title: SK-MEL-147_4_Tcells_sgCTR_Rep2


title: SK-MEL-147_4_IFNgamma_sgCTR_Rep1

status: Public on Feb 24 2022

type: SRA

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

library_source: transcriptomic

data_processing:
Fastq files were mapped to the human reference genome (Homo.sapiens.GRCh38.v77) using Tophat v2.1 with default settings for single-end data. The samples were used to generate read count data using HTSeq-count (V0.10.0).
Genome_build: hg38
Supplementary_files_format_and_content: Text fie with read count data

molecule: total RNA

organism: Homo sapiens

source_name: Melanoma cell line

growth_protocol: Cells were cultured with DMEM supplemented with 9% FBS and pen/strep in 5% CO2 incubator at 37 degree

extract_protocol:
RNA was extracted using RLT buffer (Qiagen, 79216)
Librararies were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2*106 D10 and SK-MEL-147 melanoma cells expressing either sgCtrl or sgSTUB1 were plated per dish in 10 cm cell culture dishes 48 hours prior to IFNγ treatment. Melanoma cells were subsequently treated with 25 ng/ml IFNγ or vehicle for 8 hours.

tag: cell line

tag: time (hours)

tag: treatment

value: IFNgamma

tag: guide

value: sgCTR

tag: replicate


title: DOX5

city: Vienna

first: Dominika

last: Lukovic

address: Waehringer Guertel 18-20

department: Internal Medicine II

country: Austria

institute: Medical University of Vienna

data_processing:
Alignment [code: STAR    --runThreadN 32    --outSAMattributes All    --outSAMtype BAM SortedByCoordinate    --quantMode GeneCounts    --genomeDir Sscrofa11.1_index    --readFilesIn rawReads    --outFileNamePrefix 15619    --readFilesCommand gunzip -c    --outReadsUnmapped Fastx    --outWigType wiggle ]
Counting reads into genes [EnsemblIDs](code: python3 -m HTSeq.scripts.count -f bam -r pos -t exon --additional-attr=gene_name stranded=reverse  15618Aligned.sortedByCoord.out.bam genes.gtf > 15618.counts). Mapped reads were counted into the Ensembl  Sscrofa 11.1 gene model using HTSeq Python package (Python3 Version 3.9, HTSeq-Count Version 0.11.1)9 applying parameters:  -m union stranded=revers.
Differential expression analysis[comparison between experimental group and control group]; (code: deseq2Data <- DESeqDataSetFromMatrix(countData=rawCounts, colData=sampleData, design= ~ treatment). Raw reads were transformed based on library size using DESeq2 package with subsequent rlog transformation. Statistically significantly deregulated genes were determined by generalized linear models fitted to the corresponding contrast (each treatment versus control group). The estimated coefficients and standard errors for all contrasts were used for calculation of moderated t-statistics, moderated F-statistics, and the log-odds of differential expression by empirical Bayes shrinkage of the standard errors towards a common value.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: counted reads in .txt files

organism: Sus scrofa

source_name: anterior wall

extract_protocol:
The specimens were homogenized using Precellys lysing kit CK28 beads (VWR, Vienna, Austria) in Qiazol lysis buffer (Qiagen, Hilden, Germany) and total RNA was isolated using the RNeasy® Tissue kit (Qiagen, Hilden, Germany).
The total RNA fractions of the myocardial samples were subjected to mRNA deep sequencing using the Illumina (San Diego, CA, USA) platform. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) was utilized for mRNA fragmentation and enrichment. Fragmented and primed mRNA was reverse transcribed to cDNA. The cDNA library was synthesized and enriched using the NEBNext Ultra Directional RNA Library Kit (New England Biolabs, Ipswich, MA, USA). Sequencing was performed on the HiSeq 2500 platform to a mean depth of 15–20 million paired-end reads per sample at the Core Facility of the Medical University of Vienna.

treatment_protocol:
Nineteen pigs (Sus scrofa, female large whites) were included into five groups receiving either Doxorubicin (DOX, n=5) or liposomal encapsulated Doxorubicin, Myocet (MYO, n=5), undergoing reperfused myocardial infarction (RemoLV, n=3) or induced artificial aortic isthmus stenosis (Hyper, n=3). The fifth group served as sham-operated control group (Control, n=3). Animals in groups DOX and MYO received either Doxorubicin (DOX) or liposomal doxorubicin-citrate complex (Myocet®, MYO) in 3 cycles (Day 1, 22, 43) of cytostatic treatment in doses equivalent to human treatment regimens (60 mg/m2 body surface area). The DOX and MYO experiments had to be prematurely terminated after 3 months (FUP) due to bad health conditions of the animals.  Domestic pigs in the group RemoLV were sedated by subcutaneous administration of 12mg/kg ketamine hydrochloride, 1mg/ kg xylazine, and 0.04 mg/kg atropine after overnight fasting. After endotracheal intubation, the anesthesia was deepened with 1.5-2.5 vol % isoflurane, 1.6- 1.8 vol % O2, and 0.5 vol % N2O. A 6F introduction sheath (Terumo Medical Corporation, Somerset, NJ, USA) was inserted into the right femoral artery. Following administration of 200 IU/kg of heparin, 6F right coronary guiding catheters were introduced into the left and right coronary ostium to perform selective angiography of the left and right coronary arteries.  Catheter-based reperfused anterior wall myocardial infarction was induced by the inflation of a coronary-angioplasty balloon (2.75 mm diameter, 15 mm length; Maverick, Boston Natick, MA, USA) at 5 atm for 90 min in the mid part of the left anterior descending coronary artery. Reperfusion was initiated via balloon deflation. The animals were allowed to recover from the anesthesia. FUP investigations and myocardial tissue sampling was performed at 6-month.  For pressure overload-induced myocardial fibrosis (Hyper), a bare metal stent (9 mm of diameter, 20 mm of length, Cordis S.M.A.R.T. CONTROL, Cordis, Fremont, California) was implanted in the descending thoracic aorta of the juvenile pigs. Natural enlargement of thoracic aorta by growing animals reaching the diameter of 1.8 cm resulted in induced artificial aortic thoracic stenosis by constant 9 mm stent. The developing artificial aortic isthmus stenosis resulted in a slowly developing severe myocardial hypertrophy and diffuse myocardial fibrosis during the 6 Mo FUP.  After the predefined FUP, the animals were euthanized, and the hearts were explanted. Myocardial samples from the anterior wall in groups DOX, MYO and Hyper were collected, while remote posterior wall myocardial area from the remodeled LV was excised in group RemoLV.  Sham operated animals in the same age of the animals of other groups served as Controls (n=3).
Myocardial tissue samples (~30mg) of the left ventricle (for RemoLV, non-ischemic myocardium) were washed with PBS, minced into small pieces and transferred into cryotubes containing 1.2 ml RNAlater®(Ambion, Austin, TX, USA). The samples were firstly incubated overnight at 4°C, then transferred to -80 °C.

tag: tissue

value: Myocardium

tag: follow-up (fup)

value: 3 months after 1st injection

value: Doxorubicin treated


title: SK-MEL-147_0_CTR_sgCTR_Rep2

value: CTR


title: SK-MEL-147_4_Tcells_sgCTR_Rep1

value: Tcells


title: MYO1

value: Myocet treated


title: SK-MEL-147_0_CTR_sgCTR_Rep1


title: DOX4


title: DOX3


title: DOX2


title: DOX1


title: D10_4_IFNgamma_sgSTUB1_Rep1


title: HiC DN3 Tcf7-KO rep2

city: Philadelphia

first: Wenliang

last: Wang

state: PENNSYLVANIA

address: 421 Curie Boulevard

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Raw reads for each Hi-C sample were processed with HiC-Pro (version v2.5.0) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE = GATCGATC and GENOME_FRAGMENT generated for MboI restriction enzyme.
The validPairs from HiC-Pro were converted to .hic and .cool files for downstream analysis
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: Scid.adh cell line

extract_protocol:
HiC libraries were generated on 106 cells using with Arima-HiC+ kit (Arima Genomics) and Accel-NGS @S Plus DNA Library kit (21024 Swift Biosciences), according to the manufacturer’s recommendations.
Libraries were validated for quality and size distribution using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851) and TapeStation 2200 (Agilent). Libraries were paired-end sequenced (66bp+66bp) on NovaSeq 6000 (Illumina).

tag: genotype


title: D10_4_Tcells_sgSTUB1_Rep2


title: D10_4_IFNgamma_sgSTUB1_Rep2


title: D10_4_Tcells_sgSTUB1_Rep1


title: D10_0_CTR_sgSTUB1_Rep2


title: MYO4


title: D10_0_CTR_sgSTUB1_Rep1


title: VldlrKO-P14_C57B6_retina_rep2

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

description: VLDLRKO

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.4.0.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: WT and VldlrKO samples were merged together into a single matrix. log(1+10,000*(DGE normalized to total transcripts per cell)) calculated on DGE.
Supplementary_files_format_and_content: Digital expression matrices. Compressed, flat text files with tab delimiters.

source_name: P14 retinal cells

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads.
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.

tag: laboratory

value: JS JOYAL

tag: original replicate

tag: study replicate

value: Vldlr KO


title: VldlrKO-P14_C57B6_retina_rep3

description: VLDLRKO


title: WT-P14_C57B6_retina_rep1

description: CTL

value: WT


title: VldlrKO-P14_C57B6_retina_rep1

description: VLDLRKO


title: Oligo_library_STARRseq_hk_rep3

city: Wien

first: Bernardo

middle: P

last: de Almeida

address: Campus-Vienna-Biocenter 1

institute: Research Institute of Molecular Pathology (IMP)

data_processing:
Library strategy: STARR-seq
Oligo library UMI-STARR-seq RNA and DNA input reads (150 bp) were mapped to a reference containing 249 bp long sequences containing both wildtype and mutated fragments from the Drosophila library using Bowtie v.1.2.2. We demultiplexed reads by the i5 and i7 indexes and subsequently by the oligo identity, since this library contained oligos from other experiments. Mapping reads with the correct length, strand and with no mismatches (to identify all sequence variants) were kept. Both DNA and RNA reads were collapsed by UMI (10 bp, allowing one mismatch; UMI sequences are in the sequencing read name) to ensure the counting of unique reporter transcripts.
We excluded oligos with less than 10 reads in any of the input replicates and added one read pseudocount to oligos with zero RNA counts. The enhancer activity of each oligo in each screen was calculated as the log2 fold-change over input, using both replicates, using DESeq2. We used the counts of wildtype negative regions in each library as scaling factors between samples. This normalization only changes the position of the zero and consequently does not affect the calculation of log2 fold-changes or the p-values for the statistical tests used.
Genome_build: dm3 (custom oligo library)
Supplementary_files_format_and_contentTable of all 23,959 Drosophila melanogaster enhancer sequences and their motif-mutant sequences included in the oligo library, with genomic coordinates, oligo sequence, experiment, mutated motif, read counts for each screen and final developmental and housekeeping enhancer activity (log2).

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Schneider 2 cells were grown in Schneider’s Medium (Gibco; 21720-024) supplemented with 10% heat inactivated FBS (Sigma; F7524) at 27ºC. Cells were passaged every 2-3 days.

extract_protocol: 24h after electroporation, total RNA was extracted using the RNeasy Maxi kit (Qiagen; cat. no. 75162), followed by polyA+ RNA isolation using Invitrogen Dynabeads Oligo(dT)25 (scaling up the manufacturer   s protocol accordingly; cat. no. 61005) and DNase treatment with Ambion Turbo DNase (cat. no. AM2239) at a concentration of at most 200 ng/  l for 45 minutes (min) at 37C. The reactions were then subjected to cleanup with Beckman-Coulter AMPure XP beads (Product No: A63881), at a ratio of 1:1.8. STARR-seq transcripts were specifically reverse transcribed using a gene specific primer (CTCATCAATGTATCTTATCATGTCTG), followed by RNaseA digest. After second strand synthesis (primer: TTGGTAAAGCCACCATGGAAAAG*G) we introduced a 10 bp unique molecular identifier (UMI) at the 3' end of the STARR-seq transcript (primer:  CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNGTGACTGGAGTTCAGACGTGT*G), followed by a PCR step across the spliced intron junction of the mature STARR-seq transcript (primers: AAGCCACCATGGAAAAG*G*C*C*A*T and CAAGCAGAAGACGGCATACG*A). Samples were amplified for Illumina sequencing with an Illumina i5 adapter and a custom i7 index primer (CAAGCAGAAGACGGCATACGAGA*T). All PCR steps were performed using the KAPA HiFi HotStart ReadyMix (Roche; Material Number 7958927001), and cleaned up with Beckman-Coulter AMPure XP beads (Product No: A63881) at an appropriate ratio. See Neumayr et al., Curr. Protoc. Mol. Biol. 2019 for more details.

tag: sample type

value: PCR amplified cDNA (STARR-seq transcript)

tag: promoter

value: housekeeping (RpS12)


title: D10_4_IFNgamma_sgCTR_Rep2


title: D10_4_IFNgamma_sgCTR_Rep1


title: D10_4_Tcells_sgCTR_Rep2


title: D10_4_Tcells_sgCTR_Rep1


title: Oligo_library_STARRseq_hk_rep2


title: Oligo_library_STARRseq_hk_rep1


title: D10_0_CTR_sgCTR_Rep2


title: Oligo_library_STARRseq_dev_rep3

value: developmental (DSCP)


title: Oligo_library_input_hk_rep2

organism: synthetic construct

source_name: oligo library (in STARR-seq vector)

value: PCR amplified Plasmid library


title: Oligo_library_STARRseq_dev_rep2


title: Oligo_library_STARRseq_dev_rep1


title: D10_0_CTR_sgCTR_Rep1


title: Oligo_library_input_hk_rep1


title: Oligo_library_input_hk_rep3


title: Oligo_library_input_dev_rep2


title: E6.5_ZW_rep1

city: Midlothian

first: Kennosuke

last: Ichikawa

address: Easter Bush Campus

department: The Roslin Institute

country: United Kingdom

institute: The University of Edinburgh

data_processing:
The quality of the sequencing results was assessed using FastQC (ver. 0.11.9).
Trimming and quality filtering of the raw reads were performed using Trimmomatic (ver. 0.39) (Bolger et al., 2014) as well as Trim Galore (ver. 0.6.6) with Cutadapt (ver. 3.1) (Marcel, 2011).
The trimmed and filtered reads were mapped to the chicken reference genome (GRCg6a) using STAR (ver. 2.7.3a) (Dobin et al., 2013).
The uniquely mapped reads in each gene were counted using the featureCounts tool (ver. 2.0.1) (Liao et al., 2014). While detection of sex-biased genes was performed using the DE-seq2 tool (ver. 1.20.0) (Love et al., 2014).
Genome_build: GRCg6a
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

organism: Gallus gallus

source_name: Primordial germ cells

extract_protocol:
Male and female primordial germ cells  were isolated from the blood of E2.5 embryos and from the gonads of E4.5 and E6.5, embryos using FACS. Two pools of sorted PGCs from to 6-14 individuals of each sex and stage were used as templates. Since the yield of total RNA was very low, cDNA libraries were prepared using SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa Bio, Kusatsu, Japan).
Nextera XT DNA Library Preparation Kit (Illumina Inc., San Diego, CA, USA) was used to make cDNA libraries suitable for Illumina sequencing.

tag: developmental stage

tag: Sex

value: Female

tag: cell type

value: Primordial germ cells


title: E6.5_ZW_rep2


title: Oligo_library_input_dev_rep3


title: Oligo_library_input_dev_rep1


title: E6.5_ZZ_rep2

value: Male


title: E6.5_ZZ_rep1


title: E4.5_ZW_rep2


title: E4.5_ZW_rep1


title: E4.5_ZZ_rep2


title: RoCAST_025nM_16h_undigested_rep2

city: Würzburg

first: Chase

middle: Lawrence

last: Beisel

address: Josef-Schneider Straße 2

department: Helmholtz-Institute for RNA-based Infection Research (HIRI)

country: Germany

institute: Helmholtz Centre for Infection Research (HZI)

data_processing:
For PAM-DETECT samples (samples with "digested" or "undigested" in their name) processed according to https://doi.org/10.1016/j.molcel.2016.02.031
Transposon insertion point of samples with "CRISPRdependent" or "CRISPRindependent" in their name was assessed by extracting, counting and sorting sequences containing part of the transposon terminal left end and ~15 nts long sequences 5' of the transposon terminal left end.
Genome_build: not applicable
Supplementary_files_format_and_content: All processed data files are uploaded as text files. Processed data files for PAM-DETECT samples (samples with "digested" or "undigested" in their name) contain 5nts sequences corresponding the PAM library with "R2" files containing reverse complement sequences. Processed data files for transposon insertion points (samples with "CRISPRdependent" or "CRISPRindependent" in their name) contain sequences spanning part of the transposon terminal left end and ~15 nts long sequences 5' of the transposon terminal left end.

source_name: plasmid DNA

extract_protocol:
DNA was extracted with EtOH precipitation prior to PCR amplification
See SAMPLES section
Samples were PCR amplified twice. The first PCR added the Illumina sequencing primer sites while the second PCR added the unique dual indices and the Illumina flow cell binding site.

tag: environment

value: in vitro:myTXTL from Arbor Biosciences

tag: grna

value: targets next to the randomized PAM library

value: undigested


title: E2.5_ZW_rep2


title: RoCAST_025nM_16h_digested_rep2

value: digested with PacI


title: RoCAST_025nM_16h_undigested_rep1


title: RoCAST_025nM_16h_digested_rep1


title: E2.5_ZW_rep1


title: RoCAST_3nM_16h_undigested_rep2


title: E2.5_ZZ_rep2


title: 200102_NB501850_A_L1-4_APZX-3-1 [stress_root_rep3]

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

data_processing:
The adapter sequence was removed from the obtained raw reads with FASTX-Toolkit
Clean reads were mapped to Glycine soja, Brachypodium distachyon, Oryza sativa, Triticum aestivum, Hordeum vulgare, Arabidopsis thaliana, Arabidopsis lyrata, Zea mays, Aegilops taushii, Brassica napus, Brassica rapa, Brassica oleracea, Glycine max, Cucumis melo, Cucumis sativus, Medicago truncatula, Physcomitrella patens, Sorghum bicolor miRNAs from miRBase (release 22.1) using script countreads_mirna.pl (Eminaga et al., 2013).
The script was applied to each fastq file for every biological replicate (n = 3).
A table with raw read counts was used to calculate fold change and p-value with the usage of R-package DESeq2.
Genome_build: Ensembl
Supplementary_files_format_and_content: raw read counts; columns with '*.x' contain raw counts read number and with '*.y' contain normalized values (counts per million)

organism: Hordeum vulgare

source_name: nitrogen excess_root

growth_protocol: Seeds of spring barley were germinated on wet, sterile Whatman filter paper for 3 days in a growth chamber under long-day (16 h) conditions at 23 °C until white hypocotyls were visible. Then, two seedlings were then transferred to a single pot that contained perlite.

extract_protocol:
Two week-old barley plants were collected in three biological replicates. The extraction of total RNA was performed using Direct-zol RNA Mini Prep Kit (Zymo Research) according to the manufacturer’s protocol.
Libraries were constructed using the TruSeq SmallRNA Library Preparation Kit (Illumina) as described in the manual.

treatment_protocol: Two seedlings were transferred to a single pot that contained perlite that was amended with medium containing: 28 mM NH4NO3, 20 mM KH2PO4, 4 mM K2SO4, 16 mM MgSO4x7H2O, 53 μM H3BO3, 8 μM CuSO4, 4 μM MnSO4xH2O, and 120 μM FeCl3x6H2O. In the nitrogen excess experiment the same medium was used - except that the concentration of NH4NO3 was 280 mM. The plants were subsequently grown under controlled conditions, which included a 16 h day/8 h night photoperiod at a temperature of 22 °C

tag: cultivar

value: Golden Promise

tag: culture condition

value: nitrogen excess

value: root

tag: molecule subtype

value: small RNA


title: 190517_SNK268_B_L007_APZX-2-7 [stress_shoot_rep3]

source_name: nitrogen excess_shoot

value: shoot


title: RoCAST_3nM_16h_undigested_rep1

tag: treatment


title: 190517_SNK268_B_L007_APZX-2-4 [stress_root_rep2]

tag: tissue


title: RoCAST_3nM_16h_digested_rep2


title: Ec_CRISPRdependent_TniQTnsD_T

description: crRNA-dependent transposition of RoCAST with Cascade, TnsABC, Cargo, TniQ, TnsD and gRNA targeting genomic DNA

data_processing:
paired-end (only R2 reads were used, thus R1 is not provided)
For PAM-DETECT samples (samples with "digested" or "undigested" in their name) PAM wheels were generated according to https://doi.org/10.1016/j.molcel.2016.02.031 and generation of Nucleotide Enrichment Plots was adapted to  https://bitbucket.org/csmaxwell/crispr-txtl-pam-counting-script/src/master/ by changing the script to visualize the probability of a given nucleotide at a given position by depicting the percentage of the nucleotide in that position.
Transposon insertion point of samples with "CRISPRdependent" or "CRISPRindependent" in their name was assessed by extracting, counting and sorting sequences containing part of the transposon terminal left end and ~15 nts long sequences 5' of the transposon terminal left end. The 5' sequences were then matched to the targeted plasmid or genome and the distance between the insertion point and the PAM upstream of the protospacer or the end of the tRNA-Leu gene was noted. Only insertion points with more than 20 reads were noted.
Genome_build: not applicable for PAM-DETECT samples. "TXTL_CRISPRdependent_TniQ_T", "TXTL_CRISPRdependent_TnsD_T", "TXTL_CRISPRdependent_TniQTnsD_T" and "TXTL_CRISPRdependent_TnsABC_T" were aligned to following plasmid sequence: https://benchling.com/s/seq-M9ye6lFOwoUiok5QLPTq. "TXTL_CRISPRindependent_TnsD" and "Ec_CRISPRindependent_TnsD" were aligned to following plasmid sequence: https://benchling.com/s/seq-9n9CTDGabZGf395XmgT9. "Ec_CRISPRdependent_TniQ_T", "Ec_CRISPRdependent_TnsD_T" and "Ec_CRISPRdependent_TniQTnsD_T" were aligned to E. coli BL21 (NC_000913.3)
Supplementary_files_format_and_content: All processed data files are uploaded as text files. Processed data files for PAM-DETECT samples (samples with "digested" or "undigested" in their name) contain 5nts sequences corresponding the PAM library with "R2" files containing sequences in reverse complement. Processed data files for transposon insertion points (samples with "CRISPRdependent" or "CRISPRindependent" in their name) contain sequences spanning part of the transposon terminal left end and ~15 nts long sequences 5' of the transposon terminal left end.

organism: Escherichia coli

source_name: genomic DNA

extract_protocol:
gDNA was isolated prior to PCR amplification
Samples were PCR amplified twice. The first PCR added the Illumina sequencing primer sites while the second PCR added the unique dual indices and the Illumina flow cell binding site.

value: in vivo:E. coli BL21(DE3)

value: Targets next to ATG PAM

value: Electroporated samples were plated on selective LB-plates and incubated for 20h at 37°C. Formed colonies were scraped and resuspendet in LB liquid medium. A fraction of the cell suspension was re-plated on selective LB-plates supplemented with 0.01mM IPTG and incubated for 20h at 37°C. All the formed colonies were scraped and resuspendend in LB liquid medium and a fraction was subjected to gDNA isolation.


title: 190517_SNK268_B_L007_APZX-2-5 [control_shoot_rep3]

value: control


title: 190517_SNK268_B_L007_APZX-2-6 [control_root_rep3]


title: RoCAST_3nM_16h_digested_rep1


title: 190517_SNK268_B_L007_APZX-2-3 [stress_shoot_rep2]


title: Ec_CRISPRindependent_TnsD

description: crRNA-independent transposition of RoCAST with TnsABC, Cargo, TnsD targeting a plasmid with tRNA-Leu

extract_protocol:
gDNA was isolated prior to PCR amplification
See SAMPLES section
Samples were PCR amplified twice. The first PCR added the Illumina sequencing primer sites while the second PCR added the unique dual indices and the Illumina flow cell binding site.

value: no gRNA

value: Electroporated samples were plated on selective LB-plates and incubated for 20h at 37°C. Formed colonies were scraped and resuspended in LB liquid medium. A fraction of the cell suspension was re-plated on selective LB-plates supplemented with 0.01mM IPTG and incubated for 20h at 37°C. All the formed colonies were scraped and resuspendend in LB liquid medium and a fraction was subjected to gDNA isolation.


title: VcCAST_025nM_6h_undigested_rep2


title: 190517_SNK268_B_L007_APZX-2-1 [control_shoot_rep2]


title: 190517_SNK268_B_L007_APZX-2-2 [control_root_rep2]


title: Ec_CRISPRdependent_TnsD_T

description: crRNA-dependent transposition of RoCAST with Cascade, TnsABC, Cargo, TnsD and gRNA targeting genomic DNA

value: targets next to ATG PAM


title: VcCAST_025nM_6h_undigested_rep1


title: Ec_CRISPRdependent_TniQ_T

description: crRNA-dependent transposition of RoCAST with Cascade, TnsABC, Cargo, TniQ and gRNA targeting genomic DNA


title: 180919_SNK268_B_L008_APZX-1-8 [stress_root_rep1]


title: E4.5_ZZ_rep1

value: Male

value: Primordial germ cells


title: 180919_SNK268_B_L008_APZX-1-6 [stress_shoot_rep1]


title: VcCAST_025nM_6h_digested_rep2

value: in vitro:myTXTL from Arbor Biosciences

value: targets next to the randomized PAM library


title: 180919_SNK268_B_L008_APZX-1-7 [control_root_rep1]


title: 180919_SNK268_B_L008_APZX-1-5 [control_shoot_rep1]


title: HCT116_oligo_library_input_rep2

data_processing:
Library strategy: STARR-seq
Oligo library UMI-STARR-seq RNA and DNA input reads (150 bp) were mapped to a reference containing 249 bp long sequences containing both wildtype and mutated fragments from the Drosophila library using Bowtie v.1.2.2. We demultiplexed reads by the i5 and i7 indexes and subsequently by the oligo identity, since this library contained oligos from other experiments. Mapping reads with the correct length, strand and with no mismatches (to identify all sequence variants) were kept. Both DNA and RNA reads were collapsed by UMI (10 bp, allowing one mismatch; UMI sequences are in the sequencing read name) to ensure the counting of unique reporter transcripts.
We excluded oligos with less than 10 reads in any of the input replicates and added one read pseudocount to oligos with zero RNA counts. The enhancer activity of each oligo in each screen was calculated as the log2 fold-change over input, using both replicates, using DESeq2. We used the counts of wildtype negative regions in each library as scaling factors between samples. This normalization only changes the position of the zero and consequently does not affect the calculation of log2 fold-changes or the p-values for the statistical tests used.
Genome_build: hg19 (custom oligo library)
Supplementary_files_format_and_content: Table of all 22,900 human enhancer sequences and their motif-mutant sequences included in the oligo library, with genomic coordinates, oligo sequence, experiment, mutated motif, read counts for each screen and final enhancer activity (log2).

source_name: oligo library (in human STARR-seq vector)

growth_protocol: Human colon cancer cell line HCT116 was grown in DMEM (Gibco; 52100-047) supplemented with 10% heat inactivated FBS (Sigma; F7524) and 1% L-Glutamine (Sigma; G7513) at 37ºC. Cells were passaged every 2-3 days.

extract_protocol: 6h after electroporation, total RNA was extracted using the RNeasy Maxi kit (Qiagen; cat. no. 75162), followed by polyA+ RNA isolation using Invitrogen Dynabeads Oligo(dT)25 (scaling up the manufacturer's protocol accordingly; cat. no. 61005) and DNase treatment with Ambion Turbo DNase (cat. no. AM2239) at a concentration of at most 200 ng/ul for 45 minutes (min) at 37C. The reactions were then subjected to cleanup with Beckman-Coulter AMPure XP beads (Product No: A63881), at a ratio of 1:1.8. STARR-seq transcripts were specifically reverse transcribed using a gene specific primer (CTCATCAATGTATCTTATCATGTCT), followed by RNaseA digest. After second strand synthesis (primer: GTCGTGAGGCACTGGGCA*G) we introduced a 10 bp unique molecular identifier (UMI) at the 3'end of the STARR-seq transcript (primer: CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNGTGACTGGAGTTCAGACGTGT*G), followed by a PCR step across the spliced intron junction of the mature STARR-seq transcript (primers: TCGTGAGGCACTGGGCAG*G*T*G*T*C and CAAGCAGAAGACGGCATACG*A). Samples were amplified for Illumina sequencing with an Illumina i5 adapter and a custom i7 index primer (CAAGCAGAAGACGGCATACGAGA*T). All PCR steps were performed using the KAPA HiFi HotStart ReadyMix (Roche; Material Number 7958927001) and cleaned up with Beckman-Coulter AMPure XP beads (Product No: A63881) at an appropriate ratio. See Neumayr et al., Curr. Protoc. Mol. Biol. 2019 for more details.

tag: cell line

value: PCR amplified Plasmid library


title: HCT116_oligo_library_input_rep1


title: E2.5_ZZ_rep1


title: Sfb SNU423 r2

city: seville

first: laura

last: Contreras Bernal

state: Seville

address: c/ Antonio Maura Montaner s/n. IBiS

department: Genetic

country: Spain

institute: University of Seville

data_processing:
Raw reads for the same sample from different lanes were merged using zcat command on linux CentOS 7.
Quality control was performed using Fastqc v0.11.7 on merged raw reads.
Adapter and quality trimming was performed with Cutadapt v1.15 with the following settings: -u -1 -U -1 --nextseq-trim=20 -m 70
Reads were aligned with HISAT v2.1.0 from miARmaSeq pipeline v1.7.2.
Gene expression quantification at exon level was calculated using feactureCounts v1.5.0-p1 from miARmaSeq pipeline with the following settings: -s 2 -t exon -g gene_name -C -M -O -T 16 -Q 10 -p -a
Differential expression analysis was performed with edgeR and NOISeq modules from miARmaSeq pipeline
Genome_build: GRCh38 release 96 (soft-masked)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hepatocellular carcinoma cells

growth_protocol: Cells were cultured in minimal essential medium (MEM) with Earle's balanced salts with L-glutamine suplemented with 10% fetal bovine serum, 1% sodium pyruvate, 1% non-essential amino acids and penicillin-streptomycin solution; cells were grown in culture flasks at 37 ºC in a humidified incubator with 5% CO2 until reaching a density of 100,000 cells/cm2.

extract_protocol:
Total RNA was extracted from each sample using a RNeasy mini kit according to the manufacturer’s instructions (QIAGEN, Germany).
Libraries were prepared using RNA of cells treated either with the vehicle or with Sorafenib. Total RNA concentration and quality of the RNA were assessed with Qubit (Qubit™ DNA HS assay) and a 2100 Bioanalyzed Nano Chip (Agilent Technologies Genomics, USA), respectively. RNA Integrity Number (RIN) values were > 9 in all the RNA samples. Polyadenylated RNA was isolated from the total RNA using NEBNext Oligo d(T)25 beads (New England Biolabs, USA) according to the manu-facturer's instructions. Samples were normalised to an equivalent concentration of 67.3 ng/µl and prepared for RNA Ilumina Sequencing.

treatment_protocol: Sorafenib was added at the concentration of 10 µM at 24 h hours after plating, and lysates were obtained after 12 h treatment. Controls cells were treated in parallel with dimethyl sulfoxide (DMSO), vehicle in wich Sorafenib is dossolved.

tag: differentiation stage

value: moderately-differentiated cells

value: In frame p53 gene truncation of amino acids 126 to 134

value: Sorafenib 10 uM 12h


title: S2_hk_STARRseq_input

data_processing:
Library strategy: STARR-seq
Paired-end genome-wide UMI-STARR-seq RNA and DNA input reads (36 bp) were mapped to the Drosophila genome (dm3), excluding chromosomes U, Uextra, and the mitochondrial genome, using Bowtie v.1.2.2. Mapping reads with up to three mismatches and a maximal insert size of 2kb were kept. For paired-end RNA reads that mapped to the same positions, we collapsed those that have identical UMIs (10 bp, allowing one mismatch; UMI sequences are in the sequencing read name) to ensure the counting of unique reporter transcripts. We further computationally selected both RNA and input fragments of length 150-250 bp to only capture active sequences derived from short fragments.
After processing the two biological replicates separately, we pooled both replicates for developmental and housekeeping screens for further analyses.
Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of STARR-seq and input. We performed hypergeometric tests to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
Peaks that had a hypergeometric p-value <= 0.001 and a corrected enrichment over input greater than 3 were defined as enhancers.
Genome_build: dm3
Supplementary_files_format_and_content: BigWig files contain normalized genome-wide coverage. Plain text files contain enhancer peaks, including the chromosome, the summit position, the enrichment over input at the summit, and the p-value.

source_name: whole genome library (in STARR-seq vector)

growth_protocol: Schneider 2 cells were grown in Schneider’s Medium supplemented with 10% heat inactivated FBS (Sigma; F7524) at 27ºC. Cells were passaged every 2-3 days.

tag: genotype

value: y; cn bw sp - sequenced strain (Adams et al. 2000)

value: housekeeping (RpS12)


title: Sfb SNU423 r1

value: In frame p53 gene truncation of amino acids 126 to 133


title: VcCAST_3nM_16h_undigested_rep2

value: undigested


title: VcCAST_025nM_6h_digested_rep1

value: digested with PacI


title: Control SNU423 r2

value: DMSO


title: VcCAST_3nM_16h_undigested_rep1


title: TXTL_CRISPRdependent_TnsABC_T

description: crRNA-dependent transposition of RoCAST with Cascade, TnsABC, Cargo and gRNA targeting a plasmid

extract_protocol:
Sample was diluted 1:100 prior to PCR amplification
Samples were PCR amplified twice. The first PCR added the Illumina sequencing primer sites while the second PCR added the unique dual indices and the Illumina flow cell binding site.

value: Targets next to ATG PAM


title: VcCAST_3nM_16h_digested_rep2


title: AGS-siOTUB1-2

city: xinxiang city

first: cheng

last: Yan

address: Jinsui Road 191#

country: China

institute: xinxiang univerisity

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample

source_name: AGS cellline

growth_protocol: AGS cells were plated in 12-well plates at 30% fusion per well

extract_protocol:
Lysis of cells with Trizol reagent and harvesting of RNA
RNA libraries were prepared for sequencing using BGISEQ-500 protocols

treatment_protocol: AGS cells were transfected with siControl or siOTUB1

value: AGS


title: AGS-siOTUB1-3


title: AGS-siOTUB1-1


title: TXTL_CRISPRdependent_TniQTnsD_T

description: crRNA-dependent transposition of RoCAST with Cascade, TnsABC, Cargo, TniQ, TnsD and gRNA targeting a plasmid


title: TXTL_CRISPRindependent_TnsD

extract_protocol:
TXTL sample was diluted 1:100 prior to PCR amplification
See SAMPLES section
Samples were PCR amplified twice. The first PCR added the Illumina sequencing primer sites while the second PCR added the unique dual indices and the Illumina flow cell binding site.

value: no gRNA


title: Sfb HepG2 r3

value: well-differentiated cells

value: Wild type


title: VcCAST_3nM_16h_digested_rep1

value: in vitro:myTXTL from Arbor Biosciences


title: Sfb HepG2 r2


title: AGS-siNC-3

value: si-NC


title: TXTL_CRISPRdependent_TnsD_T

description: crRNA-dependent transposition of RoCAST with Cascade, TnsABC, Cargo, TnsD and gRNA targeting a plasmid

value: targets next to ATG PAM


title: AGS-siNC-2


title: TXTL_CRISPRdependent_TniQ_T

description: crRNA-dependent transposition of RoCAST with Cascade, TnsABC, Cargo, TniQ and gRNA targeting a plasmid


title: Sfb HepG2 r1


title: Control HepG2 r3


title: RNAiMARS_4h_C

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

data_processing:
Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases. Ribosomal RNA where removed using SortMeRNA (v2.1)
trimmed reads were aligned to the TAIR10 genome using STAR (2.7.2a)
Reads were counted on each Araport11 features using featureCounts from subreads package (v1.6.5) using strand specific mode.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

organism: Arabidopsis thaliana

source_name: RNAi-MARS 4h after ABA spray replicate C

growth_protocol: Media = MS/2, pH 5.8, 1% Surose hygrometry = 33% humidity Temperature = 24°C day/ 21°c night Light = 16 hours day / 8 hours night for 12 days.

extract_protocol:
Total RNA was isolated using TRI Reagent (Sigma-Aldrich) and treated with DNase (Fermentas) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA

treatment_protocol: seedling were spray with a solution of 10µM of ABA dilluted in water.

value: RNAi-MARS

value: 12 days

value: Whole seedling

value: Abscisic acid, 10 micromole, 4h


title: RNAiMARS_4h_B

source_name: RNAi-MARS 4h after ABA spray replicate B


title: AvCAST_undigested_rep1

value: targets next to the randomized PAM library


title: AvCAST_digested_rep1


title: Control HepG2 r2


title: Control HepG2 r1


title: Control SNU423 r1

value: moderately-differentiated cells

value: In frame p53 gene truncation of amino acids 126 to 132


title: RNAiMARS_4h_A

source_name: RNAi-MARS 4h after ABA spray replicate A


title: Me49-3

city: Guangzhou

first: shilan

last: zhu

address: wuShan street

institute: South China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling
CPM: The calculation formula is: CPM=C/N*1000000, where C is the number of reads aligned to the gene, and N is the total number of reads aligned to the gene.
The genomes of ensembl mice were used for target gene analysis
Supplementary_files_format_and_content: CPM: The calculation formula is: CPM=C/N*1000000, where C is the number of reads aligned to the gene, and N is the total number of reads aligned to the gene.

source_name: exosome

growth_protocol: Bone marrow cells were isolated from the tibia and femur of wild-type C57/BL6J mice aged 4-5 weeks. After euthanasia of mice, a 1 mL syringe was used to inject sterile PBS to repeatedly wash the bone marrow cavity to collect bone marrow cells. The isolated cells were filtered through a 70 μm filter to obtain a single cell suspension and mixed with 8 mL 1 × Red Blood Cell lysis buffer and let to stand for 5 min to lyse RBCs. The cell suspension was washed twice with phosphate buffer saline (PBS) and centrifuged at 1000 rpm for 5 min at room temperature. Cells were counted and seeded at a density of 1 × 107 cells in a 10 cm cell culture plate. Then, a 10 mL of RPMI 1640 complete medium was added to each plate and incubated at 37°C, 5% CO2 in a cell incubator. This RPMI 1640 medium contained 10% exosome-depleted FBS (prepared by ultracentrifugation at 100,000 g for 12 h), 1% PS, 10 ng/mL granulocyte-macrophage colony-stimulating factor (GM-CSF) and 10 ng/mL interleukin 4. RPMI 1640, FBS, and PS were purchased from Gibco, ThermoFisher Scientific (Waltham, MA, USA ), while GM-CSF and IL-4 were obtained from PeproTech Inc. (Cranbury, NJ, USA). After that, fresh medium was replaced every two days until cells differentiated into dendritic cells at 8-9 days.

extract_protocol:
T. gondii Me49 strain was incubated with DC/RPMI 1640 culture containing 10% exosome-depleted FBS and 1% PS for 12 h at 37°C, 5% CO2. T. gondii Me49-infected DC and uninfected DC culture supernatants were collected by centrifugation at 500 g for 10 min. The supernatants were centrifuged at 16,500 g for 30 min, filtered through a 0.22 μm filter, and then centrifuged at 120,000 g for 90 min to precipitate exosomes. The pellets were resuspended in 200 μL of PBS after being washed with PBS and centrifuged at 120,000 g for 90 min twice. All the above-mentioned centrifugal steps were carried out at 4°C.Total RNA was extracted from samples using exoRNeasy Serum/Plasma Maxi Kit (Qiagen, Hilden, Germany). The purity and integrity of total RNA were detected by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). TruSeq Small RNA Sample Prep Kit was used to construct small RNA libraries from RNA samples that passed quality control. After enrichment, purification, quality inspection, and quantification, six sets of samples were sequenced using the Illumina HiSeqTM 2500 sequencing platform (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dendritic Cells

value: Toxoplasma gondii Me49-infected

tag: strain

value: exosome miRNA


title: Me49-2


title: Me49-1


title: XalbIF1_undigested_rep2

value: undigested


title: RNAiMARS_0h_C

source_name: RNAi-MARS no ABA replicate C

value: NO


title: DC-3

value: uninfected


title: AvCAST_undigested_rep2


title: XalbIF1_digested_rep2

value: digested with PacI


title: XalbIF1_undigested_rep1

value: in vitro:myTXTL from Arbor Biosciences


title: AGS-siNC-1

value: AGS

value: si-NC


title: RAW264.7 infected with WT strain TMAWT2-1

city: Wuhan

first: Peng

last: Xu

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

description: RAW264.7 infected with WT strain

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mus musculus
Supplementary_files_format_and_content: gene_expression_mouse.xls file includes FPKM values for each Sample

extract_protocol: none provided by the submitter

value: infected with WT strain


title: RAW264.7 infected with WT strain TMAWT1-1

description: RAW264.7 infected with WT strain


title: RAW264.7 infected with WT strain TMAWT3-1

description: RAW264.7 infected with WT strain


title: DC-2


title: RNAiMARS_0h_B

source_name: RNAi-MARS no ABA replicate B

value: RNAi-MARS

value: 12 days


title: RAW264.7 infected with KO strain TMAKO3-1

description: RAW264.7 infected with KO strain

value: infected with KO strain


title: AvCAST_digested_rep2

value: targets next to the randomized PAM library


title: RNAiMARS_0h_A

source_name: RNAi-MARS no ABA replicate A

value: Whole seedling


title: DC-1


title: XalbIF1_digested_rep1


title: XalbIC_undigested_rep2


title: Col0_4h_C

source_name: Col0 4h after ABA spray replicate C

value: wild type

value: Abscisic acid, 10 micromole, 4h


title: RAW264.7 infected with KO strain TMAKO2-1

description: RAW264.7 infected with KO strain


title: XalbIC_undigested_rep1


title: RCC_N_2

city: Shanghai

first: Yuchen

last: Gao

state: Shanghai

address: No.301, Yanchang Middle Road, Jing'an District, Shanghai

department: Department of Urology

institute: Shanghai Tenth People's Hospital, Tongji University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm39 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm39
Supplementary_files_format_and_content: tab-delimited text files include gene.count values for each Sample ...

source_name: Tumor-Adjacent Tissues

extract_protocol:
The 786-o cells were cultured in a 10 cm dish. When the cell density was 70-80%, the cells were collected, mixed into a cell suspension with 100 µl sterile phosphate-buffered saline solution, and injected into the right back of a nude mouse at approximately the midpoint of the spinal column and right lower limb. Before injection, 0.5 cm of tissue was taken from the tail of each nude mouse. One month later, three mice with tumor diameter of 1-1.5 cm were selected for the next study. Mice were euthanized in a carbon dioxide box, and the tumor and tumor-adjacent tissues (more than 1 cm from tumor tissue capsule) were removed. All tissues were stored in liquid nitrogen and sent to Shanghai Majorbio company for RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: Tumor-Adjacent Tissues

tag: age

value: post natal day 28


title: RCC_N_3


title: RAW264.7 infected with KO strain TMAKO1-1

description: RAW264.7 infected with KO strain


title: Col0_4h_B

source_name: Col0 4h after ABA spray replicate B


title: Col0_4h_A

source_name: Col0 4h after ABA spray replicate A


title: XalbIC_digested_rep2

source_name: plasmid DNA


title: RAW264.7 infected with OE strain TMACS3-1

description: RAW264.7 infected with OE strain

value: infected with OE strain


title: RCC_N_1


title: Col0_0h_C

source_name: Col0 no ABA replicate C

value: NO


title: RCC_pre_3

source_name: Tail

value: Tail


title: RAW264.7 infected with OE strain TMACS2-1

description: RAW264.7 infected with OE strain


title: Col0_0h_B

source_name: Col0 no ABA replicate B


title: RAW264.7 infected with OE strain TMACS1-1

description: RAW264.7 infected with OE strain


title: Sth_undigested_rep2

value: in vitro:myTXTL from Arbor Biosciences

value: undigested


title: RCC_pre_2


title: Col0_0h_A

source_name: Col0 no ABA replicate A


title: uninfected RAW264.7 TMACK3-1

description: uninfected RAW264.7

value: uninfected


title: uninfected RAW264.7 TMACK2-1

description: uninfected RAW264.7


title: Sth_digested_rep2

value: digested with PacI


title: RCC_3

source_name: Renal Cell Carcinoma Transplanted Tumors


title: Sth_undigested_rep1


title: RCC_pre_1


title: RCC_2

value: Renal Cell Carcinoma Transplanted Tumors


title: Sth_digested_rep1


title: Sr_undigested_rep2


title: uninfected RAW264.7 TMACK1-1

description: uninfected RAW264.7


title: Sr_undigested_rep1


title: RCC_1


title: HiC DP Tcf7-KO

description: DPKO

source_name: CD4+ CD8+ Thymocytes

extract_protocol:
HiC libraries were generated on 106 cells using with Arima-HiC+ kit (Arima Genomics) and Accel-NGS @S Plus DNA Library kit (21024 Swift Biosciences), according to the manufacturer’s recommendations.
Libraries were validated for quality and size distribution using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851) and TapeStation 2200 (Agilent). Libraries were paired-end sequenced (66bp+66bp) on NovaSeq 6000 (Illumina).

value: Tcf7eGFP fl/fl Cre+

value: Thymus

value: 6-10 weeks


title: HiC DP Cre+

description: DPWT

value: Vav-iCre transgenic mice

value: Vav-iCre+


title: HiC DN3 Tcf7-KO rep1

source_name: Scid.adh cell line


title: Sr_digested_rep2

value: targets next to the randomized PAM library


title: XalbIC_digested_rep1


title: 2-hemin

city: Beijing

first: Danmin

last: Shen

address: No. 10, xitoutiao, youanmenwai

institute: Capital Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
RSEM was used for read counting
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include expected count and  FPKM values for each Sample .

source_name: OPC

growth_protocol: Single cells were prepared from neonatal mouse (P0-2) cortices. Primary OPCs were obtained from C57BL/6 pups using magnetic activated cell sorting (MACS) with the CD140 (PDGFRα) MicroBead Kit. Primary OPCs were plated into poly-D,L-ornithine–coated (P0421, Sigma) culture plates, and expanded in growth medium for 3 days.

extract_protocol:
OPCs were collected, and RNA was harvested using Trizol reagent.  The mRNA was enriched and amplified by PCR, and then construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary OPCs were treated with 50 uM Hemin (7084–24–4, Frontier Scientific, USA) or vehicle (0.25% DMSO) for 12 hours.

value: brain

value: Oligodendrocyte progenitor cells (OPCs)

value: post natal day 1

value: wild type

value: Hemin


title: 1-hemin


title: HiC DN3 WT


title: 3-hemin


title: Ps_undigested_rep2


title: Sr_digested_rep1


title: Ps_digested_rep2


title: Ps_undigested_rep1


title: Estrogen rep4

city: Erlangen

first: Zhen

last: Lin

address: Schloßplatz 4

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2
In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow B cells

extract_protocol:
bone were dissected and B cells was sorted by MACS from bome marrow, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT

tag: stress

value: Hypoxia

value: bone marrow B cells

value: Estrogen


title: 3-vehicle

value: DMSO


title: Estrogen rep3


title: 2-vehicle


title: Estrogen rep2


title: Vehicle rep4

value: Vehicle


title: 1-vehicle


title: THP-1_INPUT

first: Jia

last: Yuan

address: Yueyang road 320, Xuhui, Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

data_processing:
Reads were aligned to the (hg38) reference human genome.
Use Markduplicates to examine aligned records in BAM datasets to locate duplicate molecules
Use MACS2 callpeak to call peaks from alignment results
Use bamCoverage generates a coverage bigWig file from a given BAM or CRAM file.
Use computeMmatrix prepares data for plotting a heatmap or a profile of given regions.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph files

growth_protocol: THP1 was cultured in 1640 medium containing 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and nucleus proteins-DNA complexes were isolated with indicated antibodies. And then the immunoprecipitated DNA were purified and subjected to high-throughput sequencing
Libraries were prepared according to standard Illumina protocols.

treatment_protocol: treated with PMA for 24h

tag: chip antibody

value: PMA for 24h


title: CHIP-seq_THP1 H3K27ac

value: H3K27ac (Abcam, ab4729)


title: CHIP-seq_THP1 SIRT1

value: Sirt1 (CST, 8469S)


title: Vehicle rep1


title: Mb_undigested_rep2

extract_protocol:
DNA was extracted with EtOH precipitation prior to PCR amplification
See SAMPLES section
Samples were PCR amplified twice. The first PCR added the Illumina sequencing primer sites while the second PCR added the unique dual indices and the Illumina flow cell binding site.

value: in vitro:myTXTL from Arbor Biosciences

value: undigested


title: Ms_digested_rep1

value: targets next to the randomized PAM library

value: digested with PacI


title: HIF1a KO rep3 (Hypoxia)

value: HIF1a KO


title: scRNA-Seq DRG1

city: Chengdu

first: Donghang

last: Zhang

state: Sichuan

address: No.37, guoxue lane, wuhou district, chengdu city, sichuan province

institute: West China Hospital of Sichuan University

data_processing:
Basecalls performed using  bcl2fastq tools.
Raw single-cell RNA-seq data were processed using 10X Genomics Cell Ranger (v5.0.1), including demultiplexing the FASTQ reads, aligning them to the human reference genome (GRCh38, v3.0.0, from 10X Genomics), and counting the unique molecular identifier (UMI) (by using ‘cellranger count’ function).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices.
Supplementary_files_format_and_content: peak text files

source_name: DRG

extract_protocol:
Nuclei were isolated using a Nucleus Isolation Kit (catalogue no. 52009-10, SHBIO, China) according to the manufacturer’s instructions. Nuclei suspension was loaded onto a Chromium single cell controller (10x Genomics) to generate single-nucleus gel beads in the emulsion (GEM) using single cell 3' Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074) according to the manufacturer’s protocols.
The 10x snRNA-seq library was established using Single Cell 3’ Library and Gel Bead Kit V3.1, according to the manufacturer’s instructions.

value: DRG

value: 35 years old


title: Mb_digested_rep2


title: Chronic_ESOTcells_Round3_S2

city: Cambridge

first: Julia

last: Joung

state: MA

address: 75 Ames St

institute: Broad Institute

data_processing:
bcl2fastq 2.20.0
custom Python script to determine sgRNA distribution (see Methods)
Genome_build: CRISPR activation library (Addgene 1000000057) sgRNA target sequences
Supplementary_files_format_and_content: Aggregated sgRNA counts determined using custom Python script for each condition

source_name: A375 melanoma cells

extract_protocol:
genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo D4075)
Libraries were prepared by PCR amplification of sgRNA target sites using custom primers (see Methods)
Other: PCR amplified library (see Methods)

value: A375 melanoma cells

tag: screen type

value: Chronic

tag: screen condition

value: ESO T cell round 3


title: Chronic_ESOTcells_Round3_S1

tag: cell type


title: Ps_digested_rep1

tag: environment


title: Estrogen rep1

value: WT

value: Hypoxia

value: bone marrow B cells


title: HIF1a KO rep2 (Hypoxia)


title: Ms_undigested_rep2

tag: grna


title: HIF1a KO rep1 (Hypoxia)


title: scRNA-Seq Spinal 3

description: Spinal 3

source_name: Spinal cord

value: Spinal cord

value: 46 years old


title: Mb_digested_rep1


title: Chronic_noTcells_Round3_S2

value: no T cell control round 3


title: Chronic_noTcells_Round3_S1


title: Ms_undigested_rep1


title: scRNA-Seq Spinal 2

description: Spinal 2

value: 38 years old


title: Vehicle rep3

value: Vehicle


title: Ms_digested_rep2

value: in vitro:myTXTL from Arbor Biosciences


title: scRNA-Seq Spinal 1

description: Spinal 1


title: HIF1a KO rep3 (Normoxia)

value: Normoxia


title: Vehicle rep2


title: scRNA-Seq DRG3


title: scRNA-Seq DRG2


title: Mb_undigested_rep1

value: targets next to the randomized PAM library

value: undigested


title: HIF1a KO rep2 (Normoxia)

value: HIF1a KO


title: Chronic_ESOTcells_Round2_S1

value: ESO T cell round 2


title: Lm_digested_rep2

value: digested with PacI


title: HIF1a KO rep1 (Normoxia)


title: Chronic_noTcells_Round2_S2

value: A375 melanoma cells

value: Chronic

value: no T cell control round 2


title: Lm_digested_rep1


title: Chronic_noTcells_Round2_S1


title: WT rep3 (Hypoxia)

value: WT

value: Hypoxia


title: WT rep1 (Hypoxia)

value: bone marrow B cells


title: WT rep2 (Hypoxia)


title: Lm_undigested_rep2


title: Chronic_ESOTcells_Round1_S1

value: ESO T cell round 1


title: Lm_undigested_rep1


title: Chronic_ESOTcells_Round1_S2


title: En_undigested_rep1


title: En_digested_rep2


title: Chronic_ESOTcells_Round2_S2


title: WT rep3 (Normoxia)


title: En_undigested_rep2


title: Chronic_noTcells_Round1_S2

value: no T cell control round 1


title: En_digested_rep1


title: Chronic_noTcells_Round1_S1


title: WT rep2 (Normoxia)


title: WT rep1 (Normoxia)


title: Acute_ESOTcells_S2

value: Acute

value: ESO T cell


title: Sham rep3 RNA-seq

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2
In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome build: mm10
Matrix table with raw gene counts for every gene and every sample

value: Sham


title: Acute_ESOTcells_S1


title: Acute_Tcells_S2

value: T cell control


title: Eh_undigested_rep1

data_processing:
For PAM-DETECT samples (samples with "digested" or "undigested" in their name) processed according to https://doi.org/10.1016/j.molcel.2016.02.031
Transposon insertion point of samples with "CRISPRdependent" or "CRISPRindependent" in their name was assessed by extracting, counting and sorting sequences containing part of the transposon terminal left end and ~15 nts long sequences 5' of the transposon terminal left end.
Genome_build: not applicable
Supplementary_files_format_and_content: All processed data files are uploaded as text files. Processed data files for PAM-DETECT samples (samples with "digested" or "undigested" in their name) contain 5nts sequences corresponding the PAM library with "R2" files containing reverse complement sequences. Processed data files for transposon insertion points (samples with "CRISPRdependent" or "CRISPRindependent" in their name) contain sequences spanning part of the transposon terminal left end and ~15 nts long sequences 5' of the transposon terminal left end.

value: in vitro:myTXTL from Arbor Biosciences

value: targets next to the randomized PAM library


title: Eh_digested_rep2


title: Eh_undigested_rep2

value: undigested


title: Sham rep1 RNA-seq


title: Eh_digested_rep1


title: Ac3_undigested_rep2


title: Ac3_undigested_rep1


title: OVX rep2 RNA-seq

value: OVX


title: OVX rep1 RNA-seq


title: Ac3_digested_rep2

value: digested with PacI


title: Input background ChIP-seq

data_processing:
Nanodrop: Preliminary quantitation
Agarose Gel Electrophoresis: tests RNA degradation and potential contamination
 Paired-end sequencing libraries are sequenced by Illumina high-throughput sequencer.
The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.
Genome build: mm10
bigwig files were generated using Galaxy

extract_protocol:
Lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Libraries were sequenced on the Illumina HiSeq nova 6000 following the manufacturer's protocols.


title: OVX rep3 RNA-seq


title: Sham rep2 RNA-seq


title: scCUT&Tag-pro H3K27me3 HTO

city: New York

first: Bingjie

state: New York

address: New York Genome Center, 101 Avenue of the Americas, 7th

institute: New York Genome Center

data_processing:
Library strategy: CUT&TAG
We use salmon alevin for the alignment and quantification of single-cell antibody-derived tags (ADT) and hashtag oligos (HTO), using a custom index that is constructed only from known ADT and HTO barcode sequences. We apply a threshold of 10 protein and 10 hashing antibody counts. Cells that pass these thresholds are used as input to the HTODemux() function in Seurat for demultiplexing and doublet removal. Antibody data was normalized using the centered log ratio transformation. In order to visualize cells on the basis of their ADT profiles, we performed PCA using all features as input, and retained the first 25 principal components to construct a nearest-neighbor graph and perform UMAP visualization.
We use cellranger-atac v1.2 pipeline with default settings to align reads to the hg38 human reference annotation and generate fragment files. We filter the fragment file to keep the cellular barcodes (CBs) that were present in the filtered ADT and HTO libraries, and also contained at least 100 fragments. We use the AggregateTiles function from the Signac package to quantify the fragment coverage based on 5,000bp genomic windows, remove windows with less than 5 counts, and then merge adjacent windows.  We next perform modified TD-IDF normalization, which corrects for differences in cellular sequencing depth and weights each window based on its average fragment abundance across all cells. We next run singular value decomposition (SVD) on the TF-IDF matrix to generate the low dimensional representation of the data. We use dimensions 2:30 for UMAP visualization, as the first dimensional is highly correlated with sequencing depth.
We utilize the Seurat v4 Weighted Nearest Neighbor (WNN) framework to generate a multimodal representation of the scCUT&Tag-pro datasets. We use the FindMultiModalNeighbors function to generate a WNN graph, using dimensions 1:25 (ADT modality) and dimensions 2:30 (scCUT&Tag modality).
Genome_build: hg38
Supplementary_files_format_and_content: For CUT&tag data, processed data provided as a fragment file, each line represents a unique genomic DNA fragment captured by the assay. For ADT and HTO data, processed data provided as a TSV expression matrix where the rows correspond to protein and the columns to single cells.

molecule: other

source_name: Human peripheral blood mononuclear cell (PBMC)

growth_protocol: Primary cells

extract_protocol: A step-by-step protocol for scCUT&Tag-pro is available here: https://www.protocols.io/private/57E45A034D5311ECA43B0A58A9FEAC02.

tag: sample type

value: Cell hashing tags


title: Ac3_digested_rep1


title: Acute_Tcells_S1

value: A375 melanoma cells


title: Acute_noTcells_S1

value: no T cell control


title: Ac2_undigested_rep2


title: scCUT&Tag-pro H3K27me3 histone

value: CUT&Tag

tag: antibody

value: Antibody:H3K27me3 (1:100, Cell Signaling Technology, 9733)


title: HIF-1a ChIP-seq

value: bone marrow B cells

value: HIF1 alpha Antibody(NB100-105)


title: scCUT&Tag-pro H3K27me3 ADT

value: Cell surface protein tags

value: TotalSeq-A conjugated antibody panel (BioLegend (399907)


title: optic nerve OD #3 3

city: Wenzhou City

first: Yu

last: Zhonghao

state: Zhejiang Province, China

address: 270 Xueyuan West Road

institute: The Eye Hospital, School of Ophthalmology & Optometry

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ARS1 (Capra hicus) genome using Tophat2 software
Cufflinks are used for assemble transcripts and remap and quantity gene-expression level which is estimate by FPKM value.
Genome_build: Saanen_v1
Supplementary_files_format_and_content: text files include raw count and FPKM values for each Sample.

organism: Capra hircus

source_name: right pre-chiasmatic optic nerve

extract_protocol:
Total RNA of each sample was extracted following the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
RNA libraries were prepared for sequencing using standard illumina protocols.

treatment_protocol: Left pre-chiasmatic optic nerve crush was treated with hypothermia treatment immediately one day before collected samples.

value: optic nerve

tag: breed

value: Saanen dairy goat

tag: injured or uninjured site

value: uninjured

tag: treatment or non-treatment

value: non-treatment


title: optic nerve OD #1 3

source_name: right retrobulbar optic nerve

tag: tissue


title: scCUT&Tag-pro H3K27ac rep2 ADT


title: Ac2_undigested_rep1

value: in vitro:myTXTL from Arbor Biosciences

value: targets next to the randomized PAM library

tag: treatment


title: Ac2_digested_rep1


title: optic nerve OS #3 3

source_name: left pre-chiasmatic optic nerve

value: injured

value: treatment


title: scCUT&Tag-pro H3K27ac rep2 HTO

value: Cell hashing tags


title: scCUT&Tag-pro H3K27ac rep2 histone

value: Antibody:H3K9me3 (1:100, Abcam, ab8898)


title: optic nerve OS #1 3

source_name: left retrobulbar optic nerve


title: scCUT&Tag-pro H3K27ac rep1 HTO


title: optic nerve OD #3 2


title: Ac1_undigested_rep1

source_name: plasmid DNA

value: undigested


title: Ac2_digested_rep2

value: digested with PacI


title: scCUT&Tag-pro H3K27ac rep1 ADT


title: Acute_noTcells_S2

value: A375 melanoma cells

value: Acute

value: no T cell control


title: Ac1_undigested_rep2


title: scCUT&Tag-pro H3K27ac rep1 histone

value: CUT&Tag

value: Antibody:H3K27ac (1:100, Abcam, ab177178)


title: Ac1_digested_rep2


title: optic nerve OD #1 2

value: optic nerve


title: optic nerve OS #3 2

value: Saanen dairy goat


title: scCUT&Tag-pro H3K9me3 HTO


title: optic nerve OS #1 2

value: uninjured


title: Ec_025nM_6h_undigested_rep2


title: ESQ-32731

type: genomic

city: Mexico City

first: José Jaime

last: Martínez Magaña

state: Mexico City

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan,

country: Mexico

institute: Instituto Nacional de Medicina Genómica

description: clozapine treated sample

hyb_protocol: The bisulfite-converted DNA was amplified, fragmented, and hybridized with the Infinium MethylationEPIC BeadChip, Illumina using the standard Illumina protocol.

scan_protocol: Standard Illumina iScan settings for Methylation EPIC

data_processing:
Raw data was read by minfi package (version 3.14) from IDAT files and converted to rgset from this we calculate the methylated and unmethylated intensities for each sample and probe.
Unmethylated and methylated signal intensities

label: cy3, cy5

source_name: peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from peripheral blood leukocytes was entered using standard techniques.

tag: gender

value: Male

tag: treatment status

value: Clozapine

value: peripheral blood leukocytes


title: scCUT&Tag-pro H3K9me3 ADT

value: Cell surface protein tags

value: TotalSeq-A conjugated antibody panel (BioLegend (399907)


title: Ec_025nM_6h_undigested_rep1

value: in vitro:myTXTL from Arbor Biosciences

value: targets next to the randomized PAM library


title: Ac1_digested_rep1


title: ESQ-33843

description: clozapine treated sample

value: Female


title: optic nerve OD #3 1

value: non-treatment


title: scCUT&Tag-pro H3K9me3 histone


title: Ec_025nM_6h_digested_rep2

value: digested with PacI


title: optic nerve OD #1 1


title: ESQ-33136

description: clozapine treated sample


title: ESQ-38564

description: clozapine treated sample


title: ESQ-32328

description: clozapine treated sample


title: ESQ-27056

description: clozapine treated sample


title: ESQ-31316

description: clozapine treated sample


title: ESQ-31215

description: clozapine treated sample


title: optic nerve OS #3 1

value: injured

value: treatment


title: scCUT&Tag-pro H3K4me3 HTO

value: Cell hashing tags


title: Ec_025nM_6h_digested_rep1


title: scCUT&Tag-pro H3K4me3 ADT


title: ESQ-36362

description: clozapine treated sample


title: optic nerve OS #1 1


title: Ec_3nM_16h_undigested_rep2

value: undigested


title: Ec_3nM_16h_undigested_rep1


title: vFLIP_mut 3

city: Nanjing

first: Liuxue

last: Sheng

state: Jiangsu

address: Tian Yuan East Road

institute: Nanjing Medical University

description:
all.circ_expression_anno.xls
mRNA_exp.xls
ncRNA_exp.xls
K13-3

data_processing:
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters,then mapped to hg19 whole genome using HISAT2 and BWA-MEM or Tophat.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model.
Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs.
Back-spliced junction reads identified in CIRI2 were combined and scaled to RPM (Reads Per Million mapped reads) to quantify every circRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw counts and RPM(or RPKM) values for each sample

source_name: iSLK-puro

extract_protocol:
Standared RNA extraction protocol
The purified RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).

treatment_protocol: Doxycycline treatment for 72 h.

value: iSLK-RGB-K13 mutant

value: treated with Doxycycline for 72 h


title: ESQ-01134

description: clozapine treated sample


title: scCUT&Tag-pro H3K4me2 HTO


title: ESQ-33338

description: clozapine treated sample


title: ESQ-33141

description: clozapine treated sample


title: ESQ-32126

description: clozapine treated sample


title: ESQ-30407

description: clozapine treated sample


title: Ec_3nM_16h_digested_rep2

first: Chase

address: Josef-Schneider Straße 2


title: ESQ-37068

description: clozapine treated sample


title: scCUT&Tag-pro H3K4me2 ADT


title: ESQ-37775

description: clozapine treated sample


title: vFLIP_mut 1

description:
all.circ_expression_anno.xls
mRNA_exp.xls
ncRNA_exp.xls
K13-1


title: Ec_3nM_16h_digested_rep1


title: ESQ-30306

description: clozapine treated sample


title: Kidney endothelial cells - RbpjDEC 3

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (v1.4.2), an analysis pipeline for RNA sequencing data of the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden.
Adapters were removed using Trim Galore (v0.6.4) and aligned to the reference genome using STAR (v2.6.1d).
Counts per gene were summarized using featureCounts of the subread package (v.1.6.4).
Genome_build: mm10 (GRCm38.p6)
Supplementary_files_format_and_content: tab-separated text file of featureCounts output (i.e. raw counts per sample (in columns) per gene (in rows)). The first 2 columns of the file contain the Ensembl gene ID and the gene symbol of each gene, followed by the count data per sample. Sample genotype (wild-type or knockout) is indicated within each sample's name.

source_name: kidney endothelium

extract_protocol:
Single cell suspensions were prepared from kidneys. After Fc block and subsequent staining with anti-CD31-PE and anti-CD45-FITC, cells were washed and incubated with 1:5 diluted anti-PE microbeads (Miltenyi Biotech, 130-048-801 for 15 min. Positive selection of magnetically labeled cells was performed using LS columns and MidiMax Separator in combination with MACS Multistand (all from Miltenyi Biotec according to manufacturer’s instructions. After elution from columns, cells were pelleted, filtered through 40µm mesh and proceeded for sorting on a FACSAria IIu cell sorter (Becton-Dickinson.  Total yield of EC (CD31+CD45- cells was about 5x10^5 to 1x10^6 live cells per kidney. Bulk EC RNA was isolated using a Qiagen RNEasy micro kit according to the manufacturer's protocol.
2ng of total RNA were used for library preparation with the ‘SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian’ (#634413; Takara/Clontech according to conditions recommended in user manual #063017. Generated libraries were barcoded by dual indexing approach and were finally amplified with 12 cycles of PCR. . Fragment length distribution of generated libraries was monitored using the ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies. Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific.

treatment_protocol: Cdh5CreERT2/-; Rbpjf/f  mice and their cre-negative littermates were treated with 5x 1.5mg Tamoxifen at 8wk age to induce endothelial-specific loxP recombination. Organ harvest at 12 weeks after induction.

value: Kidney

value: endothelial cells

tag: mouse line

tag: genotype

value: Cre +/-; Rbpjf/f

value: Tamoxifen 5x 1.5mg i.p. at 8wk age

tag: age


title: vIRF1_mut 3

description:
all.circ_expression_anno.xls
mRNA_exp.xls
ncRNA_exp.xls
q-3

value: iSLK-RGB-K9 mutant


title: Kidney endothelial cells - RbpjDEC 2


title: scCUT&Tag-pro H3K4me1 rep2 HTO


title: scCUT&Tag-pro H3K4me1 rep2 ADT

value: Cell surface protein tags

value: TotalSeq-A conjugated antibody panel (BioLegend (399907)


title: S2_hk_STARRseq_rep2

city: Wien

first: Bernardo

last: de Almeida

address: Campus-Vienna-Biocenter 1

institute: Research Institute of Molecular Pathology (IMP)

data_processing:
Library strategy: STARR-seq
Paired-end genome-wide UMI-STARR-seq RNA and DNA input reads (36 bp) were mapped to the Drosophila genome (dm3), excluding chromosomes U, Uextra, and the mitochondrial genome, using Bowtie v.1.2.2. Mapping reads with up to three mismatches and a maximal insert size of 2kb were kept. For paired-end RNA reads that mapped to the same positions, we collapsed those that have identical UMIs (10 bp, allowing one mismatch; UMI sequences are in the sequencing read name) to ensure the counting of unique reporter transcripts. We further computationally selected both RNA and input fragments of length 150-250 bp to only capture active sequences derived from short fragments.
After processing the two biological replicates separately, we pooled both replicates for developmental and housekeeping screens for further analyses.
Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of STARR-seq and input. We performed hypergeometric tests to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
Peaks that had a hypergeometric p-value <= 0.001 and a corrected enrichment over input greater than 3 were defined as enhancers.
Genome_build: dm3
Supplementary_files_format_and_content: BigWig files contain normalized genome-wide coverage. Plain text files contain enhancer peaks, including the chromosome, the summit position, the enrichment over input at the summit, and the p-value.

source_name: S2 cells

extract_protocol: 24h after electroporation, total RNA was extracted using the RNeasy Maxi kit (Qiagen; cat. no. 75162), followed by polyA+ RNA isolation using Invitrogen Dynabeads Oligo(dT)25 (scaling up the manufacturer   s protocol accordingly; cat. no. 61005) and DNase treatment with Ambion Turbo DNase (cat. no. AM2239) at a concentration of at most 200 ng/  l for 45 minutes (min) at 37C. The reactions were then subjected to cleanup with Beckman-Coulter AMPure XP beads (Product No: A63881), at a ratio of 1:1.8. STARR-seq transcripts were specifically reverse transcribed using a gene specific primer (CTCATCAATGTATCTTATCATGTCTG), followed by RNaseA digest. After second strand synthesis (primer: TTGGTAAAGCCACCATGGAAAAG*G) we introduced a 10 bp unique molecular identifier (UMI) at the 3' end of the STARR-seq transcript (primer:  CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNGTGACTGGAGTTCAGACGTGT*G), followed by a PCR step across the spliced intron junction of the mature STARR-seq transcript (primers: AAGCCACCATGGAAAAG*G*C*C*A*T and CAAGCAGAAGACGGCATACG*A). Samples were amplified for Illumina sequencing with an Illumina i5 adapter and a custom i7 index primer (CAAGCAGAAGACGGCATACGAGA*T). All PCR steps were performed using the KAPA HiFi HotStart ReadyMix (Roche; Material Number 7958927001), and cleaned up with Beckman-Coulter AMPure XP beads (Product No: A63881) at an appropriate ratio. See Neumayr et al., Curr. Protoc. Mol. Biol. 2019 for more details.

tag: cell line

value: PCR amplified cDNA (STARR-seq transcript)

tag: promoter

value: housekeeping (RpS12)


title: scCUT&Tag-pro H3K4me1 rep2 histone

value: CUT&Tag

value: Antibody:H3K4me1 (1:100, Abcam, ab8895)


title: ESQ-33237

description: clozapine treated sample

value: Male

value: Clozapine

tag: cell type

value: peripheral blood leukocytes


title: vFLIP_mut 2

description:
all.circ_expression_anno.xls
mRNA_exp.xls
ncRNA_exp.xls
K13-2


title: ESQ-33540

description: clozapine treated sample

value: Female


title: Kidney endothelial cells - RbpjDEC 1


title: scCUT&Tag-pro H3K4me3 histone

value: Antibody:H3K4me3 (1:100, Abcam, ab213224)


title: S2_hk_STARRseq_rep1


title: Kidney endothelial cells - CTRL3

value: Cre -/-; Rbpjf/f


title: ESQ-30512

description: clozapine treated sample


title: KSHV 3

description:
all.circ_expression_anno.xls
mRNA_exp.xls
ncRNA_exp.xls
k-3

value: iSLK-RGB BAC16

value: treated with Doxycycline for 72 h


title: ESQ-31924

description: clozapine treated sample


title: scCUT&Tag-pro H3K4me1 rep1 HTO

value: Cell hashing tags


title: S2_dev_STARRseq_rep2

value: developmental (DSCP)


title: Kidney endothelial cells - CTRL2

value: Kidney

value: endothelial cells

value: Tamoxifen 5x 1.5mg i.p. at 8wk age


title: KSHV 2

description:
all.circ_expression_anno.xls
mRNA_exp.xls
ncRNA_exp.xls
k-2


title: scCUT&Tag-pro H3K4me1 rep1 ADT

value: Cell surface protein tags

value: TotalSeq-A conjugated antibody panel (BioLegend (399907)


title: Kidney endothelial cells - CTRL1


title: ESQ-31114

description: clozapine treated sample


title: KSHV 1

description:
all.circ_expression_anno.xls
mRNA_exp.xls
ncRNA_exp.xls
k-1


title: scCUT&Tag-pro H3K4me1 rep1 histone

value: CUT&Tag


title: KD1_72

status: Public on Feb 23 2022

first: Qi

last: Zhu

state: Guangdong

address: Sun Yat-sen University, Guangzhou, Guangdong, 510006, China

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
The adapter and low-quality reads were filtered out through cutadapt (version 1.11).
Clean reads were mapped to the mm10 reference transcripts by Hisat2 (version 2.1.0), allowing up to two mismatches.
These genes were subjected to alignment against public protein databases; Pfam (Pfam Protein families), Uniprot (Swiss-Prot). It comprised RSEM (v1.2.6) for transcript abundance estimation and normalization of expression values as FPKM (Fragments per kilobase of transcript per million fragments mapped).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: preadipocytes

extract_protocol:
Total RNA was extracted using the RNAprep Pure Kit DP432 (TIANGEN Biotech Co.,Ltd., Beijing, China), following the manufacturer’s instructions. All the RNA samples were assessed for their integrity using Qsep1 instrument. To construct RNA libraries with the MGIEasy mRNA Library Prep Kit, 3 μg of total RNA was used
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 3T3-L1 cells

tag: genotype/variation

value: treated with MDI for 72 hours


title: vIRF1_mut 1

description:
all.circ_expression_anno.xls
mRNA_exp.xls
ncRNA_exp.xls
q-1

value: iSLK-RGB-K9 mutant


title: KD2_72


title: KD3_72


title: NC3_72

value: NC


title: NC2_72


title: NC1_72


title: KD3_24

value: treated with MDI for 24 hours


title: KD2_24


title: KD1_24


title: NC3_24


title: S2_dev_STARRseq_rep1

value: PCR amplified cDNA (STARR-seq transcript)


title: NC2_24


title: ESQ-37472

description: clozapine treated sample

value: Female

value: Clozapine

value: peripheral blood leukocytes


title: NC1_24


title: Hippocampus MRL-lpr+MSC1

first: Han

last: Xiaojuan

address: Zhongshan Road 321

institute: Nanjing Drum Tower Hospital,  The Affiliated Hospital of Nanjing University Medical School

data_processing:
Illumina Casava1.7 software used for basecalling.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hippocampus

extract_protocol:
Hippocampus was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated sing NEBNext®  UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following  manufacturer’s recommendations and index codes were added to attribute sequences  to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo- attached magnetic beads. Fragmentation was carried out using divalent cations under  elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First  strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H  -). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to  prepare for hybridization. In order to select cDNA fragments of preferentially 250~300  bp in length, the library fragments were purified with AMPure XP system (Beckman  Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size- selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before  PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified  (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100  system.

tag: strain

value: Hippocampus

value: post natal week 6

value: MRL-lpr

value: treated with mesenchymal stem cell


title: Hippocampus MRL-lpr3

value: untreated


title: scCUT&Tag-pro H3K4me2 histone

tag: sample type

value: Antibody:H3K4me2 (1:100, Abcam, ab32356)


title: Hippocampus MRL-lpr+MSC3


title: Hippocampus MRL-lpr+MSC2


title: Hippocampus MRL-lpr2


title: Hippocampus WT3

value: wild type


title: Hippocampus MRL-lpr1


title: Hippocampus WT2


title: ESQ-30508

description: clozapine treated sample


title: PostCovid_13

city: Madison

first: Andy

last: Madrid

state: Wisconsin

address: 600 Highland Ave

department: Neurological Surgery

institute: University of Wiconsin - Madison

description:
blood from COVID-19 patient one year after infection
Sample name: PC2015

hyb_protocol: hybridized to Illumina HumanMethylationEPIC arrays using standard Illumina instructions

scan_protocol: arrays were imaged using BeadArray Readerusing standard recommended settings

data_processing:
minfi
matrix processed file:  average beta
matrix signal file:  Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: standard illumina protocol

extract_protocol: genomic DNA from whole blood tissue was extracted using tehe GeneJET whole blood kit according to the manufacturer's recommendations

tag: individual

tag: disease state

value: post COVID-19

tag: time

value: one year after infection

value: whole blood


title: ESQ-32933

description: clozapine treated sample

value: Male


title: PostCovid_14

description:
blood from COVID-19 patient one year after infection
Sample name: PC2018


title: Hippocampus WT1


title: PostCovid_15

description:
blood from COVID-19 patient one year after infection
Sample name: PC2019


title: PostCovid_11

description:
blood from COVID-19 patient one year after infection
Sample name: PC2012


title: vIRF1_mut 2

description:
all.circ_expression_anno.xls
mRNA_exp.xls
ncRNA_exp.xls
q-2

value: iSLK-RGB-K9 mutant

value: treated with Doxycycline for 72 h


title: PostCovid_12

description:
blood from COVID-19 patient one year after infection
Sample name: PC2013


title: PostCovid_10

description:
blood from COVID-19 patient one year after infection
Sample name: PC2011


title: PostCovid_8

description:
blood from COVID-19 patient one year after infection
Sample name: PC2009


title: PostCovid_9

description:
blood from COVID-19 patient one year after infection
Sample name: PC2010


title: PostCovid_7

description:
blood from COVID-19 patient one year after infection
Sample name: PC2008


title: PostCovid_6

description:
blood from COVID-19 patient one year after infection
Sample name: PC2007


title: PostCovid_4

description:
blood from COVID-19 patient one year after infection
Sample name: PC2005


title: PostCovid_5

description:
blood from COVID-19 patient one year after infection
Sample name: PC2006


title: PostCovid_3

description:
blood from COVID-19 patient one year after infection
Sample name: PC2004


title: PostCovid_2

description:
blood from COVID-19 patient one year after infection
Sample name: PC2003


title: PostCovid_1

description:
blood from COVID-19 patient one year after infection
Sample name: PC2002


title: ESQ-32539

description: clozapine treated sample


title: ESQ-36261

description: clozapine treated sample


title: ESQ-37361

description: clozapine treated sample


title: ESQ-36564

description: clozapine treated sample


title: ESCs producing MGA that lacks  T-box domain

type: RNA

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

country: Japan

institute: Saitama Medical University

hyb_protocol: Affymetrix Standard WT Plus Protocol.

scan_protocol: AGCC Standard Protocol.

data_processing: The data were background-subtracted and normalized using the Transcriptome Analysis Console Software (TAC4.0, ThermoFisher, https://www.thermofisher.com/jp/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/affymetrix-transcriptome-analysis-console-software.html).

label: biotin

label_protocol: Affymetrix WT Plus Kit.

growth_protocol: Culture under conventional ES culture condition with LIF (1000 units/ml) and 10% serum.

extract_protocol: Total RNAs were isolated from ESCs with RNeasy Mini Kit (QUIAGEN, 74106)

tag: Sex

value: ES cells


title: ESQ-30205

description: clozapine treated sample

value: Female


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P110

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'oligo' (v1.58.0).

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P110

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The study population consisted of 110 healthy abdominally obese men and women, aged 40-70 years at time of recruitment. Subjects were recruited from the NQPlus cohort, a database of the Wageningen University, and local advertisements. Abdominal obesity was defined as a BMI >27kg/m2 or a waist circumference >88cm (women) or >102cm (men). Exclusion criteria were: earlier diagnosed with diabetes or diagnosed during our screening (OGTT, fasting glucose >7mmol/L, after 2h >11.1mmol/L), daily alcohol intake of >20g (women) or 30g (men), smoking, unstable body weight (weight gain or loss of >3kg in the past three months), diagnosed with a long-term medical condition, using medication known to interfere with glucose or lipid homeostasis, being allergic to fish oil or restricted to a vegetarian dietary regime. All subjects gave written informed consent. The study was approved by the Medical Ethics Committee of Wageningen University and registered at ClinicalTrials.gov, identifier: NCT02194504.

extract_protocol: RNA from frozen adipose tissue samples was isolated using a TRIzol/chloroform extraction (Thermo Fisher Scientific, Waltham, USA) and purified using the Qiagen Mini column kit according to manufacturers’ protocol (Qiagen, Hilden, Germany). RNA yield was quantified on a NanoDrop ND 1000 spectrophotometer (NanoDrop Technologies, Wilmington, USA) while RNA integrity was measured on an Agilent 2100 BioAnalyzer with RNA 6000 Nanochips (Agilent Technologies, Santa Clara, USA). Samples with RNA integrity (RIN) score of 6.2 and higher were included, average RIN-score was 8.0.

treatment_protocol: This study was a parallel-designed randomized 12-week intervention that examined the effects of a 25% energy restriction (ER) high nutrient quality diet; a 25% ER low nutrient quality diet; or a habitual diet on cardiometabolic risk factors by using an array of outcome measures, including subcutaneous adipose tissue (AT) transcriptomics. AT transcriptomics were determined at the fasted state, and 4 hrs postprandial of a standardized mixed meal shake challenge, both before (0 wk) and after the intervention (12 wk). An energy restriction of 25% was applied to the calculate estimated energy requirement (EER) of each participant. The two ER diets were iso-caloric and matched for alcohol, sodium, and total fat. The differences between the two ER diets was that the high nutrient quality ER diet was, compared to the low nutrient quality ER diet, enriched in monounsaturated fatty acids (MUFA; 13.4 vs. 9.3 En%), n-3 polyunsaturated fatty acids (PUFA; 7.7 vs. 4.1 En%), fiber (3.1 vs. 2.2 En%) and plant protein (10.3 vs. 5.7 En%), and reduced in fructose content (3.4 vs. 7.0 En%). The composition of the diets formed the basis of daily meal plans provided to the participant during the intervention. To increase the intake of n-3 PUFA in the high nutrient quality ER diet, a daily capsule providing 400 mg EPA and 300 mg DHA was included in the meal plan. Participants visited the facility weekly for an individual session with a qualified dietician, after which the key food products were provided for the following week. Adherence to the diet was determined based on the collection of leftovers of the supplied products, and on the participant's food diary, in which deviations from the protocol were reported. To calculate reported intake of energy and nutrients, the meal plans with reported deviations were used. Additional consumed food items were added to the intake while leftovers were subtracted. Metabolizable energy of the two diets was calculated using specific Atwater values. On a separate study day at the start of the study and after the 12 week intervention, measurements on metabolic health were conducted before and during a mixed meal shake challenge at Wageningen University, The Netherlands. Prior to this day, participants were asked to refrain from alcohol, avoid strenuous exercise, ensure a sufficient night's rest, and consume a low-fat standardized meal before 8pm, after which they had to fast. Subcutaneous adipose tissue biopsies were taken caudally from the umbilicus under local anesthesia (1% lidocaine) using a small liposuction cannula in the fasted state, as well as 4 hrs after consumption of a mixed meal shake. The mixed meal was a shake consisting of 320g water, 20g protifar, 83.5g dextrose, 60g palm olein, and 20 drops vanilla oil, equalling to 3833kJ and 76.3g carbohydrates, 17.6g protein, and 60g fat. Adipose tissue biopsies were taken by trained nurses on sagittal different locations to prevent analysis of acute inflammation and wound healing mediators. Biopsies were rinsed with phosphate-buffered saline to eliminate blood and immediately frozen in liquid nitrogen and stored at -80 ºC until RNA isolation.

tag: intervention

tag: specification intervention diet

value: 25% energy restricted (ER), low nutrient quality

tag: moment of adipose tissue sampling

value: 0 weeks (baseline)

tag: time of adipose tissue sampling

value: 4 hours after a mixed-meal challenge (postprandial)

tag: tissue

value: subcutaneous white adipose tissue (WAT)


title: ESCs producing MGA that lacks  bHLHZ domain


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P109

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P109

value: 25% energy restricted (ER), high nutrient quality

value: 12 weeks after intervention


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P110

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P110

value: 0 hours (before/fasted)


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P109

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P109


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P111

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P111


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P111

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P111


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P109

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P109


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P110

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P110


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P107

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P107


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P110

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P110


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P107

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P107


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P109

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P109


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P107

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P107


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P108

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P108

value: habitual diet


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P108

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P108