title: rend_LB_GLB115

data_processing:
Base calls performed using Casava version 1.7.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position. The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peak shadows were not removed. Matched ribosome profiling data in WT LB in Lalanne et al, 2018.
genome build: NC_000964.3
processed data files format and content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position.
Library strategy: Rend-Seq

tag: strain

value: GLB115, see Data S1 in paper for strain details

value: LB


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D6_ad012

status: Public on Nov 28 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: age

tag: tissue

value: brain

tag: source

value: PTLp

tag: target

value: SC

tag: gender

value: female


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D5_ad008

value: male


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D5_ad007


title: RNAseq_E3_D7_GLB430

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

country: Canada

institute: University of Montreal

description: Sequence reads were trimmed for poly A stretches at the 3’ ends.

library_source: transcriptomic

data_processing:
Base calls performed using Casava version 1.7.
Poly A tails were stripped, and the resulting reads aligned to the NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 1, and the 3’ ends of mapped reads were summed at each genomic position.
genome build: NC_000964.3
processed data files format and content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position.

molecule: total RNA

organism: Bacillus subtilis

source_name: Bacteria

growth_protocol: Overnight cultures started from fresh colonies were diluted to OD600 = 0.01. At OD600 =0.1, cultures were diluted to OD600 = 0.0001 in 25 mL pre-warmed medium. The culture was kept in a 125 mL flask at 37C with aeration (200 rpm) until OD600 reached 0.3.

extract_protocol:
10 mL of culture were collected and mixed with 1 mL of 10:1 ethanol/phenol stop solution by rapid inversion. Cells were pelleted at 3000 rcf for 10 min at 4C. The supernatant was decanted and cell pellets stored at -80C until RNA extraction. RNA was extracted using the RNeasy plus kit with gDNA eliminator column (Qiagen) following manufacturer’s instructions.
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 1 min 45 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740), dephosphorylated at the 3’ end and poly-A tailed using T4 PNK (NEB). Revese transcription was performed using indexed poly-dT primer using SSIII (Thermo Fisher). After reverse transcription, cDNA in the range 100 to 120 nt were size selected, and ligated to an adapter with T4 DNA ligase (NEB). The ligated cDNA was size selected (135 to 155 nt) and PCR amplified.

value: GLB430, see Data S1 in paper for strain details

tag: growth medium

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with inducers. See Data S3 from paper for details.


title: Tumorsphere-A1471_PD173074-treated_24h

first: Alain

last: Pacis

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Illumina bcl2fastq software used for basecalling
Reads were mapped to mouse genome version mm10 using Spliced Transcripts Alignment to a Reference (STAR).
Read counts for each sample are obtained using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
A1005, A1129, and A1471 tumourspheres treated with inhibitors (DMSO, Crizotinib, PD173074, or drug combination for 24h) were collected and total RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions. High RNA quality was verified using the Bioanalyzer RNA 6000 Nano assay (Agilent).
The samples were sequenced using a NextSeq500 sequencer (Illumina) by the Genomics Core Facility of the Institute of for Research in Immunology and Cancer, Université de Montréal.

value: breast tumour

tag: genotype

tag: treatment


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D4_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D6_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D5_ad002

value: RSP


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D4_ad008


title: RNAseq_E3_D6_GLB426

value: GLB426, see Data S1 in paper for strain details


title: Tumorsphere-A1471_DMSO-treated_24h

value: DMSO


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D4_ad007


title: RNAseq_E3_D7_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D4_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D4_ad004


title: Tumorsphere-A1471_Crizotinib-treated_24h

value: Crizotinib


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D3_ad010


title: RNAseq_E3_D5_GLB426


title: Tumorsphere-A1129_COMBO-treated_24h

value: Combo


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D3_ad002


title: RNAseq_E3_D4_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D4_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D3_ad006


title: Tumorsphere-A1129_DMSO-treated_24h


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D3_ad001


title: Tumorsphere-A1129_Crizotinib-treated_24h


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D2_ad008


title: RNAseq_E3_D3_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D2_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D3_ad004


title: RNAseq_E3_D1_GLB430


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D2_ad002


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D2_ad004


title: Tumorsphere-A1005_COMBO-treated_24h


title: RNAseq_E3_D2_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D1_ad010


title: RNAseq_E3_D4_GLB430


title: Tumorsphere-A1005_PD173074-treated_24h


title: Tumorsphere-A1005_DMSO-treated_24h


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D1_ad008


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D1_ad007


title: RNAseq_E3_D1_GLB426


title: Tumorsphere-A1129_PD173074-treated_24h


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D1_ad006


title: RNAseq_E3_C7_GLB430


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D1_ad004


title: Tumorsphere-A1005_Crizotinib-treated_24h


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D2_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D1_ad002


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D12_ad008


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D1_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D12_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D12_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D12_ad007


title: RNAseq_E3_C4_GLB426


title: RNAseq_E3_C6_GLB426


title: RNAseq_E3_C5_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D12_ad004


title: RNAseq_E3_C3_GLB430


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D12_ad002


title: Chinese Red Steppes 6 [RC6]

city: Changchun

first: Xibi

last: Fang

address: No. 5333 Xian Road

country: China

institute: Jilin University

description:
fat deposition
RC6_LD

data_processing:
The raw sequencing data are also evaluated by FAST-QC including quality distribution of nucleotides, position specific sequencing quality, GC content, the proportion of PCR duplication, kmer frequency etc.
Then Hisat2 were used for RNA-seq alignment.
the EB-Seq algorithm was applied to filter differentially expressed genes for the WC_LC and RC_LC groups and the URL of the GTF file used to annotate the EB-Seq is ftp://ftp.ensembl.org/pub/release-79/gtf/bos_taurus/Bos_taurus.UMD3.1.79.gtf.gz.
After significance analysis and FDR (false discovery rate) analysis, we selected the DEGs according to the Log2FC >0.585 or <-0.585, FDR <0.05.
Genome_build: Bos taurus UMD_3.1.1
Supplementary_files_format_and_content: FPKM;

organism: Bos taurus

source_name: Chinese Red Steppes_longissimus muscle

growth_protocol: Three longissimus muscle (LM) tissue samples of Japanese black cattle (28 months old) and three LM samples of Chinese Red Steppes cattle (28 months old) were provided by the National Research Center for Animal Transgenic Bio-technology, Inner Mongolia University and Branch of Animal Science, Jilin Academy of Agricultural Sciences, respectively.

extract_protocol:
Total RNA was isolated from longissimus dorsi muscles using Trizol Reagent (Invitrogen, USA) according to the manufacturer's instructions. Total RNA was treated with DNase I (NEB, Beijing, China), extracted with phenol-chloroform, and precipitated with ethanol. The quality and quantity of total RNA were determined using an Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA).
The mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. 1.5 µg of mRNA from each sample was used to construct six cDNA libraries for sequencing. The mRNA was treated with a Thermomixer (Eppendorf AG, Hamburg, Germany) to generate fragments with an average size of 200 bp (200 ± 25 bp) for the paired-end libraries. The fragmented mRNA was then used as templates for synthesizing the first-strand cDNA. The double-stranded cDNAs were purified and ligated to adaptors for Illumina paired-end sequencing. Library concentration was quantified by qPCR and a Qubit® 2.0 Flurometer (Life Technologies, CA, USA), and the insert size was checked on an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA).

tag: breed

value: Chinese Red Steppes cattle

value: 28 months

value: longissimus muscle


title: Chinese Red Steppes 5 [RC5]

description:
fat deposition
RC5_LD


title: Chinese Red Steppes 4 [RC4]

description:
fat deposition
RC4_LD

value: Chinese Red Steppes  cattle


title: wagyu 120921 [WC921]

description:
fat deposition
WC921_LD

source_name: Wagyu_longissimus muscle

value: Japanese black (Wagyu) cattle


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D12_ad001

value: brain


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D11_ad012

value: PTLp

value: SC


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D11_ad007

value: male


title: RNAseq_E3_C2_GLB426


title: wagyu 120719 [WC719]

description:
fat deposition
WC719_LD


title: RNAseq_E3_C7_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D11_ad006

value: female


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D11_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D12_ad012


title: OtA0637 Obese 3

city: Salt Lake City

first: Katsuhiko

last: Funai

state: UT

department: Molecular Medicine

institute: University of Utah

data_processing:
Sequenced on an Illumina HiSeq2000 by Otogenetics Corp (Norcross, GA)
At least 20 million 2X101 paired end reads per sample
Reads were aligned to the NCBI GRCh37 reference genome with TopHat
RefSeq annotations were used as the gene model and differential expression was assessed with Cufflinks, correcting for multiple comparisons
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file with RPKM values

organism: Homo sapiens

source_name: Subject 637

growth_protocol: Primary myoblasts were maintained in DMEM + 10% FBS supplemented with 0.5 mg/ml BSA, 0.5 mg/ml fetuin, and 100 ug/ml penicillin/streptomycin. At ~80% confluence, primary myoblasts were switched to low-serum (2% horse serum) media to induce differentiation into myotubes.

extract_protocol:
Total RNA from three samples per group was isolated by Qiagen RNeasy kit and quality was assessed on a bioanalyzer (RIN>8 for each sample).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

treatment_protocol: Myotubes washed in PBS and frozen immediately.

tag: cell type

value: Primary myotube

tag: phenotype

value: obese

tag: subject id

value: Subject 637


title: RNAseq_E3_C1_GLB430

value: GLB430, see Data S1 in paper for strain details

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with inducers. See Data S3 from paper for details.


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D11_ad002

value: RSP


title: OtA0636 Obese 2

source_name: Subject 636

value: Subject 636


title: RNAseq_E3_C1_GLB426

value: GLB426, see Data S1 in paper for strain details


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D10_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D10_ad010


title: RNAseq_E2_C9_GLB446

value: GLB446, see Data S1 in paper for strain details


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D10_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D10_ad008


title: OtA0634 Lean 3

source_name: Subject 634

value: lean

value: Subject 634


title: wagyu 120616 [WC616]

description:
fat deposition
WC616_LD

value: Japanese black (Wagyu) cattle

value: 28 months

value: longissimus muscle


title: RNAseq_E3_C3_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D11_ad010

value: brain

value: PTLp

value: SC


title: RNAseq_E2_C9_GLB442

value: GLB442, see Data S1 in paper for strain details


title: OtA0632 Lean 1

source_name: Subject 632

value: Primary myotube

value: Subject 632


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D10_ad006

value: female


title: OtA0633 Lean 2

source_name: Subject 633

value: Subject 633


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D10_ad002

value: RSP


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C9_ad008

value: male


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D10_ad001


title: RNAseq_E2_C8_GLB438

value: GLB438, see Data S1 in paper for strain details

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with inducers. See Data S3 from paper for details.


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C9_ad007


title: RNAseq_E2_C9_GLB115

value: GLB115, see Data S1 in paper for strain details


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C8_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C9_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D11_ad001


title: RNAseq_E2_C7_GLB438


title: OtA0635 Obese 1

source_name: Subject 635

value: obese

value: Subject 635


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C8_ad010


title: RgRg_infl_TraPR

city: Potsdam

first: Heinrich

last: Bente

address: Am Muehlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

description: TraPR-enriched sRNAs

data_processing:
bam-file generation and demultipexing was done by sequencing facility
bam-files were converted to fastq-files using BEDtools bamtofastq (Version 2.29.2)
Adapters were trimmed and reads were size-selected to the length of 18-26 nt using cutadapt (v1.9.1 ; options: -a AGATCGGA-g CGACGATC -m 18 -M 26 -discard-untrimmed)
Reads were aligned to the Arabidopsis thaliana genome (TAIR10) and the transgenic epiallele (plus upstream/downstream flanking regions) using Bowtie2 (2.2.5 ; options: -k 500 -no-unal)
Genome_build: TAIR10
Supplementary_files_format_and_content: For each sample two tab-delimited text files including distinct sequences and reads count values. One file for the sequences at the HPT-epiallele, one file for the sequences against the TAIR10 genome.

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol:
Growth conditions soil culture: 21°C, 16 h light 8 h dark, 60% humidity.
Growth conditions seedlings: 14 d on germination medium plates, 21°C, 16 h light 8 h dark.
Inflorescence samples were taken from 35-d-old soil-grown plants.

extract_protocol:
total RNA extraction with Trizol
TraPR RISC purification followed by RNA extraction with Trizol
NEBnext E7300 followed by size selection on PAGE gel

treatment_protocol: mock grown, no treatment

tag: ecotype

tag: ploidy

value: inmature inflorescence, closed flower buds

tag: growth condition

value: soil grown

value: 35 days


title: RgRgRgRg_infl_TraPR

description: TraPR-enriched sRNAs


title: RR_infl_TraPR

description: TraPR-enriched sRNAs


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C8_ad008

value: brain

value: PTLp


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C8_ad007

value: SC


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C8_ad006


title: RRRR_infl_TraPR

description: TraPR-enriched sRNAs


title: RNAseq_E2_C5_GLB446

value: GLB446, see Data S1 in paper for strain details


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C7_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C8_ad004


title: RNAseq_E2_C9_GLB438


title: RNAseq_E2_C6_GLB438


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_D10_ad004


title: RNAseq_E2_C5_GLB438


title: SgSgSgSg_infl_TraPR

description: TraPR-enriched sRNAs


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C7_ad010


title: RNAseq_E2_C5_GLB442

value: GLB442, see Data S1 in paper for strain details


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C7_ad008


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C8_ad002

value: female


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C7_ad007


title: SgSg_infl_TraPR

description: TraPR-enriched sRNAs


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C7_ad006


title: R∆2R∆2_infl_TraPR

description: TraPR-enriched sRNAs


title: R∆2R∆2R∆2R∆2_infl_TraPR

description: TraPR-enriched sRNAs


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C8_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C7_ad004


title: RNAseq_E2_C5_GLB424

value: GLB424, see Data S1 in paper for strain details


title: RNAseq_E2_C5_GLB115


title: SS_infl_TraPR

description: TraPR-enriched sRNAs


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C7_ad002

value: RSP


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C6_ad012


title: RNAseq_E2_C4_GLB438


title: SSSS_infl_TraPR

description: TraPR-enriched sRNAs


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C6_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C6_ad008

value: male


title: RNAseq_E2_C3_GLB438

value: GLB438, see Data S1 in paper for strain details


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C6_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C6_ad006


title: RNAseq_E2_C2_GLB438

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with inducers. See Data S3 from paper for details.


title: F1_RRSS_infl_TraPR

description: TraPR-enriched sRNAs


title: RNAseq_E2_C1_GLB442


title: RNAseq_E2_C1_GLB438


title: SSSS_infl_nrpd1_TraPR

description: TraPR-enriched sRNAs


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C5_ad008


title: SSSS_infl_ctr_TraPR

description: TraPR-enriched sRNAs


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C5_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C5_ad007


title: RNAseq_E2_C1_GLB446


title: WW_seedl

description: prepared from totalRNA

source_name: seedlings

value: seedlings, aerial parts

value: grown on germination medium plates

value: 14 days


title: RNAseq_E1_C9_GLB434

value: GLB434, see Data S1 in paper for strain details


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C3_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C5_ad012


title: SS_seedl

description: prepared from totalRNA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C4_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C3_ad012


title: F1_SSRR_infl_TraPR

description: TraPR-enriched sRNAs

value: inmature inflorescence, closed flower buds

value: soil grown


title: RNAseq_E1_C9_GLB426

value: GLB426, see Data S1 in paper for strain details


title: RR_seedl

description: prepared from totalRNA


title: WWWW_seedl

description: prepared from totalRNA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C3_ad007

value: brain

value: PTLp


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C3_ad008

value: SC


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C6_ad002


title: RNAseq_E1_C9_GLB115

value: GLB115, see Data S1 in paper for strain details


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C3_ad004


title: SSSS_seedl

description: prepared from totalRNA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C3_ad006

value: female


title: RNAseq_E2_C1_GLB115


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C5_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C5_ad002


title: RNAseq_E1_C8_GLB426


title: RNAseq_E1_C7_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C3_ad002


title: RD shSNAI2 RNA-seq

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description:
shSNAI2.coding.TPM.matrix.txt
Sample_RD_shSNAI2_10d_T_UTHSCSA

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using STAR
Gene expression values were calculated as Transcripts per million (TPM) using RSEM and the UCSC reference at the gene level.
Differential gene expression was determined using custom R scripts (https://github.com/GryderArt/VisualizeRNAseq)
Genome_build: hg19
Supplementary_files_format_and_content: TPM files are provided in txt format at the gene-level

source_name: RMS cell line

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
RNA was extracted from FN-RMS cell lines using the RNeasy mini kit (Qiagen). For HiChIP, the Dovetail MNase HiChIP kit (Catalogue # 21007) was used.  Briefly, cells were fixed with DSG and 1% formaldehyde, treated with MNase, and immunoprecipitated with anti-H3K27ac antibody (Cell Signalling, Rabbit mAb #8173).  On-bead bridge incorporation (AGGTTCGTCCATCGATCGATGGACGAACCT) and religation was performed, followed by reversal of crosslinks and proteinase K treatment and DNA purification.
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: Control shRNA cells (pLKO1) and shSNAI2.1 shRNA infected cells cells were selected in 500ug/ml for three days and at day 10 post selection cells were trypsinized, washed and transferred to RLT buffer

tag: cell line

value: RD

tag: chip antibody

tag: enrichment target

tag: mechanistic classifications of chip protein target

tag: passages

tag: treatment time

value: 7 day


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C3_ad001

tag: strain

tag: age

tag: tissue

tag: source

value: RSP

tag: target

tag: gender

value: male


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C2_ad008


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C2_ad007


title: RRRR_seedl

description: prepared from totalRNA


title: RNAseq_E1_C6_GLB426

tag: growth medium

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with inducers. See Data S3 from paper for details.


title: RD shCtr RNA-seq

description:
shSNAI2.coding.TPM.matrix.txt
Sample_RD_shScr_10d_T_UTHSCSA

tag: treatment

value: shControl


title: RNAseq_E1_C5_GLB434


title: SMS-CTR shSNAI2 RNA-seq

description:
shSNAI2.coding.TPM.matrix.txt
Sample_CTR_shSNAI2_10d_T_UTHSCSA

value: SMS-CTR


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C1_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C2_ad006


title: RNAseq_E1_C5_GLB430

value: GLB430, see Data S1 in paper for strain details


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C2_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C1_ad010


title: SMS-CTR shCtr RNA-seq

description:
shSNAI2.coding.TPM.matrix.txt
Sample_CTR_shScr_10d_T_UTHSCSA


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C1_ad007


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C1_ad002


title: RNAseq_E1_C5_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C1_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C12_ad012


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C12_ad010


title: RNAseq_E1_C4_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C6_ad004


title: G62_S15_L003

city: Amherst

first: Daniel

last: Hebert

state: MA

address: 240 Thatcher Road LSL

institute: University of Massachusetts

description: RNAseq matrix table results

data_processing:
Sequence quality was assessed using FastQC (Andrews) and MultiQC (Ewels et al., 2016).
Reads were aligned to the hg38 human reference genome using STAR (Dobin et al., 2013).
Transcript abundance was quantified using RSEM (Li and Dewey, 2011) and normalized to counts per million (CPM) in R using the edgeR software package (Robinson et al., 2010).
Analyses to compare gene expression between cell types was conducted in Excel by finding the average CPM in the pool of genes of interest for the associated cell type and determining the standard deviation away from the average for each gene of interest.
Supplementary_files_format_and_content: All processed data is found in the RNAseq matrix table provided. Data is presented as CPM for each biological replicate for each cell line.

source_name: Biological replicate 3, technical replicate 3

growth_protocol: Cells were cultured in DMEM (Sigma) supplemented with certified 10% fetal bovine serum (Gibco) at 37 °C at 5% CO2. Cells were tested for the presence of mycoplasma using a universal mycoplasma detection kit (ATCC, Cat # 30-012K).

extract_protocol:
Three million cells for each indicated cell line were plated in 10 cm plates and allowed to grow for 48 hr. Cells were then lysed in TRIzol buffer and RNA was isolated using RNA Clean Concentrate Kit with in-column DNase-I treatment (Zymo Research Corp), following manufacturer instructions. The quantity of RNA was assayed on Qubit using RNA BR assay (Life Technologies Corp), and quality was assessed on Agilent 2100 Bioanalyzer using RNA 6000 Nano Assay (Agilent Technologies Inc). Total RNA was used to isolate poly(A) mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module, and libraries were prepared using NEBNext UltraII Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer instructions. The quantity of library was assayed using Qubit DNA HS assay (Life Technologies Corp), and quality was analyzed on Bioanalyzer (Agilent Technologies Inc). Libraries were sequenced on Illumina NextSeq 500 platform using NextSeq 500/550 High Output v2 kit (150 cycles) with 76 bp paired-end sequencing chemistry.
Reads were aligned to the hg38 human reference genome using STAR (Dobin et al., 2013). Transcript abundance was quantified using RSEM (Li and Dewey, 2011) and normalized to counts per million (CPM) in R using the edgeR software package (Robinson et al., 2010).

value: WT Hek293-EBNA1-6E


title: G62_S15_L004

description: RNAseq matrix table results

source_name: Biological replicate 3, technical replicate 4


title: RNAseq_E1_C3_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C12_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C12_ad007


title: G62_S15_L002

description: RNAseq matrix table results

source_name: Biological replicate 3, technical replicate 2


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C12_ad004


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C2_ad004


title: RNAseq_E1_C2_GLB426


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C12_ad002


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C12_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C11_ad010


title: G62_S15_L001

description: RNAseq matrix table results

source_name: Biological replicate 3, technical replicate 1


title: RNAseq_E1_C1_GLB434

value: GLB434, see Data S1 in paper for strain details


title: G62_S14_L004

description: RNAseq matrix table results

source_name: Biological replicate 2, technical replicate 4


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C11_ad008

source_name: C57BL/6J P56 Mouse Brain


title: RNAseq_E1_C1_GLB430

source_name: Bacteria


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C11_ad007


title: SMS-CTR H3K27ac HiChIP

data_processing:
Library strategy: HiChIP
HiChIP data was processed by first trimming the bridge sequence (AGGTTCGTCCATCGATCGATGGACGAACCT), followed by use of the HiC-Pro pipeline (https://github.com/nservant/HiC-Pro) where the enzymatic digestion enzyme parameter was left blank, to account for MNase digestion methodology.
Processed file for Juicebox visualization was generated by hicpro2juicebox.sh (HiC-Pro tools) and Juicer tools (https://github.com/aidenlab/juicer).
Genome_build: hg19
Supplementary_files_format_and_content: hic

value: anti-H3K27ac antibody (Cell Signalling, Rabbit mAb #8173)

value: Active enhancers

value: 6 hours

value: DMSO


title: G62_S14_L003

description: RNAseq matrix table results

source_name: Biological replicate 2, technical replicate 3


title: RNAseq_E1_C5_GLB115


title: RNAseq_E1_C1_GLB426

value: GLB426, see Data S1 in paper for strain details


title: G62_S14_L002

description: RNAseq matrix table results

source_name: Biological replicate 2, technical replicate 2


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C11_ad004

value: brain

value: SC


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C11_ad002

value: female


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C11_ad006


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C12_ad008

value: PTLp


title: RNAseq_E1_C1_GLB115

value: GLB115, see Data S1 in paper for strain details

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020)


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C10_ad012


title: G62_S14_L001

description: RNAseq matrix table results

source_name: Biological replicate 2, technical replicate 1


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C10_ad008

value: male


title: G62_S13_L004

description: RNAseq matrix table results

source_name: Biological replicate 1, technical replicate 4


title: ribo_MCC2_GLB115

description: Sequence reads were trimmed for adaptor sequences.

data_processing:
Base calls performed using Casava version 1.7.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position. The footprint reads with size between 15 to 44 nucleotides in length were mapped to the genome using the center-weighted approach: for each footprint read, the center residues that are at least 10 nucleotides away from either ends were given a weight of one over the length of the fragment (minus the 10 nucleotides on both ends) to generate the wig file, for footprint <21 nt long, the read count of 1 was added at the center of the footprint.
genome build: NC_000964.3
processed data files format and content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position.
Library strategy: Ribo-Seq (ribosome protected mRNA)

growth_protocol: Overnight cultures were diluted to OD600 0.0003 in 250 mL fresh media. The culture was kept in a 2.8 L flask at 37C with aeration (200 rpm) until OD600 reached between 0.15 to  0.3.

extract_protocol:
Extraction was performed as described in detail previously (Li et al., Cell 2014 and Lalanne et al, 2018). 250 mL of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 mL canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C.
Ribosome protected mRNA fragments were size selected via gel purification, dephosphorylated at the 3’ end and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 500 uM IPTG, 0.5% w/v xylose


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C10_ad004

value: RSP


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C10_ad007


title: ribo_MCC1_GLB115

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C10_ad006


title: G62_S13_L003

description: RNAseq matrix table results

source_name: Biological replicate 1, technical replicate 3

value: WT Hek293-EBNA1-6E


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C10_ad010


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C10_ad001


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_C10_ad002


title: ribo_CRISPRi_RF1

value: CRISPRi targeting RF1, CAG74829 , lacA::Pxyl-dcas9(ErmR),  amyE::Pveg-sgRNA_prfA(CmR)

value: LB with 0.04% w/v xylose


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B9_ad010


title: 25DAG_02KN_258-3

city: Taipei

first: Yi-Fang

last: Tsay

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
To obtain 150 bp paired-end reads, base-calling with bcl2fastq (version 2.17.1.14) Conversion Software was used to demultiplex data and convert BCL files to FASTQ.
All reads were trimmed and quality-filtered using CLC Genomics Workbench 10 (Qiagen), with settings of removal of low quality sequence (limit=0.01), no ambiguous nucleotides allowed, and removal of reads smaller than 10 nucleotides.
The trimmed reads were mapped to the TAIR10 genome using the RNA-seq mapping algorithm implemented in CLC Genomics Workbench 10 and allowing only unique mapping with a maximum of two mismatches.
The expression level of each gene was calculated as Count Per Millilon (CPM).
Genome_build: TAIR10 genome
Supplementary_files_format_and_content: text files include CPM values for each sample

source_name: shoot

growth_protocol: grown hydroponically with 0.2 or 2 mM KNO3 for 16 or 25 days

extract_protocol:
Total RNA was extracted from the shoot using TRIzol reagent (Gibco BRL), and subjected to quality control with an Agilent 2100 Bioanalyzer.
Libraries were prepared using a TruSeq Stranded mRNA LT set A/B Sample Preparation kit

tag: genotype

value: shoot

tag: days after sawing

tag: nitrate concentration


title: ribo5_GLB452

value: GLB452, see Data S1 in paper for strain details

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 500 uM IPTG


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B9_ad007


title: G62_S13_L001

description: RNAseq matrix table results

source_name: Biological replicate 1, technical replicate 1

tag: cell line


title: G62_S13_L002

description: RNAseq matrix table results

source_name: Biological replicate 1, technical replicate 2


title: ribo_CRISPRi_RF2

value: CRISPRi targeting RF2, CAG74815, lacA::Pxyl-dcas9(ErmR),  amyE::Pveg-sgRNA_prfB(CmR)

value: LB with 0.05% w/v xylose


title: G62_S12_L004

description: RNAseq matrix table results

value: Hek293-EBNA1-6E ALG6/UGGT12-/-


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B9_ad012

value: brain

value: SC

value: female


title: G62_S12_L003

description: RNAseq matrix table results


title: 25DAG_02KN_258-2


title: G62_S12_L002

description: RNAseq matrix table results


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B9_ad006


title: ribo4_GLB452

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 25 uM IPTG, 0.015% w/v xylose


title: 25DAG_02KN_258-1


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B9_ad004

value: male


title: ribo2_GLB455

value: GLB455, see Data S1 in paper for strain details

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 1 mM IPTG, 0.5% w/v xylose


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B9_ad002

value: RSP


title: 25DAG_02KN_NC1-3

value: wild type


title: G62_S12_L001

description: RNAseq matrix table results


title: ribo2_GLB452

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 500 uM IPTG, 0.5% w/v xylose


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B9_ad001


title: 25DAG_02KN_NC1-2


title: ribo1_GLB455

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 0.2% w/v xylose,  100 uM IPTG


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B8_ad012

value: PTLp


title: 25DAG_02KN_NC1-1

value: shoot


title: G62_S11_L003

description: RNAseq matrix table results


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B8_ad010


title: ribo1_GLB452

value: GLB452, see Data S1 in paper for strain details

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 10 uM IPTG


title: G62_S11_L002

description: RNAseq matrix table results


title: ribo3_GLB452

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 10 uM IPTG, 0.5% w/v xylose


title: 25DAG_2KN_258-3

value: 2 mM


title: 25DAG_2KN_258-2


title: rend_MCC2_GLB115

data_processing:
Base calls performed using Casava version 1.7.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 2 -m 2. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position. The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peak shadows were not removed.
genome build: NC_000964.3
processed data files format and content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position.
Library strategy: Rend-Seq

extract_protocol:
10 mL of cell culture was added to 1 mL of 10:1 ethanol/phenol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 25 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.

value: GLB115, see Data S1 in paper for strain details


title: G62_S11_L001

description: RNAseq matrix table results

value: Hek293-EBNA1-6E ALG6/UGGT12-/-


title: rend_MCC1_GLB115

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B8_ad007

value: brain

value: SC


title: 25DAG_2KN_258-1


title: rend_CRISPRi_RF2

data_processing:
Base calls performed using Casava version 1.7.
Trimmed reads were aligned to NC_000964.3 using Bowtie v1.0.1 with options -v 1 -k 1. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position. The 5' and 3' ends of mapped reads between 15 and 45 nt in sizes were added separately at genomic positions to generate the wig file (thus leading to 4 wig files: 3’ forward, 3’ reverse, 5’ forward, 5’ reverse). Peak shadows were not removed.
genome build: NC_000964.3
processed data files format and content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position.
Library strategy: Rend-Seq

extract_protocol:
5 mL of cell culture was added to 5 mL of cold (-30C) methanol, mixed by inversion and spun down at 3000 rcf for 10 min at 4C. The supernatant was decanted and the cell pellet frozen at -80C. RNA was extracted using the RNAeasy kit (QIAGEN).
Ribosomal RNA was depleted using the MICROBExpress kit (Thermo Fisher). The resulting RNA was fragmented for 25 s at 95C using RNA fragmentation reagents (Thermo Fisher, AM 8740). Fragments in the 15 to 45 nt range were selected, dephosphorylated at the 3’ end and ligated to a 5’ adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.

value: CRISPRi targeting RF2, CAG74815, lacA::Pxyl-dcas9(ErmR),  amyE::Pveg-sgRNA_prfB(CmR)

value: LB with 0.05% w/v xylose


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B8_ad006

value: RSP

value: female


title: G62_S10_L003

description: RNAseq matrix table results


title: rend_CRISPRi_RF1

value: CRISPRi targeting RF1, CAG74829 , lacA::Pxyl-dcas9(ErmR),  amyE::Pveg-sgRNA_prfA(CmR)

value: LB with 0.04% w/v xylose


title: 25DAG_2KN_NC1-3

value: wild type


title: 25DAG_2KN_NC1-2

value: shoot


title: input_H3K36R_embryo_rep2

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

institute: Max Planck Institute of Biochemistry

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization)
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of H3K36me2 enriched regions in 21-24 hr wt embryos and in wt 3rd instar larvae.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the H3K36me2 and H3K27me3 ChIP-seq datasets from H3K36A and H3K36R mutants to the corresponding wild-type H3K36me2 and H3K27me3 ChIP-seq datasets respectively.
Genome_build: dm6
Supplementary_files_format_and_content: Bedgraph files (for visualizing ChIP-seq datasets) contain the normalized number of reads per million reads per 200 bp bins covering the 7 chromosomal arms of the Drosophila genome.

organism: Drosophila melanogaster

source_name: 21-24 hr old H3K36R mutant embryos

growth_protocol: Drosophila embryos were grown on standard medium at 25˚C

extract_protocol:
Lysates were clarified from sonicated fixed nuclei (for embryos) and from sonicated fixed hand-dissected CNS and imaginal disc tissues (for 3rd instar larvae). Histone-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in at a 1:1 ratio of dm / dp chromatin before the addition of the antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq kit.

tag: genotype/variation

value: H3K36R mutant

tag: devepmental stage

value: 21-24 hr old embryo


title: input_H3K36R_embryo_rep1


title: 25DAG_2KN_NC1-1


title: G62_S10_L001

description: RNAseq matrix table results


title: rend4_GLB452

value: GLB452, see Data S1 in paper for strain details

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 25 uM IPTG, 0.015% w/v xylose


title: H3K36me2_H3K36R_embryo_rep2

tag: chip antibody

value: H3K36me2 (Abcam ab9049)


title: 16DAG_02KN_258-3


title: G62_S9_L004

description: RNAseq matrix table results

value: Hek293-EBNA1-6E ALG6/UGGT2-/-


title: 181113_CEMBA_mm_P56_P63_RS2_181113_P7_181113_P8_B8_ad008

value: PTLp

value: male


title: G62_S9_L003

description: RNAseq matrix table results


title: G62_S10_L004

description: RNAseq matrix table results

value: Hek293-EBNA1-6E ALG6/UGGT12-/-


title: 16DAG_02KN_258-2


title: rend3_GLB452

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 10 uM IPTG, 0.5% w/v xylose


title: G62_S9_L002

description: RNAseq matrix table results


title: 16DAG_02KN_258-1


title: H3K27me3_H3K36R_embryo_rep2

value: H3K27me3 (Cell Signaling (#9733))


title: 16DAG_02KN_NC1-3


title: rend1_GLB455

value: GLB455, see Data S1 in paper for strain details

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 0.2% w/v xylose,  100 uM IPTG


title: H3K27me3_H3K36R_embryo_rep1


title: G62_S9_L001

description: RNAseq matrix table results


title: G62_S8_L004

description: RNAseq matrix table results


title: 16DAG_02KN_NC1-2


title: G62_S10_L002

description: RNAseq matrix table results


title: rend5_GLB452

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 500 uM IPTG


title: input_H3K36R_larvae_rep2

source_name: H3K36R mutant 3rd instar larvae

tag: developmental stage

value: 3rd instar larvae

tag: antibody


title: input_H3K36R_larvae_rep1


title: G62_S8_L003

description: RNAseq matrix table results


title: 16DAG_02KN_NC1-1

value: wild type


title: H3K36me2_H3K36R_larvae_rep2


title: rend1_GLB452

tag: strain

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 10 uM IPTG


title: competition_amplicons_pilot_I

description: UMI collapsed barcode for each strain wer tallied and demultiplexed for PCR1 and PCR2 indices.

data_processing:
Base calls performed using Casava version 1.7.
UMIs collapsed barcode counts for each strain in each condition (demultiplexed from PCR indices in the read) were counted using custom Matlab scripts. See Data S6 from paper for details on amplicon.
genome build: N/A
Library strategy: PCR amplicons with cell barcodes, UMIs, and multiplexing indices.

growth_protocol: Overnight cultures started from fresh colonies were pooled and diluted to OD600 = 0.01. At OD600 =0.1, the pool were diluted to OD600 = 0.0001 in 25 mL pre-warmed medium. The culture was kept in a 125 mL flask at 37C with aeration (200 rpm) until OD600 reached 0.3.

extract_protocol:
8 mL of culture (from the pool of barcoded strains in competition) was collected at OD600=0.1 and mixed with 0.8 mL of 10:1 ethanol/phenol stop solution by rapid inversion. Cells were pelleted at 3000 rcf at 4∘C for 10 min and the supernatant decanted. The cell pellets were stored at -80∘C until DNA extraction. To extract genomic DNA (gDNA), we used the Promega Wizard gDNA extraction kit, following the manufacturer’s protocol (scaling reagents volumes by 1/3×).
Amplicons were generated by two rounds of nested PCRs to append UMIs, multiplexing indices, and sequencing adapters.

value: strains GLB115, GLB452, GLB434, GLB435, see Data S1 in paper for strain details

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020), with 500 uM IPTG.


title: H3K36me2_H3K36R_embryo_rep1

value: H3K36R mutant

value: 21-24 hr old embryo


title: G62_S8_L002

description: RNAseq matrix table results


title: H3K36me2_H3K36R_larvae_rep1

value: H3K36me2 (Abcam ab9049)


title: rend2_GLB452

value: GLB452, see Data S1 in paper for strain details

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 500 uM IPTG, 0.5% w/v xylose


title: 16DAG_2KN_258-3

value: shoot

value: 2 mM


title: competition_amplicons_pilot_H

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with 25 uM IPTG, 0.015% w/v xylose.


title: rend2_GLB455

value: Conditioned MCC medium (Parker et al, Cell Syst. 2020) with 1% glycerol, 1 mM IPTG, 0.5% w/v xylose


title: 16DAG_2KN_258-2


title: G62_S8_L001

description: RNAseq matrix table results

value: Hek293-EBNA1-6E ALG6/UGGT2-/-


title: competition_amplicons_pilot_F

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with 15 uM IPTG, 0.035% w/v xylose.


title: H3K27me3_H3K36R_larvae_rep2

value: H3K27me3 (Cell Signaling (#9733))


title: competition_amplicons_pilot_G

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with 25 uM IPTG, 0.035% w/v xylose.


title: G62_S7_L004

description: RNAseq matrix table results


title: 16DAG_2KN_258-1


title: G62_S7_L003

description: RNAseq matrix table results


title: G62_S7_L002

description: RNAseq matrix table results


title: competition_amplicons_pilot_E

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020) with 10 uM IPTG, 0.5 w/v xylose.


title: input_wt_larvae_rep2

source_name: H3K36 wild-type 3rd instar larvae

value: 3rd instar larvae

value: wildtype


title: H3K27me3_H3K36R_larvae_rep1


title: competition_amplicons_E3_TGACCA

value: Pool of strains, see Data S1 in paper for strains included in pool

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020). Amplicon pool corresponding to multiple samples grown in different inducer concentrations. Refer to Data S3 in paper for details of each competition pool.


title: 16DAG_2KN_NC1-2

value: wild type


title: 16DAG_2KN_NC1-3


title: competition_amplicons_E3_GGCTAC


title: H3K36me2_wt_larvae_rep2

value: H3K36me2 (Abcam ab9049)


title: Pri-cis3

city: Shanghai

first: sujuan

last: xu

address: No.180, Fenglin Road

institute: Zhongshan Hospital

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: wild type PTEC

growth_protocol: solation of proximal tubular cells was performed as previously described .After reaching 70∼80% confluence, the cells were switched to medium without FBS at least 12 h before the experiments .

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: Wild-type PTECs treated cisplatin and infected with Ad-FXRα2 or Ad-VP16

tag: infection

value: Male

value: kidney


title: competition_amplicons_E3_GATCAG


title: Pri-cis2

tag: tissue


title: input_wt_larvae_rep1


title: G62_S6_L004

description: RNAseq matrix table results

source_name: Biological replicate 3, technical replicate 4

value: Hek293-EBNA1-6E ALG6/UGGT1-/-


title: G62_S6_L002

description: RNAseq matrix table results

source_name: Biological replicate 3, technical replicate 2


title: G62_S6_L003

description: RNAseq matrix table results

source_name: Biological replicate 3, technical replicate 3


title: H3K36me2_wt_larvae_rep1


title: Pri-cis1


title: competition_amplicons_E3_CAGATC


title: Pri-cis-FXR3


title: competition_amplicons_E3_ACTTGA


title: G62_S6_L001

description: RNAseq matrix table results

source_name: Biological replicate 3, technical replicate 1


title: G62_S5_L004

description: RNAseq matrix table results

source_name: Biological replicate 2, technical replicate 4


title: input_H3K36A_embryos_rep2

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization)
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of H3K36me2 enriched regions in 21-24 hr wt embryos and in wt 3rd instar larvae.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the H3K36me2 and H3K27me3 ChIP-seq datasets from H3K36A and H3K36R mutants to the wild-type H3K36me2 and H3K27me3 ChIP-seq datasets respectively.
Genome_build: dm6
Supplementary_files_format_and_content: Bedgraph files (for visualizing ChIP-seq datasets) contain the normalized number of reads per million reads per 200 bp bins covering the 7 chromosomal arms of the Drosophila genome.

source_name: 21-24 hr old H3K36A mutant embryos

value: 21-24 hr old embryo

value: H3K36A mutant


title: G62_S7_L001

description: RNAseq matrix table results


title: competition_amplicons_E3_CGATGT

source_name: Bacteria


title: H3K27me3_wt_larvae_rep2


title: competition_amplicons_E3_ACAGTG


title: G62_S5_L003

description: RNAseq matrix table results

source_name: Biological replicate 2, technical replicate 3


title: Pri-cis-FXR1


title: input_H3K36A_embryos_rep1


title: 16DAG_2KN_NC1-1

value: shoot

value: 2 mM


title: Pri-cis-FXR2


title: competition_amplicons_E2_T4


title: G62_S5_L002

description: RNAseq matrix table results

source_name: Biological replicate 2, technical replicate 2


title: input_wt_embryos_rep2

source_name: 21-24 hr old Oregon R embryos


title: Choroid plexus, embryo-3 (E16.5)_TRAP-seq

city: Boston

first: Maria

last: Lehtinen

address: 300 Longwood Ave

department: Pathology

institute: Boston Children's Hospital

description:
E_2
ChP-tagged mRNAs

data_processing:
The raw fastq data of 50-bp single-end sequencing reads were aligned to the mouse mm10 reference genome using STAR 2.4.0 RNA-Seq aligner.
The mapped reads were processed with cufflinks software to calculate gene FPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

source_name: Choroid plexus, embryo

extract_protocol:
Translating Ribosome Affinity Purification
Clonetech SMARTer Pico with ribodepletion
The quality of prepared bar-coded libraries was assessed using an Advanced Analytical-fragment Analyzer before mixing for sequencing on the Illumina HiSeq platform at the MIT BioMicro Center.

tag: age at harvest

value: embryonic day 16.5

value: FoxJ1:cre x bacTRAP (EGFP:L10a)

value: choroid plexus (ChP)


title: competition_amplicons_E2_T3


title: input_wt_embryos_rep1


title: G62_S5_L001

description: RNAseq matrix table results

source_name: Biological replicate 2, technical replicate 1


title: H3K27me3_wt_larvae_rep1

value: H3K27me3 (Cell Signaling (#9733))


title: competition_amplicons_E2_T2


title: H3K36me2_wt_embryos_rep2


title: competition_amplicons_E2_T1


title: G62_S4_L004

description: RNAseq matrix table results

source_name: Biological replicate 1, technical replicate 4


title: H3K36me2_H3K36A_embryos_rep1


title: competition_amplicons_E1_T3


title: Choroid plexus, adult-3 (P60)_TRAP-seq

description:
AM_2
ChP-tagged mRNAs

source_name: Choroid plexus, adult

value: 60 days


title: Choroid plexus, embryo-1 (E16.5)_TRAP-seq

description:
E_0
ChP-tagged mRNAs


title: competition_amplicons_E2_T0


title: Choroid plexus, adult-1 (P60)_TRAP-seq

description:
AM_0
ChP-tagged mRNAs


title: G62_S4_L002

description: RNAseq matrix table results

source_name: Biological replicate 1, technical replicate 2


title: Choroid plexus, embryo-2 (E16.5)_TRAP-seq

description:
E_1
ChP-tagged mRNAs


title: G62_S3_L003

description: RNAseq matrix table results

value: Hek293-EBNA1-6E ALG6-/-


title: H3K36me2_H3K36A_embryos_rep2


title: G62_S4_L003

description: RNAseq matrix table results

source_name: Biological replicate 1, technical replicate 3


title: competition_amplicons_E1_T2

value: Pool of strains, see Data S1 in paper for strains included in pool


title: H3K27me3_H3K36A_embryos_rep2


title: G62_S3_L004

description: RNAseq matrix table results


title: t0_MCCM_REP3

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

description: total RNA with depletion of rRNA

data_processing:
The quality of cDNA reads was analyzed using FastQC (version 0.11.2). Paired-end reads were aligned to the LUZ19 and P. aeruginosa PAO1 reference genomes (NC_010326.1 and NC_002516.2) using Bowtie 2. Next, the aligned reads were assigned to gene features using featureCounts. Reads that mapped to rRNA (60-80%,) were removed in silico.
Subsequently, counts were first normalized by gene length and then by the number of non-ribosomal reads in each sample to obtain RPKM values. Samples variance was analyzed using Principal Component Analysis (PCA) in R and outliers were excluded for further analysis, namely samples from assay MCCM_3 were discharged for further analysis being considered samples from two independent assays in MCCM and samples from three independent assays for LB medium for further analysis.
Differential gene expression analysis was performed using negative binomial distribution test from DESeq Bioconductor package in R. ANOVA test was performed to identify the most significantly up- or down-regulated genes. The p-values were adjusted using the “BH” method, which is the standard method built into the DEseq package) and are referred to as “padj”.
Genome_build: NC_002516.2
Genome_build: NC_010326.1
Supplementary_files_format_and_content: csv file containing RPKM values for all LUZ19 and PA01 genes in every sample
Supplementary_files_format_and_content: xlsx containing differential expression analysis of PA01 genes between different media (MCCM vs LB) without phage infection (0m)
Supplementary_files_format_and_content: xlsx containing differential expression analysis of LUZ19 and PA01 genes between timepoints in each medium

organism: Pseudomonas aeruginosa PAO1

source_name: early exponential bacteria

growth_protocol: P. aeruginosa PAO1 overnight cultures were diluted 1:100 in 25 mL of either fresh LB or MCCM medium and grown to the early-exponential phase (OD600nm = 0.3, corresponding to approximately 2×108 CFU/mL). At this point, the number of colony forming units of the culture (CFU/mL) were counted by plating serial dilutions in LB plates (21) and a sample of 4.5 mL of culture was taken simultaneously (t=0 min). This sample was immediately mixed with 1:10 vol of an ice-cold stop solution (1:10 buffered phenol, 9:10 absolute EtOH) and kept on ice to stabilize RNA.

extract_protocol:
Total RNA was extracted from cell pellets using the Purelink RNA Mini Kit (Invitrogen), according to the manufacturer’s instructions.. Subsequently, each sample was treated with TURBO DNAse (Invitrogen) at 37°C to remove genomic DNA (gDNA) and then co-precipitated overnight at -20°C with 1:10 (v/v) NaOAc and 2.5 vol of absolute EtOH.   Precipitated RNA samples were centrifuged (16,000 g, 4 °C, 1h) and pellets were washed twice with 70% (v/v) EtOH. The air-dried RNA pellets were dissolved in 60 µl of DNAse and RNAse free water (Invitrogen). Total RNA concentration and purity were measured on a Nanodrop 2000 Spectrophotometer (Thermo Scientific, MA, USA) and on a Qubit 4 Fluorometer (ThermoFisher Scientific). In addition, the absence of gDNA contamination was confirmed by PCR using specific primers for both phage LUZ19 (Forward: 5’-ccgacaagatcgtccgcatgc-3’, Reverse: 5’-ggctgaagctacgcttggcc-3’) and its host (Forward: 5’-cggtcggaatctctacgcacc-3’, Reverse: 5’-cgacgccaacaacgccacg-3’). To assess RNA integrity, samples were analyzed on a Bioanalyzer (Agilent, Santa Clara, California, US) with a RNA 6000 Nano Kit (Agilent) according to manufacturer’s instructions. Samples with good RNA integrity (RNA integrity number (RIN) > 8) were treated with RiboMinus™ Transcriptome Isolation Kit (bacteria) (Invitrogen) to deplete ribosomal RNA (rRNA), according to the manufacturer’s instructions.
Depleted rRNA samples were precipitated and washed as mentioned previously and resuspended in 18-19 µL of Fragment Prime Finish mix from TruSeq Stranded mRNA Library Prep (Illumina). Successful rRNA depletion was verified on a Bioanalyzer and the final concentrations were determined using the Qubit 4 Fluorometer (Invitrogen).rRNA-depleted samples were processed immediately, according to TruSeq Stranded mRNA Library Prep recommendations. In the end, cDNA libraries were evaluated on a Bioanalyzer (Agilent) to confirm average fragments between the range of 200-300 bp and final concentrations were measured on a Qubit. The libraries’ normalization and pooling were performed according to MiniSeq System Denature and Dilute Libraries Guide: protocol A from Illumina. For each run, a library of three samples with equimolar amounts was combined with PhiX control (spike-in of 0.5-2%) and paired end sequenced (2×75 bp) on an in-house Illumina Miniseq sequencer.

treatment_protocol: At t=5 (early infection), t=10 (middle infection) and t=15 (late infection) minutes post-infection, 4.5 mL of culture was mixed with chilled stop solution and placed on ice. Immediately after, all collected samples were frozen at -80°C to block RNA transcription and degradation until sample processing.  Biologically independent infection experiments, showing a CFU reduction of at least 95% within 5 min post-infection (only 5% bacterial culture survival to LUZ19 infection) were considered as synchronized infection. Triplicate samples from synchronized infections were used for total RNA extraction.

tag: medium

value: MCCM

tag: Stage

value: early exponential

tag: treatment time

value: untreated

tag: phage moi

value: phage wasn't added

tag: bacteria strain


title: t0_MCCM_REP2

description: total RNA with depletion of rRNA


title: H3K27me3_wt_embryos_rep2

tag: genotype

value: wildtype


title: H3K27me3_H3K36A_embryos_rep1


title: G62_S3_L002

description: RNAseq matrix table results


title: Choroid plexus, adult-2 (P60)_TRAP-seq

description:
AM_1
ChP-tagged mRNAs


title: G62_S4_L001

description: RNAseq matrix table results

source_name: Biological replicate 1, technical replicate 1

value: Hek293-EBNA1-6E ALG6/UGGT1-/-


title: competition_amplicons_E1_T4

tag: growth medium

value: Conditioned MCC medium with 1% glycerol (Parker et al, Cell Syt. 2020). Amplicon pool corresponding to multiple samples grown in different inducer concentrations. Refer to Data S3 in paper for details of each competition pool.


title: H3K36me2_wt_embryos_rep1

value: 21-24 hr old embryo

value: H3K36me2 (Abcam ab9049)


title: t0_MCCM_REP1

description: total RNA with depletion of rRNA


title: competition_amplicons_E1_T1


title: competition_amplicons_E1_T0


title: G62_S3_L001

description: RNAseq matrix table results

tag: cell line


title: t0_LB_REP3

description: total RNA with depletion of rRNA

value: LB


title: SARS-CoV-2 WA1 viral stock

city: Atlanta

first: Thomas

middle: H

last: Vanderford

state: GA

address: 954 Gatewood Rd.

department: Yerkes National Primate Research Center

institute: Emory University

data_processing:
Trimmomatic v0.36 with 'SLIDINGWINDOW:4:15' and 'MINLEN:36'
blat alignment of ready to SARS-CoV-2 WA1 (MT246667.1) with '-fastMap'
Custom Python scripts to count reads with deletions and mutations at the Spike Furin cleavage site

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Tissue culture expansion

growth_protocol: SARS-CoV-2 was obtained from BEI Resources and grown on Vero E6 cells and frozen.

extract_protocol:
An aliquot of the stock was extracted using the QiaAmp viral RNA mini kit.
First strand synthesis was performed with the Life Technologies' Superscript III RT followed by second strand synthesis with NEBNext Ultra II RNA Second Strand Synthesis kit. A MiSeq library was made using the Nextera XT DNA Library prep kit for single-end sequencing on an Illumina MiSeq.

value: WA1 viral stock


title: G62_S2_L004

description: RNAseq matrix table results


title: G62_S2_L003

description: RNAseq matrix table results


title: IMQ4

first: Xilin

last: Zhang

state: Shanghai

address: No. 1278#, Baode Rd, Jingan District

department: Dermatology

institute: Shanghai Skin Disease Hospital

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the human genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using KEGG database and GSEA plots
Genome_build: Mus_musculus.GRCm38.90,ftp://ftp.ensembl.org/pub/release-90/gtf/mus_musculus/ Mus_musculus.GRCm38.90.chr.gtf.gz
Supplementary_files_format_and_content: gene_exp_with_symbol_LC.txt

source_name: Epidermis

extract_protocol:
RNA was isolated using the standard TRIzol protocol.
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

treatment_protocol: Mice were randomly allocated into the following groups: control group and IMQ group.

tag: cell type

value: Epidermal Langerhans cells

value: Epidermis

tag: age

value: 8 weeks

value: wild type

tag: treatment

value: IMQ application on shaved back skin for 3 days


title: G62_S2_L001

description: RNAseq matrix table results

value: Hek293-EBNA1-6E ALG6-/-


title: IMQ3


title: IMQ1


title: t0_LB_REP1

description: total RNA with depletion of rRNA


title: 140 C>T CT_1

first: Tatsuya

last: Kobayashi

address: 50 Blossom st

department: Endocrine unit

institute: Massachusetts general hospital

data_processing:
Low quality reads were filtered with adaptors and reads with unknown bases with software SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05 -A 0.25. Mapped clean reads to mm9 reference using HISAT2 V. 2.0.4 with the parameters, --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM; readcounts

source_name: 140 C>T CT

extract_protocol: Rib cartilage was treated with .2% Collagenase II in Dmem 10% FBS medium overnight. Cells were filtered and plated. RNA was extracted using trizol reagent.

tag: genotype/variation

value: C>T base change

value: 10 day-old

value: Rib cartilage

value: Chondrocyetes


title: G62_S11_L004

description: RNAseq matrix table results

source_name: Biological replicate 2, technical replicate 4

value: Hek293-EBNA1-6E ALG6/UGGT12-/-


title: 140 C>T CT_2


title: G62_S2_L002

description: RNAseq matrix table results


title: IMQ2


title: G62_S1_L004

description: RNAseq matrix table results


title: Hairpin_L

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

data_processing:
Fastq trimmed to remove adapters using Fastx clipper
Fastq aligned to N. brasiliensis coding sequences (WBPS v14)
Alignment Bam fles converted to bed files using Bedtools v2
22G and 23G RNAs selected using custom perl script
counts mapping to transcripts quantified using bedtools v2 intersectBed
Genome_build: nippostrongylus_brasiliensis.PRJEB511.WBPS14.CDS_transcripts
Supplementary_files_format_and_content: #transcript #start #end #counts

organism: Nippostrongylus brasiliensis

source_name: Whole organism

extract_protocol:
RNA was extracted using trizol reagent and treated with RppH (NEB) to remove 5' phosphates
Illumina Truseq small RNA

tag: lentivirus

value: long hairpin

tag: 5' treatment

value: RppH

tag: molecule subtype

value: small RNA (18-30nt)


title: 140 CG WT-2

source_name: 140 CG WT

tag: strain

value: wild type for the CG mutants

tag: tissue


title: Hairpin_Hyb

value: long hairpin hybrid


title: WT3

value: Vaseline application on shaved back skin for 3 days


title: Hairpin_S

value: shot hairpin


title: H3K27me3_wt_embryos_rep1

tag: developmental stage

value: 21-24 hr old embryo

tag: antibody

value: H3K27me3 (Cell Signaling (#9733))

value: wildtype


title: t0_LB_REP2

description: total RNA with depletion of rRNA

tag: medium

value: LB

tag: Stage

value: early exponential

tag: treatment time

value: untreated

value: phage wasn't added


title: G62_S1_L003

description: RNAseq matrix table results

value: Hek293-EBNA1-6E ALG6-/-


title: miR

value: shRNAmir in 3UTR of mcherry


title: 140 C>T WT _1

source_name: 140 C>T WT

value: wild type for the C>T mutant

value: 10 day-old

value: Rib cartilage

value: Chondrocyetes


title: 140 C>T WT _2


title: WT2

value: Epidermal Langerhans cells

value: Epidermis

value: 8 weeks

tag: genotype

value: wild type


title: G62_S1_L002

description: RNAseq matrix table results


title: 140 CG CG-1

source_name: 140 CG CG

value: 3p seed region mutation


title: WT1

value: Vaseline application on shaved back skin for 3 days


title: WT control

value: RppH

value: small RNA (18-30nt)


title: WT4


title: 140 CG WT-1

value: wildtype for the CG mutants


title: G62_S1_L001

description: RNAseq matrix table results


title: EV

value: Empty vector control


title: 140 CG CG-2


title: GRO_xrn1_raw_data_t0

status: Public on Nov 27 2020

type: RNA

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
TR data at time t0
GRO labelling for xrn1 strain, t0: before adding KCl, Replicate 1

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a Fujifilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines (RA data) or uracils (TR data) present in each probe-coding strand as described in García-Martinez et al. 2004.

organism: Saccharomyces cerevisiae

source_name: xrn1 haploid strain

label_protocol: For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For mRNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Cells were grown in YPD at 30ºC for at least 15 hours to reach early exponential phase at 0.4 OD600. Then, we added KCl to 0.6M. At the indicated times after KCl addition cells were spun-down and collected. Each sample was done in triplicate, except for the cDNA experiment in xrn1 strain that was only one replicate

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

value: BY4741 xrn1


title: GRO_xrn1_raw_data_t15

description:
TR data at time t15 after KCl addition
GRO labelling for xrn1 strain, t15: 15 min after adding KCl, Replicate 1


title: GRO_xrn1_raw_data_t8

description:
TR data at time t8 after KCl addition
GRO labelling for xrn1 strain, t8: 8 min after adding KCl, Replicate 1


title: GRO_wt_raw_data_t45

description:
TR data at time t45 after KCl addition
GRO labelling for wt strain, t45: 45 min after adding KCl, Replicate 1

source_name: wild type haploid strain


title: GRO_wt_raw_data_t8

description:
TR data at time t8 after KCl addition
GRO labelling for wt strain, t8: 8 min after adding KCl, Replicate 1


title: Streptomyces coelicolor_M1146+ACT_30h

city: Suita

first: Katsuaki

last: Nitta

state: Osaka

address: Yamadaoka 2-1

country: Japan

institute: Osaka University

data_processing:
Generating reference genome by software STAR ver. 2.7
Read mapping to reference genome by software STAR ver. 2.7
Read counting by R-package feature counts
RLE normalized counts were generated by R-package DESeq2
Genome_build: ASM20383v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Streptomyces coelicolor

source_name: Streptomyces coelicolor

growth_protocol: Bacterial strains were grown in 50 mL liquid minimum nutrition medium with same composition as previous study in well siliconized 250 mL flasks containing stainless-steel springs. For inoculation, 1×109 CFU of spores were inoculated to the 50 mL medium. Incubation speed and temperature was set to 220 rpm and 30°C respectively.

extract_protocol:
Cells were disaggregated by double autoclaved empty tip and 0.17 mL of 15 mg/mL lysozyme was added to the cells and incubated at 30°C for 10 minutes. The solution including cells were transferred to tube containing lysing matrix E (MPbio medicals) and 0.6 mL RLT buffer (Qiagen) supplemented with beta-mercaptoethanol (100: 1, v/v), and vortexed for 5 seconds. Three pulses were applied to the tube by Fast Prep (6.5 m/s, 30s) while the tubes were kept on ice between pulses for 30 seconds. The tubes were centrifuged at 10000 rpm and 4°C for 1 minute and the lysate was recovered. After centrifuging heavy PLG tube to pack the resine for 1min, 0.65 mL recovered lysate was transferred to the heavy PLG tube. 0.65 mL chloroform, isoamyl alcohol and acid phenol mixture was added to the lysate in heavy PLG tube and mixed by inversion for 1 minute. The heavy PLG tubes containing extracts were centrifuged for 5 minutes and superior aqueous phase was recovered. RNA purification was performed with Direct-zol RNA MiniPrep Plus (Zymo research). After 0.6 mL ethanol was added to recovered 0.6 mL of aqueous phase and mixing by pipette, Zymo-spin ⅢCG column was assembled to collection tube, and 0.6 mL mixture solution was transferred to the assembled column-collection tube, and centrifuged at 10000 rpm for 30 seconds. Flow through from the collection tube was discarded and remaining 0.6 mL of mixture of aqueous extract and ethanol was transferred to the assembled column-collection tube, consequently centrifuged at 10000 rpm for 30 seconds. The flow through in the collection tube was discarded again. RNA wash buffer completed with ethanol (0.4 mL) was added to the column, centrifuged at 10000 rpm for 30 seconds and the flow-through was discarded. To the column matrix, 80 µL of DNase (6 U/µL) was added and incubated at 30°C for 15 minutes. After incubation, two cycles of RNA washing (Adding 0.4 mL of Direct-zol RNA prewash to the column, centrifuging at 10000 rpm for 30 seconds and discarding the flow through). To the column, 0.7 mL RNA wash buffer was added and centrifuged for 2 minutes to ensure complete removal of wash buffer. Consequently, the column was transferred to new RNase-free tube, 50 µL of DNase/RNase-free water was added and incubated at room temperature for 1 minute. The column with sample containing water was centrifuged at 10000 rpm for 1 minute, and tube with RNA sample was frozen by liquid nitrogen until next step.
The rRNA depleted RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at　4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand　cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The　first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end　of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high　fidelity DNA polymerase. The TruSeq barcode sequences,　which are part of the 5' and 3'TruSeq sequencing adapters, are included in Table 2. The cDNA was　purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by　capillary electrophoresis

treatment_protocol: Before sampling, all materials for sampling was autoclaved two times to avoid RNase contamination. Based on growth curve, expectedly more than 2.0 mg DCW cell cultures was sampled and mixed with the twice amount of RNA protection reagent (Qiagen) immediately. The cells were vortexed for 10 seconds, kept for 5 minutes at room temperature and centrifuged at 10000 rpm, 20°C for 10 minutes. Supernatant was eliminated as much as possible, and the cells were quenched by liquid nitrogen immediately and kept at -80°C until RNA isolation.

tag: time


title: Streptomyces coelicolor_M1146+ACT_50h


title: Streptomyces coelicolor_M1146+ACT_44h


title: Streptomyces coelicolor_M145_cAMP_50h_2

treatment_protocol: cAMP was supplemented at 48h and samples were collected at 50h. Before sampling, all materials for sampling was autoclaved two times to avoid RNase contamination. Based on growth curve, expectedly more than 2.0 mg DCW cell cultures was sampled and mixed with the twice amount of RNA protection reagent (Qiagen) immediately. The cells were vortexed for 10 seconds, kept for 5 minutes at room temperature and centrifuged at 10000 rpm, 20°C for 10 minutes. Supernatant was eliminated as much as possible, and the cells were quenched by liquid nitrogen immediately and kept at -80°C until RNA isolation.

value: cAMP


title: Streptomyces coelicolor_M145_50h_1

value: control


title: Streptomyces coelicolor_M145_50h_2


title: Streptomyces coelicolor_M145_50h_3


title: Streptomyces coelicolor_M145_cAMP_50h_3


title: Streptomyces coelicolor_M145_cAMP_50h_1


title: Streptomyces coelicolor_M1146+ACT_28h


title: Streptomyces coelicolor_M1146+ACT_22h


title: Streptomyces coelicolor_M1146+ACT_26h


title: Streptomyces coelicolor_M1146+ACT_34h


title: Streptomyces coelicolor_M1146+ACT_38h


title: Streptomyces coelicolor_M1146+ACT_32h


title: GRO_wt_raw_data_t30

description:
TR data at time t30 after KCl addition
GRO labelling for wt strain, t30: 30 min after adding KCl, Replicate 1


title: GRO_wt_raw_data_t15

description:
TR data at time t15 after KCl addition
GRO labelling for wt strain, t15: 15 min after adding KCl, Replicate 1


title: GRO_xrn1_raw_data_t30

description:
TR data at time t30 after KCl addition
GRO labelling for xrn1 strain, t30: 30 min after adding KCl, Replicate 1


title: Streptomyces coelicolor_M1146_50h


title: Streptomyces coelicolor_M1146+ACT_18h


title: GRO_xrn1_raw_data_t45

description:
TR data at time t45 after KCl addition
GRO labelling for xrn1 strain, t45: 45 min after adding KCl, Replicate 1


title: P_HC_C1

city: Heifei

first: Ming-Yue

address: Anhui Medical University of meishan road 81

institute: Anhui Medical University

description: circRNA expression in plasma from healthy volunteer C1

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: To asses the array images Agilent Feature Extraction software was applied. Quantile normalization and subsequent data processing were performed with the GeneSpring GX v11.5.1 software package (Agilent Technologies).After quantile normalization of the raw data, circRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were retained for further analyses..Differentially expressed circRNAs with statistical significance were identified through Volcano Plot filtering and Hierarchical Clustering.

source_name: Plasma, HC

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then,circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).  The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from plasma by using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacture’s protocol. The purity and concentration of RNA was evaluated with the NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).

treatment_protocol: The blood was centrifuged by spinning at 2000 × g for 10 min at room temperature. Plasma was then carefully transferred to a fresh RNase-free tube and stored at –80°C.

value: Plasma

tag: gender

value: female


title: GRO_wt_raw_data_t0

description:
TR data at time t0
GRO labelling for wt strain, t0: before adding KCl, Replicate 1


title: P_SLE_S21

description: circRNA expression in plasma from patient S21

source_name: Plasma, SLE


title: Streptomyces coelicolor_M1146_38h


title: P_HC_C5

description: circRNA expression in plasma from healthy volunteer C5


title: Streptomyces coelicolor_M1146_44h


title: P_SLE_S22

description: circRNA expression in plasma from patient S22


title: P_HC_C2

description: circRNA expression in plasma from healthy volunteer C2


title: P_HC_C4

description: circRNA expression in plasma from healthy volunteer C4


title: P_SLE_S42

description: circRNA expression in plasma from patient S42


title: Streptomyces coelicolor_M1146_34h


title: P_SLE_S19

description: circRNA expression in plasma from patient S19


title: Streptomyces coelicolor_M1146_26h


title: Streptomyces coelicolor_M1146_28h


title: Streptomyces coelicolor_M1146_22h


title: Streptomyces coelicolor_M1146_30h


title: Streptomyces coelicolor_M1146_32h


title: EV10 mRNA-Seq r0 replicate 1

city: Beijing

first: Hui

last: Jiang

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to R64-1-1 whole genome using STAR v2.6.1a with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: R64-1-1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

molecule: polyA RNA

organism: Saccharomyces cerevisiae W303

source_name: W303-1A, r0, polyA RNA

growth_protocol: Yeast cells were grown in SCD (0.67% yeast nitrogen base without amino acids, 0.079% complete supplement mixture, and 2% glucose) to mid-log phase (OD 0.5-0.8).

extract_protocol:
Total RNA was isolated using hot phenol method (Lyne et al., 2003), then polyA RNA was purified from total RNA by Oligo d(T)25 Magnetic beads (NEB). Ribosome protected mRNA was isolated as described previously (Ingolia et al., 2012; Ingolia et al., 2009). Briefly, cells were treated with 100 μg/ml cycloheximide for 2 min, and flash-frozen in polysome lysis buffer. Cell lysates were treated with 7.5 μl RNase Ⅰ (Ambion) at room temperature for 1 hour, and separated by sucrose density gradient centrifugation. Monosome fractions were collected, and RNA was extracted by Trizol reagent.
Libraries for mRNA abundance examination was prepared by using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Libraries for ribosome footprints examination was prepared by linker ligation, reverse transcription, circularization as described previously (Ingolia et al., 2012).

tag: growth phase

value: mid-log phase


title: EV10 mRNA-Seq r0 CUP1p-INH1 replicate 2

source_name: W303-1A, r0  CUP1p-INH1, polyA RNA

value: rho0 CUP1p-INH1


title: EV10 mRNA-Seq r0 replicate 2


title: EV9 mRNA-Seq snf1D mig1D EB treatment replicate 1

source_name: W303-1A, snf1D mig1D EB treatment, polyA RNA

value: snf1 mig1

value: 25 µg/ml Ethidium Bromide, 48 hour


title: EV10 mRNA-Seq r0 replicate 3


title: EV10 mRNA-Seq WT replicate 3

source_name: W303-1A, polyA RNA

value: WT


title: EV10 mRNA-Seq r0 CUP1p-INH1 replicate 3


title: EV10 mRNA-Seq r0 CUP1p-INH1 replicate 1


title: EV9 mRNA-Seq snf1D mig1D EB treatment replicate 3


title: EV10 mRNA-Seq r0 CUP1p-INH1+Cu2+ replicate 2

source_name: W303-1A, r0 CUP1p-INH1+Cu2+, polyA RNA

value: 10mM CuSO4 12 hour


title: EV9 mRNA-Seq snf1D mig1D EB treatment replicate 2


title: EV9 mRNA-Seq snf1D EB treatment replicate 2

source_name: W303-1A, snf1D EB treatment, polyA RNA


title: EV10 mRNA-Seq WT replicate 2


title: Streptomyces coelicolor_M1146_18h


title: EV9 mRNA-Seq snf1D EB treatment replicate 3


title: EV8 mRNA-Seq snf1D EB treatment replicate 1


title: EV8 mRNA-Seq EB treatment replicate 3

source_name: W303-1A, EB treatment, polyA RNA


title: EV8 mRNA-Seq EB treatment replicate 2


title: EV8 mRNA-Seq snf1D EB treatment replicate 2


title: EV8 mRNA-Seq snf1D EB treatment replicate 3


title: EV9 mRNA-Seq snf1D EB treatment replicate 1


title: EV8 mRNA-Seq EB treatment replicate 1


title: EV10 mRNA-Seq r0 CUP1p-INH1+Cu2+ replicate 3


title: EV8 mRNA-Seq snf1D replicate 3

source_name: W303-1A, snf1D, polyA RNA


title: EV10 mRNA-Seq r0 CUP1p-INH1+Cu2+ replicate 1


title: EV8 mRNA-Seq snf1D replicate 1


title: EV8 mRNA-Seq WT replicate 2


title: EV10 mRNA-Seq WT replicate 1


title: EV8 mRNA-Seq WT replicate 3


title: EV7 mRNA-Seq r0 puf3-15A replicate 2

source_name: W303-1A, r0 puf3-15A, polyA RNA

value: puf3-15A rho0


title: EV7 mRNA-Seq r0 puf3-15A replicate 1


title: EV4 mRNA-Seq r0 replicate 3


title: EV7 mRNA-Seq r0 puf3-15A replicate 3


title: EV7 mRNA-Seq r0 replicate 3


title: EV4 mRNA-Seq r0 puf3D replicate 2

source_name: W303-1A, r0 puf3D, polyA RNA

value: puf3 rho0


title: EV8 mRNA-Seq WT replicate 1


title: EV8 mRNA-Seq snf1D replicate 2


title: EV4 mRNA-Seq r0 puf3D replicate 3


title: EV7 mRNA-Seq r0 replicate 2


title: EV7 mRNA-Seq puf3-15A replicate 1

source_name: W303-1A, puf3-15A, polyA RNA


title: EV7 mRNA-Seq r0 replicate 1


title: EV7 mRNA-Seq puf3-15A replicate 3


title: EV4 mRNA-Seq atp7D puf3D replicate 3

source_name: W303-1A, atp7D puf3D, polyA RNA

value: atp7 puf3


title: EV4 mRNA-Seq atp7D replicate 1

source_name: W303-1A, atp7D, polyA RNA


title: EV4 mRNA-Seq atp7D replicate 2


title: EV4 mRNA-Seq atp7D replicate 3


title: EV4 mRNA-Seq r0 replicate 2


title: EV4 mRNA-Seq atp7D puf3D replicate 1


title: EV4 mRNA-Seq puf3D replicate 1

source_name: W303-1A, puf3D, polyA RNA


title: EV4 mRNA-Seq atp7D puf3D replicate 2


title: EV4 mRNA-Seq r0 puf3D replicate 1


title: EV7 mRNA-Seq WT replicate 2


title: EV4 mRNA-Seq r0 replicate 1


title: EV4 mRNA-Seq puf3D replicate 3


title: EV7 mRNA-Seq puf3-15A replicate 2


title: EV4 mRNA-Seq puf3D replicate 2


title: EV7 mRNA-Seq WT replicate 1


title: EV7 mRNA-Seq WT replicate 3


title: EV4 mRNA-Seq WT replicate 2


title: EV4 mRNA-Seq WT replicate 3


title: EV3 Ribo-Seq puf3D replicate 1

data_processing:
Library strategy: Ribo-Seq
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to R64-1-1 whole genome using STAR v2.6.1a with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: R64-1-1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: W303-1A, puf3D, Ribosome protected mRNA


title: EV3 Ribo-Seq r0 puf3D replicate 1

source_name: W303-1A, r0 puf3D, Ribosome protected mRNA


title: EV3 Ribo-Seq puf3D replicate 2


title: EV3 Ribo-Seq r0 puf3D replicate 2


title: EV4 mRNA-Seq WT replicate 1


title: EV3 Ribo-Seq r0 replicate 1

source_name: W303-1A, r0, Ribosome protected mRNA


title: EV3 Ribo-Seq r0 replicate 2


title: EV1 mRNA-Seq WT replicate 6


title: EV1 mRNA-Seq r0 replicate 1

source_name: W303-1A, r0, polyA RNA


title: EV3 Ribo-Seq replicate 2

source_name: W303-1A, Ribosome protected mRNA


title: EV3 Ribo-Seq replicate 1


title: EV1 mRNA-Seq r0 replicate 2


title: EV1 mRNA-Seq atp7D replicate 2


title: EV1 mRNA-Seq WT replicate 4


title: EV1 mRNA-Seq WT replicate 5


title: EV1 mRNA-Seq atp7D replicate 3


title: EV1 mRNA-Seq cor1D replicate 3

source_name: W303-1A, cor1D, polyA RNA


title: EV1 mRNA-Seq cox9D replicate 3

source_name: W303-1A, cox9D, polyA RNA


title: EV1 mRNA-Seq cor1D replicate 2


title: EV1 mRNA-Seq WT replicate 3

source_name: W303-1A, polyA RNA


title: Wild-type brain, small RNA, replicate 3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Base calling was performed using casava.
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1).
Preliminary adapter trimming was performed on each of the samples to remove the Illumina TruSeq Small RNA adapter and primer sequences using Trimmomatric v0.33.
A second round of adapter trimming was performed using the mirdeep2 clip_adapters program.
QA/QC of the retrimmed data was performed with fastqc.  The distribution of the trimmed reads fall into two main distributions around 22 nt and 32 nt, indicating miRNAs and piRNAs are likely sequenced.
The resulting collapsed sequences were searched first against the Drosophila melanogaster (dm) piRNA sequences obtained from piRBase v1.0. Sequences that do not have a corresponding match to piRBase were searched against mature dm miRNA sequences obtained from miRBase. Sequences that do not match either piRBase or miRBase, but are between 18-22 nt in length were matched against miRBase for partial overlaps.  Anything not passing this final filter were then considered as undefined.  The large majority of these undefined sequences appear to be partial rRNA sequences.
The unique piRNA sequences identified in brain and ovary were searched against the small RNA library types in order to remove piRNAs annotated by piRBase that were actually other types of small RNAs.
The files were further filtered for a minimum count of 10 sequences found across (1) all samples; (2) wild-type samples; and (3) mutant samples.
The filtered minimum count list for the mutant and wild type for the brain and ovary were then compared to determine differential expression using edgeR.
Genome_build: dm6

source_name: brain

extract_protocol:
RNA isolation was done using the mirVana miRNA isolation kit
Libraries were prepared using the TruSeq Small RNA; Illumina Catalog# RS-200-0012.

tag: condition

value: wild type

value: brain


title: EV1 mRNA-Seq cor1D replicate 1

tag: treatment


title: EV1 mRNA-Seq cox9D replicate 2


title: EV1 mRNA-Seq r0 replicate 3


title: EV1 mRNA-Seq WT replicate 2


title: EV1 mRNA-Seq cox9D replicate 1


title: EV1 mRNA-Seq atp7D replicate 1


title: EV1 mRNA-Seq WT replicate 1


title: Wild-type brain, small RNA, replicate 2


title: Wild-type brain, small RNA, replicate 1


title: Wild-type ovary, small RNA, replicate 2

source_name: ovary

value: ovary


title: Wild-type ovary, small RNA, replicate 3


title: Mutant Tudor brain, small RNA, replicate 1

value: mutant Tudor


title: Wild-type ovary, small RNA, replicate 1


title: Mutant Tudor ovary, small RNA, replicate 2


title: Mutant Tudor ovary, small RNA, replicate 3


title: Mutant Tudor ovary, small RNA, replicate 1