title: WT poly(I:C) treatment replicate2

city: Boulder

first: Roy

middle: Robert

last: Parker

state: CO

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

data_processing:
Read quality was assessed using fastqc.
Reads were trimmed using Trimmomatic 0.32 in paired and (PE) mode.
Reads were aligned using Tophat (version 2.0.6) and Bowtie2 (version 2.0.2) and the following parameters:–b2 –fast –microexon-search.
Differential expression analysis was performed using Cuffdiff (version 2.2.1) with the default parameters (Trapnell et al., 2013)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: SupplementalTablePolyIC contains cuffdiff output and other parameters used for analysis

source_name: WT poly(I:C) treatment

growth_protocol: Cells were grown in DMEM with 10% FBS.

extract_protocol:
Trizol was used to isolate Total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols by the BioFrontiers sequencing facility.

treatment_protocol: Cells were transfected with or without 500 ng poly(I:C) for6 hours.

tag: cell line background

value: parental (WT)

tag: treatment

value: poly(I:C) (500-ng/ml) transfection

tag: time point

value: 6-hours post-transfection


title: WT poly(I:C) treatment replicate1

status: Public on Jul 10 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: genotype/variation


title: WT poly(I:C) treatment replicate3


title: WT untreated replicate 3

source_name: WT untreated


title: Patient 12/13 PBMCs ex vivo

type: RNA

city: New York

first: Erin

middle: Heather

last: Doyle

state: New York

address: 1425 Madison Ave

department: Liver

institute: Icahn School of Medicine at Mount Sinai

description:
Biological replicate 2
A12-13PE

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio software

label: biotin

source_name: Human PBMCs

label_protocol: Illumina protocol

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Bioanalyser.

tag: patients

tag: tissue

value: Blood

tag: stimulation

value: Ex vivo


title: Patient 11/3 PBMCs media

description:
Biological replicate 1
A11-3PM

value: Media


title: WT untreated replicate 1


title: RLKO knockout poly(I:C) treatment replicate 2

source_name: RLKO knockout poly(I:C) treatment

value: RNase L knockout (RLKO)


title: RLKO knockout poly(I:C) treatment replicate 3


title: Patient 11/3 PBMCs ex vivo

description:
Biological replicate 1
A11-3PE


title: Patient 20/4 LMCs Poly I:C

description:
Biological replicate 6
A20-4LP

source_name: Human LMCs

value: Liver

value: Poly I:C


title: RLKO knockout poly(I:C) treatment replicate 1


title: RLKO knockout untreated replicate 2

source_name: RLKO knockout untreated


title: RLKO knockout untreated replicate 1


title: TT-seq_Raji-CDK9as_CDK9inhibited_HS30_rep2

city: Göttingen

first: Björn

last: Schwalb

address: Fassberg 11

country: Germany

institute: MPI

data_processing:
TT-seq and RNA-seq data preprocessing and global normalization parameters. Paired-end 75 base reads with additional 6 base reads of barcodes were obtained for each of the samples (Supplementary Table 1).  Reads were demultiplexed and mapped with STAR 2.3.0 (Dobin and Gingeras 2015) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li, Handsaker et al. 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. We used a spike-in (RNAs) normalization strategy essentially as described (Schwalb, Michel et al. 2016) to allow observation of global shifts (sequencing depth) , cross-contamination rate  (proportion of unlabeled reads purified in the TT-seq samples) and antisense bias ratio  (ratio of spurious reads originating from the opposite strand introduced by the reverse transcription reaction). Read counts (kij) for spike-ins were calculated using HTSeq (Anders, Pyl et al. 2015).
Calculation of the number of transcribed bases. Of all fragments, only those were kept that exhibited a positive inner mate distance. The number of transcribed bases (tbj) for all samples was calculated as the sum of the coverage of evident (sequenced) fragment parts (read pairs only) for all fragments with an inner mate interval not entirely overlapping a Refseq annotated intron (UCSC RefSeq GRCh38, ~ 98.5% of all fragments) in addition to the sum of the coverage of non-evident fragment parts (entire fragment). Number of transcribed bases per base (coverage). Coverages were calculated upon antisense bias corrected number of transcribed bases (tbj) falling into the region of a cTUs divided by its length in bases. Based on the antisense bias corrected coverages a subgroup of expressed cTUs was defined to comprise all cTUs with a coverage of 5 or higher in one of two summarized replicates of TT-seq (HS15, HS30 or control).
mNET-seq data preprocessing. Paired-end 75 base reads with additional 6 base reads of barcodes were obtained for each of the samples (Supplementary Table 1). Reads were demultiplexed, trimmed for adapter content with cutadapt (Martin 2011) -O 12 -m 25 -a TGGAATTCTCGG -A GATCGTCGGACT) and mapped with STAR 2.3.0 (Dobin and Gingeras 2015) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li, Handsaker et al. 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. Antisense bias (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) was determined using positions in regions without antisense annotation with a coverage of at least 100 according to Refseq annotated genes (UCSC RefSeq GRCh38). Coverage tracks for further analysis were restricted to the last nucleotide incorporated by the polymerase in the aligned mNET-seq reads.
mNET-seq data preprocessing and normalization. We first identified a subgroup of RefSeq-TUs with unchanged behavior over the response to heat shock in the spike-ins normalized TT-seq data via k-means clustering. On the resulting 3,416 RefSeq-TUs i, size factors for each sample j were determined as in (Anders and Huber 2010) and was used to correct for library size and sequencing depth variations.
GenoSTAN annotation of transcription units (TUs, K562 and Raji). Annotation of different transcript classes was done as in (Schwalb, Michel et al. 2016) with minor differences. In brief, genome-wide coverage was calculated from all TT-seq fragment midpoints in consecutive 200 bp bins throughout the genome. In order to create a comprehensive annotation independent of heat shock induced length differences, two replicate tracks were constructed by taking the maximum of each bin over the first and second replicates, respectively, regardless of treatment. A two-state hidden Markov model with a Poisson-Log-Normal emission distribution was learned in order to segment the genome into ‘transcribed’ and ‘untranscribed’ states. Consecutive ‘transcribed’ states were joined, if its gaps were smaller than 200 bp, within a validated GENCODE mRNA or lincRNA (version 22) or showed uninterrupted coverage supported by all TT-seq samples. Subsequently, TU start and end sites were refined to nucleotide precision by finding borders of abrupt coverage increase or decrease between two consecutive segments in the four 200 bp bins located around the initially assigned start and stop sites via fitting a piecewise constant curve to the TT-seq coverage profiles for both replicates using the segmentation method from the R/Bioconductor package "tilingArray" (Huber, Toedling et al. 2006). GRO-cap TSS refinement of TUs (cTUs, K562). For all TUs i, the GRO-cap refined transcription start site tss* was determined as the maximum of GRO-cap signal (Core, Martins et al. 2014) in a window of 500 bp around the start of the TUs. Note that all TUs without a non-zero GRO-cap site were not used. Transcript sorting (K562 and Raji). We sorted each cTU into one of the following seven classes: eRNA, sincRNA, asRNA, conRNA, uaRNA, lincRNA and mRNA (see also Supplementary Figure 3a). First, cTUs reciprocally overlapping by at least 50% with a validated GENCODE mRNA or lincRNA (version 22) in the same strand were classified as mRNAs and lincRNAs. cTUs reciprocally overlapping by less than 50% with a validated GENCODE mRNA or lincRNA (version 22) in the same strand were not classified. Next, cTUs located on the opposite strand of either a mRNA or lincRNA were classified as asRNA if the TSS was located > 1 kb downstream of the sense TSS, as uaRNA if its TSS was located < 1 kb upstream of the sense TSS, and as conRNA if its TSS was located < 1 kb downstream of the TSS. For K562, each of the remaining cTUs did not overlap with a validated GENCODE mRNA or lincRNA (version 22) and was classified as sincRNA. Every ncRNA (sincRNA, asRNA, conRNA or uaRNA) was re-classified as eRNA if its TSS fell into a K562 enhancer state (Zacher, Michel et al. 2017). This resulted in 11,325 non-ambiguously classified RNAs (transcript.annotation.timecourse.refined.TSS.corrected.gtf) (825 eRNA, 1,582 sincRNA, 564 asRNA, 502 conRNA, 1,064 uaRNA, 239 lincRNA and 6,549 mRNA). For Raji, each of the remaining TUs did not overlap with a validated GENCODE mRNA or lincRNA (version 22) and was classified into eRNA – if its TSS exhibited a high (>1) ratio H3K4me1/H3K4me3 – or as sincRNA – if its TSS exhibited a low (<1) ratio of H3K4me1/H3K4me3. This resulted in 16,452 non-ambiguously classified RNAs (transcript.annotation.timecourse.refined.gtf) (3,451 eRNA, 3,479 sincRNA, 1,398 asRNA, 326 conRNA, 565 uaRNA, 243 lincRNA and 6,990 mRNA).
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigwig files containing the coverage

source_name: Raji Burkitt's (B) lymphoma cells (CDK9as)

growth_protocol: Human K562 erythroleukemia cells were obtained from DSMZ (Cat.# ACC-10). Human Raji Burkitt’s (B) lymphoma cells (CDK9as) carry homozygous mutation of phenylalanine (F) 103 to alanine (A) at the CDK9 gene loci and were generated using the CRISPR-Cas9 system (Gressel, Schwalb et al. 2017). K562 and Raji B (CDK9as) cells were cultured antibiotic-free in accordance with the DSMZ Cell Culture standards in RPMI 1640 medium (Thermo Fisher Scientific, Waltham, MA USA) containing 10 % heat inactivated fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA USA), and 1x GlutaMAX supplement (Thermo Fisher Scientific, Waltham, MA USA) at 37 °C in a humidified 5 % CO2 incubator. Both cell lines used in this study display the phenotypic properties, including morphology and proliferation rate, that have been described in literature. Cells were verified to be free of mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen, San Diego, CA USA). Both cell lines were authenticated using DNA profiling according to the documentary standard (ASN-0002). Biological replicates were cultured independently.

extract_protocol:
Ovation Universal RNA-Seq System (NuGEN)
TT-seq, RNA-seq (Schwalb et al., 2016), or mNET-seq (Nojima et al., 2016; Schlackow et al., 2017).

treatment_protocol: To avoid transcriptional changes by freshly added growth medium, cells were expanded 24 h prior to heat shock treatments to a density of 0.3 x 10^6 cells/mL. Heat shock treatments of K562 or Raji B (CDK9as) cells were performed in T175 flasks in a volume of 50 mL at 0.6 x 10^6 cells/mL in a water bath (LAUDA, Aqualine AL12) at 42 °C. Temperature was monitored by thermometer. It took 5 min until the cell suspension reached 42 °C. For TT-seq, RNA-seq and mNET-seq experiments, cells were treated for 0 (Ctrl), 15 min (HS15) or 30 min (HS30).

tag: cell line

tag: treatment conditions

value: 5 uM 1-NA-PP1 for 35 min; 42 oC for 30 min; incl. 4sU (Sigma) labeling during the last 5 minutes.

tag: molecule

value: 4sU-labeled RNA


title: TT-seq_Raji-CDK9as_Solvent_HS30_rep2

value: Raji Burkitt's (B) lymphoma cells (CDK9as)

value: DMSO for 35 min; 42 oC for 30 min; incl. 4sU (Sigma) labeling during the last 5 minutes.


title: TT-seq_Raji-CDK9as_CDK9inhibited_HS30_rep1


title: TT-seq_Raji-CDK9as_CDK9inhibited_rep2

value: 5 uM 1-NA-PP1 for 35 min; incl. 4sU (Sigma) labeling during the last 5 minutes.


title: TT-seq_Raji-CDK9as_CDK9inhibited_rep1


title: TT-seq_Raji-CDK9as_Solvent_rep1

value: DMSO for 35 min; incl. 4sU (Sigma) labeling during the last 5 minutes.


title: TT-seq_Raji-CDK9as_Solvent_rep2


title: TT-seq_Raji-CDK9as_Solvent_HS30_rep1


title: Patient 16 HCV+ Whole liver tissue

description:
Biological replicate 7
mHCV_16

source_name: Human Liver Tissue


title: mNET-seq_K562_HS30_rep2

source_name: K562 erythroleukemia cells

extract_protocol:
TruSeq Small RNA Library (Illumina)
TT-seq, RNA-seq (Schwalb et al., 2016), or mNET-seq (Nojima et al., 2016; Schlackow et al., 2017).

tag: antibody

value: MABI0601 (BIOZOL)

value: 42 oC for 30 min.

value: Total Pol II-associated RNA


title: WT untreated replicate 2

value: parental (WT)


title: mNET-seq_K562_HS15_rep2

value: 42 oC for 15 min.


title: Rp rep3

city: CABA

first: Carlos

middle: Esteban

last: Hernando

state: Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

description: RNA was extracted from whole seeds

data_processing:
Base-calling by default setting of Illumina HiSeq 1500
Aligment to to Arabidopsis thaliana TAIR10 genome using TopHat v2.1.1
Generation of BAM files with SAMtools V1.3
Data analysis with ASpli R-package 1.6.0
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: All processed data files are .txt count tables containing the number of raw counts in each sample for all the sequenced gene trasncripts of Arabidopsis thaliana genome.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: seeds

growth_protocol: Col-0 seeds were sown in clear plastic boxes, each containing 10 mL of 0.8 % (w/v) agar in demineralized water. To establish a minimum and equal photo-equilibrium, seeds were imbibed for 2 hours in darkness and then irradiated for 20 min with a saturated far-red pulse (FRp, calculated Pfr/P= 0.03, 42 µmol.m-2.s-1) in order to minimize the quantities of Pfr formed during their development in the mother plant. Seeds were then stratified at 5 °C in darkness for 3 days prior light pulses.

extract_protocol:
In the transcriptional profiling assay total RNA was extracted with Spectrum™ Plant Total RNA Kit (Sigma) following the manufacturer’s protocols.
Libraries were prepared following the TrueSeq RNA Sample Preparation Guide (Illumina). Briefly, 3 μg of total RNA was polyA-purified and fragmented, first-strand cDNA synthesized by reverse transcriptase (SuperScript III; Invitrogen) using random hexamers. This was followed by RNA degradation and second-strand cDNA synthesis. End repair process and addition of a single A nucleotide to the 3′ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included size and purity assessment with the Agilent 2100 Bioanalyzer and the Agilent DNA1000 kit (Agilent Technologies). Samples were pooled to create 6 multiplexed DNA libraries, which were pair-end sequenced with an Illumina HiSeq1500.

treatment_protocol: Twenty minutes with a saturated red pulse (Rp, calculated Pfr/P= 0.87, 0.05 µmol.m-2.s-1) or FRp, after the 3 days of stratification. Three biological replicates of each condition were collected 12 hours after the corresponding R and FR light pulses.

tag: life stage

value: imbibed seeds 12 h after light pulse

tag: genotype

value: wt Col-0

tag: growth conditions

value: imbibed seeds, stratified for 3 days, red-light pulse for 20 min, collected 12 h after the light pulse


title: FRp rep1

description: RNA was extracted from whole seeds

value: imbibed seeds, stratified for 3 days, far red pulse for 20 min, collected 12 h after the light pulse


title: FRp rep2

description: RNA was extracted from whole seeds


title: FRp rep3

description: RNA was extracted from whole seeds


title: mNET-seq_K562_HS30__rep1


title: Rp rep2

description: RNA was extracted from whole seeds


title: mNET-seq_K562_Ctrl_rep2

value: 37 oC


title: Rp rep1

description: RNA was extracted from whole seeds


title: mNET-seq_K562_HS15_rep1


title: RNA-seq_K562_HS30_rep2

value: 4sU (Sigma) labeling for 5 minutes.

value: Total fragmented RNA


title: mNET-seq_K562_Ctrl_rep1


title: RLKO knockout untreated replicate 3

value: RNase L knockout (RLKO)


title: RNA-seq_K562_Ctrl_rep2


title: RNA-seq_K562_Ctrl_rep1


title: RNA-seq_K562_HS15_rep1


title: RNA-seq_K562_HS30__rep1


title: TT-seq_K562_HS15_rep2

value: 42 oC for 15 min; incl. 4sU (Sigma) labeling during the last 5 minutes.

value: 4sU-labeled RNA


title: TT-seq_K562_HS30_rep2

value: 42 oC for 30 min; incl. 4sU (Sigma) labeling during the last 5 minutes.


title: TT-seq_K562_HS15_rep1


title: Patient 18 HCV+ Whole liver tissue

description:
Biological replicate 9
mHCV_18

value: Liver


title: TT-seq_K562_Ctrl_rep2

value: 37 oC, 4sU (Sigma) labeling for 5 minutes.


title: RNA-seq_K562_HS15_rep2


title: TT-seq_K562_HS30__rep1


title: morulae/blastocysts with Trim21 mRNA and anti-TEAD4 antibody_rep a

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

institute: Max Planck Institute Muenster

description:
Blastocyst pool 6a
Pool of 10 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit was used, for 16 h (+/- 1h) at 45°C with 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: The robust multiarray averaging method was applied for background correction, normalization, and probe summarization using the Affymetrix Expression Console.

organism: Mus musculus

source_name: preimplantation mouse embryo

label_protocol: Biotinylated cDNA was prepared using GeneChip WT Pico kit, reverse-transcribing 20 micrograms cRNA and, of these, subjecting 5.5 micrograms to labeling

growth_protocol: Zygotes from B6C3F1 x CD1 mating (stimulated cycle, PMSG + hCG given 48 hours apart) were collected from the oviducts and cultured in KSOM(aa) medium using a 4-well plate under 5% CO2 in air at 37 degrees C. At the mid-pronuclear stage (9-11 am) the ooplasm was injected with mRNA or mRNA+antibody, followed by culture in a 96-well plate for additional 72 hours.

extract_protocol: 72 hours post-injection, pools of 10 embryos were lysed in in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water according to the manufacturer's instructions.

treatment_protocol: At the mid-pronuclear stage (9-11 am on the day of vaginal plug) the ooplasm was injected microinjected with Trim21 mRNA and dextran beads (named 'group 4'), or Trim21 mRNA, dextran beads and anti-GFP antibody (named 'group 5'), or Trim21 mRNA, dextran beads and anti-TEAD4 antibody (named 'group 6'), two replicates each ('a' and 'b').

tag: genetic background

value: B6C3F1 x CD1

tag: age

value: Theiler stage 5; 4 dpc (96h IVC)

tag: formation of blastocyst cavity

value: cavity absent or small/aberrant

value: Trim21 mRNA + anti-TEAD4 antibody


title: WT4_17

city: Mölndal

first: Lisa

last: Öberg

address: Pepparedleden 1

department: Translational Science and Experimental Medicine

country: Sweden

institute: Research and Early Development, Respiratory Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden

data_processing:
Base calling were done by bcl2fastq from Illumina
Reads were mapped with HiSat2 (2.0.2-beta)
Counts were generated with featurecounts (1.4.4)
TPMs were generated using Sailfish (0.9.0)
All processing was wrapped together with bcbio 0.9.7
Genome_build: hg38
Supplementary_files_format_and_content: combined.counts -- A text file with all combined counts for all genes as obtained from the pipeline specified above.

growth_protocol: U-937 cell were purchased from the American type culture collection (ATCC) and grown in RPMI 1640 medium with L-glutamine (Gibco, Life Technologies), 10% heat-inactivated fetal bovine serum (FBS, Gibco) and 1% Penicillin/Streptomycin (Gibco) in a 37oC humidified 5% CO2 incubator.CRISPR/Cas9-generated A20 C103A KI (3 clones), A20 KO (4 clones) and WT (7 clones) U-937 cells were differentiated into macrophage-like cells by stimulation with 10 ng/mL phorbol 12-myristate 13-acetate (PMA, Sigma-Aldrich) for 48 hours. Cells were then washed with PBS and cultured overnight in fresh medium before stimulation.

extract_protocol:
RNA was extracted using RNeasy Plus Mini kit (Qiagen). RNA integrity was assessed by Bioananalyzer 2100 (Agilent) and RIN>9,2 were obtained for all samples.
RNA was diluted to 20 ng/ul and used as input to create mRNA libraries using TruSeq Stranded mRNA kit (Illumina, CA, USA) with dual indexing following standard instructions. Libraries were validated on the Fragment Analyzer platform (AATI, IA, USA) using standard sensitivity NGS fragment analysis kit and the concentration was determined using Quant-iT dsDNA High Sensitivity assay kit on the Qubit fluorometer (Thermo Fisher, MA, USA). Sample libraries were pooled in equimolar concentrations and diluted and denatured according to Illumina guidelines. Sequencing was performed using a High Output 2 x 76 bp kit on an Illumina NextSeq500.

treatment_protocol: Cells were  treated with 10 ng/mL LPS (InvivoGen) or vehicle (H20) for 6 hours.

value: WT A20 for comparison with KI

value: no LPS

tag: clone


title: WT6_19

tag: treatment


title: Parthenogenetic blastomere 10a

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 10a parth. KSOM(aa)

source_name: blastomere pair 10 (after parthenogenesis and 2-cell stage bisection)

growth_protocol: Metaphase II oocytes from B6C3F1 mice (stimulated cycle, PMSG + hCG given 48 hours apart) were collected from the oviducts and activated in Ca-free alpha-MEM supplemented with 10 mM SrCl2 and 10 micromolar Latrunculin, for 6 hours,  using a 4-well plate under 5% CO2 in air at 37 degrees C. After activation, embryos were cultured in KSOM(aa). At the 2-cell stage the sister blastomeres were separated from each other and lysed immediately, keeping track of the original pair associations.

extract_protocol: Individual blastomeres were lysed in in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water according to the manufacturer's instructions.

treatment_protocol: At the 2-cell stage embryos were split and the blastomeres were lysed in Zymo buffer.

value: parthenogenetic 2-cell embryo

value: Theiler stage 2; 1 day post activation (20h IVC)

tag: total cell number

value: single cell


title: Patient 14/17 LMCs R848

description:
Biological replicate 3
A14-17LR


title: WT6_LPS_25

value: LPS


title: morulae/blastocysts with Trim21 mRNA and anti-TEAD4 antibody_rep b

description:
Blastocyst pool 6b
Pool of 10 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water


title: blastocyst with Trim21 mRNA_rep b

description:
Blastocyst pool 4b
Pool of 10 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water

value: cavity formation normal

value: Trim21 mRNA


title: Parthenogenetic blastomere 8a

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 8a parth. KSOM(aa)

source_name: blastomere pair 8 (after parthenogenesis and 2-cell stage bisection)


title: WT5_LPS_24


title: Parthenogenetic blastomere 9a

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 9a parth. KSOM(aa)

source_name: blastomere pair 9 (after parthenogenesis and 2-cell stage bisection)


title: TT-seq_K562_Ctrl_rep1


title: blastocysts with Trim21 mRNA and anti-GFP antibody_rep b

description:
Blastocyst pool 5b
Pool of 10 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water

value: Trim21 mRNA + anti-GFP antibody


title: Parthenogenetic blastomere 7a

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 7a parth. KSOM(aa)

source_name: blastomere pair 7 (after parthenogenesis and 2-cell stage bisection)


title: WT4_LPS_23


title: blastocysts with Trim21 mRNA and anti-GFP antibody_rep a

description:
Blastocyst pool 5a
Pool of 10 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water


title: Parthenogenetic blastomere 5a

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 5a parth. KSOM(aa)

source_name: blastomere pair 5 (after parthenogenesis and 2-cell stage bisection)


title: blastocyst with Trim21 mRNA_rep a

description:
Blastocyst pool 4a
Pool of 10 embryos was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water


title: KI2_21

value: A20 C103A knock-in mutation (DUB-inactive)


title: KI3_22


title: KI1_20


title: Parthenogenetic blastomere 10b

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 10b parth. KSOM(aa)


title: KI3_LPS_28


title: Parthenogenetic blastomere 8b

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 8b parth. KSOM(aa)


title: Medical Bypass replicate 8

city: Dublin

first: Meera

last: Nair

address: Conway Institute

country: Ireland

institute: University College Dublin

description:
NormalizedBySizeFactor.9.csv
261

data_processing:
Fastq files were merged using Unix commands
The quality was checked using fastqc/0.11.2 and the reports were combined using multiqc/0.9.
Quality filtering was performed using prinseq/0.20.3
The reads were mapped to the rat reference genome using Star/2.5.2b. The amount of reads mapped to reference genes are calculated using htseq/0.6.1p1
differential expression analysis was performed using DEseq2
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: [NormalizedBySizeFactor.9.tsv] TAB-separated counts normalized by size factors in DESeq2

organism: Rattus norvegicus

source_name: kidney cortex

extract_protocol:
Kidney cortical sections were flash frozen in liquid nitrogen.  RNA was isolated using the RNEasy mini kit (Qiagen 74104). Library preparation was carried out using the TruSeq ® Stranded mRNA NeoPrep™ Kit (Illumina NP-202-1001)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney cortex

tag: strain

value: ZDF fa/fa

tag: diabetic status

value: diabetic

tag: treatment group

value: Medical Bypass


title: Parthenogenetic blastomere 5b

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 5b parth. KSOM(aa)

tag: tissue


title: Medical Bypass replicate 7

description:
NormalizedBySizeFactor.9.csv
257


title: Medical Bypass replicate 9

description:
NormalizedBySizeFactor.9.csv
263


title: Parthenogenetic blastomere 9b

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 9b parth. KSOM(aa)


title: Parthenogenetic blastomere 7b

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 7b parth. KSOM(aa)


title: KI1_LPS_26


title: Parthenogenetic blastomere 4b

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 4b parth. KSOM(aa)

source_name: blastomere pair 4 (after parthenogenesis and 2-cell stage bisection)


title: WT3_04

value: wt A20 for comparison with KO


title: Parthenogenetic blastomere 3a

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 3a parth. KSOM(aa)

source_name: blastomere pair 3 (after parthenogenesis and 2-cell stage bisection)


title: WT2_03


title: Parthenogenetic blastomere 3b

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 3b parth. KSOM(aa)


title: Parthenogenetic blastomere 2b

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 2b parth. KSOM(aa)

source_name: blastomere pair 2 (after parthenogenesis and 2-cell stage bisection)


title: Medical Bypass replicate 4

description:
NormalizedBySizeFactor.9.csv
247


title: Parthenogenetic blastomere 1b

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 1b parth. KSOM(aa)

source_name: blastomere pair 1 (after parthenogenesis and 2-cell stage bisection)


title: Parthenogenetic blastomere 1a

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 1a parth. KSOM(aa)


title: Parthenogenetic blastomere 2a

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 2a parth. KSOM(aa)


title: Medical Bypass replicate 6

description:
NormalizedBySizeFactor.9.csv
256


title: WT_Unsort_01

value: WT


title: Medical Bypass replicate 3

description:
NormalizedBySizeFactor.9.csv
240


title: WT3_LPS_12


title: Medical Bypass replicate 2

description:
NormalizedBySizeFactor.9.csv
238


title: WT2_LPS_11


title: WT1_02


title: WT1_LPS_10


title: WT_Unsort_LPS_09


title: Medical Bypass replicate 1

description:
NormalizedBySizeFactor.9.csv
234


title: KO4_07

value: A20 KO


title: KO5_08


title: Parthenogenetic blastomere 4a

description:
Single blastomere was lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water
Blastomere 4a parth. KSOM(aa)


title: RYGB replicate 6

data_processing:
Fastq files were merged using Unix commands
The quality was checked using fastqc/0.11.2 and the reports were combined using multiqc/0.9.
Quality filtering was performed using prinseq/0.20.3
The reads were mapped to the rat reference genome using Star/2.5.2b. The counts of reads mapped to reference genes are calculated using htseq/0.6.1p1
differential expression analysis was performed using DEseq2
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: TAB-separated counts normalized by size factors in DESeq2

value: RYGB surgical intervention


title: RYGB replicate 5


title: KO1_05

value: no LPS


title: RYGB replicate 2


title: RYGB replicate 3


title: KO5_LPS_16


title: disease replicate 6

value: disease control


title: KO4_LPS_15


title: disease replicate 4


title: RYGB replicate 1


title: RYGB replicate 4


title: KO2_LPS_14


title: Medical Bypass replicate 5

description:
NormalizedBySizeFactor.9.csv
252


title: disease replicate 3


title: disease replicate 2


title: WSU-NHL

city: St. Louis

first: Jason

middle: Paul

last: Wong

state: MO

address: Neuroscience Research Building

department: Pediatrics

institute: Washington University in St. Louis

data_processing:
QC-passed reads were aligned to hg19 using MapSplice (Wang et al., 2010).
Picard Tools v1.64 was used to determine the alignment profile.
Aligned reads were sorted and indexed using SAMtools and translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UBU v1.0 (Li et al., 2009).
Transcript abundance estimates were performed using an Expectation-Maximization algorithm (Li, 2011).
Genome_build: hg19
Supplementary_files_format_and_content: Excel matrix file includes RSEM values for individual genes for each sample

source_name: Pleural effusion

growth_protocol: Cells were grown in complete medium (see details in paper) and harvested during log-phase of growth.

extract_protocol:
Cells were spun down and RNA was harvested using the RNeasy Plus Mini Kit according to manufacturer’s instructions.
mRNA-Seq libraries were generated using the Stranded mRNA-Seq kit and multiplexed with Illumina TruSeq adapters. Samples were run on two 75-cycle single-end sequencing runs with an Illumina NextSeq-500.

tag: cell line

value: WSU-NHL

tag: nhl subtype

value: Diffuse large B-cell lymphoma

value: 48 yrs

tag: cell type

value: B-cell


title: VG1

value: Primary effusion lymphoma

value: 59 yrs


title: disease replicate 1


title: KO1_LPS_13

value: LPS


title: healthy control replicate 6

value: kidney cortex

value: ZDF fa/+

value: non-diabetic

value: lean healthy control


title: WT5_18

value: WT A20 for comparison with KI


title: KO2_06


title: Toledo

source_name: Peripheral blood

value: Toledo

value: Adult


title: REC-1

source_name: Lymph node

value: Mantle cell lymphoma

value: 57 yrs


title: disease replicate 5

value: ZDF fa/fa

value: diabetic

value: disease control


title: healthy control replicate 5


title: healthy control replicate 4


title: healthy control replicate 1


title: healthy control replicate 3


title: Ocl-Ly1

source_name: Bone marrow

value: Diffuse large B-cell lymphoma

value: 44 yrs


title: Ocl-Ly3

value: 52 yrs

value: B-cell


title: Karpas422

value: Follicular lymphoma

value: 72 yrs


title: Raji

source_name: Lymphoblast

value: Raji

value: Burkitt's lymphoma

value: 11 yrs


title: Pfieffer

value: Pfieffer


title: JSC1

source_name: Ascites

value: Primary effusion lymphoma


title: SuDHL16

value: Adult


title: Jeko-1

value: Mantle cell lymphoma

value: 78 yrs


title: No29_p

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

country: Japan

institute: Kanazawa University

description: chronic hepatitis patients undergoing nucleoside analogue treatment

hyb_protocol: Biotin-labeled cDNA was suspended in 220 ul of hybridization cocktail (NuGen) and 200 ul was used for hybridization to the Affymetrix Human 133 Plus 2.0 microarray chip containing 54,675 probes.GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: After stringent washing, the microarray chips were stained with streptavidin-phycoerythrin and probe hybridization was determined using a GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. If the detection call contained 'Absent', the probe set was removed from analysis.

label_protocol: Aliquots of total RNA (50 ng) isolated from cells were subjected to amplification using the Ovation Pico WTA System V2 3302-12 (AS ONE, Japan) according to the manufacturer’s instructions. Approximately 10 ug of cDNA was amplified from 50 ng of total RNA, and 5 ug of cDNA was used for fragmentation and biotin labeling using the FL-Ovation cDNA Biotin Module V2 (NuGen) according to the manufacturer’s instructions.

extract_protocol: After separation of pDCs, RNA was extracted with the RNAqueousTM-Micro Total RNA Isolation Kit AM1931 (Thermo Fisher Scientific K.K., Yokohama, Japan) according to the manufacturer's instructions.

value: Blood

value: Plasmacytoid dendritic cells

tag: diagnosis


title: No30_p

source_name: chronic hepatitis patients undergoing nucleoside analogue treatment


title: Ramos

value: Ramos

value: 3 yrs


title: healthy control replicate 2

value: kidney cortex

value: ZDF fa/+

value: non-diabetic

value: lean healthy control


title: Granta

value: Granta

value: 58 yrs

value: B-cell


title: FL18

value: Follicular lymphoma

value: 68 yrs


title: No23_p

value: chronic hepatitis patients undergoing nucleoside analogue treatment


title: No28_p


title: DB

value: DB

value: Diffuse large B-cell lymphoma

value: 45 yrs


title: No18_p

value: Blood


title: Daudi

value: Daudi

value: Burkitt's lymphoma

value: 16 yrs


title: No11_p

value: Plasmacytoid dendritic cells


title: No7_p


title: BL41

source_name: missing

value: 8 yrs


title: No27_p


title: BCP1

value: Primary effusion lymphoma

value: 92 yrs


title: JVM-2

value: Mantle cell lymphoma

value: 63 yrs


title: BJAB

source_name: Inguinal tumor

value: BJAB

value: 5 yrs

value: B-cell


title: BC1

value: 46 yrs


title: BC3

value: 85 yrs


title: 2452_6B: ISN5

city: Pittsburgh

first: Parmjeet

last: Randhawa

state: Pennsylvania

address: E737 UPMC Montefiore Hospital, 3459 Fifth Ave

department: Pathology

institute: University of Pittsburgh

description: Non-transplant native interstitial nephritis

data_processing:
Raw sequence files (fastq) were aligned to the human transcriptome (hg19) reference sequences in StrandNGS software.
Gene and transcript annotations were retrieved from the Ensembl database to generate  aligned SAM files
Data was filtered on read quality (>15), alignment score (≥90), match count (≤1) and mapping quality (≥25).
Genome_build: human transcriptome (hg19)

growth_protocol: not applicable

extract_protocol:
Follow the instruction in Invitrogen PureLink™ FFPE RNA Isolation Kit (Catalog number:  K156002)
cDNA libraries were constructed from 100 ng total RNA obtained using the Ion Ampliseq Transcriptome Human Gene Expression Kit  from Life Technologies (Cat# A26325) and the manufacturers recommended protocol.

treatment_protocol: formalin fixed tissue was cut into I mm pieces,then added 300 µl Melting Buffer 72°C for 10min, followed by 20ul Proteinase K for 10min, ~3hours at 60°C.

value: Kidney


title: No6_p

value: chronic hepatitis patients undergoing nucleoside analogue treatment


title: No109_p

description: untreated chronic hepatitis patients

source_name: untreated chronic hepatitis patients

value: Blood

value: untreated chronic hepatitis patients


title: No9_p


title: No3_p


title: No110_p

description: untreated chronic hepatitis patients


title: No86_p

description: untreated chronic hepatitis patients


title: 2288_5: ISN1

source_name: Non-transplant native interstitial nephritis


title: 2457_17: BKVN5

description: Polyomavirus BKV nephropathy

source_name: Polyomavirus BKV nephropathy


title: 2456_16: BKVN4

description: Polyomavirus BKV nephropathy


title: No85_p

description: HBV carriers with normal liver function

source_name: HBV carriers with normal liver function

value: HBV carriers with normal liver function


title: No108_p

description: untreated chronic hepatitis patients


title: No79_p

description: HBV carriers with normal liver function


title: No73_p

description: HBV carriers with normal liver function


title: No75_p

description: HBV carriers with normal liver function


title: No111_p

description: untreated chronic hepatitis patients


title: 2455_15: BKVN3

description: Polyomavirus BKV nephropathy


title: No112_p

description: untreated chronic hepatitis patients


title: 2290_7: ISN3


title: 2291_8: ISN4


title: 2289_6: ISN2


title: 2454_14: BKVN2

description: Polyomavirus BKV nephropathy


title: No119_p

description: healthy controls

source_name: healthy controls

value: healthy controls


title: No70_p

description: HBV carriers with normal liver function

value: Plasmacytoid dendritic cells


title: 2453_13: BKVN1

description: Polyomavirus BKV nephropathy


title: 2490_12D: IFTA_4

description: Interstitial fibrosis and tubular atrophy with T-cell mediated rejection


title: 2250_12: IFTA_5

source_name: Interstitial fibrosis and tubular atrophy with T-cell mediated rejection


title: No118_p

description: healthy controls


title: No58_p

description: HBV carriers with normal liver function


title: 2489_12C: IFTA_3


title: WGBS_RDM1_FLAG_16

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

country: China

institute: Zhejiang University

library_source: genomic

data_processing:
Raw reads were aligned to TAIR10 genome using BSMAP with –v 2 (allowing maximal two mismatches) and –n 1 (aligning to both strands). Reads were discarded if there were more than 3 consecutive methylated CHH sites within the reads (for 50 bp long read). Methylation levels at each cytosine were calculated as #C/(#C+#T). DMRs between WS and rdm1 were defined using R package DMRcaller. To define CHH DMRs, parameters were applied as before (Stroud et al. Cell 152, 352–364 (2013). Basically, 100 bp bins with more than 4 cyotosines and each cytosines with more than 4 read coverage as well as more than 0.1 difference between rdm1 and WS were used as cut-off. DMRs within 200 bp of each other were merged for further analysis. Cytosine methylation over rdm1 hypo CHH DMR were extracted and plotted in R. WGBS tracks displayed in Fig. 1b correspond to wild-type Col-0 samples as described in Stroud et al. Cell 152, 352–364 (2013)..
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: leaves

growth_protocol: Plants were grown in on soil in a greenhouse in long days condition

extract_protocol:
Genomic DNA from Wassilewskija (WS), rdm1-3 and two independent lines expressing RDM1-3xFlag was extracted using the DNAeasy Plant Mini Kit (Qiagen).
DNA were sheared to 300 bp with a Covaris S2 (Covaris). Libraries, including bisulfite conversion, were made with the NuGEN Ultralow Methyl-seq kit (NuGEN) and EpiTect Bisulfite kit (Qiagen) following manufacturer’s instructions.

value: leaves

value: RDM1-Flag in rdm1-3

tag: ecotype

value: WS


title: 2488_12B: IFTA_2


title: WGBS_RDM1_FLAG_2

tag: genotype


title: WGBS_rdm1_3


title: 2487_9D: TCMR_4

description: T-cell mediated rejection

source_name: T-cell mediated rejection


title: No26_p


title: WGBS_WT_WS

value: wild type


title: 2485_9B: TCMR_2

description: T-cell mediated rejection


title: 2248_10: TCMR_5

description: T-cell mediated rejection


title: 2249_11: IFTA_1


title: 2247_9: TCMR_1

description: T-cell mediated rejection


title: 2451_3D: ATI_5

description: Acute tubular injury

source_name: Acute tubular injury


title: 2450_3C: ATI_4

description: Acute tubular injury


title: 2449_3B: ATI_3

description: Acute tubular injury


title: 2287_4: ATI_2

description: Acute tubular injury


title: 2286_3: ATI_1

description: Acute tubular injury


title: 2447_2B: STA4

description: Stable allograft function

source_name: Stable allograft function


title: 2448_2C: STA5

description: Stable allograft function


title: 2446_1B: STA3

description: Stable allograft function


title: KI2_LPS_27

value: A20 C103A knock-in mutation (DUB-inactive)

value: LPS


title: 2246_2: STA2

description: Stable allograft function


title: Pcz-1

city: Missouri

first: Qiuming

last: Yao

address: Life Science Center

institute: University of Missouri

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab:Pcz)
WC6

data_processing:
Tuxedo pipeline
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: Excel files for log2 FPKM fold change of treatment samples versus mock-treated samples.

organism: Glycine max

source_name: 5 mM Pcz

growth_protocol: williams 82 were grown for 10 days

extract_protocol:
soybean seedlings were collected
RNA TruSeq Stranded mRNA LT sample prep

treatment_protocol: Brassinosteroid 1 hour and 8 hours; V1 stage plants were irrigated with water containing high concentration  Brassinosteroid (BR)  synthesis inhibitor or combined together with low concentration  exogenous brassinolide (BL), or add high  concentration BL afterwards  (Pcz: 5 mM propiconazole Pcz;  Pcz-lowBL: 5 mM Pcz with 10 nM BL; Pcz-BL-1h:  5 mM Pcz then with 1 mM BL 1h; Pcz-BL-8h:  5 mM Pcz with 1 mM BL for 8h).

tag: cultivar

value: williams 82

value: 10 days

tag: developmental stage

value: vegetative 1 (v1) stage

value: seedling


title: Pcz-BL-8h-3

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab:Pcz-BL-8h)
WC2

source_name: 5 mM Pcz with 1 mM BL for 8h

tag: age


title: Pcz-BL-1h-2

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab:Pcz-BL-1h)
WC11

source_name: 5 mM Pcz then with 1 mM BL 1h


title: control-2

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab: Pcz-BL)
WC4

source_name: mock treated


title: Pcz-3

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab:Pcz)
WC8


title: Pcz-BL-1h-1

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab:Pcz-BL-1h)
WC14


title: Pcz-lowBL-1

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab: Pcz-BL)
WC7

source_name: 5 mM Pcz with 10 nM BL


title: Pcz-lowBL-3

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab: Pcz-BL)
WC9


title: Pcz-lowBL-2

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab: Pcz-BL)
WC10


title: control-3

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab: Pcz-BL)
WC3


title: Pcz-BL-8h-2

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab:Pcz-BL-8h)
WC15


title: control-1

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab: Pcz-BL)
WC1


title: 2245_1: STA1

description: Stable allograft function

value: Kidney


title: Pcz-BL-8h-1

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab:Pcz-BL-8h)
WC13


title: Pcz-2

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab:Pcz)
WC5


title: mock.no4sU

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description:
bulk RNA-Seq (TruSeq kit)
bulk.tsv

data_processing:
Data has been processed using GRAND-SLAM 1.1. Briefly, reads were trimmed using Trimmomatic 0.36 (Smart-Seq libraries: CTGTCTCTTATACACATCTCCGAGCCCACGAGA and CTGTCTCTTATACACATCTGACGCTGCCGACGA, TruSeq Libraries: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT). Trimmed reads were mapped to a combined reference of the mouse (Ensembl v90) and MCMV (BAC clone C5X) genomes  and the ERCC spike-in sequences using STAR 2.5.3a in end to end mode and allowing for 20 mismatches. For TruSeq libraries, the first ten bases were ignored by GRAND-SLAM via its -trim5p 10 parameter. For Smart-seq libraries, the first 25 bases were ignored. Identified SNPs from the combined TruSeq libraries were used for the Smart-seq libraries by copying the .snpdata file. Linear regression parameters were learned from the no4sU samples on plate 1 and specified for libraries from plates 2 and 3 via the parameters -errlm 'TA*0.663' -errlm2 'TA*2.802'.
Genome_build: mouse (Ensembl v90) and MCMV (BAC clone C5X) genomes
Supplementary_files_format_and_content: tsv-files; Output of GRAND-SLAM containing read counts, estimated new/total ratios (with credible interval), beta approximation parameters as well as C-to-T mismatch statistics for each gene and library

source_name: NIH-3T3 fibroblasts

growth_protocol: Murine NIH-3T3 fibroblasts were cultured and passaged in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% newborn calf serum (NCS) and Penicillin Streptomycin. 10?5 cells per well were seeded overnight on a 24-well plate.

extract_protocol:
Single cells were immediately sorted using a FACSaria III (BD Biosciences; device: 48-well plate; precision: single-cell; nozzle: 100 ?m) into different wells from a 48-well plate ?lled with 4 µl of a hypotonic lysis buffer made of 2U/µL RNase inhibitor and 0.2 % Triton-X-100 in Nuclease-free water. Single-sorted cells were spun down, immediately chilled in a 4°C and stored at ?80 °C.
After thawing the plates 3 min at room temperature, 0.4 µL of 10X PBS (pH=7.4, Ambion) was added in every well followed by dispensing 4.4 µL of 2X Iodoacetamide (IAA) (Thermo Scientific) to reach a final concentration of 10mM IAA and 50% DMSO. The reaction mixture was incubated for 5 min at 50°C. IAA reaction was quenched with 1.3 µL of 0.1 M DTT (final concentration of 15 mM) for 5 min at room temperature. ERCC spike-in control (Thermo Fisher, mix 1, dilution 1:2 millions) was added in every well (except the negative control). RNA was isolated before Reverse Transcription and PCR using a 1:1 volume of RNA XP magnetic beads (Beckman Coulter). After 10 min incubation at room temperature, the beads were washed twice with 50 µl 80% freshly-prepared EtOH on the magnetic stand and the dried beads pellets were resuspended in 4 µL elution buffer (RNAse inhibitor 1/200 Takara, CDS primer 0.5 µL in RNAse free water) immediately followed by an incubation at 72°C for 3 min. All the following experimental steps were performed using the Smart-seq v4 low input kit (Takara) with one-quarter of the recommended reagent volumes. The PCR amplification was performed according to the manual using 24 cycles. Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent).0.5 ng of every library was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using one-quarter of the recommended reagent volumes, 10 min for tagmentation at 55 °C and 1 min extension time during PCR for multiplexing. After PCR, the libraries were purified using AMPure XP beads and resuspended in 15 µl of resuspension buffer.

treatment_protocol: The cells were infected the next day with WT C5X MCMV strain at a MOI =10 followed by spinoculation of the virus at 800xg for 30min. 4sU (initially dissolved in DMSO at a concentration of 50 mM) was added right before the spinoculation in complete medium to reach a final concentration of 500 µM. RNA metabolic labeling was performed for 2hr at 37°C by replacing the medium with the 4sU-complemented medium. Cells were detached using trypsin and washed twice in cold PBS after centrifugation at 1,400 rpm and finally resuspended in 700 µL cold PBS.

tag: condition

tag: replicate

value: A


title: Pcz-BL-1h-3

description:
transcriptome
Processed+RNA+seq+data.xlsx (tab:Pcz-BL-1h)
WC12


title: mcmv.B

description:
bulk SLAM-Seq (TruSeq kit)
bulk.tsv

value: mcmv-infected

value: B


title: mock.B

description:
bulk SLAM-Seq (TruSeq kit)
bulk.tsv

value: mock


title: mcmv.A

description:
bulk SLAM-Seq (TruSeq kit)
bulk.tsv


title: K3174 DOT1L Low

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
kallisto to get read counts
DEseq2 to normalize and detect DE genes
star aligner to align reads
star-fusion to detect gene fusion
genome build: mm10
Supplementary_files_format_and_content: read counts

source_name: KMT2A-MLLT3 leukemia cells with low levels of DOT1L overexpressed

growth_protocol: Mouse leukemia cells were grown in DMEM supplemented with 10% FBS, 1% Pen/Strept, mIL3, mIL6 and mSCF

extract_protocol:
mRNA was isolated from cells three days after sort using qiagen RNeasy kit
Library prep was performed using Illumina HiSeq, 2x150bp configuration. ~350M raw paired-end reads per lane

treatment_protocol: Bone marrow from moribound mice with KMT2A-MLLT3 driven AML was transduced with DOT1L and high and low expressing populations were sorted. Three days after sort cells were collected for RNA-Seq.

value: mouse leukemia cells

tag: genotype/variation

value: low levels of DOT1L overexpressed


title: K3174 DOT1L High

source_name: KMT2A-MLLT3 leukemia cells with high levels of DOT1L overexpressed

value: high levels of DOT1L overexpressed


title: No103_p

description: healthy controls

value: Blood

value: Plasmacytoid dendritic cells

value: healthy controls


title: K3117 DOT1L High


title: K3117 NT

source_name: KMT2A-MLLT3 leukemia cells


title: K3174 NT


title: mock.A

description:
bulk SLAM-Seq (TruSeq kit)
bulk.tsv


title: mock.test2.sc12

description:
single-cell SLAM-Seq (Smart-Seq kit)
testplate.tsv


title: mock.no4sU.sc11

description:
single-cell RNA-Seq (Smart-Seq kit)
testplate.tsv


title: mock.no4sU.sc13


title: mock.no4sU.sc15


title: K3117 DOT1L Low


title: No78_p

description: HBV carriers with normal liver function

value: HBV carriers with normal liver function


title: mock.no4sU.sc09


title: K3174 DOT1L High, H3K79me2_ChIP

data_processing:
BWA Alignment
MACS2 peak calling
ngsplot for profile plot
samtools convert files
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file

extract_protocol:
Briefly, samples were crosslinked, lysed, sonicated and immunoprecipated with H3K79me2 overnight. After a series of washes they were reverse crosslinked overnight and DNA extracted.
Library prep was performed using Illumina HiSeq, 2x150bp configuration, single index, per lane. ~350M raw paired-end reads per lane

treatment_protocol: Bone marrow from moribound mice with KMT2A-MLLT3 driven AML was transduced with DOT1L and high and low expressing populations were sorted. Three days after sort cells were collected for H3K79me2 ChIP.

tag: disease state

value: KMT2A-MLLT3 AML

tag: spike-in

value: drosophila melanogaster (S2) cells spiked in at a 1:2 ratio

tag: treatment

value: DOT1L transduction

tag: cell population

value: high expressing population

tag: chip antibody

value: H3K79me2 (Abcam:ab3594)


title: mcmv.test2.sc14


title: No107_p

description: healthy controls

tag: tissue


title: No117_p

description: healthy controls


title: No100_p

description: healthy controls


title: K3174 DOT1L Low, H3K79me2_ChIP

value: low expressing population


title: K3174 DOT1L High, Input


title: mock.test2.sc08


title: K3174 DOT1L Low, Input


title: No120_p

description: healthy controls


title: K3174 NT, Input

value: control


title: K3174 NT, H3K79me2_ChIP


title: mock.test1.sc06


title: K3117 DOT1L High, Input


title: mcmv.test3.sc05

value: mcmv-infected


title: K3117 DOT1L High, H3K79me2_ChIP


title: K3117 DOT1L Low, H3K79me2_ChIP


title: K3117 DOT1L Low, Input


title: K3117 NT, Input


title: mcmv.test3.sc07


title: K3117 NT, H3K79me2_ChIP


title: WT-BM1

city: Seoul

first: In byung

last: Park

address: 145, Anam-ro, Seongbuk-gu, Seoul

country: South Korea

institute: Korea University

data_processing:
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the reference genome using HISAT v2.0.5
HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2.
Transcript assembly and abundance estimation using StringTie
After alignment, StringTie v1.3.3b was used to assemble aligned reads into transcripts and to estimate their abundance. It provides the relative abundance estimates as FPKM values (Fragments Per Kilobase of exon per Million fragments mapped) of transcript and gene expressed in each sample
Genes with one more than zeroed FPKM values in the samples were excluded. To facilitate log2 transformation, 1 was added to each FPKM value of filtered genes
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Excel spreadsheet format which includes contents; 1) Gene_symbol, 2) NCBI Protein accession ID, 3) Product, 4) Fold change, 5) Volume, 6) GOmap stat, 7) GOmap genes, 8) KEGG stat, 9) KEGG genes

source_name: wild type_bone marrow

extract_protocol:
Bone marrow cells were isolated from the femurs and tibias of 8-week-old mice. Total RNA was isolated using TRIzol reagent according to the manufacturer's instructions.
In order to construct cDNA libraries with the TruSeq RNA library kit, 1ug of total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina HiSeq4000

tag: strain background

value: wild type

value: Bone marrow


title: KO-BM9

source_name: Phc2 knockout_bone marrow

value: Phc2+/- (Phc2 heterozygote)


title: WT-BM7


title: WT-BM3


title: mock.test1.sc00

value: mock


title: mcmv.A.sc95

description:
single-cell SLAM-Seq (Smart-Seq kit)
96.tsv

value: A


title: mcmv.A.sc93


title: mock.test1.sc02


title: mock.no4sU.50c00

description:
50-cell RNA-Seq (Smart-Seq kit)
testplate.tsv


title: mock.test1.sc04


title: mock.no4sU.50c01


title: mcmv.A.sc94


title: KO-BM4


title: mcmv.B.sc91

value: B


title: TFAMKO_RNA_clone5_CN2_4

city: Baltimore

first: Christina

middle: A

last: Castellani

state: MD

address: 733 N Broadway

department: McKusick-Nathans Department of Genetic Medicine

institute: Johns Hopkins University School of Medicine

data_processing:
Libraries were uniquely barcoded and pooled for sequencing. DNA sequencing was performed in duplicate on an Illumina® HiSeq 2500 instrument using standard protocols for paired end 150 bp sequencing.
Illumina HiSeq reads were processed through Illumina’s Real-Time Analysis (RTA) software generating base calls and corresponding base call quality scores.  CIDRSeqSuite 7.1.0 was used to convert compressed bcl files into compressed fastq files.
Each independent cell-line was sequenced twice. RNA sequencing fastq files were pseudoaligned to Genome Reference Consortium Human Build 37 (GRCh37) using Kallisto(Bray et al. 2016). 100 bootstraps were performed using Kallisto.
The R package Sleuth was used for RNA sequencing analysis(Pimentel et al. 2017)
Genome_build: 19
Supplementary_files_format_and_content: Per gene TPMs

source_name: TFAM CRISPR

growth_protocol: HEK293T cells were grown in DMEM containing 10% FBS and 1% penicillin-streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from confluent T75 culture flasks of TFAM CRISPR Negative Control and KO cell lines (p32) using the AllPrep DNA/RNA/Protein Kit (Qiagen #80004).
Illumina’s TruSeq Stranded Total RNA kit protocol was used to generate libraries.  Specifically, total RNA is converted to cDNA and size selected to 150 to 200 bp in length with 3' or 5' overhangs. End repair is performed where 3' to 5' exonuclease activity of enzymes removes 3' overhangs and the polymerase activity fills in the 5' overhangs. An ‘A’ base is then added to the 3' end of the blunt phosphorylated DNA fragments which prepares the DNA fragments for ligation to the sequencing adapters, which have a single ‘T’ base overhang at their 3' end. Ligated fragments are subsequently size selected through purification using SPRI beads and undergo PCR amplification techniques to prepare the ‘libraries’.

treatment_protocol: The stable TFAM CRISPR-Cas9 knockout was generated in HEK293T cells using the Origene TFAM – Human Gene Knockout Kit via CRISPR (catalog number: KN215488) following the manufacturer’s protocol. The following sgRNA guide sequence was used to generate the stable TFAM knockout lines: GCGTTTCTCCGAAGCATGTG. Lipofection was conducted using Turbofectin 8.0 (catalog number: TF81001). Puromycin was used for selection at a concentration of 1.5 µg/mL. Fluorescence-activated cell sorting (FACS) was used for single cell sorting and clonal expansion.

tag: cell line

value: TFAM CRISPR


title: TFAMKO_RNA_clone11_CN2_6


title: mcmv.B.sc90


title: TFAMKO_RNA_NC2_CN2_2

source_name: No CRISPR

value: No CRISPR


title: mcmv.test3.sc03


title: mock.B.sc88


title: mock.B.sc87


title: KO-BM8


title: mcmv.B.sc92


title: BCBL1

source_name: Pleural effusion

tag: nhl subtype

value: Primary effusion lymphoma

value: 40 yrs

tag: cell type

value: B-cell


title: Selected translatome mixed bat1∆

city: Heidelberg

first: Kristina

middle: Rebekka

last: Doering

state: Baden-Württemberg

address: Im Neuenheimer Feld 282

department: University of Heidelberg

institute: ZMBH

data_processing:
Library strategy: Ribosome profiling
Barcode and linker removal using Cutadapt 1.11
Alignment to rRNA using Bowtie2.2.5.0
Alignment to genome using TopHat2.0.13
center weighting of ribosomal footprints (custom python script)
normalization to total read number per sample (custom python script)
Genome_build: NCBI build 3.1
Supplementary_files_format_and_content: NormReads-files: column1: chromosome number, column2: nt position, column3: normalized reads on plus strand, column4: normalized reads on minus strand

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Cultures were grown in YPD at 30°C and 150 rpm

extract_protocol:
RNA was extracted using the hot acid phenol method (for details see Becker et al. 2013)
DNA libraries were generated following previously published protocoles (Ingolia et al. 2009, Becker et al. 2013)

treatment_protocol: Cultures were mixed (deletion strain with GFP-tagged Ssb and WT culture), filtered, flash frozen and lysed in frozen state using a mixer mill. Ribosomes were pelleted through a sucrose cushion and resuspended. From this a part was used for RNA extraction (total RNCs) and the rest was used to purify GFP-tagged Ssb using a GFP-antibody coupled to sepharose-beads (Ssb-bound RNCs).

tag: strain

tag: genotype

value: MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0 ssb2{delta}::natMX4 Ssb1-GFP::kanMX4 bat1{delta}::hphNT1 mixed with MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0


title: TFAMKO_RNA_NC3_CN2_3


title: TFAMKO_RNA_NC2_CN1_2


title: TFAMKO_RNA_NC1_CN2_1


title: mcmv.A.sc83


title: mock.A.sc85


title: mock.A.sc84


title: mock.A.sc86


title: TFAMKO_RNA_clone6_CN2_5


title: Total translatome mixed rtn1∆

value: MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0 ssb2{delta}::natMX4 Ssb1-GFP::kanMX4 rtn1{delta}::hphNT1 mixed with MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0


title: mock.B.sc89


title: TFAMKO_RNA_clone5_CN1_4


title: TFAMKO_RNA_clone11_CN1_6


title: mcmv.test3.sc01


title: TFAMKO_RNA_NC3_CN1_3


title: Total translatome mixed bat1∆


title: TFAMKO_RNA_clone6_CN1_5


title: Selected translatome mixed pmt1∆

value: MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0 ssb2{delta}::natMX4 Ssb1-GFP::kanMX4 pmt1{delta}::hphNT1 mixed with MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0


title: Selected translatome mixed tal1∆

value: MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0 ssb2{delta}::natMX4 Ssb1-GFP::kanMX4 tal1{delta}::hphNT1 mixed with MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0


title: mcmv.A.sc81


title: TFAMKO_RNA_NC1_CN1_1


title: mcmv.A.sc82


title: Total translatome mixed tal1∆


title: Selected translatome mixed rtn1∆


title: mcmv.B.sc80


title: mcmv.B.sc79


title: Total translatome mixed pmt1∆


title: mock.B.sc77


title: mcmv.B.sc78


title: mock.B.sc76


title: mock.A.sc74


title: 2486_9C: TCMR_3

description: T-cell mediated rejection

source_name: T-cell mediated rejection

value: Kidney


title: Cortisol6 IVS: Septum_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 6

city: Gainesville

first: Maureen

last: Keller-Wood

state: Florida

address: 1225 Center Dr

department: Pharmacodynamics

institute: University of Florida

description: Gene expression in septum of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 6

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >13.7 pmol Cy3/µg cRNA) was fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) design 019921 by the ICBR facility at the University of Florida according to Agilent's methodology.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal. The limma package was employed to import the raw data into R (http://www.r-project.org), perform background correction and normalize the data by the quantile normalization method. Control probes and low expressed probes were filtered out, retaining for further analysis the probes that were at least 10% brighter than the negative controls on at least six arrays.

organism: Ovis aries

source_name: Heart intraventricular septum, cortisol lamb

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent, Newcastle DE) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from left vetnricular free wall and intraventricular septum with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen RNeasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols.Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer.

treatment_protocol: Pregnant ewes were treated with no or 0.5mg/kg/day cortisol; the 2 week old lamb offspring hearts were studied. Lambs were not treated directly, their cortisol increased secondary to maternal treatment.

value: Heart intraventricular septum

value: 14 days


title: Cortisol4 IVS: Septum_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 4

description: Gene expression in septum of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 4


title: Cortisol3 IVS: Septum_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 3

description: Gene expression in septum of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 3


title: Cortisol7 IVS: Septum_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 7

description: Gene expression in septum of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 7


title: Cortisol5 IVS: Septum_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 5

description: Gene expression in septum of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 5


title: Cortisol8 IVS: Septum_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 8

description: Gene expression in septum of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 8


title: mock.A.sc73


title: mcmv.A.sc69

value: mcmv-infected


title: mcmv.A.sc70


title: mcmv.A.sc71


title: mock.A.sc72


title: mock.B.sc75


title: Cortisol1 IVS: Septum_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 1

description: Gene expression in septum of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 1


title: Cortisol2 IVS: Septum_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 2

description: Gene expression in septum of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 2


title: Single blastocyst in SAGE 1step 18b

description:
18b
Half embryo in SAGE 1step

source_name: preimplantation mouse embryo

label_protocol: Biotinylated cDNA was prepared using GeneChip WT Pico kit, reverse-transcribing 20 micrograms cRNA and, of these, subjecting 5.5 micrograms to labeling.

growth_protocol: Zygotes from B6C3F1 x CD1 mating (stimulated cycle, PMSG + hCG given 48 hours apart) were collected from the oviducts and cultured to the 2-cell stage in KSOM(aa) medium using a 4-well plate under 5% CO2 in air at 37 degrees C. At the 2-cell stage the sister blastomeres were separated from each other and cultured individually in ART medium (GM501 CULT or SAGE 1-Step) or in KSOM(aa) medium in a 96-well plate for additional 72 hours (approx. 96 hours in total).

extract_protocol: Individual blastocysts were lysed in Zymo buffer (Quick RNA micro prep) and total RNA was eluted in water according to the manufacturer's instructions.

treatment_protocol: At the 2-cell stage embryos were split, cultured individually to blastocyst stage, and these blastocysts were lysed in Zymo buffer.

tag: genetic background

value: B6C3F1 x CD1

value: Single blastocyst

value: Theiler stage 5; 4 dpc (96h IVC)

tag: medium

value: SAGE 1step

tag: cell number

value: approx 40-50 cells per blastocyst


title: Single blastocyst in SAGE 1step 16b

description:
16b
Half embryo in SAGE 1step

tag: age


title: Single blastocyst in SAGE 1step 14b

description:
14b
Half embryo in SAGE 1step


title: Single blastocyst in SAGE 1step 12b

description:
12b
Half embryo in SAGE 1step


title: Control6 IVS: Septum_Control_Lamb_Replicate 6

description: Gene expression in control lamb septum at 14 days of age-Replicate 6

source_name: Heart intraventricular septum, control lamb


title: Single blastocyst in SAGE 1step 15b

description:
15b
Half embryo in SAGE 1step


title: Control7 IVS: Septum_Control_Lamb_Replicate 7

description: Gene expression in control lamb septum at 14 days of age-Replicate 7


title: Single blastocyst in SAGE 1step 17b

description:
17b
Half embryo in SAGE 1step


title: Single blastocyst in SAGE 1step 13b

description:
13b
Half embryo in SAGE 1step


title: Single blastocyst in SAGE 1step 9b

description:
9b
Half embryo in SAGE 1step


title: Control8 IVS: Septum_Control_Lamb_Replicate 8

description: Gene expression in control lamb septum at 14 days of age-Replicate 8


title: mcmv.B.sc68

tag: condition

tag: replicate

value: B


title: mcmv.B.sc67


title: Single blastocyst in SAGE 1step 10b

description:
10b
Half embryo in SAGE 1step


title: Single blastocyst in SAGE 1step 11b

description:
11b
Half embryo in SAGE 1step


title: Single blastocyst in GM501 cult 18a

description:
18a
Half embryo in GM501 cult

value: GM501 cult


title: mcmv.B.sc66


title: mock.B.sc65

value: mock


title: mock.B.sc64


title: Control5 IVS: Septum_Control_Lamb_Replicate 5

description: Gene expression in control lamb septum at 14 days of age-Replicate 5


title: mock.B.sc63


title: Control4 IVS: Septum_Control_Lamb_Replicate 4

description: Gene expression in control lamb septum at 14 days of age-Replicate 4


title: mock.A.sc61

value: A


title: mock.A.sc62


title: Control3 IVS: Septum_Control_Lamb_Replicate 3

description: Gene expression in control lamb septum at 14 days of age-Replicate 3


title: mock.A.sc60


title: mcmv.A.sc59


title: Single blastocyst in GM501 cult 16a

description:
16a
Half embryo in GM501 cult


title: Control1 IVS: Septum_Control_Lamb_Replicate 1

description: Gene expression in control lamb septum at 14 days of age-Replicate 1


title: Control2  IVS: Septum_Control_Lamb_Replicate 2

description: Gene expression in control lamb septum at 14 days of age-Replicate 2


title: mcmv.A.sc58

description:
single-cell SLAM-Seq (Smart-Seq kit)
96.tsv


title: Single blastocyst in GM501 cult 15a

description:
15a
Half embryo in GM501 cult


title: mcmv.A.sc57


title: Cortisol8 LV: Left_Ventricle_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 8

description: Gene expression in left ventricle of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 8

source_name: Heart left ventricle,  cortisol lamb

value: Heart left ventricular free wall


title: Single blastocyst in GM501 cult 14a

description:
14a
Half embryo in GM501 cult


title: Cortisol7 LV: Left_Ventricle_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 7

description: Gene expression in left ventricle of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 7


title: Single blastocyst in GM501 cult 13a

description:
13a
Half embryo in GM501 cult


title: Cortisol4 LV: Left_Ventricle_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 4

description: Gene expression in left ventricle of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 4


title: Cortisol5 LV: Left_Ventricle_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 5

description: Gene expression in left ventricle of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 5


title: Cortisol6 LV: Left_Ventricle_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 6

description: Gene expression in left ventricle of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 6


title: Single blastocyst in GM501 cult 12a

description:
12a
Half embryo in GM501 cult


title: Single blastocyst in GM501 cult 10a

description:
10a
Half embryo in GM501 cult


title: Cortisol3 LV: Left_Ventricle_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 3

description: Gene expression in left ventricle of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 3


title: Single blastocyst in GM501 cult 11a

description:
11a
Half embryo in GM501 cult


title: Single blastocyst in GM501 cult 9a

description:
9a
Half embryo in GM501 cult


title: Single blastocyst in KSOM(aa) 8b

description:
8b
Half embryo in KSOM(aa)

value: KSOM(aa)


title: Single blastocyst in KSOM(aa) 7b

description:
7b
Half embryo in KSOM(aa)


title: Single blastocyst in KSOM(aa) 8a

description:
8a
Half embryo in KSOM(aa)


title: mcmv.B.sc56


title: mcmv.B.sc55


title: Single blastocyst in KSOM(aa) 7a

description:
7a
Half embryo in KSOM(aa)


title: Cortisol1 LV: Left_Ventricle_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 1

description: Gene expression in left ventricle of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 1

source_name: Heart left ventricle, cortisol lamb


title: Single blastocyst in KSOM(aa) 6b

description:
6b
Half embryo in KSOM(aa)


title: mock.B.sc53


title: Cortisol2 LV: Left_Ventricle_Maternal cortisol 0.5 mg/kg/d_Lamb_Replicate 2

description: Gene expression in left ventricle of lamb at 14 days of age after maternal cortisol treatment 0.5mg/kg/d -Replicate 2


title: mcmv.B.sc54


title: mock.B.sc51


title: Control7  LV: Left_Ventricle_Control_Lamb_Replicate 7

description: Gene expression in control lamb left ventricle at 14 days of age-Replicate 7

source_name: Heart left ventricle, control lamb


title: Control8  LV: Left_Ventricle_Control_Lamb_Replicate 8

description: Gene expression in control lamb left ventricle at 14 days of age-Replicate 8


title: pan1 Inf 4

city: La Jolla

first: Paula

last: Doblas Ibanez

state: California

address: 9500 Gilman Dr

institute: UCSD

data_processing:
Library strategy: 3'Tag-RNA-Seq
Raw reads were processed with HTStream (https://ibest.github.io/HTStream/) to remove adapter contamination and low quality sequences. On average, 0.10% of reads were removed.
The trimmed reads were aligned to the Zea mays AGPv4 genome with Ensembl gene annotation v.37 using the aligner STAR v. 2.6.0c to generate raw counts per gene.
Genome_build: Maize B73 AGPv4
Supplementary_files_format_and_content: two matrix tables: (1) raw counts of reads for gene and (2) normalized abundance expressed in counts per million mapped reads (CPM)

organism: Zea mays

source_name: leaf 4 tissue

growth_protocol: Maize plants were grown in individual 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA.

extract_protocol:
Total RNA from each sample was isolated using RNeasy Plant Mini kit (QIAGEN) according to the manufacturer’s protocol.
Gene expression profiling was carried out using a 3'Tag-RNA-Seq protocol. Barcoded sequencing libraries were prepared using the QuantSeq FWD kit (Lexogen) for multiplexed sequencing. The libraries were sequenced (100 bp single-end reads) on a HiSeq 4000 System (Illumina), generating an average of 8 million reads per sample.

treatment_protocol: Major veins of leaf 4 from 20 day-old plants were scratch-inoculated with P. stewartii-GFP or inoculation buffer (mock inoculation). Tissue collection was carried out 1 day after inoculation (1 dpi). Half leaves containing mock- or bacteria-inoculated veins were collected, starting at 0.3 cm from the scratch site and taking 1 cm long pieces in basipetal direction, excluding the midrib. Each sample consisted of the pooled tissue of ~15 plants of the same genotype and treatment group. Inoculation and tissue collection were performed at the same time of the day across the different replicates.

value: pan1-Mu/pan1-Mu (R2)

tag: agent

value: infected with P. stewartii-GFP


title: mock.B.sc52

source_name: NIH-3T3 fibroblasts


title: mock.A.sc49


title: mock.A.sc48


title: mcmv.A.sc47


title: Control3 LV: Left_Ventricle_Control_Lamb_Replicate 3

description: Gene expression in control lamb left ventricle at 14 days of age-Replicate 3


title: mcmv.A.sc46


title: mcmv.A.sc45


title: B73 Inf 4

value: B73 (wild type)


title: mock.A.sc50


title: Control6  LV: Left_Ventricle_Control_Lamb_Replicate 6

description: Gene expression in control lamb left ventricle at 14 days of age-Replicate 6


title: Control1 LV: Left_Ventricle_Control_Lamb_Replicate 1

description: Gene expression in control lamb left ventricle at 14 days of age-Replicate 1


title: Control5  LV: Left_Ventricle_Control_Lamb_Replicate 5

description: Gene expression in control lamb left ventricle at 14 days of age-Replicate 5


title: Control4 LV: Left_Ventricle_Control_Lamb_Replicate 4

description: Gene expression in control lamb left ventricle at 14 days of age-Replicate 4


title: Single blastocyst in KSOM(aa) 6a

description:
6a
Half embryo in KSOM(aa)

data_processing: The robust multiarray averaging method was applied for background correction, normalization, and probe summarization using the Affymetrix Expression Console.


title: Control2 LV: Left_Ventricle_Control_Lamb_Replicate 2

description: Gene expression in control lamb left ventricle at 14 days of age-Replicate 2


title: Single blastocyst in KSOM(aa) 5a

description:
5a
Half embryo in KSOM(aa)


title: B73 Inf 3


title: mcmv.B.sc44

description:
single-cell SLAM-Seq (Smart-Seq kit)
96.tsv


title: Single blastocyst in KSOM(aa) 2a

description:
2a
Half embryo in KSOM(aa)


title: Single blastocyst in KSOM(aa) 3a

description:
3a
Half embryo in KSOM(aa)


title: Single blastocyst in KSOM(aa) 4a

description:
4a
Half embryo in KSOM(aa)


title: B73 Inf 2


title: pan1 Inf 2


title: mcmv.B.sc43


title: pan1 Inf 3


title: Single blastocyst in KSOM(aa) 5b

description:
5b
Half embryo in KSOM(aa)


title: Single blastocyst in KSOM(aa) 4b

description:
4b
Half embryo in KSOM(aa)


title: Single blastocyst in KSOM(aa) 3b

description:
3b
Half embryo in KSOM(aa)


title: Single blastocyst in KSOM(aa) 2b

description:
2b
Half embryo in KSOM(aa)


title: Single blastocyst in KSOM(aa) 1b

description:
1b
Half embryo in KSOM(aa)


title: mcmv.B.sc42


title: pan1 Inf 1


title: B73 Inf 1


title: mock.B.sc41


title: pan1 Mock 4

value: Mock (inoculated with PBST)


title: mock.B.sc40


title: mock.B.sc39


title: mock.A.sc38


title: mock.A.sc37


title: B73 Mock 4


title: pan1 Mock 3


title: mock.A.sc36


title: NSCs_WT-S5V5_SETD5

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

data_processing:
Sequenced reads quality was assessed using fastQC
Sequenced reads were aligned to the mouse genome (GRCm38/mm10) by using Bowtie2 version 2.2.3
In order to find the regions of ChIP-seq enrichment over background, we used SICER V1.1 (window size = 200; gap size = 200; FDR 0.01 for K4me1/3, K27ac, K27me3; window size = 4000; gap size = 800; FDR 0.01 for K36me2/3 and SETD5).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The bed files contains the genomic regions of the peaks identified after peak calling

source_name: mouse neural stem cells

growth_protocol: NSCs were routinely cultured in suspension as neurospheres. Cells were cultured in neural inducing medium (NIM) composed of: DMEM/F12 (Sigma-Aldrich) supplemented with Hormon Mix (DMEM/F12, 0,6% Glucose (Sigma-Aldrich) (30%in phosphate buffer (PBS) (Euroclone)), Insulin (Sigma-Aldrich) 250μg/ml, putrescin powder (Sigma-Aldrich) 97μg/ml, apotransferrin powder (Sigma Aldrich), sodium selenite 0,3μM, progesterone 0,2μM), 1mg/ml penicillin/streptomycin (Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich), 0,66% Glucose (30% in phosphate buffer salt (PBS) (Euroclone)), Heparin 4μg/ml, 10 ng/ml bFGF (basic fibroblast growth factor) (ThermoFisher Scientific) and 10 ng/ml EGF (epithelial growth factor) (ThermoFisher Scientific).

extract_protocol:
Cells were cross-linked adding formaldehyde directly to the cell culture media to reach a final concentration of 1%, then were incubated for 10’ at room temperature RT. The reaction was quenched adding glycine to a final concentration of 125 mM. Medium was then removed and cells were washed 3 times with cold, sterile PBS+protease inhibitor, then cells were gently scraped and collected for centrifugation at 4°C for 5’ at 1200 rpm.
Five nanograms of immunoprecipitaded and purified DNA were used to generate ChIP-seq libraries. Briefly, end repair of DNA fragments was achieved by sequential 15 min incubations at 12°C and 25°C with T4 PNK (10U/μl), T4 POL (3U/μl) and 0.1 mM dNTPs. A-base addition was performed by incubating end-repaired DNA fragments with Klenow (3’ → 5’ exo, 5U/μl) and 167 μM dATP for 30 min at 30°C. Adaptor ligation was achieved by using the NEB Quick ligation kit (M2200L) and perfoming an incubation of 15 min at 25°C. Processed DNA fragments were finally amplified with a thermal cycler for 14 cicles, by using the Agilent PfuUltra II Fusion HS DNA Pol kit (600674). All DNA purification steps between the different enzymatic reactions were performed by using Agencourt AMPure XP SPRI beads (Beckman, A63882). The obtained libraries were subjected to quality control on Agilent Bioanalyzer (Agilent Technologies, G2943CA).
ChIP-seq single-read 50bp

treatment_protocol: Cells were plated in adherent condition using Matrigel coated 15mm plates at a density of 6x10^6 per plate. When the plates reached 90% of confluence, cells were fixed.

value: NSCs were derived from telencephalic cortex of embryos at E14.5

value: anti-V5 Tag  R960-25 Life Technologies


title: B73 Mock 3


title: NSCs_WT-S5V5_INPUT

value: none (genomic DNA)


title: mcmv.A.sc35

value: mcmv-infected


title: pan1 Mock 2


title: B73 Mock 2


title: NSCs_SETD5+/-_H3K36me3

value: anti-trimethyl histone H3 Lys36 9050 Abcam


title: NSCs_SETD5+/-_H3K36me2

value: anti-dimethyl histone H3 Lys36  07-369 Millipore


title: Normal 3

city: Guangzhou

first: Jin

last: Tao

state: Guangdong

address: 600 Tianhe Road, Guangzhou

department: Department of Gastroenterology

institute: The Third Affiliated Hospital of Sun Yat-Sen University

description: Colonic mucosa acquired from normal individual 3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: colonic mucosal sample

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA containing small RNA was extracted from colonic mucosal samples by using the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacter’s protocol.

value: colonic mucosa

tag: diagnosis

value: healthy control


title: pan1 Mock 1


title: Single blastocyst in KSOM(aa) 1a

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

institute: Max Planck Institute Muenster

description:
1a
Half embryo in KSOM(aa)

value: B6C3F1 x CD1

value: Single blastocyst

value: Theiler stage 5; 4 dpc (96h IVC)

value: approx 40-50 cells per blastocyst


title: mcmv.A.sc34

value: A


title: mcmv.A.sc33


title: Normal 2

description: Colonic mucosa acquired from normal individual 2


title: Normal 1

description: Colonic mucosa acquired from normal individual 1


title: UC patient 2

description: Colonic mucosa acquired from UC patient 2

value: ulcerative colitis


title: UC patient 3

description: Colonic mucosa acquired from UC patient 3


title: Single blastocyst in GM501 cult 17a

description:
17a
Half embryo in GM501 cult

value: GM501 cult


title: NSCs_SETD5+/-_H3K27me3

value: anti-trimethyl histone H3 Lys27 07-449 Millipore


title: HCC 3

city: Beijing

first: Yanying

last: Wang

address: 15 Datun Road, Chaoyang District,Beijing 100101, China

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Gene expression data from CSCs and non-CSC of HCC 3

hyb_protocol: Labelled cDNA hybridised using the MWG Gene-Frame system. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.

scan_protocol: Arrays scanned using an Affymetrix 428 scanner and Imagene version 4 software.

data_processing: Data analysis was carried out using Imagene, version 5.1 and Genesight version 4 (Biodiscovery Inc). The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy5/Cy3 fluorescence ratios from each patient.

source_name: sorted CSCs

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

extract_protocol: Total RNA was isolated with Trizol from cells according to the manufacturer's instructions.

treatment_protocol: Hepatocytes were isoloated from liver tumor tissues. Cells were incubated with the following commercial antibodies: phycoerythrin (PE)-anti-human CD133 (Miltenyi Biotec) and fluorescein isothiocyanate (FITC)- anti-human CD13 (eBioscience) on ice for 30 minutes. Then, cells were washed with phosphate buffered saline (PBS) for three times, followed by sorting with FACS Aria III (BD Immunocytometry Systems, San Jose, CA, USA).

tag: subject status

value: Hepatocellular carcinoma (HCC) patient

tag: gender

value: male

value: liver tumor

value: cell stem cell (CSC); CD13+CD133+

source_name: soted non-CSCs

value: non cell stem cell (non-CSC):CD13-CD133-


title: HCC 1

description: Gene expression data from CSCs and non-CSC of HCC 1

tag: tissue


title: B73 Mock 1

value: B73 (wild type)

value: Mock (inoculated with PBST)


title: UC patient 1

description: Colonic mucosa acquired from UC patient 1

value: colonic mucosa


title: HCC 2

description: Gene expression data from CSCs and non-CSC of HCC 2


title: NSCs_SETD5+/-_H3K27ac

value: NSCs were derived from telencephalic cortex of embryos at E14.5

tag: chip antibody

value: anti-acethyl histone H3 Lys27 4729 Abcam


title: mcmv.B.sc32

value: mcmv-infected

value: B


title: WTCHG_261086_286: Alphoid Cnp1 before deletion

city: Nottingham

first: William

last: Brown

address: Queens Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

data_processing:
The software Burrows-Wheeler Aligner (BWA) (v0.7.15-r1142-dirty) was used for all the alignments using algorithm “mem” with standard parameters.
Samtools (v1.3.1) was used to select the reads mapped in correct orientation and within insert size.
Coverage vectors were created for using the R package Bioconductor (v3.6).
Coverage plots were created in R (http://www.r-project.org) and were smoothed using the default running medians scatter plot smoothing in R.
Supplementary_files_format_and_content: no processed data because tracks are not applicable to the engineered strains

organism: Schizosaccharomyces pombe

source_name: fission yeast cells

extract_protocol: Material was quantified using Qubit (Invitrogen) and the size profile analysed on the 2200 or 4200 TapeStation (Agilent, dsDNA HS Assay). Input material was normalised to 5 ng or maximum available prior to library preparation. Automated library preparation was performed using the Apollo prep system (Wafergen, PrepX ILMN 32i, 96 sample kit) and standard Illumina multiplexing adapters following manufacturer’s protocol up to pre-PCR amplification. Libraries were PCR amplified (18 cycles) on a Tetrad (Bio-Rad) using the NEBNext High-Fidelity 2X PCR Master Mix (NEB) and using in-house unique dual indexing primers (based on DOI: 10.1186/1472-6750-13-104). Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer. Paired end sequencing was performed using a HiSeq4000 75bp platform (Illumina, HiSeq 3000/4000 PE Cluster Kit and 150 cycle SBS Kit), generating a raw read count of >8 million reads per sample.

value: fission yeast cells


title: WTCHG_543859_214128: GC rich Cnp1 before deletion


title: WTCHG_543859_213140: GC rich Cnp1 before deletion


title: WTCHG_261086_285: Alphoid Cnp1 before deletion


title: NSCs_SETD5+/-_H3K4me3

value: anti-trimethyl histone H3 Lys4 07-473 Millipore


title: mcmv.B.sc31


title: mcmv.B.sc30


title: pan1_het_Inf_4

data_processing:
Raw reads were processed with HTStream (https://ibest.github.io/HTStream/) to remove adapter contamination and low quality sequences. The paired-end reads were also deduplicated with HTStream.On average, 24% of reads were removed.
The trimmed reads were aligned to the B73 AGPv4 genome with Ensembl gene annotation v.37 using the aligner STAR v.2.5.2b to generate raw counts per gene.
Genome_build: Maize B73 AGPv4
Supplementary_files_format_and_content: two matrix tables: (1) raw counts of reads for gene and (2) normalized abundance expressed in counts per million mapped reads (CPM)

extract_protocol:
Total RNA from each sample was isolated using RNeasy Plant Mini kit (QIAGEN) according to the manufacturer’s protocol.
cDNA libraries were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina), and sequenced (100 bp paired-end reads) on a HiSeq 4000 System (Illumina), generating 21-27 million reads per sample.

treatment_protocol: Major veins of leaf 4 from 20 day-old plants were scratch-inoculated with P. stewartii-GFP or inoculation buffer (mock inoculation). Tissue collection was carried out 1 day after inoculation (1 dpi). Half leaves containing mock- or bacteria-inoculated veins were collected, starting at 0.3 cm from the scratch site and taking 1 cm long pieces in basipetal direction, excluding the midrib. Each sample consisted of the pooled tissue of ~30 plants of the same genotype and treatment group. Inoculation and tissue collection were performed at the same time of the day across the different replicates.

value: infected with P. stewartii-GFP


title: WTCHG_543859_277144: (A/T)n>(AC/GT)n 5.3kb Cnp1 before deletion


title: NSCs_SETD5+/-_H3K4me1

value: anti-monomethyl histone H3 Lys4 8895 Abcam


title: B73_Inf_4


title: mock.B.sc29

value: mock


title: WTCHG_543859_286131: Cen8  at neo_cen


title: pan1_Inf_4

value: pan1-ems/pan1-ems (R1)


title: pan1_het_Inf_3


title: NSCs_SETD5+/-_INPUT

value: none (genomic DNA)


title: NSCs_WT_H3K36me3

value: anti-trimethyl histone H3 Lys36 9050 Abcam


title: mock.B.sc28


title: mock.B.sc27


title: pan1_Inf_3


title: WTCHG_543859_285143: Cen8  at neo_cen


title: NSCs_WT_H3K36me2

value: anti-dimethyl histone H3 Lys36  07-369 Millipore


title: WTCHG_261086_294: Cen8 ade6


title: B73_Inf_3


title: pan1_het_Inf_2


title: mock.A.sc25

value: A


title: WTCHG_543859_278132: (A/T)n>(AC/GT)n 5.3kb Cnp1 before deletion


title: WTCHG_261086_293: Cen8 ade6


title: WTCHG_543859_276156: Art cen 6.2kb Cnp1 after deletion


title: NSCs_WT_H3K27ac


title: WTCHG_543859_275168: Art cen 6.2kb Cnp1 after deletion


title: NSCs_WT_H3K4me3


title: mock.A.sc24


title: NSCs_WT_H3K4me1


title: WTCHG_543859_270133: Art cen 6.2kb Cnp1 before deletion


title: B73_Inf_2

value: B73 (wild type)


title: pan1_het_Inf_1


title: NSCs_WT_INPUT


title: mcmv.A.sc22


title: mcmv.A.sc21


title: mcmv.B.sc20


title: WTCHG_543859_224103: Cen1 Cnp1 after deletion - Long Term

value: Nott638 Cen1 ura- final pool


title: WTCHG_543859_223115: Cen1 Cnp1 after deletion - Long Term


title: pan1_het_ Mock_4

value: Mock (inoculated with PBST)


title: mock.A.sc26


title: mcmv.B.sc19


title: pan1_Mock_4


title: pan1_Inf_2


title: NSCs_WT_H3K27me3

value: NSCs were derived from telencephalic cortex of embryos at E14.5

value: anti-trimethyl histone H3 Lys27 07-449 Millipore


title: WTCHG_543859_220151: Cen1 Cnp1 after deletion - Pool

value: Nott584 ura- pool


title: mcmv.B.sc18

value: mcmv-infected

value: B


title: mcmv.A.sc23


title: mock.B.sc17


title: WTCHG_543859_269145: Art cen 6.2kb Cnp1 before deletion

value: fission yeast cells


title: B73_Mock_4


title: WTCHG_261086_278: Cen5 Cnp1 after deletion


title: WTCHG_543859_219163: Cen1 Cnp1 after deletion - Pool


title: 3-NPA 1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Transformed E12 rat mescencephalic neuronal stem cells, dopamine producing, used for neurotoxin studies

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Agilent's Rat Gene Expression  8x60k Array (AMADID: 028279). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift normalization method.

source_name: Immortalised Rat mescencephalic dopaminergic neurons

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: N27 cells were grown in RPMI medium and passaged once in two days by trypsinization

extract_protocol: RNA extraction was perforemd by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: Cells were treated with 150 µM and 250 µM of Mn or MPP+ respectively, for 48 h

tag: cell line

value: N27 Dopaminergic Neural Cell Line

tag: treatment


title: B73_Inf_1

value: infected with P. stewartii-GFP


title: pan1_Inf_1


title: pan1_Mock_3


title: pan1_het_Mock_3


title: mock.B.sc15

value: mock


title: mock.B.sc16


title: B73_Mock_3