title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P1_Pool96_P2_E7_ad004

status: Public on May 02 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

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 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
Assembly: mm10
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
Library strategy: snmC-seq2 & 3

source_name: 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-seq (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.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The 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, 2x1012 to 1x1013 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.

value: brain

tag: source

value: VTA

tag: target

value: SSp

value: male


title: INPUT-P-siRNA

status: Public on Apr 28 2023

type: SRA

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

description: Input from NHA-IDH WT

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads
Reads were aligned to the hg38 genome assembly using Bowtie2 (see materials and methods main paper)
htseq software was used to estimate the raw gene counts
peaks were called using MACS2 with the following setting: ChIP threshold FDR (0.1)
Assembly: hg38
Supplementary files format and content: bedgraph and bigWig files are generated from MACS2 peak calling output using bamtools

molecule: genomic DNA

organism: Homo sapiens

source_name: Normal human astrocytes

extract_protocol:
Sample fixation and nuclei preparation: After 48 hrs of transfection, all cells were fixed with 37% formaldehyde for 15 min at room temperature. After on, aspirated media, washed 1x with cold PBS and collected cells in 2ml of PBS/plate . The cells were spin at 850 rpm for 10 min at 4C. The supernatant was discard and resuspend the pellet in hypotonic buffer containing fresh protease inhibitors. Cells were incubated in ice for 5 min, then added 10% NP-40 to final concentration of 0.5% , and incubated on ice for 5 min. Cells were centrifuged at 1500 rpm 10 min at 4C. Discard the supernatant and pellet was resuspended in 2mll of TE buffer containing 2x protease inhibitors..
Sonication and DNA quantitation:  The nuclei was sonicated in 15 ml conical vial on cool chamber at optimal settings (5) 10 sec pulses at 60% , which needs to be determined per cell line. For this cells was 6 rounds which was 300 seconds. After sonications, samples were split into (2) 1.7 ml eppendorf tubes and was centrifuges 14,000 rpm 15 min at 4C. Samples were collected and mix in same supernatants and DNA was measures in triplicate using nanodrop. Measurements was averaged and dived the number by 1000.Samples were aliquoted in maximal amount of DNA but less the 500 ul total volume that was normalized in TE buffer.
Immunoprecipitaion: To the 500 ul of aliquots, 500 ul 2x RIPA buffer containing protease inhibitors.  40ul protein A-agarose DNA bead was added using large orifice tips and rotate 30 min at 4C. Samples were spin down at 14,000 rmp for 1 min and transferred the supernatant to a new chilled tube. 1/10th volume from each tube was removed and transfer to a new tube as INPUT, and brough the volume to 500 ul and kept at -20C until needed for next day. To the remaining volume (IP),  our protein of interest H3K27Me3 (cs # 9733) was added at 1:50 dilution and let rotate overnight at 4C. Next day, 50 ul of protein A-agarose DNA bead was added and let rotate for 2 hrs.  Samples were spin at 2500 rpm at 4C for 3 min. Supernatant was removed and pellet was washed once in order of low salt, high salt, LiCL, and twice 1X TE in 1 ml volume at RT by mixing on nutator 3-5 min and spin at 2500 rpm at RT for 3 min in between each wash.
GENEWIZ DataAnalysisReport

treatment_protocol: For siRNA, 20nM NFKBIS siRNA ( A-004765-13-0020, Dharmacon) and 20nM CT siRNA (D-001910-01-05, Dharmacon) was used to transfect the cells using Lipofectamine 2000 transfection reagents for 48 hrs to get the proper knockdown of protein.

tag: tissue

value: Normal human astrocytes

tag: cell type

value: pLNCX2-neo-IDH WT

tag: chip antibody

value: Tri-Methyl-Histone H3 (Lys27) Endogenous, Rabbit IgG


title: INPUT-P-CT

description: Input from NHA-IDH WT


title: E11.5 XY Cdyl_KO_3

status: Public on Apr 27 2023

city: Suita

first: Naoki

last: Okashita

address: 1-3 Yamadaoka

country: Japan

institute: Osaka university

library_source: transcriptomic

data_processing:
Raw sequence reads were mapped to mm10 using STAR aligner.
FPKM were calculated with an in-house Perl script at K.K. DNAFORM using raw counts obtained with featureCounts (v1.6.4) (a software program in the Subread package).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: E11.5 gonads

extract_protocol:
hCD271-positive cells (gonadal somatic cells) were isolated by MACS. Total RNA from gonadal somatic cells was extracted using the Direct-zol RNA MicroPrep kit (ZYMO RESEACH).
The libraries of the samples were prepared using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa) following manufacturer's protocols..

value: E11.5 gonads

value: Gonadal somatic cells

tag: strain

tag: genotype

value: Cdyl-KO, Nr5a1-hCD271

tag: developmental stage

tag: Sex


title: E11.5 XY Cdyl_KO_2


title: E11.5 XY Cdyl_Het_3

value: Cdyl-Het, Nr5a1-hCD271


title: IP-P-CT

description: H3K27me3 ChIP-seq from NHA-IDH WT


title: E11.5 XY Cdyl_KO_1


title: INPUT-P-KO

description: Input from NHA-IDH WT


title: IP-P-siRNA

description: H3K27me3 ChIP-seq from NHA-IDH WT


title: H2B CUT&RUN for ATF3-iKO skeletal muscle stem cells rep2

city: Hong Kong

first: Feng

last: Yang

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

country: China

institute: The Chinese University of Hong Kong

data_processing:
Raw data were first pre-processed by initial quality assessment, adaptors trimming, and low-quality filtering and then mapped to the mouse reference genome (mm9) using bowtie2, and only the non-redundant  reads were kept.
Bigwig file was converted by bam file using bamCoverage
Assembly: mm9
Supplementary files format and content: bigwig: signal of H2B binding
Library strategy: CUT&RUN

source_name: satellite cell

extract_protocol:
In brief, FISCs were harvested and washed by cell wash buffer, then bound to concanavalin A-coated magnetic beads. Digitonin Wash Buffer was used for permeabilization. After that, cells were incubated with 5 μg of H2A or H2B antibody (Abcam) overnight at 4 °C with shaking. Then, cell-bead slurry was washed with Digitonin Wash Buffer and incubated with Protein A-MNase for 1 h at 4 °C with shaking. After washing with Digitonin Wash Buffer, CaCl2 was added into the cell-bead slurry to initiate Protein A-MNase digestion, which was then incubated in 4°C for half an hour. Then 2x Stop Buffer was added to the reaction to stop the digestion. CUT&RUN fragments were released by incubation for 30 min at 37 °C followed by centrifugation. After centrifugation, the supernatant was recovered, and the DNA purification was performed by using Phenol/Chloroform (Thermo).
For DNA library construction，a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S) was used according to the manufacturer’s instructions. Bioanalyzer analysis and qPCR were used to measure the quality of DNA libraries including the DNA size and purity. Finally, DNA libraries were sequenced on the Illumina Genome Analyzer II platform.

tag: cell line

value: satellite cell

tag: treatment

value: Genomic DNA

tag: time

value: paired-end


title: H2B CUT&RUN for WT skeletal muscle stem cells rep1

value: WT


title: H2B CUT&RUN for WT skeletal muscle stem cells rep3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P1_Pool96_P2_E7_ad006

country: USA

value: female


title: PAO1 ∆phrS pPhrS∆seed replicate C

status: Public on May 03 2023

city: Iowa City

first: Michael

middle: J

last: Gebhardt

state: IA

address: 431 Newton Road, 200A EMRB

department: Department of Microbiology and Microbiology

institute: University of Iowa

description: Sample 3C

data_processing:
fastq records trimming (cutadapt 2.10) (Samples 5 - 8)
Quality control and adapter trimming (bcl2fastq 2.20.0.445) (Samples 9-10)
short reads mapping (bowtie2 2.4.4) (Samples 5-10)
BED file conversion (bedtools 2.30.0) (Samples 5-10)
bigwig file conversion (bedGraphToBigWig 2.9) (Samples 5-10)
Read quantification (htseq-count 2.0.2) (Samples 9-10)
Assembly: P. aerugionsa PAO1, NC_002516.2
Supplementary files format and content: Supplementary_files_format_and_content: bigwig format for samples 5 - 10.

organism: Pseudomonas aeruginosa

source_name: ∆phrS strain with vector for pulsed expression of PhrS-∆seed allele (pMJG448)

growth_protocol: Bacterial strains were grown at 37˚C , shaking at 200 rpm, in LB rich medium and samples 1&2 were collected at OD ≈ 0.5, samples 3&4 were collected at OD ≈ 2.0.

extract_protocol:
Standard TRI Reagent protocol was used for RNA extraction
Libary construction was carried out based on the RNAtag-Seq methodology (Shishkin, et al., 2015) for samples 5 - 8.

treatment_protocol: Cells were harvested by centrifugation, washed with 1X PBS, and cell pellets snap frozen in a dry ice - ethanol bath.

value: {delta}phrS pMJG448

value: Growth:OD ≈ 2.0 in LB + gentamicin (30 µg/mL)

value: 20 minutes pulse of 0.2% (w/v) arabinose


title: H2B CUT&RUN for ATF3-iKO skeletal muscle stem cells rep1


title: IP-P-KO

description: H3K27me3 ChIP-seq from NHA-IDH WT


title: E11.5 XY Cdyl_Het_1


title: E11.5 XY Cdyl_Het_2


title: adult whole fly,dec2P384R, biol rep 3 (Nanopore, long read)

status: Public on Apr 26 2023

city: Baton Rouge

first: Kerr

last: Wall

state: LA

address: 202 Life Science Bldg

department: Biological Sciences

institute: Louisiana State University

data_processing:
For Illumina reads, clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality
Clean reads were mapped to a reference genome (r6.39) of Drosophila melanogaster (Gramates et al., 2022) using HISAT2 (Pertea et al., 2016)
We then used featureCounts v1.5.0-p3 (Liao et al., 2014) to count the reads mapped to each gene and calculate FPKM
For the Nanopore reads, we mapped the reads to the reference genome using Minimap2 (Li, 2018) with arguments (p=80 and N=100) as described in (Soneson et al., 2019)
We then used Salmon (Patro et al., 2017) to quantify gene expression in alignment-based mode.
For both the Illumina and Nanopore data, differential expression analysis among the 3 conditions (three biological replicates per condition) were performed using the DESeq2 (Love et al., 2017) R package (1.20.0).
Supplementary files format and content: For both Illumina and Nanopore, we have provided both tab-delimented gene count files and differential expression output for each comparison (WT vs dec2WT, WT vs dec2P384R, dec2WT vs dec2P384R)

organism: Drosophila melanogaster

source_name: whole animal

growth_protocol: Fly stocks were raised at 25oC with 12:12h L:D cycle and fed on a standard cornmeal molasses medium. The  fly strains were obtained from the Bloomington Drosophila Stock Center (BDSC): GMR23E10-gal4 (49032), UAS-dec2WT (64227), UAS-dec2P384R (64228).

extract_protocol:
Drosophila melanogaster were reared on standard cornmeal molasses meduim, under controlled environment with temperature of 25oC and L:D cycle of 12:12. Flies for RNA extraction were collected at ZT 3, the time in which we observed the most significant difference in their daytime sleep. RNA was extraction from whole animal (~ 70 flies) using standard a TRIzol TM reagent protocol (Thermo Fisher Scientific, cat# 15596018) for both Illumina and nanopore sequencing. For illumina sequencing:  After RNA extraction, genomic DNA was removed using a GeneJet RNA-purification kit (Thermo Fisher Scientific, cat# K0702). RNA quality was measured using a Bioanalyzer and around 1.5-2 µg of purified RNA with RIN above 6 for each replicates was sent to Novogene (Sacramento, CA) in dry ice. Novogene prepared cDNA library using polyA enrichment library preparation procedure  and then performed Illumina sequencing (Illumina NovaSeq 6000 PE 150).  For nanopore: 10 μg of total RNA was used to prepare mRNA using NEXTflex Poly(A) Beads (BIOO Scientific cat # NOVA-512980). mRNA was assessed using a Bioanalyzer. 200 ng of input mRNA was used to prepare cDNA libraries using a Direct cDNA sequencing (SQK-DCS109) kit and these were prepared according to the Oxford Nanopore recommended protocol. Around 60ng total cDNA libraries were sequenced on a MinION using R9.4 flow cells. For each genotype, three independent biological replicates were sequenced.
1.5-2 µg of purified RNA  was sent to Novogene (Sacramento, CA). Novogene prepared cDNA library using polyA enrichment library preparation procedure to performed Illumina sequencing (Illumina NovaSeq 6000 ). For nanopore: 200 ng of mRNA was used to prepare cDNA libraries using a Direct cDNA sequencing (SQK-DCS109) kit following Oxford Nanopore recommended protocol. Around 60ng total cDNA libraries were sequenced on a MinION using R9.4 flow cells. For each genotype, three independent biological replicates were sequenced.

value: whole animal


title: H2B CUT&RUN for ATF3-iKO skeletal muscle stem cells rep3


title: PAO1 ∆phrS pEV replicate A

description: Sample 1A

source_name: ∆phrS strain with empty vector (pKH6)

value: {delta}phrS pKH6


title: H2B CUT&RUN for WT skeletal muscle stem cells rep2


title: BMMSC 2D 1

city: Tallahassee

first: li

last: sun

email: lsun2@fsu.edu, davidgmeckes@gmail.com

state: FL

address: 1115 west call st.

department: College of medicine

institute: Florida State University

data_processing:
RAW data were uploaded to BaseSpace (Illumina) for quality control and base calling.
Qulified reads were aligned to the hg38 human reference genome.
Data was uploaded to NetworkAnalyst 3.0 for further analysis and network visualization.
Total counts were filtered by following specifications: counts less than 10, variance less than 10% and unannotated, and then normalized by Log2-counts per million.
Assembly: hg38
Supplementary files format and content: Process counts file (xlsx) was generated and normalized by NetworkAnalyst.

source_name: Bone marrow

growth_protocol: hMSCs were expanded and maintained in complete culture media (CCM) containing α-MEM with 10% fetal bovine serum and 1% Penicillin/Streptomycin in a standard incubator at 37°C with 5% CO2 and 20% O2. For hypoxia 2D culture, hMSCs were seeded at a density of 1500 cells/cm2 and incubated under hypoxia (2% O2) in an oxygen-controlled chamber.

extract_protocol:
Cell total RNA was isolated with Trizol under manufacturer's protocol.
Isolated RNA was incubated with DNase I to remove trace genomic DNA contamination. Then, mRNA library was prepared by combination of NEBNext Ultra RNA Library Prep Kit (NEB, E7530) and NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). The library ran on Bioanalyzer with HS DNA chip (Agilent; 5067-4626) for quality control and quantified by KAPA library qPCR kit (KAPA; KR0405).

treatment_protocol: Each triplicate of cell group was cultured under 2D or hypoxia condition.

value: Mesenchymal Stem Cell

value: Bone marrow derived


title: BMMSC 2D 2


title: BMMSC-Hypo 3

value: Hypoxia


title: BMMSC 2D 3


title: adult whole fly,dec2P384R, biol rep 2 (Nanopore, long read)


title: adult whole fly,dec2WT, biol rep 1 (Nanopore, long read)


title: adult whole fly,WT, biol rep 3 (Nanopore, long read)


title: adult whole fly,dec2WT, biol rep 2 (Nanopore, long read)


title: BMMSC-Hypo 2


title: adult whole fly,WT, biol rep 1 (Nanopore, long read)


title: adult whole fly,dec2P384R, biol rep 1 (Illumina)


title: adult whole fly,dec2WT, biol rep 3 (Illumina)


title: adult whole fly,dec2P384R, biol rep 3 (Illumina)


title: adult whole fly,dec2P384R, biol rep 2 (Illumina)


title: adult whole fly,WT, biol rep 2 (Nanopore, long read)


title: BMMSC-Hypo 1


title: adult whole fly,dec2WT, biol rep 1 (Illumina)


title: adult whole fly,WT, biol rep 1 (Illumina)


title: adult whole fly,dec2WT, biol rep 2 (Illumina)


title: Fat body, Male 3rd instar larvae 3

status: Public on Apr 25 2023

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

data_processing:
Transcriptome analysis was performed using pseudo-alignment with salmon [PMID 28263959] using the D. melanogaster transcriptome (version dmel_r6.48_FB2022_05). DESeq2 (version 1.40.1) was used for differential expression analysis. Pathway analysis was performed using gProfiler (version 0.2.1). All code is available at: https://github.com/rnabioco/reis-rbi-pilot-fat-body
Assembly: dmel_r6.48_FB2022_05
Supplementary files format and content: salmon_quant.sf

source_name: Fat body

growth_protocol: w1118 [Bloomington Drosophila Stock Center stock number (BL) 3605] All animals were reared at 25°C, 60% humidity and fed a modified Bloomington media (1L: yeast 35g, soy flour 9.2 g, yellow cornmeal 65 g, light malt extract 42.4 g, agar 5.3 g, light corn syrup 70mL, propionic acid 4.4 ml, Tegosept in ethanol 8.4 ml). Food was made fresh each week and was used for no longer than one week . Parental animals were no older than 2 weeks. Eggs were collected for 5 hours on grape plates at 25°C and 50 first-instar larvae were transferred 22-24hrs later into a vial with experimental media.

extract_protocol:
Total RNA from 50 dissected sexed, third-instar-larval fat bodies was extracted from 50 third-instar FBs dissected from sexed larvae using 500uL of TRIzol (ambion Cat # 15596018cat number), volumes and purified using the Direct-zol Miniprep Plus kit digested with DNase I (Zymo Cat # R2072cat number). cDNA was generated with 500ng of RNA sequencing and library prep was performed at the University of Colorado Anschutz medical campus Genomics Core. Libraries were prepped according to the manufacturer’s protocol using the TECAN Universal Plus mRNA-Seq library prerparation kit with NuQant.
cDNA was generated with 500ng of RNA sequencing and library prep was performed at the University of Colorado Anschutz medical campus Genomics Core. Libraries were prepped according to the manufacturer’s protocol using the TECAN Universal Plus mRNA-Seq library prerparation kit with NuQant.

treatment_protocol: larvae were sexed and separated into male vs female

value: Fat body

value: male


title: adult whole fly,WT, biol rep 2 (Illumina)


title: Fat body, Male 3rd instar larvae 2

value: w1118 [Bloomington Drosophila Stock Center stock number (BL) 3605]


title: Fat body, Male 3rd instar larvae 1


title: Fat body, Female 3rd instar larvae 3


title: Fat body, Female 3rd instar larvae 1


title: adult whole fly,dec2P384R, biol rep 1 (Nanopore, long read)


title: Fat body, Female 3rd instar larvae 2


title: adult whole fly,dec2WT, biol rep 3 (Nanopore, long read)


title: pre-miR-31-tail RNA 5% DMS

status: Public on Apr 24 2023

city: Boston

first: Silvi

last: Rouskin

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Microbiology

institute: Harvard Medical School

description: pre-miR-31-tail RNA modified with 5% DMS

data_processing:
The reads from the fast were adapter trimmed using Trim Galore and aligned using bowtie2 (“bowtie2 --local --no-unal --no-discordant --no-mixed --phred33 40 -L 12”).
Each read was compared to its reference sequence to count how many mutations occurred at each nucleotide. All sequencing reads were combined together to calculate the average mutations per base and create a mutational profile.
Assembly: mir31
Supplementary files format and content: 3x 180905Rou_D18-8477_mutational_profile.tar.gz contains several documents, the most important being the population average of the mutations per residue in the reference sequence

source_name: in vitro transcription

extract_protocol:
Preparation of RNA: RNAs were prepared by in vitro transcription in 1× transcription buffer [40 mM Tris base, 5 mM dithiothreitol (DTT), 1 mM spermidine and 0.01% Triton-X (pH = 8.5)] with addition of 3–6 mM ribonucleoside triphosphates (NTPs), 10–20 mM magnesium chloride (MgCl2), 30–40 ng/μL DNA template, 0.2 unit/mL yeast inorganic pyrophosphatase (New England Biolabs)[61], ∼15 μM T7 RNA polymerase and 10–20% (v/v) dimethyl sulfoxide (DMSO). Reaction mixtures were incubated at 37 °C for 3–4 h, with shaking at 70 rpm, and then quenched using a solution of 7 M urea and 500 mM ethylenediaminetetraacetic acid (EDTA), pH = 8.5. Reactions were boiled for 3 min and then snap cooled in ice water for 3 min. The transcription mixture was loaded onto preparative-scale 10% denaturing polyacrylamide gels for purification. Target RNAs were visualized by UV shadowing and gel slices with RNA were excised. Gel slices were placed into an elutrap electroelution device (The Gel Company) in 1X TBE buffer. RNA was eluted from the gel at constant voltage (120 V) for ~24 h. The eluted RNA was spin concentrated, washed with 2 M high-purity sodium chloride, and exchanged into water using Amicon-15 Centrifugal Filter Units (Millipore, Sigma). RNA purity was confirmed on 10% analytical denaturing gels. RNA concentration was quantified via UV-Vis absorbance.
Dimethyl sulfate (DMS) modification of in vitro-transcribed RNA: 3 μg of pre-miR-31-tail RNA was denatured at 95 ℃ for 1 min and incubated on ice for another 3 min. Refolding buffer (300 mM sodium cacodylate and 6 mM MgCl2) was added to reach total volume of 97.5 uL (for the 0% control), 97.5 μL (for 2.5% modified sample) or 95 μL (for 5% modified sample). The RNA was incubated in refolding buffer at 37 ℃ for 40 min. The RNA was treated with either 2.5 µL DMSO (0% DMS), 2.5 μL DMS (2.5% DMS) or 5 μL DMS (5% DMS) followed by incubation at 37 ℃ while shaking at 250 rpm for 10 min. 60 μL β-mercaptoethanol was added to each reaction to neutralize the residual DMS. The modified RNA was purified using RNA Clean and Concentrator-5 kit (Zymo) according to manufacturer's instructions.
RT–PCR with DMS-modified RNA:  0.2 μM DMS-modified RNA, 2 μl 5× first strand buffer (ThermoFisher Scientific), 1 μl 10 μM reverse primer, 1 μl dNTP, 0.5 μl 0.1 M DTT, 0.5 μl RNaseOUT and 0.5 μl TGIRT-III (Ingex) were mixed. The mixture was incubated at 57 ℃ for 30 min. After the 30 min incubation, the temperature was increased to 85 ℃ for 5 min. 1 μL RNase H (New England Biolabs) was added to the mixture to digest the RNA. PCR amplification was achieved using Phusion (NEB) for 27 cycles according to the manufacturer’s instruction. The PCR product was purified by GeneJET PCR purification kit (Thermoscientific).
DMS-MaPseq

value: in vitro transcription

tag: library type

value: pre-miRNA


title: pre-miR-31-tail RNA 2.5% DMS

description: pre-miR-31-tail RNA modified with 2.5% DMS


title: pre-miR-31-tail RNA control (0% DMS)

description: pre-miR-31-tail RNA modified with 0% DMS


title: FADu+CAP-D

status: Public on Apr 17 2023

type: protein

city: Daegu

first: Soo hyun

last: Kang

address: 2177 Dalgubeol-daero

country: South Korea

institute: kyungpook university

hyb_protocol: Biotin labeled extract was hybridized with antibody-spotted slide for 2hr at room temperature. After hybridization, slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water. Detection Buffer including Cy3-Streptavidin (fullmoon Bio) was treated for 20min at room temperature. And slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water.

scan_protocol: Scanned on an GenePix 4100 scanner.

data_processing: GenePix Software (v 6.0) was used for data extraction.

label: biotin

molecule: protein

source_name: FaDu, primary OSCC CAF cells

label_protocol: 50ug of protein extract was labeled with Biotin and label buffer (Fullmoon Bio).

growth_protocol: We cocultured FaDu spheroids (bottom well) with FaDu, CAF-P, or CAF-D cells for 48h in a Transwell. The antibody array was performed for each CM.

extract_protocol: Debris was removed by filtration centrifuged conditioned medium.

value: FaDu, primary OSCC CAF cells

tag: growth protocol

value: (FaDu spheroid + CAP-D) co-culture conditioned media

value: CAP-D


title: adult whole fly,WT, biol rep 3 (Illumina)


title: FADu_Control

value: (FaDu spheroid + FaDu cells) co-culture conditioned media


title: PT1_rep2_mtDOGMA_ATAC

status: Public on Apr 13 2023

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: ATAC from multiome

library_source: genomic single cell

data_processing:
Fastqs were generated using CellRanger-Arc mkfastq v1.0
Sequencing reads were aligned using CellRanger-Arc count to the hg38 reference genome and transcriptome
RNA/ATAC data were aggregated using CellRanger-Arc aggr v1.0 between the two replicates
Assembly: hg38
Supplementary files format and content: Aggregated gene expression counts with cells x peaks matrix (h5), ATAC fragments (tsv), and surface proteins (.csv) per cell

source_name: peripheral blood mononuclear cells

growth_protocol: Cryopreserved cells were thawed in RPMI with 10% FBS and washed in media prior to single cell genomics processing.

extract_protocol:
10x Genomics multiome protocol
10x Genomics multiome scRNA-seq with adaptations for mtDNA and surface proteins described here: https://www.nature.com/articles/s41587-021-00927-2 (DOGMA-seq)

value: peripheral blood mononuclear cells


title: SLAMseq_THP1_4sUwashout_T1hr

city: Melbourne

first: Izabela

last: Todorovski

state: VIC

address: 305 Grattan Street

department: Cancer Research Division

country: Australia

institute: Peter MacCallum Centre

description:
SLAMseq_THP1_ReadCounts_Total.tsv
SLAMseq_THP1_ReadCounts_Nascent.tsv

data_processing:
Single-end reads were demultiplexed using bcl2fastq (v2.17.1.14) and resulting FASTQ files were trimmed for adapter sequences using Trim_galore (v0.6.5) with a stringency overlap of 3bp.
Trimmed FASTQ files were processed with SLAM-dunk (v0.4.3), enabling multi-mapper reconciliation and using a threshold of at least 2 T > C conversions to mark a read as converted. The no 4sU control sample was processed first to find single nucleotide polymorphisms (SNPs), which was then used to filter the subsequent samples.
Decay rates for each gene were determined using nonlinear regression to fit an exponential curve to the decreasing quantity of SLAM-seq labelled reads measured post-washout of 4-thiouridine.
Assembly: hg19 and dm3
Supplementary files format and content: SLAMseq_THP1_ReadCounts_Total.tsv (raw total RNA counts)
Supplementary files format and content: SLAMseq_THP1_ReadCounts_Nascent.tsv (raw nascent RNA counts)
Library strategy: SLAM-seq

source_name: THP-1 cell line

growth_protocol: THP-1 cells were cultured in Roswell Park Memorial Institute (RPMI) medium containing 10% (v/v) heat-inactivated fetal bovine serum (HI-FBS), penicillin (100 U/ml), streptomycin (100 μg/ml) and 2 mM GlutaMAX at 37°C and 5% carbon dioxide.

extract_protocol:
Cells were washed in ice-cold PBS and resuspended in 300μL TRIzol. To extract RNA, one-fifth volume of chloroform was added to TRIzol lysates, followed by shaking, incubation at room temperature for 2 minutes and centrifugation (16000g at 4°C for 15 minutes). The aqueous phase was isolated and RNA was precipitated using DTT (10mM), 100% isopropanol (1 volume) and GlycolBlue co-precipitant, incubated at room temperature for 10 minutes and centrifuged (16000g at 4°C for 20 minutes). Supernatant was removed, RNA pellets were washed in 75% (v/v) ethanol and DTT (100μM) and centrifuged (7500g at room temperature for 5 minutes). Supernatant was removed and RNA pellets dried for 10 minutes prior to reconstitution in Ultrapure DNAse/RNAse-free distilled water supplemented with DTT (1mM) and incubation at 55°C for 10 minutes. Thiol-containing bases were reduced by incubating RNA (10μg) with IAA (10mM, 50 mM NaPO4 pH 8.05 and 50% (v/v) DMSO) in a final volume of 50μL for 15 minutes at 55°C. Reaction was stopped by quenching IAA with DTT (20μM). RNA was precipitated using 3M NaOAc pH 5.2 (5μL), 100% ethanol (125μL) and GlycolBlue co-precipitant, incubated at -80°C for 30 minutes and centrifuged (16000g at 4°C for 30 minutes). Supernatant was removed and RNA pellet was washed in 75% (v/v) ethanol and centrifuged (16000g at 4°C for 10 minutes) twice, dried at room temperature for 10 minutes and reconstituted in Ultrapure DNAse/RNAse-free distilled water. RNA clean-up was performed by incubating RNA solution in 2 volumes of AMPure XP Beads, for 2 minutes at room temperature. Beads were washed in 80% (v/v) ethanol twice, dried at room temperature for 3 minutes and resuspended in Ultrapure DNAse/RNAse-free distilled water. Eluate was collected and S2 spike-in material (5%) was added to RNA.
QuantSeq 3′mRNA-seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria)
3'mRNA-seq

treatment_protocol: THP- cells were treated with 30μM 4-thiouridine for 12 hours at 37°C and 5% carbon dioxide, whereby culture medium was exchanged every 3 hours for the duration of the pulse. THP-1 cells were then washed in sterile ice-cold PBS twice and resuspended in pre-warmed (37°C) culture medium containing 3mM uridine. THP-1 cells were then harvested at 0- ,0.3-, 0.6-, 1-, 2-, 8- and 12- hours post-uridine chase.

value: Acute Myeloid Leukemia

value: THP-1 cell line

tag: time point

value: 1 hour post 4-thiouridine wash-out


title: SLAMseq_THP1_4sUwashout_T20min

value: 20 minutes hours post 4-thiouridine wash-out


title: SLAMseq_THP1_4sUwashout_T8hr

value: 8 hours post 4-thiouridine wash-out


title: SLAMseq_THP1_4sUwashout_T40min

value: 40 minutes hour post 4-thiouridine wash-out


title: HUDEP2 RNA [100353]

status: Public on Apr 10 2023

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

data_processing:
Sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/)
Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR
Gene quantification was done via RSEM
Assembly: hg38
Supplementary files format and content: tab-separated values, TPM and counts

source_name: umbilical cord blood

extract_protocol:
RNA was extracted from 1 million cells, using the RNeasy Mini Kit (Qiagen).
The TruSeq Stranded mRNA Library Prep Kit (Illumina) was used to enrich for polyA+ RNA and to create libraries for HiSeq2000 sequencing (Illumina).

value: umbilical cord blood

value: Human Umbilical Cord Blood-Derived Erythroid Progenitor cell line 2, abbreviated HUDEP2, expresses beta-globin upon induced differentiation


title: PT1_rep1_mtDOGMA_GEX

description: RNA/Gene expression from multiome

library_source: transcriptomic single cell


title: PT1_rep1_mtDOGMA_ATAC

description: ATAC from multiome


title: CD34E RNA [100356]

source_name: blood

value: blood

value: CD34+ HSPCs differentiated ex vivo into erythroblasts, abbreviated CD34_E


title: SLAMseq_THP1_4sUwashout_T2hr

value: 2 hours post 4-thiouridine wash-out


title: SLAMseq_THP1_no4sU_control

value: No 4-thiouridine control


title: CD34E RNA [100357]


title: SLAMseq_THP1_4sUwashout_T0hr

value: 0 hours post 4-thiouridine wash-out


title: HUDEP2 RNA [100354]


title: SLAMseq_THP1_4sUwashout_T12hr

value: 12 hours post 4-thiouridine wash-out


title: HUDEP1 RNA [100351]

value: Human Umbilical Cord Blood-Derived Erythroid Progenitor cell line 1, abbreviated HUDEP1, expresses gamma-globin upon induced differentiation


title: Col-0 Air replicate 1

status: Public on Apr 06 2023

city: Bundoora

first: Mathew

middle: G

last: Lewsey

address: AgriBio, 5 Ring Rd

department: Animal, Plant and Soil Sciences

institute: La Trobe University

data_processing:
base-calling using RTA 2.7.7
Fastq files were trimmed using Trimglore V0.4.4 and trimmed reads were mapped to the Arabidopsis TAIR10 genome using Bowtie2 V2.2.9. Shiftsize was calculated using phantompeakqualtools and default parameters
Peaks called with MACS2 version 2.1.0 (parameters options–nomodel –shiftsize  –g 1.19e8 –q 0.05). A concatenated file of all non-transgenic control IP reads was used as the control in peak calling
ChIPseeker with default parameters  was used for annotation. gene ontology enrichment was assessed using clusterProfiler and ClueGO
supplementary files format and content: Binding sites region output created by MACS2 in narrowpeak format.

organism: Arabidopsis thaliana

source_name: Three day old etiolated seedlings

growth_protocol: Seeds were sterilised using bleach then plated on 1.2% agar Linsmaier and Skoog medium plates. Stratification was at 4 celsius in the dark for three days. Plates were exposed to the light at room temperature for 2 h to induce germinaiton, then returned to the dark at 22 celsius. Plates were incubated for three days, after which treatments were conducted.

extract_protocol:
Conducted as described in O'Malley et al. 2016 (doi: 10.1016/j.cell.2016.04.038) and Chang et al. 2013 (10.7554/eLife.00675). Harvested seedlings were crosslinked with 1% formaldehyde under vacuum for 20 minutes then snap-frozen in liquid nitrogen. Nuclei were extracted from frozen, ground seedlings according to Qiao et al. 2016 (10.1126/science.1225974) then sonicated according to Chang et al .2016 using a Diagenode bioruptor to yield an average DNA fragment size of approximately 150-300 bases. Transcription-factor DNA complexes were isolated by immunoprecipitation with polyclonal anti-GFP raised in goat from David Dreschel (Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany) or, for non-transgenic controls, IgG from goat (supplied by Covance). These complexes were then retrieved using Protein G Dynabeads (Life Technologies).
Conducted as described in (Zander,M et al., 2020) DOI: 10.1038/Nat Plants 6: 290-302

treatment_protocol: Air or hormone treated for 2 h. In detail, BR and SA treatments were applied by spraying the plants until run-off occurred then samples were harvested at each time point. BR treatment was conducted using 10 nM epibrassinolide (Sigma, E1641), SA treatment using 0.5 mM SA (Sigma, S7401). JA and ET treatments were performed as previously described (Chang et al., 2013; Zander et al., 2020).

tag: plant line

value: Goat IgG whole molecule

value: Col-0 Air treatment

tag: genome build


title: Col-0 Air replicate 2


title: Col-0 TGA5::TGA5-Ypet SA for 2h replicate 1

value: Col-0 TGA5::TGA5-Ypet

value: Goat anti-GFP

value: Col-0 TGA5::TGA5-Ypet SA treatment for 2h


title: HUDEP1 RNA [100350]


title: Col-0 TCP3::TCP3-Ypet BR for 2h replicate 1

value: Col-0 TCP3::TCP3-Ypet

value: Col-0 TCP3::TCP3-Ypet BR treatment for 2h


title: FADu+CAP-P

value: FaDu, primary OSCC CAF cells

value: (FaDu spheroid + CAP-P) co-culture conditioned media


title: Col-0 EDF2::EDF2-Ypet JA for 2h replicate 2

value: Col-0 EDF2::EDF2-Ypet

value: Col-0 EDF2::EDF2-Ypet JA treatment for 2h


title: Col-0 EIN3::EIN3-Ypet JA for 2h replicate 2

value: Col-0 EIN3::EIN3-Ypet

value: Col-0 EIN3::EIN3-Ypet JA treatment for 2h


title: Col-0 ERF1::ERF1-Ypet JA for 2h replicate 3

value: Col-0 ERF1::ERF1-Ypet

value: Col-0 ERF1::ERF1-Ypet JA treatment for 2h


title: Col-0 BES1::BES1-Ypet BR for 2h replicate 1

value: Col-0 BES1::BES1-Ypet

value: Col-0 BES1::BES1-Ypet BR treatment for 2h


title: Col-0 EIN3::EIN3-Ypet JA for 2h replicate 1


title: PT1_rep2_mtDOGMA_GEX

description: RNA/Gene expression from multiome

value: peripheral blood mononuclear cells


title: Col-0 ANAC055::ANAC055-Ypet JA for 2h replicate 2

value: Col-0 ANAC055::ANAC055-Ypet

value: Col-0 ANAC055::ANAC055-Ypet JA treatment for 2h


title: JA_ChIP-Seq Col-0 ANAC055::ANAC055-Ypet  Air for 2h replicate 2

value: Goat anti-GFP

value: JA_ChIP-Seq Col-0 ANAC055::ANAC055-Ypet  Air treatment for 2h


title: Col-0 ANAC055::ANAC055-Ypet JA for 2h replicate 3


title: Col-0 ANAC055::ANAC055-Ypet JA for 2h replicate 1


title: Col-0 EDF2::EDF2-Ypet JA for 2h replicate 1


title: Col-0 STZ::STZ-Ypet JA for 2h replicate 1

value: Col-0 STZ::STZ-Ypet

value: Col-0 STZ::STZ-Ypet JA treatment for 2h


title: Col-0 STZ::STZ-Ypet JA for 2h replicate 2


title: JA_ChIP-Seq Col-0 STZ::STZ-Ypet Air for 2h replicate 1

value: JA_ChIP-Seq Col-0 STZ::STZ-Ypet Air treatment for 2h


title: JA_ChIP-Seq Col-0 RAP2.6L::RAP2.6L-Ypet Air for 2h replicate 1

value: Col-0 RAP2.6L::RAP2.6L-Ypet

value: JA_ChIP-Seq Col-0 RAP2.6L::RAP2.6L-Ypet Air treatment for 2h


title: Col-0 OBP2::OBP2-Ypet JA for 2h replicate 2

value: Col-0 OBP2::OBP2-Ypet

value: Col-0 OBP2::OBP2-Ypet JA treatment for 2h


title: JA_ChIP-Seq Col-0 ANAC055::ANAC055-Ypet  Air  for 2h replicate 1

value: JA_ChIP-Seq Col-0 ANAC055::ANAC055-Ypet  Air  treatment for 2h


title: Col-0 TCP3::TCP3-Ypet JA for 2h replicate 1

value: Col-0 TCP3::TCP3-Ypet

value: Col-0 TCP3::TCP3-Ypet JA treatment for 2h


title: JA_ChIP-Seq Col-0 OBP2::OBP2-Ypet Air for 2h replicate 1

value: JA_ChIP-Seq Col-0 OBP2::OBP2-Ypet Air treatment for 2h


title: Col-0 MYC2::MYC2-Ypet JA for 2h replicate 3

value: Col-0 MYC2::MYC2-Ypet

value: Col-0 MYC2::MYC2-Ypet JA treatment for 2h


title: JA_ChIP-Seq Col-0 MYC2::MYC2-Ypet Air for 2h replicate 3

value: JA_ChIP-Seq Col-0 MYC2::MYC2-Ypet Air treatment for 2h


title: JA_ChIP-Seq Col-0 TCP3::TCP3-Ypet Air for 2h replicate 2

value: JA_ChIP-Seq Col-0 TCP3::TCP3-Ypet Air treatment for 2h


title: Col-0 MYC2::MYC2-Ypet JA for 2h replicate 1

value: Goat anti-GFP


title: Col-0 MYC2::MYC2-Ypet JA for 2h replicate 2


title: JA_ChIP-Seq Col-0 TCP3::TCP3-Ypet Air for 2h replicate 1


title: JA_ChIP-Seq Col-0 MYC2::MYC2-Ypet Air for 2h replicate 1


title: JA_ChIP-Seq Col-0 MYC2::MYC2-Ypet Air for 2h replicate 2


title: Col-0 ERF1::ERF1-Ypet JA for 2h replicate 2

value: Col-0 ERF1::ERF1-Ypet

value: Col-0 ERF1::ERF1-Ypet JA treatment for 2h


title: Col-0 MYC3::MYC3-Ypet JA for 2h replicate 3

value: Col-0 MYC3::MYC3-Ypet

value: Col-0 MYC3::MYC3-Ypet JA treatment for 2h


title: Col-0 ERF1::ERF1-Ypet JA for 2h replicate 1


title: JA_ChIP-Seq Col-0 MYC3::MYC3-Ypet Air for 2h replicate 3

value: JA_ChIP-Seq Col-0 MYC3::MYC3-Ypet Air treatment for 2h


title: Col-0 MYC3::MYC3-Ypet JA for 2h replicate 1


title: Col-0 MYC3::MYC3-Ypet JA for 2h replicate 2


title: Col-0 RAP2.6L::RAP2.6L-Ypet JA for 2h replicate 1

value: Col-0 RAP2.6L::RAP2.6L-Ypet

value: Col-0 RAP2.6L::RAP2.6L-Ypet JA treatment for 2h


title: Col-0 OBP2::OBP2-Ypet JA for 2h replicate 1

value: Col-0 OBP2::OBP2-Ypet

value: Col-0 OBP2::OBP2-Ypet JA treatment for 2h


title: Col-0 TCP3::TCP3-Ypet JA for 2h replicate 2

value: Col-0 TCP3::TCP3-Ypet


title: JA_ChIP-Seq Col-0 MYC3::MYC3-Ypet Air for 2h replicate 2


title: Col-0 EDF2::EDF2-Ypet ET for 2h replicate 3

value: Col-0 EDF2::EDF2-Ypet

value: Col-0 EDF2::EDF2-Ypet ET treatment for 2h


title: Col-0 EDF2::EDF2-Ypet ET for 2h replicate 1


title: JA_ChIP-Seq Col-0 MYC3::MYC3-Ypet Air for 2h replicate 1


title: Col-0 EDF2::EDF2-Ypet  Air for 2h replicate 2

value: Col-0 EDF2::EDF2-Ypet  Air treatment for 2h


title: Col-0 EDF2::EDF2-Ypet  Air  for 2h replicate 1

value: Col-0 EDF2::EDF2-Ypet  Air  treatment for 2h


title: Col-0 EDF2::EDF2-Ypet ET for 2h replicate 2


title: Col-0 ANAC055::ANAC055-Ypet ET for 2h replicate 3

value: Col-0 ANAC055::ANAC055-Ypet

value: Col-0 ANAC055::ANAC055-Ypet ET treatment for 2h


title: Col-0 ANAC055::ANAC055-Ypet ET for 2h replicate 2

value: Goat anti-GFP


title: Col-0 ANAC055::ANAC055-Ypet  Air  for 2h replicate 1

value: Col-0 ANAC055::ANAC055-Ypet  Air  treatment for 2h


title: Col-0 ANAC055::ANAC055-Ypet  Air for 2h replicate 2

value: Col-0 ANAC055::ANAC055-Ypet  Air treatment for 2h


title: Col-0 ANAC055::ANAC055-Ypet  Air  for 2h replicate 3


title: Col-0 TCP3::TCP3-Ypet ET for 2h replicate 3

value: Col-0 TCP3::TCP3-Ypet ET treatment for 2h


title: Col-0 BES1::BES1-Ypet Air for 2h replicate 2

value: Col-0 BES1::BES1-Ypet

value: Col-0 BES1::BES1-Ypet Air treatment for 2h


title: Col-0 TCP3::TCP3-Ypet  Air  for 2h replicate 3

value: Col-0 TCP3::TCP3-Ypet  Air  treatment for 2h


title: Col-0 ANAC055::ANAC055-Ypet ET for 2h replicate 1


title: Col-0 BES1::BES1-Ypet  Air  for 2h replicate 1

value: Col-0 BES1::BES1-Ypet  Air  treatment for 2h


title: Col-0 TCP3::TCP3-Ypet ET for 2h replicate 2


title: Col-0 TCP3::TCP3-Ypet ET for 2h replicate 1


title: Col-0 TCP3::TCP3-Ypet  Air  for 2h replicate 1


title: Col-0 BES1::BES1-Ypet ET for 2h replicate 1

value: Col-0 BES1::BES1-Ypet ET treatment for 2h


title: Col-0 TGA5::TGA5-Ypet ET for 2h replicate 2

value: Col-0 TGA5::TGA5-Ypet

value: Col-0 TGA5::TGA5-Ypet ET treatment for 2h


title: Col-0 TGA5::TGA5-Ypet  Air  for 2h replicate 2

value: Col-0 TGA5::TGA5-Ypet  Air  treatment for 2h


title: Col-0 STZ::STZ-Ypet ET for 2h replicate 1

value: Col-0 STZ::STZ-Ypet

value: Col-0 STZ::STZ-Ypet ET treatment for 2h


title: Col-0 MYC2::MYC2-Ypet ET for 2h replicate 1

value: Col-0 MYC2::MYC2-Ypet

value: Col-0 MYC2::MYC2-Ypet ET treatment for 2h


title: Col-0 MYC2::MYC2-Ypet ET for 2h replicate 2


title: Col-0 TGA5::TGA5-Ypet  Air  for 2h replicate 1


title: Col-0 MYC2::MYC2-Ypet  Air  for 2h replicate 3

value: Col-0 MYC2::MYC2-Ypet  Air  treatment for 2h


title: Col-0 TGA5::TGA5-Ypet ET for 2h replicate 1

value: Goat anti-GFP


title: Col-0 MYC2::MYC2-Ypet  Air for 2h replicate 2

value: Col-0 MYC2::MYC2-Ypet  Air treatment for 2h


title: Col-0 MYC2::MYC2-Ypet  Air  for 2h replicate 1


title: Col-0 OBP2::OBP2-Ypet  Air  for 2h replicate 1

value: Col-0 OBP2::OBP2-Ypet

value: Col-0 OBP2::OBP2-Ypet  Air  treatment for 2h


title: Col-0 OBP2::OBP2-Ypet ET for 2h replicate 1

value: Col-0 OBP2::OBP2-Ypet ET treatment for 2h


title: Col-0 OBP2::OBP2-Ypet ET for 2h replicate 2


title: Col-0 OBP2::OBP2-Ypet  Air  for 2h replicate 2


title: Col-0 EIN3::EIN3-Ypet ET for 2h replicate 1

value: Col-0 EIN3::EIN3-Ypet

value: Col-0 EIN3::EIN3-Ypet ET treatment for 2h


title: Col-0 EIN3::EIN3-Ypet ET for 2h replicate 2


title: Col-0 EIN3::EIN3-Ypet  Air  for 2h replicate 2

value: Col-0 EIN3::EIN3-Ypet  Air  treatment for 2h


title: Col-0 TCP3::TCP3-Ypet  Air for 2h replicate 2

value: Col-0 TCP3::TCP3-Ypet

value: Col-0 TCP3::TCP3-Ypet  Air treatment for 2h


title: Col-0 EIN3::EIN3-Ypet  Air  for 2h replicate 1


title: Col-0 EIN3::EIN3-Ypet ET for 2h replicate 3


title: Col-0 EDF1::EDF1-Ypet  Air  for 2h replicate 1

value: Col-0 EDF1::EDF1-Ypet

value: Col-0 EDF1::EDF1-Ypet  Air  treatment for 2h


title: Col-0 MYC3::MYC3-Ypet  Air  for 2h replicate 3

value: Col-0 MYC3::MYC3-Ypet

value: Col-0 MYC3::MYC3-Ypet  Air  treatment for 2h


title: Col-0 MYC3::MYC3-Ypet ET for 2h replicate 1

value: Col-0 MYC3::MYC3-Ypet ET treatment for 2h


title: Col-0 EDF3::EDF3-Ypet ET for 2h replicate 1

value: Col-0 EDF3::EDF3-Ypet

value: Col-0 EDF3::EDF3-Ypet ET treatment for 2h


title: Col-0 EDF1::EDF1-Ypet ET for 2h replicate 2

value: Goat anti-GFP

value: Col-0 EDF1::EDF1-Ypet ET treatment for 2h


title: Col-0 EDF3::EDF3-Ypet ET for 2h replicate 2


title: Col-0 MYC3::MYC3-Ypet  Air for 2h replicate 2

value: Col-0 MYC3::MYC3-Ypet  Air treatment for 2h


title: Col-0 EDF1::EDF1-Ypet ET for 2h replicate 1


title: Col-0 RAP2.6L::RAP2.6L-Ypet  Air for 2h replicate 2

value: Col-0 RAP2.6L::RAP2.6L-Ypet

value: Col-0 RAP2.6L::RAP2.6L-Ypet  Air treatment for 2h


title: Col-0 MYC3::MYC3-Ypet  Air  for 2h replicate 1


title: Col-0 RAP2.6L::RAP2.6L-Ypet ET for 2h replicate 1

value: Col-0 RAP2.6L::RAP2.6L-Ypet ET treatment for 2h


title: Col-0 RAP2.6L::RAP2.6L-Ypet ET for 2h replicate 2


title: Col-0 MYC3::MYC3-Ypet ET for 2h replicate 2


title: mpk6 SA 1h replicate 3

data_processing:
base-calling using RTA 2.7.7
Sequencing reads were quality trimmed using Trimglore V0.4.4, then quantification of transcripts was performed using Salmon v0.8.1 in conjunction with AtRTD2-QUASI reference transcriptome.
Tximport pipeline was used to summarize transcript-level abundance to gene-level abundance.
Differentially expressed genes were identified using the edgeR 3.28.1 package in R
supplementary files format and content: csv files include readcount and TPM values for each samples

growth_protocol: Wild type (Columbia-0) and mpk6 mutant seeds were sterilised using chlorine gas (mixing 3 mL of HCl with 100 mL of bleach) in a desiccator for 3 hours. The seeds were then plated out on ½ MS media supplemented with 1 % sucrose and 1.5 % agar, pH 5.7. The plates were wrapped, and seeds were stratified for 3 days at 4 °C. The plates were then brought to 22 °C under the light for two hours before wrapping up again with aluminium foil and growing for another 3 days. Plates were taken to a dark room that was illuminated with a green light (light bulb covered with Lee Sheet 736 Twickenham Green).

extract_protocol:
RNA extractions were carried out using Sigma Spectrum Plant Total RNA Kit, supplemented with Sigma On-Column DNase I Digestion Set, according to the manufacturer’s instructions.
Two µg of RNA was used for RNA sequencing library construction, using Illumina TruSeq Stranded Total RNA kit. Procedures were carried out according to the manufacturer’s instructions. All RNA-sequencing libraries were then pooled into one and sequenced using NovaSeq S1 Flow-cell, 100 bp single-end reaction

treatment_protocol: Three-day-old seedlings were sprayed with hormones [1-aminocyclopropanecarboxylic acid 10 µM, salicylic acid 0.5 mM, epibrassinolide 10 nM, abscisic acid 10 µM, rac-GR24 (synthetic strigolactone) 5 µM] or treated with methyl-jasmonic acid (JA). Methyl-JA treatment was carried by adding 1 µL of methyl-JA on a 5x5 mm2 filter paper and placing this filter paper on the seedling plate (with lid removed) and placed the seedling plate in a sealed 1 L container. All hormone treatments last for an hour, covered in aluminium foil and under 22 °C. Seedling collection was carried out in a dark room illuminated with a green light. Samples were collected and snapped frozen in liquid nitrogen.

value: SA treatment for 1 h


title: Col-0 RAP2.6L::RAP2.6L-Ypet  Air  for 2h replicate 1

value: Col-0 RAP2.6L::RAP2.6L-Ypet  Air  treatment for 2h


title: mpk6 JA 1 h replicate 3

value: JA (MeJA) treatment for 1 h


title: Col-0 EDF3::EDF3-Ypet ET for 2h replicate 3


title: mpk6 JA 1 h replicate 2


title: mpk6 SA 1h replicate 2


title: mpk6 JA 1 h replicate 1


title: mpk6 ET 1 h replicate 2

value: ET (ACC)  treatment for 1 h


title: mpk6 ET 1 h replicate 3


title: mpk6 ET 1 h replicate 1


title: mpk6 SA 1h replicate 1


title: Col-0 MYC3::MYC3-Ypet ET for 2h replicate 3


title: mpk6 ABA 1 h replicate 2

value: ABA treatment for 1 h


title: mpk6 ABA 1 h replicate 3


title: mpk6 ABA 1 h replicate 1


title: mpk6 non-hormone 1 h replicate 3

value: non hormone treatment for 1 h


title: mpk6 non-hormone 1 h replicate 2


title: Col-0 SA 1h replicate 2


title: Col-0 SA 1h replicate 1


title: Col-0 JA 1 h replicate 2


title: Col-0 ABA 1 h replicate 3


title: Col-0 ABA 1 h replicate 2


title: edf1234 air treated 2h replicate 3

description: air treatment for 2h

data_processing:
base-calling using RTA 2.7.7
Sequencing reads were quality trimmed using Trimglore V0.4.4, then quantification of transcripts was performed using Salmon v0.8.1 in conjunction with AtRTD2-QUASI reference transcriptome.
For ethylene data, Trimmed RNA-seq reads for ethylene RNA-seq time-series data were mapped onto the Arabidopsis genome with the Araport11 annotation using HiSat2 V2.0.5.Read counting in genome features was performed using Htseq V0.8.0
Tximport pipeline was used to summarize transcript-level abundance to gene-level abundance.
Differentially expressed genes were identified using the edgeR 3.28.1 package in R
TAIR10 and AtRTD2-QUASI
csv files include readcount and TPM values for each samples

extract_protocol:
RNeasy Plant Mini Kit (74903, Qiagen)
cDNA library preparation and subsequent single read sequencing was carried as previously described (Zander,M et al., 2020) DOI: 10.1038/Nat Plants 6: 290-302

treatment_protocol: SA or BR or GR24 treatment in time series 0-24 h; ethylene treatment for 2h

value: edf1234 quadruple mutant


title: Col-0 SA 1h replicate 3


title: Col-0 ET 1 h replicate 2


title: mpk6 non-hormone 1 h replicate 1


title: Col-0 ET 1 h replicate 3


title: Col-0 ABA 1 h replicate 1


title: Col-0 ET 1 h replicate 1


title: Col-0 JA 1 h replicate 3


title: Col-0 non-hormone 1 h replicate 2


title: Col-0 non-hormone 1 h replicate 1


title: edf1234 ethylene treated 2h replicate 3

description: ethylene treatment for 2h


title: edf1234 ethylene treated 2h replicate 1

description: ethylene treatment for 2h


title: edf1234 ethylene treated 2h replicate 2

description: ethylene treatment for 2h


title: Col-0 non-hormone 1 h replicate 3


title: edf1234 air treated 2h replicate 1

description: air treatment for 2h


title: edf1234 air treated 2h replicate 2

description: air treatment for 2h


title: Col-0 ethylene treated 2h replicate 3

description: ethylene treatment for 2h


title: Col-0 ethylene treated 2h replicate 1

description: ethylene treatment for 2h


title: Col-0 air treated 2h replicate 2

description: air treatment for 2h


title: Col-0 JA 1 h replicate 1


title: Col-0 air treated 2h replicate 1

description: air treatment for 2h


title: Col-0 air treated 2h replicate 3

description: air treatment for 2h


title: Col-0 RAP2.6L::RAP2.6L-Ypet  Air  for 2h replicate 3


title: Col-0 SL_KAR treated 8h replicate 1

description: GR24 treatment for 8h


title: Col-0 SL_KAR treated 4h replicate 3

description: GR24 treatment for 4h


title: Col-0 SL_KAR treated 4h replicate 2

description: GR24 treatment for 4h


title: Col-0 ethylene treated 2h replicate 2

description: ethylene treatment for 2h


title: Col-0 SL_KAR treated 8h replicate 2

description: GR24 treatment for 8h


title: Col-0 SL_KAR treated 8h replicate 3

description: GR24 treatment for 8h


title: Col-0 SL_KAR treated 24h replicate 3

description: GR24 treatment for 24h


title: Col-0 SL_KAR treated 24h replicate 1

description: GR24 treatment for 24h


title: Col-0 SL_KAR treated 2h replicate 3

description: GR24 treatment for 2h


title: Col-0 SL_KAR treated 4h replicate 1

description: GR24 treatment for 4h


title: Col-0 SL_KAR treated 24h replicate 2

description: GR24 treatment for 24h


title: Col-0 SL_KAR treated 1h replicate 2

description: GR24 treatment for 1h


title: Col-0 SL_KAR treated 1h replicate 1

description: GR24 treatment for 1h


title: Col-0 SL_KAR treated 2h replicate 1

description: GR24 treatment for 2h


title: Col-0 SL_KAR treated 12h replicate 3

description: GR24 treatment for 12h


title: Col-0 SL_KAR treated 2h replicate 2

description: GR24 treatment for 2h


title: Col-0 SL_KAR treated 1h replicate 3

description: GR24 treatment for 1h


title: Col-0 SL_KAR treated 0h replicate 2

description: GR24 treatment for 0h


title: Col-0 SL_KAR treated 12h replicate 2

description: GR24 treatment for 12h


title: Col-0 SL_KAR treated 0.5 h replicate 2

description: GR24 treatment for 0.5h


title: Col-0 SL_KAR treated 0.5 h replicate 3

description: GR24 treatment for 0.5h


title: Col-0 SL_KAR treated 0.25 h replicate 3

description: GR24 treatment for 0.25h


title: Col-0 SL_KAR treated 0.5 h replicate 1

description: GR24 treatment for 0.5h


title: Col-0 SL_KAR treated 0.25 h replicate 2

description: GR24 treatment for 0.25h


title: Col-0 SL_KAR treated 0.25 h replicate 1

description: GR24 treatment for 0.25h


title: Col-0 BR treated 8h replicate 3

description: BR treatment for 8h


title: Col-0 BR treated 8h replicate 2

description: BR treatment for 8h


title: Col-0 BR treated 8h replicate 1

description: BR treatment for 8h


title: Col-0 BR treated 4h replicate 2

description: BR treatment for 4h


title: Col-0 BR treated 4h replicate 1

description: BR treatment for 4h


title: Col-0 BR treated 2h replicate 3

description: BR treatment for 2h


title: Col-0 BR treated 24h replicate 3

description: BR treatment for 24h


title: Col-0 SL_KAR treated 0h replicate 1

description: GR24 treatment for 0h


title: Col-0 SL_KAR treated 0h replicate 3

description: GR24 treatment for 0h


title: Col-0 SL_KAR treated 12h replicate 1

description: GR24 treatment for 12h


title: Col-0 BR treated 12h replicate 1

description: BR treatment for 12h


title: Col-0 BR treated 24h replicate 2

description: BR treatment for 24h


title: Col-0 BR treated 24h replicate 1

description: BR treatment for 24h


title: Col-0 BR treated 1h replicate 2

description: BR treatment for 1h


title: Col-0 BR treated 1h replicate 3

description: BR treatment for 1h


title: Col-0 BR treated 2h replicate 1

description: BR treatment for 2h


title: Col-0 BR treated 12h replicate 3

description: BR treatment for 12h


title: Col-0 BR treated 2h replicate 2

description: BR treatment for 2h


title: Col-0 BR treated 1h replicate 1

description: BR treatment for 1h


title: Col-0 BR treated 0h replicate 1

description: BR treatment for 0h


title: Col-0 BR treated 0.5 h replicate 3

description: BR treatment for 0.5h


title: Col-0 BR treated 0.25 h replicate 2

description: BR treatment for 0.25h


title: Col-0 BR treated 4h replicate 3

description: BR treatment for 4h


title: Col-0 BR treated 0.5 h replicate 1

description: BR treatment for 0.5h


title: Col-0 BR treated 0.5 h replicate 2

description: BR treatment for 0.5h


title: Col-0 SA treated 8h replicate 2

description: SA treatment for 8h


title: Col-0 BR treated 0.25 h replicate 1

description: BR treatment for 0.25h


title: Col-0 SA treated 8h replicate 3

description: SA treatment for 8h


title: Col-0 SA treated 4h replicate 2

description: SA treatment for 4h


title: Col-0 SA treated 4h replicate 3

description: SA treatment for 4h


title: Col-0 BR treated 12h replicate 2

description: BR treatment for 12h


title: Col-0 SA treated 4h replicate 1

description: SA treatment for 4h


title: Col-0 SA treated 8h replicate 1

description: SA treatment for 8h


title: Col-0 BR treated 0h replicate 2

description: BR treatment for 0h


title: Col-0 SA treated 2h replicate 3

description: SA treatment for 2h


title: Col-0 SA treated 24h replicate 1

description: SA treatment for 24h


title: Col-0 SA treated 2h replicate 2

description: SA treatment for 2h


title: Col-0 BR treated 0h replicate 3

description: BR treatment for 0h


title: Col-0 SA treated 1h replicate 2

description: SA treatment for 1h


title: Col-0 SA treated 24h replicate 3

description: SA treatment for 24h


title: Col-0 SA treated 1h replicate 3

description: SA treatment for 1h


title: Col-0 SA treated 1h replicate 1

description: SA treatment for 1h


title: Col-0 SA treated 12h replicate 2

description: SA treatment for 12h


title: Col-0 SA treated 12h replicate 1

description: SA treatment for 12h


title: Col-0 SA treated 2h replicate 1

description: SA treatment for 2h


title: Col-0 SA treated 12h replicate 3

description: SA treatment for 12h


title: Col-0 SA treated 0h replicate 2

description: SA treatment for 0h


title: Col-0 SA treated 0h replicate 3

description: SA treatment for 0h


title: Col-0 SA treated 0.5 h replicate 3

description: SA treatment for 0.5h


title: Col-0 SA treated 0.5 h replicate 2

description: SA treatment for 0.5h


title: Col-0 SA treated 0.5 h replicate 1

description: SA treatment for 0.5h


title: Col-0 SA treated 0.25 h replicate 2

description: SA treatment for 0.25h


title: Col-0 SA treated 0.25 h replicate 3

description: SA treatment for 0.25h


title: Col-0 SA treated 0.25 h replicate 1

description: SA treatment for 0.25h


title: Col-0 SA treated 24h replicate 2

description: SA treatment for 24h


title: Col-0 Air treatment replicate 1

description: air treatment for 2h

data_processing:
base-calling using RTA 2.7.7
Fastq files were trimmed using Trimglore V0.4.4 and trimmed reads were mapped to the Arabidopsis TAIR10 genome using Bowtie2 V2.2.9
Shiftsize was calculated using phantompeakqualtools and default parameters
Peaks called with MACS2 version 2.1.0 (parameters options–nomodel –shiftsize  –g 1.19e8 –q 0.05). A concatenated file of all non-transgenic control IP reads was used as the control in peak calling
ChIPseeker with default parameters  was used for annotation. gene ontology enrichment was assessed using clusterProfiler and ClueGO
TAIR10
Binding sites region output created by MACS2 in narrowpeak format.

treatment_protocol: Air or ethylene treated for 2h

value: Goat IgG whole molecule


title: Col-0 EIN3::EIN3-Ypet ET treatment for 2h replicate 2

description: ethylene treatment for 2h

value: Col-0 EIN3::EIN3-Ypet


title: Col-0 EIN3::EIN3-Ypet ET treatment for 2h replicate 1

description: ethylene treatment for 2h


title: Col-0 EIN3::EIN3-Ypet ET treatment for 2h replicate 3

description: ethylene treatment for 2h


title: Col-0 SA treated 0h replicate 1

description: SA treatment for 0h


title: Col-0 EDF3::EDF3-Ypet ET treatment for 2h replicate 2

description: ethylene treatment for 2h

value: Col-0 EDF3::EDF3-Ypet


title: Col-0 EDF2::EDF2-Ypet ET treatment for 2h replicate 2

description: ethylene treatment for 2h

value: Col-0 EDF2::EDF2-Ypet


title: Col-0 EDF3::EDF3-Ypet ET treatment for 2h replicate 3

description: ethylene treatment for 2h

value: Goat anti-GFP


title: Col-0 EDF3::EDF3-Ypet ET treatment for 2h replicate 1

description: ethylene treatment for 2h


title: Col-0 EIN3::EIN3-Ypet  Air  treatment for 2h replicate 3

description: ethylene treatment for 2h


title: Col-0 EIN3::EIN3-Ypet  Air  treatment for 2h replicate 2

description: ethylene treatment for 2h


title: Col-0 EIN3::EIN3-Ypet  Air  treatment for 2h replicate 1

description: ethylene treatment for 2h


title: Col-0 EDF3::EDF3-Ypet  Air  treatment for 2h replicate 1

description: ethylene treatment for 2h


title: Col-0 EDF3::EDF3-Ypet  Air  treatment for 2h replicate 2

description: ethylene treatment for 2h


title: Col-0 EDF3::EDF3-Ypet  Air  treatment for 2h replicate 3

description: ethylene treatment for 2h


title: Col-0 EDF2::EDF2-Ypet ET treatment for 2h replicate 1

description: ethylene treatment for 2h


title: Col-0 EDF2::EDF2-Ypet  Air  treatment for 2h replicate 1

description: ethylene treatment for 2h


title: Col-0 EDF2::EDF2-Ypet  Air  treatment for 2h replicate 2

description: ethylene treatment for 2h


title: Col-0 EDF1::EDF1-Ypet ET treatment for 2h replicate 2

description: ethylene treatment for 2h

value: Col-0 EDF1::EDF1-Ypet


title: Col-0 EDF1::EDF1-Ypet  Air  treatment for 2h replicate 3

description: ethylene treatment for 2h


title: Col-0 EDF1::EDF1-Ypet  Air  treatment for 2h replicate 1

description: ethylene treatment for 2h


title: Col-0 EDF1::EDF1-Ypet ET treatment for 2h replicate 1

description: ethylene treatment for 2h


title: MRPL41 [RNCMPT01885]

status: Public on Mar 31 2023

type: RNA

city: Toronto

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description:
C152_2.txt
channel 1

hyb_protocol: Hybridizations were carried out for 20 hours at 42°C and washed for 30 seconds in 6 x SSPE, 0.005% sarcosine and 30 seconds in 0.06x SPE in a HS4800 Pro Hybridization Station (Tecan).

scan_protocol: Arrays were scanned on a microarray scanner at 5 micron resolution (Axon Instruments GenePix 4000B). Images were quantified using Imagene 8.0.

data_processing: Experimental data is contained in a matrix where rows correspond to microarray probes and columns are the normalized intensities of the Cy3- or Cy5-labeled RNA from the GST-RBP pulldown assay. For the data processing, first, low quality spots due to spatial trends or other problems related to image analysis are discarded. Next, quantile normalization was applied to calibrate multiple arrays. Background signal and other nonspecific binding effects are removed by subtracting from each spot the row median value across all experiments, and dividing by the robust estimate of standard deviation, calculated across all the experiments. Finally, the same robust z-score transformation is applied to each column (i.e. experiment). NOTE: For the raw data files, the "N" in the headers  (linked below as a supplementary file) stands for "Normalized". The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, therefore the data under the headings should be interpreted without the "N" (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).

organism: synthetic construct

source_name: Pulldown RNA labeled with Cy3

label_protocol: Purified RBP-specific pulldown RNA are labeled with Cy3 or Cy5 according to the manufacturer's recommended protocol (Kreatech, Cat# EA-021).

extract_protocol: Bound RNA from an RNA pulldown assay is eluted in STE Buffer (1% SDS, 10 mM Tris pH 7.5, 2 mM EDTA) by heating at 90°C for 5 minutes and purified by phenol-chloroform extraction followed by ethanol precipitation.

tag: protocol

value: GST-tagged RNA-binding protein pulldown


title: MRPL4 [RNCMPT01884]

description:
C152_2.txt
channel 2

source_name: Pulldown RNA labeled with Cy5


title: C1orf52 [RNCMPT01882]

description:
C151_2.txt
channel 2


title: Col-0 Air treatment replicate 2

description: air treatment for 2h


title: MRPL3 [RNCMPT01878]

description:
C149_2.txt
channel 2


title: SREK1IP1 [RNCMPT01879]

description:
C149_2.txt
channel 1


title: Col-0 BR treated 0.25 h replicate 3

description: BR treatment for 0.25h


title: MRPL21 [RNCMPT01877]

description:
C148_2.txt
channel 1


title: Col-0 EDF3::EDF3-Ypet  Air  for 2h replicate 1

value: Col-0 EDF3::EDF3-Ypet  Air  treatment for 2h


title: Col-0 EDF1::EDF1-Ypet  Air  treatment for 2h replicate 2

description: ethylene treatment for 2h


title: MRPL20 [RNCMPT01876]

description:
C148_2.txt
channel 2


title: MRPL14 [RNCMPT01874]

description:
C147_2.txt
channel 2


title: MRPL15 [RNCMPT01875]

description:
C147_2.txt
channel 1


title: MRPL11 [RNCMPT01873]

description:
C146_2.txt
channel 1


title: METTL16 [RNCMPT01871]

description:
C145_2.txt
channel 1


title: MRPL39 [RNCMPT01883]

description:
C151_2.txt
channel 1


title: LSM14B [RNCMPT01866]

description:
C143_2.txt
channel 2


title: HIST1H1E [RNCMPT01859]

description:
C139_2.txt
channel 1


title: LRRC47 [RNCMPT01863]

description:
C141_2.txt
channel 1


title: NUP153 [RNCMPT01880]

description:
C150_2.txt
channel 2


title: MCAT [RNCMPT01869]

description:
C144_2.txt
channel 1


title: MAK16 [RNCMPT01867]

description:
C143_2.txt
channel 1


title: LSM14A [RNCMPT01865]

description:
C142_2.txt
channel 1


title: ISY1 [RNCMPT01862]

description:
C141_2.txt
channel 2


title: HIST1H1B [RNCMPT01857]

description:
C138_2.txt
channel 1


title: IBA57 [RNCMPT01861]

description:
C140_2.txt
channel 1


title: MAZ [RNCMPT01868]

description:
C144_2.txt
channel 2


title: HLA-A [RNCMPT01860]

description:
C140_2.txt
channel 2


title: HARS2 [RNCMPT01854]

description:
C137_2.txt
channel 2


title: MECP2 [RNCMPT01870]

description:
C145_2.txt
channel 2


title: HDAC2 [RNCMPT01855]

description:
C137_2.txt
channel 1


title: HDGF [RNCMPT01856]

description:
C138_2.txt
channel 2


title: GTF2F1 [RNCMPT01850]

description:
C135_2.txt
channel 2


title: HADHB [RNCMPT01853]

description:
C136_2.txt
channel 1


title: H1FX [RNCMPT01852]

description:
C136_2.txt
channel 2


title: GTPBP10 [RNCMPT01851]

description:
C135_2.txt
channel 1


title: GRWD1 [RNCMPT01849]

description:
C134_2.txt
channel 1


title: LRRC59 [RNCMPT01864]

description:
C142_2.txt
channel 2


title: GRN [RNCMPT01848]

description:
C134_2.txt
channel 2


title: HIST1H1D [RNCMPT01858]

description:
C139_2.txt
channel 2


title: NOP53 [RNCMPT01844]

description:
C132_2.txt
channel 2


title: MRPL10 [RNCMPT01872]

description:
C146_2.txt
channel 2


title: DBR1 [RNCMPT01840]

description:
C130_2.txt
channel 2


title: GNL3L [RNCMPT01845]

description:
C132_2.txt
channel 1


title: FSCN1 [RNCMPT01842]

description:
C131_2.txt
channel 2


title: FARSA [RNCMPT01837]

description:
C128_2.txt
channel 1


title: FDPS [RNCMPT01838]

description:
C129_2.txt
channel 2


title: FYTTD1 [RNCMPT01843]

description:
C131_2.txt
channel 1


title: FKBP4 [RNCMPT01839]

description:
C129_2.txt
channel 1


title: FLYWCH2 [RNCMPT01841]

description:
C130_2.txt
channel 1


title: ERI3 [RNCMPT01830]

description:
C125_2.txt
channel 2


title: DYNC1LI1 [RNCMPT01828]

description:
C124_2.txt
channel 2


title: EXOSC6 [RNCMPT01831]

description:
C125_2.txt
channel 1


title: CHTOP [RNCMPT01827]

description:
C123_2.txt
channel 1


title: EIF2AK2 [RNCMPT01829]

description:
C124_2.txt
channel 1


title: DCN [RNCMPT01826]

description:
C123_2.txt
channel 2


title: FAM46A [RNCMPT01834]

description:
C127_2.txt
channel 2


title: DBR1 [RNCMPT01824]

description:
C122_2.txt
channel 2


title: FAM133B [RNCMPT01833]

description:
C126_2.txt
channel 1


title: CRKL [RNCMPT01822]

description:
C121_2.txt
channel 2


title: GPATCH4 [RNCMPT01847]

description:
C133_2.txt
channel 1


title: FAM98A [RNCMPT01835]

description:
C127_2.txt
channel 1


title: CLNS1A [RNCMPT01821]

description:
C120_2.txt
channel 1


title: EXOSC9 [RNCMPT01832]

description:
C126_2.txt
channel 2


title: GOT2 [RNCMPT01846]

description:
C133_2.txt
channel 2


title: CISD2 [RNCMPT01820]

description:
C120_2.txt
channel 2


title: CWC15 [RNCMPT01823]

description:
C121_2.txt
channel 1


title: CDC42EP4 [RNCMPT01818]

description:
C119_2.txt
channel 2


title: vig2 [RNCMPT01817]

description:
C118_2.txt
channel 1


title: CDKN2A [RNCMPT01819]

description:
C119_2.txt
channel 1


title: FAM98B [RNCMPT01836]

description:
C128_2.txt
channel 2


title: FDY [RNCMPT01816]

description:
C118_2.txt
channel 2


title: PPHLN1 [RNCMPT01812]

description:
C116_2.txt
channel 2


title: USP17L24 [RNCMPT01815]

description:
C117_2.txt
channel 1


title: MRPL45 [RNCMPT01810]

description:
C115_2.txt
channel 2


title: NOSIP [RNCMPT01811]

description:
C115_2.txt
channel 1


title: ZNF622 [RNCMPT01808]

description:
C114_2.txt
channel 2


title: ZNF579 [RNCMPT01807]

description:
C113_2.txt
channel 1


title: ZNF346 [RNCMPT01805]

description:
C112_2.txt
channel 1


title: ZNF326 [RNCMPT01804]

description:
C112_2.txt
channel 2


title: ZNF207 [RNCMPT01803]

description:
C111_2.txt
channel 1


title: ZNF385A [RNCMPT01806]

description:
C113_2.txt
channel 2


title: DCAF13 [RNCMPT01825]

description:
C122_2.txt
channel 1


title: YTHDF1 [RNCMPT01795]

description:
C107_2.txt
channel 1


title: YARS [RNCMPT01793]

description:
C106_2.txt
channel 1


title: YWHAG [RNCMPT01797]

description:
C108_2.txt
channel 1


title: YTHDF3 [RNCMPT01796]

description:
C108_2.txt
channel 2


title: ZCCHC24 [RNCMPT01798]

description:
C109_2.txt
channel 2


title: ZCCHC7 [RNCMPT01800]

description:
C110_2.txt
channel 2


title: ZCCHC3 [RNCMPT01799]

description:
C109_2.txt
channel 1


title: XIRP1 [RNCMPT01792]

description:
C106_2.txt
channel 2


title: GADD45A [RNCMPT01814]

description:
C117_2.txt
channel 2


title: ZYX [RNCMPT01813]

description:
C116_2.txt
channel 1


title: KRT18 [RNCMPT01809]

description:
C114_2.txt
channel 1


title: SNHG28 [RNCMPT01790]

description:
C105_2.txt
channel 2


title: UTP23 [RNCMPT01789]

description:
C104_2.txt
channel 1


title: RCC1L [RNCMPT01791]

description:
C105_2.txt
channel 1


title: UBFD1 [RNCMPT01786]

description:
C103_2.txt
channel 2


title: UBE2I [RNCMPT01784]

description:
C102_2.txt
channel 2


title: TRMT10A [RNCMPT01782]

description:
C101_2.txt
channel 2


title: TRMT6 [RNCMPT01783]

description:
C101_2.txt
channel 1


title: UTP15 [RNCMPT01788]

description:
C104_2.txt
channel 2


title: TRIP6 [RNCMPT01781]

description:
C100_2.txt
channel 1


title: ZCCHC9 [RNCMPT01801]

description:
C110_2.txt
channel 1


title: ZMAT3 [RNCMPT01802]

description:
C111_2.txt
channel 2


title: TPD52L2 [RNCMPT01779]

description:
C99_2.txt
channel 1


title: SURF6 [RNCMPT01776]

description:
C98_2.txt
channel 2


title: TBL2 [RNCMPT01777]

description:
C98_2.txt
channel 1


title: TCF20 [RNCMPT01778]

description:
C99_2.txt
channel 2


title: SUMO1 [RNCMPT01775]

description:
C97_2.txt
channel 1


title: TPT1 [RNCMPT01780]

description:
C100_2.txt
channel 2


title: STIP1 [RNCMPT01773]

description:
C96_2.txt
channel 1


title: PURG [RNCMPT01769]

description:
C94_2.txt
channel 1


title: SRP14 [RNCMPT01771]

description:
C95_2.txt
channel 1


title: NUSAP1 [RNCMPT01768]

description:
C94_2.txt
channel 2


title: SPATS2L [RNCMPT01770]

description:
C95_2.txt
channel 2


title: SRP54 [RNCMPT01772]

description:
C96_2.txt
channel 2


title: UBE2L3 [RNCMPT01785]

description:
C102_2.txt
channel 1


title: SNTB2 [RNCMPT01764]

description:
C92_2.txt
channel 2


title: SPATS2 [RNCMPT01765]

description:
C92_2.txt
channel 1


title: SNRPB [RNCMPT01763]

description:
C91_2.txt
channel 1


title: SNIP1 [RNCMPT01761]

description:
C90_2.txt
channel 1


title: SNRNP40 [RNCMPT01762]

description:
C91_2.txt
channel 2


title: SLC25A5 [RNCMPT01760]

description:
C90_2.txt
channel 2


title: SERPINH1 [RNCMPT01757]

description:
C88_2.txt
channel 1


title: SCG3 [RNCMPT01756]

description:
C88_2.txt
channel 2


title: SAMSN1 [RNCMPT01753]

description:
C86_2.txt
channel 1


title: SBDS [RNCMPT01755]

description:
C87_2.txt
channel 1


title: SARS2 [RNCMPT01754]

description:
C87_2.txt
channel 2


title: SF3A2 [RNCMPT01758]

description:
C89_2.txt
channel 2


title: SUCLG1 [RNCMPT01774]

description:
C97_2.txt
channel 2


title: RRP8 [RNCMPT01748]

description:
C84_2.txt
channel 2


title: RRP9 [RNCMPT01749]

description:
C84_2.txt
channel 1


title: RRS1 [RNCMPT01750]

description:
C85_2.txt
channel 2


title: RPS6 [RNCMPT01744]

description:
C82_2.txt
channel 2


title: RPS5 [RNCMPT01743]

description:
C81_2.txt
channel 1


title: RPUSD3 [RNCMPT01746]

description:
C83_2.txt
channel 2


title: RSRC2 [RNCMPT01751]

description:
C85_2.txt
channel 1


title: RPUSD2 [RNCMPT01745]

description:
C82_2.txt
channel 1


title: RPS24 [RNCMPT01741]

description:
C80_2.txt
channel 1


title: NDUFV3 [RNCMPT01767]

description:
C93_2.txt
channel 1


title: RRP36 [RNCMPT01747]

description:
C83_2.txt
channel 1


title: CCDC9 [RNCMPT01766]

description:
C93_2.txt
channel 2


title: RPP30 [RNCMPT01737]

description:
C78_2.txt
channel 1


title: RPL24 [RNCMPT01735]

description:
C77_2.txt
channel 1


title: RPS11 [RNCMPT01738]

description:
C79_2.txt
channel 2


title: RPL32 [RNCMPT01736]

description:
C78_2.txt
channel 2


title: RPF1 [RNCMPT01734]

description:
C77_2.txt
channel 2


title: RPS2 [RNCMPT01740]

description:
C80_2.txt
channel 2


title: RCC2 [RNCMPT01732]

description:
C76_2.txt
channel 2


title: YARS2 [RNCMPT01794]

description:
C107_2.txt
channel 2


title: RARS2 [RNCMPT01731]

description:
C75_2.txt
channel 1


title: PTPN1 [RNCMPT01728]

description:
C74_2.txt
channel 2


title: REXO4 [RNCMPT01733]

description:
C76_2.txt
channel 1


title: CAVIN1 [RNCMPT01729]

description:
C74_2.txt
channel 1


title: SLBP [RNCMPT01759]

description:
C89_2.txt
channel 1


title: POU5F1 [RNCMPT01723]

description:
C71_2.txt
channel 1


title: PURB [RNCMPT01730]

description:
C75_2.txt
channel 2


title: PRPF38A [RNCMPT01725]

description:
C72_2.txt
channel 1


title: PSMD4 [RNCMPT01727]

description:
C73_2.txt
channel 1


title: PHF6 [RNCMPT01722]

description:
C71_2.txt
channel 2


title: PARP1 [RNCMPT01720]

description:
C70_2.txt
channel 2


title: PES1 [RNCMPT01721]

description:
C70_2.txt
channel 1


title: RTCA [RNCMPT01752]

description:
C86_2.txt
channel 2


title: P4HB [RNCMPT01719]

description:
C69_2.txt
channel 1


title: MRPL37 [RNCMPT01711]

description:
C66_2.txt
channel 2


title: RPS3 [RNCMPT01742]

description:
C81_2.txt
channel 2


title: RPS13 [RNCMPT01739]

description:
C79_2.txt
channel 1


title: NKAP [RNCMPT01710]

description:
C65_2.txt
channel 1


title: ZC3H7B [RNCMPT01708]

description:
C64_2.txt
channel 1


title: TAF15 [RNCMPT01706]

description:
C63_2.txt
channel 1


title: IFIT3 [RNCMPT01707]

description:
C64_2.txt
channel 2


title: NGRN [RNCMPT01701]

description:
C61_2.txt
channel 2


title: NIP7 [RNCMPT01700]

description:
C60_2.txt
channel 1


title: NAP1L4 [RNCMPT01698]

description:
C59_2.txt
channel 1


title: PRMT1 [RNCMPT01724]

description:
C72_2.txt
channel 2


title: MTERF1 [RNCMPT01695]

description:
C58_2.txt
channel 2


title: MRPS26 [RNCMPT01694]

description:
C57_2.txt
channel 1


title: NSUN5 [RNCMPT01712]

description:
C66_2.txt
channel 1


title: NAF1 [RNCMPT01697]

description:
C59_2.txt
channel 2


title: vig2 [RNCMPT01608]

description:
C2_2.txt
channel 1


title: MRPS14 [RNCMPT01692]

description:
C56_2.txt
channel 1


title: HABP4 [RNCMPT01603]

description:
B191_2.txt
channel 2


title: NAA38 [RNCMPT01696]

description:
C58_2.txt
channel 1


title: MRPS21 [RNCMPT01693]

description:
C57_2.txt
channel 2


title: vig [RNCMPT01600]

description:
B189_2.txt
channel 1


title: NSRP1 [RNCMPT01604]

description:
B191_2.txt
channel 1


title: MRPL42 [RNCMPT01689]

description:
C55_2.txt
channel 2


title: MRPL43 [RNCMPT01690]

description:
C55_2.txt
channel 1


title: RANBP2 [RNCMPT01601]

description:
B190_2.txt
channel 2


title: ZCCHC11 [RNCMPT01599]

description:
B189_2.txt
channel 2


title: NUDT14 [RNCMPT01602]

description:
B190_2.txt
channel 1


title: NUDT1 [RNCMPT01597]

description:
B188_2.txt
channel 2


title: SPOUT1 [RNCMPT01596]

description:
B187_2.txt
channel 1


title: ARCN1 [RNCMPT01595]

description:
B187_2.txt
channel 2


title: CAPN15 [RNCMPT01709]

description:
C65_2.txt
channel 2


title: ADK [RNCMPT01594]

description:
B186_2.txt
channel 1


title: ZCCHC3 [RNCMPT01593]

description:
B186_2.txt
channel 2


title: NIP7 [RNCMPT01702]

description:
C61_2.txt
channel 1


title: RTL3 [RNCMPT01590]

description:
B184_2.txt
channel 1


title: FDY [RNCMPT01607]

description:
C2_2.txt
channel 2


title: NUDT19 [RNCMPT01587]

description:
B183_2.txt
channel 2


title: PPYR1 [RNCMPT01586]

description:
B182_2.txt
channel 1


title: MRPL9 [RNCMPT01691]

description:
C56_2.txt
channel 2


title: C14orf93 [RNCMPT01585]

description:
B182_2.txt
channel 2


title: ZRANB3 [RNCMPT01584]

description:
B181_2.txt
channel 1


title: PRPF6 [RNCMPT01582]

description:
B180_2.txt
channel 1


title: IDI1 [RNCMPT01580]

description:
B179_2.txt
channel 1


title: C11orf68 [RNCMPT01583]

description:
B181_2.txt
channel 2


title: IFIT1B [RNCMPT01576]

description:
B177_2.txt
channel 1


title: serbp1b [RNCMPT01577]

description:
B178_2.txt
channel 2


title: BYSL [RNCMPT01581]

description:
B180_2.txt
channel 2


title: CCDC47 [RNCMPT01574]

description:
B176_2.txt
channel 1


title: NUDT6 [RNCMPT01572]

description:
B175_2.txt
channel 1


title: RBM4B [RNCMPT01571]

description:
B175_2.txt
channel 2


title: RYBP [RNCMPT01568]

description:
B173_2.txt
channel 1


title: CCT4 [RNCMPT01567]

description:
B173_2.txt
channel 2


title: PRPF38B [RNCMPT01726]

description:
C73_2.txt
channel 2


title: CD3EAP [RNCMPT01564]

description:
B171_2.txt
channel 1


title: NUDT16 [RNCMPT01562]

description:
B170_2.txt
channel 1


title: ZCCHC12 [RNCMPT01561]

description:
B170_2.txt
channel 2


title: CFAP20 [RNCMPT01559]

description:
B169_2.txt
channel 2


title: ZCCHC13 [RNCMPT01558]

description:
B168_2.txt
channel 1


title: GADD45B [RNCMPT01556]

description:
B167_2.txt
channel 1


title: SHARPIN [RNCMPT01557]

description:
B168_2.txt
channel 2


title: ZCCHC14 [RNCMPT01555]

description:
B167_2.txt
channel 2


title: ZCCHC10 [RNCMPT01551]

description:
B165_2.txt
channel 2


title: ARL6IP4 [RNCMPT01550]

description:
B164_2.txt
channel 1


title: CCT3 [RNCMPT01549]

description:
B164_2.txt
channel 2


title: NAA15 [RNCMPT01573]

description:
B176_2.txt
channel 2


title: EIF1 [RNCMPT01548]

description:
B163_2.txt
channel 1


title: IFIT1 [RNCMPT01546]

description:
B162_2.txt
channel 1


title: ZCCHC7 [RNCMPT01547]

description:
B163_2.txt
channel 2


title: RPL27A [RNCMPT01544]

description:
B161_2.txt
channel 1


title: CCDC137 [RNCMPT01543]

description:
B161_2.txt
channel 2


title: HABP4 [RNCMPT01541]

description:
B160_2.txt
channel 2


title: PNMA3 [RNCMPT01539]

description:
B159_2.txt
channel 2


title: DCD [RNCMPT01537]

description:
B158_2.txt
channel 2


title: CCDC9B [RNCMPT01534]

description:
B156_2.txt
channel 1


title: PPP5C [RNCMPT01535]

description:
B157_2.txt
channel 2


title: YAF2 [RNCMPT01533]

description:
B156_2.txt
channel 2


title: AATF [RNCMPT01529]

description:
B154_2.txt
channel 2


title: TEX13A [RNCMPT01528]

description:
B153_2.txt
channel 1


title: NUDT5 [RNCMPT01523]

description:
B151_2.txt
channel 2


title: ZCCHC2 [RNCMPT01520]

description:
B149_2.txt
channel 1


title: HABP4 [RNCMPT01519]

description:
B149_2.txt
channel 2


title: SNRPG [RNCMPT01516]

description:
B147_2.txt
channel 1


title: LIN28B [RNCMPT01542]

description:
B160_2.txt
channel 1


title: ZCCHC24 [RNCMPT01517]

description:
B148_2.txt
channel 2


title: RTL4 [RNCMPT01513]

description:
B146_2.txt
channel 2


title: ZCCHC9 [RNCMPT01588]

description:
B183_2.txt
channel 1


title: SRP72 [RNCMPT01514]

description:
B146_2.txt
channel 1


title: NPLOC4 [RNCMPT01540]

description:
B159_2.txt
channel 1


title: NUDT14 [RNCMPT01509]

description:
B144_2.txt
channel 2


title: NUDT8 [RNCMPT01508]

description:
B143_2.txt
channel 1


title: MDM4 [RNCMPT01506]

description:
B142_2.txt
channel 1


title: NUDT18 [RNCMPT01538]

description:
B158_2.txt
channel 1


title: CNOT10 [RNCMPT01530]

description:
B154_2.txt
channel 1


title: EWSR1 [RNCMPT01505]

description:
B142_2.txt
channel 2


title: APOBEC3B [RNCMPT01500]

description:
B139_2.txt
channel 1


title: MDM2 [RNCMPT01499]

description:
B139_2.txt
channel 2


title: C19orf47 [RNCMPT01497]

description:
B138_2.txt
channel 2


title: FKBP4 [RNCMPT01502]

description:
B140_2.txt
channel 1


title: NUDT10 [RNCMPT01496]

description:
B137_2.txt
channel 1


title: RBCK1 [RNCMPT01494]

description:
B136_2.txt
channel 1


title: NUDT7 [RNCMPT01493]

description:
B136_2.txt
channel 2


title: CCT6A [RNCMPT01489]

description:
B134_2.txt
channel 2


title: ANXA11 [RNCMPT01579]

description:
B179_2.txt
channel 2


title: ZCCHC6 [RNCMPT01511]

description:
B145_2.txt
channel 2


title: RPP38 [RNCMPT01575]

description:
B177_2.txt
channel 2


title: C4BPA [RNCMPT01477]

description:
B128_2.txt
channel 2


title: SECISBP2 [RNCMPT01482]

description:
B130_2.txt
channel 1


title: NEIL3 [RNCMPT01483]

description:
B131_2.txt
channel 2


title: CPSF4 [RNCMPT01471]

description:
B125_2.txt
channel 2


title: GADD45G [RNCMPT01475]

description:
B127_2.txt
channel 2


title: ZCCHC17 [RNCMPT01468]

description:
B123_2.txt
channel 1


title: RBBP6 [RNCMPT01487]

description:
B133_2.txt
channel 2


title: ZCCHC8 [RNCMPT01460]

description:
B119_2.txt
channel 1


title: NUDT22 [RNCMPT01466]

description:
B122_2.txt
channel 1


title: RNF31 [RNCMPT01464]

description:
B121_2.txt
channel 1


title: Serbp1 [RNCMPT01473]

description:
B126_2.txt
channel 2


title: NUDT4 [RNCMPT01458]

description:
B118_2.txt
channel 1


title: DCP2 [RNCMPT01457]

description:
B118_2.txt
channel 2


title: NUDT12 [RNCMPT01465]

description:
B122_2.txt
channel 2


title: ANP32A [RNCMPT01472]

description:
B125_2.txt
channel 1


title: MRPS12 [RNCMPT01455]

description:
B117_2.txt
channel 2


title: SECISBP2L [RNCMPT01453]

description:
B116_2.txt
channel 2


title: ZCCHC18 [RNCMPT01486]

description:
B132_2.txt
channel 1


title: NHP2 [RNCMPT01448]

description:
B113_2.txt
channel 1


title: SF1 [RNCMPT01452]

description:
B115_2.txt
channel 1


title: APOBEC3F [RNCMPT01480]

description:
B129_2.txt
channel 1


title: RPP25L [RNCMPT01443]

description:
B111_2.txt
channel 2


title: CDC40 [RNCMPT01445]

description:
B112_2.txt
channel 2


title: NSA2 [RNCMPT01442]

description:
B110_2.txt
channel 1


title: TAB2 [RNCMPT01510]

description:
B144_2.txt
channel 1


title: PURA [RNCMPT01439]

description:
B109_2.txt
channel 2


title: ETF1 [RNCMPT01438]

description:
B108_2.txt
channel 1


title: RPP25 [RNCMPT01441]

description:
B110_2.txt
channel 2


title: RPS15A [RNCMPT01411]

description:
B95_2.txt
channel 2


title: DARS [RNCMPT01410]

description:
B94_2.txt
channel 1


title: SSBP1 [RNCMPT01403]

description:
B91_2.txt
channel 2


title: CNBP [RNCMPT01406]

description:
B92_2.txt
channel 1


title: HMGB2 [RNCMPT01398]

description:
B88_2.txt
channel 1


title: CCBL2 [RNCMPT01409]

description:
B94_2.txt
channel 2


title: PDIA3 [RNCMPT01397]

description:
B88_2.txt
channel 2


title: LGALS3 [RNCMPT01401]

description:
B90_2.txt
channel 2


title: RSL1D1 [RNCMPT01402]

description:
B90_2.txt
channel 1


title: PRPF31 [RNCMPT01394]

description:
B86_2.txt
channel 1


title: RPS19 [RNCMPT01396]

description:
B87_2.txt
channel 1


title: BAG4 [RNCMPT01446]

description:
B112_2.txt
channel 1


title: LYAR [RNCMPT01393]

description:
B86_2.txt
channel 2


title: HSD17B10 [RNCMPT01389]

description:
B84_2.txt
channel 2


title: GNB2L1 [RNCMPT01391]

description:
B85_2.txt
channel 2


title: HSPB1 [RNCMPT01386]

description:
B82_2.txt
channel 1


title: THUMPD1 [RNCMPT01383]

description:
B81_2.txt
channel 2


title: SERBP1 [RNCMPT01384]

description:
B81_2.txt
channel 1


title: IFIT2 [RNCMPT01382]

description:
B80_2.txt
channel 1


title: KPNA2 [RNCMPT01412]

description:
B95_2.txt
channel 1


title: EMG1 [RNCMPT01380]

description:
B79_2.txt
channel 1


title: GAR1 [RNCMPT01437]

description:
B108_2.txt
channel 2


title: ZRANB1 [RNCMPT01578]

description:
B178_2.txt
channel 1


title: HSPD1 [RNCMPT01381]

description:
B80_2.txt
channel 2


title: RPS21 [RNCMPT01378]

description:
B78_2.txt
channel 1


title: PDAP1 [RNCMPT01377]

description:
B78_2.txt
channel 2


title: LSM6 [RNCMPT01376]

description:
B77_2.txt
channel 1


title: ALDH6A1 [RNCMPT01404]

description:
B91_2.txt
channel 1


title: RPS27A [RNCMPT01373]

description:
B76_2.txt
channel 2


title: RPL23A [RNCMPT01367]

description:
B73_2.txt
channel 2


title: MRPL13 [RNCMPT01372]

description:
B75_2.txt
channel 1


title: ZRANB2 [RNCMPT01366]

description:
B72_2.txt
channel 1


title: NUDT21 [RNCMPT01369]

description:
B74_2.txt
channel 2


title: IFIT2 [RNCMPT01371]

description:
B75_2.txt
channel 2


title: MRPL32 [RNCMPT01364]

description:
B71_2.txt
channel 1


title: DEK [RNCMPT01362]

description:
B70_2.txt
channel 1


title: NUCKS1 [RNCMPT01718]

description:
C69_2.txt
channel 2


title: DIMT1 [RNCMPT01360]

description:
B69_2.txt
channel 1


title: ZRANB2 [RNCMPT01357]

description:
B68_2.txt
channel 2


title: MRPS5 [RNCMPT01358]

description:
B68_2.txt
channel 1


title: NME1 [RNCMPT01356]

description:
B67_2.txt
channel 1


title: SERBP1 [RNCMPT01359]

description:
B69_2.txt
channel 2


title: C11orf31 [RNCMPT01355]

description:
B67_2.txt
channel 2


title: CS [RNCMPT01385]

description:
B82_2.txt
channel 2


title: RPL4 [RNCMPT01353]

description:
B66_2.txt
channel 2


title: HMGN5 [RNCMPT01352]

description:
B65_2.txt
channel 1


title: SNRPC [RNCMPT01351]

description:
B65_2.txt
channel 2


title: HIST1H1C [RNCMPT01350]

description:
B64_2.txt
channel 1


title: TCP1 [RNCMPT01346]

description:
B62_2.txt
channel 1


title: TWF2 [RNCMPT01345]

description:
B62_2.txt
channel 2


title: RPS27L [RNCMPT01338]

description:
B58_2.txt
channel 1


title: PEG10 [RNCMPT01344]

description:
B61_2.txt
channel 1


title: RPL8 [RNCMPT01340]

description:
B59_2.txt
channel 1


title: ANXA7 [RNCMPT01347]

description:
B63_2.txt
channel 2


title: RPS18 [RNCMPT01337]

description:
B58_2.txt
channel 2


title: NUDT16L1 [RNCMPT01334]

description:
B56_2.txt
channel 1


title: RPS12 [RNCMPT01363]

description:
B71_2.txt
channel 2


title: PURA [RNCMPT01333]

description:
B56_2.txt
channel 2


title: NAP1L1 [RNCMPT01331]

description:
B55_2.txt
channel 2


title: FAU [RNCMPT01329]

description:
B54_2.txt
channel 2


title: DUT [RNCMPT01328]

description:
B53_2.txt
channel 1


title: CNBP [RNCMPT01327]

description:
B53_2.txt
channel 2


title: CALR [RNCMPT01326]

description:
B52_2.txt
channel 1


title: RPL14 [RNCMPT01325]

description:
B52_2.txt
channel 2


title: RPS20 [RNCMPT01323]

description:
B51_2.txt
channel 2


title: ALDOA [RNCMPT01321]

description:
B50_2.txt
channel 2


title: NUDT21 [RNCMPT01322]

description:
B50_2.txt
channel 1


title: CNBP [RNCMPT01314]

description:
B46_2.txt
channel 1


title: RPL18A [RNCMPT01318]

description:
B48_2.txt
channel 1


title: HOXB6 [RNCMPT01315]

description:
B47_2.txt
channel 2


title: RPL35A [RNCMPT01320]

description:
B49_2.txt
channel 1


title: PEG10 [RNCMPT01313]

description:
B46_2.txt
channel 2


title: CPNE3 [RNCMPT01311]

description:
B45_2.txt
channel 2


title: FCF1 [RNCMPT01310]

description:
B44_2.txt
channel 1


title: C7orf50 [RNCMPT01308]

description:
B43_2.txt
channel 1


title: PPIB [RNCMPT01307]

description:
B43_2.txt
channel 2


title: RPS14 [RNCMPT01349]

description:
B64_2.txt
channel 2


title: RPL36 [RNCMPT01303]

description:
B41_2.txt
channel 2


title: MRM1 [RNCMPT01332]

description:
B55_2.txt
channel 1


title: PKM [RNCMPT01335]

description:
B57_2.txt
channel 2


title: MRPL28 [RNCMPT01302]

description:
B40_2.txt
channel 1


title: RPL22 [RNCMPT01297]

description:
B38_2.txt
channel 2


title: RPP25 [RNCMPT01299]

description:
B39_2.txt
channel 2


title: NHP2L1 [RNCMPT01301]

description:
B40_2.txt
channel 2


title: RPL11 [RNCMPT01296]

description:
B37_2.txt
channel 1


title: ATP5C1 [RNCMPT01295]

description:
B37_2.txt
channel 2


title: H1F0 [RNCMPT01292]

description:
B35_2.txt
channel 1


title: EIF5A [RNCMPT01291]

description:
B35_2.txt
channel 2


title: YWHAE [RNCMPT01289]

description:
B34_2.txt
channel 2


title: ETF1 [RNCMPT01286]

description:
B32_2.txt
channel 1


title: COA6 [RNCMPT01281]

description:
B30_2.txt
channel 2


title: TFB2M [RNCMPT01317]

description:
B48_2.txt
channel 2


title: MRPL54 [RNCMPT01282]

description:
B30_2.txt
channel 1


title: SERBP1 [RNCMPT01283]

description:
B31_b_2.txt
channel 2


title: RPL27 [RNCMPT01280]

description:
B29_2.txt
channel 1


title: HMGB3 [RNCMPT01288]

description:
B33_2.txt
channel 1


title: RPL30 [RNCMPT01277]

description:
B28_2.txt
channel 2


title: CCDC59 [RNCMPT01305]

description:
B42_2.txt
channel 2


title: ZRANB2 [RNCMPT01306]

description:
B42_2.txt
channel 1


title: RPL7A [RNCMPT01275]

description:
B27_2.txt
channel 2


title: MRPS28 [RNCMPT01274]

description:
B26_2.txt
channel 1


title: UCHL5 [RNCMPT01276]

description:
B27_2.txt
channel 1


title: RPL36A [RNCMPT01271]

description:
B25_2.txt
channel 2


title: RANBP2 [RNCMPT01552]

description:
B165_2.txt
channel 1


title: serbp1a [RNCMPT01570]

description:
B174_2.txt
channel 1


title: FRG1 [RNCMPT01270]

description:
B24_2.txt
channel 1


title: RPL6 [RNCMPT01300]

description:
B39_2.txt
channel 1


title: GAR1 [RNCMPT01267]

description:
B23_2.txt
channel 2


title: RPL3 [RNCMPT01265]

description:
B22_2.txt
channel 2


title: BCCIP [RNCMPT01259]

description:
B19_2.txt
channel 2


title: RPL13A [RNCMPT01261]

description:
B20_2.txt
channel 2


title: ENO1 [RNCMPT01262]

description:
B20_2.txt
channel 1


title: NSA2 [RNCMPT01253]

description:
B16_2.txt
channel 2


title: RP9 [RNCMPT01252]

description:
B15_2.txt
channel 1


title: EIF1AX [RNCMPT01258]

description:
B18_2.txt
channel 1


title: MRPS35 [RNCMPT01249]

description:
B14_2.txt
channel 2


title: SNRPA1 [RNCMPT01248]

description:
B13_2.txt
channel 1


title: PTRH1 [RNCMPT01250]

description:
B14_2.txt
channel 1


title: ATP5A1 [RNCMPT01240]

description:
B9_2.txt
channel 1


title: IFIT5 [RNCMPT01229]

description:
B4_2.txt
channel 2


title: RPS26 [RNCMPT01234]

description:
B6_2.txt
channel 1


title: SRFBP1 [RNCMPT01239]

description:
B9_2.txt
channel 2


title: TFB1M [RNCMPT01226]

description:
B2_2.txt
channel 1


title: RPL17 [RNCMPT01221]

description:
A430_2_N.txt
channel 2


title: SRP19 [RNCMPT01218]

description:
A428_2_N.txt
channel 1


title: FAM32A [RNCMPT01222]

description:
A430_2_N.txt
channel 1


title: KCTD12 [RNCMPT01223]

description:
B1_2.txt
channel 2


title: PSMC1 [RNCMPT01216]

description:
A427_2_N.txt
channel 1


title: RPS9 [RNCMPT01217]

description:
A428_2_N.txt
channel 2


title: TES [RNCMPT01215]

description:
A427_2_N.txt
channel 2


title: EIF5 [RNCMPT01214]

description:
A426_2_N.txt
channel 1


title: RPL37A [RNCMPT01256]

description:
B17_2.txt
channel 1


title: TUFM [RNCMPT01210]

description:
A424_2_N.txt
channel 1


title: GDI2 [RNCMPT01209]

description:
A424_2_N.txt
channel 2


title: ACAA2 [RNCMPT01212]

description:
A425_2_N.txt
channel 1


title: PA2G4 [RNCMPT01208]

description:
A423_2_N.txt
channel 1


title: RPL15 [RNCMPT01247]

description:
B13_2.txt
channel 2


title: FKBP3 [RNCMPT01207]

description:
A423_2_N.txt
channel 2


title: EIF3H [RNCMPT01213]

description:
A426_2_N.txt
channel 2


title: S100A4 [RNCMPT01225]

description:
B2_2.txt
channel 2


title: C2orf15 [RNCMPT01195]

description:
A418_2_N.txt
channel 2


title: SNRPD1 [RNCMPT01200]

description:
A419_2_N.txt
channel 1


title: POP7 [RNCMPT01199]

description:
A419_2_N.txt
channel 2


title: PPP1CC [RNCMPT01206]

description:
A422_2_N.txt
channel 1


title: ERH [RNCMPT01204]

description:
A421_2_N.txt
channel 1


title: RPL5 [RNCMPT01219]

description:
A429_2_N.txt
channel 2


title: S100A16 [RNCMPT01202]

description:
A420_2_N.txt
channel 1


title: LSM4 [RNCMPT01205]

description:
A422_2_N.txt
channel 2


title: RPL7A [RNCMPT01194]

description:
A417_2_N.txt
channel 1


title: JUN [RNCMPT01201]

description:
A420_2_N.txt
channel 2


title: TFAM [RNCMPT01193]

description:
A417_2_N.txt
channel 2


title: RPL7 [RNCMPT01191]

description:
A416_2_N.txt
channel 2


title: AHNAK [RNCMPT01196]

description:
A418_2_N.txt
channel 1


title: MRPL1 [RNCMPT01189]

description:
A415_2_N.txt
channel 2


title: MRPS15 [RNCMPT01188]

description:
A414_2_N.txt
channel 1


title: ARF1 [RNCMPT01187]

description:
A414_2_N.txt
channel 2


title: PEBP1 [RNCMPT01186]

description:
A413_2_N.txt
channel 1


title: RPLP0 [RNCMPT01190]

description:
A415_2_N.txt
channel 1


title: RPS15 [RNCMPT01184]

description:
A412_2_N.txt
channel 1


title: RPL26 [RNCMPT01185]

description:
A413_2_N.txt
channel 2


title: EIF4E2 [RNCMPT01182]

description:
A411_2_N.txt
channel 1


title: MRPL32 [RNCMPT01183]

description:
A412_2_N.txt
channel 2


title: CHCHD1 [RNCMPT01203]

description:
A421_2_N.txt
channel 2


title: APEX1 [RNCMPT01179]

description:
A410_2_N.txt
channel 2


title: MRTO4 [RNCMPT01180]

description:
A410_2_N.txt
channel 1


title: TSNAX [RNCMPT01178]

description:
A409_2_N.txt
channel 1


title: RPL10 [RNCMPT01177]

description:
A409_2_N.txt
channel 2


title: LSM4 [RNCMPT01278]

description:
B28_2.txt
channel 1


title: GLRX3 [RNCMPT01192]

description:
A416_2_N.txt
channel 1


title: ASS1 [RNCMPT01172]

description:
A406_2_N.txt
channel 1


title: MRPS9 [RNCMPT01170]

description:
A405_2_N.txt
channel 1


title: MRPS5 [RNCMPT01168]

description:
A404_2_N.txt
channel 1


title: PIN4 [RNCMPT01173]

description:
A407_2_N.txt
channel 2


title: RPS7 [RNCMPT01164]

description:
A402_2_N.txt
channel 1


title: CCBL2 [RNCMPT01169]

description:
A405_2_N.txt
channel 2


title: RPL29 [RNCMPT01176]

description:
A408_2_N.txt
channel 1


title: NQO1 [RNCMPT01163]

description:
A402_2_N.txt
channel 2


title: ERAL1 [RNCMPT01171]

description:
A406_2_N.txt
channel 2


title: CSRP1 [RNCMPT01160]

description:
A400_2_N.txt
channel 1


title: LSM1 [RNCMPT01175]

description:
A408_2_N.txt
channel 2


title: RPS17 [RNCMPT01166]

description:
A403_2_N.txt
channel 1


title: RPS8 [RNCMPT01157]

description:
A399_2_N.txt
channel 2


title: NTPCR [RNCMPT01158]

description:
A399_2_N.txt
channel 1


title: MRPL22 [RNCMPT01162]

description:
A401_2_N.txt
channel 1


title: C14orf166 [RNCMPT01161]

description:
A401_2_N.txt
channel 2


title: MRPL2 [RNCMPT01181]

description:
A411_2_N.txt
channel 2


title: SNRPD2 [RNCMPT01156]

description:
A398_2_N.txt
channel 1


title: GRB2 [RNCMPT01159]

description:
A400_2_N.txt
channel 2


title: RPL22 [RNCMPT01155]

description:
A398_2_N.txt
channel 2


title: RPL31 [RNCMPT01154]

description:
A397_2_N.txt
channel 1


title: SMNDC1 [RNCMPT01152]

description:
A396_2_N.txt
channel 1


title: PFN1 [RNCMPT01153]

description:
A397_2_N.txt
channel 2


title: RPL12 [RNCMPT01150]

description:
A395_2_N.txt
channel 1


title: MRPL54 [RNCMPT01151]

description:
A396_2_N.txt
channel 2


title: RPL23A [RNCMPT01149]

description:
A395_2_N.txt
channel 2


title: RPS27 [RNCMPT01148]

description:
A394_2_N.txt
channel 1


title: TEFM [RNCMPT01167]

description:
A404_2_N.txt
channel 2


title: HMGN2 [RNCMPT01174]

description:
A407_2_N.txt
channel 1


title: MRPL13 [RNCMPT01147]

description:
A394_2_N.txt
channel 2


title: LSM6 [RNCMPT01140]

description:
A390_2_N.txt
channel 1


title: EIF4E [RNCMPT01146]

description:
A393_2_N.txt
channel 1


title: LSM3 [RNCMPT01145]

description:
A393_2_N.txt
channel 2


title: RPL21 [RNCMPT01142]

description:
A391_2_N.txt
channel 1


title: SAP18 [RNCMPT01144]

description:
A392_2_N.txt
channel 1


title: HRSP12 [RNCMPT01138]

description:
A389_2_N.txt
channel 1


title: RPL7L1 [RNCMPT01141]

description:
A391_2_N.txt
channel 2


title: RPS12 [RNCMPT01143]

description:
A392_2_N.txt
channel 2


title: GTF2E2 [RNCMPT01136]

description:
A388_2_N.txt
channel 1


title: SUMO2 [RNCMPT01139]

description:
A390_2_N.txt
channel 2


title: HMGB1 [RNCMPT01134]

description:
A387_2_N.txt
channel 1


title: NUDT16L1 [RNCMPT01135]

description:
A388_2_N.txt
channel 2


title: MAGOH [RNCMPT01133]

description:
A387_2_N.txt
channel 2


title: RPS18 [RNCMPT01137]

description:
A389_2_N.txt
channel 2


title: MRPL44 [RNCMPT01128]

description:
A384_2_N.txt
channel 1


title: MRPS7 [RNCMPT01132]

description:
A386_2_N.txt
channel 1


title: BST2 [RNCMPT01131]

description:
A386_2_N.txt
channel 2


title: RPSA [RNCMPT01127]

description:
A384_2_N.txt
channel 2


title: RPL35A [RNCMPT01130]

description:
A385_2_N.txt
channel 1


title: MRPS11 [RNCMPT01129]

description:
A385_2_N.txt
channel 2