title: NEG.rep1 DO-RIP

city: Durham

first: Matthew

middle: Burk

last: Friedersdorf

state: NC

address: 207 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

data_processing:
Library strategy: DO-RIP-Seq
Adapter removal. Cutadapt V1.0. To process raw reads from the digestion-optimized RIP libraries, adapter sequences up to, but not including, the five-nucleotide random sequences were removed using Cutadapt. These trimmed reads that still contained the five random nucleotides were then collapsed to unique sequences. The random five-nucleotide regions were removed prior to mapping.
Genome alignment. Tophat2 (v2.0.8) with following options: -N 1 --read-gap-length 1 -g 10 --library-type fr-secondstrand -G GencodeV19.gtf -. Processed reads were mapped to hg19 with Gencode V19 transcriptome.
Binding Site/Peak Calling. Reads were binned in 5nt intervals, counts of uniquely mapped reads were summed and a pseudocount of 1 added to intervals with 0 reads. Binned reads were normalized to library size (per million reads) and log2 transformed. Applied single-tailed paired t-test to calculated p-values. High pass filter of 7 or more reads per bin was applied. Ratio of HuR IP reads to negative IP reads were calculated per bin. Mixture model was generated using mixtools in R for ratios. LOD calculated from log10 of posterior probabilities ratio. Binding sites were called when at least three consecutive intervals with LOD>0 and p<0.05 (p value only applicable to binding sites calculated from all libraries).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bed files contain HuR-binding sites with LOD>0 (enrichment over matched negative), fifth column (score column) is mean LOD of binding site, rep bed files are sites for the individual replicates, allHuR bed files include all three replicates in binding site determination with pval05 bed file containing only the significantly reproduced binding sites.

source_name: HEK293, negative control

growth_protocol: HEK293 cells were grown in 10x15-cm dishes until they were 80-90% confluent (approximately 12 x 10^6 cells per dish).

extract_protocol:
HEK293 cells were lysed on ice by resuspending and repeated pipetting with 1.5 cell pellet volumes of polysome lysis buffer (10 mM HEPES pH 7.0, 100 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 1X cOmpleteTM protease inhibitor cocktail (Roche), 100 Units/ml RNaseOUT (Life Technologies), 0.5% IGEPAL, and 1 mM DTT). Lysates were incubated on ice for 5 min and then stored at -80 °C. These lysates were thawed on ice and then centrifuged at 4 °C to clear the cell debris. The cleared lysates were digested in 300 μl volumes (the volume used in the optimization experiment) using 30 gel Units MNase/μg RNA. As described above, digestions were performed by incubating the lysate with micrococcal nuclease for 5 min at 30 °C, and inactivating the enzyme by adding EGTA to a final concentration of 10 mM. Digested lysates were pooled and then evenly added to immunoprecipitation reactions with either magnetic protein G beads coupled to mouse anti-HuR (3A2) antibodies, or to normal mouse serum antibodies. Immunoprecipitations were performed at 4 °C for 2 h with constant mixing, and then the bead-antibody complexes washed 4 times with ice-cold NT2 buffer. RNA fragments from the IP were extracted, dephosphorylated, and radiolabeled as described above. Since these RNA fragments were going to be used for cDNA libraries, 10 nmol of non-radioactive ATP was added to the radiolabeling reaction after the 30 min incubation with [γ-P32]ATP, and incubated for an additional 10 min at 37 °C to ensure complete labeling of the ends. As described above, end-labeled fragments were separated by polyacrylamide gel electrophoresis, and the gel visualized using a phosphor-imaging scanner. RNA fragments corresponding to 25-70 nucleotides in length were cut from the gel, and extracted overnight by constantly mixing the gel slices in 400 μl of 0.4 M NaCl at 4 °C. The supernatant containing the radiolabeled RNA fragments was transferred to a new microcentrifuge tube. 200 μl of 0.4 M NaCl was then added to the gel slices and constantly mixed at 4C for 1h to wash. The supernatant from the wash was pooled with the supernatant from the overnight extraction, and supernatants were precipitated with 1ml 100% EtOH and glycogen at -20 °C for at least 1h or -80 °C for 30 min. The RNA fragments were centrifuged at 17,000 g, 4 °C for 20 min, washed once with 80% ethanol, centrifuged at 10,000 g, 4 °C for 5 min, and air-dried.
NEBNext small RNA library prep protocol (New England BioLabs); Adapters and Primers for HuR.1 and Neg.1 DO-RIP-seq libraries = 5' RNA adapter: GUUCAGAGUUCUACAGUCCGACGAUC; 3' DNA adapter: /5rApp/NNNNNTCGTATGCCGTCTTCTGCTTG/3ddC/; 5' PCR DNA primer: AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA; 3' PCR DNA primer: CAAGCAGAAGACGGCATACGA. Adapters and Primers for HuR.2 and Neg.2 DO-RIP-seq libraries = 5' RNA adapter: GUUCAGAGUUCUACAGUCCGACGAUC; 3' DNA adapter: /5rApp/NNNNNTCGTATGCCGTCTTCTGCTTG/3ddC/; 5' PCR DNA primer: AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA; 3' PCR DNA primer for HuR.2: GTCAAGCAGAAGACGGCATACGA; 3' PCR DNA primer for Neg.2: ACCAAGCAGAAGACGGCATACGA. Adapters and Primers for HuR.3 and Neg.3 DO-RIP-seq libraries = 5' RNA adapter: GUUCAGAGUUCUACAGUCCGACGAUC; 3' DNA adapter: /5rApp/NNNNNAGATCGGAAGAGCACACGT/3ddC/; 5' PCR DNA primer: AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA; First strand synthesis DNA primer: ACGTGTGCTCTTCCGATCT; 3' HuR.3 Index primer: CAAGCAGAAGACGGCATACGAGATGTGACGAGTTCATTGGCACGTGTGCTCTTCCGATCT; 3' Neg.3 Index primer: CAAGCAGAAGACGGCATACGAGATGTGACGAGTTCTACAAGACGTGTGCTCTTCCGATCT

tag: ip antibody

value: normal mouse sera


title: NEG.rep3 DO-RIP

status: Public on Oct 13 2016

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: NEG.rep2 DO-RIP


title: 3.Ctrl

city: London

first: Marc

last: Dionne

address: Level 0, Flowers Building

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: control replicate 3

data_processing:
Illumina RTA software was used for basecalling.
Sequenced reads were demultiplexed and adaper trimmed using Illumina bcl2fastq software, then mapped to Drosophila melanogaster genome version 6.26 using STAR 2.4.0j. Command line: STAR  --outSJfilterCountUniqueMin 5   2   2   2     --outSJfilterCountTotalMin 5   2   2   2      --outFilterType BySJout
Mapped reads were associated with genes using the FeatureCounts command in Rsubread. Differentially-expressed genes were identified using Limma.
Genome_build: BDGP6.26
Supplementary_files_format_and_content: tab-delimited text spreadsheet of non-normalized counts mapping to genes

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole adult male flies

extract_protocol:
For each sample, 5 male flies were lysed in 200 ul TRIzol reagent and total RNA was extracted according to the manufacturer's instructions, followed by an extra round of ethanol precipitation.
Libraries were prepared using Illumina TruSeq Stranded mRNA v2, with the following changes from the manufacturer’s protocol: starting samples were 250ng total RNA; fragmentation was performed for 10 minutes at 94°; no spike-ins were used; and 14 cycles of PCR were used to enrich libraries. Libraries were sequenced on an Illumina NextSeq 500 using v1 chemistry.

tag: genotype

tag: age

value: 5-10 days posteclosion


title: 2.Ctrl

description: control replicate 2


title: 23.Mef2.IR

description: Mef2 knockdown replicate 3


title: 1.Ctrl

description: control replicate 1


title: Sample_180_4_K27Ac

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description: H3K27Ac ChIP in mouse cells with shCrebbp 180_4

library_source: genomic

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: mouse mm10 build
Supplementary_files_format_and_content: bigwig and bigbed formats

molecule: genomic DNA

organism: Mus musculus

source_name: splenic B220+ lymphocytes

growth_protocol: Cells were isolated from mouse spleens upon sacrifice.

extract_protocol:
Chromatin was sheared to 200-400bp, incubated with H3K27ac antibody (abcam 4729) overnight at 4C on a rocker, antibody chromatin complex was captured by ProteinA agarose beads, washed with low salt, high salt, LiCl, and TE buffer, eluted and then de-crosslinked at 65C with 0.3M NaCl final for at least 6 hr.  Final chormatin was purified using Qiagen PCR purification columns.
Libraries were prepared using the Illumina Truseq ChIPseq Library preparation Kit following the manufacture’s instructions (Illumina, CA).

tag: cell type

value: lymphoma cells

tag: genotype/variation

value: Crebbp knock-down

tag: chip antibody

value: H3K27Ac (ab4729, Rabbit, 2 ug)


title: Sample_180_5_Input

description: input DNA for H3K27Ac ChIP in mouse cells with shCrebbp 180_5


title: HuR.rep2 DO-RIP

source_name: HEK293, HuR IP

value: anti-HuR (3A2)


title: HuR.rep3 DO-RIP


title: GM12878_FACS_sorted_G1_low_1

city: Palo Alto

first: Xingqi

last: Chen

address: 269 Campus Drive

institute: Stanford University

data_processing:
Library strategy: ATAC-seq
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard. Peaks were called using the ZINBA algorithm, which was first applied to each dataset independently, using the following parameters: a 300bp window, 50bp offset, background and enriched components were modeled using the intercept, while the zero-inflated component was modeled using alignability, a posterior probability of 0.99 was used to select the set of significant regions. The peak sets from the same cell-type and number of cells were merged.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab seperated format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand

source_name: ATCC cell line GM12878

growth_protocol: ATCC cell lines (GM12878, HT1080) were purchesed from ATCC and maintained in standerd protocol according to the instruction, and sorted with FACS.

extract_protocol:
50K cells were used for ATAC-seq lib in every group of FACS sorted cells
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit and using custom-made Tn5 transposase ( where Atto-590 labled adaptor)

treatment_protocol: cells were fixed and sorted based on DAPI staining and ATAC-see color intensity

value: FACS sorted G1 low group


title: GM12878_FACS_sorted_G1_high_1

value: FACS sorted G1 high group


title: Sample_180_4_Input

description: input DNA for H3K27Ac ChIP in mouse cells with shCrebbp 180_4


title: FXR ChIP-seq, Liver, Metformin

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

data_processing:
Reads were mapped to the mouse genome (mm10) using Bowtie 1
Bigwig files report signal intensity at 25 bp resolution normalized to the library size.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig (signal intensity at 25 bp resolution normalized to the library size).

source_name: Liver

growth_protocol: C57BL6/J mice were purchased from Charles River Laboratories and housed in a temperature-controlled room (22–24°C) with a relative humidity of 36%–80%, and 12-hour light/12-hour dark cycles. Mice were fed ad libitum, with free access to water.

extract_protocol:
ChIP was performed as described in Flajollet,S., Lefebvre,B., Rachez,C., and Lefebvre,P. 2006. Distinct Roles of the Steroid Receptor Coactivator 1 and of MED1 in Retinoid-induced Transcription and Cellular Differentiation. J. Biol. Chem. 281:20338-20348.
Libraries were prepared using NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina (E6240 and E7335 from New England Biolabs) according to the manufacturer's instructions

treatment_protocol: Mice received either (a) a standard rodent chow diet (A03-10 UAR, control) (CHOW), (b) a standard rodent chow diet and metformin (0.5 g/l in drinking water, ca 50–80 mpk/d) (MET), (c) a standard rodent chow diet containing 0.5% (wt/wt) TCA (TCA), or (d) a standard rodent chow diet containing 0.5% (wt/wt) TCA and metformin for 5 days (TCA+MET). Mice were sacrificed by cervical dislocation after 6 hours of fasting.

tag: strain

tag: Sex

value: male

tag: treatment

value: Metformin

tag: antibody


title: GM12878_FACS_sorted_G1_high_2


title: GM12878_FACS_sorted_G1_low_2


title: HuR.rep1 DO-RIP


title: C2C12 Klf5 ChIP-seq day2

status: Public on Oct 14 2016

city: Bunkyo

first: Yumiko

last: Oishi

state: Tokyo

address: 1-5-45, Yushima

department: Department of Cellular and Molecular Medicine

country: Japan

institute: Tokyo Medical and Dental University

description: formaldehyde cross-linked

data_processing:
For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm9 genome using RNA-Star. Aligned read files were analyzed with HOMER (http://homer.salk.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif- and other analyses in the study.
Genome_build: mm9

source_name: C2C12 myoblast

growth_protocol: C2C12 cells were purchased from ATCC (Rockville, MD) and cultured in DMEM (Nakarai) containing 10% FBS and 1% penicillin-streptomycin at sub-confluent densities.

extract_protocol: ChIP-Seq: Sequencing libraries were prepared from collected DNA by using NEB next Ultra DNA library prep kit for Illumina. Libraries were PCR-amplified for 12-15 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2500 (Illumina) for 51 cycles.

treatment_protocol: C2C12 cells were differentiated into myotubes by replacing Growth Medium with media containing 2% horse serum with antibiotics (differentiation medium, DM). For knockdown Klf5 in C2C12 cells, siKlf5 (Thermo scientific, Dharmacon, siRNA-SMARTpool, M-062477-01-0005) treatment were performed with RNAiMAX (Life Technologies) according to manufacturer’s instructions.

value: C2C12 myoblast

tag: differentiation stage


title: CLIP-ALKBH1-replicate3

city: Chicago

first: Guan-Zheng

last: Luo

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

data_processing:
Raw reads from CLIP samples were first trimmed according to recommended settings  using cutadpt with a minimum length of 15 nucleotides
Processed  reads were combined to unique sequences then mapped to the human small RNA database (Rfam)
Genome_build: hg19

growth_protocol: HeLa cell line was purchased from ATCC (CCL-2) and grown in DMEM (Gibco, 11965) media supplemented with 10% FBS (Gibco, 10438-026) and 1× Pen/Strep (Gibco, 15140).

extract_protocol: RNA Clean & Concentrator was used to further clean the final recovered RNA sample (Zymo Research) followed by library construction with small-RNA sample preparation kit (New England BioLabs Inc) prior to the cDNA reverse transcription. To avoid the sequencing bias, which is caused by the heavily modified status of tRNAs, we used TGIRT reverse transcriptase enzyme. Using the TGIRT reverse transcriptase enzyme, we also constructed the input library with the same procedure with the exception of the ALKBH1 immunoprecipitation step.

value: HeLa


title: FXR ChIP-seq, Liver, TCA+Metformin

value: TCA+Metformin


title: CLIP-control replicate 1

source_name: CLIP-control replicate 1


title: CLIP-ALKBH1-replicate2


title: Sample_180_3_K27Ac

description: H3K27Ac ChIP in mouse cells with shCrebbp 180_3


title: CLIP-ALKBH1-replicate1


title: FXR ChIP-seq, Liver, TCA

value: TCA


title: Sample_180_1_K27Ac

description: H3K27Ac ChIP in mouse cells with shCrebbp 180_1


title: Sample_180_3_Input

description: input DNA for H3K27Ac ChIP in mouse cells with shCrebbp 180_3


title: Sample_180_2_K27Ac

description: H3K27Ac ChIP in mouse cells with shCrebbp 180_2


title: Sample_180_5_K27Ac

description: H3K27Ac ChIP in mouse cells with shCrebbp 180_5


title: RUES2-BMP-24h

city: New York

first: Albert

last: Ruzo

state: NY

address: 1230 York Avenue

department: Laboratory of Stem Cell Biology and Molecular Embryology

institute: The Rockefeller University

data_processing:
Reads were aligned using the STAR aligner
featureCounts was used to assign reads to Gencode v18 gene annotations.
DESeq2 was used to normalize the count matrix.
Genome_build: NCBI genome build 37
Supplementary_files_format_and_content: normalized gene count matrix

source_name: embryonic stem cells

growth_protocol: hESCs were cultured as 500um diameter discs (CYTOO micropatterned coverslips) in MEF-conditioned medium in presence of 20ng/ml bFGF.

extract_protocol:
Trizol and Rneasy mini kit (QIAGEN)
Illumina TruSeq RNA Sample Prep Kit v2

treatment_protocol: BMP4 50ng/ml

tag: time point

tag: agent


title: tRNA-seq Alkbh1 KO MEF Replicate 1

data_processing:
Raw reads from tRNA-seq samples were first trimmed according to recommended settings using Trimmomatic with a minimum length of 18 nucleotides with custom Python scripts to fully remove any trace of adapter.
Processed reads were aligned to culled mouse tRNA genome sequences using Bowtie1.0 according to the paramters of -v 3 -m 1- --best --strata -p 12.
Further processing using C and Python scripts were used to map reads onto specific tRNA isodecoders for accurate counting statistics.
Raw reads from CLIP samples were first trimmed according to recommended settings using cutadpt with a minimum length of 15 nucleotides
Processed reads were combined to unique sequences then mapped to the human small RNA database (Rfam)
Genome_build: hg19, mm10

source_name: tRNA-seq Alkbh1 KO MEF

growth_protocol: HeLa cell line was purchased from ATCC (CCL-2) and grown in DMEM (Gibco, 11965) media supplemented with 10% FBS (Gibco, 10438-026) and 1× Pen/Strep (Gibco, 15140). MEF cells  were grown in DMEM (Gibco, 11965) media supplemented with 10% FBS (Gibco, 10438-026) and 1× Pen/Strep (Gibco, 15140).

extract_protocol:
RNA Clean & Concentrator was used to further clean the final recovered RNA sample (Zymo Research) followed by library construction with small-RNA sample preparation kit (New England BioLabs Inc) prior to the cDNA reverse transcription.
To avoid the sequencing bias, which is caused by the heavily modified status of tRNAs, we used TGIRT reverse transcriptase enzyme.
Using the TGIRT reverse transcriptase enzyme, we also constructed the input library with the same procedure with the exception of the ALKBH1 immunoprecipitation step.

value: mouse embryonic fibroblast (MEFs)

value: Alkbh1 KO


title: Sample_180_1_Input

description: input DNA for H3K27Ac ChIP in mouse cells with shCrebbp 180_1


title: tRNA-seq Alkbh1 KO MEF Replicate 2


title: RUES2-BMP-12h


title: Sample_167_5_Input

description: input DNA for H3K27Ac ChIP in mouse cells with scramble shRNA control 167_5

value: Crebbp wild-type


title: RUES2-BMP-0h


title: FXR ChIP-seq, Liver, No treatment (Chow)

value: No treatment (Chow)


title: RUES2-BMP-4h


title: CLIP-control replicate 2

source_name: CLIP-control replicate 2


title: Sample_167_3_Input

description: input DNA for H3K27Ac ChIP in mouse cells with scramble shRNA control 167_3


title: Sample_167_2_K27Ac

description: H3K27Ac ChIP in mouse cells with scramble shRNA control 167_2


title: Sample_167_3_K27Ac

description: H3K27Ac ChIP in mouse cells with scramble shRNA control 167_3


title: Sample_180_2_Input

description: input DNA for H3K27Ac ChIP in mouse cells with shCrebbp 180_2


title: tRNA-seq wild-type MEF Replicate 1

source_name: tRNA-seq wild-type MEF

value: wild type


title: control RPF biological replicate

city: Potsdam

first: Radoslaw

last: Lukoszek

address: Karl-Liebknecht-Strasse 24-25

country: Germany

institute: University of Potsdam

description: biological replicate of control RPF sample

data_processing:
Library strategy: ribosome profiling
Quality trimming (done by own scripts)
Adapter cutting (done by own scripts)
Genome mapping using Bowtie, version 1.0.0, parameters used -v 2 -m 1 --strata --best -y, only uniquely mapped reads were kept for further analysis
Read counts for the longest transcript for each gene were normalized by reads per million feature mapped reads (rpkm; done by own scripts)
Genome_build: Arabidopsis thaliana genome, ENSEMBL version 21
Supplementary_files_format_and_content: Column 1 gives AGI identifier, column 2 gives the rpkm values. Files XXX_mrna_rpkm_CDS contain information about rpkm values for the exon bases of the longest transcript from RNA-seq libraries, files XXX_rpf_rpkm_CDS contain information about rpkm values for the exon bases of the longest transcript from Ribo-seq libraries, files XXX_xxx_rpkm_5UTR contain information about rpkm values for the 5'UTRs of the longest transcripts, files XXX_xxx_rpkm_3UTR contain information about rpkm values for the 3'UTRs of the longest transcripts.

molecule: cytoplasmic RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana_control_RPF

growth_protocol: Arabidopsis thaliana Col-0 plant were grown in the greenhouse conditions at 23°C in long day conditions (16h/8h), light intensity ~140μmol*m^-2*s^-1, humidity 60%.

extract_protocol:
Total RNA was extracted using  standard Trizol extraction protocol and spiked-in with ERCC RNA spike-in Mix (Ambion). rRNA was depleted using RiboMinus Plant Kit (Ambion), and randomly fragmented by alkaline lysis in alkaline fragmentation solution (2 mM EDTA, 12 mM Na2CO3, 87 mM NaHCO3) at 95°C for 40 min. The randomly fragmented RNA was recovered by precipitation in the presence of glycogen. Polysomes were isolated according to {Mustroph, 2009 #490} with some modifications. Briefly, approximately 10 g of leave material was thawed in polysome extraction buffer (0.2 M Tris pH 7.4, 0.2 M KCl, 0.025 M EGTA, 0.035 M MgCl2, 1% Brij-35, 1% Triton X-100, 1% Igepal CA 630, 1% Tween 20, 1% DOC, 1% PTE, 5 mM DTT, 1 mM AEBSF, 100 µg/mL cyclohexamide, 100 µg/mL chloramphenicol) and homogenized using glass homogenizer, filtered through four layers of sterile cheese cloth and two layers of sterile Miracloth (Calbiochem) and incubated on ice for 10 minutes. The supernatant after centrifugation (4°C, 16,000xg for 15 min) was additionaly filtered through Miracloth and transferred onto a sucrose cushion solution (0.4 M Tris pH 7.4, 0.2 M KCl, 0.005 M EGTA, 0.035 M MgCl2, 1.75 M sucrose, 5 mM DTT, 100 µg/mL cyclohexamide, 100 µg/mL chloramphenicol) and centrifuged at 4°C, 170,000xg for 3 h. The ribosome-containing pellet was gently resuspended in ice-cold resuspension buffer (0.2 M Tris pH 7.4, 0.2 M KCl, 0.025 M EGTA, 0.035 M MgCl2, 5 mM DTT, 100 µg/mL cyclohexamide, 100 µg/mL chloramphenicol) and applied onto 15%-60% sucrose gradient (0.04 M Tris pH 7.4, 0.02 M KCl, 0.01 M MgCl2, 100 µg/mL cyclohexemide, 100 µg/mL chloramphenicol) and centrifuged at 4°C, 237,000xg for 1.5 h. Purified polysomes were digested with RNAse I (1.5U/1OD/1µl) at 22°C for 10 min, loaded directly onto 15%-60% sucrose gradient and centrifuged at 4°C, 237,000xg for 1.5 h. Monosome fraction was concentrated with Amicon-Ultra4 Centrifugal Unit (MWL 100 kDa) and RPFs were released by adding the release buffer (20 mM HEPES-KOH pH 7.4, 100 mM KCl, 1 mM EDTA, 2mM DTT, 2 µl/ml Ribolock) and incubated for 10 min on ice and centrifuged at 4°C, 1900xg for 30 min. RNA was extracted using hot acid phenol method and depleted of rRNA using RiboMinus Plant Kit (Ambion).
RNA-size selection and generation of the cDNA libraries was performed as described (Ingolia, 2009).

treatment_protocol: For the heat stress, the plants were placed in the growth chamber at 37°C, light intensity ~140μmol*m^-2*s^-1, humidity 60%. Control plants were placed in the growth chamber at 23°C, light intensity ~140μmol*m^-2*s^-1, humidity 60%.

tag: ecotype

value: 3 week-old plants

tag: type of stress

tag: tissue

value: leaf


title: Sample_167_5_K27Ac

description: H3K27Ac ChIP in mouse cells with scramble shRNA control 167_5

value: lymphoma cells

value: H3K27Ac (ab4729, Rabbit, 2 ug)


title: heat stress RNA

data_processing:
Quality trimming (done by own scripts)
Adapter cutting (done by own scripts)
Genome mapping using Bowtie, version 1.0.0, parameters used -v 2 -m 1 --strata --best -y, only uniquely mapped reads were kept for further analysis
Read counts for the longest transcript for each gene were normalized by reads per million feature mapped reads (rpkm; done by own scripts)
Genome_build: Arabidopsis thaliana genome, ENSEMBL version 21
Supplementary_files_format_and_content: Column 1 gives AGI identifier, column 2 gives the rpkm values. Files XXX_mrna_rpkm_CDS contain information about rpkm values for the exon bases of the longest transcript from RNA-seq libraries, files XXX_rpf_rpkm_CDS contain information about rpkm values for the exon bases of the longest transcript from Ribo-seq libraries, files XXX_xxx_rpkm_5UTR contain information about rpkm values for the 5'UTRs of the longest transcripts, files XXX_xxx_rpkm_3UTR contain information about rpkm values for the 3'UTRs of the longest transcripts.

source_name: Arabidopsis thaliana_heat_stress_RNA

value: heat stress 3h at 37°C


title: Sample_167_2_Input

description: input DNA for H3K27Ac ChIP in mouse cells with scramble shRNA control 167_2


title: heat stress RPF

source_name: Arabidopsis thaliana_heat_stress_RPF


title: Sample_167_1_Input

description: input DNA for H3K27Ac ChIP in mouse cells with scramble shRNA control 167_1


title: control RPF


title: control RNA

source_name: Arabidopsis thaliana_control_RNA


title: control RNA biological replicate

description: biological replicate of control RNA sample


title: RNA-seq of hsf-1(sy441) L2 larvae at 34°C, replicate 2

status: Public on Oct 12 2016

city: Evanston

first: Jian

last: Li

address: 2205 Tech Drive, Hogan 2-100

department: Molecular Biosciences

institute: Northwestern University

data_processing:
RNA-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using TopHat2 (Kim et al. 2013) with default settings except that the proper intron size for C. elegans genes (10 to 22000 bp) was used.
Expression analyses were done using Cuffdiff (Trapnell et al. 2010) with quartile normalization. The exon model used in the analyses was based on the gtf file queried from Wormbase (WS220).
Genome_build: ce10/WS220
Supplementary_files_format_and_content: tab-delimited text file includes differentially expressed genes upon heat shock (FDR 0.05).

organism: Caenorhabditis elegans

source_name: L2 larvae

growth_protocol: Age synchronization was achieved by treatment of alkaline hypochlorite solution and eggs were hatched in M9. L1 larvae were transferred to 10 cm NGM plates seeded with OP50 and grown at 20°C to mid-L2.

extract_protocol:
RNA was extracted using Trizol and QIAGEN RNeasy RNA extraction kit with on-column DNaseI digestion as per manufacturer’s instructions.
polyA selection and library construction were done following the Illumina Truseq RNA sample preparation protocol

treatment_protocol: Worms were either directly collected or subjected to heat shock performed in a water bath pre-heated to 34°C. For heat shock, NGM plates were wrapped with parafilm and submerged for 30 min.

tag: developmental stage

value: L2 larvae

value: whole animal


title: RNA-seq of hsf-1(sy441);rmSi1[hsf-1::gfp] L2 larvae at 34°C, replicate 2

value: unc-119(ed9)III; rmSi1 II; hsf-1(sy441) I


title: RNA-seq of hsf-1(sy441);rmSi1[hsf-1::gfp] L2 larvae at 20°C, replicate 3


title: RNA-seq of hsf-1(sy441) L2 larvae at 34°C, replicate 3


title: RNA-seq of hsf-1(sy441);rmSi1[hsf-1::gfp] L2 larvae at 34°C, replicate 3


title: tRNA-seq wild-type MEF Replicate 2


title: RNA-seq of hsf-1(sy441);rmSi1[hsf-1::gfp] L2 larvae at 20°C, replicate 2


title: Sample_167_1_K27Ac

description: H3K27Ac ChIP in mouse cells with scramble shRNA control 167_1


title: RNA-seq of hsf-1(sy441);rmSi1[hsf-1::gfp] L2 larvae at 34°C, replicate 1


title: RNA-seq of hsf-1(sy441) L2 larvae at 34°C, replicate 1


title: RNA-seq of hsf-1(sy441) L2 larvae at 20°C, replicate 3


title: RNA-seq of hsf-1(sy441);rmSi1[hsf-1::gfp] L2 larvae at 20°C, replicate 1


title: RNA-seq of hsf-1(sy441) L2 larvae at 20°C, replicate 1


title: RNA-seq of hsf-1(sy441) L2 larvae at 20°C, replicate 2


title: TY1072 MYS-1 RNAi L3 rep5

city: Ann Arbor

first: Gyorgyi

last: Csankovszki

state: MI

address: 830 N. University Ave.

department: MCDB

institute: University of Michigan

data_processing:
Reads were trimmed for quality using the TrimGalore program from Babraham Bioinformatics and aligned to the C. elegans genome version WS235 with Tophat v 2.0.13. Default parameters allow up to 20 hits for each read. Gene expression was quantified using Cufflinks v2.2.1 with use of “rescue method” for multi-reads and supplying gene annotation for WS235. Gene count estimation was performed using HTSeq-count tool v0.6.0 in the default “union” mode.  Differential expression analysis was performed using DESeq2 v1.6.3 in R version 3.2.3. All analyses were performed which genes that had average expression level above 1 RPKM (reads per kilobase per million, as calculated by Cufflinks).
supplementary_files_format_and_content: tab-delimited text files include RPKM values, and values from DESeq2 (log2 fold change of (mutant/control) and p-values after adjustment for multiple test correction)
Genome_build: C. elegans genome version WS235

source_name: L3 worms

growth_protocol: Worms were synchronized by bleaching gravid adults to isolate embryos and allowing worms to hatch overnight. Newly hatched L1 larval worms were plated and grown for 24 hours on NGM plates or RNAi plates with OP50 or RNAi construct.

extract_protocol:
RNA was extracted and precipitated using the manufacturer's instructions. Total RNA was cleaned using the Qiagen RNeasy kit.
Non-stranded mRNA-seq libraries were prepared using TruSeq RNA Library Preperation Kit.

treatment_protocol: Packed larvae were resuspended in 10V of Trizol and frozen at -80C.


title: TY1072 MYS-1 RNAi L3 rep4


title: TY1072 MYS-1 RNAi L3 rep3


title: TY1072 MYS-1 RNAi L3 rep1


title: TY1072 Vector RNAi L3 rep5


title: TY1072 Vector RNAi L3 rep4


title: TY1072 Vector RNAi L3 rep2


title: TY1072 Vector RNAi L3 rep3


title: TY1072 Vector RNAi L3 rep1


title: EKM71 L3 rep2


title: EKM71 L3 rep3


title: N2 L3 rep3


title: N2 L3 rep4


title: RNA-seq of hsf-1(ok600); rmSi1[hsf-1::gfp], replicate 2

data_processing:
RNA-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using TopHat2 (Kim et al. 2013) with default settings except that the proper intron size for C. elegans genes (10 to 22000 bp) was used.
Expression analyses were done using Cuffdiff (Trapnell et al. 2010) with quartile normalization. The exon model used in the analyses was based on the gtf file queried from Wormbase (WS220).
Genome_build: ce10/WS220
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and gene differential expression testing results

growth_protocol: Age synchronization was achieved by egg lay in a 2h period and 500 L2 larvae (30h post egg lay) were pooled from multiple collections for one experiment. hsf-1(ok600) animals were  collected by picking GFP negative young larvae hatched from eggs of OG576 hsf-1(ok600)I/hT2[bli-4(e937) let-?(q782) qIs48 [pmyo-2::gfp; ppes-10::gfp; pges-1::gfp](I;III).

extract_protocol:
RNA was extracted using Trizol and QIAGEN RNeasy RNA extraction kit with on-column DNaseI digestion as per manufacturer’s instructions.
PrepX SPIA RNA-Seq library protocol using Nugen Ovation RNA-Seq V2 kit

value: hsf-1(ok600); rmSi1[hsf-1::gfp]


title: N2 L3 rep1


title: Input DNA for ChIPs in YA animals

data_processing:
ChIP-seq reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie 1.1.2 (Langmead 2010) with default settings. Given that several classical heat shock genes (eg. hsp-16.41/hsp-16.2 and F44E5.4/F44E5) are duplicated in C. elegans genome, in addition to uniquely aligned reads, reads with two reportable alignments were also kept. This setting significantly improved occupancy measure and peak calling at the duplicated HSP gene promoters without changing the overall analysis at other loci. Aligned reads were filtered against ModENCODE blacklists (Araya et al. 2014).
The insert size was determined with tools on GeneTrack (Albert et al. 2008) and aligned ChIP-seq reads from both strands were shifted accordingly towards the center.
ChIP-seq data were normalized against the total aligned reads for comparison between experiments. The bedgraph files were generated with bedtools for combined reads from two replicates.
Genome_build: ce10/WS220
Supplementary_files_format_and_content: The bedgraph files were generated with bedtools for combined reads from two replicates and show normalized coverage as reads per million (RPM).

source_name: young adults

growth_protocol: Age synchronization was achieved by treatment of alkaline hypochlorite solution and eggs were hatched in M9. L1 larvae were transferred to 10 cm NGM plates seeded with OP50 and grown at 20°C to desired stage.

extract_protocol:
Worms were collected and washed in cold M9 buffer, crosslinked with 2% formaldehyde at room temperature for 15 min., re-suspended in FA buffer, lysed by douncing in a Kontes 2 ml glass dounce and sonicated in Bioruptor to yield 200 bp–800 bp size DNA fragments. Extracts corresponding to 200 μg of protein from L2 Larvae or 400 μg of protein from young adults was used for each pull-down. For ChIP-seq analysis of HSF-1 and Pol II, 5 μl of antibody against GFP (clontech, polyclonal) or 2.5 μl of antibody against Pol II (Novus) was used in each immunoprecipitation. DNA was pooled from 6 immunoprecipitations for each ChIP-seq experiment.
Libraries were prepared following PrepX DNA library protocol with Appollo 324 system.

value: young adults

value: unc-119(ed9)III, rmSi1[hsf-1p(4kb)::hsf-1(minigene)::gfp::3'UTR(hsf-1)+Cbrunc-119(+)] II; hsf-1(ok600)I

value: Input


title: RNA-seq of N2, replicate 3


title: RNA-seq of N2, replicate 1


title: RNA-seq of hsf-1(ok600); rmSi1[hsf-1::gfp], replicate 3


title: RNA-seq of hsf-1(ok600), replicate 3


title: RNA-seq of N2, replicate 2


title: ChIP-seq of Pol II in YA animals at 34°C, replicate 2

description: Processed data file: YA-HS-PolII_combined.bedgraph


title: EKM71 L3 rep1


title: RNA-seq of hsf-1(ok600), replicate 1


title: Input DNA for ChIPs in L2 Larvae


title: ChIP-seq of Pol II in YA animals at 20°C, replicate 2

description: Processed data file: YA-control-PolII_combined.bedgraph


title: ChIP-seq of Pol II in YA animals at 34°C, replicate 1


title: ChIP-seq of HSF-1 in YA animals at 34°C, replicate 2

description: Processed data file: YA-HS-HSF_combined.bedgraph

value: anti-GFP (clontech, #632592)


title: EKM71 L3 rep4


title: ChIP-seq of Pol II in YA animals at 20°C, replicate 1


title: ChIP-seq of HSF-1 in YA animals at 20°C, replicate 2

description: Processed data file: YA-control-HSF_combined.bedgraph


title: ChIP-seq of HSF-1 in YA animals at 34°C, replicate 1


title: ChIP-seq of Pol II in L2 larvae at 34°C, replicate 2

description: Processed data file: L2-HS-PolII_combined.bedgraph


title: RNA-seq of hsf-1(ok600); rmSi1[hsf-1::gfp], replicate 1


title: N2 L3 rep2


title: ChIP-seq of Pol II in L2 larvae at 34°C, replicate 1


title: RNA-seq of hsf-1(ok600), replicate 2


title: TY1072 MYS-1 RNAi L3 rep2


title: ChIP-seq of Pol II in L2 larvae at 20°C, replicate 2

description: Processed data file: L2-control-PolII_combined.bedgraph


title: ChIP-seq of HSF-1 in L2 larvae at 34°C, replicate 2

description: Processed data file: L2-HS-HSF_combined.bedgraph


title: ChIP-seq of Pol II in L2 larvae at 20°C, replicate 1


title: ChIP-seq of HSF-1 in L2 larvae at 20°C, replicate 2

description: Processed data file: L2-control-HSF_combined.bedgraph


title: ChIP-seq of HSF-1 in L2 larvae at 20°C, replicate 1


title: RNA-seq of L2 larvae at 34°C, replicate 3


title: RNA-seq of L2 larvae at 34°C, replicate 1


title: RNA-seq of L2 larvae at 34°C, replicate 2


title: RNA-seq of L2 larvae at 20°C, replicate 2


title: RNA-seq of L2 larvae at 20°C, replicate 1


title: s293T

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

data_processing:
Tophat (ver. 2.0.7) and Cufflinks (ver. 2.1.1; https://main.g2.bx.psu.edu/) software suites were used to analyze the RNA deep sequencing data according to Trapnell et al. (2010).
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562-578 (2012) (PMID 22383036).
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: embryonic kidney cell line, 293T

growth_protocol: The human breast cancer cell line MCF-7 and human embryonic kidney cell line 293T were cultured in Dulbecco’s modified Eagle’s medium (Hyclone) containing 10% FBS (Hyclone), 100 U/mL penicillin (Sigma), and 100 µg/mL streptomycin (Sigma).

extract_protocol:
Total RNA was isolated from the cells [monolayer (mMCF-7 and m293T) and sphere (sMCF-7 and s293T) culture conditions] using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated with RNase-free DNase I (Promega, Madison, WI, USA) to eliminate DNA contamination. The RNA concentration and quality were determined using a NanoDrop® ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and the Agilent RNA Integrity number (RIN) (Schroeder et al., 2006) was evaluated using the Agilent 2100 Bioanalyzer and the Agilent RNA 6000 Nano kit (Agilent Technology, Santa Clara, CA, USA). The absorbance ratio at 260:280 nm for all samples was >1.8 and the RIN value was > 9. The integrity of RNA samples was also ascertained by the presence of distinct 28S and 18S ribosomal RNA bands in agarose gels after electrophoretic resolution.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For 3D-sphere culture, cells were plated at a density of 1×104 cells/mL in DMEM/F-12 medium (Hyclone) supplemented with B27 (Gibco), 10 ng/ mL bFGF (Gibco) and 20 ng/ mL EGF (Sigma) on 0.5% poly(2-hydroxyethyl methacrylate) (poly-HEMA; Sigma)-coated dishes.

tag: cell line

tag: culture condition

value: sphere (s) forming cell

tag: type

value: wild type (WT)


title: mMCF7

source_name: breast cancer cell line, MCF7

value: monolayer (m) cultured cell


title: RNA-seq of L2 larvae at 20°C, replicate 3

tag: genotype

value: wild type


title: m293T


title: E14_MS13T84

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description:
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E14.
Long-tailed macaque (M. f. fascicularis) -- Brunei, Cambodia, Indonesia, Malaysia, Philippines, Singapore, Thailand, and Vietnam.
Processed data file: expression_RPM.txt

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-c -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the Cynomolgus monkey genome Macaca_fascicularis_5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the "—no-coverage-search" option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the "—compatible-hits-norm", "—no-length-correction" and "—library-type fr-secondstrand" options and Macaca_fascucularis_5.0 reference gene annotations with extended TTSs. We also set the cufflinks option "—max-mle-iterations" to 50,000, because default iterations (5,000) resulted in "FAILED" when estimating the expression levels of some genes. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: expression_RPM.txt: Tab-delimited text file includes RPM values for each Sample.

organism: Macaca fascicularis

source_name: Cynomolgus monkey embryo E14

extract_protocol:
RNA preparation, cDNA synthesis and amplification from single cells were performed essentially as reported in Kurimoto, K.et al., Nucleic Acids Research, 34(5), e42.
Library constructions for SOLiD System were performed as reported in Nakamura et al., Nucleic Acids Res. (2015).

tag: subspecies

value: fascicularis

value: embryo


title: ChIP-seq of HSF-1 in YA animals  at 20°C, replicate 1

tag: chip antibody


title: E55m_MS11T44

description:
Single cell transcriptome of amplified cDNA from cynomolgus monkey gonadal cells at E55.
Long-tailed macaque (M. f. fascicularis) -- Brunei, Cambodia, Indonesia, Malaysia, Philippines, Singapore, Thailand, and Vietnam.
Processed data file: expression_RPM.txt

source_name: Gonads of male cynomolgus monkey E55

value: gonad

tag: gender

value: male


title: E55m_MS11T45


title: E17_MS11T50

description:
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E17.
Long-tailed macaque (M. f. fascicularis) -- Brunei, Cambodia, Indonesia, Malaysia, Philippines, Singapore, Thailand, and Vietnam.
Processed data file: expression_RPM.txt

source_name: Cynomolgus monkey embryo E17


title: sMCF7


title: E47m_MS11T43

description:
Single cell transcriptome of amplified cDNA from cynomolgus monkey gonadal cells at E47.
Long-tailed macaque (M. f. fascicularis) -- Brunei, Cambodia, Indonesia, Malaysia, Philippines, Singapore, Thailand, and Vietnam.
Processed data file: expression_RPM.txt

source_name: Gonads of male cynomolgus monkey E47


title: E36m_MS11T42

description:
Single cell transcriptome of amplified cDNA from cynomolgus monkey gonadal cells at E36.
Long-tailed macaque (M. f. fascicularis) -- Brunei, Cambodia, Indonesia, Malaysia, Philippines, Singapore, Thailand, and Vietnam.
Processed data file: expression_RPM.txt

source_name: Gonads of male cynomolgus monkey E36


title: E36m_MS11T39


title: E36m_MS11T37


title: E36m_MS11T40


title: E36m_MS11T36


title: E13_MS10T42

description:
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E13.
Long-tailed macaque (M. f. fascicularis) -- Brunei, Cambodia, Indonesia, Malaysia, Philippines, Singapore, Thailand, and Vietnam.
Processed data file: expression_RPM.txt

source_name: Cynomolgus monkey embryo E13


title: E13_MS10T41


title: ChIP-seq of HSF-1 in L2 larvae at 34°C, replicate 1

tag: strain


title: E16_MS09T64

description:
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E16.
Long-tailed macaque (M. f. fascicularis) -- Brunei, Cambodia, Indonesia, Malaysia, Philippines, Singapore, Thailand, and Vietnam.
Processed data file: expression_RPM.txt

source_name: Cynomolgus monkey embryo E16


title: E13_MS10T38


title: E17_MS11T51


title: E20_MS09T80

description:
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E20.
Long-tailed macaque (M. f. fascicularis) -- Brunei, Cambodia, Indonesia, Malaysia, Philippines, Singapore, Thailand, and Vietnam.
Processed data file: expression_RPM.txt

source_name: Cynomolgus monkey embryo E20


title: E16_MS09T61


title: E16_MS09T62


title: E16_MS09T63


title: E16_MS09T59


title: E16_MS09T55


title: E16_MS09T58


title: E16_MS09T56


title: E16_MS09T54


title: E16_MS09T57


title: E20_MS08T85


title: E20_MS08T84


title: E20_MS08T82


title: E20_MS08T81


title: E20_MS08T78


title: E36m_MS11T41


title: E20_MS08T79


title: E20_MS08T83


title: sRNAs from Fusarium graminearum mutant strain Fgago1 Fgago2 at 5 days after sexual induction

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

institute: Seoul National University

description: small RNA

data_processing:
Removed adaptors. Sequences without adapters were discarded. Small RNA sequences that did not match tRNA and rRNA sequences were selected.
Genome_build: FGDB_v32  (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/)
Supplementary_files_format_and_content: tab-delimited text files include small RNA sequences and raw counts

organism: Fusarium graminearum

source_name: Fungi culture

growth_protocol: Fungal strain was grown at 25 ºC under near UV light for 5 days after sexual induction

extract_protocol: Illumina Small RNA Sample Preparation Kit v1 and sequenced with Illumina HiSeq2000.

value: Fusarium graminearum Fgago1 Fgago2 mutant strain


title: sRNAs from Fusarium graminearum mutant strain Fgago1 at 5 days after sexual induction

description: small RNA

value: Fusarium graminearum Fgago1 mutant strain


title: sRNAs from Fusarium graminearum mutant strain Fgago2 at 5 days after sexual induction

description: small RNA

value: Fusarium graminearum Fgago2 mutant strain


title: mRNAs from Fusarium graminearum mutant strain Fgago1 Fgago2 at 5 days after sexual induction

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample.

extract_protocol: Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol, and sequenced with Illumina HiSeq2000.

value: Fgago1 Fgago2 mutant

value: fungal culture

value: 5 days after sexual induction


title: sRNAs from Fusarium graminearum mutant strain Fgdicer1 Fgdicer2 at 5 days after sexual induction

description: small RNA

value: Fusarium graminearum Fgdicer1 Fgdicer2 mutant strain


title: mRNAs from Fusarium graminearum mutant strain Fgago2 at 5 days after sexual induction

value: Fgago2 mutant


title: mRNAs from Fusarium graminearum mutant strain Fgago1 at 5 days after sexual induction

value: Fgago1 mutant


title: E16_MS09T60


title: mRNAs from Fusarium graminearum mutant strain Fgdicer1 Fgdicer2 at 5 days after sexual induction

value: Fgdicer1 Fgdicer2 mutant


title: sRNAs from Fusarium graminearum mutant strain Fgdicer2 at 5 days after sexual induction

description: small RNA

value: Fusarium graminearum Fgdicer2 mutant strain


title: mRNAs from Fusarium graminearum mutant strain Fgdicer2 at 5 days after sexual induction

value: Fgdicer2 mutant


title: Input TY1072 L3 rep3

data_processing:
Reads were trimmed for quality using the Trim Galore! v0.3.7 program from Babarham Bioinformatics and aligned to the C. elegans genome version WS235 with Bowtie 1.1.1. We allowed up to two mismatches, returned only the best alignment, and restricted a read to map to at most four locations in the genome. MACS2 version 2.1.0 was first used to filter duplicates reads and to correct for bias downsampling was performed in either the input or the ChIP. Multiple replicates (input and ChIP) were input into MACS2 callpeak with options --broad and p-value (-p 1e-5) for peak calling and genome-wide coverage. MACS2 coverage reads were normalized to the genome-wide median coverage, excluding the mitochondrial chromosome and final ChIP enrichment scores per base were obtained by subtracting the input coverage. For XO hermaphrodites, X and autosomes were normalized separately, due to having half the amount of X reads compared to autosomes. MACS2 coverage reads on the autosomes were normalized to the genome-wide median coverage, whereas MACS2 coverage reads on X chromosome were normalized to half the genome-wide median coverage and final ChIP enrichment scores were combined after normalization. Lastly datasets were standardized by z-score transformation of the ChIP enrichment values based on the presumed background. Annotation of ChIP binding sites was done using the cis-regulatory element annotation system (CEAS) with default settings. The ChIP-seq data was visualized by IGV browser.
supplementary_files_format_and_content: Bed files were generated by MACS2  inputing all replicates with options --broad and p-value (-p 1e-5). Wig files were generated using MACS2 coverage reads and were normalized and standardized by z-score transformation.
Genome_build: C. elegans genome version WS235

extract_protocol:
The pellet was resuspended in one volume of FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) plus protease and phosphatase inhibitors. To obtain chromatin fragments lysate was sonicated on high, for 30 seconds on 30 seconds off, two times for 10 minutes and one time for 15 minutes. 50 ul of the lystate was used to make IP input library. 3 ug of anti-H4K16ac (Millipore 07-329) was added to 400 ul of lysate (containing approximately 50 ug DNA) for ChIP.
ChIP DNA were ligated to Illumina adaptors and amplified by PCR. Library DNA between 200-550 bp in size.

treatment_protocol: Frozen synchronized L3 worm pellets were crushed (pulverized by grinding in liquid nitrogen with a mortar and pestle) and crosslinked in ten volumes of 1.1% formaldehyde in PBS plus protease and phosphatase inhibitors. The lysate was rotated at room temperature for 20 minutes. 2.5 M glycine was added to a final concentration of 125mM and rocked gently for 5 minutes at room temperature to quench formaldehyde. Lysate was spun at 4000 x g for 3 minutes and the supernatant was removed. The pellet was resuspended in 10 ml of cold PBS plus protease and phosphatase inhibitors and pelleted by spinning at 4000 x g for 3 minutes.


title: mRNAs from Fusarium graminearum wild-type strain Z-3639 at 5 days after sexual induction

value: wild-type


title: Input TY1072 L3 rep2


title: Input TY1072 L3 rep1


title: Input N2 L3 rep3

data_processing:
Reads were trimmed for quality using the Trim Galore! v0.3.7 program from Babarham Bioinformatics and aligned to the C. elegans genome version WS235 with Bowtie 1.1.1. We allowed up to two mismatches, returned only the best alignment, and restricted a read to map to at most four locations in the genome. MACS2 version 2.1.0 was first used to filter duplicates reads and to correct for bias downsampling was performed in either the input or the ChIP. Multiple replicates (input and ChIP) were input into MACS2 callpeak with options --broad and p-value (-p 1e-5) for peak calling and genome-wide coverage. MACS2 coverage reads were normalized to the genome-wide median coverage, excluding the mitochondrial chromosome and final ChIP enrichment scores per base were obtained by subtracting the input coverage. Lastly datasets were standardized by z-score transformation of the ChIP enrichment values based on the presumed background. Annotation of ChIP binding sites was done using the cis-regulatory element annotation system (CEAS) with default settings. The ChIP-seq data was visualized by IGV browser.
supplementary_files_format_and_content: Bed files were generated by MACS2  inputing all replicates with options --broad and p-value (-p 1e-5). Wig files were generated using MACS2 coverage reads and were normalized and standardized by z-score transformation.
Genome_build: C. elegans genome version WS235


title: H4K16ac TY1072 L3 rep1


title: H4K16ac TY1072 L3 rep2


title: Input N2 L3 rep1


title: H4K16ac N2 L3 rep3


title: sRNAs from Fusarium graminearum mutant strain Fgdicer1 at 5 days after sexual induction

description: small RNA

value: Fusarium graminearum Fgdicer1 mutant strain


title: H4K16ac N2 L3 rep1


title: DNA input_T47D

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: DNA from T47D cells treated with E2

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 with the default configurations
peaks were called using MACS Peak Calling with default setting
PeakAnalyzer_1.4 and HOMER peak analysis software was used to annotate peaks
Genome_build: hg19
Supplementary_files_format_and_content: bed file with peaks called by MACS.  During Peak calling ERa_E2 was treated as Chip and Input as control.

source_name: T47D breast cancer cell line

growth_protocol: Cells were maintained in 10% FBS containing media.

extract_protocol:
Lysates were clarified from sonicated nuclei and ERα complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured in steroid depleted media for 48 h and treated with 10 nM 17β-estradiol for 45 min.

tag: cell type

value: ERalpha-positive breast cancer cells


title: sRNAs from Fusarium graminearum wild-type strain Z-3639 at 5 days after sexual induction

description: small RNA

value: Fusarium graminearum wild-type strain


title: H4K16ac N2 L3 rep2


title: FireFighter_1_IP_Male

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

data_processing:
Library strategy: MIRA-seq
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to hg19 using bwa
bed files were generated from bam files using the bedtools package
Further analysis based on bed files were done using the MEDIPS R package
Genome_build: hg19
Supplementary_files_format_and_content: Bed and wig with normalized reliative methylation score (rms) files for MIRA-Seq data.

source_name: whole blood

extract_protocol:
DNA was extracted from whole blood using DNeasy Blood & Tissue kit (Qiagen, Valencia, CA)
MIRA-seq libraries were firstly constructed using Illumina’s TruSeq DNA Sample Preparation Kit-Set A/B (P/N FC-121-1001/1002). Briefly, ends of MIRA enriched methylated DNA (~40-100ng) were repaired and an ‘A’ base added to the 3’ for ligating DNAs to the adapters. Following ligation, the DNA resolved in 2% agarose gel was size-selected, with200±25bp fragments for library amplification.

treatment_protocol: Two different population

value: blood cells

tag: group

value: exposed

tag: Sex

value: Male


title: FireFighter_1_IN_Male


title: Control_1_IN_Male

value: non-exposed


title: mRNAs from Fusarium graminearum mutant strain Fgdicer1 at 5 days after sexual induction

value: Fgdicer1 mutant


title: Bcl6Cd4cre Th1 Rep1

city: Kisarazu

first: Osamu

last: Ohara

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Technology Development

institute: Kazusa DNA Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Read alignment: TopHat2 v2.0.8 with default settings
expression level: Cufflinks v2.1.1 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM (FPKM) values for each Sample .

source_name: helper T cell

extract_protocol:
Spleen were removed, stained TH1 cells or TFH cells were sorted using flow cytometer, and RNA was harvested using Trizol reagent.
RNA sequencing libraries were prepared using a kit from Illumina (TruSeq sample prep kit v2; for samples 1-7) or New England Biolabs (NEBNext Ultra RNA Library Prep kit; the rest of samples)
RNA sequencing was done with an Illumina HiSeq1500 on a 50-base single-end mode.

value: spleen

tag: age

value: 8 weeks

value: Bcl6f/f Cd4cre


title: Control_1_IP_Male


title: WT Th1 Rep1

value: wild type


title: Bcl6Cd4cre CXCR3+CXCR5dull Rep2


title: Bcl6Cd4cre CXCR3+CXCR5dull Rep1


title: H4K16ac TY1072 L3 rep3


title: WT Th1 Rep2


title: Bcl6Cd4cre Th1 Rep2


title: Bcl6Mb1cre Th1 Rep2

value: Bcl6f/f Mb1cre


title: CXCR3+CXCR5- Rep2


title: Bcl6Mb1cre Th1 Rep1


title: CXCR3+CXCR5dull Rep2


title: CXCR5+ Rep2


title: CXCR5+ Rep1


title: CXCR3+CXCR5dull Rep1


title: CXCR3+CXCR5- Rep1


title: Input N2 L3 rep2


title: CXCR3+CXCR5+


title: CXCR3-CXCR5+


title: ERα_ChIPseq_E2_T47D

description: ERalpha antibody used in T47D cells treated with E2

value: ERalpha (H-20, Santa Cruz)


title: Th17


title: IFNg+CXCR3+


title: Tfh


title: Sample_1_DLBCL3

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

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

source_name: DLBCL patient

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

value: DLBCL


title: Th2


title: Th1


title: Naïve CD4T


title: single cell RNAseq normal B cells [1350H09_Normal_H09]

status: Public on Oct 11 2016

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

data_processing:
Sequenced reads were mapped to the human gemome (hg19) by Bowtie/Tophat using the Broad pipeline.
Only single cell samples with at least 100.000 paired-end reads and a minimum of 20% aligning to the genome were retained for further analysis.
FeatureCounts was used to count features based on the Gencode v19 transcriptome annotation.
Only features detected in at least 10 single cell samples were used and further refinement of high quality samples was based on feature complexity, read distribution and number of features detected.
DESeq2 was used with raw counts to estimate differential expression between tumor and normal cells.
Counts were normalized according to their library size and displayed as log2(normalized counts + 1).
Genome_build: hg19
Supplementary_files_format_and_content: fcount_primary_output: matrix of raw feature counts

extract_protocol:
Live CD45+ and CD19+ cells were sorted in 2ul of Qiagen TCL buffer in 96-well plates
SmartSeq2 protocol with modifications (Trombetta et al., 2014)

tag: condition

value: Normal

value: B cells


title: single cell RNAseq normal B cells [1350H10_Normal_H10]


title: single cell RNAseq normal B cells [1350H11_Normal_H11]


title: single cell RNAseq tumor B cells [1350H10_Tumor_H10]

value: Tumor


title: single cell RNAseq tumor B cells [1350H12_Tumor_H12]


title: single cell RNAseq tumor B cells [1350H09_Tumor_H09]


title: single cell RNAseq tumor B cells [1350H06_Tumor_H06]


title: single cell RNAseq tumor B cells [1350H08_Tumor_H08]


title: single cell RNAseq normal B cells [1350H07_Normal_H07]


title: single cell RNAseq normal B cells [1350H06_Normal_H06]


title: single cell RNAseq tumor B cells [1350H04_Tumor_H04]


title: single cell RNAseq tumor B cells [1350H05_Tumor_H05]


title: single cell RNAseq tumor B cells [1350H07_Tumor_H07]


title: single cell RNAseq tumor B cells [1350H03_Tumor_H03]


title: single cell RNAseq tumor B cells [1350H02_Tumor_H02]


title: iTreg


title: single cell RNAseq normal B cells [1350H03_Normal_H03]


title: Sample_1_DLBCL1


title: single cell RNAseq normal B cells [1350H01_Normal_H01]


title: single cell RNAseq tumor B cells [1350H01_Tumor_H01]


title: single cell RNAseq normal B cells [1350G12_Normal_G12]


title: Sample_2_DLBCL2


title: single cell RNAseq normal B cells [1350H02_Normal_H02]


title: single cell RNAseq tumor B cells [1350G11_Tumor_G11]


title: single cell RNAseq normal B cells [1350H08_Normal_H08]


title: single cell RNAseq tumor B cells [1350H11_Tumor_H11]


title: single cell RNAseq tumor B cells [1350G12_Tumor_G12]


title: single cell RNAseq normal B cells [1350H05_Normal_H05]


title: single cell RNAseq normal B cells [1350H04_Normal_H04]


title: single cell RNAseq normal B cells [1350G08_Normal_G08]


title: single cell RNAseq tumor B cells [1350G08_Tumor_G08]


title: single cell RNAseq normal B cells [1350G07_Normal_G07]


title: single cell RNAseq tumor B cells [1350G07_Tumor_G07]


title: single cell RNAseq tumor B cells [1350G05_Tumor_G05]


title: single cell RNAseq tumor B cells [1350G09_Tumor_G09]


title: single cell RNAseq tumor B cells [1350G10_Tumor_G10]


title: single cell RNAseq normal B cells [1350G10_Normal_G10]


title: single cell RNAseq tumor B cells [1350G06_Tumor_G06]


title: single cell RNAseq tumor B cells [1350G04_Tumor_G04]


title: single cell RNAseq normal B cells [1350G06_Normal_G06]


title: single cell RNAseq tumor B cells [1350G03_Tumor_G03]


title: single cell RNAseq normal B cells [1350G09_Normal_G09]


title: single cell RNAseq normal B cells [1350G03_Normal_G03]


title: single cell RNAseq normal B cells [1350G04_Normal_G04]


title: single cell RNAseq normal B cells [1350G05_Normal_G05]


title: single cell RNAseq tumor B cells [1350G02_Tumor_G02]


title: single cell RNAseq tumor B cells [1350G01_Tumor_G01]


title: single cell RNAseq tumor B cells [1350F12_Tumor_F12]


title: single cell RNAseq normal B cells [1350G01_Normal_G01]


title: single cell RNAseq normal B cells [1350G02_Normal_G02]


title: single cell RNAseq normal B cells [1350F12_Normal_F12]


title: single cell RNAseq normal B cells [1350F11_Normal_F11]


title: single cell RNAseq tumor B cells [1350F11_Tumor_F11]


title: single cell RNAseq tumor B cells [1350F10_Tumor_F10]


title: single cell RNAseq normal B cells [1350G11_Normal_G11]


title: single cell RNAseq tumor B cells [1350F09_Tumor_F09]


title: single cell RNAseq normal B cells [1350F10_Normal_F10]


title: single cell RNAseq normal B cells [1350F09_Normal_F09]


title: single cell RNAseq tumor B cells [1350F08_Tumor_F08]


title: single cell RNAseq normal B cells [1350F08_Normal_F08]


title: single cell RNAseq normal B cells [1350F07_Normal_F07]


title: single cell RNAseq tumor B cells [1350F06_Tumor_F06]


title: single cell RNAseq normal B cells [1350F05_Normal_F05]


title: single cell RNAseq normal B cells [1350F06_Normal_F06]


title: single cell RNAseq tumor B cells [1350F05_Tumor_F05]


title: single cell RNAseq tumor B cells [1350F04_Tumor_F04]


title: single cell RNAseq tumor B cells [1350F03_Tumor_F03]


title: single cell RNAseq normal B cells [1350F02_Normal_F02]


title: single cell RNAseq tumor B cells [1350F02_Tumor_F02]


title: single cell RNAseq normal B cells [1350F04_Normal_F04]


title: single cell RNAseq normal B cells [1350F01_Normal_F01]


title: single cell RNAseq tumor B cells [1350E10_Tumor_E10]


title: single cell RNAseq normal B cells [1350F03_Normal_F03]


title: single cell RNAseq normal B cells [1350E11_Normal_E11]


title: single cell RNAseq normal B cells [1350E12_Normal_E12]


title: single cell RNAseq tumor B cells [1350E11_Tumor_E11]


title: single cell RNAseq tumor B cells [1350E12_Tumor_E12]


title: single cell RNAseq tumor B cells [1350F01_Tumor_F01]


title: single cell RNAseq normal B cells [1350H12_Normal_H12]


title: single cell RNAseq normal B cells [1350E10_Normal_E10]


title: single cell RNAseq tumor B cells [1350E09_Tumor_E09]


title: single cell RNAseq tumor B cells [1350E08_Tumor_E08]


title: single cell RNAseq normal B cells [1350E08_Normal_E08]


title: single cell RNAseq tumor B cells [1350E07_Tumor_E07]


title: single cell RNAseq normal B cells [1350E09_Normal_E09]


title: single cell RNAseq tumor B cells [1350F07_Tumor_F07]


title: single cell RNAseq tumor B cells [1350E06_Tumor_E06]


title: single cell RNAseq normal B cells [1350E06_Normal_E06]


title: single cell RNAseq normal B cells [1350E04_Normal_E04]


title: single cell RNAseq tumor B cells [1350E05_Tumor_E05]


title: single cell RNAseq tumor B cells [1350E03_Tumor_E03]


title: single cell RNAseq normal B cells [1350E02_Normal_E02]


title: single cell RNAseq tumor B cells [1350E02_Tumor_E02]


title: single cell RNAseq normal B cells [1350E03_Normal_E03]


title: single cell RNAseq tumor B cells [1350E01_Tumor_E01]


title: single cell RNAseq normal B cells [1350D12_Normal_D12]


title: single cell RNAseq normal B cells [1350E01_Normal_E01]


title: single cell RNAseq normal B cells [1350D11_Normal_D11]


title: single cell RNAseq tumor B cells [1350D08_Tumor_D08]


title: single cell RNAseq tumor B cells [1350D10_Tumor_D10]


title: single cell RNAseq tumor B cells [1350D11_Tumor_D11]


title: single cell RNAseq normal B cells [1350D10_Normal_D10]


title: single cell RNAseq tumor B cells [1350D12_Tumor_D12]


title: single cell RNAseq tumor B cells [1350D07_Tumor_D07]


title: single cell RNAseq normal B cells [1350D07_Normal_D07]


title: single cell RNAseq tumor B cells [1350D06_Tumor_D06]


title: single cell RNAseq normal B cells [1350D08_Normal_D08]


title: single cell RNAseq tumor B cells [1350D05_Tumor_D05]


title: single cell RNAseq normal B cells [1350D05_Normal_D05]


title: single cell RNAseq normal B cells [1350E07_Normal_E07]


title: single cell RNAseq normal B cells [1350D09_Normal_D09]


title: single cell RNAseq tumor B cells [1350D04_Tumor_D04]


title: single cell RNAseq normal B cells [1350D04_Normal_D04]


title: single cell RNAseq normal B cells [1350E05_Normal_E05]


title: single cell RNAseq tumor B cells [1350D03_Tumor_D03]


title: single cell RNAseq tumor B cells [1350E04_Tumor_E04]


title: single cell RNAseq tumor B cells [1350D02_Tumor_D02]


title: single cell RNAseq tumor B cells [1350D09_Tumor_D09]


title: single cell RNAseq normal B cells [1350D03_Normal_D03]


title: single cell RNAseq normal B cells [1350D02_Normal_D02]


title: single cell RNAseq tumor B cells [1350C12_Tumor_C12]


title: single cell RNAseq tumor B cells [1350D01_Tumor_D01]


title: single cell RNAseq normal B cells [1350C12_Normal_C12]


title: single cell RNAseq normal B cells [1350C11_Normal_C11]


title: single cell RNAseq normal B cells [1350C10_Normal_C10]


title: single cell RNAseq normal B cells [1350C09_Normal_C09]


title: single cell RNAseq tumor B cells [1350C11_Tumor_C11]


title: single cell RNAseq tumor B cells [1350C08_Tumor_C08]


title: single cell RNAseq tumor B cells [1350C10_Tumor_C10]


title: single cell RNAseq normal B cells [1350C08_Normal_C08]


title: single cell RNAseq tumor B cells [1350C06_Tumor_C06]


title: single cell RNAseq tumor B cells [1350C07_Tumor_C07]


title: single cell RNAseq normal B cells [1350C07_Normal_C07]


title: single cell RNAseq tumor B cells [1350C05_Tumor_C05]


title: single cell RNAseq tumor B cells [1350C04_Tumor_C04]


title: single cell RNAseq normal B cells [1350C06_Normal_C06]


title: single cell RNAseq normal B cells [1350C05_Normal_C05]


title: single cell RNAseq normal B cells [1350D06_Normal_D06]


title: single cell RNAseq normal B cells [1350C04_Normal_C04]


title: single cell RNAseq normal B cells [1350C03_Normal_C03]


title: single cell RNAseq tumor B cells [1350C01_Tumor_C01]


title: single cell RNAseq tumor B cells [1350C02_Tumor_C02]


title: single cell RNAseq tumor B cells [1350B12_Tumor_B12]


title: single cell RNAseq normal B cells [1350C01_Normal_C01]


title: single cell RNAseq normal B cells [1350D01_Normal_D01]


title: single cell RNAseq tumor B cells [1350B11_Tumor_B11]


title: single cell RNAseq normal B cells [1350B12_Normal_B12]


title: single cell RNAseq tumor B cells [1350B10_Tumor_B10]


title: single cell RNAseq tumor B cells [1350C09_Tumor_C09]


title: single cell RNAseq normal B cells [1350B11_Normal_B11]


title: single cell RNAseq normal B cells [1350B10_Normal_B10]


title: single cell RNAseq normal B cells [1350B08_Normal_B08]


title: single cell RNAseq tumor B cells [1350B09_Tumor_B09]


title: single cell RNAseq normal B cells [1350B09_Normal_B09]


title: single cell RNAseq normal B cells [1350B07_Normal_B07]


title: single cell RNAseq tumor B cells [1350B06_Tumor_B06]


title: single cell RNAseq tumor B cells [1350B07_Tumor_B07]


title: single cell RNAseq tumor B cells [1350C03_Tumor_C03]


title: single cell RNAseq tumor B cells [1350B08_Tumor_B08]


title: single cell RNAseq normal B cells [1350B06_Normal_B06]


title: single cell RNAseq normal B cells [1350B04_Normal_B04]


title: single cell RNAseq tumor B cells [1350B03_Tumor_B03]


title: single cell RNAseq tumor B cells [1350B04_Tumor_B04]


title: single cell RNAseq tumor B cells [1350B05_Tumor_B05]


title: single cell RNAseq normal B cells [1350C02_Normal_C02]


title: single cell RNAseq tumor B cells [1350B02_Tumor_B02]


title: single cell RNAseq tumor B cells [1350B01_Tumor_B01]


title: single cell RNAseq normal B cells [1350B03_Normal_B03]


title: single cell RNAseq normal B cells [1350B02_Normal_B02]


title: single cell RNAseq normal B cells [1350B05_Normal_B05]


title: single cell RNAseq tumor B cells [1350A12_Tumor_A12]


title: single cell RNAseq normal B cells [1350A12_Normal_A12]


title: single cell RNAseq tumor B cells [1350A11_Tumor_A11]


title: single cell RNAseq tumor B cells [1350A10_Tumor_A10]


title: single cell RNAseq normal B cells [1350A11_Normal_A11]


title: single cell RNAseq normal B cells [1350A10_Normal_A10]


title: single cell RNAseq normal B cells [1350A09_Normal_A09]


title: single cell RNAseq tumor B cells [1350A08_Tumor_A08]


title: single cell RNAseq tumor B cells [1350A09_Tumor_A09]


title: single cell RNAseq tumor B cells [1350A07_Tumor_A07]


title: single cell RNAseq normal B cells [1350A08_Normal_A08]


title: single cell RNAseq normal B cells [1350A07_Normal_A07]


title: single cell RNAseq tumor B cells [1350A05_Tumor_A05]


title: single cell RNAseq tumor B cells [1350A04_Tumor_A04]


title: single cell RNAseq normal B cells [1350A04_Normal_A04]


title: single cell RNAseq tumor B cells [1350A06_Tumor_A06]


title: single cell RNAseq normal B cells [1350A06_Normal_A06]


title: single cell RNAseq tumor B cells [1350A03_Tumor_A03]


title: single cell RNAseq normal B cells [1350A03_Normal_A03]


title: single cell RNAseq tumor B cells [1350A02_Tumor_A02]


title: single cell RNAseq normal B cells [1350A02_Normal_A02]


title: single cell RNAseq normal B cells [1350A01_Normal_A01]


title: C57BL/6 x Cast female, repeat 4

city: Worcester

first: Ingolf

last: Bach

state: MA

address: 364 Plantation St

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
Sequenced reads were aligned to the mouse genome (mm10) using TopHat (version 2.0.14) with default setting except set parameter read-mismatches to 2
HTSeq (version 0.6.1p1) was used to count the features after the alignment
Bioconductor packages edgeR (version 3.10.0 ) and ChIPpeakAnno (version 3.2.0)  for transcriptome quantification, differential gene expression analysis and annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the raw count values from HTSeq for each sample. Row names are gene symbols, and column names are the sample names.

source_name: WT female_whole embryo

extract_protocol:
Whole embryos were dissected at the indicated timepoints and the correct stage was verified under the binocular. Single embryos/trophoblast cells were placed in 10ul TCL Buffer (Qiagen) supplemented with 1% BME, and snap frozen.
RNA libraries were prepared for sequencing using standard Illumina protocols.  The embryo, trophoblast or mock samples were distributed on two 96-well plates and thawed at RT for 10 minutes prior to RNA purification using Ampure RNA beads (Beckmann-Coulter). RNA samples were re-suspended in solution containing 3’ RT primer and dNTPs. Reverse transcription was performed with SSII (Life Technologies), whose terminal transferase activity allows incorporation of a PCR binding site at the 3’ end of the cDNA using a template-switching oligonucleotide (custom synthesized from Exiqon) as a template. Subsequently, cDNA was amplified using 12 cycles of PCR, followed by tagmentation with Nextera kit (Illumina). Final libraries were amplified by 12 cycles of PCR and sequenced on a NextSeq 500. The average insert size and standard deviation (for the fastq files) were calculated with Picard Tools CollectInsertSizeMetrics.

value: C57BL/6 x Cast

tag: Stage

value: female

value: WT


title: C57BL/6 x Cast female, repeat 3


title: C57BL/6 x Cast male, repeat 4

source_name: WT male_whole embryo

value: male


title: HVpos_Ssea1pos_H3K4me3_ChIP

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

data_processing:
Basecalls performed using CASAVA version 1.5
Reads were aligned to the mm9 genome assembly using Bowtie.
Bowtie output SAM files were converted into interval files using the 'sam2interval' tool on a local instance of the Galaxy server (Genome Research. 2005 Oct; 15(10):1451-5). These interval files were then converted into .wig (aka bedgraph) files.
processed data files format and content: wig files (aka bedgraph). Scores represent raw read depth.
Genome_build: mm9

source_name: ES cells. HV+S+ FACs sorted population

growth_protocol: E14 Tg2a ESCs (129/Ola background) and the derivative line HV5.1 (Canham et al., 2010) were cultured on 0.1% gelatin (Sigma G1890) coated Corning flasks in ESC medium (GMEM (Sigma G5154) supplemented with 10% foetal calf serum (FCS), 1x MEM non-essential amino acids (Life Technologies 11140-036), 0.1 μM 2-Mercaptoethanol (Sigma M6250), 2 mM L-Glutamine (Life Technologies 25030-024), 1 mM Sodium Pyruvate (Life Technologies 11360-039), and 1,000 U/ml of Lif. For passaging, 60-90% confluent culture flasks were washed in PBS, incubated for 2-3 mins at 37°C in attenuated trypsin (0.025% trypsin (Invitrogen 15090-046), 1.27 mM EDTA, and 1% Chicken serum (Sigma C5405) in PBS (Sigma D8537)), and tapped to release ESCs from the flasks. Attenuated trypsin was inactivated by adding nine volumes of ESC medium and this mixture was repeatedly pipetted to obtain a single cell suspension. ESCs were centrifuged, resuspended in ESC medium and replated onto gelatin coated flasks at a ratio of between 1:2 and 1:10, or at ~5 x 104 cells/cm2. All centrifugation steps with live cells were performed at 330g for 3 min at room temperature (RT).

extract_protocol:
Approximately 1 x 10^6 FACS purified ESCs were centrifuged at 500g for 3 mins, washed twice in ice-cold PBS and were resuspended in 200ml of NBA buffer (85mM NaCl, 5.5% Sucrose, 10 mM TrisHCl pH 7.5, 0.2 mM EDTA, 0.2 mM PMSF, 1 mM DTT, 1x Protease inhibitors (Calbiochem, 539134-1SET )). Cells were lysed by the addition of an equal volume of NBB buffer (NBA + 0.1% NP40; SigmaAldrich - I8896) followed by incubation on ice for 3 mins. Nuclei were pelleted at 1000g for 3 mins at 4ºC, then washed with NBR buffer (85 mM NaCl, 5.5% Sucrose, 10 mM TrisHCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF and 1 mM DTT) and pelleted at 2000g for 3 mins at 4ºC. Nuclei were resuspended in NBR supplemented with RNaseA (to 20mg/ml) at a concentration of 16.7x10^6 nuclei per ml and incubated at 20 ºC for 5 mins. Chromatin was then fragmented for 10 mins at 20 ºC with the addition of 0.133 U/μl micrococcal nuclease (Boehringer units; SigmaAldrich - N3755-500UN; titrated to give predominantly mono-nucleosomes). Micrococcal Digestion was stopped with the addition of an equal volume of STOP buffer (215 mM NaCl, 10 mM TrisHCl pH 8, 20 mM EDTA, 5.5 %, Sucrose, 2 % TritonX 100, 0.2 mM PMSF, 1 mM DTT, 2X Protease Inhibitors). Digested nuclei were left on ice overnight to release soluble, fragmented chromatin. Chromatin was then centrifuged at 12,000g for 10 mins at 4ºC and the soluble chromatin (supernatant) transferred to a fresh tube. 20% of the released chromatin was retained as an input reference and the remainder incubated for 3 hours at 4ºC on a rotating wheel with anti-H3K4me3 (07-473; Millipore) antibody pre-coupled to protein A dynabeads (Life Technologies; 10002D; 1mgs of antibody bound to 10ml of dynabeads slurry per immunoprecipitation). Immune complexes bound to beads were washed three times with wash buffer 1 (150 mM NaCl, 10 mM TrisHCl pH 8, 2 mM EDTA, 1% NP40 and 1 % sodium deoxycholate) and twice in 1x TE buffer (10mM Tris pH8 and 10mM EDTA) at 4ºC on a rotating wheel for 10 mins. Chromatin was released from the beads by incubation with elution buffer (0.1 M NaHCO3 and 1 % SDS) for 15 mins at 37 ºC followed by the addition of proteinase K and Tris pH6.8 (final concentration of 100ug/ml and 100mM respectively) and incubation at 55ºC overnight. Dynabeads were removed using a magnetic rack and the chromatin purified using MinElute PCR Purification columns (Qiagen) according to manufacturer’s instructions.
ChIP libraries were prepared as previously described (Clouaire et al., 2012; PMID 22855832) with the following modifications. The end repair step was removed and the A-tailing reaction (reaction 2) was supplemented with 10 U of Polynucleotide Kinase (NEB) and 1mM ATP. Following heat inactivation, the samples were supplemented with ligation reagents (400 U of T4 DNA ligase (NEB), 1x buffer 2 (NEB), 7.5% PEG-6000, 1mM ATP and 13.3nM of annealed Illumina adaptors (PE or AU)) and incubated at 16°C overnight. Ligated DNA was purified using MinElute PCR columns (Qiagen) and eluted in 2x10 μl water. Purified libraries were amplified as previously described (Clouaire et al., 2012) and DNA fragments corresponding to mono- to tri-nucleosomes excised from an agarose gel and purified using the QIAEX II gel extraction kit according to manufacturer’s instructions (Qiagen).

treatment_protocol: For cell surface marker analysis by flow cytometry, 60-90% confluent ESC cultures were trypsinized and subsequently inactivated using nine volumes of FC buffer (10% FCS in PBS). After obtaining a single cell suspension, cells were centrifuged and resuspended in Ssea1 Mouse anti-Mouse IgM-kappa primary antibody (clone MC480; Developmental Studies Hybridoma Bank; 1:1500 in FC buffer) and incubated on ice for 15 mins. After two washes in ice cold FC buffer (10% FCS in PBS), cells were incubated in alexa647-conjugated Goat anti-Mouse secondary antibody (Molecular Probes A21238; 1:1000 in FC buffer) on ice for 15 mins, washed twice in FC buffer, and resuspended in 1 μg/ml DAPI in FC buffer to label dead cells. E14 ESCs labelled with secondary antibody and DAPI were used as negative controls. Forward and side scatter were used to filter out debris and cell clumps and DAPI staining was used to remove dead cells. Cells were run through a cell strainer (Corning 352235) prior to sorting on a BD FACSAriaIII. Sorted cells were collected at 4°C in 15 ml falcon tubes (Corning 352054) containing FC buffer. Different populations used in the same experiment were collected simultaneously and when multiple tubes of sorted cells were required, full tubes were stored on ice and pooled at the end of the sorting session. Sorted cells were checked for sufficient purity (>80% of cells detected as being in the original sorting gate) by running ~1000 cells through the sorter again.

value: mESCs. HexVenus Reporter line derived from E14Tg2a cells.

tag: purification antibody

value: anti-H3K4me3 (07-473; Millipore)


title: HVneg_Ssea1pos_H3K4me3_ChIP

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the mm9 genome assembly using Bowtie.
Bowtie output SAM files were converted into interval files using the 'sam2interval' tool on a local instance of the Galaxy server (Genome Research. 2005 Oct; 15(10):1451-5). These interval files were then converted into .wig (aka bedgraph) files.
processed data files format and content: wig files (aka bedgraph). Scores represent raw read depth.
Genome_build: mm9

source_name: ES cells. HV-S+ FACs sorted population


title: C57BL/6 x Cast female, repeat 2


title: C57BL/6 x Cast male, repeat 2


title: C57BL/6 x Cast male, repeat 3


title: C57BL/6 x Cast female, repeat 1


title: single cell RNAseq normal B cells [1350A05_Normal_A05]


title: single cell RNAseq normal B cells [1350B01_Normal_B01]


title: Xist KO female Trophoblast, repeat 2 [Xist KO]

description: Sample name: XK178

data_processing:
Sequenced reads were aligned to the mouse genome (mm10) using TopHat (version 2.0.14) with default setting except set parameter read-mismatches to 2.
HTSeq (version 0.6.1p1) was used to count the features after the alignment.
Bioconductor packages edgeR (version 3.10.0 ) and ChIPpeakAnno (version 3.2.0) for transcriptome quantification, differential gene expression analysis and annotation.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file includes the raw count values from HTSeq for each sample. Row names are gene symbols, and column names are the sample names.

source_name: Whole embryo, Xist KO, trophoblast, female

extract_protocol:
Whole embryos were dissected at the indicated timepoints and the correct stage was verified under the binocular. Single embryos/trophoblast cells were placed in 10ul TCL Buffer (Qiagen) supplemented with 1% BME, and snap frozen.
RNA libraries were prepared for sequencing using standard Illumina protocols. The embryo, trophoblast or mock samples were distributed on two 96-well plates and thawed at RT for 10 minutes prior to RNA purification using Ampure RNA beads (Beckmann-Coulter). RNA samples were re-suspended in solution containing 3' RT primer and dNTPs. Reverse transcription was performed with SSII (Life Technologies), whose terminal transferase activity allows incorporation of a PCR binding site at the 3' end of the cDNA using a template-switching oligonucleotide (custom synthesized from Exiqon) as a template. Subsequently, cDNA was amplified using 12 cycles of PCR, followed by tagmentation with Nextera kit (Illumina). Final libraries were amplified by 12 cycles of PCR and sequenced on a NextSeq 500.

tag: strain/background

tag: genotype/variation

value: Xist KO

value: trophoblast

tag: tissue

value: whole embryo


title: Xist KO female Trophoblast, repeat 3 [Xist KO]

description: Sample name: XK181

tag: developmental stage


title: Xist KO female Trophoblast, repeat 1 [Xist KO]

description: Sample name: XK177


title: WT male Trophoblast, repeat 14 [Xist KO]

description: Sample name: XK182

source_name: Whole embryo, WT, trophoblast, male


title: WT male Trophoblast, repeat 9 [Xist KO]

description: Sample name: XK95


title: WT male Trophoblast, repeat 11 [Xist KO]

description: Sample name: XK175


title: WT male Trophoblast, repeat 7 [Xist KO]

description: Sample name: XK93


title: WT male Trophoblast, repeat 8 [Xist KO]

description: Sample name: XK94


title: WT male Trophoblast, repeat 12 [Xist KO]

description: Sample name: XK179


title: WT male Trophoblast, repeat 6 [Xist KO]

description: Sample name: XK92


title: WT male Trophoblast, repeat 5 [Xist KO]

description: Sample name: XK91


title: single cell RNAseq tumor B cells [1350A01_Tumor_A01]


title: WT male Trophoblast, repeat 4 [Xist KO]

description: Sample name: XK90


title: WT male Trophoblast, repeat 3 [Xist KO]

description: Sample name: XK89


title: WT male Trophoblast, repeat 1 [Xist KO]

description: Sample name: XK85


title: WT male Trophoblast, repeat 2 [Xist KO]

description: Sample name: XK87


title: C57BL/6 x Cast male, repeat 1


title: Xist KO female E4.5, repeat 10 [Xist KO]

description: Sample name: XK172

source_name: Whole embryo, Xist KO, E4.5, female


title: Xist KO female E4.5, repeat 7 [Xist KO]

description: Sample name: XK162


title: Xist KO female E4.5, repeat 5 [Xist KO]

description: Sample name: XK80


title: Xist KO female E4.5, repeat 6 [Xist KO]

description: Sample name: XK81


title: Xist KO female E4.5, repeat 8 [Xist KO]

description: Sample name: XK170


title: Xist KO female E4.5, repeat 2 [Xist KO]

description: Sample name: XK77


title: Xist KO female E4.5, repeat 3 [Xist KO]

description: Sample name: XK78


title: Xist KO female E4.5, repeat 4 [Xist KO]

description: Sample name: XK79


title: WT male Trophoblast, repeat 13 [Xist KO]

description: Sample name: XK180


title: WT male Trophoblast, repeat 10 [Xist KO]

description: Sample name: XK174


title: Xist KO female E4.5, repeat 1 [Xist KO]

description: Sample name: XK74


title: WT male E4.5, repeat 12 [Xist KO]

description: Sample name: XK173

source_name: Whole embryo, WT, E4.5, male


title: WT male E4.5, repeat 11 [Xist KO]

description: Sample name: XK169


title: WT male E4.5, repeat 8 [Xist KO]

description: Sample name: XK165


title: WT male E4.5, repeat 5 [Xist KO]

description: Sample name: XK83


title: WT male E4.5, repeat 9 [Xist KO]

description: Sample name: XK166


title: WT male E4.5, repeat 4 [Xist KO]

description: Sample name: XK82


title: WT male E4.5, repeat 3 [Xist KO]

description: Sample name: XK76


title: WT male E4.5, repeat 2 [Xist KO]

description: Sample name: XK75


title: WT male E4.5, repeat 1 [Xist KO]

description: Sample name: XK73


title: WT male E4.5, repeat 7 [Xist KO]

description: Sample name: XK164


title: Xist KO female E4, repeat 6 [Xist KO]

description: Sample name: XK160

source_name: Whole embryo, Xist KO, E4, female


title: Xist KO female E4, repeat 4 [Xist KO]

description: Sample name: XK158


title: Xist KO female E4, repeat 2 [Xist KO]

description: Sample name: XK153


title: Xist KO female E4, repeat 1 [Xist KO]

description: Sample name: XK150


title: Xist KO female E4, repeat 5 [Xist KO]

description: Sample name: XK159


title: WT male E4, repeat 11 [Xist KO]

description: Sample name: XK157

source_name: Whole embryo, WT, E4, male


title: WT male E4, repeat 12 [Xist KO]

description: Sample name: XK161


title: Xist KO female E4, repeat 3 [Xist KO]

description: Sample name: XK154


title: WT male E4, repeat 10 [Xist KO]

description: Sample name: XK156


title: WT male E4, repeat 9 [Xist KO]

description: Sample name: XK155


title: WT male E4, repeat 8 [Xist KO]

description: Sample name: XK152


title: WT male E4, repeat 6 [Xist KO]

description: Sample name: XK71


title: WT male E4, repeat 7 [Xist KO]

description: Sample name: XK151


title: WT male E4, repeat 4 [Xist KO]

description: Sample name: XK65


title: WT male E4, repeat 2 [Xist KO]

description: Sample name: XK63


title: WT male E4.5, repeat 6 [Xist KO]

description: Sample name: XK84


title: WT male E4, repeat 1 [Xist KO]

description: Sample name: XK62


title: Xist KO female E4.5, repeat 9 [Xist KO]

description: Sample name: XK171


title: WT male E4.5, repeat 10 [Xist KO]

description: Sample name: XK167


title: WT male E4, repeat 3 [Xist KO]

description: Sample name: XK64


title: Xist KO female E3.5, repeat 6 [Xist KO]

description: Sample name: XK148

source_name: Whole embryo, Xist KO, E3.5, female


title: Xist KO female E3.5, repeat 1 [Xist KO]

description: Sample name: XK50


title: Xist KO female E3.5, repeat 3 [Xist KO]

description: Sample name: XK52


title: Xist KO female E3.5, repeat 5 [Xist KO]

description: Sample name: XK147


title: WT male E3.5, repeat 7 [Xist KO]

description: Sample name: XK146

source_name: Whole embryo, WT, E3.5, male


title: WT male E3.5, repeat 8 [Xist KO]

description: Sample name: XK149


title: WT male E3.5, repeat 5 [Xist KO]

description: Sample name: XK144


title: WT male E3.5, repeat 6 [Xist KO]

description: Sample name: XK145


title: WT male E4, repeat 5 [Xist KO]

description: Sample name: XK68


title: WT male E3.5, repeat 3 [Xist KO]

description: Sample name: XK55


title: WT male E3.5, repeat 4 [Xist KO]

description: Sample name: XK56


title: WT male E3.5, repeat 2 [Xist KO]

description: Sample name: XK53


title: WT male E3.5, repeat 1 [Xist KO]

description: Sample name: XK49


title: Xist KO female E3, repeat 5 [Xist KO]

description: Sample name: XK42

source_name: Whole embryo, Xist KO, E3, female


title: Xist KO female E3, repeat 8 [Xist KO]

description: Sample name: XK140


title: Xist KO female E3, repeat 6 [Xist KO]

description: Sample name: XK47


title: Xist KO female E3, repeat 4 [Xist KO]

description: Sample name: XK41


title: Xist KO female E3, repeat 1 [Xist KO]

description: Sample name: XK38


title: Xist KO female E3, repeat 3 [Xist KO]

description: Sample name: XK40


title: Xist KO female E3, repeat 2 [Xist KO]

description: Sample name: XK39


title: WT male E3, repeat 6 [Xist KO]

description: Sample name: XK139

source_name: Whole embryo, WT, E3, male


title: WT male E3, repeat 4 [Xist KO]

description: Sample name: XK136


title: WT male E3, repeat 5 [Xist KO]

description: Sample name: XK138


title: WT male E3, repeat 3 [Xist KO]

description: Sample name: XK45


title: Xist KO female E3.5, repeat 4 [Xist KO]

description: Sample name: XK54


title: Xist KO female E3.5, repeat 2 [Xist KO]

description: Sample name: XK51


title: Xist KO female E2.5, repeat 10 [Xist KO]

description: Sample name: XK130

source_name: Whole embryo, Xist KO, E2.5, female


title: WT male E3, repeat 2 [Xist KO]

description: Sample name: XK43


title: WT male E3, repeat 1 [Xist KO]

description: Sample name: XK37


title: Xist KO female E2.5, repeat 11 [Xist KO]

description: Sample name: XK131


title: Xist KO female E2.5, repeat 4 [Xist KO]

description: Sample name: XK32


title: Xist KO female E2.5, repeat 6 [Xist KO]

description: Sample name: XK34


title: Xist KO female E2.5, repeat 5 [Xist KO]

description: Sample name: XK33


title: Xist KO female E2.5, repeat 3 [Xist KO]

description: Sample name: XK31


title: Xist KO female E3, repeat 7 [Xist KO]

description: Sample name: XK135


title: Xist KO female E2.5, repeat 2 [Xist KO]

description: Sample name: XK30


title: WT male E2.5, repeat 8 [Xist KO]

description: Sample name: XK134

source_name: Whole embryo, WT, E2.5, male


title: WT male E2.5, repeat 7 [Xist KO]

description: Sample name: XK129


title: Xist KO female E2.5, repeat 1 [Xist KO]

description: Sample name: XK29


title: WT male E2.5, repeat 6 [Xist KO]

description: Sample name: XK126


title: WT male E2.5, repeat 4 [Xist KO]

description: Sample name: XK36


title: WT male E2.5, repeat 5 [Xist KO]

description: Sample name: XK122


title: WT male E2.5, repeat 3 [Xist KO]

description: Sample name: XK35


title: WT male E2.5, repeat 1 [Xist KO]

description: Sample name: XK26


title: WT male E2.5, repeat 2 [Xist KO]

description: Sample name: XK28


title: Xist KO female 8 cell, repeat 12 [Xist KO]

description: Sample name: XK121

source_name: Whole embryo, Xist KO, 8 cell stage, female

value: 8 cell


title: Xist KO female 8 cell, repeat 10 [Xist KO]

description: Sample name: XK116


title: Xist KO female 8 cell, repeat 4 [Xist KO]

description: Sample name: XK19


title: Xist KO female 8 cell, repeat 9 [Xist KO]

description: Sample name: XK115


title: Xist KO female E2.5, repeat 7 [Xist KO]

description: Sample name: XK124


title: Xist KO female 8 cell, repeat 3 [Xist KO]

description: Sample name: XK17


title: Xist KO female 8 cell, repeat 7 [Xist KO]

description: Sample name: XK24


title: Xist KO female E2.5, repeat 9 [Xist KO]

description: Sample name: XK128


title: Xist KO female 8 cell, repeat 11 [Xist KO]

description: Sample name: XK117


title: Xist KO female 8 cell, repeat 8 [Xist KO]

description: Sample name: XK112


title: Xist KO female E2.5, repeat 8 [Xist KO]

description: Sample name: XK125


title: Xist KO female 8 cell, repeat 5 [Xist KO]

description: Sample name: XK20


title: Xist KO female 8 cell, repeat 6 [Xist KO]

description: Sample name: XK22


title: Xist KO female 8 cell, repeat 2 [Xist KO]

description: Sample name: XK16


title: Xist KO female 8 cell, repeat 1 [Xist KO]

description: Sample name: XK14


title: WT male 8 cell, repeat 3 [Xist KO]

description: Sample name: XK23

source_name: Whole embryo, WT, 8 cell stage, male


title: WT male 8 cell, repeat 6 [Xist KO]

description: Sample name: XK120


title: WT male 8 cell, repeat 2 [Xist KO]

description: Sample name: XK21


title: WT male 8 cell, repeat 1 [Xist KO]

description: Sample name: XK18


title: Xist KO female 4 cell, repeat 7 [Xist KO]

description: Sample name: XK101

source_name: Whole embryo, Xist KO, 4 cell stage, female

value: 4 cell


title: Xist KO female 4 cell, repeat 9 [Xist KO]

description: Sample name: XK106


title: Xist KO female 4 cell, repeat 6 [Xist KO]

description: Sample name: XK100


title: Xist KO female 4 cell, repeat 5 [Xist KO]

description: Sample name: XK99


title: Xist KO female 4 cell, repeat 4 [Xist KO]

description: Sample name: XK98


title: Xist KO female 4 cell, repeat 3 [Xist KO]

description: Sample name: XK97


title: WT male 4 cell, repeat 6 [Xist KO]

description: Sample name: XK102

source_name: Whole embryo, WT, 4 cell stage, male


title: WT male 4 cell, repeat 9 [Xist KO]

description: Sample name: XK107


title: WT male 8 cell, repeat 5 [Xist KO]

description: Sample name: XK114


title: WT male 4 cell, repeat 5 [Xist KO]

description: Sample name: XK10


title: WT male 4 cell, repeat 4 [Xist KO]

description: Sample name: XK9


title: WT male 4 cell, repeat 3 [Xist KO]

description: Sample name: XK8


title: WT male 4 cell, repeat 7 [Xist KO]

description: Sample name: XK103


title: Xist KO female 4 cell, repeat 8 [Xist KO]

description: Sample name: XK104


title: WT male 4 cell, repeat 8 [Xist KO]

description: Sample name: XK105


title: WT male 4 cell, repeat 1 [Xist KO]

description: Sample name: XK4


title: KO male Trophoblast, repeat 9 [Rlim KO]

data_processing:
The bcl2fastq 2.16.0.10 software package was used to convert base call (BCL) files generated on the NextSeq system to fastq files
Sequenced reads were aligned to the mouse genome (mm10) using TopHat (version 2.0.12) with default setting except set parameter read-mismatches to 2
HTSeq (version 0.6.1p1) was used to count the features after the alignment
Bioconductor packages edgeR (version 3.10.0 ) and ChIPpeakAnno (version 3.2.0)  for transcriptome quantification, differential gene expression analysis and annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the raw count values from HTSeq for each sample

source_name: Whole embryo

extract_protocol:
Whole embryos were dissected at the indicated timepoints and the correct stage was verified under the binocular. Single embryos/trophoblast cells were placed in 10ul TCL Buffer (Qiagen) supplemented with 1% BME, and snap frozen.
RNA libraries were prepared for sequencing using standard Illumina protocols.  A total of 187 samples were distributed on two 96-well plates (plus 5 mock wells) and thawed at RT for 10 minutes prior to RNA purification using Ampure RNA beads (Beckmann-Coulter). RNA samples were re-suspended in solution containing 3’ RT primer and dNTPs. Reverse transcription was performed with SSII (Life Technologies), whose terminal transferase activity allows incorporation of a PCR binding site at the 3’ end of the cDNA using a template-switching oligonucleotide (custom synthesized from Exiqon) as a template. Subsequently, cDNA was amplified using 12 cycles of PCR, followed by tagmentation with Nextera kit (Illumina). Final libraries were amplified by 12 cycles of PCR and sequenced on a NextSeq 500.

value: Rlim KO

value: Trophoblast


title: KO female Trophoblast, repeat 5 [Rlim KO]


title: KO female Trophoblast, repeat 6 [Rlim KO]


title: KO female Trophoblast, repeat 2 [Rlim KO]


title: KO female Trophoblast, repeat 4 [Rlim KO]


title: KO female Trophoblast, repeat 1 [Rlim KO]


title: KO male Trophoblast, repeat 8 [Rlim KO]


title: KO female Trophoblast, repeat 3 [Rlim KO]


title: Xist KO female 4 cell, repeat 10 [Xist KO]

description: Sample name: XK108


title: KO male Trophoblast, repeat 6 [Rlim KO]


title: KO male Trophoblast, repeat 7 [Rlim KO]


title: WT male 8 cell, repeat 4 [Xist KO]

description: Sample name: XK113


title: KO male Trophoblast, repeat 5 [Rlim KO]


title: KO male Trophoblast, repeat 2 [Rlim KO]


title: KO male Trophoblast, repeat 3 [Rlim KO]


title: Xist KO female 4 cell, repeat 2 [Xist KO]

description: Sample name: XK11


title: KO male Trophoblast, repeat 4 [Rlim KO]


title: Xist KO female 4 cell, repeat 1 [Xist KO]

description: Sample name: XK3


title: KO male Trophoblast, repeat 1 [Rlim KO]


title: WT male 4 cell, repeat 2 [Xist KO]

description: Sample name: XK5


title: WT female Trophoblast, repeat 2 [Rlim KO]


title: WT female Trophoblast, repeat 3 [Rlim KO]


title: WT female Trophoblast, repeat 1 [Rlim KO]


title: WT male Trophoblast, repeat 3 [Rlim KO]


title: WT male Trophoblast, repeat 4 [Rlim KO]


title: WT male Trophoblast, repeat 1 [Rlim KO]


title: KO female E4.5, repeat 6 [Rlim KO]


title: KO female E4.5, repeat 7 [Rlim KO]


title: WT male Trophoblast, repeat 2 [Rlim KO]


title: KO female E4.5, repeat 5 [Rlim KO]


title: KO male E4.5, repeat 12 [Rlim KO]


title: KO female E4.5, repeat 4 [Rlim KO]


title: KO female E4.5, repeat 2 [Rlim KO]


title: KO male E4.5, repeat 7 [Rlim KO]


title: KO male E4.5, repeat 9 [Rlim KO]


title: WT female E4.5, repeat 5 [Rlim KO]


title: KO male E4.5, repeat 10 [Rlim KO]


title: KO male E4.5, repeat 2 [Rlim KO]


title: KO female E4.5, repeat 3 [Rlim KO]


title: KO male E4.5, repeat 6 [Rlim KO]


title: KO female E4.5, repeat 1 [Rlim KO]


title: KO male E4.5, repeat 11 [Rlim KO]


title: WT female E4.5, repeat 4 [Rlim KO]


title: KO male E4.5, repeat 3 [Rlim KO]


title: KO male E4.5, repeat 8 [Rlim KO]


title: KO male E4.5, repeat 4 [Rlim KO]