title: 11_RNA-seq_Δcdc73_strain_hyphae_rep1

status: Public on Nov 30 2023

type: SRA

city: Chuncheon-si

first: Shinae

last: Park

address: Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

library_source: transcriptomic

data_processing:
The Illumina Hiseq generates raw images utilizing HCS(HiSeq Control Software v2.2) for system control
Base calling through an integrated primary analysis software called RTA(Real Time Analysis. v1.18)
The BCL(base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq(v1.8.4)
Adapters are not trimmed away from the reads.
bedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: CASC5314
Supplementary files format and content: bigwig

molecule: total RNA

organism: Candida albicans

growth_protocol: Cells are cultured at 10ml YPD (1% Yeast extract, 2% Peptone, 2% Glucose) in 100ml flask (30℃, 230rpm) and harvested at OD600=1.0

extract_protocol:
RNA was harvested according to the MN RNA-isolation kit(MN;#7409555) standard protocols. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina(NEB #E7420S) 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: Hyphae induction was performed using YPD with 10% FBS under 37 ℃.

tag: tissue

value: hyphae

tag: genotype


title: 10_RNA-seq_Δleo1_strain_hyphae_rep2


title: 7_RNA-seq_Δctr9_strain_hyphae_rep1


title: 6_RNA-seq_SC5314_WT_strain_hyphae_rep2

source_name: wild-type

value: wild-type


title: 8_RNA-seq_Δctr9_strain_hyphae_rep2


title: 9_RNA-seq_Δleo1_strain_hyphae_rep1


title: 5_RNA-seq_SC5314_WT_strain_hyphae_rep1


title: 4_RNA-seq_Δctr9_strain_yeast_rep2

tag: cell type

value: yeast cells


title: 12_RNA-seq_Δcdc73_strain_hyphae_rep2


title: 3_RNA-seq_Δctr9_strain_yeast_rep1


title: 2_RNA-seq_SC5314_WT_strain_yeast_rep2


title: 1_RNA-seq_SC5314_WT_strain_yeast_rep1


title: hTERT RPE-1 pA-DamID gatc counts for Dam only control replicate r7

city: Amsterdam

first: Ruben

last: Schep

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

library_source: genomic

data_processing:
The full protocol is described in Van Schaik 2022; the constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts; remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17; reads overlapping GATC fragments were counted per GATC coordinate.
Assembly: hg38
Supplementary files format and content: tsv table of the read counts per 'gatc' coordinate
Library strategy: pA-DamID

molecule: genomic DNA

organism: Homo sapiens

source_name: retina

extract_protocol:
1 million permeabilized cells were processed with pA-DamID (van Schaik, 2020) with a primary antibody and for a Dam control condition, to specifically deposit m6A marks at chromatin nearby the primary antibody. Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit; 2.
The full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at m6A-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified and further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters

value: retina

tag: cell line

value: hTERT RPE-1

value: cell line

tag: treatment


title: hTERT RPE-1 pA-DamID gatc counts for H3K9me2 replicate r7


title: hTERT RPE-1 pA-DamID gatc counts for H3K9me3 replicate r5


title: hTERT RPE-1 pA-DamID gatc counts for H3K9me2 replicate r6


title: hTERT RPE-1 pA-DamID gatc counts for Dam only control replicate r4


title: hTERT RPE-1 pA-DamID gatc counts for H3K9me3 replicate r8

description:
pADamID-RPE_CT_r8_H3K9me3
These processed files for R8 & R9 originate from three sequencing runs of the same library, two on a NovaSeq 6000 and one, the largest, on a HiSeq 2500, reads were concatenated in the processing, sepatare raw sequencing files available on SRA


title: hTERT RPE-1 pA-DamID gatc counts for H3K9me2 replicate r9

description:
pADamID-RPE_CT_r9_H3K9me2
These processed files for R8 & R9 originate from three sequencing runs of the same library, two on a NovaSeq 6000 and one, the largest, on a HiSeq 2500, reads were concatenated in the processing, sepatare raw sequencing files available on SRA


title: hTERT RPE-1 pA-DamID gatc counts for Dam only control replicate r5


title: hTERT RPE-1 pA-DamID gatc counts for H3K9me3 replicate r4


title: hTERT RPE-1 pA-DamID gatc counts for H3K9me3 replicate r7


title: hTERT RPE-1 pA-DamID gatc counts for H3K27me3 replicate r9

description:
pADamID-RPE_CT_r9_H3K27me3
These processed files for R8 & R9 originate from three sequencing runs of the same library, two on a NovaSeq 6000 and one, the largest, on a HiSeq 2500, reads were concatenated in the processing, sepatare raw sequencing files available on SRA


title: hTERT RPE-1 pA-DamID gatc counts for H3K9me3 replicate r9

description:
pADamID-RPE_CT_r9_H3K9me3
These processed files for R8 & R9 originate from three sequencing runs of the same library, two on a NovaSeq 6000 and one, the largest, on a HiSeq 2500, reads were concatenated in the processing, sepatare raw sequencing files available on SRA


title: hTERT RPE-1 pA-DamID gatc counts for H3K9me2 replicate r8

description:
pADamID-RPE_CT_r8_H3K9me2
These processed files for R8 & R9 originate from three sequencing runs of the same library, two on a NovaSeq 6000 and one, the largest, on a HiSeq 2500, reads were concatenated in the processing, sepatare raw sequencing files available on SRA


title: hTERT RPE-1 pA-DamID gatc counts for H3K27me3 replicate r4


title: hTERT RPE-1 pA-DamID gatc counts for H3K27me3 replicate r8

description:
pADamID-RPE_CT_r8_H3K27me3
These processed files for R8 & R9 originate from three sequencing runs of the same library, two on a NovaSeq 6000 and one, the largest, on a HiSeq 2500, reads were concatenated in the processing, sepatare raw sequencing files available on SRA


title: hTERT RPE-1 pA-DamID gatc counts for Dam only control replicate r9

description:
pADamID-RPE_CT_r9_Dam
These processed files for R8 & R9 originate from three sequencing runs of the same library, two on a NovaSeq 6000 and one, the largest, on a HiSeq 2500, reads were concatenated in the processing, sepatare raw sequencing files available on SRA


title: Hi-C_Hae3_Alu1, replicate 1

city: Philadelphia

first: Yuanqing

last: Feng

state: Pennsylvania

address: 430 Clinical Research Building, 415 Curie Boulevard

department: Genetics

country: USA

institute: University of Pennsylvania

description: Hae3 and Alu1 digestion

data_processing:
Hi-C and H3K27ac HiChIP data analyses were performed using a customized pipeline. The pair-end reads from Hi-C and HiChIP were first transformed into chromatin interaction matrix (.cool and .mcool files). Briefly, the 150bp pair-end reads were merged using FLASH v1.2.11 with settings (-m 25 -M 150 -t 8 -p 33), then and all merged or unmerged reads were spited into pairs by the linker sequence. Paired fragments were filtered using fastp V0.20.1 with parameter “--thread 3 --disable_adapter_trimming --disable_quality_filtering --length_required 20”, and the filtered paired reads were mapped to hg38 genome using BWA V0.7.17 with options (-5SP -p). Then mapped reads were selected using SAM Flag “-F 2316” and processed by “bedtools (v2.29.2,) bamtobed -bedpe -i {input.bam} |awk '{if ($0 !~ /chrEBV|random|chrUn_/) print $0}'” to make bedpe files from interleaved paired-bam file. Next, the bedpe files were first processed by awk command “awk '{print $7, $1, int(($2+$3)/2), $4, int(($5+$6)/2), $9, $10, "UU"}' OFS="\t" ”, and then were transformed into 4D Nucleome (4DN) pairs format using pairtools (v1.01) sort and dedup. The pair files were indexed using pairix and transformed into cool/mcool files using cooler. The resolutions of mcool files are: 1000,2000,5000,10000,50000,100000,500000. For HiC but not Hi-ChIP data, option “--balance” were used to normalize the raw matrix.
For Hi-C data, compartments were called using cooltools (v0.5.1) call-compartments at 100kb resolution. Insulation scores were called using 4DN scripts with 100kb sliding window at 5kb resolution (python get_insulation_scores_and_boundaries.py --binsize 5000 --window 100000 --bweak 0.2 --bstrong 0.5 --cutoff 2 --pixels_frac 0.66). Nested TADs were called using OnTAD (v1.4)  at 5kb resolution with default settings. Loops were called using cooltools call-dots  (binsize 5kb), mustache (v1.0.1)  (-r 5kb -st 0.8 -pt 0.1 and -r 2kb -st 0.7 -pt 0.1), and cLoops (v0.93) (-w -j -s -plot -eps 2500,5000 -minPts 20,40 -hic).
For HiChIP data, loops were called using cLoops (v0.93)  with parameters (-w -j -s -plot -eps 5000,7500,10000 -minPts 15,20 -hic), and FitHiChIP (v10.0) with 2.5kb bin size and peak_to_all models. Loops, TADs and interaction matrix were visualized in UCSC browser or using R “plotgardener” (v1.2.10).
Assembly: hg38
Supplementary files format and content: hic

growth_protocol: MNT-1 cells (ATCC, #CRL- 3450), a gift from Dr. Michael S. Marks at Children’s Hospital of Philadelphia Research Institute, were grown in DMEM (Gibco, #11965084) supplemented with 20% Fetal Bovine Serum (FBS), 1% GlutaMAX (Gibco, #35050061), 1% NEAA (Gibco, #10370021),1% penicillin/streptomycin (Gibco, #15140122), and 10% AIM-V (Gibco, # 12055-091). WM88 cells, a melanocytic patient-derived melanoma tumor cell line, a gift from Dr. Ashani Weeraratna at Wistar Institute, were cultured in Tumor Specialized medium (80% MCDB153, 20% Leibovitz’s L-15, supplemented with 2% fetal bovine serum (FBS) and 1.68 mM CaCl2).

extract_protocol:
To lyse cell pellet, we prepared 2 ml of ice-cold Hi-C lysis buffer (10 mM Tris·Cl, pH 8.0, 10 mM NaCl, 0.2% Igepal) with protease inhibitors. The cross-linked cells (10M) were resuspended with 1 ml of Hi-C lysis buffer. The cell lysis was incubated on ice for 20 min with rotation at 4°C and then centrifuged at 1500g for 3 min at 4 °C to discard supernatant. The pellet was washed once with 0.5 ml ice-cold Hi-C lysis buffer. The pellet was resuspended with 250 μL 0.5% SDS and incubated for 7 min at 62 °C. 725 μL of water and 125 μL of 10% Triton X-100 was added to quench the SDS. The mix was incubated at 37°C for 5 min and then was spun down at 1500g for 3 min at room temperature to discard supernatant. The pellet was washed once with 1ml 1× PBS (0.1% Tritonx-100) and transferred to a new tube. Then, 500 μL 1× CutSmart (0.1% Tritonx-100) with 200U Hae3 (10M cells) was added, and the chromatin was digested at least 4hr at 37 °C with rotation. The mix was span down at 1000g for 3 min at 4 °C to discard supernatant. To fill in restriction fragment overhangs and mark DNA ends with biotin, 400 μL of Klenow (3`-5`exo-) solution (40 μL NEB buffer2, 8 μL 10 mM dATP, 40 μL 10% TritonX-100, 308 μL H2O, and 4 μL Klenow (3`-5`exo-, 5U/μL, NEB M0212L) was added to the digested chromatin and incubated at 37°C for 1hr with rotation. The mix was centrifuged at 1000g for 3 min at 4 °C to discard supernatant. The pellet was washed once with 1ml 1× PBS (0.5% Tritonx-100) and once with 200 μL 1× T4 DNA ligase buffer. The pellet was resuspended with 1200μL of proximity ligation solution (946 μL H2O, 120 μL T4 DNA ligase buffer, 120 μL 10% TritonX-100, 8 μL T4 DNA ligase (400U/μL, NEB M0202L), 6 μL 20 mg/ml BSA, 4 μL Bridge linker (100 ng/μL)). The mix was rotated at room temperature for 4hr or 4 °C overnight.  Here, we saved ¼ of the ligation products for HiC and the remaining ¾ for H3K27ac HiChIP (see below). To remove open-DNA and linkers, ligation products were centrifuged at 1000g for 3 min at 4 °C to discard supernatant. Then, 700 μL Exonuclease mix (70 μL 10×lambda cut buffer, 3 μL lambda exonuclease (5U/μL, NEB M0262S), 3 μL exonuclease I (20U/μL, NEB M0293S), 624 μL H2O, 3.5 μL 10% Tritonx-100) was added and rotated at 37 °C for 1hr. The mix was centrifuged at 1000g for 3 min at 4 °C to discard supernatant. The pellet was washed once with 1ml 1× PBS (0.1% Tritonx-100). To remove protein and purify DNA, the pellet was resuspended in 500 μL 1×Protease lysis buffer (10mM Tris·HCl (pH 8), 100mM NaCl, 25mM EDTA, 0.5%SDS, 0.2mg/ml protease K). The sample was incubated for 5-10h at 65 °C. The mix was centrifuged at 12,000g for 5 min at RT and supernatant was saved into a new tube. Then, 2×volume 100% ethanol was added to the supernatant and placed at -20°C for 10 mins. The mix was centrifuged at 12,000g for 10 min at 4°C to pellet the DNA. The DNA pellet was washed with 70% ethanol and spun down at 12,000g for 10 min at 4°C. The DNA pellet was dissolved in 140 μL 10 mM Tris-HCl (pH 8) buffer and incubated at 65°C for 5 min. Then, the solution was centrifuged at 12,000g for 5 min to remove melanin. To make biotinylated DNA suitable for high-throughput sequencing, DNA was sheared to 300-400 bp with a Covaris M220 (Use 20ug DNA in a 130 μL Covaris microtube. Peak incident power 50; duty factor 20%; cycle per burst 200; time: 65 seconds). To capture biotinylated DNA fragments, 30μL Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602) was washed once with 500 μL 1×TWB (5 mM Tris-HCl pH 7.5, 1M NaCl, 0.5 mM EDTA, 0.05% Tween20), once with 500 μL 1× binding and washing buffer (B&W, 10 mM Tris-HCl pH 7.5, 2 M NaCl, 1 mM EDTA), and then the beads were resuspended using 200 μL 2× B&W and added to the 200 μL biotinylated DNA. The mix was incubated for 30min at RT with rotation. Beads were separated magnet and the supernatant was discarded. Beads were washed 2 times with 600 μL 2×SSC/0.5% SDS, once with 600 μL of 1X TWB and transferred to a new tube. The beads were heated on a Thermomixer at 55°C for 2 min with mixing, and then resuspended with 50 μL 5 mM Tris (pH 8) and transferred to a new PCR tube.To enrich H3K27ac mediated interactions, sonicated chromatin was centrifuged at 12,000g for 15 min at 4°C and supernatant was transferred to a new tube. Then, 10μL of protein G beads (10M cells) were added to the chromatin and incubated for 1 hour at 4°C with rotation. Beads were separated on a magnetic stand and supernatant was transferred to a new tube. Then, 7.5 μg of H3K27ac antibody (Abcam, ab4729) was added to the tube and incubated 2 hours at 4°C on a rotator. Then, 50μL of protein G beads (10M cells) was added to the sample and incubated for 2 hours at 4°C on a rotator. Beads was collected using a magnetic stand and washed 3 times with 1 mL of high salt buffer (pH 8.0, 20mM Tris, 500mM NaCl, 1mM EDTA, 1mM EGTA, 1% TX-100, 0.1% sodium deoxycholate, 0.1% SDS); 3 times with 1 mL of LiCl wash buffer (pH 8.0, 20 mM Tris, 1mM EDTA, 250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 0.1% SDS); once with 1 mL of TE salt buffer (pH 8.0, 10 mM Tris, 1 mM EDTA, 50 mM NaCl). Beads were resuspended in 100μL of elution buffer (50 mM Tris, 10 mM EDTA, 1% SDS) and incubated at 65°C for 15 minutes to elute. Then, 1 μL of 33 mg/mL RNase A was added to the elution and incubated at 37°C for 30min. Then, 5 μL of 20 mg/mL proteinase K was added to the mix and incubated at 55°C for 30 minutes. Samples were then incubated at 65°C for 5 hours to reverse cross-links. DNA was then purified using Zymo ChIP columns (Zymo, D5102) according to manufacturer’s protocol and eluted in 30 μL water. The amount of eluted DNA was quantified by the Qubit kit. To prepare the ChIP DNA for sequencing, the eluted DNA was transferred to a 55 μL sonication tube and sheared to a size of 250-350 bp using Covaris M220 with the following parameters: peak incident power 75; duty factor 10%; cycle per burst 200; Time: 110 seconds). Then, 20 μL Dynabeads MyOne Streptavidin T1 beads (Life technologies, #65602) was added to 200 μL sonicated ChIP DNA and incubated for 20 mins at room temperature with rotation. Beads were collected on a magnet and washed 3 times with 600 μL 2×SSC/0.5% SDS and transferred to a new tube. Then, beads were washed with 600 μL of 1X TWB and the mixture was transferred to a new tube. Beads were heated on a Thermomixer at 55°C for 2 min. The beads were transferred to a new tube and washed 3 times with 600 μL 1×TE. Beads were washed once with 600 μL 5mM Tris (PH 8.0) and resuspended with 50 μL 5 mM Tris, pH 8.0.
DNA library preparation was performed on-beads using NEBNext Ultra™ II DNA Library Prep Kit (NEB, E7545S). Hi-C libraries were amplified by KAPA HiFi HotStart ReadyMix (Roche, 07145446001) for 8 cycles. Libraries were purified with AMPure beads (250-500bp) and sequenced on an Illumina HiSeq2000 with 150 bp paired-end reads.

treatment_protocol: MNT-1 were cultured under recommended conditions to around 80% confluence. Adherent cells were detached with trypsin, counted, and collected by centrifugation for 5 min at 300g, room temperature. Cells were resuspended in fresh medium at 1 M cells per 1 mL medium. 16% formaldehyde solution was added to a final concentration of 1% (v/v) and the mix was incubated at room temperature for 10 min on a tube roller. Then 2.5 M glycine was added to a final concentration of 0.2 M to quench the formaldehyde. The mix was incubated at room temperature for 5 min on a tube roller, and then centrifuged for 5 min at 300g, 4°C. The cell pellet was resuspended in 1 ml of cold PBS and spin for 5 min at 300g, 4°C. The supernatant was discarded, and cell pellets were store at -80°C.

value: melanoma cells

tag: antibody

tag: time


title: HiChIP_Hae3, replicate 1

description: Hae3 digestion

data_processing:
Hi-C and H3K27ac HiChIP data analyses were performed using a customized pipeline. The pair-end reads from Hi-C and HiChIP were first transformed into chromatin interaction matrix (.cool and .mcool files). Briefly, the 150bp pair-end reads were merged using FLASH v1.2.11 with settings (-m 25 -M 150 -t 8 -p 33), then and all merged or unmerged reads were spited into pairs by the linker sequence. Paired fragments were filtered using fastp V0.20.1 with parameter “--thread 3 --disable_adapter_trimming --disable_quality_filtering --length_required 20”, and the filtered paired reads were mapped to hg38 genome using BWA V0.7.17 with options (-5SP -p). Then mapped reads were selected using SAM Flag “-F 2316” and processed by “bedtools (v2.29.2,) bamtobed -bedpe -i {input.bam} |awk '{if ($0 !~ /chrEBV|random|chrUn_/) print $0}'” to make bedpe files from interleaved paired-bam file. Next, the bedpe files were first processed by awk command “awk '{print $7, $1, int(($2+$3)/2), $4, int(($5+$6)/2), $9, $10, "UU"}' OFS="\t" ”, and then were transformed into 4D Nucleome (4DN) pairs format using pairtools (v1.01) sort and dedup. The pair files were indexed using pairix and transformed into cool/mcool files using cooler. The resolutions of mcool files are: 1000,2000,5000,10000,50000,100000,500000. For HiC but not Hi-ChIP data, option “--balance” were used to normalize the raw matrix.
For Hi-C data, compartments were called using cooltools (v0.5.1) call-compartments at 100kb resolution. Insulation scores were called using 4DN scripts with 100kb sliding window at 5kb resolution (python get_insulation_scores_and_boundaries.py --binsize 5000 --window 100000 --bweak 0.2 --bstrong 0.5 --cutoff 2 --pixels_frac 0.66). Nested TADs were called using OnTAD (v1.4)  at 5kb resolution with default settings. Loops were called using cooltools call-dots  (binsize 5kb), mustache (v1.0.1)  (-r 5kb -st 0.8 -pt 0.1 and -r 2kb -st 0.7 -pt 0.1), and cLoops (v0.93) (-w -j -s -plot -eps 2500,5000 -minPts 20,40 -hic).
For HiChIP data, loops were called using cLoops (v0.93)  with parameters (-w -j -s -plot -eps 5000,7500,10000 -minPts 15,20 -hic), and FitHiChIP (v10.0) with 2.5kb bin size and peak_to_all models. Loops, TADs and interaction matrix were visualized in UCSC browser or using R “plotgardener” (v1.2.10).
Assembly: hg38
Supplementary files format and content: hic
Library strategy: HiChIP

value: H3K27Ac (abcam, # ab4729)


title: Hi-C_Hae3, replicate 2

description: Hae3 digestion


title: HiChIP_Hae3_Alu1, replicate 1

description: Hae3 and Alu1 digestion


title: HiChIP_Hae3_Alu1, replicate 2

description: Hae3 and Alu1 digestion


title: HiChIP_Hae3, replicate 2

description: Hae3 digestion


title: Hi-C_Hae3_Alu1, replicate 2

description: Hae3 and Alu1 digestion


title: hTERT RPE-1 pA-DamID gatc counts for Dam only control replicate r8

description:
pADamID-RPE_CT_r8_Dam
These processed files for R8 & R9 originate from three sequencing runs of the same library, two on a NovaSeq 6000 and one, the largest, on a HiSeq 2500, reads were concatenated in the processing, sepatare raw sequencing files available on SRA


title: exosomes derived from human bone marrow mesenchymal stem cells that were exposed to oxaliplatin 2

city: Zhengzhou

first: Wei

last: Shen

state: Henan

address: 127 Dongming Road

department: Department of Medical Oncology

country: China

institute: The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital

data_processing:
MiRDeep2 was used to identity known mature miRNAs based on miRBase21 (www.mirBase.org) and to predict novel miRNAs. Expression data were were normalized in Reads Per Million (RPM).
The identification of differentially expressed miRNAs was performed using the DESeq2 package within R software, employing the default parameters.
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: Bone marrow

extract_protocol:
Total RNA was extracted utilizing a RNeasy mini kit (Qiagen, Duesseldorf, Germany). The mRNA concentration and quality were subsequently assessed by a Qubit 3.0 fluorometer (Life Technologies, Gaithersburg, USA) and a Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., Waltham, USA), respectively. The integrity of the total RNA was evaluated using an Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, USA), and only samples with RNA integrity number (RIN) values exceeding 7.0 were selected for subsequent experiments.
For the cDNA library construction, approximately 1 μg of total RNA was used, following the manufacturer's instructions for the TruSeq Small RNA sample prep kits (Illumina, San Diego, USA). The procedure encompassed ligation of the RNA to 3ʹ adapters, and the attachment of 5′ adapters to the other end of the RNA molecules. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified using a low number of cycles. Post-PCR amplification, the libraries were pooled and purified via a PAGE gel.

value: exosomes

value: hBM-MSCs

value: oxaliplatin


title: exosomes derived from human bone marrow mesenchymal stem cells that were exposed to oxaliplatin 3


title: hTERT RPE-1 pA-DamID gatc counts for H3K27me3 replicate r5


title: exosomes derived from human bone marrow mesenchymal stem cells 3

value: control


title: exosomes derived from human bone marrow mesenchymal stem cells 1


title: exosomes derived from human bone marrow mesenchymal stem cells that were exposed to oxaliplatin 1


title: Healthy donor 7 CD8+ CAR T cells (mixed) (day 14) [Sample_Healthy_Donor-Redo_mix_CD8]

city: Seattle

first: Brian

last: Till

state: WA

address: 1100 Fairview Ave N, D3-100

institute: Fred Hutchinson Cancer Center

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequenced reads were aligned to iGenome's UCSC hg38 using STAR2 aligner v2.7.1a (samples 1-12) or v2.5.2a (samples 13-24).
Subread featureCounts was used with GENCODE v31 (samples 1-12) or UCSC's refFlat converted to gtf (samples 13-24) annotations to generate gene-level raw counts
Assembly: hg38
Supplementary files format and content: tab-delimited file containing raw gene counts per sample

source_name: T cells

growth_protocol: Day 0 stimulation with anti-CD3/28 beads, day 1 transduction with anti-CD20 lentivirus (1.5.3-NQ-28-BB-z), day 4 magnetic bead removal, day 8 harvest (for day 8 samples), or day 7 restimulation with CD20+ LCL line and then harvest at day 14-15 (for day 14 samples)

extract_protocol:
Total RNA was isolated from FACS-sorted CD8+ CAR T cells using the Qiagen RNeasy kit. Total RNA integrity was assessed using an Agilent 4200 TapeStation (Agilent) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences). RNA-seq libraries were prepared from total RNA using the TruSeq RNA Exome library prep kits (Illumina) (day 8 samples) or SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) and the Nextera XT DNA Library Preparation Kit (Illumina) (day 14 samples). Library size distribution was validated using an Agilent 4200 TapeStation. Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using a Qubit 2.0 Fluorometer (Life Technologies-Invitrogen).
RNA-seq libraries for samples 1 through 12 were prepared from total RNA using the TruSeq RNA Exome library prep kits (Illumina, Inc., San Diego, CA, USA) following the manufacturer's protocols. RNA-seq libraries for samples 13 through 24 were prepared from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, Inc., Mountain View, CA, USA) and the Nextera XT DNA Library Preparation Kit (Illumina, Inc., San Diego, CA, USA) following the manufacturer's protocols.

treatment_protocol: RNA-seq data from CD8+ CAR T cells sorted after culture either in isolation or in co-culture with CD4+ CAR T cells

value: T cells

value: CD8+ T cells

value: CAR+

value: Day 14 post stimulation


title: Hi-C_Hae3, replicate 1

description: Hae3 digestion


title: Healthy donor 7 CD8+ CAR T cells (separate) (day 14) [Sample_Healthy_Donor-Redo_sep_CD8]


title: Healthy donor 5 CD8+ CAR T cells (mixed) (day 14) [Sample_Healthy_Donor-2_mix_CD8]


title: Healthy donor 5 CD8+ CAR T cells (separate) (day 14) [Sample_Healthy_Donor-2_sep_CD8]


title: exosomes derived from human bone marrow mesenchymal stem cells 2


title: Healthy donor 4 CD8+ CAR T cells (mixed) (day 14) [Sample_23857_mix_CD8]


title: Healthy donor 2 CD8+ CAR T cells (separate) (day 14) [Sample_22871_sep_CD8_R1_001.190404]


title: Healthy donor 2 CD8+ CAR T cells (mixed) (day 14) [Sample_22871_mix_CD8_R1_001.190404]


title: Healthy donor 4 CD8+ CAR T cells (separate) (day 14) [Sample_23857_sep_CD8]


title: hTERT RPE-1 pA-DamID gatc counts for Dam only control replicate r6


title: Healthy donor 3 CD8+ CAR T cells (separate) (day 8) [Sample_HD1_Sep_CD8]

value: Day 8 post stimulation


title: Lymphoma patient 3 CD8+ CAR T cells (mixed) (day 14) [Sample_2154-S02_mix_CD8]


title: Healthy donor 4 CD8+ CAR T cells (mixed) (day 8) [Sample_HD2_Mix_CD8]


title: Healthy donor 2 CD8+ CAR T cells (mixed) (day 8) [Sample_22871_Mix_CD8_R1.191228]


title: Healthy donor 3 CD8+ CAR T cells (mixed) (day 8) [Sample_HD1_Mix_CD8]


title: Healthy donor 1 CD8+ CAR T cells (separate) (day 8) [Sample_22526_Sep_CD8]


title: Healthy donor 2 CD8+ CAR T cells (separate) (day 8) [Sample_22871_Sep_CD8_R1.191228]


title: Healthy donor 1 CD8+ CAR T cells (mixed) (day 8) [Sample_22526_Mix_CD8]


title: Healthy donor 6 CD8+ CAR T cells (mixed) (day 14) [Sample_Healthy_Donor-4_mix_CD8]


title: Healthy donor 4 CD8+ CAR T cells (separate) (day 8) [Sample_HD2_Sep_CD8]


title: Lymphoma patient 2 CD8+ CAR T cells (separate) (day 8) [Sample_2154-S03_Sep_CD8]


title: Lymphoma patient 3 CD8+ CAR T cells (separate) (day 14) [Sample_2154-S02_sep_CD8]


title: Lymphoma patient 1 CD8+ CAR T cells (separate) (day 8) [Sample_1191-SD_Sep_CD8]


title: siTAZ3

city: Durham

first: KUO

last: DU

state: NC

address: 905 SOUTH LASALLE STREET, Room 1063

department: Medicine

institute: Duke Universty

data_processing:
Trim_galore trim off adapter and low quality reads
STAR aligning the reads (STAR/2.5.0c-fasrc01)
Samtools index sorted bam files
Picard remove duplicates
HTSeq quantify Gene Expression Data
Assembly: mm10_STAR_genome_idx
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

growth_protocol: LX2 hepatic stellate cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were transfected with siRNA using Lipofectamine® RNAiMAX Reagent (Thermofisher). Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the medium was refleshed every three days.
RNA was harvested using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: To investigate how YAP and TAZ affect the HSC biology, we treated the cells with either non-targeting siRNA, or siRNA targeting YAP or TAZ  (20nM, Horizon) for 7 days.

value: Liver

value: TAZ knockdown

value: Hepatic stellate cells

value: TAZ-targeting siRNAs


title: Lymphoma patient 2 CD8+ CAR T cells (mixed) (day 8) [Sample_2154-S03_Mix_CD8]


title: Healthy donor 6 CD8+ CAR T cells (separate) (day 14) [Sample_Healthy_Donor-4_sep_CD8]


title: siYAP3

value: YAP knockdown

value: YAP-targeting siRNAs


title: Lymphoma patient 1 CD8+ CAR T cells (mixed) (day 8)   [Sample_1191-SD_Mix_CD8]


title: siYAP1


title: GC, rep3

city: JiangSu

first: An

last: Fangmei

address: NO. 299, QingYang Road, Wuxi, Jiangsu

institute: Wuxi Public Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the human reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPM/COUNT values for each Sample

source_name: gastric mucosa

extract_protocol:
Total RNA was isolated by using Trizol (Invitrogen,USA).
The quantity and integrity of RNA yield was assessed by using the Qubit®2.0 (Life Technologies, USA) and Agilent 2200 TapeStation (Agilent Technologies, USA) separately. 1µg total RNA of each samples were used to prepare small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB,USA) according to manufacturer’sinstructions. The libraries were sequenced by HiSeq 2500 (Illumina,USA) with single-end 50bp at Ribobio Co. Ltd (Ribobio,China).

value: gastric mucosa

tag: disease state

value: Gastric Cancer


title: siNT1

value: WT

value: Non-targeting siRNAs


title: GC, rep2


title: siNT2


title: siYAP2


title: siNT3


title: Dys, rep2

value: Dysplasia


title: Dys, rep3


title: Dys, rep1


title: CSG, rep3

value: Chronic Superficial Gastritis


title: siTAZ2


title: CAG, rep3

value: Chronic Atrophic Gastritis + Intestinal Metaplasia


title: PKD1+/+ 1383D2-derived ureteric bud tip cells Rep2

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for HiSeq output.
Sequence reads were trimmed for adaptor sequence using Fastp v0.20.0
Trimmed sequence reads were mapped to hg38 using Hisat2 v2.1.0
Gene count was performed using FeatureCounts 1.6.5 in Subread package.
Assembly: hg38

source_name: Kidney

growth_protocol: Ureteric bud organoids derived from human iPS cells were dissociated into single cells and sedded onto soft hydrogel. After 1-week-treatment of 6 factors (GDNF, FGF1, CHIR99021, TTNPB, Thiazovivin, A83-01), these cells formed ureteric bud tip cell colonies. These colonies were passaged once a week and cultured for additional 5 weeks.

extract_protocol:
Total RNA was isolated using an RNeasy kit (Qiagen) according to the manufacturer’s recommendations.
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit following manufacturer's protocols.

value: Kidney

value: 1383D2-iPS cell

value: renal progenitor cells

value: PKD1 WT

value: Human iPS cell-derived ureteric bud tip cells that were cultured for 6 weeks.


title: PKD1-/- 1383D2-derived ureteric bud tip cells Rep3

value: PKD1 KO


title: siTAZ1

value: Liver

value: TAZ knockdown

value: Hepatic stellate cells


title: CAG, rep1


title: PKD1+/+ 1383D2-derived ureteric bud tip cells Rep3


title: PKD1-/- 1383D2-derived ureteric bud tip cells Rep1


title: PKD1+/+ 1383D2-derived ureteric bud tip cells Rep1


title: DDBM182

city: Lille

first: David

last: Blum

state: Cedex

address: 1 place de Verdun

department: Lille Neurosience & Cognition

country: France

institute: Inserm

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using STAR 2.5.3a.
Quantification : Gene expression was quantified using HTSeq v0.6.1p1 (union mode) and Ensembl release 94 annotations.
Differential gene expression analysis were performed using DESeq2 version 1.16.1 with Wald test and Benjamin and Hochberg correction for multiple testing.
Assembly: mm10
Supplementary files format and content: Excel file containing raw read counts in each sample and results of differential expression analysis.

organism: Mus musculus

source_name: Hippocampus (brain)

extract_protocol:
Total RNA was extracted from hippocampi and purified using the RNeasy Lipid Tissue Mini Kit (Qiagen, France).
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Hippocampus (brain)


title: DDBM176


title: DDBM181


title: DDBM179


title: CAG, rep2

value: gastric mucosa


title: DDBM173


title: DDBM172


title: DDBM168


title: DDBM170


title: CSG, rep2


title: PKD1-/- 1383D2-derived ureteric bud tip cells Rep2


title: CSG, rep1


title: DDBM166


title: DDBM164


title: DDBM162


title: DDBM160


title: DDBM161


title: DDBM169


title: DDBM178


title: DDBM152

value: APP/PS1 A2A


title: DDBM155


title: adult liver, scRNAseq

city: Hangzhou

first: Mingshan

last: Zhou

state: Zhejiang

address: No. 600 Dunyu Road Sandun Town

institute: Westlake University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequenced reads were aligned to mouse reference genome GRCm38 using CellRanger package (v6.1.1), and further analysis was done by R package Seurat (v.4.0.0) with customized parameters.
Assembly: mm10
Supplementary files format and content: wt_liver.rdata: Seurat object rdata file.

source_name: liver

extract_protocol:
Mouse primary hepatocytes were isolated by the two-step collagenase perfusion method, which was modified from a previous protocol (Charni-Natan and Goldstein, 2020). Briefly, mice were anesthetized with pentobarbital intraperitoneal (80 mg/kg body weight). The abdomen was then incised, and the liver is exposed with inferior vena cava and portal vein. The portal vein was cut and the liver was perfused with perfusion buffer (containing 0.5 mM EGTA) for 5-10 minutes followed by digestion buffer containing type I collagenase (Invitrogen) for about 10 minutes. The liver was then taken out and transferred into a petri dish filled with RPMI 1640 medium containing 2% FBS at 4°C. The liver was then torn gently to help the hepatocytes dissociation, and the cell suspension was filtered through a 70 μm cell strainer (BD Falcon), followed by centrifugation at 50 x g for 2 minutes at 4°C. Cells were in Percoll/RPMI 1640/10 x PBS (1:1:0.1) mixture and centrifuged at 300 x g for 5 min at 4°C. Purified hepatocytes were collected for single-cell RNA sequencing.
cDNA library construction was performed using Single Cell 3′ Library Kit (v3.1 chemistry, 10x Genomics). Sequencing was performed on an Illumina HiSeq4000 platform (Illumina, one lane, 150 PE).

value: liver

value: hepatocyte

tag: age

value: 8 weeks


title: DDBM153


title: liver，MCDDRUG2，week5

city: Nanjing

first: Hang

last: Chu

address: No.24, Tongjiaxiang

institute: China Pharmacuetical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads   containing sequencing adapter
Removing reads whose low-quality base ratio (base   quality less than or equal to 5) is more than 20%
Removing reads whose unknown   base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored   in FASTQ format. The clean reads were mapped to the reference genome using HISAT2   (v2.0.4)
Bowtie2 (v2.2.5) [3] was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
The heatmap was drawn by pheatmap (v1.0.8) [5] according to the gene expression in different samples.
Supplementary files format and content: tab-delimited text files include TPM, FPKM values for each Sample

extract_protocol:
otal RNA was isolated from mice fed either with vehicle or QZTGT using extracted with RNA-easy Isolation Reagent (Vazyme)
RNA libraries for RNA-seq were prepared using Vazyme Kit following manufacturer's protocols.

tag: diet

value: MCDDRUG

value: WT

tag: time point

value: Week 5


title: liver，MCDDRUG3，week5


title: liver，MCDDRUG5，week5

value: Week 6


title: liver，MCD7，week5

value: MCD


title: liver，MCD1，week5


title: liver，CHOW2，week5

value: CHOW


title: liver，CHOW1，week5


title: liver，CHOW5，week5


title: DDBM154


title: GFP in vitro R2

city: Chapel Hill

first: Mark

last: Woodcock

address: 170 Manning Drive

institute: University of North Carolina at Chapel Hill

data_processing:
Alignment: STAR (v.2.7.6a)
Quantification: Salmon (v.1.4.0)
QA: FastQC (v0.11.9)
QA: Picard (v2.22.4) CollectRnaSeqMetrics
Assembly: Ensembl release 99, GRCh38
Supplementary files format and content: Salmon count data

source_name: In vitro

growth_protocol: Buffy coats from healthy volunteer blood donors were purchased from the Gulf Coast Regional Blood Center (Houston, Texas, USA). Peripheral blood mononuclear cells (PBMCs) were isolated by Lymphoprep (Accurate Chemical and Scientific Corporation) density gradient centrifugation. NKTs were purified from PBMCs as previously described. NKTs were transduced in retronectin coated plates on day 5 and further expanded for 10 days in the presence of IL-2 and then used for functional assays.

extract_protocol:
Total RNA was extracted from NKTs using the Rneasy Plus Mini kit (Qiagen) per manufacturers instructions.
Messenger RNA libraries were prepared (TruSeq Stranded mRNA LibraryPrep, Illumina) and sequenced on the Illumina HiSeq4000 platform (UNC High-Throughput Sequencing Facility) using paired-end 100-bp reads, with 44 million reads on average (range, 1.5-149 million).

treatment_protocol: All retroviral vectors were generated using the SFG backbone. The sequence of the p40 and p35 subunits of IL-12 were obtained from the NCBI website (NM_002187.2 and NM_000882.2 respectively) and were linked together with a flexible linker described from Anderson R. et al. through overlapping PCR. The whole IL-12 cassette was cloned into the SFG retroviral vector containing the IRES and GFP or ∆NGFR. As control the vector SFG containing the IRES and GFP or ∆NGFR only was used. The GD2.CAR, CSPG4.CAR and CD19.CAR were previously described. IL-12 was then cloned in the CAR cassettes separated by the IRES element (GD2.CAR(I)IL12, CSPG4.CAR(I)IL12 and CD19.CAR(I)IL12). The sequence of CD62L (SELL) was obtained from NCBI (NM_000655) and made by gene synthesis (Genewiz, Azenta Life Sciences) and cloned in the SFG vector containing the IRES and the ∆NGFR as selection marker. The sequence of CD1d (CD1D) was obtained from NCBI (NM_001766.3) and made by gene synthesis (Genewiz, Azenta Life Sciences) and cloned in the SFG vector. To generate the membrane-bound IL-12 we added the CD8α stalk with the mutations C164S and C181S to prevent dimerization with the CAR. Retroviral supernatants were prepared by transient transfection of 293T cells.

value: In vitro

value: Human NKT

value: GFP transduced


title: GFP in vitro R3


title: Control-3

city: beijing

first: lei

last: zhang

address: xueyuan road 38th

department: heath science center

institute: peking university

data_processing:
We used the extract tool in UMI-tools v0.5.4 to extract and add the 8-bp barcode sequence and UMIs to the read name of sequencing read pairs. Subsequently, we trimmed the template switch oligo sequence and poly-A tail sequence in read1 and removed adapter contamination and low-quality bases using costumed script and seqtk tool v1.0. We then aligned the clean reads to GRCh38 human reference genome using STAR v2.6.0a, followed by the addition of genomic features to the reads using FeatureCounts from Subread v1.6.2 to count the number of reads uniquely aligned with each gene. We then used the count tool in UMI-tools to remove PCR duplicates based on the barcode and UMI information.
Assembly: GRCh38
Supplementary files format and content: comma-delimited csv file includes raw counts for each cell

source_name: lumbar disc herniation

growth_protocol: Collagenase-treated ligament chips were washed with DMEM and placed in a 25-cm2 cell culture flask containing DMEM supplemented with 10% fetal bovine serum (Gibco), 100 U/mL penicillin, and 100 pg/mL streptomycin, followed by incubation at 37°C in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol:
After isolation, a single cell was suspended in a lysis buffer using a mouth pipette. Reverse transcription was performed using a 25-nt oligo(dT) primer anchored with an 8-nt cell-specific barcode and 8-nt unique molecular identifiers (UMIs). The 3ʹ-terminals of the amplified cDNAs were purified using Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific).
Libraries were constructed using the KAPA Hyper Prep Kit (KAPA Biosystems)

value: lumbar disc herniation

value: Mesenchymal cells

value: non-OPLL

value: Primary culture


title: Control-2


title: Control-4


title: T-OPLL-4

source_name: Thoracic PLL specimens

value: Thoracic PLL specimens

value: OPLL


title: GC, rep1

value: gastric mucosa

value: Gastric Cancer


title: T-OPLL-3


title: T-OPLL-5


title: T-OPLL-6


title: T-OPLL-2


title: T-OPLL-1


title: IL12(I)GFP in vitro R1

value: IL12 + GFP transduced


title: P-S7 control replicate 3

city: Lubbock

first: Mauricio

last: Ulloa

state: Texas

address: 3810 4th Street

department: PA, CSRL

institute: USDA-ARS

description: FOV4 susceptible genotype

data_processing:
We first performed quality assessment of the resulting reads from the Illumina platform using FastQC (version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and processed sequencing libraries using Trimmomatic (version 0.39;) to remove adapter read sequences.
We then quantified gene expression using the pseudo-alignment RNA-seq quantification program kallisto version 0.46.1.
We then integrated transcript-level abundances from kallisto tocount-based statistical analysis in edgeR (version 3.13) to produce the table of read counts per locus.
Assembly: TheG. barbadense P-S6 genome release was used as a reference genome to align the reads(https://doi.org/10.1186/s12864-022-09102-6)
Supplementary files format and content: The table of counts is a tab-separated plaint text file (.txt) which contains the counts per million reads corresponding to each locus per library (rows), and each RNA-seq library sample (columns) is named according to genotype, condition and biological replicate (for example SJ2_ctl1 would be Acala SJ2-control conditions-replicate 1; rkn means root-knot nematode infested).

organism: Gossypium barbadense

source_name: Root tissue (18 days-old plants)

growth_protocol: Cotton plants were grown in a Greenhouse in pots with soil. Air temperatures in the greenhouse were maintained between 280 C and 350 C during the day and 240 C at night.

extract_protocol:
The root samples from each genotype were grounded in liquid nitrogen, and total RNA was isolated three biological replicates following the manufacturer’s instructions using Spectrum TM Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA). The yield and purity of RNA were analyzed with a ND-1000 Spectrophotometer (Nano Drop Technology, Wilmington, DE, USA). Only RNA samples with 1.8 - 2.2 ratio of absorbance 260/280 nm were used for analysis.
For each genotype, 2 mg of RNA from each of the three biological-replicates used for cDNA library preparation. The cDNA libraries were prepared following the TruSeq RNA Sample Preparation v2 low sample (LS) protocol guide (Illumina Inc., San Diego, CA USA)

treatment_protocol: Two treatments control (ctl) and FOV4 infected  (FOV4) plants.  To produce inoculum, the isolate was grown in 9-cm-diameter Petri dishes containing 20 ml potato dextrose agar (PDA) with 3 mM streptomycin per liter at room temperature for 1 week. Then a few patches of 2-3-mm-squre of fresh grown culture were cut and put into 500 ml flasks containing potato dextrose liquid medium with 3 mM streptomycin at 28 oC with rotation for 3-4 days.  The conidial suspension was then filtered through eight layers of cheesecloth to remove hyphae, quantified with the aid of a hemacytometer, and diluted with water to obtain 1 x 106 conidia per ml. Cultivars or genotypes were germinated in seedling trays for one week and then seedlings were uprooted. Roots were rinsed with tap water and immediately dipped for 3 min into an aqueous suspension of FOV4 inoculum containing 1 x 106 conidia per ml. The non-inoculated control plants were processed the same way except they were dipped into water without FOV4. Seedlings were then transplanted into steam-sterilized U.C. Mix #2 (Baker, 1957) soil in new pots with five plants in each pot and placed in a warm greenhouse maintained between 24-28 degrees Celcius. At 11 days after inoculation (dai), the plant and soil ball were removed from the pots, and the soil removed gently from roots by washing under continuous water flow. The washed roots were placed immediately in 50ml screw-top plastic vials, liquid nitrogen was added, and the vials placed in a -80 C freezer with the tops off to allow vaporization of the liquid N.

value: Control (ctl)


title: P3-79 control replicate 3

description: FOV4 susceptible genotype

value: Pima 3-79


title: GFP in vitro R1


title: P-S7 FOV4 replicate 3

description: FOV4 susceptible genotype

value: FOV4 infected (FOV4)


title: liver，MCD2，week5

value: liver

value: MCD

value: WT

value: Week 5


title: P3-79 replicate 3

description: FOV4 susceptible genotype


title: IL12(I)GFP in vitro R3

value: In vitro

value: Human NKT


title: IL12(I)GFP in vitro R2


title: Control-1

value: lumbar disc herniation

value: Mesenchymal cells


title: m6A meRIP spa134 dark replicate 2

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
The adapter sequence of m6A meRIP raw reads were trimmed by trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The trimmed reads were aligned to the TAIR10 reference genome with Bowtie2 (Langmead and Salzberg, 2012) (v2.1.0) with default settings. meRIP track files in BigWig format were generated using bamCoverage of deeptools (v3.1.3) with RPKM normalization (Ramirez et al., 2016) from de-duplicated reads of Samtools (Li et al., 2009). m6A peaks were called by MACS2 (v2.1.1) and annotated using ChIPseeker (Yu et al., 2015; Zhang et al., 2008). Differential peaks were called with a threshold of p-value < 0.05 and Fold Change > 1.5. m6A data metaplots were plotted by deeptools (v2.5.1) (Ramirez et al., 2014).
Assembly: TAIR10
Supplementary files format and content: bigwig: meRIP intensity.
Supplementary files format and content: *RPKM.txt: signal intensity of m6A peaks
Library strategy: meRIP-Seq

organism: Arabidopsis thaliana

growth_protocol: A light-emitting diode was used to generate monochromatic blue light (peak 450 nm; half-bandwidth of 20 nm) and cool white fluorescent tubeswere used for white light. The Arabidopsis seedlings used in these experiments were grown in either a growth chamber (Conviron, model no. E7/2) or growth room at 21 °C under different light regimes.

extract_protocol:
TRAP of polysomes was performed as described previously (Mustroph et al., 2009). Briefly, 1 mL of pulverized tissue was added to a 15 mL tube containing 5 mL of polysome extraction buffer (PEB: 200 mM Tris, pH 9.0, 200 mM KCl, 25 mM EGTA, 35 mM MgCl2, 1% PTE, 1 mM DTT, 1 mM PMSF, 100 μg/mL cycloheximide, 50 μg/mL chloramphenicol) and 1% detergent mix [20% (w/v) polyoxyethylene(23), 20% (v/v) Triton X-100, 20% (v/v) Octylphenyl-polyethylene glycol, 20% (v/v) Polyoxyethylene sorbitan monolaurate 20] and incubated until thawed on ice, before homogenized with a glass homogenizer. The homogenized mixture was incubated on ice for ten minutes before being centrifuged at 16,000g at 4 degrees Celsius for fifteen minutes. After centrifugation, the supernatant was transferred to a fresh tube and filtered through sterile Miracloth (Millipore) to create an extract that had been clarified. 10% of the total cleared extract was preserved to be used as an input for isolating RNA. Anti-FLAG M2 Protein beads (1.5 mL) that were pre-washed twice with wash buffer [WB; 200 mM Tris (pH 9.0), 200 mM KCl, 25 mM EGTA, 35 mM MgCl2, 1 mM DTT, 1 mM PMSF, 100 g/mL cycloheximide, 50 g/mL chloramphenicol] were added to the clar The binding of ribosome-mRNA complexes with a FLAG epitope tag was achieved by incubating them at 4°C for two hours while gently shaking the tubes. Remove the supernatant and carefully resuspend the beads in 6 mL WB for 2 minutes at 4°C while rocking. This procedure was performed twice more before the beads were resuspended in 1 mL WB. The beads were washed twice more with 1 mL WB, and then the supernatant was extracted. Added 300μL of WB with 200ng/μL of FLAG3 peptide and 20U/μL RNase inhibitor (Cat. # N8080119 Themo Fisher) and incubated for 30 mins at 4°C with shaking. Centrifuged and collected the supernatant for RNA purification. For meRIP, WT and mutant seedlings grown in the dark or in blue light (30 μmol m−2 s−1) for 6 days were used for m6A-seq.Total RNA was isolated using Direct-zol RNA Miniprep Kits (Zymo, Cat no. R2052). MeRIP-seq was performed as described previously (Wang et al., 2021).The libraries from two biological repeats for each sample were sequenced on Illumina Novaseq6000 instruments in pair-end mode with 100 bp per reads.
The RNA was used for preparation of RNA-seq libraries with TruSeq RNA library prep kit (Illumina). The libraries from 3 biological repeats for each sample were sequenced on the Illumina HiSeq 2500 sequencing systems.

tag: chip antibody

value: EpiMark m6A antibody

value: spa134 mutant

tag: ecotype

value: dark


title: input for m6A meRIP spa134 blue light replicate 2

value: none (input)

value: blue light


title: input for m6A meRIP spa134 blue light replicate 1


title: input for m6A meRIP spa134 dark replicate 1


title: P-S6 control replicate 3

description: FOV4 resistant genotype


title: input for m6A meRIP spa134 dark replicate 2


title: input for m6A meRIP mta dark replicate 2

data_processing:
Cleaned reads of Ribo-tag and input samples were aligned to the TAIR10 reference genome with Bowtie2 (v2.1.0) (Langmead and Salzberg, 2012). Translation efficiency abundance was measured by RSEM using the default parameters (Li and Dewey, 2011).Translation efficiency was estimated with (RPKM in Ribotag +1)/ (RPKM in input +1). Differential translation efficiency analysis was conducted using edgeR (Robinson et al., 2010)with a threshold of p-value < 0.05 and Fold Change > 1.5 was used to determine whether there were any significant differences in translation efficiency between samples.
The adapter sequence of m6A meRIP raw reads were trimmed by trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The trimmed reads were aligned to the TAIR10 reference genome with Bowtie2 (Langmead and Salzberg, 2012) (v2.1.0) with default settings. meRIP track files in BigWig format were generated using bamCoverage of deeptools (v3.1.3) with RPKM normalization (Ramirez et al., 2016) from de-duplicated reads of Samtools (Li et al., 2009). m6A peaks were called by MACS2 (v2.1.1) and annotated using ChIPseeker (Yu et al., 2015; Zhang et al., 2008). Differential peaks were called with a threshold of p-value < 0.05 and Fold Change > 1.5. m6A data metaplots were plotted by deeptools (v2.5.1) (Ramirez et al., 2014).
Assembly: TAIR10
Supplementary files format and content: bigwig: meRIP intensity.
Supplementary files format and content: *RPKM.txt: signal intensity of m6A peaks
Supplementary files format and content: *results: gene expression level
Library strategy: meRIP-Seq

value: mta mutant


title: input for m6A meRIP fio1 blue light replicate 2

value: fio1 mutant


title: input for m6A meRIP fio1 dark replicate 1


title: input for m6A meRIP mta dark replicate 1


title: m6A meRIP spa134 blue light replicate 1


title: input for m6A meRIP fio1 dark replicate 2


title: input for m6A meRIP cry1cry2 blue light replicate 2

value: cry1cry2 mutant


title: input for m6A meRIP mta blue light replicate 1


title: input for m6A meRIP Col dark replicate 2


title: input for m6A meRIP cry1cry2 dark replicate 2


title: input for m6A meRIP cry1cry2 blue light replicate 1


title: input for m6A meRIP mta blue light replicate 2


title: input for m6A meRIP Col blue light replicate 2


title: input for m6A meRIP Col dark replicate 1


title: input for m6A meRIP cry1cry2 dark replicate 1


title: m6A meRIP mta blue light replicate 1


title: m6A meRIP mta dark replicate 1


title: m6A meRIP mta blue light replicate 2


title: m6A meRIP fio1 blue light replicate 1


title: m6A meRIP mta dark replicate 2


title: m6A meRIP fio1 dark replicate 1


title: m6A meRIP spa134 blue light replicate 2


title: m6A meRIP fio1 blue light replicate 2


title: input for m6A meRIP Col blue light replicate 1


title: m6A meRIP fio1 dark replicate 2


title: P-S6 FOV4 replicate 3

description: FOV4 resistant genotype

value: FOV4 infected (FOV4)


title: m6A meRIP spa134 dark replicate 1


title: input for m6A meRIP fio1 blue light replicate 1


title: m6A meRIP cry1cry2 dark replicate 2


title: m6A meRIP cry1cry2 dark replicate 1


title: m6A meRIP cry1cry2 blue light replicate 2


title: m6A meRIP Col dark replicate 2


title: m6A meRIP Col blue light replicate 2


title: m6A meRIP cry1cry2 blue light replicate 1


title: m6A meRIP Col blue light replicate 1


title: m6A meRIP Col dark replicate 1


title: input for ribotag blue mta replicate 3

data_processing:
Cleaned reads of Ribo-tag and input samples were aligned to the TAIR10 reference genome with Bowtie2 (v2.1.0) (Langmead and Salzberg, 2012). Translation efficiency abundance was measured by RSEM using the default parameters (Li and Dewey, 2011).Translation efficiency was estimated with (RPKM in Ribotag +1)/ (RPKM in input +1). Differential translation efficiency analysis was conducted using edgeR (Robinson et al., 2010)with a threshold of p-value < 0.05 and Fold Change > 1.5 was used to determine whether there were any significant differences in translation efficiency between samples.
The adapter sequence of m6A meRIP raw reads were trimmed by trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The trimmed reads were aligned to the TAIR10 reference genome with Bowtie2 (Langmead and Salzberg, 2012) (v2.1.0) with default settings. meRIP track files in BigWig format were generated using bamCoverage of deeptools (v3.1.3) with RPKM normalization (Ramirez et al., 2016) from de-duplicated reads of Samtools (Li et al., 2009). m6A peaks were called by MACS2 (v2.1.1) and annotated using ChIPseeker (Yu et al., 2015; Zhang et al., 2008). Differential peaks were called with a threshold of p-value < 0.05 and Fold Change > 1.5. m6A data metaplots were plotted by deeptools (v2.5.1) (Ramirez et al., 2014).
Assembly: TAIR10
Supplementary files format and content: bigwig: meRIP intensity.
Supplementary files format and content: *RPKM.txt: signal intensity of m6A peaks
Supplementary files format and content: *results: gene expression level
Library strategy: Ribo-tag


title: input for ribotag blue mta replicate 2


title: input for ribotag blue mta replicate 1


title: input for ribotag blue fio1 replicate 2


title: input for ribotag blue cry1cry2 replicate 3


title: input for ribotag blue fio1 replicate 3


title: input for ribotag dark mta replicate 1


title: input for ribotag blue cry1cry2 replicate 1


title: input for ribotag dark cry1cry2 replicate 3


title: input for ribotag dark fio1 replicate 3


title: input for ribotag dark mta replicate 2


title: input for ribotag blue fio1 replicate 1


title: input for ribotag blue WT replicate 1


title: input for ribotag blue WT replicate 3


title: input for ribotag dark fio1 replicate 2


title: input for ribotag dark fio1 replicate 1


title: input for ribotag blue WT replicate 2


title: input for ribotag blue cry1cry2 replicate 2


title: input for ribotag dark mta replicate 3


title: input for ribotag dark WT replicate 3


title: input for ribotag dark cry1cry2 replicate 1


title: input for ribotag dark cry1cry2 replicate 2


title: input for ribotag dark WT replicate 2


title: input for ribotag dark WT replicate 1


title: ribotag blue fio1 replicate 3

value: Anti-FLAG M2


title: ribotag blue mta replicate 2


title: ribotag blue mta replicate 1


title: ribotag blue mta replicate 3


title: ribotag blue fio1 replicate 2


title: ribotag blue cry1cry2 replicate 3


title: ribotag blue cry1cry2 replicate 1


title: ribotag blue WT replicate 3


title: ribotag blue WT replicate 2


title: ribotag blue cry1cry2 replicate 2


title: ribotag blue WT replicate 1


title: ribotag dark mta replicate 3


title: ribotag dark fio1 replicate 1


title: ribotag dark fio1 replicate 2


title: ribotag dark cry1cry2 replicate 2


title: ribotag dark mta replicate 1


title: ribotag dark fio1 replicate 3


title: ribotag dark cry1cry2 replicate 1


title: ribotag dark WT replicate 3


title: ribotag dark cry1cry2 replicate 3


title: ribotag dark WT replicate 2


title: Brain-dCA1, 3_Psmc5-siRNA Trained

city: Blacksburg

first: Timothy

last: Jarome

state: VA

address: 175 W Campus Dr

institute: Virginia Polytechnic Institute and State University

description:
Group3_3
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv

data_processing:
Sequence read is trimmed using trimgalore (--paired --phred33 --fastqc --illumina -q 30 --length 30)
Trimmed sequence is mapped to Rat genome (Rattus_norvegicus.Rnor_6.0.99)
featureCounts v2.0.1 is used to quantify the mapping results (featureCounts" "-T" "32" "-p" "-t" "exon" "-g" "gene_id" "-a) and generate count matrix
Assembly: Rattus_norvegicus.Rnor_6.0.99
Supplementary files format and content: comma-separated values file includes the raw count for each sample
Supplementary files format and content: comma-separated values file includes the DESeq2 normalized count for each sample

organism: Rattus norvegicus

growth_protocol: Frozen brain tissue, from 8-9 week old Sprague Dawley rats

extract_protocol:
RNA was extracted usin Rneasy mini plus kit (Qiagen)
Illumina TruSeq Stranded mRNA HT Sample Prep Kit, enriched by 14 cycles of PCR, validated using Agilent TapeStation and quantified by qPCR

treatment_protocol: Streotaxic injection of siRNAs into dorsal CA1 area of the hippocampus

tag: strain

value: Sprague-Dawley

value: All brain cell types

tag: Sex

value: Male

value: Psmc5-siRNA Trained


title: ribotag dark WT replicate 1

value: WT


title: ribotag blue fio1 replicate 1


title: Brain-dCA1, 13_Psmc5-siRNA Trained

description:
Group3_13
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv


title: Brain-dCA1, 17_Psmc5-siRNA Trained

description:
Group3_17
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv


title: ATCC49619, normal [B-R1

city: LuZhou

first: Zhikun

last: Zhang

state: Sichuan

address: Xianglin Road 1#

institute: Southwest Medical University

data_processing:
Illumina HiSeq 2500 results were applied in CASAVA Base Calling analysis into raw sequenced reads
Raw reads were trimmed for adaptor sequence/low-quality sequence to get clean reads on Sickle/SeqPrep
clean reads were mapped to reference genome by Bowtie2
Read count extraction and normalization were analyzed by RNA-seq
Assembly: AP018938.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Streptococcus pneumoniae

growth_protocol: Logarithmic pneumococcal cells were collected by centrifugation. The collected cells were then suspended in fresh BHI and BHI-M1 (12mM phosphate) medium, incubated at 37°C for 2h.

extract_protocol:
RNA samples were isolated by TRizol reagent
The mRNA was enriched by removing rRNA using the Ribo-zero kit. mRNA was subsequently broken into short fragments by adding fragmentation buffer, and one-stranded cDNA was synthesized using six-base random primers (random hexamers) with mRNA as the template, followed by the addition of buffer, dNTPs (dTTP in dNTP was replaced by dUTP) and DNA polymerase I and RNase H. The double-stranded cDNA was then purified with AMPure XP beads, followed by degradation of the second strand of cDNA containing U with USER enzyme. The purified double-stranded cDNA was first end-repaired, A-tailed, and sequencing junction ligated, and then fragment size selection was performed with AMPure XP beads. Finally, PCR amplification was performed and the PCR products were purified with AMPure XP beads to obtain the final library.

value: pneumococcal cell


title: Brain-dCA1, 5_Scr-siRNA-Trained

description:
Group2_5
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv

value: Scr-siRNA-Trained


title: ribotag dark mta replicate 2


title: Brain-dCA1, 19_Psmc5-siRNA Trained

description:
Group3_19
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv


title: ETV2plus NCs, scRNAseq

city: Leuven

first: Yoke Chin

last: Chai

state: Leuven

address: Herestraat 49, ON5

department: Development & Regeneration

country: Belgium

institute: KU Leuven

description: 10x Genomics

data_processing:
The Cell Ranger version 6.1.1 was used to process, align, and summarize unique molecular identifier (UMI) counts against the 10X Genomics pre-built human GRCh38 reference genome datasets (2020-A, July 7, 2020). Each sample was processed using the semi-supervised machine learning classifier – Debris Identification using Expectation Maximization (DIEM) to eliminate debris and empty droplets. More specifically, Debris and test sets were specified for droplets using set debris_test_set(sce, min_counts = 200, min_genes = 100) and genes with no expression were filtered out with filter_genes(sce, cpm_tresh = 10). Cell type clustering was initialized by performing PCA analysis using get_pcs(sce, n_var_genes = 2000, min_genes = 200, n_pcs = 30, threads = 8, seedn = 1234) and k-means algorithm using init(sce, k_init = 20, nstart_init = 30, min_size_init = 10, threads = 8). We run expectation maximization algorithm run_em(sce, threads = 8, model = ”DM”) to estimate the parameters of the multinomial mixture model and assign clusters for each droplet in the test set using assign_clusers(sce). We removed clusters that were assigned as debris using the command function call_targets(sce, clusters = "debris", thresh_score = NULL, min_genes = 0).
Assembly: GRCh38
Supplementary files format and content: rds

source_name: hiPSC H9

extract_protocol:
For nuclei isolation, all following steps were performed on ice with pre-cooled buffers and centrifugation steps were performed at 4 oC. In brief, the snap-frozen samples were thawed using 500 µl ice-cold homogenization buffer [HB; consisting of 320 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris pH 7.8, 0.1 mM EDTA, 0.1% NP40, 1X complete protease inhibitor (Roche), 1 mM β-mercaptoethanol and RNase-In inhibitor (Promega)] for 5 min to prevent the nuclei from rupturing. The samples were then homogenized with pestle A (5 gentle strokes) and pestle B (15 gentle strokes) and incubated on ice for 5 min.  The homogenates were filtered using FlowmiTM 70 µm cell strainers and the filtrates were centrifuged at 500g for 5 min. The resulting pellets were resuspended in 2.65 ml washing buffer (HB without NP40) and 2.65 ml gradient medium (5 mM CaCl2, 50% Optiprep, 3 mM magnesium acetate, 10 mM Tris pH 7.8, 1X complete protease inhibitor, 1 mM β-mercaptoethanol and RNase-In inhibitor) and the resulting solution was added gently on top of a cushion solution (29% Optiprep, 150 mM KCl, 30 mM MgCl2, 60 mM Tris pH 7.8 and  250 mM sucrose) for centrifugation at 7700 rpm for 30 min at 4 oC. The nuclei pellets were resuspended in 25 µl resuspension buffer (1X PBS, 2% BSA), filtered using FlowmiTM 40 µm cell strainers and performed nuclei counting using LUNA automated cell counter (Logos Biosystems) according to the manufacturer’s instructions
The diluted nuclei suspensions were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) (Next GEM Single Cell 3’ library and Gel Bead Kit v3.1) according to the manufacturer’s protocol (10x User Guide; CG000204, Revision D). Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT cleanup, complementary DNA amplification and library construction were all performed according to the manufacturer’s protocol. Individual sample quality was assessed using a Tapestation (Agilent). Qubit 2.0 (ThermoFisher Scientific) was used for library quantification before pooling libraries. The final library pool was sequenced on NextSeq2000 (Illumina) instrument using NextSeq 1000/2000 P3 kit v3 for 2 lanes of 100-base-pair paired-end reads.

value: hiPSC H9

value: vascularized


title: NCs, scRNAseq

description: 10x Genomics

value: non-vascularized


title: Brain-dCA1, 6_Scr-siRNA-Trained

description:
Group2_6
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv


title: Brain-dCA1, 16_Scr-siRNA-Trained

description:
Group2_16
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv


title: Brain-dCA1, 15_Scr-siRNA-Trained

description:
Group2_15
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv


title: Brain-dCA1, 7_Psmc5-siRNA Trained

description:
Group3_7
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv


title: 6hpa (8 rep) and 1dpa (8 rep) regeneration

city: Vestec by Prague

first: Radek

last: Sindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

description: Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomic Space Ranger function (v. 1.2.2)
Binary base call files were demultiplexed using mkfastq function with default parameters.
fastq files were mapped separately to Space ranger reference (XENLA_10.1_GCF) using count function which takes a microscope slide image and fastq files, performs alignment, tissue detection, fiducial detection, and barcode/UMI counting.
Spatial regeneration and refractory datasets were analyzed using Seurat (v. 5). Spots with greater than 20% reads for the mitochondrial genes were removed. Each dataset was normalized using SCTransform using vst.flavor v2.
Assembly: Xenopus laevis genome (v 10.1)
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz: raw list of spatial barcodes
Supplementary files format and content: features.tsv.gz: raw list of gene IDs
Supplementary files format and content: matrix.mtx.gz: raw gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: processed_metadata.xlsx - metadata of the filtered and processed data, including the conditions and sample annotations used for downstream analysis
Library strategy: Spatial transcriptomics

molecule: polyA RNA

organism: Xenopus laevis

source_name: tail

growth_protocol: Xenopus laevis females were stimulated with 500 U of human chorionic gonadotropin (Sigma-Aldrich). Eggs were collected the following day and fertilized by testes suspension which were surgically obtained from the male. After the removal of jelly coats by the 2% cysteine treatment, embryos were incubated in 0.1x MBS until the experimental procedure. Embryonic stages were determined based on Nieuwkoop and Faber table. Embryos were immediately transferred to the 0.1x MMR solution with gentamycin. Solution was changed every day.

extract_protocol:
Dissected tissues were embedded and oriented in 50% optimal cutting temperature (OCT) medium, rapidly frozen using dry ice and then transferred to -80°C for a maximum of six weeks of storage. Samples were sectioned sagitally (20 µm thickness) using Leica CM1950 cryostat (Leica Microsystems). Sections collected for the 10X Visium Spatial Gene Expression processing were then stored at -80°C.
Sequencing libraries were prepared according to the manufacturer’s manual “Visium Spatial Gene Expression Reagent Kits User Guide” (CG000239).

treatment_protocol: Amputation was performed manually (removal of ~30% of tail tissue) using tricaine anesthetized tadpoles at stage 40 (regenerative) and stage 46 (refractory). The tail was amputated after the following time periods: 1) regenerative 6 hpa and 1 dpa, 2) refractory 6 hpa and 1 dpa, 3) regenerative and refractory 3 dpa.

value: tail

value: amputated


title: Brain-dCA1, 1_Scr-siRNA-Naïve

description:
Group1_1
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv

value: Scr-siRNA-Naïve


title: Brain-dCA1, 2_Scr-siRNA-Naïve

description:
Group1_2
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv


title: 3dpa (6 rep) regeneration and 3dpa (6 rep) refractory

description: Spatial transcriptome sequencing


title: 0, 1, 3, 12 hpa regeneration

description: 10x Genomics

data_processing:
Data were processed using STAR v2.7.9a. Reads were aligned and counted against Xenopus laevis genome (v 10.1) with annotation XENLA_10.1_GCF obtained from Xenbase
Raw unfiltered data were processed using R packages. Firstly, droplets with cells were selected using DropletUtils v1.14.1 using command emptyDrops with parameter ”lower = 1000” and FDR <= 0.001. Filtered matrix were used for next processing using Seurat v4.1.0.
Assembly: Xenopus laevis genome (v 10.1)
Supplementary files format and content: barcodes.tsv: raw cell barcodes
Supplementary files format and content: features.tsv: raw list of gene IDs
Supplementary files format and content: matrix.mtx: raw gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: processed_metadata.xlsx: metadata of the filtered and processed data, including the time points and cell type annotations

extract_protocol:
Tissue was resuspended in 200 μl of dissociation solution I containing papain , BSA (40 μg/ml,), ActD (50 μg/ml), protease (0.5 mg/ml) and DNase I (50 μg/ml). Dissociation was gently resuspended using P200 wide-bore tip for one minute and gently rotated for 2 minutes. After three repeated resuspending/rotating steps, samples were shortly spun down, supernatant with cells were collected into tubes with 1 ml of fetal bovine serum (FBS, Gibco) prechilled on ice. Undissociated pieces were resuspended in another 200 μl of dissociation solution I and dissociated for another three steps of resuspending and rotating. Supernatant with cells was collected into a new tube with 1 ml of FBS. Next, the tissue was resuspended in 200 μl of dissociation solution II (papain with CaCl2 (5 mM), BSA (40 μg/ml), ActD (50 μg/ml), protease (5 mg/ml) and DNase I (50 μg/ml)) and dissociation was performed for three rounds of 10 minutes dissociation the same as described above. In total, five tubes with single-cell suspension in FBS were collected per sample. This allowed for both the preservation of the quality of sensitive cells (released first) and also the collection of the inner cells (collected last).
Sequencing libraries were prepared according to the manufacturer’s manual “Chromium Single Cell 3' Reagent Kits User Guide (v 3.1)”.
In total 2400 cells per sample were loaded into the Chromium chip. Library quality was tested by capillary electrophoresis on Fragment Analyzer (Agilent, NGS High Sensitivity kit, DNF-474). The sample libraries were then pooled and sequenced on Illumina NovaSeq 2000 targeting 100000 read pairs per cell.

treatment_protocol: Single cell experiment was performed using 0, 1, 3, 12 hpa of Xenopus tail at stage 42. To avoid artificial activation of gene expression and keep cells at a low temperature, the process of the whole tissue dissociation was done in a refrigerated room at 4 °C. Embryos were anesthetized and the regenerating part was dissected and collected into 0.5 ml of 2/3 PBS (Sigma D8537, diluted by RNase-free water) with Actinomycin D (ActD, 50 μg/ml; Sigma A1410, storage solution 5 mg/ml in DMSO). Tail pieces from 50 embryos were collected per one sample.


title: 6hpa (6 rep) and 1dpa (6 rep) refractory

description: Spatial transcriptome sequencing


title: Pancreas, Male, TH, HF, Age 5 Week, Replicate 6

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

data_processing:
Reads were trimmed using Trimmomatic version 0.39 in PE mode, to remove Illumina adapters, to remove the first 12 bases from the reads, to crop to a maximum of 37 bases in length, to remove low quality reads, and to filter any reads less than 25 bases in length. Parameters: ILLUMINACLIP TruSeq3-PE-2.fa:2:30:10 HEADCROP:12 CROP:37 SLIDINGWINDOW:4:15 MINLEN:25
Reads were aligned to the mouse genomeGRCm39 using HISAT2 version 2.2.1 with default parameters
Alignment files were sorted by name using samtools sort -n with samtools version
Mate coordinate and insert size fields were added to alignment files with samtools fixmate using samtools version
Alignment files were sorted by position using samtools sort with samtools version
Duplicate reads were removed using samtools markdup -r with samtools version
Gene level counts were generated using the makeTxDbFromGFF and exonsBy functions from the Bioconductor package GenomicFeatures, version and the summarizeOverlaps function from the Bioconductor package GenomicAlignments, version. The latter was run with parameters mode="IntersectionStrict", singleEnd=F, ignore.strand=T, fragments=F
Gene counts were normalized using the DESeq function, and FPKM values computed using the fpkm function from Bioconductor package DESeq2 version
Assembly: Genome GRCm39 Mus_musculus.GRCm39.dna.toplevel.fa from Ensembl. Gene annotations used in creating read counts are Ensembl Genes version 108, Mus_musculus.GRCm39.108.gtf
Supplementary files format and content: raw_counts.csv is a comma deliminted file containing the raw read counts from each sample
Supplementary files format and content: normalized_counts.csv is a comma delimited file containing the normalized counts (using the DESeq function from Bioconductor package DESeq2) from each sample
Supplementary files format and content: fpkm.csv is a comma delimited file containing the FPKM values (computed using the fpkm function from Bioconductor package DESeq2) for each sample

source_name: Pancreas

extract_protocol:
Total RNA was isolated from the tissue using RNeasy Plus Universal Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.
All RNA samples were assessed using the Bioanalyzer 2100 and quantified using the Thermo Fisher Qubit RNA assay. Each RNA sample with a RIN value above 8 and a quantity of 1000ng was utilized to generate a Poly(A)-based RNAseq library following the Illumina TruSeq stranded mRNA protocol. Briefly, the poly(A) RNAs were purified using oligo dT magnetic beads and were then fragmented with divalent cations, followed by reverse transcription into cDNA. The Illumina paired-end oligo adapters were ligated to the cDNA fragments, and the RNAseq libraries were amplified using PCR. The finished libraries were purified and analyzed on an Agilent Bioanalyzer 2100, revealing an average library size ranging from 285 to 300 base pairs. To determine the quantity of these libraries, they were further measured using the Thermo Fisher Qubit HS dsDNA assay.

treatment_protocol: At 4 weeks of age, male and female TALLYHO/Jng (TH) and C57BL/6J (B6) mice were weaned onto either standard chow or high fat diets and maintained on the respective diets. After 1 and 16 weeks of feeding (5 and 20 weeks of age), mice were euthanized by CO2 inhalation followed by cervical dislocation and exsanguination via cardiac puncture. Tissues including liver, gonadal fat, soleus muscle, and pancreas were then collected for RNA isolation.

value: Pancreas

value: M

value: TH

value: HF


title: Pancreas, Male, TH, HF, Age 5 Week, Replicate 4


title: Brain-dCA1, 10_Scr-siRNA-Trained

description:
Group2_10
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv

value: Sprague-Dawley


title: Brain-dCA1, 9_Scr-siRNA-Naïve

description:
Group1_9
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv

value: All brain cell types


title: Pancreas, Male, TH, HF, Age 5 Week, Replicate 3


title: Pancreas, Male, TH, HF, Age 5 Week, Replicate 2


title: Brain-dCA1, 11_Scr-siRNA-Naïve

description:
Group1_11
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv

value: Male


title: Pancreas, Male, TH, HF, Age 5 Week, Replicate 1


title: soleus, Male, TH, HF, Age 5 Week, Replicate 6

source_name: soleus

value: soleus


title: Brain-dCA1, 12_Scr-siRNA-Naïve

description:
Group1_12
raw.counts.group123.csv
DESeq2.normalized.counts.group123.csv

value: WT


title: samples in nlrc3 MO rep1

first: shuyang

last: Cai

address: 866     Yuhangtang Road

institute: Zhejiang university

description: GFP+ cells in Tg(fli1a:eGFP) zebrafish embryos at 28 hpf with nlrc3 MO

data_processing:
Illunima Casava 1.8 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.
Supplementary files format and content: FPKM values for each Sample.

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GFP+ cells in Tg(fli1a:eGFP)

tag: passage

value: 28 hpf embryos

tag: culture

value: no culture


title: samples in nlrc3 MO rep2

tag: tissue


title: samples in nlrc3 MO rep3


title: liver, Male, TH, HF, Age 5 Week, Replicate 6

value: liver


title: samples in control MO rep2

description: GFP+ cells in Tg(fli1a:eGFP) zebrafish embryos at 28 hpf with control MO


title: samples in control MO rep3


title: ATCC49619, 12mM phosphate [P1-R1]

value: pneumococcal cell

tag: genotype

value: BHI medium, incubated at 37°C for 2h.


title: Pancreas, Male, TH, HF, Age 5 Week, Replicate 5


title: samples in control MO rep1


title: fat, Male, TH, HF, Age 5 Week, Replicate 6

source_name: fat

value: fat


title: soleus, Male, TH, HF, Age 5 Week, Replicate 5


title: ABwt_rep2

city: Liège

first: Marc

last: Muller

address: B34 Sart Tilman

department: Life Sciences

institute: Université de Liège

description: AB wt larvae rep2 at 10dpf

data_processing:
Approximatively 20–25 M reads were sequenced per sample. The sequencing reads were processed through the Nf-core rnaseq pipeline 3.0 (Ewels, Peltzer et al. 2020) with default parameters and using the zebrafish reference genome (GRCz11) and the annotation set from Ensembl release 103 (www.ensembl.org; accessed 1 May 2020)
Differential gene expression analysis was performed using the DESeq2 pipeline (Love, Huber et al. 2014).
Assembly: zebrafish reference genome (GRCz11) and the annotation set from Ensembl release 103
Supplementary files format and content: Table_counts_fbln1/wt.csv containing individual counts: Ensembl gene Id, gene name,fbln1-WT-i_R1,fbln1-WT-ii_R1,fbln1-WT-iii_R1,fbln1-mu-i_R1,fbln1-mu-ii_R1,fbln1-mu-iii_R1
Supplementary files format and content: Table_fbln1/wt.csv containing:  Ensembl gene ID,gene name,log2FoldChange,lfcSE,stat,pvalue,padj,Mu_baseMean,WT_baseMean,baseMean

source_name: larvae heads

growth_protocol: Zebrafish (Danio rerio) of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA-Institute, Liege, Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10-h light/dark. Embryos were used and staged as described [28, 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding, adult male and female zebrafish were set up in several breeding tanks, separated by a clear plastic wall. After the light was turned on the next morning, walls are removed, and eggs are generated by natural mating and then collected from 30 minutes to 2 hours after spawning. After sorting, fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium (5 mM Na Cl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, 0.00001% Methylene Blue). The age of the embryos and larvae is indicated as hours post fertilization (hpf)

extract_protocol:
Three independent batches of wt and fbln1-/- pooled heads (n= 21controls & 21 mutants) were prepared and the RNAlater solution was eliminated. RNA was extracted using the RNA mini extraction kit (Qiagen, Hilden, Germany). Samples were lysed in RLT+ buffer with β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO, USA) and homogenized at least 10 times with a 26-gauge needle in a 1 mL syringe. An amount of 22 μL of RNAse free water was used to resuspend total RNA. RNA extract was treated with DNAseI (Qiagen, Hilden, Germany) to avoid DNA contamination. Quantity (ng/μL) and quality (260/280 and 260/230 ratios) of each extract was assessed by nanodrop spectrophotometer measurements. The pellets were purified by lithium chloride precipitation, followed by 2 times pellet washing with 70% ethanol, and resuspended in 51 µL of RNAse-free water and stored at −80 °C. The integrity of total RNA extracts was assessed using the BioAnalyzer (Agilent, Santa Clara, CA, USA). RIN (RNA integrity number) scores were > 9 for each sample.
From the mRNAs extracted from wt and fbln1 mutants, the cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Homozygous mutants were obtained by crossing heterozygous parents carrying the desired mutation. Resulting larvae were first sacrificed by exposure to MS-222 (Ethyl 3-aminobenzoate methane sulfonate; Merck, Overijse, Belgium), 10dpf larvae were stored in RNA later (Fisher Scientific, Merelbeek, Belgium). Individual fish were decapitated, the heads (anterior) of each individual were stored in a 96 well plate for later RNA extraction, whereas the body (posterior) was used for DNA extraction and genotyping using q-PCR. Once the genotypes were known, the heads were recovered and pooled to constitute wt and fbln1-/- batches of 21 individuals.

value: larvae heads

tag: strain background

value: AB

value: ABwt

value: 10 dpf


title: liver, Male, TH, HF, Age 5 Week, Replicate 5

value: M

value: TH

value: HF


title: ABwt_rep1

description: AB wt larvae rep1 at 10dpf


title: liver, Male, TH, HF, Age 5 Week, Replicate 4


title: fat, Male, TH, HF, Age 5 Week, Replicate 5


title: fbln_rep2

description: fbln1 mutants rep2 at 10dpf


title: fbln_rep3

description: fbln1 mutants rep3 at 10dpf


title: fat, Male, TH, HF, Age 5 Week, Replicate 4


title: liver, Male, TH, HF, Age 5 Week, Replicate 3


title: soleus, Male, TH, HF, Age 5 Week, Replicate 4


title: fbln_rep1

description: fbln1 mutants rep1 at 10dpf


title: soleus, Male, TH, HF, Age 5 Week, Replicate 3


title: RR6a-4dpf osteoblasts P2 rep 4

description:
RR6a-P2 rep 4
Osteo Table_Counts_P1-P2.csv
Osteo Table_P2:P1.csv

data_processing:
The sequencing reads were processed through the Nf-core rnaseq pipeline 3.0 (Ewels, P. A., et al.,  Nat Biotechnol 2020, 38, (3), 276-278) with default parameters and using the zebrafish reference genome (GRCz11) and the annotation set from Ensembl release 103 (www.ensembl.org).
Differential gene expression analysis was performed using DESeq2 pipeline
Assembly: zebrafish reference genome (GRCz11) and the annotation set from Ensembl release 103
Supplementary files format and content: Osteo Table_P2/P1.csv containing: Ensembl gene ID, gene name, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, P2_baseMean, P1_baseMean
Supplementary files format and content: Osteo Table_Counts_P1-P2.csv: individual sample count files. Ensembl gene ID,Gene name,RR6a-P2, RR8b-P1, RR3a-P2, RR4b-P1,RR3b-P1,RR2b-P1,RR2a-P2,RR7b-P1

source_name: 4dpf osteoblasts

extract_protocol:
Cells coming from cell sorting (about 30-50000 cells) were immediately lysed in 0.5% Triton X-100 containing 2U/µl RNAsin and stored at -80°C. cDNAs were prepared from these lysed cells according to the SMART-Seq 2.0 protocol (Illumina, San Diego, CA, USA) for low input RNA sequencing.
Libraries were prepared using the Nextera XT DNA library kit (Ma, X., Y. W. Wang, M. Q. Zhang and A. F. Gazdar (2013). "DNA methylation data analysis and its application to cancer research." Epigenomics 5(3): 301-316.)

treatment_protocol: A Tg(sp7:sp7-GFP) heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non-transgenic offspring. At 3dpf, the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf, around 100-150 larvae were euthanized and transferred to gentleMACS™ C tubes (Miltenyi Biotec, Leiden, Netherlands)in an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1,5 ml of De-yolk buffer prepared in house. The larvae were de-yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS- buffer (without Ca+2 and Mg+2 ions and phenol red free) and the supernatant was discarded. The larvae are resuspended in 1,5ml digestion buffer at 28º C, dissociation was performed running the protocols m_brain_01 and m_brain_03 (according to the manufacturer's instructions in the Neural Tissue Dissociation Kit (T) 130-093-231) once on a gentleMACS™ Dissociator machine (Miltenyi Biotec, Leiden, Netherlands), followed by three runs of m_brain_03, 2 runs of protocol m_brain_02, five runs of m_brain_03, each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m_brain_01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec (Neural Tissue Dissociation Kit (T) 130-093-231) followed by 4 additional runs of the m_brain_03 protocol, separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS- buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide (Fisher Scientific, Merelbeek, Belgium) was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter (P18100055) and the green fluorescent cells are sorted into a 1,5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non-transgenic siblings to ensure that the GFP-positive cells were truly due to transgene expression, not to autofluorescence.  De-yolk buffer (4ml):  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer (4ml):  1x HBSS- buffer (without Ca+2 and Mg+2 ions and phenol red free)  10mM HEPES (0.5%)  2mM EDTA  1% BSA  Filter using 0,22µm filter and store at 4ºC.    Digestion buffer (2ml):  1,8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x (Thermo Fisher Scientific, Merelbeke, Belgium)  10µl Proteinase K 20µg/µl (Thermo Fisher Scientific, Merelbeke, Belgium)  10µl Collagenase-2 20mg/ml (Thermo Fisher Scientific, Merelbeke, Belgium)

tag: cell type

value: 4dpf osteoblasts

tag: cell population

value: high (P2) fluorescence

value: ulg071 Tg

value: FACS


title: RR3a-4dpf osteoblasts P2 rep 2

description:
RR3a-P2 rep 2
Osteo Table_Counts_P1-P2.csv
Osteo Table_P2:P1.csv

tag: treatment


title: RR2a-4dpf osteoblasts P2 rep 1

description:
RR2a-P2 rep 1
Osteo Table_Counts_P1-P2.csv
Osteo Table_P2:P1.csv


title: soleus, Male, TH, HF, Age 5 Week, Replicate 2

value: soleus


title: fat, Male, TH, HF, Age 5 Week, Replicate 3


title: soleus, Male, TH, HF, Age 5 Week, Replicate 1


title: fat, Male, TH, HF, Age 5 Week, Replicate 2


title: liver, Male, TH, HF, Age 5 Week, Replicate 2


title: RR3b-4dpf osteoblasts P1 rep 2

description:
RR3b-P1 rep 2
Osteo Table_Counts_P1-P2.csv
Osteo Table_P2:P1.csv

value: low (P1) fluorescence


title: RR4b-4dpf osteoblasts P1 rep 3

description:
RR4b-P1 rep 3
Osteo Table_Counts_P1-P2.csv
Osteo Table_P2:P1.csv


title: RR2b-4dpf osteoblasts P1 rep 1

description:
RR2b-P1 rep 1
Osteo Table_Counts_P1-P2.csv
Osteo Table_P2:P1.csv


title: liver, Male, TH, HF, Age 5 Week, Replicate 1

value: liver


title: ABwt_rep3

description: AB wt larvae rep3 at 10dpf


title: fat, Male, TH, HF, Age 5 Week, Replicate 1


title: Drought6_86d_rep3

city: Tsukuba

first: FUMIYUKI

last: SOMA

state: Ibaraki

address: 2-1-2 Kan-non-dai

department: Institute of Crop Science

institute: National Agriculture and Food Research Organization

data_processing:
Reads were mapped to the IRGSP-1.0 genome assembly and MSU7 gene models using the STAR aligner (Dobin et al., 2013)
Read counts were quantified using the featureCounts (Liao et al., 2014) with option” -S 2 -p -B -C -T”.
Supplementary files format and content: Tab-delimited text files include row counts for each Sample

organism: Oryza sativa

growth_protocol: Rice plants were grown in a growth chamber under a 14 h light/10 h dark photoperiod, with 50% R.H. at daytime and 60% R.H. at nighttime. The temperature in the growth chamber varied from 25°C to 30℃ at daytime,

extract_protocol:
Total RNA was extracted using TRIzol RNA Isolation Reagents (Thermo Fisher) according to manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional mRNA-seq kit (New England Biolabs)

treatment_protocol: The water level in each pot was maintained at 6 cm above the bottom of the pot under WW conditions. Drought stress was initiated at each indicated days after sowing by withdrawing water supply.

value: Nipponbare


title: Drought6_86d_rep2


title: Pancreas, Male, TH, HF, Age 20 Week, Replicate 7

value: Pancreas


title: Drought6_86d_rep1


title: Pancreas, Male, TH, HF, Age 20 Week, Replicate 6


title: Drought5_86d_rep3


title: Pancreas, Male, TH, HF, Age 20 Week, Replicate 4


title: Drought5_86d_rep2


title: Pancreas, Male, TH, HF, Age 20 Week, Replicate 5


title: RR8b-4dpf osteoblasts P1 rep 6

description:
RR8b-P1 rep 6
Osteo Table_Counts_P1-P2.csv
Osteo Table_P2:P1.csv


title: Drought5_86d_rep1


title: Well-watered3_86d_rep3


title: Pancreas, Male, TH, HF, Age 20 Week, Replicate 3


title: Well-watered3_86d_rep2


title: Pancreas, Male, TH, HF, Age 20 Week, Replicate 1


title: Pancreas, Male, TH, HF, Age 20 Week, Replicate 2


title: soleus, Male, TH, HF, Age 20 Week, Replicate 6


title: Drought6_83d_rep3


title: fat, Male, TH, HF, Age 20 Week, Replicate 6

value: fat


title: soleus, Male, TH, HF, Age 20 Week, Replicate 5


title: Drought6_83d_rep1


title: liver, Male, TH, HF, Age 20 Week, Replicate 6


title: Well-watered3_86d_rep1


title: Drought5_83d_rep3


title: liver, Male, TH, HF, Age 20 Week, Replicate 5


title: Drought5_83d_rep1


title: RR7b-4dpf osteoblasts P1 rep 5

description:
RR7b-P1 rep 5
Osteo Table_Counts_P1-P2.csv
Osteo Table_P2:P1.csv


title: fat, Male, TH, HF, Age 20 Week, Replicate 5


title: Drought6_83d_rep2


title: Drought5_83d_rep2


title: soleus, Male, TH, HF, Age 20 Week, Replicate 4


title: soleus, Male, TH, HF, Age 20 Week, Replicate 3


title: fat, Male, TH, HF, Age 20 Week, Replicate 4


title: Well-watered3_83d_rep2


title: liver, Male, TH, HF, Age 20 Week, Replicate 4


title: fat, Male, TH, HF, Age 20 Week, Replicate 3


title: Drought6_80d_rep3


title: Drought6_80d_rep2


title: Drought6_80d_rep1


title: fat, Male, TH, HF, Age 20 Week, Replicate 2


title: Drought5_80d_rep3


title: Drought5_80d_rep2


title: Drought5_80d_rep1


title: Well-watered3_80d_rep3


title: liver, Male, TH, HF, Age 20 Week, Replicate 2


title: fat, Male, TH, HF, Age 20 Week, Replicate 1


title: Well-watered3_83d_rep3


title: Well-watered3_80d_rep2


title: liver, Male, TH, HF, Age 20 Week, Replicate 3


title: soleus, Male, TH, HF, Age 20 Week, Replicate 1


title: Drought6_77d_rep3


title: Pancreas, Male, TH, Chow, Age 5 Week, Replicate 6

value: Chow


title: Pancreas, Male, TH, Chow, Age 5 Week, Replicate 5


title: liver, Male, TH, HF, Age 20 Week, Replicate 1


title: Drought6_77d_rep2


title: Well-watered3_83d_rep1


title: Pancreas, Male, TH, Chow, Age 5 Week, Replicate 4


title: fat, Male, TH, Chow, Age 5 Week, Replicate 6


title: Drought5_77d_rep3


title: soleus, Male, TH, HF, Age 20 Week, Replicate 2


title: fat, Male, TH, Chow, Age 5 Week, Replicate 5


title: Drought5_77d_rep2


title: Drought5_77d_rep1


title: soleus, Male, TH, Chow, Age 5 Week, Replicate 5


title: Well-watered3_77d_rep3


title: fat, Male, TH, Chow, Age 5 Week, Replicate 4


title: Well-watered3_77d_rep2


title: liver, Male, TH, Chow, Age 5 Week, Replicate 5


title: soleus, Male, TH, Chow, Age 5 Week, Replicate 4


title: Drought4_92d_rep3


title: Drought6_77d_rep1


title: soleus, Male, TH, Chow, Age 5 Week, Replicate 3


title: fat, Male, TH, Chow, Age 5 Week, Replicate 3


title: liver, Male, TH, Chow, Age 5 Week, Replicate 4


title: liver, Male, TH, Chow, Age 5 Week, Replicate 3


title: Drought3_92d_rep3


title: Drought3_92d_rep2


title: soleus, Male, TH, Chow, Age 5 Week, Replicate 1


title: Well-watered2_92d_rep3


title: Drought3_92d_rep1


title: liver, Male, TH, Chow, Age 5 Week, Replicate 6


title: liver, Male, TH, Chow, Age 5 Week, Replicate 2


title: Well-watered2_92d_rep1


title: Drought2_92d_rep3


title: Pancreas, Male, TH, Chow, Age 5 Week, Replicate 2


title: Drought2_92d_rep2


title: soleus, Male, TH, Chow, Age 5 Week, Replicate 2


title: liver, Male, TH, Chow, Age 5 Week, Replicate 1


title: Well-watered2_92d_rep2


title: Well-watered3_77d_rep1


title: fat, Male, TH, Chow, Age 5 Week, Replicate 1


title: Drought4_92d_rep2


title: Drought1_92d_rep3


title: Drought4_92d_rep1


title: Drought2_92d_rep1


title: Pancreas, Male, TH, Chow, Age 5 Week, Replicate 1


title: Drought1_92d_rep1


title: Pancreas, Male, TH, Chow, Age 20 Week, Replicate 9


title: Well-watered1_92d_rep3


title: Drought1_92d_rep2


title: Pancreas, Male, TH, Chow, Age 20 Week, Replicate 8


title: Pancreas, Male, TH, Chow, Age 5 Week, Replicate 3


title: Pancreas, Male, TH, Chow, Age 20 Week, Replicate 6


title: Well-watered1_92d_rep1


title: Drought6_74d_rep3


title: Well-watered1_92d_rep2


title: Pancreas, Male, TH, Chow, Age 20 Week, Replicate 5


title: Drought6_74d_rep2


title: Pancreas, Male, TH, Chow, Age 20 Week, Replicate 4


title: Pancreas, Male, TH, Chow, Age 20 Week, Replicate 10


title: Pancreas, Male, TH, Chow, Age 20 Week, Replicate 1


title: Drought5_74d_rep2


title: Drought5_74d_rep3


title: Drought5_74d_rep1


title: fat, Male, TH, Chow, Age 5 Week, Replicate 2


title: Well-watered3_74d_rep3


title: Well-watered3_74d_rep2


title: liver, Male, TH, Chow, Age 20 Week, Replicate 6


title: Pancreas, Male, TH, Chow, Age 20 Week, Replicate 7


title: fat, Male, TH, Chow, Age 20 Week, Replicate 6


title: soleus, Male, TH, Chow, Age 20 Week, Replicate 5


title: liver, Male, TH, Chow, Age 20 Week, Replicate 5


title: Drought6_71d_rewater1_rep3