title: WT_C_3

status: Public on Mar 19 2023

city: Calgary

first: Vanina

last: Zaremberg

state: Alberta

address: 2500 University Dr NW

department: Biological Sciences

institute: University of Calgary

description:
Poly(A) Enriched mRNA
WT3_C.kallisto
read_counts_matrix.txt

data_processing:
Analysis was performed by the Cumming School of Medicine's Centre for Health Genomics and Informatics, University of Calgary
Reads were mapped to the reference transcriptome using Kallisto.
Statistical analysis was performed in R following http://achri.blogspot.com/2016/10/using-kallisto-sleuth.html
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Saccharomyces cerevisiae

growth_protocol: S cerevisiae cells were grown into log phase at 30C with shaking at 200rpm in synthetic defined medium

extract_protocol:
RNA was harvested using using the hot acid phenol protocol. 1ug of total RNA input was used for all libraries.
NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770, E7775) were used to prepare the libraries according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with either 0.095% ethanol or 20uM edelfosine for 60 minutes.

tag: biological replicate


title: WT_C_2

type: SRA

country: Canada

description:
Poly(A) Enriched mRNA
WT2_C.kallisto
read_counts_matrix.txt

library_source: transcriptomic

molecule: polyA RNA

tag: strain

tag: treatment


title: WT_E_2

description:
Poly(A) Enriched mRNA
WT2_E.kallisto
read_counts_matrix.txt

value: 20uM edelfosine


title: WT_E_3

description:
Poly(A) Enriched mRNA
WT3_E.kallisto
read_counts_matrix.txt


title: WT_E_1

description:
Poly(A) Enriched mRNA
WT1_E.kallisto
read_counts_matrix.txt


title: HTNV infected HUVECs [HV-1]

city: wuhan

first: xin

last: wang

address: Donghu road

country: China

institute: wuhan university

data_processing:
Illumina HiSeq 2500 sequencing 50nt original sequence set, through the removal of the two ends of the reads, remove the low-quality reads, decontamination and other processes to complete the preliminary filtering of the data to obtain a clean sequence, the sequence length distribution statistics and the common sequences between samples statistics
Using BWA software to compare clean reads in the sequencing data to the reference genome
After comparing reads to the entire genome of the target species, analyze the distribution of sRNA throughout the genome. The results are shown in Circos pictures
Compare the filtered reads with authoritative miRNA (miRBase version 21), rRNA, tRNA, snRNA, snoRNA (Rfam12.1), and then annotate the known ncRNA
Compare the obtained sequencing data with the sequences of all miRNA mature species of this species in the miRBase (version21) database to calculate the expression level
Genome_build: hg19
Supplementary_files_format_and_content: expression level by counts, normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: HTNV infected HUVECs

growth_protocol: exosomes were separated from HTNV infected/uninfected HUVECs

extract_protocol:
Total RNAs from exosomes were fractionated by 15% Tris-borate-EDTA (TBE) polyacrylamide gel (Invitrogen) to extract small RNAs ranging between 18 and 30 nt, which were subsequently used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols,the Illumina HiSeq 2500 platform were employed for deep sequencing of exosomal miRNA profiles.

tag: cell type

value: primary human umbilical vein endothelial cells (HUVECs)

tag: passages

tag: infection

value: Hantaan virus (HTNV)-infected


title: HTNV infected HUVECs [HV-2]


title: uninfected HUVECs [NC]

source_name: uninfected HUVECs

value: uninfected


title: DTG_Rx4

city: Houaton

first: Ali

middle: J

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

country: USA

institute: UTHSC, Houston

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCm38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw count xlsx file

organism: Mus musculus

source_name: Cardiac Myocyte

extract_protocol:
Samples with a RNA Integrity Number (RIN) read out of more than 8 were used to prepare sequencing library using the Illumina TruSeq stranded total RNA library preparation kit. The samples were sequenced on the Illumina HiSeq 4000 instrument using the paired-end sequencing reagents to generate 75 base pair runs.
RNA-Seq

treatment_protocol: RNA-Sequencing (RNA-Seq):  Total RNA was isolated from cardiac myocytes of 3-week old WT and Myh6-Cre:LmnaF/F-Vehicle treated and Myh6-Cre:LmnaF/F-JQ1 treated mice. RNA-seq was performed on the on ribosome-depleted RNA.

value: Myocytes

value: Freshly isolated

tag: genotype

tag: agent


title: DTG_Rx3


title: DTG_Rx2


title: WT2_snRNA

status: Public on Mar 20 2023

city: Göttingen

first: Ting

last: Sun

state: Germany (DEU)

address: Hermann-Rein-Straße 3

department: Neurogenetics

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciencesi

data_processing:
raw data was aligned to reference profile pre-mRNA mm10 using 10x genomics toolkit CellRanger v3.0.2
Single-nuclei UMI matrices were extracted and nuclei with less then 200 detected genes or less than 500 total transcripts were filtered out
Genome_build: premRNA_mm10
Supplementary_files_format_and_content: Tab-delimited matrix include raw UMI counts for single-cells collected from all samples
Supplementary_files_format_and_content: Tab-delimited matrix of single-cell meta data which includes cell basic information and annotation during analysis
Supplementary_files_format_and_content: Tab-delimited matrix include raw UMI counts for microglia cells
Supplementary_files_format_and_content: Tab-delimited matrix of microglia meta data which includes cell basic information and annotation during analysis

source_name: Cortex and corpus callosum

extract_protocol:
Frozen tissue was transferred into 2ml of pre-chilled homogenization buffer (320mM sucrose, 0.1% NP40, 0.1mM EDTA, 5mM CaCl2, 3mM Mg(Ac)2, 10mM pH 7.8 Tris, 167uM β-mercaptoethanol and 1x protease inhibitor (Roche)). Tissue was carefully homogenized and filtered through a 80um strainer, and further centrifuged for 1min under 100 rcf. For each sample, 400 ul supernatant was collected into a pre-chilled 2ml eppendorf low-binding eppendorf tube, followed by adding 400ul 50% iodixanol solution (in 1x homogenization buffer containing 480mM sucrose) to reach a 25% iodixanol concentration. By layering 600ul of 29% iodixanol underneath the 25% iodixanol mixture, then 600ul of 35% iodixanol underneath the 29% iodixanol, two clear interfaces between different concentrations of buffers were created, and the tube was centrifuged for 20 min under 3000 rcf. After centrifuge, nuclei were collected from the band between the 29% and the 35% iodixanol layers and transferred to a fresh pre-chilled tube. The isolated nuclei were washed and resuspended in pre-chilled resuspension buffer (1xPBA, 1% BSA, 0.1U/ul RNase inhibitor).
Single-nucleus RNA libraries were prepared using 10x genomics chromium single-cell 3’ protocol and sequenced by Illumina Novaseq 6000

tag: age

value: WT

tag: tissue

value: Cortex and corpus callosum

tag: mouse model

value: Alzheimer’s disease (AD)


title: DTG_Rx1


title: DTG_2

value: 10 percent DMSO and 10 percent (2-Hydroxypropyl)-beta-cyclodextrin


title: DTG_4


title: DTG_1


title: DTG_3


title: WT_4


title: WT_1


title: WT_3


title: WT_C_1

description:
Poly(A) Enriched mRNA
WT1_C.kallisto
read_counts_matrix.txt


title: WT_2


title: 109_C'_L

type: RNA

city: Vandœuvre-lès-Nancy

first: Hélène

last: Dubois-Pot-Schneider

address: Site CRAN/Faculté de Médecine - Bâtiment D, 1er étage 9 avenue de la Forêt de Haye, BP 184

department: CRAN

country: France

institute: Université de Lorraine - UMR7039 CRAN

description: Gene expression of patient sample 109_C'_L

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (profile Agilent G3-GX-1color).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using protocol GE1_1200_Jun14 _ssSurogates and Grid: 072363_D_F_20190204. Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Filtration by flag and signal intensity was applied. Briefly, were retained only the entities in which at least 100% of the values in at least one condition  had a detected flag (i.e. a positive  and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which 100% of the values in at least one condition were within the range of interest (i.e. 20-100th percentile).

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labelling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop (Thermo Fischer Scientific, Waltham, MA).  amplification yield was 4.04 ± 0.53 µg cRNA and specific activity was 11.97 ± 0.98 pmol Cy3 per µg cRNA.

growth_protocol: Samples collection has been conducted and promoted by the Plastic Surgery Department of the Metz-Thionville Regional Hospital in the frame of the SpectroLive clinical trial. Only individuals with Fitzpatrick type I or II skin characteristics, such as fair skin, freckles, light-colored eyes (blue or green) and blonde or red hair were included in the clinical trial. All included patients provide written informed consent. Patient records and information were anonymized and de-identified prior to analysis. For each patient, samples were acquired on the lesion (L or AK), on the perilesional (PL) i.e. safety surgical margin area (often containing AK) and on the non-lesional (NL) parts of the elliptical surgical excision. Punch biopsies (2 mm) of NL, PL, AK and L obtained at the time of surgical resection are immediately collected in RNA-later for RNA stabilization.

extract_protocol: RNA extractions were performed with EZNA HP Total RNA (Omega Bio-Tek)  following the manufacturer's recommendations. RNA was qualified using a Nanodrop 2000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA).

tag: patient number

tag: sample localisation

value: Ear

tag: lesion type

value: Lesion


title: 122_A_NL

description: Gene expression of patient sample 122_A_NL

value: Vertex

value: Non Lesion


title: 109_C'_AK_2

description: Gene expression of patient sample 109_C'_AK number 2

value: Actinic Keratosis

tag: lesion number (if applicable)


title: 115_F_NL

description: Gene expression of patient sample 115_F_NL

value: Cheek


title: 125_C'_L

description: Gene expression of patient sample 125_C'_L


title: 119_C_AK_1

description: Gene expression of patient sample 119_C_AK number 1

value: Temple


title: 109_C'_NL

description: Gene expression of patient sample 109_C'_NL


title: 123_L_L

description: Gene expression of patient sample 123_L_L

value: Shoulder


title: 110_B_L

description: Gene expression of patient sample 110_B_L

value: Forehead


title: 110_C_L

description: Gene expression of patient sample 110_C_L


title: 091_A_L

description: Gene expression of patient sample 091_A_L


title: 082_B_AK_2

description: Gene expression of patient sample 082_B_AK number 2


title: 119_C_AK_2

description: Gene expression of patient sample 119_C_AK number 2


title: 115_F_AK

description: Gene expression of patient sample 115_F_AK


title: 090_A_AK

description: Gene expression of patient sample 090_A_AK


title: 091_J_NL

description: Gene expression of patient sample 091_J_NL

value: Neck anterior surface


title: 077_B_AK_2

description: Gene expression of patient sample 077_B_AK number 2


title: 109_C'_AK_1

description: Gene expression of patient sample 109_C'_AK number 1


title: 077_B_AK_1

description: Gene expression of patient sample 077_B_AK number 1


title: 077_J_NL

description: Gene expression of patient sample 077_B_NL


title: 075_U_L_2

description: Gene expression of patient sample 075_U_L number 2

value: Hand dorsum


title: 075_U_NL

description: Gene expression of patient sample 075_U_NL


title: 077_B_L

description: Gene expression of patient sample 077_B_L


title: 075_U_L_1

description: Gene expression of patient sample 075_U_L number 1


title: 082_al_NL

description: Gene expression of patient sample 082_al_NL

value: Leg anterior surface


title: 110_B_NL

description: Gene expression of patient sample 110_B_NL


title: 082_B_AK_1

description: Gene expression of patient sample 082_B_AK number 1


title: 090_A_NL

description: Gene expression of patient sample 090_A_NL


title: 075_U_AK

description: Gene expression of patient sample 075_U_AK


title: L7128

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

library_source: genomic

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the lastest bovine reference genome (ARS-UCD1.2) using the software package Bismark (version 0.20.1).
Methylation calling and extraction were performed using Bismark methylation extractor (version 0.20.1).
Assembly: Cow genome assembly: ARS-UCD1.2
Supplementary files format and content: Tab-delimited text files including chromosome, genomic start position, genomic end position, percentage of methylation at that position, number of Cs methylated, and number of Cs non-methylated

molecule: genomic DNA

organism: Bos taurus

source_name: Liver

extract_protocol:
Total DNA was extracted from 10 mg of homogenized liver tissue and purified using magnetic beads (#OSR-M40, Tiangen Biotech, Beijing).
Bisulfite treatment, library preparation and subsequent sequencing were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China).

value: Liver

tag: breed

value: Holstein

value: postnatal heat stress


title: 119_C_NL

description: Gene expression of patient sample 119_C_NL


title: L7071


title: L7139


title: L7061


title: L7054


title: L7147

value: postnatal cooling


title: 082_al_AK

description: Gene expression of patient sample 082_al_AK


title: L7094


title: L7117


title: L7084


title: 057_C_NL

description: Gene expression of patient sample 057_C_NL


title: 056_B_NL

description: Gene expression of patient sample 056_B_NL


title: 074_C'_NL

description: Gene expression of patient sample 074_C'_NL


title: 048_F_NL

description: Gene expression of patient sample 048_F_NL


title: L7062


title: 048_F_AK

description: Gene expression of patient sample 048_F_AK


title: 041_A_AK

description: Gene expression of patient sample 041_A_AK


title: L7151


title: 074_C'_L

description: Gene expression of patient sample 074_C'_L


title: 045_J_NL

description: Gene expression of patient sample 045_J_NL


title: 035_A_L_2

description: Gene expression of patient sample 035_A_L number 2


title: 056_B_AK

description: Gene expression of patient sample 056_B_AK


title: 057_C_L

description: Gene expression of patient sample 057_C_L


title: 041_J_NL

description: Gene expression of patient sample 041_J_NL


title: 029_C_NL

description: Gene expression of patient sample 029_C_NL


title: 029_C_AK

description: Gene expression of patient sample 029_C_AK


title: 029_C_L

description: Gene expression of patient sample 029_C_L


title: 056_B_L

description: Gene expression of patient sample 056_B_L


title: 028_F_AK

description: Gene expression of patient sample 028_F_AK


title: 028_C'_PL

description: Gene expression of patient sample 028_C'_PL

value: Peri Lesion


title: max3, biological rep2

city: Saint Lucia

first: Alicia

middle: May

last: Hellens

state: Queensland

address: Mansfield Place

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

hyb_protocol: hybridized to whole‐genome Arabidopsis ATH1 GeneChips according to manufacturers reccommendations

scan_protocol: scanned with an Affymetrix GCS3000 Scanner according to manufacturers reccommendations

data_processing: The scanned probe array images (.DAT files) were converted into .CEL files using the GeneChip Operating Software (Affymetrix). Probe intensities were normalized for background correction using the robust multiarray average method corrected for GC content of the oligo, an algorithm known as GCRMA using affy and simpleaffy and the statistical language and environment R version 3.2.2.

label: biotin

organism: Arabidopsis thaliana

source_name: 2-week old arabidopsis hypocotyls from max3 mutants

label_protocol: High‐quality biotin‐labeled complementary RNA (cRNA) was prepared from 4‐μg total RNA per sample according to the standard Affymetrix protocol

growth_protocol: Arabidopsis seeds were stratified for 72 h at 4°C and then sown on University of California potting mix type C and vermiculite (3:2 v/v). The plants were grown for 2 weeks (until they had five to six leaves expanded) in a temperature‐ and humidity‐controlled growth chamber under 24°C with 16‐h light/21°C with 8‐h dark photoperiod providing 180 μmol m−2 s−1

extract_protocol: Total RNA was isolated using NucleoSpin RNA plant kits (Machery‐Nagel, Düren, Germany) and further purified and concentrated using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany) according to manufacturer's protocol. RNA was quantified using a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Wilmington, Delaware, USA).

treatment_protocol: Treatments for each replicate were performed simultaneously, and each biological replicate was harvested over a period of 60–80 min at 24 h after treatment. Hypocotyls were collected as three biological replicates of 120–150 plants per treatment or mutant and flash frozen in liquid nitrogen and stored at −80°C.

value: Hypocotyl

value: two-weeks

value: lanolin (<10% EtOH)


title: max2, biological rep3

source_name: 2-week old arabidopsis hypocotyls from max2 mutants


title: max3, biological rep1


title: max2, biological rep2


title: max3, biological rep3


title: 028_C'_NL

description: Gene expression of patient sample 028_C'_NL

value: Ear

value: Non Lesion


title: max2, biological rep1


title: max1, biological rep2

source_name: 2-week old arabidopsis hypocotyls from max1 mutants


title: id_12 - Cancer - FOAM low

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

data_processing:
Sequencing reads were preprocessed with fastp v0.21.0 (Chen et al., 2018) in default settings to remove reads associated with a low quality (phred quality <Q15), shorter than 15 nt reads, or with more than 5 Ns.
Reads passing the filtering step were aligned to the human Gencode v36 transcriptome using Salmon v1.4.0 (Patro et al., 2017) with option --validateMappings, --seqBias, and --gcBias.
Gene expression levels were normalized using tximport v.1.18 while DESeq2 v1.30.1 was applied for the differential expression analysis
Assembly: hg38
Supplementary files format and content: TPM-normalized gene expression levels

source_name: CRC

extract_protocol:
RNA was harvested using Maxwell RSC miRNA tissue kit on Maxwell RSC Instrument (Promega). The RNA concentration was assessed with a Qubit 4 fluorometer (ThermoFisher). RNA purity was assessed as 260/280 and 269/230 ratios by spectometric analysis and  RNA quality was verified on a 2100 bioanalyzer (Agilent Techn.).
200-800 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared with the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina Inc.).

value: CRC

tag: foam content

value: low

tag: class

value: FC depleted CRC stage (I or II)


title: id_15 - Cancer - FOAM low


title: max1, biological rep3


title: id_13 - Cancer - FOAM low


title: 028_C'_L

description: Gene expression of patient sample 028_C'_L

value: Lesion


title: 026_C_PL

description: Gene expression of patient sample 026_C_PL

value: Temple


title: max1, biological rep1


title: Wild type, NPA, biological rep3

source_name: Wild type 2-week old arabidopsis hypocotyls treated with NPA for 24 h

value: wild type (Col-0)

value: 3 mg/mL NPA in lanolin (<10% EtOH)


title: 035_A_L_1

description: Gene expression of patient sample 035_A_L number 1

value: Vertex


title: 018_B_NL

description: Gene expression of patient sample 018_B_NL

value: Forehead


title: 018_B_PL

description: Gene expression of patient sample 018_B_PL


title: Wild type, NPA, biological rep1


title: Wild type, Decapitated + Auxin (IAA), biological rep3

source_name: Wild type 2-week old arabidopsis hypocotyls treated with auxin (IAA) for 24 h

value: Decapitated + 3 mg/mL IAA in lanolin (<10% EtOH)


title: 018_B_L_2

description: Gene expression of patient sample 018_B_L number 2


title: 018_B_L_3

description: Gene expression of patient sample 018_B_L number 3


title: Wild type, Decapitated + Auxin (IAA), biological rep2


title: Wild type, Decapitated + Auxin (IAA), biological rep1


title: id_14 - Cancer - FOAM low


title: id_11 - Cancer - FOAM low


title: Wild type, NPA, biological rep2


title: 026_C_NL

description: Gene expression of patient sample 026_C_NL


title: id_10 - Cancer - FOAM high

value: high

value: FC enriched CRC stage (I or II)


title: Headneck, AS-17

city: Singapore

first: Abner

last: Lim

address: 30 Hospital Boulevard

department: Division of Medical Oncology

country: Singapore

institute: National Cancer Center Singapore

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000
Sequenced libraries were processed using SpaceRanger 1.3.1
Assembly: GRCh38
Supplementary files format and content: Processesed data files contains 24-bit color brightfield microscopy input image, Market Exchange Format (MEX) containing feature (row) and barcode (columns) and the associated matrix and the HDF5 binary version of the corresponding file generated.
Library strategy: Spatial transcriptomics

source_name: Tumor

extract_protocol:
Sectioned snap frozen tissues were placed onto 10x Visium library preparation slides. The tissues were fixed, stained with H&E and imaged. Subsequently, the tissues were permeabilized to release mRNA before library construction.
construction of sequencing libraries were done following Visium Spatial Expression User Guide

tag: disease state

value: Head and Neck Angiosarcoma

value: Tumor

tag: ethnicity

value: Asian


title: Headneck, AS-52


title: id_6 - Cancer - FOAM high

tag: treatment

value: High


title: id_4 - Cancer - FOAM high


title: Headneck, AS-03


title: 018_B_L_1

description: Gene expression of patient sample 018_B_L number 1


title: 017_A_L

description: Gene expression of patient sample 017_A_L


title: 8-week  mice CD4+CD25+ splenocytes biol replicate 4

city: Shanghai

first: Yile

last: Zhou

address: 180 Fenglin Road

institute: Fudan University

data_processing:
Sequencing library was generated from cDNA following Illumina Nextera XT protocol and the final library was sequenced on Illumina
On average about 15 million 150bp paired end reads were generated per sample.
Assembly: mm10
Supplementary files format and content: NO file includes raw counts for each sample,

source_name: CD4+CD25+ splenocytes

extract_protocol:
RNA was harvested using Trizol (TAKARA). 1 ug of total RNA was used for the construction of sequencing libraries.
cDNA library was prepared from cells using the SMART-Seq v4 Ultra Low RNA Kit （Clonetech）following manufacturers instructions.

tag: cell type

value: CD4+CD25+ splenocytes

value: WT

tag: developmental stage

value: young

value: 8-week old


title: 8-week  mice CD4+CD25+ splenocytes biol replicate 3

tag: genotype


title: RPMI8226 0.4 μM CDDO-2P-Im rep2

city: Cleveland

first: George

last: Luo

state: OH

address: 2103 Cornell Rd. Wolstein Research Bldg/Rm 3501

institute: Case Western Reserve University

data_processing:
Cutadapt was used to remove reads with contamination/low quality
HISAT2 was used to map reads to genome
StringTie used to assembled and estimate transcription levels
edgeR used to estimate expression levels
Assembly: tp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
Supplementary files format and content: tab-delimited text files include RPKM values

growth_protocol: Cells were grown in RPMI1640 medium with 10% FBS with 1% pen/strep

extract_protocol:
Cells were extracted with Purelink RNA Mini Kit
Illumina’s TruSeq-stranded-mRNA sample preparation protocol

treatment_protocol: Cells were treated with 1% DMSO or CDDO-2P-Im dissolved in DMSO for 6 hours

tag: cell line

value: Myeloma

value: 0.4 uM CDDO-2P-Im


title: RPMI8226 0.1 μM CDDO-2P-Im rep3

value: 0.1 uM CDDO-2P-Im


title: RPMI8226 0.4 μM CDDO-2P-Im rep3


title: RPMI8226 0.4 μM CDDO-2P-Im rep1


title: 8-week  mice CD4+CD25+ splenocytes biol replicate 2

tag: age


title: Wild type, Decapitated, biological rep2

source_name: Wild type 2-week old arabidopsis hypocotyls from plants decapitated for 24 h

value: wild type (Col-0)

tag: tissue

value: Hypocotyl

value: two-weeks

value: Decapitated + lanolin (<10% EtOH)


title: Wild type, Decapitated, biological rep3


title: Headneck, AS-07


title: Wild type, Decapitated, biological rep1


title: RPMI8226 0.1 μM CDDO-2P-Im rep2


title: Wild type, Intact, biological rep3

source_name: Wild type 2-week old arabidopsis hypocotyls

value: lanolin (<10% EtOH)


title: 016_B_NL

description: Gene expression of patient sample 016_B_NL

value: Forehead

value: Non Lesion


title: Wild type, Intact, biological rep2


title: L7128

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using Hisat2 sofware (version 2.1.0).
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Assembly: Cow genome assembly: ARS-UCD1.2
Supplementary files format and content: Tab-delimited text files including ensembl gene id and number of mapped reads.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal Mini Kit (Qiagen, Valencia, CA; #73404).
Library preparation and subsequent RNA sequencing were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China).

value: Liver

value: Holstein

value: postnatal heat stress


title: L7061


title: L7071


title: L7139


title: L7136


title: 016_B_AK

description: Gene expression of patient sample 016_B_AK

value: Actinic Keratosis


title: Wild type, Intact, biological rep1


title: 017_A_AK

description: Gene expression of patient sample 017_A_AK

value: Vertex


title: 016_B_L

description: Gene expression of patient sample 016_B_L

value: Lesion


title: 006_B_NL

description: Gene expression of patient sample 006_B_NL


title: 006_B_PL

description: Gene expression of patient sample 006_B_PL

value: Peri Lesion


title: 8-week  mice CD4+CD25+ splenocytes biol replicate 1

value: CD4+CD25+ splenocytes

value: WT

value: young

value: 8-week old


title: L7054


title: 18-month  mice CD4+CD25+ splenocytes biol replicate 3

value: aged

value: 18-month old


title: RPMI8226 DMSO rep3

value: Myeloma

value: DMSO


title: L7151

value: postnatal cooling


title: L7147


title: 18-month  mice CD4+CD25+ splenocytes biol replicate 1


title: RPMI8226 0.1 μM CDDO-2P-Im rep1

value: 0.1 uM CDDO-2P-Im


title: 006_B_L

description: Gene expression of patient sample 006_B_L

value: Forehead


title: RPMI8226 DMSO rep2


title: L7117

value: Liver

value: Holstein


title: M1910

city: Gainesville

first: Tongjun

last: Gu

state: FL

address: 2033 Mowry Road

department: ICBR

institute: The University of Florida

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality reads were trimmed or removed. The high quality reads were then mapped to GRCm38 using STAR 2.7.6a
Fragments Per Kilobase of exon per Megabase of library size (FPKM), Transcript Per Million (TPM) and extimated read counts were calculated using RSEM 1.3.3
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol: Total RNA was extracted using RNeasy Plus Mini kit (Qiagen, Hilden, Germany) from Pi*M and Pi*Z liver samples (n=6). The quantity and quality of the RNA were determined using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: liver

tag: strain background

value: Pi*M

value: LPS


title: M1904


title: RPMI8226 DMSO rep1


title: L7094


title: L7084


title: jazD cdk8-1_rep 3

city: East Lansing

first: Qiang

last: Guo

state: MI

address: 612 Wilson Rd

department: Plant Research Laboratories

institute: Michigan State University

data_processing:
Reads received as FASTQ files. Reads were assessed for quality and filtered with Illumina quality control tools filters and FASTX toolkit (http://hannonlab.cshl.edu /fastx_toolkit/).
RSEM v1.2.25 (Li and Dewey, BMC Bioinformatics, 2011) used to map reads to the Arabidopsis genome using the Illumina iGenomes TAIR10 index with default parameters. Transcript abundances expressed as transcripts per million (TPM; reads per kilobase of model per million mapped reads normalized to transcript coverage).
Genome_build: TAIR10
Supplementary_files_format_and_content: expression data (jazDcdk8_expression.txt) in tab-delimited matrix table for TPM (transcripts per million) values for all samples, as determined by RSEM
Supplementary_files_format_and_content: count data (jazDcdk8_counts.txt) in tab-delimited matrix table for read counts for all samples, as determined by RSEM

source_name: whole rosette

growth_protocol: Trays of soil-grown plants were covered with a transparent plastic dome for 10 days after seed sowing. Plants were maintained under a 16-h light (100 μE m-2 s-1) and 8-h dark photoperiod at 20 ºC

extract_protocol:
For each replicate sample, approximately 10 plants (whole rosette, excluding roots) per genotype were pooled and immediately frozen in liquid nitrogen and stored at -80 ºC until processing. Wild-type Col-0 and mutant plants were grown in the same tray to minimize tray-to-1tray variation. Three independent samples (biological replicates) were sequenced per genotype. Total RNA was isolated using a Macherey-Nagel NucleoSpin RNA plant kit with Macherey-Nagel on-column DNase treatment to remove genomic DNA. RNA integrity was assessed with a 2100 Bioanalyzer (Agilent Bioanalyzer) and all samples had an integrity score of at least 6.5.
Barcoded sequencing libraries were prepared using the BGI transcriptome kit. Normalized libraries were sequenced on the BGI DNBseq platform.

tag: replicate


title: ΔpvfA-D, batch 2, biological replicate 3

city: Chapel Hill

first: Bo

last: Li

state: North Carolina

address: Genome Sciences Building 3244, 250 Bell Tower Drive

department: Chemistry

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were aligned to the Pseudomonas entomophila L48 genome (Vodovar et al. 2006) using bbmap (Bushnell 2014).
The GTF annotation file was obtained from the Pseudomonas Genome Database (Winsor et al. 2016).
The count table was generated by featureCounts (Liao et al. 2014), then further analyzed with DESeq2 (Love et al. 2014).
Assembly: RefSeq accession number: GCF_000026105.1
Supplementary files format and content: featureCounts_Count_Table.txt contains raw count values for genes in each sample.
Supplementary files format and content: DeSeq2_Results_Table.txt contains log2 fold changes between wildtype and ΔpvfA-D samples for each gene.

organism: Pseudomonas entomophila L48

source_name: bacterial cell

growth_protocol: 25 mL Lennox Luria broth (LSLB) cultures of P. entomophila wildtype and ΔpvfA-D (3 biological replicates of each) were grown for 24 hr at 30 °C with 225 rpm shaking. Strains were cultured on two separate occasions, resulting in two "batches."

extract_protocol:
1 mL of culture was harvested by centrifugation and then RNA was extracted with TRIzol (ThermoFisher Scientific). RNA was treated with TURBO Dnase (Invitrogen) then purified with Mag-Bind TotalPure NGS beads (Omega Bio-tek).
RNA samples were submitted to BGI for sequencing. Vazyme Ribo-off rRNA removal kit was used for rRNA depletion. The BGI DNBSEQ-G400 platform was used for library construction and sequencing. Libraries were non-stranded and 100 bp paired-end reads were obtained. BGI removed adapters, contamination, and poor-quality reads.

value: bacterial cell

value: {delta}pvfA-D

tag: growth phase

value: stationary phase planktonic cells

tag: medium

value: Lennox Luria Broth (LSLB)


title: ΔpvfA-D, batch 2, biological replicate 2


title: jazD cdk8-1_rep 1


title: H1540

value: Pi*Z


title: ΔpvfA-D, batch 2, biological replicate 1


title: 001_C_L

description: Gene expression of patient sample 001_C_L

tag: patient number

tag: sample localisation

value: Temple

tag: lesion type

value: Lesion


title: H1547


title: 006_A_AK

description: Gene expression of patient sample 006_A_AK

value: Vertex

value: Actinic Keratosis


title: hNKX2-8

first: Lei

address: 8 College Road Singapore

department: Cardiovascular & Metabolic Disorders Program

institute: DUKE-NUS Medical School

data_processing:
fastqc (v.0.11.2) used for the quality of the RNA-seq data
RNA-seq data were mapped to GRCh37 genome using STAR (v.2.6.0c)
featureCount (v.1.6.3) used for the calling of read counts for every gene and every sample
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: 293T cell

extract_protocol:
TRIzol (iNtRON Biotechnology, Cat#17061) was used to dissolve cell components and minimize RNA degradation during cell lysis. Total RNAs were extracted with addition of chloroform (Sigma, Cat#C2432), followed by precipitation and purification.
NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (Cat#E7760S) was used for library construction. High quality libraries were generated with1 ug of total RNA according to the instruction manual.

value: 293T cell


title: 001_C_AK

description: Gene expression of patient sample 001_C_AK


title: hTFCP2


title: H1527


title: hRORA

description: hRORA


title: wildtype, batch 2, biological replicate 2

value: wildtype


title: wildtype, batch 2, biological replicate 3


title: jazD_rep 1

value: jazD


title: jazD_rep 2


title: jazD cdk8-1_rep 2


title: 001_C_NL

description: Gene expression of patient sample 001_C_NL

value: Non Lesion


title: wildtype, batch 2, biological replicate 1


title: ΔpvfA-D, batch 1, biological replicate 3


title: cdk8-1_rep 3


title: H1306


title: hHOXA11


title: 18-month  mice CD4+CD25+ splenocytes biol replicate 2

value: CD4+CD25+ splenocytes

value: WT

value: aged

value: 18-month old


title: hZBTB7A


title: 026_A_NL

description: Gene expression of patient sample 026_A_NL


title: H1324

value: liver

value: LPS


title: cdk8-1_rep 1


title: ΔpvfA-D, batch 1, biological replicate 2

value: bacterial cell

value: {delta}pvfA-D

value: stationary phase planktonic cells


title: Col-0_rep 3


title: hE2F4


title: S-898359

value: Pi*M


title: hEGR1


title: S-898353


title: wildtype, batch 1, biological replicate 3

value: Lennox Luria Broth (LSLB)


title: cdk8-1_rep 2


title: ΔpvfA-D, batch 1, biological replicate 1


title: S-890849


title: wildtype, batch 1, biological replicate 1


title: Col-0_rep 1


title: S-894411


title: blank

description: blank

value: blank


title: hNRF1


title: wildtype, batch 1, biological replicate 2


title: H1301

value: Pi*Z


title: NFE2L3_NC_3

status: Public on Mar 18 2023

city: Jinan

first: Zenghui

address: 44 Wenhua West Road, Lixia District

institute: Shandong university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of Homo sapiens from ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/ using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: ensembl release 87

source_name: siControl

extract_protocol:
Total RNAs were extracted from siNFE2L3 and siControl using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

treatment_protocol: Knock down NFE2L3 786-O cells and control 786-O cells

value: clear cell renal cell carcinoma cells


title: NFE2L3_Si_3

value: NFE2L5 knockdown


title: NFE2L3_Si_1

value: NFE2L3 knockdown


title: NFE2L3_Si_2

value: NFE2L4 knockdown


title: NFE2L3_NC_2


title: RNA-seq_dTAG-24h_mDPY30-dTAG_ES_Rep1

first: Aixia

last: Song

address: Dong'an Road

data_processing:
Raw reads were trimmed by Trim Galore v0.6.6, followed by mapping to the hg19 or mm10 genome using STAR v2.7.5c with parameter ‘‘--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 3’’
Low mapping quality reads and PCR duplicates were removed using SAMtools v1.9 and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
Strand-specific normalized bigwigs were generated by deeptools v3.5.0.
We collected the counts per gene by the featureCounts tool from Rsubread R package v2.0.1, differential expression analysis was then performed using DESeq2 R package v1.26.0.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: mESCs were cultured in knockout DMEM (Gibco) with 15% fetal bovine serum (BVES500, Biovision), 1 mmol/L L-glutamine (Gibco), 1× Sodium pyruvate (Gibco), 1× NEAA (Gibco), 0.11 mmol/L 2-mercaptoethanol, 103 U/mL LIF (Millipore) and 1× penicillin/streptomycin (Gibco)  at 37 °C and 5% CO2.

extract_protocol:
RNA was isolated with TRIzol. 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to  ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with dTAG 13 for 24h.

value: embryonic stem cells

value: treated with dTAG13 for 24 hours


title: ChIP_RPB1-NTD_dTAG-12h_KDM-C70-12h_mRBBP5-dTAG_ES_Rep2

data_processing:
The raw ChIP-Rx reads were trimmed by Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 with default parameters.
Low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9 and Picard v2.23.3 (https:// broadinstitute.github.io/picard/).
We then collected the spike-in read number for each of the ChIP-Rx samples with SAMtools v1.9 and generated the normalization factor as 1e6/spike-in_count.
The ENCODE blacklist regions were removed using bedtools v2.29.2.
Peak calling was performed by macs2 v2.2.6 with a q-value threshold of 0.05.
DiffBind R package v2.16.2 was used to identify differential binding peaks.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: mRBBP5-dTAG E14TG2a

growth_protocol: mESCs were cultured inknockout DMEM (Gibco) with 15% fetal bovine serum (BVES500, Biovision), 1 mmol/L L-glutamine (Gibco), 1×  Sodium pyruvate (Gibco), 1× NEAA (Gibco), 0.11 mmol/L 2-mercaptoethanol, 103U/mL LIF (Millipore) and 1× penicillin/streptomycin (Gibco)  at 37 °C and 5% CO2.

extract_protocol:
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with dTAG 13 for 6, 12,or 24 hours.

value: mRBBP5-dTAG E14TG2a

tag: chip antibody


title: NFE2L3_ip

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of Homo sapiens from ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/ using STAR software (version 2.5.3a) with default parameters. The RSeQC（version 2.6）was used for reads distribution analysis.The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis. The differentially binding peaks were identified by a python script，using fisher test. The Homer（version 4.10）was used for motifs analysis. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for annotated genes were both implemented by KOBAS software (version: 2.1.1) with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Assembly: ensembl release 87

extract_protocol:
Total RNA from 786-o cells was extracted by trizol method.After flag antibody pull-down Flag-NFe2L3 was used for chip-seq experiment, and NFE2L3 binding mRNA was obtained by the CST’s SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads)（9003S）.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: flag-NFE2L3 antibody


title: RNA-seq_dTAG-24h_mRBBP5-dTAG_ES_Rep2


title: input

value: none (input)


title: PRO_DMSO-24h_mRBBP5-dTAG_ES

data_processing:
The paired PRO-seq reads were trimmed by Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with read length >15 bp.
After removal of molecular barcode (UMI) with fastp v0.21.0, ribosomal RNA reads were discarded using Bowtie v2.3.5.1 with ‘‘--un-conc-gz’’.
Then the remaining reads were aligned to the hg19 or mm10 genome using Bowtie v2.3.5.1 with ‘‘--local --sensitive-local’’.
The mapped data were next deduplicated with UMI-tools to remove PCR duplicates based on the UMI sequences.
We generated the normalization factor as described in ChIP-Rx and built strand-specific coverage tracks with deeptools v3.5.0.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: mESCs were cultured in knockout DMEM (Gibco) with 15% fetal bovine serum (BVES500, Biovision), 1 mmol/L L-glutamine (Gibco), 1×  Sodium pyruvate (Gibco), 1× NEAA (Gibco), 0.11 mmol/L 2-mercaptoethanol, 103 U/mL LIF (Millipore) and 1× penicillin/streptomycin (Gibco)  at 37 °C and 5% CO2.

extract_protocol:
RNA was isolated with TRIzol.
Enriched RNA was ligated with RNA adapters. Reverse transcription (RT) was performed using the Superscript III enzyme (Invitrogen). The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix.  Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

value: untreated


title: RNA-seq_DMSO-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_RPB1-NTD_DMSO-12h_mRBBP5-dTAG_ES_Rep2


title: ChIP_RPB1-NTD_dTAG-12h_mRBBP5-dTAG_ES_Rep1


title: ChIP_RPB1-NTD_dTAG-12h_KDM-C70-12h_mRBBP5-dTAG_ES_Rep1


title: RNA-seq_dTAG-24h_mDPY30-dTAG_ES_Rep2


title: ChIP_input_dTAG-24h_mRBBP5-dTAG_ES (for TAF1, TAF3, BAP18, INTS11 and INTS5)

value: input


title: ChIP_INTS5_dTAG-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_input_DMSO-24h_mRBBP5-dTAG_ES (for TAF1, TAF3, BAP18, INTS11 and INTS5)


title: Col-0_rep 2

value: wildtype


title: RNA-seq_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_RPB1-NTD_DMSO-12h_mRBBP5-dTAG_ES_Rep1


title: ChIP_INTS5_DMSO-24h_mRBBP5-dTAG_ES_Rep2


title: RNA-seq_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_SPT5_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_SPT5_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_INTS5_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_INTS11_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: NFE2L3_NC_1

value: WT


title: RNA-seq_DMSO-24h_mDPY30-dTAG_ES_Rep2


title: ChIP_INTS11_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_BAP18_dTAG-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_INTS11_dTAG-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_RPB1-NTD_dTAG-12h_mRBBP5-dTAG_ES_Rep2


title: ChIP_BAP18_DMSO-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_TAF3_DMSO-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_TAF3_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_TAF1_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_TAF3_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_INTS5_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_TAF1_dTAG-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_INTS11_DMSO-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_TAF1_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_input_dTAG-12h_Tpl-10min_mRBBP5-dTAG_ES


title: ChIP_TAF3_dTAG-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_input_DMSO-12h_Tpl-10min_mRBBP5-dTAG_ES


title: ChIP_input_DMSO-12h_Tpl-20min_mRBBP5-dTAG_ES


title: ChIP_BAP18_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_input_dTAG-12h_Tpl-0min_mRBBP5-dTAG_ES


title: ChIP_BAP18_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_input_DMSO-12h_Tpl-0min_mRBBP5-dTAG_ES


title: ChIP_RPB1-NTD_dTAG-12h_Tpl-20min_mRBBP5-dTAG_ES_Rep2


title: ChIP_RPB1-NTD_dTAG-12h_Tpl-20min_mRBBP5-dTAG_ES_Rep1


title: ChIP_RPB1-NTD_dTAG-12h_Tpl-10min_mRBBP5-dTAG_ES_Rep2


title: ChIP_RPB1-NTD_dTAG-12h_Tpl-10min_mRBBP5-dTAG_ES_Rep1


title: ChIP_TAF1_DMSO-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_RPB1-NTD_dTAG-12h_Tpl-0min_mRBBP5-dTAG_ES_Rep1


title: ChIP_RPB1-NTD_DMSO-12h_Tpl-20min_mRBBP5-dTAG_ES_Rep1


title: ChIP_RPB1-NTD_DMSO-12h_Tpl-10min_mRBBP5-dTAG_ES_Rep2


title: ChIP_RPB1-NTD_DMSO-12h_Tpl-10min_mRBBP5-dTAG_ES_Rep1


title: ChIP_RPB1-NTD_DMSO-12h_Tpl-0min_mRBBP5-dTAG_ES_Rep2


title: ChIP_input-RPB1_dTAG-24h_mRBBP5-dTAG_ES (for RPB1 and SPT5)


title: ChIP_RPB1-NTD_DMSO-12h_Tpl-0min_mRBBP5-dTAG_ES_Rep1


title: ChIP_input-RPB1_DMSO-24h_mRBBP5-dTAG_ES (for RPB1 and SPT5)


title: ChIP_RPB1-S5_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_RPB1-NTD_dTAG-6h_mRBBP5-dTAG_ES_Rep1


title: ChIP_RPB1-NTD_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_input-H3K4_dTAG-6h_mDPY30-dTAG_ES (for H3K4me1/2/3 and Flag)

source_name: mDPY30-dTAG E14TG2a

value: mDPY30-dTAG E14TG2a


title: ChIP_RPB1-NTD_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_input-H3K4_DMSO-24h_mDPY30-dTAG_ES (for H3K4me1/2/3 and Flag)


title: ChIP_input-H3K4_dTAG-12h_mDPY30-dTAG_ES (for H3K4me1/2/3 and Flag)


title: ChIP_input-H3K4_dTAG-6h_mRBBP5-dTAG_ES (for H3K4me1/2/3 and Flag)


title: PRO_dTAG-24h_mRBBP5-dTAG_ES


title: ChIP_input-H3K4_dTAG-24h_mRBBP5-dTAG_ES (for H3K4me1/2/3 and Flag)


title: ChIP_input-H3K4_dTAG-12h_mRBBP5-dTAG_ES (for H3K4me1/2/3 and Flag)


title: ChIP_RPB1-NTD_dTAG-12h_Tpl-0min_mRBBP5-dTAG_ES_Rep2


title: ChIP_input-H3K4_DMSO-24h_mRBBP5-dTAG_ES (for H3K4me1/2/3 and Flag)


title: ChIP_Flag_dTAG-6h_mDPY30-dTAG_ES_Rep2

value: Flag


title: ChIP_Flag_dTAG-6h_mDPY30-dTAG_ES_Rep1


title: ChIP_Flag_dTAG-24h_mDPY30-dTAG_ES_Rep1


title: ChIP_Flag_dTAG-12h_mDPY30-dTAG_ES_Rep1


title: ChIP_input_dTAG-12h_Tpl-20min_mRBBP5-dTAG_ES


title: ChIP_Flag_DMSO-24h_mDPY30-dTAG_ES_Rep2


title: ChIP_Flag_dTAG-6h_mRBBP5-dTAG_ES_Rep2


title: ChIP_Flag_DMSO-24h_mDPY30-dTAG_ES_Rep1


title: ChIP_Flag_dTAG-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_Flag_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_Flag_dTAG-12h_mRBBP5-dTAG_ES_Rep2


title: ChIP_Flag_dTAG-12h_mRBBP5-dTAG_ES_Rep1


title: ChIP_RPB1-S5_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me1_dTAG-6h_mDPY30-dTAG_ES_Rep2


title: ChIP_H3K4me1_dTAG-12h_mDPY30-dTAG_ES_Rep2


title: ChIP_H3K4me1_dTAG-12h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me1_DMSO-24h_mDPY30-dTAG_ES_Rep2


title: ChIP_H3K4me1_DMSO-24h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me1_dTAG-24h_mDPY30-dTAG_ES_Rep1


title: ChIP_Flag_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me1_dTAG-6h_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me1_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me1_dTAG-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me1_dTAG-6h_mRBBP5-dTAG_ES_Rep1


title: ChIP_input-H3K4_dTAG-24h_mDPY30-dTAG_ES (for H3K4me1/2/3 and Flag)


title: ChIP_H3K4me1_dTAG-6h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me1_dTAG-12h_mRBBP5-dTAG_ES_Rep2


title: L7062

source_name: Liver

value: Liver

tag: breed

value: Holstein

value: postnatal cooling


title: ChIP_H3K4me1_dTAG-12h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me1_DMSO-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me1_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_Flag_dTAG-24h_mDPY30-dTAG_ES_Rep2


title: ChIP_H3K4me2_dTAG-6h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me2_dTAG-6h_mDPY30-dTAG_ES_Rep2


title: ChIP_H3K4me1_dTAG-24h_mDPY30-dTAG_ES_Rep2


title: ChIP_RPB1-NTD_DMSO-12h_Tpl-20min_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me2_dTAG-24h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me2_dTAG-24h_mDPY30-dTAG_ES_Rep2


title: ChIP_H3K4me2_dTAG-12h_mDPY30-dTAG_ES_Rep2


title: RNA-seq_DMSO-24h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me2_dTAG-12h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me2_dTAG-6h_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me2_dTAG-6h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me2_DMSO-24h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me2_dTAG-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me2_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me2_DMSO-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me2_dTAG-12h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me2_DMSO-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me3_dTAG-6h_mDPY30-dTAG_ES_Rep2


title: ChIP_H3K4me3_dTAG-12h_mDPY30-dTAG_ES_Rep2


title: ChIP_H3K4me3_dTAG-24h_mDPY30-dTAG_ES_Rep2


title: ChIP_H3K4me3_dTAG-24h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me3_dTAG-6h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me3_dTAG-6h_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me3_DMSO-24h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me3_DMSO-24h_mDPY30-dTAG_ES_Rep2


title: ChIP_H3K4me3_dTAG-12h_mDPY30-dTAG_ES_Rep1


title: ChIP_H3K4me3_dTAG-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_Flag_DMSO-24h_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me3_dTAG-24h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me2_dTAG-12h_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me3_dTAG-12h_mRBBP5-dTAG_ES_Rep2


title: ChIP_H3K4me3_dTAG-12h_mRBBP5-dTAG_ES_Rep1


title: ChIP_H3K4me3_DMSO-24h_mRBBP5-dTAG_ES_Rep2


title: E14T_mit_input_2391422_rep3

city: Memphis

first: Zhexin

last: Zhu

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to mouse genome assembly mm10 by BWA(0.7.17） by internal automatically mapping pipeline.
Uniquely mapped reads for ChIP-seq were obtained using samtools (V1,10), with parameter “-q 10 -F1024".
Stringent peaks for each replicate were called by MACS2 (V 2.1.1.20160309, with default parameters using Input (for ChIP-seq) as control and filtered with fold enrichment cutoff: 5 and p-value threshold: 1e-9.
RPM was applied to the normalized read counts to generate bigwig tracks
Assembly: mm10
Supplementary files format and content: bigwig files of normalized read counts and subtracted by input
Supplementary files format and content: narrowPeak from MACS2

source_name: embryonic stem cells

growth_protocol: mESCs were cultured in Knockout DMEM supplemented with 15% ES-qualified FBS, 1% NEAA, 1% GlutaMAX, 0.5 mM beta-mercaptoethanol, and 10 ng/ml mLIF on 0.1% gelatin-coated tissue culture dishes.

extract_protocol:
truChIP® Chromatin Shearing Kit (https://www.covaris.com/products-services/kits-reagents/truchip)
KAPA Hyper Prep Kit (KK8504)

treatment_protocol: For mitotic synchronization, mESCs were treated with 100 ng/ml nocodazole for 6 hours, and then mitotic cells were collected by gently shake-off.

value: mouse embryonic stem cells

tag: strain

value: nocodazole synchronization

tag: antibody


title: E14T_asyn_sox2_2391420_rep3

tag: cell type

tag: treatment

value: SOX2 (R&D Systems, AF2018)


title: E14T_mit_sox2_2391423_rep3


title: E14T_asyn_input_2391419_rep3


title: ChIP_Flag_dTAG-12h_mDPY30-dTAG_ES_Rep2

value: embryonic stem cells


title: E14T_mit_input_2381327_rep2


title: E14T_mit_sox2_2381328_rep2


title: ChIP_H3K4me3_dTAG-6h_mDPY30-dTAG_ES_Rep1


title: E14T_asyn_sox2_2381325_rep2


title: E14T_asyn_input_2381324_rep2


title: E14T_mit_input_2381321_rep1


title: E14T_asyn_input_2381318_rep1


title: EB_Smarce1_MD30_rep1

data_processing:
Total stranded RNA sequencing data were mapped to mouse genome assembly mm10 using an internal AutoMapper pipeline.
Briefly, the raw reads were trimmed with trim galore (V0.60) and mapped to mouse genome mm10 using STAR V2.7.1a. Then the read counts were computed using RSEM (V1.3.0) based on GENCODE vM23.
Counts were further normalized and differentially expressed genes were calculated using DESeq2
Assembly: mm10
Supplementary files format and content: read counts from RSEM

source_name: embryonic body

extract_protocol: none provided by the submitter

value: mouse embryonic body

value: untreatment


title: EB_Smarce1_MD30_rep2


title: EB_Smarce1_MD09_rep2


title: EB_Smarce1_MD09_rep1


title: ChIP_H3K4me3_DMSO-24h_mRBBP5-dTAG_ES_Rep1

value: mRBBP5-dTAG E14TG2a


title: EB_Smarce1_MDR42AA10_rep1


title: EB_Smarce1_MDR42AA04_rep2


title: EB_Smarce1_MDR42AA04_rep1


title: AID_iaa_30min_baf57_rep02.CnR

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to mouse genome assembly mm10 by BWA(0.7.17） by internal automatically mapping pipeline.
Properly paired uniquely mapped reads were obtained using samtools (V1.10, with parameters “-q 10 -F 1804”)
We only kept CUT&RUN fragments with length shorter than 2000 bp for further analysis.
Stringent peaks for each replicate were called by MACS2 (V 2.1.1.20160309, with default parameters using IgG (for CUT&RUN) and filtered with fold enrichment cutoff: 5 and p-value threshold: 1e-9.
Assembly: mm10
Supplementary files format and content: bigwig files of normalized read counts subtracted by IgG.
Supplementary files format and content: narrowPeak from MACS2

extract_protocol:
https://doi.org/10.1038/nprot.2018.015
KAPA Hyper Prep Kit (KK8504)

treatment_protocol: For mitotic synchronization, mESCs were treated with 100 ng/ml nocodazole for 6 hours, and then mitotic cells were collected by gently shake-off. For mitotic release, mitotic cells were washed out three times by fresh mESC culture medium to remove residual nocodazole and then cultured in mESC medium for the indicated time.

value: IAA

value: SMARCE1 (Bethyl, A300-810A)


title: E14T_mit_sox2_2381322_rep1


title: E14T_asyn_sox2_2381319_rep1

value: untreated


title: AID_iaa_30min_IgG_rep01.CnR

value: Rabbit (DA1E) mAb IgG XP Isotype Control (CST#3900S)


title: AID_iaa_30min_Sox2_rep01.CnR


title: AID_dmso_30min_baf57_rep02.CnR


title: AID_iaa_30min_baf57_rep01.CnR


title: AID_iaa_30min_IgG_rep02.CnR


title: AID_iaa_30min_Sox2_rep02.CnR


title: AID_iaa_30min_Esrrb_rep02.CnR

value: ESRRB (R&D Systems, PP-H6705-00)


title: AID_dmso_30min_Esrrb_rep02.CnR


title: AID_iaa_30min_Ezh2_rep01.CnR


title: AID_dmso_30min_Sox2_rep02.CnR


title: AID_iaa_30min_Esrrb_rep01.CnR


title: AID_iaa_30min_Ezh2_rep02.CnR


title: AID_dmso_30min_Ezh2_rep02.CnR


title: EB_Smarce1_MDR42AA10_rep2


title: AID_dmso_30min_baf57_rep01.CnR


title: AID_dmso_30min_IgG_rep02.CnR


title: AID_dmso_30min_Esrrb_rep01.CnR


title: AID_dmso_30min_IgG_rep01.CnR


title: AID_dmso_30min_Sox2_rep01.CnR


title: ChIP_Flag_dTAG-6h_mRBBP5-dTAG_ES_Rep1


title: e14t_mitotic_IgG_rep03


title: e14t_mitotic_SOX2_rep03


title: e14t_mitotic_SOX2_rep02


title: e14t_mitotic_SOX2_rep01


title: e14t_mitotic_IgG_rep02


title: e14t_asynchronous_IgG_rep03


title: e14t_mitotic_IgG_rep01


title: e14t_asynchronous_SOX2_rep03


title: e14t_asynchronous_SOX2_rep02


title: e14t_asynchronous_IgG_rep02


title: e14t_asynchronous_SOX2_rep01


title: AID_dmso_30min_Ezh2_rep01.CnR


title: jazD_rep 3

tag: genotype

value: jazD


title: Smarce1-MD(R42A) #A10 BRM014_BAF57_2433171

value: BRM014 + MD mutatn


title: Smarce1-MD(R42A) #A10 BRM014_SOX2_2433170


title: Smarce1-MD(R42A) #A04 BRM014_IgG_2433166


title: Smarce1-MD(R42A) #A04 BRM014_SOX2_2433167


title: Smarce1-MD(R42A) #A10 DMSO_IgG_2433163

value: DMSO + MD mutatn


title: Smarce1-MD(R42A) #A04 DMSO_BAF57_2433162


title: Smarce1-MD(R42A) #A10 DMSO_SOX2_2433164


title: Smarce1-MD(R42A) #A04 BRM014_BAF57_2433168


title: Smarce1-MD(R42A) #A04 DMSO_SOX2_2433161


title: Smarce1-MD #30 BRM014_SOX2_2433158

value: BRM014 + MD


title: Smarce1-MD(R42A) #A04 DMSO_IgG_2433160


title: Smarce1-MD #30 BRM014_IgG_2433157


title: Smarce1-MD #09 BRM014_BAF57_2433156


title: Smarce1-MD #09 BRM014_SOX2_2433155


title: Smarce1-MD #09 BRM014_IgG_2433154


title: Smarce1-MD #30 DMSO_BAF57_2433153

value: DMSO + MD


title: Smarce1-MD #30 DMSO_SOX2_2433152

value: mouse embryonic stem cells


title: Smarce1-MD(R42A) #A10 BRM014_IgG_2433169


title: e14t_asynchronous_IgG_rep01


title: Smarce1-MD(R42A) #A10 DMSO_BAF57_2433165


title: Smarce1-MD09_0.2ng_rep2

value: BMP4 rescue 0.2ng


title: Smarce1-MD30_0.1ng_rep2

value: BMP4 rescue 0.1ng


title: Smarce1-MD #09 DMSO_IgG_2433148


title: Smarce1-MD #30 BRM014_BAF57_2433159


title: Smarce1-MDR42A10_0.2ng_rep2


title: Smarce1-MD #30 DMSO_IgG_2433151


title: Smarce1-MDR42A10_0ng_rep2


title: Smarce1-MD09_0ng_rep2


title: Smarce1-MDR42A04_0.2ng_rep2


title: Smarce1-MD #09 DMSO_BAF57_2433150


title: Smarce1-MD30_0.2ng_rep2


title: Smarce1-MDR42A04_0.1ng_rep2


title: Smarce1-MDR42A04_0ng_rep2


title: Smarce1-MD30_0.2ng_rep1


title: Smarce1-MD09_0.1ng_rep2


title: Smarce1-MD #09 DMSO_SOX2_2433149

value: SOX2 (R&D Systems, AF2018)


title: Smarce1-MD30_0.1ng_rep1


title: Smarce1-MD30_0ng_rep2


title: Smarce1-MD30_0ng_rep1


title: Smarce1-MDR42A10_0.2ng_rep1


title: Smarce1-MD09_0ng_rep1


title: Smarce1-MDR42A10_0.1ng_rep1


title: Smarce1-MD09_0.1ng_rep1


title: Smarce1-MDR42A10_0ng_rep1


title: Smarce1-MDR42A04_0.1ng_rep1


title: Smarce1-MDR42A04_0.2ng_rep1


title: Smarce1-MDR42A10_0.1ng_rep2


title: Smarce1-MDR42A04_0ng_rep1


title: Smarce1 - MD BRM014 release 90min ATAC rep1

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to mouse genome assembly mm10 by BWA(0.7.17） by internal automatically mapping pipeline.
Properly paired uniquely mapped reads were obtained using samtools (V1.10, with parameters “-q 10 -F 1804”)
We only kept nucleosome free fragments with length shorter than 109 bp for further analysis.
Stringent peaks for each replicate were called by MACS2 (V 2.1.1.20160309, with False Positive Rate corrected p-value 0.05
Assembly: mm10
Supplementary files format and content: bigwig files of normalized read counts.
Supplementary files format and content: narrowPeak from MACS2

value: BRM014 treated 90 min after mitotic release

value: ATAC-seq


title: Smarce1 - MD (R42A) BRM014 release 90min ATAC rep1


title: Smarce1 - MD DMSO release 90min ATAC rep1

value: DMSO treated 90 min after mitotic release


title: Smarce1 - MD (R42A) BRM014 release 90min ATAC rep2


title: Smarce1 - MD (R42A) DMSO release 90min ATAC rep2


title: Smarce1 - MD BRM014 release 90min ATAC rep2


title: Smarce1-AID_1day_r2

extract_protocol: KAPA Hyper Prep Kit (KK8504)

value: Treated with IAA for 1days


title: Smarce1 - MD DMSO release 90min ATAC rep2


title: Smarce1-MD09_0.2ng_rep1


title: Smarce1-AID_3day_r2

value: Treated with IAA for 3days


title: Smarce1-AID_7day_r1

value: Treated with IAA for 7days


title: Smarce1-AID_480min_r2

value: Treated with IAA for 480min


title: Smarce1-AID_3day_r1


title: Smarce1-AID_30min_r2

value: Treated with IAA for 30min


title: Smarce1-AID_60min_r2

value: Treated with IAA for 60min


title: Smarce1-AID_240min_r1

value: Treated with IAA for 240min


title: Smarce1-AID_0min_r2

value: untreatment


title: Smarce1-AID_480min_r1


title: Smarce1-AID_0min_r1


title: Smarce1-AID_1day_r1


title: ChIP_H3K4me2_DMSO-24h_mDPY30-dTAG_ES_Rep2

tag: cell line

value: mDPY30-dTAG E14TG2a

value: embryonic stem cells


title: Smarce1-AID_30min_r1

value: mouse embryonic stem cells


title: Smarce1-AID_60min_r1


title: Smarce1_MD30_release90min_IgG_rep03

value: 90 min after mitotic release

value: Rabbit (DA1E) mAb IgG XP Isotype Control (CST#3900S)


title: Smarce1_MD30_release90min_Brg1_rep01

value: SMARCA4 (Abcam, ab110641)


title: Smarce1-AID_7day_r2


title: Smarce1_MD30_release90min_BAF57_rep01

value: SMARCE1 (Bethyl, A300-810A)


title: Smarce1 - MD (R42A) DMSO release 90min ATAC rep1

value: ATAC-seq


title: Smarce1-AID_240min_r2


title: Smarce1_MDR42AA10_release90min_BAF57_rep03


title: Smarce1_MD09_release90min_Brg1_rep01


title: Smarce1_MDR42AA10_release90min_IgG_rep03


title: Smarce1_MD09_release90min_IgG_rep03


title: Smarce1_MDR42AA10_release90min_Brg1_rep01


title: Smarce1_MDR42AA04_release90min_BAF57_rep01


title: Smarce1_MDR42AA04_release90min_BAF57_rep03


title: mitotic mESCs_SMARCA4_rep2

value: nocodazole synchronization


title: Smarce1_MD09_release90min_BAF57_rep01


title: mitotic mESCs_BRD9_rep2

value: BRD9 (ACTIVE MOTIF, 61537)


title: Smarce1_MDR42AA04_release90min_BAF57_rep02


title: Smarce1_MDR42AA10_release90min_BAF57_rep02


title: mitotic mESCs_IgG_rep7


title: Smarce1_MDR42AA10_release90min_BAF57_rep01


title: mitotic mESCs_SMARCA4_rep1


title: Smarce1_MDR42AA04_release90min_IgG_rep03


title: mitotic mESCs_BRD9_rep1


title: Smarce1_MDR42AA04_release90min_Brg1_rep01


title: mitotic mESCs_ARID1A_rep1

value: ARID1A (SIGMA, HPA005456-100UL)


title: mitotic mESCs_CTCF_rep2.ChIP

description: mitotic mESCs_CTCF_1940868

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to mouse genome assembly mm10 by BWA(0.7.17） by internal automatically mapping pipeline.
Uniquely mapped reads for ChIP-seq were obtained using samtools (V1,10), with parameter “-q 10 -F1024".
Stringent peaks for each replicate were called by MACS2 (V 2.1.1.20160309, with default parameters using Input (for ChIP-seq) as control and filtered with fold enrichment cutoff: 5 and p-value threshold: 1e-9.
RPM was applied to the normalized read counts to generate bigwig tracks
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of normalized read counts.
Supplementary_files_format_and_content: narrowPeak from MACS2

value: CTCF (Abcam, ab70303)


title: asynchronous mESCs_CTCF_rep2.ChIP

description: asynchronous mESCs_CTCF_1940859


title: mitotic mESCs_CTCF_rep1.ChIP

description: mitotic mESCs_CTCF_1938715


title: mitotic mESCs_input_rep13.ChIP

description: mitotic mESCs_input_1938710


title: mitotic mESCs_ARID1A_rep2


title: asynchronous mESCs_CTCF_rep1.ChIP

description: asynchronous mESCs_CTCF_1938706


title: asynchronous mESCs_input_rep13.ChIP

description: asynchronous mESCs_input_1938701


title: asynchronous mESCs_SOX2_rep2.ChIP

description: asynchronous mESCs_SOX2_1910806

value: SOX2 (R&D Systems, AF2018)


title: asynchronous mESCs_input_rep12.ChIP

description: asynchronous mESCs_input_1910803


title: mitotic mESCs_input_rep12.ChIP

description: mitotic mESCs_input_1910815


title: mitotic mESCs_IgG_rep6


title: mitotic mESCs_SOX2_rep2.ChIP

description: mitotic mESCs_SOX2_1910818


title: mitotic mESCs_H4K20me3_rep4.ChIP

description: mitotic mESCs_H4K20me3_2163946

value: H4K20me3 (Abcam, ab9053)


title: asynchronous mESCs_H3K36me3_rep2.ChIP

description: asynchronous mESCs_H3K36me3_2163942


title: mitotic mESCs_H3K36me3_rep2.ChIP

description: mitotic mESCs_H3K36me3_2163948


title: mitotic mESCs_H3K9me3_rep4.ChIP

description: mitotic mESCs_H3K9me3_2163944

value: H3K9me3 (Active Motif, 39161)


title: asynchronous mESCs_input_rep11.ChIP

description: asynchronous mESCs_input_2163937


title: asynchronous mESCs_H3K9me3_rep4.ChIP

description: asynchronous mESCs_H3K9me3_2163938


title: mitotic mESCs_H3K36me3_rep1.ChIP

description: mitotic mESCs_H3K36me3_2163936


title: mitotic mESCs_H3K9me3_rep3.ChIP

description: mitotic mESCs_H3K9me3_2163932


title: asynchronous mESCs_H3K36me3_rep1.ChIP

description: asynchronous mESCs_H3K36me3_2163930


title: mitotic mESCs_H4K20me3_rep1.ChIP

description: mitotic mESCs_H4K20me3_2163933

value: H4K20me3 (Active Motif, 39671)


title: mitotic mESCs_input_rep10.ChIP

description: mitotic mESCs_input_2163931


title: asynchronous mESCs_input_rep10.ChIP

description: asynchronous mESCs_input_2163925

value: untreatment


title: mitotic mESCs_H4K20me3_rep2.ChIP

description: mitotic mESCs_H4K20me3_2163934


title: asynchronous mESCs_H3K9me3_rep3.ChIP

description: asynchronous mESCs_H3K9me3_2163926


title: asynchronous mESCs_H4K20me3_rep1.ChIP

description: asynchronous mESCs_H4K20me3_2163927


title: mitotic mESCs_H4K20me3_rep3.ChIP

description: mitotic mESCs_H4K20me3_2163945


title: mitotic mESCs_H3K27ac_rep4.ChIP

description: mitotic mESCs_H3K27ac_1996888

value: H3K27ac (Abcam, ab4729)


title: mitotic mESCs_H3K27me3_rep4.ChIP

description: mitotic mESCs_H3K27me3_1996887


title: asynchronous mESCs_H4K20me3_rep2.ChIP

description: asynchronous mESCs_H4K20me3_2163928


title: mitotic mESCs_H3K4me3_rep4.ChIP

description: mitotic mESCs_H3K4me3_1996886


title: mitotic mESCs_input_rep9.ChIP

description: mitotic mESCs_input_1996885


title: asynchronous mESCs_H3K27ac_rep4.ChIP

description: asynchronous mESCs_H3K27ac_1996883


title: mitotic mESCs_input_rep11.ChIP

description: mitotic mESCs_input_2163943


title: asynchronous mESCs_H4K20me3_rep3.ChIP

description: asynchronous mESCs_H4K20me3_2163939


title: mitotic mESCs_H3K27ac_rep3.ChIP

description: mitotic mESCs_H3K27ac_1996878


title: asynchronous mESCs_input_rep9.ChIP

description: asynchronous mESCs_input_1996880


title: asynchronous mESCs_H3K4me3_rep4.ChIP

description: asynchronous mESCs_H3K4me3_1996881


title: asynchronous mESCs_H3K27me3_rep4.ChIP

description: asynchronous mESCs_H3K27me3_1996882


title: asynchronous mESCs_H4K20me3_rep4.ChIP

description: asynchronous mESCs_H4K20me3_2163940


title: mitotic mESCs_H3K4me3_rep3.ChIP

description: mitotic mESCs_H3K4me3_1996876


title: mitotic mESCs_H3K27me3_rep3.ChIP

description: mitotic mESCs_H3K27me3_1996877


title: mitotic mESCs_input_rep8.ChIP

description: mitotic mESCs_input_1996875


title: asynchronous mESCs_H3K27ac_rep3.ChIP

description: asynchronous mESCs_H3K27ac_1996873


title: asynchronous mESCs_H3K4me3_rep3.ChIP

description: asynchronous mESCs_H3K4me3_1996871


title: asynchronous mESCs_input_rep8.ChIP

description: asynchronous mESCs_input_1996870


title: asynchronous mESCs_H3K4me1_rep4.ChIP

description: asynchronous mESCs_H3K4me1_1983276

value: H3K4me1 (EPICYPHER, 13-0040)


title: mitotic mESCs_H3K4me1_rep3.ChIP

description: mitotic mESCs_H3K4me1_1983271

value: mouse embryonic stem cells


title: mitotic mESCs_H3K4me1_rep4.ChIP

description: mitotic mESCs_H3K4me1_1983281


title: mitotic mESCs_input_rep7.ChIP

description: mitotic mESCs_input_1983280


title: asynchronous mESCs_input_rep6.ChIP

description: asynchronous mESCs_input_1983265


title: asynchronous mESCs_H3K4me1_rep3.ChIP

description: asynchronous mESCs_H3K4me1_1983266


title: mitotic mESCs_H3K27ac_rep2.ChIP

description: mitotic mESCs_H3K27ac_1951712


title: mitotic mESCs_input_rep5.ChIP

description: mitotic mESCs_input_1951709


title: mitotic mESCs_input_rep6.ChIP

description: mitotic mESCs_input_1983270


title: mitotic mESCs_H3K27me3_rep2.ChIP

description: mitotic mESCs_H3K27me3_1951711


title: asynchronous mESCs_H3K27ac_rep2.ChIP

description: asynchronous mESCs_H3K27ac_1951707


title: asynchronous mESCs_H3K4me3_rep2.ChIP

description: asynchronous mESCs_H3K4me3_1951705


title: asynchronous mESCs_input_rep5.ChIP

description: asynchronous mESCs_input_1951704


title: mitotic mESCs_H3K27me3_rep1.ChIP

description: mitotic mESCs_H3K27me3_1951701


title: mitotic mESCs_input_rep4.ChIP

description: mitotic mESCs_input_1951699


title: mitotic mESCs_H3K27ac_rep1.ChIP

description: mitotic mESCs_H3K27ac_1951702


title: mitotic mESCs_H3K4me3_rep1.ChIP

description: mitotic mESCs_H3K4me3_1951700


title: asynchronous mESCs_H3K4me3_rep1.ChIP

description: asynchronous mESCs_H3K4me3_1951695


title: asynchronous mESCs_input_rep4.ChIP

description: asynchronous mESCs_input_1951694


title: asynchronous mESCs_H3K27me3_rep3.ChIP

description: asynchronous mESCs_H3K27me3_1996872


title: mitotic mESCs_H3K9me3_rep2.ChIP

description: mitotic mESCs_H3K9me3_1951690

value: H3K9me3 (Abcam, ab8898)


title: mitotic mESCs_H3K4me1_rep2.ChIP

description: mitotic mESCs_H3K4me1_1951689


title: asynchronous mESCs_H3K27me3_rep1.ChIP

description: asynchronous mESCs_H3K27me3_1951696


title: mitotic mESCs_input_rep3.ChIP

description: mitotic mESCs_input_1951688


title: asynchronous mESCs_H3K4me1_rep2.ChIP

description: asynchronous mESCs_H3K4me1_1951683


title: asynchronous mESCs_input_rep3.ChIP

description: asynchronous mESCs_input_1951682


title: asynchronous mESCs_input_rep7.ChIP

description: asynchronous mESCs_input_1983275


title: mitotic mESCs_H3K4me3_rep2.ChIP

description: mitotic mESCs_H3K4me3_1951710


title: asynchronous mESCs_H3K27me3_rep2.ChIP

description: asynchronous mESCs_H3K27me3_1951706


title: asynchronous mESCs_input_rep2.ChIP

description: asynchronous mESCs_input_1884805


title: mitotic mESCs_H3K4me1_rep1.ChIP

description: mitotic mESCs_H3K4me1_1940864


title: mitotic mESCs_input_rep1.ChIP

description: mitotic mESCs_input_1940863


title: asynchronous mESCs_H3K4me1_rep1.ChIP

description: asynchronous mESCs_H3K4me1_1940855


title: asynchronous mESCs_SOX2_rep1.ChIP

description: asynchronous mESCs_SOX2_1884812


title: mitotic mESCs_H3K9me3_rep1.ChIP

description: mitotic mESCs_H3K9me3_1940865


title: mitotic mESCs_input_rep2.ChIP

description: mitotic mESCs_input_1884813


title: mitotic mESCs_SOX2_rep1.ChIP

description: mitotic mESCs_SOX2_1884820


title: asynchronous mESCs_input_rep1.ChIP

description: asynchronous mESCs_input_1940854


title: Smarce1- MD #30_release 90min_SOX2_rep1

description:
Smarce1- MD #30_release 90min_SOX2_2106618
Smarce1- MD #30_release 90min_SOX2_2106618

data_processing:
Library strategy: CUT&RUN-seq
Basecalls performed using CASAVA version 1.4
Reads were aligned to mouse genome assembly mm10 by BWA(0.7.17） by internal automatically mapping pipeline.
Properly paired uniquely mapped reads were obtained using samtools (V1.10, with parameters “-q 10 -F 1804”)
We only kept CUT&RUN fragments with length shorter than 2000 bp for further analysis.
Stringent peaks for each replicate were called by MACS2 (V 2.1.1.20160309, with default parameters using IgG (for CUT&RUN) and filtered with fold enrichment cutoff: 5 and p-value threshold: 1e-9.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of normalized read counts.
Supplementary_files_format_and_content: narrowPeak from MACS2

value: 90 min after mitotic release


title: Smarce1- MD #30_release 90min_SOX2_rep2

description:
Smarce1- MD #30_release 90min_SOX2_2109686
Smarce1- MD #30_release 90min_SOX2_2109686


title: Smarce1- MD #30_release 90min_IgG_rep2

description:
Smarce1- MD #30_release 90min_IgG_2109683
Smarce1- MD #30_release 90min_IgG_2109683

value: Rabbit (DA1E) mAb IgG XP® Isotype Control (CST#3900S)


title: asynchronous mESCs_H3K27ac_rep1.ChIP

description: asynchronous mESCs_H3K27ac_1951697


title: Smarce1- MD #30_release 90min_IgG_rep1

description:
Smarce1- MD #30_release 90min_IgG_2106615
Smarce1- MD #30_release 90min_IgG_2106615


title: Smarce1- MD #30_release 90min_ESRRB_rep2

description:
Smarce1- MD #30_release 90min_ESRRB_2109687
Smarce1- MD #30_release 90min_ESRRB_2109687

value: ESRRB (R&D Systems, PP-H6705-00)


title: Smarce1- MD #09_release 90min_SOX2_rep2

description:
Smarce1- MD #09_release 90min_SOX2_2109680
Smarce1- MD #09_release 90min_SOX2_2109680


title: Smarce1- MD #09_release 90min_SOX2_rep1

description:
Smarce1- MD #09_release 90min_SOX2_2106612
Smarce1- MD #09_release 90min_SOX2_2106612


title: Smarce1- MD #30_release 90min_EZH2_rep1

description:
Smarce1- MD #30_release 90min_EZH2_2106620
Smarce1- MD #30_release 90min_EZH2_2106620


title: Smarce1- MD #09_release 90min_IgG_rep2

description:
Smarce1- MD #09_release 90min_IgG_2109677
Smarce1- MD #09_release 90min_IgG_2109677


title: asynchronous mESCs_H3K9me3_rep2.ChIP

description: asynchronous mESCs_H3K9me3_1951684


title: Smarce1- MD #30_release 90min_EZH2_rep2

description:
Smarce1- MD #30_release 90min_EZH2_2109688
Smarce1- MD #30_release 90min_EZH2_2109688


title: Smarce1- MD #30_release 90min_ESRRB_rep1

description:
Smarce1- MD #30_release 90min_ESRRB_2106619
Smarce1- MD #30_release 90min_ESRRB_2106619


title: Smarce1- MD #09_release 90min_IgG_rep1

description:
Smarce1- MD #09_release 90min_IgG_2106609
Smarce1- MD #09_release 90min_IgG_2106609


title: Smarce1- MD #09_release 90min_EZH2_rep1

description:
Smarce1- MD #09_release 90min_EZH2_2106614
Smarce1- MD #09_release 90min_EZH2_2106614


title: Smarce1- MD #09_release 90min_EZH2_rep2

description:
Smarce1- MD #09_release 90min_EZH2_2109682
Smarce1- MD #09_release 90min_EZH2_2109682


title: Smarce1- MD #09_release 90min_ESRRB_rep2

description:
Smarce1- MD #09_release 90min_ESRRB_2109681
Smarce1- MD #09_release 90min_ESRRB_2109681


title: Smarce1- MD #09_release 90min_ESRRB_rep1

description:
Smarce1- MD #09_release 90min_ESRRB_2106613
Smarce1- MD #09_release 90min_ESRRB_2106613


title: Smarce1- MD (42A)#A10_release 90min_SOX2_rep2

description:
Smarce1- MD (42A)#A10_release 90min_SOX2_2109674
Smarce1- MD (42A)#A10_release 90min_SOX2_2109674


title: Smarce1- MD (42A)#A10_release 90min_IgG_rep2

description:
Smarce1- MD (42A)#A10_release 90min_IgG_2109671
Smarce1- MD (42A)#A10_release 90min_IgG_2109671


title: asynchronous mESCs_H3K9me3_rep1.ChIP

description: asynchronous mESCs_H3K9me3_1940856


title: Smarce1- MD (42A)#A10_release 90min_EZH2_rep2

description:
Smarce1- MD (42A)#A10_release 90min_EZH2_2109676
Smarce1- MD (42A)#A10_release 90min_EZH2_2109676


title: Smarce1- MD (42A)#A10_release 90min_SOX2_rep1

description:
Smarce1- MD (42A)#A10_release 90min_SOX2_2106606
Smarce1- MD (42A)#A10_release 90min_SOX2_2106606


title: Smarce1- MD (42A)#A10_release 90min_ESRRB_rep1

description:
Smarce1- MD (42A)#A10_release 90min_ESRRB_2106607
Smarce1- MD (42A)#A10_release 90min_ESRRB_2106607


title: Smarce1- MD (42A)#A10_release 90min_ESRRB_rep2

description:
Smarce1- MD (42A)#A10_release 90min_ESRRB_2109675
Smarce1- MD (42A)#A10_release 90min_ESRRB_2109675


title: Smarce1- MD (42A)#A10_release 90min_EZH2_rep1

description:
Smarce1- MD (42A)#A10_release 90min_EZH2_2106608
Smarce1- MD (42A)#A10_release 90min_EZH2_2106608


title: Smarce1- MD (42A)#A04_release 90min_SOX2_rep2

description:
Smarce1- MD (42A)#A04_release 90min_SOX2_2109668
Smarce1- MD (42A)#A04_release 90min_SOX2_2109668


title: Smarce1- MD (42A)#A04_release 90min_SOX2_rep1

description:
Smarce1- MD (42A)#A04_release 90min_SOX2_2106600
Smarce1- MD (42A)#A04_release 90min_SOX2_2106600


title: Smarce1- MD (42A)#A04_release 90min_IgG_rep2

description:
Smarce1- MD (42A)#A04_release 90min_IgG_2109665
Smarce1- MD (42A)#A04_release 90min_IgG_2109665


title: Smarce1- MD (42A)#A04_release 90min_IgG_rep1

description:
Smarce1- MD (42A)#A04_release 90min_IgG_2106597
Smarce1- MD (42A)#A04_release 90min_IgG_2106597


title: Smarce1- MD (42A)#A04_release 90min_ESRRB_rep2

description:
Smarce1- MD (42A)#A04_release 90min_ESRRB_2109669
Smarce1- MD (42A)#A04_release 90min_ESRRB_2109669


title: Smarce1- MD (42A)#A04_release 90min_EZH2_rep1

description:
Smarce1- MD (42A)#A04_release 90min_EZH2_2106602
Smarce1- MD (42A)#A04_release 90min_EZH2_2106602


title: Smarce1- MD (42A)#A04_release 90min_ESRRB_rep1

description:
Smarce1- MD (42A)#A04_release 90min_ESRRB_2106601
Smarce1- MD (42A)#A04_release 90min_ESRRB_2106601


title: Smarce1- MD (42A)#A04_release 90min_EZH2_rep2

description:
Smarce1- MD (42A)#A04_release 90min_EZH2_2109670
Smarce1- MD (42A)#A04_release 90min_EZH2_2109670


title: mitotic mESCs_SOX2_rep4

description:
mitotic mESCs_CUT&RUN_SOX2_2041767
mitotic mESCs_CUT&RUN_SOX2_2041767


title: mitotic mESCs_SOX2_rep3

description:
mitotic mESCs_CUT&RUN_SOX2_2035551
mitotic mESCs_CUT&RUN_SOX2_2035551


title: mitotic mESCs_SOX2_rep1

description:
mitotic mESCs_CUT&RUN_SOX2_1930486
mitotic mESCs_CUT&RUN_SOX2_1930486


title: mitotic mESCs_SMARCE1_rep2

description:
mitotic mESCs_CUT&RUN_SMARCE1_2029023
mitotic mESCs_CUT&RUN_SMARCE1_2029023

value: SMARCE1 (Bethyl, A300-810A)


title: mitotic mESCs_SMARCE1_rep3

description:
mitotic mESCs_CUT&RUN_SMARCE1_2035546
mitotic mESCs_CUT&RUN_SMARCE1_2035546

value: nocodazole synchronization


title: mitotic mESCs_SOX2_rep2

description:
mitotic mESCs_CUT&RUN_SOX2_2029028
mitotic mESCs_CUT&RUN_SOX2_2029028


title: mitotic mESCs_SMARCE1_rep1

description:
mitotic mESCs_CUT&RUN_SMARCE1_1930484
mitotic mESCs_CUT&RUN_SMARCE1_1930484


title: mitotic mESCs_SMARCB1_rep3

description:
mitotic mESCs_CUT&RUN_SMARCB1_2035544
mitotic mESCs_CUT&RUN_SMARCB1_2035544

value: SMARCB1 (Bethyl, A301-087A)


title: mitotic mESCs_SMARCE1_rep4

description:
mitotic mESCs_CUT&RUN_SMARCE1_2041762
mitotic mESCs_CUT&RUN_SMARCE1_2041762


title: mitotic mESCs_SMARCB1_rep4

description:
mitotic mESCs_CUT&RUN_SMARCB1_2041760
mitotic mESCs_CUT&RUN_SMARCB1_2041760


title: Smarce1- MD (42A)#A10_release 90min_IgG_rep1

description:
Smarce1- MD (42A)#A10_release 90min_IgG_2106603
Smarce1- MD (42A)#A10_release 90min_IgG_2106603


title: mitotic mESCs_SMARCB1_rep2

description:
mitotic mESCs_CUT&RUN_SMARCB1_2029021
mitotic mESCs_CUT&RUN_SMARCB1_2029021


title: mitotic mESCs_IgG_rep4

description:
mitotic mESCs_CUT&RUN_IgG_2041757
mitotic mESCs_CUT&RUN_IgG_2041757


title: mitotic mESCs_IgG_rep3

description:
mitotic mESCs_CUT&RUN_IgG_2035541
mitotic mESCs_CUT&RUN_IgG_2035541


title: mitotic mESCs_IgG_rep2

description:
mitotic mESCs_CUT&RUN_IgG_2029018
mitotic mESCs_CUT&RUN_IgG_2029018


title: mitotic mESCs_IgG_rep1

description:
mitotic mESCs_CUT&RUN_IgG_1930477
mitotic mESCs_CUT&RUN_IgG_1930477


title: Validation2 S100Ahigh Neu2

city: Tianjin

first: Tao

last: Cheng

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

description: Validation2 S100Ahigh Neu2

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were first truncated and processed by fastp to filter out low-quality reads (more than 15 “N” or more than 50% bases with quality value ≤ 5). Then, the template switch oligo (TSO) sequence, the polyA tail sequence and short reads were discarded for each separated single cell using Cutadapt. The clean reads were aligend and quantified by STARsolo (version 2.7.9a) with human reference genome GRCh38/hg38.
processed data provided as .tsv (UMI matrix of single cells)

source_name: G-CSF mobilized peripheral blood

extract_protocol: After lysing the erythrocytes, total nucleated cells from G-CSF-mobilized grafts by apheresis were magnetically labeled with CD34 MicroBead Kit according to the manufacturer’s instructions (Miltenyi Biotec). After CD34 purification, cells were stained with conjugated anti-human lineage cocktail (CD3, CD14, CD16, CD19, CD20, CD56), CD34, CD66b and CD177 antibody for 30 min at 4 °C. Cells were washed twice with sorting buffer (PBS supplemented with 2% FBS) and filtered through a 70-μm cell strainer. Finally, single-cell suspensions were added with DAPI and loaded onto a BD FACS Aria III cell instrument for index-sorting. Lin-CD34+CD66b+CD177+SSChigh cells were sorted into every single well of 96-well plates containing cell lysis buffer and preserved at −80 °C before preparation for Single-Cell Tagged Reverse Transcription RNA sequencing (STRT-seq).

value: G-CSF mobilized peripheral blood

value: S100Ahigh Neu2

tag: patient id

tag: group or_sampling_time

value: Donor

tag: Sex

tag: age

tag: sample type

value: fresh G-CSF mobilized peripheral blood


title: Validation1 S100Ahigh Neu2

description: Validation1 S100Ahigh Neu2

tag: tissue


title: D10 lin-CD34+

description: D10 lin-CD34+

extract_protocol: Grafts collected by apheresis from donors were incubated on ice for no more than 10 min to lyse red blood cells. The single-cell suspensions were prepared for FACS. Cells were stained with conjugated anti-human lineage cocktail (CD3, CD14, CD16, CD19, CD20, CD56), CD34 and CD38 antibody for 30 min at 4 °C. Cells were washed twice with sorting buffer (PBS supplemented with 2% FBS) and filtered through a 70-μm cell strainer. Finally, single-cell suspensions were added with DAPI and loaded onto a BD FACS Aria III cell instrument to sort Lin-CD34+ cells. Live Lin-CD34+ cells were sorted into every single well of 96-well plates containing cell lysis buffer and preserved at −80 °C before preparation for Single-Cell Tagged Reverse Transcription RNA sequencing (STRT-seq).

value: lin-CD34+ cells

value: Female


title: mitotic mESCs_ESRRB_rep3

description:
mitotic mESCs_CUT&RUN_ESRRB_2041768
mitotic mESCs_CUT&RUN_ESRRB_2041768


title: D9 lin-CD34+

description: D9 lin-CD34+


title: mitotic mESCs_ESRRB_rep2

description:
mitotic mESCs_CUT&RUN_ESRRB_2035552
mitotic mESCs_CUT&RUN_ESRRB_2035552


title: mitotic mESCs_ESRRB_rep1

description:
mitotic mESCs_CUT&RUN_ESRRB_2029029
mitotic mESCs_CUT&RUN_ESRRB_2029029


title: D8 lin-CD34+

description: D8 lin-CD34+

value: Male


title: D5 lin-CD34+

description: D5 lin-CD34+


title: D3 lin-CD34+

description: D3 lin-CD34+


title: asynchronous mESCs_SOX2_rep2

description:
asynchronous mESCs_CUT&RUN_SOX2_2029016
asynchronous mESCs_CUT&RUN_SOX2_2029016

value: untreatment

value: SOX2 (R&D Systems, AF2018)


title: asynchronous mESCs_SOX2_rep4

description:
asynchronous mESCs_CUT&RUN_SOX2_2041755
asynchronous mESCs_CUT&RUN_SOX2_2041755

value: mouse embryonic stem cells


title: asynchronous mESCs_SOX2_rep3

description:
asynchronous mESCs_CUT&RUN_SOX2_2035539
asynchronous mESCs_CUT&RUN_SOX2_2035539


title: D7 lin-CD34+

description: D7 lin-CD34+


title: asynchronous mESCs_SOX2_rep1

description:
asynchronous mESCs_CUT&RUN_SOX2_1930470
asynchronous mESCs_CUT&RUN_SOX2_1930470


title: D2 lin-CD34+

description: D2 lin-CD34+


title: asynchronous mESCs_SMARCE1_rep3

description:
asynchronous mESCs_CUT&RUN_SMARCE1_2035534
asynchronous mESCs_CUT&RUN_SMARCE1_2035534


title: P10 d90 lin-CD34+ cells

description: P10 d90 lin-CD34+ cells

source_name: bone marrow

extract_protocol: BM samples were incubated on ice for no more than 10 min to lyse red blood cells. The single-cell suspensions were prepared for FACS. BM cells were stained with conjugated anti-human lineage cocktail (CD3, CD14, CD16, CD19, CD20, CD56), CD34 and CD38 antibody for 30 min at 4 °C. Cells were washed twice with sorting buffer (PBS supplemented with 2% FBS) and filtered through a 70-μm cell strainer. Finally, single-cell suspensions were added with DAPI and loaded onto a BD FACS Aria III cell instrument to sort Lin-CD34+ cells. Live Lin-CD34+ cells were sorted into every single well of 96-well plates containing cell lysis buffer and preserved at −80 °C before preparation for Single-Cell Tagged Reverse Transcription RNA sequencing (STRT-seq).

value: bone marrow

value: 90 days after transplantation

value: fresh bone marrow


title: N3 lin-CD34+ cells

description: N3 lin-CD34+ cells

value: health control


title: P10 d60 lin-CD34+ cells

description: P10 d60 lin-CD34+ cells

value: 60 days after transplantation


title: asynchronous mESCs_SMARCE1_rep4

description:
asynchronous mESCs_CUT&RUN_SMARCE1_2041750
asynchronous mESCs_CUT&RUN_SMARCE1_2041750

value: SMARCE1 (Bethyl, A300-810A)


title: asynchronous mESCs_SMARCE1_rep2

description:
asynchronous mESCs_CUT&RUN_SMARCE1_2029011
asynchronous mESCs_CUT&RUN_SMARCE1_2029011


title: mitotic mESCs_SMARCB1_rep1

description:
mitotic mESCs_CUT&RUN_SMARCB1_1930482
mitotic mESCs_CUT&RUN_SMARCB1_1930482

value: nocodazole synchronization

value: SMARCB1 (Bethyl, A301-087A)


title: P10 d14 lin-CD34+ cells

description: P10 d14 lin-CD34+ cells

value: 14 days after transplantation


title: asynchronous mESCs_SMARCE1_rep1

description:
asynchronous mESCs_CUT&RUN_SMARCE1_1930468
asynchronous mESCs_CUT&RUN_SMARCE1_1930468


title: P10 d1 lin-CD34+ cells

description: P10 d1 lin-CD34+ cells

value: 1 day after transplantation


title: asynchronous mESCs_SMARCB1_rep3

description:
asynchronous mESCs_CUT&RUN_SMARCB1_2035532
asynchronous mESCs_CUT&RUN_SMARCB1_2035532


title: P10 d30 lin-CD34+ cells

description: P10 d30 lin-CD34+ cells

value: 30 days after transplantation


title: asynchronous mESCs_SMARCB1_rep2

description:
asynchronous mESCs_CUT&RUN_SMARCB1_2029009
asynchronous mESCs_CUT&RUN_SMARCB1_2029009


title: asynchronous mESCs_SMARCB1_rep4

description:
asynchronous mESCs_CUT&RUN_SMARCB1_2041748
asynchronous mESCs_CUT&RUN_SMARCB1_2041748


title: P9 d90 lin-CD34+ cells

description: P9 d90 lin-CD34+ cells

value: lin-CD34+ cells


title: asynchronous mESCs_SMARCB1_rep1

description:
asynchronous mESCs_CUT&RUN_SMARCB1_1930466
asynchronous mESCs_CUT&RUN_SMARCB1_1930466


title: asynchronous mESCs_SMARCA4_rep4

description:
asynchronous mESCs_CUT&RUN_SMARCA4_2041747
asynchronous mESCs_CUT&RUN_SMARCA4_2041747

value: SMARCA4 (Abcam, ab110641)


title: asynchronous mESCs_SMARCA4_rep3

description:
asynchronous mESCs_CUT&RUN_SMARCA4_2035531
asynchronous mESCs_CUT&RUN_SMARCA4_2035531


title: P9 d1 lin-CD34+ cells

description: P9 d1 lin-CD34+ cells

value: Male


title: asynchronous mESCs_SMARCA4_rep2

description:
asynchronous mESCs_CUT&RUN_SMARCA4_2029008
asynchronous mESCs_CUT&RUN_SMARCA4_2029008

value: untreatment


title: asynchronous mESCs_SMARCA4_rep1

description:
asynchronous mESCs_CUT&RUN_SMARCA4_1930465
asynchronous mESCs_CUT&RUN_SMARCA4_1930465


title: P8 d60 lin-CD34+ cells

description: P8 d60 lin-CD34+ cells


title: P8 d90 lin-CD34+ cells

description: P8 d90 lin-CD34+ cells


title: P8 d30 lin-CD34+ cells

description: P8 d30 lin-CD34+ cells


title: asynchronous mESCs_IgG_rep5

description:
asynchronous mESCs_CUT&RUN_IgG_2041745
asynchronous mESCs_CUT&RUN_IgG_2041745

value: Rabbit (DA1E) mAb IgG XP® Isotype Control (CST#3900S)


title: unsplit Prime Editor 2

city: Munich

first: Elvir

last: Becirovic

state: Bavaria

address: Butenandtstrasse 7

department: Faculty for Chemistry and Pharmacy

institute: LMU Munich - Pharmacology for Natural Sciences

data_processing: The samples were sent to GENEWIZ by Azenta Life Science for subsequent processing, NGS and data analysis.

source_name: kidney, Embryo

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (high glucose) GlutaMAXTM (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS, Biochrom) and with 1 % penicillin/streptomycin (P/S, Biochrom) at 37 °C and 10 % CO2. Cells were passaged at a confluence of approximately 90 %.

extract_protocol:
Transfected cells were detached by scraping them off into remaining culture medium. The cells suspension was centrifuged (10 min, 5000 x g, 4 °C) and the cell pellet resuspended in a cell lysis buffer (RLT buffer, Qiagen) supplemented with 1% β-mercaptoethanol. Cells were then disrupted using a mixer mill at 30 Hz for 1 min. The lysates were centrifuged (10 min,500 x g, 4 °C) and supernatant was added to gDNA extraction columns. The columns were centrifuged for 4 min at 1500 x g and 1 min at 10000 x g at RT and incubated with 400 µl of RNase wash (Genomic lysis buffer (Zymo Research) supplemented with RNase A (Sigma-Aldrich), 1:5000) for 10 min followed by a 2 min centrifugation at RT. Next, 400 µl of DNA Pre-Wash buffer (Zymo Research) and 600 µl of g-DNA Wash buffer (Zymo Research) were added and with intermediate centrifugation steps for 1 min at 10000 x g. 600 µl of g-DNA Wash buffer was added again and centrifuged for 2 min at 10000 x g. To elute gDNA, 100 µl of H2O were added to the column, incubated for 20 min at RT and centrifuged for 2 min at 10000 x g. gDNA concentrations und purity were measured using the NanodropTM 2000c spectrophotometer.
For amplification of the respective target locus, 100 ng of the extracted gDNA were used in a PCR reaction with the Q5 high-fidelity DNA polymerase (New England Biolabs) according to the manufacturer’s instructions. The PCR was performed using primers containing Illumina partial adapters. The PCR product was validated via gel electrophoresis. Subsequently, the PCR-amplified DNA was purified from the agarose gel with the QIAquick gel extraction kit (Qiagen) according to the manufacturer’s instructions.
The purified PCR product was sent to next-generation sequencing (GENEWIZ, Azenta Life Sciences).

treatment_protocol: Cells were transfected using the standard calcium phosphate technique. Briefly, 24 h after seeding, a transfection mix (6 µg of plasmid DNA and 5% CaCl2 (2.5 M) in 1x borate buffer solution) was added directly to the medium. The medium was exchanged after another 24 h.

value: HEK293T cell line

value: kidney, Embryo

tag: biomaterial provider

value: Clontech, Takara


title: P8 d14 lin-CD34+ cells

description: P8 d14 lin-CD34+ cells

value: bone marrow

value: fresh bone marrow


title: REVeRT (split) Prime Editor 2


title: asynchronous mESCs_IgG_rep4

description:
asynchronous mESCs_CUT&RUN_IgG_2035529
asynchronous mESCs_CUT&RUN_IgG_2035529

value: mouse embryonic stem cells


title: P8 d1 lin-CD34+ cells

description: P8 d1 lin-CD34+ cells


title: P7 d90 lin-CD34+ cells

description: P7 d90 lin-CD34+ cells

value: 90 days after transplantation

value: Female


title: P9 d60 lin-CD34+ cells

description: P9 d60 lin-CD34+ cells

value: 60 days after transplantation


title: P7 d30 lin-CD34+ cells

description: P7 d30 lin-CD34+ cells


title: P7 d14 lin-CD34+ cells

description: P7 d14 lin-CD34+ cells

value: 14 days after transplantation


title: P7 after d180 lin-CD34+ cells

description: P7 after d180 lin-CD34+ cells

value: one year after transplantation


title: asynchronous mESCs_IgG_rep2

description:
asynchronous mESCs_CUT&RUN_IgG_1930461
asynchronous mESCs_CUT&RUN_IgG_1930461


title: P7 d1 lin-CD34+ cells

description: P7 d1 lin-CD34+ cells

value: 1 day after transplantation


title: asynchronous mESCs_ESRRB_rep3

description:
asynchronous mESCs_CUT&RUN_ESRRB_2041756
asynchronous mESCs_CUT&RUN_ESRRB_2041756

value: ESRRB (R&D Systems, PP-H6705-00)


title: P9 d30 lin-CD34+ cells

description: P9 d30 lin-CD34+ cells

value: lin-CD34+ cells

value: 30 days after transplantation


title: P9 d14 lin-CD34+ cells

description: P9 d14 lin-CD34+ cells

value: Male


title: P6 d90 lin-CD34+ cells

description: P6 d90 lin-CD34+ cells


title: P6 d60 lin-CD34+ cells

description: P6 d60 lin-CD34+ cells


title: P6 d30 lin-CD34+ cells

description: P6 d30 lin-CD34+ cells


title: P5 after d180 lin-CD34+ cells

description: P5 after d180 lin-CD34+ cells

value: half a year after transplantation


title: 4C_IP

data_processing:
Briefly, 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). After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Acetylated sites on RNAs (peaks) were identified by MACS software. Differentially acetylated 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.
GO and Pathway enrichment analysis were performed by the differentially acetylated protein coding genes,.

source_name: kidney

growth_protocol: ccRCC and paracancer tissues were preserved in liquid nitrogen

extract_protocol:
Total RNA was rRNA depleted with Ribo-zero (Illumina) and then subjected to immunoprecipitation with the GenSeqTM ac4C-IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions
The ac4C-IP-Seq service was provided by CloudSeq Inc. (Shanghai, China). Total RNA was rRNA depleted with Ribo-zero (Illumina) and then subjected to immunoprecipitation with the GenSeqTM ac4C-IP Kit (GenSeq Inc., China) 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 ac4C 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. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction. RNA libraries for IP and input samples were then constructed with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a Novaseq 6000 platform (Illumina)

value: kidney

tag: disease state

value: ccRCC tissue

tag: rip antibody

value: GenSeqTM ac4C-IP Kit


title: 3C_IP


title: 2C_IP


title: P6 d14 lin-CD34+ cells

description: P6 d14 lin-CD34+ cells

value: bone marrow


title: asynchronous mESCs_ESRRB_rep2

description:
asynchronous mESCs_CUT&RUN_ESRRB_2035540
asynchronous mESCs_CUT&RUN_ESRRB_2035540

value: untreatment


title: asynchronous mESCs_BRD9_rep3

description:
asynchronous mESCs_CUT&RUN_BRD9_2041754
asynchronous mESCs_CUT&RUN_BRD9_2041754

value: mouse embryonic stem cells

value: BRD9 (ACTIVE MOTIF, 61537)


title: asynchronous mESCs_IgG_rep3

description:
asynchronous mESCs_CUT&RUN_IgG_2029006
asynchronous mESCs_CUT&RUN_IgG_2029006

value: Rabbit (DA1E) mAb IgG XP® Isotype Control (CST#3900S)


title: 1C_IP


title: 4C_input


title: control sequence

value: HEK293T cell line

value: kidney, Embryo

value: Clontech, Takara


title: P5 d60 lin-CD34+ cells

description: P5 d60 lin-CD34+ cells

value: 60 days after transplantation

value: Female

value: fresh bone marrow


title: P5 d90 lin-CD34+ cells

description: P5 d90 lin-CD34+ cells

value: lin-CD34+ cells

value: 90 days after transplantation


title: P5 d14 lin-CD34+ cells

description: P5 d14 lin-CD34+ cells

value: 14 days after transplantation


title: asynchronous mESCs_BRD9_rep2

description:
asynchronous mESCs_CUT&RUN_BRD9_2035538
asynchronous mESCs_CUT&RUN_BRD9_2035538


title: 3C_input

value: kidney


title: P5 d30 lin-CD34+ cells

description: P5 d30 lin-CD34+ cells

value: 30 days after transplantation


title: P3 after d180 lin-CD34+ cells

description: P3 after d180 lin-CD34+ cells

value: one year after transplantation

value: Male


title: P3 d90 lin-CD34+ cells

description: P3 d90 lin-CD34+ cells

value: bone marrow


title: asynchronous mESCs_BRD9_rep1

description:
asynchronous mESCs_CUT&RUN_BRD9_2029015
asynchronous mESCs_CUT&RUN_BRD9_2029015

value: mouse embryonic stem cells

value: untreatment