title: 25C_mut-16_ATAC_3

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

data_processing:
Libraries were sequenced on the  Illumina NextSeq500 (PE 75-bp reads)
Sequences were parsed from adapters  using NGMerge and aligned to the WS258 genome using Bowtie2, and analysed using deepTools2.
Genome_build: WS258
Supplementary_files_format_and_content: tab-delimited text files including total reads mapping to genomic bins

organism: Caenorhabditis elegans

source_name: isolated germline nuclei

extract_protocol:
Synchronized L1s of wild-type and mut-16(pk710) worms were plated on enriched peptone plates and cultured at 20°C and 25°C. One million animals per sample, in biological triplicates, were harvested as adults (~68hrs at 20°C and ~48hrs at 25°C). Germline nuclei were isolated as previously described (49). Nuclei were flash frozen in liquid nitrogen and stored at -80°C.
For each sample, roughly 50,000 isolated germline nuclei were used. We prepared our ATAC-seq libraries as previously described (50). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit (ThermoFisher Q32851). Libraries were sequenced on the Illumina NextSeq500 (PE 75-bp reads) platform. Three biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.

value: Day 1 Adult


title: 25C_mut-16_ATAC_2

status: Public on Mar 06 2020

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

growth_protocol: Synchronized L1s of wild-type and mut-16(pk710) worms were plated on enriched peptone plates and cultured at 20°C and 25°C.

tag: Stage

tag: strain


title: 25C_N2_ATAC_3

value: N2 - wild-type


title: EOC67: Female high grade serous ovarian cancer, primary tumor

type: genomic

city: Omaha

first: Adam

middle: R

last: Karpf

state: NE

address: S 42nd &, Emile St

institute: UNMC

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Rnbeads Version 1.0.0

label: Cy3, Cy5

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Isolated genomic DNA using the Puregene Tissue Kit (Qiagen), which includes RNAse treatment

tag: gender

value: Female

tag: patient age

tag: tumor histology

value: serous

value: IIIC

tag: grade

tag: tissue


title: EOC7: Female high grade serous ovarian cancer, primary tumor

value: IV


title: H3K4me1_ChIP_CTCF-AID_NPC_d6_ctl_rep2

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
fastq: Illumina's HiSeq Control Software
Each fastq file was mapped to mouse genom (mm10) with BWA -aln (Li and Durbin, 2009) and PCR duplicates were removed using Picard MarkDuplicate. The bigWig files were created using deepTools (Ramírez et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (bigWig) were created using deepTools (Ramírez et al., 2016).

organism: Mus musculus

source_name: neural precursor cells

growth_protocol: Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2

extract_protocol:
ChIP and input library preparation for histone modifications (H3K4me1, H3K4me3, H3K27ac) were carried out as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol” in https://www.encodeproject.org/documents/), and ChIP and input library preparation for CTCF were also performed as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol for MicroChIP” in https://www.encodeproject.org/documents/).
ChIP-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 or HiSeq2500 protocols (Illumina, San Diego, CA).

treatment_protocol: To deplete CTCF, 1 ul 500 mM auxin per 1 ml medium was added, and medium with auxin was changed every 24 hours. Cells were harvested 24 or 48 hours after stating auxin treatment. Neural cell differentiation treatment was performed with or without auxin treatment, and the neural precursor cells were harvested on day 4, 6 or 2 days after washing out auxin from the day 4, 6 sample.

tag: cell line

value: F123 mouse neural precursor cell

tag: chip antibody

value: H3K4me1 (abcam, ab8895)


title: ceIL12Aoff5

city: Wuhan

first: chen

last: peng

address: College of Life Sciences, Wuhan University

department: College of Life Sciences

country: China

institute: Wuhan University

data_processing:
The clean data was generated by trimming low quality bases at both ends of read and remove short fragments, this work was completed by sequencing company
For PAM depletion assay, we used custom Python or R scripts to get the result
For guide-seq, the sequencing data was processed by corresponding software named guideseq,the human genome version used in the analysis is hg19;
For deep-seq, the data was handled by CRISPRessoPooled
Genome_build: hg19
Supplementary_files_format_and_content: txt files include DNA sequences for each sample

source_name: HEK 293 cells

extract_protocol:
Cells were collected after 48h post-transfection for genomic DNA extraction using FastPure Cell/Tissue DNA Isolation Mini Kit(Vazyme)
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme)

value: embryonic kidney

value: HEK 293

tag: genotype

value: wild type


title: 25C_mut-16_ATAC_1


title: 25C_N2_ATAC_2


title: H3K4me1_ChIP_CTCF-AID_NPC_d4_auxin_rep1


title: 25C_N2_ATAC_1


title: EOC60: Female high grade serous ovarian cancer, primary tumor


title: 20C_mut-16_ATAC_3


title: ceIL12Aoff3


title: H3K4me1_ChIP_CTCF-AID_NPC_d4_auxin_rep2


title: ceIL12Aoff1


title: ceIL12Aoff2


title: 20C_mut-16_ATAC_1


title: EOC44: Female high grade serous ovarian cancer, primary tumor


title: H3K4me1_ChIP_CTCF-AID_NPC_d4_ctl_rep2


title: H3K4me1_ChIP_CTCF-AID_NPC_d2_auxin_rep2


title: H3K4me1_ChIP_CTCF-AID_NPC_d4_ctl_rep1


title: ceIL12Aoff4


title: EOC54: Female high grade serous ovarian cancer, primary tumor


title: EOC82: Female high grade serous ovarian cancer, primary tumor


title: EOC43: Female high grade serous ovarian cancer, primary tumor


title: ceHBBoff8


title: EOC57: Female high grade serous ovarian cancer, primary tumor


title: H3K4me1_ChIP_CTCF-AID_NPC_d2_auxin_rep1


title: EOC5: Female high grade serous ovarian cancer, primary tumor


title: EOC66: Female high grade serous ovarian cancer, primary tumor


title: 20C_mut-16_ATAC_2


title: 20C_N2_ATAC_2


title: EOC12: Female high grade serous ovarian cancer, primary tumor


title: ceHBBoff7


title: ceHBBtarget


title: H3K4me1_ChIP_CTCF-AID_NPC_d2_ctl_rep1


title: H3K4me1_ChIP_CTCF-AID_NPC_d2_ctl_rep2


title: 12-mut-16_25C_small_RNA_3

description: size selected RNA from total RNA

library_source: transcriptomic

data_processing:
Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
Sequences were parsed from adapters using Cutadapt(Martin, 2011) and mapped to the C. elegans genome, WS258, using HISAT2(Kim, Langmead, & Salzberg, 2015) and the transcriptome using Salmon(Patro, Duggal, Love, Irizarry, & Kingsford, 2017). Data analysis was done using R, Excel, and custom Python scripts.
Genome_build: WS258
Supplementary_files_format_and_content: tab-delimited text files including total reads mapping to each gene

molecule: total RNA

source_name: whole animal

extract_protocol:
8,000 animals per sample were harvested as adults (~68hrs at 20°C and ~48hrs at 25°C) for RNA extraction. Worms were washed off plates using water and then settled on ice to form a pellet. Water was aspirated off and worm pellets were resuspended in 1mL TRIzol reagent (Life Technologies) and freeze-thawed on dry ice followed by vortexing. Worm carcasses were pelleted using centrifugation and the supernatant containing RNA was collected. 0.2 volume chloroform was add to supernatant, vortexed, centrifuged, and then the aqueous phase was transferred to a new tube. Samples were precipitated using isopropanol and rehydrated in 50μL nuclease-free H2O.
mRNA-seq library preparation. Nuclease-free H2O was added to 7.5μg of each RNA sample, extracted from whole animals, to a final volume of 100μL. Samples were incubated at 65°C for 2 minutes then incubated on ice. The Dynabeads mRNA Purification Kit (ThermoFisher 61006) was used according to the manufacturer’s protocol. 20μL of Dynabeads was used for each sample. 100ng of each mRNA sample was used to prepare libraries with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S) according to the manual, using NEBNext multiplex oligos for Illumina (NEB E7335S). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit (ThermoFisher Q33231). Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform. Three biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.Small RNA library preparation. Small RNAs (18- to 30- nt) were size selected on denaturing 15% polyacrylamide gels (Criterion 3450091) from total RNA samples. Libraries were prepared as previously described(Montgomery et al., 2012). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit. Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform. Three biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.


title: H3K4me1_ChIP_CTCF-AID_auxin_48hr_rep2

source_name: embryonic stem cells

value: F123 mouse ES cell


title: ceHBBoff4


title: ceHBBoff6


title: EOC59: Female high grade serous ovarian cancer, primary tumor


title: ceHBBoff5


title: H3K4me1_ChIP_CTCF-AID_auxin_48hr_rep1


title: ceHBBoff3


title: 20C_N2_ATAC_1


title: EOC100: Female high grade serous ovarian cancer, primary tumor

value: carcinosarcoma


title: H3K4me1_ChIP_CTCF-AID_auxin_24hr_rep2


title: H3K4me1_ChIP_CTCF-AID_auxin_24hr_rep1


title: 10-mut-16_25C_small_RNA_1

description: size selected RNA from total RNA


title: 9-mut-16_20C_small_RNA_3

description: size selected RNA from total RNA


title: H3K4me1_ChIP_CTCF-AID_auxin_0hr_rep2


title: ceDNMT1target


title: 11-mut-16_25C_small_RNA_2

description: size selected RNA from total RNA


title: H3K4me1_ChIP_CTCF-AID_auxin_0hr_rep1


title: ceHBBoff1


title: EOC1: Female high grade serous ovarian cancer, primary tumor


title: 6-N2_25C_small_RNA_3

description: size selected RNA from total RNA


title: ceHBBoff2


title: ceDNMT1off9


title: 5-N2_25C_small_RNA_2

description: size selected RNA from total RNA


title: 9297953022_R01C01

city: Exeter

first: Stefania

last: Policicchio

state: Devon

address: RILD building, BARRACK ROAD, Albion Place

country: United Kingdom

institute: University of Exeter, Medical School

hyb_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) and arrays were imaged using a Illumina iScan System (Illumina).

data_processing: llumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization).   Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on   Illumina’s database and probes identified by Chen et al.* were removed. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: Cy3 and Cy5

source_name: postmortem brain

label_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) standard protocol.

extract_protocol: Genomic DNA was isolated from post mortem human brain using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

tag: age

tag: groupid *

value: F


title: 7-mut-16_20C_small_RNA_1

description: size selected RNA from total RNA


title: H3K27ac_ChIP_CTCF-AID_NPC_d6_washout_rep2

value: H3K27ac (Active Motif, 39133)


title: ceDNMT1off8


title: H3K27ac_ChIP_CTCF-AID_NPC_d6_washout_rep1


title: ceDNMT1off7


title: 4-N2_25C_small_RNA_1

description: size selected RNA from total RNA


title: 9297953016_R01C01

value: M


title: EOC150: Female high grade serous ovarian cancer, primary tumor


title: 8-mut-16_20C_small_RNA_2

description: size selected RNA from total RNA


title: ceDNMT1off6


title: 9297953073_R02C01


title: 3-N2_20C_small_RNA_3

description: size selected RNA from total RNA


title: H3K27ac_ChIP_CTCF-AID_NPC_d6_auxin_rep2


title: 9297953016_R02C02


title: 9297953009_R03C01


title: H3K27ac_ChIP_CTCF-AID_NPC_d6_auxin_rep1


title: ceDNMT1off3


title: ceDNMT1off4


title: H3K27ac_ChIP_CTCF-AID_NPC_d6_ctl_rep1


title: 2-N2_20C_small_RNA_2

description: size selected RNA from total RNA


title: 1-N2_20C_small_RNA_1

description: size selected RNA from total RNA


title: H3K27ac_ChIP_CTCF-AID_NPC_d6_ctl_rep2


title: ceDNMT1off2


title: 12-25C-RE-mut-16-pk710-mRNA-3

description: total RNA


title: ceDNMT1off1


title: 9297953016_R05C01


title: H3K27ac_ChIP_CTCF-AID_NPC_d4_washout_rep2


title: 11-25C-RE-mut-16-pk710-mRNA-2

description: total RNA


title: 3998998206_R05C01


title: H3K27ac_ChIP_CTCF-AID_NPC_d4_washout_rep1


title: CeCTLA4target


title: 3998998206_R04C01


title: 9-25C-RE-N2-mRNA-3

description: total RNA


title: H3K27ac_ChIP_CTCF-AID_NPC_d4_auxin_rep2


title: ceB2Mtarget


title: H3K27ac_ChIP_CTCF-AID_NPC_d4_auxin_rep1


title: ceB2Moff8


title: 20C_N2_ATAC_3


title: 8-25C-RE-N2-mRNA-2

description: total RNA


title: H3K27ac_ChIP_CTCF-AID_NPC_d4_ctl_rep2


title: H3K27ac_ChIP_CTCF-AID_NPC_d4_ctl_rep1


title: EOC11: Female high grade serous ovarian cancer, primary tumor

value: IIIB


title: 3998998172_R05C01


title: 3998998172_R03C02


title: 3998998206_R02C02


title: 10-25C-RE-mut-16-pk710-mRNA-1

description: total RNA

value: Day 1 Adult


title: ceB2Moff6


title: ceB2Moff7


title: 6-20C-mut16-pk710-mRNA-3

description: total RNA


title: H3K27ac_ChIP_CTCF-AID_NPC_d2_auxin_rep2


title: ceB2Moff5


title: 5-20C-RE-mut16-pk710-mRNA-2

description: total RNA


title: ceB2Moff4


title: ceB2Moff3


title: H3K27ac_ChIP_CTCF-AID_NPC_d2_ctl_rep1


title: H3K27ac_ChIP_CTCF-AID_NPC_d2_auxin_rep1


title: ceB2Moff2


title: 2-20C-RE-N2-mRNA-2

description: total RNA

value: N2 - wild-type


title: H3K27ac_ChIP_CTCF-AID_NPC_d2_ctl_rep2


title: 3998998172_R01C01


title: 3998998172_R02C01


title: ceB2Moff1


title: 3998998172_R03C01


title: 7-25C-RE-N2-mRNA-1

description: total RNA


title: 3998998160_R06C01


title: 1-20C-RE-N2-mRNA-1

description: total RNA


title: 3998998160_R04C02


title: H3K27ac_ChIP_CTCF-AID_auxin_48hr_rep1


title: EOC96: Female high grade serous ovarian cancer, primary tumor

hyb_protocol: Hybridizations were performed according to manufactures recomendation for Affymetrix Cytoscan HD microarrays

scan_protocol: Microarray scans were performed according to manufactures recomendation for Affymetrix Cytoscan HD microarrays

data_processing:
The total number and size (segments) of CNA per sample were determined using the Affymetrix Chromosome Analysis Suite (ChAS) Software. A CNA index was calculated for each sample based on the percent of the genome that resulted in either a copy number loss or gain.
*Segments.txt: Total number and size of copy number gain and loss segments across genome

label: biotin

label_protocol: Probe labeling was performed according to manufactures recomendation for Affymetrix Cytoscan HD microarrays

extract_protocol: Genomic DNA was isolated using the Puregene Tissue Kit (Qiagen)

value: female

tag: histotype


title: 3998998206_R05C02


title: BfVEGFAtarget


title: EOC4: Female high grade serous ovarian cancer, primary tumor

value: serous


title: H3K27ac_ChIP_CTCF-AID_auxin_48hr_rep2


title: 3998998161_R02C02


title: H3K27ac_ChIP_CTCF-AID_auxin_24hr_rep2


title: EOC53: Female high grade serous ovarian cancer, primary tumor


title: BfB2Mtarget


title: BfTRBCtarget


title: H3K27ac_ChIP_CTCF-AID_auxin_0hr_rep2


title: H3K27ac_ChIP_CTCF-AID_auxin_24hr_rep1


title: 3998998172_R05C02


title: 3998998160_R04C01


title: AsPOLQtarget


title: H3K27ac_ChIP_CTCF-AID_auxin_0hr_rep1


title: AsPOLQoff6


title: EOC99: Female high grade serous ovarian cancer, primary tumor


title: 3998998206_R01C02


title: OV_30h_3 [miRNA-seq]

city: Haikou

first: Feng

last: Pang

address: Renmin Road 58

institute: Hainan University

data_processing:
Single-end sequencing on Illumina HiSeq 2500
ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using, Student t test . The significance threshold was set to be 0.01 and 0.05 in each test
Genome_build: GCF_001704415.1

organism: Capra hircus

source_name: GSF cells infected by ORFV at 30h.p.i

extract_protocol:
Ambion mirVana miRNA Isolation Kit (Thermo Fisher Scientific)
TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA)

tag: tissue source

value: skin

tag: cell type

value: primary goat skin fibroblast (GSF) cells

tag: treatment

value: GSF cells infected by ORFV at 30h.p.i


title: EOC80: Female high grade serous ovarian cancer, primary tumor


title: 3998998206_R02C01


title: AsPOLQoff5


title: 3998998206_R06C01


title: OV_30h_2 [miRNA-seq]


title: Input_mChIP_CTCF-AID_NPC_d4_washout_rep1

value: F123 mouse neural precursor cell


title: 3998998172_R06C02


title: 3-20C-N2-mRNA-3

description: total RNA


title: Input_mChIP_CTCF-AID_NPC_d4_washout_rep2


title: EOC5: Female high grade serous ovarian cancer, primary tumor


title: AsPOLQoff3

value: embryonic kidney


title: Input_mChIP_CTCF-AID_NPC_d4_auxin_rep2


title: AsPOLQoff2

value: HEK 293


title: EOC30: Female high grade serous ovarian cancer, primary tumor


title: 3998998161_R03C02


title: OV_18h_3 [miRNA-seq]

source_name: GSF cells infected by ORFV at 18h.p.i

value: GSF cells infected by ORFV at 18h.p.i


title: EOC142: Female high grade serous ovarian cancer, primary tumor


title: Input_mChIP_CTCF-AID_NPC_d4_auxin_rep1


title: OV_18h_2 [miRNA-seq]


title: AsPOLQoff1

value: wild type


title: Input_mChIP_CTCF-AID_NPC_d4_ctl_rep1


title: AsIL12Atarget


title: DG_3 [miRNA-seq]

source_name: mock-infected control

value: mock-infected control


title: Input_mChIP_CTCF-AID_NPC_d2_auxin_rep2


title: Input_mChIP_CTCF-AID_NPC_d2_auxin_rep1


title: AsIL12Aoff9


title: AsIL12Aoff10


title: OV_18h_1 [miRNA-seq]


title: DG_2 [miRNA-seq]


title: AsIL12Aoff8


title: Input_mChIP_CTCF-AID_NPC_d4_ctl_rep2


title: Input_mChIP_CTCF-AID_NPC_d2_ctl_rep2


title: EOC66: Female high grade serous ovarian cancer, primary tumor


title: AsIL12Aoff7


title: EOC89: Female high grade serous ovarian cancer, primary tumor


title: Input_mChIP_CTCF-AID_NPC_d2_ctl_rep1


title: EOC139: Female high grade serous ovarian cancer, primary tumor


title: EOC46: Female high grade serous ovarian cancer, primary tumor


title: AsIL12Aoff6


title: DG_1 [miRNA-seq]


title: EOC107: Female high grade serous ovarian cancer, primary tumor


title: AsIL12Aoff4


title: Input_mChIP_CTCF-AID_auxin_48hr_rep1

value: F123 mouse ES cell


title: EOC43: Female high grade serous ovarian cancer, primary tumor


title: 3998998172_R02C02


title: 3998998161_R03C01


title: 3998998161_R06C01


title: EOC67: Female high grade serous ovarian cancer, primary tumor


title: AsIL12Aoff5


title: 4-20C-RE-mut16-pk710-mRNA-1

description: total RNA


title: EOC12: Female high grade serous ovarian cancer, primary tumor


title: Input_mChIP_CTCF-AID_auxin_24hr_rep2


title: 3998998160_R03C02


title: EOC150: Female high grade serous ovarian cancer, primary tumor


title: EOC1: Female high grade serous ovarian cancer, primary tumor


title: EOC57: Female high grade serous ovarian cancer, primary tumor


title: EOC78: Female high grade serous ovarian cancer, primary tumor


title: Input_mChIP_CTCF-AID_auxin_24hr_rep1


title: Input_mChIP_CTCF-AID_auxin_0hr_rep1


title: Input_mChIP_CTCF-AID_auxin_48hr_rep2


title: Input_mChIP_CTCF-AID_auxin_0hr_rep2


title: EOC33: Female high grade serous ovarian cancer, primary tumor


title: AsHBBtarget


title: Rad21_mChIP_CTCF-AID_auxin_48hr_rep2

value: Rad21 (Santa Cruz, sc-98784)


title: EOC6: Female high grade serous ovarian cancer, primary tumor


title: Rad21_mChIP_CTCF-AID_auxin_48hr_rep1


title: AsHBBoff8


title: EOC143: Female high grade serous ovarian cancer, primary tumor


title: Rad21_mChIP_CTCF-AID_auxin_24hr_rep2


title: 3998998160_R01C02

value: M


title: EOC7: Female high grade serous ovarian cancer, primary tumor


title: AsIL12Aoff2


title: Rad21_mChIP_CTCF-AID_auxin_24hr_rep1


title: AsHBBoff6


title: AsIL12Aoff1


title: AsHBBoff5


title: EOC85: Female high grade serous ovarian cancer, primary tumor


title: AsHBBoff7


title: 3998998172_R01C02

value: F


title: 3998998160_R02C02


title: OV_30h_1 [miRNA-seq]


title: Rad21_mChIP_CTCF-AID_auxin_0hr_rep2


title: 3998998161_R01C02


title: EOC98: Female high grade serous ovarian cancer, primary tumor


title: Rad21_mChIP_CTCF-AID_auxin_0hr_rep1


title: EOC11: Female high grade serous ovarian cancer, primary tumor


title: CTCF_mChIP_CTCF-AID_NPC_d4_washout_rep2

value: CTCF (Active  Motif, 61311)


title: AsHBBoff4


title: AsHBBoff2


title: EOC54: Female high grade serous ovarian cancer, primary tumor


title: EOC42: Female high grade serous ovarian cancer, primary tumor


title: AsHBBoff1


title: EOC91: Female high grade serous ovarian cancer, primary tumor


title: AsB2Moff18


title: CTCF_mChIP_CTCF-AID_NPC_d4_auxin_rep1


title: EOC151: Female high grade serous ovarian cancer, primary tumor


title: EOC28: Female high grade serous ovarian cancer, primary tumor


title: AsB2Moff17


title: AsB2Moff16


title: CTCF_mChIP_CTCF-AID_NPC_d4_ctl_rep1


title: CTCF_mChIP_CTCF-AID_NPC_d4_ctl_rep2


title: AsB2Moff15


title: CTCF_mChIP_CTCF-AID_NPC_d2_auxin_rep2


title: EOC147: Female high grade serous ovarian cancer, primary tumor


title: AsB2Moff14


title: EOC60: Female high grade serous ovarian cancer, primary tumor


title: EOC44: Female high grade serous ovarian cancer, primary tumor


title: AsHBBoff3


title: AsB2Moff13


title: CTCF_mChIP_CTCF-AID_NPC_d2_auxin_rep1


title: CTCF_mChIP_CTCF-AID_NPC_d4_washout_rep1


title: AsB2Moff12


title: EOC50: Female high grade serous ovarian cancer, primary tumor


title: CTCF_mChIP_CTCF-AID_NPC_d2_ctl_rep2


title: AsB2Moff10


title: CTCF_mChIP_CTCF-AID_NPC_d4_auxin_rep2


title: EOC82: Female high grade serous ovarian cancer, primary tumor


title: CTCF_mChIP_CTCF-AID_NPC_d2_ctl_rep1


title: CTCF_mChIP_CTCF-AID_auxin_48hr_rep1


title: AsB2Moff9


title: EOC74: Female high grade serous ovarian cancer, primary tumor


title: CTCF_mChIP_CTCF-AID_auxin_24hr_rep2


title: AsB2Moff7


title: CTCF_mChIP_CTCF-AID_auxin_24hr_rep1


title: EOC61: Female high grade serous ovarian cancer, primary tumor


title: AsB2Moff8


title: CTCF_mChIP_CTCF-AID_auxin_0hr_rep2


title: AsB2Moff6


title: CTCF_mChIP_CTCF-AID_auxin_0hr_rep1


title: AsB2Moff5


title: EOC59: Female high grade serous ovarian cancer, primary tumor


title: CTCF_mChIP_CTCF-AID_auxin_48hr_rep2


title: 452_0WT

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

data_processing:
We used rsem-calculate-expression with default options in RSEM version 1.3.1 to quantify mRNA expression.
Alignment was performed STAR 2.7.0f using GRCm38.primary_assembly.genome.fa from ENSEMBL.
Gene annotation was based on gencode.vM22.primary_assembly.annotation.gtf.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited file expected counts, TPM and FPKM values

source_name: Wildtype Baseline

extract_protocol: RNA was isolated using the miRNeasy kit from Qiagen according to the manufacturer's protocol. Purified RNA samples were then cleaned and resuspended in nuclease-free water using the RNeasy MinElute Cleanup kit from Qiagen according to the manufacturer’s protocol. RNA quantity was measured using the Nanodrop 1000. Quality of RNA samples was quantitatively assessed by computation of RNA integrity numbers (RINs) using the Agilent RNA 6000 Pico kit (Agilent) following the manufacturer’s protocol. RNA samples with RINs ≥ 7 were selected for RNA-sequencing (RNA-Seq). Libraries were then prepared from poly-A RNAs using the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific) according to the manufacturer’s protocol for barcoded whole-transcriptome libraries. Size distribution of samples was assessed using the Agilent 2100 Bioanalyzer and 6000 RNA Pico kit. Library concentrations were quantified using the Agilent DNA 1000 assay and the 2100 Bioanalyzer according to the manufacturer’s instructions. Reactions were loaded onto Ion PI Chips v3 (Thermofisher) for sequencing on an Ion Proton sequencer according to the manufacturer’s protocol.

tag: genotype/variation

value: wildtype

value: 6-8 weeks

tag: time point

value: prior to NNK exposure

value: Mouse airway epithelia


title: AsB2Moff4


title: PLAC_H3K4me3_NPC_d4_dcas9alone_vcan_rep2

data_processing:
fastq: Illumina's HiSeq Control Software
PLAC-seq reads were aligned as single end reads using BWA with default parameters. Uniquely mapping reads were manually paired using in an in house pipeline. PCR duplicate reads were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (pgl) were generated useing MAPS (Juric and Yu et al., 2019) and FitHiChIP (Bhattacharyya et al., 2019).

extract_protocol:
PLAC-seq experiments were performed according to previous publication (Fang and Yu et al., 2014, Juric and Yu et al., 2019).
PLAC-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 protocols (Illumina, San Diego, CA).
PLAC-seq

treatment_protocol: To deplete CTCF, 1 ul 500 mM auxin per 1 ml medium was added, and medium with auxin was changed every 24 hours. Cells were harvested 24 or 48 hours after stating auxin treatment. Neural cell differentiation treatment was performed with or without auxin treatment, and the neural precursor cells were harvested on day 4 or 2 days after washing out auxin from the day 4 sample.


title: PLAC_H3K4me3_NPC_d4_dcas9alone_vcan_rep1


title: 448_0WT


title: AsB2Moff11


title: 450_0WT


title: 454_0WT


title: AsB2Moff3


title: 289_0WT


title: PLAC_H3K4me3_NPC_d4_dcas9CTCF_vcan_bottom_rep1


title: 697HF_E2APBX1-HF_ChIPSeq

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the HG19 human genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best". RNA-seq reads were alined to the HG19 human genome sequence using TopHat with the default parameters.
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
Tiled data files (TDF) were generated by igvtools with parameters "-z 5 -w 10 -e 200" for ChIP-seq ; bigWig files were generated by Homer software with makeUCSCfile with defauld parameters for RNA-seq .
The gene expression profiling was analyzed by HOMER software
Genome_build: HG19
Supplementary_files_format_and_content: Tiled data files (TDF) and bigWig for gene track visilization; tab-delimited text files include MACS peak calling output and analyzed RPKM values for each RNA-seq samples.

source_name: pre-B leukemic 697 cells

growth_protocol: The human pre-B leukemia 697 cell line was grown in RPMI1640 (Sigma) supplemented with 10% fetal bovine serum at 37 °C.

extract_protocol:
Total RNAs were extrated using Quick-RNA Miniprep kit (Zymo Research) . Chromatin lysates were prepared by sonication and protein-DNA complexes were isolated with indicated antibodies followed by purification with PCR purification kit (Qiagen).
Multiplexing libraries were prepared for sequencing using Illumina standard protocol.

treatment_protocol: The cells were treated with indicated shRNAs before RNA extraction or without treatment for ChIP-seq analysis.

value: pre-B leukemic cell line 697

value: Inducible 697 expressing E2APBX1-HF

value: anti-HA tag (ab9110, Abcam)


title: PLAC_H3K4me3_NPC_d4_dcas9CTCF_vcan_top_rep2

value: F123 mouse neural precursor cell


title: AsB2Moff1

value: embryonic kidney

value: HEK 293


title: AsB2Moff2

value: wild type


title: 697HF_E2A-HF_ChIPSeq

value: Inducible 697 expressing E2A-HF


title: 295_0WT


title: HA ChIP for TOP2-6HA T=3h

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description:
processed data file:
AH7688B-141013-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis.
For ChIP-seq, 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
For ChIP-seq, the input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Bedgraph fileswere created from pooled replicates of ChIP-seq. Only 1 replicate available for TOP2-6HA sample.
Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph

organism: Saccharomyces cerevisiae

source_name: Ha ChIP for TOP2-6HA T=3h

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C, except for H7606  which was innoculated at OD600 = 0.8 in BYTA medium and grown for 20 hours at room temperature. H7797 was also grown in BYTA medium at room temperature for the 34C experiments. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)).

extract_protocol:
For ChIP-seq samples, 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched with 125 mM glycine. ChIP-seq samples were processed as described in (Blitzblau et al., 2012).
For ChIP-seq, libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). Quality of all libraries was checked on 2200 Tapestation or Agilent 2100 Bioanalyzer. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads.

treatment_protocol: For 34C experiments, strains were shaken in SPO medium at room temperature for 1 hour and shifted to 34 degrees Celsius for the remaining time.

tag: genetic background

value: 3 hour

tag: strain id

value: anti-Ha


title: 697HF_HA_ChIPSeq

value: Inducible 697, vector control


title: PLAC_H3K4me3_CTCF-AID_NPC_d4_auxin_rep1

description:
plac_h3k4me3_npc_d4_auxin_maps_peak.pgl
plac_h3k4me3_npc_d4_auxin_fithichip_peaks.pgl


title: TOP2-6HA T=3h input

source_name: TOP2-6HA T=3h input


title: 697HF_input


title: PLAC_H3K4me3_CTCF-AID_NPC_d4_auxin_rep2


title: PLAC_H3K4me3_CTCF-AID_NPC_d4_ctl_rep2


title: 697_PBX1C_ChIPSeq

value: parental 697

value: anti-PBX1/2/3 (sc-888, Santa Cruz)


title: PLAC_H3K4me3_NPC_d4_dcas9CTCF_vcan_bottom_rep2


title: 697_p300_ChIPSeq

value: anti-p300 (sc-585, Santa Cruz)


title: PLAC_H3K4me3_CTCF-AID_ESC_auxin_48hr_rep2

value: F123 mouse ES cell


title: PLAC_H3K4me3_CTCF-AID_ESC_auxin_48hr_rep1

description:
plac_h3k4me3_esc_auxin_maps_peak.pgl
plac_h3k4me3_esc_auxin_fithichip_peaks.pgl


title: PLAC_H3K4me3_CTCF-AID_ESC_auxin_0hr_rep2


title: 697_input


title: HiC_CTCF-AID_auxin_0hr_clone2

data_processing:
fastq: Illumina's HiSeq Control Software
Hi-C reads were aligned as single end reads using BWA with default parameters. Uniquely mapping reads were manually paired using in an in house pipeline. PCR duplicate reads were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (HIC) were generated useing juicebox pre (Neva et al., 2016).

extract_protocol:
Hi-C experiments were conducted using Mbo1 according to previous publication (Rao et al., 2014).
Hi-C library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 protocols (Illumina, San Diego, CA).


title: 2-7ko

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description:
2ug
CKO2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: WT_CK.anno.txt: contains count and statistics for all samples.
Supplementary_files_format_and_content: CKO1_WT1.anno.txt: contains count and normalized count and statistics for WT1 and CKO1 only.

source_name: Brain

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

tag: strain

value: telencephalic tissue

tag: developmental stage

value: STINGf/f;Nestin-Cre


title: WT_single-cell RNA-seq

data_processing:
CellRanger software used for basecalling.
STAR peforms splicing-aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic,  intronic, and intergenic, and by whether the reads align (confidently) to the genome.The adopted alignment are as follows:1) A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise.2)Reads that align to a single exonic locus but also align to 1 or more non-exonic loci, the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255.3)Reads that are confidently mapped to the transcriptome are used for UMI counting.
In Cell Ranger v2.x and earlier, the following algorithm is used to determine the cutoff for calling a barcode cell-associated:1)Rank-sort the total UMI counts across all of the detected barcodes that passed the 16bp barcode whitelist filtering criteria.2)Determine the 99th percentile of the UMI counts among the top N barcodes where N is the provided 'expected recovered cell' parameter passed to the pipeline (--expect-cells=3000 by default).3)All barcodes with total UMI counts greater than or equal to 10% of the 99th percentile value are classified as cells.
The Seurat R package was applied to identify major cell types. RandomForest was applied to identify subtypes.
The graphs of principal component analysis (PCA) and T-distributed stochastic neighbor embedding (t-SNE) were produced following the scaling process.
Genome_build: mm9
Supplementary_files_format_and_content: 1. matrix.mtx: the gene expression results were stored in coordinate format, and three columns of information were used to represent the total number of unique UMI in a cell.  2. genes.tsv ：A file that records the ID and name of a gene. 3. barcodes.tsv：The file of cell barcode mark is recorded. The number of lines where the cell barcode is located is the sample. 4. all_cell.csv ：Total gene expression in samples. 5. all_UMI.csv：UMI expression of genes in each cell, each row represents a gene, and each column represents a cell. 6. markers.anno: Annotation information of marker gene in each cluster.
Supplementary_files_format_and_content: C1* processed data files on the series record include the sum analysis of wt and ko.

extract_protocol:
After collection of cells , centrifuge at a speed not exceeding 400rcf (adjust the speed and centrifugation time according to the cell types ). Carefully discard the supernatant and retain the cell precipitation.  The cell pellet was resuspended by 1mL 1X PBS containin g 0.04% BSA and the washing procedure was repeate d twice. After washing, appropriate volume PBS was added to the cell precipitation to obtain single cell dispersion suspension with a concentration c lose to  the goal number. A type of wide bore pipette tip was used in cell resuspension for a lower cell dam age. If necessary, cell filter should be applied to remove cell debris and clusters ( eg. 30 µm MACS SmartStrainers and 40 µm Flowmi TM Cell Strainer).  Automatic cytometry was used to determine the cell concentration. And the sample volume was calcul ated based on the optimal cell sampling concentration supplied by 10X official website and the target capture number . If the calculated concentration is too high, adjust the liquid volume to the appr opriate concentration and repeat counting once more. Once the desired cell suspension was obtained , immediately place the samples on ice for subsequent GEMs preparation and reverse transcription.
RNA libraries sequencing  was performed using standard Illumina protocols. 1) Interrupt, end repair and add A base. Finally the SPRIselect beads was used to purify the product. 2) Adaptor ligation and SPRIselect purification. 3) Index PCR and SPRIselect purification. 4) Qubit® 3.0 Flurometer Life Technologies, CA, USA  was used to determine the library  concentration.

value: WT


title: CKO_single-cell RNA-seq


title: N2+FW1256_4 [NH4]

city: Singapore

first: Jan

last: Gruber

address: Singapore

department: Science/Biochemistry

country: Singapore

institute: Yale-NUS College/National University of Singapore

description: processed data file: FW_vs_wt

data_processing:
reads mapped to reference transcriptome using kallisto (v0.46.0)
estimated counts were summarized to gene-level in length scaled TPM units using the tximport package (v1.12.3)
DESeq2 package (v1.24.0) was used to identify differentially expressed genes and produce the processed csv files. Of notice the adaptive shrinkage estimator from the ashr package option was used.
Genome_build: WBcel235
Supplementary_files_format_and_content: the gene-level summarized length scaled TPM counts of a given sample; a pairwise comparision between each treatment group and the control group, including:  the adjusted counts, log2 fold changes, standard error of log 2 fold changes, the p-value and adjusted p-value for each gene detected.

growth_protocol: Nematodes were cultivated on standard petri-dishes containing nematode growth medium (NGM) agar seeded with Escherichia coli OP50-1

extract_protocol:
Approximately 1000 of nematodes at age of day 6 were harvested and total RNA was extracted using RNeasy Micro kits from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nematodes that were exposed to 500µM of FW1256 from L1 stage larvae onwards.

value: Bristol N2

value: whole body

value: age of day 6


title: 2-3nes

description:
2ug
WT2


title: N2+FW1256_2 [NH2]

description: processed data file: FW_vs_wt

value: 500µM of FW1256 from L1 stage larvae onwards


title: N2+FW1256_1 [NH1]

description: processed data file: FW_vs_wt


title: HiC_CTCF-AID_NPC_d4_washout_rep2

value: F123 mouse neural precursor cell


title: 2-1wt

description:
2ug
WT1


title: 2-4ko

description:
2ug
CKO1


title: HiC_CTCF-AID_NPC_d4_washout_rep1


title: PLAC_H3K4me3_CTCF-AID_NPC_d4_ctl_rep1

description:
plac_h3k4me3_npc_d4_ctl_maps_peak.pgl
plac_h3k4me3_npc_d4_ctl_fithichip_peaks.pgl


title: N2(wild type)_4 [NC4]

description: processed data file: eat2_vs_wt.csv, FW_vs_wt

source_name: N2(wild type)

value: wild type


title: N2(wild type)_2 [NC2]


title: 697_MED1_ChIPSeq

value: pre-B leukemic cell line 697

value: anti-MED1 (A300-793A, Lot no. 2, Bethyl)


title: N2(wild type)_1 [NC1]


title: PLAC_H3K4me3_CTCF-AID_ESC_auxin_0hr_rep1

description:
plac_h3k4me3_esc_ctl_maps_peak.pgl
plac_h3k4me3_esc_ctl_fithichip_peaks.pgl


title: DA1116(eat-2)_4 [DC4]

description: processed data file: eat2_vs_wt.csv

value: eat-2 mutant


title: DA1116(eat-2)_3 [DC3]

description: processed data file: eat2_vs_wt.csv


title: AsIL12Aoff3

value: embryonic kidney

value: HEK 293


title: N2+FW1256_3 [NH3]

description: processed data file: FW_vs_wt


title: P Sox10_Input

city: Kensington

first: Kristopher

middle: A

last: Kilian

state: UNSW

address: Hilmer Building 740

country: Australia

institute: University of New South Wales

description: PvsNP-ChIP-data

data_processing:
Sequence data were mapped with Bowtie2 (Langmead and Salzberg 2012) to the UCSC Mus musculus mm9 genome.
Mapped sequence data were analyzed for peaks using HOMER (Hypergeometric Optimization of Motif EnRichment) v4.7 (Heinz et al. 2010).
Samples were converted into tag directories, and QC was performed using read mapping and GC bias statistics.
Histone peaks were  called from the Tag Directories with default factor settings, except local filtering was disabled (-L 0) and input filtering was set at three-fold over background (-F 3), to increase the sensitivity of the peak calling and identify individual subunits of multihistone peaks.
After peak calling, peak files were annotated to the mouse mm9 genome using HOMER’s annotation script to assign peaks to genes, and associate peaks with differential expression data.
Genome_build: mm9
Supplementary_files_format_and_content: .xlsx format conatining ChiP-seq data sets for patterned and non-patterned

source_name: B16F0 melanoma cancer cells

growth_protocol: Murine B16F0 melanoma cancer cells were cultured on patterned or non-patterned substrates for 5 days.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

tag: disease state

value: skin melanoma

tag: substrate

value: pattern


title: NP H3Input_ChipSeq

description: PvsNP-ChIP-data

value: non-pattern


title: P Sox10_ChIPSeq

description: PvsNP-ChIP-data


title: NP Sox10_ChIPSeq

description: PvsNP-ChIP-data


title: NP Sox10_Input

description: PvsNP-ChIP-data


title: DA1116(eat-2)_2 [DC2]

description: processed data file: eat2_vs_wt.csv

tag: tissue


title: P H3Input_ChipSeq

description: PvsNP-ChIP-data

tag: chip antibody


title: HiC_CTCF-AID_auxin_24hr

tag: cell line

value: F123 mouse ES cell


title: P H3K4me2_ChIPSeq

description: PvsNP-ChIP-data

value: H3K4me2 (Cell Signaling, 9725)


title: NP H3K4me2_ChIPSeq

description: PvsNP-ChIP-data


title: NP H3K9ac_ChIPSeq

description: PvsNP-ChIP-data

value: H3K9ac (Cell Signaling, 9649)


title: L-80-2

city: Stockholm

first: Sourav

middle: Prasanna

last: Mukherjee

address: IMM, Karolinska Institutet

country: Sweden

institute: KI

data_processing:
bcl2fastq_v2.19.1.403 from Illumina CASAVA software suite for Bcl to FastQ conversion
the preprocessed sequencing reads were aligned against the Homo sapiens (GRCh37) reference genome using STAR version 2.5.1b
the read-counts to genes were generated using a software featureCounts version 1.5.1
Full-length transcripts representing multiple splice variants for each gene locus were assembled and quantitated using StringTie version 1.3.3
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample and one tab-delimited text file include the merged read counts for each gene provided in the reference gtf file for all samples

source_name: Bronchial epithelial cell line

growth_protocol: The immortalized human bronchial epithelial cell line, BEAS 2B (European Collection of Cell Cultures) was maintained in bronchial epithelial cell growth medium (BEGM, Lonza) supplemented with BEGM bullet-kit (Lonza) [recombinant epidermal growth factor (EGF), bovine pituitary extract, GA-1000 (gentamicin sulfate and amphotericin-B), hydrocortisone, insulin, retinoic acid, transferrin, triiodothyronine and epinephrine]. Cells were cultured in flasks and plates pre-coated with 0.01 mg/mL fibronectin, 0.03 mg/mL bovine collagen type I, and 0.01 mg/mL bovine serum albumin in BEGM additive free medium for 2 h prior to the seeding. Cells were maintained in a humidified atmosphere at 37°C, 5% CO2 and sub-cultured at 80% confluency.

extract_protocol:
Total RNA was extracted from cells harvested at 48 h, 7 days, and 28 days of exposure to GO-US, GO-S, and GO-L using the RNeasy Mini Columns (Qiagen) in accordance with manufacturer’s instructions (including the purification step with DNase I). Total RNA concentration was determined spectrophotometrically using NanoDrop (NanoDrop Technologies). Quality control was conducted using the Bioanalyzer 2100 (Agilent Technologies) and all samples had RNA integrity numbers (RIN) above 8. Triplicates of each sample at different time-points and exposures were submitted for sequencing.
Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA, USA) was used to prepare mRNA sequencing libraries. Briefly, 1000 ng of total RNA was used for mRNA isolation using poly dT-coated beads

treatment_protocol: For short-term exposure (48 h), BEAS-2B were seeded in 6 well-plates (2.5x104 cells/mL) and were allowed to attach for 3 h prior to the exposure. For long-term exposure (up to 28 days), BEAS-2B were seeded in T25 flasks (2.5x104 cells/mL) and allowed to attach for 3 h prior to the exposure. After cell attachment, cells were exposed to GO. For long-term experiments, cells were exposed for 7 and 28 days, in triplicate, to 1 μg/mL and 5 μg/mL GO. To this end, the cells were split, counted, reseeded twice a week (2.5x104 cells/mL) and re-exposed to the respective GOs. While for short term exposure, cells were exposed for 48 h to 8 μg/mL, 40 μg/mL, or 80 μg/mL.

value: Immortalized normal human bronchial epithelial cell line

tag: exposure time

value: 1 day

tag: go dose

value: 80 ug/ml


title: L-80-1


title: P H3K9ac_ChIPSeq

description: PvsNP-ChIP-data


title: N2(wild type)_3 [NC3]

value: Bristol N2

value: whole body

tag: age

value: age of day 6


title: L-40-3

value: 40 ug/ml


title: Ctnnb1_OV_placenta_E8.5 [Ex3KO_RPKM]

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

description: Sample 2 (Ctnnb1_OV)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: E8.5 placenta

extract_protocol:
Placenta were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Ctnnb1 overexpression

value: Placenta


title: L-40-1

tag: cell type


title: WT_placenta_E8.5 [WT_RPKM]

description: Sample 1 (wt)

value: wild type


title: CHIR treated differentiated TSC

description: Sample 2(TCF_CHIR)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 with default parameters
MACS2 was used to call the peaks of TCF binding using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: pileup peaks

source_name: differentiated TSC

growth_protocol: Established TS cells were maintained in a proliferative state in the media containing 70% embryonic fibroblast-conditioned medium (FCM), 30% TS cell medium, FGF4 (25 ng/ml) and heparin (1 µg/ml). For TS cells differentiation, TS cell medium was used but without supplementation of bFGF, heparin, and FCM, in the presence of CHIR99021 (Biovision) or not. Then differentiated trophoblast cells were collected at indicated times for further examination.

extract_protocol:
TS cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified.
ChIP was performed according to the reported previousl with slight modification. Briefly, about 2x10^6 TS cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified. The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150.

value: Non-phospho (Active) β-Catenin (Ser33/37/Thr41) (D13A1),Cell signaling Technology (CST); #8814;  lot 4


title: L-8-3

value: 8 ug/ml


title: L-8-2


title: 4C_dCas9_GB1_e

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
Library strategy: 4C-seq
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Reads were aligned to the reference mouse genome (NCBI37/mm9) using the Bowtie program (version 1.2.2)
File format is  transformed to BAM using samtools version 1.9
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: zipped bedGraph files include RPM values for each Sample

source_name: Neuro-2A cell

growth_protocol: Mouse Neuro-2A cells were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.

extract_protocol:
The cells were centrifuged at 500 g for 5 min and the pellets were used for QHR-4C experiments. The cell pellets were suspended for crosslinking in 900 ml 2% formaldehyde at room temperature for 10 min. The crosslinking reaction was stopped by adding and mixing with 100 ml of 2M glycine for a final concentration of 200 mM. The fixed cells were spin down at 800 g at 4 °C for 5 min and washed twice by suspending briefly in 1 ml ice-cold PBS. Cells were then permeabilized twice with 200 ml ice-cold 4C permeabilization buffer each for 10 min (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, and 1× protease inhibitors).
The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions.  The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).

treatment_protocol: Neuro-2A cell at ~80% confluency is used for transfection. Briely, for each well in the 6-well plate, 1.25ug of dCas9 plasmid and 1.25ug of sgRNA plasmid (For multiple sgRNA combination, all sgRNA share the 1.25ug) is transfected using the Lipofectamine 3000 transfection reagent. 48 hr after transfection, puromycin (Sigma) was added to the culture medium at a final concentration of 2ug/ml. The culture medium was replaced every day with puromycin for a total of 3 days. Puromycin was then removed and cells were cultured in normal culture medium for 2 days.

value: Neuro-2A cells

tag: genotype

value: CBS e blocked


title: L-80-3


title: 4C_dCas9_GB1_f

value: CBS f blocked


title: RNAseq, D3, Replicate 2

city: PARIS

first: Mengliang

last: YE

address: 26 Rue d'ULM

country: France

institute: Institut Curie

data_processing:
RNAseq were aligned to the unique locations of the mouse reference genome mm10 using Tophat v2.0.6.
ATAC-seq and ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.1.0 with the following configurations : Method: Global alignment - 1 mismatch in seed alignment ; Algorithm used: Choose uniquely the alignment with the best score;
ATAC data were filtered using the following specifications : MAPQ30 ; ChIP data were filtered using the following specifications : MAPQ20
H3K4me3-normalized.wig files were generated using SICER version 1.1 (each with its own Input) with the following setting: windows size w = 500, gap size g = 1500, FDR = 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using Deeptools v3.1.1 :  bamCoverage –normalizeUsing BPM, --binSize 10
Supplementary_files_format_and_content: H3K4me3-normalized.wig files were generated using SICER version 1.1

source_name: CD8+ T cells

growth_protocol: Naive T cells were isolated from C57BL/6J TCR transgenic mice (OT-I) and either used non-activated (D0) or seeded in plates coated with 10μg/mL of CD3e, in the RPMI medium supplemented with 10% of FCS, rhIL-2 (40UmL), 2-mercaptoethanol, Pen-Strep, L-glutamine, non-essential amino acids and 1μg/mL of anti-CD28 antibodies

extract_protocol:
For ATAC-Seq, 50 000 cells were lysed and treated with Tn Transposase, then purified using MinElute PCR purification kit (Qiagen). For ChIP-Seq, histone-DNA complexes were isolated from sonicated nuclei using bead-immobilized antibody. DNA was isolated by phenol/chloroform extraction. For RNAseq, cells were lysed in Trizol, and total RNA was isolated using Qiagen columns. RNA was treated with DNAse once on-column and once in-tube using Turbo DNAse kit (Thermo FIsher).
ATAC-Seq libraries were prepared using Nextera PCR primers (Illumina). ChIP-Seq libraries were prepared using TruSeq ChIP Libary Preparation Kit (Illumina). RNAseq libraries were prepared using KAPA Stranded RNA-Seq with RiboErase Kit (Roche/KAPA Biosystems)


title: DA1116(eat-2)_1 [DC1]

description: processed data file: eat2_vs_wt.csv

tag: genotype/variation

value: eat-2 mutant


title: RNAseq, D3, Replicate 1

tag: time point


title: L-8-1


title: 4C_dCas9_GB1_de

value: CBS de blocked


title: S-80-3

value: Immortalized normal human bronchial epithelial cell line


title: L-40-2

value: 1 day


title: RNAseq, D1, Replicate 3


title: S-80-2

value: 80 ug/ml


title: 4C_dCas9_GB1_d

value: CBS d blocked


title: 4C_dCas9_GB1_ctr

value: Control


title: DMSO treated differentiated TSC

description: Sample 1 (TCF_DMSO)


title: RNAseq, D1, Replicate 2


title: S-80-1


title: 151483C_T-1

type: RNA

city: Tianjin

first: chunyang

last: jiang

address: 190 Jieyuan Road, Hongqiao District, Tianjin

institute: Tianjin Union Medical Center

hyb_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by the Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. After purification with Nucleospin ® Extract II kit, the elution volume was about 30 L.Two tubes of cy3-dctp labeled purified products were mixed.Hybrid system and hybrid reaction.Chip cleaning and scanning.

scan_protocol: Agilent chip scanner (G2565CA) was used to scan the cleaned chip and obtain the hybrid picture

data_processing:
Agilent Feature Extraction (v10.7) software was used to analyze the hybrid images and extract the data.Then, Agilent GeneSpring software was used to normalize and analyze the data.
Scan the tiff image with the Feature Extraction software to obtain the original data file (.txt). Import the original data file (.txt) into GeneSpring software and write the grouping and other parameter information.Conduct data normalization and QC analysis for each sample.Normalization (standardization) method: The default method is the normalization of GeneSpring GX's Percentile 75 method (with each chip itself) Divide the 75 percentile values of the data to get the ratio), and then take the value generated after log2;Another alternative approach. The other method is the normalization of Quantile method of GeneSpring GX software, and then the value generated after log2.

source_name: BMs from  LADC

label_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

extract_protocol: Total RNA was first extracted from the specimens using Trizol reagent and purified with Total RNA was first extracted from the specimens using Trizol reagent and purified with NucleoSpin ® RNA clean-up

tag: gender

value: female

tag: Stage

value: Ⅳ

value: lung adenocarcinoma (LADC)

value: bone marrow cells (BM)


title: RNAseq, D0, Replicate 4

tag: strain


title: 151483C_T-3

value: male


title: 151483C_T-2


title: RNAseq, D1, Replicate 1


title: 4C_dCas9_GB1_be

value: CBS be blocked


title: 4C_dCas9_GB1_bcd

value: CBS bcd blocked


title: S-40-2

value: 40 ug/ml


title: S-40-3


title: 151483C_N-1

source_name: Adjacent to carcinoma

value: paired paracancerous tissue


title: 4C_dCas9_GB1_bc

value: Neuro-2A cells

value: CBS bc blocked


title: 1201Cvs1201P

description:
JD-YX-2015-1483-JSFU-01
1201Cvs1201P:cy5ByCy3Signal(normalized)

hyb_protocol: cDNA labeled with a fluorescent dye (Cy3 or Cy5-dCTP) was produced by the Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. After purification with Nucleospin ® Extract II kit, the elution volume was about 30 L.Two tubes of cy3 or Cy5-dCTP labeled purified products were mixed.Hybrid system and hybrid reaction.Chip cleaning and scanning.

source_name: Lung cancer

label_protocol: 1.5 ug of Cy3 or Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

tag: tumor stage

value: Ⅱb

tag: alternative id

source_name: adjacent to carcinoma


title: 0801Cvs0801P

description:
JD-YX-2015-1483-JSFU-01
0801Cvs0801P:cy5ByCy3Signal(normalized)

value: Ⅱa


title: Top2 spike-in ChIP for top2-1 T=3 34C rep1

description: AH7606-3h_rep1_spikein-191118_YueSK1_S288C_PM_SPMR_FE.bdg

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The quantitative ChIP-seq reads were mapped to concatenated genome assemblies of SK1 and S288c genomes (Yue et al., 2017) using Bowtie (Langmead et al., 2009). Only reads that mapped to a single position and also matched perfectly to the SK1 or S288c genomes were retrieved for further analysis.
The 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. The input and ChIP read counts were used to calculate spike-in normalization factor.
The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used.
Genome_build: SK1 and S288c (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph, txt (read counts)

extract_protocol:
For quantitative ChIP-seq samples, 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched with 125 mM glycine. S288c crosslinked meiotic cells were added to respective samples at 20% prior to ChIP processing (Vale Silva et al., 2018). Samples were processed as described in (Blitzblau et al., 2012).
Libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). Quality of all libraries was checked on 2200 Tapestation. Libraries were quantified using qPCR. The libraries were sequenced on Illumina NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 100 bp single-end reads.

value: SK1/ S288c spike-in

tag: treatment

value: 3 hour 34C

tag: strain id

tag: antibody


title: RNAseq, D0, Replicate 2


title: RNAseq, D0, Replicate 3


title: top2-1 T=3 spike-in input 34C rep2

description: AH7606-3h_rep2_spikein-191118_YueSK1_S288C_PM_SPMR_FE.bdg

source_name: top2-1 T=3 spike-in input 34C rep2

tag: chip antibody

value: none (input)


title: Top2 spike-in ChIP for top2-1 T=3 34C rep2


title: S-8-3

value: Immortalized normal human bronchial epithelial cell line

tag: exposure time

value: 1 day

value: 8 ug/ml


title: top2-1 T=3 spike-in input 34C rep1

source_name: top2-1 T=3 spike-in input 34C rep1


title: 151483C_N-3

value: Ⅳ

tag: tissue


title: 1703Cvs1703P

description:
JD-YX-2015-1483-JSFU-01
1703Cvs1703P:cy5ByCy3Signal(normalized)

value: lung adenocarcinoma (LADC)


title: 1101Cvs1101P

description:
JD-YX-2015-1483-JSFU-01
1101Cvs1101P:cy5ByCy3Signal(normalized)

value: female


title: 2002Cvs2002P

description:
JD-YX-2015-1483-JSFU-01
2002Cvs2002P:cy5ByCy3Signal(normalized)

value: male


title: 4C_dCas9_GB1_ae

value: CBS ae blocked


title: 151483C_N-2

tag: age

value: bone marrow cells (BM)


title: RNAseq, D0, Replicate 1


title: S-8-2

tag: go dose


title: S-40-1

tag: cell type

value: 40 ug/ml


title: 4C_dCas9_GB1_af

value: Neuro-2A cells

tag: genotype

value: CBS af blocked


title: S-8-1


title: WT T=3 spike-in input 30C rep3

description: AH7797-3h_spikein-191118_YueSK1_S288C_PM_SPMR_FE.bdg

source_name: WT T=3 spike-in input 30C rep3

tag: genotype/variation

value: 3 hour


title: 4C_dCas9_GB1_a

value: CBS a blocked


title: Top2 spike-in ChIP for WT T=3 30C rep3

source_name: Top2 spike-in ChIP for WT T=3 30C rep3

value: SK1/ S288c spike-in


title: US-80-3

value: 80 ug/ml


title: H3K4me3 ChIPseq, D3, Replicate 2

tag: time point


title: WT T=0 spike-in input rep3

description: AH7797-0h_spikein-191118_YueSK1_S288C_PM_SPMR_FE.bdg

source_name: WT T=0 spike-in input rep3

value: none (input)


title: US-80-2

value: Immortalized normal human bronchial epithelial cell line


title: Input DNA,D3, Replicate 1


title: Top2 spike-in ChIP for WT T=0 rep3

source_name: Top2 spike-in ChIP for WT T=0 rep3


title: 4C_dCas9_CBSg_e

value: CBS e blocked


title: H3K4me3 ChIPseq, D3, Replicate 1


title: US-80-1

value: 1 day


title: 4C_dCas9_CBSg_de

value: CBS de blocked


title: WT T=3 spike-in input 34C rep2

description: AH7797-34C-3h-rep2_spikein-191219_YueSK1_S288C_PM_SPMR_FE.bdg

source_name: WT T=3 spike-in input 34C rep2

value: 3 hour 34C


title: US-40-3


title: Top2 spike-in ChIP for WT T=3 34C rep2

source_name: Top2 spike-in ChIP for WT T=3 34C rep2


title: 4C_dCas9_CBSg_d

value: CBS d blocked


title: Input DNA,D0, Replicate 1


title: H3K4me3 ChIPseq, D0, Replicate 2


title: 4C_dCas9_CBSg_be

value: CBS be blocked


title: Top2 spike-in ChIP for WT T=3 34C rep1

description: AH7797-34C-3h_spikein-191219_YueSK1_S288C_PM_SPMR_FE.bdg

source_name: Top2 spike-in ChIP for WT T=3 34C rep1


title: US-40-2

source_name: Bronchial epithelial cell line


title: Input DNA,D3, Replicate 2


title: US-40-1


title: 4C_dCas9_CBSg_f

value: CBS f blocked


title: WT T=3 spike-in input 34C rep1

source_name: WT T=3 spike-in input 34C rep1


title: 4C_dCas9_CBSg_bcd

source_name: Neuro-2A cell

value: CBS bcd blocked


title: H3K4me3 ChIPseq, D0, Replicate 1

source_name: CD8+ T cells


title: US-8-3

value: 8 ug/ml


title: 4C_dCas9_CBSg_bc

value: Neuro-2A cells

value: CBS bc blocked


title: ATACseq, D3, Replicate 2


title: Top2 spike-in ChIP for spo11 T=3 rep2

description: AH5184-3h_spikein-191118_YueSK1_S288C_PM_SPMR_FE.bdg

source_name: Top2 spike-in ChIP for spo11 T=3 rep2

value: 3 hour


title: spo11 T=3 spike-in input for Top2 chip rep2


title: ATACseq, D3, Replicate 1


title: 4C_dCas9_CBSg_ctr

value: Control


title: Top2 spike-in ChIP for spo11 T=3 rep1

description: AH5184spikein-3h-032718_YueSK1_S288C_PM_SPMR_PE_FE.bdg

source_name: Top2 spike-in ChIP for spo11 T=3 rep1

value: SK1/ S288c spike-in


title: US-8-2


title: US-8-1


title: ATACseq, D1, Replicate 2


title: Control-3

value: 0 ug/ml


title: 4C_dCas9_CBSg_af

value: CBS af blocked


title: Input DNA,D0, Replicate 2


title: 4C_dCas9_CBSg_ae

value: CBS ae blocked


title: spo11 T=3 spike-in input for Top2 chip rep1

value: none (input)


title: 4C_dCas9_CBSg_a

value: CBS a blocked


title: Control-2

value: Immortalized normal human bronchial epithelial cell line

value: 1 day


title: Control-1


title: rec8 T=3 spike-in input for Top2 chip rep2

description: AH5187-3h_rep2_spikein-191118_YueSK1_S288C_PM_SPMR_FE.bdg


title: Top2 spike-inChIP for rec8 T=3 rep2

source_name: Top2 spike-inChIP for rec8 T=3 rep2


title: 4C_dCas9_CBSf_f


title: 4C_dCas9_CBSf_e

value: CBS e blocked


title: ATACseq, D1, Replicate 1


title: ATACseq, D0, Replicate 2


title: GO-L_28D-5-2

value: 28 days

value: 5 ug/ml


title: ATACseq, D0, Replicate 1


title: Top2 spike-in ChIP for rec8 T=3 rep1

description: AH5187-3h_rep1_spikein-191118_YueSK1_S288C_PM_SPMR_FE.bdg

source_name: Top2 spike-in ChIP for rec8 T=3 rep1


title: 4C_p0-cortex_HS5-1_WT_rep4

data_processing:
Library strategy: 4C-seq
Sequenced reads were trimmed for adaptor sequence and the bait sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3).
Genome_build: hg19 for human, mm9 for mouse
Supplementary_files_format_and_content: bedGraph files: the reads per million (RPM) value in 4C-seq experiments.

source_name: P0 cortex

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). Human K562 cells (ATCC) were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.

extract_protocol:
After cross-linking with 2% formaldehyde, cells were lysed twice with cold lysis buffer, digested with DpnII, ligated with T4 DNA ligase.
4C libraries were generated by PCR.

value: P0 cortex

value: wildtype

tag: affected genomic coordinate


title: 4C_dCas9_CBSf_de

value: Neuro-2A cells

value: CBS de blocked


title: rec8 T=3 spike-in input for Top2 chip rep1

value: 3 hour


title: GO-L_28D-5-1


title: 4C_p0-cortex_HS5-1_WT_rep2


title: GO-L_28D-1-3

value: 1 ug/ml


title: 4C_dCas9_CBSf_ctr

value: Control


title: 4C_p0-cortex_HS5-1_WT_rep3


title: GO-L_28D-1-1


title: GO-L_28D-1-2


title: 4C_dCas9_CBSf_be

value: CBS be blocked


title: GO-S_28D-5-3


title: 4C_p0-cortex_HS5-1_HS5-1bdel_rep4

value: HS5-1b deletion


title: 4C_p0-cortex_HS5-1_WT_rep1


title: 4C_dCas9_CBSf_bcd

value: CBS bcd blocked


title: 4C_dCas9_CBSf_bc

value: CBS bc blocked


title: 4C_dCas9_CBSf_af

value: CBS af blocked


title: 4C_p0-cortex_HS5-1_HS5-1bdel_rep2


title: GO-S_28D-5-2

value: Immortalized normal human bronchial epithelial cell line


title: Top2 ChIP for WT T=3 spike-in rep2

description:
processed data file:
Top2-WT3h-748-847-reps_S288C_SK1_Yue_PM_SPMR_FE.bdg

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq and MNase-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). SNP-ChIP library reads were aligned to concatenated genome assemblies of SK1 and S288c genomes.  Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis. The RNA-seq reads were mapped to the SK1 genome using Tophat2 with first strand library type, no novel junctions, and otherwise default options.
For ChIP-seq, 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses. For MNase-seq, 3' ends were extended to a final length of 146 and bandwidth was set to 350 using MACS2 2.1.1. MNase-seq pileups were SPMR-normalized, which was used for further analyses. For RNA-seq, mapped reads were counted using featureCounts and statistical analysis was performed using a count-based workflow with the edgeR Bioconductor package.
For ChIP-seq, the input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses. For MNase-seq, the pileup was SPMR-normalized and used for further analyses. For RNA-seq, gene counts were normalized to counts per million and were then gene length-corrected for transcripts per million (tpm).
Bedgraph files and peak files for some samples were created from pooled replicates of ChIP-seq. MNase-seq data was pooled with published MNase-seq data from (Pan et al 2011). CSV file was created for RNA-seq.
Genome_build: SK1 and S288c (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph, BED6+3, CSV (RNA-seq)

source_name: Top2 ChIP for WT T=3 spike-in rep2

extract_protocol:
For ChIP-seq samples, 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. For MNase-seq samples, 50 ml of the meiotic cells were collected at the 3-hr time point and fixed for 30 min in 1% formaldehyde.  The formaldehyde was quenched with 125 mM glycine. ChIP-seq samples were processed as described in (Blitzblau et al., 2012). MNase-seq samples were processed as described in (Pan et al., 2011). For quantitative ChIP-Seq (SNP-ChIP), S288c crosslinked meiotic cells were added to respective samples at 20% prior to ChIP processing (Vale Silva et al., 2018). For RNA-seq, 1.5 ml meiotic culture was taken at the 3-hr time point and RNA was extracted from mechanically lysed cells using the Qiagen RNeasy RNA isolation Kit and mRNA was extracted using Sera-Mag oligo-dT beads and fragmented.
For MNase-seq and ChIP-seq, libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). For RNA-seq, libraries were prepared according to the Illumina TruSeq Stranded mRNA sample preparation kit, and sequencing libraries were prepared by PCR from the cDNA samples after ligation of adapters. Quality of all libraries was checked on 2200 Tapestation. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads, 75 bp single-end reads, or 100 bp single-end reads.

tag: genetic background

value: SK1/ S288c spike-in


title: WT T=3 input spike-in rep2

source_name: WT T=3 input spike-in rep2

value: none (input)


title: GO-S_28D-5-1

value: 28 days


title: 4C_dCas9_CBSf_ae

value: CBS ae blocked


title: 4C_p0-cortex_HS5-1_HS5-1bdel_rep1

value: P0 cortex


title: GO-S_28D-1-3


title: WT T=3 input spike-in rep1

source_name: WT T=3 input spike-in rep1


title: 4C_dCas9_CBSf_a

value: CBS a blocked


title: 4C_p0-cortex_HS5-1_HS5-1adel_rep2

value: HS5-1a deletion


title: 4C_dCas9_CBSf_d

value: Neuro-2A cells

value: CBS d blocked


title: 4C_dCas9_B17_f

value: CBS f blocked


title: GO-S_28D-1-2

value: 1 ug/ml


title: Top2 ChIP for WT T=0 spike-in rep2

description:
processed data file:
Top2-WT0h-747-846-reps_S288C_SK1_Yue_PM_SPMR_FE.bdg

source_name: Top2 ChIP for WT T=0 spike-in rep2

value: 0 hour


title: Top2 ChIP for WT T=3 spike-in rep1

source_name: Top2 ChIP for WT T=3 spike-in rep1

value: 3 hour


title: GO-US_28D-5-1

value: 5 ug/ml


title: 4C_p0-cortex_HS5-1_HS5-1adel_rep1


title: GO-S_28D-1-1


title: 4C_p0-cortex_HS5-1_HS5-1bdel_rep3

value: HS5-1b deletion


title: 4C_p0-cortex_b3_WT_rep4

value: wildtype


title: WT T=0 input spike-in rep2

source_name: WT T=0 input spike-in rep2


title: Top2 ChIP for WT T=0 spike-in rep1

source_name: Top2 ChIP for WT T=0 spike-in rep1


title: 4C_dCas9_B17_e

value: CBS e blocked


title: 4C_dCas9_B17_de

value: CBS de blocked


title: 4C_p0-cortex_b3_WT_rep3


title: WT T=0 input spike-in rep1

source_name: WT T=0 input spike-in rep1

value: SK1/ S288c spike-in

value: none (input)


title: 4C_dCas9_B17_d


title: 4C_p0-cortex_b3_WT_rep2


title: 4C_dCas9_B17_be

value: CBS be blocked


title: GO-US_28D-1-2

source_name: Bronchial epithelial cell line

value: Immortalized normal human bronchial epithelial cell line

value: 28 days


title: 4C_p0-cortex_b3_WT_rep1

value: P0 cortex


title: 4C_dCas9_B17_ctr

value: Neuro-2A cells

value: Control


title: 4C_p0-cortex_b3_HS5-1bdel_rep4


title: GO-US_28D-1-1


title: WT T=3 input 34C for Red1 rep3

description:
processed data file:
Red1-WT-34C-410-495-528-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: WT T=3 input 34C for Red1 rep3

value: 3 hour 34C


title: 4C_dCas9_B17_bcd

source_name: Neuro-2A cell

value: CBS bcd blocked


title: 4C_dCas9_B17_bc

value: CBS bc blocked


title: 4C_p0-cortex_b3_HS5-1bdel_rep2


title: 4C_dCas9_B17_af

value: CBS af blocked


title: 4C_p0-cortex_b3_HS5-1bdel_rep1


title: Control_28D-2

value: 0 ug/ml


title: Top2 ChIP for top2-1 T=3 34C rep2

description:
processed data file:
Top2-top2-4-496-537-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Top2 ChIP for top2-1 T=3 34C rep2


title: Red1 ChIP for WT T=3 34C rep3

source_name: Red1 ChIP for WT T=3 34C rep3


title: 4C_dCas9_B17_ae

value: CBS ae blocked


title: 4C_p0-cortex_b3_HS5-1bdel_rep3

value: HS5-1b deletion


title: GO-L_7D-5-3

value: 7 days

value: 5 ug/ml


title: 4C_p0-cortex_b3_HS5-1adel_rep1

value: HS5-1a deletion


title: GO-US_28D-1-3

value: 1 ug/ml


title: GO-L_7D-5-2


title: 4C_dCas9_B17_a

value: CBS a blocked


title: Top2 ChIP for WT T=3 34C rep2

description:
processed data file:
Top2-wildtype-34C-493-533-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Top2 ChIP for WT T=3 34C rep2


title: Control_28D-1

value: Immortalized normal human bronchial epithelial cell line


title: PM_2

city: Lexington

first: Elizabeth

middle: Anne

last: Schroder

state: KY

address: 800 Rose Street, MS508

department: Physiology

institute: University of Kentucky

description: Wild Type

data_processing:
Basecalling, alignment, filtering, peak calling, normalized ambundance measurements were performed by the Novogene company.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM, readcount

source_name: left ventricle

extract_protocol:
Mice were euthanized with CO2 and LV tissue was removed and snap frozen.  Total RNA was harvested using trizol. Construction of sequencing libraries was performed by Novogene (250~300 bp insert cDNA library, (eukaryotic mRNA non-directional Library--NEB))
250~300 bp insert cDNA library, (eukaryotic mRNA non-directional Library--NEB) Library construction was performed bo Novogene company.

tag: strain

value: left ventricle

value: Wild Type

value: 12 months


title: Control_28D-3

value: 28 days


title: Top2 ChIP for WT T=3 34C rep1

source_name: Top2 ChIP for WT T=3 34C rep1

value: 3 hour 34C


title: GO-L_7D-1-3


title: GO-L_7D-1-2


title: AM_2

description: Wild Type


title: GO-L_7D-1-1


title: AM_1

description: Scn5aΔ/+ (ΔKPQ)

value: Scn5adelta/+ (deltaKPQ)


title: 4C_p0-cortex_b3_HS5-1adel_rep2

source_name: P0 cortex

value: P0 cortex


title: GO-L_7D-5-1


title: GO-S_7D-5-3


title: GO-S_7D-5-2


title: GO-S_7D-5-1


title: PM_1

description: Scn5aΔ/+ (ΔKPQ)


title: GO-S_7D-1-3


title: GO-S_7D-1-2


title: GO-US_7D-5-3


title: Myc ChIP for WT no tag T=3h rep2

description:
processed data file:
AH7797Myc-190130-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Myc ChIP for WT no tag T=3h rep2

value: 3 hour

value: anti-Myc


title: GO-S_7D-1-1


title: Vehicle replicate 4, GFP- cells from 3 mice [4V-_101816_(Clariom_S_Mouse)_2.sst-rma-gene-full-Signal ]

first: Timothy

middle: S

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

institute: University of kentucky

description: mRNA abundance data

hyb_protocol: after fragmentation cRNA was hybridized for 16 hr at 45C on Clariom S Arrays. These were washed and stained in an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 7G Scanner

data_processing: The data were analyzed with Affymetrix Gene Expression Console software using default analysis settings and global scaling as normalization method.

source_name: Olfactory mucosa; Vehicle-stimulated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 - 100 ng of total RNA.

growth_protocol: 24 mice of both sexes, ages 7 - 12 weeks, were placed individuallly in clean air chambers for 40 hrs under air flow of 3.1L/min

extract_protocol: Mice were euthanized, olfactory mucosa were dissected, dissociated, and subjected to FACS.

treatment_protocol: After 26 hrs, half the mice were intermittently stimulated with vehicle (filtered air) or odorant for 10 sec every 20 min.

tag: agent

value: Vehicle-stimulated

value: FACS sample, GFP-


title: ASD-5 ELUTED

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description: Pool of two ASD cases

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)

molecule: polyA RNA

source_name: Prefrontal Cortex BA8

label_protocol: 5 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2). Amplification was performed for 21 cycles. 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Brain specimens used in this study from frontal and temporal cortex of ASD patients and controls were provided by University of Maryland Brain and Tissue Bank, NIH NeuroBioBank (NBB) (Baltimore,MD). Written informed consent for brain removal after death for diagnostic and research purposes was obtained from brain donors and/or next of kin. Procedures, information and consent forms have been approved by the Bioethics Subcommittee.

extract_protocol: Prefrontal cortex samples were homogenized and total RNA (Input) was extracted using the Maxwell® 16 LEV simplyRNA Tissue Kit (Promega). The poly(A) RNA fraction was purified by poly(U) chromatography (Poly(U)-agarose, Sigma). Differential elution with 25% or 90% formamide yielded two fractions of mRNAs enriched for short (WASH) or long (ELUTED) poly(A)-tails, respectively. The RNA of the two poly(A) fractions was precipitated with isopropanol and purified by Phenol:Chloroform protocol.

tag: group

value: ASD

tag: material

value: ELUTED

tag: postmorten interval (h)

tag: hybridization batch

value: B

value: Prefrontal Cortex BA8

tag: rna fraction

value: Enriched in long poly(A)-tail RNA


title: Vehicle replicate 4, GFP+ cells from 3 mice [4V+_101816]

description: mRNA abundance data

value: FACS sample, GFP+


title: GO-US_7D-5-2

value: Immortalized normal human bronchial epithelial cell line

tag: exposure time

value: 7 days

value: 5 ug/ml


title: WT no tag T=3h input for MYC rep2

source_name: WT no tag T=3h input for MYC rep2

tag: treatment

tag: strain id

tag: chip antibody

value: none (input)


title: Vehicle replicate 2, GFP- cells from 3 mice [2V-_101816]

description: mRNA abundance data

tag: cell type


title: Vehicle replicate 3, GFP+ cells from 3 mice [3V+_101816]

description: mRNA abundance data


title: Vehicle replicate 1, GFP- cells from 3 mice [1V-_101816]

description: mRNA abundance data


title: GO-US_7D-5-1

tag: go dose


title: ASD-4 INPUT

source_name: Prefrontal Cortex BA8/9

value: INPUT

tag: age

tag: tissue

value: Prefrontal Cortex BA8/9

value: total RNA


title: Myc ChIP for WT no tag T=3h rep1

description:
processed data file:
AH7797Myc-181030-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Myc ChIP for WT no tag T=3h rep1

value: 3 hour


title: Odor replicate 4, GFP- cells from 3 mice [4CA-_101816]

description: mRNA abundance data

source_name: Olfactory mucosa; citrus accord-stimulated

value: 100 percent citrus accord-stimulated


title: ASD-5 INPUT

description: Pool of two ASD cases


title: Vehicle replicate 3, GFP- cells from 3 mice [3V-_101816]

description: mRNA abundance data

value: Vehicle-stimulated


title: ASD-5 WASH

description: Pool of two ASD cases

value: WASH

value: Enriched in short poly(A)-tail RNA


title: Odor replicate 4, GFP+ cells from 3 mice [4CA+_101816]

description: mRNA abundance data


title: Vehicle replicate 2, GFP+cells from 3 mice [2V+_101816]

description: mRNA abundance data


title: ASD-4 WASH

value: ASD


title: Odor replicate 3, GFP- cells from 3 mice [3CA-_101816]

description: mRNA abundance data

value: FACS sample, GFP-


title: ASD-3 ELUTED

source_name: Prefrontal Cortex BA9

value: ELUTED

value: B

value: Prefrontal Cortex BA9


title: Vehicle replicate 1, GFP+ cells from 3 mice [1V+_101816]

description: mRNA abundance data

value: FACS sample, GFP+


title: ASD-4 ELUTED

value: Enriched in long poly(A)-tail RNA


title: Top2 ChIP for top2-1 T=3 34C rep1

source_name: Top2 ChIP for top2-1 T=3 34C rep1

value: 3 hour 34C


title: ASD-3 WASH


title: GO-US_7D-1-3

source_name: Bronchial epithelial cell line

value: Immortalized normal human bronchial epithelial cell line

value: 7 days

value: 1 ug/ml


title: WT no tag T=3h input for MYC rep1

source_name: WT no tag T=3h input for MYC rep1

value: none (input)


title: GO-US_7D-1-2


title: GO-US_7D-1-1


title: A549 infected with Zika virus 3

city: Chengdu

first: Xinzhong

last: Liao

state: Sichuan

address: Institute of Blood Transfusion (IBT) Chinese Academy of Medical Sciences (CAMS)and Peking Union Medical College (PUMC)  Chengdu,Sichua

institute: Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Clean data(clean reads) were obtained by removing readscontaining adapter, reads on containing ploy-N and low quality reads from raw data.At the same time, Q20, Q30 and GC content of the clean data werecalculated.
Index of the reference genome was built using HISAT2 (Kim et al., 2015).
The mapped reads of each sample were assembled by StringTie (v1.3.3) (MihaelaPertea.et al. 2016) and Cufflinks(Trapnell et al., 2012).
Quantififcation and differential expression analysis was done using edgeR,ClusterProfiler(Yu G et al.,2012)and rMATS(Shen S et al., 2014).
Genome_build: GO and KEGG Enrichment were used GOseq,KOBAS,DESeq2(Michael et al., 2014),IRESfiner(Zhao et al., 2018),CPC2(Kang Y. J et al., 2017）,find_circ(Sebastian Memczak et al., 2013),CIRI(Fangqing Zhao et al., 2015),PFAM(S. El-Gebali et al.,2019）and CNCI(Liang Sun et al.,2013).
Supplementary_files_format_and_content: Transcript_FPKM.xlsx

growth_protocol: A549 cells were seeded in 12-wells plate, cells were laid overnight.

extract_protocol:
RNA purity ,concentration and integrity were assessed using NanoPhotometer® spectrophotometer (IMPLEN, CA, USA),Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer(Life Technologies, CA, USA)and the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: A549 cellscells were infected Zika virus at MOI of 0.5 for 4hrs,total RNA or protein of the cells was harvested at 48hrs.

tag: cell line

tag: infection

value: Zika virus


title: A549 infected with Zika virus 2


title: Control_7D-3

value: 0 ug/ml


title: A549 infected with Zika virus 1


title: Control_7D-2


title: A549 Control 3

value: control


title: ASD-3 INPUT

value: INPUT

value: total RNA


title: A549 Control 2


title: Control_7D-1


title: A549 Control 1


title: Odor replicate 3, GFP+ cells from 3 mice [3CA+_101816]

description: mRNA abundance data

value: 100 percent citrus accord-stimulated


title: CTRL-4 ELUTED

description: Pool of two CTRL individuals

value: CTRL


title: Odor replicate 1, GFP- cells from 3 mice [1CA-_101816]

description: mRNA abundance data

value: FACS sample, GFP-


title: Hi-C: SA2-AID clone 2 auxin

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institut für Pathologie

country: Germany

institute: Universitätsmedizin Göttingen

data_processing:
Raw reads were mapped, annotated, and corrected for biases using the Juicer suite 1.5 with default parameters.
After ensuring replicate reproducibility using HiCRep, data from the same treatments were merged for all downstream analyses also using Juicer 1.5 suite.
Compartment analysis was performed using the signal of the first principal component of the Pearson's Hi-C contact matrices.
TAD boundaries were identified using TADtool with default settings.
Chromatin contacts (loops) were called using Fit-Hi-C 2.0.5 with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Juicer suite's .hic contact matrices

source_name: HCT116 cells

growth_protocol: SA1-AID and SA2-AID cells were cultured in McCoy's 5A medium supplemented with 10% FBS and PSG. For all auxin degradation experiments using SA1-AID and SA2-AID cells auxin or the solvent ethanol as control were added for 12 hours.

extract_protocol:
Biotynilated DNA (Hi-C ligation junctions) was isolated using standard phenol/chloroform extraction followed by EtOH precipitation, sonicated to ~800 bp and repurified.
Libraries were prepared as described (Zirkel et al, Mol Cell, 2018) on the basis of the Illumina Mate-Pair protocol, by ligating sequencing linkers onto streptavidin-captured biotinylated DNA. All resulting DNA libraries were paired-end sequenced on an Illumina HSeq4000 platform to ~300 million read pairs each on a HiSeq4000 platform (Illumina).

treatment_protocol: mAIDmClover neomycin cassette (plasmid pMK289 obtained from Addgene) was inserted at the 3' end of the SA1 and SA2 genes, 500-800nt homology arms were inserted left and right to the cassette present in the pMK289 plasmid. A gRNA targeting the 3' end of the SA1 or SA2 gene in front of the stop codon was cloned into a Cas9 expression construct (Addgene p48193). Both, the gRNA/Cas9 plasmid as well as the plasmid carrying homology arms and mAID-mClover neomycin cassette were transfected into HCT116 CMV-OsTIR1 cells using FuGene HD (Promega). After 6 days selection with 700 µg/ml G418 the cells were FACS-sorted for mClover expression and seeded into 96 well plates to grow single clones. To induce protein degradation 500 µM indole-3-acetic acid (auxin, IAA) dissolved in ethanol was added to the cells.

value: HCT116 CMV-OsTIR1

tag: genotype

tag: library id

value: auxin


title: Odor replicate 2, GFP+ cells from 3 mice [2CA+_101816]

description: mRNA abundance data

tag: agent

value: FACS sample, GFP+


title: CTRL-3 WASH

tag: group

tag: material

value: WASH

value: B

value: Prefrontal Cortex BA8/9

value: Enriched in short poly(A)-tail RNA


title: CTRL-3 INPUT

tag: postmorten interval (h)

tag: hybridization batch


title: CTRL-4 WASH

description: Pool of two CTRL individuals

value: Prefrontal Cortex BA9

tag: rna fraction


title: Hi-C: SA2-AID clone 2 noauxin

tag: treatment

value: no auxin


title: Odor replicate 2, GFP- cells from 3 mice [2CA-_101816]

description: mRNA abundance data


title: Odor replicate 1, GFP+ cells from 3 mice [1CA+_101816]

description: mRNA abundance data