title: RNA-Seq P9-T

data_processing:
The raw data (raw reads) from Illumina NovaSeq6000 sequencing.
Clean reads were compared with the reference genome to obtain the distribution map of whole-genome reads.
Clean reads were classified andannotated,  and the expression was calculated for the identified RNA differential expression was analyzed between samples. CIRI2 detects the paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment with BWA-MEM and combines with systematic filtering steps to remove potential false positives. CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.
Supplementary files format and content: excel table files include read counts for each Sample

extract_protocol:
Total RNA was extracted from cells or tissues with TRIzol reagent according to the manufacturer’s instruction.
The total RNA of the samples were extracted and connected to the 3-terminal and 5-terminal joints first and then reverse-transcribed into cDNA. For circRNA-seq, the RNA was treated with RNase (R). PCR amplification was carried out and then the gel was cut to recover the target fragment library. Computer sequencing was performed on the library that passed the quality inspection. Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. CIRI2 detects the paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment with BWA-MEM and combines with systematic filtering steps to remove potential false positives. CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.


title: B3_144_SU193_N

status: Public on Oct 08 2023

type: SRA

city: Palo Alto

first: Gunsagar

middle: Singh

last: Gulati

state: CA

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Bcl2fastq2 v2.18 (Illumina) was used to extract the data and generate FASTQ files for each sample by using unique barcode combinations from the Nextera preparation. Raw paired-end FASTQ reads were then aligned to GENCODE v25 reference transcripts (GRCh38.p7) with Salmon v0.7.2 using the --seq-bias flag and otherwise default parameters. Salmon results were merged into a single gene-level TPM matrix using the R package, tximport v1.4.0. Low quality cells, identified as cells expressing <1,000 detectable genes, were excluded from further analysis. Using Seurat, clusters were identified by running ‘FindClusters’ on the first 10 principal components of the data with the resolution parameter set to 0.6. Cell labels for known epithelial subpopulations were assigned according to the expression of previously described marker genes (KRT14high, MYLKhigh = basal; MMP7high, RARRES1high = luminal progenitor; MUC1high, AREGhigh = mature luminal; FAPhigh, PDGFRAhigh = fibroblast; CDH5high, EMCNhigh, PECAM1high = endothelial cell, CD3high, CD4high = CD4 T cell, CD3high, CD8high = CD8 T cell, CD19high = B cell, CD14high = macrophages).
Genome_build: GENCODE v25 (GRCh38.p7)
Supplementary_files_format_and_content: Tab-delimited text files include (1) Transcripts per million (TPM) values for each single cell (2) Metadata for each single cell

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Tumor biopsies from human breast cancer patients (n = 18) were obtained from the primary site (n =16), lymph nodes (n = 1; paired primary), or brain metastasis (n = 2) during surgical resection of breast tumors at Stanford Hospital and City of Hope National Medical Center. Samples were mechanically dissociated into < 1-2 mm3 pieces with a razor blade and then digested at 37 oC with 1500 U collagenase and 500 U hyaluronidase in Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mM Glutamax (Invitrogen), and an antibiotic/antimycotic mix containing 120 μg/ml penicillin, 100 μg/ml streptomycin, and 0.25 μg/ml amphotericin-B (PSA) for 4-6 hrs with hourly pipetting for 5 min. After digestion, cells were treated with ACK lysis buffer to deplete red blood cells and then incubated with 10 U dispase to further dissociate the tissue into single cells and 1000 U DNase I to prevent cell clumping. Cells were filtered through a 70 μm nylon mesh and washed with staining buffer containing 2% fetal bovine serum (FBS) and PSA in Hank’s Balanced Salt Solution (HBBS). Single cell suspensions of fresh breast tissue were then stained with fluorescent antibodies to prepare for FACS. To reduce nonspecific antibody binding, single cells were blocked with 10 μg/mL rat IgG on ice for 10 minutes. Cells were then stained, in the dark, on ice for 30 minutes. FACS was performed with a 130 μm nozzle on a BD FACSAria II with BD FACSDiva software. Side scatter and forward scatter profiles (area and width) were used to eliminate debris and cell doublets. Dead cells were eliminated by excluding 4’,6-diamidino-2-phenylindole (DAPI) positive cells. Breast epithelial cells were enriched by negative gating of lineage cells expressing CD45, CD31, CD3, CD16, or CD64. Human breast basal cells were then gated as CD49fhighEPCAMmed-low, luminal progenitors as CD49fhighEPCAMhigh, mature luminal cells as CD49flowEPCAMhigh, and cancer-associated fibroblasts (CAFs) and endothelial cells (ECs) as CD49f–EpCAM–. Although ECs are generally CD31+, the chemical digestion for tumor isolation cleaves surface CD31, so these cells are detected on flow cytometry as CD31–. CAFs and ECs were then distinguished based on transcriptional expression of FAP and PDGFRA in CAFs and CDH5, EMCN, and PECAM1 in ECs. Hematopoietic populations were sorted separately based on surface expression of CD45 followed by CD14+ for macrophages, CD3+CD4+ for CD4 T cells, CD3+CD8+ for CD8 T cells, and CD19+ for B cells.
cDNA libraries were constructed using a modified Smart-seq2 protocol and machine-automated pipeline by the Stanford Functional Genomic Facility (SFGF), as described previously (PMIDs: 24385147, 30241615, and 31974247). Notably, 21 to 27 cycles of PCR amplification were required to obtain cDNA amounts within range of the recommended concentrations (0.05 – 0.32 ng/μL) for downstream tagmentation. Wells with over-amplified cDNA were diluted. Libraries were prepared using the Nextera XT DNA Library Prep (Illumina) kit and sequenced on a NextSeq 500 (Illumina) to obtain 2x76 or 2x151 bp paired-end reads.

tag: tissue

value: Normal

value: Primary

value: Basal


title: B3_042_SU9_O

value: Other

value: Endothelial cell


title: B3_012_COH87_O

value: Brain metastasis


title: RNA-Seq P9-N

city: Guangzhou

first: Zhu

last: Xiaofeng

address: 107 Yan Jinag West Road

country: China

institute: Sun Yat-Sen University

source_name: normal

value: normal

tag: diagnosis

value: breast cancer

tag: Sex

value: female

tag: age

tag: tumor stage

value: II


title: RNA-Seq P8-T

source_name: tumor

value: tumor


title: RNA-Seq P8-N


title: B3_139_SU22_O


title: B2_184_SU196_O

value: CD8+ T cell


title: B2_145_SU193_N


title: RNA-Seq P7-T


title: RNA-Seq P7-N


title: B5_045_SU11_T

value: Tumor


title: RNA-Seq P12-T


title: RNA-Seq P12-N


title: B2_142_SU193_N


title: RNA-Seq P11-T


title: B12_184_SU196_O


title: B2_042_SU9_O


title: B12_145_SU193_N


title: RNA-Seq P10-T


title: B12_144_SU193_N


title: B3_145_SU193_N


title: TCR-pentamer-positive, T-4

description: Pentamer positive_TCR

data_processing:
The raw data (raw reads) from Illumina NovaSeq6000 sequencing.
Clean reads were compared with the reference genome to obtain the distribution map of whole-genome reads.
Clean reads were classified and annotated,  and the expression was calculated for the identified RNA differential expression was analyzed between samples
Assembly: hg19
Library strategy: scTCR-Seq

source_name: circFam53b epitope pentamer positive T cells

extract_protocol:
After exposure to the cell lysis buffer, the polyadenylated RNA molecules hybridized to the beads. The beads were then transferred into a single tube for reverse transcription.
Single cells were sorted into 0.6µL of 1% NP-40 buffer in a 384-well plate. Beads with unique molecular identifiers (UMIs) and cell barcodes were loaded into PBMCs in suspension in a nearly saturated state, so that each cell was paired with beads (Gel Bead-in Emulsion). After exposure to the cell lysis buffer, the polyadenylated RNA molecules hybridized to the beads. The beads were then transferred into a single tube for reverse transcription. During cDNA synthesis, each cDNA molecule was labelled with UMI and a cell tag at the 5′ end of its source cell. To prepare a library, sequencing was used to randomly interrupt the whole transcriptome amplification product to enrich the 3′ end of the transcript connected to the cell barcode and UMI. All remaining procedures, including library construction, were conducted in accordance with standard manufacturing protocols. The sequencing library was quantified using a high-sensitivity DNA chip (Agilent) and Qubit high-sensitivity DNA analysis (Thermo Fisher Scientific) on bioanalyzer 2100. The library was sequenced on Illumina Novaseq.

tag: cell type


title: TCR-pentamer-positive, T-3

description: Pentamer positive_TCR

value: circFam53b epitope pentamer positive T cells


title: B12_136_SU22_O


title: B12_045_SU11_T


title: TCR-pentamer-positive, T-2

description: Pentamer positive_TCR


title: B11_184_SU196_O


title: TCR-pentamer-positive, T-1

description: Pentamer positive_TCR


title: B12_042_SU9_O


title: TCR-pentamer-negative, T-3

description: Pentamer negative_TCR

source_name: circFam53b epitope pentamer negative T cells


title: TCR-pentamer-negative, T-4

description: Pentamer negative_TCR

value: circFam53b epitope pentamer negative T cells


title: B11_144_SU193_N


title: TCR-pentamer-negative, T-2

description: Pentamer negative_TCR


title: TCR-pentamer-negative, T-1

description: Pentamer negative_TCR


title: pentamer-positive, T-4

description:
Pentamer positive_pentamer negative_differential_genes
positive_barcodes.tsv.gz
positive_features.tsv.gz
positive_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
The raw data (raw reads) from Illumina NovaSeq6000 sequencing.
Clean reads were compared with the reference genome to obtain the distribution map of whole-genome reads.
Clean reads were classified and annotated,  and the expression was calculated for the identified RNA differential expression was analyzed between samples
Assembly: hg19


title: B2_045_SU11_T


title: B11_045_SU11_T


title: B10_145_SU193_N


title: RNA-Seq P10-N


title: B10_144_SU193_N


title: pentamer-positive, T-1


title: B10_045_SU11_T


title: pentamer-positive, T-3


title: pentamer-negative, T-4

description:
Pentamer positive_pentamer negative_differential_genes
negative_barcodes.tsv.gz
negative_features.tsv.gz
negative_matrix.mtx.gz


title: pentamer-negative, T-3


title: B10_042_SU9_O


title: B1_184_SU196_O


title: B1_145_SU193_N


title: pentamer-negative, T-2


title: B12_039_SU9_O


title: pentamer-negative, T-1


title: B1_144_SU193_N


title: B1_136_SU22_O


title: B11_145_SU193_N


title: T6 (circRNA-seq)

data_processing:
The raw data (raw reads) from Illumina NovaSeq6000 sequencing.
Clean reads were compared with the reference genome to obtain the distribution map of whole-genome reads.
Clean reads were classified andannotated,  and the expression was calculated for the identified RNA differential expression was analyzed between samples. CIRI2 detects the paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment with BWA-MEM and combines with systematic filtering steps to remove potential false positives. CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.
Assembly: hg19
Supplementary files format and content: Tissues circRNA_expression.xls reports counts and RPMs for circRNAs

source_name: cancer tissue

extract_protocol:
Total RNA was extracted from cells or tissues with TRIzol reagent according to the manufacturer’s instruction.
The total RNA of the samples were extracted and connected to the 3-terminal and 5-terminal joints first and then reverse-transcribed into cDNA. For circRNA-seq, the RNA was treated with RNase (R). PCR amplification was carried out and then the gel was cut to recover the target fragment library. Computer sequencing was performed on the library that passed the quality inspection. Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. CIRI2 detects the paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment with BWA-MEM and combines with systematic filtering steps to remove potential false positives. CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.
lncRNA or circRNA Seq

tag: ethnicity

value: Han nationality

tag: tumor grade

tag: outcome

value: recovery

value: breast cancer tissue


title: T5 (circRNA-seq)


title: B1_045_SU11_T

value: Primary


title: B10_184_SU196_O


title: T4 (circRNA-seq)


title: T2 (circRNA-seq)

value: III


title: T3 (circRNA-seq)


title: pentamer-positive, T-2


title: A9_145_SU193_N

value: Normal

value: Basal


title: A9_042_SU9_O

value: Other

value: Endothelial cell


title: A9_144_SU193_N


title: N6 (circRNA-seq)

source_name: normal tissue

value: normal tissue


title: A8_184_SU196_O

value: B cell


title: N5 (circRNA-seq)

value: female

value: II


title: A9_039_SU9_O


title: A8_145_SU193_N


title: N4 (circRNA-seq)


title: A8_144_SU193_N


title: N3 (circRNA-seq)


title: N2 (circRNA-seq)


title: N1 (circRNA-seq)


title: A9_184_SU196_O


title: A8_066_SU42_T

value: Brain metastasis


title: T5 (RNA-seq)

data_processing:
The raw data (raw reads) from Illumina NovaSeq6000 sequencing.
Clean reads were compared with the reference genome to obtain the distribution map of whole-genome reads.
Clean reads were classified andannotated,  and the expression was calculated for the identified RNA differential expression was analyzed between samples
Assembly: hg19
Supplementary files format and content: Patients.lncRNA._expression.xlsx

extract_protocol:
Total RNA was extracted from cells or tissues with TRIzol reagent according to the manufacturer’s instruction.
The total RNA of the samples were extracted and connected to the 3-terminal and 5-terminal joints first and then reverse-transcribed into cDNA. PCR amplification was carried out and then the gel was cut to recover the target fragment library. Computer sequencing was performed on the library that passed the quality inspection


title: T1 (circRNA-seq)


title: IP_Col-0_FLAG_rep2

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

library_source: genomic

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
ChIP-enriched peaks were called uing MACS2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with GFP, FLAG, H4K5Ac, H2Aub antibodies.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

value: seedlings

tag: chip antibody

tag: genotype

value: wild type


title: T6 (RNA-seq)


title: IP_Col-0_FLAG_rep1


title: T3 (RNA-seq)


title: A8_042_SU9_O


title: T2 (RNA-seq)


title: T4 (RNA-seq)


title: input_Col-0_FLAG


title: A8_012_COH87_T

value: Tumor


title: T1 (RNA-seq)

value: Han nationality


title: A8_045_SU11_T


title: N6 (RNA-seq)

value: recovery


title: epl1a-1b_rep3

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates for 12 days, under a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis plants with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing).

value: Arabidopsis seedlings

value: epl1a-/- epl1b-/-

tag: time


title: A7_184_SU196_O

value: Primary


title: epl1a-1b_rep2


title: 399_Prolapse_Females

city: Werribee

first: Ramya

middle: Sindhoora

last: Ephraim

state: VIC

address: 235 Hoppers Ln

country: Australia

institute: Victoria University

data_processing:
MGIEasy V2 chemistry set was used for generating a library using 4sequencinglanes and at least 400 m raw reads per lane with paired-end 100b reads for accuracy and processing to compressed fastq files.
Raw fastq files were analysed using the RNAsik pipeline version 1.5.4 using STAR aligner and theMus musculusreference,GRCm38 (Genbank accessionGCA_000001635.2).
Reads were quantified using featureCounts producing the raw genes count matrix and various quality control metrics.
Raw counts were then analysed with Degust, a web tool that performs differential expression analysis using limma voom normalisation, producing counts per million library size normalisation and trimmed mean of M values normalisation for RNA composition normalisation.
Supplementary files format and content: Comma-separated values (CSV) file contains raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Distal Colon

growth_protocol: Mice were housed in a temperature-controlled environment with 12-hour day/night cycles and had limited access to food and water.

extract_protocol:
TRIzolTM (Invitrogen, VIC Australia) was used to extract total RNA, which was purified using the RNeasy® Mini kit (Qiagen, Hilden, Germany), including column DNase treatment.
The RNA-Seq library was formulated by starting with >100 ng of RIN 8+ total RNA, including RNA quality control (CE integrity analysis by AATI Fragment Analyser, Fluorimetric quantitation by Invitrogen Qubit).
The Poly-A mRNA was chosen, and MGIEasy stranded mRNA chemistry was carried out. All samples were quantified and analysed using Qubit and Bioanalyser and passedthe QNAQC standard.

treatment_protocol: Mice were culled and similar sections of distal colon segments were collected from each mouse, immediately placed into liquid nitrogen, and stored at -80 ºC until RNA extraction was performed.

value: Distal Colon

tag: cell line

value: Winnie Prolapse

value: Severely Inflammed

value: Female

tag: treatment


title: 2086_Prolapse_Females


title: 21st_Jun_19_Prolapse_Females


title: A8_139_SU22_O

value: Other

value: Endothelial cell


title: epl1a-1b_rep1


title: N5 (RNA-seq)

value: female

value: normal tissue


title: A7_145_SU193_N

value: Normal

value: Basal


title: ham1-2_rep3


title: N4 (RNA-seq)

value: II


title: ham1-2_rep2


title: N3 (RNA-seq)

value: III


title: 391_Prolapse_Males

value: Male


title: A7_136_SU22_T

value: Tumor


title: ham1-2_rep1

value: Arabidopsis seedlings


title: A7_045_SU11_T


title: N1 (RNA-seq)

value: Han nationality

value: recovery


title: 452_Prolapse_Males

value: Distal Colon


title: 389_Winnie_Females

value: Winnie

value: Inflammed


title: N2 (RNA-seq)


title: A7_144_SU193_N

value: Primary


title: epcr1-2_rep2

value: epcr1-/- epcr2-/-


title: A7_042_SU9_O

value: Other

value: Endothelial cell


title: 388_Winnie_Females

value: Female


title: SCC 11T

city: New York

first: Xiaohan

last: Tang

state: New York

address: 1300 York Ave.

institute: Weill Cornell Medicine

description:
raw_counts.SCC.txt
normalized_counts.SCC.txt

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt v1.9.1; then mapped to the human hg19 reference genome using Tophat2 v2.0.11.
Raw read counts were quantified using HTSeq-count v0.11.2.
Differential expression analysis were performed using DESeq2 v1.26.0.
Assembly: hg19
Supplementary files format and content: tab-delimited txt files including raw and normalized gene counts for each sample

source_name: Epithelium

extract_protocol:
RNA was extracted using Qiagen RNeasy kit
RNAseq libraries were prepared using the TruSeq Stranded mRNA Library Preparation kit (Illumina) according to the manufacturer's instuctions.

value: Epithelium

tag: pathology

value: SCC


title: A6_184_SU196_O

value: B cell


title: 387_Winnie_Females


title: 554_Prolapse_Males

value: Winnie Prolapse

value: Severely Inflammed


title: SCC 10T


title: SCC 11M

value: Margin


title: pwwp1-2_rep3

value: Arabidopsis seedlings

value: pwwp1-/- pwwp2-/-


title: A6_145_SU193_N

value: Normal

value: Basal


title: 386_Winnie_Females

value: Distal Colon

value: Winnie


title: pwwp1-2_rep2


title: 17-7_B_Prolapse_Males

value: Male


title: SCC 10M


title: epcr1-2_rep3

value: epcr1-/- epcr2-/-


title: pwwp1-2_rep1


title: W4_Winnie_Males

value: Inflammed


title: A6_139_SU22_T

value: Tumor

value: Primary


title: SCC 9T

value: Epithelium


title: A6_144_SU193_N


title: A6_064_SU42_O

value: Other

value: Brain metastasis

value: Endothelial cell


title: SCC 9M


title: ubp5-c326s_rep3

value: ubp5-3 complemented with 1305-UBP5-C326S-Flag construct (in col-0)


title: W3_Winnie_Males


title: 2034_Winnie_Males


title: RNA-Seq P11-N

value: normal

value: breast cancer

value: female

value: II


title: ubp5-c326s_rep2

value: Arabidopsis seedlings


title: epcr1-2_rep1


title: A6_061_COH69_T

value: Basal


title: SCC 8T

value: SCC


title: SCC 8M

value: Margin


title: ubp5-c326s_rep1


title: 5C7_C57BLK6_Females

value: Distal Colon

value: Control

value: Wild Type

value: Female


title: Col-0_rep3

value: wild type


title: A6_012_COH87_O

value: Other


title: 4C5_C57BLK6_Females


title: SCC 7T

value: Epithelium


title: A6_042_SU9_O

value: Primary

value: Endothelial cell


title: SCC 7M


title: Col-0_rep2


title: 4C2_C57BLK6_Females


title: A5_184_SU196_O

value: B cell


title: Col-0_rep1


title: A7_066_SU42_T

value: Tumor

value: Brain metastasis


title: A5_145_SU193_N

value: Normal


title: 4C1_C57BLK6_Females


title: SCC 6T


title: SCC 6M


title: 4C8_C57BLK6_Males

value: Male


title: SCC 5T


title: Col-0_H3K27me3_rep1

value: Arabidopsis seedlings


title: A5_144_SU193_N

value: Basal


title: 4C6_C57BLK6_Males


title: 3C5_C57BLK6_Males


title: Col-0_H3K27me3_rep2


title: pwwp1-2_H2Aub_rep2

value: pwwp1-/- pwwp2-/-


title: 3C4_C57BLK6_Males

value: Distal Colon


title: A5_045_SU11_T


title: SCC 4T

value: SCC


title: A4_184_SU196_O


title: pwwp1-2_H2Aub_rep1


title: SCC 4M

value: Margin


title: SCC 3T


title: mWake(Cre/+), Lateral amygdala, snRNA, LA4A

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description: snRNA-Seq

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V3 was used to perform downstream analysis following the standard pipeline.
Assembly: mm10
Supplementary files format and content: h5

extract_protocol:
For scRNA-Seq, tissues were dissociated in papain (Worthington) and debris was removed using OptiPrep density gradient media following cell dissociation. Cells were then processed immediately for scRNA-Seq.
scRNA-Seq following 10x V3.1 guideline
For snRNA-Seq, tissues were processed following a modified 10x Genomics protocol. Lysis buffer containing (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet-P40, 0.01% Digitonin, 1 U/ml Rnase inhibitor, 1% BSA) was added into a tube containing the lateral amygdalae and incubated on ice for 15 min with gentle pestle grinding (5 strokes every 3 min).  Wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.2 U/ml RNase inhibitor, 1% BSA) was added, and nuclei were raw through a 50 μm filter. Debris was removed using OptiPrep density gradient media and nuclei morphology was accessed under the light microscope.  Nuclei were then immediately processed for snRNA-Seq.

tag: strain

value: Lateral amygdala

value: mWake-expressing neurons

value: 2 months old


title: ubp5-c326s_H2Aub_rep2

value: ubp5-3 complemented with 1305-UBP5-C326S-Flag construct (in col-0)


title: mWake(Cre/+), Lateral amygdala, scRNA, LA3A

description: scRNA-Seq


title: mWake(Cre/+), Lateral amygdala, scRNA, LA3

description: scRNA-Seq


title: A4_144_SU193_N

value: Primary


title: A4_183_SU196_O

value: Other

value: Fibroblast


title: Col-0_H2Aub_rep1

value: wild type


title: ubp5-c326s_H2Aub_rep1


title: mWake(Cre/+), Lateral amygdala, snRNA, LA4

description: snRNA-Seq


title: Col-0_H2Aub_rep2


title: A5_139_SU22_O

value: Endothelial cell


title: SCC 3M

value: Epithelium


title: mWake(Cre/+), Lateral amygdala, snRNA, LA2

description: snRNA-Seq

value: Male


title: SCC 2T


title: SCC 5M


title: A4_136_SU22_O


title: A4_042_SU9_O


title: epl1a-1b_H4K5Ac_rep1

value: epl1a-/- epl1b-/-

value: Arabidopsis seedlings


title: A3_184_SU196_O

value: B cell


title: SCC 2M


title: SCC 1T


title: ham1-2_H4K5Ac_rep2


title: AtTERPax7_ATAC_Mim_60h_Tam48h

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.4 (--no-unal --no-mixed --no-discordant).
Bam files were created and duplicated reads removed using view (-b) and markdup (-r) from SAMtools/1.12.
Reads from multiple biological replicates were merged (if applicable).
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing BPM) from deepTools/3.5.
Peaks were called using callpeak (-f BAMPE -p 1e-3/1e-5 -g mm -- min-length 100 --max-gap 50) from MACS/2.2.7.1.
Assembly: mm10
Supplementary files format and content: Bigwig, unit: counts per million

source_name: Cell line

growth_protocol: AtT-20 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) and antibiotics (penicillin, streptomycin).

extract_protocol:
Nuclei from 50,000 cells were isolated and transposition was performed using Tagment DNA kit following Illumina’s recommendations.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Cell line

value: Corticotrope

value: Mim 60 h, Tam 48 h


title: SCC 1M

value: Margin


title: ham1-2_H4K5Ac_rep1


title: AtTERPax7_ATAC_Mim_60h

value: Mim 60 h


title: OPMD 9T

description:
raw_counts.OPMD.txt
normalized_counts.OPMD.txt

value: OPMD


title: A3_144_SU193_N

value: Normal

value: Basal


title: OPMD 9M


title: AtTERPax7_ATAC_Tam48h

value: Tam 48 h


title: epcr1-2_H4K5Ac_rep2

value: epcr1-/- epcr2-/-


title: A4_045_SU11_T

value: Tumor

value: Primary


title: AtTERPax7_ATAC


title: epcr1-2_H4K5Ac_rep1


title: OPMD 8T

value: Epithelium


title: epl1a-1b_H4K5Ac_rep2


title: A3_136_SU22_O

value: Other

value: Endothelial cell


title: A3_139_SU22_O


title: mWake(Cre/+), Lateral amygdala, scRNA, LA1

description: scRNA-Seq

value: Lateral amygdala

value: mWake-expressing neurons

value: 2 months old

value: Male


title: OPMD 8M


title: Col-0_H4K5Ac_rep4

value: wild type

value: Arabidopsis seedlings


title: A3_064_SU42_O

value: Brain metastasis


title: AtTPax7_Lsd1

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-500 bp were kept for library preparation.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Cell line

value: Corticotrope


title: A3_045_SU11_T

value: Basal


title: OPMD 7T

value: OPMD


title: AtTNeo_Lsd1


title: A3_145_SU193_N

value: Normal


title: AtTNeo_LaminB1


title: OPMD 7M

value: Margin


title: pwwp1-2_H4K5Ac_rep2

value: pwwp1-/- pwwp2-/-


title: pwwp1-2_H4K5Ac_rep1


title: OPMD 6T

value: Epithelium


title: A2_145_SU193_N

value: Primary


title: ubp5-c326s_H4K5Ac_rep2

value: ubp5-3 complemented with 1305-UBP5-C326S-Flag construct (in col-0)


title: A2_144_SU193_N


title: OPMD 6M


title: AtTERPax7_H3K4me1_Tam36h

value: Tam 36 h


title: A2_045_SU11_T

value: Tumor


title: ubp5-c326s_H4K5Ac_rep1


title: Col-0_H4K5Ac_rep3


title: AtTERPax7_H3K4me1_Tam18h

value: Tam 18 h


title: A2_042_SU9_O

value: Other

value: Endothelial cell


title: Col-0_H4K5Ac_rep1

value: wild type

value: Arabidopsis seedlings


title: Col-0_H4K5Ac_rep2


title: OPMD 5M


title: A12_184_SU196_O

value: B cell


title: OPMD 5T


title: AtTERPax7_H3K4me1_Tam12h

value: Corticotrope

value: Tam 12 h


title: A2_184_SU196_O


title: OPMD 4T

value: OPMD


title: A12_145_SU193_N

value: Normal

value: Basal


title: OPMD 4M

value: Margin


title: IP_HAM1_FLAG_rep2

value: 1305-HAM1-Flag transformed plants (in col-0)


title: AtTERPax7_H3K4me1_Mim60h_Tam48h

value: Mim 60 h, Tam 48 h


title: OPMD 3T

value: Epithelium


title: IP_HAM1_FLAG_rep1


title: A12_045_SU11_T

value: Primary


title: AtTNeo_H1


title: AtTERPax7_H3K4me1_Tam48h

value: Tam 48 h


title: input_HAM1_FLAG


title: OPMD 3M


title: A12_037_SU17_O


title: AtTERPax7_H3K4me1


title: IP_EPL1B_FLAG_rep2

value: 1305-EPL1B-Flag transformed plants (in col-0)


title: OPMD 2T


title: AtTERPax7_H3K4me1_Mim60h

value: Mim 60 h


title: A11_184_SU196_O

value: Other


title: A11_145_SU193_N


title: Melan-a-3 (circRNA-seq)

data_processing:
The raw data (raw reads) from Illumina NovaSeq6000 sequencing.
Clean reads were compared with the reference genome.  CIRI2 detects the paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment with BWA-MEM and combines with systematic filtering steps to remove potential false positives. CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.
If a circRNA can be detected by both methods, it will be considered as an identified circRNA. The DEseq/DESeq2/edgeR/DEGseq package in Bioconductor was used to determine differently expressed circRNA.
Assembly: mm10
Supplementary files format and content: Txt files report counts and RPMs for circRNAs

source_name: Melan-a

extract_protocol:
Total RNA was extracted from cells or tissues with TRIzol reagent according to the manufacturer’s instruction.
The total RNA  of the samples were extracted and treated with RNase (R), and connected to the 3-terminal and 5-terminal joints first and then reverse-transcribed into cDNA. PCR amplification was carried out and then the gel was cut to recover the target fragment library. Computer sequencing was performed on the library that passed the quality inspection. Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. CIRI2 detects the paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment with BWA-MEM and combines with systematic filtering steps to remove potential false positives. CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.

value: Melan-a

value: melanocyte cell


title: AtTERPax7_H3K4me1_Mim60h_Tam12h

value: Mim 60 h, Tam 12 h


title: IP_EPL1B_FLAG_rep1

value: Arabidopsis seedlings


title: Melan-a-1 (circRNA-seq)


title: OPMD 1T


title: Melan-a-2 (circRNA-seq)


title: OPMD 1M


title: A11_144_SU193_N


title: Eph4-ev-3 (circRNA-seq)

value: breast epithelial cell


title: Eph4-ev-2 (circRNA-seq)


title: OPMD 2M


title: IP_EPCR1_FLAG_rep2

value: epcr1 complemented with 1305-EPCR1-Flag construct (in col-0)


title: A11_061_COH69_T

value: Tumor


title: A10_184_SU196_O

value: B cell


title: shRNA2_2

data_processing:
Raw FASTQ reads were aligned to the GENCODE v29 reference transcripts (GRCh38.p12) using Salmon v0.12 with flags -l IU, --seqBias, --gcBias, --posBias, --useVBOpt, --rangeFactorizationBins 4 and --validateMapping. A gene-level count matrix was created by importing the quantification data from Salmon using tximport (version 1.10.1). Differential gene expression analysis was performed used the R package DESEq2 (version 1.22.2) following the authors’ instructions.
Genome_build: GENCODE v29 (GRCh38.p12)
Supplementary_files_format_and_content: Tab-delimited text file containing raw count values for each bulk RNA-seq sample

source_name: MDA-MB-468 breast adenocarcinoma cell line

extract_protocol:
200,000 MDA-MB-468 cells infected with either pSicoR, shLMO2-1 or shLMO2-2 were harvested and RNA extraction was performed using the RNeasy Micro Kit (Qiagen #74034). mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490).
cDNA libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (#E7770, #E7775). Libraries were fragment analyzed by LabChip and quantified by qPCR using the KAPA Library Quantification kit (#KR0405).

tag: transfected plasmid


title: input_EPCR1_FLAG

tag: tissue


title: A10_145_SU193_N

value: Normal

value: Basal


title: B16F10-3 (circRNA-seq)

value: melanoma cell


title: IP_PWWP1_FLAG_rep2

value: pwwp1 complemented with 909-PWWP1-Flag construct (in col-0)


title: shRNA2_1


title: IP_PWWP1_FLAG_rep1


title: input_EPL1B_FLAG


title: A10_144_SU193_N

value: Primary


title: shRNA1_3


title: A10_136_SU22_O

value: Endothelial cell


title: input_PWWP1_FLAG


title: B16F10-1 (circRNA-seq)


title: IP_EPCR1_FLAG_rep1


title: shRNA2_3


title: UBP5_GFP_rep2

value: 1305-UBP5-GFP transformed plants (in col-0)


title: A10_045_SU11_T


title: 4T1-3 (circRNA-seq)

value: breast cancer cell


title: A1_144_SU193_N


title: shRNA1_1


title: shRNA1_2


title: Control_3


title: UBP5_GFP_rep1


title: A1_136_SU22_O

value: Other


title: Col-0_GFP_rep2

value: wild type


title: 4T1-2 (circRNA-seq)


title: Control_2


title: A1_045_SU11_T


title: Eph4-ev-1 (circRNA-seq)


title: Col-0_GFP_rep1


title: A1_022_SU2_O


title: B16F10-2 (circRNA-seq)


title: Control_1


title: 12_8

status: Public on Oct 07 2023

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

description: WDA12 males.txt

data_processing:
27 samples were sequenced using BGISEQ platform
HISAT was used to align the clean reads to the reference genome.
Bowtie2 was used to align the clean reads to the reference genes
Assembly: GRCm38.p6
Supplementary files format and content: Matrix table with raw gene counts for every sample

source_name: liver

extract_protocol:
Livers were removed,  and RNA was harvested using Qiagen RNA miniprep kit.
RNA libraries were prepared for sequencing using standard BGI protocols

value: liver

value: male

value: Kdm5b fl/fl

value: WDA 16 weeks + AAV-control + 4 weeks resolution


title: 12_13

description: WDA12 females.txt

value: female


title: 12_3

description: WDA12 females.txt

value: WDA 16 weeks + AAV-CMV-Cre + 4 weeks resolution


title: 12_12

description: WDA12 females.txt


title: Mutp53 (R280K)

type: RNA

city: Taichung

first: Wei-Chien

last: Huang

address: 9F, No.6, Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

description: Mutant p53 expressed

data_processing:
Housekeeping gene: 18s rRNA was used for normalization. Target LncRNA signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = Ct_Target, Ct_18s rRNA.
Fold-change data: Wtp53/pcDNA6A-Flag; Mutp53/pcDNA6A-Flag.

label: SYBR Green

label_protocol: The RT-PCR was performed with 1 μg total RNA, M-MLV Reverse Transcriptase (InvitrogenTM, Thermo Fisher Scientific Inc., Waltham, MA, USA), Random Hexamer, dNTP, 5X M-MLV buffer, and DTT.

growth_protocol: HEK-293T cells were subcultured less than 10 passage for transfection. Cells were seeded around 50% full of the well in 6 well plate, and plasmids were transiently transfected in next day. After incubation with the transfection complex for 6 hours, culture medium was refreshed and cells were collected after 2 days transfection.

extract_protocol: Cells were lysed with TRIzol™ Reagent (Thermo Fisher Scientific Inc., Waltham, MA, USA), and total RNA was isolated by chloroform/isopropanol strategy.

treatment_protocol: 2μg of plasmids were transiently transfected into HEK-293T cells by Lipofetamine2000 transfection reagent and incubate for 2 days.

tag: transfected with


title: Mutp53 (R273H)

description: Mutant p53 expressed


title: Mutp53 (E285K)

description: Mutant p53 expressed


title: 12_7

description: WDA12 males.txt

tag: Sex


title: 12_4

description: WDA12 females.txt


title: Mutp53 (R175H)

description: Mutant p53 expressed


title: 12_2

description: WDA12 females.txt


title: 11_7

description: WDA11 females.txt

value: AAV8-control + WDA 8 weeks


title: 4T1-1 (circRNA-seq)


title: 12_9

description: WDA12 males.txt


title: pcDNA6A-Flag

description: Control vector

value: Control vector


title: 12_1

description: WDA12 females.txt


title: Mutp53 (L194F)

description: Mutant p53 expressed


title: 12_5

description: WDA12 males.txt


title: 12_11

description: WDA12 males.txt


title: Wtp53

description: Wild-type p53 expressed

value: Wild-type p53


title: 11_6

description: WDA11 females.txt


title: 11_5

description: WDA11 females.txt


title: 11_3

description: WDA11 females.txt

value: AAV8-CMV-Cre + WDA 8 weeks


title: 11_2

description: WDA11 females.txt


title: 11_20

description: WDA11 males.txt


title: 11_19

description: WDA11 males.txt


title: 11_21

description: WDA11 males.txt


title: 12_6

description: WDA12 males.txt


title: 11_18

description: WDA11 males.txt


title: 11_1

description: WDA11 females.txt


title: 11_17

description: WDA11 males.txt


title: 11_15

description: WDA11 females.txt

value: AAV8-TBG-Cre + WDA 8 weeks


title: 11_13

description: WDA11 females.txt


title: 11_16

description: WDA11 males.txt


title: HDM-specific, IgE sorted, Plasma cells,  Lung, biological replicate 2, scRNAseq

city: Tarrytown

first: Joseph

middle: Cooper

last: Devlin

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

description:
10x Genomics
HDM_barcodes.tsv.gz
HDM_features.tsv.gz
HDM_matrix.mtx.gz
HDM_bcr_table.csv.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The single cell-count matrix was filtered for by calculating the ratio of the total number of annotated genes divided by the log10 of the total number of UMIs counted. Cells with a gene to UMI ratio below about 0.1 were filtered out. Cells with more than four times the interquartile range of the total number of UMIs were filtered out. Cells with more than about 80% of reads map to a mitochondrial gene were filtered out. High quality cells with a gene to UMI ratio above about 0.1, with less than about four times the interquartile range of the total number of UMIs counted, and with less than 80% of reads mapping to a mitochondrial gene were retained. The count matrices from each individual sample capture were normalized to a total count of 10,000 and batch corrected using the Harmony algorithm to generate a combined uniform manifold approximation and projection (UMAP). Unsupervised clustering by the Leiden algorithm was then used to determine cell type clusters and a Wilcox test was used to identify specific cell type and cluster marker genes.
Assembly: GRCm38, GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
HDM mouse: For IgE TRAPnSeq, IgEVenus Blimp1mCherry mice were exposed to 50 mg of HDM extract (Greer) diluted in 20 mL of saline solution intranasally three times per week for 15 weeks. At the end of the experiment, bone marrow and lung draining lymph nodes were collected and processed. Draining lymph nodes were mashed on 12-well, 70-mm filter plates (Corning Costar) in RPMI 1640 media to generate single cell suspensions. For BM extraction, femurs were cut at both ends, placed in a PCR plate with holes punched at the bottom, and spun down for 3 min at 500g. RBC lysis was performed on single cell suspensions from draining lymph nodes and bone marrow. B cells and plasma cells were isolated using EasySep mouse pan-B cell isolation kit (STEMCELL, cat: 19844) by negative selection to remove unwanted cells (CD4, CD8, CD11c, CD49b, CD90.2, Ly-6C/G (Gr-1), TER119). Purified cells were processed and secretion trap was assembled as described in the previous paragraph. Secreted IgE was captured using StAv-ectoFceRIa for 1 h at 37_x0004_C with shaking at 400 rpm. Following IgE secretion trap, cells were washed and stained with an antibody mix containing B220 (RA3-6B2), CD138 (281-2), IgG1 (A85-1), IgE (R35-72), DUMP (IgM (II/41), IgD (11-26c.2a), TCRb (H57-597), Ly6G (1A8-Ly6g), CD49b (DX5), and CD11b (M1/70)) along with barcoded antigens (Der p1, Der p2, Der f1, and Ole e1). Finally, cells were labeled with DAPI before they were sorted on a BD Symphony S6.
Allergic human: Frozen human allergic and non-allergic BM mononuclear cells (BM MNCs) and matching donor sera were obtained from BioIVT. The allergy status of each donor sera was checked by ImmunoCAP (Phadia, Thermo Fisher Scientific) following the manufacturer’s instructions. Frozen BM MNCs were carefully thawed in complete RPMI media (with Penicillin-Streptomycin, Glutamine, 2-Mercaptoethanol, 10% Fetal Bovine Serum and Dnase I), washed 1x and rested at 37 for 1h. To obtain mononuclear cells from fresh allergic BM from STEMCELL, 80-120mL of BM aspirate was diluted 7:1 with PBS and 2mM EDTA and loaded onto Ficoll in SepMate tubes (STEMCELL). Samples were spun in SepMate tubes at 1200g for 20 min. The top layer of cells was removed, and cells were washed twice with autoMacs rinsing solution at 300g for 8 min. B cells and antibody secreting cells were isolated using magnetic bead depletion from single cell suspensions of allergic bone marrow cells according to manufacturer’s protocol. Human Pan-B cells were blocked using Fc Block (BD) for 15 to 30 min at 4_x0004_C, followed by incubation with antibody mix for 30 min at 4_x0004_C in PBS with 5% BSA. Antibodies mix included CD20 (2H7), CD38 (HB7), IgE (G7-26), IgD (IA6-2), IgM (MHM88), CD3 (UCHT1), CD11b (ICRF44), CD14 (M5E2), CD16 (3G8), and CD123 (7G3). Finally, cells were labeled with DAPI before they were sorted using BD Symphony.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Cells captured by secretion trap were suspended in PBS with 0.04% w/v BSA and loaded onto a Chromium® Controller device (10x Genomics) at 15,000 cells per lane. Partitions of the cells in barcoded beads were formed and the cells lysed. Reverse transcription was performed followed by breakdown of the partition. RNA-seq, Feature Barcode, and V(D)J libraries were prepared using a Chromium® Next GEM Single Cell 5’ Kit, v.2 (10x Genomics). After amplification of the libraries, cDNA was split into separate RNA-seq, Feature Barcode, and V(D)J aliquots. To enrich the V(D)J aliquot for BCR sequences, the Chromium® Automated Single Cell Mouse and Human BCR Amplification & Library Construction Kit (10x Genomics) was used. Feature Barcode libraries for DNA-barcoded Antigens or DNA-barcoded cell surface proteins were prepared using a Chromium® 5’ Feature Barcode Library Construction kit (10x Genomics). Paired-end sequencing was performed on an Illumina NovaSeq® 6000 sequencing system for RNA-seq, feature barcode, and V(D)J libraries. For RNA-seq and Feature Barcode libraries, the Cell Ranger Single-Cell Software Suite, version 6.1.1 (10x Genomics) was used to perform sample de-multiplexing, alignment, filtering, and UMI counting.

value: Plasma cells

value: lung

tag: age

value: 25 weeks


title: RING1B_ChIP_D6_Yaf2_knockout_rep2

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Adaptors and low-quality reads were trimmed with Trim_Galore.
For RYBP, YAF2, RING1B and H3K27ac ChIP-seq experiments, the trimmed reads were aligned to mouse mm10 genome using bowtie2 with parameter “--very-sensitive --end-to-end --no-unal”. For H2AK119ub and H3K27me3 ChIP-seq experiments, the trimmed reads were mapped to mm10 (mouse) and dm6 (drosophila melanogaster) reference genome using bowtie2 with parameters “--very-sensitive --end-to-end --no-unal --no-mixed --no-discordant”. For EZH2, JARID2 and MTF2 ChIP-seq, the trimmed reads were mapped to mm10 (mouse) and hg38 (human) reference genome using bowtie2 with the same parameters as above.
The mapped reads with the quality lower than 30 were filtered out. Duplicated reads were removed with sambamba. The reads overlapped with mouse mm10 blacklist regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists) were excluded.
For calibrated ChIP-seq (cChIP-seq), the reads mapped to mm10, dm6 or hg38 genome were extracted and calculated for calibration as previously described (Bonhoure et al., 2014).
The reads mapped to mm10 genome were used to identify peaks by MACS2 in broad mode with the default parameters. bamCoverage from deepTools was used to generate the normalized bigwig files with parameter “--normalizeUsing RPGC” for normal ChIP-seq and “--normalizeUsing RPGC --scaleFactor” for cChIP-seq.
For RING1B ChIP-seq, unique mapped reads for each sample were subsampled to 10 million, and replicates were subjected to Diffbind for differential binding analysis.
Assembly: mm10
Supplementary files format and content: Normalized bigWig and peak file for each sample.

source_name: 46C mESCs

growth_protocol: 46C Sox1-GFP mES cell lines were cultured on 0.2% gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) high-glucose medium containing 15% Fetal bovine serum, 1% Glutamax, 0.1 mM 2-mercaptoethanol, 1% Non-Essential Amino Acids, 1% Sodium Pyruvate, and 1000 U/ml leukemia inhibitory factor and the 2i inhibitors (3 μM CHIR99021 and 1 μM PD0325901).

extract_protocol:
107 cells were crosslinked with 1% formaldehyde at RT for 10 min and stopped by adding 0.125 M glycine. Crosslinked cells were lysed in ChIP SDS lysis buffer, then sonicated to achieve chromatin fragments sized of 200-400 bp.
ChIPed DNA was eluted using 200 μl freshly prepared elution buffer, reverse-crosslinked and purified using MinElute PCR Purification Kit. ChIP-seq libraries were constructed using VAHTS Universal V3 DNA Library Prep Kit for Illumina according to the manufacturer's instructions.

treatment_protocol: Rybp-/- and Yaf2-/- mESC lines were generated by using CRISPR/Cas9-mediated genome editing.

value: 46C mESCs

value: embryonic stem cells

value: Yaf2 knockout


title: HDM-specific, Plasma cells,  Bone Marrow, biological replicate 4, scRNAseq

source_name: bone marrow

value: bone marrow


title: HDM-specific, Plasma cells,  Bone Marrow, biological replicate 2, scRNAseq


title: RING1B_ChIP_D6_Yaf2_knockout_rep1


title: HDM-specific, Plasma cells,  Bone Marrow, biological replicate 5, scRNAseq


title: HDM-specific, Plasma cells,  Bone Marrow, biological replicate 1, scRNAseq


title: HDM-specific, IgE sorted, Plasma cells,  Bone Marrow, biological replicate 2, scRNAseq


title: HDM-specific, IgE sorted, Plasma cells,  Lymph Node, biological replicate 4, scRNAseq

source_name: lymph node

value: lymph node


title: HDM-specific, IgE sorted, Plasma cells,  Lymph Node, biological replicate 1, scRNAseq


title: HDM-specific, IgE sorted, Plasma cells,  Lymph Node, biological replicate 3, scRNAseq


title: HDM-specific, IgE sorted, Plasma cells,  Bone Marrow, biological replicate 4, scRNAseq


title: RING1B_ChIP_D6_Rybp_knockout_rep2

value: Rybp knockout


title: RING1B_ChIP_D6_Rybp_knockout_rep1


title: RING1B_ChIP_D6_wild_type_rep2

value: WT


title: RING1B_ChIP_D6_wild_type_rep1


title: RING1B_ChIP_D0_Yaf2_knockout_rep2


title: HDM-specific, IgE sorted, Plasma cells,  Bone Marrow, biological replicate 3, scRNAseq


title: HDM-specific, IgE sorted, Plasma cells,  Bone Marrow, biological replicate 1, scRNAseq


title: HDM-specific, Plasma cells,  Bone Marrow, biological replicate 6, scRNAseq


title: HDM-specific, Plasma cells,  Bone Marrow, biological replicate 3, scRNAseq


title: 11_14

description: WDA11 females.txt

value: liver

value: female

value: Kdm5b fl/fl


title: HDM-specific, IgE sorted, Plasma cells,  Lung, biological replicate 1, scRNAseq


title: HDM-specific, IgE sorted, Plasma cells,  Lymph Node, biological replicate 2, scRNAseq


title: RING1B_ChIP_D0_Yaf2_knockout_rep1


title: RING1B_ChIP_D0_Rybp_knockout_rep2


title: RING1B_ChIP_D0_Rybp_knockout_rep1


title: RING1B_ChIP_D0_wild_type_rep1


title: OT1 + wildtype  IL2-pos scTCR

city: Chicago

first: Jun

state: IL

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

data_processing:
The cellranger multi (10x Genomics, version 7.1.0) pipeline was used to jointly map and quantify the coupled single-cell RNA-seq (scRNA) and single-cell TCR-seq (scTCR) data for each sample. The reference genome and TCR pre-assembly reference were all based on mm10 and provided by 10X (refdata-gex-mm10-2020A for scRNA; refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0 for scTCR). The resultant clonotype and filtered contig annotation data for each sample were used for downstream analyses.
Assembly: mm10
Supplementary files format and content: 10x scRNA output raw counts (.mtx)
Supplementary files format and content: 10x scTCR output clonotypes (.csv)

source_name: Spleen

growth_protocol: T cell blasts were either pretreated with 1 μM TAPI-0 (Sigma, SML1292) (for TNF-α) or incubated with 10 μL IL-2 cytokine catch reagent (Miltenyi Biotec,130-090-491) (for IL-2). After being washed twice, 1% of labeled OT1 CD8+ T cells were added into the wild-type mouse splenocytes repertoire. OVA/H-2Kb pMHC functionalized hexapods were added to the T cells mixture and apply magnetic force. The mixture of hexapods and the T cell blasts were incubated in a cell culture incubator maintained at 37℃ and 5% CO2 to allow the secretion of cytokines.

extract_protocol:
NA
Fifteen-thousand sorted cytokine-positive CD8+ T cells (CD3+CD8+IL-2+ or CD3+CD8+TNFα+) were separately partitioned into droplets for single-cell omics assays via Chromium Next GEM Single-Cell 5’Kit v2 (10x Genomics, 1000263). RNA-seq libraries were prepared according to manufacturer protocols. TCR-seq libraries were prepared via the Chromium Single Cell Mouse TCR Amplification Kit (10x Genomics, 1000254). All sequencing libraries (RNA-seq, TCR-seq) were quantified via the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851), quality-checked for fragment sizes via high-sensitivity D5000 ScreenTapes (Agilent, 5067-5592), pooled, and sequenced (Illumina, Novaseq-6000).
paired scRNA-seq and scTCR-seq

treatment_protocol: Following 6 hours of incubation, the hexapod and cell mixtures were carefully washed with cold FACS buffer (PBS, 2% BSA, 0.05% sodium azide). Fc receptors were blocked with Mouse TruStain FcX (BioLegend, 156604) at 1:50 dilution for 5 minutes at 4℃. Then, cells were incubated for 30 minutes at 4°C in the dark with a staining solution containing BV421-labeled anti-mouse CD45 (clone: 30-F11, BioLegend,103133), BUV395-labeled anti-Mouse CD3ε (clone: 145-2C11, BD Biosciences, 563565), AF488-labeled anti-mouse CD8α (clone: 53-6.7, BioLegend, 100723) or AF488-labeled anti-mouse CD4 (clone: RM4-5, BioLegend, 100529), and PE-labeled anti-TNFα (clone: MP6-XT22, BioLegend, 506306) or mouse IL-2 detection antibody (Miltenyi Biotec,130-090-491) for activated CD8+ or CD4+ T-cell phenotyping and detection. Subsequently, stained cells were conjugated with LIVE/DEAD Fixable Near-IR viability dye (Invitrogen, L34975) at 1:1000 dilution in PBS for 15 minutes at 4°C. Finally, cells were washed three times in cold cell media (RPMI 1640, 10% FBS) before fluorescence-activated cell sorting (BD Biosciences, FACSAria Fusion).

value: Spleen

tag: target strain

tag: control strain

tag: subpopulation

value: IL-2 positive


title: OT1 + wildtype TNFa-pos scTCR

tag: cell type

value: TNF-alpha positive


title: 5CC7 + wildtype TNFa-pos scTCR


title: OT1 + wildtype TNFa-pos scRNA


title: RJ-4914

city: Shanghai

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

data_processing:
HiSeq 2500 instrument (Illumina) and single-end 50-bp read flow cells were used in this study
Sequenced reads were trimmed for adaptor sequence by trimmomatic(v0.36), then mapped to human genome(hg19) by Hisat2(V2.0.5), and counted by featureCounts(v1.5.2)
data was filterd under the standization that a gene expressed at least in 3 cells and a cells must express at leat 200 features
Assembly: hg19
Supplementary files format and content: txt file include raw count values for each cell

source_name: perianal fistula tissue of the patients with Crohn's disease

growth_protocol: tissues collected were transferred into pre-warmed DMEM medium containing 2 mg/ml collagenase P (Roche) and 10 U/µl DNase I (Roche).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We gently pipetted the mixture and then digested for 60 min at 37 °C to fully release single cells. The cell suspension solution was filtered and centrifuged. The pellet was resuspended and 2 mM ethylene diamine tetraacetic acid in phosphate-buffered saline. We employed fluorescence activated cell sorting (FACS) to ensure the living cell selections.

tag: prognosis

value: healed

tag: disease state

value: Crohn’s disease

value: perianal fistula


title: RJ-4918

value: unhealed


title: OT1 + wildtype IL2-pos scRNA


title: ATAC_D0_Rybp_knockout_rep1

data_processing:
Paired-ends reads were treated with trim_galore to remove adapters and low-quality reads, and then aligned to the mm10 by using bowtie2 with parameters “--very-sensitive --end-to-end --no-unal -X 2000”. The alignment files were further processed with sambamba to remove low quality mapped reads and duplicates. The reads overlapped with mouse mm10 blacklist regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists) were filtered out. Accessible regions were identified using MACS2 without control using the default parameters
The alignment files were further processed with sambamba to remove low quality mapped reads and duplicates. The reads overlapped with mouse mm10 blacklist regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists) were filtered out.
Accessible regions were identified using MACS2 without control using the default parameters.
Assembly: mm10
Supplementary files format and content: Normalized bigwig and peak file for each sample.

source_name: embryonic stem cells

extract_protocol:
DNAs were isolated using MinElute PCR Purification Kit.
ATAC-seq libraries were generated using TruePrep DNA Library Prep Kit V2 for Illumina and purified with AMPure XP beads.

treatment_protocol:
Rybp-/- mESC lines were generated by using CRISPR/Cas9-mediated genome editing.
Cells were dissociated and plated at a density of 1 × 104 cells/cm2 on Attachment Factor-coated plates in DMEM/F12 (1:1) medium supplemented with 0.5% N2, 1% B27, 1% non-essential amino acids, 1% glutamax, and 0.1 mM 2-mercaptoethanol. Fresh culture medium was changed every other day.

value: 46C mESCs

tag: genotype


title: input_ChIP_D0_Rybp_knockout

data_processing:
Adaptors and low-quality reads were trimmed with Trim_Galore.
For RYBP, YAF2 and H3K27ac ChIP-seq experiments, the trimmed reads were aligned to mouse mm10 genome using bowtie2 with parameter “--very-sensitive --end-to-end --no-unal”. For H2AK119ub and H3K27me3 ChIP-seq experiments, the trimmed reads were mapped to mm10 (mouse) and dm6 (drosophila melanogaster) reference genome using bowtie2 with parameters “--very-sensitive --end-to-end --no-unal --no-mixed --no-discordant”. For EZH2, JARID2 and MTF2 ChIP-seq, the trimmed reads were mapped to mm10 (mouse) and hg38 (human) reference genome using bowtie2 with the same parameters as above.
The mapped reads with the quality lower than 30 were filtered out. Duplicated reads were removed with sambamba. The reads overlapped with mouse mm10 blacklist regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists) were excluded.
For calibrated ChIP-seq (cChIP-seq), the reads mapped to mm10, dm6 or hg38 genome were extracted and calculated for calibration as previously described (Bonhoure et al., 2014).
The reads mapped to mm10 genome were used to identify peaks by MACS2 in broad mode with the default parameters.
bamCoverage from deepTools was used to generate the normalized bigwig files with parameter “--normalizeUsing RPGC” for normal ChIP-seq and “--normalizeUsing RPGC --scaleFactor” for cChIP-seq.
Assembly: mm10
Supplementary files format and content: Normalized bigWig and peak file for each sample.

value: embryonic stem cells

tag: chip antibody


title: input_ChIP_D6_Rybp_knockout

tag: cell line


title: input_ChIP_D6_Yaf2_knockout

value: Yaf2 knockout


title: ATAC_D0_Rybp_knockout_rep2


title: input_ChIP_D0_wild_type


title: input_ChIP_D0_Yaf2_knockout


title: input_ChIP_D6_wild_type


title: ATAC_D0_wild_type_rep1


title: RJ-4913


title: YAF2_ChIP_D6_Rybp_knockout


title: ATAC_D0_wild_type_rep2


title: YAF2_ChIP_D6_wild_type


title: 5CC7 + wildtype TNFa-pos scRNA


title: H3K27ac_ChIP_D0_wild_type


title: YAF2_ChIP_D0_wild_type


title: leaf, cenh3-4/WT, JZ336

city: Beijng

first: Jing

last: Wang

address: No. 2, Yard 1, Beichen West Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
For chromosome dosage plot analyses, 150 bp single reads were mapped to the Glycine max reference genome sequence (GCF_000004515.6_Glycine_max_v4.0) using BWA.
The software Control-FREEC (Version：11.5) was used to detect copy number variations (CNV). The window size set in this project is 50000bp, the sliding step size is 10000bp, the species chromosome ploidy is 2, and CNV detection and quantitative statistics are carried out for each sample.
This project used python for data processing, and uses python's matplotlib library for picture drawing: First, the data in the Ratio column is processed so that its maximum value is 3; secondly, the species analyzed in this project are diploid species, so the value of Ratio column is then multiplied by 2 to make its maximum value 6; lastly, plot a scatter plot using data: the X-axis is the starting position of the CNV quantity statistical area, and the Y-axis is the Ratio value.
Assembly: GCF_000004515.6_Glycine_max_v4.0
Supplementary files format and content: *.bam_ratio.txt includes ratios and predicted copy number alterations for each window
Library strategy: DNA-seq

organism: Glycine max

source_name: leaf

extract_protocol:
For library preparation of genome-resequencing, genomic DNA was prepared using a modified CTAB protocol. 1cm2 leaf tissue was stored at −80ºC before use. The tissue was ground in centrifuge tube cooled by liquid nitrogen using 0.5mm diameter small steel ball and tissue grinder at 30Hz for 15sec twice. The CTAB buffer was preheated to 65ºC in a water bath and 600μL hot CTAB buffer was added to dissolve tissue powder. After incubating at 65ºC for 30min, the liquid was short centrifuged and 500μL supernatant was moved to a clean centrifuge tube. 500μL chloroform: isoamyl alcohol (24:1) was added and mixed gently for 5min. The mixture was centrifuged for 20 min at 12000rpm and 400μL supernatant was taken out to mix with 270μL isopropanol and 30μL 3M sodium acetate (pH=5.6) in a clean centrifuge tube. After -20°C overnight, the liquid was centrifuged for 50 min at 12000rpm and the sediment was washed once using 800μL 70% ethanol. The dried sediment was dissolved with 100μL ddH2O and 1μL RNase was added to degrade RNA at 37 ºC for 1h. The solution was stored at −80ºC for library preparation.
2 μg of DNA were used for a PCR-free library preparation with a PCR-free protocol BGI-NGS-JK-DNA-003. Samples were subjected to quality control according to sample type and products requirements. Genomic DNA was randomly fragmented. The fragmented genomic DNA was selected to a certain average size. The fragments were subjected to end-repair and then was 3’ adenylated. And then adaptors were ligated to the ends of these 3’ adenylated fragments. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded adaptor ligation products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: leaf


title: RING1B_ChIP_D0_wild_type_rep2


title: leaf, cenh3-3/WT, JZ420


title: RYBP_ChIP_D6_Yaf2_knockout

value: RYBP


title: RJ-4911


title: RJ-4915


title: RJ-4916


title: H3K27ac_ChIP_D0_Rybp_knockout

value: Rybp knockout


title: RYBP_ChIP_D6_wild_type

value: WT


title: JARID2_ChIP_D0_wild_type


title: RJ-4909


title: JARID2_ChIP_D0_Rybp_knockout


title: RYBP_ChIP_D0_wild_type


title: MTF2_ChIP_D0_wild_type


title: leaf, WT, J


title: MTF2_ChIP_D0_Rybp_knockout


title: leaf, cenh3-1/cenh3-4, J308


title: RJ-4907


title: H3K27me3_ChIP_D6_Rybp_knockout


title: RJ-4910


title: RJ-4905


title: Sample t72

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

description: Glioblastoma grade 4

data_processing:
Base calling using Illumina CASAVA software
DRAGEN RNA Pipeline 3.7.5 (Illumina)
Assembly: Human GRCh38/hg38
Supplementary files format and content: tab-delimited text file with Ensembl ID and read counts for all the samples

source_name: Brain tumor

extract_protocol:
Total RNA from glioma tissues was extracted using TRI Reagent (Sigma-Aldrich), and the quality was determined using the Qubit RNA IQ Assay Kit in a Qubit 4 Fluorometer (Thermo Fisher) according to the manufacturers’ instructions. Only the RNA samples with integrity values > 6 were used for subsequent DNase treatment with the TURBO DNA-free Kit (Thermo Fisher) and retrotranscription into cDNA with the RevertAid First-Strand cDNA Synthesis Kit (Fermentas, Thermo Fisher).
The starting amount of total RNA was 100 ng following Illumina’s recommendations for preparing the sequencing library using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus.

value: Brain tumor


title: leaf, cenh3-3/cenh3-4, 523


title: EZH2_ChIP_D0_wild_type


title: RJ-4906


title: leaf, cenh3-1/cenh3-4, 609


title: H3K27me3_ChIP_D6_Yaf2_knockout


title: H3K27me3_ChIP_D6_wild_type


title: Sample t70

description: Glioblastoma grade 4


title: RJ-4908


title: H3K27me3_ChIP_D0_Rybp_knockout


title: H3K27me3_ChIP_D0_Yaf2_knockout


title: Sample t68

description: Glioblastoma grade 4


title: H3K27me3_ChIP_D0_wild_type


title: H2Aub_ChIP_D6_Yaf2_knockout


title: WR-3

city: Shenzhen

first: YINZHONG

last: MA

state: Guangdong

address: 1068 Xueyuan Avenue

department: Research Center for Protein and Cell-based Drugs

institute: Shenzhen Institutes of Advanced Technology，Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The neural stem cells were derived from hippocampus and subependymal regions of the brain of an embryonic C57BL/6 mouse at 12.5 days gestation. The cells were cultured (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in Mouse neural stem cell complete medium (cat# MUBNF -90011, Cyagen, China)

extract_protocol:
Cell were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three replicates were treated with 50 ng/ml of Wnt3a plus 50 ng/ml of Rspondin 1 for 24 hours

value: neural stem cell

value: embryo brain

tag: treatment


title: EZH2_ChIP_D0_Rybp_knockout


title: WR-1

source_name: derived from hippocampus and subependymal regions of the brain of an embryonic C57BL/6 mouse at 12.5 days gestation


title: Sample t56

description: Glioblastoma grade 4


title: Sample t62

description: Glioblastoma grade 4


title: MCF_12

city: RICHMOND

first: Shanwei

last: Shen

state: VA

address: 1101 E Marshall St

department: Pathology

institute: Virginia Commonwealth University

data_processing:
Raw FASTQ sequences were inspected for quality using the tool FastQC
Samples were aligned to the GRCh38 human soft masked primary assembly genome accessed at https://ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/dna/ using STAR aligner. Paired end 151bp reads were aligned with STAR version 2.7.9a. with default parameters. Alignment files (BAM files) were inspected for quality with the tool Qualimap. The featureCounts tool from the SourceForge Subread package (https://subread.sourceforge.net/) was used to generate the raw counts.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: human breast

growth_protocol: MCF10AT  cells were grown in were maintained in DMEM/F12 HEPES (11330032, Thermo Fisher Scientific) supplemented with following additives: 5% horse serum (16050122, Thermo Fisher Scientific), 0.5 mg/mL hydrocortisone (H0888, Sigma-Aldrich), 100 ng/mL cholera toxin (C8052, Sigma-Aldrich), 10 μg/mL insulin (I0516, Sigma-Aldrich), 100 µg/ml penicillin/streptomycin (15140122, Thermo Fisher Scientific), and 20 ng/mL EGF (PHG0311L, Thermo Fisher Scientific). For serum starvation studies, DMEM/F-12 was supplemented with 0.1% bovine serum albumin

extract_protocol:
After treatment, cells were washed with 37 °C PBS and mRNA was isolated RNA was extracted in phenol: chloroform: isoamyl alcohol followed by ethanol precipitation. DNA was removed by DNase I treatment.
mRNA library was prepared by polyA selection with ≥500 ng RNA using the Universal Plus mRNA-Seq Library Preparation Kit (NuGEN) following manufacturer’s protocol.

treatment_protocol: Following 24 hour serum starvation, (DMEM/F12 supplemented with 0.1% BSA), three biological replicates were treated with PRL (250 ng/ml) for two hours.

value: human breast

value: epithelial cell

value: hPRLrL/hPRLrI I-tail deleted

value: treated with PRL for 2 hours


title: Control-3

value: untreated


title: H2Aub_ChIP_D6_wild_type


title: H2Aub_ChIP_D6_Rybp_knockout


title: H2Aub_ChIP_D0_Yaf2_knockout


title: Sample t60

description: Glioblastoma grade 4


title: WR-2


title: H2Aub_ChIP_D0_wild_type


title: H2Aub_ChIP_D0_Rybp_knockout


title: Sample t54

description: Glioblastoma grade 4


title: Control-2


title: RNAseq_D6_Rybp_knockout_rep2

data_processing:
The raw paired end reads were trimmed using Trim_Galore, then mapped and quantified to mouse mm10 genome with STAR-RSEM pipeline using RSEM.
Transcript-level counts were collapsed to gene-level counts using tximport, and differential gene expression was analyzed with DESeq2. Genes with fold change larger than 2 and q-value less than 0.05 were considered as differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include normalized count values from DESeq2.

extract_protocol:
Total RNAs were extracted with RaPure Total RNA Micro Kit.
In brief, 500 ng of total RNAs were used for RNA-seq library construction. Poly(A)-containing mRNAs were isolated by poly(A) selection beads and further reverse transcribed to cDNAs. cDNAs were ligated with adapters, amplified by PCR and purified with AMPure XP beads to obtain the final sequencing library.RNA sequencing libraries were constructed using a VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina according to the manufacturer's instructions.

treatment_protocol:
Rybp-/- and Yaf2-/- mESC lines were generated by using CRISPR/Cas9-mediated genome editing.
Cells were dissociated and plated at a density of 1 × 104 cells/cm2 on Attachment Factor-coated plates in DMEM/F12 (1:1) medium supplemented with 0.5% N2, 1% B27, 1% Non-Essential Amino Acids, 1% Glutamax, and 0.1 mM 2-mercaptoethanol. Fresh culture medium was changed every other day.

value: neural differentiation

tag: time

value: Day 6


title: MCF_8


title: MCF_10

value: hPRLrL/hPRLrI


title: Sample t53

description: Glioblastoma grade 4


title: RNAseq_D6_Yaf2_knockout_rep1

value: 46C mESCs

value: embryonic stem cells


title: Control-1

tag: strain


title: MCF_9


title: Sample t65

description: Glioblastoma grade 4


title: Sample t50

description: Glioblastoma grade 4


title: ZHX2_3

city: WuHan

first: 思源

last: 樊

state: HuBei

address: Address: No.13, Hangkong Road, Wuhan, Hubei, P.R.

institute: Huazhong University of Science and Technology

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 data were mapped to the reference genome of rat from https://ftp.ensembl.org/pub/ 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).
RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and a fold-change cutoff of 1 were used to judge the statistical significance of gene expression differences.
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: Primary VSMCs

growth_protocol: The cells were subsequently cultured in SMCM medium and cultured in a humidified atmosphere containing 5% CO2 at 37°C

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO15596026) following the methods by Chomczynski et al. 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 QubitTMRNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTMStranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer's instruction. PCR products corresponding to 200-500 bps were enriched.

treatment_protocol: After being treated by Ad-Control or Ad-ZHX2 and PDGF-BB 20mg/ml for 24h，cells were used for extracting total RNA.

value: Primary VSMCs

value: ZHX2 overexpression


title: Sample t49

description: Glioblastoma grade 4


title: MCF_11


title: RNAseq_D6_Yaf2_knockout_rep2

value: Yaf2 knockout


title: RNAseq_D6_Rybp_knockout_rep1

value: Rybp knockout


title: Allergic human, Plasma cells, Bone Marrow

description:
10x Genomics
Human_allergic_BM_barcodes.tsv.gz
Human_allergic_BM_features.tsv.gz
Human_allergic_BM_matrix.mtx.gz
Human_allergic_BM_bcr_table.csv.gz

value: Plasma cells

value: bone marrow


title: ZHX2_2


title: RNAseq_D6_wild_type_rep2

value: WT


title: ZHX2_1


title: MCF_6

value: human breast


title: MCF_7

value: epithelial cell


title: MCF_5


title: Control_3

value: Control

value: Ad-Control


title: RNAseq_D3_Yaf2_knockout_rep2

value: Day 3


title: Sample t48

description: Glioblastoma grade 4

value: Brain tumor


title: Sample t45

description: Glioblastoma grade 4


title: RNAseq_D6_wild_type_rep1

value: neural differentiation

value: Day 6


title: Control_2


title: MCF_4

value: hPRLrL/hPRLrI I-tail deleted

value: treated with PRL for 2 hours


title: Sample t40

description: Glioblastoma grade 4


title: Control_1

value: Primary VSMCs


title: ZHX2_Input

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 mapped to the reference genome of rat from https://ftp.ensembl.org/pub/ using STAR software (version 2.5.3a) with default parameters.
The RSeQC (version 2.6) was used for read distribution analysis.
The MACS2 software (Version 2.1.1) was used for peak calling.
Assembly: rn6
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
The tissue was collected and frozen in liquid nitrogen. The cells were treated with cell lysis buffer, and the nucleus was collected by centrifuging at 2000g for 5 min. The nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA. The 10% lysis sonicated chromatin was stored as "input", and 90% was used in immunoprecipitation reactions with anti-ZHX2 antibody (Proteintech, 20136-1-AP) named "IP". The DNA of input and IP was extracted by the phenol-chloroform method.
The high-throughput DNA sequencing libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Catalog NO. ND607, Vazyme). The library products corresponding to 200-500 bps were enriched.

treatment_protocol: The tissue/cell was fixed in 1% formaldehyde for 10 min at room temperature, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction.


title: Sample t39

description: Glioblastoma grade 4


title: RNAseq_D3_Rybp_knockout_rep2

value: 46C mESCs

value: embryonic stem cells


title: Sample t29

description: Astrocytoma grade II


title: ZHX2_IP


title: MCF_2

value: hPRLrL/hPRLrI


title: RNAseq_D3_Rybp_knockout_rep1

value: Rybp knockout


title: RNAseq_D3_wild_type_rep2


title: RW3

description: Under OGD and normoxia condition, cells were treated with 100ng/ml of Wnt3a plus 50ng/ml of Rspondin 1

source_name: brain

growth_protocol: Cortical neurons were cultured from E19 embryo brains of Sprague Dawley rats. In brief, after digested by 2 mg/ml papain (cat. #LS003126, Worthington) at 37°C for 30 min, the dissociated cells were suspended in Neurbasal-A (cat. #10888022, Thermo Fisher) culture medium containing 1% Glutamax (cat. #35050061, Thermo Fisher) and 2% B27 supplement (cat. #A3653401, Thermo Fisher). These cells were plated onto 6-well plates at a cell density of 5 x 105/well

treatment_protocol: Three replicates were Wnt3a+Rspondin1 treated for 24 hours.

value: brain

value: cortical neurons

value: primary neuron

value: Sprague Dawley

tag: developmental stage

value: Under OGD and normoxia condition, cells were treated with Wnt3a plus Rspondin 1


title: RNAseq_D3_wild_type_rep1

value: WT


title: MCF_1

tag: tissue

value: human breast

value: epithelial cell

value: untreated


title: Sample t38

description: Glioblastoma grade 4

value: Brain tumor


title: MCF_3

value: hPRLrL/hPRLrI I-tail deleted


title: RW1


title: RW2


title: snRNA-seq of LAND-treated glioblastoma nuclei with 10x Multiome (DEFND-seq RNA library) - PTO037

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
snRNA-seq data were processed as described previously [Yuan and Sims, Scientific Reports, 2016]. The code is available at (https://github.com/simslab/DropSeqPipeline8). Briefly, we aligned the transcriptomic reads (read 2) to the human or mouse genome and transcriptome annotation using STAR v2.7.0d [Dobin et al, Bioinformatics, 2013]. For human data sets other than the mixed species experiment, we used GRCh38/Gencode v24. For the mixed species data set, we used a concatenated genome and annotation comprised of GRCh38/Gencode v32 and GRCm38/Gencode vM23. Because we are analyzing nuclei that contain a significant amount of unspliced mRNA, we identified reads that uniquely and strand-specifically aligned to the entire gene body of each gene (including exons, introns, intron-exon junctions, and exon-exon junctions), assigning an address to each aligned read containing the gene name, cell-identifying barcode sequence, and unique molecular identifier (UMI) extracted from read 1. Next, we demultiplexed the resulting table, correcting sequencing errors in the barcodes as described in Yuan and Sims [Yuan and Sims, Scientific Reports, 2016] to produce a count matrix for each sample.
snDNA-seq and snATAC-seq data were processed using a custom pipeline available here (https://github.com/simslab/dna10x). The pipeline attempts to mimic some of the basic data processing procedures that are implemented in the 10x Genomics Cell Ranger software packages for analysis of snATAC-seq and Multiome data, including the formatting of output files. We generated sample-demultiplexed fastq files using the mkfastq command in cellranger-atac v2.0.0 (10x Genomics). We aligned paired-end reads 1 and 2 to the human or mouse genome using bwa mem v0.7.17-r1188 [Li, arXiv, 2013] after removing a standard adapter sequence (CTGTCTCTTATACACATCT) from each read using cutadapt v2.8 [Martin, EMBnet.journal, 17, 1, 2011].  We then extracted all reads with an alignment score that was >90% of the read length and insert size <1 kb. We also implemented an error correction procedure for the cell-identifying barcodes from read 3. Briefly, for cell-identifying barcodes that do not appear in the standard list provided by 10x Genomics, we first determine the frequency falt of each barcode in the standard list in the data set. For each observed barcode sequence that has a Hamming distance of one from a sequence on the standard list, we estimate the posterior probability palt that the barcode deviates from the standard list due to sequencing error using the quality scores for the putatively errant base provided by Illumina or Element palt = falt10-q/10 where q is the quality score. If palt>0.975 for any alternative barcodes, then we replace the errant barcode with the alternative barcode from the standard list with the highest value of palt. Finally, we establish read addresses for each alignment that passes the filter described above comprised of a cell-identifying barcode, chromosome, a fragment start position, a fragment end position and collapse identical fragments. Finally, we sort the fragments by alignment position on the genome and output a table in the format of the “fragments.tsv” file that is typically produced by Cell Ranger.
Assembly: human-only libraries: GRCh38/Gencode v24; human/mouse mixture: GRCm38/Gencode vM23/GRCh38/Gencode v32
Supplementary files format and content: gzip-compressed, tab-delimited file containing the scRNA-seq count matrix where each row is a gene (labeled by a gene ID and gene symbol) and each column is a cell (with a header containing the cell-identifying barcode and cluster number)

source_name: glioblastoma tissue

growth_protocol: 3T3 cells (ATCC #CRL-1658) and U87 MG cells (ATCC #HTB-14) were cultured in Dulbecco's Modified Eagle's Medium (ATCC #30-2002) supplemented with 10% feline bovine serum (FBS, ThermoFisher # A3160401). Eagle’s Minimum Essential Medium (ATCC #30-2003) was used to culture BJ cells (ATCC CRL-2522). TrypLE Express Enzyme (ThermoFisher #12605010) was used for dissociating cells during cell passages .

extract_protocol:
snATAC-seq: Nuclei were prepared from cryopreserved BJ fibroblasts. Frozen cells were thawed and added to a Dounce homogenizer containing 1 mL of nuclei isolation buffer (NIB: 10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal (Millipore Sigma #18896), and 1 x protease inhibitors (Millipore Sigma #118735800001)). The sample was gently homogenized on ice with 5 strokes of the loose pestle and 5 strokes of the tight pestle. The cells were transferred to a conical and 5 mL of PBS (Gibco #10010-031) was added. The sample was spun down at 500 g for 5 minutes, washed with 10 mL of PBS and resuspended in 100 µL of 10x Genomics Nuclei Buffer (10x Genomics, #2000207).  xSDS snDNA-seq: Nuclei that were cross-linked and then treated with sodium dodecyl sulfate (SDS) to remove nucleosomes (xSDS) were prepared following Adey et al. Briefly, BJ fibroblasts were washed with 10 mL of PBS and covered in 3 mL of TrypLE (ThermoFisher #12605028) for 10 minutes at 37 °C. Then 9 mL of media was added, quenching the dissociation, and cells were spun down. The cells were resuspended in 10 mL of media with 406 µL of 37% formaldehyde (Millipore Sigma #252549) and gently rotated at room temperature for 10 minutes. 2.5 M glycine (800 µL) was then added and the suspension was incubated on ice for 5 minutes. Cells were centrifuged at 500 g for 8 minutes and washed with 10 mL of PBS. 5 mL of NIB was added to the pellet and the suspension was incubated for 20 minutes at 4 °C under rotation. Cells were then spun down at 500 g for 5 minutes and washed with 900 µL of NEBuffer 2.1 (New England Biolabs #B7202). The cells were pelleted (500 g for 5 minutes) and resuspended in NEBuffer 2.1 with 12 µL of 20% SDS. The solution was placed in a gentleMACS and vigorously shaken at 42 °C for 30 minutes. 200 µL of 10 % Triton-X (Millipore Sigma #T8787) was added and the cells were again shaken at 42 °C for 30 minutes.  LAND snDNA-seq/DEFND-seq: The LAND protocol for adherent cells using 10x reagents was adapted from the LAND protocol. BJ fibroblasts were first washed with 10 mL of PBS and dissociated with 3 mL of TrypLE for 10 minutes at 37 C. Media (9 mL) was used to quench the dissociation reaction and collect the cells. The cells were spun down (300 g for 5 minutes) and 200 µL of DEFND buffer (175 µL NIB, 10 µL 1 mg/mL protease inhibitor (Millipore Sigma #11429868001), 25 µL 100 mM lithium diiodosalicylate (Millipore Sigma #653-14-5)), was added and incubated on ice for 5 minutes. Immediately following this incubation, 10 mL of nuclei isolation buffer was added and the nuclei were centrifuged at 4 °C for 5 minutes at 500 g. The supernatant was removed and 100 µL of 10x Genomics Nuclei Buffer. A fraction of nuclei was stained with SYBR green and counted on a Countess with a GFP filter set.  GBM Cryopreserved Tissue DEFND-seq: A cryopreserved IDH wildtype Grade IV GBM sample was obtained from excess material collected for clinical purposes from de-identified brain tumor specimens. Nuclei were prepared from this anonymous sample according to XXXXX . Frozen tissue was placed in a Dounce homogenizer containing 1 mL of homogenization buffer (HB: 1 µM DTT, 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM tris, 1x protease inhibitor, 0.4 U/µL RNAse, 0.2 U/µL SUPERase In) and subjected to 15 strokes using the loose piston and 15 strokes using the tight piston. The homogenate was divided into 5 volumes and each was strained twice. The filtered homogenate was combined into a tube and centrifuged at 1000 g for 10 minutes at 4 °C. The pellet was resuspended in 1000 µL of HB and strained with 4 strainers (250 µL of homogenate for each strainer). The strained homogenate was again combined into a tube and centrifuged at 1000 g for 10 minutes at 4 °C. The pellet was resuspended in 250 µL of HB to which 250 µL of 50% iodixanol dilution media (IDM: 250 mM sucrose, 150 mM KCl, 30 mM MgCl2, 60 mM tris) was added resulting in a 25% IDM/nuclei suspension. This suspension was carefully layered on top of a tube containing 50% IDM at the bottom and 29% IDM at the surface, and centrifuged at 18,000 g for 23 minutes at 4 C. The nuclei formed a white pellet or sheet in the middle of the tube between the layers. All solution around this pellet was removed – first from the top and then from the bottom, and the pellet was resuspended in 1 mL of chilled PBS and centrifuged (500 g for 5 minutes at 4 °C). The supernatant was removed and the pellet was then treated with DEFND buffer for 5 minutes on ice. Immediately following this incubation, 5 mL of NIB with RNAse inhibitors was added at the nuclei were centrifuged at 500 g for 5 minutes at 4 °C.
snATAC-seq: Single-cell ATAC libraries were prepared with these nuclei using the 10x Genomics Single Cell ATAC kit (10x Genomics #1000176, #1000162, and #1000212) according to the manufacturer’s protocol. xSDS snDNA-seq: The cells were pelleted (500 g for 5 minutes) and resuspended in 100 µL of 10x Genomics Nuclei Buffer, counted, and tagmented following the Chromium Single Cell ATAC protocol. Tagmented nuclei were loaded onto a 10x Chromoium controller and libraries were prepared according to the Chromimum Single Cell ATAC protocol (10x Genomics #1000176, #1000162, and #1000212). LAND snDNA-seq: Nuclei were then tagmented and prepared for single-cell sequencing with the Chromium Single Cell ATAC kit (10x Genomics #1000176, #1000162, and #1000212) and protocol. DEFND-seq: Nuclei were then tagmented and prepared for single-cell sequencing with the Chromium Single Cell Multiome kit (10x Genomics #1000285, #1000230, #1000215).
DEFND-seq/10x Multiome (snRNA/DNA-seq), snATAC-seq, snDNA-seq

value: glioblastoma tissue


title: MuSC rep2, Pax7CreERT2/+::Yapflox/floxTazflox/flox:: Rosa-YFP, 48 hrs

first: Anwen

last: Shao

address: 3520 San Martin Drive

department: Department of Embryology

institute: Carnegie Instituition for Science

description:
YapTaz cKO_biol rep2
YAPTAZ_cKO_3_48_GTTTCG

data_processing:
Illumnia's bcll2fastq/2.20.0 was used to generate Fastq files with default parameters.
RNA-seq reads were mapped to mm9 genome using HISAT/2.2.1. Then the alignments were processed through Stringtie/1.3.5 to assemble and quantify the transcripts for each sample. Samtools/1.10 and Htseq/0.10.0 to get the raw counts. Differentially expressed gene (DEG) analysis was performed with DESeq2.
Assembly: mm9
Supplementary files format and content: tab-delimited text files
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: hindlimb muscles

growth_protocol: FACS isolated SCs were cultured on Matrigel-coated plates in growth medium (DMEM with 20% FBS, 5% horse serum, 1% pen-strep, 1% glutamax, 0.1% chick embryo extract and 2 ng/mL FGF2).

extract_protocol:
Growth medium was removed and TriZol was directly added to the SCs. Direct-zol RNA Miniprep Kits (Zymo) were used for RNA purification.
Total RNA was subjected to rRNA depletion using Ribo-Zero rRNA Removal Kit (illumina) and libraries were generated using the TruSeq RNA Library Prep Kit according to illumina manual.

value: hindlimb muscles

value: muscle stem cells

value: YapTaz knockout

value: dish-cultured for 48 hrs


title: MuSC rep1, Pax7CreERT2/+::Yapflox/floxTazflox/flox:: Rosa-YFP, 48 hrs

description:
YapTaz cKO_biol rep1
YAPTAZ_cKO_2_48_GTGAAA


title: DNAJC12, VEC3

city: Chengdu

first: MENGJIA

last: SHEN

address: 37 Guoxue Alley

institute: West China School of Medicine/West China Hospital of Sichuan University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include readcount and FPKM values for each Sample

value: Breast cancer cells

value: MDA-MB-231 transfected with empty vector

value: control


title: RNAseq_D0_Yaf2_knockout_rep2

value: 46C mESCs

value: embryonic stem cells

value: Yaf2 knockout

value: neural differentiation

value: Day 0


title: V3

description: Cells were moved into a Hypoxia Incubator Chamber (cat. #27310, Stem Cell Technologies) contained 1% O2 with Neurobasal-A Medium without D-glucose and sodium pyruvate (cat. #A2477501, Thermo Fisher) for 4.5 hr and then returned to normoxia condition with regular medium mentioned below.

value: brain

value: cortical neurons

value: primary neuron

value: Sprague Dawley

value: OGD and normoxia


title: RNAseq_D0_Yaf2_knockout_rep1


title: MuSC rep1, Pax7CreERT2/+::Amotflox/flox:: Rosa-YFP, 48 hrs

description:
Amot cKO_biol rep1
Ag_cko_1_48_CGTACG

value: hindlimb muscles

value: Amot knockout


title: V2


title: RNAseq_D3_Yaf2_knockout_rep1

value: Day 3


title: DNAJC12, VEC1


title: MuSC rep2, Pax7CreERT2/+::Mpp7flox/flox:: Rosa-YFP, 48 hrs

description:
Mpp7 cKO_biol rep2
Mpp7_cko_3_48_GTGGCC

value: muscle stem cells

value: Mpp7 knockout

value: dish-cultured for 48 hrs


title: RNAseq_D0_Rybp_knockout_rep2

value: Rybp knockout


title: V1


title: DNAJC12, OE3

value: Breast cancer cells

value: MDA-MB-231 transfected with DNAJC12v

value: DNAJC12 overexpression


title: MuSC rep1, Pax7CreERT2/+::Mpp7flox/flox:: Rosa-YFP, 48 hrs

description:
Mpp7 cKO_biol rep1
Mpp7_cko_2_48_AGTTCC


title: RNAseq_D0_Rybp_knockout_rep1

value: 46C mESCs

value: embryonic stem cells

value: neural differentiation


title: MuSC rep2, Pax7CreERT2/+:: Rosa-YFP, 48 hrs

description:
Con_biol rep2
Y3_48_TAGCTT

value: Control


title: C3

description: untreated

value: brain

value: cortical neurons

value: primary neuron

value: untreated


title: RNAseq_D0_wild_type_rep2

value: WT

value: Day 0


title: DNAJC12, OE2


title: DNAJC12, OE1


title: C2

description: untreated

value: Sprague Dawley


title: MuSC rep1, Pax7CreERT2/+:: Rosa-YFP, 48 hrs

description:
Con_biol rep1
Y2_48_ACTTGA

value: hindlimb muscles

value: muscle stem cells


title: RNAseq_D0_wild_type_rep1


title: C1

description: untreated


title: DNAJC12, VEC2

value: MDA-MB-231 transfected with empty vector

value: control


title: MuSC rep2, Pax7CreERT2/+::Amotflox/flox:: Rosa-YFP, 48 hrs

description:
Amot cKO_biol rep2
Ag_cko_2_48h_GAGTGG

value: Amot knockout

value: dish-cultured for 48 hrs


title: MAPK1_IP-1

status: Public on Oct 06 2023

city: Changchun

first: yue

last: wang

address: 2699 Qianjin Street

institute: Jilin University

data_processing:
The libraries were created following the manufacturer's instructions and used with the Illumina NovaSeq 6000 system for 150 nt paired-end sequencing in high-throughput sequencing.
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
ChIP-seq reads were aligned to the GRCh38 genome using Bowtie2. Only uniquely mapping reads with at most four mismatches were retained.
We utilized model-based analysis for ChIP-seq version 1.4 to find the binding locations of MAPK1
The peaks' locations in relation to the transcription start site (TSS) were assigned using DeepTools
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: AGS cells

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, sonication of cell lysates resulted in DNA fragments of 200-500 bp being centrifuged at   403 12,000g for 10 min.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit. 10 ng of DNA was used as starting material for input and ip samples.

value: AGS cells

value: IP


title: MAPK1_IP-2


title: input-1

value: input


title: C73_B1_VISIUM

city: Toronto

first: Diana

last: Nakib

state: ON

address: 101 College Street

institute: University of Toronto

description: Spatial transcriptomics on OCT-embedded tissue

data_processing:
*library strategy: Spatial transcriptomics
Reads were QCed, mapped, and UMIs were quantilfied using cell-ranger (v3).
Viable cells were identified using EmptyDrops (v1.2.0), and ambient RNA was removed using SoupX (v1.2.2) with known markers
Feature selection, and dimensionality reduction was done with Seurat (v3)
Samples were integrated using Harmony (v1.0), and clustered using Seurat (v3)
Clusters were manually annotated.
Assembly: GRCh38-2020-A transcriptome
supplementary files format and content:
barcodes.tsv.gz: list of spatial barcodes (raw feature matrix)
features.tsv.gz: list of gene IDs (raw feature matrix)
matrix.mtx.gz: gene expression count data in Matrix Market Exchange format (raw feature matrix)
aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
detected_tissue_image.jpg.gz: image of tissue and spots
scalefactors_json.json.gz: scalefactors in json format
tissue_hires_image.png.gz: hires image of tissue
tissue_lowres_image.png.gz: low-res image of tissue
tissue_positions_list.cv.gz: list of spatial barcodes and the coordinates specifying spots
GEX_Merged.tif: higher resolution tif of tissue slice
metrix_summary.csv: summary of key sample metrics

molecule: cytoplasmic RNA

source_name: Adult Liver

extract_protocol:
Tissue was prepared for Visium Spatial transcriptomics as previously described (https://doi.org/10.1002/hep4.1854)]. Briefly, liver tissue was embedded in OCT media, frozen, and cryosectioned with 16-um thickness at -10ºC (cryostar NX70 HOMP). Sections were placed on a chilled Visium Tissue Optimization Slide (10x Genomics) and processed following the Visium Spatial Gene Expression User Guide. Tissue was permeabilized for 12 minutes, based on an initial optimizations trial. Libraries were prepared according to the Visium Spatial Gene Expression User Guide and samples sequenced on a NovaSeq 6000.
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Adult Liver

value: M


title: siMAPK1_2

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by Bowtie2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The edgeR package version 3.18.1 (R Bioconductor package), which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC>1.5 or <0.67) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the SUVA pipeline described previously . The frequency and proportion of reads of SUVA AS events (pSAR) were calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: MAPK1 knockdown in AGS cell


title: C73_D1_VISIUM


title: NC_3

value: AGS cell(control plasmid)


title: NC_2