title: 5xFAD_12_F [GT19.12897]

city: Bar Harbor

first: Christoph

last: Preuss

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

hyb_protocol: manufacturer's protocol

scan_protocol: manufacturer's protocol

data_processing: The NanoString Mouse AD gene expression panel was used for gene expression profiling on the nCounter platform (NanoString, Seattle, WA) as described by the manufacturer. nSolver software was used for analysis of NanoString gene expression values.Normalization was done by dividing counts within a lane by geometric mean of the housekeeping genes from the same lane. For the downstream analysis, counts were log-transformed from normalized count values.

label_protocol: manufacturer's protocol

growth_protocol: All mice were bred and housed in a 12/12 hour light/dark cycle. All experiments were performed on a unified genetic background (C57BL/6J).

extract_protocol: Upon arrival at the terminal endpoint for each aged mouse cohort, individual animals were weighed prior to intraperitoneal administration of ketamine (100mg/kg) and xylazine (10mg/kg). First confirming deep anesthetization via toe pinch, an incision was made along the midline to expose the thorax and abdomen followed by removal of the lateral borders of the diaphragm and ribcage revealed the heart. A small cut was placed in the right atrium to relieve pressure from the vascular system before transcardially perfusing the animal with 1XPBS via injection into the left ventricle. With the vascular system cleared, the entire brain was carefully removed and weighed before hemisecting along the midsagittal plane. Hemispheres were immediately placed in a cryovial and snap-frozen on dry ice. Brain samples were stored at -80°C until RNA extraction was performed. RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher, Waltham, MA). Brain hemispheres were thawed to 0°C and were lysed and homogenized in TRIzol Reagent (ThermoFisher). After the addition of chloroform, the RNA-containing aqueous layer was removed for RNA isolation according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA Total RNA Nano assay (Agilent Technologies, Santa Clara, CA).

tag: strain

tag: genotype/variation

value: 5xFAD mouse model carrying transgenes with a total of five AD-linked familial mutations in APP and PSEN1

tag: age (months)

value: F

value: Brain hemisphere


title: ω3LC1_T7_1: Liver_diet_fish1

status: Public on Feb 03 2020

type: RNA

city: St. John's

first: Xi

last: Xue

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: Equal quantities (825 ng) of each labeled aRNA (refer to label protocol) from one experimental sample and the common reference were pooled, fragmented following the manufacturer's instructions and co-hybridized to a cGRASP-designed Agilent 44K salmonid oligonucleotide microarray (GEO accession # GPL11299) as per the manufacturer’s instructions (Agilent, Mississauga, ON). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately following hybridization as per the manufacturer's instructions.

scan_protocol: Each microarray was scanned at 5 µm resolution and 90% of laser power using a ScanArray Gx Plus scanner and ScanArray Express software (v4.0; Perkin Elmer, Woodbridge, ON) with photomultiplier tube (PMT) set to balance fluorescence signal between channels.

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (median background + 2 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene.

molecule: total RNA

organism: Salmo salar

source_name: Liver tissue, ω3LC1 diet, individual fish

label_protocol: Eight individual fish from each experimental diet groups were used in the microarray analysis using a common reference design. An equal quantity of each DNase I-treated, column-purified liver total RNA sample involved in the microarray experiment was pooled to make a common reference for the microarray hybridizations. Anti-sense amplified RNA (aRNA) was in vitro transcribed from 1 µg of each experimental RNA or reference pooled RNA using Ambion's Amino Allyl MessageAmp II aRNA Amplification kit (Life Technologies), following the manufacturers' instructions. The quality and quantity of aRNA were assessed using UV spectrophotometry and agarose gel electrophoresis. Twenty µg of aRNA was precipitated overnight following standard molecular biology procedures and re-suspended in coupling buffer; the resulting solution was used in a labeling reaction following the manufacturer's protocol. Resulting aRNA was labeled with either Cy3 (for the common reference) or Cy5 (for the experimental individuals) fluor (GE HealthCare, Mississauga, ON) through a dye-coupling reaction, following the manufacturer's instructions. The labeling efficiency was measured using the microarray function of the NanoDrop spectrophotometer.

growth_protocol: Atlantic salmon post-smolts (average weight 178 g) were randomly distributed among 12 tanks (500 L) with flow-through seawater  (~12°C, dissolved oxygen ≥ 10 mg L-1), and all fish were kept on a photoperiod of 12 hours light / 12 hours dark. Quadruplicate tanks of fish were fed each experimental diet to apparent satiety, twice each day for a period of 14 weeks. At the end of trial, 5 fish from each tank were euthanized with 400 mg L-1 of tricaine-methane-sulfonate (TMS; Syndel Laboratories, Vancouver, BC) after 24 h of fasting. Body weight and fork length of fish were measured and recorded. Liver tissues (50-100 mg sample-1) were rapidly dissected from fish, placed in RNase-free 1.5 mL tubes, flash-frozen in liquid nitrogen, and stored at -80°C until RNA extractions were performed.

extract_protocol: Liver samples were homogenized in 1 ml of TRIzol reagent (Invitrogen/Life Technologies, Burlington, ON) with stainless steel beads (5 mm; QIAGEN, Mississauga, ON) using a TissueLyser (QIAGEN), frozen on dry ice and stored at -80°C. Frozen homogenates were slowly thawed on wet ice and the TRIzol total RNA extractions were then completed following the manufacturer’s instructions. Due to low 260/230 ratios (i.e. ranging from 0.9 to 1.7) following TRIzol extraction, all RNA samples were re-extracted using the phenol-chloroform phase separation method. Briefly, to separate the TRIzol-extracted RNA from organic materials, an equal volume of acid phenol:chloroform:isoamyl alcohol (125:24:1) (pH 4.5) (AM9720; Ambion/Life Technologies) was added to the samples, vortexed for 30 sec and centrifuged at 16,100 x g at 4°C for 20 min. The RNA was then recovered from the aqueous layer from the previous step by precipitation with 0.1 volumes of 3 M sodium acetate (pH 5.5) (Ambion/Life Technologies) and 2.5 volumes of anhydrous ethyl alcohol (Commercial Alcohols Inc., Brampton, ON) at -80°C for 1 h, followed by centrifugation at 16,100 x g at 4°C for 30 min. To wash the resulting RNA pellet, 1 ml of 75% ethanol was added and centrifuged at 16,100 x g at 4°C for 20 min. The ethanol was removed, and the RNA pellet was air-dried at room temperature for 10 min and resuspended in nuclease-free water (Invitrogen/Life Technologies). Total RNA of each sample was then treated with DNase I (QIAGEN) to degrade residual genomic DNA, and all samples were purified from salts, proteins and nucleotides using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s protocols.

tag: tissue

value: Liver

tag: life stage

value: Juvenile

source_name: pool of RNAs from liver tissues invovled in the microarray experiment (i.e. FO, 100COSEFM10CM)


title: ω3LC1_T34_1: Liver_diet_fish5


title: HEK293 WT

type: SRA

city: Miyazaki City

first: Hideki

last: Nishitoh

state: Miyazaki Prefecture

address: 5200 Kihara, Kiyotake

department: Department of Medical Sciences

country: Japan

institute: University of Miyazaki

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using tophat2 v2.0.13 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

organism: Homo sapiens

source_name: Human embryonic kidney

extract_protocol:
mRNAs were isolated from total RNA by NEBNEXT Poly(A) mRNA Magnetic Isolation Module (NEBE7490).
NEBNext mRNA Library Prep Master Mix Set for Illumina (E6110) was used with 250 ng of mRNA for the construction of sequencing libraries according to the manufacturer's protocol.

value: Human embryonic kidney

tag: cell line

tag: genotype

value: wild-type

tag: passage


title: 5xFAD_6_M [GT19.12892]

country: USA

organism: Mus musculus

tag: gender

value: M


title: ω3LC1.4_T3_4: Liver_diet_fish2

source_name: Liver tissue, ω3LC1.4 diet, individual fish


title: 5xFAD_4_F [GT19.12896]


title: 5xFAD_12_M [GT19.12893]


title: ω3LC0_T35_3: Liver_diet_fish8

source_name: Liver tissue, ω3LC0 diet, individual fish


title: ω3LC1.4_T26_1: Liver_diet_fish5


title: SmallRNA.mouse.testis.wt.adult.Untreat.ox.rep1

city: Rochester

first: Xin

last: Li

state: NY

address: 601 Elmwood Ave.

department: Biochemistry and biophysics

institute: University of Rochester Med Center

description:
Small RNAseq
small RNA

data_processing:
Analyses were performed using piPipes v1.4. All data from the small RNA sequencing, ribosome profiling (Ribo-seq), RNA sequencing, and degradome sequencing were analyzed using the latest mouse genome release mm10 (GCA_000001635.7), and green lizard genome release anoCar2 (GCA_000090745.1). Generally, one mismatch is allowed for genome mapping.
For small RNA sequencing, libraries were normalized to the sum of total miRNA reads; spike-in RNA was used to normalize the libraries with and without RNase treatment. Uniquely mapping reads >23 nt were selected for further piRNA analysis. To ensure precision of the mapping, a piRNA is counted only when the 5´-end of the piRNA maps to the uORF or UDR of a transcript.
For RNA-seq reads, the expression per transcript was normalized to the top quartile of expressed transcripts per library calculated by Cuffdiff, and the tpm (transcripts per million) value was quantified using the Salmon software.
For Ribo-seq analysis, uniquely mapping reads between 26 nt and 32 nt were selected for further analysis. Libraries from harringtonine treatment were further normalized to the sum of reads mapping to mitochondrial coding sequences. Libraries from puromycin treatment were further normalized to the sum of reads mapping to the 5´-UTR of mRNAs.
For Degradome data, reads were aligned to the genome using TopHat 2.0.12. Reads were mapped uniquely using the ‘-g 1’ flag. Uniquely mapping reads were selected for further analysis. Libraries were normalized to the sum of reads mapping to mRNA protein-coding regions, assuming that mRNA cleavage was largely unchanged during spermatogenesis.
Genome_build: Mouse: mm10 (GCA_000001635.7, GRCm38), Lizard: anoCar2 (GCA_000090745.1, AnoCar2.0).
Supplementary_files_format_and_content: For Small RNAseq, Ribo-seq and Degradome, processed data files are unique genome alignment results in BED2 format (https://github.com/bowhan/piPipes/wiki/smallRNA-seq). RNAseq quantification results are .sf files output by Salmon software.

source_name: testis

growth_protocol: Animals mice were maintained and used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester. Lizards were used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560), and rRNAs were depleted from total RNAs with complementary DNA oligomers (IDT) and RNaseH (Invitrogen, Waltham, MA, USA).
Small RNAseq: Small RNA libraries were constructed and sequenced using oxidation to enrich for piRNAs by virtue of their 2´-O-methyl-modified 3´ termini. The oxidation procedure selects against in vitro-digested products with a 3´ phosphate. A 25-mer RNA with 2´-O-methyl-modified 3´ termini (5´-UUACAUAAGAUAUGAACGGAGCCCmG -3´) was used as a spike-in control. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG.

treatment_protocol: The mice were anesthetized with Ketamine/Xylazine mixture (Ketamine 100 mg/kg; Xylazine 25 mg/kg) via intraperitoneal injection. After complete anesthesia, testes were exteriorized with a longitudinal incision around 1 cm at the center of abdomen. The tunica albuginea was penetrated using a sharp 26 G needle (BD, Franklin Lakes, NJ, USA, 30511) 1 mm from the vascular pedicle, and the needle was withdrawn to generate path for introducing a blunt end Hamilton needle (Hamilton, Reno, NV, USA, 7786-02). PBS containing 0.02% Fast Green FCF (Thermo Fisher Scientific, Waltham, MA, USA) with harringtonine (LKT labs, 0.5 μg/μl in a total volume of 10 μl) or puromycin dihydrochloride (Invitrogen, 2.5 μg/μl in a total volume of 10 μl) was slowly injected using a Hamilton microsyringe (1705RN) into one testis, and vehicle control without drug was injected into the other testis. The needle was held in place for 30 seconds before removal to prevent back flow of the solution. Successful completion of injection was indicated by testis filled with green solution. The testes were returned to the abdominal cavity after injection. The incisions were sutured. At the end point, the mice were euthanized by cervical dislocation, and the testes were collected.

value: whole testis

tag: strain/background

value: wt

tag: age

value: adult


title: ω3LC1_T38_3: Liver_diet_fish8


title: ω3LC1_T20_2: Liver_diet_fish4


title: ω3LC0_T35_1: Liver_diet_fish7


title: SmallRNA.mouse.testis.wt.adult.RNase.ox.rep1

description:
Small RNAseq
small RNA


title: ω3LC1_T20_1 : Liver_diet_fish3


title: ω3LC0_T23_3: Liver_diet_fish4


title: 5xFAD_4_F [GT19.12889]


title: Treat_023_RBG18944

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: Treated_ICGScluster2_011_HSCs (CD31+kit+CD45-)

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.6.0) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

source_name: the Aorta surrounded by Gonads and Mesonephros tissues (AGM)

extract_protocol:
CD31+kit+CD45- cells were FACS-purified.
Cells were sorted in 2.3 µl of lysis buffer containing 0.2% Triton X-100 (Sigma-Aldrich) and 1U of Superase-In RNase Inhibitor (Ambion) and processed following the Smart-Seq2 protocol.
Following preamplification, all samples were purified using Ampure XP beads (Beckman Coulter) at a ratio of 1:0.6. The cDNA was then quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher) and size distributions were checked on high-sensitivity DNA chips (Agilent Bioanalyzer).
Libraries were prepared using the Illumina Nextera XT DNA preparation kit.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 4000.
Samples were used to construct Nextera XT libraries (Illumina) from 125 pg of preamplified cDNA. Libraries were purified and size selected (0.5X-0.7X) using Ampure XP beads. Then, libraries were quantified using KAPA qPCR quantification kit (KAPA Biosystems).

tag: cell type

value: Hematopoietic stem cells (CD31+kit+CD45-)

tag: treatment

tag: icgs cluster


title: ω3LC0_T8_3: Liver_diet_fish2


title: ω3LC0_T31_2: Liver_diet_fish5


title: ω3LC0_T31_4: Liver_diet_fish6


title: ω3LC0_T8_2: Liver_diet_fish1


title: ω3LC1_T38_2: Liver_diet_fish7


title: SmallRNA.mouse.testis.Mov10l1Tg.Neurog3-cre.adult.unox.rep3

description:
Small RNAseq
small RNA


title: Treat_022_RBG18932

description: Treated_ICGScluster1_005_HSCs (CD31+kit+CD45-)


title: Ctrl_067_RBG19207

description: Ctrl_ICGScluster1_034_HSCs (CD31+kit+CD45-)

value: Ctrl


title: SmallRNA.mouse.testis.Mov10l1Tg.Neurog3-cre.adult.unox.rep1

description:
Small RNAseq
small RNA


title: SmallRNA.mouse.testis.Mov10l1Tg.Neurog3-cre.adult.ox.rep3

description:
Small RNAseq
small RNA


title: SmallRNA.mouse.testis.Mov10l1Control.adult.unox.rep3

description:
Small RNAseq
small RNA


title: SmallRNA.mouse.testis.Mov10l1Tg.Neurog3-cre.adult.ox.rep2

description:
Small RNAseq
small RNA


title: SmallRNA.mouse.testis.Mov10l1Tg.Neurog3-cre.adult.unox.rep2

description:
Small RNAseq
small RNA


title: Treat_027_RBG18992

description: Treated_ICGScluster3_003_HSCs (CD31+kit+CD45-)


title: 5xFAD_4_M [GT19.12877]


title: 5xFAD_6_M [GT19.12879]


title: 5xFAD_12_M [GT19.12888]


title: Ctrl_066_RBG19195

description: Ctrl_ICGScluster1_033_HSCs (CD31+kit+CD45-)


title: SmallRNA.mouse.testis.Mov10l1Control.adult.unox.rep2

description:
Small RNAseq
small RNA


title: Ctrl_065_RBG19183

description: Ctrl_ICGScluster2_021_HSCs (CD31+kit+CD45-)


title: Ctrl_064_RBG19171

description: Ctrl_ICGScluster4_001_HSCs (CD31+kit+CD45-)


title: Ctrl_063_RBG19159

description: Ctrl_ICGScluster2_020_HSCs (CD31+kit+CD45-)


title: SmallRNA.mouse.testis.Mov10l1Control.adult.ox.rep3

description:
Small RNAseq
small RNA


title: SmallRNA.mouse.testis.Mov10l1Control.adult.unox.rep1

description:
Small RNAseq
small RNA


title: SmallRNA.mouse.testis.Mov10l1Control.adult.ox.rep2

description:
Small RNAseq
small RNA


title: SmallRNA.mouse.testis.Mov10l1Control.adult.ox.rep1

description:
Small RNAseq
small RNA


title: RNAseq.mouse.testis.wt.adult.Untreat.rep1

description:
Strand-specific RNA-seq
rRNA depleted RNA

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560), and rRNAs were depleted from total RNAs with complementary DNA oligomers (IDT) and RNaseH (Invitrogen, Waltham, MA, USA).
Strand-specific RNA-seq: Libraries were constructed following the TruSeq RNA sample preparation protocol.


title: SmallRNA.mouse.testis.Mov10l1Tg.Neurog3-cre.adult.ox.rep1

description:
Small RNAseq
small RNA


title: Ctrl_062_RBG19147

description: Ctrl_ICGScluster2_019_HSCs (CD31+kit+CD45-)


title: RNAseq.mouse.testis.Tdrd5CKOTg.Stra8-cre.adult.rep1


title: RNAseq.mouse.testis.wt.adult.Puromycin.rep1


title: RNAseq.mouse.testis.Tdrd5CKOControl.Stra8-cre.adult.rep1


title: Ctrl_061_RBG19135

description: Ctrl_ICGScluster1_032_HSCs (CD31+kit+CD45-)


title: 5xFAD_4_M [GT19.12864]


title: 5xFAD_6_M [GT19.12867]


title: 5xFAD_6_F [GT19.12870]


title: 5xFAD_12_F [GT19.12858]


title: 5xFAD_12_M [GT19.12868]


title: 5xFAD_6_F [GT19.12852]


title: 5xFAD_12_F [GT19.12846]


title: 5xFAD_6_F [GT19.12844]


title: RNAseq.mouse.testis.Mov10l1Control.adult.rep2


title: RNAseq.mouse.testis.Mov10l1Tg.Neurog3-cre.adult.rep2


title: Riboseq.mouse.testis.wt.adult.rep2

description: Ribosome footprints

data_processing:
Library strategy: Ribo-seq
Analyses were performed using piPipes v1.4. All data from the small RNA sequencing, ribosome profiling (Ribo-seq), RNA sequencing, and degradome sequencing were analyzed using the latest mouse genome release mm10 (GCA_000001635.7), and green lizard genome release anoCar2 (GCA_000090745.1). Generally, one mismatch is allowed for genome mapping.
For small RNA sequencing, libraries were normalized to the sum of total miRNA reads; spike-in RNA was used to normalize the libraries with and without RNase treatment. Uniquely mapping reads >23 nt were selected for further piRNA analysis. To ensure precision of the mapping, a piRNA is counted only when the 5´-end of the piRNA maps to the uORF or UDR of a transcript.
For RNA-seq reads, the expression per transcript was normalized to the top quartile of expressed transcripts per library calculated by Cuffdiff, and the tpm (transcripts per million) value was quantified using the Salmon software.
For Ribo-seq analysis, uniquely mapping reads between 26 nt and 32 nt were selected for further analysis. Libraries from harringtonine treatment were further normalized to the sum of reads mapping to mitochondrial coding sequences. Libraries from puromycin treatment were further normalized to the sum of reads mapping to the 5´-UTR of mRNAs.
For Degradome data, reads were aligned to the genome using TopHat 2.0.12. Reads were mapped uniquely using the ‘-g 1’ flag. Uniquely mapping reads were selected for further analysis. Libraries were normalized to the sum of reads mapping to mRNA protein-coding regions, assuming that mRNA cleavage was largely unchanged during spermatogenesis.
Genome_build: Mouse: mm10 (GCA_000001635.7, GRCm38), Lizard: anoCar2 (GCA_000090745.1, AnoCar2.0).
Supplementary_files_format_and_content: For Small RNAseq, Ribo-seq and Degradome, processed data files are unique genome alignment results in BED2 format (https://github.com/bowhan/piPipes/wiki/smallRNA-seq). RNAseq quantification results are .sf files output by Salmon software.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560), and rRNAs were depleted from total RNAs with complementary DNA oligomers (IDT) and RNaseH (Invitrogen, Waltham, MA, USA).
Ribo-seq: Testes samples were lysed, RNase T1 & A treated and loaded on sucrose gradients, and 80S monosomes were recovered for library construction. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG and has been trimmed in the raw data.


title: RNAseq.mouse.testis.Mov10l1Tg.Neurog3-cre.adult.rep1


title: Riboseq.mouse.testis.wt.adult.rep1

description: Ribosome footprints


title: RNAseq.mouse.testis.Mov10l1Tg.Neurog3-cre.adult.rep3


title: RNAseq.mouse.testis.Mov10l1Control.adult.rep3


title: RNAseq.mouse.testis.Mov10l1Control.adult.rep1


title: Ctrl_057_RBG18979

description: Ctrl_ICGScluster1_030_HSCs (CD31+kit+CD45-)


title: Ctrl_052_RBG19194

description: Ctrl_ICGScluster3_005_HSCs (CD31+kit+CD45-)


title: Ctrl_060_RBG19123

description: Ctrl_ICGScluster1_031_HSCs (CD31+kit+CD45-)


title: Ctrl_056_RBG18967

description: Ctrl_ICGScluster2_017_HSCs (CD31+kit+CD45-)


title: Ctrl_050_RBG19170

description: Ctrl_ICGScluster2_016_HSCs (CD31+kit+CD45-)


title: Ctrl_054_RBG18943

description: Ctrl_ICGScluster7_002_HSCs (CD31+kit+CD45-)


title: Ctrl_059_RBG19015

description: Ctrl_ICGScluster3_006_HSCs (CD31+kit+CD45-)


title: Ctrl_055_RBG18955

description: Ctrl_ICGScluster1_029_HSCs (CD31+kit+CD45-)


title: Ctrl_049_RBG19158

description: Ctrl_ICGScluster1_026_HSCs (CD31+kit+CD45-)


title: Ctrl_053_RBG18931

description: Ctrl_ICGScluster1_028_HSCs (CD31+kit+CD45-)


title: Ctrl_058_RBG19003

description: Ctrl_ICGScluster2_018_HSCs (CD31+kit+CD45-)


title: Ctrl_051_RBG19182

description: Ctrl_ICGScluster1_027_HSCs (CD31+kit+CD45-)


title: APOE4_12_F [GT18.01750]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: 5xFAD_4_F [GT19.12834]


title: APOE4Trem2_6_F [GT18.01749]

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)


title: 5xFAD_4_M [GT19.12840]


title: APOE4Trem2_6_M [GT18.01746]


title: Trem2_6_M [GT18.01747]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2


title: Trem2_12_F [GT18.01748]


title: APOE4Trem2_6_F [GT18.01745]


title: APOE4Trem2_2_F [GT18.01743]


title: Riboseq.mouse.testis.wt.adult.PuromycinUntreat.rep1

description: Ribosome footprints


title: Ctrl_047_RBG19134

description: Ctrl_ICGScluster3_004_HSCs (CD31+kit+CD45-)


title: Ctrl_045_RBG19014

description: Ctrl_ICGScluster5_001_HSCs (CD31+kit+CD45-)


title: APOE4_12_F [GT18.01741]

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (APOE-ε4)


title: Ctrl_043_RBG18978

description: Ctrl_ICGScluster1_023_HSCs (CD31+kit+CD45-)


title: Riboseq.mouse.testis.wt.adult.Harringtonine.rep1

description: Ribosome footprints


title: Riboseq.mouse.testis.wt.adult.HarringtonineUntreat.rep1

description: Ribosome footprints


title: Riboseq.mouse.testis.wt.adult.In-vitro-shearedRNA.rep1

description: Ribosome footprints


title: Riboseq.mouse.testis.wt.adult.polysome.rep1

description: Ribosome footprints


title: C57BL/6J_12_F [GT18.01742]

value: Wild type mouse used as control

value: F


title: Riboseq.mouse.testis.wt.adult.monosome.rep1

description: Ribosome footprints


title: Riboseq.mouse.testis.wt.adult.mono-mitochondria.rep1

description: Ribosome footprints


title: Ctrl_044_RBG19002

description: Ctrl_ICGScluster1_024_HSCs (CD31+kit+CD45-)


title: Riboseq.mouse.testis.wt.adult.HighSalt.rep2

description: Ribosome footprints


title: Ctrl_048_RBG19146

description: Ctrl_ICGScluster2_015_HSCs (CD31+kit+CD45-)


title: Riboseq.mouse.testis.wt.adult.mono-80S.rep1

description: Ribosome footprints


title: Ctrl_046_RBG19122

description: Ctrl_ICGScluster1_025_HSCs (CD31+kit+CD45-)


title: Riboseq.mouse.testis.wt.adult.Harringtonine.rep2

description: Ribosome footprints


title: Riboseq.mouse.testis.wt.adult.HighSalt.rep1

description: Ribosome footprints


title: Riboseq.mouse.testis.Tdrd5CKOTg.Stra8-cre.adult.rep3

description: Ribosome footprints


title: Trem2_2_F [GT18.01739]

value: Brain hemisphere


title: Trem2_2_M [GT18.01738]


title: APOE4Trem2_6_M [GT18.01740]


title: Riboseq.mouse.testis.Tdrd5CKOTg.Stra8-cre.adult.rep2

description: Ribosome footprints


title: ω3LC0_T23_1: Liver_diet_fish3

value: Liver

value: Juvenile


title: Riboseq.mouse.testis.wt.adult.Puromycin.rep1

description: Ribosome footprints


title: ω3LC1_T7_3: Liver_diet_fish2


title: Ctrl_042_RBG18966

description: Ctrl_ICGScluster3_003_HSCs (CD31+kit+CD45-)


title: Riboseq.mouse.testis.Tdrd5CKOControl.Stra8-cre.adult.rep3

description: Ribosome footprints


title: APOE4_2_F [GT18.01721]


title: Trem2_2_M [GT18.01720]


title: APOE4Trem2_2_F [GT18.01722]


title: Ctrl_038_RBG19205

description: Ctrl_ICGScluster1_019_HSCs (CD31+kit+CD45-)


title: Riboseq.mouse.testis.PNLDC1Tg.adult.rep1

description: Ribosome footprints


title: Riboseq.mouse.testis.Tdrd5CKOControl.Stra8-cre.adult.rep1

description: Ribosome footprints


title: Ctrl_039_RBG18930

description: Ctrl_ICGScluster1_020_HSCs (CD31+kit+CD45-)


title: Ctrl_037_RBG19193

description: Ctrl_ICGScluster2_014_HSCs (CD31+kit+CD45-)


title: Ctrl_035_RBG19169

description: Ctrl_ICGScluster7_001_HSCs (CD31+kit+CD45-)


title: Riboseq.mouse.testis.Tdrd5CKOControl.Stra8-cre.adult.rep2

description: Ribosome footprints


title: Ctrl_036_RBG19181

description: Ctrl_ICGScluster6_002_HSCs (CD31+kit+CD45-)


title: C57BL/6J_2_F [GT18.01718]


title: Riboseq.mouse.testis.Neurog3-cre.Ribotag.Input.adult.rep1

description: Ribosome footprints


title: Trem2_2_M [GT18.01716]


title: Riboseq.mouse.testis.Neurog3-cre.Ribotag.Input.adult.rep3

description: Ribosome footprints


title: Riboseq.mouse.testis.Neurog3-cre.Ribotag.HAIP.adult.rep3

description: Ribosome footprints


title: Riboseq.mouse.testis.Tdrd5CKOTg.Stra8-cre.adult.rep1

description: Ribosome footprints


title: APOE4Trem2_12_F [GT18.01712]


title: C57BL/6J_12_F [GT18.01714]


title: APOE4_6_F [GT18.01713]


title: Riboseq.mouse.testis.Neurog3-cre.Ribotag.HAIP.adult.rep2

description: Ribosome footprints


title: Ctrl_034_RBG19157

description: Ctrl_ICGScluster2_013_HSCs (CD31+kit+CD45-)


title: Trem2_6_M [GT18.01711]


title: Ctrl_031_RBG19001

description: Ctrl_ICGScluster1_017_HSCs (CD31+kit+CD45-)


title: Ctrl_032_RBG19013

description: Ctrl_ICGScluster1_018_HSCs (CD31+kit+CD45-)


title: Riboseq.mouse.testis.Mov10l1CKOTg.Neurog3-cre.adult.rep3

description: Ribosome footprints


title: Riboseq.mouse.testis.Neurog3-cre.Ribotag.HAIP.adult.rep1

description: Ribosome footprints


title: Riboseq.mouse.testis.Mov10l1CKOTg.Neurog3-cre.adult.rep2

description: Ribosome footprints


title: Riboseq.mouse.testis.Mov10l1CKOTg.Neurog3-cre.adult.rep1

description: Ribosome footprints


title: C57BL/6J_2_F [GT18.01710]


title: AD pt5

city: Cambridge

first: Madison

middle: R

last: Mack

state: Massachusetts

address: 350 Water St

department: Immunology & Inflammation Research

institute: Sanofi

data_processing:
Sequences were aligned with STAR v2.0.4b
Gene counts were determined with Subread:featureCount v1.4.5
Transcript abundance was determined with Sailfish v0.6.3
Sequence performace was assessed with RSeQC v2.3
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files are the counts tables from Subread:featureCount for each sample as a text file, as well as a compiled csv file of RPKMs for each sample

source_name: PBMC CD56dim NK cells

extract_protocol:
Cells were sorted directly into lysis buffer containing TCEP according to manufacturer's instructions, vortexed for 30 seconds, and then frozen on dry ice. Total RNA was extracted from 30-100,000 sorted NK cells using the Macherey-Nagel RNA Nucleospin XS kit.
Libraries were constructed using the CloneTech SMARTer cDNA amplification kit with 10 ng of total RNA.

treatment_protocol: Peripheral blood mononuclear cells were isolated from whole blood by Ficoll gradient centrifugation and frozen in 90% serum 10% DMSO at -80 until use. PBMCs were thawed on the day of sorting and immediately stained for FACS.

tag: sort population

value: Live CD45+ CD13- CD3- CD56dim

tag: disease state

value: atopic dermatitis

tag: barcode

value: GTATCCT


title: Ctrl_028_RBG18965

description: Ctrl_ICGScluster2_011_HSCs (CD31+kit+CD45-)


title: APOE4_12_F [GT18.01735]

tag: strain


title: Ctrl_029_RBG18977

description: Ctrl_ICGScluster1_015_HSCs (CD31+kit+CD45-)


title: Control pt5

value: control

value: TCGTGCG


title: Ctrl_033_RBG19145

description: Ctrl_ICGScluster2_012_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)


title: Riboseq.mouse.testis.Mov10l1CKOControl.adult.rep3

description: Ribosome footprints

value: whole testis

tag: genotype/variation

value: adult


title: Riboseq.mouse.testis.Mov10l1CKOControl.adult.rep2

description: Ribosome footprints


title: AD pt4

value: GGTGAAT


title: Ctrl_026_RBG18941

description: Ctrl_ICGScluster2_010_HSCs (CD31+kit+CD45-)

value: Ctrl


title: Control pt4

value: GGCAGCG


title: Ctrl_030_RBG18989

description: Ctrl_ICGScluster1_016_HSCs (CD31+kit+CD45-)


title: C57BL/6J_2_M [GT18.01733]

tag: age (months)

value: M


title: Trem2_2_M [GT18.01732]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2

tag: tissue


title: Control pt3

value: GGCAAGA


title: Riboseq.mouse.testis.Mov10l1CKOControl.adult.rep1

description: Ribosome footprints


title: Degradome.mouse.testis.wt.adult.PuromycinUntreated.rep1

description:
Degradome
RNA degradation products

data_processing:
Library strategy: Degradome-Seq
Analyses were performed using piPipes v1.4. All data from the small RNA sequencing, ribosome profiling (Ribo-seq), RNA sequencing, and degradome sequencing were analyzed using the latest mouse genome release mm10 (GCA_000001635.7), and green lizard genome release anoCar2 (GCA_000090745.1). Generally, one mismatch is allowed for genome mapping.
For small RNA sequencing, libraries were normalized to the sum of total miRNA reads; spike-in RNA was used to normalize the libraries with and without RNase treatment. Uniquely mapping reads >23 nt were selected for further piRNA analysis. To ensure precision of the mapping, a piRNA is counted only when the 5´-end of the piRNA maps to the uORF or UDR of a transcript.
For RNA-seq reads, the expression per transcript was normalized to the top quartile of expressed transcripts per library calculated by Cuffdiff, and the tpm (transcripts per million) value was quantified using the Salmon software.
For Ribo-seq analysis, uniquely mapping reads between 26 nt and 32 nt were selected for further analysis. Libraries from harringtonine treatment were further normalized to the sum of reads mapping to mitochondrial coding sequences. Libraries from puromycin treatment were further normalized to the sum of reads mapping to the 5´-UTR of mRNAs.
For Degradome data, reads were aligned to the genome using TopHat 2.0.12. Reads were mapped uniquely using the ‘-g 1’ flag. Uniquely mapping reads were selected for further analysis. Libraries were normalized to the sum of reads mapping to mRNA protein-coding regions, assuming that mRNA cleavage was largely unchanged during spermatogenesis.
Genome_build: Mouse: mm10 (GCA_000001635.7, GRCm38), Lizard: anoCar2 (GCA_000090745.1, AnoCar2.0).
Supplementary_files_format_and_content: For Small RNAseq, Ribo-seq and Degradome, processed data files are unique genome alignment results in BED2 format (https://github.com/bowhan/piPipes/wiki/smallRNA-seq). RNAseq quantification results are .sf files output by Salmon software.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560), and rRNAs were depleted from total RNAs with complementary DNA oligomers (IDT) and RNaseH (Invitrogen, Waltham, MA, USA).
Degradome: The RNAs were first oxidized at room temperature for 30 minutes with sodium periodate (Sigma, St. Louis, MO, USA) to block the 3´-ends from ligation, and were then size-selected to isolate RNA ≥ 200 nt (DNA Clean & Concentrator™-5, Zymo Research). 5´ adaptors were attached using T4 RNA ligase (Ambion) at 20°C for 3 hours. The ligated products were subjected to rRNA depletion with complementary DNA oligomers (IDT) and RNaseH (invitrogen). The rRNA depleted ligation products were reverse transcribed using a degenerate primer (5´-GCACCCGAGAATTCCANNNNNNNNC-3´). cDNA was amplified by PCR using KAPA HIFI Hotstart polymerase (Kapa Biosystems, Wilmington, MA, USA), and 250–350 nt dsDNA was isolated on 8% native PAGE gels.

value: wt


title: APOE4Trem2_2_M [GT18.01736]

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)

value: Brain hemisphere


title: AD pt3

value: Live CD45+ CD13- CD3- CD56dim

value: GCCTCCC


title: Trem2_12_M [GT18.01731]


title: Treat_021_RBG19204

description: Treated_ICGScluster2_010_HSCs (CD31+kit+CD45-)


title: Degradome.mouse.testis.wt.adult.Puromycin.rep1

description:
Degradome
RNA degradation products


title: Treat_020_RBG19192

description: Treated_ICGScluster6_001_HSCs (CD31+kit+CD45-)


title: Control pt1

value: ACGCGGG


title: Degradome.mouse.testis.Neurog3-cre.Ribotag.adult.HAIP.rep1

description:
Degradome
RNA degradation products


title: C57BL/6J_2_F [GT18.01726]

value: Wild type mouse used as control

value: F


title: Treat_019_RBG19180

description: Treated_ICGScluster1_004_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)


title: Ctrl_025_RBG18929

description: Ctrl_ICGScluster2_009_HSCs (CD31+kit+CD45-)


title: AD pt2

value: atopic dermatitis

value: AATACGC


title: Treat_018_RBG19168

description: Treated_ICGScluster2_009_HSCs (CD31+kit+CD45-)


title: [ChIP-seq, FLAG] mESC rtTA IP

city: Singapore

first: Qian Yi

last: Lee

address: Biopolis Drive

department: R&D

country: Singapore

institute: Nuevocor

library_source: genomic

data_processing:
Reads were aligned to the mm10 reference sequence using Bowtie 2.1.0 with an additional -5 10 parameter.
Peak calling was performed using MACS 2.1.1 .
Higher confidence peaks were selected based on a cutoff of q ≤ 0.05 and signal score ≥ 5
Genome_build: mm10
Supplementary_files_format_and_content: For flagAscl1/Myod1 IP: bed files containing significant peaks based on q ≤ 0.05 and signal score ≥ 5 cutoff. mESC rtTA-IP and input (control): bed files containing all uniquely aligned reads.

molecule: genomic DNA

source_name: V6.5 mESC

growth_protocol: A CAGGS promoter driven rtTA-t2a-puroR cassette was targeted into the ROSA26 locus of the V6.5 ES cell line using the protocol previously described (Beard et al., 2006). Successfully targeted clones were confirmed by Southern blots. RtTA-containing mESCs were then infected with TetO-flagAscl1 or TetO-flagMyod1 lentivirus to establish dox-inducible flagAscl1 or flagMyod1 ES cell lines. Successfully infected clones were confirmed by immunofluorescence using the anti-FLAG M2 antibody, as well as by an iN reprogramming assay to check that the cells can successfully reprogram into neurons or muscles under the presence of dox and neural media.

extract_protocol:
FLAG-tagged TFs were immunoprecipitated using FLAG M2 antibody conjugated beads (Sigma F2426). Approximately 60-100 million cells were used per replicate. Beads (~100uL slurry per sample) were washed thrice with IP dilution buffer (1% Triton X-100, 2mM EDTA pH8.0, 20mM Tris-HCl pH8.0, 150mM NaCl, 1mM DTT, 100uM PMSF), blocked overnight in IP dilution buffer with 0.1% BSA and 0.06% sheared salmon sperm DNA (Thermo Fisher; AM9680), then washed again three times with IP dilution buffer before use. Nuclei were isolated by incubating with cell lysis buffer (5mM HEPES pH7.9, 85mM KCl, 0.5% NP40, 100uM PMSF, protease inhibitors from Roche) for 10min on ice and centrifuged at 5000rpm for 5min at 4°C, then lysed with nuclear lysis buffer (50mM Tris-HCl pH8.0, 10mM EDTA pH8.0, 1% SDS, 100uM PMSF, protease inhibitors) for 10min on ice. Chromatin was sheared using either the Bioruptor (Diagenode) or Covaris sonicator until DNA was fragmented to 200-500bp. Sheared chromatin was diluted using 3X volume of IP dilution buffer and pre-cleared for at least 4hr at 4°C using IgG beads (Sigma A0919). 1% of pre-cleared chromatin was kept as input, and the remainder was incubated with FLAG beads overnight at 4°C. Beads were washed 8 times with IP wash buffer (20mM Tris-HCl pH8.0, 2mM EDTA pH8.0, 250mM NaCl, 1% NP40, 0.05% SDS, 100uM PMSF) and once with TE buffer with 100uM PMSF. Beads and 1% input samples were reverse cross-linked overnight in IP elution buffer (50mM NaHCO3, 1% SDS) at 65°C. Isolated DNA was RNase treated for 30min at 37°C, purified using QIAquick PCR purification columns (Qiagen) and eluted in DEPC water.
ChIP-seq libraries were prepared using the NEBNext library prep kit (NEB; E6240) following the supplier’s protocols with slight modifications. Adaptor ligation was performed using regular T4 ligase and ligase buffer. Size selection (200-500bp) was performing after adaptor ligation and PCR enrichment using 2% low-melt agarose gel (Lonza; 50080), and DNA was purified using the QiaQuick gel extraction columns from Qiagen.

treatment_protocol: mESCs (containing either rtTA alone or with flagAscl1 or flagMyod1 were cultured in mESC media: DMEM (Gibco) containing 12% KSOR (Gibco), 3% cosmic calf serum (CCS; Hyclone), beta-mercaptoethanol (Sigma), non-essential amino acids, sodium pyruvate, penicillin/streptomycin (all from Invitrogen) and 0.1% LIF on feeders (mouse embryonic fibroblast). Prior to TF induction with doxycycline, cells were expanded in the absence of feeders for 1-2 passages. Cells are then cultured in N3 media containing: DMEM/F12 (Gibco), Insulin, ApoTransferrin, Progesterone, Putrescine and Sodium Selenite, supplemented with 2 µg/ml dox (all from Sigma) for 48h.

value: V6.5 mESC

value: Mouse embryonic stem cells

tag: transgenes

value: rtTA

tag: days post transgene induction

value: 2 days

tag: chip antibody

value: FLAG-conjugated beads (Sigma F2426)


title: C57BL/6J_2_F [GT18.01725]


title: AD pt1

description: Sample was excluded from study due to sort impurities

value: AAATGCA


title: APOE4_2_F [GT18.01724]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: Treat_017_RBG19156

description: Treated_ICGScluster1_003_HSCs (CD31+kit+CD45-)


title: Trem2_6_M [GT18.01695]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2

value: M

value: Brain hemisphere


title: Control pt2

value: Live CD45+ CD13- CD3- CD56dim

value: control

value: CGCTACA


title: C57BL/6J_2_F [GT18.01727]

value: Wild type mouse used as control

value: F


title: [ChIP-seq, FLAG] mESC flagMyod1 IP

tag: cell line

value: flagMyod1 + rtTA


title: APOE4_2_F [GT18.01693]

tag: gender


title: Treat_016_RBG19144

description: Treated_ICGScluster2_008_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)


title: [ChIP-seq, FLAG] mESC combined input

value: V6.5 mESC

value: Mouse embryonic stem cells

value: combined input file

value: input


title: Treat_015_RBG19132

description: Treated_ICGScluster5_001_HSCs (CD31+kit+CD45-)


title: S2 input rep a

city: Montreal

first: Celia

last: Alecki

state: QC

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

institute: McGill University

description:
RNA:DNA hybrid
library strategy: DRIP-Seq

data_processing:
adapters were trimmed using Trimmomatic(PE -phred33)
reads with both mate pairs were aligned to the dm3 genome using bowtie2/2.3.1 (fr--no-mixed--no-unal), and sorted .bam files generated with samtools/1.4.1
duplicate reads were removed with Picard/2.17.3 (default parameters)
strand specific .bam files were generated according to sam flags using samtools/1.4.1 (forward strand: samtools view -f 99, samtools view -f 147; reverse strand: samtools view -f 83, samtools view -f 163; the two resulting .bam files for each strand were merged)
bigwig files were generated usig deepTools/2.5.3 bamCoverage (binSize 10 normalizeUsingRPKM)
peaks were called with MACS2/2.1.1.20160309  callpeak (-f BAMPE --bw 250 -g dm --mfold 10 30 -q 0.01) with the input or RNH_IP as control file
bedtools intersect (-u) was used on Galaxy to first filter for peaks present in both DRIPvs. INPUT and DRIP vs RNH-IP for each replicate, and then to filter for peaks present in both replicates, which were used for further analysis
Genome_build: dm3
Supplementary_files_format_and_content: bigwig (all samples); bed (filtered peaks from both replicates)

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol:
S2 cells (gibco) were grown into Gibco media supplemented with 10% FBS at 2.10^6 cells/mL in suspension at 27c.
OregonR flies wre grown at c. Embryos were collected on apple juice plates.

extract_protocol:
Total nucleic acids were extracted from embryos and S2 cells using phenol-chloroform. RNA:DNA hybrids were immunoprecipitated using S9.6 antibody.
Library were prepared with NEBNext Ultra II RNA Library Prep Kit for Illumina according to the instruction but by starting at the second strand synthesis step.

value: S2 cells


title: Halauxifen-methyl 6 HAT Rep 4

city: West Lafayette

first: Cara

last: McCauley

state: INDIANA

address: 915 West State Street

department: Botany and Plant Pathology

institute: Purdue University

data_processing:
Sequence quality was assessed using FastQC (v 0.11.2) for all samples and quality trimming was done using FASTX toolkit (v 0.0.14) to remove bases with less than Phred33 score of 30 and resulting reads of at least 50 bases were retained (typically more than 99% of total reads).
The quality trimmed reads were mapped against the STAR-indexed reference horseweed genome downloaded from NCBI using STAR (v 2.5.2b) with default parameters.
HTSeq (v 0.6.1) was used to generate raw read counts from each sample for each gene feature using STAR output and the gtf predicted by GeneMark (Since NCBI gff file failed to contain predicted gene information)
DE pairwise analysis between samples  using read counts matrix generated by HTSeq was performed using ‘R’ (Version 3.3.2) and two different methods (DESeq2,edgeR) and also using Cufflinks.
Any genes with 0 counts in all samples were removed from the count matrix and genes that had counts in some samples but not in others were changed from 0 to 1 in order to avoid having infinite values calculated for the fold change.
Genome_build: GCA_000775935.1 (ASM77593v1)
Supplementary_files_format_and_content: Counts

organism: Erigeron canadensis

source_name: Halauxifen-methyl 6 HAT

growth_protocol: Horseweed seed was grown in commercial potting media in a greenhouse with supplemental light set to a 16-hr photoperiod.

extract_protocol:
Individual leaves were removed, flash frozen with liquid nitrogen, and RNA was extracted according to Qiagen RNeasy Plant Mini Kit protocol (Cat# 74904).
RNA libraries were prepared for sequencing using standard Illumina protocols. Individual samples were dual-barcoded pool prior to sequencing.

tag: developmental stage

value: rosette

tag: biotype

value: glyphosate-resistant

tag: agent

value: Halauxifen-methyl

tag: time

value: 6 HAT

value: leaf


title: S2 input rep b


title: S2 RNaseH DRIP-seq rep b


title: C57BL/6J_6_F [GT18.01692]

value: Brain hemisphere


title: APOE4Trem2_12_F [GT18.01689]

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)


title: Halauxifen-methyl 6 HAT Rep 3


title: Treat_014_RBG19120

description: Treated_ICGScluster2_007_HSCs (CD31+kit+CD45-)

tag: cell type

tag: treatment

tag: icgs cluster


title: S2 RNaseH DRIP-seq rep a


title: Trem2_2_M [GT18.01737]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2

value: M


title: Ctrl_024_RBG19012

description: Ctrl_ICGScluster2_008_HSCs (CD31+kit+CD45-)

value: Ctrl


title: Halauxifen-methyl 6 HAT Rep 2


title: APOE4_2_M [GT18.01688]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: [ChIP-seq, FLAG] mESC flagAscl1 IP

value: V6.5 mESC

value: flagAscl1 + rtTA

value: 2 days

value: FLAG-conjugated beads (Sigma F2426)


title: Ctrl_023_RBG19000

description: Ctrl_ICGScluster1_013_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)


title: APOE4Trem2_6_F [GT18.01687]

value: F


title: Ctrl_041_RBG18954

description: Ctrl_ICGScluster1_022_HSCs (CD31+kit+CD45-)


title: Ctrl_027_RBG18953

description: Ctrl_ICGScluster1_014_HSCs (CD31+kit+CD45-)


title: APOE4_2_F [GT18.01723]


title: Halauxifen-methyl 6 HAT Rep 1

value: rosette

value: glyphosate-resistant


title: Ctrl_022_RBG18988

description: Ctrl_ICGScluster3_002_HSCs (CD31+kit+CD45-)


title: Dicamba 6 HAT Rep 4

source_name: Dicamba 6 HAT

value: Dicamba

value: 6 HAT


title: S2 DRIP-seq rep a

value: S2 cells


title: 10-14H input rep b

source_name: 10-14H Oregon R embryos

value: 10-14H embryo

value: Oregon R


title: Ctrl_021_RBG18976

description: Ctrl_ICGScluster1_012_HSCs (CD31+kit+CD45-)


title: Trem2_6_M [GT18.01686]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2

value: M

value: Brain hemisphere


title: 10-14H input rep a


title: APOE4Trem2_12_M [GT18.01685]

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)


title: APOE4_12_F [GT18.01684]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: Ctrl_020_RBG18964

description: Ctrl_ICGScluster2_007_HSCs (CD31+kit+CD45-)

value: Ctrl


title: Ctrl_019_RBG18952

description: Ctrl_ICGScluster2_006_HSCs (CD31+kit+CD45-)


title: 10-14H RNaseH DRIP-seq rep b


title: Dicamba 6 HAT Rep 1

value: leaf


title: Dicamba 6 HAT Rep 2


title: S2 DRIP-seq rep b


title: Riboseq.mouse.testis.Neurog3-cre.Ribotag.Input.adult.rep2

description: Ribosome footprints

value: whole testis

tag: strain/background

tag: age

value: adult


title: 10-14H RNaseH DRIP-seq rep a

tag: strain


title: Ctrl_040_RBG18942

description: Ctrl_ICGScluster1_021_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)


title: 2,4-D 6 HAT Rep 4

value: rosette

value: glyphosate-resistant


title: Trem2_6_M [GT18.01683]

tag: genotype/variation

tag: age (months)


title: Ctrl_018_RBG18940

description: Ctrl_ICGScluster2_005_HSCs (CD31+kit+CD45-)


title: Ctrl_017_RBG18928

description: Ctrl_ICGScluster1_011_HSCs (CD31+kit+CD45-)


title: 2,4-D 6 HAT Rep 3

value: 6 HAT

tag: tissue


title: APOE4Trem2_2_M [GT18.01680]


title: 10-14H DRIP-seq rep a


title: Dicamba 6 HAT Rep 3

value: Dicamba


title: Trem2_12_F [GT18.01715]

value: F


title: Treat_013_RBG19203

description: Treated_ICGScluster2_006_HSCs (CD31+kit+CD45-)


title: 10-14H DRIP-seq rep b

value: 10-14H embryo

value: Oregon R


title: C57BL/6J_12_M [GT18.01709]

value: Wild type mouse used as control

value: M


title: APOE4Trem2_12_M [GT18.01708]

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)

value: Brain hemisphere


title: 2,4-D 6 HAT Rep 2


title: Treat_012_RBG19191

description: Treated_ICGScluster3_002_HSCs (CD31+kit+CD45-)


title: C57BL/6J_6_M [GT18.01707]


title: 2,4-D 6 HAT Rep 1


title: 2-6H input rep a

source_name: 2-6H Oregon R embryos

value: 2-6H embryo


title: Treat_011_RBG19179

description: Treated_ICGScluster4_002_HSCs (CD31+kit+CD45-)


title: Treat_010_RBG19167

description: Treated_ICGScluster7_001_HSCs (CD31+kit+CD45-)


title: APOE4_6_M [GT18.01706]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: Water 6 HAT Rep 4

source_name: Water 6 HAT

value: Water

value: leaf


title: 2-6H RNaseH DRIP-seq rep b

description:
RNA:DNA hybrid
library strategy: DRIP-Seq


title: Water 6 HAT Rep 3


title: 2-6H RNaseH DRIP-seq rep a


title: APOE4Trem2_12_M [GT18.01705]


title: Treat_009_RBG19155

description: Treated_ICGScluster2_005_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)


title: APOE4_12_M [GT18.01704]


title: Water 6 HAT Rep 2

value: rosette


title: Water 6 HAT Rep 1

value: glyphosate-resistant


title: Halauxifen-methyl 1 HAT Rep 4

source_name: Halauxifen-methyl 1 HAT

value: Halauxifen-methyl

value: 1 HAT


title: Treat_008_RBG19143

description: Treated_ICGScluster2_004_HSCs (CD31+kit+CD45-)


title: 2-6H DRIP-seq rep a


title: Ctrl_016_RBG19011

description: Ctrl_ICGScluster6_001_HSCs (CD31+kit+CD45-)

value: Ctrl


title: C57BL/6J_2_M [GT18.01703]


title: 2-6H DRIP-seq rep b


title: Treat_007_RBG19131

description: Treated_ICGScluster4_001_HSCs (CD31+kit+CD45-)


title: 2-6H input rep b


title: A3_3

city: New Delhi

first: Rita

last: Sharma

state: Delhi

address: SCIS, JNU

department: School of Computational & Integrative Sciences

country: India

institute: Jawaharlal Nehru University

data_processing:
Low-quality reads with Phred score<30 were filtered
Adapter triming using AdapterRemoval-v2 (2.2.0)
ribosomal RNA sequences removal by aligning the reads with silva database using bowtie2 (2.2.9)
read alignment to the genome using STAR
estimation of gene expression and transcript abundance using StringTie (1.3.3b)
pairwise differential expression analysis using cuffdiff
Genome_build: Phytozome v3.3.1
Supplementary_files_format_and_content: FPKM values in excel format

organism: Sorghum bicolor

growth_protocol: Soghum bicolor M35-1 plants were raised in an open field

extract_protocol:
Total RNA was isolated using a modified trizol method
Libraries were prepared using TruSeq® Stranded Total RNA kit using manufacturer’s instructions

tag: cultivar

value: Pollen

value: male gametophyte


title: APOE4Trem2_12_M [GT18.01702]


title: A3_2


title: Halauxifen-methyl 1 HAT Rep 3


title: Trem2_12_F [GT18.01701]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2

value: F


title: Ctrl_015_RBG18999

description: Ctrl_ICGScluster2_004_HSCs (CD31+kit+CD45-)


title: Halauxifen-methyl 1 HAT Rep 2


title: Trem2_2_F [GT18.01700]


title: Ctrl_014_RBG18987

description: Ctrl_ICGScluster1_010_HSCs (CD31+kit+CD45-)


title: APOE4Trem2_12_M [GT18.01734]

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)

value: M


title: Halauxifen-methyl 1 HAT Rep 1


title: A3_1


title: Ctrl_013_RBG18975

description: Ctrl_ICGScluster1_009_HSCs (CD31+kit+CD45-)


title: A2_3

value: Microspore


title: C57BL/6J_2_M [GT18.01698]

value: Wild type mouse used as control

value: Brain hemisphere


title: Dicamba 1 HAT Rep 4

source_name: Dicamba 1 HAT

value: Dicamba


title: A2_2


title: Ctrl_012_RBG18963

description: Ctrl_ICGScluster1_008_HSCs (CD31+kit+CD45-)


title: C57BL/6J_12_M [GT18.01665]


title: Dicamba 1 HAT Rep 3

value: leaf


title: A2_1


title: Dicamba 1 HAT Rep 2


title: A1_3

source_name: Meiotic to tetrad_anther

value: Meiotic to tetrad


title: APOE4Trem2_12_M [GT18.01663]


title: A1_2


title: Ctrl_010_RBG18939

description: Ctrl_ICGScluster1_007_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)


title: 2,4-D 1 HAT Rep 4

value: rosette

value: glyphosate-resistant


title: APOE4Trem2_2_F [GT18.01662]


title: Ctrl_009_RBG18927

description: Ctrl_ICGScluster1_006_HSCs (CD31+kit+CD45-)


title: A1_1


title: C57BL/6J_12_M [GT18.01661]


title: APOE4_12_M [GT18.01660]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: Trem2_12_M [GT18.01699]


title: Treat_005_RBG19178

description: Treated_ICGScluster3_001_HSCs (CD31+kit+CD45-)


title: IFD6

city: Calgary

first: Matthew

last: Workentine

state: Alberta

address: 3280 Hospital Drive NW

institute: University of Calgary

data_processing:
SOLiD 5500xl Lifescope v2.1 software used for basecalling.
Reads produced by 5500XL SOLiD system were mapped to the mouse reference genome (mm10) using Tophat v2.0.13 with default parameters.
Sam alignments were converted to sorted bams using samtools.
Sequences were mapped using software using default parameters against the M. musculus mm10 reference genome (NCBI assembly accession number, GCA_000001635.2).
Quality of alignments was assessed using JMP Genomics v7 software.
Transcript abundances and differential expression tested using Cufflinks package v2.2.1, with default parameters, excepting the inclusion of quartile normalization and bias correction, were expressed in fragments per kilobase per million mapped reads (FPKM), and were thresholded based on an adjusted-p value (q<0.05).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for each sample and Entrez ID and gene name

source_name: Interfollicular dermal cells (IFD)

extract_protocol:
Back skin from adult postnatal day 26-27 male Sox2:GFP/aSMA:dsRed mice was treated with dispase/collagenase, stained with respective antibodies and each cell population was FACS-isolated and total RNA was immediately harvested using the Dynabeads mRNA DIRECT Micro Purification Kit (Ambion).
RNA libraries were prepared for sequencing using standard Life Technologies SOLiD protocols

value: post-natal day ~26-27

tag: Sex

value: male

value: Adult mouse back skin

tag: hair stage

value: Early anagen

value: Interfollicular dermal cells (IFD)


title: Dicamba 1 HAT Rep 1

value: 1 HAT


title: Treat_004_RBG19166

description: Treated_ICGScluster1_001_HSCs (CD31+kit+CD45-)


title: IFD2


title: 2,4-D 1 HAT Rep 1


title: Ctrl_011_RBG18951

description: Ctrl_ICGScluster3_001_HSCs (CD31+kit+CD45-)

value: Ctrl


title: 2,4-D 1 HAT Rep 2


title: Trem2_12_M [GT18.01657]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2

tag: gender

value: M


title: Treat_006_RBG19190

description: Treated_ICGScluster1_002_HSCs (CD31+kit+CD45-)


title: IFD1


title: Treat_003_RBG19154

description: Treated_ICGScluster2_003_HSCs (CD31+kit+CD45-)


title: APOE4_6_F [GT18.01659]

value: F

value: Brain hemisphere


title: 2,4-D 1 HAT Rep 3

tag: developmental stage

value: leaf


title: DSL1

source_name: Dermal sheath cells (DS)

value: Dermal sheath cells (DS)


title: Water 1 HAT Rep 3

source_name: Water 1 HAT

value: rosette

tag: biotype

value: Water


title: Treat_002_RBG19142

description: Treated_ICGScluster2_002_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)


title: C57BL/6J_6_F [GT18.01658]

value: Wild type mouse used as control


title: DS5

value: post-natal day ~26-27


title: Water 1 HAT Rep 2

value: glyphosate-resistant

tag: agent


title: Treat_001_RBG19130

description: Treated_ICGScluster2_001_HSCs (CD31+kit+CD45-)


title: DS4

value: male

value: Adult mouse back skin


title: Trem2_2_F [GT18.01656]


title: Water 1 HAT Rep 1

tag: time


title: Ctrl_008_RBG19010

description: Ctrl_ICGScluster1_005_HSCs (CD31+kit+CD45-)

tag: cell type


title: C57BL/6J_2_M [GT18.01655]


title: C57BL/6J_2_F [GT18.01654]


title: FarS rep 3 [FarS target identification]

city: Jena

first: Malte

last: Siemers

address: Winzerlaer Straße 2

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University

description:
MHF3_GATCAG
processed data file: FarS pulse_read_counts.xlsx

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, Munich, Blum group).
cDNA reads were imported into CLC Genomics Workbench v11.0.
Adaptor- and quality trimming was performed using the trim reads command with the following settings: sequence=NEB P7:AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, NEB P5:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; reads: all; when an adapter is found: trim 3'end; for reads without adapters: keep the read; scores=mismatch:2, gapcost:3, cutoff:10; cutoff at end: 4.
The trimmed reads were checked for quality and mapped with CLC Genomics Workbench v12.0.3 to the V. cholerae reference genome (NCBI Acc.number: NC_002505.1, NC_002506.1) using the following settings: Mismatch cost=2, Insertion cost=3, Deletion cost=3, Length fraction=0.8, Similarity fraction=0.8, Global alignment=yes, Strand specific=reverse, Maximum number of hits for a read=10.
Reads mapping in CDS were counted and differential expression was calculated using the CLC "Differential expression for RNA-seq" tool. Genes with a fold-change > 2.0 and a FDR adjusted p-value ≤ 0.05 were considered to be differentially expressed.
Genome_build: NC_002505.1, NC_002506.1
Supplementary_files_format_and_content: FarS_pulse_read_counts.xlsx

organism: Vibrio cholerae

source_name: whole bacterial cells

growth_protocol: V. cholerae C6706 wild-type cells carrying pBAD-ctr or pBAD-farS were cultivated to exponential phase (OD600=0.5) in 50 ml LB media containing 50 µg/ml kanamycin.

extract_protocol:
RNA was isolated using Tri-reagent according to standard protocols. Prepared RNA was DNase digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using the Ribo-Zero rRNA Removal kit (Epicentre) for gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760), according to the manufacturer's instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: L-arabinose (0.2% final conc.) was added, when cells reached exponential phase (OD600=0.5). After 15 minutes of treatment 4 OD600 units of cells were harvested in tubes containing 1/5 "stop-mix" (95%ethanol, 5%phenol) and snap frozen in liquid nitrogen until further processing.

value: wt pBAD-farS

tag: growth phase

value: exponential phase

tag: treatment

value: 0.2% L-arabinose


title: DP2

source_name: Dermal papilla cells (DP)

value: Early anagen

value: Dermal papilla cells (DP)


title: DP4


title: Ctrl_006_RBG18986

description: Ctrl_ICGScluster1_004_HSCs (CD31+kit+CD45-)

source_name: the Aorta surrounded by Gonads and Mesonephros tissues (AGM)

value: Ctrl

tag: icgs cluster


title: DP1

tag: age


title: Water 1 HAT Rep 4

value: 1 HAT


title: APOE4_6_F [GT18.01678]

tag: strain

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)

value: F

value: Brain hemisphere


title: APOE4Trem2_6_M [GT18.01679]

tag: genotype/variation

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)

value: M


title: Ctrl_005_RBG18974

description: Ctrl_ICGScluster2_002_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)


title: DC4

source_name: Hair follicle dermal stem cells (hfDSCs)

value: post-natal day ~26-27


title: C57BL/6J_2_M [GT18.01677]

value: Wild type mouse used as control

tag: age (months)


title: FarS rep 1 [FarS target identification]

description:
MHF1_CAGATC
processed data file: FarS pulse_read_counts.xlsx


title: control rep 3 [FarS target identification]

description:
MHC3_TTAGGC
processed data file: FarS pulse_read_counts.xlsx

value: wt pBAD-ctr


title: APOE4_2_F [GT18.01676]

tag: tissue


title: FarS rep 2 [FarS target identification]

description:
MHF2_ACTTGA
processed data file: FarS pulse_read_counts.xlsx

value: wt pBAD-farS


title: Ctrl_003_RBG18950

description: Ctrl_ICGScluster1_003_HSCs (CD31+kit+CD45-)


title: DC2

value: male

value: Adult mouse back skin

value: Hair follicle dermal stem cells (hfDSCs)


title: DC1

value: Early anagen


title: Ctrl_002_RBG18938

description: Ctrl_ICGScluster1_002_HSCs (CD31+kit+CD45-)

value: Ctrl


title: control rep 1 [FarS target identification]

description:
MHC1_ATCACG
processed data file: FarS pulse_read_counts.xlsx

value: exponential phase

value: 0.2% L-arabinose


title: APOE4_2_F [GT18.01674]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: Ctrl_001_RBG18926

description: Ctrl_ICGScluster1_001_HSCs (CD31+kit+CD45-)


title: control rep 2 [FarS target identification]

description:
MHC2_CGATGT
processed data file: FarS pulse_read_counts.xlsx


title: Hfq::3XFLAG stationary rep II [Hfq RIP-seq]

description:
MH8_GGCTAC
RNA co-immunoprecipitation
processed data file: Hfq RIP-seq_read_counts.xlsx

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, Munich, Blum group).
cDNA reads were imported into CLC Genomics Workbench v9.5.4.
3'adaptor- and quality trimming was performed using the trim reads command with the following settings: sequence=GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT; strand=minus; action=remove adapter; scores=mismatch: 2, gapcost: 3, cutoff: 10, cutoff at end: 4.
The trimmed reads were checked for quality and mapped with CLC Genomics Workbench v12.0.3 to the V. cholerae reference genome (NCBI Acc.number: NC_002505.1, NC_002506.1) using the following settings: Mismatch cost=2, Insertion cost=3, Deletion cost=3, Length fraction=0.8, Similarity fraction=0.8, Global alignment=no, Strand specific=forward, Maximum number of hits for a read=10.
Reads mapping to gene were counted and fold enrichment in the hfq::3XFLAG-tagged samples over the untagged control samples was calculated using the CLC "Differential expression for RNA-seq" tool, independently for each condition. Genes with a fold-change > 2.0 and a p-value ≤ 0.05 were considered to be enriched.
Genome_build: NC_002505.1, NC_002506.1
Supplementary_files_format_and_content: Hfq_RIP-seq_read_counts.xlsx

growth_protocol: V. cholerae wild-type and hfq::3XFLAG-tagged strains were grown in LB medium to low (OD600 of 0.2) and high cell densities (OD600 of 2.0).

extract_protocol:
RNA was isolated using Phenol-Chloroform-Isopropanol extraction. Extracted RNA was DNase digested and cleaned up using standard nucleic acid precipitation procedures.
cDNA libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina (NEB E7300), according to the manufacturer's instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: Cells equivalent to 50 OD600 units were collected and subjected to RNA co-immunoprecipitation.

value: stationary (OD600 of 2.0)

tag: antibody

value: monoclonal anti-FLAG antibody (Sigma, #F1804)


title: Trem2_12_F [GT18.01675]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2

value: F

value: Brain hemisphere


title: Hfq::3XFLAG stationary rep I [Hfq RIP-seq]

description:
MH7_ACAGTG
RNA co-immunoprecipitation
processed data file: Hfq RIP-seq_read_counts.xlsx


title: miR-7KD mice (#3)

city: zunyi

first: xu

last: lin

address: zunyi medical University

institute: zunyi medical University

description: This sample is a brain tissue cell from a wild type mouse. This cell is a representative sample of three wild-type biological replicates used in this experiment.

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: brain

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wild type

value: brain


title: control stationary rep II [Hfq RIP-seq]

description:
MH6_TAGCTT
RNA co-immunoprecipitation
processed data file: Hfq RIP-seq_read_counts.xlsx

value: wild-type


title: Ctrl_004_RBG18962

description: Ctrl_ICGScluster2_001_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)


title: C57BL/6J_12_F [GT18.01673]

extract_protocol: Upon arrival at the terminal endpoint for each aged mouse cohort, individual animals were weighed prior to intraperitoneal administration of ketamine (100mg/kg) and xylazine (10mg/kg). First confirming deep anesthetization via toe pinch, an incision was made along the midline to expose the thorax and abdomen followed by removal of the lateral borders of the diaphragm and ribcage revealed the heart. A small cut was placed in the right atrium to relieve pressure from the vascular system before transcardially perfusing the animal with 1XPBS via injection into the left ventricle. With the vascular system cleared, the entire brain was carefully removed and weighed before hemisecting along the midsagittal plane. Hemispheres were immediately placed in a cryovial and snap-frozen on dry ice. Brain samples were stored at -80°C until RNA extraction was performed. RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher, Waltham, MA). Brain hemispheres were thawed to 0°C and were lysed and homogenized in TRIzol Reagent (ThermoFisher). After the addition of chloroform, the RNA-containing aqueous layer was removed for RNA isolation according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA Total RNA Nano assay (Agilent Technologies, Santa Clara, CA).

value: Wild type mouse used as control


title: control stationary rep I [Hfq RIP-seq]

description:
MH5_TGACCA
RNA co-immunoprecipitation
processed data file: Hfq RIP-seq_read_counts.xlsx


title: R2 Pos H3K9ac Chipseq

first: Cristina

last: Pina

address: Long Road

department: Department of Haematology Cambridge Biomedical Campus NHS - Blood and Transplant

country: United Kingdom

institute: University of Cambridge

data_processing:
ChIP-seq reads were aligned to mm10 genome assembly using BWA algorithm.
MACS2 peak-calling algorithm was used to call peaks.
ENCODE2 guidelines were followed while peak-calling for histone marks. All the histone marks were evaluated using “narrow peak-calling” step. Q-value was set at 0.05 for all the marks.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Bed files containing narrowPeak and bedgraph files generated by MACS2.

source_name: Bone marrow

growth_protocol: MLL-AF9 AMLs generated from lineage-depleted BM cells retrovirally (RV)-transduced for expression of the MLL-AF9 fusion oncogene and transplanted into lethally irradiated mouse recipients.

extract_protocol:
5.10^5 (H3K27ac and H3K4me1) - 5.10^6 (H3K9ac and H3K4me3) cells per condition were cross-linked in 1% formaldehyde, lysed and sonicated as described (Tzelepis et al, 2016), using 33 cycles of 30'' ON/30''OFF. Chromatin was immunoprecipitated with anti-H3K9ac (Millipore 07-352), anti-H3K27ac (abcam -ab4729), anti-H3K4me1 (abcam ab8895) or anti-H3K4me3 (abcam ab8580) antibodies and captured with 1:1 protein A and protein G magnetic beads. After reverse cross-linking, immunoprecipitated and input DNA were purified using a Zymo DNA clean and concentrator5 kit.
Standard Illumina ChIP library protocols with Nextera indices

treatment_protocol: Kat2a Flox/Flox Mx1-Cre -/- (WT) or Mx1-Cre+/- (KO) mice were treated with pIpC for locus excision and BM collected 4-6 weeks later for RV transduction and injection into irradiated recipients. Terminal AML BM samples were pooled (WT - 5; KO - 4) for chromatin preparation.

tag: disease state

value: MLL-AF9 leukemia

value: Bone marrow

value: Kat2a KO

tag: chip antibody

value: anti-H3K9ac (Millipore 07-352)


title: APOE4Trem2_6_F [GT18.01669]

data_processing: The NanoString Mouse AD gene expression panel was used for gene expression profiling on the nCounter platform (NanoString, Seattle, WA) as described by the manufacturer. nSolver software was used for analysis of NanoString gene expression values.Normalization was done by dividing counts within a lane by geometric mean of the housekeeping genes from the same lane. For the downstream analysis, counts were log-transformed from normalized count values.

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)

tag: gender


title: Hfq::3XFLAG exponential rep II [Hfq RIP-seq]

description:
MH4_ACTTGA
RNA co-immunoprecipitation
processed data file: Hfq RIP-seq_read_counts.xlsx

value: exponential (OD600 of 0.2)


title: Trem2_12_F [GT18.01670]


title: Hfq::3XFLAG exponential rep I [Hfq RIP-seq]

description:
MH3_CGATGT
RNA co-immunoprecipitation
processed data file: Hfq RIP-seq_read_counts.xlsx


title: WT  MICE (#7)

description: This sample is a brain tissue cell from a wild type mouse. This cell is a representative sample of three miR-7deficiency biological replicates used in this experiment.

value: miR-7 KD


title: APOE4_2_M [GT18.01668]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)

value: M


title: APOE4Trem2_12_F [GT18.01671]

value: F


title: control exponential rep II [Hfq RIP-seq]

description:
MH2_CAGATC
RNA co-immunoprecipitation
processed data file: Hfq RIP-seq_read_counts.xlsx

value: monoclonal anti-FLAG antibody (Sigma, #F1804)


title: R1 Neg H3K9ac Chipseq

value: Kat2a WT


title: R2 Neg H3K9ac Chipseq


title: H1 ESCs

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 1

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for PrimeView Human Gene Expression Array

data_processing: The data were normalized using RMA normalization from R/Bioconductor

label: biotin

source_name: embryonic stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Urine samples were collected from 10 healthy donors with diverse age, gender and ethnicity (Table 1). Ethical approval (Number: 5704) was granted by the ethical committee of the medical faculty of Heinrich Heine University, Düsseldorf, Germany. Isolation and expansion of the UdRPCs followed the established protocols of Zhou et al. (2011) and Bohndorf et al. (2017). For differentiation of the UdRPCs 10µM CHIR99021 was added to the cell culture medium for 2 days.

extract_protocol: RNA was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research, CA, USA) according to provider guidelines. After checking the quality of mRNA, 500 ng of RNA were used for complementary DNA synthesized with the TaqMan Reverse Transcription Kit (Applied Biosystems).

treatment_protocol: UdRPCs were reprogrammed into iPSCs using an integration-free episomal based transfection system without pathway inhibition. Briefly, UdRPCs were nucleofected with two plasmids pEP4 E02S ET2K (Addgene plasmid #20927) and pEP4 E02S CK2M EN2L (Addgene plasmid #20924) expressing a combination of pluripotency factors including OCT4, SOX2, LIN28, c-MYC, KLF4, and NANOG using the Amaxa 4D-Nucleofector Kit according to the manufacturer’s guidelines. The nucleofected cells were cultured on Matrigel coated 6-well plate containing StemMACs or mTeSR media under hypoxic conditions. Emerging colonies were picked and transferred to a new plate and cultured under normoxic conditions. After few passaging, vector-dilution PCR and genomic DNA fingerprinting were performed. Karyotyping was performed at the Institute of Human Genetics and Anthropology, Heinrich Heine University, Düsseldorf. Finally, embryoid body (EB) formation and analysis were carried out as previously described (Bohndorf et al. 2017).

value: embryonic stem cells

tag: ethnicity


title: H9 ESCs

description: replicate 1


title: C57BL/6J_12_M [GT18.01653]

value: Brain hemisphere


title: B4_HFF_iPS

description: replicate 1

source_name: induced pluripotent stem cells from human foreskin fibroblasts (HFF)


title: UM27_CHIR

description: replicate 1

source_name: UdRPCs treated with CHIR99021

value: urine derived renal progenitor cells (UdRPCs)

value: Caucasian


title: R2 Pos H3K4me3 Chipseq

value: MLL-AF9 leukemia

value: anti-H3K4me3 (Abcam ab8580)


title: control exponential rep I [Hfq RIP-seq]

description:
MH1_ATCACG
RNA co-immunoprecipitation
processed data file: Hfq RIP-seq_read_counts.xlsx

value: wild-type


title: R1 Pos H3K9ac Chipseq

value: Bone marrow

value: Kat2a KO

value: anti-H3K9ac (Millipore 07-352)


title: R1 Pos H3K4me3 Chipseq


title: R2 Neg H3K4me3 Chipseq


title: Ctrl_007_RBG18998

description: Ctrl_ICGScluster2_003_HSCs (CD31+kit+CD45-)

value: Hematopoietic stem cells (CD31+kit+CD45-)

value: Ctrl


title: UF45_CHIR

description: replicate 1


title: hREPCs

description: replicate 1

source_name: renal epithelial proximal cells

value: renal epithelial proximal cells


title: C57BL/6J_6_M [GT18.01666]

value: Wild type mouse used as control

value: M


title: UF21

description: replicate 1

source_name: urine derived renal progenitor cells (UdRPCs)

value: F


title: APOE4_2_M [GT18.01652]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: APOE4_12_M [GT18.01650]

value: Brain hemisphere


title: R1 Neg H3K4me3 Chipseq

value: Kat2a WT


title: R2 Pos H3K4me1 Chipseq

value: anti-H3K4me1 (Abcam ab8895)


title: C57BL/6J_6_F [GT18.01651]


title: C57BL/6J_6_M [GT18.01649]


title: R1 Pos H3K4me1 Chipseq

value: MLL-AF9 leukemia


title: APOE4_12_F [GT18.01648]


title: R2 Neg H3K4me1 Chipseq


title: R1 Neg H3K4me1 Chipseq


title: APOE4Trem2_6_F [GT18.01647]

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)


title: C57BL/6J_12_M [GT18.01646]


title: UM51

description: replicate 1

value: urine derived renal progenitor cells (UdRPCs)

value: African


title: APOE4_2_M [GT18.01644]


title: UF31

description: replicate 1


title: R2 Pos H3K27ac Chipseq

value: Bone marrow

value: Kat2a KO

value: anti-H3K27ac (Abcam ab4729)


title: Trem2_2_F [GT18.01643]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2


title: UF45

description: replicate 1

value: Caucasian


title: iPS_UF45

description: replicate 1

source_name: induced pluripotent stem cells from UdRPCs


title: Trem2_6_F [GT18.01642]


title: R2 Neg H3K27ac Chipseq


title: iPS_UM51

description: replicate 1

value: induced pluripotent stem cells from UdRPCs


title: R1 Pos H3K27ac Chipseq


title: Trem2_12_F [GT18.01641]


title: UM51_CHIR

description: replicate 1

value: M


title: iPS_UM27

description: replicate 1


title: R1 Neg H3K27ac Chipseq


title: R2 Pos Input H3K9ac


title: UF61

description: replicate 1

source_name: mesenchymal stem cells derived from AF1

value: mesenchymal stem cells derived from AF1

value: F


title: APOE4_6_M [GT18.01626]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: UM27

description: replicate 1


title: UM48

description: replicate 1


title: UF60

description: replicate 1


title: iPS_UF21

description: replicate 1


title: rip_rep3

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Anti-Flag pull down

data_processing:
cDNA libraries were prepared  using SMARTer RNA-Seq Pico Input kit and sequenced as 75bp paired-end reads on Illumina Nextseq 500 machine. Raw sequencing reads were demultiplexed into Fastq file format using Illumina’s bcl2fastq v2.20.
Reads were aligned to UCSC genome dm6 with STAR aligner (version STAR_2.6.1c), using Ensembl 96 gene models.
Only uniquely mapped reads were selected for downstream analysis using Samtools. Duplicated reads were also removed using Picard to correct PCR amplification bias between samples.
Genome_build: dm6
Supplementary_files_format_and_content: Bigwig files

source_name: Ovary

growth_protocol: Drosophila cultured at 29 degree for 3 days, ovaries were dissected and diassociated with type II collagenase, and mature eggs were fltered and discarded.

extract_protocol:
For M5C-seq, total RNA were extracted with Qiagen RNeasy Midi Kit and RNA were isolated with antibody. For RIP-seq, tissues were lysated with 1X polysome lysis buffer and RNA-protrein complexes were isolated with antibody.
Libraries were prepared according to TAKARA SMARTer RNA-Seq Pico Input kit
M5C-seq/RIP-seq

value: Ovary


title: rip_rep2

description: Anti-Flag pull down


title: APOE4Trem2_12_M [GT18.01627]

value: Brain hemisphere


title: Trem2_6_M [GT18.01623]


title: UM54

description: replicate 1


title: rip_rep1

description: Anti-Flag pull down


title: R1 Neg Input H3K9ac

value: MLL-AF9 leukemia

value: Kat2a WT


title: R2 Pos Input H3K4me3


title: R2 Neg Input H3K9ac


title: m5c_rep2

description: Anti-5-methylcytosine (5-mC) antibody pull down


title: R1 Pos Input H3K4me3


title: Trem2_2_M [GT18.01621]


title: R1 Pos Input H3K9ac


title: APOE4Trem2_2_F [GT18.01620]

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)


title: C57BL/6J_12_F [GT18.01624]

value: Wild type mouse used as control


title: APOE4Trem2_2_M [GT18.01619]


title: m5c_rep1


title: R2 Neg Input H3K4me3

value: Bone marrow


title: APOE4Trem2_12_M [GT18.01618]


title: R1 Neg Input H3K4me3


title: Trem2_12_M [GT18.01617]


title: striatum, KI-96, rep3

city: Guangzhou

first: Su

last: Yang

address: Huangpu Avenue

institute: Jinan University

data_processing:
Sequencing adapters were trimmed by BBduk (minlen=100 ktrim=r k=23 mink=11 hdist=1 tpe tbo; http://jgi.doe.gov/data-and-tools/bb-tools/). Reads with length under 100 bp after trimming were discarded.
lipped reads were aligned to mouse genome GRCm38 (primary assembly) by STAR aligner with default settings. Read counts for genes were obtained by using HTSeq.
All mRNA differential expression analyses were performed in R using the Bioconductor package DESeq2 version 1.24.0. We removed one WT sample identified as a potential outlier and used the default settings with ‘sac’ as a covariate variable.
We tested differential expression in two-sample tests of KI (KI-96 and E1) samples versus wild type (WT) samples.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for all samples

source_name: Striatum tissue

growth_protocol: Mice were housed and handled in accordance with policies of the Emory University Environmental Enrichment Program for Research Animals. The Animal Care Facility at Emory University meets the requirements of Federal Law (89-544, 91-579) and NIH regulations; the facility is accredited by the American Association for Accreditation of Laboratory Care (AAALC). The Department of Animal Resources provides veterinary care by laboratory animal veterinarians who are well trained in the laboratory use of these species. The mice (5 per cage maximum) were housed in a 12-hour light (7:00 AM - 7:00 PM) and 12-hour dark (7:00 PM - 7:00 AM) cycle at a controlled temperature (22℃), and fed ad libitum a regular chow diet.

extract_protocol:
RNAs from the striatum of WT, KI-96, and E1 mice at 6 months of age were extract using RNeasy Lipid Tissue Kit (Qiagen).
Library was constructed by Novogene.

value: 6-month old

tag: mouse id

value: Striatum


title: R2 Pos Input H3K4me1

description: The same input file was used for two different markers in GSM3333432 and GSM3333436

value: Kat2a KO


title: APOE4Trem2_2_M [GT18.01622]

first: Christoph

last: Preuss

institute: The Jackson Laboratory


title: m5c_rep3


title: striatum, KI-96, rep2


title: APOE4Trem2_12_F [GT18.01615]


title: R1 Pos Input H3K4me1

description: The same input file was used for two different markers in GSM3333431 and GSM3333435


title: striatum, KI-96, rep1


title: R2 Neg Input H3K4me1

description: The same input file was used for two different markers in GSM3333430 and GSM3333434


title: Trem2_2_F [GT18.01640]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2


title: striatum, KI-96, rep4


title: striatum, E1, rep4


title: APOE4_2_M [GT18.01639]


title: R1 Neg Input H3K4me1

description: The same input file was used for two different markers in GSM3333429 and GSM3333433


title: striatum, E1, rep3


title: R2 Pos Input H3K27ac


title: PCM9

type: genomic

city: New York

first: Varshini

last: Vasudevaraja

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

description: FFPE

hyb_protocol: The DNA is bisulfite-converted using the EZ-96 DNA Methylation Kit from Zymo Research.  After bisulfite conversion, the DNA then undergoes restoration using the Illumina Infinium HD FFPE DNA Restore Kit. The DNA then undergoes a whole-genome overnight amplification.  The amplified DNA is then enzymatically fragmented using end-point fragmentation.  The DNA is then isolated and precipitated in isopropanol and re-suspended in Illumina RA1 buffer.  The re-suspended DNA is then denatured at 95⁰C, and the resulting single-stranded DNA is dispensed directly onto the Illumina Array for hybridization.  The DNA hybridizes with the array overnight in an oven at 48⁰C.  After hybridization, the BeadChips are then washed with Illumina PB1 buffer to remove any unhybridized and non-specifically hybridized DNA.

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: minfi- R package was used to analyze the data. Data was preprocessed, quantile normalized and poor samples and probes were removed based on mean detection Pvalues per sample. 'dmpFinder' was used to identify the differenitally methylated probes between MPNSTs and DMs. qvalue < 0.01 are considered significant.

label: Cy5 and Cy3

source_name: Skin melanoma

label_protocol: Standard Illumina Protocol

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens with the Maxwell® 16 FFPE Plus LEV DNA Purification Kit

tag: cancer type

value: PCM

value: Skin melanoma


title: C57BL/6J_2_M [GT18.01638]

city: Bar Harbor

address: 600 Main Street

value: M


title: striatum, E1, rep2


title: Trem2_6_F [GT18.01637]

value: F


title: R1 Pos Input H3K27ac


title: PCM12

description: FFPE


title: striatum, E1, rep1


title: PCM2

description: FFPE


title: PALM23

description: FFPE

value: PALM


title: PCM10

description: FFPE


title: R2 Neg Input H3K27ac


title: PCM1

description: FFPE


title: PALM25

description: FFPE


title: APOE4_2_M [GT18.01636]

value: APOE4 KI

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: striatum, WT, rep7

value: WT


title: PCM4

description: FFPE


title: PCM7

description: FFPE


title: PALM26

description: FFPE


title: APOE4_12_M [GT18.01635]

value: Brain hemisphere


title: R1 Neg Input H3K27ac

value: MLL-AF9 leukemia

value: Kat2a WT


title: PALM22

description: FFPE


title: striatum, WT, rep6


title: St_2

city: Beijing

first: Wenkai

last: Hui

state: Beijing

address: Qinghua East Street

institute: Beingjing Forestry University

data_processing:
The unigenes were de novo assembled using Trinity v2.4.0 software
Sequence adaptors, N’s more than 10% and low-quality reads (Q phred ≤ 20 for >50% read) were removed by Illumina Casava v1.8 software.
The read count of each unigene among the samples was calculated and converted to expect number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) as described by Trapnell et al (2010).
Genome_build: FASTA file is available on the series record.
Supplementary_files_format_and_content: read count and FPKM

organism: Zanthoxylum armatum

source_name: Stems

extract_protocol:
Total RNA of each sample was separately extracted using Magen Plant RNA Kit (HiPure HP Plant RNA Mini Kit, Guangzhou) following the instructions of the manufacturer. The quality of total RNA was investigated by agarose gel electrophoresis and Nanodrop 2100 (Agilent, USA).
The fifteen cDNA libraries were constructed and sequenced using the Illumina HiSeq™ 4000 (Illumina, USA) platform at Novegene Bioinformatics Technology Co. Ltd (Beijing, China).

value: Stems

tag: sampling time


title: striatum, WT, rep4


title: NALM9

description: FFPE

value: NALM


title: APOE4Trem2_2_F [GT18.01634]

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)


title: Trem2_6_F [GT18.01632]


title: Trem2_12_M [GT18.01631]


title: St_1


title: RO_3

source_name: Roots

value: Roots


title: striatum, WT, rep3

value: 6-month old

value: Striatum


title: PALM19

description: FFPE


title: striatum, WT, rep2


title: PALM17

description: FFPE


title: APOE4Trem2_2_M [GT18.01630]


title: PALM16

description: FFPE


title: St_3


title: Trem2_6_F [GT18.01628]

value: Homozygous Trem2*R47H model harboring a rare deleterious missense variant in TREM2


title: striatum, WT, rep1


title: PALM14

description: FFPE

value: Skin melanoma


title: striatum, WT, rep5


title: RO_1


title: PALM11

description: FFPE


title: ML_3

source_name: mature leaves

value: mature leaves


title: ML_2


title: APOE4Trem2_6_F [GT18.01613]

value: F


title: PALM13

description: FFPE

value: PALM


title: ML_1


title: PCM11

description: FFPE

value: PCM


title: PALM20

description: FFPE


title: APOE4Trem2_12_F [GT18.01612]


title: PALM12

description: FFPE


title: LB_3

source_name: leaf buds

value: leaf buds


title: C57BL/6J_12_M [GT18.01614]

value: Wild type mouse used as control

value: M


title: Trem2_2_F [GT18.01610]

value: Brain hemisphere


title: RO_2


title: LB_2


title: PCM5

description: FFPE


title: APOE4Trem2_6_M [GT18.01609]


title: PALM9

description: FFPE


title: Fr_3

source_name: Fruits

value: Fruits


title: Trem2_6_F [GT18.01633]


title: Fr_2


title: Trem2_12_M [GT18.01605]


title: C57BL/6J_12_F [GT18.01606]


title: APOE4Trem2_6_M [GT18.01604]


title: PALM15

description: FFPE


title: RMNT3RV

city: La Jolla

first: Paul

middle: A

last: Insel

state: CA

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

data_processing:
FASTQC to inspect quality of sequencing.
Kallisto v0.43.1 on rat reference transcriptome, ensembl release 79, with bias correction, yielding transcript-level TPM and counts estimates.
Transcript-level expression was converted to gene-level expression using tximport.
Differential expression analysis was performed using gene-level counts estimates as input for edgeR
Sets of differentially expressed genes were subsequently analyzed via tools such as Enrichr, GSEA and STRING
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: excel files with gene expression in TPM and estimated counts, obtained from tximport

organism: Rattus norvegicus

source_name: Right Ventricle

extract_protocol:
Snap-frozen ventricular tissue was homogenized in RLT Lysis buffer (Qiagen). RNA from this lysate was extracted using the RNeasy mini kit (Qiagen) with on-column DNase-1 digestion.
Libraries were constructed at the UCSD IGM core using the Illumina Truseq stranded mRNA protocol, using ~0.5-1 ug of total RNA as input.
RNA-sequencing on a Hiseq-4000, 12 samples multiplexed on a single lane (~25-30 million single reads per sample)

treatment_protocol: Adult rats were kept in either normoxia or hypoxia (10% O2) for 2 weeks before euthanizing and collecting cardiac tissue.

value: Sprague-Dawley

value: 3-4 months

value: Right Ventricle


title: APOE4_6_M [GT18.01730]

value: APOE4 KI

value: Mouse to human gene prioritization resulted in the selection of 760 key mouse genes targeting a subset of highly co-expressed human genes, which explained a significant proportion of the observed variance across the 30 human AMP-AD co-expression modules.


title: C57BL/6J_6_M [GT18.01719]


title: RMNT3LV

source_name: Left Ventricle

value: Left Ventricle


title: Fr_1


title: RMNT2RV


title: C57BL/6J_6_F [GT18.01717]


title: APOE4_6_F [GT18.01697]

value: Mouse model carrying a humanized version of the strongest LOAD associated risk allele (Homozygous APOE-ε4)


title: APOE4Trem2_2_F [GT18.01607]

value: Mouse model harboring both, the common (Homozyogus APOE-ε4)  and rare AD risk variants (Homozygous Trem2*R47H)


title: RMNT2LV


title: APOE4_6_M [GT18.01696]


title: PALM2

description: FFPE

value: Skin melanoma


title: APOE4_6_F [GT18.01691]

value: F


title: RMNT1LV


title: C57BL/6J_6_M [GT18.01682]


title: PALM4

description: FFPE

value: PALM


title: RMCH4RV


title: PALM10

description: FFPE


title: PALM5

description: FFPE


title: LB_1


title: NALM8

description: FFPE

value: NALM


title: NALM6

description: FFPE


title: C57BL/6J_6_F [GT18.01681]


title: RMCH4LV


title: PALM8

description: FFPE


title: RMCH2RV


title: PALM7

description: FFPE


title: RMCH2LV


title: APOE4_6_M [GT18.01672]


title: PALM1

description: FFPE


title: C57BL/6J_6_F [GT18.01645]


title: RMCH1RV


title: APOE4_6_F [GT18.01616]


title: C57BL/6J_6_M [GT18.01611]


title: Sample_3-1L

status: Public on Feb 02 2020

city: New Haven

first: Stefania

last: Nicoli

state: CT

address: 300 George street

department: Internal Medicine

institute: Yale University

description: mRNA

data_processing:
After sequencing, reads were filtered based on qc and the Illumina adapter was removed.
Alignment against total human genome (GRCh38, GTF= GENECODE v 27) was performed using STAR with params=' --runThreadN 12  --outFilterMismatchNmax 4  --quantMode GeneCounts  '
Total number of reads for each individual human mRNA were counted by STAR software.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.ReadsPerGene.tab: Tab-delimited files containing: column 1 – gene ID; column 2 – counts for unstranded RNA-seq; column 3 – counts for the 1st read strand aligned with RNA; column 4 – counts for the 2nd read strand aligned with RNA.

source_name: HUVEC

growth_protocol: HUVEC cells were grown in EGM Bullet Kit medium in culture. PDMS matrix with a 3 or 30 kPa module were made, and 4 dishes for each condition were coated overnight with 1% fibronectin.

extract_protocol:
Cells were lysated using TRIzol follow the company protocols.
Total RNA were used to prepare Illumina libraries using the Lexogen SPLIT kit.

treatment_protocol: No cell treatment.

tag: cell type

value: Human umbilical vein endothelial cell (HUVEC)

tag: growth condition

value: 3 kPa


title: NALM2

description: FFPE


title: NALM7

description: FFPE


title: NALM5

description: FFPE


title: Sample_3-2L

description: mRNA


title: Sample_30-3L

description: mRNA

value: 30 kPa


title: Sample_30-1L

description: mRNA


title: PALM6

description: FFPE


title: RMNT1RV


title: MALM9

description: FFPE

value: MALM


title: Sample_3-3L

description: mRNA


title: Dl3vg_1

city: Hilo

first: Kelsey

last: Coffman

state: HI

address: 64 Nowelo St

department: Tropical Pest Genetics and Molecular Biology Research Unit

institute: USDA-ARS

description: Venom glands were collected in triplicate.

data_processing:
Reads were filtered with the fastx toolkit (hannonlab.cshl.edu/fastx_toolkit/) to retain reads with >90% of bases with a PHRED score of 30 or higher for both reads in a pair.
Genome_build: de novo assembly

organism:
Diachasmimorpha longicaudata
Diachasmimorpha longicaudata entomopoxvirus

source_name: wasp venom gland

growth_protocol: D. longicaudata wasps were reared with a 16L:8D photoperiod at 26-27 °C and 55-60% relative humidity.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN) with on-column DNase digestion, followed by a secondary DNase treatment using the TURBO DNA-free Kit after RNA isolation.
Illumina-compatible stranded RNA library was constructed with the Kapa Biosystems RNA library preparation chemistry using 1ug RNA from each venom gland sample. Library was sequenced on one run of an Illumina NextSeq instrument, which generated 75bp paired-end reads.

tag: developmental stage

value: unemerged adult

tag: Sex

value: female

value: venom gland


title: NALM3

description: FFPE


title: Sample_3-3S

description: microRNA

data_processing:
After sequencing, reads were filtered based on qc and the Illumina adapter was removed.
Alignment against total human genome (GRCh38, GTF= GENECODE v 27) was performed using STAR with params=' --runThreadN 16  --outFilterMismatchNmax 1  --outFilterMultimapScoreRange 0  --quantMode TranscriptomeSAM GeneCounts  --outReadsUnmapped Fastx  --outSAMtype BAM SortedByCoordinate  --outFilterMultimapNmax 10  --outSAMunmapped Within  --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0  --outFilterMatchNmin 16  --alignSJDBoverhangMin 1000  --alignIntronMax 1  --outWigType wiggle  --outWigStrand Stranded  --outWigNorm RPM
Total number of reads for each individual human microRNA were counted by STAR software.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.ReadsPerGene.tab: Tab-delimited files containing: column 1 – gene ID; column 2 – counts for unstranded RNA-seq; column 3 – counts for the 1st read strand aligned with RNA; column 4 – counts for the 2nd read strand aligned with RNA.

extract_protocol:
Cells were lysated using TRIzol follow the company protocols. Total RNA were run in a 15% denaturizing gel with 7 M urea (0.8 ml 10x TBE, 1.4 ml water, 3.8 g urea, 3 ml acrylamide, 64 ul 10% APS, 4 ul TEMED). The region between 15 and 31 nt was cut and small RNA fraction was extracted from the gel using 0.3 M NaCl-TE overnight and purified using isopropanol.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: Sample_3-2S

description: microRNA


title: Sample_3-1S

description: microRNA


title: Sample_30-3S

description: microRNA