title: ESR1-Y537S-Palbo_1


title: 644621

status: Public on Nov 12 2024

type: SRA

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

country: USA

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
Data were processed using a previoulsy published method[https://pubmed.ncbi.nlm.nih.gov/24972667/]. In brief, reads were quality controlled using FASTQC. Reads were mapped against hg38 genome using STAR aligner. HT-Seq was utilized to analyzed the aligned reads and generate gene-wise counts using Ensemble version 78 transcriptome. Extracted read data was processed using edgeR software. Timmed means of M-values method was utilized to normalized reads that were provided in the file named 20231208-For-GEO-Raw-Counts.tsv".
Assembly: hg38
Supplementary files format and content: 20231208-For-GEO-Raw-Counts.tsv; tab-delimited; Raw gene-count matrix

molecule: total RNA

organism: Homo sapiens

source_name: heart muscle

extract_protocol:
mRNA was extracted using Trizol and stored in RNAlater.
mRNA library was constructed using Illumina TruSeq Stranded kit following manufacturer's recommendations.
Paired end library strategy was utilized

tag: tissue

value: heart muscle

tag: group

value: HCM


title: ESR1-Y537S-Veh_3

city: Dallas

first: Chang-Ching

last: Lin

state: TX

address: 4554 Glenwick Ln, Apt 2203

department: Harold C. Simmons Comprehensive Cancer Center

institute: UT Southwestern Medical Center

data_processing:
Aligning sequencing reads to the human reference genome GRCh38 using STAR
DESeq2 was used to assess the statistical significance of differentially expressed genes
Assembly: GRCh38
Supplementary files format and content: TSV file include raw counts for each sample (Expression_Matrix_CPM)
Supplementary files format and content: TSV file include differential gene expression (DEG_full_adjP1_fc1)

growth_protocol: MCF7 cells were maintained in DMEM containing 10% FBS and 1x antibiotic-antimycotic.

extract_protocol:
Total RNA was extracted using Promega Maxwell RSC simply RNA extraction kit.
mRNA libraries were prepared using TruSeq Stranded mRNA Library prep kit (Illumina)

treatment_protocol: Cells were treated with vehicle (DMSO) or 200 nM palbociclib alone or in combination with estrogen-deprived media or 1 nM fulvestrant.

tag: cell line

tag: cell type

value: Breast cancer

tag: genotype

value: ESR1 Y537S

tag: treatment

value: DMSO


title: 639649


title: Genomic DNA methylation from 9422492042_R01C01

type: genomic

city: Barcelona

first: Joan

address: Carrer del Doctor Aiguader, 88

country: Spain

institute: Hospital del Mar Research Institute

hyb_protocol: The bisulfite converted DNA was processed and hybridized to the 450K or EPIC BeadChip (Illumina, Inc.), according to the manufacturer's instructions.

scan_protocol: The BeadChip images were scanned on the iScan system and the data was extracted into GenomeStudio software v2011.1, using default analysis settings.

data_processing: Idat files were loaded with Minfi. CpGs with a detection rate lower than 99% (detection p-value > 0.05) or having a beadcount lower than 1% in at least 5% of samples were excluded. Additionally, CpGs at multi-hit or single-nucleotide polymorphism locations (MethylToSNP) were also excluded. Samples having a call-rate lower than 95% or sex mismatch were excluded. DNA methylation was expressed as beta values and we applied preprocessnoob and BMIQ normalizations

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Blood DNA

label_protocol: Bisulfite conversion was performed using 500 ng genomic DNA input using the EZ DNA Methylation Gold Kit (Zymo Research)

extract_protocol: DNA was extracted from whole peripheral blood collected in 10mL EDTA tubes during the first 24h after stroke onset.

value: Blood DNA

tag: Sex

value: male

value: no


title: ESR1-Y537S-Veh_1


title: Sample 2

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes
map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: oviAri3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Ovis aries

source_name: testis

extract_protocol: Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V3 (10x Genomics Inc., Pleasanton, CA, USA) following the manufacture’s introduction.

tag: age

value: Eight months

value: testis


title: 638751


title: ESR1-Y537S-Palbo and fulv_2

value: Palbociclib + fulvestrant


title: Sample 1

description: Control

value: Control


title: Genomic DNA methylation from 9422491083_R06C02

value: yes


title: 649284


title: Genomic DNA methylation from 9422492042_R01C02


title: Genomic DNA methylation from 9422492042_R05C01

value: female


title: 635263


title: ESR1-Y537S-Palbo_3

value: Palbociclib


title: ESR1-WT-Palbo and fulv_2

value: ESR1 WT


title: Genomic DNA methylation from 9422491083_R06C01


title: 634021


title: Whole brain, TNFR1ff, remyelination, rep6

city: Athens

first: Lesley

last: Probert

state: Attiki

address: Vassilisis Sofias 127

department: Immunology

country: Greece

institute: Hellenic Pasteur Institute

data_processing:
Quality Control and pre-processing was conducted using FastQC and Cutadapt.
Alignment of the trimmed reads was conducted in a splice-aware manner using the STAR aligner.
Gene-level quantification was performed using RSEM.
Differential expression analysis was conducted using edgeR’s quasi-likelihood negative binomial generalized log-linear model (FDR <0.05).
Assembly: GRCm39
Supplementary files format and content: Unfiltered gene-level quantification results by RSEM (tab-delimited).

molecule: polyA RNA

organism: Mus musculus

source_name: whole brain

extract_protocol:
Total brain RNA isolation was performed using TRIzol reagent (Thermo Fisher Scientific, T9424) according to the manufacturer’s instructions. RNA purity and quantification were assessed using NanoDrop 2000 spectrophotometer data.
Samples with 381-448 ng of total RNA were processed using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, K01524) for library preparation. The libraries were assessed for molarity and median library size using Bioanalyzer High Sensitivity DNA Analysis (Agilent, 5067-4627).

value: whole brain

value: remyelination


title: Whole brain, TNFR1ff, remyelination, rep5


title: ESR1-WT-Palbo and fulv_1


title: ESR1-WT-Palbo and fulv_3


title: Genomic DNA methylation from 9422491083_R05C01


title: Whole brain, TNFR1ff, remyelination, rep7


title: ESR1-WT-Palbo and E2_3

value: Palbociclib + E2 deprivation


title: ESR1-Y537S-Veh_2

value: Breast cancer


title: 633573

value: heart muscle

value: HCM


title: 639124


title: 633322


title: Genomic DNA methylation from 9422491083_R04C02

value: Blood DNA


title: Whole brain, TNFR1ff, remyelination, rep4


title: Genomic DNA methylation from 9422491083_R04C01


title: ESR1-WT-Palbo and E2_2


title: Whole brain, TNFR1ff, remyelination, rep3


title: Genomic DNA methylation from 9422491083_R03C02


title: 632093


title: ESR1-WT-Palbo and E2_1


title: Whole brain, TNFR1ff, remyelination, rep2


title: 631132


title: Genomic DNA methylation from 9422491083_R03C01


title: ESR1-WT-Palbo_3


title: 631131


title: Whole brain, TNFR1ff, remyelination, rep1


title: Genomic DNA methylation from 9422491083_R02C02

value: male


title: ESR1-WT-Palbo_2


title: Whole brain, TNFR1ff, naive, rep7

value: naïve


title: ESR1-WT-Palbo_1


title: 629740


title: Genomic DNA methylation from 9422491059_R06C01

value: no


title: Whole brain, TNFR1ff, naive, rep6


title: Genomic DNA methylation from 9422491059_R05C02


title: Whole brain, TNFR1ff, naive, rep5


title: 610700


title: Genomic DNA methylation from 9422491059_R04C02


title: ESR1-WT-Veh_2

value: DMSO


title: ESR1-WT-Veh_1


title: Whole brain, TNFR1ff, naive, rep4


title: 588103


title: 587005


title: 370118


title: Whole brain, TNFR1ff, naive, rep2


title: Whole brain, TNFR1ff, naive, rep3


title: 49


title: Genomic DNA methylation from 9422491058_R02C02


title: Whole brain, TNFR1ff, naive, rep1


title: 56


title: Genomic DNA methylation from 9422491058_R05C01


title: Genomic DNA methylation from 9422491058_R02C01


title: Whole brain, mgTNFR1KO, remyelination, rep6


title: 48


title: ESR1-WT-Veh_3


title: Whole brain, mgTNFR1KO, remyelination, rep5


title: Genomic DNA methylation from 9422491058_R01C02


title: 619278


title: 47


title: Whole brain, mgTNFR1KO, remyelination, rep4


title: 46


title: Genomic DNA methylation from 9422491059_R04C01


title: Genomic DNA methylation from 9422491042_R06C02


title: 44


title: mK562_360m_B1_T2

city: Los Angeles

first: Marty

middle: G

last: Yang

state: CA

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

description: K562 cells were treated with 10 uM BrdU for varying timepoints to label newly replicated chromatin, nuclei were isolated and treated with EcoGII for footprinting of protein-DNA contacts, and DNA was purified and prepared into PacBio SMRTbell libraries for sequencing on the PacBio Sequel II platform.

library_source: genomic

data_processing:
Reads are demultiplexed using lima to produce a .bam file for subreads for each sample.
Circular consensus sequences (CCS) were generated for each sample using ccs to produce a corresponding .bam file per sample.
Supplementary files format and content: Processed data is shared in .pickle format.
Library strategy: Replication-Aware Single-molecule Accessibility Mapping (RASAM)

growth_protocol: K562 cells (ATCC) were grown for at least three days in standard media containing RPMI 1640 + L-Glutamine (Hyclone) supplemented with 10% Fetal Bovine Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). mESC E14 cells were grown on 0.2% gelatin and maintained in standard media containing DMEM + Glutamax (ThermoFisher 10566-016), 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 1X Non-Essential Amino Acids (ThermoFisher 11140-50), 1 mM Sodium Pyruvate (ThermoFisher 11360-070), 0.128mM 2-Mercaptoethanol (BioRad 1610710XTU), and 1X Leukemia Inhibitory Factor (purified and gifted by Barbara Panning Lab at UCSF). mESCs were passaged every 1-2 days using TrypLE Express Enzyme (1X) (12605010). Media was changed daily when cells were not passaged. All cell lines were regularly tested negative for mycoplasma contamination. Standard media was added to mESC E14 or K562 cells with a final concentration of 10 uM BrdU (abcam ab142567). Cells were incubated in BrdU-containing media for between 5 minutes and 24 hours. After labeling, mESC E14 plates were rinsed three times with 1x PBS and collected using TrypLE Express Enzyme (1X) (12605010). K562s were collected and spun down (300xg, 5 minutes) immediately after labeling.

extract_protocol:
To the methylation reaction, 2.65 uL 10% SDS and 2.65 uL of 20 mg/mL Proteinase K (Thermo Scientific AM2548) were added and incubated at 65oC for at least 2 hours and up to overnight. To extract the DNA, an equal volume of Phenol-Chloroform was added and mixed vigorously by shaking. The samples were then spun at max speed for 2 min and the aqueous portion was removed. To the aqueous extraction, 0.1x volumes of 3M NaOAc, 1 uL GlycoBlue, and 3x volumes of cold 100% EtOH were added, mixed by inversion and incubated overnight at -20oC or for 2 hours at -80oC. Samples were then spun at max speed for 30 minutes at 4oC, washed with 500 uL 70% EtOH, spun again at max speed for 2 minutes at 4oC. The resulting pellet was air dried and resuspended in 40 uL EB.
Purified DNA from mESCs and K562s was sheared using a Covaris g-tube (520079) in a 5424 rotor at 7,000 RPM for 6 passes for a target size between 6,000 and 8,000 bp. Sheared DNA was used as input for the PacBio HiFi SMRTbell Library Preparation protocol using the SMRTbell Express Template Prep Kit 2.0. Briefly, samples underwent removal of single stranded overhangs, DNA damage repair, end-repair, A-tailing, barcoded SMRTbell adapter ligation, and exonuclease cleanup according to manufacturer’s protocol followed by a 1X AMPure PB bead cleanup. Final sample concentration was measured via Qubit High Sensitivity DNA Assay and library size was measured on an Agilent Bioanalyzer DNA chip. Libraries were sequenced on PacBio Sequel II 8M SMRTcells.

treatment_protocol: Briefly, all nuclei were collected by centrifugation (300xg, 5 min), washed in ice cold 1X PBS, spun again (300xg, 5 min), and resuspended in 1 mL Nuclear Isolation Buffer (20mM HEPES, 10mM KCl, 1mM MgCl2, 0.1% Triton X-100, 20% Glycerol, and 1X Protease Inhibitor (Roche 4693132001)) per 10 million cells by gently pipetting 5x with a wide-bore pipette tip. The suspension was incubated on ice for 5 minutes, and nuclei were pelleted (600xg, 4oC, 5 min), washed with Buffer M (15mM Tris-HCl pH 8.0, 15 mM NaCl, 60mM KCl, 0.5mM Spermidine), and spun once again (600xg, 4oC, 5 min). Nuclei were resuspended in 200 uL of Methylation Reaction Buffer (Buffer M containing 1mM S-adenosylmethionine (SAM; New England BioLabs B9003S)). 10uL high-concentration EcoGII was added per 1e6 nuclei and the nuclei suspension was incubated at 37oC for 30 minutes. An additional 1 uL of 32 mM SAM was supplemented after 15 minutes. Any unmethylated controls were treated similarly with the addition of SAM, but EcoGII was excluded from those reactions.

value: EcoGII treated; 6h BrdU


title: Whole brain, mgTNFR1KO, remyelination, rep3


title: Genomic DNA methylation from 9422491059_R01C02


title: Genomic DNA methylation from 9422491042_R06C01


title: Genomic DNA methylation from 9422491058_R06C02


title: 43


title: Genomic DNA methylation from 9422491042_R05C02


title: Genomic DNA methylation from 9422491042_R04C02


title: Whole brain, mgTNFR1KO, remyelination, rep2


title: Whole brain, mgTNFR1KO, remyelination, rep7


title: 41


title: Whole brain, mgTNFR1KO, remyelination, rep1


title: 39


title: Whole brain, TNFR1ff, demyelination, rep6

value: demyelination


title: 38


title: Whole brain, TNFR1ff, demyelination, rep7


title: Genomic DNA methylation from 9422491042_R04C01


title: Genomic DNA methylation from 9422491042_R03C02

value: yes


title: Genomic DNA methylation from 9422491042_R03C01


title: Whole brain, TNFR1ff, demyelination, rep5


title: Whole brain, TNFR1ff, demyelination, rep4


title: 37


title: 36


title: Genomic DNA methylation from 9422491019_R06C01

value: female


title: Whole brain, TNFR1ff, demyelination, rep3


title: 33


title: 30


title: Whole brain, TNFR1ff, demyelination, rep2


title: Genomic DNA methylation from 9422491019_R03C02


title: Genomic DNA methylation from 9422491019_R02C02


title: Whole brain, TNFR1ff, demyelination, rep1


title: 28


title: WT E. coli MG1655 at OD600=0.33 in Lennox LB

city: Boston

first: Jeffrey

last: Moffitt

state: MA

address: 200 Longwood Ave

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

data_processing:
We built a salmon (v1.8.0) index  with default parameters on the synthetic operon transcriptome (synthetic_operons.fasta) used for the construction of the MERFISH probe libraries.
We applied the salmon quant function (parameters -l A) to measure transcripts per million (TPM), mapped counts, and effective transcript lengths.
Assembly: We constructed the synthetic operon transcriptome from the EcoCyc 27.1 Escherichia coli K-12 substr. MG1655 reference genome and transcription unit annotations.
Supplementary files format and content: tab delimited file containing the name, length, effective length, TPM, and number of reads for each transcript

organism: Escherichia coli str. K-12 substr. MG1655

source_name: WT

growth_protocol: LB sample: we inoculated a single colony of Escherichia coli (E. coli) K-12 MG1655 (#7740, CGSG, Yale Coli Genetic Stock Center) in ~5 mL Lennox Broth (LB) media (Thermo Scientific Chemicals, AC612725000). We grew the inoculate aerobically at 37°C with shaking (220 rpm) overnight. The next day, we diluted the overnight culture 1:100 in 30 mL fresh LB and grew the cells aerobically at 37°C with shaking. We drew a 4.5 ml culture sample at an optical density (OD600) of 0.33 for bulk RNA sequencing. Diauxic samples: We grew an overnight culture of E. coli MG1655 in 5 mL MOPS minimal media (Teknova, M2106) supplemented with 0.2% w/v glucose (Teknova, G0520) in a closed 50 mL tube at 37°C with shaking (220 rpm). The following day, we pelleted the overnight culture, resuspended it in 2 mL fresh MOPS minimal media, and measured the resulting OD600. We then diluted the resuspended sample in glucose-xylose diauxic growth medium (0.025% w/v glucose and 0.025% w/v xylose [Sigma-Aldrich, X3877] in MOPS minimal media) to a final OD600 of 0.004. We incubated the culture aerobically at 37°C with shaking, periodically drawing small volumes (~2 mL) and measuring their OD600 to monitor growth. We drew 4.5 mL of culture at OD600=0.18 (glucose growth phase) and OD600=0.47 (xylose phase) for sequencing.

extract_protocol:
We followed the RNAsnap protocol to extract the RNA of all the samples. In short, we mixed 4.5 mL of culture with 0.5 mL of ice cold RNAsnap stop solution (10% pH 6.6 phenol [Fisher BioReagents, BP1750I-100] in ethanol), pelleted the sample for 8 minutes at 600 g, and discarded the supernatant. We resuspended the pellet in 0.5 mL RNAsnap extraction buffer (9.5 mL 100% formamide [Invitrogen, AM9342], 360 µL 0.5 M EDTA [Invitrogen, AM9849], 25 µL 10% Sodium Dodecyl Sulfate [Invitrogen, AM9823], and 100 µL 100% 2-Mercaptoethanol [Fisher Chemical, O3446I-100]), heated the sample at 95°C for 1 minute, and stored it at -20°C before RNA purification. To purify the RNA, we used the Zymo Direct-zol RNA miniprep plus kit, first mixing 100 µL RNA in RNAsnap extraction buffer with 200 µL of Zymo RNA binding buffer, and then following manufacturer's instructions.
Library preparation and sequencing for the diauxic media samples were performed by the Harvard Medical School Biopolymers Core using the Ribo-Erase kit for rRNA depletion, the KAPA HyperPrep kit for library preparation, and 150-bp paired-end sequencing on an Illumina NextSeq500. Library preparation and sequencing for the LB sample were performed by Azenta using TURBO DNase for DNA depletion, the QIAGEN FastSelect rRNA HMR Kit for rRNA depletion, and the NEBNext Ultra II RNA Library Preparation Kit for Illumina for library preparation according to the manufacturer’s recommendations. The library was 150 bp paired-end sequenced on an Illumina HiSeqNovaSeq 6000.

value: WT


title: 27


title: Genomic DNA methylation from 9422491019_R01C02


title: Genomic DNA methylation from 9422491019_R01C01


title: 20


title: OE_CD51_ICD_3

city: shenzhen

first: bing

last: zeng

state: Guangdong

address: huaqiang road

institute: Shenzhen Aier Eye Hospital

data_processing:
Raw reads were filtered using fastp57 (version 0.13.1, default parameters) and mapped to hg38, using HISAT263 (version 2.1.0) with parameters “--rna-strandness RF –dta”. Read counts per gene were calculated in strand-specific manner using featureCounts64. Differential expression analysis was performed using DESeq265, and genes with mean TPM ≥ 1, FDR < 0.05, and fold change > 1.5 were identified as significantly differentially expressed.
Assembly: hg38
Supplementary files format and content: gene coutns, rpkm

source_name: Retinal pigment epithelial cells

extract_protocol:
RNA was extracted from cells using TRNzol Universal Reagent (TIANGEN, cat. no. DP424) or Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054) by following the manufacturers’ protocols
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacture's protocols

value: Retinal pigment epithelial cells

value: CD51_ICD over expression


title: OE_CD51_ICD_2


title: OE_CD51_ICD_1


title: Genomic DNA methylation from 9422491012_R05C02


title: 14


title: p14_control_saline

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

data_processing:
Sequencing outputs were demultiplexed using mkfastq option of Cell Ranger
Fastq files were aligned to Mus musculus RGCm38 (mm10) reference using count option of Cell Ranger
All main processing steps were performed with Monocle3 v0.2.3.0 (R package) (https://cole-trapnell-lab.github.io/monocle3/docs/starting/).25  All processing was performed for each sample. The thresholds for minimum read count per cell were 500 reads. The thresholds for minimum gene number per cell were 39 (RA group) and 56 (O2+NS group, O2+HMGB1 group). All mitochondrial and sex chromosomal genes were removed from analysis. All samples were assembled into one monocle cds object. Cells were visualized using principal component analysis (PCA) and UMAP in order to informatively display genetic distance and relatedness between the cell population. Gene expression data was normalized and PC was calculated by preprocess_cds() function. Top 15 PCs were used for UMAP embedding. Clustering was defined using a resolution of 10-5. On the other hand, Subclustering was defined using a resolution of 10-4. Cell types were annotated by SingleR (v1.4.0) R package. Default settings were used for the parameters excecpt for number of dimension = 15 in preprocess_Cds().
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text file containing raw or normalized gene counts

source_name: Lung

growth_protocol: Time-dated pregnant C57BL/6 mice were obtained from CLEA Japan (Tokyo, Japan) at E14-E15 days of gestation.  All mice were housed in individual cages with 12-h light-dark cycles. Standard rodent diet and water was provided ad libitum.

extract_protocol:
The lungs obtained from two pups in each group were analyzed for scRNA-seq. The lungs obtained for scRNA-seq  were rinsed with Dulbecco’s PBS (Nacalai, kyoto, Japan).followed by ice-cold 10%FBS-RPMI (Nacalai, kyoto, Japan). Then the tissues were minced in a Petri dish on ice.  Lung pieces were transferred to a GentleMACS C tubes (Miltenyi Biotec, Bergisch Gladbach, Germany), using an enzyme mix containing dispase (50 caseinolytic units/ml, Corning, New York, USA), collagenase (2mg/ml, Wako, Osaka, Japan), elastase (1mg/ml, Worthington Biochemical Corporation, New Jersey, USA), and DNase (10unit/ml, Takara, Shiga, Japan). Samples were homogenized using a GentleMACS Dissociators (Miltenyi Biotec, Bergisch Gladbach, Germany), filtered using a 70 μm strainer, and pelleted by centrifugation at 300 g for 5 min, resuspended in ice-cold RBC lysis buffer (Bio Legend; 420301) for red blood cell lysis, and then counted.
Live cells were sorted and collected using FACS AriaⅢ (Becton Dickinson, New Jersey, USA). The cells were washed twice with PBS with 0.1% BSA and suspended to 1x106cells/ml. Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1(10x Genomics, California, USA) was used to prepare the library according to the manufacturer's protocol. Cells were loaded to a target of 6,000 cells.  The sequencing libraries were sequenced on the NextSeq 2000 platform using NextSeq 2000 P3 Reagents (100 Cycles) (illumine, California, USA). The read length was set to 28 (read 1) + 8 (i7) + 0 (i5) + 91 (read 2) bases.

treatment_protocol: Within 12 hours of birth, Newborn pups from six different litters were pooled and randomly assigned into three groups, room air treated with normal saline as vehicle (RA+NS group), hyperoxia exposure treated with normal saline as vehicle (O2+NS group), and hyperoxia exposure treated with HMGB1 peptide (O2+HMGB1 group). Each litter consisted of 7 pups to control for the effect of litter size on nutrition and growth. The pups in hyperoxia exposure group were continuously reared in an atmosphere containing 90% O2 from Postnatal Day 1 to 14 with a brief interruption for animal care (less than 10min/day).

tag: strain background

tag: genotype/varaition

value: control

value: Lung

value: postnatal day 14

value: saline


title: NC_3


title: Genomic DNA methylation from 9422491012_R05C01


title: 13

value: heart muscle

value: HCM


title: NC_2


title: 10


title: p14_BPD_saline

value: bronchopulmonary dysplasia (BPD) model


title: p14_BPD_HMGB1

value: HMGB1 peptide


title: Genomic DNA methylation from 9422491019_R05C01

value: Blood DNA

value: male

value: no


title: Genomic DNA methylation from 9422491012_R03C01


title: K562, dMLL3/4, H3, ChIP, rep2

city: Busan

first: Jin

last: Kang

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Department of Molecular Biology

country: South Korea

institute: Pusan National University

description: K dMLL H3_R2

data_processing:
ChIP-seq raw reads were filtered to remove input read ends with poor quality values (quality score 20) and then aligned to hg19 Canonical genome using Bowtie2. Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files. Bigwig files generated from BAM files using BamCompare to normalize data against histone H3. Bigwig files for ChIP-seq data without spike-in control were generated using BamCoverage and BigwigCompare to normalize data against H3.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: K562 cells were cultured in RPMI mediun containing 10% FBS, 20 mM HEPES, 10% P/S, and 2 mM L-Glutamine.

extract_protocol:
Nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein A agarose beads.
ChIP DNA (10 ng for H3K4ac, H3K4me1, H3K4me2, and H3 and and 5 ng for H3K4me3) was processed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with NEBNext adaptors. Adaptor-ligated DNA was selected at 175 bp size using NEBNext sample purification bead and amplified using the adaptor primers. The fragments are purified using NEBNext sample purification beads.

treatment_protocol: Lentiviral vectors containing a sgRNA and a Cas9 gene were transduced into K562 cells. sgRNA for eGFP was used as experimental control.

value: erythroleukemia cells

tag: chip antibody

value: H3 (Abcam, ab1791)


title: Genomic DNA methylation from 9422491019_R02C01

value: female


title: NC_1

value: WT


title: Control Spleen R4

city: San Diego

first: sanjeeb

middle: k

last: sahu

address: Lajolla

institute: AltosLabs

description: Single end

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9 for mouse or hg19 for Human samples
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Tissue

extract_protocol:
Tissues were removed, flash frozen on liquid N2, and RNA was harvested using Trizol reagent.
NEBNext Ultra II Directional RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: strain

value: Spleen

value: post natal day 135

value: LAKI -/-


title: Genomic DNA methylation from 9422491012_R01C02


title: K562, dMLL3/4, H3K4me3,ChIP, rep2

description: K dMLL H3K4me3_R2

value: H3K4me3 (Millipore, 04-745)


title: 22


title: Control Liver R4

description: Single end

value: Liver


title: tuSz[1] rep3

city: Normal

first: Nathan

middle: T

last: Mortimer

state: IL

address: Campus Box 4120

department: School of Biological Sciences

institute: Illinois State University

data_processing:
Quality control to trim reads below a quality score threshold of 30 using FastQC (version 0.11.8)
Reads were mapped to the D. melanogaster reference genome dm6 using HISAT2 (version 2.1.0)
Read counts for each gene in the reference genome annotation were generated using featureCounts (version 1.6.3)
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited txt files with read counts for each gene for each sample. Generated by featureCounts

organism: Drosophila melanogaster

source_name: whole larvae

growth_protocol: Larvae were grown on standard Drosophila medium at 28°C

extract_protocol:
In total, three biological replicates were prepared with each biological replicate consisting of 20 pooled larvae. RNA was extracted from whole larvae using Trizol (Thermo Fisher Scientific) followed by QIAGEN RNeasy Micro clean-up (QIAGEN; both according to manufacturer’s instructions). RNA concentration was measured using a nanodrop and the integrity was verified using agarose gel electrophoresis.
Libraries with 250-300bp insert size were prepared for sequencing using standard Illumina protocols

value: whole larvae

tag: growth temperature


title: Genomic DNA methylation from 9422491012_R02C01


title: Genomic DNA methylation from 9422491012_R01C01


title: tuSz[1] rep1


title: Control Skin R4

description: Single end

value: Skin


title: Genomic DNA methylation from 9403904130_R06C02


title: tuSz[1] rep2


title: hop[Tum] rep3

value: hop[Tum]


title: K562, dMLL3/4, H3K4me1, ChIP, rep2

description: K dMLL H3K4me1_R2

value: H3K4me1 (Abcam, ab8895)


title: K562, dMLL3/4, H3K4ac, ChIP, rep2

description: K dMLL H3K4ac_R2

value: H3K4ac (Active Motif, 39481)


title: Control Bone marrow R3

description: Single end

value: Bone marrow


title: Genomic DNA methylation from 9403904130_R05C02

value: Blood DNA

value: male


title: hop[Tum] rep2


title: K562, dp300, H3, ChIP, rep2

description: K dp300 H3_R2

value: erythroleukemia cells


title: Control Bone marrow R2

description: Single end


title: Genomic DNA methylation from 9403904130_R04C01

value: yes


title: K562, dp300, H3K4me3,ChIP, rep2

description: K dp300 H3K4me3_R2


title: hop[Tum] rep1


title: w[1118] rep3


title: Genomic DNA methylation from 9403904130_R03C02

value: no


title: Genomic DNA methylation from 9403904130_R03C01

value: female


title: OSK Bone marrow R3

description: Single end


title: K562, dp300, H3K4me2,ChIP, rep2

description: K dp300 H3K4me2_R2

value: H3K4me2 (Millipore, 07-030)


title: w[1118] rep2


title: OSK Bone marrow R2

description: Single end

value: post natal day 135


title: K562, dp300, H3K4me1, ChIP, rep2

description: K dp300 H3K4me1_R2


title: w[1118] rep1


title: Genomic DNA methylation from 9403904130_R02C02


title: K562, dp300, H3K4ac, ChIP, rep2

description: K dp300 H3K4ac_R2


title: Genomic DNA methylation from 9403904130_R02C01


title: Genomic DNA methylation from 9403904115_R06C02


title: highfat_Week3_rep3

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
FastQC files were pre-processed by TrimGalore
and mapped against the mm10 mouse genome assembly using bowtie2, keeping only unique alignments
FeatureCount was used for counting reads mapped to miRBase v21 miRNAs
Assembly: mm10
Supplementary files format and content: gzipped csv file with read counts for mirBase v21 miRNAs.

source_name: subcutaneous adipose tissue

extract_protocol:
Total RNA was purified using TRizol (Invitrogen) according to the manufacturer’s instructions and 1 μg of total RNA was used for library preparation
NEBNextâ Multiplex Small RNA library Prep Set (Illuminaâ kit E7300) was used for small RNA library preparation following the manufacturer’s instructions.

value: subcutaneous adipose tissue

tag: diet

value: highfat

tag: timepoint


title: K562, Con, H3, ChIP, rep2

description: K Con H3_R2

value: Control

value: H3 (Abcam, ab1791)


title: highfat_Week3_rep2


title: Control Skin R3

description: Single end

value: Skin

value: LAKI -/-


title: Control Bone marrow R1

description: Single end


title: highfat_Week3_rep1


title: Genomic DNA methylation from 9403904115_R05C02


title: Genomic DNA methylation from 9403904115_R05C01


title: Control Spleen R2

description: Single end

value: Spleen


title: K562, Con, H3K4me1, ChIP, rep2

description: K Con H3K4me1_R2

value: H3K4me1 (Abcam, ab8895)


title: Control Liver R3

description: Single end

value: Liver


title: highfat_Week1_rep4


title: Genomic DNA methylation from 9403904115_R04C02

value: Blood DNA


title: K562, Con, H3K4me2,ChIP, rep2

description: K Con H3K4me2_R2


title: OSK Bone marrow R1

description: Single end

value: Bone marrow


title: K562, Con, H3K4ac, ChIP, rep2

description: K Con H3K4ac_R2

value: erythroleukemia cells

value: H3K4ac (Active Motif, 39481)


title: K562, dMLL3/4, H3_Sp, ChIP, rep1

description: K dMLL H3_R1_Sp


title: highfat_Week1_rep2


title: Control Spleen R3

description: Single end


title: highfat_Week3_rep4


title: Genomic DNA methylation from 9403904115_R03C02

value: male

value: no


title: Control Spleen R1

description: Single end


title: K562, dMLL3/4, H3K4me3_Sp,ChIP, rep1

description: K dMLL H3K4me3_R1_Sp

value: H3K4me3 (Millipore, 04-745)


title: Control Liver R2

description: Single end

value: post natal day 135


title: highfat_Week1_rep1

value: subcutaneous adipose tissue


title: Genomic DNA methylation from 9403904115_R03C01

value: female


title: highfat_Day1_rep4

value: highfat


title: Genomic DNA methylation from 9403904115_R02C02

value: yes


title: K562, Con, H3K4me3,ChIP, rep2

description: K Con H3K4me3_R2

value: Control


title: highfat_Day1_rep3


title: K562, dMLL3/4, H3K4me1_Sp,ChIP, rep1

description: K dMLL H3K4me1_R1_Sp


title: Genomic DNA methylation from 9403904115_R04C01


title: highfat_Day1_rep2


title: OSK Spleen R5

description: Single end

value: LAKI -/-


title: Control Skin R1

description: Single end

value: Skin


title: K562, dMLL3/4, H3K4me2_Sp,ChIP, rep1

description: K dMLL H3K4me2_R1_Sp

value: H3K4me2 (Millipore, 07-030)


title: Genomic DNA methylation from 9403904115_R02C01


title: OSK Skin R5

description: Single end


title: K562, dp300, H3_Sp, ChIP, rep1

description: K dp300 H3_R1_Sp

value: H3 (Abcam, ab1791)


title: K562, dMLL3/4, H3K4ac_Sp, ChIP, rep1

description: K dMLL H3K4ac_R1_Sp


title: Genomic DNA methylation from 9403904115_R01C02

value: Blood DNA


title: Control Liver R1

description: Single end

value: Liver


title: Genomic DNA methylation from 9403904094_R05C01


title: OSK Liver R5

description: Single end


title: highfat_Day1_rep1


title: control_Week3_rep4

value: control


title: OSK Spleen R4

description: Single end

value: Spleen


title: K562, dp300, H3K4me2_Sp,ChIP, rep1

description: K dp300 H3K4me2_R1_Sp

value: erythroleukemia cells


title: control_Week3_rep3


title: OSK Skin R4

description: Single end


title: Genomic DNA methylation from 9403904094_R03C01

value: no


title: K562, dp300, H3K4me1_Sp,ChIP, rep1

description: K dp300 H3K4me1_R1_Sp

value: H3K4me1 (Abcam, ab8895)


title: control_Week3_rep2


title: Genomic DNA methylation from 9403904094_R01C01

value: male


title: OSK Liver R4

description: Single end

value: post natal day 135


title: K562, dp300, H3K4ac_Sp, ChIP, rep1

description: K dp300 H3K4ac_R1_Sp

value: H3K4ac (Active Motif, 39481)


title: control_Week3_rep1

value: subcutaneous adipose tissue


title: Genomic DNA methylation from 9403904087_R06C02

value: female


title: Genomic DNA methylation from 9403904087_R06C01

value: yes


title: control_Week1_rep4


title: OSK Skin R3

description: Single end

value: LAKI -/-


title: control_Week1_rep3


title: Genomic DNA methylation from 9403904087_R04C01


title: K562, Con, H3K4me3_Sp,ChIP, rep1

description: K Con H3K4me3_R1_Sp

value: Control

value: H3K4me3 (Millipore, 04-745)


title: K562, Con, H3K4me2_Sp,ChIP, rep1

description: K Con H3K4me2_R1_Sp

value: H3K4me2 (Millipore, 07-030)


title: control_Week1_rep2


title: Genomic DNA methylation from 9403904094_R04C01

value: Blood DNA


title: K562, dp300, H3K4me3_Sp,ChIP, rep1

description: K dp300 H3K4me3_R1_Sp


title: OSK Liver R3

description: Single end

value: Liver


title: OSK Spleen R2

description: Single end


title: Genomic DNA methylation from 9403904087_R03C02


title: control_Week1_rep1

value: control


title: K562, Con, H3K4me1_Sp,ChIP, rep1

description: K Con H3K4me1_R1_Sp


title: Genomic DNA methylation from 9403904087_R02C02


title: K562, Con, H3K4ac_Sp, ChIP, rep1

description: K Con H3K4ac_R1_Sp


title: Genomic DNA methylation from 9403904087_R01C02


title: OSK Liver R2

description: Single end


title: OSK Spleen R3

description: Single end

value: Spleen


title: control_Day1_rep3


title: K562, Con, H3_Sp, ChIP, rep1

description: K Con H3_R1_Sp

value: erythroleukemia cells

value: H3 (Abcam, ab1791)


title: Genomic DNA methylation from 9403904087_R01C01

value: no


title: OSK Spleen R1

description: Single end


title: neuron CRISPRi-hypr-seq screen rep2, XC164

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

data_processing:
Filter reads with fastp
Extract cell barcodes with UMI-Tools
Map reads to custom index with Bowtie
Convert to bam files with SAMTools
Generate count tables with UMI-Tools
Assembly: hg38
Supplementary files format and content: count tables (cells by probes or cells by genes) for all cells that passed QC
Library strategy: HyPR-Seq

extract_protocol:
The papain-dissociated single neurons were fixed in 4% formaldehyde solution followed with permeabilization in 70% ice-cold ethanol. The probes were pooled to a concentration of 20nM/probe and incubated with the neurons at 37°C overnight. The neurons were then harvested for the hybridization with B1H1 hairpin (Molecular Instruments) followed by ligation with readout oligo at 37°C for one hour, respectively. After ligation, cells were filtered through a 20-μm pluriStrainer (cat. #43-0020-01). The single-cell suspension was checked and counted for the emulsion droplet generation.
We made a 20-μL reaction with 1x EvaGreen Supermix (Bio-Rad cat. #186-4033), 500 nM indexing primer, 20,000 barcoded beads (Chemgenes) and 2,000 cells. The emulsions were generated by using QX200 Digital Droplet Generator (Bio-Rad 1864002) based on the instruction. Following the generation of droplets, the emulsions were UV-treated (6.5 J/cm2 at 365 nm) for 5 mins, with a distance from the UV bulb for 5 cm. Then the droplet PCR amplification was performed with the following program: 94°C for 30 sec for denaturation; 94°C for 5 sec, 64°C for 30 sec, and 72°C for 30 sec for 25 cycles; 72°C for 5 mins final extension. All PCR cycling steps were carried out with 50% ramp rate (2°C/min). To release the library cDNAs, all PCR products were combined, and the emulsions were broken and cleaned with introduction of 1/2 volume of 97% 1H,1H,2H,2H-Perfluoro-1-octanol (Sigma-Aldrich 370533). Then by vortexing and centrifugation, the top aqueous phase was collected and cleaned with 1.8x SPRI beads. Next, the purified libraries were ready for the deep sequencing step with customer primers.

value: excitatory neurons


title: control_Day1_rep2


title: Genomic DNA methylation from 9403904085_R06C02

value: male


title: OSK Skin R1

description: Single end

value: Skin

value: post natal day 135


title: neuron CRISPRi-hypr-seq screen rep2, XC163


title: OSK Liver R1

description: Single end


title: neuron CRISPRi-hypr-seq screen rep1, XC151


title: Genomic DNA methylation from 9403904085_R05C02

value: female


title: control_Day1_rep1

value: subcutaneous adipose tissue


title: Genomic DNA methylation from 9403904085_R06C01


title: OSK Skin R2

description: Single end

value: LAKI -/-


title: Genomic DNA methylation from 9403904085_R05C01


title: control_Day1_rep4


title: Adipocyte control 3

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

data_processing:
reads were first aligned using STAR v.2.4.2a with parameters ‘--outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.07 --outFilterMultimapNmax 10’ to the reference mouse genome (mm10/genocode,vM8). Gene expression was measured using RESM/1.2.22 with expression values normalized into FPKM.
Genome_build: vM8
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample, a separate file contains read quality data

source_name: Inguinal Fat

extract_protocol:
RNA from freshly isolated ear cartilage lipochondrocytes or adipocytes was harvested using a modified TRIzol reagent protocol. For stages P8, P10, and P13, ear cartilage from Wnt1-Cre2;TdTomato mice was dissected and digested in 1% Collagenase II in DMEM to generate a single cell suspension. Cells were then collected via FACS using a TdTomato High gate, followed by RNA extraction. For stages P21 and P33, ear cartilage was dissected carefully avoiding adipocytes and digested as described to generate a single cell suspension. Cells were centrifuged at 400g for 5 minutes and the buoyant fraction was collected for RNA extraction. For adipocyte controls, inguinal fat was minced, digested, and centrifuged as described. The buoyant fraction was collected for RNA extraction. For RNA extraction, all tissues were homogenized in TRIzol reagent using a tissue homogenizer after isolation. After homogenization, any lipid layers were avoided by collecting the other fraction of the homogenate.Chloroform was added to the homogenates, followed by vortexing and centrifugation according to protocol. The aqueous phase was collected and ran through a QIAGEN RNeasy micro kit, and the manufacturer's instructions were followed. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: postnatal day

value: Inguinal Fat

tag: background strain


title: neuron CRISPRi-hypr-seq screen rep2, XC167


title: Adipocyte control 2

tag: tissue


title: QDG2

city: Fuzhou

first: Daxin

last: Chen

address: Qiuyang Rd, MinhouShangjie, Fuzhou, Fujian 350122, China.

institute: fujian univerity of TCM

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:： Check the sample for contamination and, if there is pollution, remove it If the reads contains a joint sequence, the joint sequence is cut off first a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window; Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed; if the truncated read length is less than 50 bp, the entire read is removed Remove unmatched reads Q30，Q20 explanation： Q30 indicates that the sequencing error rate of the base is 0.1%. Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: renal tissue

extract_protocol:
The kidney were dissected and renal tissues were stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with Trizol (Tiangen, Beijing, China). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: renal tissue

value: Hypertension+QDG


title: Genomic DNA methylation from 9403904085_R04C02

value: Blood DNA


title: neuron CRISPRi-hypr-seq screen rep1, XC123


title: Adipocyte control 1


title: QDG3


title: QDG1


title: Postnatal day 33 Lipochondrocyte 3

source_name: Ear cartilage plate

value: Ear cartilage plate


title: Genomic DNA methylation from 9403904085_R03C02


title: human neurons, differentiated, WTC11, 2-week, H3K4me3, rep2 (PLAC-seq)

description:
Merged-Human_on-hg38.fastp.5k.2.sig3Dinteractions.bedpe
consensus-humanAnchors_from-merged-Chimp+Human-peaks.sorted.lifted-to-human.bed

data_processing:
Samples were processed using Arima MAPS v2.0 pipeline using 2Mbp binning range, 5kbp bin size, X chromosome processing, pospoisson model, and 1kbp length cutoff
Anchor peaks were generated by calling peaks with default MACS2 settings “--broad --nolambda --broad-cutoff 0.3” from 20 million short BAM reads extracted from each replicate and merged.
Peaks were cross lifted to each genome and combined to generate a consensus peakset for each genome
Peaks were then used to rerun the maps pipline serving as the anchorset.
Samples were then merged and normalized by usable reads/FRiPs determined calculated from anchor peak bins multiplied by "LR Frips er Peak Bin" to call final interaction loops.
Assembly: hg38
Supplementary files format and content: bedpe files
Library strategy: PLAC-Seq

extract_protocol:
2% PFA crosslinked cells comprising 15 μg of genomic DNA were used per PLAC-seq reaction, which corresponds to 4~5 M human or chimpanzee neurons according to estimation. Then the crosslinked chromatin was digested using a restriction enzyme (RE) cocktail followed by the fill-in step of the 5’-overhangs with a biotinylated nucleotide. Next, the spatially proximal digested ends of DNA were ligated while capturing the genomic structure. The proximally-ligated chromatin is then fragmented by sonicator (Covaris S220), immunoprecipitated with anti-H3K4me3 antibody (Millipore 04-745) conjugated Dynabeads (M-280 sheep anti-rabbit IgG, invitrogen #11203D), and purified to yield fragmented proximally-ligated DNA.
PLAC-seq was performed according to the protocol from Arima-HiC+ Kit (Arima Genomics, #P/N A101020).

value: H3K4me3 (Millipore, #04-745)


title: M3

value: Hypertension


title: human neurons, differentiated, WTC11, 2-week, H3K4me3, rep1 (PLAC-seq)


title: Postnatal day 33Lipochondrocyte 2


title: neuron CRISPRi-hypr-seq screen rep1, XC125


title: M2


title: Postnatal day 33 Lipochondrocyte 1


title: Postnatal day 21 Lipochondrocyte 3


title: M1


title: Genomic DNA methylation from 9403904085_R01C01


title: Genomic DNA methylation from 9403904067_R06C02


title: WT3

value: Normal


title: human neurons, differentiated, WTC11, 2-week, rep2 (ATAC-seq)

description: raw_hg38_2percent-idr.conservative_peak.narrowPeak.gz

data_processing:
All libaries were processed using the ENCODE ATAC-seq pipeline (v1.10.0) using default settings and idr cutoff at 2%
Briefly, reads were mapped to bowtie2, duplicates removed by picard and peaks were called by MACS2
Assembly: hg38, pantro5
Supplementary files format and content: bigwig, idr conserivative at 2%

growth_protocol: A well-characterized human iPSC line with a wildtype genetic background (WTC11) and a 2nd human iPSC F12468 iPSC line with the Ngn2 transgene were used for human cell culture. For chimpanzee cell culture, the iPS cell lines (C3649 and C3624), a gift from Yoav Gilad’s Lab, were used. iPSC lines were maintained on Matrigel-coated (Corning, 354277) plates with fresh mTeSR medium (StemCell Technologies, 5850) every two days. Both human and chimpanzee iPSCs were passaged using Accutase (STEMCELL Technologies, 07922) and mTeSR medium containing 10uM Rock inhibitor Y-27632 (STEMCELL Technologies, 72302). Human embryonic kidney (HEK) 293T cells were cultured in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) supplemented with 10% fetal bovine serum (CPS Serum, FBS-500). HEK 293T cells were passaged with trypsin-EDTA (Gibco, 25200072). All cells were grown at 37°C with 5% CO2. Culture medium was routinely assessed for mycoplasma contamination with the MycoAlert Mycoplasma Detection Kit (LONZA, LT07-218).

extract_protocol:
Generally, live cells were washed once with ice-cold 1xPBS containing protease inhibitor then resuspended in ice-cold nuclei extraction buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA630, and 1× protease inhibitor) for 5 min. Next, counted 50,000 cells per reaction and exchanged into 50 μL 1× buffer TD, and added 2.5 μL TDE1 enzyme for 30 min at 37 °C with rotation for transposition. The fully transposed DNA was purified with Qiagen MinElute spin columns (Qiagen#28006), PCR amplified, and AMPure XP beads size-selected for fragments between 300 and 1,000 bp. Libraries were subjected to paired-end 150 bp sequencing on the Novaseq 6000.
ATAC-seq was performed by using the Nextera DNA Library Prep Kit (Illumina FC-121-1030).

treatment_protocol: Human and chimp excitatory neurons were generated by integration of the AAVS1 safe harbor locus of human iPSCs (i3N iPSCs). Based on the similarity (99%) of conserved sequence of AAVS1 between human and chimpanzee genome, the same iNgn2 cassette used in human iPSCs was knocked in chimpanzee AAVS1 safe harbor locus. The iPSCs were dissociated and seeded in Matrigel coated plate in N2 medium containing BDNF (PeproTech, #450-02), NT-3 (PeproTech, #450-03), mouse laminin (Lifetechnology, #23017-015), Doxycycline (Sigma, #D9891) and Rock Inhibitor (STEMCELL Technologies, 72302), and changed medium for the following two days without Rock Inhibitor. After three days in N2 medium, the pre-differentiated cells were dissociated and seeded in a Poly-L-Ornithine coated plate in Maturation medium containing those above factors except Rock Inhibitor. For the following differentiation procedures, half medium change was applied for the cells every 7 days.

value: WT

value: differentiation

tag: time

value: 2 week


title: Genomic DNA methylation from 9403904067_R06C01

value: male

value: no


title: Postnatal day 21 Lipochondrocyte 2


title: Postnatal day 21 Lipochondrocyte 1


title: human neurons, differentiated, WTC11, 2-week, rep1 (ATAC-seq)

tag: cell line

value: excitatory neurons


title: WT2


title: Genomic DNA methylation from 9403904067_R05C02

value: female


title: Postnatal day 13 Lipochondrocyte 3


title: MDA-MB-468 cells, Glyceollin I 24 hours, Biological replicate 2

city: Ariake, Koto-ku, Tokyo

first: Tatsuro

last: Yamamoto

department: Division of Cancer Biology

institute: The Cancer Institute of JFCR

data_processing:
Alignment to the hg38 human reference genome was performed using STAR v2.6.0b
Mapped reads were counted using featureCounts v2.0.0
Differential gene-expression analysis and normalized of reads counts were performed by DESeq2 v1.24.0
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw reads count
Supplementary files format and content: tab-delimited text files include normalized reads counts using Deseq2
Supplementary files format and content: tab-delimited text files include differential gene expression analysis data using Deseq2

source_name: Breast; Mammary gland

growth_protocol:
MCF7 and MDA-MB-468 cells were cultured in RPMI 1640 supplemented with 10% FBS.
To establish MCF7-LTED cells, MCF7 cells were grown in phenol red-free RPMI 1640 containing 4% dextran-coated charcoal-stripped FBS for 2–4 months.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen)
RNA-seq library was prepared by Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: Cells were treated with 10 µM Glyceollin I, and harvested in 6, 12 and 24 hours after treatment.

value: Breast; Mammary gland

tag: cell type

value: epithelial cell

tag: disease

value: Adenocarcinoma

value: Glyceollin I

value: 24 hours


title: WT1

value: renal tissue

tag: treatment


title: Genomic DNA methylation from 9403904067_R04C02

data_processing: Idat files were loaded with Minfi. CpGs with a detection rate lower than 99% (detection p-value > 0.05) or having a beadcount lower than 1% in at least 5% of samples were excluded. Additionally, CpGs at multi-hit or single-nucleotide polymorphism locations (MethylToSNP) were also excluded. Samples having a call-rate lower than 95% or sex mismatch were excluded. DNA methylation was expressed as beta values and we applied preprocessnoob and BMIQ normalizations

extract_protocol: DNA was extracted from whole peripheral blood collected in 10mL EDTA tubes during the first 24h after stroke onset.

value: Blood DNA

tag: Sex


title: human neurons, differentiated, WTC11, 2-week, rep2 (RNA-seq)

data_processing:
Raw paired-end fastq RNA-seq libraries were trimmed to 51bp using FastP v0.20.1
FastP filtered reads were mapped to hg38 using STAR 2.7.9a with ENCODE recommended parameters
Gene expression levels (TPM and expected_counts) were calculated using RSEM rsem-calculate-expression (v1.3.1)  with gencode.v38.chr_patch_hapl_scaff.annotation.gtf as annotation
Assembly: hg38
Supplementary files format and content: tab-delimited .genes.result files

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

tag: genotype


title: Genomic DNA methylation from 9403904085_R01C02


title: WT E. coli MG1655 at OD600=0.47 (xylose phase) in glucose-xylose diauxic media


title: Postnatal day 13 Lipochondrocyte 2

value: Ear cartilage plate


title: Genomic DNA methylation from 9403904067_R04C01


title: MDA-MB-468 cells, Glyceollin I 12 hours, Biological replicate 2

value: 12 hours


title: Genomic DNA methylation from 9403904067_R03C01

value: yes


title: Genomic DNA methylation from 9403904067_R02C02


title: Postnatal day 10 Lipochondrocyte 3


title: Hs_Chondro-Pellet_CultureD45_Replicate5

data_processing:
Reads were first aligned using STAR v.2.4.2a with parameters ‘--outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.07 --outFilterMultimapNmax 10’ and mapped to GRCh38. Gene expression levels were quantified using RSEM v.1.2.25 with expression values normalized into Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files contain TPM and FPKM values

growth_protocol: See PMCID: PMC6685424

extract_protocol:
RNA was extracted using an Rneasy micro kit.
Libraries were prepared using a TruSeq RNA Library Prep Kit v2 according to manufacturer's instructions.

treatment_protocol: See PMCID: PMC6685424

value: Human embryonic stem cell

value: Chondrogenic media, 45 days


title: Hs_Chondro-Pellet_CultureD45_Replicate4


title: K562, dMLL3/4, H3K4me2,ChIP, rep2

description: K dMLL H3K4me2_R2

value: erythroleukemia cells

value: H3K4me2 (Millipore, 07-030)


title: human neurons, differentiated, WTC11, 2-week, rep1 (RNA-seq)

value: WT

value: differentiation

value: 2 week


title: MDA-MB-468 cells, Glyceollin I 6 hours, Biological replicate 2

value: Breast; Mammary gland

value: 6 hours


title: Genomic DNA methylation from 9403904067_R02C01

value: male

value: no


title: Postnatal day 10 Lipochondrocyte 2


title: Hs_Chondro-Pellet_CultureD45_Replicate3


title: Genomic DNA methylation from 9403904067_R01C02

value: female


title: MDA-MB-468 cells, Glyceollin I 6 hours, Biological replicate 1

value: epithelial cell

value: Adenocarcinoma

value: Glyceollin I


title: MDA-MB-468 cells, Glyceollin I 24 hours, Biological replicate 1

value: 24 hours


title: Hs_Chondro-Pellet_CultureD45_Replicate2


title: Genomic DNA methylation from 9403904067_R01C01

value: Blood DNA

value: yes


title: MDA-MB-468 cells, control, Biological replicate 2

value: no treatment


title: WT E. coli MG1655 at OD600=0.18 (glucose phase) in glucose-xylose diauxic media


title: Postnatal day 13 Lipochondrocyte 1

value: Ear cartilage plate


title: MDA-MB-468 cells, control, Biological replicate 1


title: Postnatal day 8 Lipochondrocyte 2


title: Postnatal day 8 Lipochondrocyte 3


title: Hs_Chondro-Pellet_CultureD45_Replicate1

value: Human embryonic stem cell

value: Chondrogenic media, 30 days


title: Genomic DNA methylation from 9403904043_R04C01


title: Hs_Chondro-Pellet_CultureD30_Replicate5


title: MDA-MB-468 cells, Glyceollin I 12 hours, Biological replicate 1

value: WT

value: 12 hours


title: MCF7-LTED cells, Glyceollin I 24 hours, Biological replicate 2

value: Breast; Mammary gland

value: MCF7 cells after 3 to 8 months of estrogen deprivation


title: Postnatal day 8 Lipochondrocyte  1


title: Genomic DNA methylation from 9403904043_R03C01

value: male


title: Hs_Chondro-Pellet_CultureD30_Replicate4


title: MCF7-LTED cells, Glyceollin I 24 hours, Biological replicate 1


title: Genomic DNA methylation from 9403904043_R02C02

value: no


title: Postnatal day 10 Lipochondrocyte 1


title: MCF7-LTED cells, Glyceollin I 12 hours, Biological replicate 2


title: Hs_Chondro-Pellet_CultureD30_Replicate3


title: Individual 3, stimulated

city: Montreal

first: Christopher

middle: E.

last: Rudd

state: Quebec

address: 5345 Boulevard de l'Assomption

department: Département of Médecine

country: Canada

institute: Université de Montréal

data_processing:
The NGS data were analyzed using MiXCR.
TCR repertoire analysis was performed using R and Python.
The diversity of TCR repertoires was evaluated by the Gini, Gini-Simpson and D50 diversity coefficients.
The graphs of TCR alpha chain and beta chain were drawn with packages dplyr and tidyr in the environment of R (4.4.1).
Assembly: MiXCR reference library
Supplementary files format and content: Comma-seperated values file including V and D hits scores.

source_name: Peripheral blood

growth_protocol: PBMCs were cultured in RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 100U/ml penicillin at 37C.

extract_protocol:
RNA was isolated with Qiagen miRNeasy Mini Kit (Cat. 217004). 200 ng of RNA (each sample) were used for library preparation.
RNA library for TCR profilling was prepared with SMARTer Human TCR a/b Profiling Kit from Takara Bio following manufacturer's protocol.

treatment_protocol: For samples of the P3 stimulation group, PBMC were incubated with the peptide on day 2 for 6 days.

value: Peripheral blood

value: CD8 T-cell


title: Genomic DNA methylation from 9403904043_R02C01

value: female


title: Individual 3, resting


title: MCF7-LTED cells, Glyceollin I 12 hours, Biological replicate 1

value: epithelial cell

value: Adenocarcinoma

value: Glyceollin I


title: Individual 2, stimulated


title: Hs_Chondro-Pellet_CultureD30_Replicate2


title: Genomic DNA methylation from 9403904043_R01C02

value: Blood DNA


title: Genomic DNA methylation from 9403904043_R01C01


title: Individual 2, resting


title: Genomic DNA methylation from 9403904041_R06C02


title: Hs_Chondro-Pellet_CultureD30_Replicate1


title: MCF7-LTED cells, Glyceollin I 6 hours, Biological replicate 1

value: 6 hours


title: MCF7-LTED cells, Glyceollin I 6 hours, Biological replicate 2


title: Individual 1, stimulated


title: MCF7-LTED cells, control, Biological replicate 2

value: no treatment


title: Hs_Chondro-Pellet_CultureD21_Replicate3

value: Human embryonic stem cell

value: Chondrogenic media, 21 days


title: Hs_Chondro-Pellet_CultureD21_Replicate4


title: Genomic DNA methylation from 9403904041_R06C01


title: Control Skin R2

description: Single end

value: Skin

tag: age

value: post natal day 135

value: LAKI -/-


title: MCF7-LTED cells, control, Biological replicate 1

value: Breast; Mammary gland

value: MCF7 cells after 3 to 8 months of estrogen deprivation


title: highfat_Week1_rep3

value: subcutaneous adipose tissue

value: highfat


title: Genomic DNA methylation from 9403904041_R05C02

value: yes


title: Hs_Chondro-Pellet_CultureD21_Replicate2


title: MCF7 cells, Glyceollin I 24 hours, Biological replicate 2

value: WT

value: 24 hours


title: Genomic DNA methylation from 9403904041_R02C02

value: female


title: MCF7 cells, Glyceollin I 12 hours, Biological replicate 2

value: epithelial cell

value: Adenocarcinoma

value: Glyceollin I

value: 12 hours


title: 661W with choline

type: RNA

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

institute: The University of Tokyo

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit and hybridized with a Whole Mouse Genome Microarray (4x44K, Agilent Technologies). Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: The slides were scanned  immediately after washing on SureScan Microarray Scanner (Agilent Technologies) using one color scan setting for 4x44k array slides (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was obtained using the Agilent Feature Extraction software (v12.1.1.1) with set to default for all parameters.

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: The mouse photoreceptor cell line 661W  was cultured in DMEM /F12 (Sigma-Aldrich) with penicillin streptomycin (100 units/ml) and 10% (v/v) fetal bovine serum (FBS, ThermoFischer-Gibco) in a 5% CO2 incubator at 37°C.

extract_protocol: Total RNA was extracted from cells and purified, and the quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 661W was cultured in choline-deficinent or choline-sufficient (8.98 g/L) DMEM/f12 for 3 days.

value: with choline


title: Genomic DNA methylation from 9403904025_R06C02

city: Barcelona

first: Joan

institute: Hospital del Mar Research Institute

value: Blood DNA

value: male

value: no


title: Genomic DNA methylation from 9403904025_R05C02


title: Individual 1, resting

value: Peripheral blood

value: CD8 T-cell


title: ARPE19_PNPLA6 (overexpression)

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit and hybridized with a Whole Human Genome Microarray (4x44K, Agilent Technologies). Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

growth_protocol: ARPE-19 (CRL-2302, ATCC) was cultured in DMEM /F12 (Sigma-Aldrich) with penicillin streptomycin (100 units/ml) and 10% (v/v) fetal bovine serum in a 5% CO2 incubator at 37°C.

treatment_protocol: A target-specific Silencer Select siRNA (Thermo Fischer Scientific) for PNPLA6 and a Silencer® Select Negative Control No. 1 siRNA (Thermo Fischer Scientific), or mammalian expression vector with PNPLA6 and mock vector were transfected with Lipofectamine 3000 reagent (Thermo Fischer Scientific), respectively. Each cell was collected 72 hours after transfection.

value: PNPLA6 overexpression


title: Genomic DNA methylation from 9403904025_R05C01


title: MCF7 cells, Glyceollin I 6 hours, Biological replicate 2

value: Breast; Mammary gland

value: 6 hours


title: 661W without choline

value: without choline


title: Lpar1-/- cocultured 3T3 24 h

data_processing:
Data was obtained using the Agilent Feature Extraction software (v12.1.1.1) with set to default for all parameters.
The microarray data were analyzed using GeneSpring GX software (v14.9; Agilent Technologies). Normalized signal intensity (Shift to 75 percentile).

source_name: Lpar1-/- cocultured 3T3 24 h

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: Preparation of BMMCs: Mouse BM cells were cultured in DMEM (Nissui) supplemented with 0.2% (w/v) sodium bicarbonate, 100 units/ml penicillin, 100 µg/ml streptomycin, 292 µg/ml L-glutamine, 1 x nonessential amino acids solution, 10% (v/v) FBS (Biosera), and 10 ng/ml recombinant mouse IL-3, which was obtained by the baculovirus expression system. After 4-6 weeks of culture, >97% of the cells were identified as c-Kit+FcεRIα+ MCs by flow cytometry.; Generation of CRISPR/Cas9-based Lpar1-deficient Swiss 3T3 fibroblasts: A single guide RNA (sgRNA) sequence targeting a region adjacent to exon 3 of Lpar1, which is located upstream of the first transmembrane region on the Lpar1 locus, was cloned into an expression vector. The expression vector of sgRNA and Cas9 was transfected into Swiss 3T3 cells (Japanese Collection of Research Bioresources). Then, 24 h after transfection, the cells were subjected to single-cell cloning and the Lpar1 gene was sequenced.

treatment_protocol: The fibroblast-directed maturation of immature BMMCs toward CTMC-like cells was described previously Ogasawara et al. J Immunol 158, 393-404, 1997. Briefly, BMMCs were seeded onto the monolayer of Swiss 3T3 and cocultured for 24 h in the presence of 100 ng/ml mouse SCF (Peprotech). The cells after coculture were trypsinized with TrypLE Select (Thermo Fischer Scientific Gibco) and reseeded in culture dishes, and adherent fibroblasts and nonadherent MCs were collected, or pure fibroblasts were isolated using mouse CD117 MicroBead kit and autoMACS Pro Separator (both from Miltenyi Biotec).

value: Swiss 3T3 fibroblasts

value: Lpar1-/- cocultured 3T3 24 h


title: Genomic DNA methylation from 9403904025_R04C02

value: female


title: MCF7 cells, Glyceollin I 12 hours, Biological replicate 1

value: epithelial cell

value: WT


title: MCF7 cells, Glyceollin I 6 hours, Biological replicate 1

value: Adenocarcinoma

value: Glyceollin I


title: Lpar1+/+ cocultured 3T3 24 h

source_name: Lpar1+/+ cocultured 3T3 24 h

value: Lpar1+/+ cocultured 3T3 24 h


title: Genomic DNA methylation from 9403904025_R04C01

value: Blood DNA


title: MCF7 cells, control, Biological replicate 2

value: no treatment


title: Genomic DNA methylation from 9403904041_R04C02

value: male

value: yes


title: Hs_Chondro-Pellet_CultureD21_Replicate1

value: Human embryonic stem cell

value: Chondrogenic media, 21 days


title: MCF7 cells, control, Biological replicate 1

value: Breast; Mammary gland


title: MCF7 cells, Glyceollin I 24 hours, Biological replicate 1

value: 24 hours


title: Genomic DNA methylation from 9403904025_R03C01

value: no


title: ARPE19_Control siRNA

value: Control knockdown


title: Lpar1-/- cocultured 3T3 0 h

source_name: Lpar1-/- cocultured 3T3 0 h

value: Swiss 3T3 fibroblasts

value: Lpar1-/- cocultured 3T3 0 h


title: EBV(-) B cell line, biological rep1

city: Stanford

first: Jiaying

last: Toh

address: 1201 Welch Road

institute: Stanford University

description: Gene expression data from B cell line from EBV(-) diffuse large B cell lymphoma

hyb_protocol: Samples were hybridised to Clariom™ S Assays, human (Affymetrix/Applied Biosystems™) using the GeneChip™ Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 (Affymetrix).

data_processing: Background reduction and quantile normalization were first carried out on CEL files using the Signal Space Transformation-Robust Multi-array Average (SST-RMA) method from Transcriptome Analysis Software v4.0 (Applied Biosystems). The SST-RMA method includes GC Correction Version 4 (GC4) background reduction and SST intensity normalization.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All cell lines were cultured in RPMI-1640 (Cytiva) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS; Corning) and 1% (v/v) Glutamax (Gibco) at 37°C with 5% CO2.

extract_protocol: Cells were harvested from healthy cell cultures in the log-phase of growth, washed in ice-cold phosphate-buffered saline, and immediately stored at -80°C for later use. Total RNA was isolated from cell pellets using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in the supplied RNase-free water. Total RNA was checked for quality and integrity using a BioAnalyzer (Agilent).


title: Genomic DNA methylation from 9403904025_R02C02

address: Carrer del Doctor Aiguader, 88

source_name: Blood DNA


title: RNA Polymerase II C&R native

city: Baltimore

first: Patricia

middle: J

last: Gearhart

state: Maryland

address: 251 Bayview Blvd, Rm 06009C

department: Laboratory of Molecular Biology and Immunology

institute: NIH/NIA

description: No fixation

data_processing:
Demultiplexing using bcl2convert
Adapter trimming using trimgalore
Alignment using bowtie2
Duplicate marking and removal using SAMtools
Peak calling using MACS2
IDR analysis using idr
Assembly: GRCm39 (mm39)
Supplementary files format and content: BED files containing all mapped and QC'd reads are provided
Supplementary files format and content: Bedgraph files containing peak data are provided for non-IgG samples (IgG used as control for peak calling within experiments)
Library strategy: CUT&RUN

source_name: Splenic

growth_protocol: Primary B cells purified from mouse spleens were stimulated in RPMI 1640 supplemented with 10% FBS, 1% GlutaMAX, 1% Pen/Strep, 50 micromolar 2-me. Cells were cultured at 37C 5% CO2 for 48 hours

extract_protocol:
Cells were fixed with 0.1% formaldehyde for 1 minute and quenched with glycine. Nuclei were isolated and used for CUT&RUN modified for primary B cells
EpiCypher Library Prep Kit

value: Splenic

value: Follicular B cells

tag: antibody

value: RNA Polymerase II

value: 48 hour stim w anti-CD40 and IL-4


title: IgG C&R native

description: No fixation

value: IgG


title: Genomic DNA methylation from 9403904025_R01C02

value: Blood DNA


title: ARPE19_Mock

value: Mock overexpression


title: ARPE19_PNPLA6 siRNA (knockdown)

value: PNPLA6 knockdown


title: H3K4me3 C&R native

description: No fixation


title: EBV(-) B cell line, biological rep2

source_name: B cell line from EBV(-) diffuse large B cell lymphoma


title: Genomic DNA methylation from 9403904025_R01C01

value: male


title: EBV(+) B cell line, biological rep5

description: Gene expression data from spontaneous lymphoblastoid B cell line derived from patient with EBV(+) B cell PTLD, DLBCL morphology

source_name: Spontaneous lymphoblastoid cell line from EBV(+) B cell PTLD


title: Lpar1+/+ cocultured 3T3 0 h

source_name: Lpar1+/+ cocultured 3T3 0 h

value: Lpar1+/+ cocultured 3T3 0 h


title: CTCF.PBM14451.HK

status: Public on Nov 11 2024

type: protein

city: Toronto

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street, Room 1350

department: Terrence Donnelly Centre for Cellular and Biomolecular Research

institute: University of Toronto

hyb_protocol: We used 150 ng of plasmid DNA in a 15 μL in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37°C, 12.5 μL of the mix was added to 137.5 μL of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per mL BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Alexa 647-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mM zinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 uM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing:
We provide several scores for each 8-mer in each experiment. VALUE - median kmer intensity; Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots.  Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.
Median intensity for the 8mer sequence

label: Alexa 647

molecule: protein

source_name: CTCF.PBM14451.HK PBM, HK design

label_protocol: We used Alexa 647-labeled anti-GST antibody to detect the GST-tagged DNA binding proteins.

extract_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned into pTH6838, a modified T7-driven GST expression vector. We used 150 ng of plasmid DNA in a 15 μL in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate to produce the proteins.

tag: design

value: HK


title: NFKB1.PBM14452.HK

source_name: NFKB1.PBM14452.HK PBM, HK design


title: NR4A2.PBM14360.HK

source_name: NR4A2.PBM14360.HK PBM, HK design


title: WT BMMCs cocultured with Lpar1-/- Swiss 3T3 fibroblasts

treatment_protocol: The fibroblast-directed maturation of immature BMMCs toward CTMC-like cells was described previously Ogasawara et al. J Immunol 158, 393-404, 1997. Briefly, BMMCs were seeded onto the monolayer of Swiss 3T3 and cocultured for 4 days in the presence of 100 ng/ml mouse SCF (Peprotech), with medium change at 2-day intervals. The cells after coculture were trypsinized with TrypLE Select (Thermo Fischer Scientific Gibco) and reseeded in culture dishes, and adherent fibroblasts and nonadherent MCs were collected, or pure MCs were isolated using mouse CD117 MicroBead kit and autoMACS Pro Separator (both from Miltenyi Biotec).

value: BMMCs


title: SOX5.PBM14450.HK

source_name: SOX5.PBM14450.HK PBM, HK design


title: JUN.PBM14357.HK

source_name: JUN.PBM14357.HK PBM, HK design


title: GCM1.PBM14359.HK

source_name: GCM1.PBM14359.HK PBM, HK design


title: YY1.PBM14358.HK

source_name: YY1.PBM14358.HK PBM, HK design


title: Pla2g3+/+, BMMCs cocultured with WT Swiss 3T3 fibroblasts

source_name: Pla2g3+/+ BMMCs cocultured with WT Swiss 3T3 fibroblasts


title: Pla2g3-/-, BMMCs

source_name: Pla2g3-/- BMMCs

value: Pla2g3-/- BMMCs


title: PAX7.PBM14356.HK

source_name: PAX7.PBM14356.HK PBM, HK design


title: Pla2g3+/+, BMMCs

source_name: Pla2g3+/+ BMMCs

value: Pla2g3+/+ BMMCs


title: Pla2g3-/-, BMMCs cocultured with WT Swiss 3T3 fibroblasts

source_name: Pla2g3-/- BMMCs cocultured with WT Swiss 3T3 fibroblasts


title: EBV(+) B cell line, biological rep4

value: Spontaneous lymphoblastoid cell line from EBV(+) B cell PTLD


title: EBV(+) B cell line, biological rep2


title: EBV(+) B cell line, biological rep1


title: GABPA.PBM14352.HK

source_name: GABPA.PBM14352.HK PBM, HK design


title: RARA.PBM14354.HK

source_name: RARA.PBM14354.HK PBM, HK design


title: FLI1.PBM14351.HK

source_name: FLI1.PBM14351.HK PBM, HK design


title: LEF1.PBM14349.HK

source_name: LEF1.PBM14349.HK PBM, HK design


title: RORB.PBM14353.HK

source_name: RORB.PBM14353.HK PBM, HK design


title: EBV(+) B cell line, biological rep3

source_name: Spontaneous lymphoblastoid cell line from EBV(+) B cell PTLD


title: LHX6.PBM14348.HK

source_name: LHX6.PBM14348.HK PBM, HK design


title: FOSL2.PBM14347.HK

source_name: FOSL2.PBM14347.HK PBM, HK design


title: ZSCAN4.PBM14320.HK

source_name: ZSCAN4.PBM14320.HK PBM, HK design


title: POU5F1.PBM14346.HK

source_name: POU5F1.PBM14346.HK PBM, HK design


title: RXRA.PBM14321.HK

source_name: RXRA.PBM14321.HK PBM, HK design


title: JUNB.PBM14345.HK

source_name: JUNB.PBM14345.HK PBM, HK design


title: MYF6.PBM14377.HK

source_name: MYF6.PBM14377.HK PBM, HK design


title: SOX15.PBM14319.HK

source_name: SOX15.PBM14319.HK PBM, HK design


title: SOX2.PBM14378.HK

source_name: SOX2.PBM14378.HK PBM, HK design


title: VDR.PBM14350.HK

source_name: VDR.PBM14350.HK PBM, HK design


title: SRY.PBM14318.HK

source_name: SRY.PBM14318.HK PBM, HK design


title: MAX.PBM14317.HK

source_name: MAX.PBM14317.HK PBM, HK design


title: NFKB1.PBM14436.ME

source_name: NFKB1.PBM14436.ME PBM, ME design

value: ME


title: WT BMMCs cocultured with Lpar1+/+ Swiss 3T3 fibroblasts

value: Swiss 3T3 fibroblasts


title: YY1.PBM14342.ME

source_name: YY1.PBM14342.ME PBM, ME design


title: NR4A2.PBM14344.ME

source_name: NR4A2.PBM14344.ME PBM, ME design


title: GCM1.PBM14343.ME

source_name: GCM1.PBM14343.ME PBM, ME design


title: SOX5.PBM14434.ME

source_name: SOX5.PBM14434.ME PBM, ME design


title: CTCF.PBM14435.ME

source_name: CTCF.PBM14435.ME PBM, ME design


title: NR1H4.PBM14355.HK

source_name: NR1H4.PBM14355.HK PBM, HK design


title: JUN.PBM14341.ME

source_name: JUN.PBM14341.ME PBM, ME design


title: PAX7.PBM14340.ME

source_name: PAX7.PBM14340.ME PBM, ME design


title: RARA.PBM14338.ME

source_name: RARA.PBM14338.ME PBM, ME design


title: NR1H4.PBM14339.ME

source_name: NR1H4.PBM14339.ME PBM, ME design


title: GABPA.PBM14336.ME

source_name: GABPA.PBM14336.ME PBM, ME design


title: RORB.PBM14337.ME

source_name: RORB.PBM14337.ME PBM, ME design


title: FLI1.PBM14335.ME

source_name: FLI1.PBM14335.ME PBM, ME design


title: VDR.PBM14334.ME

source_name: VDR.PBM14334.ME PBM, ME design


title: LEF1.PBM14333.ME

source_name: LEF1.PBM14333.ME PBM, ME design


title: FOSL2.PBM14331.ME

source_name: FOSL2.PBM14331.ME PBM, ME design


title: LHX6.PBM14332.ME

source_name: LHX6.PBM14332.ME PBM, ME design


title: ZSCAN4.PBM14304.ME

source_name: ZSCAN4.PBM14304.ME PBM, ME design


title: RXRA.PBM14305.ME

source_name: RXRA.PBM14305.ME PBM, ME design


title: POU5F1.PBM14330.ME

source_name: POU5F1.PBM14330.ME PBM, ME design


title: JUNB.PBM14329.ME

source_name: JUNB.PBM14329.ME PBM, ME design


title: MYF6.PBM14361.ME

source_name: MYF6.PBM14361.ME PBM, ME design


title: SOX15.PBM14303.ME

source_name: SOX15.PBM14303.ME PBM, ME design


title: SRY.PBM14302.ME

source_name: SRY.PBM14302.ME PBM, ME design


title: SOX2.PBM14362.ME

source_name: SOX2.PBM14362.ME PBM, ME design


title: MAX.PBM14301.ME

source_name: MAX.PBM14301.ME PBM, ME design


title: THAP9.PBM13968.HK

source_name: THAP9.PBM13968.HK PBM, HK design


title: THAP9.PBM13952.ME

source_name: THAP9.PBM13952.ME PBM, ME design


title: THAP8.PBM13951.ME

source_name: THAP8.PBM13951.ME PBM, ME design


title: THAP8.PBM13967.HK

source_name: THAP8.PBM13967.HK PBM, HK design


title: THAP8.PBM13950.ME

source_name: THAP8.PBM13950.ME PBM, ME design


title: THAP7.PBM13964.HK

source_name: THAP7.PBM13964.HK PBM, HK design


title: THAP7.PBM13949.ME

source_name: THAP7.PBM13949.ME PBM, ME design


title: THAP7.PBM13948.ME

source_name: THAP7.PBM13948.ME PBM, ME design


title: THAP8.PBM13966.HK

source_name: THAP8.PBM13966.HK PBM, HK design


title: THAP6.PBM13947.ME

source_name: THAP6.PBM13947.ME PBM, ME design


title: THAP5.PBM13962.HK

source_name: THAP5.PBM13962.HK PBM, HK design


title: THAP5.PBM13946.ME

source_name: THAP5.PBM13946.ME PBM, ME design


title: THAP6.PBM13963.HK

source_name: THAP6.PBM13963.HK PBM, HK design


title: THAP5.PBM13961.HK

source_name: THAP5.PBM13961.HK PBM, HK design


title: THAP5.PBM13945.ME

source_name: THAP5.PBM13945.ME PBM, ME design


title: THAP4.PBM13896.ME

source_name: THAP4.PBM13896.ME PBM, ME design


title: THAP2.PBM13910.HK

source_name: THAP2.PBM13910.HK PBM, HK design


title: THAP4.PBM13911.HK

source_name: THAP4.PBM13911.HK PBM, HK design


title: THAP4.PBM13912.HK

source_name: THAP4.PBM13912.HK PBM, HK design


title: THAP11.PBM13893.ME

source_name: THAP11.PBM13893.ME PBM, ME design


title: THAP11.PBM13909.HK

source_name: THAP11.PBM13909.HK PBM, HK design


title: THAP2.PBM13894.ME

source_name: THAP2.PBM13894.ME PBM, ME design


title: THAP11.PBM13892.ME

source_name: THAP11.PBM13892.ME PBM, ME design


title: THAP10.PBM13907.HK

source_name: THAP10.PBM13907.HK PBM, HK design


title: THAP10.PBM13890.ME

source_name: THAP10.PBM13890.ME PBM, ME design


title: THAP10.PBM13906.HK

source_name: THAP10.PBM13906.HK PBM, HK design


title: THAP10.PBM13891.ME

source_name: THAP10.PBM13891.ME PBM, ME design


title: TBPL1.PBM13889.ME

source_name: TBPL1.PBM13889.ME PBM, ME design


title: TBPL1.PBM13905.HK

source_name: TBPL1.PBM13905.HK PBM, HK design


title: SP140L.PBM13763.ME

source_name: SP140L.PBM13763.ME PBM, ME design


title: THAP7.PBM13965.HK

source_name: THAP7.PBM13965.HK PBM, HK design


title: SP140L.PBM13779.HK

source_name: SP140L.PBM13779.HK PBM, HK design


title: SP140.PBM13957.ME

source_name: SP140.PBM13957.ME PBM, ME design


title: SP140.PBM13778.HK

source_name: SP140.PBM13778.HK PBM, HK design


title: SP140.PBM13762.ME

source_name: SP140.PBM13762.ME PBM, ME design


title: SP140L.PBM13888.ME

source_name: SP140L.PBM13888.ME PBM, ME design


title: SP110.PBM13777.HK

source_name: SP110.PBM13777.HK PBM, HK design


title: THAP4.PBM13895.ME

source_name: THAP4.PBM13895.ME PBM, ME design


title: SP140L.PBM13904.HK

source_name: SP140L.PBM13904.HK PBM, HK design


title: SP140.PBM13973.HK

source_name: SP140.PBM13973.HK PBM, HK design


title: SP100.PBM13776.HK

source_name: SP100.PBM13776.HK PBM, HK design


title: SP100.PBM13760.ME

source_name: SP100.PBM13760.ME PBM, ME design


title: SP100.PBM13956.ME

source_name: SP100.PBM13956.ME PBM, ME design


title: RFX8.PBM13903.HK

source_name: RFX8.PBM13903.HK PBM, HK design


title: RFX8.PBM13902.HK

source_name: RFX8.PBM13902.HK PBM, HK design


title: RFX8.PBM13887.ME

source_name: RFX8.PBM13887.ME PBM, ME design


title: THAP11.PBM13908.HK

source_name: THAP11.PBM13908.HK PBM, HK design


title: TMF1.PBM13775.HK

source_name: TMF1.PBM13775.HK PBM, HK design


title: TMF1.PBM13759.ME

source_name: TMF1.PBM13759.ME PBM, ME design


title: TET2.PBM13773.HK

source_name: TET2.PBM13773.HK PBM, HK design


title: TCF20.PBM13756.ME

source_name: TCF20.PBM13756.ME PBM, ME design


title: TET2.PBM13757.ME

source_name: TET2.PBM13757.ME PBM, ME design


title: THYN1.PBM13758.ME

source_name: THYN1.PBM13758.ME PBM, ME design


title: TCF20.PBM13772.HK

source_name: TCF20.PBM13772.HK PBM, HK design


title: SNAPC5.PBM13357.HK

source_name: SNAPC5.PBM13357.HK PBM, HK design


title: SNAPC5.PBM13341.ME

source_name: SNAPC5.PBM13341.ME PBM, ME design


title: SNAPC2.PBM13755.ME

source_name: SNAPC2.PBM13755.ME PBM, ME design


title: SNAPC2.PBM13771.HK

source_name: SNAPC2.PBM13771.HK PBM, HK design


title: SP110.PBM13761.ME

source_name: SP110.PBM13761.ME PBM, ME design


title: SMYD3.PBM14325.HK

source_name: SMYD3.PBM14325.HK PBM, HK design


title: SMYD3.PBM13770.HK

source_name: SMYD3.PBM13770.HK PBM, HK design


title: SP100.PBM13972.HK

source_name: SP100.PBM13972.HK PBM, HK design


title: SMYD3.PBM13960.ME

source_name: SMYD3.PBM13960.ME PBM, ME design


title: SCMH1.PBM13769.HK

source_name: SCMH1.PBM13769.HK PBM, HK design


title: SCMH1.PBM13753.ME

source_name: SCMH1.PBM13753.ME PBM, ME design


title: SMYD3.PBM13754.ME

source_name: SMYD3.PBM13754.ME PBM, ME design


title: SAFB2.PBM13736.ME

source_name: SAFB2.PBM13736.ME PBM, ME design


title: RFX8.PBM13886.ME

source_name: RFX8.PBM13886.ME PBM, ME design


title: SMYD3.PBM14309.ME

source_name: SMYD3.PBM14309.ME PBM, ME design


title: SAFB2.PBM13752.HK

source_name: SAFB2.PBM13752.HK PBM, HK design


title: RAG1.PBM13750.HK

source_name: RAG1.PBM13750.HK PBM, HK design


title: THYN1.PBM13774.HK

source_name: THYN1.PBM13774.HK PBM, HK design


title: SAFB.PBM13751.HK

source_name: SAFB.PBM13751.HK PBM, HK design


title: RAG1.PBM13734.ME

source_name: RAG1.PBM13734.ME PBM, ME design


title: PURG.PBM13733.ME

source_name: PURG.PBM13733.ME PBM, ME design


title: PURB.PBM14454.HK

source_name: PURB.PBM14454.HK PBM, HK design


title: PURB.PBM14324.HK

source_name: PURB.PBM14324.HK PBM, HK design


title: PURB.PBM13748.HK

source_name: PURB.PBM13748.HK PBM, HK design


title: PREB.PBM13784.HK

source_name: PREB.PBM13784.HK PBM, HK design


title: PURB.PBM14308.ME

source_name: PURB.PBM14308.ME PBM, ME design


title: PREB.PBM13768.ME

source_name: PREB.PBM13768.ME PBM, ME design


title: PURB.PBM13732.ME

source_name: PURB.PBM13732.ME PBM, ME design


title: PREB.PBM13747.HK

source_name: PREB.PBM13747.HK PBM, HK design


title: PLSCR1.PBM13746.HK

source_name: PLSCR1.PBM13746.HK PBM, HK design


title: PREB.PBM13731.ME

source_name: PREB.PBM13731.ME PBM, ME design


title: PLSCR1.PBM13730.ME

source_name: PLSCR1.PBM13730.ME PBM, ME design


title: PHF19.PBM13782.HK

source_name: PHF19.PBM13782.HK PBM, HK design


title: PHF19.PBM13766.ME

source_name: PHF19.PBM13766.ME PBM, ME design


title: PHF19.PBM13767.ME

source_name: PHF19.PBM13767.ME PBM, ME design


title: PCGF6.PBM13729.ME

source_name: PCGF6.PBM13729.ME PBM, ME design


title: PHF19.PBM13783.HK

source_name: PHF19.PBM13783.HK PBM, HK design


title: PCGF2.PBM13744.HK

source_name: PCGF2.PBM13744.HK PBM, HK design


title: PCGF2.PBM13728.ME

source_name: PCGF2.PBM13728.ME PBM, ME design


title: SAFB.PBM13735.ME

source_name: SAFB.PBM13735.ME PBM, ME design


title: PA2G4.PBM13727.ME

source_name: PA2G4.PBM13727.ME PBM, ME design


title: PA2G4.PBM13743.HK

source_name: PA2G4.PBM13743.HK PBM, HK design


title: NME2.PBM13959.ME

source_name: NME2.PBM13959.ME PBM, ME design


title: NME2.PBM14438.ME

source_name: NME2.PBM14438.ME PBM, ME design


title: PURG.PBM13749.HK

source_name: PURG.PBM13749.HK PBM, HK design


title: NME2.PBM13340.ME

source_name: NME2.PBM13340.ME PBM, ME design


title: NME2.PBM13356.HK

source_name: NME2.PBM13356.HK PBM, HK design


title: NKRF.PBM13742.HK

source_name: NKRF.PBM13742.HK PBM, HK design


title: NACC2.PBM13741.HK

source_name: NACC2.PBM13741.HK PBM, HK design


title: NACC2.PBM13725.ME

source_name: NACC2.PBM13725.ME PBM, ME design


title: KCNIP3.PBM13724.ME

source_name: KCNIP3.PBM13724.ME PBM, ME design


title: GPBP1.PBM13722.ME

source_name: GPBP1.PBM13722.ME PBM, ME design


title: GPBP1L1.PBM13723.ME

source_name: GPBP1L1.PBM13723.ME PBM, ME design


title: GPBP1L1.PBM13739.HK

source_name: GPBP1L1.PBM13739.HK PBM, HK design


title: GPBP1.PBM13781.HK

source_name: GPBP1.PBM13781.HK PBM, HK design


title: GPBP1.PBM13738.HK

source_name: GPBP1.PBM13738.HK PBM, HK design


title: PCGF6.PBM13745.HK

source_name: PCGF6.PBM13745.HK PBM, HK design


title: GLMP.PBM13651.HK

source_name: GLMP.PBM13651.HK PBM, HK design


title: GLMP.PBM13635.ME

source_name: GLMP.PBM13635.ME PBM, ME design


title: DRAP1.PBM13619.HK

source_name: DRAP1.PBM13619.HK PBM, HK design


title: DR1.PBM13737.HK

source_name: DR1.PBM13737.HK PBM, HK design


title: DRAP1.PBM13603.ME

source_name: DRAP1.PBM13603.ME PBM, ME design


title: DACH2.PBM13601.ME

source_name: DACH2.PBM13601.ME PBM, ME design


title: DR1.PBM13721.ME

source_name: DR1.PBM13721.ME PBM, ME design


title: CSRNP3.PBM13599.ME

source_name: CSRNP3.PBM13599.ME PBM, ME design


title: CSRNP3.PBM13615.HK

source_name: CSRNP3.PBM13615.HK PBM, HK design


title: CSRNP2.PBM13613.HK

source_name: CSRNP2.PBM13613.HK PBM, HK design


title: NKRF.PBM13726.ME

source_name: NKRF.PBM13726.ME PBM, ME design


title: DACH1.PBM13616.HK

source_name: DACH1.PBM13616.HK PBM, HK design


title: CSRNP1.PBM13612.HK

source_name: CSRNP1.PBM13612.HK PBM, HK design


title: DACH2.PBM13602.ME

source_name: DACH2.PBM13602.ME PBM, ME design


title: CSRNP2.PBM13597.ME

source_name: CSRNP2.PBM13597.ME PBM, ME design


title: DACH2.PBM13618.HK

source_name: DACH2.PBM13618.HK PBM, HK design


title: KCNIP3.PBM13740.HK

source_name: KCNIP3.PBM13740.HK PBM, HK design


title: CSRNP1.PBM13611.HK

source_name: CSRNP1.PBM13611.HK PBM, HK design


title: CSRNP2.PBM13614.HK

source_name: CSRNP2.PBM13614.HK PBM, HK design


title: CSRNP2.PBM13598.ME

source_name: CSRNP2.PBM13598.ME PBM, ME design


title: CGGBP1.PBM13543.ME

source_name: CGGBP1.PBM13543.ME PBM, ME design


title: CHCHD3.PBM13672.ME

source_name: CHCHD3.PBM13672.ME PBM, ME design


title: CGGBP1.PBM13559.HK

source_name: CGGBP1.PBM13559.HK PBM, HK design


title: CENPX.PBM13558.HK

source_name: CENPX.PBM13558.HK PBM, HK design


title: CENPT.PBM13557.HK

source_name: CENPT.PBM13557.HK PBM, HK design


title: CENPS.PBM13687.HK

source_name: CENPS.PBM13687.HK PBM, HK design


title: DACH1.PBM13600.ME

source_name: DACH1.PBM13600.ME PBM, ME design


title: CENPT.PBM13541.ME

source_name: CENPT.PBM13541.ME PBM, ME design


title: GPBP1.PBM13765.ME

source_name: GPBP1.PBM13765.ME PBM, ME design


title: CENPS.PBM13671.ME

source_name: CENPS.PBM13671.ME PBM, ME design


title: DACH2.PBM13617.HK

source_name: DACH2.PBM13617.HK PBM, HK design


title: CSRNP1.PBM13595.ME

source_name: CSRNP1.PBM13595.ME PBM, ME design


title: CENPA.PBM13540.ME

source_name: CENPA.PBM13540.ME PBM, ME design


title: CENPA.PBM13556.HK

source_name: CENPA.PBM13556.HK PBM, HK design


title: BRF2.PBM13686.HK

source_name: BRF2.PBM13686.HK PBM, HK design


title: ARHGAP35.PBM13685.HK

source_name: ARHGAP35.PBM13685.HK PBM, HK design


title: AEBP1.PBM13684.HK

source_name: AEBP1.PBM13684.HK PBM, HK design


title: AEBP1.PBM13668.ME

source_name: AEBP1.PBM13668.ME PBM, ME design


title: CSRNP1.PBM13596.ME

source_name: CSRNP1.PBM13596.ME PBM, ME design


title: ARHGAP35.PBM13669.ME

source_name: ARHGAP35.PBM13669.ME PBM, ME design


title: NFXL1.PBM13885.ME

source_name: NFXL1.PBM13885.ME PBM, ME design


title: NFX1.PBM13884.ME

source_name: NFX1.PBM13884.ME PBM, ME design


title: BRF2.PBM13670.ME

source_name: BRF2.PBM13670.ME PBM, ME design


title: NFXL1.PBM13901.HK

source_name: NFXL1.PBM13901.HK PBM, HK design


title: CHCHD3.PBM13688.HK

source_name: CHCHD3.PBM13688.HK PBM, HK design


title: NFX1.PBM13900.HK

source_name: NFX1.PBM13900.HK PBM, HK design


title: MYRFL.PBM13899.HK

source_name: MYRFL.PBM13899.HK PBM, HK design


title: CENPX.PBM13542.ME

source_name: CENPX.PBM13542.ME PBM, ME design


title: TTF1.PBM13667.ME

source_name: TTF1.PBM13667.ME PBM, ME design


title: TERF1.PBM13898.HK

source_name: TERF1.PBM13898.HK PBM, HK design


title: MYRFL.PBM13883.ME

source_name: MYRFL.PBM13883.ME PBM, ME design


title: TTF1.PBM13683.HK

source_name: TTF1.PBM13683.HK PBM, HK design


title: TERF1.PBM13882.ME

source_name: TERF1.PBM13882.ME PBM, ME design


title: TERF1.PBM13897.HK

source_name: TERF1.PBM13897.HK PBM, HK design


title: TERF1.PBM13881.ME

source_name: TERF1.PBM13881.ME PBM, ME design


title: MYSM1.PBM13681.HK

source_name: MYSM1.PBM13681.HK PBM, HK design


title: MYSM1.PBM13665.ME

source_name: MYSM1.PBM13665.ME PBM, ME design


title: MYPOP.PBM13680.HK

source_name: MYPOP.PBM13680.HK PBM, HK design


title: MYPOP.PBM13664.ME

source_name: MYPOP.PBM13664.ME PBM, ME design


title: MYPOP.PBM13864.ME

source_name: MYPOP.PBM13864.ME PBM, ME design


title: MYPOP.PBM13880.HK

source_name: MYPOP.PBM13880.HK PBM, HK design


title: MSANTD4.PBM13679.HK

source_name: MSANTD4.PBM13679.HK PBM, HK design


title: MTERF4.PBM13879.HK

source_name: MTERF4.PBM13879.HK PBM, HK design


title: DMTF1.PBM13678.HK

source_name: DMTF1.PBM13678.HK PBM, HK design


title: MTERF4.PBM13863.ME

source_name: MTERF4.PBM13863.ME PBM, ME design


title: DMTF1.PBM13662.ME

source_name: DMTF1.PBM13662.ME PBM, ME design


title: MTERF3.PBM13878.HK

source_name: MTERF3.PBM13878.HK PBM, HK design


title: MBD1.PBM13780.HK

source_name: MBD1.PBM13780.HK PBM, HK design


title: MBD1.PBM13971.HK

source_name: MBD1.PBM13971.HK PBM, HK design


title: MTERF2.PBM13877.HK

source_name: MTERF2.PBM13877.HK PBM, HK design


title: MTERF2.PBM13861.ME

source_name: MTERF2.PBM13861.ME PBM, ME design


title: SETDB2.PBM13860.ME

source_name: SETDB2.PBM13860.ME PBM, ME design


title: MBD1.PBM13955.ME

source_name: MBD1.PBM13955.ME PBM, ME design


title: SETDB2.PBM13876.HK

source_name: SETDB2.PBM13876.HK PBM, HK design


title: MBD1.PBM13764.ME

source_name: MBD1.PBM13764.ME PBM, ME design


title: MBD4.PBM13873.HK

source_name: MBD4.PBM13873.HK PBM, HK design


title: PIN1.PBM13875.HK

source_name: PIN1.PBM13875.HK PBM, HK design


title: MBD6.PBM13874.HK

source_name: MBD6.PBM13874.HK PBM, HK design


title: TERB1.PBM13682.HK

source_name: TERB1.PBM13682.HK PBM, HK design


title: PIN1.PBM13859.ME

source_name: PIN1.PBM13859.ME PBM, ME design


title: TERB1.PBM13666.ME

source_name: TERB1.PBM13666.ME PBM, ME design


title: MBD4.PBM13857.ME

source_name: MBD4.PBM13857.ME PBM, ME design


title: MBD3.PBM13872.HK

source_name: MBD3.PBM13872.HK PBM, HK design


title: MSANTD1.PBM13677.HK

source_name: MSANTD1.PBM13677.HK PBM, HK design


title: HSFX2.PBM13676.HK

source_name: HSFX2.PBM13676.HK PBM, HK design


title: MBD3.PBM13856.ME

source_name: MBD3.PBM13856.ME PBM, ME design


title: MSANTD1.PBM13871.HK

source_name: MSANTD1.PBM13871.HK PBM, HK design


title: MSANTD4.PBM13663.ME

source_name: MSANTD4.PBM13663.ME PBM, ME design


title: MSANTD1.PBM13661.ME

source_name: MSANTD1.PBM13661.ME PBM, ME design


title: MSANTD1.PBM13855.ME

source_name: MSANTD1.PBM13855.ME PBM, ME design


title: MTERF3.PBM13862.ME

source_name: MTERF3.PBM13862.ME PBM, ME design


title: HSFX2.PBM13650.HK

source_name: HSFX2.PBM13650.HK PBM, HK design


title: HSFX1.PBM13870.HK

source_name: HSFX1.PBM13870.HK PBM, HK design


title: HSFX2.PBM13634.ME

source_name: HSFX2.PBM13634.ME PBM, ME design


title: HSFX2.PBM13660.ME

source_name: HSFX2.PBM13660.ME PBM, ME design


title: HSFX1.PBM13649.HK

source_name: HSFX1.PBM13649.HK PBM, HK design


title: HSFX1.PBM13633.ME

source_name: HSFX1.PBM13633.ME PBM, ME design


title: POU5F2.PBM13869.HK

source_name: POU5F2.PBM13869.HK PBM, HK design


title: MBD6.PBM13858.ME

source_name: MBD6.PBM13858.ME PBM, ME design


title: ZHX3.PBM13852.ME

source_name: ZHX3.PBM13852.ME PBM, ME design


title: ZHX3.PBM13867.HK

source_name: ZHX3.PBM13867.HK PBM, HK design


title: ZHX2.PBM13866.HK

source_name: ZHX2.PBM13866.HK PBM, HK design


title: ZHX2.PBM13865.HK

source_name: ZHX2.PBM13865.HK PBM, HK design


title: TPRX1.PBM13659.ME

source_name: TPRX1.PBM13659.ME PBM, ME design


title: TPRX1.PBM13944.HK

source_name: TPRX1.PBM13944.HK PBM, HK design


title: ZHX2.PBM13849.ME

source_name: ZHX2.PBM13849.ME PBM, ME design


title: TPRX1.PBM13675.HK

source_name: TPRX1.PBM13675.HK PBM, HK design


title: POU5F2.PBM13853.ME

source_name: POU5F2.PBM13853.ME PBM, ME design


title: ZHX3.PBM13851.ME

source_name: ZHX3.PBM13851.ME PBM, ME design


title: TPRX1.PBM13928.ME

source_name: TPRX1.PBM13928.ME PBM, ME design


title: NANOGNB.PBM13674.HK

source_name: NANOGNB.PBM13674.HK PBM, HK design


title: NANOGNB.PBM13658.ME

source_name: NANOGNB.PBM13658.ME PBM, ME design


title: MKX.PBM13673.HK

source_name: MKX.PBM13673.HK PBM, HK design


title: MKX.PBM13943.HK

source_name: MKX.PBM13943.HK PBM, HK design


title: MKX.PBM13657.ME

source_name: MKX.PBM13657.ME PBM, ME design


title: HSFX1.PBM13854.ME

source_name: HSFX1.PBM13854.ME PBM, ME design


title: MKX.PBM13927.ME

source_name: MKX.PBM13927.ME PBM, ME design


title: LEUTX.PBM13720.HK

source_name: LEUTX.PBM13720.HK PBM, HK design


title: LEUTX.PBM14307.ME

source_name: LEUTX.PBM14307.ME PBM, ME design


title: ZHX3.PBM13868.HK

source_name: ZHX3.PBM13868.HK PBM, HK design


title: ADNP2.PBM13528.HK

source_name: ADNP2.PBM13528.HK PBM, HK design


title: ADNP2.PBM13512.ME

source_name: ADNP2.PBM13512.ME PBM, ME design


title: LEUTX.PBM13704.ME

source_name: LEUTX.PBM13704.ME PBM, ME design


title: ZHX2.PBM13850.ME

source_name: ZHX2.PBM13850.ME PBM, ME design


title: HMGN3.PBM13703.ME

source_name: HMGN3.PBM13703.ME PBM, ME design


title: HMG20A.PBM13976.HK

source_name: HMG20A.PBM13976.HK PBM, HK design


title: ADNP.PBM13510.ME

source_name: ADNP.PBM13510.ME PBM, ME design


title: ADNP.PBM13526.HK

source_name: ADNP.PBM13526.HK PBM, HK design


title: ADNP2.PBM13527.HK

source_name: ADNP2.PBM13527.HK PBM, HK design


title: GRHL3.PBM13646.HK

source_name: GRHL3.PBM13646.HK PBM, HK design


title: HMG20A.PBM13632.ME

source_name: HMG20A.PBM13632.ME PBM, ME design


title: HMG20A.PBM13647.HK

source_name: HMG20A.PBM13647.HK PBM, HK design


title: GTF2IRD2B.PBM13926.ME

source_name: GTF2IRD2B.PBM13926.ME PBM, ME design


title: HMG20A.PBM13648.HK

source_name: HMG20A.PBM13648.HK PBM, HK design


title: ADNP.PBM13525.HK

source_name: ADNP.PBM13525.HK PBM, HK design


title: HMGN3.PBM13719.HK

source_name: HMGN3.PBM13719.HK PBM, HK design


title: ADNP.PBM13509.ME

source_name: ADNP.PBM13509.ME PBM, ME design


title: ADNP2.PBM13511.ME

source_name: ADNP2.PBM13511.ME PBM, ME design


title: GRHL3.PBM13630.ME

source_name: GRHL3.PBM13630.ME PBM, ME design


title: ZGLP1.PBM13718.HK

source_name: ZGLP1.PBM13718.HK PBM, HK design


title: GATAD2B.PBM13644.HK

source_name: GATAD2B.PBM13644.HK PBM, HK design


title: ZGLP1.PBM13941.HK

source_name: ZGLP1.PBM13941.HK PBM, HK design


title: ZGLP1.PBM13925.ME

source_name: ZGLP1.PBM13925.ME PBM, ME design


title: ZGLP1.PBM13702.ME

source_name: ZGLP1.PBM13702.ME PBM, ME design


title: LEUTX.PBM14323.HK

source_name: LEUTX.PBM14323.HK PBM, HK design


title: GATAD2B.PBM13628.ME

source_name: GATAD2B.PBM13628.ME PBM, ME design


title: GATAD2A.PBM13643.HK

source_name: GATAD2A.PBM13643.HK PBM, HK design


title: GATAD2A.PBM13627.ME

source_name: GATAD2A.PBM13627.ME PBM, ME design


title: GATAD2B.PBM13629.ME

source_name: GATAD2B.PBM13629.ME PBM, ME design


title: GATAD2B.PBM13645.HK

source_name: GATAD2B.PBM13645.HK PBM, HK design


title: GTF2IRD2B.PBM13942.HK

source_name: GTF2IRD2B.PBM13942.HK PBM, HK design


title: FLYWCH1.PBM14312.ME

source_name: FLYWCH1.PBM14312.ME PBM, ME design