title: Liver_Control_Refed_s7RLL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
7RL


title: leaf_21DAS_Col-0_rep2

status: Public on Apr 21 2021

type: SRA

city: Beijing

first: Wenwen

last: Liu

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
Quality control was conducted using fastp version 0.20.0 with the parameter length_required set to 150
Quantification of transcript expression was performed using Salmon version 1.0.0 against a reference transcript dataset for Arabidopsis, AtRTDv2_QUASI_19April2016 (Zhang et al., 2017) with parameters salmon index --type puff -k 31 and salmon quant -l IU --numBootstraps 30 --seqBias --validateMappings
The transcript-level quantifications were merged to the gene-level and then the length scaled transcripts per kilobase million (TPM) and estimated read counts were calculated for genes using the R package tximport version 1.12.3 with the option “lengthScaledTPM”
Genome_build: Arabidopsis Thaliana Reference Transcript Dataset 2 (AtRTD2), a comprehensive, non-redundant, high quality transcript reference dataset developed for RNA-seq analysis. It is generated by integration of transcript assemblies of ca. 8.5 billion pairs of reads from 285 RNA-seq data sets obtained from 129 RNA-seq libraries and merged along with the previous version, AtRTD (which covers TAIR10 transcripts and transcripts from Marquez et al., 2012), and Araport11 transcript assemblies
Supplementary_files_format_and_content: Matrix table with TPM value for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: The plants were grown on MS plates containing 1% sucrose under long-day condition (16-h light with intensity of 18 W/m2 at 22 °C and 8-h dark at 18 °C) after surface-sterilization followed by 7-day stratification of the seeds.

extract_protocol:
flash frozen in liquid nitrogen, and RNA was extracted using an RNeasy Plant Mini Kit (Qiagen), followed by on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: tissue

value: the first true leaf

tag: age

value: 21DAS (days after sowing)


title: SB-1092 Non-tumor 16S rRNA

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

country: USA

institute: Stony Brook University

data_processing:
Salmon (version 0.10.2) was used to process RNA-seq data. Human genome assembly GRCh37 was used as reference. After alignment, DEseq2 was used to concatenate all individual samples and run comparative analysis. For 16S rRNA data, llumina Miseq paired-end reads were aligned to human reference genome hg19 with Bowtie2. SINA/SILVA classifier was used for classification. Operational taxonomic units (OTUs) were produced by binning sequences with identical taxonomic assignments.
Genome_build: hg19
Supplementary_files_format_and_content: concatenated results from Salmon for each sample, OTUs

organism: Homo sapiens

source_name: colorectal

extract_protocol:
DNA and RNA was extracted from the archived frozen tissues using the Qiagen Allprep DNA/RNA/miRNA kits (Qiagen,  Hilden, Germany) according to the manufacturer’s protocol.  DNA and RNA was extracted from sections of FFPE tumor and non tumor samples using the Qiagen Allprep DNA/RNA FFPE (Qiagen, Hilden, Germany) kits according to the manufacturer’ protocol except that xylene was used to de-paraffinize the FFPE samples.
RNA sequence libraries were prepared with the Kapa RNA kit with RiboErase (Roche Sequencing and Life Science Kapa Biosystems, Wilmington, MA) according to the manufacturer’s protocol. 16S rRNA libraries were constructed by generating broad-range PCR amplicons using barcoded primers that target the V3V4 variable region of the 16S rRNA gene: primers 338F (5’ ACTCCTACGGGAGGCAGCAG) and 806R (5’ GGACTACHVGGGTWTCTAAT), Illumina paired-end sequencing was performed on the Miseq platform with versions v2.4 of the Miseq Control Software and of MiSeq Reporter, using a 600 cycle version 3 reagent kit.

tag: sample type

value: Non-tumor

tag: molecule subtype

value: rRNA


title: Liver_Control_Refed_s7RL1

city: Madison

first: Cara

middle: Leanne

last: Green

state: Wisconsin

address: 2214 Kendall Ave

department: Medicine

institute: University of Wisconsin-Madisin

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
7R

data_processing:
To remove any genes that exhibited no or a very low number of mapped reads, only genes that had more than 1 count per million in at least 4 samples across all treatments were retained for further analysis. This resulted in a total of 14211 unique genes. Raw counts were normalized using the trimmed mean of M values (TMM normalization) (Robinson and Oshlack 2010). Differential gene expression was modeled using the edgeR package (Robinson, McCarthy et al. 2010) in R (version 3.5.3) and pairwise comparisons were conducted between Fasted Control or Refed Ctrl AA and either Low AA or Low Ile. To control for type I errors, the Benjamini Hochberg adjusted p-value was used (5% FDR). We tested for over-representation of gene ontology (GO) terms or KEGG pathways in each comparison, using the limma package (Ritchie, Phipson et al. 2015).
Supplementary_files_format_and_content: raw counts and statistical analysis

organism: Mus musculus

source_name: Liver, Control Diet, Refed

growth_protocol: Diet started at 10 weeks of age

extract_protocol:
Liver tissues were harvested and snap frozen in liquid nitrogen. Transcriptional profiling: RNA was extracted from liver as previously described (Cummings et al., 2018). Concentration and purity of RNA was initially determined using a Nanodrop 2000c, and then submitted to the University of Wisconsin-Madison Biotechnology Center Gene Expression Center & DNA Sequencing Facility. RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide Rev. E.
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide Rev. E.
Sample libraries were combined and striped across three lanes, the data from each lane was merged into a single sample file prior to expression estimation

treatment_protocol: Mice were placed on either a control or low isoleucine diet

value: liver

tag: Sex

value: male

value: 13 weeks

tag: diet

value: Control

tag: feeding state

value: Refed


title: Liver_Low Isoleucine_Fasted_s2LL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
2L

source_name: Liver, Low Isoleucine Diet, Fasted

value: Low Isoleucine

value: Fasted


title: leaf_21DAS_Col-0_rep1


title: Liver_Low Isoleucine_Fasted_s2NL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
2N


title: Liver_Low Isoleucine_Fasted_s2RL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
2R


title: Liver_Low Isoleucine_Fasted_s2RLL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
2RL


title: leaf_20DAS_Per-1_rep3

value: 20DAS (days after sowing)


title: leaf_20DAS_Per-1_rep2


title: leaf_20DAS_Per-1_rep1


title: SB-1092 Tumor 16S rRNA

value: Tumor


title: leaf_20DAS_F1_rep3

value: Col-0 x Per-1 F1


title: leaf_20DAS_F1_rep2


title: SB-541 Non-tumor 16S rRNA


title: SB-521 Tumor 16S rRNA


title: SB-738 Tumor 16S rRNA


title: SB-541 Tumor 16S rRNA


title: SB-1035 Tumor 16S rRNA


title: SB-1035 Non-tumor 16S rRNA


title: SB-967 Non-tumor 16S rRNA


title: SB-526 Non-tumor 16S rRNA


title: SB-867 Tumor 16S rRNA


title: SB-867 Non-tumor 16S rRNA


title: SB-920 Tumor 16S rRNA


title: SB-521 Non-tumor 16S rRNA


title: SB-920 Non-tumor 16S rRNA


title: SB-501 Non-tumor 16S rRNA


title: leaf_20DAS_F1_rep1


title: Liver_Control_Fasted_s1NL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
1N

source_name: Liver, Control Diet, Fasted


title: Liver_Control_Fasted_s1LL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
1L


title: leaf_20DAS_Col-0_rep3


title: CLIP-seq IgG_CLIP_rep2

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

description: CLIP-seq

data_processing:
First, raw reads quality and adapter sequences were checked using fastqc (version 0.11.5). Cutadapt (version 1.17) and trim_galore were used to filter adaptor and poor quality sequences.
In case of RNA-seq experiments, clean reads were mapped to the mm10 reference mouse genome using Star (version 2.6). HTSeq (version 0.6.1) facilitated to counting RNA-seq reads at gene-level with parameters ‘-f bam -r name -a 10 -t exon -s no -i gene_id -m union’. Finally, DESeq2 (version 1.20.0) was subsequently applied on gene counts to identify genes differentially expressed between TCRβ+DP cells isolated from WT or TCRβ+DP Srsf1fl/flLckcre/+ mice after removing entries that exhibited zero counts in all replicates.
In case of CLIP-seq experiments, bowtie2 (version 2.1.0) was used to map clean reads to the mm10 mouse reference genome with parameters ‘-p 10 -L 15 -N 1 -D 50 -R 50 --phred33 --qc-filter --very-sensitive --end-to-end’. CLIP-seq peaks were identified by Piranha (version 1.2.1) with the following parameters ‘-s -b 20 -d ZeroTruncatedNegativeBinomial -p 0.05’. Homer (version 4.9.1) was used for peak annotation based on the mm10 genome assembly and for SRSF1 binding motif analysis.
Genome_build: mm10
Supplementary_files_format_and_content: txt format. Read counts for each gene
Supplementary_files_format_and_content: bw format.

source_name: Total thymocytes

extract_protocol:
RNA was isolated with Saturated phenol
RNA was isolated with Saturated phenol (Ambion, AM9712), and ligated with adaptor, converted to cDNA. cDNA was synthesized by SuperScript III First-strand kit (Invitrogen, 18080-051). cDNA was amplified by PCR to prepare the libraries, and then sequenced on the Hiseq 2500 Illumina platform.

tag: strain

value: thymus

value: 6~8 weeks

value: WT

tag: cell sorting strategy

tag: clip antibody

value: Normal mouse IgG


title: Liver_Control_Fasted_s1RL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
1R


title: leaf_20DAS_Col-0_rep2

value: the first true leaf


title: Liver_Control_Fasted_s1RLL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
1RL


title: CLIP-seq IgG_CLIP_rep1

description: CLIP-seq


title: leaf_20DAS_Col-0_rep1


title: CLIP-seq SRSF1_CLIP_rep2

description: CLIP-seq


title: leaf_19DAS_Per-1_rep1

value: 19DAS (days after sowing)


title: leaf_19DAS_Per-1_rep3


title: leaf_19DAS_F1_rep3


title: leaf_19DAS_Per-1_rep2


title: SB-262 Tumor 16S rRNA

value: rRNA


title: leaf_19DAS_F1_rep1


title: SB-157 Tumor 16S rRNA


title: leaf_19DAS_F1_rep2


title: SB-262 Non-tumor 16S rRNA

value: Non-tumor


title: SB-157 Non-tumor 16S rRNA


title: leaf_19DAS_Col-0_rep3


title: SB-141 Tumor 16S rRNA


title: leaf_19DAS_Col-0_rep1


title: leaf_18DAS_Per-1_rep3

value: 18DAS (days after sowing)


title: SB-108 Tumor 16S rRNA


title: P90_SCI_rep2_3days

city: Norwich

first: Darrell

address: Earlham Road

department: Norwich Medical School

country: United Kingdom

institute: University of East Anglia

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis.
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format.
The reads were mapped to the reference genome, allowing 00 mis-matches and 0 gaps using PatMaN [Pruffer et al. 2008].
The reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRBase, release 21.
The abundances of the reads were normalized using the RPM method [Mortazavi et al. 2008].
The differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20.
Genome_build: GRCm38
Supplementary_files_format_and_content: *csv; Comma-separated text files include raw abundances.

source_name: sensorimotor cortex, P90, SCI, 3d

growth_protocol: All procedures involving live animals were performed according to European Community Council Directive of 24 November 1986 (86/609/EEC) and University of Turin's institutional guidelines on animal welfare (DL 116/92). C57BL/6J mice were bred in Neuroscience Institute Cavalieri Ottolenghi animals facility. All animals had free access to food and water and were used for SCI surgery.

extract_protocol:
Twelve hours or three days after injury, WT and SCI mice were sacrificed by cervical dislocation, the brains removed and the sensorimotor cortex rapidly isolated: under a dissecting microscope we isolated the sensorimotor cortex. The samples were collected individually and stored at -80°C until the total RNA extraction.
HD sRNA libraries created with HiSeq2500 adapters (Xu et al. 2015).
The sequencing was done at the Earlham Institute (UK), single end, 50nt reads.

treatment_protocol: Postnatal day 15 (P15) and adult (P90) C57BL/6J male mice were used to produce the SCI model or control group (WT). Animals were deeply anaesthetized with 3% isoflurane vaporized in O2/N2O 50:50 in order to perform the spinal cord transection. The cervical spine was exposed, the spinal muscles displaced laterally and the lesion performed as follows: using a 27-gauge½ needle, the entire spinal cord was dorsally exposed and transacted at C5/6 level. In the control group, the spinal cord was simply exposed without any damage.

tag: strain/background

tag: gender

value: male

value: sensorimotor cortex

tag: treatment

value: spinal cord injury

tag: time point

value: 3 days post injury


title: SB-064 Tumor 16S rRNA


title: P90_SCI_rep3_3days


title: P90_SCI_rep1_3days


title: SB-463 Tumor 16S rRNA


title: SB-298 Non-tumor 16S rRNA


title: SB-296 Tumor 16S rRNA


title: SB-300 Tumor 16S rRNA


title: SB-396 Non-tumor 16S rRNA


title: SB-478 Non-tumor 16S rRNA


title: SB-463 Non-tumor 16S rRNA


title: SB-470 Non-tumor 16S rRNA


title: SB-478 Tumor 16S rRNA


title: SB-470 Tumor 16S rRNA


title: SB-300 Non-tumor 16S rRNA


title: CLIP-seq SRSF1_CLIP_rep1

description: CLIP-seq


title: SB-396 Tumor 16S rRNA


title: SB-108 Non-tumor 16S rRNA


title: SB-298 Tumor 16S rRNA


title: SB-296 Non-tumor 16S rRNA


title: SB-452 Non-tumor 16S rRNA


title: SB-452 Tumor 16S rRNA


title: SB-118 Non-tumor 16S rRNA


title: leaf_19DAS_Col-0_rep2


title: leaf_18DAS_Per-1_rep2


title: SB-118 Tumor 16S rRNA


title: SB-064 Non-tumor 16S rRNA


title: P90_wt_rep3_3days

source_name: sensorimotor cortex, P90, control, 3d

tag: genotype/variation

value: wild type

value: control


title: SB-036 Non-tumor 16S rRNA


title: leaf_18DAS_Per-1_rep1


title: SB-010 Tumor 16S rRNA

value: Tumor


title: P90_wt_rep2_3days


title: SB-010 Non-tumor 16S rRNA


title: leaf_18DAS_F1_rep3

value: Col-0 x Per-1 F1


title: P90_wt_rep1_3days


title: leaf_18DAS_F1_rep2


title: P90_SCI_rep3_12h

source_name: sensorimotor cortex, P90, SCI, 12h

value: 12h post injury


title: P90_SCI_rep1_12h


title: P90_SCI_rep2_12h


title: SB-036 Tumor 16S rRNA


title: wfikkn1-mut-TCDD-rep3_S15

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

description:
fastqc file of wfikkn1 mutant_TCDD rep3
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx

data_processing:
Reads were trimmed using Cutadapt (version 1.8.1) to remove the adapter sequencesTrimmed files were aligned using HISAT2 (version 2.2.0) against the zebrafish build 11 (Danio rerio GRCz11 release 97) genome
Number of mapped reads was counted, sorted, and converted to BAM files using Samtools (version 1.10)
Read counts were estimated using HTSeq (version 0.12.4)
Normalization of counts and differential expression analysis were conducted using Bioconductor's edgeR
Genome_build: Outliers (WT DMSO 2 and WT TCDD 2) were removed after multidimensional scaling

organism: Danio rerio

source_name: 48 hpf whole zebrafish

growth_protocol: Tropical 5D wildtype zebrafish and wfikkn1 mutant zebrafish embryos were grown to 4 hpf in glass petridishes at 28.5˚C.

extract_protocol:
Total RNA was extracted from 48 hpf whole embryos using RNAzol (Molecular Research Center, Inc; Cincinnati, OH) and a bullet blender with 0.5 mM zirconium oxide beads (Next Advance, Averill Park, New York) as recommended by the manufacturer. The RNA was purified using the Direct-zol MiniPrep kit (Zymo Research; Irvine, CA) and included an in-column DNase 1 digestion. RNA quality and quantity was assessed using a SynergyMix microplate reader with the Gen5 Take3 module. RNA integrity was confirmed (RIN score > 8) with an Agilent Bioanalyzer 2100.
Total RNA samples were sent to Oregon State University Center for Genome Research and Biocomputing Core facilities for library preparation and sequencing. Samples were prepared using the Robotic PolyA Enrichment Library Prep and Robotic Stranded RNA Library Prep Kits (WaferGen, Fremont, CA).
Libraries were randomized across 6 lanes and sequenced with 100bp single-end reads using the Illumina HiSeq 3000. Raw sequence reads were quality checked prior to processing.

treatment_protocol: The two zebraifsh lines were exposed to either 0.1 % DMSO (vehicle control) or 1 ng/mL TCDD (chemical) for 1 hour at 4 hpf. Exposures were conducted in 20 mL glass vials with 100 uL/embryo exposure solution. To ensure even mixing, vials were placed on a rocker for the duration of the exposure, and every 15 minutes were manually shaken. After exposure, zebrafish were rinsed three times with embryo media (EM) and grown to 48 hpf in 60 mm Petridishes with at 28.5˚C. Each individual biorep (n=9 fish) was in a different Petridish.

value: wfikkn1 mutant

tag: agent

value: 1 ng/mL TCDD

tag: developmental stage

value: 48 hpf


title: leaf_18DAS_Col-0_rep1

tag: genotype

tag: tissue

value: the first true leaf


title: WT-TCDD-rep4_S14

description:
fastqc file of WT_TCDD rep4
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx

value: Wildtype


title: WT-TCDD-rep3_S13

description:
fastqc file of WT_TCDD rep3
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: wfikkn1-mut-TCDD-rep4_S16

description:
fastqc file of wfikkn1 mutant_TCDD rep4
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: P90_wt_rep3_12h

source_name: sensorimotor cortex, P90, control, 12h

tag: age


title: leaf_18DAS_F1_rep1


title: P90_wt_rep2_12h


title: WT-DMSO-rep4_S10

description:
fastqc file of WT_DMSO rep4
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx

value: 0.1% DMSO


title: wfikkn1-mut-DMSO-rep3_S11

description:
fastqc file of wfikkn1 mutant_DMSO rep3
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: WT-DMSO-rep3_S9

description:
fastqc file of WT_DMSO rep3
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: P90_wt_rep1_12h


title: leaf_18DAS_Col-0_rep2


title: leaf_18DAS_Col-0_rep3


title: leaf_17DAS_Per-1_rep3

value: 17DAS (days after sowing)


title: leaf_17DAS_Per-1_rep2


title: leaf_17DAS_Per-1_rep1


title: leaf_17DAS_F1_rep2


title: wfikkn1-mut-TCDD-rep2_S8

description:
fastqc file of wfikkn1 mutant_TCDD rep2
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: leaf_17DAS_F1_rep3


title: WT-TCDD-rep1_S5

description:
fastqc file of WT_TCDD rep1
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: wfikkn1-mut-DMSO-rep4_S12

description:
fastqc file of wfikkn1 mutant_DMSO rep4
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: WT-TCDD-rep2_S6


title: wfikkn1-mut-DMSO-rep2_S4

description:
fastqc file of wfikkn1 mutant_DMSO rep2
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: wfikkn1-mut-TCDD-rep1_S7

description:
fastqc file of wfikkn1 mutant_TCDD rep1
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: WT-DMSO-rep2_S2

description:
fastqc file of WT_DMSO rep2
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: wfikkn1-mut-DMSO-rep1_S3

description:
fastqc file of wfikkn1 mutant_DMSO rep1
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: P15_SCI_rep2_3days

source_name: sensorimotor cortex, P15, SCI, 3d


title: leaf_17DAS_F1_rep1


title: P15_wt_rep3_3days

source_name: sensorimotor cortex, P15, control, 3d


title: WT-DMSO-rep1_S1

description:
fastqc file of WT_DMSO rep1
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx


title: P15_SCI_rep1_3days


title: P15_wt_rep2_3days


title: P15_SCI_rep3_3days


title: leaf_17DAS_Col-0_rep3


title: ATAC-seq_Fruiting stage replicate 2

city: Boston

first: Eric

last: Greer

state: MA

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

library_source: genomic

data_processing:
Real-Time Analysis (RTA) software
The raw fastq files were trimmed for the adaptor sequences, the multiqc was use to summarize the fastQC results, and the trimmed files were mapped to the Dictyostelium discoideum genome using bowtie2
The mitochondria genome was removed in the alignment process
The duplicated reads were removed by picard
The bam files were shifted for +4bp and -5bp for positive and negative strand, respectively
The sorted bam files were subject to peak calling with MACS2
Open chromatin regions and peak annotation were deducted with Diffbind and ChIPSeeker, respectively
Genome_build: AX4
Supplementary_files_format_and_content: Peak files for open chromatin regions

molecule: genomic DNA

organism: Dictyostelium discoideum

source_name: Fruiting stage cell nuclei

growth_protocol: We cultured te strain at 22 °C shaken in the incubator at 180 rpm in HL5 medium with 300 μg/ml streptomycin

extract_protocol:
Dictyostelium were physically dissociated and washed twice with PBS with 0.04% BSA and lysed with 10 mM Tris-HCL (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.5% Tween 20, 0.5% NP-50, 0.05% digitonin (Promega G944A), 1% BSA, and 0.5% cellulase on ice or room temperature for 30 minutes to fully lyse the cells. Validation of equivalent ATACseq lysine of different stages was performed by trypan blue staining and optimized by real-time PCR detection of ribosomal RNA release.
Nuclei were transposed using the Nextera DNA Library Prep Kit.  Transposed libraries were amplified for 11 cycles and size selected for fragments ranging 200-1000 bp. ATAC-seq experiments were sequenced to a minimum depth of 25 million reads/sample.

value: Fruiting


title: iPS on LM 111E8(p5)

type: RNA

city: Kyoto

first: Koji

last: Eto

address: 53 Kawahara-cho, Shogoin Kawahara-cho, Sakyo-ku

department: CiRA

country: Japan

institute: Kyoto University

hyb_protocol: Labelled cDNA was hybridized with SurePrint G3 Human 8x60K slides (Agilent Technologies)

scan_protocol: Arrays were scanned on an Agilent Microarray using the AgilentG3_GX_1Color profile.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028004_D_F_20150612) to obtain non-background subtracted and spatially detrended processed signal intensities.

source_name: iPSCs

label_protocol: Total RNA of 200 ng was labeled with cyanine 3-CTP.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and an RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: 6-well plates were precoated with LM-E8s (LM521-E8, LM421-E8, LM411-E8, LM321-E8, LM311-E8, LM121-E8, and LM111-E8)  for 1 h at 37°C in CO2 incubators. The PSCs mainteind on those LM-E8s were cultured in AK02N medium (Ajinomoto, Tokyo, Japan) with 10 μM Y27632 (Wako, Osaka, Japan).


title: leaf_17DAS_Col-0_rep2


title: P15_SCI_rep3_12h

source_name: sensorimotor cortex, P15, SCI, 12h

value: male


title: P15_wt_rep1_3days

value: sensorimotor cortex


title: ATAC-seq_Fruiting stage replicate 3


title: iPS on LM 411E8(p5)


title: ATAC-seq_Mound stage replicate 2

source_name: Mound cell nuclei

value: Mound


title: P15_SCI_rep2_12h

value: spinal cord injury


title: iPS on LM 321E8(p5)


title: iPS on LM 311E8(p5)


title: iPS on LM 521E8(p5)


title: ATAC-seq_Streaming stage replicate 3

source_name: Streaming cell nuclei

value: Streaming


title: ATAC-seq_Mound stage replicate 1


title: P15_SCI_rep1_12h


title: iPS on LM 421E8(p5)


title: ATAC-seq_Mound stage replicate 3


title: ATAC-seq_Streaming stage replicate 2


title: leaf_16DAS_Per-1_rep3

source_name: seedling

value: 16DAS (days after sowing)


title: ATAC-seq_Vegetative stage replicate 2

source_name: Vegetative cell nuclei

value: Vegetative


title: ATAC-seq_Vegetative stage replicate 3


title: P15_wt_rep2_12h

source_name: sensorimotor cortex, P15, control, 12h

value: wild type

value: control


title: leaf_16DAS_Per-1_rep1


title: iPS on LM 121E8(p5)


title: ATAC-seq_Fruiting stage replicate 1


title: ATAC-seq_Mound stage replicate 4


title: leaf_16DAS_F1_rep3

value: Col-0 x Per-1 F1


title: ATAC-seq_Vegetative stage replicate 1


title: P15_wt_rep3_12h

value: 12h post injury


title: leaf_16DAS_Per-1_rep2


title: leaf_17DAS_Col-0_rep1


title: leaf_16DAS_F1_rep2


title: Mettl3KO_rep2 [RNA-seq]

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Nuclear RNA of WT26, Mettl14 KO, RBC and Mettl3 KO ES cells was isolated and processed for HiSeq RNA sequencing as described in Materials and methods. The quality of raw and trimmed Fastq reads was verified using FastQC (Andrews 2010). Reads were trimmed using cutadapt version 1.8.1 (Martin 2011). Reads were then aligned to the GRCm38 genome from Ensembl using STAR version 2.6.0c (Dobin et al. 2013). Differential analysis was carried out using DESeq2 version 1.26.0 (Love, Huber, and Anders 2014) on the count matrices output from snakePipes version 2.1.0 (Bhardwaj et al. 2019). For MA plots, transcripts with a baseMean > 50 reads were considered and significant differences in gene expression have absolute(log2FC) > 1 changes and adjusted p-values of < 0.05. The p-values attained by the Wald test are corrected for multiple testing using the Benjamini and Hochberg (BH) method. Data visualization was performed using ggplot2 (Wickham 2009). Heatmaps for gene expression of genes encoding core components of chromatin, transcription machinery and m6A RNA pathway were generated using pheatmap in R (pheatmap: Pretty heatmaps. R package version 1.0.8. https://CRAN.Rproject.org/package=pheatmap). GO enrichment analysis was performed with the enrichGO function from clusterProfiler R package version 3.14.3 (Yu et al. 2012) using the Biological Process ontology. P-values were adjusted using the BH method. Dotplots represent significant pathways (adjusted p-value < 0.05).
Genome_build: GRCm38
Supplementary_files_format_and_content: Individual fastq and raw counts files uploaded

growth_protocol: The growth protocols have been described in our study (Duda et al). Mouse ES cells are grown in ES medium with 15% Serum Replacement and LIF, on a 2% gelatin-coated dishes.

extract_protocol:
RNA was extracted with Trizol, DNase treated and column-purified
RNA libraries were prepared using standard TruSeq Stranded Total RNA (Gold) protocol

value: Rosa26 BirA-V5, Cre-ERT2, Mettl3 KO

tag: cell type

value: Mouse Embryonic Stem cells (mESCs)


title: RBC_rep2 [RNA-seq]

value: Rosa26 BirA-V5, Cre-ERT2


title: leaf_16DAS_Col-0_rep3

value: the first true leaf


title: ATAC-seq_Streaming stage replicate 1


title: Mettl14KO_rep2 [RNA-seq]

value: Mettl14 KO


title: RBC_rep1 [RNA-seq]


title: leaf_16DAS_F1_rep1


title: Mettl14KO_rep1 [RNA-seq]


title: WT26_rep1 [RNA-seq]


title: WT26_rep2 [RNA-seq]


title: leaf_16DAS_Col-0_rep2


title: Mettl3KO_rep1 [RNA-seq]


title: mES_Mettl3KO_ip1

description: Mettl3 KO m6A IP

data_processing:
Library strategy: m6A MeRIP-seq
Unprocessed reads were trimmed using cutadapt (Martin 2011) version 1.8.1. Reads were then aligned to the GRCm38 genome from Ensembl using STAR (Dobin et al. 2013) version 2.6.0c, with settings (--sjdbOverhang 100 –winAnchorMultimapNmax 200 --outFilterMultimapNmax 100) that identify repeat reads as recommended by TEtranscripts (Jin et al. 2015). GTF files of repeat annotations were generated from the RepeatMasker (Smit et al. 2010) obtained from UCSC genome database (Karolchik et al. 2003). Repeat reads were quantified using TEtranscripts version 2.0.3 with settings (--mode multi --minread 1 -i 10 --padj 0.05)
Genome_build: GRCm38
Supplementary_files_format_and_content: Individual fastq and raw counts files uploaded

source_name: mES

extract_protocol:
RNA was extracted with Trizol, DNase treated, column-purified and sonicated. 'IP' RNA was subjected to immunoprecipitation as described in our study (Duda et al.). 'Input' RNA served as control.
RNA libraries were prepared using TruSeq Stranded Total RNA (Gold) protocol without fragmentation step

value: Mouse Embryonic Stem cells

tag: molecule subtype

value: m6A MeRIP-seq


title: mES_Mettl3KO_input2

description: Mettl3 KO input

value: Total RNA


title: leaf_15DAS_Per-1_rep3

value: 15DAS (days after sowing)


title: leaf_16DAS_Col-0_rep1


title: mES_RBC_input2

description: control for Mettl3 KO input


title: mES_RBC_ip2

description: control for Mettl3 KO m6A IP


title: mES_Mettl3KO_input1

description: Mettl3 KO input


title: mES_Mettl3KO_ip2

description: Mettl3 KO m6A IP


title: P15_wt_rep1_12h

value: male

value: sensorimotor cortex


title: leaf_15DAS_F1_rep3


title: mES_RBC_input1

description: control for Mettl3 KO input


title: mES_Mettl14KO_input2

description: Mettl14 KO input


title: mES_Mettl14KO_ip2

description: Mettl14 KO m6A IP


title: mES_WT26_ip2

description: control for Mettl14 KO m6A IP


title: leaf_15DAS_F1_rep2


title: mES_Mettl14KO_ip1

description: Mettl14 KO m6A IP


title: Keratinocytes treated with IFNG and HSV-2 infected 1 [200406290036_D]

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

institute: University of Washington

description:
200406290036_D.AVG_Signal
IFNG+HSV-2_1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using CubicSpline with background subtraction using Illumina Genome Studio (V2010.3)

label: biotin

label_protocol: cRNA were biotin labled using Illumina TotalPrep RNA Amplification Kit

extract_protocol: Total RNA extracted from keratinpcuytes using Qiagen RNeasy Mini Kit.

value: Human primary keratinocytes

value: treated with IFNG and HSV-2 infected


title: Keratinocytes treated with IFNG and HSV-2 infected 2 [200406290036_H]

description:
200406290036_H.AVG_Signal
IFNG+HSV-2_2


title: Keratinocytes untreated and HSV-2 infected 2 [200406290036_I]

description:
200406290036_I.AVG_Signal
Untreated+HSV-2_2

value: untreated and HSV-2 infected


title: leaf_15DAS_Per-1_rep2


title: Keratinocytes untreated and HSV-2 infected 1 [200406290036_F]

description:
200406290036_F.AVG_Signal
Untreated+HSV-2_1


title: mES_RBC_ip1

description: control for Mettl3 KO m6A IP


title: mES_WT26_ip1

description: control for Mettl14 KO m6A IP

value: wild type


title: leaf_15DAS_F1_rep1

value: Col-0 x Per-1 F1


title: mES_WT26_input2

description: control for Mettl14 KO input


title: mES_WT26_input1

description: control for Mettl14 KO input


title: Zmynd8_KOmin_RNAseq_rep2

city: Shanghai

first: Qiang

last: Pan

address: 320 Yue Yang Road

institute: Chinese Academy of Sciences

data_processing:
For RNA seq, paired-end reads were aligned to the mouse reference genome mm10 with HISAT2.The whole samples expression levels were presented  as RPKM. The statistically significant DE genes were obtained by an adjusted P-value <0.05 and foldchange > 1.5 using the DEGseq software.
For ChIP sequencing analysis: The 75-nt sequence reads generated by Illumina equencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
For ChIP-seq determination of Fragment Density: Since the 5′-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3′-ends to a length of 150-250 bp, depending on the average fragment length in the size selectedlibrary (normally 200 bp). To identify the density of fragments (extended tags) along the genome,the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can bevisualized in genome browsers (see Section V.).
For ChIP-seq, the generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009). MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II). Both methods look for significant enrichments in the ChIP/IP data file when compared to the Input data file (~ random background).
Genome_build: mm10 for RNAseq; hg38 for ChIPseq

source_name: crypt cell

extract_protocol:
For RNA seq, total RNA was from small intestinal crypts from 2-month-old APCmin and APCmin; ZMYND8 IEC-/- mice. RNA was libraried by NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) and  sequencing (2×150 bp) by HiSeq3000. HCT116 cells (107 cells) were harvested and followed by ChIP-seq (Active Motif, Inc.) using the antibody against ZMYND8 (Bethyl A302-090A).
Fro RNA seq, libraries were prepared according to instructions of NEBNext® Ultra™ RNA LibraryPrep Kit for Illumina (NEB, USA).

treatment_protocol: For ChIP seq, HCT116 cells were cultured with 10% FBS for 24 hours.

value: small intestinal crypt cells

value: 2 months

value: untreated

value: APCmin+; Zmynd8IEC-/-


title: Keratinocytes treated with IFNG and mock infected 2 [200406290036_G]

description:
200406290036_G.AVG_Signal
IFNG+Mock_2

value: treated with IFNG and mock infected


title: leaf_15DAS_Per-1_rep1

value: the first true leaf


title: Keratinocytes treated with IFNG and mock infected 1 [200406290036_B]

description:
200406290036_B.AVG_Signal
IFNG+Mock_1


title: Zmynd8_KOmin_RNAseq_rep1


title: leaf_15DAS_Col-0_rep2


title: Keratinocytes untreated and mock infected 2 [200406290036_L]

description:
200406290036_L.AVG_Signal
Untreated+Mock_2

value: untreated and mock infected


title: WTmin_RNAseq_rep2

value: APCmin+


title: WTmin_RNAseq_rep1


title: leaf_15DAS_Col-0_rep1


title: mES_Mettl14KO_input1

description: Mettl14 KO input

value: Mouse Embryonic Stem cells

value: Mettl14 KO

value: Total RNA


title: Pt33_ctrl [5957899023_I]

source_name: Genital skin_ctrl

tag: subject status

value: patients with recurrent HSV-2 infection

value: genital skin biopsies

value: ctrl


title: facs2 ncfp

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

description: run_3022_s_6_withindex_sequence.txt_TCTGTTGCGG-TCACGACCAC

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were aligned to the Ensembl release 95 v2 primary assembly with STAR version 2.5.3a.
The raw gene count matrix was imported into Partek Flow software, version 8.0. Normalization size factors were calculated for all gene counts by CPM to adjust for differences in sequencing depth. Ribosomal genes and genes not expressed in the smallest group size minus samples greater than one count-per-million were excluded from further analysis.
Gene-specific analysis was then performed using the lognormal with shrinkage model (limma-trend method) to analyze for differential expression between the three groups of samples
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing normalized gene counts for each sample and also output from GSA differential analysis

source_name: TVZ neuroglial progenitor cells

growth_protocol: Nestin-CFPnuc were maintained on a C57/BL6 background and housed in barrier facilities with controlled light-dark cycles (12:12 hour) and harvested at postnatal day one. NCFP samples express the cyan fluorescent protein under the Nestin promoter.

extract_protocol:
Neural stem cells were isolated from the TVZ and separated by FACS based on expression of CFP and CD133.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq

treatment_protocol: No treatment

value: TVZ neuroglial progenitor cells

tag: cell population

value: nestin+

tag: passage


title: leaf_15DAS_Col-0_rep3

value: 15DAS (days after sowing)


title: facs3 ncfp cd133

description: run_3022_s_6_withindex_sequence.txt_TCTCCTAGCA-ATCCAAGTAG

value: cd133+ and nestin+


title: Keratinocytes untreated and mock infected 1 [200406290036_C]

description:
200406290036_C.AVG_Signal
Untreated+Mock_1

value: Human primary keratinocytes


title: facs3 cd133

description: run_3022_s_6_withindex_sequence.txt_CGACTAACGT-CTCTATACTG


title: facs1 ncfp cd133

description: run_3022_s_6_withindex_sequence.txt_CATTCCGCAA-ACAATCCGGC


title: leaf_14DAS_Per-1_rep2

value: 14DAS (days after sowing)


title: leaf_14DAS_Per-1_rep3


title: leaf_14DAS_Per-1_rep1


title: facs1 ncfp

description: run_3022_s_6_withindex_sequence.txt_AGAACAGTGA-TGCTGAACGC


title: facs2 cd133

description: run_3022_s_6_withindex_sequence.txt_AGATAGCACA-ATGGCGTACG


title: leaf_14DAS_F1_rep3

value: Col-0 x Per-1 F1


title: facs3 ncfp

description: run_3022_s_6_withindex_sequence.txt_AAGAGAGAAG-GCGACTCGTA


title: facs1 cd133

description: run_3022_s_6_withindex_sequence.txt_AACACGCTTG-TATCATGTCG


title: miniCAFE.gIL1RN.22nt-3

city: GuangZhou

first: Yongfei

last: Hu

state: GUangDong

address: Road LuJing

institute: Dermatology Hospital of Southern Medical University

description: which figure to present this data: fig.4H

data_processing:
Deep-seq was used to determine the indel frequency. Briefly, On-target sites were amplified by PCR with indexed forward and indexed reverse primers. After purification and concentration normalization, PCR products were pooled into different libraries. Completed libraries were generated by a second round of PCR using the pooled libraries as templates and sequenced with 150-bp paired-end reads on Illumina HiSeq instrument. Pooled samples were demultiplexed according to the indexes within forward and reverse primers for the first round PCR. The primers were trimmed from the raw reads, and clean reads were mapped to the gene sequences with software BWA v0.7.17. SAMtools v0.1.18 was used to obtain sorted bam files. Finally, R package Genomic Alignments were used to count Indels in alignment results, and all figures were ploted using R package ggplot2.
Hisat2 v2.0.52 was used to build the index of the reference genome and align the RNA-Seq paired-end clean reads with the reference genome. Then, StringTie v2.23 was used to count the read numbers mapped to each gene. Fragments Per Kilobase per Million (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression was defined by a Benjamini-Hochberg adjusted p value (q value | FDR) of <0.05 and fold change of >2 or <0.5. All figures were plotted using R package ggplot2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each sample. samples.indel.counts.tar.gz: the results of insertion and deletion frequency in particular gene locs with gene editing.[three genes were edited in 6F data files(FANCF, MYOD, Site6), three genes were edited in Deep-1/Deep-2 data files(FGF21, HBG, IL1RN)], more detailed information is annotated in the figure legends.

source_name: HEK293T (embryonic kidney cell)

extract_protocol:
The RNA-seq analysis has been described in our previous work. Briefly, total RNA was isolate with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and mRNA was enriched and fragmented. Deep-seq was used to determine the indel frequency. Briefly, total DNA was extracted using sarkosyl lysis buffer and on-target sites were amplified by PCR.
RNA libraries were constructed by the following steps: the first strand synthesis, the second strand synthesis, adaptor adding, and PCR amplification. After verification and quantification, libraries were sequenced by HiSeq instrument with 150bp paired-end module. DNA libraries were constructed by the following steps: on-target sites were amplified by PCR with indexed forward and indexed reverse primers. After purification and concentration normalization, PCR products were pooled into different libraries. Completed libraries were generated by a second round of PCR using the pooled libraries as templates and sequenced with 150-bp paired-end reads on Illumina HiSeq instrument.

value: transfected with plasmids miniCAFE with sgRNAs targeting gene IL1RN


title: facs2 ncfp cd133

description: run_3022_s_6_withindex_sequence.txt_CACAGCATGA-TACAGCCTTG


title: Pt32_8wks [5957899023_B]

source_name: Genital skin_8wks


title: Pt34_8wks [5957899020_I]


title: MECPGK3DT14C

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

country: Italy

institute: IRCCS, Ospedale San Raffaele

description: 3D cultured cells, RNA extracted after 14 days - replicate 3

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39).
The remaining reads were mapped to the reference human genome GRCh38, using STAR aligner (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts (version1.6.4). Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode realise 31).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: MEC1 cell line

growth_protocol: Cells of some samples were grown in a 3D hydrogel matrix.

extract_protocol:
RNA extraction was performed according to the standard manufacturer's instructions using TRIzol reagent (Ambion) for 3D bioprinted scaffolds (at day 7 and 14 of culture)  and ReliaPrep RNA Cell Miniprep System® (Promega) for 2D cell lines. 3D bioprinted cells were further treated with DNase I (Thermo Fisher Scientific) and Ambion™ RNase Inhibitor (Thermo Fisher Scientific) for 15 minutes at 37°C, and eventually a second RNA extraction was performed by using ReliaPrep RNA Cell Miniprep System® (Promega).
NGS libraries were generated with the SMART-Seq® v4 Ultra® Low Input RNA (TaKaRa) protocol, starting from 2ng of RNA. Libraries were barcoded, pooled and sequenced on an Illumina Nova-Seq 6000 sequencing system in SR (single read) mode, with reads 100nt long.

tag: cell line

value: Chronic Lymphocytic Leukemia

tag: culture method

tag: time


title: DEEP-2_FKDL202590568-1a

description:
which figure to present this data: fig.3E and fig S4H
samples.indel.counts.tar.gz

data_processing:
Library strategy: Deep-seq
Deep-seq was used to determine the indel frequency. Briefly, On-target sites were amplified by PCR with indexed forward and indexed reverse primers. After purification and concentration normalization, PCR products were pooled into different libraries. Completed libraries were generated by a second round of PCR using the pooled libraries as templates and sequenced with 150-bp paired-end reads on Illumina HiSeq instrument. Pooled samples were demultiplexed according to the indexes within forward and reverse primers for the first round PCR. The primers were trimmed from the raw reads, and clean reads were mapped to the gene sequences with software BWA v0.7.17. SAMtools v0.1.18 was used to obtain sorted bam files. Finally, R package Genomic Alignments were used to count Indels in alignment results, and all figures were ploted using R package ggplot2.
Hisat2 v2.0.52 was used to build the index of the reference genome and align the RNA-Seq paired-end clean reads with the reference genome. Then, StringTie v2.23 was used to count the read numbers mapped to each gene. Fragments Per Kilobase per Million (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression was defined by a Benjamini-Hochberg adjusted p value (q value | FDR) of <0.05 and fold change of >2 or <0.5. All figures were plotted using R package ggplot2.
Genome_build: hg38
Supplementary_files_format_and_content: samples.FPKM.Matrix.tar.gz: tab-delimited excel files include FPKM values for each sample. samples.indel.counts.tar.gz: the results of insertion and deletion frequency in particular gene locs with gene editing.[three genes were edited in 6F data files(FANCF, MYOD, Site6), three genes were edited in Deep-1/Deep-2 data files(FGF21, HBG, IL1RN)], more detailed information is annotated in the figure legends.

value: embryonic kidney cell

value: transfected with plasmids V-D or V-WT with sgRNAs


title: MECPGK3DT14B

description: 3D cultured cells, RNA extracted after 14 days - replicate 2


title: Pt32_ctrl [5957899020_F]


title: leaf_14DAS_Col-0_rep3

value: the first true leaf


title: Pt34_ctrl [5957899023_F]


title: 6F


title: leaf_14DAS_F1_rep1


title: MECPGK3DT7C

description: 3D cultured  cells, RNA extracted after 7 days - replicate 3


title: MECPGK3DT7B

description: 3D cultured cells, RNA extracted after 7 days - replicate 2


title: Pt33_8wks [5957899020_D]


title: leaf_14DAS_Col-0_rep1


title: leaf_14DAS_Col-0_rep2


title: MECPGK3DT14A

description: 3D cultured cells, RNA extracted after 14 days - replicate 1


title: Pt31_8wks [3998479055_L]


title: Pt31_2wks [3998479055_I]

source_name: Genital skin_2wks


title: DEEP-1_FKDL202590567-1a


title: leaf_13DAS_Per-1_rep3

value: 13DAS (days after sowing)


title: MECPGK2DC

description: 2D cultured cells -  replicate 3


title: MECPGK2DB

description: 2D cultured cells -  replicate 2


title: MECPGK3DT7A

description: 3D cultured cells, RNA extracted after 7 days - replicate 1


title: Pt30_8wks [3998479055_G]


title: Pt30_ctrl [3998479055_F]


title: MECPGK2DA

description: 2D cultured cells -  replicate 1


title: leaf_13DAS_Per-1_rep2


title: FCN3_overexpression_rep2

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

country: South Korea

institute: Korea Institute of Science and Technology Information

data_processing:
Quality trimming using FastQC and Fastx-toolkit
Alignment using STAR v2.6.1d to hg19
Differential expression analysis using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include expected count, FPKM, and TPM values for each sample

source_name: lung epithelial

growth_protocol: A549 cells were cultured in RPMI-1640(WELGENE, Korea), supplemented with 10% fetal bovine serum (Giboco, Grand Island), and 1% penicillin/streptomycin (Gibco, Carlsbad, CA, USA) at humidifed cell incubator at 37ºC with 5% CO2.

extract_protocol:
Total RNA of 1 ug was extracted from each sample after 48 hours of infection using miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufactturer's instruction.
The mRNA library (insert size of ~300 bp) was created using the Truseq Stranded mRNA Prep kit (Illumina)

treatment_protocol: Control virus and FCN3 expressing virus was infected to A549 cells.

value: lung cancer cell line

tag: transfection


title: V-D.gMYOD_2

description:
which figure to present this data: fig.2F
samples.FPKM.Matrix.tar.gz

data_processing:
Deep-seq was used to determine the indel frequency. Briefly, On-target sites were amplified by PCR with indexed forward and indexed reverse primers. After purification and concentration normalization, PCR products were pooled into different libraries. Completed libraries were generated by a second round of PCR using the pooled libraries as templates and sequenced with 150-bp paired-end reads on Illumina HiSeq instrument. Pooled samples were demultiplexed according to the indexes within forward and reverse primers for the first round PCR. The primers were trimmed from the raw reads, and clean reads were mapped to the gene sequences with software BWA v0.7.17. SAMtools v0.1.18 was used to obtain sorted bam files. Finally, R package Genomic Alignments were used to count Indels in alignment results, and all figures were ploted using R package ggplot2.
Hisat2 v2.0.52 was used to build the index of the reference genome and align the RNA-Seq paired-end clean reads with the reference genome. Then, StringTie v2.23 was used to count the read numbers mapped to each gene. Fragments Per Kilobase per Million (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression was defined by a Benjamini-Hochberg adjusted p value (q value | FDR) of <0.05 and fold change of >2 or <0.5. All figures were plotted using R package ggplot2.
Genome_build: hg38
Supplementary_files_format_and_content: samples.FPKM.Matrix.tar.gz: tab-delimited excel files include FPKM values for each sample. samples.indel.counts.tar.gz: the results of insertion and deletion frequency in particular gene locs with gene editing.[three genes were edited in 6F data files(FANCF, MYOD, Site6), three genes were edited in Deep-1/Deep-2 data files(FGF21, HBG, IL1RN)], more detailed information is annotated in the figure legends.

tag: treatment

value: transfected with plasmids V-D with sgRNA targeting gene MYOD


title: Pt31_ctrl [3998479055_K]

value: patients with recurrent HSV-2 infection

value: genital skin biopsies

tag: time point


title: Pt31_lesion [3998479055_H]

source_name: Genital skin_lesion

value: lesion


title: leaf_13DAS_Per-1_rep1

data_processing:
Quality control was conducted using fastp version 0.20.0 with the parameter length_required set to 150
Quantification of transcript expression was performed using Salmon version 1.0.0 against a reference transcript dataset for Arabidopsis, AtRTDv2_QUASI_19April2016 (Zhang et al., 2017) with parameters salmon index --type puff -k 31 and salmon quant -l IU --numBootstraps 30 --seqBias --validateMappings
The transcript-level quantifications were merged to the gene-level and then the length scaled transcripts per kilobase million (TPM) and estimated read counts were calculated for genes using the R package tximport version 1.12.3 with the option “lengthScaledTPM”
Genome_build: Arabidopsis Thaliana Reference Transcript Dataset 2 (AtRTD2), a comprehensive, non-redundant, high quality transcript reference dataset developed for RNA-seq analysis. It is generated by integration of transcript assemblies of ca. 8.5 billion pairs of reads from 285 RNA-seq data sets obtained from 129 RNA-seq libraries and merged along with the previous version, AtRTD (which covers TAIR10 transcripts and transcripts from Marquez et al., 2012), and Araport11 transcript assemblies
Supplementary_files_format_and_content: Matrix table with TPM value for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample


title: FCN3_overexpression_rep1


title: Pt30_2wks [3998479055_D]


title: Pt29_8wks [3998479055_B]


title: Pt30_lesion [3998479055_C]


title: V-D.gMYOD_1


title: V-D.Ctrl_2

value: transfected with plasmid V-D only


title: Control_rep2

value: empty vector


title: leaf_13DAS_F1_rep2


title: Control_rep1


title: V-D.Ctrl_1


title: leaf_13DAS_F1_rep1


title: Pt29_2wks [3998479046_K]


title: Pt29_lesion [3998479046_J]


title: leaf_13DAS_Col-0_rep3


title: S-D.gMYOD_2

description:
which figure to present this data: fig.1F
samples.FPKM.Matrix.tar.gz

value: transfected with plasmids S-D with sgRNA targeting gene MYOD


title: leaf_13DAS_Col-0_rep2


title: S-D.gMYOD_1


title: S-D.Ctrl_2

value: transfected with plasmid S-D only


title: leaf_13DAS_Col-0_rep1


title: leaf_13DAS_F1_rep3


title: S-D.Ctrl_1


title: CAD5

first: Congcong

last: Zhang

address: Anzhen Road 2

institute: Beijing Institute of Heart Lung and Vascular Disease

data_processing:
software SOAPnuke to filter reads, followed as:1) Remove reads with adaptors;2) Remove reads in which unknown bases(N) are more than 10%;3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read).
SOAPnuke:version：v1.5.2  parameters: -l 15 -q 0.5 -n 0.1
we map clean reads to reference genome using HISAT
HISAT2:Version: v2.0.4  Parameters: -p 8 --phred64 --sensitive -I 1 -X 1000
We mapped clean reads to reference using Bowtie2, and then calculate gene expression  level with RSEM .
RSEM :Version: v1.2.12
Bowtie2 :  Version: v2.2.5  Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k200
We detect DEGs with DEGseq as requested
DEGseq:  Parameters: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Supplementary_files_format_and_content: txt file include FPKM values for every gene in each Sample

source_name: epicardial adipose tissue

extract_protocol:
epicardial adipose tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC.  RNA concentration, RIN value,28S/18S and the fragment length distribution.
RNA libraries were prepared for sequencing using standard BGISEQ-  500 platform

tag: disease state

value: Coronary atherosclerotic disease


title: leaf_12DAS_Per-1_rep3

extract_protocol:
flash frozen in liquid nitrogen, and RNA was extracted using an RNeasy Plant Mini Kit (Qiagen), followed by on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 12DAS (days after sowing)


title: TS576 cells in 3D stiff hydrogel_rep2

city: La Jolla

first: Rana

last: Tariq

state: California

address: 9500 Gilman Dr

department: Pedatrics

institute: University of California, San Diego

data_processing:
Illumina was used for base-calling.
STAR was used for alignment. Sequenced reads were mapped to gencode.v33.
htseq-count was used to generate counts.
Differentially expressed genes were identified using DESeq2.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_count.txt: Tab-delimited text files include raw counts for each Sample.

source_name: glioblastoma cells

growth_protocol: 2D samples were cultured as spheres. 3D samples were cultured one sample per well using the same medium as 2D samples.

extract_protocol:
Sphere cultured cells were dissociated using Accutase. 3D hydrogels were first digested with collagenase and hyaluronidase to release the cells, and the cells were dissociated with Accutase. RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols for Illumina NovaSeq 6000.

value: Glioblastoma cells

tag: culture condition

value: 3D stiff hydrogel


title: TS576 cells in sphere culture_rep2

value: Sphere


title: TS576 cells in 3D stiff hydrogel_rep1


title: TS576 cells in 3D soft hydrogel_rep2

value: 3D soft hydrogel


title: TS576 cells in sphere culture_rep1


title: Pt28_8wks [3998479046_I]


title: Pt29_ctrl [3998479055_A]

value: ctrl


title: Pt28_2wks [3998479046_F]


title: CAD4


title: leaf_12DAS_Per-1_rep1

first: Wenwen

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

value: the first true leaf


title: Pt27_ctrl [3998479046_D]


title: Pt28_ctrl [3998479046_H]


title: serum_free_cultured_rep5 [serum-free culture-BC13]

city: Los Angeles

first: Jiwen

address: 635 Charles E. Young Dr. S.

institute: UCLA

data_processing:
FASTQ files were mapped using STAR, then use the output BAM files do HTSEQ or Rsubread to generate count files. We calculated RPKM by running EdgeR-Limma-Voom in R.
Genome_build: GRCm38 and GRCh38
Supplementary_files_format_and_content: excel spreadsheet includes RPKM values for each sample.

growth_protocol: Except that serum selected astrocyte samples were cultured in serum medium, other cultured samples were cultured in defined serum-free medium.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen, 217004) under the protocols of the manufacturer
We used the Ovation RNA-seq system V2 (Nugen 7102) to perform first and second-strand cDNA synthesis. We then used the Next Ultra RNA-seq library prep kit for Illumina (NEB E7530) and NEBNext® multiplex oligos for Illumina (NEB E7710 E7500 E7730) to perform end repair, adaptor ligation, and 9-10 cycles of PCR enrichment according to manufacturer’s instructions.

treatment_protocol: All treatments were proceeded on 3DIV in serum-free medium. Astrocytes were treated by TNFα for 48hr, by Poly I:C for 72hr, or by hypoxia for 72hr.

value: brain; cortex

value: Astrocytes


title: Pt27_8wks [3998479046_E]

value: patients with recurrent HSV-2 infection


title: TS576 cells in 3D soft hydrogel_rep1


title: serum_free_cultured_rep4 [serum-free culture-BC12]


title: leaf_12DAS_F1_rep3

value: Col-0 x Per-1 F1


title: CAD2


title: leaf_12DAS_F1_rep2


title: CAD3


title: serum_free_cultured_rep3 [serum-free culture-BC11]


title: Pt27_2wks [3998479046_B]

value: genital skin biopsies


title: leaf_12DAS_Col-0_rep3


title: leaf_12DAS_F1_rep1


title: Pt26_ctrl [3998498050_K]


title: serum_free_cultured_rep2 [serum-free culture-BC10]


title: CAD1


title: serum_free_cultured_rep1 [serum-free culture-BC9]


title: acutely_purified_rep4 [acute-BC7]


title: CON2

value: Healthy control


title: Pt27_lesion [3998479046_A]

value: lesion


title: CON1


title: leaf_12DAS_Col-0_rep1


title: Pt26_lesion [3998498050_I]


title: leaf_12DAS_Col-0_rep2


title: acutely_purified_rep3 [acute-BC6]


title: Pt26_8wks [3998498050_L]


title: Pt25_8wks [3998498050_H]


title: acutely_purified_rep2 [acute-BC3]


title: leaf_11DAS_Per-1_rep2

value: 11DAS (days after sowing)


title: acutely_purified_rep1 [acute-BC2]


title: Pt25_ctrl [3998498050_G]


title: serum_selected_rep3 [serum selected-BC8]


title: RNA-Seq of 24 hours post radiation, replicate 2 [h24-2]

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

institute: NARO

data_processing:
Basecalling and de-multiplexing with bcl2fastq
Raw reads were mapped to R. varieornatus coding sequences with bowtie2 and quantified with RSEM by the align_and_estimate_abundance.pl from the Trinity suite
Differential gene expression was tested with DESeq2 using the run_DE_analysis.pl from Trinity suite.
Gene ontology enrichment analysis was done with GOStat
Genome_build: Ramazzottius varieornatus genome v101 http://download.tardigrades.org
Supplementary_files_format_and_content: TSV file containing the gene expression matrix

organism: Ramazzottius varieornatus

source_name: 24 hours post radiation_whole body

growth_protocol: R. varieornatus was cultured based on our previous study (Horikawa et al 2008, Astrobiology).

extract_protocol:
Total RNA was extracted from 30 indivuals with DirectZOL
Illumina sequencing library was constructed with NEBNext Ultra RNA

treatment_protocol: R. varieornatus specimens were exposed to 500 Gy 60Co gamma ray (2,003 Gy/h, 15 min) and was incubated at 22˚C until sampling

tag: treatment/time point

value: 24 hours post radiation

value: whole body


title: RNA-Seq of 24 hours post radiation, replicate 1 [h24-1]


title: RNA-Seq of 21 hours post radiation, replicate 3 [h21-3]

source_name: 21 hours post radiation_whole body

value: 21 hours post radiation


title: leaf_11DAS_F1_rep3

city: Beijing

last: Liu

source_name: seedling

tag: genotype


title: serum_selected_rep2 [serum selected-BC4]

last: Li

tag: tissue


title: RNA-Seq of 24 hours post radiation, replicate 3 [h24-3]


title: Pt25_2wks [3998498050_E]


title: Pt25_lesion [3998498050_D]


title: Pt24_8wks [3998498050_C]


title: leaf_11DAS_F1_rep2

tag: age


title: leaf_11DAS_Per-1_rep3


title: Pt24_ctrl [3998498050_B]


title: Pt24_2wks [3998498030_L]


title: serum_selected_rep1 [serum selected-BC1]

tag: cell type


title: leaf_11DAS_F1_rep1


title: RNA-Seq of 18 hours post radiation, replicate 3 [h18-3]

source_name: 18 hours post radiation_whole body

value: 18 hours post radiation


title: leaf_11DAS_Col-0_rep3


title: Pt23_8wks [3998498030_J]


title: leaf_11DAS_Per-1_rep1


title: Pt24_lesion [3998498030_K]


title: leaf_11DAS_Col-0_rep2


title: RNA-Seq of 21 hours post radiation, replicate 2 [h21-2]


title: RNA-Seq of 18 hours post radiation, replicate 1 [h18-1]


title: leaf_11DAS_Col-0_rep1


title: RNA-Seq of 15 hours post radiation, replicate 3 [h15-3]

source_name: 15 hours post radiation_whole body

value: 15 hours post radiation


title: leaf_10DAS_Per-1_rep3

value: 10DAS (days after sowing)


title: Pt23_2wks [3998498030_G]


title: leaf_10DAS_Per-1_rep2


title: RNA-Seq of 15 hours post radiation, replicate 1 [h15-1]


title: RNA-Seq of 21 hours post radiation, replicate 1 [h21-1]


title: leaf_14DAS_F1_rep2

value: 14DAS (days after sowing)


title: Pt23_lesion [3998498030_F]


title: CON3


title: Pt22_8wks [3998498030_E]


title: leaf_10DAS_Per-1_rep1


title: Pt23_ctrl [3998498030_I]

value: ctrl


title: leaf_10DAS_F1_rep3

value: the first true leaf


title: leaf_10DAS_F1_rep2


title: RNA-Seq of 12 hours post radiation, replicate 3 [h12-3]

source_name: 12 hours post radiation_whole body

value: 12 hours post radiation


title: RNA-Seq of 12 hours post radiation, replicate 2 [h12-2]


title: RNA-Seq of 12 hours post radiation, replicate 1 [h12-1]


title: Pt22_ctrl [3998498030_D]


title: leaf_10DAS_F1_rep1


title: RNA-Seq of 09 hours post radiation, replicate 3 [h09-3]

source_name: 09 hours post radiation_whole body

value: 09 hours post radiation


title: Pt22_2wks [3998498030_B]

value: patients with recurrent HSV-2 infection


title: leaf_10DAS_Col-0_rep3


title: RNA-Seq of 15 hours post radiation, replicate 2 [h15-2]


title: RNA-Seq of 18 hours post radiation, replicate 2 [h18-2]


title: RNA-Seq of 09 hours post radiation, replicate 2 [h09-2]


title: leaf_10DAS_Col-0_rep2


title: leaf_10DAS_Col-0_rep1


title: RNA-Seq of 06 hours post radiation, replicate 3 [h06-3]

source_name: 06 hours post radiation_whole body

value: 06 hours post radiation


title: leaf_9DAS_Per-1_rep3

value: 9DAS (days after sowing)


title: RNA-Seq of 09 hours post radiation, replicate 1 [h09-1]


title: RNA-Seq of 06 hours post radiation, replicate 2 [h06-2]


title: Pt21_ctrl [200796240037_J]

source_name: Genital skin_ctrl

value: genital skin biopsies


title: Pt21_8wks [200796240037_H]


title: leaf_9DAS_Per-1_rep2


title: Pt19_ctrl [200796240037_I]


title: Pt22_lesion [3998498030_A]

value: lesion


title: Pt19_8wks [200796240037_G]


title: Pt21_lesion [200796240037_F]


title: RNA-Seq of 06 hours post radiation, replicate 1 [h06-1]


title: Pt20_lesion [200796240037_K]


title: Pt20_ctrl [200796240037_D]


title: RNA-Seq of 04 hours post radiation, replicate 3 [h04-3]

source_name: 04 hours post radiation_whole body

value: 04 hours post radiation


title: Pt19_lesion [200796240037_C]


title: leaf_9DAS_F1_rep2

value: Col-0 x Per-1 F1


title: leaf_9DAS_F1_rep3


title: leaf_9DAS_F1_rep1


title: RNA-Seq of 04 hours post radiation, replicate 2 [h04-2]

value: whole body


title: RNA-Seq of 04 hours post radiation, replicate 1 [h04-1]


title: RNA-Seq of Ctrl hours post radiation, replicate 3 [Ctrl-3]

source_name: Ctrl hours post radiation_whole body

value: Ctrl hours post radiation


title: leaf_9DAS_Col-0_rep2


title: leaf_9DAS_Col-0_rep3


title: Pt20_8wks [200796240037_B]

source_name: Genital skin_8wks


title: leaf_9DAS_Per-1_rep1


title: RNA-Seq of Ctrl hours post radiation, replicate 2 [Ctrl-2]


title: Pt18_8wks [200796240037_A]


title: RNA-Seq of Ctrl hours post radiation, replicate 1 [Ctrl-1]


title: leaf_12DAS_Per-1_rep2

value: 12DAS (days after sowing)


title: leaf_8DAS_Per-1_rep3

value: 8DAS (days after sowing)


title: L6WH_C

city: Urrbrae

first: Haipei

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

data_processing:
Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed.
Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam, Repbase and durum wheat NCBI mRNA entries as references. Unique sRNA sequences were then obtained for each library.
Conserved mature miRNAs and 5p- or 3p-derived miRNA variants were identified using BLAST search against the plant miRBase (Release 22.1). MIR (microRNA gene locus) and miRNA sequences from common plant species in the miRBase were used as references. Sequences mapped to the mature miRNA in the hairpin were identified as conserved mature miRNAs. Sequences mapped to the opposite arm of mature miRNA in the hairpin were identified as 5p- or 3p-derived variants. Single mismatch within the sequence and length variation at both 5p and 3p were allowed in the alignment.
All the mapped miRNAs were aligned to the durum wheat genome (NCBI UID 3439611, assembly Svevo.v1) to determine their genomic location. The remaining unmatched sRNA sequences were used to identify novel durum miRNAs. Sequences were BLASTed to the durum wheat genome.
To identify miRNA precursors, secondary hairpin structures containing matched sequences were predicted using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) from 120nt of flanking genome sequences.
Genome_build: Durum wheat genome (NCBI UID 3439611, assembly Svevo.v1)
Supplementary_files_format_and_content: Matrix table with normalized reads count of each microRNA in each library

organism: Triticum turgidum subsp. durum

source_name: Seedling shoot tissue

growth_protocol: Young seedlings were grown in controlled glasshouse environment (24/18 °C, 16/8 h photoperiod). Each treatment group had 12 individual biological replicates (one plant per pot). Each pot contained 1.2 kg of N40 sand with 0.5% CaCO3.

extract_protocol:
Total RNA was extracted from frozen seedling shoot material using the Tri reagent as previously described (Sigma-Aldrich, North Ryde, Australia). Extracted total RNA samples were treated with TURBO DNase (ThermoFisher Scientific, Scoresby, Australia) following the manufacturer’s instructions. The concentration, quantity and quality of purified total RNA samples were measured on a NanoDrop Lite spectropho-tometer (ThermoFisher Scientific, Scoresby, Australia). RNA integrity was assessed by agarose gel electrophoresis and Bioanalyzer measurement. High-quality RNA samples from the six biological replicates per treatment group were equally pooled for small RNA sequencing purpose.
High-quality RNA samples from the six biological replicates per treatment group were equally pooled for small RNA sequencing purpose. A total of eight small RNA libraries (AuCG_C, AuCG_N, AuWH_C, AuWH_N, L6CG_C, L6CG_N, L6WH_C, L6WH_N) were made using the TruSeq Small RNA Sample Prep Kit
Small RNA sequencing (single-end, 50 bp) was performed on an Illumina NovaSeq 6000 at LC-Bio (Hangzhou, China).

treatment_protocol: Complete basal nutrient solution was provided to progeny control treatment groups (AuCG_C, AuWH_C, L6CG_C, L6WH_C). The progeny N starvation treatment groups (AuCG_N, AuWH_N, L6CG_N, L6WH_N) were supplied with the basal nutrient solution without the nitrogen component.

tag: parental treatment

value: Water-deficit & heat stress group parents

tag: progeny treatment

value: Control group


title: L6WH_N

value: Nitrogen starvation group


title: Pt17_ctrl [200796240018_J]

tag: subject status

value: ctrl


title: leaf_9DAS_Col-0_rep1

value: the first true leaf


title: Pt17_8wks [200796240018_H]


title: leaf_8DAS_Per-1_rep2


title: leaf_8DAS_Per-1_rep1


title: leaf_8DAS_F1_rep2


title: Pt18_lesion [200796240018_L]


title: L6CG_C

value: Control group parents


title: AuWH_N

value: DBA Aurora


title: AuWH_C


title: Pt16_ctrl [200796240018_D]

value: patients with recurrent HSV-2 infection


title: leaf_8DAS_Col-0_rep3


title: Pt17_lesion [200796240018_F]


title: Pt14_ctrl [200406290064_L]


title: Pt16_lesion [200796240018_K]


title: Pt12_lesion [200406290064_I]


title: leaf_8DAS_Col-0_rep2


title: leaf_8DAS_F1_rep1


title: L6CG_N


title: leaf_8DAS_F1_rep3


title: Pt14_lesion [200406290064_H]


title: noZn-Rep2

city: Honolulu

first: Sladjana

last: Prisic

state: HI

address: 1800 East-West Rd

institute: University of Hawaii

data_processing:
fastQC of raw reads in .fastq format
trimmomatic to remove adapter sequences, trim ends and revove reads with low quality scores
bowtie2 for alignment of trimmed files to Mtb genome
featureCounts to define tagwise abundances from BAM files (Bowtie2)
Genome_build: Mycobacterium tuberculosis H37Rv, Mycobrowser, R3
Supplementary_files_format_and_content: Text (.csv) files of gene abundances from featureCounts

organism: Mycobacterium tuberculosis

growth_protocol: Mtb were grown in 7H9-ADC broth until mid-log phase (OD600 ~0.8). Cultures were centrifuged and the pellets were resuspended in Sauton's medium without added Zn2+ and grown for 4 days at 37°C with 120rpm.

extract_protocol:
Treatments were centrifuged at 4°C, and cell pellets were resuspended in TRIzol. TRIzol extractions were homogenized by bead beating and RNA was extracting following the manufacturer's protocol.
Ribosomal RNA was depleted from the samples using Ribo-Zero plus rRNA depletion kit (Illumina®, Cat. #:20037135) before being sequenced on an Illumina® HiSeq platform for generation of 150 base pair paired end reads. RNA sequencing (RNAseq) was performed by GENEWIZ® (South Plainfield, NJ 07080).

treatment_protocol: 4 day old cultures in Sauton's without Zn2+ were centrifuged and resuspended in Sauton's medium with 500μM Zn2+, 6μM Zn2+, no added Zn2+, 0.35mg/mL recombinant CP, and 0.8μM TPEN, each in biological triplicate. Treatments were incubated at 37°C with 120rpm for 24hrs.

tag: strain


title: noZn-Rep3


title: leaf_7DAS_Per-1_rep3

value: 7DAS (days after sowing)


title: Pt16_8wks [200796240018_B]

value: genital skin biopsies


title: leaf_7DAS_Per-1_rep2


title: 500uM_Zn-Rep3


title: Pt13_8wks [200406290064_F]


title: Pt12_8wks [200406290064_K]


title: 500uM_Zn-Rep2


title: Pt11_8wks [200406290064_E]


title: Pt12_ctrl [200406290064_B]


title: 500uM_Zn-Rep1


title: leaf_7DAS_F1_rep2


title: leaf_7DAS_F1_rep1


title: noZn-Rep1


title: AuCG_C


title: Ovary_Input_N

city: Bergen

first: Pavla

last: Navratilova

address: Thorm hlensgt. 55

department: Sars International Centre for Marine Molecular Biology

country: Norway

institute: University of Bergen

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence using cutadapt (v1.9.1), and masked for low-complexity or low-quality sequence.
Paired-end reads were mapped using bowtie2 (v2.2.4) with the following parameters: -k 1,
Alignments were deduplicated (samtools rmdup) and filtered for sufficient alignment quality (samtools view -q 30) and all unpaired or discordant alignments were excluded.
RPKM normalized log2 bigWig tracks for alignments were generated at 20 bp resolution using deeptools v2
Genome_build: od01
Supplementary_files_format_and_content: BigWig files generated using deeptools v2

organism: Oikopleura dioica

source_name: ovary

growth_protocol: Oikopleura dioica animals were grown in synchronous cultures in 6 l beakers as described in (Bouquet et al., 2009). Tailbud stage larvae were collected from individual IVFs. Maturing gonads were dissected manually form day 5 animals

extract_protocol:
ChIP was performed according to (Navratilova et al. 2017), finalized by library preparation using NEBNext Ultra II. Histone modification antibodies as listed in the Supplemental Table 1 were used.
Following ChIP-seq, fragments were purified using Phenol-chlorophorm extractions and ethanol precipitation followed by Qiagen MinElute PCR Purification Kit. NEBNext UltraII Library preparation kit was used for library preparation. The number of cycles for final amplification varied between 8-15 cycles. Fragment sizes of barcoded libraries were assessed using Bioanalyzer libraries were purified using AMPure beads before pooling and sequencing. Pooled libraries were sequenced in a 2x75bp Paired-End format on HiSeq2500/4000 or HiSeq X-ten platform yielding about 50M reads per sample.
Illumina (NEBnext UltraII library preparation kit)

value: ovary

tag: antibody


title: Pt11_lesion [200406290064_A]

source_name: Genital skin_lesion

value: lesion


title: AuCG_N


title: Pt13_lesion [200406290064_D]


title: leaf_7DAS_Col-0_rep3


title: Testis_CenH3_L

source_name: testis

value: testis

value: custom against Od CenH3


title: Pt8_8wks [200769890019_K]


title: Pt14_8wks [200406290064_J]


title: Ovary_CenH3_N


title: leaf_7DAS_Per-1_rep1


title: leaf_7DAS_Col-0_rep2


title: Pt11_ctrl [200406290064_G]


title: Testis_Input_L


title: TPEN-Rep3

source_name: 0.8μM TPEN


title: leaf_7DAS_Col-0_rep1


title: Pt8_ctrl [200769890019_I]


title: leaf_7DAS_F1_rep3

value: Col-0 x Per-1 F1


title: Pt7_ctrl [200769890019_G]


title: TB_Input_O

source_name: tailbud

value: tailbud


title: Pt10_ctrl [200769890019_F]


title: TPEN-Rep2


title: shoot_8DAS_Per-1_rep3

value: seedling shoot

value: 8DAS (days after sowing)


title: Pt10_8wks [200769890019_H]


title: TB_Input_XE


title: shoot_8DAS_Per-1_rep2


title: TPEN-Rep1


title: TB_Input_XD


title: shoot_8DAS_Per-1_rep1


title: shoot_8DAS_F1_rep3


title: TB_Input_L


title: TB_Input_C


title: shoot_8DAS_F1_rep2


title: TB_Input_H


title: TB_Input_XC


title: shoot_8DAS_Col-0_rep3


title: TB_Input_XB


title: Pt7_8wks [200769890019_E]


title: TB_Input_XA


title: Pt7_2wks [200769890019_A]

source_name: Genital skin_2wks


title: shoot_8DAS_Col-0_rep2

source_name: seedling


title: Pt9_8wks [200769890019_D]


title: ZLM Rep3

source_name: Zinc-limited Mtb

growth_protocol: Mtb were grown in 7H9-ADC broth medium until mid-log phase (OD ~0.8) and centrifuged. The 7H9-ADC supernatant was completely aspirated and the cell pellets were resuspended in Sauton's medium without zinc. Zinc sulfate was added to 6uM to the zinc-replete cultures. Cultures were grown for 10 days at 37oC with shaking at 120rpm. On day 10, cultures were centrifuged at 4oC and the cell pellets were resuspended in 1mL TRIzol.

extract_protocol:
Cultures were centrifuged at 4°C, and cell pellets were resuspended in TRIzol. TRIzol extractions were homogenized by bead beating and RNA was extracting following the manufacturer's protocol.
Ribosomal RNA was depleted from the samples using Ribo-Zero plus rRNA depletion kit (Illumina®, Cat. #:20037135) before being sequenced on an Illumina® HiSeq platform for generation of 150 base pair paired end reads. RNA sequencing (RNAseq) was performed by GENEWIZ® (South Plainfield, NJ 07080).

tag: zinc status

value: Limited


title: ZLM Rep1


title: ZRM Rep3

source_name: Zinc-replete Mtb

value: Replete


title: ZLM Rep2


title: shoot_8DAS_Col-0_rep1


title: TB_Input_B


title: Pt9_ctrl [200769890019_B]

value: ctrl


title: Pt7_lesion [200769890002_J]


title: shoot_8DAS_F1_rep1


title: TB_Input_A


title: ZRM Rep1


title: shoot_7DAS_Per-1_rep3


title: Pt5_ctrl [200769890002_G]


title: TB_Lamin1_XE

value: custom against Od lamin1


title: shoot_7DAS_Per-1_rep2


title: Pt6_ctrl [200769890002_H]


title: Pt6_lesion [200769890002_I]


title: Osteoarthritis-modeled joint 3

first: jiang

middle: xiao

last: yu

address: 15 Datun Road Chaoyang District

institute: institute of zoology, CAS

description: RNA sequencing of Osteoarthritis-modeled joint

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human or mm10 mouse reference genome using hisat2 software.
Genome_build: hg19 for Homo sapiens and mm10 for Mus musculus
Supplementary_files_format_and_content: Txt file of read count for RNA-seq.

source_name: joint

extract_protocol: For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: cell type/tissue

value: joint

value: Osteoarthritis-modeled


title: shoot_7DAS_Per-1_rep1


title: Pt5_8wks [200769890002_E]

data_processing: The data were normalised using CubicSpline with background subtraction using Illumina Genome Studio (V2010.3)

value: patients with recurrent HSV-2 infection


title: Pt6_8wks [200769890002_F]


title: Pt6_2wks [200769890002_B]


title: TB_Lamin1_XD


title: shoot_7DAS_F1_rep3

value: 7DAS (days after sowing)


title: Osteoarthritis-modeled joint 2


title: ZRM Rep2


title: TB_CTCF_XE

value: custom against Od CTCF


title: shoot_7DAS_F1_rep2


title: TB_CTCF_XD


title: Exosome-treated joint 3

description: RNA sequencing of Exosome-treated joint

value: Exosome-treated


title: Pt5_2wks [200769890002_A]

value: genital skin biopsies


title: Pt5_lesion [200761430009_J]

value: lesion


title: Osteoarthritis-modeled joint 1


title: TB_CTCF_XC


title: shoot_7DAS_F1_rep1


title: Pt4_lesion [200761430009_I]


title: Pt4_ctrl [200761430009_H]


title: shoot_7DAS_Col-0_rep3


title: TB_CTCF_XB


title: TB_SMC1_XC

value: custom against Od SMC1


title: Exosome-treated joint 1

description: RNA sequencing of Exosome-treated joint


title: Exosome-treated joint 2

description: RNA sequencing of Exosome-treated joint


title: Control joint 3

description: RNA sequencing of Control joint

value: Control


title: TB_SMC1_XB

value: tailbud


title: shoot_7DAS_Col-0_rep1

value: seedling shoot


title: shoot_7DAS_Col-0_rep2


title: shoot_6DAS_Per-1_rep3

value: 6DAS (days after sowing)


title: TB_SMC1_XA


title: leaf_8DAS_Col-0_rep1

value: the first true leaf

value: 8DAS (days after sowing)


title: Control joint 2

description: RNA sequencing of Control joint


title: Pt3_8wks [200761430009_G]


title: Control joint 1

description: RNA sequencing of Control joint


title: shoot_6DAS_Per-1_rep2


title: RNA-seq SRSF1KO_rep1

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

institute: China Agricultural University

description: count.txt

data_processing:
First, raw reads quality and adapter sequences were checked using fastqc (version 0.11.5). Cutadapt (version 1.17) and trim_galore were used to filter adaptor and poor quality sequences.
In case of RNA-seq experiments, clean reads were mapped to the mm10 reference mouse genome using Star (version 2.6). HTSeq (version 0.6.1) facilitated to counting RNA-seq reads at gene-level with parameters ‘-f bam -r name -a 10 -t exon -s no -i gene_id -m union’. Finally, DESeq2 (version 1.20.0) was subsequently applied on gene counts to identify genes differentially expressed between TCRβ+DP cells isolated from WT or TCRβ+DP Srsf1fl/flLckcre/+ mice after removing entries that exhibited zero counts in all replicates.
In case of CLIP-seq experiments, bowtie2 (version 2.1.0) was used to map clean reads to the mm10 mouse reference genome with parameters ‘-p 10 -L 15 -N 1 -D 50 -R 50 --phred33 --qc-filter --very-sensitive --end-to-end’. CLIP-seq peaks were identified by Piranha (version 1.2.1) with the following parameters ‘-s -b 20 -d ZeroTruncatedNegativeBinomial -p 0.05’. Homer (version 4.9.1) was used for peak annotation based on the mm10 genome assembly and for SRSF1 binding motif analysis.
Genome_build: mm10
Supplementary_files_format_and_content: txt format. Read counts for each gene
Supplementary_files_format_and_content: bw format.

extract_protocol:
Rneasy Plus Mini Kit
Libraries are constructed according to the standard protocol for Smart-seq2

value: thymus

value: 6~8 weeks

tag: cell sorting strategy

value: FACS-sorted

tag: clip antibody


title: RNA-seq SRSF1KO_rep2

description: count.txt


title: TB_H3K36me3_L

value: Abcam ab9050


title: TB_H3K36me3_O


title: shoot_6DAS_F1_rep3

value: Col-0 x Per-1 F1


title: TB_H3K36me3_H


title: RNA-seq WT_rep3

description: count.txt

value: WT


title: shoot_6DAS_F1_rep2


title: Pt3_2wks [200761430009_C]

extract_protocol: Total RNA extracted from keratinpcuytes using Qiagen RNeasy Mini Kit.

value: patients with recurrent HSV-2 infection

tag: time point


title: Pt4_2wks [200761430009_B]


title: Pt4_8wks [200761430009_F]


title: Pt3_lesion [200757770053_L]


title: Pt2_8wks [200757770053_J]


title: Pt1_ctrl [200757770053_K]

value: ctrl


title: TB_H3K36me3_C


title: TB_H3K9me3_K

value: Abcam ab8898


title: RNA-seq WT_rep1

description: count.txt


title: shoot_6DAS_F1_rep1


title: H3_S5: rep3, epimastigotes supplemented with haemoglobin

city: Nottingham

first: Fei

last: Sang

address: QMC

department: School of Life Sciences

institute: University of Nottingham

data_processing:
Raw PE reads were trimmed against adaptor sequences by scythe (v0.981), and quality trimmed by sickle (v1.33) using default settings.
Trimmed reads were directionally separately aligned to the haploid genome of T. cruzi strain CL Brener Esmeraldo and Nonesmeraldo-like available at triTrypDB using bowtie2 (version 2.3.5) with -very-sensitive-local option.
Uniquely and correctly mapped reads were extracted for the downstream analysis. featureCounts was used to count the number of reads aligned to each gene.
Gene expression level was calculated and normalised by Fragments Per Kilobase Per Million (FPKM). Genes with FPKM < 10 on both conditions were removed from the posterior analysis.
Genome_build: T. cruzi strain CL Brener Esmeraldo and Nonesmeraldo-like available at triTrypDB

organism: Trypanosoma cruzi

source_name: Trypanosoma cruzi epimastigotes

growth_protocol: Epimastigote forms of Trypanosoma cruzi, clone CL Brener were grown in 50 mL medium BHI with 10% FCS in the presence of 30 μMheme to 28˚C for 7 days in culture bottle cells with 25 cm2 surface area

extract_protocol:
RNA samples of epimastigotes incubated with or without heme were extracted from samples by using TRIzol method. Total RNA was measured using Qubit RNA assay kit (Life technologies, USA). The mRNA enrichment was performed in a NEBNext Poly(A) mRNA Magnetic Isolation Module
cDNA libraries were synthesized by Illumina
TruSeq RNA Sample Preparation Kit.

treatment_protocol: 20 mM heme stock solution was freshly prepared by dissolving in 0.1 N NaOH, and after it was buffered in PBS (100 mM sodium phosphate buffer and 150 mM NaCl at pH 7.4). The stock solution was diluted immediately before use to 5 mM in the same PBS buffer or in culture medium.

value: epimastigote


title: shoot_6DAS_Col-0_rep3

growth_protocol: The plants were grown on MS plates containing 1% sucrose under long-day condition (16-h light with intensity of 18 W/m2 at 22 °C and 8-h dark at 18 °C) after surface-sterilization followed by 7-day stratification of the seeds.


title: TB_H3K9me3_H


title: shoot_6DAS_Per-1_rep1


title: RNA-seq WT_rep2

description: count.txt


title: H2_S3: epimastigotes rep2, supplemented with haemoglobin


title: TB_H3K4me1_L

value: Abcam ab8895


title: shoot_6DAS_Col-0_rep2


title: H1_S9: epimastigotes rep1, supplemented with haemoglobin


title: Pt1_8wks [200757770053_I]

first: Tao

address: 1100 Fairview Ave N/FHCRC/E5-110

institute: University of Washington

value: genital skin biopsies


title: TB_H3K4me1_K

value: tailbud


title: shoot_5DAS_Per-1_rep3

value: seedling shoot

value: 5DAS (days after sowing)


title: TB_H3K9me3_C


title: f3_S1: epimastigotes rep2, control


title: Pt2_2wks [200757770053_F]


title: Pt2_lesion [200757770053_B]

value: lesion


title: Pt1_2wks [200757770053_E]


title: Pt1_lesion [200757770053_A]


title: TB_H3K4me1_O


title: shoot_6DAS_Col-0_rep1

value: 6DAS (days after sowing)


title: f2_S14: epimastigotes rep1, control


title: TB_H3K4me1_H


title: shoot_5DAS_Per-1_rep1


title: shoot_5DAS_Per-1_rep2


title: shoot_5DAS_F1_rep2


title: Rpb3 ChIP (Rep-1) Sonicated Chromatin

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

description:
ChIP-DNA
Biological replicate 1

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive --no-mixed --no-unal, to map sequences up to 1 kb with maximum accuracy.
The PCR duplicates were removed by Samtool Rmdup tool
The .Bam files were used to generate the profiles using BamR (https://github.com/rchereji/bamR)
Supplementary_files_format_and_content: bigwig

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Cells were grown to OD600 0.8 before being formaldehyde crosslinked and harvested

extract_protocol:
Mnase-digested or sonicated extracts were used to ChIP for either Sth1myc or Rpb3. ChIPs and corresponding inputs were reverse-crosslinked, extracted with chloroform:IAA, then precipitated with ethanol.
Libraries were constructed using NEBNext Ultra II kit and Biooscientific NEXTFLEX ChIP-Seq adapters. Protocol was slightly modified from NEBNext manufacturer instuctions.

value: Sth1-MYC tagged

tag: protocol

value: Formadehyde Crosslinked and Sonicated

value: MATa his3delta_1 leu2delta_0 met15delta_0 ura3delta_0 STH1-myc13::HIS3


title: TB_H3K4me1_C


title: TB_H3K27me3_B

value: Millipore 07-449


title: Sth1-Myc ChIP (Rep-2) MNase Chromatin

description:
ChIP-DNA
Biological replicate 2

value: Formadehyde Crosslinked and Mnase digested


title: Rpb3 ChIP (Rep-2) Sonicated Chromatin

description:
ChIP-DNA
Biological replicate 2


title: FXR2_1

city: Ulm

first: Axel

last: Freischmidt

address: Albert-Einstein-Allee 11

institute: Ulm University

description: low molecular weight RNA copurifying with the second RG-domain of FXR2

hyb_protocol: according to the instructions in the FlashTagTM Biotin HSR RNA Labeling Kit

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix Expression Console 1.4.1.46 for normalization (RMA+DBAG; human only); BRB Array tools for statistical analysis

label_protocol: FlashTagTM Biotin HSR RNA Labeling Kit (Genisphere, LLC, Hatfield, PA, USA) according to the instructions of the manufacturer

growth_protocol: HEK293 cells were grown under standard conditions (37° C; 5% CO2) in DMEM (Thermo Fisher Scientifc #41965039) supplemented with 10% fetal bovine serum.

extract_protocol: Low molecular weight RNA from HEK293 cells was isolated using RNAzol RT (Sigma-Aldrich #R4533) and further purified with the Direct-zol RNA MicroPrep Kit (Zymo Research #R2060). After incubation of the RGG/RG-domains with the low molecular weight RNA, recombinant proteins were recovered using Ni-NTA-Agarose (Qiagen) and the co-purifying RNA isolated directly from the beads using RNAzol RT and the Direct-zol RNA Microprep Kit.

tag: cell line

tag: recombinant proteins

value: amino acid 458-521 of FXR2 with a N-terminal GST and a C-terminal His-tag


title: FXR1_3

description: low molecular weight RNA copurifying with the RGG-domain of FXR1

value: amino acid 414-479 of FXR1 (variant 1) with a N-terminal GST and a C-terminal His-tag


title: FXR2_3


title: Sth1-Myc ChIP (Rep-1) MNase Chromatin

description:
ChIP-DNA
Biological replicate 1

tag: genotype


title: TB_H4ac_K

tag: tissue

value: Millipore 06-866


title: FXR1_2


title: shoot_5DAS_F1_rep1

value: Col-0 x Per-1 F1

tag: age


title: FXR2_2


title: TB_H3K27me3_A


title: MNase Input (Rep-2) MNase Chromatin

description:
Genomic-DNA
Biological replicate 2


title: shoot_5DAS_Col-0_rep2


title: TB_H4ac_H


title: shoot_5DAS_Col-0_rep1


title: MNase Inputs (Rep-1) MNase Chromatin

description:
Genomic-DNA
Biological replicate 1


title: shoot_5DAS_F1_rep3


title: TB_H4ac_C


title: Rpb3 ChIP (Rep-2) MNase Chromatin

description:
ChIP-DNA
Biological replicate 2


title: FMR1_3

description: low molecular weight RNA copurifying with the RGG-domain of FMR1

value: amino acid 505-570 of FMR1 ISO1 with a N-terminal GST and a C-terminal His-tag


title: TB_H3K27ac_B

value: Abcam ab4729


title: Rpb3 ChIP (Rep-1) MNase Chromatin

description:
ChIP-DNA
Biological replicate 1


title: FXR1_1


title: shoot_5DAS_Col-0_rep3


title: FMR1_1


title: FMR1_2


title: shoot_4DAS_F1_rep3

value: 4DAS (days after sowing)


title: TB_H3K4me3_B

value: tailbud

value: Millipore 04-745


title: TB_H3K4me3_A


title: shoot_4DAS_Per-1_rep1

value: seedling shoot


title: Input_2

description: low molecular weight RNA of HEK293 cells

source_name: Input


title: 2-month-old young mice cortex

first: Rui

last: Zhan

address: 38 Xueyuan Road, Haidian District

description: Single-nucleus RNA

data_processing:
Quality control was performed by the Cell Ranger package v.2.0.1.
Fastq format were aligned with the mm10 reference genome. The aligned reads were filtered by cell barcodes and the unique molecular identifier (UMI) to establish filtered gene-barcode matrices.
The pre-processed digital gene expression profiling (DGE) matrices were imported utilizing the Seurat package (v.3.1) in R (v.4.0.2).
The data were screened for detecting genes in more than 3 cells, cells with from 200 to 10000 genes, UMI from 1000 to 30000, and mitochondrial genes less than 10%.
The snRNA-seq datasets were subsequently analyzed by Seurat as described previously(Zhou et al., 2020). In brief, cells were grouped by cell clusters with uniform manifold approximation and projection (UMAP) as determined by the function FindClusters of Seurat that calculated with 10 principal component analysis (PCA) components with resolution 0.1–1.0, leading to 15–25 clusters. A resolution of 0.6 was chosen for the following analysis.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Brain

growth_protocol: Normal diet feeding 2-18 months

extract_protocol:
Frozen cortices from mice were homogenized in 0.025% NP-40 lysis buffer, incubated on ice for 30 min, filtered through a 30 μm filter, and centrifuged at 500 × g for 5 min at 4 °C. Nuclei were washed, filtered twice, and resuspended in 500 μL nuclei wash buffer and 900 μL 1.8 M sucrose. The mixture was mixed, layered, and centrifuged at 12,000 × g for 1 h to separate the nuclei from cell debris. The nuclei pellets were resuspended in nuclei wash buffer at 1,000 nuclei/μL and filtered through a 40 μm cell strainer.
Isolated nuclei from 2-month-old young and 18-month-old (n = 3 each group, pooled) mouse cortices were loaded on a 10x Genomics Chromium chip. Reverse transcription and library preparation were performed via a 10x Genomics Single Cell Reagent Kit, following the manufacturer's protocol(Hu et al., 2017).

value: Cerebral cortex

value: Wild type

value: 2 months old


title: 18-month-old aging mice cortex

description: Single-nucleus RNA

value: 18 months old


title: shoot_4DAS_F1_rep2


title: CD45+ cells_aortas_regression anti-miR-33

city: New York

first: Emily

last: Brown

address: 435 E 30th St

institute: NYU Langone

data_processing:
quality control, Cell Ranger Single Cell Software Suite
sample de-multiplexing, Cell Ranger Single Cell Software Suite
barcode processing, Cell Ranger Single Cell Software Suite
single cell 3' gene counting, Cell Ranger Single Cell Software Suite
alignment, Cell Ranger Single Cell Software Suite
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene expression by cell, file with barcodes and file with expressed genes.  Files are ready to be import into Seurat package or similar.

source_name: CD45+ cells

extract_protocol: The whole aorta was carefully isolated, and the perivascular fat was removed. Then the aortic tissue was cut into as small pieces as possible and incubated at 37°C for 15 minutes with enzyme mixture containing DNase I (40 U/ml), liberase (4 U/ml), hyaluronidase (60 U/ml). Live CD45+ cells were sorted out using BD FACSAriaIII. The cells are resuspended in final concentration of ~500 cells/µL in 1X HBSS containing 0.04% BSA to minimize cell loss and aggregation. ~12,000 cells are partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum recovery of 10,000 individual cells per sample. Utilizing the v2 Chromium™ Single Cell 3' Library Kit and Chromium instrument (10x Genomics), poly-adenylated mRNA from an individual cell is tagged with a unique 16bp 10x barcode and 10bp Unique Molecular Identifier. Full length cDNA is then amplified to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size (~400bp) for library construction. The final library is sequence ready and contains four unique sample indexes. The concentration of the 10x single cell library will be accurately determined through qPCR (Kapa Biosystems) to produce cluster counts appropriate for the HiSeq4000 platform (Illumina). 26x98nt read lengths are generated targeting 50,000 reads per cell.

value: atherosclerotic lesion

value: Ldlr-/-

tag: disease state

value: atherosclerosis regression