title: C57BL/6J_Male_NaiveCD4+Tcell_90


title: C57BL/6J_Male_NaiveCD4+Tcell_79

status: Public on Dec 15 2017

type: SRA

city: Cambridge

first: Nicolas

last: Walker

address: Downing Street

department: Genetics

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic

data_processing:
The 125bp paired-end reads libraries were aligned using STAR v2.5.0a 1 (Dobin et al., 2013) against a custom reference genome containing the GRCm38 version of the mouse reference genome plus the sequence of the ERCC Spike-in RNAs and the ENSEMBL v76 annotation with the following parameters -- outFilterType BySJout -- alignSJoverhangMin 8 -- alignSJDBoverhangMin 1 -- outFilterMismatchNoverLmax 0.3 -- alignIntronMin 20 -- outFilterMismatchNmax 999 -- alignIntronMax 1000000 -- alignMatesGapMax 1000000 -- outFilterMultimapNmax 1 -- outSAMattrIHstart 0 -- outSAMmultNmax 1 -- outSAMstrandField intronMotif -- outSAMtype BAM SortedByCoordinate. Gene expression levels were estimated using HTSeq count (v0.5.4p3)2 (Anders et al., 2014) with parameters (-m intersection- nonempty -a 10 -i gene_id -s no) to count the number of unique read pairs that mapped to the genes in the ENSEMBL annotation v76 of the mouse Genome.
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

growth_protocol: C57BL/6 mice at 6-8 weeks of age were used for spleen collection purposes.

extract_protocol:
Naïve CD4+ T lymphocytes were purified from single-cell suspensions by MACS depletion of non-CD4+ T cells as well as regulatory T cells and TCRγ/δ+ T cells, using a cocktail of specific biotin conjugated antibodies against CD8a (Ly-2), CD45R (B220), CD49b (DX5), CD11b (Mac-1), Ter-119, CD25 and TCRγ/δ+ using the CD4+ CD62L+ T Cell Isolation Kit II (Miltenyi) to obtain an unlabeled pre-enriched CD4+ T cell fraction. Collected cells were suspended in PBS containing 2% FBS and Fc receptors were blocked with FcR blocking reagent for 10 minutes at 4°C (Miltenyi). Cells were further fluorescently stained with a combination of CD4-FITC (Miltenyi), CD44-APC clone IM7 (eBioscience), CD62L clone MEL-14 (BD Pharmingen), eFluor® 450 CD25 clone PC61.5 (eBioscience), for 10 minutes at 4°C, washed and then stained with DAPI (Life Technologies) to cell sort the live population of naïve CD4+, CD62Lhi, CD44lo, CD25- T lymphocytes using the MoFlo XDP system (Beckman Coulter). Samples were gated on single cells for doublet discrimination and non-viable cells were excluded using the viability dye 4’, 6 – diamidine – 2 – phenylindole (DAPI). AllPrep DNA/RNA Mini Kit (Qiagen) was used to perform simultaneous isolation of RNA and DNA from 10^6 sorted naïve CD4+ T cells and resting B cells.  All RNA samples were subjected to in-column RNase-Free DNase treatment (Qiagen) to remove traces of DNA contamination. RNA integrity was subsequently assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies) by using the RNA 6000 Pico Kit (Agilent Technologies). For each sample type 3 biological replicates were generated from male and female samples.
Purified male quiescent naïve CD4+ T and resting B cells were loaded onto a 5-10 μm C1 Single-Cell Auto Prep Integrated Fluidic Circuits (IFC) and captured following manufactures’ instructions. Capture efficiency for each cell type and IFC was determined using a microscope in order to remove in further analysis samples with no cell capture, debris or with two or more cells captured. Synthetic ERCC ExFold RNA Spike-In Mixes (Ambion®) were added at a 1:5000 (B cells) and 1:1000 (T cells) dilution to the cell lysis mix as controls to estimate the level of technical noise in further analysis. Cell lysis, reverse transcription and cDNA pre-amplification was performed in the Fluidigm C1™ Single-Cell Auto Prep System using the C1 Single-Cell Auto Prep Array (IFCs), the Auto Prep Reagent Kit for mRNA Seq (Fluidigm) and the SMARTer® Ultra™ Low RNA Kit (Clontech). Universal amplification was performed utilising the Advantage® 2 PCR Kit (Clontech). cDNA was harvested, quantified by Qubit® assays and diluted to 0.1–0.3 ng/ml. Single cell RNAseq libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina) and the Nextera Index Kit (Illumina) following the instructions in the Fluidigm manual ‘‘Using the C1TM Single-Cell Auto Prep System to Generate mRNA from Single Cells and Libraries for Sequencing.’’ Libraries were pooled, and 125bp paired-end sequencing was performed over two lanes of an Illumina HiSeq2000 instrument.

tag: strain

tag: Sex

value: Male

tag: cell type

value: Naive CD4+ T cell


title: C57BL/6J_Male_NaiveCD4+Tcell_76


title: Ler x Col rep 1

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description:
mRNA-seq
colholdoutgeneIDsnrpd1.txt
Barcode: CAGATC

data_processing:
Read filtering was performed using cutadapt (-0 6 -m 26 -discard-untrimmed) and trim_galore (-t 10; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove low quality bases from the 5' end of reads. Trimmed reads were assessed with fastqc.
Reads were aligned to TAIR10 using tophat (-N 2 -read-edit-dist 2; v2.0.13)
Following alignment, reads were classified by strain (Col or Ler) using SNPs (Pignatta et al., eLife, 2014). If classification at two SNP positions within the same read conflicted, that read was discarded.
Allele-specific read counts for each locus were generated by running ht-seq count on the reads classifed by strain (-m intersection-strict -stranded=no).
In the case of libraries originating from crosses including a parent with the nrpd1 allele in the Ler background, reads originating from genes that retained the Col genotype even after multiple backcrosses into Ler were removed from downstream analysis. These loci are listed in colholdoutgeneIDsnrpd1.txt.
genome build: TAIR10, resequenced Ler-0 genome
processed data files format and content: allele_counts files contain RNA-seq data in tab-delimited format for each sample, with one row per gene.  Contains gene ID (locus_name), Col-assigned reads (Col), Ler-assigned reads (Ler), and total number of RNA-seq reads aligned to gene (total).
processed data files format and content: colholdoutgeneIDsnrpd1.txt file is the list of gene IDs not to be included in analysis for the nrpd1a-4 (Ler) female x nrpd1a-4 (Col) male samples (three reps) or their wild type counterparts, Ler female x Col male 6 days after pollination (2 reps). These loci remain as Col genotype in at least one of the the nrpd1a-4 (Ler) plants even after four backcrosses of nrpd1a-4 (Col) to Ler.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Ler x Col

growth_protocol: Plants were grown in a greenhouse with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at six DAP (approximately torpedo stage of embryogenesis).

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total endosperm RNA isolated using the Ambion RNAqueous Micro Kit.
DNase I-treated RNA (Invitrogen, Life Technologies Corporation, Carlsbad, CA) was used to prepare mRNA-seq libraries using the Truseq Stranded mRNA Library Prep Kit as directed (Illumina Inc., San Diego, CA). Amplification was for 15 cycles. Libraries were sequenced with 100x100 base paired end reads on an Illumina HiSeq 2000 machine.

treatment_protocol: no treatment

tag: genotype

value: Ler female x Col male

tag: developmental stage

value: 6 days after pollination

tag: tissue

value: Endosperm


title: C57BL/6J_Male_NaiveCD4+Tcell_77


title: 20140304.A-20140114_NS_pBBR

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Bc H111 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: H111 genome sequence (accession no. HG938370, HG938371, and HG938372)
Supplementary_files_format_and_content: CLC exported tab-delimited text files include RPKM and mean values for each sample

organism: Burkholderia cenocepacia H111

source_name: H111 /pBBR5

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . Ds cDNA was produced and nugen librairies obtained.
RNA libraries were prepared using Ovation® Complete Prokaryotic RNA-Seq Library System

value: Bc H111 planktonic cells

tag: treatment

value: empty vector control

tag: growth

value: planktonic cells, OD600 equal 2.0

tag: medium

value: LB


title: C57BL/6J_Male_NaiveCD4+Tcell_78


title: C57BL/6J_Male_NaiveCD4+Tcell_69


title: C57BL/6J_Male_NaiveCD4+Tcell_71


title: Cvi x Cvi rep 1_Embryo

description:
sRNA-seq
Barcode: TTAGGC
At_emb_v_endo_24nt_300bp_stats.txt

data_processing:
Analysis of sRNA libraries began with the trimming of low-quality read ends (fastq_quality_trimmer, -t 20 and -l 25; http://hannonlab.cshl.edu/fastx_toolkit/). Adapters were removed with cutadapt (-0 6 -m 26 ?discard-untrimmed).
sRNA libraries prepared using the NEXTflex sRNA-Seq Kit v2 are appended with 4 base randomized barcodes immediately 3' and 5' of the sRNA read itself. These barcodes were used to remove PCR duplicates (any read of the same sRNA sequence with identical flanking barcodes on both ends) before being removed themselves.
Reads were aligned using Bowtie 1.1.1 with two mismatches allowed (-v 2 --best; Langmead et al., 2009), using a metagenomic approach to reduce mapping bias. In the case of crosses between A. thaliana Col and Ler ecotypes, a metagenome was constructed using the TAIR10 genome and the published Ler genome (Gan et al.,Nature, 2011). In the case of crosses between Col and Cvi ecotypes, a metagenome was constructed using a Cvi pseudogenome (1bp indels and SNP substitutions introduced into TAIR10 base genome) and the TAIR10 genome. Following alignment, reads aligning to either parent genome were converted back to TAIR10 coordinates. For A. lyrata, reads were aligned in the same manner to the published MN47 genome (Hu et al., Nat Genet, 2011).
Reads were classified by strain using SNPs (Pignatta et al., eLife, 2014, Klosinska et al., Nat Plants, 2016). If classification at two SNP positions within the same read conflicted, that read was discarded. All reads that overlapped annotated tRNAs, snRNAs, rRNAs, or snoRNAs were removed.
Spike-ins consisting of sRNAs isolated from Candida albicans were added to A. thaliana libraries during preparation.  Ultimately, spike-ins were not utilized in normalization, with library size-based normalization used instead.  Reads that mapped to the C. albicans genome (either uniquely or in addition to mapping to the Arabidopsis thaliana genome) were removed from further analysis.
A single base read depth value was created for 24nt sRNAs  ?  each base of a read would contribute 1/24 of a read to an overlapping genomic position. Alignment files were run through bedtools genomecov (-d -scale: adjusted to account for individual library size; bedtools v. 2.23.0, bedtools.readthedocs.io/en/latest/index.html). Per-position values for all libraries pooled within a given analysis were averaged.
For *_emb_v_endo_24nt_300bp_stats.txt: 24nt sRNAs were binned into 300 base windows with 150 base overlaps, such that every position in the genome was covered by exactly 2 windows. Overlapping was performed using bedtools coverage (bedtools v. 2.23.0, bedtools.readthedocs.io/en/latest/index.html). sRNA window read values, classified as either embryo or endosperm, were used as input for DESeq2, with the sizeFactors command used to provide RPM normalization between libraries (Love et al., 2014). Output values were used to calculate average sRNA levels for all libraries at a given locus (mean log2 total counts) and the ratio of embryo expression to endosperm expression (log2 embryo/endosperm counts)
genome build: For A. thaliana libraries, TAIR10, resequenced Ler-0 genome (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/fasta/UNMASKED/ler_0.v7.fas), Cvi pseudogenome (TAIR10+Cvi1.fa.gz). For A. lyrata libraries, published MN47 genome (Hu et al., Nat Genet, 2011).
processed data files format and content: singlebasecompilation and singlebase.bed files: bed files detailing every position of the genome, with the fourth column providing a normalized sRNA read coverage value for all embryo, endosperm, or seed coat libraries in the study. For A. thaliana, all libraries of the same tissue type were combined. For A. lyrata, KarxMN47 replicates of the same tissue type were combined and for MN47xMN47 replicates of the same tissue type were combined. Prefix designations for A. lyrata are K=Kar, M=MN47, E=embryo, N=endosperm, S=seedcoat. Female in cross listed first. For MN47xMN47 endosperm, only replicates MMN2 and MMN3 were combined. MMN1 was not used.
processed data files format and content: *_emb_v_endo_24nt_300bp_stats.txt: tab delimited text file including window position, mean sRNA coverage for all libraries, endosperm libraries, and embryo libraries, the log2 fold change between endosperm and embryo mean values, and associated statistical quantities. At = A. thaliana, KM = A. lyrata Kar female x MN47 male, MM = A. lyrata MN47 female x MN47 male.
processed data files format and content: *_allele_specific_24_300bp_values_*reps.txt: tab deliminted text file including chr/scaffold, start, end and allele-specific 24nt sRNA read counts in 300 bp windows across the genome. CLN = A. thaliana Col female x Ler male endosperm, LCN = A. thaliana Ler female x  Col male endosperm, CVN = A. thaliana Col female x Cvi male endosperm, VCN = A. thaliana Cvi female x Col male endosperm, KME = A. lyrata Kar female x MN47 male embryo, KMN = A. lyrata Kar female x MN47 male endosperm

source_name: Cvi x Cvi

growth_protocol: Plants were grown in a greenhouse with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at six DAP (approximately torpedo stage of embryogenesis). A. lyrata plants were grown in a growth chamber with 16-hour days at 20 C. Seeds were dissected at ~15 days after pollination, corresponding to the late torpedo/walking stick stage of embryogenesis.

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total embryo, endosperm, or seed coat RNA isolated using the Ambion RNAqueous Micro Kit.
The small RNA pool was separated from the larger RNA pool by sequential ethanol addition and filtering. The larger RNA pool was collected on filters after the addition of ethanol equivalent to 60% of the sample volume, and the small RNA pool was collected on filters after the addition of ethanol equivalent to 50% of the flowthrough volume from the larger RNA filter binding step.  Libraries for Illumina sequencing were constructed using the NEXTflex Small RNA-Seq Kit v2 as directed (Bioo Scientific Corporation, Austin, Texas). 40 base single-end sequencing of sRNA libraries was performed on an Illumina HiSeq 2000 machine.

value: Cvi female x Cvi male

value: Embryo


title: C57BL/6J_Male_NaiveCD4+Tcell_75


title: C57BL/6J_Male_NaiveCD4+Tcell_67


title: 20130523.B-20130425_NS_C

source_name: H111 /pRpfRAAL

value: high c-di-GMP level


title: Ler x Col rep 2

description:
mRNA-seq
colholdoutgeneIDsnrpd1.txt
Barcode: CTTGTA


title: C57BL/6J_Male_NaiveCD4+Tcell_65


title: 20130402.X-20130228_NS_C


title: C57BL/6J_Male_NaiveCD4+Tcell_72


title: 20130523.B-20130425_NS_A


title: M3_nB_neg

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Bowtie-1.1.1
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files are normalized to reads per peak million (rpm) using R/Bioconductor

molecule: genomic DNA

source_name: naïve B cells

extract_protocol:
Three days post-LPS naïve B cell (nB, B220+GL7-CD138-) and plasmablast (Pb, CD138+) populations were isolated by FACS from the spleens of chimeric mice.
2000-4000 cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg. Tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

treatment_protocol: Chimeric mice were generated by transferring CD45.1/2 CRE negative and CD45.2 CRE positive Ezh2-floxed bone marrow into lethally irradiated CD45.1 wild-type mice.  After allowing the immune system to reconstitute the animals were treated with tamoxifen to induce deletion of Ezh2 and subsequently inoculated with LPS.

value: female

tag: sorting markers

tag: organ

value: spleen

tag: stimulation

value: LPS

tag: ezh2 status

value: wild-type


title: 20130523.B-20130425_NS_B

value: low c-di-GMP level


title: C57BL/6J_Male_NaiveCD4+Tcell_70

value: Male


title: C57BL/6J_Male_NaiveCD4+Tcell_73

value: Naive CD4+ T cell


title: 20130402.X-20130228_NS_A


title: C57BL/6J_Male_NaiveCD4+Tcell_68


title: M3_Pb_neg

source_name: Plasmablasts


title: C57BL/6J_Male_NaiveCD4+Tcell_62


title: 20130402.X-20130228_NS_B


title: M3_nB_pos

value: knockout


title: C57BL/6J_Male_NaiveCD4+Tcell_63


title: C57BL/6J_Male_NaiveCD4+Tcell_57


title: C57BL/6J_Male_NaiveCD4+Tcell_66


title: C57BL/6J_Male_NaiveCD4+Tcell_59


title: C57BL/6J_Male_NaiveCD4+Tcell_64


title: M3_Pb_pos


title: C57BL/6J_Male_NaiveCD4+Tcell_54


title: C57BL/6J_Male_NaiveCD4+Tcell_60


title: C57BL/6J_Male_NaiveCD4+Tcell_61


title: C57BL/6J_Male_NaiveCD4+Tcell_52


title: C57BL/6J_Male_NaiveCD4+Tcell_53


title: M2_Pb_neg


title: M2_nB_pos


title: C57BL/6J_Male_NaiveCD4+Tcell_49


title: M1_Pb_pos


title: C57BL/6J_Male_NaiveCD4+Tcell_56


title: C57BL/6J_Male_NaiveCD4+Tcell_58


title: M1_Pb_neg


title: C57BL/6J_Male_NaiveCD4+Tcell_44


title: M2_Pb_pos


title: C57BL/6J_Male_NaiveCD4+Tcell_50


title: M1_nB_neg


title: C57BL/6J_Male_NaiveCD4+Tcell_41


title: C57BL/6J_Male_NaiveCD4+Tcell_45


title: C57BL/6J_Male_NaiveCD4+Tcell_48


title: C57BL/6J_Male_NaiveCD4+Tcell_55


title: C57BL/6J_Male_NaiveCD4+Tcell_51


title: M2_nB_neg


title: C57BL/6J_Male_NaiveCD4+Tcell_89


title: Control_654

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Tophat2 and the UCSC mm9 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique RefSeq gene using the HOMER package v4.8.2.
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing FPKM normalized read counts for each sample.

source_name: LPS induced splenic CD138+ Pb

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Kit.
500ng of total RNA was used as input for the KAPA Biosystems Stranded mRNA-seq kit with polyA selection beads.

treatment_protocol: Three days following LPS stimulation, CD138+ cells were magentically enriched from the spleens of wild-type and EZH2-deficient mice.

tag: genotype/variation

value: wild type

value: male

tag: drug treatment

value: Tamoxifen

value: Plasmablasts


title: C57BL/6J_Male_NaiveCD4+Tcell_38


title: C57BL/6J_Male_NaiveCD4+Tcell_36


title: C57BL/6J_Male_NaiveCD4+Tcell_46


title: Control_660


title: C57BL/6J_Male_NaiveCD4+Tcell_43


title: Ezh2KO_653


title: C57BL/6J_Male_NaiveCD4+Tcell_42


title: Control_655


title: C57BL/6J_Male_NaiveCD4+Tcell_39


title: Ezh2KO_659


title: C57BL/6J_Male_NaiveCD4+Tcell_37


title: C57BL/6J_Male_NaiveCD4+Tcell_47


title: C57BL/6J_Male_NaiveCD4+Tcell_35


title: C57BL/6J_Male_NaiveCD4+Tcell_34


title: C57BL/6J_Male_NaiveCD4+Tcell_30


title: Ezh2KO_656


title: C57BL/6J_Male_NaiveCD4+Tcell_33


title: HEK293_24h_R1

city: Toronto

first: Olivia

last: Rissland

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

description:
HEK293.4SU.exon.csv
HEK293.4SU.intron.csv
HEK293.1.4SU.introns.preDRUID.csv
HEK.4SU.HL.one.csv
HEK.4SU.HL.DRUID.one.csv

data_processing:
Basecalling was performed using Illumina Real-Time Analysis v1.18.54 or later, and bcl2fastq2 v2.17 was used to convert to fastq format (by The Center for Applied Genetics (SickKids)).
Library quality was assessed using FastQC v0.11.5.
Reads were trimmed and clipped for Illumina adaptors using Trimmomatic v0.36 with the following options LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Reads were aligned to merged reference genome hg38 (human) + dm6 (fly) + sacCer3 (yeast)' obtained using the UCSC Table Browser and kentUtils v302 on 08 Aug 2015. Reads were mapped using STAR version 2.5.2a_modified. STAR was used with default settings, aside from: outFilterMultimapNmax 10, outFilterMismatchNoverLmax 0.05, outFilterScoreMinOverLread 0.75, outFilterMatchNminOverLread 0.85, alignIntronMax 1, and outFilterIntronMotifs RemoveNoncanonical.
Mapped reads were quantified using two different methods. Firstly, an in-house R script using the GenomicFeatures and rtracklayer packages from Bioconductor and the plyr package was used to select the longest transcript for every gene and create gtf files containing exon and intron annotations. Any introns that overlapped with an exon in any other isoform were not included in the gtf. The htseq-count script from the HTSeq 0.6.1p2 was used to count reads mapping to introns and exons. In addition to HTSeq, an in-house intersection method based around the tools provided by BEDTools suite v2.26.0 was used. Briefly, rather than counting the number of reads mapping to a feature, coverage was determined at the nucleotide level and subsequently averaged at the feature level.
Genome_build: hg38, dm6, sacCer3
Supplementary_files_format_and_content: Comma separated values files containing: gene read counts and coverage determined for reads mapping to exonic and intronic regions for each gene in each sample, half-lives determined using different methods.

organism: Homo sapiens

source_name: HEK293 cells

growth_protocol: Human HEK293 epithelial cells (ATCC CRL1573) were cultured in Eagle’s Minimum Essential Medium (EMEM) supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin solution. Mammalian cell lines were cultured at 37°C in a humidified incubator with 5% CO2. Drosophila melanogaster Schneider 2 (S2) cells were cultured in ExpressFive SFM media (Thermo Fisher Scientific) supplemented with 10% FBS (heat-inactivated) and 20mM L-Glutamine, at 28°C. Saccharomyces cerevisiae USY006 was grown in liquid YPD (20 g/L bacto peptone, 10g/L yeast extract, 950 mL water) at 30°C on a shaker at 200 rpm to mid-exponential phase.

extract_protocol:
Following PBS washes, cell pellets were lysed in TRI Reagent (Sigma-Aldrich) according to manufacturer’s instructions. Briefly, 100 µL of 1-bromo-3-chloropropane was added to each sample, and samples were vortexed for 15 seconds and incubated at room temperature for 2 minutes. Sample were centrifuged in a prechilled centrifuge at 4°C at 15500 x g for 15 min. Aqueous phase was transferred to a new tube and 500µL isopropanol and 2µL glycoblue were added.  Samples were vortexed for 10 s and then incubated for 10 min at room temperature. Samples were then centrifuged at 4°C at 15500 x g for 10 min. Supernatant was discarded and pellet was washed with 1 mL of 75% ethanol and centrifuged at 4°C, 9000 x g for 5 min. Ethanol was removed and pellet was resuspended in 20 µL Milli-Q water.   For Saccharomyces cerevisiae 10 ml of the liquid culture was pelleted for 3 min at 1500 x g at 4°C. Supernatant was discarded and pellet was resuspended in 1 ml of ice-cold milli-Q water and pelleted again. The cell pellet was resuspended in 400 µL TES solution (10 mM Tris-Cl pH 7.5, 10mM EDTA, 0.5% SDS). 400 µL Phenol:Chloroform 5:1 was added, and the sample was vortexed vigorously for 10 s. After incubating at 65°C for 60 min with periodic vortexing, the sample was then centrifuged for 5 min at 21000 x g at 4°C. The aqueous phase was transferred to a new tube and reextracted with acid phenol and then again with chloroform. The aqueous phase was transferred, and RNA was precipitated with 40 µL of 3M sodium acetate, pH5.3 and 1 mL of ice-cold 100% ethanol. RNA was pelleted at 21000 x g for 5 min at 4°C. The RNA pellet was washed with ice-cold 70% ethanol and resuspended in 50 µL of milli-Q water.  For Caenorhabditis elegans, sample volumes were brought up to 100 µL with UltraPure water and resuspended in 4X volume of TRI-Reagent. Samples were vortexed for 10 minutes at room temperature. 10% volume of 1-bromo-3-chloropropane was added and samples vortexed for an additional 10 minutes at room temperature. Samples were then centrifuge for 8 minutes at 10,000 x g at 4 degrees and top aqueous layer was transferred to a new tube. RNA was precipitated with 20 µg glycogen and 4X volume of 100% ethanol for at least 1 hour at -20°C.  For transcription inhibition samples, 4 µg sample RNA was combined with 10 % Saccharomyces cerevisiae RNA.   For metabolically labeled samples a 1 mg/mL solution of HPDP-biotin (Thermo Fisher Scientific) in dimethylformamide was incubated at 37°C for 30 minutes. 40-100 µg of RNA was combined with 20% w/w unlabeled yeast RNA (C. elegans N2 RNA for 293_not_enough samples gifted by the Claycomb lab), 20% w/w 4SU-labeled fly RNA and 120 µL of 2.5x citrate buffer (25 mM citrate pH 4.5, 2.5 mM EDTA) in a total volume of 240 µL. 60 µL of HPDP-biotin solution was added, and the solution was incubated at 37°C for 2 hr, covered and shaking at 200 rpm. Equal volume acid phenol was added, and samples were vortexed and separated at 21000 x g for 5 min at 4°C. Aqueous layer was re-extracted with acid phenol and again with chloroform. RNA was precipitated with 18 µL of 5M NaCl, 750 µL of 100% ethanol, and 2 µL glycoblue for a minimum of 60 min at –20°C. RNA was pelleted for 30 min at 21000 x g at 4°C and supernatural discarded. RNA pellet was resuspended in 200 µL 1x wash buffer (10 mM Tris-Cl pH 7.4, 50 mM NaCl, 1 mM EDTA).  50 µL MACS microbeads (Miltenyi Biotec) were incubated with 48 µL of 1x wash buffer and 2 µL yeast tRNA for 20 min at room temperature with rotation. The microcolumns (Miltenyi Biotec) were washed with 100 µL nucleic acid equilibration buffer (Miltenyi Biotec) and then five times with 100 µL 1x wash buffer. Beads were applied to the column in 100 µL aliquots and washed five times with 100 µL 1x wash buffer. Columns were demagnetized, and beads eluted with two 100 µL washes with 1x wash buffer. 200 µL of bead solution was combined with RNA sample and rotated at room temperature for 20 min. Sample was then applied to the remagnetized column in 100 µL aliquots. Columns were washed three times with 400 µL of wash 1 buffer (10mM Tris-Cl pH 7.4, 6M urea, 10mM EDTA) prewarmed to 65°C and then three times with 400 µL wash 2 buffer (10 mM Tris-Cl pH 7.4, 1M NaCl, 10mM EDTA). Selected RNA was eluted with five washes of 1x wash buffer with 0.1M dithiothreitol. RNA was precipitated for at least 1 hr at –20°C with 30 µL 5M NaCl, 1 mL ethanol, and 2 µL glycoblue and then pelleted for 30 min at 21000 x g and 4°C.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Sample preparation kit (Illumina) per the manual (Rev. E).

treatment_protocol: For metabolic labeling experiments cells were treated with 100 µM 4SU and harvested after 1, 2, 4, 8, 12, and 24 hr. HEK293 and S2 cells treated with 100µM 4SU for 24 h were used for the generation of labeled spike-ins.

tag: length of treatment

value: 24 hr

tag: 4su selected

value: TRUE


title: C57BL/6J_Male_NaiveCD4+Tcell_32

tag: strain


title: C57BL/6J_Male_NaiveCD4+Tcell_28

tag: Sex


title: C57BL/6J_Male_NaiveCD4+Tcell_29

tag: cell type


title: C57BL/6J_Male_NaiveCD4+Tcell_23


title: C57BL/6J_Male_NaiveCD4+Tcell_24


title: AMPK_NULL_H3K27me3_ChIPSeq

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

data_processing:
Basecalls performed using Illuminal CASAVA software.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie v1.1.2 with only uniquely mapped reads retained.
Peaks were called using MACS2 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file

source_name: mouse embryonic fibroblast cells

growth_protocol: The WT and AMPKa DKO MEFs were cultured in DMEM with 10% FBS.

extract_protocol:
Chromatin immunoprecipitation was performed following standard protocol. Basically, 8-10 X10^6 cells were crosslinked with 1% formaldehyde at room temperature for 10 min, and then lysed with RIPA buffer containing 0.3 M NaCl. Specific H3K27me3 antibody was added to the sheared chromatin of 200-700 bp size, and rotated at 4°C for overnight. ChIP'd DNA was purified using PCR Purification Kit (Qiagen) and then quantified by Quant-iT dsDNA HS Assay Kit (Invitrogen).
Equal amounts of ChIP enriched DNA (5 ng) under each experimental condition (WT and NULL) were prepared for ChIP-Seq libraries. ThruPLEX-FD Prep Kit (Rubicon Genomics, Cat# R400427) was used to construct the sequencing libraries according to the manufacturer's protocol, and the final products were sequenced on the HiSeq2000.

value: ES-derived neural progenitor cells

tag: chip antibody


title: HEK293_SS_R1

value: FALSE


title: C57BL/6J_Male_NaiveCD4+Tcell_40


title: C57BL/6J_Male_NaiveCD4+Tcell_31


title: Pb.H3K27me3.ChIPseq.1

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Bowtie
Peaks were called using HOMER with the settings '-style histone'.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files are normalized to reads per peak per million (rppm) using R/Bioconductor

source_name: FACS sorted CD138+ B220int splenic plasmablasts

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717). Briefly, 10^7 B cells or 1^6 Plasmablasts were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp. Chromatin was immunoprecipitated with 1 ug anti-H3K27me3 antibody over night at 4 degrees. Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified.
ChIP-seq libraries were constructed from total IP DNA using the KAPA HyperPrep Kit


title: C57BL/6J_Male_NaiveCD4+Tcell_27


title: Pb.H3K27me3.ChIPseq.2


title: HEK293_12h_R1

value: 12 hr


title: C57BL/6J_Male_NaiveCD4+Tcell_19


title: C57BL/6J_Male_NaiveCD4+Tcell_25


title: C57BL/6J_Male_NaiveCD4+Tcell_22


title: C57BL/6J_Male_NaiveCD4+Tcell_18


title: C57BL/6J_Male_NaiveCD4+Tcell_17


title: HEK293_8h_R1

value: 8 hr


title: Bcell.H3K27me3.ChIPseq.2

source_name: MACS sorted CD43- splenic B cells

value: female

value: B cells


title: HEK293_1h_R1

value: 1 hr


title: AMPK_WT_H3K27me3_ChIPSeq


title: Bcell.H3K27me3.ChIPseq.1


title: HEK293_4h_R1

value: 4 hr


title: C57BL/6J_Male_NaiveCD4+Tcell_21

value: Male


title: C57BL/6J_Male_NaiveCD4+Tcell_20

value: Naive CD4+ T cell


title: C57BL/6J_Male_NaiveCD4+Tcell_13


title: C57BL/6J_Male_NaiveCD4+Tcell_10


title: C57BL/6J_Male_NaiveCD4+Tcell_26


title: HEK293_2h_R1

value: 2 hr


title: C57BL/6J_Male_NaiveCD4+Tcell_9


title: C57BL/6J_Male_NaiveCD4+Tcell_5


title: C57BL/6J_Male_NaiveCD4+Tcell_4


title: C57BL/6J_Male_NaiveCD4+Tcell_6


title: C57BL/6J_Male_NaiveCD4+Tcell_16


title: C57BL/6J_Male_NaiveCD4+Tcell_14


title: C57BL/6J_Male_NaiveCD4+Tcell_11


title: C57BL/6J_Male_NaiveCD4+Tcell_15


title: C57BL/6J_Male_NaiveCD4+Tcell_8


title: MN47 x MN47 seed coat rep3

description:
sRNA-seq
Barcode: GTGAAA
MMS_24_overallavg_comp_singlebase.bed.gz

data_processing:
Analysis of sRNA libraries began with the trimming of low-quality read ends (fastq_quality_trimmer, -t 20 and -l 25; http://hannonlab.cshl.edu/fastx_toolkit/). Adapters were removed with cutadapt (-0 6 -m 26 —discard-untrimmed).
sRNA libraries prepared using the NEXTflex sRNA-Seq Kit v2 are appended with 4 base randomized barcodes immediately 3’ and 5’ of the sRNA read itself. These barcodes were used to remove PCR duplicates (any read of the same sRNA sequence with identical flanking barcodes on both ends) before being removed themselves.
Reads were aligned using Bowtie 1.1.1 with two mismatches allowed (-v 2 --best; Langmead et al., 2009), using a metagenomic approach to reduce mapping bias. In the case of crosses between A. thaliana Col and Ler ecotypes, a metagenome was constructed using the TAIR10 genome and the published Ler genome (Gan et al.,Nature, 2011). In the case of crosses between Col and Cvi ecotypes, a metagenome was constructed using a Cvi pseudogenome (1bp indels and SNP substitutions introduced into TAIR10 base genome) and the TAIR10 genome. Following alignment, reads aligning to either parent genome were converted back to TAIR10 coordinates. For A. lyrata, reads were aligned in the same manner to the published MN47 genome (Hu et al., Nat Genet, 2011).
Reads were classified by strain using SNPs (Pignatta et al., eLife, 2014, Klosinska et al., Nat Plants, 2016). If classification at two SNP positions within the same read conflicted, that read was discarded. All reads that overlapped annotated tRNAs, snRNAs, rRNAs, or snoRNAs were removed.
Spike-ins consisting of sRNAs isolated from Candida albicans were added to A. thaliana libraries during preparation.  Ultimately, spike-ins were not utilized in normalization, with library size-based normalization used instead.  Reads that mapped to the C. albicans genome (either uniquely or in addition to mapping to the Arabidopsis thaliana genome) were removed from further analysis.
A single base read depth value was created for 24nt sRNAs  —  each base of a read would contribute 1/24 of a read to an overlapping genomic position. Alignment files were run through bedtools genomecov (-d -scale: adjusted to account for individual library size; bedtools v. 2.23.0, bedtools.readthedocs.io/en/latest/index.html). Per-position values for all libraries pooled within a given analysis were averaged.
For *_emb_v_endo_24nt_300bp_stats.txt: 24nt sRNAs were binned into 300 base windows with 150 base overlaps, such that every position in the genome was covered by exactly 2 windows. Overlapping was performed using bedtools coverage (bedtools v. 2.23.0, bedtools.readthedocs.io/en/latest/index.html). sRNA window read values, classified as either embryo or endosperm, were used as input for DESeq2, with the sizeFactors command used to provide RPM normalization between libraries (Love et al., 2014). Output values were used to calculate average sRNA levels for all libraries at a given locus (mean log2 total counts) and the ratio of embryo expression to endosperm expression (log2 embryo/endosperm counts)
Genome_build: For A. thaliana libraries, TAIR10, resequenced Ler-0 genome (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/fasta/UNMASKED/ler_0.v7.fas), Cvi pseudogenome (TAIR10+Cvi1.fa.gz  ). For A. lyrata libraries, published MN47 genome (Hu et al., Nat Genet, 2011).
Supplementary_files_format_and_content: singlebasecompilation and singlebase.bed files: bed files detailing every position of the genome, with the fourth column providing a normalized sRNA read coverage value for all embryo, endosperm, or seed coat libraries in the study. For A. thaliana, all libraries of the same tissue type were combined. For A. lyrata, KarxMN47 replicates of the same tissue type were combined and for MN47xMN47 replicates of the same tissue type were combined. Prefix designations for A. lyrata are K=Kar, M=MN47, E=embryo, N=endosperm, S=seedcoat. Female in cross listed first. For MN47xMN47 endosperm, only replicates MMN2 and MMN3 were combined. MMN1 was not used.
Supplementary_files_format_and_content: *_emb_v_endo_24nt_300bp_stats.txt: tab delimited text file including window position, mean sRNA coverage for all libraries, endosperm libraries, and embryo libraries, the log2 fold change between endosperm and embryo mean values, and associated statistical quantities. At = A. thaliana, KM = A. lyrata Kar female x MN47 male, MM = A. lyrata MN47 female x MN47 male.
Supplementary_files_format_and_content: *_allele_specific_24_300bp_values_*reps.txt: tab deliminted text file including chr/scaffold, start, end and allele-specific 24nt sRNA read counts in 300 bp windows across the genome. CLN = A. thaliana Col female x Ler male endosperm, LCN = A. thaliana Ler female x  Col male endosperm, CVN = A. thaliana Col female x Cvi male endosperm, VCN = A. thaliana Cvi female x Col male endosperm, KME = A. lyrata Kar female x MN47 male embryo, KMN = A. lyrata Kar female x MN47 male endosperm

organism: Arabidopsis lyrata

source_name: Seed Coat

growth_protocol: A. thaliana plants were grown in a greenhouse with 16-hour days at ~21 C. Flowers were emasculated 2 days before pollination. Seeds were dissected at six DAP (approximately torpedo stage of embryogenesis). A. lyrata plants were grown in a growth chamber with 16-hour days at 20 C. Seeds were dissected at ~15 days after pollination, corresponding to the late torpedo/walking stick stage of embryogenesis.

extract_protocol:
Seeds from crosses between multiple individuals were hand-dissected and total embryo,endosperm, or seed coat RNA isolated using the Ambion RNAqueous Micro Kit.
The small RNA pool was separated from the larger RNA pool by sequential ethanol addition and filtering. The larger RNA pool was collected on filters after the addition of ethanol equivalent to 60% of the sample volume, and the small RNA pool was collected on filters after the addition of ethanol equivalent to 50% of the flowthrough volume from the larger RNA filter binding step.  Libraries for Illumina sequencing were constructed using the NEXTflex Small RNA-Seq Kit v2 as directed (Bioo Scientific Corporation, Austin, Texas). 40 base single-end sequencing of sRNA libraries was performed on an Illumina HiSeq 2000 machine.

tag: genotype

value: MN47 female x MN47 male

tag: developmental stage

value: 15 days after pollination

value: Seed Coat


title: C57BL/6J_Male_NaiveCD4+Tcell_2


title: C57BL/6J_Male_NaiveCD4+Tcell_1


title: C57BL/6J_Male_NaiveCD4+Tcell_12


title: C57BL/6J_Male_NaiveCD4+Tcell_7


title: C57BL/6J_Male_NaiveCD4+Tcell_3


title: LSD1_ChIPseq_C2C12_AD

city: Freiburg

first: Roland

last: Schuele

state: Baden-Württemberg

address: Breisacherstr. 66

department: Urologie, Uniklinik Freiburg

country: Germany

institute: Zentrale Klinische Forschung

data_processing:
peak finding algorithm MACS 1.41
All peaks with FDR greater than 1 % were excluded from further analysis
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2
Genome_build: mm10

source_name: C2C12 cells

extract_protocol:
Arrigoni et al. 2015. Standardizing chromatin research: a simple and universal method for ChIP-seq. Nucleic Acids Res. 2016 Apr 20;44(7):e67. doi: 10.1093/nar/gkv1495. Epub 2015 Dec 23. For ChIP-seq experiment, C2C12 cells were fixed for 6 minutes with 1 % PFA at 4 °C followed by 5 minutes blocking in 125 mM glycine. Nuclei preparation was performed using previously described NEXON protocol37, by sonicating the cells with Covaris E220 focused ultrasonicator for 2 minutes at peak power 75 W, duty factor 2 % and 200 Cycles/burst at 4 °C. Chromatin was sheared using Covaris E220 focused ultrasonicator to obtain a fragment size distribution of 100–800 bp (peak power: 140 W; Duty factor: 5 %; Cycles/burst: 200, water temperature 4 °C). Chromatin was immunopercipitated using homemade antibody directed against C-terminus of Lsd1 protein (Biogenes, 20752) as described (Dutel et al., 2014)
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).

treatment_protocol: adipogenic differentiation: DMEM high glucose (4.5 g/l)  (Lonza, BE12-614F) supplemented with 10 % FCS, 1% L-glutamine and 1 % penicillin/streptomycin, 0.5 mM isobutylmethylxanthine, 125 nM indomethacin, 5 μM dexamethasone, 850 nM insulin, 1 nM T3, and 1 μM rosiglitazone for 3 days, followed by DMEM high glucose (4.5 g/l)  (Lonza, BE12-614F) supplemented with 10 % FCS, 1% L-glutamine and 1 % penicillin/streptomycin, 850 nM insulin, 1 nM T3, and 1 μM rosiglitazone; myogenic differentiation DMEM high glucose (4.5 g/l)  (Lonza, BE12-614F) supplemented with1% L-glutamine and 1 % penicillin/streptomycin, 2% horse serum

tag: differentiation stage

value: adipogenic differentiation day1

value: wild-type

tag: passages

value: LSD1 (20752, homemade, Schüle lab)


title: MN47 x MN47 seed coat rep2

description:
sRNA-seq
Barcode not provided
MMS_24_overallavg_comp_singlebase.bed.gz

tag: tissue


title: MN47 x MN47 endosperm rep2

description:
sRNA-seq
Barcode: CGATGT
MMN2_3_24_overallavg_comp_singlebase.bed.gz
MM_emb_v_endo_24nt_300bp_stats.txt

source_name: Endosperm

value: Endosperm


title: MN47 x MN47 endosperm rep1

description:
sRNA-seq
Barcode: ACAGTG


title: Input_C2C12_HS

growth_protocol: DMEM high glucose (4.5 g/l)  (Lonza, BE12-614F) supplemented with 10 % FCS, 1% L-glutamine and 1 % penicillin/streptomycin

value: myogenic differentiation day1


title: MN47 x MN47 embryo rep1

description:
sRNA-seq
Barcode: TGACCA
MME_24_overallavg_comp_singlebase.bed.gz
MM_emb_v_endo_24nt_300bp_stats.txt

source_name: Embryo

value: Embryo


title: LSD1_ChIPseq_C2C12_HS


title: Input_C2C12_AD


title: C2C12_pSlik-LSD1_ad_2

data_processing:
We aligned these reads to the mm10 build of the mouse genome using TopHat version 2
The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR
Genome_build: mm10

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

value: overexpression


title: C2C12_pSlik-LSD1_ad_3


title: C2C12_pSlik_ad_1

value: Control


title: C2C12_pSlik_ad_2


title: C2C12_pSlik_ad_3


title: LSD1_ChIPseq_C2C12_OELsd1_AD

value: Overexpression


title: C2C12_pSlik-LSD1_ad_1


title: MN47 x MN47 endosperm rep3

description:
sRNA-seq
Barcode: CTTGTA
MMN2_3_24_overallavg_comp_singlebase.bed.gz
MM_emb_v_endo_24nt_300bp_stats.txt


title: Input_C2C12_OELsd1_AD


title: Kar x MN47 seed coat rep1

description:
sRNA-seq
Barcode: GATCAG
KMS1_24_singlebase.bed.gz

value: Kar female x MN47 male


title: MN47 x MN47 embryo rep3

description:
sRNA-seq
Barcode: TAGCTT
MME_24_overallavg_comp_singlebase.bed.gz
MM_emb_v_endo_24nt_300bp_stats.txt


title: Kar x MN47 endosperm rep3

description:
sRNA-seq
Barcode: TAGCTT
KMN_24_overallavg_comp_singlebase.bed.gz
KM_emb_v_endo_24nt_300bp_stats.txt
KMN_allele_specific_24_300bp_values_3reps.txt


title: C2C12_pSLik_hs_1


title: C57BL/6J_Male_NaiveCD4+Tcell_B5

description:
C57BL/6J_Male_NaiveCD4+Tcell_B5
T_B_M_2_B5

data_processing:
trim_galore   -o $outputfile --fastqc --gzip --paired --stringency 3  $fastq1 $fastq2
For alignment we used the STAR aligner (Dobin,2012). star --runThreadN 4 --genomeDir $genome_dir --readFilesIn $fastq1 $fastq2 --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 10 --outFilterMismatchNmax 999 –outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --limitBAMsortRAM 40000000000 --chimSegmentMin 10 --alignSoftClipAtReferenceEnds No
We produced unstranded coverage files using: STAR  --runThreadN 4 --runMode inputAlignmentsFromBAM --inputBAMfile Aligned.sortedByCoord.out.bam --outWigType bedGraph --outWigStrand Unstranded --outWigReferencesPrefix chr
To quantify gene expression we used the isolator framework (Jones,2016) isolator analyze --threads 1 -g /data/genomes/mm10/mm10-ercc.fa --output isolator-output.hdf5 gencode.vM3.annotation.gtf C57BL6-isolator.yaml > out ; We then use isolator summarize gene-expression --credible=0.95 --normalize isolator-output.hdf5 to produce estimates for gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: from CD4+CD62L+ T cells

extract_protocol:
Naïve CD4+ T lymphocytes were purified from single-cell suspensions by MACS depletion of non-CD4+ T cells as well as regulatory T cells and TCRγ/δ+ T cells, using a cocktail of specific biotin conjugated antibodies against CD8a (Ly-2), CD45R (B220), CD49b (DX5), CD11b (Mac-1), Ter-119, CD25 and TCRγ/δ+ using the CD4+ CD62L+ T Cell Isolation Kit II (Miltenyi) to obtain an unlabeled pre-enriched CD4+ T cell fraction. Collected cells were suspended in PBS containing 2% FBS and Fc receptors were blocked with FcR blocking reagent for 10 minutes at 4°C (Miltenyi). Cells were further fluorescently stained with a combination of CD4-FITC (Miltenyi), CD44-APC clone IM7 (eBioscience), CD62L clone MEL-14 (BD Pharmingen), eFluor® 450 CD25 clone PC61.5 (eBioscience), for 10 minutes at 4°C, washed and then stained with DAPI (Life Technologies) to cell sort the live population of naïve CD4+, CD62Lhi, CD44lo, CD25- T lymphocytes using the MoFlo XDP system (Beckman Coulter). Samples were gated on single cells for doublet discrimination and non-viable cells were excluded using the viability dye 4’, 6 – diamidine – 2 – phenylindole (DAPI). AllPrep DNA/RNA Mini Kit (Qiagen) was used to perform simultaneous isolation of RNA and DNA from 10^6 sorted naïve CD4+ T cells and resting B cells.  All RNA samples were subjected to in-column RNase-Free DNase treatment (Qiagen) to remove traces of DNA contamination. RNA integrity was subsequently assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies) by using the RNA 6000 Pico Kit (Agilent Technologies). For each sample type 3 biological replicates were generated from male and female samples.
RNA was extracted from 1 million cells and spiked-in with synthetic ERCC ExFold RNA Spike-In Mixes (Ambion®) according to manufacturer’s instructions. RNA-sequencing libraries were prepared at the Wellcome Trust Sanger Institute using the bespoke pipeline and the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (Illumina) following manufacturer’s instructions with minor modifications. 400ng of RNA per sample type were subjected to rRNA-depletion with RiboZero Gold, fragmented for 6 min using metal-ion catalysed hydrolysis. Following the adaptor ligation step an Uracil-Specific Excision enzymatic treatment (NEB) was incorporated to introduce nicks in U positions of the second strand and ensure optimal stranded library preparation. The libraries were amplified with 8 cycles of PCR using the KAPA HiFi HotStart DNA Polymerase (Kapa Biosystems), cleaned up with AMPure XP Beads, quantified and pooled in equimolar amounts. The pools were sequenced at the Wellcome Trust Sanger Institute on the Illumina HiSeq 2000 platform using 100bp paired-end read length.

value: spleen

value: CD4+CD62L+ T cells

tag: gender

value: male


title: MN47 x MN47 embryo rep2

description:
sRNA-seq
Barcode: ATCACG
MME_24_overallavg_comp_singlebase.bed.gz
MM_emb_v_endo_24nt_300bp_stats.txt


title: Kar x MN47 endosperm rep2

description:
sRNA-seq
Barcode: CGATGT
KMN_24_overallavg_comp_singlebase.bed.gz
KM_emb_v_endo_24nt_300bp_stats.txt
KMN_allele_specific_24_300bp_values_3reps.txt


title: C57BL/6J_Male_NaiveCD4+Tcell_B6

description:
C57BL/6J_Male_NaiveCD4+Tcell_B6
T_B_M_2_B6


title: C2C12_pSLik_hs_3


title: C2C12_pSLik_hs_2


title: C2C12_siCtrl_ad_3


title: C57BL/6J_Female_NaiveCD4+Tcell_A5

description:
C57BL/6J_Female_NaiveCD4+Tcell_A5
T_B_F_1_A5

value: female


title: C57BL/6J_Female_NaiveCD4+Tcell_A6

description:
C57BL/6J_Female_NaiveCD4+Tcell_A6
T_B_F_1_A6


title: C2C12_siCtrl_ad_2


title: C57BL/6J_Male_NaiveCD4+Tcell_B4

description:
C57BL/6J_Male_NaiveCD4+Tcell_B4
T_B_M_2_B4


title: C2C12_siLsd1_ad_2

value: knock-down


title: C2C12_siLsd1_ad_1


title: RNA-Seq WT rep2

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b with default parameters. Refseq transcripts were supplied in GTF format file.
featureCounts v1.5.1 was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen, Cat#74104) according to the manufacturer's instructions.
1 ug of total RNA was used to construct the libraries using Illumina True-seq RNA sample preparation kit (RS-122-2001). Samples were sequenced using Illumina HiSeq2000 platform.

value: mouse embryonic fibroblast cells

value: wild type


title: C2C12_siCtrl_ad_1

value: adipogenic differentiation day1


title: Kar x MN47 endosperm rep1

description:
sRNA-seq
Barcode: TGACCA
KMN_24_overallavg_comp_singlebase.bed.gz
KM_emb_v_endo_24nt_300bp_stats.txt
KMN_allele_specific_24_300bp_values_3reps.txt

value: 15 days after pollination


title: Kar x MN47 embryo rep3

description:
sRNA-seq
Barcode: GATCAG
KME_24_overallavg_comp_singlebase.bed.gz
KM_emb_v_endo_24nt_300bp_stats.txt
KME_allele_specific_24_300bp_values_3reps.txt


title: RNA-Seq AMPK-KO rep2

value: AMPK-/-


title: C2C12_siLsd1_ad_3


title: C57BL/6J_Female_NaiveCD4+Tcell_A4

description:
C57BL/6J_Female_NaiveCD4+Tcell_A4
T_B_F_1_A4


title: C57BL/6J_Male_RestingBcell_B1

description:
C57BL/6J_Male_RestingBcell_B1
B_B_M_1_B1

source_name: from CD43- B cells

value: CD43- B cells


title: C57BL/6J_Male_RestingBcell_B3

description:
C57BL/6J_Male_RestingBcell_B3
B_B_M_1_B3


title: RNA-Seq AMPK-KO rep1


title: Kar x MN47 embryo rep1

description:
sRNA-seq
Barcode: ATCACG
KME_24_overallavg_comp_singlebase.bed.gz
KM_emb_v_endo_24nt_300bp_stats.txt
KME_allele_specific_24_300bp_values_3reps.txt


title: C57BL/6J_Male_RestingBcell_B2

description:
C57BL/6J_Male_RestingBcell_B2
B_B_M_1_B2


title: C57BL/6J_Female_RestingBcell_A3

description:
C57BL/6J_Female_RestingBcell_A3
B_B_F_2_A3


title: Lola O Dam Lola O replicate 2

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

institute: University of Lausanne

description: Dam-Lola-O fusion protein expressed in neurons

data_processing:
Library strategy: DamID-seq
fastq files were mapped to BDGP6 of the Drosophila melanogaster genome, binned to GATC fragments and normalised using the damidseq_pipeline (Marshall and Brand, 2015). Bedgraph files from the pipeline were converted into bigwig tracks using KentUtils.
For the Lola-O binding data, a False Discovery Rate (FDR) Perl script was used to identify two or more consecutive GATC fragments that form a peak with a FDR less than 0.01 (0.1%). Any gene (genome release 6.11) that was within 5 kb of a peak (unless there is a gene in between) was identified as a target.
Genome_build: BDGP6
Supplementary_files_format_and_content: bigwig tracks normalised to sequencing depth (on sample records) and  log2 normalised foldchanges between DAM pulldown and Control pulldown as bigwig tracks (as produced by the damidseq_pipeline) (on series record).

organism: Drosophila melanogaster

source_name: Dam methylase Dam-Lola-O

growth_protocol: Flies were maintained on apple juice plates supplemented with fresh yeast.

extract_protocol:
Genomic DNA was isolated,RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors (Marshall et al., 2016).
Libraries were generated using the NebNext Ultra II DNA Library Kit

treatment_protocol: Embryos were collected for two hours at 25°C and subsequently developed for 20 hours, collected and frozen.

value: embryo

value: 22+/- 2 hours after fertilization

value: elav-Gal4; UAS-Dam-Lola-O


title: C57BL/6J_Female_RestingBcell_A2

description:
C57BL/6J_Female_RestingBcell_A2
B_B_F_2_A2


title: C57BL/6J_Male_NaiveCD4+Tcell_H3K27me3

data_processing:
Raw reads from Illumina next-generation sequencing were pre-processed using FastQC v0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TrimGalore v0.2.7 (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove poor-quality bases (with Phred score ≥20) and adapter sequences. Post-QC reads were aligned to mouse reference genome GRCm38/mm10 using BWA v0.6.2
using default parameters and the UCSC and RefSeq annotation. The mapped data were subject to further QC using SAMtools to remove unmapped, unpaired reads and reads with mapping quality score ≤20. PCR duplicates were removed using Picard tool ‘MarkDuplicates’ function. Multi-mapped reads were not included in bam files. Peaks were identified using MACS2 with default parameters (Vilagos et al., 2012), and were subsequently annotated against UCSC genome annotation (including promoter, exons, introns, upstream (-20kb to -1kb to gene TSS) and downstream (transcription end site to 20kb downstream) using a custom Perl script
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: big wig

source_name: NaiveCD4+ T cell

extract_protocol:
Naïve CD4+ T lymphocytes were purified from single-cell suspensions by MACS depletion of non-CD4+ T cells as well as regulatory T cells and TCRγ/δ+ T cells, using a cocktail of specific biotin conjugated antibodies against CD8a (Ly-2), CD45R (B220), CD49b (DX5), CD11b (Mac-1), Ter-119, CD25 and TCRγ/δ+ using the CD4+ CD62L+ T Cell Isolation Kit II (Miltenyi) to obtain an unlabeled pre-enriched CD4+ T cell fraction. Collected cells were suspended in PBS containing 2% FBS and Fc receptors were blocked with FcR blocking reagent for 10 minutes at 4°C (Miltenyi). Cells were further fluorescently stained with a combination of CD4-FITC (Miltenyi), CD44-APC clone IM7 (eBioscience), CD62L clone MEL-14 (BD Pharmingen), eFluor® 450 CD25 clone PC61.5 (eBioscience), for 10 minutes at 4°C, washed and then stained with DAPI (Life Technologies) to cell sort the live population of naïve CD4+, CD62Lhi, CD44lo, CD25- T lymphocytes using the MoFlo XDP system (Beckman Coulter). Samples were gated on single cells for doublet discrimination and non-viable cells were excluded using the viability dye 4’, 6 – diamidine – 2 – phenylindole (DAPI). AllPrep DNA/RNA Mini Kit (Qiagen) was used to perform simultaneous isolation of RNA and DNA from 10^6 sorted naïve CD4+ T cells and resting B cells.
Purified naïve CD4+ T and B cells were fixed with 1% freshly prepared formaldehyde (Thermofisher) for 10minutes at room temperature with agitation. Fixation was stopped with glycine to final concentration of 125 mM and cells washed three times in ice-cold PBS. 15x106 cells were suspended in 1 mL of lysis buffer (20 mM Hepes, pH 7.6, 1% SDS) supplemented with protease inhibitors (Complete Protease Inhibitor Cocktail, Roche). The chromatin was sheared to an average size of 200bp using a Bioruptor® Pico (Diagenode) with 10 high-energy cycles (30 s on/30 s off) at 4°C and then centrifuged for 5 minutes at 13.000 rpm at room temperature. ChIP was performed on pre-cleared chromatin diluted ten-fold with IP buffer (1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris pH 8, 167 mM NaCl) supplemented with protease inhibitors (Roche). For each immunoprecipitation, reactions of 33 l of chromatin were incubated with each one of the following antibodies: anti-H3K4me3 (1 µg, A5051-001P, Diagenode), anti-H3K36me3 (1 µg, A1847-001P, Diagenode), anti-H3K27ac (1.5 µg, A1723-0040, Diagenode), anti-H3K27me3 (2 µg A1811-001P, Diagenode) and rabbit-IgG (C15410206, Diagenode), overnight at 4°C on a rotating wheel. Chromatin was precipitated with 20μl of a mix of 1:1 protein A to protein G magnetic beads (Dynabeads, Invitrogen) dissolved in IP buffer (containing 0.15% SDS, 0.1% BSA) added to each chromatin-antibody mix and incubated at 4°C for an hour. The complexes chromatin-antibody-beads were washed once in buffer 1 (1 % Triton X-100, 0.1 % SDS, 2 mM EDTA, 150 mM NaCl and 20 mM Tris pH 8), twice in buffer 2 (1 % Triton X-100, 0.1 % SDS, 2 mM EDTA, 500 mM NaCl and 20 mM Tris pH 8) and twice in TE buffer (1 mM EDTA, 10 mM Tris pH 8). The bound fraction was eluted into elution buffer (1 % SDS, 0.1 M NaHCO3) for 20 minutes at room temperature, followed by crosslink reversal (200mM NaCl final concentration) and proteinase K protein digestion for at least 4 hours. DNA was extracted with MinElute PCR Purification Kit (QIAGEN). ChIP-seq libraries for H3K36me3 and H3K4me3 and their respective inputs were prepared at the Wellcome Trust Sanger Institute from ChIP enriched DNA using the NEBnext library prep kit (E6000B-SS) and sequenced using 75bp pair-end reads sequencing on an Illumina HiSeq 2500 platform. ChIP-seq libraries for H3K27me3 and H3K27ac and their respective inputs were prepared at the Radboud University Nijmegen from ChIP enriched DNA using the NEXTflex™ Illumina ChIP-Seq Library Prep Kit from Bioo Scientific and sequenced using 42bp single-end reads sequencing on an Illumina HiSeq 2000 platform.


title: Lola O Dam Control replicate 1

description: Dam alone control expressed in neurons (used for normalization)

source_name: Dam methylase control


title: C57BL/6J_Male_RestingBcell_H3K27me3

source_name: RestingB cell

value: RestingBcell


title: RNA-Seq WT rep1


title: Lola O Dam Control replicate 2


title: C57BL/6J_Female_NaiveCD4+Tcell_H3K27ac


title: C57BL/6J_Male_RestingBcell_H3K27ac


title: C57BL/6J_Female_RestingBcell_A1

description:
C57BL/6J_Female_RestingBcell_A1
B_B_F_2_A1


title: C57BL/6J_Male_NaiveCD4+Tcell_INPUT_REP1


title: C57BL/6J_Female_RestingBcell_H3K27ac


title: C57BL/6J_Male_NaiveCD4+Tcell_INPUT_REP2


title: C57BL/6J_Male_NaiveCD4+Tcell_H3K4me3_REP2


title: Kar x MN47 embryo rep2

value: Embryo


title: C57BL/6J_Male_NaiveCD4+Tcell_H3K27ac


title: C57BL/6J_Male_NaiveCD4+Tcell_H3K4me3_REP1


title: C57BL/6J_Female_RestingBcell_H3K27me3


title: Lola O Dam Lola O replicate 1


title: C57BL/6J_Male_RestingBcell_INPUT_REP2


title: C57BL/6J_Male_RestingBcell_INPUT_REP1


title: Cells deleted for MftR grown with urate_KU_3

city: Baton Rouge

first: Anne

last: Grove

state: LA

address: 131 LSB

department: Biological Sciences

institute: Louisiana State University

description:
KU
KU3_3_1

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v1.8.4 conversion software (Illumina).
Sequence reads were aligned to the indexed genome using Bowtie2
Samtools was used to convert the aligned SAM files obtained from Bowtie2 to BAM files
The BAM files were used to count the number of sequence reads aligned to CDS regions in the genome using the HTSeq python package
The differentially expressed genes for control and experimental conditions were identified using DEGseq
Genome_build: Burkholderia thailandensis E264
Supplementary_files_format_and_content: relative abundance

organism: Burkholderia thailandensis

source_name: Burkholderia thailandensis_cells deleted for MftR_urate

growth_protocol: cells grown in liquid culture, 2X YT media, to OD~0.6

extract_protocol:
Cells were collected by centrifugation followed by twice washing with chilled DEPC-treated water. Total RNA was isolated from three replicates of each condition using illustra RNAspin Mini Isolation kit (GE Healthcare).
All samples were rRNA depleted using Ribo-Zero rRNA removal kit (Bacterial (Illumina)). The strand specific libraries were prepared using TruSeq stranded RNA sample kit (Illumina).

value: cells deleted for MftR

tag: growth condition

value: 2X YT with urate


title: C57BL/6J_Male_NaiveCD4+Tcell_H3K36me3_REP2

value: spleen


title: Cells deleted for MftR grown with urate_KU_2

description:
KU
KU2_2_1


title: C57BL/6J_Male_RestingBcell_H3K4me3_REP1

value: male


title: C57BL/6J_Male_RestingBcell_H3K36me3_REP2


title: C57BL/6J_Female_NaiveCD4+Tcell_H3K27me3

value: female


title: Cells deleted for MftR_KN_1

description:
KN
KN1_1_2

source_name: Burkholderia thailandensis_cells deleted for MftR

value: 2X YT


title: C57BL/6J_Male_RestingBcell_H3K4me3_REP2


title: Cells deleted for MftR_KN_3

description:
KN
KN3_3_2


title: C57BL/6J_Male_RestingBcell_H3K36me3_REP1


title: Wild-type grown with urate_WU_3

description:
WU
WU3_3_1

value: wild-type


title: C57BL/6J_Male_NaiveCD4+Tcell_H3K36me3_REP1


title: Wild-type grown with urate_WU_1

description:
WU
WU1_1_1


title: Obba rivulosa 3 A-2 8 weeks growth replicate 1

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, reads with unknown bases (N) >10% and low quality reads (more than 50% of the bases with quality values<5%) were removed. Clean reads were mapped to the genome sequence using BWA/Bowtie (Langmead et al., 2009; Li and Durbin, 2010)
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using RSEM tool (Li et al. 2009)
Genome_build: O. rivulosa 3A-2 (v1.0 annotation, http://genome.jgi.doe.gov/Obbri1)
Supplementary_files_format_and_content: File includes gene length, expected count and FPKM for each sample.

organism: Obba rivulosa

source_name: Solid culture Norway spruce wood sticks

growth_protocol: The fungus was maintained on 2% malt extract agar plates (MEA) (2% (w/v) malt extract, 2% (w/v) agar agar). For pre-cultures, the fungus was cultivated for 7 days at 28°C in 100 ml liquid low-nitrogen-asparagine-succinate medium (LN-AS), pH 4.5 (Hatakka and Uusi-Rauva, 1983), supplemented with 0.05% glycerol, in 250 ml Erlenmeyer flasks, which were inoculated with five mycelium-covered agar plugs (⌀ 7 mm) from MEA plates. After the homogenization (Waring Blender, USA), 4 ml of mycelial suspension was used for the inoculation of spruce wood solid cultures, which consisted of 2 g (dry weight) of Norway spruce (Picea abies) wood sticks (approx. 2 x 0.2 x 0.3 cm in size) on 1% (w/v) water agar (Mäkelä et al., 2002). Cultures were incubated stationary at 28°C in the dark for 2, 4, and 8 weeks.

extract_protocol:
Total RNA was extracted from the spruce cultures by using a CsCl gradient ultracentrifugation as described previously (Patyshakuliyeva et al., 2014). Quality and quantity of RNA were determined by using the RNA6000 Nano Assay (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA, USA). Purification of mRNA, synthesis of cDNA library, and sequencing (RNA-seq) was performed at the BGI Tech Solutions Co. Ltd. (Hong Kong, China) as described in Patyshakuliyeva et al., 2015.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After reaching the specific time point, mycelium-colonized wood sticks were flash frozen in liquid nitrogen followed by subsequent RNA extraction.

tag: monokaryotic strain

value: monokaryon 3 A-2

tag: dikaryotic strain

tag: substrate

value: Norway spruce wood stricks + 1% (w/v) water agar

tag: sampling time

value: 8 weeks

tag: sample type

value: Solid culture Norway spruce wood sticks


title: Obba rivulosa 3 A-2 4 weeks growth replicate 2

value: 4 weeks


title: LW_Liver_90d_RNA-seq

city: Wuhan

first: Yuhua

last: Fu

state: Hubei

address: No.1, Shizishan Street, 430070, Wuhan, China

department: College of Animal Science and Technology

country: China

institute: Huazhong Agricultural University

data_processing:
To avoid reads with low-quality, we removed the following types of reads: (a) reads with ≥ 10% unidentified nucleotides (N); (b) reads with > 10 nt aligned to the adapter, allowing ≤ 10% mismatches; and (c) reads with > 50% bases having phred quality < 5.
High-quality RNA-seq data were aligned to the swine Sscrofa10.2 reference genome using Tophat (v2.1.0) with 2 nt fault tolerance
Reads count for each protein-coding gene were extracted by using the HTseq (v 0.6.1) and only uniquely aligned reads were remained.
The reads count were normalized by using TMM method from R package edgeR (v 3.16.3)
Genome_build: Sus scrofa (Sscrofa10.2)
Supplementary_files_format_and_content: Reads count for each gene in three library

organism: Sus scrofa

source_name: Liver

growth_protocol: The liver tissues were obtained from three male pigs at Postnatal day 90.

extract_protocol:
Total RNA was extracted from the three liver samples using TRIzol (Invitrogen). RNase-free DNase I (TaKaRa) was used to remove genomic DNA from the RNA samples. The integrity of total RNA was determined by the Agilent Technologies of Bioanalyzer 2100 and RNA 6000 Nano Labchip Kit (Agilent, CA, USA) with RIN number >6.0.
Three libraries were sequenced by Illumina Hiseq 2500 (Illumina, San Diego, CA, USA) with 125 bp paired-end reads according to the manufacturer’s instructions.

tag: breeds

value: Large White pig

tag: age

value: Postnatal 90 day


title: Cells deleted for MftR grown with urate_KU_1

description:
KU
KU1_1_1

tag: strain


title: WB_Liver_90d_RNA-seq

value: Chinese wild boar

tag: Sex


title: Wild-type_WN_3

description:
WN
WN3_3_2

source_name: Burkholderia thailandensis_wild-type


title: Obba rivulosa 3 A-2 8 weeks growth replicate 2


title: HoxB7cre_WT_SCR18

city: PARIS

first: Silvia

last: Cereghini

address: 9 Quai Saint Bernard BatC 7ET

department: Developmental Biology

country: France

institute: IBPS- UMR7622 CNRS -UPMC

data_processing:
RNA sequencing was performed on an Ion Proton™ System, according to the manufacturer's instructions.
The prepared libraries were quantified and pooled together in duplicates at the required concentration.
The library pools were then processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (ThermoFisher Scientific) and sequencing with the Ion PI™Sequencing 200 Kit on Ion Proton PI™ chips (ThermoFisher Scientific) according to commercial protocols.
The resulting RNA-Seq BAM files were analyzed with the Bioconductor package metaseqR (Moulos and Hatsis, Nucleic Acids Res 43, e25 (2015) and applying the edgeR (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) methodology for differential expression analysis with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: Hoxb7 Hnf1b raw_counts_table.txt: raw counts of the 4 samples (SCR16, SCR17,SCR18,SCR19)
Hoxb7cre Hnf1b normalized_counts_table.txt: nrmalized counts of the 4 samples (SCR16, SCR17,SCR18,SCR19)

source_name: Embryonic kidneys_wildtype

extract_protocol:
RNA from microdissected kidneys was extracted by Tryzol using the miRNA mini kit Qiagen for extraction of total and miRNAs. The quality of the RNA samples was assessed on the Agilent Bioanalyzer system using the Agilent RNA 6000 Nano Kit  (Agilent Technologies) and RNA with a Ring higher than 8 was used.
1-2 μg of total RNA were used for mRNA isolation using the Dynabeads® mRNA DIRECT™ Micro Kit (ThermoFisher Scientific).
mRNA was digested with RNase III, purified, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA‐Seq Kit v2 (ThermoFisher Scientific).

tag: background strain

value: kidneys


title: Obba rivulosa 3 A-2 4 weeks growth replicate 1


title: HoxB7cre_WT_SCR19

tag: genotype


title: ES_Liver_90d_RNA-seq

value: Enshi black pig


title: HoxB7cre_HET_SCR17

source_name: E15.5 Embryonic kidneys_mutant

tag: developmental stage


title: Cells deleted for MftR_KN_2

description:
KN
KN3_3_1

value: cells deleted for MftR


title: Wild-type_WN_2

description:
WN
WN2_2_1


title: Obba rivulosa 3 A-2 2 weeks growth replicate 2

value: 2 weeks


title: S-morphotype (smooth) RNA-seq

city: Daejeon

first: Haeyoung

last: Jeong

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

data_processing:
Sequence reads were produced from an Illumina HiSeq 2500 instrument (HCS v2.2) at Macrogen (Seoul, Korea) at January, 2016. TruSeq SBS Kit v4 was used for the sequencing reagent.
Paired reads, imported in CLC Genomics Workbench, were first trimmed (low quality limit 0.01, max 1 ambiguous nucleotide allowed per read, min length 50 nt) and subject to RNA-seq analysis v2.1 using the PGAP annotation for gene and mRNA information.
Read mapping parameters for the analysis process were as follows: costs for mismatch:insertion:deletion = 2:3:3, length and similarity fraction = 0.8, max number of hits for a reads = 10). Quantile normalization was applied to genes having 1 or more RPKM in both samples.
Genome_build: MVGR00000000.1 (assembly KWv02)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

organism: Microcystis aeruginosa KW

source_name: cell culture

growth_protocol: BG11 medium under 50 μmol/m2/s1 at 25℃ with no aeration or agitation for 3 weeks.

extract_protocol:
Each type of cells were harvested and grounded in liquid nitrogen followed by RNA extraction using PureLink RNA Mini Kit (Invitrogen)
After removing ribosomal RNA using Ribo-Zero rRNA Removal Kit (Bacteria), libraries were constructed using TruSeq RNA Sample Prep Kit v2 (Part # 15026495 Rev. F) from each morphoype without replicates.

treatment_protocol: No treatment was required because M. aeruginosa KW strain showed distinct morphotypes spontanously when grown in static microscosms in laboratory conditions.

value: KW

tag: morphotype

value: S-type


title: W-morphotype (wrinkle) RNA-seq

source_name: Cell culture

value: W-type


title: Wild-type_WN_1

description:
WN
WN1_1_1

value: 2X YT


title: Obba rivulosa 3 A-2 2 weeks growth replicate 1


title: d_rnr O2 w/propionate 2

status: Public on Dec 14 2017

city: Karlsruhe

first: Andreas

last: Doetsch

address: Haid-und-Neu-Str. 9

department: Physiology and Biochemistry of Nutrition

institute: Max Rubner-Institute

data_processing:
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina).
The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923).
Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'.
Genome_build: NC_000913.3 E. coli K12 substr. MG1655
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI.

organism: Escherichia coli K-12

source_name: delta-rnr mutant_oxic_glycerol + propionate

growth_protocol: Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions.

extract_protocol:
Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany).
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides.

treatment_protocol: No further treatment was applied.

tag: genotype/variation

value: K-12 delta-rnr mutant (JW5741-1)

tag: oxic/anoxic

value: oxic

tag: carbon source

value: glycerol + propionate

tag: molecule subtype

value: total RNA (ribosome-depleted)


title: Wild-type grown with urate_WU_2

description:
WU
WU2_2_2

value: wild-type

tag: growth condition

value: 2X YT with urate


title: d_rnr NO3 2

source_name: delta-rnr mutant_anoxic (NO3)_glycerol

value: anoxic (NO3)

value: glycerol


title: d_rnr O2 2

source_name: delta-rnr mutant_oxic_glycerol


title: d_rnr O2 1


title: d_rnr NO3 w/propionate 1

source_name: delta-rnr mutant_anoxic (NO3)_glycerol + propionate


title: d_rnr O2 w/propionate 1


title: d_rnr NO3 1


title: WT O2 w/propionate 2

source_name: wild type_oxic_glycerol + propionate

value: K-12 wild type


title: WT O2 w/propionate 1


title: WT NO3 w/propionate 2

source_name: wild type_anoxic (NO3)_glycerol + propionate


title: WT NO3 w/propionate 1


title: WT O2 2

source_name: wild type_oxic_glycerol


title: WT NO3 1

source_name: wild type_anoxic (NO3)_glycerol


title: WT NO3 2


title: WT O2 1


title: input

city: Manhattan

first: Ross

last: Levine

state: NY

address: RRL

institute: MSKCC

data_processing:
H3K27Ac and H3K4Me1 FASTQ reads are aligned to mouse reference genome (build mm9) using bowtie2 (Langmead and Salzberg, 2012) after trimming adaptors with trim-galore tool.
Duplicated reads are marked with Picard tools and removed from aligned BAM files.
Alignment BAMs are sorted and indexed using samtools (Li, 2011; Li et al., 2009).
Enriched ChIP-seq peaks genome-wide are called with MACS (v1.4) (Zhang et al., 2008)
Genome coverage is calculated for individual BAM using bedtools (v2.17) (Quinlan and Hall, 2010) and normalized to 10 million reads.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: MPN progenitor cells

growth_protocol: MPLW5151L-positive p65fl/fl;Mx1-Cre, Ikk2fl/fl;Mx1-Cre or floxed Cre-negative control cells were seeded at a density of 10 000 cells/replicate into cytokine-supplemented methylcellulose medium (Methocult M3434; STEMCELL Technologies).

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library  prep kit following the manufacturer’s recommended protocol (New England  Biolabs, Ipswich, MA, USA).

treatment_protocol: MPLW515L retroviral bone marrow transplantation experiments and secondary Jak2V617F bone marrow transplantation experiments were performed as previously described (Kleppe et al., 2015).

tag: cell type

value: MPN progenitor cells

value: mutant

tag: antibody


title: MEP-H3K4me1


title: MIGRI-H3K4me1

value: control


title: HoxB7cre_HET_SCR16

tag: tissue

value: kidneys


title: H3K27ac


title: d_rnr NO3 w/propionate 2


title: H3K27ac control


title: NES_Input_rep2

first: William

last: Mallard

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description:
HEK293T NES-APEX2 input
NES-APEX2.gene_exp.diff.gz

data_processing:
Reads were mapped to human genome using TopHat v2.1.1 with the flags, "--no-coverage-search" and "--GTF gencode.v19.annotation.gtf".
Gene expression was quantified against the Gencode v19 reference transcriptome (gencode.v19.annotation.gtf, genecodegenes.org) with Cufflinks v2.2.1.
The statistical significance of differential expression was assessed using CuffDiff2, with the flags, "--dispersion-method per-condition" and "--seed 42".
ROC analysis was perfomed in Microsoft Excel, using true positive and false positive gene lists culled from the literature.
Genome_build: hg19

source_name: HEK293T cells

growth_protocol: HEK 293T cells (ATCC) were cultured in 6-well dishes, in growth media consisting of 1:1 DMEM:MEM (Cellgro), supplemented with 10% Fetal Bovine Serum (FBS), 50 units/mL penicillin, and 50 _g/mL streptomycin, at 37 ¡C and under 5% CO2. Cells were discarded at 25 passages, and were periodically tested for Mycoplasma contamination using Universal Mycoplasma Detection kit (ATCC).

extract_protocol:
All buffers used during RNA isolation were supplemented to 0.1 U/uL RNaseOUT (Thermo Fisher), 1xEDTA-free proteinase inhibitor cocktail (Thermo Fisher) and 0.5 mM DTT, final. Labeled, crosslinked cell pellets were lysed by incubation in 1 mL ice-cold RIPA buffer (50 mM Tris, 150 mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate, 1% Triton X-100, 5 mM EDTA), supplemented with 10 mM ascorbate and 5 mM Trolox, for 5 min at 4 ¡C with end-over-end agitation. Samples were then sheared using a Branson Digital Sonifier 250 at 10% amplitude for three 30-s intervals (0.7 s on + 1.3 s off), with 30-s resting steps between intervals. Samples were held in ice-cold metal thermal blocks throughout sonication. Lysates were then clarified by centrifugation at 15,000xg for 5 min at 4 ¡C, moved to fresh tubes and each diluted with 1 mL Native lysis buffer (NLB: 25mM Tris pH 7.4, 150 mM KCl, 0.5% NP-40, 5 mM EDTA), supplemented with ascorbate and trolox. ÒInputÓ samples corresponded to 20% of these lysates. To the remainder was added 50 uL of streptavidin-coated magnetic bead slurry (Pierce) that had been equilibrated by two washes in 1:1 RIPA:NLB. Samples were incubated for 2 h at 4 ¡C with end-over-end agitation. Beads were subsequently washed with the following series of buffers (1 mL each, 5 min per wash, 4 ¡C, with gentle end-over-end agitation): (1) RIPA buffer, supplemented with trolox and ascorbate, (2) RIPA buffer without radical quenchers, (3) high salt buffer (1 M KCl, 50 mM Tris, pH 8.0, 5 mM EDTA), (4) urea buffer (2 M Urea, 50 mM Tris, pH 8.0, 5 mM EDTA), (5) RIPA Buffer, (6) 1:1 RIPA: NLB, (7) NLB, and (8) TE (10 mM Tris, pH 7.4, 1 mM EDTA). Input and enriched RNAs were harvested and reverse-crosslinked by proteolysis in 100 uL of Elution Buffer (2% N-lauryl sarcoside, 10mM EDTA, 5mM DTT, in 1X PBS, supplemented with 200 ug proteinase K (Ambion) and 4 U RNaseOUT) at 42 ¡C for 1h, followed by 55 ¡C for 1h, as previously described. Eluted samples were cleaned up using Agencourt RNAClean XP magnetic beads (Beckman Coulter), following the manufacturer's 1.5 mL tube format protocol, and eluted into 85 uL H2O. Thereafter, contaminating DNA was removed by digestion with 5 U RQ1 RNase-free DNase I (Promega) in 100 uL of the manufacturer's supplied buffer (1X final concentration) at 37 ¡C for 30 min. Purified RNAs were again cleaned up using Agencourt RNAClean XP magnetic beads, as above, and eluted into 30 uL H2O.
Purified RNA samples were depleted of ribosomal RNA using the Ribo-Zero Gold rRNA removal kit (Illumina), generally in accordance with the manufacturer's protocol. Briefly, RNA concentration and integrity were quantified on an Agilent 2100 Bioanalyzer, using ÒRNA PicoÓ and, where appropriate, ÒRNA NanoÓ kits. Samples were not concentrated prior to rRNA depletion, which can accommodate a maximum input volume of 17 uL. Therefore, samples with total input masses of 0-20 ng or 20-100 ng were mixed with 1 uL or 2 uL of Ribo-Zero rRNA Removal Solution, respectively, in 1x RiboZero Reaction Buffer, at a final volume of 20 uL. Reaction mixes were incubated at 68¡C for 10 minutes, followed by 25¡C for 5 minutes more, and thereafter added to 32.5 uL magnetic beads (90 uL bead slurry; washed with water and equilibrated in Magnetic Bead Resuspension Buffer, supplemented with RiboGuard RNase Inhibitor) by extensive pipetting. Binding reactions were incubated at room temperature for 5 minutes, gently vortexed for 5 seconds, and incubated for 5 minutes at 50¡C, in a thermocycler. The supernatant, containing rRNA-depleted RNA, was diluted in water to 50 uL final volume, cleaned up with 50 uL Agencourt RNAClean XP beads and eluted with 19.5 uL of Elute, Prime, Fragment mix from the TruSeq RNA sample preparation kit, v2 (Illumina). Thereafter, libraries were prepared using the TruSeq RNA sample preparation kit, according to the manufacturer's instructions, starting from ÒIncubate RFPÓ step.

treatment_protocol: For mitochondrial APEX-RIP experiments, cells were grown to 90% confluency in 6-well plates, and incubated in fresh growth media supplemented with 500 uM Biotin-phenol (BP) for 30 minutes at 37 ¡C, after which H2O2 was added to a final concentration of 1 mM. After 1 min, the media was replaced with 5 mL crosslink-quench solution (0.1% (v/v) formaldehyde, 10 mM sodium ascorbate, and 5 mM Trolox, in PBS) for one minute, to simultaneously quench the APEX2 BP labeling reaction and initiate formaldehyde crosslinking. Thereafter, cells were washed and incubated in 5 mL of fresh crosslink-quench for two additional 1-minute incubation steps, followed by a third, 8-minute wash. Thereafter, crosslinking was terminated by the addition of Glycine. For all other subcellular compartments, treatment was identical, except that, following BP-labeling, and prior to the addition of crosslink-quench solution, cells were incubated in 2 mL azide-free quenching solution (10 mM ascorbate and 5 mM Trolox, in PBS) for one minute. Subsequently, cells were subjected to only two (1 and 9 minute) treatments in crosslink-quench solution. Thereafter, crosslinking was terminated by the addition of Glycine.

tag: cell line

value: HEK293T cells

tag: expression construct

tag: input or rip

value: Input


title: NES_RIP_rep3

description:
HEK293T NES-APEX2 RIP
NES-APEX2.gene_exp.diff.gz

value: RIP


title: NES_RIP_rep2


title: NES_RIP_rep1


title: NES_Input_rep3


title: NES_Input_rep1


title: NLS_RIP_rep2

description:
HEK293T NLS-APEX2 RIP
NLS-APEX2.gene_exp.diff.gz


title: NLS_RIP_rep1


title: NLS_RIP_rep3


title: NLS_Input_rep3

description:
HEK293T NLS-APEX2 input
NLS-APEX2.gene_exp.diff.gz


title: NLS_Input_rep2


title: NLS_Input_rep1


title: KDEL_RIP_rep2

description:
HEK293T KDEL-HRP RIP
KDEL-HRP.gene_exp.diff.gz

value: KDEL-HRP


title: KDEL_RIP_rep1


title: KDEL_Input_rep2

description:
HEK293T KDEL-HRP input
KDEL-HRP.gene_exp.diff.gz


title: KDEL_Input_rep1


title: input control


title: Mito_RIP_NegCtrl_rep2

description:
HEK293T Mito-APEX2 RIP -H2O2
Mito-APEX2.gene_exp.diff.gz


title: Mito_Input_NegCtrl_rep1

description:
HEK293T Mito-APEX2 input -H2O2
Mito-APEX2.gene_exp.diff.gz


title: Mito_Input_NegCtrl_rep2


title: Mito_RIP_NegCtrl_rep1


title: Mito_RIP_rep3

description:
HEK293T Mito-APEX2 RIP
Mito-APEX2.gene_exp.diff.gz


title: Mito_RIP_rep1


title: Mito_Input_rep2

description:
HEK293T Mito-APEX2 input
Mito-APEX2.gene_exp.diff.gz


title: Mito_Input_rep3


title: Mito_Input_rep1


title: at-pollen-sRNA_col_rdr6

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description:
small RNA
Arabidopsis thaliana Pollen of rdr6 Columbia-0

data_processing:
small-RNA: Adapters were removed from the 50 bp long single-end sRNA reads in each library. The resulting18-30 bp long reads were mapped to a Col genome (TAIR10) masked for Ler SNPs using bowtie (-v 2 –best). All reads mapping to chloroplast and mitochondria and to structural noncoding RNAs (tRNAs, snRNAs, rRNAs, or snoRNAs) were removed. Mapped reads from both replicates were pooled together, sorted in two categories (21-22-nt and 24-nt long) and remapped to the same reference masked genome mentioned above using ShorStack (--mismatches 2 --mmap f) in order to improve the localization of sRNAs mapping to multiple genomic locations. We normalized the alignments by converting coverage values to reads per million mapped reads (RPM) values.
genome build: TAIR10
processed data files format and content: small-RNA: Unique small RNAs (between 18-30 nts)  that mapped to the Ler masked TAIR10 genome, after removal of chloroplast, mitochondria and structural noncoding RNAs. Accumulation number (raw reads) are represented in a three column format file: <sequence_smallRNA> <number_of_reads><read_length_bp> for each sample.

source_name: AT Pollen rdr6 Columbia

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
Mature pollen was harvested by manual collection of open flowers into a 18% sucrose collection buffer placed on ice. Tubes containing the extraction buffer and open flowers were vortexed for 5 minutes and centrifuged for 3 minutes at 3,000 rpm in a centrifuge equipped with a tilt rotor. Pollen RNA was extracted with TRIzol reagent according to manufacturer instructions. Small RNA was enriched by cutting the 17-29nt small RNA fraction from a polyacrylamide gel and subsequent elution and precipitation.  Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit
For the library preparation the Illumina TrueSeq small RNA protocol was followed and the libraries were sequenced with an Illumina HiSeq2500 in 50-bp single-end fashion.

treatment_protocol: Material was generated by manual extraction of pure mature pollen from Col-0 rdr6 plants.

value: pollen

value: rdr6 (Col)


title: at-pollen-sRNA_col_wt_control

description:
small RNA
Arabidopsis thaliana Pollen of Columbia-0

source_name: AT Pollen wt-control Columbia

treatment_protocol: Material was generated by manual extraction of pure mature pollen from Col-0 wt plants.

value: Col


title: at-pollen-sRNA_col_dcl4_rdr6

description:
small RNA
Arabidopsis thaliana Pollen of dcl4 rdr6 Columbia-0

source_name: AT Pollen dcl4_rdr6 Columbia

treatment_protocol: Material was generated by manual extraction of pure mature pollen from Col-0 dcl4 rdr6 plants.

value: dcl4 rdr6 (Col)


title: at-endosperm-RNAseq_replicate2_ler_wt_x_col_pol4

description:
endo_RNAseq_total_rpkm.txt.gz
Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with nrpd1a-3 (male)

data_processing:
RNA-seq: For each replicate, 50 bp long reads were mapped to the Arabidopsis (TAIR10) genome, masked for rRNA genes, using TopHat v2.1.0 (Trapnell et al, 2009) (parameters adjusted as -g 1 -a 10 -i 40 -I 5000 -F 0 -r 130). Gene and TE expression was normalized to reads per kilobase per million mapped reads (RPKM) using GFOLD.
genome build: TAIR10
processed data files format and content: RNA-seq: expression levels (RPKM) are shown for genes and transposable elements in TAIR10 for each condition and replicate.

source_name: AT F1-Endosperm Landsberg x pol4 Columbia

extract_protocol:
For RNA sequencing, endosperm from seeds derived from indicated crosses were dissected in biological duplicates. RNA was extracted following a modified protocol for the RNAqueous kit (Ambion, Life Technologies). RNA was purified by Qiagen RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) after residual DNA was removed by adding 2 uL DNaseI (Thermo-Scientific, Waltham, USA).
Libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, USA) and sequenced in 50-bp single-end mode.

treatment_protocol: Material was generated by manually crossing of pistillata (Ler) mutants with pollen of nrpd1a plants.

value: endosperm

value: Ler x nrpd1a (Col)


title: at-endosperm-RNAseq_replicate1_ler_wt_x_col_wt

description:
endo_RNAseq_total_rpkm.txt.gz
Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with Columbia-0 (male)

source_name: AT F1-Endosperm Landsberg x Columbia

treatment_protocol: Material was generated by manually crossing of pistillata (Ler) mutants with pollen of Col plants.

value: Ler x Col


title: at-endosperm-RNAseq_replicate2_ler_wt_x_col_pol4_osd1

description:
endo_RNAseq_total_rpkm.txt.gz
Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with nrpd1a-3 osd1-1 (male)

source_name: AT F1-Endosperm Landsberg x pol4 osd1 Columbia

treatment_protocol: Material was generated by manually crossing of pistillata (Ler) mutants with pollen of 4x nrpd1a plants.

value: Ler x nrpd1a osd1 (Col)


title: at-endosperm-RNAseq_replicate1_ler_wt_x_col_osd1

description:
endo_RNAseq_total_rpkm.txt.gz
Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with osd1-1 (introgressed into Col) (male)

source_name: AT F1-Endosperm Landsberg x osd1 Columbia

treatment_protocol: Material was generated by manually crossing of pistillata (Ler) mutants with pollen of 4x Col plants.

value: Ler x osd1 (Col)


title: at-endosperm-RNAseq_replicate1_ler_wt_x_col_pol4_osd1


title: at-endosperm-RNAseq_replicate1_ler_wt_x_col_pol4

value: Ler x nrpd1a  (Col)


title: at-pollen-sRNA_col_nrpd1a_2n

description:
small RNA
Arabidopsis thaliana Pollen of 4x nrpd1a-3 (Columbia-0)

source_name: AT Pollen nrpd1a-2n Columbia

treatment_protocol: Material was generated by manual extraction of pure mature pollen from 4x Col-0 nrpd1a plants (2n pollen).

value: 4x nrpd1a (Col)


title: at-pollen-sRNA_col_nrpd1a_1n

description:
small RNA
Arabidopsis thaliana Pollen of nrpd1a-3 (Columbia-0)

source_name: AT Pollen nrpd1a-1n Columbia

treatment_protocol: Material was generated by manual extraction of pure mature pollen from Col-0 nrpd1a plants (1n pollen).

value: nrpd1a (Col)


title: at-pollen-sRNA_col_wt_2n

description:
small RNA
Arabidopsis thaliana Pollen of 4x Columbia-0

source_name: AT Pollen wt-2n Columbia

treatment_protocol: Material was generated by manual extraction of pure mature pollen from 4x Col-0 wt plants (2n pollen).

value: 4x Col


title: at-pollen-sRNA_col_wt_1n

source_name: AT Pollen wt-1n Columbia

treatment_protocol: Material was generated by manual extraction of pure mature pollen from Col-0 wt plants (1n pollen).


title: at-seed-sRNA_replicate2_ler_wt_x_col_wt

description:
small RNA
Arabidopsis thaliana F1-seed of pistillata (Landsberg-0) (female) crossed with Columbia-0 (male)

source_name: AT F1-Seed 6DAP Landsberg x Columbia

extract_protocol:
For each genotype 1000 seeds at 6-7 DAP were collected in duplicates in RNA later (Sigma–Aldrich) and homogenized (Silamat S5) using glass beads. Total RNAs of seeds were extracted using mirVana miRNA isolation kit (Ambion/Life Technologies) and sRNAs were isolated by FDF-PAGE.
SRNA libraries were generated using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina and the libraries were sequenced with an Illumina HiSeq2500 in 50-bp single-end fashion.

treatment_protocol: Material was generated by manually crossing of emasculated pistillata (Ler) with pollen of Col plants.

value: seed

value: pistillata (Ler) x Col


title: KDEL_Input_rep3

value: HEK293T cells

value: Input


title: at-seed-sRNA_replicate2_ler_wt_x_4x nrpd1a

description:
small RNA
Arabidopsis thaliana F1-seed of pistillata (Landsberg-0) (female) crossed with 4x nrpd1a-3 (male)

source_name: AT F1-Seed 6DAP Landsberg x pol4 4x Columbia

treatment_protocol: Material was generated by manually crossing of emasculated pistillata (Ler) with pollen of 4x nrpd1 (Col) plants.

value: pistillata (Ler) x 4x nrpd1a (Col)


title: at-seed-sRNA_replicate1_ler_wt_x_4x nrpd1a


title: at-seed-sRNA_replicate1_ler_wt_x_col_wt


title: at-seed-sRNA_replicate1_ler_wt_x_4x Col

description:
small RNA
Arabidopsis thaliana F1-seed of pistillata (Landsberg-0) (female) crossed with 4x Columbia-0 (male)

source_name: AT F1-Seed 6DAP Landsberg x 4x Columbia

treatment_protocol: Material was generated by manually crossing of emasculated pistillata (Ler) with pollen of 4x Col plants.

value: pistillata (Ler) x 4x Col


title: at-seed-sRNA_replicate2_ler_wt_x_nrpd1a

description:
small RNA
Arabidopsis thaliana F1-seed of pistillata (Landsberg-0) (female) crossed with nrpd1a-3 (male)

source_name: AT F1-Seed 6DAP Landsberg x pol4 Columbia

treatment_protocol: Material was generated by manually crossing of emasculated pistillata (Ler) with pollen of nrpd1 (Col) plants.

value: pistillata (Ler) x nrpd1a (Col)


title: at-seed-sRNA_replicate2_ler_wt_x_4x Col


title: at-endosperm-BS_replicate2_ler_wt_x_col_wt

description: Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with Columbia-0 (male)

data_processing:
Bisulfite-seq: For each mutant, the 125 bp reads from the Illumina BS sequence libraries from the two replicates were merged and trimmed to 100 bp by cutting 5 bp from the start and 20 bp from the end of each read. After this first trimming, each read was split in two 50 bp long reads in order to improve mapping efficiency.  Reads were mapped to the TAIR10 Arabidopsis genome using the Bismark read mapper (Krueger and Andrews, 2011) allowing up to one mismatch per read. Duplicated reads (aligning to the same genomic position) were eliminated before reporting methylation levels.
genome build: TAIR10
processed data files format and content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format:  <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>

extract_protocol:
Genomic DNA of hand-dissected endosperm  from 18-28 siliques was purified using MagJET Plant Genomic DNA kit (Thermo Fisher Scientific) and sonicated in Bioruptor (Diagenode) for 30 cycles (30 sec ON, 30 sec OFF at high power) using a Bioruptor (Diagenode). The bisulfite conversion was done using the EpiTect Fast DNA Bisulfite Kit (Qiagen) during the library preparation.
Bisulfite libraries were generated using Ovation Ultralow Methyl-Seq Library Systems (NuGEN) following the manufacturer's protocol using 20 ng of starting DNA.

treatment_protocol: Material was generated by manually crossing of emasculated wt (Ler) with pollen of wt (Col) plants.


title: at-endosperm-RNAseq_replicate2_ler_wt_x_col_wt


title: at-seed-sRNA_replicate1_ler_wt_x_nrpd1a

value: pistillata (Ler) x nrpd1a  (Col)


title: at-endosperm-BS_replicate2_ler_wt_x_col_pol4

description: Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with nrpd1a-3 (male)

treatment_protocol: Material was generated by manually crossing of emasculated wt (Ler) with pollen of nrpd1 (Col) plants.

value: endosperm


title: at-endosperm-BS_replicate2_ler_wt_x_col_pol4_osd1

description: Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with nrpd1a-3 osd1-1 (male)

treatment_protocol: Material was generated by manually crossing of emasculated wt (Ler) with pollen of nrpd1a osd1 (Col) plants.


title: at-endosperm-BS_replicate1_ler_wt_x_col_pol4


title: Mito_RIP_rep2

description:
HEK293T Mito-APEX2 RIP
Mito-APEX2.gene_exp.diff.gz

treatment_protocol: For mitochondrial APEX-RIP experiments, cells were grown to 90% confluency in 6-well plates, and incubated in fresh growth media supplemented with 500 uM Biotin-phenol (BP) for 30 minutes at 37 ¡C, after which H2O2 was added to a final concentration of 1 mM. After 1 min, the media was replaced with 5 mL crosslink-quench solution (0.1% (v/v) formaldehyde, 10 mM sodium ascorbate, and 5 mM Trolox, in PBS) for one minute, to simultaneously quench the APEX2 BP labeling reaction and initiate formaldehyde crosslinking. Thereafter, cells were washed and incubated in 5 mL of fresh crosslink-quench for two additional 1-minute incubation steps, followed by a third, 8-minute wash. Thereafter, crosslinking was terminated by the addition of Glycine. For all other subcellular compartments, treatment was identical, except that, following BP-labeling, and prior to the addition of crosslink-quench solution, cells were incubated in 2 mL azide-free quenching solution (10 mM ascorbate and 5 mM Trolox, in PBS) for one minute. Subsequently, cells were subjected to only two (1 and 9 minute) treatments in crosslink-quench solution. Thereafter, crosslinking was terminated by the addition of Glycine.

value: RIP


title: at-endosperm-RNAseq_replicate2_ler_wt_x_col_osd1


title: at-endosperm-BS_replicate1_ler_wt_x_col_pol4_osd1


title: at-endosperm-BS_replicate1_ler_wt_x_col_osd1

description: Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with osd1-1 (introgressed into Col) (male)

treatment_protocol: Material was generated by manually crossing of emasculated wt (Ler) with pollen of osd1 (Col) plants.


title: at-endosperm-BS_replicate2_ler_wt_x_col_osd1


title: Adult ABX Female Replicate 3

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description:
SMARTseq + Nextera XT
A2M_ABX_Female

data_processing:
reads were mapped to mouse reference genome GRCm38 using STAR. Reads per gene were counted using featureCounts. Mouse reference genome .fasta file and gene annotation .gtf file were downloaded from Gencode version M9
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

source_name: Brain microglia

extract_protocol: RNA libraries were prepared for sequencing using SMART-Seq (TAKARA) protocole and Nextera XT DNA library (Illumina)

tag: strain

tag: age

value: Adult (2 months)

tag: antibiotics treatment

value: Specfic-pathogen-free (SPF) treated with ABX


title: Adult SPF Male Replicate 2

description:
SMARTseq + Nextera XT
A2M_SPF_Male

value: Specfic-pathogen-free (SPF)


title: Adult ABX Male Replicate 1

description:
SMARTseq + Nextera XT
A2M_ABX_Male


title: Adult SPF Male Replicate 1

description:
SMARTseq + Nextera XT
A2M_SPF_Male


title: Adult ABX Male Replicate 2

description:
SMARTseq + Nextera XT
A2M_ABX_Male


title: Adult ABX Male Replicate 3

description:
SMARTseq + Nextera XT
A2M_ABX_Male


title: Adult SPF Male Replicate 3

description:
SMARTseq + Nextera XT
A2M_SPF_Male


title: Adult ABX Female Replicate 1

description:
SMARTseq + Nextera XT
A2M_ABX_Female


title: Adult SPF Female Replicate 2

description:
SMARTseq + Nextera XT
A2M_SPF_Female