title: CDK9 inhibitor 8hr

city: emeryville

first: Zhenhai

last: Gao

state: California

address: 4560 Horton street

institute: Novartis Institute for Biomedical Research

description: CDK9 inhibitor treatment 8hr

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg19 genome using bowtie v.2.1.0
Aligned reads were filtered to remove reads with mapping quality < 20
PCR duplicate reads were marked using Picard v1.99 MarkDuplicates
Peaks were called and bedGraph files generated by running MACS v1.4.2 with options -B --nomodel --shiftsize 125 -g hs
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph for coverage, xls for peaks

source_name: HeLa cell line

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS. Cells were maintained at 37 °C under 5% CO2.

extract_protocol:
Nuclei were extracted from HeLa cells and sonicated using the Covaris instrument. The resulting chromatin was isolated from clarified from sonicated nuclei. The histone-DNA complexes were immunoprecipitated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the truseq chip-seq kit from illumina (IP-202-1012). Briefly the ends of DNA are repaired using a combination of T4 DNA polymerase and Klenow DNA polymerase. An 'A' base is then added to the blunt and phosphorylated ends using the Klenow fragment (3' to 5' exo minus), this prepares the fragments for ligation of the adapters which have a 'T' overhang in their 3' end. The illumina specific adapters are then ligated to the DNA fragments and the library is amplified by PCR. The resulting, size selected libraries were sequenced in the Illumina Hiseq 2000.

treatment_protocol: HeLa cells treated with DMSO or 0.3 μM i-CDK9 for 8 hr were cross-linked with 1% formaldehyde for 10 min. Cross-linking was quenched by the addition of glycine (0.125 M) for 5 min.

value: cell line

value: α-Pol II (Santa Cruz Biotechnology, sc-899 X)


title: CDK9 inhibitor 2hr

status: Public on Jun 17 2015

type: SRA

country: USA

description: CDK9 inhibitor treatment 2hr

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: chip antibody


title: DMSO 8hr

description: DMSO treatment 8hr


title: AOM_3 (RNA-seq)

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

library_source: transcriptomic

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
Transcriptome-mapping: tophat 2.0
Evaluation of differential expression: DESeq
Genome_build: mm9
Supplementary_files_format_and_content: Matrix-format created by DESeq containing the expression levels and p-values for differential expression

molecule: total RNA

organism: Mus musculus

source_name: colon epithel

extract_protocol:
For epithelial cell preparation from colon, colon was flushed with ice-cold PBS, cut open longitudinally. Distal and proximal colon region were processed separately. Each part was minced into small pieces in cold PBS. Enterocytes were mechanically isolated by shaking in PBS with 30 mM EDTA, at 37oC. Crypts were recovered and then stored at -80°C for RNA extraction. Only samples from distal colon were used in our study. Total RNA from the samples was isolated using the Fibrous Tissue Kit (Qiagen) according to the manufacturer’s instructions. The Poly(A)Purist™ MAG Kit (Ambion) was used for mRNA selection.
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.

tag: treatment

value: Treatment with DSS following treatment with AOM


title: AOM_1 (RNA-seq)


title: AOM_2 (RNA-seq)


title: DSS_4 (RNA-seq)

value: Treatment with DSS


title: Heatshock_rep2seqrep2

city: Palo Alto

first: Kevin

last: Van Bortle

state: CA

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

description: Small RNA

data_processing:
Small RNA-sequencing reads were mapped to the Dm6 release of the Drosophila genome using bowtie1.0.0, allowing one mismatch, and randomly assigning multi-mapping reads single alignment to the highest scoring region
Duplicate reads were removed using Samtools
Genome_build: Drosophila Dm6

organism: Drosophila melanogaster

source_name: Drosophila Kc167 cells

growth_protocol: Kc167 cells were grown in HyClone SFX cell culture medium.

extract_protocol:
Small RNAs were extracted using the mirVana isolation kit (Life technologies cat# AM1560)
Libraries were prepared and sequenced using Illuminia 50bp paired-end sequencing by the Genomics Services Lab at HudsonAlpha

treatment_protocol: For ecdysone treatment, cells were plated to 0.5 × 106 cells/mL and grown overnight. Cells were treated the following morning with 20-hydroxyecdysone (Sigma) at a final concentration of 5 × 10−7 M for 3 or 48 hr. Cells in both control, 0 h experiments were treated with ethanol.

value: Late-stage embryonic plasmatocyte

tag: cell line

value: 20min heat shock (37 degrees celcius)


title: Heatshock_rep1seqrep2

description: Small RNA


title: DMSO 2hr

description: DMSO treatment 2hr


title: MethylC-seq_VIP_neurons_rep1

city: Baltimore

first: Alisa

last: Mo

state: MD

address: 725 N. Wolfe St. PCTB805

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2014 (in submission)
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/ and Lister et al., 2013) for alignment and mC calling
MethylC-seq: DMRs were identified using methylpy (https://bitbucket.org/schultzmattd/methylpy/). For DMR calling, data from this study was combined with mouse whole fetal cortex (E13) and adult glia samples from Lister et al., 2017
MethylC-seq: UMRs and LMRs were identified using MethylSeekR [Burger et al. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155 (2013)] using m (methylation) = 0.5 and 5% FDR.
sample_supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
sample_supplementary_files_format_and_content: tab delimited text files of DMRs; columns in DMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - category (a 1 indicates the hypo-methylated cell type(s) using the order: Fetal, Excitatory, PV, VIP, Glia)
sample_supplementary_files_format_and_content: tab delimited text files of UMRs and LMRs; columns in UMRs/LMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - UMR or LMR
Genome_build: mm10

source_name: Vasoactive intestinal peptide-positive inhibitory neurons from mouse neocortex

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
The neocortex was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
MethylC-seq libraries were constructed as previously described [Lister R. et al. Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905 (2013)], except that samples were PCR amplified with KAPA HiFi HotStart Uracil+ ReadyMix (Kapa Biosystems KK2802) using the following PCR conditions: 2 minutes at 95°C, 4 cycles of [15 seconds at 98°C, 30 seconds at 60°C, 4 minutes at 72°C], and 10 minutes at 72°C. Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.

tag: strain

tag: genotype

value: VIP-cre; R26-LSL-CAG-Sun1-GFP-myc

tag: tissue

value: brain (neocortex)

value: vasoactive intestinal peptide-positive (VIP) inhibitory neurons

tag: age

value: 8 to 11 weeks

tag: Sex

value: male


title: IgG control

description: antibody isotype control

value: cell signaling cat. 2729S


title: Heatshock_rep1seqrep1

description: Small RNA


title: HMLER_Bound_MeDP

city: LYON cedex

first: Robert

last: Dante

address: Centre Léon Bérard 28, rue Laennec

department: Tumoral escape

country: France

institute: Cancer Research Center of Lyon

data_processing:
Reads were aligned on the UCSC Homo sapiens hg19 genome using Bowtie (0.12.7).
Duplicate reads were filtered using SAMTools rmdup.
Preliminary peak detection was performed using MACS 1.4.2.
Over sequenced regions were defined as 500 bp regions containing more than 3 times the median number of reads in at least 1 of the 2 inputs. Peaks were filtered against these over sequenced regions, as they represent suspicious false positive regions.
Peaks in HMEC-hTERT and HMLER were compared using MAnorm, and final peak lists were build as peaks common to both cell lines and cell line specific peaks (p value ≤ 0.01).
Reads were extended to 300 bp using Bedtools slop.
Bedgraph coverage files were obtained using Betools genomecov. Coverage value were converted in FPM using -scale.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks bed files contain 3 columns (chr, start, end). Begraph coverage files contain 4 columns (chr, start, end, FPM)

source_name: cell line

growth_protocol: HMEC-hTERT and HMLER cell lines were kindly provided by Anne-Pierre Morel (CRCL, Lyon, France). They were cultivated as previously described (Morel et al. PLoS One 2008).

extract_protocol:
Genomic DNA was sheared to a mean fragment length of 300-500 bp through sonication. Methylated-DNA precipitation (MeDP) was carried out using the MethylMiner Methylated DNA Enrichment Kit (Life Technologies) from 1µg of sheared DNA. Pools of 5 independent experiments, library preparation and high throughput sequencing (single-end 50 bp sequencing on Illumina HiSeq 2000) were performed at Beijing Genomics Institute (Hong-Kong, China). MBD2 Chromatin Immunoprecipitations (ChIP) were performed as previously described (Auriol et al. Nucleic Acids Research 2005). Briefly, sheared chromatin (with a mean fragment length between 300 and 500 bp) was obtained by sonication of formaldehyde cross-linked nuclei. ChIP was then performed with a custom-made rabbit polyclonal serum obtained after immunization with peptides corresponding to the N-terminal part of the MBD2 protein (Covalab, Villeurbanne, Lyon) (Perriaud et al. Curr. Pharm. Des 2013) using the ChIP Assay Kit (Merck Millipore, Saint-Quentin-en-Yvelines, France) as specified by the manufacturer’s instruction. Precipitated DNA was finally purified using NucleoSpin Gel and PCR Clean-up kit, (Macherey-Nagel) according to the manufacturer’s protocol “DNA clean-up of samples containing SDS”.
DNA-end was repaired to overhang a 3'-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification.

treatment_protocol: No treatments.

value: HMLER

tag: protocol

value: sonication, MeDP

tag: methylated dna capture

value: using a biotinylated MBD domain from MBD2 protein


title: 48hr20HE_rep2seqrep2

description: Small RNA

value: 48 hour ecdysone


title: DSS_1 (RNA-seq)


title: DSS_2 (RNA-seq)


title: HMEC-hTERT_Bound_MeDP

value: HMEC-hTERT


title: Control 2

city: Iowa City

first: xiangbing

last: meng

state: IA

address: 375 Newton Road

institute: University of Iowa

data_processing:
Illumina HiSeq 2000 and Off-Line Basecaller software(OLB V1.8.0) were used for basecalling.
Subsequently, 3’ adapter sequences were trimmed from clean reads (reads that passed Solexa CHASTITY quality filter) and any reads shorter than 15nt were discarded. Next the 3’-adapter-trimmed-reads (≥ 15nt) were aligned to the latest known human reference miRNA precursor set (Sanger miRBase 19) using Novoalign (v2.07.11). Reads (counts < 2) were discarded when calculating miRNA expression. In order to characterize the isomiR variability, any sequences that matched the miRNA precursors in the mature miRNA region ±4nt (no more than one mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin.
For piRNAs, the 3’-adapter-trimmed reads (length ≥ 15nt) were aligned to the latest piRNA set in piRNAbank using Novoalign software (v2.07.11). Expression of each piRNA was defined as the mapped tag counts.
Genome_build: n/a
Supplementary_files_format_and_content: counts

source_name: Testis

extract_protocol:
Testes were removed, flash frozen on dry ice, and RNA was harvested using the mirVana™ miRNA Isolation Kit reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: testis

value: post natal 6 months

value: wild type


title: 48hr20HE_rep2seqrep1

description: Small RNA


title: Control_3 (RNA-seq)

value: No treatment


title: Heatshock_rep2seqrep1

description: Small RNA

value: Late-stage embryonic plasmatocyte


title: Control_1 (RNA-seq)


title: 48hr20HE_rep1seqrep2

description: Small RNA


title: 3hr20HE_rep2seqrep2

description: Small RNA

value: 3 hour ecdysone


title: 3hr20HE_rep2seqrep1

description: Small RNA


title: 48hr20HE_rep1seqrep1

description: Small RNA


title: 121-3

city: Birmingham

first: Charles

last: Landen

state: AL

address: 619 19th St S

department: Obstetrics and Gynecology

institute: University of Alabama at Birmingham

data_processing:
The raw fastq files were aligned to human genome hg19 of a local instance of Partek Flow software package (Saint Louis, MO). Pre-alignment was conducted to determine if trimming is needed based on reads quality score.  Aligner STAR was used for best recovery.
The BAM files were loaded into Partek Genomics Suite 6.6 (Saint Louis, MO) for further analysis. The reads per kilobase of exon model per million mapped reads (RPKM)-normalized reads were calculated and the expression levels of genes were estimated.
Additional filter was applied to exclude genes of low expression.  The differential expressions were determined by using paired t-test.
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq-PDX-paired-tr-vs-untr_allintensity-filtered.txt: This file contains the RPKM for all mapped reads for all samples tested (treated and untreated ovarian PDX)

source_name: Treated Patient-Derived Xenograft (PDX)

growth_protocol: PDX tumors were established in the subcutaneou compartment of SCID mice using metastatic disease from ovarian cancer patients. Once tumors developed, each PDX line (one per patient) was stratified into treatment vs no treatment.

extract_protocol:
One week of the last dose of treatment, both treated and untreated PDX mice were sacrificed according to IACUC protocol. Fresh tumor tissue was harvested and snap frozen in liquid nitrogen or stored in RNAlater.
Sample preparation, raw data prepressing, quality control were conducted in UAB Genomics Core .  For RNA-seq, total RNA quality was assessed and the rRNA depleted and concentrated. The RNA-Seq libraries were prepared, validated and quantified using the TruSeq RNA library prep kit from Illumina following the manufacturer's directions.

treatment_protocol: PDX tumors that were in the treatment catergory received 4 doses of intraperitoneal combination chemotherapy once a week. Therapy was 90 mg/kg of carboplatin and 20 mg/kg of paclitaxel.

value: Human ovarian PDX tumor


title: 116-3


title: 115-6


title: Control_2 (RNA-seq)


title: 121-2

source_name: Untreated Patient-Derived Xenograft (PDX)


title: DSS_3 (RNA-seq)

value: Treatment with DSS


title: 3hr20HE_rep1seqrep2

description: Small RNA


title: 116-2b


title: 136-3


title: 115-2


title: AOM_3

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig-format containing the genomic methylation ratios of the respective sample

extract_protocol:
For epithelial cell preparation from colon, colon was flushed with ice-cold PBS, cut open longitudinally. Distal and proximal colon region were processed separately. Each part was minced into small pieces in cold PBS. Enterocytes were mechanically isolated by shaking in PBS with 30 mM EDTA, at 37oC. Crypts were recovered and then stored at -80°C for DNA extraction. Only samples from distal colon were used in our study.
5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

value: Treatment with DSS following treatment with AOM


title: 108-3


title: 136-2c


title: DSS_3


title: AOM_1


title: AOM_2


title: 3hr20HE_rep1seqrep1

description: Small RNA


title: 108-2


title: 0hr20HE_rep2seqrep2

description: Small RNA

value: 0 hour ecdysone


title: 0hr20HE_rep2seqrep1

description: Small RNA


title: 106-3


title: DSS_2


title: DSS_1


title: 0hr20HE_rep1seqrep2

description: Small RNA


title: 106-2


title: Control_3


title: 0hr20HE_rep1seqrep1

description: Small RNA


title: Control_1


title: FAIRE_Dmel_CS_EA

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

data_processing:
Reads with residual adapter sequences were discarded (FastX cliper version 0.012 option -M15)
Reads were mapped against their own-species genome by  Bowtie2 (default parameters)
Species alignments were converted to D.melanogaster coordinates by liftOver tool from UCSC (minMatch=0.1)
F-Seq (Boyle et al. 2008) was used to detect nucleosome-free regions in relation to background signal (parameters l=200)
HT-Seq was used to count the number of reads falling within a called peak
Genome_build: Drosophila melanogaster FB5
Supplementary_files_format_and_content: Peak position and original as well as normalized counts

source_name: eye-antennal imaginal disc

growth_protocol: All flies were raised at 25 degrees Celsius on standard fly food

extract_protocol:
Nucleosome-depleted regions were extracted with phenol/chloroform followed by ethanol precipitation and RNAse A treatment.
Libraries were prepared for sequencing using standard Illumina Truseq protocols

treatment_protocol: FAIRE-Seq was perfomed in accordance to (Giresi et al. 2007). Eye-antennal imaginal discs were dissected in PBT and cross-linked in 4% formaldehyde for 10 min. Chromatin was isolated using a 3-step lysis protocol and next it was subjected to a ten-cycle sonication (30 seconds on/off).

tag: developmental time point

value: third instar wandering larvae

value: eye-antennal imaginal disc

value: Canton S

tag: stock


title: Control_2


title: FAIRE_Dmel_FRT82_EA


title: AE9aId1fl_fl4OHT48H-1

status: Public on Jun 16 2015

city: Miami

first: Lan

last: Wang

address: 1501 NW 10TH AVE BRB 701

institute: University of Miami

data_processing:
Illumina Casava1.80 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 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 cuffdiff (FPKM model).
Genome_build: mm9
Supplementary_files_format_and_content: text files contain gene ID, locus, FPKM value, fold change and p value.

source_name: leukemia cell

extract_protocol:
RNA was isolated from AE9a cells  using the Qiagen RNeasy Plus® mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leukemia cell


title: AE9aId1CBD15uM16H-1


title: AE9aId1fl_fl4OHT48H-2


title: AE9aId1fl_flControl_2


title: AE9aId1fl_flControl-1


title: AE9aId1CBD15uM16H-2


title: H3K9me2-ChIP-Seq-in-Mutant-newborn-mouse-liver

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by BGI, Shenzhen
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with only unique mapped reads were kept
Data were filtered using samtools to remove potential PCR duplicates
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension 300 bp, and then normalized to 10 M of depth.

extract_protocol:
Chromatin Immunoprecipitation were performed according to Diagenode IDeal ChIP-seq Kit with minor modifications. Briefly, 2 million cells were harvested in PBS and crosslinked in 1% formaldehyde for 2 minutes. After sonication, chromatin from 1 million cells was subjected to ChIP using IDeal ChIP-seq Kit. For RNA-Seq, RNA samples were extracted using Trizol reagent, and genomic DNA contaminations were eliminated with TurboTM DNase (Life technologies).
ChIP-seq libraries were constructed with KAPA Library Preparation Kits and single-end sequenced with Hiseq 2000. For RNA-Seq, total RNA were extracted and the subsequent library preparation steps were carried out according to standard Illumina procedures at the NIBS sequencing center and subjected to single-end sequencing.

treatment_protocol: For RA induction, 1 uM all-trans retinoic acid was added into medium and LIF was withdrawn simultaneously.

value: liver

tag: developmental stage

value: newborn

tag: strain background

value: C57BL/6 (mixed)

tag: genotype/variation

value: GLP mutant (GLP 3A) homozygous

value: H3K9me2, mAbcam 1220


title: input-of-H3K9me2-in-Mutant-newborn-mouse-liver


title: H3K9me2-ChIP-Seq-in-WT-newborn-mouse-liver

source_name: WT-newborn-mouse-liver

value: wild type


title: input-of-H3K9me2-in-WT-newborn-mouse-liver


title: MNase-seq Low MNase concentration rep1

city: La Jolla

first: Haruhiko

last: Ishii

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

data_processing:
CASAVA 1.8.2 was used for base-calling.
Reads for all the data except for the RNA-seq data were mapped using bowtie to the mm9 genome assembly using the options -X 500 -y -v 3 -m 1 --best --strata --time -p 4 -S. When the read length was 100, the reads were trimmed using the option --trim3 50.
Reads for RNA-seq data were mapped using TopHat using options --bowtie1 -r 100 -p 20 --keep-tmp --no-coverage-search.
Genome_build: mm9

source_name: J1 Embryonic Stem Cells

growth_protocol: J1 mouse embryonic stem cells were maintained on a feeder layer of irradiated mouse embryonic fibroblasts (Global Stem) on gelatin-coated plates in medium composed of Dulbecco's modified Eagle's medium (DMEM) with 4.5 g/L glucose, L-glutamine and sodium pyruvate (Corning 10-013-CV), supplemented with 15% heat-inactivated FBS (Hyclone), 0.1mM 2-mercaptoethanol, 0.1mM nonessential amino acids (Gibco), 2 mM L-alanyl-L-glutamine dipeptide (Gibco), penicillin-streptomycin (Gibco), and 1000 units/mL Leukemia Inhibitory Factor (EMD Millipore). Before the experiments, J1 cells were passaged twice on feeder-free gelatin-coated plates.

extract_protocol:
Nuclei were treated with MNase. The reaction was quenched by addition of EDTA to 10 mM. Proteins were removed by digestion with proteinase K, extraction with phenol and chloroform, and precipitation with ethanol. RNA was removed by digestion with RNase A, extraction with phenol and chloroform, and precipitation with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.

value: Embryonic Stem Cells


title: MNase-seq Standard MNase concentration rep2


title: MPE-seq 30 min rep2

data_processing:
Library strategy: MPE-Seq
CASAVA 1.8.2 was used for base-calling.
Reads for all the data except for the RNA-seq data were mapped using bowtie to the mm9 genome assembly using the options -X 500 -y -v 3 -m 1 --best --strata --time -p 4 -S. When the read length was 100, the reads were trimmed using the option --trim3 50.
Reads for RNA-seq data were mapped using TopHat using options --bowtie1 -r 100 -p 20 --keep-tmp --no-coverage-search.
Genome_build: mm9

extract_protocol:
Nuclei were treated with MPE-Fe(II). The reaction was quenched by addition of bathophenanthroline to ~6 mM. Proteins were removed by digestion with proteinase K, extraction with phenol and chloroform, and precipitation with ethanol. RNA was removed by digestion with RNase A, extraction with phenol and chloroform, and precipitation with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.


title: MPE-seq 10 min rep2


title: MPE-seq 20 min rep2


title: Genomic DNA digested with MNase rep2

extract_protocol:
Genomic DNA was treated with MNase. The reaction was quenched by addition of EDTA to 16 mM. The sample was digested with proteinase K, was extracted with phenol and chloroform, and was precipitated with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.


title: Rev-erbalpha_ChIP-exo_rep1

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

description: antibody: Rev-erba (Cell Signaling Technology #2124)

data_processing:
Library strategy: ChIP-exo
Sequenced reads from two biological replicates were pooled and aligned to the mouse genome (mm9) using bowtie v1.1.1(Langmead et al., 2009) with parameters ‘–n 1 and –m 1’. ChIP-exo peak call on the forward and reverse strands was performed using MACE-1.0 (Liguo Wang et al.,2014) with default parameters. The most prevalent ChIP-exo peaks were selected from within published Rev-erbalpha ChIP-seq peaks (Bin Fang et al., 2014).
Genome_build: mm9
Supplementary_files_format_and_content: UCSC genome browser tracks (bigwig files) and ChIP-seq peak calls (bed files) were generated by HOMER.ChIP-exo peak calls (bed files) were generated by MACE.

source_name: liver

extract_protocol:
The ChIP-exo portion of the protocol was performed as sdescribed (4) with modifications making the assay compatible with the Illumina sequencing platform. Briefly, it was performed in essentially the same way as ChIP-seq, except that after the end repair and nick repair, the DNA was digested by the lambda (M0262, NEB) and RecJf exonucleases (M0264, NEB), while it is still on the agarose beads. Then, the DNA samples were eluted from the beads and are analyzed by high-throughput sequencing.
The ChIP-exo portion of the protocol was performed as sdescribed (H. S. Rhee and B. F. Pugh, 2011) with modifications making the assay compatible with the Illumina sequencing platform. Briefly, it was performed in essentially the same way as ChIP-seq, except that after the end repair and nick repair, the DNA was digested by the lambda (M0262, NEB) and RecJf exonucleases (M0264, NEB), while it is still on the agarose beads. Then, the DNA samples were eluted from the beads and are analyzed by high-throughput sequencing.

tag: time

value: ChIP-exo

tag: target

value: Rev-erbalpha

tag: genome build

value: C57BL/6J Wild Type


title: HDAC3_KO_liver_ZT10_rep2

description: antibody: HDAC3 (Abcam ab7030)

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm9) using Bowtie v0.12.8 (Langmead et al., 2009) with parameters with parameters ‘-n 2 -l 30 -m 1’. Only one uniquely aligning read per genomic position was kept for further analysis. Aligned reads from biological replicates were pooled together and peak calling was performed with HOMER (Heinz et al., 2010), using corresponding input in the same tissue.
Genome_build: mm9
Supplementary_files_format_and_content: UCSC genome browser tracks (bigwig files) and ChIP-seq peak calls (bed files) were generated by HOMER.ChIP-exo peak calls (bed files) were generated by MACE.

extract_protocol:
ChIP experiments were performed as described (Feng et al. 2011) with minor changes. Mouse liver, brain (ventral tegmental area), and epididymal white adipose tissue (eWAT) were harvested, minced and cross-linked in 1% formaldehyde for 20min, followed by quenching with 1/20 volume of 2.5M glycine solution for 5 min, and two washes with 1×PBS. Nuclear extracts were prepared by Dounce homogenization in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC). Chromatin fragmentation was performed by sonication in lysis buffer (50mM Tris-HCL ph 8.0, 0.1%SDS, 10mM EDTA), using the Bioruptor (Diagenode). Proteins were immune-precipitated in ChIP buffer, and crosslinking was reversed overnight at 65°C in SDS buffer (50mM Tris-HCL, 10mM EDTA, 1% SDS, pH 8), and DNA isolated using phenol/chloroform/isoamyl alcohol.
DNA was amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina, using adaptor oligo and primers from Illumina, enzymes from New England Biolabs and PCR Purification Kit and MinElute Kit from Qiagen.

value: ChIP-seq

value: C57BL/6J HDAC3 KO


title: HDAC3_KO_liver_ZT10_rep1

description: antibody: HDAC3 (Abcam ab7030)


title: FAIRE_Dpse_EA

organism: Drosophila pseudoobscura

value: Dpse\wild-type


title: HDAC3_liver_reverbalphaKO_betaKD_ZT10

description: antibody: HDAC3 (Abcam ab7030)

value: C57BL/6J Rev-erbaKO/bKD


title: RORgamma_liver_ZT22

description: antibody: RORg (Santa Cruz Biotechnology sc28559)

value: RORgamma

value: C57BL/6J RORg KO


title: Rev-erbalpha_ChIP-exo_rep2


title: Genomic DNA digested with MPE-Fe(II) rep2

extract_protocol:
Genomic DNA was treated with MPE-Fe(II). The reaction was quenched by addition of bathophenanthroline to ~6 mM. DNA was precipitated with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.

tag: cell type


title: RORgamma_liver_ZT10


title: Rev-erbalpha_brain_ZT10

source_name: brain(ventral tegmental area)

value: brain(ventral tegmental area)


title: Rev-erbalpha_WT_liver_ZT10_rep2

value: liver


title: input_eWAT

description: antibody: none

source_name: eWAT

value: eWAT


title: HDAC3_liver_ZT10

description: antibody: HDAC3 (Abcam ab7030)


title: HDAC3_liver_reverbGFP_ZT10_rep2

description: antibody: HDAC3 (Abcam ab7030)

value: C57BL/6J Rev-erba/b floxed/AAV-GFP


title: HDAC3_liver_Rev-erbsflCRE(DBDm)_ZT10_rep1

description: antibody: HDAC3 (Abcam ab7030)

value: C57BL/6J Rev-erba DBD mutant/b KO


title: HDAC3_liver_reverbGFP_ZT10_rep1

description: antibody: HDAC3 (Abcam ab7030)


title: HDAC3_liver_Rev-erbsflCRE(DBDm)_ZT10_rep2

description: antibody: HDAC3 (Abcam ab7030)


title: MNase-seq Low MNase concentration rep2

tag: cell line


title: RORalpha_liver_ZT10

description: antibody: RORa (Santa Cruz Biotechnology sc28612)

tag: strain

value: RORalpha

value: C57BL/6J RORa KO


title: Rev-erbalpha_DBD_mutant_liver_ZT10_rep2

tag: genotype


title: Rev-erbalpha_DBD_mutant_liver_ZT10_rep1

tag: tissue


title: SUPeR-seq_zygote5

first: Xiaoying

last: Fan

state: Beijing

address: 5 Yiheyuan Road

department: College of Life Sciences

institute: Peking University

description:
extracted from female mouse
single cell RNA-seq

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the mouse refference genome (mm10) using BWA software
gene expression level was estimated using comstomized Perl scripts.
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: txt files reflect FPKM of each gene in Refseq.

source_name: mouse zygote

growth_protocol: Mouse embryonic stem cells were maintained without feeders on gelatinlized dishes in the presence of 1,000U/ml leukemia inhibitory factor (LIF, Millipore) in Dulbecco's Modification of Eagle's Medium (DMEM/F-12, Gibco) containing 20% fetal calf serum (FCS, Gibco) for routine passage while the HKE293T cells were cultured in DMEM/High glucose. Metaphse II oocytes ,zygotes and 2-cell embryos (after mating with CD-1 male mice) were recovered from the oviduct ampulla of super-ovulated mice of CD-1 strain.

extract_protocol:
Single cells were picked into the lysis buffer which contained Rnase inhibitor to prevent RNA degration
Cells were picked into the lysis buffer to release all RNAs; then the released RNAs were reverse transcribed with SuperScript III(Invitrogen), then digested the unreacted primers with ExoSAP-IT(USB) and tailed the first strand cDNA with a poly(A) sequence with terminal deoxynucleotidyl transferase (TdT, Invitrogen) , then used poly(T) primers to synthesize the sencond strand cDNA.the cDNAs were then enriched by two rounds of PCR amplifications each with size-selection by 2% agarose gel recovery.then the library construction waa conducted following the illumina library preparing protocol. The quality-ensured libraries were used for pair-end deep sequencing on Illumina HiSeq Sequencer.

treatment_protocol: To validate the zygotic genes in mouse embryonic development, we treated the mouse zygotes with 0.1mg/ml a-Amanitine and then collected the 2-cell embryos to build libraries with SUPeR-seq

value: zygote

tag: gender

value: female


title: SUPeR-seq_TE5

source_name: mouse blastocyst

value: blastocyst


title: SUPeR-seq_TE2


title: Rev-erbalpha_129mice_WT_liver_ZT10_rep1

value: Rev-erbalpha

value: 129S1/SvlmJ Wild Type


title: Small RNA Solexa Sequencing of Regulatory Dendritic Cells

city: Shanghai

first: Xiaoping

last: Su

address: 800 Xiangyin Road

institute: National Key Laboratory of Medical Immunology & Institute of Immunology

description: 18-30 nt small RNA

data_processing:
Sequence alignments were performed using BWI.
Sequencing data alignments were mainly analyzed using the SOAP (Short Oligonucleotide Alignment Program) (http://soap.genomics.org.cn) algorithm.
Genome_build: miRBase release 19.0
Supplementary_files_format_and_content: Text file that is linked to the Sample (GSMxxx) record includes miRNA sequences and raw counts.
Supplementary_files_format_and_content: Text file that is linked to the Series (GSE45882) record includes miRNA names, sequences, and normalized counts.

source_name: immune cells, DCreg

growth_protocol: To purify HSCs, bone-marrow cells were stained with antibodies, and the c-Kit+ Sca1+ Lineage- population was sorted using a MoFlo XDP cell sorter (Beckman Coulter), the purity of which was confirmed to be >95%. Bone marrow mononuclear cells were prepared from mouse (5–6 weeks old) femur bone marrow suspensions by depletion of red cells, and mouse imDCs were prepared from bone marrow progenitors by culturing in 10 ng/mL rmGM-CSF and 1 ng/mL rmIL-4 as described previously. Nonadherent cells were gently washed out on day 4 of culture; the remaining loosely adherent clusters were cultured for an additional 4 to 5 days in the presence of 10 ng/mL LPS. At day 8, maDCs were positively selected using CD11c magnetic microbeads (Miltenyi Biotec, Auburn, CA). The cells cultured only with the same concentrations of GM-CSF and IL-4 for 6 days were harvested as imDCs. DCreg were generated as described previously. Once monolayers of endothelial-like splenic stromal cells (ESSCs) had reached 50% to 60% confluence, maDCs were seeded at a density of 2 ×10^6 per 5 mL/well in 6-well plates in RPMI1640 medium supplemented with 5% FCS for at least 7 days. DCreg were washed off the layer using 0.1% trypsin and 5 mM EDTA, and purified using CD11c magnetic microbeads.

extract_protocol:
Total RNA, containing miRNA, was extracted using the mirVana miRNA Isolation Kit (Ambion) and passed the RNA quality control for Solexa sequencing.
Briefly, after PAGE purification of small RNA molecules under 30 bases and ligation of a pair of Solexa adaptors to their 5' and 3' ends, the small RNA molecules were amplified using the adaptor primers for 12 cycles and the fragments around 90 bp (small RNA+adaptors) were isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's Solexa Sequencer according to the manufacturer's instructions. Then the image files generated by the sequencer were processed to produce digital-quality data. The subsequent procedures performed with Solexa were summarizing data production, evaluating sequencing quality, calculating length distribution of small RNA reads and filtrating reads contaminated by rRNA, tRNA, mRNA, snRNA, and snoRNA. Finally, clean reads were compared with a miRBase database (release 19.0) and the copy numbers of each unique sequence were calculated.

value: regulatory dendritic cells


title: Small RNA Solexa Sequencing of Mature Dendritic Cells

description: 18-30 nt small RNA

source_name: immune cells, maDC

value: mature dendritic cells


title: SUPeR-seq_morula3

source_name: mouse morula

value: morula


title: input_brain

description: antibody: none

value: ChIP-seq

value: C57BL/6J Wild Type


title: Rev-erbalpha_eWAT_ZT10_rep2


title: Rev-erbalpha_WT_liver_ZT10_rep1


title: rRNA-mRNA-depleted-1

description: rRNA-mRNA-depleted RNA-seq

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the mouse refference genome (mm10) using BWA software
gene expression level was estimated using comstomized Perl scripts.
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: txt files reflect RPKM of each gene in Refseq.

source_name: human HEK293T cell

value: human HEK293T cell

tag: passage

value: diluted from HEK293T cell total RNA


title: Small RNA Solexa Sequencing of Immature Dendritic Cells

description: 18-30 nt small RNA

source_name: immune cells, imDC

value: immature dendritic cells


title: Rev-erbalpha_eWAT_ZT10_rep1

value: eWAT


title: SUPeR-seq_zygote4


title: SUPeR-seq_zygote3


title: SUPeR-seq_ICM2


title: SUPeR-seq_ICM5


title: SUPeR-seq_ICM1


title: Rev-erbalpha_129mice_WT_liver_ZT10_rep2

value: liver


title: SUPeR-seq_TE1


title: SUPeR-seq_morula2


title: SUPeR-seq_morula1


title: SUPeR-seq_blastocyst3


title: Small RNA Solexa Sequencing of Hematopoietic Stem Cells

description: 18-30 nt small RNA

source_name: immune cells, HSC

value: hematopoietic stem cells


title: SUPeR-seq_blastocyst2


title: HEK-pool-spllt-9

description: single cell RNA-seq


title: RNASeq H9RET rep2

city: Bethesda

first: Peng

last: Li

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: treated with H9RET for 4h

data_processing:
For RNA-Seq and ChIP-Seq, basecalls performed using CASAVA 1.8
Raw reads were aligned to the hg18 human genome assembly using Bowtie 0.12.4
Aligned reads are converted to BED format (for RNA-Seq analysis) or BED format with duplicated reads removed (for ChIP-Seq analysis) using unpublished python and perl scripts
For RNA-Seq, reads per kilobase of exon per megabase of library size (RPKM) were calculated using hg18 RefSeq database
For ChIP-Seq, peaks are called using MACS 1.4.2 and visualized using IGV browser
Genome_build: hg18 (NCBI build 36.1)
Supplementary_files_format_and_content: BED files are generated using CASAVA pipeline 1.8 and unpublished python scripts

source_name: Pre-activated CD8+ T cells

growth_protocol: Buffy coats were obtained from healthy donors from the NIH Blood Bank, and peripheral blood mononuclear cells (PBMCs) were isolated by gradient centrifugation using lymphocyte separation medium (Mediatech, Inc., VA). Cells were isolated using the human CD8+ T-cell Isolation kit I (Miltenyi Biotec, Germany). For pre-activating cells, 6- well plates were pre-coated with 2 μg/ml of plate-bound anti-CD3 mAb (BD Biosciences). Cells were seeded at 1 x 106 cells/ml in complete medium (RPMI medium supplemented with glutamine, penicillin, streptomycin, and 10% FBS) with 1 μg/ml  soluble anti-CD28 mAb (BD Biosciences) for 3 days and then rested for 48 h in fresh medium.

extract_protocol:
For RNA-Seq,  RNA from 5 donors was pooled, and 1 μg of the pooled RNA was used to synthesize cDNA 220-400 bp fragments were isolated using 2% E-Gel (Invitrogen), ends were repaired, adaptor was added using T4 DNA ligase (New England Biolabs), and amplified for 17 cycles using PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs). For ChIP-Seq, Chromatin from 10-20 million cells was sonicated into 250-500 bp fragments, DNA ends were repaired using polynucleotide kinase and Klenow enzyme, and treated with Taq polymerase to generate a protruding 3’ “A” nucleotide. DNA fragments of ~250-450 bp were purified from agarose gels and used for cluster generation and sequencing. Antibody against STAT5B was used for immunoprecipitation.
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform.

treatment_protocol: For RNA-Seq, pre-activated human CD8+ T-cells were rested for two days in complete medium, stimulated for 4 hr with 1 μg/ml of wild type IL-2, H9, H9-RET, or H9-RETR, and total RNA from 5 x 106 cells was isolated (RNeasy kit, Qiagen, Valencia, CA). For ChIP-Seq, pre-activated CD8+ T-cells were treated with different cytokines for 90 min and then chemically cross-linked with 1% paraformaldehyde.

value: Peripheral blood

value: Pre-activated CD8+ T cells


title: RNASeq H9 rep2

description: treated with H9 for 4h


title: RNASeq IL2 rep2

description: treated with IL-2 for 4h


title: RNASeq H9RETR rep2

description: treated with H9RETR for 4h


title: rRNA-mRNA-depleted-2

description: rRNA-mRNA-depleted RNA-seq


title: HEK-pool-spllt-8

description: single cell RNA-seq


title: SUPeR-seq_8-cell3

source_name: mouse 8-cell

value: 8-cell embryo

value: female


title: SUPeR-seq_blastocyst1

value: blastocyst


title: SUPeR-seq_8-cell2


title: SUPeR-seq_4-cell3

source_name: mouse 4-cell

value: 4-cell embryo


title: SUPeR-seq_8-cell1


title: HEK-pool-spllt-7

description: single cell RNA-seq


title: RNASeq Control rep2

description: untreated


title: HEK-pool-spllt-10

description: single cell RNA-seq


title: SUPeR-seq_4-cell1


title: SUPeR-seq_2-cell3

source_name: mouse 2-cell

value: 2-cell embryo


title: SUPeR-seq_4-cell2


title: SUPeR-seq_2-cell1


title: HEK-pool-spllt-4

description: single cell RNA-seq


title: HEK-pool-spllt-6

description: single cell RNA-seq


title: SUPeR-seq_2-cell2


title: mouse_ESC_total_RNA_bulk

description:
22-25
illumina RNA sequencing

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the reference genome using BWA software
gene expression level was estimated using comstomized Perl scripts.
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: txt files reflect RPKM of each gene in Refseq.

source_name: mouse ES cell

extract_protocol:
Single cells were picked into the lysis buffer which contained Rnase inhibitor to prevent RNA degration
Cells were picked into the lysis buffer to release all RNAs; then the released RNAs were reverse transcribed with SuperScript III(Invitrogen), then digested the unreacted primers with ExoSAP-IT(USB) and tailed the first strand cDNA with a poly(A) sequence with terminal deoxynucleotidyl transferase (TdT, Invitrogen) , then used poly(T) primers to synthesize the sencond strand cDNA.the cDNAs were then enriched by two rounds of PCR amplifications each with size-selection by 2% agarose gel recovery then the library construction waa conducted following the illumina library preparing protocol. The quality-ensured libraries were used for pair-end deep sequencing on Illumina HiSeq2000 and Illumina HiSeq2500 Sequencers.

value: ES cell


title: RNASeq H9RETR rep1

description: treated with H9RETR for 4h


title: RNASeq H9RET rep1

description: treated with H9RET for 4h


title: HEK-pool-spllt-5

description: single cell RNA-seq


title: HEK-pool-spllt-3

description: single cell RNA-seq


title: HEK-pool-spllt-1

description: single cell RNA-seq


title: SUPeR-seq_a-AM_treated_2-cell2-2

description: single cell RNA-seq

source_name: mouse 2-cell embryo


title: SUPeR-seq_2-cell3-2

description: single cell RNA-seq


title: RNASeq Control rep1

description: untreated


title: SUPeR-seq_a-AM_treated_2-cell1-2

description: single cell RNA-seq


title: SUPeR-seq_a-AM_treated_2-cell2-1

description: single cell RNA-seq


title: SUPeR-seq_2-cell2-1

description: single cell RNA-seq


title: SUPeR-seq_2-cell2-2

description: single cell RNA-seq


title: SUPeR-seq_2-cell3-1

description: single cell RNA-seq


title: Tang2009-HEK293T3

description: single cell RNA-seq


title: ChIPSeq H9RETR STAT5B rep2

description:
treated with H9RETR
ChIP against STAT5B

tag: chip antibody

value: STAT5B (Invitrogen, 135300, LOT-1477602A)


title: Tang2009-HEK293T2

description: single cell RNA-seq


title: ChIPSeq H9RET STAT5B rep2

description:
treated with H9RET
ChIP against STAT5B


title: HEK-pool-spllt-2

description: single cell RNA-seq


title: RNASeq IL2 rep1

description: treated with IL-2 for 4h


title: SUPeR-seq_2-cell1-1

description: single cell RNA-seq


title: ChIPSeq H9 STAT5B rep2

description:
treated with H9
ChIP against STAT5B


title: SUPeR-seq_2-cell1-2

description: single cell RNA-seq


title: RNASeq H9 rep1

description: treated with H9 for 4h


title: SUPeR-seq_zygote2

description: single cell RNA-seq

value: zygote


title: ChIPSeq IL2 STAT5B rep2

description:
treated with IL-2
ChIP against STAT5B


title: ChIPSeq Control STAT5B rep2

description:
untreated
ChIP against STAT5B


title: SUPeR-seq_zygote1

description: single cell RNA-seq


title: SUPeR-seq_a-AM_treated_2-cell1-1

description: single cell RNA-seq


title: SUPeR-seq__HEK293T7

description: single cell RNA-seq


title: SUPeR-seq_oocyte3

description: single cell RNA-seq

source_name: mouse oocyte

value: oocyte


title: Tang2009-HEK293T1

description: single cell RNA-seq


title: SUPeR-seq__HEK293T6

description: single cell RNA-seq


title: ChIPSeq H9RETR STAT5B rep1

description:
treated with H9RETR
ChIP against STAT5B


title: SUPeR-seq_oocyte1

description: single cell RNA-seq


title: SUPeR-seq__HEK293T5

description: single cell RNA-seq


title: SUPeR-seq_oocyte2

description: single cell RNA-seq


title: SUPeR-seq_oocyte5

description: single cell RNA-seq


title: SUPeR-seq_oocyte4

description: single cell RNA-seq


title: SUPeR-seq_1ng2

description: single cell RNA-seq

value: diluted from ESC total RNA


title: SUPeR-seq__HEK293T4

description: single cell RNA-seq


title: ChIPSeq H9RET STAT5B rep1

description:
treated with H9RET
ChIP against STAT5B


title: SUPeR-seq_1ng1

description: single cell RNA-seq


title: SUPeR-seq__HEK293T3

description: single cell RNA-seq


title: ChIPSeq H9 STAT5B rep1

description:
treated with H9
ChIP against STAT5B


title: SUPeR-seq_10pg4

description: single cell RNA-seq


title: SUPeR-seq_100pg2

description: single cell RNA-seq


title: SUPeR-seq_100pg1

description: single cell RNA-seq


title: SUPeR-seq_10pg3

description: single cell RNA-seq


title: ChIPSeq Control STAT5B rep1

description:
untreated
ChIP against STAT5B


title: SUPeR-seq_10pg1

description: single cell RNA-seq


title: Tang2009_ESC2

description:
22-25
single cell RNA-seq


title: SUPeR-seq_10pg2

description: single cell RNA-seq


title: rRNA-depleted_HEK293T4

description:
diluted from HEK293T cell total RNA
rRNA-depleted RNA sequencing

tag: rna type

value: rRNA-depleted RNA prep


title: Tang2009_ESC1

description:
22-25
single cell RNA-seq


title: rRNA-depleted_HEK293T3


title: Tang2009_ESC3

description:
22-25
single cell RNA-seq


title: SUPeR-seq_ESC3

description:
22-25
single cell RNA-seq


title: SUPeR-seq_ESC1

description:
22-25
single cell RNA-seq


title: rRNA-depleted_HEK293T2


title: SUPeR-seq_ESC2

description:
22-25
single cell RNA-seq


title: rRNA-depleted_HEK293T1

description:
diluted from HEK293T cell total RNA
rRNA-depleted RNA sequencing
RNA-seq (single cell)

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the mouse refference genome (mm10) using BWA software
gene expression level was estimated using comstomized Perl scripts.
Genome_build: mm10
Supplementary_files_format_and_content: txt files reflect FPKM of each gene in Refseq.


title: ChIPSeq IL2 STAT5B rep1

description:
treated with IL-2
ChIP against STAT5B


title: Bulk_mRNA_HEK293T2

description:
diluted from HEK293T cell total RNA
illumina RNA sequencing
RNA-seq (single cell)

value: Bulk mRNA prep


title: Bulk_mRNA_HEK293T4


title: Bulk_mRNA_HEK293T3


title: SUPeR-seq__HEK293T2

description: single cell RNA-seq


title: CD11c+Ia low cells

description: 18-30 nt small RNA

data_processing:
Sequencing data alignment were mainly analyzed using SOAP (Short Oligonucleotide Alignment Program) (http://soap.genomics.org.cn) algorithm.
Then the image files generated by the sequencer were processed to produce digital-quality data. The subsequent procedures performed with Solexa were summarizing data production, evaluating sequencing quality, calculating length distribution of small RNA reads and filtrating reads contaminated by rRNA, tRNA, mRNA, snRNA, and snoRNA. Finally, clean reads were compared with a miRBase database (release 19.0) and the copy numbers of each unique sequence were calculated.
Supplementary_files_format_and_content: Text files containing clean tags, 18-30 nt, tab delimited, length | number | sequence

source_name: immune cells

growth_protocol: To purify CD11c+Ia high and CD11c+Ia low cells, CD11c+ cells enriched by CD11c-conjugated microbeads from spleen were stained with fluorescently labeled anti-Ia-FITC, and then CD11c+Ialow cells and CD11c+Iahigh cells were sorte  using a MoFlo XDP cell sorter (Beckman Coulter), the purity of which was confirmed to be >95%.

extract_protocol: Briefly, after PAGE purification of small RNA molecules under 30 bases and ligation of a pair of Solexa adaptors to their 5' and 3' ends, the small RNA molecules were amplified using the adaptor primers for 12 cycles and the fragments around 90 bp (small RNA+adaptors) were isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's Solexa Sequencer according to the manufacturer's instructions.

treatment_protocol: Total RNA, containing miRNA, was extracted using mirVana miRNA Isolation Kit (Ambion) and passed the RNA quality control for Solexa sequencing.

value: dendritic cells


title: Bulk_mRNA_HEK293T1


title: C666 PAR-CLIP

city: Durham

first: Dong

last: Kang

state: North Carolina

address: BOX 3025 213 Research Drive, Duke University

department: Molecular Genetics and Microbiology

institute: Duke University

description:
barcode: TCGTATGCCGTCTTCTGCTTGT
Protocol: PAR-CLIP

data_processing:
reads were first filtered allowing for up to three mismatches but with only one or zero non-T-to-C mutations. Subsequently, reads that aligned to a unique genomic location, that contained at least one T-to-C mutation and that overlapped by at least one nucleotide were grouped together as clusters. Clusters with a read depth of at least five reads were presented as miRNA:mRNA interaction sites in the PAR-CLIP dataset. Each cluster in the PAR-CLIP dataset was further examined for canonical miRNA seed match sites, using the miRNA expression data generated from the small RNA deep sequencing library derived in parallel, and miRNAs with seed matches equal to or greater than 7mer1A (perfect base pairing to seed nt 2-7 with an A across from nt 1 of the miRNA) to the cluster were identified as candidate miRNAs putatively responsible for the cluster.
genome build: hg19 and EBV-WT strain AJ507799.2
processed data files format and content: Based off of BED format.  Columns are:  Chromosome, start coordinate, end coordinate, reads per million library reads, sense.

source_name: nasopharyngeal carcinoma_PAR-CLIP

extract_protocol:
C666 cells were first expanded to 30 150-mm dishes at ~80% confluency, and were then cultured in the presence of 100 µM 4-thiouridine (4SU) for ~20 hours. The cells were then UV radiated at 365 nm for 1 minute, harvested and lysed on ice in NP40 lysis buffer.
Cross-linked Ago:RNA complexes were then immunoprecipitated using a pan-Ago antibody (ab57113; Abcam) and protein G Dynabeads (Invitrogen). Ago-bound RNAs were digested with RNaseT1, radio-labeled, gel purified, proteinase K treated, phenol-chloroform extracted, ethanol precipitated and ligated to 3’ and 5’ Illumina adapters.

treatment_protocol: treated with 4-SU for 20 hours before harvest

value: nasopharyngeal carcinoma

tag: antibody

value: pan-Ago antibody (ab57113; Abcam)


title: SUPeR-seq__HEK293T1

description: single cell RNA-seq


title: Apical Resection+Vagotomy_rep2

city: Cambridge

first: Caitlin

middle: C

last: O'Meara

state: MA

address: 65 landsdowne street

department: Medicine

institute: Brigham and Women's hospital

description:
Surgery performed postnatal day 1, hearts collected postnatal day 2
M24VR2

data_processing:
Illumina Cassava 1.8.2 software used for basecalling
the reads were mapped to grcm38 whole genome using tophat v2.0.9 with default parameters aside from: --library-tpe=fr-firststrand
Cufflinks v2.1.1 was used to assemble transcripts and to estimate transcript abundances with default parameters aside from: --library-tpe=fr-firststrand
Cuffdiff v2.1.1 was used to perform differential expression analysis (with the following parameters -u -b)
Cummerbund was used to extract FPKMs from the output
Genome_build: grcm38
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for all Samples
Supplementary_files_format_and_content: cuff diff output of differentially expressed genes comparing resected vs sham and Resected+vagotomy vs resected
Supplementary_files_format_and_content: abundance measurements all samples FPKM
Supplementary_files_format_and_content: differential gene expression file comparing resected+vagotomy to resection
Supplementary_files_format_and_content: differential gene expression file comparing resected to sham

source_name: heart ventricle

extract_protocol:
Animals were sacrificed by decapitation and hearts were removed, washed in ice cold PBS, and bottom 1/3 of ventricular apex was dissected and snap frozen. Total RNA was extracted using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: post natal day 2

tag: treatment

value: ventricular apical resection and left vagotomy


title: Apical Resection_rep3

description:
Surgery performed postnatal day 1, hearts collected postnatal day 2
M24_r7

value: ventricular apical resection


title: Apical Resection+Vagotomy_rep3

description:
Surgery performed postnatal day 1, hearts collected postnatal day 2
M24VR3


title: Apical Resection+Vagotomy_rep1

description:
Surgery performed postnatal day 1, hearts collected postnatal day 2
M24VR1


title: Apical Resection_rep2

description:
Surgery performed postnatal day 1, hearts collected postnatal day 2
M24_r2


title: Sham operation_rep2

description:
Surgery performed postnatal day 1, hearts collected postnatal day 2
M24_s2

value: sham surgery


title: Apical Resection_rep1

description:
Surgery performed postnatal day 1, hearts collected postnatal day 2
M24_r1


title: Sham operation_rep1

description:
Surgery performed postnatal day 1, hearts collected postnatal day 2
M24_s1


title: relysis_1ng-1

description: single cell RNA-seq

value: mouse ES cell


title: relysis_100pg-1

description: single cell RNA-seq


title: mouse blastocyst-5b

description: single cell RNA-seq

source_name: mouse blastocyst

value: mouse blastocyst


title: relysis_100pg-2

description: single cell RNA-seq


title: relysis_1ng-2

description: single cell RNA-seq


title: CD11c+Ia high cells

description: 18-30 nt small RNA


title: mouse blastocyst-5a

description: single cell RNA-seq


title: mouse blastocyst-4b

description: single cell RNA-seq


title: C666 small RNA

description: barcode: TCGTATGCCGTCTTCTGCTTGT

data_processing:
sequencing reads were pre-processed using the FAST-X toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), and were aligned to the human genome (hg19) and EBV1 wild type genome using Bowtie with up to two mismatches allowed.
genome build: hg19 and EBV-WT strain AJ507799.2
processed data files format and content: Based off of BED format.  Columns are:  Chromosome, start coordinate, end coordinate, reads per million library reads, sense.

source_name: nasopharyngeal carcinoma_miRNA-Seq

extract_protocol:
C666 total RNA was first harvested using TRIzol (Ambion), and the small RNA fraction (~18 to ~24 nt) was subsequently isolated using 15% TBE-Urea polyacrylamide gels (Bio-Rad).
The harvested RNAs were then ligated to 3’ and 5’ Illumina adapters, reverse transcribed using SSIII (Invitrogen) and subjected to Illumina deep sequencing.


title: mouse blastocyst-4a

description: single cell RNA-seq


title: RpoN_overexpressed_sample1 [growth condition]

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

description: transitional growth conditions sample 5

data_processing:
RNA-seq reads were mapped to the PA14 genome using the Stampy aligner with default settings.
The Reads-per-Gene were calculated from the SAM files counting only the reads that were located within the gene boundaries
Genome_build: gi|116048575|ref|NC_008463.1|
Supplementary_files_format_and_content: The processed files in TXT format include Genes and Reads-per-gene

organism: Pseudomonas aeruginosa

source_name: RpoN_overexpressed_transitional growth

growth_protocol: Cultures growing in LB medium at 37 °C were harvested after reaching an OD600 of 2.0

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Briefly, eukariotic RNA was depleted using MICROBEnrich Kit (both for tumor samples and control sampels), subsequently bacterial rRNA was depleted using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmented by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.

treatment_protocol: Cells from 3 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation.

value: PA14 wild type

tag: environmental condition

value: transitional growth

tag: culture type

value: planktonic culture


title: RpoN_overexpressed_sample2 [growth condition]

description: transitional growth conditions sample 7


title: mouse morula-5a

description: single cell RNA-seq

source_name: mouse morula

value: mouse morula


title: RpoS_wildtype [growth condition]

description: transitional growth conditions sample 3

source_name: RpoS_wildtype_transitional growth


title: mouse morula-4b

description: single cell RNA-seq


title: mouse morula-5b

description: single cell RNA-seq


title: RpoS_empty_vector_sample1 [growth condition]

description: transitional growth conditions sample 2

source_name: RpoS_empty_vector_transitional growth


title: RpoN_wildtype_sample1 [growth condition]

description: transitional growth conditions sample 4

source_name: RpoN_wildtype_transitional growth


title: Sham operation_rep3

description:
Surgery performed postnatal day 1, hearts collected postnatal day 2
M24_s9


title: mouse morula-4a

description: single cell RNA-seq


title: PA14_wt_stat_sample1 [growth condition]

description: stationary phase conditions sample 1

growth_protocol: Cultures growing in LB medium at 37 °C were harvested after 12 h of incubation

value: stationary phase


title: PA14_wt_stat_sample2 [growth condition]

description: stationary phase conditions sample 2


title: mouse 8-cell-5a

description: single cell RNA-seq

value: mouse 8-cell


title: SigX_wildtype_sample3 [growth condition]

description: low osmolarity conditions sample 4

source_name: SigX_wildtype_low osmolarity

growth_protocol: Cultures were cultivated in LB medium with low osmolarity containing 8 mM NaCl and were harvested after reaching an OD600 of 1.0

value: low osmolarity


title: mouse 8-cell-4b

description: single cell RNA-seq

source_name: mouse 8-cell


title: SigX_empty_vector_sample2 [growth condition]

description: low osmolarity conditions sample 3

source_name: SigX_empty_vector_low osmolarity


title: mouse 8-cell-5b

description: single cell RNA-seq


title: mouse 8-cell-4a

description: single cell RNA-seq


title: mouse 4-cell-5b

description: single cell RNA-seq

source_name: mouse 4-cell

value: mouse 4-cell


title: SigX_empty_vector_sample1 [growth condition]

description: low osmolarity conditions sample 1


title: RpoS_wildtype_sample1 [growth condition]

description: transitional growth conditions sample 6


title: mouse 4-cell-5a

description: single cell RNA-seq


title: FecI_wildtype_sample1 [growth condition]

description: iron starvation conditions sample 8

source_name: FecI_wildtype_iron starvation

growth_protocol: Iron starvation was induced by growing cultures in 50 % LB medium (diluted with H2O) to an OD600 of 1.5 and incubation with the iron-chelating agents 2,2’-bipyridl for 70 minutes prior to harvesting

value: iron starvation


title: mouse 4-cell-4b

description: single cell RNA-seq


title: mouse 4-cell-4a

description: single cell RNA-seq


title: PvdS_wildtype_sample1 [growth condition]

description: iron starvation conditions sample 6

source_name: PvdS_wildtype_iron starvation


title: SigX_wildtype_sample2 [growth condition]

description: low osmolarity conditions sample 2


title: FpvI_wildtype_sample1 [growth condition]

description: iron starvation conditions sample 4

source_name: FpvI_wildtype_iron starvation


title: RpoS_wildtype_sample2 [growth condition]

description: transitional growth conditions sample 1


title: mouse 2-cell-5b

description: single cell RNA-seq

source_name: mouse 2-cell

value: mouse 2-cell


title: mouse 2-cell-4b

description: single cell RNA-seq


title: mouse 2-cell-4a

description: single cell RNA-seq


title: mouse 2-cell-5a

description: single cell RNA-seq


title: mouse zygote-7a

description: single cell RNA-seq

source_name: mouse zygote

value: mouse zygote


title: mouse zygote-6b

description: single cell RNA-seq


title: AlgU_empty_vector_sample2 [growth condition]

description: heat shock (50°) conditions sample 3

source_name: AlgU_empty_vector_heat shock (50°)

growth_protocol: Cultures were grown in LB to an OD600 of 2.2, exposed to temperatures of 50 °C

value: heat shock (50°)


title: FpvI_empty_vector_sample1 [growth condition]

description: iron starvation conditions sample 3

source_name: FpvI_empty_vector_iron starvation


title: FecI2_empty_vector_sample1 [growth condition]

description: iron starvation conditions sample 1

source_name: FecI2_empty_vector_iron starvation


title: AlgU_wildtype_sample1 [growth condition]

description: heat shock (50°) conditions sample 2

source_name: AlgU_wildtype_heat shock (50°)


title: mouse zygote-6a

description: single cell RNA-seq


title: mouse zygote-7b

description: single cell RNA-seq


title: FecI2_wildtype_sample1 [growth condition]

description: iron starvation conditions sample 2

source_name: FecI2_wildtype_iron starvation


title: mouse oocyte-7b

description: single cell RNA-seq

source_name: mouse oocyte

value: mouse oocyte


title: AlgU_empty_vector_sample1 [growth condition]

description: heat shock (50°) conditions sample 1


title: mouse oocyte-7a

description: single cell RNA-seq


title: RpoH_wildtype [growth condition]

description: heat shock (42°) conditions sample 2

source_name: RpoH_wildtype_heat shock (42°)

growth_protocol: Cultures were grown in LB to an OD600 of 2.2, exposed to temperatures of 42 °C

value: heat shock (42°)


title: FecI_empty_vector_sample1 [growth condition]

description: iron starvation conditions sample 7

source_name: FecI_empty_vector_iron starvation


title: mouse oocyte-6b

description: single cell RNA-seq


title: PA14_tumor_sample2 [growth condition]

description: ex vivo tumor sample 2

growth_protocol: Ex-vivo samples were obtained by using a mouse model in which intravenously administered planktonic P. aeruginosa PA14 bacteria are enriched in transplantable subcutaneous mouse tumors (model was described in Komor et al., 2012)

value: ex vivo tumor


title: RpoH_empty_control [growth condition]

description: heat shock (42°) conditions sample 1

source_name: RpoH_empty_control_heat shock (42°)


title: RNA-seq

source_name: J1 Embryonic Stem Cells

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to manufacturer's instruction. Ribosomal RNA was removed using RiboMinus Eukatyote Kit (Invitrogen). The mRNA libraries were prepared for strand-specific sequencing as described previously (Parkhomchuk et al. 2009).
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.

value: Embryonic Stem Cells


title: PvdS_empty_vector_sample1 [growth condition]

description: iron starvation conditions sample 5

source_name: PvdS_empty_vector_iron starvation


title: PA14_tumor_sample1 [growth condition]

description: ex vivo tumor sample 1


title: MNase Low-ChIP-seq Input rep2

extract_protocol:
Nuclei were treated with MNase. The reaction was quenched by addition of EDTA to 10 mM and the soluble fraction was extracted. Then the sample was treated wtih proteinase K and was extracted with phenol and chloroform to remove proteins. The DNA was isolated by precipitation with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.


title: FliA_empty_vector_sample1 [growth condition]

description: exponential growth conditions sample 5

growth_protocol: Cultures growing in LB medium at 37 °C were harvested after reaching an OD600 of 1.0

value: exponential growth


title: MNase Low-ChIP-seq H3 rep2

extract_protocol:
Nuclei were treated with MNase. The reaction was quenched by addition of EDTA to 10 mM and the soluble fraction was extracted. The sample was immunoprecipitated with an antibody against histone H3 (Abcam ab1791). After elution, the sample was treated with RNase A to remove RNA. Then the sample was treated wtih proteinase K and was extracted with phenol and chloroform to remove proteins. The DNA was isolated by precipitation with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.

value: Histone H3 (Abcam, ab1791)


title: MNase Low-ChIP-seq Input rep1


title: AlgU_wildtype_sample2 [growth condition]

description: heat shock (50°) conditions sample 4

value: PA14 wild type


title: FliA_wildtype_sample2 [growth condition]

description: exponential growth conditions sample 6

value: planktonic culture


title: RpoD_overexpressed_sample1 [growth condition]

description: exponential growth conditions sample 3


title: MNase Low-ChIP-seq H2B rep2

extract_protocol:
Nuclei were treated with MNase. The reaction was quenched by addition of EDTA to 10 mM and the soluble fraction was extracted. The sample was immunoprecipitated with an antibody against histone H2B (Abcam ab1790). After elution, the sample was treated with RNase A to remove RNA. Then the sample was treated wtih proteinase K and was extracted with phenol and chloroform to remove proteins. The DNA was isolated by precipitation with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.

value: Histone H2B (Abcam, ab1790)


title: MPE-ChIP-seq Input rep2

extract_protocol:
Nuclei were treated with MPE-Fe(II). The reaction was quenched by addition of bathophenanthroline to ~6 mM and the soluble fraction was extracted. Then the sample was treated wtih proteinase K and was extracted with phenol and chloroform to remove proteins. The DNA was isolated by precipitation with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.


title: PA14_wt_lowP_sample2 [growth condition]

description: low phosphate conditions sample 2

growth_protocol: Cultures were grown in DeMoss Medium under low phosphate conditions and harvested after reaching an OD600 of 2.0

value: low phosphate


title: MNase Low-ChIP-seq H2B rep1


title: MNase Low-ChIP-seq H3 rep1


title: FliA_wildtype_sample1 [growth condition]

description: exponential growth conditions sample 4


title: PA14_wt_exp_sample1 [growth condition]

description: exponential growth conditions sample 1


title: MPE-ChIP-seq Input rep1


title: PA14_wt_lowP_sample1 [growth condition]

description: low phosphate conditions sample 1


title: PA14_wt_exp_sample2 [growth condition]

description: exponential growth conditions sample 2


title: mouse oocyte-6a

description: single cell RNA-seq


title: MPE-ChIP-seq H3 rep1

extract_protocol:
Nuclei were treated with MPE-Fe(II). The reaction was quenched by addition of bathophenanthroline to ~6 mM and the soluble fraction was extracted. The sample was immunoprecipitated with an antibody against histone H3 (Abcam ab1791). After elution, the sample was treated with RNase A to remove RNA. Then the sample was treated wtih proteinase K and was extracted with phenol and chloroform to remove proteins. The DNA was isolated by precipitation with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.


title: PA14_wt_bf48_sample1 [growth condition]

description: biofilm 48h conditions sample 1

growth_protocol: Biofilm cultures were incubated in 96-well plates as described previously (Dötsch et al., PloS ONE, 2012) and harvested after 48 h

value: biofilm 48h


title: MPE-ChIP-seq H3 rep2


title: MPE-ChIP-seq H2B rep2

extract_protocol:
Nuclei were treated with MPE-Fe(II). The reaction was quenched by addition of bathophenanthroline to ~6 mM and the soluble fraction was extracted. The sample was immunoprecipitated with an antibody against histone H2B (Abcam ab1790). After elution, the sample was treated with RNase A to remove RNA. Then the sample was treated wtih proteinase K and was extracted with phenol and chloroform to remove proteins. The DNA was isolated by precipitation with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.


title: Genomic DNA digested with MNase rep1

extract_protocol:
Genomic DNA was treated with MNase. The reaction was quenched by addition of EDTA to 16 mM. The sample was digested with proteinase K, was extracted with phenol and chloroform, and was precipitated with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.


title: PA14_wt_bf48_sample2 [growth condition]

description: biofilm 48h conditions sample 2


title: Genomic DNA digested with MPE-Fe(II) rep1

extract_protocol:
Genomic DNA was treated with MPE-Fe(II). The reaction was quenched by addition of bathophenanthroline to ~6 mM. DNA was precipitated with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.


title: MPE-ChIP-seq H2B rep1


title: PA14_wt_bf24_sample2 [growth condition]

description: biofilm 24h conditions sample 2

growth_protocol: Biofilm cultures were incubated in 96-well plates as described previously (Dötsch et al., PloS ONE, 2012) and harvested after 24 h

value: biofilm 24h


title: PA14_wt_att_sample2 [growth condition]

description: attachment conditions sample 2

growth_protocol: The overnight culture of P. aeruginosa PA14 was diluted to an OD600 of 0.1 in 10 ml M9 medium and inoculated for 1 h in a cell harvesting system

value: attachment


title: MNase-seq Standard MNase concentration rep1

growth_protocol: J1 mouse embryonic stem cells were maintained on a feeder layer of irradiated mouse embryonic fibroblasts (Global Stem) on gelatin-coated plates in medium composed of Dulbecco's modified Eagle's medium (DMEM) with 4.5 g/L glucose, L-glutamine and sodium pyruvate (Corning 10-013-CV), supplemented with 15% heat-inactivated FBS (Hyclone), 0.1mM 2-mercaptoethanol, 0.1mM nonessential amino acids (Gibco), 2 mM L-alanyl-L-glutamine dipeptide (Gibco), penicillin-streptomycin (Gibco), and 1000 units/mL Leukemia Inhibitory Factor (EMD Millipore). Before the experiments, J1 cells were passaged twice on feeder-free gelatin-coated plates.

extract_protocol:
Nuclei were treated with MNase. The reaction was quenched by addition of EDTA to 10 mM. Proteins were removed by digestion with proteinase K, extraction with phenol and chloroform, and precipitation with ethanol. RNA was removed by digestion with RNase A, extraction with phenol and chloroform, and precipitation with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.


title: PA14_wt_att_sample1 [growth condition]

description: attachment conditions sample 1


title: PA14_wt_att_control_sample2 [growth condition]

description: attachment control conditions sample 2

growth_protocol: The overnight culture of P. aeruginosa PA14 was diluted to an OD600 of 0.1 in 10 ml M9 medium and incubated for 1 hour at RT with agitation

value: attachment control


title: MPE-seq 30 min rep1

extract_protocol:
Nuclei were treated with MPE-Fe(II). The reaction was quenched by addition of bathophenanthroline to ~6 mM. Proteins were removed by digestion with proteinase K, extraction with phenol and chloroform, and precipitation with ethanol. RNA was removed by digestion with RNase A, extraction with phenol and chloroform, and precipitation with ethanol.
DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP.  The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.


title: PA14_wt_anox_sample2 [growth condition]

description: anoxic conditions sample 2

growth_protocol: Anoxic PA14 cultures were harvested after 16h incubation in an Whitley anaerobic workstation at 37°C in PYG-KNO3 [DSMZ_Medium 104, supplemented with 100 mM KNO3]

value: anoxic


title: MPE-seq 20 min rep1


title: MPE-seq 10 min rep1


title: PA14_wt_anox_sample1 [growth condition]

description: anoxic conditions sample 1


title: wrky33 mock rep 3

status: Public on Jun 15 2015

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the Arabidopsis genome (TAIR10) using tophat v2.0.10 with parameters -a 10 -g 10 --library-type fr-unstranded -G TAIR10_GFF3_genes.gff
Read counts per gene per sample were obtained using the bedTools suite  v2.16.2 (function coverageBed) with option -split
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: 4 week old mature leaves

growth_protocol: Arabidopsis Col-0 plants were grown for 4 weeks under short-day conditions in closed cabinets (Schneijder chambers: 16 h light/ 8 h dark cycle at 22-24°C, 60% relative humidity) on 42mm Jiffy-7 pots (Jiffy) to prevent contaminations from garden soil. Before sewing, the Jiffy pot peat pellets were re-hydrated in water containing 0.1% liquid fertilizer Wuxal (Manna). B. cinerea strain 2100 was cultivated on potato dextrose plates at 22°C for 10 days. Spores were collected, washed, and frozen at -80C in 0.8% NaCl at a concentration of 10 to the power of 7 spores mL-1.

extract_protocol:
Total RNA was extracted from mock treated (14 hpi) and B. cinerea inoculated (14 hpi) 4-week old plants (WT and wrky33) with using the RNeasy Plant Mini (Qiagen) according to the manufacturer’s instructions.
mRNA sequencing libraries were constructed with barcodes using the TrueSeq RNA Sample Preparation Kit (Illumina).

treatment_protocol: For inoculation of Arabidopsis plants the spores were diluted in Vogel buffer. 2.5x10 to the power of 5 spores mL-1 were used for spray inoculations of 4-week old intact plants. For mock treatment, Vogel buffer was used. Plants were kept prior to and during infection under sealed hoods at high humidity.

value: leaves

tag: ecotype

value: wrky33 mutant

value: 14 hour mock control


title: wrky33 mock rep 1


title: ES_Tsix-stop_HiC

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

data_processing:
Library strategy: HiC
Initial data processing and base calling was performed using the Illumina Analysis Pipeline. FASTQ files were mapped using GSNAP version 2011-03-10 (Wu et al., 2010). To avoid bias in the mapping of either the Cast- or the 129-derived reads, the alternative alleles of polymorphic sites between the 129- and Cast-genome (see above) are included in the reference during mapping (GSNAP SNP-tolerant mapping; flag –v). Only sequence tags aligning to a single position on the genome were considered for further analysis on the 32-42 bp aligned sequence reads. Further analysis was performed with the 32-42 bp aligned sequence.
The data was converted to Browser Extensible Data (BED) files for downstream analysis. To compensate for differences in sequencing depth and mapping efficiency among samples, the total number of unique reads of each sample was uniformly equalized relative to the sample with the lowest number of sequence reads, allowing quantitative comparisons. Wiggle (WIG) files for viewing the data in the UCSC Genome Browser were generated from the normalized files.
To obtain RNA-Seq gene expression values (RPKM), we used Genomatix (www.genomatix.de; ElDorado 12-2010) selecting RefSeq genes.
Known polymorphic sites between the mouse species 129 and Cast were collected using polymorphic sites determined by (i) the Sanger mouse sequencing project using the March 2011 release (Keane et al., 2011; Yalcin et al., 2011) (http://www.sanger.ac.uk/resources/mouse/genomes/; we used the ftp-mouse.sanger.ac.uk/REL-1003/20100301-high-confidence-snps.tab file for the species 129S1, C57BL and CAST) and (ii) the NIEHS/Perlegen mouse resequencing project (Frazer et al., 2007) (http://phenome.jax.org/db/q?rtn=projects/projdet&reqprojid=198; we used the b04_Chr*_genotype.dat files for the species 129S1/SvImJ, CAST/EiJ and the C57BL/6J reference genome of NCBI Build 36 (Waterston et al., 2002)). This resulted in a total of 20,785,351 polymorphic sites between the genomes of 129 and Cast.
Within the individual samples, we used the mapped tags to determine the sequence tag coverage per allele for each of the 20,785,351 polymorphic sites using GSNAP tally. A total of 7,854,031 polymorphic sites were covered at least once in any of the samples used for this study. Per single polymorphic nucleotide, the pile-ups were subsequently assigned to either the 129- or the Cast-allele using custom Perl-based scripts (see supplementary table Polymorphic_sites_of_Tsix_stop_with_counts.txt.gz). To avoid including counts from positions which were reported to be polymorphic in the Sanger sequencing project and/or the NIEHS/Perlegen resequencing projects, but which were not present in the genotypes used for the current study, we selected polymorphic sites that were covered at least twice from both the 129 and the Cast allele. This resulted in a total of 1,121,809 polymorphic sites used in further analysis. Counts over polymorphic sites within exons of individual RefSeq genes for either 129 or Cast were summed to obtain allele-specific gene expression counts for both species. The ratio between the 129 counts or the Cast counts versus the total counts (129 + Cast) represent the relative contribution of the 129 or Cast allele, respectively, to expression of a particular gene. To calculate allele specific expression values, we multiplied the relative contribution of either 129 or Cast with the total RPKM expression value of a gene. For the ESC differentiation timecourse, only genes that contained a count of >80 over the complete timecourse from both the 129 as well as from the Cast allele were included for further analysis.
For HiC, reads were mapped to the reference mouse genome (mm9) using BWA MEM (Li et al., 2014) with default parameters. Reads were filtered based on mapping quality score (mapQ>=10) and PCR duplicates were removed. (Normalized) interaction matrices at a resolution of 40 kb and the corresponding two-dimensional heat maps were generated as previously described by Lieberman-Aiden et al. (2009) using optimized LGF normalization (normLGF) from the R package HiTC (Servant et al., 2012). The Hi-C Domain Caller package was used to calculate the directionality index from the normalized interaction matrix and to determine domains and boundaries using default parameters (Dixon et al., 2012; see Domains.txt).
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated according to general instructions and were used for analysis; Wig files can be directly uploaded to the UCSC genome browser. The domains within Domains.txt were determined using the HiC data

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: ESCs were cultured without feeders in the presence of leukemia inhibitory factor (LIF; 1000 U ml-1) either in Glasgow modification of Eagles medium (GMEM) containing 10% fetal calf serum (called “serum” medium), or in serum-free N2B27 supplemented with MEK inhibitor PD0325901 (1 μM), GSK3 inhibitor CH99021 (3 μM), penicillin (100 U ml-1), streptomycin (100 mg ml-1), glutamine (1 mM), non-essential amino acids (0.1 mM), β-mercaptoethanol (0.1 mM) (together called “2i” medium; Ying et al., 2008). For adaptation to 2i, serum ESCs were transferred to 2i medium and cultured for >12 days (>6 passages) in 2i medium. ESCs used in this study include the female lines ES_Tsix-stop (Luikenhuis et al., 2001), ES_Xist-del (a polymorphic 129:Cast female ESC line that show non-random XCI due to a deletion in the Xist gene on the 129 allele; Csankovszki et al. (1999)), TNGA (Chambers et al., 2007) and XT67E1 (a polymorphic 129:PGK female ESC line that show non-random XCI due to a deletion in the Xist gene on the 129 allele; Penny et al., 1996), and the male ESC lines E14Tg2a (E14) and Rex1GFPd2 lines (Wray et al., 2011; Marks et al., 2012). Derivation and culture of the EpiSCs was described previously (Maruotti et al. 2010; Veillard et al., 2014). Derivation of NPC lines, including culture conditions and further details, has been described in Splinter et al. (2011).

extract_protocol:
Total RNA was isolated with Trizol (Invitrogen) according to the manufacturer’s recommendations. 100 μg total RNA was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit; QIAGEN), followed by DNaseI treatment (QIAGEN). 100–200 ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 s and purified (RNAeasy Minelute Kit; QIAGEN). cDNA was synthesized using 5 μg random hexamers by Superscript III Reverse Transcriptase (Invitrogen). Ds cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer’s recommendations and purified (Minelute Reaction Cleanup Kit; QIAGEN). Strand-specific rRNA depleted ds cDNA profiling used for the NPC lines was performed with the ScriptSeq kit (cat. no. SS10924) from Illumina, according to the instructions of the manufacturer. rRNA depletion was performed with the Ribo-Zero rRNA Removal Kit using 5 μg of total RNA (Human/Mouse/Rat; cat. no. RZH110424). Collection of the cells for Hi-C and the HiC sample preparation procedure was performed as previously described (Lieberman-Aiden et al., 2009), with the slight modification that DpnII was used as restriction enzyme during initial digestion.
For the PolyA+ samples, cDNA was prepared for sequencing by end repair of 20 ng ds cDNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and 14 cycles of PCR amplification. Quality control of the adaptor-containing DNA libraries of both PolyA+ and ScriptSeq samples was performed by qPCR and by running the products on a Bioanalyzer (BioRad). Cluster generation and sequencing (32-42 bp) was performed with the Illumina Genome Analyzer IIx or Hi-Seq 2000 platforms according to standard Illumina protocols. For HiC, paired-end libraries were prepared according to Lieberman-Aiden et al. (2009) and sequenced on the NextSeq 500 platform using 2*75 bp sequencing.

treatment_protocol: Induction of ESC differentiation has been described by Barakat et al. (2011). In short, ESCs were split, and pre-plated on non-gelatinised cell culture dishes for 60 minutes. ESCs were then seeded in non-gelatinised bacterial culture dishes containing differentiation medium to induce embryoid body (EB) formation. EB-medium consisted of IMDM-glutamax, 15% foetal calf serum, 100 U ml-1 penicillin, 100 mg ml-1 streptomycin, non-essential amino acids, 37.8 μl l-1 monothioglycerol and 50 μg ml-1 ascorbic acid. EBs were plated on coverslips 1 day prior to harvesting, and allowed to grow out.

value: ESCs

tag: strain background

value: 129/SV-Jae x Cast

tag: measurement

value: HiC

value: Undifferentiated in Ndiff and 2i+LIF


title: wrky33 mock rep 2


title: wrky33 Bc 14h rep 3

value: 14 hour post inoculation with spores of Botrytis cinerea 2100


title: wrky33 Bc 14h rep 2


title: WT Bc 14h rep 3

value: WT


title: WT Bc 14h rep 2


title: PA14_wt_bf24_sample1 [growth condition]

description: biofilm 24h conditions sample 1

value: PA14 wild type

value: planktonic culture


title: WT Bc 14h rep 1


title: WT mock rep 2


title: WT mock rep 1


title: WK33-HA Bc 14h input rep2

description: Negative control for peak calling only (for Sample 6)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Trimming and filtering of LinDA adapters and low quality sequences was performed using 1) cutadapt  v1.2.1 with options –e 0.2, -n 2 and –m 36 and 2) PRINSEQ lite v0.20.2 with options –trim_qual_right/left 20, trim_tail_right/left 3 –min_len 36, -min_qual_mean 25
Sequenced reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie v0.12.7 with options –best –m 1
Peak calling was performed for each replicate using the program QuEST v2.4 in transcription factor mode (option “2”) with permissive parameter settings (option “3”) and suppling the corresponding input or mock-treated sample as negative controls in peak calling
For samples where several negative controls were available, only peaks that were identified against all used negative controls (high confidence peaks) were retained for further analysis
Annotation of peak locations with respect to annotated gene features in TAIR10 was performed using the annotatePeaks.pl function from the Homer suite
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files with peak coordinates, enrichment scores, and annnotation information

extract_protocol:
Lysates were clarified from sonicated nuclei and WRKY33-DNA complexes were isolated with an HA antibody. ChIP DNA was purified using a QIA quick PCR Purification kit (Qiagen) and subjected to a linear DNA amplification (LinDA) protocol (Shankaranarayanan et al., 2011) which included two rounds of ‘in vitro transcription’ by T7 RNA polymerase.
The resulting LinDA DNA was used to generate sequencing libraries bearing barcodes using a NEBNext ChIP-Seq Library Pre Reagent Set for Illumina kit (New England Biolabs).


title: WT mock 14h rep2

description: Negative control for peak calling only (for Sample 10)

value: rabbit polyclonal antibodies to HA (Sigma)

value: 14 hour mock treated


title: WT mock rep 3


title: WK33-HA Bc 14h input rep1

description: Negative control for peak calling only (for Sample 5)


title: WK33-HA Bc 14h rep1


title: WK33-HA mock 14h input rep2

description: Negative control for peak calling only (for Sample 2)


title: PA14_wt_att_control_sample1 [growth condition]

description: attachment control conditions sample 1


title: WK33-HA mock 14h rep1

description: No peaks identified in peak calling against input


title: WK33-HA mock 14h input rep1

description: Negative control for peak calling only (for Sample 1)


title: wrky33 Bc 14h rep 1


title: scnRNAs co-IPed with Twi1p from wild-type cells @10.5 hpm

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

institute: Institute of Human Genetics, CNRS

data_processing:
Following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed.
Supplementary_files_format_and_content: Normalized numbers (RPKM) of sequenced 26-32-nt RNAs that map uniquely to the compiled 1462 MIC genome supercontigs (ordered by their lengths) are shown as histograms with 100-b bin. The 1,464 supercontigs (Tetrahymena Comparative Sequencing Project, Broad Institute of Harvard and MIT) were ordered by length, concatenated as 157.7 Mb of linear DNA, and used as the MIC genome for this study.

organism: Tetrahymena thermophila

source_name: Conjugating cells at 10.5 hpm

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30 °C. For conjugation, growing cells (~5-7 x 105/ml) of two different mating types were washed, pre-starved (~12-24 hr) and mixed in 10 mM Tris (pH 7.5) at 30 °C.

extract_protocol: RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24

tag: genotype/variation

value: wild-type