title: spinal cord, Naive, VZC00104.D06


title: spinal cord, Naive, VZC00104.C22

status: Public on Dec 24 2021

type: SRA

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic

data_processing:
Illumina sequencing BCL basecall files were converted into FASTQ files with the Illumina bcl2fastq software.
Adapter and other non-genomic content are trimmed away using Trimgalore.
Continuous reads were aligned to a reference genome (GRCm38) using STAR accounting for spliced alignments.
Following removal of duplicate reads HT-seq was used for obtaining raw transcript counts.
Quality control wells (bulk and empty wells), ERCC, non-genes and genes present in zero genes were removed.
Normalized counts per million (CPM) was estimated for each gene and cell by dividing the counts for each gene and cell with the sum of all counts for that particular cell, multiplying by 10^6 and adding 1 (pseudocount) prior to log2-transformation.
Cells with Actb expression in the 1st percentile were removed.
Cells with a count less than 2^16 were removed.
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

molecule: total RNA

organism: Mus musculus

source_name: spinal cord

growth_protocol: NA, this is an in vivo experiment

extract_protocol:
Spinal cords were harvested following perfusion with 1xPBS, spinal cords were stored on ice. Spinal cords were dissociated using papain by trituration. Myelin was removed using a 30 % Percoll gradient. Fc receptor was blocked using CD16/32 antibody. Cells were stained for CD45, CD14, CD64 and CD11b using pre-conjugated antibodies for index sorting. Dead cells were removed using MACS® Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) using manufacturer’s protocol. CD45+ cells were isolated using a SONY FACS SH800S cell sorter and placed in 2 ul lysis buffer (H2O 1:53, Recombinant RNase Inhibitor 1:40, ERCC 1:600000 1:40, 10 % TritonTM X-100 1:50, 10 mM dNTP 1:4 ,100 µM dT 1:40 according to the Smart-Seq2 protocol).
Full-length cDNA and sequencing libraries were prepared using the Smart-Seq2 protocol . Briefly,primers were annealed at 72oC for 3 min (Bio-Rad, 1000C TouchTM Thermal Cycler) followed by immediate reverse transcription and template switching by adding 3 µl (Eppendorf, epMotion 5073) reverse transcription mix to each well and kept at 42oC for 90 min and 70oC for 5 min. DNA was pre-amplified by adding 7.5 µl of pre-amplification mix into each well and kept at 37oC for 30 min, 95oC for 3 min, 22 cycles of: 98oC for 20 s; 67oC for 15 s; 72oC for 4 min followed by 72oC for 5 min. DNA was purified by adding solid phase reversible immobilization (SPRI) beads at a ratio of 0.75:1, incubated for 5 min at room temperature (RT), washed twice with 30 µl 80 % EtOH (Solveco, 1000), air dried for 15 min and eluted in 15 µl EB buffer (Qiagen, 19086). A magnetic plate (custom made) was used for separation of the beads during processing. DNA concentration was measured in 16 random wells from each 384-well plate using a step-wise pattern with QUBITTM dsDNA HS Assay Kit (Q33231). 3 µl sample was added to 97 µl buffer in a 96-well plate (InvitrogenTM, M33089) and concentrations were measured and compared to standard (Tecan spark 10M, ex/em 485/528 nm). DNA was then diluted to a concentration of 0.15 µg/µl using RNase-free H2O. Tagmentation was performed by adding 1.8 µl Tn5 mix to each well in a 384-well plate (Table 5). 0.7 µl cDNA was then added into each well containing the Tn5 mix. The plate was vortexed (Thermo Fisher, 88880017TS), centrifuged and kept at 55oC for 10 min. Tn5 was inactivated by adding 1 µl 0.1 % SDS (Sigma, 71725) to each well. Plate was vortexed and incubated at RT for 7 min. Libraries were barcoded by adding 19.5 µl PCR/barcode mix into each well now containing 3.5 µl sample (Table 5). 2 µl primer (3.75 µM/primer) was finally added to each well. PCR/barcoding was then conducted at 72oC for 3 min, 95oC for 3 min followed by 12 cycles of: 95oC for 15 s; 55oC for 30 s; 72oC for 45 s. DNA was pooled (5 µl from each well) into an Eppendorf® tube. Clean-up, as described above, was repeated and DNA was eventually eluted in 30 µl EB buffer.
Smart-Seq2 (full-length cDNA of single cells)

treatment_protocol: Contusion spinal cord injury (75kdyn) using the IH-impactor was induced in mice with C57BL/6J background.

tag: strain

tag: tissue

value: spinal cord

value: No

value: Naive


title: spinal cord, Naive, VZC00104.D03


title: spinal cord, Naive, VZC00104.D07


title: spinal cord, Naive, VZC00104.C19


title: spinal cord, Naive, VZC00104.C20


title: spinal cord, Naive, VZC00104.D16


title: spinal cord, Naive, VZC00104.D11


title: spinal cord, Naive, VZC00104.C18


title: spinal cord, Naive, VZC00104.C24


title: spinal cord, Naive, VZC00104.C23


title: spinal cord, Naive, VZC00104.D01


title: spinal cord, Naive, VZC00104.C16


title: spinal cord, Naive, VZC00104.C17


title: spinal cord, Naive, VZC00104.D04


title: spinal cord, Naive, VZC00104.D12


title: spinal cord, Naive, VZC00104.C15


title: spinal cord, Naive, VZC00104.C14


title: spinal cord, Naive, VZC00104.D10


title: spinal cord, Naive, VZC00104.C13


title: spinal cord, Naive, VZC00104.C12


title: spinal cord, Naive, VZC00104.C07


title: spinal cord, Naive, VZC00104.C11


title: spinal cord, Naive, VZC00104.C08


title: spinal cord, Naive, VZC00104.C09


title: spinal cord, Naive, VZC00104.C05


title: spinal cord, Naive, VZC00104.C06


title: spinal cord, Naive, VZC00104.C04


title: spinal cord, Naive, VZC00104.C02


title: spinal cord, Naive, VZC00104.C03


title: spinal cord, Naive, VZC00104.B17


title: spinal cord, Naive, VZC00104.B16


title: spinal cord, Naive, VZC00104.B12


title: spinal cord, Naive, VZC00104.B22


title: spinal cord, Naive, VZC00104.B10


title: spinal cord, Naive, VZC00104.B11


title: spinal cord, Naive, VZC00104.B19


title: spinal cord, Naive, VZC00104.B09


title: spinal cord, Naive, VZC00104.B13


title: spinal cord, Naive, VZC00104.B15


title: spinal cord, Naive, VZC00104.B07


title: spinal cord, Naive, VZC00104.B08


title: spinal cord, Naive, VZC00104.B06


title: spinal cord, Naive, VZC00104.B20


title: spinal cord, Naive, VZC00104.B14


title: spinal cord, Naive, VZC00104.B21


title: spinal cord, Naive, VZC00104.B04


title: spinal cord, Naive, VZC00104.B03


title: spinal cord, Naive, VZC00104.B02


title: spinal cord, Naive, VZC00104.B01


title: spinal cord, Naive, VZC00104.A22


title: spinal cord, Naive, VZC00104.A21


title: spinal cord, Naive, VZC00104.B05


title: spinal cord, Naive, VZC00104.A20


title: spinal cord, Naive, VZC00104.A19


title: spinal cord, Naive, VZC00104.B18


title: spinal cord, Naive, VZC00104.C01


title: spinal cord, Naive, VZC00104.A16


title: spinal cord, Naive, VZC00104.A18


title: spinal cord, Naive, VZC00104.A17


title: spinal cord, Naive, VZC00104.A13


title: spinal cord, Naive, VZC00104.A03


title: spinal cord, Naive, VZC00104.A06


title: spinal cord, Naive, VZC00104.A11


title: spinal cord, Naive, VZC00104.A15


title: spinal cord, Naive, VZC00104.A10


title: spinal cord, Naive, VZC00104.A14


title: spinal cord, Naive, VZC00104.A12


title: spinal cord, Naive, VZC00104.A09


title: Col_2

city: Cambridge

first: Bernhard

last: Blob

address: 47 Bateman Street

country: United Kingdom

institute: Sainsbury Laboratory, Cambridge University

description:
FPKM_SE6.txt
processed data header: Col_2

data_processing:
Analysis was performed by Novogene (Beijing, China). In short, raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads. The filtering process is as follows: (1) Discard reads with adaptor contamination. (2) Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%). (3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read. RNA-seq Adapter sequences (Oligonucleotide sequences of adapters from TruSeqTM RNA and DNA Sample Prep Kits): RNA 5' Adapter (RA5), part # 15013205: 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' RNA 3' Adapter (RA3), part # 15013207: 5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC(6-nucleotide index)ATCTCGTATGCCGTCTTCTGCTTG-3'. TopHat2 was used for aligment to TAIR10. The mismatch parameter is set to two, and other parameters are set to default.  Appropriate parameters are also set, such as the longest intron length. Only filtered reads are used to analyze the mapping status of RNA-seq data to the reference genome. the gene expression level is estimated by counting the reads that map to genes or exons. HTSeq software was used to analyze the gene expression levels in this experiment, using the union mode. The result files present the number of genes with different expression levels and the expression level of single genes. In general, an FPKM value of 0.1 or 1 is set as the threshold for determining whether the gene is expressed or not.
Genome_build: TAIR10
Supplementary_files_format_and_content: read counts or FPKM values, as tab delimeted tables in .txt files

organism: Arabidopsis thaliana

source_name: whole root meristems

growth_protocol: Arabidopsis seeds were surface sterilized in a bleach solution (5% sodium hypochlorite with 0.02% tween 20) for 5 minutes with gentle rotation. Seeds were then thoroughly washed at least 8 times with sterile distilled water and imbibed for 2 – 5 days at 4 °C in the dark. Seeds were germinated on 1/2 strength Murashige and Skoog (½ MS) agar medium containing 1% sucrose and 0.8% difco agar. Seedlings and adult plants were grown under long-day condition – 16 hours light (188 μmol m−2 s−1) and 8 hours dark at 23 °C. For confocal imaging, anatomical analysis, and RNA-seq experiments, 5-day-old vertically grown seedlings were used, unless otherwise specified.

extract_protocol: 5 days old seedlings were transferred to 1/2 MS medium plates with 5% agar in batches of 15 for easier dissection. Root meristems were cut off with a syringe needle and immediately transferred to RNAlater solution. All meristems were collected in total volume of 20ul of RNAlater. Total RNAs were extracted using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.  Library preparation and sequencing was done by Novogene (beijing, China) as follows: After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads.  The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and  reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the  second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR  enrichment.

tag: age

value: 5day old seedlings

tag: induction time

tag: line

value: Col-0 Wildtype


title: SE6_4

description:
FPKM_SE6.txt
processed data header: SE6_4

extract_protocol: 5 days old seedlings were transferred to 1/2 MS medium plates with 5% agar in batches of 15 for easier dissection. Root meristems were cut off with a syringe needle and immediately transferred to RNAlater solution. All meristems were collected in total volume of 20ul of RNAlater. Total RNAs were extracted using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.  Library preparation and sequencing was done by Novogene (beijing, China) as follows: After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the  mRNA. The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and  reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the  second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR  enrichment.

value: pear sextuple mutant


title: spinal cord, Naive, VZC00104.A02


title: spinal cord, Naive, VZC00104.A05


title: Col_1

description:
FPKM_SE6.txt
processed data header: Col_1


title: SE6_3

description:
FPKM_SE6.txt
processed data header: SE6_3


title: SE6_2

description:
FPKM_SE6.txt
processed data header: SE6_2


title: Col_4

description:
FPKM_SE6.txt
processed data header: Col_4


title: 0.75%h2s 1

city: Urbana

first: Sichong

last: Pei

state: IL

address: 600 S Mathews, RM210

department: Chemical and biomolecular engineering

country: USA

institute: University of Illinois Urbana-Champaign

data_processing:
Basecalling
Trimming reads by Trimmomatic trimmomatic SE -threads 4 -phred33 \  ${INPUT_DIR}/${line}.fastq \  ${OUTPUT_DIR}/${line}_trimmed.fastq \  ILLUMINACLIP:/home/n-z/pei3/rnaseq_analysis/se_adapter.fa:2:15:10 LEADING:28 TRAILING:28 MINLEN:30
Aligning reads by BWA-MEM.  bwa mem -t=8 -v=1 \  bwamem/bwa_index/b_index \  results/trim/${line}_trimmed.fastq|samtools sort -@8 -o bwamem/${line}_sorted.bam -
Genes were counted by FeatureCounts from package edgeR. (For source codes of following steps, please refer to github page https://github.com/raogroupuiuc)
Raw count matrix were normalized based on library size and sequencing depth, and a pseudocount matrix was generated with prior count=1 (to avoid log zero) and statistal analysis was performed on pseudocount matrix
Genome_build: Methylococcus capsulatus str Bath. NCBI entry: NC_002977.6
Supplementary_files_format_and_content: Raw count matrix including all 15 samples and all genes in txt format
Supplementary_files_format_and_content: Pseudocount matrix in tab limited format
Supplementary_files_format_and_content: Raw count for each sample (listed individually)

molecule: polyA RNA

organism: Methylococcus capsulatus str. Bath

source_name: Bacteria

growth_protocol: A fresh overnight culture was inoculated into AMS medium so that OD=0.03. Headspace is filled with 50% CH4 and 50% air with 2atm. Grown at 37C at 200rpm.

extract_protocol:
When OD reaches ~0.8, RNA protect reagent was added into culture and RNAs were extracted by Rneasy mini kit immediately after collection.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Different amount of H2S is injected into headspace to reach 0.1%, 0.5% and 0.75%, and grown as the control. The H2S shock treatment is to inject H2S into a control culture's headspace at mid-log phase(OD~0.6) and incubate for 1hr before collection.

tag: treatment


title: 0.5%h2s 1


title: 0.75%h2s 2


title: 0.5%h2s 3


title: 0.75%h2s 3


title: 0.1%h2s 3


title: 0.1%h2s 2


title: spinal cord, Naive, VZC00104.A08


title: spinal cord, Naive, VZC00104.A07


title: h2s shock2

value: H2S shock


title: h2s shock3


title: 0.1%h2s 1


title: h2s shock1


title: control1

value: Control


title: control2


title: control3


title: OsSRT1-RNAi_H3K9ac_ChIA_20h_rep1

city: Wuhan

first: Baibai

last: Gao

address: 1 Shizishan Street, Hongshan District

country: China

institute: National Key Laboratory of Crop Genetic Improvement

library_source: genomic

data_processing:
ChIA-PET raw reads were processed using modified ChIA-PET Tool pipeline
First, the linker filtering was carried out for the PET sequence reads.
Next, the PET sequences were mapped to the MH63 rice reference genome using BWA with up to two mismatches allowed.
The mapped PETs were then used for further classification as self-ligation, inter-ligation and other PETs.
Genome_build: MH63
Supplementary_files_format_and_content: bedpe

molecule: genomic DNA

organism: Oryza sativa

source_name: OsSRT1-RNAi mature leaf

growth_protocol: Rice [Oryza sativa L. ssp. indica cv. Minghui 63 (MH63)] seeds were sown on May 19, 2017 in a paddy field. At 20 days after germination, the seedlings were transplanted into a paddy field of Huazhong Agricultural University at Wuhan, China, and grown under normal agricultural conditions. In the paddy field, the plants were transplanted at a density of one plant per 15 × 30 cm area.

extract_protocol:
Sample was ground in liquid nitrogen into a fine powder and resuspended in 100 ml of EB1 buffer. The mixture was then filtered through Miracloth, and the filtrate was centrifuged at 1,800 × g for 10 min at 4 °C. The pellet was washed three times in 5 ml of EB2 buffer and centrifuged at 2,000 × g for 10 min at 4 °C. Next, the pellet was washed in 2 ml of EB3 buffer and centrifuged at 2,000 × g for 1 h at 4 °C. The final pellet was resuspended in 1 ml of NLB buffer, and chromatin was fragmented into 1-3 kb by sonication. After centrifugation at 2,000 × g for 10 min at 4 °C, the supernatant was transferred to a new tube for chromatin immunoprecipitation (ChIP). The antibody (80 µg; RNAPII, BioLegend, 920102) was mixed with 800 µl suspended protein G magnetic beads, and incubated at 4°C for 8 h with rotation to coat the magnetic beads. All of the chromatin was extracted to the antibody-loaded beads in a new tube and incubated at 4°C overnight with rotation. The supernatant was discarded and the beads were sequentially washed with 5 mL 0.1% SDS FA cell lysis buffer (0.05 M HEPES-KOH, 0.15 M NaCl, 0.001 M EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS) for three times, 5 mL High salt ChIP buffer (0.05 M HEPES-KOH, 0.35 M NaCl, 0.001 M EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS) twice, 5 mL ChIP wash buffer (0.01 M Tris–HCl, 0.25 M LiCl, 0.001 M EDTA, 2.5% NP-40, and 0.5% sodium deoxycholate) once and 5 mL 1 × TE buffer (pH 8.0, Ambion, cat. no. AM9849) twice. ChIP DNA was used for end-repair and A-tailing using T4 DNA polymerase (Promega, cat. no. M421F) and Klenow enzyme (NEB, cat. no. M0212L). Proximity ligation of ChIP DNA was performed using biotinylated bridge-linker (forward strand: 5′-[5Phos] CGCGATATC/iBIOdT/TATCTGACT-3′, reverse strand: 5′-[5Phos]GTCAGATAAGATATCGCGT-3′).
Protein-DNA complex was reverse cross-linked and the ChIA-PET libraries were prepared by using Tn5 transposase (VAHTS; cat. no. TD501). The libraries were sequenced (2 × 150 bp) using Illumina Hiseq X-Ten (Beijing AnnoRoad Company).

treatment_protocol: Rice leaves were dual cross-linked with 1% formaldehyde for 20 min and quenched with 0.2 M glycine. Next, EGS was added to a final concentration of 1.5 mM in PBS buffer and incubated for another 40 min at room temperature.

value: mature leaf

tag: development stage

value: mature leaves harvested at 20:00 at floral induction stage

tag: cultivar

tag: chip antibody


title: OsSRT1-RNAi_H3K9ac_ChIA_20h_rep2


title: 0.5%h2s 2


title: H3K9ac_ChIA_8h_rep2

source_name: MH63 mature leaf

value: mature leaves harvested at 8:00 at floral induction stage

value: Minghui 63


title: H3K27ac_ChIA_8h_rep1


title: H3K9ac_ChIA_20h_rep2


title: H3K9ac_ChIA_20h_rep1


title: OsSRT1-RNAi_H3K9ac_ChIA_8h_rep2


title: H3K27ac_ChIA_20h_rep1


title: H3K9ac_ChIA_8h_rep1


title: H3K27ac_ChIA_20h_rep2


title: H3K27ac_ChIA_8h_rep2


title: H3K9me2_ChIA_20h_rep2


title: H3K9me2_ChIA_20h_rep1


title: H3K9me2_ChIA_8h_rep1


title: H3K9me2_ChIA_8h_rep2


title: DNAmeth_8h

data_processing:
The sequence quality of the whole-genome bisulfite sequencing (WGBS) libraries was evaluated using FastQC, and the adapter sequences and low-quality reads were filtered using Trimmomatic
The cleaned reads were then mapped to the MH63 reference genome using BatMeth
The uniquely mapped reads were used for further analysis. Individual cytosines with coverage of at least 3 were considered for methylation-level calling.
The DNA methylation level of each cytosine was obtained by dividing the depth of methylated reads by the total coverage of individual cytosines
Genome_build: MH63
Supplementary_files_format_and_content: bigWig files

extract_protocol:
Genomic DNA was extracted using a DNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 69104).
Bisulfite conversion of DNA was conducted using the EZ DNA Methylation-GoldTM kit (ZYMO, D5005), and the bisulfite-treated DNA libraries were constructed using the Illumina TruSeq DNA sample prep kit, following the manufacturers’ instructions.

treatment_protocol: Fresh samples are frozen using liquid nitrogen.

tag: time point


title: DNAmeth_0h

value: mature leaves harvested at 0:00 at floral induction stage


title: OsSRT1-RNAi_RNAPII_ChIP_20h

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the duplication reads
peaks were called using MACS.2.2.1 with narrow parameters
Genome_build: MH63
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads)

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 20 min and quenched with 0.2 M glycine at room temperature.

value: RNAPII


title: DNAmeth_20h


title: DNAmeth_12h

value: mature leaves harvested at 12:00 at floral induction stage


title: MH63_RNAPII_ChIP_20h


title: DNAmeth_4h

value: mature leaves harvested at 4:00 at floral induction stage


title: OsSRT1-RNAi_H3K9ac_ChIA_8h_rep1


title: MH63_RNAPII_ChIP_8h


title: OsSRT1-RNAi_H3K27ac_ChIP_20h


title: OsSRT1-RNAi_RNAPII_ChIP_8h


title: OsSRT1-RNAi_H3K27ac_ChIP_8h


title: MH63_H3K27ac_ChIP_20h


title: MH63_H3K27ac_ChIP_8h


title: OsSRT1-RNAi_H3K9ac_ChIP_20h


title: OsSRT1-RNAi_H3K9ac_ChIP_8h


title: MH63_H3K9ac_ChIP_8h


title: MH63_H3K9ac_ChIP_20h


title: H3K9ac_ChIP_20h_rep1


title: H3K9ac_ChIP_20h_rep2


title: H3K9ac_ChIP_16h_rep1

value: mature leaves harvested at 16:00 at floral induction stage


title: H3K9ac_ChIP_12h_rep2


title: H3K9ac_ChIP_8h_rep2


title: H3K9ac_ChIP_8h_rep1


title: H3K9ac_ChIP_16h_rep2


title: H3K9ac_ChIP_4h_rep2


title: H3K9ac_ChIP_4h_rep1


title: H3K9ac_ChIP_0h_rep1


title: H3K9ac_ChIP_0h_rep2


title: H3K4me1_ChIP_20h_rep2


title: H3K4me1_ChIP_12h_rep2


title: H3K4me1_ChIP_16h_rep1


title: H3K4me1_ChIP_8h_rep2


title: H3K4me1_ChIP_8h_rep1


title: H3K4me1_ChIP_0h_rep2


title: H3K9ac_ChIP_12h_rep1


title: H3K27me3_ChIP_20h_rep2


title: H3K27me3_ChIP_16h_rep1


title: H3K4me1_ChIP_20h_rep1


title: H3K4me1_ChIP_16h_rep2


title: H3K27me3_ChIP_12h_rep2


title: H3K27me3_ChIP_20h_rep1


title: H3K27me3_ChIP_12h_rep1


title: H3K27me3_ChIP_8h_rep2


title: H3K27ac_ChIP_16h_rep2


title: H3K27me3_ChIP_4h_rep2


title: H3K27me3_ChIP_0h_rep2


title: H3K27me3_ChIP_16h_rep2


title: H3K4me1_ChIP_12h_rep1


title: H3K27ac_ChIP_12h_rep2


title: H3K27ac_ChIP_12h_rep1


title: H3K27ac_ChIP_16h_rep1


title: H3K27ac_ChIP_8h_rep2


title: H3K4me1_ChIP_0h_rep1


title: H3K4me1_ChIP_4h_rep2


title: H3K27ac_ChIP_4h_rep2


title: H3K27ac_ChIP_0h_rep1


title: H3K9me2_ChIP_20h_rep2


title: H3K27ac_ChIP_0h_rep2


title: H3K9me2_ChIP_20h_rep1


title: H3K9me2_ChIP_16h_rep2


title: H3K27ac_ChIP_8h_rep1


title: H3K4me1_ChIP_4h_rep1


title: H3K9me2_ChIP_12h_rep2


title: H3K27ac_ChIP_20h_rep2


title: H3K27ac_ChIP_4h_rep1


title: H3K9me2_ChIP_8h_rep2


title: H3K27ac_ChIP_20h_rep1


title: H3K9me2_ChIP_8h_rep1


title: H3K9me2_ChIP_16h_rep1


title: H3K9me2_ChIP_0h_rep2


title: H3K4me3_ChIP_20h_rep2


title: H3K9me2_ChIP_0h_rep1


title: H3K4me3_ChIP_20h_rep1


title: H3K4me3_ChIP_16h_rep1


title: H3K4me3_ChIP_12h_rep1


title: H3K4me3_ChIP_4h_rep2


title: H3K4me3_ChIP_8h_rep2


title: H3K9me2_ChIP_12h_rep1


title: H3K4me3_ChIP_12h_rep2


title: H3K9me2_ChIP_4h_rep2


title: H3K4me3_ChIP_0h_rep2


title: H3K4me3_ChIP_8h_rep1


title: H3K4me3_ChIP_0h_rep1


title: Roots, 24hpt, Az39, B

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

country: Canada

institute: University of Manitoba

data_processing:
Adaptors and low-quality bases removed with Trimmomtatic v. 0.36
Reads aligned to Arabidopsis thaliana TAIR10 reference genome with HISAT2 v. 2.2.1
Genes quantified with featureCounts
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole roots

growth_protocol: Arabidopsis thaliana (WT Col.) seed were surface sterilized in ethanol and aseptically transferred onto MS-nutrient agar plates (1.1 g/L MS, 1% sucrose, 0.8% agar). Plates were orientated in a vertical manner and incubated in growth chambers with the following settings: 22oC, 16 hours light (150 µE/m2/s) and 8 hours of dark.

extract_protocol:
Root systems were collected at 24 hours and 7 days post treatment and flash frozen in liquid nitrogen. Two biological replicates were collected for each time point with each replicate consisting of at least 50 root systems. Root tissue was homogenized with Invitrogen PureLink Plant RNA Reagent (Thermo Fisher Scientific, Waltham, MA, USA) to isolate nucleic acids, and DNA contamination was removed by treating the samples with Ambion TURBO-DNA-free ( Thermo Fisher Scientific, Waltham, MA, USA) per the manufacturer’s protocol. RNA quantity was determined with a Nanodrop spectrophotometer and RNA quality was determined with an RNA nanochip on the Agilent 2100 bioanalyzer system
Reverse transcription, fragmentation, end repair, adapter ligation, and PCR enrichment were conducted with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, Whitby, ON, Canada) per the manufacturer’s protocols. Library size distribution was determined with a high sensitivity DNA chip on the Agilent 2100 bioanalyzer system. Library concentration and molarity was determined with the NEBNext Library Quant Kit (New England Biolabs, Whitby, ON, Canada) in conjunction with PerfeCTa qPCR ToughMix (QuantaBio, Beverly, MA, USA) and PicoGreen fluorospectrophotometry. Libraries were sent to Genome Québec (Montréal, QC, Canada) for 150 bp single-end sequencing on the Illumnia HiSeq 4000 platform.

treatment_protocol: Lysogeny broth agar plates were inoculated with WT A. brasilense strain 39 and A. brasilense ipdc. Plates were incubated at 37oC for 48 hours. Isolated colonies were used to inoculate lysogeny broth and incubated for 24 hours in a rotary shaker at 37oC and 250 rpm. The pellets were washed and resuspended in 0.9% sterile saline and adjusted to a final OD595 = 1. Arabidopsis seedlings were treated four days after initial planting with 2 uL (OD595 = 1) Azospirillum suspension or 2 uL of 0.9% saline.

value: Whole roots

value: Azospirillum brasilense Az39

tag: time

value: 24hpt (hours post treatment )


title: Roots, 24hpt, ipdc, B

value: Azospirillum brasilense Az39 -ipdc mutant


title: Roots, 24hpt, ipdc


title: Roots, 7dpt, Az39, B

value: 7dpt (days post treatment )


title: Roots, 24hpt, Az39


title: Roots, 24hpt, NaCl, B

value: NaCl


title: H3K9me2_ChIP_4h_rep1


title: TOC1_DAP_rep1

data_processing:
Library strategy: DAP-Seq
Trimmomatic fitered the raw reads
DAP-seq reads were aligned to the MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the  duplication reads
peaks were called using MACS.2.2.1 with narrow parameters
Genome_build: MH63
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

extract_protocol:
Genomic DNA was extracted from rice mature leaves using the DNeasy plant mini kit (QIAGEN, 69104) according to the manufacturer’s instructions. One micrograms of genomic DNA were diluted in EB (10 mM Tris-HCl, pH 8.5) and sonicated to 200-bp fragments in a Bioruptor (Diagenode). Purified samples were then end-repaired, and ligated with an adaptor using the NEBNext® Ultra™ II DNA library prep kit (New England BioLabs, E7645) according to the manufacturer’s recommendations. DNA libraries were purified by bead cleaning using a 1:1 bead:DNA ratio, eluted from the beads in 30 μl of EB, and quantified with the Qubit HS fluorometric assay. Fifty microliters of purified Halo-OsTOC1 protein (2 μg plasmids per reaction) was diluted in 400 μl of 1X phosphate-buffered saline (PBS) containing 25 μl of washed Magne®HaloTag® beads (Promega) for 1 h at room temperature on a rotator to encourage the protein binding to the beads. In addition to the Halo-OsTOC1 samples, a negative control Halo sample was run simultaneously using protein expressed in the TNT wheatgerm expression system (Promega). The beads were washed four times in 1X PBS + NP40 (0.005%) and resuspended in 100 μl of 1X PBS. Fifty nanograms of the genomic DNA library was diluted to a final volume of 60 μl in 1X PBS and added to the protein-bound beads. Protein-bound beads and gDNA were rotated for 1 h at room temperature. The beads were washed four times in 1X PBS + NP40, followed by two washes with 1X PBS, transferred to a new tube, and DNA was recovered by resuspending in 25 μl EB and boiling for 10 min at 98 °C.
Eluted samples were enriched and tagged with dual indexed multiplexing barcodes by performing six cycles of PCR in a 50-μl reaction. Samples were pooled and sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads).

treatment_protocol: Samples for DNA isolation were immediately frozen in liquid nitrogen and stored at -80°C until use.


title: Input_rep2


title: Roots, 7dpt, NaCl


title: TOC1_DAP_rep2


title: Roots, 24hpt, NaCl


title: Roots, 7dpt, ipdc, B


title: SLX_17313_i728_i522

data_processing:
De-multiplexed fastq files were aligned using HISAT2
Picard SortSam was used to create .bam from .sam files, Picard Merge2 to merge .bam files where necessary
Cuffquant was used to create abundance files
Cuffnorm was used with all abundance files from all cells to get read counts.
Genome_build: TAIR10, Release 36
Supplementary_files_format_and_content: tab-delimited text file with read counts for each cells and gene

source_name: phloem root meristem

growth_protocol: Arabidopsis seeds were surface sterilized in a bleach solution (5% sodium hypochlorite with 0.02% tween 20) for 5 minutes with gentle rotation. Seeds were then thoroughly washed at least 5 times with sterile distilled water and imbibed for 2 – 5 days at 4 °C in the dark. Seeds were germinated on 1/2 strength Murashige and Skoog (½ MS) agar medium which contains 1% sucrose and 0.8% difco agar. Seedlings and adult plants were grown under long-day condition – 16 hours light (188 μmol m−2 s−1) and 8 hours dark at 23 °C.

extract_protocol:
Arabidopsis root protoplasts were isolated according to the published protocol (Clark et al., 2018). In short, sterilized seeds were plated onto the nylon mesh (57-103, Nitex) placed on the top of MS agar media. Two rows of seeds comprising approximately 100-150 seeds per row were then grown vertically for 5 days in long-day growth condition. To isolate root protoplasts, ⅓ of the root was cut and chopped on the surface of the mesh and collected in buffer containing cell wall degrading enzymes - 1.5 g Cellulase (C1794, Sigma) and 0.1 g Pectolyase (P3026, Sigma) in 100 ml protoplasting solution. After 1 hour of incubation with occasional stirring, the protoplasts were spun down (200 rcf for 6 min) in 15 ml Falcon tube and after removal of supernatant, cells were resuspended in 700 ul protoplasting solution without enzymes. After filtering with 70 um and 40 um cell strainers sequentially, FACS was performed using 70 micron nozzle at 10 psi. Fluorescence positive cells were collected in a round-bottom polystylene tube that contains 150 - 200 ul RLT buffer with beta-mercaptoethanol (10 ul / 1 ml RLT buffer, RNeasy micro kit protocol, Qiagen). Cell sorting was performed for about 15 min and collected cells were immediately frozen on dry ice and kept in -80 °C for up to one week. For single cell transcriptomics, protoplasts were produced and isolated as described here, but sorted individually into 96-well plates.
Libraries were prepared using Illumina Nextera XT DNA preparation kit and either Nextera XT index kit – 96 indexes or Nextera XT index kit v2.

tag: reporter line

tag: possible cell type

value: PSE/MSE/procambium/columella

tag: developmental stage

value: protoplast of 5 day old root meristems


title: SLX_17313_i729_i517


title: SLX_17313_i729_i513


title: Roots, 7dpt, NaCl, B


title: Roots, 7dpt, Az39


title: H3K4me3_ChIP_16h_rep2

value: mature leaf


title: Roots, 7dpt, ipdc


title: SLX_17313_i729_i518


title: SLX_17313_i729_i521


title: SLX_17313_i729_i515


title: SLX_17313_i728_i521


title: SLX_17313_i729_i520


title: SLX_17313_i728_i518


title: H3K4me3_ChIP_4h_rep1


title: SLX_17313_i728_i515


title: SLX_17313_i728_i517


title: SLX_17313_i727_i521


title: SLX_17313_i727_i518


title: SLX_17313_i727_i516


title: SLX_17313_i728_i513


title: SLX_17313_i727_i522


title: SLX_17313_i728_i520


title: SLX_17313_i729_i522


title: SLX_17313_i727_i513


title: SLX_17313_i726_i518


title: SLX_17313_i729_i516


title: SLX_17313_i726_i521


title: SLX_17313_i727_i515


title: SLX_17313_i726_i522


title: SLX_17313_i724_i522


title: SLX_17313_i726_i516


title: SLX_17313_i728_i516


title: SLX_17313_i726_i513


title: SLX_17313_i724_i518


title: SLX_17313_i727_i520


title: SLX_17313_i724_i516


title: SLX_17313_i726_i515


title: SLX_17313_i724_i521


title: SLX_17313_i724_i520


title: SLX_17313_i724_i515


title: SLX_17313_i726_i517


title: SLX_17313_i724_i517


title: SLX_17313_i724_i513


title: SLX_17313_i727_i517


title: SLX_17313_i723_i522


title: SLX_17313_i726_i520


title: SLX_17313_i723_i521


title: SLX_17313_i723_i518


title: SLX_17313_i723_i517


title: SLX_17313_i723_i515


title: SLX_17313_i722_i522


title: SLX_17313_i723_i520


title: SLX_17313_i722_i521


title: SLX_17313_i723_i516


title: SLX_17313_i723_i513


title: SLX_17313_i722_i518


title: SLX_17313_i722_i513


title: SLX_17313_i722_i520


title: SLX_17313_i721_i520


title: SLX_17313_i722_i516


title: SLX_17313_i722_i517


title: SLX_17313_i721_i521


title: SLX_17313_i721_i518


title: SLX_17313_i722_i515


title: SLX_17313_i720_i521


title: SLX_17313_i721_i513


title: SLX_17313_i721_i516


title: SLX_17313_i721_i517


title: SLX_17313_i721_i515


title: SLX_17313_i720_i520


title: SLX_17313_i720_i517


title: SLX_17313_i720_i518


title: SLX_17313_i720_i522


title: SLX_17313_i720_i515


title: SLX_17313_i720_i516


title: SLX_17313_i720_i513


title: SLX_17313_i719_i522


title: SLX_17313_i719_i520


title: SLX_17313_i719_i521


title: SLX_17313_i719_i517


title: SLX_17313_i719_i518


title: SLX_17313_i719_i516


title: H3K27me3_ChIP_0h_rep1


title: SLX_17313_i718_i522


title: SLX_17313_i719_i513


title: SLX_17313_i719_i515


title: SLX_17313_i718_i521


title: SLX_17313_i718_i518


title: SLX_17313_i718_i520


title: H3K27me3_ChIP_4h_rep1


title: SLX_17313_i718_i513


title: SLX_17313_i716_i521


title: SLX_17313_i718_i515


title: SLX_17313_i716_i522


title: SLX_17313_i718_i517


title: SLX_17313_i716_i518


title: SLX_17313_i716_i517


title: SLX_17313_i716_i520


title: SLX_17313_i716_i515


title: SLX_17313_i715_i508


title: SLX_17313_i716_i513


title: SLX_17313_i715_i511


title: SLX_17313_i716_i516


title: SLX_17313_i715_i507


title: SLX_17313_i715_i505


title: SLX_17313_i715_i510


title: SLX_17313_i715_i506


title: SLX_17313_i715_i503


title: SLX_17313_i715_i502


title: SLX_17313_i718_i516


title: SLX_17313_i714_i508


title: SLX_17313_i714_i505


title: SLX_17313_i714_i502


title: SLX_17313_i714_i506


title: SLX_17313_i712_i511


title: SLX_17313_i714_i507


title: SLX_17313_i712_i510


title: SLX_17313_i714_i510


title: SLX_17313_i712_i507


title: SLX_17313_i712_i508


title: SLX_17313_i712_i506


title: SLX_17313_i712_i505


title: SLX_17313_i712_i503


title: SLX_17313_i712_i502


title: SLX_17313_i714_i511


title: SLX_17313_i711_i510


title: SLX_17313_i710_i511


title: SLX_17313_i711_i502


title: SLX_17313_i711_i505


title: SLX_17313_i711_i503


title: SLX_17313_i710_i510


title: SLX_17313_i711_i507


title: SLX_17313_i711_i508


title: SLX_17313_i710_i508


title: SLX_17313_i710_i506


title: SLX_17313_i711_i506


title: SLX_17313_i710_i507


title: SLX_17313_i714_i503


title: SLX_17313_i710_i505


title: SLX_17313_i710_i503


title: SLX_17313_i707_i506


title: SLX_17313_i707_i510


title: SLX_17313_i710_i502


title: SLX_17313_i707_i511


title: SLX_17313_i707_i505


title: SLX_17313_i711_i511


title: SLX_17313_i707_i508


title: SLX_17313_i707_i502


title: SLX_17313_i707_i503


title: SLX_17313_i706_i510


title: SLX_17313_i706_i508


title: SLX_17313_i706_i506


title: SLX_17313_i706_i507


title: SLX_17313_i705_i511


title: SLX_17313_i706_i502


title: SLX_17313_i705_i505


title: SLX_17313_i706_i505


title: SLX_17313_i705_i502


title: SLX_17313_i705_i510


title: SLX_17313_i706_i503


title: SLX_17313_i704_i508


title: SLX_17313_i705_i508


title: SLX_17313_i705_i506


title: SLX_17313_i705_i503


title: SLX_17313_i704_i507


title: SLX_17313_i707_i507


title: SLX_17313_i705_i507


title: SLX_17313_i704_i510


title: SLX_17313_i706_i511


title: SLX_17313_i704_i503


title: SLX_17313_i704_i502


title: SLX_17313_i703_i511


title: SLX_17313_i703_i510


title: SLX_17313_i703_i508


title: SLX_17313_i703_i506


title: SLX_17313_i703_i507


title: SLX_17313_i703_i503


title: SLX_17313_i702_i511


title: SLX_17313_i702_i510


title: SLX_17313_i702_i507


title: SLX_17313_i703_i502


title: SLX_17313_i702_i506


title: SLX_17313_i702_i505


title: SLX_17313_i701_i511


title: SLX_17313_i704_i506


title: SLX_17313_i701_i507


title: SLX_17313_i701_i506


title: SLX_17313_i701_i510


title: SLX_17313_i702_i508


title: SLX_17313_i701_i505


title: SLX_17313_i701_i502


title: SLX_17313_i702_i503


title: SLX_17312_i729_i522


title: SLX_17312_i729_i520


title: SLX_17313_i703_i505


title: SLX_17312_i729_i521


title: SLX_17313_i701_i503


title: SLX_17313_i704_i505


title: SLX_17312_i729_i518


title: SLX_17312_i729_i513


title: SLX_17312_i729_i516


title: SLX_17312_i729_i515


title: SLX_17313_i702_i502


title: SLX_17312_i728_i522


title: SLX_17312_i728_i521


title: SLX_17312_i728_i520


title: SLX_17312_i728_i518


title: SLX_17312_i728_i515


title: SLX_17312_i728_i516


title: SLX_17312_i727_i517


title: SLX_17312_i727_i516


title: SLX_17312_i728_i517


title: SLX_17312_i727_i515


title: SLX_17312_i727_i522


title: SLX_17312_i729_i517


title: SLX_17312_i726_i522


title: SLX_17312_i727_i513


title: SLX_17312_i727_i520


title: SLX_17312_i727_i521


title: SLX_17312_i726_i521


title: SLX_17312_i726_i520


title: SLX_17312_i726_i516


title: SLX_17312_i726_i517


title: SLX_17312_i726_i518


title: SLX_17312_i726_i515


title: SLX_17312_i724_i522


title: SLX_17312_i726_i513


title: SLX_17312_i724_i518


title: SLX_17312_i724_i517


title: SLX_17312_i728_i513


title: SLX_17312_i724_i520


title: SLX_17312_i727_i518


title: SLX_17312_i724_i513


title: SLX_17312_i723_i522


title: SLX_17312_i724_i516


title: SLX_17312_i723_i521


title: SLX_17312_i724_i515


title: SLX_17312_i723_i520


title: SLX_17312_i723_i517


title: SLX_17312_i723_i516


title: SLX_17312_i723_i515


title: SLX_17312_i723_i513


title: SLX_17312_i723_i518


title: SLX_17312_i722_i522


title: SLX_17313_i701_i508


title: SLX_17312_i722_i518


title: SLX_17312_i722_i516


title: SLX_17312_i722_i521


title: SLX_17312_i721_i521


title: SLX_17312_i722_i515


title: SLX_17312_i722_i513


title: SLX_17312_i721_i522


title: SLX_17312_i721_i520


title: SLX_17312_i721_i517


title: SLX_17312_i721_i515


title: SLX_17312_i721_i518


title: SLX_17312_i721_i516


title: SLX_17312_i720_i522


title: SLX_17312_i721_i513


title: SLX_17312_i720_i518


title: SLX_17312_i720_i517


title: SLX_17312_i720_i516


title: SLX_17312_i719_i521


title: SLX_17312_i720_i513


title: SLX_17312_i722_i520


title: SLX_17312_i719_i520


title: SLX_17312_i720_i515


title: SLX_17312_i719_i518


title: SLX_17312_i719_i517


title: SLX_17312_i722_i517


title: SLX_17312_i719_i516


title: SLX_17312_i719_i515


title: SLX_17312_i718_i521


title: SLX_17312_i719_i513


title: SLX_17312_i718_i516


title: SLX_17312_i718_i517


title: SLX_17312_i718_i518


title: SLX_17312_i720_i521


title: SLX_17312_i720_i520


title: SLX_17312_i716_i521


title: SLX_17312_i716_i520


title: SLX_17312_i718_i520


title: SLX_17312_i716_i518


title: SLX_17312_i718_i515


title: SLX_17312_i716_i513


title: SLX_17312_i718_i513


title: SLX_17312_i715_i511


title: SLX_17312_i716_i517


title: SLX_17312_i716_i522


title: SLX_17312_i715_i506


title: SLX_17312_i716_i516


title: SLX_17312_i715_i505


title: SLX_17312_i715_i507


title: SLX_17312_i715_i502


title: SLX_17312_i714_i511


title: SLX_17312_i714_i508


title: SLX_17312_i714_i507


title: SLX_17312_i714_i503


title: SLX_17312_i714_i506


title: SLX_17312_i714_i510


title: SLX_17312_i715_i503


title: SLX_17312_i718_i522


title: SLX_17312_i715_i508


title: SLX_17312_i714_i505


title: SLX_17312_i712_i508


title: SLX_17312_i712_i511


title: SLX_17312_i714_i502


title: SLX_17312_i712_i507


title: SLX_17312_i715_i510


title: SLX_17312_i716_i515


title: SLX_17312_i712_i505


title: SLX_17312_i712_i502


title: SLX_17312_i711_i508


title: SLX_17312_i711_i511


title: SLX_17312_i711_i507


title: SLX_17312_i712_i506


title: SLX_17312_i712_i503


title: SLX_17312_i710_i511


title: SLX_17312_i710_i510


title: SLX_17312_i711_i505


title: SLX_17312_i712_i510


title: SLX_17312_i711_i502


title: SLX_17312_i710_i508


title: SLX_17312_i724_i521


title: SLX_17312_i710_i507


title: SLX_17312_i707_i507


title: SLX_17312_i707_i511


title: SLX_17312_i710_i502


title: SLX_17312_i707_i510


title: SLX_17312_i710_i506


title: SLX_17312_i710_i503


title: SLX_17312_i707_i508


title: SLX_17312_i706_i508


title: SLX_17312_i706_i503


title: SLX_17312_i706_i510


title: SLX_17312_i707_i506


title: SLX_17312_i711_i506


title: SLX_17312_i707_i503


title: SLX_17312_i707_i505


title: SLX_17312_i707_i502


title: SLX_17312_i705_i505


title: SLX_17312_i704_i511


title: SLX_17312_i706_i507


title: SLX_17312_i710_i505


title: SLX_17312_i711_i503


title: SLX_17312_i706_i505


title: SLX_17312_i704_i507


title: SLX_17312_i706_i506


title: SLX_17312_i705_i508


title: SLX_17312_i706_i502


title: SLX_17312_i705_i510


title: SLX_17312_i705_i506


title: SLX_17312_i704_i508


title: SLX_17312_i704_i510


title: SLX_17312_i706_i511


title: SLX_17312_i705_i502


title: SLX_17312_i704_i505


title: SLX_17312_i705_i503


title: SLX_17312_i705_i507


title: SLX_17312_i704_i503


title: SLX_17312_i703_i511


title: SLX_17312_i705_i511


title: SLX_17312_i703_i508


title: SLX_17312_i703_i507


title: SLX_17312_i702_i510


title: SLX_17312_i702_i508


title: SLX_17312_i704_i502


title: SLX_17312_i703_i510


title: SLX_17312_i702_i505


title: SLX_17312_i703_i505


title: SLX_17312_i703_i506


title: SLX_17312_i702_i506


title: SLX_17312_i704_i506


title: SLX_17312_i703_i503


title: SLX_17312_i701_i502


title: SLX_17312_i701_i511


title: SLX_17312_i702_i503


title: SLX_17312_i702_i502


title: SLX_17312_i702_i507


title: SLX_17312_i701_i503


title: SLX_17312_i701_i505


title: SLX_17312_i701_i510


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title: SLX_14254_i710_i508


title: SLX_14254_i711_i505


title: SLX_14254_i712_i502


title: SLX_14254_i711_i503


title: SLX_14254_i710_i507


title: SLX_14254_i710_i517


title: SLX_14254_i711_i508


title: SLX_14254_i710_i506


title: SLX_14254_i710_i504


title: SLX_14254_i711_i502


title: SLX_14254_i710_i503


title: SLX_14254_i709_i508


title: SLX_14254_i710_i502


title: SLX_14254_i709_i517


title: SLX_14254_i709_i507


title: SLX_14254_i709_i505


title: SLX_14254_i711_i507


title: SLX_14254_i709_i504


title: SLX_14254_i709_i503


title: SLX_14254_i709_i506


title: SLX_14254_i711_i504


title: SLX_14254_i708_i507


title: SLX_14254_i709_i502


title: SLX_14254_i710_i505


title: SLX_14254_i708_i504


title: SLX_14254_i708_i508


title: SLX_14254_i708_i517


title: SLX_14254_i708_i505


title: SLX_14254_i707_i508


title: SLX_14254_i707_i504


title: SLX_14254_i707_i505


title: SLX_14254_i707_i507


title: SLX_14254_i708_i506


title: SLX_14254_i707_i503


title: SLX_14254_i707_i502


title: SLX_14254_i706_i508


title: SLX_14254_i708_i503


title: SLX_14254_i707_i517


title: SLX_14254_i707_i506


title: SLX_14254_i706_i506


title: SLX_14254_i706_i505


title: SLX_14254_i706_i504


title: SLX_14254_i706_i503


title: SLX_14254_i706_i502


title: SLX_14254_i705_i508


title: SLX_14254_i708_i502


title: SLX_14254_i705_i506


title: SLX_14254_i705_i507


title: SLX_14254_i705_i505


title: SLX_14254_i706_i517


title: SLX_14254_i706_i507


title: SLX_14254_i705_i504


title: SLX_14254_i704_i507


title: SLX_14254_i704_i506


title: SLX_14254_i704_i504


title: SLX_14254_i705_i503


title: SLX_14254_i704_i505


title: SLX_14254_i703_i505


title: SLX_14254_i705_i502


title: SLX_14254_i703_i504


title: SLX_14254_i703_i503


title: SLX_14254_i703_i502


title: SLX_14254_i704_i503


title: SLX_14254_i703_i507


title: SLX_14254_i703_i517


title: SLX_14254_i703_i508


title: SLX_14254_i705_i517


title: SLX_14254_i702_i505


title: SLX_14254_i702_i506


title: SLX_14254_i702_i507


title: SLX_14254_i702_i517


title: SLX_14254_i702_i504


title: SLX_14254_i702_i503


title: SLX_14254_i704_i517


title: SLX_14254_i702_i502


title: SLX_14254_i701_i508


title: SLX_14254_i703_i506


title: SLX_14254_i701_i506


title: SLX_14254_i701_i505


title: SLX_14254_i704_i508


title: SLX_14254_i704_i502


title: SLX_14254_i701_i507


title: SLX_14253_i712_i508


title: SLX_14253_i712_i517


title: SLX_14253_i712_i503


title: SLX_14253_i712_i502


title: SLX_14253_i712_i504


title: SLX_14253_i712_i507


title: SLX_14254_i701_i502


title: SLX_14253_i711_i517


title: SLX_14253_i712_i505


title: SLX_14254_i702_i508


title: SLX_14253_i711_i507


title: SLX_14253_i711_i505


title: SLX_14253_i710_i517


title: SLX_14253_i711_i503


title: SLX_14253_i710_i507


title: SLX_14253_i711_i502


title: SLX_14253_i710_i508


title: SLX_14253_i711_i506


title: SLX_14253_i710_i505


title: SLX_14253_i711_i504


title: SLX_14253_i710_i506


title: SLX_14253_i710_i504


title: SLX_14254_i701_i503


title: SLX_14253_i712_i506


title: SLX_14253_i710_i502


title: SLX_14253_i710_i503


title: SLX_14253_i709_i517


title: SLX_14253_i709_i508


title: SLX_14253_i709_i507


title: SLX_14253_i709_i505


title: SLX_14253_i711_i508


title: SLX_14253_i708_i517


title: SLX_14253_i709_i506


title: SLX_14253_i709_i504


title: SLX_14253_i709_i503


title: SLX_14253_i708_i508


title: SLX_14254_i701_i504


title: SLX_14253_i708_i506


title: SLX_14253_i708_i507


title: SLX_14253_i708_i505


title: SLX_14253_i708_i503


title: SLX_14253_i708_i504


title: SLX_14253_i707_i508


title: SLX_14253_i708_i502


title: SLX_14253_i707_i507


title: SLX_14253_i707_i506


title: SLX_14253_i707_i505


title: SLX_14253_i707_i517


title: SLX_14253_i707_i503


title: SLX_14253_i707_i504


title: SLX_14253_i706_i517


title: InVitro_4hr_HSC-3_PL

type: RNA

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

description: Gene expression after 24hr in Ato-C-treated K562 cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F-026652) for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37℃ GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The OSCC cell lines were incubated in a RPMI 1640 medium supplemented with 5% heat-inactivated fetal bovine serum. The cells were then treated with PL (5 μmol/L) for 4 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell

value: OSCC cell line

tag: gender

value: male

value: 4hr, PL, 5 umol/L


title: InVitro_4hr_SAS_None

description: Gene expression after 24hr in untreated K562 cells

source_name: SAS

value: female

value: 4hr, no treatment


title: InVitro_4hr_HSC-3_None

description: Gene expression after 24hr in CDDP-treated K562 cells


title: InVitro_4hr_SAS_PL

description: Gene expression after 24hr in ATO-treated K562 cells


title: SLX_14253_i707_i502


title: SLX_14253_i709_i502


title: SLX_14253_i706_i507


title: SLX_14253_i706_i506


title: SLX_14253_i706_i508


title: SLX_14253_i706_i505


title: 14D-Ctrl3

city: Heidelberg

first: Andreas

last: Fischer

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

data_processing:
base calling bcl2fastq 2.17.1.14
low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) with 90 percent of the read needing a quality phred score > 20.
Homertools 4.7 (Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432) were used for PolyA-tail trimming, and reads with a length < 17 were removed
Genomic mapping was performed with STAR 2.3 (Bioinformatics. 2013 Jan 1;29(1):15-21, STAR: ultrafast universal RNA-seq aligner, Dobin A1, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR)  for the filtered reads with mouse genome 38
The genes were counted with htseq-count version 0.6.0 of the sam file to gencode.vM8.annotation.gtf. Raw counts were translated to RPKM values by a  perl script.
Genome_build: Mouse Genome 38 (mm10)
Supplementary_files_format_and_content: Raw-count table and RPKM table for  14d-Keto, tab delimited (tsv) text file.

source_name: Heart

extract_protocol:
Cardiac endothelial cells were isolated using CD31 antibodies coupled to Dynabeads to separate cells through magnetic isolation. RNA was extracted using the RNAeasy mini kit (Qiagen). Libraries were prepared with an input of 10 ng RNA per sample using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara). Samples were sequenced on a HiSeq 2000 v4 system (Ilumina) with a depth of 50 base pairs in single-read mode.
SmarTer Ultra Low Input RNA and NEBNext ChIP-Seq

treatment_protocol: Mice were fed one of the following diets from Research Diets: D12359 or D17011501 for 14 days

tag: organ

value: heart

tag: cell type

value: endothelial cells

tag: diet

value: control


title: 14D-Ctrl1


title: 14D-Ctrl2


title: SLX_14253_i706_i504


title: SLX_14253_i706_i503


title: SLX_14253_i706_i502


title: 14D-Keto5

value: ketogenic


title: 14D-Keto1


title: 14D-Keto3


title: 14D-Keto2


title: SLX_14253_i705_i517


title: SLX_14253_i705_i507


title: 14D-Ctrl4


title: 14D-Ctrl5


title: SLX_14253_i705_i505


title: SLX_14253_i705_i502


title: SLX_14253_i705_i504


title: SLX_14253_i705_i503


title: SLX_14253_i704_i517


title: rtf2_rtf1-intronless_RTS1_ON_d

city: Brighton

first: Alice

last: Budden

address: Science Park Road

department: GDSC

institute: University of Sussex

data_processing:
Library strategy: Pu-Seq (Polymerase-usage Sequencing)
Reads mapped using Bowtie2
Polymerase usage determined as previously described (Keszthelyi et al., 2015)
Genome_build: Schizosaccharomyces pombe reference sequence (http://www.pombase.org/downloads/genome-datasets) with inserted replication fork barrier RTS1, 10xrDNA barrier as previously described (Naiman et al., 2021)
Supplementary_files_format_and_content: Two CSV files per sample containing read counts in 300 bp bins, one file for each strand

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe

growth_protocol: Cells were grown to mid log phase in YE media at 30C

extract_protocol:
As previously described (Keszthelyi et al., 2015)
As previously described (Keszthelyi et al., 2015)

tag: strain number

tag: genotype

value: II::RTS1-ura4-10xrRFB, RTS1{delta}::Phleo, rtf1{delta}int:HYG, rtf2{delta}::NAT, rnh201{delta}::KAN, cdc6L591G, ade6-704, leu1-32, ura4-d18


title: rtf2_RTS1_A-delete_ON_e

value: II::RTS1-A{delta}-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::kan, rtf2{delta}::NAT, cdc20_M630F, ade6-704, leu1-32, ura4-d18


title: rtf2_rtf1-intronless_RTS1_ON_e

value: II::RTS1-ura4-10xrRFB, RTS1{delta}::Phleo, rtf1{delta}int:HYG, rtf2{delta}::NAT, rnh201{delta}::KAN, cdc20M630F, ade6-704, leu1-32, ura4-d18


title: SLX_14253_i704_i508


title: rtf1-intronless_RTS1_ON_e

value: II::RTS1-ura4-10xrRFB, RTS1{delta}::Phleo, rtf1{delta}int:HYG, rnh201{delta}::KAN, cdc20M630F, ade6-704, leu1-32, ura4-d18


title: 14D-Keto4


title: SLX_14253_i704_i506


title: rtf2_RTS1_A-delete_ON_d

value: II::RTS1-A{delta}-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::kan, rtf2{delta}::NAT, cdc6L591G, ade6-704, leu1-32, ura4-d18


title: SLX_14253_i704_i507

value: protoplast of 5 day old root meristems


title: RTS1_A-delete_ON_e

value: II::RTS1-A{delta}-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::kan, cdc20M630F, ade6-704, leu1-32, ura4-d18


title: RTS1_A-delete_OFF_d

value: II::RTS1-A{delta}-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::kan, rtf1{delta}::HYG, cdc6L591G, ade6-704, leu1-32, ura4-d18


title: SLX_14253_i704_i505

value: PSE


title: RTS1_A-delete_ON_d

value: II::RTS1-A{delta}-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::kan, cdc6L591G, ade6-704, leu1-32, ura4-d18


title: rtf2_RTS1_ON_e

value: II::RTS1-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::KAN, rtf2{delta}::NAT, cdc20_M630F, ade6-704, leu1-32, ura4-d18


title: RTS1_A-delete_OFF_e

value: II::RTS1-A{delta}-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::kan, rtf1{delta}::HYG, cdc20M630F, ade6-704, leu1-32, ura4-d18


title: SLX_14253_i705_i508


title: SLX_14253_i704_i503


title: SLX_14253_i705_i506


title: SLX_14253_i704_i504


title: SLX_14253_i703_i517


title: WT_RTS1_OFF_d

value: II:RTS1-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::KAN, rtf1{delta}::HYG, cdc6L591G, ade6-704, leu1-32, ura4-d18


title: rtf1-intronless_RTS1_ON_d

value: II::RTS1-ura4-10xrRFB, RTS1{delta}::Phleo, rtf1{delta}int:HYG, rnh201{delta}::KAN, cdc6L591G, ade6-704, leu1-32, ura4-d18


title: SLX_14253_i703_i508


title: SLX_14253_i704_i502


title: WT_RTS1_OFF_e

value: II::RTS1-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::KAN, rtf1{delta}::HYG, cdc20M630F, ade6-704, leu1-32, ura4-d18


title: rtf2_RTS1_ON_d

value: II::RTS1-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::KAN, rtf2{delta}::NAT, cdc6L591G, ade6-704, leu1-32, ura4-d18


title: WT_RTS1_ON_d

value: II::RTS1-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::KAN, cdc6L591G, ade6-704, leu1-32, ura4-d18


title: WT_RTS1_ON_e

value: II::RTS1-ura4-10xrRFB, RTS1{delta}::Phleo, rnh201{delta}::KAN, cdc20M630F, ade6-704, leu1-32, ura4-d18


title: SLX_14253_i703_i506


title: SLX_14253_i703_i507


title: P_DDDY5

city: Guangzhou

first: shanshan

last: Zhuang

state: Guangdong

address: Guangzhou, Guangdong, 510225, China

department: College of Light Industry and Food

institute: Zhongkai College of Agriculture and Engineering

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: genes.read.txt

organism: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa was incubated in TSB at 37 C for 8 h. During the logarithmic phase, 200 μL of bacterial solution was added to 200 mL of liquid medium, 200 μL of sterile water (control group; P_CK), or 50 mg/mL of DDDY solution (treatment group; P_DDDY). The bacteria were then cultured on a shaking table at 150 R/min and 37 C for 24 h, centrifuged at 6000 R/min and 4 C for 10 min, washed with PBS three times, and then collected and stored at -80 C.

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The bacteria were then cultured on a shaking table at 150 R/min and 37 C for 24 h.

tag: strain

value: ATCC 9027

tag: agent

value: DDDY


title: SLX_14253_i703_i505


title: SLX_14253_i703_i504


title: P_DDDY4


title: SLX_14253_i703_i503


title: P_DDDY2


title: P_CK5

value: untreated


title: SLX_14253_i703_i502


title: P_DDDY3


title: SLX_14253_i702_i517


title: SLX_14253_i702_i508


title: P_CK4


title: SLX_14253_i702_i507


title: P_CK3


title: SLX_14253_i702_i506


title: P_CK2


title: P_CK1


title: SLX_14253_i702_i505


title: SLX_14253_i702_i504


title: SLX_14253_i702_i503


title: SLX_14253_i702_i502


title: SLX_14253_i701_i508


title: P_DDDY1


title: SLX_14253_i701_i507


title: SLX_14253_i701_i505


title: MiaPaCa-2 control repl-2

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

data_processing:
Base calling and generation of FASTQ files were performed using standard CASAVA pipeline
RNA-seq quality was checked by running FastQC, and TrimGalore was used for adapter and quality trimming. RNA-seq reads were mapped against hg38 using STAR (v 2.7.0e) aligner with default parameters.
Differential gene expression analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of normalized abundance measurements.

source_name: Pancreatic cancer cell line

growth_protocol: Cells were maintained in medium recommended by the supplier.

extract_protocol:
Total RNA was extracted using PureLink RNA isolation (Life Technologies, 12183025) and treated with DNase (Life Technologies, AM2222).
Strandspecific RNA-seq library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Ipswich, MA) according to the manufacturer's protocols.

treatment_protocol: Low glucose for 48 hours (2.5 mM glucose)

tag: cell line

tag: treatment

tag: supplier

value: ATCC


title: MiaPaCa-2 low glucose repl-3

value: low glucose


title: MiaPaCa-2 control repl-1


title: SLX_14253_i701_i506

value: protoplast of 5 day old root meristems


title: MiaPaCa-2 control repl-3


title: SLX_14253_i701_i504


title: SLX_14253_i701_i503


title: SLX_14253_i701_i502


title: SLX_14252_i712_i508


title: WT-NHS-Rep2

city: Beijing

first: Shipeng

last: Shao

state: Please Select

address: No.5 Yiheyuan Road Haidian District, Bei, jing,china

institute: Peking University

data_processing:
Library strategy: CUT&TAG
The paired-end reads were aligned to human genome build GRCh38/hg18 using Subread-align
The SEACR software was used for peak identification with data from IgG1 input as controls and default parameters
Homer (ver 4.10.0) ‘annotatePeaks’ and ‘find-MotifsGenome’ functions were used to annotate the called peaks and to find enriched motifs in these called peaks
Alignment files in the bam format were also transformed into read coverage files (bigwig format) using DeepTools
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

source_name: HeLa cells S6

growth_protocol: Human cancer cell line HeLa S6 was cultured in DMEM (Gibco) containing 10% FBS (Lifetech), 50 μg/mL penicillin and streptomycin (Lifetech). Cells were maintained at 37 °C in a humidified incubator with an atmosphere containing 5% CO2.

extract_protocol:
We performed the Cut&Tag experiments according to the manufacturer’s instructions (Vazyme, cat. no. TD901-TD902). HeLa Cells were harvested, counted, and centrifuged for 3 mins at 600g at RT. Aliquots of cells (about 100000 cells) were washed twice in 1.5 mL Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1×Protease inhibitor cocktail) by gentle pipetting. 10 μL of Concanavalin A beads (Bangs Laboratories) were activated and added to each sample. The mixture was rotated and incubated for 15 mins at RT. The supernatant was removed and bead-bound cells were resuspended in 50 μL Dig-wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1× Protease inhibitor cocktail, 0.05% Digitonin) containing 2 mM EDTA and a 1:50 dilution of primary antibodies. The incubation was rotated for 2 h at RT. Then primary antibodies were removed by pulling off all of the supernatants after placing the tube on the magnet stand. The second antibody (goat anti-Rabbit IgG) was diluted 1:50 in 50 μL of Dig-Wash buffer and incubated at RT for 30 mins. Cells were washed 3× for 5 mins in 800 μL Dig-Wash buffer to remove unbound antibodies. A 1:200 pG-Tn5 adapter complex (~0.04 μM) was prepared in Dig-300 Buffer (0.05% Digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1×Protease inhibitor cocktail) and added to cells. Then cells were rotated and incubated with transposase at RT for 1 h. Cells were washed 3× for 5 min in 800 μL Dig-300 Buffer to remove unbound pG-Tn5 protein. Next, cells were resuspended in 100 μL Tagmentation buffer (10 mM MgCl2 in Dig-300 Buffer) and incubated at 37 °C for 1 h. 10 μL of 0.5 M EDTA, 3 μL of 10% SDS and 2.5 μL of 20 mg/mL Proteinase K was added to the sample, which was incubated at 55 °C for 60 min to stop tagmentation. Then the total DNA was extracted using Phenol-chloroform-isoamyl alcohol 25:24:1 (Invitrogen, cat. no. 15593049).
To amplify libraries, 21 μL DNA was mixed with 2 μL of a uniquely barcoded i5 and an i7 primer, (Vazyme, cat. no. TD202) using a different barcode for each sample. A volume of 25 μL NEBNext HiFi 2×PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap-filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 4 °C. Post-PCR clean-up was performed by adding 1.1×volume of Ampure XP beads (Beckman Counter), and libraries were incubated with beads for 10 mins at RT, washed twice gently in 80% ethanol, and eluted in 23 μL 10mM Tris pH 8.0. The concentration of each sample was measured using Invitrogen Qubit 4. The size distribution of libraries was determined by fragment analysis capillary electrophoresis, using 2 μL sample following the manufacturer’s instructions. Run a bead selection to choose the DNA fragment size from 300 to 500 bp using Ampure XP beads. Then the library was pooled together with an equal molar and performed paired-end sequencing on a single lane of an Illumina NovaSeq system yielding 150-bp paired-end (PE150) reads.

treatment_protocol: One day before transfection, the cells were passaged into a 35-mm petri-dish at approximately 50% density. Transfection of cells was performed using Lipofectamine 3000 (Lifetech) in accordance with the manufacturer’s protocol. For Hex group, cells were treated with 1.5% 1,6-hexanediol for 60 mins during HS at 42 °C before lysed.

value: Cancer Cell Line HeLa S6

value: WT cells

tag: chip antibody

value: HSF1 primary antibodies (CST, D3L8I, Rabbit mAb #12972)


title: SLX_14252_i712_i506

value: PSE


title: WT-HS-Hex-Rep2

value: Heat shock at 42 C for 30 min and treated with 1.5% 1,6-hexanediol for 30 min


title: WT-HS-Hex-Rep1


title: Pol_II-NHS-Rep2

value: Recombinant Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody [EPR18855-87]-ChIP Grade (abcam, ab238146)


title: Pol_II-NHS-Rep1


title: WT-HS-Rep2

value: Heat shock at 42 C for 30 min


title: SLX_14252_i712_i505


title: WT-HS-Rep1


title: Pol_II-HS-Rep2


title: SLX_14252_i712_i504


title: M3-NHS_Rep2

value: HSF1 KO and transfected with HSF1 M3


title: WT-NHS-Rep1


title: M3-NHS_Rep1


title: SLX_14252_i712_i503


title: SLX_14252_i712_i502


title: SLX_14252_i711_i508


title: M3-HS_Rep1


title: SLX_14252_i711_i517


title: M1-NHS-Rep1

value: HSF1 KO and transfected with HSF1 M1


title: SLX_14252_i711_i507


title: M3-HS_Rep2


title: M1-NHS-Rep2


title: SLX_14252_i712_i507


title: SLX_14252_i712_i517


title: M1-NHS-Hex-Rep1

value: treated with 1.5% 1,6-hexanediol for 30 min


title: SLX_14252_i711_i505


title: SLX_14252_i711_i506


title: Pol_II-HS-Rep1


title: SLX_14252_i711_i503


title: SLX_14252_i711_i504


title: SLX_14252_i711_i502


title: SLX_14252_i710_i517


title: SLX_14252_i710_i508


title: CYCT1-HS-Rep2

value: Recombinant Anti-Cyclin T1 antibody [EPR17982] (abcam,ab184703)


title: CYCT1-HS-Rep1


title: BRD4-NHS-Rep2

value: Recombinant Anti-Brd4 antibody [EPR5150(2)] (abcam, ab128874)


title: BRD4-NHS-Rep1


title: SLX_14252_i710_i507


title: BRD4-HS-Rep2


title: SLX_14252_i710_i506


title: M1-NHS-Hex-Rep2


title: BRD4-HS-Rep1


title: SLX_14252_i710_i505


title: SLX_14252_i710_i504


title: SLX_14252_i710_i503


title: Nasal, Control-024-ND7

city: Cincinnati

first: Brian

middle: Michael

last: Varisco

address: 3333 Burnet Avenue, MLC 7006

department: Critical Care Medicine

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Specimens were sequenced, demultiplexed and each  aligned and counted using STAR.
Illumina Novaseq 6000
STAR Alignment to GRCh38
DESeq2
ToppGene
Genome_build: GRCh38
Supplementary_files_format_and_content: fastq

source_name: Nasal

extract_protocol:
Specimens stored in RNAProtect. 1:100 beta-mercaptoethanol added during thawing, cells extracted and RNA collected using QIAShredder and RNEasy columns.
RNA barcoded and amplified using NEBNext Low-Input RNA Kit.

tag: group

value: Control

tag: subgroup

tag: time

value: study day 7


title: Nasal, Control-023-ND14

value: study day 14


title: Nasal, Control-022-ND7

value: Control-developed ALI


title: Nasal, Control-024-ND1

value: study day 1


title: Nasal, Control-024-ND3

value: study day 3


title: SLX_14252_i709_i507

tag: reporter line

tag: possible cell type

tag: developmental stage

value: protoplast of 5 day old root meristems


title: SLX_14252_i709_i517


title: Nasal, Control-022-ND3


title: SLX_14252_i709_i508


title: Nasal, Control-022-ND1


title: CYCT1-NHS-Rep2

value: Cancer Cell Line HeLa S6

value: untreated

value: WT cells


title: SLX_14252_i710_i502

value: PSE


title: Nasal, Control-021-ND3


title: Nasal, Control-021-ND1


title: Nasal, Control-020-ND7


title: SLX_14252_i709_i502


title: SLX_14252_i709_i504


title: SLX_14252_i709_i506


title: SLX_14252_i709_i503


title: SLX_14252_i708_i508


title: SLX_14252_i708_i517


title: SLX_14252_i708_i507


title: Nasal, Control-019-ND7


title: Nasal, Control-020-ND1


title: Nasal, Control-019-ND3


title: SLX_14252_i708_i504


title: Nasal, Control-019-ND1


title: SLX_14252_i709_i505


title: Nasal, Control-018-ND3


title: SLX_14252_i708_i506


title: SLX_14252_i708_i505


title: SLX_14252_i707_i508


title: CYCT1-NHS-Rep1


title: Nasal, Control-018-ND7


title: Nasal, Control-020-ND3


title: SLX_14252_i708_i502


title: Nasal, Control-021-ND7


title: Nasal, Control-018-ND1


title: SLX_14252_i707_i517


title: Nasal, Control-017-ND7


title: Nasal, Control-020-ND14


title: SLX_14252_i707_i504


title: Nasal, Control-017-ND3


title: SLX_14252_i707_i503


title: SLX_14252_i707_i507


title: Nasal, Control-015-ND7


title: SLX_14252_i707_i506


title: Nasal, Control-017-ND1


title: SLX_14252_i707_i505


title: SLX_14252_i706_i517


title: SLX_14252_i706_i508


title: SLX_14252_i706_i506


title: SLX_14252_i706_i507


title: Nasal, Control-013-ND3


title: Nasal, Control-013-ND1


title: Nasal, Control-012-ND1


title: Pak1 +/+ cells #1

city: Tlalnepantla de Baz

first: Luis

middle: E.

last: Arias-Romero

email: larias@unam.mx, lear1607@hotmail.com

address: Av. de los Barrios #1

department: UBIMED

country: Mexico

institute: FES-Iztacala, UNAM

description: WT 1

hyb_protocol: To prepare the antibody microarray, it was blocked with blocking solution for 30 min at room temperature, rinsed with Milli-Q grade water, and dried with compressed nitrogen. Next, the array was incubated with the biotin-labeled proteins at 4°C overnight, the arrays were washed three times with 60 mL of wash solution, and the conjugated-labeled proteins were detected using Cy3-streptavidin.

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

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) and Grid: 026655_D_F_20100123). Mean Signals were quantile normalized.
Slides were scanned and interpreted by FullMoonBio. Data include 1) signal intensity for each sample, 2) average signal intensity for replicates, 3) ratio of WT vs. KO antibody signal.
Normalized data = Average Signal Intensity of Replicate Spots / Median Signal. Fold change = Treatment Sample / Control Sample. Ratio analysis = (Signal Intensity of Phospho Site-Specific Antibody) / (Signal Intensity of Site-Specific Antibody)

label: biotin

source_name: Pak1 +/+ cells #1

label_protocol: 100 μg of cell lysates were diluted in 50 μL of reaction mixture and labeled with biotin in 10 μg/μL N,N-dimethyformamide. The biotin-labeled proteins were diluted 1:20 in coupling solution before applying to the array for conjugation.

growth_protocol: Primary breast cancer cells derived from MMTV-Neu:Pak1+/+ and MMTV-Neu:Pak1−/− animals were maintained in low calcium medium supplemented with 5% horse serum.

extract_protocol: RIPA buffer supplemented with proteases and phosphatases inhibitors.

treatment_protocol: Serum starved by 3 hr and stimulated with EGF 15 min.

value: Primary breast cancer cells


title: Pak1 -/- cells #1

description: KO 1

source_name: Pak1 -/- cells #1


title: Pak1 -/- cells #2

description: KO 2

source_name: Pak1 -/- cells #2


title: Pak1 +/+ cells #2

description: WT 2

source_name: Pak1 +/+ cells #2


title: SLX_14252_i706_i504


title: WT48h rep3

city: Kunming

first: yang

last: le

address: No.2 of Cuihubeilu

institute: Yunnan university

description: Arthrobotrys oligospora

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome of Arthrobotrys oligospora from https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1 using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A FDR corrected p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by OmicShare tools (https://www.omicshare.com/tools), with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Genome_build: AOL24927 1.0
Supplementary_files_format_and_content: genes_rpkm_expression.txt: Tab-delimited text file includes RPKM values for each Sample.

organism: Orbilia oligospora

source_name: mixed A. oligospora and C. elegans sample

extract_protocol:
Mix samples, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: hyphae

tag: age

value: wild type


title: WT48h rep2

description: Arthrobotrys oligospora


title: WT48h rep1

description: Arthrobotrys oligospora


title: Nasal, Control-010-ND3

description: RNA-Only


title: SLX_14252_i706_i502


title: WT36h rep3

description: Arthrobotrys oligospora


title: SLX_14252_i707_i502


title: SLX_14252_i705_i517


title: SLX_14252_i705_i508


title: Nasal, Control-003-ND1


title: WT36h rep2

description: Arthrobotrys oligospora


title: Nasal, Control-009-ND14

description: RNA-Only


title: SLX_14252_i705_i506


title: SLX_14252_i706_i505


title: Nasal, Control-002-ND3

description: RNA-Only


title: SLX_14252_i705_i504


title: SLX_14252_i706_i503


title: Nasal, Control-002-ND1-NEB


title: SLX_14252_i705_i502


title: SLX_14252_i704_i504


title: Nasal, Control-001-ND1

description: RNA-Only

value: Control-developed PARDS


title: Nasal, CHOP-ARDS-006-ND7

value: PARDS

value: C


title: SLX_14252_i704_i508


title: WT12h rep3

description: Arthrobotrys oligospora


title: SLX_14252_i704_i503


title: SLX_14252_i704_i507


title: SLX_14252_i705_i507


title: Nasal, CHOP-ARDS-006-ND3

value: A


title: SLX_14252_i704_i502


title: SLX_14252_i705_i505


title: SLX_14252_i703_i517


title: Nasal, CHOP-ARDS-006-ND1


title: WT12h rep1

description: Arthrobotrys oligospora


title: WT12h rep2

description: Arthrobotrys oligospora


title: SLX_14252_i703_i508


title: WT24h rep3

description: Arthrobotrys oligospora


title: Nasal, CHOP-ARDS-005-ND3


title: SLX_14252_i703_i506


title: WT24h rep2

description: Arthrobotrys oligospora


title: SLX_14252_i703_i505


title: WT0h rep3

description: Arthrobotrys oligospora

value: 0 h


title: WT24h rep1

description: Arthrobotrys oligospora


title: Nasal, CHOP-ARDS-005-ND1


title: WT0h rep2

description: Arthrobotrys oligospora


title: SLX_14252_i703_i503


title: Nasal, CHOP-ARDS-004-ND14

value: study day 14


title: Nasal, CHOP-ARDS-004-ND1


title: SLX_14252_i703_i502


title: SLX_14252_i702_i508


title: WT0h rep1

description: Arthrobotrys oligospora


title: SLX_14252_i702_i517


title: SLX_14252_i702_i507


title: SLX_14252_i703_i507


title: SLX_14252_i702_i505


title: Nasal, CHOP-ARDS-002-ND7

value: study day 7


title: SLX_14252_i702_i503


title: SLX_14252_i702_i502


title: Nasal, CHOP-ARDS-002-ND3

value: B


title: SLX_14252_i703_i504


title: Nasal, CHOP-ARDS-002-ND1

value: study day 1


title: SLX_14252_i701_i508

value: protoplast of 5 day old root meristems


title: Nasal, CHOP-ARDS-001-ND7


title: SLX_14252_i701_i504


title: SLX_14252_i701_i505


title: Nasal, CHOP-ARDS-003-ND1


title: SLX_14252_i702_i506


title: Nasal, CHOP-ARDS-001-ND3

value: study day 3


title: SLX_14252_i701_i506


title: SLX_14252_i702_i504


title: SLX_14252_i701_i502


title: SLX_14252_i701_i503


title: Nasal, CHOP-ARDS-001-ND14


title: SLX_14251_i712_i517


title: THP-1 monocyte incubated with CF Proband's Mother Plasma, 5034.03 (mRNA)

city: Denver

first: Hara

last: Levy

state: CO

address: 1400 Jackson Street

department: Pediatrics

institute: National Jewish Health

description:
Gene expression data from THP-1 monocytes incubated with proband's mother serum
Sample name: 5034.03

hyb_protocol: The labeled samples were then hybridized onto two arrays: Human Clariom D array (ThermoFisher Scientific),  GeneChip miRNA 4.0 array (ThermoFisher Scientific) for 16hrs at 45C

scan_protocol: GeneChips were scanned using a 7G Affymetrix Genechip Scanner

data_processing: Profiling data was normalized in the robust multi-array average (RMA) procedure and then processed using Transcriptome Analysis Console (ThermoFisher Scientific, version 4)

label: Biotin

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix protocol from at least 300ng RNA

growth_protocol: THP-1 cells were maintained in RPMI 1640 medium supplemented with 10% FBS and 2 mmol/L L-glutamine. THP-1 monocytes were differentiated into macrophages by adding 200 nM PMA to the media for 48 hours.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) according to manufacturer's  protocol.

treatment_protocol: THP-1 monocytes and macrophages were co-cultured for 9 hours with plasma (without PMA) collected from the enrolled subjects and healthy controls

tag: disease state

value: no known disease

tag: cell type

value: THP-1 monocyte

value: incubated with proband's mother serum


title: THP-1 monocyte incubated with CF Proband's Mother Plasma, 5064.03 (mRNA)

description:
Gene expression data from THP-1 monocytes incubated with proband's mother serum
Sample name: 5064.03


title: Nasal, CHOP-ARDS-001-ND1

value: D


title: THP-1 monocyte incubated with CF Proband Plasma, 5059.01 (mRNA)

description:
Gene expression data from THP-1 monocytes incubated with proband serum
Sample name: 5059.01

value: classical CF

value: incubated with proband serum


title: SLX_14251_i712_i507

value: PSE


title: SLX_14252_i701_i507


title: THP-1 monocyte incubated with CF Proband Plasma, 5064.01 (mRNA)

description:
Gene expression data from THP-1 monocytes incubated with proband serum
Sample name: 5064.01


title: SLX_14251_i712_i508


title: SLX_14251_i712_i506


title: SLX_14251_i712_i504


title: Nasal, Bronch-003-N

value: Control


title: SLX_14251_i712_i503


title: Bronchial, Bronch-005-B

source_name: Bronchial

value: C


title: SLX_14251_i712_i502


title: Bronchial, Bronch-003-B

value: A


title: SLX_14251_i711_i517


title: SLX_14251_i711_i508


title: Nasal, Bronch-002-N


title: WT36h rep1

description: Arthrobotrys oligospora

value: hyphae

tag: genotype

value: wild type


title: SLX_14251_i712_i505


title: SLX_14251_i711_i507


title: Bronchial, Bronch-002-B


title: SLX_14251_i711_i506


title: Nasal, ARDS-033-ND7

value: PARDS

value: study day 7


title: AC and PVP-3

city: Hefei

first: manman

last: Wang

address: 103 Meishan Road

institute: Anhui University of Chinese Medicine

description: Mixed samples of seed embryo seedling roots, stems and leaves in medium supplemented with both AV and PVP

data_processing:
De novo transcriptome assemblies
Quantification for assembled transcripts
Functional annotation of transcripts
Sequence mapping and differential expression analysis
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample…

organism: Paeonia suffruticosa

source_name: Roots, stems and leaves mixed

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extractibn kit,which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry.
The library was sequenced using the Illumina NovaSeq 6000 sequencing platform (Paired end150) to generate raw reads

value: Roots, stems and leaves mixed

value: Tissue culture 30 days after rooting

value: AC and PVP


title: AC and PVP-1


title: AC and PVP-2


title: SLX_14251_i711_i505

value: protoplast of 5 day old root meristems


title: CK-3

description: mixed samples of seed embryo seedling roots, stems and leaves in medium without any anti-browning agent

value: CK


title: Nasal, ARDS-033-ND3

value: study day 3


title: PBMCs, Healthy Control, C6 (mRNA)

description:
Gene expression data from PBMCs
Sample name: C6

source_name: Healthy Control

value: healthy

value: +/+CFTR

value: Peripheral Blood Mononuclear cells (PBMCs)


title: PBMCs, Healthy Control, C8 (mRNA)

description:
Gene expression data from PBMCs
Sample name: C8


title: PBMCs, Mother of proband, 7102.03 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7102.03

source_name: Mother of proband

value: no known disease

value: -/+ CFTR


title: PBMCs, Healthy Control, C7 (mRNA)

description:
Gene expression data from PBMCs
Sample name: C7


title: PBMCs, CF proband, 7100.01 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7100.01

source_name: CF proband

value: classical CF

value: -/- CFTR


title: PBMCs, Mother of proband, 7098.03 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7098.03


title: PBMCs, CF proband, 7102.01 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7102.01


title: PBMCs, Mother of proband, 7100.03 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7100.03


title: SLX_14251_i711_i504

source_name: phloem root meristem

value: PSE


title: PBMCs, CF proband, 7098.01 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7098.01


title: CK-2


title: SLX_14251_i711_i502


title: PBMCs, Mother of proband, 7018.03 (mRNA)

description:
Gene expression data from PBMCs
Sample name: 7018.03


title: Nasal, ARDS-032-ND7

value: C


title: CK-1


title: Nasal, ARDS-033-ND1

value: PARDS

value: D

value: study day 1