title: CD8+_T_cells_BGI

description: Illumina HiSeq 2000 (BGI)

source_name: Cells

value: CD8+ T cells

value: Human (donor B)


title: single H9 hESC cell [H9_Batch1.004]

status: Public on Jul 21 2016

type: SRA

city: Madison

first: Ning

last: Leng

state: WI

address: 330 N Orchard St

country: USA

institute: Morgridge Institute for Research

description:
H9 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
sc_cell_type_ec.csv
H9_Batch1.004

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequencing reads were mapped to hg19 using bowtie 0.12.8
Gene expected counts were calculated using RSEM 1.2.3
Genome_build: hg19
Supplementary_files_format_and_content: Expected counts

molecule: total RNA

organism: Homo sapiens

source_name: undifferentiated human embryonic stem cells

growth_protocol: Growth can treatment conditions were listed in additional columns in the SAMPLE section

extract_protocol:
Single-cell suspentions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
For scRNA-seq, diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). Libraries were multiplexed at 24 libraries per lane, and single-end reads of 67-bp sequencing was performed on an Illumina HiSeq 2500 system. For bulk RNAseq, mRNA is isolated from purified 100 ng total RNA using oligo-dT beads. Isolated mRNA is fragmented in reverse transcription buffer with heat and then reverse-transcribed with SmartScribe reverse transcriptase using a random hexamer oligo.After reverse transcription, RNA is removed by RNaseA and RNaseH treatment. A partial Illumina 5′ adaptor is then ligated to the single stranded cDNA using T4 RNA ligase 1 and incubated overnight at 22°C. After purification, ligated cDNA is amplified by 18 cycles of PCR using oligos that contain full Illumina adaptors. Indexed cDNA libraries are pooled and sequenced on an Illumina HiSeq2500 with a single 51 bp read and a 10 bp index read.

tag: passage

value: passage 30-35

tag: facs sorting

value: not sorted


title: single H9 hESC cell [H9_Batch1.003]

description:
H9 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
sc_cell_type_ec.csv
H9_Batch1.003

treatment_protocol: Growth can treatment conditions were listed in additional columns in the SAMPLE section


title: single H9 hESC cell [H9_Batch1.005]

description:
H9 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
sc_cell_type_ec.csv
H9_Batch1.005


title: single H9 hESC cell [H9_Batch1.001]

description:
H9 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
sc_cell_type_ec.csv
H9_Batch1.001


title: Monocytes_BGI

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description: Illumina HiSeq 2000 (BGI)

data_processing:
Trim low quality reads and adapters using Trimmomatic software
Mapping trimmed reads to human reference genome using TopHat software
Transcript assembly and quantification using Cufflinks software
Genome_build: GRCh37
Supplementary_files_format_and_content: Table-delimited text files include FPKM value of 156600 transcripts across 28 samples

growth_protocol: Donor E is a fetus, donor A and B were adults

extract_protocol:
Total RNA was extracted from tissue by using the miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All the samples were histologically confirmed to be normal

tag: tissue type

value: Monocytes

tag: donor


title: PPL05TRGP_2Y

city: Chongqing

first: Qingzhu

last: Jia

address: Xinqiao

department: Department of Onoclogy

institute: XinQiao Hospital

data_processing:
Library strategy: T-cell repertoire sequencing
Basecall using IonTorrent built-in software
Raw repertoire reads were aligned to the mus musculus T-cell receptor beta-chain using MATLAB
V- and J-segment usage were determined according to sequence alignment
Abundance of unique T-cell clones were calculated based on aligned tcr nucleotide sequence/amino acid sequence
Supplementary_files_format_and_content: Saved as .MAT format including TCR NT/AA sequence, frequencies, V- and J-segment usage, and basic information of this sample

organism: Mus musculus

source_name: Labeled regulatory T-cell from Peyer's Patch

extract_protocol:
Total RNA was extracted from trizol-lysed samples using the RNeasy Mini Kit according to standard protocol
A multiplex PCR system was introduced to amplify the CDR3 region of rearranged TCRB loci

treatment_protocol: TCRδCreERR26ZsGreen mice (4-week old) were treated with 3 doses of 1mg tamoxifen i.p. every other for long-term tracing day

tag: tissue

value: Peyer's Patch

tag: cell type

value: T cell

tag: strain

tag: tracking

value: 1.5 years


title: Ovary_BGI

description: Illumina HiSeq 2000 (BGI)

source_name: Tissue

value: Ovary

value: Human (donor E)


title: B_cells_BGI

description: Illumina HiSeq 2000 (BGI)

value: B cells


title: PPL05TRGN_2Y

source_name: Non-labeled regulatory T-cell from Peyer's Patch


title: single H9 hESC cell [H9_Batch1.002]

description:
H9 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
sc_cell_type_ec.csv
H9_Batch1.002


title: CD4+_T_cells_BGI

description: Illumina HiSeq 2000 (BGI)

value: CD4+ T cells


title: Testis_BGI

description: Illumina HiSeq 2000 (BGI)

value: Testis

value: Human (donor A)


title: SPL01TCGN_2Y

source_name: Non-labeled conventional T-cell from spleen

value: spleen


title: PPL05TCGP_2Y

source_name: Labeled conventional T-cell from Peyer's Patch


title: PPL05TCGN_2Y

source_name: Non-labeled conventional T-cell from Peyer's Patch


title: bulk H9 hESCs differentiated for 96 hours [H9_96h_rep2]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_96h_rep2

source_name: H9 cells differentiated for 96 hours


title: PPL04TRGP_2Y


title: bulk H9 hESCs differentiated for 96 hours [H9_96h_rep1]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_96h_rep1


title: bulk H9 hESCs differentiated for 72 hours [H9_72h_rep3]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_72h_rep3

source_name: H9 cells differentiated for 72 hours


title: Colon_BGI

description: Illumina HiSeq 2000 (BGI)

value: Colon


title: PPL04TRGN_2Y


title: PPL04TCGP_2Y


title: bulk H9 hESCs differentiated for 72 hours [H9_72h_rep2]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_72h_rep2


title: PPL06TCGN_2Y


title: grayMatterRNAseq_5353G

city: New York

first: Aslihan

last: Dincer

address: 1470 Madison Ave, 9th Floor Room 202

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing libraries were prepared according to the NuGen Ovation RNASeq version 2 protocol, and run on the paired-end 50 bp module in Illumina HiSeq 2000(Eurofins MWG; Operon). RNA-seq raw reads were aligned to the UCSC Homo sapiens reference genome build 19 using the STAR aligner. Mapped reads on gene were counted using HTSeq python framework. S Anders, T P Pyl, W Huber: HTSeq — A Python framework to work with high-throughput sequencing data. bioRxiv 2014. doi: 10.1101/002824.
Genome_build: hg19
Supplementary_files_format_and_content: text file for gene's raw count for each sample

source_name: Cortical Gray Matter

extract_protocol: NuGen Ovation RNASeq

value: Cortical Gray Matter


title: PPL04TCGN_2Y


title: grayMatterRNAseq_26G


title: bulk H9 hESCs differentiated for 36 hours [H9_36h_rep3]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_36h_rep3

source_name: H9 cells differentiated for 36 hours


title: PPL03TRGP_2Y


title: bulk H9 hESCs differentiated for 36 hours [H9_36h_rep2]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_36h_rep2


title: bulk H9 hESCs differentiated for 96 hours [H9_96h_rep3]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_96h_rep3


title: PPL03TRGN_2Y


title: grayMatterRNAseq_25G


title: grayMatterRNAseq_1970G


title: grayMatterRNAseq_2149G


title: bulk H9 hESCs differentiated for 36 hours [H9_36h_rep1]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_36h_rep1


title: PPL03TCGP_2Y


title: bulk H9 hESCs differentiated for 24 hours [H9_24h_rep2]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_24h_rep2

source_name: H9 cells differentiated for 24 hours


title: PPL03TCGN_2Y


title: PPL02TRGN_2Y


title: Prostate_BGI

description: Illumina HiSeq 2000 (BGI)

value: Prostate


title: bulk H9 hESCs differentiated for 24 hours [H9_24h_rep1]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_24h_rep1


title: Esophagus_BGI

description: Illumina HiSeq 2000 (BGI)

value: Esophagus


title: bulk H9 hESCs differentiated for 24 hours [H9_24h_rep3]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_24h_rep3

value: passage 30-35


title: grayMatterRNAseq_1756G


title: whiteMatterRNAseq_26W

source_name: Subcortical White Matter

value: Subcortical White Matter


title: PPL02TRGP_2Y


title: whiteMatterRNAseq_5353W


title: bulk H9 hESCs differentiated for 72 hours [H9_72h_rep1]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_72h_rep1

value: not sorted


title: bulk H9 hESCs differentiated for 12 hours [H9_12h_rep3]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_12h_rep3

source_name: H9 cells differentiated for 12 hours


title: whiteMatterRNAseq_25W


title: whiteMatterRNAseq_2149W


title: PPL02TCGN_2Y

value: Peyer's Patch


title: whiteMatterRNAseq_1970W


title: bulk TB derived from H1 hESC [TB_rep2]

description:
H1 were seeded in E7 (E8 minus FGF2) with 50ng/ml BMP4 and SB431542
bulk_cell_type_ec.csv
TB_rep2

source_name: trophoblast-like cells differentiated from H1

value: FACS sorted by TROP2+


title: PPL02TCGP_2Y

value: T cell

value: 1.5 years


title: bulk H9 hESCs differentiated for 12 hours [H9_12h_rep2]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_12h_rep2


title: whiteMatterRNAseq_1756W


title: PPL01TCGP_2Y


title: bulk TB derived from H1 hESC [TB_rep1]

description:
H1 were seeded in E7 (E8 minus FGF2) with 50ng/ml BMP4 and SB431542
bulk_cell_type_ec.csv
TB_rep1


title: bulk NPC derived from H1 hESC [NPC_rep2]

description:
The NPC differentiation medium consists of E6 (E8 minus FGF2, minus TGFb1), with 5 mg/ml insulin, SB431542 (10 _M) and 100ng/ml Noggin
bulk_cell_type_ec.csv
NPC_rep2

source_name: neuronal progenitor cells differentiated from H1

value: FACS sorted  by mCherry+


title: bulk NPC derived from H1 hESC [NPC_rep1]

description:
The NPC differentiation medium consists of E6 (E8 minus FGF2, minus TGFb1), with 5 mg/ml insulin, SB431542 (10 _M) and 100ng/ml Noggin
bulk_cell_type_ec.csv
NPC_rep1


title: SPL03TRGP_2M

source_name: Labeled regulatory T-cell from spleen

value: 2 month


title: SPL03TCGN_2M


title: SPL03TRGN_2M

source_name: Non-labeled regulatory T-cell from spleen


title: bulk HFF  [HFF_rep3]

description:
Human foreskin fibroblast is cultured in DMEM/F12 with 10% FBS
bulk_cell_type_ec.csv
HFF_rep3

source_name: human foreskin fibroblast

value: passage 8-12


title: PPL01TRGP_2Y

source_name: Labeled regulatory T-cell from Peyer's Patch


title: bulk HFF  [HFF_rep1]

description:
Human foreskin fibroblast is cultured in DMEM/F12 with 10% FBS
bulk_cell_type_ec.csv
HFF_rep1


title: bulk EC derived from H1 hESC [EC_rep3]

description:
H1 were seeded in E8 with BMP4 (5ng/ml) and Activin A (25ng/ml) for the first 2 days, then switched to supplement with VEGF and WNT for 3 days
bulk_cell_type_ec.csv
EC_rep3

source_name: endothelial cells differentiated from H1

value: FACS sorted by CD31+/CD34+


title: SPL02TRGP_2M


title: bulk EC derived from H1 hESC [EC_rep1]

description:
H1 were seeded in E8 with BMP4 (5ng/ml) and Activin A (25ng/ml) for the first 2 days, then switched to supplement with VEGF and WNT for 3 days
bulk_cell_type_ec.csv
EC_rep1


title: bulk EC derived from H1 hESC [EC_rep2]

description:
H1 were seeded in E8 with BMP4 (5ng/ml) and Activin A (25ng/ml) for the first 2 days, then switched to supplement with VEGF and WNT for 3 days
bulk_cell_type_ec.csv
EC_rep2


title: bulk H9 hESCs differentiated for 12 hours [H9_12h_rep1]

description:
H9 cells were differentiated in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 2 days. Cells are sampled at the indicated time.
bulk_time_course_ec.csv
H9_12h_rep1


title: SPL02TRGN_2M


title: bulk HFF  [HFF_rep2]

description:
Human foreskin fibroblast is cultured in DMEM/F12 with 10% FBS
bulk_cell_type_ec.csv
HFF_rep2


title: SPL02TCGP_2M

source_name: Labeled conventional T-cell from spleen


title: SPL01TRGP_2M


title: SPL01TCGP_2M


title: PPL01TRGN_2Y

source_name: Non-labeled regulatory T-cell from Peyer's Patch


title: bulk DEC derived from H1 hESC [DEC_rep1]

description:
H1 cells were seeded in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 3 days.
bulk_cell_type_ec.csv
DEC_rep1

source_name: definitive endoderm cell differentiated from H1

value: FACS sorted by CXCR4+


title: bulk H9 hESC cell [H9_rep3]

description:
H9 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
bulk_cell_type_ec.csv
H9_rep3

source_name: undifferentiated human embryonic stem cells


title: PPL01TCGN_2Y

source_name: Non-labeled conventional T-cell from Peyer's Patch


title: SPL01TRGN_2M

value: spleen


title: SPL03TCGP_2M


title: bulk H9 hESC cell [H9_rep2]

description:
H9 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
bulk_cell_type_ec.csv
H9_rep2


title: SPL01TCGN_2M

source_name: Non-labeled conventional T-cell from spleen


title: bulk H9 hESC cell [H9_rep1]

description:
H9 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
bulk_cell_type_ec.csv
H9_rep1


title: SPL03TRGP_2W

value: 2 weeks


title: bulk H1 hESC cell [H1_rep4]

description:
H1 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
bulk_cell_type_ec.csv
H1_rep4


title: SPL03TRGN_2W


title: SPL03TCGP_2W


title: bulk H1 hESC cell [H1_rep2]

description:
H1 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
bulk_cell_type_ec.csv
H1_rep2


title: SPL02TRGP_2W


title: SPL02TCGN_2M


title: SPL03TCGN_2W


title: bulk H1 hESC cell [H1_rep3]

description:
H1 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
bulk_cell_type_ec.csv
H1_rep3


title: bulk DEC derived from H1 hESC [DEC_rep2]

description:
H1 cells were seeded in E8 with BMP4 (5ng/ml), Activin A (25ng/ml) and CHIR99021 (1uM) for the first 2 days, then withdraw CHIR99021 for 3 days.
bulk_cell_type_ec.csv
DEC_rep2


title: bulk H1 hESC cell [H1_rep1]

description:
H1 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel
bulk_cell_type_ec.csv
H1_rep1


title: SPL02TRGN_2W


title: N3KD0h_2

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: Sample 6

data_processing:
Illumina software used for basecalling.
Fastq files were aligned with hg19 genome (iGenomes, Illumina) using TopHat v. 2.0.9 and output as bam files.
Bam files were grouped and compared using cuffdiff v. 2.2.1 using the genes.gtf transcript map provided for hg19 by iGenomes (archive-2012-03-09-03-24-41).
Cuffdiff output was loaded into the R/Bioconductor package cummeRbund for analysis and visualization
The processed data was output using the repFpkmMatrix() function in cummeRbund
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are FPKM for each replicate sample, summarized by RefSeq ID.  Format is csv.

source_name: MCF-7 Cells infected with lentivirus (MISSION TRC shRNA against Nudt3, TRCN0000299497))

growth_protocol: MCF-7 cells were grown according to ATCC-recommended protocols

extract_protocol:
Total cellular RNA was prepared by extraction with Trizol following standard methods
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with shRNA-expressing lentiviruses.

tag: cell line

value: MCF-7 is a human breast adenocarcinoma cell line

tag: treatment

value: Expressing shRNA targeting Nudt3


title: N3KD0h_1

description: Sample 5


title: SPL02TCGP_2W


title: AUF1 KO-2

city: NY

first: Devon

last: Chenette

address: 450 East 29 Street

institute: NYU School of Medicine

data_processing:
Sequenced reads were mapped to mm9 whole genome using tophat v2.0.9 with default parameters
Library size (RPKM) and differential expression were calculated with cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: RPKM and differential expression values

source_name: AUF1 KO_satellite cell

extract_protocol:
Skeletal muscle hindlimb from 4 month old mice was digested in collagenase and subject to FACs sorting using Sdc4 as a positive marker, RNA was isolated using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 4 months

tag: genotype/variation

value: AUF1-null (KO)

value: Skeletal muscle hindlimb

value: primary satellite cells


title: SPL01TRGP_2W


title: Con0h_2

description: Sample 3

source_name: MCF-7 Cells infected with lentivirus (MISSION TRC shRNA against non-mammalian control, SHC002V)

value: Expressing non-mammalian control shRNA


title: SPL02TCGN_2W


title: AUF1 KO-3


title: AUF1 KO-1


title: Con0h_1

description: Sample 2


title: SPL01TRGN_2W


title: SPL01TCGP_2W


title: Con0h_0

description: Sample 1


title: WT-3

source_name: WT_satellite cell

value: wild type (WT)


title: SPL01TCGN_2W

value: T cell


title: WT-2


title: hos1-3 rep3

city: Harpenden

first: Dana

middle: Reid

last: MacGregor

state: Hertfordshire

address: Rothamsted Research

department: Biointeractions and Crop Protection

country: United Kingdom

institute: Rothamsted Research

data_processing:
The resulting FASTQ files contained 262,407,174 reads for Col and 258,662,478 reads for hos1-3.
These were then filtered using the fastq-mcf program from the ea-utils package (http://code.google.com/p/ea-utils/) with the parameters -x 0.01 -q 20 -p 10 -u. Spike-in reads were removed using Bowtie and the lower limit of detection quantified using custom scripts.
The remaining reads were aligned using Tophat v1.4.1 and the following parameters: -I 10,000 -r 50–mate-std-dev 100 –library-type fr-unstranded.
The Cufflinks package was used to quantify gene and isoform abundance using the -G flag. The 17 cuffcompare and cuffdiff components of Cufflinks were used to quantify gene and isoform differential expression (Trapnell et al., 2012).
Genome_build: The TAIR10 reference sequence was used.
Supplementary_files_format_and_content: cufflinks output file; Gene counts provided

organism: Arabidopsis thaliana

source_name: hos1-3_14 day old seedlings

growth_protocol: Col and hos1-3 seeds were surface sterilized and stratified at 4°C for 2 to 4 d on Murashige and Skoog (MS) agar (Melford) and 0.9% agar (Sigma-Aldrich) with no Suc added to the media, grown for 14 days at 22°C in 12:12 light and harvested at dawn into liquid Nitrogen.

extract_protocol:
RNA was extracted using the standard protocols for Qiagen RNeasy plant mini kit with the additional steps for DNase treatment.
Five micrograms of RNA was submitted to sequencing using standard protocols for Illumina TruSeq (version 3) technologies. The input material was spiked with ∼1% Ambion ERCC RNA spike-in mix. Samples may also contain 1-2% PhiX which is used as a control. Samples are pre-filtered using Bowtie to remove reads matching this sequence.

treatment_protocol: Col and hos1-3 materials were treated identically.

tag: ecotype background

value: Col

tag: developmental stage

value: 14 day old seedlings


title: hos1-3 rep2


title: Wild type Columbia rep3

source_name: WT_14 day old seedlings

value: wild type


title: hos1-3 rep1


title: WT-1


title: Wild type Columbia rep2


title: MFB

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

description: Double fimbriae mutant (MFB)

data_processing:
Illumina Casava1.8 software used for base-calling and demultiplexing
Genome_build: Ensembl70
Supplementary_files_format_and_content: cuffdiff.txt, including values of rpkm, log2foldchage, p-value

source_name: Monocyte-derived dendritic cells (MoDCs)_MFB

growth_protocol: Porphyromonas gingivalis strains:- Four P. gingivalis strains were used in this study; 1) Pg381, which expresses both minor (Mfa1) and major (FimA) fimbriae, 2) isogenic minor fimbria-deficient mutant (FimA+Pg), which expresses only the major fimbriae, 3) isogenic major fimbria-deficient mutant (Mfa1+Pg), which expresses only the minor fimbriae and 4) the double fimbriae mutant (MFB). P. gingivalis strains were maintained anaerobically in (10% H2, 10% CO2, and 80% N2) in a Forma Scientific anaerobic system glove box model 1025/1029 at 37°C in Difco anaerobe broth MIC. Mutant strains were maintained using erythromycin (5 μg/ml) for mutant Mfa1+Pg, tetracycline (2 μg/ml) for mutant FimA+Pg and both erythromycin and tetracycline for double fimbriae mutant MFB.

extract_protocol:
For RNA isolation:- Total RNA was isolated using RNeasy kit (Cat. no. 74104) according to the manufacturer’s instruction (Qiagen, Valencia, CA).  Illumina TruSeq RNA Sample Prep Kit (Cat# FC-122-1001) was used with 800 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: DC infection with Porphyromonas gingivalis:- Bacterial suspensions were washed five times in PBS and re-suspended for spectrophotometer reading at OD 660 nm of 0.11, which previously determined to be equal to 5 x 107 CFU. For bacterial CFSE staining, the suspension were washed (3 times) and re-suspended in 5 μM of CFSE in PBS. The bacteria were incubated for 30 min at 37°C in the dark. MoDCs were pulsed with Pg381, DPG3, MFI and MFB at 10 MOI and incubated with the MoDCs for 12 hours.

tag: pathogen strain

value: MFB

tag: pathogen genotype

value: Pg mfa1-/fimA-

tag: incubation duration


title: DPG3

description: Isogenic major fimbria-deficient mutant (Mfa1+Pg), which expresses only the minor fimbriae.

source_name: Monocyte-derived dendritic cells (MoDCs)_DPG3


title: Pg381-WT

description: Pg381, which expresses both minor (Mfa1) and major (FimA) fimbriae.

source_name: Monocyte-derived dendritic cells (MoDCs)_Pg381

value: Porphyromonas gingivalis strain 381


title: N3KD0h_0

description: Sample 4


title: Wild type Columbia rep1


title: Control_Un-infected

description: Control_Un-infected (no bacteria)

source_name: Monocyte-derived dendritic cells (MoDCs)_no_bacteria

value: Control_ No P.g. strain

value: Control_no P. gingivalis


title: MFI

description: Isogenic minor fimbria-deficient mutant (FimA+Pg), which expresses only the major fimbriae.

source_name: Monocyte-derived dendritic cells (MoDCs)_MFI

value: MFI


title: C1

city: Nanjing

first: Xiwu

last: Qi

state: Jiangsu

address: No 1, Qianhuhoucun

institute: Institute of Botany, Jiangsu Province and Chinese Academy of Sciences

description: small RNA

data_processing:
Illumina Casava software was used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence and less than 18nt sequence to obtain the clean data. All identical sequences were counted and eliminated from the initial data set
The unique reads were mapped onto the Glehnia littoralis unigene (trancriptome SRX547159) using the program Bowtie
Supplementary_files_format_and_content: [.txt] tab-delimited text file including the length, number of reads, unique sequences

organism: Glehnia littoralis

source_name: control, leaf

growth_protocol: The Glehnia littoralis seedings cultivated in a green house for six month. Before treatments, plants were tranferred into distilled water for a week in a growth chamber under 12 h light at 23°C.

extract_protocol:
Fresh samples of young leaves were collected for RNA extraction. Total RNA of the three G. littoralis samples was extracted using TRIzol reagent (Invitrogen) according to the manufactures’ instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For salt treatment, plants were transferred to 250 mM NaCl for 1 h under the same light. For salt recovery, the salt stressed plants were put back into distilled water for 1 h.

tag: genotype

value: leaf

tag: stress

value: control


title: S1

description: small RNA

source_name: salt stress, leaf

value: 250 mM NaCl treated for 1 h


title: S2

description: small RNA

source_name: recovery from salt stress, leaf

value: salt recovery


title: L. major H3V-KO + DMOG rep 1

status: Public on Jul 20 2016

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
adapter and quality trimming: Trimmomatic v0.32 using TruSeq3 adapters, removing leading and trailing bases with quality less than 15, and removing reads with average quality less than 20 and reads shorter than 50 bp; quality based on Phred 33 scores
alignment: Bowtie2 v2.2.3 using sensitive local alignment mode
sorting: Samtools v1.2 using default parameters
expression level of replicates: Cuffnorm (from Cufflinks v2.2.1) using the reference annotation and library type fr-firststrand; replicates were considered individual samples
expression level of condition: Cuffdiff (from Cufflinks v2.2.1) using reference annotation and library type fr-firststrand; the three replicates combined were considered a sample
Genome_build: Leishmania major Friedlin (v9.0 from TriTrypDB.org)
Supplementary_files_format_and_content: tab-delimited text file; column 1 - gene (gene ID); column 2 - locus (gene coordinates); column 3 - individual replicate FPKM; column 4 - treatment FPKM (combined replicates)

molecule: polyA RNA

organism: Leishmania major

source_name: H3VKO parasite

growth_protocol: Leishmania major Friedlin strain promastigotes were grown at 26°C in M199 media supplemented with 10% FBS, as described by Kapler et al., 1990

extract_protocol:
Total RNA was isolated from log phase Leishmania major cultures using Trizol, according to the manufacturer’s instructions. 5x107 cells were used for each prep.
RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.

treatment_protocol: DMOG treatment of wild type and H3.V knockout cells was performed by supplementing media with 5mM DMOG for 2 days. Control cells were treated with equal concentrations of vehicle (DMSO)

tag: strain, lifestage

value: Strain Friedlin, promastigote form

tag: sample

value: polyA enriched RNA (mRNA)


title: L. major H3V-KO rep 1


title: L. major WT + DMOG rep 2

source_name: WT parasite


title: L. major H3V-KO rep 2


title: L. major H3V-KO + DMOG rep 2


title: L. major WT + DMOG rep 1


title: L. major WT rep 2


title: L. major WT rep 1


title: Phage-P3_3.5_rep3

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description:
Phage RNA recovered after 3.5min post infection
Phage-infect-P3_T3.5-T13_statistics.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced were mapped to Pseudomonas aeruginosa PAK whole genome sequence or Phage P3 sequence complemented by the manually annotated ncRNA using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES -l 20
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied on each strand coverage count with the 13M value as a reference for reporting the expression data of 0M.
Genome_build: Pseudomonas aeruginosa PAK (KK037225.1)
Supplementary_files_format_and_content: Genome annotation (Gene ID), Raw Counts (0M, 13M), Normalized Counts (0M, 13M), Statistics (FC, pvalue, significant)

organism: Pseudomonas phage PAK_P3

source_name: Pseudomonas phage PAK P3

growth_protocol: Pseudomonas cells were grown in LB supplemented with 10mM MgCl2 at 37°C until OD600nm   ̴ 0,3

extract_protocol:
Cells were then lyzed in TRIzol,® total RNA was purified through a standard organic extraction and ethanol precipitation followed by DNase treatment (TURBO DNAse®) and rRNA depletion (Ribo-Zero rRNA Removal Kit)
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq stranded RNA seq kit

treatment_protocol: Synchronous infection with bacteriophage PAK_P3 for 0min, 3,5min or 13min (MOI = 50) and halted by rapid cooling in diluted phenol

tag: subsp.

value: phage PAK

tag: time point

value: 3.5 min post infection


title: Phage-P3_3.5_rep2

tag: strain


title: Phage-P3_3.5_rep1

description:
Phage RNA recovered after 3.5 min post infection
Phage-infect-P3_T3.5-T13_statistics.xls


title: Phage-P3_13_rep1

description:
Phage RNA recovered after 13min post infection
Phage-infect-P3_T3.5-T13_statistics.xls

value: 13 min post infection


title: Host-P3_13_rep1

description:
Host RNA recovered after 13min post infection
Host-infect-P3_T0-T13_statistics.xls

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa PAK

value: Host PAK

value: PAK


title: Host-P3_13_rep3


title: Phage-P3_13_rep2


title: Phage-P3_13_rep3


title: Host-P3_0_rep2

description:
Host RNA recovered after 0min post infection
Host-infect-P3_T0-T13_statistics.xls

value: 0 min post infection


title: Host-P3_0_rep3


title: Host-P3_13_rep2


title: Host-P3_0_rep1


title: sl-nm

first: Ping

last: Wu

address: 163 Xianlin Avenue

institute: Nanjing University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequences were mapped to Solanum lycopersicum whole genome using bowtie
The counts of reads were normalized by the formula: actual miRNA count/ total count of clean reads*1000000
Genome_build: Solanum lycopersicum (Assembly number: GCA_000188115.2)
Supplementary_files_format_and_content: abundance measurements

organism: Solanum lycopersicum

source_name: root

growth_protocol: Seeds of tomato (Solanum lycopersicum) were surfaced sterilized with 8% sodium hypochlorite for 6 min by gently shaking, and rinsed six times in sterile distilled water. Surface sterilized tomato seed were germinated at 24 °C for two days on 0.8% water Agar. After germinating, the seeds were transferred to a plastic pot filled with 650g sands. Plants were cultivated under 16h light (300 μmol photons m–2 s–1) at 24 °C and 8h dark at 22 °C. All plants were watered two times per week with half-strength Hoagland solution containing 20 μM phosphate (Arnon and Hoagland 1940).

extract_protocol:
Total RNA from tomato roots were isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For mycorrhizal treatment, plants were  inoculated with Rhizophagus irregularis (BGC HEB07D,  a mixture of soil, spores, hyphae and root material from Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences).

tag: inoculated with

tag: tissue

value: root


title: Islet Dnase 130313

city: Cambridge

first: David

last: Gifford

state: MA

address: 32 Vassar St

institute: MIT

description: Dnase-seq on human pancreatic islet cells

library_source: genomic

data_processing:
Alignments done via bcbio-nextgen with BWA with default settings
Peak calling for NRF performed via GEM with default settings
SLOT sequence merging and reconstruction via FLASH -m 50 -M 150 -x 0.3
Dnase-seq data was used to train the synergistic sequence model, and parameters were dumped as a binary file that is then zipped into an archive.
Genome_build: mm10/hg19
Supplementary_files_format_and_content: NRF binding sites in the .csv file, .zip file contains fitted model parameters and input data. Input directory contains genome and read files in compressed binary format necessary to reproduce the run. Output contains model parameters in binary format with VARIABLENAME_loopid.bin where loopid determines the regularization value (stored in ETA_loopid.bin). All bin files are binary vectors of floats that can be parsed 8-bytes at a time. Summary contains parsed outputs including summary plots (pdf format) and binary prediction vectors over the genome used in the paper.

molecule: genomic DNA

source_name: Pancreatic islet

growth_protocol: Mouse embryonic stem cell culture was performed according to previously published protocols(Sherwood et al., 2014 PMID 24441470). Undifferentiated 129P2/OlaHsd mouse ES cells were maintained on gelatin-coated plates feeder-free in mES media composed of Knockout DMEM (Life Technologies) supplemented with 15% defined fetal bovine serum (FBS) (HyClone), 0.1mM nonessential amino acids (Life Technologies), Glutamax (Life Technologies), 0.55mM 2-mercaptoethanol (Sigma), 1X ESGRO LIF (Millipore), 5 nM GSK-3 inhibitor XV and 50 nM UO126.

extract_protocol: ChIP was performed according to the “Mammalian ChIP-on-chip” protocol (Agilent) using a polyclonal antibody against Nrf1 antibody (ab34682, Abcam) and Protein G Dynabeads (Life Technologies). 10-100 million cells were used for each experiment. qPCR using positive and negative control primers was performed to ensure ChIP enrichment. Library preparation and Illumina HiSeq were performed by the MIT BioMicroCenter. DNase-seq was performed as described previously (Sherwood et al., 2014 PMID 24441470). 10-100 million cells were digested with 60-100 units of DNase I (Promega) per 107 nuclei. 50-125 bp hypersensitive DNA was collected using E-Gel SizeSelect Agarose 2% gels (Life Technologies). Library preparation and Illumina HiSeq were performed by the MIT BioMicroCenter.

value: Pancreatic islet


title: sl-myc

value: Rhizophagus irregularis


title: Nrf ChIP-seq (sr8)

description:
NRF ChIP-seq on mouse ES cells
nrf_GEM_events_mm10.txt

source_name: embryonic stem cell

tag: antibody

value: anti-Nrf1 antibody (ab34682, Abcam)

value: embryonic stem cell


title: Mouse Dnase 130801

description: Dnase-seq on mouse ES cells


title: Nrf ChIP-seq (sr3)


title: Nrf ChIP-seq (dox)


title: Fraction6 rep1

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

data_processing:
Illumina Casava1.9 software used for basecalling.
Flexbar was used for adapter removal with the following parameters: -u 2 -m 48 -ae RIGHT -at 2 -ao 1 (Dodt et al, 2012). Then the first 15-nt of the 1st read derived from the random primer region were further removed due to potential high mismatches.
Read pairs that were concordantly mapped to the reference sequences of rRNA, tRNA, snRNA, snoRNA and miscRNAs (available from Ensembl and RepeatMasker annotation) using Bowtie2 (version 2.1.0) (Langmead & Salzberg, 2012) with default parameters (in --end-to-end & --sensitive mode) were excluded.
The remaining reads were then mapped to the mouse reference genome (mm10) using Tophat2 (version 2.0.10) with the parameters --mate-inner-dist 200 --mate-std-dev 100 -N 3 --read-gap-length 2 --read-edit-dist 3 --min-anchor 6 --library-type fr-firststrand --segment-mismatches 2 --segment-length 25 with the input of Ensembl mouse gene annotation (Release 72).
The number of 5'ends of the 2nd reads in read pairs were counted for each detected TSS clusters in each fraction.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample.

source_name: NIH3T3 fibroblast cells

growth_protocol: Mouse NIH 3T3 cells were used and cultivated in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Gibco) at 37°C with 5% CO2 and split every second or third day.

extract_protocol:
The supernatant was layered onto a 10mL linear sucrose gradient (10%-50% [w/v], supplemented with 10 mM HEPES pH 7.4,150 mM KCl,10 mM MgCl2, 0.5 mM DTT,100μg/ml cycloheximide), and centrifuged in a SW41Ti rotor (Beckman) for 120 min at 160,000 g at 4°C. Fractions were manually collected according to the A254 peaks that indicate the number of ribosomes.
3mg total RNA collected from each fraction were reverse transcribed using random primer (N15-oligo) tailed with 3’ part of Illumina TruSeq Universal Adaptor sequence. 5’ complete single-stranded cDNAs were captured based on a protocol from Takahashi et al, 2012 with minor modification. 5'end-sequencing

treatment_protocol: Prior to lysis, cells were treated with cycloheximide (100 mg/ml) for 10 mins at 37°C.

tag: cell type

value: fibroblast

tag: ribosome number

value: 6-8 ribsoomes


title: Fraction1 rep2

value: free RNP


title: Fraction4 rep2

value: 2-3 ribosomes


title: Fraction6 rep2


title: Nrf ChIP-seq (nodox)


title: Fraction7 rep2

value: 9+ ribosomes


title: Fraction5 rep2

value: 4-5 ribosomes


title: Fraction2 rep2


title: Fraction5 rep1


title: Fraction4 rep1


title: SLOT (MPRA) run 6 140619

description: Massively parallel reporter asssay tags for chromatin accessibility screening


title: Fraction3 rep1

value: 80s monosome


title: pro-B Setdb1 Thermo Scientific

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

data_processing:
RNA-seq reads were mapped to the mouse genome (mm10) using tophat2 (Kim et al., 2013). Expression of genes in FPKM was calculated with cuffdiff and cummerbund (Trapnell et al., 2013).
Paired end ChIP-seq reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009). Reads mapping to multiple locations were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking file was generated using cuffdiff; bedgraph files were generated from homerr tag directories using makeUCSCfile

source_name: pro-B cells

extract_protocol:
Rneasy Plus Mini Kit, Dynabeads mRNA purification kit / phenol-chloroform extraction
2-5 ng of cDNA, ChIP-precipitated DNA were used as starting material for the generation of single-end sequencing libraries as described by Illumina’s ChIP Sequencing sample preparation protocol. DNA fragments of the following sizes were selected for the different experiments: 200–350 bp for ChIPseq and 150–700 bp for RNA-seq. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were modified with uracil-N-glycosylase (New England Biolabs) unable to generate second strand. The barcode containing adaptor was used for tagging and PCR amplification. Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS library quantification kit. library construction protocol

tag: chip antibody

value: Setdb1 Themo Scientific PA5-30334


title: pro-B Setdb1 Santa Cruz

value: Setdb1 Santa Cruz SC-66884X


title: pro-B Input


title: pro-B H3K9ac

value: H3K9ac Millipore #07-352


title: RNA-seq control

value: control


title: pro-B H3K9me3

value: H3K9me3 Diagenode pAb-056-050


title: Sample_2_Input

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq data was aligned to hg18 using ELAND
ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2)
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited ChIPseeqer peak file containing following columns;
Chromosome: chromosome name
Start_Position: the first (genomic) coordinate of the peak
End_Position: the second (genomic) coordinate of the peak
Avg_p-value : average log p-value of the nucleotides in the normalized peak region
Score: score estimated as the average ChIP reads/length of peak (minus the average INPUT reads/length of peak - if INPUT is available)
Posmaxpeakheight: the position of the maximum height of the peak
Maxpeakheight: the maximum peak height (in reads)
RelPosMaxPeakHeight(%): the relative position of the maximum height of the peak, e.g., 50% means the highest point is at the middle of the peak
Peak_Size: the size of the peak (in bp)
Mid_point: the middle position of the peak
Summit_dist_from_mid: the distance of the maximum height from the middle of the peak

extract_protocol:
DNA was purified using QIAGEN MiniElute column after reverse cross-linking.
Rabbit polyclonal antibody was raised against human KDM2B and affinity purified (Gearhart, et al. Mol Cell Biol 2006; 26:6880-6889)
Libraries were prepared using the Illumina ChIP-Seq sample kits, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

tag: cell line

value: diffuse large B cell lymphoma (DLBCL) cell line


title: Fraction2 rep1


title: RNA-seq ko

value: Setdb1 ko


title: Sample_1_KDM2B

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq data was aligned to hg18 using ELAND
ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2)
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited ChIPseeqer peak file containing following columns;
Chromosome: chromosome name
Start_Position: the first (genomic) coordinate of the peak
End_Position: the second (genomic) coordinate of the peak
Avg_p-value: average log p-value of the nucleotides in the normalized peak region
Score: score estimated as the average ChIP reads/length of peak (minus the average INPUT reads/length of peak - if INPUT is available)
Posmaxpeakheight: the position of the maximum height of the peak
Maxpeakheight: the maximum peak height (in reads)
RelPosMaxPeakHeight(%): the relative position of the maximum height of the peak, e.g., 50% means the highest point is at the middle of the peak
Peak_Size: the size of the peak (in bp)
Mid_point: the middle position of the peak
Summit_dist_from_mid:the distance of the maximum height from the middle of the peak


title: Fraction3 rep2


title: Human ES S6 DALT Dnase 131220

description: Dnase-seq on human ES cells


title: HCT116 p53-/- INZ (8)

city: New Orleans

first: HUA

last: LU

state: LA

address: 1430 Tulane Ave

department: Biochemistry and Molecular Biology

institute: TULANE UNIVERSITY

description: This sample is p53-null HCT116 cells treated with INZ.  It is the second of two biological replicates.

data_processing:
After sequencing images generated, image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8.0).
3’ adapter sequences were trimmed from clean reads (reads that passed Solexa CHASTITY quality filter) and the tags shorter than 15nt were discarded. Then the 3’-adapter-trimmed reads (length >= 15nt) were aligned to the latest known human reference miRNA precursor set (Sanger miRBase 19) using Novoalign software (v2.07.11).
The unmapped reads were discarded as unusable reads.
Any sequence that matched the mature miRNA region ±4nt within a known pre-miRNA hairpin were grouped and the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin were also indicated. To correct for the difference in tag counts between samples, the tag counts were scaled to tpm (the copy number of transcripts per million) based on the total number of tag aligned to known human pre-miRNAs in miRBase 19.
Genome_build: miRBase 19
Supplementary_files_format_and_content: txt file reports tag counts

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin and 0.1 mg/ml streptomycin at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol:
Total RNA was extracted using TriZol  (Invitrogen, USA). RNA quality was confirmed by agarose electrophoresis and only those samples showing no degradation (ratios approaching 2:1 for the 28S and 18S bands) were sent to Arraystar Inc. (Rockville, MD)
Total RNA of each sample was used to prepare the miRNA sequencing library which included the following steps: 1) 3'-adapter ligation with T4 RNA ligase 2 (truncated); 2) 5'-adapter ligation with T4 RNA ligase; 3) cDNA synthesis with RT primer; 4) PCR amplification; 5) extraction and purification of ~120-140 bp PCR amplified fragments (correspond to ~15-35 nt small RNAs) from the PAGE gel.

treatment_protocol: Cells were plated in 10-cm cell culture dishes and were treated with 4μM INZ at 70% confluency and harvested at 18 hours post treatment

value: HCT116 colorectal carcinoma cell line

value: p53 null

tag: agent

value: INZ


title: HCT116 p53-/- DMSO (6)

description: This sample is p53-null HCT116 cells treated with DMSO.  It is the second of two biological replicates.

source_name: HCT116 p53-/- DMSO

value: DMSO


title: HCT116 p53-/- INZ (7)

description: This sample is p53-null HCT116 cells treated with INZ.  It is the first of two biological replicates.


title: Fraction7 rep1

value: fibroblast


title: HCT116 p53-/- DMSO (5)

description: This sample is p53-null HCT116 cells treated with DMSO.  It is the first of two biological replicates.


title: Fraction1 rep1

value: free RNP


title: HCT116 p53+/+ INZ (4)

description: This sample is wild-type p53 harboring HCT116 cells treated with INZ.  It is the second of two biological replicates.

value: Wild-type p53


title: PP242E24h2

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

data_processing:
The paired-end read data from the HiSeq 2000 were processed and analyzed through a series of steps. Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2. FASTQ files were trimmed using FASTQ Trimmer (version 1.0.0).  TopHat2 (version 0.5) was employed to map paired end RNA-Seq reads to version hg19 of the Homo sapiens reference genome in the UCSC genome browser, in conjunction with the RefSeq genome reference annotation hg19. Gene expression values (raw read counts) from BAM files were calculated using StrandNGS (version 2.1) Quantification tool.  Partial reads were considered and option of detecting novel genes and exons were selected.  Default paramteres for finding novel exons and genes were specified.  DESeq normalization algorithm using default values was selected.  Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene for each treatment relative to the vehicle control. We considered genes with fold-change >3 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Inhibitor.txt (raw expression file for inhibitor experiment), timecourse.txt (raw expression file for inhibitor experiment)

growth_protocol: MCF-7 cells were obtained from and grown as recommended by the American Type Culture Collection. Receptor expression was verified by Q-PCR and western blotting and gene expression and proliferative response to estradiol was monitored regularly. For experiments with E2 and PaPE treatment, cells were maintained in the corresponding phenol red-free medium for 7 days prior to use. At the 7th day, cells were treated with Veh (0.1% EtOH), 10 nM E2 or 1 uM PaPE for 4h or 24h.  For inhibitor experiments, cells were pretreated with 1 uM PP242 or 1 uM AZD6244 for 30 min.  Then, cells were treated witn Veh, E2 or PaPE in the presence or absence of intibitors for 4h.

extract_protocol: Once the sample quality and replicate reproducibility was verified 2 samples from each group were subjected to sequencing. RNA at a concentration of 100 ng/µL in nuclease-free water was used for library construction.The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNAseq Sample Prep kit.  The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000  using a TruSeq SBS sequencing kit version 3. Fastq files were generated with the software Casava 1.8.2 (Illumina).. Briefly, the poly-A containing mRNA was purified from total RNA, RNA was fragmented, double-stranded cDNA was generated from fragmented RNA, and adapters were ligated to the ends.

treatment_protocol: For gene expression analysis, total RNA was extracted from 3 biological replicates for each ligand treatment using Trizol reagent and further cleaned using the RNAeasy kit from QIAGEN. For time course studies, MCF-7 cells were treated with Veh (0.1% EtOH), 10 nM E2 or 1 μM PaPE for 4h and 24 hours. For inhibitor studies, MCF-7 were pretreated with Ctrl (0.1% DMSO), 1 μM PP242 (mTOR pathway inhibitor) or 1 μM AZD6244 (MAPK inhibitor) for 1 h and then treated with Veh (0.1% EtOH), 10 nM E2 or 1 μM PaPE in the presence or absence of inhibitors for 4 h.

tag: Sex

value: Female

value: Breast

tag: treatment time

tag: inhibitor

tag: treatment

value: 10 nM E2


title: Ctrl_Veh_24h_1

value: Ctrl

value: Veh


title: Ctrl_E2_4h_1


title: Ctrl_Veh_1_4h


title: PP242E24h1


title: PP242334h1

value: 1 uM PaPE


title: Ctrl_SPE1_24h_2


title: HCT116 p53+/+ INZ (3)

description: This sample is wild-type p53 harboring HCT116 cells treated with INZ.  It is the first of two biological replicates.

tag: genotype


title: Ctrl_SPE1_4h_2


title: HCT116 p53+/+ DMSO (2)

description: This sample is wild-type p53 harboring HCT116 cells treated with DMSO.  It is the second of two biological replicates.

source_name: HCT116 p53+/+ DMSO


title: PP242Veh4h2


title: HCT116 p53+/+ DMSO (1)

description: This sample is wild-type p53 harboring HCT116 cells treated with DMSO.  It is the first of two biological replicates.


title: PP242334h2


title: AZDVeh4h2

value: 1 uM AZD6422


title: PP242Veh4h1


title: Ctrl_E2_4h_2


title: AZD334h1


title: Ctrl_SPE1_4h_1


title: Ctrl_SPE1_24h_1


title: Ctrl_Veh_2_4h


title: AZDE24h2


title: AZD334h2


title: Ctrl_E2_24h_1


title: Sample_16_SUDHL4_79-6.1085_R1

data_processing:
genome build: hg19
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
CPM were obtained using Rsubread
Supplementary_files_format_and_content: tab-delimited

source_name: SUDHL4 cell line

extract_protocol: RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

value: treated with 10uM 79-6.1085 for 12h


title: Sample_17_SUDHL4_79-6.1085_R2


title: Ctrl_Veh_24h_2


title: Sample_18_SUDHL4_79-6.1085_R3


title: Sample_11_Farage_79-6.1085_R2

source_name: Farage cell line

value: Farage


title: Sample_10_Farage_79-6.1085_R1


title: Sample_12_Farage_79-6.1085_R3


title: Sample_14_SUDHL4_DMSO_R2

value: treated with DMSO for 12h


title: Sample_7_Farage_DMSO_R1


title: Sample_13_SUDHL4_DMSO_R1


title: Sample_15_SUDHL4_DMSO_R3


title: Sample_8_Farage_DMSO_R2


title: Sample_5_SUDHL6_79-6.1085_R2

source_name: SUDHL6 cell line


title: AZDE24h1


title: Sample_9_Farage_DMSO_R3


title: Sample_2_SUDHL6_DMSO_R2


title: Ctrl_E2_24h_2


title: Sample_1_SUDHL6_DMSO_R1

description: Gene expression ratios were determined in cells treated with 79-6.1085 compared to cells treated with DMSO and were identified using Rsubread.


title: 1187

city: Atlanta

first: Peng

last: Jin

address: 615 Michael St

institute: Emory University

description:
Protocol: hMe-Seal
processed_data_file: UK_DhMLs_1000_2.txt

data_processing:
Library strategy: hMe-Seal
Genome alignment: Bowtie
Identification of differential regions: diffReps, window = 1000, step = 100, fragment = 300, other settings default
Genome_build: hg19
Supplementary_files_format_and_content: txt, regions of differential 5hmC identified by diffReps

source_name: University of Kentucky ADRC

extract_protocol:
Genomic DNA was isolated from brain samples with standard protocols. Tissues were homogenized on ice and then treated with proteinase K (0.667 µg/µl) in digestion buffer (100 mM Tris-HCl (pH 8.5), 5 mM EDTA, 0.2% SDS (vol/vol), 200 mM NaCl) overnight at 55 °C. On the second day, an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1, saturated with 10 mM Tris (pH 8.0) and 1 mM EDTA; P-3803, Sigma) was added, mixed completely, centrifuged for 5 min at 20,817xg, and precipitated with an equal volume of isopropanol. Genomic DNA was recovered in 10 mM Tris-HCl (pH 8.0) and sonicated to ~500 bp by Misonix 3000 (microtip, 4 pulses of 27 s each, 1-min rest on ice, output 2).
5-hmC enrichment was performed as previously described [18]. 5-hmC labeling reactions were performed in a 100 µl solution containing 50 mM HEPES buffer (pH 7.9), 25 mM MgCl2, 300 ng/µl sonicated genomic DNA (100-500 bp), 250 µM UDP-6-N3-Glu, and 2.25 µM wild-type _-glucosyltransferase. Reactions were incubated for 1 h at 37°C. DNA substrates were purified via Qiagen DNA purification kit or by phenol-chloroform precipitation and reconstituted in H2O. Click chemistry was performed by adding of 150 µM dibenzocyclooctyne-modified biotin into the DNA solution and incubating for 2 h at 37°C. Samples were purified by Pierce Monomeric Avidin Kit (Thermo) following the manufacturer's recommendations. After elution, biotin-5-N3-gmC-containing DNA was concentrated with 10 K Amicon Ultra 0.5-ml Centrifugal Filters (Millipore) and purified using a Qiagen DNA purification kit. Libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A). We used 25 ng of input genomic DNA or 5-hmC–captured DNA to initiate the protocol. DNA fragments of ~150–300 bp were gel-purified after the adaptor ligation step. PCR-amplified DNA libraries were quantified on an Agilent 2100 Bioanalyzer and diluted to 6–8 pM for cluster generation and sequencing. We performed 38-cycle single-end sequencing Generation using Version 4 Cluster Generation and Sequencing Kits (Part #15002739 and #15005236 respectively) and Version 7.0 recipes. Image processing and sequence extraction were done using the standard Illumina Pipeline.

value: prefrontal cortex

tag: diagnosis

value: Control


title: ACT3

description:
Protocol: hMe-Seal
processed_data_file: ACT_DhMLs_1000.txt

source_name: Emory ADRC


title: 1196

value: Alzheimer's


title: ACT2


title: 1186


title: 1159


title: 1161


title: ACT8


title: 1121


title: ACT7


title: Sample_6_SUDHL6_79-6.1085_R3


title: Sample_4_SUDHL6_79-6.1085_R1


title: Sample_3_SUDHL6_DMSO_R3


title: Monocytes M_01

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description:
total white blood cells enriched from total peripheral blood through red blood cell lysis, then either directly resuspended in Trizol (unsorted) or stained with antibodies for sort
Cells were stained with following antibodies: CD33 PE (BD Bioscience 555450), CD34 APC (BD Bioscience 555824), CD3 FITC (BD Bioscience 555332), CD19 PE-Cy7 (BD Bioscience 557835), CD14 APC-Cy (BioLegend 325620) and PI for 30 minutes in the dark
cells were sorted on a BD Aria Sorter. First, different populations were gated according to FSC/SSC, then further defined by positivity for CD33, CD3, CD19, CD34 and CD14 as indicated above.

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: healthy adult

extract_protocol: TruSeq RNA v3

value: Monocytes

tag: sorted by surface marker

value: CD14+ within monocyte gate

tag: pooled or single individual?

value: single individual

value: peripheral blood


title: T-cells T_01

value: T-cells

value: CD3+ within lymphocyte gate


title: T-cells T_04


title: Monocytes M_05


title: T-cells T_03


title: Monocytes M_03


title: Granulocytes G_05

value: Granulocytes

value: CD33+ within granulocyte gate


title: Monocytes M_02


title: Granulocytes G_03


title: T-cells T_05


title: Monocytes M_04


title: Granulocytes G_02


title: T-cells T_02


title: B-cells B_04

value: B-cells

value: CD19+ within lymphocyte gate


title: AZDVeh4h1

value: Female

value: Breast

value: 1 uM AZD6422

value: Veh


title: B-cells B_03


title: B-cells B_02


title: Total white blood cells 0_03

value: Total white blood cells

value: unsorted


title: Granulocytes G_01


title: B-cells B_05


title: B-cells B_01


title: Total white blood cells 0_02


title: 31-08H012-MeBIO

source_name: AML patient sample

growth_protocol: 2-3x10^6 cells in 2-3ml serum-free medium

extract_protocol:
cells were harvested after 16 hours, resuspended in 1ml Trizol prior to RNA-extraction
TruSeq RNA v3

treatment_protocol: compounds were diluted in medium 1:1000 (final DMSO concentration 0.1% in all conditions), compound concentrations as indicated above

tag: modulating agent

tag: exposure time


title: Granulocytes G_04

tag: tissue


title: peripheral blood CD34+ cells pooled_CD34pB

value: peripheral blood CD34+ cells

value: CD34+ within lymphocyte gate

value: sorted from pooled WBC of 4 individuals


title: 30-08H012-BIO


title: Total white blood cells 0_01

value: single individual


title: 28-08H012-DMSO

value: peripheral blood


title: 27-08H012-T0


title: 32-08H012-BIO-SR1


title: 29-08H012-SR1


title: 23-09H043-SR1


title: 16-04H112-DMSO

value: bone marrow


title: 20-04H112-BIO-SR1


title: 26-09H043-BIO-SR1


title: 15-04H112-T0


title: 14-12H030-MeBIO-SR1


title: 25-09H043-MeBIO


title: 7-05H163-MeBIO-SR1


title: 22-09H043-DMSO


title: 21-09H043-T0


title: 6-05H163-BIO-SR1


title: 11-12H030-BIO


title: 24-09H043-BIO


title: 18-04H112-BIO


title: 17-04H112-SR1


title: 5-05H163-MeBIO


title: 2-05H163-DMSO


title: 12-12H030-MeBIO


title: 13-12H030-BIO-SR1


title: 19-04H112-MeBIO


title: 9-12H030-DMSO


title: PPARg2-Med+Low SsVAT nuclei

data_processing:
Library strategy: TAB–seq
Data were mapped to the Sus scrofa Sscrofa10.2 (GCA_000003025.4) reference genome
TAB-seq analysis were performed as described in Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012, 149, 1368-1380.
Genome_build: Sus scrofa Sscrofa10.2 (GCA_000003025.4) reference genome
Supplementary_files_format_and_content: tab delimited text file,  column headers:
Supplementary_files_format_and_content: Column1: chromosome
Supplementary_files_format_and_content: Column2: cytosine position
Supplementary_files_format_and_content: Column3: strand
Supplementary_files_format_and_content: Column4: CNN (N = A, T, C, G)
Supplementary_files_format_and_content: Column5: methylated cytosines in this site
Supplementary_files_format_and_content: Column6: totally detected cytosines in this site

organism: Sus scrofa

source_name: PPARg2-Med+Low SsVAT nuclei

growth_protocol: SsVAT nuclei are isolated and sorted into PPARg2-High, PPARg2-Med+Low and PPARg2-Neg subpopulation based on PPARg2 staining using fluorescence-activated nuclear sorting.

extract_protocol: Genomic DNA (gDNA) was purified from PPARg2-High, PPARg2-Med+Low and PPARg2-Neg SsVAT nuclei using DNeasy kit (Qiagen, Frederick, MD, USA #69504), according to the manufacturer’s instructions. TAB-seq libraries were constructed according to Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012, 149, 1368-1380.

tag: cell subpopulation


title: PPARg2-Neg SsVAT nuclei

source_name: PPARg2-Neg SsVAT nuclei


title: eWAT, Rev-erb alpha ChIP-seq

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Deeping sequencing was performed using Illumina Genome Analyzer IIx, and sequencing reads were obtained using Solexa analysis pipeline and mapped to the mouse genome (UCSC mm9) using Bowtie. BigWig files for RPM-normalized stack-height profiles were generated using bedtools and SRA tool kit.
Genome_build: mm9
Supplementary_files_format_and_content: Read-per-million (RPM) normalized stack-height profile in bigWig format

source_name: Epididymal white adipose tissue

extract_protocol:
Mice were euthanized, and tissue was harvested immediately, quickly minced, and cross-linked in 1% formaldehyde for 20 min, followed by quenching with 1/20 volume of 2.5 M glycine solution and two washes with PBS. Cell lysates with fragmented chromatin were prepared by probe sonication in ChIP dilution buffer (50mMHEPES, 155mMNaCl, 1.1% Triton X-100, 0.11% sodium deoxycholate, 0.1% SDS, 1mM phenylmethylsulfonyl fluoride [PMSF], and a complete protease inhibitor tablet [pH 7.5]).   ChIP was performed using 2-10 µg of antibodies.
For ChIP-seq, material from three to four mice was pooled prior to library generation. ChIP DNA was prepared for sequencing according to the amplification protocol provided by Illumina.

treatment_protocol: Mice were maintained on a standard diet under 12h-light/12h-dark (LD) cycles. The experiments were performed on 12-15 weeks-old males. The tissues were harvested at Zeitgeber Time (ZT) 10 (5PM) when Rev-erb alpha protein level peaks in wild type (WT) mice.

value: Epididymal white adipose tissue

tag: time

tag: strain

tag: gender

value: male

tag: age

value: 12-15 weeks-old

value: Rev-erb alpha (Cell Signaling, catalog number CS2124, rabbit antibody)


title: 10-12H030-SR1


title: 05B3-1 rep3

city: Hangzhou

first: Jianping

last: Lu

state: Zhejiang

address: 866 Yuhantang Road

department: College of Life Sciences

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Magnaporthe oryzae 70-15 (MG8) whole genome using tophat 2.0.8b with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1
Genome_build: MG8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Pyricularia oryzae

source_name: Mycelium

growth_protocol: The strains were cultured in liquid CM medium at 25˚C with shaking at 180 rpm for 2 d

extract_protocol:
Total RNA was extracted from ground mycelia in liquid nitrogen with RNeasy Plant mini kit (QIAGEN)
RNA libraries were prepared for sequencing using NEBNext RNA sample preparation kit (NEB) with standard Illumina protocols

treatment_protocol: The mycelia were collected and incubated in H2O at 25˚C for 4 h

value: Mycelia under starvation


title: WT rep2

value: wild type


title: 3-05H163-SR1


title: 4-05H163-BIO


title: 8-12H030-T0


title: 1-05H163-T0


title: DarrowHuntley-2015-HIC010

status: Public on Jul 19 2016

first: Miriam

last: Huntley

address: 29 Oxford Street

institute: Harvard University

description: Processed data files were not available at the time of accessioning.

data_processing:
The paired end reads were aligned separately using BWA against the b37 (human), mm10 (mouse), or rheMac2 (rhesus macaque).
PCR duplicates, low mapping quality and unligated reads were removed using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al, Cell 2014l)
Contact matrices were constructed at various resolutions and normalized using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al, Cell 2014)
genome build: b37 (human), mm10 (mouse), rheMac2 (rhesus macaque)
processed data files format and content: Contact matrices: a text file with the raw observed contact matrix in sparse matrix notation at a given resolution. Only the upper triangle of the matrix is provided (i.e. i<=j), the matrix is symmetric, so M_i,j = M_j,i. At this stage of processing, read pairs where one or both ends do not align to the reference genome have already been removed, as well as chimeric ambiguous reads (see Section II.a.2 of the Extended Experimental Procedures of Rao, Huntley, et al., Cell 2014 for a definition of chimeric ambiguous reads). In addition, duplicate reads (reads where both ends align to within +/- 4bp of each other) have been removed as well (see Section II.a.3 of the Extended Experimental Procedures of Rao, Huntley, et al., Cell 2014 for a full description of duplicate removal). Full details of the Hi-C processing pipeline used in this study are provided in Section II.a. of the Extended Experimental Procedures of Rao, Huntley, et al., Cell 2014.
processed data files format and content: Normalization files: normalization vectors that can be used to transform the raw contact matrices M into normalized matrices M*.  Each file is ordered such that the first line of the normalization vector file is the norm factor for the first row/column of the corresponding raw contact matrix, the second line is the factor for the second row/column of the contact matrix, and so on. To normalize, an entry M_i,j in a *RAWobserved file, divide the entry by the corresponding norm factors for i and j. (See section II.b of the Extended Experimental Procedures of Rao, Huntley, et al., Cell, 2014 for more information about the different types of normalizations.)
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); fields 9-12 are the component scores used in the Arrowhead algorithm (see Rao, Huntley, et al)
processed data files format and content: merged_nodups.txt files contain filtered, "normal" contacts. Each line represents a single Hi-C read pair that has passed the alignment and duplicate removal stages. The format of each line of the file is: read_name, strand1, chromosome1, position1, fragment-index1, strand2, chromosome2 ,position2, fragment-index2, mapq1, mapq2
processed data files format and content: collisions.txt.gz files contain the contacts that have 3 or more loci.

source_name: Retinal Pigmented Epithelial Cells

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 with MboI and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared and then biotinylated ligation junctions were recovered with streptavidin beads.
Standard Illumina library construction protocol was performed, and libraries were sequenced on the HiSeq X Ten/NextSeq/HiSeq2500 following the manufacturer's protocols.

tag: cell line

tag: cell type

value: Retinal Pigmented Epithelial Cells

tag: protocol

value: in situ Hi-C


title: DarrowHuntley-2015-HIC013


title: DarrowHuntley-2015-HIC009


title: eWAT, Input

tag: chip antibody

value: Input


title: 05B3-1 rep2


title: WT rep3


title: 05B3-1 rep1


title: WT rep1


title: CA755, repeat

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0).
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and ht-seq-count.
Non-protein coding and mitochondrial genes were filtered out.
Samples were selected for further analysis by using these criteria: unpaired reads examined/FASQ total read >0.75 and median CV coverage <1. Samples that had total counts less than one million were excluded.
Genes expressed (counts per million >1) in less than 3 samples were removed. Data normalization (TMM) and differential expression analysis were performed in R using "edgeR" package.
Genome_build: GRCh38
Supplementary_files_format_and_content: mexico2_data.csv is a comma-separated matrix. The first column contains the Ensembl gene ID and the second contains the HGNC symbol. The remaining columns include read counts assigned for each library. Data represents all processing steps up to read counting, not including gene filtering, normalization, and analysis with edgeR.
Supplementary_files_format_and_content: mexico2_combined_metrics.csv is a comma-separated matrix. The first column contains sample ID, remaining columns include RNA sequencing and alignment metrics.

source_name: Whole blood

extract_protocol:
Total RNA was isolated using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Ambion, TX) and RNA sample was globin reduced wit GLOBINclear (Ambion, TX) according to manufacturer’s instructions.
Libraries were prepared from globin reduced RNA samples using the Illumina TrueSeq RNA Sample Preparation kit according to manufacturer's instructions.

tag: group

value: Diarrhea

value: 2 year-old or older

tag: organisms

value: Rotavirus

tag: flowcell

value: C

tag: lane


title: CA848, repeat

value: <2 year-old


title: DarrowHuntley-2015-HIC012


title: PPARg2-High SsVAT nuclei

source_name: PPARg2-High SsVAT nuclei


title: DarrowHuntley-2015-HIC011


title: CT056, repeat

value: Control

value: Negative


title: CT026, repeat


title: DarrowHuntley-2015-HIC008


title: DarrowHuntley-2015-HIC020

organism: Macaca mulatta

source_name: Skin Fibroblasts

value: Skin Fibroblasts


title: DarrowHuntley-2015-HIC007

value: RPE1 WT


title: DarrowHuntley-2015-HIC006


title: DarrowHuntley-2015-HIC005


title: DarrowHuntley-2015-HIC003


title: DarrowHuntley-2015-HIC004


title: DarrowHuntley-2015-HIC002


title: CA1019

value: Norovirus


title: CA1000


title: DarrowHuntley-2015-HIC001


title: CA838, repeat


title: CA750, repeat


title: CA858, repeat


title: CA1022


title: CA933

value: Adenovirus


title: CA910


title: CO196


title: CO193


title: CA925


title: Input-K

city: Zhengzhou

first: Jinlian

last: Ma

state: Henan

address: 100 Kexue Avenue

department: School of Pharmaceutical Sciences

institute: Zhengzhou University

description: treat sample

data_processing:
Basecalls performed using CASAVA version 1.4
Rawdata was filtered to get clean data.
Clean data was aligned to the Homo_sapiens.GRCh38.76 genome by "bwa aln" with the default configurations.After aligning,data was filtered to get the uniqe reads aligned to the genome.
Peaks were called by "Macs14" with the data aligned to the genome.Configurations we used are "--bw 300 -s 125 -g hs -p 0.001 -w --space 50 -m 10,30'.
While calling peaks with treatment data, Macs14 produces "control_afterfiting_all.wig" files and "treat_afterfiting_all.wig" files.
Peaks in different samples were compared by "MAnorm" with the following configuartions"-fold-change_cutoff_unbiased 0.5 -fold-change_cutoff_biased 1  -log10p_cutoff_biased 3".
Genome_build: Homo_sapiens.GRCh38.76
Supplementary_files_format_and_content: [.wig] files represent reads depth of peak related sites on the genome.  "control_afterfiting_all.wig" file keeps the depth of peaks related sites in control sample. "treat_afterfiting_all.wig" file keeps the depth of peaks related sites in treated (LSD1 KO) sample.

source_name: gastric cancer cells

growth_protocol: Cells were cultured in DMEM medium with 10% FBS. After the cells attached, puromycin was added in the culture medium at a final concentration of 0.5 μg/ml for 3 days to select the stably LSD1 knockout cell line

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

tag: Sex

value: male

value: stomach

value: MGC803 gastric cancer cell line

tag: genotype/variation

value: LSD1 KO


title: CO059


title: CT057, repeat


title: H3K9me2K_ChIPSeq

description: treat sample

value: anti-H3K9me2 (Abcam, catalog# ab1220, lot# GR139816-1)


title: CA967


title: CO188


title: CT030, repeat


title: CA968


title: CA1024


title: CO246


title: CA934


title: CA930


title: CA954


title: CO187


title: CA945


title: CA1032


title: CA928


title: H3K4me2C_ChIPSeq

description: control sample

value: control

value: anti-H3K4me2 (Abcam, catalog# ab32356, lot# GR26908-7)


title: CO186


title: CO191

value: 2 year-old or older


title: DarrowHuntley-2016-RNA006

data_processing:
Reads were aligned to hg19 using STAR.
Aligned reads were split into maternal and paternal reads using our standard human diploid pipeline  (see Rao, Huntley, et al, Cell 2014).
kallisto was used (indexed to GRCh37 cdna) to calculate transcript abundances on the maternal and paternal allele of each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contain transcript abundances for the maternal and paternal allele of each sample.

source_name: Retinal Pigmented Epithelial Cells (hTERT-RPE1)

extract_protocol:
Total RNA was extracted with the NucleoSpin RNA® kit (Macherey-Nagel, Cat. 740955.250)
RNA-Seq libraries were constructed using 500ng of total RNA as input for the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Cat. E7420S). The NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat. E7490) was used to select for polyadenylated RNA and NEBNext Multiplex Oligos for Illumina (Cat. E7335) were used for multiplexing.

value: RNA-seq


title: CO213

value: Diarrhea

value: C


title: H3K4me2K_ChIPSeq

description: treat sample


title: CO215


title: DarrowHuntley-2016-RNA002

value: Retinal Pigmented Epithelial Cells (hTERT-RPE1)


title: CO220

value: <2 year-old


title: CO190

value: Control

value: Negative


title: DarrowHuntley-2016-RNA005


title: DarrowHuntley-2016-RNA004


title: CO079


title: H3K9me2C_ChIPSeq

description: control sample


title: CO120


title: CO104


title: small RNA DIS3L2 mut rep3

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description: HEK293 DIS3L2 mut

data_processing:
base caling CASAVA v1.8.2
aligmnent STAR v2.4.0
further processing, filtering, counting, QC  - custom scripts emploing samtools v1.2-10, HTSeq v0.6.1, RSeQ v2.6.1, FastQC v0.11.3
differential expression analysis DESeq2 v1.8.2
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files (corected for library size) and count tables (htseq-count output file or FPKM_count.py)

source_name: small RNA DIS3L2 mut

growth_protocol: Cells were cultured as monolayers in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) at 37 °C in a 5% CO2 incubator.

extract_protocol:
For RNA isolation, cell lines were treated with doxycycline (100 ng/ml) for 3 days before RNA was isolated using the standard TRI Reagent (Sigma-Aldrich) procedure according to the manufacturer’s guidelines. For RNA-Seq we used RNA samples treated with DNase (Ambion) and rRNA-depleted using a Ribo-Zero Kit (Epicentre) according to the manufacturer’s protocol.
For samples labeled "total-rRNA" strand-specific RNA libraries were prepared in triplicate using a TruSeq RNA Sample Preparation Kit (Illumina) as per the manufacturer’s protocol with several previously described modifications (Szczepinska et al. Genome Res. 2015); For samples labeled "small RNA" RNA molecules underwent additional TAP (Epicentre) treatment. Next we used RA3, RA5 and RTP, RP1 and RPI_X (Illumina) for library preparation (detailed protocol can be sent on demand). Prepared libraries were size selected through gel purification.

treatment_protocol: To induce exogenous gene expression, doxycycline (100 ng/ml) was added to the medium.

value: producing mut DIS3L2

tag: molecule subtype

value: total RNA, after library preparation size selected for RNAs 20-200 nt


title: small RNA DIS3L2 WT rep2

description: HEK293 DIS3L2 WT

source_name: small RNA DIS3L2 WT

value: producing WT DIS3L2


title: CO075


title: CO214

value: Adenovirus


title: DarrowHuntley-2016-RNA003

value: RPE1 WT


title: DarrowHuntley-2016-RNA001


title: CO078


title: CO081


title: CO071


title: small RNA DIS3L2 WT rep3

description: HEK293 DIS3L2 WT


title: small RNA DIS3L2 mut rep2

description: HEK293 DIS3L2 mut


title: CO072


title: CO068


title: small RNA DIS3L2 mut rep1

description: HEK293 DIS3L2 mut


title: total RNA DIS3L2 WT rep1

description: HEK293 DIS3L2 WT

source_name: total RNA DIS3L2 WT

value: total RNA, rRNA depleated


title: small RNA DIS3L2 WT rep1

description: HEK293 DIS3L2 WT


title: total RNA DIS3L2 WT rep2

description: HEK293 DIS3L2 WT


title: CO083


title: total RNA DIS3L2 mut rep2

description: HEK293 DIS3L2 mut

source_name: total RNA DIS3L2 mut


title: total RNA DIS3L2 mut rep3

description: HEK293 DIS3L2 mut


title: total RNA DIS3L2 WT rep3

description: HEK293 DIS3L2 WT


title: U-87_24-4-15

city: Haifa

first: Arie

last: Admon

state: select a state

address: Kiryat Technion- Emerson building

department: Department of Biology

country: Israel

institute: Technion - Israel Institute of Technology, Haifa, Israel

data_processing:
The experiment was performed by Illumina HiSeq 2500 in 50 base pair single read mode
The RNA-seq reads were mapped to the GRCh38 genome using TopHat version 2.0.13
Only uniquely mapped reads were counted in the analysis, using the HTSeq-count package version 0.6.1 with ‘union’ mode
The counts normalization and the differential expression analysis were done using the DESeq2 package version 1.8.1
Genome_build: GRCh38 genome
Supplementary_files_format_and_content: Excel file includes normalized counts

source_name: Glioblastoma cultured cells

growth_protocol: Three human Glioblastoma cell lines, U-87, T98G and LNT-229 (obtained from the ATCC) were maintained in DMEM supplemented with 10% FBS, 1% L-glutamine, 1% Na-pyruvate, 0.1 mg/ml streptomycin and 100 μ/ml penicillin and 0.1% HEPES. The cells were kept in 5% CO2 humidified incubator at 37°C.

extract_protocol:
Total RNA was prepared from between 1 to 2*106 GBM cells, using the Total RNA Purification Plus kit (Norgen biotec) as per the kit instructions. The isolated total RNA was quantified using Qubit 2.0 machine (Invitrogen) before the sequencing library preparation. The mRNA population in each sample was enriched by removing ribosomal RNA (rRNA) using the Epicenter ScriptSeq Complete kit (human, Illumina) as per the kit instructions.
The experiment was performed by Illumina HiSeq 2500 in 50 base pair single read mode in the Technion Genome Center. The RNA-seq reads were mapped to the GRCh38 genome using TopHat version 2.0.13. Only uniquely mapped reads were counted in the analysis, using the HTSeq-count package version 0.6.1 with ‘union’ mode. The counts normalization and the differential expression analysis were done using the DESeq2 package version 1.8.1.

treatment_protocol: Cells were counted and plated in new 150 mm Petri dishes one day prior to the treatment. The following day, the media was removed and replaced with fresh medium with or without 1 μM of 5'-Aza-2'-deoxycytidine (Decitabine, Enco diagnostics, AdooQ bioscience). After incubation with Decitabine for 72 hours, the cells were harvested, counted and prepared for RNA sequencing.

tag: tissue

value: Brain tumor cell line

tag: treatment

value: Not treated


title: CO070


title: U-87_DAC_22-3-15

value: Cells following treatment with Decitabine


title: T98G_DAC_29-4-15


title: T98G_DAC_15-3-15


title: U-87_22-3-15


title: total RNA DIS3L2 mut rep1

description: HEK293 DIS3L2 mut


title: T98G_29-4-15


title: T98G_15-3-15


title: Input DNA_Pol

city: Nankang, Taipei

first: Der-Hwa

last: Huang

state: Taiwan

address: 128, Sec2, Academia Rd.

department: Insititute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Raw sequences were aligned to Drosophila Release 5.47 genome sequence by using mapping software CLC Genomics Workbench vision 7
Peaks of ChIP-enriched sequences were identified by using PICS (Probabilistic Inference for ChIP-Seq) with mapping software Avadis-NGS vision 1.2
Reads were adjusted by using RPKM (reads per kilobase per million) for each data sets
Genome_build: Dmel_Release_5.4
Supplementary_files_format_and_content: text file with called peaks.

organism: Drosophila melanogaster

source_name: Or-R

growth_protocol: Fly grew at 25 degree C, harvest at 3rd instar stage

extract_protocol:
Lysates were prepared from sonicated nuclei and GAF-DNA complexes were isolated with antibody.  The GAF antibodies were custom-made by this lab while anti-RNA Pol II antibodies were provided by the lab of Dr. John T. Lis.
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments.  This fragment range corresponds to a ChIP fragment range of about 200 -300bp. Size selected fragments were PCR amplified for 12 cycles . Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment.

tag: genotype

value: wildtype

value: Imaginal discs and salivary glands

tag: developmental stage

value: 3rd instar stage

tag: antibody

value: none (input)


title: WT_Pol

value: anti-PolII


title: Input DNA_GAF


title: LNT-229_DAC_20-4-15


title: DarrowHuntley-2015-HIC016

source_name: Mouse Embryonic Kidney Fibroblasts

value: Patski

value: Mouse Embryonic Kidney Fibroblasts

value: in situ Hi-C


title: GAFm_Pol

source_name: GAF mutant

value: GAF mutant


title: DarrowHuntley-2015-HIC015


title: AZM microbiome seq_pooled sample

city: New York

first: Leopoldo

middle: Nicolas

last: Segal

address: 462 First Avenue NBV 6N5-6N8

department: Medicine

institute: NYU School of Medicine

data_processing:
demultiplexing and filtering of short (<150 nt) and low quality reads
de novo clustering of the sequences into operational taxonomic units (OTUs) with the UCLUST program using a 97% similarity threshold
taxonomical assignment of each OTU by running the RDP Classifier(8) at 80% bootstrap confidence on a selected representative sequence from each OTU;
alignment of representative sequences using PyNAST(9) with the Greengenes core-set alignment template
phylogenetic tree reconstruction from the representative sequences for each OTUs using the FASSTTREE program
UniFrac distance calculations
Supplementary_files_format_and_content: abundance measurement

organism: human lung metagenome

source_name: Lung BAL_pooled

extract_protocol:
ion exchange column (Qiagen)
Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25μl reactions with the following reaction conditions: 11μl PCR-grade H2O, 10μl Hot MasterMix (5 Prime Cat# 2200410), 2μl of forward and reversed barcoded primer (5μM) and 2μl template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94°C for 3 min followed by 35 cycles of denaturation at 94°C for 45 seconds, annealing at 58°C for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72°C. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions

treatment_protocol: Twenty smokers with emphysema received AZM 250 mg or placebo daily for 8 weeks

tag: subject status

value: patients with COPD

tag: time point

value: Pre- or post-treatment (pooled)

tag: treated with

value: Placebo or azithromycin (pooled)

value: Lung BAL

tag: barcode sequence

value: provided in the 'complete_metadata.txt' for each sample

tag: linker primer sequence

value: CCGGACTACHVGGGTWTCTAAT


title: MDA-MB453_PIAS1_R1881_rep2

status: Public on Jul 18 2016

city: Kuopio

first: Sari

last: Toropainen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description:
Chromatin IP against PIAS1 in MDA-MB453 cells
processed data file: MDA_PIAS1_R1881_rep1+2_peaks.bed

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.7) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
Individual background was generated for each AR and PIAS1 ChIP-seq sample. The read ration of IgG/ChIP-seq sample was set to same for all ChIP-seq samples by randomly removing IgG reads.
The peak detection was done by using HOMER software (4.1). Binding sites were determined with findPeaks command (using -factor mode and individual IgG samples as a background).
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks (found in both replicates).

growth_protocol: The cells were grown in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), 25 U/ml penicillin and 25 mg/ml streptomycin in a 5% CO2 atmosphere at 37 C.

extract_protocol:
Lysates were derived from sonicated nuclei and AR- and PIAS1-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocol, as utilized at the Functional Genomics Unit, Helsinki, Finland.

treatment_protocol: ChIP-seq samples transfected with siNON or siPIAS1 were seeded onto plates in DMEM supplemented with 5% charcoal-stripped FBS. After four days of plating the cells, the cells were exposed to R1881 (10 nM) for 2 h.

tag: origin

value: Metastatic carcinoma of the breast

tag: cell line

value: MDA-MB453 breast cancer cell line

value: 10 nM R1881 for 2hrs

tag: chip antibody

value: PIAS1 (Abcam 77231)


title: WT_MNase

data_processing:
Raw sequences were aligned to Drosophila Release 5.47 genome sequence by using mapping software CLC Genomics Workbench vision 7
Unique read pairs identifying both ends of fragments >=120 bp and =<180 bp in length were selected
The center of each read was used to identify as its position, and were smoothed with 10bp bin.
Reads were adjusted by using formula described in supplemental material and methods.
Genome_build: Dmel_Release_5.4
Supplementary_files_format_and_content: The processed data files contain the center position bp of each nucleosome read at each single-base pair position for +/- 500 bp surrounding the TSS of each indicated gene.

extract_protocol:
MNase-digested chromatin was prepared as described previously (Petesch and Lis 2008; Gilchrist et al. 2009; Gilchrist et al. 2010) except that 200 µl chromatin was digested with 20 units MNase (Worthington) for 3 hours at 25 degrees C. Following gel purification, mono-nucleosome sized fragments (100-200 bp) were subjected to paired-end sequencing using the Illumina paired-end protocol.
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments.  This fragment range corresponds to a ChIP fragment range of about 200 -300bp. Size selected fragments were PCR amplified for 12 cycles . Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment.

value: wildtype

value: Imaginal discs and salivary glands

value: 3rd instar stage


title: GAFm_MNase


title: Input-C

description: control sample

value: male

value: stomach

value: MGC803 gastric cancer cell line

tag: age

value: control


title: MDA-MB453_AR_siPIAS1_R1881_rep1

description:
Chromatin IP against AR in MDA-MB453 cells
processed data file: MDA_AR_siPIAS1_R1881_rep1+2_peaks.bed

tag: transfected with

value: PIAS1 siRNA

value: rabbit antiserum against AR


title: LNT-229_20-4-15

value: Brain tumor cell line

value: Not treated


title: MDA-MB453_AR_siPIAS1_R1881_rep2


title: MDA-MB453_AR_siNON_R1881_rep1

description:
Chromatin IP against AR in MDA-MB453 cells
processed data file: MDA_AR_siNON_R1881_rep1+2_peaks.bed

value: control siRNA (siNON, Non-targeting pool)


title: DarrowHuntley-2015-HIC019

value: Patski

tag: cell type

value: Mouse Embryonic Kidney Fibroblasts

tag: protocol

value: in situ Hi-C


title: DarrowHuntley-2015-HIC014


title: LNT-229_5-2-15

tag: tissue


title: LNT-229_DAC_5-2-15

tag: treatment

value: Cells following treatment with Decitabine


title: DarrowHuntley-2015-HIC021

source_name: B-lymphoblastoids

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was digested with CviJI in CviJI reaction buffer and ligated with T4 DNA ligase. The library was enriched for ligation products after proximity ligation using size selection on an agarose gel.
Standard Illumina library construction protocol was performed, and libraries were sequenced on the HiSeq X Ten/NextSeq/HiSeq2500 following the manufacturer's protocols.

value: B-lymphoblastoids

value: COLA Hi-C


title: IP Sync-TRAP cKO P12 CB3

city: Evanston

first: Yue

last: Yang

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

description: Ribosome-bound RNA

data_processing:
Reads were aligned to mm9 using bowtie. The number of reads in each sample was normalized by library size and ChIP-Seq datasets were input subtracted. Peak calling was performed using the Sicer program.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated by merging replicate bam files and using bedtools and bedGraphToBigWig. Total reads were normalized to 10 million reads.
Supplementary_files_format_and_content: Bed files were generated by first calling H3K4me3 or H3K27ac peaks using Sicer. H3K4me3 peaks that overlapped with Refseq TSS were considered H3K4me3-bound TSS. H3K27ac peaks that were >1000bp away from Refseq TSS and did not overlap with H3K4me3 peaks were considered H3K27ac-bound enhancers.
Supplementary_files_format_and_content: Txt files are a tabular matrix file generated from RNA-seq datasets. Gene and exon level differential expression was estimated through pair-wise negative binomial tests with EdgeR and DEXSeq, respectively. The Benjamini-Hochberg false discovery rate (FDR) was calculated for all genes. Significantly differentially expressed genes (FDR < 0.05) are indicated.

source_name: cerebellum

extract_protocol:
For ChIP, lysates were purified from sonicated nuclei and histone-DNA complexes were isolated with the indicated antibodies. Total RNA was harvested with Trizol. For Sync-TRAP, ribosome-bound RNA were purified and amplified with Ovation RNA-Seq System V2 (NuGEN)
ChIP-Seq libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit and RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Chd4 cKO

value: P12, 6 days post-electroporation

value: cerebellum


title: IP Sync-TRAP cKO P12 CB2

description: Ribosome-bound RNA

tag: developmental stage


title: DarrowHuntley-2015-HIC018


title: IP Sync-TRAP WT P12 CB2

description: Ribosome-bound RNA

value: WT


title: IP Sync-TRAP WT P12 CB1

description: Ribosome-bound RNA


title: input Sync-TRAP cKO P12 CB1


title: DarrowHuntley-2015-HIC017


title: MDA-MB453_AR_siNON_R1881_rep2

value: Metastatic carcinoma of the breast

value: MDA-MB453 breast cancer cell line

value: 10 nM R1881 for 2hrs