title: 2-HPC-iPSC-16 H3K4me3 ChIPseq

description: Sample 31

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_16_peaks.bed: mm9


title: R1-ESC H3K4me3 ChIPseq

status: Public on Dec 06 2013

type: SRA

city: Beijing

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute Of Biological Sciences, Beijing (NIBS)

description: Sample 28

library_source: genomic

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_R1_peaks.bed: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: ESC H3K4me3 ChIPseq

growth_protocol: ES cells and iPS cells were maintained in ES cell media containing 15% FBS and 1,000 Uml-1 of LIF.MEF and APCs were cultured in DMEM supplemented with 10% FBS and penicillin/streptomycin. HPCs was freshly isolated from bone marrow

extract_protocol: 1.5x108 cells were resuspended in lysis buffer and digested with micrococcal nuclease about 5 minutes at 37℃.Then, the lysate was immunoprecipitated with antibody anti-H3K4me2, anti-H3K4me3, anti-H3K27me3; meanwhile, retaining a fraction of input ‘whole-cell extract’ as sequencing control. Immunoprecipitation-enrichment of chromatin fragments were defined and the bound DNA were purified using phenol:chloroform extractions. Chiped DNA was quantified by Qubit 2.0 Fluorometer (life technologies) and Q-PCR was performed to validate the enrichment efficiency. Then the enriched DNA was sonicated to 100-500bp fragments. DNA-end was repaired to overhang a 3’-dA, then adapters was ligated to the end DNA fragments. DNA fragments about 100-300bp, were recovered and amplified to construct the sequencing library. Thirty-nine ChIP library and thirteen input controls were used for sequencing.

tag: strain

tag: cell type

value: embryonic stem cells

tag: passage

tag: chip antibody

tag: chip antibody vendor

value: abcam

tag: chip antibody cat #

tag: chip antibody lot #


title: 1-MEF-iPSC-37 H3K4me3 ChIPseq

description: Sample 29

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_37_peaks.bed: mm9

source_name: MEF-iPSC H3K4me3 ChIPseq

value: MEF-derived induced pluripotent stem cells


title: 2-APC-iPSC-32 H3K4me3 ChIPseq

description: Sample 30

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me3_32_peaks.bed: mm9

source_name: APC-iPSC H3K4me3 ChIPseq

value: APC-derived induced pluripotent stem cells


title: 3-APC H3K27me3 ChIPseq

description: Sample 27

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_BSC_peaks.bed: mm9

source_name: APC H3K27me3 ChIPseq

value: mouse adipose progenitor cells

value: Millipore


title: 2-APC H3K27me3 ChIPseq

description: Sample 25

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_ASC_peaks.bed: mm9


title: 2-HPC H3K27me3 ChIPseq

description: Sample 26

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_HSC_peaks.bed: mm9

source_name: HPC H3K27me3 ChIPseq

value: mouse hematopoietic progenitor cells


title: BDI09 Leaf 2

city: NEWARK

first: Dong-Hoon

last: Jeong

state: DE

address: 15 Innovation Way

country: USA

institute: University of Delaware

description: small RNA

library_source: transcriptomic

data_processing:
The raw sequencing data was converted to SCARF format, trimmed of adapters, matched to the Brachypodium Genome 8X Assembly (ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Bdistachyon/)  by custom Perl scripts
Genome_build: 8X
Supplementary_files_format_and_content: Text containing distinct small RNAs or mRNAs with their raw abundance after removing the adapter sequences

molecule: total RNA

organism: Brachypodium distachyon

source_name: Leaf

growth_protocol: Brachypodium (Line Bd21) was used for all libraries. For the BDI small RNA and PARE libraries, seeds were germinated in soil and the plants were grown in a growth chamber at a constant 20°C, under a 20 h-light, 4 h-dark cycle. Leaf, stem, and panicle tissues were harvested from six-week old plants. Leaf tissue was the blade of first and second leaf from the top, not including the leaf sheath.  Stem tissue was harvested from just above the first top node to just below the second node, including both nodes as well as the leaf sheath of the second leaf.  Panicle tissue was harvested from plants with immature, unfertilized flowers from the tip of the spikelet to just above, but not including, the panicle node at approximately 10 h into the subjective day. To collect root tissue, seeds were husked, surface-sterilized with a 50% bleach solution, rinsed with sterile water, and germinated on half-strength Murashige and Skoog (MS) medium containing 0.2% (w/v) Phytagel in sterile plastic boxes. Root tissue was harvested from three-week old plants from the tip of the root to just below, but not including the seed. For the OBD set of small RNA libraries from tissues, Brachypodium plants were grown with supplemental light on a 16 h photoperiod at 25°C. For OBD02, leaf and stem tissues were collected at day 7-8, 14-15, and 27-28 and pooled. Panicle tissue was collected at day 28-35 at 4 time point intervals of 0700 (dawn), 1300, 1900, 0100 hours. For OBD03 seedlings, the following whole seedlings including roots were pooled. Two samples were soil grown under a 16 h photoperiod and tissues were collected from 3- and 4-day old plants. Two additional samples included 5-day old etiolated seedlings and light-grown seedlings grown on moistened filter paper.

extract_protocol:
Total RNAs were isolated using Trizol reagent (Molecular Research Center).
Small RNA libraries were constructed as previously described (Lu et al., 2007) and PARE libraries were constructed as described (German et al., 2008). All the libraries were sequenced on llumina IIGX analyzer. Sequencing was performed at Illumina or the Delaware Biotechnology Institute.

treatment_protocol: Stress treatments and controls except phosphate starvation and its control for BDI small RNA libraries were done using three-week old plants planted in soil under normal growth conditions with a 20 h photoperiod as above. Stresses began 5-6 h after the lights came on.  For heat stress, plants were moved to 40°C for 12 h.  For cold stress, plants were moved to 4°C in a cold room for 12 h.  For drought stress, plants were removed from the soil and rinsed, blotted dry with paper towels, and air-dried for 12 h.  For salt stress, the base of the plant pot was submerged in 300mM NaCl solution for 12 h to the depth of approximately 1 inch, not covering the soil.  For submergence stress, plants were fully submerged in 20°C water for 24 h.  For phosphate starvation stress, seeds were planted in MS media with KH2PO4 omitted, and control plants were planted in MS media; plants were harvested at three weeks, 5-6 h after lights on.  Control plants were sampled at the same time as the stress treatments. For OBD04, tissues from plants treated with abiotic, biotic, and mechanical stresses were pooled. For abiotic stress, leaves and stems were collected from plants subjected to heat (37°C), cold (4°C), salt (200 mM NaCl), and osmotic (300 mM Mannitol) treatments. For biotic stress, leaves were collected from plants with the following treatments: Bacterial treatments were (Pseudomonas fluorescens and Pseudomonas syringae pv. tomato DC3000 [Pto DC3000]) delivered to 28-29 day old Brachypodium leaves under vacuum at 1x107 cfu/mL. Leaves of four-week old plants were placed in a 1.5 ml microcentrifuge tube containing 20 µg/mL victorin. Tissue was harvested 24 h after treatment with victorin. Mechanical stress was applied by crushing the leaves of 29-30 day old plants with tweezers. Unless otherwise indicated, libraries were made from a pool of samples collected every 4 h after the stress began, i.e. 4h+8h+12h+16h+20h+24h.

tag: tissue

value: leaf

tag: plant line

tag: treatment

value: untreated


title: 1-MEF H3K27me3 ChIPseq

description: Sample 24

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_MEF_peaks.bed: mm9

source_name: MEF H3K27me3 ChIPseq

value: mouse embryonic fibroblast


title: BDI08 Root

description: small RNA

source_name: Root

value: root


title: 1-MEF-iPSC-42 H3K27me3 ChIPseq

description: Sample 20

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_42_peaks.bed: mm9

source_name: MEF-iPSC H3K27me3 ChIPseq


title: 2-APC-iPSC-4 H3K27me3 ChIPseq

description: Sample 21

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_4_peaks.bed: mm9

source_name: APC-iPSC H3K27me3 ChIPseq


title: 3-APC-iPSC-3 H3K27me3 ChIPseq

description: Sample 19

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_3_peaks.bed: mm9


title: polII chipseq rep2

city: Houston

first: Stephen

middle: D

last: Ayers

state: Texas

address: 6565 Fannin Street F8-060

department: Genomic Medicine

institute: Methodist Hospital Research Institute

description: Sample 8

data_processing:
Basecalls performed using CASAVA version 1.6
Data quality was assessed with fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 0.12.7 using --trim5 2 --trim3 5
Peaks of enriched binding were generated using QuEST version 2.4.
Genome_build: mm9
Supplementary_files_format_and_content: Standard bed format, containing reads mapped by bowtie.  Lines adhere to the specification on: http://genome.ucsc.edu/FAQ/FAQformat.html#format1, and each line contains the fields: chrom, chromstart, chromend.

source_name: polII ChIP-seq

growth_protocol: mESCs and miPSCs were cultured in mESC medium (DMEM with 15% FBS, 1 mM L-glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma) and 1,000 U ml−1 LIF (Santa cruz)) on irradiated feeder cells.

extract_protocol:
Clarified lysates were prepared from sonicated nuclei and histone-DNA complexes were isolated according to manufacturer's standard protocols, with antibodies specific for PHF20 (Cell signaling Cat# 3934S lot#1), Wdr5 (Bethyl Cat# A302-429A lot# A302-429A-1) or PolII (abcam cat#ab5408 lot#gr258-5).
Libraries were prepared with Illumina's DNA ChIP-Seq Sample Kit (Part# 0801-0303), according to manufacturer's standard protocols. Briefly, DNA was end-repaired using T4 DNA polymerase, E. Coli DNA Pol I large fragment and T4 polynucleotide kinase. Blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base (A-Tailing) for ligation of Illumina's adapters. After adapter ligation, DNA was PCR-amplified with Illumina primers for 15 cycles and library fragments of ~250 bp purified. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina MiSeq following  manufacturer's protocols.

treatment_protocol: ChIP assay was performed according to the Imprint Ultra Chromatin Immunoprecipitation Kit manual (Sigma), Briefly, cells were grown to an approximate final count of 1-5×107 cells for each reaction. Cells were cross-linked with 1% formaldehyde solution for 10 min at room temperature with gentle agitation and quenched with 0.125M glycine. Cells were rinsed twice with 1×PBS, flash frozen and stored at –80°C. Cells were resuspended, lysed, and sonicated to solubilize and shear crosslinked DNA. The resulting chromatin extract was incubated overnight at 4°C with 10 mg antibody. Next day, each sample was added 15 ml blocked beads and then incubated at 4°C for 1 h. Beads were washed 5 times with RIPA buffer, once with TE containing 50 mM NaCl and complexes were eluted from beads in elution buffer by heating at 65°C. Reverse crosslinking was performed overnight at 65°C. Input DNA (reserved from sonication) was concurrently treated for crosslink reversal. DNA were treated with RNaseA, proteinase K and purified. Primary antibodies used for IP were: PHF20 (PHF20 antibody Cell signaling Cat# 3934S lot#1), Wdr5 (Wdr5 antibody Bethyl Cat# A302-429A lot# A302-429A-1), mouse/rabbit IgG and RNA Polymerase II (Polymerase II antibody abcam cat#ab5408 lot#gr258-5). Relative fold enrichments were calculated by determining the immunoprecipitation efficiency (ratios of the amount of immunoprecipitated DNA to that of the input sample).

tag: strain background

tag: cell type origin

value: ES-derived neural progenitor cells

value: Polymerase II antibody

value: Abcam

tag: chip antibody cat. #


title: 2-HPC-iPSC-16 H3K27me3 ChIPseq

description: Sample 18

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_16_peaks.bed: mm9

source_name: HPC-iPSC H3K27me3 ChIPseq

value: HPC-derived induced pluripotent stem cells


title: wdr5 chipseq rep2

description: Sample 7

source_name: wdr5 ChIP-seq

value: Wdr5 antibody

value: Bethyl


title: 1-MEF-iPSC-37 H3K27me3 ChIPseq

description: Sample 16

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_37_peaks.bed: mm9


title: phf20 chipseq rep2

description: Sample 6

source_name: phf20 ChIP-seq

value: embryonic stem cells

value: PHF20 antibody

value: Cell signaling


title: 2-APC-iPSC-32 H3K27me3 ChIPseq

description: Sample 17

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_32_peaks.bed: mm9

value: APC-derived induced pluripotent stem cells


title: R1-ESC H3K27me3 ChIPseq

description: Sample 15

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_R1_peaks.bed: mm9

source_name: ESC H3K27me3 ChIPseq


title: control sample rep2

description: Sample 5

source_name: control sample


title: 2-HPC input DNA

description: Sample 13

data_processing: The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.

source_name: HPC input DNA


title: 3-APC input DNA

description: Sample 14

source_name: APC input DNA

value: mouse adipose progenitor cells


title: 2-HPC* input DNA

description: Sample 12


title: 3-APC-iPSC-9 input DNA

description: Sample 9

source_name: APC-iPSC input DNA


title: wdr5 chipseq rep1

description: Sample 3


title: 2-APC input DNA

description: Sample 11


title: phf20 chipseq  rep1

description: Sample 2


title: control sample rep1

description: Sample 1


title: 3-APC-iPSC-9 H3K27me3 ChIPseq

description: Sample 23

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_9_peaks.bed: mm9

value: Millipore


title: 2-APC-iPSC-4 input DNA

description: Sample 7


title: 1-MEF-iPSC-42 input DNA

description: Sample 6

source_name: MEF-iPSC input DNA

value: MEF-derived induced pluripotent stem cells


title: 3-APC-iPSC-3 input DNA

description: Sample 5


title: 2-HPC-iPSC-18 input DNA

description: Sample 8

source_name: HPC-iPSC input DNA


title: 2-HPC-iPSC-16 input DNA

description: Sample 4


title: 2-APC-iPSC-32 input DNA

description: Sample 3


title: 2-HPC-iPSC-18 H3K27me3 ChIPseq

description: Sample 22

data_processing:
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K27me3_18_peaks.bed: mm9


title: R1-ESC input DNA

description: Sample 1

source_name: ESC input DNA


title: 2-APC small RNA

description: Sample 11

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_ASC_uniq_counts.txt: mm9

source_name: APC_small RNAseq

extract_protocol: S-RNAs about 18-30 nt were first separated from the 5μg-10μg total RNA by size fractionation with 15% TBE urea polyacrylamide gel(TBU).Next,the 5’ RNA adapter(GUUCAGAGUUCUACAGUCCGACGAUC-3’) was ligated to the RNA pool with T4 RNA ligase.Ligated RNA was size-fractionated on a 15% agarose gel,and a 40-65 nt fraction excised.The 3’RNA adapter(5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’;p,phosphate;idT,inverted deoxythymidine) was subsequently ligated to precipitated RNA using T4 RNA ligase.Ligate RNA was size-fractionated on a 10% agarose gel,and the 70-90 nt fraction excised.Through the RT- PCR amplification of 15 cycles and purified,small RNA libraries were produced.

value: mouse adipose progenitor cells (APC)


title: 1-MEF-iPSC-37 input DNA

description: Sample 2


title: 3-APC small RNA

description: Sample 13

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_BSC_uniq_counts.txt: mm9


title: 2-HPC small RNA

description: Sample 12

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_HSC_uniq_counts.txt: mm9

source_name: HPC_small RNAseq

value: mouse hematopoietic progenitor cells (HPC)


title: 3-APC-iPSC-9 small RNA

description: Sample 9

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_9_uniq_counts.txt: mm9

source_name: APC-iPSC_small RNAseq


title: 1-MEF small RNA

description: Sample 10

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_MEF_uniq_counts.txt: mm9

source_name: MEF_small RNAseq

value: mouse embryonic fibroblast (MEF)


title: polII chipseq rep1

description: Sample 4


title: 2-HPC-iPSC-18 small RNA

description: Sample 8

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_18_uniq_counts.txt: mm9

source_name: HPC-iPSC_small RNAseq


title: 3-APC-iPSC-3 small RNA

description: Sample 5

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_3_uniq_counts.txt: mm9


title: 1-MEF-iPSC-42 small RNA

description: Sample 6

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_42_uniq_counts.txt: mm9

source_name: MEF-iPSC_small RNAseq


title: 1-MEF input DNA

description: Sample 10

source_name: MEF input DNA

value: mouse embryonic fibroblast


title: 1-MEF-iPSC-37 small RNA

description: Sample 2

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_37_uniq_counts.txt: mm9


title: 2-HPC-iPSC-16 small RNA

description: Sample 4

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_16_uniq_counts.txt: mm9


title: 2-APC-iPSC-32 small RNA

description: Sample 3

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_32_uniq_counts.txt: mm9


title: 3-APC rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_BSC_rep1.fpkm: mm9

extract_protocol: Total RNA was isolated from cell pellets using TRIZOL regent (Invitrogen) according to the manufacture’s instructions. RNA integrity was confirmed using the 2100 Bioanalyzer (Agilent Technologies) with a minimum RNA integrity number (RIN) of 8. mRNA was enriched by using the oligo(dT) magnetic beads and interrupted to short frangments about 200bp. cDNA was synthesized by random hexamer-primer and purified with PCR product extraction kit (Qiagen). Finally, sequencing primers linked cDNA fragments approximately 200bp were isolated by gel electrophoresis and enriched through PCR amplification to construct the library. And Illumina HiSeqTM 2000 was used for sequencing analysis.


title: 2-HPC rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_HSC_rep2.fpkm: mm9


title: R1-ESC small RNA

description: Sample 1

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_R1_uniq_counts.txt: mm9

source_name: ESC_small RNAseq


title: 3-APC rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_BSC_rep2.fpkm: mm9


title: 2-APC rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_ASC_rep1.fpkm: mm9


title: 2-APC rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_ASC_rep2.fpkm: mm9


title: 2-HPC rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_HSC_rep1.fpkm: mm9


title: FROZ_TruSeq_MCJBCR028

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

data_processing:
Basecalls made by standard Illumina pipleline (Bustard)
The pair end reads were aligned to the human genome build 37.1 using TopHat (1.4.0) and Bowtie (0.12.7). HTSeq (0.5.3p3) was used to perform gene counting while BEDTools (2.7.1) was used to count the reads mapping to individual exons according to RefSeq gene annotations (Feb 2009, GRCh37/hg19) with 23,113 genes.
Genome_build: hg19
Supplementary_files_format_and_content: text; gene level expression count

organism: Homo sapiens

source_name: Fresh-frozen breast tumor

extract_protocol:
RNA was extracted from FFPE tissue using the Qiagen AllPrep FFPE kit including treatment with DNase. RNA was extracted from the fresh-frozen tumors using the Qiagen Rneasy including treatment with DNase.
For Illumina libraries we used 200ng total RNA and followed the manufacturer's instructions for TruSeq RNA sample preparation V2 (catalogue number: RS-122-2001). For the RiboZeroGold/ScriptSeq V2 libraries (catalogue number: LIMC1204/SSV21124) we used 200-400ng total RNA and followed the manufacturers instructions, with the exception for FFPE libraries, we extended the cDNA synthesis 37C step to 90 minutes.

tag: tissue id

tag: er/pr/her2 status

tag: tumor size

tag: tumor grade

tag: molecule subtype

value: polyA enriched RNA


title: FROZ_TruSeq_BRB277


title: 3-APC-iPSC-9 rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_9_rep2.fpkm: mm9

tag: strain

tag: cell type


title: 1-MEF rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_MEF_rep1.fpkm: mm9

tag: passage


title: FROZ_TruSeq_BRB248


title: FROZ_TruSeq_BRB215


title: 2-APC-iPSC-4 rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_4_rep2.fpkm: mm9


title: 2-HPC-iPSC-18 rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_18_rep1.fpkm: mm9


title: 2-APC-iPSC-4 small RNA

description: Sample 7

data_processing:
The raw files were split according to barcode sequence by Perl scripts. Adapter sequences were removed using “vectorstrip” in EMBOSS package (version 6.4.0.0). Then, the unique reads were classified and counted.
Genome Build:
sRNA_4_uniq_counts.txt: mm9


title: 2-APC-iPSC-4 rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_4_rep1.fpkm: mm9


title: 1-MEF-iPSC-42 rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_42_rep2.fpkm: mm9


title: FROZ_TruSeq_BRB212


title: 1-MEF-iPSC-42 rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_42_rep1.fpkm: mm9


title: 3-APC-iPSC-3 rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_3_rep2.fpkm: mm9


title: FROZ_TruSeq_BRB157


title: 3-APC-iPSC-3 rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_3_rep1.fpkm: mm9


title: 2-HPC-iPSC-16 rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_16_rep2.fpkm: mm9


title: FROZ_TruSeq_BRB147


title: 2-HPC-iPSC-16 rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_16_rep1.fpkm: mm9


title: 3-APC-iPSC-9 rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_9_rep1.fpkm: mm9


title: 2-APC-iPSC-32 rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_32_rep2.fpkm: mm9


title: FROZ_TruSeq_BRB144


title: 2-APC-iPSC-32 rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_32_rep1.fpkm: mm9


title: 1-MEF rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_MEF_rep2.fpkm: mm9


title: FROZ_ScriptSeq_BRB277

data_processing:
Basecalls made by standard Illumina pipleline (Bustard)
The pair end reads were aligned to the human genome build 37.1 using TopHat (1.4.0) and Bowtie (0.12.7). HTSeq (0.5.3p3) was used to perform gene counting while BEDTools (2.7.1) was used to count the reads mapping to individual exons according to RefSeq gene annotations (Feb 2009, GRCh37/hg19) with 23,113 genes.
Genome_build: hg19
Supplementary_files_format_and_content: text; gene level expression count

value: rRNA depleted RNA


title: R1-ESC rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_R1_rep1.fpkm: mm9


title: R1-ESC rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_R1_rep2.fpkm: mm9


title: FROZ_ScriptSeq_BRB248


title: FROZ_ScriptSeq_BRB215


title: FROZ_TruSeq_BRB123


title: 1-MEF-iPSC-37 rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_37_rep2.fpkm: mm9


title: FROZ_ScriptSeq_MCJBCR028


title: 1-MEF-iPSC-37 rep1 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_37_rep1.fpkm: mm9


title: FROZ_ScriptSeq_BRB147


title: FROZ_ScriptSeq_BRB157


title: FROZ_ScriptSeq_BRB123


title: FROZ_ScriptSeq_BRB144


title: FROZ_ScriptSeq_BRB212


title: FFPE_ScriptSeq_BRB215

source_name: FFPE breast tumor


title: FFPE_ScriptSeq_BRB157


title: FFPE_ScriptSeq_BRB277


title: FFPE_ScriptSeq_MCJBCR028


title: FFPE_ScriptSeq_BRB212


title: FFPE_ScriptSeq_BRB248


title: FFPE_ScriptSeq_BRB147


title: FFPE_ScriptSeq_BRB123


title: FFPE_ScriptSeq_BRB144


title: MCF7 profiling library 2

status: Public on Dec 05 2013

city: Berlin

first: Markus

last: Landthaler

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine

description:
ProtOccProf library 1
Binding Profile
barcode for 4SU_Library2_1.qfa: TCTCACGTCGTATGCCGTCTTCTGCTTG
barcode for 4SU_Library2_2.qfa: TCTCACGTCGTATGCCGTCTTCTGCTTG
barcode for 4SU_Library2_3.qfa: TCTCACGTCGTATGCCGTCTTCTGCTTG
barcode for 4SU_Library2_4.qfa: TCTCACGTCGTATGCCGTCTTCTGCTTG
barcode for 4SU_Library2_5.qfa: TCTTTTATCGTATGCCGTCTTCTGCTTG
barcode for 4SU_Library2_6.qfa: TCTTTTATCGTATGCCGTCTTCTGCTTG
barcode for 4SU_Library2_7.qfa: TCTTTTATCGTATGCCGTCTTCTGCTTG
barcode for 4SU_Library2_8.qfa: TCTTTTATCGTATGCCGTCTTCTGCTTG

data_processing:
Read demultiplexing, read filtering and adapter trimming was done using flexbar (Dodt et al, 2012). Reads belonging to the same library were pooled.
Further read processing was performed using the Poppi pipeline. We used TopHat2 (version 2.06) (Trapnell et al., 2009 and Kim et al. 2013) for spliced alignment of strand-specific protein occupancy profiling reads to the human reference genome sequence (hg18).
We separated all reads by strand and generate two strand-specific mpileup read coverage files with samtools (version 0.1.18) (Li et al., 2009). These file are subsequently used to produce a separate bedgraph file for each strand (Watson / Crick). Additionally, a single bedgraph file for strand-specific T-C conversions is produced in a similar manner. T-C transitions sites are only included in the final file if at least two conversion events are observed on average.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph

source_name: MCF7 cell culture

growth_protocol: MCF-7 cells were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin.

extract_protocol: Eluted protein-RNA complexes were RNase I treated, followed by ammonium sulfate precipitation. Precipitate was separated by SDS-PAGE and transferred onto a nitrocellulose membrane. RNA was extracted from membrane by proteinase K treatment and phenol/chloroform extraction. Recovered RNA was dephosphorylated using CIP. After dephosphorylation RNA was phenol/chloroform extracted, ethanol precipitated and 50 end labeled with T4 PNK. Radiolabeled RNA was extracted and subsequent small RNA cloning and adaptor ligations were performed as described previously in small RNA cloning protocol (Hafner et al. 2008 Methods).

treatment_protocol: MCF-7 cells were grown in medium supplemented with 4-thiouridine at a final concentration of 200 microM for 16 hours. Cells were UV-crosslinked at 365 nm.

tag: cell line

tag: purification

value: oligo(dT) beads


title: wt zebrafish heart

first: Xiangjun

last: Tong

address: Yiheyuan Road No. 5

department: College of Life Sciences

institute: Peking University

data_processing:
sequenced by the Illumina Hiseq 2000 platform
Around 200 million 50-bp single-end reads were obtained per sample.
Reads were aligned to zebrafish genome Zv9 using tophat, with up to 2 mismatches allowed.
Differential expression analysis was performed using DESeq.
Genome_build: zebrafish genome Zv9
Supplementary_files_format_and_content: excel file of relative gene expression level between the wt and the kctd10 mutant.
Supplementary_files_format_and_content: tab delimited txt files of gene raw counts and DESeq processed relative gene expression level between the wt and the kctd10 mutant.

organism: Danio rerio

source_name: heart

extract_protocol:
Total RNAs from wild-type and kctd10 mutant fish hearts were isolated with RNeasy Mini Kit (Qiagen), purified with RNeasy columns (QIAGEN).
Next generation sequencing libraries were prepared with the Illumina TruSeq preparation kit (Illumina) according to manufacturer's protocol

value: AB

tag: development stage

value: 48 hpf

tag: genotype/variation

value: wt (wild type)

value: heart


title: kctd10 mut zebrafish heart

value: kctd10 -/- (kctd10 mutant)

tag: tissue


title: transcriptome_TCBQ

first: Zechen

last: Chong

address: NO. 7 Beitucheng West Road

institute: Beijing Institute of Genomics

description: processed data file: gene_exp.diff.txt

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using BWA version 0.5.9-r16
Peaks were called using MACS version 1.4.2 with default parameter
We aligned those high quality reads to the masked Homo sapiens reference genome (hg19) genome and junction sequences using BWA 0.5.8 software allowing up to four mismatches. All the uniquely mapped reads were used to define gene expression level based on our developed method. We modified the RPKM (measured in reads per kilobase of exon per million mapped sequence reads, which is a normalized measure of exonic read density) calculation described by Mortazavi and colleagues to include junction fragments. By including reads that map to junction fragments, we ensure that genes with many introns are not under represented in the RPKM estimate. To examine differential expression, we used a MARS (MA-plot-based method with Random Sampling model) method to identify differentially expressed genes which described in DEGseq. For each gene, the P-value and Q-value were computed, and the fold changes were also calculated. Those genes with p < 0.001 and q-value < 0.05 were defined as DEGs.
Genome_build: hg19
Supplementary_files_format_and_content: The files are generated by MACS version 1.4.2, including chr, start, end, length, summit, tags, -10*log10(pvalue),fold_enrichment. The file of differitially expressed genes includes Gene, GeneNames, value1, value2, log2(Fold_change), log2(Fold_change) normalized, z-score, p-value, q-value(Benjamini et al. 1995), q-value(Storey et al. 2003), Signature(p-value < 0.001).

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from TCBQ/DMSO treated MRC-5 cells using RNAzol (Molecular Research Center, Inc.)
Poly(A) RNA from 1 ug of total RNA was used to generate the  cDNA  library  according  to  TruSeq  RNA  Sample  Prep  Kit  protocol  which  was then sequenced using the Illumina system.

treatment_protocol: TCBQ powder was dissolved in DMSO with the concentration of 20mM for stock. MRC-5 cells with about 50% confluence were treated with TCBQ or DMSO diluted in culture media to the final concentration of 20uM for 24 hours.

value: human fetal lung fibroblast Cell


title: transcriptome_DMSO

description: processed data file: gene_exp.diff.txt


title: MCF7 profiling library 1

description:
ProtOccProf library 1
Binding Profile
barcode for 4SU_Library1_1.qfa: TCTCGTATCGTATGCCGTCTTCTGCTTG
barcode for 4SU_Library1_2.qfa: TCTCGTATCGTATGCCGTCTTCTGCTTG


title: 2-HPC-iPSC-18 rep2 RNAseq

data_processing:
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_18_rep2.fpkm: mm9

value: HPC-derived induced pluripotent stem cells


title: 5hmC_TCBQ

extract_protocol:
Genomic DNA was extracted from the harvested cells using a Genomic DNA Purification Kit (Promega, Madison, WI, USA), according to the manufacturer’s instructions. 0.1 mM DFO was added in the processes of DNA extraction and purification.
Genomic DNA from TCBQ or DMSO treated MRC-5 cells was purified by using Wizard genomic DNA purification kit (Promega) with additional Proteinase K treatment and rehydrated in 10 mM Tris (pH 8.0). Genomic DNA samples were further sonicated into short fragments (about 300bp) by using Covaris DNA shearing (Covaris S2 SonoLAB Single) with microTUBEs according to manufacturer’s instructions. Sonicated DNA was then purified with phenol/chloroform/isoamyl alcohol (25:24:1) precipitation. 5hmC was pulled down as described previously (Song et al., 2011). After purification, 10ng of the pull-down 5hmC containing DNA was end-repaired, adenylated, ligated to adapters and single-end sequenced on an HiSeq 2000 system (Illumina) according to the manufacturer’s recommendations for Illumina ChIP-Seq to identify peak enrichment

tag: enrichment method

value: The Hydroxymethyl Collector™ Kit


title: 5hmC_DMSO


title: input mix

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
Sequence data was generated and demultiplexed using the Illumina pipeline
Reads were aligned to hg19 with BWA version 0.5.10 using the default parameters
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) version 1.4.1. A  p-value cutoff 1e-7 was used.
Genome_build: hg19

source_name: breast carcinoma

extract_protocol:
Lysates were clarified from sonicated nucle.Lysate was split into 3 equal volumes and for each ChIP (ER, H3K4me3, H3K27me3) protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: primary tumor tissue was cryosectioned, 30x 30um sections were used

value: primary breast tumor

tag: procedure

value: whole cell lysate


title: poor outcome_5_ER

value: ChIP-seq

tag: chip antibody

value: SC-543 (Santa Cruz)

tag: aromatase inhibitor treatment outcome

value: poor


title: poor outcome_5_H3K27me3

value: 07-449 (millipore)


title: poor outcome_6_H3K4me3

value: ab8580 (Abcam)


title: poor outcome_7_ER


title: poor outcome_7_H3K4me3


title: poor outcome_6_H3K27me3


title: poor outcome_6_ER


title: poor outcome_3_H3K27me3


title: poor outcome_4_H3K27me3


title: poor outcome_5_H3K4me3


title: poor outcome_3_H3K4me3


title: poor outcome_4_ER


title: poor outcome_1_ER


title: poor outcome_7_H3K27me3


title: poor outcome_1_H3K27me3


title: poor outcome_2_H3K27me3


title: good outcome_4_H3K4me3

value: good


title: poor outcome_3_ER


title: good outcome_5_ER


title: good outcome_4_ER


title: poor outcome_2_ER


title: good outcome_4_H3K27me3


title: poor outcome_1_H3K4me3


title: poor outcome_4_H3K4me3


title: good outcome_3_H3K27me3


title: good outcome_2_H3K27me3


title: good outcome_1_H3K27me3


title: good outcome_5_H3K4me3


title: good outcome_3_ER


title: IN17

city: San Francisco

first: Peter

middle: James

last: Turnbaugh

state: CA

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: University of California San Francisco

data_processing:
Pre-processing of raw reads: binned according to barcode, trimmed ends to min score = 20 and minimum length = 20
Mapped reads to 539 human-associated genomes (http://www.hmpdacc.org/) using SSAHA (version 2; parameters: -best 1 -score 20 -solexa)
The number of transcripts assigned to each gene was then tallied.
Supplementary_files_format_and_content: Counts files were generated. The column1 identifiers are the gene IDs used in the draft genomes downloadable from the HMP DACC, with annotation added to the end. Column2 and column3 values are total reads assigned and fraction reads assigned (#reads/total reads), respectively.

organism: human gut metagenome

source_name: Fecal microbial community

growth_protocol: Fresh fecal samples were collected and stored temporarily at -20C before transfer to -80C

extract_protocol: Microbial cells were lysed by a bead beater (BioSpec Products), total RNA was extracted with phenol:chloroform:isoamyl alcohol (pH 4.5, 125:24:1, Ambion 9720), purified using MEGAClear columns (Ambion), and rRNA was depleted via subtractive hybridization (MICROBExpress, Ambion, in addition to custom depletion oligos). The presence of genomic DNA contamination was assessed by PCR with universal 16S rDNA primers. cDNA was synthesized using SuperScript II and random hexamers (Invitrogen), followed by second strand synthesis with RNaseH and E.coli DNA polymerase (New England Biolabs). Samples were prepared for sequencing with an Illumina HiSeq instrument after enzymatic fragmentation (NEBE6040L/M0348S). The size distribution of each library was quantified on an Agilent HS-DNA chip.

treatment_protocol: Subjects were sampled during baseline timepoints and during the 5 day consumption of a plant- or animal-based diet.

tag: subject

tag: time

value: Day 4

tag: diet

value: animal-based

tag: sample type (source of extracted total rna)

value: fecal sample (microbial cells)


title: good outcome_2_H3K4me3


title: IN18


title: good outcome_2_ER


title: IN16


title: IN13


title: IN15


title: IN23

value: Day 3


title: good outcome_5_H3K27me3


title: IN14


title: IN24


title: good outcome_3_H3K4me3


title: IN3

value: Day -1


title: IN25


title: IN7


title: IN22


title: IN21


title: IN5


title: IN27


title: IN6


title: IN1


title: IN2


title: BB20

value: plant-based


title: BB28


title: good outcome_1_ER


title: IN28


title: BB26


title: MCF7 flow-through

data_processing:
Read demultiplexing, read filtering and adapter trimming was done using flexbar (Dodt et al, 2012).
We used TopHat2 (version 2.06) (Trapnell et al., 2009 and Kim et al. 2013) for spliced alignment of reads to the human reference genome sequence (hg18).
mRNA half-lives were determined as described in Schwanhaeusser et al. Nature 2011 from the three fractions total/4suRNA/flowthrough
Genome_build: hg18
Supplementary_files_format_and_content: text format indicating mRNA half-life in minutes for replicate 1 and 2 (rep1 and rep2) determined as described in Schwanhaeusser et al. Nature 2011

growth_protocol: HEK293 or MCF-7 cells were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen). 4SU residues were biotinylated using EZ-Link biotin-HPDP (Thermo Fisher Scientific). Biotinylated 4SU-labled RNA was separated from non-labeled RNA using μMACS Streptavidin MicroBeads (Miltenyi) and 4SU-labeled RNA was eluted from μColumns by addition of 100 mM DTT. RNA was recovered from the flow-though and 4SU-labeled fractions using MinElute Spin columns (Qiagen). Input (total), flow-though (non-labeled RNA) and eluted (4SU-labled RNA) samples were used for poly(A)+ mRNA library preparation following the TruSeq RNA sample Prep v2 LS protocol (Illumina). The libraries were sequenced on an Illumina HiSeq2500 for 100 cycles (multiplexed 1× 101 + 7 index). mRNA half-lives were computed as previously described (Schwanhausser et al., 2011)

treatment_protocol: For global mRNA for half-life measurements, MCF-7 and HEK293 cells were labeled with 700 µM 4SU for 60 min.

value: oligo(dT) beads

tag: sample type

value: non-labeled RNA


title: good outcome_1_H3K4me3


title: IN4


title: BB25


title: MCF7 total RNA

value: input or total RNA


title: MCF7 4suRNA

value: 4SU-labeled RNA


title: BB24


title: BB34


title: BB19


title: IN26


title: BB29


title: BB35


title: BB37


title: BB30


title: BB36


title: BB31


title: BB32


title: BB21


title: BB22


title: BB27


title: HEK293 flow-through

source_name: HEK293 cell culture


title: BB23


title: HEK293 4suRNA


title: LE2

city: SAN ANTONIO

first: Timothy

last: ANDERSON

state: TEXAS

department: Genetics

institute: Texas Biomedical Research Institute

data_processing:
Illumina Casava1.8.2 pipeline used for basecalling.
The RNA-Seq libraries were aligned using bowtie (version 0.12.7) - The latest S. mansoni genome assembly was used as reference
The gene transcripts were quantified using cufflinks (version 2.1.1) - The gene reference file (GFF) was obatined directly from the S. mansoni genome project (file name => v4.19.05.11.chado.filtered.gff)
Genome_build: sma_v5.0.chr.fa
Supplementary_files_format_and_content: tab-delimited text file including FPKM values for each sample type (replicate combined) and p-values from the samples comparison

organism: Schistosoma mansoni

source_name: Worms

extract_protocol:
Total RNA were extracted using the mirVana™ miRNA Isolation Kit (Life Technologies, USA)
RNA-seq libraries were prepared using the TruSeq™ RNA Sample Preparation Guide

treatment_protocol: Adult worms previously stored in RNAlater® (Life Technologies, USA) were disrupted using a homogenizer (Fisher Scientific, USA)

tag: population

value: LE

tag: country

value: Brazil

tag: phenotype

value: oxamniquine susceptible

tag: lab host

value: hamsters and mice


title: BB38


title: LE1


title: HR2

value: HR

value: Puerto Rico

value: oxamniquine resistant


title: BB18

value: Day 1


title: shSetd2_KD

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

description: total RNA extracted with Trizol reagent processed for mRNA library preparation

data_processing:
Low quality bases from 3' end of the read were trimmed. Only 45bp from 5' end were considered for analysis. Sequencing data is aligned to mouse (mm9) genome in a reference guided manner by tophat. Further, cuffdiff was used for identifying differentialy expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: RNA from E14 ES cells interfered with shSetd2

growth_protocol:
ES cell lines were grown on 0.1% gelatinized tissue culture dishes in GMEM in presence of 15% Serum and Leukemia inhibitory factor.
Cells were transduced with pLKO.1 lentiviral vector coding for indicated shRNA molecule, selected with puromycin and harvested at day 4 post selection

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying theTruSeq RNA Sample Preparation Kit v2 ( RS-122-2001 )

treatment_protocol: total RNA was extracted lysing growing cells by Trizol reagent according to manifacturer's protocol

tag: background strain

tag: cell type

value: embryonic stem cells

value: Setd2 knock-down


title: HEK293 total RNA

tag: cell line

tag: purification


title: Ebs_EedKO

source_name: RNA from Embryoid Bodies (Ebs) Eed KO

growth_protocol:
ES cell lines were grown on 0.1% gelatinized tissue culture dishes in GMEM in presence of 15% Serum and Leukemia inhibitory factor.
Undifferentiated ES cells were induced to differentiate into embryoid bodies (EBs) by LIF removal in hanging drops containing 1,000 cell/20 µl drop on the lid of 15 cm petri dishes for 48 h. EBs were then collected from the drops and stimulated between day 2 and 5 with 0.5 µM all-trans-retinoic acid (ATRA). EBs were left in culture in non-coated petri dishes up to day 9 in ES medium without LIF. Medium was replaced every second day.

value: embroid bodies

tag: genotype/variation

value: EED knock-out


title: ES_EedKO

source_name: RNA from E36 Eed KO ES cells

growth_protocol: ES cell lines were grown on 0.1% gelatinized tissue culture dishes in GMEM in presence of 15% Serum and Leukemia inhibitory factor.


title: BB11

value: Day -1

value: plant-based

value: fecal sample (microbial cells)


title: BB16


title: shCtrl

source_name: RNA from E14 ES cells interfered with sh scrambled control

value: wild type


title: BB14


title: Ebs_WT

source_name: RNA from Embryoid Bodies (Ebs) E36


title: HR1


title: BB17


title: BB3

value: Day -4


title: BB15


title: BB6


title: BB4


title: BB8


title: HR3


title: ES_WT

source_name: RNA from E36 ES cells


title: Ebs_WT_K36me3

description:
Embryoid Bodies (Ebs)_WT_ChIP H3K36me3
Immuno-precipitation of chromatin using a specific antibody against H3K36me3.

data_processing:
Alignment: Short reads were mapped onto the mouse July, 2007 genome release (mm9) using Bowtie. The alignments were performed allowing zero to two mismatches and keeping only the reads that align to unique positions in the genome.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: mm9
Supplementary_files_format_and_content: Alignment file generated by Bowtie is converted to SAM file format which is compressed to generate BAM file using SAMTools. Wig files generated by MACS are converted to bigWig format using UCSC wigToBigwig tool.

source_name: E36 Ebs cells

growth_protocol: Undifferentiated ES cells were induced to differentiate into embryoid bodies (EBs) by LIF removal in hanging drops containing 1,000 cell/20 µl drop on the lid of 15 cm petri dishes for 48 h. EBs were then collected from the drops and stimulated between day 2 and 5 with 0.5 µM all-trans-retinoic acid (ATRA). EBs were left in culture in non-coated petri dishes up to day 9 in ES medium without LIF. Medium was replaced every second day.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: Exponentially growing ES cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with specific antibody, which was further purified using protein A coupled beads, and recovered DNA was used for high-throughput sequencing.


title: Ebs_WT_K27me1

description:
Embryoid Bodies (Ebs)_WT_ChIP H3K27me1
Immuno-precipitation of chromatin using a specific antibody against H3K27me1.


title: BB9


title: BB1


title: BB13


title: BB5


title: Ebs_EedKO_K36me3

description:
Embryoid Bodies (Ebs)_EedKO_ChIP H3K36me3
Immuno-precipitation of chromatin using a specific antibody against H3K36me3.

source_name: E36 Ebs cells EED KO


title: ES_WT_K36me3

description:
ES_WT_ChIP H3K36me3
Immuno-precipitation of chromatin using a specific antibody against H3K36me3.

source_name: E36 ES cells

growth_protocol: ES cell lines were grown on 0.1% gelatinaized tissue culture dishes in GMEM in presence of 15% Serum and Leukemia inhibitory factor.


title: BB2


title: BB12


title: BB7


title: ES_EedKO_K27me2

description:
ES_EedKO_ChIP H3K27me2
Immuno-precipitation of chromatin using a specific antibody against H3K27me2.

source_name: E36 ES cells EED KO


title: ES_EedKO_K36me3

description:
ES_EedKO_ChIP H3K36me3
Immuno-precipitation of chromatin using a specific antibody against H3K36me3.


title: C646_K27ac

description:
p300 HAT inhibitor C646 treated ESc -ChIP H3K27ac
Immuno-precipitation of chromatin using a specific antibody against H3K27ac.

source_name: E14 ES cells

growth_protocol:
ES cell lines were grown on 0.1% gelatinaized tissue culture dishes in GMEM in presence of 15% Serum and Leukemia inhibitory factor.
ES cells were grown as indicated in the presence of 30uM C646 p300 HAT inhibitor for 48hrs


title: ES_WT_K27me3

description:
ES_WT_ChIP H3K27me3
Immuno-precipitation of chromatin using a specific antibody against H3K27me3.


title: C646_K27me2

description:
p300 HAT inhibitor C646 treated ESc -ChIP K27me2
Immuno-precipitation of chromatin using a specific antibody against H3K27me2.


title: ES_EedKO_K27me3

description:
ES_EedKO_ChIP H3K27me3
Immuno-precipitation of chromatin using a specific antibody against H3K27me3.


title: BB33

value: Day 3


title: Ebs_EedKO_K27me1

description:
Embryoid Bodies (Ebs)_EedKO_ChIP H3K27me1
Immuno-precipitation of chromatin using a specific antibody against H3K27me1.


title: footprint S2 cell 250 replicate B

first: Joshua

middle: Griffin

last: Dunn

state: California

address: 1700 4th Street, BH404

department: Cellular & Molecular Pharmacology

institute: UCSF / HHMI

description:
RIbosome profiling
ribosome-associated RNA

data_processing:
Basecalls performed using Casava versions 1.6 or 1.7
Sequenced reads were trimmed for adaptor sequence
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to Drosophila rRNA, the S288C yeast genome, and phiX genome allowing three mismatches. Reads aligning to any of these indices were discarded
The remaining reads were aligned using Bowtie v0.12.7 against Drosophila melanogaster genome build dm3 using parameters “-v2 -p4 –best -m1”. Reads which did not align to dm3 were then aligned against a bowtie index of sequences spanning splice junctions annotated in FlyBase genome annotation version 5.43, or splice junctions discovered in our own data using HMMSplicer v0.95 also using parameters “-v2 -p4 –best -m1”.
Bowtie alignments against chromosomes and splice junctions were converted to wiggle files in the genomic coordinate space of Drosophia melanogaster genome build dm3.  In this stage, each read was counted once. For the mRNA samples  the entire length of each read alignment was used (i.e. the genomic positions corresponding to the entire alignment were each incremented by 1/alignment_length, so that each alignment is counted once), for the ribosome footprints samples the caculated postion of the ribosome P-site was used. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme.
Genome_build: dm3
Supplementary_files_format_and_content: wiggle file

organism: Drosophila melanogaster

source_name: S2 cell

extract_protocol:
Samples were lysed using the indicated strategies in the indicated buffers. For ribosome profiling samples, monosomes were resolved by digestion with micrococcal nuclease,  isolated by sucrose cushions or gradients as indicated and  RNA was isolated from monosome fractions using acid:Phenol and chloroform extractions. For RNA-seq samples, RNA was extracted with Trizol
For RNA-seq, poly(A)+ RNA was selected on oligo dT(25) dynabeads, randomly fragmented to approximately 50 nt in length, and size-selected to 40-60mers via gel purification. For ribosome profiling, 28-34mers were size-selected via gel purification. All fragments were then dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circulizarized, PCR amplified, and subjected to 50-57 cycles of sequencing on an Illumina HiSeq, as indicated

tag: strain

value: Oregon R

tag: monosome enrichment strategy

value: sucrose cushion

tag: lysis buffer ion concentrations

tag: lysis strategy

value: Dounce homogenizeation


title: footprint S2 cell 150 replicate B

value: 150 mM Na+, 5 mM Mg++


title: footprint S2 cell 250 replicate A


title: footprint S2 cell 150 replicate A


title: footprint 0-2 hour embryo cushion replicate A

source_name: whole 0-2 hour Drosophila embryo

value: y w

tag: tissue

value: whole 0-2 hour embryo

value: Cryolysis


title: mRNA 0-2 hour embryo replicate B

description:
RNA-Seq
polyA RNA


title: footprint 0-2 hour embryo replicate B


title: footprint 0-2 hour embryo replicate A


title: footprint 0-2 hour embryo gradient replicate B

value: sucrose gradient


title: BB10

tag: subject

tag: time

tag: diet


title: footprint 0-2 hour embryo gradient replicate A


title: mRNA 0-2 hour embryo replicate A

description:
RNA-Seq
polyA RNA


title: ES_WT_K27me2

description:
ES_WT_ChIP H3K27me2
Immuno-precipitation of chromatin using a specific antibody against H3K27me2.

value: embryonic stem cells


title: 24hpi_CtE_Hep2_MOI_1_rRNApolyAdep

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

description:
heterogeneous RNA-Seq (hRNA-Seq)
Poly(A)-depleted and rRNA-depleted
Chlamydia trachomatis serovar E

data_processing:
Base calls were performed using the bulit in Illumina basecaller.
Sequenced reads were mapped to the Chlamydia trachomatis serovar E v.1 genome using bowtie.
RPKM values were calculated for the genes present in the Chlamydia trachomatis genome.
Genome_build: HE601870.1
Supplementary_files_format_and_content: Tab-delimited .txt files report RPKM values.

organism:
Chlamydia trachomatis
Homo sapiens

source_name: Hep-2, Chlamydia trachomatis infected, 24hpi

growth_protocol: HEp-2 cells were infected with C. trachomatis serovar E as previously described (Tan et al., 2009) in 100 mm TC dishes.  Five TC dishes were mock-infected with SPG buffer only.  The infection was allowed to proceed 48 hours prior to EB harvest (REF).  C. trachomatis EBs and mock-infected cell lysates were used to infect HeP-2 monolayers for hRNA-Seq.

extract_protocol:
Total RNA was purified from frozen HEp-2/C. trachomatis lysates using the MasterPure RNA Purification kit (Epicentre, Cat. No. MCR85102).  Carryover DNA was treated twice with Turbo DNase free (Ambion, Cat. No. AM1907) according to the manufacturer’s protocol for rigorous DNAse treatment.  Total DNA removal was verified by qPCR.
After rRNA reduction, each sample was split and one half subjected to poly-A depletion by the Poly(A)Purist Mag purification kit (Ambion).  Briefly, poly(A) tailed mRNAs were bound to magnetic beads and removed from solution using a magnet.  Poly(A)-depleted and rRNA-depleted eluates were further purified using Zymo-Spin IC columns (Zymo Research).
Illumina mRNA-Seq libraries were prepared from poly(A)-depleted and rRNA-depleted samples using the TruSeq RNA Sample Prep kit (Illumina, San Diego, CA) per the manufacturer’s protocol with IGS-specific optimizations. Adapters containing 6 nucleotide indexes were ligated to the double-stranded cDNA. The DNA was purified with AMPure XT beads (Beckman Coulter Genomics, Danvers, MA) between enzymatic reactions and size selection steps (~250 to 300bp).

treatment_protocol: HEp-2 cells were grown in 6 x 100mm TC dishes until 90% confluent.  3 dishes were infected with C. trachomatis serovar E in 3.5 ml SPG buffer for an MOI = 1. HEp-2 monolayers were also mock-infected using mock-infected cell lysates.  Each treatment was incubated at 25°C for 2h, then supplemented with 10 mL fresh medium (DMEM + 10% FBS, 25 ug/ml gentamycin, 1.25 ug/ml fungizone) and incubated at 37°C, 5% CO2.  One dish per treatment was harvested at 1, 6, and 24 hours post-infection by scraping and resuspending in 300 uL PBS.  Samples were stored at -80°C.

tag: specific host

value: Homo sapiens

tag: host cell

tag: host cell infected with

value: Chlamydia trachomatis


title: footprint 0-2 hour embryo cushion replicate B


title: 24hpi_CtE_Hep2_MOI_1_rRNAdep

description:
heterogeneous RNA-Seq (hRNA-Seq)
rRNA-depleted
Chlamydia trachomatis serovar E

data_processing:
Base calls were performed using the bulit in Illumina basecaller.
Sequenced reads were mapped to the Chlamydia trachomatis serovar E v.1 genome using bowtie.
RPKM values were calculated for the genes present in the Chlamydia trachomatis genome.  We calculate the RPKM values internally using the alignment files.
Genome_build: HE601870.1
Supplementary_files_format_and_content: Tab-delimited .txt files report RPKM values.

extract_protocol:
Total RNA was purified from frozen HEp-2/C. trachomatis lysates using the MasterPure RNA Purification kit (Epicentre, Cat. No. MCR85102).  Carryover DNA was treated twice with Turbo DNase free (Ambion, Cat. No. AM1907) according to the manufacturer’s protocol for rigorous DNAse treatment.  Total DNA removal was verified by qPCR.
Illumina mRNA-Seq libraries were prepared from rRNA-depleted samples using the TruSeq RNA Sample Prep kit (Illumina, San Diego, CA) per the manufacturer’s protocol with IGS-specific optimizations. Adapters containing 6 nucleotide indexes were ligated to the double-stranded cDNA. The DNA was purified with AMPure XT beads (Beckman Coulter Genomics, Danvers, MA) between enzymatic reactions and size selection steps (~250 to 300bp).


title: 1hpi_CtE_Hep2_MOI_1_rRNApolyAdep

source_name: Hep-2, Chlamydia trachomatis infected, 1hpi


title: LaeBOE

city: Jinan

first: Yuqi

last: Qin

address: 27 Shanda Nan Lu

institute: Shandong University

description: Beauveria bassiana overexpression LaeB in LaeA deletion stain grown in SDB

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 21-nt long tags. Then low quality tags, one copy tags and tags which are not 21-nt long were removed to generate clean tags. Reference 21-nt tag databases were created from predicted P. decumbens transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to TPM (number of transcripts per million clean tags) for differential expression analysis.
Genome_build: Whole Genome Shotgun project in GenBank under the accession number ADAH00000000

organism: Beauveria bassiana

source_name: Fungal mycelia

growth_protocol: The conidia of Beauveria bassiana were inoculated to SDB for 48 h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis.
The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 35bp.

value: overexpression LaeB in LaeA deletion strains

tag: medium

value: SDB

value: 48 h after  after inoculating the fresh conidia


title: LaeAKO

description: Beauveria bassiana LaeA deletion stain grown in SDB

value: LaeA deletion

value: 48 h after after inoculating the fresh conidia


title: E36_Eed_-/-_H3K27me1

description: Chromatin precipitatin using a specific antibody against H3K27me1

data_processing:
Alignment: Short reads were mapped onto the mouse July, 2007 genome release (mm9) using Bowtie. The alignments were performed allowing zero to two mismatches and keeping only the reads that align to unique positions in the genome.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome_build: mm9
Supplementary_files_format_and_content: Alignment file generated by Bowtie is converted to SAM file format which is compressed to generate BAM file using SAMTools. Wig files generated by MACS were normalized to sequencing depth and converted to bigWig format using UCSC wigToBigwig tool.

growth_protocol: ES cell lines were grown on 0.1% gelatinized tissue culture dishes in GMEM supplemented with 15% fetal calf serum, 2 mM glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin, 0.1 mM non-essential aminoacids, 1 mM Na-Pyruvate, 50 μM β-mercaptoethanol-phosphate-buffered saline and Leukemia Inhibitory Factor.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the Illumina ChIPSeq Sample Prep kit (IP-102-1001) and multiplexing oligonucleotide kit (PE-400-1001).

treatment_protocol: Exponentially growing ES cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with specific antibody, which was further purified using proteinA coupled beads and recovered DNA was used for highthrouput sequencing.

value: E36 ES cells

tag: chip antibody

value: H3K27me1 (Active Motif, cat No:61015, Lot:08711001)


title: E36_Eed_-/-_H3K27ac

description: Chromatin precipitatin using a specific antibody against H3K27ac

tag: cell type

value: E36 ES cells (Abcam, cat No:4729, Lot:GR55451-1)


title: E36_Eed_-/-_H3K4me3

description: Chromatin precipitatin using a specific antibody against H3K4me3

value: H3K4me3 (Active Motif, catNo:39159, Lot:01609004)


title: E36_Eed_+/+_H3K4me3


title: E36_Eed_+/+_H3K4me1

description: Chromatin precipitatin using a specific antibody against H3K4me1


title: E36_Eed_-/-_H3K4me1


title: E36_Eed_+/+_H3K27ac


title: BBA-WT

description: Beauveria bassiana wild type stain grown in SDB

value: Beauveria bassiana wild type

value: 48 h after inoculating the fresh conidia


title: E36_Eed_-/-_Input

description: Chromatin


title: E36_Eed_+/+_H3K27me1


title: E36_Eed_+/+_Input

description: Chromatin


title: 1229969_MeDIPseq

status: Public on Dec 04 2013

city: London

first: Jordana

last: Bell

address: St Thomas' Hospital, Westminster Bridge Rd

department: Department of Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

description: Family 24 monozygotic twin 2

data_processing:
In the sample of 50 monozygotic (MZ) twins with paired-end MeDIP-seq data there were on average 50 million paired-end reads of length 50bp per individual. Alignment to hg18 was performed using Maq (v0.7.1). QC of the aligned data took into account base quality scores (no exclusions), read mapping scores (threshold maq q > 10), removal of duplicate PE reads, proper PE pairing criteria, and insert-size distribution checks. On average, 60% of reads passed alignment QC per individual. We used the post-QC PE reads to reconstruct MeDIP-fragments per individual. We quantified coverage of MeDIP-fragments per base-pair (bp) across the genome, and binned coverage into overlapping 1kb bins (overlap of 500bp). For each bin we calculated a normalized methylation score, the relative methylation quantification (RMQ) score, which was the sum of the MeDIP-fragment coverage of each bp in that bin, divided by the overall number of autosomal post-QC reads per individual. For pain-DMR analysis we only considered bins with RMQ variance > 0, where at least 10% of the sample had RMQ scores > 0.
In the sample of 50 unrelated individuals with single-end MeDIP-seq data there were on average 25 million single-end (SE) reads of length 50bp per individual. Sequence alignment to the human genome (hg18) was performed in Bwa (v0.5.9). Data were subject to quality control checks for base composition (no exclusions), read mapping quality (threshold bwa q > 10), and removal of duplicate reads. On average, 53% of reads passed alignment QC per individual. Post-QC single-SE reads were then extended by 175bp equilaterally to produce MeDIP-fragments of size 225bp. We quantified coverage of MeDIP-fragments per base-pair (bp) across the genome, and binned coverage per bp into overlapping 1kb bins (overlap of 500bp). For each bin we calculated the normalized methylation score (RMQ), , which was the sum of the MeDIP-fragment coverage of each bp in that bin, divided by the overall number of autosomal post-QC reads per individual. In the pain-DMR analyses we only considered bins with RMQ variance > 0, where at least 10% of the sample had RMQ scores > 0.
Genome_build: hg18
Supplementary_files_format_and_content: Each processed data file contains RMQ scores over a 1kb window for each individual in bed file format. The files consist of four tab-delimited columns: the chromosome, the start bp of the 1kb bin, the end bp of hte 1kb bin, and the RMQ score for that individual in that bin. The processed files can include genomic regions where the majority or all individuals had RMQ scores of 0, and these regions can be filtered out in the downstream analyses.

source_name: Whole blood

extract_protocol:
MeDIP-sequencing was performed and analyzed separately in the MZ twin and unrelated samples.
In the MZ twin sample 5 µg genomic DNA from each sample was sonicated on a Diagenode Bioruptor to produce a median fragment length of 180-230, and prepared for next generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps. Samples were quantified and size checked using a 2100 Bioanalyzer and DNA1000 chips (Agilent).  1 µg of each adapter-ligated sample was spiked with ~5x10-7pmoles methylated/unmethylated control DNA and subjected to methylated immunoprecipitation with 150 ng anti-5-methylcytidine using automation according to manufacturer’s reagents and protocols (Diagenode); 100ng was reserved as input for MeDIP quality control, which was conducted using qPCR with primers designed to amplify methylated / unmethylated control DNA.  MeDIP DNA was then purified (Zymo Reasearch) and amplified by 18 cycles adapter-mediated PCR.  PCR products were purified (QIAGEN) and run out on separate 2% low-melting point agarose gels. PCR fragments were excised and purified (QIAGEN).  The resulting libraries (300-350bp) were quality controlled using an Agilent 2100 Bioanalyzer and DNA1000 chips and qPCR. The samples were sequenced on Illumina GA2, using two lanes per sample, to produce on average 50 million paired-end reads of length 50bp.
In the unrelated samples 1.5µg of original genomic DNA was fragmented to DNA smear between 200bp to 500bp using a Bioruptor NGS (Diagenode) sonication system. End repair, <A> base addition and adaptor ligation steps were performed using Illumina’s Paired-End DNA Sample Prep kit following the manufacturer’s instructions.  Then, the methylated DNA fractions were immunoprecipitated using the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode, catalog number: mc-magme-048) with small adjustments. Briefly, 1.5µl of each two control templates (methylated and unmethylated DNA controls) with different sequences were mixed with adapter ligated DNA and heat denatured (95°C, 3min) in a final reaction volume of 90µl within the provided reagents of 24µl MagBuffer A and 6µl MagBuffer B. 7.5µl aliquot of the denatured genomic DNA was saved as input and another 75µl was immunoprecipitated with 5µl of prepared anti-5mC antibody and 20µl of prepared Magbeads. The DNA-antibody-magbeads mixture was incubated overnight at 4°C on a rotating wheel. The DNA-antibody-magbeads mixture was then washed twice using each of 150µl ice-cold MagWash Buffer-1 and washed once with 150µl of ice-cold MagWash Buffer-2. For each buffer, the washing reaction was incubated for 4min at 4°C on a rotating wheel. The input DNA and immunoprecipitated products were then in parallel treated with protease K and purified with ZYMO DNA Clean & Concentrator-5 (ZYMO). The efficiency and sensitivity of immunoprecipitation reaction were detected by qPCR using the enriched DNA and the unbound input DNA. MeDIP-seq library was constructed by PCR amplification with the enriched DNA as template. PCR reaction was performed in 50µl of reaction volume consisting of 20µl MeDIP enriched DNA, 5µl of 2.5mM dNTP, 2µl primers, 5µl of 10X pfx Amplification Buffer, 2µl of 50mM MgSO4, 15.2µl sterilized water and 0.8µl of Platinum pfx DNA polymerase (Invitrogen). The program of amplification was 94°C 2 min, 10 cycles of 94 °C 15s, 62°C 30s and 72°C 30 then prolong with 10min at 72°C. The products could be kept at 12°C. The PCR products were purified using Agencourt Ampure Beads (Beckman Counlter). After analyzing by the Bioanalyzer analysis system (Agilent, Santa Clara, USA) and quantified by the real time PCR, the prepared library was sequenced using Illumina HiSeq2000 with SE50 read length.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual

value: Family 24, monozygotic twin 2

tag: age

tag: pain temperature

tag: medip antibody

value: anti-5-methylcytidine (Diagenode, Catalog# mc-magme-048)

tag: medip-seq id


title: 382248_MeDIPseq

description: Family 25 monozygotic twin 1

value: Family 25, monozygotic twin 1


title: 712976_MeDIPseq

description: Family 23 monozygotic twin 1

value: Family 23, monozygotic twin 1


title: WT H3K27me3_ChIPSeq

first: Liguo

last: Zhang

address: South Zhongguancun Street

institute: Chinese Academy of Agricultural Sciences

description: High-throughput profiling of H3K27me3 in WT (wild type).

data_processing:
Basecalls were performed using CASAVA version 1.4.
Clean: After completing the sequencing, we removed the low-quality sequences, the adaptor sequences, and the pollutants.
Alignment: Sequence reads were obtained and mapped to the rice (Orazy JP_6.1) genome using Bowtie (Langmead et al., 2009) allowing up to two mismatches. Reads with unique locations were retained for further analysis.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm. The default parameters were bandwidth, 200bp; mfold, 32; P-value of 1.00e-05.
Genome_build: Orazy JP_6.1
Supplementary_files_format_and_content: WIG files were generated using the MACS program.

organism: Oryza sativa

source_name: Wild type seedling, H3K27me3 ChIP

growth_protocol: Surface-sterilized seeds of the WT and Epi-df plants were soaked in water for 3 d and then placed in artificial soil for three weeks.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-H3K27me3 antibody (Millipore,cat no. 07-449). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters, which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 100-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No treatment.

tag: variety

value: japonica

tag: genotype/variation

value: wild type

value: seedling

value: 3 weeks


title: 283836_MeDIPseq

description: Family 24 monozygotic twin 1

value: Family 24, monozygotic twin 1


title: Epi-df H3K27me3_ChIPSeq

description: High-throughput profiling of H3K27me3 in Epi-df (mutant).

source_name: Epi-df seedling, H3K27me3 ChIP

value: Epi-df mutant

tag: tissue


title: 477815_MeDIPseq

description: Family 25 monozygotic twin 2

value: Family 25, monozygotic twin 2


title: 445615_MeDIPseq

description: Family 23 monozygotic twin 2

value: Family 23, monozygotic twin 2


title: 483852_MeDIPseq

description: Family 22 monozygotic twin 1

value: Family 22, monozygotic twin 1


title: 559111_MeDIPseq

description: Family 21 monozygotic twin 2

value: Family 21, monozygotic twin 2


title: 403215_MeDIPseq

description: Family 22 monozygotic twin 2

value: Family 22, monozygotic twin 2


title: 1hpi_CtE_Hep2_MOI_1_rRNAdep

value: Homo sapiens

value: Chlamydia trachomatis


title: 79872_MeDIPseq

description: Family 21 monozygotic twin 1

value: Family 21, monozygotic twin 1


title: 79762_MeDIPseq

description: Family 20 monozygotic twin 1

value: Family 20, monozygotic twin 1

value: anti-5-methylcytidine (Diagenode, Catalog# mc-magme-048)


title: 487641_MeDIPseq

description: Family 17 monozygotic twin 2

value: Family 17, monozygotic twin 2


title: 766282_MeDIPseq

description: Family 17 monozygotic twin 1

value: Family 17, monozygotic twin 1


title: 160449_MeDIPseq

description: Family 13 monozygotic twin 2

value: Family 13, monozygotic twin 2


title: 588430_MeDIPseq

description: Family 15 monozygotic twin 2

value: Family 15, monozygotic twin 2


title: 356052_MeDIPseq

description: Family 16 monozygotic twin 1

value: Family 16, monozygotic twin 1


title: 602196_MeDIPseq

description: Family 12 monozygotic twin 2

value: Family 12, monozygotic twin 2


title: 588020_MeDIPseq

description: Family 14 monozygotic twin 1

value: Family 14, monozygotic twin 1


title: 176409_MeDIPseq

description: Family 14 monozygotic twin 2

value: Family 14, monozygotic twin 2


title: 470736_MeDIPseq

description: Family 15 monozygotic twin 1

value: Family 15, monozygotic twin 1


title: 374374_MeDIPseq

description: Family 13 monozygotic twin 1

value: Family 13, monozygotic twin 1


title: 118686_MeDIPseq

description: Family 16 monozygotic twin 2

value: Family 16, monozygotic twin 2


title: 450657_MeDIPseq

description: Family 11 monozygotic twin 2

value: Family 11, monozygotic twin 2


title: 650936_MeDIPseq

description: Family 11 monozygotic twin 1

value: Family 11, monozygotic twin 1


title: 63446_MeDIPseq

description: Family 9 monozygotic twin 2

value: Family 9, monozygotic twin 2


title: 249910_MeDIPseq

description: Family 10 monozygotic twin 1

value: Family 10, monozygotic twin 1


title: 877393_MeDIPseq

description: Family 20 monozygotic twin 2

value: Family 20, monozygotic twin 2


title: 101515_MeDIPseq

description: Family 7 monozygotic twin 2

value: Family 7, monozygotic twin 2

value: anti-5-methylcytidine (Diagenode, Catalog# mc-magme-048)


title: 499830_MeDIPseq

description: Family 10 monozygotic twin 2

value: Family 10, monozygotic twin 2


title: 180816_MeDIPseq

description: Family 8 monozygotic twin 1

value: Family 8, monozygotic twin 1


title: 293839_MeDIPseq

description: Family 8 monozygotic twin 2

value: Family 8, monozygotic twin 2


title: 285498_MeDIPseq

description: Family 9 monozygotic twin 1

value: Family 9, monozygotic twin 1


title: 93815_MeDIPseq

description: Family 6 monozygotic twin 2

value: Family 6, monozygotic twin 2


title: 182718_MeDIPseq

description: Family 7 monozygotic twin 1

value: Family 7, monozygotic twin 1


title: 159406_MeDIPseq

description: Family 19 monozygotic twin 2

value: Family 19, monozygotic twin 2


title: 844344_MeDIPseq

description: Family 18 monozygotic twin 1

value: Family 18, monozygotic twin 1


title: 150096_MeDIPseq

description: Family 6 monozygotic twin 1

value: Family 6, monozygotic twin 1


title: 147224_MeDIPseq

description: Family 5 monozygotic twin 2

value: Family 5, monozygotic twin 2


title: 281452_MeDIPseq

description: Family 18 monozygotic twin 2

value: Family 18, monozygotic twin 2


title: 220824_MeDIPseq

description: Family 5 monozygotic twin 1

value: Family 5, monozygotic twin 1


title: 1036126_MeDIPseq

description: Family 19 monozygotic twin 1

value: Family 19, monozygotic twin 1


title: 200728_MeDIPseq

description: Family 12 monozygotic twin 1

value: Family 12, monozygotic twin 1


title: 13812_MeDIPseq

description: Family 4 monozygotic twin 1

value: Family 4, monozygotic twin 1


title: 1293_MeDIPseq

description: Family 3 monozygotic twin 2

value: Family 3, monozygotic twin 2


title: 7752_MeDIPseq

description: Family 3 monozygotic twin 1

value: Family 3, monozygotic twin 1

value: anti-5-methylcytidine (Diagenode, Catalog# mc-magme-048)


title: dsDcr1, Ago1-IP

city: New York

first: Jakub

middle: Orzechowski

last: Westholm

state: NY

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan-Kettering Cancer Center

data_processing:
Genome_build: n/a
trim adaptors using fastx_clipper
trim 4 random nucleotides from each end, using custom script
collapse identical reads using fastq_collapser
Supplementary_files_format_and_content: read count table files (columns are read read sequence and number of reads)

source_name: S2R+ cells with  MT-DsRed-mir-144/451 vector

growth_protocol: dsRNA (75 mg total) knockdown experiments were carried out in 10-ml MT-  DsRed-mir-144/451 S2R+ cells for 8 days, with CuSO4 added on the 5th day to induce the miRNA construct.

extract_protocol:
The cells were lysed with IP/Extract buffer, and cleared by centrifugation at 14,000 rpm for 15 min at 4°C. The extracted RNA were resuspended in water and spiked in with 10 index small RNA oligos along with with 32P-labeled 19bp and 29bp oligos bearing PmeI sites.
AGO1-associated RNA was extracted using randomized 3’ adaptor (5’rAppNNNNTGGAATTCTCGGGTGCCAAGG/ 3ddC/) and randomized 5’ adaptor (5'GUUCAGAGUUCUACAGUCCGACGAUCNNNN). The ligated RNA products were reverse transcribed (RT primer 5’GCCTTGGCACCCGAGAATTCCA) at 50°C for 1 hr with SuperScript III (Life Technologies) and heat to 70°C for 15 min. The cDNAs were amplified by standard Taq polymerase (NEB) using RP1 forward primer (5’AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA) and different 5' index primers RPI (x) (NEBNext® Multiplex Oligos, Illumina) for each sample, followed by digestion of the index oligos by PmeI at 37°C for 3h.

treatment_protocol: Cells were treated with dsRNA (75 µg total) during entire growth

tag: cell line

tag: ip antibody

tag: knockdown


title: 366_MeDIPseq

description: Family 1 monozygotic twin 2

value: Family 1, monozygotic twin 2


title: 35911_MeDIPseq

description: Unrelated individual 50

value: Unrelated individual 50


title: 110504_MeDIPseq

description: Family 4 monozygotic twin 2

value: Family 4, monozygotic twin 2


title: 13563_MeDIPseq

description: Family 2 monozygotic twin 2

value: Family 2, monozygotic twin 2


title: dsGFP, Ago1-IP

value: dsGFP


title: 6160_MeDIPseq

description: Family 2 monozygotic twin 1

value: Family 2, monozygotic twin 1


title: 35891_MeDIPseq

description: Unrelated individual 46

value: Unrelated individual 46


title: 35847_MeDIPseq

description: Unrelated individual 49

value: Unrelated individual 49


title: 35874_MeDIPseq

description: Unrelated individual 47

value: Unrelated individual 47


title: 35968_MeDIPseq

description: Unrelated individual 48

value: Unrelated individual 48


title: 35841_MeDIPseq

description: Unrelated individual 45

value: Unrelated individual 45


title: 35966_MeDIPseq

description: Unrelated individual 44

value: Unrelated individual 44