title: rbESC_R1T2S2

description: 2x150bp reads


title: HEK293, no drug, RNAseq, rep2 [ND2.RNA]

status: Public on Jan 19 2025

type: SRA

city: Durham

first: Nikoleta

middle: G

last: Tsvetanova

state: NC

address: 308 Research Drive

department: Pharmacology & Cancer Biology

country: USA

institute: Duke University

description:
Novogene
MK2

library_source: transcriptomic

data_processing:
Samples were trimmed with BBDuk (BBMap version #38.63) to remove adaptors.
Sequences aligning to ncRNA, tRNA, and rRNA were removed using Bowtie (version 2.3.5)
Cleaned files were aligned to the Genome Reference Consortium Human Build 38 (GRCh38) using STARaligner (version 2.7.5)
FeatureCounts (Subread version 1.6.3) was used to align and quantify coding sequences, with RPF reads being narrowed to reads of length 26 to 34 nucleotides.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of raw reads for each Sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS. For the experiment, cells were cultured in DMEM without FBS

extract_protocol:
All samples were lysed in Riboseq lysis buffer (20 mM Tris, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100ug/mL cyclohexamide, 25 u/mL DNase I). RNAseq samples were purified with Qiagen RNeasy Plus Mini Kit. Ribo-seq samples were purified on Zymo-Spin IIC columns, then ribosome protected fragments were size-selected on 15% TBE-Urea gels. rRNA for Ribo-seq samples was depleted with Galen Molecular Human riboPOOL for Ribosome Profiling RNA kit.
RNAseq samples were prepared the NEBNext Ultra II RNA Library Prep Kit for Illumina. Riboseq samples were prepared with NEBNext Multiplex Small RNA Library Prep Kit for Illumina

treatment_protocol: 20 minutes of DMSO or 30uM Dyngo, then 2 hours of 1 uM isoproterenol or left untreated

tag: cell line

tag: cell type

value: Human embryonic kidney cell

tag: genotype

value: WT

tag: treatment

value: DMSO, no drug


title: rbESC_R2T2

city: München

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description: 2x150bp reads

data_processing:
Reads were mapped to the appropriate reference genome using STAR
Internal fragments and 5' transcript ends were distinguished using a custom python script available on github. For smart-seq2 and smart-seq2-polyA libraries, reads were not seperated by 5' or internal fragments and all reads were processed together
BigWig files were generated from unique mapping reads, rRNA removed and rpm normalized, using bedtools and ucsc bedGraphToBigWig
TEs and genes were quantified from unique and multimapping reads from 5' fragments using TEtranscript
For more information see (gitlab link)
Assembly: GRCm38 (Mus musculus), Sscrofa11.1 (Sus scrofa), Btau_5.0.1 (Bos taurus), OryCun2.0 (Oryctolagus cuniculus), Mmul_8.0.1 (Macaca mulatta)
Supplementary files format and content: merged bigWig files, 2 files per species/stage seperated for 5' fragments ("FivePrime") and internal fragments ("Else")
Supplementary files format and content: table txt file containing gene and TE counts for each species using 5' fragments (Smart-seq+5') or all fragments (Smart-seq2)

molecule: total RNA

organism: Oryctolagus cuniculus

source_name: rabbit embryonic stem cells

growth_protocol:
Oocyte and preimplantation stages were collected from mouse, pig, cow, rabbit and rhesus.
Stem cells were cultured in appropriate medium and collected at least 48hr since last cell split. rbESC were seperated from feeder cells by FACS using the Oct4-GFP marker. For more information see methods of accompaning paper

extract_protocol:
For each library a single embryo from was used originating from the listed species and developmental stage. For stem cells, RNA was extracted using the ReliaPrep kit. 250pg was used as input for the Smart-seq+5 protocol. For more information see methods of accompaning paper
An adapted version of Smart-seq2 (called Smart-seq+5') was used to capture both 5' transcript information as well as internal transcript fragments. For Smart-seq2 libraries (SS2), embryos were processed as described in published protocol (Picelli et. al. 2014). For Smart-seq2-polyA libraries (SS2-PA), an additional polyadenylation step was preformed at the start of the protocol. See methods of accompaning paper for more information
Smart-seq+5'

treatment_protocol: Mouse and rabbit embryos were collected after natural mating. Pig, cow and rhesus embryos were harvested by IVF. For more information see methods of accompaning paper

tag: tissue

value: rabbit embryonic stem cells


title: JJ012-Ant-2

status: Public on Jan 18 2025

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

description:
Library name: Sample 4
Column name in all.fpkm_anno.xls: JJ012-Antcin-K-2_count & JJ012-Antcin-K-2_FPKM

data_processing:
To remove technical sequences (e.g., adapters, PCR primers) and bases with quality scores below 20, fastq data passing the filter were processed with Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, N proportion: 0.1) to obtain high-quality clean data.
First, reference genome sequences and gene model annotations for relevant species were downloaded from genome websites like UCSC, NCBI, and ENSEMBL. Next, Hisat2 (v2.2.1) was used to index the reference genome. Finally, clean data were aligned to the reference genome using Hisat2 (v2.2.1).
First, transcripts in fasta format were generated from the known GFF annotation file and properly indexed. Then, using this file as the reference, HTSeq (v0.6.1) estimated gene and isoform expression levels from the paired-end clean data.
Assembly: hg38
Supplementary files format and content: xls file include raw counts and FPKM values for each Sample

source_name: Bone

growth_protocol: The JJ012 cells were cultured 50%/50% in a Dulbecco’s Modified Eagle Medium (DMEM)/alpha-minimum essential medium (α-MEM) medium, 10% fetal bovine serum (FBS) and antibiotics then maintained in a humidified incubator at 37 °C in 5% CO2

extract_protocol:
RNA was haversted using TRIzol reagent
Libraries with different indices were multiplexed and sequenced on an Illumina NovaSeq 6000 instrument using a 2×150 paired-end (PE) configuration per the manufacturer’s instructions.

treatment_protocol: Chondrosarcoma cell line JJ012 was treated with Antcin K (10 μM) for 24 h in the culture medium.

value: Bone

value: cancer cell

value: Antcin K


title: JJ012-Ant-1

description:
Library name: Sample 3
Column name in all.fpkm_anno.xls: JJ012-Antcin-K-1_count & JJ012-Antcin-K-1_FPKM


title: rbESC_R2T1

description: 2x150bp reads


title: HEK293, Iso, RNAseq, rep1 [ISO1.RNA]

description:
Novogene
MK4

value: DMSO, 1uM Isoproterenol (2 hr)


title: HEK293, no drug, RNAseq, rep1 [ND1.RNA]

description:
Novogene
MK1


title: PC3 cells, ST6GAL1 OE, biol rep 3

city: Newcastle upon Tyne

first: Jennifer

last: Munkley

state: Tyne & Wear

address: International Centre for Life

country: United Kingdom

institute: Newcastle University

description:
Library name: Sample 6
6-OE3-PC3-ST6GAL1
PC3_ST6GAL1_OE_Counts.txt

data_processing:
Analysis was conducted in Galaxy version 22.01
Quality control was performed with FastQC
Reads were quantified using featureCounts
Differential gene expression analysis was performed with limma-voom
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of raw read counts for each sample

source_name: Prostate cancer

extract_protocol:
RNEasy Kit following manufacturer's protocol (Qiagen)
TruSeq Stranded mRNA Sequencing Library Prep Kit following manufacturer's protocols.

value: Prostate cancer

value: ST6GAL1 overexpression


title: JJ012-2

description:
Library name: Sample 2
Column name in all.fpkm_anno.xls: control-JJ012-2_count & control-JJ012-2_FPKM

value: non


title: OS cell lines-143B NC1

city: shanghai

first: tao

last: zhang

address: 650 new songjiang road

country: China

institute: Department of Orthopedics,Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using HISAT2 soft
HTSeq statistics were used to compare the Read Count value of each gene as the original expression level of the gene, and the expression level was standardized by the number of fragments per million from a gene per thousand base length (FPKM).
We adopt DESeq for differences in gene expression analysis, screening of differentially expressed genes conditions as follows: the expression differences multiples | log2FoldChange | > 1, significant P - value < 0.05.  The differential genes were analyzed by ggploT2 and Pheatmap, and the protein network interaction was mapped by Cytoscape.
Genome_build: Ensembl Homo_sapiens（102.38）
Supplementary_files_format_and_content: The Expression file provides the normalized Expression data (FPKM) for each sample
Supplementary_files_format_and_content: The DESeq file provided the differential expression multiple and P value of each gene in different comparison groups.

source_name: osteosarcoma

extract_protocol:
Total RNA of Cells was isolated using the Trizol Reagent (Invitrogen Life Technologies) and quantified in a NanoDrop (ThermoFisher). 3 μg of total RNA were used for the RNA sample preparations. Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was sequenced on a Hiseq platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd.
Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

value: osteosarcoma cell line

value: Targeting NC-shRNA

tag: cell  line


title: PC3 cells, ST6GAL1 OE, biol rep 2

description:
Library name: Sample 5
5-OE2-PC3-ST6GAL1
PC3_ST6GAL1_OE_Counts.txt


title: JJ012-1

description:
Library name: Sample 1
Column name in all.fpkm_anno.xls: control-JJ012-1_count & control-JJ012-1_FPKM


title: Lacrimal Gland, Csk(CKO) and WT pooled. scRNAseq

city: New york

first: Xin

last: Zhang

state: New york

department: Ophthalmology

institute: Columbia University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The barcoding, demultiplexing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest). The normalized gene x cell matrix was used as input for the Seurat package. Cells with <200 or > 4000 genes, as well as those exhibiting >15% expression of mitochondrial genes, were filtered out prior to dataset normalization and scaling. Dimensionality reduction was achieved through Principal Component Analysis (PCA) and non-linearly with Uniform Manifold Approximation and Projection (UMAP) with dimensions = 1:20. Following the integration of control and mutant datasets through canonical correlation analysis (CCA), clustering was performed using “RunUMAP” and annotated based on known marker genes. Differential gene expression testing was conducted using the “FindMarkers” and “FindAllMarkers” functions in Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

organism: Mus musculus

source_name: Whole lacrimal gland

extract_protocol:
Lacrimal glands obtained from P1 pups underwent a PBS wash for 2-5 minutes and were digested with dispase (2000 units/ml) and papain (20 units/ml) for 30 minutes at room temperature. After gently removing the digestion enzyme mixture, the glands were washed with PBS and mechanically disrupted through vigorous pipetting until single-cell dispersion was observed under the microscope. They were pelleted with three washes in PBS and centrifugation at 3000 rpm at  4°C.
Control and CskCKO mutant cells were treated with cell multiplexing oligos (CMO) in 24 accordance with the 10x Genomics 3’ cellplex kit manual. The cells were then pooled together in a single collection tube for library preparation and subsequent sequencing at Columbia University's single-cell sequencing core.

value: Whole lacrimal gland

tag: age

value: Postnatal Day 2

value: Csk(CKO) and WT combined


title: PC3 cells, OEControl, biol rep 1

description:
Library name: Sample 1
1-C1-PC3
PC3_ST6GAL1_OE_Counts.txt

value: Lenti-ORF control


title: PC3 cells, OEControl, biol rep 3

description:
Library name: Sample 3
3-C3-PC3
PC3_ST6GAL1_OE_Counts.txt


title: PC3 cells, ST6GAL1 OE, biol rep 1

description:
Library name: Sample 4
4-OE1-PC3-ST6GAL1
PC3_ST6GAL1_OE_Counts.txt


title: Normal-eGFR IgAN2

city: Zhengzhou

first: Junpeng

last: You

state: Henan

address: No.1, Jianshe Road, Erqi District

department: Department of Nephrology

institute: The First Affiliated Hospital of Zhengzhou University

description:
Library name: Sample5
10x Genomics

data_processing:
Cell Ranger software (7.0.0) was downloaded from the 10x Genomics website. Alignment, filtering, barcode counting, and UMI counting were performed using the cellranger count module to generate the feature-barcode matrix and identify cell clusters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Kidney biopsy tissue

extract_protocol:
Single-cell libraries were prepared using the 10x Genomics Single Cell 3' Library and Gel Bead Kit V3 (Catalog #1000075) and the Chromium Single Cell B Chip Kit (Catalog #1000074). The cell suspension, containing 300-600 viable cells per microliter (quantified using Count Star), was loaded onto the Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion, following the manufacturer's protocol. Briefly, cells were resuspended in PBS with 0.04% BSA, and approximately 16,000 cells were added to each channel, with an expected recovery of around 8,000 cells. Captured cells were lysed, and the released RNA was barcoded during reverse transcription within individual GEMs. Reverse transcription was performed on a Bio-Rad S1000™ Touch Thermal Cycler at 53°C for 45 minutes, followed by 85°C for 5 minutes, with a final hold at 4°C. The cDNA was then generated, amplified, and assessed for quality using the Agilent 4200 (analysis performed by CapitalBio Technology, Beijing).
Single-cell RNA-seq libraries were constructed using the Single Cell 3' Library and Gel Bead Kit V3 (10x Genomics), according to the manufacturer’s instructions. The libraries were then sequenced on an Illumina NovaSeq 6000 with a sequencing depth of at least 20,000 reads per cell, using a paired-end 150 bp (PE150) read strategy (performed by CapitalBio Technology, Beijing).

value: Kidney biopsy tissue

tag: diagnosis

value: IgA nephropathy (IgAN)


title: Low-eGFR IgAN2

description:
Library name: Sample2
10x Genomics


title: Normal-eGFR IgAN1

description:
Library name: Sample4
10x Genomics


title: Low-eGFR IgAN3

description:
Library name: Sample3
10x Genomics


title: rbESC_R1T2

description: 2x150bp reads


title: primary tumor, rep1

city: Beijing

first: haoran

last: Huang

state: Beijing Municipality

address: Peking Union Medical College Hospital (East), No.1 Shuaifuyuan,Wangfujing, Dongcheng District

institute: Peking Union Medical College Hospital

data_processing:
Cell Ranger pipeline was applied for sample demultiplexing of sequencing results, barcode processing, read alignment, filtering of estimated droplets, and the generation of gene/barcode matrices.
Assembly: GRCh38
Supplementary files format and content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively
Supplementary files format and content: matrix.mtx: Filtered gene-barcode matrix file

source_name: pancreas

growth_protocol: Primary pancreatic tumors and paired liver metastases

extract_protocol:
Pancreatic and liver tumor samples were excised and mechanically dissociated into single cells using pancreatic digestive enzymes. the cell suspension (300–600 living cells/L, confirmed by Count Star) were loaded onto the Chromium single-cell controller (10x Genomics) using the Single Cell 3' GEM, Library & Gel Bead Kit V3.1 (10x Genomics, California, USA) and Chromium Single Cell B Chip Kit (10x Genomics, California, USA).
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V2 following the manufacture’s introduction. Finally sequencing was performed on an Illumina Novaseq6000 with a sequencing depth of at least 100,000 reads per cell and pair end 150bp (PE150).

treatment_protocol: Three patients diagnosed with PC and LM at Peking Union Medical College Hospital (PUMCH) were enrolled in this study, which strictly followed the guidelines of the Ethics Committee of PUMCH (ethical approval number, 1-22PJ138). All patients did not receive any antitumor therapy before surgery, and all provided written informed consent for sample collection and data analysis. All patients were in good physical condition and underwent surgery. All patients and their family have a strong desire for surgery. All patients had limited liver metastases, less than three, with low metastatic load, and tumor marker CA199 less than 1000U/ml.

value: pancreas


title: Low-eGFR IgAN1

description:
Library name: Sample1
10x Genomics


title: ABBV-075_1000nM

city: New York

first: Shipra

last: Shukla

state: NY

address: 417 East 68th Street

institute: MSKCC

data_processing:
RNA sequencing reads werealigned to human genome assembly hg20 with STAR v2.6 using default parameters.
RPKM values were generated using default parameters
Assembly: hg20
Supplementary files format and content: RPKM values

source_name: Prostate

growth_protocol: MSK-PCa17 cells were grown in matrigel in previously defined media (PMID: 25201530)

extract_protocol:
RNA was extracted using trizole
RNA-seq was performed by MSKCC genomics core facility using poly-A capture

treatment_protocol: Organoids were treated with increasing doses of ABBV-075 for 4 hours

value: Prostate

value: prostate cancer organoid


title: primary tumor,spatial transcriptome

description: Library name: 220857C_PC_3_SP

data_processing:
Space Ranger pipeline was applied for sample demultiplexing of sequencing results, barcode processing, read alignment, filtering of estimated droplets, and the generation of gene/barcode matrices.
Assembly: GRCh38
Supplementary files format and content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively
Supplementary files format and content: matrix.mtx: Filtered gene-barcode matrix file

extract_protocol:
Tissue sections were generated from the collected patients’ samples and tested on the machine after determining the morphology.
Spatial RNA-seq data from two 10X Visium capture areas, in which each contained 5,000 barcoded spots, were first processed by Space Ranger analysis software.


title: liver metastasis,spatial transcriptome

description: Library name: 220857C_LM_3_SP

source_name: liver

value: liver


title: ABBV-075_10nM


title: HNF4G_BRD4_DMSO

library_source: genomic

data_processing:
The sequenced reads from fastq files were mapped to hg19 using Bowtie 2.0
Peaks were called using MACS2. Downstream analysis were performed using Homer.
Assembly: hg19
Supplementary files format and content: narrowPeak

molecule: genomic DNA

growth_protocol: Cells were grown in RPMI medium with 10% FBS

extract_protocol:
Chromatin was isolated and sheared. Following antibody was used; anti-BRD4 (Bethyl laboratories, A301-985A100)
Purified ChIP DNA was blunt-ended, ligated to adaptors, amplified with 8-12-cycles of PCR, and sequenced.

treatment_protocol: Cells were treated with either ABBV-075 (25 nM)  or DMSO control for 4 hours.

value: Human Prostate cancer

tag: chip antibody

value: DMSO


title: primary tumor, rep2


title: liver metastasis, rep3


title: PC3 cells, OEControl, biol rep 2

description:
Library name: Sample 2
2-C2-PC3
PC3_ST6GAL1_OE_Counts.txt

value: Prostate cancer


title: Normal-eGFR IgAN3

description:
Library name: Sample6
10x Genomics


title: GFP_BRD4_DMSO


title: ABBV-075_1nM


title: ABBV-075_100nM


title: liver metastasis, rep2


title: 22Rv1-HNF4G-DMSO-1

data_processing:
RNA sequencing reads werealigned to human genome assembly hg20 with STAR v2.6 using default parameters.
Assembly: hg20
Supplementary files format and content: Normalized counts in an excel file

extract_protocol:
RNA was harvested using Trizol reagent and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq was performed by MSKCC genomics core facility using poly-A capture

treatment_protocol: Cells were treated with either ABBV-075 (25 nM)  or DMSO control for 24 hours.


title: DMSO


title: 22Rv1-HNF4G-ABBV-075-2


title: HNF4G_BRD4_ABBV-075

value: ABBV-075 (25 nM X 4 hrs)


title: GFP_BRD4_ABBV-075


title: 22Rv1-HNF4G-ABBV-075-1


title: 22Rv1-GFP-ABBV-075-2


title: 22Rv1-HNF4G-DMSO-2


title: 22Rv1-GFP-ABBV-075-1


title: primary tumor, rep3


title: 22Rv1-GFP-DMSO-2


title: FSTD8_20

city: California

first: Natalia

middle: Faraj

last: Murad

state: CA

address: 500 Parnassus Ave

department: HemOnc

institute: University of California, San Francisco

description:
Library name: Sample 40
Column name in counts.csv file: FSTD8_20

data_processing:
Paired-end clean reads were aligned to the reference genome Felis_catus_9.0 using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p380 was used to count the reads numbers mapped to each gene.
Assembly: Felis_catus_9.0
Supplementary files format and content: tab delimited file including raw counts for each sample

organism: Felis catus

source_name: oral cavity

extract_protocol:
RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research) according to the manufacturer’s modified protocol for “RNA purification from the aqueous phase after Tri Reagent extraction”.
Tumor samples were crushed in liquid nitrogen, mixed with 500µL Trizol, and further lysed using a bead mill. Chloroform (100 µL) was added to the lysate, mixed well, and the mixture subjected to centrifugation. The aqueous phase was removed, mixed with an equal volume of 100% ethanol and added to a Zymo-Spin IICR column. After centrifugation and a quick wash, on-column DNA digestion was performed, followed by additional washes. Total RNA was eluted with 50 µL of RNAse/DNAse-free water and 1 µg was submitted to Novogene Co. for quality testing, library prep, and sequencing.

value: oral cavity

value: mucosal surface

value: tumor

tag: time

value: Day 8

tag: batch


title: liver metastasis, rep1


title: FSTD8_19

description:
Library name: Sample 39
Column name in counts.csv file: FSTD8_19

growth_protocol: Tumor samples were crushed in liquid nitrogen, mixed with 500µL Trizol, and further lysed using a bead mill


title: FSTD8_18

description:
Library name: Sample 38
Column name in counts.csv file: FSTD8_18


title: FSTD8_17

description:
Library name: Sample 37
Column name in counts.csv file: FSTD8_17


title: FSTD8_16

description:
Library name: Sample 36
Column name in counts.csv file: FSTD8_16


title: 22Rv1-GFP-DMSO-1


title: FSTD8_15

description:
Library name: Sample 35
Column name in counts.csv file: FSTD8_15


title: Pelabresib+Enza 1

description: Sample_35CR_CPI0610-Enz_23.disambiguatedSorted_hg20.bam

data_processing:
RNA sequencing reads werealigned to human genome assembly hg20 with STAR v2.6 using default parameters.
RNA-Seq alignments were assembled into potential transcripts using StringTie
Assembly: hg20
Supplementary files format and content: Gene count matrix in an excel file

source_name: Prostate cancer PDX

growth_protocol: CB17 male SCID mice (Charles River) were castrated and, 2 weeks after castration, were implanted with tumor bits of LuCaP 35CR.

extract_protocol:
To isolate RNA from xenograft tumor explants, the tumor samples were ground in 1 ml Trizol (Invitogen) using a PowerGen homogenizer (Fisher Scientific), followed by the addition of 200 µL chloroform. The samples were then centrifuged at 10,000 g for 15 minutes. The upper phase was mixed with an equal volume of 70% ethanol, and the RNA was further purified using the E.Z.N.A total RNA kit (Omega).
RNA-seq was performed by MSKCC genomics core facility using poly-A capture

treatment_protocol: When tumors exceeded 100 mm3, animals were randomized to control and treatment groups (n = 3 per group).

value: Prostate cancer PDX

value: LuCaP 35CR

value: CB17 SCID

value: Pelabresib+enza


title: Pelabresib+Enza 2

description: Sample_35CR_CPI0610-Enz_12.disambiguatedSorted_hg20


title: FSTD8_12

description:
Library name: Sample 32
Column name in counts.csv file: FSTD8_12


title: FSTD8_13

description:
Library name: Sample 33
Column name in counts.csv file: FSTD8_13


title: Pelabresib 1

description: Sample_35CR_CPI0610_1.disambiguatedSorted_hg20

value: Pelabresib


title: Pelabresib 3

description: Sample_35CR_CPI0610_21.disambiguatedSorted_hg20


title: Pelabresib+Enza 3

description: Sample_35CR_CPI0610-Enz_8.disambiguatedSorted_hg20


title: FSTD8_11

description:
Library name: Sample 31
Column name in counts.csv file: FSTD8_11


title: Pelabresib 2

description: Sample_35CR_CPI0610_6.disambiguatedSorted_hg20


title: Enzalutamide 1

description: Sample_35CR_Enz_14.disambiguatedSorted_hg20

value: Enzalutamide


title: Enzalutamide 2

description: Sample_35CR_Enz_16.disambiguatedSorted_hg20


title: FSTD8_8

description:
Library name: Sample 28
Column name in counts.csv file: FSTD8_8


title: Vehicle 3

description: Sample_35CR_VEH_27.disambiguatedSorted_hg20

value: Vehicle


title: Vehicle 2

description: Sample_35CR_VEH_15.disambiguatedSorted_hg20


title: FSTD8_4

description:
Library name: Sample 24
Column name in counts.csv file: FSTD8_4


title: LuCaP 70CR tumors, Vehicle replicate 2

description: 10x Genomics

data_processing:
Reads obtained from the 10x Genomics scRNAseq platform were mapped to human and mouse combined genome (GRCh38 + mm10) using Cell Ranger (10X Genomics). True cells were distinguished from empty droplets using scCB2 package (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02054-8). Cells were removed if they had less than 2000 total counts, more than 60,000 total counts, less than 100 total genes, or greater than 20% mitochondrial reads. Genes detected in less than 20 cells and all mitochondrial genes were removed for subsequent analyses. Putative doublets were removed using the Doublet Detection package
To visualize single cells of the global atlas, we used Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP). Cell types were determined using a combination of marker genes identified from the literature and gene ontology for cell types using the web-based tool Panglao DB (https://panglaodb.se/)
Differentially expressed genes between different clusters were found using MAST package (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0844-5)
Assembly: GRCh38 + mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PDX

extract_protocol:
SCID mice were euthanized and PDX tumors were harvested after vehicle or pelabresib treatment (n=2 mice for each condition). The tumors were dissociated into single-cell suspension using the tumor dissociation kit (Miltenyi Biotec, 130-095-929) following the manufacturer’s protocol.
Cells were directly processed with 10X genomics Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 according to manufacturer’s specifications. For each sample, 200 million reads were acquired on NovaSeq platform S4 flow cell.

value: PDX

value: LuCaP 70CR

value: 6 Days


title: FSTD8_5

description:
Library name: Sample 25
Column name in counts.csv file: FSTD8_5


title: FSTD8_7

description:
Library name: Sample 27
Column name in counts.csv file: FSTD8_7


title: Vehicle 1

description: Sample_35CR_VEH_13.disambiguatedSorted_hg20


title: FSTD8_14

description:
Library name: Sample 34
Column name in counts.csv file: FSTD8_14


title: LuCaP 70CR tumors, Vehicle replicate 1

description: 10x Genomics


title: FSTD8_3

description:
Library name: Sample 23
Column name in counts.csv file: FSTD8_3


title: LuCaP 70CR tumors, Pelabresib replicate 2

description: 10x Genomics


title: LuCaP 70CR tumors, Pelabresib replicate 1

description: 10x Genomics


title: FSTD8_1

description:
Library name: Sample 21
Column name in counts.csv file: FSTD8_1


title: Enzalutamide 3

description: Sample_35CR_Enz_30.disambiguatedSorted_hg20


title: LuCap 77CR_Pelabresib+Enzalutamide 1

data_processing:
RNA sequencing reads werealigned to human genome assembly hg20 with STAR v2.6 using default parameters.
Transcripts per million (TPM) data were generated via TPMCalculator  using default parameters
Assembly: hg20
Supplementary files format and content: Transcript per million in an excel file

growth_protocol: CB17 male SCID mice (Charles River) were castrated and, 2 weeks after castration, were implanted with tumor bits of LuCaP 70CR.

treatment_protocol: When tumors exceeded 100 mm3, animals were randomized to control and treatment groups (n = 3–6 per group). Treatment with enzalutamide (50 mg/kg, once a day), pelabresib (30 mg/Kg, twice daily), enazalutamide and pelabresib combination or vehicle was begun at a tumor size of 100 mm3. Mice were treated until the end of the experiments.

value: LuCaP 77CR


title: FSTD1_19

description:
Library name: Sample 19
Column name in counts.csv file: FSTD1_19

value: pre-treatment

value: Day 1


title: FSTD8_2

description:
Library name: Sample 22
Column name in counts.csv file: FSTD8_2

value: oral cavity


title: LuCap 77CR_Pelabresib 2

value: Prostate cancer


title: FSTD8_9

description:
Library name: Sample 29
Column name in counts.csv file: FSTD8_9

value: mucosal surface

value: tumor


title: FSTD1_16

description:
Library name: Sample 16
Column name in counts.csv file: FSTD1_16


title: FSTD1_15

description:
Library name: Sample 15
Column name in counts.csv file: FSTD1_15


title: FSTD1_18

description:
Library name: Sample 18
Column name in counts.csv file: FSTD1_18


title: FSTD1_20

description:
Library name: Sample 20
Column name in counts.csv file: FSTD1_20


title: LuCap 77CR_Pelabresib 1

value: Prostate cancer PDX


title: LuCap 77CR_Enzalutamide 2


title: LuCap 77CR_Enzalutamide 1


title: FSTD1_14

description:
Library name: Sample 14
Column name in counts.csv file: FSTD1_14


title: LuCap 77CR_Vehicle 1


title: LuCap 77CR_Vehicle 2


title: FSTD1_12

description:
Library name: Sample 12
Column name in counts.csv file: FSTD1_12


title: FSTD1_13

description:
Library name: Sample 13
Column name in counts.csv file: FSTD1_13


title: FSTD1_11

description:
Library name: Sample 11
Column name in counts.csv file: FSTD1_11


title: PD WT Sample4

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

description:
PD_WT_Sample-4
Raw_Counts.txt

data_processing:
Raw reads for RNAseq samples were quality trimmed using cutadapt (v3.4) and aligned using STAR (v2.5.4b).
Aligned reads were quantified using featureCounts (v1.4.6-p4) from the subreads package.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file containing raw counts for each sample

source_name: PD iPSC

growth_protocol: Stem cells were mainatined in mTeSR media on Vitronectin coated cultureware.

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit according to the manufacturer's instructions(Takara Bio)
RNA-seq library preparation was performed using the KAPA RNA HyperPrep Kit with RiboErase (Roche) per the manufacturer’s instructions.

value: cortical interneurons

value: PD iPSC

tag: passage

tag: timepoint

value: PD WT


title: PD WT Sample2

description:
PD_WT_Sample-2
Raw_Counts.txt


title: FSTD1_17

description:
Library name: Sample 17
Column name in counts.csv file: FSTD1_17


title: PD WT Sample3

description:
PD_WT_Sample-3
Raw_Counts.txt


title: FSTD1_7

description:
Library name: Sample 7
Column name in counts.csv file: FSTD1_7


title: CR_Smad23_2

city: Ithaca

first: Megan

last: Rothstein

address: 526 Campus Road Rm 433

institute: Cornell University

data_processing:
library strategy: CUT&RUN
Demultiplexing, bcl2fastq
Trimming, CutAapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25
Alignment, bowtie2 v2.4.2, “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000
Filtering, samtools v1.10 view "-f 2 -F 780 -bh", sort, index
Peak calling, SEACR v1.3 "0.005 non stringent"
Generate bigwigs, bamCoverage "--outFileFormat bigwig --binSize 5 --normalizeUsing RPKM"
Genome_build: UCSC galGal6
Supplementary_files_format_and_content: .bigwig files displaying read coverage across the genome

organism: Gallus gallus

source_name: chicken HH9 cranial neural fold dissections

growth_protocol: Fertilized chicken embryos (Leghorn White) were incubated at 37℃ until they reached the desired developmental stage

extract_protocol:
Neural fold dissections were performed on HH9/HH14 embryos to obtain cranial/trunk neural crest cells (10 embryos/20 neural folds per experiment). Cells were dissociated in Accumax (Innovative Cell Technologies, AM105) cell dissociation solution for 20 min at RT under mild agitation. CUT&RUN experiments were performed as previously described (Skene and Henikoff, 2017).
CUT&RUN libraries were prepared using the NEBNext ultra II DNA library prep kit (New England Biolabs E7645) according to the kit's protocol.

tag: breed

value: Leghorn White

tag: developmental stage

tag: tissue/cell type

value: cranial/trunk neural crest cells

tag: tag


title: FSTD1_5

description:
Library name: Sample 5
Column name in counts.csv file: FSTD1_5


title: LuCap 77CR_Pelabresib+Enzalutamide 2

tag: cell line

value: CB17 SCID

value: Pelabresib+enza


title: FSTD1_9

description:
Library name: Sample 9
Column name in counts.csv file: FSTD1_9

tag: cell type


title: FSTD1_10

description:
Library name: Sample 10
Column name in counts.csv file: FSTD1_10

tag: genotype


title: CR_Smad23_1


title: CAP-LPS 3

first: Zijing

last: Liu

address: Fengtai District, #20 East St.

institute: Beijing Institute of Biotechnology

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions.
Clean data were obtained by removing reads containing adapters, reads containing ploy-N sequences and low-quality reads from the raw data.
Hisat2 tools soft were used to map with reference genome.
Gene expression levels were quantified as fragments per kilobase of transcript per million fragments mapped. Genes with an adjusted P- value < 0.01 and a fold change ≥ 2 according to DESeq2 were considered differentially expressed.
Assembly: Mus_musculus GRCm38
Supplementary files format and content: Matrix file of expression levels of all genes (number of comparison fragments)

source_name: spleen

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies).
A total of 1 μg of RNA per sample was used for RNA sample preparation. Sequencing libraries were generated using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology) following the manufacturer’s instructions, and index codes were added to attribute sequences to each sample.

value: spleen

tag: strain

value: 8 weeks

value: wild type

tag: treatment

value: CAP is injected s.c. into the nape 30 min before LPS administration


title: FSTD1_4

description:
Library name: Sample 4
Column name in counts.csv file: FSTD1_4

tag: tissue

value: pre-treatment

value: Day 1


title: PD S707QfsX56 Clone2 Sample4

description:
PD_S707QfsX56-Clone2_Sample-4
Raw_Counts.txt

value: PD S707QfsX56


title: CAP-LPS 2

tag: age


title: PD WT Sample1

description:
PD_WT_Sample-1
Raw_Counts.txt


title: FSTD1_3

description:
Library name: Sample 3
Column name in counts.csv file: FSTD1_3

value: oral cavity

value: mucosal surface


title: FSTD1_8

description:
Library name: Sample 8
Column name in counts.csv file: FSTD1_8

value: tumor


title: FSTD1_2

description:
Library name: Sample 2
Column name in counts.csv file: FSTD1_2


title: CAP-LPS 1


title: FSTD1_1

description:
Library name: Sample 1
Column name in counts.csv file: FSTD1_1


title: LPS 3

value: LPS is injected i.p.


title: ST rep 2

city: Toronto

first: Kai

middle: Howson

last: Ellis

state: ON

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description:
Library name: Sample 11
ST_2

data_processing:
Differentially expressed mRNA transcripts analysis were completed by Novogene Co. LTD. Briefly, clean reads were obtained by removing reads containing adapters, greater than 10% unidentifiable bases, and low quality reads (Qscore of over 50% bases £ 5). Clean reads were mapped to a reference genome using HISAT2.
Assembly: Hg38
Supplementary files format and content: CSV file containing a raw counts matrix

growth_protocol: Human umbilical vein endothelial cells (HUVECs; ECs, LONZA) were cultured in Endothelial Cell Medium (ECM, ScienCell) supplemented with 5% Fetal Bovine Serum (FBS) and Endothelial Cell Growth Supplement (ScienCell). ECs were detached using Trypsin-EDTA (0.25%) and used at passages 5-7. THP1 monocytes were cultured in RPMI 1640 medium (WISENT) with 10% FBS (WISENT).

extract_protocol:
RNA was isolated using TRIzolTM Reagent from THP1 cells (mono-culture and co-culture) after LPS stimulation according to the manufacturer’s instructions. RNA concentration and quality was measured using the Agilent 2100 Bioanalyzer (Total RNA Pico Chip).
Preparation of RNA library and mRNA sequencing was completed by Novogene Co. LTD (Sacramento, CA, USA) using the Illumina NovaSeq X Plus Series (PE150) Sequencing System of samples meeting minimum input requirements [amount ≥ 200 ng, RIN>8, purity (A260/280 ≥ 1.8, A260/230 ≥ 1.8)].

treatment_protocol: For co-culture experiments, ECs were seeded in 10 cm plates +/- DMSO, Etoposide, or Etoposide + EGCG. Cells were collected, washed and counted before co-culture experiments. ECs were then plated onto 6-well plates (500,000 cells/well) and cultured in complete ECM for 2h to allow to adherence. After 2h, THP1 cells (400,000 cells/well) were seeded in the upper chamber of transwell membrane inserts (1 µm pore size selected to ensure passage of whole secretome, STERLITECH), and co-cultured with control ECs, or senescent ECs (senECs) or EGCG-treated senECs in complete ECM. THP1 cells were grown in complete ECM without ECs (mono-culture) as a control. Following 24h of mono-culture or co-culture, THP1 cells were removed and stimulated with 100 ng/ml LPS (Sigma-Aldrich) for 2h.

value: human leukemia monocytic cell line

value: WT

value: Co-culture with normal EGCG-treated senescent endothelial cells

value: 24 Hours


title: LPS 2


title: PD S707QfsX56 Clone2 Sample2

description:
PD_S707QfsX56-Clone2_Sample-2
Raw_Counts.txt

value: cortical interneurons

value: PD iPSC


title: ST rep 1

description:
Library name: Sample 10
ST_1


title: ST rep 5

description:
Library name: Sample 12
ST_5


title: PD S707QfsX56 Clone1 Sample4

description:
PD_S707QfsX56-Clone1_Sample-4
Raw_Counts.txt


title: SEN rep 5

description:
Library name: Sample 9
SEN_5

value: Co-culture with normal senescent endothelial cells


title: SEN rep 1

description:
Library name: Sample 7
SEN_1


title: LPS 1

value: spleen

value: 8 weeks


title: PD S707QfsX56 Clone2 Sample1

description:
PD_S707QfsX56-Clone2_Sample-1
Raw_Counts.txt


title: SEN rep 2

description:
Library name: Sample 8
SEN_2


title: CAP 3

value: wild type

value: CAP is injected s.c. into the nape


title: CAP 2


title: PD S707QfsX56 Clone1 Sample3

description:
PD_S707QfsX56-Clone1_Sample-3
Raw_Counts.txt


title: CAP 1


title: NT rep 1

description:
Library name: Sample 4
NT_1

value: Co-culture with normal endothelial cells


title: knock down NC,biol rep 2

city: Zhuhai

first: lixin

last: Tai

address: Hengqin

institute: University of Macau

description:
Library name: Sample8
Column name in fpkm_All_sample.txt: NC_2

data_processing:
the data were subjected to QC analyses using the FastQC tool. The reads were further mapped to the human genome (hg38) using the spliced read aligner bowtie2, Version 2.4.4. Unique gene hit counts were calculated by using feature Counts v2.0.3.
Assembly: hg38
Supplementary files format and content: .txt formate,  fpkm_All_sample.txt file contain all fpkm counts of each sample

source_name: Breast; Mammary gland

growth_protocol: MCF-7 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
MCF-7 cells were transfected with TRIM28, CtBP1/2, Ctrl(NC) siRNA for 2days using Lipofectamin 3000 Transfection Reagent according to the product manual. RNA was extracted using the RNEasy Plus Micro kit (Qiagen, 74034). 1μg of total RNA was used to prepare libarary construction.
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Beijing, China) using standard Illumina protocols.

value: Breast; Mammary gland

value: epithelial cell

value: Control Knock down

value: Control siRNA

value: Day 2


title: NT rep 2

description:
Library name: Sample 5
NT_2

value: human leukemia monocytic cell line


title: PD S707QfsX56 Clone2 Sample3

description:
PD_S707QfsX56-Clone2_Sample-3
Raw_Counts.txt

value: PD S707QfsX56


title: Control 3

value: Saline is injected s.c. into the nape


title: knock down NC,biol rep 1

description:
Library name: Sample7
Column name in fpkm_All_sample.txt: NC_1


title: PD S707QfsX56 Clone1 Sample2

description:
PD_S707QfsX56-Clone1_Sample-2
Raw_Counts.txt


title: H1 WT Sample4

description:
H1_WT_Sample-4
Raw_Counts.txt

source_name: H1 hESC

value: H1 hESC

value: H1 WT


title: PD S707QfsX56 Clone1 Sample1

description:
PD_S707QfsX56-Clone1_Sample-1
Raw_Counts.txt

value: cortical interneurons

value: PD iPSC


title: ThP rep 3

description:
Library name: Sample 3
ThP_3

value: WT

value: Mono-culture

value: 24 Hours


title: H1 WT Sample3

description:
H1_WT_Sample-3
Raw_Counts.txt


title: knock down TRIM28,biol rep 3

description:
Library name: Sample6
Column name in fpkm_All_sample.txt: TRIM28_3

value: TRIM28 Knock down

value: TRIM28 siRNA


title: ThP rep 1

description:
Library name: Sample 1
ThP_1


title: NT rep 3

description:
Library name: Sample 6
NT_3

value: Co-culture with normal endothelial cells


title: knock down TRIM28,biol rep 1

description:
Library name: Sample4
Column name in fpkm_All_sample.txt: TRIM28_1

value: Breast; Mammary gland

value: epithelial cell


title: H1 WT Sample1

description:
H1_WT_Sample-1
Raw_Counts.txt


title: H1 WT Sample2

description:
H1_WT_Sample-2
Raw_Counts.txt


title: CKO438

city: Guangzhou

first: Jiancheng

state: Guangdong

address: NO.74, Zhongshan er Road

institute: Sun Yat-sen University

data_processing:
The raw FASTQ data were first processed through fastp v 0.23.2 and all the downstream analyses were based on high-quality clean data.
An index of the reference genome was built and paired-end clean reads were aligned to the reference genome (mm10) using HISAT2 v2.2.1.
Differential expression analysis was performed using the DESeq2 R package (1.34.0).
The selected differentially expressed genes were used to construct heatmaps with the pheatmap R package (1.0.12).
Gene Ontology (GO) enrichment analysis of the differentially expressed genes was performed by the clusterProfiler R package (v4.2.2).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM value for each sample

source_name: Spleen

extract_protocol:
Total RNA was extracted from spleen lymphocytes with TRIzol following the manufacture's protocol.
The entire mRNAseq library was generated using the ALFA-SEQ Directional RNaLib Prep Kit according to the manufacturer's recommendations.

value: Spleen

value: lymphocytes

value: Npc1 cko


title: knock down NC,biol rep 3

description:
Library name: Sample9
Column name in fpkm_All_sample.txt: NC_3

value: Control Knock down

value: Control siRNA

value: Day 2


title: P1 ctrl + CORT (biological replicate 2)

city: Bologna

first: Gabriele

last: D'Uva

address: via Massarenti 9

country: Italy

institute: University of Bologna

description: Library name: P1 ctrl + CORT 2

data_processing:
The softwares used for data analysis are the following (in order): NextSeq Control Software v2.2.0.4 (base-calling) BCL to FASTQ file converter bcl2fastq (demultiplexing) cutadapt v1.16 (Trimming) FastQC v0.11.7 multiqc v1.5 STAR v2.5.4a (Alignment) featureCounts v1.6.2 (Counting) DESeq2 v1.18.1 (Differential expression)
Assembly: mmu_GRCm38.90_ERCC_SIRV
Supplementary files format and content: tab-delimited text files include raw gene counts

source_name: neonatal cardiomyocytes

growth_protocol: Cells were  purified using the immuno-magnetic cell sorting MACS Neonatal Isolation System (130-100-825, Miltenyi biotech) and cultured in gelatine-coated (0.1%, G1393, Sigma) wells with DMEM/F12 (Aurogene) supplemented with L-glutamine, sodium pyruvate, non- essential amino acids, penicillin, streptomycin, 5% horse serum and 10% FBS  at 37°C and 5% CO2

extract_protocol:
RNA extraction was performed with NucleoSpin RNA II kit (Macherey Nagel); 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD following manufacturer's protocols.

treatment_protocol: 48 hours later, medium was changed and cells were starved with medium without serum for 24h

value: postnatal-day-1 (P1)

value: ctrl

value: neonatal cardiomyocytes


title: P1 ctrl + CORT (biological replicate 3)

description: Library name: P1 ctrl + CORT 3


title: knock down CtBP,biol rep 3

description:
Library name: Sample3
Column name in fpkm_All_sample.txt: CtBP_3

value: CtBP1/2 Knock down

value: CtBP1/2 siRNA


title: CKO435


title: ThP rep 2

description:
Library name: Sample 2
ThP_2

value: human leukemia monocytic cell line

value: WT

value: Mono-culture

value: 24 Hours


title: RNA_NoInd_2

data_processing:
Demultiplexing, bcl2fastq
Trimming, CutAapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25
Alignment, hisat2 v2.2.0 "--phred33 --rna-strandness R --no-unal"
Sort, samtools v1.10 view "-bh", sort, index
Quantification, featureCounts v2.0.0  "-p -t exon -s 2 -g gene_id"
Genome_build: UCSC hg38
Supplementary_files_format_and_content: hiNCC_featureCounts.txt, (Tab delim) all samples gene-level quantification

source_name: hESCs

growth_protocol: human induced neural crest cells were cultured in matrigel(Corning 354277)-coated 6-well tissue culture plates in a 37 degree 5% CO2 incubator in DMEM/F12 media supplemented with 1% B27 and 0.5%BSA.

extract_protocol:
RNA isolation and RNA-seq library preparation was performed on 500,000 hiNCCs after Day 5 of induction. RNA was isolated using the RNAqueous-micro total RNA isolation kit (Thermo Fisher Scientific AM1931) according to the kit's protocol.
RNA was poly(A) selected using the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs E7490). TruSeq-barcoded RNA-seq libraries were generated with the NEBNext Ultra II directional RNA library prep kit (New England Biolabs E7760).

treatment_protocol: hiNCCs were treated with 3uM CHIR99021 (low Wnt) or 10uM CHIR99021 (high Wnt) for hours 0-72 of induction +/- 10uM SB431542 or 5ng/uL recombinant human TGF-beta 1 protein for hours 0-120 of induction.

value: uninduced embryonic stem cells

tag: condition


title: H1 VKI-S707QfsX56 Clone2 Sample4

description:
H1_VKI-S707QfsX56-Clone2_Sample-4
Raw_Counts.txt

value: cortical interneurons

value: H1 hESC

value: H1 VKI-S707QfsX56


title: knock down CtBP,biol rep 1

description:
Library name: Sample1
Column name in fpkm_All_sample.txt: CtBP_1

value: Breast; Mammary gland

value: epithelial cell


title: WT430

value: Spleen

value: lymphocytes

value: wt


title: P1 ctrl + CORT (biological replicate 1)

description: Library name: P1 ctrl + CORT 1

value: postnatal-day-1 (P1)

value: ctrl


title: RNA_NoInd_1


title: CKO433

value: Npc1 cko


title: WT427


title: knock down CtBP,biol rep 2

description:
Library name: Sample2
Column name in fpkm_All_sample.txt: CtBP_2

value: CtBP1/2 Knock down

value: CtBP1/2 siRNA

value: Day 2


title: H1 VKI-S707QfsX56 Clone2 Sample2

description:
H1_VKI-S707QfsX56-Clone2_Sample-2
Raw_Counts.txt


title: Control 2

value: spleen

value: 8 weeks

value: wild type

value: Saline is injected s.c. into the nape


title: Control-3

city: Shanghai

first: Lan

last: Rong

address: Zhizaoju road No.639,Huangpu District,Shanghai,China

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Trimmomatic v.0.36; Hisat2 v.2.0.5; Featurecount v.1.6.3; R edgeR package R3.6.3
Trimmomatic is used for removing reads with adapter and low-quality sequences(illuminaclip:adapters.fa:2:30:10 slidingwindow:4:15 minlen:75)
Clean reads were mapped to the reference coding gene set using Hisat2 software (-p 16 --dta-cufflinks)
Gene expression levels were calculated using the FPKM method, and the edgeR R package was used to analyze the differentially expressed genes
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each samples

source_name: HaCaT cells

growth_protocol: Cells are cultured in DMEM supplemented with 12% FBS and penicillin/streptomycin in a humidified air incubator of 5% CO2 at 37℃. For lentiviral packaging, psPAX2, pMD2.0G, and lentiCRISPR v2-pX330-sgSTUB1/sgControl are co-transfected into HEK-293FT cells. Supernatants are collected 48 hours after transfection. After 48 hours of lentiviral infection, selection is carried out in the presence of polybrene to establish stable cell lines expressing the indicated sgRNAs. Cells are sorted and seeded into 96-well plates. Colonies are cultured for a further 15 days and subjected to anti-STUB1 immunoblotting to determine knockout efficiency.

extract_protocol:
Total RNA is isolated using TRIzol Universal and chloroform. Afetr centrifugation, the aqueous phase containing RNA is collected and precipitated using isopropanol. After precipitation and centrifugation, RNA forms a pellet, which is washed to remove impurities and dissolved in DEPC water.
RNA-seq library preparation follows the protocol of the Illumina TruSeq™ RNA Sample Prep Kit. Poly-A mRNA is enriched using Oligo(dT) magnetic beads, then fragmented ultrasonically. Using these mRNA fragments, first-strand cDNA is synthesized with random primers and M-MuLV reverse transcriptase, followed by RNA degradation with RNase H. Second-strand cDNA synthesis is done with DNA Polymerase I. The double-stranded cDNA is purified, end-repaired, A-tailed, and sequencing adapters are added. AMPure XP beads select ~200 bp fragments, followed by PCR amplification and another purification to yield the final library.

value: HaCaT cells

value: immortalized keratinocyte cell

value: WT

value: no special treatment


title: Control 1


title: WT45

value: Spleen


title: knock down TRIM28,biol rep 2

description:
Library name: Sample5
Column name in fpkm_All_sample.txt: TRIM28_2

value: Breast; Mammary gland

value: epithelial cell

value: TRIM28 Knock down

value: TRIM28 siRNA


title: H1 VKI-S707QfsX56 Clone2 Sample1

description:
H1_VKI-S707QfsX56-Clone2_Sample-1
Raw_Counts.txt

value: cortical interneurons

value: H1 hESC

value: H1 VKI-S707QfsX56


title: Control-2


title: H1 VKI-S707QfsX56 Clone1 Sample4

description:
H1_VKI-S707QfsX56-Clone1_Sample-4
Raw_Counts.txt


title: ATAC_TGFB1CHIR3_3

data_processing:
Trimming of Nextera adapter sequences was performed using cutadapt (version 3.4)(Martin, 2011a) using the following parameters: “-a CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG --minimum-length=25”.
Trimmed reads were aligned to the galGal6 chicken reference genome using bowtie2 (version 2.4.4)(Langmead and Salzberg, 2012) with the following arguments: “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000”.
Bam alignment files were indexed using samtools (version 1.10), followed by marking of duplicate reads using Picard’s (version 2.26.2) MarkDuplicates function.
Duplicate reads were then removed using samtools view with the following arguments: “-F 1804 -f 2”.
Peaks were called with macs2 (version 2.2.7.1)(Zhang et al., 2008) using the parameters: “-f BAMPE -g 1e9 -q 0.05 --call-summits”.
Assembly: galGal6 (UCSC)
Supplementary files format and content: bw

source_name: neural crest explant

growth_protocol: Fertilized chicken embryos (Leghorn White) were incubated at 37℃ until they reached the desired developmental stage. Neural crest explants were derived via microdissection of neural folds of HH9 embryos. The dissected tissues were then transferred to 96-well cell culture plates and cultured in DMEM (1x) (Gibco, 11965) + 10% FBS (Gibco, 10437028). Explants were incubated at 37°C in a CO2 incubator for 24hrs.

extract_protocol:
Five neural crest explants following the treatment conditions described above were pooled and dissociated in Accumax (Innovative Cell Technologies, #AM105).
Cell suspensions were washed and processed using the OMNI-ATAC-Seq protocol(Corces et al., 2017).

treatment_protocol: Culture media was supplemented with either DMSO, 10ng/mL recombinant hTGFβ1, 10ng/mL recombinant hTGFβ1 + 3uM CHIR99021,  or 10ng/mL recombinant hTGFβ1 + 10uM CHIR99021

value: neural crest explant

value: neural crest


title: Control-1


title: RNA_lowWNT_TGFB_1

source_name: hNCC induction day 5

value: Day 5 induced neural crest cells

value: low Wnt


title: H1 VKI-S707QfsX56 Clone1 Sample3

description:
H1_VKI-S707QfsX56-Clone1_Sample-3
Raw_Counts.txt


title: RNA_lowWNT_SB4_2


title: H1 VKI-S707QfsX56 Clone2 Sample3

description:
H1_VKI-S707QfsX56-Clone2_Sample-3
Raw_Counts.txt


title: H1 VKI-S707QfsX56 Clone1 Sample2

description:
H1_VKI-S707QfsX56-Clone1_Sample-2
Raw_Counts.txt


title: ATAC_TGFB1CHIR3_2

value: 10ng/mL recombinant hTGFβ1 + 3uM CHIR99021


title: STUB1 Knockout-2

value: HaCaT cells

value: STUB1 knockout


title: RNA_lowWNT_SB4_1


title: ATAC_TGFB1CHIR3_1


title: STUB1 Knockout-1

value: immortalized keratinocyte cell


title: H1 WT IgG Sample2

data_processing:
Raw reads were processed using CutRunTools2.1 for trimming, alignment, bigWig generation and peak calling
Assembly: hg38
Supplementary files format and content: bigWig density file, data normalized to sample read depth
Supplementary files format and content: narrowPeak file containing output from MACS2 peakcalling
Library strategy: CUT&RUN

growth_protocol: Embryonic stem cells were maintained in mTeSR media on Laminin coated cultureware.

extract_protocol:
Genomic DNA was processed using CUT&RUN after the manufacturer's instructions (Epicypher).
After PCR amplification, samples with unique dual-end indexes were pooled in equimolar concentrations.

value: embryonic stem cells

tag: antibody

value: IgG


title: STUB1 Knockout-3

value: no special treatment


title: ATAC_TGFB1CHIR10_3

value: 10ng/mL recombinant hTGFβ1 + 10uM CHIR99021


title: RNA_lowWNT_2


title: ATAC_TGFB1CHIR10_2


title: H1 WT IgG Sample1


title: KYSE150_ETS1_ ChIP-Seq

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

data_processing:
Pair-end 150bp reads were trimmed for adaptor sequence, and then mapped to hg38 reference genome using BWA
PCR duplicate reads were removed using sambamba software.
Blacklist regions were removed using ENCODE blacklist file in ChIP-seq.
Peaks were called subsequently using macs2 with “-q 0.01 --keep-dup 1” parameters.
Bigwig files were generated by deepTools bamCompare function (version 3.1.3) with “--normalizeUsing CPM --extendReads 146 --binSize 20” parameters.
Assembly: hg38
Supplementary files format and content: bigwig files

growth_protocol: KYSE150 cells were cultured in RPMI-1640 medium (Corning, #10-040-CV) supplemented with 10% Fetal Bovine Serum (FBS) (Omega, Tarzna, #FB-02), 1% Penicillin/Streptomycin (Thermofisher Scientific, 30-002-CI).

extract_protocol:
DNA framgents were collected after reverse crosslink using 5M NaCl and purified using Qiaquick PCR purification kit (Qiagen, #28104) according to manufacturer's protocol
Standard Illumina library preparation protocol

treatment_protocol: KYSE150 cell line was harvested and fixed using 1% formalin. Sample then sonicated using sonicator and pulled down uisng either ETS1 antibody(Cell Signaling Technology, 14069S) and Dynabeads. DNA framgents were collected after reverse crosslink using 5M NaCl and purified using Qiaquick PCR purification kit according to manufacturer's protocol

value: Esophageal squamous cell carcinoma cell line


title: RNA_lowWNT_TGFB_2


title: ATAC_TGFB1CHIR10_1


title: RNA_highWNT_TGFB_2

value: high Wnt


title: HEK-293T cells, transduced with Cas9 and sg2-THAP1, replicate3

city: Cambridge

first: Richard

last: Timms

address: Cambridge Biomedical Campus, Hills Road

department: CITIID, Department of Medicine

institute: University of Cambridge

data_processing:
Trimmed of Illumina adaptors (Cutadapt)
Aligned to GRCh38 genome_tran reference using HISAT2
RNA-seq quantitation pipeline in SeqMonk
Assembly: GRCh38
Supplementary files format and content: csv file with read counts for each gene

extract_protocol:
RNeasy Mini Kit (Qiagen)
Strand-specific polyA+ library prep (Genewiz)

value: Expressing sgRNA targeting THAP1


title: RNA_highWNT_TGFB_1


title: H1 WT MYT1L Sample4

value: H1 hESC


title: HEK-293T cells, transduced with Cas9 and sg2-THAP1, replicate2


title: RNA_highWNT_SB4_2


title: ATAC_TGFB1_3

value: 10ng/mL recombinant hTGFβ1


title: HEK-293T cells, transduced with Cas9 and sg2-THAP1, replicate1


title: H1 WT MYT1L Sample3


title: RNA_highWNT_SB4_1


title: H1 WT MYT1L Sample2


title: RNA_lowWNT_1


title: ATAC_TGFB1_1

value: neural crest explant


title: H1 VKI-S707QfsX56 Clone1 Sample1

description:
H1_VKI-S707QfsX56-Clone1_Sample-1
Raw_Counts.txt

value: cortical interneurons

value: H1 VKI-S707QfsX56


title: RNA_highWNT_2

value: Day 5 induced neural crest cells


title: ATAC_TGFB1_2

value: neural crest


title: ATAC_Ctrl_3

value: DMSO


title: RNA_highWNT_1


title: H1 WT MYT1L Sample1


title: IgG

city: Wuhan

first: Jingchun

state: HUBEI

address: Zhangzhidong road

institute: Renmin Hospital of Wuhan University

data_processing:
Library strategy: CUT & Tag
Cells were harvested, counted and centrifuged for 3 min at 600 × g at room temperature.
Primary antibody incubation was performed on a rotating platform for overnight at 4℃.
Nucleus were washed in wash Buffer to remove unbound pA-Tn5 protein
The library DNA was purified and amplified for sequencing with the Illumina NovaSeq 6000.
Genome_build: hg38
Supplementary_files_format_and_content: peak
Supplementary_files_format_and_content: peakcount

source_name: IgG

extract_protocol:
Cells were harvested, counted and centrifuged
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ovarian cancer cells(SKOV3) treated with 2DG


title: ATAC_Ctrl_2


title: 2DG


title: HEK-293T cells, transduced with Cas9 and sg1-THAP1, replicate3


title: HEK-293T cells, transduced with Cas9 and sg1-THAP1, replicate1


title: IFNg+LNMA_3

city: Bangalore

first: Avik

last: Chattopadhyay

state: Karnataka

address: Devasandra Layout

department: Department of Biochemistry

country: India

institute: Indian Institute of Science

description: Library name: sample_12

data_processing:
Raw sequence data were processed to remove adapter sequences and low-quality bases using fastp, and aligned to the indexed Mouse reference genome (GRCm 38.90) using STAR v2 aligner.
After alignment, PCR and optical duplicates were removed using Picard tools, and gene-level expression counts were obtained using featureCounts.
The resulting raw counts were then normalized to generate normalized expression values for downstream analysis.
The normalization method used was RPKM (Reads Per Kilobase Million), which accounts for both sequencing depth and gene length, allowing for the comparison of gene expression levels across samples.
Assembly: Aligned to the indexed Mouse reference genome (GRCm38.p6)
Supplementary files format and content: The normalized expression data for each sample is provided in an Excel sheet, with genes listed in rows and samples in columns, where each cell represents the normalized expression value for a specific gene in a specific sample.

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS, maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using a phenol-chloroform based method (TRIzol reagent) according to the manufacturer’s protocol.
RNA libraries were prepared using the Illumina TruSeq RNA Library Prep Kit v2 with polyA enrichment, followed by sequencing on an Illumina HiSeq platform.

treatment_protocol: Cells were treated with 10 U/mL IFN-γ, with or without 200 µM LNMA, for 6 hours.

value: Monocyte/ macrophage

value: WT

value: IFN-gamma 10 Units/mL and LNMA 200 uM


title: HEK-293T cells, transduced with Cas9 and sg2-Control, replicate3

value: Expressing control sgRNA


title: ATAC_Ctrl_1


title: HEK-293T cells, transduced with Cas9 and sg2-Control, replicate2


title: Control

source_name: Control


title: Pharynx_TMA_Right

type: RNA

city: Pittsburgh

first: Zhentao

state: PA

address: 5051 CENTRE AVE, HCC SUITE

institute: UMPC Hillman Cancer Center

hyb_protocol: RNA ISH probes were denatured and hybridized overnight at 37°C. After hybridization, samples were washed and incubated with antibody cocktails and DAPI

scan_protocol: The prepared samples were loaded onto the SMI instrument for scanning. Reporter probes were hybridized and imaged over multiple cycles to capture RNA and protein signals. Z-stack images were acquired for each field of view

data_processing: The raw count data were processed using standard Seurat workflow. Each cell was normalized by sequencing depth and then transformed by log1p transformation.

source_name: Head and neck squamous cell carcinoma

label_protocol: Fluorophore-conjugated antibodies and DAPI were used for staining, targeting proteins such as CD298/B2M, PanCK, CD45, and CD68.

growth_protocol: Tissue samples were prepared on VWR® Superfrost® Plus slides and baked overnight at 60°C to ensure adherence. The samples underwent deparaffinization, proteinase K digestion, and heat-induced epitope retrieval (HEIR). These treatments exposed the target RNAs and epitopes

treatment_protocol: Samples were treated with Proteinase K at 40°C for 30 minutes and HEIR at 100°C for 15 minutes. Fiducials were added, followed by fixation with 10% neutral buffered formalin (NBF). Samples were blocked with N-succinimidyl acetate (NHS-acetate) before further preparation.

value: Pharynx


title: IFNg+LNMA_1

description: Library name: sample_10


title: RNA_TGFB1MO_T2

data_processing:
Paired-end sequencing reads were trimmed using Cutadapt (Martin, 2011b) using the following arguments: “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25”.
Reads were aligned using HISAT2 (Kim et al., 2019) with the following arguments: --phred33 --rna-strandness R --no-unal”.
Counts were assigned to genes using featureCounts (Liao et al., 2014).
Assembly: galGal6 (UCSC)
Supplementary files format and content: tab-delimited raw counts .txt file

source_name: dorsal neural fold

extract_protocol:
RNA was isolated using the RNAqueous-micro total RNA isolation kit (Thermo Fisher Scientific AM1931) according to the kit's protocol.
RNA was poly(A) selected using the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs E7490). TruSeq-barcoded RNA-seq libraries were generated with the NEBNext Ultra II directional RNA library prep kit (New England Biolabs E7760).

treatment_protocol: Embryos were bilaterally injected with the TGFβ1 morpholino and the GTBlue-Control morpholino at a final concentration of 1 mM. Embryos were cultured until HH9 and dorsal neural folds of TGFβ1 morpholino-treated and GTBlue-Control morpholino-treated sides of the same embryo were dissected and subjected to RNA isolation and RNA-seq library preparation.

value: dorsal neural fold

value: TGFB1 knockdown


title: HEK-293T cells, transduced with Cas9 and sg1-Control, replicate3


title: RNA_TGFB1MO_T1


title: PAB6, Male SD rat, PAB, week 4

city: Luzhou

first: Huiling

last: Cai

address: Longmatan District, Luzhou City, Sichuan Province

institute: Southwest Medical University

description:
Library name: PAB6
exp_PAB6

data_processing:
RNA integrity and concentration were  assessed using an Agilent 2100 Bioanalyzer (Agilent, CA, USA).
SE50 sequencing was performed on a G400 sequencer (BGI-Shenzhen, China).
Use SOAPnuke to filter the downlink data to get clean tags (Parameter-Q 2 -q -z 15)
Clean data was compared to the reference genome using Bowtie2 (v2.2.9) (Parameter-q -L 16 -p 6 --phred64 --rdg 1,10 --rfg 1,10)
Differential analysis of miRNAs was performed using DESeq2.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: gene_expression xlsx files include FPKM values for each samlple

organism: Rattus norvegicus

source_name: blood serum

growth_protocol: -80°C storage

extract_protocol:
Total RNA (including miRNAs) was extracted using the miRNeasy serum Kit (QIAGEN, Germany) kit and an amount of total RNA was used for sequencing library preparation.
Small RNA sequencing libraries were prepared using the MGIEasy Small RNA Library Prep Kit ( BGI - Shenzhen, China) according to the manufacturer's protocol.

value: blood serum

value: Rat Serum (SD)

value: PAB

value: week 4


title: LNMA_3

description: Library name: sample_9

value: LNMA 200 uM


title: HEK-293T cells, transduced with Cas9 and sg2-Control, replicate1


title: HEK-293T cells, transduced with Cas9 and sg1-THAP1, replicate2

value: Expressing sgRNA targeting THAP1


title: HEK-293T cells, transduced with Cas9 and sg1-Control, replicate2


title: PAB5, Male SD rat, PAB, week 4

description:
Library name: PAB5
exp_PAB5


title: RNA_TGFB1MO_C2


title: LNMA_1

description: Library name: sample_7


title: HEK-293T cells, transduced with Cas9 and sg1-Control, replicate1


title: LNMA_2

description: Library name: sample_8


title: HEK-293T cells, untransduced, replicate3

value: Wild-type


title: IFNg_2

description: Library name: sample_5

value: IFN-gamma 10 Units/mL


title: PAB4, Male SD rat, PAB, week 4

description:
Library name: PAB4
exp_PAB4


title: PAB3, Male SD rat, PAB, week 4

description:
Library name: PAB3
exp_PAB3


title: RNA_TGFB1MO_T3

value: neural crest


title: RNA_TGFB1MO_C3


title: CR_H3K27ac_trunk_2

data_processing:
library strategy: CUT&RUN
Demultiplexing, bcl2fastq
Trimming, CutAapt v2.1.0, -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25
Alignment, bowtie2 v2.4.2, “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 1000
Filtering, samtools v1.10 view "-f 2 -F 780 -bh", sort, index
Peak calling, SEACR v1.3 "0.005 non stringent"
Generate bigwigs, bamCoverage "--outFileFormat bigwig --binSize 5 --normalizeUsing RPKM"
Genome_build: UCSC galGal6
Supplementary_files_format_and_content: .bigwig files displaying read coverage across the genome

source_name: chicken HH14 trunk neural fold dissections

value: Leghorn White

value: cranial/trunk neural crest cells


title: PAB2, Male SD rat, PAB, week 4

description:
Library name: PAB2
exp_PAB2

value: WT


title: IFNg+LNMA_2

description: Library name: sample_11

value: Monocyte/ macrophage

value: IFN-gamma 10 Units/mL and LNMA 200 uM


title: HEK-293T cells, untransduced, replicate2


title: PAB1, Male SD rat, PAB, week 4

description:
Library name: PAB1
exp_PAB1


title: IFNg_1

description: Library name: sample_4


title: CR_H3K27ac_trunk_1


title: Control_2

description: Library name: sample_2

value: No treatment


title: RNA_TGFB1MO_C1

value: dorsal neural fold


title: CR_H3K27ac_cranial_2


title: Control1, Male SD rat, sham operation, week 4

description:
Library name: Control1
exp_Control1

value: Sham operation


title: RNA-Seq of Riemerella anatipestifer CH-1 under normal condition

city: chengdu

first: Hongmeng

last: Ma

address: No. 211 Huimin Road, Wenjiang District

institute: sichuan agricultural university

description: Library name: CH-1

data_processing:
Sequencing on NovaSeqXPlus platform 1 Qubit 4.0 quantitative, according to the proportion of data mixed on the machine ;  2 Bridge PCR amplification was performed on cBot to generate clusters ; 3 On-machine sequencing.The sequencing platform converts the sequencing image signal into a text signal by CASAVA Base Calling and stores it in a fastq format as the original data.
Assembly: ASM29565v1
Supplementary files format and content: processed data files are in xlsx format and the content is the difference in gene expression between the CH-1_zntR and the CH-1.

organism: Riemerella anatipestifer

extract_protocol:
Total RNA was extracted from the bacterial pellet using an RNAprep Pure Cell/Bacteria Kit (TIANGEN). We used a NanoDrop 2000 to assess the concentration and quality of RNA samples.
Library preparation for RNA transcriptome sequencing was performed using the TruSeqTM Stranded Total RNA Library Prep Kit. The rRNA was first removed from total RNA, and the mRNA was cleaved into ~200 bp fragments using fragmentation buffer. Single-stranded cDNA was synthesized with random primers and the second-strand cDNA was synthesized with dUTP instead of dTTP. The ends of double-stranded cDNA were blunted with the End Repair Mix and an A base was added at the 3’ end. The cDNA was then digested with the UNG enzyme to remove the second-strand.


title: Control_3

description: Library name: sample_3


title: Control_1

description: Library name: sample_1


title: Control2, Male SD rat, sham operation, week 4

description:
Library name: Control2
exp_Control2

value: blood serum


title: CR_H3K27ac_cranial_1

extract_protocol:
Neural fold dissections were performed on HH9/HH14 embryos to obtain cranial/trunk neural crest cells (10 embryos/20 neural folds per experiment). Cells were dissociated in Accumax (Innovative Cell Technologies, AM105) cell dissociation solution for 20 min at RT under mild agitation. CUT&RUN experiments were performed as previously described (Skene and Henikoff, 2017).
CUT&RUN libraries were prepared using the NEBNext ultra II DNA library prep kit (New England Biolabs E7645) according to the kit's protocol.


title: Ctrl7

status: Public on Jan 17 2025

city: Limoges

first: christophe

last: sirac

address: 2 Rue du Pr Descottes

country: France

institute: university of Limoges

description: Library name: D18

data_processing:
Paired-end reads were processed through the bioinformatic pipeline nf-core/rnaseq v3.12 in reverse strandedness mode
Alignment to the GRCm38 mouse genome with STAR and quantification by Salmon with the corresponding genome annotation from the ENSEMBL release 111 database
batch effect  was taken into account through ComBat adjustment
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes gene id (column 1), gene name (column 2) and library name with raw counts for each Sample

source_name: Heart (Apical)

extract_protocol:
Total RNA was extracted from the apical part of the hearts using the miRNeasy Mini Kit (Qiagen) on the TRIzol reagent
Libraries were generated from 500 ng of total RNA using the Truseq Stranded mRNA Kit (Illumina), quantified with the Qubit dsDNAHS Assay Kit (Invitrogen).

value: Heart (Apical)

tag: group

value: DH control heart

value: DH


title: LS1

description: Library name: Scoeur-41

value: Transgenic AL- heart

value: DH-lambdaS

tag: batch


title: Ctrl6

description: Library name: D17


title: IFNg_3

description: Library name: sample_6


title: Ctrl3

description: Library name: SCoeur-47


title: RNA-Seq of Riemerella anatipestifer CH-1_zntR under normal condition

description: Library name: CH-1_zntR

value: zntR mutant


title: LS4

description: Library name: Scoeur-44


title: LS3

description: Library name: Scoeur-43


title: LS2

description: Library name: Scoeur-42


title: AL9

description: Library name: S55

value: Transgenic AL+ heart


title: Ctrl1

description: Library name: SCoeur-45


title: AL8

description: Library name: S53


title: Ctrl5

description: Library name: D16


title: AL7

description: Library name: SCoeur-32


title: AL6

description: Library name: SCoeur-31


title: AL5

description: Library name: SCoeur-30


title: HEK-293T cells, untransduced, replicate1

value: Wild-type


title: Control3, Male SD rat, sham operation, week 4

description:
Library name: Control3
exp_Control3

value: Rat Serum (SD)

value: week 4


title: AL2

description: Library name: SCoeur-26


title: AL4

description: Library name: SCoeur-29


title: Ctrl4

description: Library name: SCoeur-48


title: AL3

description: Library name: SCoeur-28


title: AL1

description: Library name: SCoeur-25


title: Ctrl2

description: Library name: SCoeur-46


title: ChIP_shK_input_rep2

city: Boston

first: Jeannie

middle: T

last: Lee

state: MA

address: Massachusetts General Hospital, 185 Cambridge street

department: molbio

institute: Massachusetts  General Hospital, Harvard Medical School

data_processing:
Paired end 150 adapters were removed using software cutadapt (version 1.4.2; -e 0.2 -q 20 -a AGATCGGAAGAGC  -m 20 –overlap 12). The resulting reads were aligned using bowtie2 (version 2.2.2; -p 4 -x mm10plushg38 --no-mixed --no-discordant) to three hybrid genomes mm10plushg38 mm10musplushg38 mm10casplushg38. Sambamba (version 0.6.6; markdup) was used to remove duplicate alignments. To calibrate across different IPs, reads from hg38 spike-in cells and mouse mm10 are quantified using Unix grep and wc -l or their associated read fragment using samtools flagstats, collecting with\ itself\ and\ mate\ mapped and singletons (mates/2+singletons). Uniquely aligned mouse reads were normalized to human spike-in by subsampling mm10 reads so total number of hg38 reads was matched between samples. Input-subtracted calibrated ChIP coverage profiles were generated with SPP (R version 3.0.0) (Kharchenko et al, 2008) with smoothing using 1kb windows recorded every 500 bp, as described (Simon et al., 2013). Two biological replicates for each cell line showed similar results.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: MEFs (CAST/Ei x 129/Sv/Jae)

growth_protocol: MEF media [DMEM, high glucose, GlutaMAX supplement, pyruvate (10569044, Thermo Fisher Scientific), 10% FBS, 25 mM HEPES pH 7.2-7.5 (15630130, Thermo Fisher Scientific), 1X MEM non-essential amino acids (11140076, Thermo Fisher Scientific), 1X Pen/Strep (15140163, Thermo Fisher Scientific), and 0.1 mM b-mercaptoethanol (21985023, Thermo Fisher Scientific)].with 200ug/ml Hygromycin B (10687010, Thermo Fisher Scientific) and 2ug/ml Puro (A1113803, Thermo Fisher Scientific).

extract_protocol:
Calibrated ChIP-seq was performed as described previously with minor modifications (Kriz et al., 2021). Briefly, MEF cells were trypsinized, resuspended in 1 million cells/mL of media and mixed with 50,000 HEK293 cells per 5 million mouse cells. Cells were crosslinked with 1% formaldehyde for 10 min at room temperature with rotation, and quenched with 0.2 M glycine for 5 min. Crosslinked cells were washed once with cold PBS, pelleted, and snap frozen in an EtOH/dry ice bath. Cell pellets were stored at -80C until further processing. 5-10 million cross-linked cells per IP were thawed on ice and resuspended in 300ul Lysis Buffer 1 (25mM HEPES pH 7.2-7.5, 25mM EDTA, 0.5% SDS). Nuclei were sonicated (Qsonica Q800 Sonicator) in polystyrene tubes at 40% power setting, 30s ON/30s OFF for a total sonication (ON) time of 6 min. After sonication, 1.2 mL of Lysis Buffer 2 (25mM HEPES pH 7.2-7.5, 187.5mM NaCl, 1.25% Triton X-100, 0.625% Na-deoxycholate, 6.25% glycerol, 1x cOmplete EDTA-free protease inhibitor cocktail) was added. 30ul of Dynabeads Protein G (Thermo Fisher Scientific) per IP were washed 3 times with ChIP Wash Buffer 1 (25mM HEPES pH 7.2-7.5, 150mM NaCl, 5mM EDTA, 1% Triton X-100, 0.5% Na-deoxycholate, 5% glycerol, 1x cOmplete EDTA-free protease inhibitor cocktail) and resuspended in 60ul ChIP Wash Buffer 1. Each IP was blocked with 20ul washed beads for 2 hours at 4C with rotation. The other 40ul of washed beads were incubated with antibody (5ul of RAD21 antibody or 2ul of H3K27me3 antibody/IP) for 2 hours at 4C. 5% input was taken from blocked lysates. Beads conjugated to antibody were added to blocked lysates and IP allowed to proceed overnight at 4C with rotation. IPs were then washed 3 times with cold ChIP Wash Buffer 1, 3 times with cold ChIP Wash Buffer 2 (25mM HEPES pH 7.2-7.5, 300mM NaCl, 5mM EDTA, 1% Triton X-100, 0.5% Na-deoxycholate, 5% glycerol, 1x cOmplete EDTA-free protease inhibitor cocktail). And 1 time with cold TENG (50mM Tris-HCl pH 8, 1mM EDTA, 50mM NaCl, 5% glycerol, 1x cOmplete EDTA-free protease inhibitor cocktail). All washes were performed by inverting tubes and setting aside for ~2 minutes per wash. IPs were then resuspended in 500ul TENG with 100ug RNAse A (Thermo Fisher Scientific) and incubated for 30 min at 37C. IPs were then washed 2 times with cold ChIP Wash Buffer 2 and 2 times with cold TENG without protease inhibitors. IPs were resuspended in 200ul elution buffer (50mM Tris-HCl pH 7.5, 10mM EDTA, 1% SDS) and incubated 15 min at 65C. Eluate was then transferred to a new tube and 198ul TE buffer (Ambion) and 40ug Proteinase K (Sigma) added. Inputs were thawed, TE buffer added to equalize volume to IPs and 200ul elution buffer and 40ug Proteinase K added. Inputs and IPs were then incubated for 2h at 45C and crosslinks reversed overnight at 65C. DNA was purified with phenol-chloroform extraction and resuspended in 50ul TE. Efficiency of ChIP was assayed via qPCR, with samples displaying over 10-fold enrichment of positive regions over negative control prepared for sequencing.  Experiments were performed in two biological replicates.
Libraries were prepared from ~500ng of input or IP DNA using the NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to kit instructions.

value: MEFs (CAST/Ei x 129/Sv/Jae)

value: MEFs

value: shHNRNPK

value: shRNA, overexpression plasmids


title: ChIP_shK_WT_input_rep2

value: shHNRNPK and WT-HNRNPK overexpression


title: ChIP_shK_6A_input_rep2

value: shHNRNPK and 6A-HNRNPK mutant overexpression


title: ChIP_shScr_input_rep2

value: shScramble


title: snRNAseq_d30pi_combined

city: La Jolla

first: Miguel

last: Reina-Campos

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
cellranger was used to process the raw sequencing files to generate count matrices per cell
Assembly: mm10
Supplementary files format and content: "h5ad" file containing combined total nuclei profiled from all mice and regions of the gastrointestinal tract

source_name: Small Intestine

extract_protocol:
Female CD45.1+ CD8+ P14 T cells were adoptively transferred into male CD45.2+ recipients (1×105 cells/mouse) 30 minutes prior to infection with LCMV-Armstrong. At 28 days post infection, mice were euthanized and small intestine was dissected, flayed, and washed in cold PBS; Peyer’s patches were excised from the small intestine. The small intestine was divided into three equal sections designated as the proximal, middle, and distal small intestine. Tissue sections were cut into ~3 mm pieces and flash-frozen in liquid nitrogen for 2 min. Nuclei isolation was performed with 10x Genomics Chromium Nuclei Isolation Kit per the manufacturer’s instructions. Briefly, 30-50 mg of flash-frozen tissue per sample was dissociated with a pestle, incubated for 10 minutes on ice, and washed. Dissociated tissue was passed through a Nuclei Isolation Column, and flowthrough nuclei were washed in Debris Removal Buffer and Wash and Resuspension Buffer. Nuclei were quantified with Nexcelom Bioscience Cellometer. For maximum targeted recovery, 40,000 nuclei per sample were loaded for GEM generation.
Samples were processed via the Chromium Next Gem Single Cell 3’ HT Dual Index v3.1 protocol and sequenced to a depth of 550 million read pairs per sample (~23,000 read pairs per nucleus) on a NovaSeq 6000 system (Illumina).

value: Small Intestine

value: LCMV infection


title: Small Intestine Infected LCMV d8 pi

data_processing:
BCL files were demultiplexed into FASTQ files using spaceranger mkfastq followed by spaceranger count to generate the spatial representation of gene counts by matrix at 2 and 8 mm resolution binning
Assembly: mm10
Supplementary files format and content: Standard 10X Cellranger outputs for VisiumHD data
Library strategy: VisiumHD spatial transcriptomics

extract_protocol:
NA
Following Manufacturer's protocol

treatment_protocol: A 7 um thick section from a day 8 pi FFPE sample was placed in a histology slide, dried at 42 for 3 hours, dehydrated overnight, baked at 60C for 30 min and deparaffinized following the VisiumHD standard protocol (CG000685). The mouse reagents (Visium HD, Mouse Transcriptome, 6.5 mm, 4 rxns, PN -1000676) were used to obtain a high-quality H&E picture, hybridize, RNA removal and amplify probes, analyte transfer to the VisiumHD slide using the Cytassist with the 2.0 software

value: LCMV infection and P14 CD8 T cell transfer


title: ChIP_shK_WT_rep2


title: ChIP_shK_6A_input_rep1


title: ChIP_shK_WT_input_rep1


title: ChIP_shK_rep2


title: ChIP_shScr_rep2


title: ChIP_shK_input_rep1


title: ChIP_shScr_input_rep1


title: ChIP_shK_6A_rep2


title: CHART_6A_input_rep2

data_processing:
Paired end 150 adapters were removed using software cutadapt (version 1.4.2; -e 0.2 -q 20 -a AGATCGGAAGAGC  -m 20 –overlap 12). The resulting reads were aligned using bowtie2 (version 2.2.2; -p 4 -x mm10plushg38 --no-mixed --no-discordant) to three hybrid genomes mm10plushg38 mm10musplushg38 mm10casplushg38. Sambamba (version 0.6.6; markdup) was used to remove duplicate alignments. To calibrate across different IPs, reads from hg38 spike-in cells and mouse mm10 are quantified using Unix grep and wc -l or their associated read fragment using samtools flagstats, collecting with\ itself\ and\ mate\ mapped and singletons (mates/2+singletons). Uniquely aligned mouse reads were normalized to human spike-in by subsampling mm10 reads so total number of hg38 reads was matched between samples. Input-subtracted calibrated ChIP coverage profiles were generated with SPP (R version 3.0.0) (Kharchenko et al, 2008) with smoothing using 1kb windows recorded every 500 bp, as described (Simon et al., 2013). Two biological replicates for each cell line showed similar results.
Assembly: mm10
Supplementary files format and content: Wig
Library strategy: CHART-seq

source_name: mESCs (CAST/Ei x 129/Sv/Jae)

growth_protocol: Undifferentiated ES cells were grown on gama-irradiated MEF feeders for 2 days in media containing DMEM, high glucose, GlutaMAX supplement, pyruvate, 15% Hyclone FBS (Sigma), 25 mM HEPES pH 7.2-7.5, 1x MEM non-essential amino acids, 1x Pen/Strep, 0.1 mM bME, and 500 U/mL ESGRO recombinant mouse Leukemia Inhibitory Factor (LIF) protein (Sigma, ESG1107) at 37°C with 5% CO2. ES cell colonies were trypsinized and feeders removed (day 0). ES cells were then switched to medium lacking LIF to induce differentiation and grown in suspension for 4 days, forming embryoid bodies (EBs). EBs were settled down onto gelatin-coated plates at day 5, and allowed to further differentiate until at day 7.

extract_protocol: Xist CHART-seq was performed as previously described (Wang et al., 2018). Briefly, 25M cells were resuspended in 1XPBS and crosslinked with 1% formaldehyde for 10 min at room temperature. The formaldehyde was quenched with addition of 0.125M glycine, washed three times with PBS-0.05% tween-20, and cell pellets were snap freeze in liquid nitrogen. Cell pellets were thawed on ice with 1ml sucrose buffer (10mM HEPES pH7.5, 0.3M sucrose, 1% Triton X-100, 100mM potassium acetate, 0.1mM EGTA, supplemented with 0.5mM spermidine, 0.15mM spermine, 1mM DTT, 1X Protease Inhibitor Cocktail (11873580001, Sigma), 10U/mL SUPERaseIN RNase Inhibitor (AM2694, Thermo Fisher Scientific) freshly), resuspended and rotated for 10min at 4C. then cells were dounced 20 times with dounce homogenizer (357544, Wheaton) in 3ml sucrose buffer. The cells were layered on a cushion of 7.5ml glycerol buffer (10mM HEPES pH7.5, 25% glycerol, 1mM EDTA, 0.1mM EGTA, 100mM potassium acetate, freshly supplemented with 0.5mM spermidine, 0.15mM spermine, 1mM DTT, 1X PIC, and 5U/mL SUPERaseIN) and centrifugated for 10min in 4C at 1500g. pellets were resuspended in 3ml 1X PBS and 3ml of 6% formaldehyde in 1X PBS (3% formaldehyde final) was added for second fixation, that was carried in rotated for 30 minutes at room temperature. Next, the cells were centrifugated at 1000g for 5min in 4C, and washed 3 times with cold PBS-0.05% tween-20. The pellets were resuspended in 1ml nuclear extraction buffer (50mM HEPES pH 7.5, 250mM NaCl, 0.1mM EGTA, 0.5% N-lauroylsarcosine, 0.1% sodium deoxycholate, 5mM DTT, 10U/mL SUPERaseIN), rotated 10 minutes at 4C, spinned-down at 400g for 5 minutes at 4C and nuclei were resuspended in sonication buffer (50mM HEPES pH 7.5, 75mM NaCl, 0.1mM EGTA, 0.5% N-lauroylsarcosine, 0.1% sodium deoxycholate, 0.1% SDS, 5mM DTT, 10U/mL SUPERaseIN). The lysate was divided to two Covaris microtubes, with 130μl in each and sonication was preformed with Covaris E220 sonicator at power: 140W, duty factor: 10%, cycles per burst: 200 for 5 minutes at 4C. Chromatin was pooled, cleared by centrifugation at full speed for 20 minutes at 4C, supernatant was taken to new tube, and volume was adjusted to 390μl. The lysate was pre-cleared with addition of 640μl 2X hybridization buffer (50mM Tris-HCl pH 7.0, 750mM NaCl, 1% SDS, 1mM EDTA, 15% formamide, 1mM DTT, 1mM PMSF, 1X PIC, and 100U/mL SUPERaseIN) and 60μl of washed Dynabeads™ MyOne™ Streptavidin C1 beads (Invitrogen) in rotation at room temperature for 1 hour. Then, supernatant was divided to two tubes for probe hybridization, each reaction with 520μl. 1% was kept frozen for input. Each tube received 3.6μl from a 10μM mix of 10 Xist probes and hybridization was performed at room temperature in rotation overnight. Next, 120μl of washed beads were added for each reaction and the tubes were incubated in rotation at 37C for 1 hour. Then beads were washed once with 1X hybridization buffer (33% sonication buffer, 67% 2X hybridization buffer) for 10 min, 5 times with 2% SDS buffer (10mM HEPES pH 7.6, 250mM NaCl, 2% SDS, 2mM EDTA, 2mM EGTA, and 1mM DTT) for 5 min and twice with 0.5% NP40 buffer (10mM HEPES pH7.6, 250mM NaCl, 0.5% NP-40, 3mM MgCl2, and 10mM DTT) for 5min, at 37C. Beads were resuspended with 180μl of 0.5% NP40 buffer and 20μl RNase H (5U/μl, NEB) for 20 minutes in room temperature to elute the DNA twice. Input DNA was also resuspended with 0.5% NP40 buffer to 400μl. Eluted DNA was spined down at full speed for 1 min to pellet residual beads, 10μl RNase A (12091-021,Thermo Fisher Scientific) was added to the supernatant, and DNA was incubated for 1h at 37C in rotation. Next, DNA was treated with 10μl of Proteinase K (20mg/ml), SDS to 1% final, and EDTA to 10mM final concentration and the samples were incubated at 55°C for 1 hour. To reverse crosslinking the DNA, NaCl was added to 300mM and the samples were incubated at 65°C overnight. DNA was extracted with phenol-chloroform extraction. Xist pulldown was validated by qPCR with primers around Xist-promoter and compared to primers of Gapdh promoter. To proceed for sequencing, DNA was diluted to 130µl in TE and sonicated in Covaris microtubes at power: 140W, duty factor: 10%, cycles per burst: 200 for 2min at 4C. DNA was cleaned up with 1.8X ampure XP beads (A63881, Beckman Coulter). For each sample 2pg of drosophila S2 cells sonicated DNA was spike-in. sequencing libraries were than prepared with NEBNext® Ultra II DNA Library Prep Kit for Illumina (#E7645S). Libraries were sequenced using Ilumina novaseq generating 150bp pair-end reads.

value: mESCs (CAST/Ei x 129/Sv/Jae)

value: Day 7 differentiated mouse embryonic stem cells

value: HNRNPK 6A mutant


title: ChIP_shK_WT_rep1


title: ChIP_shK_6A_rep1


title: CHART_6A_input_rep1


title: CHART_WT_input_rep1

value: WT


title: CHART_WT_input_rep2


title: CHART_6A_rep2


title: ChIP_shK_rep1


title: CHART_WT_rep2


title: CHART_6A_rep1


title: CHART_WT_rep1


title: RNAseq_6A_D14_rep2

data_processing:
PE150 reads were preprocessed using software trim Galor (version 0.4.3) and cutadapt (version 1.4.2) to remove 2 adaptors (AGATCGGAAGAGCACACGT, AGATCGGAAGAGCGTCGTGT). Unique reads were produces by adhoc methods from fastq files. Allelic alignments were preformed similar to the ChIP-seq pipeline only using references mm10_cas and mm10_mus in a 2 pass STAR (version 2.7.10a) alignment (--outSAMprimaryFlag AllBestScore --outMultimapperOrder Random  --outSAMtype BAM Unsorted --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.05 --peOverlapNbasesMin 5 --peOverlapMMp 0.05 --outFilterIntronMotifs RemoveNoncanonical).
Assembly: mm10
Supplementary files format and content: txt

growth_protocol: Undifferentiated ES cells were grown on -irradiated MEF feeders for 2 days in media containing DMEM, high glucose, GlutaMAX supplement, pyruvate, 15% Hyclone FBS (Sigma), 25 mM HEPES pH 7.2-7.5, 1x MEM non-essential amino acids, 1x Pen/Strep, 0.1 mM bME, and 500 U/mL ESGRO recombinant mouse Leukemia Inhibitory Factor (LIF) protein (Sigma, ESG1107) at 37°C with 5% CO2. ES cell colonies were trypsinized and feeders removed (day 0). ES cells were then switched to medium lacking LIF to induce differentiation and grown in suspension for 4 days, forming embryoid bodies (EBs). EBs were settled down onto gelatin-coated plates at day 5, and allowed to further differentiate until at day 14.

extract_protocol: Total cell RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific), from which rRNA was depleted using RiboMinus™ Eukaryote Kit v2 (A15020) (Life Technologies Corporation) as per manufacturer’s instructions. RNA-seq libraries were prepared in two biological replicates using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer’s instructions. Libraries were sequenced on Ilumina Novaseq, generating 150bp pair-end reads.

value: Day 14 differentiated mouse embryonic stem cells


title: RNAseq_WT_D14_rep2


title: RNAseq_6A_D0_rep2

value: Day0 mouse embryonic stem cells


title: RNAseq_WT_D0_rep2


title: RNAseq_WT_D14_rep1


title: RNAseq_6A_D14_rep1


title: Other3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: lung

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: lung

value: other lung myeloid cells

value: Cx3cr1-Cre/VeDTR (deltaFRT)


title: AM2

value: alveolar macrophage


title: AM1


title: ChIP_shScr_rep1

value: MEFs (CAST/Ei x 129/Sv/Jae)

value: MEFs

value: shRNA, overexpression plasmids


title: RNAseq_WT_D0_rep1


title: AM3


title: DSS-N-2

first: Zhe

last: Cui

address: No.1058, Huan Zhen Bei Road, Baoshan District, Shanghai

institute: Department of General Surgery, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the human genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: colon

extract_protocol:
RNA was isolated using the standard TRIzol protocol.
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

value: colitis

value: colon

value: DSS+normal saline


title: DSS-T-3

value: DSS+thymopentin


title: RNAseq_6A_D0_rep1

value: mESCs (CAST/Ei x 129/Sv/Jae)


title: Other1


title: DSS-T-2


title: TNB-T-3

value: TNBS+thymopentin


title: TNB-N-3

value: TNBS+normal saline


title: TNB-T-2

value: WT


title: TNB-N-2


title: Other2


title: DSS-N-1


title: TNB-N-1


title: HiC_shK_6A

data_processing:
Reads were trimmed using cutadapt with the options–adaptor = GATCGATC (MboI ligation junction) and–minimum-length = 20. Reads of each pair were individually mapped to the mus (Xi) and cas (Xa) reference genomes using Bowtie2 and merged into Hi-C summary files and filtered using HOMER as previously described (Minajigi et al., 2015). Hi-C contact maps were generated from reads in the filtered HOMER mus and cas tag directories using the ‘pre’ command of Juicer tools with the genomeID mm10 (Durand et al., 2016b). The resulting Hi-C contact maps in .hic format were visualized and normalized with the ‘Coverage Square Root’ option in Juicebox version 1.8.8 (Durand et al., 2016a).
Assembly: mm10
Supplementary files format and content: hic files

source_name: MEFs

extract_protocol:
In situ Hi-C: As described in Rao et al. (2014), 5 million cells were crosslinked with 1% formaldehyde for 10min. Crosslinked cell pellets were lysed with 300uL ice-cold HiC lysis buffer (10mM Tris HCl pH 8, 10mM NaCl, 0.2% Igepal CA630) with protease inhibitors (Roche). Cell suspension was incubated for 30min at 4C with rotation, then pelleted at 2500xg for 5min. Pelleted nuclei were then washed with 500ul ice-cold HiC lysis buffer and resuspended in 50uL 0.5% SDS solution and incubated at 62C for 10min. 145ul H2O and 25ul 10% Triton X-100 were added to quench SDS and nuclei incubated at 37C for 15min. 26.1ul of 10X NEB Buffer 2 and 100U of MboI restriction enzyme were added and nuclei digested overnight at 37C with rotation. MboI was then heat activated at 62C for 20min, then nuclei cooled to room temperature. To fill in MboI fragment overhangs and mark DNA ends with biotin, 50ul of fill-in master mix was added (37.5ul 0.4mM biotin-14-dATP, 1.5ul 10mM dCTP, 1.5ul 10mM dGTP, 1.5ul 10mM dTTP, 8ul 5U/ul DNA Polymerase I, Large (Klenow) Fragment) and mixed by pipetting. Nuclei were then incubated at 37C for 1h with rotation. To ligate biotinylated DNA ends together, 900ul ligation master mix was added (649ul H2O, 120ul 10X NEB T4 ligase buffer, 100ul 10% Triton X-100, 6ul of 20mg/ml BSA, 25ul of 400U/ul T4 DNA ligase). Reaction was mixed by inverting and incubated at room temperature for 4h with rotation. Reaction was then centrifuged at 1700xg for 5min at room temperature. Pelleted nuclei were resuspended in 750ul TES buffer (1mM EDTA, 10mM Tris-HCl pH 8, 0.5% SDS), 50ul Proteinase K (20mg/ml) added and incubated at 55C for 1h with rotation. To reverse crosslinks, 88.9ul 3M NaCl was added and crosslinks reversed by incubated overnight at 65C with shaking (Eppendorf thermomixer, 950rpm). Samples were cooled to room temperature and DNA extracted with phase-lock gel tubes (5Prime). RNA was digested from purifying DNA by adding 2ul RNAse A (20mg/ml) and incubating at 37C for 1h. DNA was then extracted with phase-lock gel tubes (5Prime) and resuspended in 130ul 1X Tris buffer (10mM Tris-HCl, pH 8). To ensure complete resuspension, DNA was then incubated at 37C for 15min. DNA was then sonicated to a size of 300-500bp using a Covaris with the following parameters: 140W, 10% duty cycle, 200 bursts/cycle, 100s. Samples were then size selected to 300-500bp using AMPure XP beads and eluted in 300ul 1X Tris buffer. To pulldown biotinylated ligation products, 30ul (per sample) of MyOne Streptavidin C1 beads were washed with 400ul of 1X Tween washing buffer (5mM Tris-HCl pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) and resuspended in 300ul 2X binding buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 2M NaCl). Beads were then added to purified DNA and sample incubated at room temperature for 15min with rotation. Beads were washed twice with 600ul 1X Tween Washing buffer. Subsequent library preparation steps were then done directly on beads.
30ul of Dynabeads MyOne Streptavidin C1 beads was used per sample. After adaptor-ligation with 3 ml of 15uM  NEBNext adaptor for Illumina (included in NEBNext Multiplex Oligos for Illumina; NEB, E7335S) at RT for 15 min, the C1 beads were separated on a magnet, washed with 600 ml of 1X TWB (5mM Tris-HCl, pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) twice at 55 C for 2 min and washed briefly with 100 ml of 1X NEBuffer 2.1 at RT. The resulting C1 beads were resuspended in 50 ml of 1XNEBuffer 2.1 with 3 ml USER enzyme (included in NEBNext Multiplex Oligos for Illumina; NEB, E7335S) and incubated at 37C for
20 min with rotation. After the buffer was discarded, the beads were resuspended in 100 ml of 1X PCR master mix [50 ml of Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531S), 2.5 ml of universal primer (NEBNext Multiplex Oligos for Illumina; NEB,E7335S), 2.5 ml of index primer (NEBNext Multiplex Oligos for Illumina; NEB, E7335S, 45 ml of water]. In situ Hi-C libraries were directly amplified from the beads with 12 cycles. Libraries were generated in two biological replicates.

value: CAST/Ei x 129/Sv/Jae

value: shHNRNPK and 6A-HNRNPK mutant overexpression


title: HiC_shK_WT

value: shHNRNPK and WT-HNRNPK overexpression


title: HiC_shK

value: shHNRNPK


title: TNB-T-1