title: Rice-scATAC-Spikelet-s6-Rep2

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

institute: Chinese Academy of Agricultrual Sciences

description:
Library name: Sample12
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).

data_processing:
Raw sequencing data were converted to fastq format using ‘cellranger-arc mkfastq’. The multiome raw sequencing data for scRNA-seq and scATAC-seq were processed using CellRanger ARC (v2.0.2). Rice MSU 7.0 was used as the reference genome.
Assembly: MSU7
Supplementary files format and content: tsv,h5

organism: Oryza sativa

source_name: Spikelet

extract_protocol:
The nuclei isolation procedure was modified from the product information sheet of the CelLyticTM PN Isolation/Extraction Kit by Sigma. Briefly, the rice frozen organ was chopped in 1x NIBTA buffer (1 mM DL-Dithiothreitol solution, 1x ProtectRNA TM RNase Inhibitor, 1x cOmplete™, EDTA-free Protease Inhibitor Cocktail, 1x NIB, 0.3% Triton X-100) on pre-chilled plates. Transfer the homogenates to a new 15 mL tube. The tube was shaken for 5 min on ice. The lysate was transferred into a 30-μm Smartstrainer and collected using a new 15 mL tube. Spin the 15 mL tube for 10 min at 1,260 × g. Decant the supernatant and resuspend the pellet in 4 mL of 1x NIBTA buffer. Put 5 mL of 75% PercoII® solution (3.75 mL PercoII and 1.25 mL NIBTA buffer) in a new 15 mL tube and carefully transfer the lysate on top of the Percoll® layer. Centrifuge for 30 min at 650 × g. Most of the nuclei are banded at the interface between the 1x NIBTA buffer and the PercoII® layers. Gently collect the nuclei band in a new 15 mL tube, and 1x NIBTA buffer was added to 10 mL. Centrifuge for 5 min at 1260 × g. Wash the nucleus pellet twice with 1x NIBTA buffer. Nuclei were resuspended in diluted nuclei buffer (10x Genomics) to a final concentration of 4,000 nuclei per µL and used as input for single-cell multiome ATAC + gene expression and scRNA-seq library preparation (5 µL; approximately 20,000 nuclei).
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).

value: Spikelet

value: Nipponbare

value: WT


title: Rice-scRNA-Spikelet-s6-Rep2

status: Public on May 28 2025

type: SRA

country: China

description:
Library name: Sample11
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).

library_source: transcriptomic single cell

molecule: nuclear RNA

tag: tissue

tag: genotype

tag: treatment


title: HD_176

city: Verona

first: Barbara

last: Mariotti

state: Verona

address: strada le grazie 8

department: Medicine

country: Italy

institute: University of Verona

library_source: transcriptomic

data_processing:
Basecalls performed using bcl2fastq2
The quality of sequenced reads obtained from each sample was assessed using FastQC software. UMI sequences were extracted using UMI-Tools (v1.0.1). Raw reads were trimmed to remove low-quality ends, polyA tails, and adapters sequences using bbduk (v38.86).
Trimmed reads were aligned to the reference human genome (GRCh38) using STAR (v2.7.3a).
After mapping, PCR duplicates were removed from the BAM files based on UMI sequence using UMI-tools. The number of reads mapping to each gene was determined using HTSeq-count (v0.11.2). Reads counts were normalized with the FPM normalization method implemented in DESeq2. Batach correction of FPM counts were done with limma.
Assembly: GrCh38
Supplementary files format and content: tab delimited file containing batch adjusted FPM value

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: Neutrophils were purified from peripheral blood of COPD patients and control donors by density gradient centrifugation.

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen, Venlo, Limburg, Netherlands). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation.
RNA libraries for RNA-seq were prepared using QUANTSEQ 3' mRNA-seq library prep Kit (LEXOGENE) following manufacturer's protocols.

treatment_protocol: freshly isolated cells

value: peripheral blood

tag: cell line

value: primary cells

tag: cell type

value: neutrophils

tag: Sex

value: Male

tag: disease state

value: control


title: US22502722_253949444819_1_4- 0896-007

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

description: US22502722_253949444819_1_4- 0896-007

hyb_protocol: cRNA was hybridized to a human genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing:
Agilent Feature Extraction Software (v 10.7) was used for background subtraction and GeneSpring v.10.1 (Agilent Technologies, Inc., CA) software was used to conduct the preliminary data filtration and statistical analysis.
processed_data: Logratio (test/reference)

source_name: Whole Blood

label_protocol: Total RNA (200-2000ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol: Total RNA was isolated using the PAXgene Blood RNA kit (Qiagen, Valencia, CA) following manufacturer directions

treatment_protocol: treatment protocol is not applicable

tag: age

tag: gender

value: Female

value: Alive

tag: timepoint

source_name: Agilent's Universal Human Reference RNA

tag: reference

value: Agilent's Universal Human Reference RNA


title: US22502722_253949444819_2_4- 0896-017

description: US22502722_253949444819_2_4- 0896-017


title: HD_166


title: US22502722_253949444820_1_3- 0896-006

description: US22502722_253949444820_1_3- 0896-006


title: Rice-scRNA-Spikelet-s6-Rep1

description:
Library name: Sample9
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).


title: US22502722_253949444819_1_3- 0896-005

description: US22502722_253949444819_1_3- 0896-005


title: US22502722_253949444820_2_2- 0896-013

description: US22502722_253949444820_2_2- 0896-013


title: HD_161


title: Rice-scATAC-Spikelet-s4-Rep2

description:
Library name: Sample8
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).

library_source: genomic

molecule: genomic DNA


title: HD_159


title: US22502722_253949444820_1_1- 0896-002

description: US22502722_253949444820_1_1- 0896-002


title: SG16374548_253949448111_1_1_0894-018-900_hr168


title: US22502722_253949444819_1_1- 0896-001

description: US22502722_253949444819_1_1- 0896-001


title: HD_157


title: Rice-scRNA-Spikelet-s4-Rep2

description:
Library name: Sample7
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).


title: HD_158


title: SG16374548_253949448110_1_2_0894-016-900_hr144


title: Rice-scRNA-Spikelet-s4-Rep1

description:
Library name: Sample5
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).


title: SG16374548_253949448104_2_1_0894-017-900_hr156


title: SG16374548_253949448109_1_3_0894-015-900_hr132


title: US22502722_253949444820_1_4- 0896-008

description: US22502722_253949444820_1_4- 0896-008


title: HD_150


title: SG16374548_253949448095_1_4_0894-014-900_hr120


title: SG16374548_253949448108_1_4_0894-013-900_hr108


title: Rice-scATAC-Spikelet-s6-Rep1

description:
Library name: Sample10
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).


title: SG16374548_253949448103_2_4_0894-011-900_hr84


title: HD_149


title: Rice-scRNA-Spikelet-s3-Rep2

description:
Library name: Sample3
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).


title: SG16374548_253949448102_2_3_0894-010-900_hr72


title: HD_148


title: US22502722_253949444820_1_2- 0896-004

description: US22502722_253949444820_1_2- 0896-004


title: US22502722_253949444819_1_2- 0896-003

description: US22502722_253949444819_1_2- 0896-003


title: SG16374548_253949448309_2_1_0894-009-900_hr60


title: Rice-scATAC-Spikelet-s3-Rep1

description:
Library name: Sample2
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).


title: SG16374548_253949448100_2_1_0894-008-900_hr48


title: HD_146


title: SG16374548_253949447599_2_1_0894-007-900_hr36


title: Rice-scATAC-Spikelet-s4-Rep1

description:
Library name: Sample6
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).


title: SG16374548_253949447597_1_3_0894-006-900_hr24


title: SG16374548_253949447596_1_2_0894-004-900_hr8


title: SG16374548_253949447552_1_1_0894-002-900_hr2


title: HD_135


title: Rice-scRNA-Spikelet-s3-Rep1

description:
Library name: Sample1
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).


title: HD_143


title: Rice-scATAC-Spikelet-Rep2

description: 10x Genomics

library_source: genomic single cell

data_processing:
Raw sequencing data were converted to fastq format using ‘cellranger-arc mkfastq’. The multiome raw sequencing data for scRNA-seq and scATAC-seq were processed using CellRanger ARC (v2.0.2). Rice MSU 7.0 was used as the reference genome.
Raw count matrix data were imported into R using the Seurat (V.4.3.0) package for further data analysis. Low-quality cells were removed by filtering out cells that had fewer than 500 genes or 1,000 unique molecular identifiers (UMIs). Doublets and multiplets were filtered out using DoubletFinder. The core statistical parameters of DoubletFinder (nExp and pK) used to build artificial doublets for true doublet classification were determined automatically using recommended settings.The top 2000 highly variable genes were used for principal component analysis (PCA) dimensionality reduction. The first 20 principal components (PCs) were selected according to the PCA elbow plot and used for clustering with a suitable resolution parameter. Cluster stability was assessed using Clustree across a range of resolution values (0.1 to 2.0). Based on the results obtained from Clustree, a suitable resolution value was selected to determine the number of clusters. This process was performed separately for each sample. The clusters were visualized and explored by and UMAP .
To integrate count matrix data from different sources, the scRNA-seq data from each sample were combined into one single object. Variable genes were selected using the SCtransform function with default parameters. The FindIntegrationAnchors function command used default parameters (dims = 1:20) to discover integration anchors across all samples. The IntegrateData function was run on the anchor set with default additional arguments. ScaleData and RunPCA were then performed on the integrated assay to compute 20 PCs. UMAP dimensionality reduction was carried out and a shared nearest neighbor (SNN) graph constructed using dimensions 1:20 as input features and default PCA reduction. Clustering analysis was performed on the integrated assay at a resolution of 0.5.
Assembly: Rice MSU 7.0
Supplementary files format and content: Rdata of scRNA and scATAC

extract_protocol: A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).

tag: Stage

tag: library type

value: ATAC-seq

value: normal


title: SG16374548_253949447592_1_1_0894-005-900_hr12


title: Rice-scATAC-Spikelet-s3-Rep2

description:
Library name: Sample4
A total of 20,000 nuclei from each rice sample were pooled for single-cell multiome library generation using the 10X genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The nuclei were counted by Luna FL (Logos Biosystems). GEMs were generated using the 10X Chromium Controller with one lane of GEM chip (Chromium Next GEM Chip J) for each sample. scATAC and gene expression libraries from each pool were generated Glbizzia Biosciences following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide. In brief, nuclei were incubated in a transposition mix that includes transposases that enter the nuclei and fragment DNA in open regions of chromatin, while simultaneously adaptor sequences are added to the fragments. Single Cell Multiome ATAC + GEX Gel Beads capture the adaptor sequences on DNA fragments as well as the poly-A tail of mRNA and GEMs are generated and incubated, resulting in 10x barcoded DNA from the transposed DNA (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). cDNA was then purified, amplified and sequenced per the manufacturer’s recommendations (10x Genomics). The libraries were sequenced with Illumina NovaSeq 6000 under the modes of PE150 (scRNA-seq library) and PE50 (scATAC-seq library).


title: SG16374548_253949447272_1_2_0894-003-900_hr4


title: Rice-scRNA-Spikelet-Rep2

description: 10x Genomics

value: RNA-Seq


title: SG16374548_253949446603_1_1_0894-001-900_hr0


title: HD_132


title: SG16374548_253949448308_2_1_0892-001-900_hr0


title: HD_125.5


title: US22502722_253949444822_2_4- 0886-020

description: US22502722_253949444822_2_4- 0886-020


title: Rice-scRNA-Spikelet-Rep1

description: 10x Genomics


title: HD_122


title: US22502722_253949444822_2_3- 0886-018

description: US22502722_253949444822_2_3- 0886-018


title: US22502722_253949444775_2_2- 0886-017

description: US22502722_253949444775_2_2- 0886-017


title: HD_121


title: Rice-scATAC-Tiller_Bud-Rep1

description: 10x Genomics

source_name: Tiller Bud

value: Tiller Bud


title: Rice-scATAC-Tiller_Bud-Rep2

description: 10x Genomics


title: US22502722_253949444821_2_4- 0886-019

description: US22502722_253949444821_2_4- 0886-019


title: US22502722_253949444822_2_2- 0886-015

description: US22502722_253949444822_2_2- 0886-015


title: US22502722_253949444821_2_2- 0886-014

description: US22502722_253949444821_2_2- 0886-014


title: Rice-scATAC-Spikelet-Rep1

description: 10x Genomics


title: US22502722_253949444821_2_3- 0886-016

description: US22502722_253949444821_2_3- 0886-016


title: HD_120


title: US22502722_253949444822_2_1- 0886-013

description: US22502722_253949444822_2_1- 0886-013


title: US22502722_253949444822_1_4- 0886-011

description: US22502722_253949444822_1_4- 0886-011


title: Rice-scRNA-Tiller_Bud-Rep1

description: 10x Genomics


title: HD_111


title: US22502722_253949444822_1_3- 0886-009

description: US22502722_253949444822_1_3- 0886-009


title: Rice-scRNA-Tiller_Bud-Rep2

description: 10x Genomics


title: f3hR3

description:
Unknown_AR742-13T0012
raw_counts.txt

data_processing:
The fastp was used to remove adapter and filter out low-quality reads with more than 20% low-quality bases (quality <20), The clean reads were mapped to rice reference genome MSU7 by HISAT2. The gene expression level was calculated by featureCounts using default parameters. The DEseq package was used for identification and analysis of differential genes, and gene functional enrichment analysis was performed using agriGO v2.0 online software.
Assembly: MSU7
Supplementary files format and content: raw_counts.txt

source_name: Root

growth_protocol: Rice plants were cultivated hydroponically from germination using the Kimura nutrient solution. The nutrient solution was replaced every other day. The rice plants were grown in a growth chamber under the following conditions: temperature of 28 degrees Celsius and a 12-hour light/12-hour dark cycle.

extract_protocol:
RNA extraction was performed using the RNAprep pure Plant Total RNA Extraction Kit (Tiangen). A total of 1 μg of total RNA was used for library construction.
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (yeasen) following manufacturer's protocols

value: Root

value: one-month-old

value: f3h knockdown


title: US22502722_253949444775_2_1- 0886-008

description: US22502722_253949444775_2_1- 0886-008


title: US22502722_253949444821_1_3- 0886-007

description: US22502722_253949444821_1_3- 0886-007


title: US22502722_253949444822_1_2- 0886-006

description: US22502722_253949444822_1_2- 0886-006


title: f3hR2

description:
Unknown_AR742-13T0011
raw_counts.txt


title: SG16374548_253949448331_1_3_0897-009-900_hr60


title: HD_109


title: HD_105


title: US22502722_253949444821_1_2- 0886-005

description: US22502722_253949444821_1_2- 0886-005


title: f3hR1

description:
Unknown_AR742-13T0010
raw_counts.txt


title: US22502722_253949444775_1_4 - 0886-004

description: US22502722_253949444775_1_4 - 0886-004


title: US22502722_253949444822_1_1- 0886-003

description: US22502722_253949444822_1_1- 0886-003


title: K27M-RYBP-Rep3

city: Edinburgh

first: Gerry

last: Brien

address: Western General Hospital  Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University  of Edinburgh

description: 10% mouse cells was used as spike-in chromatin.

data_processing:
Analysis of CUT&RUN-Rx data involved adding the 'mm10_' prefix to chromosome names, creating a human/mouse hybrid genome by combining hg38 with mm10, aligning reads with Bowtie2 (v 2.3.5.1), filtering, and converting to BAM format using SAMtools (v 1.10).  Normalization was performed using the spike-in reads, and RRPM-normalized bigwig files were generated with deepTools' bamCoverage ( v 3.3.0). Peaks were called using macs2 (v 2.2.7.1) with paramaters broad --broad-cutoff 0.05, converted to bed format, and processed to generate consensus peak sets using MSPC (-r Bio -w 1e-4 -s 1e-8 -c 2) (v 5.4.0) and bedtools. Finally, peaks were annotated with HOMER
QuantSeq: Reads were trimmed using BBDUK to remove the first 11 nucleotides from reads, polyA tails, TruSeq adapters, low quality nucleotides with a q below 10, and reads smaller than 20 nucleotides in length. Reads were aligned to the hg38 genome using the STAR aligner (v2.7.3a). Gene abundance was quantified using htseq-count (v 0.11.2) and DESeq2 (v 1.36.0) was utilised to identify differentially expressed genes ( >1.5 fold change and a <0.05 Benjamini-Hochberg adjusted P value)
Assembly: hg38
Supplementary files format and content: txt files contain the output from DESeq, i.e. differentially expressed genes in H3K27M-KO or drug treated conditions compared to DIPGXIII untreated cells.
Library strategy: CUT&RUN-Rx

source_name: Brain

growth_protocol: All cell lines were grown as monolayers on CellBIND plates (Fisher Scientific) with DMEM/F12 (1:1) supplemented with Penicillin-Streptomycin (100U/mL; Gibco), Bovine albumin fraction V solution (7.5%; Gibco), MEM Non-essential amino acids solution (100X; Gibco), beta-mercaptoethanol (50mM; Gibco), N2 and B27 (Life Technologies), Laminin (R&D Systems; 2μg/mL), epidermal growth factor and fibroblast growth factor 2 (Peprotech; 10 ng/mL) as previously described (Conti et al. 2005).

extract_protocol:
CUT&RUN-Rx library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol. QuantSeq libraries were generated using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen; 015.24) in accordance with the manufacturer’s instructions.
Quantseq: Illumina NextSeq 500, 75-bp single end. CUT&RUN-Rx: Illumina NextSeq 500, 38-bp paired end.

treatment_protocol: Cells were treated with 2µM Tazemetostat or DMSO for 3, 6 and 9 days for Quantseq. For CUT&RUN, DIPGXIII cells were treated with 2µM Tazemetostat or DMSO for 6 days where indicated (with TAZ or DMSO in the file and sample names). Otherwise, DIPGXIII (Parental) and DIPGXIII-KO cells were untreated for CUT&RUN (indicated by P or KO in the file and sample names).

value: SU-DIPGXIII

value: H3K27M-positive SU-DIPGXIII cells

value: Brain

tag: antibody

value: DEDAF (Millipore, AB3637)


title: US22502722_253949435655_2_4 - 0884-019

description: US22502722_253949435655_2_4 - 0884-019


title: US22502722_253949435655_2_3 - 0884-018

description: US22502722_253949435655_2_3 - 0884-018


title: K27M-RYBP-Rep2


title: US22502722_253949444821_2_1- 0886-012

description: US22502722_253949444821_2_1- 0886-012


title: ZH11R2

description:
Unknown_AR742-13T0008
raw_counts.txt

value: WT


title: US22502722_253949435655_2_2 - 0884-017

description: US22502722_253949435655_2_2 - 0884-017

value: Male


title: HD_112

value: peripheral blood

value: primary cells

value: neutrophils

value: control


title: ZH11R1

description:
Unknown_AR742-13T0007
raw_counts.txt


title: US22502722_253949435655_2_1 - 0884-016

description: US22502722_253949435655_2_1 - 0884-016

value: Alive

value: Agilent's Universal Human Reference RNA


title: US22502722_253949435655_1_4 - 0884-015

description: US22502722_253949435655_1_4 - 0884-015


title: US22502722_253949435655_1_3 - 0884-013

description: US22502722_253949435655_1_3 - 0884-013


title: KO-RYBP-Rep3

value: SU-DIPGXIII-KO

value: H3K27M knock-out cells (derived from parental SU-DIPGXIII cell line)


title: K27M-RYBP-Rep1


title: f3hL3

description:
Unknown_AR742-13T0006
raw_counts.txt

source_name: Leaf

value: Leaf


title: US22502722_253949435655_1_2 - 0884-012

description: US22502722_253949435655_1_2 - 0884-012


title: US22502722_253949435655_1_1 - 0884-011

description: US22502722_253949435655_1_1 - 0884-011


title: f3hL2

description:
Unknown_AR742-13T0005
raw_counts.txt

value: one-month-old


title: KO-RYBP-Rep2


title: US22502722_253949435654_2_4 - 0884-010

description: US22502722_253949435654_2_4 - 0884-010


title: US22502722_253949435654_2_3 - 0884-009

description: US22502722_253949435654_2_3 - 0884-009


title: US22502722_253949444821_1_1- 0886-002

description: US22502722_253949444821_1_1- 0886-002

value: Female


title: US22502722_253949435654_2_2 - 0884-008

description: US22502722_253949435654_2_2 - 0884-008


title: KO-RYBP-Rep1


title: ZH11R3

description:
Unknown_AR742-13T0009
raw_counts.txt

value: Root


title: f3hL1

description:
Unknown_AR742-13T0004
raw_counts.txt

value: f3h knockdown


title: ZH11L3

description:
Unknown_AR742-13T0003
raw_counts.txt


title: HD_101


title: TAZ-SUZ12-Rep3

value: SU-DIPGXIII

value: H3K27M-positive SU-DIPGXIII cells treated with 2µM Tazemetostat for 6 days

value: Brain

value: SUZ12 (Cell Signalling, 3737S)


title: US22502722_253949435654_2_1 - 0884-007

description: US22502722_253949435654_2_1 - 0884-007

value: Male


title: US22502722_253949435654_1_4 - 0884-006

description: US22502722_253949435654_1_4 - 0884-006


title: ZH11L2

description:
Unknown_AR742-13T0002
raw_counts.txt

value: WT


title: TAZ-SUZ12-Rep2


title: US22502722_253949435654_1_3 - 0884-003

description: US22502722_253949435654_1_3 - 0884-003


title: US22502722_253949435654_1_2 - 0884-002

description: US22502722_253949435654_1_2 - 0884-002


title: US22502722_253949435654_1_1 - 0884-001

description: US22502722_253949435654_1_1 - 0884-001


title: TAZ-SUZ12-Rep1


title: ZH11L1

description:
Unknown_AR742-13T0001
raw_counts.txt


title: SG16374548_253949448308_2_3_0883-019-900_Day14


title: Rice-scATAC-Culm-Rep1

description:
10x Genomics
ST-TileSize-100-normMethod-ReadsInTSS-ArchR.bw

data_processing:
Raw sequencing data were converted to fastq format using ‘cellranger-arc mkfastq’. The multiome raw sequencing data for scRNA-seq and scATAC-seq were processed using CellRanger ARC (v2.0.2). Rice MSU 7.0 was used as the reference genome.
Raw count matrix data were imported into R using the Seurat (V.4.3.0) package for further data analysis. Low-quality cells were removed by filtering out cells that had fewer than 500 genes or 1,000 unique molecular identifiers (UMIs). Doublets and multiplets were filtered out using DoubletFinder. The core statistical parameters of DoubletFinder (nExp and pK) used to build artificial doublets for true doublet classification were determined automatically using recommended settings.The top 2000 highly variable genes were used for principal component analysis (PCA) dimensionality reduction. The first 20 principal components (PCs) were selected according to the PCA elbow plot and used for clustering with a suitable resolution parameter. Cluster stability was assessed using Clustree across a range of resolution values (0.1 to 2.0). Based on the results obtained from Clustree, a suitable resolution value was selected to determine the number of clusters. This process was performed separately for each sample. The clusters were visualized and explored by and UMAP .
To integrate count matrix data from different sources, the scRNA-seq data from each sample were combined into one single object. Variable genes were selected using the SCtransform function with default parameters. The FindIntegrationAnchors function command used default parameters (dims = 1:20) to discover integration anchors across all samples. The IntegrateData function was run on the anchor set with default additional arguments. ScaleData and RunPCA were then performed on the integrated assay to compute 20 PCs. UMAP dimensionality reduction was carried out and a shared nearest neighbor (SNN) graph constructed using dimensions 1:20 as input features and default PCA reduction. Clustering analysis was performed on the integrated assay at a resolution of 0.5.
Assembly: Rice MSU 7.0
Supplementary files format and content: Seurat of scRNA; bw and arrow file of scATAC

source_name: Culm

value: Culm

value: Nipponbare

value: normal


title: SG16374548_253949447551_1_4_0883-018-900_hr168

value: Alive

value: Agilent's Universal Human Reference RNA


title: TAZ-MEL18-Rep3

value: PCGF2 (Diego Passini Lab)


title: SG16374548_253949448306_2_2_0883-015-900_hr132


title: TAZ-MEL18-Rep2


title: SG16374548_253949448305_1_1_0883-016-900_hr144


title: Rice-scRNA-Culm-Rep2

description: 10x Genomics


title: SG16374548_253949447270_1_4_0883-017-900_hr156


title: TAZ-MEL18-Rep1


title: SG16374548_253949448110_2_1_0883-012-900_hr96


title: SG16374548_253949448095_2_3_0883-010-900_hr72


title: SG16374548_253949448109_2_3_0883-011-900_hr84


title: TAZ-H3K27me3-Rep2

value: H3K27me3 (Cell Signalling, 9733T)


title: TAZ-H3K27me3-Rep3


title: Rice-scATAC-SP-Rep2

description:
10x Genomics
SP-TileSize-100-normMethod-ReadsInTSS-ArchR.bw

source_name: Young Spike

value: Young Spike


title: Rice-scATAC-SP-Rep1


title: SG16374548_253949448097_1_1_0883-009-900_hr60


title: TAZ-H3K27me3-Rep1


title: Rice-scRNA-Culm-Rep1

description: 10x Genomics


title: SG16374548_253949448098_1_3_0883-008-900_hr48


title: SG16374548_253949448331_2_1_0883-007-900_hr36


title: Rice-scRNA-SP-Rep2

description: 10x Genomics


title: TAZ-CBX8-Rep3

value: CBX8 (Cell Signalling, 14696S)


title: Rice-scRNA-SP-Rep1

description: 10x Genomics


title: SG16374548_253949447595_2_1_0883-004-900_hr8


title: SG16374548_253949448329_2_3_0883-006-900_hr24


title: SG16374548_253949448327_2_2_0883-005-900_hr12


title: SG16374548_253949448112_2_4_0883-013-900_hr108


title: TAZ-CBX8-Rep2


title: SG16374548_253949446602_1_4_0883-003-900_hr4


title: SG16374548_253949447593_1_3_0883-002-900_hr2


title: SG16374548_253949447555_2_3_0883-001-900_hr0


title: TAZ-CBX8-Rep1


title: US22502722_253949444818_2_4- 0882-020

description: US22502722_253949444818_2_4- 0882-020

value: Female


title: Rice-scATAC-Culm-Rep2


title: Rice-scATAC-SAM-Rep1

description:
10x Genomics
SAM-TileSize-100-normMethod-ReadsInTSS-ArchR.bw

source_name: Shoot apical meristem

value: Shoot apical meristem


title: Rice-scATAC-SAM-Rep2


title: US22502722_253949444775_1_3 - 0882-019

description: US22502722_253949444775_1_3 - 0882-019


title: Rice-scRNA-SAM-Rep2

description: 10x Genomics


title: US22502722_253949444818_2_3- 0882-017

description: US22502722_253949444818_2_3- 0882-017


title: TAZ-CBX4-Rep2

value: SU-DIPGXIII

value: CBX4 (Cell Signalling, 30559S)


title: Rice-scRNA-SAM-Rep1

description: 10x Genomics


title: TAZ-CBX4-Rep3

value: H3K27M-positive SU-DIPGXIII cells treated with 2µM Tazemetostat for 6 days

value: Brain


title: US22502722_253949444818_2_2- 0882-015

description: US22502722_253949444818_2_2- 0882-015


title: US22502722_253949444817_2_4- 0882-018

description: US22502722_253949444817_2_4- 0882-018


title: SG16374548_253949446591_1_3_0883-014-900_hr120

value: Male


title: US22502722_253949444817_2_2- 0882-014

description: US22502722_253949444817_2_2- 0882-014


title: US22502722_253949444818_2_1- 0882-013

description: US22502722_253949444818_2_1- 0882-013


title: TAZ-CBX4-Rep1


title: Rice-scATAC-Root-Rep2

description:
10x Genomics
Root-TileSize-100-normMethod-ReadsInTSS-ArchR.bw

source_name: Crown Root

value: Crown Root


title: Rice-scATAC-Root-Rep1


title: TAZ-BMI1-Rep3

value: BMI1 (Cell Signalling, 5694S)


title: US22502722_253949444775_1_2 - 0882-012

description: US22502722_253949444775_1_2 - 0882-012


title: TAZ-BMI1-Rep2


title: US22502722_253949444817_2_1- 0882-011

description: US22502722_253949444817_2_1- 0882-011


title: US22502722_253949444818_1_4- 0882-010

description: US22502722_253949444818_1_4- 0882-010


title: Rice-scRNA-Root-Rep2

description: 10x Genomics

value: Nipponbare


title: TAZ-BMI1-Rep1


title: US22502722_253949444818_1_3- 0882-008

description: US22502722_253949444818_1_3- 0882-008


title: US22502722_253949444817_1_4- 0882-009

description: US22502722_253949444817_1_4- 0882-009


title: US22502722_253949444817_1_3- 0882-007

description: US22502722_253949444817_1_3- 0882-007


title: Rice-scRNA-Root-Rep1

description: 10x Genomics

value: normal


title: US22502722_253949444818_1_1- 0882-003

description: US22502722_253949444818_1_1- 0882-003

value: Alive


title: US22502722_253949444818_1_2- 0882-006

description: US22502722_253949444818_1_2- 0882-006

value: Agilent's Universal Human Reference RNA


title: DMSO-SUZ12-Rep1

value: H3K27M-positive SU-DIPGXIII cells treated with DMSO

value: SUZ12 (Cell Signalling, 3737S)


title: US22502722_253949444817_1_1- 0882-002

description: US22502722_253949444817_1_1- 0882-002


title: DMSO-SUZ12-Rep2


title: Rice-scRNA-Leaf-Rep2

description: 10x Genomics

source_name: Third Leaf

value: Third Leaf


title: DMSO-MEL18-Rep3

value: PCGF2 (Diego Passini Lab)


title: US22502722_253949444817_1_2- 0882-004

description: US22502722_253949444817_1_2- 0882-004

value: Female


title: DMSO-SUZ12-Rep3


title: US22502722_253949444775_1_1 - 0882-005

description: US22502722_253949444775_1_1 - 0882-005


title: Rice-scATAC-Leaf-Rep1

description:
10x Genomics
leaf-TileSize-100-normMethod-ReadsInTSS-ArchR.bw


title: SG16374548_253949448107_2_3_0877-008-900_hr48


title: Rice-scRNA-Leaf-Rep1

description: 10x Genomics


title: SG16374548_253949448109_1_4_0877-009-900_hr60


title: DMSO-MEL18-Rep2


title: SG16374548_253949448308_1_4_0877-011-900_hr84


title: SG16374548_253949448106_2_3_0877-007-900_hr36


title: SG16374548_253949448103_2_2_0877-006-900_hr24


title: Rice-scATAC-Flag_Leaf-Rep2

description:
10x Genomics
Flag-TileSize-100-normMethod-ReadsInTSS-ArchR.bw

source_name: Flag Leaf

value: Flag Leaf


title: Rice-scATAC-Flag_Leaf-Rep1


title: DMSO-MEL18-Rep1

value: SU-DIPGXIII


title: SG16374548_253949448097_1_4_0877-004-900_hr8


title: Rice-scATAC-Leaf-Rep2


title: SG16374548_253949447601_1_4_0877-002-900_hr2


title: DMSO-H3K27me3-Rep2

value: H3K27me3 (Cell Signalling, 9733T)


title: DMSO-H3K27me3-Rep3


title: SG16374548_253949448331_2_2_0877-003-900_hr4


title: Rice-scRNA-Flag_Leaf-Rep2

description: 10x Genomics


title: US22502722_253949444816_1_4- 0875-014

description: US22502722_253949444816_1_4- 0875-014


title: DMSO-H3K27me3-Rep1


title: Rice-scRNA-Flag_Leaf-Rep1

description: 10x Genomics


title: US22502722_253949444816_1_2- 0875-009

description: US22502722_253949444816_1_2- 0875-009


title: US22502722_253949435660_2_1 - 0875-010

description: US22502722_253949435660_2_1 - 0875-010


title: US22502722_253949444816_1_3- 0875-011

description: US22502722_253949444816_1_3- 0875-011


title: DMSO-CBX8-Rep3

value: CBX8 (Cell Signalling, 14696S)


title: E11.5 Pbx1/2 mutant replicate 4

city: New York

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

description: Library name: M4

data_processing:
RNAseq fastq files from all samples were aligned using STAR with GENCODE vM27 genome annotation. Feature counting was done using featureCounts.
Processing of count matrix, which includes variance stabilization, PCA and differential expression analysis, was done using DEseq2 R package.
Assembly: mm10
Supplementary files format and content: CSV files of integer raw counts estimated by featureCounts

molecule: polyA RNA

organism: Mus musculus

source_name: lambdoidal junctions

growth_protocol: Mouse embryos were generated using previously described mutant alleles and genotyping methods for conditional and constitutive alleles of Pbx1 and Pbx2. Wild-type Swiss Webster mice, sourced from Charles River Laboratories, were bred via natural timed mating using female mice over 6 weeks of age. Embryos were collected at gestational day E11.5 defined as noon on the day a vaginal plug was detected, following euthanasia of the pregnant females. Due to genetic complexity, genotyping of mice and embryos was necessary before proceeding with analyses. Both male and female embryos were analyzed without sex discrimination, as the observed phenotypes in Pbx1/2 mutants are fully penetrant across all specimens.

extract_protocol:
Epithelium and mesenchyme cells were sorted using FACS (Sony SH800S) as described earlier, collecting Epcam positive and negative cells directly into separate tubes containing RLT RNA extraction buffer. Post-genotyping of individual embryos, RNA from 4 embryos per group (Pbx1/2 mutant and control) was pooled. A total of four biological replicates were analyzed for each genotype. RNA extraction was performed using the RNeasy Plus Micro Kit (Qiagen, #74034), and RNA quantity was assessed using the Qubit RNA HD Assay Kit (Invitrogen, Q32852). RNA quality was checked using an RNA 6000 Pico kit (Agilent, Cat: 5067-1513) on a 2100 Bioanalyzer (Agilent), ensuring all samples for library preparation had an RIN greater than 9. PolyA RNAs were isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490). RNA sequencing libraries were prepared from 100ng of RNA using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, #E7775). The library size and quality were verified on an Agilent 2100 Bioanalyzer using the High Sensitivity DNA kit (Agilent, Cat: 5067-4626), and library DNA concentrations were measured using the Qubit dsDNA HS Assay Kit (Invitrogen, Q32854).
RNA libraries were prepared according to 10X protocol.

value: lambdoidal junctions

value: Mouse stem cells

value: Epithelial cells

value: Pbx1/2 mutant


title: E11.5 Pbx1/2 mutant replicate 3

description: Library name: M3


title: SG16374548_253949448102_1_4_0877-005-900_hr12

value: Male


title: US22502722_253949444816_1_1- 0875-007

description: US22502722_253949444816_1_1- 0875-007


title: US22502722_253949435660_1_3 - 0875-006

description: US22502722_253949435660_1_3 - 0875-006


title: US22502722_253949435660_2_4 - 0875-005

description: US22502722_253949435660_2_4 - 0875-005


title: E11.5 Pbx1/2 mutant replicate 1

description: Library name: M1


title: DMSO-CBX8-Rep1

value: Brain


title: E11.5 Pbx1/2 mutant replicate 2

description: Library name: M2


title: US22502722_253949435660_1_2 - 0875-004

description: US22502722_253949435660_1_2 - 0875-004

value: Alive


title: SG16374548_253949447600_1_4_0877-001-900_hr0

value: Agilent's Universal Human Reference RNA


title: US22502722_253949435660_2_3 - 0875-003

description: US22502722_253949435660_2_3 - 0875-003


title: US22502722_253949435660_1_1 - 0875-002

description: US22502722_253949435660_1_1 - 0875-002


title: E11.5 WT replicate 4

description: Library name: CC4

value: WT


title: DMSO-CBX4-Rep2

value: H3K27M-positive SU-DIPGXIII cells treated with DMSO

value: CBX4 (Cell Signalling, 30559S)


title: DMSO-CBX4-Rep1


title: SG16374548_253949448307_1_2_0874-001-900_hr0


title: US22502722_253949435660_2_2 - 0875-012

description: US22502722_253949435660_2_2 - 0875-012


title: E11.5 WT replicate 3

description: Library name: CC3


title: US22502722_253949444773_2_4- 0873-019

description: US22502722_253949444773_2_4- 0873-019


title: DMSO-CBX8-Rep2


title: E11.5 WT replicate 2

description: Library name: CC2


title: DMSO-BMI1-Rep2

value: BMI1 (Cell Signalling, 5694S)


title: US22502722_253949444775_2_4- 0873-014

description: US22502722_253949444775_2_4- 0873-014

value: Female


title: US22502722_253949444774_1_3- 0873-007

description: US22502722_253949444774_1_3- 0873-007


title: US22502722_253949444773_1_4- 0873-008

description: US22502722_253949444773_1_4- 0873-008


title: E11.5 WT replicate 1

description: Library name: CC1


title: US22502722_253949444774_2_1- 0873-013

description: US22502722_253949444774_2_1- 0873-013


title: DMSO-BMI1-Rep1


title: US22502722_253949444773_1_2- 0873-004

description: US22502722_253949444773_1_2- 0873-004


title: US22502722_253949444773_1_3- 0873-006

description: US22502722_253949444773_1_3- 0873-006


title: Bulk RNA, postnatal day 9, replicate 3

city: Munich

first: Monika

last: Leischner-Brill

address: Arcisstr. 21

department: School of Medicine and Health

country: Germany

institute: Technical University of Munich

description: Library name: MUC7131

data_processing:
Read counts were extracted using htseq-count with strict intersection.
Assembly: mm9
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

molecule: cytoplasmic RNA

source_name: spinal cord

extract_protocol:
Spinal cords were homogenized (buffer in RNase-free water in mM: 50 TrisCl, pH 7.5, 100 KCl, 12 MgCl2, 1 % NP-40, 1 X dithiothreitol (DTT), 1 X protease inhibitors, 1 mg/ml heparin, 100 µg/ml cycloheximide, RNAseOUT. The mRNA-ribosome complex was precipitated using a polyclonal HA-antibody (Sigma #H6908) and Dynabeads Protein G.
Ribosome-bound mRNA was isolated with RNeasy Plus Micro Kit (Qiagen #74034) per manufacturer's instructions.

treatment_protocol: Dissected spinal cords were kept at -80 °C until pull-down of labeled ribosomes.

value: spinal cord

value: ChAT-Cre +, RiboTag fl/fl, Spast fl/fl

tag: developmental stage

value: postnatal day 9

value: Bulk spinal cord RNA

value: not applicable


title: US22502722_253949444774_1_2- 0873-005

description: US22502722_253949444774_1_2- 0873-005


title: Bulk RNA, postnatal day 9, replicate 1

description: Library name: MUC7129


title: KO-SUZ12-Rep3

value: SU-DIPGXIII-KO

value: H3K27M knock-out cells (derived from parental SU-DIPGXIII cell line)

value: SUZ12 (Cell Signalling, 3737S)


title: DMSO-BMI1-Rep3

value: SU-DIPGXIII


title: KO-SUZ12-Rep1

value: Brain


title: US22502722_253949444773_2_2- 0873-015

description: US22502722_253949444773_2_2- 0873-015

value: Alive


title: US22502722_253949444773_1_1- 0873-002

description: US22502722_253949444773_1_1- 0873-002

value: Agilent's Universal Human Reference RNA


title: US22502722_253949444775_2_3- 0873-001

description: US22502722_253949444775_2_3- 0873-001


title: KO-SUZ12-Rep2


title: US22502722_253949422282_2_4  -  0871-017

description: US22502722_253949422282_2_4  -  0871-017

value: Male


title: KO-RING1B-Rep3

value: RING1B (Cell Signalling, 5694S)


title: Bulk RNA, postnatal day 5, replicate 3

description: Library name: MUC7128

value: postnatal day 5


title: Bulk RNA, postnatal day 5, replicate 2

description: Library name: MUC7127


title: US22502722_253949422282_2_3  -  0871-016

description: US22502722_253949422282_2_3  -  0871-016


title: US22502722_253949422282_2_1  -  0871-014

description: US22502722_253949422282_2_1  -  0871-014


title: KO-RING1B-Rep2


title: KO-RING1B-Rep1


title: US22502722_253949422282_1_2  -  0871-011

description: US22502722_253949422282_1_2  -  0871-011


title: Negative control, pooled

description: Library name: MUC7125

value: ChAT-Cre -, RiboTag fl/fl

value: pooled sample

value: RiboTagged RNA


title: US22502722_253949422282_1_4  -  0871-013

description: US22502722_253949422282_1_4  -  0871-013


title: US22502722_253949422282_1_1  -  0871-010

description: US22502722_253949422282_1_1  -  0871-010


title: Bulk RNA, postnatal day 9, replicate 2

description: Library name: MUC7130

value: spinal cord

value: ChAT-Cre +, RiboTag fl/fl, Spast fl/fl


title: KO-MEL18-Rep3

value: PCGF2 (Diego Passini Lab)


title: US22502722_253949444774_1_1- 0873-003

description: US22502722_253949444774_1_1- 0873-003

value: Female


title: US22502722_253949422281_2_4  -  0871-009

description: US22502722_253949422281_2_4  -  0871-009


title: KO-MEL18-Rep2

value: SU-DIPGXIII-KO


title: RiboTag, spast, postnatal day 14, replicate 1

description: Library name: MUC6912

value: postnatal day 14


title: RiboTag, postnatal day 7, replicate 3

description: Library name: MUC6911

value: ChAT-Cre +, RiboTag fl/fl

value: postnatal day 7


title: US22502722_253949422281_2_3  -  0871-008

description: US22502722_253949422281_2_3  -  0871-008


title: US22502722_253949422282_2_2  -  0871-015

description: US22502722_253949422282_2_2  -  0871-015


title: US22502722_253949422281_2_2   -  0871-007

description: US22502722_253949422281_2_2   -  0871-007


title: RiboTag, spast, postnatal day 5, replicate 3

description: Library name: MUC6909


title: US22502722_253949422281_1_2  -  0871-002

description: US22502722_253949422281_1_2  -  0871-002


title: US22502722_253949422281_1_1 - 0871-001

description: US22502722_253949422281_1_1 - 0871-001


title: KO-IgG3-Rep3

description: 10% mouse cells was used as spike-in chromatin.

value: H3K27M knock-out cells (derived from parental SU-DIPGXIII cell line)

value: Brain

value: IgG (Cell Signalling, 2729S)


title: KO-MEL18-Rep1


title: US22502722_253949422282_1_3  -  0871-012

description: US22502722_253949422282_1_3  -  0871-012

value: Male

value: Alive

value: Agilent's Universal Human Reference RNA


title: Bulk RNA, postnatal day 5, replicate 1

description: Library name: MUC7126

value: postnatal day 5

value: Bulk spinal cord RNA

value: not applicable


title: US22502722_253949423800_2_4 - 0870-016

description: US22502722_253949423800_2_4 - 0870-016


title: KO-IgG3-Rep2


title: KO-IgG3-Rep1


title: RiboTag, spast, postnatal day 9, replicate 3

description: Library name: MUC6910

value: spinal cord

value: postnatal day 9

value: RiboTagged RNA


title: RiboTag, postnatal day 11, replicate 3

description: Library name: MUC6908

value: postnatal day 11


title: US22502722_253949423800_2_2 - 0870-014

description: US22502722_253949423800_2_2 - 0870-014

value: Female


title: US22502722_253949423800_2_1 - 0870-013

description: US22502722_253949423800_2_1 - 0870-013


title: US22502722_253949423800_1_4 - 0870-012

description: US22502722_253949423800_1_4 - 0870-012


title: KO-IgG2-Rep3

value: SU-DIPGXIII-KO


title: US22502722_253949423800_1_3 - 0870-011

description: US22502722_253949423800_1_3 - 0870-011


title: RiboTag, postnatal day 7, replicate 2

description: Library name: MUC6906

value: ChAT-Cre +, RiboTag fl/fl


title: KO-IgG2-Rep2


title: US22502722_253949422281_1_3   -  0871-003

description: US22502722_253949422281_1_3   -  0871-003


title: US22502722_253949423800_1_1 - 0870-009

description: US22502722_253949423800_1_1 - 0870-009


title: RiboTag, spast, postnatal day 9, replicate 2

description: Library name: MUC6905

value: ChAT-Cre +, RiboTag fl/fl, Spast fl/fl


title: US22502722_253949423799_2_4 - 0870-008

description: US22502722_253949423799_2_4 - 0870-008


title: US22502722_253949423799_2_3 - 0870-007

description: US22502722_253949423799_2_3 - 0870-007


title: KO-IgG2-Rep1

value: H3K27M knock-out cells (derived from parental SU-DIPGXIII cell line)


title: RiboTag, postnatal day 7, replicate 1

description: Library name: MUC6904

value: postnatal day 7


title: US22502722_253949423799_2_2 - 0870-006

description: US22502722_253949423799_2_2 - 0870-006


title: US22502722_253949423800_2_3 - 0870-015

description: US22502722_253949423800_2_3 - 0870-015


title: US22502722_253949423799_2_1 - 0870-005

description: US22502722_253949423799_2_1 - 0870-005


title: US22502722_253949423799_1_4 - 0870-004

description: US22502722_253949423799_1_4 - 0870-004


title: US22502722_253949423799_1_3 - 0870-003

description: US22502722_253949423799_1_3 - 0870-003


title: RiboTag, spast, postnatal day 9, replicate 1

description: Library name: MUC6903


title: KO-IgG1-Rep1

value: Brain

value: IgG (Cell Signalling, 2729S)


title: RiboTag, postnatal day 11, replicate 2

description: Library name: MUC6907

value: Male


title: RiboTag, spast, postnatal day 5, replicate 2

description: Library name: MUC6902


title: KO-IgG1-Rep2


title: US22502722_253949423799_1_1 - 0870-001

description: US22502722_253949423799_1_1 - 0870-001

value: Alive

value: Agilent's Universal Human Reference RNA


title: RiboTag, postnatal day 14, replicate 3

description: Library name: MUC6901

value: postnatal day 14


title: SG16374548_253949448304_1_1_0869-001-900_hr0


title: KO-H3K27me3-Rep3

value: H3K27me3 (Cell Signalling, 9733T)


title: US22502722_253949423800_1_2 - 0870-010

description: US22502722_253949423800_1_2 - 0870-010


title: US22502722_253949435656_2_2 - 0867-006

description: US22502722_253949435656_2_2 - 0867-006


title: US22502722_253949423799_1_2 - 0870-002

description: US22502722_253949423799_1_2 - 0870-002


title: KO-H3K27me3-Rep2


title: US22502722_253949435656_1_4 - 0867-004

description: US22502722_253949435656_1_4 - 0867-004


title: RiboTag, postnatal day 9, replicate 3

description: Library name: MUC6899

value: spinal cord


title: US22502722_253949435656_1_3 - 0867-003

description: US22502722_253949435656_1_3 - 0867-003


title: KO-H3K27me3-Rep1


title: KO-IgG1-Rep3


title: RiboTag, postnatal day 14, replicate 2

description: Library name: MUC6898


title: US22502722_253949435656_1_2 - 0867-002

description: US22502722_253949435656_1_2 - 0867-002


title: KO-CBX8-Rep3

value: CBX8 (Cell Signalling, 14696S)


title: SG16374548_253949447595_1_2_0866-007-900_hr36

value: Deceased


title: SG16374548_253949447598_2_2_0866-008-900_hr48


title: KO-CBX8-Rep1


title: SG16374548_253949447592_1_2_0866-006-900_hr24


title: RiboTag, postnatal day 11, replicate 1

description: Library name: MUC6896

value: postnatal day 11

value: RiboTagged RNA


title: RiboTag, spast, postnatal day 5, replicate 1

description: Library name: MUC6900

value: postnatal day 5

value: Female


title: SG16374548_253949446591_2_3_0866-001-900_hr0


title: SG16374548_253949446602_2_4_0866-003-900_hr4


title: RiboTag, postnatal day 5, replicate 3

description: Library name: MUC6894

value: ChAT-Cre +, RiboTag fl/fl


title: KO-CBX4-Rep2

value: SU-DIPGXIII-KO

value: H3K27M knock-out cells (derived from parental SU-DIPGXIII cell line)

value: CBX4 (Cell Signalling, 30559S)


title: US22502722_253949435656_2_1 - 0867-005

description: US22502722_253949435656_2_1 - 0867-005


title: KO-CBX4-Rep1

value: Brain


title: US22502722_253949435659_2_4 - 0865-019

description: US22502722_253949435659_2_4 - 0865-019

value: Male


title: SG16374548_253949446603_1_3_0866-004-900_hr8


title: RiboTag, postnatal day 9, replicate 2

description: Library name: MUC6895

value: postnatal day 9


title: RiboTag, postnatal day 5, replicate 2

description: Library name: MUC6893


title: US22502722_253949435658_2_4 - 0865-018

description: US22502722_253949435658_2_4 - 0865-018

value: Alive

value: Agilent's Universal Human Reference RNA


title: US22502722_253949444816_2_3- 0865-017

description: US22502722_253949444816_2_3- 0865-017


title: US22502722_253949435656_1_1 - 0867-001

description: US22502722_253949435656_1_1 - 0867-001


title: KO-BMI1-Rep3

value: BMI1 (Cell Signalling, 5694S)


title: US22502722_253949435659_2_3 - 0865-016

description: US22502722_253949435659_2_3 - 0865-016


title: RiboTag, postnatal day 9, replicate 1

description: Library name: MUC6892

value: spinal cord


title: RiboTag, postnatal day 14, replicate 1

description: Library name: MUC6897

value: postnatal day 14


title: KO-BMI1-Rep2


title: US22502722_253949435659_2_2 - 0865-014

description: US22502722_253949435659_2_2 - 0865-014


title: US22502722_253949435658_2_3 - 0865-015

description: US22502722_253949435658_2_3 - 0865-015


title: KO-CBX4-Rep3


title: KO-BMI1-Rep1


title: SG16374548_253949447554_1_4_0866-005-900_hr12

value: Deceased


title: US22502722_253949435659_2_1 - 0865-012

description: US22502722_253949435659_2_1 - 0865-012


title: 12M_VEH_SOL_2

city: Los Angeles

first: Russell

last: Rogers

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description: Library name: 12M_VEH_SOL-2

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Assembly: mm10
Supplementary files format and content: rsem_count.txt (tab-delimited text file includes raw count values for each Sample)

source_name: skeletal muscle

growth_protocol: 8-week-old mdx mice (Jackson Labs) were aged 6- or 12-months with or without intervention.

extract_protocol:
RNA isolation using the miRNeasy Mini Kit (Qiagen)
library was constructed using the TruSeq Stranded mRNA library preparation kit

treatment_protocol: Mouse CDCs (passage 5) or human CDC-EVs were administered intravenously by femoral vein infusion, once monthly until endpoint.

value: skeletal muscle

value: mdx

value: Vehicle


title: US22502722_253949444816_2_2- 0865-011

description: US22502722_253949444816_2_2- 0865-011


title: US22502722_253949435659_1_4 - 0865-009

description: US22502722_253949435659_1_4 - 0865-009


title: K27M-SUZ12-Rep3

value: SU-DIPGXIII

value: H3K27M-positive SU-DIPGXIII cells

value: SUZ12 (Cell Signalling, 3737S)


title: 12M_VEH_SOL_1

description: Library name: 12M_VEH_SOL-1


title: US22502722_253949435658_1_3 - 0865-006

description: US22502722_253949435658_1_3 - 0865-006


title: US22502722_253949435658_2_1 - 0865-010

description: US22502722_253949435658_2_1 - 0865-010


title: US22502722_253949435659_1_2 - 0865-005

description: US22502722_253949435659_1_2 - 0865-005


title: US22502722_253949435659_1_3 - 0865-007

description: US22502722_253949435659_1_3 - 0865-007


title: K27M-RING1B-Rep3

value: RING1B (Cell Signalling, 5694S)


title: K27M-SUZ12-Rep2


title: K27M-SUZ12-Rep1


title: US22502722_253949435658_1_2 - 0865-004

description: US22502722_253949435658_1_2 - 0865-004


title: 12M_CDC_SOL_2

description: Library name: 12M_CDC_SOL-2

value: CDCs


title: 12M_CDC_SOL_1

description: Library name: 12M_CDC_SOL-1


title: US22502722_253949444816_2_1- 0865-002

description: US22502722_253949444816_2_1- 0865-002


title: RiboTag, postnatal day 5, replicate 1

description: Library name: MUC6891

value: ChAT-Cre +, RiboTag fl/fl

value: postnatal day 5

value: RiboTagged RNA

value: Female


title: US22502722_253949435658_2_2 - 0865-013

description: US22502722_253949435658_2_2 - 0865-013

value: Male

value: Alive

value: Agilent's Universal Human Reference RNA


title: Dsred_2

city: Shenzhen

first: Tao

last: Yu

address: Academic Building, 1120 Lianhua Road

institute: Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center

description: Library name: Dsred_2

data_processing:
Raw reads were first aligned to zebrafish reference genome danRer11 using STAR aligner with default parameters.
Read count per gene was then calculated using the FeatureCount program with default parameters.
TPM(transcripts per million) was calculated according to standard formula.
Assembly: GRCz11 - danRer11 - Genome
Supplementary files format and content: Comma-separated values file including read counts and TPM values for each sample

organism: Danio rerio

source_name: microglia

extract_protocol:
Cells of interest were manually picked and transferred by the glass needle to lysis buffer.  Then the cell lysate was used for reverse-transcription and amplification with the Smart-Seq2 method
Library construction for RNA-seq was prepared using Nextera XT DNA sample preparation kit

value: microglia


title: Dsred_3

description: Library name: Dsred_3


title: US22502722_253949435658_1_1 - 0865-001

description: US22502722_253949435658_1_1 - 0865-001


title: US22502722_253949435659_1_1 - 0865-003

description: US22502722_253949435659_1_1 - 0865-003


title: K27M-RING1B-Rep2

value: Brain


title: Dsred_1

description: Library name: Dsred_1


title: US22502722_253949423801_2_4 - 0864-018

description: US22502722_253949423801_2_4 - 0864-018


title: K27M-RING1B-Rep1


title: K27M-MEL18-Rep3

value: PCGF2 (Diego Passini Lab)


title: US22502722_253949423802_2_1 - 0864-016

description: US22502722_253949423802_2_1 - 0864-016


title: GFP_3

description: Library name: GFP_3


title: US22502722_253949423802_1_2 - 0864-009

description: US22502722_253949423802_1_2 - 0864-009


title: K27M-MEL18-Rep2


title: GFP_2

description: Library name: GFP_2


title: US22502722_253949423802_1_1 - 0864-008

description: US22502722_253949423802_1_1 - 0864-008


title: US22502722_253949423801_2_3 - 0864-007

description: US22502722_253949423801_2_3 - 0864-007


title: GFP_1

description: Library name: GFP_1


title: K27M-IgG3-Rep3

value: IgG (Cell Signalling, 2729S)


title: K27M-MEL18-Rep1


title: US22502722_253949423801_2_1 - 0864-005

description: US22502722_253949423801_2_1 - 0864-005


title: K27M-IgG3-Rep2


title: US22502722_253949423801_1_3 - 0864-003

description: US22502722_253949423801_1_3 - 0864-003


title: US22502722_253949423801_1_4 - 0864-004

description: US22502722_253949423801_1_4 - 0864-004


title: US22502722_253949423801_1_1 - 0864-001

description: US22502722_253949423801_1_1 - 0864-001


title: SW480 NDF-KO, MT4_Rescue_Rep1

city: Piscataway

first: Jia

last: Fei

state: NJ

address: 604 Allison Rd

department: Department of Molecular Biology and Biochemistry

institute: Rutgers University

description: Library name: Sample 17

data_processing:
Raw sequencing data were trimmed and aligned to the hg19 reference genome using Bowtie2, and PCR duplicates were removed with samtools. Normalized bigwig files and metagene analysis were prepared by Homer or Deeptools. The mapped BAM files were used for analyzing the wave peak and elongation speed as previously described with slight modifications. Calculations were restricted to genes > 30 kb with non-overlapping transcription units (corresponding to 3709 hg19 transcripts), and gene ranges were extended around their TSSs (−2 kb to +30 kb); extensions beyond chromosome limits were dropped.
Assembly: hg19
Supplementary files format and content: bigWig for TT-seq; bedGraph for Bru-seq
Library strategy: BRU-Seq

growth_protocol: Hela and SW480 cells were cultured in DMEM (Corning) supplemented with 10% FBS (Corning) and 100 U/mL penicillin-streptomycin (ThermoFisher). Cells were maintained in a humidified incubator at 37°C with 5% CO₂.

extract_protocol:
After labeling, cells were quickly washed with 1× cold PBS, residual liquid was quickly removed from the culture plate, and 3 ml Trizol LS (ThermoFisher) was added directly to the cells. RNA was purified twice using a standard Trizol RNA extraction protocol.
RNA libraries were prepared with the NEBNext Small RNA Library Prep Set (NEB) according to kit instructions.

treatment_protocol: For TT-seq, cells were pre-treated with 0.1 mM DRB (TCI) for 3 hours. For the 5-minute DRB release condition, cells were washed with warm PBS and immediately incubated in culture medium containing 1 mM 4-thiouridine (4sU; Sigma) for 5 minutes. For the 10-minute DRB release, cells were first incubated in fresh culture medium for 5 minutes following the PBS wash, then switched to medium containing 1 mM 4sU for an additional 5 minutes. For Bru-seq, cells were incubated with culture medium containing 2 mM 5-bromouridine (5-BrU; MilliporeSigma, 850187) and returned to the incubator (37 °C, 5% CO₂) for 10 minutes to allow incorporation of 5-BrU into nascent RNA.

value: NDF KO + NDF MT4

value: No


title: K27M-IgG3-Rep1

value: SU-DIPGXIII

value: H3K27M-positive SU-DIPGXIII cells


title: SW480 NDF-KO, MT2_Rescue_Rep2

description: Library name: Sample 16

value: NDF KO + NDF MT2


title: K27M-IgG2-Rep3


title: US22502722_253949435658_1_4 - 0865-008

description: US22502722_253949435658_1_4 - 0865-008


title: SG16374548_253949448332_1_4_0862-019-900_Day14


title: US22502722_253949423801_1_2 - 0864-002

description: US22502722_253949423801_1_2 - 0864-002


title: SW480 NDF-KO, MT2_Rescue_Rep1

description: Library name: Sample 15


title: US22502722_253949423802_1_3 - 0864-012

description: US22502722_253949423802_1_3 - 0864-012


title: SG16374548_253949448097_2_3_0862-020-900Day21


title: K27M-IgG2-Rep2


title: SG16374548_253949448330_1_1_0862-017-900_hr156


title: US22502722_253949423802_1_4 - 0864-014

description: US22502722_253949423802_1_4 - 0864-014


title: SW480 NDF-KO, WT_Rescue_Rep2

description: Library name: Sample 14

value: NDF KO + NDF WT


title: K27M-IgG2-Rep1


title: SG16374548_253949448329_1_3_0862-015-900_hr132


title: US22502722_253949423801_2_2 - 0864-006

description: US22502722_253949423801_2_2 - 0864-006


title: SG16374548_253949448328_2_3_0862-014-900_hr120


title: SW480 NDF-KO, WT_Rescue_Rep1

description: Library name: Sample 13


title: K27M-IgG1-Rep3


title: SG16374548_253949448094_2_1_0862-016-900_hr144


title: SG16374548_253949448327_1_4_0862-013-900_hr108


title: SG16374548_253949447600_1_2_0862-012-900_hr96


title: SG16374548_253949447598_1_3_0862-011-900_hr84


title: Hela NDF-KO,DRB_10min_Rep2

description:
Library name: Sample 12
TT-seq

data_processing:
Raw sequencing data were trimmed and aligned to the hg19 reference genome using Bowtie2, and PCR duplicates were removed with samtools. Normalized bigwig files and metagene analysis were prepared by Homer or Deeptools. The mapped BAM files were used for analyzing the wave peak and elongation speed as previously described with slight modifications. Calculations were restricted to genes > 30 kb with non-overlapping transcription units (corresponding to 3709 hg19 transcripts), and gene ranges were extended around their TSSs (−2 kb to +30 kb); extensions beyond chromosome limits were dropped.
Assembly: hg19
Supplementary files format and content: bigWig for TT-seq; bedGraph for Bru-seq

source_name: Hela

value: Hela

value: NDF KO

value: DRB 3 hours, and release from DRB for 10 min


title: K27M-IgG1-Rep2


title: SG16374548_253949447596_2_4_0862-010-900_hr72

source_name: Whole Blood

value: Female


title: SW480 NDF-KO, MT4_Rescue_Rep2

description: Library name: Sample 18


title: SG16374548_253949447595_1_1_0862-009-900_hr60

source_name: Agilent's Universal Human Reference RNA


title: SG16374548_253949448093_1_3_0862-018-900_hr168


title: Hela NDF-KO,DRB_0min_Rep2

description:
Library name: Sample 10
TT-seq

value: DRB 3 hours


title: K27M-IgG1-Rep1


title: SG16374548_253949447556_2_2_0862-007-900_hr36

value: Alive


title: Hela NDF-KO,DRB_5min_Rep2

description:
Library name: Sample 11
TT-seq

value: DRB 3 hours, and release from DRB for 5 min


title: SG16374548_253949447594_1_4_0862-008-900_hr48

value: Agilent's Universal Human Reference RNA


title: K27M-H3K27me3-Rep2

value: Brain

value: H3K27me3 (Cell Signalling, 9733T)


title: SG16374548_253949447272_1_4_0862-005-900_hr12


title: Hela NDF-WT,DRB_10min_Rep2

description:
Library name: Sample 9
TT-seq

value: NDF WT


title: SG16374548_253949447554_1_1_0862-006-900_hr24


title: SG16374548_253949447552_2_2_0862-004-900_hr8


title: Hela NDF-WT,DRB_5min_Rep2

description:
Library name: Sample 8
TT-seq


title: K27M-H3K27me3-Rep1


title: SG16374548_253949446602_2_3_0862-002-900_hr2


title: K27M-CBX8-Rep3

value: CBX8 (Cell Signalling, 14696S)


title: Hela NDF-WT,DRB_0min_Rep2

description:
Library name: Sample 7
TT-seq


title: SG14244409_253949422267_2_2 0859-003-900

value: Male

value: Deceased


title: SG16374548_253949447270_2_4_0862-001-900_hr0


title: Hela NDF-KO,DRB_10min_Rep1

description:
Library name: Sample 6
TT-seq


title: K27M-CBX4-Rep3

value: SU-DIPGXIII

value: H3K27M-positive SU-DIPGXIII cells

value: CBX4 (Cell Signalling, 30559S)


title: SG14244409_253949422271_2_4 0856-020-900


title: Hela NDF-KO,DRB_5min_Rep1

description:
Library name: Sample 5
TT-seq

value: Hela


title: K27M-CBX8-Rep1


title: K27M-CBX4-Rep2


title: SG14244409_253949422270_1_1 0856-017-900


title: SG14244409_253949422271_2_3 0856-019-900


title: SG14244409_253949422269_2_3 0856-016-900


title: SG14244409_253949422269_1_4 0859-002-900


title: Hela NDF-KO,DRB_0min_Rep1

description:
Library name: Sample 4
TT-seq

value: NDF KO


title: Hela NDF-WT,DRB_10min_Rep1

description:
Library name: Sample 3
TT-seq

value: DRB 3 hours, and release from DRB for 10 min


title: Hela NDF-WT,DRB_5min_Rep1

description:
Library name: Sample 2
TT-seq


title: K27M-BMI1-Rep3

value: BMI1 (Cell Signalling, 5694S)


title: K27M-CBX4-Rep1


title: K27M-BMI1-Rep2


title: SG14244409_253949422269_2_4 0856-014-900


title: SG14244409_253949422271_1_4 0856-011-900


title: SG14244409_253949422271_2_1 0856-013-900


title: SW480 NDF-KO, WT_Rescue, NDF, ChIP_Input

description: Library name: Sample 15

data_processing:
ChIP-Seq sequencing data were trimmed with Fastp and Trim Galore! Programs and aligned to the hg19 reference genome using Bowtie2. PCR duplicates were removed with the samtools. Normalized bigwig files and metagene analysis were prepared by Homer or Deeptools.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% formaldehyde (Sigma) for 10 min, after quenching and lysis, chromatin was sonicated with a Covaris S220 focused-ultrasonicator.
ChIP-seq libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB E7645S) according to kit instructions.

treatment_protocol: Cells were either treated with 0.1 mM DRB in culture medium for 3 hours or, following DRB treatment, washed three times with warm PBS. Fresh culture medium was then added, and cells were returned to the humidified incubator at 37°C with 5% CO₂ for 5, 10, or 20 minutes before crosslinking with 1% PFA.

tag: chip antibody

value: antisera against hNDF

value: NDF KO + NDF WT

value: No


title: Hela NDF-WT,DRB_0min_Rep1

description:
Library name: Sample 1
TT-seq

value: DRB 3 hours


title: SG14244409_253949422271_2_2 0856-018-900

value: Alive

value: Agilent's Universal Human Reference RNA


title: SG14244409_253949422270_1_4 0856-010-900


title: SG14244409_253949422270_1_3 0856-009-900


title: K27M-BMI1-Rep1

value: Brain


title: SG14244409_253949422270_2_1 0856-008-900


title: SW480 NDF-KO, MT4_Rescue, NDF, ChIP_Rep2

description: Library name: Sample 14

value: NDF KO + NDF MT4


title: SG14244409_253949422270_2_4 0859-001-900

value: Male


title: SG14244409_253949422269_2_2 0856-006-900


title: Quantseq_KO_Day3_Rep3

data_processing:
Analysis of CUT&RUN-Rx data involved adding the 'mm10_' prefix to chromosome names, creating a human/mouse hybrid genome by combining hg38 with mm10, aligning reads with Bowtie2 (v 2.3.5.1), filtering, and converting to BAM format using SAMtools (v 1.10).  Normalization was performed using the spike-in reads, and RRPM-normalized bigwig files were generated with deepTools' bamCoverage ( v 3.3.0). Peaks were called using macs2 (v 2.2.7.1) with paramaters broad --broad-cutoff 0.05, converted to bed format, and processed to generate consensus peak sets using MSPC (-r Bio -w 1e-4 -s 1e-8 -c 2) (v 5.4.0) and bedtools. Finally, peaks were annotated with HOMER
QuantSeq: Reads were trimmed using BBDUK to remove the first 11 nucleotides from reads, polyA tails, TruSeq adapters, low quality nucleotides with a q below 10, and reads smaller than 20 nucleotides in length. Reads were aligned to the hg38 genome using the STAR aligner (v2.7.3a). Gene abundance was quantified using htseq-count (v 0.11.2) and DESeq2 (v 1.36.0) was utilised to identify differentially expressed genes ( >1.5 fold change and a <0.05 Benjamini-Hochberg adjusted P value)
Assembly: hg38
Supplementary files format and content: txt files contain the output from DESeq, i.e. differentially expressed genes in H3K27M-KO or drug treated conditions compared to DIPGXIII untreated cells.

value: SU-DIPGXIII-KO

value: H3K27M knock-out cells treated with DMSO for 3 days


title: SG14244409_253949422270_1_2 0856-007-900


title: SW480 NDF-KO, MT4_Rescue, NDF, ChIP_Rep1

description: Library name: Sample 13


title: SG14244409_253949422271_1_3 0856-005-900


title: Quantseq_KO_Day3_Rep2


title: SG14244409_253949422270_2_3 0856-015-900


title: SG14244409_253949422271_1_2 0856-004-900


title: Quantseq_KO_Day3_Rep1


title: SW480 NDF-KO, MT2_Rescue, NDF, ChIP_Rep1

description: Library name: Sample 11

value: NDF KO + NDF MT2


title: SW480 NDF-KO, MT2_Rescue, NDF, ChIP_Rep2

description: Library name: Sample 12


title: SG14244409_253949422271_1_1 0856-003-900


title: Quantseq_K27M_TAZ_Day9_Rep3

value: H3K27M-positive SU-DIPGXIII cells treated with 2µM Tazemetostat for 9 days


title: SG14244409_253949422269_2_1 0856-002-900


title: SG14244409_253949422268_2_1 0856-001-900


title: SG14244409_253949422267_1_3 0855-019-900


title: SG14244409_253949422268_2_2 0855-020-900


title: Quantseq_K27M_TAZ_Day9_Rep2


title: SW480 NDF-KO, WT_Rescue, NDF, ChIP_Rep2

description: Library name: Sample 10


title: SG14244409_253949422268_1_4 0855-018-900


title: Quantseq_K27M_TAZ_Day9_Rep1


title: SW480 NDF-KO, WT_Rescue, NDF, ChIP_Rep1

description: Library name: Sample 9


title: SG14244409_253949422270_2_2 0856-012-900


title: SG14244409_253949422266_2_4 0855-015-900


title: SG14244409_253949422267_1_2 0855-016-900


title: SG14244409_253949422267_1_4 0855-017-900


title: Quantseq_K27M_TAZ_Day6_Rep3

value: H3K27M-positive SU-DIPGXIII cells treated with 2µM Tazemetostat for 6 days


title: Hela NDF-KO, Pol II, ChIP_DRB_10min

description: Library name: Sample 7

value: RPB2 (GeneTex, GTX102535)

value: Hela

value: NDF KO


title: SG14244409_253949422268_2_3 0855-014-900


title: SG14244409_253949422267_2_1 0855-013-900


title: Quantseq_K27M_TAZ_Day6_Rep2


title: Hela NDF-KO, Pol II, ChIP_DRB_5min

description: Library name: Sample 6

value: DRB 3 hours, and release from DRB for 5 min


title: SG14244409_253949422267_1_1 0855-012-900


title: Quantseq_K27M_TAZ_Day6_Rep1


title: SG14244409_253949422269_1_3 0855-011-900


title: Hela NDF-KO, Pol II, ChIP_DRB_0min

description: Library name: Sample 5


title: SG14244409_253949422269_1_2 0855-010-900


title: Quantseq_K27M_TAZ_Day3_Rep3

value: H3K27M-positive SU-DIPGXIII cells treated with 2µM Tazemetostat for 3 days


title: SG14244409_253949422268_2_4 0855-009-900


title: SG14244409_253949422266_2_3 0855-008-900


title: SG14244409_253949422268_1_3 0855-007-900


title: Quantseq_K27M_TAZ_Day3_Rep2


title: Hela NDF-WT, Pol II, ChIP_DRB_20min

description: Library name: Sample 4

value: NDF WT

value: DRB 3 hours, and release from DRB for 20 min


title: SG14244409_253949422268_1_2 0855-006-900

value: Alive


title: Hela NDF-WT, Pol II, ChIP_DRB_10min

description: Library name: Sample 3

value: DRB 3 hours, and release from DRB for 10 min


title: Quantseq_K27M_TAZ_Day3_Rep1

value: Brain


title: SG14244409_253949422269_1_1 0855-005-900

value: Agilent's Universal Human Reference RNA


title: SG14244409_253949422268_1_1 0855-004-900

value: Male


title: SG14244409_253949422267_2_4 0855-003-900


title: Hela NDF-KO, Pol II, ChIP_DRB_20min

description: Library name: Sample 8


title: SG14244409_253949422267_2_3 0855-002-900


title: Hela NDF-WT, Pol II, ChIP_DRB_0min

description: Library name: Sample 1

value: DRB 3 hours


title: SG14244409_253949422266_2_2 0855-001-900


title: Quantseq_K27M_DMSO_Day9_Rep2

value: SU-DIPGXIII-KO

value: H3K27M-positive SU-DIPGXIII cells treated with DMSO for 9 days


title: SG14244409_253949423793_1_2 0851-020-900 d21


title: SG14244409_253949423792_1_3  0851-018-900 hr 168


title: Quantseq_K27M_DMSO_Day9_Rep1


title: SG14244409_253949423791_2_2  0851-017-900 hr 156


title: Quantseq_K27M_DMSO_Day6_Rep3

value: H3K27M-positive SU-DIPGXIII cells treated with DMSO for 6 days


title: SG14244409_253949423792_2_3  0851-014-900 hr 120


title: SG14244409_253949423792_2_2  0851-016-900 hr 144


title: Quantseq_K27M_DMSO_Day6_Rep2


title: SG14244409_253949423791_2_4  0851-015-900 hr 132


title: SG14244409_253949423791_1_2  0851-013-900 hr 108


title: Quantseq_K27M_DMSO_Day6_Rep1


title: SG14244409_253949423791_1_3  0851-011-900 hr 84


title: Hela NDF-WT, Pol II, ChIP_DRB_5min

description: Library name: Sample 2


title: SG14244409_253949423791_1_1  0851-009-900 hr 60


title: Quantseq_K27M_DMSO_Day3_Rep3

value: H3K27M-positive SU-DIPGXIII cells treated with DMSO for 3 days


title: TAZ.T14C.br5

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

description:
TAZ knockout screened in IMDM (rich) + 10% FBS
Moffat_1821

data_processing:
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Assembly: TKOv3 sgRNA library
Supplementary files format and content: tab-delimited read count matrix
Library strategy: CRISPRseq

source_name: haematopoeitic

growth_protocol: Cells were cultured in IMDM media supplemented with 10% FBS and 1% Penicillin/Streptomycin and serially passaged for up to 18 days (propagated in biological triplicates).  Aliquots were pelleted at indicated timepoints for gDNA extraction and quantification by next-generation sequencing.

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer’s instructions
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.

value: haematopoeitic

value: chronic myelogenous leukemia-derived

value: TAZ 4bp deletion(HAP1)   (HZGHC004024c008)

value: TKOv3 (lentiCRISPRv2)


title: Quantseq_K27M_DMSO_Day9_Rep3


title: SG14244409_253949423792_1_2  0851-012-900 hr 96


title: K27M-H3K27me3-Rep3

value: SU-DIPGXIII

value: H3K27M-positive SU-DIPGXIII cells

value: H3K27me3 (Cell Signalling, 9733T)


title: Quantseq_K27M_DMSO_Day3_Rep2


title: Quantseq_K27M_DMSO_Day3_Rep1


title: SG14244409_253949423791_1_4  0851-006-900 hr 24

value: Alive


title: SG14244409_253949423791_2_3  0851-005-900 hr 12


title: SG14244409_253949423792_2_4  0851-008-900 hr 48


title: maize crown root, inoculum TRI_G_W, Well_watered, plantID_792

city: Lawrence

first: Maggie

middle: R

last: Wagner

state: KS

address: 1200 Sunnyside Avenue

institute: University of Kansas

description:
Library name: plantID_792
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

data_processing:
UMIs were removed from all sequences and added to the read headers using UMI-tools. Next, cutadapt version 4.2 was used to remove the first four bases of each read, remove poly-A tails (if present), remove spurious poly-G runs using the --nextseq-trim=10 parameter, and remove adapter sequences. Reads that were <10 bp long or that aligned to maize rRNA gene sequences were removed; the remaining reads were aligned to the maize reference genome B73 RefGen_v550 using HISAT2 version 2.2.1. Aligned reads were converted to BAM format, sorted, and indexed using samtools version 1.9. We then used UMI-tools to de-duplicate reads that both shared a UMI and had identical mapping coordinates. Finally, we used the FeatureCounts function of the subread package version 2.0.5 with the maize genome annotation version Zm00001eb.1 and parameters -O --fraction -M --primary -g ID -t gene to generate a table of gene expression estimates.
Assembly: maize reference genome B73 RefGen_v5
Supplementary files format and content: tab-delimited FeatureCounts output (transcript counts per sample/library)

organism: Zea mays

source_name: crown root

growth_protocol: growth chamber; multiple microbiome treatments; drought or well-watered

extract_protocol:
Macherey-Nagel NucleoSpin RNA Plant kit + Invitrogen DNA-Free kit
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

treatment_protocol: flash frozen

value: crown root

tag: plant id

tag: inoculum type

value: live

tag: inoculum origin

value: TRI

tag: inoculum conditioning_host

value: gamagrass

tag: inoculum conditioning_water

tag: testphase water_treatment


title: SG14244409_253949423792_2_1  0851-004-900 hr 8

value: Male

value: Agilent's Universal Human Reference RNA


title: TAZ.T14A.br5

description:
TAZ knockout screened in IMDM (rich) + 10% FBS
Moffat_1819

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: SG14244409_253949423791_2_1  0851-003-900 hr 4

tag: age

tag: gender

tag: timepoint

tag: reference


title: SG14244409_253949423792_1_4  0851-002-900 hr 2


title: maize crown root, inoculum WEL_N_D, Well_watered, plantID_790

description:
Library name: plantID_790
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: WEL


title: SG14244409_253949423793_1_1 0851-001-900 hr 0


title: TAZ.T0.br5

description:
TAZ knockout screened in IMDM (rich) + 10% FBS
Moffat_1818


title: TAZ.T20C.br4

description:
TAZ knockout screened in IMDM (rich) + 5% FBS
Moffat_1523

value: TAZ 5bp deletion (HAP1)   (HZGHC004024c009)


title: maize crown root, inoculum SVR_G_D, Well_watered, plantID_788

description:
Library name: plantID_788
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: SVR


title: plate6_day6

city: Cambridge

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

data_processing:
Data was processed following recommended guidelines for scPBAT data (https://felixkrueger.github.io/Bismark/bismark/library_types/), as such all files were treated as single-end
Trim Galore (version 0.4.2) was used to trim reads, to remove the first 6 bp from their 5' end, and for auto-detection of adapter and poor quality from their 3' end
Bismark (version 0.16.3) was used to align DNA reads to the bisulfite converted GRCh38 genome (with the flag --non_directional specified), deduplicate reads, and finally perform methylation calling.
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files for each processed cell are provided, these are files are tab separated and contain DNA methylation data with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Library strategy: scPBAT

source_name: Embryo

growth_protocol: Supernumerary blastocysts, cryopreserved at D5 or D6, were thawed using commercial kits specified by the clinic from which they were donated. Embryos were cultured in N2B27 medium (made in house) under mineral oil (Sage, #ART-4008) in a humidified incubator at 37oC, 7% CO2 and 5% O2. The zona pellucida surrounding the blastocyst was removed by short incubation in Tyrode Acid solution (Sigma, #T1788) prior to incubation in anti-human antibody (Sigma, H8765) diluted 1:4 in N2B27, for 1 hour at 37oC, 7% CO2 and 5% O2. The embryos were then rinsed in N2B27 and placed in N2B27 containing 2:5 non-heat inactivated rat serum (prepared in house) for 45 minutes.46 As outer cells became swollen and lysed, the whole blastocyst was transferred to N2B27 for 1 hour prior to manual removal of the degraded outer cells by pipetting using appropriately sized capillaries. For specific experiments, 50 μM Cycloheximide (Sigma, 4859), 1 μM Actinomycin D (ToCris, #1229) or 10 μM MG132 (ToCris, #1748) were added during immunosurgery to block protein translation, RNA transcription and protein degradation respectively. Following IS, ICMs were incubated in Accutase (Biolegend, 423201) on a warming pad for 10 mins. ICMs were dissociated into single cells using glass capillaries and transferred to a 96-well plate.

extract_protocol:
AMPure XP
Embryos from embryonic days 5-6 were collected in Corujo-Simon et al. in which scRNA-seq was performed using the RNA half of the scNMT-seq method. In this study we used the gDNA from the same cells to generate DNA methylation and chromatin accessibility data using the published scNMT-seq protocol (52). Briefly, genomic DNA was purified using AMPure XP beads then bisulfite converted with the Zymo EZ-96 DNA Methylation-Direct MagPrep kit. Sequencing libraries were then prepared from bisulfite converted fragments via random primed synthesis using oligos containing Illumina primer sequences, followed by indexing PCR.

value: Embryo


title: SG16374548_253949448330_1_3_0846-017-900_hr156


title: SG14244409_253949423792_1_1  0851-007-900 hr 36


title: TAZ.T14B.br5

description:
TAZ knockout screened in IMDM (rich) + 10% FBS
Moffat_1820

value: haematopoeitic

value: chronic myelogenous leukemia-derived


title: TAZ.T20A.br4

description:
TAZ knockout screened in IMDM (rich) + 5% FBS
Moffat_1521

value: TKOv3 (lentiCRISPRv2)


title: maize crown root, inoculum SVR_G_D, Well_watered, plantID_787

description:
Library name: plantID_787
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG16374548_253949448095_2_2_0846-015-900_hr132


title: SG16374548_253949447599_1_2_0846-016-900_hr144


title: TAZ.T20B.br4

description:
TAZ knockout screened in IMDM (rich) + 5% FBS
Moffat_1522


title: TAZ.T0.br4

description:
TAZ knockout screened in IMDM (rich) + 5% FBS
Moffat_1520


title: SG16374548_253949448094_2_3_0846-013-900_hr108


title: SG16374548_253949448331_1_4_0846-014-900_hr120


title: plateC_day6

data_processing:
Data was processed following recommended guidelines for scNMT data (https://felixkrueger.github.io/Bismark/bismark/library_types/), as such all files were treated as single-end
Trim Galore (version 0.6.2) was used to trim reads, to remove the first 6 bp from their 5' end, and for auto-detection of adapter and poor quality from their 3' end
Bismark (version 0.22.1) was used to align DNA reads to the bisulfite converted GRCh38 genome (with the flag --non_directional specified), deduplicate reads, and finally perform methylation calling.
To reduce unwanted biases from the data (as discussed here: https://felixkrueger.github.io/Bismark/bismark/methylation_extraction/#optional-nome-seq-or-scnmt-seq) the bismark.cov.gz files were passed to the coverage2cytosine module of bismark (with the flag --nome-seq specified)
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files for each processed cell are provided and each genomic layer (CpG methylation or GpC accessibility), these are files are tab separated and contain DNA methylation data with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>


title: maize crown root, inoculum TRI_N_D, Well_watered, plantID_784

description:
Library name: plantID_784
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: plateB_day6


title: SG16374548_253949447592_2_2_0846-011-900_hr84

data_processing:
Agilent Feature Extraction Software (v 10.7) was used for background subtraction and GeneSpring v.10.1 (Agilent Technologies, Inc., CA) software was used to conduct the preliminary data filtration and statistical analysis.
processed_data: Logratio (test/reference)


title: SG16374548_253949448093_2_3_0846-010-900_hr72


title: maize crown root, inoculum WEL_N_W, Well_watered, plantID_782

description:
Library name: plantID_782
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG16374548_253949447600_1_3_0846-018-900_hr168


title: SG16374548_253949447556_2_3_0846-009-900_hr60


title: SG16374548_253949447593_1_4_0846-008-900_hr48


title: TAZ.T19B.br3

description:
TAZ knockout screened in IMDM (rich) + 10% FBS
Moffat_1518


title: SG16374548_253949446602_1_2_0846-007-900_hr36


title: TAZ.T19A.br3

description:
TAZ knockout screened in IMDM (rich) + 10% FBS
Moffat_1517


title: maize crown root, inoculum TRI_N_D, Well_watered, plantID_777

description:
Library name: plantID_777
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: plate1_day5


title: SG16374548_253949447551_1_2_0846-005-900_hr12


title: TAZ.T0.br3

description:
TAZ knockout screened in IMDM (rich) + 10% FBS
Moffat_1516


title: SG16374548_253949447595_1_3_0846-003-900_hr4


title: SG16374548_253949447270_1_2_0846-004-900_hr8


title: maize crown root, inoculum CWR_N_D, Well_watered, plantID_783

description:
Library name: plantID_783
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module

value: CWR


title: SG16374548_253949446591_1_1_0846-002-900_hr2


title: SG16374548_253949448332_2_2_0846-012-900_hr96


title: maize crown root, inoculum CWR_N_D, Well_watered, plantID_775

description:
Library name: plantID_775
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: TAZ.T19B.br2

description:
TAZ knockout screened in DMEM (minimal) + 10% FBS
Moffat_1427

value: TAZ 4bp deletion(HAP1)   (HZGHC004024c008)


title: maize crown root, inoculum CWR_N_D, Well_watered, plantID_771

description:
Library name: plantID_771
Lexogen QuantSeq 3’ mRNA-Seq V2 kit with unique dual sequences and the unique molecular identifier (UMI) module


title: SG14244409_253949423790_2_1 0839-020-900 d21


title: TAZ.T19C.br3

description:
TAZ knockout screened in IMDM (rich) + 10% FBS
Moffat_1519


title: SG16374548_253949447594_1_1_0846-001-900_hr0_baseline


title: TAZ.T19A.br2

description:
TAZ knockout screened in DMEM (minimal) + 10% FBS
Moffat_1426


title: SG14244409_253949423790_1_1 0839-019-900 d14


title: SG14244409_253949423790_2_3 0839-017-900 hr 156


title: SG14244409_253949423789_2_4  0839-016-900 hr 144