title: NS364_3+10

description:
10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (biological replicate #3)
NS364_NoCvsGlu; NS364vsGT23_NoC

data_processing:
files were converted to fastqsanger using FASTQ Groomer
reads were mapped to the B. thetaiotaomicron genome using Bowtie2 (v.2.3.4)
the mapped reads were quantifed using  featureCounts (v1.6.3)
differential gene expression was measured using DEseq2 (v1.18.1)
Genome_build: NC_004.fastq.gz663
Supplementary_files_format_and_content: Excel spreadsheet with computed log2 fold differences between each genotype and condition

molecule: cytoplasmic RNA

growth_protocol: Cells were grown to mid-exponential phase in minimal media containing glucose (OD600 = ~0.45-0.6; samples designated -5) and switched to media lacking a carbon source (samples designated +10)

extract_protocol:
Rneasy (Qiagen), TurboDnase (ThermoFisher), Rneasy (Qiagen)
Libraries were prepared according to Illumina's instructions accompanying the ScriptSeq v2 kit (Illumina) following depletion of rRNA and tRNA using RiboZero Bacteria Kit (Illumina)

treatment_protocol: Frozen cell pellets were treated with RNAProtect (Qiagen)

value: delta-tdk delta-BT4338


title: SCLC tumor, sgp130_6637T1

status: Public on Dec 19 2019

type: SRA

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

country: USA

institute: MIT

library_source: transcriptomic

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options. Estimated counts from rsem were upper-quartile normalized where the 75th percentile was set to 1000.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel files include estimated read counts (from rsem) per gene for each sample and normalized counts per gene for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Small cell lung cancer tumor

extract_protocol:
Tumors were dissected from lungs upon necropsy and flash-frozen in liquid nitrogen, followed by storage at -80C. Total RNA was isolated from frozen tumors using the AllPrep DNA/RNA Mini Kit (QIAGEN #80204).
Libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche #08098123702), according to the manufacturer's protocols.

tag: strain

value: mixed C57BL/6;129/Sv

tag: genotype

tag: crispr-mediated mutation

tag: tissue

value: Small cell lung cancer tumor


title: SCLC tumor, sgp130_6638T4


title: Holder pasteurized  whole milk from donor B

city: Lodz

first: Urszula

last: Smyczyńska

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

description:
excluded from expression analysis due to low miRNA read count
mirna_count_table.txt
Milk-2B

data_processing:
Read adapters were trimmed and UMI sequences were extracted by UMI-tools v1.0.0. Maximum 2bp mismatch in a 19bp-long adapter sequence (AACTGTAGGCACCATCAAT) was allowed. Reads with incomplete UMI sequence (<12nt) and shorter than 15bp after trimming were excluded from the downstream analyses.
Trimmed reads were mapped to miRBase v22 mature human miRNA sequences. Prior to mapping, mature miRNA records with identical sequences were collapsed to allow unique mapping. Bowtie2 v2.3.4.1 local alignment with following parameters was used: “-N1 -L9 --norc -k10 --local --score-min L,4,1.3 --mp 4”. Reads mapping to multiple miRNAs with equal scores were excluded. Uniquely mapped reads were deduplicated based on UMI using the “unique" method in UMI-tools. Next, SAMtools v1.9 idxstats was used to obtain read counts for each miRNA. The counts are in mirna_count_matrix.txt
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited matrix of miRBase mapping read counts

organism: Homo sapiens

source_name: breast milk

extract_protocol:
Serum/Plasma Advanced Kit (Qiagen), according to manufacturers instructions.
QIAseq miRNA Library Kit (Qiagen), according to manufacturers instructions.

treatment_protocol: HPP samples: subjected to HPP in 62.5°C for 30 minutes in Human Milk Pasteurizer S90 Eco (Sterifeed, Medicare Colgate Ltd, England, Cullompton). HoP samples: HoP using U 4000/65 apparatus (Unipress Equipment, Poland, Celestynow). Control samples: untreated. Storage: frozen at -20°C before further processing.

tag: material

value: whole milk

tag: treatment

value: HoP

tag: donor

value: B


title: high-pressure processed whole milk from donor B

description:
excluded from expression analysis due to low miRNA read count
mirna_count_table.txt
Milk-3B

value: HPP


title: MDA_EV(wox+)-1

type: RNA

city: Jerusalem

first: Rami

last: Aqeilan

address: Hadassah medical school

department: Immunology and Cancer Research

country: Israel

institute: Hebrew University

hyb_protocol: hybridized using Affymetrix GeneChip® Human Genome U133 Plus 2.0 arrays.

scan_protocol: The quality assurance, calibration, data normalization and principal component analysis for the Affymetrix cell format files were performed by Partek Genomics Suite 6.5 (Partek Genomics, St Louis, MO, USA).

data_processing: Differentially expressed genes were analyzed using the Enricher dataset (http://amp.pharm.mssm.edu/Enrichr/) and the KEGG database.

label: biotin

source_name: metastatic melanoma cancer

label_protocol: standard Affymetrix protocol

growth_protocol: cells were grown in DMEM (Gibco) supplemented with 10% FBS, glutamine and penicillin/streptomycin

extract_protocol: Total RNA was prepared using TRI reagent, BIO TRI (Biolab, Israel) as described by the manufacturer.

treatment_protocol: Stable clones for WWOX overexpression were produced using a lenti-viral vector (pDEST12.2TM destination vector, Gateway Cloning Technology) containing either WT or mutated (WFPA) WWOX. Clones were selected using 2mg/ml G418 (Gibco 11811031).

tag: cell line

tag: lenti-viral vector

value: WT WWOX protein


title: NS364_2+10

city: HERSHEY

first: Guy

last: Townsend

state: PA

address: 500 University Drive, BMR Rm. C6820

department: Biochemistry & Molecular Biology

institute: Penn State College of Medicine

description:
10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (biological replicate #2)
NS364_NoCvsGlu; NS364vsGT23_NoC

organism: Bacteroides thetaiotaomicron

source_name: human gut bacteria

tag: condition

value: No C


title: Holder pasteurized  whole milk from donor A

description:
excluded from expression analysis due to low miRNA read count
mirna_count_table.txt
Milk-2A

value: A


title: NS364_1+10

description:
10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (biological replicate #1)
NS364_NoCvsGlu; NS364vsGT23_NoC


title: SCLC tumor, sgp107_6631T1


title: SCLC tumor, sgp107_6630T3


title: SCLC tumor, sgp107_6630T2


title: SCLC tumor, sgp107_6629T1


title: unprocessed whole milk from donor B

description:
excluded from expression analysis due to low miRNA read count
mirna_count_table.txt
Milk-1B

value: untreated


title: NS364_3-5

description:
mid-exposnential phase growth in minimal media containging glucose as the sole carbon source (biological replicate #3)
NS364_NoCvsGlu; NS364vsGT23_Glu

value: glu


title: SCLC tumor, sgp107_6627T2


title: unprocessed whole milk from donor C

description:
mirna_count_table.txt
Milk-1C

value: C


title: NS364_2-5

description:
mid-exposnential phase growth in minimal media containging glucose as the sole carbon source (biological replicate #2)
NS364_NoCvsGlu; NS364vsGT23_Glu


title: unprocessed whole milk from donor A

description:
mirna_count_table.txt
Milk-1A


title: NS364_1-5

description:
mid-exposnential phase growth in minimal media containging glucose as the sole carbon source (biological replicate #1)
NS364_NoCvsGlu; NS364vsGT23_Glu


title: SCLC tumor, sgp107_6627T1


title: GT23_3+10

description:
10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (biological replicate #3)
GT23_NoCvsGlu; NS364vsGT23_NoC

value: delta-tdk


title: Control sample num 337

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

data_processing:
Alignment: STAR 2.4.0
Quantitation: featureCounts 1.4.4
Normalization & Differential Expression: DESeq2 1.4.5
Genome_build: GRCm38
Supplementary_files_format_and_content: xu-counts.csv: contains raw gene-level counts against GRCm38 GENCODE genes

source_name: Region I epididymis tissue

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit (Valencia, CA) according to manufacturer's instructions.
Total RNA was extracted and an mRNA library was prepared using Illumina TruSeq platform and followed by transcriptome sequencing using an Illumina HiSeq 2000.

treatment_protocol: Mice carrying loxP-flanked Pten allele (Pten flox/flox) were purchased from The Jackson Laboratory (Bar Harbor, Maine). Tg(Rnase10-Cre) mice were a generous gift from Dr. Huhtaniemi (Imperial College London, UK) (Krutskikh et al., 2012). Mice were bred and genotyped based upon the information provided by The Jackson Laboratory (Bar Harbor, Maine).

value: Control

value: Region I epididymis


title: SCLC tumor, sgp107_6631T2


title: PTEN KO sample num 345

value: PTEN knockout


title: PTEN KO sample num 336


title: Control sample num 335


title: DU145-miR-205* rep 2

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

description:
DU145 cells transfected with miR-205* synthetic mimic
5591989038_E

hyb_protocol: Standard Illumina DASL hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were log2 transformed and normalized with robust spline normalization using the lumi package from Bioconductor.

source_name: prostate cancer cells

label_protocol: Biotinylated cRNA was prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays

growth_protocol: DU145 cells were maintained at 37°C/5% CO2 in RPMI medium supplemented with 10% fetal bovine serum

extract_protocol: Trizol (Invitrogen/Life Technologies) according to the manufacturer's protocol

treatment_protocol: Transfection of Ambion® Pre-miR™ miRNA Precursors (Life Technologies) at 20 nM final concentration using Lipofectamine reagent.


title: PTEN KO sample num 333


title: SCLC tumor, sgp107_6629T2


title: GT23_1+10

description:
10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (biological replicate #1)
GT23_NoCvsGlu; NS364vsGT23_NoC


title: GT23_2-5

description:
mid-exposnential phase growth in minimal media containging glucose as the sole carbon source (biological replicate #2)
GT23_NoCvsGlu; NS364vsGT23_Glu


title: GT23_3-5

description:
mid-exposnential phase growth in minimal media containging glucose as the sole carbon source (biological replicate #3)
GT23_NoCvsGlu; NS364vsGT23_Glu


title: S20_YFP_FC_CRT_1

city: Storrs

first: Linnaea

last: Ostroff

state: CT

address: 75 N Eagleville Rd. U-3156

institute: University of Connecticut

description: processed data file: Counts_and_DGE_results_eYFP.txt

data_processing:
Read mapping was performed using Tophat 2.0.9 against the rn6 rat reference genome.
BAM alignment files were processed using the HTSeq 0.6.1 python framework and respective rn6 GTF gene annotation, obtained from the UCSC database.
The Bioconductor package DESeq2(3.2) was used to identify differentially expressed genes (DEG). The resulting values were then adjusted using the Benjamini and Hochberg’s method for controlling the false discovery rate (FDR).  Genes with an adjusted p-value < 0.05 were determined to be differentially expressed.
Genome_build: rn6
Supplementary_files_format_and_content: Tab-delimited text files DESeq2 output and FPKM values for TRAP and eYFP samples

molecule: polyA RNA

organism: Rattus norvegicus

growth_protocol: Adult (8-10 week old) Sprague-Dawley rats were given 1ul bilateral injections of lenti.CMV.eYFP-L10a or lenti.CMV.eYFP into auditory cortical area TE3 and allowed to recover for at least two weeks.

extract_protocol:
RNA was extracted and purified with the Stratagene Absolutely RNA Nanoprep Kit (Agilent Technologies) according to the manufacturer's instructions.
Libraries were made using the SMART-Seq v4 Ultra Low Input RNA Kit for Illumina Sequencing, with the Low Input Library Prep kit v2 (Clontech, Cat # 634890 and 634899, respectively), using 50-200 pg of total RNA. 16 cycles of PCR were used for the cDNA amplification step, and 5 PCR cycles to amplify the library prep.

treatment_protocol: Rats were given either Pavlovian fear conditioning consisting of five pairings of an auditory tone and a mild footshock or control exposure to the conditioning box. Two hours later animals were euthanized and tissue from the cortical injection sites and the amygdala was frozen on liquid nitrogen.

value: Sprague-Dawley

tag: ge

value: Adult (8-10 week old)

tag: training group

value: Fear conditioned

value: Cortex

tag: ip bait

value: eYFP

tag: rna sample

value: total RNA


title: S20_YFP_FC_CRT_2


title: GT23_1-5

description:
mid-exposnential phase growth in minimal media containging glucose as the sole carbon source (biological replicate #1)
GT23_NoCvsGlu; NS364vsGT23_Glu


title: S20_YFP_FC_AMY_1

value: Amygdala


title: Control sample num 344


title: S20_YFP_FC_AMY_2


title: S20_YFP_BOX_CRT_2

value: Box control


title: S20_YFP_BOX_CRT_1


title: GT23_2+10

description:
10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (biological replicate #2)
GT23_NoCvsGlu; NS364vsGT23_NoC

value: No C


title: S20_YFP_BOX_AMY_1


title: IP_YFP_FC_CRT_2

value: IP


title: S20_YFP_BOX_AMY_2


title: Peritoneal macrophages, oleic acid

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.50.0).

source_name: Pool of peritoneal macrophages, treated with 500 µM oleic acid (C18:1) complexed with BSA for 6 hrs.

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction.A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: To harvest peritoneal macrophages, 8-12 week old wild type C57Bl/6 mice were injected intraperitoneally with 1mL 4% thioglycolic acid. Three days post-injection, mice were anesthetised with isoflurane and euthanized by CO2. Peritoneal cells were harvested by washing the peritoneal cavity with ice-cold RPMI-1630 supplemented with 10% heat-inactivated FCS (BioWest) and 1% P/S. Cells were plated after lysis of erythrocytes and non-adherent cells were washed away three hours post plating.

extract_protocol: Total RNA was isolated from samples using the RNeasy kit (Qiagen) according to the manufacturer’s protocol. RNA quality was verified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) using 6000 Nano Chips according to manufacturer’s instructions. RNA was considered suitable for array hybridization only if RNA integrity number exceeded 8.0. RNA from 3 samples per group was pooled for microarray analysis.

treatment_protocol: Peritoneal macrophages were incubated with 500uM final concentrations of fatty acids. All fatty acid stocks were initially reconstituted in absolute ethanol. Sub-stocks of fatty acids at 25 mM were prepared in filter-sterilised KOH at 70 mM. Complete RPMI-1630 medium supplemented with fatty acid-free BSA (Sigma-Aldrich, St. Louis, MO) was filter sterilised, and incubated for 30 min with fatty acids to complex BSA to fatty acids. Ratio of BSA to fatty acids were approximately 1:2. Vehicle control treatments only contained equivalent mixture of ethanol and KOH.

tag: cell type

value: Peritoneal macrophages

value: oleic acid complexed with BSA

tag: fatty acid concentration (micromolar)

tag: incubation time (hrs)


title: Peritoneal macrophages, palmitic acid

source_name: Pool of peritoneal macrophages, treated with 500 µM palmitic acid (C16:0) complexed with BSA for 6 hrs.

tag: strain

value: palmitic acid complexed with BSA


title: L47

city: Toulouse

first: Francoise

middle: B.

last: LENFANT

address: 1 avenue J. Poulhès

department: Team 9- I2MC

country: France

institute: INSERM U1048

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624) All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 16 out of 20 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 32849 spots out of 62976 were selected.  The mean signal of the 11 first samples and 8 last were substracted to individuals signals to correct the batch effect of the 2 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 30207 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: mammary luminal cells

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 25 ng of total RNA using the One-Color Quick Amp  Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt  Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked using Dropsense™  96 UV/VIS droplet reader (Trinean, Belgium). 600 ng of Cy3-labelled cRNA were hybridized on the microarray slides  following the manufacturer’s instructions.

growth_protocol: Mice were housed since birth in 12h light/12h dark period and fed a Safe 04 chow diet.

extract_protocol: Total RNA was extracted with RNeasy micro kit qiagen according to the manufacturer's instructions. RNA amounts were determined by Fragment analyzer and the RNA quality was assessed using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were ovariectomized at 24 days, 10 days later mice receive a pellet of E2 0.01mg/60 days or E2 0.01 + Pg 1.5 mg/60 days

tag: gender

value: female

tag: genotype

value: WT

tag: treatement

value: E2 + Pg


title: L21


title: L72


title: MDA_mut-1

value: WFPA MUT WWOX protein


title: L52


title: IP_YFP_FC_CRT_1

value: Sprague-Dawley

tag: tissue


title: L63


title: IP_YFP_FC_AMY_2

value: Adult (8-10 week old)


title: IP_YFP_BOX_CRT_2


title: Peritoneal macrophages, linoleic acid

source_name: Pool of peritoneal macrophages, treated with 500 µM linoleic acid (C18:2) complexed with BSA for 6 hrs.

tag: treatment

value: linoleic acid complexed with BSA


title: IP_YFP_FC_AMY_1

value: Fear conditioned


title: Peritoneal macrophages, control

source_name: Pool of peritoneal macrophages, treated with BSA only (control) for 6 hrs.

value: bovine serum album (BSA) only, control


title: L76


title: L27


title: IP_YFP_BOX_CRT_1

value: Cortex

value: eYFP


title: L44


title: L61


title: L53


title: L51


title: S20_FC_AMY_1

description: processed data file: Counts_and_DGE_results_TRAP.txt

value: Amygdala

value: total RNA


title: IP_YFP_BOX_AMY_2

value: Box control

value: IP


title: S20_FC_AMY_2


title: S20_FC_CRT_2


title: L50


title: L18


title: TALE2041HG_170224_JC_006_1

type: protein

city: Boston

first: James

last: Anderson

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

description:
Notes from NEB: PURExpress® is a reconstituted protein synthesis system based on the PUREsystem™ (Shimizu et al., 2001) where all necessary components needed for in vitro transcription and translation are purified from E. coli.
Assay for protein-DNA sequence specificity

scan_protocol: PBM arrays were scanned using a GenePix 4400A Microarray Scanner (Molecular Devices), and scan images were analyzed by GenePix Pro (Molecular Devices).

data_processing: PBM data quantification:  Raw data files were processed using the same general approach as used for universal PBMs. Briefly, masliner software was used to combine Alexa488 scans at three different laser power levels and to resolve the signal intensity in spots that are saturated at high laser power settings. Cy3 scans were performed at a single laser power level. If a data set had any negative background-subtracted intensity (BSI) values (which can occur if the region surrounding a spot is brighter than the spot itself), a pseudocount was added to all BSI values for that experiment such that all values were then positive. The custom PBM design included ten replicate probes for each sequence. For each experiment and for each set of probes with identical sequences, we calculated the median-adjusted BSI, median absolute deviation (MAD) and the robust standard deviation estimate from the MAD. Any individual replicate probe with a normalized adjusted BSI value more than 3 s.d. away from the median of the replicate probes was omitted from subsequent analysis, to avoid confounding statistical tests or incorrect choice of parameter settings in model fitting. For each TALE protein, we defined a background set of probes that comprises all the probes on the array designed to represent binding sites for other TALE proteins (not the one being assayed in a given experiment). The array median level was then calculated as the median normalized adjusted BSI of all probes in the background set. The standard deviation of the background set SIs was calculated robustly using the asymptotic approximation σ = 1.4826 x MAD. The z-score for each probe was calculated relative to the median and standard deviation of its corresponding background probes. These z-scores represent a linear transformation of the median SIs for each probe, and therefore facilitate interpretation but do not affect the PWM fitting procedure, which performs its own linear scaling adjustments.

label: Alexa488-conjugated anti-GST primary antibody (Invitrogen A-11131)

molecule: protein

organism: synthetic construct

source_name: Protein expressed by NEB PureExpress IVT kit (NEB product # E6800L)

label_protocol: Lastly, the array was incubated for 20 min with an Alexa488-conjugated anti-GST antibody (Invitrogen A-11131), and washed with 0.05% Tween in PBS and PBS.

extract_protocol:
Cloning of TALE proteins: TALE vectors were assembled by a combination of REAL assembly and REAL-Fast assembly . The REAL assembly and REAL-Fast plasmid vectors do not include plasmids encoding non-canonical RVDs, so these non-canonical plasmids were cloned by site-directed mutagenesis on the canonical RVD plasmids. Plasmid vectors expressing one-, two-, or four-long TALE repeats (within the pUC57-ΔBsaI backbone) were ligated in a serial, hierarchical progression to assemble full TALE repeat arrays bearing the proper sequence of repeat variable diresidues (RVDs) to target the DNA sequence of interest. Generally, this assembly involved restriction enzyme digest of each N-terminal TALE repeat vector with BsaI and BamHI, followed by digest of its neighboring C-terminal TALE repeat vector with BsaI and BamHI, and finally ligation of these neighboring repeats by T4 DNA ligase. TALEN expression vectors  were digested with SacII and BamHI to obtain the DNA-binding domain comprising the ∆152 N-terminal domain, the RVD repeats, and the +63 C-terminal domain. This fragment was ligated into a modified pDONR221 vector (Invitrogen), with SacII and BamHI restriction sites internal to attL recombination sites, to create Gateway-compatible TALE Entry clones.  The TALE constructs were then transferred by Gateway recombinational cloning into the pDEST15 expression vector, which adds an N-terminal glutathione S-transferase (GST) tag (Invitrogen), by an LR reaction. All clones were full-length sequence-verified (Supplementary Data).
Custom PBM design: Target sites for each TALE protein were determined using the canonical TALE code (NI: A, HD: C, NN: G, NG: T), and are preceded by the 5’ T to create the full target site. The constant flanking regions were the same as that used in a prior custom PBM design and do not contain binding sites for any of the TALE proteins in this study . Probe set descriptions, including the array design versions on which they are included, are provided in Supplementary Note. The Agilent AMAD ID for this custom array is 084120.
TALE protein expression: Proteins were expressed using the PURExpress In Vitro Transcription and Translation Kit (New England Biolabs). Protein concentrations were determined by anti-GST western blots with a dilution series of recombinant GST (Sigma). Proteins were stored at 4oC until being used in PBM assays. The duration of storage at 4oC between protein expression and PBM experiments was typically one day, but never greater than three days.
PBM experiments: PBM experiments were performed as follows: briefly, custom-designed microarrays were first double-stranded by an on-slide primer extension reaction. In the PBM assay, arrays were blocked with 2% milk in PBS for 1 h, washed with 0.1% Tween-20 in PBS and 0.01% TX-100 in PBS, then incubated with protein mixture (PBS, 2% milk, 0.2 mg ml-1 BSA, and 0.3 ug ml-1 salmon testes DNA) for 1 h. The final concentration of TALE protein in the PBM reactions was 200 nM, unless otherwise indicated (Supplementary Table 1). Arrays were washed with 0.5% Tween-20 in PBS and 0.01% TX-100 in PBS.

tag: protein class

value: TALE


title: TALE2041Ref_170224_JC_006_1


title: S20_FC_CRT_1


title: IP_YFP_BOX_AMY_1


title: S20_BOX_CRT_1


title: TALE2037VG_160907_JC_001_2


title: S20_BOX_AMY_2


title: TALE2039Ref_170629_JC_009_1


title: S20_BOX_AMY_1


title: S20_BOX_CRT_2


title: L58


title: IP_FC_CRT_1


title: IP_FC_CRT_2


title: L67


title: L62


title: L57


title: IP_FC_AMY_2


title: TALE2037VA_160907_JC_001_2


title: IP_FC_AMY_1


title: TALE2037HG_160907_JC_001_2


title: TALE2036Ref_161202_JC_004_1


title: IP_BOX_CRT_2


title: TALE2036GN_161202_JC_004_1


title: TALE2023Ref_161122_JC_003_1


title: TALE2037Ref_160907_JC_001_2


title: SH-SY5Y SDCCA8 KO SS 2

city: Galway

first: Mairead

last: Flynn

address: Corrib village, NUI Galway

department: Centre for Chromosome Biology

country: Ireland

institute: NUI Galway

data_processing:
Raw fastq files were aligned to GR37 using STAR
Reads were aggregated by gene using HTSeq-counts
Genome_build: GR37
Supplementary_files_format_and_content: HTSEQ files containing reads aggregated by gene

source_name: Immature neuronal cells (SH-SY5Y)

growth_protocol: Baseline conditions 10% FBS

extract_protocol:
Rneasy
TruSeq

treatment_protocol: Cells were grown in 0.1% FBS for 48 hours

value: SDCCAG8 KO

value: Serum starved

value: Immature neuronal cells (SH-SY5Y)


title: IP_BOX_AMY_1


title: SH-SY5Y WT SS 3

value: Wildtype


title: pks-rad-2

city: Washington

first: Zheng

last: Wang

state: DC

address: 4555 Overlook Ave. SW.

department: Center for Bio/Molecular Science and Engineering

institute: US Naval Research Laboratory

description: pks irradiated replica 2

data_processing:
Used hisat2 ( https://ccb.jhu.edu/software/hisat2/index.shtml ) and samtools ( http://www.htslib.org/ ) to build sorted-bam files that map raw RNA-seq to supercontigs of Exophiala dermatitidis NIH / ut8656_1_supercontigs.fasta
Used Trinity ( https://github.com/trinityrnaseq/trinityrnaseq ) to build genome-guided assembly from all RNAseq samples using the sorted-bam files.
Used eXpress ( https://pachterlab.github.io/eXpress/index.html ) for transcript quan-tification to get estimated counts, FPKM & TPM measures for each putative genes.
Used Trinity pipeline to build differential expression matrix, MA plots and gene expression heatmaps.
Used downstream analysis of Trinity to obtain over- and under-expressed genes in different conditions
Genome_build: sed blast to obtain the function of differentially expressed genes as available.

organism: Exophiala dermatitidis

source_name: fungal cells

growth_protocol: Fungal cells grew in YPD for 48 hours at 30 oC

extract_protocol:
RiboPure™ RNA Purification Kit for yeast (ThermoFisher)
iIllumina RNA-seq library standard protocol

treatment_protocol: Cells were irradiated with 1000 Gy gamma radiation (Co60)

value: pks1 mutant

value: irradiated


title: TALE2020VA_161110_JC_002_2


title: IP_BOX_AMY_2

value: Sprague-Dawley

value: Adult (8-10 week old)


title: L4

value: female


title: pks-control-1

description: pks control replica 1

value: control


title: SH-SY5Y SDCCA8 KO SS 1


title: SH-SY5Y WT SS 2


title: TALE2020VG_161110_JC_002_2


title: pks-control-2

description: pks control replica 2


title: pks-rad-1

description: pks irradiated replica 1


title: SH-SY5Y SDCCA8 KO Bas 3

value: Baseline


title: SH-SY5Y SDCCA8 KO Bas 2


title: WT-rad-1

description: wilde type irradiated replica 1

value: wild type

tag: resouce


title: WT-control-2

description: wild type control replica 2


title: SH-SY5Y SDCCA8 KO Bas 1


title: WT-control-1

description: wild type control replica 1


title: SH-SY5Y WT Bas 3


title: SH-SY5Y WT SS 1


title: L56

value: E2 + Pg


title: Endo Rep 5

first: Fasih

middle: Mubtasim

last: Ahsan

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
Fibroblasts, iPSCs, and MSCs were each sequenced in biological triplicates and technical duplicates (n = 60 total samples) to account for variation in extraction and culturing. Raw sequencing reads were converted into fastq files and filtered for low quality reads and Illumina sequencing adapter contamination using bcl2fastq (Illumina). Reads were then quasi-mapped and quantified to the Homo sapiens GENCODE 28 (GRCh38.p12, Ensembl 92, April 2018) transcriptome using the alignment-free transcript level quantifier Salmon v0.9.1 8-10. A quasi-mapping index was prepared using parameters “salmon index -k 31 –type quasi”, and comprehensive transcript level estimates were calculated using parameters “salmon quant -l A –seqBias –gcBias --discardOrphansQuasi”. Transcript level counts were collapsed to gene level (HGNC) counts, transcripts per million abundances (TPM) and estimated lengths using R Bioconductor package tximport v1.6.0 11.
The resulting sample gene count matrix was size factor normalized and analyzed for pairwise differential gene expression using R Bioconductor package DESeq2 v1.18.1. Expression changes were estimated using an empirical Bayes procedure to generate moderated fold change values with design “~ Batch + Sample”, modeling batch effect variation due to day of RNA extraction 12,13.  Significance testing was performed using the Wald test, and resulting P values were adjusted for multiple testing using the Benjamini-Hochberg procedure 14. DEGs were filtered using an adjusted false discovery rate (FDR) q value < 0.05 and an absolute log2 transformed fold-change > 1.
Variance stabilized transform (VST) values in the gene count matrix were calculated and plotted for PCA using R Bioconductor packages DESeq2, FactoMineR, and factoextra 12,13. Whole transcriptome PCA was performed with comparison to existing RNA-sequencing data of nutrient balanced trilineage differentiations previously provided in GEO: GSE101655 1. RNA-sequencing samples were batch effect normalized across library preparation differences between this study and previously published reports 1 using limma v3.34.9 15. PCA of nucleus-encoded mitochondrial protein and mtDNA transcripts were extracted using localization evidence derived from MitoMiner v4.0, subsetting VST matrices using genes listed in MitoCarta 2.0 16,17. Scatterplots and MA plots of gene expression fold-changes between fibroblasts, iPSCs, and MSCs were performed, and Pearson/Spearman correlation coefficients calculated, using R package ggpubr v0.1.6 (https://cran.r-project.org/web/packages/ggpubr/index.html). Genes of interest were extracted and averaged clonal heatmaps were prepared using R Bioconductor packages pheatmap v1.0.8 and gplots v3.0.1 18,19. Venn diagram intersections of DEG lists were generated using Venny 2.1.0 (http://bioinfogp.cnb.csic.es/tools/venny/index.html)
Genome_build: Homo sapiens GENCODE 28 (GRCh38.p12, Ensembl 92, April 2018)
Supplementary_files_format_and_content: Salmon v0.9.1 quantification output files for each respective sample after quasi-mapping to the GENCODE 28 reference transcriptome. Columns are (in order): (1) Name of transcript from GENCODE 28 reference, (2) Length of the transcript (nt), (3) Effective length of the transcript, correcting for sequencing and GC fragment bias, (4) transcripts per million of the transcript (TPM), and (5) number of estimated reads mapping to each quantified transcript.

source_name: H9-derived hPSC differentiation culture

growth_protocol: All work with human embryonic stem cells (hESCs) has been approved under the UCLA Institutional Biosafety Committee (IBC) and UCLA Embryonic Stem Cell Research Oversight (ESCRO) Committee under Protocol # 2007-003-12. H9 (WA09 – Female; RRID:CVCL_9773), H1 (WA01 – Male; RRD:CVCL_9771), HSF-1 (Male; RRID:CVCL-D003), hiPS2 (Male; RRID: CVCL_B508) and UCLA-1 (Female; RRID:CVCL_9951) primed human pluripotent stem cells (hPSCs) were provided low-passage and contamination tested through the UCLA BSCRC hESC Core Bank (Jerome Zack, UCLA). Following receipt, hPSCs were shifted to feeder-free Matrigel (Corning) in mTeSR1 medium (Stemcell Technologies) and passaged using Gentle Cell Dissociation Reagent (Stemcell Technologies). 6-wells plates were coated with 1:10 Matrigel (Corning) and incubated for 30 minutes prior to seeding. 80-90% confluent hPSCs were incubated in Gentle Cell Dissociation Reagent (Stemcell Technologies) for 8 minutes at 37C, dissociated to single cells using a 40μm cell strainer, and harvested in plain media (DMEM/F12; Gibco) for counting. Cells were centrifuged at 450xg for 5 minutes.

extract_protocol:
All cells were grown to 70-80% confluence and purified using the RNeasy Mini Kit (Qiagen) and RNase-free DNase (Qiagen) following the manufacturer’s protocols. All samples showed a A260/280 ratio > 1.99 (Nanodrop; Thermo Scientific). For RNA-Sequencing, prior to library preparation, quality control of the RNA was performed using the Advanced Analytical Technologies Fragment Analyzer (Advanced Analytical, Inc.) and analyzed using PROSize 2.0.0.51 software. RNA Quality Numbers (RQNs) were computed per sample between 8.1 and 10, indicating intact total RNA per sample prior to library preparation.
Strand-specific ribosomal RNA (rRNA) depleted RNA-Seq libraries were prepared from 1 µg of total RNA using the KAPA Stranded RNA-Seq Kit with Ribo-Erase (Kapa Biosystems, Roche). Briefly, rRNA was depleted from total RNA samples, the remaining RNA was heat fragmented, and strand-specific cDNA was synthesized using a first strand random priming and second strand dUTP incorporation approach. Fragments were then A-tailed, adapters were ligated, and libraries were amplified using high-fidelity PCR. All libraries were prepared in technical duplicates per sample (n = 30 samples, 60 libraries total), and resulting raw sequencing reads merged for downstream alignment and analysis. Libraries were paired-end sequenced at 2x150 bp on an Illumina NovaSeq 6000.

treatment_protocol: Ectoderm Differentiation:  1.2 x 106 cells were seeded in each well of a 6 well plate in mTeSR1 media (Stemcell Technologies) with 10 μM ROCK inhibitor (Y-27632; Stemcell Technologies). Media was changed to differentiation media 24 hours after seeding. hPSCs were differentiated over a 5-day period by culturing in a 50% DMEM/F12 and 50% IMDM-based medium (Gibco) supplemented with 450 μM monothioglycerol (Millipore Sigma), 1 mg/ml BSA (Gibco), 0.11 μM 2-mercaptoethanol (Gibco), 1% Glutamax (Gibco), 1% N2 supplement (Thermofisher), 2% B27 supplement (Thermofisher), 10 μM SB43154 (Stemgent), and 0.2 μM Dorsomorphin (Stemgent).     Mesoderm Differentiation:  1.8 x 106 cells were seeded in each well of a 6 well plate in mTeSR1 media with 10 μM ROCK inhibitor (Y-27632; Stemcell Technologies). hPSCs were differentiated over a 5-day period by culturing in a 50% DMEM/F12 and 50% IMDM-based medium (Gibco) supplemented with 450 μM monothioglycerol (Millipore Sigma), 1 mg/ml BSA (Gibco), 0.11 μM 2-mercaptoethanol (Gibco), 1% Glutamax (Gibco), 0.7 µg/mL insulin (Millipore Sigma), 15 µg/mL transferrin (Millipore Sigma), 1 mL/100mL chemically-defined lipid concentrate (Gibco), 100 ng/mL VEGF-165 (Stemcell Technologies), 100 ng/mL BMP4 (Peprotech), and 20 ng/mL FGF2 (Peprotech). Medium for the first 24 hours of differentiation was supplemented with 100 ng/mL Activin A (Stemcell Technologies).    Endoderm Differentiation:  1.8 x 106 cells were seeded in each well of a 6 well plate in mTeSR1 media with 10 μM ROCK inhibitor (Y-27632; Stemcell Technologies). hPSCs were differentiated over a 3-day period by culturing in a 50% DMEM/F12 and 50% IMDM-based medium (Gibco) supplemented with 450 μM monothioglycerol (Millipore Sigma), 1 mg/ml BSA (Gibco), 0.11 µM 2-mercaptoethanol (Gibco), and 1% Glutamax (Gibco). Medium for the first 24 hours was supplemented with 100 ng/mL Activin A (Stemcell Technologies), 2 µM CHIR99021 (Cayman Chemicals), and 50 nM PI-103 (Fisher Scientific). Medium after the first 24 hours was supplemented with 100 ng/mL Activin A (Stemcell Technologies), and 250 nM LDN 1931189 (Stemgent).    Embryoid Body Differentiation :  3.5 x 106 cells per well were seeded in AggreWell EB Formation Media (Stemcell Technologies) with 10 μM ROCK inhibitor (Y-27632; Stemcell Technologies) into 6-well AggreWell 400 plates (Stemcell Technologies) for consistent size and shape. Within 24 hours, embryoid bodies were harvested through a cell strainer and transferred to 6-well Ultra-Low Attachment plates (Corning Costar) and grown in DMEM/F12 (Gibco) supplemented with 20% KnockOut Serum Replacement (Gibco), 1% Glutamax (Gibco), 1% Penicillin/Streptomycin (Corning), 1% Non-Essential Amino Acids (Corning), and 0.1 mM 2-mercaptoethanol (Gibco). Media was changed every day throughout 21 days of differentiation. For DCA treated condition, media was supplemented with 1mM dichloroacetate (DCA; Millipore Sigma). For glutamine deprivation condition, DMEM/F12 without glutamine (Gibco) was used and Glutamax (Gibco) was excluded from media preparation.

tag: lineage day

tag: passage number

value: Unknown

tag: experiment date

tag: rna extraction date

tag: lineage

value: Endo

tag: number of cells


title: SH-SY5Y WT Bas 2

tag: condition

tag: cell type


title: DLD1 KO2

city: Hangzhou

first: Kefeng

last: Ding

state: Zhejiang Province

address: 88 Jiefang Road

department: Department of Colorectal Surgery

country: China

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

data_processing:
data filtering was performed using trim Galore(version 0.3.7)
reads were aligned to the hg19 using STAR(version 2.5)
sequence assembly was performed using cufflinks(version 2.2.1)
differentially expressed genes were screened using DESeq(version 1.22.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: DLD1_BEX2 KO

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

tag: cell line

value: colorectal cancer cell line

tag: tumor stage

value: III

tag: genotype/variation

value: BEX2 knocked out


title: TALE2020HG_161110_JC_002_2

value: TALE


title: TALE2017HG_161205_JC_004_2


title: TALE2020Ref_161110_JC_002_2


title: WT-rad-2

description: wilde type irradiated replica 2

tag: strain

tag: genotype


title: TALE2017Ref_161205_JC_004_2


title: DLD1 KO1


title: Ecto Rep 6

value: Ecto


title: TALE2016Ref_161202_JC_004_1


title: Meso Rep 6

value: Meso


title: DLD1


title: TALE2016NHv6_170428_JC_007_2


title: TALE2017VG_161205_JC_004_2


title: TALE2016NHv4_170428_JC_007_2


title: TALE2016NHv3_170428_JC_007_2


title: hPSC Rep 7

value: hPSC


title: RPE1 SDCCA8 KO SS 2

source_name: Retinal epithelial cells (hTERT-RPE1)

value: SDCCAG8 KO

value: Serum starved

value: Retinal epithelial cells (hTERT-RPE1)


title: SH-SY5Y WT Bas 1

value: Wildtype

value: Immature neuronal cells (SH-SY5Y)


title: Endo Rep 4


title: TALE2016NHv2_170428_JC_007_2


title: TALE2016NHv1_170428_JC_007_2


title: TALE2016NHv5_170428_JC_007_2


title: RPE1 SDCCA8 KO SS 3


title: Ecto Rep 5


title: RPE1 WT SS 3


title: RPE1 WT SS 2


title: RPE1 WT SS 1


title: Meso Rep 5


title: TALE2016GNv6_170525_JC_004_3


title: TALE2016GNv5_170525_JC_004_3


title: RPE1 SDCCA8 KO Bas 2

value: Baseline


title: RPE1 SDCCA8 KO Bas 1


title: Bulk_RNAseq_adult_rep3

city: Houston

first: Hongjie

last: Li

state: TX

address: one Baylor Plaza

institute: Baylor College of Medicine

description: RNAseq

data_processing:
Sequencing libraries were prepared from amplified cDNA using tagmentation (Nextera XT, Illumina). Sequencing was performed using the Nextseq 500 platform (Illumina) with paired-end 75 bp reads.
Reads were aligned to the Drosophila melanogaster genome (r6.10) using STAR (2.4.2a)
Uniquely mapped reads that overlap with genes were counted using HTSeq-count (0.7.1) (Anders et al., 2015) with default settings except "–m intersection–strict".
To normalize for comparison among samples, we rescaled gene counts to counts per million (CPM). All analyses were performed after converting gene counts to logarithmic space via the transformation log2(CPM+1).
Genome_build: Drosophila melanogaster genome (r6.10)
Supplementary_files_format_and_content: CSV file with gene expression normalized as Log2(CPM+1)

organism: Drosophila melanogaster

source_name: olfactory projection neurons

growth_protocol: Drosophila were raised on standard cornmeal medium with a 12h/12h light cycle at 25°C,

extract_protocol:
Cells are FACS sorted using GFP marker
SMART-seq2

treatment_protocol: No treatment

tag: age

value: 5d adult

tag: cell collection

value: FACS

tag: cell number


title: RPE1 SDCCA8 KO Bas 3


title: hPSC Rep 6

value: Unknown


title: RPE1 WT Bas 3


title: Ecto Rep 4


title: Meso Rep 4


title: Bulk_RNAseq_adult_rep2

description: RNAseq


title: hPSC Rep 5


title: A549-shCTRL, biological rep1

city: guangzhou

first: Dongcheng

last: Liu

state: guangdong

address: zhongshan 2nd road

department: Institute of Human Virology and Ministry of Education Key Laboratory of Tropical Disease Control

institute: Sun Yat-sen University

description: Gene expression data from A549 cells treated with shcontrol lentivirus

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: A549 cell infected with shcontrol lentivirus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A549 cells were cultured in RPMI-1640 with 10% FBS

extract_protocol: Total RNA  was extracted with a Qiagen RNeasy Mini Kit according to the manufacturer’s instructions.

treatment_protocol: A549 cells were infected with shMETTL7B or shcontrol lentivirus.

value: NSCLC A549 cell


title: TALE2016GNv4_170525_JC_004_3

tag: protein class


title: A549-shCTRL, biological rep2


title: TALE2016GNv3_170525_JC_004_3


title: Bulk_RNAseq_adult_rep1

description: RNAseq


title: hPSC Rep 4

tag: lineage day


title: RPE1 WT Bas 2


title: A549-shCTRL, biological rep3


title: TALE2016GNv1_170525_JC_004_3


title: RPE1 WT Bas 1


title: A549-shMETTL7B, biological rep2

description: Gene expression data from A549 cells treated with shMETTL7B  lentivirus

source_name: A549 cell infected with shMETTL7B lentivirus


title: A549-shMETTL7B, biological rep3


title: Bulk_RNAseq_development_rep3

description: RNAseq

value: 36h APF


title: hPSC Rep 3

tag: passage number


title: A549-shMETTL7B, biological rep1


title: Ecto Rep 3

tag: experiment date


title: TALE2016ENv6_170503_JC_008_1


title: Bulk_RNAseq_development_rep2

description: RNAseq


title: Bulk_RNAseq_development_rep1

description: RNAseq


title: TALE2016ENv3_170503_JC_008_1


title: TALE2016ENv5_170503_JC_008_1


title: TALE2016ENv4_170503_JC_008_1


title: TALE2016ENv2_170503_JC_008_1


title: Endo Rep 3

tag: rna extraction date

value: Endo


title: SH-SY5Y SDCCA8 KO SS 3


title: hPSC Rep 2

tag: lineage


title: Zebrafish_larva, EM_32_rep1

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

data_processing:
High-throughput sequencing raw image data files were converted to reads using fqtools_plus analysis.
We used FastqC (v0.11.8) to evaluate the raw read quality statistics.
Reads were mapped to the zebrafish genome (Ensembl v95) by Hisat2 (v2.0.5) with parameters “--dta -x --rna-strandness RF” and “--known-splicesite-infile” followed by gene annotation in GTF format (Ensembl v95).
The output of Hisat2 were converted to BAM format and sorted by Samtools (v1.5).
Genome_build: GRCz11
Supplementary_files_format_and_content: HTSeq (0.9.1) was used to count reads mapped to each gene with parameters “-t exon –i gene_id -r pos -s reverse”.

organism: Danio rerio

source_name: EM 32d replicates1

growth_protocol: Zebrafish (AB strain) were obtained from China Zebrafish Resource Center and maintained at 28.5 oC with a light/dark cycle of 14/10 h.  For each juvenile sample, fifty embryos of zebrafish were maintained in a petri dish from 0 dpf, and transferred to a three-litter tank in the recirculation systems at 5 dpf. They were fed with paramecium at 5-15 dpf and fairy shrimp at 16-32 dpf twice a day.

extract_protocol:
RNA samples from each individual were exacted using Trizol (Invitrogen) according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL, RNA purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA), quantified its concentration with Qubit 3.0 Flurometer (Life Technologies, CA, USA), RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
All the sequencing libraries were prepared at Annoroud (Beijing, China)using VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme Biotech) following the official protocol.

treatment_protocol: The AI EM (6-methylenandrosta-1, 4-diene-3, 17-dione, ≥ 98% purity, Bervita) used for  juvenile zebrafish was dissolved in 10 μg/L DMSO. Two groups of juvenile zebrafish were also raised in continuous exposure to 10 μg/L EM or the solvent control for 32 days.

tag: tissue

value: Whole body

value: AB

tag: treatment

tag: library type

value: fr-firststrand (dUTP)


title: Zebrafish_larva, EM_32_rep3

source_name: EM 32d replicates3


title: Zebrafish_larva, EM_32_rep2

source_name: EM 32d replicates2


title: 10x, sample 2

first: Rory

last: Kirchner

address: 677 Huntington Ave

department: Department of Biostatistics

institute: Harvard T.H. Chan School of Public Health

data_processing:
inDrop FASTQ files were transformed to put the cellular barcodes, UMI and sample barcodes into the read name and demultiplexed into the two samples using umis (https://github.com/vals/umis).
Demultiplexed FASTQ files were filtered by matching known cellular barcodes for inDrop-v3, correcting for an edit distance of one.
FASTQ files were aligned to FlyBase gene build r6.27 of Drosophila using RapMap and reads per gene were counted using the umis repository.
A sparse matrix of UMI deduped reads-per-gene-per cell was generated as a gene x cell sparse matrix for both samples combined.
10x data was run through CellRanger v3.1.0 against Flybase build r6.27 of Drosophila
The sparse matrix was filtered for low quality cells, inspecting a combination of genes per cell, UMI counts per cell, mitochondrial content per cell, transcriptome complexity per cell and other metrics.
Genome_build: Drosophila, FlyBase release r6.27
Supplementary_files_format_and_content: counts.csv.gz: A gzipped CSV gene x cell matrix (16986 x 10606) of UMI deduped counts. metadata.csv.gz: a gzipped CSV of cells x metadata (10606 x 16). metadata-code-book.md describes each of the columns in the metadata.csv file.

growth_protocol: Drosophila guts were dissociated to single cells as previously described (Dutta et al., 2015) with a few modifications. Guts were dissected from 7-day old adult esg-sfGFP/+, pros- Gal4>RFP/+ females. After pulling out the gut, the crop and midgut/hindgut junction (where the Malpighian tubules branch out of the gut) and Malpighian tubules were removed. Five flies at a time were dissected and immediately transferred into cold PBS containing 1% BSA to avoid exposing the midgut tissue to room temperature for a long period of time. Once 40 guts were dissected, they were transferred to a dissection plate and chopped into small pieces using a razor blade. These small fragments were immediately transferred to an eppendorf tube containing 400 ul of 1 mg/ml elastase/PBS solution (Sigma E0258) and incubated on a shaker at 27  ̊C for 30 min. 1% of BSA in PBS (final concentration) was used to stop the digestion reaction and prevent cells from aggregating. The cell suspension was passed through 100 m and then a 25 um cell strainer and loaded on the top of Optiprep with density gradient 1.12 g/ml. Viable cells were isolated from the top layer of the sample after centrifugation at 800xg for 20 min. Cell viability and number were assessed by 0.4% trypan blue and hemocytometer.

extract_protocol:
Cells (>160 cells/ul) were encapsulated at the Single Cell Core from ICCB-Longwood screening facility with inDrop (Zilionis et al., 2017).
For inDrop samples: Reverse transcription and library preparation were done at the same facility as previously described (Zilionis et al., 2017). 10x cells were prepared following the manufacturer's protocol.

value: esg-sfGFP/+, pros- Gal4>RFP/+

value: 7-day old adult

tag: Sex

value: female

value: gut

tag: technology


title: inDrop, sample 2

tag: genotype/variation

value: inDrop


title: inDrop, sample 1


title: Meso Rep 3

value: Meso

tag: number of cells


title: Ecto Rep 2

value: Ecto


title: Meso Rep 2


title: Zebrafish_larva, DMSO_32_rep1

source_name: DMSO 32d replicates1

tag: strain


title: Zebrafish_larva, DMSO_32_rep2

source_name: DMSO 32d replicates2

tag: age


title: Zebrafish_larva, DMSO_32_rep3

source_name: DMSO 32d replicates3


title: 10x, sample 1


title: Z6_Zebrafish_gonad_adult_female_R2

growth_protocol: Zebrafish (AB strain) were obtained from China Zebrafish Resource Center and maintained at 28.5℃ with a light/dark cycle of 14/10 h.  three pairs of adult zebrafish were kept in a three-liter tank in the recirculation systems and fed twice a day with fairy shrimp.

extract_protocol:
RNA samples from each individual were exacted using Trizol (Invitrogen) according to the manufacturer's protocol. RNA was enriched from total RNA by removing rRNA using NEBNext rRNA Depletion Kit (New England Biolabs). We assessed the overall quality of extracted RNA by GEL, RNA purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA), quantified its concentration with Qubit 3.0 Flurometer (Life Technologies, CA, USA), RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
All the sequencing libraries were prepared at Meiyin (Beijing, China) using VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme Biotech) following the official protocol.

treatment_protocol: None.

value: ovary

value: adult


title: Endo Rep 2


title: TALE2016ENv1_170503_JC_008_1

value: TALE


title: TALE2016DNv5_170426_JC_007_1


title: Endo Rep 1


title: Z1_Zebrafish_gonad_adult_female_R1


title: O

city: Trondheim

first: Tonje

middle: Marita Bjerkan

last: Heggeset

address: Postboks 4760 Torgarden

department: Industry

country: Norway

institute: SINTEF

data_processing:
Adaptor sequences, reads with >5% unknown bases, or with >20% bases with below Q10 quality were removed by filtering by BGI, Hong Kong, China using BGI proprietary software, resulting in the clean reads (the raw data files provided here), which were used as basis for functional annotation of the Aurantiochytrium sp. T66 draft genome (GenBank assembly accession: GCA_001462505.1, performed by BGI, Hong Kong, China) in combination with de novo prediction, and for transcript abundance measurements.
Tandem repeats were identified using Tandem Repeats Finder (TRF) and transposable elements by a combination of a homology-based and de novo approaches, using RepeatMasker and RepeatProteinMask, with the database of known repeats, Repbase.
RepeatModeler, Piler, and LTR-Finder were used to build a de novo repeat library from the T66 genome, and to search for long terminal repeat retrotransposons (LTR).
De novo gene prediction was performed based on the repeat-masked genome using AUGUSTUS, SNAP, and GlimmerHMM. Homologous proteins of the species Aureococcus anophagefferens, Nannochloropsis gaditana, Phaeodactylum tricornutum, Phytophthora infestans, Phytophthora sojae, and Thalassiosira pseudonana were mapped to the genome using tblastn with an E-value cutoff 1·e-5. The aligned sequences as well as their corresponding query proteins were then filtered and passed to GeneWise to search for accurately spliced alignments. Source evidences generated from these approaches were then integrated by GLEAN  to produce a consensus gene set.
Cleaned RNA-seq reads were aligned against the genome using TopHat to identify candidate exon regions and the donor and acceptor sites. Then Cufflinks was used to assemble the alignments into transcripts. Finally, open reading frames were predicted based on the assembled candidate transcript sequences using HMM-based training parameters, and the GLEAN set was combined with the transcripts from the RNA-Seq to generate a final gene set.
Gene functions were assigned by blastP searches against the Swissprot and TrEMBL databases, while Gene Ontology identifiers were assigned by InterProScan.
Finally the functional annotation of genes of interest was further curated by manual inspection and evaluation of blastn, blastp, and Position-Specific Iterated BLAST, PSI-blast, alignments with the hits from the NCBI nucleotide collection (nr/nt) and the non-redundant protein sequences (nr) in combination with the best hits from Swissprot and TrEMBL, in particular taking into consideration the fraction of the gene aligning to the hits (denoting all with less than 50% of the overall length as fragments) and the identity scores in the case of hits from multiple enzyme classes.
By comparison to the Thraustochytrium sp. ATCC 26185 and Hondaea fermentalgiana FCC1311 draft assemblies, 4 genes, encoding pfaA (T66011701), pfaC (T66011702), pfaD (T66011703), and glutamine synthase (T66011704) that were fragmented/missing in the original gene list were reconstructed, yielding a final list of coding sequences (supplementary file T66_Genemodels.fa), which was used as the reference file for read alignment.
Transfer-RNAs (tRNAs) were found by tRNAscan-SE. Small nuclear RNA (snRNA) and microRNA (miRNA) were identified by blastn followed by INFERNAL searches against the Rfam database. Ribosomal RNA (rRNA), were found by blastN searches against rRNA.
Read alignment and expression analysis was performed in CLC Genomics Workbench v. 11.0 (QIAGEN). Raw reads were mapped onto the reference sequence T66_Genemodels by the RNA-Seq Analysis 2.16 tool in the "One reference sequence per transcript" mode, selecting for RPKM as the expression value. Expression levels in the samples were compared pairwise using the Differential Expression for RNA-Seq 1.0 tool. The data files were then combined by the Create Expression Browser 1.0 tool.
Columns with functional gene annotation were finally added to the resulting gene expression table, generating the T66_RNA-Seq.txt table file.
Genome_build: T66_Genemodels.fa
Supplementary_files_format_and_content: T66_RNA-Seq.txt is a tab-delimited text file and includes the output from the RNA-Seq analysis pipeline integrated with curated functional annotation for genes of interests as well as best hit annotation from BLAST-queries against the Swissprot/TREmbl databases; T66_Genemodels.fa is the reference file used for read alignment

organism: Aurantiochytrium sp. T66

source_name: T66 culture

growth_protocol: Aurantiochytrium sp T66 (ATCC PRA-276) was cultivated in 3 l bioreactors with 1.5 l culture medium, which were inoculated with 60 ml (4 %) actively growing culture. The fermentation medium contained initially (g/l): Glycerol 90, Sodium-glutamate hydrate 25, NaCl 14.4, CaCl2·2H2O 0.5, MgCl2 0.8, KCl 0.4, KH2PO4 4.0, Na2SO4 3.0, maleic acid 5.8, 6.1 Tris base 6.1, cyanocobalamin 5·10-6, thiamine·HCl 5·10-5, trace mineral solution 1.5 ml (Jakobsen et al. 2007)[12], Sodium-ampicillin (0.3), and streptomycin sulphate (0.3). The antibiotics were used as a general precaution against bacterial contamination. Antifoam (Clerol FBA 622) was added as required. The bioreactors containing the medium were heat sterilized at 121°C for 30 min. Phosphate was autoclaved separately, and the trace mineral and vitamin solutions were filter sterilized. The glycerol concentration was always kept above 15 g/l, by subsequent additions (3-4 times). The temperature was 28°C, and pH was controlled at 7.0 ±0.2 by addition of 3 N NaOH or 3N H2SO4. The aeration rate was 0.3 vvm (0.45 l/min), and the dissolved oxygen was controlled at 20 % of saturation by automatically adjustment. Inoculum for the fermentations was cultivated in 500 ml baffled Erlenmeyer flasks with 100 ml medium, on a rotary shaker (28°C, 150 rpm). The medium was the same as the fermentation medium, but with glycerol reduced to 30 g/l. Four replicate fermentations were run at each of the two conditions (N-starvation and O2-limitation) and sampling for RNA-extraction was made from 3 of the replicates.

extract_protocol:
RNA was isolated using the Spectrum™ Plant Total RNA Kit (Sigma). The On-Column DNase I Digest Set (SIGMA) was used to remove DNA. RNA integrity was evaluated on a Bioanalyzer 2100 with the Plant RNA Nano assay and software v. 1.3 resulting in RIN values of 8.9 – 9.5 for the 12 samples. The RNA concentrations were measured on a Qubit 2.0 Fluorometer using the QubitTM BR Assay Kit (Invitrogen), while RNA purity was evaluated by nanodrop spectroscopy, where a A260/280 ratio of ~2.0 generally was accepted as pure for RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols by BGI, Hong Kong, China.

treatment_protocol: Five ml culture was centrifuged (3500 x g, 10 min at room temperature). All supernatant was carefully removed. The pellet was resuspended in deionized water to a standardised optical density and centrifuged (12 000 g, 5 min), the supernatant removed, and the pellet frozen at -80°C.

tag: growth stage

value: Late O2-starvation


title: TALE2016DNv6_170426_JC_007_1


title: N2

value: Late N-starvation


title: hPSC Rep 1

value: hPSC

value: Unknown


title: Ecto Rep 1


title: Z51_Zebrafish_gonad_adult_male_R2

value: testis

value: male


title: E

value: Exponential growth


title: TALE2016DNv4_170426_JC_007_1


title: Z46_Zebrafish_gonad_adult_male_R1

value: AB

value: fr-firststrand (dUTP)


title: N1

value: Close to N-depletion


title: TALE2016DNv1_170426_JC_007_1


title: TALE2016DNv3_170426_JC_007_1


title: CK

status: Public on Dec 18 2019

city: Beijing

first: Guohong

address: 17 Qing Hua East Road, Hai Dian District

institute: China Agricultural University

description: Sample 1

data_processing:
Image analysis and base-calling takes place automatically on the computer that runs the sequencer in real time, or Real Time Analysis (RTA). CASAVA (Version: 1.8.2) is used to convert BCLs into FASTQ file.
BWA (Version: 0.5.9-r16) is used to align reads to reference genome.
Cufflinks (Version: 2.0.0)  is utilized to calculate FPKM (Fragments Per Kilobase of transcript per Million fragments mapped).
DEGseq (Version: 1.10.0) is used to identify differentially expressed genes. MARS (MA-plot-based method with Random Sampling model, Wang et al. 2009) method is used to identify differentially expressed genes.
Genome_build: ASM892v1 (GCA_000008925.1)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene of sample.

organism: Ligilactobacillus salivarius str. Ren

source_name: L. salivarius Ren growing in the absence (CK) of oxgall

growth_protocol: Volumes of 200 ml of fresh MRS were inoculated at 1% (v/v) with fresh overnight cultures and incubated anaerobically at 37 °C.

extract_protocol:
Total RNA isolation was carried out using TRIzol reagent (Invitrogen) as the manufacturer’s instructions, and purified using a Ribo-Zero rRNA Removal Kit (Illumina) to eliminate ribosomal RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For bile stress treatment, oxgall (Sigma) was added to a final concentration of 0.75 g liter-1. Cultures were harvested when the optical density at mid-exponential phase (OD600 of 0.6).

value: Ren

tag: stress


title: Mpeg 14 days post injury Round2_cryo2

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

description: 2 trangenic alleles: mpeg1 BAC driving biotin ligase and ubiqutously-driven Avi-tagged nuclear envelope protein

data_processing:
Reads were mapped using STAR (v.2.4.2a) to danRer10 and read counts were obtained using subreads FeatureCounts
Differential Expression analysis was performed using DESeq2 R package.
Genome_build: danRer10

source_name: Mpeg 14 days post injury Round2_cryo2

extract_protocol:
For nuclei isolation, hearts were dissected at appropriate time points and  washed in hypotonic buffer H (20 mM HEPES (pH 7.9), 15 mM MgCl2, 10 mM KCl, 1 mM DTT, and 1 X Complete protease inhibitor) and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B, every 5 minutes for 15 minutes. Nuclei were collected by centrifugation (2000 g, 4 °C) and resuspended in 1 mL buffer NDP (10 mM HEPES (pH 7.9), 40 mM NaCl, 90 mM KCl, 0.5 mM EDTA, 0.5 mM spermidine, 0.15 mM spermine, 1 mM dithiothreitol and 1 X Complete protease inhibitor). For nuclei purification, nuclei were incubated with 5 mg of M-280 streptavidin-coated dynabeads with rotation for 30 minutes at 4 °C. A flow-based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette (VWR, cat # 8913-898) attached to a 1 mL micropipette tip (Rainin reach pipet tip, cat # RT-L1000S), both pre-treated with NPB/BSA for 30 minutes, and added to a MiniMACS separator magnet (OctoMACS Separator, Miltenyl Biotec, cat # 130-042-109). A two-way stopcock (Biorad cat # 732-8102) was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing (Fisher Scientific, cat # 8220) and the flow-rate set to ~0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X-100 (NPBt) and added to the slow-flow setup. The tip was subsequently removed from the stand and the nuclei-beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow-flow setup. Nuclei-beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand (DynaMag TM-2 magnet, Invitrogen, cat # 12321D). Nuclei-beads were then processed for RNA extraction.
RNA extraction and DNAse treatment were carried out using the RNAqueous®-Micro Kit (Life Technologies, cat # AM1931). RNA integrity was checked with a RNA pico chip (Agilent Technologies, cat # 5067-1513) using the Agilent 2100 Bioanalyzer.
cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART-seqTMv4 ultra low input kit for RNA (Clontech laboratories, cat #’s 634888, 634889, 634890, 634891, 634892, 634893, and 634894). Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads (150 cycles) (Illumina, cat # FC-404-1002).

tag: development

value: Adult

tag: stage post injury

value: 14 days post injury

value: macrophages

value: In vivo Biotinylated Macrophage Nuclei

value: cryoinjury

tag: strand

value: reverse


title: Mpeg 14 days post injury Round2_cryo3

source_name: Mpeg 14 days post injury Round2_cryo3


title: BS

description: Sample 2

source_name: L. salivarius Ren growing in the presence (BS) of oxgall

value: 0.075% oxgall


title: TALE2009Ref_170224_JC_006_1

source_name: Protein expressed by NEB PureExpress IVT kit (NEB product # E6800L)

tag: protein class

value: TALE


title: IP_BOX_CRT_1

value: Sprague-Dawley

tag: ge

value: Adult (8-10 week old)

tag: training group

value: Box control

value: Cortex

tag: ip bait

tag: rna sample

value: IP


title: Mpeg 14 days post injury Round2_sham3

source_name: Mpeg 14 days post injury Round2_sham3

tag: tissue

tag: treatment

value: sham injury


title: Mpeg 14 days post injury Round1_sham2

source_name: Mpeg 14 days post injury Round1_sham2


title: Mpeg 14 days post injury Round1_sham1

source_name: Mpeg 14 days post injury Round1_sham1


title: Mpeg 14 days post injury Round1_sham3 merged


title: Mpeg 5 days post injury resec2

source_name: Mpeg 5 days post injury resec2

value: 5 days post injury

value: resection


title: Mpeg 14 days post injury Round2_cryo1 merged


title: Mpeg 5 days post injury cryo1

source_name: Mpeg 5 days post injury cryo1


title: Mpeg 5 days post injury resec1

source_name: Mpeg 5 days post injury resec1


title: Mpeg 5 days post injury cryo4

source_name: Mpeg 5 days post injury cryo4


title: TALE2003Ref_161123_JC_003_3


title: TALE2016DNv2_170426_JC_007_1


title: Mpeg 5 days post injury sham3

source_name: Mpeg 5 days post injury sham3


title: TALE2003NH_161123_JC_003_3


title: TALE2009NH_170224_JC_006_1


title: Mpeg 1days post injury resec3

source_name: Mpeg 1days post injury resec3

value: 1 days post injury


title: Mpeg 1 days post injury cryo2

source_name: Mpeg 1 days post injury cryo2

value: Adult


title: Mpeg 1 days post injury sham2

source_name: Mpeg 1 days post injury sham2


title: Mpeg 1 days post injury cryo3

source_name: Mpeg 1 days post injury cryo3


title: Mpeg 5 days post injury sham2 merged

source_name: Mpeg 5 days post injury sham2 merged


title: Mpeg 1days post injury resec2

source_name: Mpeg 1days post injury resec2


title: WT primary hepatocyte EV_Chow Diet_12 week

city: Nanjing

first: YUE

last: ZHAO

state: Jiangsu

address: Rm 2113, MengMinWei Building, Gulou Campus

department: Medical School

institute: Nanjing University

description: miRNA expression after 12-week CD-induced WT mice primary hepatocytes-derived EV

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings. Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary hepatocyte of  WT mice, chow diet

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVanaTM PARISTM (Cat # AM1556, Ambion, Austin, TX, US), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Primary hepatocytes isolated from WT or LKO mice were incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2, followed by EV extraction and purification.

tag: gender

value: male

value: 20 week


title: KO primary hepatocyte EV_HFD_12 week

description: miRNA expression after 12-week HFD-induced LKO mice primary hepatocytes-derived EV

source_name: primary hepatocyte of Ggpps LKO mice, high fat diet


title: SCbeta_rep3_entrained_RNA-seq_CT56

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Sequencing reads were mapped to the human hg38 reference genome assembly using STAR (Dobin et al., 2013) with default parameters. Gene expression based on GENCODE annotations (Harrow et al., 2012) was determined using RSEM (Li and Dewey 2011). Genes with expected count values >=10 across all samples were retained, normalized by library scaling using DESeq2 (Love, et al. 2014), and used for downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files containing RSEM output for each sample

source_name: HUES 8 hESC line

growth_protocol: Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ºC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).

extract_protocol:
Total RNA was isolated using the miRNeasy kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was depleted from total RNA using the Ribo-Zero Gold Kit (Epicentre, Madison, WI).
Directional cDNA libraries were prepared using a KAPA Biosystems Stranded RNA-seq Library Preparation kit, pooled, and sequenced on an Illumina HiSeq2000 platform across multiple lanes.

tag: cell line

value: HUES 8 hESC line

value: hPSC-derived islet

value: entrained to circadian metabolic rhythms


title: SCbeta_rep3_entrained_RNA-seq_CT64


title: Mpeg 1 days post injury resec4

source_name: Mpeg 1 days post injury resec4

value: macrophages

value: In vivo Biotinylated Macrophage Nuclei

value: reverse


title: SCbeta_rep3_entrained_RNA-seq_CT68


title: SCbeta_rep3_entrained_RNA-seq_CT52


title: SCbeta_rep3_entrained_RNA-seq_CT44


title: SCbeta_rep3_entrained_RNA-seq_CT40


title: SCbeta_rep3_entrained_RNA-seq_CT36


title: SCbeta_rep3_entrained_RNA-seq_CT32


title: TALE2003GN_161123_JC_003_3

source_name: Protein expressed by NEB PureExpress IVT kit (NEB product # E6800L)

value: TALE


title: SCbeta_rep3_entrained_RNA-seq_CT48


title: Mpeg 1 days post injury sham3

source_name: Mpeg 1 days post injury sham3


title: KO primary hepatocyte EV_Chow Diet_12 week

description: miRNA expression after 12-week chow diet-induced LKO mice primary hepatocytes-derived EV

source_name: primary hepatocyte of Ggpps LKO mice, chow diet


title: SCbeta_rep3_entrained_RNA-seq_CT60


title: Mpeg 1 days post injury sham1

source_name: Mpeg 1 days post injury sham1


title: SCbeta_rep3_entrained_RNA-seq_CT20


title: SCbeta_rep3_entrained_RNA-seq_CT28


title: SCbeta_rep3_entrained_RNA-seq_CT24


title: SCbeta_rep3_entrained_RNA-seq_CT12


title: WT primary hepatocyte EV_HFD_12 week

description: miRNA expression after 12-week HFD-induced WT mice primary hepatocytes-derived EV

source_name: primary hepatocyte of WT mice, high fat diet


title: SCbeta_rep3_entrained_RNA-seq_CT16


title: SCbeta_rep3_Mock-treated_RNA-seq_CT16

value: mock-treated


title: SCbeta_rep3_entrained_RNA-seq_CT0


title: SCbeta_rep3_entrained_RNA-seq_CT8


title: SCbeta_rep3_entrained_RNA-seq_CT4


title: SCbeta_rep3_Mock-treated_RNA-seq_CT20


title: SCbeta_rep3_Mock-treated_RNA-seq_CT8


title: SCbeta_rep3_Mock-treated_RNA-seq_CT4


title: SCbeta_rep3_Mock-treated_RNA-seq_CT0


title: SCbeta_rep2_entrained_RNA-seq_CT68


title: SCbeta_rep3_Mock-treated_RNA-seq_CT12


title: SCbeta_rep2_entrained_RNA-seq_CT64


title: SCbeta_rep2_entrained_RNA-seq_CT56


title: SCbeta_rep2_entrained_RNA-seq_CT60


title: SCbeta_rep2_entrained_RNA-seq_CT44


title: SCbeta_rep2_entrained_RNA-seq_CT28


title: SCbeta_rep2_entrained_RNA-seq_CT48


title: SCbeta_rep2_entrained_RNA-seq_CT36


title: SCbeta_rep2_entrained_RNA-seq_CT40


title: SCbeta_rep2_entrained_RNA-seq_CT20


title: SCbeta_rep2_entrained_RNA-seq_CT52


title: SCbeta_rep2_entrained_RNA-seq_CT24


title: SCbeta_rep2_entrained_RNA-seq_CT32


title: SCbeta_rep2_entrained_RNA-seq_CT8


title: SCbeta_rep2_entrained_RNA-seq_CT12


title: SCbeta_rep2_entrained_RNA-seq_CT16


title: SCbeta_rep2_entrained_RNA-seq_CT4


title: SCbeta_rep2_entrained_RNA-seq_CT0


title: SCbeta_rep2_Mock-treated_RNA-seq_CT0


title: SCbeta_rep1_entrained_RNA-seq_CT68


title: SCbeta_rep2_Mock-treated_RNA-seq_CT4


title: SCbeta_rep2_Mock-treated_RNA-seq_CT12


title: SCbeta_rep2_Mock-treated_RNA-seq_CT8


title: SCbeta_rep1_entrained_RNA-seq_CT64


title: SCbeta_rep1_entrained_RNA-seq_CT56


title: SCbeta_rep1_entrained_RNA-seq_CT52


title: SCbeta_rep1_entrained_RNA-seq_CT48


title: SCbeta_rep1_entrained_RNA-seq_CT40


title: SCbeta_rep1_entrained_RNA-seq_CT44


title: SCbeta_rep1_entrained_RNA-seq_CT60


title: SCbeta_rep1_entrained_RNA-seq_CT36


title: SCbeta_rep1_entrained_RNA-seq_CT28


title: SCbeta_rep1_entrained_RNA-seq_CT16


title: SCbeta_rep1_entrained_RNA-seq_CT24


title: SCbeta_rep1_entrained_RNA-seq_CT8


title: SCbeta_rep1_entrained_RNA-seq_CT12


title: SCbeta_rep1_Mock-treated_RNA-seq_CT20


title: SCbeta_rep1_entrained_RNA-seq_CT20


title: SCbeta_rep1_Mock-treated_RNA-seq_CT8


title: SCbeta_rep2_Mock-treated_RNA-seq_CT20


title: SCbeta_rep2_Mock-treated_RNA-seq_CT16


title: SCbeta_rep1_Mock-treated_RNA-seq_CT4


title: SCbeta_rep1_Mock-treated_RNA-seq_CT12


title: HI_entrained_RNA-seq_CT52

source_name: Primary human adult islets

value: Primary human adult islet


title: SCbeta_rep1_Mock-treated_RNA-seq_CT0


title: HI_entrained_RNA-seq_CT48


title: HI_entrained_RNA-seq_CT60


title: HI_entrained_RNA-seq_CT64


title: HI_entrained_RNA-seq_CT36


title: HI_entrained_RNA-seq_CT56


title: HI_entrained_RNA-seq_CT40


title: HI_entrained_RNA-seq_CT24


title: HI_entrained_RNA-seq_CT32


title: HI_entrained_RNA-seq_CT16


title: HI_entrained_RNA-seq_CT28


title: SCbeta_rep1_entrained_RNA-seq_CT4


title: HI_entrained_RNA-seq_CT12


title: SCbeta_rep1_entrained_RNA-seq_CT32


title: SCbeta_rep1_entrained_RNA-seq_CT0


title: SCbeta_rep1_Mock-treated_RNA-seq_CT16


title: HI_entrained_RNA-seq_CT8


title: HI_entrained_RNA-seq_CT4


title: HI_Mock-treated_RNA-seq_CT16


title: HI_Mock-treated_RNA-seq_CT12


title: HI_entrained_RNA-seq_CT0


title: HI_Mock-treated_RNA-seq_CT8


title: HI_Mock-treated_RNA-seq_CT4


title: HI_Mock-treated_RNA-seq_CT0


title: AJ76_RNA_rep5

city: Seattle

first: David

last: Hawkins

state: WA

address: 1959 NE Pacific St, HSB K226

department: Division of Medical Genetics, Department of Genome Sciences

institute: University of Washington

description: STARR-seq reporter RNA

data_processing:
Library strategy: STARR-seq
STARR-seq raw reads were checked for adapter sequences and low quality reads (q score < 20) using FASTQC and trimmed using TrimGalore package. Trimmed reads were mapped to human genome (hg19) using the Bowtie2 aligner. The mapped reads were quantified against all tested sequences using ‘featureCounts’ function from Rsubread package.
We retained tested sequences for downstream analysis only if it contain reads at minimum in three biological replicates for both RNA and plasmid libraries. The RNA and plasmid read counts were normalized by respective library size and the normalized silencer element activity (fold change) is defined as ratio of RNA to plasmid counts averaged over biological replicates divided by mean ratio of RNA to plasmid counts of random control regions for each tested sequence. One-tailed t-test was used to find significant differences in tested silencer activity over control random regions activity. The computed P-values are adjusted with Benjamini-Hochberg method to control for false discovery rate. Then, the potential silencers were identified as sequences with fold change less than one and adjusted P-value < 0.05.
Genome_build: hg19

source_name: Synthetic Oligos

extract_protocol:
Qiagen RNeasy Plus Mini kit and Qiagen Plasmid Plus Mini kit, mRNA enrichment was done using polyT Dynabeads and  RT was performed by superscript III reverse trascriptase.
Reporter-specific libraries were generate by first using reporter-specific primers during RT and PCR. Sequencing libraries were prepared according to Illumina's instructions. A standard flow cell adapters and indexes were added to all DNA and cDNA reactions through an 6 cycles of PCR.The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Nextseq 500/550 v2 75 cycle mid-output kit following the manufacturer's protocols.

tag: cell type


title: AJ86_DNA_rep4

description: STARR-seq reporter plasmid DNA

library_source: genomic

molecule: genomic DNA


title: AJ87_DNA_rep5

description: STARR-seq reporter plasmid DNA


title: AJ85_DNA_rep3

description: STARR-seq reporter plasmid DNA


title: AJ84_DNA_rep2

description: STARR-seq reporter plasmid DNA


title: AJ72_RNA_rep1

description: STARR-seq reporter RNA


title: AJ74_RNA_rep3

description: STARR-seq reporter RNA


title: AJ75_RNA_rep4

description: STARR-seq reporter RNA


title: AJ73_RNA_rep2

description: STARR-seq reporter RNA


title: D1_Uninfected

city: Fort WORTH

first: Kathleen

last: Borgmann

address: 3500 Camp Bowie Blvd

department: Pharmacology and Neuroscience

institute: University of North Texas Health Science Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4).
Data were quality trimmed using fastq-mcf (ea-utils/v1.1.2-806).
Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat.
Duplicates were marked using picard-tools (v1.127 https://broadinstitute.github.io/picard/).
Read counts were generated using featureCounts (36) and the differential expression analysis was performed using edgeR.
Genome_build: hg19 (UCSC version from igenomes)
Supplementary_files_format_and_content: tab-delimited text file

source_name: primary astrocytes Donor 1

growth_protocol: Human astrocytes were isolated from brain tissues recovered from first- and early second-trimester conceptual tissues by mechanical dissociation and passaging until 99% pure.

extract_protocol:
Total RNA was extracted from sorted cell populations using the Trizol reagent method (Thermofisher).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Red/Green-HIV-1-WT/D116A were obtained from NIH AIDS Reagent Program (#12427 and #12428, respectively). Astrocytes were spinoculated with VSVG-psuedotyped R/G-HIV at 35,000 unit of reverse transcriptase activity/ml. R/G-HIV exposed astrocytes were cultured for two weeks and were passaged every seven days. Cells were sorted by Fluorescent activated cell sorting (Sony) by mCherry and GFP reporter expression.

value: fetal brain

tag: passage(s)

tag: Sex

value: unknown

tag: gestational age (days)

tag: condition

value: no infection


title: D3_Uninfected

source_name: primary astrocytes Donor 3

value: Female


title: D3_RGH_D116A

value: integrase deficient infection (R-/G-)


title: D1_RGH_WT_plus_plus

value: active infection (R+/G+)


title: D3_RGH_WT_plus_plus


title: D1_RGH_WT_plus_minus

value: latent infection (R+/G-)


title: D2_RGH_D116A

source_name: primary astrocytes Donor 2

value: Male


title: D2_RGH_WT_plus_plus


title: D1_RGH_D116A


title: single cell RNAseq [Patient 4]

city: Miami

first: Michael

last: Durante

state: FL

department: Ophthalmology

institute: University of Miami Miller School of Medicine

data_processing:
CellRanger (3.0.2) “mkfastq” command was used to generate fastq files from Illumina bcl files.
CellRanger (3.0.2) “count” command was used to generate bam files and raw gene-barcode matrices aligned to the GRCh38 Ensembl build 93 genome.
Genome_build: GRCh38 Ensembl build 93
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mx

source_name: human respiratory epithelium

extract_protocol:
Single cell suspensions from olfactory and respiratory epithelium were generated and run on the 10X genomics Chromium instrument using the 3' single cell RNA-seq v2 and v3 kits.
10X genomics 3' single cell RNA-seq v2 and v3.

value: Respiratory epithelium

tag: age

value: Adult


title: single cell RNAseq [Patient 3]

source_name: human olfactory epithelium

value: Olfactory epithelium


title: single cell RNAseq [Patient 1]


title: AJ83_DNA_rep1

description: STARR-seq reporter plasmid DNA


title: D3_RGH_WT_plus_minus


title: N703 OVX1

city: Sydney

last: Gallego Ortega

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

description: scRNAseq Dropseq

data_processing:
Data has been processed using the instructions in the McCarroll lab:
http://mccarrolllab.org/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf
Data visualisation and analuysis has been generated using the Seurat package version 2
Genome_build: mm10
Supplementary_files_format_and_content: DGE (txt matrix genes by cells)

source_name: vaginal epithelium

extract_protocol: Cell suspensions were generated as described in Ali et al. Cell Reports 2019, briefly: vaginae were dissected out, washed with Ca2+ and Mg2+ free Hanks Balanced Salt Solution (HBSS), and were slit open to expose the epithelium during subsequent enzymatic digestion. The tissues were placed in DMEM/F12 containing 1mg/ml pronase (Sigma) and 0.5mg/ml DNase1 (Sigma) at 4°C overnight with slow shaking. Enzymatic digestion was stopped by adding DMEM/F12 medium (Sigma) supplemented with 10% fetal bovine serum. The epithelium was then squeezed out with the help of a pair of forceps under the dissecting microscope. Following two successive washes in DMEM/F12, the single cell suspension was prepared using 40µm cell strainer before capture.

treatment_protocol: OVX mice were surgically ovarectimised

value: vaginal epithelium

value: Ovarectomised

tag: strain


title: N704 OVX2

description: scRNAseq Dropseq


title: N702 WT2

description: scRNAseq Dropseq

value: WT


title: D2_RGH_WT_plus_minus


title: D2_Uninfected


title: N701 WT1

description: scRNAseq Dropseq


title: single cell RNAseq [Patient 2]


title: HFD.34wk.3.technical_replicate.3

city: Cambrdge

first: Ramya

last: Gamini

address: 1 Portland st

institute: Pfizer Inc.,

data_processing:
Base calling, de-multiplexing and adapter removal were performed using Illumina BaseSpace. The encoding version is Illumina 1.9
Reads were aligned to the GRCm38.2 (mm10, patch release 2) mouse genome assembly with STAR (Version 2.5).
Alignment: STAR v2.5.2b was used for alignment with the following settings: "--alignSJDBoverhangMin 1 $limitBAMsortRAM --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0.90 --outFilterMatchNminOverLread 0.90 --alignIntronMax 1000000"
Gene level counts were calculated using FeatureCounts -subread(Version 1.5.1) with following parameter: --minOverlap 25
The raw read counts for each gene is the combined sum of read counts of the three (3) technical replicates
Normalization using edgeR-TMM and differential expression with voom and limma using default parameters in R3.4
Genome_build: Genome_build: GRCm38.2 (mm10, patch release 2)
Supplementary_files_format_and_content: comma separated normalized value (CPM) for each expressed gene (in rows) in each sample (in columns)

source_name: perigonadal adipocytes

growth_protocol: Perigonadal adipose tissue was harvested from male C57/Bl6 mice at the end of treatment time.

extract_protocol:
Isolated adipocytes were snap frozen in trizol were thawed on ice and then transferred to Fastprep matrix D lysing tubes (Mp Biomedicals) for homogenization using a Qialyzer instrument (Qiagen). Cells were homogenized with 2 cycles of 2 minutes at 20 1/s frequency, rotating tubes within holders (outside to inside and vice-versa) between rounds. RNA was extracted from the adipocyte homogenates using the RNeasy Lipid Tissue Mini kit and the Qiagen user-developed protocol titled Purification of total RNA from fatty tissues using the RNeasy® Lipid Tissue Mini Kit and MaXtract High Density (Qiagen). On-column DNA digest was performed for all samples according to manufacturer protocol (Qiagen). RNA was quantified using a Nanodrop 8000 spectrophotometer and quality was assessed using an Agilent 4100 Bioanalyzer (Agilent).
cDNA libraries for RNA-seq analysis were prepared from total RNA (isolated as described above) according to Illumina TruSeq stranded mRNA sample prep LS protocol.

treatment_protocol: Male C57/Bl6 mice were fed either chow diet or high fat diet for 8, 20 or 34 weeks.

tag: tag

value: adipocytes

tag: treatment duration

value: 6 weeks + 34 weeks

tag: genotype

value: HFD


title: HFD.34wk.1.technical_replicate.3


title: CD.34wk.7.technical_replicate.3

value: CD


title: HFD.34wk.6.technical_replicate.3


title: CD.34wk.8.technical_replicate.3


title: HFD.34wk.4.technical_replicate.3


title: HFD.34wk.2.technical_replicate.3


title: HFD.34wk.5.technical_replicate.3


title: CD.34wk.6.technical_replicate.3


title: CD.34wk.3.technical_replicate.3


title: CD.34wk.4.technical_replicate.3


title: CD.34wk.5.technical_replicate.3


title: HFD.20wk.3.technical_replicate.3

value: 6 weeks + 20 weeks


title: HFD.20wk.5.technical_replicate.3


title: HFD.20wk.4.technical_replicate.3


title: CD.20wk.6.technical_replicate.3


title: HFD.20wk.6.technical_replicate.3


title: HFD.20wk.1.technical_replicate.3


title: CD.34wk.2.technical_replicate.3


title: CD.34wk.1.technical_replicate.3


title: HFD.20wk.2.technical_replicate.3


title: CD.20wk.4.technical_replicate.3


title: CD.20wk.1.technical_replicate.3


title: CD.20wk.5.technical_replicate.3


title: HFD.8wk.5.technical_replicate.3

value: 6 weeks + 8 weeks


title: HFD.8wk.6.technical_replicate.3


title: CD.20wk.2.technical_replicate.3


title: HFD.8wk.4.technical_replicate.3


title: HFD.8wk.3.technical_replicate.3


title: HFD.34wk.4.technical_replicate.2


title: CD.8wk.4.technical_replicate.3


title: CD.8wk.5.technical_replicate.3


title: Meso Rep 1

city: Boston

source_name: H9-derived hPSC differentiation culture

extract_protocol:
All cells were grown to 70-80% confluence and purified using the RNeasy Mini Kit (Qiagen) and RNase-free DNase (Qiagen) following the manufacturer’s protocols. All samples showed a A260/280 ratio > 1.99 (Nanodrop; Thermo Scientific). For RNA-Sequencing, prior to library preparation, quality control of the RNA was performed using the Advanced Analytical Technologies Fragment Analyzer (Advanced Analytical, Inc.) and analyzed using PROSize 2.0.0.51 software. RNA Quality Numbers (RQNs) were computed per sample between 8.1 and 10, indicating intact total RNA per sample prior to library preparation.
Strand-specific ribosomal RNA (rRNA) depleted RNA-Seq libraries were prepared from 1 µg of total RNA using the KAPA Stranded RNA-Seq Kit with Ribo-Erase (Kapa Biosystems, Roche). Briefly, rRNA was depleted from total RNA samples, the remaining RNA was heat fragmented, and strand-specific cDNA was synthesized using a first strand random priming and second strand dUTP incorporation approach. Fragments were then A-tailed, adapters were ligated, and libraries were amplified using high-fidelity PCR. All libraries were prepared in technical duplicates per sample (n = 30 samples, 60 libraries total), and resulting raw sequencing reads merged for downstream alignment and analysis. Libraries were paired-end sequenced at 2x150 bp on an Illumina NovaSeq 6000.

tag: lineage day

tag: passage number

tag: experiment date

tag: rna extraction date

tag: lineage

value: Meso

tag: number of cells


title: HFD.8wk.2.technical_replicate.3

tag: tissue


title: HFD.34wk.6.technical_replicate.2


title: CD.20wk.3.technical_replicate.3


title: HFD.34wk.5.technical_replicate.2


title: HFD.34wk.2.technical_replicate.2


title: CD.34wk.8.technical_replicate.2


title: CD.34wk.7.technical_replicate.2


title: CD.8wk.2.technical_replicate.3


title: CD.8wk.6.technical_replicate.3


title: HFD.34wk.1.technical_replicate.2


title: CD.34wk.3.technical_replicate.2


title: CD.34wk.4.technical_replicate.2


title: HFD.34wk.3.technical_replicate.2


title: CD.34wk.5.technical_replicate.2


title: CD.34wk.1.technical_replicate.2


title: CD.34wk.2.technical_replicate.2


title: HFD.20wk.6.technical_replicate.2


title: CD.8wk.1.technical_replicate.3


title: HFD.20wk.4.technical_replicate.2


title: HFD.20wk.3.technical_replicate.2


title: HFD.20wk.2.technical_replicate.2


title: HFD.8wk.1.technical_replicate.3


title: CD.8wk.3.technical_replicate.3


title: CD.34wk.6.technical_replicate.2


title: CD.20wk.5.technical_replicate.2


title: HFD.20wk.1.technical_replicate.2


title: HFD.20wk.5.technical_replicate.2


title: CD.20wk.1.technical_replicate.2


title: CD.20wk.3.technical_replicate.2


title: CD.20wk.2.technical_replicate.2


title: CD.20wk.6.technical_replicate.2


title: HFD.8wk.6.technical_replicate.2


title: HFD.8wk.5.technical_replicate.2


title: HFD.8wk.2.technical_replicate.2


title: HFD.8wk.1.technical_replicate.2


title: CD.8wk.6.technical_replicate.2


title: CD.8wk.5.technical_replicate.2


title: HFD.8wk.3.technical_replicate.2


title: HFD.34wk.5.technical_replicate.1


title: HFD.34wk.6.technical_replicate.1


title: CD.8wk.2.technical_replicate.2


title: HFD.34wk.3.technical_replicate.1


title: HFD.34wk.4.technical_replicate.1


title: CD.8wk.3.technical_replicate.2


title: HFD.34wk.1.technical_replicate.1


title: HFD.34wk.2.technical_replicate.1


title: CD.34wk.8.technical_replicate.1


title: CD.34wk.6.technical_replicate.1


title: CD.34wk.7.technical_replicate.1


title: CD.34wk.5.technical_replicate.1


title: CD.20wk.4.technical_replicate.2


title: HFD.8wk.4.technical_replicate.2


title: CD.34wk.2.technical_replicate.1


title: CD.8wk.4.technical_replicate.2


title: CD.34wk.1.technical_replicate.1


title: CD.34wk.4.technical_replicate.1


title: CD.34wk.3.technical_replicate.1


title: HFD.20wk.5.technical_replicate.1


title: CD.8wk.1.technical_replicate.2


title: CD.20wk.6.technical_replicate.1


title: HFD.20wk.3.technical_replicate.1


title: HFD.20wk.2.technical_replicate.1


title: CD.20wk.5.technical_replicate.1


title: CD.20wk.2.technical_replicate.1


title: CD.20wk.1.technical_replicate.1


title: HFD.20wk.1.technical_replicate.1


title: CD.20wk.4.technical_replicate.1


title: HFD.8wk.5.technical_replicate.1


title: HFD.8wk.4.technical_replicate.1


title: HFD.8wk.3.technical_replicate.1


title: CD.20wk.3.technical_replicate.1


title: HFD.8wk.1.technical_replicate.1


title: CD.8wk.5.technical_replicate.1


title: CD.8wk.4.technical_replicate.1


title: HFD.8wk.2.technical_replicate.1


title: CD.8wk.6.technical_replicate.1


title: CD.8wk.3.technical_replicate.1


title: HFD.20wk.4.technical_replicate.1


title: HFD.20wk.6.technical_replicate.1


title: CD.8wk.1.technical_replicate.1


title: CD.8wk.2.technical_replicate.1


title: HFD.8wk.6.technical_replicate.1


title: P7_day7_2

first: Thomas

middle: J

last: Cahill

address: Sherrington Building, Sherrington Rd

department: Department of Physiology, Anatomy, & Genetics

institute: University of Oxford

data_processing:
Reads were mapped to the mouse genome (Mm10) using TopHat15 v2.1.10, with Bowtie16 v.2.2.6
Cuffdiff used for pair-wise comparisons
DESeq2 was used to identify genes showing differential temporal regulation and STEM v.1.3.8 was used for temporal clustering
Genome_build: Mm10

extract_protocol:
Single cell cardiac tissue suspensions were prepared by mincing hearts and gentle agitation in collagenase 500 units per ml in HBSS solution for 1 hour at 37degC. Samples were passed through a 70um filter, washed and resuspended in 2% FBS/PBS. Samples were incubated with FcR-block, and then labelled with anti-CD45 (Biolegend 103124, 1:200), anti-CD11b (Biolegend 101206, 1:100), anti-Ly6G (Biolegend 127636, 1:200), anti-F4/80 (Biolegend 123110, 1:100), anti-Ly6C (Biolegend 128026 1:800), anti-CD206 (Biolegend 141721, 1:100). Macrophages were identified as CD45+ CD11b+ Ly6G- F4/80+ cells
RNA extraction and DNAse treatment were carried out using the RNAqueous®-Micro Kit (Life Technologies, cat # AM1931). RNA integrity was checked with a RNA pico chip (Agilent Technologies, cat # 5067-1513) using the Agilent 2100 Bioanalyzer.
cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART-seqTMv4 ultra low input kit for RNA (Clontech laboratories, cat #’s 634888, 634889, 634890, 634891, 634892, 634893, and 634894). Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads (150 cycles) (Illumina, cat # FC-404-1002).

tag: development

value: Neonate P7

tag: stage post injury

value: Day 7 post MI

value: Macrophages

value: FACS

tag: treatment

value: Myocardial infarction

tag: strand

value: reverse


title: P7_day7_0


title: P7_day7_1


title: P7_day4_1

value: Day 4 post MI


title: P7_day4_0


title: P1_day7_1

value: Neonate P1


title: P7_pre_2

value: Baseline


title: P7_pre_1


title: P1_pre_2


title: P1_day4_2


title: P1_day7_2


title: P1_day4_1


title: P1_pre_1


title: P7_pre_0


title: P1_day7_0