title: E15.5Heart, HighFatDiet, Rep1


title: 39-125-2017-3-29-2017_S39

status: Public on Sep 18 2024

type: SRA

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

country: USA

institute: Texas A&M University

library_source: transcriptomic

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 36 bases, and leading and trailing basepairs below a quality score of 3
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.2; parameters -p 14 --dta -x GCF_002263795.1_ARS-UCD1.2
Read assembly and quantification was performed with StringTie v2.1.7 with parameters -p 14 -G GCF_002263795.1_ARS-UCD1.2_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.1_ARS-UCD1.2_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE.py with parameters python prepDE.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.32.1.
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: comma-delimited text file of gene counts for each sample

molecule: polyA RNA

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library preparation kits, using standard Illumina protocols

treatment_protocol: All blood samples were collected in Tempus blood tubes (Applied Biosystem). Samples were stored per product recommendation.

tag: brd severity

tag: year

tag: sample day

tag: Sex

value: Male

tag: animal id

tag: developmental stage

value: Bull


title: 40-130-2017-3-29-2017_S40

value: Healthy


title: E15.5Heart, HighFatDiet, Rep2

city: Houston

first: Yun

last: Huang

address: 2121 W HOLCOMBE blvd, Room 429

department: Health Science Center

library_source: genomic

data_processing:
Adaptor trimming of raw reads was performed by TrimGalore v0.5.0 with default parameters.
High-quality reads (Q ≥ 20) were uniquely aligned to the mm10 reference genome using Bowtie2 with the ‘--very-sensitive’ option
The resulting alignment of each sample (with two biological replicates) was analyzed by Genrich v.0.5 (https://github.com/jsh58/Genrich) with ATAC-seq mode (option: -j, -q 0.05, -d 150)
Bedtools merge was used to count the reads that fell into non-overlapped peak regions
Differential chromatin accessible regions were detected using DESeq2 with normalized peak signals (fold change ≥ 2; FDR < 0.05)
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: E15.5 embryonic heart

growth_protocol: Timed mating was applied and the day when a vaginal plug was found was defined as E0.5. At E15.5, embryonic hearts were dissected out to perform the ATAC-seq analysis.

extract_protocol:
To isolate the nuclei for ATAC-seq, embryonic heart tissues were first rinsed with ice-old PBS. Nuclei were then extracted using a dounce homogenizer in ATAC lysis buffer.
ATAC-seq libray preparation was performed using the ATAC-seq kit (Active motif, 53150) in accordance with the manufacturer’s instructions.

treatment_protocol: For the maternal high-fat diet experiments, female mice at 8–10 weeks old were fed with high-fat diet (60 kcal% fat, D12492i, Research Diets, USA) for 9 weeks before timed mating. The age-matched mice were fed normal diet (10 kcal% fat, D12450Ji, Research Diets) for 9 weeks before timed mating and used as control.

tag: tissue

value: E15.5 embryonic heart

tag: cell line

value: embryonic heart cell

tag: genotype

value: WT

tag: treatment

value: high-fat diet


title: SKOV3_Pae_2

city: Wuhan

first: Jingchun

last: Liu

state: HUBEI

address: Zhangzhidong road

country: China

institute: Renmin Hospital of Wuhan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database  of splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)  (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel  network flow algorithm as well as an optional de novo assembly step to assemble and  quantitate fulllength transcripts representing multiple splice variants for each gene  locus.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 4 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Genome_build: Homo_sapiens_AR109
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: cisplatin‑sensitive human epithelial  ovarian cancer cell line

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
A total amount of 1 µg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached  magnetic beads. Fragmentation was carried out using divalent cations under elevated  temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand  cDNA was synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase(RNase H-  ). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments of  preferentially 250~300 bp in length, the library fragments were purified with AMPure  XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA)  was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5  min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA  polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products  were purified (AMPure XP system) and library quality was assessed on the Agilent  Bioanalyzer 2100 system.

tag: agent

value: Paeonol


title: SKOV3_1


title: 36-114-2017-3-29-2017_S36


title: OUMS-36T-3F cells, cHSF3_3

type: RNA

city: Ube

first: Ryosuke

last: Takii

state: Yamaguchi

address: minami-kogushi, 1-1-1

department: Biochemistry and Molecular Biology

country: Japan

institute: Yamaguchi university

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: OUMS-36T-3F cells, cHSF3

label_protocol: Biotinylated cDNA were prepared from 200 ng total RNA with WT PLUS Reagent Kit (Thermo Fisher).

growth_protocol: DMEM containing 10% fetal boviine serum at 37C

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).

treatment_protocol: no


title: SKOV3_2


title: 37-115-2017-3-29-2017_S37

value: Steer


title: OUMS-36T-3F cells, cHSF3_1


title: OUMS-36T-3F cells, cHSF3_2


title: OUMS-36T-3F cells, cHSF1_3

source_name: OUMS-36T-3F cells, cHSF1


title: ATAC WT, donor4

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

description: Illumina

data_processing:
Sequences were aligned using Bowtie. Peaks were identified using MACS on Galaxy tools.  Differential peak analysis was done using Diffbound on Galaxy tools.
Assembly: Mustela purorius furo, assembly ASM1176430v1.1
Supplementary files format and content: BED files

organism: Mustela putorius furo

source_name: Polarized pancreatic ductal epithelia

growth_protocol: Pancreata were removed from 1-3 day old newborn WT and CF ferrets and digested in 5 mg/ml collagenase for 20 min at 37oC. The digested pancreas was incubated overnight in PneumaCult™-Ex Plus medium (STEMCELL Technologies, MA, USA) on 804G-coated culture dishes overnight at 37oC in a 5% CO2 incubator. The 804G coating procedure is as previously described for airway basal cells {Mou, 2016 #413}. Ductal structures that adhered to the plate were aspirated on the following day and cultured on fresh 804G-coated culture dishes in PneumaCult™-Ex Plus medium until near confluence. These cells were then passaged by incubating with Accutase (STEMCELL Technologies, MA, USA) for 5 min at 37oC. The cells were passaged continuously for 10 passages to eliminate contaminating cells and obtain a morphologically homogenous population of duct cells. Passage-10 cells were harvested using Accutase and transferred to 804G-coated transwell inserts (Corning, NY, USA) at a density of 100,000 cells per well. Following seeding, transwells were cultured in PneumaCult™-Ex Plus medium on both apical and basolateral chambers for 3 days. The medium in both the apical and basolateral chamber was then switched to PneumaCult™-ALI (STEMCELL Technologies, MA, USA) for 1 day. Air liquid interface (ALI) was established the following day by aspirating the medium from the apical chamber. Cultures were maintained at an ALI for 2 weeks before use in experiments at which time transepithelial resistance should be greater than 1000 ohms.

extract_protocol:
Fully differentiated WT and CF ferret PDE cultures grown at ALI for 14 days were dissociated using Accutase. Cells were dissociated using Accutase and ~50,000 cells from each PDE culture were lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40: Sigma). Transposition was performed using 25 μl tagmentation reaction mix from Tagment DNA kit (Illumina, CA, USA). Tagged DNA was amplified indexed, using the NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs, MA, USA) and with Nextera DNA CD Indexes (Illumina, CA, USA), using the following settings: 72°C for 5 minutes; 98°C for 30 seconds; 12 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. The indexed library was purified with 1.8 times the volume of Ampure XP beads (Beckman Coulter, CA, USA). Library quality was assessed using a BioAnalyzer 2100 High Sensitivity DNA Chip (Agilent Technologies, MA, USA). All DNA libraries that exhibited the correct nucleosome pattern were pooled and processed for 150bp paired-end sequencing using a HiSeq4000 (Illumina) in the University of Iowa Genomics Division.
Cells were dissociated using Accutase and ~50,000 cells from each PDE culture were lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40: Sigma). Transposition was performed using 25 μl tagmentation reaction mix from Tagment DNA kit (Illumina, CA, USA). Tagged DNA was amplified indexed, using the NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs, MA, USA) and with Nextera DNA CD Indexes (Illumina, CA, USA), using the following settings: 72°C for 5 minutes; 98°C for 30 seconds; 12 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. The indexed library was purified with 1.8 times the volume of Ampure XP beads (Beckman Coulter, CA, USA).

value: Polarized pancreatic ductal epithelia

tag: cell type

value: Ductal


title: ATAC WT, donor1

description: Illumina


title: 34-105-2017-3-29-2017_S34


title: 35-109-2017-3-29-2017_S35


title: 33-104-2017-3-29-2017_S33


title: SCNT, LatA&TSA&UNC0638-treated, rep1

city: Tsukuba

first: Inoue

last: Kimiko

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

institute: RIKEN

description: SMART HiSeq HT

data_processing:
Sequence reads were trimmed for adaptor sequence using trimmomatic.
Trimmed sequence reads were mapped to the mouse genome build mm10 using STAR.
Read count extraction and normalization were performed using featureCounts and R, respectively.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw read counts for genes and transposal elements in each sample.

source_name: Embryo

growth_protocol: C57BL/6N female mice at 4–20 weeks of age were superovulated by injection of 7.5 IU equine chorionic gonadotropin  or anti-inhibin serum, followed 46–52 h later by injection of 7.5 IU human chorionic gonadotropin. Female mice were euthanized by cervical dislocation 16 h after the hCG injection, and then cumulus–oocyte complexes were collected from the ampullae of excised oviducts 16 h after the hCG injection, and placed in 100-μL droplets of human tubal fluid medium. For in vitro fertilization, spermatozoa were collected from the cauda epididymidis of adult DBA2 male mice and preincubated for at least 30 min in a 400-μL droplet of HTF. After preincubation, 3–5 μL of the sperm suspension was added to the oocyte cultures. At 3 h post-insemination, morphologically normal fertilized embryos were collected and cultured in potassium simplex optimized medium. For somatic cell nuclear transfer, cumulus cells used as nuclear donors were collected from wild-type female mice with a BDF1 (C57BL/6N ×DBA2) genetic background. Recipient oocytes were collected from BDF1 female mice following superovulation as above, and placed in KSOM droplets containing 0.1% bovine testicular hyaluronidase to remove cumulus cells. The cumulus-free oocytes were enucleated in Hepes-buffered KSOM containing 7.5 μg/mL cytochalasin B using a Piezo-driven pipette. After being cultured in fresh KSOM for 1 h, the enucleated oocytes were injected with cumulus cell nuclei in Hepes-buffered KSOM at room temperature. After 1 h culture, the injected oocytes were activated by culture in a Ca2+-free KSOM containing 3 mM strontium chloride and 5 μg/mL cytochalasin B for 1 h. The reconstructed oocytes were cultured in KSOM containing 5 μg/mL cytochalasin B for 5 h. After being washed thoroughly, the embryos were further cultured in KSOM.

extract_protocol:
Five to 10 IVF- and SCNT-derived embryos were collected at 28–29 h post-insemination/activation, washed twice in 0.05% bovine serum albumin in phosphate-buffered saline.
RNA-seq libraries were constructed by using SMART-Seq HT kits.

treatment_protocol: Some SCNT-derived embryos were injected with 10 pL of 1500 ng/μL mouse Kdm3a or Kdm4d mRNA at 5–6 h post-activation. Some other SCNT embryos were treated with G9a inhibitors (24h at 1uM) and/or trichostatin A (TSA; 8h at 25 nM).

value: Embryo

value: Wildtype

value: SCNT, LatA&TSA&UNC0638-treated


title: ATAC WT, donor2

description: Illumina


title: SCNT, LatA&TSA&UNC0638-treated, rep2

description: SMART HiSeq HT


title: E15.5Heart, NormalDiet, Rep3

value: normal diet


title: 32-192-2017-3-3-2017_S32


title: ATAC CFTRKO knockout, donor2

description: Illumina

value: CFTR KO/KO


title: E15.5Heart, NormalDiet, Rep2


title: E15.5Heart, NormalDiet, Rep1


title: ATAC CFTRKO knockout, donor3

description: Illumina


title: OUMS-36T-3F cells, cHSF1_1


title: SCNT, LatA&TSA&R701-treated, rep2

description: SMART HiSeq HT

value: SCNT, LatA&TSA&R701-treated


title: OUMS-36T-3F cells, KO_3

source_name: OUMS-36T-3F cells, KO

value: KO


title: OUMS-36T-3F cells, cHSF1_2


title: OUMS-36T-3F cells, KO_2


title: 31-166-2017-3-3-2017_S31

value: Male

value: Bull


title: SCNT, LatA&TSA&R701-treated, rep1

description: SMART HiSeq HT


title: SCNT, LatA&TSA&A366-treated, rep2

description: SMART HiSeq HT

value: SCNT, LatA&TSA&A366-treated


title: WT, donor3

description: Illumina

data_processing:
Sequences from  bulk RNA-seq were aligned using RSEM, using the ferret ASM1176430v1.1 genome and gtf file. Differential gene expression analysis was done using PyMINR.
Assembly: Mustela purorius furo, assembly ASM1176430v1.1
Supplementary files format and content: Tab separated values, comma separated values, matrix files

extract_protocol:
Fully differentiated WT and CF ferret PDE cultures grown at ALI for 14 days were dissociated using Accutase followed by DNase treatment. Qiagen RNEasy mini kit was used to extract RNA from cells. Two transwells per donor were combined. RNA samples with RIN>9 were used for library prep and sequencing.
Sequencing libraries were generated by following 10X Genomics recommendations (Document CG000315). Briefly, single cells and reverse transcription master mix were partitioned into Gel Beads in partitioning oil in the 10X Chromium controller. After reverse transcription, cDNA libraries were amplified and fragmentated, followed by adaptor ligation and sample index PCR reaction. Libraries were sequenced on NovaSeq 6000 platform by the University of Iowa Genomics Division.


title: 30-147-2017-3-3-2017_S30


title: 29-114-2017-3-3-2017_S29


title: WT, donor2

description: Illumina


title: WT, donor1

description: Illumina


title: ATAC CFTRKO knockout, donor1

description: Illumina


title: CFTRKO knockout, donor3

description: Illumina


title: SCNT, LatA&R701-treated, rep3

description: SMART HiSeq HT

value: SCNT, LatA&R701-treated


title: SCNT, LatA&TSA&A366-treated, rep1

description: SMART HiSeq HT


title: 28-40-2015-3-30-2015_S18


title: CFTRKO knockout, donor2

description: Illumina


title: 28-85-2015-5-11-2015_S28


title: OUMS-36T-3F cells, KO_1


title: HUVEC_Ang Ⅱ-2 [SAMPLE 5]

city: Shanghai

first: Hao

last: Lin

state: Shanghai

address: No. 389, Xincun Road

department: Department of Cardiology

institute: Tongji Hospital, School of Medicine, Tongji University,

data_processing:
Raw reads form the sequencing data, after removal the adaptors and filtering out low quality reads, were labeled Cleandata. Then, rRNA residues were removed by comparing known rRNA to get statistical data.
It needs to align twice, due to the particularity of splice site reads. Firstly, one normal alignment of reads using Tophat2 software and exclude fusion gene alignments, thereby gain the reads which cannot align to the reference genome. For unmapped reads of gene fusion align, we used Tophat-fusion of Tophat2 software. And to acquire potential looping reads.This two-step alignment procedure was the 2 basic steps for circRNAs prediction.
The circRNA were identified and performed by RiboBio (Guangzhou, China). Then, to compare the positions of the two ends of the identified circRNA splicing site on the genome using the ANNOVAR software, and to annotate circRNAs by aligning against multiple databases. At last, the origin of circRNA in the genome was predicted according to the origin of the sequences at both ends of the circular RNA splicing site.
The circRNA expression level was based on the predicted circRNA sequence, and was obtained by counting the number of circRNA reads and calculating its RPM (Reads Per Million mapped reads). RiboBio uses HTseq software to calculate the count value for each circRNA, and then further calculate its RPM value. The formula for calculating the RPM value is as follows, RPM = (circRNA readCount*1,000,000)/total mapped reads.
Assembly: Hg19
Supplementary files format and content: We used HTseq software to calculate the count value for each circRNA, and then further calculate its RPM value. The formula for calculating the RPM value is as follows, RPM = (circRNA readCount*1,000,000)/total mapped reads.

source_name: HUVEC

growth_protocol: HUVEC cultured in Dulbecco’s Modified Eagle Medium (DMEM, low glucose, Hyclone) supplemented with 5% FBS (Gibco), 3% penicillin/streptomycin (Gibco)

extract_protocol:
Then total RNA of above HUVECs were extracted using mirVanaTM RNA Isolation Kit. Total RNA concentration was determined using NanoDrop ND-2000 (Thermo Scientific) and RNA integrity was examined with Agilent Bioanalyzer 2100 (Agilent Technologies).
RNA libraries for RNA-seq were constructed by RiboBio (Guangzhou, China) following illumina protocols.

value: HUVEC

value: ea.hy 926

value: human umbilical vein endothelial cells

value: WT

value: Ang Ⅱ treatment


title: CFTRKO knockout, donor1

description: Illumina

value: Polarized pancreatic ductal epithelia

value: Ductal


title: SCNT, LatA&R701-treated, rep1

description: SMART HiSeq HT

value: Embryo

value: Wildtype


title: OUMS-36T-3F cells, WT_2

source_name: OUMS-36T-3F cells, WT


title: 28-123-2017-3-29-2017_S38


title: 27-75-2015-5-11-2015_S27


title: SCNT, LatA&A366-treated, rep2

description: SMART HiSeq HT

value: SCNT, LatA&A366-treated


title: OUMS-36T-3F cells, WT_3


title: OUMS-36T-3F cells, WT_1


title: 120CHpB

city: Stellenbosch

first: Evelyn

last: Maluleke

state: Western cape

address: Victoria street

department: Viticulture and Oenology

country: South Africa

institute: Stellenbosch University

data_processing:
STAR 2.6.1
Sequencing reads underwent quality and adaptor contamination checks both before and after trimming using FastQC 0.11.9. Trim Galore 0.6.5 was then employed to eliminate low-quality reads (Q <20), polyA reads, ambiguous reads containing N, and those shorter than 20 nt, while Cutadapt 1.7.1 was used to trim adapters from the remaining reads.
Trimmed sequence reads were mapped to a concatenated genome (Hypbu1+B05. 10). Parameters (Mismatch= (--outFilterMismatchNmax 10)
The GeneCounts function from STAR was used to obtain read counts
Assembly: Hypbu1 and B05. 10
Supplementary files format and content: tab-delimited txt file for each timepoint

organism:
Botrytis cinerea
Hyphopichia pseudoburtonii

source_name: co-culture, treatment, 120h

growth_protocol: H. pseudoburtonii Y963 and B .cinerea were maintained on WL agar and Malt extract agar respectively. Bothe cultures were grown at 25°C

extract_protocol:
total RNA was extracted using a modified version of the hot acidic phenol method originally described by Collart and Oliviero
RNA libraries for RNAISeq were prepared using the Ion Total Transcriptome Sequencing Kit v2

treatment_protocol: H. pseudoburtonii was co-cultured with B. cinerea (coculture/treated), and controlas were prepared by growing H. pseudonurtonii in the absence of B. cinerea (monoculture/control)

value: eukaryotic

tag: hp strain

tag: bc strain

value: co-culture, treatment, 120h


title: 23-40-2015-5-11-2015_S23


title: 48CHpB

source_name: co-culture, treatment, 48h

value: co-culture, treatment, 48h


title: 22-28-2015-5-11-2015_S22

value: Healthy

value: Male


title: SCNT, LatA&A366-treated, rep1

description: SMART HiSeq HT


title: 48AHpB


title: 120BHpB


title: 25-68-2015-5-11-2015_S25

value: Bull


title: 21-20-2015-5-11-2015_S21

value: Steer


title: SCNT, Kdm3a-injected, rep1

description: SMART HiSeq HT

value: SCNT, Kdm3a-injected


title: 120AHpB


title: SCNT, Kdm4d-injected, rep2

description: SMART HiSeq HT

value: SCNT, Kdm4d-injected


title: SCNT, LatA&R701-treated, rep2

description: SMART HiSeq HT

value: SCNT, LatA&R701-treated


title: 26-71-2015-5-11-2015_S26


title: 24BHpB

source_name: co-culture, treatment, 24h

value: co-culture, treatment, 24h


title: SCNT, Kdm4d-injected, rep1

description: SMART HiSeq HT


title: 19-60-2015-3-30-2015_S19


title: SCNT, Kdm3a-injected, rep2

description: SMART HiSeq HT


title: 48BHpB


title: P. putida_100hr_aerob_rep2

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

country: Germany

institute: Saarland University

description: Gene expression of P. putida after 100 hr in anoxic BES

hyb_protocol: 600 ng labeled RNA with a specific activity of 15 (pmol Cy3) μg−1 was hybridized onto the microarray at 65 °C for 17 h in a hybridization chamber (Gene Expression Hybridization Kit, SureHyb chamber Agilent Technologies).

scan_protocol: After washing slides were scanned immediately with the SureScan Microarray Scanner (G4900DA) using the AgilentG3_GX_1color scanner protocol with 3 μm double resolution.

data_processing: Data extraction and processing was performed using microarray and feature extraction software (Version 12.1.1.1, Agilent Technologies) using default parameters to obtain background substracted Processed Signal Intensities. For statistical analysis, a moderated t-test was applied considering asymptotic computation of p-values adjusted for multiple testing (Benjamini-Hochberg method) and a q-value cut-off of 0.05.

organism: Pseudomonas putida KT2440

source_name: P. putida, 100hr, anaerob, replicate 2

label_protocol: 50 ng RNA were used as input for direct chemical labelling (Low Input Quick Amp WT Labeling One-Color Kit, RNA Spike-In One-Color Kit, Agilent Technologies) according to the manufacturer's protocol. Labelled RNA was subsequently purified (RNeasy Mini Spin Columns, Agilent Technologies).

growth_protocol: Aerob control: Grown in defined M9 glucose media (DM9) supplemented with 5g/L glucose at 30°C, and 230 rpm in shake flask (<15% filling volume). Cells were harvested during exponential growth. Anaerobic BES: Cultivated in DM9 media supplemented with 1.5g/L glucose in a bioelectrochemical system with the anode as the working electrode and [Fe(CN)6] as the mediator. Potential at the anode was set to 0.5V. Cells were harvested after 24 hr and 100 hr of cultivation.

extract_protocol: Total RNA of P. putida was isolated, and cleaned up with RNeasy Mini Kit (Qiagen, Hilden, Germany), and TURBO DNA-free Kit (Thermo Fisher Scientific, Waltham, MA, USA). RNA quality was assessed (RNA 6000 Nano Kit, 2100 Bioanalyzer System, Agilent Technologies). The RNA integrity number (RIN) of all samples was >8 as a criterion for sufficient quality.

treatment_protocol: Samples from pre-culture or BES were taken, centrifuged (13,000 rpm, RT, 30sec), the supernatent was discarded and pellet snap frozen in liquid N2. Samples were stored at -80°C.

tag: condition

value: anaerobic BES

tag: time


title: SCNT, LatA-treated control, rep2

description: SMART HiSeq HT

value: SCNT, LatA-treated


title: SCNT, LatA&TSA-treated, rep2

description: SMART HiSeq HT

value: SCNT, LatA&TSA-treated


title: 20-71-2015-3-30-2015_S20


title: SCNT, LatA-treated control, rep1

description: SMART HiSeq HT

value: Embryo


title: SCNT, cont, rep2

description: SMART HiSeq HT

value: Wildtype

value: SCNT, non-treated


title: 24CHpB

value: eukaryotic


title: 45-156-2017-3-29-2017_S45


title: SCNT, LatA&TSA-treated, rep1

description: SMART HiSeq HT


title: ATAC WT, donor3

description: Illumina

value: Polarized pancreatic ductal epithelia

value: Ductal

value: WT


title: 05-68-2015-3-2-2015_S5

value: Male


title: P. putida_100hr_aerob_rep1

source_name: P. putida, 100hr, anaerob, replicate 1


title: P. putida_100hr_aerob_rep4

source_name: P. putida, 100hr, anaerob, replicate 4


title: P. putida_24hr_aerob_rep3

description: Gene expression of P. putida after 24 hr in anoxic BES

source_name: P. putida, 24hr, anaerob, replicate 3


title: 24-60-2015-5-11-2015_S24

source_name: Whole blood

value: Healthy


title: P. putida_100hr_aerob_rep3

source_name: P. putida, 100hr, anaerob, replicate 3


title: 04-60-2015-3-2-2015_S4

value: Steer


title: IVF, rep3

description: SMART HiSeq HT

value: IVF


title: 03-40-2015-3-2-2015_S3

value: Bull


title: P. putida_24hr_aerob_rep4

source_name: P. putida, 24hr, anaerob, replicate 4


title: 16-28-2015-3-30-2015_S16


title: IVF, rep2

description: SMART HiSeq HT


title: 24AHpB


title: 17-33-2015-3-30-2015_S17


title: SCNT, cont, rep1

description: SMART HiSeq HT


title: 15-20-2015-3-30-2015_S15


title: iPSC

first: Guoyu

last: Chen

address: Xuhui District Yueyang Road 320

institute: PICB

data_processing:
raw sequencing reads were mapped to mm10/gencode vM25 using STAR
raw read counts were quantified using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: iPSC

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
From purified polyA RNA

value: iPSC

value: wild type


title: sample 4_ZsGreen ECs-biol rep 2

first: Hongxin

last: Li

address: Yueyang Road 320

department: Shanghai Institute of Biochemistry and Cell Biology

institute: University of Chinese Academy of Sciences

data_processing:
Sequencing reads were filtered with SOAPnuke by (v1.5.6) to remove sequencing adapter and reads with low-quality base ratio.
Trimmed and filtered reads were mapped to mm10 (GRCm38) using HISTA2 (v2.1.0) with the default parameter.
RSEM (v1.3.1) was used to quantify gene expression. DESeq2 (v1.4.5) was used to analyze differentially expressed genes.
Assembly: mm10 (GRCm38)
Supplementary files format and content: tab-delimited text file includes FPKM, TPM, read counts and normal read counts for each sample

source_name: Lung (Pulmonary)

extract_protocol:
Total RNA was extracted from cells using RNeasy Micro kit (QIAGEN, GER) according to the manual instruction.
Library preparation is performed using TruePrep DNA Library Prep Kit for MGI (VAZYME，China). Less than 4μL RNA are used as a template and amplified by Discover-sc WTA Kit V2 (VAZYME，China).

value: Lung (Pulmonary)

tag: group

value: ZsGreen ECs

value: pulmonary endothelial cell

value: Tamoxifen x5, TAC 6w


title: P. putida_0hr_aerob_rep1

description: Gene expression of P. putida from aerobic pre-culture

source_name: P. putida, 0hr, aerob, replicate 1

value: aerobic pre-culture


title: IVF, rep4

description: SMART HiSeq HT

source_name: Embryo

value: Embryo

value: Wildtype


title: IVF, rep1

description: SMART HiSeq HT


title: P. putida_24hr_aerob_rep1

source_name: P. putida, 24hr, anaerob, replicate 1

value: anaerobic BES


title: MCC

source_name: myeloid-like cell complex

value: myeloid-like cell complex


title: sample 2_tdTomato ECs-biol rep 2

value: tdTomato ECs


title: P. putida_24hr_aerob_rep2

source_name: P. putida, 24hr, anaerob, replicate 2


title: iMac, scRNA-seq (oligo)

library_source: transcriptomic single cell

data_processing:
The demutiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: induced macrophage

extract_protocol:
iMac cells were digested with PBS containing 5mM EDTA, washed and resuspended in PBS.
Library was constructed using a DNBelab C4 system. In brief, the single-cell suspension underwent droplet encapsulation, emulsion breakage, reverse transcription, cDNA amplification and purification,and sequencing according to the manufacturer’s protocol.

value: induced macrophage

tag: library type

value: oligo


title: PB

source_name: plasma blood cells

value: plasma blood cells

value: blood cells


title: P. putida_0hr_aerob_rep4

source_name: P. putida, 0hr, aerob, replicate 4


title: P. putida_0hr_aerob_rep3

source_name: P. putida, 0hr, aerob, replicate 3


title: iMac, scRNA-seq (cDNA)

value: cDNA


title: MCC (single-cell)

source_name: MEF tranformed cells

growth_protocol: Cell were cultured in a iPSC medium.

extract_protocol:
RNA from the single cells was isolated, following the 10X protocol.
According to the manufactor's instructions (single cell 3' ve protocol, 10X genomics)

value: MEF tranformed cells


title: 319-1 [miRNA]

description: miRNA expression after overexpression of hsa_circ_0122319 and hsa_circ_0002457 in HUVEC

hyb_protocol: The labeled RNA was purified and hybridized with the chip, and the original image was scanned with the Agilent Scanner G2505C (Agilent Technologies) after elution.

scan_protocol: The original image was scanned with the Agilent Scanner G2505C (Agilent Technologies) after elution.

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 13.1, Agilent Technologies) was employed to finish the basic analysis with the raw data.

label_protocol: Total RNA is dephosphorylated, denatured, and then further labeled with Cyanine-3-CTP (Cy3).

extract_protocol: Then total RNA of above HUVECs were extracted using mirVanaTM RNA Isolation Kit. Total RNA concentration was determined using NanoDrop ND-2000 (Thermo Scientific) and RNA integrity was examined with Agilent Bioanalyzer 2100 (Agilent Technologies).

value: HUVEC

value: overexpression of hsa_circ_0122319


title: 319 [miRNA]


title: 02-20-2015-3-2-2015_S2

tag: brd severity

tag: year

value: Male

value: Steer


title: RNA_ESC_Gabpa_dTAG_24h_rep1

status: Public on Sep 17 2024

city: Boston

first: Yi

last: Zhang

state: MA

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

data_processing:
CUT&RUN data analysis: The raw reads were trimmed with Trimmomatic (v0.39) to remove sequencing adaptors then mapped to GRCm38 reference genome using bowtie2 (v2.4.2). PCR duplicates were removed with Picard MarkDuplicates (v2.23.4). Reads with mapping quality less than 30 were removed. The mapped reads were further filtered to only retain proper paired reads with fragment length between 10 and 120. Peaks were called with MACS2 (v2.2.7.1). Reproducible peaks were generated with the IDR framework using two replicates, with IDR threshold of 0.05. For E4.5 ICM and ESC, we further filtered the peaks to keep the ones with q-value ≤ 10-30 to remove very weak peaks. The signal tracks were generated with deeptools bamCoverage (v3.5.1) with bin size of 1 and normalization using CPM. For z-score normalized signal tracks, we first used bamCoverage with bin size of 100 to generate FPKM signals then used a customized script to calculate the z-score of each bin. The peaks were annotated with R package ChIPseeker. Peaks within -1000 to +500 around TSS were considered as promoter peaks. The heatmaps of binding profiles were calculated with deeptools computeMatrix (v3.5.1) using bigwig signal tracks as input and bin size of 10, and visualized in R with packages profileplyr and EnrichedHeatmap.
ATAC-seq data analysis: ATAC-seq data were analyzed with the ENCODE ATAC‐seq pipeline with default parameters (v2.1.2, https://github.com/ENCODE-DCC/atac-seq-pipeline).
Assembly: mm10
Supplementary files format and content: bigwig files contain CUT&RUN signals and ATAC-seq fold changes; txt files contain gene-level reads counts of RNA-seq

source_name: mESC

growth_protocol: Female mice (7-8 weeks) were superovulated through an initial injection of 7.5 IU pregnant mare serum gonadotropin (PMSG, BioVendor, RP1782725000), followed 48 hours later by a 7.5 IU injection of human chorionic gonadotropin (hCG, Sigma, C1063). Oocyte-cumulus complexes (OCCs) were collected 14 hrs post hCG injection. Sperm was then harvested from the cauda epididymis of adult male mice (8-12 weeks). The sperm suspension was capacitated for 1 h in 200 μl HTF medium (Millipore, MR-070-D). Subsequently, OCCs were exposed to spermatozoa for a 6-hour incubation. The time when sperm were added to OCCs was considered as 0 hpf. Two-nuclear zygotes were cultured in the KSOM medium (Millipore, MR-106-D) under a humidified atmosphere of 5% CO2 at 37°C for further development.

extract_protocol:
For mESC CUT&RUN with more than 10K, cells were resuspended in 50 μl wash buffer (20 mM HEPES/pH=7.5, 150 mM NaCl, 0.5 mM spermidine and 1× protease inhibitor) with activated Concanavalin A Magnetic Beads (Polysciences, 86057-3) for 10 mins at RT, then samples were included with anti-GABPA (1:40, Proteintech, 21542-1-AP, lot#00018047) overnight at 4°C. Samples were included with 2.8 ng/μl pA-MNase (home-made) for 2 hrs at 4 °C. Subsequently, samples were included with 200 μl pre-cooled 0.5 μM CaCl2 for 20 mins at 4 °C and quench by adding 23 μl 10×stop buffer (1700 mM NaCl, 20 mM EGTA, 100 mM EDTA , 0.02% Digitonin, 250 µg/ml glycogen and 250 µg/ml RNase A). DNA Fragments were released by incubation at 37°C for 15 mins. 2.5 μl 10% SDS and 2.5 μl 20 mg/ml Protease K (Thermo Fisher) was added and incubated at 55 °C for at least 1 h. DNA was extracted by phenol-chloroform followed by ethanol precipitation.
For low input CUT&RUN, mESC, zona-free embryos or isolated ICM were resuspended in 50 μl wash buffer with activated Concanavalin A Magnetic Beads for 10 mins at RT, then samples were fixed with 1% formaldehyde for 1 min. After three times wash with wash buffer, samples were included with anti-GABPA overnight at 4°C. The followed protocol is same as previous one. Sequencing libraries were prepared with NEBNext Ultra II DNA library preparation kit for Illumina (New England Biolabs, E7645S).  For ATAC-seq, ESC and isolated ICM were digested with adapter-loaded Tn5 for 15 mins at 37°C, and stopped by stop buffer (100 mM Tris/pH=8.0, 100 mM NaCl, 40 µg/ml Proteinase K and 0.4% SDS) and incubated overnight at 55°C. 5 µl of 25% Tween-20 was added to quench SDS. Sequencing libraries were prepared with NEBNext High-Fidelity 2×PCR Master Mix (NEB, M0541S).  For RNA-seq, fresh ESC or embryos were collected. Reverse transcription and cDNA amplification were performed with SMART-Seq™ v4 Ultra™ Low Input RNA Kit (Clontech, 634890), followed cDNA fragmentation, adaptor ligation, and amplification using Nextera® XT DNA Sample Preparation Kit kit (Illumina, FC-131-1024).

treatment_protocol: dTAG13 (Tocris, 6605) was reconstituted in DMSO to a 5 mM stock. For Gabpa-dTAG/dTAG mESC treatment, dTAG13 was dilute in mESC culture medium to 0.5 μM. For Gabpa-dTAG/dTAG embryos treatment, dTAG13 was dilute in KSOM to 1 μM. Specific time-point embryos were washed with KSOM/dTAG13 for at least three times, then culture in KSOM with dTAG13 for further development.

value: mESC

value: Gabpa-dTAG/dTAG

value: dTAG13 for 24h


title: RNA_ESC_Gabpa_dTAG_24h_rep2


title: P. putida_0hr_aerob_rep2

source_name: P. putida, 0hr, aerob, replicate 2

value: aerobic pre-culture


title: NC [miRNA]

source_name: NC

value: NC


title: 01-71-2015-3-2-2015_S1

source_name: Whole blood

value: Healthy

tag: sample day

tag: Sex

value: Bull


title: sample 3_ZsGreen ECs-biol rep 1

value: Lung (Pulmonary)

value: ZsGreen ECs

value: pulmonary endothelial cell

value: Tamoxifen x5, TAC 6w


title: RNA_E45_ICM_Gabpa_DMSO_rep2

source_name: embryo

value: embryo

value: E4.5 ICM

value: DMSO


title: BM

source_name: bone marrow

value: bone marrow

value: wild type


title: MEF

source_name: MEF

value: MEF


title: RNA_morula_Gabpa_dTAG_rep2

value: morula


title: RNA_morula_Gabpa_dTAG_rep1

value: Gabpa-dTAG/dTAG


title: 457-1 [miRNA]

value: HUVEC

value: overexpression of hsa_circ_0002457


title: RNA_morula_Gabpa_DMSO_rep1


title: RNA_L2C_Gabpa_dTAG_rep2

value: late 2-cell


title: RNA_L2C_Gabpa_dTAG_rep1


title: sample 1_tdTomato ECs-biol rep 1

source_name: Lung (Pulmonary)

value: tdTomato ECs


title: RNA_L2C_Gabpa_DMSO_rep3


title: RNA_L2C_Gabpa_DMSO_rep2


title: H3K27ac_E45_ICM_Gabpa_dTAG_rep1

data_processing:
CUT&RUN data analysis: The raw reads were trimmed with Trimmomatic (v0.39) to remove sequencing adaptors then mapped to GRCm38 reference genome using bowtie2 (v2.4.2). PCR duplicates were removed with Picard MarkDuplicates (v2.23.4). Reads with mapping quality less than 30 were removed. The mapped reads were further filtered to only retain proper paired reads with fragment length between 10 and 120. Peaks were called with MACS2 (v2.2.7.1). Reproducible peaks were generated with the IDR framework using two replicates, with IDR threshold of 0.05. For E4.5 ICM and ESC, we further filtered the peaks to keep the ones with q-value ≤ 10-30 to remove very weak peaks. The signal tracks were generated with deeptools bamCoverage (v3.5.1) with bin size of 1 and normalization using CPM. For z-score normalized signal tracks, we first used bamCoverage with bin size of 100 to generate FPKM signals then used a customized script to calculate the z-score of each bin. The peaks were annotated with R package ChIPseeker. Peaks within -1000 to +500 around TSS were considered as promoter peaks. The heatmaps of binding profiles were calculated with deeptools computeMatrix (v3.5.1) using bigwig signal tracks as input and bin size of 10, and visualized in R with packages profileplyr and EnrichedHeatmap.
ATAC-seq data analysis: ATAC-seq data were analyzed with the ENCODE ATAC‐seq pipeline with default parameters (v2.1.2, https://github.com/ENCODE-DCC/atac-seq-pipeline).
Assembly: mm10
Supplementary files format and content: bigwig files contain CUT&RUN signals and ATAC-seq fold changes; txt files contain gene-level reads counts of RNA-seq
Library strategy: CUT&RUN


title: 457 [miRNA]


title: H3K27ac_E45_ICM_Gabpa_DMSO_rep1


title: ATAC_ESC_Gabpa_dTAG_24h_rep2

value: mESC

value: dTAG13 for 24h


title: RNA_ESC_Gabpa_DMSO_rep1


title: RNA_E45_ICM_Gabpa_dTAG_rep1


title: RNA_E45_ICM_Gabpa_dTAG_rep2


title: ATAC_ESC_Gabpa_DMSO_rep2


title: ATAC_ESC_Gabpa_DMSO_rep1


title: ATAC_E45_ICM_Gabpa_dTAG_rep2


title: RNA_E45_ICM_Gabpa_DMSO_rep1


title: RNA_morula_Gabpa_DMSO_rep2


title: RNA_ESC_Gabpa_DMSO_rep2


title: GABPA_dTAG_CUTrun_2cell_rep2


title: RNA_L2C_Gabpa_DMSO_rep1


title: H3K27ac_E45_ICM_Gabpa_dTAG_rep2


title: H3K27ac_E45_ICM_Gabpa_DMSO_rep2


title: GABPA_CUTrun_E45_ICM_rep2

value: untreated


title: GABPA_CUTrun_E35_ICM_rep1

value: E3.5 ICM


title: ATAC_ESC_Gabpa_dTAG_24h_rep1


title: ATAC_E45_ICM_Gabpa_DMSO_rep2


title: GABPA_CUTrun_2cell_rep2


title: GABPA_CUTrun_2cell_rep1


title: RNA_L2C_Gabpa_dTAG_rep3


title: GABPA_dTAG_CUTrun_E45_ICM_rep1


title: GABPA_dTAG_CUTrun_E45_ICM_rep2


title: GABPA_dTAG_CUTrun_2cell_rep1


title: GABPA_CUTrun_ESC_500


title: GABPA_CUTrun_ESC_rep1


title: GABPA_CUTrun_ESC_rep2


title: H3_TaDRIM-Seq-Rice-young leaves-rep2

first: guoting

last: chen

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
splitting data into DNA-end and RNA-end data, mapping DNA-end data to the reference genome by BWA
RNA-end data to the reference genome by HISAT2 and Bowtie2
Extracting the uniquely matched reads
Converting bam files to BigWig files
Assembly: genome build by BWA and assembly by HISAT2 and Bowtie2
Supplementary files format and content: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: The hic format file was converted by juicer_tools

molecule: nuclear RNA

organism: Oryza sativa Indica Group

source_name: young leaves

growth_protocol: Human K562 cells (ATCC) were cultured in DMEM containing 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco) and growing at 37 °C and 5% CO2 in a cellmate CO2 incubator (Esco Scientific). Cells were cross-linked with 1% formaldehyde (Sigma-Aldrich) in 1×PBS (Thermo Fisher) for 10 min with rotation at room temperature, followed by quenching with 0.2M glycine for 5 min at room temperature with rotation. Cells were washed three times with 1×PBS and stored at -80 °C.Rice Xian/indica cv. Minghui 63 (MH63) seeds were used and sown in May. Germinated seedlings were transplanted into a paddy field (Huazhong Agricultural University at Wuhan, China), and grown under normal agricultural conditions. Mature leaves were collected on July, and were immediately single cross-linked with 1% formaldehyde and stored at -80 °C.

extract_protocol:
Approximately1×106- 1×107 crosslinked cells were used per replicate. Cell nuclei were isolated in 1 mL lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2% NP40, 1×protease inhibitors, 0.2 U/μl RiboLock RNase) (Thermo Fisher), and incubated for 10min on ice followed by centrifugation for 3min at 2500g and 4°C. The nuclei were washed twice with 300µl 1×wash buffer A (20mM HEPES pH 7.6, 150mM NaCl, 0.5mM Spermidine, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), and nuclei were collected by centrifugation for 3min at 2500g and 4 °C. Nuclei were then resuspended in Antibody buffer (495μl 1×wash buffer A, 5μl 5% digitonin, 2μl 0.5M EDTA, 1.6μl 30%BSA, 10μg antibody (H3K4me3, Abcam, ab8580; H3K9ac, Abcam, ab10812; CTCF, Abcam, ab188408), and incubated at 4°C for 2h with rotation. Nuclei were pelleted for 3 min at 2500g and washed five times with 300μl 1×wash buffer A, resuspended 500µl 1×transposase incubation buffer (20mM HEPES pH 7.6, 300mM NaCl, 0.5mM Spermidine, 0.01% digitonin, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), followed by adding 5μl TTE Mix, and incubated at 4°C for 1h with rotation. Nuclei were collected and washed five times with 300µl 1×transposase incubation buffer and resuspended in tagmentation buffer (500µl 1×transposase incubation buffer, 5µl 1M MgCl2), and incubated at 37°C for 1h. Next, 500µl of 40mM EDTA (Thermo Fisher) was added to stop the reaction. The isolated nuclei were washed twice with 500µl 1×PBS (Thermo Fisher) and then incubated in 200µl permeabilization buffer (190µl nuclease-free water, 10µl 10% SDS) (Thermo Fisher) at 62°C for 10min, and immediately quenched the SDS reaction by adding add 580μl of nuclease-free water and 100μl of 10% (vol/vol) Triton X-100 (Sigma-aldrich), and incubated at 37°C for 15min with rotation.The isolated nuclei were washed twice with 500µl 1×wash buffer B (20mM Tris-HCl, pH 7.5, 10mM MgCl2 and 0.2% Tween 20) and resuspended in 500µl 1× CutSmart buffer (NEB), followed by adding 1.6µl RNase If (NEB) with dilution tenfold in 1× PBS, and incubated at 37°C for 3min with rotation followed by incubation for 5min on ice. Nuclei were collected by centrifugation, then resuspended by 400µl PNK solution containing 1×T4 PNK reaction buffer, 1mM ATP, 1U/μl RiboLock RNase and 1U/μl T4 PNK (Thermo Fisher) at 37°C for 40min with rotation. The specific bridge linker was designed containing 5ʹ phosphorylation [5Phos] and Internal Biotin dT [ibiodT] chemical modifications. The forward strand is: 5′-[5APP]CCTCGATAC/iBIOdT/TGAGCTGAC-3′, and reverse strand is 5′-[5Phos]GTCAGC/iBIOdT/CAAGTATCGAG-3′. The 5′App ends of forward strand was treated by using a DNA 5′ Adenylation Kit (NEB). The isolated nuclei were washed twice with 500µl 1×wash buffer B and resuspended in 400µl of RNA ligation solution (1×T4 RNA ligase reaction buffer, 1U/μl RiboLock RNase, 10U/μl T4 RNA Ligase 2 truncated, 1.5pmol/μl bridge linker, 15% (w/v) PEG 8000, 0.1% Triton X-100) (NEB), and incubated overnight at 16 °C with rotation. The nuclei were pelleted by centrifugation, resuspended in 400 μl reverse transcription solution (1×MMLV buffer, 0.5mM dNTP, 8U/μl MMLV (RNase H-), 1U/μl RiboLock RNase) (Promega), and then incubated at 42 °C for 1 h. The isolated nuclei were washed five times with 500μl 1×wash buffer B, resuspended in T4 DNA ligation solution (1×DNA ligase reaction buffer with 10mM ATP, 4U/μl T4 DNA ligase, 0.1% (vol/vol) Triton X-100 and 0.1 mg/mLBSA) (NEB), incubated overnight at 16 °C with rotation. The isolated nuclei were resuspended in proteinase K solution (50 mM Tris-HCl, pH 7.5, 1% SDS, 100mM NaCl, 1mM EDTA and 1mg/mL proteinase K) at 65 °C for 3h with shaking at 800 rpm. RNA/DNA complex was extracted and dissolved in nuclease-free water (Thermo Fisher). The purified RNA/DNA complexes were incubated with gap-filling solution (10×NEBuffer r2.1,1mM dNTP and 0.18U/μl T4 DNA polymerase) (NEB) at room temperature for 40min to repair the pG-Tn5 transposition gap, followed by second-strand cDNA synthesis.
DNA-cDNA complexes were converted to DNA library according to the TruePrep DNA Library Prep Kit for Illumina (Vazyme, cat. no. TD501). The fragments containing biotinylated bridge-linker were enriched by M280 beads (Thermo Fisher) before PCR, and enriched library DNA is size-selected by using AMPure XP beads (Beckman), and sequenced (2×150 bp) using Illumina Hiseq X-Ten (Annoroad Gene Technology).

treatment_protocol: Approximately1×106- 1×107 crosslinked cells were used per replicate. Cell nuclei were isolated in 1 mL lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2% NP40, 1×protease inhibitors, 0.2 U/μl RiboLock RNase) (Thermo Fisher), and incubated for 10min on ice followed by centrifugation for 3min at 2500g and 4°C. The nuclei were washed twice with 300µl 1×wash buffer A (20mM HEPES pH 7.6, 150mM NaCl, 0.5mM Spermidine, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), and nuclei were collected by centrifugation for 3min at 2500g and 4 °C. Nuclei were then resuspended in Antibody buffer (495μl 1×wash buffer A, 5μl 5% digitonin, 2μl 0.5M EDTA, 1.6μl 30%BSA, 10μg antibody (H3K4me3, Abcam, ab8580)), and incubated at 4°C for 2h with rotation. Nuclei were pelleted for 3 min at 2500g and washed five times with 300μl 1×wash buffer A, resuspended 500µl 1×transposase incubation buffer (20mM HEPES pH 7.6, 300mM NaCl, 0.5mM Spermidine, 0.01% digitonin, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), followed by adding 5μl TTE Mix, and incubated at 4°C for 1h with rotation. Nuclei were collected and washed five times with 300µl 1×transposase incubation buffer and resuspended in tagmentation buffer (500µl 1×transposase incubation buffer, 5µl 1M MgCl2), and incubated at 37°C for 1h. Next, 500µl of 40mM EDTA (Thermo Fisher) was added to stop the reaction. The isolated nuclei were washed twice with 500µl 1×PBS (Thermo Fisher) and then incubated in 200µl permeabilization buffer (190µl nuclease-free water, 10µl 10% SDS) (Thermo Fisher) at 62°C for 10min, and immediately quenched the SDS reaction by adding add 580μl of nuclease-free water and 100μl of 10% (vol/vol) Triton X-100 (Sigma-aldrich), and incubated at 37°C for 15min with rotation.The isolated nuclei were washed twice with 500µl 1×wash buffer B (20mM Tris-HCl, pH 7.5, 10mM MgCl2 and 0.2% Tween 20) and resuspended in 500µl 1× CutSmart buffer (NEB), followed by adding 1.6µl RNase If (NEB) with dilution tenfold in 1× PBS, and incubated at 37°C for 3min with rotation followed by incubation for 5min on ice. Nuclei were collected by centrifugation, then resuspended by 400µl PNK solution containing 1×T4 PNK reaction buffer, 1mM ATP, 1U/μl RiboLock RNase and 1U/μl T4 PNK (Thermo Fisher) at 37°C for 40min with rotation. The specific bridge linker was designed containing 5ʹ phosphorylation [5Phos] and Internal Biotin dT [ibiodT] chemical modifications. The forward strand is: 5′-[5APP]CCTCGATAC/iBIOdT/TGAGCTGAC-3′, and reverse strand is 5′-[5Phos]GTCAGC/iBIOdT/CAAGTATCGAG-3′. The 5′App ends of forward strand was treated by using a DNA 5′ Adenylation Kit (NEB). The isolated nuclei were washed twice with 500µl 1×wash buffer B and resuspended in 400µl of RNA ligation solution (1×T4 RNA ligase reaction buffer, 1U/μl RiboLock RNase, 10U/μl T4 RNA Ligase 2 truncated, 1.5pmol/μl bridge linker, 15% (w/v) PEG 8000, 0.1% Triton X-100) (NEB), and incubated overnight at 16 °C with rotation. The nuclei were pelleted by centrifugation, resuspended in 400 μl reverse transcription solution (1×MMLV buffer, 0.5mM dNTP, 8U/μl MMLV (RNase H-), 1U/μl RiboLock RNase) (Promega), and then incubated at 42 °C for 1 h. The isolated nuclei were washed five times with 500μl 1×wash buffer B, resuspended in T4 DNA ligation solution (1×DNA ligase reaction buffer with 10mM ATP, 4U/μl T4 DNA ligase, 0.1% (vol/vol) Triton X-100 and 0.1 mg/mLBSA) (NEB), incubated overnight at 16 °C with rotation. The isolated nuclei were resuspended in proteinase K solution (50 mM Tris-HCl, pH 7.5, 1% SDS, 100mM NaCl, 1mM EDTA and 1mg/mL proteinase K) at 65 °C for 3h with shaking at 800 rpm. RNA/DNA complex was extracted and dissolved in nuclease-free water (Thermo Fisher). The purified RNA/DNA complexes were incubated with gap-filling solution (10×NEBuffer r2.1,1mM dNTP and 0.18U/μl T4 DNA polymerase) (NEB) at room temperature for 40min to repair the pG-Tn5 transposition gap, followed by second-strand cDNA synthesis.

value: young leaves

value: no

value: Indica Group wild-type

value: WT


title: oscoi2, control, rep3

city: Montpellier

first: Anne-Sophie

last: PETITOT

address: 911 avenue Agropolis

department: UMR DIADE

country: France

institute: IRD

data_processing:
The quality of each library was controlled using FastQC.
Reads were trimmed with CutAdapt using the following criteria: the first 12 bases of all reads were eliminated, contaminating adapters were removed, low quality bases (Q<30) were trimmed out from both the 5- and 3-ends of reads, and reads less than 35nt were discarded.
Clean reads were mapped against the Oryza sativa subsp. japonica ‘Nipponbare’ reference genomes (MSU7 and RAP-DB) using HiSat2. Mapped reads were assembled into transcripts with StringTie using  reference annotations. Count files were generated from GTF files with an in-house script.
Assembly: msu7 and rapdb
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Oryza sativa

source_name: crown root tips

growth_protocol: Disinfected seeds were germinated on half‐strength Murashige & Skoog (½MS) medium including Gamborg B5 vitamins (Duchefa) supplied with 0.7% plant agar (Duchefa) for 2 days.Two days after germination, seedlings were transferred into glass tubes containing 20 ml of ½MS including Gamborg B5 vitamins supplied with 0.2% phytagel (Sigma) and grown in a growth chamber at 26°C under a 12h-day/12h-night photoperiod with a 70% relative humidity

extract_protocol:
Total RNAs were extracted from rice root samples using the RNeasy Plant mini kit (Qiagen) with addition of an on-column DNase I digestion.
cDNA libraries preparation and sequencing were performed by Novogene (Novogene, Cambridge, UK) using the Illumina NovaSeq platform generating 150-bp paired-end reads.

treatment_protocol: Six days old plants were transferred  in 1/2MS liquid media containing either Jasmonate (5 µM) or DMSO (control) for 6h. Crown root tips (around 1 cm) from 20-24 plants were collected and immediatly frozen in liquid nitrogen

value: crown root tips

value: oscoi2 edited lines

value: control


title: GABPA_CUTrun_E45_ICM_rep1

value: embryo

value: E4.5 ICM


title: H3K9ac-CUT&Tag-Rice-mature leaves-rep1

source_name: mature leaves

value: mature leaves


title: oscoi1ab, jasmonate, 6h, rep3

value: oscoi-1a/1b edited lines

value: jasmonate 6h


title: GABPA_CUTrun_8cell_rep2

value: Gabpa-dTAG/dTAG


title: ATAC_E45_ICM_Gabpa_DMSO_rep1

value: DMSO


title: oscoi1ab, jasmonate, 6h, rep2


title: ATAC_E45_ICM_Gabpa_dTAG_rep1


title: oscoi1ab, control, rep3


title: GABPA_CUTrun_8cell_rep1


title: oscoi1ab, control, rep1


title: H3K27me3-CUT&Tag-Rice-mature leaves-rep1


title: H3_TaDRIM-Seq-Rice-young leaves-rep1


title: WT, control, rep2

value: Kitaake


title: WT, control, rep1


title: oscoi2, jasmonate, 6h, rep2


title: oscoi2, jasmonate, 6h, rep1


title: oscoi2, control, rep2


title: GABPA_CUTrun_E35_ICM_rep2

value: untreated


title: Arabidopsis,overexpression2 ,three weeks

city: 上海市

first: bo

last: li

state: 上海

address: 上海市徐汇区枫林路300号植物生理生态研究所

institute: SIPPE

data_processing:
The libraries from each genotypes were sequenced on an illumine HiSeq 2000 (100 base paired end reads).
After filtering, the clean Illumina sequencing reads were mapped to the TAIR10 Arabidopsis genome using SOAPalibner/soap2.
The RPKM (Reads Per Kb per Million reads) method was used to determine gene differential expression (Fold Change>2; FDR0.001).

organism: Arabidopsis thaliana

source_name: inflorescence stem

extract_protocol:
total RNA isolation using the E.Z.N.A Plant RNA Kit (R6827; Omega Bio-tek). All total RNA samples were treated with DNase I during extraction. RNA quality and concentration (>200 ng/μl) was examined by electrophoresis and cDNA from 50 ng total RNA was generated.
Then 3 µg of the cDNA was fragmented, and 400 ng of the fragmented cDNA was used with an average size of 400 bp for library preparation (QiaQuick PCR extraction kit; QIAGEN). The libraries from each genotypes were sequenced on an illumine HiSeq 2000 (100 base paired end reads).

value: inflorescence stem

value: Arabidopsis

value: stem

value: overexpression


title: Arabidopsis,wide type ,three weeks

address: 上海市徐汇区枫林路300号植物生理生态研究所

value: WT


title: Arabidopsis,man6 mutant ,three weeks

address: 上海市徐汇区枫林路300号植物生理生态研究所

value: MAN6 knockout


title: Arabidopsis,man6 mutant2 ,three weeks

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: 339_14_Lung Parenchyma - BI1015550 2.5mg per kg Bleomycin 1mg per kg

city: Biberach (Riss)

first: Katrin

last: Fundel-Clemens

address: Birkendorferstr. 65

department: gCBDS

institute: Boehringer Ingelheim Pharma GmbH&Co KG

data_processing:
Basecalling has been done with bcl2fastq v2.20.0.422.
Alignment has been performed with STAR v2.5.2 using hg38 genome reference.
Read counts has been obtained with featureCounts v1.5.1.
Demultiplexing was performed using bcl2fastq v2.20.0.422 from Illumina (https://emea.support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html). Sequencing reads from the RNA-seq experiment were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline (also described in (Schlager et al., 2020)): filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner (Dobin et al., 2013) allowing for soft clipping of adapter sequences.  For quantification, we used transcript annotation files from Ensembl version 86, which corresponds to GENCODE 25 for human. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) (Li and Dewey, 2011) and featureCounts (v1.5.1) (Liao, Smyth and Shi, 2014). Quality controls were implemented using FastQC (v0.11.5) [ Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ], picardmetrics (v0.2.4) [ Slowikowski K. (2016): Available online at: https://github.com/slowkow/picardmetrics ] and dupRadar (v1.0.0) (Sayols, Scherzinger and Klein, 2016) at the respective steps.
Assembly: Rnor_6.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Lung Parenchyma

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using Tru-seq mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Lung Parenchyma


title: 339_17_Lung Parenchyma - BI1015550 2.5mg per kg Bleomycin 1mg per kg


title: oscoi2, control, rep1

value: crown root tips

value: oscoi2 edited lines

value: control


title: oscoi1ab, jasmonate, 6h, rep1


title: 339_9_Lung Parenchyma - Bleomycin 1mg per kg

value: Bleomycin 1mg per kg


title: oscoi1ab, control, rep2

value: oscoi-1a/1b edited lines


title: WT, jasmonate, 6h, rep3

value: jasmonate 6h


title: oscoi2, jasmonate, 6h, rep3


title: WT, jasmonate, 6h, rep1


title: WT, jasmonate, 6h, rep2


title: 339_8_Lung Parenchyma - Bleomycin 1mg per kg


title: 339_7_Lung Parenchyma - Bleomycin 1mg per kg


title: WT, control, rep3


title: 339_6_Lung Parenchyma - Control NaCl

value: NaCl


title: 339_4_Lung Parenchyma - Control NaCl


title: Arabidopsis,overexpression ,three weeks

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: total, 30min, replicate3

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center

data_processing:
Reads were aligned with STAR (v2.7.6) and counted with RSEM (v1.3.3).
Library sizes were normalized using genes with known half-lives greater than 14 hours (Herzog et al, 2017). Samples of each time series were further normalized to the corresponding t=0 time point.
We fitted a simple exponential decay model per compartment for roughly 10,000 genes, giving the aggregated subcellular turnover rates, in contrast to the rates of transition from one compartment to the next.
Assembly: mm10
Supplementary files format and content: {sample}_norm_read_count.txt files provide normalized read counts per gene.

growth_protocol: E14TG2a mESCs [Iacovino, M., Roth, M. E. & Kyba, M. Rapid genetic modification of mouse embryonic stem cells by Inducible Cassette Exchange recombination. Methods Mol. Biol. 1101, 339–351 (2014)] were cultured in 0.1% gelatin [w/v] coated plates in “2i + LIF” ES medium [Advanced DMEM/F12 (12634028, Thermo Fisher Scientific) – Neurobasal (21103049, Thermo Fisher Scientific) – Knockout™ DMEM (10829018, Thermo Fisher Scientific) (1 : 1 : 0.5), 14% Fetal Bovine Serum qualified for ES cells (16141079, Life Technologies), 1X N2 (17502048, Thermo Fisher Scientific), 1X B27 (17504001, Thermo Fisher Scientific), 1X GlutaMax (35050061, ThermoFisher Scientific), 1X MEM Non-Essential Amino Acid (11140050, Thermo Fisher Scientific), 1X Nucleosides (ES-008-D, Merck Millipore), 100 µM β-mercaptoethanol (21985023, Thermo Fisher Scientific), 3 μM CHIR99021 (SML1046-5MG, Invitrogen) and 1 μM PD0325901 (PZ0162-5MG, Invitrogen), 1000 U/ml Leukemia inhibitory factor (ESG1107, Merck Millipore)], under a controlled atmosphere at 5% CO2 and 37°C. mESCs were seeded the day before the experiments at a density of 3× 105 cells/ml.

extract_protocol:
Cells were harvested at 0, 30, 60, 120 and 180 min after addition of flavopiridol followed by cell fractionation. Briefly, medium was aspirated, 5 ml of ice-cold PBS supplemented with 100 µM cycloheximide (A0879,0001, Biochemika) was added to the plates, cells were scraped from the plates, transferred to 15ml falcon and spun down. Pellet was resuspended in 500 µl of ice-cold permeabilization buffer (110 mM KOAc, 25 mM K-HEPES pH 7.2, 2.5 mM Mg(OAc)2, 1 mM EGTA with freshly added 0.015% digitonin, 1 mM DTT, 100 μg/ml cycloheximide, 1X Complete Protease Inhibitor Cocktail and 40 U/mL RNaseOUT™). 100 µl of the sample was taken aside as Total extract and rest was incubated for 10 min at 4°C with rotation, followed by centrifugation at 3000 g 5 min at 4°C. Supernatant (corresponding to the Cytosolic fraction) was transferred to new tube while the pellet was resuspended in 5ml of wash buffer (110 mM KOAc, 25 mM K-HEPES pH 7.2, 2.5 mM Mg(OAc)2, 1 mM EGTA with freshly added 0.004% digitonin, 1mM DTT, 100μg/ml cycloheximide) and spun down again at 3000 g 5 min at 4°C. After centrifugation washed pellet was mixed with 500 µl of ice-cold lysis buffer (400 mM KOAc, 25 mM K-HEPES pH 7.2, 15 mM Mg(OAc)2, 0.5% (v/v) NP-40 and freshly added 1 mM DTT, 100 μg/ml cycloheximide, 1X Complete Protease Inhibitor Cocktail, 40 U/mL RNase Out) and incubated for 5 min on ice followed by centrifugation at 3000 g 5 min at 4°C to collect the supernatant (corresponding to the Membrane fraction) and the pellet (insoluble and the nuclear fraction). For additional purity nuclei were loaded on 10% sucrose cushion in lysis buffer and centrifuged at 200 g 5 min at 4°C. The cytosolic and membrane fractions were clarified at 7500 g 10 min at 4°C to remove cell debris.Obtained fractions were mixed with Trizol LS and RNA was isolated following the manufacturer instructions.
One microgram of total RNA was used as an input for TruSeq Stranded mRNA Library Prep Kit according to the instructions of the manufacturer.
TruSeq Stranded mRNA Library Paired-End

treatment_protocol: Three independently passaged biological replicates of mESCs (~3.5 × 107 cells per replicate) were cultured in “2i + LIF” ES medium supplemented with 1µM flavopiridol to block the transcription.

tag: fraction

value: total

tag: time point

value: mESC

value: 1microM flavopiridol


title: total, 60min, replicate2

tag: cell line


title: 339_18_Lung Parenchyma - BI1015550 2.5mg per kg Bleomycin 1mg per kg

tag: tissue

tag: genotype


title: total, 60min, replicate3

tag: treatment


title: 339_15_Lung Parenchyma - BI1015550 2.5mg per kg Bleomycin 1mg per kg


title: total, 60min, replicate1

tag: cell type


title: total, 30min, replicate1


title: 339_13_Lung Parenchyma - BI1015550 2.5mg per kg Bleomycin 1mg per kg


title: 339_16_Lung Parenchyma - BI1015550 2.5mg per kg Bleomycin 1mg per kg


title: 339_12_Lung Parenchyma - Bleomycin 1mg per kg


title: 339_1_Lung Parenchyma - Control NaCl


title: 339_3_Lung Parenchyma - Control NaCl


title: 339_11_Lung Parenchyma - Bleomycin 1mg per kg


title: total, 0min, replicate3


title: total, 120min, replicate3


title: total, 240min, replicate1


title: total, 120min, replicate1


title: nucleus, 60min, replicate2

value: nucleus


title: total, 120min, replicate2


title: total, 240min, replicate3


title: total, 240min, replicate2


title: 339_2_Lung Parenchyma - Control NaCl


title: nucleus, 60min, replicate1


title: 339_5_Lung Parenchyma - Control NaCl


title: total, 0min, replicate2


title: nucleus, 60min, replicate3


title: nucleus, 30min, replicate1


title: nucleus, 30min, replicate2


title: nucleus, 30min, replicate3


title: nucleus, 120min, replicate1


title: nucleus, 120min, replicate2


title: nucleus, 0min, replicate3


title: total, 30min, replicate2


title: membrane, 60min, replicate2

value: membrane


title: nucleus, 240min, replicate3


title: nucleus, 0min, replicate2


title: nucleus, 240min, replicate2


title: membrane, 30min, replicate3


title: nucleus, 240min, replicate1


title: nucleus, 120min, replicate3


title: nucleus, 0min, replicate1


title: membrane, 60min, replicate3


title: membrane, 120min, replicate1


title: total, 0min, replicate1


title: cytosol, 60min, replicate3

value: cytosol


title: membrane, 0min, replicate3


title: membrane, 30min, replicate2


title: membrane, 240min, replicate3


title: membrane, 240min, replicate1


title: membrane, 240min, replicate2


title: cytosol, 60min, replicate1


title: membrane, 120min, replicate3


title: cytosol, 30min, replicate2


title: cytosol, 240min, replicate3


title: membrane, 0min, replicate1


title: membrane, 60min, replicate1


title: membrane, 0min, replicate2


title: cytosol, 60min, replicate2


title: cytosol, 30min, replicate1


title: cytosol, 240min, replicate2


title: membrane, 30min, replicate1


title: cytosol, 120min, replicate3


title: cytosol, 240min, replicate1


title: membrane, 120min, replicate2


title: cytosol, 120min, replicate2


title: cytosol, 120min, replicate1


title: SCO PCB40 4

city: Mississippi State,

first: Adam

last: Thrash

state: MS

address: 2 Research Blvd., Box 9627

department: Institute for Genomics, Biocomputing & Biotechnology

institute: Mississippi State University

description: Scorton Creek 16

data_processing:
mapped and quantified using salmon (v1.3.0) against the reference transcriptome
Tximport (v1.16.1) was used to import transcript-level estimates from salmon and summarize this data to the gene level
genes were filtered such that only genes with an average log Counts per Million > 1 across all samples were retained
EdgeR (v3.30.3) was used to determine differentially expressed genes (DEGs)
Assembly: NCBIFundulus heteroclitusannotation release 102; assembly MU-UCD_Fhet_4.1
Supplementary files format and content: tab-delimited text files containing information about how reads mapped to transcripts

organism: Fundulus heteroclitus

source_name: Embryo Whole Brain

extract_protocol:
Total RNA was isolated from 6 embryos’ brains per treatment from individual 17 dpf embryos using the Qiagen RNeasy® Micro Kit (Germantown, MD, USA) following the Purification of Total RNA from Animal and Human Tissues protocol in the RNeasy® Micro Handbook with slight modifications.  The modification included homogenization of brain tissue in 350 µL of RLT buffer using a pellet pestle and elution of Total RNA using 15 µL of RNase-free water.
RNA quality was assayed using the Agilent High Sensitivity RNA ScreenTape System (Waldbronn, Germany) for the Agilent 2200 TapeStation (Palo Alto, CA, USA), and RNA was quantified using the NanoDrop 2000 (ThermoFisher Scientific, Waltham, MA).

value: Embryo Whole Brain

tag: population

value: Scorton Creek

value: SCO PCB40 4


title: SCO PCB40 3

description: Scorton Creek 15

value: SCO PCB40 3


title: SCO PCB40 6

description: Scorton Creek 18

value: SCO PCB40 6


title: SCO PCB40 2

description: Scorton Creek 14

value: SCO PCB40 2


title: cytosol, 0min, replicate2


title: SCO PCB40 5

description: Scorton Creek 17

value: SCO PCB40 5


title: cytosol, 0min, replicate1


title: SCO Hg Fed 6

description: Scorton Creek 12

value: SCO Hg Fed 6


title: SCO PCB40 1

description: Scorton Creek 13

value: SCO PCB40 1


title: cytosol, 30min, replicate3


title: cytosol, 0min, replicate3


title: total, 60min, rep6

data_processing:
Alignment of raw reads was done with STAR (v2.7.6).
Reads in exons were counted with HTSeq-count (v0.11.1) and exon and TPM values were obtained by RSEM (v.1.3.3) using default parameters.
Based on a binomial mixture model by Juerges et al. (2018) we determined the conversion rate per sample. With the conversion rates, T and T2C conversion counts the fraction of new to total RNA was calculated on intron/exon level, which was used later on as input for the kinetic model.
Gene set enrichment analyses were performed with fgsea (v1.28.0) with the GSEA parameter set to 0 and gene set sizes limited from 30 to 900.
Fitting was performed throughout with the python package lmfit (v1.0.3) using the Levenberg-Marquardt “least-squares” algorithm to minimize the chi-squared unless otherwise specified. Summarizing different models and genes, the following kinetic rates were estimated: transcript elongation rate, intron removal rate, nuclear export rate, nuclear degradation rate, cytosolic degradation rate, cytosolic transport rate and membrane degradation rate.
Assembly: mm10
Supplementary files format and content: {sample}.txt files provide raw read counts per gene, reads counted in exons with HTSeq-count
Supplementary files format and content: {sample}_t2c_counts.txt files give gene and exon-wise T2C metrics: conversion probability (p_conv), number of Ts in gene/exon/intron (T_exon, T_intron), number of T2C transitions in gene/exon/intron (T2C_exon, T2C_intron) and share of T2C vs total T counts divided by conversion probability per gene/exon/intron (T2C_over_T_exon, T2C_over_T_intron).

extract_protocol:
Briefly, medium was aspirated, 5 ml of ice-cold PBS supplemented with 100 µM cycloheximide (A0879,0001, Biochemika) was added to the plates, cells were scraped from the plates, transferred to 15ml falcon and spun down. Pellet was resuspended in 500 µl of ice-cold permeabilization buffer (110 mM KOAc, 25 mM K-HEPES pH 7.2, 2.5 mM Mg(OAc)2, 1 mM EGTA with freshly added 0.015% digitonin, 1 mM DTT, 100 μg/ml cycloheximide, 1X Complete Protease Inhibitor Cocktail and 40 U/mL RNaseOUT™). 100 µl of the sample was taken aside as Total extract and rest was incubated for 10 min at 4°C with rotation, followed by centrifugation at 3000 g 5 min at 4°C. Supernatant (corresponding to the Cytosolic fraction) was transferred to new tube while the pellet was resuspended in 5ml of wash buffer (110 mM KOAc, 25 mM K-HEPES pH 7.2, 2.5 mM Mg(OAc)2, 1 mM EGTA with freshly added 0.004% digitonin, 1mM DTT, 100μg/ml cycloheximide) and spun down again at 3000 g 5 min at 4°C. After centrifugation washed pellet was mixed with 500 µl of ice-cold lysis buffer (400 mM KOAc, 25 mM K-HEPES pH 7.2, 15 mM Mg(OAc)2, 0.5% (v/v) NP-40 and freshly added 1 mM DTT, 100 μg/ml cycloheximide, 1X Complete Protease Inhibitor Cocktail, 40 U/mL RNase Out) and incubated for 5 min on ice followed by centrifugation at 3000 g 5 min at 4°C to collect the supernatant (corresponding to the Membrane fraction) and the pellet (insoluble and the nuclear fraction). For additional purity nuclei were loaded on 10% sucrose cushion in lysis buffer and centrifuged at 200 g 5 min at 4°C. The cytosolic and membrane fractions were clarified at 7500 g 10 min at 4°C to remove cell debris. 20 µl of all fractions were taken for Western analysis while rest were mixed with Trizol LS (10296028, Thermo Fisher Scientific) for subsequent RNA isolation.
One microgram of total RNA was used as an input for TruSeq Stranded mRNA Library Prep Kit according to the instructions of the manufacturer.
TruSeq Stranded mRNA Library Paired-End

treatment_protocol: Two independently passaged biological replicates of mESCs (~3.5 × 107 cells per replicate) were separately labelled in “2i + LIF” ES medium supplemented with 500 µM (for 0, 15, 20, 30, 40 min) or 100 µM (for 60, 120 and 180 min) 4-thiouridine (4sU, RP-2304, ChemGenes) and fractionated by sequential detergent extraction, as described previously [Jagannathan et al. 2011] with minor modifications.

value: 100uM 4-thiouridine


title: SCO Hg Fed 5

description: Scorton Creek 11

value: SCO Hg Fed 5


title: total, 60min, rep4


title: SCO Hg Fed 4

description: Scorton Creek 10

value: SCO Hg Fed 4


title: total, 60min, rep3

value: mESC


title: SCO Hg Fed 2

description: Scorton Creek 8

value: SCO Hg Fed 2


title: total, 40min, rep4

value: 500uM 4-thiouridine


title: SCO Hg Fed 1

description: Scorton Creek 7

value: SCO Hg Fed 1


title: total, 40min, rep3


title: total, 30min, rep2


title: SCO Control 6

description: Scorton Creek 6

value: SCO Control 6


title: SCO Control 3

description: Scorton Creek 3

value: Embryo Whole Brain

value: SCO Control 3


title: SCO Control 4

description: Scorton Creek 4

value: Scorton Creek

value: SCO Control 4


title: SCO Control 5

description: Scorton Creek 5

value: SCO Control 5


title: total, 30min, rep1


title: total, 20min, rep4


title: SCO Control 2

description: Scorton Creek 2

value: SCO Control 2


title: total, 20min, rep3


title: total, 20min, rep1


title: NBH PCB400 6

description: New Bedford Harbor 18

value: New Bedford Harbor

value: NBH PCB400 6


title: SCO Control 1

description: Scorton Creek 1

value: SCO Control 1


title: total, 180min, rep5

value: 100uM 4-thiouridine


title: total, 60min, rep5


title: SCO Hg Fed 3

description: Scorton Creek 9

value: SCO Hg Fed 3


title: total, 180min, rep4


title: NBH PCB400 3

description: New Bedford Harbor 15

value: NBH PCB400 3


title: total, 15min, rep2

value: mESC


title: NBH PCB400 1

description: New Bedford Harbor 13

value: NBH PCB400 1


title: total, 180min, rep3


title: NBH PCB40 6

description: New Bedford Harbor 12

value: NBH PCB40 6


title: total, 15min, rep1

value: 500uM 4-thiouridine


title: total, 120min, rep5


title: total, 120min, rep6


title: NBH PCB40 5

description: New Bedford Harbor 11

value: NBH PCB40 5


title: NBH PCB40 4

description: New Bedford Harbor 10

value: Embryo Whole Brain

value: NBH PCB40 4


title: total, 20min, rep2


title: total, 120min, rep4


title: NBH PCB400 4

description: New Bedford Harbor 16

value: NBH PCB400 4


title: NBH PCB40 2

description: New Bedford Harbor 8

value: NBH PCB40 2


title: total, 120min, rep3


title: NBH Control 5

description: New Bedford Harbor 5

value: NBH Control 5


title: NBH PCB40 1

description: New Bedford Harbor 7

value: NBH PCB40 1


title: total, 180min, rep6


title: total, 0min, rep3


title: NBH PCB400 5

description: New Bedford Harbor 17

value: New Bedford Harbor

value: NBH PCB400 5


title: total, 0min, rep4


title: NBH Control 3

description: New Bedford Harbor 3

value: NBH Control 3


title: NBH Control 6

description: New Bedford Harbor 6

value: NBH Control 6


title: nucleus, 60min, rep4

value: 100uM 4-thiouridine


title: NBH Control 2

description: New Bedford Harbor 2

value: NBH Control 2


title: NBH Control 1

description: New Bedford Harbor 1

value: NBH Control 1


title: NBH PCB400 2

description: New Bedford Harbor 14

value: NBH PCB400 2


title: NBH Control 4

description: New Bedford Harbor 4

value: NBH Control 4


title: nucleus, 60min, rep5

value: mESC


title: WT_S40_Rep5

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

data_processing:
Untrimmed reads were mapped to the Maize Genome v4 using Hisat2 with default parameters.
The resulting bam file was analyzed using Strigtie package and the gff3 file from AGP v4 version with default paramenters, resulting in a mapping gtf file for each sample.
Assembly: Zea_mays.AGPv4.dna.toplevel.fa
Supplementary files format and content: gtf files of mapping reads

organism: Zea mays

source_name: Leaf

growth_protocol: Z. mays seedlings were grown under controlled temperature and humidity conditions throughout with a 16 h light and 8 h dark cycle. U. maydis sporidia were grown at 28ºC under constant shaking at 200 rpm till OD600 of the culture reached 0.8. At this stage the cells were harvested and used for infection.

extract_protocol:
RNA was extracted from all the different samples using TRIzol method following the manufacturer’s protocol.
We used the commertial kit NEB Ultra II stranded

treatment_protocol: The Z. mays seedlings were infected with a suspension of U. maydis sporidia in sterile water using a syringe infection method.

value: Leaf

tag: u. maydis_strain

value: WT


title: nucleus, 30min, rep1

value: 500uM 4-thiouridine


title: nucleus, 60min, rep3


title: nucleus, 60min, rep6


title: nucleus, 40min, rep4


title: total, 0min, rep1


title: NBH PCB40 3

description: New Bedford Harbor 9

value: Embryo Whole Brain

value: NBH PCB40 3


title: WT_P40_Rep2


title: nucleus, 20min, rep3


title: WT_P40_Rep1


title: nucleus, 20min, rep1


title: WT_LSW_Rep2

value: LSW


title: nucleus, 30min, rep2


title: nucleus, 40min, rep3


title: nucleus, 180min, rep6


title: WT_LSW_Rep1


title: nucleus, 20min, rep4


title: WT_S40_Rep1


title: WT_P40_Rep5


title: nucleus, 20min, rep2


title: nucleus, 180min, rep5


title: nucleus, 180min, rep4


title: WT_LSW_Rep5


title: WT_S40_Rep2


title: UI_S40_Rep1

value: UI


title: UI_S40_Rep2


title: nucleus, 180min, rep3


title: UI_S40_Rep3


title: nucleus, 15min, rep2


title: UI_P40_Rep3


title: nucleus, 15min, rep1


title: UI_P40_Rep1


title: nucleus, 120min, rep5


title: UI_P40_Rep2


title: UI_LSW_Rep3


title: nucleus, 120min, rep6


title: H3K27me3-d2-float-untr

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
Reads were aligned to the mm10 genome in paired-end mode using bowtie2 v2.2.9 using --very-sensitive-local as a parameter.
Peaks and depth coverages were obtained using macs2 v2.1.1.
Assembly: mm10
Supplementary files format and content: narrowPeak file containing peak coordinates
Supplementary files format and content: bigWig file containing genome-wide depth coverage

source_name: in-vitro -derived d2 floating haematopoietic progenitors

growth_protocol: ESCs expressing an inducible dominant negative FOS (dnFOS), generated in Obier et al. 2016, were differentiated for 2d to floating hematopoietic progenitors.

extract_protocol:
Cells were crosslinked with Di(N-succinimidyl) glutarate (DSG) and formaldehyde. ChIP on double-crosslinked chromatin was performed using an anti-RUNX1 antibody (Abcam #23980).
Sequencing libraries were prepared using the KAPA Hyper Prep Kit as exactly described in Obier et al 2016.

treatment_protocol: ESCs were grown with or without Doxycycline induction and materials were processed exactly as described in Obier et al. 2016.

tag: antibody

value: Tet-on dominant-negative FOS

value: Doxycycline


title: H3K27me3-d2-float-DOX

value: in-vitro -derived d2 floating haematopoietic progenitors


title: untreated-RUNX1


title: UI_LSW_Rep2


title: nucleus, 120min, rep3


title: 42D_4

city: Leicester

first: Mrinal

last: Das

state: Leicestershire

address: University Road, Leicester

country: United Kingdom

institute: University of Leicester

description:
MD15
total RNA

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts
Assembly: mm10
Supplementary files format and content: tab limited raw count for each sample

source_name: liver

extract_protocol:
RNA from whole tissue was extracted using trizol and RNAeasy kit
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following

treatment_protocol: aerosol infection

value: liver

tag: strain

value: infected for 42 day


title: nucleus, 120min, rep4

value: 100uM 4-thiouridine


title: UI_LSW_Rep1


title: nuc3_S40_Rep4


title: 42D_1

description:
MD9
total RNA


title: DOX-RUNX1


title: 42D_3

description:
MD12
total RNA


title: nucleus, 0min, rep3


title: nucleus, 0min, rep1


title: 21D_3

description:
MD7
total RNA

value: infected for 21 day


title: nuc3_S40_Rep2


title: 21D_4

description:
MD8
total RNA


title: 21D_2

description:
MD6
total RNA


title: nuc3_S40_Rep1


title: Uninf_4

description:
MD14
total RNA

value: uninfected


title: Uninf_3

description:
MD4
total RNA


title: Uninf_2

description:
MD3
total RNA


title: membrane, 60min, rep5


title: membrane, 60min, rep6


title: nuc3_P40_Rep4


title: nuc3_P40_Rep2


title: membrane, 60min, rep4


title: 42D_2

description:
MD10
total RNA


title: Uninf_1

description:
MD1
total RNA


title: membrane, 60min, rep3


title: 21D_1

description:
MD5
total RNA


title: membrane, 40min, rep4


title: nuc3_LSW_Rep2


title: membrane, 40min, rep3


title: nuc3_LSW_Rep1


title: 07_KO_CT18_A

city: Kyoto

first: Masao

last: Doi

department: Department of Systems Biology

institute: Kyoto University, Graduate School of Pharmaceutical Sciences

hyb_protocol: The labeled, fragmented ssDNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix) in a GeneChip Hybridization Oven 640 at 45°C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix GeneChip Scanner 3000 7G system and the software Genechip Command Console Software (AGCC).

data_processing: The data were analyzed with the GeneSpring GX software (version 11.5.1, Agilent Technologies) in the following settings: Summarization Algorithm, RMA16; Confidence level, All; Baseline Options, Do not perform baseline transformation.

source_name: Suprachiasmatic Nuclei

label_protocol: Ambion WT Expression kit was used to prepare the cDNA, which was then labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

extract_protocol: RNA was extracted using Qiagen Rneasy kit.

tag: circadian time


title: 05_KO_CT6_A


title: 08_KO_CT18_B


title: 06_KO_CT6_B


title: NUC1-nuc2_S40_Rep4


title: membrane, 30min, rep2


title: V4645

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

description: sample_id in count_matrix: V4645

data_processing:
Raw fastq files (pair-end) were aligned to human GRCh38.p13 genome using STAR 2.7.11 with GENCODE 35 annotations.
Counts were collected from the output of each STAR run and merged into one count matrix
Assembly: hunan GRCh38.p14 (hg38)
Supplementary files format and content: FASTQ
Supplementary files format and content: tab-delimited text included raw counts per sample

source_name: iPS Cells

growth_protocol: The hiPSCs were maintained in mTeSRPlus (StemCell #100-0276) with primocin (Invitrogen #ant-pm-1) on tissue culture plates coated with matrigel (Fisher Scientific #08-774-552) or geltrex (Fisher Scientific #A1413202) throughout the mutagenesis process. The Institutional Review Board (IRB) of NorthShore University HealthSystem approved study.

extract_protocol:
Total RNA was extracted using Qiagen RNEasy mini spin columns and the concentrations verified by NanoDrop
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.Sequencing was performed on NovaX with 2x150 bp paired read

treatment_protocol: The cell culture, DNA base editing/sgRNA transfection, and cell sorting for LoF mutagenesis were performed in batches, each containing 23 genes and a non-transfected control (NTC) on a 24-well plate format. The base editor system (pEF-AncBE4max, pEF-BFP, and pDT-sgRNA) contains a reporter gene that makes cells that have undergone C to T editing turn from blue to green . LipofectamineSTEM was used for cell transfection.  After cell transfection for 72 hrs, single hiPSC from the post-transfection culture were sorted into 96-well plates with one cell per well using a BD FACSAria Fusion Flow Cytometer in the presence of CEPT cocktail (1:10,000 chroman 1, emricasan, and transISRIB; 1:1,000 polyamine supplement) (Tristan et al., 2023). The sorted single cells were cultured on a 96-well plate with media changes every other day for 10-14 days until colonies appeared with an appropriate size to pick for Sanger sequencing genotyping.

tag: cell line_barcode

value: iPS Cells

value: iPSC

tag: age

value: Female

tag: ancestry

value: EA

tag: lof target_gene

tag: chromosome of_gene

tag: variant type

value: Homo

tag: crispr type

tag: passage #


title: 04_WT_CT18_B

value: wild-type


title: NUC1-nuc2_S40_Rep2

tag: tissue

value: Leaf

tag: fraction


title: membrane, 20min, rep4

tag: cell line

value: mESC

tag: treatment

value: 500uM 4-thiouridine


title: V4647

description: sample_id in count_matrix: V4647

tag: cell type

tag: Sex

value: Hetero


title: NUC1-nuc2_S40_Rep1

tag: u. maydis_strain

tag: genotype


title: V4639

description: sample_id in count_matrix: V4639


title: nuc3_P40_Rep1


title: 03_WT_CT18_A

tag: strain

tag: circadian time


title: 02_WT_CT6_B


title: 01_WT_CT6_A


title: membrane, 20min, rep3


title: NUC1-nuc2_P40_Rep4


title: V4615

description: sample_id in count_matrix: V4615

tag: cell line_barcode

tag: age


title: nuc3_LSW_Rep4

value: LSW


title: membrane, 20min, rep2


title: V4617

description: sample_id in count_matrix: V4617

tag: ancestry

tag: lof target_gene

value: Negative Control


title: V4600

description: sample_id in count_matrix: V4600

tag: chromosome of_gene

tag: variant type


title: V4593

description: sample_id in count_matrix: V4593

tag: crispr type

tag: passage #


title: NUC1-nuc2_P40_Rep2

tag: tissue

tag: fraction


title: V4563

description: sample_id in count_matrix: V4563

tag: cell line

value: Male


title: membrane, 30min, rep1

tag: cell type

tag: treatment


title: membrane, 20min, rep1


title: NUC1-nuc2_P40_Rep1

tag: u. maydis_strain


title: V4628

description: sample_id in count_matrix: V4628

tag: Sex


title: V4558

description: sample_id in count_matrix: V4558


title: V4561

description: sample_id in count_matrix: V4561


title: V4542

description: sample_id in count_matrix: V4542


title: membrane, 180min, rep3


title: V4567

description: sample_id in count_matrix: V4560

value: TRIO


title: TRAP, mix, control, 3

city: Irapuato

first: Obed

middle: Ramirez

last: Sanchez

state: Guanajuato

address: Km. 9.6 Libramiento NorteCarr. Irapuato-León

department: langebio

country: Mexico

institute: cinvestav

description: Four week-old A. thaliana leaves mixed with cultured BcRPL23-YFP B.cinerea were subjected to TRAP RNA profiling, biological repeat 3

data_processing:
Library strategy: TRAP-seq
Fastq libraries were aligned to a concatenated genome composed of A. thaliana (TAIR10) and B. cinerea B05 (ASM83294v1) using STAR parameters --outFilterMismatchNoverLmax 0.3,  and --outFilterMismatchNoverReadLmax 0.1
Gene quantifciation was obtanied with featureCounts using default parameters
Genome_build: TAIR10/ASM83294v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism:
Arabidopsis thaliana
Botrytis cinerea

source_name: plant leaves, fungal hyphae

growth_protocol: All A. thaliana lines used were 4 week-old in the Columbia background (Col-0). A. thaliana plants were grown in a controlled environment glasshouse at 23°C with 55% humidity and 12 h light d-1 . B. cinerea was cultured on Potato Dextrose Agarat (PDA) at room temperature.

extract_protocol:
Total RNAs were extracted from the above samples using the TRIzol reagent and treated with DNase I.
NEB Next Poly(A) mRNA Magnetic Isolation Module kit (NEB #E7490) coupled with NEBNext® Ultra™ Directional RNA Library Prep Kit (NEB #E7420) were used to make the libraries for Illumina sequencing based on the manufacturer’s protocols.

tag: host ecotype

value: mixed with cultured BcRPL23-YFP B.cinerea B05

value: plant leaves, fungal hyphae


title: membrane, 180min, rep6

value: 100uM 4-thiouridine


title: NUC1-nuc2_LSW_Rep4

tag: genotype


title: membrane, 180min, rep5


title: V4520

description: sample_id in count_matrix: V4556

tag: cell line_barcode

value: iPS Cells


title: membrane, 180min, rep4


title: NUC1-nuc2_LSW_Rep2


title: V4548

description: sample_id in count_matrix: V4548

value: iPSC

tag: age


title: NUC1-nuc2_LSW_Rep1


title: V4539

description: sample_id in count_matrix: V4539

value: Female

tag: ancestry


title: V4536

description: sample_id in count_matrix: V4536

value: EA

tag: lof target_gene


title: membrane, 15min, rep2


title: V4538

description: sample_id in count_matrix: V4538

tag: chromosome of_gene

value: Homo


title: membrane, 15min, rep1


title: V4565

description: sample_id in count_matrix: V4514

tag: variant type


title: membrane, 120min, rep6


title: V4551

description: sample_id in count_matrix: V4551

tag: crispr type


title: V4509

description: sample_id in count_matrix: V4509

tag: passage #


title: TRAP, mix, control, 2

description: Four week-old A. thaliana leaves mixed with cultured BcRPL23-YFP B.cinerea were subjected to TRAP RNA profiling, biological repeat 2

tag: tissue


title: V4512

description: sample_id in count_matrix: V4512


title: V4535

description: sample_id in count_matrix: V4535

value: chrX


title: membrane, 120min, rep5


title: TRAP, infected, 2

description: Four week-old A. thaliana leaves infected by B.cinerea transformant expressing YFP-tagged ribosome subunit BcRPL23-YFP were collected and subjected to Translating Ribosome Affinity Purification (TRAP) profiling, biological repeat 2

value: infected with BcRPL23-YFP B.cinerea B05


title: V4503

description: sample_id in count_matrix: V4503


title: TRAP, mix, control, 1

description: Four week-old A. thaliana leaves mixed with cultured BcRPL23-YFP B.cinerea were subjected to TRAP RNA profiling, biological repeat 1


title: V4502

description: sample_id in count_matrix: V4502


title: V4522

description: sample_id in count_matrix: V4522


title: TRAP, infected, 1

description: Four week-old A. thaliana leaves infected by B.cinerea transformant expressing YFP-tagged ribosome subunit BcRPL23-YFP were collected and subjected to Translating Ribosome Affinity Purification (TRAP) profiling, biological repeat 1


title: V4508

description: sample_id in count_matrix: V4508


title: membrane, 120min, rep3

value: mESC


title: V4506

description: sample_id in count_matrix: V4506


title: At, total, control, 2

description: mRNAs isolated from 4-week old B.cinerea infected A. thaliana leaves, biological repeat 2

data_processing:
Fastq libraries were aligned to a concatenated genome composed of A. thaliana (TAIR10) and B. cinerea B05 (ASM83294v1) using STAR parameters --outFilterMismatchNoverLmax 0.3,  and --outFilterMismatchNoverReadLmax 0.1
Gene quantifciation was obtanied with featureCounts using default parameters
Genome_build: TAIR10/ASM83294v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: infected with B.cinerea B05

tag: sample type

value: total tissue


title: membrane, 120min, rep4

tag: cell line


title: At, total, control, 3

description: mRNAs isolated from 4-week old B.cinerea infected A. thaliana leaves, biological repeat 3


title: V3969

description: sample_id in count_matrix: V3997

tag: cell type


title: At, total, control, 1

description: mRNAs isolated from 4-week old B.cinerea infected A. thaliana leaves, biological repeat 1

tag: treatment


title: V3997

description: sample_id in count_matrix: V3996


title: V4489

description: sample_id in count_matrix: V4500


title: membrane, 0min, rep4

value: 500uM 4-thiouridine


title: V3943

description: sample_id in count_matrix: V3999


title: membrane, 0min, rep1


title: V4000

description: sample_id in count_matrix: V4002


title: TRAP, infected, 3

description: Four week-old A. thaliana leaves infected by B.cinerea transformant expressing YFP-tagged ribosome subunit BcRPL23-YFP were collected and subjected to Translating Ribosome Affinity Purification (TRAP) profiling, biological repeat 3


title: V3996

description: sample_id in count_matrix: V3994


title: membrane, 0min, rep3


title: cytosol, 60min, rep6


title: D_Etoposide_STM_2_B_NEAT1

city: Würzburg

first: Redmond

last: Smyth

state: Bayern

address: Josef-Schneider-Straße 2, D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Basecalling
Demuliplexing
Alignment with last against Neat1 transcript
Mutations counted with rf_count
Assembly: Neat1 transcript
Supplementary files format and content: Binary file containing mutation counts (https://rnaframework-docs.readthedocs.io/en/latest/rf-count/)

extract_protocol:
RNAhot extract with Trizol
Reverse transcribed with MarathonRT and amplified with specific primers
Nanopore DNA sequencing (with barcoding)

value: Etoposide

tag: replicate

tag: dms treatment

value: DMS


title: V3991

description: sample_id in count_matrix: V3988

tag: Sex

value: Male

value: Hetero


title: V3981

description: sample_id in count_matrix: V3991


title: D_Etoposide_STM_1_B_NEAT1


title: V4501

description: sample_id in count_matrix: V4501


title: V3982

description: sample_id in count_matrix: V3977


title: D_STM_1_B_NEAT1

value: STM


title: V3979

description: sample_id in count_matrix: V3959


title: D_STM_2_B_NEAT1


title: V3967

description: sample_id in count_matrix: V3972


title: cytosol, 60min, rep3

value: 100uM 4-thiouridine


title: V3964

description: sample_id in count_matrix: V3962

value: iPS Cells


title: D_Etoposide_2_B_NEAT1


title: V3925

description: sample_id in count_matrix: V3948

value: iPSC


title: D_Etoposide_1_B_NEAT1


title: V3983

description: sample_id in count_matrix: V3947


title: V3917

description: sample_id in count_matrix: V3953

value: Female

value: TRIO


title: V3975

description: sample_id in count_matrix: V3958

value: EA


title: cytosol, 40min, rep4


title: V3936

description: sample_id in count_matrix: V3936

value: Homo


title: D_Untreated_2_B_NEAT1

value: Untreated


title: cytosol, 40min, rep3

value: mESC


title: cytosol, 30min, rep2


title: V3928

description: sample_id in count_matrix: V3928


title: V3932

description: sample_id in count_matrix: V3932


title: D_Untreated_1_B_NEAT1


title: cytosol, 60min, rep4


title: V3972

description: sample_id in count_matrix: V3964


title: cytosol, 30min, rep1


title: cytosol, 60min, rep5


title: V3923

description: sample_id in count_matrix: V3923


title: V3921

description: sample_id in count_matrix: V3921


title: E_Untreated_2_B_NEAT1


title: V3909

description: sample_id in count_matrix: V3909


title: V3870

description: sample_id in count_matrix: V3911


title: E_Untreated_1_B_NEAT1


title: V3897

description: sample_id in count_matrix: V3897

value: chrX


title: cytosol, 20min, rep3


title: cytosol, 20min, rep4


title: D_Etoposide_STM_2_A_NEAT1


title: V3900

description: sample_id in count_matrix: V3894


title: V3929

description: sample_id in count_matrix: V3889


title: D_Etoposide_STM_1_A_NEAT1


title: V3877

description: sample_id in count_matrix: V3877


title: cytosol, 20min, rep1


title: V3873

description: sample_id in count_matrix: V3873


title: cytosol, 20min, rep2


title: V3880

description: sample_id in count_matrix: V3880


title: cytosol, 180min, rep6


title: D_STM_2_A_NEAT1


title: V3968

description: sample_id in count_matrix: V3865

value: Negative Control


title: D_STM_1_A_NEAT1


title: V3866

description: sample_id in count_matrix: V3866


title: V3864

description: sample_id in count_matrix: V3864


title: V3857

description: sample_id in count_matrix: V3862


title: cytosol, 180min, rep5


title: D_Etoposide_2_A_NEAT1


title: V3860

description: sample_id in count_matrix: V3860


title: cytosol, 180min, rep4


title: D_Untreated_2_A_NEAT1


title: V3888

description: sample_id in count_matrix: V3855


title: V3858

description: sample_id in count_matrix: V3858


title: V3842

description: sample_id in count_matrix: V3842


title: D_Untreated_1_A_NEAT1


title: V3882

description: sample_id in count_matrix: V3882


title: cytosol, 15min, rep2

value: 500uM 4-thiouridine


title: V3850

description: sample_id in count_matrix: V3850


title: E_Untreated_2_A_NEAT1