title: gtf_shNT2


title: FLAG-ZBTB24-5

status: Public on Jul 31 2018

type: SRA

city: Rochester

first: Keith

middle: Darrell

last: Robertson

state: MN

address: 200 First Street SW, Stabile 12-70

department: Pharmacology

country: USA

institute: Mayo Clinic

library_source: genomic

data_processing:
ChIP-seq peak calling was performed with MACS2 package and corrected for input. Narrow peak calling was performed on sequences from the FLAG-ZBTB24 (FDR cut-off = 0.01) lines and broad peak calling on the FLAG-DNMT3B lines (FDR cut-off = 0.005)
Raw reads were mapped to the hg19 genome and transcripts were assembles using HISAT2. Transcripts from all RNAseq samples were merged using Stringtie and differential expression was, defining log2 fold change, was performed on pooled samples using CuffLinks.
Genome_build: hg19
Supplementary_files_format_and_content: peak bed, FPKM, TPM, foldchange

molecule: genomic DNA

organism: Homo sapiens

source_name: Cell line

growth_protocol: HCT116 cells were grown in McCoy's 5A supplemented with FBS and L-glutamine. Stable FLAG-expressing lines and shRNA lines were created by lentiviral infection followed by selection in puromycin (0.75µg/mL). For FLAG-tagged lines, single cell clones were isolated by limiting dilution and propagated post screening by Western and immunofluoresence.

extract_protocol:
Genomic DNA was isolated and purified from cells in culture using a serial phenol: chloroform extraction. Trizol reagent was used for extracting total RNA following the manufacturer’s protocol.
RNA samples are converted to Illumina sequencing libraries using Illumina’s Truseq Stranded Total RNA Library Preparation Kit;ChIP-seq library is prepared with ThruPLEX DNA-seq kit.

tag: cell line

value: colorectal cancer cell line - HCT116

tag: stale expression

tag: chip antibody


title: gtf_shNT1

library_source: transcriptomic

molecule: total RNA

value: shNT (shRNA against no target control)


title: Control_knockdown_Rep2_5C_library

status: Public on May 22 2017

city: St. Louis

first: Jennifer

middle: E.

last: Phillips-Cremins

state: MO

address: 4515 McKinley Ave

department: Bioengineering

institute: Washington University in St. Louis

description: Chromosome-Conformation-Capture-Carbon-Copy (5C) Library

data_processing:
Paired-end reads were aligned to a pseudo-genome consisting of all 5C primers using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead, 2010). Only reads with one unique alignment were considered for downstream analyses. Interactions were counted when both paired-end reads could be uniquely mapped to the 5C primer pseudo-genome. Only interactions between forward-reverse primer pairs were tallied as a true count. Counts were converted to contact matrices for each genomic region queried (i.e. ~1-2 Megabase regions around developmentally regulated genes Nanog, Oct4, Sox2, Nestin, Olig, Klf4). Only the Sox2 and Klf4 regions were queried in the YY1 and Control siRNA samples.
To correct for bias related to intrinsic properties of restriction fragments (i.e. G-C content; fragment size) and procedural batch effects, we converted our raw .counts data to ‘Observed’ values through a series of pre-processing steps. Briefly, raw .counts matrices were (i) trimmed of primers with less than 10 total counts in any replicate, (ii) quantile normalized across biological conditions, (iii) normalized for primer biases using an adaptation of the 'Express' matrix-balancing algorithm (Sauria 2015) , (iv) trimmed of low information primer-primer pairs as described below, (v) log transformed, (vi) binned into 4 kilobase(kb)-sized bins and (vii) smoothed using a sliding 16 kb smoothing windows with 4 kb step-size. A primer-primer pair was set to NaN and removed from downstream analyses if it did not cross a threshold of 10 counts in at least three replicates. Four kb bins were withheld from downstream processing if greater than 80% of the primer-primer pairs within that bin’s smoothing window were NaN. Next, we developed an empirical ‘Expected’ model of the local background level of non-specific chromatin interactions. We computed our ‘Expected’ values locally  by first averaging the observed values across all bin-bin pairs representing equidistant interactions, then for each bin-bin pair correcting this distance-dependence expected with local 'Donut' and 'Lower Left' correction factors as described previously (Rao 2014); we retained the maximum of the Donut and Lower Left background calculations as our 'Expected' value for that bin-bin pair. We then assigned each bin-bin pair a “log2(Observed/Expected)” value by subtracting the region-specific Expected value for a given bin-bin contact distance from the Observed value of bins at the same distance. To compute p-values for each individual bin-bin pair, we modeled our ‘Observed over Expected’ values as a Logistic distribution with location/scale parameters computed independently for each region and each biological replicate. The resulting ‘Interaction Score’ (computed as -10*log2(p-value)) was comparable within and between replicates and allowed for robust detection of fragment-to-fragment looping interactions that were significant above the expected background signal for each genomic region. The processed data file Beagan_et_al_Processed_Data_File_2_22_2017.txt was created for 6 sample (ES 2i Rep1, ES 2i Rep2, ES Serum Rep1, ES Serum Rep2, pNPC Rep1, pNPC Rep2) experimental analyses. The processed data file Beagan_et_al_YY1_Knockdown_5C_Processed_Data_File_2_22_2017.txt was created for 4 sample (Control_siRNA_Rep1, Control_siRNA_Rep2, YY1_siRNA_Rep1, YY1_siRNA_Rep2) experimental analyses.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files Beagan_et_al_Processed_Data_File_2_22_2017.txt and Beagan_et_al_YY1_Knockdown_5C_Processed_Data_File_2_22_2017.txt contain the following information for each bin-bin pair:  “Region” (5C Region), “Bin1 ID” (unique identifier of the downstream bin), “Bin2 ID” (unique identifier of the upstream bin), “Chromosome” (chromosome containing the 5C region),  “Bin1 Start” (genomic coordinate of the start of the downstream bin), “Bin1 End” (genomic coordinate of the end of the downstream bin), “Bin2 Start” (genomic coordinate of the start of the upstream bin), “Bin2 End” (genomic coordinate of the end of the upstream bin), “Distance” (mid-to-mid distance between interaction bins), “_observed.counts” (normalized, logged, binned and smoothed interaction counts between Bin1 and Bin2), “_expected.counts” (expected interaction counts as determined by the maximum of the Donut and Lower Left local background models), “_obs_over_max_donut_ll.counts” (calculated by subtracting Expected counts from Observed counts) “_obs_over_max_donut_ll_pvalues.counts” (p-value for a specific bin-bin interaction calculated by fitting Observed over Expected counts to a Logistic distribution), "_obs_over_exp_int_scores_diag_trimmed.counts" (-10*log2(p-value) of each p-value, with on diagonal pixels trimmed - used to plot interaction score heatmaps). The processed data files Beagan_et_al_Processed_Data_File_2_22_2017.txt also contains an additional column "obs_over_exp_int_scores_diag_cluster_trimmed.counts" from which noisey loops have been removed - this file is used to calculate annotation enrichments, etc.The processed data file Beagan_et_al_Processed_Data_File_2_22_2017.txt  was created for 6 sample (ES_2i_Rep1, ES_2i_Rep2, ES_Serum_Rep1, ES_Serum_Rep2, pNPC_Rep1, pNPC_Rep2) experimental analysis. The processed data file Beagan_et_al_YY1_Knockdown_5C_Processed_Data_File_2_22_2017.txt  was created for 4 sample (Control_siRNA_Rep1, Control_siRNA_Rep2, YY1_siRNA_Rep1, YY1_siRNA_Rep2) experimental analysis.    The raw primer bed file (BED_314-ES-NPC-LOCI_mm9.bed) contains the following information for each individual primer used in the 5C experiment: “Chromosome” (chromosome containing the 5C region), “Start Site” (genomic coordinate of the start of the primer fragment), “End Site” (genomic coordinate of the end of the primer fragment), “Primer ID” (unique identifier within our primer set). The primer bed file Beagan_et_al_Primer_Bedfile_for_YY1_knockdown.bed provides the same information but only for the primers utilized for the analysis of the control and YY1 siRNA replicates.    The binned primer bed files (Beagan_et_al_Binned_Bedfile_2_22_17.bed,Beagan_et_al_YY1_knockdown_Binned_Bedfile_2_22_17.bed) contain the following information for each bin: “Chromosome” (chromosome containing the 5C region), “Start Site” (genomic coordinate of the start of the bin), “End Site” (genomic coordinate of the end of the bin), “Bin ID” (unique identifier within our primer set).    The raw counts files (ES_2i_Rep1.counts, ES_2i_Rep2.counts, ES_Serum_Rep1.counts, ES_Serum_Rep2.counts, pNPC_Rep1.counts, pNPC_Rep2.counts, Control_siRNA_Rep1_5C.counts, Control_siRNA_Rep2_5C.counts, YY1_siRNA_Rep1_5C.counts, YY1_siRNA_Rep2_5C.counts) were generated by first aligning paired-end reads to a pseudo-genome consisting of all 5C primers using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead, 2010). Only reads with one unique alignment were considered for downstream analyses. Interactions were counted when both paired-end reads could be uniquely mapped to the 5C primer pseudo-genome. Only interactions between forward-reverse primer pairs were tallied as a true count. Counts were converted to contact matrices for each genomic region queried (i.e. ~1-2 Megabase regions around developmentally regulated genes Nanog, Oct4, Sox2, Nestin, Olig, Klf4). Only Sox2 and Klf4 were queried for the siRNA experiments. The raw counts files (ES_2i_Rep1.counts, ES_2i_Rep2.counts, ES_Serum_Rep1.counts, ES_Serum_Rep2.counts, pNPC_Rep1.counts, pNPC_Rep2.counts, Control_siRNA_Rep1_5C.counts, Control_siRNA_Rep2_5C.counts, YY1_siRNA_Rep1_5C.counts, YY1_siRNA_Rep2_5C.counts) contain the following information for each primer-primer pair used for downstream analyses: “Forward primer ID” (the forward primer in this primer-primer pair), “Reverse primer ID” (the reverse primer in this primer-primer pair), “Co

organism: Mus musculus

source_name: Neural Progenitor Cells

growth_protocol: Neural progenitor cells were isolated from whole brains of P1 129SvJae x C57/BL6, Sox2-eGFP mice and cultured as neurospheres in Neural Stem Cell media: DMEM/F12 media (Invitrogen 12100-046 and 21700-075) containing 72 mM glucose, 120 mM Sodium Bicarbonate, 5.6 mM Hepes (Sigma H-0887), 27.5 nM Sodium Selenite (Sigma S-9133), 18 nM progesterone (Sigma P0130), 90 ug/mL Apo-transferrin (Sigma T1428), 23 ug/mL insulin (Sigma I6634), 100 uM putrescine (Sigma P-7505), 2 mM L-glutamine (Gibco 25030-081), 1% Pen/Strep (Sigma P0781), 2 ug/mL heparin, 20 ng/mL rhEGF (R&D Systems) , and 10 ng/mL rhFGF (R&D systems). Neurospheres were passaged every 3-4 days to prevent the formation of necrotic cores. After two passages, neurospheres were dissociated with Accutase and plated on Poly-D-Lysine Hydrobromide (100 ug/mL, Sigma P6407), and laminin (8 ug/mL, Corning 354232) coated plates at 20,000 cells/cm^2. After allowing the cells to adhere and grow, cells were treated with 20 nM siRNA targeting YY1 (Dharmacon # L-050273-00-0005) for 78 hours, replacing the media and siRNA every 24 hours. Cells were fixed for 3C with formaldehyde at the conclusion of 78 hours.

extract_protocol: 3C templates were generated using HindIII with an in situ 3C protocol similar to that previously described in Rao et al. 2014. 5C libraries were generated from 3C templates using an alternating primer design across 1-2 Mb regions around Oct4, Nanog, Sox2, Nestin, Olig1-Olig2, Klf4, and a gene desert negative control  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009).

tag: cell type

value: Neural Progenitor Cells

tag: developmental stage

tag: strain

value: 129SvJae x C57BL/6; Sox2-eGFP


title: Control_knockdown_Rep1_5C_library


title: YY1_knockdown_Rep2_5C_library


title: YY1_knockdown_Rep1_5C_library


title: gtf_shZB2

value: shZBTB24 (shRNA against ZBTB24)


title: 5C-insitu-mEs-2i-GenomeCopies-1k

status: Public on May 07 2018

description: 3C and 5C

data_processing:
[5C data processing]
Paired-end reads were aligned to a pseudo-genome consisting of all 5C primers using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead, 2010). Only reads with one unique alignment were considered for downstream analyses. Interactions were counted when both paired-end reads could be uniquely mapped to the 5C primer pseudo-genome. Only interactions between forward-reverse primer pairs were tallied as a true count. Counts were converted to contact matrices for each genomic region queried (i.e. ~1-3.5 Megabase regions around developmentally regulated genes Sox2, Klf4, Nanog, Dppa2, Rex1.
To correct for bias related to intrinsic properties of restriction fragments (i.e. G-C content; fragment size) and procedural batch effects, we converted our raw .counts data to ?Observed? values through a series of pre-processing steps. Briefly, raw .counts matrices were (i) 75th percentile scalar normalized for Figure 2 and 3 or quantile normalized for Figure 4 across biological conditions, (ii) binned into 4 kilobase(kb)-sized bins and (iii) smoothed using a sliding 12 kb smoothing windows, (iv) matrix balanced using ICE balancing algorithm using default parameters (Imakaev et al 2012).
Next, we developed an empirical ?Expected? model of the local background level of non-specific chromatin interactions. We computed our ?Expected? values locally  by first averaging the observed values across all bin-bin pairs representing equidistant interactions, then for each bin-bin pair correcting this distance-dependence expected with local 'Donut' as described previously (Rao 2014); We then assigned each bin-bin pair a "log2(Observed/Donut Expected)" value by subtracting the region-specific Donut Expected value for a given bin-bin contact distance from the Observed value of bins at the same distance. To compute p-values for each individual bin-bin pair, we modeled our ?Observed over Donut Expected? values as a Logistic distribution with location/scale parameters computed independently for each region. The resulting ?Interaction Score? (computed as -10*log2(p-value)) allowed for robust detection of fragment-to-fragment looping interactions that were significant above the expected background signal for each genomic region.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files ending with "_iced.counts" contain the following information for each bin-bin pair:  "Bin1 ID" (unique identifier of the downstream bin), "Bin2 ID" (unique identifier of the upstream bin),  "Counts" (quantile normalized and binned/smoothed counts after ICE balancing).
The processed data files ending with "_pvalues.counts" contain the following information for each bin-bin pair:  "Bin1 ID" (unique identifier of the downstream bin), "Bin2 ID" (unique identifier of the upstream bin), "Counts" (p-value for a specific bin-bin interaction calculated by fitting Observed over Expected counts to a Logistic distribution)
The processed data files ending with "_int_scores.counts" contain the following information for each bin-bin pair:  "Bin1 ID" (unique identifier of the downstream bin), "Bin2 ID" (unique identifier of the upstream bin), "Counts" (-10*log2(p-value) of each p-value, with on diagonal pixels trimmed - used to plot interaction score heatmaps)
The raw primer bed file (BED_6697-mm9-pluripotent.bed) contains the following information for each individual primer used in the 5C experiment: "Chromosome" (chromosome containing the 5C region), "Start Site" (genomic coordinate of the start of the primer fragment), "End Site" (genomic coordinate of the end of the primer fragment), "Primer ID" (unique identifier within our primer set), "Orientations" (primer orientations)
The binned primer bed files for Figure 2 (Figure2_single_alt_pixelmap.bed, Figure2_dbl_alt_pixelmap.bed) and Figure 3-4 (4000_pixelmap.bed) contain the following information for each bin: "Chromosome" (chromosome containing the 5C region), "Start Site" (genomic coordinate of the start of the bin), "End Site" (genomic coordinate of the end of the bin), "Bin ID" (unique identifier within our primer set).
The raw counts files (proj017-LCN-exp3-5C-dilution-mEs-2i-GC200k-Rep1-JK3C2-WG5C1-S1_S2.counts, proj017-LCN-exp3-5C-insitu-mEs-2i-GC200k-Rep1-JK3C2-WG5C1-S1_S5.counts, proj017-LCN-exp3-5C-insitu-mEs-2i-GC100k-Rep1-JK3C2-WG5C1-S1_S3.counts, proj017-LCN-exp3-5C-insitu-mEs-2i-GC50k-Rep1-JK3C2-WG5C1-S1_S4.counts, proj017-LCN-exp3-5C-insitu-mEs-2i-GC10k-Rep1-JK3C2-WG5C1-S1_S1.counts, proj017-LCN-exp3-5C-insitu-mEs-2i-GC5k-Rep1-JK3C2-WG5C1-S1_S6.counts, proj017-LCN-exp3-5C-insitu-mEs-2i-GC1k-Rep1-JK3C2-WG5C1-S1_S7.counts) were generated by first aligning paired-end reads to a pseudo-genome consisting of all 5C primers using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead, 2010). Only reads with one unique alignment were considered for downstream analyses. Interactions were counted when both paired-end reads could be uniquely mapped to the 5C primer pseudo-genome. Only interactions between forward-reverse primer pairs were tallied as a true count. Counts were converted to contact matrices for each genomic region queried (i.e. ~1-3.5 Megabase regions around developmentally regulated genes Sox2, Klf4, Nanog, Rex1, Dppa1). The raw counts files contain the following information for each primer-primer pair used for downstream analyses: "Forward primer ID" (the forward primer in this primer-primer pair), "Reverse primer ID" (the reverse primer in this primer-primer pair), "Count" (the number of mapped reads to this primer-primer pair).

source_name: mouse embryonic stem cells v6.5

growth_protocol: Mouse embryonic stem cells v6.5 were cultured in 2i culture media as previously described in Beagan et al 2016. The cells were routinely grown on feeder layer, and passaged twice on gelatin-coated culture dishes before crosslink.

extract_protocol:
3C templates were generated using HindIII with a in situ 3C protocol similar to that previously described in Rao et al. 2014. 5C libraries were generated from 1,000 genome copies of 3C templates using double alternating 5C primer design across ~1-3.5 Mb regions around Sox2, Klf4, Dppa2, Rex1, Nanog  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009; Hnisz et al 2016).
Library was constructed using NEBNExt Ultra DNA Library prep kit for Illumina kit according to manufacturer's protocol. Each library was quantitated using qPCR-based Kapa Library Quantification Kit, and equal molecular number of each libarary was pooled before sequencing.

tag: passages

tag: culture conditions

value: V6.5 ES cells cultured under 2i/LIF conditions

value: 129SvJae x C57BL/6

tag: gender

value: male

tag: protocol

value: 5C on 1,000 genome copies of in situ 3C templates


title: 5C-insitu-mEs-2i-GenomeCopies-5k

description: 3C and 5C

extract_protocol:
3C templates were generated using HindIII with a in situ 3C protocol similar to that previously described in Rao et al. 2014. 5C libraries were generated from 5,000 genome copies of 3C templates using double alternating 5C primer design across ~1-3.5 Mb regions around Sox2, Klf4, Dppa2, Rex1, Nanog  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009; Hnisz et al 2016).
Library was constructed using NEBNExt Ultra DNA Library prep kit for Illumina kit according to manufacturer's protocol. Each library was quantitated using qPCR-based Kapa Library Quantification Kit, and equal molecular number of each libarary was pooled before sequencing.

value: 5C on 5,000 genome copies of in situ 3C templates


title: 5C-insitu-mEs-2i-GenomeCopies-100k

description: 3C and 5C

extract_protocol:
3C templates were generated using HindIII with a in situ 3C protocol similar to that previously described in Rao et al. 2014. 5C libraries were generated from 100,000 genome copies of 3C templates using double alternating 5C primer design across ~1-3.5 Mb regions around Sox2, Klf4, Dppa2, Rex1, Nanog  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009; Hnisz et al 2016).
Library was constructed using NEBNExt Ultra DNA Library prep kit for Illumina kit according to manufacturer's protocol. Each library was quantitated using qPCR-based Kapa Library Quantification Kit, and equal molecular number of each libarary was pooled before sequencing.

value: 5C on 100,000 genome copies of in situ 3C templates


title: 5C-insitu-mEs-2i-GenomeCopies-200k

description: 3C and 5C

extract_protocol:
3C templates were generated using HindIII with a in situ 3C protocol similar to that previously described in Rao et al. 2014. 5C libraries were generated from 200,000 genome copies of 3C templates using double alternating 5C primer design across ~1-3.5 Mb regions around Sox2, Klf4, Dppa2, Rex1, Nanog  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009; Hnisz et al 2016).
Library was constructed using NEBNExt Ultra DNA Library prep kit for Illumina kit according to manufacturer's protocol. Each library was quantitated using qPCR-based Kapa Library Quantification Kit, and equal molecular number of each libarary was pooled before sequencing.

value: 5C on 200,000 genome copies of in situ 3C templates


title: 5C-insitu-mEs-2i-GenomeCopies-50k

description: 3C and 5C

extract_protocol:
3C templates were generated using HindIII with a in situ 3C protocol similar to that previously described in Rao et al. 2014. 5C libraries were generated from 50,000 genome copies of 3C templates using double alternating 5C primer design across ~1-3.5 Mb regions around Sox2, Klf4, Dppa2, Rex1, Nanog  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009; Hnisz et al 2016).
Library was constructed using NEBNExt Ultra DNA Library prep kit for Illumina kit according to manufacturer's protocol. Each library was quantitated using qPCR-based Kapa Library Quantification Kit, and equal molecular number of each libarary was pooled before sequencing.

value: 5C on 50,000 genome copies of in situ 3C templates


title: 5C-insitu-mEs-2i-GenomeCopies-10k

description: 3C and 5C

extract_protocol:
3C templates were generated using HindIII with a in situ 3C protocol similar to that previously described in Rao et al. 2014. 5C libraries were generated from 10,000 genome copies of 3C templates using double alternating 5C primer design across ~1-3.5 Mb regions around Sox2, Klf4, Dppa2, Rex1, Nanog  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009; Hnisz et al 2016).
Library was constructed using NEBNExt Ultra DNA Library prep kit for Illumina kit according to manufacturer's protocol. Each library was quantitated using qPCR-based Kapa Library Quantification Kit, and equal molecular number of each libarary was pooled before sequencing.

value: 5C on 10,000 genome copies of in situ 3C templates


title: 5C-dilution-mEs-2i-GenomeCopies-200k

description: 3C and 5C

extract_protocol:
3C templates were generated using HindIII with a dilution 3C protocol as previously described in Beagan et al 2016. 5C libraries were generated from 200,000 genome copies of 3C templates using double alternating 5C primer design across ~1-3.5 Mb regions around Sox2, Klf4, Dppa2, Rex1, Nanog  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009; Hnisz et al 2016).
Library was constructed using NEBNExt Ultra DNA Library prep kit for Illumina kit according to manufacturer's protocol. Each library was quantitated using qPCR-based Kapa Library Quantification Kit, and equal molecular number of each libarary was pooled before sequencing.

value: 5C on 200,000 genome copies of dilution 3C templates


title: ES_Serum_Rep2_5C_library

description:
Processed data file(s):
BED_314-ES-NPC-LOCI_mm9.bed
Beagan_et_al_Processed_Data_File_7_30_2016.txt
Beagan_et_al_Classified_Results_7_30_16.txt
2i_Pipeline_PP_RemovalBED_binned_mm9_16kbbin_4kbstep.bed
NOTE: Raw data files are equivalent to sample GSM1974096, but processed data files are different.

data_processing:
Paired-end reads were aligned to a pseudo-genome consisting of all 5C primers using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead, 2010). Only reads with one unique alignment were considered for downstream analyses. Interactions were counted when both paired-end reads could be uniquely mapped to the 5C primer pseudo-genome. Only interactions between forward-reverse primer pairs were tallied as a true count. Counts were converted to contact matrices for each genomic region queried (i.e. ~1-2 Megabase regions around developmentally regulated genes Nanog, Oct4, Sox2, Nestin, Olig, Klf4).
To correct for bias related to intrinsic properties of restriction fragments (i.e. G-C content; fragment size) and procedural batch effects, we converted our raw .counts data to ‘Observed’ values through a series of pre-processing steps. Briefly, raw .counts matrices were (i) trimmed of primers with less than 100 total counts in any replicate, (ii) quantile normalized across biological conditions, (iii) normalized for primer biases using an adaptation of the 'Express' matrix-balancing algorithm (Sauria 2015) , (iv) trimmed of low information primer-primer pairs as described below, (v) log transformed, (vi) binned into 4 kilobase(kb)-sized bins and (vii) smoothed using a sliding 16 kb smoothing windows with 4 kb step-size. A primer-primer pair was set to NaN and removed from downstream analyses if it did not cross a threshold of 15 counts in at least three replicates. Four kb bins were withheld from downstream processing if greater than 80% of the primer-primer pairs within that bin’s smoothing window were NaN. Next, we developed an empirical ‘Expected’ model of the local background level of non-specific chromatin interactions. We computed our ‘Expected’ values locally  by first averaging the observed values across all bin-bin pairs representing equidistant interactions, then for each bin-bin pair correcting this distance-dependence expected with local 'Donut' and 'Lower Left' correction factors as described previously (Rao 2014); we retained the maximum of the Donut and Lower Left background calculations as our 'Expected' value for that bin-bin pair. We then assigned each bin-bin pair a “log2(Observed/Expected)” value by subtracting the region-specific Expected value for a given bin-bin contact distance from the Observed value of bins at the same distance. To compute p-values for each individual bin-bin pair, we modeled our ‘Observed over Expected’ values as a Logistic distribution with location/scale parameters computed independently for each region and each biological replicate. The resulting ‘Interaction Score’ (computed as -10*log2(p-value)) was comparable within and between replicates and allowed for robust detection of fragment-to-fragment looping interactions that were significant above the expected background signal for each genomic region. The processed data file Beagan_et_al_Processed_Data_File_7_30_2016.txt was created for 6 sample (ES 2i Rep1, ES 2i Rep2, ES Serum Rep1, ES Serum Rep2, pNPC Rep1, pNPC Rep2) experimental analyses.
Supplementary_files_format_and_content: The processed data file Beagan_et_al_Processed_Data_File_7_30_2016.txt contains the following information for each bin-bin pair:  “Chromosome” (chromosome containing the 5C region), “Region” (5C Region), “Bin1 ID” (unique identifier of the downstream bin), “Bin2 ID” (unique identifier of the upstream bin), “Bin1 Start” (genomic coordinate of the start of the downstream bin), “Bin1 End” (genomic coordinate of the end of the downstream bin), “Bin2 Start” (genomic coordinate of the start of the upstream bin), “Bin2 End” (genomic coordinate of the end of the upstream bin), “Distance” (mid-to-mid distance between interaction bins), “_obs.counts” (normalized, logged, binned and smoothed interaction counts between Bin1 and Bin2), “_exp.counts” (expected interaction counts as determined by the maximum of the Donut and Lower Left local background models), “_obs_over_exp.counts” (calculated by subtracting Expected counts from Observed counts) “_obs_over_exp_pvalues.counts” (p-value for a specific bin-bin interaction calculated by fitting Observed over Expected counts to a Logistic distribution). The processed data file Beagan_et_al_Processed_Data_File_7_30_2016.txt was created for 6 sample (ES_2i_Rep1, ES_2i_Rep2, ES_Serum_Rep1, ES_Serum_Rep2, pNPC_Rep1, pNPC_Rep2) experimental analysis.
Supplementary_files_format_and_content: The raw primer bed file (BED_314-ES-NPC-LOCI_mm9.bed) contains the following information for each individual primer used in the 5C experiment: “Chromosome” (chromosome containing the 5C region), “Start Site” (genomic coordinate of the start of the primer fragment), “End Site” (genomic coordinate of the end of the primer fragment), “Primer ID” (unique identifier within our primer set).
Supplementary_files_format_and_content: The binned primer bed file (2i_Pipeline_PP_RemovalBED_binned_mm9_16kbbin_4kbstep.bed) contains the following information for each bin: “Chromosome” (chromosome containing the 5C region), “Start Site” (genomic coordinate of the start of the bin), “End Site” (genomic coordinate of the end of the bin), “Bin ID” (unique identifier within our primer set).
Supplementary_files_format_and_content: The raw counts files (ES_2i_Rep1.counts, ES_2i_Rep2.counts, ES_Serum_Rep1.counts, ES_Serum_Rep2.counts, pNPC_Rep1.counts, pNPC_Rep2.counts) were generated by first aligning paired-end reads to a pseudo-genome consisting of all 5C primers using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead, 2010). Only reads with one unique alignment were considered for downstream analyses. Interactions were counted when both paired-end reads could be uniquely mapped to the 5C primer pseudo-genome. Only interactions between forward-reverse primer pairs were tallied as a true count. Counts were converted to contact matrices for each genomic region queried (i.e. ~1-2 Megabase regions around developmentally regulated genes Nanog, Oct4, Sox2, Nestin, Olig, Klf4). The raw counts files (ES_2i_Rep1.counts, ES_2i_Rep2.counts, ES_Serum_Rep1.counts, ES_Serum_Rep2.counts, pNPC_Rep1.counts, pNPC_Rep2.counts) contain the following information for each primer-primer pair used for downstream analyses: “Forward primer ID” (the forward primer in this primer-primer pair), “Reverse primer ID” (the reverse primer in this primer-primer pair), “Count” (the number of mapped reads to this primer-primer pair).
Supplementary_files_format_and_content: The final interaction classification file (Beagan_et_al_Classified_Results_7_30_16.txt) contains the following information for each bin-bin pair that falls into one of our classifications: “Chromosome” (chromosome containing the 5C region), “Region” (5C Region), “Classification” (classification for that bin-bin pair), “Bin1 ID” (unique identifier of the downstream bin), “Bin2 ID” (unique identifier of the upstream bin), “Bin1 Start” (genomic coordinate of the start of the downstream bin), “Bin1 End” (genomic coordinate of the end of the downstream bin), “Bin2 Start” (genomic coordinate of the start of the upstream bin), “Bin2 End” (genomic coordinate of the end of the upstream bin), “Distance” (mid-to-mid distance between interaction bins), “_obs.counts” (normalized, logged, binned and smoothed interaction counts between Bin1 and Bin2), “_exp.counts” (expected interaction counts as determined by the maximum of the Donut and Lower Left local background models), “_obs_over_exp.counts” (calculated by subtracting Expected counts from Observed counts) “_obs_over_exp_pvalues.counts” (p-value for a specific bin-bin interaction calculated by fitting Observed over Expected counts to a Logistic distribution).
Genome_build: mm9

source_name: V6.5 ES cells

growth_protocol: Murine V6.5 ES cells were expanded on Mitomycin-C-inactivated MEF feeder layers in pluripotent media (containing serum) supplemented with LIF.  After initial expansion, ES cells were passaged onto 0.1% gelatin to remove contaminating feeder cells.  Cells were grown to ~7e6 cells per 15 cm dish at the time of fixation with 1% formaldehyde before downstream assay.

extract_protocol:
3C templates were generated   using HindIII as previously described (Dekker et al., 2002; van Berkum and Dekker, 2009). 5C libraries were generated from 3C templates using an alternating primer design across 1-2 Mb regions around Oct4, Nanog, Sox2, Nestin, Olig1-Olig2, Klf4, and a gene desert negative control  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009).
3C and 5C

value: V6.5 ES cells

tag: culture condition

value: standard serum/LIF conditions


title: NPC_Rep1_5C_library

description:
Processed data file(s):
BED_314-ES-NPC-LOCI_mm9.bed
Beagan_et_al_Processed_Data_File_7_30_2016.txt
Beagan_et_al_Classified_Results_7_30_16.txt
2i_Pipeline_PP_RemovalBED_binned_mm9_16kbbin_4kbstep.bed
NOTE: Raw data files are equivalent to sample GSM1974109, but processed data files are different.

growth_protocol: Neural progenitor cells were   isolated from whole brains of P1 129SvJae x C57/BL6, Sox2-eGFP mice and cultured as neurospheres in Neural Stem Cell media: DMEM/F12 media (Invitrogen 12100-046 and 21700-075) containing 72 mM glucose, 120 mM Sodium Bicarbonate, 5.6 mM Hepes (Sigma H-0887), 27.5 nM Sodium Selenite (Sigma S-9133), 18 nM progesterone (Sigma P0130), 90 ug/mL Apo-transferrin (Sigma T1428), 23 ug/mL insulin (Sigma I6634), 100 uM putrescine (Sigma P-7505), 2 mM L-glutamine (Gibco 25030-081), 1% Pen/Strep (Sigma P0781), 2 ug/mL heparin, 20 ng/mL rhEGF (R&D Systems) , and 10 ng/mL rhFGF (R&D systems). Neurospheres were passaged every 3-4 days to prevent the formation of necrotic cores. After two passages, neurospheres were dissociated with Accutase and plated on Poly-D-Lysine Hydrobromide (100 ug/mL, Sigma P6407),   and laminin  (8 ug/mL, Corning 354232) coated plates at 60,000 cells/cm^2. Cells were fixed with 1% formaldehyde one day after adherent plating.

value: Neural Progenitor cells

tag: genotype/variation


title: NPC_Rep2_5C_library

description:
Processed data file(s):
BED_314-ES-NPC-LOCI_mm9.bed
Beagan_et_al_Processed_Data_File_7_30_2016.txt
Beagan_et_al_Classified_Results_7_30_16.txt
2i_Pipeline_PP_RemovalBED_binned_mm9_16kbbin_4kbstep.bed
NOTE: Raw data files are equivalent to sample GSM1974110, but processed data files are different.


title: ES_2i_Rep1_5C_library

description:
Processed data file(s):
BED_314-ES-NPC-LOCI_mm9.bed
Beagan_et_al_Processed_Data_File_7_30_2016.txt
Beagan_et_al_Classified_Results_7_30_16.txt
2i_Pipeline_PP_RemovalBED_binned_mm9_16kbbin_4kbstep.bed
NOTE: Raw data files are equivalent to sample GSM1974097, but processed data files are different.

growth_protocol: Murine V6.5 ES cells were expanded on Mitomycin-C-inactivated MEF feeder layers in 2i serum-free media containing LIF, CHIR99021, PD0325901 (Axon Medchem), as previously described (Rais et al., 2013).  After initial expansion, ES cells were passaged onto 0.1% gelatin to remove contaminating feeder cells.  Cells were grown to ~7e6 cells per 15 cm dish at the time of fixation with 1% formaldehyde before downstream assay.

value: 2i/LIF conditions


title: NPC_Input_ChIPseq_library

description:
Processed data file(s):
NPC-CTCF-IP_MACS2_rendition_1E-8_downsampled.narrowPeak

data_processing:
First, ChIP-Seq data was aligned to the mm9 reference genome, duplicate counts were filtered, and replicates were downsampled to equivalent read depths. Subsequently, the MACS2 software was utilized for ChIP peak calling, with a p-value cutoff of 1e-8. The cell-type matched whole cell extract (WCE) library was used as the background.
Supplementary_files_format_and_content: The ChIP-seq processed data files are in the ENCODE narrowPeak format.
Genome_build: mm9

extract_protocol:
Approximately 20 million cells were fixed in serum-free culture media supplemented with formaldehyde added to a final concentration of 1%. After 10 minute incubation at room temperature, fixation was terminated by adding 2.5M glycine stock to a final concentration of 125 mM glycine. Cross-linking termination was carried out for 5 minutes at room temperature followed by 15 minutes at 4°C. Cells were harvested with silicone scraper and pelleted, washed once with PBS, snap-frozen and stored at -80°C until processing.   Cell pellets were thawed for 10 min on ice before use. Nuclei were isolated by resuspending each pellet in 1 mL Cell Lysis Buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP-40/Igepal, Protease Inhibitor, PMSF), incubating on ice for 10 min, and spinning to pellet. Nuclei were resuspended in 500 uL Nuclear Lysis Buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS, Protease Inhibitor, PMSF) and incubated on ice for 20 min. After bringing the samples up to volume by the addition of 300 uL IP Dilution Buffer (20 mM Tris pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triston X-100, 0.01% SDS, Protease Inhibitor, PMSF), samples were sonicated for 45 minutes using an Epishear sonicator set at 100% amplitude, with cycles of 30 seconds on and 30 seconds off. The resulting sheared chromatin was spun down, and the supernatant was transferred to a preclearing solution of 3.7 mL IP Dilution Buffer, 0.5 mL Nuclear Lysis Buffer, 175 uL of Agarose Protein A/G beads, and 50 ug Rabbit IgG, and rotated at 4°C. 35 uL Protein A/G agarose beads were pre-bound with 10 uL anti-CTCF antibody (Millipore #07-729) and incubated for 2 hours during the pre-clear stage. After a two hour pre-clear incubation, the beads were pelleted, and 4.5 mL supernatant was removed. 200 uL was reserved for input control, while the remaining supernatant was transferred to agarose beads pre-bound with antibody and rotated overnight at 4°C. Bound bead complexes were washed once with 1 mL IP Wash Buffer 1 (20 mM Tris pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), twice with 1 mL High-Salt Buffer (20 mM Tris pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP Wash Buffer 2 (10 mM Tris pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% NP-40/Igepal, 1% Na-deoxycholate), and finally once with 1x TE. Complexes were eluted by twice resuspending bound beads in 110 uL Elution Buffer (100 mM NaHCO3, 1% SDS), pelleting the beads after each elution and transferring 100 uL supernatant to a new tube. Finally, 12 uL of 5M NaCl and 20 ug RNase A were added to both 200 uL IP and input samples and incubated at 65 degrees for 1 hour, followed by the addition of 60 ug of Proteinase K and overnight incubation at 65 degrees. DNA was isolated via phenol-chloroform extraction and ethanol precipitation, and concentration was quantified using Qubit fluorometer.
Libraries were prepared for sequencing using the NEBNext Ultra Library Prep Kit (NEB #E7370) and following the manufacturer’s protocol for ChIP-seq library preparation. No size selection step was performed following adapter ligation. The libraries were amplified over 18 PCR cycles using NEBNext Multiplex Oligos for Illumina (NEB #E7335). The final ChIP libraries were eluted in 30 uL 0.1x TE from the Agencourt AMPure XP beads, at which point we confirmed the library contained DNA fragments ranging from 250 to 1200 bp, including the adapters, by running a High-Sensitivity DNA assay on an Agilent Bioanalyzer. The concentration of these libraries was assayed via the KAPA Illumina Library Quantification Kit (#KK4835), diluted to equivalent concentrations and pooled, and finally sequenced with 75-cyles per paired-end on the Illumina NextSeq500.

value: input


title: ES_Serum_Rep1_5C_library

description:
Processed data file(s):
BED_314-ES-NPC-LOCI_mm9.bed
Beagan_et_al_Processed_Data_File_7_30_2016.txt
Beagan_et_al_Classified_Results_7_30_16.txt
2i_Pipeline_PP_RemovalBED_binned_mm9_16kbbin_4kbstep.bed
NOTE: Raw data files are equivalent to sample GSM1974095, but processed data files are different.


title: ES_2i_Rep2_5C_library

description:
Processed data file(s):
BED_314-ES-NPC-LOCI_mm9.bed
Beagan_et_al_Processed_Data_File_7_30_2016.txt
Beagan_et_al_Classified_Results_7_30_16.txt
2i_Pipeline_PP_RemovalBED_binned_mm9_16kbbin_4kbstep.bed
NOTE: Raw data files are equivalent to sample GSM1974098, but processed data files are different.


title: ES_Serum_Input_ChIPseq_library

description:
Processed data file(s):
ES-CTCF-IP_MACS2_rendition_1E-8_downsampled.narrowPeak


title: ES_Serum_CTCF_ChIPseq_library

value: anti-CTCF (Millipore #07-729)


title: ES_2i_CTCF_ChIPseq_library

description:
Processed data file(s):
ES-2i-CTCF-IP_MACS2_rendition_1E-8_downsampled.narrowPeak


title: iPS_2i_Rep1_RNA_seq_library

status: Public on May 05 2016

description:
RNA-seq
Beagan_et_al_normalized_10sample_gene_expression_w_coordinates_1_29_2016.txt

data_processing:
RNA-seq reads were aligned to the mouse genome (build mm9) using the Tophat (Tophat v2.1.0) alignment tool (Trapnell et al., 2009) with the parameters: -r 100 --no-coverage-search --library-type fr-firststrand and UCSC gene annotations. Gene level read counts were computed using the htseq-count tool (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) with parameters: -m union --stranded=reverse and UCSC gene annotations.
To generate Beagan_et_al_normalized_10sample_gene_expression_w_coordinates_1_29_2016.txt:   In experimental analyses of 10 replicates (ES_Rep1, ES_Rep2, pNPC_Rep1, pNPC_Rep2, iPS_Rep1, iPS_Rep2, ES2i_Rep1, ES2i_Rep2, iPS2i_Rep1, iPS2i_Rep2), genes with more than three counts in at least five libraries were retained, resulting in a total of 11,767 genes analyzed. To account for library-specific differences in sequencing depth, log2-transformed libraries were normalized by read depth of the 75%tile gene. Libraries were assessed for the absence of batch effects before proceeding to downstream biological analyses.
Supplementary_files_format_and_content: RNA-seq processed data files format and content: The processed data file Beagan_et_al_normalized_10sample_gene_expression_w_coordinates_1_29_2016.txt was created for a 10 sample experiment (ES_Rep1, ES_Rep2, pNPC_Rep1, pNPC_Rep2, iPS_Rep1, iPS_Rep2, ES2i_Rep1, ES2i_Rep2, iPS2i_Rep1, iPS2i_Rep2). For each gene, data are listed as log2-transformed, sequencing depth-normalized counts. Prior to downstream analyses, libraries were confirmed to have minimal batch effects.
Supplementary_files_format_and_content: The concatenated counts files (v65ES_Rep1_S11_concatenated_counts_11_29_2015.txt, v65ES_Rep2_S12_concatenated_counts_11_29_2015.txt, v65ESw2i_Rep1_S9_concatenated_counts_11_29_2015.txt, v65ESw2i_Rep2_S10_concatenated_counts_11_29_2015.txt, pNPC_Rep1_S3_concatenated_counts_11_29_2015.txt, pNPC_Rep2_S4_concatenated_counts_11_29_2015.txt, iPS_Rep1_S1_concatenated_counts_11_29_2015.txt, iPS_Rep3_S2_concatenated_counts_11_29_2015.txt, iPSw2i_Rep1_S5_concatenated_counts_11_29_2015.txt, iPSw2i_Rep2_S6_concatenated_counts_11_29_2015.txt) were generated by aligning RNA-seq reads to the mouse genome (build mm9) using the Tophat (Tophat v2.1.0) alignment tool (Trapnell et al., 2009) with the parameters: -r 100 --no-coverage-search --library-type fr-firststrand and UCSC gene annotations. Gene level read counts were computed using the htseq-count tool (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) with parameters: -m union --stranded=reverse and UCSC gene annotations. After ensuring the absence of batch effects between sequencing runs, counts files for the same sample from two sequencing runs were concatenated to generate the counts files. For each gene, data are listed as mapped counts.

source_name: NPC-derived Induced Pluripotent Stem Cells

growth_protocol: Induced pluripotent stem cells were derived from primary NPCs as described by (Eminli et al., 2008). After reprogramming and initial expansion, iPS cells were cultured on Mitomycin-C inactived MEFs in 2i serum-free media containing LIF, CHIR99021, PD0325901 (Axon Medchem), as previously described (Rais et al., 2013).  After 2i expansion, iPS cells were passaged onto 0.1% gelatin to remove contaminating feeder cells.

extract_protocol: 0.9 million cells were lysed with Trizol (Life Technologies 15596-026) and snap frozen. Total RNA was then extracted and purified using the miRvana miRNA Isolation Kit (Ambion AM 1561). RNA integrity was assessed using the Agilent BioAnalyer and samples with RIN scores >9 were carried forward for sequencing. 350 ng total RNA was prepared for sequencing using the Illumina TruSeq Stranded Total RNA Library Prep kit with RiboZero (Illumina RS-122-2202).  Paired-end sequencing was performed on the NextSeq 500 with 75 cycles per end.


title: NPC_CTCF_ChIPseq_library


title: v6.5_2i_rep1_RNA_seq_library

growth_protocol: Murine V6.5 ES cells were expanded on Mitomycin-C-inactivated MEF feeder layers in 2i serum-free media containing LIF, CHIR99021, PD0325901 (Axon Medchem), as previously described (Rais et al., 2013).  After initial expansion, ES cells were passaged onto 0.1% gelatin to remove contaminating feeder cells.


title: v6.5_Rep1_RNA_seq_library

growth_protocol: Murine V6.5 ES cells were expanded on Mitomycin-C-inactivated MEF feeder layers in pluripotent media supplemented with LIF.  After initial expansion, ES cells were passaged onto 0.1% gelatin to remove contaminating feeder cells.


title: v6.5_2i_rep2_RNA_seq_library


title: iPS_2i_Rep2_RNA_seq_library

value: NPC-derived Induced Pluripotent Stem Cells


title: v6.5_Rep2_RNA_seq_library


title: iPS_2i_Rep1_5C_library

description:
Chromosome-Conformation-Capture-Carbon-Copy (5C) Library
BED_ES-NPC-iPS-LOCI_mm9.bed
Beagan_et_al_5C_processed_data_file_2_23_2016_10samples.txt
BED_binned_mm9_20kbbin_4kbstep-10samples.bed

data_processing:
Paired-end reads were aligned to a pseudo-genome consisting of all 5C primers using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead, 2010). Only reads with one unique alignment were considered for downstream analyses. Interactions were counted when both paired-end reads could be uniquely mapped to the 5C primer pseudo-genome. Only interactions between forward-reverse primer pairs were tallied as a true count. Counts were converted to contact matrices for each genomic region queried (i.e. ~1-2 Megabase regions around developmentally regulated genes Nanog, Oct4, Sox2, Nestin, Olig, Klf4) to generate the raw .counts file for each sample.
To correct for bias related to intrinsic properties of restriction fragments (i.e. G-C content; fragment size) and procedural batch effects, we converted our raw .counts data to ‘Observed’ values through a series of pre-processing steps. Briefly, raw .counts matrices were (i) trimmed of primers with less than 100 total counts in any replicate, (ii) quantile normalized across biological conditions, (iii) normalized for primer biases as previously described (Phillips-Cremins et al. 2013), (iv) trimmed of low information primer-primer pairs as described below, (v) log transformed, (vi) binned into 4 kilobase(kb)-sized bins and (vii) smoothed using a sliding 20 kb smoothing windows with 4 kb step-size. A primer-primer pair was set to NaN and removed from downstream analyses if it did not cross a threshold of 10 counts in any one library. Four kb bins were withheld from downstream processing if greater than 80% of the primer-primer pairs within that bin’s smoothing window were NaN. Next, we developed an empirical ‘Expected’ model of the distance-dependent background level of non-specific chromatin interactions. We computed our ‘Expected’ values locally (i.e. for each developmentally regulated region independently) by averaging the observed values across all bin-bin pairs representing equidistant interactions in each region. We then assigned each bin-bin pair a “log2(Observed/Expected)” value by subtracting the region-specific Expected value for a given bin-bin contact distance from the Observed value of bins at the same distance. To compute p-values for each individual bin-bin pair, we modeled our ‘Observed over Expected’ values as a Logistic distribution with location/scale parameters computed independently for each region and each biological replicate. The resulting ‘Interaction Score’ (computed as -10*log2(p-value)) was comparable within and between replicates and allowed for robust detection of fragment-to-fragment looping interactions that were significant above the expected background signal for each genomic region. The processed data files Beagan_et_al_5C_processed_data_file_2_23_2016_6samples.txt  and Beagan_et_al_5C_processed_data_file_2_23_2016_10samples.txt were created for 6 sample (V6.5_Rep1, V6.5_Rep2, pNPC_Rep1, pNPC_Rep2, iPS_Rep1, iPS_Rep2) and 10 sample (V6.5_Rep1, V6.5_Rep2, pNPC_Rep1, pNPC_Rep2, iPS_Rep1, iPS_Rep2, V6.52i_Rep1, V6.52i_Rep2, iPS2i_Rep1, iPS2i_Rep2) experimental analyses.
Supplementary_files_format_and_content: The processed data files (Beagan_et_al_5C_processed_data_file_2_23_2016_6samples.txt, Beagan_et_al_5C_processed_data_file_2_23_2016_10samples.txt) contain the following information for each bin-bin pair:  “Chromosome” (chromosome containing the 5C region), “Region” (5C Region), “Bin1 ID” (unique identifier of the downstream bin), “Bin2 ID” (unique identifier of the upstream bin), “Bin1 Start” (genomic coordinate of the start of the downstream bin), “Bin1 End” (genomic coordinate of the end of the downstream bin), “Bin2 Start” (genomic coordinate of the start of the upstream bin), “Bin2 End” (genomic coordinate of the end of the upstream bin), “Distance” (mid-to-mid distance between interaction bins), “_obs.counts” (normalized, logged, binned and smoothed interaction counts between Bin1 and Bin2), “_exp.counts” (expected interaction counts as determined by distance-dependent expected model), “_obs_over_exp.counts” (calculated by subtracting Expected counts from Observed counts) “_obs_over_exp_pvalues.counts” (p-value for a specific bin-bin interaction calculated by fitting Observed over Expected counts to a Logistic distribution). The processed data files Beagan_et_al_5C_processed_data_file_2_23_2016_6samples.txt  and Beagan_et_al_5C_processed_data_file_2_23_2016_10samples.txt were created for 6 sample (V6.5_Rep1, V6.5_Rep2, pNPC_Rep1, pNPC_Rep2, iPS_Rep1, iPS_Rep2) and 10 sample (V6.5_Rep1, V6.5_Rep2, pNPC_Rep1, pNPC_Rep2, iPS_Rep1, iPS_Rep2, V6.52i_Rep1, V6.52i_Rep2, iPS2i_Rep1, iPS2i_Rep2) experimental analyses. NOTE: Figures comparing chromatin architecture between only ES, NPC, and iPS cells were generated using the ‘6 sample’ processed data, while figures including the ES in 2i and iPS in 2i conditions were generated from the ’10 sample’ processed data.
Supplementary_files_format_and_content: The raw primer bed file (BED_ES-NPC-iPS-LOCI_mm9.bed) contains the following information for each individual primer used in the 5C experiment: “Chromosome” (chromosome containing the 5C region), “Start Site” (genomic coordinate of the start of the primer fragment), “End Site” (genomic coordinate of the end of the primer fragment), “Primer ID” (unique identifier within our primer set).
Supplementary_files_format_and_content: The binned primer bed file (BED_binned_mm9_20kbbin_4kbstep-6samples.bed, BED_binned_mm9_20kbbin_4kbstep-10samples.bed) contains the following information for each bin: “Chromosome” (chromosome containing the 5C region), “Start Site” (genomic coordinate of the start of the bin), “End Site” (genomic coordinate of the end of the bin), “Bin ID” (unique identifier within our primer set). BED_binned_mm9_20kbbin_4kbstep-6samples.bed and BED_binned_mm9_20kbbin_4kbstep-10samples.bed were created for 6 sample (V6.5_Rep1, V6.5_Rep2, pNPC_Rep1, pNPC_Rep2, iPS_Rep1, iPS_Rep2) and 10 sample (V6.5_Rep1, V6.5_Rep2, pNPC_Rep1, pNPC_Rep2, iPS_Rep1, iPS_Rep2, V6.52i_Rep1, V6.52i_Rep2, iPS2i_Rep1, iPS2i_Rep2) experimental analyses.
Supplementary_files_format_and_content: The raw counts files (v65_Rep1.counts, v65_Rep2.counts, v65_2i_Rep1.counts, v65_2i_Rep2.counts, pNPC_Rep1.counts, pNPC_Rep2.counts, iPS_Rep1.counts, iPS_Rep2.counts, iPS_2i_Rep1.counts, iPS_2i_Rep2.counts) were generated by first aligning paired-end reads to a pseudo-genome consisting of all 5C primers using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead, 2010). Only reads with one unique alignment were considered for downstream analyses. Interactions were counted when both paired-end reads could be uniquely mapped to the 5C primer pseudo-genome. Only interactions between forward-reverse primer pairs were tallied as a true count. Counts were converted to contact matrices for each genomic region queried (i.e. ~1-2 Megabase regions around developmentally regulated genes Nanog, Oct4, Sox2, Nestin, Olig, Klf4). The raw counts files (v65_Rep1.counts, v65_Rep2.counts, v65_2i_Rep1.counts, v65_2i_Rep2.counts, pNPC_Rep1.counts, pNPC_Rep2.counts, iPS_Rep1.counts, iPS_Rep2.counts, iPS_2i_Rep1.counts, iPS_2i_Rep2.counts) contain the following information for each primer-primer pair used for downstream analyses: “Forward primer ID” (the forward primer in this primer-primer pair), “Reverse primer ID” (the reverse primer in this primer-primer pair), “Count” (the number of mapped reads to this primer-primer pair).
Supplementary_files_format_and_content: The final interaction classification file (Beagan_et_al_5C_processed_classification_data_file_2_23_2016_6samples.txt) contains the following information for each bin-bin pair that falls into one of our classifications: “Chromosome” (chromosome containing the 5C region), “Region” (5C Region), “Classification”

growth_protocol: Induced pluripotent stem cells were derived from primary NPCs as described by (Eminli et al., 2008). After reprogramming and initial expansion, iPS cells were cultured on Mitomycin-C inactived MEFs in 2i serum-free media containing LIF, CHIR99021, PD0325901 (Axon Medchem), as previously described (Rais et al., 2013).  After 2i expansion, iPS cells were passaged onto 0.1% gelatin to remove contaminating feeder cells.  Cells were grown to ~7e6 cells per 15 cm dish at the time of fixation with 1% formaldehyde before downstream assay.

extract_protocol: 3C templates were generated   using HindIII as previously described (Dekker et al., 2002; van Berkum and Dekker, 2009). 5C libraries were generated from 3C templates using an alternating primer design across 1-2 Mb regions around Oct4, Nanog, Sox2, Nestin, Olig1-Olig2, Klf4, and a gene desert negative control  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009).


title: iPS_Rep2_5C_library

description:
Chromosome-Conformation-Capture-Carbon-Copy (5C) Library
BED_ES-NPC-iPS-LOCI_mm9.bed
Beagan_et_al_5C_processed_data_file_2_23_2016_6samples.txt
Beagan_et_al_5C_processed_data_file_2_23_2016_10samples.txt
BED_binned_mm9_20kbbin_4kbstep-6samples.bed
Beagan_et_al_5C_processed_classification_data_file_2_23_2016_6samples.txt
BED_binned_mm9_20kbbin_4kbstep-10samples.bed

growth_protocol: Induced pluripotent stem cells were derived from primary NPCs as described by (Eminli et al., 2008). iPS cells were cultured on Mitomycin-C inactived MEFs in KO DMEM supplemented with 15% FBS, Glutamax, non-essential AA, pen-strep, b-mercaptoethanol and Leukemia Inhibitory Factor (LIF). After initial expansion, iPS cells were passaged onto 0.1% gelatin to remove contaminating feeder cells.  Cells were grown to ~7e6 cells per 15 cm dish at the time of fixation with 1% formaldehyde before downstream assay.


title: iPS_Rep1_5C_library


title: pNPC_Rep2_RNA_seq_library

growth_protocol: Neural progenitor cells were   isolated from whole brains of P1 129SvJae x C57/BL6, Sox2-eGFP mice and cultured as neurospheres in Neural Stem Cell media: DMEM/F12 media (Invitrogen 12100-046 and 21700-075) containing 72 mM glucose, 120 mM Sodium Bicarbonate, 5.6 mM Hepes (Sigma H-0887), 27.5 nM Sodium Selenite (Sigma S-9133), 18 nM progesterone (Sigma P0130), 90 ug/mL Apo-transferrin (Sigma T1428), 23 ug/mL insulin (Sigma I6634), 100 uM putrescine (Sigma P-7505), 2 mM L-glutamine (Gibco 25030-081), 1% Pen/Strep (Sigma P0781), 2 ug/mL heparin, 20 ng/mL rhEGF (R&D Systems) , and 10 ng/mL rhFGF (R&D systems). Neurospheres were passaged every 3-4 days to prevent the formation of necrotic cores. After two passages, neurospheres were dissociated with Accutase and plated on Poly-D-Lysine Hydrobromide (100 ug/mL, Sigma P6407),   and laminin  (8 ug/mL, Corning 354232) coated plates at 60,000 cells/cm^2.

value: Neural Progenitor Cells


title: iPS_Rep2_RNA_seq_library

growth_protocol: Induced pluripotent stem cells were derived from primary NPCs as described by (Eminli et al., 2008). iPS cells were cultured on Mitomycin-C inactived MEFs in KO DMEM supplemented with 15% FBS, Glutamax, non-essential AA, pen-strep, b-mercaptoethanol and Leukemia Inhibitory Factor (LIF). After initial expansion, iPS cells were passaged onto 0.1% gelatin to remove contaminating feeder cells.

value: 129SvJae x C57BL/6


title: O3

status: Public on Jul 18 2016

type: RNA

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

organism: Rattus norvegicus

source_name: aged replicate 3

label_protocol: biotinylated cRNA using Illumina TotalPrep RNA Amplification kit (Ambion, UK)

extract_protocol: RNA was extracted from immature and aged rat primordial follicles was measured by Qubit® Fluorometer.  The quality of RNA was analyzed by using Agilent RNA 6000 Nano Kit and Agilent 2100 electrophoresis Bio-anlyzer according to the manufacturer’s instructions by subjecting 1µl of the diluted RNA on to a Nano chip. The quality of total RNA was obtained as electropherogram profile and RNA integrity number (RIN) generated by the Bioanalyzer software.

value: rat primordial follicles


title: Y2

source_name: immature replicate 2


title: Y3

source_name: immature replicate 3


title: genomic DNA from HCT116 cells infected with shRNA against ZBTB24 [850K_shZB1]

type: genomic

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated and purified from cells in culture using a serial phenol: chloroform extraction. Trizol reagent was used for extracting total RNA following the manufacturer’s protocol.

tag: shRNA

tag: age

value: patient-derived Xenograph glioma stem cells


title: O2

source_name: aged replicate 2


title: pNPC_Rep1_RNA_seq_library


title: O1

source_name: aged replicate 1


title: iPS_Rep1_RNA_seq_library


title: iPS_2i_Rep2_5C_library


title: pNPC_Rep2_5C_library


title: v65_2i_Rep1_5C_library

value: male


title: v65_Rep1_5C_library

growth_protocol: Murine V6.5 ES cells were expanded on Mitomycin-C-inactivated MEF feeder layers in pluripotent media supplemented with LIF.  After initial expansion, ES cells were passaged onto 0.1% gelatin to remove contaminating feeder cells.  Cells were grown to ~7e6 cells per 15 cm dish at the time of fixation with 1% formaldehyde before downstream assay.


title: pNPC_Rep1_5C_library


title: v65_2i_Rep2_5C_library


title: genomic DNA from HCT116 cells infected with shRNA against No Target Control [850K_shNT3]

value: No Target Control


title: genomic DNA from HCT116 3BKO (DNMT3B knockout) cell line [850K_3BKO]

source_name: HCT116 3BKO

value: 3BKO (DNMT3B knockout)


title: v65_Rep2_5C_library


title: genomic DNA from HCT116 cells infected with shRNA against No Target Control [850K_shNT2]


title: Y1

source_name: immature replicate 1


title: genomic DNA from HCT116 cells infected with shRNA against ZBTB24 [850K_shZB2]


title: genomic DNA from HCT116 cell line [850K_WT]

value: wildtype


title: genomic DNA from HCT116 cells infected with shRNA against No Target Control [850K_shNT1]


title: ES_2i_Input_ChIPseq_library


title: 786-O_SETD2_KO2

status: Public on Sep 30 2015

description:
KO2
786-O human cells depleted of SETD2 by zinc finger nucleases

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi.

source_name: DNA from 786-O ccRCC cell line depleted of SETD2 clone 2

label_protocol: Standard Illumina Infinium HD Methylation assay protocol

growth_protocol: 786-O parental and SETD2 KO derivatives were grown in RPMI medium (Hyclone) supplemented with 10% heat-inactivated fetal bovine serum (Hyclone) and 2mm  L-glutamine (Mediatech). NCCIT  were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone).

extract_protocol: Genomic DNA was extracted by proteinase K treatment, phenol:chloroform extraction, and ethanol precipitation.

treatment_protocol: NCCIT cells were transfected (PepMute reagent) with siRNA (Dharmacon)  against SETD2 expression following the manufacturer's protocol (SignaGen)

value: SETD2 KO


title: 786-O_SETD2_KO1

description:
KO1
786-O human cells depleted of SETD2 by zinc finger nucleases

source_name: DNA from 786-O ccRCC cell line depleted of SETD2 clone 1


title: HCT116_DNMT1/DNMT3B_overexpression

status: Public on Oct 20 2014

description:
DKI
HCT116 DNMT1/DNMT3B overexpression human colorectal carcinoma cells.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

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

data_processing: Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi. The 'GSE54840_methylated_unmethylated_signals.txt' file contains methylated and unmethylated signal intensities.

source_name: DNA from HCT116 DNMT1/DNMT3B overexpression human colorectal carcinoma cells

label_protocol: Standard Illumina Protocol.

growth_protocol: NCCIT and HCT116 cells were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone). HCT116 overexpression cells were selected under G418 (750 µg/ml).

treatment_protocol: NCCIT cells were transfected (PepMute reagent) with siRNA (Dharmacon) against DNMT expression following the manufacturer's protocol (SignaGen).

value: colorectal carcinoma cells

value: DNMT1/DNMT3B overexpression


title: NCCIT input all

description: Sample 3

data_processing:
Basecalls performed using CASAVA version 1.7
MBD-seq reads were aligned to the hg19 genome assembly using BWA version 0.5.9.
Mapped reads were filtered if they were mapped to multiple locations and to unique location with 5% or more mismatches and indels of read lengths.
peaks were called using SICER version 1.1 with the following setting: Window Size (200),Gap Size (400), Effective genome size (0.854).
differential peaks were called using SICER version 1.1 with the following setting: Window Size (200),Gap Size (400).
Genome_build: hg19
Supplementary_files_format_and_content: bed.gz files were generated using bamToBed and gzip
Supplementary_files_format_and_content: bigwig files were generated using wigToBigWig; Scores represent read depth.

source_name: NCCIT human cells treated with a control non-targeting siRNA

growth_protocol: NCCIT cells were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone).

extract_protocol:
Genomic DNA was isolated by proteinase digestion and phenol:chloroform extraction.  Affinity purification was performed according to manufacturers' protocols.
DNA sequencing libraries were constructed according to Illumina's protocol for TruSeq DNA sample preparation kit

treatment_protocol: NCCIT cells were transfected with siRNA (Dharmacon) against DNMT3B, and a  no-target control (NTC)

value: NCCIT

value: embryonic carcinoma cells

tag: transfected with

value: control non-targeting siRNA


title: NCCIT siNTC 5mC-seq

description: Sample 1

tag: affinity purification method

value: MethylMagnet mCpG DNA isolation (Ribomed)


title: 786-O_Parental

description:
Parental
786-O Parental human cells

source_name: DNA from Parental 786-O ccRCC cell line

value: WT


title: NCCIT_siRNA_NTC (biological replicate 2)

status: Public on Oct 21 2014

description:
NTC-2
NCCIT human cells treated with a control non-targeting siRNA.

source_name: DNA from NCCIT human cells treated with a control non-targeting siRNA


title: NCCIT siDNMT3B 5mC-seq

description: Sample 2

source_name: NCCIT human cells depleted of DNMT3B by siRNA

value: siRNA against DNMT3B


title: NCCIT_siRNA_DNMT3B (biological replicate 3)

description:
DNMT3B-2
NCCIT human cells depleted of DNMT3B by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT3B by siRNA


title: NCCIT_siRNA_DNMT1 (biological replicate 3)

description:
DNMT1-2
NCCIT human cells depleted of DNMT1 by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT1 by siRNA

value: siRNA against DNMT1


title: NCCIT_siRNA_DNMT3B (biological replicate 2)

description:
DNMT3B-1
NCCIT human cells depleted of DNMT3B by siRNA.


title: NCCIT_siRNA_3B+3L (biological replicate 3)

description:
3B+3L-2
NCCIT human cells depleted of DNMT3B and DNMT3L by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT3B and DNMT3L by siRNA

value: siRNA against DNMT3B and DNMT3L


title: HCT116_DNMT1_overexpression

description:
1KI
HCT116 DNMT1 overexpression human colorectal carcinoma cells.

source_name: DNA from HCT116 DNMT1 overexpression human colorectal carcinoma cells

value: DNMT1 overexpression


title: NCCIT_siRNA_3B+3L (biological replicate 2)

description:
3B+3L-1
NCCIT human cells depleted of DNMT3B and DNMT3L by siRNA.


title: NCCIT 3A+3B+3L rep1

hyb_protocol: Following labeling, cDNAs were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6).  Differential expressions were calculated using ANOVA of Partek package.

label: biotin

source_name: NCCIT_DNTM3A, DNMT3B, and DNMT3L depletion

label_protocol: Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

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

treatment_protocol: NCCIT cells were transfected (PepMute reagent) with siRNA (Dharmacon)  against DNMT expression following the manufacturer's protocol (SignaGen)

value: siRNA against DNMT3A, DNMT3B, and DNMT3L transcript

value: DNTM3A, DNMT3B, and DNMT3L depletion


title: NCCIT_siRNA_DNMT1 (biological replicate 2)

description:
DNMT1-1
NCCIT human cells depleted of DNMT1 by siRNA.


title: NCCIT_siRNA_SETD2

description:
siSETD2
NCCIT human cells depleted of SETD2 by siRNA

source_name: DNA from NCCIT human cells depleted of SETD2 by siRNA

tag: sirna


title: HCT116_DNMT1/DNMT3B_KO

description:
DKO
HCT116 DNMT1/DNMT3B genetic knockout human colorectal carcinoma cells.

source_name: DNA from HCT116 DNMT1/DNMT3B genetic knockout human colorectal carcinoma cells

tag: cell line

value: DNMT1/DNMT3B genetic knockout


title: HCT116_WT

description:
WT
HCT116 parental human colorectal carcinoma cells.

source_name: DNA from HCT116 parental human colorectal carcinoma cells

value: parental


title: NCCIT 3B+3L rep2

source_name: NCCIT_DNMT3B and DNMT3L depletion

value: siRNA against DNMT3B and DNMT3L transcript

value: DNMT3B and DNMT3L depletion


title: NCCIT_siRNA_D1+3A+3B

description:
D1+3A+3B
NCCIT human cells depleted of DNMT1, DNMT3A, and DNMT3B by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT1, DNMT3A, and DNMT3B by siRNA

value: siRNA against DNMT1, DNMT3A, and DNMT3B


title: NCCIT_siRNA_3A+3L

description:
3A+3L
NCCIT human cells depleted of DNMT3A and DNMT3L by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT3A and DNMT3L by siRNA

value: siRNA against DNMT3A and DNMT3L


title: NCCIT_siRNA_3A+3B

description:
3A+3B
NCCIT human cells depleted of DNMT3A and DNMT3B by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT3A and DNMT3B by siRNA

value: NCCIT

value: siRNA against DNMT3A and DNMT3B


title: NCCIT_siRNA_D1+3A

description:
D1+3A
NCCIT human cells depleted of DNMT1 and DNMT3A by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT1 and DNMT3A by siRNA

value: embryonic carcinoma cells

value: siRNA against DNMT1 and DNMT3A


title: NCCIT 3B+3L rep1


title: NCCIT_siRNA_3A+3B+3L

description:
3A+3B+3L
NCCIT human cells depleted of DNTM3A, DNMT3B, and DNMT3L by siRNA.

source_name: DNA from NCCIT human cells depleted of DNTM3A, DNMT3B, and DNMT3L by siRNA

value: siRNA against DNTM3A, DNMT3B, and DNMT3L


title: NCCIT_Undifferentiated

description:
UD
NCCIT undifferentiated human cells.

source_name: DNA from NCCIT undifferentiated human cells

tag: cell subtype

value: undifferentiated cells


title: NCCIT 3A+3L rep2

source_name: NCCIT_DNMT3A and DNMT3L depletion

value: siRNA against DNMT3A and DNMT3L transcript

value: DNMT3A and DNMT3L depletion


title: HCT116_DNMT3B_KO

description:
3BKO
HCT116 DNMT3B genetic knockout human colorectal carcinoma cells.

source_name: DNA from HCT116 DNMT3B genetic knockout human colorectal carcinoma cells

value: colorectal carcinoma cells

value: DNMT3B genetic knockout


title: NCCIT 3A+3B rep2

source_name: NCCIT_DNMT3A and DNMT3B depletion

value: siRNA against DNMT3A and DNMT3B transcript

value: DNMT3A and DNMT3B depletion


title: NCCIT_siRNA_DNMT3L

description:
DNMT3L
NCCIT human cells depleted of DNMT3L by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT3L by siRNA

value: siRNA against DNMT3L


title: NCCIT 3A+3B rep1


title: NCCIT_siRNA_DNMT3A

description:
DNMT3A
NCCIT human cells depleted of DNMT3A by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT3A by siRNA

value: siRNA against DNMT3A


title: NCCIT_siRNA_3B+3L (biological replicate 1)

description:
3B+3L-0
NCCIT human cells depleted of DNMT3B and DNMT3L by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT3B and DNMT3L by siRNA

value: siRNA against DNMT3B and DNMT3L


title: NCCIT 3A+3L rep1


title: NCCIT_siRNA_D1+3B

description:
D1+3B
NCCIT human cells depleted of DNMT1 and DNMT3B by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT1 and DNMT3B by siRNA

value: siRNA against DNMT1 and DNMT3B


title: HCT116_DNMT1_KO

description:
1KO
HCT116 DNMT1 genetic knockout human colorectal carcinoma cells.

source_name: DNA from HCT116 DNMT1 genetic knockout human colorectal carcinoma cells

value: DNMT1 genetic knockout


title: NCCIT siDNMT3B rep2

source_name: NCCIT_DNMT3B depletion

value: NCCIT

value: siRNA against DNMT3B transcript

value: DNMT3B depletion


title: NCCIT siDNMT3L rep1

source_name: NCCIT_DNMT3L depletion

value: embryonic carcinoma cells

value: siRNA against DNMT3L transcript

value: DNMT3L depletion


title: NCCIT_RA_Differentiated

description:
DF
NCCIT retinoic acid induced differentiated human cells.

source_name: DNA from NCCIT retinoic acid induced differentiated human cells

value: retinoic acid induced differentiated cells


title: NCCIT_siRNA_DNMT1 (biological replicate 1)

description:
DNMT1-0
NCCIT human cells depleted of DNMT1 by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT1 by siRNA

value: siRNA against DNMT1


title: NCCIT siDNMT3B rep1


title: NCCIT_siRNA_NTC (biological replicate 1)

description:
NTC-1
NCCIT human cells treated with a control non-targeting siRNA.

source_name: DNA from NCCIT human cells treated with a control non-targeting siRNA

value: control non-targeting siRNA


title: NCCIT_siRNA_DNMT3B (biological replicate 1)

description:
DNMT3B-0
NCCIT human cells depleted of DNMT3B by siRNA.

source_name: DNA from NCCIT human cells depleted of DNMT3B by siRNA

value: siRNA against DNMT3B


title: NCCIT siD1+3A+3B rep1

source_name: NCCIT_DNMT1, DNMT3A, and DNMT3B depletion

value: siRNA against DNMT1, DNMT3A, and DNMT3B transcript

value: DNMT1, DNMT3A, and DNMT3B depletion


title: NCCIT siD1+3A rep1

source_name: NCCIT_DNMT1 and DNMT3A depletion

value: siRNA against DNMT1 and DNMT3A transcript

value: DNMT1 and DNMT3A depletion


title: NCCIT siD1+3B rep2

source_name: NCCIT_DNMT1 and DNMT3B depletion

value: siRNA against DNMT1 and DNMT3B transcript

value: DNMT1 and DNMT3B depletion


title: NCCIT siD1+3A+3B rep2


title: NCCIT siD1+3A rep2


title: NCCIT siDNMT3A rep2

source_name: NCCIT_DNMT3A depletion

value: siRNA against DNMT3A transcript

value: DNMT3A depletion


title: NCCIT 3A+3B+3L rep2

source_name: NCCIT_DNTM3A, DNMT3B, and DNMT3L depletion

value: NCCIT

value: siRNA against DNMT3A, DNMT3B, and DNMT3L transcript

value: DNTM3A, DNMT3B, and DNMT3L depletion


title: NCCIT siNTC-2 rep1

value: embryonic carcinoma cells

value: control siRNA

value: control


title: NCCIT siD1+3B rep1


title: NCCIT siNTC-2 rep2


title: NCCIT siDNMT1 rep1

source_name: NCCIT_DNMT1 depletion

value: siRNA against DNMT1 transcript

value: DNMT1 depletion


title: NCCIT siDNMT3A rep1


title: NCCIT siNTC-1 rep1


title: NCCIT siNTC-1 rep2


title: unclassified-17

status: Public on Sep 16 2014

data_processing: Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi. The file Unmethylated_and_methylated_signal_intensities.txt contains the raw unmethylated and methylated signal intensities and is available on the series record.

source_name: liver

growth_protocol: Normal hepatocytes were prepared as previously described (Zhu et al)

tag: disease status

value: unclassified

tag: tissue

value: liver


title: unclassified-20


title: NCCIT siDNMT1 rep2

tag: cell type


title: unclassified-19


title: NCCIT siDNMT3L rep2

value: siRNA against DNMT3L transcript

value: DNMT3L depletion


title: unclassified-21


title: unclassified-18


title: unclassified-16


title: unclassified-9


title: unclassified-10


title: unclassified-8


title: Plated_hepatocyte8


title: unclassified-11


title: unclassified-3


title: unclassified-15


title: unclassified-12


title: unclassified-5


title: unclassified-14


title: Plated_hepatocyte9


title: Plated_hepatocyte14


title: unclassified-7


title: unclassified-4


title: unclassified-6


title: unclassified-2


title: Plated_hepatocyte15


title: unclassified-13


title: unclassified-1


title: Plated_hepatocyte12


title: Plated_hepatocyte16


title: Plated_hepatocyte2


title: Plated_hepatocyte5


title: Plated_hepatocyte17


title: Plated_hepatocyte13


title: HCV HCC-12

value: HCCHCV


title: Plated_hepatocyte11


title: Metastatic Tumor-7

value: HM


title: Plated_hepatocyte7


title: Metastatic Tumor-8


title: Plated_hepatocyte6


title: HCV HCC-10


title: Metastatic Tumor-4


title: Plated_hepatocyte10


title: HCV HCC-8


title: Plated_hepatocyte1


title: Metastatic Tumor-5


title: Metastatic Tumor-6


title: Plated_hepatocyte3


title: HCV HCC-6


title: Metastatic Tumor-1


title: Metastatic Tumor-3


title: Metastatic Tumor-2


title: HCV HCC-7


title: HCV HCC-5


title: HCV HCC-11


title: HCV HCC-9


title: Plated_hepatocyte4


title: HCV HCC-3


title: HCV HCC-4


title: Ethanol HCC-8

value: HCCEtOH


title: HCV HCC-2


title: Ethanol HCC-15


title: HCC cell line-3

value: HCC cell line


title: Ethanol HCC-13


title: Ethanol HCC-10


title: Ethanol HCC-3


title: Ethanol HCC-4


title: Ethanol HCC-12


title: Ethanol HCC-6


title: HCC cell line-5


title: HCC cell line-1

description: FLNEO


title: Cryptogenic HCC-2

value: HC


title: HCC cell line-6


title: Ethanol HCC-9


title: Ethanol HCC-1


title: HCV HCC-1


title: Cryptogenic HCC-4


title: HCV Cirrhosis-39

value: CirrHCV


title: Ethanol HCC-11


title: Ethanol HCC-2


title: Ethanol HCC-5


title: HCC cell line-8


title: Ethanol HCC-7


title: Biliary Tumor-2

value: Hbil


title: HCC cell line-2


title: Cryptogenic HCC-3


title: HCC cell line-7


title: Cryptogenic HCC-1


title: HCV Cirrhosis-38


title: Cryptogenic HCC-5


title: Biliary Tumor-1


title: HCV Cirrhosis-34


title: Ethanol HCC-14


title: HCV Cirrhosis-35


title: HCV Cirrhosis-37


title: HCC cell line-4


title: HCV Cirrhosis-36


title: HCV Cirrhosis-33


title: HCV Cirrhosis-29


title: HCV Cirrhosis-31


title: HCV Cirrhosis-21


title: HCV Cirrhosis-30


title: HCV Cirrhosis-16


title: HCV Cirrhosis-19


title: HCV Cirrhosis-23


title: HCV Cirrhosis-26


title: HCV Cirrhosis-20


title: HCV Cirrhosis-22


title: HCV Cirrhosis-12


title: HCV Cirrhosis-32


title: HCV Cirrhosis-15


title: HCV Cirrhosis-17


title: HCV Cirrhosis-25


title: HCV Cirrhosis-24


title: HCV Cirrhosis-10


title: HCV Cirrhosis-18


title: HCV Cirrhosis-13


title: HCV Cirrhosis-7


title: HCV Cirrhosis-14


title: HCV Cirrhosis-6


title: HCV Cirrhosis-9


title: HCV Cirrhosis-8


title: HCV Cirrhosis-11


title: HCV Cirrhosis-27


title: HCV Cirrhosis-2


title: HCV Cirrhosis-28


title: HCV Cirrhosis-5


title: HCV Cirrhosis-3


title: Ethanol Cirrhosis-20

value: CirrEtOH


title: HCV Cirrhosis-1


title: HCV Cirrhosis-4


title: Ethanol Cirrhosis-17


title: Ethanol Cirrhosis-14


title: HBV Cirrhosis-6

value: CirrHBV


title: Ethanol Cirrhosis-5


title: HBV Cirrhosis-3


title: HBV Cirrhosis-5


title: Ethanol Cirrhosis-13


title: HBV Cirrhosis-1


title: HBV Cirrhosis-4


title: Ethanol Cirrhosis-21


title: Ethanol Cirrhosis-9


title: HBV Cirrhosis-2


title: Ethanol Cirrhosis-16


title: Ethanol Cirrhosis-3


title: Ethanol Cirrhosis-11


title: Ethanol Cirrhosis-1


title: Ethanol Cirrhosis-6


title: Ethanol Cirrhosis-2


title: Ethanol Cirrhosis-7


title: Ethanol Cirrhosis-18


title: Ethanol Cirrhosis-19


title: Ethanol Cirrhosis-15


title: Genetic Cirrhosis-2

value: CG


title: Ethanol Cirrhosis-4


title: Ethanol Cirrhosis-12


title: Genetic Cirrhosis-4


title: Genetic Cirrhosis-1


title: Cryptogenic Cirrhosis-3

value: CC


title: Normal-33

value: Normal


title: Normal-25


title: Normal-28


title: Biliary Cirrhosis-2

value: Cbil


title: Ethanol Cirrhosis-10


title: Normal-26


title: Ethanol Cirrhosis-8


title: Normal-20


title: Biliary Cirrhosis-1


title: Cryptogenic Cirrhosis-2


title: Normal-30


title: Normal-23


title: Normal-31


title: Immune Cirrhosis-1

value: CI


title: Immune Cirrhosis-2

value: liver


title: Normal-29


title: Genetic Cirrhosis-3


title: Normal-22


title: Normal-24


title: Cryptogenic Cirrhosis-1


title: Normal-27


title: Normal-32


title: Normal-34


title: Normal-16


title: Normal-19


title: NCCIT siNTC 5mC-seq

status: Public on Jul 14 2014

data_processing:
Basecalls performed using CASAVA version 1.8
MBD-seq reads were aligned to the hg19 genome assembly using BWA version 0.5.9.
Mapped reads were filtered if they were mapped to multiple locations and to unique location with 5% or more mismatches and indels of read lengths.
peaks were called using SICER version 1.1 with the following setting: Window Size (200),Gap Size (400), Effective genome size (0.833).
differential peaks were called using SICER version 1.1 with the following setting: Window Size (200),Gap Size (400), Effective genome size (0.833).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using wigToBigWig; Scores represent read depth.

source_name: NCCIT human cells treated with a control non-targeting siRNA

value: NCCIT

value: human embryonic carcinoma cells

value: control siRNA

value: MethylMagnet mCpG DNA isolation (Ribomed)


title: Normal-14


title: NCCIT siEED+siRNF2 5mC-seq

source_name: NCCIT human cells depleted of EED and RNF2 by siRNA

value: siRNA against EED and RNF2 transcripts


title: NCCIT siWDR5 5mC-seq

source_name: NCCIT human cells depleted of WDR5 by siRNA

value: siRNA against WDR5 transcript


title: NCCIT siRNF2 5mC-seq

source_name: NCCIT human cells depleted of RNF2 by siRNA

value: siRNA against RNF2 transcript


title: NCCIT siEED 5mC-seq

source_name: NCCIT human cells depleted of EED by siRNA

value: siRNA against EED transcript


title: Normal-18


title: Normal-11


title: Normal-15


title: Normal-21


title: NCCIT siNTC rep2 [re-analysis]

data_processing: Intensities of arrays have been quantile-normalized using GC-RMA in Partek Genomic Suite (v6.6). Differential expressions were calculated using ANOVA of Partek package.

source_name: NCCIT human cells_control non-targeting siRNA


title: NCCIT siNTC rep1 [re-analysis]


title: NCCIT siSETD2 5mC-seq

source_name: NCCIT human cells depleted of SETD2 by siRNA

value: siRNA against SETD2 transcript


title: Normal-13


title: NCCIT siWDR5 rep2

source_name: NCCIT human cells_WDR5 by siRNA


title: NCCIT siWDR5 rep1


title: Normal-3


title: NCCIT siCBX4 5mC-seq

source_name: NCCIT human cells depleted of CBX4 by siRNA

value: siRNA against CBX4 transcript


title: NCCIT siEED+RNF2 rep1

source_name: NCCIT human cells_EED and RNF2 by siRNA


title: NCCIT siRNF2 rep2

source_name: NCCIT human cells_RNF2 by siRNA


title: Normal-6


title: NCCIT siRNF2 rep1


title: NCCIT siSETD2 rep2

source_name: NCCIT human cells_SETD2 by siRNA


title: NCCIT siSETD2 rep1


title: NCCIT siEED rep2

source_name: NCCIT human cells_EED by siRNA


title: NCCIT siEED rep1


title: Normal-2


title: NCCIT siEED+RNF2 rep2


title: Normal-8


title: Normal-17


title: NCCIT siCBX4 rep2

source_name: NCCIT human cells_CBX4 by siRNA


title: NCCIT siCBX4 rep1


title: Normal-1


title: Normal-9


title: Normal-4


title: Normal-7


title: Normal-10


title: NCCIT pluripotent input

status: Public on Jun 14 2014

data_processing:
Basecalls performed using CASAVA version 1.7
MBD-seq reads were aligned to the hg19 genome assembly using BWA version 0.5.9.
Mapped reads were filtered if they were mapped to multiple locations and to unique location with 5% or more mismatches and indels of read lengths.
peaks were called using SICER version 1.1 with the following setting: Window Size (200),Gap Size (400), Effective genome size (0.833).
differential peaks were called using SICER version 1.1 with the following setting: Window Size (200),Gap Size (400), Effective genome size (0.833).
Genome_build: hg19
Supplementary_files_format_and_content: bed.gz files were generated using bamToBed and gzip
Supplementary_files_format_and_content: bigwig files were generated using wigToBigWig; Scores represent read depth.

source_name: NCCIT human cells

value: embryonic carcinoma

tag: transfectant


title: NCCIT siNTC input


title: NCCIT 7-day differentiated 5mC-seq

description: reanalysis of GSM952552

source_name: NCCIT human cells differentiated with retinoic acid for 7 days


title: NCCIT 7-day differentiated 5hmC-seq

value: Hydroxymethyl Collector (Active Motif)


title: NCCIT siNTC 5mC-seq


title: NCCIT siTET3 5hmC-seq

source_name: NCCIT human cells depleted of TET3 by siRNA

value: siRNA against TET3 transcript


title: NCCIT pluripotent 5mC-seq

description: reanalysis of GSM952551


title: NCCIT siTET2 5mC-seq

source_name: NCCIT human cells depleted of TET2 by siRNA

value: siRNA against TET2 transcript


title: NCCIT siTET1 5mC-seq

source_name: NCCIT human cells depleted of TET1 by siRNA

value: siRNA against TET1 transcript


title: NCCIT siTET3 5mC-seq


title: NCCIT siNTC 5hmC-seq

source_name: NCCIT human cells treated with a control non-targeting siRNA


title: NCCIT siTET1 5hmC-seq


title: NCCIT siTET3 rep1

source_name: RNA from NCCIT human cells depleted of TET3 by siRNA


title: NCCIT siNTC rep1

source_name: RNA from NCCIT human cells treated with a control non-targeting siRNA


title: NCCIT siTET2 5hmC-seq


title: NCCIT siNTC rep2


title: Normal-12

source_name: liver

value: Normal


title: NCCIT siTET3 rep2


title: NCCIT siTET1 rep2

source_name: RNA from NCCIT human cells depleted of TET1 by siRNA


title: NCCIT siTET2 rep1

source_name: RNA from NCCIT human cells depleted of TET2 by siRNA


title: NCCIT pluripotent 5hmC-seq


title: NCCIT siTET2 rep2


title: Normal-5

value: liver


title: NCCIT siTET1 rep1

value: NCCIT