title: LT122DAF14Lumen SHADINGDelayedR1

tag: days after flowering

tag: sowing date

tag: replicate


title: SC061DAF7SolarCONTROL OptimalR1

status: Public on Mar 25 2021

type: SRA

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

library_source: transcriptomic

data_processing:
Sequenced reads were pseudo-aligned to the publicly available Brassica napus transcriptome obtained from Ensembl Plants using kallisto (v0.46)
RNA-seq data was normalized using the R package sleuth
Genome_build: AST_PRJEB5043_v1
Supplementary_files_format_and_content: tab-delimited text files include tpm values for each sample

molecule: total RNA

organism: Brassica napus

growth_protocol: A ﬁeld experiment in two sowing dates was carried out at the Austral Farming Exper-imental Station in Valdivia, Chile (39° 47’ S., 73° 14’ W.). In this experiment three sources of variation were evaluated in rapeseed: (i) genotype (two adapted spring rapeseed hy-brids: Lumen and Solar (chosen for having similar phenology and adapted to southern Chile), (ii) sowing date (optimum and late sowing date) and (iii) source-sink (S-Sratio) ra-tios (control without manipulation and a reduced S-Sratio with black nets intercepting 75% of solar radiation from the beginning of flowering [BBCH 61] to 15 days after flowering (DAF)). Treatments were arranged in a split–split-plot design with three replicates, where sowing date was assigned to main plots, the S-Sratio to subplots and genotypes to sub-sub plots [16]. The rapeseed plants were sown at a plant density of 55 plants m-2

extract_protocol:
Total RNA extraction was performed using a method adapted for Brassica seeds (Graeber et al., 2011;doi:10.1105/tpc.111.084103) with 100 mg of each sample and using NucleoSpin® Gel and PCR columns
RNA quality analysis, libraries construction and sequencing were performed by Novogene (Beijing, China) using standard Illumina protocols

tag: genotype

value: Solar

tag: treatment

value: CONTROL

value: Optimal


title: LT106DAF7Lumen SHADINGDelayedR3

value: Lumen

value: SHADING

value: Delayed


title: sgControl SAR-seq for sgXRCC1 in iNeuron rep1

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

country: China

library_source: genomic

data_processing:
Library strategy: SAR-seq
SAR-seq, END-seq, ChIP-seq, SEAL, and ATAC-seq reads were aligned to the reference genome (hg19 for human i3Neuron and iMuscle, mm10 for mouse pre B cells or rn6 for rat primary neurons) using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
We used MACS (v1.4.3) to call SAR-seq, XRCC1 ChIP-seq and ATAC-seq peaks. SAR-seq XRCC1, and CTCF ChIP-seq peaks with >10 fold-enrichment over background were kept. Peaks of hisone modification determined by ChIP-seq peaks were called by SICER with default parameters. Peaks within blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered. As peaks of ddN S1-END-seq are always clustered, subpeaks were called by the PeakSplitter tool of PeakAnalyzer with parameters -c 15 -v 0.6.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
.
Genome_build: hg19 for human, mm10 for mourse, rn6 for rat.
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: iNeuron

growth_protocol: For neuronal differentiation, 20-25 million iPSCs were plated on day 0 onto a 15 cm plate in N2 media composed of knockout DMEM/F12 media (Life Technologies Corporation, Cat. No. 12660012) with N2 supplement (Life Technologies Corporation, Cat. No. 17502048), 1x GlutaMAX (Thermofisher Scientific, Cat. No. 35050061), 1x MEM nonessential amino acids (NEAA) (Thermofisher Scientific, Cat. No. 11140050), 10 µM ROCK inhibitor (Y-27632; Selleckchem, Cat. No. S1049), and 2 µg/mL doxycycline (Clontech, Cat. No. 631311). N2 media was changed once a day for two more days. Day 3 cells were replated onto freshly-prepared poly-L-ornithine- (PLO; 0.1 mg/ml; Sigma, Cat. No. P3655-10MG) coated dishes as follows: Cells were washed with PBS, dissociated with accutase for 10 minutes at 37°C, washed and plated in i3Neuron Culture Media: BrainPhys media (STEMCELL Technologies, Cat. No. 05790) supplemented with 1x B27 Plus Supplement (ThermoFisher Scientific, Cat. No. A3582801), 10 ng/mL BDNF (PeproTech, Cat. No. 450-02), 10 ng/mL NT-3 (PeproTech, Cat. No. 450-03), 1 mg/mL mouse laminin (Sigma, Cat. No. L2020-1MG), and 2 µg/mL doxycycline (Clontech, Cat. No. 631311).For 10 cm plates used in SAR-seq or CHIP-seq, 12-15 million neurons were plated. For 15 cm plates 30-45 million neurons were plated. For ibidi slides used in imaging experiments, 0.2 million neurons per well were plated. Unless otherwise noted, i3Neurons were fed on day 6 during a half media change and harvested on day 7. For i3Neurons cultured beyond 7 days, half media changes were conducted three times per week. In some experiments pre-differentiated i3Neurons were frozen on day 3 in 90% fetal bovine serum (Sigma Aldrich, Cat. No. ES-009-B) and 10% DMSO (Mediatech Inc., Cat. No. 25-950-CQC), and then thawed rapidly at 37°C, followed by removal of FBS/DMSO and plating in i3Neuron Culture Media. We did not detect any differences for experiments where day 3 neurons were thawed or plated immediately following differentiation.

extract_protocol:
Cells were washed with PBS, incubated with accutase for 5-10 mins, collected with a cell scrapper, pelleted at 200 × g for 5 minutes and resuspended in cold 0.1% BSA in PBS. Cold methanol was then added dropwise during slow vortexing to 80% final concentration. Samples were kept on ice for 20 minutes and then stored at -20C until processing.
Copper catalyzes azide-alkyne click chemistry. For biotin labeling via Click-iT reaction, cells were first washed 1x in PBS, permeabilized with 0.2% Triton-X100/PBS for 10 minutes on ice, and then washed 1x in PBS. Then the following were added in order: 3 mM copper sulfate (Sigma), 50 M biotin azide (ThermoFisher, Cat. No. B10184), and 1X Click-iT additive (ThermoFisher, Cat. No. C10424) for 2 hours shaking at room temperature. Cells were then washed one time in PBS and lysed in 50 mM Tris pH 8.0 with 1% SDS and Proteinase K overnight at 37°C. DNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) according to manufacturer’s instructions, followed by 2.5:1 volume ethanol and 1:10 volume sodium acetate precipitation. DNA pellets were resuspended in TE buffer and sheared to 150-200 bp fragments using Covaris S220 sonicator at 10% duty cycle, 175 peak incident power, 200 cycles per burst, for 240 seconds. DNA was again precipitated by 2.5:1 volume ethanol and 1:10 volume sodium acetate and resuspended in TE buffer. Biotin-EdU fragments were pulled down using MyOne Streptavidin C1 Beads (ThermoFisher, Cat. No. 650-01). Before pulldown, 35 L of Dynabeads were washed two times with 1 mL 1X Wash and Binding buffer (1X W&B) (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1 M NaCl, 0.1% Tween20) on a DynaMag-2 magnetic separator (Invitrogen, Cat. No. 12321D) and resuspended in 2X W&B (10 mM Tris-HCl pH8.0, 2 mM EDTA, 2 M NaCl, 0.2% Tween20). Equal volume of Dynabeads in 2X W&B were added to DNA in TE and incubated at 24°C shaking in a ThermoMixer C at 800 rpm for 30 minutes. Dynabeads bound to biotin-EdU fragments were washed three times in 1 mL of 1X W&B, two times in 1 mL EB, and one time in 1mL 1X T4 DNA Ligase Buffer (NEB). Dynabeads were resuspended in 50 L end-repair reaction mix (1X T4 DNA Ligase Buffer, 0.4 mM of dNTPs, 2.7 U of T4 DNA polymerase (NEB), 9 U of T4 Polynucleotide Kinase (NEB), and 1 U of Klenow fragment (NEB)) and incubated at 24°C shaking at 800 rpm for 30 minutes. Dynabeads were washed one time in 1mL 1X W&B, two times in 1mL EB, and one time in 1 mL NEBuffer 2 (NEB) and resuspended in 50 L of A-tailing reaction mix (1X NEB dA-Tailing Buffer and 20 U Klenow fragment exo- (NEB)), followed by incubation at 37°C shaking at 800 rpm for 30 minutes. Dynabeads were then washed again 1x in 1 mL NEBuffer 2 and resuspended in 115 L of ligation reaction mix (1X Quick Ligase Buffer (NEB), 6000 U Quick Ligase (NEB), 5 nM annealed TruSeq truncated adapter) and incubated at 25°C shaking at 600 rpm for 20 minutes. Ligation reaction was stopped by adding 50 mM EDTA, and Dynabeads were washed three times in 1 mL 1X W&B, three times in 1 mL EB, and finally resuspended in 8 L EB + 10 L 2X Kapa HiFI HotStart Ready Mix (Kapa Biosciences). 10 mM primers 5’-CAAGCAGAAGACGGCATACGA- GATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T-3’ and 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCC CTACACGACGCTCTTCCGATC*T-3’ (* indicates a phosphothiorate bond and a NNNNNN TruSeq index sequence) were added with 37 L PCR reaction mix (20 L 2X Kapa HiFI HotStart Ready Mix, 17 L H2O) for final volume of 60 L. DNA was amplified using PCR program: 98°C, 45 seconds; 15 cycles [98°C, 15 seconds; 63°C, 30 seconds; 72°C, 30 seconds]; 72°C, 5 minutes. PCR products were separated from DynaBeads and cleaned using 1.8X volume AMPure Beads XP. 150-200 bp bands were isolated on 2% agarose gel and purified using QIA-quick Gel Extraction Kit (Qiagen). Prior to sequencing using Illumina NextSeq 550 (75 bp single read), library concentrations were calculated by KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems).    To specifically sequence only EdU-incorporated strands of DNA (Strand-Specific SAR-seq), SAR-seq was followed exactly as above with additional steps prior to PCR amplification. After washing three times in 1 mL 1X W&B and three times in 1 mL EB post-ligation, Dynabeads were washed in 50 L 1X SSC buffer and resuspended in 20 L of 0.15 M NaOH for 10 minutes at room temperature to denature DNA strands. Beads were placed back on the DynaMag-2 magnetic separator and washed one time with 20 L 0.1 M NaOH, one time with 1 mL 1X W&B, two times with 1 mL EB, and resuspended in 8 L EB + 10 L 2X Kapa HiFI HotStart Ready Mix. Primers and PCR reaction mix were added as above.

treatment_protocol: Neurons and iMuscle cells were incubated with 20 M EdU for 18 hours, unless otherwise noted.

tag: cell type

value: neuron differentiated from iPSC

value: sgControl

value: NT

tag: dose

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: LeftvsRight_8_dHC_Right_0min

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

description: polyA RNA

data_processing:
Adaptor trimmed with cutadapt (v 1.15), maximum error rate of 0.05 and a minimum length of 15
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Genome_build: GRCm38
Supplementary_files_format_and_content: .h5 files with kallisto output (pseudoaligned read counts). Files are futher zipped

molecule: polyA RNA

organism: Mus musculus

source_name: hippocampus

growth_protocol: Mice are originally all from a C57BL/6J Background. More details about mouselines can be found in the metadata. Age of the mice is between 2 and 3 months

extract_protocol:
Trizol
illumina TrueSeq or Illumina Smartseq2 (see samples)

treatment_protocol: Homecage (no stress, control group) or 6 min 18°C swim stress

tag: condition

value: Homecage

tag: timepoint

tag: region

value: dHC

tag: Sex

value: Male

tag: hemisphere

value: Right

tag: animalnumber

tag: experiment

value: LeftvsRight

tag: block

tag: mousetype

value: WT

tag: mouseline

tag: libraryprotocol

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: genomic DNA from Labial salivary gland tissue 57

type: genomic

city: Berkeley

first: Xiaorong

last: Shao

state: CA

address: 431 Stanley Hall

country: USA

institute: University of California, Berkeley

description: Case

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K/Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting

data_processing: Minfi

label: Cy5 and Cy3

source_name: Labial salivary gland tissue 57

label_protocol: Standard Illumina Protocol

extract_protocol: Qiagen Allprep DNA/RNA mini kit

tag: gender

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: Sjogrens Syndrome


title: genomic DNA from Labial salivary gland tissue 56

description: Non-case

source_name: Labial salivary gland tissue 56

value: symptomatic not Sjogrens


title: LeftvsRight_9_vHC_Left_45min

description: polyA RNA

value: Swim

value: vHC

value: Left


title: LT102DAF7Lumen SHADINGDelayedR2

tag: days after flowering

tag: genotype

value: Lumen

tag: treatment

value: SHADING

tag: sowing date

value: Delayed

tag: replicate


title: sgXRCC1 SAR-seq in iNeuron rep2

institute: Center for Excellence in Molecular Cell Science

tag: cell type

value: neuron differentiated from iPSC

value: NT

tag: dose

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: LT098DAF7Lumen SHADINGDelayedR1


title: sgControl SAR-seq for sgPARP1 in iNeuron rep1

value: sgControl


title: sgXRCC1 SAR-seq in iNeuron rep1


title: LT130DAF14Lumen SHADINGDelayedR3


title: LeftvsRight_5_vHC_Left_0min

description: polyA RNA

tag: condition

value: Homecage

tag: timepoint

tag: region

tag: Sex

value: Male

tag: hemisphere

tag: animalnumber

tag: experiment

value: LeftvsRight

tag: block

value: WT


title: LT078DAF14Lumen SHADINGOptimalR2

tag: days after flowering

value: Optimal


title: sgPARP1 SAR-seq in iNeuron rep2

tag: genotype


title: LeftvsRight_6_dHC_Left_0min

description: polyA RNA

value: dHC

tag: mousetype

tag: mouseline

tag: libraryprotocol

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: LT082DAF14Lumen SHADINGOptimalR3

tag: treatment

tag: sowing date

tag: replicate


title: genomic DNA from Labial salivary gland tissue 54

description: Case

source_name: Labial salivary gland tissue 54

tag: gender

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: Sjogrens Syndrome


title: LeftvsRight_4_dHC_Right_45min

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

tag: Sex

value: Right


title: LeftvsRight_11_vHC_Right_45min

description: polyA RNA

value: vHC

tag: hemisphere

tag: animalnumber

tag: experiment

tag: block


title: genomic DNA from Labial salivary gland tissue 53

description: Non-case

source_name: Labial salivary gland tissue 53

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 51

description: Non-case

source_name: Labial salivary gland tissue 51


title: genomic DNA from Labial salivary gland tissue 52

description: Case

source_name: Labial salivary gland tissue 52


title: LeftvsRight_7_vHC_Right_0min

description: polyA RNA

tag: mousetype

tag: mouseline


title: LeftvsRight_3_vHC_Right_45min

description: polyA RNA

tag: libraryprotocol

tag: sampleprocessing


title: sgPARP1 SAR-seq in iNeuron rep1

tag: cell type

value: neuron differentiated from iPSC

tag: genotype

tag: treatment

value: NT

tag: dose

tag: harvested day

tag: molecule subtype

value: EdU incorporated DNA


title: genomic DNA from Labial salivary gland tissue 50

description: Case

source_name: Labial salivary gland tissue 50

tag: gender

tag: tissue

tag: disease status


title: genomic DNA from Labial salivary gland tissue 68

description: Non-case

source_name: Labial salivary gland tissue 68


title: LeftvsRight_2_dHC_Left_45min

description: polyA RNA

tag: condition

tag: timepoint

tag: region

tag: Sex

value: Male

tag: hemisphere

value: Left


title: LT058DAF7Lumen SHADINGOptimalR3

tag: days after flowering

value: Lumen

value: SHADING

tag: sowing date

tag: replicate


title: LeftvsRight_1_vHC_Left_45min

description: polyA RNA

tag: animalnumber

tag: experiment

value: LeftvsRight

tag: block

tag: mousetype

value: WT

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: NT SAR-seq for PARPi in iNeuron

tag: cell type

tag: genotype

tag: treatment

tag: dose

tag: harvested day

tag: molecule subtype


title: PARPi (Veliparib) SAR-seq in iNeuron

value: 18hrs Veliparib

value: 10 uM


title: POLB sg1 SAR-seq in iNeuron rep2

value: sgPOLB


title: LT054DAF7Lumen SHADINGOptimalR2

value: Optimal


title: LT050DAF7Lumen SHADINGOptimalR1


title: LC129DAF14Lumen CONTROL DelayedR3

value: CONTROL

value: Delayed


title: FSTFemale45min4h_27_vHC_45min

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

value: vHC

tag: Sex

value: Female

tag: hemisphere

value: both

value: illumina TruSeq

value: WholeRNA


title: FSTFemale45min4h_28_vHC_0min

description: polyA RNA

value: Homecage

value: Male

tag: animalnumber

tag: experiment


title: LT074DAF14Lumen SHADINGOptimalR1

tag: days after flowering

value: Lumen

value: SHADING

tag: sowing date

tag: replicate


title: PARPi (Olaparib) SAR-seq in iNeuron

value: neuron differentiated from iPSC

value: WT

value: 18hrs Olaparib

value: 10 µM

value: EdU incorporated DNA


title: FSTFemale45min4h_26_vHC_4h

description: polyA RNA

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: NT SAR-seq for POLAi in iNeuron

tag: cell type

tag: genotype

tag: treatment

value: NT

tag: dose

tag: harvested day


title: LC125DAF14Lumen CONTROL DelayedR2

value: CONTROL

value: Delayed


title: PARPi (Talazoparib) SAR-seq in iNeuron

value: 18hrs Talazoparib

value: 1 uM

tag: molecule subtype


title: genomic DNA from Labial salivary gland tissue 46

description: Non-case

source_name: Labial salivary gland tissue 46

tag: gender

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 49

description: Case

source_name: Labial salivary gland tissue 49

value: Sjogrens Syndrome


title: genomic DNA from Labial salivary gland tissue 45

description: Non-case

source_name: Labial salivary gland tissue 45


title: genomic DNA from Labial salivary gland tissue 48

description: Non-case

source_name: Labial salivary gland tissue 48


title: genomic DNA from Labial salivary gland tissue 47

description: Case

source_name: Labial salivary gland tissue 47


title: LC121DAF14Lumen CONTROL DelayedR1

tag: days after flowering


title: FSTFemale45min4h_25_vHC_0min

description: polyA RNA

tag: condition

value: Homecage

tag: timepoint

tag: region

value: vHC

tag: Sex

tag: hemisphere

value: both

tag: animalnumber

tag: experiment

value: illumina TruSeq

value: WholeRNA


title: POLAi SAR-seq in iNeuron rep2

tag: cell type

value: neuron differentiated from iPSC

value: WT

value: 14 hrs Adarotene (Pol Alpha inhibitor) with EdU (also 14hrs)


title: POLAi SAR-seq in iNeuron rep1

tag: genotype

value: EdU incorporated DNA


title: LC105DAF7Lumen CONTROL DelayedR3

value: Lumen

tag: treatment

value: CONTROL

tag: sowing date

tag: replicate


title: FSTFemale45min4h_24_vHC_0min

description: polyA RNA

value: Male

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: genomic DNA from Labial salivary gland tissue 44

description: Non-case

source_name: Labial salivary gland tissue 44

tag: gender

tag: tissue

tag: disease status


title: genomic DNA from Labial salivary gland tissue 43

description: Non-case

source_name: Labial salivary gland tissue 43


title: LC101DAF7Lumen CONTROL DelayedR2

tag: days after flowering

value: Delayed


title: FSTFemale45min4h_22_vHC_4h

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

tag: Sex

tag: hemisphere


title: genomic DNA from Labial salivary gland tissue 42

description: Case

source_name: Labial salivary gland tissue 42

value: Female

value: Labial salivary gland tissue


title: FSTFemale45min4h_21_vHC_4h

description: polyA RNA

source_name: hippocampus

tag: animalnumber

tag: experiment


title: LC097DAF7Lumen CONTROL DelayedR1

tag: genotype

tag: treatment

tag: sowing date

tag: replicate


title: LC081DAF14Lumen CONTROL OptimalR3

value: Optimal


title: genomic DNA from Labial salivary gland tissue 55

description: Case

source_name: Labial salivary gland tissue 55

value: Sjogrens Syndrome


title: FSTFemale45min4h_19_vHC_0min

description: polyA RNA

value: Homecage

value: vHC

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: NT SAR-seq for HU in iNeuron

source_name: iNeuron

tag: cell type

value: NT

tag: dose

tag: harvested day

tag: molecule subtype


title: HU SAR-seq in iNeuron

value: 4 days HU

value: 10 mM


title: FSTFemale45min4h_20_vHC_45min

description: polyA RNA

tag: condition

tag: timepoint

tag: region

value: both

value: WT

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: FSTFemale45min4h_23_vHC_45min

description: polyA RNA

tag: Sex

tag: hemisphere

tag: animalnumber

tag: experiment


title: SAR-seq in iNeuron rep1

value: neuron differentiated from iPSC

tag: genotype

tag: treatment

value: EdU incorporated DNA


title: LC073DAF14Lumen CONTROL OptimalR1

tag: days after flowering

value: Lumen

value: CONTROL

tag: sowing date

tag: replicate


title: FSTFemale45min4h_18_vHC_4h

description: polyA RNA

value: Swim

value: Female

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: genomic DNA from Labial salivary gland tissue 41

description: Case

source_name: Labial salivary gland tissue 41

tag: gender

tag: tissue

value: Labial salivary gland tissue

tag: disease status


title: LC057DAF7Lumen CONTROL OptimalR3

value: Optimal


title: SAR-seq in iNeuron rep3

tag: cell type

tag: dose

tag: harvested day

tag: molecule subtype


title: input for SAR-seq in iNeuron


title: LC077DAF14Lumen CONTROL OptimalR2


title: SAR-seq in iNeuron rep2


title: HiC in iNeuron rep2

data_processing:
Using Juicer software (Durand et al., 2016b), .hic files were generated, and normalized ligation frequency matrices and observed over expected normalized ligation frequency matrices were obtained with a dump command. Loop or domain calls were also done by juicer software (Durand et al, 2016a). Interaction matrices were visualized by Juicebox software. After processing two replicates, final map is generated by merging these two replicates. The final bin resolution of the Hi-C map is 1 kb and fragment resolutions are not generated. From 2.1B raw reads generated by together with QC and data-generation runs, we obtained 1.5B final total contacts which are over Q30.
Genome_build: hg19
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)

growth_protocol: For neuronal differentiation, 20-25 million iPSCs were plated on day 0 onto a 15 cm plate in N2 media composed of knockout DMEM/F12 media (Life Technologies Corporation, Cat. No. 12660012) with N2 supplement (Life Technologies Corporation, Cat. No. 17502048), 1x GlutaMAX (Thermofisher Scientific, Cat. No. 35050061), 1x MEM nonessential amino acids (NEAA) (Thermofisher Scientific, Cat. No. 11140050), 10 M ROCK inhibitor (Y-27632; Selleckchem, Cat. No. S1049), and 2 g/mL doxycycline (Clontech, Cat. No. 631311). N2 media was changed once a day for two more days. Day 3 cells were replated onto freshly-prepared poly-L-ornithine- (PLO; 0.1 mg/ml; Sigma, Cat. No. P3655-10MG) coated dishes as follows: Cells were washed with PBS, dissociated with accutase for 10 minutes at 37°C, washed and plated in i3Neuron Culture Media: BrainPhys media (STEMCELL Technologies, Cat. No. 05790) supplemented with 1x B27 Plus Supplement (ThermoFisher Scientific, Cat. No. A3582801), 10 ng/mL BDNF (PeproTech, Cat. No. 450-02), 10 ng/mL NT-3 (PeproTech, Cat. No. 450-03), 1 mg/mL mouse laminin (Sigma, Cat. No. L2020-1MG), and 2 g/mL doxycycline (Clontech, Cat. No. 631311).For 10 cm plates used in SAR-seq or CHIP-seq, 12-15 million neurons were plated. For 15 cm plates 30-45 million neurons were plated. For ibidi slides used in imaging experiments, 0.2 million neurons per well were plated. Unless otherwise noted, i3Neurons were fed on day 6 during a half media change and harvested on day 7. For i3Neurons cultured beyond 7 days, half media changes were conducted three times per week. In some experiments pre-differentiated i3Neurons were frozen on day 3 in 90% fetal bovine serum (Sigma Aldrich, Cat. No. ES-009-B) and 10% DMSO (Mediatech Inc., Cat. No. 25-950-CQC), and then thawed rapidly at 37°C, followed by removal of FBS/DMSO and plating in i3Neuron Culture Media. We did not detect any differences for experiments where day 3 neurons were thawed or plated immediately following differentiation.

extract_protocol: In situ Hi-C consists of 7 steps: (1) crosslinking cells with formaldehyde, (2) DNA digestion using MboI, (3) filling in and marking ends with Biotin, (4) proximity ligation, (5) DNA shearing, (6) pulling down the biotinylated ligation junctions with streptavidin beads, and (7) paired end sequencing. As quality control (QC), we confirmed efficient restriction, ligation and DNA shearing with an agarose DNA gel and for appropriate size selection in using Agilent 4200 TapeStation system after steps (5) and (6). For the final QC, we performed 75 paired end sequencing on the Illumina Nextseq to assess quality of the libraries based on percent of Intra-chromosomal reads, long Range (>20Kb) reads, and Library Complexity. The HiC libraries were sequenced on 100 paired end sequencing using Illumina Novaseq 6000.


title: FSTFemale45min4h_16_vHC_45min

description: polyA RNA

tag: condition

tag: timepoint

tag: region

tag: Sex

tag: hemisphere

tag: animalnumber

tag: experiment

tag: sampleprocessing


title: genomic DNA from Labial salivary gland tissue 38

description: Case

source_name: Labial salivary gland tissue 38

value: Sjogrens Syndrome


title: LC049DAF7Lumen CONTROL OptimalR1

tag: days after flowering

tag: genotype

tag: treatment

tag: sowing date

tag: replicate


title: genomic DNA from Labial salivary gland tissue 39

description: Case

source_name: Labial salivary gland tissue 39

tag: gender

tag: tissue

tag: disease status


title: genomic DNA from Labial salivary gland tissue 37

description: Non-case

source_name: Labial salivary gland tissue 37

value: symptomatic not Sjogrens


title: FSTFemale45min4h_15_vHC_45min

description: polyA RNA

value: vHC

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: HCT116 shID4

city: Hsinchu City

first: Cam-Thu

last: Ha

address: No. 101, Section 2, Guangfu Road

department: Institute of Biotechnology

country: Taiwan

institute: National Tsing Hua University

data_processing:
bcl2fastq2 conversion Software v2.19 used for basecalling.
Trimmomatic v0.32 used for sequenced reads trimming. Clipping adapters and remove low quality reads/bases from the the 3' end using a sliding windows approach.
HISAT2 used for aligning trimmed read to human whole genome (GRCh38.p10)
Reads count and FPKM (Fragments Per Kilobase of transcript per Million) were calculated by cufflinks v2.2.1.
Differential expression analysis based on cuffdiff, a part of the cufflinks package.
Differential expressed genes of each experiment design would followed by enrichment test for functional assay by clusterProfiler 3.5.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: RPKM

source_name: colorectal carcinoma

growth_protocol: HCT116 cells were cultured in RPMI medium, then transduced with lentiviral particles encoding scrambled control (SC) or shID4

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).
All RNA Sample preparation procedures were carried out according to the official Illumina protocol.  Agilent's SureSelect Strand Specific RNA Library Preparation Kitwere used for library construction followed by AMPure XP Beads size selection.  The sequence was directly determined using sequencing-by-synthesis technology. Sequencing data were generated by Welgene's pinepline which based on Illumina bcl2fastq v2.1.7 and expected to generate.

tag: transduction

value: HCT116 cells were transduced with lentiviral particles encoding shID4

tag: cell line


title: FSTFemale45min4h_14_vHC_4h

description: polyA RNA

tag: condition

tag: timepoint

tag: region

tag: Sex

value: Male

tag: hemisphere

tag: animalnumber


title: 1372-RP-227

city: Frederick

first: Mohamed Diwan M.

last: AbdulHameed

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

description: Treatment

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the Cavia porcellus transcriptome (Cavpor3.0) downloaded from the Ensembl website.
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o guinea_pig/"$sample"  $DATA_DIR/1372-RP-"$sample"_R1_001.fastq.gz $DATA_DIR/1372-RP-"$sample"_R2_001.fastq.gz -t 10
Genome_build: Cavia porcellus transcriptome (Cavpor3.0)
Supplementary_files_format_and_content: tab-delimited text files, including abundance measurements

organism: Cavia porcellus

source_name: Liver

extract_protocol:
Total RNA was isolated from the liver using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The isolated RNA samples to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing.
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 150-bp double-end sequencing with the Illumina NovaSeq600 system (Illumina, San Diego, CA) according to the manufacturer’s protocol. Bcl2fastq2 Conversion Software v2.20 (Illumina) was used to generate de-multiplexed Fastq files.

tag: breed

value: Hartley Guinea Pig

value: Liver

tag: duration

tag: dose

value: Low (25 mg/kg Thioacetamide)


title: 1372-RP-226

description: Treatment

tag: tissue

value: High (100 mg/kg Thioacetamide)


title: genomic DNA from Labial salivary gland tissue 33

description: Non-case

source_name: Labial salivary gland tissue 33

tag: gender

tag: disease status


title: HCT116 Scramble

value: HCT116 cells were transduced with lentiviral particles encoding scrambled control (SC)


title: genomic DNA from Labial salivary gland tissue 35

description: Case

source_name: Labial salivary gland tissue 35


title: NT for Nt.BspQ1 S1-END-seq in iNeuron

data_processing:
Library strategy: END=seq
SAR-seq, END-seq, ChIP-seq, SEAL, and ATAC-seq reads were aligned to the reference genome (hg19 for human i3Neuron and iMuscle, mm10 for mouse pre B cells or rn6 for rat primary neurons) using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
bigwig files were made for positive (*.pos.bw) and negativ (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).

tag: cell type

value: neuron differentiated from iPSC

tag: treatment

tag: in-situ treatment

value: 20 U of Nt.BspQI @ 50 degrees C for 30 mins

tag: harvested day


title: FSTFemale45min4h_13_vHC_0min

description: polyA RNA

value: Homecage

value: both

tag: experiment

tag: block

tag: mousetype

value: WT

tag: mouseline

tag: libraryprotocol

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: LC053DAF7Lumen CONTROL OptimalR2

tag: days after flowering

tag: genotype

value: Lumen

value: CONTROL

tag: sowing date

value: Optimal

tag: replicate


title: HiC in iNeuron rep1


title: genomic DNA from Labial salivary gland tissue 40

description: Non-case

source_name: Labial salivary gland tissue 40

value: Female

tag: tissue

value: Labial salivary gland tissue

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 32

description: Non-case

source_name: Labial salivary gland tissue 32

tag: gender


title: Nt.BspQ1 S1-END-seq in iNeuron

value: 20 U of Nt.BspQI @ 50 degrees C for 30 mins; wash in EB; 1.8 U of S1 nuclease @15 mins on ice, followed by 37 degrees C for 20 mins.


title: FSTFemale45min4h_12_vHC_0min

description: polyA RNA

tag: condition

tag: timepoint

tag: region

value: vHC

tag: Sex

tag: hemisphere

tag: animalnumber


title: genomic DNA from Labial salivary gland tissue 36

description: Non-case

source_name: Labial salivary gland tissue 36

tag: disease status


title: FSTFemale45min4h_11_vHC_45min

description: polyA RNA

value: Swim

tag: experiment

tag: block

tag: mousetype


title: 1372-RP-224

description: Treatment

tag: breed

value: Hartley Guinea Pig

value: Liver

tag: duration

value: 9 h

tag: dose

value: High (100 mg/kg Thioacetamide)


title: END-seq in iNeuron

tag: cell type

value: neuron differentiated from iPSC

tag: treatment

tag: in-situ treatment

tag: harvested day


title: 1372-RP-225

description: Control

tag: tissue

value: Vehicle (3 ml/kg Saline)


title: Human Wharton’s jelly-derived mesenchymal stem cells - 5 μg/mL of Diesel exhaust particle treated 1

city: Seoul

first: Hyun Sung Park

last: Park

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea, 200 Dong 4204 Ho

department: College of Agriculture and Life Science

country: South Korea

institute: Seoul National University

data_processing:
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts.
Filtered reads were mapped to the reference genome related to the species using the aligner TopHat (Trapnell C. et al, 2009).
Gene expression level was measured with Cufflinks v2.1.1 (Trapnell C. et al, 2010) using the gene annotation database of the species. To improve the accuracy of the measurement, multi-read-correction and frag-bias-correct options were applied. All other options were set to default values.
Genome_build: hg19
Supplementary_files_format_and_content: xls file include FPKM values of each genes and transcripts

growth_protocol: WJ-MSCs were cultured in DMEM (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS, Tissue Culture Biologicals, Tulare, CA, USA), 1% Glutamax (Gibco), 1% antibiotic/antimycotic solution (Gibco), EGF 25 µg/mL (Peprotech, Rocky Hill, NJ, US), and bFGF 50 ng/ml (Peprotech) in a humidified atmosphere containing 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) in WJ-MSC treated with or without 5 µg/mL of DEP.
Library construction using Illumina Truseq RNA protocol

value: human Wharton's jelly-derived mesenchymal stem cells

value: 5 ug/ml of Diesel exhaust particles


title: NT for ddN S1-END-seq in iNeuron

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37 degrees C for 20 mins.


title: Human Wharton’s jelly-derived mesenchymal stem cells - Control 2

treatment_protocol: 5 μg/mL of Diesel exhaust particle treated

value: untreated


title: genomic DNA from Labial salivary gland tissue 30

description: Case

source_name: Labial salivary gland tissue 30

tag: gender

value: Sjogrens Syndrome


title: FSTFemale45min4h_17_vHC_0min

description: polyA RNA

tag: condition

value: Homecage

tag: timepoint

tag: region

value: Male

value: both

value: WT

tag: mouseline

tag: libraryprotocol

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: ddN END-seq in iNeuron

value: 5 uM of each of ddA, ddT, ddG, and ddC chain-terminating nucleosides (20 uM total); 18 hours


title: genomic DNA from Labial salivary gland tissue 29

description: Case

source_name: Labial salivary gland tissue 29

value: Female

value: Labial salivary gland tissue

tag: disease status


title: 1372-RP-223

description: Treatment

value: Hartley Guinea Pig

value: Liver

value: High (100 mg/kg Thioacetamide)


title: 1372-RP-222

description: Control

value: Vehicle (3 ml/kg Saline)


title: FSTFemale45min4h_8_vHC_45min

description: polyA RNA

value: Swim

value: vHC

tag: Sex

tag: hemisphere

tag: animalnumber

tag: experiment

tag: block

tag: mousetype


title: HiC in iNeuron rep4

tag: cell type

value: neuron differentiated from iPSC


title: FSTFemale45min4h_10_vHC_4h

description: polyA RNA


title: ddN S1-END-seq in iNeuron

tag: treatment

tag: in-situ treatment

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37 degrees C for 20 mins.

tag: harvested day


title: FSTFemale45min4h_9_vHC_4h

description: polyA RNA

tag: condition


title: 1372-RP-220

description: Control

tag: breed

tag: tissue

tag: duration

value: 9 h

tag: dose


title: 1372-RP-221

description: Control


title: input in iNeuron

data_processing:
SAR-seq, END-seq, ChIP-seq, SEAL, and ATAC-seq reads were aligned to the reference genome (hg19 for human i3Neuron and iMuscle, mm10 for mouse pre B cells or rn6 for rat primary neurons) using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
We used MACS (v1.4.3) to call SAR-seq, XRCC1 ChIP-seq and ATAC-seq peaks. SAR-seq XRCC1, and CTCF ChIP-seq peaks with >10 fold-enrichment over background were kept. Peaks of hisone modification determined by ChIP-seq peaks were called by SICER with default parameters. Peaks within blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered. As peaks of ddN S1-END-seq are always clustered, subpeaks were called by the PeakSplitter tool of PeakAnalyzer with parameters -c 15 -v 0.6.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
Genome_build: hg19 for human, mm10 for mourse, rn6 for rat.
Supplementary_files_format_and_content: bigwig, bed

extract_protocol:
Cells were fixed in 1% formaldehyde. Cells were sonicated, lysates clarified, and protein-DNA complexes immunoprecipitated.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).  libraries were prepared and sequenced following standard Illumina protocols

value: NT

tag: chip antibody


title: HiC in iNeuron rep3


title: FSTFemale45min4h_7_vHC_0min

description: polyA RNA

value: Homecage

tag: timepoint

tag: region

value: both

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: genomic DNA from Labial salivary gland tissue 34

description: Non-case

source_name: Labial salivary gland tissue 34

tag: gender

tag: disease status

value: symptomatic not Sjogrens


title: 1372-RP-219

description: Control


title: Human Wharton’s jelly-derived mesenchymal stem cells - Control 1

tag: cell type

value: human Wharton's jelly-derived mesenchymal stem cells

value: untreated


title: FSTFemale45min4h_6_vHC_4h

description: polyA RNA

source_name: hippocampus

tag: Sex

value: Female

tag: hemisphere

tag: animalnumber

tag: experiment

tag: block

tag: mousetype

value: WT

value: illumina TruSeq

value: WholeRNA


title: Pol II ChIP-seq in iNeuron

tag: treatment

tag: harvested day


title: 1372-RP-218

description: Treatment

tag: breed

value: Hartley Guinea Pig

tag: tissue

value: Liver

tag: duration

tag: dose

value: Low (25 mg/kg Thioacetamide)


title: genomic DNA from Labial salivary gland tissue 31

description: Non-case

source_name: Labial salivary gland tissue 31

value: Labial salivary gland tissue


title: XRCC1 ChIP-seq in iNeuron

source_name: iNeuron

value: neuron differentiated from iPSC

tag: chip antibody


title: FSTFemale45min4h_5_vHC_0min

description: polyA RNA

tag: condition

tag: timepoint

tag: region

value: vHC

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: 1372-RP-217

description: Control

value: Vehicle (3 ml/kg Saline)


title: PAR ChIP-seq in iNeuron

tag: cell type

value: 10 uM PARG inhibitor; 20 minutes prior to harvest

value: 5 ug, Millipore-Sigma MABE1016


title: THP-1 control_3

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

description: Control for 48h

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

source_name: THP-1 cell line treated with control 3

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

tag: cell line

value: incubating with control for 48 h

value: DMSO as control


title: FSTFemale45min4h_3_vHC_45min

description: polyA RNA

value: Swim

tag: Sex

tag: hemisphere

value: both

tag: animalnumber

tag: experiment

tag: block


title: THP-1 treated with JOA_2

description: 2 μ M JOA treatment for 48 h

source_name: THP-1 cell line treated with JOA 2

tag: treatment

value: incubating with JOA for 48 h

value: 2 uM JOA


title: THP-1 treated with JOA_1

description: 2 μ M JOA treatment for 48 h

source_name: THP-1 cell line treated with JOA 1


title: H3K27me3 ChIP-seq in iNeuron

value: NT

value: 5 ug, Millipore, Cat. No. 07-449

tag: harvested day


title: H3K9me3 ChIP-seq in iNeuron

value: 10 ug, Active Motif, Cat. No. 39765


title: FSTFemale45min4h_2_vHC_4h

description: polyA RNA

value: Female

tag: mousetype

value: WT

value: illumina TruSeq

value: WholeRNA


title: 1372-RP-216

description: Treatment

tag: breed

value: Hartley Guinea Pig

tag: tissue

value: Liver

tag: duration

tag: dose

value: High (100 mg/kg Thioacetamide)


title: 1372-RP-215

description: Treatment

value: 9 h


title: THP-1 control_2

description: Control for 48h

source_name: THP-1 cell line treated with control 2

value: incubating with control for 48 h


title: THP-1 control_1

description: Control for 48h

source_name: THP-1 cell line treated with control 1

value: DMSO as control


title: H3K36me3 ChIP-seq in iNeuron

value: neuron differentiated from iPSC

tag: chip antibody

value: 5 ug, Abcam #9050


title: FSTFemale45min4h_4_vHC_45min

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

value: vHC

value: Male

value: both

tag: mouseline

tag: libraryprotocol


title: 1372-RP-213

description: Treatment

source_name: Liver

value: Low (25 mg/kg Thioacetamide)


title: FSTFemale45min4h_1_vHC_0min

description: polyA RNA

value: Homecage

tag: Sex

tag: hemisphere

tag: sampleprocessing


title: H3K4me3 ChIP-seq in iNeuron

tag: cell type

value: NT

value: 6 uL, Abcam #8580


title: 1372-RP-212

description: Treatment


title: KO_IL1_YFP_NEG, rep3

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina adapters were removed, along with the first 12 base pairs using BBDuk and reads <50bp after trimming were discarded
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl mouse transcriptome (GRCm38.p6, release 96)
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset
Differential gene expression was calculated using the voom function in limma
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file containing STAR gene count values. Differential expression tables produced by the limma R package.

source_name: Mice transplanted with KO, recipient WT MPP3, rep3

growth_protocol: MPP3 cells were sorted from recipient mice directly into RLT Buffer.

extract_protocol:
Total RNA isolated using RNeasy Micro Kit (Qiagen).
Library construction using the SMARTer® Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara)
paired-end sequencing performed on the NovaSeq 6000 instrument (Illumina)

treatment_protocol: Mice were treated with PBS or IL-1β (0.5 µg (Peprotech) per injection per mouse) for 20 days.

tag: treatment

tag: yfp

tag: sample genotype

value: WT

tag: mouse genotype

value: KO


title: MOLM-13 treated with JOA_2

description: 0.5 μ M JOA treatment for 48 h

source_name: MOLM-13 cell line treated with JOA 2

tag: cell line

value: incubating with JOA for 48 h

value: 0.5 uM JOA


title: CTCF ChIP-seq in iNeuron

value: 6 ul, Millipore, Cat. No. 07-729

tag: harvested day


title: THP-1 treated with JOA_3

description: 2 μ M JOA treatment for 48 h

source_name: THP-1 cell line treated with JOA 3

value: 2 uM JOA


title: MLL4 ChIP-seq in iNeuron

value: MLL4 homemade ab courtesy of Kai Ge Lab


title: 1372-RP-211

description: Control

tag: breed

value: Hartley Guinea Pig

tag: tissue

value: Liver

tag: duration

value: 9 h

tag: dose

value: Vehicle (3 ml/kg Saline)


title: MOLM-13 treated with JOA_1

description: 0.5 μ M JOA treatment for 48 h

source_name: MOLM-13 cell line treated with JOA 1


title: 1372-RP-214

description: Treatment


title: 1372-RP-210

description: Treatment


title: KO_IL1_YFP_POS, rep3

source_name: Mice transplanted with KO, donor MPP3, rep3


title: MOLM-13 control_2

description: Control for 48h

source_name: MOLM-13 cell line treated with control 2

value: incubating with control for 48 h

value: DMSO as control


title: H3K27ac ChIP-seq in iNeuron

value: neuron differentiated from iPSC

tag: chip antibody

value: 5 ug, Abcam #4729


title: KO_IL1_YFP_NEG, rep1

source_name: Mice transplanted with KO, recipient WT MPP3, rep1


title: H3K4me1 ChIP-seq in iNeuron

value: NT

value: 5 ug, Abcam #8895


title: KO_IL1_YFP_POS, rep2

source_name: Mice transplanted with KO, donor MPP3, rep2


title: 1372-RP-208

description: Treatment

value: High (100 mg/kg Thioacetamide)


title: KO_IL1_YFP_POS, rep1

source_name: Mice transplanted with KO, donor MPP3, rep1

value: KO


title: 1372-RP-209

description: Treatment


title: ATAC-seq

data_processing:
SAR-seq, END-seq, ChIP-seq, SEAL, and ATAC-seq reads were aligned to the reference genome (hg19 for human i3Neuron and iMuscle, mm10 for mouse pre B cells or rn6 for rat primary neurons) using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
We used MACS (v1.4.3) to call SAR-seq, XRCC1 ChIP-seq and ATAC-seq peaks. SAR-seq XRCC1, and CTCF ChIP-seq peaks with >10 fold-enrichment over background were kept. Peaks of hisone modification determined by ChIP-seq peaks were called by SICER with default parameters. Peaks within blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered. As peaks of ddN S1-END-seq are always clustered, subpeaks were called by the PeakSplitter tool of PeakAnalyzer with parameters -c 15 -v 0.6.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, bed

extract_protocol: i3Neurons were grown on 96-well plates (0.05x106 cells per well). Cells were washed gently with PBS. Then, 100 L of accutase per well was added and removed, and the plate was incubated at 37°C for 5 minutes. 50 μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) was added directly to the well for 10 minutes. Cells were then pipetted 10-20 times to break clumps and centrifuged at 500 × g for 10 minutes at 4°C. The nuclei pellet was resuspended in the Nextera transposition reaction mix (25 μL 2x TD Buffer, 2.5 μL Nextera Tn5 transposase (Illumina, Cat. No. FC-121-1030), and 22.5 μL nuclease free H2O) on ice, then incubated for 30 minutes at 37°C. The tagmented DNA was purified using the Qiagen MinElute kit and eluted with 10 μL Elution Buffer. Following purification, library fragments were amplified using the Nextera index kit (Illumina, Cat. No. FC-121-1011) under the following cycling conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute for a total of five cycles. To prevent saturation due to over-amplification, a 5 µL aliquot was then removed and subjected to qPCR for 20 cycles for calculation of the optimal number of cycles needed for the 45 µL reaction that remained. The number of additional cycles required was determined by plotting linear Rn vs. Cycle and calculating the cycle number corresponding to a quarter of the maximum fluorescence intensity. Adding seven cycles to this estimate was found to yield optimal libraries. PCR reactions were subsequently cleaned with Agencourt AMPure XP beads (Beckman Coulter), run on a 2% agarose gel and a smear of 200-800 bp was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina Nextseq550 (75 bp paired-end reads).


title: MOLM-13 control_3

description: Control for 48h

source_name: MOLM-13 cell line treated with control 3


title: MOLM-13 treated with JOA_3

description: 0.5 μ M JOA treatment for 48 h

source_name: MOLM-13 cell line treated with JOA 3

value: incubating with JOA for 48 h


title: 1372-RP-207

description: Treatment

value: Low (25 mg/kg Thioacetamide)


title: HeLa-3

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Samples were pooled and sequenced on one Illumina NovaSeq 6000 S1 run.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Reads were aligned to the reference genome (hg38 + HPV18) using STAR 2.7.0f with the following parameters: "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3  --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 clip3pAdapterSeq - --readFilesCommand zcat --runThreadN 32 --outSAMtype BAM Unsorted --chimSegmentMin 20"
Genome_build: hg38
Supplementary_files_format_and_content: TXT files containing predicted junctions containing HPV sequences (in STAR junction.out format)

source_name: HeLa cell

growth_protocol: All cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Thermo Fisher Scientific, Waltham, MA) with 10% fetal bovine serum (FBS, GE Healthcare, Logan, UT) at 37°C under a 5% CO2 atmosphere.

extract_protocol:
Total RNA from frozen tissues was extracted after homogenization using TriPure Isolation reagent (Roche) and treated with TURBO DNA-free™ Kit (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HeLa

tag: gender

value: female

tag: cancer type

value: Cervical


title: MOLM-13 control_1

description: Control for 48h

source_name: MOLM-13 cell line treated with control 1


title: HEK293T polyA RNA MgR-OED-rep3

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Cutadapt (v2.8) was used to cut the adapters of the paired-end reads with the following parameters: cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 15 -e 0.15.
The paired-end reads without adapters were further merged using FLASH software(v1.2.11) with following parameters: -z -m 10 -M 135 -x 0.25.
fastx_collapser software was used to collapse the reads with the default parameters. We included one 5’-end and one 3’-end tetramer barcode (NNNN) ligated to the insert fragments during library construction. These random sequences were used to identify or remove PCR duplicates. Reads with fully identical sequences, including the same barcode and insert fragment, were marked as PCR duplicates, and only one of the identical sequences was retained for subsequent analysis.
The random barcodes of the reads at the two termini were cut with Cutadapt (v2.8) with the parameters -u 4 –u -4.
These filtered reads were subsequently mapped to the human reference genome (hg38) and transcriptome with STAR software with the following parameters: --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 30 --outFilterMismatchNmax 15 --outFilterMismatchNoverLmax 0.1 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15 --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts.
To identify significantly enriched Nm sites, we calculated the coverage of the 3′ ends of the sequencing reads at each position in all annotated transcripts. We reasoned that the coverage of a candidate Nm site should be significantly higher over the one nucleotide upstream and downstream and over the corresponding position in the matched input sample. Finally, we developed the computational software endSeeker to calculate the 3’-end coverage of the candidate Nm sites (endCov), the one nucleotide upstream (upCov) and the one nucleotide downstream (downCov) in the MgR, MgR-OED and input data. To avoid the side-effects of random fragment experiments, for the one nucleotide upstream (upCov) and the one downstream nucleotide (downCov), the average coverage around the 3’-end sites in the input data was used. A positive signal had to meet the following criteria: (1) upFC=endCov/upCov≥3; (2) downFC=endCov/downCov≥3; (3) upCtrlFC=upFC_Nm/upFC_Input≥3; (4) downCtrlFC=downFC_Nm/downFC_Input≥3. A candidate Nm site was retained when it med the above criteria in all three replicates of the MgR and MgR-OED experiments. These stringent parameters allowed us to identify the highest-confidence candidate Nm sites.
Genome_build: hg38
Supplementary_files_format_and_content: wiggle files were generated using bamToWig software and big wiggle files were generated by wigToBigWig.
Supplementary_files_format_and_content: known Nm sites and novel Nm sites in the text files

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin-streptomycin under conditions of 37℃ and 5% CO2.

extract_protocol:
RNA was collected using RNAzol1, and polyA+ RNA was purified by Oligo d(T)25 Magnetic Beads (New England Biolabs) following the manufacturer’s instructions.
Total RNA or polyA+ RNA was chemically fragmented in to 20-200-nucleotides-long by RNA Fragmentation Reagents (Thermo Fisher Scientific). After purification and 3’ end repairation, the RNA was subjected to MgR digestion and followed by Oxidation-Elimination-Dephosphorylation treatment. The remaining RNA was 5‘end repaired and  then prepared for sequencing using small RNA library protocols except using the  high-definition 3'- and 5'- adaptors.

treatment_protocol: Untreated

value: treated with MgR and OED


title: 1372-RP-206

description: Treatment

value: Hartley Guinea Pig

value: Liver


title: KO_IL1_YFP_NEG, rep2

source_name: Mice transplanted with KO, recipient WT MPP3, rep2

value: WT


title: KO_PBS_YFP_NEG, rep2

value: PBS


title: HeLa-2


title: HEK293T polyA RNA MgR-OED-rep2


title: KO_PBS_YFP_NEG, rep3


title: KO_PBS_YFP_NEG, rep1


title: HEK293T polyA RNA MgR-OED-rep1


title: 1372-RP-204

description: Treatment


title: HeLa-1


title: KO_PBS_YFP_POS, rep3


title: 1372-RP-203

description: Control

value: Vehicle (3 ml/kg Saline)


title: 1372-RP-205

description: Treatment

value: 9 h


title: KO_PBS_YFP_POS, rep2


title: dCas9-KRAB_sgNeg_rep3

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Adapter sequences and low quality reads were trimmed using Trim Galore with "--illumina --fastqc -q 20 --stringency 3 --length 20".
Reads were then aligned to UCSC hg38 genome using bowtie2 (version 2.3.3.1) with "--end-to-end --sensitive".
Low-quality alignments and PCR duplicates were removed using Samtools and Picard MarkDuplicates.
Gene expression was counted using htseq-count with "-s no -m union -t exon".
Genome_build: Human (hg38)
Supplementary_files_format_and_content: Tab-delimited text files include gene expression count values for each sample.

growth_protocol: Protocol was according to ATCC.

extract_protocol:
RNA was extracted using TRIzol Reagent (cat# 15596018; ThermoFisher).
Library was constructed at CCHMC DNA Sequencing and Genotyping Core.

treatment_protocol: A549 cells were infected with lentiviral vectors carrying dCas9-KRAB and rat Nkx2-1 and then selected by puromycin (10 ug/ml) for dCas9-KRAB and by GFP sorting for rat NKX2-1.

value: lung carcinoma cell line A549

tag: genotype

value: constitutively expressing dCas9-KRAB and NKX2-1

value: dCas9 w/sgNon-Targeting Negative Control


title: 1372-RP-202

description: Control


title: dCas9-KRAB_sgSFTPB#2_rep3

value: dCas9 w/sgSFTPB#2


title: HEK293T polyA RNA MgR-rep1

value: treated with MgR


title: KO_PBS_YFP_POS, rep1

value: KO


title: 1372-RP-201

description: Treatment

value: Low (25 mg/kg Thioacetamide)


title: HEK293T polyA RNA MgR-rep2


title: dCas9-KRAB_sgSFTPB#2_rep2


title: HEK293T polyA RNA input-rep3

value: untreated


title: dCas9-KRAB_sgNeg_rep2


title: 1372-RP-200

description: Treatment

value: High (100 mg/kg Thioacetamide)


title: dCas9-KRAB_sgSFTPB#2_rep1


title: WT_IL1_YFP_NEG, rep2

source_name: Mice transplanted with WT, recipient MPP3, rep2


title: dCas9-KRAB_sgNeg_rep1


title: 1372-RP-199

description: Treatment

source_name: Liver


title: HEK293T polyA RNA input-rep2


title: HEK293T polyA RNA input-rep1


title: WT_IL1_YFP_NEG, rep1

source_name: Mice transplanted with WT, recipient MPP3, rep1


title: 1372-RP-198

description: Control


title: HEK293T total RNA MgR-OED-rep3


title: 6b4 ibm1

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

country: France

institute: Institut Jean-Pierre Bourgin - INRAE

data_processing:
Pre-processed high quality reads were mapped to the TAIR10 genome using bismark (v0.20.0) with default settings for paired-end libraries (Krueger and Andrews, 2011)
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files with cytosine methylation levels in CG,CHG and CHH contexts.

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Plants were grown under short day conditions for five weeks (experiment 1: 6b4-1, 6b4 jmj14, 6b4 jmj14 cmt3 drm2, 6b4 cmt3 drm2) or eight weeks (experiment 2: 6b4-2, 6b4 nac50 nac52, 6b4 ibm1)

extract_protocol:
Genomic DNA was isolated from leaf tissue using the Nucleospin Plant II Maxi kit (Macharey Nagel).
Library preparation and sequencing was performed by BGI Genomics (Hong Kong). Briefly, genomic DNA was fragmented to 100-300bp by Sonication, end-repaired and ligated to methylated adaptors. Bisulfite treatment was then performed using the EZ DNA Methylation-Gold kit (Zymo), and the bisulfite-treated fragments were PCR amplified and sequenced as paired-end 100bp reads (PE100) with DNBSEQ technology.

value: Leaf

value: 6b4 transgene in ibm1 mutant

tag: developmental stage

value: 8 weeks


title: WT_IL1_YFP_POS, rep3

source_name: Mice transplanted with WT, donor MPP3, rep3


title: HEK293T polyA RNA MgR-rep3


title: mouse_Liver 3

city: Cleveland

first: Brian

middle: P

last: Rubin

address: 9620 Carnegie Ave NE2-215

department: Cancer Biology

institute: Cleveland Clinic

data_processing:
Gapped aligment was performed to the mm10 genome with HISAT2 v2.1.0
Raw counts were created with Featurescounts v1.6.4
FPKM abundance measurements were generated with Cufflinks v2.2.1.3
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Tumors and control tissue were cold preserved at -80˚C till sample processing. Total RNA was isolated with the Qiagen RNAeasy kit.
RNA libraries were prepared for sequencing using the standard DNBSeq protocol (BGI).

tag: strain

tag: tissue location

value: Liver

value: liver


title: Nickase with DOX S1-END-seq in MCF10A

tag: cell type

tag: treatment

value: 5 µM Palbociclib for 48 hours to arrest cells in G1; 3 µg/mL doxycycline added for last 24 hours to induce Cas9D10A

tag: in-situ treatment

value: 1.8 U of S1 nuclease @15 mins on ice, followed by 37 degrees C for 20 mins.


title: HEK293T total RNA MgR-OED-rep2

value: treated with MgR and OED


title: WT_IL1_YFP_NEG, rep3

source_name: Mice transplanted with WT, recipient MPP3, rep3

tag: yfp

tag: sample genotype

value: WT

tag: mouse genotype


title: WT_IL1_YFP_POS, rep2

source_name: Mice transplanted with WT, donor MPP3, rep2


title: mouse_Liver 1


title: mouse_Liver 2


title: WT_IL1_YFP_POS, rep1

source_name: Mice transplanted with WT, donor MPP3, rep1


title: 6b4-2

value: 6b4 transgene in wild-type Col-0


title: Nickase without DOX S1-END-seq in MCF10A

value: 5 µM Palbociclib for 48 hours to arrest cells in G1

tag: harvested day


title: HEK293T total RNA MgR-OED-rep1

tag: cell line


title: mouse_EHE 3

source_name: EHE Tumor

value: Peritoneal Surface

tag: tissue

value: Epithelioid hemangioendothelioma (EHE)


title: WT_PBS_YFP_NEG, rep3

value: PBS


title: HEK293T total RNA MgR-rep2

value: treated with MgR


title: Human Wharton’s jelly-derived mesenchymal stem cells - 5 μg/mL of Diesel exhaust particle treated 2

value: human Wharton's jelly-derived mesenchymal stem cells

value: 5 ug/ml of Diesel exhaust particles


title: WT_PBS_YFP_NEG, rep2


title: HEK293T total RNA MgR-rep3


title: 6b4 drm2 cmt3

value: Leaf

value: 6b4 transgene in drm2/cmt3 mutant

value: 5 weeks


title: 6b4 jmj14 drm2 cmt3

value: 6b4 transgene in jmj14/drm2/cmt3 mutant


title: WT_PBS_YFP_NEG, rep1


title: HEK293T total RNA MgR-rep1


title: 6b4-1


title: 6b4 jmj14

value: 6b4 transgene in jmj14 mutant


title: mouse_EHE 2


title: WT_PBS_YFP_POS, rep3


title: WT_PBS_YFP_POS, rep2


title: 6b4 nac50 nac52

value: 6b4 transgene in nac50 nac52 mutant

value: 8 weeks


title: WT_PBS_YFP_POS, rep1


title: Dongjin(WT)_rep2

status: Public on Mar 24 2021

city: Pyeongchang

first: Jun Sung

last: Seo

state: Gangwon

address: Pyeongchangdaero 1447

department: Company-affiliated research institute

institute: LaSemilla Co. Ltd.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to IRGSP-1.0 whole genome using HISAT2 through bowtie2 aligner
Gene/transcript was assemblied using reference gene model by StringTie program. Trancript abundance measurement was calculated by read count and FPKM value.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Gtf files by Stringtie include FPKM values for each Sample.

organism: Oryza sativa Japonica Group

source_name: rice leaf

growth_protocol: Rice plants were grown in soil for 4 weeks at 28 °C with a cycle of 16 h light/ 8 h dark having light intensity of 200 µmol m-2 s-1

extract_protocol:
4-week-old rice leaves were ground with liquid nitrogen, and total RNA was extracted using Rneasy plant mini kit (Qiagen). Illumina TruSeq mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: No treatment

tag: growth stage

tag: cultivar

value: Dongjin

value: leaf


title: vRIC-seq_SARS-CoV-2_rep1

city: Beijing

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description: replicates were merged for processing

data_processing:
library strategy: virus-suitable RNA in situ conformation sequencing (vRIC-seq)
Illumina bcl2fastq conversion software (v.2.16) was used for base calling.
After the sequencing of vRIC-seq libraries, adapters and PCR duplicates were trimmed off using the Trimmomatic program (v.0.36) (Bolger et al., 2014) and homemade scripts, respectively. The poly(N) tails at the 3’ end were further clipped using the Cutadapt program (v.1.15) (Martin, 2011).
After filtering, the paired reads were first aligned to human 45S pre-rRNA, and the unmapped reads were further aligned to a pan-genome which consist of Chlorocebus sabaeus reference genome (genome assembly version: chlSab2) and SARS-CoV-2 reference genome (Refseq accession number NC_045512.2) using the STAR software (v020201) (Dobin et al., 2013). The parameters used were as follows: STAR --runMode alignReads --genomeDir index --readFilesIn read.fq --outFileNamePrefix outprefix --outFilterMultimapNmax 100 --outSAMattributes All --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --alignSJoverhangMin 15 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5.
The low-quality and secondary mapping results were filtered using the SAMtools package (v.0.1.19).
Genome_build: NC_045512.2
Supplementary_files_format_and_content: genome-wide RNA-RNA interaction in hic format produced by Juicebox

organism: Severe acute respiratory syndrome coronavirus 2

growth_protocol: Inactivated SARS-CoV-2 coronavirus was generated and purified as previously described (Gao et al. Science. 2020 Jul 3;369(6499):77-81. PMID: 32376603)

extract_protocol:
After pCp-biotin labelling and proximity ligation, 200 μl of proteinase K buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and 50 μl of proteinase K were applied to beads and sequentially incubated at 37 °C for 60 min and 56 °C for 15 min. The supernatant was isolated by magnet stand and transferred to a new EP tube. The RNA was extracted with 750 μl of TRIzol LS and 220 μl of chloroform following the manufacture’s instruction.
For fragmentation, 16 μl of total RNA was mixed with 4 μl of 5 × first-strand buffer (250 mM Tris-HCl pH 8.3, 375 mM KCl, 15 mM MgCl2) and incubated at 94 °C for 5 min, and then quickly put on ice. To enrich pCp-biotin marked chimeric RNAs, 20 μl of pre-blocked MyOne Streptavidin C1 beads, 30 μl of NF-H2O and 50 μl of 2 × TWB buffer were applied to each RNA sample and incubated at room temperature for 30 min by rotating. After washing four times with 1× TWB buffer, the beads were resuspended in 100 μl of PK buffer (100 mM NaCl, 10 mM Tris-HCl pH 7.0, 1 mM EDTA, 0.5% SDS) and incubated in Thermomixer at 95 °C for 10 min (1000 rpm). The tube was quickly placed on a magnet stand for 1 min and the supernatant was transferred to a new EP tube. This elution process was repeated two more times. Finally, the enriched RNAs were extracted with acid Phenol: chloroform and precipitated at the final concentration of 300 mM NaCl, with 3 volumes of -20°C ethanol and 1 μl of glycoblue. RNA was pelleted at 13,000 rpm and washed twice with 75% ETOH before resuspending in 10 μl of nuclease-free water. To synthesis first-strand cDNA, 0.5 μl of N6 primer (0.1 μg/μl) was added to the mixture and incubated at 65 °C for 5 min, followed by rapid placement on ice for at least 2 min. Reverse transcription was performed by further addition of 5.5 μl of reverse transcription mix (3 μl of 5 × first-strand buffer, 1 μl of 10 mM dNTPs, 0.5 μl of 100 mM DTT, 0.5 μl of RNase inhibitor, 0.5 μl of Superscript II reverse transcriptase) to the mixture and incubation at 25 °C for 10 min, 42 °C for 40 min and then 70 °C for 15 min. We next created dUTP second strand cDNA by adding the following reaction mixture (10 μl of 5 × second-strand buffer, 0.8 μl of 25 mM dNTPs with 80% of the dTTP replaced by dUTP, 20.5 μl of RNase-free water, 0.2 μl of 5 U/μl RNase H and 2.5 μl of E. coli DNA polymerase I) to the first-strand cDNA mixture, and incubated at 16 °C for 2 h. The double-stranded (ds)DNA products were purified using 1.8 × AMPure beads following the manufacturer’s protocol and end-repaired with a mixture of T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. The end-repaired DNA was then treated with Klenow exo- to add an adenine to the 3’ ends. For paired-end library construction, adaptors were ligated to dsDNA using quick T4 DNA ligase and incubated at 20 °C for 15 min. Subsequently, the ligated DNA product was purified twice with AMPure beads. The adaptor-ligated cDNA was mixed with 1 μl of 10 μM Illumina PE1.0, 1 μl of 10 μM index primer, 1 μl of 50 mM MgSO4, 2.5 μl of 10 × Pfx buffer, 0.4 μl of 25 mM dNTPs, 0.4 μl of 2.5 U/μl Platinum Pfx DNA polymerase (Thermo Fisher, 11708-013) and 3 μl of USER enzyme (NEB, M5505S). The mixture was incubated at 37 °C for 15 min to allow the USER enzyme to digest the dUTP strand, then at 94 °C for 2 min. PCR was performed with the following programme: 11 to 13 cycles of 94 °C for 15 s, 62 °C for 30 s and 72 °C for 30 s. The 200 to 450 bp of PCR products were purified from agarose gel by Qiaqucik mini Elute Kit. The DNA concentration was measured by Qubit and sequenced by Illumina paired-end sequencing.

treatment_protocol: To capture the virus particles, 150 μl BioMag®Plus Concanavalin A beads were washed twice with binding buffer (20 mM HEPS-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). The tube was placed on a magnet stand for 1 min, and discard the supernatant. Resuspended the beads with 100 μl virus particles mixed with 400 μl binding buffer and incubate for 10 min at room temperature. After washing three times with binding buffer and once with PBST buffer (1 × PBS, 0.1% Tween 20), the beads were resuspended in 1 ml PBST buffer. Add 27 μl formaldehyde and incubate for 10 min at room temperature with rotating at 20 rpm and then quenched by 0.125 M glycine. After washing three times with PBST buffer, the beads were resuspended in 1 ml of permeabilization buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP-40, 0.3% Triton X-100, 0.1% Tween 20, 1× protease inhibitors, 2 U/ml SUPERase In RNase inhibitor), mixed briefly and incubated on ice for 15 min. After washing three times with 1 × PNK buffer (50 mM Tris-HCl pH7.4, 10 mM MgCl2, 0.1% Tween 20), the beads were briefly incubated with 200 μl of 1 × MN mixture (50 mM Tris-HCl pH 8.0, 5 mM CaCl2, 0.03 U/μl micrococcal nuclease) for 10 min at 37 °C. The reaction was stopped by washing twice with 1 × PNK + EGTA buffer (50 mM Tris- HCl pH7.4, 20 mM EGTA 0.1% Tween 20) and twice with 1 × PNK buffer (50 mM Tris-HCl pH7.4, 10 mM MgCl2, 0.1% Tween 20).

tag: sample type

value: Inactivated SARS-CoV-2 coronavirus


title: OsGRP3 KD_rep2

value: OsGRP3 Knock-down


title: vRIC-seq_SARS-CoV-2_rep2

description: replicates were merged for processing


title: Dongjin(WT)_rep1

value: WT


title: EHE 1

data_processing:
Alignment to the mm10 genome, demultiplexing, and counting was performed with CellRanger v3.0.2
Genome_build: mm10
Supplementary_files_format_and_content: Barcode, features, MTX matrix and h5 files from CellRanger

extract_protocol:
Tumors were cryopreserved in 10%DMSO in fetal bovine serum and slow frozen to -80˚C. Following histologic confirmation, samples were rewarmed and dissociated with the MACS tumor dissociation kit.
Single Cell library preparations with the 10X genomics platform

value: Peritoneal Surface

tag: tissue type

value: Epithelioid hemangioendothelioma (EHE) tumor


title: 111617p4_H9_S381

city: Boston

first: Lauren

last: Mifflin

state: MA

address: 260 Longwood Ave

department: Department of Cell Biology

institute: Harvard Medical School

description: Optn KO-2

data_processing:
scumi pipeline, The samples which are not showing up in the processed data were filtered out during QC.
Genome_build: mm10
Supplementary_files_format_and_content: nextseq_180111_rsem.genes.tpm.matrix

source_name: Spinal cord

extract_protocol:
Spinal cords were digested in Accutase; myelin was removed using a 0.25% BSA spin, cells were stained for CD45, CD11b, and CX3CR1 and single cells were isolated into plates using FACS Aria II
Samples were prepared according to the SmartSeq2 protocol

tag: genotype

value: Optn KO


title: EHE 2


title: OsGRP3 OX_rep2

value: Overexpressing OsGRP3

value: Nakdong


title: Nakdong(WT)_rep1


title: OsGRP3 OX_rep1


title: 111617p4_H7_S379

description: Optn KO-2


title: Nakdong(WT)_rep2


title: 111617p4_H5_S377

description: Optn KO-2


title: 111617p4_H8_S380

description: Optn KO-2


title: 111617p4_H3_S375

description: Optn KO-2


title: mouse_EHE 1

value: Epithelioid hemangioendothelioma (EHE)


title: 111617p4_H6_S378

description: Optn KO-2


title: HEK293T total RNA input-rep3

value: untreated


title: 111617p4_H4_S376

description: Optn KO-2


title: 111617p4_H2_S374

description: Optn KO-2


title: 111617p4_H12_S384

description: Optn KO-2


title: 111617p4_H1_S373

description: Optn KO-2


title: 111617p4_H11_S383

description: Optn KO-2


title: HEK293T total RNA input-rep2


title: HEK293T total RNA input-rep1


title: 111617p4_H10_S382

description: Optn KO-2


title: 111617p4_G9_S369

description: Optn KO-2


title: OsGRP3 KD_rep1


title: 111617p4_G8_S368

description: Optn KO-2


title: 111617p4_G7_S367

description: Optn KO-2


title: 111617p4_G6_S366

description: Optn KO-2


title: 111617p4_G5_S365

description: Optn KO-2


title: 111617p4_G4_S364

description: Optn KO-2


title: 111617p4_G3_S363

description: Optn KO-2


title: 111617p4_G2_S362

description: Optn KO-2


title: 111617p4_G1_S361

description: Optn KO-2


title: 111617p4_G11_S371

description: Optn KO-2


title: 111617p4_G10_S370

description: Optn KO-2


title: 111617p4_G12_S372

description: Optn KO-2


title: 111617p4_F5_S353

description: Optn KO-2


title: 111617p4_F6_S354

description: Optn KO-2


title: 111617p4_F1_S349

description: Optn KO-2


title: 111617p4_F3_S351

description: Optn KO-2


title: 111617p4_F4_S352

description: Optn KO-2


title: 111617p4_F8_S356

description: Optn KO-2


title: 111617p4_F11_S359

description: Optn KO-2


title: 111617p4_F2_S350

description: Optn KO-2


title: 111617p4_F9_S357

description: Optn KO-2


title: 111617p4_E7_S343

description: Optn KO-2


title: 111617p4_E8_S344

description: Optn KO-2


title: 111617p4_E9_S345

description: Optn KO-2


title: 111617p4_E6_S342

description: Optn KO-2


title: 111617p4_E5_S341

description: Optn KO-2


title: 111617p4_E2_S338

description: Optn KO-2


title: 111617p4_E4_S340

description: Optn KO-2


title: 111617p4_E3_S339

description: Optn KO-2


title: 111617p4_E12_S348

description: Optn KO-2


title: 111617p4_E1_S337

description: Optn KO-2


title: 111617p4_F7_S355

description: Optn KO-2


title: 111617p4_F12_S360

description: Optn KO-2


title: 111617p4_D9_S333

description: Optn KO-2


title: 111617p4_E10_S346

description: Optn KO-2


title: 111617p4_D8_S332

description: Optn KO-2


title: 111617p4_D5_S329

description: Optn KO-2


title: 111617p4_D3_S327

description: Optn KO-2


title: 111617p4_D4_S328

description: Optn KO-2


title: 111617p4_D1_S325

description: Optn KO-2


title: 111617p4_D2_S326

description: Optn KO-2


title: 111617p4_F10_S358

description: Optn KO-2


title: 111617p4_D12_S336

description: Optn KO-2


title: 111617p4_C7_S319

description: Optn KO-2


title: 111617p4_C8_S320

description: Optn KO-2


title: 111617p4_C5_S317

description: Optn KO-2


title: 111617p4_C6_S318

description: Optn KO-2


title: 111617p4_D10_S334

description: Optn KO-2


title: 111617p4_C9_S321

description: Optn KO-2


title: 111617p4_C4_S316

description: Optn KO-2


title: 111617p4_D11_S335

description: Optn KO-2


title: 111617p4_C2_S314

description: Optn KO-2


title: 111617p4_C3_S315

description: Optn KO-2


title: 111617p4_C1_S313

description: Optn KO-2


title: 111617p4_C12_S324

description: Optn KO-2


title: 111617p4_C11_S323

description: Optn KO-2


title: 111617p4_C10_S322

description: Optn KO-2


title: 111617p4_D7_S331

description: Optn KO-2


title: 111617p4_D6_S330

description: Optn KO-2


title: 111617p4_B8_S308

description: Optn KO-2


title: 111617p4_B6_S306

description: Optn KO-2


title: 111617p4_B5_S305

description: Optn KO-2


title: 111617p4_B7_S307

description: Optn KO-2


title: 111617p4_B4_S304

description: Optn KO-2


title: 111617p4_B12_S312

description: Optn KO-2


title: 111617p4_B3_S303

description: Optn KO-2


title: 111617p4_B2_S302

description: Optn KO-2


title: 111617p4_A9_S297

description: Optn KO-2


title: 111617p4_E11_S347

description: Optn KO-2


title: 111617p4_B11_S311

description: Optn KO-2


title: 111617p4_B10_S310

description: Optn KO-2


title: 111617p4_A2_S290

description: Optn KO-2


title: 111617p4_A4_S292

description: Optn KO-2


title: 111617p4_A8_S296

description: Optn KO-2


title: 111617p4_A1_S289

description: Optn KO-2


title: 111617p4_A11_S299

description: Optn KO-2


title: 111617p4_A12_S300

description: Optn KO-2


title: 111617p3_H8_S284

description: Optn KO-2


title: 111617p4_A5_S293

description: Optn KO-2


title: 111617p4_A7_S295

description: Optn KO-2


title: 111617p3_H7_S283

description: Optn KO-2


title: 111617p4_A3_S291

description: Optn KO-2


title: 111617p4_B9_S309

description: Optn KO-2


title: 111617p4_A10_S298

description: Optn KO-2


title: 111617p3_H5_S281

description: Optn KO-2


title: 111617p3_H9_S285

description: Optn KO-2


title: 111617p3_H6_S282

description: Optn KO-2


title: 111617p3_H4_S280

description: Optn KO-2


title: 111617p4_B1_S301

description: Optn KO-2


title: 111617p3_H1_S277

description: Optn KO-2


title: 111617p3_H11_S287

description: Optn KO-2


title: 111617p3_H2_S278

description: Optn KO-2


title: 111617p3_H3_S279

description: Optn KO-2


title: 111617p3_H12_S288

description: Optn KO-2


title: 111617p4_A6_S294

description: Optn KO-2


title: 111617p3_G7_S271

description: Optn KO-2


title: 111617p3_G5_S269

description: Optn KO-2


title: 111617p3_G6_S270

description: Optn KO-2


title: 111617p3_G8_S272

description: Optn KO-2


title: 111617p3_G2_S266

description: Optn KO-2


title: 111617p3_G3_S267

description: Optn KO-2


title: 111617p3_G12_S276

description: Optn KO-2


title: 111617p3_G1_S265

description: Optn KO-2


title: 111617p3_F9_S261

description: Optn KO-2


title: 111617p3_G9_S273

description: Optn KO-2


title: 111617p3_F4_S256

description: Optn KO-2


title: 111617p3_F5_S257

description: Optn KO-2


title: 111617p3_F6_S258

description: Optn KO-2


title: 111617p3_G10_S274

description: Optn KO-2


title: 111617p3_F7_S259

description: Optn KO-2


title: 111617p3_F3_S255

description: Optn KO-2


title: 111617p3_F1_S253

description: Optn KO-2


title: 111617p3_F2_S254

description: Optn KO-2


title: 111617p3_F12_S264

description: Optn KO-2


title: 111617p3_F11_S263

description: Optn KO-2


title: 111617p3_H10_S286

description: Optn KO-2


title: 111617p3_E9_S249

description: Optn KO-2


title: 111617p3_F10_S262

description: Optn KO-2


title: 111617p3_E7_S247

description: Optn KO-2


title: 111617p3_E8_S248

description: Optn KO-2


title: 111617p3_E5_S245

description: Optn KO-2


title: 111617p3_G4_S268

description: Optn KO-2


title: 111617p3_E3_S243

description: Optn KO-2


title: 111617p3_E2_S242

description: Optn KO-2


title: 111617p3_E4_S244

description: Optn KO-2


title: 111617p3_G11_S275

description: Optn KO-2


title: 111617p3_E1_S241

description: Optn KO-2


title: 111617p3_F8_S260

description: Optn KO-2


title: 111617p3_E10_S250

description: Optn KO-2


title: 111617p3_D9_S237

description: Optn KO-2


title: 111617p3_D8_S236

description: Optn KO-2


title: 111617p3_D5_S233

description: Optn KO-2


title: 111617p3_D6_S234

description: Optn KO-2


title: 111617p3_D3_S231

description: Optn KO-2


title: 111617p3_D12_S240

description: Optn KO-2


title: 111617p3_E6_S246

description: Optn KO-2


title: 111617p3_D2_S230

description: Optn KO-2


title: 111617p3_D1_S229

description: Optn KO-2


title: 111617p3_D10_S238

description: Optn KO-2


title: 111617p3_C8_S224

description: Optn KO-2


title: 111617p3_D11_S239

description: Optn KO-2


title: 111617p3_C9_S225

description: Optn KO-2


title: 111617p3_C5_S221

description: Optn KO-2


title: 111617p3_C7_S223

description: Optn KO-2


title: 111617p3_C4_S220

description: Optn KO-2


title: 111617p3_C6_S222

description: Optn KO-2


title: 111617p3_C1_S217

description: Optn KO-2


title: 111617p3_C3_S219

description: Optn KO-2


title: 111617p3_E11_S251

description: Optn KO-2


title: 111617p3_C10_S226

description: Optn KO-2


title: 111617p3_E12_S252

description: Optn KO-2


title: 111617p3_B9_S213

description: Optn KO-2


title: 111617p3_C2_S218

description: Optn KO-2


title: 111617p3_D7_S235

description: Optn KO-2


title: 111617p3_D4_S232

description: Optn KO-2


title: 111617p3_B7_S211

description: Optn KO-2


title: 111617p3_B6_S210

description: Optn KO-2


title: 111617p3_B5_S209

description: Optn KO-2


title: 111617p3_B8_S212

description: Optn KO-2


title: 111617p3_B3_S207

description: Optn KO-2


title: 111617p3_B4_S208

description: Optn KO-2


title: 111617p3_B2_S206

description: Optn KO-2


title: 111617p3_B12_S216

description: Optn KO-2


title: 111617p3_B10_S214

description: Optn KO-2


title: 111617p3_B11_S215

description: Optn KO-2


title: 111617p3_A9_S201

description: Optn KO-2


title: 111617p3_A8_S200

description: Optn KO-2


title: 111617p3_B1_S205

description: Optn KO-2


title: 111617p3_C11_S227

description: Optn KO-2


title: 111617p3_A5_S197

description: Optn KO-2


title: 111617p3_A6_S198

description: Optn KO-2


title: 111617p3_C12_S228

description: Optn KO-2


title: 111617p3_A4_S196

description: Optn KO-2


title: 111617p3_A1_S193

description: Optn KO-2


title: 111617p3_A12_S204

description: Optn KO-2


title: 111617p3_A2_S194

description: Optn KO-2


title: 111617p3_A3_S195

description: Optn KO-2


title: 111617p3_A11_S203

description: Optn KO-2


title: 111617p2_H5_S185

description: Optn KO-1


title: 111617p2_H7_S187

description: Optn KO-1


title: 111617p2_H6_S186

description: Optn KO-1


title: 111617p2_H9_S189

description: Optn KO-1


title: 111617p2_H8_S188

description: Optn KO-1


title: 111617p2_H3_S183

description: Optn KO-1


title: 111617p2_H1_S181

description: Optn KO-1


title: 111617p2_H2_S182

description: Optn KO-1


title: 111617p3_A10_S202

description: Optn KO-2


title: 111617p2_H10_S190

description: Optn KO-1


title: 111617p2_H11_S191

description: Optn KO-1


title: 111617p2_H4_S184

description: Optn KO-1


title: 111617p2_G8_S176

description: Optn KO-1


title: 111617p2_G6_S174

description: Optn KO-1


title: 111617p2_G9_S177

description: Optn KO-1


title: 111617p2_G4_S172

description: Optn KO-1


title: 111617p2_G5_S173

description: Optn KO-1


title: 111617p2_G3_S171

description: Optn KO-1


title: 111617p2_G7_S175

description: Optn KO-1


title: 111617p3_A7_S199

description: Optn KO-2


title: 111617p2_G11_S179

description: Optn KO-1


title: 111617p2_G1_S169

description: Optn KO-1


title: 111617p2_G10_S178

description: Optn KO-1


title: 111617p2_F9_S165

description: Optn KO-1


title: 111617p2_F8_S164

description: Optn KO-1


title: 111617p2_F6_S162

description: Optn KO-1


title: 111617p2_F2_S158

description: Optn KO-1


title: 111617p2_H12_S192

description: Optn KO-1


title: 111617p2_F3_S159

description: Optn KO-1


title: 111617p2_G12_S180

description: Optn KO-1


title: 111617p2_F7_S163

description: Optn KO-1


title: 111617p2_F1_S157

description: Optn KO-1


title: 111617p2_F4_S160

description: Optn KO-1


title: 111617p2_F11_S167

description: Optn KO-1


title: 111617p2_F5_S161

description: Optn KO-1


title: 111617p2_E6_S150

description: Optn KO-1


title: 111617p2_E9_S153

description: Optn KO-1


title: 111617p2_E8_S152

description: Optn KO-1


title: 111617p2_E7_S151

description: Optn KO-1


title: 111617p2_E5_S149

description: Optn KO-1


title: 111617p2_G2_S170

description: Optn KO-1


title: 111617p2_E4_S148

description: Optn KO-1


title: 111617p2_E3_S147

description: Optn KO-1


title: 111617p2_E1_S145

description: Optn KO-1


title: 111617p2_E11_S155

description: Optn KO-1


title: 111617p2_E12_S156

description: Optn KO-1


title: 111617p2_E10_S154

description: Optn KO-1


title: 111617p2_F10_S166

description: Optn KO-1


title: 111617p2_D9_S141

description: Optn KO-1


title: 111617p2_D6_S138

description: Optn KO-1


title: 111617p2_D8_S140

description: Optn KO-1


title: 111617p2_D5_S137

description: Optn KO-1


title: 111617p2_D7_S139

description: Optn KO-1


title: 111617p2_F12_S168

description: Optn KO-1


title: 111617p2_D4_S136

description: Optn KO-1


title: 111617p2_D2_S134

description: Optn KO-1


title: 111617p2_D10_S142

description: Optn KO-1


title: 111617p2_D11_S143

description: Optn KO-1


title: 111617p2_D3_S135

description: Optn KO-1


title: 111617p2_D1_S133

description: Optn KO-1


title: 111617p2_C9_S129

description: Optn KO-1


title: 111617p2_D12_S144

description: Optn KO-1


title: 111617p2_C8_S128

description: Optn KO-1


title: 111617p2_C7_S127

description: Optn KO-1


title: 111617p2_C5_S125

description: Optn KO-1


title: 111617p2_C6_S126

description: Optn KO-1


title: 111617p2_C3_S123

description: Optn KO-1


title: 111617p2_C4_S124

description: Optn KO-1


title: 111617p2_C12_S132

description: Optn KO-1


title: 111617p2_C11_S131

description: Optn KO-1


title: 111617p2_C10_S130

description: Optn KO-1


title: 111617p2_B7_S115

description: Optn KO-1


title: 111617p2_B6_S114

description: Optn KO-1


title: 111617p2_C2_S122

description: Optn KO-1


title: 111617p2_E2_S146

description: Optn KO-1


title: 111617p2_B3_S111

description: Optn KO-1


title: 111617p2_C1_S121

description: Optn KO-1


title: 111617p2_B2_S110

description: Optn KO-1


title: 111617p2_B4_S112

description: Optn KO-1


title: 111617p2_B1_S109

description: Optn KO-1


title: 111617p2_A9_S105

description: Optn KO-1


title: 111617p2_B5_S113

description: Optn KO-1


title: 111617p2_B11_S119

description: Optn KO-1


title: 111617p2_A5_S101

description: Optn KO-1


title: 111617p2_B8_S116

description: Optn KO-1


title: 111617p2_A7_S103

description: Optn KO-1


title: 111617p2_B10_S118

description: Optn KO-1


title: 111617p2_A3_S99

description: Optn KO-1


title: 111617p2_A12_S108

description: Optn KO-1


title: BCU002519_Low-Saffron

city: Piacenza

first: Marcello

last: Del Corvo

address: Via Emilia Parmense, 84

department: Institute of Zootechnics, Faculty of Agricultural, Food and Environmental Sciences

country: Italy

institute: Università Cattolica del S. Cuore

data_processing:
Library strategy: Methylation-sensitive restriction enzyme sequencing (MRE-seq)
All sequence reads were cleaned to guarantee high quality data by removing adaptor reads, ambiguous reads, low quality regions (Q30), and short sequences (<50 bp) using bowtie2 (version 2.0.5; Langmead and Salzberg, 2012), samtools (version 1.2; Li et al., 2009), and bedtools (version v2.24.0; Quinlan and Hall, 2010). Then, sequence reads were analysed using the same pipeline for their origin from potential repetitive elements (RE-dat database (Nussbaumer et al., 2013), ribosomal data (using ribosomal sequences from NCBI and unpublished in-house data), chloroplast and mitochondrial DNA. Because of the absence of a reference genome for saffron crocus, the rice genome Oryza sativa ssp. japonica release 7 (Kawahara et al., 2013) was used as a reference.
All the high quality (HQ) read pairs were tested to detect whether their ends overlapped with a minimal overlap of 10 bp and a maximal overlap of 250 bp using Flash (version: 1.2.10; Magoc and Salzberg, 2011).
The de novo assembly for each accession and for the combined dataset was performed using Trinity (version: 2.1.1; Haas et al., 2013) with a minimal contig length of 100 bp. The resulting contigs were evaluated by mapping the high-quality reads used for the assembly to the assembled contig sequences using bowtie2 with default settings (version 2.0.5; Langmead and Salzberg, 2012), and only contigs consisting of at least five reads were retained. The resulting files were further processed using samtools (version 1.2; Li et al., 2009) and bedtools (version v2.24.0; Quinlan and Hall, 2010).
To identify single nucleotide polymorphisms (SNP), the per base coverage was estimated using mpileup included in the samtools software package (version 1.2; Li et al., 2009) with the parameter –AB. All SNPs and Indels were identified using picard tools (version 2.2.1; http://broadinstitute.github.io/picard) and HaplotypeCaller of GATK (version 3.5-0-g36282e4; DePristo et al., 2011; McKenna et al., 2010). The difference of each position was calculated based on the base occurrences at that position. The base counts for each position were regarded as vectors and normalised for each trait with the coverage of the position resulting in comparable vectors. The resulting difference score represented the sum of the absolute values over all base possibilities. It ranged from 0 to 200. True SNPs were considered in the presence of a difference score higher than 180.
Genome_build: Oryza sativa ssp. Japonica
Supplementary_files_format_and_content: For each sample were generated a vcf (variant call format) text file.

organism: Crocus sativus

source_name: Leaves

growth_protocol: Five accessions from the WSCC (World Saffron and Crocus Collection, located in the Centro de Investigación Agroforestal de Albadalejito, Cuenca, Spain) germplasm showing stable alternative phenotypes were selected for the study. The five accessions were co-cultivated in the same field for at least 8 consecutive years before the analysis. The experimental farm of Cuenca is located at an altitude of 950–1,000 metres a.s.l. The edaphic characteristics of the fields are those common for the area, with sandy loams, alkaline pH (7.6–8.4), normal electrical conductivity (<400 mmhos/cm) and a low 104 organic matter content (1–2.5%).

extract_protocol:
Leaves were lyophilised and preserved at -80°C until analysis. DNA extractions were carried out using the commercial kit GeneElute Plant Genomic DNA Miniprep Kit (Sigma-Aldrich) according to the manufacturer’s instructions with one minor modification. In detail, we added 4% w/w of PVP (polyvinylpyrrolidone; Soffritti et al., 2016) to each sample during DNA extraction to facilitate the removal of secondary metabolites, such as polyphenols, and to produce a purer DNA for the subsequent analysis.
To carry out the methyl filtration enrichment of gene-related sequences, genomic DNA was digested using the restriction enzyme HpaII. This enzyme was selected because it is able to achieve very good gene space coverage and very good depletion of transposable elements, as also reported in Wischnitzki et al. (2015). In brief, the steps of the MRE-seq analysis are: 1) digestion of 300 ng of genomic DNA with the restriction enzyme HpaII and contemporary ligation of double strand adaptors to the generated fragments; 2) PCR amplification of the adaptor- ligated DNA; 3) removal of the adaptor sequences by PmeI digestion (the sequence of the adaptor includes the rare cutting site of the enzyme GTTTAAAC). This step is important to increase the length of the informative sequences; 4) sequencing of the generated DNA fragments was done on an Illumina MiSeq platform (300 bp paired-end reads). All steps were carried out exactly as reported in detail in Wischnitzki et al. (2015).

tag: origin

value: Spain

tag: phenotype

value: Low saffron

value: Leaves


title: 111617p2_B12_S120

description: Optn KO-1


title: 111617p2_A1_S97

description: Optn KO-1


title: BCU001754_Diff-Pigmentation

value: India

value: Different pigmentation


title: 111617p2_B9_S117

description: Optn KO-1


title: BCU001668_Late-Flowering

value: Late flowering


title: 111617p2_A11_S107

description: Optn KO-1


title: 111617p2_A10_S106

description: Optn KO-1


title: 111617p2_A4_S100

description: Optn KO-1


title: BCU001610_High-Saffron

value: High saffron


title: 111617p1_H9_S93

description: Optn KO-1


title: 111617p1_H8_S92

description: Optn KO-1


title: 111617p2_A2_S98

description: Optn KO-1


title: BCU001637_Early-Flowering

value: Early flowering


title: 111617p1_H7_S91

description: Optn KO-1


title: SC207_IPAH_36year_female

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

data_processing:
FASTQ files were generated by using CellRanger mkfastq, a wrapper for bcl2fastq
Aligned to the 10X Genomics human reference genome, refdata-cellranger-GRCh38-3.0.0, with Cell Ranger 3.0.2 using cellranger count function
Cell Ranger output of raw_feature_bc_matrix.h5 was analyzed in R using the Seurat package
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data file is in hierarchical data format (HDF).  It contains a gene x cell matrix with mRNA counts per cell of each gene.  Genes are in rows and cells are designated by barcodes in each column with UMI (unique molecular identifier) counts for each gene provided.

source_name: whole lung

extract_protocol:
Explanted lungs were finely diced and digested for 1 hour in a mix of collagenase A/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v1 and Single Cell 3’ Reagent Kits v2 User Guide
single cell RNA-seq

tag: chemistry

value: 10X Genomics 3Prime V2 chemistry

tag: disease state

value: IPAH

tag: protocol

value: digested into single cell suspension

value: whole lung


title: 111617p1_H6_S90

description: Optn KO-1

value: Optn KO


title: 111617p1_H3_S87

description: Optn KO-1


title: miRNA-HepG2

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

institute: Peking University

data_processing:
For PolyA(+) RNA-seq,Adapteor was removed by trimmomatic-0.39, HISAT2 software was used to align sequencing reads to reference mRNA. For small RNA-seq, homemade PERL software was used to  remove adaptor sequences, and Bowtie sofeware was used to align sequencing reads to miRNA database
For polyA(+) RNA-seq,mouse Cdna database(UCSC, NCBI37)  was used for alignment. For small RNA-seq, 20-25nt small RNAs was aligned to known mature miRNA sequences(miRBase)
Both polyA(+) and small RNA-seq, Reads per Million was calculated for the normalization
Genome_build: mm9
Supplementary_files_format_and_content: csv

source_name: WT

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina)。Small RNA-seq libraries preparation using NEBNext® Small RNA Library Prep Set for Illumina kit。

value: WT