title: LNCaP_2509_2MK4_replicate 1

city: Ann Arbor

first: Armand

last: Bankhead

state: MI

address: 1415 Washington Heights

department: Biostatistics

institute: University of Michigan

description: processed data file: diffReps_SP2509_mock_2MK4.txt

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2, with default parameters
Differential H3K4me3 and H3K9me2 regions were identified with diffReps 1.55.4, with these parameters: -gn hg19 -nproc 16 -me nb -bkg 2.0  -nsd 2
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg19
Supplementary_files_format_and_content: Aligned BAM files were converted to bedGraph format using bedtools2 genomeCoverageBed function, and then to bigWig using the UCSC genome brower utility function "bedGraphToBigWig". Scores represent reads per million

organism: Homo sapiens

source_name: LNCaP prostate cancer cell line_2509_H3K4me2

growth_protocol: LNCaP cells were plated in 15cm dish with 3.5 million cells per well in RPMI+10%FBS.

extract_protocol:
For each ChIP reaction, 3 million formaldehyde cross-linked cells were lysed and sonicated with a digital probe sonicator to shear chromatin. 5µg of anti-dimethylated histone H4 Lysine 4 were used to immunoprecipitate DNA overnight at 4°C. One percent of chromatin was used as input. Immune complexes were collected with 30 µl protein A magnetic beads. After extensive washing, immune complexes were eluted, cross-links were reversed, and DNA from 4 replicate samples were pooled and  purified with miniElute PCR purification kit and eluted with 20 µl of elution buffer.
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:
Plated LNCaP cells were trasfected with siRNA for 6 hrs then changed to fresh RPMI+10%FBS and grown for 96hrs.
Plated LNCaP cells were treated with 2uM SP-2509 or vehicle (DMSO) for72hrs.

tag: cell line

value: LNCaP

value: prostate cancer

tag: chip antibody


title: LNCaP_mock_2MK9_replicate 1

status: Public on Jun 30 2016

type: SRA

country: USA

description: processed data file: diffReps_SP2509_mock_2MK9.txt

library_source: genomic

molecule: genomic DNA

source_name: LNCaP prostate cancer cell line_mock_H3K9me2

tag: cell type


title: T. brucei H3VKO DMOG3

city: Athens

first: David

last: Reynolds

state: Georgia

address: 120 E Green St

department: Biochemistry and Molecular Biology

institute: University of Georgia

library_source: transcriptomic

data_processing:
Smalll RNA reads were quality and adapter trimmed using Cutadapt [81] and reads shorter than 18 nucleotides were discarded. Reads were mapped to the T. brucei reference genome using Bowtie2 version 2.2.3 with the following parameters “-a -D 10 -R 5 -N 1 -L 15 -i S,1,0.50“ [78] and further processed using Samtools 1.2 [79], BEDTools [82], and custom scripts.
Genome_build: Trypanosoma brucei Lister 427 (v6.0 from TriTrypDB.org) [http://tritrypdb.org/common/downloads/release-6.0/TbruceiLister427/fasta/data/TriTrypDB-6.0_TbruceiLister427_Genome.fasta]
Supplementary_files_format_and_content: .wig and .bedgraph report small RNAseq data (not ChIP-seq data)

molecule: total RNA

organism: Trypanosoma brucei

source_name: H3VKO parasite

growth_protocol: Bloodstream form T. brucei cells were grown as described in Hirumi et al. (1980). Parasitology 80, 371–382.

extract_protocol:
For small RNA sequencing by the Georgia Genomics Facility (GGF), total RNA was isolated from log phase T. brucei using Trizol according to the manufacturer's instructions. 5x10^7 cells were used for each prep. For all other small RNA sequencing libraries, small RNAs were isolated using a Qiagen miRNEASY kit according to the manufacturer's instructions. 5x10^7 cells were used for each prep.
For small RNA sequencing by GGF, the small RNA-seq libraries were prepared using approximately 250ng total RNA using the Illumina-compatible NEBNext small RNA library preparation kit following the manufacturer protocol (New England Biolabs). For remaining small RNA-seq samples, libraries were prepared using approximately 250ng small RNA by Vertis Biotechnology AG. The small RNA sample was poly(A)-tailed using poly(A) polymerase. Then, the 5'PPP and CAP structures were removed using tobacco acid pyrophosphatase (TAP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/μL using a high fidelity DNA polymerase. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: DMOG treatment of cells was performed by supplementing media with 1mM DMOG for 5 days in T. brucei

tag: strain

value: 221a of strain 427

tag: lifestage

value: bloodstream form

tag: genotype/variation

tag: treatment

value: DMOG (an inhibitor of J synthesis)

tag: sample

value: small RNA


title: T. brucei WT DMOG1

source_name: WT parasite

value: WT


title: LNCaP_2509_input_replicate 1

source_name: LNCaP prostate cancer cell line_2509_input


title: T. brucei WT2


title: T. brucei H3VKO DMOG2


title: T. brucei H3VKO DMOG1


title: neuron_cultures_ehmt1_shrna_ttx_rna_seq_rep3

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

country: Spain

institute: CNAG,Centro Nacional de Análisis Genómico

data_processing:
alignment was done with GSNAP-gmap-2015-06-23
read counting was performed with custom C++ script
DEseq2 was used to call the expression changes
GO enrichment was performed in GENE DAVID
Genome_build: rn6
Supplementary_files_format_and_content: Excel tables including the normalized read counts for all the samples, as well as the DEseq2 pvalues for each of the comparisons. The normalized counts are found in the columns. The values in these columns represent the deseq-normalized counts multiplied by 42 (bp coverage of tag) divided by the gene length. There are 5 pair-wise comparisons of expression and each has its table. Wt_ttx and shrna_ttx for the study of ttx effect in wt samples or transduced sampes. Startpoint_wt_shrna_VS_wt for the effect of shrna alone on wt neurons. Endpoint_ttx_shrna_VS_ttx for the effect of shrna on the TTX treated samples. Rattus_shrna_total_6vs_6_effect for the effect of shrna regardless to the TTX treatment. Gene David GO enrichments for the TT down-regulated genes (Down-reg), their shrna blocked subset (Blocked_shrna) and shrna independent subset (Common).

organism: Rattus norvegicus

source_name: cortical neurons

extract_protocol:
Total RNA was Trizol extracted from 3 wild-type, 3 wildtype ttx samples, 3 ehmt1 kd and 3 emht1 kd ttx samples. RNA was treated with DNase (Qiagen, 79254) and purified on the RNeasy MinElute Cleanup Kit (Qiagen, 74204). 2000 ng of total RNA were treated with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; Illumina MRZH11124). Depleted RNA was precipitated 1 h at -80°C in three volumes of ethanol plus 1 µg of glycogen. RNA was then washed and resuspended in 36 µl of RNase free water. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution and the RNA was fragmented by incubation at 95°C for 3 minutes. For reverse transcription, cDNA first strand synthesis was performed with random examer primers. cDNA second strand synthesis was performed with dUNTPs, to ensure strand specificity.
The RNA-seq library was synthetized with KAPA Hyper prep kit (KK8504), a treatment with USER enzyme (NEB, M5505L) was added to digest the unspecific strand. The libraries were pooled (4/lane) and sequenced on the illumina HiSeq, which yielded approximately 40 million single-end reads per sample.

value: Wistar

tag: culture

value: primary cortical neuronal cultures

tag: tissue

value: brain

value: cortical neuron

tag: age


title: LNCaP_2509_2MK9_replicate 2

source_name: LNCaP prostate cancer cell line_2509_H3K9me2


title: LNCaP_2509_2MK9_replicate 1


title: T. brucei H3VKO3


title: LNCaP_2509_2MK4_replicate 2


title: T. brucei WT1


title: T. brucei H3VKO1


title: neuron_cultures_ehmt1_shrna_rna_seq_rep2


title: LNCaP_mock_input_replicate 2

source_name: LNCaP prostate cancer cell line_mock_input


title: LNCaP_mock_2MK4_replicate 1

source_name: LNCaP prostate cancer cell line_mock_H3K4me2


title: H36

city: Wuxi

first: Xian

last: Yin

address: Lihu road 1800

department: school of biotechnology

country: China

institute: Jiangnan University

data_processing:
fastx(version:0.0.13) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to H915-1 whole genome using tophat (version:2.0.9)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks (version:2.1.1)
Genome_build: genome of Aspergillus niger H915-1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Aspergillus niger

source_name: Aspergillus niger

extract_protocol:
Pellets were harvested with miracloth, flash frozen in liquid nitrogen, and RNA was extracted using Rneasy Mini Kit(Cat#74106, Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: air volume/culture volume/min


title: LNCaP_mock_input_replicate 1


title: H48


title: T. brucei WT DMOG3


title: LNCaP_mock_2MK9_replicate 2


title: T. brucei WT3


title: LNCaP_mock_2MK4_replicate 2


title: LNCaP_2509_iput_replicate 2


title: LNCaP_siLUC_input_replicate 2

source_name: LNCaP prostate cancer cell line_siLUC_input


title: neuron_cultures_ehmt1_wt_ttx_rna_seq_rep1


title: LNCaP_siLUC_input_replicate 1


title: LNCaP_siLUC_2MK9_replicate 1

description: processed data file: diffReps_siLSD1_siLUC_2MK9.txt

source_name: LNCaP prostate cancer cell line_siLUC_H3K9me2


title: H24


title: 1.5vvm


title: LNCaP_siLUC_2MK4_replicate 1

description: processed data file: diffReps_siLSD1_siLUC_2MK4.txt

source_name: LNCaP prostate cancer cell line_siLUC_H3K4me2


title: LNCaP_siLUC_2MK4_replicate 2


title: neuron_cultures_ehmt1_shrna_rna_seq_rep3


title: LNCaP_siLUC_2MK9_replicate 2


title: LNCaP_siLSD1_input_replicate 2

source_name: LNCaP prostate cancer cell line_siLSD1_input


title: H6


title: LNCaP_siLSD1_2MK4_replicate 2

source_name: LNCaP prostate cancer cell line_siLSD1_H3K4me2


title: LNCaP_siLSD1_2MK9_replicate 1

source_name: LNCaP prostate cancer cell line_siLSD1_H3K9me2


title: NT2 RNA-seq, rep 2

city: Davis

first: Yoong Wearn

last: Lim

state: CA

address: One Shields Avenue

department: Molecular and Cellular Biology

institute: University of California, Davis

description: PolyA RNA

data_processing:
DRIPc-seq, DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf before mapping.
DRIPc-seq, DRIP-seq: Trimmed fastq reads were mapped to hg19 or mm9 using BWA 0.6.1 and Bowtie2.2.1. Peak calling was performed using a custom HMM algorithm.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: wig files, bed files, bedGraph files.

source_name: pluripotent testicular embryonic carcinoma cell line

extract_protocol: Standard Illumina protocols.


title: NT2 MethylC-seq

data_processing:
Library strategy: MethylC-Seq
DRIPc-seq, DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf before mapping.
DRIPc-seq, DRIP-seq: Trimmed fastq reads were mapped to hg19 or mm9 using BWA 0.6.1 and Bowtie2.2.1. Peak calling was performed using a custom HMM algorithm.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: wig files, bed files, bedGraph files.


title: NT2 RNA-seq, rep 1

description: PolyA RNA


title: LNCaP_siLSD1_input_replicate 1


title: K562 DRIP-seq

description:
RNA/DNA hybrids
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.

data_processing:
Library strategy: DRIP-Seq
DRIPc-seq, DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf before mapping.
DRIPc-seq, DRIP-seq: Trimmed fastq reads were mapped to hg19 or mm9 using BWA 0.6.1 and Bowtie2.2.1. Peak calling was performed using a custom HMM algorithm.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: wig files, bed files, bedGraph files.

source_name: erythromyeloblastoid leukemia cell line


title: LNCaP_siLSD1_2MK4_replicate 1


title: NT2 DRIP-seq RNaseH


title: LNCaP_siLSD1_2MK9_replicate 2


title: NT2 DRIP-seq RNaseA


title: NT2 DRIP-seq, 1


title: NT2 DRIP-seq, 2

description:
RNA/DNA hybrids
Genomic DNA was fragmented using BamHI, NcoI, ApaL1, NheI and PvuII.


title: NT2 DRIPc-seq, rep 2

description:
RNA/DNA hybrids
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.
Processed data file: NT2_DRIPc_peaks.bed.gz

data_processing:
Library strategy: DRIPc-Seq
DRIPc-seq, DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf before mapping.
DRIPc-seq, DRIP-seq: Trimmed fastq reads were mapped to hg19 or mm9 using BWA 0.6.1 and Bowtie2.2.1. Peak calling was performed using a custom HMM algorithm.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: wig files, bed files, bedGraph files.


title: H12


title: NPC-747T

city: Shanghai

first: Hua

last: Dong

address: 199 Liangjing Rd.

institute: astrazeneca

data_processing:
Illumina HiSeq Control Software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by illumina HiSeq Analysis Software
Raw fastq data was mapped to human genome(Human.B37) and transcriptome(Gene model:RefGene) by ArrayStudiuo V7.0
Sequenced Fragments Per Kilobase of exon per Million fragments mapped to human genome (FPKM) were calculated using ArrayStudiuo V7.0. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Human NCBI genome build 37 and Gene model:RefGene
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample ...

source_name: Nasopharyngeal

extract_protocol:
Total RNA were extracted from the snap-frozen NPC or control nasopharyngeal tissues.  25 ug total RNA prepared for sequencing for each sample
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tumor

tag: who class

value: III

tag: gender

value: female


title: NPC-755T

value: male


title: NPC-751T


title: NPC-752T


title: NPC-754T


title: NPC-756T


title: NPC-757T


title: NPC-749T


title: NPC-748T


title: Selplg-/- 1

city: La Jolla

first: Linda

middle: M

last: Bradley

address: 10901 N. Torrey Pines Rd.

department: Inflammatory Diseases

institute: Sanford Burnham Prebys Discovery Institute

data_processing:
Base-calling software is Real-Time Analysis (RTA) version 1.18.64 (http://support.illumina.com/sequencing/sequencing_software/real-time_analysis_rta.html)
To remove the least reliable data from the analysis results, which is often derived from overlapping clusters, raw data are filtered to remove any reads that do not meet the overall quality as measured by the Illumina chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities (chastity = brightest intensity/(brightest intensity + second brightest intensity)).
Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6.

organism: Mus musculus

source_name: H2-Db+GP33-41+ CD8+ T cell

extract_protocol:
Sorted WT or PSGL-1 KO CD8+ T cells were washed, pelleted, and frozen in RLT +BME Buffer (Quiagen RNeasy Micro Kit Cat. no. 74004). Total RNA extraction was completed using Quiagen Kit following manufactuer's instructions.
1ug of Total subjected to Ribo depletion to remove rRNA and then Multiplexed library was constructed using Illumina's Truseq Stranded Total RNA LT Kit Cat # RS-122-2201

value: Spleen

tag: cell population

value: CD8+ T cell

tag: lcmv cl 13 infection

value: 9 days post-infection

value: PSGL-1 KO


title: Selplg-/- 2


title: NPC-743T

value: II


title: NPC-744T


title: WT 1

value: Wildtype


title: WT 2


title: NPC-737T


title: NPC-740T

description:
740T
only single end raw data '740T_merged_R1.fastq.gz' provided by submitter.


title: NPC-736T


title: NPC-735T


title: nonNPC-742T

value: Control


title: NPC-741T


title: NPC-732T


title: NPC-730T


title: NPC-729T


title: NPC-728T


title: NPC-733T


title: nonNPC-727T


title: NPC-746T


title: NPC-722T


title: nonNPC-721T


title: NPC-724T


title: NPC-720T


title: NPC-716T


title: NPC-723T


title: NPC-713T


title: NPC-714T


title: NPC-712T


title: NPC-711T


title: NPC-710T


title: NPC-708T


title: NPC-706T


title: M_Input_ZT15_rep2

city: East Lansing

first: Dae Kwan

last: Ko

address: 612 Wilson Rd.  Plant Biology RM 122

department: Plant Research Laboratories

institute: Michigan State University

data_processing:
Raw reads were subjective to quality trimming and adaptor clipping using FASTX-Toolkit (hannonlab.cshl.edu/fastx_toolkit) followed by removing orphan reads.
For B73 or Mo17, the filtered pair-end reads were mapped to the maize B73 reference genome (release 5b.60), or the Mo17 reference genome (reference-guided assembly based on the B73 genome), respectively. For hybrids, the filtered pair-end reads were mapped to both B73 and Mo17 reference genomes and the best alignment was selected for each read.
The latest version of MACS (version 2.0.1) algorithm was used to identify enriched peaks on each ChIP-seq file against the corresponding input file using a mappable genome size of –g 2.07e+09 and cut off p-value of 1e-3. Peaks were defined if they overlapped in both biological replicates.
To make a master-peak list from the three time-points, the peaks obtained from each time-point were merged for each genotype.
Genome_build: B73 RefGen_v2, Mo17
Supplementary_files_format_and_content: tab-delimited text files include peak coordinates for each genotype ...

organism: Zea mays

source_name: Aerial tissues

growth_protocol: All maize plants were grown at 600 µmol/m2/sec under 16L:8D cycle with temperature 28 °C (light) and 23 °C (dark) except for photosynthesis, starch and sucrose measurements for which natural sunlight was supplemented. The plants were placed in a randomized design by rotating around the growth room on a daily basis to minimize positional effects.

extract_protocol:
Lysates were clarified from sonicated nuclei and ZmCCA1b-DNA complexes were isolated with antibody.
ChIP-seq libraries for ChIP and input samples from two biological replicates were constructed using the standard NEB protocol (New England BioLabs) using custom made adapters containing barcodes for pooling multiple samples per each sequencing lane. Adapter and barcode sequences are listed in Supplementary Table 3. ChIPed DNA was subjective to end repair, dA-tailing, ligation with the adapters, and amplification by 18 cycles of PCR using NEBNext High-Fidelity 2× PCR Master Mix (New England BioLabs). 100-bp pair-end sequencing was performed on an Illumina Hi-Seq 2500.

tag: genotype

tag: antibody

value: Input

value: 5 days after planting

tag: time-point (zt)


title: MB_Input_ZT15_rep2

description: MB.txt

value: Mo17 x B73


title: BM_Input_ZT15_rep2

description: BM.txt

value: B73 x Mo17


title: NPC-731T


title: NPC-702T


title: NPC-701T


title: M_ChIP_ZT15_rep2


title: nonNPC-703T


title: NT2 DRIPc-seq, rep 1

tag: cell line


title: T. brucei H3VKO

source_name: H3VKO parasite

tag: strain

value: 221a of strain 427

value: bloodstream form

value: small RNA


title: NPC-718T

value: Tumor

value: III


title: NPC-719T

value: female


title: MB_ChIP_ZT15_rep2

description: MB.txt


title: BM_ChIP_ZT15_rep2

description: BM.txt


title: B_ChIP_ZT15_rep2


title: NPC-704T

value: male


title: NPC-707T


title: MB_Input_ZT15_rep1

description: MB.txt


title: T. brucei WT

source_name: WT parasite

tag: lifestage

value: WT


title: BM_Input_ZT15_rep1

description: BM.txt


title: M_ChIP_ZT15_rep1


title: BM_ChIP_ZT15_rep1

description: BM.txt


title: M_Input_ZT15_rep1


title: NPC-725T


title: B_Input_ZT15_rep1


title: B_ChIP_ZT15_rep1


title: MB_Input_ZT9_rep2

description: MB.txt


title: B_Input_ZT15_rep2


title: BM_Input_ZT9_rep2

description: BM.txt


title: MB_ChIP_ZT15_rep1

description: MB.txt


title: B_Input_ZT9_rep2


title: M_Input_ZT9_rep2


title: M_ChIP_ZT9_rep2


title: MB_ChIP_ZT9_rep2

description: MB.txt


title: BM_ChIP_ZT9_rep2

description: BM.txt


title: T. brucei H3VKO DMOG

tag: genotype/variation

value: DMOG (an inhibitor of J synthesis)


title: M_Input_ZT9_rep1


title: B_ChIP_ZT9_rep2


title: MB_Input_ZT9_rep1

description: MB.txt


title: siChaer PE

city: Los Angeles

first: Yibin

last: Wang

state: Ca

institute: University of California Los Angeles

data_processing:
Reads were aligned to rn5 using tophat2 with parameters -r 200 -a 13 -g 1 --no-mixed --no-discordant.
RPKM was calculated using in-house scripts for Ensembl genes plus H19 from Refseq.
Genome_build: rn5
Supplementary_files_format_and_content: Tab-delimited text files contain read counts and RPKM.

source_name: neonatal rat ventricular myocytes_siChaer_phenylephrine

growth_protocol: Neonatal rat ventricular myocytes were isolated from 2-day neonatal rat hearts, plated on 100 mm dishes and cultured with 1% ITS medium.

extract_protocol:
Total RNAs were extracted with TRIzol reagents.
TruSeq Stranded RNA library prep with 8 base indexing

treatment_protocol: After 6-h transfection with Chaer-specific siRNA (siChaer) and negative control siRNA (siNeg), mediums were changed with phenylephrine (50 microM) and collected after 48 h.

value: Sprague Dawley

value: Heart

tag: cell type

value: ventricular myocytes

value: 2-day neonatal


title: siNeg

source_name: neonatal rat ventricular myocytes_siNeg


title: siChaer

source_name: neonatal rat ventricular myocytes_siChaer


title: siNeg PE

source_name: neonatal rat ventricular myocytes_siNeg_phenylephrine


title: 97_SF/SCL isthmus

city: Pirassununga

first: Angela

middle: Maria

last: Gonella

state: SP

address: Rua Duque de Caxias Norte, 255

department: Departamento de Reprodução Animal

country: Brazil

institute: Universidade de São Paulo

data_processing:
CASAVA v1.8.2.
seqyClean v1.3.12. (https://bitbucket.org/izhbannikov/seqyclean/get/stable.zip) using 26 Phred quality parameter for maximum average error, and vector and adaptor sequences from the Univec database (https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/) were use as guide to remove possible contaminants. Only high quality paired-end sequences were kept for further analyses
The reads were mapped with Tophat v.2.0.8 and Bowtie2 v2.1.0 on the masked bovine genome assembly (Bos taurus UMD 3.1, NCBI).
The mapping file was sorted using SAMTools v 0.1.18 and read counts were obtained using the script from HTSeq-count v0.5.4p2 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html). The differential expression analysis was performed with package DESEq v1.12.1, from R/Bioconductor.
Using the function estimateSizeFactors, the normalized counts were obtained (baseMean values, which are the number of reads divided by the size factor or normalization constant). The standard deviation along the baseMean values was also calculated for each transcript. In order to avoid artifacts caused by low expression profiles and high expression variance, only transcripts that had an average of baseMean > 5 and the mean greater than the standard variation were analyzed.
The method to test for differential expression was the negative binonial distribution, through the nbinomTest function on DESeq. The threshold for evaluating significance was obtained by applying a p-value of 0.05 FDR- Benjamini-Hochberg.
Genome_build:  Bos taurus (assembly Bos_taurus_UMD_3.1.1)

organism: Bos indicus

source_name: Isthmus

extract_protocol:
Total RNA was extracted from frozen ampulla and isthmus samples using the AlLrep® DNA/RNA/Protein Mini kit (No. 80004, Qiagen), as recommended by manufacturer’s instructions. cDNA was generated by a routine RNA library preparation TruSeq protocol developed by Illumina Technologies (San Diego, CA) using 1 μg of total RNA as input.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were pre-synchronized by intramuscular injection of Prostaglandin F2α analog (PGF; 0.5 mg of sodium cloprostenol; Sincrocio, Ouro Fino, Cravinhos, Brazil) and, 7 days later an injection of GnRH agonist (1 µg of buserelin acetate; Sincroforte, Ouro Fino, Cravinhos, Brazil). At this day (D-20) animals received an Estrotect device and estrus detection was performed twice daily from D-20 to D-10. All animals received a new intravaginal P4-releasing device (1g; Sincrogest) on D-10 along with an intramuscular injection of 2 mg estradiol benzoate (Sincrodiol, Ouro Fino). Simultaneously, cows in the LF-LCL received an intramuscular injection of PGF. Additionally, P4 device removal was performed earlier in animals of the LF-LCL group. Specifically, devices were removed 42h and 30 h before the GnRH injection in the LF-LCL and the SF-SCL groups, respectively. All animals received a PGF injection at P4 device removal and a second PGF injection 6h later. Ovulation was induced by an injection of GnRH agonist on D0. On day 4, cows were stunned using captive bolt and euthanized by jugular exsanguination at the University slaughterhouse.

tag: developmental stage

value: multiparous cows

tag: health status

value: Healthy

tag: breed

value: Nelore

value: isthmus


title: B_Input_ZT9_rep1

value: Input

tag: age

value: 5 days after planting


title: Brassica_epi_Sh2

first: Carl

last: Procko

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2)
Reads were aligned to Arabidopsis TAIR10 or B. rapa FPsc v1.3 using TopHat version 2.0.9 and Bowtie 2.1.0 (strand-specific).
Cufflinks, Cuffmerge and Cuffdiff versions 2.1.1 were used for transcriptome assembly and differential expression analysis using default parameters.
In addition, Brassica samples were analyzed using multi-mapped read correction parameter in Cufflinks and Cuffdiff.
Genome_build: TAIR10 (Arabidopsis) or FPsc v1.3 (Brassica)
Supplementary_files_format_and_content: Excel spreadsheets showing differential gene expression for relevant pairwise comparisons as given from the Cuffdiff gene expression output; showing fpkm, log2 fold change, and fold-change significance.

molecule: polyA RNA

organism: Brassica rapa

source_name: hypocotyl epidermal peels

growth_protocol: Seedlings are grown in continuous W light on 1/2 LS 0.7% agar plates.

extract_protocol:
RNA was extracted using Qiagen RNeasy micro kit and digested with DNase I. Agilent Tape Station was used to determine RNA integrity (RIN) numbers prior to library preparation.
Stranded mRNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions. Libraries were then quantified, pooled and sequenced at single-end 50 base-pair reads using the Illumina HiSeq 2500 platform. Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2).

treatment_protocol: Seedlings are treated with W light or shade (low red:far red light).

value: FPsc wild-type

tag: treatment

value: Shade


title: Brassica_epi_Sh3


title: Brassica_epi_Sh1


title: M_ChIP_ZT9_rep1


title: 489215_SF/SCL isthmus

tag: tissue


title: MB_ChIP_ZT9_rep1

description: MB.txt

value: Mo17 x B73


title: 527_LF/LCL isthmus


title: 856_SF/SCL isthmus


title: B_ChIP_ZT9_rep1


title: BM_ChIP_ZT9_rep1

description: BM.txt

value: B73 x Mo17


title: Brassica_epi_W3

value: W light


title: Brassica_epi_W2


title: Brassica_wholehyp_Sh3

source_name: whole hypocotyl tissue


title: 79_LF/LCL isthmus


title: 617_LF/LCL isthmus


title: Plasma

city: Madrid

first: Lidia

middle: Ángeles

last: Daimiel-Ruiz

state: Madrid

address: Ctra. Cantoblanco, Km 8

department: Nutritional Genomics of Cardiovascular Disease and Obesity

institute: Institute IMDEA Food

data_processing:
Standard Ion PGM basecalling procedure
Sequenced reads were trimmed for adaptor sequences
Then samples aligning with the MS2 carrier were removed
Quality control included a Phred QC 20 filtering
Samples with a QC value higher than 20 were aligned against Viridiplanate clade using Bowtie 2
Supplementary_files_format_and_content: tab-delimited text files

source_name: pool of 5 samples

extract_protocol: miRCury RNA Extraction kit - biofluids

treatment_protocol: ingestion of 40 mL of EVOO, 2 h

value: plasma


title: M_Input_ZT3_rep2


title: BM_Input_ZT9_rep1

description: BM.txt


title: Brassica_epi_W1


title: BM_Input_ZT3_rep2

description: BM.txt


title: Brassica_wholehyp_Sh1


title: Brassica_wholehyp_Sh2


title: B_Input_ZT3_rep2


title: MB_Input_ZT3_rep1

description: MB.txt


title: BM_Input_ZT3_rep1

description: BM.txt


title: WT

first: Hui

last: Wan

state: Jiangsu

address: No 1800 Lihu Avenue

data_processing:
FastQC v0.11.3 software used for basecalling.
Cutadapt software used forremoving the adapter sequences using Cutadapt software,and then removed low overall quality reads which base qulity values Q≤20 is over 50% using FASTX-ToolKit software, and then filter reads containing ambiguous bases or trimming flanking ambiguous bases using NGS QC Toolkit.
The aligment of clean reads were mapped against the G. oxydans genome WSH003  using Bowtie 2.
To obtain and visualize the differences data in gene expression between two samples, Cufflinks and cummeRbund were used according to the described.
Genome_build: ASM31176v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Gluconobacter oxydans

source_name: Gluconobacter oxydans cells

extract_protocol:
The bacterial total RNA extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer’s instructions and adding lysozyme (Sinopharm, Shanghai, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: Gluconobacter oxydans WSH003

tag: culture phase

value: exponential growth phase


title: Brassica_wholehyp_W3


title: Brassica_wholehyp_W1


title: B_Input_ZT3_rep1


title: M_ChIP_ZT3_rep2


title: B_ChIP_ZT3_rep2


title: MB_ChIP_ZT3_rep1

description: MB.txt


title: MB_ChIP_ZT3_rep2

description: MB.txt


title: TB

value: pqqB-overexpression mutant


title: BM_ChIP_ZT3_rep1

description: BM.txt


title: M_ChIP_ZT3_rep1


title: M_Input_ZT3_rep1


title: MB_Input_ZT3_rep2

description: MB.txt


title: trf5-2

status: Public on Jun 29 2016

city: Houston

first: Ambro

last: van Hoof

state: TX

address: 6431 Fannin Street

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center-Houston

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) for sequencing was removed from the raw reads. After removing the 3' adaptor, reads with the length less than 10 were excluded.
Reads were mapped with Bowtie to features annotated at ftp.ensembl.org/pub/release-77/fasta/saccharomyces_cerevisiae/dna/
differentially expressed genes were identified using RSEM and EdgeR

organism: Saccharomyces cerevisiae

source_name: cell

growth_protocol: cells grown in SC-LEU media at 30°C to an OD of 0.6

extract_protocol:
RNA was harvested using phenol TE and chloroform method
RNA libraries were prepared according to standard Illumina protocols for Directional mRNA-Seq Sample Preparation

value: trf4delta, trf5delta with plasmid holding trf5-delta98-117


title: BM_ChIP_ZT3_rep2

description: BM.txt


title: trf5-1


title: Brassica_wholehyp_W2


title: WT-1

value: trf4delta, trf5delta with plasmid holding wild type TRF5


title: PhyC_WT_rep2_3

city: Harpenden

first: Stephen

last: Pearce

state: Hertfordshire

address: West Common

department: Sustainable Soils and Crops

country: United Kingdom

institute: Rothamsted Research

data_processing:
Bases were called at the UC Davis Genome Center using CASAVA1.5
Raw reads were trimmed for adapter contamination using "Scythe" (Default options, https://github.com/vsbuffalo) and for quality using “Sickle” (Default options except –l 25 –q 25, https://github.com/najoshi/sickle).
Trimmed reads were mapped to a reference set of genomic contigs from the hexaploid wheat variety ‘Chinese Spring’. This reference was assembled from flow-sorted A and B chromosomes and provided by the International Wheat Genome Sequencing Consortium (http://plants.ensembl.org/Triticum_aestivum/Info/Index, v2.2). Reads were aligned using GSNAP(l) (version 05-09-2013, default parameters except -m 2 -n 1 -N 1 -A sam).
Uniquely mapped reads were counted with ht-seq count (-m union) (http://www-huber.embl.de/users/anders/HTSeq/doc/index.html) using a custom-made GFF file describing 150,754 transcribed genomic loci.
Gene loci with a low number of counts were removed using the R script "noleaven" (http://topherconley.github.io/noleaven/).

organism: Triticum turgidum subsp. durum

source_name: Fully-extended third leaf

growth_protocol: Plants were grown in a Conviron PGR15 growth chamber at UC Davis, CA, in 16hr light/8hr dark conditions with a light intensity of 260µM m-2 s-1 and 20 °C day/ 18 °C night temperatures.

extract_protocol:
Total RNA was extracted from the third fully-expanded leaf of four-week-old plants using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO).
RNA-seq libraries were constructed using the TruSeq™ RNA library prep kit v2 (Illumina, San Diego, CA) according to the manufacturer's instructions and their quality determined by running samples on a high-sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).


title: phyCnull_rep2_2

value: phyC null mutants


title: PhyC_WT_rep2_4


title: phyCnull_rep2_1


title: PhyC_WT_rep2_1


title: phyCnull_rep2_4


title: PhyC_WT_rep2_2


title: phyCnull_rep1_3


title: B_ChIP_ZT3_rep1


title: phyCnull_rep1_4


title: phyCnull_rep1_2


title: WT-2


title: PhyC_WT_rep1_3


title: PhyC_WT_rep1_4


title: PhyC_WT_rep1_2


title: phyCnull_rep1_1


title: phyBnull_rep1_4

value: phyB null mutants


title: phyBnull_rep2_2


title: phyCnull_rep2_3


title: PhyB_WT_rep2_3


title: phyBnull_rep1_2


title: phyBnull_rep1_3


title: phyBnull_rep2_3


title: phyBnull_rep2_4


title: PhyB_WT_rep2_2


title: PhyB_WT_rep2_4


title: PhyB_WT_rep2_1


title: PhyB_WT_rep1_2


title: PNH3-CD8Naive

city: Shenzhen

first: Wangmin

last: Qiao

address: Building NO.7, BGI Park, No.21 Hongan 3rd Street, Yantian District

institute: BGI

description: PNH3 CD8+ naïve T cells

data_processing:
We define "dirty" raw reads as reads which contain the sequence of adapter, high content of unknown bases and low quality reads.
Clean reads are mapped to rRNA  reference using short reads alignment software SOAPaligner/SOAP2 (4)  to remove the remain rRNA reads.
we use Cuffdiff 2 version 2.1.1 to calculate gene and transcript expression levels in more than one condition and test them for significant differences on the basis of FPKM value.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples

source_name: T cells

extract_protocol:
RNeasy Mini kit (Qiagen)
Samples were prepared with the Illumina TruSeq Stranded Total RNA Library Prep Kit

tag: diagnosis

value: paroxysmal nocturnal hemoglobinuria (PNH)

value: CD8+ naive T cells

value: blood


title: PhyB_WT_rep1_4


title: PNH3-CD8Memory

description: PNH3 CD8+ memory T cells

value: CD8+ memory T cells


title: PNH3-CD4Naive

description: PNH3 CD4+ naïve T cells

value: CD4+ naive T cells


title: phyBnull_rep1_1


title: phyBnull_rep2_1


title: PhyC_WT_rep1_1


title: PhyB_WT_rep1_3


title: PNH2-CD8Memory

description: PNH2 CD8+ memory T cells


title: PNH2-CD8Naive

description: PNH2 CD8+ naïve T cells


title: PNH2-CD4Memory

description: PNH2 CD4+ memory T cells

value: CD4+ memory T cells


title: PNH2-CD4Naive

description: PNH2 CD4+ naïve T cells


title: PNH1-CD4Naive

description: PNH1 CD4+ naïve T cells


title: Healthy3-CD8Memory

description: Healthy3 CD8+ memory T cells

value: healthy


title: Healthy3-CD8Naive

description: Healthy3 CD8+ naïve T cells


title: Healthy2-CD4Naive

description: Healthy2 CD4+ naïve T cells


title: Healthy3-CD4Naive

description: Healthy3 CD4+ naïve T cells


title: Healthy3-CD4Memory

description: Healthy3 CD4+ memory T cells


title: Healthy2-CD8Naive

description: Healthy2 CD8+ naïve T cells


title: Healthy2-CD8Memory

description: Healthy2 CD8+ memory T cells


title: Rev-erba ChIP-seq at ZT10 (HNF6 KO) Replicate 3

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

data_processing:
Bowtie 1 was used to align ChIP-seq samples to mm9 genome, followed by peak-calling and generation of ucsc visualization files using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig, peaks bed

source_name: liver

growth_protocol: C57BL/6 mice were grown on normal chow on normal light/dark schedule

extract_protocol:
DNA or RNA is extracted using Qiagen kits
Library contruction follows illumina kits
Standard illumina method was used

treatment_protocol: no specific treatment was performed

value: 12 weeks old male

value: HNF6 KO

tag: Sex

value: male

value: Rev-erba, Cell Signaling Technology (CST#2124)


title: Healthy1-CD8Naive

description: Healthy1 CD8+ naïve T cells


title: Healthy1-CD8Memory

description: Healthy1 CD8+ memory T cells


title: Rev-erba ChIP-seq at ZT10 (HNF6 KO) Replicate 2


title: PNH1-CD4Memory

description: PNH1 CD4+ memory T cells


title: Healthy1-CD4Naive

description: Healthy1 CD4+ naïve T cells


title: Healthy1-CD4Memory

description: Healthy1 CD4+ memory T cells


title: Rev-erba ChIP-seq at ZT10 (Wild Type) Replicate 3

value: WT


title: PhyB_WT_rep1_1

value: wild type


title: Healthy2-CD4Memory

description: Healthy2 CD4+ memory T cells


title: PNH3-CD4Memory

description: PNH3 CD4+ memory T cells


title: Rev-erba ChIP-seq at ZT10 (Wild Type) Replicate 2


title: dukeepi2948rep2

city: New York

first: Erin

middle: L

last: Heinzen

state: NY

department: Institute for Genomic Medicine

institute: Columbia University

data_processing:
Base calling with Casava 1.9
Adapters trimmed
Reads aligned with Tophat2
Transcripts assembled with Cufflinks
Raw reads counted from bam file with Subread
Genome_build: UCSC hg19 and NCBI 37
Supplementary_files_format_and_content: tab-delimited text files including raw read counts for each aligned sample

source_name: dentate granule cells

extract_protocol:
Approximately 800 to 1000 dentate granule cells were extracted with laser capture microdissection from flash frozen surgically-resected hippocampal tissue.  RNA was extracted using the ARCTURUS PicoPure RNA Isolation Kit and amplified using the Clontech SMARTer Ultra Low RNA Kit according to the manufacturer’s instructions.
Sequencing libraries were then prepared using the TruSeq RNA Sample Preparation Kit.

tag: gender

value: M

value: mesial temporal lobe epilepsy


title: dukeepi3956rep1

value: F


title: dukeepi2948rep1


title: PNH1-CD8Naive

description: PNH1 CD8+ naïve T cells


title: PNH1-CD8Memory

description: PNH1 CD8+ memory T cells


title: Rev-erba ChIP-seq at ZT10 (Wild Type) Replicate 1

tag: antibody


title: dukeepi1895rep2


title: dukeepi2953cap2


title: dukeepi1895rep1


title: dukeepi2953cap1


title: dukeepi2638cap1

value: mesial temporal lobe epilepsy with hippocampal sclerosis


title: DKO_BEC 1

city: DaeJon

first: Da-Hye

last: Lee

address: 335 Gwahangno

department: Biological science

country: South Korea

institute: KAIST

description: replicate 6

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

source_name: in vitro differentiatied biliary epithelilal cells

growth_protocol: hepatoblasts were isolated from control and Lats1/2 deficient E14.5 fetal livers and cultured on collagen coated plates

extract_protocol:
Total mRNA was extracted with QIAGEN RNeasy Mini kit according to manufaturer's protocol
index labeled cDNAs were obtained by Illumina TruSeq RNA sample prep v2 Kit

treatment_protocol: for hepatocyte differentiation, we treated 12.5ng/ml oncostatin M for 5 days and for biliary epithelial cell differentiation, we cultured hepatoblasts on Matrigel for 14 days

value: B6;129 mixed

value: liver

tag: genotype


title: con_BEC

description: replicate 5


title: DKO_BEC 2

description: replicate 6


title: Rev-erba ChIP-seq at ZT10 (HNF6 KO) Replicate 1


title: dukeepi4000rep3


title: dukeepi3949rep3


title: dukeepi3169rep2


title: dukeepi4000rep2


title: dukeepi1046cap2


title: DKO_HP 2

description: replicate 4

source_name: in vitro differentiated heptocytes


title: dukeepi1930rep2


title: DKO_HP 1

description: replicate 4


title: dukeepi3956rep2


title: dukeepi3949rep2


title: DKO_HB

description: replicate 2

source_name: in vitro cultured hepatoblasts


title: dukeepi3169rep3


title: dukeepi1513rep2


title: MA9-LPE-shTcf4-654 (9-5-14)

city: Melbourne

first: Margherita

last: Ghisi

state: Victoria

address: St Andrews Place

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

description:
MLL-AF9-shTcf4-654 (9-5-14)
FACS-sorted GFP-positive MLL-AF9 AML cells 2 days after transduction with the shTcf4#654-GFP vector

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the mouse reference genome (mm10) using Tophat2 with default parameters.
Counts per gene were obtained using HTSeq with mode intersection-nonempty and Ensembl gtf. Counts were normalised using the limma-voom method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing limma-voom normalised log2 values for each Sample

source_name: Acute myeloid leukemia (AML) driven by MLL-AF9 linked to cherry reporter and an oncogenic form of NRAS (MLL-AF9;NRAS AML)

growth_protocol: Primary MLL-AF9;NRAS AMLs were generated by reconstituting lethally irradiated congenic mice with fetal liver cells co-transduced with a MLL-AF9 expressing  vector and a second vector co-expressing NRASG12D. AML cells were harvested form the spleen of  leukemic animals.

extract_protocol:
Cells were lysated and total RNA was extracted using Trizol reagent. Illumina TruSeq V2 RNA-seq kit was used with 400 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MLL-AF9;NRAS AML cells were  transduced in vitro with shTcf4-GFP (hairpin #654 or #3646) or shRen-GFP retroviral vectors and GFP-positive cells were FACS-sorted 2 days after transduction.

tag: strain background

tag: origin

value: MLL-AF9 primary AML cells obtained from the spleen of terminally sick mice

tag: traduced with

value: shTcf4#654-GFP vector

tag: time point

value: 2 days after transduction


title: MLL-AF9-shTcf4-3646 (14-4-14)

description:
MLL-AF9-shTcf4-3646 (14-4-14)
FACS-sorted GFP-positive MLL-AF9 AML cells 2 days after transduction with the shTcf4#3646-GFP vector

value: shTcf4#3646-GFP vector

tag: cell type


title: MLL-AF9-shTcf4-654 (14-4-14)

description:
MLL-AF9-shTcf4-654 (14-4-14)
FACS-sorted GFP-positive MLL-AF9 AML cells 2 days after transduction with the shTcf4#654-GFP vector


title: dukeepi2213cap2


title: MLL-AF9-shRen (14-4-14)

description:
MLL-AF9-shRen (14-4-14)
FACS-sorted GFP-positive MLL-AF9 AML cells 2 days after transduction with the shRen-GFP vector

value: shRen-GFP vector


title: dukeepi1930rep3


title: dukeepi1513rep3


title: dukeepi2213cap1


title: con_HP

description: replicate 3

tag: strain

tag: developmental stage


title: MA9-LPE-shTcf4-3646 (9-5-14)

description:
MLLAF9-shTcf4-3646 (9-5-14)
FACS-sorted GFP-positive MLL-AF9 AML cells 2 days after transduction with the shTcf4#3646-GFP vector


title: 28-TRIMA1-M4B1-DOX-R

description:
28-TRIMA1-M4B1-DOX-R
NormalizedMatrix_TRIMA4dDOX_Paper.txt

source_name: Acute myeloid leukemia (AML) driven by Tet-regulated MLL-AF9 and an oncogenic form of NRAS (Tet-Off MLL-AF9 AML)

growth_protocol: Primary Tet-Off MLL-AF9 AMLs were generated by reconstituting lethally irradiated congenic mice with foetal liver cells co-transduced with a Tet-Off-MLL-AF9-dRED retroviral vector and a second vector co-expressing NRASG12D together with the Tet-Off responsive transcriptional activator. AML cells were harvested form the spleen of  leukemic animals.

treatment_protocol: Tet-Off MLL-AF9 AML cells were treated in vitro with doxycycline (DOX) for 4 days to inactivate MLL-AF9 expression or left untreated (UT); or transduced in vitro with an Id2-GFP  or a control-GFP retroviral vector and GFP-positive cells were FACS-sorted 2 days after transduction.

value: Tet-Off MLL-AF9 AML cells

tag: protocol

value: doxycycline (DOX) for 4 days


title: 24-TRIMA2-M3B1-DOX-R

description:
24-TRIMA2-M3B1-DOX-R
NormalizedMatrix_TRIMA4dDOX_Paper.txt


title: 22-TRIMA2-M1B1-DOX-R

description:
22-TRIMA2-M1B1-DOX-R
NormalizedMatrix_TRIMA4dDOX_Paper.txt


title: 27-TRIMA1-M4B1-UT

description:
27-TRIMA1-M4B1-UT
NormalizedMatrix_TRIMA4dDOX_Paper.txt

value: untreated


title: 23-TRIMA2-M3B1-UT

description:
23-TRIMA2-M3B1-UT
NormalizedMatrix_TRIMA4dDOX_Paper.txt


title: 25-TRIMA2-M4B1-UT

description:
25-TRIMA2-M4B1-UT
NormalizedMatrix_TRIMA4dDOX_Paper.txt


title: 6-3-MA9-ID2

description:
6-3-MA9-ID2
ID2-CNT_log_dig_matrix.txt

value: FACS-sorted GFP-positive Tet-Off MLL-AF9 AML cells

value: 2 days after transduction with the Id2-GFP vector


title: 5-3-MA9-CNT

description:
5-3-MA9-CNT
ID2-CNT_log_dig_matrix.txt

value: 2 days after transduction with the Control-GFP vector


title: 21-TRIMA2-M1B1-UT

description:
21-TRIMA2-M1B1-UT
NormalizedMatrix_TRIMA4dDOX_Paper.txt


title: 3-2-MA9-CNT

description:
3-2-MA9-CNT
ID2-CNT_log_dig_matrix.txt


title: 4-2-MA9-ID2

description:
4-2-MA9-ID2
ID2-CNT_log_dig_matrix.txt


title: MA9-LPE-shRen (9-5-14)

description:
MLL-AF9-shRen (9-5-14)
FACS-sorted GFP-positive MLL-AF9 AML cells 2 days after transduction with the shRen-GFP vector


title: con_HB

description: replicate 1

value: wild type


title: 1-1-MA9-CNT

description:
1-1-MA9-CNT
ID2-CNT_log_dig_matrix.txt


title: 16-BM3-Kplus-Iminus

source_name: MLL-AF9-positive acute myeloid leukemia (AML)

growth_protocol: Primary MLL-AF9+ AMLs were generated by reconstituting lethally irradiated congenic mice with foetal liver cells obtained from Id2-GFP reporter mice and transduced with a retroviral vector co-expressing MLL-AF9 and the cherry reporter protein.

treatment_protocol: KitHI–Id2HI (3 BM_Kplus-Iplus), KitHI–Id2LOW (3 BM_Kplus-Iminus), KitLOW–Id2HI (3 BM_Kminus-Iplus) and KitLOW–Id2LOW (3 BM_Kminus-Iminus) MLL-AF9-positive primary AML cells were purified from the bone marrow of leukemic animals

value: FACS-sorted MLL-AF9 AML subpopulations characterized by differential expression of Id2 and Kit

value: MLL-AF9 AML cells obtained from the bone marrow of terminally sick mice

tag: cell subtype


title: 13-BM2-Kminus-Iplus


title: 15-BM3-Kplus-Iplus


title: 18-BM3-Kminus-Iminus


title: 11-BM2-Kplus-Iplus


title: 2-1-MA9-ID2

description:
2-1-MA9-ID2
ID2-CNT_log_dig_matrix.txt


title: 26-TRIMA2-M4B1-DOX

description:
26-TRIMA2-M4B1-DOX
NormalizedMatrix_TRIMA4dDOX_Paper.txt


title: 17-BM3-Kminus-Iplus


title: 12-BM2-Kplus-Iminus


title: 10-BM1-Kminus-Iminus


title: 8-BM1-Kplus-Iminus


title: 9-BM1-Kminus-Iplus


title: 7-BM1-Kplus-Iplus


title: GTPP sample 3

status: Public on Jun 28 2016

city: Boston

first: Christian

last: Munch

address: 240 Longwood Avenue

department: Cell Biology

institute: Harvard Medical School

data_processing:
FastQC
tophat2 v1.2 data analysis pipeline at HMS research computing
tophat vs hg19
cufflinks
cuffmerge
cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: text delimited file containing FPKM values for each sample, fold-changes with p-values, and sequecinging status

source_name: HeLa cells

extract_protocol:
NucleoSpin miRNA (Macherey-Nagel)
ribosomal depletion with RiboZero, directional RNA-seq library preparation, and 12 cycle amplification using LongAmp (New England BioLabs) and indexed primers (Integrated DNA Technologies)

tag: cell line

value: HeLa


title: CDDO sample 1


title: DMSO sample 1


title: DMSO sample 3


title: GTPP sample 2


title: CDDO sample 2


title: CDDO sample 3


title: Zfp281_WT_FA-rep2

first: Jianlong

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

data_processing:
Reads were aligned to the genome using TopHat (v2.0.10) and Bowtie2 (v2.1.0) with the default parameter settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.1.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files - tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks.

source_name: Embryonic stem cells

growth_protocol: Feeder-free mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated plates under standard conditions (Metastable pluripotent state or SL: DMEM supplemented with 15% fetal calf serum (FBS), 1000 units/mL recombinant leukemia inhibitory factor (LIF), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix (100X stock, Sigma), and 50 U/mL Penicillin/Streptomycin). For chemically defined naïve culture conditions (2iL), mESCs were cultured on 0.1% gelatin-coated plates using serum-free N2B27 medium (DMEM/F12 and Neurobasal medium mixed at a ratio of 1:1, 1x B27 supplement, 1x N2 supplement, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, and 50 U/mL Penicillin/Streptomycin ) supplemented with Gsk3β inhibitor (CHIR99021, 3 μM) and Mek inhibitor (PD0325901, 1 μM) and LIF. For defined primed culture conditions (FA), mESCs and EpiSCs were culture on fibronectin-coated plates (10 μg/mL/cm2) in N2B27 medium supplemented with activin A (20 ng/mL) and Fgf2 (12 ng/mL).

extract_protocol:
Total RNA was isolated using the RNeasy kit (#74136, Qiagen) according to manufacturer’s instructions.
Up to 2 μg of total RNA for each sample was taken for Ribo-Zero RNA-seq libraries preparation, and massively parallel sequencing was performed with the Illumina HiSeq 2500 Sequencing System. 100-bp single end reads were generated for each sample.

value: mESC 3+/+

tag: genotype/variation

value: WT

tag: mouse strain

value: mESCs were cultured on fibronectin-coated plates under FA condition (N2B27 medium supplemented with Fgf2 an Activin A) for 48 hrs


title: 14-BM2-Kminus-Iminus


title: GTPP sample 1


title: Zfp281_WT_2iL-rep2

value: mESCs were cultured on gelatin-coated plates under 2iL condition (N2B27 medium supplemented with Gsk3β and Mek inhibitors (2i) and LIF) for 48 hrs


title: Zfp281_WT_SL-rep2

value: mESCs were cultured on gelatin-coated plates under SL conditions:DMEM supplemented with serum and LIF


title: Zfp281_WT_2iL-rep1

value: mESC CJ7


title: WT_Primed

source_name: Epiblast stem cells

value: mEpiSC OEC2

value: mEpiSCs were cultured on fibronectin-coated plates under FA condition (N2B27 medium supplemented with Fgf2 an Activin A)


title: Zfp281_KO_2iL-rep2

value: mESC 7-/-

value: Zfp281 KO


title: WT_Naive

value: mESCs were cultured long time (>16 days) on gelatin-coated plates under 2iL condition (N2B27 medium supplemented with Gsk3β and Mek inhibitors (2i) and LIF)


title: Zfp281_KO_2iL-rep1


title: Zfp281_KO_SL-rep2


title: Zfp281_WT_FA-rep1


title: CJ7_mESC_ChIPseq_Zfp281

description: CJ7 mouse embryonic stem cells grown under ESC growth condition (serum plus LIF)

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality
Reads were aligned to the mouse genome (NCBI build 37, mm9) using the bowtie (v1.0.0) program, with parameters -m 1.
The mapped reads were sorted and converted to a binary bam file using samtools (v0.1.19)
Zfp281 ChIP-seq peaks were determined by MACS program (v.2.0.10), using input ChIP-seq as the control data, and all other parameters followed the default settings.
Bedgraph files were converted from bam files by Bedtools suite (v2.18.1) genomecov component with -bg parameter
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files of ChIP-seq reads and bed file of MACS called peaks.

growth_protocol: Feeder-free mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated plates under standard conditions: DMEM supplemented with 15% fetal calf serum (FBS), 1000 units/mL recombinant leukemia inhibitory factor (LIF), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix (100X stock, Sigma), and 50 U/mL Penicillin/Streptomycin).

extract_protocol:
ChIP was performed as previously described (Lee et al., 2006) by using Zfp281 antibody (Abcam #ab101318).
25 μl of 70 ng/μl input and 5 ng/μl Zfp281-ChIPed DNA to prepare input and Zfp281 ChIP-seq libraries. Massively parallel sequencing was performed with the Illumina HiSeq 2500 Sequencing System according to the manufacturer’s protocol.


title: Zfp281_KO_FA-rep1


title: Zfp281_KO_SL-rep1


title: DMSO sample 2


title: Zfp281_KO_FA-rep2


title: CJ7_mESC_ChIPseq_Input


title: Zfp281_WT_SL-rep1


title: MEF_Day7_Scrambled_shRNA, replicate3

city: PARKVILLE

first: Denise

last: Miles

state: VIC

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The reads were sequenced using a stranded protocol and aligned against the mouse genome, build 38, using Tophat 2.0.12 with bowtie 1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count. Genes that have no expression across all samples are removed from the dataset.
Genome_build: mouse build 38
Supplementary_files_format_and_content: The file readcounts.txt contains the absolute number of reads per gene for each sample.

source_name: mouse embryonic fiblroblasts containing FUW-OSKM and FUW-M2rtTA

growth_protocol: Cells were grown on irradiated feeder MEFs in ES media with or without induction of OSKM via doxycycline

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

treatment_protocol: Cells were treated for 7 days

tag: treatment

value: no doxycycline

tag: days treatment

value: MEF

tag: knockdown

value: no


title: MEF_OSKM_induced_Day7_Trim28_shRNA_Setdb1_shRNA, replicate 1

value: doxycyline

value: in vitro reprogrammed cells


title: MEF_OSKM_induced_Day7_Trim28_shRNA_Setdb1_shRNA, replicate 3


title: MEF_Day7_Scrambled_shRNA, replicate2


title: MEF_OSKM_induced_Day7_Trim28_shRNA, replicate 1


title: MEF_OSKM_induced_Day7_Trim28_shRNA_Setdb1_shRNA, replicate 2


title: MEF_Day7_Scrambled_shRNA, replicate1


title: MEF_OSKM_induced_Day7_Scrambled_shRNA, replicate2


title: asthenozoospermia

city: Nanjing

first: Zhen

last: Zhou

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

data_processing:
Illumina Casava1.6 software used for basecalling.
The final clean reads were obtained by getting rid of short reads (< 10 nucleotides) and contaminant reads (including reads with 5’ primer contaminants or poly A and reads without 3’ primer).
Sequenced reads with no more than 2 mismatches were identified as one piRNA and formed the final piRNA expression profiles.
After masking the adaptor sequences, the clean reads were aligned to the reference human (Homo sapiens) genome. The sequences that correspond to known piRNAs were determined by perfect sequence matching to the NCBI database.
 Finally, the total sequencing frequency of each sample was adjusted to an equal scale of 10,641,029 (same as the total reads of healthy controls).
Supplementary_files_format_and_content: tab-delimited text files include piRNA names and counts in each sample

source_name: Seminal plasma

extract_protocol:
Total RNA was extracted from 5ml of seminal plasma from fertile healthy controls/asthenozoospermia patients/azoospermia patients using the Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: fertility diagnosis

value: asthenozoospermia

tag: tissue

value: seminal plasma


title: MEF_OSKM_induced_Day7_Scrambled_shRNA, replicate3


title: MEF_OSKM_induced_Day7_Trim28_shRNA, replicate 2


title: MEF_OSKM_induced_Day7_Scrambled_shRNA, replicate1


title: MEF_OSKM_induced_Day7_Trim28_shRNA, replicate 3


title: fertile healthy controls

value: fertile healthy


title: azoospermia

value: azoospermia


title: DMSO sample 2

data_processing:
Processing with the RNA-seq pipeline in http://bcbio-nextgen.readthedocs.org/en/latest/
FastQC
cutadapt
alignment with STAR
FastQC/RNA-SeQC
featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files containing coverage data across the mitochondrial genome.

value: HeLa


title: GTPP sample 3


title: GTPP sample 1


title: DMSO sample 1


title: GTPP sample 2


title: 2.5 days post-fertilization embryos

city: Lexington

first: Mark

last: Evers

state: Kentucky

address: 800 Rose Street

department: College of Medicine

institute: University of Kentucky

data_processing:
Align to reference transcriptome using RSEM
Calculate raw transcript expression for each time point using RSEM
Calculate expression fold change and probability of differential expression using Ebseq
Genome_build: Sea lamprey transcriptome (Pmarinus_7.0, Jan 2011)
Supplementary_files_format_and_content: "genes.results.txt" files contain transcript abundance estimates generated by RSEM. ".results files" (in GSE_differential_expression.tar series supplementary file) contain differential expression estimates generated by Ebseq. Differential expression was calculated between time points, in reference to D1, and in reference to testes.

organism: Petromyzon marinus

source_name: Whole Embryos

extract_protocol:
embryos were frozen in liquid nitrogen, homogenized in Trizol and extracted using Trizol extraction
HudsonAlpha paired-end RNAseq with NEBnext library prep

value: Whole Embryos

value: 2.5 days post-fertilization embryos


title: 5 days post-fertilization embryos

value: 5 days post-fertilization embryos


title: 2 days post-fertilization embryos

value: 2 days post-fertilization embryos


title: 3 days post-fertilization embryos

value: 3 days post-fertilization embryos


title: 4 days post-fertilization embryos

value: 4 days post-fertilization embryos


title: Total_NOG4

first: Vrutant

middle: V

last: Shah

address: 1515 Holcombe Blvd #1000

department: EMC

institute: UT MD Anderson Cancer Center

description: Processed data file: total_cabr_nog_above10.txt

data_processing:
Sequences were trimmed and quality was checked using fastQC.
For small RNA-seq: Trimmed reads are aligned to Xenopus laevis genome assembly 9.1. For Ago-IP- & total RNA-seq: Trimmed reads are aligned to Xenopus laevis transcriptome using bowtie-2.
For small RNA-seq: Reads were re-aligned to miRBase 21 using miRdeep2. For Ago-IP- & total RNA-seq: Aligned reads were counted using Express.
For Ago-IP & total RNA-seq: Read counts were analyzed using DESeq package for R.
Genome_build: Xenopus laevis v9.1
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts using Express tool.

organism: Xenopus laevis

source_name: whole embryo, noggin

extract_protocol:
For small RNAs and total RNAs: Tissue samples were lysed in Trizol, and RNA was extracted and treated with DNaseI using the Direct-zol RNA mini-prep kit (Zymo).
For AGO IP RNA: Ago-RNP immunoprecipitations were carried out as a modification of Keene et al. (2006).
RNA samples were processed for library preparation using the NEBNext Multiplex Small RNA Library Prep Set for Illumina kit according to manufacturer's instructions.
Sequencing libraries were prepared from the immunoprecipitated RNA samples using the ScriptSeqTM Complete Gold Kit - Low Input (Epicentre Technologies), with rRNA depleted protocol.

treatment_protocol: Embryos were injected at the 2-cell stage, and animal caps were isolated manually when the embryos reached stg. 8. Isolated animal caps were maintained in 1X MMR.

tag: strain/background

value: NXR

value: mid-gastrula embryo

value: whole embryo

value: noggin

tag: ip antibody


title: Total_CABR6

source_name: whole embryo, CABR

value: constitutively active BMP4 receptor (CABR)


title: Total_NOG6


title: Total_NOG3


title: Total_CABR3


title: Total_CABR4


title: DMSO sample 3


title: AC_AGO_IP_U3

description:
RIP RNA
Immunoprecipitation, non-specific binding

data_processing:
Library strategy: RIP-Seq
Sequences were trimmed and quality was checked using fastQC.
For small RNA-seq: Trimmed reads are aligned to Xenopus laevis genome assembly 9.1. For Ago-IP- & total RNA-seq: Trimmed reads are aligned to Xenopus laevis transcriptome using bowtie-2.
For small RNA-seq: Reads were re-aligned to miRBase 21 using miRdeep2. For Ago-IP- & total RNA-seq: Aligned reads were counted using Express.
For Ago-IP & total RNA-seq: Read counts were analyzed using DESeq package for R.
Genome_build: Xenopus laevis v9.1
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts using Express tool.

source_name: animal caps, untreated, IP

value: animal caps

value: anti-Myc, monoclonal 9E10 (Sigma Aldrich, St. Louis, MO; cat# 05-419, lot# 2712325)


title: miR-93 mimic 2

first: Shawn

middle: Samson

last: Badal

address: 2121 W. Holcombe Blvd

department: Nephrology

institute: MD Anderson Cancer Center

description:
immortalized cultured cell
mouse podocytes transfected with pre-miR-93 mimic rep 1

data_processing:
Data quality assessed by FastQC software
Adaptor presence was tested using trimmomatic
Reads were aligned to NCBI mouse genome build 37.2 using Tophat2 v2.0.4
Transcript quantification, normalization and assembly were carried out using  default Cufflinks settings
Cuffdiff2 was used to identify feature differentially expressed between conditions.
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output file; Sample_1 is miR-93 mimic and Sample_2 is NT mimic

source_name: podocyte

growth_protocol: Cells were grown under normal differentiation conditions in DMEM (glucose 1g/L) supplemented with 5% FBS and 1% Anti-Anti, for 12 days.

extract_protocol:
Trizol Reagent Followed by PureLink RNA mini Kit Cleanup
RNA libraries were prepared for sequencing following standard illumina protocols

treatment_protocol: Cells were transfected with 50 nM of a pre-miR-93 mimic or a pre-nontargeting control mimic, oligos were introduced with Lipofectamine 2000. Transfected cells were incubated for 48 hours and RNA extracted as below

value: kidney

value: epithelial cell


title: miR-93 mimic 1


title: AC_AGO_IP_U1


title: AC_AGO_IP_U2


title: NT mimic 1

description:
immortalized cultured cell
mouse podocytes transfected with nontargeting mimic rep 1


title: AC_AGO_IP_N4

description:
RIP RNA
Immunoprecipitation

source_name: animal caps, noggin, IP


title: NT mimic 2


title: AC_AGO_IP_N3

description:
RIP RNA
Immunoprecipitation


title: 1 day post-fertilization embryos

value: 1 day post-fertilization embryos


title: gDNA Input

description: immortalized cultured cell

data_processing:
Basecalls performed using CASAVA version 1.8.2 with no mismatches
DNAse-seq reads were aligned to the mm10 genome assembly using Bowtie Short Read Aligner with default parameters
Duplicate reads were then filtered, reads were shifted 50nt downstream of their mapped location. The number of complete reads that mapped within 500nt of each unique Transcription start site as defined by Ensembl vGRCm38.73. TSSs that had at least the equivalent of 10 reads/million in a single condition, relative to the condition with the largest number of mapped reads were kept for subsequent analysis.
Peaks were valled using the MACS2 peak calling algorithm using the parameters recommended by Zhang et al., 2012, Genome Biology
Pathway analysis was carried out on the top 200 most differentially enriched TSSs in each of the conditions
Genome_build: mm10
Supplementary_files_format_and_content: merged peak files for each condition and list of DHS scores for TSS sites and aligned bam files

growth_protocol: Cells were cultured in normal glucose (5mM) or high glucose (25mM) for 36 hours following growth arrest in reduced serum media

extract_protocol:
Nuclei were isolated and subjected to DNAse digestion. DNA was isolated by phenol:chloroform extraction and ethanol precipitation. Gel purified DNA ranging in size from 50-500bp was further purified using Qiagen PCR purification kits
DNA libraries were prepared according to standard illumina protocols

treatment_protocol: Cells cultured in high glucose conditions were transfected with 50nM of a nontargeting mimic or a miR-93 mimic.Normal glucose cells served as control

tag: condition

value: genomic DNA input control


title: HG+NT 2

description: immortalized cultured cell

value: High glucose (25mM) + NT mimic Rep 2


title: HG+miR-93 2

description: immortalized cultured cell

value: High glucose (25mM) + miR-93 mimic Rep 2


title: HG+miR-93 1

description: immortalized cultured cell

value: High glucose (25mM) + miR-93 mimic Rep 1


title: AC_AGO_IP_N1

description:
RIP RNA
Immunoprecipitation


title: AC_AGO_IP_C4

description:
RIP RNA
Immunoprecipitation

source_name: animal caps, CABR, IP


title: AC_AGO_IP_C3

description:
RIP RNA
Immunoprecipitation


title: AC_AGO_IP_C2

description:
RIP RNA
Immunoprecipitation


title: HG+NT 1

description: immortalized cultured cell

value: High glucose (25mM) + NT mimic Rep 1


title: miR_NOG5

description: Small RNA

source_name: animal caps, noggin


title: NG 2

description: immortalized cultured cell

value: Normal glucose (5mM) rep 2


title: NG 1

description: immortalized cultured cell

value: Normal glucose (5mM) rep 1


title: miR_NOG3

description: Small RNA

value: NXR


title: miR_CABR2

description: Small RNA

source_name: animal caps, CABR

value: mid-gastrula embryo


title: AC_AGO_IP_C1

description:
RIP RNA
Immunoprecipitation


title: miR_CABR5

description: Small RNA


title: miR_NOG2

description: Small RNA


title: miR_CABR3

description: Small RNA


title: AC_AGO_IP_N2

description:
RIP RNA
Immunoprecipitation


title: directional RNA-seq, mCherry+GFP-marked gametocyte population

city: Nijmegen

first: Richard

middle: Csaba

last: Bartfai

address: Geert Groteplein 26-26

department: Department of Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
Illumina Casava 1.8.2 software was used for base calling. We only used the bcl to fast conversion.
The single-end RNA-seq samples were mapped with BWA (Version 0.6.2-r126, default parameters) to either the complete P. falciparum assembly for the genomic tracks or the spliced transcriptome (PlasmoDB 6.1 and 9.1) and filtered to mapping quality ≥15.
Genome_build: PlasmoDB 6.1, PlasmoDB 9.1
Supplementary_files_format_and_content: .raw.bedGraphFull: Raw coverage by 92 bp reads for single-end.
Supplementary_files_format_and_content: .scale1.bedGraphFull: Normalized coverage per site (ni) calculated as ni = ri × g/b, where ri is the raw coverage (.raw.bedGraphFull) covering the sites i in the sample, b is the total number of bases in fragments, and g is the genome size. Therefore, a normalized coverage value of 1 represents the coverage expected if fragments are randomly distributed across the genome.
Supplementary_files_format_and_content: .tsv: tab-delimited tables of raw read counts or RPKM normalized read counts.

organism: Plasmodium falciparum

growth_protocol: PfDynGFP/P47mCherry gametocyte cultures were performed in the semi-automated shaker system and were started at 5% hematocrit and 0.5% parasiteamia. Gametocyte cultures were treated with N-acetyl-glucosamine on day 7 to eliminate asexual parasites. Gametocytes were concentrated in 37ºC culture medium and separated from erythrocytes and culture debris using a 63% and a 33% percoll density gradient and subsequently taken up in a 4ºC suspended activation (SA) buffer (10 mM Tris, pH 7.3, 170 mM. NaCl, 10 mM glucose). Gametocytes were further purified by magnetic separation from uninfected red blood cells using MACS columns.

extract_protocol:
Gametocytes were FACS-sorted using the Coulter Epics Elite flow cytometer (Beckman Coulter) at 4ºC in SA buffer into GFP+ (1.1 x 10^6 male gametocytes), GFP+/Cherry+ (6.3 x 10^6 male gametocytes) and Cherry+ (13.2 x 10^6 female gametocytes) populations.
cDNA synthesis and preparation of strand-specific RNA-seq libraries:  RNA was isolated on RNeasy collumns using an on-collumn DNaseI treatment and subsequently enriched for polyA+ mRNA using oligo-dT selection (Qiagen, Oligotex mRNA mini kit). RNA hydrolysis, cDNA synthesis and strand-specific RNA-Seq was performed as in (10.1093/nar/gkv1214). In short, PolyA+ RNA was fragmented by hydrolysis and first strand synthesis was initiated using AT-corrected nonamer primers in the presence of 0.2 ug Actinomycin D, followed by a heat inactivation and DNA clean-up. During second strand synthesis dTTP was replaced by dUTP, resulting in a "U"-base containing second cDNA strand. Up to 2ng of double-stranded cDNA was used for sequencing library preparation, which included an additional degradation step of "U"-base containing second strand cDNA by USER enzyme (New England Biolabs) before Pre-PCR to ensure maintenance of strand-specific information as in (10.1093/nar/gkv1214). Libraries were amplified for a total of 16 cycles (4 cycles Pre-size-selection PCR, 12 cycles Post-size-selection PCR) using a P. falciparum optimized Kapa PCR protocol (KAPA Biosystems) and fragments of 300-400bp were isolated for sequencing. Libraries were sequenced for 92 cycles single-end (TruSeq SR Cluster Kit v3, Sequencing reagents v3) on a HiSeq2000 system (Illumina).

value: NF54 pDynGFP/p47mCherry

tag: Stage

value: stage IV-V

tag: gender

value: male

value: gametocyte

tag: mcherry

value: positive

tag: gfp


title: directional RNA-seq, GFP-marked gametocyte population

source_name: GFP-marked gametocyte population

tag: strain

tag: cell type

value: negative


title: directional RNA-seq, mCherry-marked gametocyte population

source_name: mCherry-marked gametocyte population

value: female


title: cFD + spt cMO_replicate 4

status: Public on Jun 27 2016

city: Stanford

first: James

last: Chen

address: 269 W. Campus Drive, CCSR 3150

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
Basecalls performed using HiSeq control software v 1.5.15
Paired-end reads passing initial QC from two sequencing lanes were concatenated head-to-tail
Data was processed according to the CEL-seq protocol (Hashimshony, T et al.  Cell Reports. 2012) using custom scripts (http://yanailab.technion.ac.il):
De-multiplexing of read_1 file using a unique 8 bp barcode, filtering/truncation of read_2 (quality  score >20; 35 bp), alignment of read_2 35 bp reads to Zv8 reference, and feature counting
Count files analyzed using EdgeR to identify differentially expressed genes
Genome_build: Zv8
Supplementary_files_format_and_content: Tab-delimited text files of raw counts and normalized abundance measurements from EdgeR analysis

organism: Danio rerio

source_name: embryo

growth_protocol: Zebrafish embryos were obtained from natural spawning

extract_protocol:
After collection of 5 biological replicates, total RNA was obtained from each sample using the RNAqueous-Micro Total RNA Isolation Kit (Ambion) and RNA integrity was assessed by bioanalyzer analysis (RIN 8.1 - 9.9)
Libraries were constructed according to the CEL-seq protocol (Hashimshony, T et al.  Cell Reports. 2012).  Barcode information on read_1 of paired-end reads: cntrl_1, CATCACGC; cntrl_2, GTCGTTCC; cntrl_3, GTCGTGAA; cntrl_4, TCACACGC; cntrl_5, TCACAGAG; cMO_1, TGATGCGC; cMO_2, ACGACTCC; cMO_3, ACGACGAA; cMO_4, ATGTGCGC; cMO_5, CGTGTGAG.

treatment_protocol: 1-cell stage embryos were injected with either caged fluorescein-dextran (cFD) alone or in combination were the spt caged morpholino (cMO) and allowed to develop until 6 hours post-fertilization (hpf).  Embryos were then irradiated with UV light using a 100 μm-diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single-cells.  Fluorescein-positive cells were isolated using fluorescence-activated cell-sorting (FACS) directly into lysis buffer (RNAqueous-Micro Total RNA Isolation Kit; Ambion) and immediately lysed.  Lysed cells in lysis buffer were then stored in -80 °C until all samples for 5 biological replicates were obtained.

value: WT AB

value: ventral somite progenitors

value: late gastrulation (9 hpf)

value: cFD and the spt cMO


title: cFD only_replicate 5

value: cFD alone


title: cFD + spt cMO_replicate 2


title: cFD + spt cMO_replicate 5


title: cFD only_replicate 3


title: cFD + spt cMO_replicate 1


title: cFD only_replicate 2


title: cFD + spt cMO_replicate 3


title: Crz1_B_T20

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

institute: UNIVERSITAT AUTONOMA BARCELONA

description: IP genomic DNA

data_processing:
Libraries were sequenced with the MiSeq Reagent Kit v2 (300 cycle) to provide reads of around 150 nt.
Base calling was performed with MiSeq Reporter v2.2. (CASAVA v1.8). Sequenced reads were trimmed for adaptor sequence and demultiplexed.
Reads were aligned with Bowtie2-2.1.0 (end-to-end) and default settings.
Peak calling and abundance measurements were performed with SeqMonk v.0.24. intergenic regions and information on the flanking genes were obtained from the Saccharomyces Genome Database using the YeastMine tool. This information was loaded into SeqMonk as an Annotation set and was used to generate 6303 intergenic probes. Subsequently, each of these probes was tiled in contiguous sections (bins) of 50 nt. This generated a total number of 65198 probes that were quantitated by the read count quantitation method, with identical reads removed and correction for total read count referred to the largest Dataset.
Genome_build: S. cerevisiae EF4

growth_protocol: Strain SP020 (CRZ1:3xHA) was grown overnight to mid-exponential phase at 28°C in liquid rich medium (YPD; 10 g/l yeast extract, 20 g/l peptone and 20 g/l dextrose) and then resuspended in fresh YPD media containing 50 mM TAPS adjusted to pH 5.5 to OD600 = 0.2. Cells were grown for 4-5 hours to reach OD600 = 0.6-0.8.

extract_protocol:
Forty ml of cultures were taken at the appropriate times and made 1% formaldehyde to crosslink proteins and DNA. From this point the procedure was as described in (González et al., 2013;Serra-Cardona et al., 2014) with the following modifications: i) chromatin was fragmented using a Bioruptor Plus UCD-300 equipment (Diagenode) provided with a cooling system (4°C) for 30 cycles (high intensity; 30 s of sonication followed by 60 s pause) to generate fragments of ≤ 500 bp length; ii) the supernatant was pre-cleared with protein G sepharoseTM fast flow (GE Healthcare, #17-0618-01) beads for 1 h at 4°C and then, the pre-cleared cell lysate was incubated with 1 µg of polyclonal anti-HA ChIP-grade (Abcam, #ab9110) antibody overnight at 4°C; iii) anti-HA-Crz1-DNA complexes were collected with protein-G-sepharose beads incubating for 1 hour at 4°C,  and iv) after reverse crosslinking, DNA was extracted using a NucleoSpin® Gel and PCR Clean-up kit (Macherey Nagel, #740609) and NTB buffer (Macherey-Nagel, #740595).
ChiP libraries were prepared using the TruSeq ChIP Sample Preparation Kit (Illumina) and then subjected to paired-end deep sequencing.

treatment_protocol: At time 0, the pH of the culture was raised to 8.0 by adding 1 M KOH and growth resumed.

value: SP020 (CRZ1:3xHA)

value: whole cell


title: cFD only_replicate 4


title: cFD only_replicate 1


title: Crz1_B_T2

description: IP genomic DNA


title: Crz1_B_T5

description: IP genomic DNA


title: Squamous (NLSCLC)_H226

city: Baltimore

first: Priti

last: Kumari

state: MD

address: 801 W Baltimore St

department: Institute For Genome Sciences

institute: University Of Maryland Baltimore School Of Medicine

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Human (hg19) whole genome reference using Bowtie v0.12.9
Raw read count were calculated for each sample.
Differential expression of piRNA were computed between Immortalized(control) and Tumor samples
Genome_build: H. sapiens (hg 19)
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: piRNA Library Lung

growth_protocol: Human NSCLC cells were cultured in RPMI 1640 with 10% FBS, Human HBE cell lines were cultured in Keratinocyte-SFM with L-Glutamine, prequalified human recombinant Epidermal Growth Factor 1-53.

extract_protocol:
Total RNA including snRNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were washed in PBS before RNA extraction.

tag: cell line

value: Squamous (NLSCLC)

value: Lung


title: Squamous (NLSCLC)_SKMES1


title: Crz1_B_T1

description: IP genomic DNA


title: Adenocarcinoma (NSCLC)_H1944

value: Adenocarcinoma (NSCLC)


title: Squamous (NLSCLC)_H596


title: Crz1_A_T2

description: IP genomic DNA


title: Adenocarcinoma (NSCLC)_H1437


title: Crz1_A_T20

description: IP genomic DNA


title: Squamous (NLSCLC)_H157


title: Crz1_A_T1

description: IP genomic DNA


title: Adenocarcinoma (NSCLC)_H1792


title: Adenocarcinoma (NSCLC)_H522


title: Crz1_A_T5

description: IP genomic DNA


title: Immortalized bronchial epithelial_HBE4

value: Immortalized bronchial epithelial


title: Setdb1FplusZP3_rep1

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

data_processing:
Basecalls performed using RTA version 1.13.48
Demultiplexing and fastq generation was performed with bcl2fastq (bcl2fastq-1.8.3)
Illumina adaptor sequences (GATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were removed from the 3’ end of RNA sequencing reads and spliced alignment of reads to the genome was created using STAR of version 2.5.0a with parameters –outFilterMultimapNmax 300 –outMultimapperOrder Random -outSAMmultNmax 1 -outSAMmapqUnique 255 –alignSJoverhangMin 8, tracking up to 300 matches and choosing only one random match for reads with multiple alignments, gapped alignments with overhang shorter than 8 bp were removed.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for bins of 100 bp were generated by QuasR package (version 1.10.1) using only uniquely  mapped reads (minimum mapping quality 255) and  the output values in the bigWig files were linearly scaled by the total number of aligned reads per sample.
Supplementary_files_format_and_content: TXT with table of RPKM values (Reads Per Kilobase per Million of mapped reads) for each RefSeq transcript and each RNA-Seq sample was produced using uniquely mapped reads.

growth_protocol: GV-oocytes were isolated in M2 medium containing 2.5mM milrinone (Sigma).

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen). cDNA was generated and amplified from 1.2 ng with the NuGen ovation RNA-seq System V2 (Part no. 7102; NuGen).
50 ng of the resulting SPIA cDNA was fragmented and sequencing libraries were prepared using TruSeq DNA Sample Preparation Kit (low-throughput protocol) (Part no. 15005180 Rev. C; NuGen).

tag: strain background

tag: genotype/variation

value: Setdb1 F/+; ZP3-cre

value: GV-oocyte


title: Setdb1FplusZP3_rep4


title: Immortalized bronchial epithelial_HBE3


title: Setdb1FminusZP3_rep2

value: Setdb1 F/-; ZP3-cre


title: Setdb1Fminus_rep2

value: Setdb1 F/-


title: Setdb1FminusZP3_rep1


title: Bcl11bYFP-on DN2 cells #2

city: Seattle

first: Hao Yuan

last: Kueh

state: WA

address: 3720 15th Ave NE

department: Division of Biology

institute: University of Washington

data_processing:
Sequence reads from each sample were trimmed to remove the adapter sequences and the resulting 50 bp reads were mapped to the NCBI37/mm9 mouse genome assembly
Alignment was done using Tophat (v.2.0.6). command: tophat --no-novel-juncs --library-type fr-unstranded -G Mus_musculus.NCBIM37.66.gtf
Abundance measurements were done using Cufflinks (v.2.1.1). cufflinks (fpkm) command: cuffdiff --dispersion-method blind --library-type fr-unstranded --no-effective-length-correction --library-norm-method quartile -u -b mm9.fa --emit-count-tables Mus_musculus.NCBIM37.66.gtf
Genome_build: UCSC mm9, NCBI37
Supplementary_files_format_and_content: Tab-delimited files with fpkm values generated from Cufflinks

source_name: cultured bone marrow progenitors from Bcl11b-YFP mice

growth_protocol: Bone marrow progenitors from 2-3 month old Bcl11b-YFP reporter mice were cultured on OP9-DL1 stromal cells with IL-7 and Flt3L (5 ng/ml each) for 6 days to obtain early DN stage cells.

extract_protocol:
Sorted cells were lysed in the TRIzol reagent (Invitrogen) and total RNA was extracted as per the manufacturer’s protocol. polyA+ mRNA was isolated using the Dynabeads mRNA purification kit (Invitrogen), then fragmented, converted cDNA by random priming.  cDNA was then subject to end repair, adaptor ligation, size selection and one round of PCR amplification
polyA+ mRNA was isolated by two rounds of selection with Dynabeads (Invitrogen), fragmented to an average size of 200 bp by Mg2+ mediated hydrolysis and used to synthesize cDNA by random priming. The cDNA was end-repaired, the blunt ends were phosphorylated and Illumina adapters were ligated to the fragments. ~300 bp cDNA fragments were then purified by gel electrophoresis and SPRI (Agencourt AMPure XP catalog #A63880) beads were used to remove shorter fragments (<100 bp). The cDNA was then PCR amplified for 15 cycles and the resulting DNA fragments were purified once again with SPRI beads and sequenced on the Illumina HiSeq 2000 sequencer following the manufacturer's protocol.

treatment_protocol: Fetal liver derived DN cells were harvested from OP9-DL1 co-cultures and sorted for DN1 (Kit+CD44+CD25) or DN2 (Kit+CD44+CD25+) populations

tag: genotype

value: in vitro-differentiated DN2 cells


title: Setdb1Fminus_rep1


title: Bcl11bYFP-low DN2 cells #2


title: Bcl11bYFP-off DN2 cells #2


title: Immortalized bronchial epithelial_HBE2


title: Bcl11bYFP-on DN2 cells #1


title: DN1 cells [all Bcl11bYFP(off)] #2

value: in vitro-differentiated DN1 cells


title: Crz1_B_T0

description: IP genomic DNA


title: Bcl11bYFP-low DN2 cells #1


title: Setdb1FminusZP3_rep3


title: Setdb1FplusZP3_rep3


title: Setdb1FplusZP3_rep2


title: Crz1_A_T0

description: IP genomic DNA


title: Setdb1FminusZP3_rep4


title: Bcl11bYFP-off DN2 cells #1


title: DN1 cells [all Bcl11bYFP(off)] #1


title: LTearly_3_M4grLT3

data_processing:
HiSeq 2000 was run with HCS 2.0.12 and base calling was performed with RTA 1.17.21.3
The 3′ adaptor was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least seven or ten bases, respectively. Low-complexity reads were filtered out based on their dinucleotide entropy. All the reads that were shorter than 14 nucleotides were removed. Alignments to the Mus musculus genome (May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/) were performed by the software bowtie (version 0.9.9.1) ( Langmead et al., 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. To track genomically untemplated hits (e.g., exon-exon junctions or missing parts in the current assembly), the reads were also mapped to an annotation database containing known sequences (http://www.sanger.ac.uk/Projects/S_pombe/). In that case, all best hits with at most two mismatches were tracked. Each alignment was weighted by the inverse of the number of hits. In the cases where a read had more hits to an individual sequence from the annotation database than to the whole genome, the former number of hits was selected to ensure that the total weight of a read does not exceed one. Genomic read coverage plots were based on weighted alignments.
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
Reads mapping to mouse RefSeq mRNAs (fasta sequences downloaded from http://www.ncbi.nlm.nih.gov/nuccore on 2012-08-13) were counted per gene and per sample
Genome_build: mm9

source_name: bone marrow

growth_protocol: The cDNA of human MLL-AF9 fusion gene (a kind gift from J. Hess, University of Michigan, USA) was subcloned into the pLox-Cre vector backbone. 20 μg of p2Low-MLL-AF9 vector DNA were  electroporated into the A2Lox-cre targeting cells pretreated with doxycycline in order to active Cre recombinase and then selected using 300 μg/ml G418. Selected clones were used to generate chimeric transgenic lines using the aggregation method and standard protocols. Chimeric mice were backcrossed with C57BL/6 for up to 10 generations. Double heterozygous female mice were identified using genotyping PCR and then used for subsequent animal experiments.

extract_protocol:
Total RNA was isolated using the Arcuturus PicoPure RNA Isolation kit (and DNAse treated according to the kits manual.
RNA-seq libraries were prepared with the ScriptSeq Complete Kit (Human/Mouse/Rat) - Low Input (EpiCentre) starting from 150ng total RNA.

treatment_protocol: Isolated bone marrow cells were first stained with lineage cocktail antibodies against Cd5, Cd11b, Cd45R/B220, Ly-6G (Gr-1) and Ter119 (R&D Systems) and counter selected using magnetic beads. Cells were then stained with streptavidin Pacific Blue conjugated, biotinconjugated FcγRII/III, Alexa Fluor 647-conjugated Cd34, allophycocyanin-conjugated c-Kit and phycoerythrin-Cy7-conjugated Sca-1 monoclonal antibodies. The following sorting scheme were applied for FACS experiments:  Granuolocyte macrophage progenitor cells (GMPs): IL-7Rα-, Lin- ,Sca-1-, c-Kit+, Cd34+, FcγRII/III-high; Long-term hematopoietic stem cells (LT-HSCs) Lin-, Sca-1+, c-Kit+, Cd34-, Cd48-, Cd150+

tag: tissue type

value: bone marrow


title: LTearly_4_M2_grLT5


title: LTlate_3_M3grD2


title: wtGMP_4


title: LTlate_4_M3grG2


title: BMTGMP_4_M1grX


title: wtGMP_3


title: BMTGMP_2_M2grV


title: LTlate_2_M6grLT3


title: wtGMP_2


title: LTearly_2_M3grE2


title: LTearly_1_M2grLT3


title: BMTGMP_1_M1grV


title: LTearly_1_M2grD2


title: wtGMP_1


title: Jurkat_Pol2_Combo_THZ1_JQ1_4h

city: Cambridge

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: T-ALL

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

treatment_protocol: Jurkat cells treated with THZ1 (50 nM) and JQ1 (500 nM) in combination for 4 hours. RNA Pol2 ChIP-seq

value: Jurkat T-ALL cells

tag: treated with

value: THZ1 (50 nM) and JQ1 (500 nM) in combination for 4hrs

tag: chip antibody

value: RNA Pol II (Rpb1 N-terminus)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: THZ1_WCE

treatment_protocol: Jurkat cells treated with THZ1 (50 nM) for 4 hours -- this is WCE

value: THZ1 (50 nM) for 4hrs


title: Jurkat_Pol2_THZ1_50nM_4h

treatment_protocol: Jurkat cells treated with THZ1 (50 nM) for 4 hours. RNA Pol2 chip-seq


title: Combo_WCE

treatment_protocol: Jurkat cells treated with THZ1 (50 nM) and JQ1 (500 nM) for 4 hours -- this is WCE

value: THZ1 (50 nM) and JQ1 (500 nM) for 4hrs


title: Jurkat_Pol2_DMSO_4h

treatment_protocol: Jurkat cells treated with DMSO for 4 hours. RNA Pol2 chip-seq

value: DMSO for 4hrs


title: MYC

value: c-Myc


title: CDK7

value: Bethyl Labs


title: JQ1_WCE

treatment_protocol: Jurkat cells treated with JQ1 (500 nM) for 4 hours -- WCE

value: JQ1 (500 nM) for 4hrs


title: Jurkat_WCE


title: BRD4

value: Bethyl


title: Erythroid_H3K27me3

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
FASTQ format sequencing reads were mapped to the human genome (hg19 NCBI Build 37) using the BWA version 0.6.1 alignment program with default parameters.
The Model-based Alignment of ChIP-Seq (MACS) program version 1.4.0rc2 was used to identify CTCF and SA1 peaks using default parameters.
The SICER program version 1.1 was used to identify broad regions bound by H3K27me3
Genome_build: hg19
Supplementary_files_format_and_content: The CTCF and SA1 macs1.4 peaks bed output files have a fifth field that is -10*log10(pvalue).  The H3K27me3 files have additional SICER fields ChIP_island_read_count, CONTROL_island_read_count,p_value, fold_change, FDR_threshold

source_name: Erythroid Cell

growth_protocol: To obtain primary human erythroid cells, CD34+ cells were cultured and selected as described.(Panzenbock, B., Bartunek, P., Mapara, M. Y., and Zenke, M. (1998) Blood 92, 3658-3668.  Migliaccio, A. R., Migliaccio, G., Di Baldassarre, A., and Eddleman, K. (2002) Bone Marrow Transplant 30, 75-80) Briefly, Human CD34-selected stem and progenitor cells were cultured in StemSpan SF expansion medium (StemSpan 09650) with estradiol (100 ng/ml), dexamethasone (10 ng/ml), human transferrin (200 ng/ml), insulin (10 ng/ml), Flt3 ligand (100 ng/ml), stem cell factor (100 ng/ml), interleukin-3 (50 ng/ml), interleukin-6 (20 ng/ml), insulin-like growth factor 1 (50 ng/ml), and erythropoietin (3 U/ml) for 9 to 14 days. FACS analysis was used to analyze cellular expression of CD71 (transferrin receptor) and CD235a (glycophorin A). These cells represent the R3/R4 cell population of nucleated erythroid cells defined by Zhang et al.(Zhang, J., Socolovsky, M., Gross, A. W., and Lodish, H. F. (2003) Blood 102, 3938-3946)

extract_protocol:
ChIP assays were performed as previously described with minor variations (Steiner, L. A., Maksimova, Y., Schulz, V., Wong, C., Raha, D., Mahajan, M. C., Weissman, S. M., and Gallagher, P. G. (2009) Mol Cell Biol). 1 × 107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, followed by Dounce homogenization. Cross-linked nuclei were isolated, followed by sonication with a Covaris S2 shearing device (duty cycle 10%, intensity 5, 15 minutes), to obtain chromatin-containing DNA fragments with an average size of ~200-400bp. For each ChIP, 20 μg of antibody was used. Samples were immunoprecipitated with antibodies against antibody against CTCF (Millipore,07-729),  the SA-1 subunit of cohesin (Abcam, ab4457), trimethyl histone 3 lysine 27 (Abcam ab6002) or nonspecific rabbit IgG (sc-2091, Santa Cruz). The antigen-antibody complex was captured on protein G beads, washed four times with radioimmunoprecipitation assay buffer, and then washed with phosphate-buffered saline. The DNA-protein complex was eluted from the protein G beads with 1% sodium dodecyl sulfate at 65°C, and cross-linking of DNA-protein adducts was reversed by overnight incubation at 65°C.   After proteinase K and RNase digestion of the reverse-cross-linked sample, DNA was extracted with phenol-chloroform, precipitated with ethanol, then cleaned with the QIAquick PCR Purification Kit (Qiagen) according to manufacturer instructions.
ChIP libraries were prepared using the KAPA Library Preparation Kit (KAPA Biosystems) per the manufacturer's protocol. Briefly, ChIP DNA was end repaired, followed by addition of an adenine base at the 3' and NEXTflex ChIP-Seq Barcodes (BiooScientific) adaptor ligation. The modified DNA was then size selected on a 2% agarose and purified by using a gel extraction kit (Qiagen).  One microliter of size-selected adaptor ligated DNA was initially analyzed by SYBR Green Q-PCR to determine the number of cycles required to reach 50% of complete amplification.  Adaptor ligated DNA was PCR amplified with one initial heating step of 98°C for 45 second, followed by the pre-determined number of cycles with a melting temperature of 98°C for 15 s, an annealing temperature of 65°C for 30 s, and a product extension at 72°C for 30 s. At the end of the amplification, a final extension at 72°C for 1 min was performed. Amplified ChIP DNA was subjected to deep sequencing using standard Yale Center for Genome analysis protocols.

value: Erythroid

tag: antibody source

value: Abcam, ab6002


title: Erythroid_Total_Input

value: TI


title: Erythroid_SA1_2

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
FASTQ format sequencing reads were mapped to the human genome (hg19 NCBI Build 37) using the BWA version 0.6.1 alignment program with default parameters.
The Model-based Alignment of ChIP-Seq (MACS) program version 1.4.0rc2 was used to identify CTCF and SA1 peaks using default parameters.
The SICER program version 1.1 was used to identify broad regions bound by H3K27me3
Genome_build: hg19
Supplementary_files_format_and_content: The CTCF and SA1 macs1.4 peaks bed output files have a fifth field that is -10*log10(pvalue).  The H3K27me3 files have additional SICER fields ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold

value: Abcam, ab4457


title: Erythroid_rep3

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
FASTQ format sequencing reads were aligned to the hg19 genome using TopHat Version 2.0.4 software with default parameters
Reads in every gene were counted using htseq-count (http://www.ncbi.nlm.nih.gov/pubmed/25260700). Read counts per gene and log2 reads per kilobase per million reads were obtained using the edgeR package.
Genome_build: hg19
Supplementary_files_format_and_content: Counts per gene and log2 RPKM

extract_protocol:
RNA was prepared using the Qiagen RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.
Single end RNA libraries were prepared for sequencing using standard Illumina protocols at the Yale Center for Genome Analysis.