title: TOSO-WT-TGFB1_IL6-96h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_TOSO-WT-T16-96-1
sample date (yymmdd): 140219


title: MATa deltaRE_right 5C Rep2

status: Public on Nov 20 2015

type: SRA

city: Worcester

first: Bryan

middle: R

last: Lajoie

state: MA

address: 368 Plantation St.

department: Program in Systems Biology

country: USA

institute: UMMS

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB22-R2

library_source: genomic

data_processing:
[Hi-C, mapping] Iterative mapping and error correction of the chromatin interaction data were performed as previously described (Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999-1003, doi:10.1038/nmeth.2148 (2012))
[Hi-C normalization] The total read count for each library was normalized to a common value
[Hi-C, comparisons] subtractions and log2 ratios were performed
[5C, mapping] fastq files were mapped to the 5C probe pool using our in-house 5C mapping pipeline.  Each side of the paired-end reads was mapped independently to the 5C probe pool using the novoalign mapping software (V2.05 novocraft.com) and 5C interactions were assembled from those paired end reads where both sides mapped uniquely to a single 5C primer of opposite type (forward-reverse or reverse-forward).  Since our experiments were carried out using strains which have a different background than that for which the probes were designed to, we lifted the probe coordinates over to the correct genome assembly.  For SK1 the 5C probes were aligned to the SK1 genome produced by Scott Keeney’s Group (http://cbio.mskcc.org/public/SK1_MvO/) using the BLAST command line tool blastall (http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/) using the blastn program and a 20bp word size.  This genome assembly contained what appeared to be a 29,701bp translocation from chromosome XI inserted at position 3,623 in the left arm of Chr. III.  Our 5C data did not show evidence for a large insertion in Chr. III.  Therefore this region of the assembly is likely an assembly error so we manually removed this region from the SK1 genomic sequence (chrIII:3,623-33,324).Once the probes were aligned to the genome they were manually curated to remove those which blasted to the wrong chromosome or to multiple chromosomes.  Probes were also filtered if they no longer aligned adjacent to a HindIII restriction site in the SK1 genome. Finally, since the length of the rDNA on the right arm of chromosome XII contains many copies of the rDNA repeats which could, in reality be up to 2Mbps of DNA, we decided to treat the left and right portions of chromosome XII as separate chromosome in our analysis.  We did this by changing the chromosome name of these probes to the right of the rDNA to chr12R and restarting the coordinates at 0.  The procedure for mapping to the 5C datasets from the strains used for the microscopy experiments (Supplemental Figure S8) was the same as for mapping to the SK1 genome, except that the W303 genome.
[5C, filtering] Prior to correcting the 5C counts using the Iterative Correction algorithm it was necessary to filter the data of any outliers.  First, the 70kb around Centromere-centromere and telomere-telomere interactions were removed to prevent from filtering high 5C counts from these regions which are known to interact and thus will have a higher signal than expected.  Then single data points which were greater than or equal to 7 standard deviations from the local mean, based on genomic distance, were removed for intra-chromosomal interactions.  For inter-chromosomal interactions a cutoff of 8 standard deviations from the mean of the inter-quartile (25%-50%) were removed.  Finally, we removed the highest and lowest 7.5% (15% total) of rows and columns from the dataset which were determined by summing all of the inter-chromosomal interactions for each 5C fragment.  The centromeres and telomeres were replaced and used for all further correction/analysis. The data was binned into 10kb x 10kb bins.  The median of the interactions in each 10kb x 10kb region was used to represent that region.  The iterative correction algorithm assumes that all bins should have the same sum of interactions.  This assumption is valid when genome wide Hi-C data is being considered.  However, the 5C design is comprehensive enough to approximate this assumption.  The row and column sums were calculated for each 10kb bin.  Then each row and column was multiplied by a factor that would raise or lower its sum to match the average of all the sums.  This was done iteratively until the row and column sums deviated very little from each other.  Figure S3 shows the sums of each row in the dataset before and after applying the iterative correction algorithm.
[5C, comparisons] In order to call significant differences between pairs of 5C datasets, we tested for the difference in the ranks of interaction frequencies obtained between two pairs of genomic regions.  To this end, we first bin the 5C data into 30Kb by 30Kb bins that overlap each other by 10Kb.  For each of these bins we pool all 5C interactions that fall within it across the three biological replicates for that strain.  We use this list of pooled values for the first strain and perform a two-tailed rank sum test with the list of corresponding values for the second strain.  We correct for multiple testing and plot the log2 of the median of strain 1 divided by the median of strain 2 for that bin in the heat map if the corrected p-value from the test between these two bins is less than or equal to a 5% FDR.Filtering, correction, and normalization of 5C data. Prior to correcting the 5C counts using the Iterative Correction algorithm it was necessary to filter the data of any outliers.  First, the 70kb around Centromere-centromere and telomere-telomere interactions were removed to prevent from filtering high 5C counts from these regions which are known to interact and thus will have a higher signal than expected.  Then single data points which were greater than or equal to 7 standard deviations from the local mean, based on genomic distance, were removed for intra-chromosomal interactions.  For inter-chromosomal interactions a cutoff of 8 standard deviations from the mean of the inter-quartile (25%-50%) were removed.  Finally, we removed the highest and lowest 7.5% (15% total) of rows and columns from the dataset which were determined by summing all of the inter-chromosomal interactions for each 5C fragment.  The centromeres and telomeres were replaced and used for all further correction/analysis.  The data was binned into 10kb x 10kb bins.  The median of the interactions in each 10kb x 10kb region was used to represent that region.  The iterative correction algorithm assumes that all bins should have the same sum of interactions.  This assumption is valid when genome wide Hi-C data is being considered.  However, the 5C design is comprehensive enough to approximate this assumption.  The row and column sums were calculated for each 10kb bin.  Then each row and column was multiplied by a factor that would raise or lower its sum to match the average of all the sums.  This was done iteratively until the row and column sums deviated very little from each other.  Figure S3 shows the sums of each row in the dataset before and after applying the iterative correction algorithm.  The 5C data for each dataset was first normalized to a standard read depth.  Each interaction in the dataset was calculated as a percentage of the total number of reads for the dataset.  This percentage was then multiplied by the arbitrary value of 1,000,000. Finally, 5C data was normalized relative to the expected value for pairs of loci separated by a give genomic distance (as decribed in (Sanyal et al., 2012)). This distance-dependent expected value was calculated using the ârobust lowessâsmoothing method which takes an âoutlier filteredâ weighted average across a percentage of the data (here we used 5%) for each genomic distance.    #5C data analysis.  In order to call significant differences between pairs of 5C datasets, we tested for the difference in the ranks of interaction frequencies obtained between two pairs of genomic regions.  To this end, we first bin the 5C data into 30Kb by 30Kb bins that overlap each other by 10Kb.  For each of these bins we pool all 5C interactions that fall within it across the three biological

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: MATa deltaRE_right 5C

growth_protocol: Yeast from glycerol stocks were streaked out onto agar plates with the appropriate media and incubated at 30°C.  Three colonies were picked and grown over night in a 6ml culture of the appropriate media at 30°C while shaking at 250 RPM.  The culture was backed down to an OD600 of 0.2 in 100ml of media and grown over night at 30°C with shaking.  The culture was diluted to an OD600 of 0.2 in 400ml of media and incubated to mid-log phase at 30˚C with shaking.

extract_protocol:
Crosslinked cells were lysed by grinding in a cold mortar and pestle
[Hi-C] The yeast culture was crosslinked with 37% formaldehyde to a final concentration of 3% in the culture media for 20 min at 25˚C.  The crosslinking was quenched by adding 2X the volume of formaldehyde used of 2.5M Glycine to the culture and incubated culture for 5 min at 25˚C.  Cells were lyses by grinding in a cold mortar and pestle.  The chromatin was solubilized by adding 1% w/v SDS and Incubating at 65˚C water bath for 10 min.  Excess SDS was quenched using 10% v/v Triton X-100.  The chromatin was digested with HindIII at 37˚C overnight in a water bath.  Digested ends were filled in with biotin-14-dCTP with Klenow at 37˚C for 2 hr in a water bath.  The klenow was inactivated by Incubating in a 65˚C water bath for 20 min.  Crosslinked and digested fragments were ligated together in a dilute reaction inorder to favor intra-molecular ligation in a 16˚C water bath for 8 hr.  Crosslinkes were reversed by incubating the ligation mixture with proteinase K in a 65˚C water bath.  Ligation products were purified with phenol (pH 8.0):chloroform and precipitated with sodium acetate pH 5.2 and ethanol.  The precipitated DNA was resuspended in 1X TE and then the DNA was re-extracted with phenol (pH 8.0):chloroform and precipitated with sodium acetate pH 5.2 and ethanol.  The DNA pellet was dried thoroughly and excess salt was washed out of the solution using an amicon 30kDa spin column using 1X TE.  Then the sample was concentrated using a 30kDa amicon column.  RNA was degrade using DNase free RNase A at 37˚C for 1 hr.  The Hi-C library was quantified on a 0.8% agarose gel in 0.5X TBE by comparing it to known concentration standards.  The Hi-C efficiencey was accessed by first PCR amplifing a neighboring interaction in the Hi-C library.  This amplicon was split and the aliquots were digested with either HindIII, NheI, or HindIII and NheI at 37˚C overnight.  The digested products were quantified on a gel and the percent Hi-C efficiency was calculated as the percent digested with NheI divided by the percent digested in the NheI and HindIII combined reaction.  Biotin was removed from un-ligated ends using T4 DNA polymerase at 20˚C for 4hrs and then at 75˚C for 20 min to inactivate the enzyme. The DNA was sheared to 50-700bp using the Covaris S2 sonicator. The DNA ends were repaired using T4 DNA Polymerase, T4 Polynucleotide Kinase, and Klenow fragment of DNA Polymerase I at 20˚C for 30 min.  The DNA was purified with one Qiagen MinElute Column.  A dATP was added to the 3’ end of the molecules by using Klenow Fragment (exo-) at 37˚C for 30 min and then at 65˚C for 20 min to inactivate the enzyme.  The end repaired and A-tailed library was fractionated to 100-300bp using 0.9x and then 1.1x ampure XP extractions.  For each 1.0 ng of biotinylated ligation products, 1.0 µl of Dynabeads MyOne Strepavidin C1 beads were used to enrich the library.  Illumina PE adapters were ligated to the library using NEB Quick Ligase at room temperature for 15 min.  The library was amplified using Illumina primers PE1.0 and PE2.0 for as few cycles as possible.  Cycle number was determined by a titration experiment that revealed which cycle would produce enough library for sequencing but didn’t produce higher molecular weight artifacts.  The library was purified once more with 1.8x Ampure XP to remove primers and primer dimers.  The final library was quantified on a bioanalyzer.  The libraries were sequenced on either the GAII or HiSeq platforms.
[5C] The yeast culture was crosslinked with a final volume of 3% formaldehyde (37% w/v, Fisher, Catalog #: BP531-500) in the culture media at 25˚C for 20mins with shaking.  The remaining formaldehyde was quenched with an excess of 2.5M glycine.  The yeast cells were harvested by centrifugation and lysed by grinding with a mortar and pestle in the presence of liquid nitrogen.  The chromatin was digested with HindIII (NEB, R0104S) and the resulting crosslinked restriction fragments were ligated with T4 DNA polymerase (Invitrogen, 15224-090) in a dilute reaction so that intra-molecular ligation was favored.  The crosslinking was reversed by incubating overnight at 65˚C in the presence of proteinase K (Invitrogen, 25530-015).  The chimeric DNA molecules were purified with a series of phenol:chloroform pH 8.0 (1:1) extractions and precipitated with 100% cold ethanol and 3M sodium acetate pH 5.2.  The RNA was degraded with RNase A (Roche, Catalog #: 10109169001) and the yield was quantified using molecular weight standards run on an agarose gel.  3C-PCR was performed on all 3C libraries with 3C PCR primers which represent a variety of genomic distances.  Libraries which showed the characteristic, exponential decay of 3C-PCR product abundance relative to genomic distance passed quality control.  For one 5C reaction, 4 million genome copies (53.3ng) worth of 3C library were mixed with 1fmol of each of the 5C probes in a 40 µl reaction.  The reaction was heated to 95˚C for 9mins to melt the DNA, then slowly cooled to 55˚C to allow for the 5C probes to anneal to the 3C ligation products for a minimum of 4hrs and a maximum of 16hrs.  The annealed probes were then ligated together using Taq DNA Ligase (New England Biolabs, M0208S) at 55˚C for 1hr.  The 5C products were amplified with a high fidelity polymerase (Amplitaq Gold, Life technologies, 4398813) and 1.6µM of each of the universal primers (Universal_forward: 5’ -/5Phos/CCTCTCTATGGGCAGTCGGTGAT – 3’, Universal_reverse: 5’ – /5Phos/CTGCCCCGGGTTCCTCATTCTCT – 3’).  Five 5C reactions for a total of 20 million genome copies were used to produce each 5C library.  The Illumina Paired-end sequencing adapters and primers were used to add the Illumina Paired-end sequences to the 5C molecules in order to prepare them for sequencing on either the Illumina GAII or HiSeq platforms.

tag: genotype

value: MATa, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3,RE_right::KanMX5

tag: strain

tag: media

value: -ura

tag: tag


title: PLZP-KO-IL1B_IL6_IL23-48h (population, rep1)

city: Berkeley

first: Nir

last: Yosef

state: CA

address: Berkeley

department: EECS

institute: UC Berkeley

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_PLZP-KO-B623-48-1
sample date (yymmdd): 140224

library_source: transcriptomic

data_processing:
base calling software
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using TopHat (Trapnell et al., 2009). The resulting alignments were processed by Cufflinks to evaluate the expression of transcripts from RefSeq.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text. Standard cufflinks output with columns for: (tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status)

molecule: total RNA

organism: Mus musculus

source_name: CD4 T cells

growth_protocol: C57BL/6 WT and CD4-/-(2663) mice were obtained from Jackson Laboratory. IL-17A–GFP+ mice were obtained from Biocytogen. All animals, unless noted otherwise, were housed and maintained in a conventional pathogen-free facility at the Harvard Institute of Medicine in Boston. All experiments were performed in accordance to the guidelines outlined by the Harvard Medical Area Standing Committee on Animals at the Harvard Medical School. In addition, spleens and lymph nodes from GPR65−/− mice were provided by Li Yang (IACUC protocol: J195b), originally generated by Dr. Owen Witte. PLZP−/− mice were provided by Pier Paolo Pandolfi at the Beth Israel Deaconess Medical Center (IACUC protocol: 082-2014), and TOSO−/− mice were generously provided by John Coligan at the National Institute of Allergy and Infectious Diseases.

extract_protocol:
Cells were washed, stained and sorted for CD3 (Biolegend), CD4 (Biolegend), 7AAD and IL-17A-GFP+.
population controls were generated by extracting total RNA using a RNeasy plus Micro RNA kit (Qiagen) according to manufacturer’s recommendations. Subsequently, 1 μL of RNA in water was added to 2  μL of lysis reaction mix, thermocycled using cycling conditions I described in Supplementary Experimental Procedures in corresponding publication. Next, 4  μL of the RT Reaction Mix were added, and the mixture was thermocycled using cycling conditions II. Finally, 1  μL of the total RT reaction was added to 9 μL of PCR mix, and that mixture was thermocycled using cycling conditions III. Products were quantified, diluted to 0.125 ng/ μL, and libraries were prepared, cleaned, and tested as described in Supplementary Experimental Procedures in corresponding publication.

treatment_protocol: CD4+ T cells were purified from spleen and LNs using anti-CD4 microbeads (Miltenyi Biotech) and then stained in PBS with 1% FCS for 20 min at room temperature with anti-CD4-PerCP, anti-CD62L-APC and anti-CD44-PE antibodies (all Biolegend). Naive CD4+CD62lhighCD44low T cells were sorted using a BD FACSAria cell sorter, or provided by collaborator as sorted cells, shipped on ice overnight. Sorted cells were activated with plate-bound anti-CD3 (2 μg/ml) and anti-CD28 (2 μg/ml) in the presence of cytokines. For Th17 differentiation, the following reagents were used: 2 ng/ml recombinant human TGF-β1 (Miltenyi Biotec), 25 ng/ml recombinant mouse IL-6 (Miltenyi Biotec), 20 ng/ml recombinant mouse IL-23 (R&D Biosystems) and 20 ng/ml recombinant mouse IL-1β (Miltenyi Biotec).

tag: cell type

value: CD4 T cells


title: MATa deltaRE_right 5C Rep1

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB22-R1

value: MATa, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3,RE_right::KanMX4


title: EAE-LN-IL17A/GFP+ (population, rep2)

description: Gaublomme_et_al_2015_populations_invivo_EAE-IL17A-LN_2

growth_protocol: C57BL/6 WT and CD4-/-(2663) mice were obtained from Jackson Laboratory. IL-17A–GFP+ mice were obtained from Biocytogen. All animals, unless noted otherwise, were housed and maintained in a conventional pathogen-free facility at the Harvard Institute of Medicine in Boston. All experiments were performed in accordance to the guidelines outlined by the Harvard Medical Area Standing Committee on Animals at the Harvard Medical School.

extract_protocol:
At the peak of disease (EAE), T cells were collected from the draining LNs and the CNS. For isolation from the CNS, mice were perfused through the left ventricle of the heart with cold PBS. The brain and the spinal cord were flushed out with PBS by hydrostatic pressure. CNS tissue was minced with a sharp razor blade and digested for 20 min at 37°C with collagenase D (2.5 mg/ml; Roche Diagnostics) and DNaseI (1 mg/ml; Sigma). Mononuclear cells were isolated by passage of the tissue through a cell strainer (70 μm), followed by centrifugation through a Percoll gradient (37% and 70%). After removal of mononuclear cells, the lymphocytes were washed, stained and sorted for CD3 (Biolegend), CD4 (Biolegend), 7AAD and IL-17A-GFP+.
Population controls were generated by extracting total RNA using a RNeasy plus Micro RNA kit (Qiagen) according to manufacturer’s recommendations. Subsequently, 1 μL of RNA in water was added to 2  μL of lysis reaction mix, thermocycled using cycling conditions I described in Supplementary Experimental Procedures in corresponding publication. Next, 4  μL of the RT Reaction Mix were added, and the mixture was thermocycled using cycling conditions II. Finally, 1  μL of the total RT reaction was added to 9 μL of PCR mix, and that mixture was thermocycled using cycling conditions III. Products were quantified, diluted to 0.125 ng/ μL, and libraries were prepared, cleaned, and tested as described in Supplementary Experimental Procedures in corresponding publication.

treatment_protocol: For active induction of EAE, mice were immunized by subcutaneous injection of 100 μg MOG35-55  (MEVGWYRSPFSRVVHLYRNGK) in CFA, and then received 200 ng pertussis toxin intraperitoneally (List Biological Laboratory) on days 0 and 2. Mice were monitored and were assigned scores daily for development of classical and atypical signs of EAE according to the following criteria (Jager et al., 2009): 0, no disease; 1, decreased tail tone or mild balance defects; 2, hind limb weakness, partial paralysis or severe balance defects that cause spontaneous falling over; 3, complete hind limb paralysis or very severe balance defects that prevent walking; 4, front and hind limb paralysis or inability to move body weight into a different position; 5, moribund state.


title: PLZP-KO-TGFB1_IL6-48h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_PLZP-KO-T16-48-1
sample date (yymmdd): 140224


title: MATalpha deltaRE_right 5C Rep3

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB21-R3

source_name: MATalpha deltaRE_right 5C

value: MATalpha, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3,RE_right::KanMX6


title: MATalpha deltaRE_right 5C Rep2

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB21-R2

value: MATalpha, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3,RE_right::KanMX5


title: TOSO-WT-No_cytokines_added-96h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_TOSO-WT-Th0-96-1
sample date (yymmdd): 140219


title: MATalpha deltaRE_whole 5C Rep2

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB23-R2

source_name: MATalpha deltaRE_whole 5C

value: MATalpha, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3,RE_whole::KanMX5


title: MATalpha deltaRE_right 5C Rep1

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB21-R1

value: MATalpha, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3,RE_right::KanMX4


title: MATa HiC Rep1

description:
library strategy: Hi-C
yHiC-yJB2__sk1-rmv__genome__H-10000-iced.matrix.gz-n2r.txt
yHiC-yJB2-R2___yHiC-yJB2-R4.log2ratio.matrix.gz
yHiC-yJB2-R2___yHiC-yJB2-R4.subtract.matrix.gz
yHiC-yJB2-R2

source_name: MATa HiC

value: MATa, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3


title: PLZP-WT-IL1B_IL6_IL23-48h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_PLZP-WT-B623-48-1
sample date (yymmdd): 140224


title: PLZP-WT-TGFB1_IL6-48h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_PLZP-WT-T16-48-1
sample date (yymmdd): 140224


title: MATalpha deltaFkh1 5C Rep3

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB16-R3

source_name: MATalpha deltaFkh1 5C

value: MATalpha, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3, Fkh1delta::KanMX4


title: PLZP-WT-No_cytokines_added-48h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_PLZP-WT-Th0-48-1
sample date (yymmdd): 140224


title: MATalpha deltaFkh1 5C Rep1

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB16-R1


title: MATalpha deltaFkh1 5C Rep2

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB16-R2


title: GPR65-KO-IL1B_IL6_IL23-96h (population, rep2)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-KO-B623-96-1
sample date (yymmdd): 140219


title: EAE-IL17A-CNS_130124_CNS_IL17a_SC6_58

description:
Gaublomme_et_al_2015_single-cells_EAE-IL17A-CNS_130124_CNS_IL17a_SC6_58
IL17-GFP+ T cells collected from the CNS of EAE-induced mice. Cells were colected at the peak of disease (14 days post immunization)
sample date (yymmdd): 130124

data_processing:
base calling software
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using TopHat (Trapnell et al., 2009). The resulting alignments were processed by Scripture (Guttman et al., 2010) to evaluate the expression of transcripts from RefSeq (Pruitt et al., 2007).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files output by the scripture software (Guttman et al. 2010);  columns: (1--3) genomic location (4) gene name (5) RPKM

source_name: EAE-CNS-IL-17A/GFP+ (single cell batch 4)

extract_protocol:
At the peak of disease, T cells were collected from the draining LNs and the CNS. For isolation from the CNS, mice were perfused through the left ventricle of the heart with cold PBS. The brain and the spinal cord were flushed out with PBS by hydrostatic pressure. CNS tissue was minced with a sharp razor blade and digested for 20 min at 37°C with collagenase D (2.5 mg/ml; Roche Diagnostics) and DNaseI (1 mg/ml; Sigma). Mononuclear cells were isolated by passage of the tissue through a cell strainer (70 mm), followed by centrifugation through a Percoll gradient (37% and 70%). After removal of mononuclear cells, the lymphocytes were washed, stained and sorted for CD3 (Biolegend), CD4 (Biolegend), 7AAD and IL-17A-GFP+.
Cell lysis and SMART-Seq (Ramskold et al., 2012) whole transcriptome amplification (WTA) was performed on the C1 chip using the Fluidigm C1 Single-Cell Auto Prep System (C1 System) with the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech). WTA products were harvested from the C1 chip, and cDNA libraries were prepared using Nextera XT DNA Sample preparation reagents (Illumina) as per manufacturer’s recommendations, with minor modifications. Specifically, reactions were run at ¼ the recommended volume, the tagmentation step was extended to 10 minutes, and the extension time during the PCR step was increased from 30s to 60s. After the PCR step, all 96 samples were pooled without library normalization, cleaned twice with 0.9x AMPure XP SPRI beads (Beckman Coulter), and eluted in buffer TE. The pooled libraries were quantified using Quant-IT DNA High-Sensitivity Assay Kit (Invitrogen) and examined using a high sensitivity DNA chip (Agilent). Finally, samples were sequenced deeply using either a HiSeq 2000 or a HiSeq 2500 sequencer.


title: MATa deltaFkh1 5C Rep3

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB15-R4

source_name: MATa deltaFkh1 5C

value: MATa, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3, Fkh1delta::KanMX4


title: MATa deltaRE_right 5C Rep3

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB22-R3

value: MATa, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3,RE_right::KanMX6


title: MATalpha deltaRE_whole 5C Rep1

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB23-R1

value: MATalpha, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3,RE_whole::KanMX4


title: GPR65-KO-TGFB1_IL6-96h (population, rep2)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-KO-T16-96-1
sample date (yymmdd): 140219


title: GPR65-KO-No_cytokines_added-96h (population, rep2)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_GPR65-KO-Th0-96-1
sample date (yymmdd): 140219


title: input_cdk9i_s0_merged_set2

city: Daegu

first: Heeyoun

last: Bunch

address: 80 Daehak-ro, Kyungpook National University, Agriculture and Life Sciences Building #1, Room 207

department: Applied Biosciences

country: South Korea

institute: Kyungpook National University

data_processing:
Demultiplex/Base calls with CASAVA(?)
Alignment against GRCh37.75 genome using BWA mem
Duplicates removed with PicardTools and filtered to retain only primary alignments
Peaks called with HOMER (v4.7) with default parameters of 4 fold-change and Poisson p-value of 1e-4.  Matched input sample used for background distribution
Genome_build: Ensembl GRCh37.75
Supplementary_files_format_and_content: Homer-format peak files, with locus, fold change, and additional fields in tab-delimited format.

organism: Homo sapiens

extract_protocol:
none provided by submitter
none provided by submitter

tag: ip target

value: input

tag: treatment (those ending with 'i' indicate inhibitor)

tag: time

tag: matched input


title: PLZP-KO-No_cytokines_added-48h (population, rep1)

description:
Gaublomme_et_al_2015_populations_invitro_knockouts_PLZP-KO-Th0-48-1
sample date (yymmdd): 140224


title: input_cdk9i_s15_merged_set2


title: MATa deltaFkh1 5C Rep2

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB15-R3


title: input_dmso_s0_merged_set2

source_name: dmso

value: dmso


title: input_dnapki_s0_merged_set2

source_name: dnapki

value: dnapki


title: MATa deltaFkh1 5C Rep1

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB15-R1


title: MATa deltaRE_left 5C Rep3

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB5-R4

source_name: MATa deltaRE_left 5C

value: MATa, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3, REdelta::KanMX4


title: MATalpha deltaRE_left 5C Rep2

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB4-R3

source_name: MATalpha deltaRE_left 5C

value: MATalpha, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3, REdelta::KanMX4


title: MATalpha deltaRE_left 5C Rep3

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB4-R4

value: -ura


title: input_dmso_s15_merged_set2


title: MATa deltaRE_left 5C Rep2

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB5-R3


title: MATa deltaRE_left 5C Rep1

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB5-R1


title: input_topIIi_s0_merged_set2

source_name: topIIi

value: topIIi


title: input_topIIi_s15_merged_set2


title: diploid 5C Rep2

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB3-R3

source_name: diploid 5C

value: nuc1D::LEU2, pGAL::HO::URA3


title: input_dnapki_s15_merged_set2


title: s2polII_dnapki_s15_merged_set2


title: MATa 5C Rep3

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB2-R4

source_name: MATa 5C


title: s2polII_dmso_s15_merged_set2


title: s2polII_dnapki_s0_merged_set2


title: MATa 5C Rep2

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB2-R2


title: s2polII_dmso_s0_merged_set2


title: s2polII_cdk9i_s15_merged_set2


title: diploid 5C Rep1

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB3-R1


title: s2polII_cdk9i_s0_merged_set2


title: MATalpha 5C Rep3

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB1-R4

source_name: MATalpha 5C

value: MATalpha, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3


title: MATa 5C Rep1

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB2-R1


title: polII_dnapki_s15_merged_set2

value: polII


title: MATalpha 5C Rep1

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB1-R1


title: MATalpha 5C Rep2

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB1-R2


title: polII_dnapki_s0_merged_set2


title: input_dmso_s15_merged_set1


title: input_gh2ax_dmso_s15_merged_set1


title: input_ICRF_s15_merged_set1

source_name: ICRF

value: ICRF


title: polII_dmso_s0_merged_set2


title: diploid 5C Rep3

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB3-R4


title: input_ICRF_s0_merged_set1


title: polII_dmso_s15_merged_set2


title: h2ax_topIIi_s0_merged_set2


title: h2ax_topIIi_s15_merged_set2


title: input_gh2ax_dmso_s0_merged_set1


title: input_dmso_s0_merged_set1


title: h2ax_dnapki_s15_merged_set2


title: trim28_dmso_s15_merged_set1


title: ATF4 SC_WT

city: Beijing

first: dan

last: liu

address: NO.1 Beichen West Road, Chaoyang District, Beijing

country: China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

data_processing:
RNA sequencing reads were aligned to the mouse reference genome mm9 from UCSC using TopHat with a tolerance of 2 mismatches.Only unique mapped reads were used for further analysis.
A Python package HTSeq(version 0.5.3p9) can get each gene reads count number.R package named DEseq(v1.16.0) test for differential expression genes,which is based on the negative binomial distribution models.
Genome_build: mm9
Supplementary_files_format_and_content: Processed_data_file is in txt format.With the following columns:gene ,KO(counts),WT(counts)

source_name: Embryo cell

growth_protocol: primary fetal liver cells sorted by FASC

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment by Doxcycline or any other solutions

tag: tissue

value: fetal liver

tag: developmental stage

tag: doxcycline treatment

value: No

value: wild type

value: LSK


title: trim28_dmso_s0_merged_set1


title: topoIIB_dmso_s0_merged_set1

value: topoIIB


title: h2ax_dmso_s0_merged_set2


title: 4-3907_KO

city: Philadelphia

first: Mark

middle: Jakob

last: Ferreira

state: PA

address: 3400 Civic Center Blvd Bldg 421

department: Genetics

institute: University of Pennsylvania School of Medicine

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation .
Differential expression analysis was carried out using a custom script implementing EdgeR software.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file of raw read counts and tab-delimited file of RPKM normalized read counts

source_name: Primary mouse pancreatic ductal cells

extract_protocol:
RNA was collected and isolated from treated primary ductal cells using the Qiagen RNeasy Mini Kit. Illumina TruSeq RNA Sample Prep v2 Kit was used with 77-210ng total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Primary mouse pancreatic ductal cells


title: h2ax_cdk9i_s15_merged_set2


title: polII_dmso_s15_merged_set1


title: h2ax_dmso_s15_merged_set2


title: h2ax_cdk9i_s0_merged_set2


title: 1-3898_Ctrl

value: HhexL/L


title: 3-3903_KO


title: polII_dmso_s0_merged_set1

value: dmso


title: 2-3900_Ctrl


title: polII_ICRF_s15_merged_set1


title: polII_ICRF_s0_merged_set1


title: CordBlood_CD4+_Act+IL4_72h_rep1

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

country: Finland

institute: Turku Centre for Biotechnology

description: CD4+ cell culture from cord blood of human neonates

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were mapped to hg19 reference transcriptome using tophat 1.4.1using default parameters.
Feature count table was obtained using htseq-count and normalized using DESeq package in R.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file includes normalized values of all samples

source_name: human cord blood CD4+ cells, Act+IL4

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen) according to manufacturers instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cord blood

value: CD4+ T cells


title: CordBlood_CD4+_Act+IL4_72h_rep3


title: gh2ax_dmso_s15_merged_set1


title: gh2ax_dmso_s0_merged_set1


title: CordBlood_CD4+_Act+IL4_72h_rep2


title: h2ax_dnapki_s0_merged_set2

value: dnapki


title: CordBlood_CD4+_Act+IL12_72h_rep2

source_name: human cord blood CD4+ cells, Act+IL12


title: ATF4 SC_KO

value: ATF4 KO


title: CordBlood_CD4+_Act_72h_rep2

source_name: human cord blood CD4+ cells, Act


title: topoIIB_dmso_s15_merged_set1


title: dnapk_dmso_s0_merged_set1

value: dnapk


title: CordBlood_CD4+_Act_72h_rep3


title: CordBlood_CD4+_Act_72h_rep1


title: CordBlood_CD4+_naive_precursor_rep2

source_name: human cord blood CD4+ cells, naive


title: CordBlood_CD4+_Act+IL12_72h_rep3


title: CordBlood_CD4+_naive_precursor_rep3


title: CordBlood_CD4+_naive_precursor_rep1


title: dnapk_dmso_s15_merged_set1


title: CordBlood_CD4+_Act+IL12_72h_rep1


title: SUS2_2

status: Public on Nov 19 2015

city: Daejeon

first: Namil

last: Lee

address: Daehakro

department: Biological science

institute: KAIST

data_processing:
CLC genomics work bench 6.5.1 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CHO-K1 draft genome Nat. Biotechnol. 2013 Aug;31(8):759-65 with parameters mismatch costs=2, length fraction=0.5, and similarity fraction=0.8
DESeq normalized value were calculated DESeq algorithm in program R. Genome Biology 2010, 11:R106
Genome_build: C_griseus_v1.0; GenBank :AMDS00000000
Supplementary_files_format_and_content: tab-delimited text files include DESeq values for each Sample

organism: Cricetulus griseus

source_name: ovary

growth_protocol: CHO cell was adaptated in SFM4CHO media

extract_protocol:
RNA was harvested using Trizol reagent.rRNA was specifically removed using Ribo-Zero kit (Epicentre, Madison, WI). TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., San Diego, CA) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., San Diego, CA) according to manufacturer's instructions

tag: cell line

tag: passage


title: SUS2_1


title: SUS1_2


title: SUS4_1


title: SUS3_1


title: SUS0_2


title: SUS3_2


title: SUS1_1


title: SUS4_2


title: SARS_Vero_Gleevec_24hrs

city: Baltimore

first: David

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

data_processing:
NOT PROVIDED
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: NOT PROVIDED

organism: Chlorocebus sabaeus

source_name: Vero E6 cells

growth_protocol: Vero E6 cells were grown in MEM with 10% Fetal Bovine Serum

extract_protocol:
RNA was extracted using Trizol from cells infected in culture.
Poly-A RNA was isolated and indexed libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RNA was isolated at 24 and 48 hours post infection at an MOI of 0.1 and 3 with each virus.

value: Vero E6


title: SARS_Vero_Gleevec_48hrs


title: SARS_VEROlowMOI_48hr_2


title: SUS0_1


title: SARS_Vero_IFNbeta_24hrs


title: SARS_VEROlowMOI_48hr_1


title: SARS_VEROHighMOI_24hr_3


title: SARS_VEROHighMOI_24hr_1


title: SARS_VEROlowMOI_24hr_3


title: Vero-3_20ulEMC_24hrs_RNA1


title: Vero-3_2ulEMC_24hrs_RNA3


title: SARS_VEROHighMOI_24hr_2


title: Vero-3_2ulEMC_24hrs_RNA1


title: Vero-3_2ulEMC_24hrs_RNA2


title: PBS_VERO_24hr_2


title: PBS_VERO_24hr_3


title: PBS_VERO_24hr_1


title: MATalpha deltaRE_left 5C Rep1

description:
library strategy: 5C
supplemental_table_3_5Cprobes_mapped_and_filtered_to_SK1.xlsx
supplemental_table_4_5Cprobes_mapped_and_filtered_to_w303.xlsx
supplemental_table_S1_all5Cprobes.xlsx
supplemental_readme.txt
significant_differences_1repVs1rep.tar.gz
significant_differences_3repVs3rep.tar.gz
y3512LR_SK1v3-yJB4-R2

value: MATalpha, ho::LYS2, lys2, ura3, nuc1D::LEU2, pGAL::HO::URA3, REdelta::KanMX4

value: -ura


title: SARS_Vero_IFNbeta_48hrs


title: Timecourse 3 5 minute labeling

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description:
3' adapter sequence: 5'AGATCGGAAGAGCACACGTCTG-3'
5' barcode sequence: NNNNNNTGACCAN

data_processing:
Raw fastq files were demultiplexed using pyBarcodeFilter version 2.3.3 from the pyCRAC tool suite (Webb et al Genome Biology 2014; version 1.2.2.3).
Quality trimming and removal of 3' Adapter sequences (5'AGATCGGAAGAGCACACG-3' ) was removed using Flexbar (version 2.4)
Reads were aligned to the Saccharomyces_cerevisiae.R64-1-1.75  reference genome using STAR (version 2.4.2a) at default settings. Read counts (FPKMs) were calculated using pysam
The splicing ratio, i.e., the mRNA proportion is then calculated from the aligned reads either by direct methods or using a probabilistic method (details provided in supplementary data of the manuscript); code for the probabilistic method is available at http://isplice.sourceforge.net.
Genome_build: Saccharomyces_cerevisiae.R64-1-1.75 (ENSEMBL)
Supplementary_files_format_and_content: Processed data files are Excel spreadsheets containing the data used for generating the figures in the manuscript.

source_name: Nascent RNA isolated using an ultrashort 4-thio-Uracil

growth_protocol: Cultures were grown in SD -Ura–Leu to OD600 of 0.8. Cultures remained at 30ºC and were shaken throughout the experiment. Large (600 ml) cultures were used for es4tU-seq experiments.

extract_protocol:
RNA was isolated using a standard hot-phenol extraction. Biotinylation was performed on 2 mg of RNA. The incubation at 65°C was for only 15 minutes to reduce RNA degradation. The RNA was purified using 2ml Zeba columns (Thermo), as per manufacturer's instructions, and ethanol precipitated. Biotinylated RNA was extracted using streptavidin C1 Dynabeads (Life Technologies).  Fifty µl of beads were equilibrated in NaPTMg (i.e. 0.2M NaCl, 0.1M Sodium phosphate pH 6.8, 25mM MgCl2 and 0.4% Tween) then blocked in NaPTMg and 1µg/µl glycogen for 20minutes.  The biotinylated RNA was purified for 30 minutes with the dynabeads at 4°C in NaPTMg.  The beads were washed 3 times in NaPTMg and twice with TEN1000 (i.e. 10mM Tris Cl pH 7.5, 1mM EDTA pH8 and 1M NaCl). All bead block, incubation and wash volumes were 400µl.  The RNA was eluted twice with 50µl of 0.7M beta-mercaptoethanol for 5 minutes at room temperature before being ethanol precipitated with 20µg glycogen -20°C for at least 2hours and re-suspended in 10µl DEPC treated H2O.
RNA-seq libraries were produced essentially as described previously (Hector et al Nucleic Acids Research 2014). Briefly, between 100-250ng of (thiolated) RNA was fragmented in Superscript reverse transcription buffer for five minutes at 95ºC.  Fragmented RNA was subsequently randomly primed as described (Hector et al Nucleic Acids Research 2014). The cDNAs were ligated to 5' adapters (see barcodes below) using CircLigase 2 for six hours at 65ºC according to manufacturer's procedures. Libraries were amplified using PCR primers listed below. The cDNA products were amplified (16-20 cycles) using Pfu Polymerase (Promega) using standard cycling conditions (Tm = 55ºC)
P5_forward_PCR_oligonucleotide: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’
P3_reverse_PCR_oligonucleotide: 5’-CAAGCAGAAGACGGCATACGAGAT(6nt barcode)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’

treatment_protocol: Cells were treated with 500 µM 4tU for the appropriate time. Cells were snap frozen in methanol at -70ºC to rapidly halt transcription

tag: assayed molecule

value: thiolated RNA


title: Timecourse 3 rRNA depleted total RNA

description:
3' adapter sequence: 5'AGATCGGAAGAGCACACGTCTG-3'
5' barcode sequence: NNNNNNACAGTGN

source_name: Ribosomal RNA depleted total RNA

value: rRNA depleted total RNA


title: Timecourse 3 1.5 minute labeling

description:
3' adapter sequence: 5'AGATCGGAAGAGCACACGTCTG-3'
5' barcode sequence: NNNNNNCGATGTN


title: Timecourse 3 2.5 minute labeling

description:
3' adapter sequence: 5'AGATCGGAAGAGCACACGTCTG-3'
5' barcode sequence: NNNNNNTTAGGCN


title: Timecourse 1 2.5 minute labeling


title: Timecourse 2 rRNA depleted total RNA

description:
3' adapter sequence: 5'AGATCGGAAGAGCACACGTCTG-3'
5' barcode sequence: NNNNNNGCCAATN


title: Timecourse 1 rRNA depleted total RNA


title: Timecourse 1 5 minute labeling


title: Timecourse 2 5 minute labeling


title: Timecourse 2 2.5 minute labeling


title: Timecourse 1 1.5 minute labeling

description:
3' adapter sequence: 5'AGATCGGAAGAGCACACGTCTG-3'
5' barcode sequence: NNNNNNATCACGN


title: 3T3-L1_si-Mcaf1_SETDB1

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

country: Japan

institute: Akita University Graduate School of Medicine

data_processing:
All bound DNA fragments were mapped UCSC build mm9 assembly of the mouse genome by the mapping program ELAND.
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format.
Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files

source_name: 3T3-L1 preadipocytes

growth_protocol: TT2 embryonic stem cells (ESCs) were maintained in Dulbecco’s modified Eagle’s medium containing 10% Knockout serum replacement (Invitrogen), 1% fetal bovine serum, leukemia-inhibiting factor, penicillin/streptomycin, L-glutamine, non-essential amino acids and β-mercaptoethanol at 37 °C. 10T1/2 mesenchymal stem cells (MSCs) and 3T3-L1 preadipocytes were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37 °C.

extract_protocol:
Sonicated nuclear fraction was incubated with each antibody and histone-DNA or SETDB1-DNA complexes were isolated. Sonicated DNA was incubated with MBD domain of MBD1 and m5CpG was isolated.
Libraries were prepared according to Illumina's instructions.

value: 3T3-L1 preadipocytes

tag: ChIP

tag: day

value: Day 0

tag: sirna/shrna

value: siRNA targeting Mcaf1


title: 3T3-L1_D0_Input

value: Input


title: 3T3-L1_si-Ctr_SETDB1

value: Negative control siRNA


title: 3T3-L1_Ctr_SETDB1


title: 3T3-L1_sh-Setdb1_SETDB1

value: shRNA targeting Setdb1


title: 3T3-L1_si-Mbd1_SETDB1

value: siRNA targeting Mbd1


title: 3T3-L1_si-Setdb1_Pol2

value: PolII

value: siRNA targeting Setdb1


title: 3T3-L1_si-Setdb1_H3K9me3


title: 3T3-L1_si-Ctr_H3K9me3


title: 3T3-L1_si-Ctr_Pol2


title: 3T3-L1_D6_SETDB1

source_name: 3T3-L1 adipocytes

value: 3T3-L1 adipocytes

value: Day 6


title: 3T3-L1_si-Ctr_H3K4me3


title: 3T3-L1_D6_Pol2


title: 3T3-L1_D6_m5CpG


title: 3T3-L1_D6_H3K9me3


title: Timecourse 2 1.5 minute labeling

tag: strain

tag: genotype


title: 3T3-L1_D8_H3K4me3

value: Day 8


title: 3T3-L1_D0_Pol2


title: 3T3-L1_D0_MBD1_repB


title: 3T3-L1_D0_MBD1_repA


title: 3T3-L1_D0_H3K9me3_repB


title: 3T3-L1_D0_m5CpG


title: 3T3-L1_D0_SETDB1_repA


title: 3T3-L1_si-Setdb1_H3K4me3


title: TT2_m5CpG

source_name: TT2 ESCs

value: TT2 embryonic stem cells


title: 10Thalf_H3K4me3

source_name: 10T1/2 MSCs

value: 10T1/2 mesenchymal stem cells


title: 10Thalf_SETDB1


title: 10Thalf_Input


title: 3T3-L1_D0_H3K27me3


title: 3T3-L1_D0_H3K9me3_repA


title: TT2_SETDB1


title: 10Thalf_H3K9me3


title: 3T3-L1_D0_H3K4me3


title: 10Thalf_H3K27me3


title: 10Thalf_m5CpG


title: TT2_H3K9me3


title: TT2_H3K27me3


title: SD_1

city: St. Louis

first: Joseph

middle: C

last: Corbo

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

data_processing:
Basecalls were made with Casava 1.8.
Raw reads were demultiplexed and aligned to Mus musculus Ensembl release 72 with Tophat v2.0.9 and Bowtie2 v2.1.0.
HTseq was used to estimate gene abundance.
Differential expression analysis was conducted with EdgeR.
Genome_build: Mus musculus Ensembl release 72

molecule: polyA RNA

source_name: Eye

extract_protocol:
Eyes were harvested and rapidly dissected in the dark. The anterior portion of the eye including the lens was removed, and the remaining tissue (posterior sclera, choroid, RPE, and retina) was rinsed in cold sterile HBSS with calcium and magnesium (Gibco) and stored in TRIzol (Invitrogen) at -80 C. For extraction, the tissue was homogenized with a pestle and then passage through a needle. Total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen) with on-column DNaseI digestion (Qiagen).
Polyadenylated mRNA was obtained from total RNA using Dynabeads (Invitrogen), fragmented, and reverse-transcribed to cDNA using random hexamers. The cDNA was blunt-ended, 3’-adenylated, and ligated to sequencing adapters. Ligated fragments were amplified for 12 cycles with primers to incorporate sample indices. All four samples were run on a single lane of HiSeq 2500 (1x50 bp).

tag: condition

value: Subjective day

value: eye


title: OD_2

value: Objective day


title: TM2

first: Maija

last: Hollmén

address: Tykistökatu 6A 4th floor

institute: University of Turku

description: processed data file: T-VS-TM2.GeneDiffExp.txt

data_processing:
RNA from both monocytes/macrophages (n = 3) and cancer cells (n = 3) in single and co-culture was sent to BGI China and sequenced according to BGI standard protocols using Illumina HiSeqTM 2000. Monocyte donor 2 samples collected in single culture (2.52 μg) or with T47D cells (2.42 μg) did not reach a desired amount > 3 μg of RNA and were left out of the analysis.
High-quality reads were aligned to the human reference genome with SOAPaligner/SOAP244. The matched reads were then aligned to Human Refseq mRNA (NCBI).
The expression levels for each gene were normalized to reads per kilobase per million mapped reads (RPKM) to facilitate the comparison of transcripts among samples.
A mean log2Ratio (RPKM of macrophages (MΦ) co-cultured with MDA-MB-231 or T47D cells vs. MΦ single culture; RPKM of MDA-MB-231 or T47D cells co-cultured with MΦ/MDA-MB-231 or T47D cell line cultured alone of each gene was calculated. To identify genes differentially expressed between groups, an algorithm was used45 with a correction for false positive (type I) and false negative (type II) errors using the FDR method46. The genes were regarded as differentially expressed when their FDRs were less than 0.05. Further, genes were classified as up-regulated when their mean log2Ratio was larger than 0.5 or down-regulated when their log2 ratio was less than −0.5.
Supplementary_files_format_and_content: text files with gene expression difference single vs. co-culture are available in a tar archive on the series record.

growth_protocol: The monocytes and cancer cells (T47D or MDA-MB-231) wete co-cultured for five days in a transwell system (PET membrane pore size 0.4 micro meters)

extract_protocol:
Total RNA isolation using the Trizol protocol
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) were used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments. Then cDNA was synthesized using the mRNA fragments as templates. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. The short fragments were connected with adapters. After agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used in quantification and qualification of the sample library. At last, the library was sequenced using Illumina HiSeqTM 2000

tag: cell type

value: Breast cancer

tag: culture condition

value: co-culture

tag: immunopathological classification

value: ER pos


title: TM3

description: processed data file: T-VS-TM3.GeneDiffExp.txt


title: 3T3-L1_D0_SETDB1_repB

value: 3T3-L1 preadipocytes

value: Day 0


title: MM3

description: processed data file: M-VS-MM3.GeneDiffExp.txt

value: TNBC


title: MM1

description: processed data file: M-VS-MM1.GeneDiffExp.txt


title: MM2

description: processed data file: M-VS-MM2.GeneDiffExp.txt


title: M3T

description: processed data file: M3C-VS-M3T.GeneDiffExp.txt, M1C-VS-M3T.GeneDiffExp.txt

source_name: Monocyte donor 3

value: Monocyte


title: T

description: processed data file: T-VS-TM1.GeneDiffExp.txt, T-VS-TM2.GeneDiffExp.txt, T-VS-TM3.GeneDiffExp.txt

value: single


title: TT2_Input

value: Input


title: M2M

description: processed data file: M1C-VS-M2M.GeneDiffExp.txt, M3C-VS-M2M.GeneDiffExp.txt

source_name: Monocyte donor 2


title: OD_1


title: TT2_H3K4me3


title: M

description: processed data file: M-VS-MM1.GeneDiffExp.txt, M-VS-MM2.GeneDiffExp.txt, M-VS-MM3.GeneDiffExp.txt


title: SD_2


title: M1M

description: processed data file: M1C-VS-M1M.GeneDiffExp.txt, M3C-VS-M1M.GeneDiffExp.txt

source_name: Monocyte donor 1


title: h1975_r1

city: San Francisco

first: Saurabh

last: Asthana

address: 1450 Third Street, Room HD276

department: Helen Diller Family Comprehensive Cancer Center

institute: UCSF

description: RNAseq replicate from H1975 (parental) cells

data_processing: Reads were aligned against NCBI build 37 (hg19) of the human genome using the NCBI Ensembl transcript annotation (version 75) with RSEM, which also yielded gene-level expression quantification. Supplementary files are standard output from RSEM, please consult RSEM documentation for details.

source_name: H1975 cells

extract_protocol: RNA from each of the indicated cell lines was extracted by RNeasy kit (Qiagen). In total, 2 μg of total RNA was used for deep sequencing library preparation using Illumina Truseq sample prep kits (Illumina) according to the manufacturer’s protocols. Sequencing libraries with different indices were pooled and sequenced in paired end format to a length of 100bp using the HiSeq2000 platform at Center for Advanced Technology at UCSF.

tag: tumor type

value: Lung adenocarcinoma

value: H1975 (parental)


title: m2_r0

description: RNAseq replicate from erlotinib-resistant H1975 cells (strain M2)

value: H1975 erlotinib-resistant H1975 cells (strain M2)


title: h1975

description: Exome capture from parental H1975 cells

data_processing: Reads were aligned against NCBI build 37 (hg19) of the human genome using BWA. Copy number segmentation was performed with CNVKit. Supplementary files are segmentation output from CNVKit, please consult CNVKit documentation for details.

extract_protocol: Whole exome library was captured using SeqCap EZ Human Exome Library v5.0 from Roche NimbleGen.


title: M1C

description: processed data file: M1C-VS-M1M.GeneDiffExp.txt, M1C-VS-M1T.GeneDiffExp.txt, M1C-VS-M2M.GeneDiffExp.txt, M1C-VS-M3M.GeneDiffExp.txt, M1C-VS-M3T.GeneDiffExp.txt


title: M3C

description: processed data file: M3C-VS-M1M.GeneDiffExp.txt, M3C-VS-M1T.GeneDiffExp.txt, M3C-VS-M2M.GeneDiffExp.txt, M3C-VS-M3T.GeneDiffExp.txt, M3C-VS-M3T.GeneDiffExp.txt


title: m1_r1

description: RNAseq replicate from erlotinib-resistant H1975 cells (strain M1)

value: H1975 erlotinib-resistant H1975 cells (strain M1)


title: m1_r0


title: m2

description: Exome capture from erlotinib-resistant H1975 cells (strain M2)


title: m1

description: Exome capture from erlotinib-resistant H1975 cells (strain M1)


title: TM1

description: processed data file: T-VS-TM1.GeneDiffExp.txt


title: RNA-seq Asp5 knock-out infected 1

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for base-calling
Reads were aligned to the human genome by Rsubread version 1.16.1
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: hg19 (NCBI build 37)
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Human foreskin fibroblast

growth_protocol: Primary human foreskin fibroblasts were grown to confluency in DME supplemented with 10% v/v fetal calf serum

extract_protocol:
Total parasite and host RNA was extracted using the QIAGEN RNeasy kit following the manufacturer's protocol
DNA libraries were prepared using the Illumina TruSeq v2 protocol and sequenced on an Illumina HiSeq 2000 at the Australian Genome Research Facility (AGRF) Melbourne, following the manufacturer's protocol

treatment_protocol: Parasites were added at an MOI = 5 and at 18 hours were washed with PBS to remove extracellular parasites then dislodged with trypsin

tag: infection

value: Infected with Toxoplasma gondii

tag: strain, toxoplasma gondii

tag: genotype/variation


title: h1975_r0


title: RNA-seq Asp5 knock-out infected 2


title: RNA-seq wild type infected 2


title: RNA-seq wild type infected 3


title: M3M

description: processed data file: M1C-VS-M3M.GeneDiffExp.txt, M3C-VS-M3M.GeneDiffExp.txt


title: M1T

description: processed data file: M1C-VS-M1T.GeneDiffExp.txt, M3C-VS-M1T.GeneDiffExp.txt


title: RNA-seq uninfected 3

value: Uninfected


title: RNA-seq wild type infected 1


title: m2_r1


title: RNA-seq uninfected 1


title: RNA-seq uninfected 2


title: Xrn2 ChIP-seq HA-Xrn2 WT

city: Aurora

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

description: Chromatin IP against Xrn2

data_processing:
Single-end 50 base reads (after removing barcodes) were mapped to the hg19 UCSC human genome  with Bowtie version 0.12.5
Genome_build: GRCh37/hg19 assembly

source_name: HEK293 Flp-in T-REx pcDNA5 HA-Xrn2 WT

growth_protocol: HEK293 Flp-in cell lines were grown in DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin, and pen/strep

extract_protocol:
cross-linked Chromatin was sonicated with a Bioruptor
IPs from 1-2 mg of cross-linked extract were immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: Amr Rpb1 was induced with doxycycline (2.0 mg/ml)  for 12-16 hr then treated with a-amanitin (2.5 mg/ml) for a further 42 hr before cross-linking and harvesting for ChIP-seq. HA tagged WT and mutant (D235A) Xrn2 were induced with doxycycline (2.0 mg/ml) for 24 hrs.

tag: growth conditions

value: DMEM 10% FCS,+ hygromycin + blasticidin + doxycycline

tag: antibody

value: rabbit anti-Xrn2 (aa402-537, affinity pure Brannan et al Mol Cell 46, 311-324, 2012 )


title: RNA pol II ChIP-seq HA-Xrn2 WT shXrn2 Rep2

description: Chromatin IP against RNA pol II

source_name: HEK293 Flp-in T-REx pcDNA5 HA-Xrn2 WT shXrn2

tag: cell line

value: DMEM 10% FCS,+ hygromycin + blasticidin + doxycycline + puromycin

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: RNA pol II ChIP-seq HA-Xrn2 D235AshXrn2 Rep1

description: Chromatin IP against RNA pol II

source_name: HEK293 Flp-in T-REx pcDNA5 HA-Xrn2 D235AshXrn2


title: RNA pol II ChIP-seq HA-Xrn2 D235A

description: Chromatin IP against RNA pol II

source_name: HEK293 Flp-in T-REx pcDNA5 HA-Xrn2 D235A


title: RNA pol II ChIP-seq HA-Xrn2 D235AshXrn2 Rep2

description: Chromatin IP against RNA pol II


title: RNA pol II ChIP-seq HA-Xrn2 WT

description: Chromatin IP against RNA pol II


title: RNA pol II ChIP-seq Rpb1 WT Rep2

description: Chromatin IP against RNA pol II

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT

value: DMEM 10% FCS,+ hygromycin + blasticidin + doxycycline + a-amanitin


title: RNA-seq Asp5 knock-out infected 3


title: RNA pol II ChIP-seq Rpb1 E1126G Rep 2

description: Chromatin IP against RNA pol II

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr E1126G


title: RNA pol II ChIP-seq 21NT

description: Chromatin IP against RNA pol II

source_name: 21NT breast epithelial cells

value: DMEM 10% FCS,


title: RNA pol II ChIP-seq HAP1

description: Chromatin IP against RNA pol II

source_name: Hap1 lymphoma cells

value: IMDM 10% FBS


title: Long RNA-seq: RBC_3

city: Durham

first: Jen-Tsan

middle: Ashley

last: Chi

state: North Carolina

address: 101 Science Drive

department: MGM

institute: Duke University

description: Red blood cell #3

data_processing:
RNA-seq data was processed using the TrimGalore toolkit to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only pairs where both reads were 20nt or longer were kept for further analysis.
Reads were mapped to the GRCh37r73 version of the human genome and transcriptome using the STAR RNA-seq alignment tool.  Reads were kept for subsequent analysis if they mapped to a single genomic location. RNA-Seq quality control was generated with the RSeQC toolkit.
Gene expression in reads per million per kilobase (RPKM) value were calculated using the cufflinks algorithm.
Genes that had an RPKM value >= 0.5 in at least one sample were kept for subsequent analysis.
Genome_build: GRCh37r73
Supplementary_files_format_and_content: table with normalized expression across samples

source_name: Purified human mature erythrocytes

extract_protocol:
Blood samples were obtained from healthy adults via venipuncture into vacutainer tubes. Blood was washed three times with PBS, centrifuged, and plasma and buffy coat removed. Leukocytes were then depleted from the sample using a Purecell® Leukocyte Reduction Filtration System. Reticulocytes (immature red blood cells) were removed in the CD71 positive fraction using CD71 microbeads with the autoMACS® Separator (Miltenyi Biotec). The erythrocyte purification protocol reflects methods previously described (Sangokoya et. al, Methods in Molecular Biology, 2010). RNA was extracted using the miRVana miRNA Isolation kit (Life Technologies).
Total RNA-seq libraries were prepared with 1ug purified total RNA input using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo‐Zero Globin (Illumina). Samples were muliplexed, libraries pooled, and run on two flowcells with the Illumina HiSeq 2000 sequencing system. Barcode IDs are as follows: RBC_1-CGATGT, RBC_2-TGACCA, RBC_3-ACAGTG, PBMC_1-GCCAAT, PBMC_2-CAGATC, PBMC_3-CTTGTA, D8_1-AGTCAA, D8_3-GTCCGC.

value: Erythrocyte


title: Long RNA-seq: D8_1

description: Day 8 Erythroid Progenitor #1

source_name: Cultured differentiating erythroid progenitors (Day 8)

extract_protocol:
Mobilized Peripheral Blood CD34+ Cells (AllCells) were grown in StemLine II media containing Glutamine (Sigma) with 20% BIT (StemCell Technologies) and 1% Penicillin/Streptomycin (Gibco). Cells were supplemented with growth factors IL-3 at 20ng/mL (Invitrogen), SCF at 50ng/mL (Invitrogen), and Erythropoietin (Epo) at 3U/mL (Calbiochem). Cells were isolated on Day 8 of in vitro erythroid differentiation. The cells were rinsed twice in cold PBS, then RNA was extracted using the miRVana miRNA Isolation kit (Life Technologies).
Total RNA-seq libraries were prepared with 1ug purified total RNA input using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo‐Zero Globin (Illumina). Samples were muliplexed, libraries pooled, and run on two flowcells with the Illumina HiSeq 2000 sequencing system. Barcode IDs are as follows: RBC_1-CGATGT, RBC_2-TGACCA, RBC_3-ACAGTG, PBMC_1-GCCAAT, PBMC_2-CAGATC, PBMC_3-CTTGTA, D8_1-AGTCAA, D8_3-GTCCGC.

value: Cultured erythroid progenitors


title: Long RNA-seq: PBMC_1

description: Peripheral Blood Mononuclear Cell #1

source_name: Purified human PBMCs

extract_protocol:
Blood samples were obtained from healthy adults via venipuncture into vacutainer tubes. A buffy coat was separated from whole blood using a Ficoll-Paque (GE Healthcare) centrifugation gradient, and remaining erythrocytes were lysed using a red cell lysis buffer (Qiagen). RNA was extracted using the miRVana miRNA Isolation kit (Life Technologies).
Total RNA-seq libraries were prepared with 1ug purified total RNA input using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo‐Zero Globin (Illumina). Samples were muliplexed, libraries pooled, and run on two flowcells with the Illumina HiSeq 2000 sequencing system. Barcode IDs are as follows: RBC_1-CGATGT, RBC_2-TGACCA, RBC_3-ACAGTG, PBMC_1-GCCAAT, PBMC_2-CAGATC, PBMC_3-CTTGTA, D8_1-AGTCAA, D8_3-GTCCGC.

value: Peripheral Blood Mononuclear Cell (PBMC)


title: Long RNA-seq: RBC_1

description: Red blood cell #1


title: Long RNA-seq: PBMC_2

description: Peripheral Blood Mononuclear Cell #2


title: Long RNA-seq: PBMC_3

description: Peripheral Blood Mononuclear Cell #3


title: 1488_input_neuroblastoma tumor

city: Ghent

first: Anneleen

last: Decock

address: De Pintelaan 185

country: Belgium

institute: Ghent University

data_processing:
Quality control by FastQC (version 0.9.2)
Paired-end read mapping to the human reference genome using Bowtie2 (version 2.0.0 beta7) and SAMtools (version 0.1.18)
Marking PCR duplicates by Picard (version 1.79)
Mapping quality control by SAMStat (version 1.08) and bamUtil (version 1.0.2)
Peak calling using MACS (version 1.4.0 beta)
Genome_build: hg19
Supplementary_files_format_and_content: .bam: .bam format was used as output file type for read mapping (Bowtie2; duplicates are removed); .bed: location and score of the identified peaks (MACS); .wig.gz: visualization (MACS); .tdf: visualization of the methyl-seq data in IGV.

source_name: primary tumor

extract_protocol:
DNA fragmentation by shearing, followed by MBD capture (MethylCap kit of Diagenode)
PrepX ILM DNA Library Kit (IntegenX) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)

tag: age of the patient at diagnosis (months)

tag: inss stage

tag: mycn amplification status

value: non-amplified

tag: overall survival time (days)

tag: overall survival status

value: alive

tag: event-free survival time (days)

tag: event-free survival status

value: no event


title: 1509_input_neuroblastoma tumor


title: 1646_input_neuroblastoma tumor


title: 1486_input_neuroblastoma tumor


title: 1039_input_neuroblastoma tumor


title: RNA pol II ChIP-seq HA-Xrn2 WT shXrn2 Rep1

description: Chromatin IP against RNA pol II


title: RNA pol II ChIP-seq Rpb1 R749H Rep2

description: Chromatin IP against RNA pol II

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H


title: 1476_input_neuroblastoma tumor


title: Long RNA-seq: D8_3

description: Day 8 Erythroid Progenitor #3

tag: cell type


title: Q3SC-2

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: iPSC line made from subject Q3 with a reversion of one allele to become heterozygous for the gene ATM

data_processing:
Illumina software used for base calling
Fastq files of reads were aligned with genome using TopHat (default settings) with the UCSC genes.gtf hg19 transcript map from the Illumina iGenomes archive
Bam files were compared and fragments per kilobase per million reads (FPKM) was determined by CuffDiff
Results were loaded into the R/BioConductor package cummeRbund for analysis.  repFpkmMatrix was used to output the processed data file.
Genome_build: hg19
Supplementary_files_format_and_content: The FPKM value is shown for each transcript ID (RefSeq) and each Sample.

source_name: iPSC culture

growth_protocol: iPSC are grown in mTeSR on a Matrigel-coated surface under 4% O2 and 5% CO2 atmosphere at 37C

extract_protocol:
Trizol
Illumina TruSeq

treatment_protocol: No treatment

value: SC

tag: passage

value: Induced pluripotent stem cells (iPSC)


title: Q3SA-2

description: iPSC line made from subject Q3 with a bi-allelic mutation in the ATM gene

value: SA


title: 1038_input_neuroblastoma tumor


title: 1483_input_neuroblastoma tumor


title: 1469_input_neuroblastoma tumor


title: Q1SA-2

description: iPSC line made from subject Q1 with a bi-allelic mutation in the ATM gene


title: 1028_input_neuroblastoma tumor


title: Long RNA-seq: RBC_2

description: Red blood cell #2


title: Q3SC-1


title: 823_input_neuroblastoma tumor


title: Q1-1


title: Q3SA-1


title: 822_input_neuroblastoma tumor


title: 1863_input_neuroblastoma tumor

value: event


title: 820_input_neuroblastoma tumor


title: FA_Saline_5

first: Kenneth

last: Eyring

address: 12700 East 19th Avernue, 8611

department: Department of Medicine

institute: University of Colorado School of Medicine

data_processing:
aligned with bwa-meth
extraced counts with bwa-meth (via samtools mpileup)
Genome_build: mm10
Supplementary_files_format_and_content: text files were generated; counts.txt represents total read counts at site; methylated.txt represents total counts called as methylated

source_name: whole lung

extract_protocol:
Lungs were perfused with phosphate buffered saline then removed and flash frozen in liquid nitrogen.  DNA was extraced using Qiagen's Dneasy Columns.  Agilent's SureSelect Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing kit was used with 4 ug of DNA for the construction of sequencing libraries.
Methyl-seq libraries were preapared for sequencing using SureSelect Human Methyl-Seq Protocol Version B using SureSelect Methyl-Seq Reagent Kit and Mouse Methyl-Seq Capture Library.

tag: strain

tag: tissue

value: whole lung

tag: in utero exposure

value: filtered air

tag: treatment

value: saline


title: FA_Saline_6


title: total small RNA-seq in Piwi-KD

city: Vienna

first: Grzegorz

last: Sienski

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

data_processing:
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings
after adapter removal, reads were collapsed, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini) from sequence as well using HomerTools, version 4.2;  reads ranging in size from 19-42 nt were taken into further analysis
reads were filtered against contaminants (Drosophila and human rRNA, C virus, mitochondrial sequences) and mapped with bowtie v0.12.7 (-a --best --strata -v 1) to D. mel. genome (dm3) and processed with Samtools v 0.1.16 and BedTools v2.16.1
reads mapped to the dm3 genome were further taken and mapped to TE consensus file (with bowtie as above); details in Supplementary materials
Supplementary_files_format_and_content: RNA-seq: file contains strand-specific density coverage of uniquely mapped reads to dm3
Supplementary_files_format_and_content: ChIP-seq: file contains density coverage of uniquely mapped reads to dm3
Supplementary_files_format_and_content: ncRNA-seq: file contains collapsed, dm3 genome-aligned reads
Genome_build: dmel_release 5

organism: Drosophila melanogaster

source_name: Ovarian Somatic Cells (OSC)

growth_protocol: OSC were cultured as described in Niki et al 2007

extract_protocol:
for RNA-seq and small RNA-seq the total RNA was extracted using TRIZOL Reagent (Invitrogen)
for ChIP chromatin was prepared and extracted as in Lee et all 2006
small-RNAs were cloned as described in Senti et al 2015

treatment_protocol: OSC were transfected twice with siRNAs and analyzed after 4 days

tag: genotype/variation

value: Piwi-KD


title: 1484_input_neuroblastoma tumor


title: FA_Saline_4


title: total small RNA-seq in SetDB1-KD


title: 1803_input_neuroblastoma tumor

value: amplified


title: total small RNA-seq in HP1-KD


title: total small RNA-seq in GFP-KD

value: GFP-KD


title: FA_Saline_3


title: FA_Saline_2


title: total small RNA-seq in Armi-KD

value: Armi-KD


title: 912_input_neuroblastoma tumor


title: FA_Saline_1


title: CS_Saline_6

value: cigarette smoke


title: Input small RNA-seq rep2


title: CS_Saline_4


title: CS_Saline_5


title: Piwi-IP followed by small RNA-seq rep1

value: Piwi-IP


title: Piwi-IP followed by small RNA-seq rep2


title: CS_Saline_3


title: anti-Rpb3 ChIP-seq in Su(var)3-9-KD used in Fig6

data_processing:
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
reads were trimmed to bases 6-45 using HomerTools, version 3.9;  N-containing reads were discarded; smaller than 40nt-long reads were discarded
reads were mapped with bowtie v0.12.7 (-v 1 -k 1 -m 1 --best --strata)  to D. mel. genome (dm3) and BigWig files were created with Samtools v 0.1.16 and BedTools v2.16.1
Supplementary_files_format_and_content: RNA-seq: file contains strand-specific density coverage of uniquely mapped reads to dm3
Supplementary_files_format_and_content: ChIP-seq: file contains density coverage of uniquely mapped reads to dm3
Supplementary_files_format_and_content: ncRNA-seq: file contains collapsed, dm3 genome-aligned reads
Genome_build: dmel_release 5

tag: chip-seq antibody

value: anti-Rpb3 (Adelman et al. Mol Cell 2005)


title: CG9754-IP followed by small RNA-seq rep1


title: CS_Saline_1


title: FA_HDM_8

value: house dust mite


title: FA_HDM_9


title: CG9754-IP followed by small RNA-seq rep2


title: CS_Saline_2


title: anti-Rpb3 ChIP-seq in SetDB1-KD used in Fig6


title: anti-Rpb3 ChIP-seq in HP1-KD used in Fig6


title: FA_HDM_6


title: FA_HDM_7


title: anti-Rpb3 ChIP-seq in G9a-KD used in Fig6


title: FA_HDM_5


title: anti-Rpb3 ChIP-seq in CG9754-KD used in Fig6


title: anti-Rpb3 ChIP-seq in GFP-KD used in Fig6


title: FA_HDM_4


title: anti-Rpb3 ChIP-seq in CG9754-KD used in Fig3


title: anti-HP1 ChIP-seq with C1A9 Ab in Piwi-KD

value: anti-HP1, DSHB (#C1A9)

value: C1A9 Ab in Piwi-KD


title: Input small RNA-seq rep1


title: FA_HDM_2


title: FA_HDM_3


title: anti-HP1 ChIP-seq with C1A9 Ab in GFP-KD

value: C1A9 Ab in GFP-KD


title: RNA pol II ChIP-seq Rpb1 R749H Rep1

description: Chromatin IP against RNA pol II

tag: growth conditions

value: DMEM 10% FCS,+ hygromycin + blasticidin + doxycycline + a-amanitin

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: FA_HDM_1


title: RNA pol II ChIP-seq Rpb1 WT Rep1

description: Chromatin IP against RNA pol II

tag: cell line


title: anti-HP1 ChIP-seq with 291C Ab in Piwi-KD

value: anti-HP1, Covance (#291C)

value: 291C Ab in Piwi-KD


title: RNA pol II ChIP-seq Rpb1 E1126G Rep 1

description: Chromatin IP against RNA pol II


title: CS_HDM_8

value: whole lung


title: anti-HP1 ChIP-seq with 291C Ab in GFP-KD

value: 291C Ab in GFP-KD


title: CS_HDM_7


title: anti-H3K9me3 ChIP-seq in Su(var)3-9-KD used in Fig6

value: anti-H3K9me3, Active Motif (#39161)


title: AAD_CEBPG

city: Frederick

first: Peter

middle: F

last: Johnson

address: 1050 Boyles Street

department: Mouse Cancer Genetics Program

institute: NCI-Frederick

description: MEFs immunoprecipitated with CEBPG antibody under AAD conditions

data_processing:
Base-calling was carried out using Illumina Real Time Analysis software (RTA 1.8.70.0)
Reads were trimmed and filtered for residual adaptor contamination using Trimmomatic
Trimmed and adaptor-filtered reads were aligned to the mouse mm10 reference genome using BWA mapper
Significant peaks were called using MACS (v1.4.2) algorithm using default parameters (tag size: auto, p-value cutoff: 1e-04, bandwidth: 152), followed by Audic-claverie algorithm for differential analysis (thresholds: log2(fold-change) > 1 for enrichment, log2(fold-change)<1 for depletion, adjusted p-value = 0.05)
Peak annotation was carried out using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: BED format file containing significant peaks

source_name: Mouse embryonic fibroblasts

growth_protocol: WT MEFs were isolated at E13.5 and passaged 2-3 times.

extract_protocol:
Formaldehyde fixed cells were sonicated, cleared, and chromatin was immunoprecipitated overnight with GFP, CEBPG, and ATF4 antibodies
NEB ChIP-Seq library prep kit was used for constructing single-end libraries from 5-10 ng of each ChIP-enriched, fragmented DNA sample. Sequencing was carried out on Illumina GAIIx with 36bp length, using Illumine TruSeq v3 sequencing chemistry. The libraries were subjected to high-throughput sequencing using the Illumina GAIIx sequencer, with one sample on each lane of the flow cell

treatment_protocol: At time of experiment, cells were first plated in media for 24 hours and then replaced with AAD media for a subsequent 3 hours

value: Mouse embryonic fibroblasts

tag: passages

tag: chip antibody

value: CEBPG C-terminal antiserum (our lab)


title: AAD_GFP

description: MEFs immunoprecipitated with GFP antibody under AAD conditions

value: GFP (Santa Cruz; FL)


title: anti-H3K9me3 ChIP-seq in SetDB1-KD used in Fig6


title: CS_HDM_5

value: cigarette smoke


title: CS_HDM_6


title: anti-H3K9me3 ChIP-seq in HP1-KD used in Fig6


title: CS_HDM_4


title: anti-H3K9me3 ChIP-seq in GFP-KD used in Fig6

value: GFP-KD


title: CS_HDM_3


title: CS_HDM_2


title: anti-H3K9me3 ChIP-seq in CG9754-KD used in Fig6


title: CS_HDM_1


title: anti-H3K9me3 ChIP-seq in G9a-KD used in Fig6


title: 1793_input_neuroblastoma tumor

tag: age of the patient at diagnosis (months)

tag: inss stage

tag: mycn amplification status

value: amplified

tag: overall survival time (days)

value: alive

value: no event


title: 1649_input_neuroblastoma tumor

tag: overall survival status

tag: event-free survival time (days)

tag: event-free survival status


title: anti-H3K9me3 ChIP-seq in CG9754-KD used in Fig3


title: AAD_ATF4

description: MEFs immunoprecipitated with ATF4 antibody under AAD conditions

tag: strain

tag: cell type

value: ATF4 (Santa Cruz; C-20)


title: 1647_input_neuroblastoma tumor


title: mRNA-seq from Su(var)3-9-KD siRNA #2

data_processing:
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
fastq files containing 2nd mate were reverse complemented and used together with fastq files containing 1st mate as single-end library; N-containing reads were discarded
reads were trimmed to high-quality bases 6-46 using HomerTools, version 4.1 and after filtering (masking reads aliging to Drosophila and human rRNA, C virus, mitochondrial sequences ), mapped to genome dm3 with bowtie v0.12.7 (-m 1 -k 1 --best --strata -v 1) using in-house developed pipeline
RPKM was calculated using HomerTools (analyzeRepeats.pl rna -count exons -condenseGenes -rpkm -strand +); for differential gene expression counts were calculated with HomerTools (analyzeRepeats.pl rna dm3 -count exons -condenseGenes -noadj -strand +) follwed by (getDiffExpression.pl -repeats -DESeq)
Supplementary_files_format_and_content: RNA-seq: file contains strand-specific density coverage of uniquely mapped reads to dm3
Supplementary_files_format_and_content: ChIP-seq: file contains density coverage of uniquely mapped reads to dm3
Supplementary_files_format_and_content: ncRNA-seq: file contains collapsed, dm3 genome-aligned reads
Genome_build: dmel_release 5

value: Su(var)3-9-KD siRNA


title: 1515_input_neuroblastoma tumor

value: non-amplified


title: 1501_input_neuroblastoma tumor

value: event


title: mRNA-seq from Su(var)3-9-KD siRNA #1


title: mRNA-seq from SetDB1-KD siRNA #3

value: SetDB1-KD siRNA


title: 1384_input_neuroblastoma tumor


title: 1794_input_neuroblastoma tumor


title: 1800_input_neuroblastoma tumor


title: MEL non-induced Rep2

city: Oxford

first: Supat

last: Thongjuea

address: Headington

department: MRC Molecular Haematology Unit

institute: The Weatherall Institute of Molecular Medicine

description: processed data file: MEL non-induced Rep2

data_processing:
For ChIP-seq, reads were mapped against NCBI build 37.1 of the mouse genome using Bowtie (Langmead et al. 2009). Uniquely mapped reads were extended to 200 bp in the 3' direction and were transformed into a genome-wide read density (coverage) using custom R scripts. MACS (Zhang et al. 2008), CCAT (Xu et al. 2010), and in-house peak calling software with default parameters were used to comprehensively identify binding sites. We combined binding sites identified by all three methods to define consensus-binding regions using GenomicRanges (Lawrence et al. 2013). Consensus-binding regions were given p-values based on a negative binomial distribution (Rozowsky et al. 2009) and assigned p-values were adjusted using the Benjamini-Hochberg (BH) method.
For RNA-seq, raw reads were mapped with Tophat2 (Daehwan Kim, et al., Genome Biology 2013) against the mouse genome (mm9) NCBI build 37.1 with default parameters using "no-coverage-search", and "segment-length 18" as the input options. We next quantified the expression per UCSC RefSeq (mm9) gene to obtain read count and RPKM values using the rpkmforgenes software (Ramsköld D, et al., PLos Comput Biol., 2009). The non-adjusted read counts for each gene were used for statistical calculation of global differential expression using DESeq2 (Michael I Love, et al., Genome Biology, 2014).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files, tab-delimited text files

source_name: MEL_MEL non-induced

growth_protocol: Mouse erythroleukemia (MEL) cells were maintained in DMEM containing 10% FCS and penicillin/streptomycin. ETO2-V5-Bio MEL cells expressing BirA were generated and maintained as previously described (Soler et al. 2010; Soler et al. 2011).

extract_protocol:
For endogenous co-immunoprecipitations, MEL nuclear extracts were diluted to reach 100mM KCl salt concentration using Heng 0 buffer (20mM HEPES KOH pH7.9, 20% glycerol, 0.25mM EDTA, 0.05% Np40). For co-IP experiments in MEL cells, 0.5 mg nuclear extract was used per IP. Extracts were treated with 1U Benzonase nuclease (Millipore). For RNA-seq, total RNA was extracted from MEL or E13.5 sorted fetal liver populations using the RNeasy mini kit (Qiagen).
Libraries were prepared according to Illumina's standard instructions

value: Mouse erythroleukemia (MEL) cells

value: MEL non-induced


title: MEL non-induced Rep1

description: processed data file: MEL non-induced Rep1


title: Lsd1 KD rep2

description: processed data file: Lsd1_WT_Vs_KD.txt

source_name: MEL_Lsd1 KD

value: Lsd1 KD


title: MEL induced Rep2

description: processed data file: MEL_non-Induced_Vs_Induced.txt

source_name: MEL_MEL induced

value: MEL induced


title: Lsd1 KD rep1

description: processed data file: Lsd1_WT_Vs_KD.txt


title: 1382_input_neuroblastoma tumor


title: 1381_input_neuroblastoma tumor


title: mRNA-seq from SetDB1-KD siRNA #2


title: mRNA-seq from SetDB1-KD siRNA #3 + Su(var)3-9-KD siRNA #2

value: SetDB1-KD siRNA + Su(var)3-9-KD siRNA


title: mRNA-seq from SetDB1-KD siRNA #2 + Su(var)3-9-KD siRNA #1


title: 1789_input_neuroblastoma tumor


title: 1030_input_neuroblastoma tumor


title: mRNA-seq from Piwi-KD

value: Piwi-KD


title: Lsd1 WT rep1

description: processed data file: Lsd1_WT_Vs_KD.txt

source_name: MEL_Lsd1 WT

value: Lsd1 WT


title: 11_input_neuroblastoma tumor


title: 1796_input_neuroblastoma tumor

value: died of disease


title: Irf2bp2 KD-sh1 Rep2

description: processed data file: Irf2bp2_WT_Vs_KD.txt

source_name: MEL_Irf2bp2 KD-sh1

value: Irf2bp2 KD-sh1


title: Irf2bp2 KD-sh1 Rep1


title: mRNA-seq from Luc-KD

value: Luc-KD


title: mRNA-seq from GFP-KD

value: GFP-KD


title: MEL induced Rep1


title: Irf2bp2 WT Rep1

source_name: MEL_Irf2bp2 WT

value: Irf2bp2 WT


title: Irf2bp2 WT Rep2


title: mRNA-seq from G9a-KD siRNA #2

value: G9a-KD siRNA


title: 1795_input_neuroblastoma tumor


title: Gfi1b KD Rep2

description: processed data file: Gfi1b_WT_Vs_KD.txt

source_name: MEL_Gfi1b KD

value: Gfi1b KD


title: mRNA-seq from G9a-KD siRNA #2 + Su(var)3-9-KD siRNA #2

value: G9a-KD siRNA + Su(var)3-9-KD siRNA


title: 1791_input_neuroblastoma tumor

value: non-amplified

value: event


title: 1790_input_neuroblastoma tumor


title: 1786_input_neuroblastoma tumor

value: amplified


title: mRNA-seq from G9a-KD siRNA #2 + SetDB1-KD siRNA #3

value: G9a-KD siRNA + SetDB1-KD siRNA


title: Gfi1b KD Rep1

description: processed data file: Gfi1b_WT_Vs_KD.txt

value: Mouse erythroleukemia (MEL) cells


title: Gfi1b WT Rep1

description: processed data file: Gfi1b_WT_Vs_KD.txt

source_name: MEL_Gfi1b WT

value: Gfi1b WT


title: 1784_input_neuroblastoma tumor


title: mRNA-seq from G9a-KD siRNA #1 + Su(var)3-9-KD siRNA #1


title: mRNA-seq from G9a-KD siRNA #1 + SetDB1-KD siRNA #2


title: 1783_input_neuroblastoma tumor


title: mRNA-seq from G9a-KD siRNA #1


title: mRNA-seq from CG9754-KD siRNA #2

value: CG9754-KD siRNA


title: 1780_input_neuroblastoma tumor


title: Eto2 KD-sh3 Rep1

description: processed data file: Eto2_WT_Vs_KD.txt

source_name: MEL_Eto2 KD-sh3

value: Eto2 KD-sh3


title: Eto2 KD-sh2 Rep2

description: processed data file: Eto2_WT_Vs_KD.txt

source_name: MEL_Eto2 KD-sh2

value: Eto2 KD-sh2


title: 1713_input_neuroblastoma tumor

value: died of disease


title: 1782_input_neuroblastoma tumor


title: mRNA-seq from CG9754-KD siRNA #1


title: 1507_input_neuroblastoma tumor


title: Eto2 KD-sh2 Rep1

description: processed data file: Eto2_WT_Vs_KD.txt


title: 1430_input_neuroblastoma tumor


title: Eto2 WT Rep2

description: processed data file: Eto2_WT_Vs_KD.txt

source_name: MEL_Eto2 WT

value: Eto2 WT