title: Nb A&Z

description:
Sample name: NB19
Oryza sativa japonica cv. Nipponbare
Extrachromosomal circular-DNA enriched genomic DNA

data_processing:
Quality control of FASTQ files was evaluated using the FastQC tool (version 0.10.1).
To remove any read originating from organelle circular genomes, reads were mapped against the mitochondria and chloroplast genomes using the program Bowtie2 version 2.2.2 71 with --sensitive local mapping.
Unmapped reads were mapped against the reference genome IRGSP-1.0 (http://rgp.dna.affrc.go.jp/E/IRGSP/Build5/build5.html) using the following parameters: --sensitive local, -k 1. DNA from both mitochondria and chloroplast genomes integrated in nuclear genomes was masked (1,697,400 bp). The TE containing regions cover 194,224,800 bp in O. sativa.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: bigWig files

organism: Oryza sativa Japonica Group

source_name: Aerial part of 10-day-old seedlings, alpha-amanitin and zebularine

growth_protocol: Germination and growth for 10 days at 12 h at 28 °C (day) and 27 °C (night) on solid ½ MS medium (1% sucrose, 0.5% Phytagel (Sigma), pH 5.8).

extract_protocol:
Total DNA of seedlings was extracted as previously reported (Mette, M. F. et al. (1999) EMBO J 18, 241-248). Enrichment of extrachromosomal circular DNA was performed according to (Lanciano et al. submitted). 5 μg of genomic DNA for each sample were purified using a Geneclean kit (MPBio, USA) according to the manufacturer's instructions. ecDNA was isolated from the GeneClean product using the PlasmidSafe DNase (Epicentre, USA) according to the manufacturer's instructions, except that the 37°C incubation was performed for 17h. DNA samples were precipitated by adding 0.1 volume of 3M sodium acetate (pH 5.2), 2.5 volumes of ethanol and 1 μl of glycogen (Fisher, USA) and incubating overnight at -20°C. The precipitated circular DNA was amplified by random rolling circle amplification using the Illustra TempliPhi kit (GE Healthcare, USA) according to the manufacturer's instructions except that the incubation was performed for 65h at 28°C. The DNA concentration was determined using the DNA PicoGreen kit (Invitrogen, USA) using a LightCycler480 (Roche, USA).
One nanogram of amplified ecDNA from each sample was used to prepare the libraries using the Nextera XT library kit (Illumina, USA) according to the manufacturer's instructions.
Samples were pooled and loaded onto a MiSeq platform (Illumina, USA) and 2x250 nucleotides paired-end sequencing was performed.

treatment_protocol: Treatment with alpha-amanitin and zebularine: Germination and growth on solid ½ MS medium (1% sucrose, 0.5% Phytagel (Sigma), pH 5.8) supplemented with sterile filtrated zebularine (Sigma, stock: 5 mg/ml in DMSO) and α-amanitin (5 µg/ml) (Sigma, stock: 1 mg/ml in water).

tag: cultivar

value: Nipponbare

value: Aerial part of seedlings

value: 10 days

tag: treatment

value: alpha-amanitin and zebularine


title: Beaf-32 RNAi Hi-C biological rep A

status: Public on Jun 26 2017

type: SRA

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
[processed data file:]
Beaf32_KD_merge_corrected_score.bedgraph

library_source: genomic

data_processing:
mapping : each mate aligned separately to drosophla genome (dm3, ensembl) using bwa mem with parameters ` -E50 -L0`
build hic matrix : using hicBuildMatrix (HiCExplorer v1.7.0, using restriction fragment resoltiion) with parameters `-rs <dpn2.bed> `
correct hic Matrix : using hicCorrectMatrix (HiCExplorer v1.7.0)
find TADs : using hicFindTADs (HiCExplorer v1.7.0) with parameters `TAD_score --minDepth 10000 --maxDepth 40000 --step 2500` followed by `find_TADs --pvalue 0.001 --delta 0.01`
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph format. The bedgraph files contain TAD separation scores in windows over the genome, calculated using HiCExplorer. A HiC matrix was created for each sample using HiCExplorer and matrices for replicates for each sample were merged. Matrices were then normalized using ICE correction and TAD separation score was calculated in windows.

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were cultured in Express Five SFM (Thermo Fisher Scientific) supplemented with glutamax, at 27°C at a density of 1-16 million/ml.

extract_protocol:
S2 cells have been fixed with 2% formaldehyde for 10 minutes at room temperature. Glycine at 125 mM final concentration has been added to the plates followed by 5 minutes incubation. After two washes in PBS, cells have been scraped off the plate and pelleted. Each pellet (10-50 million of cells) has been resuspended in 1 ml of lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% IGEPAL CA-630) and nuclei have been extracted by sonication (Arrigoni et al. 2016) using Covaris E220 sonicator (settings: 75W peak power, 2% duty factor, 200 cycles/burst), for 60-90 seconds until about 70% of intact nuclei have been released.
10-50 ng of DNA bound to beads have been used for library preparation using a modification of the NEBNext Ultra II DNA library preparation workflow (NEB, E7645). DNA bound to beads have been end-repaired, A-tailed, adaptor-ligated using manufacturer’s instruction. Beads were reclaimed on a magnet, washed once in EB and eluted at 98 °C for 10 minutes. DNA has been USER-treated to open the adapters in meantime to PCR amplification.

treatment_protocol: For knockdown experiments, 7.5 million cells transfected with 100μg of dsRNA on 10cm dishes, using Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific). The M1BP knockdown lasted for 7 days while that of Beaf-32 lasted for 4 days. For M1BP-Beaf-32 double knockdown, cells were first treated with M1BP dsRNA at day 1, followed by treatment with Beaf-32 dsRNA at day 3, and were collected at day 7. All knockdown experiments were carried out in duplicate.

tag: cell line


title: GST RNAi Hi-C biological rep B

description:
[processed data file:]
GST_merge_rf_corrected_score.bedgraph


title: Beaf-32 RNAi Hi-C biological rep B


title: M1BP RNAi Hi-C biological rep A technical rep 2

description:
[processed data file:]
M1BP_KD_merge_corrected_score.bedgraph


title: WT replicate4

city: Dallas

first: Hao

last: Zhu

state: TX

address: 5323 Harry Hines Boulevard

country: USA

institute: UT Southwestern Medical Center

description: HWT437 - WT4

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed to remove adaptor and low quality sequences (Phred score<20) using trim_galore package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed reads were aligned to mouse reference genome GRCm38/mm10 with HiSAT226. After duplicates removal by SAMtools27 and Picard (http://broadinstitute.github.io/picard.), read counts were generated for the annotated genes based GENCODE V2028 using featureCounts29. Differential gene analysis was performed use edgeR30, using FDR < 0.05 as cutoff. Enriched pathways were analyzed through the use of QIAGEN’s Ingenuity® Pathway Analysis (IPA®,QIAGEN RedwoodCity,www.qiagen.com/ingenuity). Heatmaps to visualize the data were generated by using GENE-E (www.broadinstitute.org/cancer/software/GENE-E).
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values

molecule: total RNA

organism: Mus musculus

source_name: frozen whole hippocampus_WT

extract_protocol:
Whole hippocampus was harvested using Trizol reagent and the Qiagen miRNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Nugen library protocols.

treatment_protocol: Whole hippocampus was collected from 80 days old male mice to extract RNA.

tag: strain background

tag: genotype/variation

value: WT

tag: gender

value: male

tag: age

value: postnatal day 80

tag: tissue

value: hippocampus


title: SKNO1 ASXL2 SH2 25

city: New York

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave.

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The reads were aligned to genome assembly hg19 using STAR
Number of reads on each transcript was counted using featurecounts
Differentially expressed genes were determined using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Transcript read counts. 1st column is NCBI accession id, 2nd column is gene symbol, 3rd column is number of reads

organism: Homo sapiens

source_name: SKNO1 cells

extract_protocol:
BM cells were harvested, Liniage-ckit+ScaI+ fractions were sorted by flow cytometry, and RNA was harvested using RNAeasy micro kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: fusion protein

value: AML-ETO


title: SH_B_TRAM_2

status: Public on Jun 25 2017

city: Chicago

first: Alexander

last: Misharin

state: IL

address: 240 E Huron M-300

department: Medicine - Pulmonary

institute: Northwestern University Feinberg School of Medicine

description:
Multiplexed with 32 total samples as part of "Batch C" for a single RNA-seq run
processed data file: shielded_chimera_norm_counts

data_processing:
Trimming was performed using Trimmomatic v0.33 with default parameters and alignment was performed using Tophat v2.1.0 with default parameters
Illumina bcl2fastq2 v2.17 was used for demultiplexing and conversion to FASTQ files.
Trimming was performed using Trimmomatic v0.33
Alignment was performed using Tophat v2.1.0
The gRanges R package was used to generate read counts
Normalized counts were estimated using edgeR v3.14.0
Genome_build: mm10
Supplementary_files_format_and_content: normalized mRNA molecule count values for each sample

molecule: polyA RNA

extract_protocol:
sequencing was performed on the Illumina NextSeq 500 instrument using the V2 chemistry high-output 75 cycles sequencing kit (Illumina).
Monocyte and macrophage subpopulations were isolated via FACSorting on BD FACSAria III instrument, 0.5–1.5x105 cells were sorted into capture media (PBS, 2% BSA and 0.05% EDTA), spun down and immediately lysed in 350 ul of RLT-plus buffer (QIAGEN) supplemented with β2-mercaptoethanol. Total RNA was extracted using RNeasy Plus Mini kit (QIAGEN) and eluted in 35 ul of nuclease free water. RNA quality and quantity were assessed using Bioanalyzer 2100 instrument and RNA Pico chip.
RNA-seq libraries were prepared in 96-well plate format using NEBNext Poly(A) mRNA Magnetic Isolation Module, NEBNext Ultra RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) according to the protocol. Fifty ng of total RNA were enriched for poly(A) mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module, mRNA subjected to chemical fragmentation in the presence of divalent cations at 94°C for 15 min and cDNA was generated using random primers and ProtoScript II reverse transcriptase in the presence of murine RNase inhibitor using the following program: 10 min at 25°C, 15 min at 42°C, 15 min and 70°C. Second strand DNA was generated using NEBNext Second Strand Synthesis Enzyme module (DNA Polymerase I, RNase H, E. coli DNA ligase) for 60 minutes at 16°C. Resulting double stranded DNA was purified using 1.8X volume of AMPure XP Beads (Beckman Coulter), eluted in 0.1X TE buffer, DNA ends were repaired using NEBNext End Prep Enzyme Mix (T4 PNK and T4 DNA polymerase) for 30 min at 20°C  and 30 min and 65°C , followed by NEBNext adaptor for Illumina ligation using Blunt/TA Ligase master mix (T4 DNA ligase) for 15 min at 20°C and incubation with USER enzyme for 15 min at 37°C. After another round of purification using 1X volume of AMPure XP Beads, adaptor-ligated DNA was amplified using NEBNext Q5 Hot Start HiFi DNA polymerase in the presence of NEBNext multiplex oligos (dual index primers) for 14 cycles. PCR-enriched libraries were purified using 0.9X volume of AMPure XP Beads and their quality was assessed using Bioanalyzer 2100 instrument and High Sensitivity DNA chip. Equimolar amount of libraries were pooled and sequenced using an Illumina NextSeq 500.

tag: strain

value: lung

tag: cell type

value: Macrophages


title: Nb Z

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

country: France

institute: IRHS

description:
Sample name: NB18
Oryza sativa japonica cv. Nipponbare
Extrachromosomal circular-DNA enriched genomic DNA

source_name: Aerial part of 10-day-old seedlings, zebularine

treatment_protocol: Treatment with zebularine: Germination and growth on solid ½ MS medium (1% sucrose, 0.5% Phytagel (Sigma), pH 5.8) supplemented with sterile filtrated zebularine (Sigma, stock: 5 mg/ml in DMSO).

value: zebularine


title: SH_B_TRAM_3


title: Beaf-32 + M1BP RNAi Hi-C biological rep A technical rep 1

description:
[processed data file:]
Beaf32_M1BP_KD_merge_rf_corrected_score.bedgraph


title: SH_B_TRAM_1


title: SH_B_MoAM_3


title: SH_B_MoAM_4


title: SH_B_MoAM_2


title: LysMC8flxRIPK3_Sflow_D20_2

description:
Multiplexed with 78 total samples as part of "Batch B" for a single RNA-seq run
processed data file: macrophage_ontogeny_norm_counts

data_processing:
Trimming was performed using Trimmomatic v0.33 with the following parameters: "LEADING:30 TRAILING:30 SLIDINGWINDOW:20:28 MINLEN:20"; Alignment was performed using Tophat v2.1.0 with read-edit-dist: 8 and read-mismatches:8 and otherwise default parameters
Illumina bcl2fastq2 v2.17 was used for demultiplexing and conversion to FASTQ files.
Trimming was performed using Trimmomatic v0.33
Alignment was performed using Tophat v2.1.0
The gRanges R package was used to generate read counts
Normalized counts were estimated using edgeR v3.14.0
Genome_build: mm10
Supplementary_files_format_and_content: normalized mRNA molecule count values for each sample

extract_protocol:
sequencing was performed on the Illumina NextSeq 500 instrument using the V1 chemistry high-output 150 cycles sequencing kit (Illumina).
Monocyte and macrophage subpopulations were isolated via FACSorting on BD FACSAria III instrument, 0.5–1.5x105 cells were sorted into capture media (PBS, 2% BSA and 0.05% EDTA), spun down and immediately lysed in 350 ul of RLT-plus buffer (QIAGEN) supplemented with β2-mercaptoethanol. Total RNA was extracted using RNeasy Plus Mini kit (QIAGEN) and eluted in 35 ul of nuclease free water. RNA quality and quantity were assessed using Bioanalyzer 2100 instrument and RNA Pico chip.
RNA-seq libraries were prepared in 96-well plate format using NEBNext Poly(A) mRNA Magnetic Isolation Module, NEBNext Ultra RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) according to the protocol. Fifty ng of total RNA were enriched for poly(A) mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module, mRNA subjected to chemical fragmentation in the presence of divalent cations at 94°C for 15 min and cDNA was generated using random primers and ProtoScript II reverse transcriptase in the presence of murine RNase inhibitor using the following program: 10 min at 25°C, 15 min at 42°C, 15 min and 70°C. Second strand DNA was generated using NEBNext Second Strand Synthesis Enzyme module (DNA Polymerase I, RNase H, E. coli DNA ligase) for 60 minutes at 16°C. Resulting double stranded DNA was purified using 1.8X volume of AMPure XP Beads (Beckman Coulter), eluted in 0.1X TE buffer, DNA ends were repaired using NEBNext End Prep Enzyme Mix (T4 PNK and T4 DNA polymerase) for 30 min at 20°C  and 30 min and 65°C , followed by NEBNext adaptor for Illumina ligation using Blunt/TA Ligase master mix (T4 DNA ligase) for 15 min at 20°C and incubation with USER enzyme for 15 min at 37°C. After another round of purification using 1X volume of AMPure XP Beads, adaptor-ligated DNA was amplified using NEBNext Q5 Hot Start HiFi DNA polymerase in the presence of NEBNext multiplex oligos (dual index primers) for 14 cycles. PCR-enriched libraries were purified using 0.9X volume of AMPure XP Beads and their quality was assessed using Bioanalyzer 2100 instrument and High Sensitivity DNA chip. Equimolar amount of libraries were pooled and sequenced using an Illumina NextSeq 500.

value: Alveolar Macrophages


title: SH_B_MoAM_1


title: Nb A

description:
Sample name: NB17
Oryza sativa japonica cv. Nipponbare
Extrachromosomal circular-DNA enriched genomic DNA

source_name: Aerial part of 10-day-old seedlings, alpha-amanitin

treatment_protocol: Treatment with alpha-amanitin: Germination and growth on solid ½ MS medium (1% sucrose, 0.5% Phytagel (Sigma), pH 5.8) supplemented with sterile filtrated α-amanitin (5 µg/ml) (Sigma, stock: 1 mg/ml in water).

value: alpha-amanitin


title: Nb C

description:
Sample name: NB15
Oryza sativa japonica cv. Nipponbare
Extrachromosomal circular-DNA enriched genomic DNA

source_name: Aerial part of 10-day-old seedlings, control

treatment_protocol: Control: Germination and growth on solid ½ MS medium (1% sucrose, 0.5% Phytagel (Sigma), pH 5.8).

value: control


title: LysMC8flxRIPK3_Sflow_D14_4


title: LysMC8flxRIPK3_Sflow_D20_1

description:
Multiplexed with 77 total samples as part of "Batch A" for a single RNA-seq run
processed data file: macrophage_ontogeny_norm_counts


title: LysMC8flxRIPK3_Sflow_D14_3


title: LysMC8flxRIPK3_Sflow_D14_2


title: LysMC8flxRIPK3_Sflow_D14_1


title: LysMC8flxRIPK3_Sfhi_D20_2


title: LysMC8flxRIPK3_Sfhi_D14_4


title: LysMC8flxRIPK3_Sfhi_D20_1


title: LysMC8flxRIPK3_Sfhi_D14_3


title: LysMC8flxRIPK3_mono_D20_2

value: Lung Monocytes


title: LysMC8flxRIPK3_Sfhi_D14_2


title: LysMC8flxRIPK3_Sfhi_D14_1


title: LysMC8flxRIPK3_mono_D14_4


title: LysMC8flxRIPK3_mono_D20_1


title: LysMC8flxRIPK3_IM_D20_2

value: Interstitial Macrophages


title: LysMC8flxRIPK3_IM_D20_1


title: LysMC8flxRIPK3_mono_D14_1


title: LysMC8flxRIPK3_mono_D14_2


title: LysMC8flxRIPK3_IM_D14_1


title: LysMC8flxRIPK3_IM_D14_2


title: LysMC8flxRIPK3_IM_D14_4


title: LysMC8flx_Sflow_D20_4


title: LysMC8flxRIPK3_IM_D14_3


title: LysMC8flx_Sflow_D20_2


title: LysMC8flx_Sflow_D20_3


title: LysMC8flx_Sflow_D20_1


title: LysMC8flx_Sflow_D14_3


title: SH_B_TRAM_4


title: LysMC8flx_Sflow_D14_4


title: LysMC8flx_Sflow_D14_2


title: LysMC8flx_Sflow_D14_1


title: LysMC8flx_Sfhi_D20_3


title: LysMC8flx_Sfhi_D20_4


title: LysMC8flxRIPK3_mono_D14_3


title: LysMC8flx_Sfhi_D14_4


title: LysMC8flx_Sfhi_D20_2


title: LysMC8flx_Sfhi_D20_1


title: LysMC8flx_Sfhi_D14_3


title: LysMC8flx_Sfhi_D14_1


title: LysMC8flx_Sfhi_D14_2


title: LysMC8flx_Sfhi_D0_4


title: LysMC8flx_Sfhi_D0_3


title: LysMC8flx_Sfhi_D0_1


title: LysMC8flx_mono_D20_3


title: LysMC8flx_mono_D20_4


title: LysMC8flx_Sfhi_D0_2


title: LysMC8flx_mono_D14_3


title: LysMC8flx_mono_D14_4


title: LysMC8flx_mono_D20_2


title: LysMC8flx_mono_D14_1


title: LysMC8flx_IM_D20_4


title: LysMC8flx_IM_D20_3


title: LysMC8flx_IM_D20_2


title: LysMC8flx_IM_D14_3


title: LysMC8flx_IM_D14_4


title: CD11cC8flxRIPK3_Sflow_D21_2


title: LysMC8flx_IM_D14_2


title: CD11cC8flxRIPK3_Sflow_D14_4


title: CD11cC8flxRIPK3_Sflow_D21_1


title: LysMC8flx_IM_D20_1


title: CD11cC8flxRIPK3_Sflow_D14_3


title: CD11cC8flxRIPK3_Sflow_D14_2


title: CD11cC8flxRIPK3_Sfhi_D21_2


title: CD11cC8flxRIPK3_Sfhi_D14_3


title: CD11cC8flxRIPK3_Sfhi_D14_4


title: LysMC8flx_mono_D20_1


title: CD11cC8flxRIPK3_Sflow_D14_1


title: CD11cC8flxRIPK3_Sfhi_D14_2


title: LysMC8flx_mono_D14_2


title: CD11cC8flxRIPK3_Sfhi_D14_1


title: CD11cC8flxRIPK3_Sfhi_D21_1


title: CD11cC8flxRIPK3_mono_D14_3


title: CD11cC8flxRIPK3_mono_D14_2


title: CD11cC8flxRIPK3_mono_D21_2


title: CD11cC8flxRIPK3_mono_D14_4


title: CD11cC8flxRIPK3_mono_D14_1


title: CD11cC8flxRIPK3_mono_D21_1


title: CD11cC8flxRIPK3_IM_D14_4


title: CD11cC8flxRIPK3_IM_D21_1


title: CD11cC8flxRIPK3_IM_D21_2


title: LysMC8flx_IM_D14_1


title: CD11cC8flxRIPK3_IM_D14_3


title: CD11cC8flxRIPK3_IM_D14_2


title: CD11cC8flx_Sflow_D20_2


title: CD11cC8flx_Sflow_D20_1


title: CD11cC8flx_Sflow_D14_3


title: CD11cC8flx_Sflow_D20_4


title: CD11cC8flx_Sflow_D20_3


title: CD11cC8flx_Sflow_D14_2


title: CD11cC8flx_Sflow_D14_1


title: CD11cC8flx_Sfhi_D20_4


title: CD11cC8flx_Sfhi_D20_3


title: CD11cC8flx_Sfhi_D20_2


title: CD11cC8flx_Sfhi_D14_2


title: CD11cC8flx_Sfhi_D14_3


title: CD11cC8flx_Sfhi_D14_1


title: CD11cC8flx_Sfhi_D0_3


title: CD11cC8flx_Sfhi_D0_4


title: CD11cC8flx_Sfhi_D0_2


title: CD11cC8flx_mono_D20_4


title: CD11cC8flx_mono_D20_3


title: CD11cC8flx_mono_D14_3


title: CD11cC8flx_mono_D14_2


title: CD11cC8flx_Sfhi_D0_1


title: CD11cC8flx_IM_D20_4


title: CD11cC8flx_IM_D20_3


title: CD11cC8flx_IM_D20_2


title: CD11cC8flx_mono_D14_1


title: CD11cC8flxRIPK3_IM_D14_1


title: CD11cC8flx_IM_D20_1


title: CD11cC8flx_Sfhi_D20_1


title: CD11cC8flx_IM_D14_2


title: CD11cC8flx_IM_D14_1


title: C8flx_Sflow_D19_5


title: CD11cC8flx_IM_D14_3


title: CD11cC8flx_mono_D20_2


title: CD11cC8flx_mono_D20_1


title: C8flx_Sflow_D19_3


title: C8flx_Sflow_D19_2


title: C8flx_Sflow_D19_1


title: C8flx_Sflow_D14_4


title: C8flx_Sflow_D14_2


title: C8flx_Sfhi_D19_5


title: C8flx_Sflow_D14_1


title: C8flx_Sfhi_D19_3


title: C8flx_Sflow_D19_4


title: C8flx_Sfhi_D14_4


title: C8flx_Sfhi_D14_3


title: C8flx_Sfhi_D14_2


title: C8flx_Sfhi_D0_2


title: C8flx_Sfhi_D0_3


title: C8flx_mono_D19_5


title: C8flx_mono_D19_4


title: C8flx_mono_D19_2


title: C8flx_Sflow_D14_3


title: C8flx_mono_D14_3


title: C8flx_mono_D14_1


title: C8flx_IM_D19_4


title: C8flx_IM_D19_2


title: C8flx_IM_D19_3


title: C8flx_mono_D14_2


title: C8flx_mono_D19_1


title: C8flx_Sfhi_D19_4


title: C8flx_Sfhi_D19_2


title: C8flx_IM_D14_3


title: C8flx_IM_D19_5


title: C8flx_IM_D14_2


title: C8flx_IM_D14_1


title: C8flx_IM_D14_4


title: C8flx_Sfhi_D14_1


title: C8flx_Sfhi_D19_1


title: H1_EED_FK_DOX_D28_2

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

description: H1-EED-/-/EED-OE, +DOX

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38/hg38 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: hg19
Supplementary_files_format_and_content: TPM

source_name: Human embryonic stem cell with inducible knockout of EED, +DOX

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human embryonic stem cell

tag: genotype

value: inducible knockout of EED

value: +DOX


title: H1_EED_FK_DOX_D28_1

description: H1-EED-/-/EED-OE, -DOX，Day28

source_name: Human embryonic stem cell with inducible knockout of EED, -DOX, day 28

value: -DOX

tag: time

value: day 28


title: H1_EED_FK_DOX_D24

description: H1-EED-/-/EED-OE, -DOX，Day24

source_name: Human embryonic stem cell with inducible knockout of EED, -DOX, day 24

value: day 24


title: C8flx_Sfhi_D0_1


title: H1_EED_FK_DOX_D16

description: H1-EED-/-/EED-OE, -DOX，Day16

source_name: Human embryonic stem cell with inducible knockout of EED, -DOX, day 16

value: day 16


title: C8flx_mono_D19_3


title: H1_EED_FK_DOX_D20

description: H1-EED-/-/EED-OE, -DOX，Day20

source_name: Human embryonic stem cell with inducible knockout of EED, -DOX, day 20

value: day 20


title: H1_SUZ12_LPR_DK89

source_name: Human embryonic stem cell with deletion of SUZ12

value: SUZ12 knockout


title: H1_EED_FK_DOX_D12

description: H1-EED-/-/EED-OE, -DOX，Day12

source_name: Human embryonic stem cell with inducible knockout of EED, -DOX, day 12

value: day 12


title: C8flx_mono_D14_4

value: lung


title: H1_SUZ12_LPR_DK30


title: C8flx_IM_D19_1


title: H1_EED_LPR_DK2

source_name: Human embryonic stem cell with deletion of EED

value: EED knockout


title: H1_EED_LPR_DK1_DK10


title: H1_E2K_PN32

source_name: Human embryonic stem cell with deletion of EZH2

value: EZH2 knockout


title: H1_E2K_E1DK1

source_name: Human embryonic stem cell with deletion of EZH1 and EZH2

value: EZH1 and EZH2 knockout


title: H1_E1K_P26

source_name: Human embryonic stem cell with deletion of EZH1

value: EZH1 knockout


title: H1_E2K_E1DK2


title: H1_EED_FK_DOX_D8

description: H1-EED-/-/EED-OE, -DOX，Day8

source_name: Human embryonic stem cell with inducible knockout of EED, -DOX, day 8

value: day 8


title: H1_E1K_P3


title: Smc1a ChIP-seq  Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 6

city: Stanford

first: Paul

last: Khavari

state: CA

address: 269 Campus Drive, CCSR 2150

institute: Stanford University

description: Sample 15

data_processing:
Reads were aligned with bowtie2 using default parameters.
Aligned reads were filtered for MAPQ > 30 and deduplicated with samtools.
Signal tracks were generated by first using the bedtools genomeCoverageBed to produce bedGraph files.
The UCSC utility bedGraphToBigWig was used with default parameters to generate bigwig files.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for each ChIP experiment are in UCSC format.

source_name: Primary Epidermal Keratinocyte - Differentiation Day 6

growth_protocol: Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiated for three or six days as previously described (Zarnegar et al., 2012)

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with an antibody.
NEB Next ChIP-seq library prep kit was used.

treatment_protocol: In the case of siRNA knockdown, progenitor keratinocytes were nucleofected with scrambled control, KLF4, ZNF750, or EHF targeting siRNAs

value: primary epidermal keratinocyte

tag: differentiation state

value: Late differentiation (Day 6)

tag: individual

tag: Sex

value: male

tag: chip antibody

value: Smc1a (Bethyl, catalog#  A300-055A, lot# A300-055-5)


title: Smc1a ChIP-seq  Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3

description: Sample 14

source_name: Primary Epidermal Keratinocyte - Differentiation Day 3

value: Early Differentiation (Day 3)


title: EHF ChIP-seq Primary Epidermal Keratinocyte - Differentiation Day 3

description: Sample 16

value: Donors not specified for single biological replicate experiments

value: EHF (Santa Cruz, catalog#  sc-166653, lot# C0910)


title: H1

source_name: Human embryonic stem cell

value: Human embryonic stem cell

value: control


title: Smc1a ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3

description: Sample 11


title: Smc1a ChIP-seq  Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 0

description: Sample 13

source_name: Primary Epidermal Keratinocyte - Differentiation Day 0

value: Undifferentiated (Day 0)


title: Smc1a ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 6

description: Sample 12


title: H1_2


title: Promoter capture HiC Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3

description:
Sample 11
Processed data file(s): CHiC_contacts_b2g.bed, CHiC_contacts_b2b.bed

data_processing:
Library strategy: CHiC-Seq
Sequencing reads were aligned and paired, filtered for valid long-range contacts, and removed of duplicates using the HiCUP pipeline.
The CHiCAGO tool was used to identify signicant contacts between captured baits on other fragments at an FDR < 0.01.
Bait to bait interactions (b2b) reaching FDR < 0.01 on any of Day 0, Day 3, or Day 6 are included with supporting read counts from each replicate.
Bait to non-bait (or bait to "genome") interactions (b2g) reaching FDR < 0.01 and associated with an H3K27ac peak on any of Day 0, Day 3, or Day 6 are included with supporting read counts from each replicate.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file reports one contact per row. Interacting HindIII fragments are represented in bed format (chr/start/stop) with bait (or upstream bait, in the case of b2b contacts) listed first. The following fields correspond to a unique contact ID, fragment IDs for first and second fragments, and raw read counts supporting contacts in each replicates.

extract_protocol:
Cells were cross-linked in 2% formaldehyde for 10 min at RT and flash frozen. After digestion of nuclei with HindIII, DNA ends were labeled with biotin-14–dATP (Life Technologies) in a Klenow end-filling reaction and ligated in nuclei overnight. DNA was sheared, end repaired, A-tailed and subjected to pull down with streptavidin beads.
Paired-end adaptors were ligated (Illumina) and libraries were PCR-amplified and either sequenced directly or enriched for promoter fragments with RNA oligonucleotide baits.

tag: restriction enzyme

value: HindIII


title: RNA-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 6

description: Sample 3

data_processing:
Paired end RNA-seq reads were aligned to the Gencode V19 transcriptome in hg19 using STAR aligner version 2.4.1d with default settings.
RSEM version 1.2.21 was then used to calculate expected read counts per protein-coding gene.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file contains RSEM read count estimates for each Gencode V19 mRNA, in addition to transcription start site and transcription end site positions.

extract_protocol:
Cell pellets were frozen at -80 C, and RNA was later purified using Qiagen RNeasy Mini Kit.
The TruSeq Stranded mRNA Library Prep Kit was used.


title: Promoter capture HiC Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 6

description:
Sample 12
Processed data file(s): CHiC_contacts_b2g.bed, CHiC_contacts_b2b.bed


title: Smc1a ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 0

description: Sample 10


title: RNA-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 0

description: Sample 1


title: RNA-seq Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 0

description: Sample 4


title: RNA-seq Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3

description: Sample 5


title: Promoter capture HiC Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 0

description:
Sample 10
Processed data file(s): CHiC_contacts_b2g.bed, CHiC_contacts_b2b.bed


title: RNA-seq Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 6

description: Sample 6


title: H1_E2K_PN21


title: Promoter capture HiC Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 6

description:
Sample 9
Processed data file(s): CHiC_contacts_b2g.bed, CHiC_contacts_b2b.bed


title: HiC Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 6

description:
Sample 6
Processed data file(s): HiC_matrices_norm_Day6.tar.gz

data_processing:
Library strategy: HiC-Seq
Sequencing reads were aligned and paired, filtered for valid long-range contacts, and removed of duplicates using the HiCUP pipeline.
The CHiCAGO tool was used to identify signicant contacts between captured baits on other fragments at an FDR < 0.01.
Bait to bait interactions (b2b) reaching FDR < 0.01 on any of Day 0, Day 3, or Day 6 are included with supporting read counts from each replicate.
Bait to non-bait (or bait to "genome") interactions (b2g) reaching FDR < 0.01 and associated with an H3K27ac peak on any of Day 0, Day 3, or Day 6 are included with supporting read counts from each replicate.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file reports one contact per row. Interacting HindIII fragments are represented in bed format (chr/start/stop) with bait (or upstream bait, in the case of b2b contacts) listed first. The following fields correspond to a unique contact ID, fragment IDs for first and second fragments, and raw read counts supporting contacts in each replicates.


title: Promoter capture HiC Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 0

description:
Sample 7
Processed data file(s): CHiC_contacts_b2g.bed, CHiC_contacts_b2b.bed


title: HiC Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3

description:
Sample 5
Processed data file(s): HiC_matrices_norm_Day3.tar.gz


title: Promoter capture HiC Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3

description:
Sample 8
Processed data file(s): CHiC_contacts_b2g.bed, CHiC_contacts_b2b.bed


title: HiC Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 0

description:
Sample 4
Processed data file(s): HiC_matrices_norm_Day0.tar.gz


title: HiC Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3

description:
Sample 2
Processed data file(s): HiC_matrices_norm_Day3.tar.gz


title: HiC Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 6

description:
Sample 3
Processed data file(s): HiC_matrices_norm_Day6.tar.gz


title: HiC Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 0

description:
Sample 1
Processed data file(s): HiC_matrices_norm_Day0.tar.gz


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 0

description: Sample 1

value: H3K27ac (Abcam, catalog# ab4729, lot# GR45787-1)


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 6

description: Sample 3


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3

description: Sample 2


title: ADAR_KD_Riboseq_replicate2

city: Haifa

first: Oz

last: Solomon

address: Technion

country: Israel

institute: Technion

description:
mRNA
Processed data file: RPKM_table.all_samples.txt

data_processing:
Library strategy: Ribo-Seq
Adapters were trimmed using cutadapt.
PARSseq, RNAseq and Riboseq reads were aligned to the human genome hg19, using Bowtie2 (--local). Only uniquely mapped aligned reads were retained for further analysis. To count (in PARSseq) the number of reads which start at certain position in the genome, we took into account only reads which their start 5’ matched the reference by at least five bases without gap, carefully paying attention to the read orientation as PARS-seq protocol is strand specific. Samples were normalized such that at the end of the normalization step, the sum of all read-starts in each sample was equal.
PARSseq reads were also aligned to UCSC knownCanonical genes mRNA sequences using bowtie2. We only used uniquely aligned reads that their 5' matched with no gaps for at least five bases (considering the read orientation). Read starts at each position of the transcriptome were counted. Samples were normalized such that at the end of the normalization step, the sum of all read-starts in each sample was equal.
PARSscores were calculated as in Kertez et al. (2010).
RNA editing sites were detected as in Porath et al. (2014).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files (with genome aligned reads starts count)
RPKM_table.all_samples.txt: Tab-delimited text file includes RPKM values.
read start counts files  (tab delim- 1st column: ucsc_id, 2nd column: read starts per base seprated by ";")

extract_protocol:
Total RNA from HepG2 cells was isolated using Trizol (Invitrogen) and treated with DNase I (Invitrogen). Poly-A mRNA was isolated using mRNA Sequencing Sample Preparation kit (Illumina Proprietary). Random-primed cDNA synthesis was done on 2μg of total RNA using M-MLV reverse transcriptase (Invitrogen). qPCRs for ADAR were done as described. Analysis was performed by the SDS 2.3 software using the absolute quantification method with ABL for the normalization. All reactions were run on ABI 7900HT genetic analyzer (Applied Biosystems). Probing the mRNA with S1 nuclease (digest at un-paired bases) and RNase V1 (digest at paired bases) was done as described in Kertesz et al. (2010).
Libraries were prepared as described in the PARS-seq protocol, using the TruSeq Small RNA sample preparation kit of the Illumina. We ligated the 5' adapter as described in the TruSeq Small RNA sample preparation protocol (Illumina) and stopped the reaction with 1µl stop solution (a component of the TruSeq Small RNA sample preparation kit) in 28C for 15 min. 3' end treatment with Antarctic phosphatase was done as described in the directional mRNA-Seq sample preparation protocol, followed by its inactivation with ethanol precipitation. 3' adapter ligation, reverse transcription and PCR amplification were performed as described in the TruSeq Small RNA sample preparation protocol. The cDNA was size selected and cleaned using E-Gel 4% agarose (Invitrogen) and Agencourt AMPure XP beads (Beckman Coulter). The library was quantified using Qubit (Invitrogen) and validated using Agilent 2100 Bioanalyzer. Libraries were sequenced on Illumina Hiseq2500 machine.

treatment_protocol: HepG2 cells were stably transfected with validated siADAR1 or scrambled siRNA.

tag: sirna


title: CDYL_ChIP-Seq

city: Beijing

first: yongqing

last: liu

address: 38 Xue Yuan Road

department: Department of Biochemistry and Molecular Biology

institute: Peking University Health Science Center

description: ChIP

data_processing:
Quality control of raw data based on FastQC
Read alignment through Bowtie version 2
Peak calling through MACS version2
Peak annotation by CEAS
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Bam files from read alignment which contain mapping reads; bed file from peak calling which contains binding sites of CDYL

source_name: Hippocampus

growth_protocol: Hippocampi from adult wild-type C57BL/6 mice

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The chromatin DNA precipitated by either normal rabbit IgG (control) or polyclonal antibody against mouse CDYL was purified with the Qiagen PCR purification kit. After cross linking, chromatin complexes were isolated and sonicated for appropriate fragmentation for sequencing.

value: 6-8 weeks

value: hippocampus


title: control_Riboseq_replicate1

tag: cell line

value: scrambled


title: ADAR_KD_Riboseq_replicate1


title: control_Riboseq_replicate2


title: ADAR_KD_RNAseq

data_processing:
Adapters were trimmed using cutadapt.
PARSseq, RNAseq and Riboseq reads were aligned to the human genome hg19, using Bowtie2 (--local). Only uniquely mapped aligned reads were retained for further analysis. To count (in PARSseq) the number of reads which start at certain position in the genome, we took into account only reads which their start 5’ matched the reference by at least five bases without gap, carefully paying attention to the read orientation as PARS-seq protocol is strand specific. Samples were normalized such that at the end of the normalization step, the sum of all read-starts in each sample was equal.
PARSseq reads were also aligned to UCSC knownCanonical genes mRNA sequences using bowtie2. We only used uniquely aligned reads that their 5' matched with no gaps for at least five bases (considering the read orientation). Read starts at each position of the transcriptome were counted. Samples were normalized such that at the end of the normalization step, the sum of all read-starts in each sample was equal.
PARSscores were calculated as in Kertez et al. (2010).
RNA editing sites were detected as in Porath et al. (2014).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files (with genome aligned reads starts count)
RPKM_table.all_samples.txt: Tab-delimited text file includes RPKM values.
read start counts files  (tab delim- 1st column: ucsc_id, 2nd column: read starts per base seprated by ";")


title: control_RNAseq


title: V1_ADAR_KD_replicate1

data_processing:
Library strategy: PARS-Seq
Adapters were trimmed using cutadapt.
PARSseq, RNAseq and Riboseq reads were aligned to the human genome hg19, using Bowtie2 (--local). Only uniquely mapped aligned reads were retained for further analysis. To count (in PARSseq) the number of reads which start at certain position in the genome, we took into account only reads which their start 5’ matched the reference by at least five bases without gap, carefully paying attention to the read orientation as PARS-seq protocol is strand specific. Samples were normalized such that at the end of the normalization step, the sum of all read-starts in each sample was equal.
PARSseq reads were also aligned to UCSC knownCanonical genes mRNA sequences using bowtie2. We only used uniquely aligned reads that their 5' matched with no gaps for at least five bases (considering the read orientation). Read starts at each position of the transcriptome were counted. Samples were normalized such that at the end of the normalization step, the sum of all read-starts in each sample was equal.
PARSscores were calculated as in Kertez et al. (2010).
RNA editing sites were detected as in Porath et al. (2014).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files (with genome aligned reads starts count)
RPKM_table.all_samples.txt: Tab-delimited text file includes RPKM values.
read start counts files  (tab delim- 1st column: ucsc_id, 2nd column: read starts per base seprated by ";")

tag: nuclease

value: RNase V1


title: V1_control_replicate2


title: V1_ADAR_KD_replicate2


title: S1_ADAR_KD_replicate2


title: S1_ADAR_KD_replicate1


title: S1_control_replicate1


title: CTCF ChIP-seq Primary Epidermal Keratinocyte - Differentiation Day 6

description: Sample 9

value: CTCF (Millipore, catalog#  07-729, lot# JBC1881349)


title: V1_control_replicate1


title: CTCF ChIP-seq Primary Epidermal Keratinocyte - Differentiation Day 3

description: Sample 8

value: primary epidermal keratinocyte


title: CTCF ChIP-seq Primary Epidermal Keratinocyte - Differentiation Day 0

description: Sample 7


title: H3K27ac ChIP-seq  Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3

description: Sample 5

value: H3K27ac (Abcam, catalog# ab4729, lot# GR103379-1)


title: H3K27ac ChIP-seq  Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 6

description: Sample 6

value: Late differentiation (Day 6)

value: male


title: Input DNA

description: input


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3 - EHF siRNA

description: Sample 8

source_name: H3K27ac ChIP-seq Primary Epidermal Keratinocyte - Differentiation Day 3 - EHF siRNA

value: Differentiated (Day 3)

tag: genotype/variation

value: EHF knockdown


title: H3K27ac ChIP-seq  Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 0

description: Sample 4


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3 - EHF siRNA

description: Sample 7


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3 - ZNF750 siRNA

description: Sample 6

source_name: H3K27ac ChIP-seq Primary Epidermal Keratinocyte - Differentiation Day 3 - ZNF750 siRNA

value: ZNF750 knockdown


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3 - Control siRNA

description: Sample 2

source_name: H3K27ac ChIP-seq Primary Epidermal Keratinocyte - Differentiation Day 3 - Control siRNA

value: Control


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3 - KLF4 siRNA

description: Sample 4

source_name: H3K27ac ChIP-seq Primary Epidermal Keratinocyte - Differentiation Day 3 - KLF4 siRNA

value: KLF4 knockdown


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3 - Control siRNA

description: Sample 1


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3 - KLF4 siRNA

description: Sample 3


title: S1_control_replicate2


title: UMI-4C Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3 - EHF siRNA

description: Sample 9

data_processing:
Sequencing reads were aligned and paired, filtered for valid long-range contacts, and removed of duplicates using the HiC-Pro pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited BED 6 file contains processed read counts supporting contact between two 5kb regions of the genome.
Column 1: Bin #1 - chromosome
Column 2: Bin #1 - start position
Column 3: Bin #1 - end position
Column 4: Bin #2 - chromosome
Column 5: Bin #2 - start position
Column 6: Bin #2 - end position
Column 7: HiC-Pro filtered read counts

source_name: Primary Epidermal Keratinocyte - Differentiation Day 3 - EHF siRNA

extract_protocol:
Cells were cross-linked in 2% formaldehyde for 10 min at RT and flash frozen.  Nuclei were digested with MboI and ligated in nuclei overnight.
UMI-4C universal adapter was ligated and custom two-step bait primers were used for library PCR.

treatment_protocol: Progenitor keratinocytes were nucleofected with scrambled control, KLF4, ZNF750, or EHF targeting siRNAs


title: UMI-4C Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3 - ZNF750 siRNA

description: Sample 7

source_name: Primary Epidermal Keratinocyte - Differentiation Day 3 - ZNF750 siRNA


title: UMI-4C Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3 - KLF4 siRNA

description: Sample 6

source_name: Primary Epidermal Keratinocyte - Differentiation Day 3 - KLF4 siRNA


title: UMI-4C Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3 - KLF4 siRNA

description: Sample 5


title: UMI-4C Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3 - Control siRNA

description: Sample 4

source_name: Primary Epidermal Keratinocyte - Differentiation Day 3 - Control siRNA


title: UMI-4C Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 0 - Control siRNA

description: Sample 2

source_name: Primary Epidermal Keratinocyte - Differentiation Day 0 - Control siRNA

value: Undifferentiated (Day 0)


title: UMI-4C Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3 - EHF siRNA

description: Sample 10


title: RNA-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3

description: Sample 2

value: Early Differentiation (Day 3)


title: UMI-4C Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3 - ZNF750 siRNA

description: Sample 8


title: UMI-4C Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3 - Control siRNA

description: Sample 3


title: UMI-4C Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 0 - Control siRNA

description: Sample 1


title: sox11crush.C

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Removal of low expressed transcripts (minimum of 10 counts for at least one condition (all replicates)
Normalization (TMM) and removal of unwanted variation using residual (k=1) with R-package RUVSeq
Genome_build: mm10
Supplementary_files_format_and_content: Complete_geneList_EdgeR_Zhigang.csv

source_name: RGCs

growth_protocol: Mice were approximately 3-4 weeks when starting. Mice were pseudo-randomly sorted from litters into treatment groups, and approximately balanced for age and sex between treatment groups.

extract_protocol:
After sacrifice, retinas were dissected in serum-free culture media and kept cool on ice. 3 retinas were pooled for each treatment condition for each replicate. Then, retinas were dissociated with papain, quenched with trypsin inhibitor, triturated, and stained with anti-Thy1-PE-Cy7 antibody and SYTOX live-dead cell stain. Cells were then sorted directly into Arcturus PicoPure extraction buffer, lysed immediately, and RNA was extracted according to manufacturer's instructions.
Nugen Ovation RNA Ultra Low Input (500 pg) +TruSeq Nano

treatment_protocol: Eyes were injected with either AAV-Control or AAV-Sox11 for 2 weeks. Each replicate of each treatment group consisted of 3 retinas (from 3 different animals). Then, optic nerve crush was performed 3 days before sacrifice.

value: retina

value: retinal ganglion cell

tag: rna sample type

value: Sorted by FACS

tag: condition

value: crushed


title: sox11crush.B

tag: tissue


title: H3K27ac ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3 - ZNF750 siRNA

description: Sample 5

value: H3K27ac (Abcam, catalog# ab4729, lot# GR45787-1)


title: plupcrush.B

value: AAV-PLAP


title: plupcrush.C


title: sox11crush.A


title: STING KO T cells CMA 3

status: Public on Jun 24 2017

city: Lausanne

first: Muhammet

middle: Fatih

last: Gulen

state: VD

address: Station 19

department: GHI

country: Switzerland

institute: EPFL

description:
STING KO T cells CMA 3
Sample name: 52

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3, Martin 2011) and filtered for low complexity with seq_crumbs (v. 0.1.8).
Reads were aligned against Mus musculus.GRCm38.75 genome using STAR (v. 2.4.0f1, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Mus musculus.GRCm38.75 gene annotation. Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Reads were also aligned to the Mus musculus.GRCm38.75 transcriptome using STAR (v. 2.4.0f1, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.16, Li and Dewey 2011).
Genome_build: GRCm38.75
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample. Normalized read counts are available in file on series record.

source_name: Primary splenic mouse T cells

extract_protocol:
Total RNA was isolated from the cells using the RNAeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using 1000 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina) on a Sciclone liquid handling robot (PerkinElmer) using a PerkinElmer-developed automated script

value: spleen

value: CD4+ T cells

tag: passages

value: STING KO

tag: stimulation

value: 10-carboxymethyl-9-acridanone (CMA)


title: plupcrush.A

tag: cell type


title: STING KO T cells CMA 1

description:
STING KO T cells CMA 1
Sample name: 82

tag: strain

tag: genotype


title: DC90_0h

city: Nanning

first: Jijing

last: Luo

state: Guangxi

address: 100 Daxue Rd.(East)

institute: Guangxi University

data_processing:
Base calling using Illumina Casava1.7
Raw data (raw reads) were firstly processed through in-house perl scripts to remove reads containing adapter and low-quality reads to obtain clean data (clean reads). Paired-end clean reads were aligned to the reference genome using TopHatv2.0.12
HTSeq v0.6.1 was used to count the numbers of reads mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
The identifiers in fpkm.xls (e.g. EPlOING00000031521, BGIOSGA034166 etc.) are accession numbers of gene models of indica rice. They were generated in indica rice genome annotation by Beijing Institute of Genomics, Chinese Academy of Sciences. Indica rice reference genome and gene model annotation files were downloaded   from ensembl FTP server:
FA link (ftp://ftp.ensemblgenomes.org/pub/release-23/plants/fasta/oryza_sativa/dna/)
GTF link (ftp://ftp.ensemblgenomes.org/pub/release-23/plants/gtf/oryza_indica/)
Genome_build: Indica rice 9311 assembly, ASM465v1
Supplementary_files_format_and_content: excel files include FPKM values for each Sample (identifiers available at: http://plants.ensembl.org/Oryza_indica/Info/Index)

organism: Oryza sativa

source_name: rice plant

extract_protocol:
Whole plants of each sample (three replicates for each) were harvested for each genotype before and 36h time point of chilling treatment, respectively. Total RNA of each sample was isolated by TRIZOL. Equal amount (3 µg) total RNA isolated from three replicates of each sample were mixed to get four group pooled samples.
A total amount of 3 µg RNA of each pooled group was used as input material for generating sequencing libraries using NEB Next® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s instruction.

tag: line

value: chilling tolerance chromosome substitution line (CSL)

tag: age

value: 3-leaf stage seedling

value: whole plant

tag: time point

value: before chilling treatment


title: YD6_36h (YD6 the same as 9311)

value: chilling-sensitive recurrent parent

value: 36h of chilling treatment


title: YD6_0h (YD6 the same as 9311)


title: STING KO T cells DMSO 2

description:
STING KO T cells DMSO 2
Sample name: 71

value: DMSO


title: WT T cells CMA 3

description:
WT T cells CMA 3
Sample name: 12

value: wildtype


title: STING KO T cells DMSO 1

description:
STING KO T cells DMSO 1
Sample name: 81


title: WT T cells CMA 2

description:
WT T cells CMA 2
Sample name: 32


title: STING KO T cells DMSO 3

description:
STING KO T cells DMSO 3
Sample name: 51


title: DC90_36h


title: WT T cells DMSO 3

description:
WT T cells DMSO 3
Sample name: 11


title: WT T cells DMSO 2

description:
WT T cells DMSO 2
Sample name: 31


title: WT T cells DMSO 1

description:
WT T cells DMSO 1
Sample name: 41


title: H3K4me3 WM164 Dabrafenib (D2)

city: Woolloongabba

first: Helmut

last: Schaider

state: Queensland

address: level 7, 37 Kent Street

department: Diamantina Institute

country: Australia

institute: The University Of Queensland

description: Chip Sample

data_processing:
Sequencing was done on Hiseq2000. Demultiplexing was done using bcl2fastq 2.17.1.14 pipeline.
Data QC was done using fastqc, trim_galore, blast
Alignment was performed using bowtie2 (v2.2.5). Samtools was used to sort bam files.
R packages SPP v1.13 (Kharchenko, Tolstorukov, and Park,2008) and bioMart were used to call peaks and run annotation.
Genome_build: hg19
Supplementary_files_format_and_content: TDF

source_name: WM164 melanoma cells

growth_protocol: Cells were maintained in Fully supplemented RPMI media.

extract_protocol:
The extraction was done according to active motif enzymatic chip kit(53009)
Illumina Truseq ChIP library preparation, with Pippin prep size selection

treatment_protocol: Cells were treated with 50nM dabrafenib every 3 days for 50 days.

tag: chip antibody

value: H3K4me3 Active motif  (39159)


title: P4_Hes1N

city: Minato-ku, Tokyo

first: Sumiko

last: Watanabe

address: 4-6-1 Shirokane-dai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

data_processing:
bcl2fastq-1.8.4 used for basecalling with default parameters
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using TopHat (v2.0.8b) with the option (--coverage-search --max-multihits 50)
fragments per kilobase of exon per million mapped fragments (FPKM) was calculated from the aligned reads by using CuffLinks (v2.1.1) with the default option
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Retina

growth_protocol: SPF with normal feeding

extract_protocol:
total RNA was extracted using RNeasy Plus Micro Kit (Qiagen), and RNA quality was confirmed using a 2100
The first-strand cDNA was synthesized using random primers and SuperScript II (Invitrogen), and the second-strand cDNA was synthesized using RNaseH and DNA pol I (Illumina). Illumina GA sequencing adaptors were ligated to the cDNA ends. Double-stranded cDNA was size-fractionated by 6% PAGE, and cDNAs of 200 bp were recovered. cDNAs were amplified by 15 PCR cycles using Phusion DNA Polymerase (Finnzymes). Thirty-six-base-pair single-end-read RNA Seq tags were generated using an Illumina GA sequencer according to the standard protocol.

treatment_protocol: no particular treatment

value: FVB/N

value: retina

value: postnatal day 4


title: P1_Hes1N

value: postnatal day 1


title: P1_Hes1P


title: H3K4me3 WM164 Dabrafenib (D1)

description: Chip Sample


title: Input WM164 Dabrafenib treated (input)

description: Input

value: none (input)


title: H3K4me3 WM164 Parent (P1)

description: Chip Sample


title: P4_Hes1P


title: STING KO T cells CMA 2

description:
STING KO T cells CMA 2
Sample name: 62

value: spleen

value: CD4+ T cells


title: PCB-00082

city: Beaverton

first: Noah

last: Berlow

address: 12655 SW Beaverdam Rd

institute: CC-TDI

data_processing:
raw reads were aligned to the GRCh38.87 human genome using STAR aligner in paired end mode
aligned transcripts were quantified used RSEM-calculate-expression function in paired end mode
Genome_build: GRCh38.87
Supplementary_files_format_and_content: result files are In genes.results file format. These files have quantified RPKM and TPM values

source_name: autopsy

extract_protocol:
RNA extraction was performed at Beijing Genomics Institute (BGI)
RNA extraction was performed at  Oregon Health and Science University's Gene Profiling Shared Resource (OHSU GPSR)
library construction was performed at Beijing Genomics Institute (BGI)
library construction was performed at  Oregon Health and Science University's Gene Profiling Shared Resource (OHSU GPSR)

tag: disease diagnosis

value: embryonal rhabdomyosarcoma

tag: gender

value: female

value: 14 years


title: PCB-00380

source_name: resection

value: alveolar rhabdomyosarcoma

value: 2 years


title: CF-00017

value: metastatic Ewing's sarcoma

value: 22 years


title: CF-00016_3

value: metastatic alveolar rhabdomyosarcoma


title: CF-00014

value: male

value: 8 years


title: CF-00015

value: Diffuse Intrinsic Pontine Glioma

value: 4 years


title: HEB KO, rep3

first: Yang

last: Li

address: Xueyuan Road 38,Haidian District

institute: Peking University

data_processing:
First strand cDNA was generated using random primers, followed by second strand cDNA synthesis, and adapter-ligated PCR-enriched products were used to create cDNA libraries.
A single “A” base was added and adapter ligated, followed by purification and enrichment with PCR, to create cDNA libraries, which were sequenced for paired ends using the Illumina platform.
Reads for each sample were aligned to the hg19 assembly of the human genome using the Tophat v2.1.0 and Bowtie v2.2.6  software packages.
RNA-Sequencing expression calculation and normalization (FPKM) was performed by using Tophat software.
Genome_build: hg19
Supplementary_files_format_and_content: single EXCEL sheet includes normalized expression of all samples

source_name: embryonic stem cells

growth_protocol: Human H1 ESCs were maintained and expanded on plates coated with growth-factor-reduced Matrigel (Corning) in serum-free, defined TeSR-E8 medium (Stem Cell Technologies). Cells were passaged by non-enzymatic dissociation using 0.5 mM EDTA.

extract_protocol:
Total RNA was isolated from cells using TRIZOL (Invitrogen) according to the manufacturer's protocol
Libraries were prepared using TruSeq Stranded Total RNA kit (Illumina), and ribosomal RNA depleted using Ribo-zero Gold rRNA beads.

value: embryonic stem cells

tag: cell line

value: HEB KO


title: CF-00013

value: 24 years


title: CF-00002

value: 6 years


title: CF-00001

value: 1.6 years


title: whib4.input.rep2.chipseq

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

institute: Institut Pasteur

description:
Strain overexpressing WhiB4 from pEXWhiB4 plasmid.
Processed data file: WhiB4_peaks.bed

data_processing:
Samples were aligned to the Mtb H37Rv reference sequence, using BWA (version 0.7).
SAM files thus obtained were converted to BAM files using samtools view command.
BAM files of each ChIP biological replicate and the input replicate samples were converted to .bed format using bedtools.
.bed files of each ChIP biological replicate and the input replicate samples were used in the MACS2 peak caller for peak calling.
Genome_build: Mtb H37Rv reference sequence (ASM19595v2)
Supplementary_files_format_and_content: WhiB4_peaks.bed

organism: Mycobacterium tuberculosis H37Rv

source_name: Mtb cells, FLAG-tagged WhiB4, input

growth_protocol: Cells were grown to early exponential phase in 7H9 medium containing ADS (Albumin, Dextrose, Sodium chloride) as supplement.

extract_protocol:
Cells were fixed in the required growth phase in formaldehyde, quenched, washed and lysed. Fragmented DNA - protein complex were pulled using the anti-FLAG antibody. The complex was then washed, reverse cross-linked and obtained DNA purified using phenol-chloroform extraction.
TruSeq ChIP kit was used for the library preparation. DNA was end repaired and adapters were ligated. After ligation, purify ligation products and then amplify.

treatment_protocol: At OD600nm = 0.3, cells were induced with 200 ng/ml of anhydrotetracycline for 16 hrs.

tag: strain/background

tag: overexpression

value: FLAG-tagged WhiB4

tag: growth phase

value: exponential


title: CF-00004

value: 36 years


title: wildtype, rep3

value: wild type


title: HEB KO, rep2


title: HEB KO, rep1


title: whib4.input.rep1.chipseq


title: H3K4me3 WM164 Parent (P2)

description: Chip Sample

value: H3K4me3 Active motif  (39159)


title: WT T cells CMA 1

description:
WT T cells CMA 1
Sample name: 42

value: spleen

value: CD4+ T cells

value: wildtype

value: 10-carboxymethyl-9-acridanone (CMA)


title: whib4.rep2.chipseq

source_name: Mtb cells, FLAG-tagged WhiB4, FLAG ChIP

value: Anti-FLAG M2 Magnetic Beads (Sigma, M8823)


title: wildtype, rep2


title: ChGA_1_RNASeq

status: Public on Jun 23 2017

city: San Francisco

first: Duncan

last: Leitch

state: California

department: Physiology

institute: University of California - San Francisco

data_processing:
The quality of all raw sequence reads was analyzed via FASTQC, and adapters were trimmed using Scythe.
All reads were trimmer for low complexity or low quality ends (Sickle version 1.3).
Reads were then aligned to the annotated mouse reference genome (mm10) using TopHat2 (version 0.7).
Transcripts were assembled and relative abundance was estimated using Cufflinks and Cuffdiff tools.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with FPKM values for each sample

source_name: ChGA, GFP-

growth_protocol: Intestinal organoids were generated from ChgA-GFP reporter mice. The small intestine was isolated and washed with cold PBS and crypts were isolated following dissociation in EDTA. Isolated crypts were suspended in Matrigel. Following polymerization, organoid growth media containing murine epidermal growth factor,  noggin,  and 10% R-spondin conditioned media was added and refreshed every 3-4 days. Organoids were maintained at 37°C, 5% CO2 and propagated weekly

extract_protocol:
Intestinal epithelial cells from organoids were dissociated and immediately sorted by fluorescence-activated cell sorting. ~1% of total epithelial cells were GFP+ and collected. The remaining GFP- cells were retained for comparison. RNA from GFP+ and GFP- subgroups was then extracted and prepared for cDNA library generations using the SMARTer Ultra Low Input RNA kit.
The Low Input Library Prep Kit (version 2, Clontech Laboratories, Inc.).  cDNA quality was assessed via bioanalyzer using the High Sensitivity DNA kit (Agilent Technologies), and high quality samples were preserved for sequencing

value: ChgA-GFP

tag: organoid

value: Intestinal organoid

value: Intestinal epithelial cells

tag: cell subgroup

value: GFP- fluorescently sorted cells


title: ChGA_2_RNASeq

source_name: ChGA, GFP+

value: GFP+ fluorescently sorted cells


title: wildtype, rep1

value: embryonic stem cells


title: Input WM164 parent (input)

description: Input

value: none (input)


title: whib4.rep1.chipseq

value: FLAG-tagged WhiB4


title: TPC1-Vector rep1 RNA-seq

first: Weiwei

last: Liang

address: 58 Zhongshan Road II

institute: The First Affiliated Hospital of Sun Yat-sen University

description:
Vector control
processed data file: processed results.xls

data_processing:
Basecalling was done using CASAVA.
Reads Count was counted by Cufflinks v2.1.1, and FPKM was then calculated to estimate the expression level of genes.
Cuffdiff was used to assess differential expression.
Genome_build: hg38
Supplementary_files_format_and_content: processed results.xls: Excel file includes normalized results.

source_name: thyroid cancer cells

growth_protocol: TPC1 cells were maintained in DMEM plus 10% FBS.

extract_protocol:
Total RNA was extracted using Trizol.
Libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

treatment_protocol: Cells were transfected with vector control, or vector expressing C1orf106. Stable cell lines were selected by treatment with 0.5 μg/mL puromycin for two weeks.

value: papillary thyroid cancer cells

tag: transfection

value: Vector


title: TPC1-C1orf106 rep1 RNA-seq

description:
C1orf106 overexpression
processed data file: processed results.xls


title: Control Pravastatin biological replicate 2

city: London

first: ian

middle: james

last: holt

address: 1 Midland Road

country: United Kingdom

institute: Crick Institute

description:
Strand-specific RNA-Seq
allSamples_RNASeq_RSEM_TPM.tsv.gz

data_processing:
The RSEM package (version 1.2.29) (Li and Dewey, 2011) was used for the alignment and subsequent gene-level counting of the sequenced reads with respect to hg19 Ensembl genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 14th April 2016.
Differential expression analysis was performed with DESeq2 (version 1.10.1) (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

source_name: human fibroblasts

growth_protocol: Cells were grown in Dulbecco's minimum essential medium (DMEM) containing 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
Total cell RNA was prepared from ~8 million cells using Trizol reagent (Sigma) following the manufacturer's protocol.
Purified total RNA was quantified by Nano drop and quality checked using the Agilent Bioanalyser. Samples that showed minimal degradation as measured by RNA integrity number (RIN) > 8.0 were further processed for Illumina sequencing with the TruSeq Stranded mRNA HT Sample Prep Kit (Illumina, Part# RS-122-2103). The starting amount of total RNA for all samples was 1ug. Resulting libraries were quantified and quality control checked for size and primer dimer contamination. Libraries with sizes below 500bp and very low (<5%) primer dimer contamination were sequenced on the Illumina HiSeq 4000 with the paired-end 101bp dual indexing protocol. FastQ files were generated using CASAVA BCL to FastQ (version 2.16).

treatment_protocol: Samples labeled pravastatin were from cells grown in the presence of 5 µM pravastatin for 7 days prior to RNA extraction.

tag: treatment

value: Pravastatin


title: Control Pravastatin biological replicate 3


title: Patient 2 ATAD3F Pravastatin biological replicate 2


title: Patient 2 ATAD3F Pravastatin biological replicate 3


title: Control Pravastatin biological replicate 1


title: Patient 2 ATAD3F Pravastatin biological replicate 1


title: Control biological replicate 2

value: untreated


title: Patient 1 ATAD3CAS Pravastatin biological replicate 2


title: Control biological replicate 1


title: Patient 2 ATAD3F biological replicate 3


title: Patient 1 ATAD3CAS biological replicate 1


title: Patient 1 ATAD3CAS Pravastatin biological replicate 1


title: TAA_Low_7day_47

city: Jefferson

first: Yuping

last: Wang

state: AR

address: 3900 NCTR RD

department: National Center for Toxicological Research

institute: Food and Drug Administration

data_processing:
The sequencing data were de-multiplexed and transformed to fastq data files.
The miRNA sequencing data first underwent 3’ end adapter trimming.
The trimmed reads were then filtered by read length between 18-25 nt.
The quality of samples was assessed by FastQC tool and all the samples passed the Phred quality score cutoff of 30 (99.9% base call accuracy).
The miRDeep2 pipeline was utilized for the mapping of the reads to miRBase Release 21 and the quantification.
Genome_build: UCSC rn5
Supplementary_files_format_and_content: tabular, read count

organism: Rattus norvegicus

source_name: liver tissue

extract_protocol:
Total RNA was isolated from approximately 15 mg liver sections using miRVanaTM isolation kit (Ambion® ThermoFisher Scientific, Grand Island, NY, USA) according to manufacturer's protocol. The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260 nm (Nanodrop-1000, Thermo Scientific, Wilmington, DE, USA). The quality of RNA samples was characterized on an Agilent BioAnalyzer (Agilent Technologies, Santa, Clara, CA, USA) using an RNA6000 Nano Chip (Agilent Technologies). RNA integrity numbers (RINs) greater than 8.0 were used for NGS analysis with an average of 9.2 for all samples.
1 µg of extracted total RNA was used for miRNA-seq library preparation using Illumina TruSeq small RNA sample preparation kit. Each RNA sample was processed individually by adding special bar-coded adaptors and reverse transcriptase and amplified. The quantity and quality of each library was measured by Picogreen DNA quantification and Bioanalyzer high sensitive Pico chips (Agilent Technologies). Forty eight barcoded libraries were then pooled by mixing equi-molar of DNA. The pooled libraries were then loaded onto 6% high resolution PAGE gel for separation of miRNA from other RNAs. The bands with the molecular weight between 145-160 bp were excised into recovery tubes for gel purification. The recovered barcoded libraries were then sequenced by the Illumina HiSeq2000 platform with single end base pair reads.

tag: dose

value: Low

tag: treatment duration

value: 7 days

tag: Sex

value: male

value: Sprague-Dawley (SD)


title: TAA_Low_7day_48

tag: strain


title: TAA_Low_3day_45

value: 3 days


title: TAA_Low_3day_44


title: TPC1-Vector rep2 RNA-seq

tag: cell type


title: Patient 1 ATAD3CAS Pravastatin biological replicate 3


title: TPC1-C1orf106 rep2 RNA-seq


title: TAA_Low_14day_42

value: 14 days


title: TAA_Low_3day_43


title: TAA_Low_7day_46


title: TAA_Low_14day_40


title: TAA_Low_14day_41


title: TAA_Middle_28day_38

value: Middle

value: 28 days


title: TAA_Middle_28day_39


title: TAA_Middle_7day_36


title: TAA_Middle_28day_37


title: TAA_Middle_7day_35


title: TAA_Middle_7day_34


title: TAA_Middle_14day_32


title: TAA_Middle_14day_33


title: Patient 2 ATAD3F biological replicate 2


title: Patient 2 ATAD3F biological replicate 1


title: TAA_Low_28day_29


title: TAA_Middle_14day_31


title: TAA_High_7day_26

value: High


title: TAA_High_7day_27


title: TAA_Low_28day_28


title: RNA_IFN_TL_rep2

city: New York

first: Lionel

last: Ivashkiv

address: 535 E 70th St

institute: Hospital For Special Surgery

description:
mRNA-seq
RNA_IFN_TL_rep2.fastq

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed(http://www.bioinformatics.babraham.ac.uk/project/trim_galore).
Sequenced reads were mapped to reference human genome (hg19 assembly) using STAR aligner (2.5.2b, Dobin et al., 2013 Bioinformatics) with default parameters.
Cufflinks version 2.2.1 (Trapnell et al., 2012 Nat Protoc) was used to estimate the abundance of transcripts.
Genome_build: hg19

source_name: Primary human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).

extract_protocol:
RNA extraction kit from QIAGEN, according to company's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with or without TNF (10ng/ml) and IFNA (25ng/ml) for 24 hours and LPS (10ng/ml) for 3 hours.

tag: tissue

value: peripheral blood

value: monocytes


title: RNA_IFN_TL_rep1

description:
mRNA-seq
RNA_IFN_TL_rep1.fastq


title: TAA_High_7day_25


title: RNA_IFN_T_rep3

description:
mRNA-seq
RNA_IFN_T_rep3.fastq


title: TAA_High_3day_24


title: RNA_IFN_TL_rep3

description:
mRNA-seq
RNA_IFN_TL_rep3.fastq


title: RNA_IFN_T_rep2

description:
mRNA-seq
RNA_IFN_T_rep2.fastq


title: TAA_High_3day_22


title: RNA_IFN_L_rep3

description:
mRNA-seq
RNA_IFN_L_rep3.fastq


title: TAA_High_28day_21


title: RNA_IFN_L_rep2

description:
mRNA-seq
RNA_IFN_L_rep2.fastq


title: TAA_High_28day_20


title: TAA_High_3day_23


title: RNA_IFN_L_rep1

description:
mRNA-seq
RNA_IFN_L_rep1.fastq


title: RNA_IFN_rep2

description:
mRNA-seq
RNA_IFN_rep2.fastq


title: TAA_High_28day_19


title: Control_28day_18

value: Control


title: Control_28day_17


title: TAA_Low_28day_30


title: RNA_IFN_T_rep1

description:
mRNA-seq
RNA_IFN_T_rep1.fastq


title: RNA_IFN_rep3

description:
mRNA-seq
RNA_IFN_rep3.fastq


title: RNA_IFN_rep1

description:
mRNA-seq
RNA_IFN_rep1.fastq


title: Control_28day_16


title: Control_14day_15


title: RNA_TL_rep2

description:
mRNA-seq
RNA_TL_rep2.fastq


title: RNA_TL_rep3

description:
mRNA-seq
RNA_TL_rep3.fastq


title: Control_14day_14


title: RNA_T_rep3

description:
mRNA-seq
RNA_T_rep3.fastq


title: RNA_TL_rep1

description:
mRNA-seq
RNA_TL_rep1.fastq


title: RNA_T_rep2

description:
mRNA-seq
RNA_T_rep2.fastq


title: RNA_T_rep1

description:
mRNA-seq
RNA_T_rep1.fastq


title: Control_14day_13


title: RNA_L_rep3

description:
mRNA-seq
RNA_L_rep3.fastq


title: TAA_Middle_3day_10


title: TAA_High_14day_9


title: TAA_Middle_3day_11


title: RNA_L_rep1

description:
mRNA-seq
RNA_L_rep1.fastq


title: TAA_High_14day_7


title: TAA_High_14day_8


title: Control_7day_6


title: Control_7day_5


title: RNA_N_rep3

description:
mRNA-seq
RNA_N_rep3.fastq


title: RNA_N_rep1

description:
mRNA-seq
RNA_N_rep1.fastq


title: Control_3day_2


title: Control_3day_3


title: ChIP_IRF1_N

description:
antibody: anti-IRF1 (SantaCruz Tech sc-497)
ChIP_IRF1_N.fastq

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed.
Sequenced reads were mapped to reference human genome (hg19 assembly) using BWA with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: peak

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit.


title: ChIP_p65_T

description:
antibody: anti-p65 (SantaCruz Tech sc-372)
ChIP_p65_T.fastq


title: Control_7day_4


title: ChIP_H3K27ac_TL

description:
antibody: anti-H3K27ac (Abcam ab4729)
ChIP_H3K27ac_TL.fastq


title: ChIP_p65_N

description:
antibody: anti-p65 (SantaCruz Tech sc-372)
ChIP_p65_N.fastq


title: HPIP2 ChIPseq

first: Quanbo

last: Ji

address: #28, Fuxing Road.

institute: The 301 hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP was performed as previously described. Briefly, For HPIP ChIP, 3×106 chondrocytes were fixed in 37% formaldehyde, pelleted, and resuspended in lysis buffer. The cells were sonicated and centrifuged to remove insoluble material. The supernatants were collected, and Pellet Protein G magnetic beads were added and incubated for 1 hour at 4°C with anti-HPIP (Proteintech, 1:50, 12102-1-AP). The chromatin was collected, purified, and de-crosslinked at 62°C for 2 h, followed by incubation at 95°C for 10 min. The DNA was isolated using the ChIP DNA Clean & Concentrator (Zymo Research Corp.) according to the manufacturer’s instructions. 100ng DNA fragments were used per ChIP. Sequencing libraries were prepared from collected HPIP ChIP and corresponding input DNA by blunting, A-tailing, adaptor ligation using NEXTFlex barcoded adapters (Bioo Scientific). Libraries were PCR-amplified for 16 cycles, fragments size of 300bp were processed using the Covaris Focused-ultrasonicators (Covaris, Inc. S220). Sequencing was performed using the Hi-Seq 2500 (Illumina) platform
Data were filtered using the following specifications…
Genomic binding peaks for HPIP were identified using the findPeaks command from HOMER (http://homer.salk.edu/homer/) with 8-fold enrichment over the input sample. Peaks were annotated using the annotatePeaks command. HPIP-related transcription factor binding motifs were performed with command findMotifsGenome.pl using a standard background as the random genomic sequence.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig files are created using the program wigToBigWig, files include genomic binding peaks value and fold enrichments for each sample

source_name: Cartilage

extract_protocol:
Lysates were clarified from sonicated nuclei and HPIP-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Chondrocytes

tag: passages

value: Primary

tag: chip antibody

value: HPIP antibody (Proteintech, 2102-1-AP)


title: ChIP_IRF1_IFN_T

description:
antibody: anti-IRF1 (SantaCruz Tech sc-497)
ChIP_IRF1_IFN_T.fastq


title: Control_3day_1


title: HPIP1 ChIPseq


title: TAA_Middle_3day_12


title: ChIP_H3K27ac_T

description:
antibody: anti-H3K27ac (Abcam ab4729)
ChIP_H3K27ac_T.fastq


title: Input1 DNA


title: RNA_N_rep2

description:
mRNA-seq
RNA_N_rep2.fastq


title: HPIP KO RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

extract_protocol:
Total RNA was extracted and reverse-transcribed into cDNA using a RNeasy Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cartilage


title: Input2 DNA


title: ChIP_H3K27ac_N

description:
antibody: anti-H3K27ac (Abcam ab4729)
ChIP_H3K27ac_N.fastq


title: ChIP_H4ac_L

description:
antibody: anti-H4ac (Millipore 06-866)
ChIP_H4ac_L.fastq


title: ChIP_H4ac_TL

description:
antibody: anti-H4ac (Millipore 06-866)
ChIP_H4ac_TL.fastq


title: ChIP_H4ac_N

description:
antibody: anti-H4ac (Millipore 06-866)
ChIP_H4ac_N.fastq


title: Flag-NF90 iCLIP rep2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome with the UCSC Genes annotation (hg19 knownGene.txt updated at 2013/6/30) using TopHat2 (Kim et al., 2013) 2.0.9 (parameters: -g 1 -a 6 --microexon-search -m 2).
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: bed file

source_name: Flag-NF90 iCLIP

growth_protocol: HeLa cells (Human cervical cancer cells) were cultured with DMEM medium supplemented with 10% FBS.

extract_protocol:
For iCLIP-seq, The UV-crosslinked cells were resuspended in lysis buffer and sonicated for 20s x 6 times on 25% duty. by immunoprecipitaiton with 8 µg anti-Flag (ShangHai Genomics) antibody at 4°C for 2 hours. Beads with protein-RNA complexes with 5 µg yeast tRNAs were treated with 5 Kunz U/ml of micrococcal nuclease for 5 min at 37°C, and RNA 3’ ends were dephosphorylated by PNK at pH6.5. Then pre-adenylated linker L3 (3’ modification with biotin) was linked to 3’ end of RNA at 16°C overnight. 5’ end of RNA was labeled with [γ- 32P] ATP and eluted with 1x Nupage loading buffer (Invitrogen) at 70°C for 10 min. Protein-RNA complexes were eluted with 1xNuPAGE loading buffer. Complexes were separated on 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane and exposure to a Fuji film at -80℃. Protein-RNA complexes were digested with proteinase K and RNA were reverse transcribed by Superscript III reverse transcriptase (Invitrogen) with Rclip primers. cDNAs were separated on 6% TBE-urea gel, then three bands were cut at 120-200 nt (high), 85-120 nt (medium) and 70-85 nt (low). cDNAs were circularized by Circligase II (Epicentre). Single-stranded cDNAs were hybridized with cut_oligo, and then digested by BamHI. Linearized cDNAs were PCR amplified and purified on PAGEs to obtain iCLIP libraries.
For iCLIP-seq, the protein-RNA complexes were treated with 5 Kunz U/ml of micrococcal nuclease with 5 μg yeast tRNAs for 5 min at 37°C, and RNA 3’ ends were dephosphorylated by PNK at pH6.5. Then pre-adenylated linker L3 (3’ modification with biotin) was linked to 3’ end of RNA at 16°C overnight. 5’ end of RNA was labeled with [γ-32P] ATP and eluted with 1x Nupage loading buffer (Invitrogen) at 70°C for 10 min. Complexes were separated on 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane and exposure to a Fuji film at -80℃. Protein-RNA complexes were digested with proteinase K, and RNA were reverse transcribed by Superscript III reverse transcriptase (Invitrogen) with Rclip primers. cDNAs were separated on 6% TBE-urea gel, then three bands were cut at 120-200 nt (high), 85-120 nt (medium) and 70-85 nt (low).cDNAs were circularized by Circligase II (Epicentre). Single-stranded cDNAs were hybridized with cut_oligo, and then digested by BamHI. Linearized cDNAs were PCR amplified and purified on PAGEs to obtain iCLIP libraries, which were subjected to Illumina HiSeq 2500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For iCLIP-seq, Flag-NF90 overexpressed Hela cells were washed with cold 1xPBS, and UV cross-linked at 400mJ/cm2 and collected by scraper.

value: HeLa

tag: genotype/variation

value: expressing Flag-NF90

tag: antibody

value: anti-Flag

tag: barcode sequence

value: NNNGCCGNN


title: Ctrl1 RNA-seq


title: Flag-NF90 iCLIP

description:
Flag-NF90 iCLIP
HeLa_iCLIP_NF90.bed

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome with the UCSC Genes annotation (hg19 knownGene.txt updated at 2013/6/30) using TopHat2 (Kim et al., 2013) 2.0.9 (parameters: -g 1 -a 6 --microexon-search -m 2).
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: HeLa cells

extract_protocol:
For total RNA, 10μg of total RNAs isolated from HeLa cells were separated into polyadenylated and nonpolyadenylated fractionations by oligo(dT) magnetic beads (Invitrogen). The polyadenylated RNA population was purified by oligo(dT) magnetic beads and followed by DNase I treatment at 37 °C for 30 mins (Ambion, DNA-freeTM Kit). Ribosomal RNAs were further depleted by using RiboMinus kit (Invitrogen) (Yang et al., 2011) to get the poly (A)-/ribo- RNA population. Then poly (A)-/ribo- RNAs were subjected to Trizol extraction.
For nascent RNA, 100-140 μg total RNA was used for biotinylation and purification of 4sU labeled nascent RNA. 4sU labeled RNA was biotinylated in biotinylation buffer (10 mM Tris pH 7.4, 1 mM EDTA) with 0.2 mg/ml EZ-link biotin-HPDP (Pierce, 21341), which was dissolved in dimethylformamide (DMF, Sigma, D4551) at a concentration of 1 mg/ml, and incubated at room temperature for 1.5 h with rotation. Unbound biotin-HPDP was removed by equal volume chloroform extraction twice, and RNA was precipitated at 1,3000 rpm for 15min at 4℃ with 1:10 volume of 5 M NaCl and an equal volume of isopropanol. The RNA pellet was washed twice with 75% ethanol and resuspended in 150 μl DEPC•H2O. RNA quality was checked by electrophoretical analysis to exclude RNA degradation. 4sU labeled and unlabeled RNA was separated by using Streptavidin-coated magnetic beads (Invitrogen). Biotinylated RNA was incubated with 150 μl Streptavidin beads at room temperature for 20 min. Beads were washed four times with 0.9 ml of 65 ℃ washing buffer (100 mM Tris pH 7.4, 10 mM EDTA, 1 M NaCl, 0.1% Tween 20), followed by four times with 0.9 ml of room temperature washing buffer. Nascent RNA was eluted with 100 μl 0.1 M dithiotheitol (DTT) twice, and RNA was precipitated with 40 μl of 4 M LiCl, 2 μl glycogen and 600 μl ice-cold ethanol. Before preparation of nascent RNA-seq library, ribosomal RNA was depleted from 4sU labeled RNAs with RiboMinusTM Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01) according to the manufacturer’s protocol.
For iCLIP-seq, The UV-crosslinked cells were resuspended in lysis buffer and sonicated for 20s x 6 times on 25% duty. by immunoprecipitaiton with 8 µg anti-Flag (ShangHai Genomics) antibody at 4°C for 2 hours. Beads with protein-RNA complexes with 5 µg yeast tRNAs were treated with 5 Kunz U/ml of micrococcal nuclease for 5 min at 37°C, and RNA 3’ ends were dephosphorylated by PNK at pH6.5. Then pre-adenylated linker L3 (3’ modification with biotin) was linked to 3’ end of RNA at 16°C overnight. 5’ end of RNA was labeled with [γ- 32P] ATP and eluted with 1x Nupage loading buffer (Invitrogen) at 70°C for 10 min. Protein-RNA complexes were eluted with 1xNuPAGE loading buffer. Complexes were separated on 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane and exposure to a Fuji film at -80℃. Protein-RNA complexes were digested with proteinase K and RNA were reverse transcribed by Superscript III reverse transcriptase (Invitrogen) with Rclip primers. cDNAs were separated on 6% TBE-urea gel, then three bands were cut at 120-200 nt (high), 85-120 nt (medium) and 70-85 nt (low). cDNAs were circularized by Circligase II (Epicentre). Single-stranded cDNAs were hybridized with cut_oligo, and then digested by BamHI. Linearized cDNAs were PCR amplified and purified on PAGEs to obtain iCLIP libraries.
For total RNA and nascent RNA, 4sUDRB and ribo– RNA-seq libraries were prepared with Illumina TruSeq RNA Sample Prep Kit v2 (P/N 15026495) without oligo(dT) enrichment. Deep sequencing was performed on Illumina Hiseq 2500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.
For iCLIP-seq, the protein-RNA complexes were treated with 5 Kunz U/ml of micrococcal nuclease with 5 μg yeast tRNAs for 5 min at 37°C, and RNA 3’ ends were dephosphorylated by PNK at pH6.5. Then pre-adenylated linker L3 (3’ modification with biotin) was linked to 3’ end of RNA at 16°C overnight. 5’ end of RNA was labeled with [γ-32P] ATP and eluted with 1x Nupage loading buffer (Invitrogen) at 70°C for 10 min. Complexes were separated on 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane and exposure to a Fuji film at -80℃. Protein-RNA complexes were digested with proteinase K, and RNA were reverse transcribed by Superscript III reverse transcriptase (Invitrogen) with Rclip primers. cDNAs were separated on 6% TBE-urea gel, then three bands were cut at 120-200 nt (high), 85-120 nt (medium) and 70-85 nt (low).cDNAs were circularized by Circligase II (Epicentre). Single-stranded cDNAs were hybridized with cut_oligo, and then digested by BamHI. Linearized cDNAs were PCR amplified and purified on PAGEs to obtain iCLIP libraries, which were subjected to Illumina HiSeq 2500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.
RNA-Seq and RIP-seq

treatment_protocol:
For total RNA, HeLa cells (Human cervical cancer cells) were cells were washed by DPBS (GIBCO), trypsinized, and collected by centrifugation.
For nascent RNA, HeLa cells (Human cervical cancer cells) were transfected with poly (I:C) for 6 hour, then incubated with 100 μM DRB (Sigma, D1916) for 3 h to block Pol II transcription. Transcription was recovered after DRB release and newly transcribed RNA was labeled with 200 μM 4sU (Sigma, T4509). TRizol (Invitrogen) was added to stop transcription and total RNA was extracted after 2hr.
For iCLIP-seq, Flag-NF90 overexpressed Hela cells were washed with cold 1xPBS, and UV cross-linked at 400mJ/cm2 and collected by scraper.

tag: cell line

tag: type

value: HeLa with expressing Flag-NF90

value: NNNGGCGNN


title: ChIP_H3K4me3_IFN_TL

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_IFN_TL.fastq


title: HeLa nascent 2hr NF110 KD control ribo– RNA replicate 2

description:
HeLa nascent 4sU-labeled 2hr NF110 KD control ribo– RNA technical replicate 2
Hela_4sU_NF110_KD_control.bw

value: nascent RNA labeled with 4sU 2hr ribo- RNA

value: 3 hr DRB 2hr 4sU-labeling


title: ChIP_H3K4me3_IFN_T

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_IFN_T.fastq


title: ChIP_H3K4me3_IFN_L

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_IFN_L.fastq


title: HeLa nascent 2hr NF110 KD control ribo– RNA replicate 1

description:
HeLa nascent 4sU-labeled 2hr NF110 KD control ribo– RNA technical replicate 1
Hela_4sU_NF110_KD_control.bw


title: ChIP_H3K4me3_IFN

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_IFN.fastq


title: HeLa nascent 2hr NF90 KD control ribo– RNA

description:
HeLa nascent 4sU-labeled 2hr NF90 KD control ribo– RNA
Hela_4sU_NF90_KD_control.bw


title: HeLa nascent 2hr scramble poly(I:C) ribo– RNA replicate 2

description:
HeLa nascent 4sU-labeled 2hr scramble poly(I:C) ribo– RNA technical replicate 2
Hela_4sU_scramble_polyIC.bw

value: 6hr poly (I:C) 3 hr DRB 2hr 4sU-labeling


title: ChIP_H3K27ac_L

description:
antibody: anti-H3K27ac (Abcam ab4729)
ChIP_H3K27ac_L.fastq


title: ChIP_H3K4me3_TL_rep1

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_TL_rep1.fastq


title: ChIP_H3K4me3_T_rep2

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_T_rep2.fastq


title: HeLa nascent 2hr scramble poly(I:C) ribo– RNA replicate 1

description:
HeLa nascent 4sU-labeled 2hr scramble poly(I:C) ribo– RNA technical replicate 1
Hela_4sU_scramble_polyIC.bw


title: HeLa nascent 2hr scramble control ribo– RNA replicate 2

description:
HeLa nascent 4sU-labeled 2hr scramble control ribo– RNA technical replicate 2
Hela_4sU_scramble_control.bw


title: HeLa NF110 KD ribo–/poly(A)– RNA replicate 2

description:
HeLa steady-state NF110 KD ribo–/poly(A)– RNA technical replicate 2
HeLa_NF110_KD_polyAminus.bw

value: steady-state ribo-/poly(A)- RNA

value: untreated


title: ChIP_H3K4me3_TL_rep2

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_TL_rep2.fastq

value: peripheral blood

value: monocytes


title: HeLa NF110 KD ribo–/poly(A)– RNA replicate 1

description:
HeLa steady-state NF110 KD ribo–/poly(A)– RNA technical replicate 1
HeLa_NF110_KD_polyAminus.bw


title: ChIP_H3K4me3_L_rep2

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_L_rep2.fastq


title: ChIP_H3K4me3_N_rep2

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_N_rep2.fastq


title: ChIP_H3K4me3_N_rep1

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_N_rep1.fastq


title: ChIP_H3K4me3_T_rep1

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_T_rep1.fastq


title: HeLa NF90 KD ribo–/poly(A)– RNA replicate 1

description:
HeLa steady-state NF90 KD ribo–/poly(A)– RNA technical replicate 1
HeLa_NF90_KD_polyAminus.bw


title: ChIP_H2Bub_IFN_TL

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_IFN_TL.fastq


title: HeLa scramble ribo–/poly(A)– RNA replicate 2

description:
HeLa steady-state scramble ribo–/poly(A)– RNA technical replicate 2
HeLa_scramble_polyAminus.bw


title: HeLa scramble ribo–/poly(A)– RNA replicate 1

description:
HeLa steady-state scramble ribo–/poly(A)– RNA technical replicate 1
HeLa_scramble_polyAminus.bw


title: HeLa NF110 KD poly(A)+ RNA

description:
HeLa NF110 KD poly(A)+ RNA
HeLa_NF110_KD_polyAplus.bw

value: poly(A)+ RNA


title: HeLa NF90 KD poly(A)+ RNA

description:
HeLa NF90 KD poly(A)+ RNA
HeLa_NF90_KD_polyAplus.bw


title: HeLa nascent 2hr scramble control ribo– RNA replicate 1

description:
HeLa nascent 4sU-labeled 2hr scramble control ribo– RNA technical replicate 1
Hela_4sU_scramble_control.bw


title: ChIP_H2Bub_IFN

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_IFN.fastq


title: RF_M_plus_rep4

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

institute: Tel Aviv University

data_processing:
Sequenced reads were first trimmed for adaptor sequences and then aligned against the human transcriptome (each gene represented by its canonical transcript). Only uniquely mapped reads were used in subsequent analyses.
RNA expression levels and ribosome occupancy were estimated by calculating reads per kilobase of mRNA per million reads (RPKM) per transcript, taking into account either all reads that map to the transcript (for estimation of RNA levels using RNA-seq data) or only those mapping to its CDS (for estimation of ribosome occupancy).
In estimation of ribosome occupancy in CDS, 5' ends of reads were offset 12 nucleotides to the 3' direction to match the P-site location of ribosome.
Expression estimates were further normalized using quantile normalization.
Only genes with expression level of at least 1.0 RPKM, in either the treated or control conditions, in both the RNA-seq and Ribo-seq datasets were included in subsequent analyses.
Genome_build: The combined dataset includes 10,996 genes.
Supplementary_files_format_and_content: Excel file with RPKM values per sample that were further normalized using quantile normalization. To avoid inflation of FC estimates due to low levels, RPKM levels below 1.0 were set to a floor level of 1.0.

source_name: HeLa S3

growth_protocol: HeLa S3 cells or their stable shRNA expressing derivatives were cultured in DMEM supplemented with 10% fetal calf serum, 2 mM L-glutamine and 100 U/ml penicillin/streptomycin  at 37°C in 5% CO2. Synchronization was done using double-thymidine block.

extract_protocol:
Cells were harvested and lysed in lysis buffer containing 20 mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1m M DTT, 100 µg/ml Cycloheximide, 1% Triton X-100 and 25 U/ml DNase I. Samples were treated with RNase I to generate ribosome footprints, whereas an undigested portion was used to isolate total mRNA using poly-dT agarose.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Expression of shRNA and thus, induction of hnRNP C knockdown was achieved by treatment with 0.5 ug/ml Doxycyclin for 3 days.

value: treated with Dox to induce knockdown


title: HeLa scramble poly(A)+ RNA

description:
HeLa scramble poly(A)+ RNA
HeLa_scramble_polyAplus.bw


title: ChIP_H2Bub_TL_rep2

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_TL_rep2.fastq


title: RF_M_plus_rep2


title: ChIP_H2Bub_TL_rep1

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_TL_rep1.fastq


title: RF_M_plus_rep3


title: ChIP_H3K4me3_L_rep1

description:
antibody: anti-H3K4me3 (Abcam ab8580)
ChIP_H3K4me3_L_rep1.fastq


title: ChIP_H2Bub_T_rep2

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_T_rep2.fastq


title: ChIP_H2Bub_T_rep1

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_T_rep1.fastq


title: HeLa NF90 KD ribo–/poly(A)– RNA replicate 2

description:
HeLa steady-state NF90 KD ribo–/poly(A)– RNA technical replicate 2
HeLa_NF90_KD_polyAminus.bw


title: RF_M_plus_rep1


title: ChIP_H4ac_T

description:
antibody: anti-H4ac (Millipore 06-866)
ChIP_H4ac_T.fastq


title: RF_M_min_rep4


title: RF_M_min_rep3


title: ChIP_H2Bub_L_rep2

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_L_rep2.fastq


title: ChIP_H2Bub_L_rep1

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_L_rep1.fastq


title: ChIP_H2Bub_IFN_T

description:
antibody: anti-H2Bub (Cell Signaling Tech 5546)
ChIP_H2Bub_IFN_T.fastq