title: P-RPE_2

description:
Library name: P-RPE_2
Column name in mouse_RNA_reprogramming_count.csv: P.RPE.2

data_processing:
For RNA-seq data analysis, The clean reads were aligned to the mouse genome (mm10) using STAR (v2.7.11a). with the default parameter settings. The read counts of each gene were calculated using program featureCounts of Subread package. The gene counts were normalized using R package edgeR (4.0.16). The differential expression analysis was performed by R package limma (3.58.1), and the thresholds of significantly DEGs were |log2 fold change| > 1.5 and adjusted P value < 0.01. Perform unsupervised clustering analysis on the obtained differentially expressed genes using Mfuzz (2.26.0). GO analysis was performed on the genes in each cluster using the R package clusterProfiler.
Assembly: GRCm38.102, GRCh38.108
Supplementary files format and content: csv files include count values for each Sample

extract_protocol:
For RNA-seq sample collection, we scraped cells at each time point that exhibited a relatively consistent and successful induction phenotype, minimizing the inclusion of cells with failed induction. For each sample, total RNA was extracted using TRIzol reagent (Thermo) and subsequently purified using the RNeasy Mini Kit (Qiagen), following the manufacturer’s instructions. RNA-seq libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB England BioLabs, E7770L). Paired-end sequencing was performed using Illumina NovaSeq 6000 with 150 base pairs (bp) read length.
For each sample, total RNA was extracted using TRIzol reagent (Thermo) and subsequently purified using the RNeasy Mini Kit (Qiagen), following the manufacturer’s instructions.

treatment_protocol: Generation of ciRPE cells from MEFs via a two-stage chemically defined reprogramming protocol M7 reprogramming medium (RM) preparation Equal volumes of Neurobasal (Gibco) and DMEM/F12/GlutaMAX supplemented with 1% N2 (Gibco), 1% B27 supplement without vitamin A (Gibco), 7.5% BSA (Solarbio), 1% NEAA, 1% P/S, bFGF (PeproTech, 10 ng/ml) and the small molecules CHIR-99021 (3 μM, MCE), LDN193189 (0.1 mM, Selleckchem), A 83-01 (0.5 mM, Selleckchem), Hh-Ag1.5 (0.5 mM, Xcess Biosciences), RG108 (10 μM, Selleckchem), BMS-345541 (0.2 mM, MCE) and CKI-7 (5 μM, Sigma-Aldrich). M3 differentiation and maturation medium (DM) preparation DMEM/F12/GlutaMAX supplemented with 10% KSR (Gibco), 1% NEAA, 1% P/S, 0.055 mM 2-mercaptoethanol, Y27632 (10 μM, Selleckchem) and Nicotinamide (NIC, 10 mM, Sigma-Aldrich), Retinoic acid (RA, 1 μM, Sigma-Aldrich), Activin A (0.2 mM, MCE). ciRPE maintenance medium preparation ciRPE maintenance medium includes proliferation medium and function-maintaining medium. The proliferation medium consisted of DMEM/F12/GlutaMAX supplemented with 1% N2, 2% B27 without vitamin A, 1% NEAA, 1% P/S, 0.1 mM 2-mercaptoethanol, 10 ng/mL bFGF, 20 ng/mL EGF (Gibco), 10 μM Y27632, and 0.5 μM A-83-01. The function-maintaining medium consisted of DMEM/F12/GlutaMAX supplemented with 1% N2, 2% B27 with vitamin A, 1% NEAA, 1% P/S, 0.1 mM 2-mercaptoethanol, 0.2 μM Activin A, 0.5 μM RA, 1 μM BMP4, and 10 mM NIC. All chemical components are listed in the key resources table. Small molecules were dissolved and diluted in DMSO (Sigma-Aldrich) following the manufacturer’s instructions and are detailed in Table S13. Stage I: Chemical conversion of eye-field cells from MEFs (1) Four days before the chemical conversion, Matrigel was thawed overnight at 4°C. The following day, 6-well plates were pre-cooled at 4°C for a minimum of 1 hour. Matrigel was diluted 1:40 in DMEM/F12/GlutaMAX and 1 mL of this diluted Matrigel solution was added to each pre-cooled well of the 6-well plate, which was then incubated at 4°C overnight. Note: To ensure optimal performance, Matrigel must be thawed at 4°C and should not be subjected to repeated freeze-thaw cycles. (2) Two days before chemical induction, thaw the cryopreserved primary MEFs in a 37°C water bath and centrifuge to remove the cryoprotectant. Resuspend the cells in MEF medium and seed them into 6-well plates at a density of 20×104 cells per well. Prior to seeding the MEFs, pre-warm the Matrigel-coated 6-well plates at 37°C for at least 30 minutes. Note: The density of MEFs is crucial for the success of chemical induction. Ensure that cells are evenly distributed; too few cells can lead to poor proliferation and cell health, while overly dense cultures may affect the success rate of induction. Regularly monitor the health and growth of MEFs after seeding to ensure they adhere well and proliferate as expected. Proper pre-warming of Matrigel-coated plates is essential for optimal cell attachment and performance. (3) One day before chemical induction, replace the culture medium of MEFs with fresh medium and allow the cells to proliferate for one day. Regularly check the growth and condition of the MEFs to ensure that the cell health and density are optimal. Note: The health of MEFs is crucial for successful conversion. Long-term storage of MEFs in liquid nitrogen may also reduce conversion efficiency. This study used freshly prepared MEFs or those stored in liquid nitrogen for no more than 6 months. (4) On the day of chemical induction, prepare the fresh RM of Stage I, working in the dark to ensure complete dissolution of all components, particularly the chemical agents. After incubating MEFs overnight in MEF medium, wash the cells twice with 1× PBS and replace the medium with the freshly prepared RM. Refresh the RM the next day. (5) During Stage I induction, cells will rapidly proliferate within the first 1-4 days, with their morphology transitioning from elongated spindle-shaped to small oval-shaped. After one week, proliferation of the clones will slow. At this point, mechanically remove surrounding non-clonal cells using a yellow pipette tip to facilitate the continued expansion of the clones. About one week later, cells will begin to adopt a cobblestone-like morphology. Thereafter, refresh the medium daily until EF-like cells are formed. Stage II: Generation of ciRPE cells from eye-field cells For Stage II induction, the cells exhibit initial RPE cell morphology but still lack maturity and pigmentation. At this stage, replace the medium with DM of Stage II to induce pigmentation and promote further maturation of ciRPE cells. The medium is changed daily. After two weeks of treatment, the cells reach near-full maturity and show significant pigmentation. Subsequently, ciRPE cells are passaged and expanded in maintenance medium. Dynamic alternating culture for ciRPE cells To balance proliferation and RPE-specific functionality, ciRPE cells derived from MEFs were cultured using a dynamic alternating medium protocol. After the first passage, during the initial expansion phase (day 0-7), the cells were cultured in proliferation medium to maximize growth. Following this, the cells were briefly exposed to function-maintaining medium for 1–2 days every 3–5 days. This alternating approach effectively supported both cell expansion and the preservation of early RPE-like characteristics. Generation of hciRPE cells from HEFs via a two-stage chemically defined reprogramming protocol M9 RM preparation Equal volumes of Neurobasal (Gibco) and DMEM/F12/GlutaMAX supplemented with 1% N2 (Gibco), 1% B27 supplement without vitamin A (Gibco), 7.5% BSA (Solarbio), 1% NEAA, 1% P/S, bFGF (PeproTech , 10 ng/ml) and the small molecules CHIR-99021 (10 μM), LDN193189 (0.5 mM), Hh-Ag1.5 (0.5 mM), RG108 (10 μM), BMS-345541 (0.2 mM), R-268712 (10 μM, MCE), BIX-01294 (1 μM, MCE), Valproic acid (VPA, 0.2 mM, MCE) and SB-431542 (10 μM, Sigma-Aldrich). M2 DM preparation DMEM/F12/GlutaMax supplemented with 10% KSR, 1% NEAA, 1% P/S, 0.055 mM 2-mercaptoethanol, NIC (10 mM), Activin A (0.2 mM). hciRPE maintenance medium preparation The ciRPE maintenance medium is designed to support the long-term culture and functionality of mature hciRPE cells. It consists of DMEM/F12/GlutaMAX as the base, supplemented with 1% N2, 2% B27 with vitamin A, 1% NEAA, 1% P/S, and 0.1 mM 2-Mercaptoethanol. To promote cell health and expansion, 10 ng/mL bFGF and 20 ng/mL EGF are included. Additionally, low concentrations of Activin A (0.1 μM), RA (0.5 μM), and BMP4 (0.5 μM) are added to maintain RPE-specific gene expression, pigmentation, and structural integrity. The medium is freshly prepared, and all components are dissolved thoroughly before use. Stage I: Chemical conversion of OV cells from HEFs (1) Matrigel was thawed overnight at 4°C. The following day, 6-well plates were pre-cooled at 4°C for at least 1 hour. Matrigel was diluted 1:40 in DMEM/F-12/GlutaMAX, and 1 mL of this diluted Matrigel solution was added to each pre-cooled well of the 6-well plate. The plates were then incubated at 4°C overnight. (2) The next day, thaw the cryopreserved primary HEFs in a 37°C water bath, and centrifuge to remove the cryoprotectant. Resuspend the cells in 15% FBS-DMEM medium and seed them into 6-well plates at a density of 15×104 cells per well. Prior to seeding the HEFs, pre-warm the Matrigel-coated plates at 37°C for at least 30 minutes. Note: This study utilized either freshly prepared HEFs or those stored in liquid nitrogen for no longer than 2 months. (3) When the density of HEFs reaches 60-70%, chemical induction can be initiated. For Stage I induction, prepare the fresh RM in the dark to ensure the complete dissolution of all components, especially the chemical agents. Wash the HEFs twice with 1×PBS and replace the medium with the freshly prepared RM. Refresh the RM every two days. (4) During Stage I induction, the cells will rapidly proliferate within the first week, transitioning in morphology from elongated spindle-shaped to small oval-shaped. By approximately day 12, a few stable clones of uniform size and morphology will have formed. At this stage, mechanically remove surrounding non-clonal cells using a yellow pipette tip to facilitate the continued expansion of the clones.  Thereafter, refresh the medium daily until OV-like cells are formed. Stage II: Generation of hciRPE cells from OV cells For Stage II induction, replace the medium with DM to induce pigmentation and promote the further maturation of hciRPE cells. The medium is refreshed daily. After two weeks of treatment with the maturation medium, the cells exhibit RPE-like morphology and display some pigmentation. Subsequently, the hciRPE cells are passaged and expanded in maintenance medium. Maintenance culture of hciRPE cells For long-term culture, hciRPE cells are passaged using mechanical dissociation methods and seeded onto Matrigel-coated plates, maintaining a confluency of 60–80%. The maintenance medium is refreshed every 2–3 days to ensure optimal cell health. Cells are regularly monitored for RPE-specific characteristics, including morphology, pigmentation, and the expression of key markers.

value: RPE


title: MVT_LungsP_N3

status: Public on Oct 29 2025

type: SRA

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

description: MVT_LungsP_N3 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using MVT1 into FVB (Imm.competent) mouse, with vector lentiGuide-Puro

library_source: genomic

data_processing:
Mapping using bowtie2 (v2.3.5.1; parameters: -L 11 -N 1 -I S,1,0.75 --norc), allowing for one mismatch.
Normalized abundance of individual sgRNAs were obtained using MAGeCK (v0.5.9.4).
Assembly: lentiviral libraries encompassing 2215 sgRNAs against mouse immune interactome genes  or 2180 sgRNAs against the homologue human genes
Supplementary files format and content: counts.txt.gz are tab-delimited files containing raw counts for each library
Library strategy: CRISPR-seq

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
All tissue samples were processed through a common DNA extraction protocol, as described (Scheidmann et al., 2022). Briefly, tumor and metastasis-carrying organs were lysed in a FastPrep tissue homogenizer (MP) using dedicated matrix beads-containing disposable tubes (MP) in presence of a DNA extraction buffer (50 mM Tris-Cl pH 8.0, 50 mM EDTA, 1% SDS). The lysate was then digested for at least 16 hours at 65 °C in presence of Proteinase K (Qiagen) and then for 30 minutes at 37 °C in presence of RNAase A (Qiagen). Separation of genomic DNA was carried out by first adding pre-chilled 7.5 M ammonium acetate, followed by isopropanol addition to the resulting supernatant, leading the DNA to precipitate. The pellet was then washed with 70% ethanol and the genomic DNA was resuspended in Tris-EDTA buffer (Ambion) and frozen at -20 °C. Finally, DNA extraction from cultivated cells was carried out using the Dneasy kit (Qiagen). For CRISPR genomics applications, DNA samples were quantified using NanoDrop ND-1000 UV-Vis Spectrophotometer (Thermo Fisher).
Samples were processed to reach a theoretical coverage of 500–1,000× per target. For mouse samples, 10-15 µg of genomic DNA were amplified in a one-step PCR with barcoded primers targeting the pLentiGuide vector backbone (P5 and P7). The primer sequences in the table below highlight an 8 bp barcode position in blue and vector binding site in bold, mapping between the sgRNA scaffold and the U6 promoter. All pPrimers were ordered as desalted Oligos oligos at IDT (Integrated DNA Technologies)(at Integrated DNA Technologies or at Microsynth) Microsynth and resuspended in nuclease-free water. For human samples, 10 µg of gDNA were pre-amplified in a nested PCR with the external primers targeting the huTHY1insert and the upstream portion of the U6 promoter (primer sequences in table below). In the second PCR step, barcoded primers targeting the pLentiguide vector backbone (P5 and P7) were used as internal primers (primer sequences in table above). For mouse samples, PCR conditions were as follows: 100 µl as reaction volume, KAPA HiFi Hot Start Ready Mix (2X; Roche)0.02 U/µl of Q5 polymerase (New England Biosciences), and 25-31 cycles of amplification. For human samples, only 23-27 cycles of amplification were applied in the first step using KAPA HiFi Hot Start Ready Mix (2X; Roche). Since some samples did not yield any clearly detectable product after the first PCR, all products were purified with AMPure XP Beads (Beckman Coulter) or Sera-Mag Select Beads (2X, Cytiva Europa GmbH) and used as input for a second PCR (23-27 cycles) with the same primers that were used for the first PCR. When loading a second PCR, pre-amplified fragments were re-quantified using NanoDrop. To reach the theoretical coverage after sequencing, 200 ng of pre-amplified product were re-amplified using nested barcoded primers (P5 and P7). PCR conditions for the second PCR were as follows: 200 ng of pre-amplified fragments per 25 µl reaction, 0.02 U/µl of Q5 polymerase (New England Biosciences), and 27 cycles of amplification. The amplified product containing the spacer sequence with a size of 202 bp was purified by SPRI bead cleanup and a right-sided size selection to remove the genomic DNA input. Using a dual barcoding system, the final NGS amplicons were multiplexed and sequenced on an Illumina platform with 21 dark cycles (DC) in Read 1 to skip the invariable region of the primer binding side (U6 promoter).

tag: tissue

tag: cell line

tag: cell type

value: tumor

tag: genotype

value: xenograft

tag: treatment

value: NSG (Imm.deficient)

tag: crispr lib

value: Immuno Signalome (2215) sgRNA library

tag: sgrna library

tag: effect type

value: sgRNAs used as barcodes (no KO)

tag: vector

value: lentiGuide-Puro

tag: full library_complexity


title: patient 97, Day 14, Short Responder

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

country: USA

institute: Mayo Clinic

library_source: transcriptomic single cell

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Cellranger (v7.0.1) was used for demultiplexing, barcoded processing, gene counting, cell clustering, and aggregation analyses with TCR-seq. The reference database (refdata-gex-GRCh38-2020-A) was downloaded from 10X Genomics.
Seurat package 4.2.0 was used for downstream analyses.
Assembly: GRCh38/hg38.
Supplementary files format and content: HDF5 (Hierarchical Data Format).

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMC) from 10 patients at day 0 and 14 (D0 and D14) with castrate levels of testosterone (<50 mg/dL) underwent continued ADT and stereotactic body radiotherapy (SBRT) : 5 with poor response, and 5 with good response.
Library was peformed according to the manufacter's instructions (single cell 3' v2 protocol, 10xGenomics).

value: PBMC

tag: time

value: Day 14

tag: group

value: Short Responder


title: MVT_LungsP_N2

description: MVT_LungsP_N2 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using MVT1 into FVB (Imm.competent) mouse, with vector lentiGuide-Puro


title: MVT_LungsP_N1

description: MVT_LungsP_N1 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using MVT1 into NSG (Imm.deficient) mouse, with vector lentiGuide-Puro


title: 4T_LungsT_B4

description: 4T_LungsT_B4 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Thy1

value: BALB (Imm.competent)


title: D32_scRNA

city: Wenzhou

first: zhengbiao

last: zhu

state: Zhejiang

address: Ouhai District

department: The Affiliated Eye Hospital of Wenzhou Medical University

country: China

institute: Wenzhou Medical University

description:
Library name: D32_scRNA
SeekOne® Digital Droplet

data_processing:
For scRNA-seq data analysis, the demultiplexing, barcoded processing, gene counting and aggregation were performed using the SeekSoulTools (v1.2.2) software with the default parameters. All scRNA-seq reads were aligned to the mouse reference genome (mm10). The scRNA-seq expression profiles were analyzed using R package Seurat (v4.1.0). The cells within a minimum of 200 genes expressed and the percentage of mitochondrial gene counts < 10% were kept for subsequent analysis. We followed the standard Seurat pipeline by running function FindVariableFeatures, ScaleData, RunPCA, FindNeighbors, and FindClusters in order. We performed single-cell regulatory network inference and clustering (SCENIC) analysis using python package pySCENIC (0.12.1) to identify activated TFs and subnetwork of each TF (regulons) for each cell type. To calculate RNA velocity, both velocyto (v0.17) and scVelo (0.2.5)  were used to analyze reads that passed the quality control after clustering as instructed. First, the standard velocyto pipeline was run to count spliced and unspliced reads for each sample based on the filtered SeekSoulTools-generated bam files. Then the output loom file was used as input for scVelo based on the dynamic model to estimate velocity embedding.
Assembly: GRCm38.102
Supplementary files format and content: RDS data for saving single-cell data

source_name: E13.5 mouse embryos

extract_protocol:
For scRNA-seq sample collection, we scraped all cells with different induction phenotypes at each time point, aiming to analyze all cell types involved in the induction process. Cells were washed in ice-cold PBS and dissociated using SeekMate Tissue Dissociation Kits (SeekGene). DNase I treatment was applied if needed. Cell viability was assessed using a Fluorescence Cell Analyzer (Countstar® Rigel, S2), after removing erythrocytes and filtering out debris and dead cells. Fresh cells were resuspended in RPMI1640 with 2% FBS at 1×106 cells/mL.
Single-cell RNA-Seq libraries were prepared using the SeekOne® Digital Droplet Single Cell 3' Kit (SeekGene). Cells were mixed with reverse transcription reagents and loaded into SeekOne® chip S3 for droplet generation. Reverse transcription was performed at 42°C for 90 minutes, followed by inactivation at 85°C for 5 minutes. cDNA was purified, amplified, fragmented, end-repaired, and ligated to sequencing adaptors. Indexed PCR was performed to amplify the 3' polyA regions, including Cell Barcodes and Unique Molecular Indices (UMIs). Libraries were cleaned, quantified, and sequenced on an Illumina NovaSeq 6000 or DNBSEQ-T7 platform.

treatment_protocol: Generation of ciRPE cells from MEFs via a two-stage chemically defined reprogramming protocol M7 reprogramming medium (RM) preparation Equal volumes of Neurobasal (Gibco) and DMEM/F12/GlutaMAX supplemented with 1% N2 (Gibco), 1% B27 supplement without vitamin A (Gibco), 7.5% BSA (Solarbio), 1% NEAA, 1% P/S, bFGF (PeproTech, 10 ng/ml) and the small molecules CHIR-99021 (3 μM, MCE), LDN193189 (0.1 mM, Selleckchem), A 83-01 (0.5 mM, Selleckchem), Hh-Ag1.5 (0.5 mM, Xcess Biosciences), RG108 (10 μM, Selleckchem), BMS-345541 (0.2 mM, MCE) and CKI-7 (5 μM, Sigma-Aldrich). M3 differentiation and maturation medium (DM) preparation DMEM/F12/GlutaMAX supplemented with 10% KSR (Gibco), 1% NEAA, 1% P/S, 0.055 mM 2-mercaptoethanol, Y27632 (10 μM, Selleckchem) and Nicotinamide (NIC, 10 mM, Sigma-Aldrich), Retinoic acid (RA, 1 μM, Sigma-Aldrich), Activin A (0.2 mM, MCE). ciRPE maintenance medium preparation ciRPE maintenance medium includes proliferation medium and function-maintaining medium. The proliferation medium consisted of DMEM/F12/GlutaMAX supplemented with 1% N2, 2% B27 without vitamin A, 1% NEAA, 1% P/S, 0.1 mM 2-mercaptoethanol, 10 ng/mL bFGF, 20 ng/mL EGF (Gibco), 10 μM Y27632, and 0.5 μM A-83-01. The function-maintaining medium consisted of DMEM/F12/GlutaMAX supplemented with 1% N2, 2% B27 with vitamin A, 1% NEAA, 1% P/S, 0.1 mM 2-mercaptoethanol, 0.2 μM Activin A, 0.5 μM RA, 1 μM BMP4, and 10 mM NIC. All chemical components are listed in the key resources table. Small molecules were dissolved and diluted in DMSO (Sigma-Aldrich) following the manufacturer’s instructions and are detailed in Table S13. Stage I: Chemical conversion of eye-field cells from MEFs (1) Four days before the chemical conversion, Matrigel was thawed overnight at 4°C. The following day, 6-well plates were pre-cooled at 4°C for a minimum of 1 hour. Matrigel was diluted 1:40 in DMEM/F12/GlutaMAX and 1 mL of this diluted Matrigel solution was added to each pre-cooled well of the 6-well plate, which was then incubated at 4°C overnight. Note: To ensure optimal performance, Matrigel must be thawed at 4°C and should not be subjected to repeated freeze-thaw cycles. (2) Two days before chemical induction, thaw the cryopreserved primary MEFs in a 37°C water bath and centrifuge to remove the cryoprotectant. Resuspend the cells in MEF medium and seed them into 6-well plates at a density of 20×104 cells per well. Prior to seeding the MEFs, pre-warm the Matrigel-coated 6-well plates at 37°C for at least 30 minutes. Note: The density of MEFs is crucial for the success of chemical induction. Ensure that cells are evenly distributed; too few cells can lead to poor proliferation and cell health, while overly dense cultures may affect the success rate of induction. Regularly monitor the health and growth of MEFs after seeding to ensure they adhere well and proliferate as expected. Proper pre-warming of Matrigel-coated plates is essential for optimal cell attachment and performance. (3) One day before chemical induction, replace the culture medium of MEFs with fresh medium and allow the cells to proliferate for one day. Regularly check the growth and condition of the MEFs to ensure that the cell health and density are optimal. Note: The health of MEFs is crucial for successful conversion. Long-term storage of MEFs in liquid nitrogen may also reduce conversion efficiency. This study used freshly prepared MEFs or those stored in liquid nitrogen for no more than 6 months. (4) On the day of chemical induction, prepare the fresh RM of Stage I, working in the dark to ensure complete dissolution of all components, particularly the chemical agents. After incubating MEFs overnight in MEF medium, wash the cells twice with 1× PBS and replace the medium with the freshly prepared RM. Refresh the RM the next day. (5) During Stage I induction, cells will rapidly proliferate within the first 1-4 days, with their morphology transitioning from elongated spindle-shaped to small oval-shaped. After one week, proliferation of the clones will slow. At this point, mechanically remove surrounding non-clonal cells using a yellow pipette tip to facilitate the continued expansion of the clones. About one week later, cells will begin to adopt a cobblestone-like morphology. Thereafter, refresh the medium daily until EF-like cells are formed. Stage II: Generation of ciRPE cells from eye-field cells For Stage II induction, the cells exhibit initial RPE cell morphology but still lack maturity and pigmentation. At this stage, replace the medium with DM of Stage II to induce pigmentation and promote further maturation of ciRPE cells. The medium is changed daily. After two weeks of treatment, the cells reach near-full maturity and show significant pigmentation. Subsequently, ciRPE cells are passaged and expanded in maintenance medium.

value: E13.5 mouse embryos

value: Reprogramming intermediate


title: D18_scRNA

description:
Library name: D18_scRNA
SeekOne® Digital Droplet

value: M7 reprogramming medium


title: 4T_LungsT_N2

description: 4T_LungsT_N2 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into FVB (Imm.competent) mouse, with vector lentiGuide-Thy1


title: 4T_LungsT_N1

description: 4T_LungsT_N1 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into FVB (Imm.competent) mouse, with vector lentiGuide-Thy1


title: 4T_LungsT_B5

description: 4T_LungsT_B5 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Thy1


title: mouse_D32_2

description:
Library name: mouse_D32_2
Column name in mouse_RNA_reprogramming_count.csv: D32.2

library_source: transcriptomic

value: ciRPE

value: M3 differentiation and maturation medium


title: patient 97, Day 0, Short Responder

value: Day 0


title: P-RPE_1

description:
Library name: P-RPE_1
Column name in mouse_RNA_reprogramming_count.csv: P.RPE.1

value: RPE


title: 4T_LungsT_B3

description: 4T_LungsT_B3 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Thy1

value: tumor


title: mouse_D32_3

description:
Library name: mouse_D32_3
Column name in mouse_RNA_reprogramming_count.csv: D32.3


title: P1- Alpha-MSH

city: London

first: Trinidad

last: Montero

address: Charterhouse Square

department: Biochemical Pharmacology

country: United Kingdom

institute: Whilliam Harvey Research Institute, Bart's and The London School of Medicine; Queen Mary University of London

data_processing:
Data were analysed using Partek Flow Genomic Analysis Software (release no. 10.0.23.0720), inlcuding reads trimming, alignment, quentification to transcriptome and normalization.
Base trimming was based on quality score (end min quality level (Phred) 20) from both ends
Reads were aligned to the human genome (hg38) using STAR 2.7.8a
Quanfitication to transcriptome was conducted using assemby Homo sapines (human) hg38, annotation model RefSeq Transcripts 93 - 2020 - 02 - 03
Transcript quantification was conducted with TPM normalisation method
Assembly: Human Genome G38
Supplementary files format and content: RPKM values are provided for each sample in a txt file

source_name: Skin

growth_protocol: Fibroblasts were maintained in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% heat inactivated foetal bovine serum (FBS), 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin (‘complete medium’) until ~80% confluence

extract_protocol:
RNA was extracted using Direct-zol RNA MiniPrep  (Zymo Research)
RNAseq library was prepared using the KAPA mRNA HyperPrep Kit (Roche) and xGen UDI+UMI adapter set (Integrated DNA Technologies). Sequencing was performed on a NovaSeq 6000 Sequencing System (Illumina), using an S1 flow-cell and 100 cycle SBS sequencing kit.

treatment_protocol: Cells were plated on day 0 and drug treatments (BMS-470539 -10uM-, alphaMSH -10uM-, itraconazole -1uM- or vehicle -PBS-) applied on days 1, 3 and 5. Cells were collected on day 6 and RNA extracted.

value: Skin

value: Primary

value: Fibroblast

tag: individual

value: Patient 1

value: alpha-MSH


title: 4T_LungsT_B2

description: 4T_LungsT_B2 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Thy1

value: xenograft

value: Immuno Signalome (2215) sgRNA library

value: sgRNAs used as barcodes (no KO)


title: mouse_D32_1

description:
Library name: mouse_D32_1
Column name in mouse_RNA_reprogramming_count.csv: D32.1


title: 4T_LungsP_N4

description: 4T_LungsP_N4 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into NSG (Imm.deficient) mouse, with vector lentiGuide-Puro

value: NSG (Imm.deficient)

value: lentiGuide-Puro


title: 4T_LungsP_N3

description: 4T_LungsP_N3 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into NSG (Imm.deficient) mouse, with vector lentiGuide-Puro


title: patient 80, Day 14, Long Responder

value: PBMC

value: Day 14

value: Long Responder


title: mouse_D18_2

description:
Library name: mouse_D18_2
Column name in mouse_RNA_reprogramming_count.csv: D18.2

value: E13.5 mouse embryos

value: Reprogramming intermediate

value: M7 reprogramming medium


title: 4T_LungsP_B4

description: 4T_LungsP_B4 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Puro

value: tumor

value: BALB (Imm.competent)


title: 4T_LungsP_B3

description: 4T_LungsP_B3 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Puro


title: patient 74, Day 0, Short Responder

value: Day 0

value: Short Responder


title: patient 74, Day 14, Short Responder


title: 4T_LungsT_B1

description: 4T_LungsT_B1 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into NSG (Imm.deficient) mouse, with vector lentiGuide-Thy1


title: 4T_LungsP_N5

description: 4T_LungsP_N5 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into FVB (Imm.competent) mouse, with vector lentiGuide-Puro


title: patient 80, Day 0, Long Responder


title: 4T_LungsP_N2

description: 4T_LungsP_N2 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into NSG (Imm.deficient) mouse, with vector lentiGuide-Puro


title: 4T_LungsP_N1

description: 4T_LungsP_N1 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into NSG (Imm.deficient) mouse, with vector lentiGuide-Puro


title: mouse_D18_1

description:
Library name: mouse_D18_1
Column name in mouse_RNA_reprogramming_count.csv: D18.1


title: 4T_LungsP_B2

description: 4T_LungsP_B2 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Puro


title: mouse_D18_3

description:
Library name: mouse_D18_3
Column name in mouse_RNA_reprogramming_count.csv: D18.3


title: patient 71, Day 14, Long Responder


title: patient 71, Day 0, Long Responder


title: Input_S

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li H. and Durbin R. 2009) and fold enrichment bedgraphs were generated using Macs2 (Zhang Y et al, 2008).
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT). Alignments of reads from strains lacking the REII element  were to the standard genome as described but with the sequence of the REII element removed.
Supplementary files format and content: For ChIPseq, bedgraphs of Fold Enrichment of the IP over Input  (FE) or  raw pileups for the Inputs as generated by Macs2  (Zhang Y et al, 2008).

organism: Schizosaccharomyces pombe

source_name: mat1Msmt0 ade6-216 his2 ura4-DS/E otr1R(Sph1)::ura4+ raf2-myc::KanMX6 leu1+::Pnmt1-GFP-raf1

growth_protocol: Sample were grown in YEA medium at 30°C. For induction of gene under nmt1 promoter, cells were grown in PMG medium at 30°C.

extract_protocol:
For the H3K9me3 chromatin immunoprecipitation (ChIP) assay, 5x108 cells were crosslinked with 3% paraformaldehyde (PFA) for 30 minutes at room temperature, followed by quenching with 125 mM glycine. For Swi6 or Raf2 ChIPs,1x109 cells were incubated for 2 hours at 18°C, fixed in 3% PFA, and washed in ice-cold PBS. Cells were treated with 10mM Dimethyl adipimidate (DMA) at room temperature for 45 minutes. Fixed cells were resuspended in ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) supplemented with 1 mM PMSF and protease inhibitors (Roche cOmplete, Mini Protease Inhibitor Cocktail) and lysed by bead-beating ( Biospec Mini-Beadbeater-16). The lysates were sonicated with a Diagenode Bioruptor for 14-cycles on medium power setting (30 s ON, 30 s OFF) to shear DNA into 0.4–0.6 kb fragments. Cellular debris were removed by centrifugation and 2% supernatants was kept aside for whole cell extract input control. The remaining lysates were pre-cleared with agarose beads for 1 hour at 4°C. After bead removal, lysates were incubated with the appropriate antibody (2–10 μg) overnight at 4°C with slow rotation. Antibodies used includes anti-H3K9me3 (Abcam), anti-c-Myc (Santa Cruz), and home-made affinity-purified anti-Swi6. Pre-washed protein A and protein G agarose beads were added to the lysates and incubated for 4 hours at 4°C. The beads were sequentially washed, twice with Wash Buffer I (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), twice with Wash Buffer II (50 mM HEPES/KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), twice with Wash Buffer III (10 mM Tris/HCl pH 8.0, 250 mM LiCl, 0.5% IGEPAL, 0.5% sodium deoxycholate, 1 mM EDTA), and once with TE buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA). The chromatin was eluted from the beads twice with 50 μl of elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA, 1% SDS) at 65°C for 30 minutes each, with shaking (~1,200 rpm). Eluted chromatin and input control samples were reverse crosslinked overnight at 65°C. Samples were treated sequentially with RNase A (10 μg, 2 hours, 37°C) and Proteinase K (20 μg, 2 hours, 37°C), and subsequently purified using the Qiagen PCR purification kit.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

tag: strain

tag: growth

value: Growth in PMG medium 30°C + 2hr at 18°C before fixation

tag: fixation

value: 3% PFA + 10mM DMA


title: mouse_D7_2

description:
Library name: mouse_D7_2
Column name in mouse_RNA_reprogramming_count.csv: D7.2


title: RNA_raf1R576H_upf1∆_Rep2

data_processing:
Single ended short reads from RNAseq experiments were quality trimmed using fastp (Chen et al. 2018) and aligned to the reference genome using the STAR aligner (Dobin, A. et al., 2013). Wig files, normalized to counts per million mapped reads, were generated by STAR.
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: Wig format for stranded RNAseq.

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6 upf1∆::KanMX6

growth_protocol: Sample were grown in YEA medium at 30°C.

extract_protocol:
Total RNA was extracted from cells using the MasterPure Yeast RNA Purification Kit (Biosearch Technologies) according to the manufacturer's instructions.
For RNA Seq-Sequencing, libraries were prepared using ScriptSeq v2 RNA-seq library preparation kit (Illumina) or Ultra II directional RNA library prep kit for Illumina (NEB) according to the manufacturer’s protocol and analyzed using an Agilent 2100 BioAnalyzer.

value: Yeast Whole Cells

value: Growth in YEA medium at 30°C


title: RNA_raf1R576H_Rep2

source_name: mat1Msmt0 leu1-32 ade6-210 ura4-DS/E mat2P(Bg-Bs)::ura4+ raf1R576H::KanMX6


title: 4T_LungsP_B1

description: 4T_LungsP_B1 No Cas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality -whole lungs using 4T1 into BALB (Imm.competent) mouse, with vector lentiGuide-Puro

value: xenograft

value: Immuno Signalome (2215) sgRNA library

value: sgRNAs used as barcodes (no KO)


title: RNA_upf1∆_Rep1

source_name: h+ leu1-32 ade6-210 ura4-D18 upf1∆::KanMX6


title: mouse_D7_3

description:
Library name: mouse_D7_3
Column name in mouse_RNA_reprogramming_count.csv: D7.3


title: MEF_2

description:
Library name: MEF_2
Column name in mouse_RNA_reprogramming_count.csv: MEF.2

value: MEF


title: MEF_1

description:
Library name: MEF_1
Column name in mouse_RNA_reprogramming_count.csv: MEF.1


title: HCT116-Rpb1 degron, triptolide 4hr, biological replicate 3,input

city: La Jolla

first: Alon

last: Goren

state: CA

address: 9375 Gilman Dr

department: Department of Medicine

institute: University of California San Diego

description: Library name: HCT116_TRP_4hr_3_input_S61

data_processing:
Samples were sequenced on Illumina NextSeq 550 or Nextseq 2000, samples were demultiplexed with Illumina bcl2fastq.
Adapters were removed with Trimmomatic, reads with Phred score <26 over a 4bp window were truncated.
Reads were aligned to a concatenated genome containing hg38 + sacCer3 + dm6, alignment files were separated by species. If UMIs are not present in adapter sequences, PCR duplicate reads were removed with samtools markdup. When present, UMIs were deduplicated with UMI-tools dedup, with method=unique. Alignments were additionally filtered to remove reads if paired-end reads aligned >1000bp apart, or on different chromosomes.
HOMER tag directories were made; by default read counts for each species were filtered for primary alignments with MAPQ > 10, reads were extended to model approximate ChIP-seq fragment size using the option -fragLength 150. Samples were converted to bed files for normalization. Details of spike-in normalization are described in Supplement, normalized data are in bedGraph format.
Read normalized bigwig files were created with HOMER makeBigWig.pl from tag directories.
Assembly: hg38, dm6, sacCer3
Supplementary files format and content: Normalized BigWig files for hg38 genome

growth_protocol: HeLa-S3 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1x penicillin-streptomycin, L-glutamine, and 110mg/L sodium pyruvate. Cells were incubated at 37°C and 5% CO2. HCT116-EF1a-OsTIR1-Rpb1 cells were cultured in McCoy’s 5A media (Thermo Scientific 16600082) with 10% FBS and 1x antibiotic-antimycotic. Cells were incubated at 37°C and 5% CO2. Cell lines mESc E14 Dpy30-miniAID-P2A-mTagBFP2 pB-hygro-OsTIR1-P2A-mCherry and mESc E14 Rbbp5-P2A-2xHA-P2A-NEO were provided from the Helin lab, and maintained in GMEM with 15% FBS, 10uM sodium pyruvate, 1x MEM-NEAA, 50uM B-mercaptoethanol, and antibiotic/antimycotic.

extract_protocol:
HCT116 or HeLa-S3 cells were double crosslinked on plates with 2 mM DSG for 30 minutes (Fisher Scientific NC1736108) and 1% formaldehyde (Pierce ThermoFisher PI28906) for 10 minutes. Crosslinking was quenched with 1/20th volume of 2.625 M glycine (EMD Millipore 357002) and 0.5% BSA (NEB B9000S). Cells were washed by resuspending 3 times with 0.5% BSA/PBS + Protease inhibitor (PIC, Roche 11697498001), spinning down at 1200g for 5 minutes at 4°C and removing the supernatant. Washed pellets were snap frozen in dry ice then stored in -80°C. Cells were lysed with LB3 lysis buffer + PIC, then chromatin was sheared on the PIXUL sonicator (Active Motif 53130) for 108 minutes. S2 cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature, then quenched with glycine and 10% BSA to a final concentration of 0.5%, lysed in LB3 buffer, and sonicated on the PIXUL for 60 minutes. S. cerevisiae cultures in log phase were crosslinked with 0.86% formaldehyde for 30 minutes on a room temperature rotating shaker. The cell wall was digested with Zymolase at 37°C for 60 minutes, cells were washed by pelleting 3x at 5000g and washing in PBS + Protease inhibitor, then resuspended in NP-S buffer + PI. Sheared S. cerevisiae chromatin was sonicated on the PIXUL for 108 minutes. All PIXUL sonication was done with settings Pulse (N) = 50, PRF (kHz) = 1.00, Burst Rate (Hz) = 20, only Process Time was varied. Sheared chromatin from each species were clarified by centrifugation at 15000g, for 10 minutes at 4°C, then combined and inputs were taken before immunoprecipitation for each condition, to assess the relative ratios of chromatin. To HeLa-S3 cells, approximately 100k S2 and 500k S. cerevisiae cells were added per immunoprecipitation reaction. To HCT116 cells, approximately 500k S2 and 100k S. cerevisiae cells were added to each immunoprecipitation reaction. To each IP, 10uL of Protein A beads (Thermo Fisher Scientific 10002D), 1% Triton X-100 and 1x PIC were added. 1 million HCT116 cells or HeLa-S3 cells were used per immunoprecipitation reaction.
To each IP, 10uL of Protein A beads (Thermo Fisher Scientific 10002D), 1% Triton X-100 and 1x PIC were added. 1 million HCT116 cells or HeLa-S3 cells were used per immunoprecipitation reaction. Below are the volumes per IP of each antibody used: CST H3K27ac (D5E4): 1uL CST H3K4me3 (C42D8): 1uL CST H3K4me1 (D1A9): 1uL CST H3K36me3 (D5A7): 1uL CST Rpb1 NTD (D8L4Y): 4uL CST H3K9ac (C5B11): 4uL Samples were incubated overnight on a rotator at 4°C. IP Washes were performed: 3x with 180uL of WBI, 3x with 180uL of WBIII, and 2x with 185uL TET, then eluted in 25uL of cold TT Buffer. Input chromatin containing target and spike-in species’ chromatin from each biological condition were diluted 1:62.5x in TT buffer to a final volume of 25uL. Libraries were prepared with the NEB Ultra II Library Prep Kit (NEB E7645L). NEXTflex Dual-Barcode ChIP-seq Adapters (NOVA-514151) were added at 0.25uM or 0.5uM or 0.625uM. Libraries were then de-crosslinked at 55°C for 1hr, then 65°C overnight and cleaned with Speedbeads, 8.6% PEG and 0.8M NaCl and eluted in TT buffer. Next libraries were PCR amplified with 1uM Solexa 1GA and 1GB primers and NEB Ultra II Q5 Mastermix (PCR protocol: 98C for 30’’, then 12 or 13 cycles of 98C for 10’’, 60C for 15’’, 72C for 30’’, then hold at 72C for 2’). A final cleanup was done with Speedbeads, 8.5% PEG and 1M NaCl, washed twice with 80% EtOH, then the final libraries were eluted in 20uL TT. Library size was estimated by running 6uL of eluted library on a 1.8% agarose gel and concentration was quantified with Qubit HS dsDNA kit (Invitrogen Q32854). Libraries were pooled and sequenced on Illumina NextSeq 550 or NextSeq 2000.

treatment_protocol: HeLa-S3 cells were synchronized in G1/S by adding 2 mM thymidine for 16 hr, washed with PBS, released for 3 hr in fresh medium, and pro-metaphase arrested with 10uM S-trityl-L-cysteine (STC) for 12 hr then harvested. HeLa-S3 cells and HCT116 cells were treated with 500nM Triptolide for 1 or 4 hours. HCT116 cells were treated with 500uM auxin for 1 or 4 hours. mESCs were treated with either 500nM Auxin (3-indoleacetic acid, Sigma-Aldrich #I3750) for DPY30-mAID or 500nM dTAG13 (Tocris Biosciences #6605) for RBBP5-FKBP cells, for 0 and 24 hours.

tag: spike-in species

value: D. melanogaster, S. cerevisiae

value: human colon cancer

tag: chip antibody

value: Triptolide 4hr


title: HCT116-Rpb1 degron, triptolide 1hr, biological replicate 4,input

description: Library name: HCT116_TRP_1hr_4_input_S60

tag: cell line

value: Triptolide 1hr


title: Input_R

source_name: mat1Msmt0 ade6-216 his2 ura4-DS/E otr1R(Sph1)::ura4+ raf2-myc::KanMX6 leu1+::Pnmt1-GFP


title: patient 37, Day 14, Long Responder

tag: tissue

value: PBMC

value: Day 14

value: Long Responder


title: patient 70, Day 14, Long Responder


title: IgG RIP-Seq of Adar f/f b9 placenta

city: xiamen

first: Xiaogang

last: Chen

address: xiangan Campus，Xiamen University

institute: xiamen university

data_processing:
The reads were quality-checked using FastQC and deduplicated with FastUniq (v1.1). STAR (v2.5.3a) was used to align reads to the Gencode M15 transcriptome, and data normalization was done with EdgeR’s TMM method. Transposable element (TE) analysis was conducted using GTF files curated by the Hammell Lab, and RNA secondary structures were predicted using RNAfold from the ViennaRNA package (v2.4.11).
Assembly: mm39
Supplementary files format and content: CSV file for Adar1 f/f and ko placenta

source_name: placenta

extract_protocol:
Placental tissues were processed to extract input RNA using TRIzol Reagent. A seperate portion was lysed in dsRIP buffer (100 mM NaCl, 50 mM Tris-HCl pH 7.4, 3 mM MgCl2, 0.5% NP-40) with protease inhibitors and RNase inhibitor.
Lysates were incubated with 5 mg Mda5 antibody (Proteintech, 66770-1-Ig) at 4°C for 2 hours, followed by Protein G Dynabeads capture. RNA was extracted using TRIzol Reagent, rRNA was depleted, and the RNA was fragmented before sequencing on the NovaSeq platform

value: placenta

tag: genotype

value: Adar f/f


title: HCT116-Rpb1 degron, triptolide 1hr, biological replicate 3,input

description: Library name: HCT116_TRP_1hr_3_input_S59

tag: cell type

tag: treatment


title: Raf2-myc_raf1-OE_FE_Exp15_Rep2

value: Santa Cruz anti-Myc (9E10) (cat# sc-40)

value: Growth in PMG medium 30°C + 2hr at 18°C before fixation


title: patient 70, Day 0, Long Responder

value: Day 0


title: Raf2-myc_WT_FE_Exp15_Rep2

value: 3% PFA + 10mM DMA


title: patient 37, Day 0, Long Responder


title: HCT116-Rpb1 degron, auxin 4hr, biological replicate 3,input

description: Library name: HCT116_IAA_4hr_3_input_S65

value: Auxin 4hr


title: Untag_for_sample_45:46

source_name: mat1Msmt0 leu1-32 ade6-210 his2 ura4-DS/E otr1R(Sph1)::ura4+


title: mouse_D7_1

description:
Library name: mouse_D7_1
Column name in mouse_RNA_reprogramming_count.csv: D7.1

value: E13.5 mouse embryos

value: Reprogramming intermediate

value: M7 reprogramming medium


title: MEF_3

description:
Library name: MEF_3
Column name in mouse_RNA_reprogramming_count.csv: MEF.3

value: MEF


title: patient 57, Day 0, Long Responder


title: RNA_raf1R576H_Rep1

value: Yeast Whole Cells

value: Growth in YEA medium at 30°C


title: patient 42, Day 14, Short Responder

value: Short Responder


title: RNA_WT_Rep1

source_name: mat1Msmt0 ade6-210 ura4-D18 mat2P(Bg-Bs)::ura4+


title: HCT116-Rpb1 degron, triptolide 4hr, biological replicate 4,input

description: Library name: HCT116_TRP_4hr_4_input_S62

value: D. melanogaster, S. cerevisiae

value: human colon cancer

value: Triptolide 4hr


title: IgG RIP-Seq of Adar ko a3 placenta

value: placenta

value: Adar ko


title: RNA_raf1R576H_upf1∆_Rep1


title: Mda5 RIP-Seq of Adar ko a3 placenta


title: patient 42, Day 0, Short Responder

value: PBMC


title: HCT116-Rpb1 degron, auxin 4hr, biological replicate 4,input

description: Library name: HCT116_IAA_4hr_4_input_S64


title: patient 11, Day 0, Short Responder


title: IgG RIP-Seq of Adar ko b2 placenta


title: IgG RIP-Seq of Adar f/f a8 placenta

value: Adar f/f


title: HCT116-Rpb1 degron, triptolide 4hr, biological replicate 4, H3K27ac

description: Library name: HCT116_TRP_4hr_4_H3K27ac_1_S21

value: CST H3K27ac (D5E4)


title: patient 57, Day 14, Long Responder

value: Day 14

value: Long Responder


title: HCT116-Rpb1 degron, triptolide 4hr, biological replicate 3, Rpb1

description: Library name: HCT116_TRP_4hr_3_Rpb1_1_S20

value: CST Rpb1 NTD (D8L4Y)


title: HCT116-Rpb1 degron, auxin 1hr, biological replicate 4,input

description: Library name: HCT116_IAA_1hr_4_input_S66

value: Auxin 1hr


title: patient 27, Day 14, Short Responder


title: HCT116-Rpb1 degron, auxin 1hr, biological replicate 3,input

description: Library name: HCT116_IAA_1hr_3_input_S63


title: HCT116-Rpb1 degron, triptolide 4hr, biological replicate 3, H3K4me3

description: Library name: HCT116_TRP_4hr_3_H3K4me3_1_S18

value: CST H3K4me3 (C42D8)


title: Mda5 RIP-Seq of Adar f/f b9 placenta


title: HCT116-Rpb1 degron, DMSO 0hr, biological replicate 4,input

description: Library name: HCT116_DMSO_0hr_4_input_S58

value: DMSO


title: R882C_4_CTRL

first: Hector

last: Huerga Encabo

address: The Francis Crick Institute, 1 Midland Rd

institute: The Francis Crick Institute

data_processing:
fastq files were processed with the nf-core/rnaseq v 3.7 with the extra parameters “-profile crick --aligner star_rsem”.
STAR was used for read aligment and RSEM was use for gene quantification.
Differential expression analysis was performed using DESeq2 v.1.34.0
Assembly: Ensembl GRCh38 release 95
Supplementary files format and content: tab separated gene counts per gene per sample. Individual file per sample

extract_protocol:
RNA was isolated using RNAeasy minikit (Qiagen)
NEBNext Ultra II Directional PolyA mRNA

value: NO TREATMENT


title: HCT116-Rpb1 degron, triptolide 4hr, biological replicate 3, H3K36me3

description: Library name: HCT116_TRP_4hr_3_H3K36me3_1_S19

value: CST H3K36me3 (D5A7)


title: HCT116-Rpb1 degron, triptolide 4hr, biological replicate 3, H3K27ac

description: Library name: HCT116_TRP_4hr_3_H3K27ac_1_S17


title: snRNA-Seq of mus musculus: Adar1 wt placenta seq5

description:
WT2-5_S1_L001
con_filtered_feature_bc_matrix.h9
con_metrics_summary.csv

data_processing:
CellRanger (v4.0.0) processed the reads into gene expression matrices.
Assembly: mm39
Supplementary files format and content: HDF5 for Adar1 con and ko placenta

extract_protocol:
placental tissues were homogenized using a gentleMACS Dissociator in collagenase A. After digestion, homogenized tissues were washed with ice-cold 1X phosphate-buffered saline (PBS) and filtered through a cell strainer. Cell suspensions were then collected and centrifuged at 300 x g for 5 min. at 4°C. Red blood cells were lysed using a lysing buffer. Next, cells were washed with ice-cold 1X PBS and resuspended in 1X PBS for cell counting, which was performed using an automatic cell counter. Lastly, dead cells were removed from the cell suspensions using the Dead Cell Removal Kit and cells were counted again using an automatic cell counter.
Nuclei from Adar1f/f and Adar1PKO placental tissues were processed using the Chromium Single Cell 3’ Reagent V3 Kit (10X Genomics) and sequenced on a NovaSeq 6000 S4 platform.

value: Adar1 wt


title: patient 27, Day 0, Short Responder

value: Day 0

value: Short Responder


title: HCT116-Rpb1 degron, DMSO 0hr, biological replicate 3,input

description: Library name: HCT116_DMSO_0hr_3_input_S57

value: D. melanogaster, S. cerevisiae

value: human colon cancer


title: snRNA-Seq of mus musculus: Adar1 wt placenta seq4

description:
WT2-4_S1_L005
con_filtered_feature_bc_matrix.h8
con_metrics_summary.csv

value: placenta


title: HCT116-Rpb1 degron, triptolide 4hr, biological replicate 4, Rpb1

description: Library name: HCT116_TRP_4hr_4_Rpb1_1_S24

value: Triptolide 4hr


title: Mda5 RIP-Seq of Adar ko b2 placenta

value: Adar ko


title: patient 11, Day 14, Short Responder

value: PBMC


title: HCT116-Rpb1 degron, triptolide 4hr, biological replicate 4, H3K36me3

description: Library name: HCT116_TRP_4hr_4_H3K36me3_1_S23


title: HCT116-Rpb1 degron, triptolide 1hr, biological replicate 4, H3K27ac

description: Library name: HCT116_TRP_1hr_4_H3K27ac_1_S13

value: CST H3K27ac (D5E4)

value: Triptolide 1hr


title: snRNA-Seq of mus musculus: Adar1 wt placenta seq3

description:
WT2-3_S1_L003
con_filtered_feature_bc_matrix.h7
con_metrics_summary.csv


title: HCT116-Rpb1 degron, triptolide 1hr, biological replicate 3, Rpb1

description: Library name: HCT116_TRP_1hr_3_Rpb1_1_S12

value: CST Rpb1 NTD (D8L4Y)


title: R882C_4_EPO

value: EPO (3U/ml) 6 hours


title: snRNA-Seq of mus musculus: Adar1 wt placenta seq2

description:
WT2-2_S1_L002
con_filtered_feature_bc_matrix.h6
con_metrics_summary.csv


title: Mda5 RIP-Seq of Adar f/f a8 placenta

value: Adar f/f


title: HCT116-Rpb1 degron, triptolide 1hr, biological replicate 3, H3K4me3

description: Library name: HCT116_TRP_1hr_3_H3K4me3_1_S10

value: CST H3K4me3 (C42D8)


title: HCT116-Rpb1 degron, triptolide 4hr, biological replicate 4, H3K4me3

description: Library name: HCT116_TRP_4hr_4_H3K4me3_1_S22


title: HCT116-Rpb1 degron, triptolide 1hr, biological replicate 4, Rpb1

description: Library name: HCT116_TRP_1hr_4_Rpb1_1_S16


title: HCT116-Rpb1 degron, auxin 4hr, biological replicate 4, H3K4me3

description: Library name: HCT116_IAA_4hr_4_H3K4me3_1_S30

value: Auxin 4hr


title: HCT116-Rpb1 degron, triptolide 1hr, biological replicate 4, H3K4me3

description: Library name: HCT116_TRP_1hr_4_H3K4me3_1_S14


title: WT4_CTRL

value: WT

value: NO TREATMENT


title: HCT116-Rpb1 degron, triptolide 1hr, biological replicate 4, H3K36me3

description: Library name: HCT116_TRP_1hr_4_H3K36me3_1_S15

value: CST H3K36me3 (D5A7)


title: R882H_4_CTRL


title: R882H_4_EPO


title: HCT116-Rpb1 degron, triptolide 1hr, biological replicate 3, H3K36me3

description: Library name: HCT116_TRP_1hr_3_H3K36me3_1_S11


title: HCT116-Rpb1 degron, triptolide 1hr, biological replicate 3, H3K27ac

description: Library name: HCT116_TRP_1hr_3_H3K27ac_1_S9


title: snRNA-Seq of mus musculus: Adar1 ko placenta seq4

description:
KO2-4_S1_L006
ko_filtered_feature_bc_matrix.h5
ko_metrics_summary.csv

value: Adar1 ko


title: HCT116-Rpb1 degron, auxin 4hr, biological replicate 4, H3K36me3

description: Library name: HCT116_IAA_4hr_4_H3K36me3_1_S31

value: D. melanogaster, S. cerevisiae


title: snRNA-Seq of mus musculus: Adar1 wt placenta seq1

description:
WT2-1_S1_L001
con_filtered_feature_bc_matrix.h5
con_metrics_summary.csv

value: Adar1 wt


title: WT4_EPO


title: DK604_EPO


title: HCT116-Rpb1 degron, auxin 4hr, biological replicate 4, Rpb1

description: Library name: HCT116_IAA_4hr_4_Rpb1_1_S32

value: human colon cancer


title: DK604_CTRL


title: R882C_3_EPO


title: HCT116-Rpb1 degron, auxin 4hr, biological replicate 3, H3K4me3

description: Library name: HCT116_IAA_4hr_3_H3K4me3_1_S34


title: HCT116-Rpb1 degron, auxin 4hr, biological replicate 3, H3K36me3

description: Library name: HCT116_IAA_4hr_3_H3K36me3_1_S35


title: R882C_3_CTRL


title: HCT116-Rpb1 degron, auxin 4hr, biological replicate 3, H3K27ac

description: Library name: HCT116_IAA_4hr_3_H3K27ac_1_S33


title: HCT116-Rpb1 degron, auxin 4hr, biological replicate 3, Rpb1

description: Library name: HCT116_IAA_4hr_3_Rpb1_1_S36


title: HCT116-Rpb1 degron, auxin 1hr, biological replicate 4, Rpb1

description: Library name: HCT116_IAA_1hr_4_Rpb1_1_S40

value: Auxin 1hr


title: snRNA-Seq of mus musculus: Adar1 ko placenta seq3

description:
KO2-3_S1_L003
ko_filtered_feature_bc_matrix.h5
ko_metrics_summary.csv

value: placenta


title: HCT116-Rpb1 degron, auxin 1hr, biological replicate 4, H3K4me3

description: Library name: HCT116_IAA_1hr_4_H3K4me3_1_S38


title: snRNA-Seq of mus musculus: Adar1 ko placenta seq1

description:
KO2-1_S1_L001
ko_filtered_feature_bc_matrix.h5
ko_metrics_summary.csv


title: R882H_3_EPO


title: snRNA-Seq of mus musculus: Adar1 ko placenta seq2

description:
KO2-2_S1_L002
ko_filtered_feature_bc_matrix.h5
ko_metrics_summary.csv


title: snRNA-Seq of mus musculus: Adar1 ko placenta seq5

description:
KO2-5_S1_L003
ko_filtered_feature_bc_matrix.h5
ko_metrics_summary.csv


title: R882H_3_CTRL


title: HCT116-Rpb1 degron, auxin 1hr, biological replicate 4, H3K36me3

description: Library name: HCT116_IAA_1hr_4_H3K36me3_1_S39


title: HCT116-Rpb1 degron, auxin 4hr, biological replicate 4, H3K27ac

description: Library name: HCT116_IAA_4hr_4_H3K27ac_1_S29


title: DK603_EPO


title: HCT116-Rpb1 degron, auxin 1hr, biological replicate 4, H3K27ac

description: Library name: HCT116_IAA_1hr_4_H3K27ac_1_S37


title: HCT116-Rpb1 degron, auxin 1hr, biological replicate 3, H3K4me3

description: Library name: HCT116_IAA_1hr_3_H3K4me3_1_S26


title: HCT116-Rpb1 degron, auxin 1hr, biological replicate 3, Rpb1

description: Library name: HCT116_IAA_1hr_3_Rpb1_1_S28


title: TCells_Py2T_In_vivo_Thy1_rep3

data_processing:
Trim Galore! (v0.6.6; parameters: –q 20 –length 20)
Mapping using STAR (v 2.5.9a) to mouse (GRCm39)  with splice junctions from the human GENCODE annotation (release M29)
The gene-level expression counts were computed with featureCounts from the subread package (v.2.0.3; parameters: -t exon -g gene_id --minOverlap 10 -Q 10) using the human gene annotations from GENCODE (release 40)
Samples were retained for further analyses if they had at least 500’000 reads, at least 5’000 genes with non-zero expression and less than 50% of reads mapping to mitochondrial genes
Assembly: GRCm39 and GENCODE release M29
Supplementary files format and content: counts.txt.gz are tab-delimited files containing raw counts for each library

source_name: TCells_Py2T_In_vivo_Thy1_rep3 Thy1-transduced, Cd3-sorted Py2T intratumoral T cells, replicate 3

extract_protocol:
FACS-purified cells were lysed immediately upon direct sorting in 150 µL of extraction buffer from the Arcturus PicoPure RNA isolation kit (Thermo Scientific). The quality of the RNA isolated through the PicoPure kit was determined with a TapeStation RNA High sensitivity Screen Tape (Agilent).
Due to the low concentration of total RNA the SMARTer® Stranded Total RNA-Seq Kit v3 -Pico Input Mammalian (Takara Bio) was used to prepare sequencing libraries. Briefly, total RNA samples (0.27–8 ng) were mechanically fragmented (4 minutes) and reverse-transcribed using random priming into double-stranded cDNA in the presence of a template switch oligo (TSO). When the reverse transcriptase reaches the 5’ end of the RNA fragment, the enzyme’s terminal transferase activity adds non-templated nucleotides to the 3’ end of the cDNA, then the TSO pairs with the added non-templated nucleotide, enabling the reverse transcriptase to continue replicating to the end of the oligonucleotide. This procedure results in a cDNA fragment that contains sequences derived from the random priming oligo and the TSO. So, PCR amplification using primers binding to the latter sequences was performed so to add full-length Illumina adapters, including dual barcodes for multiplexing. Ribosomal cDNA was cleaved by ZapR in the presence of the mammalian-specific R-Probes. Remaining fragments were enriched with a second round of PCR amplification using primers designed to match Illumina adapters. Since RNA input concentrations was highly variable the samples were grouped into two sets of samples and PCR cycle numbers were adjusted (Group 1 = 6.5-8ng input, 12 cycles; Group 2 = 0.27-4 ng, 16 cycles). The quality and quantity of the enriched libraries were validated using a TapeStation analyzer (Agilent). The product presented as a smear with an average fragment size of approximately 300 - 360 bp. The libraries were normalized to 5nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.

value: t cells

tag: number of_cells

tag: origin

value: allograft

value: FVB

value: no


title: DK603_CTRL


title: TCells_Py2T_In_vivo_Thy1_rep2

source_name: TCells_Py2T_In_vivo_Thy1_rep2 Thy1-transduced, Cd3-sorted Py2T intratumoral T cells, replicate 2


title: HCT116-Rpb1 degron, auxin 1hr, biological replicate 3, H3K27ac

description: Library name: HCT116_IAA_1hr_3_H3K27ac_1_S25

value: CST H3K27ac (D5E4)


title: HCT116-Rpb1 degron, DMSO 0hr, biological replicate 4, H3K4me3

description: Library name: HCT116_DMSO_0hr_4_H3K4me3_1_S6

value: DMSO


title: HCT116-Rpb1 degron, DMSO 0hr, biological replicate 4, H3K36me3

description: Library name: HCT116_DMSO_0hr_4_H3K36me3_1_S7


title: HCT116-Rpb1 degron, DMSO 0hr, biological replicate 4, Rpb1

description: Library name: HCT116_DMSO_0hr_4_Rpb1_1_S8

value: CST Rpb1 NTD (D8L4Y)


title: WT3_EPO

value: EPO (3U/ml) 6 hours


title: TCells_Py2T_In_vivo_Cas9_rep2

source_name: TCells_Py2T_In_vivo_Cas9_rep2 Rejected Cas9-BROAD, Cd3-sorted Py2T intratumoral T cells, replicate 2


title: TCells_Py2T_In_vivo_Cas9_rep1

source_name: TCells_Py2T_In_vivo_Cas9_rep1 Rejected Cas9-BROAD, Cd3-sorted Py2T intratumoral T cells, replicate 1


title: HCT116-Rpb1 degron, DMSO 0hr, biological replicate 4, H3K27ac

description: Library name: HCT116_DMSO_0hr_4_H3K27ac_1_S5


title: HCT116-Rpb1 degron, DMSO 0hr, biological replicate 3, H3K4me3

description: Library name: HCT116_DMSO_0hr_3_H3K4me3_1_S2

value: CST H3K4me3 (C42D8)


title: TCells_MVT1_In_vivo_Thy1_rep3

source_name: TCells_MVT1_In_vivo_Thy1_rep3 Thy1-transduced, Cd3-sorted MVT1 intratumoral T cells, replicate 3


title: HCT116-Rpb1 degron, DMSO 0hr, biological replicate 3, H3K36me3

description: Library name: HCT116_DMSO_0hr_3_H3K36me3_1_S3


title: R882C_2_CTRL

value: NO TREATMENT


title: HelaS3, 95percent TSA, 5percent DMSO, spike3, input

description: Library name: HelaS3_95TSA_5DMSO_spike3_input

value: human cerival cancer

value: DMSO and 1uM TSA 18hr


title: TCells_MVT1_In_vivo_Thy1_rep2

source_name: TCells_MVT1_In_vivo_Thy1_rep2 Thy1-transduced, Cd3-sorted MVT1 intratumoral T cells, replicate 2


title: R882H_2_EPO


title: HelaS3, 95percent TSA, 5percent DMSO, spike3, H3K27ac

description: Library name: HelaS3_95TSA_5DMSO_spike3_H3K27ac

value: D. melanogaster, S. cerevisiae


title: HelaS3, 95percent TSA, 5percent DMSO, spike4, input

description: Library name: HelaS3_95TSA_5DMSO_spike4_input


title: HelaS3, 95percent TSA, 5percent DMSO, spike4, H3K27ac

description: Library name: HelaS3_95TSA_5DMSO_spike4_H3K27ac


title: TCells_MVT1_In_vivo_Thy1_rep1

source_name: TCells_MVT1_In_vivo_Thy1_rep1 Thy1-transduced, Cd3-sorted MVT1 intratumoral T cells, replicate 1


title: HelaS3, 95percent TSA, 5percent DMSO, spike2, H3K27ac

description: Library name: HelaS3_95TSA_5DMSO_spike2_H3K27ac


title: HelaS3, 95percent TSA, 5percent DMSO, spike1, input

description: Library name: HelaS3_95TSA_5DMSO_spike1_input


title: HCT116-Rpb1 degron, auxin 1hr, biological replicate 3, H3K36me3

description: Library name: HCT116_IAA_1hr_3_H3K36me3_1_S27

value: CST H3K36me3 (D5A7)


title: TCells_Py2T_In_vivo_Cas9_rep3

source_name: TCells_Py2T_In_vivo_Cas9_rep3 Rejected Cas9-BROAD, Cd3-sorted Py2T intratumoral T cells, replicate 3


title: TCells_MVT1_In_vivo_Cas9_rep3

source_name: TCells_MVT1_In_vivo_Cas9_rep3 Rejected Cas9-BROAD, Cd3-sorted MVT1 intratumoral T cells, replicate 3


title: HelaS3, 75percent TSA, 25percent DMSO, spike4, input

description: Library name: HelaS3_75TSA_25DMSO_spike4_input


title: TCells_MVT1_In_vivo_Cas9_rep1

source_name: TCells_MVT1_In_vivo_Cas9_rep1 Rejected Cas9-BROAD, Cd3-sorted MVT1 intratumoral T cells, replicate 1


title: DK602_EPO


title: WT2_EPO

value: WT


title: HelaS3, 75percent TSA, 25percent DMSO, spike4, H3K27ac

description: Library name: HelaS3_75TSA_25DMSO_spike4_H3K27ac


title: TCells_4T1_In_vivo_Thy1_rep3

source_name: TCells_4T1_In_vivo_Thy1_rep3 Thy1-transduced, Cd3-sorted 4T1 intratumoral T cells, replicate 3

value: BALBc


title: HelaS3, 75percent TSA, 25percent DMSO, spike3, input

description: Library name: HelaS3_75TSA_25DMSO_spike3_input


title: HCT116-Rpb1 degron, DMSO 0hr,  biological replicate 3, Rpb1

description: Library name: HCT116_DMSO_0hr_3_Rpb1_1_S4

value: human colon cancer


title: WT2_CTRL


title: HelaS3, 75percent TSA, 25percent DMSO, spike3, H3K27ac

description: Library name: HelaS3_75TSA_25DMSO_spike3_H3K27ac


title: R882C_2_EPO


title: DK602_CTRL


title: WT3_CTRL


title: HCT116-Rpb1 degron, DMSO 0hr, biological replicate 3, H3K27ac

description: Library name: HCT116_DMSO_0hr_3_H3K27ac_1_S1


title: R882H_2_CTRL


title: TCells_MVT1_In_vivo_Cas9_rep2

source_name: TCells_MVT1_In_vivo_Cas9_rep2 Rejected Cas9-BROAD, Cd3-sorted MVT1 intratumoral T cells, replicate 2

value: t cells


title: TCells_4T1_In_vivo_Thy1_rep2

source_name: TCells_4T1_In_vivo_Thy1_rep2 Thy1-transduced, Cd3-sorted 4T1 intratumoral T cells, replicate 2

value: allograft


title: HelaS3, 95percent TSA, 5percent DMSO, spike1, H3K27ac

description: Library name: HelaS3_95TSA_5DMSO_spike1_H3K27ac


title: HelaS3, 75percent TSA, 25percent DMSO, spike1, H3K27ac

description: Library name: HelaS3_75TSA_25DMSO_spike1_H3K27ac


title: TCells_4T1_In_vivo_Cas9_rep1

source_name: TCells_4T1_In_vivo_Cas9_rep1 Rejected Cas9-BROAD, Cd3-sorted 4T1 intratumoral T cells, replicate 1


title: HelaS3, 75percent TSA, 25percent DMSO, spike2, input

description: Library name: HelaS3_75TSA_25DMSO_spike2_input


title: HelaS3, 95percent TSA, 5percent DMSO, spike2, input

description: Library name: HelaS3_95TSA_5DMSO_spike2_input


title: HelaS3, 75percent TSA, 25percent DMSO, spike2, H3K27ac

description: Library name: HelaS3_75TSA_25DMSO_spike2_H3K27ac


title: HelaS3, 75percent TSA, 25percent DMSO, spike1, input

description: Library name: HelaS3_75TSA_25DMSO_spike1_input


title: TCells_4T1_In_vivo_Cas9_rep2

source_name: TCells_4T1_In_vivo_Cas9_rep2 Rejected Cas9-BROAD, Cd3-sorted 4T1 intratumoral T cells, replicate 2


title: HelaS3, 50percent TSA, 50percent DMSO, spike3, H3K27ac

description: Library name: HelaS3_50TSA_50DMSO_spike3_H3K27ac


title: R882H_1_EPO


title: R882C_1_CTRL


title: HelaS3, 50percent TSA, 50percent DMSO, spike3, input

description: Library name: HelaS3_50TSA_50DMSO_spike3_input


title: DK601_EPO


title: HelaS3, 50percent TSA, 50percent DMSO, spike1, input

description: Library name: HelaS3_50TSA_50DMSO_spike1_input


title: Py2T_In_vivo_Thy1

source_name: Py2T_In_vivo_Thy1 Thy1-transduced, Thy1.2-sorted Py2T tumor cells

value: tumor

value: FVB


title: HelaS3, 50percent TSA, 50percent DMSO, spike2, input

description: Library name: HelaS3_50TSA_50DMSO_spike2_input


title: R882H_1_CTRL


title: HelaS3, 50percent TSA, 50percent DMSO, spike2, H3K27ac

description: Library name: HelaS3_50TSA_50DMSO_spike2_H3K27ac

value: CST H3K27ac (D5E4)


title: HelaS3, 50percent TSA, 50percent DMSO, spike4, H3K27ac

description: Library name: HelaS3_50TSA_50DMSO_spike4_H3K27ac


title: HelaS3, 50percent TSA, 50percent DMSO, spike4, input

description: Library name: HelaS3_50TSA_50DMSO_spike4_input


title: DK601_CTRL


title: Py2T_In_vivo_Cas9_TREAT

source_name: Py2T_In_vivo_Cas9_TREAT Depletion_Rejected Cas9-BROAD, Thy1.2-sorted Py2T tumor cells

value: anti-CD4_anti-CD8 lymphocyte depleting antibodies


title: HelaS3, 25percent TSA, 75percent DMSO, spike4, input

description: Library name: HelaS3_25TSA_75DMSO_spike4_input


title: Py2T_In_vivo_Cas9

source_name: Py2T_In_vivo_Cas9 Rejected Cas9-BROAD, Thy1.2-sorted Py2T tumor cells

value: no


title: WT1_EPO

value: EPO (3U/ml) 6 hours


title: HelaS3, 25percent TSA, 75percent DMSO, spike4, H3K27ac

description: Library name: HelaS3_25TSA_75DMSO_spike4_H3K27ac


title: R882C_1_EPO


title: HelaS3, 25percent TSA, 75percent DMSO, spike3, H3K27ac

description: Library name: HelaS3_25TSA_75DMSO_spike3_H3K27ac


title: Py2T_In_vitro_Thy1

source_name: Py2T_In_vitro_Thy1 In vitro cultivated Py2T cells

value: cell culture


title: HelaS3, 25percent TSA, 75percent DMSO, spike3, input

description: Library name: HelaS3_25TSA_75DMSO_spike3_input


title: HelaS3, 25percent TSA, 75percent DMSO, spike2, input

description: Library name: HelaS3_25TSA_75DMSO_spike2_input


title: PKO_gOE3

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

data_processing:
Raw data (raw reads) of fastq format were processed through in-house perl scripts to remove reads containing adapter and poly-N sequences and reads with low quality.
Paired-end clean reads were aligned to the Homo Sapiens reference genome hg38 using Hisat2 v2.0.5.
Feature Counts software (v1.5.0-p3) was used to count the number of reads mapped per gene. Then, FPKM (Fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including the read count values for all 12 samples
Supplementary files format and content: tab-delimited text file including the fpkm values for all 12 samples

source_name: Xenograft tumor

extract_protocol:
Total RNA was extracted from cells using a RNeasy Mini Kit (Qiagen, Cat#74106) with DNAse I digestion (Qiagen, Cat#79254).
Libraries were prepared at Novogene Bioinformatics Technology Co., Ltd using the NEBNext Ultra II RNA Library Prep kit according to manufacturer's recommendations and sequenced as paired-end 150bp reads on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: For xenograft experiments, NSG mice 8-12 weeks of age were used for subcutaneous injection of tumor cell suspensions from four established DU145 cell lines. For PTEN knockout using the CRISPR/Cas9 system, sgRNA plasmids targeting human control CRISPR KO plasmid and human PTEN were purchased from Santa Cruz Biotechnology (Santa Cruz, Cat#sc-418922 and Cat#sc-400103, respectively). PTEN knockout was achieved to establish a PTEN-ERRγlow cell line from the parental DU145 cell line (PTEN+ERRγlow). ERRγ was overexpressed in both PTEN+ERRγlow and PTEN-ERRγlow DU145 cell lines using lentivirus to establish PTEN+ERRγ+ and PTEN-ERRγ+ cell lines, respectively.

value: Xenograft tumor

value: Human prostate cancer

value: PTEN-ERR{gamma}+

value: CRISPR/Cas9-mediated PTEN knockout + lentivirus-mediated overexpression of ERRγ


title: WT1_CTRL

value: NO TREATMENT


title: Py2T_In_vivo_Thy1_Lungs

source_name: Py2T_In_vivo_Thy1_Lungs Thy1-transduced, Thy1.2-sorted Py2T lung metastatic cells


title: HelaS3, 25percent TSA, 75percent DMSO, spike2, H3K27ac

description: Library name: HelaS3_25TSA_75DMSO_spike2_H3K27ac

value: D. melanogaster, S. cerevisiae

value: human cerival cancer

value: DMSO and 1uM TSA 18hr


title: NKCells_Py2T_In_vivo_Cas9

source_name: NKCells_Py2T_In_vivo_Cas9 Rejected Cas9-BROAD, Dx5-sorted Py2T intratumoral NK cells

value: nk cells


title: NKCells_Py2T_In_vivo_Thy1

source_name: NKCells_Py2T_In_vivo_Thy1 Thy1-transduced, Dx5-sorted Py2T intratumoral NK cells

value: allograft


title: PKO_gOE2


title: HelaS3, 25percent TSA, 75percent DMSO, spike1, H3K27ac

description: Library name: HelaS3_25TSA_75DMSO_spike1_H3K27ac


title: NKCells_MVT1_In_vivo_Thy1

source_name: NKCells_MVT1_In_vivo_Thy1 Thy1-transduced, Dx5-sorted MVT1 intratumoral NK cells


title: HelaS3, 50percent TSA, 50percent DMSO, spike1, H3K27ac

description: Library name: HelaS3_50TSA_50DMSO_spike1_H3K27ac


title: PKO_gOE1


title: PTEN_KO3

value: PTEN-ERR{gamma}low

value: CRISPR/Cas9-mediated PTEN knockout


title: NKCells_4T1_In_vivo_Thy1

source_name: NKCells_4T1_In_vivo_Thy1 Thy1-transduced, Dx5-sorted 4T1 intratumoral NK cells

value: BALBc


title: HelaS3, 100percent TSA, 0percent DMSO, spike2, input

description: Library name: HelaS3_100TSA_0DMSO_spike2_input

value: 1uM TSA 18hr


title: PTEN_KO2


title: NKCells_4T1_In_vivo_Cas9

source_name: NKCells_4T1_In_vivo_Cas9 Rejected Cas9-BROAD, Dx5-sorted 4T1 intratumoral NK cells

value: no


title: HelaS3, 100percent TSA, 0percent DMSO, spike2, H3K27ac

description: Library name: HelaS3_100TSA_0DMSO_spike2_H3K27ac

value: CST H3K27ac (D5E4)


title: HelaS3, 100percent TSA, 0percent DMSO, spike1, input

description: Library name: HelaS3_100TSA_0DMSO_spike1_input


title: PTEN_KO1


title: HelaS3, 0percent TSA, 100percent DMSO, spike4, input

description: Library name: HelaS3_0TSA_100DMSO_spike4_input

value: DMSO 18hr


title: ERRg_OE3

value: Xenograft tumor

value: PTEN+ERR{gamma}+

value: Lentivirus-mediated overexpression of ERRγ


title: Neutroph_Py2T_In_vivo_Cas9

source_name: Neutroph_Py2T_In_vivo_Cas9 Rejected Cas9-BROAD, Ly6G(pos)sorted Py2T intratumoral neutrophil-like cells

value: neutrophil like

value: FVB


title: Neutroph_Py2T_In_vivo_Thy1

source_name: Neutroph_Py2T_In_vivo_Thy1 Thy1-transduced, Ly6G(pos)sorted Py2T intratumoral neutrophil-like cells


title: HelaS3, 0percent TSA, 100percent DMSO, spike4, H3K27ac

description: Library name: HelaS3_0TSA_100DMSO_spike4_H3K27ac

value: D. melanogaster, S. cerevisiae


title: ERRg_OE2

value: Human prostate cancer


title: HelaS3, 25percent TSA, 75percent DMSO, spike1, input

description: Library name: HelaS3_25TSA_75DMSO_spike1_input

value: human cerival cancer

value: DMSO and 1uM TSA 18hr


title: HelaS3, 100percent TSA, 0percent DMSO, spike4, H3K27ac

description: Library name: HelaS3_100TSA_0DMSO_spike4_H3K27ac


title: NKCells_MVT1_In_vivo_Cas9

source_name: NKCells_MVT1_In_vivo_Cas9 Rejected Cas9-BROAD, Dx5-sorted MVT1 intratumoral NK cells

value: nk cells

value: allograft


title: HelaS3, 100percent TSA, 0percent DMSO, spike3, input

description: Library name: HelaS3_100TSA_0DMSO_spike3_input


title: HelaS3, 100percent TSA, 0percent DMSO, spike3, H3K27ac

description: Library name: HelaS3_100TSA_0DMSO_spike3_H3K27ac


title: Neutroph_MVT1_In_vivo_Thy1

source_name: Neutroph_MVT1_In_vivo_Thy1 Thy1-transduced, Ly6G(pos)sorted MVT1 intratumoral neutrophil-like cells


title: HelaS3, 0percent TSA, 100percent DMSO, spike2, input

description: Library name: HelaS3_0TSA_100DMSO_spike2_input


title: HelaS3, 100percent TSA, 0percent DMSO, spike4, input

description: Library name: HelaS3_100TSA_0DMSO_spike4_input


title: HelaS3, 0percent TSA, 100percent DMSO, spike1, input

description: Library name: HelaS3_0TSA_100DMSO_spike1_input


title: Neutroph_MVT1_In_vivo_Cas9

source_name: Neutroph_MVT1_In_vivo_Cas9 Rejected Cas9-BROAD, Ly6G(pos)sorted MVT1 intratumoral neutrophil-like cells


title: CTRL3

value: PTEN+ERR{gamma}low


title: HelaS3, 0percent TSA, 100percent DMSO, spike1, H3K27ac

description: Library name: HelaS3_0TSA_100DMSO_spike1_H3K27ac


title: Neutroph_4T1_In_vivo_Thy1

source_name: Neutroph_4T1_In_vivo_Thy1 Thy1-transduced, Ly6G(pos)sorted 4T1 intratumoral neutrophil-like cells

value: BALBc


title: HelaS3, 0percent TSA, 100percent DMSO, spike2, H3K27ac

description: Library name: HelaS3_0TSA_100DMSO_spike2_H3K27ac


title: ERRg_OE1


title: CTRL2


title: HCT116, auxin 4hr, biological replicate 2, input

description: Library name: HCT116_IAA_4hr_2_input

data_processing:
Samples were sequenced on Illumina NextSeq 550 or Nextseq 2000, samples were demultiplexed with Illumina bcl2fastq.
Adapters were removed with Trimmomatic, reads with Phred score <26 over a 4bp window were truncated.
Reads were aligned to a concatenated genome containing hg38 + sacCer3 + dm6, alignment files were separated by species. Duplicate reads were removed with samtools markdup.
HOMER tag directories were made; by default read counts for each species were filtered for primary alignments with MAPQ > 10, reads were extended to model approximate ChIP-seq fragment size using the option -fragLength 150. Samples were converted to bed files for normalization. Details of spike-in normalization are described in Supplement, normalized data are in bedGraph format.
Read normalized bigwig files were created with HOMER makeBigWig.pl from tag directories.
Assembly: hg38, dm6, sacCer3
Supplementary files format and content: Read-normalized BigWig files for hg38 genome

growth_protocol: HeLa-S3 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1x penicillin-streptomycin, L-glutamine, and 110mg/L sodium pyruvate. Cells were incubated at 37°C and 5% CO2. HCT116-EF1a-OsTIR1-Rpb1 cells were cultured in McCoy’s 5A media (Thermo Scientific 16600082) with 10% FBS and 1x antibiotic-antimycotic. Cells were incubated at 37°C and 5% CO2.

treatment_protocol: HeLa-S3 cells were synchronized in G1/S by adding 2 mM thymidine for 16 hr, washed with PBS, released for 3 hr in fresh medium, and pro-metaphase arrested with 10uM S-trityl-L-cysteine (STC) for 12 hr then harvested. HeLa-S3 cells and HCT116 cells were treated with 500nM Triptolide for 1 or 4 hours. HCT116 cells were treated with 500uM auxin for 1 or 4 hours.

value: human colon cancer

value: Auxin 4hr


title: Neutroph_4T1_In_vivo_Cas9

source_name: Neutroph_4T1_In_vivo_Cas9 Rejected Cas9-BROAD, Ly6G(pos)sorted 4T1 intratumoral neutrophil-like cells

value: no


title: HCT116, triptolide 4hr, biological replicate 2, input

description: Library name: HCT116_TRP_4hr_2_input

value: Triptolide 4hr


title: CTRL1

value: Xenograft tumor


title: HelaS3, 0percent TSA, 100percent DMSO, spike3, input

description: Library name: HelaS3_0TSA_100DMSO_spike3_input

value: DMSO 18hr


title: HelaS3, 100percent TSA, 0percent DMSO, spike1, H3K27ac

description: Library name: HelaS3_100TSA_0DMSO_spike1_H3K27ac

value: CST H3K27ac (D5E4)

value: 1uM TSA 18hr


title: HelaS3, 0percent TSA, 100percent DMSO, spike3, H3K27ac

description: Library name: HelaS3_0TSA_100DMSO_spike3_H3K27ac


title: HCT116, triptolide 1hr, biological replicate 2, input

description: Library name: HCT116_TRP_1hr_2_input

value: Triptolide 1hr


title: HCT116, DMSO treated, 0hr, biological replicate 2, input

description: Library name: HCT116_DMSO_0hr_2_input

value: D. melanogaster, S. cerevisiae

value: DMSO


title: HCT116, auxin 4hr, biological replicate 2, Rpb1 tech rep 2

description: Library name: HCT116_IAA_4hr_2_Rpb1_2

value: CST Rpb1 NTD (D8L4Y)


title: MVT1_In_vivo_Thy1_Lungs

source_name: MVT1_In_vivo_Thy1_Lungs Thy1-transduced, Thy1.2-sorted MVT1 lung metastatic cells

value: tumor

value: FVB


title: HCT116, auxin 4hr, biological replicate 2, Rpb1 tech rep 1

description: Library name: HCT116_IAA_4hr_2_Rpb1_1


title: HCT116, auxin 4hr, biological replicate 2, H3K4me1

description: Library name: HCT116_IAA_4hr_2_H3K4me1_1

value: CST H3K4me1 (D1A9)


title: Tumor_1

city: Beijing

first: Tingyao

last: Ma

address: DongchengNo.1, Dongjiao Min Alley

institute: Beijing Tongren Hospital

description: 10x Genomics

data_processing:
Illumina sequencing, Sequencing raw data, Valid barcodes, Valid UMI, Alignment with STAR, Gene-barcode Matrix, Detected Genes, UMI Normalization, PCA, t - SNE, k-means clustering, Subgroup correlation, Multiples and P values of gene expression differences in subpopulations, top20 significant genes
Use cell Ranger Single Cell V3 software to process data.The raw data contains a small number of articulated, repetitive, low-quality Reads that affect the quality of the comparison and subsequent analysis and are filtered during Cell Ranger processing.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: salivary gland

extract_protocol:
1 Around 100mg fresh sample or flash frozen tissue in liquid nitrogen is taken for next step.  2 The tissue homogenizer is inserted on ice. Add the 2 mL pre-chilled Homogeniza Buffer.  3 Transfer minced tissue to the chilled tissue homogenizer for 3-5 mins until the tissue is fully infiltrated.  4 Grind the tissue with the tissue homogenizer for around 10-15 times until grinding forces disappear. Assess if the nuclei are completely released into suspension and observe the suspension background under microscopy observation. 70 µm and 40 µm cell strainers are used to filter the tissue homogenate, followed by collection of into a 15 ml centrifuge tube.  5 Centrifuge at 500g and 4℃ for 5 mins and discard the supernatant. The cell pellets are washed twice with Wash buffer.  6 Resuspend the precipitate with the desired volume of Blocking Buffer and mix thoroughly. Observe the nuclei suspension background under microscopy observation.   7 If the suspension background is clean, cell counting can be used. Otherwise, fluorescence-activated cell sorting is needed to filter the suspension background.
After the amplification products were qualified, the sequencing library was constructed.The cDNA is first chemically broken to 200 to 300bp   The left and right fragments, cDNA fragmentation, terminal repair and addition of A, cDNA fragment screening, P7 Adaptor connector connection and PCR amplification to introduce sample Index, finally the fragment screening to obtain the cDNA library.

tag: disease

value: adenoid cystic carcinoma

value: salivary gland


title: MVT1_In_vivo_Cas9

source_name: MVT1_In_vivo_Cas9 Rejected Cas9-BROAD, Thy1.2-sorted MVT1 tumor cells

value: allograft


title: mRNA_SCI_Ctrl_D

city: Vestec

first: Ruslan

last: Klassen

address: Průmyslová 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science

description: Library name: mRNA_SCI_Ctrl_D

data_processing:
Raw reads were trimmed for adapters and low-quality bases using TrimmomaticSE v0.36. Reads mapping to mtDNA and rRNA were removed with SortMeRNA v2.1. Remaining reads were aligned to the rat genome (Rnor_6.0) using STAR v2.5.2b with default settings. Gene-level counts were obtained with htseq-count in "union" mode using Ensembl annotation Rnor_6.0.93.
Assembly: Rnor 6.0
Supplementary files format and content: mRNA_count_table.txt - Matrix of raw counts with mature miRNA names in rows and samples in columns.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: spinal cord tissue

growth_protocol: Adult male Wistar rats (10 weeks old, 300 ± 30 g) were obtained from the breeding facility of the Physiological Institute of the Academy of Sciences of the Czech Republic, Prague. Animals were housed under standard conditions (12-hour light/dark cycle) with ad libitum access to food and water. All procedures were approved by the Ethics Committee of the Institute of Experimental Medicine CAS and conformed to the Directive 2010/63/EU for animal experiments.

extract_protocol:
Animals were euthanized under deep anesthesia (ketamine 100 mg/kg, xylazine 20 mg/kg). Spinal cords were rapidly dissected, and a 2-cm-long segment centered on the injury epicenter was isolated. Tissue was immediately placed into RNAlater (Thermo Fisher Scientific) and stored at -80°C until RNA extraction. Total RNA was isolated using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer's protocol. RNA quantity and purity were assessed with NanoDrop 2000 (Thermo Fisher) and integrity evaluated using the Fragment Analyzer (Agilent); only samples with RQN >7 were used.
Libraries were prepared from 500 ng total RNA using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen), including 15 PCR amplification cycles. ERCC spike-ins (0.6 µl of 0.01× dilution) were added to each sample. Libraries were quantified using Qubit 2 fluorometer and Fragment Analyzer and sequenced on the Illumina NextSeq 500 platform using 85 bp single-end reads.

treatment_protocol: Spinal cord injury (SCI) was induced by balloon compression at the T8–T9 spinal level. Under anesthesia (3% isoflurane, buprenorphine 0.1 mg/kg), a 2F Fogarty catheter was inserted epidurally, inflated with 15 μl saline for 5 minutes, and then removed. Sham-operated animals underwent catheter insertion without balloon inflation. Post-surgery, animals received antibiotic (ampicillin 60 mg/kg daily for 5 days) and analgesic (buprenorphine 0.05–0.1 mg/kg as needed). Tissue for RNA extraction was collected at 3 hpi, 12 hpi, 24 hpi, 3 dpi, and 7 dpi, along with corresponding sham groups and intact controls.

value: spinal cord tissue

value: wild type

value: without treatment


title: MVT1_In_vivo_Thy1

source_name: MVT1_In_vivo_Thy1 Thy1-transduced, Thy1.2-sorted MVT1 tumor cells

value: no


title: HCT116, auxin 4hr, biological replicate 2, H3K36me3

description: Library name: HCT116_IAA_4hr_2_H3K36me3_1

value: human colon cancer

value: CST H3K36me3 (D5A7)

value: Auxin 4hr


title: mRNA_SCI_Ctrl_C

description: Library name: mRNA_SCI_Ctrl_C


title: HCT116, auxin 4hr, biological replicate 2, H3K4me3 tech rep 1

description: Library name: HCT116_IAA_4hr_2_H3K4me3_1

value: CST H3K4me3 (C42D8)


title: MVT1_In_vivo_Cas9_TREAT

source_name: MVT1_In_vivo_Cas9_TREAT Depletion_Rejected Cas9-BROAD, Thy1.2-sorted MVT1 tumor cells

value: anti-CD4_anti-CD8 lymphocyte depleting antibodies


title: HCT116, auxin 4hr, biological replicate 2, H3K27ac tech rep 2

description: Library name: HCT116_IAA_4hr_2_H3K27ac_2

value: D. melanogaster, S. cerevisiae

value: CST H3K27ac (D5E4)


title: HCT116, auxin 4hr, biological replicate 2, H3K4me3 tech rep 2

description: Library name: HCT116_IAA_4hr_2_H3K4me3_2


title: HCT116, auxin 4hr, biological replicate 2, H3K27ac tech rep 1

description: Library name: HCT116_IAA_4hr_2_H3K27ac_1


title: mRNA_SCI_Ctrl_B

description: Library name: mRNA_SCI_Ctrl_B


title: MVT1_In_vitro_Thy1

source_name: MVT1_In_vitro_Thy1 In vitro cultivated MVT1 cells

value: cell culture


title: HCT116, auxin 1hr, biological replicate 2, input

description: Library name: HCT116_IAA_1hr_2_input

value: Auxin 1hr


title: HCT116, auxin 1hr, biological replicate 2, Rpb1 tech rep 2

description: Library name: HCT116_IAA_1hr_2_Rpb1_2

value: CST Rpb1 NTD (D8L4Y)


title: Normal_1

description: 10x Genomics

value: Normal


title: Monocy_Py2T_In_vivo_Thy1

source_name: Monocy_Py2T_In_vivo_Thy1 Thy1-transduced, Ly6G(neg)sorted Py2T intratumoral monocyte-like cells

value: monocyte like

value: FVB


title: mRNA_SCI_Ctrl_A

description: Library name: mRNA_SCI_Ctrl_A

value: spinal cord tissue

value: Sham control surgery


title: HCT116, auxin 1hr, biological replicate 2, Rpb1 tech rep 1

description: Library name: HCT116_IAA_1hr_2_Rpb1_1


title: HCT116, auxin 1hr, biological replicate 2, H3K4me1

description: Library name: HCT116_IAA_1hr_2_H3K4me1_1

value: CST H3K4me1 (D1A9)


title: Monocy_Py2T_In_vivo_Cas9

source_name: Monocy_Py2T_In_vivo_Cas9 Rejected Cas9-BROAD, Ly6G(neg)sorted Py2T intratumoral monocyte-like cells

value: allograft

value: no


title: HCT116, auxin 1hr, biological replicate 2, H3K36me3

description: Library name: HCT116_IAA_1hr_2_H3K36me3_1

value: human colon cancer

value: CST H3K36me3 (D5A7)


title: mRNA_SCI_7D_SH_D

description: Library name: mRNA_SCI_7D_SH_D

value: wild type


title: HCT116, auxin 1hr, biological replicate 2, H3K4me3 tech rep 2

description: Library name: HCT116_IAA_1hr_2_H3K4me3_2

value: CST H3K4me3 (C42D8)


title: Monocy_MVT1_In_vivo_Thy1

source_name: Monocy_MVT1_In_vivo_Thy1 Thy1-transduced, Ly6G(neg)sorted MVT1 intratumoral monocyte-like cells


title: HCT116, auxin 1hr, biological replicate 2, H3K4me3 tech rep 1

description: Library name: HCT116_IAA_1hr_2_H3K4me3_1

value: D. melanogaster, S. cerevisiae


title: mRNA_SCI_7D_SH_C

description: Library name: mRNA_SCI_7D_SH_C


title: HCT116, auxin 1hr, biological replicate 2, H3K27ac tech rep 2

description: Library name: HCT116_IAA_1hr_2_H3K27ac_2

value: CST H3K27ac (D5E4)


title: Monocy_MVT1_In_vivo_Cas9

source_name: Monocy_MVT1_In_vivo_Cas9 Rejected Cas9-BROAD, Ly6G(neg)sorted MVT1 intratumoral monocyte-like cells


title: mRNA_SCI_7D_SH_A

description: Library name: mRNA_SCI_7D_SH_A

value: Laminotomy


title: Monocy_4T1_In_vivo_Thy1

source_name: Monocy_4T1_In_vivo_Thy1 Thy1-transduced, Ly6G(neg)sorted 4T1 intratumoral monocyte-like cells

value: BALBc


title: mRNA_SCI_7D_SH_B

description: Library name: mRNA_SCI_7D_SH_B


title: HCT116, triptolide 4hr, biological replicate 2, Rpb1 tech rep 1

description: Library name: HCT116_TRP_4hr_2_Rpb1_1

value: CST Rpb1 NTD (D8L4Y)

value: Triptolide 4hr


title: HCT116, triptolide 4hr, biological replicate 2, Rpb1 tech rep 2

description: Library name: HCT116_TRP_4hr_2_Rpb1_2


title: HCT116, auxin 1hr, biological replicate 2, H3K27ac tech rep 1

description: Library name: HCT116_IAA_1hr_2_H3K27ac_1

value: Auxin 1hr


title: HCT116, triptolide 4hr, biological replicate 2, H3K4me1

description: Library name: HCT116_TRP_4hr_2_H3K4me1_1


title: Monocy_4T1_In_vivo_Cas9

source_name: Monocy_4T1_In_vivo_Cas9 Rejected Cas9-BROAD, Ly6G(neg)sorted 4T1 intratumoral monocyte-like cells

value: monocyte like


title: mRNA_SCI_7D_B

description: Library name: mRNA_SCI_7D_B

value: spinal cord tissue


title: Fibrob_Py2T_In_vivo_Thy1

source_name: Fibrob_Py2T_In_vivo_Thy1 Depleted_Cas9-BROAD-transduced, Thy1.1-sorted Py2T fibroblasts

value: fibroblast

value: FVB


title: HCT116, triptolide 4hr, biological replicate 2, H3K4me3 tech rep 1

description: Library name: HCT116_TRP_4hr_2_H3K4me3_1


title: HCT116, triptolide 4hr, biological replicate 2, H3K36me3

description: Library name: HCT116_TRP_4hr_2_H3K36me3_1


title: HCT116, triptolide 4hr, biological replicate 2, H3K4me3 tech rep 2

description: Library name: HCT116_TRP_4hr_2_H3K4me3_2


title: HCT116, triptolide 4hr, biological replicate 2, H3K27ac tech rep 1

description: Library name: HCT116_TRP_4hr_2_H3K27ac_1


title: Fibrob_MVT1_In_vivo_Thy1

source_name: Fibrob_MVT1_In_vivo_Thy1 Depleted_Cas9-BROAD-transduced, Thy1.1-sorted MVT1 fibroblasts

value: allograft


title: mRNA_SCI_7D_A

description: Library name: mRNA_SCI_7D_A


title: mRNA_SCI_3D_SH_D

description: Library name: mRNA_SCI_3D_SH_D

value: Sham control surgery


title: HCT116, triptolide 1hr, biological replicate 2, Rpb1 tech rep 2

description: Library name: HCT116_TRP_1hr_2_Rpb1_2

value: human colon cancer

value: Triptolide 1hr


title: HCT116, triptolide 4hr, biological replicate 2, H3K27ac tech rep 2

description: Library name: HCT116_TRP_4hr_2_H3K27ac_2


title: mRNA_SCI_3D_SH_C

description: Library name: mRNA_SCI_3D_SH_C

value: wild type


title: HCT116, triptolide 1hr, biological replicate 2, Rpb1 tech rep 1

description: Library name: HCT116_TRP_1hr_2_Rpb1_1


title: DendritCells_allModels_In_vivo_Thy1

source_name: DendritCells_allModels_In_vivo_Thy1 Thy1-transduced, MHC-class2-sorted intratumoral dendritic cells, Mixture of MVT1 and Py2T tumors

value: dendritic cells

value: no


title: BCells_allModels_In_vivo_Thy1

source_name: BCells_allModels_In_vivo_Thy1 Thy1-transduced, CD19-sorted intratumoral B cells, Mixture of MVT1 and Py2T tumors

value: b cells


title: HCT116, triptolide 1hr, biological replicate 2, H3K4me1

description: Library name: HCT116_TRP_1hr_2_H3K4me1_1

value: D. melanogaster, S. cerevisiae

value: CST H3K4me1 (D1A9)


title: HCT116, triptolide 1hr, biological replicate 2, H3K36me3

description: Library name: HCT116_TRP_1hr_2_H3K36me3_1

value: CST H3K36me3 (D5A7)


title: HCT116, triptolide 1hr, biological replicate 2, H3K4me3 tech rep 2

description: Library name: HCT116_TRP_1hr_2_H3K4me3_2

value: CST H3K4me3 (C42D8)


title: 4T1_In_vivo_Thy1

source_name: 4T1_In_vivo_Thy1 Thy1-transduced, Thy1.1-sorted 4T1 tumor cells

value: tumor

value: BALBc


title: mRNA_SCI_3D_SH_A

description: Library name: mRNA_SCI_3D_SH_A

value: spinal cord tissue


title: HCT116, triptolide 1hr, biological replicate 2, H3K4me3 tech rep 1

description: Library name: HCT116_TRP_1hr_2_H3K4me3_1


title: HCT116, triptolide 1hr, biological replicate 2, H3K27ac tech rep 2

description: Library name: HCT116_TRP_1hr_2_H3K27ac_2

value: CST H3K27ac (D5E4)


title: 4T1_In_vivo_Thy1_Lungs

source_name: 4T1_In_vivo_Thy1_Lungs Thy1-transduced, Thy1.1-sorted 4T1 lung metastatic cells


title: mRNA_SCI_3D_D

description: Library name: mRNA_SCI_3D_D

value: Laminotomy


title: HCT116, DMSO treated, 0hr, biological replicate 2, Rpb1 tech rep 2

description: Library name: HCT116_DMSO_0hr_2_Rpb1_2

value: CST Rpb1 NTD (D8L4Y)

value: DMSO


title: HCT116, triptolide 1hr, biological replicate 2, H3K27ac tech rep 1

description: Library name: HCT116_TRP_1hr_2_H3K27ac_1

value: human colon cancer


title: 4T1_In_vivo_Cas9

source_name: 4T1_In_vivo_Cas9 Rejected Cas9-BROAD, Thy1.1-sorted 4T1 tumor cells

value: allograft


title: mRNA_SCI_3D_C

description: Library name: mRNA_SCI_3D_C

source_name: spinal cord tissue

value: wild type


title: 4T1_In_vivo_Cas9_TREAT

source_name: 4T1_In_vivo_Cas9_TREAT Depletion_Rejected Cas9-BROAD, Thy1.1-sorted 4T1 tumor cells

value: anti-CD4_anti-CD8 lymphocyte depleting antibodies


title: HCT116, DMSO treated, 0hr, biological replicate 2, H3K4me1

description: Library name: HCT116_DMSO_0hr_2_H3K4me1_1


title: mRNA_SCI_3D_B

description: Library name: mRNA_SCI_3D_B


title: HCT116, DMSO treated, 0hr, biological replicate 2, H3K36me3

description: Library name: HCT116_DMSO_0hr_2_H3K36me3_1


title: HCT116, DMSO treated, 0hr, biological replicate 2, H3K4me3 tech rep 2

description: Library name: HCT116_DMSO_0hr_2_H3K4me3_2


title: HCT116, DMSO treated, 0hr, biological replicate 2, Rpb1 tech rep 1

description: Library name: HCT116_DMSO_0hr_2_Rpb1_1


title: HCT116, DMSO treated, 0hr, biological replicate 2, H3K4me3 tech rep 1

description: Library name: HCT116_DMSO_0hr_2_H3K4me3_1


title: mRNA_SCI_3D_A

description: Library name: mRNA_SCI_3D_A


title: HCT116, DMSO treated, 0hr, biological replicate 2, H3K27ac tech rep 2

description: Library name: HCT116_DMSO_0hr_2_H3K27ac_2


title: 4T1_In_vitro_Thy1

source_name: 4T1_In_vitro_Thy1 In vitro cultivated 4T1 cells

value: cell culture

value: no


title: PyTCas9BROAD_FVB3 Rejected Cas9-BROAD Py2T Mammary fat pad tumor

data_processing:
Trim Galore! (v0.6.6; parameters: –q 20 –length 20)
Mapping using STAR (v 2.5.9a) to mouse (GRCm39)  with splice junctions from the human GENCODE annotation (release M29)
The gene-level expression counts were computed with featureCounts from the subread package (v.2.0.3; parameters: -t exon -g gene_id --minOverlap 10 -Q 10) using the human gene annotations from GENCODE (release 40)
Assembly: GRCm39 and GENCODE release M29 and CAS9 sequence
Supplementary files format and content: counts.txt.gz are tab-delimited files containing raw counts for each library

source_name: tumor

extract_protocol:
Individual tumor fragments were and homogenized using M-tubes (Miltenyi) and GentleMACS devices (Miltenyi) using the program RNA_001 and total RNA was isolated using the RNeasy kit (Qiagen).
The TruSeq Stranded mRNA (Illumina) was used for library preparation as described. Briefly, total RNA samples (500 ng) were poly-A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched by PCR. The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent).

value: bulk

value: FVB

tag: transduction

value: GFP-transduced


title: HCT116, auxin 4hr, biological replicate 1, H3K27ac tech rep 2

description: Library name: HCT116_IAA_4hr_1_H3K27ac_2

value: D. melanogaster, S. cerevisiae

value: Auxin 4hr


title: mRNA_SCI_3D_SH_B

description: Library name: mRNA_SCI_3D_SH_B

value: Sham control surgery


title: mRNA_SCI_24h_SH_D

description: Library name: mRNA_SCI_24h_SH_D

value: spinal cord tissue


title: PyTCas9BROAD_FVB2 Rejected Cas9-BROAD Py2T Mammary fat pad tumor

value: tumor


title: HCT116, DMSO treated, 0hr, biological replicate 2, H3K27ac tech rep 1

description: Library name: HCT116_DMSO_0hr_2_H3K27ac_1

value: CST H3K27ac (D5E4)


title: mRNA_SCI_24h_SH_C

description: Library name: mRNA_SCI_24h_SH_C


title: HCT116, auxin 1hr, biological replicate 1, H3K27ac tech rep 2

description: Library name: HCT116_IAA_1hr_1_H3K27ac_2

value: Auxin 1hr


title: HCT116, triptolide 4hr, biological replicate 1, H3K27ac tech rep 2

description: Library name: HCT116_TRP_4hr_1_H3K27ac_2

value: Triptolide 4hr


title: PyTCas9BROAD_FVB1 Rejected Cas9-BROAD Py2T Mammary fat pad tumor


title: HCT116, triptolide 1hr, biological replicate 1, H3K27ac tech rep 2

description: Library name: HCT116_TRP_1hr_1_H3K27ac_2

value: human colon cancer

value: Triptolide 1hr


title: Py2TNSG3 Rejection control Py2T Mammary fat pad tumor

value: allograft

value: NSG


title: mRNA_SCI_24h_SH_B

description: Library name: mRNA_SCI_24h_SH_B

value: wild type


title: HCT116, DMSO treated, 0hr, biological replicate 1, H3K27ac tech rep 2

description: Library name: HCT116_DMSO_0hr_1_H3K27ac_2

value: DMSO


title: mRNA_SCI_24h_SH_A

description: Library name: mRNA_SCI_24h_SH_A


title: Py2TNSG2 Rejection control Py2T Mammary fat pad tumor

value: bulk


title: Replacement_Sample5

description: Replacement_Sample5 StealTHY CRISPR KO _whole lungs in immunodeficient host_Replicate 7

source_name: CRISPR Knockout (by Cas9 transfection) of the 2180 sgRNA library (immune signalome library) through the StealTHY

value: xenograft

tag: crispr lib

value: Immuno Signalome (2180) sgRNA library

tag: sgrna library

tag: effect type

value: sgRNAs used as barcodes (no KO)

tag: vector

value: lentiGuide-THY

tag: full library_complexity


title: Replacement_Sample4

description: Replacement_Sample4 StealTHY CRISPR KO _whole tumor in immunodeficient host_Replicate 7


title: Replacement_Sample1

description: Replacement_Sample1 MDA231 Thy1 post-Cas9 transfection

source_name: Thy1 post-Cas9 transfection

value: In vitro

value: CRISPR KO


title: mRNA_SCI_24h_D

description: Library name: mRNA_SCI_24h_D

value: spinal cord tissue

value: Laminotomy


title: Py2TNSG1 Rejection control Py2T Mammary fat pad tumor

value: tumor

tag: strain

value: GFP-transduced


title: Replacement_Sample

description: Replacement_Sample MDA231 Thy1 pre-Cas9 transfection

source_name: Thy1 pre-Cas9 transfection


title: mRNA_SCI_24h_C

description: Library name: mRNA_SCI_24h_C


title: Py2T_UT_rep3 Untransduced Py2T Mammary fat pad tumor

value: FVB


title: mRNA_SCI_24h_B

description: Library name: mRNA_SCI_24h_B


title: H7Position_HumanPlate1

description: H7Position_HumanPlate1 dCas9-GFP immunogen_LN_Replicate2

source_name: dCas9 (i.e. no knockout) - SgRNAs as barcodes for studying loss of clonality


title: Py2T_UT_rep2 Untransduced Py2T Mammary fat pad tumor


title: H8Position_HumanPlate1

description: H8Position_HumanPlate1 dCas9-GFP immunogen_LN_Replicate4


title: H9Position_HumanPlate1

description: H9Position_HumanPlate1 dCas9-GFP control_LN_Replicate2


title: mRNA_SCI_24h_A

description: Library name: mRNA_SCI_24h_A


title: H5Position_HumanPlate1

description: H5Position_HumanPlate1 dCas9-THY1 immunogen_LN_Replicate2


title: H6Position_HumanPlate1

description: H6Position_HumanPlate1 dCas9-THY1 immunogen_LN_Replicate4


title: H4Position_HumanPlate1

description: H4Position_HumanPlate1 GFP immunogen_LN_Replicate4


title: Py2T_UT_rep1 Untransduced Py2T Mammary fat pad tumor


title: mRNA_SCI_12h_SH_D

description: Library name: mRNA_SCI_12h_SH_D

value: Sham control surgery