title: T0_H12.S96

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H11.S88

status: Public on Jul 18 2018

type: SRA

city: Leuven

first: Sara

last: Aibar

address: Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

description: SMARTseq2 (Picelli et a. 2014)

library_source: transcriptomic

data_processing:
BAM files were converted to merged, demultiplexed FASTQ files, cleaned using fastq-mcf (ea-utils r819), and QC checked with FastQC (0.11.4)
Reads were then mapped to the human genome (hg19) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2)
Cells with less than 100,000 reads and/or 1000 genes expressed were discarded
Furthermore, only cells with an average expression level >3 of a curated list of housekeeping genes (n=85) were kept (Tirosh et al., 2016)
low-quality cell removal: library size, genes expressed per cell, ERCCs, house-keeping gene expression and mitochondrial DNA reads (Lun et al., 2016)
GRCh37
.txt read counts

molecule: polyA RNA

organism: Homo sapiens

source_name: T0 melanoma cell

extract_protocol:
FACS sorting for dsRED+ living cells, SMARTseq2 (Picelli et a. 2014)
Nextera-XT (Illumina)

treatment_protocol: BRAFi&MEKi by oral gavage

tag: tissue

value: tumor (PDX MEL006)

tag: age

value: before treatment

tag: genotype

value: BRAFmut (V600E)


title: T0_H10.S80

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H1.S8

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G9.S71

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G8.S63

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G7.S55

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G6.S47

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G1.S7

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G12.S95

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G5.S39

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G4.S31

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G3.S23

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G2.S15

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G11.S87

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G10.S79

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F8.S62

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F7.S54

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F4.S30

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F6.S46

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F5.S38

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F3.S22

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F2.S14

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F1.S6

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F12.S94

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E9.S69

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E8.S61

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E4.S29

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E6.S45

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E2.S13

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E5.S37

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E7.S53

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E1.S5

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E12.S93

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E3.S21

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E10.S77

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D8.S60

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F11.S86

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D4.S28

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D6.S44

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D2.S12

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D3.S20

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D7.S52

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D5.S36

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C8.S59

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D10.S76

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C4.S27

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D11.S84

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C5.S35

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C3.S19

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E11.S85

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D9.S68

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C12.S91

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C10.S75

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B9.S66

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C2.S11

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C11.S83

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B7.S50

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C1.S3

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B6.S42

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B8.S58

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D1.S4

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D12.S92

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B5.S34

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C9.S67

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C7.S51

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B4.S26

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C6.S43

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B3.S18

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B2.S10

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B1.S2

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B12.S90

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B10.S74

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B11.S82

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A9.S65

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A7.S49

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A6.S41

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A5.S33

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A4.S25

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A2.S9

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A1.S1

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A3.S17

description: SMARTseq2 (Picelli et a. 2014)


title: Transplant associated SCC 4

type: RNA

city: NEW YORK

first: Melody

last: Abikhair

state: NY

address: 550 FIRST AVENUE

country: USA

institute: NYU School of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25

data_processing: GCRMA (using gcrma package from R/Bioconductor)

label: biotin

molecule: total RNA

source_name: Transplant associated squamous cell carcinoma

label_protocol: Affymetrix double amplification protocol

extract_protocol: QIAGEN Rneasy Kit

tag: immune status

value: Immunosuppressed


title: Immunocompetent SCC 7

source_name: Squamous cell carcinoma

value: Immunocompetent


title: Immunocompetent SCC 8


title: Immunocompetent SCC 4


title: Transplant associated SCC 1


title: T0_A12.S89

description: SMARTseq2 (Picelli et a. 2014)


title: Immunocompetent SCC 2


title: Transplant associated SCC 5


title: Immunocompetent SCC 5


title: T0_A11.S81

description: SMARTseq2 (Picelli et a. 2014)


title: Transplant associated SCC 3


title: T0_A8.S57

description: SMARTseq2 (Picelli et a. 2014)


title: Transplant associated SCC 2


title: Normal skin 8

source_name: Normal skin


title: Normal skin 7


title: Immunocompetent SCC 1


title: Normal skin 6


title: Immunocompetent SCC 6


title: Normal skin 9


title: Normal skin 4


title: Normal skin 5


title: GAL3

city: Melbourne

first: James

middle: Gordon

last: Ryall

state: VIC

address: Department of Physiology, The University of Melbourne

department: Physiology

country: Australia

institute: The University of Melbourne

data_processing:
Basecalls performed using bcl2fast2
Sequenced reads were trimmed of adaptor sequences, then mapped to mm10 whole genome using TopHat2 version 2.0.10
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks v2.2.0
Genome_build: mm10
Supplementary_files_format_and_content: Galaxy247-[Cuffdiff_on_data_212,_data_203,_and_others__gene_differential_expression_testing]

organism: Mus musculus

source_name: GAL, C2C12 cell

growth_protocol: High Glucose, Low Glucose and Galactose cells were cultured for 24 hrs in DMEM supplemented with 1mM sodium pyruvate, 10% fetal bovine serum, 1% penicillin/streptomycin and either 25mM or 5mM glucose or 10mM galactose

extract_protocol:
C2C12 cells were trypsinized and centrifuged to a pellet
RNA libraries were prepared using a NEBNext Ultra RNA Library Prep Kit for Illumina

tag: cell line

tag: treatment (monosaccharide substrate)

value: Galactose (10mM)


title: GAL4


title: cyp-36A1(lf) egl-9(lf) rep 2

city: Cambridge

first: Corinne

last: Pender

state: MA

address: 77 Massachusetts Ave

institute: MIT

description:
fpkm_cyp-36A1(lf)_egl-9(lf)_rep_2
150820Hor_D15-7684

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Quality control: reads were aligned against the C. elegans ce10 genome assembly using bwa 0.7.5a and samtools/0.1.19 (bwa aln/ bwa samse) and mapping rates, fraction of multiply-mapping reads, number of unique 20-mers at the 5’ end of the reads, insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.17.0 .
For expression analysis, reads were aligned against the C.elegans ce10 genome / ENSEMBL 65 annotation using RSEM 1.2.15 [Li2011] and bowtie 1.0.1 [Langmead2009], with the following parameters  -p 6 --bowtie-chunkmbs 1024  --output-genome-bam.
Genome_build: C. elegans ce10 / ENSEMBL 65
Supplementary_files_format_and_content: Tab-delimited text files with raw counts and FPKM data from RSEM (posterior mean estimates)

organism: Caenorhabditis elegans

source_name: whole animals, MT22836

growth_protocol: All strains were maintained at 22.5C on nematode growth medium seeded with OP50 E. coli for at least two generations without starvation prior to experiment.

extract_protocol:
RLT buffer (QIAGEN) was added to the frozen pellet, and worms were lysed using a BeadBug microtube homogenizer (Sigma) and 0.5 mm zirconium beads (Sigma). RNA was extracted using the RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions.
RNA integrity and concentration were checked on a Fragment Analyzer (Advanced Analytical). The mRNA was purified by polyA-tail enrichment, fragmented, and reverse transcribed into cDNA (Illumina TruSeq). cDNA samples were then end-repaired and adaptor-ligated using the SPRI-works Fragment Library System I (Beckman Coulter Genomics) and indexed during amplification. Libraries were quantified using the Fragment Analyzer (Advanced Analytical) and qPCR before being loaded for single-end sequencing using the Illumina HiSeq 2000.

treatment_protocol: 150 very young adults (0-1 eggs in uterus) were picked into M9 buffer and allowed to settle. M9 was aspirated, and worms were then rinsed twice with M9 and twice with RNase-free water. Excess liquid was aspirated and the pellet was frozen in liquid nitrogen.

tag: strain background

tag: genotype/variation

tag: developmental stage

value: Young adult

value: Whole body


title: egl-9(lf) rep 2

description:
fpkm_egl-9(lf)_rep_2
150820Hor_D15-7682

source_name: whole animals, JT307


title: egl-9(lf) hif-1(lf) rep 2

description:
fpkm_egl-9(lf)_hif-1(lf)_rep_2
150820Hor_D15-7683

source_name: whole animals, CB6088


title: GAL2


title: GAL1


title: T0_A10.S73

description: SMARTseq2 (Picelli et a. 2014)


title: N2 rep 2

description:
fpkm_N2_rep_2
150820Hor_D15-7681

source_name: whole animals, N2

value: Wild type


title: LG4

source_name: LG, C2C12 cell

value: Low glucose (5mM)


title: cyp-36A1(lf) egl-9(lf) rep 1

description:
fpkm_cyp-36A1(lf)_egl-9(lf)_rep_1
150820Hor_D15-7678


title: egl-9(lf) hif-1(lf) rep 1

description:
fpkm_egl-9(lf)_hif-1(lf)_rep_1
150820Hor_D15-7677


title: LG3


title: LG2


title: Normal skin 3


title: egl-9(lf) rep 1

description:
fpkm_egl-9(lf)_rep_1
150820Hor_D15-7676


title: N2 rep 1

description:
fpkm_N2_rep_1
150820Hor_D15-7675


title: LG1


title: HG3

source_name: HG, C2C12 cell

value: High glucose (25mM)


title: HG2


title: HG4


title: Immunocompetent SCC 3


title: Normal skin 1


title: Ctrl_M_L

city: Baltimore

first: Jennifer

middle: L.

last: Pluznick

state: Maryland

address: 725 N. Wolfe Street, WBSB 205

institute: Johns Hopkins University

description:
enriched mRNA
HalperinL
JHUJP04001_007_L

data_processing:
Illumina CASAVA 1.8.2 was used for basecalling and to convert BCL files to FASTQ files. (Default parameters were used)
Alignments were run using rsem-1.2.9 via the “rsem-calculate-expression” module used with the following options: “—calc-ci,” “—output-genome-bam,” “—paired-end,” and “—forward-prob 0.”
Reads were mapped to olfactory receptor genes using specified coordinates from Ibarra-Soria et al, PLOS Genetics 2014
Differential expression analysis was run using rsem-1.2.9 EBSeq via “rsem-run-ebseq” using an R script within rsem to run the EBSeq package. A false discovery rate of 0.05 was set as the threshold using the “FDR_rate” script within “resem-control-FDR.”
Genome and transcript alignments were performed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: control diet_renal cortex

extract_protocol:
Kidneys were harvested, then capsules were  removed, followed by manual dissection of outer cortex. Samples were immediately placed in RNA later and then flash frozen in liquid nitrogen. RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit with Ribo-Zero Gold (Cat#RS-122–2303) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were placed on diet at 6 weeks of age, and on diet for a total of 9 weeks

tag: strain

value: wild type

tag: diet

value: Control Diet

value: renal cortex


title: Normal skin 10


title: HG1


title: Ctrl_M_M

description:
enriched mRNA
HalperinM
JHUJP04001_008_M


title: Normal skin 2


title: Ctrl_M_J

description:
enriched mRNA
HalperinJ
JHUJP04001_006_J


title: Ctrl_M_I

description:
enriched mRNA
HalperinI
JHUJP04001_005_I


title: HF_M_G

description:
enriched mRNA
HalperinG
JHUJP04001_004_G

source_name: high fat diet_renal cortex

value: High Fat Diet


title: HF_M_F

description:
enriched mRNA
HalperinF
JHUJP04001_003_F


title: HF_M_B

description:
enriched mRNA
HalperinB
JHUJP04001_002_B


title: HF_M_A

description:
enriched mRNA
HalperinA
JHUJP04001_001_A


title: Input_PD14_rep2

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

country: China

institute: Chinese Academy of Sciences

description:
ChIP-seq input, rep2 (PD14)
MEF-P7Input_combined

library_source: genomic

data_processing:
Illumina bcl2fastq software was used to generate fastq files.
ChIP-seq reads were filtered to move sequencing adapters and low quality reads by cutadapt (version 1.14)
ChIP-seq reads were aligined to mm10 genome using bowtie2 (version 2.3.2), then unique mapped reads were chosed by SAMtools (Version: 1.3.1). PCR duplications were also remove by picard (version: 1.118)
Peaks were called using MACS2 (macs2 2.1.1.20160309) under the parameters: -broad -g mm -B --broad-cutoff 0.1
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated by BAM file using bamCoverage (deeptools 2.5.3), the parameter "--scaleFactor" was calculated using DESeq (R package) over the promoter reads counts.

molecule: genomic DNA

growth_protocol: MEFs were isolated from pregnant C57BL/6 mouse (13.5 days) and cultured in DMEM, supplemented with 10% fetal bovine serum (FBS, Gibco, 12800) under 5% CO2 at 37 °C. Cells were serially passaged as described in1 after reaching 80%-90% confluence. MEFs were used 2,8 and 14 population doubling (PD) levels. The number of population doubling was calculated by the formula PD=log2(Ne/N0). Ne represent the counts numbers where N0 represent the seeding numbers respectively. Cumulative PD numbers represent the sum of PD’s from all previous passages with cells derived from the primary culture considered to be at PD=0.

extract_protocol:
MEFs were cross-linked with 1% formaldehyde solution (Sigma, F8775) for 10 min at room temperature. Fixation was quenched by glycin at a final concentration of 0.125 M for 5 min. Next, chromatin was sheared using a Bioruptor sonicator until DNA was fragmented to 300-500 bp. The supernatant was pre-cleared with 20 μL salmon sperm DNA/Protein A sepharose beads (Sigma, GE17-5280). Subsequently, 250 μg fraction and 3 μg histone modification antibody were combined and agitated overnight at 4 °C. Antibody-protein-DNA complexes were pull-down by 30 μL Protein A sepharose beads slurry and washed. The eluted complexes were subsequently decross-linked at at 65 °C for 5 h. After phenol chloroform extraction step, ChIP DNA were provided for establishing sequencing libraries which followed illumina manufacturer’s protocol and the libraries were sequenced on illumina Hiseq platform (Genewiz, Corp).
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For producing the lentiviruses of interest, HEK293T cells were used to transient co-transfection with pLKO.1-shRNA coding shRNAs targeting C/EBP α (TRCN library, Sigma) and two assistant vectors psPAX and pMD2.G vectors. Culture media were replaced with DMEM supplemented 30% FBS post 18 h transfection and then viral supernatants were collected 24 h later. Young MEFs were transduced with the lentiviruses when the confluence reached 70％. 24 h later, 3 μg/μL puromycin was added to select shRNA-expressing cells. Screen for puromysin-positive cells will last at least 5 days and then cells will be harvest at middle-aged passage for further study.

tag: cell type

value: mouse embryonic fibroblasts (MEFs)

tag: passages

tag: chip antibody info.

value: input


title: Input_PD8_rep1

description:
ChIP-seq input, rep1 (PD8)
MEF-P4-Input_combined


title: H3K4me1_PD8_rep2

description:
H3K4me1 of WT MEFs, rep2 (PD8)
MEF-P4H3K4me1_combined

tag: chip antibody

value: Abcam, ab8895


title: H3K27ac_shCebpa_rep1

description:
H3K27ac of Cebpa KD MEFs, rep1
321048_combined

value: Abcam, ab4729


title: Input_PD2_rep2

description:
ChIP-seq input, rep2 (PD2)
MEF-P1Input_combined


title: Input_PD8_rep2

description:
ChIP-seq input, rep2 (PD8)
MEF-P4Input_combined


title: H3K4me1_PD14_rep2

description:
H3K4me1 of WT MEFs, rep2 (PD14)
MEF-P7H3K4me1_combined


title: H3K27ac_shCebpa_rep2

description:
H3K27ac of Cebpa KD MEFs, rep2
S009502_combined


title: H3K27ac_shControl

description:
H3K27ac of Cebpa KD control
MEF-K-D_TKD180500724_1.fq.gz


title: Input_PD2_rep1

description:
ChIP-seq input, rep1 (PD2)
MEF-P1-Input_combined


title: H3K4me1_PD14_rep1

description:
H3K4me1 of WT MEFs, rep1 (PD14)
MEF-P7-H3K4me1_combined


title: Input_PD14_rep1

description:
ChIP-seq input, rep1 (PD14)
MEF-P7-Input_combined


title: H3K27ac_PD14_rep1

description:
H3K27ac of WT MEFs, rep1 (PD14)
MEF-P7H3K27Ac_combined


title: H3K27ac_PD14_rep2

description:
H3K27ac of WT MEFs, rep2 (PD14)
MEF-P7H3K27ac_combined


title: H3K27ac_PD8_rep2

description:
H3K27ac of WT MEFs, rep2 (PD8)
MEF-P4H3K27ac_combined


title: H3K4me1_PD2_rep2

description:
H3K4me1 of WT MEFs, rep2 (PD2)
MEF-P1H3K4me1_combined


title: H3K27ac_PD8_rep1

description:
H3K27ac of WT MEFs, rep1 (PD8)
MEF-P4-H3K27Ac_combined


title: H3K4me1_PD8_rep1

description:
H3K4me1 of WT MEFs, rep1 (PD8)
MEF-P4-H3K4me1_combined


title: DSS_19083_05_merged

city: Rotterdam

first: Mark

last: Schmitt

address: Dr. Molewaterplein 40

department: Pathology

country: Netherlands

institute: Erasmus MC

description: 3% DSS in drinking water

data_processing:
The reads were aligned using STAR version 2.5.3a (Dobin et al, 2013) against the UCSC mm10 reference genome, using GENCODE annotation.gtf version M15 (GENCODE 2012 Genome Research)
Read counts on GENCODE annotation were computed using the featureCounts version 1.5.2 using --largestOverlap --primary --fracOverlap 0.8
The differentially expressed genes were called using a generalized linear negative binomial model with controlling the effect of the RNA sample preparation date. The calculations were performed by the DESeq2 R package (Anders and Huber, Genome Biology 2010)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Ensemble Gene Id  and read count

source_name: Paneth cells

extract_protocol:
Mouse intestines were opened longitudinally, washed with PBS and villi were scraped away. The intestinal tissue was then dissected in 5-10 mm long pieces and washed 3 times with PBS. Whole crypts were extracted from the small intestine by incubating the minced tissues with 2 mM EDTA for 30 min. at 4°C. Crypts were then pelleted and passed through a 70 μm strainer. Isolated crypts were first digested to single cells after incubation with TrypLE (Life Technologies) and 2000 U/ml-1 Dnase (Sigma) for 10 min. at 37°C. Dissociated cells were passed through a 40 μm strainer, stained with an APC-conjugated CD24 antibody (clone M1/69 BioLegend), and, to exclude non-epithelial cells, with the following Ab’s for 30 min. at 4°C: BV421-conjugated TER119 (Biolegend), CD31 (Biolegend), CD45 (Biolegend). For Paneth cell analysis, an additional staining with a PE-conjugated CD117 antibody (Biolegend) was also performed. Cells were then sorted by FACS (BD FACSAriaIII; BD Bioscience). Single viable epithelial cells were gated by CD24 and side scatter (SSC), and by negative selection against the above BV421-conjugated Ab’s and with DAPI to discriminate live from dead cells. Detailed FACS gating strategy for the small intestine was performed as previously described (Roth et al., 2012). RNA was isolated from isolated Paneth cells using TRIzolTM Reagent (ThermoFisher Scientific) according to the manufacturer’s instructions. RNA quality and quantity was evaluated on a 2100 Bio-analyzer (Agilent) using the Agilent RNA 6000 Pico Kit (Agilent Technologies). For RNA sequencing analysis, RNA samples were further processed by GATC-Biotech (Konstanz, Germany) according to the INVIEWTM Transcriptome Explore library preparation protocol (Illumina based).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were administered 3% dextran sulfate sodium salt (colitis-grade; MP Biomedicals) through the drinking water for seven days during which the animals were monitored for a specific set of parameters including stool consistency, blood loss, appearance, and % weight loss. Three days after removal of DSS the mice were sacrificed and analyzed. Mice left on normal water for equivalent times were used as controls

value: intestinal tissue

value: 10 weeks

tag: agent

value: DSS

tag: rna isolation date

value: 8-12 week old


title: Control_19083_06

description: Water control

tag: tissue

value: Water


title: Control_18345_11

description: Water control

tag: age

value: 12 weeks


title: DSS_17954_05

description: 3% DSS in drinking water

tag: genotype


title: H3K27ac_PD2_rep2

description:
H3K27ac of WT MEFs, rep2 (PD2)
MEF-P1H3K27ac_combined


title: H3K27ac_PD2_rep1

description:
H3K27ac of WT MEFs, rep1 (PD2)
MEF-P1-H3K27Ac_combined


title: DSS_19424_01

description: 3% DSS in drinking water


title: DSS_19083_08

description: 3% DSS in drinking water


title: Control_18346_07

description: Water control


title: RNA-seq_PD14_rep2

description:
MEFP7RNA_combined
RNA-seq of PD14 MEFs, rep2

data_processing:
Illumina bcl2fastq software was used to generate fastq files.
RNA-seq reads were filtered to move sequencing adapters and low quality reads by cutadapt (version 1.14)
RNA-seq reads were mapped to mouse reference genome (Version: mm10) by hisat2 (Version 2.0.5)
Gene expression level was measured by TPM using stringtie (Version: 1.3.1c).
Genome_build: mm10
Supplementary_files_format_and_content: csv file: the gene expression (TPM) in each samples

extract_protocol:
For RNA analysis, cells were harvested by TRIzol reagent (Invitrogene, 10296028), Strand-specific RNA libraries eliminating ribosome for sequencing were implemented to acquire mRNA and lncRNA data (rep1), RNA libraries using PloyA enrichment were also performed (rep2).
Libraries were prepared for sequencing using standard Illumina protocols

tag: molecule subtype

value: polyA enrich


title: H3K4me1_PD2_rep1

description:
H3K4me1 of WT MEFs, rep1 (PD2)
MEF-P1-H3K4me1_combined


title: RNA-seq_PD8_rep2

description:
MEFP4RNA_combined
RNA-seq of PD8 MEFs, rep2


title: RNA-seq_PD14_rep1

description:
MEF-P7_H7V5WALXX
RNA-seq of PD14 MEFs, rep1

value: eliminating ribosome


title: ATAC-seq_F121

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

institute: KU Leuven

description: ATGAGC | Sample 18 F121 (P24)

data_processing:
Single-end ATAC-seq raw data were analyzed using the ATAC-seq pipeline from the Kundaje lab (Version 0.3.3). Briefly, the raw reads were first trimmed using cutadapt (version 1.9.1) to remove adaptor sequence at the 3′ end. The trimmed reads were aligned to reference genome (mm10) using Bowtie2 (v2.2.6) using the ‘--local’ parameter. Single-end reads that aligned to the genome with mapping quality ≥30 were kept as usable reads (reads aligned to the mitochondrial genome were removed) using SAMtools (v1.2). PCR duplicates were removed using Picard’s MarkDuplicates (Picard v1.126).
Open chromatin regions (peak regions) were called using MACS2 (v2.1.0) using the ‘-g 1.87e9 -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits’ parameter.
The differential chromatin accessibility analysis and related plots were performed using the DiffBind package with ‘DESeq2, log2fold=1, FDR<=0.05’ parameter.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files containing open chromatin peaks normalized to the genome size

organism: Mus musculus musculus x Mus musculus castaneus

source_name: Embryonic Stem Cells

growth_protocol: PSCs were expanded on top of male WT feeders in mouse ESC medium (S/L condition)

extract_protocol:
Next, the cell pellets were resuspended in 50 µl of ATAC-lysis buffer (10mM Tris HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% NP40, and 0.01% Digitonin) and incubated on ice for 3 min. Wash out lysis with 1 ml of cold ATAC-lysis buffer containing 0.1% Tween-20 but No NP40 or digitonin and invert tube 3 times to mix. Nuclei were pelleted at 500 RCF for 10 min at 4°C in a fixed angle centrifuge.
Cells nuclei were resuspended in 50 µl of transposition mixture (25 ul 2x TD buffer, 2.5 ul transposase (100 nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, and 5 ul H2O) (Nextera DNA Sample Preparation Kit, Illumina, FC-121-1030). The reaction was performed  at 37°C for 30 minutes in a thermomixer with 1000 RPM mixing. The transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (D4014). DNA libraries were PCR amplified using NEBNext High-Fidelity 2x PCR Master Mix (Bioke, M0541), and size selected for 200 to 800 bp using homemade Serapure beads [60]. Library concentrations were quantified with the KAPA Library Quantification Kit (KK4854), and equimolar amounts were pooled for single-end sequencing on an Illumina HiSeq 4000 instrument (Illumina) to yield ~50 million (range 34-90 million) 51bp long reads per sample.

treatment_protocol: PSCs were feeder-depleted and 50,000 viable cells were pelleted at 500 RCF at 4°C for 5 min in a fixed angle centrifuge

value: ESC

tag: gender

value: female

tag: passage

value: WT


title: RNA-seq_PD2_rep1

description:
MEF-P1_H7V5WALXX
RNA-seq of PD2 MEFs, rep1


title: ATAC-seq_CM3 (P6)

description: CGGAAT | Sample 15 CM3 (P6)

value: male


title: ATAC-seq_CM1 (P6)

description: GAGTGG | Sample 13 CM1 (P6)


title: RNA-seq_PD8_rep1

description:
MEF-P4_H7V5WALXX
RNA-seq of PD8 MEFs, rep1


title: RNA-seq_PD2_rep2

description:
MEFP1RNA_combined
RNA-seq of PD2 MEFs, rep2


title: Hi-C_PD14_rep2

description:
MEF-P7_HF73CALXX
in situ Hi-C of PD14 MEFs

data_processing:
library strategy: Hi-C
Illumina bcl2fastq software was used to generate fastq files.
Mapping: All paired-end reads were processed by HiC-Pro (Version 2.7.8) to generate the interaction matrix, then the matrix was normalized by ICE and library size.
A/B compartment: We used HiTC (R package) for visualization the interaction matrix and calculating the A/B compartment.
TAD: The TADs was detected by the method descripted in Crane, Emily, et al (https://github.com/dekkerlab/crane-nature-2015)
Genome_build: mm10
Supplementary_files_format_and_content: ".matrix" files: The HiC-Pro outputs of normalized interaction matrix under 40-kb bins. "40000_abs.bed":  A bed file representing the chromatin locations of the bin numbers in .matrix files

extract_protocol:
2×10^6 cells fixed in 1% formaldehyde were suspended in Hi-C lysis buffer and 100U of MboI restriction enzyme (NEB, R0147) was applied to digest chromatin overnight. Biotin-14-dATP (Life Technologies, 19524016) filled DNA restriction ends distinctly before DNA proximity ligation and crosslink reversal. To make the biotin-marked DNA suitable for high-throughput sequencing using Illumina sequencers, we shear DNA into a size of 300-500 bp using Covaris LE220 (Covaris, Woburn, MA) within 135 s. Sonicated DNA was end-repaired and size selected using AMPure XP beads (Beckman Coulter, A63882), before dATP-tailing step. Biotin-marked DNA was pulled down by Dynabeads Streptavidin T1 beads (Life technologies, 65602). Bead-bound Hi-C DNA was amplified with 13 cycles PCR amplification.
Hi-C libraries were performed following NEBnext library preparation manufacturer’s protocol (NEB, E7335)

tag: restriction enzyme

value: MboI


title: ATAC-seq_CM2 (P6)

description: CCAACA | Sample 14 CM2 (P6)


title: ATAC-seq_Dusp9+/- 1

description: ATTCCT | Sample 19 6-1 (P27)


title: Hi-C_PD8_rep2

description:
MEF-P4_HF73CALXX
in situ Hi-C of PD8 MEFs

value: mouse embryonic fibroblasts (MEFs)


title: Hi-C_PD2_rep2

description:
MEF-P1_H7VVJALXX
in situ Hi-C of PD2 MEFs


title: CM1 (P5)

description: CGTACGTA | Sample 29 CM1 (P5)

data_processing:
Reads from all datasets were aligned to mouse reference genome GRCm38/mm10 using STAR (v2.5.3a) with default parameters followed with conversion to BAM sorted by coordinate.
featureCounts function from the R Bioconductor package “Rsubread” was used to assign mapped reads to genomic features. For downstream analyses, only the genes with CPM value (count-per-milion) higher than 0.5 in at least two libraries were kept.
A read count matrix was used as an input for differential expression analysis using the edgeR quasi-likelihood pipeline in R(Chen et al. 2016). Obtained P values were corrected for multiple testing with the Benjamini–Hochberg method to control the FDR. Genes were considered significantly differentially regulated on the basis of both FDR < 0.05 and fold difference = 1.5
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with matrix for all samples with CPM values normalized by the library size

extract_protocol:
Total RNA were isolated from all biological samples using TRIzol reagent following the manufacturer’s protocol.
4 µg of total RNA was used for library preparation with the KAPA stranded mRNA Library prep kit for Illumina platform (KAPA Biosystems). Library concentrations were quantified with the Qubit dsDNA HS (High Sensitivity) Assay Kit (Invitrogen, Q32854), and equimolar amounts were pooled for single-end sequencing on an Illumina HiSeq 4000 instrument (Illumina) to yield ~20 million reads (range 13–23 million) of 36 bp or 51 bp in length per sample.

tag: differentiation time

value: undifferentiated


title: CM3 (P5)

description: ACTGATAT | Sample 31 CM3 (P5)


title: ATAC-seq_Dusp9+/- 2

description: CAAAAG | Sample 20 6-41 (P27)


title: CM7 (P5)

description: ATTCCTTT | Sample 32 CM7 (P5)


title: Hi-C_PD14_rep1

description:
MEF-P7_HFL3FALXX
in situ Hi-C of PD14 MEFs


title: ATAC-seq_CM7 (P6)

description: GGTAGC | Sample 16 CM7 (P6)


title: CM2 (P5)

description: GAGTGGAT | Sample 30 CM2 (P5)


title: Hi-C_PD2_rep1

description:
MEF-P1_HFL3FALXX
in situ Hi-C of PD2 MEFs


title: mac53-I rep3

city: Changsha

first: Long

last: Ma

state: Hunan

address: Xiangya Road No.110

institute: Central South University

data_processing:
Raw data was processed with Perl scripts to ensure the quality of data used in further analysis, clean data was obtained by removing reads Vontaining adapter.
Bowtie2 was used for building the genome index, and Clean Data was mapped to the WBcel235 alignments using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count.
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

source_name: L1 worm

growth_protocol: Synchronized animals at the L1 larval stage were allowed to recover on OP50-seeded NGM agar plates with or without 5 mM NaI for 8 hrs.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) and chloroform-isopropanol.
Libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain/genotype

tag: developmental stage

tag: treatment

value: iodide


title: mac53 rep2

value: untreated


title: mac53-I rep2


title: mac53 rep3


title: mac53-I rep1


title: Hi-C_PD8_rep1

description:
MEF-P4_HFL3FALXX
in situ Hi-C of PD8 MEFs

tag: strain

tag: cell type


title: mac35-I rep3


title: mac35-I rep2


title: CON_411_SAL_M_CAGATC

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Reads were demultiplexed and fastq files were generated using CASAVA v. 1.8.2.
The fastq files were aligned to the GRCm38 (mm10) genome with Ensembl annotation v. 75 using Tophat2 v. 2.0.10 in paired-end mode with Bowtie2 v. 2.1.0 and Samtools v. 0.1.19.
Aligned reads were sorted using Samtools v. 0.1.19.
Gene tag counts were calculated using htseq-count from HTSeq v. 0.6.1.
Genome_build: Genome_build: GRCm38 (Ensembl v. 75 annotation)
Supplementary_files_format_and_content: tab-delimited tag counts generated using htseq-count.

source_name: striatum

growth_protocol: Adult male mice from generation 17 of long term selective breeding experiment for increased home cage activity were used. In brief, a starting population derived from a systematic inter-cross of 8 genetically variable inbred strains was used as the founder strain for two mouse lines: High-Active and Control.

extract_protocol:
Bilateral striatal tissue was homogenized with an RNase-free disposable pellet pestle (Thermo Fisher Scientific, Waltham, MA) and RNA was extracted using the commercially available RNeasy® Lipid Tissue Mini Kit (Qiagen Inc., Valencia, CA). Purification of the isolated RNA included treatment with DNase I (Qiagen Inc, Valencia, CA), accordingly to the manufacturer's instructions. For assessing total RNA yield, aliquot samples were measured with the Qubit® 2.0 (Life Technologies). Each sample showed a 260/280 ratio over 2.0 and yielded over 14 μg of RNA. Quality and integrity of isolated RNA samples were determined by 28S/18S rRNA analysis with the Agilent 2100 Bioanalyzer (Santa Clara, CA). All samples scored an RNA Integrity Number (RIN) over 8, indicating no signs of degradation. Quality was spot checked by choosing random samples to run on a gel, which confirmed the Bioanalyzer report.
RNA-sequencing was performed by the Roy J. Carver Biotechnology Center. RNA-Seq libraries were prepared using the TruSeq Stranded RNA Sample Prep kit with an average fragment length of 200 bp. Libraries were quantified using qPCR, pooled in a pool of 20, and multiplexed across a total of 5 lanes. The libraries were sequenced on an Illumina HiSeq 2500 for 101 cycles in 100 bp paired-end format using a TruSeq SBS sequencing reagent kit, v. 4. Read depth ranged between 41,684,484 reads and 70,449,689 reads with a median read depth of 54,516,050 reads.

treatment_protocol: Mice were phenotyped for home cage activity when they were approximately 3 months old. At approximately 6.5 months of age, all the mice were re-phenotyped for home cage activity using the same procedure, 6 days of continuous video-tracking. On the 7th day, 2 hours after the lights shut off in the animal facility, mice received an intraperitoneal (i.p.) injection (10 ml/kg) of either vehicle (0.9% saline) or amphetamine (0.25 mg/kg d-amphetamine sulfate in 0.9% saline, catalog number A-5880, Sigma-Aldrich, St. Louis, MO), and returned to their home cage for video tracking. Mice were euthanized exactly 2 hours following the injection by live decapitation. All surfaces and instruments were cleaned thoroughly with RNAse away. Brains were rapidly dissected and immediately placed on an aluminum platform on wet ice with the ventral surface exposed. Using the olfactory tubercles and optic chiasm as landmarks, a razor blade was used to cut a coronal section approximately 1.7 mm thick containing the striatum. The section was then flipped onto its caudal aspect and then the entire bilateral striatum (dorsal and ventral) was carefully dissected from the cortex, medial septum, and olfactory tubercles. The striatum was then immediately placed in a centrifuge tube on dry ice and then stored at -80°C. The entire brain extraction and dissection process occurred over approximately 2 minutes.

value: striatum

value: control

tag: amphetamine treatment

value: saline

tag: rephenotype

tag: Sex

value: CAGATC


title: CON_469_SAL_M_TAGCTT

value: TAGCTT


title: CON_454_AMP_M_ACAGTG

value: amphetamine

value: ACAGTG


title: SEL_886_SAL_M_CCGTCC

value: high-active

value: CCGTCC


title: SEL_872_AMP_M_CTTGTA

value: CTTGTA


title: CON_448_SAL_M_GATCAG

value: GATCAG


title: SEL_871_SAL_M_GTTTCG

value: male

value: GTTTCG


title: CON_883_SAL_M_GCCAAT

value: GCCAAT


title: SEL_905_AMP_M_AGTTCC

value: AGTTCC


title: SEL_415_AMP_M_AGTCAA

value: AGTCAA


title: CON_409_AMP_M_ATCACG

value: ATCACG


title: SEL_499_SAL_M_GTGGCC

value: striatum

value: GTGGCC


title: CON_457_AMP_M_CGATGT

value: control

value: CGATGT


title: SEL_487_AMP_M_ATGTCA

value: ATGTCA


title: CON_477_SAL_M_ACTTGA

value: saline

value: ACTTGA


title: SEL_483_SAL_M_GTGAAA

value: high-active

value: GTGAAA


title: mac35-I rep1

value: iodide


title: mac35 rep3

value: untreated


title: CON_407_AMP_M_TTAGGC

value: amphetamine

value: male

value: TTAGGC


title: mac35 rep2


title: mac53 rep1


title: CON_369_AMP_M_TGACCA

value: TGACCA


title: mac35 rep1


title: SEL_192_AMP_M_GGCTAC

value: GGCTAC


title: SEL_197_SAL_M_GTCCGC

value: GTCCGC


title: WT-I rep3

value: N2 (wild type)


title: WT-I rep2


title: WT-I rep1


title: WT rep1


title: WT rep2


title: WT rep3


title: reprogramming with si-Scramble (control), MEF replicate 2

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Tophat software version 2.0.10 was used to align reads to mouse mm10 reference genome
FPKM values were calculated over all genes in mm10 assembly GTF (UCSC, December 2011), using cufflinks version 2.2.1.
FC was calculated in compare to MEF siControl, replicate 1.
Genome_build: mm10

source_name: Mbd3f/- OSK2nd cell line, mouse fibroblasts

growth_protocol: Maintenance and reprogramming (Day 3 and beyond)  of murine naïve pluripotent cells were conducted in bovine serum-free N2B27-based media or KSR media:   N2B27- based media: 500ml KO-DMEM (Invitrogen), 5ml N2 supplement (Invitrogen; 17502048), 5ml B27 supplement (Invitrogen; 17504044), 15% knockout serum replacement (Invitrogen – 10828), 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin-streptomycin (Invitrogen), 5mg/ml BSA (Sigma).   KSR media: 500 ml DMEM (Invitrogen) , 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin- streptomycin (Invitrogen).   Naïve conditions for murine PSCs included 10μg recombinant human LIF (Millipore; LIF1005). Where indicated 2i was added 48 hours after OSKM induction: small-molecule inhibitors CHIR99021 (CH, 3μM- Axon Medchem) and PD0325901 (PD 0.2 or 1μM - Axon Medchem).

extract_protocol:
Total RNA was isolated from indicated cell lines, and extracted from Trizol pellets by Direct-zol RNA MiniPrep kit (Zymo) according to manufacturer’s manual.
RNA was extracted from Trizol pellets, and utilized for RNA-Seq by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s instruction.

treatment_protocol: For secondary Mbd3f/- OSK2nd production, primary MEFs from Mbd3flox/- chimeric mice were infected with FUW-TetO-STEMCCA-OKS-mCherry and FUW-M2rtTA. IPS cells were isolated and injected into BDF2 blastocysts for the isolation of secondary MEFs. Secondary MEFs were transfected at day -3 and again at day 0 (starting reprogramming by adding DOX) with siRNA for cMyc, lMyc, nMyc or control (Stealth siRNA- mix of 3 as indicated in the paper) with RNAiMAX (Invitrogen). For molecular analysis, cells were collected at day 3 and day 7 as indicated.

tag: cell line

value: Mbd3f/- + OSK 2nd cell line

tag: stage of reprogramming

value: MEF


title: BMPC 2

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

institute: University of Arizona

description: cells were double sorted from unimmunized mice

data_processing:
Transcripts were quantified using Salmon version 0.9.1 (https://github.com/COMBINE-lab/salmon.git)
Genome_build: GRCm38.p6 (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M17/gencode.vM17.pc_transcripts.fa.gz)
Supplementary_files_format_and_content: combined .txt file is provided with trancript per million values for all samples. ENSEMBL transcript names, Gene ID, and lengths estimated by Salmon are provided.

source_name: bone marrow

growth_protocol: Primary ex vivo plasma cells

extract_protocol:
RNA was extracted using Macherey-Nagel NucleoSpin XS kit according to instructions
Sequencing libraries were generated using Clontech Smartseq and Nextera DNA library kits

treatment_protocol: untreated

tag: tissue

value: bone marrow

tag: markers

value: plasma cells


title: BMPC 1


title: B220-2NBDG+ 3

source_name: spleen

value: spleen


title: B220+2NBDG+ 1


title: B220-2NBDG- 1


title: B220-2NBDG+ 1


title: B220-2NBDG+ 2


title: B220-2NBDG-

data_processing:
CellRanger v 2.1 was used for demultiplexing, alignment, filtering of cells, and generation of read count tables using default parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-separated value files containing unique molecular identifier sequences and transcript counts for all cells passing quality control

extract_protocol:
Samples were prepared using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v2
Illumina nextera


title: B220-2NBDG+


title: B220+2NBDG+ 3


title: B220+2NBDG+ 2


title: B220+2NBDG- 1


title: B220-2NBDG- 2


title: BMPC


title: B220+2NBDG+


title: B220+2NBDG-


title: B220+2NBDG- 3


title: BMPC 3


title: B220-2NBDG- 3


title: reprogramming with si-Scramble (control), MEF replicate 1


title: B220+2NBDG- 2


title: NOD_2

city: St. Louis

first: Pavel

last: Zakharov

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Wash.Univ in St. Louis

data_processing:
The average quality of sequencing reads in each sample was assessed using the fastqс utility from fastq-tools (Droop, 2016).
All libraries were aligned to the reference genome using the STAR aligner (Dobin et al., 2013)
The raw counts of the number of tags on each gene were generated using htseq-count utility from HTseq package (Anders et al., 2015)
DESeq2 package (Love et al., 2014, version 1.18.1) was used to calculate the per-gene Wald statistics with multifactor analysis to account for donor/batch effect. Specifically, paired NOD-iLN and B16A-iLN samples from one isolation (4 pairs in total) were treated as one donor group each.
The ranked list of differences based on Wald per-gene statistics was used as input for Gene Set Enrichment Analysis (GSEA, Broad Institute).
The gene expression matrix counts were adjusted for donor effect with Combat (sva package) only for heat maps and clustering.
Genome_build: mm10

source_name: T-cells

extract_protocol:
Sorted cell RNA was isolated using the Ambion RNAqueous-Micro Kit (Life Technologies) following the manufacturer’s instructions. Library preparation was performed with 1-50 ng of total RNA, integrity was determined using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).
ds-cDNA was prepared using the SeqPlex RNA Amplification Kit (Sigma) per manufacturer’s protocol. cDNA was blunt ended, had an adenosine added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-2500 using single reads extending 50 bases. All RNAseq work was performed by the Genome Technology Access Center at Washington University School of Medicine.

tag: batch

tag: barcode

value: GCCTCCC

value: NOD/ShiLtJ

value: inguinal lymph node

tag: t-cell clone


title: NOD_1

value: GGTGAAT


title: NOD_3

value: GTATCCT


title: B16A_2

value: TCGTGCG


title: B16A_1

value: GGCAAGA


title: B16A_3

value: GGCAGCG


title: B16A_4

value: CACCTCC


title: NOD_4

value: GCTTAGA


title: reprogramming with Myc inhibitor, day 3

source_name: Mbd3f/- OSK2nd cell line, day 3 of reprogramming

value: day 3


title: reprogramming with siMyc (for cMyc, nMyc, lMyc), day 3


title: OSK over expression reprogramming, day 4

source_name: Mbd3f/- cell line, day 4 of reprogramming

value: Mbd3f/- cell line

value: day 4


title: CBS12357 Maltose-2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

description: S. eubayanus CBS 12357T was grown in either SMG or SMM until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

data_processing:
RNA-Seq reads were aligned to CBS12357 reference using STAR version 2.5.3a in 2Pass mode
resulted sequence alignment file (SAM) were filtered on ambigious alignments and sorted with samtools to sorted binary alignement file (BAM)
The sorted BAM file was processed with htseq-count from the HTSeq framework version 0.9.1 with -m union and -stranded reverse to calculate the transcript counts
The raw transcript counts were normalized on fragments per kilobase million (FPKM) by applying rpkm module from edgeR package
Genome_build: CBS12357
Supplementary_files_format_and_content: Comma delimited file, normalized transcript counts

organism: Saccharomyces eubayanus

source_name: Shake flask mid exponential phase

growth_protocol: S. eubayanus batch cultures were grown on synthetic medium (SM) containing 3.0 g L-1 KH2PO4, 5.0 g L-1 (NH4)2SO4, 0.5 g L-1 MgSO4, 7 H2O, 1 mL L-1 trace element solution, and 1 mL L-1 vitamin solution. The pH was set to 6 with 2 M KOH prior to autoclaving at 120 °C for 20 min. Vitamin solutions (Verduyn et al. 1992) were sterilized by filtration and added to the sterile medium. Concentrated sugar solutions were autoclaved at 110 °C for 20 min and added to the sterile flasks to give a final concentration of 20 g L-1 carbon source (glucose (SMG), maltose (SMM)

extract_protocol:
The resulting ice pellet was gently thawed on ice and spun down at 4700 x g for 5 min at 0 o C. Pellets were then resuspended in 1.2 mL of ice-cold AE buffer (50 mM sodium acetate and 10 mM EDTA, pH 5.0), followed by addition of 1.2 mL of acid phenol/chloroform/isoamyl alcohol mix and 0.12 mL 10 % sodium dodecyl sulfate. The resulting mix was vortexed for 30 s and incubated for 5 min at 65 °C. After homogenizing for 30 sec by vortexing, 800 µL aliquots were distributed in RNase-free screw-cap tubes (Tai et al. 2005). After centrifugation (15 min at 10,000 x g), the aqueous phase was transferred to a new tube containing 0.4 mL of acid phenol/chloroform. The mix was vortexed for 30 seconds, centrifuged (15 min at 10,000 x g) and the aqueous phase was again transferred to a new tube. RNA was then ethanol precipitated and re-suspended in RNAse-free water. Prior to cDNA synthesis, purity, concentration and integrity of the RNA in the samples was assessed with the Nanodrop (Thermo Fisher Scientific), Qubit (Thermo Fisher Scientific) and Tapestation 220 with RNA Screen Tape (Agilent Technologies), respectively, according the manufacturers’ recommendations.
cDNA libraries were prepared using the TruSeq RNA V2 kit (Illumina)and sequenced on HISeq 2500 (Illumina) at Novogene (HK) Company Ltd (Hong Kong, China).

tag: carbon source

value: Maltose


title: 16 hr TNF-a BRD4 ChIP-seq

city: San Diego

first: Shannon

middle: M

last: Lauberth

state: California

address: 9500 Gilman Drive #0322, Bonner Hall 3202

department: Biological Sciences

institute: UCSD

data_processing:
Sequenced reads were mapped to the hg38 human reference genome using Bowtie2 software and default parameters.
Mapped reads were then processed to make tag directories using the HOMER module. PCR duplications were removed and only uniquely mapped reads were kept for further analyses.
Genome browser files for resulting reads were generated by using the makeUCSCfile module from HOMER.
Enrichment for BRD4 and histone modification deposition were called using findPeaks module from HOMER using preset parameters for transcription factors and histones, respectively and compared to the input samples.
Deeptools were used to generate heatmaps.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: SW480 Cells

growth_protocol: Human SW480 cells were grown in Dulbecco’s modified Eagle medium (DMEM, Gibco) medium supplemented with 10% FBS.

extract_protocol:
Lysates from sonicated nuclei were prepared and protein-DNA complexes were IP'd overnight with BRD4 antibody.
ChIP-seq libraries were prepared according to Illumina's ChIP Truseq protocol. Briefly, ChIP DNA was end-repaired and adaptors were ligated to the ends of the DNA fragments. Adaptor-ligated ChIP DNA fragments with average size of 350 bp were used to construct libraries and single-end sequenced on Illumina HiSeq 4000.

treatment_protocol: cells were treated with 12.5 ng ml-1 TNF-α(Shenandoah Biotechnology) for 0 or 16 hr before harvesting for ChIP-seq analyses.

value: Human Colon Cancer Cell Line

tag: treated with

value: 12.5 ng ml-1 TNF-α for 16 hr

tag: chip antibody

value: Anti-BRD4:Bethyl laboratories; cat# A301-985A100; lot# A301-985A100-6


title: reprogramming with siMyc (for cMyc, nMyc, lMyc), day 7

source_name: Mbd3f/- OSK2nd cell line, day 7 of reprogramming

value: Mbd3f/- + OSK 2nd cell line

value: day 7


title: CBS12357 Maltose-1

treatment_protocol: S. eubayanus CBS 12357T was grown in either SMG or SMM until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.


title: CBS12357 Glucose-1

value: Glucose


title: 0 hr TNF-a BRD4 ChIP-seq

value: 12.5 ng ml-1 TNF-α for 0hr


title: cMyc over expression reprogramming, day 4


title: OSK over expression + cMyc over expression,  reprogramming, day 4


title: CBS12357 Glucose-2


title: THP1_untreated

status: Public on Jul 17 2018

city: Bruxelles

first: Pierre

last: Coulie

address: Avenue hippocrate 74, B1.74.04

department: GECE

institute: de Duve Institute

data_processing:
Sequencing Parameters  Sequencing platform : HiSeq4000  Control Software : HD 3.4.0.38  Primary Analysis RTA : 2.7.7  Type of sequencing : 2 * 100 bases  Index size : 6  Sequencing chemistry : HiSeq 3000/4000 PE
Fastq files were aligned with STAR-2.5.3a with following options (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical)
Bam files were sorted with Samtools 1.6
Gene counts were obtained using HTSeq 0.9.1 htseq-count with union mode
Count normalisation was performed with DESeq2_1.18.1
Genome_build: GRCh38.dna.primary_assembly
Supplementary_files_format_and_content: tsv ; gene count

growth_protocol: Cell were cultured in RPMI 1640 with 10%FCS

extract_protocol:
NucleoSpin RNA II - Macherey-Nagel
Illumina TruSeq Stranded mRNA

treatment_protocol: Cells were treated or not with 300ng/ml PMA during 3 hours, washed 3 times to remove PMA, rested for 21h and treated or not with 10ng/ml LPS-LBP during 24h

value: THP1 (ATCC TIB-202)

value: human monocytic cell line

value: untreated


title: THP1_PMA_LPS-LBP

value: PMA LPS-LBP


title: THP1_PMA

value: PMA


title: Neogenin KO

type: protein

city: Tuebingen

first: Andreas

last: Körner

address: Hoppe-Seyler-Straße 3

department: Clinic of Anesthesiology and Intensive Care Medicine

country: Germany

institute: University of Tuebingen

description: Peritoneal monocytes/macrophages from WT and Neo-/- mice were used following 12 h of ZyA-induced peritonitis. Protein and phosphorylation (TGF-β Phospho Antibody Array, FullMoonBioscience, #PTG176) profiling of peritoneal monocytes (pooled lavages from 4 mice / condition) was carried out according to the manufacturer’s instructions.

hyb_protocol: 1. 6 ml Protein Coupling Solution and one tube of biotinylated sample was mixed (Protein Coupling Mix) 2. Slides were incubated in Protein Coupling Mix for 2 hours on an orbital shaker (35 rpm) 3. For Detection, 60 µl of Cy3-streptavidin (0.5 mg/ml) were added to 60 ml of Detection Buffer. 4. Slides were submerged in 30 ml of Cy3-streptavidin solution for 20 minutes on an orbital shaker (35 rpm) at room temperature in the dark.

scan_protocol: Scans were performed by Full Moon BioSystems

data_processing:
Average Signal of Replicate Spots was normalized to Median Signal. Data Normalized to Median Signal.
Processed data includes:
Text files with average signals (*average_signal.txt)
Text file (fold-change_data.txt) with protein expression ratio (PER) for KO/WT and Phospho Protein Expression Ratio (PPER)  (KO/WT).  Column headers are: Antibody name (AB), UniProt ID (ID), PER, Phosphorylation Antibody (PA), Phosphorylation Site (PS), PPER.

molecule: protein

source_name: peritoneal monocytes/macrophages

label_protocol:
1. 100 µg of protein was used and Labeling Buffer was added to bring the volume to 75 µl.
2. 3 µl of Biotin/DMF solution was added and the mixture incubated at room temperature for 2 hours with vortexing every 10 minutes.
3. 35 µl of Stop Reagent was added and solution mixed by vortexing. Incubation for 30 minutes.

extract_protocol:
1. Cells were washed 5 times with ice cold PBS and remaining PBS removed
2. 100 µl of Full Moon Lysis Buffer was added and cells detached using a cell scraper and transferred to a microcentrifuge tube. One tube of Lysis Beads was added.
3. Mixture were vortexed for 60 seconds and incubated on ice for 10 minutes. Procedure was repeated 5 times.
4. Mixture was centrifuged at 10000 g for 5 minutes at 4°C.
5. Liquid was transferred to a fresh tube and centrifuged  at 18000 g for 20 minutes at 4°C.
6. Supernatant was transferred to a fresh tube.

value: peritoneal monocytes/macrophages

tag: genotype

value: Neogenin KO


title: Neogenin WT

value: Neogenin WT


title: reprogramming with si-Scramble (control), day 7


title: T2-2 (sample 2 rep2)

city: Guangzhou

first: Pengfei

last: Pang

state: Guangdong

address: No. 600 Tianhe Road, Tianhe District

institute: The Third Affiliated Hospital,Sun Yat-Sen University

data_processing:
Raw reads were filtered to: (1) Remove reads without 3’adapter; 2) Remove reads without insert fragment; 3) Remove reads with too much poly A/T; 4) Remove reads with length out of certain range; 5) Remove the low quality reads; 6) Remove the reads which contained N base more than 5% for total bases.
Saturation analysis was then performed to determine if the number of detected genes increased along with the amount of sequencing (total tag number).
The distribution of the expression of the clean tags was used to evaluate the normality of the dataset.
The remaining reads were aligned to the reference genome （the Ensemble (http://www.ensembl.org/index.html)）using TopHat v2.0.12 software
The expression of each detected gene based on the fragments per kilobase transcript per million (FPKM) values of each sample were estimated.
A differential gene expression analysis was performed using edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: FPKMs

source_name: immortal human umbilical vein endothelial cells treated with DDX24 siRNA#2

growth_protocol: Immortal human umbilical vein endothelial cells were cultured under the vascular cell basal media (ATCC PCS100030 supplemented with endothelial cell growth kit components (ATCC PCS100041)

extract_protocol:
Purified RNA was fragmented and the cDNA was synthesized by reverse transcription. The resulting double-stranded DNA fragments were en-repaired and A-nucleotide overhangs were added.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Immortal human umbilical vein endothelial cells  were treated by two short interfering (si)RNAs targeting DDX24 .

value: iHUVECs

tag: treatment

value: DDX24 siRNA#2

value: DDX24 knockdown


title: T1-2 (sample 1 rep2)

source_name: immortal human umbilical vein endothelial cells treated with DDX24 siRNA#1

value: DDX24 siRNA#1


title: T2-1 (sample 2 rep1)


title: Ctr-2 (control rep2)

source_name: immortal human umbilical vein endothelial cells treated with DDX24 scrambled siRNA

value: DDX24 scrambled siRNA

value: control


title: T1-1 (sample 1 rep1


title: Ctr-1 (control rep1)


title: spy7361 reintro W31G/W41G K455A/K472A_H3K9me3 #15

city: Durham

first: Nahid

last: Iglesias

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

description: BARCODE SEQUENCE: AGGTCAGT

data_processing:
Raw reads were separated by barcode. Barcode sequence were removed from the reads and attached to the identifier. Reads were mapped using Bowtie's default parameters. Mapped reads were normalized to reads per million, tiled with igvtools, and visualized in Integrated Genome Viewer (IGV).
Genome_build: ASM294v2
Supplementary_files_format_and_content: Mapped reads were normalized to reads per million, tiled with igvtools for visualization in Integrated Genome Viewer (IGV).

organism: Schizosaccharomyces pombe

extract_protocol:
ChIP was performed essentially as described (Jih et al., 2017). Briefly, 50 ml of logarithmically growing cells were fixed with 1% formaldehyde for 15 min at room temperature, quenched with 130 mM glycine for 5 min, harvested and washed twice with 1x TBS (50 mM Tris-HCl, pH 7.5, 150 mM NaCl). Cells were resuspended in 500 µl lysis buffer (50 mM Hepes-KOH, pH 7.5, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% SDS, and protease inhibitors) in 2 ml screw-cap tubes and lysed by bead beating with 1 ml acid-washed 0.5 mm glass beads with 6 cycles of 30 sec at 5000 rpm on a MagNA Lyser Instrument (Roche). Extracts were sonicated for 3x20 sec at 50% amplitude using a sonicator (Branson Digital Sonifier). For H3K9me2 ChIP, 2 µg of anti-H3K9me2 antibody (Abcam, ab1220) coupled to 30 µl Dynabeads Protein A (Invitrogen, 100-02D) was used for each immunoprecipitation. For H3K9me3 ChIP, 1 µg of anti-H3K9me3 antibody (Diagenode C15500003) was first incubated with 30 µl Dynabeads M-280 Streptavidin beads (Invitrogen, 11206D), followed by blocking with 5 µM biotin, according to the manufacturer's instructions, prior to be used for each immunoprecipitation. Half (250 µl for ChIP-seq) or one fifth (100 µl for ChIP-qPCR) of sheared chromatin lysate was added to the antibody-bead mixture and incubated for 2 hr at 4°C on a rotating device.
Immunoprecipitated DNA was cleaned up using the Qiagen PCR Purification Kit after reversing cross-links, RNaseA, and proteinase K treatment. Immunoprecipitated DNA was eluted from column with the provided elution buffer (50 ul x 2), subjected to additional shearing in a Qsonica water bath sonicator at 20% amplitude for 15 minutes of total shearing time (each cycle is 15” on + 15” off), followed by vacuum centrifugation to reduce the volume to 30 ul. DNA concentration was measured using Qubit dsDNA HS Kit.1 to 10 ng of immunoprecipitated DNA was used for standard Illumina library construction using barcoded adapters and protocol described previously (Wong et al., 2013). Libraries were pooled and sequenced on the Illumina HiSeq2000 or 2500.

tag: media

value: YEA

tag: antibody

value: H3K9me3 (Diagenode C15500003)


title: SPY6908 clr4 K455R/K472R_H3K9me3

description: BARCODE SEQUENCE: TTGAGTGT


title: spy7361 reintro W31G/W41G K455A/K472A_H3K9me3 #12

description: BARCODE SEQUENCE: CTCTGTCT


title: spy7361 reintro W31G/W41G K455A/K472A_H3K9me3 #14

description: BARCODE SEQUENCE: AACCGTGT


title: SPY6897 clr4 K472R_H3K9me3

description: BARCODE SEQUENCE: GGTCCTTGA

source_name: SPY6897 clr4 K472R_H3K9me3


title: SPY7289 clr4 K455A_H3K9me3

description: BARCODE SEQUENCE: CAGATC

source_name: SPY7289 clr4 K455A_H3K9me3


title: clr4 W31G/W41G/K455A/K472A_H3K9me3 #20

description: BARCODE SEQUENCE: CAGATC


title: clr4 W31G/W41G_H3K9me3  #26

description: BARCODE SEQUENCE: TTAGGC


title: clr4 W31G/W41G/K455A/K472A_H3K9me3 #27

description: BARCODE SEQUENCE: GATCAG


title: clr4 W31G/W41G/K455A/K472A_H3K9me3 #21

description: BARCODE SEQUENCE: ACTTGA


title: spy2353_epe1∆_H3K9me3

description: BARCODE SEQUENCE: GTTGTCCCA

value: YES


title: spy2352_epe1∆_H3K9me3

description: BARCODE SEQUENCE: CAGGAGGCG


title: clr4 W31G/W41G_H3K9me3  #25

description: BARCODE SEQUENCE: CGATGT


title: SPY7283 clr4 WT_H3K9me3

description: BARCODE SEQUENCE: ATCACG

source_name: SPY7283 clr4 WT_H3K9me3


title: SPY137 clr4 WT_H3K9me3

description: BARCODE SEQUENCE: CGCATTAA

source_name: SPY137 clr4 WT_H3K9me3


title: 5-day-old etiolated WT were exposed to white light for 1 hour, biological rep3

city: Beijing

first: Yi

address: 19 Xie Jie Kou Wai Street, Hai Dian District

institute: Beijing Normal University

hyb_protocol: Affymetrix Gene 1.0 ST Array hybridizations were performed by Atlas Biolabs.

scan_protocol: Standard Affymetrix protocol

data_processing: Raw CEL files were analyzed using Bioconductor software for R (http://www.atlas-biolabs.de), and the GC Robust Multi-array Average (GC-RMA) expression estimation was obtained using the gcrma package.

organism: Arabidopsis thaliana

source_name: WT, 5-day-dark plus 1-hour light

label_protocol: Total RNA was isolated from pools of seedlings and labeling was performed using 1 μg RNA per standard Affymetrix protocol.

growth_protocol: Plants were grown on half MS medium without sucrose in darkness for 5 days and transferred into continuous white light (120 μmolm-2s-1) for 1 hour.

extract_protocol: Total RNA was purified by using the RNase Plant Mini Kit (Qiagen).

tag: ecotype

value: whole seedlings

value: WT

tag: age

value: white light


title: clr4 W31G/W41G_H3K9me3  #13

description: BARCODE SEQUENCE: ATCACG


title: E10.5 wt brain vs. lu mice brain replicate2

city: TaipeiCity

first: Yi-Chao

last: Lee

address: YuancyuSt

country: Taiwan

institute: Taipei Medical University

description: Biological replicate 2 of 2.

hyb_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies) at 535 nm for Cy3 and 625 nm for Cy5.

scan_protocol: Scanned images were analyzed by Feature extraction 10.7.3.1 software (Agilent Technologies)

data_processing: image analysis and normalization software was used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

source_name: E10.5 wild-type brain

label_protocol: Correspondingly fragmented labeled cRNA was then pooled and hybridized to an Agilent SurePrint G3 Mouse Gene Exp v2 Array Kit (Agilent Technologies) at 65°C for 17 hours. After hybridization, slides were washed sequential

growth_protocol: All animals were housed in an air-conditioned vivarium with free access to food and water and a 10/14h light/dark cycle.

extract_protocol: 0.2 g of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye) (Agilent Technologies, California, USA) during the in vitro transcription process. 0.825 g of Cy-labeled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: stain

tag: developmental stage

source_name: E10.5 luxoid brain

value: luxoid


title: 5-day-old etiolated rb10 were exposed to white light for 1 hour, biological rep1

source_name: rb10, 5-day-dark plus 1-hour light


title: 5-day-old etiolated WT were exposed to white light for 1 hour, biological rep1


title: SPY7207 clr4 K472A_H3K9me3

description: BARCODE SEQUENCE: ACAGTGCAC

source_name: SPY7207 clr4 K472A_H3K9me3


title: SPY7208 clr4 K472A

description: BARCODE SEQUENCE: CACAGTTGG

source_name: SPY7208 clr4 K472A


title: SPY7206 clr4 K472A_H3K9me3

description: BARCODE SEQUENCE: TATCTCCG

source_name: SPY7206 clr4 K472A_H3K9me3


title: SPY815 clr4∆_H3K9me3

description: BARCODE SEQUENCE: CTCTGTCT

source_name: SPY815 clr4∆_H3K9me3


title: SPY7211 clr4 K455A/K472A_H3K9me3

description: BARCODE SEQUENCE: TCGCGTAC


title: SPY7209 clr4 K455A/K472A_H3K9me3

description: BARCODE SEQUENCE: GAGTTAAC


title: SPY7205 clr4 K455A_H3K9me3

description: BARCODE SEQUENCE: GTCTACAT

source_name: SPY7205 clr4 K455A_H3K9me3


title: 5-day-old etiolated rb10, biological rep2

source_name: rb10, 5-day-dark


title: SPY7210 clr4 K455A/K472A_H3K9me3

description: BARCODE SEQUENCE: GCAGCCTC


title: 5-day-old etiolated WT were exposed to white light for 1 hour, biological rep2


title: 5-day-old etiolated rb10 were exposed to white light for 1 hour, biological rep2


title: 5-day-old etiolated rb10 were exposed to white light for 1 hour, biological rep3


title: SPY7204 clr4 K455A_H3K9me3

description: BARCODE SEQUENCE: CGCATTAA

source_name: SPY7204 clr4 K455A_H3K9me3


title: 5-day-old etiolated rb10, biological rep3


title: 5-day-old etiolated WT, biological rep3

description: 5-day-old etiolated WT, biological rep3

source_name: WT, 5-day-dark


title: 5-day-old etiolated WT, biological rep2

description: 5-day-old etiolated WT, biological rep2


title: E10.5 wt brain vs. lu mice brain replicate1

description: Biological replicate 1 of 2.


title: 5-day-old etiolated rb10, biological rep1


title: SPY137 clr4 WT H3K9me3

description: BARCODE SEQUENCE: CCATACAC

source_name: SPY137 clr4 WT H3K9me3


title: SPY7896 clr4 K472A_H3K9me2

description: BARCODE SEQUENCE: CAGATC

source_name: SPY7896 clr4 K472A_H3K9me2


title: SPY7360 clr4 K472A_H3K9me2

description: BARCODE SEQUENCE: ACTAACTGC

source_name: SPY7360 clr4 K472A_H3K9me2


title: 5-day-old etiolated WT, biological rep1

description: 5-day-old etiolated WT, biological rep1


title: SPY7059 clr4 K455A_H3K9me3

description: BARCODE SEQUENCE: GCCAAT

source_name: SPY7059 clr4 K455A_H3K9me3


title: SPY6900 clr4 K455A/K472A_H3K9me3

description: BARCODE SEQUENCE: TAGCTT


title: SPY6897 clr4 KR472_H3K9me2

description: BARCODE SEQUENCE: TGACCA

source_name: SPY6897 clr4 KR472_H3K9me2


title: SPY7057 clr4 K455A/K472A_H3K9me3

description: BARCODE SEQUENCE: ATATAGGA


title: SPY6908 clr4 K455R/K472R_H3K9me2

description: BARCODE SEQUENCE: ACAGTG


title: SPY7896 clr4 K472A_H3K9me3

description: BARCODE SEQUENCE: CAGGAGGCG

source_name: SPY7896 clr4 K472A_H3K9me3


title: SPY7357 clr4 K455R/K472R_H3K9me2

description: BARCODE SEQUENCE: GGTCCTTGA


title: spy7260_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: TTGAGTGT

source_name: spy7260_epe1_delta ago1_delta_H3K9me2

extract_protocol:
ChIP was performed essentially as described (Jih et al., 2017). Briefly, 50 ml of logarithmically growing cells were fixed with 1% formaldehyde for 15 min at room temperature, quenched with 130 mM glycine for 5 min, harvested and washed twice with 1x TBS (50 mM Tris-HCl, pH 7.5, 150 mM NaCl). Cells were resuspended in 500 µl lysis buffer (50 mM Hepes-KOH, pH 7.5, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% SDS, and protease inhibitors) in 2 ml screw-cap tubes and lysed by bead beating with 1 ml acid-washed 0.5 mm glass beads with 6 cycles of 30 sec at 5000 rpm on a MagNA Lyser Instrument (Roche). Extracts were sonicated for 3x20 sec at 50% amplitude using a sonicator (Branson Digital Sonifier). For H3K9me2 ChIP, 2 µg of anti-H3K9me2 antibody (Abcam, ab1220) coupled to 30 µl Dynabeads Protein A (Invitrogen, 100-02D) was used for each immunoprecipitation. For H3K9me3 ChIP, 1 µg of anti-H3K9me3 antibody (Diagenode C15500003) was first incubated with 30 µl Dynabeads M-280 Streptavidin beads (Invitrogen, 11206D), followed by blocking with 5 µM biotin, according to the manufacturer's instructions, prior to be used for each immunoprecipitation. Half (250 µl for ChIP-seq) or one fifth (100 µl for ChIP-qPCR) of sheared chromatin lysate was added to the antibody-bead mixture and incubated for 2 hr at 4°C on a rotating device.
Immunoprecipitated DNA was cleaned up using the Qiagen PCR Purification Kit after reversing cross-links, RNaseA, and proteinase K treatment. Immunoprecipitated DNA was eluted from column with the provided elution buffer (50 ul x 2), subjected to additional shearing in a Qsonica water bath sonicator at 20% amplitude for 15 minutes of total shearing time (each cycle is 15” on + 15” off), followed by vacuum centrifugation to reduce the volume to 30 ul. DNA concentration was measured using Qubit dsDNA HS Kit.1 to 10 ng of immunoprecipitated DNA was used for standard Illumina library construction using barcoded adapters and protocol described previously (Wong et al., 2013). Libraries were pooled and sequenced on the Illumina HiSeq2500.


title: spy7259_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: GGTCCTTGA

source_name: spy7259_epe1_delta ago1_delta_H3K9me2


title: SPY7051 clr4 K455A_H3K9me3

description: BARCODE SEQUENCE: ACAGTG

source_name: SPY7051 clr4 K455A_H3K9me3


title: spy7255_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: TATACCGT

source_name: spy7255_epe1_delta ago1_delta_H3K9me2


title: spy7258_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: CCTTTACAG

source_name: spy7258_epe1_delta ago1_delta_H3K9me2


title: spy7249_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: CCATACAC

source_name: spy7249_epe1_delta ago1_delta_H3K9me2


title: spy5210 (epe1_delta 2352, ago1_delta)_H3K9me2

description: BARCODE SEQUENCE: AACACCTAC


title: spy7252_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: GAGTTAAC

source_name: spy7252_epe1_delta ago1_delta_H3K9me2


title: spy7253_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: GCAGCCTC

source_name: spy7253_epe1_delta ago1_delta_H3K9me2


title: spy7251_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: GTCTACAT

source_name: spy7251_epe1_delta ago1_delta_H3K9me2


title: spy2353_epe1_delta_H3K9me2

description: BARCODE SEQUENCE: AGGTCAGT


title: spy5212 (epe1_delta 2353, ago1_delta)_H3K9me2

description: BARCODE SEQUENCE: GTGACTACA


title: spy4719_ago1_delta_H3K9me2

description: BARCODE SEQUENCE: ACTTGA


title: spy5211 (epe1_delta 2352, ago1_delta)_H3K9me2

description: BARCODE SEQUENCE: CCTTTACAG


title: spy7257_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: AACACCTAC

source_name: spy7257_epe1_delta ago1_delta_H3K9me2


title: spy3216_h-ago1_delta_H3K9me2

description: BARCODE SEQUENCE: CTCTGTCT


title: SPY7326 epe1_delta clr4 K455A/K472A_H3K9me2 #36

description: BARCODE SEQUENCE: GTCTACAT


title: spy7254_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: TCGCGTAC

source_name: spy7254_epe1_delta ago1_delta_H3K9me2


title: spy7250_epe1_delta ago1_delta_H3K9me2

description: BARCODE SEQUENCE: CGCATTAA

source_name: spy7250_epe1_delta ago1_delta_H3K9me2


title: SPY7324 epe1_delta clr4 K455A/K472A_H3K9me2 #23

description: BARCODE SEQUENCE: CGCATTAA


title: spy137_wt_H3K9me2

description: BARCODE SEQUENCE: CGATGT


title: SPY7315 epe1_delta clr4 K455A_H3K9me2 #66

description: BARCODE SEQUENCE: ATATAGGA


title: SPY7311 epe1_delta clr4 WT_H3K9me2 #15

description: BARCODE SEQUENCE: TAGCTT

source_name: SPY7311 epe1_delta clr4 WT_H3K9me2 #15


title: SPY7314 epe1_delta clr4 K455A_H3K9me2 #58

description: BARCODE SEQUENCE: CTTGTA


title: SPY7312 epe1_delta clr4 WT_H3K9me2 #16

description: BARCODE SEQUENCE: GGCTAC

source_name: SPY7312 epe1_delta clr4 WT_H3K9me2 #16


title: spy2352_epe1_delta_H3K9me2

description: BARCODE SEQUENCE: AACCGTGT


title: SPY7310 epe1_delta clr4 WT_H3K9me2 #14

description: BARCODE SEQUENCE: GATCAG

source_name: SPY7310 epe1_delta clr4 WT_H3K9me2 #14


title: 3_V5T3

city: Stanford

first: William

last: Greenleaf

state: CA

address: 279 Campus Drive, Beckman Center B257

department: Genetics

institute: Stanford University

description:
primary lung tumor from CMV TKO line with hypoaccessible chromatin state
merged_bams_4_summits.bed
merged_peaks_filtered_subset.bed
res_V_1vs0_comb.csv

data_processing:
Sequencing data processing: Adapters were trimmed from reads before alignment using bowtie 2 with the -X 2000 flag.  Duplicate fragments for each sample were discarded, as were reads mapping to chrM, reads with mapping quality less than 30
Determining peak summits: Peak calling was done on merged data for each sequencing batch, with peak calling done using MACS2 ( --nomodel --call-summits)  resulting in the bed files merged_bams_X_summits.bed.
Peak filtering: Peak summits were expanded by 250 bps to either side of the summit to form a region of 500 bp. Peaks were filtered to not include blacklist regions or regions that appeared to have copy number amplification.
Peak filtering2: Each peak was assessed for having at least one read in all samples, or at least one sample with large number of normalized reads (>1 std. deviation above the mean). If it did not meet either of these criterion, it was filtered out.
Merging peaks: The three peak sets (one for each sequencing batch) were concatenated. Overlapping peaks were resolved by taking the peak with the highest numbers of reads.
Determining differential accessibility: counts per sample were found within peaks, and differential accessibility was called with different contrasts using DESeq2
Genome_build: mm9 for mus musculus
Supplementary_files_format_and_content: merged_peaks_filtered_subset.bed are the set of accessible regions, after fltering and merging.  Five columns indicate chromosome, start, and end of accessible regions, a unique name, and the peak score from the MACs2 data.
Supplementary_files_format_and_content: res_G_LvsT_comb.csv gives the differential accessibility across accessible regions between CGRP liver metastasis and tumor samples (i.e. comparing samples with the label G_L vs G_T in column "CGRP model (G): tumors  (T) versus mets (L)"). The output is directly from DEseq2.  Columns appended by '_GA.5' assess signficance of abs value of log2fold change being greater than 0.5
Supplementary_files_format_and_content: res_V_1vs0_comb.csv gives the differential accessibility across accessible regions between CMV model with Nfib amplification versus not (i.e. comparing samples with the label V_1 vs V_0 in column "CMV model (V), Nfib amplifiied (1) vs not (0)"). Output is formatted exactly as for res_G_LvstT_comb.csv

source_name: lung tumor

extract_protocol:
Cells were lysed, incubated with  Tn5 transposase, and purified with Qiagen MinElute kit.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit, as per Buenrostro et al. (2013).

value: lung tumor

tag: expression vector

value: Ad-CMV-Cre

tag: not included for low atac-seq enrichment

value: FALSE

tag: nfib amplification

tag: cmv model (v), nfib amplifiied (1) vs not (0)

tag: sequencing batch

tag: sample prep batch


title: 3_V5T4_A

tag: tissue


title: 3_V5T4_B


title: SPY7328 epe1_delta clr4 K455A/K472A_H3K9me2 #42

description: BARCODE SEQUENCE: GCAGCCTC


title: 3_V5T2_B


title: clr4 K455A_H3K9me2

description: BARCODE SEQUENCE: GCCAAT

source_name: clr4 K455A_H3K9me2


title: SPY7328 epe1_delta clr4 K455A/K472A_H3K9me3 #42

description: BARCODE SEQUENCE: TATCTCCG


title: clr4 WT_H3K9me2

description: BARCODE SEQUENCE: ATCACG

source_name: clr4 WT_H3K9me2


title: SPY7326 epe1_delta clr4 K455A/K472A_H3K9me3 #36

description: BARCODE SEQUENCE: CGGACGTGG


title: SPY7325 epe1_delta clr4 K455A/K472A_H3K9me3 #34

description: BARCODE SEQUENCE: GCGTTTCGA


title: SPY7325 epe1_delta clr4 K455A/K472A_H3K9me2 #34

description: BARCODE SEQUENCE: GAGTTAAC


title: 3_V5T1_A

description:
primary lung tumor from CMV TKO line with hyperaccessible chromatin state
merged_bams_4_summits.bed
merged_peaks_filtered_subset.bed
res_V_1vs0_comb.csv

value: TRUE


title: 3_V5T1_B


title: SPY7319 epe1_delta clr4 K455A_H3K9me2 #80

description: BARCODE SEQUENCE: AACCGTGT


title: SPY7319 epe1_delta clr4 K455A_H3K9me3 #80

description: BARCODE SEQUENCE: ACGTAGCTC


title: clr4 K455A/K472A_H3K9me2

description: BARCODE SEQUENCE: ACTTGA


title: SPY7324 epe1_delta clr4 K455A/K472A_H3K9me3 #23

description: BARCODE SEQUENCE: ATCCTATTC


title: 3_V5L2

description:
liver metastasis from CMV TKO line with hyperaccessible chromatin state
merged_bams_4_summits.bed
merged_peaks_filtered_subset.bed
res_V_1vs0_comb.csv

source_name: liver metastasis

value: liver metastasis


title: SPY7315 epe1_delta clr4 K455A_H3K9me3 #66

description: BARCODE SEQUENCE: TGATCCGA


title: 3_V5N1_B

description:
lymph node metastasis from CMV TKO line with hyperaccessible chromatin state
merged_bams_4_summits.bed
merged_peaks_filtered_subset.bed
res_V_1vs0_comb.csv

source_name: lymph node metastasis

value: lymph node metastasis


title: 3_V5L1


title: SPY7314 epe1_delta clr4 K455A_H3K9me3 #58

description: BARCODE SEQUENCE: GCAAGTAGA


title: SPY7312 epe1_delta clr4 WT_H3K9me3 #16

description: BARCODE SEQUENCE: CATTCCAAG

source_name: SPY7312 epe1_delta clr4 WT_H3K9me3 #16


title: 3_V5L1_A


title: 1_V3T1_B

description:
primary lung tumor from CMV TKO line with hypoaccessible chromatin state
merged_bams_0_summits.bed
merged_peaks_filtered_subset.bed


title: 3_V5T2_A


title: 1_V3T1_A


title: SPY7310 epe1_delta clr4 WT_H3K9me3 #14

description: BARCODE SEQUENCE: TGACGCAT

source_name: SPY7310 epe1_delta clr4 WT_H3K9me3 #14


title: 1_V2L1_B

description:
liver metastasis from CMV TKO line with hypoaccessible chromatin state
merged_bams_0_summits.bed
merged_peaks_filtered_subset.bed


title: clr4 K455A_H3K9me3

description: BARCODE SEQUENCE: ACTAACTGC

source_name: clr4 K455A_H3K9me3


title: SPY7305 clr4_delta_H3K9me3_2

description: BARCODE SEQUENCE: AACACCTAC

source_name: SPY7305 clr4_delta_H3K9me3


title: clr4 WT_H3K9me3

description: BARCODE SEQUENCE: TGCGGTTA

source_name: clr4 WT_H3K9me3


title: clr4 K455A/K472A_H3K9me3_2

description: BARCODE SEQUENCE: GTTGTCCCA


title: 3_G5T2_B

description:
primary lung tumor from CGRP TKO line with hypoaccessible chromatin state
merged_bams_4_summits.bed
merged_peaks_filtered_subset.bed
res_G_LvsT_comb.csv

value: Ad-CGRP-Cre

tag: cgrp model (g)

value: tumors  (t) versus mets (l):G_T


title: SPY7385 clr4 K455A/K472A 2 copies_H3K9me2 #76

description: BARCODE SEQUENCE: GTGGGATA


title: SPY7375 clr4 K455A 2 copies_H3K9me2 #68

description: BARCODE SEQUENCE: TGATCCGA

source_name: SPY7375 clr4 K455A 2 copies_H3K9me2 #68


title: 3_G5T1_B


title: 3_G5T1_A


title: SPY7374 clr4 K455A 2 copies_H3K9me2 #55

description: BARCODE SEQUENCE: GCAAGTAGA

source_name: SPY7374 clr4 K455A 2 copies_H3K9me2 #55


title: SPY7311 epe1_delta clr4 WT_H3K9me3 #15

description: BARCODE SEQUENCE: ATCGCCAGC

source_name: SPY7311 epe1_delta clr4 WT_H3K9me3 #15


title: Splenic CD4 T Cells: M2P2_AHGLJJBGX3

city: Cambridge

first: Daniel

middle: Bartholomew

last: Graham

address: 415 Main St.

department: Infectious Disease and Microbiome

institute: Broad Institute

description: 384 mutliplexed cells

data_processing:
Demultiplexing with bcl2fastq
Alignment with BWA
Counting of transcripts with custom python script
QC with custom python script
Downstream analysis with the seurat software package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated file, cells vs genes counts matrix

source_name: Splenic CD4 T Cells

extract_protocol: 384 single cells per plate tagged and multiplexed with 5' digital gene expression strategy

tag: strain

value: Splenic CD4 T Cells

value: L. monocytogenes infection i.p. days 0 and 11

tag: time point

value: day 18 post infection

tag: biological replicate

value: mouse 2 plate 2

tag: sequencing replicate


title: SPY7384 clr4 K455A/K472A 2 copies_H3K9me2 #72

description: BARCODE SEQUENCE: TAGCTAGTA

tag: media

value: YEA

tag: antibody


title: Splenic CD4 T Cells: M1P3_AHGLJJBGX3

description: 384 mutliplexed cells

tag: treatment

value: mouse 1 plate 3


title: Splenic CD4 T Cells: M2P3_AHGLJJBGX3

description: 384 mutliplexed cells

value: mouse 2 plate 3


title: SPY7364 clr4 WT 2 copies_H3K9me2 #11

description: BARCODE SEQUENCE: TGACGCAT

source_name: SPY7364 clr4 WT 2 copies_H3K9me2 #11


title: SPY7363 clr4 WT 2 copies_H3K9me2 #1

description: BARCODE SEQUENCE: GTTGTCCCA

source_name: SPY7363 clr4 WT 2 copies_H3K9me2 #1


title: SPY7361 clr4 K455A/K472A_H3K9me2

description: BARCODE SEQUENCE: CAGGAGGCG


title: Splenic CD4 T Cells: M1P2_AHGLJJBGX3

description: 384 mutliplexed cells

value: mouse 1 plate 2


title: SPY7359 clr4 K455A_H3K9me2

description: BARCODE SEQUENCE: TTGAGTGT

source_name: SPY7359 clr4 K455A_H3K9me2


title: Splenic CD4 T Cells: M2P3_AHGL2NBGX3

description: 384 mutliplexed cells


title: SPY7385 clr4 K455A/K472A 2 copies_H3K9me3 #76

description: BARCODE SEQUENCE: TCATTAGG

value: H3K9me3 (Diagenode C15500003)


title: Splenic CD4 T Cells: M2P1_AHGL2NBGX3

description: 384 mutliplexed cells

value: mouse 2 plate 1


title: Splenic CD4 T Cells: M1P3_AHGL2NBGX3

description: 384 mutliplexed cells


title: 1_V2L1_A

tag: genotype

value: Ad-CMV-Cre


title: Splenic CD4 T Cells: M2P2_AHGL2NBGX3

description: 384 mutliplexed cells


title: Splenic CD4 T Cells: M1P2_AHGL2NBGX3

description: 384 mutliplexed cells


title: SPY7375 clr4 K455A 2 copies_H3K9me3 #68

description: BARCODE SEQUENCE: TTCTGATG

source_name: SPY7375 clr4 K455A 2 copies_H3K9me3 #68


title: SPY7384 clr4 K455A/K472A 2 copies_H3K9me3 #72

description: BARCODE SEQUENCE: GACACTCTA


title: SPY7354 clr4 WT_H3K9me2

description: BARCODE SEQUENCE: AACACCTAC

source_name: SPY7354 clr4 WT_H3K9me2


title: Splenic CD4 T Cells: M2P1_AHGLJJBGX3

description: 384 mutliplexed cells


title: 3_G5T2_A

source_name: lung tumor

value: lung tumor

value: FALSE


title: SPY7363 clr4 WT 2 copies_H3K9me3 #1

description: BARCODE SEQUENCE: GTGACTACA

source_name: SPY7363 clr4 WT 2 copies_H3K9me3 #1


title: SPY7354 clr4 WT_H3K9me3

description: BARCODE SEQUENCE: ATCCTATTC

source_name: SPY7354 clr4 WT_H3K9me3


title: clr4 K455A/K472A_H3K9me3_1

description: BARCODE SEQUENCE: CACAGTTGG


title: SPY7359 clr4 KA455_H3K9me3

description: BARCODE SEQUENCE: TATCTCCG

source_name: SPY7359 clr4 KA455_H3K9me3


title: clr4 K455R/K472R_H3K9me3

description: BARCODE SEQUENCE: GCGTTTCGA


title: d0 Tg MEF +Mybl2 only rep2 75% chimeric

city: Birmingham

first: Carl

last: Ward

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

description: Day_0_75percent_1_2_mm10_bt2_auto_SPMR_treat_pileup.bdg.gz

data_processing:
NextSeq Control Software v2.1.0.31 was used for basecalling
GenerateFASTQWorker v2.6.17.15 was used to generate fastq files
FASTQC v0.11.5 was used to trim low quality reads
bowtie2 v2.1.0 was used to align reads to genome using arguments: --very-sensitive-local
samtools v1.4 was used to convert alignes .sam to .bam
MACS v2.1.0 was used to call peaks using optional arguments: --keep-dup=auto -B --trackline -f BAMPE -g mm
bedtools
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph generated with MACS showing Tn5 accessible regions of the genome.

source_name: Mouse embryonic fibroblasts

growth_protocol: DMEM with 1% Penicillin/Streptomycin, 2mM L-glutamine, 15% ESC qualified FBS, 1% non-essential amino acids, 0.1mM 2-mercaptoethanol, 0.01% LIF and 10μg/ml vitamin C. 200ng/ul Doxycycline was added to induce reprogramming.

extract_protocol:
50,000 cells were lysed in 10mM TrisHcl ph7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL. Nuclei were incubated with Tn5 transposase and 2% Digitonin. Then DNA was purified with Qiagen MiniElute kit.
10 μl of DNA was combined with 2.5 μl of indexing primers (Nextera Customized PCR Primer 1 and barcode Nextera PCR Primer 2), 25 μl of NEBNextHigh-Fidelity 2x PCR Master Mix (New England Biolabs). DNA was then amplified for 8 cycles to enrich the tagmented DNA fragments. A PCR clean-up was then performed using AMPure XP beads (Beckman Coulter), and the small fragments were then resuspended in 32.5 μl of resuspension buffer (provided in the Nextera kit). DNA was quantified using a Qubit fluorometer (Life Technologies), and library sizes were then determined using TapeStation (Agilent Technologies)

treatment_protocol: Trasgenic (Tg) MEFs carrying doxycycline-inducible Yamanaka factors were transduced with lentiviral particles encoding AmCyan or Mybl2-AmCyan and then reprogramming was induced by addition of doxycycline. Cells were collected after 3 days of reprogramming.

tag: genotype/variation

value: Tg MEF +Mybl2 only 75% chimeric

tag: cell type

value: Mouse embryonic fibroblasts


title: d0 Tg MEF +Mybl2 only rep1 75% chimeric


title: d0 Tg MEF +Mybl2 only rep2 80% chimeric

description: Day_0_80percent_1_2_mm10_bt2_auto_SPMR_treat_pileup.bdg.gz

value: Tg MEF +Mybl2 only 80% chimeric


title: d3 Tg MEF +Mybl2 only rep1 75% chimeric

description: Day_4_75percent_1_2_mm10_bt2_auto_SPMR_treat_pileup.bdg.gz


title: d3 Tg MEF +Mybl2 only rep1 80% chimeric

description: Day_4_80percent_1_2_mm10_bt2_auto_SPMR_treat_pileup.bdg.gz


title: ChIP-exo, CEBPb, replicate 1 [mouse]

city: Philadelphia

first: David

middle: J

last: Steger

state: PA

address: 12-193 SCTR 3400 Civic Center Blvd

department: Institute of Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

description: Liver_CEBPb_AAV-CEBPa_pool.plus.bw; Liver_CEBPb_AAV-CEBPa_pool.minus.bw; cebpb.liver.1445.peaks.txt

data_processing:
Reads were mapped to the hg19 or mm9 genomes using Bowtie. Reads mapping to ambiguous contigs were excluded.
Redundant reads were preserved for the ChIP-exo samples.
genome build: hg19; mm9
processed data files format and content: 1) ChIP seq peaks and motif mapping results are in BED format 2) ChIP-exo processed data are in bigwig format with 5' tag density reported as reads per million.

source_name: liver

growth_protocol: hMSCs were cultured in low glucose DMEM supplemented with 1% glutamine, and 10% FBS.

extract_protocol:
Cultured cells and liver tissue were crosslinked in 1 % formaldehyde for 15 minutes. A 5 minute quench was performed with 125mM glycine. To prepare ChIP extracts, nuclei were prepared by hypotonic lysis followed by Dounce homogenization. Nuclei were resuspended in SDS lysis buffer (50 mM HEPES/NaOH pH 7.5, 1% SDS, 10 mM EDTA, Complete protease inhibitor), incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

treatment_protocol: For hMSCs, confluent cells were treated with DMI adipogenic induction medium for 24 hours. For mouse experiments, 8-10 week old C57B/6 WT mice treated with AAV_Null or AAV_Cebpa as described in Bauer et al. J Clin Invest 2015 PMID 26348894.

tag: chip antibody

value: CEBPb, sc-150, Santa Cruz

value: AAV-cebpa


title: ChIP-exo, CEBPa, replicate 1 [mouse]

description: Liver_CEBPa_AAV-Null_DS332.plus.bw; Liver_CEBPa_AAV-Null_DS332.minus.bw

value: CEBPa, sc-61, Santa Cruz

value: AAV-control


title: ChIP-exo, CEBPb, replicate 2 [mouse]


title: ChIP-exo, CEBPa, replicate 2 [mouse]

description: Liver_CEBPa_AAV-Null_DS333.plus.bw; Liver_CEBPa_AAV-Null_DS333.minus.bw


title: d0 Tg MEF +Mybl2 only rep1 80% chimeric


title: ChIP-seq of Mybl2 in MEF

data_processing:
NextSeq Control Software v2.1.0.31 was used for basecalling
GenerateFASTQWorker v2.6.17.15 was used to generate fastq files
bowtie2 v2.1.0 was used to align reads to genome using arguments: --very-sensitive-local
samtools v1.4 was used to convert alignes .sam to .bam
MACS v2.1.0 was used to call peaks using optional arguments: --keep-dup=auto -B --trackline -f BAM -g mm
bedtools
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph generated with MACS showing mybl2 bound regions of the genome.

growth_protocol: DMEM with 1% Penicillin/Streptomycin, 2mM L-glutamine, 10%  FBS

extract_protocol:
2 x107 cells were suspended in 30 mls PBS and incubated with 250 ul DSG (50mg/500ul DMSO) on a rotating wheel for 45 minutes at room temperature. After this step, cells were washed 4 times with PBS and then resuspended in 10 ml of PBS and used for the second cross-linking with 1% Formaldehyde for 10 minutes at room temperature. Cross-linking was then terminated by adding 4 volumes of cold PBS+0.125 M of Glycine. Following this step cells were resuspended in 300l of ice-cold ChIP Lysis Buffer (50mM HEPES-KOH pH 7.5, 1mM EDTA pH 8, 1% Triton X-100, 0.1% Na Deoxycholate and proteinase inhibitor cocktail (Roche UK, Burgess Hill, UK)), and sonicated at 4°C using a Bioruptor™ (Diagenode, Liege, Belgium) to generate fragments an average length of 400-500 bp (10 min with 30 s “ON” and “OFF” cycles, power setting high).
Kapa hyper prep Kit

treatment_protocol: MEF were transduced with lentiviral particles encoding  HA-tagged Mybl2-P2A-AmCyan

value: anti-HA


title: SPY7364 clr4 WT 2 copies_H3K9me3 #11

description: BARCODE SEQUENCE: TGAGAGTG

source_name: SPY7364 clr4 WT 2 copies_H3K9me3 #11

value: YEA


title: ATAC Mybl2 overexpression replicate 3

value: embryonic fibroblasts


title: ATAC Mybl2 overexpression replicate 2


title: clr4 K455W H3K9me3

description: BARCODE SEQUENCE: AGGTCAGT

source_name: clr4 K455W H3K9me3


title: SPY7305 clr4_delta_H3K9me3_1

description: BARCODE SEQUENCE: CGGACGTGG

source_name: SPY7305 clr4_delta_H3K9me3


title: ATAC Control replicate 3

value: control (AmCyan)


title: clr4 WT H3K9me3

description: BARCODE SEQUENCE: GGCTAC

source_name: clr4 WT H3K9me3


title: clr4 K455W H3K9me2

description: BARCODE SEQUENCE: GCCAAT

source_name: clr4 K455W H3K9me2


title: SPY7374 clr4 K455A 2 copies_H3K9me3 #55

description: BARCODE SEQUENCE: GGCAGACGA

source_name: SPY7374 clr4 K455A 2 copies_H3K9me3 #55


title: ATAC Control replicate 1


title: clr4 K455A H3K9me2

description: BARCODE SEQUENCE: TGACCA

source_name: clr4 K455A H3K9me2


title: clr4 K455R H3K9me3

description: BARCODE SEQUENCE: CTTGTA

source_name: clr4 K455R H3K9me3


title: ATAC Control replicate 2


title: clr4 K472A_H3K9me3

description: BARCODE SEQUENCE: ACAGTGCAC

source_name: clr4 K472A_H3K9me3


title: clr4 K455R H3K9me2

description: BARCODE SEQUENCE: TTAGGC

source_name: clr4 K455R H3K9me2


title: clr4 WT H3K9me2

description: BARCODE SEQUENCE: CGATGT

source_name: clr4 WT H3K9me2


title: SPY7305 clr4_delta H3K9me2

description: BARCODE SEQUENCE: ATCACG

source_name: SPY7305 clr4_delta H3K9me2


title: 1_V2T1_B (re-analysis of GSM2147572)

source_name: lung tumor

tag: expression vector

tag: not included for low atac-seq enrichment

value: TRUE

tag: nfib amplification


title: 1_V4T1_A (re-analysis of GSM2147575)

description:
primary lung tumor from CMV TKO line with hyperaccessible chromatin state
merged_bams_0_summits.bed
merged_peaks_filtered_subset.bed

tag: sequencing batch

tag: sample prep batch


title: 1_V4T1_B (re-analysis of GSM2147576)

tag: tissue


title: 1_V3T1_B (re-analysis of GSM2147574)


title: 1_V1T1_B (re-analysis of GSM2147570)

description:
primary lung tumor from CMV TKO line with hypoaccessible chromatin state
merged_bams_0_summits.bed
merged_peaks_filtered_subset.bed
res_V_1vs0_comb.csv

tag: cmv model (v), nfib amplifiied (1) vs not (0)


title: SOX9.IP.rep3.s2

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

institute: Tel Aviv University

data_processing:
Sequenced reads were aligned to the human genome (hg19) using Bowtie2
SOX9 peaks were detected using MACS2; 1146 peaks detected
Genome_build: hg19
Supplementary_files_format_and_content: processed file contains the genomic coordinates of the 1,146 peaks (bed format) and "fold_enrichment" info for the peaks

source_name: hES-RPE

growth_protocol: For RPE differentiation, hESCs colonies (Hes1 hES) were picked up using collagenase IV (1 mg/ml; 200 U/mg, Gibco-BRL, Gaithersburg, MD), and cultured using differentiation protocol including treatment with nicotinamide and activinA. After 6-10 weeks in suspension, pigmented clusters were triturated, plated on gelatin (Sigma) coated plates (Corning Incorporated, Corning, NY), and cultured in Knock out medium with 10mM nicotinamide for 3-5 weeks. The RPE cell lines were further propagated using TrypLE Select (Gibco-BRL). The cells were passaged every 2 weeks.

extract_protocol:
Sonicated chromatin from hES-RPE cells was immunoprecipitated with rabbit anti SOX9 ( Millipore, AB5535 ).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit.

value: ES-derived RPE cells

value: rabbit anti-Sox9 (Millipore, AB5535)


title: 1_V2T1_A (re-analysis of GSM2147571)

value: Ad-CMV-Cre


title: ATAC Mybl2 overexpression replicate 1


title: 1_V4L1_B (re-analysis of GSM2147569)

description:
liver metastasis from CMV TKO line with hyperaccessible chromatin state
merged_bams_0_summits.bed
merged_peaks_filtered_subset.bed

source_name: liver metastasis

value: liver metastasis


title: 1_V3T1_A (re-analysis of GSM2147573)

value: lung tumor

value: FALSE


title: SOX9.IP.rep2.s2


title: 1_V3L1_B (re-analysis of GSM2147567)


title: 1_V2L1_B (re-analysis of GSM2147565)


title: 1_V2L1_A (re-analysis of GSM2147564)


title: SOX9.IP.rep2.s1


title: 1_V4L1_A (re-analysis of GSM2147568)


title: 1_V3L1_A (re-analysis of GSM2147566)


title: SOX9.IP.rep1.s2


title: 1_V1L1_A (re-analysis of GSM2147562)

description:
liver metastasis from CMV TKO line with hyperaccessible chromatin state
merged_bams_0_summits.bed
merged_peaks_filtered_subset.bed
res_V_1vs0_comb.csv


title: SOX9.IP.rep1.s1


title: 1_V1L1_B (re-analysis of GSM2147563)


title: 2_G6T2

description:
primary lung tumor from CGRP TKO line with hypoaccessible chromatin state
merged_bams_1_summits.bed
merged_peaks_filtered_subset.bed
res_G_LvsT_comb.csv

value: Ad-CGRP-Cre

tag: cgrp model (g)

value: tumors  (t) versus mets (l):G_T


title: N2a-Scramble siRNA Rep2

city: XiaMen

first: Honghua

last: zheng

state: FuJian

address: XiaMen University xiang’an campus

institute: Institute of Neuroscience xiamen university

description: Gene expression data from N2a cell line with Scramble siRNA

hyb_protocol: Follow fragmentation, cDNA were hybridized for 16 hr at 45℃ on NimbleGen arrays which  were then washed and stained.

scan_protocol: Raw signal intensities were normalized in RMA method by NimbleScan v2.5

data_processing: Genes that Intensity ≥100.0 in all samples were chosen for further analysis.Contain Box Plot for genesafter filtering.

source_name: N2a-Scramble siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard NimbleGen microarrays protocol from 1-2μg total RNA.

growth_protocol: N2a cells were cultured in DMEM containing 10% FBS and maintainded ina 5%CO2 incubator at 37℃

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Transfected  scramble siRNA and Men1 siRNA into Neuro2a cell line respectively

tag: cell line

value: mouse neuroblastoma N2a cells

value: control


title: N2a-Men1 siRNA Rep1

description: Gene expression data from N2a cell line with Men1-siRNA

source_name: N2a-Men1 siRNA

value: Men1 knockdown


title: N2a-Men1 siRNA Rep2


title: 2_G6T1


title: SOX9.IP.rep3.s1


title: 2_G3T2


title: 2_G6L1

description:
liver metastasis from CGRP TKO line with hypoaccessible chromatin state
merged_bams_1_summits.bed
merged_peaks_filtered_subset.bed
res_G_LvsT_comb.csv

value: tumors  (t) versus mets (l):G_L


title: 2_G6L2


title: 2_G2T2


title: 2_G3L2


title: 2_G2L2


title: 2_G3L3


title: 2_G2L1


title: 2_G1T1


title: 2_G1T2


title: input.s2


title: input.s1


title: 2_G6L34


title: 2_G2T1


title: ProNeut_Neutrophil1

city: La Jolla

first: Huy

middle: Q

last: Dinh

address: 9420 Athena Circle

department: Division of Inflammation Biology

institute: La Jolla Institute

data_processing:
Read quality was QC using FastQC 0.11.7
Read mapping was done by Rsubread 1.30.5
CPM counts (log) was calculated using FeatureCount 1.22.2 and edgeR 1.30.5
Genes with at least 2 samples with CPM>1 were kept for downstream analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: NeP_log2_cpm.txt: tab-delimited text files includes log2 CPM for each samples (Column names: Gene ID, Gene Symbol, and 15 samples as described in the SAMPLES section)

extract_protocol: Universal Plus mRNA-Seq (Nugen)

treatment_protocol: Five Mouse cell subsets were FACS sorted from healthy mice fresh BM.

value: Bone marrow


title: PreNeut_Neutrophil1


title: PreNeut_Neutrophil2


title: Neutrophil_2

description: BM Neuts

source_name: Neutrophil

value: Neutrophil