title: Exp015-2_H3K4me3_1000c_Ad_BC08_15u

description: Mint-ChIP


title: Exp015-2_H3K4me3_1000c_Ad_BC07_30u

status: Public on Oct 27 2015

type: SRA

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

country: USA

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

description: Mint-ChIP

library_source: genomic

data_processing:
Provided fastq files are already demultiplexed according to adapter barcode and trimmed.
Alignment: BWA paired-end alignment to hg19
Filter1: Remove all unmapped reads and reads with X0 > 2 from bam files
Filter2: Remove all PCR duplicates using PicardTools MarkDuplicates with REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT
Filter3: Of pairs with identical R1 starting position alignment, keep only the pair with the longest fragment size.
Make tdf files using igvtools count --includeDuplicates --pairs
Genome_build: hg19
Supplementary_files_format_and_content: For visualization in IGV, tdf files are provided.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: K562 cells and mouse YAC-1 cells were cultured in RPMI with 10% FCS, penicillin-streptomycin and L-glutamine. Pfeiffer, SKM-1 and Toledo were cultured in RPMI with 20% FCS, penicillin-streptomycin, L-glutamine and β-mercaptoethanol (3.5 µl in 1000 ml).

extract_protocol:
Cell lysis immediately followed by MNase digestion of native chromatin, T7-adapter ligation, pool-and-split multiplexing, immunoprecipitation and magnetic bead isolation of immunoprecipitated DNA.
Mint-ChIP: In vitro transcription, reverse transcription, PCR (see manuscript).

treatment_protocol: K562 cells were treated for 48 hours with C646 (25 µM), 48 hours with GSK126 (2 µM), or 96 hours with KDM5-C70 (5 µM). Pfeiffer, SKM-1 and Toledo were treated for 72 hours with GSK126 (1 µM).

tag: experiment

tag: histone modification

tag: cell number

tag: mnase units

tag: treatment


title: Exp015-2_H3K4me3_5000c_Ad_BC05_150u

description: Mint-ChIP


title: Exp015-2_H3K4me3_5000c_Ad_BC06_60u

description: Mint-ChIP


title: Exp015-2_H3K27me3_80000c_Ad_BC08_15u

description: Mint-ChIP


title: Exp015-2_H3K4me3_80000c_Ad_BC06_60u

description: Mint-ChIP


title: Exp015-2_H3K27me3_80000c_Ad_BC07_30u

description: Mint-ChIP


title: Exp015-2_H3K27me3_80000c_Ad_BC06_60u

description: Mint-ChIP


title: Exp015-2_H3K4me3_1000c_Ad_BC01_300u

description: Mint-ChIP


title: Exp015-2_H3K27me3_80000c_Ad_BC01_300u

description: Mint-ChIP


title: Exp015-2_H3K4me3_500c_Ad_BC08_15u

description: Mint-ChIP


title: Exp015-2_H3K27me3_500c_Ad_BC07_30u

description: Mint-ChIP


title: Exp015-2_H3K27me3_500c_Ad_BC08_15u

description: Mint-ChIP


title: Exp015-2_H3K27me3_500c_Ad_BC05_150u

description: Mint-ChIP


title: Exp015-2_H3K27me3_500c_Ad_BC01_300u

description: Mint-ChIP


title: Exp015-2_H3K27me3_500c_Ad_BC06_60u

description: Mint-ChIP


title: Exp015-2_H3K27me3_1000c_Ad_BC05_150u

description: Mint-ChIP


title: Exp015-2_H3K27me3_5000c_Ad_BC06_60u

description: Mint-ChIP


title: Exp015-2_H3K27me3_1000c_Ad_BC07_30u

description: Mint-ChIP


title: Exp015-2_H3K27me3_5000c_Ad_BC07_30u

description: Mint-ChIP


title: Exp015-2_H3K27me3_5000c_Ad_BC05_150u

description: Mint-ChIP


title: Exp015-2_H3K27me3_1000c_Ad_BC08_15u

description: Mint-ChIP


title: Exp015-2_H3K27me3_5000c_Ad_BC01_300u

description: Mint-ChIP


title: Exp004-2_H3K4me3_500c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K4me3_500c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K4me3_500c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K4me3_5000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp015-2_H3K27me3_80000c_Ad_BC05_150u

description: Mint-ChIP


title: Exp004-2_H3K4me3_500c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3K4me3_5000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K4me3_5000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K4me3_5000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K4me3_1000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3K4me3_1000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K4me3_1000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K4me3_1000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K4me3_100000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp015-2_H3K27me3_5000c_Ad_BC08_15u

description: Mint-ChIP


title: Exp004-2_H3K4me3_100000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K4me3_100000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp015-2_H3K27me3_1000c_Ad_BC06_60u

description: Mint-ChIP


title: Exp015-2_H3K27me3_1000c_Ad_BC01_300u

description: Mint-ChIP


title: Exp004-2_H3K4me3_500c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K4me3_1000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K4me3_5000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K4me3_100000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K27me3_500c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3K27me3_500c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K27me3_5000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3K27me3_5000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K27me3_5000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K27me3_5000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K27me3_1000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3K27me3_500c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K27me3_1000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K27me3_500c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K27me3_1000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K4me3_100000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K27ac_500c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K27me3_100000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K27me3_100000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3K27me3_100000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K27ac_500c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K27me3_1000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K27me3_1000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K27me3_100000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K27ac_500c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K27ac_5000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K27ac_500c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3K27me3_5000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K27ac_500c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K27me3_500c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K27ac_5000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3K27ac_5000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K27ac_5000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K27me3_100000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K27ac_1000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K27ac_5000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K27ac_1000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K27ac_1000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3K27ac_100000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3K27ac_100000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3K27ac_100000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3K27ac_100000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3_500c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K27ac_1000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3K27ac_100000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3_5000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3_500c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3_500c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3_500c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3_5000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3_5000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3_5000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3_5000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3_1000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3_1000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3_1000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3_1000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3K27ac_1000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3_1000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp004-2_H3_100000c_Ad_BC04_10u

description: Mint-ChIP


title: Exp004-2_H3_100000c_Ad_BC03_25u

description: Mint-ChIP


title: Exp004-2_H3_100000c_Ad_BC05_4u

description: Mint-ChIP


title: Exp004-2_H3_100000c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp004-2_H3_100000c_Ad_BC01_150u

description: Mint-ChIP


title: Exp015-5_H3K4me3_30u_Ad_BC12_KDM5C703

description:
Mint-ChIP
see H3K4me3_KDM5C70.tdf for processed data


title: Exp015-5_H3K4me3_30u_Ad_BC06_KDM5C703


title: Exp015-5_H3K4me3_30u_Ad_BC08_DMSO2

description:
Mint-ChIP
see H3K4me3_DMSO.tdf for processed data

value: DMSO


title: Exp015-5_H3K4me3_30u_Ad_BC07_DMSO1


title: Exp015-5_H3K4me3_30u_Ad_BC05_KDM5C702


title: Exp015-5_H3K4me3_30u_Ad_BC10_KDM5C701


title: Exp004-2_H3_500c_Ad_BC02_62-5u

description: Mint-ChIP


title: Exp015-5_H3K4me3_30u_Ad_BC03_DMSO3


title: Exp015-5_H3K4me3_30u_Ad_BC04_KDM5C701


title: Exp015-5_H3K4me3_30u_Ad_BC02_DMSO2


title: Exp015-5_H3K4me3_30u_Ad_BC01_DMSO1


title: Exp015-5_H3K4me3_150u_Ad_BC11_DMSO2


title: Exp015-5_H3K4me3_150u_Ad_BC10_DMSO3


title: Exp015-5_H3K4me3_150u_Ad_BC08_KDM5C702


title: Exp015-5_H3K4me3_150u_Ad_BC06_DMSO1


title: Exp015-5_H3K4me3_150u_Ad_BC04_DMSO3


title: Exp015-5_H3K4me3_150u_Ad_BC05_DMSO2


title: Exp015-5_H3K4me3_150u_Ad_BC03_KDM5C701


title: Exp015-5_H3K4me3_150u_Ad_BC07_KDM5C703


title: Exp015-5_H3K4me3_150u_Ad_BC02_KDM5C702


title: Exp015-5_H3K4me3_150u_Ad_BC01_KDM5C703


title: Exp015-5_H3_30u_Ad_BC12_KDM5C703

description:
Mint-ChIP
see H3_KDM5C70.tdf for processed data


title: Exp015-5_H3K4me3_30u_Ad_BC11_KDM5C702


title: Exp015-5_H3_30u_Ad_BC10_KDM5C701


title: Exp015-5_H3_30u_Ad_BC11_KDM5C702


title: Exp015-5_H3K4me3_30u_Ad_BC09_DMSO3


title: Exp015-5_H3_30u_Ad_BC09_DMSO3

description:
Mint-ChIP
see H3_DMSO.tdf for processed data


title: Exp015-5_H3_30u_Ad_BC06_KDM5C703


title: Exp015-5_H3_30u_Ad_BC05_KDM5C702


title: Exp015-5_H3_30u_Ad_BC07_DMSO1


title: Exp015-5_H3_30u_Ad_BC08_DMSO2


title: Exp015-5_H3_30u_Ad_BC03_DMSO3


title: Exp015-5_H3K4me3_150u_Ad_BC12_DMSO1


title: Exp015-5_H3K4me3_150u_Ad_BC09_KDM5C701


title: Exp015-5_H3_30u_Ad_BC04_KDM5C701


title: Exp015-5_H3_30u_Ad_BC01_DMSO1


title: 533T

city: Rochester

first: Brooke

last: Druliner

state: MN

address: 200 First St. SW

institute: Mayo Clinic

data_processing:
Alignment and data processing bioinformatics. Casava software was used to demultiplex the indices in each lane. Illumina adapters were clipped from reads with cutadapt and aligned to the hg19 human genome assembly with bowtie2 2.1.0 with default parameters. Unpaired and non-uniquely-mapped reads were discarded with samtools. Individual nucleosome footprints were extracted from BAM files with bedtools 2.17.
Genome_build: hg19
Supplementary_files_format_and_content: Nucleosome occupancy profiles were obtained by calculating the fragments per million that mapped at each base-pair in the probed regions with bedtools. Nucleosome dyad frequencies (midpoints) were obtained by calculating the sum of nucleosome dyads (fragment centers) in 100-bp windows at a 10-bp step-size with bedtools. Data were subsequently processed in R 2.15.1

source_name: primary colorectal adenocarcinoma

extract_protocol:
Primary samples from surgically removed tumors of lung adenocarcinoma patients, and corresponding normal tissue were obtained from the University of Massachusetts Medical School (UMMS) Tissue Bank, and prepared as previously described 9. Primary samples from colorectal adenocarcinoma patients with a surgically removed tumor, and corresponding normal tissue were obtained from the Mayo Clinic through Dr. Lisa Boardman. A total of 7 tumor specimens were included in this study (LAC: two grade one, two grade three; CRC: one of each stage one, two and three), with matched normal tissue for each tumor specimen, for a total of 14 genomes that were sequenced. The tumor and normal material was snap-frozen in liquid nitrogen within 1 h after surgery. Samples were examined by board-certified pathologists, using hematoxylin and eosin staining. Samples were selected by grade and stage, and only samples with 80% or more tumor cells were included, as assessed by histological examination. Patient samples were anonymized, and we received patient history along with the samples. Harvesting of nuclei, MNase digestion and mononucleosomal isolation were performed on each sample as previously described 9. See Supplementary Table 1 for preparation information on each patient sample.
MNase digested DNA sequencing libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB #E7370S/L), starting with thirty nanograms of input mononucleosomal DNA. Following end prep and adaptor ligation, libraries were cleaned-up with AMPure® XP Beads (Beckman Coulter, Inc. #A63881) without size selection due to the original input of a size population of ~150bp. Universal and indexed sequences were added through 8 cycles of PCR, using NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, NEB #E7335S/L). The NEBNext® Multiplex Oligos kit contains indices 1-12 which correspond to the identical product if using Illumina® TruSeq primers. The libraries were quantity and quality checked using the Qubit Fluorometer High Sensitivity Kit and Agilent High Sensitivity DNA kit on the Agilent 2100 Bioanalyzer. The average size of material across all libraries was 275bp, and the average total material in this region was more than 90%; there were no adapter or primer dimers. We used a custom designed Roche Nimblegen SeqCap EZ Library SR to capture ~2kb regions flanking the TSS for every gene in the human genome, using the HG19 build. The TSS sequences were repeat masked, so only unique probes were included. We performed the sequence capture according to the manufacturer’s protocol. Following a 72 hour capture hybridization, we performed a 15 cycle PCR amplification using the TruSeq primers 1 (AAT GAT ACG GCG ACC ACC GAG A) and 2 (CAA GCA GAA GAC GGC ATA CGA G). We then performed a quantitative real-time PCR to confirm that regions within the sequence capture were successfully enriched, and that regions excluded from the capture were depleted post-capture. We selected three regions within the 2kb TSS of genes that we knew to be in the SeqCap design (on-target), and for the same three genes we selected regions outside of the 2kb TSS that were not in the SeqCap design (off-target). The on-target and off-target regions and primer sequences can be found in Supplementary Table 2. Dilutions were made in elution buffer to 10 nM stock in 0.05% Tween-20.
MNase-seq (followed by enrichment of TSS regions genome-wide for mTSS-seq)

tag: subject id

tag: subject status

value: colorectal adenocarcinoma patient

tag: tissue

value: colorectal adenocarcinoma

tag: tumor grade or stage

value: stage 4

tag: molecule subtype

value: mononucleosome and subnucleosome-protected DNA


title: 525N

source_name: primary colon epithelial tissue

value: colon epithelial; normal tissue

value: NA; normal tissue


title: Exp015-5_H3_150u_Ad_BC12_DMSO1


title: 524T

value: stage 3


title: 532N


title: Exp015-5_H3_30u_Ad_BC02_DMSO2


title: Exp015-5_H3_150u_Ad_BC11_DMSO2


title: 512T

value: stage 2


title: 513N


title: Exp015-5_H3_150u_Ad_BC10_DMSO3


title: Exp015-5_H3_150u_Ad_BC08_KDM5C702


title: Exp015-5_H3_150u_Ad_BC07_KDM5C703


title: 386T

source_name: primary lung adenocarcinoma

value: lung adenocarcinoma patient

value: lung adenocarcinoma

value: grade one, stage 1B


title: 386N

source_name: primary lung epithelial tissue

value: lung epithelial; normal tissue


title: 873N


title: Exp015-5_H3_150u_Ad_BC09_KDM5C701


title: Exp015-5_H3_150u_Ad_BC05_DMSO2


title: 873T

value: grade one, stage 2B


title: Exp015-5_H3_150u_Ad_BC06_DMSO1


title: Exp015-5_H3_150u_Ad_BC04_DMSO3


title: 4137N_rep_hiseq


title: 4137T_rep_hiseq


title: 4137T_orig_hiseq


title: 4137N_orig_hiseq


title: Exp004-9_H3K27me3_Ad_BC10_C646

description:
Mint-ChIP
This sample is missing processed data because the data was not processed beyond alignment (bam). The number of reads was simply used to generate figures for the manuscript.


title: Exp015-5_H3_150u_Ad_BC01_KDM5C703


title: Exp015-5_H3_150u_Ad_BC02_KDM5C702


title: Exp004-9_H3K27me3_Ad_BC11_GSK126


title: Exp015-5_H3_150u_Ad_BC03_KDM5C701


title: Exp004-9_H3K27me3_Ad_BC09_DMSO


title: Exp004-9_H3K27me3_Ad_BC05_DMSO


title: Exp004-9_H3K27me3_Ad_BC03_GSK126


title: Exp004-9_H3K27me3_Ad_BC02_C646


title: Exp004-9_H3K27me3_Ad_BC06_C646


title: Exp004-9_H3K27ac_Ad_BC11_GSK126


title: Exp004-9_H3K27ac_Ad_BC07_GSK126


title: Exp004-9_H3K27me3_Ad_BC01_DMSO


title: Exp004-9_H3K27ac_Ad_BC10_C646


title: Exp004-9_H3K27ac_Ad_BC09_DMSO


title: Exp004-9_H3K27ac_Ad_BC02_C646


title: Exp004-9_H3_Ad_BC07_GSK126


title: Exp004-9_H3K27ac_Ad_BC06_C646


title: Exp004-9_H3_Ad_BC10_C646


title: Exp004-9_H3K27ac_Ad_BC05_DMSO


title: Exp004-9_H3K27ac_Ad_BC03_GSK126


title: Exp004-9_H3_Ad_BC11_GSK126


title: Exp004-9_H3_Ad_BC06_C646


title: Exp004-9_H3K27ac_Ad_BC01_DMSO


title: Exp004-9_H3_Ad_BC09_DMSO


title: Exp004-9_H3_Ad_BC03_GSK126


title: Exp004-9_H3_Ad_BC02_C646


title: Exp004-8_H3K27me3_Ad_BC10_C646


title: Exp004-8_H3K27me3_Ad_BC06_C646


title: Exp004-8_H3K27me3_Ad_BC05_DMSO


title: Exp004-9_H3_Ad_BC05_DMSO


title: Exp004-9_H3_Ad_BC01_DMSO


title: Exp004-9_H3K27me3_Ad_BC07_GSK126


title: Exp004-8_H3K27me3_Ad_BC09_DMSO


title: Exp004-8_H3K27me3_Ad_BC07_GSK126


title: Exp004-8_H3K27ac_Ad_BC10_C646


title: Exp004-8_H3K27ac_Ad_BC11_GSK126


title: Exp004-8_H3K27me3_Ad_BC02_C646


title: Exp004-8_H3K27me3_Ad_BC03_GSK126


title: Exp004-8_H3K27ac_Ad_BC06_C646


title: Exp004-8_H3K27ac_Ad_BC09_DMSO


title: Exp004-8_H3K27ac_Ad_BC03_GSK126


title: Exp004-8_H3K27me3_Ad_BC11_GSK126


title: Exp004-8_H3_Ad_BC07_GSK126


title: Exp004-8_H3_Ad_BC09_DMSO


title: Exp004-8_H3_Ad_BC10_C646


title: Exp004-8_H3_Ad_BC11_GSK126


title: Exp004-8_H3_Ad_BC05_DMSO


title: Exp004-8_H3K27ac_Ad_BC01_DMSO


title: Exp004-8_H3_Ad_BC02_C646


title: Exp004-8_H3_Ad_BC03_GSK126


title: Exp004-8_H3_Ad_BC01_DMSO


title: Exp004-8_H3K27me3_Ad_BC01_DMSO


title: Exp004-5_H3K27ac_Ad_BC02_C646


title: Exp004-5_H3K27ac_Ad_BC01_DMSO


title: Exp004-5_H3K27me3_Ad_BC02_C646


title: Exp004-5_H3K27me3_Ad_BC03_GSK126


title: Exp004-5_H3K27me3_Ad_BC01_DMSO


title: Exp004-5_H3K27ac_Ad_BC03_GSK126


title: Exp004-5_H3_Ad_BC03_GSK126


title: Exp004-8_H3_Ad_BC06_C646


title: Exp004-8_H3K27ac_Ad_BC05_DMSO


title: Exp004-5_H3_Ad_BC01_DMSO


title: Exp004-8_H3K27ac_Ad_BC07_GSK126


title: Exp004-5_H3_Ad_BC02_C646


title: Exp004-8_H3K27ac_Ad_BC02_C646


title: Input T2E 2

city: Denver

first: Brian

middle: Patrick

last: OConnor

state: Colorado

address: 1400 Jackson St

department: Center for Genes, Environment and Health

institute: National Jewish Health

data_processing:
ChIP-seq sequencing reads were aligned to the human reference genome using the Ion Torrent Suite software, version 4.0.2 and version 4.4
Peak-calling from aligned reads will be performed using the Model-based Analysis for ChIP-Sequencing (MACS2) software (Zhang, 2008), comparing p300 IPs to their respective total input controls. Peak significance was determined with a false discovery rate (FDR) cutoff of 0.001.
Peaks found by ChIP-seq will be associated with the nearest gene by genomic location, using both the RefSeq, refGene, and UCSC known gene models. A gene lists based on closest called peaks was generated.
Genome_build: HG19
Supplementary_files_format_and_content: peak.bed files were generated using MACS2 as described above

source_name: Pc3 immortalized cells

growth_protocol: PC3 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA). PC3 cells were cultured in RPMI 1640 media containing L-glutamine, 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. All cell lines were maintained at 37°C and in 95% air and 5% CO2.

extract_protocol:
Chromatin was sheared using the isothermal Covaris S2 to produce approximately 100-300bp fragments for Ion Proton ChIP-seq. DNA-protein complexes were immunoprecipitated with an anti-p300 ChIP-grade antibody (Abcam #54984), captured by magnetic beads, cross-links reversed, and the genomic DNA purified (Invitrogen Magnify ChIP Kit #49-2024).
Libraries were made according to the instructions using the Ion Xpress Plus Fragment Library Kit- 4471269

treatment_protocol: PC3 cells were treated withand without 30 µm MnTE-2PyP for 24 hours, then exposed to 20 Gy of radiation. One hour after irradiation, the cells were harvested and fixed with 1% methanol-free formaldahyde.

tag: cell line type

value: Pc3 Prostate Cancer Cell Line

tag: antibody

value: 30 µm MnTE-2PyP for 24 hours


title: GBM31

city: Miami

first: Nagi

last: Ayad

state: Florida

address: 1095 NW 14th Terrace, LPLC, R48

department: Psychiatry and Behavioral Sciences

institute: University of Miami

description: GBM Sample

library_source: transcriptomic

data_processing:
Data generated with HiSeq Control Software (1.4.8), and processed with Casava (1.8).
Data screened for contamination from Salmonella, E. coli, and Mycoplasma with BLAST.
FastQC used to identify overrepresented adapter and primer sequences. CutAdapt used to trim 3' read ends with quality score < 10.
Samples mapped to hg19 human annotation (GRCh37.67) with TopHat (2.0.4).
BEDTools used to assess number of genes mapped, and to capture reads mapped to individual samples.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are bedgraph files and include the following: chromA  chromStartA  chromEndA  dataValueA
Processed data files also include CoverageBED.sort.Uniq.txt files with the following information: chr, start, stop, ensID, #reads_per_gene, gene_length_coverage, gene_length, fraction_of_gene_with_reads.^SAMPLE = GSM1532542
Data generated with HiSeq Control Software (1.4.8), and processed with Casava (1.8).
Data screened for contamination from Salmonella, E. coli, and Mycoplasma with BLAST.
FastQC used to identify overrepresented adapter and primer sequences. CutAdapt used to trim 3' read ends with quality score < 10.
Samples mapped to hg19 human annotation (GRCh37.67) with TopHat (2.0.4).
BEDTools used to assess number of genes mapped, and to capture reads mapped to individual samples.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are bedgraph files and include the following: chromA  chromStartA  chromEndA  dataValueA
Processed data files also include CoverageBED.sort.Uniq.txt files with the following information: chr, start, stop, ensID, #reads_per_gene, gene_length_coverage, gene_length, fraction_of_gene_with_reads.^SAMPLE = GSM1532542

molecule: total RNA

source_name: GBM Sample

extract_protocol:
RNA was isolated using Trizol reagent, purified with Rneasy Kit (QIAGEN) and DNase digested.
RNA libraries were prepared using the Rebo-Zero and the Epicentre Scriptseq V2 Kit

value: brain

tag: tumor stage

value: Glioma Grade IV


title: Input T2E 1


title: GBM17

description: GBM Sample

data_processing:
Data generated with HiSeq Control Software (1.4.8), and processed with Casava (1.8).
Data screened for contamination from Salmonella, E. coli, and Mycoplasma with BLAST.
FastQC used to identify overrepresented adapter and primer sequences. CutAdapt used to trim 3' read ends with quality score < 10.
Samples mapped to hg19 human annotation (GRCh37.67) with TopHat (2.0.4).
BEDTools used to assess number of genes mapped, and to capture reads mapped to individual samples.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are bedgraph files and include the following: chromA  chromStartA  chromEndA  dataValueA


title: GBM16

description: Epileptic Sample

data_processing:
Data generated with HiSeq Control Software (1.4.8), and processed with Casava (1.8).
Data screened for contamination from Salmonella, E. coli, and Mycoplasma with BLAST.
FastQC used to identify overrepresented adapter and primer sequences. CutAdapt used to trim 3' read ends with quality score < 10.
Samples mapped to hg19 human annotation (GRCh37.67) with TopHat (2.0.4).
BEDTools used to assess number of genes mapped, and to capture reads mapped to individual samples.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are bedgraph files and include the following: chromA  chromStartA  chromEndA  dataValueA
Processed data files also include CoverageBED.sort.Uniq.txt files with the following information: chr, start, stop, ensID, #reads_per_gene, gene_length_coverage, gene_length, fraction_of_gene_with_reads.^SAMPLE = GSM1532542

source_name: Epileptic Sample


title: Input PC3 2


title: PC3 ChIP p300 1

source_name: PC3 immortalized cells

value: anti-p300 antibody (Abcam #54984)


title: GBM34

description: Epileptic Sample


title: PcC3 ChIP p300 2


title: T2E ChIP p300 1


title: Input PC3 1


title: T2E ChIP p300 2


title: Exp004-5_H3K27me3_Ad_BC06_YAC-1

organism: Mus musculus


title: Exp004-5_H3K27me3_Ad_BC05_YAC-1


title: Exp004-5_H3K27ac_Ad_BC06_YAC-1


title: Exp004-5_H3_Ad_BC06_YAC-1


title: 1357N


title: 4137N_orig_miseq


title: Exp004-5_H3K27ac_Ad_BC05_YAC-1


title: Exp004-5_H3_Ad_BC05_YAC-1


title: Event2_Inflorescence_Rep2

status: Public on Oct 26 2015

city: Saint Louis

first: Jim

last: Morrell

state: Missouri

address: 800 North Lindbergh Blvd

department: Biotechnology

institute: Monsanto Co.

data_processing:
Illumina Casava V1.8.2 software was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to corn_B73_5a public transcriptome using Bowtie v0.12.8 with parameters  -S -p 5 --best --strata -k 10 -m 10 -n 2 -e 70
Up to 2 high quality (Phred score > 20) mismatches for every 28 seed sequence were allowed. If a read mapped to more that 10 transcripts, it was dropped.  If it mapped to 10 or less, it was assigned equally to all of them.
The DESeq algorithm (Simon Anders, EMBL) was used to normalize raw counts across all the samples.
Genome_build: corn_B73_5a (http://www.maizesequence.org)
Supplementary_files_format_and_content: Comma separated file (CSV) containing DESeq-normalized counts.

organism: Zea mays

source_name: Ear Inflorescence tissue_Event 2_V16

growth_protocol: Field experiments were planted in Illinois in 2012.  Standard agronomic practices used to prepare and maintain the study site were characteristic of corn production practices for the region.  Samples were collected when plants reached the V16 stage for Ear Inflorescence tissue, and the R1 growth stage for Ear tissue.

extract_protocol:
Total RNA was isolated from three biological replicates for each tissue using TRIzol (Invitrogen) according to the manufacturer's protocol. RNA quantity was determined with a Nanodrop 8000 spectrophotometer and integrity assessed by Bioanalyzer assay with RIN greater than 6.
Two µg of total RNA was used for sequencing library preparation with Illumina TruSeq RNA Sample Prep Kit V2 following manufacturer’s protocol.  qPCR (SYBR PCR Master Mix, Applied Biosystem) was utilized to quantify sequencing libraries.
Sequencing was performed with Illumina HiSeq2000 sequencing using 50 base pair reads.

treatment_protocol: There were no special environmental or stress treatments applied. Plants were harvested by cutting the stalk at soil level and separating each plant into its component parts.  Ear inflorescence and ear tissue was flash frozen in liquid nitrogen, and stored at -80C thereafter.

tag: line

value: Monsanto Elite Hybrid NN6306

tag: genotype/variation

value: expressing AtHB17delta113_event2

tag: developmental stage

value: Ear Inflorescence


title: Event2_Inflorescence_Rep1


title: Event1_Inflorescence_Rep1

source_name: Ear Inflorescence tissue_Event 1_V16

value: expressing AtHB17delta113_event1


title: Event2_Ear_Rep1

source_name: Ear tissue_Event 2_R1

value: Ear


title: Event2_Ear_Rep2


title: 4137T_orig_miseq

value: mononucleosome and subnucleosome-protected DNA


title: Event2_Inflorescence_Rep3


title: Event1_Inflorescence_Rep3


title: Event1_Ear_Rep3

source_name: Ear tissue_Event 1_R1


title: Event1_Ear_Rep2


title: H2009_e3KRAB1_Rep2

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

data_processing:
Prada alignment
Cufflinks normalization
Genome_build: hg19
Supplementary_files_format_and_content: gct, normalized expression level for each gene

source_name: Cancer cell line

growth_protocol: Cells were grown in RPMI medium supplemented with 10% FBS

extract_protocol:
RNA was extracted using Qiagen RNeasy kit (74104) and mRNA was subsequently isolated using NEB poly(A) module (E7490)
Following NEB RNA-seq library preparation kit (E7420S)
Following NEB RNA-seq library preparation kit (E7420S)

treatment_protocol: Cells were ransfected with the dCas9-KRAB fustion and subsequently transfected with guide RNAs

tag: tumor type

value: Lung adenocarcinomas

value: krab1:a guide RNA (e3 #1) recognizing the e3 enhancer region


title: H2009_e3KRAB2_Rep1

value: krab2:a guide RNA (e3 #2) recognizing the e3 enhancer region


title: WT_Inflorescence_Rep1

value: non-trangenic control WT


title: WT_Ear_Rep1

source_name: Ear tissue_non-transformed_R1


title: WT_Inflorescence_Rep3


title: WT_Ear_Rep3


title: WT_Ear_Rep2


title: Event1_Ear_Rep1


title: T2E ChIP p300 3


title: H2009_e3KRAB2_Rep2


title: 1357T

value: lung adenocarcinoma patient

value: lung adenocarcinoma

value: grade one, stage 1A


title: H2009_e3KRAB1_Rep1


title: WT_Inflorescence_Rep2


title: H2009_Control_Rep2

value: Control:a guide RNA with no target


title: Event2_Ear_Rep3


title: H2009_Empty_Rep1

value: Empty:no guide RNA


title: H2009_K27ac_e3KRAB2

data_processing:
BWA alignment
MACS Peak-calling
Genome_build: hg19
Supplementary_files_format_and_content: bed; DNA coordinates of regions significantly associated with H3K27ac

extract_protocol:
Chromatin-IP
Following NEB ChIP-seq library preparation kit (E6200S)

treatment_protocol: No treatment


title: H2009_Empty_Rep2


title: HCC95_K27ac

value: Squamous cell lung carcinomas

tag: cell line


title: H2009_K27ac_Rep1


title: H2009_K27ac_Rep2


title: Ishikawa_K27ac_Rep1

value: Endometrial carcinomas

value: Ishikawa


title: H358_K27ac_Rep2


title: Ishikawa_K27ac_Rep2


title: H2009_K27ac_Empty


title: H2009_K27ac_Control


title: H358_K27ac_Rep1


title: ATRX KO

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

data_processing:
For a global normalization, we performed a combined analysis of genes and repetitive transcripts. Transcript sequences including splice variants were downloaded from Ensembl BioMart (GRCm38.p4). Repetitive element sequences were downloaded from RepBase v20 (http://www.girinst.org/server/RepBase/). All sequences were combined into a genome file using bowtie-build.
Raw reads were mapped using Bowtie-1.1.2
Total read counts per transcript were generated using samtools idxstats function
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: text file with raw read counts (samtools idxstats)

molecule: polyA RNA

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
Total RNA was extracted from embryonic stem cells using the Qiagen Rneasy kit. 4 ug of RNA was used for library preparation.
Libraries were constructed according to the Illumina Tru-Seq protocol

tag: genotype

value: ATRX-/-

tag: clone

tag: background strain


title: DAXX KO

value: DAXX-/-


title: H2009_Control_Rep1

tag: treatment


title: MI63_treated_MCF7

city: Novato

first: Christina

last: Yau

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

data_processing:
Sequence reads are proccessed using the Illumina pipeline software Casava version 1.8
Reads were aligned to the human genome (hg19) using the ELAND algorithm.
Only uniquely mapped reads were used for further analysis.  After removing of duplicate reads, all files were normalized to the same number of alignments (~20.5 million tags per file).
The .bed files of normalized unique tags were used to identify FOXM1 bound chromosomal regions using the peak caller MACS (version 1.4) with a p value cutoff of 1E-7. Specifically,  the normalized .bed files of unique reads from each experimental condition (proliferating, confluent, MI63 treated and control) were compared to those from unenriched MCF7 input DNA to generate a set of 4 processed data files - proliferating_peaks.xls, confluent_peaks.xls, mi63_peaks.xls and control_peaks.xls .  In addition, a fifth processed data file directly comparing data from the proliferating to confluent conditions was generated.
MACS peaks are mapped to genes if they are within 5kb of a transcriptional start site of a UCSC Known Gene.
Genome_build: hg19
Supplementary_files_format_and_content: Text files generated by MACS containing the chromosomal locations of FOXM1 bound peaks passing a p value cutoff of 1e-7.

source_name: Breast Cancer Cell Line

growth_protocol: Estrogen receptor-positive (ER+) MCF-7 human breast cancer cells obtained from American Type Culture Collection (Rockville, MD) were cultured at 37°C and 5% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS and 1% insulin.

extract_protocol:
Harvested MCF-7 cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were clarified from sonicated nuclei and FOXM1-DNA complexes were isolated with antibody (Santa Cruz, sc-501, Lot. D0110).
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3’-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200-250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on Illumina GAII (36 nt reads, single-end).

treatment_protocol: Untreated replicate monolayer cultures were grown to either exponential proliferation stage (~30% confluency) or complete (~100%) confluency.  Treated replicate cultures were exposed (10 mM x 24h) to the p53wt upregulating MDM2 inhibitor, MI-63 (Ascenta Therapeutics/Sanofi Oncology) before harvest along with untreated controls plated at the same time and confluency.

tag: gender

value: female

tag: er status

value: ER+

tag: confluency

value: Low

tag: mi63 treatment

value: Yes

tag: foxm1 antibody chip


title: Control_MCF7

value: No


title: Wildtype

value: wildtype


title: MCF7_Input_DNA


title: wtDFL

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL

data_processing:
Mapping and RNA-seq analyses were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm9 (NCBIM37) with bowtie2 with parameters --end-to-end --sensitive -k 20
Reads Per Kilobase per Million reads (RPKM) for each transcript were calculated from the raw counts with program rnacounter 1.5.2 (https://pypi.python.org/pypi/rnacounter)
Genome_build: mm9
Supplementary_files_format_and_content: One density file per strand (bigWig) and one tab-delimited text file with raw counts and RPKM per transcript.

source_name: distal limb

extract_protocol:
Total RNA from E12.5 embryonnic forelimb tissues was extracted shortly after dissection in cold PBS and isolated using Trizol.
Library preparation using the Illumina TruSeq protocol is applied with a Poly A selection. Strand specific RNA-Seq.

tag: strain


title: Confluent_MCF7

value: High


title: STR_WT_2

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

department: Neuroscience

description: PROTOCOL 3

data_processing:
Single-end and Paired-end reads were aligned in a staged manner. Reads were aligned with tophat using default options to a reference sequence comprised of mitochondrial DNA (h19, mm10 from UCSC).
ChIP-seq data were aligned with tophat using default options to a reference sequence comprised of mitochondrial DNA (h19 from UCSC).
ChIP-seq was analyzed using MACS.
RNA-seq Counts values were quantified using HTSeq python suite, providing gene definitions (h19 GTF, mm10 GTF from UCSC).
RNA-seq RPKM values were then quantified using RseQC, providing gene definitions (h19 GTF, mm10 GTF from UCSC).
Gene-level RPKMs quantifications were used for all downstream processing.
Genome_build: Human h19; Mouse mm10
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample; bed-files including coordinates of the detected peaks.

growth_protocol:
PROTOCOL1: Human neural progenitor cell lines were used.
PROTOCOL2: Human neural progenitor cell line was used.
PROTOCOL3: Mouse regional brain dissections were used and frozen in liquid nitrogen.

extract_protocol:
PROTOCOL1: All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent). Samples were randomized for RNA extractions and sequencing. 2ug of total RNA were treated with Ribo-zero Removal Kit according to the manufacturer’s instructions to remove ribosomal RNA.
PROTOCOL2: DNA was purified using Qiagen MinElute Columns and quantified using a Qubit Fluorometer according to the manufacturer’s instructions.
PROTOCOL3: All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent). Samples were randomized for RNA extractions and sequencing. 2ug of total RNA were treated with Ribo-zero Removal Kit according to the manufacturer’s instructions to remove ribosomal RNA.
Libraries were prepared using an Illumina TruSeq kit according to the manufacturer’s instructions.

treatment_protocol:
PROTOCOL1: RNA was extracted after three days post-transduction using Qiagen’s RNeasy Kit according to the manufacturer’s instructions.
PROTOCOL2: DNA was collected after immunoprecipitation using Invitrogen Dynabeads according to the manufacturer’s instructions.
PROTOCOL3: RNA was extracted from frozen tissues using Qiagen’s RNeasy Kit according to the manufacturer’s instructions.

tag: tissue

value: Striatum

tag: Sex

value: M

tag: age

value: postnatal day 47


title: CTX_WT_1

description: PROTOCOL 3

value: Cortex


title: CTX_HET_2

description: PROTOCOL 3


title: CTX_WT_3

description: PROTOCOL 3


title: Proliferating_MCF7


title: CTX_WT_2

description: PROTOCOL 3


title: H_5_wholeBlood

city: Berlin

first: Nikolaus

last: Rajewsky

address: Robert Rössle Str 10 (H. 87)

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion with CASAVA-1.8.2
Alignment to human rRNA data (UCSC) using bowtie2
Aligmnment of non-rRNA reads to hg19 using bowtie2
Create 20nt anchors from both ends of non-contigiously mapping reads and map independently to hg19
Extend aligned anchor sequences and report head-to-tail splice sites
Filter resulting splicing events using the following criteria 1) GT/AG signal flanking the splice sites 2) unambiguous breakpoint detection 3) maximum of two mismatches when extending the anchor alignments 4) breakpoint no more than two nucleotides inside the alignment of the anchors 5) at least two independent reads supporting the head-to-tail splice junction 6) a minimum difference of 35 in the bowtie2 alignment score between the first and the second best alignment of each anchor 7) no more than 100 kilobases distance between the two splice sites.
Genome_build: hg19
Supplementary_files_format_and_content: BED file, score column contains # reads supporting the head-to-tail splice junction of the particular circRNA

source_name: Peripheral whole blood from healthy individual

extract_protocol:
Trizol LS (Thermo Scientific)
TruSeq RNA v2 (Illumina)

value: Peripheral whole blood

tag: diagnosis

value: healthy


title: H_3_wholeBlood


title: CTX_HET_1

description: PROTOCOL 3


title: CTX_HET_4

description: PROTOCOL 3


title: H_4_wholeBlood


title: CTX_HET_3

description: PROTOCOL 3


title: CTX_WT_4

description: PROTOCOL 3


title: STR_HET_4

description: PROTOCOL 3


title: STR_WT_1

description: PROTOCOL 3


title: H2009_K27ac_e3KRAB1

value: Lung adenocarcinomas

tag: antibody


title: H_1_rep_wholeBlood

source_name: Peripheral whole blood from healthy individual. Technical replicate of sample H_1_wholeBlood


title: STR_WT_3

description: PROTOCOL 3


title: H_1_wholeBlood


title: STR_WT_4

description: PROTOCOL 3


title: eif3a_par-iclip_replicate1

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

data_processing:
Barcodes used were NNNGGTTNN (rep1) and NNNTTGTNN (rep2)
Alignment to hg19 was performed using bowtie
Genome_build: hg19
Supplementary_files_format_and_content: Peak-calling for processed files was performed using Pyicoclip

source_name: HEK293T cells

growth_protocol: 10 million cells were incubated with 100 mM 4-thiouridine for 8 h and irradiated with 354 nm UV light prior to harvesting.

extract_protocol:
Cell lysates were isolated and crosslinked eIF3:RNA complexes were immunoprecipitated with anti-eIF3a antibody.
Library construction was performed as per the method of Huppertz et al., iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65, 274-287 (2014).

tag: cell type

value: human embryonic kidney cells

tag: antibody name

value: eIF3a (Abcam #ab86146)


title: STR_HET_2

description: PROTOCOL 3


title: STR_HET_3

description: PROTOCOL 3


title: Event1_Inflorescence_Rep2

tag: line

value: Monsanto Elite Hybrid NN6306

tag: genotype/variation

value: expressing AtHB17delta113_event1

tag: developmental stage

value: Ear Inflorescence


title: STR_HET_1

description: PROTOCOL 3


title: Proliferating_MCF7

data_processing:
Resulting reads were aligned to the transcriptome defined by UCSC hg19 Known Genes using the RNA-Seq pipeline RSEM v1.2.9 and Bowtie v1.0.0
RSEM estimated Fragments Per Kilobase Mapped (FPKMs) and Transcripts Per Million (TPMs) per transcript and isoform using an expectation maximization algorithm.
TPMs for individual read groups were used for downstream differential expression analyses
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values of UCSC known genes for each sample from 3 read groups

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen, CA) and assayed using a 2100 Bioanalyzer (Agilent, CA).
~ 0.5-1.0 µg cDNA from each was first sheared to a size ranging between 200-300 bp using the Covaris-S2 sonicator (Covaris, Woburn, MA) according to the manufacturer’s recommended protocols, and the fragmented cDNA samples were then prepared for whole transcriptome library generation using the TruSeq v1 Multiplex Sample Preparation kit (Illumina, San Diego, CA). Briefly, cDNA fragments were end-repaired, dA-tailed and ligated to multiplex adapters according to manufacturer's instructions. After ligation, DNA fragments smaller than 150 bp were removed with AmPure XP beads (Beckman Coulter Genomics, Danvers, MA). The purified adapter ligated products were enriched using polymerase chain reaction (14 cycles). The final amplified libraries were resolved on 2.0% agarose gel and manually size-selected in the range of 350–380 bp. The final RNA-Seq libraries were quantitated using the Agilent 2100 Bioanalyzer and pooled together in equal concentration for sequencing.

treatment_protocol: Untreated replicate monolayer cultures were grown to either exponential proliferation stage (~30% confluency) or complete (~100%) confluency;. and treated replicate cultures were exposed (10 mM x 24h) to the p53wt upregulating MDM2 inhibitor, MI-63 (Ascenta Therapeutics/Sanofi Oncology) before cell harvest.

tag: cell line

value: ER+

value: Low


title: H_2_wholeBlood


title: MI63_treated_MCF7

value: Yes


title: HUES65

first: Soohyun

last: Lee

state: MASSACHUSETTS

address: 10 Shattuck St.

department: Department of Biomedical Informatics

institute: Harvard Medical School

data_processing:
Sequence reads were aligned to GRCh37.67 transcriptome using bowtie 0.12.7.
TPM and readcount values were obtained using EMSAR v1.0
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited files that contains TPM and read count information.

source_name: ESC

growth_protocol: hESC lines and hiPSC lines were cultured with mouse embryonic fibroblasts (MEFs, Globalstem) pre-plated at 12-15,000 cells/cm2. Medium containing DMEM/F12, 20% knockout serum replacement, 1mM L-glutamine, 100 uM MEM non-essential amino acids, and 0.1 mM beta-mercaptoethanol was used. 10 ng/ml of FGF-2 was added after sterile filtration and cells were fed daily and passaged weekly using 6 U/mL dispase or mechanically.

extract_protocol: Undifferentiated hESC/hiPSC cells were sorted for hTRA-1-81+ to control for the homogeneity of cells before RNA extraction. The quality and quantity of total input mRNA was determined on an Agilent BioAnalyzer 2100 using Agilent RNA 6000 Nano kit. One microgram of total RNA from each sample was then used as input for library preparation using Illumina TruSeq RNA Sample Prep Kit, following manufacturer’s instructions. Each paired-end library was prepared with an adaptor with unique index sequence. The size profile and quantity of resulting libraries were than determined on the BioAnalyzer 2100 with Agilent High Sensitivity DNA kit. These libraries were then pooled together at equal molar concentration and sequenced on an Illumina HiSeq 2000. All hESC and hiPSC samples for RNA-Seq analysis were prepared on the same day by the same person, and then sequenced simultaneously on the same run (except for hiPSC lines 1, 2 and 3; this did not affect the clustering). All fibroblasts samples were prepared and sequenced in the same manner as the pluripotent samples but on different days.

tag: data set

value: nonisogenic

value: ESC


title: HUES63


title: iPS18c

source_name: iPSC

value: iPSC


title: Confluent_MCF7

tag: er status

value: High

value: No


title: HUES3


title: HUES53


title: HIP_WT_4

description: PROTOCOL 3

value: Hippocampus

value: M

value: postnatal day 47


title: HUES48


title: HIP_WT_3

description: PROTOCOL 3


title: HIP_HET_4

description: PROTOCOL 3


title: HIP_WT_2

description: PROTOCOL 3


title: HIP_WT_1

description: PROTOCOL 3


title: iPS27b


title: eif3a_par-iclip_replicate2


title: HIP_HET_3

description: PROTOCOL 3


title: HUES9


title: HUES8


title: HIP_HET_2

description: PROTOCOL 3


title: HUES64


title: HUES66


title: HIP_HET_1

description: PROTOCOL 3


title: HUES28


title: iPS11c


title: iPS11b


title: HUES62


title: HUES45


title: H1


title: H9


title: HUES49


title: iPS18b


title: iPS17b


title: iPS18


title: HUES44


title: iPS20b


title: Human_Dermal_Fibroblast

source_name: Fibroblast

value: isogenic

value: Fibroblast


title: hESC3.6 G3


title: iPS15b


title: iPS29e


title: hESC3.6 G15


title: HUES13


title: hESC3.6 G15 Fib


title: hESC3.6 G2


title: iPS27e


title: hESC3.6 G2 Fib


title: HUES1


title: hESC3.2


title: hESC3.6 G3 Fib


title: hESC3.6 Fib


title: hESC3.3


title: iPS17a


title: hESC3.1


title: hESC2.6 G5


title: hESC2.6 G13


title: hESC2.6 G12 Fib


title: hESC2.6 G5 Fib


title: hESC2.6 G13 Fib


title: hESC2.6 Fib


title: hESC2.3


title: hESC2.6 G12


title: hESC2.2


title: hiPSC8


title: hiPSC8 Fibroblast


title: hiPSC9 Fibroblast


title: hiPSC9


title: hiPSC3 Fibroblast


title: hiPSC3


title: hiPSC2


title: hiPSC1 Fibroblast


title: hiPSC2 Fibroblast


title: hiPSC11 Fibroblast


title: HF-35119

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

description:
Patient ID: HF-35119; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963050

data_processing:
Reads that passed quality filters were determined, and fastq files were generated by Illumina CASAVA v1.8
50bp Illumina paired-end reads were aligned to build 37 of the NCBI human genome using Bioconductor package, HTSeqGenie version 3.10.1 (Pau and Reeder, 2014). The alignment was performed using GSNAP (Genomic Short-read Nucleotide Alignment Program) version ’2013-03-31’ (Wu and Nacu, 2010).
The Bioconductor package, DESeq2 (version 1.2.6) (Love et al., 2014), was used to normalize expression across samples and identify genes that were significantly differentially expressed using the default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: entrez gene IDs, gene exonic counts, gene length, and RPKM values

source_name: Colonic biopsy

extract_protocol:
RNAlater® biopsies were homogenized using Tissuelyzer (Qiagen, Hilden, Germany) and ribonucleic acid (RNA) was isolated using the RNeasy® Mini Kit (Qiagen, Hilden, Germany) according to manufacturer instructions.
Total RNA (RNA integrity number > 5; 250 ng) was put into the Illumina TruSeq RNA Sample Preparation Kit v2 protocol and run in conjunction with Biomek liquid handling platforms (Beckman Coulter Life Sciences).
RNA libraries were evaluated using the Agilent 2200 TapeStation HighSensitivity D1K Tape and quantitative polymerase chain reaction (qPCR) with the KAPA Library Quantification Kit for Illumina sequencing.
2 nM of library (12 samples per lane) was loaded for cluster generation and sequenced on the Illumina HiSeq 2000 Sequencing System at 2 × 50 base pairs read length plus index read.

tag: disease state

value: UC

tag: inventory sample name

tag: tissue diagnosis

value: No Dx

tag: remission at week 10

value: Non-remitter

tag: prior anti.tnf

value: Prior anti-TNF

tag: tnf ir

value: TNF IR

value: colonic biopsy


title: HF-35634

description:
Patient ID: HF-35634; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963040

value: Naive

value: ND

tag: tissue


title: HF-35420

description:
Patient ID: HF-35420; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963062

value: Remitter


title: HF-37205

description:
Patient ID: HF-37205; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963107


title: HF-35397

description:
Patient ID: HF-35397; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963051


title: HF-34733

description:
Patient ID: HF-34733; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963035


title: HF-37228

description:
Patient ID: HF-37228; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963074


title: hESC2.1

value: ESC


title: HF-37276

description:
Patient ID: HF-37276; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963099


title: HF-37246

description:
Patient ID: HF-37246; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: NA
SAM9963089


title: HF-37273

description:
Patient ID: HF-37273; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963100


title: HF-37615

description:
Patient ID: HF-37615; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963108

value: NOS


title: HF-37432

description:
Patient ID: HF-37432; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963056


title: HF-37504

description:
Patient ID: HF-37504; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963081


title: HF-37614

description:
Patient ID: HF-37614; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963106


title: HF-35642

description:
Patient ID: HF-35642; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963095


title: hiPSC11

value: iPSC


title: HF-37282

description:
Patient ID: HF-37282; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963083


title: hiPSC1


title: HF-37237

description:
Patient ID: HF-37237; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963071


title: HF-37253

description:
Patient ID: HF-37253; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963080


title: HF-35401

description:
Patient ID: HF-35401; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963052


title: HF-37531

description:
Patient ID: HF-37531; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963087


title: HF-34774

description:
Patient ID: HF-34774; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963047


title: HF-35651

description:
Patient ID: HF-35651; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963092


title: HF-35366

description:
Patient ID: HF-35366; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963038


title: HF-37284

description:
Patient ID: HF-37284; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963057


title: HF-37535

description:
Patient ID: HF-37535; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963104


title: HF-35105

description:
Patient ID: HF-35105; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963046


title: HF-35117

description:
Patient ID: HF-35117; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963049


title: HF-37243

description:
Patient ID: HF-37243; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963084


title: HF-35357

description:
Patient ID: HF-35357; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963093


title: HF-37412

description:
Patient ID: HF-37412; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: NA
SAM9963105


title: HF-37275

description:
Patient ID: HF-37275; Tissue Diagnosis: No Dx; Remission at wk 10: NA; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963053


title: HF-35415

description:
Patient ID: HF-35415; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963067


title: HF-37225

description:
Patient ID: HF-37225; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963059


title: HF-37235

description:
Patient ID: HF-37235; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963075


title: HF-37288

description:
Patient ID: HF-37288; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963078


title: HF-35412

description:
Patient ID: HF-35412; Tissue Diagnosis: No Dx; Remission at wk 10: NA; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963090


title: HF-37286

description:
Patient ID: HF-37286; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: NA
SAM9963096


title: HF-35645

description:
Patient ID: HF-35645; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963069


title: HF-35356

description:
Patient ID: HF-35356; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963070


title: HF-34747

description:
Patient ID: HF-34747; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963042


title: HF-37390

description:
Patient ID: HF-37390; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963088


title: HF-35649

description:
Patient ID: HF-35649; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963068


title: OSC_Mate pair

city: Skolkovo

first: Ekaterina

last: Khrameeva

state: Moscow region

address: Novaya St., 100

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
Library strategy: Mate-pair-Seq
Fastq files were generated and demultiplexed with the bcl2fastq v1.8.4 Conversion Software (Illumina).
Only read pairs that contained circularization adaptor CTGTCTCTTATACACATCT were used in further analysis because they were guaranteed to come from real mate-pair fragments. The circularization adaptor was trimmed using a custom script.
Reads were mapped to the D. melanogaster reference genome (version dm3) using bowtie2 v2.2.1 with options --rf -I 5000 -X 15000.
BreakDancer v1.4.5 (with options -t -q 10 –l) and Delly v0.5.9 programs were used to predict chromosomal rearrangements relative to the D. melanogaster reference genome (version dm3).
genome build: dm3
processed data files format and content:  Rearrangements predicted by Delly program are in vcf format. The SV type can be DEL, DUP, INV or TRA for deletions, tandem duplications, inversions and translocations, respectively. Rearrangements predicted by BreakDancer program are in tab-delimited format. Columns include Chromosome 1, Position 1, Orientation 1, Chromosome 2, Position 2, Orientation 2, Type of a SV, Size of a SV, Confidence Score, Total number of supporting read pairs, Total number of supporting read pairs from each map file, Estimated allele frequency.

organism: Drosophila melanogaster

source_name: cultured cells_OSC

growth_protocol: S2 and Kc167 cells were grown at 25 C in Schneider’s Drosophila Medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco) and 50 units/ml penicillin and 50 mkg/ml streptomycin. DmBG3-c2 cells were grown in the same conditions except that half of Schneider’s Drosophila  Medium was substituted by the Shields and Sang M3 insect medium (Sigma). OSC cells were cultured in Shields and Sang M3 insect medium (Sigma) supplemented with 10% heat inactivated FBS (Gibco), 10% fly extract, 10 µg/ml insulin (Sigma), 0.6 mg/ml glutathione (Sigma), 50 units/ml penicillin and 50 mkg/ml streptomycin

extract_protocol:
High molecular weight genomic DNAs from S2, Kc167, BG3 and OSC cells were isolated by standard method (Sambrook and Russell 2001) with modifications. Briefly, cells were incubated in lysis buffer (50 mM Tris-HCl at pH 8.0, 25 mM EDTA, 0.2% Triton X-100, 1% sarcosyl) with 20 mg/mL proteinase K for 16 h at 37⁰C. DNA was sequentially extracted with phenol, phenol-chloroform, chloroform and then precipitated with 2.5 volumes of ethanol, washed 3 times with 70% ethanol, dried and dissolved in TE.
The fragmentation of genomic DNAs into 8-10 kb fragments was done by “Evrogen” (http://www.evrogen.com/) with the use of Nextera Mate Pair library Sample Prep kit (Illumina), followed by the TruSeq DNA Sample Prep kit. The libraries were quantitated by qPCR.

value: OSC

tag: development stage

value: adult

value: ovary


title: DmBG3-c2_Mate pair

source_name: cultured cells_DmBG3-c2

value: third instar larval

value: central nervous system


title: HF-37189

description:
Patient ID: HF-37189; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963103

value: UC


title: Kc167_Mate pair

source_name: cultured cells_Kc167

value: late embryonic stage

value: embryo


title: HF-34751

description:
Patient ID: HF-34751; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963045

value: No Dx

value: Non-remitter

value: Prior anti-TNF


title: HF-37512

description:
Patient ID: HF-37512; Tissue Diagnosis: NOS; Remission at wk 10: Remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963065

value: Naive

value: colonic biopsy


title: HF-35630

description:
Patient ID: HF-35630; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963072

value: Remitter

value: ND


title: HF-37593

description:
Patient ID: HF-37593; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963082

value: NOS


title: HF-35400

description:
Patient ID: HF-35400; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963076

value: TNF IR


title: S2_Mate pair

source_name: cultured cells_S2


title: HF-37428

description:
Patient ID: HF-37428; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963054


title: HF-37676

description:
Patient ID: HF-37676; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963060


title: HF-37251

description:
Patient ID: HF-37251; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963085


title: HF-37516

description:
Patient ID: HF-37516; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963109


title: HF-35653

description:
Patient ID: HF-35653; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963091


title: HF-37588

description:
Patient ID: HF-37588; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963066


title: HF-34767

description:
Patient ID: HF-34767; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963044


title: HF-35425

description:
Patient ID: HF-35425; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963086


title: HF-35631

description:
Patient ID: HF-35631; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963073


title: HF-37223

description:
Patient ID: HF-37223; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963058


title: HF-35116

description:
Patient ID: HF-35116; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963048


title: HF-35417

description:
Patient ID: HF-35417; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963039


title: HF-37283

description:
Patient ID: HF-37283; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963079


title: HF-37285

description:
Patient ID: HF-37285; Tissue Diagnosis: No Dx; Remission at wk 10: NA; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963098


title: HF-34765

description:
Patient ID: HF-34765; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963043


title: HF-37201

description:
Patient ID: HF-37201; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963037


title: HF-35399

description:
Patient ID: HF-35399; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963061


title: HF-37281

description:
Patient ID: HF-37281; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963063


title: HF-37603

description:
Patient ID: HF-37603; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963101


title: HF-37231

description:
Patient ID: HF-37231; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963064


title: HF-37605

description:
Patient ID: HF-37605; Tissue Diagnosis: NOS; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963094


title: HF-37197

description:
Patient ID: HF-37197; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963036


title: miR10b doxy no3

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

data_processing:
Adapter sequences were removed form raw reads using fqtrim (The Center for Computational Biology at Johns Hopkins University, http://ccb.jhu.edu/software/fqtrim/)
Trimmed reads were mapped to the mouse genome using STAR [default settings]
Reads were quantitated using FeatureCounts (SourceForge Subread Package) using RefSeq (hg19) annotation
Genome_build: hg19
Supplementary_files_format_and_content: Processed files contain quantitations of reads to refseq.

source_name: Human embryonic stem cells upon 14 days of neural induction. Doxyxyxline was added day11-14 in order to overexpress miR10b

growth_protocol: Expansion and transduction of hESCS: Human ESC H9 (WA09, passage 31-45) (Thomson et al., 1998) was expanded and maintained on γ-irradiated mouse embryonic fibroblasts (MEFs) in DMEM/F12, 20% KSR, 0.05 mM 2-mercaptoethanol, 0.5% Pen/ Strep, 0.5% Glutamate and 10 ng/ml FGF-2 (R&D Systems). The cells were passaged once weekly with dispase (5 mg/ml, Stemcell Tech.) or EDTA (0.5mM).   At the time of lentiviral transduction the ESCs were plated onto Matrigel (1:40, BD Biosciences) without MEFs and infected at a MOI of 50. The infected hESCs were maintained on matrigel for 3 days before plated back onto MEFs for an additional 7 days of expansion prior to differentiation.

extract_protocol:
RNA was exracted using the miRNeasy mini kit form Qiagen
RNA libraries were prepared using Illumina kits.

treatment_protocol: Neural induction, 14days. Patterning towards midbrain with CT0.8 and Shh 200ng/ml: Kirkeby A, Nelander J, Parmar M. Generating regionalized neuronal cells from pluripotency, a step-by-step protocol.  Front Cell Neurosci. 2013 Jan 3;6:64. doi: 10.3389/fncel.2012.00064.  - Kirkeby A, Grealish S, Wolf DA, Nelander J, Wood J, Lundblad M, Lindvall O, Parmar M. Generation of regionally specified neural progenitors and functional neurons from human embryonic stem cells under defined conditions. Cell Rep. 2012 Jun 28;1(6):703-14. doi: 10.1016/j.celrep.2012.04.009. Epub 2012 May 26.

tag: growth

value: 14 days of neural induction

tag: treatment

value: Doxycycline was added day 11-14


title: HF-35404

description:
Patient ID: HF-35404; Tissue Diagnosis: No Dx; Remission at wk 10: Remitter; Prior anti-TNF: Naive; TNF IR: ND
SAM9963077


title: HF-37220

description:
Patient ID: HF-37220; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963034


title: miR10b NOdoxy no3

source_name: Human embryonic stem cells upon 14 days of neural induction. No doxycycline as added. Serve as a control to sample 7-9

value: No doxycycline


title: miR10a NOdoxy no3

source_name: Human embryonic stem cells upon 14 days of neural induction. No doxycycline as added. Serve as a control to sample 1-3


title: miR10a NOdoxy no1


title: miR10b doxy no2


title: miR10a NOdoxy no2


title: Rat 713

city: Minneapolis

first: Ann

middle: Margaret

last: Parr

address: 2001 6th St SE

department: Department of Neurosurgery

institute: University of Minnesota

data_processing:
Analysis of RNA-seq data was carried out using the Galaxy software platform hosted by the Minnesota Supercomputing Institute. Reads first underwent quality control assessment with the FastQC tool and adapter sequence contamination removal with the CutAdapt tool. Because all base positions had first-quartile Phred scores greater than 20, trimming with FastQ Trimmer was not needed.
Reads were subsequently mapped to the Rattus norvegicus RN4 reference genome with TopHat (version 1.5.0) using an empirically determined insertion size of 210 base pairs.
The mapped reads were assembled into transcripts with Cufflinks (version 0.0.6) using quartile normalization.
Transcriptional datasets for each time point were pooled using CuffMerge.
Differences between strains at each time point were identified with CuffDiff.
Genome_build: RN4
Supplementary_files_format_and_content: Files containing CuffDiff results of gene differential expression testing (between strains, at each time point). In order, the columns indicate (A) tested object identifier (ID; here, equivalent to gene ID), (B) gene ID, (C) Rat Genome Database (RGD) gene ID, (D) genomic locus, (E) sample 1 (Sprague-Dawley, SD), (F) sample 2 (athymic nude, AN), (G) test status (OK = test successful), (H) FPKM for sample 1 (SD), (G) FPKM for sample 2 (AN), (H) log2(fold change) = log2(FPKM(SD)/FPKM(AN)), (I) test statistic, (J) p value, (K) q value, (L) statistically significant (if q<0.05).

organism: Rattus norvegicus

source_name: Tissue from spinal cord injury epicenter

growth_protocol: [not applicable]

extract_protocol:
A 1-mm spinal cord segment through the injury site was harvested and flash-frozen in liquid nitrogen. RNA was extracted from tissue samples using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands). RNA quantity and quality were assessed with the Aligent 2100 Bioanalyzer (Aligent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Age-matched adult (16-18 week old) female SD (Hsd:SD, N=15) and AN (Hsd:RH-rnu/rnu, N=15) rats (Charles River, Wilmington, MA) received moderate (200 kdyn) contusion injury using the Infinite Horizon impactor (Precision Systems, Lexington, KY). At 1 or 8 weeks after injury, animals were anesthetized with ketamine (100 mg/kg IP) and xylazine (10 mg/kg IP). Animals underwent transcardial perfusion with phosphate buffered saline (PBS), and a 1-mm spinal cord segment through the injury site was harvested and flash-frozen in liquid nitrogen.

tag: strain

value: athmyic nude (AN)

tag: time point

value: Chronic (8 weeks post-injury)


title: HF-37426

description:
Patient ID: HF-37426; Tissue Diagnosis: No Dx; Remission at wk 10: Non-remitter; Prior anti-TNF: Prior anti-TNF; TNF IR: TNF IR
SAM9963055

value: UC


title: miR10a doxy no3

source_name: Human embryonic stem cells upon 14 days of neural induction. Doxyxyxline was added day11-14 in order to overexpress miR10a


title: Rat 707


title: Rat 717

value: Acute (1 week post-injury)


title: Rat 714


title: Rat 608

value: Sprague-Dawley (SD)


title: GFP_IP

description: PROTOCOL 2

tag: cell type

value: Neural progenitor cells

tag: Sex

value: F

tag: chip antibody

value: mouse monoclonal anti-FLAG M2

tag: chip antibody vendor

value: Sigma-Aldrich

tag: chip antibody cat. #


title: GFP_INPUT

description: PROTOCOL 2

tag: cell line


title: FOXP1_INPUT

description: PROTOCOL 2


title: Rat 606


title: miR10b NOdoxy no2


title: miR10b doxy no1


title: FOXP1_IP

description: PROTOCOL 2


title: Rat 605


title: Rat 620


title: miR10b NOdoxy no1


title: Rat 715


title: FOXP1_GFP_3

description: PROTOCOL 1


title: FOXP1_GFP_2

description: PROTOCOL 1


title: FOXP1_GFP_1

description: PROTOCOL 1


title: OSC_PolyA RNA-seq_rep2

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped to the D. melanogaster reference genome (version dm3) and FlyBase gene annotation v5.48 using tophat2 v2.0.12 with options -g 1 -x 1 -M --no-novel-indels.
BedTools v2.16.2 was used to calculate read coverage in 20K genomic bins and genes, according to FlyBase annotation v5.48.
genome build: dm3
processed data files format and content:  Processed data files are tab-delimited text files reporting raw read counts in 20Kb genomic bins or genes. Each file has two columns: (1) gene FlyBase ID or left bin coordinate, and (2) read count.

extract_protocol:
PolyA+ RNA extraction was carried out using RNeasy Mini Kit (Qiagen, Germany) following manufacturer's instruction. RNA quality was assessed using capillary electrophoresis on Bioanalyzer 2100 (Agilent, USA).
For library preparation, TruSeq RNA Sample Prep Kit v2 (Illumina, USA) was used following manufacturer's instructions. After preparation, libraries were quantified using Qubit fluorometer and quantitative PCR

value: OSC

value: adult

value: ovary


title: Rat 619


title: Rat 618


title: miR10a doxy no2


title: FOXP1_GFP_4

description: PROTOCOL 1


title: FOXP1_OE_3

description: PROTOCOL 1


title: FOXP1_OE_4

description: PROTOCOL 1


title: FOXP1_OE_2

description: PROTOCOL 1


title: DmBG3-c2_PolyA RNA-seq_rep2

value: third instar larval

value: central nervous system


title: DmBG3-c2_PolyA RNA-seq_rep1


title: Kc167_PolyA RNA-seq_rep2

value: late embryonic stage

value: embryo


title: S2_PolyA RNA-seq_rep2


title: D14-2366_Mg

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Sequence reads were aligned to a reference transcriptome based on ensemble hg19 assembly GRCh37 release 68 using RSEM 1.2.6 with bowtie 1.0.0.
Gene expression values produced by RSEM are reported as Fragments per Kilobase of modeled exon per Million mapped reads (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file that includes Ensembl gene ID, Ensembl transcript ID and FPKM values for each sample.

growth_protocol: hTERT-RPE1 (human telomerase-immortalised retinal pigmented epithelial cells) were were cultured in DMEM (Invitrogen) supplemented with 10% FBS, 2 mM L- glutamine and 100 U/ml penicillin/streptomycin. Cells were grown at 37°C with 5% CO2 in a humidified environment.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN).  The purified RNA was the subjected to oligo (dT) selection, fragmentation and first and double strand synthesis with the Illumina Tru-Seq kit using manufacturer’s instructions. DNA fragments were purified using SPRI-TE beads according to manufacturer’s instructions. The purified DNA was end repaired and single A bases were added for adaptor ligations. The adaptor-ligated DNA was then subjected to double SPRI purification to select for DNA inserts between 150 and 350nt. These fragments were enriched and barcoded by PCR for multiplexing. A final SPRI purification at 1.5X was performed to clean up the barcoded RNA-Seq libraries. Libraries were quantified by Advanced Analytical Fragment Analyzer and by qPCR and sequenced on a HiSeq2000 for 50nt"

treatment_protocol: For RNAseq analysis cells were either treated with 0.5uM Reversine for 24 hours, then washed and harvested 48 hours later or with BafA1 (0.1uM) or MG132 (1uM) for 6 and 24 hours, respectively.

tag: treated with

value: 1 uM MG132


title: D14-2365_Mg

value: human telomerase-immortalised retinal pigmented epithelial cells


title: FOXP1_OE_1

description: PROTOCOL 1


title: D14-2364_Baf

value: 0.1uM BafA1


title: D14-2362_Baf


title: D14-2363_Baf


title: OSC_PolyA RNA-seq_rep1


title: S2_PolyA RNA_seq_rep1


title: D14-2361_Rev

value: 0.5uM Reversine


title: OSC_HindIII Hi-C library_rep1

data_processing:
Library strategy: Hi-C
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped to the D. melanogaster reference genome (version dm3) using bowtie2 v2.2.1 with --very-sensitive option in a single-end mode.
Hi-C data were processed using ICE pipeline v0.9 with 20 iterations of iterative correction as described previously (Imakaev et al, 2012) at 20Kb resolution.
genome build: dm3
processed data files format and content:  Processed data files are genome-wide maps reporting iteratively corrected values for contacts between 20Kb bins. One processed data file is supplied for each replicate (available on the sample record) plus a merge of the two replicates for each cell line (available on the series record). The files are in a plain text format (tab-delimited) in which rows and columns correspond to 20Kb genomic bins.

extract_protocol:
Hi-C experiment was performed as described previously (Belton et al. 2012) with minor modifications that are described below. 3-5 millions of cells were pelleted and resuspended in 10 ml of 1× PBS (10 mM phosphate buffer, 2.7 mM KCI, 137 mM NaCI, pH7.4) and fixed with 1% formaldehyde (Sigma) for 10 min at room temperature. The reaction was stopped by adding 2 M glycine to a final concentration of 125 mM. Cell suspension was incubated on ice for 5 min, and then cells were pelleted (10 min at 1000 g in pre-chilled (4C) centrifuge). The supernatant was removed, the cell pellet was washed with 500 μl of 1X PBS and then frozen and, if necessary, stored in a liquid nitrogen. After thawing the cells were lysed for 15 min in 1.5 ml of ice-cold lysis buffer (50 mM Tris-HCI (pH8.0), 150 mM NaCI, 0.5% (v/v) NP-40, 1% (v/v) Triton-X100, 1× Protease Inhibitor Cocktail (CALBIOCHEM #539137 of Thermo Scientific #78430)). The nuclei were harvested at 5000 g for 7 min in pre-chilled centrifuge, washed twice with 100 μl of 1.2× restriction NEBuffer 2 (NEB) and resuspended in 200 μl of 1.2× NEBuffer 2. 20% SDS was added to a final concentration of 0.3%, and nuclei were incubated at 37C for 1h with constant shaking. After incubation, 330 μl of 1.2× NEBuffer 2 were added, 20% Triton X-100 was added to a final concentration of 1.8%, and samples were incubated for 1h in the same conditions. DNA was digested overnight with 600-800 U of 100 U/μl HindIII-HF restriction endonuclease (NEB) at 37C with shaking. Next morning, 200 U of HindIII-HF were added and samples were incubated for 2h in the same conditions. Nuclei were harvested at 5000 g for 10 min at 25C and resuspended in 50 μl of the collected supernatant. Cohesive DNA ends were biotinylated by adding 7.6 μl of the biotin fill-in mixture prepared in 1× NEBuffer 2 (0.025 mM dATP (Thermo Scientific), 0.025 mM dGTP (Thermo Scientific), 0.025 mM dTTP (Thermo Scientific), 0.025 mM biotin-14-dCTP (Invitrogen), 0.8 U/ul Klenow enzyme (NEB)). Samples were incubated at 37C for 75 min with slow shaking, then 20% SDS was added to a final concentration of 1.8%, and samples were heated at 65C for 20 min to inactivate Klenow enzyme and residual HindIII-HF. The samples were transferred into 10-ml tubes with 3 ml of 1× T4 DNA ligase reaction buffer (Thermo Scientific) supplied with 1.8% Triton X-100, incubated at 37C for 1h and then cooled on ice. Next, 100 U of T4 DNA ligase (Thermo Scientific) was added and the DNA was ligated for 6 h at 22C with slow agitation. The cross-links were reversed by incubation at 65C overnight in the presence of proteinase K (100 ug/ml). After cross-link reversal, DNA was purified by single phenol-chloroform extraction followed by ethanol precipitation (tRNA (Sigma) at a concentration of 7.5 ug/ml and glycogen (Thermo Scientific) at a concentration of 20 ug/ml were used as co-precipitators due to a low amount of DNA in the samples). After precipitation, the pellets was dissolved in 500 μl 10 mM Tris-HCI pH8.0, and DNA was additionally purified to remove residual salts and DTT on AMICON Ultra Centrifugal Filter Units (0.5 ml, 30K, Millipore #UFC5030BK) by washing with 10 mM Tris-HCI pH 8.0 (after two washing steps the final volume of the DNA solution was 40-50 μl). Biotinylated nucleotides from non-ligated DNA ends were removed by incubation of Hi-C libraries in the presence of 1.5 U of T4 DNA polymerase (NEB) in NEBuffer 2 supplied with 0.025 mM dATP and 0.025 mM dGTP at 20C for 4 h. Next, DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA pellets were dissolved in 500 μl of sonication buffer (50 mM Tris-HCI (pH 8.0), 10 mM EDTA, 0.1% SDS), the samples were treated with 50 ug of RNAse A (Thermo Scientific) for 45 min at 37C, and DNA was then sheared to the size of approximately 100-1000 bp using a VirSonic 100 (VerTis). Samples were concentrated (and simultaneously purified) on AMICON Ultra Centrifugal Filter Units. Fraction of 100-500 bp DNA fragments was captured by using Agencourt AMPure XP beads (Beckman Coulter), DNA was eluted with 50 μl of 10 mM Tris-HCI (pH 8.0).
The DNA ends after the sonication step were repaired by adding 62.5 μl MQ water, 14 μl of 10× T4 DNA ligase reaction buffer, 3.5 μl of 10 mM dNTP mix, 5 μl of 3 U/μl T4 DNA polymerase (NEB), 5 μl of 10 U/μl T4 polynucleotide kinase (NEB), 1 μl of 5 U/μl Klenow DNA polymerase (NEB) and incubating at 20C for 30 min. DNA was purified with Agencourt AMPure XP beads and eluted with 50 μl of 10 mM Tris-HCI (pH 8.0). To perform an A-tailing reaction, the DNA samples were then supplemented with 6 μl 10X NEBuffer 2, 1.2 μl of 10 mM dATP, 1 μl of MQ water and 3.6 μl of 5 U/μl Klenow (exo-) (NEB). The reactions were carried out for 30 min at 37C in PCR-machine and then their enzyme was heat-inactivated by incubation at 65C for 20 min. DNA was purified using Agencourt AMPure XP beads and eluted with 100 μl of 10 mM Tris-HCI (pH 8.0). Biotin pull-down of the ligation junctions was performed as described previously (Belton et al. 2012) with minor modifications. Briefly, 4 μl of MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture biotinylated DNA, and the volumes of all buffers were decreased by 4 times. The washed beads with captured ligation junctions were resuspended in 50 μl of adapter ligation mixture composed of 41.5 μl MQ water, 5 μl 10X T4 DNA ligase reaction buffer (Thermo Scientific), 2.5 μl of Illumina TruSeq adapters and 1 μl of 5 U/μl T4 DNA ligase (Thermo Scientific). Adapter ligation was performed at 22C for 2.5 h. Then beads were sequentially washed twice with 100 μl of TWB (5 mM Tris-HCl (pH8.0), 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), once with 100 μl of 1× binding buffer (10 mM Tris-HCl (pH8.0), 1 mM EDTA, 2 M NaCl) and once with 100 μl of CWB (10 mM Tris-HCI (pH8.0), 50 mM NaCI) and then resuspended in 20 μl of MQ water. Test PCR reactions containing 4 μl of streptavidin bound Hi-C library were performed to determine the optimal number of PCR cycles needed to generate enough PCR products for sequencing. PCR reactions (volume of each reaction is 25 μl) were performed using KAPA High Fidelity DNA Polymerase (KAPA) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 min at 98C followed by 6, 9, 12, 15 and 18 cycles of 20 s at 98C, 15 s at 65C, 20 s at 72C. The PCR reactions were run on a 2% agarose gel supplied with ethidium bromide and the number of PCR cycles necessary to obtain sufficient amount of DNA was determined based on visual inspection of gels (typically 12-15 cycles). Four preparative PCR reactions were performed for each sample. PCR mixtures were combined, PCR products were purified with QIAGEN PCR Purification Kit. The DNA was eluted with 50 μl of 10 mM Tris-HCI (pH 8.0) and was run on a 1.8% agarose gel supplied with ethidium bromide. 200-600 bp DNA fragments were cut off the gel, purified on QIAGEN Gel Extraction Kit and sequenced on Illumina HiSeq 2000 by paired-end 101-nt reads.


title: OSC_HindIII Hi-C library_rep2


title: Kc167_HindIII Hi-C library_rep2


title: DmBG3-c2_HindIII Hi-C library_rep1


title: D14-2357_Control


title: D14-2358_Control


title: D14-2356_Control


title: S2_HindIII Hi-C library_rep2


title: A12/A12 adults r2

status: Public on Oct 25 2015

city: Moscow

first: Sergey

middle: A

last: Lavrov

address: Kurchatov sq. 2

department: DMBC

institute: IMG

data_processing:
Basecalling by Illumina Casava1.8 software
Preprocessing: Sequenced reads were converted to Sanger quality scores type by Galaxy tool FASTQ Groomer 1.0.4 for subsequent manipulations. Sequencing artefacts were removed by Galaxy tool Remove sequencing artifacts. Quality trimming was done by FASTQ Quality Trimmer Galaxy tool (False, 5' and 3', 1, 1, 0, >=38). Adapter trimming and short reads removal were done by Flexbar (2.4) in Galaxy (Max uncalled:1, Adapter removal:on, Trim-end mode:Any, Min-overlap:5, Threshold:3, Minimum read length:15), using adapter sequences from "2011-08-03 Illumina Adapter Sequence Letter". rRNA sequences were removed by assembly of RNA-seq reads to Drosophila rDNA sequences using Bowtie2 with default parameters and taking nonaligned sequences for further analysis.
Mapping: Transcripts were assembled by Tophat 0.6 (Galaxy tool) using preprocessed reads and dm3 R5 Drosophila genome as reference. Parameters list: (Max realign edit distance:0, Max edit distance:2, Library Type:FR Unstranded, Final read mismatches:2, Use bowtie -n mode:No, Anchor length:8, Maximum number of mismatches that can appear in the anchor region of spliced alignment:0, The minimum intron length:29, The maximum intron length:167000, Allow indel search:No, Maximum number of alignments to be allowed:20, Minimum intron length that may be found during split-segment (default) search:29, Maximum intron length that may be found during split-segment (default) search:167000, Number of mismatches allowed in each segment alignment for reads mapped independently:2, Minimum length of read segments:20, Use Coverage Search:Yes, Minimum intron length that may be found during coverage search:29, Maximum intron length that may be found during coverage search:167000, Use Microexon Search:No, Do Fusion Search:No, Set Bowtie2 settings:Yes, Use Preset options:Yes, Preset option:Very sensitive).
FPKM calculation: Was done by Cufflinks (Galaxy Tool Version 0.0.7) using Tophat bam output and dm3_genes.gtf dm3 genes list from Ensemble. Parameters: Max Intron Length:167000, Min Isoform Fraction:0.1, Pre MRNA Fraction:0.1, Reference Annotation:235: dm3_genes.gtf, Count hits compatible with reference RNAs only:not used (parameter was added after this job was run), Perform Bias Correction:Yes, Reference sequence data:cached, Using reference genome:dm3_index (value not yet validated), Use multi-read correct:Yes. Genes output table from Cufflinks was used for gene-level FPKM data.
Results: Cufflinks output gene-level FPKM tables were processed in Excel. Genes with zero FPKM or with 3x or more inter-repeat difference were removed, and the average between-repeat FPKM was calculated for the remaining (app. 9000) genes. This values were used for log2(A4(ΔP)/A12) calculation and generation of
Genome_build: D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3)
Supplementary_files_format_and_content: Individual samples: Cufflinks FPKM output, tab-delimited. Total results (on series record): calculated log2 ratios for Drosophila genes. Log2(A4/A12)L - larvae, Log2(A4/A12)A - adults

source_name: whole organism

growth_protocol: Flies were cultivated with standard media at 18C

extract_protocol:
RNA samples were prepared from 2-3 day adult and third instar larvae females of genotypes A12/A12 and A4/A4. Homozygous non-fluorescent A4/A4 female larvae were picked from A4/CyO-GFP stock. Samples were  prepared  according to standard Illumina protocol (TruSeq RNA Sample Prep Kit after rRNA depletion by Ribo-Zero™ rRNA Removal Kit (Human/Mouse/Rat), Epicentre)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: adults

tag: age

value: 2-3 days

tag: genotype

tag: gender

value: female


title: Kc167_HindIII Hi-C library_rep1

tag: tissue


title: D14-2359_Rev


title: Kc167_PolyA RNA-seq_rep1

tag: development stage


title: D14-2367_Mg


title: S2_HindIII Hi-C library_rep1


title: A12/A12 larvae r2

value: larvae

value: third instar


title: A12/A12 adults r1


title: A12/A12 larvae r1


title: DmBG3-c2_HindIII Hi-C library_rep2


title: A4/A4 adults r2


title: A4/A4 larvae r2


title: A4/A4 larvae r1


title: A4/A4 adults r1


title: D14-2360_Rev


title: s18

status: Public on Oct 24 2015

city: New Delhi

first: Dinesh

last: Gupta

state: Delhi

address: Aruna Asaf Ali Marg

department: Structural and Computational Biology

country: India

institute: ICGEB

data_processing:
The adapter sequences were trimmed and low quality sequences were filtered using FastX tool kit [http://hannonlab.cshl.edu/fastx_toolkit/], then mapped to rice genome using bowtie [http: //bowtie.cbcb.umd.edu.] with parameters -a -v 0.
The frequencies of miRNAs were normalized to 10^-7 by total number of small reads (excluding reads which did not map to the rice genome or other ncRNA’s) in each library.
Genome_build: Assembly downloaded from http://rice.genomics.org.cn/rice/link/download.jsp dated 1st August 2003.
Supplementary_files_format_and_content: tab-delimited text files include abundance values for each Sample

organism: Oryza sativa

source_name: Panicle

growth_protocol: Different rice varieties were grown under green house conditions at 30°C and relative humidity of 70%. Heat stress was given at 42°C for 6 hours. Flag leaf and root are harvested and used for RNA isolation.

extract_protocol:
Total rna was isolated using Trizol reagent and enriched with 50% PEG and 0.1% Nacl for small rna isolation. The RNA bands of corresponding size ranging between 15-30 nucleotides were gel purified. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: physiology

value: Normal

tag: character

value: Heat Tolerant

tag: cultivar


title: s17

source_name: Flag Leaf

value: Heat Stress

value: Heat Susceptible


title: s11


title: s12


title: s19


title: s6

value: Shatabdi


title: s16


title: s14

value: Lalat


title: s15


title: s13


title: SanbornRao-2015-HIC045

status: Public on Oct 23 2015

city: Houston

first: Suhas

last: Rao

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Library strategy: HiC-Seq
The paired end reads were aligned separately using BWA against the b37 human build or the mm9 mouse build
PCR duplicates, low mapping quality and unligated reads were removed using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al)
Contact matrices were constructed at various resolutions and normalized using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al)
loops were annotated using HiCCUPS (see Rao, Huntley, et al. Cell 2014), domains were annotated using Arrowhead (see Rao, Huntley, et al. Cell 2014),
genome build: b37 (human), mm9 (mouse)
processed data files format and content: HiCCUPS_looplist.txt files contain loop calls generated via HiCCUPS; first three fields represent the locus participating in the loop closer to the p-end of the chromosome; fields 4-6 represent the locus participating in the loop closer to the q-end of the chromosome; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 represents the observed number of counts at the loop; fields 9-12 represent the expected number of counts at the loop using four different expected models; fields 13-16 are the q-values over each of the expected values; field 17 is the number of enriched pixels that was clustered into a particular loop; field 18-19 are the centroid of the loop; field 20 is the radius of the loop
processed data files format and content: Arrowhead_domainlist.txt files contain domain calls generated via Arrowhead; first 6 fields represent the boundaries of the domain; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 is the corner score for the domain (see Rao, Huntley, et al. Cell 2014); fields 9-12 are the component scores used in the Arrowhead algorithm (see Rao, Huntley, et al. Cell 2014)

source_name: haploid fibroblast-like

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, 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 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq/HiSeq2500/HiSeqX following the manufacturer's protocols

tag: protocol

value: in situ HYbrid Capture Hi-C


title: SanbornRao-2015-HIC044


title: uqc3

data_processing:
The adapter sequences were trimmed and low quality sequences were filtered using FastX tool kit [http://hannonlab.cshl.edu/fastx_toolkit/], then mapped to Arabidopsis genome using bowtie [http: //bowtie.cbcb.umd.edu.] with parameters -a -v 0.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include abundance values for each Sample

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Arabidopsis plants were grown under green house conditions at 21°C and relative humidity of 50-60%. Roots are harvested and used for RNA isolation.

tag: ecotype

value: Col 0

tag: RNAi mutant

value: Wild Type


title: uqc8


title: s10


title: s9


title: t1

data_processing:
The adapter sequences were trimmed and low quality sequences were filtered using FastX tool kit [http://hannonlab.cshl.edu/fastx_toolkit/], then mapped to tomato genome using bowtie [http: //bowtie.cbcb.umd.edu.] with parameters -a -v 0.
Genome_build: SL2.40 (http://solgenomics.net/organism/Solanum_lycopersicum/genome)
Supplementary_files_format_and_content: tab-delimited text files include abundance values for each Sample

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Seeds of tomato cv. Pusa Ruby were obtained from NSC, Pusa Campus, New Delhi, were soaked in water and kept for germination. At the seedling stage (1 month) these were transferred to vermiculite in green house (28°C, 14 hours light and 10 hours dark with 70% relative humidity) for further growth of plant. To get ToLCV infected samples, agro infiltration of tomato plants were carried out using Agrobacterium tumefaciens EHA105 harbouring plasmid constructs, containing dimers of ToLCNDV ‘A’ [HQ264185.1] and ToLCNDV ‘B’ [HQ2641856.1] genome.

extract_protocol:
Total rna was isolated using Trizol reagent and enriched with 50% PEG and 0.1% Nacl for small rna isolation. The RNA bands of corresponding size ranging between 15-30 nucleotides were gel purified. The purified RNAs were ligated with 3′ and 5′ adapters; first strand cDNA synthesis was carried out with manufacturer’s instruction and then amplified using adapter specific primers. The amplified products were purified on 6% UREA-PAGE and subjected to next generation sequencing using GAII Illumina Genome Analyzer (USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Healthy

value: ToLCV Susceptible

value: Pusa Ruby


title: uqc4


title: t2

value: ToLCV infected


title: SanbornRao-2015-HIC046


title: SanbornRao-2015-HIC003

value: in situ Hi-C


title: SanbornRao-2015-HIC001


title: s5


title: pEF1del-mRFP-oligos-eGFP library total

first: Shira

last: Weingarten-Gabbay

address: 75 Ames St

institute: The Broad Institute

data_processing:
Single-end  reads in the length of 50 or 200nt  were trimmed to 45nt containing the common priming site and the unique 25nt of the oligo’s variable region.
Trimmed reads were mapped to the synthetic library sequences using Novoalign aligner
The number of reads for each designed oligo was counted in each sample.
Genome_build: Synthetic library oligonucleotides
Supplementary_files_format_and_content: Tab delimited file that holds the synthetic oligo id number, sequence, cap-independnet translation activity, promoter activitiy and cDNA/gDNA ratio

organism: synthetic construct

source_name: Designed oligonucleotides

extract_protocol:
none provided by the submitter
Illumina adaptors ligation

tag: functional assay

value: promoter activity

tag: master plasmid


title: pEF1del-mRFP-oligos-eGFP library eGFP positive population


title: s8


title: SanbornRao-2015-HIC002


title: uqc7


title: pEF1-mRFP-oligos-eGFP library total

value: cap-independent translation


title: pEF1-mRFP-oligos-eGFP library 16 expression Bins


title: SanbornRao-2015-HIC005


title: SanbornRao-2015-HIC005_Hi-C2


title: SanbornRao-2015-HIC004


title: SanbornRao-2015-HIC073