title: YOL** rep4

city: University Park

first: Nabeel

last: Ahmed

state: PENNSYLVANIA

address: 407 Chemistry Building

department: The Huck Institutes of the Life Sciences

institute: Pennsylvania State University

description: mutant yeast

data_processing:
Library strategy: Ribosome Profiling
The raw reads were first trimmed of their 3′ adapter sequence CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG using cutadapt v1.14
The reads were also subject to a quality filter of at least 20 during the cutadapt run.
Preprocessed reads were first mapped to a set of ribosomal RNA sequences using Bowtie2  and then subsequently the unmapped reads were mapped to the rest of S. cerevisiae reference genome sacCer3 using Tophat2. For each mutant strain, the sequence at the mutated nucleotide positions was altered in the reference genome for accurate mapping of reads
Gene annotations were obtained from Saccharomyces Genome Database (http://www.yeastgenome.org/) on October 30, 2014.
Custom python scripts were implemented for all downstream analyses. Mapped reads were first quantified by their 5′ ends on individual gene transcripts and A-site positions were assigned according to Table 1 in Ahmed et.al., Scientific Reports (2019).  To maintain the accuracy of read assignment, transcripts in which multiple mapped reads constitute more than 0.1% of the reads mapped to the CDS region were not considered in the analysis.
Genome_build: sacCer3
Supplementary_files_format_and_content: wig files containing coverage at chromosome position determined from 5' end of the reads

source_name: yeast

growth_protocol: 200 ml of yeast cells grown in YPD, at 30°C to an optical density (OD600) of 0.5

extract_protocol:
Thawed cell lysates were cleared by centrifugation (20,000xg, 5 min, 4°C) and digested by RNase I (AM2295, Ambion; 125 U/1mg nucleic acid) for 1 hr (25°C, 650 rpm) to obtain ribosome footprints. The reaction was stopped by adding 10 µl SUPERase-In (AM2696, Ambion). The digested lysate was loaded onto 10 50% (w/v) sucrose gradients and centrifuged at 35,000 rpm, 4°C for 2.5 hrs. Gradients were fractionated and monosome fractions were collected, pooled and used for RNA purification by hot acid-phenol extraction. 5 µg of purified RNA was depleted for rRNA using the Ribo-Zero Gold for Yeast kit (MRZY1306, Illumina).
Samples were heated at 80°C for 2 min and  50 μg of RNA  was loaded onto a 15% TBE-Urea polyacrylamide gels (Invitrogen) in 1x TBE (Ambion) and run for 65 min at 200 V. Gels were stained for 20 min with SYBR gold (Invitrogen). To recover ribosomal footprints, the gel pieces were excised that contained RNA fragments with a size between 25 and 33 nt. Gel pieces were placed into 0.5 mL gel breaker tubes, nested into a 1.5 mL tube and centrifuged for 3 min at 20,000xg. 0.5 mL 10 mM Tris-HCl pH 7.0 was added and tubes were incubated at 70°C for 10 min with maximal shaking in an Eppendorf thermomixer. Gel pieces were removed using a Spin-X cellulose acetate column (Fisher) and the flow through was transferred to a new tube. 55 μl 3 M NaOAc pH 5.5, 2 μl glycoblue and 0.55 mL isopropanol were added. After mixing, tubes were frozen at −80°C for 1 hr to 16 hr. Samples were centrifuged for 30 min at 20,000xg and 4°C and pellets were washed with ice-cold 80% ethanol and resuspended in 15 μl of 10 mM Tris-HCl pH 7.0. For dephosphorylation, 2 μl 10x T4 polynucleotide kinase buffer without ATP (NEB), 1 μl murine RNase inhibitor and 2 μl T4 polynucleotide kinase (NEB) were added to each sample. Samples were incubated at 37°C for 1 hr before heat inactivation of the enzyme for 10 min at 75°C and precipitation of nucleic acids by adding 0.5 mL 10 mM Tris-HCl pH 7.0, 55 μl 3 M NaOAc pH 5.5, 2 μl glycoblue and 0.55 mL isopropanol and incubating for 1 hr to 16 hr at −80°CSamples were centrifuged for 30 min at 20,000xg and 4°C, pellets were washed with ice-cold 80% ethanol and resuspended in 6-11 μl of 10 mM Tris-HCl pH 7.0. For linker ligation, a maximum of 5 pmol RNA in 5 μl were denatured for 2 min at 80°C before 8 μl 50% sterile filtered PEG MW 8000, 2 μl DMSO, 2 μl 10x T4 RNA Ligase 2 buffer (NEB), 1 μl murine RNase inhibitor, 1 μl 1 μg/μl linker L1 and 1 μl truncated T4 RNA Ligase 2 (NEB) were added and incubated for 2.5 hr at 37°C or 23°C. Nucleic acids were precipitated as described before and resuspended in 6 μl 10 mM Tris-HCl pH 7.0. Samples were run on a 10% TBE-Urea polyacrylamide gel (Invitrogen) in 1x TBE (Ambion) for 50 min at 200 V. Gels were stained for 20 min with SYBR gold and desired gel pieces were excised and RNA was extracted as described before. For reverse transcription, RNA was resuspended in 10 μl 10 mM Tris-HCl pH 7.0 and 1 μl 10 mM dNTP (NEB), 1 μl 25 linker L1’L2′ and 1.5 μl DEPC H20 were added to each sample. Samples were incubated at 65°C for 5 min followed by addition of 4 μl 5x FSB buffer (Invitrogen), 1 μl murine RNase inhibitor, 1 μl 0.1 M DTT (Invitrogen) and 1 μl Superscript III (Invitrogen). Samples were incubated at 50°C for 30 min and afterward 2.3 μl 1 N NaOH was added to hydrolyze RNA and samples were further incubated at 95°C for 15 min. Samples were run on a 10% TBE-Urea polyacrylamide gel for 70 min at 200 V. Gels were stained as described before and desired bands were excised and nucleic acids were extracted as mentioned earlier but using Tris-HCl pH 8.0 and precipitating nucleic acids by adding 32 μl 5 M NaCl, 1 μl 0.5 M EDTA, 2 μl glycoblue and 0.55 mL isopropanol. For circularization, DNA was resuspended in 15 μl 10 mM Tris-HCl pH 8.0 and 2 μl 10x CircLigase buffer (EPICENTRE), 1 μl 1 mM ATP, 1 μl 50 mM MnCl2 and 1 μl CircLigase™ (EPICENTRE) were added. Samples were incubated at 60°C for 1 hr. Addition of 1 μl CircLigase™ was repeated and samples were incubated for another hour at 60°C. Afterward, the enzyme was inactivated by incubating 10 min at 80°C. 5 μl of circularized DNA was used for PCR amplification. Therefore, 16.7 μl 5x HF buffer, 1.7 μl 10 mM dNTPs, 0.4 μl 100 μM PCR primer L1’, 0.4 μl 100 μM barcoding primer, 59.2 μl DEPC H20 and 0.8 μl HF Phusion (NEB) were added. 17 μl PCR mix were aliquoted to 4 separate PCR tubes and the following PCR reaction cycles were run: 1.) 98°C, 30 s; 2.) 98°C, 10 s; 3.) 60°C, 10 s; 4.) 72°C, 5 s. Steps 2 through 4 were repeated ten times and one tube was removed after cycles 7, 8, 9, 10. Samples were run on a 8% TBE polyacrylamide gel (Invitrogen) in 1x TBE (Ambion) for 45 min at 180 V. Gels were stained as mentioned before and desired bands were excised and DNA was extracted as described before. After a quality control step using a high sensitivity bioanalyzer chip (Agilent), samples were sequenced on a HiSeq 2000 (Illumina)

treatment_protocol: Cells were rapidly filtered (All-Glass Filter 90mm, Millipore), flash frozen in liquid nitrogen, mixed with 600 µL frozen lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 6 mM MgCl2, 0.1% NP-40, 0.1 mg/ml CHX, 1 mM PMSF, 2x Complete EDTA-free protease inhibitors (5056489001, Roche), 0.02 U/ml DNase I (4716728001, Roche), 20 mg/mL leupeptin, 20 mg/mL aprotinin, 10 mg/mL E-64, 40 mg/mL bestatin) and pulverized by mixer milling (2 min, 30 Hz, MM400, Retsch).

value: p.Q13P(CCU), p.G98S(AGC) and p.N105S(UCG) mutations in YOL109W


title: Sample 18: Rat1_2

status: Public on Apr 20 2020

type: SRA

city: Edinburgh

first: Clementine

last: Delan-Forino

address: Michael Swann Building 5.1, King's Buildings, Mayfield Road

country: United Kingdom

institute: University of Edinburgh - WTCCB

description: RNA bound to protein of interest

library_source: transcriptomic

data_processing:
Library strategy: CRAC
CRAC Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped. (For the raw reads uploaded here barcodes were not clipped)
CRAC Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
CRAC Length filtered: Reads were length filtered to keep ionly reads which were containing 3' linker
CRAC Collapsing reads: To remove PCR duplicates, reads with the same start and end and sharing the same 3-nucleotide random barcode sequence were collapsed using pyRemoveDuplicate.py from pyCRAC package
CRAC Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign and counts over each genomic features calculated using pyReadCounters from pyCRAC package
RNAseq Demultiplexing: Reads were indexed during library preparation and demultiplexed by the sequencing platform
RNAseq Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
RNAseq Reverse Complement: Reads were reverse complemented
RNAseq Sequences filtration: Low complexity sequences were filtered out before genome alignment
RNAseq Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign, all reads mapping to non RNA polymerase II transcripts were filtered out, and counts over each genomic features calculated using pyReadCounters from pyCRAC package
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts over genomic features of mapped reads in gff format

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: S.cerevisiae strains expressing C-terminal HTP or N-terminal FTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP-tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while HTP-protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.
CRAC (as described in Delan-Forino et al, MiMB, in press) and RNA seq (Lexogen Sense mRNA kit)

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking.

tag: tag

value: HISx6-TEV proteas cleavage site-protA

tag: tissue

value: yeast culture

tag: barcode name

value: clipped

tag: barcode sequence


title: CDK9_L60

city: Beijing

first: Li

last: Yu

address: Medicial Science Building, Tsinghua University

department: The Institution of Immunology

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
Basecal was performed using CASAVA 1.8
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 1.1.2
Reads were filtered as the unsure bases less than 10% and low quality (I<10) bases less than 50%.
Peaks were called using findPeaks program in HOMER (v4.7.2) with the following setting: FDR < 0.001)
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: Macrophages

growth_protocol: Bone marrows cells from C57BL/6 mice were cultured for 5 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate BMDMs

extract_protocol:
Lysates were clarified from sonicated nuclei and CDK9-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs  were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, InvivoGen) for 1 hour.

tag: cell type

value: Bone marrow-derived macrophages

tag: strain


title: WT_30min rep1

data_processing:
Basecal was performed using CASAVA 1.8
Tophat (v2.1.0) was used for pair-end reads alignment with the following parameters:  -i 70 -g 1 --no-novel-indels
Gene expression level were quantified by using Cufflinks (v2.2.1), and Cufflinks was also used for further differential expression analysis
Genome_build: mouse (mm10)
Supplementary_files_format_and_content: Excel file contains quantified gene expression level as FPKM and adjusted p-value for differentail expression analysis.

molecule: polyA RNA

extract_protocol:
RNA was isolated using Qiagen RNA-easy kit and total RNA was polyA enriched.
RNA libraries were prepared for sequencing using TruSeq mRNA-seq Sample Preparation Kit(Illunima)
none provided by the submitter

treatment_protocol: BMDMs  were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, InvivoGen) for indicated time.


title: YOL** rep2

country: USA

description: mutant yeast

tag: genotype


title: Nelfb_KO_30min rep1


title: YOL** rep3

description: mutant yeast


title: WT_0min rep3


title: YOL** rep1

description: mutant yeast


title: WT_0min rep2


title: WT_60min rep3


title: YOL*-II rep4

description: mutant yeast

value: p.Q13P(CCA), p.G98S(UCC) and p.N105S(UCU) mutations in YOL109W


title: 145_RSS31_JoDo01_HD_D1_M_pos_N723_S502

city: San Diego

first: Joseph

middle: Samuel

last: Dolina

state: California

address: 9420 Athena circle

institute: La Jolla Institute for Allergy and Immunology

description: High dose day 1 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr).
Filtered reads were mapped against the UCSC mouse mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand).
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4).
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

growth_protocol: Listeria monocytogenes (Lm) derived from the wild type 10403S background deficient in the actin assembly-inducing protein alone (Lm ΔactA) or expressing ovalbumin (Lm ΔactA-Ova) were obtained from the laboratory of Daniel A. Portnoy (University of California, Berkeley, CA). Bacteria were cultured in BBL brain heart infusion medium (Becton, Dickinson and Company, Sparks, MD) at 37°C, back-diluted to log-phase (OD600 0.075-0.100), washed, and re-suspended in 1×PBS.

extract_protocol:
Total RNA was purified using the Direct-zol RNA MiniPrep Plus and RNA Clean & Concentrator-25 kits (Zymo Research, Irvine, CA). RNA quality and quantity was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA) resulting in all samples producing RIN scores above 9.0. 5 ng of total RNA was then amplified using the Smart-seq2 protocol.
A 1:1 ratio of Agencourt AMPure XP beads (Beckman Coulter Inc., Brea, CA) were used to purify resulting cDNA, and 1 ng cDNA was subsequently used to prepare a sequencing library with the Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA). Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR pre-amplification cycles, and fragment size selection.
The resulting libraries were deep sequenced on the HiSeq 2500 System in Rapid Run mode (Illumina) using 50-bp single-end reads (~6.0×10^6 reads per condition).

treatment_protocol: Primary infections were conducted via intravenous (IV) injection of low dose (LD; 1×103 CFU) or high dose (HD; 1×106 CFU) Lm in the caudal vein.

value: Foxp3eGFP (C57BL/6 background)

value: spleen

value: CD4+eGFP+ (Treg)

tag: dosage

value: High Dose

tag: drug

value: Listeria {delta}actA-Ova

tag: day

value: Day 1


title: YOL*-II rep3

description: mutant yeast


title: 146_RSS31_JoDo01_HD_D1_F_pos_N723_S503

source_name: High dose day 1 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen


title: Sample 7: Trf4_Mtr4-arch

description: RNA bound to protein of interest

value: Cb

value: NNNTGGAGC


title: 144_RSS31_JoDo01_LD_D1_F_pos_N722_S511

description: Low dose day 1 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen

value: Low Dose


title: YOL*-II rep2

description: mutant yeast


title: 143_RSS31_JoDo01_LD_D1_M_pos_N722_S510

source_name: Low dose day 1 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen


title: 142_RSS31_JoDo01_Naive_F_pos_N722_S508

description: Naïve Foxp3-eGFP mouse spleen

source_name: Naïve Foxp3-eGFP mouse spleen

value: Day 0


title: 141_RSS31_JoDo01_Naive_M_pos_N722_S507

description: Naïve Foxp3-eGFP mouse spleen


title: 132_RSS31_JoDo01_HD_D1_F_neg_N721_S506


title: YHR* rep2

description: mutant yeast

value: p.L128N(AAC), p.E149K(AAA), p.V250Y(UAC) and p.V338H(CAC) mutations in YHR179W


title: 130_RSS31_JoDo01_LD_D1_F_neg_N721_S503


title: YLR* rep1

description: mutant yeast

value: p.S139G(GGU) and p.G161S(UCU) mutations in YLR109W


title: 131_RSS31_JoDo01_HD_D1_M_neg_N721_S505


title: YLR* rep2

description: mutant yeast


title: YHR* rep1

description: mutant yeast


title: YOL*-I rep2

description: mutant yeast


title: 128_RSS31_JoDo01_Naive_F_neg_N720_S511

description: Naïve Foxp3-eGFP mouse spleen


title: 127_RSS31_JoDo01_Naive_M_neg_N720_S510

description: Naïve Foxp3-eGFP mouse spleen


title: 129_RSS31_JoDo01_LD_D1_M_neg_N721_S502


title: HY5-VP16-3_set3

city: Rishon LeZion,

first: Yogev

last: Burko

address: 68 HaMaccabim Rd.,

department: Plant Biology

country: Israel

institute: Volcani Institute

data_processing:
base calling was done by RTA 1.17.20 (Illumina, CA)
demultiplexing was done by CASAVA 1.8.2 (Illumina, CA)
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie2 version 2.3.0 with with default parameters.
Peaks were called using HOMER (version 4.9.1) Findpeaks script with the following setting:  -style factor -F 3 -P 0.0001 -L 2 -LP 0.001
IP from wild-type (Col-0) or hy5 extract using anti-FLAG antibody used as a background control. COL for set 1 (HY5ox-1, HY5-VP16_1, HY5-VP16_2, HY5-SRDX_1, HY5-SRDX_2), COL_3 for set 3 (HY5ox_3, HY5-VP16_3) and hy5_2 mutant for set 2 (HY5ox_3).
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph files report genome-wide ChIP created with HOMER. Excel file with peaks and annotated genes for all samples.

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: Seeds were sterilized and plated on 0.5× Linsmaier and Skoog medium (LS; Caisson Laboratories) with 0.8% phyta-agar (Caisson Laboratories). Stratified done in the dark at 4°C for seven days. Germination induced in constant white light for one hour before the seedlings moved to the dark for three days at 21°C.

extract_protocol:
Whole seedling were collected into a nylon socks, using rasor blade, and snap-frozen in liquid nitrogen.
ChIP-seq experiments done as described in Kaufmann et al., 2010.
Illumina TruSeq libraries were constructed according to manufacturer’s protocols

treatment_protocol: 3 days dark + 2.5h simulated white light (100 µmol m−2 s−1).

tag: ecotype

value: Columbia

tag: modification type

value: HY5 with activation domain (VP16)

tag: chip antibody

value: Flag antibody IP (Sigma Cat# F1804)

tag: tag used for chip

value: FLASH2 (2xStrepII-6xHis-protease cleavage site-3xFlag)

value: Whole seedlings


title: HY5ox-3_set3

value: HY5 without modification


title: YOL*-II rep1

description: mutant yeast

value: p.Q13P(CCA), p.G98S(UCC) and p.N105S(UCU) mutations in YOL109W


title: YKL* rep1

description: mutant yeast

value: p.D31F(UUC) and p.S61G(GGU) mutations in YKL096W-A


title: YKL* rep2

description: mutant yeast


title: YMR* rep1

description: mutant yeast

value: p.P55E(GAA) mutation in YMR122W-A


title: YOL*-I rep1

description: mutant yeast


title: Col-0_set3

value: Control for set_3


title: hy5_set2

value: Control for set_2


title: 12h-BHypo_stranded_mRNAseq

data_processing:
base calling was done by RTA 1.17.20 (Illumina, CA)
demultiplexing was done by CASAVA 1.8.2 (Illumina, CA)
Sequenced reads were trimmed for adaptor sequence, then aligned to TAIR10 whole genome build using TopHat (v2.0.8), with default parameter except intron length was set to 40 minimum, 2000 maximum.
Cuffdiff (v2.1.1) was used to calculate the expression change between the different time points in the light with the dark sample on a Linux platform with default parameter.
We assign 1 and -1 to the log2FC when 0 was calculated at the denominator or at the numerator respectively.
Genome_build: TAIR10
Supplementary_files_format_and_content: CSV (Comma delimited): Normalized FPKM for all genes in all conditions generated with cuffnorm; Log2 Fold change relative to Dark at the beginning of the experiment, created with cuffdiff (include average FPKM for each sample in each comparison and q-value).

source_name: Hypocotyls

extract_protocol:
At the indicated time the roots were removed with a scalpel and two biological replicates of seedlings growing in the dark or moved to simulated white light were collected into ice cold 80% acetone. Dark samples were collected under safe green light
The cotyledons and the hypocotyl were separated under a stereomicroscope as described in (Park et al., 2012)
RNA was extracted with RNeasy Micro Kit (Qiagen cat. 74004)
500ng of total RNA was used to prepare RNA-seq libraries, using TruSeq Library prep kit-v2 (Illumina).

treatment_protocol: Seedling were grown vertically on ½ LS plates with nylon mash (100 micron, 44% open area, 40 inch width- ELKO filtering). At the indicated time the roots were removed with a scalpel and two biological replicates of seedlings growing in the dark or moved to simulated white light were collected into ice cold 80% acetone.

value: Hypocotyls

tag: condition

value: Dark 3days + 12h light


title: WT_0min rep1

value: Bone marrow-derived macrophages


title: 12h-AHypo_stranded_mRNAseq

value: Dark 3days +12h light


title: 6h-BHypo_stranded_mRNAseq

value: Dark 3days + 6h light


title: 6h-AHypo_stranded_mRNAseq


title: 3h-BHypo_stranded_mRNAseq

value: Dark 3days + 3h light


title: 3h-AHypo_stranded_mRNAseq

value: Columbia


title: 1h-BHypo_stranded_mRNAseq

value: Dark 3days + 1h light


title: YMR* rep2

description: mutant yeast


title: 1h-AHypo_stranded_mRNAseq


title: 30min-BHypo_stranded_mRNAseq

value: Dark 3days + 30 min light


title: 15min-BHypo_stranded_mRNAseq

value: Dark 3days + 15 min light


title: Dark-AHypo_stranded_mRNAseq

value: Dark 3days


title: 12h-BCot_stranded_mRNAseq

source_name: Cotyledons + SAM

value: Cotyledons + SAM


title: 6h-BCot_stranded_mRNAseq


title: 30min-AHypo_stranded_mRNAseq


title: Dark-BHypo_stranded_mRNAseq


title: 6h-ACot_stranded_mRNAseq


title: 3h-BCot_stranded_mRNAseq


title: 12h-ACot_stranded_mRNAseq


title: 15min-AHypo_stranded_mRNAseq


title: 3h-ACot_stranded_mRNAseq


title: 1h-BCot_stranded_mRNAseq


title: 1h-ACot_stranded_mRNAseq


title: R10B

type: genomic

city: Leeds

first: Frederique

last: Ponchel

state: England

address: St. James’s University Hospital

department: Leeds Institute of Rheumatic and Musculoskeletal Medicine

institute: University of Leeds

hyb_protocol: Bisulfite converted DNA was amplified using the Illumina Infinium Methylation Assay and hybridised to Illumina Human Methylation 450K Beadchips.

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

data_processing: R package Minfi using preprocessIllumina function. CpG probes which were identified to be common SNPs and cross-reactive probes that have been shown to hybridise to multiple locations in the genomes were filtered out

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Monocyte

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the Nucleon extraction kit according to manufacturers’ instructions.

tag: gender

value: F

tag: sample group

value: Early Rheumatoid Arthritis


title: 30min-ACot_stranded_mRNAseq


title: R09B

value: M


title: 30min-BCot_stranded_mRNAseq


title: R06B


title: 892-2 GFPneg KO E15.5

city: Clayton

first: Kate

middle: Ann

last: Loveland

state: VIC

address: 27-31 Wright Street

department: Molecular and Translational Sciences and Centre for Reproductive Health

country: Australia

institute: Monash University and Hudson Institute of Medical Resarch

data_processing:
RNAseq processing pipeline RNAsik v1.8.9
QC with fastqc (v0.11.5), picard (v2.9.0) and multiqc (v 1.0)
Alignment with STAR (STAR/2.5.2b)
Read counts matrix made with featureCounts (subread v1.5.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: featureCounts

source_name: testis

extract_protocol:
Paired gonads were dissected free from mesonephros, and single cell suspensions were obtained. Fluorescence Activated Cell Sorting (FACS) isolated viable GFP- somatic cells from GFP+ germ cells.
RNA libraries were prepared using ~20 ng high quality RNA (RIN 8.4 - 9.6) using the Nugen Trio Library preparation kit. Libraries were sequenced on an Illumina HiSeq3000

value: Inhba x Oct4 GFP KO

tag: age

value: embryonic E15.5


title: 15min-BCot_stranded_mRNAseq

tag: tissue


title: 855-1 GFPneg KO E15.5


title: C08B

value: Healty control


title: R01B


title: Dark-ACot_stranded_mRNAseq


title: C03B


title: R02B


title: 15min-ACot_stranded_mRNAseq


title: 1052-4 GFPneg KO E15.5


title: Dark-BCot_stranded_mRNAseq


title: R08B


title: 1052-2 GFPneg KO E15.5


title: HY5-SRDX-1_set1

value: Whole seedlings

value: HY5 with repression domain (SRDX)

value: Flag antibody IP (Sigma Cat# F1804)

value: FLASH2 (2xStrepII-6xHis-protease cleavage site-3xFlag)


title: HY5-SRDX-2_set1


title: C05B


title: R05M

source_name: memory CD4+T-cells


title: R10M


title: R09M


title: R04M


title: C01B


title: R06M


title: R05B


title: C07B


title: R01M


title: HY5-VP16-2_set1

value: HY5 with activation domain (VP16)


title: R07B


title: 995-1 GFPneg WT E15.5

value: Inhba x Oct4 GFP WT


title: R04B


title: C06B


title: HY5-VP16-1_set1

value: Columbia


title: 941-3 GFPneg WT E15.5


title: HY5ox-2_set2

description: Collected and processed separately from the other samples

value: HY5 without modification_set_2


title: R03B


title: R07M


title: HY5ox-1_set1

value: HY5 without modification


title: 855-2 GFPneg WT E15.5


title: R03M


title: Col-0_set1

value: Control for set_1


title: hy5_4h_Light-2_stranded_mRNAseq

data_processing:
base calling was done by RTA 1.17.20 (Illumina, CA)
demultiplexing was done by CASAVA 1.8.2 (Illumina, CA)
Sequenced reads were trimmed for adaptor sequence, then aligned to TAIR10 whole genome build using TopHat (v2.0.11)[Bowtie (v2.2.2.0), Samtools (v0.1.19.0)], (Kim et al. 2013) on a Linux platform with default parameter except library type set to firststrand and intron length was set to 40 minimum, 2000 maximum
Mapped reads were counted by HTSeq (v0.6.0) with default parameters except “-m intersection-strict -s reverse” (Anders et al., 2015) and analyzed by edgeR (v3.16.5) (Robinson et al., 2010). Only genes with CPM (counts-per-million) values greater than 1 in at least two samples were kept for differential expression analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files: Log2 fold change relative to hy5 and CPM for all the samples, showing all the genes with CPM (counts-per-million) values greater than 1, in at least two samples.

extract_protocol:
Whole seedling were collected (40 seedllings) and snap-frozen in liquid nitrogen. Dark samples were collected under safe green light
RNA was extracted with RNeasy Micro Kit (Qiagen cat. 74004)
Libraries were prepared according to Illumina's instructions accompanying TruSeq Stranded mRNA Library Prep Kit. Briefly, total RNA (0.5µg) from each sample was used to isolate poly(A) mRNA. Steps involved in library preparation were mRNA fragmentation, first strand cDNA synthesis followed by second strand cDNA synthesis and adaptor ligation, cDNA fragments isolation and amplification.

treatment_protocol: 3 days dark ; 3 days dark + 1.5h or 4h in simulated white light (100 µmol m−2 s−1).

value: Dark 3days + 4h light


title: SRDX_4h_Light-2_stranded_mRNAseq

value: 35S:FLASH-HY5-SRDX (hy5/hy5)


title: 1064-2 GFPneg WT E15.5


title: 928-1 GFPneg KO E13.5

value: embryonic E13.5


title: SRDX_4h_Light-1_stranded_mRNAseq


title: SRDX_1.5h_Light-2_stranded_mRNAseq

value: Dark 3days + 1.5h light


title: 832-1 GFPneg KO E13.5

value: Inhba x Oct4 GFP KO


title: C08M

value: M


title: 831-2 GFPneg KO E13.5


title: VP16_1.5h_Light-2_stranded_mRNAseq

value: 35S:FLASH-HY5-VP16 (hy5/hy5)


title: VP16_1.5h_Light-1_stranded_mRNAseq

value: Whole seedlings


title: C07M

value: F

value: Healty control


title: OX_1.5h_Light-2_stranded_mRNAseq

value: 35S:FLASH-HY5 (hy5/hy5)


title: VP16_1.5h_Light-3_stranded_mRNAseq

value: HY5 with activation domain (VP16)


title: R02M

value: Early Rheumatoid Arthritis


title: hy5_1.5h_Light-3_stranded_mRNAseq

value: Columbia


title: SRDX_1.5h_Light-1_stranded_mRNAseq

value: HY5 with repression domain (SRDX)


title: OX_1.5h_Light-1_stranded_mRNAseq

value: HY5 without modification


title: hy5_1.5h_Light-2_stranded_mRNAseq


title: 696-6 GFPneg KO E13.5


title: Col_1.5h_Light-3_stranded_mRNAseq


title: hy5_4h_Light-1_stranded_mRNAseq


title: 876-4 GFPneg WT E13.5

value: Inhba x Oct4 GFP WT


title: 900-2 GFPneg WT E13.5


title: Col_1.5h_Light-2_stranded_mRNAseq


title: C06M


title: 927-5 GFPneg WT E13.5


title: 803-2 GFPneg WT E13.5


title: Col_1.5h_Light-1_stranded_mRNAseq


title: SRDX_Dark-1_stranded_mRNAseq

value: Dark 3days


title: hy5_1.5h_Light-1_stranded_mRNAseq


title: VP16_Dark-2_stranded_mRNAseq


title: VP16_Dark-3_stranded_mRNAseq


title: VP16_Dark-1_stranded_mRNAseq


title: OX_Dark-3_stranded_mRNAseq


title: OX_Dark-2_stranded_mRNAseq


title: SRDX_Dark-2_stranded_mRNAseq

value: 35S:FLASH-HY5-SRDX (hy5/hy5)


title: C03M


title: C05M


title: OX_Dark-1_stranded_mRNAseq


title: R06N

source_name: naive CD4+T-cells


title: RNA-seq of mouse photothrombosis model(14d)

city: Chiba City

first: Atsushi

last: Yamaguchi

state: Chiba

address: 1-8-1 Inohana, Chuo-ku, Chiba City

department: Dept. Med.

country: Japan

institute: Chiba University

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of FASTQ format were processed by Trimmomatic (v0.30) to be high quality clean data.
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website (UCSC, NCBI, ENSEMBL).  Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence (mm10).  Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis: In the beginning transcripts in FASTA format are converted from known gff annotation file and indexed properly.  Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Ipsilateral Cerebral cortex

extract_protocol:
Total RNA were derived from cerebral cotex on the ipsilateral side of mouse stroke brain at each time point (1d, 3d, 7d, 14d, 28d).  Sham-operated mice at day 7 post-operation were used as control.
Strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina after poly(A) selection by the NEBNext poly(A) mRNA Isolation Module (New England Biolabs Inc.).  Samples were barcoded using the recommended NEBNext Multiplex Oligos.  Size range and quality of libraries were verified on the Agilent 2100 Bioanalyzer (Agilent Technologies).  RNA-seq libraries were quantified by quantitative polymerase chain reaction using the KAPA library quantification kit (KAPA Biosystems).  Each library was normalized to 2 nM and pooled in equimolar concentrations.  Paired-end 150 sequencing was performed on an Illumina HiSeq4000 (Illumina, San Diego, CA).  Libraries were pooled and sequenced using two lanes of one HiSeq4000 flow cell to an average depth of 33.6 million reads per sample.

tag: treatment

value: 14 d post stroke


title: RNA-seq of mouse photothrombosis model(28d)

value: 28 d post stroke


title: J3T2A

type: RNA

city: Okayama

first: Yuji

last: Matsumoto

address: 2-5-1 Shikata, kita-ku

department: Neurological Surgery

institute: Okayama University

description: Gene expression data from J3T-2A

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Canine Genome 2.0 Array. Arrays were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method.

label: biotin

organism: Canis lupus familiaris

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3' IVT PLUS Reagent Kit from 250 ng total RNA according to the manufacturer's instructions.

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum and 100U penicillin and 0.1mg ml-1 storeptomycin.

extract_protocol: Total RNA of J3T-1, J3T-2, J3T-1shA, and J3T2A were isolated using RNeasy kit according to the manufacturer's instructions.

value: glioma

tag: subclone

tag: expression

value: overexpression of annexin A2


title: J3T1shA

description: Gene expression data from J3T-1shA

value: knockdown of annexin A2


title: R05N


title: J3T2

description: Gene expression data from J3T-2

value: expressing low annexin A2


title: hy5_Dark-3_stranded_mRNAseq

value: Whole seedlings


title: hy5_Dark-2_stranded_mRNAseq


title: R08M

value: F


title: R09N

value: M


title: R10N


title: R04N


title: C01M

value: Healty control


title: J3T1

description: Gene expression data from J3T-1

value: expressing high annexin A2


title: RNA-seq of mouse photothrombosis model(7d)

value: 7 d post stroke


title: RNA-seq of mouse photothrombosis model(3d)

value: 3 d post stroke


title: POL3-3Flag mgs1∆ rad5∆ (FY1925) IP

city: Milan

first: Dana

last: Branzei

address: Via Adamello 16

country: Italy

institute: IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation

description: Binding pattern of Elg1 by ChIP-on-chip after release of cells from G1 block in medium containing 0.02% MMS for 30 min

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner.

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

label: Dynabeads Protein A invitrogen

source_name: cells

label_protocol: Sample preparation and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YP+Glucose 2% (YPD) media at 25°C in 500 ml flask for a density of 1.2×10^7 cells/ml.

extract_protocol: Binding profiles by ChIP-on-chip were determined as described in (Bermejo et al., 2009).

treatment_protocol: G1 synchronization was performed by alpha−factor treatment (3-5 μg/ml) for 120-180 minutes at 25°C and validated by microscopy. Cells were pelleted, washed once with YP and released into YPD media containing 0.2% MMS for 30 min, and fixed with 1% formaldehyde for 30 min at room temperature for further ChIP.

value: G1 arrest with alpha-factor released in 0.02% MMS for 30 mins

tag: strain

value: W303 MATa mgs1delta::hphNT1 rad5delta::URA3 pol3::POL3-3FLAG::kanMX

tag: antibody

value: Anti-FLAG M2 F1804 (SIGMA)


title: RNA-seq of mouse photothrombosis model(1d)

value: 1 d post stroke


title: R08N

value: Early Rheumatoid Arthritis


title: ND8037 null #158

city: Yokohama

first: Miyako

last: Kusano

state: Kanagawa

address: 1-7-22, Suehiro, Tsurumi

institute: RIKEN CSRS

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 17

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 h on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 integrated with Affymetrix® Microarray Suitesoftware.

data_processing: The microarray data normalization and background correction was performed using robust multi-array average (RMA) with Bioconductor package 'simpleaffy' by using R/Bioconductor.

organism: Oryza sativa Japonica Group

source_name: roots, a no-insertion null plant segregated from heterozygous ND8037, ammonium sufficient condition, 18 day-old sample

label_protocol: Biotinylated cRNA was labeled using a biotinylated nucleotide analog/ribonucleotide mix using GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: We grew samples using two different conditions. Growth condition 1 for SAMPLE 1-17: The conditions in the greenhouse at Tohoku University, Sendai, Japan were: 14 h of light at 26oC and 10 h of darkness at 23oC without humidity control; light strength, 810 μmol∙m-2∙sec-1; light source, metal halide lamp (05:30 - 18:30) and sunlight.  WT-, heterozygous Osgs1;1-, and homozygous Osgs1;2 seeds were sterilized in 3 steps: (i) seeds were immersed in 60oC water for 10 min and then washed in flowing water for 10 min, (ii) immersed in 70% ethanol for 30 sec and washed immediately, and (iii) immersed in 2% hypochlorous acid for 20 min and then washed in water for 20 min. Then they were incubated at 30oC for 2 days in the dark. Germinated seeds were hydroponically grown for 18 days in one-quarter strength basal nutrient solution that lacked an N source and contained 150 mM NaH2PO4•2H2O, 75 mM K2SO4, 75 mM CaCl2•2H2O, 100 mM MgCl2•H2O, 11.25 mM Fe•EDTA, 12.5 mM H3BO3, 2.25 mM MnSO4•5H2O, 0.075 mM CuSO4•5H2O, 0.175 mM ZnSO4•7H2O, and 0.025 mM Na2MoO4•2H2O and 1.0 mM NH4Cl to harvest root samples.  Growth condition: Plants were hydroponically grown for 18 days.

extract_protocol: Total RNA isolation was performed using RNeasy Plant Mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer's instruction.

treatment_protocol: Germinated seeds were hydroponically grown under one-quarter strength basal nutrient solution lacking a nitrogen (N) source with 1 mM of ammonium for 18 days.

tag: cultivar

value: Nipponbare

value: roots

tag: growth period

value: 18 days

tag: genotype


title: RNA-seq of mouse photothrombosis model(sham)

value: sham


title: Col_Dark-3_stranded_mRNAseq

value: Dark 3days

tag: ecotype

value: Columbia


title: Col_Dark-2_stranded_mRNAseq

value: Whole seedlings

tag: modification type


title: Hair follicle mesenchyme from 12mo mice

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

description: FACS sorted cells: 10,000 cells; Recovered: 5415 cells

data_processing:
All raw FASTQs reads were aligned to our custom mouse mm10-1.2.0_yfp_wpre [mm10 (GRCm38.p5) + eYFP pseudo gene] genome, which was generated by adding in the eYFP + WPRE sequences to the GRCm38.p5 (primary assembly) reference genome using the STAR algorithm. All reads were quantified through the 10X Genomics cellranger v2.0.1 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v2.1.0) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<400 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. A selection of highly variable genes was obtained and used to calculate up to 75 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 20 were used to run and plot a tSNE plot for all cells. Expression of selected marker genes across cell clusters identified by graph based clustering (Seurat res = 0.3). Differential and marker gene analysis of cells defined by FACS sorting sample or graph-clustering was also run in Seurat using the negative binomial test for genes expressed by at least 25% of cells in the defined cell group being compared.
Genome_build: mm10-1.2.0_yfp_wpre [mm10 (GRCm38.p5) + eYFP pseudo gene]
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

source_name: 12mo HF

growth_protocol: All transgenic mice were housed singly. We received prior approval from the University of Calgary Animal Handling Committee, and mouse were treated in full accordance to guidelines set by the Canadian Council on Animal Care.

extract_protocol:
Backskin from α-SMACreT2:RosaYFP mice at 2 months of age and 18 months of age (n = 2/ sample) were surgically removed. Isolated backskin were incubated in 5mg/mL dispase (StemCell Technologies) in Hank’s Buffered Salt Solution (HBSS; Life Technologies) for 30 mins at 37oC, then the epidermis was surgically removed. The remaining dermis was dissociated in 2mg/mL collagenase in Ham’s F12 Nutrient mixture (Thermo Fischer Scientific) for 2 hours at 37oC. Cell suspension was diluted with cold HBSS, strained through 70µm and 40µm cell filters (Falcon) and centrifuged at 280g. Re-suspended cells were stained with conjugated Integrin α-9-PE (ThermoFisher), conjugated CD200-PE (ThermoFisher) and conjugated Cd26-647 (R&D Systems) for 45 mins, then with corresponding Alexa Fluor secondary antibodies (Invitrogen) for 30 mins. eFluor 780 viability dye (eBioscience) was included in the last 5 mins to exclude dead cells and debris. FACS-isolation was performed using a FACSAria III (BD Biosciences) and analyzed using FCS Express 6 software. Single colour and appropriate isotype controls were used for compensation and gating.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 and v3 Chemistry. Single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 2727 and 1906 cells for Samples 1 and 2, respectively, with an estimated doublet rate of ≈3%. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of 100,000 reads/cell.

treatment_protocol: 1mg of 4-hydroxy-tamoxifen (4-OHT; Sigma-Aldrich) was dissociated into 300uL solution of 10% EtOH and 90% sunflower oil. Each transgenic mouse was treated with 300uL (1mg/25g) of tamoxifen oil intraperitoneally at postnatal day 3 and 4, to drive CreER recombination.

tag: transgenic strain

tag: background

tag: facs strategy

value: (TdTomato+ or Cd26+) and (Itga9+ or Cd200+)

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3


title: Hair follicle mesenchyme from 2mo mice - replicate 2

description: FACS sorted cells: 10,000 cells; Recovered: 6998 cells

source_name: 2mo HF-2


title: R02N

tag: gender

value: M

tag: sample group


title: hy5_Dark-1_stranded_mRNAseq

tag: tissue

tag: condition


title: POL3-3Flag mgs1∆ rad5∆ (FY1925) input

tag: treatment


title: ND8037 null #156

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 15


title: POL3-3Flag rad5∆ (FY1924) IP

value: W303 MATa rad5delta::URA3 pol3::POL3-3FLAG::kanMX


title: ND8037 homozygote #125

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 14

source_name: roots, a homozygous Osgs1;1 plant segregated from heterozygous ND8037, ammonium sufficient condition, 18 day-old sample


title: C08N

value: Healty control


title: POL3-3Flag rad5∆ (FY1924) input

value: G1 arrest with alpha-factor released in 0.02% MMS for 30 mins


title: C05N

value: F


title: ND8037 null #157

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 16


title: Col_Dark-1_stranded_mRNAseq


title: T72_3: T72 replicate 3

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

data_processing:
Transcript abundance was quantified using kallisto pseudoalignment software utilizing Gencode release 16-GRCm38.p5 transcript and genome information.
The DESEQ2 package was used to obtain TPM (transcript per million reads) and rlog (regularized log) expression values and to identify differentially expressed genes.
Reads were also mapped to the mm10 genome using STAR version STAR_2.5.3a
Genome_build: mm10
Supplementary_files_format_and_content: Read count per gene. TPM Transcripts per million reads.

source_name: MEDEP cells

growth_protocol: MEDEP cells (BRC5 cell line) were cultured in IMDM medium containing 15% FCS, 5mM ascorbic acid, 1X ITS complement (Sigma I3146), 0.15mM alpha-TG, 50nM SCF and 10-7M dex. Differentiation was induced by removing SCF and dex and adding 4U/ml Epo to exponentially growing cells 3. Cell density was maintained below 2x106 cells/ml during differentiation by dilution with differentiation medium.

extract_protocol:
RNA was prepared from MEDEP cells using Trizol reagent (Ambion).
Strand specific RNA sequencing libraries were created at the Yale Center for Genome Analysis.

value: MEDEP cells

tag: time, hours

tag: succinyl acetone

value: No

tag: replicate


title: ND8037 homozygote #123

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 12

tag: cultivar


title: POL3-3Flag mgs1∆ (FY1923) IP

tag: strain

value: W303 MATa mgs1∆ pol3::POL3-3FLAG::kanMX

tag: antibody

value: Anti-FLAG M2 F1804 (SIGMA)


title: T72_2: T72 replicate 2


title: POL3-3Flag mgs1∆ (FY1923) input

tag: genotype


title: OX_1.5h_Light-3_stranded_mRNAseq

tag: modification type

value: HY5 without modification

value: Dark 3days + 1.5h light

tag: ecotype

value: 35S:FLASH-HY5 (hy5/hy5)


title: gs1;2 #356

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 11

source_name: roots, homozygous Osgs1;2, ammonium sufficient condition, 18 day-old sample

value: Nipponbare

value: roots

tag: growth period

value: 18 days


title: POL3-3Flag (FY1922) input

value: W303 MATa pol3::POL3-3FLAG::kanMX


title: T48_3: T48 replicate 3


title: R07N

value: Early Rheumatoid Arthritis


title: R03N

value: M


title: T72_1: T72 replicate 1


title: C06N


title: T48_2: T48 replicate 2


title: POL3-3Flag (FY1922) IP


title: s14_3

city: Shanghai

first: Yang

last: Wang

address: Dongan road 131

institute: Fudan University

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

source_name: HBV-infected Liver hepatocytes

label_protocol: Total RNA was labeled  by Affymetrixy FL-Ovation™ cDNA Biotin Module V2(Cat#4200, NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Primary human hepatocytes (PHHs) were purchased from RIDL (Shanghai, China) was cultured in maintenance medium (Life Technologies) containing 1% DMSO and 2% FBS, the cells were plated on type I collagen coated 24-well plates at a concentration of 2.5 x 10^5 cells

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

treatment_protocol: PHH cells were infected with HBV virions at 200 viral genome equivalents (vge) per cell in the presence of 4% PEG8000 for 16 hours and then washed by PBS. 6 days later, cells were treated with IFN-α2 or IFN-α14 for 6 h.

tag: cell type

value: Primary human hepatocytes

value: treated with IFN-α14


title: T36_3: T36 replicate 3


title: ELG1-10Flag rad5∆ mgs1∆ (FY1921) input

value: G1 arrest with alpha-factor released in 0.02% MMS for 30 mins

value: W303 MATa rad5delta::URA3 mgs1delta::hphNT1 Elg1:10 FLAG::KAN


title: T48_1: T48 replicate 1

value: MEDEP cells


title: s14_1


title: R01N

value: F


title: s2_2

value: treated with IFN-α2


title: ELG1-10Flag mgs1∆ (FY1919) IP

value: W303 MATa mgs1delta::hphNT1 Elg1:10 FLAG::KAN

value: Anti-FLAG M2 F1804 (SIGMA)


title: s14_2


title: C07N

value: Healty control


title: gs1;2 #355

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 10


title: wild type # 629

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 8

source_name: roots, wild type, ammonium sufficient condition, 18 day-old sample

value: wild type


title: gs1;2 #354

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 9

value: Nipponbare


title: T36_2: T36 replicate 2

value: No


title: s2_3


title: ELG1-10Flag rad5∆ mgs1∆ (FY1921) IP


title: ND8037 homozygote #124

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 13

value: roots

value: 18 days


title: wild type # 628

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 7


title: wild type # 627

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 6


title: s2_1


title: T36_1: T36 replicate 1


title: Mock_3

value: not treated with Interferon


title: NC2373 homozygote #117

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 4

source_name: roots, a homozygous Osgs1;1 plant segregated from heterozygous NC2373, ammonium sufficient condition, 18 day-old sample


title: ELG1-10Flag mgs1∆ (FY1919) input


title: NC2373 homozygote #118

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 5


title: Mock_1


title: ELG1-10Flag rad5∆ (FY1920) IP

description: Binding pattern of Elg1 by ChIP-on-chip after release of cells from G1 block in medium containing 0.02% MMS for 30 min

value: W303 MATa rad5delta::URA3 Elg1:10 FLAG::KAN


title: Series16_A549-ACE2_SARS-CoV-2_Rux_3

city: New York

first: Daniel

last: Blanco Melo

state: NY

address: One Gustave L. Levy Place, Box 1124

department: Microbiology

institute: Icahn School of Medicine at Mount Sina

description:
Time after treatment: 24 hours
BN9-indexA9

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) or Ferret genome (MusPutFur1.0) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Differential gene expression analysis was performed using DESeq2 (implemented in the RNA Express App (v1.1.0) on Basespace (Illumina, CA)) comparing Infected samples to their correspondent mock treated sample, for each virus/cell type.
Genome_build: human (hg19), Ferret (MusPutFur1.0)
Supplementary_files_format_and_content: Tab separated value (tsv) matrix of raw read counts per gene for each sample.

source_name: SARS-CoV-2 infected A549 cells trasnduced with a vector expressing human ACE2 (1hr after Ruxolitinib pre-treatment)

extract_protocol:
TruSeq RNA Library Prep Kit v2
Total RNA was extracted using RNeasy Mini Kit (Qiagen)

value: Lung adenocarcinoma

value: SARS-CoV-2 infected (MOI 2)


title: ELG1-10Flag rad5∆ (FY1920) input

value: G1 arrest with alpha-factor released in 0.02% MMS for 30 mins


title: T24_3: T24 replicate 3


title: Series16_A549-ACE2_SARS-CoV-2_Rux_2

description:
Time after treatment: 24 hours
BN8-indexA8


title: ELG1-10Flag (HY1976) IP

value: W303 MATa Elg1:10 FLAG::KAN


title: Series16_A549-ACE2_SARS-CoV-2_Rux_1

description:
Time after treatment: 24 hours
BN7-indexA7


title: T24_1: T24 replicate 1

value: MEDEP cells


title: ELG1-10Flag (HY1976) input


title: Series16_A549-ACE2_SARS-CoV-2_3

description:
Time after treatment: 24 hours
BN6-indexA6

source_name: SARS-CoV-2 infected A549 cells trasnduced with a vector expressing human ACE2


title: T12SA_3: T12SA replicate 3

value: Yes


title: Cmi Wpp input

city: Duluth

first: Matthew

last: Slattery

state: MINNESOTA

address: 1035 University Drive, SMed 219

institute: University of Minnesota Medical School

data_processing:
ChIP-seq reads were aligned to the dm3 genome assembly using BWA allowing up to 2 edit distance in the seed region and 3 in the full read length.
Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software, version 2 (MACS2) with a qvalue cutoff of 0.05
Genome_build: dm3
Supplementary_files_format_and_content: bed

organism: Drosophila melanogaster

source_name: white prepuae

growth_protocol: S2 cells were grown according to Drosophila Genomics Resource Center recommendations; third instar larvae were collected from the sides of culture bottles at the wandering stage; prepupal animals were collected from the sides of culture bottles at the white prepupa stage

extract_protocol:
Chromatin was crosslinked at RT in 1.8% formaldehyde and homogenized for chromatin extraction. Cmi antiserum was used for immunoprecipitation.
Input and immunoprecipitated DNA were prepared for sequencing using the Illumina TruSeq ChIP Sample Preparation Kit per the manufacturer's instructions. Library construction was performed by the University of Chicago IGSB Sequencing Core.

value: Y cn bw sp


title: Cmi Wpp ChIP

value: anti-Cmi


title: T12SA_2: T12SA replicate 2


title: Series16_A549-ACE2_SARS-CoV-2_1

description:
Time after treatment: 24 hours
BN4-indexA4


title: NC2373 no insertion #153

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 2

source_name: roots, a no-insertion null plant segregated from heterozygous NC2373, ammonium sufficient condition, 18 day-old sample


title: T12SA_1: T12SA replicate 1


title: NC2373 no insertion #152

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 1


title: Series16_A549-ACE2_Mock_3

description:
NA
BN3-IndexA3

source_name: Mock treated A549 cells trasnduced with a vector expressing human ACE2

value: Mock treatment


title: Cmi W3L input

source_name: wandering third instar larvae


title: T24_2: T24 replicate 2


title: Mock_2

value: Primary human hepatocytes


title: NC2373 no insertion #154

description:
The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
SAMPLE 3


title: Cmi S2 input

source_name: S2 cells


title: perivascular_adipose_tissue_proximal _aorta_28

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

institute: Centro Cardiologico Monzino IRCCS

description:
200793810066_E
Subject_28

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Raw data were imported in the R software version 3.5.0 and analyzed with the lumi R/Bioconductor package. Variance stabilizing transformation (VST) was applied and transformed data were then normalized by robust spline normalization (RSN). Probes with a detection P‐value <0.01 in at least 30% of the samples were retained.

label: Biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: Total RNA was extracted by adding 1 mL of TRIzol Reagent to 50-100 mg of frozen adipose tissue samples. Tissues were homogenized through a 5 mm stainless steel bead in a Tissue Lyzer. After homogenization, samples underwent a second round of purification with chloroform and precipitated with isopropanol. RNA resuspended in RNase-free water was further cleaned-up by the RNeasy MinElute Cleanup kit, following the manufacturer’s instructions and, then, treated with TURBO DNase as described by the manufacturer's protocol. Infinite M200 PRO multimode microplate reader (Tecan) and the 2100 Bioanalyzer (Agilent Technologies) were used to assess RNA yield/purity and RNA integrity, respectively.

treatment_protocol: Collected adipose tissue samples were directly snap-frozen in liquid nitrogen and stored at -80°C until processing.

tag: diagnosis

value: Peripheral artery disease (PAD)

value: Periaortic adipose tissue (proximal abdominal aorta)

tag: Sex

value: Male

tag: age (years)

tag: country of origin

value: Italy

tag: subject


title: T12_2: T12 replicate 2

tag: tissue

value: No


title: subcutaneous_abdominal_fat_28

description:
200793810066_B
Subject_28

value: Subcutaneous abdominal fat


title: omental-visceral_fat_28

description:
200793810066_D
Subject_28

value: Omental-visceral fat


title: perivascular_adipose_tissue_distal_aorta_60

description:
200793810054_L
Subject_60

value: Periaortic adipose tissue (abdominal aorta)


title: perivascular_adipose_tissue_distal_aorta_28

description:
200793810066_L
Subject_28


title: Series16_A549-ACE2_Mock_1

description:
NA
BN1-indexA1

value: Lung adenocarcinoma

tag: treatment


title: T12_1: T12 replicate 1

tag: time, hours

tag: succinyl acetone


title: T0_3: T0 replicate 3

tag: replicate


title: Cmi S2 ChIP


title: Series16_A549-ACE2_SARS-CoV-2_2

description:
Time after treatment: 24 hours
BN5-indexA5

value: SARS-CoV-2 infected (MOI 2)

tag: strain


title: T12_3: T12 replicate 3


title: Cmi W3L ChIP

tag: antibody


title: perivascular_adipose_tissue_distal_aorta_58

description:
200793810054_H
Subject_58


title: T0_2: T0 replicate 2


title: Pchwild_D3T2030_rep1

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
Quality trimmed read sequences were mapped to Plasmodium chabaudi chabaudi reference genomes using TopHat2. Gene expression estimates were made as raw read counts using the Pyhton script ‘HTSeq- count’ (model type – union). Counts data were converted to counts per million (cpm) and genes were filtered if they failed to achieve a cpm value of 1 in at least 30% of libraries per conditions.
Normalization of raw read counts was done using voom tmm method and differential gene expression analysis was carried out using DeSeq2
Genome_build: Plasmodium chabaudi chabaudi
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Plasmodium chabaudi chabaudi

growth_protocol: Ring stage sr10KO (clone A and B) and wild type P. chabaudi parasites were sub-inoculated into groups of four CBA mice each (1 x 106 parasitized RBCs per mouse) by intravenous injection at 20:30 hrs corresponding to ZT13.5, day 0. Starting at ZT13.5 on day 2 post-infection, blood smears were taken for both groups every three hours for 48 hrs producing a total of 17 time points. Same procedures were adopted for P. yoelii wild type and sr10KO strains to obtain time series phenotype data using blood smears.  20µl of blood was also collected via tail snip at these time points, washed in PBS and immediately treated with 500 uL TRIzol reagent and stored shortly at 4°C and for long term at -80°C. Blood smears were briefly fixed with 100% methanol and stained with Giemsa’s solution.  The parasitic patterns were then recorded based on classification of the parasitic forms into four stages- rings, early trophozoites, late trophozoites and schizonts.

extract_protocol:
Total RNA was isolated from TRIzol treated samples according to the manufacturer’s instructions (Life Technologies).
Strand-specific mRNA libraries were prepared from total RNA using TruSeq Stranded mRNA Sample Prep Kit LS (Illumina) according to the manufacturer’s instructions. Briefly, at least 100ng of total RNA was used as starting material to prepare the libraries. PolyA+ mRNA molecules were purified from total RNA using oligo-T attached magnetic beads. First strand synthesis was performed using random primers followed by second strand synthesis where dUTP were incorporated in place of dTTP to achieve strand-specificity. Ends of the double stranded cDNA molecules were adaptor ligated and the libraries amplified by PCR for 15 cycles. Libraries were sequenced on Illumina HiSeq 4000 platform with paired-end 100/150bp read chemistry according to manufacturer’s instructions. Data from 14 timepoints were anlyzed further excluding the first three time points.econd strand synthesis where dUTP were incorporated in place of dTTP to achieve strand-specificity. Ends of the double stranded cDNA molecules were adaptor ligated and the libraries amplified by PCR for 15 cycles. Libraries were sequenced on Illumina HiSeq 4000 platform with paired-end 100/150bp read chemistry according to manufacturer’s instructions. Data from 14 timepoints were anlyzed further

value: AS

tag: genotype

value: wild type


title: Pchwild_D3T2030_rep2


title: Series16_A549-ACE2_Mock_2

description:
NA
BN2-indexA2


title: T0_1: T0 replicate 1

value: MEDEP cells


title: Pchwild_D3T1730_rep2


title: B_X2_S1

city: London

first: Adam

last: Pennycuick

address: 5 University Street

department: UCL Respiratory

institute: University College London

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software v2.19.
Raw fastq files were trimmed using fastp version 0.20.1 with default options.
Fastq files were tagged with UMI information using UMItools version 1.0.1
Reads were aligned to human genome UCSC hg38 using RNA-STAR version 2.5.2b
Duplicate reads were removed using JE-suite version 1.2.1 (using the UMI-aware markdupes method)
Reads per transcript were counted using FeatureCounts version 1.6.4
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Tab delimited text file containing non-normalised count data; columns represent samples, rows represent genes.

source_name: Paediatric_FACS sorted airway basal cells

growth_protocol: Not applicable

extract_protocol:
Sorted basal cells were centrifuged at 300 x g for 5 mins at 4°C, resuspended in a 2:1 mix of Arcturus PicoPure Extraction buffer/RNAlater (Life Technologies) and stored at -80°C until use. samples were thawed, disrupted by lysis (incubation at 42°C for 30 mins followed by incubation at room temperature for 5 mins), vortexed and filtered using RNAeasy MinElute columns (Qiagen). RNA extraction was performed using the Arcturus PicoPure RNA Isolation Kit (Life Technologies Ltd; KIT0204) as per the manufacturer’s instructions. RNA was quantified using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific).
Libraries were created by UCL Genomics Core Facility using the SMARTer Stranded Total RNAseq Kit (Clontech), cleaned using JetSeq (Bioline) and quality control analysis of RNA integrity was performed using High Sensitivity RNA ScreenTape and the TapeStation Analysis software (Agilent Technologies). RNA sequencing was performed using 0.5x NextSeq for 75 cycles (Illumina; 43PE, ~33M reads per sample; R2 contains UMI information for associated R1 file).

treatment_protocol: Bronchoscopic biopsies from the tracheal lumen were transported to the laboratory in transport medium consisting of αMEM containing penicillin/streptomycin, amphotericin B and gentamicin. Cell suspensions were generated by sequential enzymatic digestion using with dispase 16 U/mL (Corning) for 20 minutes at room temperature followed by 0.1% trypsin/EDTA (Sigma) for 30 minutes at 37°C (both in RPMI medium, Gibco). Each enzyme step was quenched with medium containing FBS, placed on ice and combined following the second digestion. Biopsies were manually homogenised using sharp dissection between digest steps and by blunt homogenization through a 100 μm cell strainer (Miltenyi Biotec). Centrifugation steps were performed at 300 x g for 5 mins at 4°C. Cells were blocked in a fluorescence-activated cell sorting (FACS) buffer composed of PBS containing 1% FBS, 25 mM HEPES buffer and 1 mM EDTA for 20 minutes in 96-well V bottomed plates (Thermo Fisher Scientific). Cells were centrifuged as above before staining for 20 minutes on ice at 4°C. The antibodies used were CD31 (BV421; Biolegend; 303124), CD45 (BV421; Biolegend; 304031), EPCAM (APC; Biolegend; 324208), PDPN (PE-Cy7; Biolegend; 337013). Cells were resuspended in FACS buffer for sorting of EPCAM+/PDPN+ live cells into epithelial cell culture medium containing Y-27632 for transport to the laboratory.

tag: group

value: Paediatric

value: fresh sorted basal cells


title: B_X8_S5

value: Bronchoscopic biopsies from the tracheal lumen


title: B_X6_S4

source_name: Adult_FACS sorted airway basal cells

value: Adult


title: Pchwild_D3T1730_rep1


title: omental-visceral_fat_60

description:
200793810054_I
Subject_60

value: Peripheral artery disease (PAD)


title: B_X5_S3


title: subcutaneous_abdominal_fat_58

description:
200793810054_K
Subject_58


title: subcutaneous_abdominal_fat_60

description:
200793810054_E
Subject_60


title: perivascular_adipose_tissue_proximal _aorta_60

description:
200793810054_F
Subject_60

value: Periaortic adipose tissue (proximal abdominal aorta)


title: Pchwild_D3T1430_rep2


title: Hair follicle mesenchyme from 2mo mice

description: FACS sorted cells: 10,000 cells; Recovered: 2604 cells

source_name: 2mo HF

extract_protocol:
Backskin from α-SMACreT2:RosaYFP mice at 2 months of age and 18 months of age (n = 2/ sample) were surgically removed. Isolated backskin were incubated in 5mg/mL dispase (StemCell Technologies) in Hank’s Buffered Salt Solution (HBSS; Life Technologies) for 30 mins at 37oC, then the epidermis was surgically removed. The remaining dermis was dissociated in 2mg/mL collagenase in Ham’s F12 Nutrient mixture (Thermo Fischer Scientific) for 2 hours at 37oC. Cell suspension was diluted with cold HBSS, strained through 70µm and 40µm cell filters (Falcon) and centrifuged at 280g. Re-suspended cells were stained with conjugated Integrin α-9-PE (ThermoFisher), conjugated CD200-PE (ThermoFisher) and conjugated Cd26-647 (R&D Systems) for 45 mins, then with corresponding Alexa Fluor secondary antibodies (Invitrogen) for 30 mins. eFluor 780 viability dye (eBioscience) was included in the last 5 mins to exclude dead cells and debris. FACS-isolation was performed using a FACSAria III (BD Biosciences) and analyzed using FCS Express 6 software. Single colour and appropriate isotype controls were used for compensation and gating.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry. Single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 2727 and 1906 cells for Samples 1 and 2, respectively, with an estimated doublet rate of ≈3%. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of 100,000 reads/cell.

tag: transgenic strain

tag: background

tag: facs strategy

value: (YFP+ or Cd26+) and (Itga9+ or Cd200+)

tag: library preparation

value: 10X Genomics Single Cell RNAseq v2


title: B_X4_S2

tag: cell type


title: perivascular_adipose_tissue_proximal _aorta_58

description:
200793810054_C
Subject_58

tag: diagnosis

tag: Sex

value: Male

tag: age (years)

value: Italy


title: Pchwild_D3T1430_rep1


title: N4

source_name: Adult_Airway epithelial cells

extract_protocol:
Samples were thawed, disrupted by lysis (incubation at 42°C for 30 mins followed by incubation at room temperature for 5 mins), vortexed and filtered using RNAeasy MinElute columns (Qiagen). RNA extraction was performed using the Arcturus PicoPure RNA Isolation Kit (Life Technologies Ltd; KIT0204) as per the manufacturer’s instructions. RNA was quantified using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific).
Libraries were created by UCL Genomics Core Facility using the SMARTer Stranded Total RNAseq Kit (Clontech), cleaned using JetSeq (Bioline) and quality control analysis of RNA integrity was performed using High Sensitivity RNA ScreenTape and the TapeStation Analysis software (Agilent Technologies). RNA sequencing was performed using 0.5x NextSeq for 75 cycles (Illumina; 43PE, ~33M reads per sample).

treatment_protocol: Bronchoscopic biopsies from the tracheal lumen were frozen in OCT and sectioned before laser-cature microdissection to isolate only the epithelium. Samples were suspended in a 2:1 mix of Arcturus PicoPure Extraction buffer and RNAlater (Life Technologies) and stored at -80°C until use.

tag: tissue

value: Airway epithelial cells


title: omental-visceral_fat_58

description:
200793810054_B
Subject_58

value: Omental-visceral fat

tag: country of origin

tag: subject


title: Hs944T-shScr replicate 1

city: Boston

first: David

middle: E.

last: Fisher

state: Massachusetts

address: 55 Fruit Street

department: Dermatology

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to the reference genome (hg19) by STAR 2.5.2.
Reads were counted by HTSeq-0.6.1 using UCSC annotation, as downloaded from the Illumina iGenomes collection.
Only reads with mapping score of 10 or more were counted.
Differentially expressed genes were detected by DESeq2, using the Wald test.

growth_protocol: Hs944T cells were routinely cultured in DMEM with 1% penicillin/streptomycin/L-glutamine and 9% FBS

extract_protocol: Total RNA was isolated from lysates using RNeasy (Qiagen)

treatment_protocol: Hs944T cells were infected with lentivirus expressing G9a-targeting or scrambled shRNAs and 72h later the cells were lysed for RNA isolation

value: melanoma cell line

tag: passages

tag: shRNA target

value: Scr negative control


title: Hs944T-shScr replicate 2


title: A5


title: N3


title: Pchwild_D3T1130_rep2

tag: strain

value: AS


title: Pchwild_D3T1130_rep1

value: wild type


title: Pchwild_D3T0830_rep2


title: perivascular_adipose_tissue_distal_aorta_15

description:
200793810047_J
Subject_15

value: Periaortic adipose tissue (abdominal aorta)


title: Hs944T-shG9a replicate 1


title: A2


title: Pchwild_D3T0830_rep1


title: Hs944T-shG9a replicate 2


title: Hair follicle mesenchyme from 18mo mice

description: FACS sorted cells: 10,000 cells; Recovered: 3776 cells

source_name: 18mo HF


title: omental-visceral_fat_15

description:
200793810047_G
Subject_15


title: Pchwild_D3T0530_rep2


title: Pchwild_D3T0530_rep1


title: perivascular_adipose_tissue_proximal _aorta_15

description:
200793810047_D
Subject_15


title: pMEL-GFP replicate 1

source_name: pMEL/hTERT/CDK4(R24C)/BRAF(V600E) cells

growth_protocol: pMEL/hTERT/CDK4(R24C)/BRAF(V600E) cells were routinely cultured in DMEM with 1% penicillin/streptomycin/L-glutamine and 9% FBS

treatment_protocol: pMEL/hTERT/CDK4(R24C)/BRAF(V600E) cells were infected with lentivirus expressing G9a or GFP and 72h later the cells were lysed for RNA isolation

value: immortalized human melanocytes expressing BRAF(V600E)

tag: overexpression

value: GFP


title: pMEL-G9a_WT replicate 2


title: pMEL-GFP replicate 3


title: Pchwild_D3T0230_rep2

tag: genotype


title: perivascular_adipose_tissue_distal_aorta_59

description:
200790250104_I
Subject_59


title: subcutaneous_abdominal_fat_15

description:
200793810047_A
Subject_15

value: Subcutaneous abdominal fat


title: P7

source_name: Paediatric_Airway epithelial cells

tag: group

value: Paediatric

value: Bronchoscopic biopsies from the tracheal lumen


title: pMEL-G9a_WT replicate 1


title: perivascular_adipose_tissue_proximal _aorta_59

description:
200790250104_J
Subject_59

value: Peripheral artery disease (PAD)

value: Periaortic adipose tissue (proximal abdominal aorta)


title: P6


title: P5


title: P4


title: omental-visceral_fat_59

description:
200790250104_G
Subject_59


title: Trr RNAi depletion CG larvae

city: Maywood

first: Andrew

last: Dingwall

state: IL

address: 2160 S First Avenue

department: Cancer Biology

institute: Loyola University Chicago

description: trr-CG

data_processing:
FASTQ files were aligned using SOAPaligner/SOAP2, then valiated with Bowtie.  Transcripts were then assembled with Cufflink.
An in house algorithm developed by BGI was used for gene expression analysis.
Genome_build: dm6
Supplementary_files_format_and_content: The processed data is formatted in a comma separated values (.csv) file.  Each column represents the following:  Gene ID, gene symbol, length of gene, and the RPKM values for each sample type.

source_name: Drosophila W3L at 25 degrees C

growth_protocol: Drosophila melanogaster wandering third instar larvae grown at 25 degrees C.

extract_protocol:
Animals (>20 of each genotype) were collected, and RNA extracted using RNAqueous (Invitrogen). Samples were DNAseI treated, RNAs selected by oligo dT and fragmented. Then cDNA is synthesized  using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short  fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent  2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using  Illumina HiSeqTM 2000. Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed. After QC,  raw reads are filtered into clean reads which will be aligned to the reference sequences with SOAPaligner/SOAP2[ 1]. QC of alignment is performed to determine if resequencing is  needed. The alignment data is utilized to calculate distribution of reads on reference genes and perform coverage analysis.
Libraries were prepared according to Illumina's instructions and performed by Beijing Genomics

tag: phenotype

value: Clear gut larvae

tag: treatment

value: shRNAi using GawB69B Gal4 driver at 25 degrees

value: Trr RNAi depletion


title: Pchwild_D2T2330_rep1


title: P3

value: Airway epithelial cells


title: Cmi RNAi depletion CG larvae

description: cmi-CG

value: Cmi RNAi depletion


title: omental-visceral_fat_57

description:
200669330063_L
Subject_57

value: Omental-visceral fat

value: Male

value: Italy


title: Cmi RNAi depletion BG larvae

description: cmi-BG

value: Blue gut larvae


title: P1


title: Pchwild_D2T2030_rep1

value: AS

value: wild type


title: Xenograft tumor, CBL_8

first: Rui

last: Guo

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

description: Table S5  rnaseq.cbl xenograft

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using Salmon v0.14.0
Quant file was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCh37.83
Supplementary_files_format_and_content: Excel file includes Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj), log2 normalized reads of genes

source_name: Xenograft tumors

growth_protocol: Burkitt Lymphoma cells were cultured in GIBCO RPMI 1650 medium (Life Technologies) with 10% fetal calf serum (FCS) and 10 mM HEPES in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
Total RNAs were subsequently isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination
To construct RNA-seq libraries, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: No specific treatment

value: Xenograft tumor


title: Wild type BG (blue gut) larvae

description: WT-BG

value: Wild type


title: perivascular_adipose_tissue_proximal _aorta_57

description:
200669330063_D
Subject_57


title: Pchwild_D2T1730_rep2


title: subcutaneous_abdominal_fat_59

description:
200790250104_H
Subject_59

value: Subcutaneous abdominal fat


title: Wild type CG (clear gut) larvae

description: WT-CG


title: Pchwild_D3T0230_rep1


title: Pchwild_D2T1730_rep1


title: Trr RNAi depletion BG larvae

description: trr-BG


title: Pchwild_D2T2330_rep2


title: Pchwild_D2T2030_rep2


title: Xenograft tumor, CBL_3

description: Table S5  rnaseq.cbl xenograft


title: Pchwild_D2T1430_rep2


title: Xenograft tumor, Ctrl_13

description: Table S5  rnaseq.cbl xenograft

value: DMSO


title: perivascular_adipose_tissue_proximal _aorta_63

description:
200669330022_K
Subject_63

value: Peripheral artery disease (PAD)


title: perivascular_adipose_tissue_distal_aorta_63

description:
200669330022_H
Subject_63

value: Periaortic adipose tissue (abdominal aorta)


title: Xenograft tumor, Ctrl_1

description: Table S5  rnaseq.cbl xenograft


title: UCB1

city: Guangzhou

first: Xinping

last: Yang

state: Guangdong

address: 1838 N. Guangzhou Ave

institute: Southern Medical University

data_processing:
Tophat2 (v2.1.1; run with parameters '-p 6 -r 50 -b2 -very-sensitive') + Picard MarkDuplicats (v2.2.2) + GATK (v3.5) pipeline was used to detect reliable variants from RNA-seq data. ANNOVAR (v2016-02-01) was used to annotate variants. A/G and C/T mismatches statistified (1) with allele frequency lower than 0.05 in East Asia population or without allele frequency, (2) VQSR marked as 'PASS' were retained as potential RNA editing sites.
Gene counts were calculated by STAR (v2.5.2b + HTSeq htseq-count (v0.9.0) pipeline. Raw counts of two umbilical cord blood were used to remove the influence of blood contamination on gene expressions in placenta.
Editing levels of potential RNA editing sites were defined as the ratio of reads with editing to total reads. If there is no read covering the editing site in a sample, editing ratio for this site in this sample would be assigned as zero.
Transcripts expressed in placenta were assembled from RNA-seq reads by StringTie (v1.3.4) and comapred with known transcripts from Ensembl (GRCh38.84) by Cufflinks cuffcompare (v2.2.1). Then the intron retention events were detected by comparing assembled transcripts with corresponding non-redunant canonical transcripts from GENCODE (v29).
For every intron retention (IR) event, the percent spliced in (PSI) was defined as the ratio of adjusted spliced-in reads and the sum of adjusted spliced-in and spliced-out reads. Adjusted spliced-in reads = number of reads supporting IR events / (IR event length + read length -1). Adjusted spliced-out reads = number of reads skipping corresponding introns / (read length -1).
Genome_build: hg38
Supplementary_files_format_and_content: For RNA editing sites: counts and editing ratios at potential RNA editing sites. Tab-delimited files are formatted as: chr, pos, ref, alt, func.refgene, gene.refgene, strand, non-edited.counts, edited.counts, editing.ratio
Supplementary_files_format_and_content: For gene expression: raw counts of expressed genes in placenta and umbilical cord blood; counts after removing blood contamination of expressed genes in placenta. Tab-delimited files are formatted as: ENSG id, raw counts (or normalized counts).
Supplementary_files_format_and_content: For intron retention (IR) events: counts and PSI values for IR events. Tab-delimited files are formatted as: stringtie transcript id, gene symbol, Chr, IR start, IR end, strand, reads supporting IR, reads not supporing IR, adjusted reads supporting IR, adjusted reads not supporting IR, PSI.

source_name: Normal_Umbilical Cord Blood

extract_protocol:
Total RNA was isolated using the RNeasy® Plus Universal Mini Kit (Qiagen, DEU) according to the manual manufacturer’s instruction.
RNAs with poly(A) tails were isolated, and double-stranded cDNA libraries were prepared using TruSeq RNA Kit (Illumina, USA).

tag: subject status

value: Normal

value: Umbilical Cord Blood


title: PHNPR41

value: Placenta


title: Xenograft tumor, Ctrl_7

description: Table S5  rnaseq.cbl xenograft


title: UCB2


title: PHNPR43


title: subcutaneous_abdominal_fat_63

description:
200669330022_B
Subject_63


title: omental-visceral_fat_63

description:
200669330022_F
Subject_63


title: Pchwild_D2T1130_rep1


title: Pchwild_D2T1130_rep2


title: Akata EBV+ cells, myc KO Rep3

description:
Table S2 myc-pxpr.deseq.lfcshrink
CJ25_Akata_myc_3

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using Salmon v0.14.0
Quant file was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCh37.83
Supplementary_files_format_and_content: comma-delimited text files include Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj), raw counts of genes

source_name: Akata EBV+ Burkitt Lymphoma cells

value: Akata EBV+ Burkitt Lymphoma cells

value: myc KO


title: perivascular_adipose_tissue_distal_aorta_57

description:
200669330063_H
Subject_57


title: PHNPR38B


title: perivascular_adipose_tissue_distal_aorta_47

description:
200667730041_L
Subject_47

value: Female


title: Pchwild_D2T0830_rep2


title: PHNPR38A


title: Pchwild_D2T1430_rep1


title: Akata EBV+ cells, myc KO Rep2

description:
Table S2 myc-pxpr.deseq.lfcshrink
CJ24_Akata_myc_2


title: Pchwild_D2T0830_rep1


title: perivascular_adipose_tissue_proximal _aorta_62

description:
200667730041_K
Subject_62

value: Periaortic adipose tissue (proximal abdominal aorta)


title: Akata EBV+ cells, myc KO Rep1

description:
Table S2 myc-pxpr.deseq.lfcshrink
CJ23_Akata_myc_1


title: omental-visceral_fat_47

description:
200667730041_H
Subject_47

value: Omental-visceral fat

value: Italy


title: subcutaneous_abdominal_fat_61

description:
200667730041_I
Subject_61

value: Male


title: PHNPR37


title: Pchwild_D2T0530_rep2

value: AS

value: wild type


title: perivascular_adipose_tissue_proximal _aorta_61

description:
200667730041_G
Subject_61


title: omental-visceral_fat_62

description:
200667730041_J
Subject_62


title: Akata EBV+ cells, Control for myc KO Rep1

description:
Table S2 myc-pxpr.deseq.lfcshrink
CJ20_Akata_pxpr_1

value: Control for myc KO


title: Akata EBV+ cells, Control for myc KO Rep2

description:
Table S2 myc-pxpr.deseq.lfcshrink
CJ21_Akata_pxpr_2


title: PchSR10KO_D3T2030_rep2


title: PHNPR35


title: PHNPR36


title: Pchwild_D2T0530_rep1


title: omental-visceral_fat_61

description:
200667730041_F
Subject_61


title: PHNPR34


title: PchSR10KO_D3T2030_rep1


title: PchSR10KO_D3T1730_rep2


title: PHNPR32


title: P3HR1 cells, tada2b KO Rep3

description:
Table S6 tada2b-pxpr.salmongc.deseq.lfcshrink
CJ19_T3_p3_tada2b_3

source_name: P3HR1 Burkitt Lymphoma cells

tag: cell line

value: Burkitt Lymphoma cells

value: tada2b KO


title: PHNPR33


title: PchSR10KO_D3T1730_rep1


title: P3HR1 cells, tada2b KO Rep1

description:
Table S6 tada2b-pxpr.salmongc.deseq.lfcshrink
CJ17_T1_p3_tada2b_1

tag: cell type


title: PHNPR31


title: perivascular_adipose_tissue_distal_aorta_61

description:
200667730041_C
Subject_61

tag: diagnosis

value: Peripheral artery disease (PAD)


title: PHNPR30


title: subcutaneous_abdominal_fat_47

description:
200667730041_D
Subject_47

value: Subcutaneous abdominal fat

tag: Sex


title: Akata EBV+ cells, Control for myc KO Rep3

description:
Table S2 myc-pxpr.deseq.lfcshrink
CJ22_Akata_pxpr_3


title: subcutaneous_abdominal_fat_62

description:
200667730041_B
Subject_62

tag: age (years)


title: PchSR10KO_D3T1430_rep2


title: perivascular_adipose_tissue_proximal _aorta_47

description:
200667730041_A
Subject_47

tag: tissue


title: perivascular_adipose_tissue_distal_aorta_62

description:
200667730041_E
Subject_62

value: Periaortic adipose tissue (abdominal aorta)

tag: country of origin


title: PHNPR29

value: Normal


title: P3HR1 cells, med12 KO Rep2

description:
Table S7 med12-pxpr.salmongc.deseq.lfcshrink
CJ15_M2_p3_med12_2

value: med12 KO


title: P3HR1 cells, tada2b KO Rep2

description:
Table S6 tada2b-pxpr.salmongc.deseq.lfcshrink
CJ18_T2_p3_tada2b_2


title: subcutaneous_abdominal_fat_22

description:
200307970061_I
Subject_22

tag: subject


title: PchSR10KO_D3T1430_rep1


title: PchSR10KO_D3T1130_rep2


title: P3HR1 cells, med12 KO Rep3

description:
Table S7 med12-pxpr.salmongc.deseq.lfcshrink
CJ16_M3_p3_med12_3


title: perivascular_adipose_tissue_distal_aorta_22

description:
200307970061_K
Subject_22


title: PHNPR28

value: Placenta


title: P3HR1 cells, med12 KO Rep1

description:
Table S7 med12-pxpr.salmongc.deseq.lfcshrink
CJ14_M1_p3_med12_1


title: PchSR10KO_D3T1130_rep1


title: PchSR10KO_D3T0830_rep2


title: P3HR1 cells, Control for med12 and tada2b KO Rep2

description:
Table S6 tada2b-pxpr.salmongc.deseq.lfcshrink, Table S7 med12-pxpr.salmongc.deseq.lfcshrink
CJ11_P2_p3_pxpr_2

value: Control for med12 and tada2b KO


title: PolII_LPS_rep2

city: Beijing

first: Li

last: Yu

address: Medicial Science Building, Tsinghua University

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads have passed Illumina filters, and been trimmed using Sickle using quality threshold >20
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 1.1.2
Peaks were called using HOMER (version4.7.2) FDR< 10^-3)
bedGraph files were generated by HOMER (version 4.7.2)
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: Macrophages

extract_protocol:
Lysates were clarified from sonicated nuclei and PolII-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow-derived macrophages

tag: agent

value: LPS

tag: antibody

value: PolII


title: PolII_LPS_rep1

tag: strain


title: PchSR10KO_D3T0830_rep1


title: PolII_UT_rep2

value: untreated


title: P3HR1 cells, Control for med12 and tada2b KO Rep1

description:
Table S6 tada2b-pxpr.salmongc.deseq.lfcshrink, Table S7 med12-pxpr.salmongc.deseq.lfcshrink
CJ10_P1_p3_pxpr_1


title: PchSR10KO_D3T0530_rep2


title: PHNPR26


title: PHNPR27A


title: PHNPR27B


title: PHNPR25


title: perivascular_adipose_tissue_proximal _aorta_22

description:
200307970061_E
Subject_22

value: Periaortic adipose tissue (proximal abdominal aorta)

value: Male

value: Italy


title: PolII_UT_rep1


title: P3HR1 cells, supt16h KO Rep3

description:
Table S4 supt16h-pxpr.salmongc.deseq.lfcshrink
CJ9_S16_3_p3_supt16h_3

value: supt16h KO


title: PHNPR24


title: P3HR1 cells, supt16h KO Rep2

description:
Table S4 supt16h-pxpr.salmongc.deseq.lfcshrink
CJ8_S16_2_p3_supt16h_2

value: Burkitt Lymphoma cells


title: Gsh2-Cre; Zeb2fl/ko #5

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

data_processing:
Illumina software was used for basecalling.
low quality reads were removed using fastq_quality_filter (FASTX-Toolkit)
alignment: Sequence reads were mapped to the mus musculus reference genome (mm10) via TopHat2 v2.0.13
counts: featureCounts v1.4.6 was used to count the number of genes for GRCm38 annotated genes with parameters -t exon and -g gene_name.
Genome_build: mm10
Supplementary_files_format_and_content: countTable.txt with gene counts

extract_protocol:
V-SVZ tissue was manually dissected and treated with papain. Cells were dissociated, washed in PBS and put over a 70um cell strainer. GFP+ cells were FACS sorted and immediately lysed in Trizol LS. RNA was isolated using the RNeasy Micro kit (Qiagen).
Libraries were prepared according to the Illumina TruSeq protocol.

value: V-SVZ

tag: age

value: Gsh2-Cre; Zeb2fl/KO


title: PchSR10KO_D3T0230_rep2

value: AS

tag: genotype


title: PchSR10KO_D3T0530_rep1


title: PHNPR23


title: Gsh2-Cre; Zeb2fl/wt #6

value: Gsh2-Cre; Zeb2fl/wt


title: P3HR1 cells, Control for med12 and tada2b KO Rep3

description:
Table S6 tada2b-pxpr.salmongc.deseq.lfcshrink, Table S7 med12-pxpr.salmongc.deseq.lfcshrink
CJ13_P3_p3_pxpr_3


title: Gsh2-Cre; Zeb2fl/wt #5


title: omental-visceral_fat_22

description:
200307970061_G
Subject_22

value: Peripheral artery disease (PAD)

value: Omental-visceral fat


title: PchSR10KO_D2T2330_rep2


title: PHNPR19

value: Normal

value: Placenta


title: P3HR1 cells, smc1a KO Rep2

description:
Table S3 smc1a-pxpr.salmongc.deseq.lfcshrink
CJ5_SM2_p3_smc1a_2

value: smc1a KO


title: Gsh2-Cre; Zeb2fl/ko #4


title: P3HR1 cells, smc1a KO Rep1

description:
Table S3 smc1a-pxpr.salmongc.deseq.lfcshrink
CJ4_SM1_p3_smc1a_1


title: Gsh2-Cre; Zeb2fl/wt #4


title: PchSR10KO_D2T2030_rep2


title: Gsh2-Cre; Zeb2fl/ko #3


title: PHNPR17


title: P3HR1 cells, Control for smc1a and supt16h KO Rep3

description:
Table S3 smc1a-pxpr.salmongc.deseq.lfcshrink, Table S4 supt16h-pxpr.salmongc.deseq.lfcshrink
CJ3_P3_p3_pxpr_3

value: Control for smc1a and supt16h KO


title: P3HR1 cells, smc1a KO Rep3

description:
Table S3 smc1a-pxpr.salmongc.deseq.lfcshrink
CJ6_SM3_p3_smc1a_3


title: PHNPR16


title: PchSR10KO_D2T2030_rep1


title: P3HR1 cells, supt16h KO Rep1

description:
Table S4 supt16h-pxpr.salmongc.deseq.lfcshrink
CJ7_S16_1_p3_supt16h_1


title: PchSR10KO_D2T1730_rep2


title: Gsh2-Cre; Zeb2fl/wt #3


title: P3HR1 cells, Control for smc1a and supt16h KO Rep2

description:
Table S3 smc1a-pxpr.salmongc.deseq.lfcshrink, Table S4 supt16h-pxpr.salmongc.deseq.lfcshrink
CJ2_P2_p3_pxpr_2


title: PHNPR21


title: P3HR1 cells, Control for smc1a and supt16h KO Rep1

description:
Table S3 smc1a-pxpr.salmongc.deseq.lfcshrink, Table S4 supt16h-pxpr.salmongc.deseq.lfcshrink
CJ1_P1_p3_pxpr_1


title: PchSR10KO_D3T0230_rep1


title: PHNPR14


title: Gsh2-Cre; Zeb2fl/wt #2


title: PHNPR18


title: PchSR10KO_D2T1730_rep1


title: Gsh2-Cre; Zeb2fl/ko #2


title: PHNPR11


title: ITGA3_neg_4

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

description:
EXP115_ITGA3_n_C (07)
ITGA3- (EPCR+CD90+CD133+CD34+CD45RA-) cells sorted from sample C after 7 day culture in UM171

data_processing:
Basecalls performed using Illumina RTA 1.18.64
Samples demultiplexed using bcl2fastq 2.17
TPM values were computed by kallisto using a transcriptome index built on human genome GRCh38 along with Ensembl 92 annotations and taking into account fragment orientation for these stranded libraries.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression files are tab delimited with columns 1) Ensembl transcript identifier, 2) transcript length , 3) effective transcript length, 4) estimated counts, and 5) transcript per million reads sequenced (TPM).

source_name: expanded cord blood

growth_protocol: cord blood cells sorted at day 0 for the CD34+CD45RA- phenotype and expanded for 7 days with UM171 (35nM). Cells are sorted for the CD34+CD45RA-CD90+EPCR+CD133+ and either ITGA3+ and ITGA3-. EPCR+CD34+ are sorted as a control.

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
TruSeq RNA Stranded Sample Preparation (Illumina)

value: cord blood cells

tag: cell population


title: PchSR10KO_D2T2330_rep1


title: PchSR10KO_D2T1430_rep1


title: ITGA3_neg_3

description:
EXP119_ITGA3_n_F (16)
ITGA3- (EPCR+CD90+CD133+CD34+CD45RA-) cells sorted from sample F after 7 day culture in UM171


title: Gsh2-Cre; Zeb2fl/wt #1


title: PchSR10KO_D2T1130_rep2


title: ITGA3_neg_2

description:
EXP119_ITGA3_n_E (15)
ITGA3- (EPCR+CD90+CD133+CD34+CD45RA-) cells sorted from sample E after 7 day culture in UM171


title: PHNPR10


title: PHNPR09


title: PHNPR08


title: ITGA3_neg_1

description:
EXP115_ITGA3_n_A (05)
ITGA3- (EPCR+CD90+CD133+CD34+CD45RA-) cells sorted from sample A after 7 day culture in UM171


title: PchSR10KO_D2T1130_rep1


title: PHNPR06


title: ITGA3_pos_3

description:
EXP119_ITGA3_p_F (13)
ITGA3+ (EPCR+CD90+CD133+CD34+CD45RA-) cells sorted from sample F after 7 day culture in UM171


title: PchSR10KO_D2T0830_rep1


title: PchSR10KO_D2T0830_rep2


title: ITGA3_pos_2

description:
EXP119_ITGA3_p_E (12)
ITGA3+ (EPCR+CD90+CD133+CD34+CD45RA-) cells sorted from sample E after 7 day culture in UM171


title: ITGA3_pos_1

description:
EXP115_ITGA3_p_A (01)
ITGA3+ (EPCR+CD90+CD133+CD34+CD45RA-) cells sorted from sample A after 7 day culture in UM171


title: PHNPR03


title: PchSR10KO_D2T0530_rep2


title: PHPR42

value: early-onset severe preeclampsia (EOSPE)


title: PchSR10KO_D2T1430_rep2


title: PHPR37


title: Gsh2-Cre; Zeb2fl/ko #1


title: Acetone G10 B

city: Beltsville

first: Wayne

middle: M

last: Jurick

state: MD

address: Building 002

department: Agricultural Research Service

institute: United States Department of Agriculture

data_processing:
FAST-QC       v. 0.11.9
Trinity de novo Alignment to reference (MD-8 genome) usegalaxy.org
Salmon transcriptome read counting usegalaxy.org
Genome_build: reference genome: GCA_000769745.1
Supplementary_files_format_and_content: gene count data from transcriptome as aligned to reference genome

organism: Penicillium crustosum

source_name: frozen mycelia

growth_protocol: biological Replicates are deliniated alphabetically with the letter after M in sample name.

extract_protocol:
trizol with bead beating in qiagen tissue lyzer
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: 5ppm difenoconazole addition to liquid shake culture for samples beginning with "D" acetone for samples beginning with "A"

value: exposed to acetone


title: PchSR10KO_D2T0530_rep1


title: PHPR33


title: Acetone G10 C