title: T-ALL Sample 215

description: taken at diagnosis


title: F123 GAM library f123_1NP_GAM180914_B01_1_S2_R1_001

status: Public on Jan 29 2025

type: SRA

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.

tag: cell line

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: Hybrid F1 S129/Jae and Cast

tag: Sex

value: male


title: T-ALL Sample 213

type: genomic

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

description: taken at diagnosis

hyb_protocol: Followed the manufacturer's (Illumina, CA, USA) specifications.

scan_protocol: Followed the manufacturer's (Illumina, CA, USA) specifications on HiScan.

data_processing:
The ChAMP package in R was used to normalize the arrays with Beta-Mixture Quantile normalization, and to filter out non-CpG probes, probes in the X and Y chromosomes, CpGs within five base pairs from European SNPs, probes aligning to multiple locations, probes with a bead count < 3 in at least 5% of samples, and probes with a detection p-value above 0.05. Beta-values (ranging from 0 to 1) were estimated after normalization and filtering.
Average Beta, unmethylated and methylated signal intensities in Series supplementary files.

label: Cy3 and Cy5

organism: Homo sapiens

source_name: T-ALL bone marrow/peripheral blood sample

growth_protocol: No growth; biobanked frozen samples.

extract_protocol: DNA was extracted by Qiagen ALLprep DNA/RNA kit (Qiagen, Hilden, Germany); sodium bisulfite converted using the EZ DNA methylation kit (Zymo Research, CA, USA) according the manufacturer's specifications.

tag: tissue

tag: tissue type

value: Tumor

tag: cimp subgroup

value: CIMP low

tag: disease

value: Pediatric T-cell acute lymphoblastic leukemia


title: T-ALL Sample 212

description: taken at diagnosis

label_protocol: Followed the manufacturer's (Illumina, CA, USA) specifications.

value: T-ALL bone marrow/peripheral blood sample

value: CIMP high


title: T-ALL Sample 214

description: taken at diagnosis


title: F123 GAM library f123_1NP_GAM180914_A12_1_S89_R1_001


title: F123 GAM library f123_1NP_GAM180914_A11_1_S81_R1_001


title: F123 GAM library f123_1NP_GAM180914_A10_1_S73_R1_001


title: T-ALL Sample 211

description: taken at diagnosis


title: T-ALL Sample 210

description: taken at diagnosis


title: F123 GAM library f123_1NP_GAM180914_A09_1_S65_R1_001


title: T-ALL Sample 209

description: taken at diagnosis


title: T-ALL Sample 207

description: taken at diagnosis


title: F123 GAM library f123_1NP_GAM180914_A08_1_S57_R1_001


title: T-ALL Sample 206

description: taken at diagnosis


title: F123 GAM library f123_1NP_GAM180914_A05_1_S33_R1_001


title: F123 GAM library f123_1NP_GAM180914_A04_1_S25_R1_001


title: T-ALL Sample 208

description: taken at diagnosis


title: T-ALL Sample 203

description: taken at diagnosis


title: T-ALL Sample 205

description: taken at diagnosis


title: F123 GAM library f123_1NP_GAM180914_A06_1_S41_R1_001


title: F123 GAM library f123_1NP_GAM180914_A03_1_S17_R1_001


title: T-ALL Sample 204

description: taken at diagnosis


title: T-ALL Sample 202

description: taken at diagnosis


title: F123 GAM library f123_1NP_GAM180914_A01_1_S1_R1_001


title: F123 GAM library f123_1NP_GAM180914_A02_1_S9_R1_001


title: UPN207_BM_Methyl_CTRL

city: Paris

first: David

last: Rombaut

address: 22 rue Méchain

country: France

institute: Institut Cochin

hyb_protocol: DNA (500ng) was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research, CA, United States). Whole genome DNA methylation was performed in accordance with Illumina manufacturer instructions for the Infinium Methylation EPIC 850K BeadChip Array (Illumina, USA).

scan_protocol: EPIC BeadChips were imaged using the Illumina iScan System (Illumina, United States).

data_processing:
Beta values are computed out of raw IDAT files by the import function of the ChAMP R package, utilizing the minfi method. Probes with a detection P-value >0.01, with a beadcount <3 in at least 5% of samples, noCG start, CpGs near a SNP (using the general EPIC SNP list), multihit CpGs, as well as CpGs from the X or Y chromosome are filtered out by ChAMP. After probes quality control, Beta values are normalized using BMIQ: beta-mixture quantile normalization.
Normalized Beta values (BMIQ) for the post-filtered 723612 CpGs.
Unmethylated, methylated signal intensities and pvalue detection for the 862927 CpGs.

label: Cy5 and Cy3

source_name: Bone marrow

label_protocol: Standard Illumina Protocol

extract_protocol: DNA were extracted from the bone marrow mononuclear cell (BM MNC) fraction isolated on Ficoll gradient using the DNA/RNA Kit (Qiagen, Hilden, Germany).

value: Healthy control

tag: progression

value: CTRL

tag: mdsdiag

value: SF3B1 WT SRSF2 WT U2AF1 WT

tag: gender

value: Male

tag: methyl batch


title: T-ALL Sample 201

description: taken at diagnosis


title: UPN206_BM_Methyl_CTRL

value: Female


title: F123 GAM library f123_1NP_GAM180812_H12_1_S96_R1_001


title: F123 GAM library f123_1NP_GAM180812_H11_1_S88_R1_001


title: F123 GAM library f123_1NP_GAM180812_H10_1_S80_R1_001


title: F123 GAM library f123_1NP_GAM180812_H10_2_S176_R1_001


title: F123 GAM library f123_1NP_GAM180812_H11_2_S184_R1_001


title: F123 GAM library f123_1NP_GAM180914_A07_1_S49_R1_001


title: UPN203_BM_Methyl_CTRL


title: UPN204_BM_Methyl_CTRL


title: UPN202_BM_Methyl_CTRL


title: F123 GAM library f123_1NP_GAM180812_H09_1_S72_R1_001


title: F123 GAM library f123_1NP_GAM180812_H08_2_S160_R1_001


title: UPN200_BM_Methyl_MDS

value: LR-MDS

value: MDS

value: RCMD-RS

value: SF3B1 MUT SRSF2 WT U2AF1 WT


title: UPN201_BM_Methyl_CTRL


title: F123 GAM library f123_1NP_GAM180812_H08_1_S64_R1_001

value: mouse embryonic stem cells


title: UPN196_BM_Methyl_MDSp

value: MDSp

value: RCMD

value: SF3B1 WT SRSF2 MUT U2AF1 WT


title: F123 GAM library f123_1NP_GAM180812_H07_1_S56_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: F123 GAM library f123_1NP_GAM180812_H07_2_S152_R1_001


title: F123 GAM library f123_1NP_GAM180812_H06_1_S48_R1_001


title: F123 GAM library f123_1NP_GAM180914_B04_1_S26_R1_001


title: F123 GAM library f123_1NP_GAM180812_H06_2_S144_R1_001


title: UPN195_BM_Methyl_MDS

value: MDS-U


title: UPN205_BM_Methyl_CTRL


title: UPN194_BM_Methyl_MDSp

value: RA


title: UPN198_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_H05_2_S136_R1_001


title: F123 GAM library f123_1NP_GAM180812_H04_2_S128_R1_001


title: UPN192_BM_Methyl_MDSp


title: F123 GAM library f123_1NP_GAM180812_H04_1_S32_R1_001


title: F123 GAM library f123_1NP_GAM180812_H09_2_S168_R1_001


title: UPN193_BM_Methyl_MDSp


title: UPN191_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_H02_1_S16_R1_001


title: F123 GAM library f123_1NP_GAM180812_H02_2_S112_R1_001


title: F123 GAM library f123_1NP_GAM180812_H03_1_S24_R1_001


title: UPN189_BM_Methyl_MDS


title: UPN188_BM_Methyl_MDS

value: RARS


title: F123 GAM library f123_1NP_GAM180812_G12_2_S191_R1_001


title: UPN199_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_H01_2_S104_R1_001


title: UPN187_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_G11_1_S87_R1_001


title: UPN184_BM_Methyl_MDS


title: UPN190_BM_Methyl_MDS


title: UPN185_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_G10_2_S175_R1_001


title: F123 GAM library f123_1NP_GAM180812_G10_1_S79_R1_001


title: UPN183_BM_Methyl_MDS


title: UPN186_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_H03_2_S120_R1_001


title: F123 GAM library f123_1NP_GAM180812_G09_2_S167_R1_001


title: UPN181_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_G09_1_S71_R1_001


title: UPN179_BM_Methyl_MDS


title: UPN178_BM_Methyl_MDSp

value: SF3B1 MUT SRSF2 WT U2AF1 MUT


title: F123 GAM library f123_1NP_GAM180812_G08_2_S159_R1_001


title: UPN176_BM_Methyl_MDS

value: SF3B1 WT SRSF2 WT U2AF1 WT


title: UPN177_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_G07_1_S55_R1_001


title: UPN173_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_G12_1_S95_R1_001


title: F123 GAM library f123_1NP_GAM180812_G06_2_S143_R1_001


title: UPN170_BM_Methyl_MDS

value: Male


title: F123 GAM library f123_1NP_GAM180812_G05_1_S39_R1_001


title: UPN167_BM_Methyl_MDS

value: Female


title: F123 GAM library f123_1NP_GAM180812_G04_2_S127_R1_001


title: F123 GAM library f123_1NP_GAM180812_G04_1_S31_R1_001


title: F123 GAM library f123_1NP_GAM180812_G05_2_S135_R1_001


title: F123 GAM library f123_1NP_GAM180812_G06_1_S47_R1_001


title: UPN169_BM_Methyl_MDS

value: LR-MDS


title: UPN168_BM_Methyl_MDS

value: MDS


title: UPN180_BM_Methyl_MDS

value: SF3B1 WT SRSF2 WT U2AF1 MUT


title: UPN165_BM_Methyl_MDSp

value: SF3B1 WT SRSF2 MUT U2AF1 MUT


title: F123 GAM library f123_1NP_GAM180812_G03_2_S119_R1_001

value: mouse embryonic stem cells


title: UPN164_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_G03_1_S23_R1_001


title: UPN163_BM_Methyl_MDS

value: SF3B1 MUT SRSF2 WT U2AF1 WT


title: F123 GAM library f123_1NP_GAM180812_G08_1_S63_R1_001


title: UPN162_BM_Methyl_MDS

value: RCMD


title: UPN161_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_G07_2_S151_R1_001


title: UPN172_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_G02_2_S111_R1_001


title: F123 GAM library f123_1NP_GAM180812_G02_1_S15_R1_001


title: UPN159_BM_Methyl_MDS


title: UPN160_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_F11_2_S182_R1_001


title: F123 GAM library f123_1NP_GAM180812_G01_1_S7_R1_001


title: F123 GAM library f123_1NP_GAM180812_F12_2_S190_R1_001


title: F123 GAM library f123_1NP_GAM180812_F11_1_S86_R1_001


title: UPN157_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_F10_1_S78_R1_001


title: UPN158_BM_Methyl_MDS

value: RCMD-RS


title: UPN156_BM_Methyl_MDS

value: SF3B1 WT SRSF2 MUT U2AF1 WT


title: F123 GAM library f123_1NP_GAM180812_F09_1_S70_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: UPN155_BM_Methyl_MDS


title: UPN152_BM_Methyl_MDS

value: RA


title: F123 GAM library f123_1NP_GAM180812_F09_2_S166_R1_001


title: F123 GAM library f123_1NP_GAM180812_F08_2_S158_R1_001


title: F123 GAM library f123_1NP_GAM180812_G01_2_S103_R1_001


title: F123 GAM library f123_1NP_GAM180812_F08_1_S62_R1_001


title: UPN153_BM_Methyl_MDS


title: UPN166_BM_Methyl_MDS

value: RARS


title: F123 GAM library f123_1NP_GAM180812_F07_2_S150_R1_001


title: UPN150_BM_Methyl_MDS


title: UPN149_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_F06_2_S142_R1_001


title: F123 GAM library f123_1NP_GAM180812_F07_1_S54_R1_001


title: UPN148_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_F06_1_S46_R1_001


title: UPN146_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_F05_2_S134_R1_001


title: UPN147_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_F05_1_S38_R1_001


title: UPN144_BM_Methyl_MDS


title: UPN143_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_F04_2_S126_R1_001


title: F123 GAM library f123_1NP_GAM180812_F03_2_S118_R1_001


title: UPN142_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_F04_1_S30_R1_001


title: F123 GAM library f123_1NP_GAM180812_F03_1_S22_R1_001


title: UPN140_BM_Methyl_MDS


title: UPN151_BM_Methyl_MDS


title: UPN141_BM_Methyl_MDS


title: UPN139_BM_Methyl_MDSp

value: MDSp

value: SF3B1 MUT SRSF2 WT U2AF1 MUT


title: UPN138_BM_Methyl_MDSp


title: UPN135_BM_Methyl_MDS

value: Male


title: F123 GAM library f123_1NP_GAM180812_F01_2_S102_R1_001


title: F123 GAM library f123_1NP_GAM180812_F02_2_S110_R1_001


title: UPN134_BM_Methyl_MDS

value: Female


title: F123 GAM library f123_1NP_GAM180812_F02_1_S14_R1_001


title: F123 GAM library f123_1NP_GAM180812_E12_1_S93_R1_001


title: UPN133_BM_Methyl_MDSp

value: LR-MDS

value: SF3B1 WT SRSF2 WT U2AF1 WT


title: F123 GAM library f123_1NP_GAM180812_F01_1_S6_R1_001


title: F123 GAM library f123_1NP_GAM180812_E11_2_S181_R1_001


title: UPN132_BM_Methyl_MDS

value: MDS


title: F123 GAM library f123_1NP_GAM180812_E11_1_S85_R1_001


title: UPN129_BM_Methyl_MDS


title: UPN126_BM_Methyl_MDS


title: UPN127_BM_Methyl_MDS

value: SF3B1 MUT SRSF2 MUT U2AF1 WT


title: F123 GAM library f123_1NP_GAM180812_E10_1_S77_R1_001

value: mouse embryonic stem cells


title: F123 GAM library f123_1NP_GAM180812_E08_2_S157_R1_001


title: UPN128_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_E08_1_S61_R1_001


title: UPN124_BM_Methyl_MDSp


title: F123 GAM library f123_1NP_GAM180812_E07_2_S149_R1_001


title: F123 GAM library f123_1NP_GAM180812_E07_1_S53_R1_001


title: UPN123_BM_Methyl_MDS

value: SF3B1 MUT SRSF2 WT U2AF1 WT


title: UPN121_BM_Methyl_MDS


title: UPN122_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_E05_2_S133_R1_001


title: UPN120_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_E05_1_S37_R1_001


title: UPN117_BM_Methyl_MDS


title: UPN118_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_E03_2_S117_R1_001


title: UPN119_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_E04_2_S125_R1_001


title: F123 GAM library f123_1NP_GAM180812_E04_1_S29_R1_001


title: F123 GAM library f123_1NP_GAM180812_E03_1_S21_R1_001


title: UPN116_BM_Methyl_MDS

value: RCMD


title: F123 GAM library f123_1NP_GAM180812_E09_1_S69_R1_001


title: UPN114_BM_Methyl_MDS


title: UPN115_BM_Methyl_MDS


title: UPN125_BM_Methyl_MDS

value: RCMD-RS


title: F123 GAM library f123_1NP_GAM180812_E02_1_S13_R1_001


title: UPN111_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_E01_2_S101_R1_001


title: UPN110_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_E06_2_S141_R1_001


title: UPN109_BM_Methyl_MDS


title: UPN108_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_E01_1_S5_R1_001


title: F123 GAM library f123_1NP_GAM180812_D11_2_S180_R1_001


title: F123 GAM library f123_1NP_GAM180812_E06_1_S45_R1_001


title: F123 GAM library f123_1NP_GAM180812_D12_2_S188_R1_001


title: UPN103_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_D10_1_S76_R1_001


title: UPN102_BM_Methyl_MDS

value: SF3B1 WT SRSF2 MUT U2AF1 WT


title: UPN106_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_D11_1_S84_R1_001

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM180812_D10_2_S172_R1_001

value: male


title: UPN105_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_D08_1_S60_R1_001


title: UPN104_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_D07_1_S52_R1_001


title: F123 GAM library f123_1NP_GAM180812_D09_1_S68_R1_001


title: UPN101_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_D08_2_S156_R1_001


title: UPN107_BM_Methyl_MDS


title: UPN94_BM_Methyl_MDSp


title: UPN96_BM_Methyl_MDS


title: UPN97_BM_Methyl_MDS


title: UPN95_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_D05_2_S132_R1_001


title: F123 GAM library f123_1NP_GAM180812_D06_2_S140_R1_001


title: F123 GAM library f123_1NP_GAM180812_D07_2_S148_R1_001


title: F123 GAM library f123_1NP_GAM180812_D06_1_S44_R1_001


title: F123 GAM library f123_1NP_GAM180812_D05_1_S36_R1_001


title: UPN100_BM_Methyl_MDS


title: UPN93_BM_Methyl_MDS


title: UPN98_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_D04_2_S124_R1_001


title: UPN92_BM_Methyl_MDSp


title: F123 GAM library f123_1NP_GAM180812_D09_2_S164_R1_001


title: F123 GAM library f123_1NP_GAM180812_D04_1_S28_R1_001


title: UPN91_BM_Methyl_MDSp

value: RA


title: UPN88_BM_Methyl_MDS

value: RARS


title: UPN90_BM_Methyl_MDSp

value: MDSp


title: UPN89_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_D03_2_S116_R1_001


title: F123 GAM library f123_1NP_GAM180812_D02_1_S12_R1_001


title: F123 GAM library f123_1NP_GAM180812_D01_1_S4_R1_001


title: UPN85_BM_Methyl_MDS


title: UPN83_BM_Methyl_MDS


title: UPN87_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C12_2_S187_R1_001


title: F123 GAM library f123_1NP_GAM180812_C12_1_S91_R1_001


title: F123 GAM library f123_1NP_GAM180812_C11_2_S179_R1_001


title: UPN80_BM_Methyl_MDSp


title: UPN78_BM_Methyl_MDSp


title: F123 GAM library f123_1NP_GAM180812_C10_2_S171_R1_001


title: UPN79_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_D03_1_S20_R1_001


title: UPN81_BM_Methyl_MDS


title: UPN82_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_D02_2_S108_R1_001


title: UPN76_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C08_1_S59_R1_001


title: UPN86_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C08_2_S155_R1_001


title: F123 GAM library f123_1NP_GAM180812_E02_2_S109_R1_001


title: F123 GAM library f123_1NP_GAM180812_D01_2_S100_R1_001


title: UPN71_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C09_2_S163_R1_001


title: UPN73_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C06_2_S139_R1_001


title: F123 GAM library f123_1NP_GAM180812_C10_1_S75_R1_001


title: UPN70_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C05_2_S131_R1_001


title: UPN66_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C05_1_S35_R1_001


title: F123 GAM library f123_1NP_GAM180812_C11_1_S83_R1_001


title: UPN69_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C04_2_S123_R1_001


title: UPN68_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C04_1_S27_R1_001


title: UPN67_BM_Methyl_MDS


title: UPN65_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C03_2_S115_R1_001


title: UPN77_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C07_1_S51_R1_001


title: F123 GAM library f123_1NP_GAM180812_C02_2_S107_R1_001


title: F123 GAM library f123_1NP_GAM180812_C03_1_S19_R1_001


title: UPN64_BM_Methyl_MDSp


title: F123 GAM library f123_1NP_GAM180812_C01_2_S99_R1_001


title: UPN61_BM_Methyl_MDS


title: UPN63_BM_Methyl_MDS


title: UPN54_BM_Methyl_MDSp


title: UPN60_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C07_2_S147_R1_001


title: F123 GAM library f123_1NP_GAM180812_C02_1_S11_R1_001


title: UPN58_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_B11_2_S178_R1_001


title: UPN52_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C01_1_S3_R1_001


title: UPN56_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_C06_1_S43_R1_001


title: F123 GAM library f123_1NP_GAM180812_B10_1_S74_R1_001


title: F123 GAM library f123_1NP_GAM180812_B09_2_S162_R1_001


title: F123 GAM library f123_1NP_GAM180812_B09_1_S66_R1_001


title: UPN46_BM_Methyl_MDS


title: UPN47_BM_Methyl_MDSp

value: SF3B1 WT SRSF2 WT U2AF1 MUT


title: UPN55_BM_Methyl_MDS

value: Male


title: F123 GAM library f123_1NP_GAM180812_B08_1_S58_R1_001


title: UPN45_BM_Methyl_MDSp

value: Female


title: UPN53_BM_Methyl_MDSp

value: LR-MDS


title: F123 GAM library f123_1NP_GAM180812_B11_1_S82_R1_001


title: F123 GAM library f123_1NP_GAM180812_B10_2_S170_R1_001


title: UPN49_BM_Methyl_MDS

value: SF3B1 WT SRSF2 WT U2AF1 WT


title: UPN50_BM_Methyl_MDS

value: MDS


title: F123 GAM library f123_1NP_GAM180812_B08_2_S154_R1_001


title: UPN48_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_B06_1_S42_R1_001


title: UPN40_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_B12_1_S90_R1_001


title: F123 GAM library f123_1NP_GAM180812_B07_2_S146_R1_001


title: F123 GAM library f123_1NP_GAM180812_B05_1_S34_R1_001


title: UPN37_BM_Methyl_MDSp


title: UPN38_BM_Methyl_MDS


title: UPN44_BM_Methyl_MDS


title: UPN39_BM_Methyl_MDS


title: UPN43_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_B03_1_S18_R1_001


title: F123 GAM library f123_1NP_GAM180812_B07_1_S50_R1_001


title: UPN41_BM_Methyl_MDSp


title: UPN34_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_B02_2_S106_R1_001


title: F123 GAM library f123_1NP_GAM180812_B05_2_S130_R1_001


title: UPN32_BM_Methyl_MDS


title: UPN31_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_A12_2_S185_R1_001


title: UPN30_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_A10_1_S73_R1_001


title: UPN28_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_B04_2_S122_R1_001


title: F123 GAM library f123_1NP_GAM180812_B04_1_S26_R1_001


title: UPN35_BM_Methyl_MDS


title: UPN26_BM_Methyl_MDSp


title: UPN36_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_B03_2_S114_R1_001


title: UPN33_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_A09_2_S161_R1_001


title: F123 GAM library f123_1NP_GAM180812_B02_1_S10_R1_001


title: UPN24_BM_Methyl_MDSp


title: F123 GAM library f123_1NP_GAM180812_B01_2_S98_R1_001


title: F123 GAM library f123_1NP_GAM180812_A07_1_S49_R1_001


title: UPN21_BM_Methyl_MDS


title: UPN29_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_B01_1_S2_R1_001


title: F123 GAM library f123_1NP_GAM180812_A06_2_S137_R1_001


title: F123 GAM library f123_1NP_GAM180812_A10_2_S169_R1_001


title: F123 GAM library f123_1NP_GAM180812_A11_2_S177_R1_001


title: UPN27_BM_Methyl_MDS


title: UPN25_BM_Methyl_MDSp


title: F123 GAM library f123_1NP_GAM180812_A09_1_S65_R1_001


title: F123 GAM library f123_1NP_GAM180812_A06_1_S41_R1_001


title: F123 GAM library f123_1NP_GAM180812_A05_2_S129_R1_001


title: F123 GAM library f123_1NP_GAM180812_A04_2_S121_R1_001


title: UPN17_BM_Methyl_MDS


title: UPN23_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_A08_1_S57_R1_001


title: F123 GAM library f123_1NP_GAM180812_A04_1_S25_R1_001


title: F123 GAM library f123_1NP_GAM180812_A08_2_S153_R1_001


title: UPN15_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_A07_2_S145_R1_001


title: UPN22_BM_Methyl_MDS


title: UPN20_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_A02_2_S105_R1_001


title: UPN19_BM_Methyl_MDS

value: MDS-U


title: UPN13_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_A02_1_S9_R1_001

value: mouse embryonic stem cells


title: F123 GAM library f123_1NP_GAM180812_A03_2_S113_R1_001


title: UPN16_BM_Methyl_MDS

value: SF3B1 MUT SRSF2 WT U2AF1 WT


title: UPN12_BM_Methyl_MDS

value: RCMD


title: UPN14_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_A03_1_S17_R1_001


title: F123 GAM library f123_1NP_GAM180812_A01_2_S97_R1_001


title: UPN11_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180716_H12_2_S192_R1_001


title: UPN10_BM_Methyl_MDS


title: UPN18_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180812_A01_1_S1_R1_001


title: UPN6_BM_Methyl_MDS


title: UPN8_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180716_H07_1_S56_R1_001


title: F123 GAM library f123_1NP_GAM180716_H11_2_S184_R1_001


title: F123 GAM library f123_1NP_GAM180716_H06_1_S48_R1_001


title: F123 GAM library f123_1NP_GAM180716_H05_2_S136_R1_001


title: UPN5_BM_Methyl_MDSp


title: UPN2_BM_Methyl_MDSp


title: UPN3_BM_Methyl_MDS


title: F123 GAM library f123_1NP_GAM180716_H04_2_S128_R1_001


title: F123 GAM library f123_1NP_GAM180716_G12_2_S191_R1_001


title: HL60, Decitabine, Normoxia, 72 hour, Rep3

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

description: Library name: R3_HL60_DAC_N_72H

data_processing:
Raw reads were trimmed in pair-end mode using Trim Galore (v0.6.5, Cutadapt v2.10, options ‘--clip_R1 9 --clip_R2 9) to exclude poor-quality calls and adaptors.
Alignment and methylation calling of trimmed reads was performed using Bismark (v0.22.3) in PBAT mode against the human GRCh38 reference assembly using a custom approach (also known as the 'dirty harry' method in which mapping is first performed in pair-end mode with unmapped singleton reads written out, followed by alignment of the singleton reads in single-end mode. ).
Mapping of trimmed reads was performed using Bismark with the following parameters: i) -- unmapped –pbat -1 <read1> -2 <read2>, ii) --pbat --single_end <unmapped_read1> iii) --pbat --single_end <unmapped_read2>.
Mapped reads were then deduplicated (using deduplcation_bismark) and methylation extraction performed (using bismark_methylation_extractor) in paired end and single end mode separately, and then merged into a single coverage file per sample.
Assembly: GRCh38 reference
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>

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:
DNA 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).
Post-bisulphite adaptor tagging (PBAT) strategy was performed as described, Nucleic Acids Res (2012)[Miura F et al. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging (2012)]. Briefly, DNA purified from treated cells underwent bisulphite conversion using the EZ-96 DNA Methylation-Direct MagPrep Kit (Zymo Research, U.S.; #D5044).Samples were then resuspended in a pre-amplification mix: 1X blue buffer, 0.4mM dNTP mix, 2uM 6NF preamplification oligo (5’-CTACACGACGCTCTTCCGATCTNNNNNN-3’), and UltraPure distilled water, and incubated at 65oC to denature the DNA. Klenow (3’  5’ exo-, 50U) (Custom Science, AUS) was added to each sample and first strand synthesis was performed by incubating as follows: 5min at 4oC, 37 repeats of +1oC every 15s, 30min at 37oC. Samples were then incubated with Exonuclease I (40U) (New England Biolabs, U.S) at 37oC for 1 hour and purified using Agencourt AMPure XP beads (0.8X) (Beckman Coulter, U.S.). For second strand synthesis, samples and beads were resuspended in a second-strand mixture, as indicated: 1X blue buffer, 0.4mM dNTP mix, 2uM 6NR_NEB adaptor 2 oligo (5’-CAGACGTGTGCTCTTCCGATCTNNNNNN-3’) and UltraPure distilled water and incubated at 95oC for 45s. Like first strand synthesis, Klenow was added to each sample and incubated on the thermocycler using the same conditions, before a second round of purification with AMPure XP beads (0.8X). To amplify the libraries for sequencing, samples and beads were resuspended in KAPA HiFi HotStart ReadyMix (1X) (Millenium Science, AUS), which contains a DNA polymerase to amplify the DNA. Following the manufacturer’s instructions, specific i7 and i5 NEBNext index pairs (5uM) (New England Biolabs, U.S) were added to each sample and incubated as follows: 1 cycle at 95oC for 2min; 6 cycles of 94oC for 80s, 65oC for 30s and 72oC for 30s; 72oC for 3min; hold at 4oC. Amplified libraries were purified using AMPure XP beads (0.8X) and eluted in UltraPure distilled water. Sequencing was performed using a MiSeq Reagent Kit v2 (Illumina, U.S.) in 150bp paired-end mode, with a loading sample concentration of 10pM and a 5% PhiX (Illumina, U.S.) spike-in.

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 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 for MOLM-13 and MV-4-11 cells, and 2000nM for HL-60 cells) (Sellekchem, U.S.), or without HMA (Untreated control, UT) made every 24 hours.

tag: processing protocol

value: PBAT

value: Peripheral blood

value: promyeloblast

tag: disease/cancer type

value: Acute promyelocytic leukemia

tag: age

tag: replicate

tag: treatment

value: 72 hour normoxia, decitabine

tag: oxygen tension

value: Normoxia (21% O2)

tag: hypomethylating agent_(hma)

value: Decitabine

tag: hypoxia pre-treatment

value: N

tag: batch


title: HL60, Azacytidine, Hypoxia, 144 hour, Rep2

description: Library name: R2_HL60_AZA_H_144H

tag: tissue

tag: cell line

tag: cell type

tag: Sex

value: 72 hour hypoxia pre-treament, 72 hour azacytidine

value: Hypoxia (1% O2)

value: Azacytidine

value: Y


title: MOLM, Decitabine, Normoxia, 72 hour, Rep3

description: Library name: R3_MOLM_DAC_N_72H

value: acute myeloid leukemia

value: Acute myeloid leukemia (M5a)

value: Male


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

description: Library name: R2_MOLM_AZA_H_144H


title: F123 GAM library f123_1NP_GAM180716_G06_2_S143_R1_001

value: mouse embryonic stem cells

tag: genotype

value: Hybrid F1 S129/Jae and Cast

value: male


title: HL60, Decitabine, Hypoxia, 144 hour, Rep2

description: Library name: R2_HL60_DAC_H_144H

value: PBAT

value: Peripheral blood

value: Female

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


title: F123 GAM library f123_1NP_GAM180716_G05_2_S135_R1_001


title: UPN9_BM_Methyl_MDS

tag: disease

value: LR-MDS

tag: progression

value: MDS

tag: mdsdiag

value: RARS

value: SF3B1 MUT SRSF2 WT U2AF1 WT


title: F123 GAM library f123_1NP_GAM180716_G04_2_S127_R1_001


title: HL60, Untreated, Normoxia, 72 hour, Rep3

description: Library name: R3_HL60_Unt_N_72H

tag: processing protocol

value: promyeloblast

value: Acute promyelocytic leukemia

value: 72 hour normoxia, untreated

value: Normoxia (21% O2)

value: Untreated

value: N


title: F123 GAM library f123_1NP_GAM180716_F12_2_S190_R1_001

value: mouse embryonic stem cells


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

description: Library name: R2_MOLM_DAC_H_144H

value: acute myeloid leukemia

tag: disease/cancer type

value: Acute myeloid leukemia (M5a)

value: Male

value: Hypoxia (1% O2)

value: Decitabine

value: Y


title: F123 GAM library f123_1NP_GAM180716_F11_2_S182_R1_001

value: Hybrid F1 S129/Jae and Cast

value: male


title: MOLM, Untreated, Normoxia, 72 hour, Rep3

description: Library name: R3_MOLM_Unt_N_72H

value: PBAT

value: Peripheral blood

tag: age


title: UPN4_BM_Methyl_MDS

value: LR-MDS

value: MDS

value: RCMD

value: SF3B1 WT SRSF2 WT U2AF1 WT

tag: gender

tag: methyl batch


title: F123 GAM library f123_1NP_GAM180716_F07_1_S54_R1_001


title: F123 GAM library f123_1NP_GAM180716_H06_2_S144_R1_001


title: F123 GAM library f123_1NP_GAM180716_F06_2_S142_R1_001


title: HL60, Azacytidine, Normoxia, 72 hour, Rep2

description: Library name: R2_HL60_AZA_N_72H

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female

tag: replicate

tag: treatment

value: 72 hour normoxia, azacytidine

tag: oxygen tension

value: Normoxia (21% O2)

value: Azacytidine


title: F123 GAM library f123_1NP_GAM180716_F06_1_S46_R1_001

value: mouse embryonic stem cells


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

description: Library name: R2_MOLM_Unt_H_144H

value: acute myeloid leukemia

value: Acute myeloid leukemia (M5a)

value: Male

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

value: Hypoxia (1% O2)

tag: hypomethylating agent_(hma)

value: Untreated

tag: hypoxia pre-treatment

tag: batch


title: MOLM, Azacytidine, Normoxia, 72 hour, Rep2

description: Library name: R2_MOLM_AZA_N_72H

value: PBAT

tag: tissue

value: Peripheral blood

tag: cell line

tag: cell type

value: N


title: F123 GAM library f123_1NP_GAM180716_G11_2_S183_R1_001

tag: genotype

value: Hybrid F1 S129/Jae and Cast

tag: Sex

value: male


title: F123 GAM library f123_1NP_GAM180716_F05_2_S134_R1_001


title: F123 GAM library f123_1NP_GAM180716_G07_1_S55_R1_001


title: HL60, Untreated, Hypoxia, 72 hour, Rep2

description: Library name: R2_HL60_Unt_H_72H

value: promyeloblast

value: Acute promyelocytic leukemia

value: 72 hour hypoxia, untreated


title: HL60, Decitabine, Normoxia, 72 hour, Rep2

description: Library name: R2_HL60_DAC_N_72H

value: Female

value: 72 hour normoxia, decitabine

value: Normoxia (21% O2)

value: Decitabine


title: F123 GAM library f123_1NP_GAM180716_F04_2_S126_R1_001

value: mouse embryonic stem cells


title: F123 GAM library f123_1NP_GAM180716_E12_2_S189_R1_001


title: MOLM, Untreated, Hypoxia, 72 hour, Rep2

description: Library name: R2_MOLM_Unt_H_72H

value: acute myeloid leukemia

value: Acute myeloid leukemia (M5a)

value: Male


title: F123 GAM library f123_1NP_GAM180716_G06_1_S47_R1_001


title: F123 GAM library f123_1NP_GAM180716_E11_2_S181_R1_001


title: MOLM, Decitabine, Normoxia, 72 hour, Rep2

description: Library name: R2_MOLM_DAC_N_72H


title: F123 GAM library f123_1NP_GAM180716_E06_2_S141_R1_001


title: HL60, Azacytidine, Hypoxia, 144 hour, Rep1

description: Library name: R1_HL60_AZA_H_144H

value: 72 hour hypoxia pre-treament, 72 hour azacytidine

value: Hypoxia (1% O2)

value: Azacytidine

value: Y


title: F123 GAM library f123_1NP_GAM180716_E06_1_S45_R1_001

value: Hybrid F1 S129/Jae and Cast


title: HL60, Untreated, Normoxia, 72 hour, Rep2

description: Library name: R2_HL60_Unt_N_72H

value: PBAT

value: Peripheral blood

value: 72 hour normoxia, untreated

value: Untreated

value: N


title: HL60, Untreated, Hypoxia, 144 hour, Rep2

description: Library name: R2_HL60_Unt_H_144H

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female

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


title: F123 GAM library f123_1NP_GAM180716_E05_2_S133_R1_001

value: mouse embryonic stem cells

value: male


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

description: Library name: R1_MOLM_AZA_H_144H

value: acute myeloid leukemia

value: Acute myeloid leukemia (M5a)

value: Male


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

description: Library name: R3_MOLM_AZA_H_144H

value: 72 hour hypoxia pre-treament, 72 hour azacytidine

value: Hypoxia (1% O2)

value: Azacytidine


title: F123 GAM library f123_1NP_GAM180716_E04_2_S125_R1_001

value: Hybrid F1 S129/Jae and Cast


title: MOLM, Untreated, Normoxia, 72 hour, Rep2

description: Library name: R2_MOLM_Unt_N_72H

value: PBAT

value: Peripheral blood

value: Normoxia (21% O2)


title: F123 GAM library f123_1NP_GAM180716_D12_2_S188_R1_001


title: F123 GAM library f123_1NP_GAM180716_D11_2_S180_R1_001


title: F123 GAM library f123_1NP_GAM180716_D06_1_S44_R1_001


title: HL60, Azacytidine, Normoxia, 72 hour, Rep1

description: Library name: R1_HL60_AZA_N_72H

value: 72 hour normoxia, azacytidine

value: N


title: F123 GAM library f123_1NP_GAM180716_D07_1_S52_R1_001


title: HL60, Decitabine, Hypoxia, 144 hour, Rep1

description: Library name: R1_HL60_DAC_H_144H

value: promyeloblast

value: Acute promyelocytic leukemia

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

value: Decitabine

value: Y


title: F123 GAM library f123_1NP_GAM180716_D06_2_S140_R1_001

value: mouse embryonic stem cells

value: male


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

description: Library name: R3_MOLM_DAC_H_144H

value: acute myeloid leukemia

value: Acute myeloid leukemia (M5a)

value: Male


title: F123 GAM library f123_1NP_GAM180716_D05_2_S132_R1_001


title: MOLM, Azacytidine, Normoxia, 72 hour, Rep1

description: Library name: R1_MOLM_AZA_N_72H

value: Azacytidine


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

description: Library name: R1_MOLM_DAC_H_144H

value: Hypoxia (1% O2)


title: F123 GAM library f123_1NP_GAM180716_D04_2_S124_R1_001

value: Hybrid F1 S129/Jae and Cast


title: HL60, Untreated, Hypoxia, 144 hour, Rep3

description: Library name: R3_HL60_Unt_H_144H

value: PBAT

value: Peripheral blood

value: Female

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

value: Untreated


title: F123 GAM library f123_1NP_GAM180716_E07_1_S53_R1_001


title: F123 GAM library f123_1NP_GAM180716_C12_2_S187_R1_001


title: HL60, Azacytidine, Hypoxia, 144 hour, Rep3

description: Library name: R3_HL60_AZA_H_144H

value: promyeloblast

value: Acute promyelocytic leukemia

value: 72 hour hypoxia pre-treament, 72 hour azacytidine


title: F123 GAM library f123_1NP_GAM180716_C11_2_S179_R1_001


title: HL60, Decitabine, Normoxia, 72 hour, Rep1

description: Library name: R1_HL60_DAC_N_72H

value: 72 hour normoxia, decitabine

value: Normoxia (21% O2)

value: Decitabine

value: N


title: HL60, Untreated, Hypoxia, 144 hour, Rep1

description: Library name: R1_HL60_Unt_H_144H

value: Y


title: F123 GAM library f123_1NP_GAM180716_C07_1_S51_R1_001

value: mouse embryonic stem cells

value: male


title: F123 GAM library f123_1NP_GAM180716_C06_2_S139_R1_001


title: F123 GAM library f123_1NP_GAM180716_C06_1_S43_R1_001


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

description: Library name: R1_MOLM_Unt_H_144H

value: acute myeloid leukemia

value: Acute myeloid leukemia (M5a)

value: Male

value: Hypoxia (1% O2)


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

description: Library name: R3_MOLM_Unt_H_144H

value: PBAT

value: Peripheral blood


title: F123 GAM library f123_1NP_GAM180716_C05_2_S131_R1_001

value: Hybrid F1 S129/Jae and Cast


title: MOLM, Decitabine, Normoxia, 72 hour, Rep1

description: Library name: R1_MOLM_DAC_N_72H


title: F123 GAM library f123_1NP_GAM180716_C04_2_S123_R1_001


title: HL60, Decitabine, Hypoxia, 144 hour, Rep3

description: Library name: R3_HL60_DAC_H_144H

value: promyeloblast

value: Female

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


title: F123 GAM library f123_1NP_GAM180716_B11_2_S178_R1_001


title: F123 GAM library f123_1NP_GAM180716_B07_1_S50_R1_001


title: HL60, Untreated, Hypoxia, 72 hour, Rep1

description: Library name: R1_HL60_Unt_H_72H

value: Acute promyelocytic leukemia

value: 72 hour hypoxia, untreated

value: Untreated


title: HL60, Untreated, Hypoxia, 72 hour, Rep3

description: Library name: R3_HL60_Unt_H_72H

value: N


title: HL60, Azacytidine, Normoxia, 72 hour, Rep3

description: Library name: R3_HL60_AZA_N_72H

value: 72 hour normoxia, azacytidine

value: Normoxia (21% O2)

value: Azacytidine


title: F123 GAM library f123_1NP_GAM180716_B06_2_S138_R1_001

value: mouse embryonic stem cells

value: male


title: MOLM, Untreated, Hypoxia, 72 hour, Rep3

description: Library name: R3_MOLM_Unt_H_72H

value: acute myeloid leukemia

value: Acute myeloid leukemia (M5a)

value: Male


title: F123 GAM library f123_1NP_GAM180716_B05_2_S130_R1_001


title: HL60, Untreated, Normoxia, 72 hour, Rep1

description: Library name: R1_HL60_Unt_N_72H

value: PBAT

value: Peripheral blood

value: 72 hour normoxia, untreated


title: MOLM, Untreated, Hypoxia, 72 hour, Rep1

description: Library name: R1_MOLM_Unt_H_72H

value: Hypoxia (1% O2)


title: F123 GAM library f123_1NP_GAM180716_B04_2_S122_R1_001

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM180716_A12_2_S185_R1_001


title: PhpC - 5 - age 32

city: HOUSTON

first: Vijay Kumar

last: M J Rao

state: Texas

address: 6431 Fannin street

department: Neurology

country: USA

institute: UTHealth Houston

description: PhpC - Age 32 vs. Control - Age 32.txt

library_source: transcriptomic

data_processing:
All primary analysis is carried out using CLC Genomics Server 22.0.2. The workflow “RNA-Seq Analysis” of CLC Genomics Server with standard parameters is used to map reads to the human genome (hg38).
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 22.0.2 was used for differential expression analysis with default settings. It is an implementation of the ‘Exact Test’ for two-group comparisons developed by Robinson and Smyth, 2008 and incorporated in the EdgeR Bioconductor package Robinson et al., 2010.
For all unsupervised analysis, only miRNAs were considered with at least 10 counts summed over all samples. A variance stabilizing transformation was performed on the raw count matrix using the function vst of the R package DESeq2 version 1.28.1. 500 genes with the highest variance were used for the principal component analysis. The variance was calculated agnostically to the pre-defined groups (blind=TRUE). 35 genes with the highest variance across samples were selected for hierarchical clustering. All primary analysis is carried out using CLC Genomics Server 22.0.2. The workflow “RNA-Seq Analysis” of CLC Genomics Server with standard parameters is used to map reads to the human genome (hg38).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: Epilepsy brain resection

growth_protocol: Human astrocytes were maintained in DMEM growth media supplemented with 10% FBS and antibiotics in humidified chamber wuth 5% CO2 and 37 degrees C

extract_protocol:
RNA was isolated from 2 million cells in 1 ml RLT using the RNeasy Mini (QIAGEN) according to manufacturer’s instructions with an elution volume of 30µl.
The library preparation was done using the QIAseq Stranded mRNA Kit (QIAGEN). From 500 ng starting material, the mRNA was enriched. The RNA was heat fragmented. After first and second strand synthesis, the cDNA was end-repaired and 3’ adenylated. Sequencing adapters were ligated to the overhangs. Adapted molecules were enriched using by 13 cycles or PCR and purified by a bead based cleanup. ). Library preparation was quality controlled using capillary electrophoresis (Tape D1000).High quality libraries are pooled based in equimolar concentrations. The library pool(s) were quantified using qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flowcell before sequencing on a MiSeq (Illumina Inc.) instrument (2x75, 2x10) according to the manufacturer instructions (Illumina Inc.).

treatment_protocol: Human astrocytes were treated with 2uM PDS and 2uM PhpC for 24 hrs.

value: Epilepsy brain resection

value: Human astrocytes

value: Primary

value: Wild-type

value: 20 µM PhpC


title: MOLM, Azacytidine, Normoxia, 72 hour, Rep3

description: Library name: R3_MOLM_AZA_N_72H

value: 72 hour normoxia, azacytidine

value: Normoxia (21% O2)

value: N


title: PhpC - 4 - age 32

description: PhpC - Age 32 vs. Control - Age 32.txt


title: MOLM, Untreated, Normoxia, 72 hour, Rep1

description: Library name: R1_MOLM_Unt_N_72H

value: Untreated


title: PhpC - 3 - age 32

description: PhpC - Age 32 vs. Control - Age 32.txt


title: F123 GAM library f123_1NP_GAM180716_A07_1_S49_R1_001

value: mouse embryonic stem cells

value: male


title: PhpC - 2 - age 32

description: PhpC - Age 32 vs. Control - Age 32.txt


title: F123 GAM library f123_1NP_GAM180716_A06_1_S41_R1_001


title: F123 GAM library f123_1NP_GAM180716_A11_2_S177_R1_001


title: F123 GAM library f123_1NP_GAM180716_A06_2_S137_R1_001


title: PDS - 5 - age 32

description: PDS - Age 32 vs. Control - Age 32.txt

value: 2 µM PDS


title: PhpC - 1 - age 32

description: PhpC - Age 32 vs. Control - Age 32.txt

data_processing:
All primary analysis is carried out using CLC Genomics Server 22.0.2. The workflow “RNA-Seq Analysis” of CLC Genomics Server with standard parameters is used to map reads to the human genome (hg38).
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 22.0.2 was used for differential expression analysis with default settings. It is an implementation of the ‘Exact Test’ for two-group comparisons developed by Robinson and Smyth, 2008 and incorporated in the EdgeR Bioconductor package Robinson et al., 2010.
For all unsupervised analysis, only miRNAs were considered with at least 10 counts summed over all samples. A variance stabilizing transformation was performed on the raw count matrix using the function vst of the R package DESeq2 version 1.28.1. 500 genes with the highest variance were used for the principal component analysis. The variance was calculated agnostically to the pre-defined groups (blind=TRUE). 35 genes with the highest variance across samples were selected for hierarchical clustering. All primary analysis is carried out using CLC Genomics Server 22.0.2. The workflow “RNA-Seq Analysis” of CLC Genomics Server with standard parameters is used to map reads to the human genome (hg38).
Assembly: hg38
Supplementary files format and content: raw and normalized counts for each sample


title: F123 GAM library f123_1NP_GAM180716_A05_2_S129_R1_001


title: F123 GAM library f123_1NP_GAM180511_H12_1_S96_R1_001


title: PDS - 3 - age 32

description: PDS - Age 32 vs. Control - Age 32.txt


title: F123 GAM library f123_1NP_GAM180716_A04_2_S121_R1_001


title: PDS - 4 - age 32

description: PDS - Age 32 vs. Control - Age 32.txt


title: F123 GAM library f123_1NP_GAM180511_H11_2_S184_R1_001


title: F123 GAM library f123_1NP_GAM180511_H12_2_S192_R1_001


title: PDS - 2 - age 32

description: PDS - Age 32 vs. Control - Age 32.txt


title: F123 GAM library f123_1NP_GAM180716_B06_1_S42_R1_001


title: Control - 4 - age 32

description: PDS - Age 32 vs. Control - Age 32.txt

value: No treatment


title: F123 GAM library f123_1NP_GAM180511_H10_1_S80_R1_001


title: F123 GAM library f123_1NP_GAM180511_H10_2_S176_R1_001


title: PDS - 1 - age 32

description: PDS - Age 32 vs. Control - Age 32.txt


title: Control - 5 - age 32

description: PDS - Age 32 vs. Control - Age 32.txt


title: F123 GAM library f123_1NP_GAM180511_H09_2_S168_R1_001


title: Control - 3 - age 32

description: PDS - Age 32 vs. Control - Age 32.txt


title: Control - 2 - age 32

description: PDS - Age 32 vs. Control - Age 32.txt


title: Control - 1 - age 32

description: PDS - Age 32 vs. Control - Age 32.txt


title: F123 GAM library f123_1NP_GAM180511_H07_2_S152_R1_001


title: F123 GAM library f123_1NP_GAM180511_H04_2_S128_R1_001


title: F123 GAM library f123_1NP_GAM180511_H06_2_S144_R1_001


title: F123 GAM library f123_1NP_GAM180511_H05_2_S136_R1_001


title: SeMC+PBS_rep2

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

country: China

institute: Yangtze University

data_processing:
Data filtering was conducted to obtain clean reads and to remove low quality reads present in the raw reads as recommended by the manufacturer. Hisat2 was used to map clean reads to the reference genome (GRCg7b), which was extracted from the NCBI genome database. The calculated reads count per gene were estimated by Htseq-count and used for comparing the difference in gene expression among samples.
Assembly: GRCg7b
Supplementary files format and content: Reads count

molecule: total RNA

organism: Gallus gallus

growth_protocol: HD11 cells were cultured in RPMI 1640 complete medium (Containing 8% of FBS, 3% of CS and 1% of penicillin-streptomycin), kept at 41°C in 5% CO2, and were passaged every three days at a ratio of 1:3.

extract_protocol:
RNA was prepared using RNAeasy mini kit (Qiagen). 2ug of total RNA was used for the construstion of the sequencing labraries
Sequencing libraries were prepared using the Illumina Truseq RNA sample preparation kit according to the manufacturer’s protocol (Illumina Inc., USA).

treatment_protocol: Approximately 12 hours before challenging, HD11 cells were seeded into 6-well cell plates at a concentration of 2×106 cells per well in RPMI 1640 containing 100 μM SeMC, the concentration of SeMC has been verified to be fit for cell viability. Cells were stimulated with 100 ng/ mL lipopolysaccharide for 6h, washed and further lysed with 1mL Trizol regent.

value: Macrophage-like

value: SeMC+PBS


title: F123 GAM library f123_1NP_GAM180511_H08_2_S160_R1_001


title: F123 GAM library f123_1NP_GAM180511_H11_1_S88_R1_001


title: F123 GAM library f123_1NP_GAM180511_H03_2_S120_R1_001


title: F123 GAM library f123_1NP_GAM180511_H02_2_S112_R1_001


title: SeMC+PBS_rep1


title: SeMC+LPS_rep3

value: SeMC+LPS


title: SeMC+LPS_rep2


title: F123 GAM library f123_1NP_GAM180511_H01_2_S104_R1_001

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM180511_G12_2_S191_R1_001


title: F123 GAM library f123_1NP_GAM180511_G12_1_S95_R1_001


title: SeMC+LPS_rep1


title: F123 GAM library f123_1NP_GAM180511_G11_2_S183_R1_001


title: LPS_rep3

value: LPS


title: LPS_rep2


title: LPS_rep1


title: Control_rep3

value: Control


title: Control_rep2


title: F123 GAM library f123_1NP_GAM180511_G10_1_S79_R1_001


title: F123 GAM library f123_1NP_GAM180511_G10_2_S175_R1_001


title: F123 GAM library f123_1NP_GAM180511_G11_1_S87_R1_001


title: Control_rep1


title: F123 GAM library f123_1NP_GAM180511_G09_2_S167_R1_001


title: SeMC+PBS_rep3


title: Rat 05, liver, clozapine(ChIP)

city: Wollongong

first: Yueqing

last: Su

address: Northfields Avenue

institute: University of Wollongong

description: Library name: Clozapine, ChIP

data_processing:
To ensure the accuracy and reliability of the sequenced data, e quality control (QC) was performed at each step, including sample testing, library preparation, and sequencing.  The raw reads from the Illumina HiSeqTM X TEN also underwent QC to determine their suitability for subsequent analysis. The filtered sequenced reads (raw reads) were cleaned through the following three filtering processes: (1) Removing reads containing adapters, (2) Removing reads with N > 10% (N represents bases that cannot be determined), and (3) Removing reads with low-quality bases (Qscore<= 5) that constitute over 50% of the total bases.
Removing reads containing adapters
Removing reads with N > 10% (N represents bases that cannot be determined)
Removing reads with low-quality bases (Qscore<= 5) that constitute over 50% of the total bases.
Assembly: Rnor_6.0
Supplementary files format and content: bigWig, narrowPeak (expect for input sample)

organism: Rattus norvegicus

source_name: Liver

growth_protocol: All animals were housed individually in temperature-controlled room (220C) with a 24-hour lighting cycle (lights on 07:00-19:00), allowed to free access water and standard laboratory chow diet (containing 3.9kcal/g, 10% fat, 16% protein and 74% carbohydrate) throughout the experiment.

extract_protocol:
According to the manufacturer’s instructions, 40 mg liver tissue was cut into small pieces and cross-linked using 1mL 1% formaldehyde in room temperature for 20 minutes, then was homogenized using Precellys®24 homogenizer (Bertin Technologies, France).
The ChIP DNA was sent to Novogene Co. (Hong Kong) for DNA paired-end library construction and high-throughput sequencing using an Illumina Hiseq2500 50SE sequencer.

treatment_protocol: Thirty-six female Sprague-Dawley rats (200g- 220g) were purchased from the Animal Resource Centre (Perth, WA, Australia).  After one week of environmental adaption, the rats were randomly assigned into three groups: olanzapine (3 mg/kg, b.i.d, orally, Zyprexa, Eli Lilly, Indianapolis, USA), clozapine (20mg/kg, b.i.d, orally, Clozaril, Novartis, Turkey), and vehicle (equivalent sweet cookie dough pellet without drugs) with 12 animals per group.  The antipsychotic drugs were mixed into 300mg sweet cookie powder (30% cornflour, 30.9% sucrose, 15.5% casein, 8.4% minerals, 6.4% fibre, 6.3% gelatine, 1.6% vitamins) and appropriate water.  Each animal was treated orallytwice a day (8:00 am and 8:00 pm, respectively) for nigh weeks, as described previously (Liu et al., 2017).  During the treatment, rats were observed to completely consume drugs pellet.  Since the rats avoided taking the cookie pellet with clozapine after 3 days’ treatment, clozapine was delivered using a 1 ml syringe via the mouth, followed by an equivalent sweet cookie dough pellet without drugs to ensure the same amount of cookie pellets was consumed.

value: Liver

value: Clozapine


title: F123 GAM library f123_1NP_GAM180511_G08_2_S159_R1_001


title: F123 GAM library f123_1NP_GAM180511_G07_2_S151_R1_001


title: F123 GAM library f123_1NP_GAM180511_G06_2_S143_R1_001


title: F123 GAM library f123_1NP_GAM180511_G05_2_S135_R1_001


title: Cortex_YB1_5

city: Moscow

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

description: Library name: KY5

data_processing:
Read trimming (Trimmomatic)
Read alignment (STAR)
Read counting (featureCounts)
Assembly: GRCm39 v.104
Supplementary files format and content: Tab-delimeted file exhibiting number of raw counts of RNA reads spanning on exonic regions of each gene (in ENSEMBL format)

source_name: Cortex

extract_protocol:
RNA was extracted using RNAzol RT (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer’s protocol. The concentration and quality of RNA were determined via a Qubit Fluorometer (Invitrogen) and an Agilent Bioanalyzer 2100, respectively, using an RNA 6000 Nano Kit (Agilent Technologies, Santa-Clara, CA, USA).
RNA with an Integrity Number (RIN) no less than 8 was taken. An Illumina NEB Next Ultra II Directional RNA Library Prep Kit (NEB, Ipswich, MA, USA) was used for the mRNA library preparation

treatment_protocol: Chaperones (4 μg of human recombinant HSP70 and 6.4 μg of recombinant YB-1 proteins) were administrated intranasally in a subchronic manner for 21 days (starting on 14 day after OB), one time per day

value: Cortex

value: NMRI


title: Cortex_YB1_4

description: Library name: KY4


title: F123 GAM library f123_1NP_GAM180511_G04_2_S127_R1_001


title: Cortex_YB1_3

description: Library name: KY3


title: F123 GAM library f123_1NP_GAM180511_G02_2_S111_R1_001


title: F123 GAM library f123_1NP_GAM180511_G03_2_S119_R1_001


title: Cortex_YB1_1

description: Library name: KY1


title: F123 GAM library f123_1NP_GAM180511_G01_2_S103_R1_001


title: Cortex_HSP70_5

description: Library name: KH5

value: HSP70 (4 μg)


title: F123 GAM library f123_1NP_GAM180511_F12_2_S190_R1_001


title: F123 GAM library f123_1NP_GAM180511_F11_1_S86_R1_001


title: Cortex_HSP70_4

description: Library name: KH4


title: Cortex_HSP70_3

description: Library name: KH3


title: F123 GAM library f123_1NP_GAM180511_F12_1_S94_R1_001


title: Cortex_HSP70_1

description: Library name: KH1


title: F123 GAM library f123_1NP_GAM180511_F09_2_S166_R1_001


title: Hippocampus_YB1_5

description: Library name: GY5

source_name: Hippocampus

value: Hippocampus


title: F123 GAM library f123_1NP_GAM180511_F10_1_S78_R1_001


title: F123 GAM library f123_1NP_GAM180511_F10_2_S174_R1_001


title: Cortex_HSP70_2

description: Library name: KH2


title: F123 GAM library f123_1NP_GAM180511_F08_2_S158_R1_001


title: Rat 08, liver, vehicle (ChIP)

description: Library name: Vehicle, ChIP

value: Vehicle


title: F123 GAM library f123_1NP_GAM180511_F07_2_S150_R1_001

value: mouse embryonic stem cells


title: Rat 09, liver，olanzapine(ChIP)

description: Library name: Olanzapine, ChIP

value: olanzapine


title: Hippocampus_YB1_1

description: Library name: GY1


title: Cortex_YB1_2

description: Library name: KY2


title: Hippocampus_YB1_2

description: Library name: GY2


title: F123 GAM library f123_1NP_GAM180511_F06_2_S142_R1_001

value: male


title: F123 GAM library f123_1NP_GAM180511_F05_2_S134_R1_001


title: Hippocampus_HSP70_5

description: Library name: GH5


title: F123 GAM library f123_1NP_GAM180511_F04_2_S126_R1_001


title: Hippocampus_HSP70_4

description: Library name: GH4


title: F123 GAM library f123_1NP_GAM180511_F02_2_S110_R1_001


title: Hippocampus_HSP70_3

description: Library name: GH3


title: F123 GAM library f123_1NP_GAM180511_F01_2_S102_R1_001


title: Hippocampus_HSP70_2

description: Library name: GH2


title: F123 GAM library f123_1NP_GAM180511_E12_1_S93_R1_001


title: zhiliaozu2

city: Shanghai

first: zhen

last: zhu

address: huanhuxisan road 222

institute: shanghai jiao tong university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
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

source_name: kidney

extract_protocol:
kidneys were removed, flash frozen on dry ice. Cell nucleus separation uses a cell nucleus separation kit (Shanghai biotechnology corporation, 52009-10). The Chromium Chip G was loaded with cell suspension, 10X barcode gel beads, and oil in  distinct compartments, creating GEMs using the 10X Genomics Chromium platform. GEM was transferred into the PCR machine for reverse transcription.
RNA libraries were prepared for sequencing using standard Illumina protocols
The cDNA library containing P5 and P7 connectors was constructed by end repair, addition of A, and connection of Read2 sequencing primers.

value: kidney

tag: strain

value: post natal week 22

value: treated with losartan


title: Hippocampus_YB1_4

description: Library name: GY4


title: F123 GAM library f123_1NP_GAM180511_E12_2_S189_R1_001


title: zhiliaozu1


title: F123 GAM library f123_1NP_GAM180511_E10_2_S173_R1_001


title: duizhaozu2

value: untreated


title: F123 GAM library f123_1NP_GAM180511_E10_1_S77_R1_001

value: Hybrid F1 S129/Jae and Cast


title: Hippocampus_YB1_3

description: Library name: GY3


title: CRPtg-db/db mice-3

city: Hong Kong

first: YIFAN

last: WANG

address: 6/F, 3 Sassoon Road, Pokfulam

department: School of Chinese Medicine

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Hisat2 (v2.0.1)
HTSeq (v0.6.1)
DESeq2
Assembly: NLRP3

source_name: Kidney

growth_protocol: Whole kidney sample were applied

extract_protocol:
Total RNA was extracted by Trizol (Invitrogen). Total 20 ug RNA was applied for RNA sequencing
RNA library construction was preparaed by Illumina HiSeq 2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Kidney

value: CRPtg-db/db

value: 32 weeks


title: CRPtg-db/db mice-2


title: F123 GAM library f123_1NP_GAM180511_E09_2_S165_R1_001


title: CRPtg-db/db mice-1


title: F123 GAM library f123_1NP_GAM180511_E08_2_S157_R1_001


title: F123 GAM library f123_1NP_GAM180511_E06_2_S141_R1_001


title: CRPwt-db/db mice-2

value: CRPwt-db/db


title: CRPwt-db/db mice-3


title: F123 GAM library f123_1NP_GAM180511_F03_2_S118_R1_001


title: CRPwt-db/db mice-1


title: F4_HFD_SEMA_T2

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
Raw reads were assessed for quality by FastQC and preprocessed with FASTQ Toolkit v.2.2.5 for adapter trimming and low quality (Q<30) filtering of the reads.
Filtered sequence reads were aligned to the reference Genome assembly version GRCm39 with salmon aligner (v.1.10) using a decoy-aware transcriptome index with k-mers of length 31 and normalizing for local GC content. GENCODE Gene Set version M27 was used for gene annotation.
Transcripts were merged to genes using Bioconductor R (v.4.3.1) package tximport (v1.28.0). To identify differentially expressed genes (DEGs), data were filtered to remove from the analysis the genes having >10 counts for at least 3 samples. Gene-level normalization and differential expression analysis were performed with R package DESeq2 v.1.40.2
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with raw counts for each Sample

source_name: pancreatic neoplastic lesion

extract_protocol:
RNA was isolated from mouse pancreatic neoplastic lesions at T1 (30 days; LFD mice n=3; HFD mice n=4) and T2 from orthotopic PaNIN lesion transplantation (90 days; LFD mice, HFD mice and  SEMA mice; n=4 for each experimental group) by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA according manufacturer’s instruction. Then, RNA integrity was verified by BioAnalyzer 2100 (Agilent) and only RNA samples with a RNA integrity number (RIN) > 7 were processed for cDNA library construction.
Sequencing was performed on rRNA-depleted total RNA (50M PE reads, 7.5Gbp) on an Illumina HiSeq 2000 platform. The resulting raw reads were assessed for quality by FastQC and preprocessed with FASTQ Toolkit v.2.2.5 for adapter trimming and low quality (Q<30) filtering of the reads.

value: pancreatic neoplastic lesion

tag: time

value: M

tag: dietary regimen

value: HFD+SEMA


title: F123 GAM library f123_1NP_GAM180511_E04_2_S125_R1_001


title: F5_HFD_SEMA_T2


title: Hippocampus_HSP70_1

description: Library name: GH1

value: Hippocampus

value: NMRI

value: HSP70 (4 μg)


title: F123 GAM library f123_1NP_GAM180511_E03_2_S117_R1_001

value: mouse embryonic stem cells


title: F123 GAM library f123_1NP_GAM180511_E11_2_S181_R1_001

value: male


title: duizhaozu1

value: kidney

tag: age


title: F123 GAM library f123_1NP_GAM180511_D12_2_S188_R1_001


title: D3_HFD_T2

value: HFD


title: F123 GAM library f123_1NP_GAM180511_E01_2_S101_R1_001


title: F123 GAM library f123_1NP_GAM180511_E02_2_S109_R1_001


title: F123 GAM library f123_1NP_GAM180511_E11_1_S85_R1_001


title: F123 GAM library f123_1NP_GAM180511_D11_1_S84_R1_001


title: D5_HFD_T2


title: D2_HFD_T2


title: D1_HFD_T2


title: C4_HFD_T1


title: C5_HFD_T1


title: F123 GAM library f123_1NP_GAM180511_D11_2_S180_R1_001


title: F123 GAM library f123_1NP_GAM180511_E07_2_S149_R1_001


title: F123 GAM library f123_1NP_GAM180511_D12_1_S92_R1_001


title: C3_HFD_T1


title: F123 GAM library f123_1NP_GAM180511_E05_2_S133_R1_001


title: C1_HFD_T1


title: F123 GAM library f123_1NP_GAM180511_D10_1_S76_R1_001


title: F123 GAM library f123_1NP_GAM180511_D10_2_S172_R1_001


title: F123 GAM library f123_1NP_GAM180511_D09_2_S164_R1_001


title: B5_LFD_T2

value: LFD


title: F123 GAM library f123_1NP_GAM180511_D08_2_S156_R1_001


title: F123 GAM library f123_1NP_GAM180511_D06_2_S140_R1_001


title: B2_LFD_T2


title: B1_LFD_T2


title: B4_LFD_T2


title: F2_HFD_SEMA_T2


title: F123 GAM library f123_1NP_GAM180511_D05_2_S132_R1_001


title: A3_LFD_T1


title: F123 GAM library f123_1NP_GAM180511_D04_2_S124_R1_001


title: A1_LFD_T1


title: A2_LFD_T1


title: F123 GAM library f123_1NP_GAM180511_D03_2_S116_R1_001


title: F123 GAM library f123_1NP_GAM180511_D01_2_S100_R1_001


title: Old_3

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:
Novogene used Illumina HiSeq 2000 (Mus musculus) 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 HISAT2
Quantifications of read counts and FPKM were calculated by the featureCounts function of the subread software.
Assembly: NCBI, Mus_musculus , GCF_000001635.26_GRCm38.p6
Supplementary files format and content: FPKM and raw gene counts for each Sample

source_name: heart tissue

growth_protocol: mice were raised in a stable environment (room temperature, 24 ± 3 °C; room humidity, 55 ± 5%) with a 12-h light/12-h dark cycle, and were fed normal chow.

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 Novogene.

value: 22 months

value: heart tissue


title: F123 GAM library f123_1NP_GAM180511_D02_2_S108_R1_001

value: Hybrid F1 S129/Jae and Cast


title: F123 GAM library f123_1NP_GAM180511_C12_2_S187_R1_001


title: Old_1


title: Old_2


title: Young_3


title: F123 GAM library f123_1NP_GAM180511_C11_2_S179_R1_001


title: Young_2


title: F123 GAM library f123_1NP_GAM180511_C12_1_S91_R1_001


title: F123 GAM library f123_1NP_GAM180511_C11_1_S83_R1_001


title: F123 GAM library f123_1NP_GAM180511_C10_2_S171_R1_001


title: Young_1


title: F123 GAM library f123_1NP_GAM180511_C10_1_S75_R1_001


title: F123 GAM library f123_1NP_GAM180511_C09_2_S163_R1_001


title: resistance exercise mice

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: plasma sample from resistance exercise mice

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: C57BL/6 mice aged 8 weeks were used. The mice were housed in polycarbonate cages with bedding and were maintained under artificial conditions at a constant temperature of 22 ± 1°C with a constant humidity of 55 ± 5% and a 12-hour dark / 12-hour light cycle. They had free access to water and food 24 hour a day. All animals were fasted overnight prior to sacrifice and euthanized under general anesthesia and analgesia at the end of the experimental period. Blood samples were taken from inferior vena cava in mouse 3 hours after each acute exercise and then centrifuged at 3,000 × g for 10 minutes at 4℃ to separate plasma. Then the plasma was centrifuged at 16,000 × g for 10 minutes at 4℃ to remove cell debris, and 100 μl of plasma was collected. For microarray analysis, the samples of three mice from the same group were mixed together to obtain enough plasma. Finally, 300 μl of plasma was obtained from each group.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

value: 8 weeks

value: plasma


title: F123 GAM library f123_1NP_GAM180511_C07_2_S147_R1_001


title: aerobic exercise mice

source_name: plasma sample from aerobic exercise mice


title: F123 GAM library f123_1NP_GAM180511_C08_2_S155_R1_001


title: 21 hours post fertilisation, Azakenpaullone treated, replicate 3

city: Cambridge

first: Elia

last: Benito Gutierrez

address: Downing Street

department: Zoology

country: United Kingdom

institute: University of Cambridge

data_processing:
Raw read quality was assessed using FastQC (version 0.11.9)
Reads were trimmed using fastp (version 0.21.0) to remove adapter contamination and poly-G tails
Transcript expression was quantified with Salmon (version 1.3.0).
Transcript level expression values were imported into R and summarized to gene level using the Bioconductor package tximport
Differential expression analysis between AZA treated and Control groups was carried out using DESeq2(version 1.30.0)
Multiple testing correction was carried out using the Benjamini-Hochberg method
Assembly: The B. lanceolatum transcriptome and genome described in Marlétaz, F. et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 564, 64–70 (2018) were downloaded via the link provided. Additionally, the FASTA files for the mitochondrial B. lanceolatum genome and transcriptome sequences, as described in Nohara, M., Nishida, M. & Nishikawa, T. New complete mitochondrial DNA sequence of the lancelet Branchiostoma lanceolatum (Cephalochordata) and the identity of this species’ sequences. Zoolog Sci 22, 671–674 (2005) were retrieved from NCBI (AB19483). The four references were used to generate a reference index using Salmon (version 1.3.0)
Supplementary files format and content: Tar archive file containing full Salmon output

organism: Branchiostoma lanceolatum

source_name: Whole organism

growth_protocol: After in vitro fertilization, embryos were raised in Petri dishes in filtered artificial salt water (ASW) in an incubator at 21°C.

extract_protocol:
Norgen Total RNA Purification Plus Kit (Catalog n° #48300)
Illumina TruSeq Stranded mRNA kit (#20020595)

treatment_protocol: Fertilized eggs were raised at 21°C. At 4.5 hpf (blastula stage) embryos were transferred into small beakers with 10ml of 10μM Azakenpaullone (AZA) or dimethylsulfoxide (DMSO as a control) in filtered ASW and left to develop at 21°C up to 12 hpf (early neurula stage) or 21 hpf (7 ss stage).

value: Whole organism

value: Azakenpaullone


title: 21 hours post fertilisation, Azakenpaullone treated, replicate 2


title: normal caged mice

source_name: plasma sample from control mice


title: F123 GAM library f123_1NP_GAM180511_C06_2_S139_R1_001


title: F123 GAM library f123_1NP_GAM180511_C05_2_S131_R1_001


title: F123 GAM library f123_1NP_GAM180511_C04_2_S123_R1_001


title: 21 hours post fertilisation, Azakenpaullone treated, replicate 1


title: 21 hours post fertilisation, control, replicate 2

value: DMSO control


title: F123 GAM library f123_1NP_GAM180511_C03_2_S115_R1_001


title: 21 hours post fertilisation, control, replicate 1


title: 22 hours post fertilisation, control, replicate 3


title: F123 GAM library f123_1NP_GAM180511_C01_2_S99_R1_001


title: F123 GAM library f123_1NP_GAM180511_B12_2_S186_R1_001


title: 12 hours post fertilisation, Azakenpaullone treated, replicate 3


title: 12 hours post fertilisation, Azakenpaullone treated, replicate 2


title: 12 hours post fertilisation, Azakenpaullone treated, replicate 1


title: 12 hours post fertilisation, control, replicate 3


title: F123 GAM library f123_1NP_GAM180511_B12_1_S90_R1_001


title: TAC_3

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, Mus_musculus , GCF_000001635.26_GRCm38.p6
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: Wild-type male mice at 2-month of age  were raised in a stable environment (room temperature, 24 ± 3 °C; room humidity, 55 ± 5%) with a 12-h light/12-h dark cycle, and were fed normal chow.

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: mices were randomly separated into sham and TAC groups, with at least 6 mice per group. Transverse aortic constriction (TAC) was performed as previously described with 27G needle. After 4 Weeks, The mice were anaesthetized with inhalational anaesthetic and euthanized by cervical dislocation. Hearts were immediately dissected and stored at -80°C.

value: Transverse aortic constriction (TAC) was performed using 27 neddle for 4 weeks


title: F123 GAM library f123_1NP_GAM180511_B10_1_S74_R1_001


title: F123 GAM library f123_1NP_GAM180511_B11_1_S82_R1_001


title: 12 hours post fertilisation, control, replicate 2


title: TAC_2


title: 12 hours post fertilisation, control, replicate 1


title: F123 GAM library f123_1NP_GAM180511_B08_2_S154_R1_001


title: F123 GAM library f123_1NP_GAM180511_B09_2_S162_R1_001


title: F123 GAM library f123_1NP_GAM180511_B07_2_S146_R1_001


title: TAC_1


title: MCF7 cells, siNSRP1_2, repeat2

city: yangzhou

first: Yu

last: Shiyi

state: Jiangsu

address: hanjiang district jiangyangzhonglu136, Hanjiang district, Jiangyangzhonglu 136

institute: yangzhou university

data_processing:
The sequencing data was filtered with SOAPnuke ( (v1.5.6))
The clean data were mapped to the GRCH38 whole genome using HISAT2 with default parameters.
The SAM files were processed with Samtools to generate BAM files.
The sorted BAM files were processed with featureCounts to calculate counts for each transcripts in GRCH38.
The differentially expressed genes were calculated by Deseq2.
Assembly: GRCH38
Supplementary files format and content: txt files with raw gene counts for every transcripts in each sample

growth_protocol: RPMI1640 medium, supplemented with 10% FBS

extract_protocol:
RNA was extracted from cells using TRIzol reagent (Invitrogen)
DNBSEQ Eukaryotic Strand-specific mRNA library strategy was applied to establish libraries.

value: breast cancer cells

value: NSRP1 knockdown


title: F123 GAM library f123_1NP_GAM180511_C02_2_S107_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


title: Sham_3

value: Sham


title: F123 GAM library f123_1NP_GAM180511_B06_2_S138_R1_001

value: mouse embryonic stem cells


title: F123 GAM library f123_1NP_GAM180511_B05_2_S130_R1_001

value: male


title: F123 GAM library f123_1NP_GAM180511_B04_2_S122_R1_001


title: MCF7 cells, siNSRP1_2, repeat1


title: F123 GAM library f123_1NP_GAM180511_B11_2_S178_R1_001


title: MCF7 cells, siNSRP1_1, repeat2


title: Sham_2


title: F123 GAM library f123_1NP_GAM180511_B02_2_S106_R1_001


title: Sham_1


title: F123 GAM library f123_1NP_GAM180511_B01_2_S98_R1_001


title: CUT&Tag of TOP1cc in shRFC3 cells rep2

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

description: Library name: shRFC3_TOP1cc_2

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: F123 GAM library f123_1NP_GAM180511_A12_1_S89_R1_001

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: MCF7 cells, siNSRP1_1, repeat1


title: F123 GAM library f123_1NP_GAM180511_A12_2_S185_R1_001


title: F123 GAM library f123_1NP_GAM180511_B10_2_S170_R1_001


title: MCF7 cells, siControl, repeat 2

value: WT


title: F123 GAM library f123_1NP_GAM180511_A11_1_S81_R1_001


title: F123 GAM library f123_1NP_GAM180511_A11_2_S177_R1_001


title: CUT&Tag of TOP1cc  in shRFC3 cells rep1

description: Library name: shRFC3_TOP1cc_1


title: F123 GAM library f123_1NP_GAM180511_A10_2_S169_R1_001


title: MCF7 cells, siControl, repeat 1


title: CUT&Tag of TOP1cc in shCtrl cells rep2

description: Library name: shCtrl_TOP1cc_2


title: F123 GAM library f123_1NP_GAM180511_A10_1_S73_R1_001


title: F123 GAM library f123_1NP_GAM180511_A09_2_S161_R1_001


title: F123 GAM library f123_1NP_GAM180511_A08_2_S153_R1_001


title: CUT&Tag of TOP1cc  in shCtrl cells rep1

description: Library name: shCtrl_TOP1cc_1


title: F123 GAM library f123_1NP_GAM180511_B03_2_S114_R1_001


title: CUT&Tag of CyclinT1 in shRFC3 cells rep2

description: Library name: shRFC3_CyclinT1_2


title: Liver, control female humanized-liver mice [Hu_C]

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

institute: Osaka Metropolitan University Graduate School of Medicine

data_processing:
Quality trimming and adapter clipping of the read data were performed using Trimmomatic version 0.38.
Trimmed reads were mapped to the transcript in the human  reference sequence hg38 using Bowtie2 aligner within RSEM.
Read count extraction and normalization were performed using edgeR program.
Assembly: hg38
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

growth_protocol: Female 8-week-old NOG mice expressing HSVtk mutant clone 30 cDNA under the control of mouse transthyretin gene enhancer/promoter (NOG-TKm30 mice) were transplanted with commercially available human hepatocytes (humanized-liver mice).

extract_protocol:
RNeasy Mini Kit was performed according to the manufacturer's instructions.
The sequencing libraries were prepared from 200 ng of total RNA with MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd.) according to the manufacturer's instructions.

treatment_protocol: Female 18-week-old humanized-liver mice were treated with 0 or 0.3% acetoaceto-o-toluidide (AAOT) for 4 weeks.

value: Liver

value: primary cultuer cell

value: female

value: Control

value: 4 weeks


title: F123 GAM library f123_1NP_GAM180511_A06_2_S137_R1_001

city: Berlin

last: Kukalev

address: Hannoversche Str., 28

institute: Max-Delbrueck Center for Molecular Medicine

value: Hybrid F1 S129/Jae and Cast


title: AldhNeg_3

city: MARSEILLE

first: Christophe

last: Ginestier

address: 27 Bd Leï Roure

institute: CRCM

description:
Library name: Sample 24
Column name in raw_counts_all_samples.txt: AldhNeg_3

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

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

value: cell line

value: Colon cancer

value: non-cancer stem cells (ALDHneg)

value: 30h DMSO


title: F123 GAM library f123_1NP_GAM180511_A05_2_S129_R1_001

first: Alexander


title: CUT&Tag of CyclinT1  in shRFC3 cells rep1

description: Library name: shRFC3_CyclinT1_1


title: F123 GAM library f123_1NP_GAM180511_A04_2_S121_R1_001


title: F123 GAM library f123_1NP_GAM180511_A03_2_S113_R1_001


title: CUT&Tag of CyclinT1 in shCtrl cells rep2

description: Library name: shCtrl_CyclinT1_2


title: AldhNeg_1

description:
Library name: Sample 22
Column name in raw_counts_all_samples.txt: AldhNeg_1


title: AldhNeg_2

description:
Library name: Sample 23
Column name in raw_counts_all_samples.txt: AldhNeg_2


title: CTRLNeg_3

description:
Library name: Sample 21
Column name in raw_counts_all_samples.txt: CTRLNeg_3

value: Breast cancer


title: CUT&Tag of CyclinT1  in shCtrl cells rep1

description: Library name: shCtrl_CyclinT1_1


title: CTRLNeg_2

description:
Library name: Sample 20
Column name in raw_counts_all_samples.txt: CTRLNeg_2


title: F123 GAM library f123_1NP_GAM180426_H09_1_S72_R1_001


title: Liver, AAOT treated female humanized-liver mice [Hu_AAOT]

value: AAOT


title: CUT&Tag of CDK9 in shRFC3 cells rep2

description: Library name: shRFC3_CDK9_2


title: CUT&Tag of CDK9  in shRFC3 cells rep1

description: Library name: shRFC3_CDK9_1


title: F123 GAM library f123_1NP_GAM180426_H08_1_S64_R1_001

value: mouse embryonic stem cells


title: CTRLNeg_1

description:
Library name: Sample 19
Column name in raw_counts_all_samples.txt: CTRLNeg_1


title: F123 GAM library f123_1NP_GAM180426_H07_1_S56_R1_001

value: male


title: F123 GAM library f123_1NP_GAM180511_A07_2_S145_R1_001


title: CUT&Tag of CDK9 in shCtrl cells rep2

description: Library name: shCtrl_CDK9_2

value: liver


title: F123 GAM library f123_1NP_GAM180426_G11_1_S87_R1_001


title: AldhPos_3

description:
Library name: Sample 18
Column name in raw_counts_all_samples.txt: AldhPos_3

value: cancer stem cells (ALDHpos)


title: F123 GAM library f123_1NP_GAM180426_G09_1_S71_R1_001


title: CUT&Tag of CDK9  in shCtrl cells rep1

description: Library name: shCtrl_CDK9_1

value: tumor cells


title: AldhPos_2

description:
Library name: Sample 17
Column name in raw_counts_all_samples.txt: AldhPos_2


title: F123 GAM library f123_1NP_GAM180511_A01_2_S97_R1_001


title: F123 GAM library f123_1NP_GAM180426_H12_1_S96_R1_001


title: AldhPos_1

description:
Library name: Sample 16
Column name in raw_counts_all_samples.txt: AldhPos_1


title: F123 GAM library f123_1NP_GAM180426_H11_1_S88_R1_001


title: F123 GAM library f123_1NP_GAM180426_G07_1_S55_R1_001


title: F123 GAM library f123_1NP_GAM180426_F11_1_S86_R1_001


title: CTRLPos_3

description:
Library name: Sample 15
Column name in raw_counts_all_samples.txt: CTRLPos_3


title: CUT&Tag of RFC3  in Late_S cells rep1

description: Library name: Late_S_RFC3_1


title: F123 GAM library f123_1NP_GAM180426_H10_1_S80_R1_001


title: F123 GAM library f123_1NP_GAM180426_F10_1_S78_R1_001


title: CTRLPos_2

description:
Library name: Sample 14
Column name in raw_counts_all_samples.txt: CTRLPos_2


title: F123 GAM library f123_1NP_GAM180426_G08_1_S63_R1_001


title: F123 GAM library f123_1NP_GAM180426_F08_1_S62_R1_001


title: F123 GAM library f123_1NP_GAM180426_F09_1_S70_R1_001


title: CUT&Tag of RFC3  in Late_S cells rep2

description: Library name: Late_S_RFC3_2


title: F123 GAM library f123_1NP_GAM180426_G12_1_S95_R1_001


title: CTRLPos_1

description:
Library name: Sample 13
Column name in raw_counts_all_samples.txt: CTRLPos_1


title: CUT&Tag of RFC3  in Early_S cells rep1

description: Library name: Early_S_RFC3_1


title: F123 GAM library f123_1NP_GAM180426_F07_1_S54_R1_001


title: CUT&Tag of RFC3  in G1/S cells rep2

description: Library name: G1_S_RFC3_2


title: AldhNegNIF_3

description:
Library name: Sample 12
Column name in raw_counts_all_samples.txt: AldhNegNIF_3

value: 30h Nifuroxazide


title: F123 GAM library f123_1NP_GAM180426_E10_1_S77_R1_001


title: CUT&Tag of RFC3  in G1/S cells rep1

description: Library name: G1_S_RFC3_1


title: AldhNegNIF_2

description:
Library name: Sample 11
Column name in raw_counts_all_samples.txt: AldhNegNIF_2


title: F123 GAM library f123_1NP_GAM180426_E08_1_S61_R1_001


title: F123 GAM library f123_1NP_GAM180426_G10_1_S79_R1_001


title: F123 GAM library f123_1NP_GAM180426_D12_1_S92_R1_001


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

description: Library name: Late_S_S5P_2


title: AldhNegNIF_1

description:
Library name: Sample 10
Column name in raw_counts_all_samples.txt: AldhNegNIF_1


title: F123 GAM library f123_1NP_GAM180426_F12_1_S94_R1_001


title: F123 GAM library f123_1NP_GAM180426_D11_1_S84_R1_001


title: NIF_ALDneg_3

description:
Library name: Sample 9
Column name in raw_counts_all_samples.txt: NIF_ALDneg_3


title: CUT&Tag of  RFC3  in Early_S cells rep2

description: Library name: Early_S_RFC3_2


title: F123 GAM library f123_1NP_GAM180426_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: CUT&Tag of RNAPII S5P  in Early_S cells rep2

description: Library name: Early_S_S5P_2


title: F123 GAM library f123_1NP_GAM180426_E09_1_S69_R1_001


title: F123 GAM library f123_1NP_GAM180426_E12_1_S93_R1_001


title: NIF_ALDneg_1

description:
Library name: Sample 7
Column name in raw_counts_all_samples.txt: NIF_ALDneg_1


title: F123 GAM library f123_1NP_GAM180426_D10_1_S76_R1_001


title: F123 GAM library f123_1NP_GAM180426_D07_1_S52_R1_001


title: NIF_ALDneg_2

description:
Library name: Sample 8
Column name in raw_counts_all_samples.txt: NIF_ALDneg_2


title: F123 GAM library f123_1NP_GAM180426_D08_1_S60_R1_001


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

description: Library name: Early_S_S5P_1


title: F123 GAM library f123_1NP_GAM180426_C11_1_S83_R1_001


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

description: Library name: Late_S_S5P_1


title: F123 GAM library f123_1NP_GAM180426_C10_1_S75_R1_001