title: WT_2_D10

description:
WT_unadj.counts.gz
WT_2_D10


title: WT_2_D1

status: Public on Aug 28 2018

type: SRA

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
WT_unadj.counts.gz
WT_2_D1

library_source: transcriptomic

data_processing:
QC was performed using FastQC and Trimmomatic
RNA-seq reads were aligned using HISAT (version 0.1.6) and ChIP-seq peaks were pre-aligned using BWA (version 0.5.9) and Stampy (--bamkeepgoodreads)
Single cell RNA-seq outliers were identified using robust PCA on alignment proportion, ERCC92 spike-in proportion, number of detectable genes, proportion of reads mapping to protein-coding genes, proportion of mitochondrial transcripts, proportion of ribosomal transcripts, 3’ to 5’ coverage bias, transcriptomic variance, cell-to-mean correlation, the proportion of the library accounted for by the top 500 transcripts and GC content. Cells passing QC are listed in the associated counts matrix (WT_unadj.counts.gz).
RNA-seq reads were assigned to genes using HTSeq (intersection non-empty)
ChIP-seq and ATAC-seq bigWig profiles and peak-calls were generated using MACS2 on deduplicated BAM files with MAPQ >10
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited files include counts for RNA-seq samples, bigWig files show ChIP/input signal and bigBed files show peak calls for ChIP-seq samples

molecule: polyA RNA

organism: Mus musculus

source_name: mTEChi

extract_protocol:
Thymic lobes were cleaned from fatty tissues and incubated with Liberase and DNaseI (Roche Diagnostics; 200μg/ml and 30μg/ml, respectively; 45min, 37ºC) to obtain a cell suspension which was subsequently filtered through a nylon mesh (100micro pore size, Sefar Nitex) to remove debris. TEC were sorted and then RNA was either isolated from single cells using the SMART-seq2 protocol. TEC for ChIP-seq and ATAC-seq were treated as detailed in Žuklys S et al. Nature Immunology 2016:17(10):1206-1215
RNA-seq libraries were prepared using the appropriate Illumina kit for SMART-seq2 or HiSeq2500 (ChIP-seq). Nextera adapters were used for single cell RNA-seq, ATAC-seq and ChIP-seq.

treatment_protocol: ChIP antibodies were (histone modification, company, cat #): H3K4me3, Diagenode, C15410003; H3K27me3, Millipore, 07-449; H3K4me1, Abcam, ab8895; H3K9ac, Abcam, ab4441; H3K4ac, Millipore, 07-539; H3K9me3, Millipore, 05-1242; H3K27ac, Abcam, ab4729.

tag: strain

tag: genotype

value: wild-type

tag: sample type

tag: cell type

value: mTEChi


title: WT_2_C8

description:
WT_unadj.counts.gz
WT_2_C8


title: WT_2_C6

description:
WT_unadj.counts.gz
WT_2_C6


title: WT_2_C7

description:
WT_unadj.counts.gz
WT_2_C7


title: WT_2_C5

description:
WT_unadj.counts.gz
WT_2_C5


title: WT_2_C4

description:
WT_unadj.counts.gz
WT_2_C4


title: WT_2_C3

description:
WT_unadj.counts.gz
WT_2_C3


title: WT_2_C12

description:
WT_unadj.counts.gz
WT_2_C12


title: WT_2_B8

description:
WT_unadj.counts.gz
WT_2_B8


title: WT_2_B9

description:
WT_unadj.counts.gz
WT_2_B9


title: WT_2_C2

description:
WT_unadj.counts.gz
WT_2_C2


title: WT_2_B7

description:
WT_unadj.counts.gz
WT_2_B7


title: WT_2_C11

description:
WT_unadj.counts.gz
WT_2_C11


title: WT_2_C10

description:
WT_unadj.counts.gz
WT_2_C10


title: WT_2_B3

description:
WT_unadj.counts.gz
WT_2_B3


title: WT_2_C1

description:
WT_unadj.counts.gz
WT_2_C1


title: WT_2_B1

description:
WT_unadj.counts.gz
WT_2_B1


title: WT_2_B6

description:
WT_unadj.counts.gz
WT_2_B6


title: WT_2_C9

description:
WT_unadj.counts.gz
WT_2_C9


title: WT_2_B5

description:
WT_unadj.counts.gz
WT_2_B5


title: WT_2_B4

description:
WT_unadj.counts.gz
WT_2_B4


title: WT_2_B11

description:
WT_unadj.counts.gz
WT_2_B11


title: WT_2_A8

description:
WT_unadj.counts.gz
WT_2_A8


title: WT_2_A5

description:
WT_unadj.counts.gz
WT_2_A5


title: WT_2_A9

description:
WT_unadj.counts.gz
WT_2_A9


title: WT_2_A4

description:
WT_unadj.counts.gz
WT_2_A4


title: WT_2_A2

description:
WT_unadj.counts.gz
WT_2_A2


title: WT_2_A12

description:
WT_unadj.counts.gz
WT_2_A12


title: WT_2_A3

description:
WT_unadj.counts.gz
WT_2_A3


title: WT_2_A6

description:
WT_unadj.counts.gz
WT_2_A6


title: WT_2_A11

description:
WT_unadj.counts.gz
WT_2_A11


title: WT_2_A10

description:
WT_unadj.counts.gz
WT_2_A10


title: WT_1_H8

description:
WT_unadj.counts.gz
WT_1_H8


title: WT_1_H9

description:
WT_unadj.counts.gz
WT_1_H9


title: WT_1_H7

description:
WT_unadj.counts.gz
WT_1_H7


title: WT_1_H6

description:
WT_unadj.counts.gz
WT_1_H6


title: WT_1_H4

description:
WT_unadj.counts.gz
WT_1_H4


title: WT_2_B2

description:
WT_unadj.counts.gz
WT_2_B2


title: WT_2_B12

description:
WT_unadj.counts.gz
WT_2_B12


title: WT_1_H5

description:
WT_unadj.counts.gz
WT_1_H5


title: WT_2_A7

description:
WT_unadj.counts.gz
WT_2_A7


title: WT_1_H3

description:
WT_unadj.counts.gz
WT_1_H3


title: Colon organoid flagellin #4

city: Berkeley

first: Gregory

last: Barton

state: CA

department: Molecular and Cell Biology

country: USA

institute: UC Berkeley

data_processing:
Base calling was performed using CASAVA bcl2fastq_v2.17
Alignment was performed with Kallisto 0.43.0, with 20 bootstraps
Genome_build: Mus_musculus.GRCm38_rel84
Supplementary_files_format_and_content: h5 files, output from Kallisto

molecule: total RNA

source_name: intestinal organoid

growth_protocol: SI and colon organoids were incubated in Advanced DMEM/F12 (Life Technologies) supplemented with glutamine, penicillin/streptomycin, HEPES, B-27 (Life Technologies), N-acetylcysteine (Sigma), mouse epidermal growth factor (Life Technologies), mouse Noggin (R&D Systems) and 10% conditioned media from 293T cells expressing human R-spondin 1 (obtained from Calvin Kuo, Stanford University). Paneth cell skewed organoids were grown in the additional presence of CHIR99021 (Stemgent) and valproic acid (Sigma) .

extract_protocol:
Organoids were washed with warm PBS and incubated in Cell Recovery Solution (Corning) for 30 minutes at 4C with slow rocking. Organoids were then moved into 15 mL conicals, and gently dissociated with repeated pipetting. Cells were washed twice in cold PBS before resuspending in RNAzol (Molecular Research Center), homogenized by passage through a 25 gauge needle, and stored at -80 C until RNA isolation. RNA was isolated using a DirectZol RNA purification kit (Zymo Research). RNA was treated with Turbo DNAse (Thermo Fisher) for 30 minutes and purified using a RNA Clean and Concentrator kit (Zymo Research). Total RNA was used for RNA-sequencing.
1 ug of total RNA was used for rRNA depletion with the RiboZero depletion kit to prepare RNA-sequencing library by using the TruSeq RNA sample prep kit (Illumina) according to manufacturer’s instructions. 50-cycle single-end RNA sequencing was performed on a HiSeq 4000 (Illumina).

treatment_protocol: Organoids were left unstimulated or were stimulated by adding 100 ng/mL Ultrapure flagellin (Invivogen) to the culture medium for 4 hours.

tag: tissue

value: intestinal organoid

tag: type of organoid

value: colon

tag: stimulation

value: flagellin


title: Colon organoid flagellin #2


title: Colon organoid flagellin #3


title: WT_2_B10

description:
WT_unadj.counts.gz
WT_2_B10


title: WT_1_H2

description:
WT_unadj.counts.gz
WT_1_H2


title: Colon organoid flagellin #1


title: WT_1_H12

description:
WT_unadj.counts.gz
WT_1_H12


title: WT_1_H10

description:
WT_unadj.counts.gz
WT_1_H10


title: Colon organoid unstim #4

value: unstimulated


title: WT_1_H11

description:
WT_unadj.counts.gz
WT_1_H11


title: WT_1_H1

description:
WT_unadj.counts.gz
WT_1_H1


title: Colon organoid unstim #3


title: Colon organoid unstim #2


title: WT_2_A1

description:
WT_unadj.counts.gz
WT_2_A1


title: WT_1_G9

description:
WT_unadj.counts.gz
WT_1_G9


title: Paneth cell organoid flagellin #6

value: Paneth cell skewed


title: Colon organoid unstim #1


title: WT_1_G7

description:
WT_unadj.counts.gz
WT_1_G7


title: WT_1_G6

description:
WT_unadj.counts.gz
WT_1_G6


title: WT_1_G5

description:
WT_unadj.counts.gz
WT_1_G5


title: Paneth cell organoid flagellin #5


title: Paneth cell organoid flagellin #3


title: WT_1_G3

description:
WT_unadj.counts.gz
WT_1_G3


title: WT_1_G8

description:
WT_unadj.counts.gz
WT_1_G8


title: WT_1_G4

description:
WT_unadj.counts.gz
WT_1_G4


title: WT_1_G2

description:
WT_unadj.counts.gz
WT_1_G2


title: Paneth cell organoid flagellin #1


title: Paneth cell organoid unstim #6


title: Paneth cell organoid unstim #5


title: WT_1_G11

description:
WT_unadj.counts.gz
WT_1_G11


title: WT_1_G12

description:
WT_unadj.counts.gz
WT_1_G12


title: WT_1_G10

description:
WT_unadj.counts.gz
WT_1_G10


title: WT_1_G1

description:
WT_unadj.counts.gz
WT_1_G1


title: Paneth cell organoid unstim #2


title: Paneth cell organoid unstim #3


title: WT_1_F9

description:
WT_unadj.counts.gz
WT_1_F9


title: Paneth cell organoid unstim #1


title: WT_1_F8

description:
WT_unadj.counts.gz
WT_1_F8


title: SI organoid flagellin #3

value: small intestine


title: WT_1_F7

description:
WT_unadj.counts.gz
WT_1_F7


title: Paneth cell organoid flagellin #4


title: WT_1_F6

description:
WT_unadj.counts.gz
WT_1_F6


title: SI organoid flagellin #2


title: Paneth cell organoid flagellin #2


title: WT_1_F5

description:
WT_unadj.counts.gz
WT_1_F5


title: WT_1_F4

description:
WT_unadj.counts.gz
WT_1_F4


title: SI organoid flagellin #1


title: SI organoid unstim #2


title: WT_1_F3

description:
WT_unadj.counts.gz
WT_1_F3


title: SI organoid unstim #1


title: WT_1_F2

description:
WT_unadj.counts.gz
WT_1_F2


title: Paneth cell organoid unstim #4


title: WT_1_F12

description:
WT_unadj.counts.gz
WT_1_F12


title: WT_1_F11

description:
WT_unadj.counts.gz
WT_1_F11


title: WT_1_F10

description:
WT_unadj.counts.gz
WT_1_F10


title: WT_1_F1

description:
WT_unadj.counts.gz
WT_1_F1


title: Colon IEC 4 weeks #1

data_processing:
Base calling was performed using CASAVA bcl2fastq_v2.17
Sequenced reads were quality-trimmed (cut-off of 30) with cutadapt 1.1
Alignment was performed with Kallisto 0.43.0, with 30 bootstraps
Genome_build: Mus_musculus.GRCm38.cdna_rel84
Supplementary_files_format_and_content: h5 files, output from Kallisto

source_name: intestinal epithelial cells

extract_protocol:
SI or colons were harvested from mice, flushed with PBS, cut open longitudinally, and incubated with 3 mM EDTA and 1 mM DTT for 30 minutes at 4C on a rocker. Supernatants were then passed through a 100 micron filter and centrifuged at 650xg for 5 minutes.  IECs were then resuspended in RNAzol, homogenized by passing repeatedly through a 25-gauge needle, and stored at -80C until RNA was isolated. RNA was isolated using a DirectZol RNA purification kit (Zymo Research). RNA was treated with Turbo DNAse (Thermo Fisher) for 30 minutes and purified using a RNA Clean and Concentrator kit (Zymo Research).
1 ug of total RNA was used for rRNA depletion with the RiboZero depletion kit to prepare RNA-sequencing library by using the TruSeq RNA sample prep kit (Illumina) according to manufacturer’s instructions; 50-cycle single-end RNA sequencing was performed on a HiSeq 4000 (Illumina)

tag: cells

value: intestinal epithelial cells

tag: age

value: 4 weeks

value: wildtype


title: Colon IEC 8 weeks #1

value: 8 weeks


title: SI IEC 8 weeks #2


title: WT_1_E9

description:
WT_unadj.counts.gz
WT_1_E9


title: WT_1_E7

description:
WT_unadj.counts.gz
WT_1_E7


title: SI IEC 4 weeks #1


title: SI IEC 4 weeks #2


title: WT_1_E6

description:
WT_unadj.counts.gz
WT_1_E6


title: WT_1_E8

description:
WT_unadj.counts.gz
WT_1_E8


title: SI IEC 8 weeks #1


title: SI organoid unstim #3


title: WT_1_E4

description:
WT_unadj.counts.gz
WT_1_E4


title: F36: Primary Cortical Neurons

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

description: Mouse primary cortical neurons were overexpressed with miR-203 or scrambled miRNA (Control) using lentiviral construct. Cells were infected at DIV0 and treated with SAHA at 2 doses and RNA isolated at DIV8 . 4 independent replicates (biological) were used for the study.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using RNA-STAR v 2.2
Counts were estimated using RNA-STAR
Genes were kept if they were expressed in 80% of the samples with >10 reads. The resulting read counts were normalized for library size using cqn function of CQN R package in R to get fragments per kilobase million mapped reads (FPKM) values. Log2 transformed FPKM values were corrected for batch and sequencing biases using linear model in  R.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include Normalized log2 FPKM values for each Sample ...

source_name: Primary Cortical Neurons

extract_protocol:
Total RNA was isolated using Nucleospin RNA XS kit, Takara following manufacture's protocol
RNA libraries were prepared for sequencing using Stranded poly-A library preparation kit, Illumina
75-bp paired end Stranded RNA-Seq using HiSeq4000

value: Primary Cortical Neurons

tag: construct

value: controlhigh

tag: saha dose

tag: batch


title: WT_1_E5

description:
WT_unadj.counts.gz
WT_1_E5


title: WT_1_E3

description:
WT_unadj.counts.gz
WT_1_E3


title: Colon IEC 8 weeks #2


title: F32: Primary Cortical Neurons


title: F34: Primary Cortical Neurons

value: DMSO


title: WT_1_E12

description:
WT_unadj.counts.gz
WT_1_E12


title: WT_1_E2

description:
WT_unadj.counts.gz
WT_1_E2


title: F35: Primary Cortical Neurons


title: F33: Primary Cortical Neurons


title: WT_1_E11

description:
WT_unadj.counts.gz
WT_1_E11


title: WT_1_E10

description:
WT_unadj.counts.gz
WT_1_E10


title: F29: Primary Cortical Neurons


title: F31: Primary Cortical Neurons

value: controlintermediate


title: F30: Primary Cortical Neurons


title: WT_1_E1

description:
WT_unadj.counts.gz
WT_1_E1


title: F27: Primary Cortical Neurons


title: WT_1_D9

description:
WT_unadj.counts.gz
WT_1_D9


title: Colon IEC 4 weeks #2


title: WT_1_D8

description:
WT_unadj.counts.gz
WT_1_D8


title: F25: Primary Cortical Neurons


title: WT_1_D7

description:
WT_unadj.counts.gz
WT_1_D7


title: F24: Primary Cortical Neurons


title: WT_1_D6

description:
WT_unadj.counts.gz
WT_1_D6


title: F23: Primary Cortical Neurons


title: WT_1_D5

description:
WT_unadj.counts.gz
WT_1_D5


title: WT_1_D4

description:
WT_unadj.counts.gz
WT_1_D4


title: F22: Primary Cortical Neurons


title: F21: Primary Cortical Neurons


title: WT_1_D3

description:
WT_unadj.counts.gz
WT_1_D3


title: F20: Primary Cortical Neurons


title: WT_1_D12

description:
WT_unadj.counts.gz
WT_1_D12


title: F18: Primary Cortical Neurons


title: WT_1_D11

description:
WT_unadj.counts.gz
WT_1_D11


title: F17: Primary Cortical Neurons


title: F16: Primary Cortical Neurons


title: WT_1_D10

description:
WT_unadj.counts.gz
WT_1_D10


title: WT_1_C9

description:
WT_unadj.counts.gz
WT_1_C9


title: WT_1_D1

description:
WT_unadj.counts.gz
WT_1_D1


title: F26: Primary Cortical Neurons


title: F14: Primary Cortical Neurons


title: F13: Primary Cortical Neurons


title: WT_1_C7

description:
WT_unadj.counts.gz
WT_1_C7


title: WT_1_C8

description:
WT_unadj.counts.gz
WT_1_C8


title: F15: Primary Cortical Neurons


title: F12: Primary Cortical Neurons


title: WT_1_C5

description:
WT_unadj.counts.gz
WT_1_C5


title: F10: Primary Cortical Neurons


title: WT_1_C4

description:
WT_unadj.counts.gz
WT_1_C4


title: F11: Primary Cortical Neurons


title: F9: Primary Cortical Neurons


title: F8: Primary Cortical Neurons


title: WT_1_D2

description:
WT_unadj.counts.gz
WT_1_D2


title: F19: Primary Cortical Neurons


title: WT_1_C3

description:
WT_unadj.counts.gz
WT_1_C3


title: F7: Primary Cortical Neurons


title: WT_1_C2

description:
WT_unadj.counts.gz
WT_1_C2


title: WT_1_C11

description:
WT_unadj.counts.gz
WT_1_C11


title: WT_1_C12

description:
WT_unadj.counts.gz
WT_1_C12


title: F5: Primary Cortical Neurons


title: WT_1_C10

description:
WT_unadj.counts.gz
WT_1_C10


title: WT_1_C1

description:
WT_unadj.counts.gz
WT_1_C1


title: F4: Primary Cortical Neurons


title: F6: Primary Cortical Neurons


title: F2: Primary Cortical Neurons


title: WT_1_C6

description:
WT_unadj.counts.gz
WT_1_C6


title: WT_1_B8

description:
WT_unadj.counts.gz
WT_1_B8


title: WT_1_B6

description:
WT_unadj.counts.gz
WT_1_B6


title: F3: Primary Cortical Neurons


title: F1: Primary Cortical Neurons


title: WT_1_B7

description:
WT_unadj.counts.gz
WT_1_B7


title: WT_1_B5

description:
WT_unadj.counts.gz
WT_1_B5


title: WT_1_B3

description:
WT_unadj.counts.gz
WT_1_B3


title: WT_1_B4

description:
WT_unadj.counts.gz
WT_1_B4


title: WT_1_B2

description:
WT_unadj.counts.gz
WT_1_B2


title: WT_1_B12

description:
WT_unadj.counts.gz
WT_1_B12


title: WT_1_B11

description:
WT_unadj.counts.gz
WT_1_B11


title: WT_1_B10

description:
WT_unadj.counts.gz
WT_1_B10


title: WT_1_A7

description:
WT_unadj.counts.gz
WT_1_A7


title: WT_1_A8

description:
WT_unadj.counts.gz
WT_1_A8


title: WT_1_B1

description:
WT_unadj.counts.gz
WT_1_B1


title: WT_1_A9

description:
WT_unadj.counts.gz
WT_1_A9


title: WT_1_A4

description:
WT_unadj.counts.gz
WT_1_A4


title: WT_1_A3

description:
WT_unadj.counts.gz
WT_1_A3


title: WT_1_A12

description:
WT_unadj.counts.gz
WT_1_A12


title: WT_1_A2

description:
WT_unadj.counts.gz
WT_1_A2


title: WT_1_A5

description:
WT_unadj.counts.gz
WT_1_A5


title: WT_1_B9

description:
WT_unadj.counts.gz
WT_1_B9


title: WT_1_A11

description:
WT_unadj.counts.gz
WT_1_A11


title: WT_1_A10

description:
WT_unadj.counts.gz
WT_1_A10


title: mTEClo_input-2

description: TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

library_source: genomic

molecule: genomic DNA

source_name: mTEClo

value: input

value: mTEClo

tag: chip antibody


title: WT_1_A1

description:
WT_unadj.counts.gz
WT_1_A1

value: wild-type

value: mTEChi


title: mTEClo_H3K4me3-2

description: mTEClo_H3K4me3-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

value: H3K4me3, Diagenode, C15410003


title: mTEClo_H3K9ac-1

description: mTEClo_H3K9ac-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

value: H3K9ac, Abcam, ab4441


title: mTEClo_input-1


title: mTEClo_H3K4me3-1


title: mTEClo_H3K4me1-2

description: mTEClo_H3K4me1-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

value: H3K4me1, Abcam, ab8895


title: mTEClo_H3K4me1-1


title: y1808: dpb3∆ without HU 40min H3K4me3 eSPAN repeat

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis.
The sequence reads mapped to the Watson and Crick strands of the reference genome were separated by in-house Perl programs and then genome-wide reads coverage was calculated by BEDTools and in-house Perl  programs.
To obtain the nucleosome occupancy, DNA fragments from 120 to 170 bp in size determined by the paired-reads were firstly selected for calculation. The length of DNA fragments were then adjusted to half of the nucleosome size (74bp) to increase the signal-to-noise ratio. Finally, the count of adjusted DNA fragments covering each base pair in the genome were used to calculate the nucleosome occupancy.
To identify BrdU-IP-ssSeq peaks, the sequence reads of both Watson and Crick strands were merged and used to call peaks using SICER software with false discovery rate (FDR) cut-off 0.01.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated for Watson and Crick strand, scores represent the normalization reads density.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: To synchronize cells at G1, alpha factor was added at cell density OD600=0.4-0.5 to achieve a final concentration of five µg/mL for yeast strains.  After three hours arrest at 25°C, the cells were released to fresh YPD medium with or without 200 mM HU.  For the histone H3 Recombination-induced Tag Exchange (RITE) experiments, yeast cells were grown overnight in YPD in the presence of hygromycin B (200 μg/mL, Invitrogen). The cells were then diluted 1:10 into two fresh YPD flask (one with, the other without hygromycin B) and incubated for 32 hours (G0 state). The cells were centrifuged by 3000 rpm for 10 minutes. The cells cultured with hygromycin B were transferred to another flask containing depleted medium without hygromycin B. Recombination was induced by the addition of 1 μM β-estradiol (E-8875, Sigma-Aldrich) and the cells were cultured for additional 16 hours. Subsequently, these cells were diluted 1:25 in fresh YPD media containing 200 mM HU and 400ul/ml BrdU. After incubation at 25 C for 90 minutes, samples were collected for ChIP and eSPAN.

extract_protocol:
All ChIP and eSPAN assays were performed as described previously except that Mnase digestion was used for chromatin fragmentation in order to map nucleosomes. Briefly, the samples were incubated with 1% fresh-made formaldehyde at 25 °C for 20 min, and then quenched with 0.125M glycine for five min.  The cells wer harvested and lysed with glass beads in ChIP lysis buffer (50 mM HEPES, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate). The resulting cell and chromatin pellet was washed with NP buffer (1.6 M sorbitol, 2 mM CaCl2, 5mM MgCl, 50 mM NaCl, 14 mM β-mercaptoethanol, 10 mM Tris-HCl (pH 7.4), 0.075% NP-40, 5 mM spermidine).  Proper amounts of Mnase was added to ensure that majority of chromatin are mono- and di-nucleosomes with incubation at 37 °C for 20 min . The reacation was terminated by adding 5ul 0.5M EDTA. Further, ¼ volume 5X ChIP lysis buffer was added into dilute thedigested chromatin. The lysates was incubated in ice for 30 minutes. After clarification of lysates by centrifugation, soluble chromatin (mainly mononucleosomes) was immunoprecipitated with a specific antibody including anti-H3K4me3 antibody (ab8580), anti-H3K56ac antibody (6), anti-HA antibody (12CA5) or anti-T7 (A190-117A BETHYL)). ChIP DNA was recovered using Chelex-100. The ChIP or total DNA was denatured at 100°C for five min and was immediately transferred to ice bath for five minutes.  The DNA was diluted at least ten times with BrdU IP solution (PBS, 0.0625% Triton X-100(v/v), 6.7 g/mL Escherichia. coli tRNA, 0.67 ul/mL BrdU antibody (BD Bioscience)).  After the samples were incubated at 4°C for two hour, 20 uL protein G beads (GE Healthcare) were added.  After incubation at 4°C for another hour, the protein G beads was washed extensively. DNA were eluted using 100 uL 1XTE buffer plus 1% SDS and incubation at 65 °C for 15 min. Eluted DNA was purified using a Qiagen Mini-elute kit.
We used the ssDNA library preparation kit to prepare library (Cat no. 10096 Swift Bioscience). The ssDNA libraries were sequenced using the paired-end method by different sequencing platform over the years including Illumina NextSeq 500, Hi-seq 2000 or 2500 machine at Mayo Clinic or Columbia University.

tag: media

value: YPD

tag: cell cycle stage

value: S

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: y1814: dpb3∆ without HU 40min H3K56ac eSPAN repeat

value: Anti-H3K56ac and Anti-BrdU Antibody


title: y1807: dpb3∆ without HU 30min H3K4me3 eSPAN repeat


title: y1881: dpb3∆ without HU 30min H3K56ac eSPAN repeat


title: y1790: dpb3∆ without HU 40min H3K4me3 ChIP-ssSeq repeat

value: Anti-H3K4me3 Antibody (ab8580)


title: WT_1_A6

description:
WT_unadj.counts.gz
WT_1_A6


title: mTEClo_H3K27me3-2

description: mTEClo_H3K27me3-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

value: H3K27me3, Millipore, 07-449


title: y1789: dpb3∆ without HU 30min H3K4me3 ChIP-ssSeq repeat


title: y1796: dpb3∆ without HU 40min H3K56ac ChIP-ssSeq repeat

value: Anti-H3K56ac antibody


title: mTEClo_H3K27me3-1


title: mTEClo_H3K27ac-2

description: mTEClo_H3K27ac-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

value: H3K27ac, Abcam, ab4729


title: mTEClo_H3K27ac-1


title: y1802: dpb3∆ without HU 40min BrdU-IP-ssSeq repeat

value: Anti-BrdU (BD BioScience, 347580)


title: y1795: dpb3∆ without HU 30min H3K56ac ChIP-ssSeq repeat


title: y1837: dpb3∆ without HU 30min BrdU-IP-ssSeq repeat


title: mTEChi_K9me3-3

description: mTEChi_K9me3-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

value: H3K9me3, Millipore, 05-1242


title: mTEClo_H3K9ac-2


title: y1784: dpb3∆ without HU 40min input MNase-ssSeq repeat


title: mTEChi_K9me3-2


title: mTEChi_K9me3-1


title: mTEChi_K9ac-3

description: mTEChi_K9ac-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb


title: y1783: dpb3∆ without HU 30min input MNase-ssSeq repeat


title: mTEChi_K9ac-2


title: mTEChi_K9ac-1


title: mTEChi_K4me1-1

description: mTEChi_K4me1-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb


title: mTEChi_K4ac-1

description: mTEChi_K4ac-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

value: H3K4ac, Millipore, 07-539


title: y1723: WT Dpb3 eSPAN

data_processing:
Library strategy: eSPAN
Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis.
The sequence reads mapped to the Watson and Crick strands of the reference genome were separated by in-house Perl programs and then genome-wide reads coverage was calculated by BEDTools and in-house Perl  programs.
To obtain the nucleosome occupancy, DNA fragments from 120 to 170 bp in size determined by the paired-reads were firstly selected for calculation. The length of DNA fragments were then adjusted to half of the nucleosome size (74bp) to increase the signal-to-noise ratio. Finally, the count of adjusted DNA fragments covering each base pair in the genome were used to calculate the nucleosome occupancy.
To identify BrdU-IP-ssSeq peaks, the sequence reads of both Watson and Crick strands were merged and used to call peaks using SICER software with false discovery rate (FDR) cut-off 0.01.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated for Watson and Crick strand, scores represent the normalization reads density.

extract_protocol:
All ChIP and eSPAN assays were performed as described previously except that Mnase digestion was used for chromatin fragmentation in order to map nucleosomes. Briefly, the samples were incubated with 1% fresh-made formaldehyde at 25 °C for 20 min, and then quenched with 0.125M glycine for five min.  The cells wer harvested and lysed with glass beads in ChIP lysis buffer (50 mM HEPES, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate). The resulting cell and chromatin pellet was washed with NP buffer (1.6 M sorbitol, 2 mM CaCl2, 5mM MgCl, 50 mM NaCl, 14 mM β-mercaptoethanol, 10 mM Tris-HCl (pH 7.4), 0.075% NP-40, 5 mM spermidine).  Proper amounts of Mnase was added to ensure that majority of chromatin are mono- and di-nucleosomes with incubation at 37 °C for 20 min . The reacation was terminated by adding 5ul 0.5M EDTA. Further, ¼ volume 5X ChIP lysis buffer was added into dilute thedigested chromatin. The lysates was incubated in ice for 30 minutes. After clarification of lysates by centrifugation, soluble chromatin (mainly mononucleosomes) was immunoprecipitated with a specific antibody including anti-H3K4me3 antibody (ab8580), anti-H3K56ac antibody (6), anti-HA antibody (12CA5) or anti-T7 (A190-117A BETHYL)). ChIP DNA was recovered using Chelex-100. The ChIP or total DNA was denatured at 100°C for five min and was immediately transferred to ice bath for five minutes.  The DNA was diluted at least ten times with BrdU IP solution (PBS, 0.0625% Triton X-100(v/v), 6.7 g/mL Escherichia. coli tRNA, 0.67 ul/mL BrdU antibody (BD Bioscience)).  After the samples were incubated at 4°C for two hour, 20 uL protein G beads (GE Healthcare) were added.  After incubation at 4°C for another hour, the protein G beads was washed extensively. DNA were eluted using 100 uL 1XTE buffer plus 1% SDS and incubation at 65 °C for 15 min. Eluted DNA was purified using a Qiagen Mini-elute kit.
We used the ssDNA library preparation kit to prepare library (Cat no. 10096 Swift Bioscience). The ssDNA libraries were sequenced using the paired-end method by different sequencing platform over the years including Illumina NextSeq 500 or HiSeq 2000 machine at Mayo Clinic or Columbia University.

value: YPD+HU

value: Anti-HA and BrdU antibody


title: y1727: WT Dpb4 eSPAN


title: y1721: WT Dpb3 ChIP-ssSeq

value: Anti-HA antibody(12CA5)


title: y1722: WT sonication BrdU-IP-ssSeq repeat 1

data_processing:
Library strategy: BrdU ChIP-seq
Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis.
The sequence reads mapped to the Watson and Crick strands of the reference genome were separated by in-house Perl programs and then genome-wide reads coverage was calculated by BEDTools and in-house Perl  programs.
To obtain the nucleosome occupancy, DNA fragments from 120 to 170 bp in size determined by the paired-reads were firstly selected for calculation. The length of DNA fragments were then adjusted to half of the nucleosome size (74bp) to increase the signal-to-noise ratio. Finally, the count of adjusted DNA fragments covering each base pair in the genome were used to calculate the nucleosome occupancy.
To identify BrdU-IP-ssSeq peaks, the sequence reads of both Watson and Crick strands were merged and used to call peaks using SICER software with false discovery rate (FDR) cut-off 0.01.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated for Watson and Crick strand, scores represent the normalization reads density.


title: y1725: WT Dpb4 ChIP-ssSeq


title: mTEChi_K27me3-2

description: mTEChi_K27me3-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

value: wild-type

value: mTEChi


title: y1724: WT sonication input ssSeq repeat 2


title: y1720: WT sonication input ssSeq repeat 1


title: y1726: WT sonication BrdU-IP-ssSeq repeat 2


title: y1558: Tagging swithching system dpb3∆ HA eSPAN repeat 2


title: y1557: Tagging swithching system dpb3∆ T7 eSPAN repeat 2

value: Anti-T7 and BrdU antibody


title: mTEChi_K27me3-1


title: mTEChi_input-4

value: input


title: mTEChi_input-3


title: y1559: Tagging swithching system dpb3∆ H3K4me3 eSPAN repeat 2

value: S


title: mTEChi_input-5


title: y1552: Tagging swithching system dpb3∆ T7 ChIP-ssSeq repeat 2

value: Anti-T7 antibody(A190-117A)


title: y1560: Tagging swithching system dpb3∆ H3K56ac eSPAN repeat 2

value: Anti-H3K56ac and Anti-BrdU Antibody


title: mTEChi_input-2


title: cTEClo_input-1

source_name: cTEClo

value: cTEClo


title: y1553: Tagging swithching system dpb3∆ HA ChIP-ssSeq repeat 2


title: mTEChi_K4me1-2

value: H3K4me1, Abcam, ab8895


title: mTEChi_K4ac-2


title: cTEClo_H3K4me1-1

description: cTEClo_H3K4me1-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb


title: y1555: Tagging swithching system dpb3∆ H3K56ac ChIP-ssSeq repeat 2

value: Anti-H3K56ac antibody


title: cTEClo_H3K27ac-1

description: cTEClo_H3K27ac-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

value: H3K27ac, Abcam, ab4729


title: cTEChi_input-1

source_name: cTEChi

value: cTEChi


title: y1556: Tagging swithching system dpb3∆ BrdU-IP-ssSeq repeat 2

value: Anti-BrdU (BD BioScience, 347580)


title: y1551: Tagging swithching system dpb3∆ input MNase-ssSeq repeat 2


title: y1700: Tagging swithching system dpb3∆ H3K4me3 eSPAN  repeat 1

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: y1699: Tagging swithching system dpb3∆ HA eSPAN  repeat 1

value: YPD+HU


title: y1698: Tagging swithching system dpb3∆ T7 eSPAN  repeat 1


title: y1694: Tagging swithching system dpb3∆ HA ChIP-ssSeq  repeat 1


title: y1701: Tagging swithching system dpb3∆ H3K56ac eSPAN  repeat 1


title: c196_H3K4me1-1

description: c196_H3K4me1-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb

value: see Zuklys S et al. Nature Immunology 2016:17(10):1206-1215

value: cTEC


title: c196_input-1


title: c196_H3K4me1-2


title: mTEChi_input-1

value: wild-type


title: c196_H3K27ac-2

description: c196_H3K27ac-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb


title: y1554: Tagging swithching system dpb3∆ H3K4me3 ChIP-ssSeq repeat 2

value: Anti-H3K4me3 Antibody (ab8580)


title: c196_H3K27ac-1


title: B6_input-2

source_name: cTEC


title: y1697: Tagging swithching system dpb3∆ BrdU-IP-ssSeq  repeat 1


title: B6_input-1


title: y1695: Tagging swithching system dpb3∆ H3K4me3 ChIP-ssSeq  repeat 1


title: B6_H3K4me1-2

description: B6_H3K4me1-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb


title: cTEChi_H3K4me1-1


title: y1692: Tagging swithching system dpb3∆ input MNase-ssSeq repeat 1


title: y1689: Tagging swithching system WT HA eSPAN

value: Anti-HA and BrdU antibody


title: cTEChi_H3K27ac-1


title: c196_input-2

value: input


title: B6_H3K4me1-1


title: y1690: Tagging swithching system WT H3K4me3 eSPAN

value: S


title: B6_H3K27ac-2

description: B6_H3K27ac-1_merged_signal_mapq_10_FE.bw, TEC_histone_marks_IDR_0.01_merged_vs_input_merged_IDR_0.01_MAPQ_10_minus_blacklist.bb, TEC_histone_marks_mapq_10.bb


title: y1691: Tagging swithching system WT H3K56ac eSPAN


title: y1684: Tagging swithching system WT HA ChIP-ssSeq

value: Anti-HA antibody(12CA5)


title: y1693: Tagging swithching system dpb3∆ T7 ChIP-ssSeq  repeat 1

value: Anti-T7 antibody(A190-117A)


title: y1685: Tagging swithching system WT H3K4me3 ChIP-ssSeq


title: B6_H3K27ac-1


title: y1696: Tagging swithching system dpb3∆ H3K56ac ChIP-ssSeq  repeat 1


title: SWHEL-Tomato B cell S98

city: Darlinghurst

first: Tri

middle: Giang

last: Phan

state: New South Wales

address: 384 Victoria St

department: Immunology Division

country: Australia

institute: Garvan Institute

data_processing:
Quality control assessed using FastQC 0.11.3
Sequenced reads were trimmed for adaptor sequence using CutAdapt 1.14 (-n 2, -m 16)
An index reference genome was created by concatenating GRCm38 and the RNA Sequins spike-in nucleotide sequence. Reads were pseudoaligned to this index and transcript abundance was quantified using kallisto 0.43.1
Genome_build: GRCm38 v89
Supplementary_files_format_and_content: tab-delimited text file containing abundance counts

source_name: lymph node

extract_protocol:
single cell sorted and processed using SMART-Seq v4 Ultra Low Input RNA kit. Each sample spiked with Sequin spike-ins (Hardwick et al., Nature Methods, 2016)
sequencing libraries were prepared from 1ng cDNA per sample using the Nextera XT DNA Sample Prep kit

tag: mouse

tag: rna processing batch

tag: pool


title: SWHEL-Tomato B cell S96


title: y1683: Tagging swithching system WT T7 ChIP-ssSeq


title: y1686: Tagging swithching system WT H3K56ac ChIP-ssSeq


title: SWHEL-Tomato B cell S94


title: SWHEL-Tomato B cell S92


title: SWHEL-Tomato B cell S95


title: SWHEL-Tomato B cell S90


title: SWHEL-Tomato B cell S88


title: SWHEL-Tomato B cell S86


title: y1688: Tagging swithching system WT T7 eSPAN

value: Anti-T7 and BrdU antibody


title: SWHEL-Tomato B cell S85


title: y1687: Tagging swithching system WT BrdU-IP-ssSeq


title: y1676: dpb3∆ without HU 30min H3K4me3 eSPAN

value: YPD


title: y1677: dpb3∆ without HU 40min H3K4me3 eSPAN


title: SWHEL-Tomato B cell S84


title: y1682: Tagging swithching system WT input MNase-ssSeq


title: y1678: dpb3∆ without HU 30min H3K56ac eSPAN

value: Anti-H3K56ac and Anti-BrdU Antibody


title: y1679: dpb3∆ without HU 40min H3K56ac eSPAN


title: SWHEL-Tomato B cell S82


title: SWHEL-Tomato B cell S78


title: y1665: dpb3∆ without HU 40min H3K4me3 ChIP-ssSeq


title: y1664: dpb3∆ without HU 30min H3K4me3 ChIP-ssSeq


title: SWHEL-Tomato B cell S73


title: y1667: dpb3∆ without HU 40min H3K56ac ChIP-ssSeq

value: Anti-H3K56ac antibody


title: SWHEL-Tomato B cell S75


title: y1666: dpb3∆ without HU 30min H3K56ac ChIP-ssSeq


title: SWHEL-Tomato B cell S70


title: SWHEL-Tomato B cell S68


title: y1673: dpb3∆ without HU 40min BrdU-IP-ssSeq


title: y1672: dpb3∆ without HU 30min BrdU-IP-ssSeq


title: y1661: dpb3∆ without HU 40min input MNase-ssSeq


title: y1660: dpb3∆ without HU 30min input MNase-ssSeq


title: SWHEL-Tomato B cell S66


title: y1675: WT without HU 40min H3K4me3 eSPAN


title: SWHEL-Tomato B cell S64


title: y1674: WT without HU 30min H3K4me3 eSPAN


title: SWHEL-Tomato B cell S62


title: SWHEL-Tomato B cell S56


title: SWHEL-Tomato B cell S58


title: SWHEL-Tomato B cell S60


title: y1663: WT without HU 40min H3K4me3 ChIP-ssSeq


title: y1681: WT without HU 40min H3K56ac eSPAN


title: SWHEL-Tomato B cell S54


title: SWHEL-Tomato B cell S76


title: y1662: WT without HU 30min H3K4me3 ChIP-ssSeq


title: SWHEL-Tomato B cell S72


title: y1669: WT without HU 40min H3K56ac ChIP-ssSeq


title: SWHEL-Tomato B cell S50


title: y1671: WT without HU 40min BrdU-IP-ssSeq


title: SWHEL-Tomato B cell S42


title: SWHEL-Tomato B cell S48


title: y1670: WT without HU 30min BrdU-IP-ssSeq


title: y1659: WT without HU 40min input MNase-ssSeq


title: y1658: WT without HU 30min input MNase-ssSeq


title: SWHEL-Tomato B cell S41


title: y1440: dpb4∆ H3K4me3 eSPAN


title: SWHEL-Tomato B cell S36


title: SWHEL-Tomato B cell S40


title: SWHEL-Tomato B cell S37


title: y1439: dpb3∆ H3K4me3 eSPAN


title: y1443: dpb4∆ H3K56ac eSPAN


title: y1680: WT without HU 30min H3K56ac eSPAN


title: SWHEL-Tomato B cell S34


title: SWHEL-Tomato B cell S30


title: y1442: dpb3∆ H3K56ac eSPAN


title: SWHEL-Tomato B cell S32


title: y1431: dpb4∆ H3K4me3 ChIP-ssSeq


title: SWHEL-Tomato B cell S28


title: SWHEL-Tomato B cell S52


title: y1430: dpb3∆ H3K4me3 ChIP-ssSeq


title: y1434: dpb4∆ H3K56ac ChIP-ssSeq


title: y1668: WT without HU 30min H3K56ac ChIP-ssSeq


title: y1433: dpb3∆ H3K56ac ChIP-ssSeq


title: SWHEL-Tomato B cell S24


title: y1437: dpb4∆ BrdU-IP-ssSeq


title: SWHEL-Tomato B cell S22


title: y1436: dpb3∆ BrdU-IP-ssSeq


title: SWHEL-Tomato B cell S18


title: SWHEL-Tomato B cell S20


title: SWHEL-Tomato B cell S146


title: y1438: WT H3K4me3 eSPAN repeat 3


title: SWHEL-Tomato B cell S26


title: SWHEL-Tomato B cell S16


title: y1441: WT H3K56ac eSPAN repeat 3


title: SWHEL-Tomato B cell S142


title: SWHEL-Tomato B cell S14


title: y1432: WT H3K56ac ChIP-ssSeq repeat 3


title: SWHEL-Tomato B cell S140


title: y1429: WT H3K4me3 ChIP-ssSeq repeat 3


title: y1435: WT BrdU-IP-ssSeq repeat 3


title: y1428: dpb4∆ input MNase-ssSeq


title: SWHEL-Tomato B cell S138


title: y1426: WT input MNase-ssSeq repeat 3


title: SWHEL-Tomato B cell S136


title: y1427: dpb3∆ input MNase-ssSeq


title: SWHEL-Tomato B cell S134


title: vel_2

type: RNA

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 2 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%).

data_processing: Data processed with FeatureExtraction v9.5 and normalized by quantile normalization of gPRocessed signal using R2.6.1 statistical software.

organism: Mytilus galloprovincialis

source_name: Veliger of Mytilus galloprovincialis

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol.

growth_protocol: Mature mussels were obtained from a commercial shellfish farm in Vigo (NW Spain) during the spawning season. Mussels spawning and larval rearing was performed as detailed in Balseiro et al., 2013.

extract_protocol: Five biological replicates were taken at each developmental stage: oocytes, trochophore, veliger, pediveliger, setted and seed. Larvae were centrifuged at -3000 g for 10 minutes at 4°C. The pellet was resuspended in 250 µl of TRIzol (Invitrogen). Total RNA isolation was conducted following the manufacturer’s specifications in combination with the RNeasy Mini kit (Qiagen) for RNA purification after DNase I treatment. Next, the concentration and purity of the RNA were measured using a NanoDrop ND1000 spectrophotometer. Finally, RNA integrity was tested on an Agilent 2100 Bioanalyzer (Agilent Technologies). Only the samples with high RNA quality and quantity were used for labeling and hybridization. 3 to 5 biological replicates were used for each developmental stage and trochophore samples were discarded due to the low RNA integrity.

value: whole body

tag: developmental stage

value: Veliger larvae (3dpf)


title: SWHEL-Tomato B cell S132


title: settled_2

source_name: Settled Mytilus galloprovincialis

value: Settled juveniles (25dpf)


title: vel_3


title: settled_5


title: SWHEL-Tomato B cell S130


title: settled_4


title: vel_4


title: SWHEL-Tomato B cell S128


title: settled_3


title: settled_1


title: seed_5

source_name: Seed of Mytilus galloprovincialis

value: Seed (30dpf)


title: ER t0 Rep 5 [t0.5]

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

institute: University of York

description:
SLX-15851.D706_D503
ER parallel Factor ChIP with CTCF spike-in 0 minutes after stimulation with Estra-2-diol, replicate 5

data_processing:
Alignement with BWA
Duplicate and blacklist reads removed
Peak calling with MACS2
Differential Binding analysed with DiffBind/Brundle
Genome_build: GRCh38
Supplementary_files_format_and_content: csv of ER peak counts.

organism: Homo sapiens

source_name: MCF7_ER t0

growth_protocol: Grown in stripped DMEM

extract_protocol: Thruplex

treatment_protocol: 100 nM Estrogen

tag: cell line

tag: replicate

tag: time

tag: control antibody

value: CTCF Cell signaling D31H2  Lot:3

tag: target antibody

value: ER Millipore 06-965 Lot:3008172

tag: factor

value: ER


title: ER t70 Rep 3 [t70.3]

description:
SLX-15851.D706_D505
ER parallel Factor ChIP with CTCF spike-in 70 minutes after stimulation with Estra-2-diol, replicate 3

source_name: MCF7_ER t70


title: SWHEL-Tomato B cell S126


title: SWHEL-Tomato B cell S123


title: ER t50 Rep 1 [t50.1]

description:
SLX-15851.D706_D506
ER parallel Factor ChIP with CTCF spike-in 50 minutes after stimulation with Estra-2-diol, replicate 1

source_name: MCF7_ER t50


title: ER t0 Rep 3_input

description:
SLX-15851.D701_D503
ER parallel Factor ChIP with CTCF spike-in 0 minutes after stimulation with Estra-2-diol, replicate 3

source_name: ER t0 Rep 3_input


title: ER t50 Rep 5 [t50.5]

description:
SLX-15851.D705_D508
ER parallel Factor ChIP with CTCF spike-in 50 minutes after stimulation with Estra-2-diol, replicate 5


title: ER t60 Rep 6 [t60.6]

description:
SLX-15851.D706_D501
ER parallel Factor ChIP with CTCF spike-in 60 minutes after stimulation with Estra-2-diol, replicate 6

source_name: MCF7_ER t60


title: seed_4

tag: tissue


title: seed_3


title: ooc_3

source_name: Oocytes of Mytilus galloprovincialis

value: Unfertilized oocytes


title: ooc_1


title: seed_2


title: seed_1


title: ooc_4


title: ER t0 Rep 3 [t0.3]

description:
SLX-15851.D706_D507
ER parallel Factor ChIP with CTCF spike-in 0 minutes after stimulation with Estra-2-diol, replicate 3


title: SWHEL-Tomato B cell S122


title: ER t90 Rep 2 [t90.2]

description:
SLX-15851.D706_D508
ER parallel Factor ChIP with CTCF spike-in 90 minutes after stimulation with Estra-2-diol, replicate 2

source_name: MCF7_ER t90


title: SWHEL-Tomato B cell S12


title: SWHEL-Tomato B cell S119


title: SWHEL-Tomato B cell S118


title: ER t10 Rep 5 [t10.5]

description:
SLX-15851.D702_D503
ER parallel Factor ChIP with CTCF spike-in 10 minutes after stimulation with Estra-2-diol, replicate 5

source_name: MCF7_ER t10


title: ER t70 Rep 4 [t70.4]

description:
SLX-15851.D707_D501
ER parallel Factor ChIP with CTCF spike-in 70 minutes after stimulation with Estra-2-diol, replicate 4


title: SWHEL-Tomato B cell S114


title: ER t40 Rep 2 [t40.2]

description:
SLX-15851.D702_D504
ER parallel Factor ChIP with CTCF spike-in 40 minutes after stimulation with Estra-2-diol, replicate 2

source_name: MCF7_ER t40


title: SWHEL-Tomato B cell S116


title: ER t10 Rep 6 [t10.6]

description:
SLX-15851.D707_D507
ER parallel Factor ChIP with CTCF spike-in 10 minutes after stimulation with Estra-2-diol, replicate 6


title: SWHEL-Tomato B cell S112


title: ER t10 Rep 3 [t10.3]

description:
SLX-15851.D706_D502
ER parallel Factor ChIP with CTCF spike-in 10 minutes after stimulation with Estra-2-diol, replicate 3


title: ER t0 Rep 2 [t0.2]

description:
SLX-15851.D702_D505
ER parallel Factor ChIP with CTCF spike-in 0 minutes after stimulation with Estra-2-diol, replicate 2


title: SWHEL-Tomato B cell S110


title: smchd1MD1.rep2

city: Toyonaka

first: Koji

last: Nagao

state: Osaka

address: 1-1 Machikaneyama

department: Graduate School of Science

country: Japan

institute: Osaka University

data_processing:
Allele-specific RNA-seq analysis was performed as described by Sakata et al., (2017) with minor modifications: (i) paired-end reads were used as single-end reads; (ii) the number of allele-specific reads in two replicates were summed; (iii) genes with the number of allele-specific reads ≥20 in both X^ΔA/X^JF1 and [X^ΔA/X^JF1; Smchd1^MD1/MD1] were considered as informative genes to assess the expression of JF1 alleles.
The numbers of maternal and paternal allele-specific reads for each gene were counted using custom scripts.
Gene expression was quantified in a non-allelic manner using Cufflinks v2.2.1 cuffdiff with option '--library-type ff-firststrand --multi-read-correct'.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include average of JF1 probability (aveJF1prob), sum of the number of allele-specific reads (sumASreads), and average of FPKM values (aveFPKM) for each genotype; JF1 probability (JF1prob) and the number of allele-specific reads (ASreads) for each sample.

source_name: E13.5 MEF

extract_protocol:
Total RNAs were extracted from MEFs using ALLPrep DNA/RNA mini kit (QIAGEN).
Total RNA (1 µg) was subjected to enrichment for polyadenylated RNA, and libraries were prepared using TruSeq stranded mRNA LT sample prep kit-set (Illumina) according to the manufacturer’s instructions.

tag: cell type

value: mouse embryonic fibroblasts

tag: genotype

value: Smchd1 MD1/MD1; Xist deltaA/+

tag: strain

value: C57BL6/J x (JF1 x C57BL6/J F1)

tag: Sex

value: female


title: smchd1MD1.rep1


title: SWHEL-Tomato B cell S106


title: ER t40 Rep 3 [t40.3]

description:
SLX-15851.D707_D502
ER parallel Factor ChIP with CTCF spike-in 40 minutes after stimulation with Estra-2-diol, replicate 3


title: ER t90 Rep 4 [t90.4]

description:
SLX-15851.D708_D501
ER parallel Factor ChIP with CTCF spike-in 90 minutes after stimulation with Estra-2-diol, replicate 4


title: smchd1WT.rep2

value: Smchd1 +/+; Xist deltaA/+


title: smchd1WT.rep1


title: ER t20 Rep 6 [t20.6]

description:
SLX-15851.D707_D503
ER parallel Factor ChIP with CTCF spike-in 20 minutes after stimulation with Estra-2-diol, replicate 6

source_name: MCF7_ER t20


title: SWHEL-Tomato B cell S104


title: ooc_2


title: SWHEL-Tomato B cell S102


title: met_5

source_name: Pediveliger of Mytilus galloprovincialis

value: Pediveliger larvae (20dpf)


title: met_3


title: ER t0 Rep 1 [t0.1]

description:
SLX-15851.D703_D502
ER parallel Factor ChIP with CTCF spike-in 0 minutes after stimulation with Estra-2-diol, replicate 1


title: y1303: WT H3K4me3 eSPAN repeat 2

source_name: whole cell

tag: media

value: YPD+HU

value: S

tag: chip antibody

value: Anti-H3K4me3 and Anti-BrdU Antibody


title: met_2

value: whole body


title: met_4


title: SWHEL-Tomato B cell S100

source_name: lymph node

tag: mouse


title: ER t50 Rep 6 [t50.6]

description:
SLX-15851.D703_D503
ER parallel Factor ChIP with CTCF spike-in 50 minutes after stimulation with Estra-2-diol, replicate 6


title: y929: WT H3K4me3 eSPAN repeat 1

tag: cell cycle stage


title: met_1


title: ER t80 Rep 2 [t80.2]

description:
SLX-15851.D702_D506
ER parallel Factor ChIP with CTCF spike-in 80 minutes after stimulation with Estra-2-diol, replicate 2

source_name: MCF7_ER t80


title: y1297: WT H3K56ac eSPAN repeat 2

value: Anti-H3K56ac and Anti-BrdU Antibody


title: SWHEL-Tomato B cell S10

tag: rna processing batch

tag: pool


title: y933: WT H3K56ac eSPAN repeat 1


title: SWHEL-Tomato B cell S08


title: SWHEL-Tomato B cell S06


title: y1279: WT H3K4me3 ChIP-ssSeq repeat 2

value: Anti-H3K4me3 Antibody (ab8580)


title: ER t70 Rep 6 [t70.6]

description:
SLX-15851.D708_D503
ER parallel Factor ChIP with CTCF spike-in 70 minutes after stimulation with Estra-2-diol, replicate 6

tag: cell line


title: SWHEL-Tomato B cell S04


title: ER t20 Rep 2 [t20.2]

description:
SLX-15851.D702_D508
ER parallel Factor ChIP with CTCF spike-in 20 minutes after stimulation with Estra-2-diol, replicate 2

tag: replicate


title: y927: WT H3K4me3 ChIP-ssSeq repeat 1


title: SWHEL-Tomato B cell S02


title: SWHEL-Tomato B cell S99


title: y931: WT H3K56ac ChIP-ssSeq repeat 1

value: Anti-H3K56ac antibody


title: ER t60 Rep 2 [t60.2]

description:
SLX-15851.D701_D504
ER parallel Factor ChIP with CTCF spike-in 60 minutes after stimulation with Estra-2-diol, replicate 2

tag: time

value: CTCF Cell signaling D31H2  Lot:3


title: y1291: WT BrdU-IP-ssSeq repeat 2

value: Anti-BrdU (BD BioScience, 347580)


title: ER t10 Rep 2 [t10.2]

description:
SLX-15851.D701_D501
ER parallel Factor ChIP with CTCF spike-in 10 minutes after stimulation with Estra-2-diol, replicate 2

tag: control antibody

value: ER Millipore 06-965 Lot:3008172

value: ER


title: SWHEL-Tomato B cell S93


title: y925: WT BrdU-IP-ssSeq repeat 1


title: ER t30 Rep 4 [t30.4]

description:
SLX-15851.D702_D507
ER parallel Factor ChIP with CTCF spike-in 30 minutes after stimulation with Estra-2-diol, replicate 4

source_name: MCF7_ER t30

tag: target antibody


title: ER t90 Rep 1 [t90.1]

description:
SLX-15851.D701_D502
ER parallel Factor ChIP with CTCF spike-in 90 minutes after stimulation with Estra-2-diol, replicate 1

tag: factor


title: ER t60 Rep 3 [t60.3]

description:
SLX-15851.D703_D505
ER parallel Factor ChIP with CTCF spike-in 60 minutes after stimulation with Estra-2-diol, replicate 3


title: SWHEL-Tomato B cell S89


title: SWHEL-Tomato B cell S87


title: y923: WT input MNase-ssSeq repeat 1


title: ER t80 Rep 5 [t80.5]

description:
SLX-15851.D709_D501
ER parallel Factor ChIP with CTCF spike-in 80 minutes after stimulation with Estra-2-diol, replicate 5


title: ER t20 Rep 3 [t20.3]

description:
SLX-15851.D703_D506
ER parallel Factor ChIP with CTCF spike-in 20 minutes after stimulation with Estra-2-diol, replicate 3


title: y1143: WT S H3K4me3 ChIP-ssSeq repeat 2


title: SWHEL-Tomato B cell S83


title: ER t30 Rep 2 [t30.2]

description:
SLX-15851.D703_D501
ER parallel Factor ChIP with CTCF spike-in 30 minutes after stimulation with Estra-2-diol, replicate 2


title: ER t70 Rep 1 [t70.1]

description:
SLX-15851.D709_D502
ER parallel Factor ChIP with CTCF spike-in 70 minutes after stimulation with Estra-2-diol, replicate 1


title: SWHEL-Tomato B cell S81


title: y1285: WT H3K56ac ChIP-ssSeq repeat 2


title: y1139: WT S input MNase-ssSeq repeat 2


title: y1273: WT input MNase-ssSeq repeat 2


title: SWHEL-Tomato B cell S97


title: ER t40 Rep 5 [t40.5]

description:
SLX-15851.D703_D507
ER parallel Factor ChIP with CTCF spike-in 40 minutes after stimulation with Estra-2-diol, replicate 5


title: SWHEL-Tomato B cell S91


title: SWHEL-Tomato B cell S80


title: ER t60 Rep 5 [t60.5]

description:
SLX-15851.D709_D503
ER parallel Factor ChIP with CTCF spike-in 60 minutes after stimulation with Estra-2-diol, replicate 5


title: ER t20 Rep 5 [t20.5]

description:
SLX-15851.D702_D501
ER parallel Factor ChIP with CTCF spike-in 20 minutes after stimulation with Estra-2-diol, replicate 5


title: y1240: WT S H3K4me3 ChIP-ssSeq repeat 1


title: y1138: WT G1 input MNase-ssSeq repeat 2

value: YPD


title: SWHEL-Tomato B cell S77


title: SWHEL-Tomato B cell S79


title: SWHEL-Tomato B cell S74


title: ER t80 Rep 1 [t80.1]

description:
SLX-15851.D703_D508
ER parallel Factor ChIP with CTCF spike-in 80 minutes after stimulation with Estra-2-diol, replicate 1


title: ER t40 Rep 1 [t40.1]

description:
SLX-15851.D708_D505
ER parallel Factor ChIP with CTCF spike-in 40 minutes after stimulation with Estra-2-diol, replicate 1


title: y1234: WT S input MNase-ssSeq repeat 1


title: y1232: WT G1 input MNase-ssSeq repeat 1


title: y1236: WT G1 H3K4me3 ChIP-ssSeq repeat 1


title: SWHEL-Tomato B cell S69


title: ER t70 Rep 2 [t70.2]

description:
SLX-15851.D701_D507
ER parallel Factor ChIP with CTCF spike-in 70 minutes after stimulation with Estra-2-diol, replicate 2


title: ER t60 Rep 4 [t60.4]

description:
SLX-15851.D708_D506
ER parallel Factor ChIP with CTCF spike-in 60 minutes after stimulation with Estra-2-diol, replicate 4


title: 382silenced_rep3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: MiR-382 24h-3_ inhibitor

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).

label: biotin

source_name: C2C12 myotubes_7 days of differentiation_24h post transfection with miR-382 silcencer

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Myoblasts were cultured in 12-well plates at a density of 100.000 cells/cm2 in growth media (DMEM 4,5g/L glucose, with 10% Fetal Bovine Serum, 2% HEPES and 1% Non-essential amino acids).  Differentiation was perfromed in differentiation medium (DMEM 4,5g/L glucose, with 2% Horse serum, 2% HEPES and 1% Non-essential amino acids) for 6 days.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Breda, the Netherlands) and column-purified using the RNeasy mini kit (Qiagen, Venlo, the Netherlands). RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Transfections were performed at day 6 of differentiation. Cells were transfected with miRNA inhibitors using lipofectamine RNAimax, according to the manufacturers protocol. The final LNA concentration was 50nM.

value: immortalized mouse myoblast

tag: transfection

value: miRNA-382-5p silencer

tag: time of cell differentiation (days)

tag: time post transfection (hrs)


title: SWHEL-Tomato B cell S67


title: y1141: WT G1 H3K4me3 ChIP-ssSeq repeat 2


title: Control_rep3

description: NegA 24h-3_Negative Control A

source_name: C2C12 myotubes_7 days of differentiation_24h post transfection with (negative) control

tag: cell type

value: negative control


title: 382silenced_rep2

description: MiR-382 24h-2_ inhibitor


title: Control_rep2

description: NegA 24h-2_Negative Control A


title: Control_rep1

description: NegA 24h-1_Negative Control A


title: ER t0 Rep 6 [t0.6]

description:
SLX-15851.D701_D508
ER parallel Factor ChIP with CTCF spike-in 0 minutes after stimulation with Estra-2-diol, replicate 6

source_name: MCF7_ER t0


title: SWHEL-Tomato B cell S71


title: ER t50 Rep 4 [t50.4]

description:
SLX-15851.D701_D505
ER parallel Factor ChIP with CTCF spike-in 50 minutes after stimulation with Estra-2-diol, replicate 4

source_name: MCF7_ER t50


title: WT_2_G2

description:
WT_unadj.counts.gz
WT_2_G2

source_name: mTEChi

tag: strain

tag: genotype

value: wild-type

tag: sample type

value: mTEChi


title: 382silenced_rep1

description: MiR-382 24h-1_ inhibitor


title: SWHEL-Tomato B cell S63

tag: mouse


title: SWHEL-Tomato B cell S65


title: ER t50 Rep 2 [t50.2]

description:
SLX-15851.D708_D507
ER parallel Factor ChIP with CTCF spike-in 50 minutes after stimulation with Estra-2-diol, replicate 2


title: SWHEL-Tomato B cell S61


title: ER t90 Rep 6 [t90.6]

description:
SLX-15851.D703_D504
ER parallel Factor ChIP with CTCF spike-in 90 minutes after stimulation with Estra-2-diol, replicate 6


title: SWHEL-Tomato B cell S59


title: ER t40 Rep 4 [t40.4]

description:
SLX-15851.D701_D506
ER parallel Factor ChIP with CTCF spike-in 40 minutes after stimulation with Estra-2-diol, replicate 4


title: PD miR-25 2

city: Herston

first: Berit

last: Genz

state: Queensland

address: 300 Herston Road

department: Cell and Molecular Biology

institute: QIMR Berghofer Medical Research Institute

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was normalized using the lumi package on R followed by differential expression between control and pull-down samples using the lmFIT and eBayes functions in the limma package. During the processing of the raw data, probes that were not detected by the Illumina array in the control samples were excluded from further analysis.  Probes with a 5% false discovery rate and fold change ≥ 2 were considered significantly enriched.

source_name: LX-2 cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: LX-2 cells were cultured in DMEM, 2% FCS, 1% Glutamin, 1% penicillin/streptomycin at 37°C, 5% CO2.

extract_protocol: Cells were harvested and lysed 24 hours post transfection. miRNA and their bound targets were enriched using streptavidin myOne C1 Dynabeads. Beads were washed before RNA extraction using an Rneasy kit (Qiagen) following manufacturer's instructions.

treatment_protocol: 50 pmol of synthetic biotin-labelled miR-25-3p duplex were transfected into LX-2 cells using Lipofectamine 2000 reagent (Life Technologies).

tag: transfection molecule

tag: pull-down

value: pull-down (enriched targets)


title: Control 2

description: Replicate 2

value: Control


title: Dearing_120min_rep3

city: minneapolis

first: Liang

last: Guo

state: MINNESOTA

address: 2001 6th Street SE

institute: University of Minnesota

description: Gene expression data from reovirus strain Dearing-infected cells 120min after adding actinomycin D

hyb_protocol: Biotinylated anti-sense cRNA was purified with the RNeasy column; 15 µg was fragmented according to Affymetrix instructions’ and hybridized to Affymetrix murine U74Av2 oligonucleotide microarrays.

scan_protocol: Microarrays were scanned on a Hewlett Packard Agilent 2200 confocal scanner.

data_processing: Normalized signal intensities were obtained using Affymetrix MAS 5.0 software as described previously

source_name: Murine L929 cells, reovirus strain Dearing-infected, 120min after actinomycin D treatment

label_protocol: The purified cDNA was used for an in vitro transcription reaction using T7 RNA polymerase and biotinylated nucleotides following the manufacturer’s protocol.

growth_protocol: Murine L929 cells were maintained as suspension cultures as described previously

extract_protocol: Total RNA was isolated at 0, 45, 90 and 120 min post-actinomycin D treatment using Trizol reagent according to the manufacturer’s instructions. Total RNA was purified with the RNeasy column.

treatment_protocol: L929 cells were plated in 150 x 25 mm tissue culture plates and were allowed to incubate at 37oC for 4 h, after which time the medium was removed and cells were mock-infected or infected with purified virions (Dearing, c87 or c8) at a multiplicity of infection of 80 plaque forming units/cell. After a 1.5 h viral adsorption at 37C, medium was added and samples were incubated at 37oC for an additional 18 h. At 19.5 h post-infection, actinomycin D was added at a final concentration of 10 µg/ml to stop transcription.

value: fibroblast cell line L929

tag: infection

value: reovirus strain Dearing-infected

tag: agent

value: actinomycin D


title: PD miR-25 3

description: Replicate 3


title: Control 1

description: Replicate 1


title: SWHEL-Tomato B cell S57

tag: rna processing batch

tag: pool


title: ER t0 Rep 4 [t0.4]

description:
SLX-15851.D708_D508
ER parallel Factor ChIP with CTCF spike-in 0 minutes after stimulation with Estra-2-diol, replicate 4

tag: cell line

tag: replicate

tag: time

tag: control antibody


title: Dearing_90min_rep3

description: Gene expression data from reovirus strain Dearing-infected cells 90min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain Dearing-infected, 90min after actinomycin D treatment


title: Dearing_45min_rep3

description: Gene expression data from reovirus strain Dearing-infected cells 45min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain Dearing-infected, 45min after actinomycin D treatment


title: PD miR-25 1

description: Replicate 1


title: Dearing_0min_rep3

description: Gene expression data from reovirus strain Dearing-infected cells 0min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain Dearing-infected, 0min after actinomycin D treatment

value: control


title: clone87_120min_rep3

description: Gene expression data from reovirus strain clone 87-infected cells 120min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone87-infected, 120min after actinomycin D treatment

value: reovirus strain clone87-infected


title: clone87_90min_rep3

description: Gene expression data from reovirus strain clone 87-infected cells 90min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone87-infected, 90min after actinomycin D treatment


title: SWHEL-Tomato B cell S53


title: SWHEL-Tomato B cell S55


title: I_Acros_TiO2_High_3

city: Durham

first: Carlton

last: Jones

address: 109 T.W. Alexander Drive

institute: U.S. Environmental Protection Agency

description:
GRC189_IA30_3
replicate 3

hyb_protocol: The global gene expression change was analyzed by using Illumina Human HT-12 v4 Expression Beadchips following the manufacturer’s protocol.

data_processing: The data processing was performed using Bioconductor’s beadarray package (version 2.4.1) for the R language (version 2.14.0). The bead-level data were loaded into a single data object using the readIllumina function, and a log2 transformation of the intensity data was performed. A probe-level summarywas produced using the summarize function by taking the median log2 intensity for each bead type. A quantile normalization of this probe-level data was performed using the normaliseIllumina function. The illuminaHumanv4.db package (version 1.12.1) containing the Illumina HumanHT12v4 annotation data was used to annotate the normalized probe-level data [29, 30].

growth_protocol: Human HepatocellularCarcinoma Cells, designation HepG2 (ATCC cat# HB-8065, Manassa, VA, USA) were obtained and expanded through passage seven using growth medium (Basal Medium Eagle, Gibco cat. 21010-046) containing 2 mM GlutaMAXTM (Gibco cat.35050-061; Life Technologies), 1mMsodium pyruvate (Gibco cat. 11360-070 Life; Technologies), and 10% fetal bovine serum and then frozen in liquid nitrogen. Cells were subsequently carefully thawed and expanded before experimentation at passage number 10–20. Cell cultures were maintained in a humidified incubator at 37°C and 95% air/5% CO2 during the study.

extract_protocol: At the end of 72 h of cell exposure to the treatment, the media was vacuum aspirated and the flasks rinsed with warm Dulbecco’s phosphate-buffered saline. cells were lysed with lysis buffer. RNA was extracted by acid phenol-chloroform, then precipitated  with ethanol, and purified through glass fiber columns. RNA integrity was assessed by the RNA 6000 LabChip kit using a 2100 bioanalyzer (Agilent-Technologies, Palo Alto, CA). The RNA Integrity number (RIN) of all samples were between 9.8 and 10.0.As the highest RIN number is 10 for completely intactRNA, RNA with a RIN number between 9.8 and 10 is of good quality.

treatment_protocol: Working stocks of each nanomaterial were prepared at 1.0 mg per mL and diluted using culture medium. Individual flasks were treated with 200 uL per cm2 of the appropriate nanomaterial dilution and incubated for 72 h. The final concentrations were 0.3 (low dose), 3 (medium dose), and 30 (high dose) μg/mL.

value: Human Hepatocellular Carcinoma Cell Line

tag: nanomaterial vendor

value: Acros

tag: nanoparticles

tag: concentration

value: 30 μg/mL


title: B_Nano Amor_CeO2_Mid_4

description:
GRC189_BNA3_4
replicate 4

scan_protocol: The global gene expression change was analyzed by using Illumina Human HT-12 v4 Expression Beadchips following the manufacturer’s protocol.

source_name: HepG2_Nano Amor_CeO2

tag: cell type

value: Nano Amor

value: 3 μg/mL


title: ER t80 Rep 4 [t80.4]

description:
SLX-15851.D704_D505
ER parallel Factor ChIP with CTCF spike-in 80 minutes after stimulation with Estra-2-diol, replicate 4

value: CTCF Cell signaling D31H2  Lot:3

tag: target antibody

value: ER Millipore 06-965 Lot:3008172

tag: factor

value: ER


title: ER t90 Rep 5 [t90.5]

description:
SLX-15851.D709_D505
ER parallel Factor ChIP with CTCF spike-in 90 minutes after stimulation with Estra-2-diol, replicate 5

source_name: MCF7_ER t90


title: B_Nano Amor_CeO2_High_2

description:
GRC189_BNA30_2
replicate 2

label_protocol: The global gene expression change was analyzed by using Illumina Human HT-12 v4 Expression Beadchips following the manufacturer’s protocol.


title: SWHEL-Tomato B cell S51

source_name: lymph node

tag: mouse


title: ER t20 Rep 1 [t20.1]

description:
SLX-15851.D704_D502
ER parallel Factor ChIP with CTCF spike-in 20 minutes after stimulation with Estra-2-diol, replicate 1

source_name: MCF7_ER t20


title: ER t30 Rep 3 [t30.3]

description:
SLX-15851.D704_D503
ER parallel Factor ChIP with CTCF spike-in 30 minutes after stimulation with Estra-2-diol, replicate 3

source_name: MCF7_ER t30


title: SWHEL-Tomato B cell S49


title: D_Alfa Aesar_CeO2_Low_1

description:
GRC189_DAA03_1
replicate 1

source_name: HepG2_Alfa Aesar_CeO2

value: Alfa Aesar

value: 0.3 μg/mL


title: SWHEL-Tomato B cell S47


title: ER t50 Rep 3 [t50.3]

description:
SLX-15851.D704_D504
ER parallel Factor ChIP with CTCF spike-in 50 minutes after stimulation with Estra-2-diol, replicate 3


title: clone87_45min_rep3

description: Gene expression data from reovirus strain clone 87-infected cells 45min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone87-infected, 45min after actinomycin D treatment


title: clone87_0min_rep3

description: Gene expression data from reovirus strain clone 87-infected cells 0min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone87-infected, 0min after actinomycin D treatment


title: clone8_120min_rep3

description: Gene expression data from reovirus strain clone 8-infected cells 120min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone8-infected, 120min after actinomycin D treatment

value: reovirus strain clone8-infected


title: SWHEL-Tomato B cell S46


title: clone8_45min_rep3

description: Gene expression data from reovirus strain clone 8-infected cells 45min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone8-infected, 45min after actinomycin D treatment


title: clone8_90min_rep3

description: Gene expression data from reovirus strain clone 8-infected cells 90min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone8-infected, 90min after actinomycin D treatment


title: C_Alfa Aesar_CeO2_Mid_4

description:
GRC189_CAA3_4
replicate 4


title: B_Nano Amor_CeO2_High_1

description:
GRC189_BNA30_1
replicate 1


title: M_Nano Amor_CeO2_Mid_1

description:
GRC189_MNA3_1
replicate 2


title: ER t10 Rep 4 [t10.4]

description:
SLX-15851.D708_D504
ER parallel Factor ChIP with CTCF spike-in 10 minutes after stimulation with Estra-2-diol, replicate 4

source_name: MCF7_ER t10


title: SWHEL-Tomato B cell S45


title: D_Alfa Aesar_CeO2_Low_2

description:
GRC189_DAA03_2
replicate 2


title: SWHEL-Tomato B cell S44


title: A_Degussa_TiO2_Mid_1

description:
GRC189_AD3_1
replicate 1

value: Degussa


title: ER t80 Rep 3 [t80.3]

description:
SLX-15851.D705_D502
ER parallel Factor ChIP with CTCF spike-in 80 minutes after stimulation with Estra-2-diol, replicate 3

source_name: MCF7_ER t80


title: SWHEL-Tomato B cell S43


title: ER t40 Rep 6 [t40.6]

description:
SLX-15851.D705_D503
ER parallel Factor ChIP with CTCF spike-in 40 minutes after stimulation with Estra-2-diol, replicate 6

source_name: MCF7_ER t40


title: WT_2_G9

description:
WT_unadj.counts.gz
WT_2_G9

source_name: mTEChi

tag: strain

tag: genotype

value: wild-type

tag: sample type

value: mTEChi


title: L_Alfa Aesar_CeO2_Low_2

description:
GRC189_LAA03_2
replicate 2


title: A_Degussa_TiO2_High_5

description:
GRC189_AD30_5
replicate 5


title: SWHEL-Tomato B cell S39


title: control_D_4

description:
GRC189_ctr_D
replicate 4

source_name: HepG2_No Treatment

value: No Treatment


title: Mock_45min_rep3

description: Gene expression data from mock-infected cells 45min after adding actinomycin D

source_name: Murine L929 cells, mock-infected, 45min after actinomycin D treatment

value: fibroblast cell line L929

tag: infection

value: mock-infected

tag: agent

value: actinomycin D


title: ER t70 Rep 5 [t70.5]

description:
SLX-15851.D704_D506
ER parallel Factor ChIP with CTCF spike-in 70 minutes after stimulation with Estra-2-diol, replicate 5

source_name: MCF7_ER t70


title: ER t10 Rep 1 [t10.1]

description:
SLX-15851.D704_D508
ER parallel Factor ChIP with CTCF spike-in 10 minutes after stimulation with Estra-2-diol, replicate 1


title: SWHEL-Tomato B cell S35

tag: rna processing batch

tag: pool


title: SWHEL-Tomato B cell S38


title: ER t30 Rep 1 [t30.1]

description:
SLX-15851.D705_D504
ER parallel Factor ChIP with CTCF spike-in 30 minutes after stimulation with Estra-2-diol, replicate 1

tag: cell line

tag: replicate


title: C_Alfa Aesar_CeO2_Mid_5

description:
GRC189_CAA3_5
replicate 5

value: Human Hepatocellular Carcinoma Cell Line


title: ER t20 Rep 4 [t20.4]

description:
SLX-15851.D705_D505
ER parallel Factor ChIP with CTCF spike-in 20 minutes after stimulation with Estra-2-diol, replicate 4

tag: time

tag: control antibody


title: clone8_0min_rep3

description: Gene expression data from reovirus strain clone 8-infected cells 0min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone8-infected, 0min after actinomycin D treatment

value: control


title: Mock_0min_rep3

description: Gene expression data from mock-infected cells 0min after adding actinomycin D

source_name: Murine L929 cells, mock-infected, 0min after actinomycin D treatment


title: M_Nano Amor_CeO2_Low_2

description:
GRC189_MNA03_2
replicate 2

source_name: HepG2_Nano Amor_CeO2

tag: nanomaterial vendor

value: Nano Amor

tag: nanoparticles


title: SWHEL-Tomato B cell S33

source_name: lymph node


title: Dearing_120min_rep2

description: Gene expression data from reovirus strain Dearing-infected cells 120min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain Dearing-infected, 120min after actinomycin D treatment

value: reovirus strain Dearing-infected


title: SWHEL-Tomato B cell S31


title: B_Nano Amor_CeO2_Low_2

description:
GRC189_BNA03_2
replicate 2

tag: cell type

tag: concentration


title: Mock_90min_rep3

description: Gene expression data from mock-infected cells 90min after adding actinomycin D

source_name: Murine L929 cells, mock-infected, 90min after actinomycin D treatment


title: Mock_120min_rep3

description: Gene expression data from mock-infected cells 120min after adding actinomycin D

source_name: Murine L929 cells, mock-infected, 120min after actinomycin D treatment


title: I_Acros_TiO2_Mid_3

description:
GRC189_IA3_3
replicate 3

value: Acros

value: 3 μg/mL


title: Dearing_0min_rep2

description: Gene expression data from reovirus strain Dearing-infected cells 0min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain Dearing-infected, 0min after actinomycin D treatment


title: ER t60 Rep 1 [t60.1]

description:
SLX-15851.D705_D507
ER parallel Factor ChIP with CTCF spike-in 60 minutes after stimulation with Estra-2-diol, replicate 1

source_name: MCF7_ER t60

value: CTCF Cell signaling D31H2  Lot:3

tag: target antibody

value: ER Millipore 06-965 Lot:3008172

tag: factor

value: ER


title: ER t30 Rep 6 [t30.6]

description:
SLX-15851.D709_D506
ER parallel Factor ChIP with CTCF spike-in 30 minutes after stimulation with Estra-2-diol, replicate 6

source_name: MCF7_ER t30


title: Dearing_45min_rep2

description: Gene expression data from reovirus strain Dearing-infected cells 45min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain Dearing-infected, 45min after actinomycin D treatment


title: A_Degussa_TiO2_High_4

description:
GRC189_AD30_4
replicate 4

value: 30 μg/mL


title: SWHEL-Tomato B cell S27

tag: mouse


title: ER t90 Rep 3 [t90.3]

description:
SLX-15851.D705_D506
ER parallel Factor ChIP with CTCF spike-in 90 minutes after stimulation with Estra-2-diol, replicate 3

source_name: MCF7_ER t90


title: H36: iPSC-derived Neurons

description: iPSC derived neurons from A152T Tau (patients) or control samples were treated with indicated SAHA dosage.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using RNA-STAR v 2.2
Counts were estimated using RNA-STAR
Genes were kept if they were expressed in 80% of the samples with >10 reads. The resulting read counts were normalized for library size using cqn function of CQN R package in R to get fragments per kilobase million mapped reads (FPKM) values. Log2 transformed FPKM values were corrected for batch and sequencing biases using linear model in  R.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Normalized log2 FPKM values for each Sample ...

source_name: iPSC-derived Neurons

tag: tissue

value: iPSC-derived Neurons

tag: diagnosis/patient

value: Patient (19-5-RC6)

tag: saha dose

value: 2.5uM SAHA

tag: batch

value: E


title: H35: iPSC-derived Neurons

value: DMSO


title: SWHEL-Tomato B cell S25

tag: rna processing batch


title: D_Alfa Aesar_CeO2_High_4

description:
GRC189_DAA30_4
replicate 4

source_name: HepG2_Alfa Aesar_CeO2

value: Alfa Aesar


title: SWHEL-Tomato B cell S23

tag: pool


title: SWHEL-Tomato B cell S29


title: H32: iPSC-derived Neurons

value: D


title: Dearing_90min_rep2

description: Gene expression data from reovirus strain Dearing-infected cells 90min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain Dearing-infected, 90min after actinomycin D treatment

tag: cell line

value: fibroblast cell line L929

tag: infection

tag: agent

value: actinomycin D


title: clone87_90min_rep2

description: Gene expression data from reovirus strain clone 87-infected cells 90min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone87-infected, 90min after actinomycin D treatment

value: reovirus strain clone87-infected

tag: time


title: H33: iPSC-derived Neurons


title: SWHEL-Tomato B cell S19


title: clone87_120min_rep2

description: Gene expression data from reovirus strain clone 87-infected cells 120min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone87-infected, 120min after actinomycin D treatment


title: SWHEL-Tomato B cell S17


title: H31: iPSC-derived Neurons


title: H_Mknano_TiO2_Low_3

description:
GRC189_HMK03_3
replicate 3

value: Human Hepatocellular Carcinoma Cell Line

tag: nanomaterial vendor

value: Mknano

value: 0.3 μg/mL


title: clone87_0min_rep2

description: Gene expression data from reovirus strain clone 87-infected cells 0min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone87-infected, 0min after actinomycin D treatment

value: control


title: L_Alfa Aesar_CeO2_Mid_1

description:
GRC189_LAA3_1
replicate 1

tag: nanoparticles

value: 3 μg/mL


title: clone8_90min_rep2

description: Gene expression data from reovirus strain clone 8-infected cells 90min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone8-infected, 90min after actinomycin D treatment

value: reovirus strain clone8-infected


title: clone8_120min_rep2

description: Gene expression data from reovirus strain clone 8-infected cells 120min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone8-infected, 120min after actinomycin D treatment


title: clone87_45min_rep2

description: Gene expression data from reovirus strain clone 87-infected cells 45min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone87-infected, 45min after actinomycin D treatment


title: H_Mknano_TiO2_High_5

description:
GRC189_HMK30_5
replicate 5

tag: cell type

value: 30 μg/mL


title: clone8_45min_rep2

description: Gene expression data from reovirus strain clone 8-infected cells 45min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone8-infected, 45min after actinomycin D treatment


title: H34: iPSC-derived Neurons

value: iPSC-derived Neurons


title: control_C_3

description:
GRC189_ctr_C
replicate 3

source_name: HepG2_No Treatment

value: No Treatment

tag: concentration


title: SWHEL-Tomato B cell S15

source_name: lymph node


title: A_Degussa_TiO2_Mid_5

description:
GRC189_AD3_5
replicate 5

value: Degussa


title: H30: iPSC-derived Neurons

value: Patient (19-5-RC6)

value: 2.5uM SAHA

value: C


title: SWHEL-Tomato B cell S147


title: SWHEL-Tomato B cell S21


title: H29: iPSC-derived Neurons


title: SWHEL-Tomato B cell S145


title: H28: iPSC-derived Neurons


title: SWHEL-Tomato B cell S143


title: B_Nano Amor_CeO2_Mid_5

description:
GRC189_BNA3_5
replicate 5

source_name: HepG2_Nano Amor_CeO2

value: Nano Amor


title: I_Acros_TiO2_Mid_5

description:
GRC189_IA3_5
replicate 5

value: Acros


title: Mock_90min_rep2

source_name: Murine L929 cells, mock-infected, 90min after actinomycin D treatment

value: fibroblast cell line L929

value: mock-infected

value: actinomycin D


title: Mock_120min_rep2

source_name: Murine L929 cells, mock-infected, 120min after actinomycin D treatment


title: SWHEL-Tomato B cell S141


title: H27: iPSC-derived Neurons

value: DMSO


title: H26: iPSC-derived Neurons

value: B


title: SWHEL-Tomato B cell S139


title: I_Acros_TiO2_High_4

description:
GRC189_IA30_4
replicate 4

value: Human Hepatocellular Carcinoma Cell Line


title: H25: iPSC-derived Neurons


title: clone8_0min_rep2

description: Gene expression data from reovirus strain clone 8-infected cells 0min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain clone8-infected, 0min after actinomycin D treatment

value: control


title: SWHEL-Tomato B cell S137


title: H24: iPSC-derived Neurons


title: SWHEL-Tomato B cell S135


title: H23: iPSC-derived Neurons


title: C_Alfa Aesar_CeO2_Low_4

description:
GRC189_CAA03_4
replicate 4

value: Alfa Aesar

value: 0.3 μg/mL


title: Mock_45min_rep2

description: Gene expression data from mock-infected cells 45min after adding actinomycin D

source_name: Murine L929 cells, mock-infected, 45min after actinomycin D treatment


title: SWHEL-Tomato B cell S133


title: H22: iPSC-derived Neurons

source_name: iPSC-derived Neurons

value: iPSC-derived Neurons

value: A


title: SWHEL-Tomato B cell S131


title: Dearing_45min_rep1

source_name: Murine L929 cells, reovirus strain Dearing-infected, 45min after actinomycin D treatment

value: reovirus strain Dearing-infected


title: Dearing_90min_rep1

source_name: Murine L929 cells, reovirus strain Dearing-infected, 90min after actinomycin D treatment


title: H21: iPSC-derived Neurons

value: Patient (19-5-RC6)


title: M_Nano Amor_CeO2_Low_4

description:
GRC189_MNA03_4
replicate 4


title: Mock_0min_rep2

description: Gene expression data from mock-infected cells 0min after adding actinomycin D

source_name: Murine L929 cells, mock-infected, 0min after actinomycin D treatment


title: Dearing_120min_rep1

description: Gene expression data from reovirus strain Dearing-infected cells 120min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain Dearing-infected, 120min after actinomycin D treatment


title: C_Alfa Aesar_CeO2_Mid_3

description:
GRC189_CAA3_3
replicate 3

source_name: HepG2_Alfa Aesar_CeO2

value: 3 μg/mL


title: H20: iPSC-derived Neurons


title: H19: iPSC-derived Neurons


title: M_Nano Amor_CeO2_High_5

description:
GRC189_MNA30_5
replicate 5

value: 30 μg/mL


title: clone87_0min_rep1

source_name: Murine L929 cells, reovirus strain clone87-infected, 0min after actinomycin D treatment

value: reovirus strain clone87-infected


title: A_Degussa_TiO2_Mid_4

description:
GRC189_AD3_4
replicate 4

value: Degussa


title: B_Nano Amor_CeO2_High_4

description:
GRC189_BNA30_4
replicate 4

value: Nano Amor


title: SWHEL-Tomato B cell S129


title: L_Alfa Aesar_CeO2_High_4

description:
GRC189_LAA30_4
replicate 4


title: clone87_90min_rep1

source_name: Murine L929 cells, reovirus strain clone87-infected, 90min after actinomycin D treatment

value: fibroblast cell line L929


title: I_Acros_TiO2_Low_2

description:
GRC189_IA03_2
replicate 2

value: Acros


title: H_Mknano_TiO2_Mid_3

description:
GRC189_HMK3_3
replicate 3

value: Mknano


title: SWHEL-Tomato B cell S125


title: clone87_120min_rep1

source_name: Murine L929 cells, reovirus strain clone87-infected, 120min after actinomycin D treatment

value: actinomycin D


title: clone8_120min_rep1

source_name: Murine L929 cells, reovirus strain clone8-infected, 120min after actinomycin D treatment

value: reovirus strain clone8-infected


title: Dearing_0min_rep1

description: Gene expression data from reovirus strain Dearing-infected cells 0min after adding actinomycin D

source_name: Murine L929 cells, reovirus strain Dearing-infected, 0min after actinomycin D treatment

value: control


title: M_Nano Amor_CeO2_High_2

description:
GRC189_MNA30_2
replicate 2

value: Human Hepatocellular Carcinoma Cell Line


title: H18: iPSC-derived Neurons

value: 2.5uM SAHA

value: E


title: SWHEL-Tomato B cell S13

source_name: lymph node


title: D_Alfa Aesar_CeO2_Mid_4

description:
GRC189_DAA3_4
replicate 4

value: Alfa Aesar


title: H17: iPSC-derived Neurons

value: iPSC-derived Neurons

value: DMSO


title: SWHEL-Tomato B cell S124


title: clone8_90min_rep1

source_name: Murine L929 cells, reovirus strain clone8-infected, 90min after actinomycin D treatment


title: SWHEL-Tomato B cell S121


title: SWHEL-Tomato B cell S117


title: H16: iPSC-derived Neurons

value: D


title: clone8_45min_rep1

source_name: Murine L929 cells, reovirus strain clone8-infected, 45min after actinomycin D treatment


title: H_Mknano_TiO2_Mid_2

description:
GRC189_HMK3_2
replicate 2

value: 3 μg/mL


title: control_A_1

description:
GRC189_ctr_A
replicate 1

source_name: HepG2_No Treatment

value: No Treatment


title: H15: iPSC-derived Neurons


title: clone8_0min_rep1

source_name: Murine L929 cells, reovirus strain clone8-infected, 0min after actinomycin D treatment


title: A_Degussa_TiO2_High_2

description:
GRC189_AD30_2
replicate 2

value: Degussa

value: 30 μg/mL


title: Mock_120min_rep1

description: Gene expression data from mock-infected cells 120min after adding actinomycin D

source_name: Murine L929 cells, mock-infected, 120min after actinomycin D treatment

value: fibroblast cell line L929

value: mock-infected


title: H14: iPSC-derived Neurons

source_name: iPSC-derived Neurons


title: SWHEL-Tomato B cell S115


title: SWHEL-Tomato B cell S111


title: H13: iPSC-derived Neurons


title: H12: iPSC-derived Neurons

value: C


title: M_Nano Amor_CeO2_Low_5

description:
GRC189_MNA03_5
replicate 1

source_name: HepG2_Nano Amor_CeO2

value: Nano Amor


title: SWHEL-Tomato B cell S11


title: H11: iPSC-derived Neurons


title: SWHEL-Tomato B cell S109


title: D_Alfa Aesar_CeO2_High_3

description:
GRC189_DAA30_3
replicate 3


title: SWHEL-Tomato B cell S108


title: C_Alfa Aesar_CeO2_High_2

description:
GRC189_CAA30_2
replicate 2


title: H10: iPSC-derived Neurons


title: D_Alfa Aesar_CeO2_High_2

description:
GRC189_DAA30_2
replicate 2


title: H9: iPSC-derived Neurons


title: SWHEL-Tomato B cell S105


title: unt-4-DIV6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with limma package in R

source_name: Primary Cortical Neurons

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: unt

tag: time point


title: H7: iPSC-derived Neurons

value: B


title: SWHEL-Tomato B cell S107


title: SWHEL-Tomato B cell S103


title: SWHEL-Tomato B cell S113


title: H_Mknano_TiO2_High_3

description:
GRC189_HMK30_3
replicate 3

value: Human Hepatocellular Carcinoma Cell Line

value: Mknano


title: H6: iPSC-derived Neurons


title: H_Mknano_TiO2_High_4

description:
GRC189_HMK30_4
replicate 4


title: unt-4-DIV8


title: Mock_0min_rep1

source_name: Murine L929 cells, mock-infected, 0min after actinomycin D treatment

value: control


title: Mock_45min_rep1

source_name: Murine L929 cells, mock-infected, 45min after actinomycin D treatment

value: actinomycin D


title: Mock_90min_rep1

description: Gene expression data from mock-infected cells 90min after adding actinomycin D

source_name: Murine L929 cells, mock-infected, 90min after actinomycin D treatment


title: unt-4-DIV13


title: SWHEL-Tomato B cell S101


title: unt-4-DIV10


title: H5: iPSC-derived Neurons

value: iPSC-derived Neurons


title: L_Alfa Aesar_CeO2_Mid_2

description:
GRC189_LAA3_2
replicate 2

source_name: HepG2_Alfa Aesar_CeO2

value: Alfa Aesar


title: SWHEL-Tomato B cell S09


title: unt-3-DIV13


title: H8: iPSC-derived Neurons

value: 2.5uM SAHA


title: H_Mknano_TiO2_Mid_4

description:
GRC189_HMK3_4
replicate 4

value: 3 μg/mL


title: unt-3-DIV8


title: M_Nano Amor_CeO2_Low_3

description:
GRC189_MNA03_3
replicate 3

value: 0.3 μg/mL


title: SWHEL-Tomato B cell S07


title: H3: iPSC-derived Neurons

value: A


title: unt-2-DIV8


title: B_Nano Amor_CeO2_High_3

description:
GRC189_BNA30_3
replicate 3

value: 30 μg/mL


title: SWHEL-Tomato B cell S05


title: A_Degussa_TiO2_Low_3

description:
GRC189_AD03_3
replicate 3

value: Degussa


title: SWHEL-Tomato B cell S03


title: SWHEL-Tomato B cell S01


title: H1: iPSC-derived Neurons

value: DMSO


title: H3K27me3_smchd1MD1

data_processing:
Data processing of ChIP-seq was performed as described by Nozawa et al., (2013) with minor modifications. The sequence reads were aligned to the mouse reference genome (UCSC mm9, without Y chromosome) and a single unit of mouse ribosomal DNA repeats (BK000964.1).
We calculated the H3K27me3 enrichment values defined as log2([ChIP RPKM]/[Input RPKM]) in each gene body. Genes with their length ≤ 1 kb or Input RPKM < 0.1 were excluded due to low read counts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include H3K27me3 enrichment values defined as log2([ChIP RPKM]/[Input RPKM]) for each genotype

source_name: E13.5 MEF

extract_protocol:
ChIP was performed as described by Nozawa et al., (2013)
ChIP-seq libraries were prepared as described by Nozawa et al., (2013)

tag: developmental stage

value: mouse embryonic fibroblasts

tag: genotype

value: Smchd1 MD1/MD1

tag: strain

tag: Sex

value: female

tag: chip antibody

value: H3K27me3 (mouse monoclonal; CMA323)


title: Input_smchd1MD1


title: unt-2-DIV13

value: unt


title: unt-2-DIV6


title: H3K27me3_WT

value: Smchd1 +/+


title: ILSGR0260r_S1_BC40

city: Cambridge

first: Luyi

last: Tian

state: MA

address: 415 main st Cambridge

institute: Broad institute

data_processing:
The data was first demultiplexed by the cell barcode sequence and then aligned and counted using Rsubread (1.5.0)  and featureCounts (1.5.0) with mm10 genome annotation. Quality control was performed using scPipe to remove low quality cells.
The distance of the percentage of cells in three DC subtype between sisters were calculated, and used together with the total cell count as the input of Mahalanobis distance for outlier detection. Random permutation on sisters described in Figure 1B were used to get a null distribution and a 0.05 p-value cut-off was used to exclude sisters with different lineage output, leaving us with 98 clones.
Genome_build: mm10
Supplementary_files_format_and_content: gene counting matrix, rows repsent genes and each column is a clone. For meta data, XXX_fill_sis1/XXX_fill_sis2 represent the fate bias of filler cells in sister wells, which is considered as population control. cDC1_sis1.. E.t.c are cell count of cDCs. The cell counts are normalized using beads so they are not integers.

source_name: hematopoietic stem and progenitor cells

growth_protocol: bone marrow cells were extracted from C57BL/6 mice and cultured at a density of 1.5 x 10^6 in 96-round bottom plates with DC culture medium and 200 ng/ml FLT3L obtained from Dr Jian-Guo Zhang (WEHI).  To generate conditioned medium that can sustain the growth and differentiation of isolated DC progenitors, medium derived from FLT3L cultures after 3.5 days was centrifuged to remove cells, then passed through a 0.22-μm filter, and frozen aliquots stored at -80°C, as described previously. This medium is referred to as DC-conditioned medium (DC-CM).

extract_protocol:
On day 2.5 after culture, each 200 μl cultured well was mixed well, then 100 µL of the contents transferred manually to a separate new well, and given approximately 30-60 minutes to settle. The 96-well plates containing sister wells derived from each single UBC-GFP LSK clone were imaged on a Nikon TiE live cell imaging system. Cells were maintained at 37 °C in a humidified atmosphere and 5% CO2. Images were acquired in DIC and fluorescence using a 4x 0.13NA plan neofluor objective, and GFP filter (FITC, ex 465-495, DM 505, em 515-555). A Z-stack of 150 μm, with interval of 50um was performed and, the best focus plane was automatically selected for analysis using an offline Metamorph software (v 7.8.2.0) licence and method for automatic segmentation and cell count. Cell count script parameters, region size and diameter, were changed per experiment, on the basis of visual inspection of the 100 single cell controls. After imaging, cell cultures were incubated in 37 °C and at 5% CO2 for 4.5 days.
Depending on cell abundance 1 – 10 cells per clone were FACS sorted for RNA sequencing. Transcriptome libraries were generated according to the CEL-Seq protocol with the exception that all column purifications were replaced by magnetic bead purifications using AMPure XP beads (Beckman Coulter A63880). Libraries were sequenced on the Illumina NextSeq500 sequencer using a 75-cycle kit.

treatment_protocol: The isolation and sorting of GFP+ progenitors was performed as described. Briefly, bone marrow from C57BL/6-TG (UBC-GFP) was extracted and cells were enriched for ckit (2B8 conjugated to APC) via magnetic activated cell sorting (MACS) positive selection. The ckit enriched fraction was subsequently stained for Sca-1 (E13 161-7conjugated to Alexa Fluor 594 or Alexa Fluor 680), IL-7R (A7R34-2.2 conjugated to biotin with streptavidin-PECy7) and FLT3 (A2F10 conjugated to Phycoerythrin). Cells with positive expression of GFP, ckit, sca-1 and FLT3, while negative for IL-7R, were deemed MPPs and sorted into FLT3L-DC "filler" cultures as single cells, with 100-cell controls in duplicate. Cells with positive expression of GFP, cKit and Sca-1 were deemed Sca1+cKit+ (SKs). Cells were sorted using the BD Influx, BD FacsARIA W and BD FacsAria L. Single SKs from UBC-GFP mice were deposited in 96 well round bottomed wells pre-seeded with 1.5 x 10^6 total C57BL/6 BM cells (filler cells) cultured in DC culture medium with and additional 200 ng/mL FLT3L 37 °C and at 5% CO2 for 2.5 days.

value: hematopoietic stem and progenitor cells

tag: description

value: no cell sorted


title: unt-3-DIV10


title: H2: iPSC-derived Neurons

tag: tissue

value: iPSC-derived Neurons

tag: diagnosis/patient

tag: saha dose

tag: batch


title: unt-2-DIV10


title: unt-1-DIV8


title: unt-1-DIV13


title: Input_WT


title: L_Alfa Aesar_CeO2_Low_3

description:
GRC189_LAA03_3
replicate 3

tag: cell line

value: Human Hepatocellular Carcinoma Cell Line

value: Alfa Aesar


title: unt-1-DIV6


title: A_Degussa_TiO2_High_3

description:
GRC189_AD30_3
replicate 3


title: H_Mknano_TiO2_High_2

description:
GRC189_HMK30_2
replicate 2

value: Mknano


title: I_Acros_TiO2_Low_3

description:
GRC189_IA03_3
replicate 3

value: Acros

value: 0.3 μg/mL


title: L_Alfa Aesar_CeO2_Mid_3

description:
GRC189_LAA3_3
replicate 3

value: 3 μg/mL


title: H_Mknano_TiO2_High_1

description:
GRC189_HMK30_1
replicate 1

value: 30 μg/mL


title: M_Nano Amor_CeO2_High_4

description:
GRC189_MNA30_4
replicate 4

value: Nano Amor


title: ILSGR0260r_S1_BC39

value: progenitor cells at day 2.5


title: M_Nano Amor_CeO2_High_3

description:
GRC189_MNA30_3
replicate 3


title: miR203-4-DIV8


title: ILSGR0260r_S1_BC38


title: I_Acros_TiO2_Mid_4

description:
GRC189_IA3_4
replicate 4


title: ILSGR0260r_S1_BC37


title: unt-1-DIV10


title: miR203-4-DIV13


title: ILSGR0260r_S1_BC36


title: miR203-4-DIV6


title: L_Alfa Aesar_CeO2_High_1

description:
GRC189_LAA30_1
replicate 1


title: ILSGR0260r_S1_BC35


title: ILSGR0260r_S1_BC34


title: ILSGR0260r_S1_BC33


title: H_Mknano_TiO2_Low_4

description:
GRC189_HMK03_4
replicate 4


title: ILSGR0260r_S1_BC32


title: miR203-3-DIV8


title: miR203-3-DIV13


title: miR203-4-DIV10


title: miR203-3-DIV6


title: M_Nano Amor_CeO2_Low_1

description:
GRC189_MNA03_1
replicate 1


title: ILSGR0260r_S1_BC31


title: miR203-2-DIV8


title: miR203-3-DIV10


title: B_Nano Amor_CeO2_Low_3

description:
GRC189_BNA03_3
replicate 3


title: ILSGR0260r_S1_BC29


title: I_Acros_TiO2_High_5

description:
GRC189_IA30_5
replicate 5


title: ILSGR0260r_S1_BC30


title: M_Nano Amor_CeO2_Mid_4

description:
GRC189_MNA3_4
replicate 5


title: miR203-2-DIV13


title: I_Acros_TiO2_Low_4

description:
GRC189_IA03_4
replicate 4


title: B_Nano Amor_CeO2_Low_4

description:
GRC189_BNA03_4
replicate 4


title: ILSGR0260r_S1_BC28


title: ILSGR0260r_S1_BC27


title: ILSGR0260r_S1_BC26


title: miR203-2-DIV6


title: miR203-2-DIV10


title: miR203-1-DIV6


title: ILSGR0260r_S1_BC25


title: miR203-1-DIV13


title: H_Mknano_TiO2_Mid_1

description:
GRC189_HMK3_1
replicate 1


title: D_Alfa Aesar_CeO2_Low_3

description:
GRC189_DAA03_3
replicate 3


title: L_Alfa Aesar_CeO2_Low_4

description:
GRC189_LAA03_4
replicate 4


title: L_Alfa Aesar_CeO2_Mid_5

description:
GRC189_LAA3_5
replicate 5


title: B_Nano Amor_CeO2_Mid_1

description:
GRC189_BNA3_1
replicate 1


title: ILSGR0260r_S1_BC23


title: ILSGR0260r_S1_BC24


title: control-4-DIV8

value: control


title: miR203-1-DIV10


title: miR203-1-DIV8


title: control-4-DIV13


title: control-4-DIV6


title: D_Alfa Aesar_CeO2_Mid_1

description:
GRC189_DAA3_1
replicate 1


title: I_Acros_TiO2_Mid_1

description:
GRC189_IA3_1
replicate 1


title: ILSGR0260r_S1_BC20


title: ILSGR0260r_S1_BC21


title: C_Alfa Aesar_CeO2_High_4

description:
GRC189_CAA30_4
replicate 4


title: M_Nano Amor_CeO2_Mid_3

description:
GRC189_MNA3_3
replicate 4


title: ILSGR0260r_S1_BC22


title: ILSGR0260r_S1_BC19


title: ILSGR0260r_S1_BC18


title: ILSGR0260r_S1_BC17


title: ILSGR0260r_S1_BC16


title: control-3-DIV8


title: control-3-DIV13


title: control-2-DIV6


title: control-3-DIV10


title: H_Mknano_TiO2_Low_2

description:
GRC189_HMK03_2
replicate 2


title: D_Alfa Aesar_CeO2_Low_4

description:
GRC189_DAA03_4
replicate 4


title: A_Degussa_TiO2_Low_2

description:
GRC189_AD03_2
replicate 2

value: Degussa


title: ILSGR0260r_S1_BC15


title: control-2-DIV8