title: HEK293T,MED23-KD-2,4SU-labelled 15min, rep2

first: Lu

last: CHENGJIANG

state: China, Mainland

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

description:
Library name: 293T23KD2-2_4SU
293T23KD2-2_4SU

data_processing:
Reads were mapped to the human genome hg19 using STAR, and RNA levels were calculated with RSEM. To identify genes with transcriptional readthrough, the following steps were performed. 1) for each gene, we divided the downstream 4 kb region of the genes into 20 bins (200 bp) and divided the gene body into 100 equal bins. 2) RNA-seq reads were counted in these bins and normalized to the total number of mapped reads and the length of the bins on each sample (TPM). Then, the expression fold changes in the 200 bp bins in the MED23-KD samples versus the WT samples were calculated. 3) To avoid the interference from the alterations in gene body expression, we first calculated the TPM values in the downstream 4 kb region and in the last exon (TTS-closest exon) for each gene in each sample and then normalized the TTS downstream expression level to the TTS-closest exon expression level.
Assembly: hg19
Supplementary files format and content: bigwig

molecule: other

growth_protocol: The cells were cultured in DMEM (HyClone) supplemented with 4500 mg/L glucose, 4.0 mM L-glutamine, sodium pyruvate, 10% fetal bovine serum (Gibco, 10091), 100 U/ml penicillin and 100 mg/ml streptomycin (Gibco, 15140163). The cells were maintained at less than 80% confluence and passaged every two days.

extract_protocol:
The labelled cells were harvested immediately with TRIzol. Total RNA was extracted with phenol/chloroform/isoamyl alcohol. The 4SU-labelled RNAs were biotinylated and enriched using streptavidin beads.
The 4SU RNAs were subjected to construct strand-specific DNA libraries using an NEBNext Ultra Directional RNA Library Prep Kit for Illumina.

treatment_protocol: 293T cells were seeded at 50% confluence in a 10 cm dish and cultured overnight. The cells were then transiently labelled with 4SU at a final concentration of 1 mM for 15 minutes.

value: cultured cell lines

value: 4SU metabolic labelling for 15min


title: HEK293T,MED23-KD-2,4SU-labelled 15min, rep1

status: Public on May 28 2025

type: SRA

city: Shanghai

country: China

description:
Library name: 293T23KD2-1_4SU
293T23KD2-1_4SU

library_source: other

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: HEK293T,MED23-KD-1,4SU-labelled 15min, rep1

description:
Library name: 293T23KD1-1_4SU
293T23KD1-1_4SU


title: HEK293T,Wildtype-1,4SU-labelled 15min, rep1

description:
Library name: 293TWT1_4SU
293TWT1_4SU

value: WT


title: HEK293T,Wildtype-1,4SU-labelled 15min, rep2

description:
Library name: 293TWT2_4SU
293TWT2_4SU


title: RA_01.IP

city: beijing

first: Cheng

last: Xiao

state: beijing

address: yinghua road

institute: China japan friendship hospital

library_source: transcriptomic

data_processing:
After sequencing by Illumina NovaSeq 6000 sequencer, image analysis, base identification and quality control, Raw reads (Raw Data) were produced. First use Q30 for quality control. Then, cutadapt[1] software (v1.9.3) was used to remove low-quality reads and obtain high-quality clean reads. The clean reads of all samples were matched to the reference genome using the Hisat2[2] software (v2.0.4). MACS [3] software was then used to identify methylated genes in each sample. Differential methylation gene identification was performed using diffReps[4] software. The peaks located on the exon of mRNA are screened using our own procedures and annotated accordingly.
Assembly: HG19
Supplementary files format and content: The differentially methylated sites were identified by diffReps with default setting.

molecule: total RNA

source_name: synovial tissues

extract_protocol:
RIP was performed using Magna RIP Kit (Millipore) following the manufacturer's instructions and a IGF2BP3 antibody. The input and immunoprecipitated RNAs were recovered using RNAiso plus and extracted according to the manufacturer's protocol.
RNA sequencing libraries were constructed using the GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) kit.

tag: tissue

value: synovial tissues

tag: disease state

value: rheumatoid arthritis (RA)


title: RA_001.IP


title: RA_01.IgG


title: OA.IP

value: osteoarthritis (OA)


title: 31_2_OA.IP


title: RA_001.IP

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (mm10) by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
Assembly: HG19
Supplementary files format and content: The differentially methylated sites were identified by diffReps with default setting.

extract_protocol:
The m6A-IP-Seq service was provided by CloudSeq Inc. (Shanghai, China). Total RNA was subjected to immunoprecipitation with the GenSeq® m6A-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified.
RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions.


title: RA_01.IP


title: RA-01.Input


title: 31_2_OA.IgG


title: HEK293T,MED23-KD-1,4SU-labelled 15min, rep2

description:
Library name: 293T23KD1-2_4SU
293T23KD1-2_4SU


title: RA_001.IgG


title: OA.IP


title: 31_2_OA.IP


title: OA.Input


title: RA-001.Input


title: 31-2-OA.Input


title: Endometrial cancer, serous, 9 (Methyl-seq)

city: Asan

first: Jeong-An

last: Gim

address: 22 Suncheonhyang-ro

country: South Korea

institute: Soonchunhyang University

library_source: genomic

data_processing:
Assembly: StringTie, FPKM and TPM were provided.
Assembly: hg38
Supplementary files format and content: *.tsv
Library strategy: Methyl-seq

molecule: genomic DNA

source_name: Endometrial cancer, serous

extract_protocol:
Total RNA was isolated by TRIzol
Library works were performed by Macrogen
SureSelect RNA Direct

value: Endometrial cancer, serous


title: Endometrial cancer, serous, 7 (Methyl-seq)


title: Endometrial cancer, serous, 6 (Methyl-seq)


title: Endometrial cancer, serous, 5 (Methyl-seq)


title: OA.IgG


title: Endometrial cancer, serous, 4 (Methyl-seq)


title: Endometrial cancer, serous, 3 (Methyl-seq)


title: Endometrial cancer, serous, 9 (RNA-seq)

data_processing:
Assembly: StringTie, FPKM and TPM were provided.
Assembly: hg38
Supplementary files format and content: *.tsv


title: Endometrial cancer, endometrioid, 1 (Methyl-seq)

source_name: Endometrial cancer, endometrioid

value: Endometrial cancer, endometrioid


title: Endometrial cancer, serous, 8 (RNA-seq)


title: Endometrial cancer, endometrioid, 7 (RNA-seq)


title: Endometrial cancer, serous, 2 (Methyl-seq)


title: Endometrial cancer, serous, 7 (RNA-seq)


title: Endometrial cancer, endometrioid, 6 (RNA-seq)


title: Endometrial cancer, endometrioid, 3 (RNA-seq)


title: Endometrial cancer, serous, 1 (Methyl-seq)


title: Endometrial cancer, serous, 5 (RNA-seq)


title: Endometrial cancer, endometrioid, 4 (RNA-seq)


title: Endometrial cancer, endometrioid, 2 (RNA-seq)


title: Endometrial cancer, serous, 4 (RNA-seq)


title: Endometrial cancer, serous, 3 (RNA-seq)


title: Endometrial cancer, serous, 2 (RNA-seq)


title: Endometrial cancer, serous, 8 (Methyl-seq)


title: Endometrial cancer, serous, 1 (RNA-seq)


title: Endometrial cancer, endometrioid, 1 (RNA-seq)


title: HT29_Cyclosporine_Rep2

city: Beijing

first: Ying

last: Guo

address: 1 Xian Nong Tan Street

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Raw reads of fastq format were firstly processed using fastp (Version: 0.20.1; Parameters: --length_required 50) and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2 (Version: 2.1.0; Parameters: --rna-strandness rf --fr) .
The sam and bam files were anlysis using samtools (Version: 1.9; Parameters: mpileup -uRf -d 1000000).
FPKM of each gene was calculated by HTSeq-count (Version: 0.11.2; Parameters: -s reverse) .
Read counts of each gene were obtained by HTSeq-count (Version: 0.11.2; Parameters: -s reverse).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for all samples.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Colon

growth_protocol: A549 and HepG2 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 IU/mL penicillin and 100 μg/mL streptomycin; HT-29 cells were cultured in DMEM/F12 supplemented with 5% FBS, 100 IU/mL penicillin and 100 μg/mL streptomycin. DMEM (Cat. No. 11965500BT), FBS (Cat. No. 10099141C), penicillin streptomycin (Cat. No. 15140122), and DMEM/F12 (Cat. No. 11320033) were purchased from Gibco (Waltham, MA, USA).

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Cat. No. 15596026; Gibco)  according to the manufacturer’s protocol.
RNA integrity was assessed by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The cDNA library was constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: A549, HepG2 and HT-29 cells were seeded in 6-well plates and incubated with the test compounds or 0.1% v/v DMSO. Briefly, HT-29 cells (colon) were treated with cyclosporine A at a final concentration of 10 µM; A549 and HepG2 cells were treated with triptolide at a final concentration of 30 nM and 10 nM, respectively.

value: Colon

value: Human colorectal adenocarcinoma cells

value: Cyclosporine 10 μM


title: HT29_DMSO_Rep2

value: DMSO


title: HT29_DMSO_Rep3


title: HT29_Cyclosporine_Rep1


title: Endometrial cancer, endometrioid, 5 (RNA-seq)


title: HT29_DMSO_Rep1


title: HepG2_Triptolide_Rep2

source_name: liver

value: liver

value: Human hepatocellular carcinoma cells

value: Triptolide 10 nM


title: HepG2_Triptolide_Rep1


title: HepG2_DMSO_Rep3


title: A549_Triptolide_Rep2

source_name: lung

value: lung

value: adenocarcinomic human alveolar basal epithelial cells

value: Triptolide 30 nM


title: A549_DMSO_Rep1


title: A549_DMSO_Rep3


title: A549_Triptolide_Rep1


title: A549_DMSO_Rep2


title: HepG2_DMSO_Rep2


title: Endometrial cancer, serous, 6 (RNA-seq)


title: HepG2_DMSO_Rep1


title: CN2_2_b

city: Tucson

first: Jiawen

last: Yang

state: Arizona

address: 1515 N Campbell Ave

department: University of Arizona Cancer Center

country: USA

institute: The University of Arizona

data_processing:
Ran fastqc to check the quality of raw data
Trimmed the adapter sequence from raw sequencing data by using trimmomatic-0.39
Performed data alignment by using STAR 2.7.10a with a hg38 reference genome (“GDC.h38.d1.vd1 STAR2 Index Files (v36)” downloaded from https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files)
The aligned data were mapped to the same reference genome by using Rsubread package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for individual sample

source_name: PrEC Hahn

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen）
Total RNA was sent to Novogene CO.for mRNA library preparation and sequencing.

value: PrEC Hahn

value: prostate epithelial cell

value: xenograft tumor cells


title: CN2_2_c


title: CN1_2_b


title: CN1_2_c


title: CN1_1_c


title: CN9_c

value: centrosome loss clone (CN9)


title: CN2_2_a


title: CN9_b


title: CN1_1_a


title: CN1_1_b


title: PrEC_c

value: parental cells (PrEC Hahn cells)


title: CN9_a


title: PrEC_b


title: PolII-MED23KD-2, 2nd

data_processing:
Raw reads were trimmed by Cutadapt v2.10 in pair-end mode
The reads were aligned to Human genecodev19 genome using Bowtie2 v2.4.1 (bowtie2 --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700)
Paired reads coverage on genome were quantified by Deeptools.
Assembly: GRCh38
Supplementary files format and content: bigWig files were generated using the Deeptools from bam files which reads with mapped quality lower than 10 were discareded.
Library strategy: CUT&Tag

source_name: Human embryonic kidney

extract_protocol:
CUT&Tag experiments were performed by following the Steven Henikoff’s protocol. The CUT&Tag DNA were extracted by phenol‒chloroform and ethanol precipitation.
The recovered DNA were amplified by 19 cycles of PCR.

value: Human embryonic kidney

value: MED23 knockdown

tag: antibody

value: Total Pol II (ACTIVEMOTIF, #91152)


title: PolII-WT-2, 2nd

value: WT


title: PrEC_a


title: CFPAC-1 cell, CGN siRNA

city: Guangzhou

first: Yuling

last: Su

state: State...

address: Guangzhou University City, Panyu District, Guangzhou City

institute: South China univerisity of technology

data_processing:
Filtering of Clean Reads: Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Alignment with Ribosome RNA (rRNA): Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
Alignment with Reference Genome: An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
Quantification of Gene Abundance:The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM[6]software.
Given FPKM(A) to be the expression of gene A, C to be number of fragments mapped to gene A, N to be total number of fragments that mapped to reference genes, and L to be number of bases on gene A. The FPKM method is able to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. Therefore, the calculated gene expression can be directly used for comparing the difference of gene expression among samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: cell line

extract_protocol:
Total RNA was isolated from CGN knockdown (CGN siRNA) or control (NC) CFPAC-1 cells using Trizol reagent (Company, City, Country). RNA quality was evaluated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked by RNase-free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched using oligo(dT) beads. The enriched mRNA was then fragmented into short fragments using fragmentation buffer and reverse transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (CAT# 7530, New England Biolabs). The purified double-stranded cDNA fragments were end repaired, added with A base, and ligated to Illumina sequencing adapters. The ligation reaction was purified using AMPure XP Beads (1.0X). Ligated fragments were size selected by agarose gel electrophoresis and amplified by polymerase chain reaction (PCR). The resulting cDNA library was sequenced by Gene Denovo Biotechnology Co. (Guangzhou, China) using Illumina Novaseq6000.

value: cell line

value: Human epithelial cell

value: KrasG12V mutation

value: CGN siRNA


title: CFPAC-1 cell, NC

value: Negative control siRNA


title: PolII-MED23KD-1, 2nd


title: PolII-WT-1, 2nd


title: 293T-MED23-KD2_1

data_processing:
The raw reads were assessed with FastQC
The adapter sequences were trimmed with Cutadapt
The trimmed reads were mapped to the hg19 genome with STAR
The RNA expression levels were quantified using RSEM.
Differential gene expression analysis was conducted with DESeq2
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample. Last six columns are corresponding to WT1, WT2, MED23-KD1-1, MED23-KD1-2, MED23-KD2-1 and MED23-KD2-2.

molecule: polyA RNA

growth_protocol: All cell lines were cultured in DMEM supplemented with 4500 mg/L glucose, 4.0 mM L-glutamine, sodium pyruvate, 10% fetal bovine serum, 100 U/ml penicillin and 100 mg/ml streptomycin in incubator with 5% CO2 at 37 °C .

extract_protocol:
RNA extraction by the TRIzol-chloroform-ethanol method
The poly (A) RNA were enriched with oligo (dT) beads and subjected to construct strand-specific DNA libraries using an NEBNext Ultra Directional RNA Library Prep Kit for Illumina.


title: 293T-MED23-KD1_2


title: 23KD-PolII-2

data_processing:
Raw reads were trimmed by Cutadapt v2.10 in pair-end mode
The reads were aligned to Human genecodev19 genome using Bowtie2 v2.4.1 (bowtie2 --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700)
Paired reads coverage on genome were quantified by Deeptools.
Assembly: GRCh37
Supplementary files format and content: bigWig files were generated using the Deeptools from bam files which reads with mapped quality lower than 10 were discareded.

extract_protocol:
CUT&Tag experiments were performed as Steven Henikoff’s protocol. The CUT&Tag DNA were extracted by phenol‒chloroform and ethanol precipitation.
The recovered DNA were amplified by 17 cycles of PCR.
CUT&Tag

tag: cutandtag antibody


title: 293T-MED23-KD2_2


title: 293T-WT_2


title: plateE_day5

city: Cambridge

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

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>

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: CN1_2_a


title: WT-PolII-1


title: 293T-MED23-KD1_1


title: 293T-WT_1


title: MED23HA1

data_processing:
Raw reads were trimmed by Cutadapt v2.10 in pair-end mode
The reads were aligned to Human genecodev19 genome using Bowtie2 v2.4.1 (bowtie2 --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700)
Paired reads coverage on genome were quantified by Deeptools.
Assembly: GRCh37
Supplementary files format and content: bigWig files were generated using the Deeptools from bam files which reads with mapped quality lower than 30 were discareded.

extract_protocol:
CUT&Tag was performed as Steven Henikoff’s protocol. The CUT&Tag DNA were extracted by phenol‒chloroform and ethanol precipitation.
The recovered DNA were amplified by 17 cycles of PCR.
CUT&Tag

value: MED23-HA kncokin

tag: cutandtag _antibody

value: anti-HA (Abcam, #ab9110)


title: WT-PolII-2


title: MED23HA2


title: con2


title: UVA-dnCLIP-MED23-rep1

data_processing:
Both 5’ and 3’ adapters were trimmed and filled by Cutadapt.
The UMI sequences were identified using umi_tools and paired reads with the same UMIs were used for further analysis.
The passed reads were aligned using Bowtie (bowtie -v 2 -m 10 --fr --best –strata --allow-contain), and duplications were removed.
Assembly: GRCh37
Supplementary files format and content: bigWig files were generated using the Deeptools

extract_protocol:
Cells were lysed under 1% SDS and sonication. Cell lysates were diluted to capture MED23-RNA complex. The MED23-enriched RNAs were partially digested by RNase T1 (25 U/µl ), dephosphorylated by intestinal alkaline phosphatase and then phosphorylated by PNK. RNAs were extracted by TRIzol-chloroform-ethanol method.
The enriched RNA fragments were subjected to small RNA library preparation with QIAseq miRNA Library Kits according to the manufacturer’s instructions
CLIP-seq

treatment_protocol: Removed the culture medium and exposed the cells to the UVC lights.

tag: clip antibody

value: anti-HA (Smart-Lifesciences, #SA068001)


title: 23KD-PolII-1


title: UVA-dnCLIP-MED23-rep2


title: UVA-dnCLIP-Ctrl-rep2


title: con1


title: input-2

data_processing:
Raw reads were trimmed by Cutadapt v2.10 in pair-end mode
The reads were aligned to Human genecodev19 genome using Bowtie2 v2.4.1
Paired reads coverage on genome were quantified by Deeptools.
Assembly: GRCh37
Supplementary files format and content: bigWig files were generated using the Deeptools from bam files

extract_protocol:
1 x 107 cells were collected and crosslinked in 5 ml PBS with 1% formaldehyde for 10 min at room temperature. After quenching and cell lysis, chromatin was sonicated using a Covaris M220 sonicator. VRC (Sigma, 94742) at a final concentration of 2 mM was added to the cell lysis buffer, nuclear lysis buffer and IP buffer after sonication to prevent RNA degradation. ChIP was performed using 10 µg of an anti-FIP1 antibody .
The ChIP and input libraries were constructed with a VAHTS Universal DNA Library Prep Kit (Vazyme, ND607) according to the manufacturer’s instructions. Libraries were amplified by distinct PCR cycles to obtain 200 ng final DNA libraries.

tag: chip antibody


title: UVA-dnCLIP-Ctrl-rep1


title: input-1


title: plateD_day3or4


title: WT-FIP1-2

value: FIP1 (Abclonal, #A7138)


title: 23KD-FIP1-1


title: WT-FIP1-1


title: SG16374548_257236351177_2_3_0842-003-900_hr4

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

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: SG16374548_257236351177_2_4_0891-003-900_hr4

value: Male


title: 23KD-FIP1-2

value: Human embryonic kidney

value: MED23 knockdown


title: SG16374548_257236351177_2_2_0880-014-900_hr120

value: Deceased


title: SG16374548_257236351177_2_1_0837-004-900_hr8


title: SG16374548_257236351177_1_2_0880-012-900_hr96


title: SG16374548_257236351177_1_3_0849-003-900_hr4


title: SG16374548_257236351154_2_4_0936-005-900_hr12


title: SG16374548_257236351154_2_3_0890-004-900_hr8


title: SG16374548_257236351154_2_2_0905-004-900_hr8


title: SG16374548_257236351154_2_1_0872-009-900_hr60


title: SG16374548_257236351154_1_2_0857-007-900_hr36


title: SG16374548_257236351154_1_1_0964-002-900_hr2


title: SG16374548_257236351154_1_3_0824-017-900_hr156


title: SG16374548_257236351153_2_2_0958-013-900_hr108


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title: UC9_saliva_UC

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

country: Japan

institute: Yamaguchi university

description:
Library name: UC9_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC9

data_processing:
FASTQ files produced by Illumina Miseq were uploaded to the Illumina BAseSpace Sequence Hub. Read classification was performed using the 16S Metagenomics app (ver 1.1.0) whithin the Illumina BaseSpace Sequence Hub, based on the Greengenes May 2013 (v13.8) database curated by Illumina, and OTU counts of bacterial reads were caluculated.
Assembly: Greengene v13.8 database curated by Illumina
Supplementary files format and content: Csv file of Family-Level Taxonomy Table
Library strategy: 16S rRNA-seq

organism: human oral metagenome

source_name: Saliva sample

extract_protocol:
DNA extraction from oral specimens Oral bacteria were collected from the periodontal pockets and tongue tissue during oral care. In the edentulous jaw, we collected bacteria only from the tongue, whereas in the case of the teeth, we collected bacteria from the periodontal pockets. The QIAamp DNA Mini Kit (Qiagen) was used to extract genomic DNA from the oral samples. Fecal samples were collected by the participants themselves following the manufacturer's instructions. DNA was extracted from 200 mg of stool using a QIAamp DNA Stool Mini Kit (Qiagen).
After determining the concentration of genomic DNA extracted from the samples using Nanodrop one (Thermo Fisher Scientific), 6.25 ng DNA was added to 25 μl of 2x KAPA HS HiFi ready mix (KAPA Biosystem). The DNA mixture was amplified using a PCR thermal cycler (C1000 Touch Thermal Cycler, Bio-Rad) programmed with an initial denaturation of 3 minutes at 95°C, followed by 25 cycles of denaturation at 95°C for 30 seconds, annealing at the temperature of 72°C for 30 seconds, and extension at 72°C for 30 seconds with the following primer pair for the V3-V4 region of 16S rRNA. Forward primer: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG, 16S amplicon Reverse primer: TCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAAT CCA. The barcode and adaptor sequence were inserted into the products by the Nextera XT Index Kit (Illumina) using a C1000 Touch Thermal Cycler (Bio-rad) programmed with an initial denaturation of 3 min at 95°C, followed by 8 cycles of denaturation at 95°C for 30 sec, annealing at the temperature of 55°C for 30 sec, and extension at 72°C for 5 min. Product concentrations were confirmed using a Qubit (Thermo Fisher Scientific). The libraries were pooled to equal molecular amounts and analyzed on an Illumina Mi-Seq DNA sequencer with a 300 bp paired-end cycle sequencing kit (Illumina).

value: Saliva sample

value: Urothelial carcinoma


title: SG16374548_257236351164_2_2_0906-002-900_hr2


title: SG16374548_257236351167_1_4_0842-001-900_hr0_baseline


title: SG16374548_257236351164_1_2_0803-002-900_hr2


title: UC6_saliva_UC

description:
Library name: UC6_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC6


title: UC5_saliva_UC

description:
Library name: UC5_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC5


title: SG16374548_257236351164_1_4_0843-015-900_hr132


title: SG16374548_257236351164_1_3_0912-011-900_hr96


title: UC8_saliva_UC

description:
Library name: UC8_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC8


title: UC56_saliva_UC

description:
Library name: UC56_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC56


title: UC43_saliva_UC

description:
Library name: UC43_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC43


title: UC41_saliva_UC

description:
Library name: UC41_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC41


title: SG16374548_257236351160_2_3_0834-002-900_hr2


title: SG16374548_257236351160_1_1_0852-005-900_hr12


title: UC40_saliva_UC

description:
Library name: UC40_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC40


title: UC48_saliva_UC

description:
Library name: UC48_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC48


title: SG16374548_257236351160_2_2_0827-001-900_hr0


title: UC46_saliva_UC

description:
Library name: UC46_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC46


title: SG16374548_257236351160_1_4_0905-001-900_hr0


title: UC34_saliva_UC

description:
Library name: UC34_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC34


title: UC45_saliva_UC

description:
Library name: UC45_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC45


title: SG16374548_257236351160_1_3_0836-012-900_hr96_Day4


title: UC30_saliva_UC

description:
Library name: UC30_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC30


title: UC49_saliva_UC

description:
Library name: UC49_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC49


title: SG16374548_257236351159_2_1_0937-001-900_hr0


title: SG16374548_257236351160_1_2_0862-004-900_hr8


title: UC4_saliva_UC

description:
Library name: UC4_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC4


title: SG16374548_257236351169_2_2_0880-007-900_hr36


title: SG16374548_257236351159_2_3_0891-001-900_hr0


title: UC33_saliva_UC

description:
Library name: UC33_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC33


title: SG16374548_257236351164_1_1_0881-005-900_hr12


title: SG16374548_257236351160_2_4_0905-005-900_hr12


title: UC27_saliva_UC

description:
Library name: UC27_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC27


title: SG16374548_257236351159_1_4_0803-003-900_hr4


title: SG16374548_257236351158_2_4_0836-002-900_hr2


title: SG16374548_257236351158_2_3_0922-005-900_hr12


title: UC14_saliva_UC

description:
Library name: UC14_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: U14


title: UC29_saliva_UC

description:
Library name: UC29_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC29


title: UC2_saliva_UC

description:
Library name: UC2_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC2


title: SG16374548_257236351159_2_4_0857-004-900_hr8


title: SG16374548_257236351159_1_3_0879-008-900_hr48


title: UC11_saliva_UC

description:
Library name: UC11_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: U11


title: UC12_saliva_UC

description:
Library name: UC12_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: U12


title: SG16374548_257236351158_1_4_0958-009-900_hr60


title: SG16374548_257236351160_2_1_0807-001-900_hr0


title: UC3_saliva_UC

description:
Library name: UC3_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC3


title: SG16374548_257236351159_2_2_0830-006-900_hr24


title: SG16374548_257236351158_2_1_0804-003-900_hr4


title: UC28_saliva_UC

description:
Library name: UC28_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: UC28


title: C9_saliva_Healthy

description:
Library name: C9_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C9

value: Healthy


title: SG16374548_257236351158_1_3_0917-013-900_hr108


title: SG16374548_257236351159_1_1_0975-009-900_hr60


title: SG16374548_257236351158_2_2_0876-004-900_hr8


title: UC13_saliva_UC

description:
Library name: UC13_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: U13


title: UC10_saliva_UC

description:
Library name: UC10_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: U10


title: SG16374548_257236351158_1_2_0872-017-900_hr156


title: SG16374548_257236351158_1_1_0975-015-900_hr132


title: SG16374548_257236351199_2_3_0905-014-900_hr120


title: C8_saliva_Healthy

description:
Library name: C8_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C8


title: SG16374548_257236351199_2_4_0906-001-900_hr0


title: C7_saliva_Healthy

description:
Library name: C7_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C7


title: C6_saliva_Healthy

description:
Library name: C6_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C6


title: SG16374548_257236351199_2_1_0905-011-900_hr84


title: SG16374548_257236351199_2_2_0917-010-900_hr72


title: SG16374548_257236351199_1_4_0827-010-900_hr72


title: C3_saliva_Healthy

description:
Library name: C3_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C3


title: C5_saliva_Healthy

description:
Library name: C5_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C5


title: C4_saliva_Healthy

description:
Library name: C4_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C4


title: SG16374548_257236351199_1_1_0821-002-900_hr2


title: C20_saliva_Healthy

description:
Library name: C20_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C20


title: SG16374548_257236351198_2_3_0917-016-900_hr144


title: C18_saliva_Healthy

description:
Library name: C18_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C18


title: SG16374548_257236351199_1_3_0959-002-900_hr2


title: C16_saliva_Healthy

description:
Library name: C16_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C16


title: C2_saliva_Healthy

description:
Library name: C2_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C2


title: C21_saliva_Healthy

description:
Library name: C21_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C21


title: SG16374548_257236351198_1_4_0964-003-900_hr4


title: C19_saliva_Healthy

description:
Library name: C19_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C19


title: SG16374548_257236351198_2_2_0975-012-900_hr96


title: SG16374548_257236351198_2_1_0944-007-900_hr36


title: SG16374548_257236351198_1_2_0975-004-900_hr8


title: C14_saliva_Healthy

description:
Library name: C14_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C14


title: C15_saliva_Healthy

description:
Library name: C15_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C15


title: C13_saliva_Healthy

description:
Library name: C13_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C13


title: SG16374548_257236351198_1_3_0958-008-900_hr48


title: C12_saliva_Healthy

description:
Library name: C12_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C12


title: SG16374548_257236351198_1_1_0866-003-900_hr4


title: SG16374548_257236351198_2_4_0872-015-900_hr132


title: SG16374548_257236351174_2_4_0845-003-900_hr4


title: C10_saliva_Healthy

description:
Library name: C10_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C10


title: SG16374548_257236351199_1_2_0815-002-900_hr2


title: C11_saliva_Healthy

description:
Library name: C11_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C11


title: SG16374548_257236351174_2_3_0873-009-900_hr60


title: C1_saliva_Healthy

description:
Library name: C1_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C1


title: SG16374548_257236351174_2_1_0939-001-900_hr0


title: SG16374548_257236351174_2_2_0821-010-900_hr72


title: SG16374548_257236351174_1_4_0975-001-900_hr0


title: SG16374548_257236351174_1_3_0878-005-900_hr12


title: C17_saliva_Healthy

description:
Library name: C17_saliva
Column name in saliva_UCvsHealthy_Family_Level_Aggregate_Counts.csv: C17


title: SG16374548_257236351173_2_4_0836-006-900_hr24


title: SG16374548_257236351174_1_2_0906-006-900_hr24


title: eastern gamagrass crown root, inoculum Mock, Well_watered, plantID_488

city: Lawrence

first: Maggie

middle: R

last: Wagner

state: KS

address: 1200 Sunnyside Avenue

institute: University of Kansas

description:
Library name: plantID_488
2x150bp

data_processing:
cutadapt to remove NEBNext adapter sequences, poly-A tails, spurious poly-G runs, and low-quality tails using the -q 20,20 parameter and other default parameters. The cleaned reads were aligned to the T. dactyloides reference genome (Td-KS_B6_1-REFERENCE-PanAnd-2.0a) using HISAT2. The alignments were name-sorted so that mate-pairs could be fixed using the fixmate function of samtools, and then re-sorted based on coordinates, de-duplicated, and converted to indexed BAM files using the same software. Finally, a table of transcript expression estimates was generated using the FeatureCounts function of the subread package with parameters -p -O --fraction -M --primary -g ID -t gene and the T. dactyloides genome annotation version Td-KS_B6_1-REFERENCE-PanAnd-2.0a_Td00002ba.2
Tripsacum dactyloides gene models were annotated based on DNA sequence homology with annotated maize genes to infer function. We used BEDtools to extract gene coordinates and protein-coding sequences from the T. dactyloides reference genome Td-KS_B6_1-REFERENCE-PanAnd-2.0a, and then used OrthoFinder to compare coding sequences from the two species (compared to Zea mays annotation Zm-B73-REFERENCE-NAM-5.0_Zm00001eb.1)
Assembly: T. dactyloides PanAnd reference genome Td-KS_B6_1-REFERENCE-PanAnd-2.0a
Supplementary files format and content: tab-delimited FeatureCounts output (transcript counts per sample/library)
Supplementary files format and content: tab-delimited OrthoFinder output (T. dactyloides genes with maize orthologs)

organism: Tripsacum dactyloides

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
NEBNext Ultra II Directional Library Kit with the oligo-dT magnetic isolation module (New England Biolabs, Ipswich, MA, USA)

treatment_protocol: flash frozen

value: crown root

tag: plant id

tag: inoculum type

value: mock

tag: inoculum origin

tag: inoculum conditioning_host

tag: inoculum conditioning_water

value: Pete

tag: testphase drought_treatment


title: eastern gamagrass crown root, inoculum SVR_G_W, Well_watered, plantID_487

description:
Library name: plantID_487
2x150bp

tag: tissue

value: live

value: SVR

value: gamagrass

tag: genotype


title: eastern gamagrass crown root, inoculum TRI_N_D, Well_watered, plantID_490

description:
Library name: plantID_490
2x150bp

value: TRI


title: eastern gamagrass crown root, inoculum SVR_G_D, Well_watered, plantID_491

description:
Library name: plantID_491
2x150bp


title: SG16374548_257236351173_2_3_0811-002-900_hr2


title: SG16374548_257236351174_1_1_0975-005-900_hr12

value: Female


title: eastern gamagrass crown root, inoculum WEL_G_D, Well_watered, plantID_486

description:
Library name: plantID_486
2x150bp

value: WEL


title: eastern gamagrass crown root, inoculum TRI_G_W, Well_watered, plantID_485

description:
Library name: plantID_485
2x150bp


title: SG16374548_257236351173_1_4_0821-015-900_hr132

value: Alive

value: Agilent's Universal Human Reference RNA


title: eastern gamagrass crown root, inoculum TRI_N_W, Well_watered, plantID_484

description:
Library name: plantID_484
2x150bp


title: eastern gamagrass crown root, inoculum CWR_G_W, Well_watered, plantID_478

description:
Library name: plantID_478
2x150bp

value: CWR


title: SG16374548_257236351173_2_2_0876-005-900_hr12


title: SG16374548_257236351173_2_1_0908-006-900_hr24

value: Male


title: SG16374548_257236351173_1_2_0958-020-900_Day21

value: Deceased


title: eastern gamagrass crown root, inoculum WEL_N_W, Well_watered, plantID_476

description:
Library name: plantID_476
2x150bp


title: eastern gamagrass crown root, inoculum TRI_G_W, Well_watered, plantID_481

description:
Library name: plantID_481
2x150bp


title: SG16374548_257236351172_2_3_0835-005-900_hr12


title: SG16374548_257236351172_2_4_0843-013-900_hr108


title: eastern gamagrass crown root, inoculum CWR_N_D, Well_watered, plantID_480

description:
Library name: plantID_480
2x150bp


title: eastern gamagrass crown root, inoculum WEL_G_W, Well_watered, plantID_479

description:
Library name: plantID_479
2x150bp


title: SG16374548_257236351173_1_3_0909-003-900_hr4


title: eastern gamagrass crown root, inoculum Mock, Well_watered, plantID_475

description:
Library name: plantID_475
2x150bp


title: SG16374548_257236351173_1_1_0862-006-900_hr24


title: eastern gamagrass crown root, inoculum CWR_G_D, Well_watered, plantID_477

description:
Library name: plantID_477
2x150bp


title: eastern gamagrass crown root, inoculum SVR_G_D, Well_watered, plantID_474

description:
Library name: plantID_474
2x150bp


title: eastern gamagrass crown root, inoculum CWR_N_W, Well_watered, plantID_472

description:
Library name: plantID_472
2x150bp


title: SG16374548_257236351172_2_1_0921-009-900_hr108


title: SG16374548_257236351172_1_4_0808-002-900_hr2


title: SG16374548_257236351172_1_3_0917-017-900_hr156


title: eastern gamagrass crown root, inoculum WEL_N_D, Well_watered, plantID_468

description:
Library name: plantID_468
2x150bp


title: SG16374548_257236351172_1_2_0815-008-900_hr48


title: SG16374548_257236351171_2_4_0896-017-900_hr156


title: SG16374548_257236351172_1_1_0871-004-900_hr8


title: eastern gamagrass crown root, inoculum WEL_N_W, Well_watered, plantID_465

description:
Library name: plantID_465
2x150bp


title: eastern gamagrass crown root, inoculum TRI_G_D, Well_watered, plantID_464

description:
Library name: plantID_464
2x150bp


title: eastern gamagrass crown root, inoculum SVR_G_D, Well_watered, plantID_460

description:
Library name: plantID_460
2x150bp


title: SG16374548_257236351171_2_2_0834-010-900_hr72


title: SG16374548_257236351171_2_1_0808-001-900_hr0


title: SG16374548_257236351172_2_2_0811-003-900_hr4


title: eastern gamagrass crown root, inoculum WEL_G_D, Well_watered, plantID_454

description:
Library name: plantID_454
2x150bp


title: SG16374548_257236351171_1_4_0872-005-900_hr12


title: SG16374548_257236351171_1_3_0878-002-900_hr2


title: eastern gamagrass crown root, inoculum WEL_G_D, Well_watered, plantID_451

description:
Library name: plantID_451
2x150bp


title: SG16374548_257236351171_1_2_0872-001-900_hr0


title: eastern gamagrass crown root, inoculum CWR_G_D, Well_watered, plantID_450

description:
Library name: plantID_450
2x150bp


title: SG16374548_257236351170_2_4_0881-002-900_hr2


title: SG16374548_257236351171_1_1_0821-012-900_hr96


title: eastern gamagrass crown root, inoculum CWR_N_D, Well_watered, plantID_449

description:
Library name: plantID_449
2x150bp


title: eastern gamagrass crown root, inoculum WEL_N_W, Well_watered, plantID_471

description:
Library name: plantID_471
2x150bp


title: eastern gamagrass crown root, inoculum SVR_N_D, Well_watered, plantID_448

description:
Library name: plantID_448
2x150bp


title: SG16374548_257236351170_2_3_0924-004-900_hr8


title: eastern gamagrass crown root, inoculum SVR_G_W, Well_watered, plantID_470

description:
Library name: plantID_470
2x150bp


title: SG16374548_257236351170_2_2_0836-008-900_hr48


title: eastern gamagrass crown root, inoculum SVR_N_W, Well_watered, plantID_447

description:
Library name: plantID_447
2x150bp


title: eastern gamagrass crown root, inoculum CWR_G_W, Well_watered, plantID_446

description:
Library name: plantID_446
2x150bp


title: eastern gamagrass crown root, inoculum CWR_N_W, Well_watered, plantID_466

description:
Library name: plantID_466
2x150bp


title: SG16374548_257236351170_2_1_0912-017-900_hr156


title: SG16374548_257236351171_2_3_0936-010-900_hr72


title: SG16374548_257236351170_1_4_0911-004-900_hr8


title: eastern gamagrass crown root, inoculum TRI_G_W, Well_watered, plantID_444

description:
Library name: plantID_444
2x150bp


title: eastern gamagrass crown root, inoculum TRI_G_D, Well_watered, plantID_443

description:
Library name: plantID_443
2x150bp


title: eastern gamagrass crown root, inoculum TRI_N_W, Well_watered, plantID_442

description:
Library name: plantID_442
2x150bp


title: SG16374548_257236351170_1_2_0922-003-900_hr4


title: eastern gamagrass crown root, inoculum CWR_N_W, Well_watered, plantID_458

description:
Library name: plantID_458
2x150bp


title: eastern gamagrass crown root, inoculum SVR_N_D, Well_watered, plantID_439

description:
Library name: plantID_439
2x150bp


title: SG16374548_257236351170_1_3_0939-005-900_hr12


title: eastern gamagrass crown root, inoculum TRI_N_W, Well_watered, plantID_452

description:
Library name: plantID_452
2x150bp


title: SG16374548_257236351170_1_1_0824-015-900_hr132


title: eastern gamagrass crown root, inoculum CWR_N_D, Well_watered, plantID_436

description:
Library name: plantID_436
2x150bp


title: SG16374548_257236351145_2_3_0872-013-900_hr108


title: SG16374548_257236351145_2_4_0827-008-900_hr48


title: eastern gamagrass crown root, inoculum SVR_N_D, Well_watered, plantID_432

description:
Library name: plantID_432
2x150bp


title: eastern gamagrass crown root, inoculum SVR_N_D, Well_watered, plantID_433

description:
Library name: plantID_433
2x150bp


title: eastern gamagrass crown root, inoculum WEL_N_W, Well_watered, plantID_429

description:
Library name: plantID_429
2x150bp


title: SG16374548_257236351145_1_4_0834-008-900_hr48


title: eastern gamagrass crown root, inoculum TRI_G_D, Well_watered, plantID_427

description:
Library name: plantID_427
2x150bp


title: eastern gamagrass crown root, inoculum WEL_G_W, Well_watered, plantID_425

description:
Library name: plantID_425
2x150bp


title: SG16374548_257236351145_1_3_0845-001-900_hr0_baseline


title: SG16374548_257236351145_1_2_0857-001-900_hr0_baseline


title: eastern gamagrass crown root, inoculum CWR_G_D, Well_watered, plantID_424

description:
Library name: plantID_424
2x150bp


title: SG16374548_257236351144_2_4_0906-008-900_hr48


title: SG16374548_257236351145_1_1_0880-009-900_hr60


title: eastern gamagrass crown root, inoculum CWR_G_D, Well_watered, plantID_422

description:
Library name: plantID_422
2x150bp


title: eastern gamagrass crown root, inoculum Mock, Well_watered, plantID_419

description:
Library name: plantID_419
2x150bp


title: SG16374548_257236351144_2_3_0880-001-900_hr0


title: eastern gamagrass crown root, inoculum TRI_N_W, Well_watered, plantID_418

description:
Library name: plantID_418
2x150bp


title: eastern gamagrass crown root, inoculum CWR_G_W, Well_watered, plantID_417

description:
Library name: plantID_417
2x150bp


title: SG16374548_257236351144_1_4_0905-013-900_hr108


title: SG16374548_257236351144_1_3_0975-014-900_hr120


title: SG16374548_257236351145_2_2_0872-011-900_hr84


title: eastern gamagrass crown root, inoculum TRI_G_D, Well_watered, plantID_412

description:
Library name: plantID_412
2x150bp


title: SG16374548_257236351144_1_1_0902-006-900_hr24


title: SG16374548_257236351144_2_1_0804-004-900_hr8


title: SG16374548_257236351145_2_1_0964-001-900_hr0


title: SG16374548_257236351144_1_2_0974-020-900_Day21


title: eastern gamagrass crown root, inoculum WEL_N_D, Well_watered, plantID_423

description:
Library name: plantID_423
2x150bp


title: SG16374548_257236351143_2_3_0917-003-900_hr4


title: eastern gamagrass crown root, inoculum SVR_G_D, Well_watered, plantID_410

description:
Library name: plantID_410
2x150bp


title: SG16374548_257236351143_2_2_0834-005-900_hr12


title: eastern gamagrass crown root, inoculum SVR_G_W, Well_watered, plantID_413

description:
Library name: plantID_413
2x150bp


title: eastern gamagrass crown root, inoculum SVR_N_W, Well_watered, plantID_408

description:
Library name: plantID_408
2x150bp


title: SG16374548_257236351143_2_1_0868-004-900_hr8


title: eastern gamagrass crown root, inoculum CWR_N_D, Well_watered, plantID_411

description:
Library name: plantID_411
2x150bp


title: eastern gamagrass crown root, inoculum CWR_G_W, Well_watered, plantID_407

description:
Library name: plantID_407
2x150bp


title: SG16374548_257236351143_1_4_0857-003-900_hr4


title: eastern gamagrass crown root, inoculum WEL_G_W, Well_watered, plantID_406

description:
Library name: plantID_406
2x150bp


title: SG16374548_257236351144_2_2_0880-006-900_hr24


title: eastern gamagrass crown root, inoculum Mock, Well_watered, plantID_416

description:
Library name: plantID_416
2x150bp


title: SG16374548_257236351143_1_2_0958-011-900_hr84


title: SG16374548_257236351143_1_3_0905-003-900_hr4


title: eastern gamagrass crown root, inoculum WEL_G_D, Well_watered, plantID_403

description:
Library name: plantID_403
2x150bp


title: SG16374548_257236351142_2_4_0868-008-900_hr48


title: eastern gamagrass crown root, inoculum TRI_N_D, Well_watered, plantID_401

description:
Library name: plantID_401
2x150bp


title: eastern gamagrass crown root, inoculum CWR_N_W, Well_watered, plantID_400

description:
Library name: plantID_400
2x150bp


title: SG16374548_257236351142_2_3_0860-003-900_hr4


title: eastern gamagrass crown root, inoculum SVR_G_W, Well_watered, plantID_404

description:
Library name: plantID_404
2x150bp


title: eastern gamagrass crown root, inoculum SVR_N_W, Well_watered, plantID_421

description:
Library name: plantID_421
2x150bp


title: eastern gamagrass crown root, inoculum TRI_N_D, Well_watered, plantID_399

description:
Library name: plantID_399
2x150bp


title: eastern gamagrass crown root, inoculum SVR_N_W, Well_watered, plantID_398

description:
Library name: plantID_398
2x150bp


title: SG16374548_257236351142_2_1_0899-001-900_hr0


title: eastern gamagrass crown root, inoculum TRI_G_W, Well_watered, plantID_396

description:
Library name: plantID_396
2x150bp


title: SG16374548_257236351142_1_3_0835-006-900_hr24


title: eastern gamagrass crown root, inoculum WEL_G_W, Well_watered, plantID_394

description:
Library name: plantID_394
2x150bp


title: eastern gamagrass crown root, inoculum CWR_G_W, Drought, plantID_388

description:
Library name: plantID_388
2x150bp

value: Drought


title: SG16374548_257236351142_1_4_0827-009-900_hr60


title: eastern gamagrass crown root, inoculum CWR_N_W, Drought, plantID_383

description:
Library name: plantID_383
2x150bp


title: SG16374548_257236351142_1_2_0824-012-900_hr96


title: SG16374548_257236351141_2_4_0912-009-900_hr60


title: eastern gamagrass crown root, inoculum SVR_N_D, Drought, plantID_380

description:
Library name: plantID_380
2x150bp


title: SG16374548_257236351141_2_3_0975-010-900_hr72


title: eastern gamagrass crown root, inoculum SVR_N_D, Drought, plantID_377

description:
Library name: plantID_377
2x150bp


title: SG16374548_257236351141_1_1_0857-002-900_hr2


title: eastern gamagrass crown root, inoculum TRI_N_W, Drought, plantID_371

description:
Library name: plantID_371
2x150bp


title: eastern gamagrass crown root, inoculum TRI_N_D, Drought, plantID_376

description:
Library name: plantID_376
2x150bp


title: SG16374548_257236351141_2_2_0906-009-900_hr60


title: SG16374548_257236351142_2_2_0938-004-900_hr8


title: SG16374548_257236351141_2_1_0912-006-900_hr24


title: SG16374548_257236351143_1_1_0902-001-900_hr0


title: SG16374548_257236351141_1_3_0936-004-900_hr8


title: eastern gamagrass crown root, inoculum SVR_G_W, Drought, plantID_366

description:
Library name: plantID_366
2x150bp


title: SG16374548_257236351141_1_4_0876-003-900_hr4


title: SG16374548_257236351134_2_4_0908-008-900_hr48


title: eastern gamagrass crown root, inoculum CWR_N_W, Drought, plantID_375

description:
Library name: plantID_375
2x150bp


title: eastern gamagrass crown root, inoculum WEL_N_W, Drought, plantID_373

description:
Library name: plantID_373
2x150bp


title: eastern gamagrass crown root, inoculum Mock, Drought, plantID_350

description:
Library name: plantID_350
2x150bp


title: eastern gamagrass crown root, inoculum WEL_N_W, Drought, plantID_362

description:
Library name: plantID_362
2x150bp


title: SG16374548_257236351134_2_3_0804-001-900_hr0


title: eastern gamagrass crown root, inoculum TRI_N_D, Drought, plantID_348

description:
Library name: plantID_348
2x150bp


title: SG16374548_257236351134_2_1_0912-002-900_hr4


title: SG16374548_257236351134_2_2_0827-006-900_hr24


title: eastern gamagrass crown root, inoculum CWR_G_D, Drought, plantID_341

description:
Library name: plantID_341
2x150bp


title: SG16374548_257236351142_1_1_0912-008-900_hr48


title: eastern gamagrass crown root, inoculum WEL_N_D, Drought, plantID_382

description:
Library name: plantID_382
2x150bp


title: SG16374548_257236351134_1_3_0830-004-900_hr8


title: eastern gamagrass crown root, inoculum TRI_N_D, Well_watered, plantID_414

description:
Library name: plantID_414
2x150bp


title: SG16374548_257236351134_1_4_0850-004-900_hr8


title: eastern gamagrass crown root, inoculum SVR_N_W, Drought, plantID_339

description:
Library name: plantID_339
2x150bp


title: SG16374548_257236351141_1_2_0811-004-900_hr8


title: eastern gamagrass crown root, inoculum CWR_N_D, Drought, plantID_368

description:
Library name: plantID_368
2x150bp


title: eastern gamagrass crown root, inoculum CWR_G_D, Drought, plantID_322

description:
Library name: plantID_322
2x150bp


title: eastern gamagrass crown root, inoculum TRI_G_W, Drought, plantID_363

description:
Library name: plantID_363
2x150bp


title: SG16374548_257236351134_1_2_0834-011-900_hr84


title: SG16374548_257236351133_2_4_0830-007-900_hr36


title: eastern gamagrass crown root, inoculum SVR_G_D, Drought, plantID_328

description:
Library name: plantID_328
2x150bp


title: eastern gamagrass crown root, inoculum SVR_G_D, Drought, plantID_327

description:
Library name: plantID_327
2x150bp


title: SG16374548_257236351133_2_3_0857-009-900_hr60


title: SG16374548_257236351133_2_2_0830-009-900_hr60


title: eastern gamagrass crown root, inoculum TRI_G_W, Drought, plantID_334

description:
Library name: plantID_334
2x150bp


title: eastern gamagrass crown root, inoculum TRI_G_D, Drought, plantID_314

description:
Library name: plantID_314
2x150bp


title: SG16374548_257236351134_1_1_0908-007-900_hr36


title: SG16374548_257236351133_1_4_0912-019-900_Day14


title: eastern gamagrass crown root, inoculum WEL_N_W, Drought, plantID_313

description:
Library name: plantID_313
2x150bp


title: eastern gamagrass crown root, inoculum Mock, Drought, plantID_318

description:
Library name: plantID_318
2x150bp


title: SG16374548_257236351133_2_1_0815-004-900_hr8


title: eastern gamagrass crown root, inoculum SVR_G_W, Drought, plantID_309

description:
Library name: plantID_309
2x150bp


title: eastern gamagrass crown root, inoculum CWR_N_W, Drought, plantID_316

description:
Library name: plantID_316
2x150bp


title: eastern gamagrass crown root, inoculum TRI_G_D, Drought, plantID_304

description:
Library name: plantID_304
2x150bp


title: SG16374548_257236351132_2_4_0835-001-900_hr0_baseline


title: eastern gamagrass crown root, inoculum CWR_N_D, Drought, plantID_303

description:
Library name: plantID_303
2x150bp


title: SG16374548_257236351132_2_3_0821-001-900_hr0


title: SG16374548_257236351132_2_2_0975-017-900_hr156


title: SG16374548_257236351133_1_2_0959-004-900_hr8


title: eastern gamagrass crown root, inoculum TRI_N_W, Drought, plantID_301

description:
Library name: plantID_301
2x150bp


title: eastern gamagrass crown root, inoculum SVR_N_D, Drought, plantID_295

description:
Library name: plantID_295
2x150bp


title: SG16374548_257236351132_2_1_0878-006-900_hr24


title: eastern gamagrass crown root, inoculum WEL_G_W, Drought, plantID_291

description:
Library name: plantID_291
2x150bp


title: SG16374548_257236351133_1_3_0927-004-900_hr8


title: eastern gamagrass crown root, inoculum CWR_G_W, Drought, plantID_284

description:
Library name: plantID_284
2x150bp


title: eastern gamagrass crown root, inoculum CWR_G_D, Drought, plantID_280

description:
Library name: plantID_280
2x150bp


title: SG16374548_257236351132_1_3_0912-011-900_hr108


title: SG16374548_257236351133_1_1_0807-003-900_hr4


title: SG16374548_257236351132_1_2_0837-003-900_hr4


title: SG16374548_257236350465_2_3_0922-001-900_hr0


title: eastern gamagrass crown root, inoculum WEL_G_W, Drought, plantID_275

description:
Library name: plantID_275
2x150bp


title: SG16374548_257236350465_2_4_0927-001-900_hr0


title: SG16374548_257236351132_1_1_0912-016-900_hr144


title: SG16374548_257236350465_2_1_0958-019-900_Day14


title: eastern gamagrass crown root, inoculum WEL_N_W, Drought, plantID_279

description:
Library name: plantID_279
2x150bp


title: eastern gamagrass crown root, inoculum SVR_G_W, Drought, plantID_269

description:
Library name: plantID_269
2x150bp


title: eastern gamagrass crown root, inoculum SVR_N_W, Drought, plantID_272

description:
Library name: plantID_272
2x150bp


title: SG16374548_257236350465_1_4_0879-003-900_hr4


title: eastern gamagrass crown root, inoculum SVR_G_W, Drought, plantID_253

description:
Library name: plantID_253
2x150bp


title: SG16374548_257236350465_1_2_0827-015-900_hr132


title: SG16374548_257236350465_2_2_0891-002-900_hr2


title: eastern gamagrass crown root, inoculum TRI_N_D, Drought, plantID_254

description:
Library name: plantID_254
2x150bp


title: eastern gamagrass crown root, inoculum SVR_G_D, Drought, plantID_257

description:
Library name: plantID_257
2x150bp


title: eastern gamagrass crown root, inoculum TRI_N_W, Drought, plantID_277

description:
Library name: plantID_277
2x150bp


title: SG16374548_257236350465_1_1_0862-001-900_hr0


title: eastern gamagrass crown root, inoculum CWR_N_D, Drought, plantID_250

description:
Library name: plantID_250
2x150bp


title: SG16374548_257236350465_1_3_0827-012-900_hr96


title: SG16374548_257236350464_2_4_0815-003-900_hr4


title: SG16374548_257236350464_2_3_0890-002-900_hr2


title: eastern gamagrass crown root, inoculum SVR_N_W, Drought, plantID_248

description:
Library name: plantID_248
2x150bp


title: SG16374548_257236351132_1_4_0899-005-900_hr12


title: eastern gamagrass crown root, inoculum CWR_G_W, Drought, plantID_245

description:
Library name: plantID_245
2x150bp


title: SG16374548_257236350464_1_4_0880-010-900_hr72


title: SG16374548_257236350464_2_2_0827-004-900_hr8


title: eastern gamagrass crown root, inoculum WEL_N_D, Drought, plantID_255

description:
Library name: plantID_255
2x150bp


title: eastern gamagrass crown root, inoculum TRI_G_D, Drought, plantID_244

description:
Library name: plantID_244
2x150bp


title: eastern gamagrass crown root, inoculum WEL_G_D, Drought, plantID_247

description:
Library name: plantID_247
2x150bp


title: SG16374548_257236350464_1_3_0852-003-900_hr4


title: eastern gamagrass crown root, inoculum Mock, Drought, plantID_243

description:
Library name: plantID_243
2x150bp


title: eastern gamagrass crown root, inoculum WEL_G_D, Drought, plantID_234

description:
Library name: plantID_234
2x150bp


title: SG16374548_257236350464_1_2_0908-001-900_hr0


title: eastern gamagrass crown root, inoculum WEL_G_D, Drought, plantID_232

description:
Library name: plantID_232
2x150bp


title: eastern gamagrass crown root, inoculum SVR_N_D, Drought, plantID_230

description:
Library name: plantID_230
2x150bp


title: SG16374548_257236350463_2_3_0830-002-900_hr2


title: SG16374548_257236350463_2_2_0975-019-900_Day14


title: SG16374548_257236350463_2_1_0821-007-900_hr36


title: SG16374548_257236350464_1_1_0876-001-900_hr0


title: eastern gamagrass crown root, inoculum CWR_N_W, Drought, plantID_227

description:
Library name: plantID_227
2x150bp


title: SG16374548_257236350463_1_4_0824-006-900_hr24


title: SG16374548_257236350463_2_4_0912-002-900_hr8


title: eastern gamagrass crown root, inoculum TRI_G_W, Drought, plantID_219

description:
Library name: plantID_219
2x150bp


title: SG16374548_257236350463_1_3_0974-019-900_Day14


title: SG16374548_257236350463_1_2_0931-004-900_hr8


title: eastern gamagrass crown root, inoculum SVR_N_W, Drought, plantID_242

description:
Library name: plantID_242
2x150bp


title: eastern gamagrass crown root, inoculum SVR_G_D, Drought, plantID_216

description:
Library name: plantID_216
2x150bp


title: eastern gamagrass crown root, inoculum WEL_N_D, Drought, plantID_228

description:
Library name: plantID_228
2x150bp


title: eastern gamagrass crown root, inoculum TRI_G_W, Drought, plantID_215

description:
Library name: plantID_215
2x150bp


title: SG16374548_257236350463_1_1_0834-006-900_hr24


title: SG16374548_257236350464_2_1_0944-001-900_hr0


title: eastern gamagrass crown root, inoculum WEL_G_D, Drought, plantID_208

description:
Library name: plantID_208
2x150bp


title: eastern gamagrass crown root, inoculum WEL_N_D, Drought, plantID_209

description:
Library name: plantID_209
2x150bp


title: eastern gamagrass crown root, inoculum TRI_N_W, Drought, plantID_202

description:
Library name: plantID_202
2x150bp


title: SG16374548_257236350462_2_3_0936-001-900_hr0


title: SG16374548_257236350462_2_2_0849-002-900_hr2


title: SG16374548_257236350462_2_4_0842-004-900_hr8


title: eastern gamagrass crown root, inoculum TRI_N_D, Drought, plantID_200

description:
Library name: plantID_200
2x150bp


title: eastern gamagrass crown root, inoculum WEL_G_W, Drought, plantID_226

description:
Library name: plantID_226
2x150bp


title: SG16374548_257236350462_1_4_0908-004-900_hr8


title: eastern gamagrass crown root, inoculum Mock, Drought, plantID_197

description:
Library name: plantID_197
2x150bp


title: SG16374548_257236350462_1_2_0866-006-900_hr24


title: eastern gamagrass crown root, inoculum CWR_G_D, Drought, plantID_196

description:
Library name: plantID_196
2x150bp


title: eastern gamagrass crown root, inoculum TRI_G_D, Drought, plantID_195

description:
Library name: plantID_195
2x150bp


title: SG16374548_257236350462_1_3_0899-004-900_hr8


title: SG16374548_257236350461_2_3_0862-002-900_hr2


title: eastern gamagrass crown root, inoculum CWR_N_D, Drought, plantID_194

description:
Library name: plantID_194
2x150bp


title: SG16374548_257236350461_2_2_0899-006-900_hr24


title: SG16374548_257236350461_2_1_0860-001-900_hr0_baseline


title: CBX2 antibody, Tazemetostat treated SU-DIPGXIII-H3K27M, rep3

city: Edinburgh

first: Gerry

last: Brien

address: Western General Hospital  Crewe Road South

department: Institute of Genetics and Cancer

institute: University  of Edinburgh

description:
Library name: TAZ-CBX2_Rep3
10% mouse cells was used as spike-in chromatin.
TAZ_CBX2.merged.sorted.av.bw

data_processing:
RNA-seq analysis involved: Paired-end reads from sequencing were aligned to the GRCh38 genome build (GCA_000001405.15 assembly) using the HISAT2 aligner (https://doi.org/10.1038/s41587-019-0201-4). Read extraction was performed with the featureCounts program (doi:10.1093/bioinformatics/btt656) using the corresponding GTF reference annotation and keeping only primary alignments. Read counts table and sample metadata were imported into R, and Differentially expressed genes were determined using DESeq2 (doi:10.1186/s13059-014-0550-8).
CUT&RUN-Rx analysis 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
Assembly: hg38
Supplementary files format and content: bigwig files contain average CUT&RUN signal for biological replicates.
Supplementary files format and content: csv files contain the output from DESeq, i.e. differentially expressed genes in sgRNA-KO conditions compared to DIPGXIII sgLUC cells, and the gene abundance data quantified using htseq-count.
Library strategy: CUT&Run

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:
For CUT&RUN-Rx, cells were harvested using Accutase (STEMCELL Technologies) and counted. Following counting mouse NSCs were spiked-in to human DIPGXIII cell suspensions (1:10 cell number ratio). Cells were fixed in culture media containing 0.1% formaldehyde at room temperature for 1 min. Formaldehyde was quenched with glycine at 0.125 M, followed by a 5-min incubation at room temperature. Fixed cells were washed with PBS. Fixed cells were incubated on ice for 10 min in nuclear extraction buffer (20mM HEPES pH 7.5, 10mM KCL, 0.1% Triton X-100, 20% Glycerol,1X protease inhibitor cocktail and 0.5mM spermidine). Extracted nuclei were collected by centrifugation (4ºC, 600g) and resuspended in cold nuclei extraction buffer (100µL per sample). CUT&RUN was performed following Epicypher CUT&RUN Protocol v1.5.1. CUT&RUN DNA was purified using the Monarch PCR & DNA Cleanup Kit (New England Biolabs) in accordance with the manufacturer’s instructions.  For RNA-seq, RNA was extracted from harvested cells (n=2 replicates) using Quick-RNA microprep kit (Zymocat#R1051).
CUT&RUN-Rx library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol. For RNA-seq, poly(A) mRNA enrichment and library preparation were performed by Genewiz.

treatment_protocol: For CUT&RUN, SU-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, SU-DIPGXIII-H3K27M (Parental) and SU-DIPGXIII-H3K27M-KO cells were untreated for CUT&RUN (indicated by P or KO in the file and sample names). For RNA-seq, SU-DIPGXIII-H3K27M cells constitutively express Cas9 and an sgRNA targeting the indicated gene.

value: Brain

tag: cell line

value: SU-DIPGXIII

tag: cell type

value: Patient-derived Diffuse Midline Glioma cells

tag: treatment

value: 2µM Tazemetostat


title: H2AK119Ub antibody, Tazemetostat treated SU-DIPGXIII-H3K27M, rep2

description:
Library name: TAZ-H2AK119Ub-Rep2
10% mouse cells was used as spike-in chromatin.
TAZ_H2AK119Ub1.merged.sorted.av.bw


title: SG16374548_257236351143_2_4_0843-012-900_hr96


title: SG16374548_257236350461_2_4_0905-006-900_hr24


title: SG16374548_257236350462_1_1_0937-005-900_hr12


title: eastern gamagrass crown root, inoculum CWR_G_W, Drought, plantID_193

description:
Library name: plantID_193
2x150bp

value: crown root

value: Pete


title: H2AK119Ub antibody, Tazemetostat treated SU-DIPGXIII-H3K27M, rep1

description:
Library name: TAZ-H2AK119Ub-Rep1
10% mouse cells was used as spike-in chromatin.
TAZ_H2AK119Ub1.merged.sorted.av.bw


title: SG16374548_257236350461_1_3_0908-002-900_hr2


title: SG16374548_257236350461_1_4_0824-018-900_hr168


title: CBX2 antibody, Tazemetostat treated SU-DIPGXIII-H3K27M, rep2

description:
Library name: TAZ-CBX2_Rep2
10% mouse cells was used as spike-in chromatin.
TAZ_CBX2.merged.sorted.av.bw


title: CBX2 antibody, Tazemetostat treated SU-DIPGXIII-H3K27M, rep1

description:
Library name: TAZ-CBX2_Rep1
10% mouse cells was used as spike-in chromatin.
TAZ_CBX2.merged.sorted.av.bw


title: SG16374548_257236350461_1_2_0849-001-900_hr0_baseline


title: H2AK119Ub antibody, DMSO treated SU-DIPGXIII-H3K27M, rep2

description:
Library name: DMSO-H2AK119Ub-Rep2
10% mouse cells was used as spike-in chromatin.
DMSO_H2AK119Ub1.merged.sorted.av.bw

value: DMSO


title: SG16374548_257236350461_1_1_0836-009-900_hr60


title: H2AK119Ub antibody, DMSO treated SU-DIPGXIII-H3K27M, rep3

description:
Library name: DMSO-H2AK119Ub-Rep3
10% mouse cells was used as spike-in chromatin.
DMSO_H2AK119Ub1.merged.sorted.av.bw


title: SG16374548_257236350462_2_1_0975-008-900_hr48


title: H2AK119Ub antibody, DMSO treated SU-DIPGXIII-H3K27M, rep1

description:
Library name: DMSO-H2AK119Ub-Rep1
10% mouse cells was used as spike-in chromatin.
DMSO_H2AK119Ub1.merged.sorted.av.bw


title: SG16374548_257236350454_2_3_0827-018-900_hr168


title: CBX2 antibody, DMSO treated SU-DIPGXIII-H3K27M, rep3

description:
Library name: DMSO-CBX2-Rep3
10% mouse cells was used as spike-in chromatin.
DMSO_CBX2.merged.sorted.av.bw


title: SG16374548_257236350454_2_1_0912-005-900_hr12


title: H2AK119Ub antibody, Tazemetostat treated SU-DIPGXIII-H3K27M, rep3

description:
Library name: TAZ-H2AK119Ub-Rep3
10% mouse cells was used as spike-in chromatin.
TAZ_H2AK119Ub1.merged.sorted.av.bw


title: SG16374548_257236350454_1_4_0912-014-900_hr120


title: SG16374548_257236350454_2_4_0827-002-900_hr2


title: SG16374548_257236350454_2_2_0939-004-900_hr8


title: CBX2 antibody, DMSO treated SU-DIPGXIII-H3K27M, rep1

description:
Library name: DMSO-CBX2-Rep1
10% mouse cells was used as spike-in chromatin.
DMSO_CBX2.merged.sorted.av.bw


title: SG16374548_257236350454_1_3_0849-006-900_hr24


title: H2AK119Ub antibody, SU-DIPGXIII_H3K27M cells, rep3

description:
Library name: K27M-H2AK119Ub-Rep3
10% mouse cells was used as spike-in chromatin.
P_H2AK119Ub.merged.sorted.av.bw


title: H2AK119Ub antibody, SU-DIPGXIII_H3K27M cells, rep2

description:
Library name: K27M-H2AK119Ub-Rep2
10% mouse cells was used as spike-in chromatin.
P_H2AK119Ub.merged.sorted.av.bw


title: SG16374548_257236350454_1_2_0909-002-900_hr2


title: SG16374548_257236350453_2_3_0834-003-900_hr4


title: SG16374548_257236350453_2_4_0821-014-900_hr120


title: H2AK119Ub antibody, SU-DIPGXIII_H3K27M-KO cells, rep3

description:
Library name: KO-H2AK119Ub-Rep3
10% mouse cells was used as spike-in chromatin.
KO_H2AK119Ub1.merged.sorted.av.bw


title: H2AK119Ub  antibody, SU-DIPGXIII_H3K27M-KO cells, rep1

description:
Library name: KO-H2AK119Ub-Rep1
10% mouse cells was used as spike-in chromatin.
KO_H2AK119Ub1.merged.sorted.av.bw


title: SG16374548_257236350454_1_1_0917-005-900_hr12


title: H2AK119Ub antibody, SU-DIPGXIII_H3K27M cells, rep1

description:
Library name: K27M-H2AK119Ub-Rep1
10% mouse cells was used as spike-in chromatin.
P_H2AK119Ub.merged.sorted.av.bw


title: CBX2 antibody, SU-DIPGXIII_H3K27M cells, rep3

description:
Library name: K27M-CBX2-Rep3
10% mouse cells was used as spike-in chromatin.
P_CBX2.merged.sorted.av.bw


title: SG16374548_257236350453_2_1_0908-003-900_hr4


title: CBX2 antibody, SU-DIPGXIII_H3K27M cells, rep2

description:
Library name: K27M-CBX2-Rep2
10% mouse cells was used as spike-in chromatin.
P_CBX2.merged.sorted.av.bw


title: SG16374548_257236350453_1_4_0827-013-900_hr108


title: SG16374548_257236350453_2_2_0834-004-900_hr8


title: CBX2 antibody, SU-DIPGXIII_H3K27M-KO cells, rep2

description:
Library name: KO-CBX2-Rep2
10% mouse cells was used as spike-in chromatin.
KO_CBX2.merged.sorted.av.bw


title: SG16374548_257236350453_1_3_0917-009-900_hr60


title: CBX2 antibody, SU-DIPGXIII_H3K27M-KO cells, rep3

description:
Library name: KO-CBX2-Rep3
10% mouse cells was used as spike-in chromatin.
KO_CBX2.merged.sorted.av.bw


title: SG16374548_257236350453_1_2_0872-007-900_hr36


title: SG16374548_257236350453_1_1_0880-008-900_hr48


title: H2AK119Ub antibody, SU-DIPGXIII_H3K27M-KO cells, rep2

description:
Library name: KO-H2AK119Ub-Rep2
10% mouse cells was used as spike-in chromatin.
KO_H2AK119Ub1.merged.sorted.av.bw


title: SG16374548_257236350452_2_3_0880-003-900_hr4


title: CBX2 antibody, SU-DIPGXIII_H3K27M-KO cells, rep1

description:
Library name: KO-CBX2-Rep1
10% mouse cells was used as spike-in chromatin.
KO_CBX2.merged.sorted.av.bw


title: SG16374548_257236350452_2_2_0908-004-900_hr12


title: PCGF4 sgRNA2, SU-DIPGXIII-H3K27M-Cas9, rep1

description:
Library name: BMI1.3_K27M+_Rep1
results_BMI1.3_K27M+_vs_LUC_K27M+.csv

data_processing:
RNA-seq analysis involved: Paired-end reads from sequencing were aligned to the GRCh38 genome build (GCA_000001405.15 assembly) using the HISAT2 aligner (https://doi.org/10.1038/s41587-019-0201-4). Read extraction was performed with the featureCounts program (doi:10.1093/bioinformatics/btt656) using the corresponding GTF reference annotation and keeping only primary alignments. Read counts table and sample metadata were imported into R, and Differentially expressed genes were determined using DESeq2 (doi:10.1186/s13059-014-0550-8).
CUT&RUN-Rx analysis 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
Assembly: hg38
Supplementary files format and content: bigwig files contain average CUT&RUN signal for biological replicates.
Supplementary files format and content: csv files contain the output from DESeq, i.e. differentially expressed genes in sgRNA-KO conditions compared to DIPGXIII sgLUC cells, and the gene abundance data quantified using htseq-count.

value: H3K27M; PCGF4 knock-down

value: sgRNA


title: PCGF4 sgRNA1, SU-DIPGXIII-H3K27M-Cas9, rep2

description:
Library name: BMI1.1_K27M+_Rep2
results_BMI1.1_K27M+_vs_LUC_K27M+.csv


title: SG16374548_257236350452_2_4_0902-012-900_hr96

value: Female


title: PCGF4 sgRNA2, SU-DIPGXIII-H3K27M-Cas9, rep2

description:
Library name: BMI1.3_K27M+_Rep2
results_BMI1.3_K27M+_vs_LUC_K27M+.csv


title: CBX2 antibody, SU-DIPGXIII_H3K27M cells, rep1

description:
Library name: K27M-CBX2-Rep1
10% mouse cells was used as spike-in chromatin.
P_CBX2.merged.sorted.av.bw


title: SG16374548_257236350452_1_4_0958-010-900_hr72


title: PCGF4 sgRNA1, SU-DIPGXIII-H3K27M-Cas9, rep1

description:
Library name: BMI1.1_K27M+_Rep1
results_BMI1.1_K27M+_vs_LUC_K27M+.csv


title: SG16374548_257236350452_1_3_0872-002-900_hr2


title: SG16374548_257236350452_1_1_0958-015-900_hr132


title: CBX8 sgRNA1, SU-DIPGXIII-H3K27M-Cas9, rep2

description:
Library name: CBX8.1_K27M+_Rep2
results_CBX8.1_K27M+_vs_LUC_K27M+.csv

value: H3K27M; CBX8 knock-down


title: CBX8 sgRNA2, SU-DIPGXIII-H3K27M-Cas9, rep2

description:
Library name: CBX8.2_K27M+_Rep2
results_CBX8.2_K27M+_vs_LUC_K27M+.csv


title: SG16374548_257236350452_2_1_0860-005-900_hr12

value: Alive


title: CBX8 sgRNA2, SU-DIPGXIII-H3K27M-Cas9, rep1

description:
Library name: CBX8.2_K27M+_Rep1
results_CBX8.2_K27M+_vs_LUC_K27M+.csv


title: SG16374548_257236350452_1_2_0860-002-900_hr2

value: Agilent's Universal Human Reference RNA


title: CBX8 sgRNA1, SU-DIPGXIII-H3K27M-Cas9, rep1

description:
Library name: CBX8.1_K27M+_Rep1
results_CBX8.1_K27M+_vs_LUC_K27M+.csv


title: SG16374548_257236350451_2_4_0938-001-900_hr0


title: EZH2 sgRNA1, SU-DIPGXIII-H3K27M-Cas9, rep2

description:
Library name: EZH2.3_K27M+_Rep2
results_EZH2.3_K27M+_vs_LUC_K27M+.csv

value: H3K27M; EZH2 knock-down


title: SG16374548_257236350451_2_3_0958-016-900_hr144

value: Male


title: EZH2 sgRNA1, SU-DIPGXIII-H3K27M-Cas9, rep1

description:
Library name: EZH2.3_K27M+_Rep1
results_EZH2.3_K27M+_vs_LUC_K27M+.csv


title: SG16374548_257236350451_2_2_0837-002-900_hr2


title: SG16374548_257236350451_2_1_0850-001-900_hr0_baseline


title: CBX2 sgRNA2, SU-DIPGXIII-H3K27M-Cas9, rep2

description:
Library name: CBX2.3_K27M+_Rep2
results_CBX2.3_K27M+_vs_LUC_K27M+.csv

value: H3K27M; CBX2 knock-down


title: CBX2 sgRNA2, SU-DIPGXIII-H3K27M-Cas9, rep1

description:
Library name: CBX2.3_K27M+_Rep1
results_CBX2.3_K27M+_vs_LUC_K27M+.csv


title: SG16374548_257236350451_1_4_0912-018-900_hr168


title: CBX2 sgRNA1, SU-DIPGXIII-H3K27M-Cas9, rep2

description:
Library name: CBX2.1_K27M+_Rep2
results_CBX2.1_K27M+_vs_LUC_K27M+.csv


title: SG16374548_257236350451_1_2_0964-004-900_hr8


title: CBX2 sgRNA1, SU-DIPGXIII-H3K27M-Cas9, rep1

description:
Library name: CBX2.1_K27M+_Rep1
results_CBX2.1_K27M+_vs_LUC_K27M+.csv


title: CBX4 sgRNA2, SU-DIPGXIII-H3K27M-Cas9, rep2

description:
Library name: CBX4.2_K27M+_Rep2
results_CBX4.2_K27M+_vs_LUC_K27M+.csv

value: H3K27M; CBX4 knock-down


title: SG16374548_257236350451_1_1_0896-019-900_Day14


title: SG16374548_253949448304_2_4_0975-003-900_hr4


title: CBX4 sgRNA1, SU-DIPGXIII-H3K27M-Cas9, rep2

description:
Library name: CBX4.1_K27M+_Rep2
results_CBX4.1_K27M+_vs_LUC_K27M+.csv

value: Brain


title: CBX4 sgRNA1, SU-DIPGXIII-H3K27M-Cas9, rep1

description:
Library name: CBX4.1_K27M+_Rep1
results_CBX4.1_K27M+_vs_LUC_K27M+.csv

value: SU-DIPGXIII


title: SG16374548_253949448327_1_3_0974-018-900_hr168


title: SG16374548_253949448307_2_2_0975-002-900_hr2


title: control luciferase sgRNA, SU-DIPGXIII-H3K27M-Cas9 cells, rep2

description: Library name: LUC_K27M+_Rep2

value: Patient-derived Diffuse Midline Glioma cells


title: control luciferase sgRNA, SU-DIPGXIII-H3K27M-Cas9 cells, rep1

description: Library name: LUC_K27M+_Rep1


title: SG16374548_253949448331_2_3_0974-017-900_hr156


title: SG16374548_253949448108_1_1_0974-016-900_hr144


title: +Rapa, Tachyzoite, biol rep 3

city: Wuhan

first: bolin

last: Fan

state: hubei

address: hubei

institute: Huazhong Agricultural University

description:
TranRaPa_3
Transcription of Dicre-iGRA1 strains treated with plus Rapamycin drug

data_processing:
Clean reads were mapped to the T. gondii GT1 genome (ToxoDB) using Hisat2 software
Transcript levels were calculated using the transcript per million (TPM) method, and differentially expressed genes were identified using DESeq2 v1.24.0 with a p-value < 0.01 and a minimum fold change of 2.
Assembly: T. gondii reference genome (TGGT1)
Supplementary files format and content: raw counts for each sample

organism: Toxoplasma gondii

source_name: Tachyzoite culture

growth_protocol: To obtain tachyzoite samples, parasites were cultured in human foreskin fibroblasts (HFF), in Dulbecco’s Modified Eagle Medium (DMEM) (Sigma-Aldrich, USA), supplemented with 2% heat-inactivated fetal bovine serum (FBS) (Gibco, USA), 1% penicillin-streptomycin, and 5 mM L-glutamine. In order to obtain samples of bradyzoites, parasites were cultured in RPMI 1640 medium (pH = 8.2) containing 1% fetal bovine serum, along with ambient CO2.

extract_protocol:
Intracellular parasites were harvested, released by needle passage, and purified by filtration through membranes with 3 μm pore size to remove host cell debris. Total RNA was extracted from purified parasites using transZol Up reagent (TransGen Biotech, China) following the manufacturer’s instructions. The RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent, USA).
Libraries for RNA sequencing were prepared using the TruSeq RNA Sample Prep Kit (Illumina, USA) and sequenced on a DNBSEQ-T7 sequencer (MGI Tech Co., Ltd, China) with the PE150 model.

treatment_protocol: To obtain tachyzoite samples, RH-Dicre-iGRA1  was grown under normal culture conditions, and  was required to be treated with plus or minus Rapamycin drug, to obtain tachyzoite samples.

value: Tachyzoite culture

value: plus Rapamycin drug


title: +Rapa, Tachyzoite, biol rep 2

description:
TranRaPa_2
Transcription of Dicre-iGRA1 strains treated with plus Rapamycin drug


title: SG16374548_253949448305_2_3_0974-013-900_hr108


title: SG16374548_257236350451_1_3_0803-008-900_hr48


title: +Rapa, Tachyzoite, biol rep 1

description:
TranRaPa_1
Transcription of Dicre-iGRA1 strains treated with plus Rapamycin drug


title: SG16374548_253949448111_2_2_0974-012-900_hr96


title: SG16374548_253949447551_2_2_0974-011-900_hr84


title: -Rapa, Tachyzoite, biol rep 4

description:
TranDMSO_4
Transcription of Dicre-iGRA1 strains treated with minus Rapamycin drug

value: minus Rapamycin drug


title: -Rapa, Tachyzoite, biol rep 3

description:
TranDMSO_3
Transcription of Dicre-iGRA1 strains treated with minus Rapamycin drug


title: -Rapa, Tachyzoite, biol rep 2

description:
TranDMSO_2
Transcription of Dicre-iGRA1 strains treated with minus Rapamycin drug


title: SG16374548_253949448106_2_4_0974-010-900_hr72


title: SG16374548_253949448096_2_4_0974-007-900_hr36


title: SG16374548_253949448105_2_1_0974-009-900_hr60


title: CBX4 sgRNA2, SU-DIPGXIII-H3K27M-Cas9, rep1

description:
Library name: CBX4.2_K27M+_Rep1
results_CBX4.2_K27M+_vs_LUC_K27M+.csv


title: -Rapa, Tachyzoite, biol rep 1

description:
TranDMSO_1
Transcription of Dicre-iGRA1 strains treated with minus Rapamycin drug