title: CUT&Tag of RNAPII S5P  in G1/S cells rep2

description: Library name: G1_S_S5P_2


title: AldhPosNIF_3

status: Public on Jan 29 2025

type: SRA

city: MARSEILLE

first: Christophe

last: Ginestier

address: 27 Bd Leï Roure

country: France

institute: CRCM

description:
Library name: Sample 6
Column name in raw_counts_all_samples.txt: AldhPosNIF_3

library_source: transcriptomic

data_processing:
FastQC and STAR for QC and alignment
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts for rach sample

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: Cell lines were grown in the standard medium as described in Charafe-Jauffret, E. et al. Cancer Res 69, 1302–1313 (2009)

extract_protocol:
Total RNA was isolated using the Maxwell RSC simply RNA Tissue Kit (AS1340)
Illumina Stranded Total RNA Prep

treatment_protocol: Cell lines were  treated in adherent conditions with Nifuroxazide (NIF) (stock concentration SC = [10 mM], Selleckchem, S4182) for 30 hours. ALDHneg and ALDHbr cells were then isolated by cell sorting

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: Colon cancer

tag: genotype

value: cancer stem cells (ALDHpos)

tag: treatment

value: 30h Nifuroxazide


title: F123 GAM library f123_1NP_GAM180426_E11_1_S85_R1_001

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip

library_source: genomic

data_processing:
Sequenced reads from each GAM library were mapped to the mouse genome assembly GRCm38 (Dec. 2011, mm10) using bowtie2 with all default settings. All non-uniquely mapped reads, reads with mapping quality < 20 were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command. Samples were checked for contamination using fastq_screen. Number of nucleotides sequenced in each genomic bin was calculated using bedtools coverage command. Next, the optimal threshold between the sequencing noise and the signal to call positive windows was calculated as the lowest coverage per bin that gives the highest percent of clustered windows (windows that have a neighboring positive window on at-least one side) for each GAM sample in the dataset. Windows were called positive when the number of nucleotides covered by the reads is higher or equal to the optimal threshold. Each dataset was assessed for quality control by determining the percentage of orphan windows, number of uniquely mapped reads to the mouse genome, and cross-well contamination for every sample. 1NP samples that passed QC were merged into in-silico 3NPs at the level of positive windows. For good quality samples, we produced raw co-segregation, as well as normalized (NPMI) pair-wise chromatin contact matrices.
Assembly: mm10
Supplementary files format and content: Processed data files are raw GAM segregation tables, non-normalized pairwise cosegregation matrices and normalized NPMI matrices in tab-delimited format.
Library strategy: WGA

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse F123 ESCs (a male, hybrid cell line, derived from S129/Jae and Cast) (Gribnau et al., 2003) were cultured in a layer of mitotically inactivated feeder murine embryonic fibroblasts under standard conditions (DMEM, supplemented with 15 % KSR, 1x Glutamax, 10 mM non-essential amino acids, 50 µM beta-mercaptoethanol , 1000 U / ml LIF). Before harvesting, mESCs were passaged onto feeder free 0.1% gelatin coated plates for at least 2 passages to remove feeder cells. As feeder-removal results in reduced levels of LIF in the culture, the LIF concentration in the media was doubled when the cells were in feeder-free culture conditions. Cells were harvested after ~ 48 h at 70 – 80 % confluency.

extract_protocol:
Fixation of F123 mESC was performed as described previously (Branco and Pombo, 2006). Briefly, cells were grown to 70 % confluency, media was removed, and cells were fixed in 4% and 8% paraformaldehyde in 250 mM HEPES-NaOH (pH 7.6; 10 min and 2 h, respectively), gently scrapped, and softly pelleted and embedded in saturated 2.1 M sucrose in PBS and frozen in liquid nitrogen on copper sample holders. Ultrathin cryosections were cut with a glass knife using an ultracryomicrotome (Leica Biosystems, EM UC7) at ~230 nm thickness, and transferred to PEN membrane steel frame slides 4.0 µm (Leica Microsystems, 11600289) for laser microdissection. Before laser microdissection, cryosections were washed in sterile-filtered 1x PBS (3 times, 5 min each), sterile-filtered H2O (3 times, 5 min each), and stained with sterile-filtered 1 % (w/v) cresyl violet (Sigma-Aldrich, C5042) in H2O for 10 min, followed by 2 washes with H2O (30 s each).  Individual NPs were isolated from the cryosection by laser microdissection using a laser microdissection microscope (Leica Microsystems, LMD7000). Cut NPs were collected in a PCR Cap Strip filled with opaque adhesive material (Carl Zeiss Microscopy, 415190-9161-000). For each collection day, 1 or 2 caps were left empty and taken through the whole genome amplification (WGA) and sequencing process as a negative control for quality control purposes.
Whole Genome Amplification (WGA) was performed as described previously (Winick-Ng et al, 2021) with minor modifications. Briefly, DNA was extracted from NPs at 60oC in the lysis buffer (20mM Tris-HCl pH 8.0, 1.4 mM EDTA, 560 mM guanidinium-HCl, 3.5% Tween-20, 0.35% Triton X-100) containing 0.75 units/ml Qiagen protease (Qiagen, 19155). After 24h of DNA extraction, the protease was heat inactivated at 75oC for 30 min and the extracted DNA was amplified via two rounds of PCR. At-first quasi-linear amplification was performed with random hexamer GAT-7N  primers with an adaptor sequence. The lysis buffer containing the extracted genomic DNA was mixed with 2x DeepVent mix buffer (2x Thermo polymerase buffer (10x), 400 µm dNTPs, 4 mM MgSO4 in ultrapure DNase free water), 0.5 µM GAT-7N primers (5′- GTG AGT GAT GGT TGA GGT AGT GTG GAG NNN NNN N) and 2 units/µl DeepVent® (exo-) DNA polymerase (New England Biolabs, M0259L) and incubated for 11 cycles in the BioRad thermocycler. The second exponential PCR amplification was performed in presence of 1x DeepVent mix, 10 mM dNTPs, 0.4 µM GAM-COM primers (5′-GTG AGT GAT GGT TGA GGT AGT GTG GAG) and 2 units/µl DeepVent (exo-) DNA polymerase in the programmable thermal cycler for 26 cycles.
After whole genome amplification, the DNA WGA product was purified withSPRI beads (1.7x) The DNA concentration of each sample was quantified using the Quant-iT® PicoGreen dsDNA assay kit (Invitrogen #P7589). Genomic sequencing library was prepared from 1ng of purified DNA using the Illumina Nextera XT library preparation kit (Illumina #FC-131-1096), following the manufacturer’s instructions or with reduce to 20% volume of reagents. After the library preparation, DNA was again purified with in-house SPRI beads (1.7x) and equal amounts of DNA from each sample was pooled together (up to 196 samples) for the sequencing. The final pool of libraries was additionally purified two more times with SPRI beads (1.7x) and analyzed using DNA High Sensitivity on-chip electrophoresis on an Agilent 2100 Bioanalyzer. The samples were sequenced on Illumina NextSeq500 machine as single-end 75 bp reads, according to manufacturer’s instructions.

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

tag: Sex

value: male


title: F123 GAM library f123_1NP_GAM180426_C09_1_S67_R1_001


title: F123 GAM library f123_1NP_GAM180426_C12_1_S91_R1_001


title: AldhPosNIF_2

description:
Library name: Sample 5
Column name in raw_counts_all_samples.txt: AldhPosNIF_2


title: F123 GAM library f123_1NP_GAM180426_C08_1_S59_R1_001


title: F123 GAM library f123_1NP_GAM180426_C07_1_S51_R1_001


title: CUT&Tag of RNAPII S5P  in G1/S cells rep1

city: hefei

first: sun

last: xuedan

address: daoxiangcun

country: China

institute: ustc

description: Library name: G1_S_S5P_1

data_processing:
(RNA-seq) Raw reads were quality-filtered using Seqtk and then aligned to the reference genome with Hisat2 (version 2.0.4). Gene fragment counts were generated using StringTie (v1.3.3b) and normalized by TMM (trimmed mean of M-values). Differential expression analysis was performed using edgeR, identifying significant differentially expressed genes (DEGs) as those with a False Discovery Rate (FDR) value below the threshold (Q < 0.05) and a fold-change greater than 2. (CUT-tag)The data analysis workflow first involved adapter trimming and removal of low-quality bases from paired-end reads were conducted using Trim Galore software. Clean reads were then aligned to the hg38 reference genome using Bowtie2, followed by the removal of PCR duplicates with Picard. Genome browser tracks in bigWig format were produced from merged replicates using samtools, and peak calling was performed with MACS2 using the parameters -f BAMPE --broad -nomodel. The resulting bigWig data were visualized using the Integrative Genomics Viewer (IGV) software from the Broad Institute, while peak visualizations were prepared using Deeptools. (scRNA)Single-cell RNA-seq data were processed with Cell Ranger count (10x Genomics Cell Ranger based on the mouse reference genome GRCm38 (mm10)). Digital gene expression matrices were analyzed in R using the Seurat package. Cells were filtered based on the number of features (less than 500 genes) and the percentage of mitochondrial genes ('percent.mt' lower than 5%). Data normalization and scaling were performed using the default parameters with Seurat functions NormalizeData and ScaleData. Principal component analysis (PCA) and UMAP dimension reduction were conducted using the top 20 principal components. A nearest-neighbor graph was calculated using FindNeighbors based on the 20 dimensions of the PCA reduction, followed by clustering with FindClusters at a resolution of 0.6. Candidate marker genes for each cell cluster were identified using the FindAllMarkers function.
Assembly: hg38/mm10
Supplementary files format and content: text files include FPKM values for each Sample for RNA-seq
Supplementary files format and content: bigwig for Cut-tag
Supplementary files format and content: matrix.mtx.gz for scRNA
Library strategy: CUT&Tag

source_name: liver

extract_protocol:
RNA sequencing libraries were prepared using the phenol/chloroform extraction method. Single-cell isolation was performed with the 10x Genomics Chromium Single Cell Solution platform. For CUT&Tag experiments, cell capture was achieved using ConA-coated magnetic beads for cell enrichment.
RNA libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® according to standard Illumina instructions. And CUT&Tag libraries were prepared according to the protocol established by Steven Henikoff's laboratory.scRNA-seq libraries were prepared following the manufacturer’s protocol (10x Genomics).

value: liver

value: tumor cells


title: CUT&Tag of RNAPII S2P  in Late_S cells rep2

description: Library name: Late_S_S2P_2


title: AldhPosNIF_1

description:
Library name: Sample 4
Column name in raw_counts_all_samples.txt: AldhPosNIF_1


title: F123 GAM library f123_1NP_GAM180426_B12_1_S90_R1_001


title: F123 GAM library f123_1NP_GAM180426_B10_1_S74_R1_001


title: F123 GAM library f123_1NP_GAM180426_B09_1_S66_R1_001


title: NIF_ALDpos_2

description:
Library name: Sample 2
Column name in raw_counts_all_samples.txt: NIF_ALDpos_2

value: Breast cancer


title: CUT&Tag of RNAPII S2P  in Early_S cells rep2

description: Library name: Early_S_S2P_2


title: F123 GAM library f123_1NP_GAM180426_A12_1_S89_R1_001


title: NIF_ALDpos_1

description:
Library name: Sample 1
Column name in raw_counts_all_samples.txt: NIF_ALDpos_1


title: F123 GAM library f123_1NP_GAM180426_B07_1_S50_R1_001


title: RNA-SEQ for shRFC3 cells rep3

description: Library name: shRFC3_3

data_processing:
(RNA-seq) Raw reads were quality-filtered using Seqtk and then aligned to the reference genome with Hisat2 (version 2.0.4). Gene fragment counts were generated using StringTie (v1.3.3b) and normalized by TMM (trimmed mean of M-values). Differential expression analysis was performed using edgeR, identifying significant differentially expressed genes (DEGs) as those with a False Discovery Rate (FDR) value below the threshold (Q < 0.05) and a fold-change greater than 2. (CUT-tag)The data analysis workflow first involved adapter trimming and removal of low-quality bases from paired-end reads were conducted using Trim Galore software. Clean reads were then aligned to the hg38 reference genome using Bowtie2, followed by the removal of PCR duplicates with Picard. Genome browser tracks in bigWig format were produced from merged replicates using samtools, and peak calling was performed with MACS2 using the parameters -f BAMPE --broad -nomodel. The resulting bigWig data were visualized using the Integrative Genomics Viewer (IGV) software from the Broad Institute, while peak visualizations were prepared using Deeptools. (scRNA)Single-cell RNA-seq data were processed with Cell Ranger count (10x Genomics Cell Ranger based on the mouse reference genome GRCm38 (mm10)). Digital gene expression matrices were analyzed in R using the Seurat package. Cells were filtered based on the number of features (less than 500 genes) and the percentage of mitochondrial genes ('percent.mt' lower than 5%). Data normalization and scaling were performed using the default parameters with Seurat functions NormalizeData and ScaleData. Principal component analysis (PCA) and UMAP dimension reduction were conducted using the top 20 principal components. A nearest-neighbor graph was calculated using FindNeighbors based on the 20 dimensions of the PCA reduction, followed by clustering with FindClusters at a resolution of 0.6. Candidate marker genes for each cell cluster were identified using the FindAllMarkers function.
Assembly: hg38/mm10
Supplementary files format and content: text files include FPKM values for each Sample for RNA-seq
Supplementary files format and content: bigwig for Cut-tag
Supplementary files format and content: matrix.mtx.gz for scRNA

molecule: polyA RNA


title: F123 GAM library f123_1NP_GAM180426_A11_1_S81_R1_001


title: F123 GAM library f123_1NP_GAM180426_A09_1_S65_R1_001


title: CUT&Tag of RNAPII S2P  in Late_S cells rep1

description: Library name: Late_S_S2P_1


title: F123 GAM library f123_1NP_GAM180426_B08_1_S58_R1_001


title: CUT&Tag of RNAPII S2P  in G1/S cells rep2

description: Library name: G1_S_S2P_2


title: F123 GAM library f123_1NP_GAM180426_A10_1_S73_R1_001


title: F123 GAM library f123_1NP_GAM180426_A07_1_S49_R1_001


title: CUT&Tag of RNAPII S2P  in Early_S cells rep1

description: Library name: Early_S_S2P_1


title: RNA-SEQ for shRFC3 cells rep2

description: Library name: shRFC3_2


title: RNA-SEQ for shRFC3 cells rep1

description: Library name: shRFC3_1


title: CUT&Tag of G4-DNA  in Late_S cells rep2

description: Library name: Late_S_G4_2


title: CUT&Tag of RNAPII S2P  in G1/S cells rep1

description: Library name: G1_S_S2P_1


title: F123 GAM library f123_1NP_GAM180410_H11_2_S184_R1_001


title: F123 GAM library f123_1NP_GAM180410_H12_2_S192_R1_001


title: F123 GAM library f123_1NP_GAM180410_H12_1_S96_R1_001


title: RNA-SEQ for shCtrl cells rep3

description: Library name: shCtrl_3


title: NIF_ALDpos_3

description:
Library name: Sample 3
Column name in raw_counts_all_samples.txt: NIF_ALDpos_3


title: CUT&Tag of G4-DNA  in Late_S cells rep1

description: Library name: Late_S_G4_1


title: F123 GAM library f123_1NP_GAM180410_H11_1_S88_R1_001


title: CUT&Tag of G4-DNA  in Early_S cells rep2

description: Library name: Early_S_G4_2


title: F123 GAM library f123_1NP_GAM180410_H10_1_S80_R1_001


title: F123 GAM library f123_1NP_GAM180426_A08_1_S57_R1_001


title: F123 GAM library f123_1NP_GAM180410_H10_2_S176_R1_001


title: RNA-SEQ for shCtrl cells rep2

description: Library name: shCtrl_2


title: CUT&Tag of G4-DNA  in Early_S cells rep1

description: Library name: Early_S_G4_1


title: F123 GAM library f123_1NP_GAM180410_H09_1_S72_R1_001


title: F123 GAM library f123_1NP_GAM180410_H07_2_S152_R1_001


title: F123 GAM library f123_1NP_GAM180410_H09_2_S168_R1_001


title: F123 GAM library f123_1NP_GAM180410_H08_2_S160_R1_001


title: CUT&Tag of TOP1 in shRFC3 cells rep2

description: Library name: shRFC3_TOP1_2


title: CUT&Tag of TOP1  in shRFC3 cells rep1

description: Library name: shRFC3_TOP1_1


title: CUT&Tag of TOP1 in shCtrl cells rep2

description: Library name: shCtrl_TOP1_2


title: F123 GAM library f123_1NP_GAM180410_H05_1_S40_R1_001


title: CUT&Tag of TOP1  in shCtrl cells rep1

description: Library name: shCtrl_TOP1_1


title: F123 GAM library f123_1NP_GAM180410_H06_2_S144_R1_001


title: siNC.H2O2_9

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
BGI used BGISEQ 500 platform for RNA-Seq
The raw data include low quality, contamination of joints, and high levels of unknown base n reads, which need to be removed before analysis to ensure the reliability of the results
The clean reads were align to the reference genome sequnence using HISAT
The clean reads were align to the reference genome sequnence using Bowtie2
Assembly: NCBI, Homo_sapiens , GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cardiomyocyte AC16 cells were cultured in DMEM/F12 and DMEM (high glucose), respectively. DMEM supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 100 U/mL penicillin, and 100 μg/ml streptomycin.

extract_protocol:
RNA  extracted according to the manufacturer's instructions using Trizol reagent.
RNA libraries were prepared for sequencing according to manufacturer's instructions of Beijing Genomics Institution (BGI)

treatment_protocol: Medium without FBS was replaced before transfection. Negative control siRNA and EP300 siRNA were transfected into AC16 cells at ~70% confluence using jetPRIME® (Polyplus-transfection, NY, USA). After 12h of transfection, AC16 cells were treated with H2O2 (200mM) for 1 h, then fresh complete medium was replaced. After 48 h, RNA  extracted according to the manufacturer's instructions using Trizol reagent.

value: siRNA  Control


title: CUT&Tag of G4-DNA  in G1/S cells rep1

description: Library name: G1_S_G4_1


title: F123 GAM library f123_1NP_GAM180410_H08_1_S64_R1_001


title: siEP300.H2O2_11


title: siEP300.H2O2_12


title: CUT&Tag of G4-DNA  in G1/S cells rep2

description: Library name: G1_S_G4_2


title: F123 GAM library f123_1NP_GAM180410_H07_1_S56_R1_001


title: F123 GAM library f123_1NP_GAM180410_H04_2_S128_R1_001


title: F123 GAM library f123_1NP_GAM180410_H05_2_S136_R1_001


title: F123 GAM library f123_1NP_GAM180410_H06_1_S48_R1_001


title: F123 GAM library f123_1NP_GAM180410_H03_2_S120_R1_001


title: F123 GAM library f123_1NP_GAM180410_H02_2_S112_R1_001


title: CUT&Tag of TBP in shRFC3 cells rep2

description: Library name: shRFC3_TBP_2


title: RNA-SEQ for shCtrl cells rep1

description: Library name: shCtrl_1


title: F123 GAM library f123_1NP_GAM180410_H02_1_S16_R1_001


title: CUT&Tag of TBP in shRFC3 cells rep1

description: Library name: shRFC3_TBP_1


title: F123 GAM library f123_1NP_GAM180410_H03_1_S24_R1_001


title: siEP300.H2O2_10


title: F123 GAM library f123_1NP_GAM180410_H01_2_S104_R1_001


title: siNC.H2O2_7


title: siNC.H2O2_8


title: siEP300_6

value: Control


title: CUT&Tag of TBP  in shCtrl cells rep1

description: Library name: shCtrl_TBP_1


title: F123 GAM library f123_1NP_GAM180410_G11_1_S87_R1_001


title: CUT&Tag of CDK7 in shRFC3 cells rep2

description: Library name: shRFC3_CDK7_2


title: siEP300_4


title: F123 GAM library f123_1NP_GAM180410_G07_2_S151_R1_001


title: CUT&Tag of CDK7 in shCtrl cells rep2

description: Library name: shCtrl_CDK7_2


title: F123 GAM library f123_1NP_GAM180410_G12_1_S95_R1_001


title: F123 GAM library f123_1NP_GAM180410_G08_2_S159_R1_001


title: F123 GAM library f123_1NP_GAM180410_G09_1_S71_R1_001


title: F123 GAM library f123_1NP_GAM180410_H01_1_S8_R1_001


title: CUT&Tag of TBP in shCtrl cells rep2

description: Library name: shCtrl_TBP_2


title: CUT&Tag of CDK7  in shRFC3 cells rep1

description: Library name: shRFC3_CDK7_1


title: F123 GAM library f123_1NP_GAM180410_G12_2_S191_R1_001


title: siEP300_5


title: F123 GAM library f123_1NP_GAM180410_G09_2_S167_R1_001


title: F123 GAM library f123_1NP_GAM180410_G07_1_S55_R1_001


title: siNC_2


title: F123 GAM library f123_1NP_GAM180410_G10_2_S175_R1_001


title: F123 GAM library f123_1NP_GAM180410_G11_2_S183_R1_001


title: siNC_3


title: F123 GAM library f123_1NP_GAM180410_G08_1_S63_R1_001


title: CUT&Tag of CDK7  in shCtrl cells rep1

description: Library name: shCtrl_CDK7_1


title: F123 GAM library f123_1NP_GAM180410_G10_1_S79_R1_001


title: CUT&Tag of NELFB in shRFC3 cells rep2

description: Library name: shRFC3_NELFB_2


title: siNC_1


title: F123 GAM library f123_1NP_GAM180410_G06_2_S143_R1_001


title: CUT&Tag of NELFB  in shRFC3 cells rep1

description: Library name: shRFC3_NELFB_1


title: F123 GAM library f123_1NP_GAM180410_G05_2_S135_R1_001


title: CUT&Tag of NELFB in shCtrl cells rep2

description: Library name: shCtrl_NELFB_2


title: siMLF1_6

extract_protocol:
RNA of NRVMs extracted according to the manufacturer's instructions using Trizol reagent.
RNA libraries were prepared for sequencing according to manufacturer's instructions of Beijing Genomics Institution (BGI)

treatment_protocol: Medium without FBS was replaced before transfection. Negative control siRNA and Mlf1 siRNA were transfected into AC16 cells at ~70% confluence using jetPRIME® (Polyplus-transfection, NY, USA). After 12 h of transfection, fresh complete medium was replaced.

value: Cardiomyocyte


title: CUT&Tag of NELFB  in shCtrl cells rep1

description: Library name: shCtrl_NELFB_1


title: F123 GAM library f123_1NP_GAM180410_G03_2_S119_R1_001


title: CUT&Tag of NELFA in shRFC3 cells rep2

description: Library name: shRFC3_NELFA_2


title: F123 GAM library f123_1NP_GAM180410_G04_2_S127_R1_001


title: F123 GAM library f123_1NP_GAM180410_G03_1_S23_R1_001


title: siMLF1_5


title: F123 GAM library f123_1NP_GAM180410_G02_2_S111_R1_001


title: CUT&Tag of NELFA in shCtrl cells rep2

description: Library name: shCtrl_NELFA_2


title: siMLF1_4


title: siNeg_3


title: F123 GAM library f123_1NP_GAM180410_G01_2_S103_R1_001


title: siNeg_2


title: CUT&Tag of NELFA  in shRFC3 cells rep1

description: Library name: shRFC3_NELFA_1


title: F123 GAM library f123_1NP_GAM180410_G01_1_S7_R1_001


title: F123 GAM library f123_1NP_GAM180410_F12_2_S190_R1_001


title: F123 GAM library f123_1NP_GAM180410_F12_1_S94_R1_001


title: siNeg_1


title: C57 mouse OE3

city: Shanghai

first: Chen

last: Yanxi

address: No. 138, Dong'an Road, Xuhui District, Shanghai

institute: Fudan University

description: Library name: LH3

data_processing:
The raw data was checked by FastQC v0.11.5
Clean reads were aligned to the Mouse genome using STAR 2.5.3a
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.16.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: auditory cortex

extract_protocol:
Total RNA was isolated from each striatum sample using Trizol
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit

value: auditory cortex

value: WNT3 Overexpressing


title: CUT&Tag of NELFA  in shCtrl cells rep1

description: Library name: shCtrl_NELFA_1


title: CUT&Tag of RNAPII S5P  in shRFC3 cells rep2

description: Library name: shRFC3_S5P_2


title: F123 GAM library f123_1NP_GAM180410_G05_1_S39_R1_001


title: F123 GAM library f123_1NP_GAM180410_F10_2_S174_R1_001


title: F123 GAM library f123_1NP_GAM180410_F10_1_S78_R1_001


title: F123 GAM library f123_1NP_GAM180410_G02_1_S15_R1_001


title: CUT&Tag of RNAPII S5P  in shCtrl cells rep2

description: Library name: shCtrl_S5P_2


title: F123 GAM library f123_1NP_GAM180410_F11_2_S182_R1_001


title: F123 GAM library f123_1NP_GAM180410_F11_1_S86_R1_001


title: F123 GAM library f123_1NP_GAM180410_F05_2_S134_R1_001


title: C57 mouse OE2

description: Library name: LH2


title: F123 GAM library f123_1NP_GAM180410_F09_2_S166_R1_001


title: F123 GAM library f123_1NP_GAM180410_F07_2_S150_R1_001


title: C57 mouse NC3

description: Library name: LC3

value: WNT3 control


title: F123 GAM library f123_1NP_GAM180410_F06_2_S142_R1_001


title: C57 mouse OE1

description: Library name: LH1


title: C57 mouse NC1

description: Library name: LC1


title: CUT&Tag of RNAPII S2P  in shRFC3 cells rep2

description: Library name: shRFC3_S2P_2


title: F123 GAM library f123_1NP_GAM180410_F08_1_S62_R1_001


title: F123 GAM library f123_1NP_GAM180410_F08_2_S158_R1_001


title: F123 GAM library f123_1NP_GAM180410_F06_1_S46_R1_001


title: CUT&Tag of RNAPII S5P  in shRFC3 cells rep1

description: Library name: shRFC3_S5P_1


title: CUT&Tag of RNAPII S2P  in shRFC3 cells rep1

description: Library name: shRFC3_S2P_1


title: F123 GAM library f123_1NP_GAM180410_F09_1_S70_R1_001


title: F123 GAM library f123_1NP_GAM180410_F07_1_S54_R1_001


title: CUT&Tag of RNAPII S5P  in shCtrl cells rep1

description: Library name: shCtrl_S5P_1


title: F123 GAM library f123_1NP_GAM180410_F04_2_S126_R1_001


title: CUT&Tag of RNAPII S2P  in shCtrl cells rep2

description: Library name: shCtrl_S2P_2


title: C57 mouse NC2

description: Library name: LC2


title: F123 GAM library f123_1NP_GAM180410_F05_1_S38_R1_001


title: F123 GAM library f123_1NP_GAM180410_F03_2_S118_R1_001


title: F123 GAM library f123_1NP_GAM180410_F02_1_S14_R1_001


title: F123 GAM library f123_1NP_GAM180410_F02_2_S110_R1_001


title: scRNA for sgRFC3 liver cancer tissues

description: Library name: sgRFC3

library_source: transcriptomic single cell

value: Liver tissues  cells


title: scRNA for sgCtrl liver cancer tissues

description: Library name: sgCtrl


title: F123 GAM library f123_1NP_GAM180410_E12_2_S189_R1_001


title: F123 GAM library f123_1NP_GAM180410_F03_1_S22_R1_001


title: ZT11Ab.female.541

city: Philadelphia

first: Thomas

middle: G

last: Brooks

address: 3400 Civic Center Blvd

department: ITMAT

country: USA

institute: University of Pennsylvania

description: Library name: ZT11Ab.female.541

data_processing:
Reads were quantified with Salmon v1.9.0 using the GRCm38 genome and Ensembl v102 annotation. Differential expression was tested using DESeq2 v1.42.0.
Assembly: GRCm38, ensembl v102
Supplementary files format and content: IL10_Ab.TPM.txt contains the complete abundance measurements.
Supplementary files format and content: Sengupta.ZT23IgG_ZT23Ab_ZT11IgG.results.xlsx contains three sub-tables, each of which contains gene-level quantified values for each sample as well as differential expression results from DESeq2 for the three pairwise comparisons. There is also an interaction term sheet.

source_name: Lung

growth_protocol: Adult C57b/6 mice 8-18 weeks in age were bred in-house or ordered from Jackson Laboratories.

extract_protocol:
RNA was extracted from the lung tissue using TRIzol (ThermoFisher Scientific, catalog no. 15596026) and RNeasy Mini Kit (Qiagen, catalog no. 74204), according to manufacturers’ protocols. After extraction, total RNA was analyzed on a Tapestation 4200 to check for integrity.
Libraries were prepared following the Illumina Stranded Total RiboZero Protocol (April 2021 protocol version)

treatment_protocol: Mice were placed in circadian boxes 2-4 weeks before infection to allow for adjustment to the reverse 12-hour light/dark schedule. Under light isoflurane anesthesia, mice were intranasally infected with 30-35 PFU of mouse-adapted H1N1 (PR8) at either ZT11 or ZT23. To block IL-10 signaling, mice were treated with IL-10R1a monoclonal antibody (Clone 1B1.3A, BioXCell BE0050) or polyclonal IgG (Clone MOPC-21, BioXCell BE0083) during the infection. Mice were treated with 100ug/10uL of IL10R1 MAb administered intranasally D0 in 10uL PBS, 150ug/100uL of IL10R1 Mab administered intraperitoneally on day 3 in 100uL of PBS, and 100ug/100uL of IL10R1 MAb administered i.p. D5.

value: Lung

value: female

tag: time

value: Ab


title: CUT&Tag of RNAPII S2P  in shCtrl cells rep1

description: Library name: shCtrl_S2P_1


title: ZT11Ab.female.5566

description: Library name: ZT11Ab.female.5566


title: F123 GAM library f123_1NP_GAM180410_E12_1_S93_R1_001


title: CUT&Tag of RFC3 in shRFC3 cells rep2

description: Library name: shRFC3_RFC3_2


title: F123 GAM library f123_1NP_GAM180410_E11_2_S181_R1_001


title: F123 GAM library f123_1NP_GAM180410_F01_1_S6_R1_001


title: ZT11Ab.female.3969

description: Library name: ZT11Ab.female.3969


title: CUT&Tag of RFC3  in shRFC3 cells rep1

description: Library name: shRFC3_RFC3_1


title: F123 GAM library f123_1NP_GAM180410_F01_2_S102_R1_001


title: F123 GAM library f123_1NP_GAM180410_E10_1_S77_R1_001


title: F123 GAM library f123_1NP_GAM180410_E09_2_S165_R1_001


title: CUT&Tag of RFC3 in shCtrl cells rep2

description: Library name: shCtrl_RFC3_2


title: CUT&Tag of G4 in shRFC3 cells rep2

description: Library name: shRFC3_G4_2


title: ZT11Ab.male.5568

description: Library name: ZT11Ab.male.5568


title: F123 GAM library f123_1NP_GAM180410_E11_1_S85_R1_001


title: CUT&Tag of RFC3  in shCtrl cells rep1

description: Library name: shCtrl_RFC3_1


title: F123 GAM library f123_1NP_GAM180410_E10_2_S173_R1_001


title: ZT11Ab.male.3966

description: Library name: ZT11Ab.male.3966


title: ZT11Ab.male.3963

description: Library name: ZT11Ab.male.3963


title: F123 GAM library f123_1NP_GAM180410_E09_1_S69_R1_001


title: CUT&Tag of G4  in shRFC3 cells rep1

description: Library name: shRFC3_G4_1


title: F123 GAM library f123_1NP_GAM180410_E08_2_S157_R1_001


title: ZT23Ab.female.396

description: Library name: ZT23Ab.female.396


title: F123 GAM library f123_1NP_GAM180410_E08_1_S61_R1_001


title: F123 GAM library f123_1NP_GAM180410_E07_2_S149_R1_001


title: F123 GAM library f123_1NP_GAM180410_E07_1_S53_R1_001


title: CUT&Tag of G4 in shCtrl cells rep2

description: Library name: shCtrl_G4_2


title: F123 GAM library f123_1NP_GAM180410_E06_2_S141_R1_001


title: CUT&Tag of G4  in shCtrl cells rep1

description: Library name: shCtrl_G4_1


title: F123 GAM library f123_1NP_GAM180410_E05_2_S133_R1_001


title: MOLM, Decitabine, Normoxia, 144 hour, Rep3

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

description:
Library name: 2_DAC_N_R3_S25
2_DAC_N_R3_S25

data_processing:
Raw reads were trimmed using Trim Galore (v0.6.5, Cutadapt v2.10) in paired-end mode with default parameters and retaining unpaired reads.
Hisat2 (v2.1.0) was used to map and align trimmed and unpaired reads using default parameters (--phred33) to the human reference genome build (GRCh38), and samtools (v1.10) was used to generate bam files.
Count tables were generated using SeqMonk (v1.47.1). Only primary alignments (from bam files) were imported and raw counts quantified by specifying library type="opposing strand specific" and 'Merge transcript isoforms'.
Assembly: GRCh38
Supplementary files format and content: tab-deliminated text file containing raw counts for all samples (Columns) per gene (row).

source_name: Peripheral blood

growth_protocol: AML cell lines were routinely cultured at 5x105 cells/mL in normoxic conditions (21% O2, 5% CO2, 37oC). MOLM-13 and MV-4-11 cell lines were cultured using RPMI-1640 medium (Sigma-Aldrich, U.S.) supplemented with 2mM GlutaMAX (Thermofisher, U.S.) and 10% Foetal Bovine Serum (Sigma-Aldrich, U.S.), while HL-60s were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (Sigma-Aldrich, U.S.) with 4mM GlutaMAX and 10% FBS. Cell lines were also tested for mycoplasma using the MycoAlert Mycoplasma detection kit (Lonza, Switzerland).

extract_protocol:
RNA was extracted and purified using Quick DNA/RNA Magbead Kit (Zymo, USA) following the manufacturer’s instructions and eluted in UltraPure distilled water (Thermofisher, U.S).
Libraries were prepared using the Illumina stranded mRNA prep kit (Illumina, US) and sequencing was carried out with a NovaSeq 6000 SP 2x100bp FlowCell plus PhiX spike-in (Illumina, US).

treatment_protocol: AML cell lines were pre-exposed to either normoxic (21% O2, 5% CO2, 37oC) or hypoxic (1% O2, 5% CO2, 37oC) conditions for 72 hours at a concentration of 4x105 cells/mL. A standard CO2 incubator was used for culture at 21% O2, while 1% O2 was maintained in a Hypoxic Glove-box Chamber (PLAS labs, U.S.). Following pre-exposure, cells were re-seeded into their respective oxygen tensions at 4x105 cells/mL and cultured for a further 72 hours, with treatments of decitabine (DAC; 100nM for all cell lines) (Sellekchem, U.S.), 5’-azacitidine (AZA; 500nM) (Sellekchem, U.S.), or without HMA (Untreated control, UT) made every 24 hours.

value: Peripheral blood

value: acute myeloid leukemia

tag: disease/cancer type

value: Acute myeloid leukemia (M5a)

value: Male

tag: age

tag: replicate

value: 72 hour pre-treatment normoxia, 72 hour decitabine

tag: oxygen tension

value: Normoxia (21% O2)

tag: hypomethylating agent_(hma)

value: Decitabine

tag: hypoxia pre-treatment

value: N

tag: batch


title: ZT23Ab.female.3958

description: Library name: ZT23Ab.female.3958


title: ZT23Ab.female.5412

description: Library name: ZT23Ab.female.5412


title: ZT23Ab.male.5569

description: Library name: ZT23Ab.male.5569

value: male


title: F123 GAM library f123_1NP_GAM180410_E05_1_S37_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM180410_E04_2_S125_R1_001


title: MOLM, Untreated, Normoxia, 144 hour, Rep3

description:
Library name: 2_UT_N_R3_S27
2_UT_N_R3_S27

value: 72 hour pre-treatment normoxia, 72 hour untreated

value: Untreated


title: F123 GAM library f123_1NP_GAM180410_E06_1_S45_R1_001


title: F123 GAM library f123_1NP_GAM180410_E03_2_S117_R1_001


title: ZT23Ab.male.3955

description: Library name: ZT23Ab.male.3955


title: F123 GAM library f123_1NP_GAM180410_E02_2_S109_R1_001


title: ZT23Ab.male.3957

description: Library name: ZT23Ab.male.3957


title: F123 GAM library f123_1NP_GAM180410_E01_2_S101_R1_001


title: F123 GAM library f123_1NP_GAM180410_E01_1_S5_R1_001


title: MOLM, Decitabine, Hypoxia, 144 hour, Rep3

description:
Library name: 1_H_DAC_R3_S20
1_H_DAC_R3_S20

value: 72 hour pre-treatment hypoxia, 72 hour decitabine

value: Hypoxia (1% O2)

value: Y


title: MOLM, Azacytadine, Normoxia, 144 hour, Rep3

description:
Library name: 2_AZA_N_R3_S23
2_AZA_N_R3_S23

value: 72 hour pre-treatment normoxia, 72 hour azacytadine

value: Azacytidine


title: F123 GAM library f123_1NP_GAM180410_E03_1_S21_R1_001


title: F123 GAM library f123_1NP_GAM180410_D12_2_S188_R1_001


title: ZT11IgG.female.5482

description: Library name: ZT11IgG.female.5482

value: Lung

value: female

value: IgG


title: MOLM, Untreated, Hypoxia, 144 hour, Rep3

description:
Library name: 1_H_UT_R3_S21
1_H_UT_R3_S21

value: Peripheral blood

value: acute myeloid leukemia

value: Acute myeloid leukemia (M5a)

value: Male

value: 72 hour pre-treatment hypoxia, 72 hour untreated


title: F123 GAM library f123_1NP_GAM180410_D12_1_S92_R1_001

value: mouse embryonic stem cells

value: male


title: F123 GAM library f123_1NP_GAM180410_D11_2_S180_R1_001

value: Hybrid F1 S129/Jae and Cast


title: MOLM, Azacytadine, Hypoxia, 144 hour, Rep3

description:
Library name: 1_H_AZA_R3_S19
1_H_AZA_R3_S19

value: 72 hour pre-treatment hypoxia, 72 hour azacytadine


title: ZT11IgG.male.5567

description: Library name: ZT11IgG.male.5567


title: F123 GAM library f123_1NP_GAM180410_D10_2_S172_R1_001


title: F123 GAM library f123_1NP_GAM180410_D11_1_S84_R1_001


title: ZT11IgG.male.5408

description: Library name: ZT11IgG.male.5408


title: ZT11IgG.female.5565

description: Library name: ZT11IgG.female.5565


title: ZT23IgG.female.5571

description: Library name: ZT23IgG.female.5571


title: F123 GAM library f123_1NP_GAM180410_D08_2_S156_R1_001


title: MOLM, Untreated, Normoxia, 144 hour, Rep2

description:
Library name: 2_UT_N_R2_S18
2_UT_N_R2_S18

value: 72 hour pre-treatment normoxia, 72 hour untreated

value: Normoxia (21% O2)

value: Untreated

value: N


title: F123 GAM library f123_1NP_GAM180410_D10_1_S76_R1_001


title: MOLM, Decitabine, Normoxia, 144 hour, Rep2

description:
Library name: 2_DAC_N_R2_S16
2_DAC_N_R2_S16

value: 72 hour pre-treatment normoxia, 72 hour decitabine

value: Decitabine


title: F123 GAM library f123_1NP_GAM180410_D09_2_S164_R1_001


title: ZT23IgG.male.557

description: Library name: ZT23IgG.male.557

value: Lung


title: F123 GAM library f123_1NP_GAM180410_D06_2_S140_R1_001


title: ZT23IgG.female.5475

description: Library name: ZT23IgG.female.5475

value: female

value: IgG


title: F123 GAM library f123_1NP_GAM180410_D05_2_S132_R1_001


title: MOLM, Azacytadine, Hypoxia, 144 hour, Rep2

description:
Library name: 1_H_AZA_R2_S10
1_H_AZA_R2_S10

value: Peripheral blood

value: acute myeloid leukemia

value: Hypoxia (1% O2)

value: Azacytidine

value: Y


title: MOLM, Untreated, Hypoxia, 144 hour, Rep2

description:
Library name: 1_H_UT_R2_S12
1_H_UT_R2_S12

value: Acute myeloid leukemia (M5a)

value: Male

value: 72 hour pre-treatment hypoxia, 72 hour untreated


title: ZT23IgG.female.5476

description: Library name: ZT23IgG.female.5476


title: F123 GAM library f123_1NP_GAM180410_D07_2_S148_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: F123 GAM library f123_1NP_GAM180410_D03_2_S116_R1_001


title: MOLM, Decitabine, Normoxia, 144 hour, Rep1

description:
Library name: 2_DAC_N_R1_S7
2_DAC_N_R1_S7

value: Normoxia (21% O2)

value: N


title: F123 GAM library f123_1NP_GAM180410_D09_1_S68_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: MOLM, Azacytadine, Normoxia, 144 hour, Rep1

description:
Library name: 2_AZA_N_R1_S5
2_AZA_N_R1_S5

value: 72 hour pre-treatment normoxia, 72 hour azacytadine


title: F123 GAM library f123_1NP_GAM180410_D02_1_S12_R1_001


title: MOLM, Decitabine, Hypoxia, 144 hour, Rep2

description:
Library name: 1_H_DAC_R2_S11
1_H_DAC_R2_S11

value: 72 hour pre-treatment hypoxia, 72 hour decitabine

value: Decitabine


title: ceAF-2

city: Wuxi

first: Fan

last: Chen

state: jiangsu

address: No. 1800 Lihu Avenue

department: Wuxi School of Medicine

institute: Jiangnan University

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Assembly: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Supplementary files format and content: Xls file includes raw counts for each sample
Supplementary files format and content: Xls file include RPKM values for each sample

source_name: Colon

extract_protocol:
1 μg total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: Colon


title: ceAF-5


title: F123 GAM library f123_1NP_GAM180410_D06_1_S44_R1_001


title: F123 GAM library f123_1NP_GAM180410_D01_2_S100_R1_001


title: MOLM, Untreated, Normoxia, 144 hour, Rep1

description:
Library name: 2_UT_N_R1_S9
2_UT_N_R1_S9

value: Peripheral blood

value: 72 hour pre-treatment normoxia, 72 hour untreated

value: Untreated


title: F123 GAM library f123_1NP_GAM180410_D05_1_S36_R1_001


title: F123 GAM library f123_1NP_GAM180410_D07_1_S52_R1_001


title: F123 GAM library f123_1NP_GAM180410_C12_2_S187_R1_001


title: ceAF-1


title: DSS-5


title: F123 GAM library f123_1NP_GAM180410_D04_2_S124_R1_001


title: F123 GAM library f123_1NP_GAM180410_D03_1_S20_R1_001


title: F123 GAM library f123_1NP_GAM180410_C11_2_S179_R1_001


title: F123 GAM library f123_1NP_GAM180410_C10_2_S171_R1_001


title: MOLM, Azacytadine, Normoxia, 144 hour, Rep2

description:
Library name: 2_AZA_N_R2_S14
2_AZA_N_R2_S14

value: acute myeloid leukemia

value: Azacytidine


title: F123 GAM library f123_1NP_GAM180410_D08_1_S60_R1_001


title: ceAF-3


title: F123 GAM library f123_1NP_GAM180410_D02_2_S108_R1_001


title: F123 GAM library f123_1NP_GAM180410_C09_2_S163_R1_001


title: Early-onset colorectal cancer tumor tissue, patient 9

city: Houston

first: Lanlan

last: Shen

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

description:
Library name: T8
Column name in processed file methyl_counts_all_samples.txt: T_8

data_processing:
FastQC v0.11.9 was used for general quality checks of sequencing reads in FASTQ files. TrimGalore v0.6.6 was used in the 'paired-end' mode to trim 5' and 3' read ends and remove adapter sequences.
BSMAP v2.90 was used in the 'paired-end' mode to align raw FASTQ reads to the hg38 reference genome. Samtools v1.11 was used to remove unmapped reads and sort aligned reads.
Methylation was quantified at the single-CpG level using a Python script adapted from BSMAP, with a minimum of 4 reads covering each CpG (-m 4) in the -x CG mode for CpG methylation (with the -p, -u, -r, and -g options for quality control of reads).
Single-CpG methylation files for samples were unified using the 'unionbedg' command of Bedtools. Dashes ('-') represent NA values for bases without reads.
Assembly: hg38
Supplementary files format and content: The processed file is a unified table of methylation at the single-CpG level for each sample. Dashes ('-') represent NA values for bases without reads. The chromosome and base position are annotated, and strands are merged.

source_name: Moderately differentiated sigmoid colon cancer

extract_protocol:
Genomic DNA was extracted from microdissected FFPE sections using the QIAamp DNA FFPE Tissue Kit.
500ng gDNA was used for library preparation. The quantity and size distribution of libraries were determined using the Pico Green fluorescence assay and the Agilent 2100 Bioanalyzer, respectively. Libraries were sequenced as 150bp paired-end reads with planned 30x coverage per sample.

tag: patient's disease_state

value: Left-sided EOCRC

tag: individual

value: Patient 9


title: F123 GAM library f123_1NP_GAM180410_C12_1_S91_R1_001


title: F123 GAM library f123_1NP_GAM180410_C08_1_S59_R1_001


title: DSS-1


title: F123 GAM library f123_1NP_GAM180410_C07_2_S147_R1_001


title: MOLM, Untreated, Hypoxia, 144 hour, Rep1

description:
Library name: 1_H_UT_R1_S3
1_H_UT_R1_S3

value: Acute myeloid leukemia (M5a)

value: Male

value: 72 hour pre-treatment hypoxia, 72 hour untreated

value: Hypoxia (1% O2)

value: Y


title: MOLM, Decitabine, Hypoxia, 144 hour, Rep1

description:
Library name: 1_H_DAC_R1_S2
1_H_DAC_R1_S2


title: F123 GAM library f123_1NP_GAM180410_D01_1_S4_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: DSS-4


title: H9565_WT

city: Tsukuba

first: ASM SAKHAWAT

last: HOSSAIN

state: Ibaraki

address: 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan

department: Graduate School of Comprehensive Human Science

country: Japan

institute: University of Tsukuba

data_processing:
CLC Genomics Workbench v 22 (RNAseq protocol)
Sequence reads were trimmed for adaptor sequence/low-quality sequence
mapped to mm10
TPM values extraction and nomalization
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: Skin

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74136), RNA quality was analyzed with Agilent 2100 bioanalyzer
NEBNext Ultra II Directional RNA Library prep kit for Illumina was used according to the manufacturer's protocol

value: Skin

value: Primary culture

value: Neonatal Dermal Fibroblast

value: Wildtype (W6)

value: No Treatment


title: ceAF-4

value: Colon


title: F123 GAM library f123_1NP_GAM180410_C06_1_S43_R1_001


title: F123 GAM library f123_1NP_GAM180410_C06_2_S139_R1_001


title: DSS-3


title: MOLM, Azacytadine, Hypoxia, 144 hour, Rep1

description:
Library name: 1_H_AZA_R1_S1
1_H_AZA_R1_S1

value: Peripheral blood

value: acute myeloid leukemia

value: 72 hour pre-treatment hypoxia, 72 hour azacytadine

value: Azacytidine


title: F123 GAM library f123_1NP_GAM180410_C11_1_S83_R1_001


title: Early-onset colorectal cancer tumor tissue, patient 10

description:
Library name: T9
Column name in processed file methyl_counts_all_samples.txt: T_9

source_name: Moderately differentiated rectosigmoid adenocarcinoma

value: Left-sided EOCRC

value: Patient 10


title: F123 GAM library f123_1NP_GAM180410_C04_2_S123_R1_001


title: H9563_homo


title: F123 GAM library f123_1NP_GAM180410_C05_1_S35_R1_001


title: F123 GAM library f123_1NP_GAM180410_C09_1_S67_R1_001


title: F123 GAM library f123_1NP_GAM180410_C08_2_S155_R1_001


title: Early-onset colorectal cancer tumor tissue, patient 8

description:
Library name: T7
Column name in processed file methyl_counts_all_samples.txt: T_7

value: Patient 8

value: Moderately differentiated sigmoid colon cancer


title: F123 GAM library f123_1NP_GAM180410_C07_1_S51_R1_001

value: mouse embryonic stem cells


title: Early-onset colorectal cancer tumor tissue, patient 6

description:
Library name: T6
Column name in processed file methyl_counts_all_samples.txt: T_6

source_name: Rectal adenocarcinoma arising from tubulovillous adenoma with high grade dysplasia

value: Patient 6


title: F123 GAM library f123_1NP_GAM180410_C03_2_S115_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: Early-onset colorectal cancer tumor tissue, patient 3

description:
Library name: T3
Column name in processed file methyl_counts_all_samples.txt: T_3

value: Patient 3


title: Early-onset colorectal cancer tumor tissue, patient 5

description:
Library name: T5
Column name in processed file methyl_counts_all_samples.txt: T_5

value: Patient 5


title: H9564_WT

value: Skin

value: Primary culture

value: Neonatal Dermal Fibroblast

value: Wildtype (W5)


title: H9561_homo

value: No Treatment


title: F123 GAM library f123_1NP_GAM180410_C05_2_S131_R1_001


title: Early-onset colorectal cancer tumor tissue, patient 1

description:
Library name: T1
Column name in processed file methyl_counts_all_samples.txt: T_1

source_name: Moderately differentiated rectal adenocarcinoma

value: Patient 1


title: Control BM cells

city: Hangzhou

first: Aiwei

last: Wu

state: Zhejiang

address: 2318 Yuhangtang Road

department: School of Basic Medical Sciences

institute: Hangzhou Normal University

data_processing:
Raw reads were processed and mapped to mouse genome mm10 to generate gene expression matrix using CeleScope (v2.0.7, https://github.com/singleron-RD/CeleScope) with default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Bone marrow

extract_protocol:
BM cells were harvested by crushing the bones (Femur, Tibia and Hip). Then, red blood cells were lysed with Ammonium-Chloride-Potassium (ACK) buffer and the remainning cells were washed twice with PBS, lineage depleted using the Lineage Cell Depletion Kit (Miltenyi), labelled with the following antibody cocktail: anti-cKit, anti Sca-1 and anti Flt3 antibodies and FACS sorted. Then, the whole BM cell, immature hematopoietic cells (c-kit+), and hematopoietic stem cells (Lin- c-kit+ sca-1+) were sorted using flow cytometry and mixed at a ratio of 1:1:4.
The mixed cells in suspensions were loaded onto microfluidic devices and scRNA-seq libraries were constructed according to the Singleron GEXSCOPE™ protocol using the GEXSCOPE™ Single-CellRNA LibraryKit (Singleron, 1110011).

treatment_protocol: All mice received TBI with 4 Gy of R-rays at a dose rate of 0.407 Gy/min. Mice in the irradiation+DDO1002 group received 50 mg/kg DDO1002 solution (5% DMSO, 30% PEG300, 10% Tween 80, and 55% ddH2O) by intraperitoneal injection every two days for 54 days, starting from six days after irradiation. Mice in the irradiation+control group received the same volume of solvent control for the same duration and frequency as mice in the irradiation+DDO1002 group. The mice were sacrificed 70 days after TBI.

value: Bone marrow

value: solvent for DDO1002


title: DSS-2

value: Colon


title: DDO1002-treated BM cells


title: F123 GAM library f123_1NP_GAM180410_C03_1_S19_R1_001


title: F123 GAM library f123_1NP_GAM180410_B11_2_S178_R1_001


title: F123 GAM library f123_1NP_GAM180410_C02_1_S11_R1_001


title: H9562_homo


title: F123 GAM library f123_1NP_GAM180410_C01_1_S3_R1_001


title: F123 GAM library f123_1NP_GAM180410_B11_1_S82_R1_001


title: Normal adjacent tissue, patient 6

description:
Library name: N6
Column name in processed file methyl_counts_all_samples.txt: N_6

source_name: Normal adjacent rectal

value: Left-sided EOCRC

value: Normal adjacent rectal


title: F123 GAM library f123_1NP_GAM180410_B12_2_S186_R1_001

value: mouse embryonic stem cells


title: PBBR5

city: Nanjing

first: Sun

last: Peng

address: 101 Longmian Avenue

institute: Nanjing Medical University

data_processing:
Filtering of Clean Reads
Alignment with Ribosome RNA (rRNA)
Alignment with Reference Genome
Quantification of Gene Abundance
Assembly: mm10
Supplementary files format and content: Text files include counts and FPKM values for each Sample.

extract_protocol:
Total RNA was extracted using Trizol reagent kit
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X). And polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: liver

value: PPAR knockdown + benzbromarone


title: Early-onset colorectal cancer tumor tissue, patient 4

description:
Library name: T4
Column name in processed file methyl_counts_all_samples.txt: T_4

value: Patient 4

value: Moderately differentiated sigmoid colon cancer


title: F123 GAM library f123_1NP_GAM180410_C01_2_S99_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: F123 GAM library f123_1NP_GAM180410_C02_2_S107_R1_001


title: F123 GAM library f123_1NP_GAM180410_B09_1_S66_R1_001


title: F123 GAM library f123_1NP_GAM180410_B12_1_S90_R1_001


title: Normal adjacent tissue, patient 4

description:
Library name: N4
Column name in processed file methyl_counts_all_samples.txt: N_4

source_name: Normal adjacent sigmoid

value: Normal adjacent sigmoid


title: F123 GAM library f123_1NP_GAM180410_B10_2_S170_R1_001


title: Normal adjacent tissue, patient 7

description:
Library name: N7
Column name in processed file methyl_counts_all_samples.txt: N_7

source_name: Normal adjacent colonic mucosal

value: Patient 7

value: Normal adjacent colonic mucosal


title: PBBR4


title: F123 GAM library f123_1NP_GAM180410_B10_1_S74_R1_001

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip


title: Early-onset colorectal cancer tumor tissue, patient 2

description:
Library name: T2
Column name in processed file methyl_counts_all_samples.txt: T_2

value: Patient 2

value: Moderately differentiated rectosigmoid adenocarcinoma


title: F123 GAM library f123_1NP_GAM180410_B09_2_S162_R1_001


title: F123 GAM library f123_1NP_GAM180410_B08_1_S58_R1_001


title: PBBR2


title: Normal adjacent tissue, patient 2

description:
Library name: N2
Column name in processed file methyl_counts_all_samples.txt: N_2

source_name: Normal adjacent rectosigmoid

value: Normal adjacent rectosigmoid


title: Normal adjacent tissue, patient 3

description:
Library name: N3
Column name in processed file methyl_counts_all_samples.txt: N_3

value: Patient 3


title: PBBR1


title: F123 GAM library f123_1NP_GAM180410_B06_1_S42_R1_001


title: F123 GAM library f123_1NP_GAM180410_B05_2_S130_R1_001


title: PBBR3


title: Normal adjacent tissue, patient 5

description:
Library name: N5
Column name in processed file methyl_counts_all_samples.txt: N_5

value: Patient 5


title: F123 GAM library f123_1NP_GAM180410_B05_1_S34_R1_001


title: F123 GAM library f123_1NP_GAM180410_B07_1_S50_R1_001


title: P5

value: PPAR knockdown


title: F123 GAM library f123_1NP_GAM180410_B08_2_S154_R1_001


title: F123 GAM library f123_1NP_GAM180410_B03_2_S114_R1_001


title: F123 GAM library f123_1NP_GAM180410_B04_2_S122_R1_001


title: P4


title: Normal adjacent tissue, patient 1

description:
Library name: N1
Column name in processed file methyl_counts_all_samples.txt: N_1

value: Left-sided EOCRC

value: Patient 1


title: F123 GAM library f123_1NP_GAM180410_B03_1_S18_R1_001

value: mouse embryonic stem cells


title: DPSCs, LV-ctrl_3

city: Guangzhou

first: Junkai

last: Zeng

state: Guangdong

address: Southern Medical University

institute: Southern Medical University

description: Library name: Sample6

data_processing:
The concentration and size distribution of the cDNA library was assessed using an Agilent 4200 Bioanalyzer prior to sequencing on an Illumina NovaSeq 6000 platform, following the manufacturer's guidelines (Illumina).
Raw sequencing reads were preprocessed with Seqtk and aligned to the reference genome using Hisat2 (version 2.0.4).
Gene fragment counts were determined using StringTie (version 1.3.3b), followed by normalization with the Trimmed Mean of M values method.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: Dental pulp

growth_protocol: Dental pulp stem cells were maintained in DMEM supplemented with 10% fetalbovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol (thermofisher, 15596018). 1 ug of total RNA was used forthe construction of seguencing libraries.
Total RNA was subjected to library preparation in accordance with the Illumina standard protocol utilizing the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®.

treatment_protocol: Odontogenic differentiation was induced by treatment of 14-day

value: Dental pulp

value: Dental pulp stem cells

value: Negative control

value: odontogenic differentiation


title: DPSCs, LV-ctrl_2

description: Library name: Sample5


title: P3

value: liver


title: F123 GAM library f123_1NP_GAM180410_B02_1_S10_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: F123 GAM library f123_1NP_GAM180410_B02_2_S106_R1_001


title: F123 GAM library f123_1NP_GAM180410_B01_2_S98_R1_001


title: DPSCs, LV-ctrl_1

description: Library name: Sample4


title: P2


title: P1


title: F123 GAM library f123_1NP_GAM180410_A12_1_S89_R1_001


title: F123 GAM library f123_1NP_GAM180410_A11_1_S81_R1_001


title: DPSCs, LV-circ1599_2

description: Library name: Sample2

value: hsa_circ_0001599 overexpression


title: BBR5

value: benzbromarone


title: F123 GAM library f123_1NP_GAM180410_A11_2_S177_R1_001


title: DPSCs, LV-circ1599_1

description: Library name: Sample1


title: BBR4


title: MCF7 cells, WT-3

city: xian

first: Xi

last: Zhang

state: Shannxi province

address: Northwest University, 229 North Taibai Road, Xi'an

department: 1 School of Life Science, Northwest University, Xi'an, Shaanxi 710069, China 2 Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, Shaanxi 710069, China

institute: Northwest University

description: Library name: Sampe 18

data_processing:
RNA sequencing data is checked for integrity of paired-end sequencing data using the MD5 code of the original file in the Linux system. Data cleanup with Cutadapt software and Python followed by quality control with FastQC. After quality filtering (FastQC, quality value > 5), over 30 billion clean reads were obtained in each library and then used for down-stream analysis.
Significant differential gene analysis was performed using the R-package DESeq and subsequent functional analysis was performed.
Assembly: Download the Human Genome File and Genome Annotation File (GRCh38/hg38) from the UCSC website (https://genome.ucsc.edu/) , build a genome index, and compare them with the STAR tool. The generated BAM file is quantified and normalized with featureCounts to obtain the FPKM value.
Supplementary files format and content: raw counts for each Sample

source_name: breast

extract_protocol:
Total RNA was isolated using Trizol(Solarbio,Beijing,China),and purity and concentration were validated using NanoDrop ND-1000 instryment(ThermoFisher Scientific, Waltham, Massachusetts, USA). Before transcriptome analysis (RNAseq) or quantitative real-time PCR (qRT-PCR),  the integrity of RNA was evaluated through the 2100 biological analyzer gel image analysis system (Agilent, Santa Clara, California, USA). 1.0µg RNA was used for the construction of sequencing libraries.
RNAseq libraries were constructed using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA).

value: breast

value: luminal A

value: WT


title: F123 GAM library f123_1NP_GAM180410_A10_2_S169_R1_001


title: F123 GAM library f123_1NP_GAM180410_A09_1_S65_R1_001


title: F123 GAM library f123_1NP_GAM180410_A08_2_S153_R1_001


title: F123 GAM library f123_1NP_GAM180410_A10_1_S73_R1_001


title: BBR3

source_name: liver


title: F123 GAM library f123_1NP_GAM180410_A09_2_S161_R1_001


title: BBR2


title: MCF7 cells, WT-2

description: Library name: Sampe 17


title: BBR1


title: DPSCs, LV-circ1599_3

description: Library name: Sample3


title: MCF7 cells, UNC0642-3

description: Library name: Sampe 15

value: UNC0642 treated


title: F123 GAM library f123_1NP_GAM180410_A07_1_S49_R1_001


title: F123 GAM library f123_1NP_GAM180410_A06_1_S41_R1_001


title: F123 GAM library f123_1NP_GAM180410_A06_2_S137_R1_001


title: MCF7 cells, WT-1

description: Library name: Sampe 16


title: F123 GAM library f123_1NP_GAM180410_B01_1_S2_R1_001


title: C5

value: control


title: F123 GAM library f123_1NP_GAM180410_A05_1_S33_R1_001


title: F123 GAM library f123_1NP_GAM180410_A05_2_S129_R1_001


title: MCF7 cells, UNC0642-2

description: Library name: Sampe 14


title: F123 GAM library f123_1NP_GAM180410_A04_2_S121_R1_001


title: MCF7 cells, UNC0642-1

description: Library name: Sampe 13


title: C4


title: F123 GAM library f123_1NP_GAM180410_A03_2_S113_R1_001


title: F123 GAM library f123_1NP_GAM180410_A03_1_S17_R1_001


title: MDA-MB-468 cells, WT-3

description: Library name: Sampe 12

value: TNBC


title: C3


title: F123 GAM library f123_1NP_GAM180410_A02_1_S9_R1_001


title: F123 GAM library f123_1NP_GAM180410_A02_2_S105_R1_001


title: F123 GAM library f123_1NP_GAM180410_A08_1_S57_R1_001


title: F123 GAM library f123_1NP_GAM180410_A01_2_S97_R1_001


title: MDA-MB-468 cells, WT-2

description: Library name: Sampe 11


title: C2


title: MDA-MB-468 cells, WT-1

description: Library name: Sampe 10


title: F123 GAM library f123_1NP_GAM180410_A01_1_S1_R1_001


title: C1


title: F123 GAM library f123_1NP_GAM180318_H09_1_S72_R1_001


title: F123 GAM library f123_1NP_GAM180318_G09_1_S71_R1_001


title: MDA-MB-468 cells, UNC0642-3

description: Library name: Sampe 9


title: F123 GAM library f123_1NP_GAM180318_H08_1_S64_R1_001


title: retina from AAV206-5

city: Guangzou

first: Xiaolai

last: Zhou

address: No. 54 Xianlie South Rd

institute: Zhongshan ophthalmic center，Sun Yat-sen university

data_processing:
Quality control, Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. paired-end clean reads were aligned to the reference genome using STAR v2.7.10b.
RSEM v1.3.1 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: Text fles include raw counts for each Sample

source_name: retina

extract_protocol:
Total RNA was extracted from retina using Trizol reagent (15596018CN, Invitrogen, USA), following the manufacturer's protocol. RNA quantity and integrity were assessed using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Libraries for RNA sequencing were prepared using NEBNext® Ultra™ RNA  Library Prep Kit for Illumina® (NEB, USA), and sequencing was performed on an Illumina NovaSeq platform to generate paired-end reads of 150 bp.

treatment_protocol: The groups received intravitreal injections of AAV2-GFP and AAV206-GFP, respectively.

value: retina

value: intravitreal injections of  AAV206-GFP


title: F123 GAM library f123_1NP_GAM180318_E09_1_S69_R1_001

value: mouse embryonic stem cells


title: MDA-MB-468 cells, UNC0642-1

description: Library name: Sampe 7


title: F123 GAM library f123_1NP_GAM180318_F08_1_S62_R1_001


title: retina from AAV206-4


title: MDA-MB-468 cells, UNC0642-2

description: Library name: Sampe 8


title: F123 GAM library f123_1NP_GAM180318_F09_1_S70_R1_001


title: retina from AAV206-3


title: retina from AAV206-1


title: MDA-MB-231 cells, WT-2

description: Library name: Sampe 5


title: F123 GAM library f123_1NP_GAM180318_E08_1_S61_R1_001


title: MDA-MB-231 cells, WT-1

description: Library name: Sampe 4


title: MDA-MB-231 cells, UNC0642-3

description: Library name: Sampe 3


title: F123 GAM library f123_1NP_GAM180318_B08_1_S58_R1_001


title: retina from AAV2-4

value: intravitreal injections of  AAV2-GFP


title: F123 GAM library f123_1NP_GAM180318_D09_1_S68_R1_001


title: MDA-MB-231 cells, WT-3

description: Library name: Sampe 6


title: F123 GAM library f123_1NP_GAM180318_D08_1_S60_R1_001


title: F123 GAM library f123_1NP_GAM180223_H09_2_S168_R1_001


title: F123 GAM library f123_1NP_GAM180318_C09_1_S67_R1_001


title: F123 GAM library f123_1NP_GAM180318_C08_1_S59_R1_001


title: shSLC25A1, Day 2, rep 5

city: Iowa City

first: Henry

last: Keen

state: IA

address: 329 EMRB

institute: University of Iowa

description: Library name: Sample 30

data_processing:
Read trimming was performed with ngmerge (version 0.3)
Trimmed reads were aligned to the human genome (build GRCh37) using the bwa mem aligner (version 0.7.15-r1140)
Peak calling was performed with Genrich (version 0.5)
Assembly: GRCh37
Supplementary files format and content: narrowPeak

source_name: Airway basal cells

extract_protocol:
DNA was harvested using ATAC-Seq Kit (Active Motif).
DNA libraries for ATAC-seq were prepared using ATAC-Seq Kit (Active Motif) following manufacturer's protocols.

value: Airway basal cells

value: mucociiliary differentiation

value: Day 2


title: F123 GAM library f123_1NP_GAM180318_B09_1_S66_R1_001

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM180223_H08_1_S64_R1_001

value: male


title: F123 GAM library f123_1NP_GAM180318_A09_1_S65_R1_001


title: shSLC25A1, Day 2, rep 4

description: Library name: Sample 29


title: F123 GAM library f123_1NP_GAM180223_H07_2_S152_R1_001


title: retina from AAV2-5


title: F123 GAM library f123_1NP_GAM180318_G08_1_S63_R1_001


title: F123 GAM library f123_1NP_GAM180318_A08_1_S57_R1_001


title: F123 GAM library f123_1NP_GAM180223_H11_2_S184_R1_001


title: retina from AAV2-3


title: MLKL_KO mouse-1, hippocampus, 14 month old

first: Jie

last: Tu

address: 1068 Xueyuan Boulevard, Nanshan, Shenzhen 518055, China

department: The Brain Cognition and Brain Disease Institute (BCBDI)

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS)

data_processing:
Raw reads were mapped to the mm10 mouse reference genome using CellRanger pipeline with include-intron mode (10 x Genomics). After performing the alignment, we used SoupX (version 1.6.2) to quantify and remove ambient mRNA contamination. The corrected count matrix was then used as input for the further quality control and downstream analysis in Seurat (version 4.3).
Assembly: mm10
Supplementary files format and content: sparse matrix contains the gene expression counts
Supplementary files format and content: barcodes identifying individual cells
Supplementary files format and content: gene names or features

source_name: Hippocampus

extract_protocol:
Nuclei were isolated from the hippocampus of 14-month-old male MLKL KO mice and WT littermates. Briefly, tissues were homogenized by Dounce homogenizer (~25 strokes/sample) in ice-old homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH, pH 7.8, 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). The lysate was mixed with equal volume of OptiPrep medium, centrifuged at 10,000 × g for 20 minutes at 4°C, and the nuclei were collected as pellets. The pellets were washed and resuspended in DMEM/F12 medium with 10% FBS to obtain a final concentration of 400 nuclei/μl. The purity of the single-nucleus suspensions was evaluated by flow cytometry, and high purity samples (DAPI+ nuclei > 95%) were used for analysis. RNAsin (Promega) was included in all buffers or solutions at 60 U/ml in nuclei extraction.
snRNA-seq libraries were generated using Chromium Single Cell 3’ Library Kit v3 (1000078; 10 x Genomics) according to the manufacturer’s instructions. The concentration of generated libraries was measured by Qubit (Thermo Fisher Scientific), and the length of fragments was analyzed by Fragment Analyzer (Advanced Analytical Technologies). The libraries were sequenced using NovaSeq 6000 system (Novogene).

value: Hippocampus

value: MLKL  knockout


title: MLKL_KO mouse-3, hippocampus, 14 month old


title: retina from AAV206-2


title: F123 GAM library f123_1NP_GAM180223_H12_2_S192_R1_001

data_processing:
Sequenced reads from each GAM library were mapped to the mouse genome assembly GRCm38 (Dec. 2011, mm10) using bowtie2 with all default settings. All non-uniquely mapped reads, reads with mapping quality < 20 were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command. Samples were checked for contamination using fastq_screen. Number of nucleotides sequenced in each genomic bin was calculated using bedtools coverage command. Next, the optimal threshold between the sequencing noise and the signal to call positive windows was calculated as the lowest coverage per bin that gives the highest percent of clustered windows (windows that have a neighboring positive window on at-least one side) for each GAM sample in the dataset. Windows were called positive when the number of nucleotides covered by the reads is higher or equal to the optimal threshold. Each dataset was assessed for quality control by determining the percentage of orphan windows, number of uniquely mapped reads to the mouse genome, and cross-well contamination for every sample. 1NP samples that passed QC were merged into in-silico 3NPs at the level of positive windows. For good quality samples, we produced raw co-segregation, as well as normalized (NPMI) pair-wise chromatin contact matrices.
Assembly: mm10
Supplementary files format and content: Processed data files are raw GAM segregation tables, non-normalized pairwise cosegregation matrices and normalized NPMI matrices in tab-delimited format.
Library strategy: WGA

extract_protocol:
Fixation of F123 mESC was performed as described previously (Branco and Pombo, 2006). Briefly, cells were grown to 70 % confluency, media was removed, and cells were fixed in 4% and 8% paraformaldehyde in 250 mM HEPES-NaOH (pH 7.6; 10 min and 2 h, respectively), gently scrapped, and softly pelleted and embedded in saturated 2.1 M sucrose in PBS and frozen in liquid nitrogen on copper sample holders. Ultrathin cryosections were cut with a glass knife using an ultracryomicrotome (Leica Biosystems, EM UC7) at ~230 nm thickness, and transferred to PEN membrane steel frame slides 4.0 µm (Leica Microsystems, 11600289) for laser microdissection. Before laser microdissection, cryosections were washed in sterile-filtered 1x PBS (3 times, 5 min each), sterile-filtered H2O (3 times, 5 min each), and stained with sterile-filtered 1 % (w/v) cresyl violet (Sigma-Aldrich, C5042) in H2O for 10 min, followed by 2 washes with H2O (30 s each).  Individual NPs were isolated from the cryosection by laser microdissection using a laser microdissection microscope (Leica Microsystems, LMD7000). Cut NPs were collected in a PCR Cap Strip filled with opaque adhesive material (Carl Zeiss Microscopy, 415190-9161-000). For each collection day, 1 or 2 caps were left empty and taken through the whole genome amplification (WGA) and sequencing process as a negative control for quality control purposes.
Whole Genome Amplification (WGA) was performed as described previously (Winick-Ng et al, 2021) with minor modifications. Briefly, DNA was extracted from NPs at 60oC in the lysis buffer (20mM Tris-HCl pH 8.0, 1.4 mM EDTA, 560 mM guanidinium-HCl, 3.5% Tween-20, 0.35% Triton X-100) containing 0.75 units/ml Qiagen protease (Qiagen, 19155). After 24h of DNA extraction, the protease was heat inactivated at 75oC for 30 min and the extracted DNA was amplified via two rounds of PCR. At-first quasi-linear amplification was performed with random hexamer GAT-7N  primers with an adaptor sequence. The lysis buffer containing the extracted genomic DNA was mixed with 2x DeepVent mix buffer (2x Thermo polymerase buffer (10x), 400 µm dNTPs, 4 mM MgSO4 in ultrapure DNase free water), 0.5 µM GAT-7N primers (5′- GTG AGT GAT GGT TGA GGT AGT GTG GAG NNN NNN N) and 2 units/µl DeepVent® (exo-) DNA polymerase (New England Biolabs, M0259L) and incubated for 11 cycles in the BioRad thermocycler. The second exponential PCR amplification was performed in presence of 1x DeepVent mix, 10 mM dNTPs, 0.4 µM GAM-COM primers (5′-GTG AGT GAT GGT TGA GGT AGT GTG GAG) and 2 units/µl DeepVent (exo-) DNA polymerase in the programmable thermal cycler for 26 cycles.
After whole genome amplification, the DNA WGA product was purified withSPRI beads (1.7x) The DNA concentration of each sample was quantified using the Quant-iT® PicoGreen dsDNA assay kit (Invitrogen #P7589). Genomic sequencing library was prepared from 1ng of purified DNA using the Illumina Nextera XT library preparation kit (Illumina #FC-131-1096), following the manufacturer’s instructions or with reduce to 20% volume of reagents. After the library preparation, DNA was again purified with in-house SPRI beads (1.7x) and equal amounts of DNA from each sample was pooled together (up to 196 samples) for the sequencing. The final pool of libraries was additionally purified two more times with SPRI beads (1.7x) and analyzed using DNA High Sensitivity on-chip electrophoresis on an Agilent 2100 Bioanalyzer. The samples were sequenced on Illumina NextSeq500 machine as single-end 75 bp reads, according to manufacturer’s instructions.


title: shSLC25A1, Day 2, rep 2

description: Library name: Sample 27


title: F123 GAM library f123_1NP_GAM180223_H04_2_S128_R1_001


title: F123 GAM library f123_1NP_GAM180223_H08_2_S160_R1_001


title: retina from AAV2-1


title: F123 GAM library f123_1NP_GAM180223_H09_1_S72_R1_001


title: MDA-MB-231 cells, UNC0642-2

description: Library name: Sampe 2

value: breast


title: retina from AAV2-2


title: MDA-MB-231 cells, UNC0642-1

description: Library name: Sampe 1


title: F123 GAM library f123_1NP_GAM180223_H03_2_S120_R1_001


title: shSLC25A1, Day 2, rep 1

description: Library name: Sample 26


title: F123 GAM library f123_1NP_GAM180223_H03_1_S24_R1_001


title: F123 GAM library f123_1NP_GAM180223_H07_1_S56_R1_001


title: MLKL_KO mouse-2, hippocampus, 14 month old


title: F123 GAM library f123_1NP_GAM180223_H05_1_S40_R1_001


title: F123 GAM library f123_1NP_GAM180223_H10_2_S176_R1_001


title: F123 GAM library f123_1NP_GAM180223_H04_1_S32_R1_001


title: F123 GAM library f123_1NP_GAM180223_H05_2_S136_R1_001


title: WT mouse-2, hippocampus, 14 month old


title: F123 GAM library f123_1NP_GAM180223_G12_2_S191_R1_001


title: F123 GAM library f123_1NP_GAM180223_H01_2_S104_R1_001


title: WT mouse-1, hippocampus, 14 month old


title: shControl, Day 2, rep 5

description: Library name: Sample 25


title: shControl, Day 2, rep 2

description: Library name: Sample 22


title: F123 GAM library f123_1NP_GAM180223_G10_1_S79_R1_001


title: shSLC25A1, Day 2, rep 3

description: Library name: Sample 28


title: H7113_homo

value: Skin

value: Primary culture

value: Neonatal Dermal Fibroblast

value: No Treatment


title: F123 GAM library f123_1NP_GAM180223_G09_2_S167_R1_001


title: F123 GAM library f123_1NP_GAM180223_H02_1_S16_R1_001


title: F123 GAM library f123_1NP_GAM180223_H02_2_S112_R1_001


title: WT mouse-3, hippocampus, 14 month old

value: WT


title: H7115_WT

value: WT (W4)


title: shControl, Day 2, rep 4

description: Library name: Sample 24


title: shControl, Day 2, rep 3

description: Library name: Sample 23


title: F123 GAM library f123_1NP_GAM180223_G09_1_S71_R1_001


title: H7114_WT

value: WT (W3)


title: F123 GAM library f123_1NP_GAM180223_G10_2_S175_R1_001

value: mouse embryonic stem cells


title: shControl, Day 2, rep 1

description: Library name: Sample 21


title: F123 GAM library f123_1NP_GAM180223_G08_1_S63_R1_001


title: F123 GAM library f123_1NP_GAM180223_H01_1_S8_R1_001


title: shSLC25A1, Day 1, rep 4

description: Library name: Sample 19

value: Day 1


title: F123 GAM library f123_1NP_GAM180223_G11_2_S183_R1_001


title: H6991_homo


title: F123 GAM library f123_1NP_GAM180223_G06_2_S143_R1_001


title: F123 GAM library f123_1NP_GAM180223_G06_1_S47_R1_001


title: H7112_homo


title: shSLC25A1, Day 1, rep 5

description: Library name: Sample 20

value: Airway basal cells


title: shSLC25A1, Day 1, rep 2

description: Library name: Sample 17

value: mucociiliary differentiation


title: F123 GAM library f123_1NP_GAM180223_G08_2_S159_R1_001


title: H6993_WT

value: WT (W2)


title: F123 GAM library f123_1NP_GAM180223_G07_1_S55_R1_001

value: Hybrid F1 S129/Jae and Cast


title: shSLC25A1, Day 1, rep 3

description: Library name: Sample 18


title: shSLC25A1, Day 1, rep 1

description: Library name: Sample 16


title: H6989_homo


title: RNA-CKO-zygote-3W-3

first: Heng-yu

last: Fan

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
Adaptor sequences were removed using Trim_galore, and quality assessment was conducted using Fastqc. Alignment to the mouse genome (mm10) was performed using Hisat2 and Samtools, and RNA raw counts were quantified using Featurecounts.
Assembly: mm10
Supplementary files format and content: "processed RNA-seq data.xlsx" file includes raw counts and FPKM for each sample

source_name: zygote

extract_protocol:
10 oocytes or zygotes from each experimental group were washed for 3 times with 0.2% BSA in PBS and pooled into a 200 μL RNase-free Eppendorf tube.
Library construction using smart-seq2 and ERCC spike-in was conducted following established protocol (Picelli, S. et al.  Nat Protoc, 2014. doi:10.1038/nprot.2014.006).

value: zygote

value: Dhx36fl/fl; Zp3-Cre


title: H6755_WT

value: WT (W1)


title: RNA-CKO-zygote-3W-2


title: shControl, Day 1, rep 4

description: Library name: Sample 14


title: F123 GAM library f123_1NP_GAM180223_G05_1_S39_R1_001

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

institute: Max-Delbrueck Center for Molecular Medicine

value: male


title: F123 GAM library f123_1NP_GAM180223_G04_2_S127_R1_001


title: F123 GAM library f123_1NP_GAM180223_G03_2_S119_R1_001


title: shControl, Day 1, rep 5

description: Library name: Sample 15


title: F123 GAM library f123_1NP_GAM180223_G04_1_S31_R1_001


title: F123 GAM library f123_1NP_GAM180223_G02_1_S15_R1_001


title: F123 GAM library f123_1NP_GAM180223_G03_1_S23_R1_001


title: F123 GAM library f123_1NP_GAM180223_G01_2_S103_R1_001


title: F123 GAM library f123_1NP_GAM180223_G02_2_S111_R1_001


title: RNA-WT-zygote-3W-3


title: F123 GAM library f123_1NP_GAM180223_G01_1_S7_R1_001


title: F123 GAM library f123_1NP_GAM180223_G05_2_S135_R1_001


title: F123 GAM library f123_1NP_GAM180223_G07_2_S151_R1_001


title: shControl, Day 1, rep 3

description: Library name: Sample 13


title: F123 GAM library f123_1NP_GAM180223_F11_2_S182_R1_001


title: F123 GAM library f123_1NP_GAM180223_F12_2_S190_R1_001


title: RNA-WT-zygote-3W-1


title: RNA-WT-zygote-3W-2


title: shSLC25A1, Day 0, rep 5

description: Library name: Sample 10

value: Day 0


title: F123 GAM library f123_1NP_GAM180223_F10_1_S78_R1_001


title: F123 GAM library f123_1NP_GAM180223_F09_1_S70_R1_001


title: shControl, Day 1, rep 1

description: Library name: Sample 11


title: F123 GAM library f123_1NP_GAM180223_F10_2_S174_R1_001


title: RNA-CKO-MII-3W-3

source_name: metaphase II oocyte

value: metaphase II oocyte


title: F123 GAM library f123_1NP_GAM180223_F07_2_S150_R1_001


title: F123 GAM library f123_1NP_GAM180223_F07_1_S54_R1_001


title: F123 GAM library f123_1NP_GAM180223_F09_2_S166_R1_001


title: shSLC25A1, Day 0, rep 2

description: Library name: Sample 7


title: RNA-CKO-MII-3w-4


title: F123 GAM library f123_1NP_GAM180223_F08_2_S158_R1_001


title: F123 GAM library f123_1NP_GAM180223_F08_1_S62_R1_001


title: shSLC25A1, Day 0, rep 4

description: Library name: Sample 9


title: shSLC25A1, Day 0, rep 1

description: Library name: Sample 6


title: shControl, Day 1, rep 2

description: Library name: Sample 12


title: shSLC25A1, Day 0, rep 3

description: Library name: Sample 8


title: RNA-CKO-MII-3W-1


title: F123 GAM library f123_1NP_GAM180223_F06_1_S46_R1_001


title: F123 GAM library f123_1NP_GAM180223_F06_2_S142_R1_001


title: F123 GAM library f123_1NP_GAM180223_F04_2_S126_R1_001


title: shControl, Day 0, rep 5

description: Library name: Sample 5


title: RNA-CKO-MII-3W-2


title: F123 GAM library f123_1NP_GAM180223_F05_2_S134_R1_001


title: RNA-WT-MII-3W-2


title: F123 GAM library f123_1NP_GAM180223_F05_1_S38_R1_001


title: RNA-WT-MII-3W-3


title: F123 GAM library f123_1NP_GAM180223_F03_1_S22_R1_001


title: RNA-CKO-zygote-3W-1


title: F123 GAM library f123_1NP_GAM180223_F04_1_S30_R1_001


title: shControl, Day 0, rep 4

description: Library name: Sample 4


title: F123 GAM library f123_1NP_GAM180223_F03_2_S118_R1_001


title: F123 GAM library f123_1NP_GAM180223_F02_1_S14_R1_001


title: shControl, Day 0, rep 3

description: Library name: Sample 3


title: RNA-WT-MII-3W-1


title: F123 GAM library f123_1NP_GAM180223_F01_2_S102_R1_001


title: RNA-CKO-FGO-4W-3

source_name: fully-grown oocyte

value: fully-grown oocyte


title: F123 GAM library f123_1NP_GAM180223_F01_1_S6_R1_001


title: F123 GAM library f123_1NP_GAM180223_E12_2_S189_R1_001


title: RNA-CKO-FGO-4W-2


title: shControl, Day 0, rep 2

description: Library name: Sample 2


title: RNA-CKO-FGO-4W-1


title: F123 GAM library f123_1NP_GAM180223_E11_2_S181_R1_001


title: F123 GAM library f123_1NP_GAM180223_E10_2_S173_R1_001


title: shControl, Day 0, rep 1

description: Library name: Sample 1


title: C10

first: FU

last: SHIHAO

address: No. 96 Jinzhai Road

institute: university of science and technology of china

description:
Library name: sample30
C10

data_processing:
1) Remove reads contaminated with adapters (the number of bases contaminated with adapters in reads is greater than 5bp. For double ended sequencing, if one end is contaminated with adapters, remove the reads at both ends); 2) Remove low-quality reads (more than 50% of the total bases in reads have a quality value Q<19. For double ended sequencing, if one end has low-quality reads, both ends will be removed); 3) Remove reads with an N ratio greater than 5% (for double ended sequencing, if one end has an N ratio greater than 5%, both ends of the reads will be removed).
Assembly: hg18
Supplementary files format and content: matrix files

source_name: left atrial

extract_protocol:
Extracting RNA from left atrial samples using the trizol method
Data processing, splitting, quality control, filtering; Construct a reference based library of common eukaryotic transcriptome types, and after passing the library quality inspection, perform high-throughput sequencing using Illumina sequencing platform with a read length of PE150

value: left atrial

tag: disease

value: control


title: F123 GAM library f123_1NP_GAM180223_E09_2_S165_R1_001


title: C9

description:
Library name: sample29
C9

tag: tissue


title: F123 GAM library f123_1NP_GAM180223_E10_1_S77_R1_001

tag: cell line


title: RNA-WT-FGO-4W-2

tag: cell type


title: C8

description:
Library name: sample28
C8


title: F123 GAM library f123_1NP_GAM180223_E09_1_S69_R1_001

tag: genotype


title: F123 GAM library f123_1NP_GAM180223_E08_2_S157_R1_001


title: F123 GAM library f123_1NP_GAM180223_E07_2_S149_R1_001


title: RNA-WT-FGO-4W-3


title: RNA-WT-FGO-4W-1


title: F123 GAM library f123_1NP_GAM180223_E07_1_S53_R1_001


title: F123 GAM library f123_1NP_GAM180223_E06_1_S45_R1_001


title: F123 GAM library f123_1NP_GAM180223_E06_2_S141_R1_001


title: C6

description:
Library name: sample26
C6


title: RNA-CKO-FGO-3W-1


title: C5

description:
Library name: sample25
C5


title: F123 GAM library f123_1NP_GAM180223_E05_1_S37_R1_001


title: RNA-WT-FGO-3W-2


title: F123 GAM library f123_1NP_GAM180223_E03_2_S117_R1_001


title: F123 GAM library f123_1NP_GAM180223_E04_2_S125_R1_001


title: C4

description:
Library name: sample24
C4


title: RNA-WT-FGO-3W-1


title: C3

description:
Library name: sample23
C3


title: F123 GAM library f123_1NP_GAM180223_E02_2_S109_R1_001


title: F123 GAM library f123_1NP_GAM180223_E08_1_S61_R1_001


title: F123 GAM library f123_1NP_GAM180223_E03_1_S21_R1_001


title: RNA-CKO-GO-2W-3

source_name: growing oocyte

value: growing oocyte


title: F123 GAM library f123_1NP_GAM180223_E01_2_S101_R1_001


title: C7

description:
Library name: sample27
C7


title: RNA-CKO-GO-2W-1


title: F123 GAM library f123_1NP_GAM180223_D12_2_S188_R1_001


title: RNA-CKO-GO-2W-2


title: C2

description:
Library name: sample22
C2


title: C1

description:
Library name: sample21
C1


title: F123 GAM library f123_1NP_GAM180223_E01_1_S5_R1_001


title: F123 GAM library f123_1NP_GAM180223_D11_2_S180_R1_001


title: AF20

description:
Library name: sample20
AF20

value: atrial fibrillation and sinus rhythm


title: RNA-CKO-FGO-3W-2


title: F123 GAM library f123_1NP_GAM180223_E05_2_S133_R1_001

value: mouse embryonic stem cells


title: F123 GAM library f123_1NP_GAM180223_D09_2_S164_R1_001


title: RNA-WT-GO-2W-2


title: F123 GAM library f123_1NP_GAM180223_D10_2_S172_R1_001


title: AF18

description:
Library name: sample18
AF18


title: F123 GAM library f123_1NP_GAM180223_D09_1_S68_R1_001


title: RNA-WT-GO-2W-1


title: AF19

description:
Library name: sample19
AF19


title: F123 GAM library f123_1NP_GAM180223_D07_2_S148_R1_001


title: F123 GAM library f123_1NP_GAM180223_D08_2_S156_R1_001


title: AF17

description:
Library name: sample17
AF17


title: F123 GAM library f123_1NP_GAM180223_E02_1_S13_R1_001


title: ATAC-CKO-GO-2

data_processing:
Adaptor removal and quality control were conducted using Trim_galore and Fastqc. Alignment to the mouse genome (mm10) was achieved with Bowtie2 and Samtools. Duplicate removal was performed using Sambamba, and mitochondrial repeats were excluded using Samtools. Bigwig files were generated using Deeptools.
Assembly: mm10
Supplementary files format and content: bw file includes quantitative information on gene expression levels across the genome for each sample

extract_protocol:
100 growing oocytes or fully-grown oocytes were removed from the zona pellucida, washed twrice with 0.2% (w/v) BSA in PBS, and  were pooled into a 1.5 mL Eppendorf tube for each experimental group.
ATAC-seq was conducted using the High-Sensitivity Open Chromatin Profile Kit 2.0 (for Illumina®) (Novoprotein, N248) following the manufacturer's instruction.


title: F123 GAM library f123_1NP_GAM180223_D07_1_S52_R1_001


title: F123 GAM library f123_1NP_GAM180223_D06_2_S140_R1_001


title: F123 GAM library f123_1NP_GAM180223_D06_1_S44_R1_001


title: ATAC-WT-GO-2


title: AF15

description:
Library name: sample15
AF15


title: F123 GAM library f123_1NP_GAM180223_D10_1_S76_R1_001


title: F123 GAM library f123_1NP_GAM180223_D05_1_S36_R1_001


title: F123 GAM library f123_1NP_GAM180223_D05_2_S132_R1_001


title: RNA-WT-GO-2W-3


title: ATAC-WT-GO-1


title: F123 GAM library f123_1NP_GAM180223_D04_2_S124_R1_001


title: AF16

description:
Library name: sample16
AF16


title: F123 GAM library f123_1NP_GAM180223_D03_2_S116_R1_001


title: F123 GAM library f123_1NP_GAM180223_D03_1_S20_R1_001


title: F123 GAM library f123_1NP_GAM180223_D04_1_S28_R1_001


title: AF12

description:
Library name: sample12
AF12


title: AF13

description:
Library name: sample13
AF13


title: ATAC-CKO-GO-1


title: ATAC-CKO-FGO-1


title: F123 GAM library f123_1NP_GAM180223_D08_1_S60_R1_001


title: ATAC-CKO-FGO-2


title: F123 GAM library f123_1NP_GAM180223_D02_1_S12_R1_001


title: AF11

description:
Library name: sample11
AF11


title: ATAC-WT-FGO-2


title: F123 GAM library f123_1NP_GAM180223_D01_2_S100_R1_001


title: F123 GAM library f123_1NP_GAM180223_D01_1_S4_R1_001


title: AF10

description:
Library name: sample10
AF10


title: AF14

description:
Library name: sample14
AF14


title: ATAC-WT-FGO-1


title: F123 GAM library f123_1NP_GAM180223_C12_2_S187_R1_001


title: AF9

description:
Library name: sample9
AF9


title: F123 GAM library f123_1NP_GAM180223_C11_2_S179_R1_001


title: F123 GAM library f123_1NP_GAM180223_C10_2_S171_R1_001


title: F123 GAM library f123_1NP_GAM180223_C10_1_S75_R1_001


title: AF8

description:
Library name: sample8
AF8


title: CR_rep3

city: Memphis

first: Yogesh

last: Dhungana

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Gene expression was quantified as fragments per kilobase of transcript per million (FPKM) mapped reads using RSEM v.1.2.28PP with the GRCm38.p6 and annotation file (Gencode v.30)
Assembly: mm10
Supplementary files format and content: normalized count matrix

source_name: BALL tumor cells

extract_protocol:
For comparison of PR and CR tumor clones, RNA was isolated from in vitro cell cultures in triplicate using the RNeasy plus mini kit (QIAgen). For in vivo comparison of CAR-T cells and tumors, mice were engrafted with CR or GPR65 KO tumors and treated with CAR-T cells 7 days later. Spleens were harvested 4 days after CAR-T treatment and RFP+ tumor cells and Thy1.1+ CAR-T cells were isolated by FACS. Tumor cells from untreated mice were isolated after 7 days of tumor engraftment. RNA was isolated from sorted cells and 3 biological replicates were submitted for RNA-sequencing
For total RNA-seq, library was constructed from RNA using Illumina TrueSeq stranded mRNA library prep kit and sequenced using the HiSeq or NovaSeq platforms (2 × 101-bp paired-end reads)

tag: group

value: CR

value: BALL tumor cells

value: Murine luciferase-expressing Arf-/- BCR-ABL1+Ph+ progenitor B-ALL cells


title: CR_rep2


title: F123 GAM library f123_1NP_GAM180223_C09_1_S67_R1_001

tag: Sex


title: AF7

description:
Library name: sample7
AF7


title: F123 GAM library f123_1NP_GAM180223_D02_2_S108_R1_001


title: F123 GAM library f123_1NP_GAM180223_C08_1_S59_R1_001


title: CR_rep1


title: AF6

description:
Library name: sample6
AF6


title: F123 GAM library f123_1NP_GAM180223_C07_1_S51_R1_001


title: PR_rep3

value: PR


title: F123 GAM library f123_1NP_GAM180223_C07_2_S147_R1_001

value: Hybrid F1 S129/Jae and Cast


title: AF4

description:
Library name: sample4
AF4


title: PR_rep2


title: F123 GAM library f123_1NP_GAM180223_C06_2_S139_R1_001


title: F123 GAM library f123_1NP_GAM180223_C06_1_S43_R1_001


title: F123 GAM library f123_1NP_GAM180223_C05_2_S131_R1_001


title: PR_rep1


title: AF3

description:
Library name: sample3
AF3


title: F123 GAM library f123_1NP_GAM180223_C04_2_S123_R1_001


title: AF2

description:
Library name: sample2
AF2


title: F123 GAM library f123_1NP_GAM180223_C05_1_S35_R1_001


title: AF1

description:
Library name: samlpe1
AF1


title: F123 GAM library f123_1NP_GAM180223_C09_2_S163_R1_001


title: S1 to S14

data_processing:
The Cell Ranger (v.7.0.0) Single-Cell software suite (10X Genomics) was implemented to process raw sequencing data from the Illumina NovaSeq 6000 run
Assembly: mm10 (GRCm38.p6)
Supplementary files format and content: cell ranger count matrix for single cells in each sample

source_name: spleen

extract_protocol:
B6 mice were injected with CR or GPR65 KO tumor cells (i.v.) followed by treatment 7 days later with 10x106 activated CAR-T cells or mock PBS injection (retro-orbital). Spleens were harvested from untreated mice at day 7 and from CAR-T treated mice at day 11 after tumor engraftment. Processed spleens were stained and sorted to isolate CR or GPR65 KO tumor cells (RFP+), and the host immune cell compartment (RFP–Thy1.1–CD45.2+)
Tumor and host cells from individual treated and untreated mice were fixed separately using the 10X Genomics CG000478 Demonstrated Protocol Cell & Nuclei Fixation Chromium Fixed RNA Profiling Rev B. After fixation, individual samples were counted and barcoded with unique sample barcodes during probe hybridization. Uniquely barcoded samples were counted using Trypan Blue stain and then pooled in equal numbers following 10X Genomics CG000565 Chromium Fixed RNA Profiling Multiplexed Samples Pooling Workbook Rev B, washed and 8000 cells were targeted from each sample to be partitioned into GEMS on Chip Q using the 10X Genomics Chromium Fixed RNA Profiling kit.

tag: strain

value: C57B6 mouse

value: 7-8 weeks

value: spleen


title: F123 GAM library f123_1NP_GAM180223_C04_1_S27_R1_001

value: male


title: CART_GPR65KO_rep3

source_name: CD19 CAR T cells

extract_protocol:
For in vivo comparison of CAR-T cells and tumors, mice were engrafted with CR or GPR65 KO tumors and treated with CAR-T cells 7 days later. Spleens were harvested 4 days after CAR-T treatment and RFP+ tumor cells and Thy1.1+ CAR-T cells were isolated by FACS.
For total RNA-seq, library was constructed from RNA using Illumina TrueSeq stranded mRNA library prep kit and sequenced using the HiSeq or NovaSeq platforms (2 × 101-bp paired-end reads)

value: CD19 CAR T cells


title: F123 GAM library f123_1NP_GAM180223_C02_2_S107_R1_001


title: F123 GAM library f123_1NP_GAM180223_C03_1_S19_R1_001


title: AF5

description:
Library name: sample5
AF5


title: F123 GAM library f123_1NP_GAM180223_C03_2_S115_R1_001


title: F123 GAM library f123_1NP_GAM180223_C08_2_S155_R1_001


title: F123 GAM library f123_1NP_GAM180223_C02_1_S11_R1_001


title: F123 GAM library f123_1NP_GAM180223_C01_2_S99_R1_001


title: F123 GAM library f123_1NP_GAM180223_C01_1_S3_R1_001


title: Fibroblast of IPF patient sample

first: Tao

last: Ren

address: No. 600, Yi Shan Road

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

data_processing:
The sequencing platform is novaseq 6000. After the data is off the machine, RTA (real time analysis) is used to convert it into the original BCL file, and the version is v3.4.4; It is split by bcl2fastq (btq) software and converted into FQ, version v2.19. Fastp software is used for quality control, version 0.19.7, involving the parameter fastp-G-Q5-U50-N 15-L150.We applied BD Rhapsody Analysis pipeline (Version:1.8 https://hub.docker.com/r/bdgenomics/rhapsody) with default parameter to align reads and generate feature-barcode matrices. The reads were mapped to hg38 genome (GENCODE version 29) utilizing STAR mapping with customized parameter from BD Rhapsody Analysis pipeline. Seurat R package (version: 3.1.5) was used for cell normalization and regression according to the UMI counts of each cell, feature filtration and mitochondrial percentage, which in turn obtained the scaled data.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: the margin of the excised lung tissue

growth_protocol: Airway basal cells were isolated from the fifth-generation bronchi by fiberoptic bronchoscopy, cultured on a lawn of irradiated 3T3-J2 feeder as previously described (Rheinwald JG. and Green H., 1975). BCs with robust self-renewal properties were selectively expanded as colonies through cell passaging at 37°C in a 7.5% CO2 atmosphere.Distal airway basal cells were isolated from the margin of the excised lung tissue by mincing and enzymatic digestion, cultured on a lawn of irradiated 3T3-J2 feeder as previously described (Rheinwald JG. and Green H., 1975). Primary BCs were expanded as colonies at 37°C in a 7.5% CO2 atmosphere.Fibroblast were isolated from the margin of the excised lung tissue by mincing and enzymatic digestion, cultured in fibroblast medium. Primary fibroblast were expanded at 37°C in a 5% CO2 atmosphere.

extract_protocol:
BCs and  fibroblasts were resuspended and followed by single-cell capture and barcoding according to BD Rhapsody workflow.
RNA libraries were prepared for sequencing using BD Rhapsody Analysis pipeline (Version: 1.8) protocols.

value: the margin of the excised lung tissue

value: Fibroblast

value: IPF


title: CART_GPR65KO_rep1


title: CART_GPR65KO_rep2


title: F123 GAM library f123_1NP_GAM180223_B11_2_S178_R1_001


title: Distal BCs of IPF patient sample

value: Distal basal cells


title: CART_CR_rep3


title: F123 GAM library f123_1NP_GAM180223_B10_1_S74_R1_001


title: CART_CR_rep2


title: F123 GAM library f123_1NP_GAM180223_B09_1_S66_R1_001


title: F123 GAM library f123_1NP_GAM180223_B09_2_S162_R1_001


title: F123 GAM library f123_1NP_GAM180223_B10_2_S170_R1_001


title: Airway BCs of healthy control2

source_name: human bronchial epithelia

value: human bronchial epithelia

value: Airway basal cells

value: healthy


title: CART_CR_rep1


title: F123 GAM library f123_1NP_GAM180223_B08_2_S154_R1_001

value: mouse embryonic stem cells


title: F123 GAM library f123_1NP_GAM180223_B08_1_S58_R1_001


title: Airway BCs of healthy control1


title: F123 GAM library f123_1NP_GAM180223_B07_1_S50_R1_001


title: Airway BCs of IPF patient3


title: CART_rep2


title: F123 GAM library f123_1NP_GAM180223_B06_2_S138_R1_001


title: F123 GAM library f123_1NP_GAM180223_B07_2_S146_R1_001


title: CART_rep1


title: F123 GAM library f123_1NP_GAM180223_B04_2_S122_R1_001


title: Airway BCs of IPF patient2


title: F123 GAM library f123_1NP_GAM180223_B06_1_S42_R1_001


title: Airway BCs of IPF patient1


title: F123 GAM library f123_1NP_GAM180223_B05_1_S34_R1_001