title: Kidney cortex biopsy_baboon_female_LS_15113

description:
LS_15113
20210119_Females_Transcripts_LS_GEO.csv

value: kidney cortex

value: female

value: Southwest national primate research center

value: Ultrasound guided biopsy snap frozen immediately in liquid nitrogen

value: Animals were sedated with ketamine (10mg/kg, IM) and maintained on isoflurane (1.3-3.0%) anesthetic throughout the procedures. Buprenorphine (0.2 mg/kg, SQ) was administered for post operative pain relief after surgery and as needed over 24-48 hour period.


title: Brain_Week5_NMF421_7

status: Public on Sep 01 2022

type: SRA

city: Bar Harbor

first: Robert

last: Burgess

state: ME

address: 600 Main St

country: USA

institute: The Jackson Laboratory

library_source: transcriptomic

data_processing:
Filtering of reads was perfomed using NGSQCToolkit/2.3 and custom perls scripts
Read alignment was done using bowtie2/2.2.0
Read count estimations were performed using rsem/1.2.12
Genome_build: We used the Mus musculus GRCm38v74 genome for this work
Supplementary_files_format_and_content: Read counts matrix from rsem

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Tissues 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).
Libraries were prepared using the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  Libraries were checked for quality and concentration using the D5000 ScreenTape assay (Agilent Technologies) and quantitative PCR (KAPA Biosystems), according to the manufacturers’ instructions.
Libraries were pooled and sequenced 70 bp single-end on the HiSeq 4000 (Illumina) using HiSeq 3000/4000 SBS Kit reagents (Illumina), targeting 30 million reads per sample.

tag: genotype

value: Nadk2 -/-

tag: strain

tag: tissue

value: Brain

tag: age

value: Week 5

tag: Sex

value: male


title: O3S2

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

country: Germany

institute: Max Planck Institute

description: each sample is genomic material from one animal.

library_source: genomic

data_processing:
The fastq reads were mapped to the mm10 genome using bowtie2 (V. 2.3.5) (Langmead & Salzberg, 2012). Duplicates were removed using MarkDuplicates program of Picard Tools (V. 2.21.4) (http://broadinstitute.github.io/picard). For mapping spike-in fragments to the yeast genome, the ‘–no-overlap–no-dovetail’ options were set and mapped to a repeat-masked version of the yeast genome (R64) to avoid crossmapping of the mouse genome to that of the yeast genome.
Peak calibration was done as described (Skene & Henikoff, 2017). The peaks were then called using the SEACR-package (V. 1.3) in ‘stringent‘-mode (Meers et al, 2019).
Assembly: mm10
Supplementary files format and content: Peak calibration was done as described (Skene & Henikoff, 2017). The peaks were then called using the SEACR-package (V. 1.3) in ‘stringent‘-mode (Meers et al, 2019).

molecule: genomic DNA

source_name: Liver tissue

extract_protocol:
50mg of 4 young and 4 old mouse liver tissues were used. 5million of nuclei were extracted using the same process described for the ATAC-seq experiment. CUT&RUN  was performed on 1 million nuclei per sample as previously described with modifications (Skene & Henikoff, 2017). Nuclei were prepared using the Nuclei EZ prep kit (Sigma-Aldrich, NUC-101). Subsequently, nuclei were washed twice with Wash Buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM Spermidine) and bound to activated Concanavalin A beads for 10 min at room temperature. Cell-bead suspension was then resuspended in antibody buffer (20 mM MHEPES, 150 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin, 2 mM EDTA) and incubated overnight at 4°C with S2-phospho (ab5095), S5-phospho (ab 5408) and PolII-CTD (ab26721) antibodies from Abcam, in a concentration 1:250. Cell-bead suspension was then washed twice with Digitonin Buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin) and incubated with 2.5 µl EpiCypher CUTANA pAG-MNase, for 10 min. After washing samples twice with Digitonin buffer, 1 µl 100 mM CaCl2 was added to samples which were incubated for 2 h at 4°C, rotating. To stop the reaction, STOP buffer (340 mM Nacl, 20 mm EDTA, 4 mM EGTA, 0.02%Digitonin, 50 µg/ml RNase A, 50 µg/ml Glycogen, sonicated yeast DNA as spike-in) was added in each tube. Samples were incubated at 37°C for 10 min at 500 rpm, and after centrifugation, liquid was collected, DNA was purified using Zymo DNA clean concentrator kit.
Libraries were prepared as described in Tessarz et al, 2014

value: liver

value: 18 months

tag: antibody


title: Kidney cortex biopsy_baboon_female_LS_14740

city: Winston Salem

first: Laura

middle: A

last: Cox

state: NC

address: 1 Medical Center Blvd

department: Internal Medicine

institute: Wake Forest School of Medicine

description:
LS_14740
20210119_Females_Transcripts_LS_GEO.csv

data_processing:
All transcripts were processed together in Partek Flow with an average read length of greater than 90 (minimum=25) and an average Phred score of greater than 30 (minimum=30).
Reads were aligned to the olive baboon genome (papAnu2.0; March 2012) identifying 53,120 transcripts.
Transcripts were excluded where the sum was less than or equal to 14 among all samples and normalized using TMM with a +1 offset to eliminate zeros for downstream analyses.
The full transcript list generated in Partek Flow was imported into Partek Genomics Suite for principal component analysis (PCA) (Partek®, Inc).
Transcripts were filtered for expression values totaling <14 among all samples and filtered for the top 20,000 transcripts based on coefficient of variation prior to diet-specific WGCNA.
The R package WGCNA was run as a Pearson’s correlation with default settings as described by Langfelder and Horvath34.
Genome_build: papAnu2.0
Supplementary_files_format_and_content: Matrix table with annotated normalized transcript counts for every transcript and WGCNA results from LS samples.
Supplementary_files_format_and_content: Matrix table with annotated normalized transcript counts for every transcript and WGCNA results from HS samples.

organism: Papio hamadryas

source_name: Kidney cortex biopsy

growth_protocol: Animals were maintained on a low salt chow diet their whole life leading up to the study.

extract_protocol:
RNA was isolated from kidney biopsy samples using the Direct-zol RNA Miniprep Plus Kit (Zymo Research). Tissue was homogenized in 600 μL of TRI reagent (Zymo Research) using a BeadBeater for 3 x 30 sec with RNA purification according to the Direct-zol RNA Miniprep Plus Kit instructions. RNA was quantified by Qubit RNA BR Assay Kit (Invitrogen) and RIN was determined by with an RNA ScreenTape Kit on the Tapestation 2200 (Agilent).
cDNA libraries were prepared using the KAPA Stranded mRNA-Seq Kit (Roche). Libraries were quantified by Qubit dsDNA Assay Kit (Invitrogen) and quality was determined by with a DNA ScreenTape Kit on the Tapestation 2200 (Agilent).

tag: animal id

tag: sample name

tag: diet

value: low salt control chow

tag: colony

tag: collection method

tag: surgery anestetic

tag: treatment

tag: diet length

value: 6 weeks

tag: sodium in diet

value: 17.3 mmol Na+/500 g food consumed


title: eyeball organization, Ac-rBc-PI-PLC-A1 protein, 24h rep2

city: wenzhou

first: Bianjin

last: Sun

state: zhejiang

address: No. 270 Xueyuan West Road, Lucheng District

country: China

institute: School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: eyeball organization from C57/B6 mouse

growth_protocol: Six- to eight-week-old C57BL/6J mice were purchased from the Chinese Academy of Sciences, Shanghai Laboratory Animal Center (SLAC) .The mice were housed in an environment on a 12 h light/12 h dark cycle.Müller glial cells were cultured in DMEM containing 10% heat-inactivated fetal bovine serum (FBS; Ausvin) and penicillin–streptomycin (50 IU/ml and 50 mg/ml, respectively, Beyotime)

extract_protocol:
RNA was harvested using RNAprep pure Cell / Bacteria Kit (Tiangen)
The RNA samples were qualified for library construction. The mRNA SEq library can be constructed in two ways: common library or strand specific library. Common library construction is used for conventional projects, and strand specific library construction is used for distinguishing the directionality of strands.

treatment_protocol: Mice were anesthetized with a mixed solution of xylazine (5 mg/kg body weight) and ketamine (70 mg/kg body weight).Then,1ul of the corresponding solution was injected by intravitreal injection.

value: eyeball organization from C57/B6 mouse

tag: cell line

value: eyeball organization

tag: cell type

value: WT

value: Ac-rBc-PI-PLC-A1 protein

tag: time


title: Brain_Week5_NMF421_6

tag: genotype

value: Nadk2 +/+

tag: strain


title: eyeball organization, Inac-rBc-PI-PLC-A1 protein, 24h rep2

tag: tissue

value: Inac-rBc-PI-PLC-A1 protein


title: Kidney cortex biopsy_baboon_female_LS_14690

description:
LS_14690
20210119_Females_Transcripts_LS_GEO.csv

value: kidney cortex

tag: Sex

value: female

tag: age

value: Southwest national primate research center

value: Ultrasound guided biopsy snap frozen immediately in liquid nitrogen


title: O2S2

tag: antibody


title: Y4CTD

value: 3 months

value: CTD


title: Kidney cortex biopsy_baboon_female_LS_14012

description:
LS_14012
20210119_Females_Transcripts_LS_GEO.csv

tag: animal id

tag: sample name

value: Animals were sedated with ketamine (10mg/kg, IM) and maintained on isoflurane (1.3-3.0%) anesthetic throughout the procedures. Buprenorphine (0.2 mg/kg, SQ) was administered for post operative pain relief after surgery and as needed over 24-48 hour period.


title: eyeball organization, Inac-rBc-PI-PLC-A1 protein, 24h rep1


title: Y2CTD

value: liver


title: Brain_Week5_NMF421_8

value: Nadk2 -/-

value: Brain

value: Week 5

value: male


title: eyeball organization, Ac-rBc-PI-PLC-A1 protein, 24h rep1

value: eyeball organization from C57/B6 mouse

value: eyeball organization


title: Brain_Week5_NMF421_4


title: Kidney cortex biopsy_baboon_female_LS_13988

description:
LS_13988
20210119_Females_Transcripts_LS_GEO.csv

tag: diet

value: low salt control chow

tag: colony

value: 6 weeks

value: 17.3 mmol Na+/500 g food consumed


title: Brain_Week5_NMF421_3

value: Nadk2 +/+


title: eyeball organization, pbs, 24h rep2

value: WT

value: PBS


title: Y1CTD


title: Y3CTD


title: eyeball organization, Ac-rBc-PI-PLC-A1 protein, 24h rep3

value: Ac-rBc-PI-PLC-A1 protein


title: BM from xenotransplanted mouse 10 collected at the end of the experiment Ampli-seq

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Data analyzed withthe CRISPResso2 pipeline:
reads were trimmed using the Trimmomatic
paired-end reads were merged using the FLASh and aligned against the reference vector
quantification around the guide cut site was performed for each found allele
Assembly: Custom reference vector AAV sequence and sgRNA
Supplementary files format and content: Tab-separated results of the different allele found with corresponding quantifications
Library strategy: amplicon sequencing

organism: Homo sapiens

source_name: Bone Marrow (BM)

extract_protocol:
gDNA was isolated with QIAamp DNA Micro Kit (QIAGEN) according to the manufacturer’s instructions.
PCR amplicons for individual samples were generated by nested PCR using primers listed in the related manuscript and starting from >50-100 ng of purified gDNA. The first PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to manufacturer instruction using the following amplification protocol: 95°C x 5’min, (95°C x 0.5 min, 60°C x 0.5 min, 72°C x 0.2 5min) x 20 cycles, 72°C x 5 min. The second PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to manufacturer instruction using 5μl of the first-step PCR product and the following amplification protocol: 95°C x 5min, (95°C x 0.5 min, 60°C x 0.5 min, 72°C x 0.3 min) x 20 cycles, 72°C x 5 min. Second-step PCR primers were endowed with tails containing P5/P7 sequences, i5/i7 Illumina tags to allow multiplexed sequencing and R1/R2 primer binding sites (Supplementary Table 5). PCR amplicons were separately purified performing double-side selection with AmpPure XP beads (Beckman Coulter) or QIAquick PCR Purification Kit (QIAGEN). Amplicons concentration and quality was assessed by QuantiFluor ONE dsDNA system and 4200 Tapestation System (Agilent). Amplicons from up to 36 differently tagged samples were multiplexed at equimolar ratios and run

value: Bone Marrow (BM)

tag: time point

value: End of Experiment

value: GE


title: O1S2

value: liver

value: 18 months


title: Brain_Week5_NMF421_5

value: Nadk2 -/-

value: Brain

value: female


title: eyeball organization, pbs, 24h rep3

value: eyeball organization from C57/B6 mouse

tag: treatment


title: Kidney cortex biopsy_baboon_female_LS_17174

description:
LS_17174
20210119_Females_Transcripts_LS_GEO.csv

value: kidney cortex

value: Southwest national primate research center

tag: collection method

value: Ultrasound guided biopsy snap frozen immediately in liquid nitrogen

tag: surgery anestetic

value: Animals were sedated with ketamine (10mg/kg, IM) and maintained on isoflurane (1.3-3.0%) anesthetic throughout the procedures. Buprenorphine (0.2 mg/kg, SQ) was administered for post operative pain relief after surgery and as needed over 24-48 hour period.

tag: diet length


title: eyeball organization, pbs, 24h rep1

tag: cell line

value: eyeball organization

tag: cell type


title: Muscle_Week13_NM2913_4

source_name: Muscle

tag: genotype

value: Muscle

value: Week 13

value: male


title: O4CTD

tag: strain

value: CTD


title: BM from xenotransplanted mouse 9 collected at the end of the experiment Ampli-seq

tag: tissue

value: Bone Marrow (BM)

value: End of Experiment


title: Brain_Week5_NMF421_1

value: Week 5

tag: Sex


title: Brain_Week5_NMF421_2

value: Nadk2 +/+

tag: age


title: BM from xenotransplanted mouse 6 collected at the end of the experiment Ampli-seq

value: GE


title: O3CTD

value: liver

value: 18 months

tag: antibody


title: BM from xenotransplanted mouse 8 collected at the end of the experiment Ampli-seq


title: BM from xenotransplanted mouse 5 collected at the end of the experiment Ampli-seq

value: GE + MSCs


title: im-scWAT, D4, JMJD1A [ChIP-seq]

city: Tokyo

first: Juro

last: Sakai

address: 4-6-1, Komaba, Meguro-ku

department: Division of Metabolic Medicine

country: Japan

institute: Research Center for Advanced Science and Technology, The University of Tokyo

data_processing:
The libraries were sequenced on HiSeq 2500 (Illumina).
Trimmomatic were used to filter out low-quality reads and adapters from ChIP-seq reads in fastq files.
ChIP-seq reads passed quality filtering were aligned to the mouse mm9 genome by using bowtie2.
SAM files generated were converted to sorted bam files by using SAMtools
PCR duplicates in ChIP-seq reads were removed by Picard.
Bigwig files of ChIP-seq were generated by using bamCoverage function of deeptools while signals in blacklist of mm9 were removed.
Assembly: mm9
Supplementary files format and content: bigWig files

source_name: im-scWAT cells

growth_protocol: Immortalized preadipocytes derived from inguinal subcutaneous white adipose tissue (im-scWAT) were cultured in the complete medium (DMEM/F12 containing 1.2 g/L NaHCO3 and 10% FBS)  at 37 °C.

extract_protocol:
Sonicated nuclear fraction was incubated with each antibody and JMJD1A-DNA complexes were isolated.
Libraries were prepared by KAPA Hyper Prep Kit (Nippon Genetics) following manufacturer's protocol.

treatment_protocol: Preadipocytes were cultured until confluent (day 0), and then treated with the culture medium containing  0.125 mM indomethacin, 5 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine, 0.5 μM rosiglitazone, 5 μg/mL insulin, and 1 nM T3) for 48 h (day 2), followed by treatment with only insulin, T3, and rosiglitazone for another 2 days (day 4).

value: im-scWAT cells

tag: time

value: Day 4

tag: chip antibody


title: WT ETP rep2

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 13th street

department: CBRC

institute: Harvard Medical School

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 (mouse genome) assembly using the genome mappers STAR
Assembly: mm10

source_name: Thymus

extract_protocol:
proB, largepreB, smallpreB (BM):  Erythroid, myeloid, T cells, NK cells and mature B lineage (Lin) cells were depleted from bone marrow cell suspensions, and Lin(–)cKitloCD19+CD43+ pro-B cells, Lin(–)CD19+CD43+BP1+ large preB cells, and Lin(–)CD19+CD43–CD25+ small preB cells were sorted by FACSAria (BD Biosciences).    ETP, DN2, DN3, preDP (Thymus):  Erythroid, myeloid, gdT, CD8+CD4+DP, CD8+T, CD4+T, NK and B lineage (Lin) cells were depleted from thymocyte cell suspensions, and Lin(–)CD44+cKit+CD25– ETP, Lin(–)CD44+cKit+CD25+ DN2, Lin(–)CD44–CD25+ DN3, and Lin(–)CD44–CD25– preDP cells were sorted by FACSAria (BD Biosciences).      smallDP, CD8+T, CD4+T (Thymus):  Erythroid, myeloid, NK and B lineage (Lin) cells were depleted from thymocyte cell suspensions, and CD8+CD4+ small DP, CD8+T, and CD4+T were sorted by FACSAria (BD Biosciences).    RNA was isolated using Trizol reagent and Direct-zol RNA prep kit (Zymo Research).
Illumina TruSeq RNA Sample Prep Kit (Illumina) or NEB Next Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB) were used for the construction of sequencing libraries.

value: Lin(-)CD44+cKit+CD25- ETP

value: WT


title: Fibroblasts from early-met lungs of mice treated with doxorubicin (Dox), biol rep 5

city: Tel Aviv

first: Nour

last: Ershaid

state: Israel

address: Postal code 2373,

country: Israel

institute: Tel Aviv University

data_processing:
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1.
Reads were mapped to the Mus musculus genome (mm10) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Fibroblasts (CD45- EpCAM- PDGFRa+)

extract_protocol:
RNA from sorted cells was isolated using the EZ-RNAII Kit (20-410-100, Biological Industries).
MARS-seq protocol was used to generate libraries. MARS-seq libraries were sequenced using Illumina NovaSeq 6000.

value: Fibroblasts (CD45- EpCAM- PDGFRa+)

value: Doxorubicin


title: O2CTD


title: DDNSe ETP rep1

value: DNSe-/-


title: BM from xenotransplanted mouse 3 collected at the end of the experiment Ampli-seq


title: WT ETP rep1


title: Fibroblasts from early-met lungs of mice treated with doxorubicin (Dox), biol rep 4


title: Muscle_Week6_NM2913_8

value: Muscle

value: Week 6

value: female


title: Muscle_Week13_NM2913_3

value: Week 13


title: BM from xenotransplanted mouse 2 collected at the end of the experiment Ampli-seq

value: Bone Marrow (BM)

value: End of Experiment


title: Muscle_Week13_NM2913_1


title: O1CTD

value: CTD


title: DDNSe ETP rep2


title: im-scWAT, D0, JMJD1A [ChIP-seq]

value: Day 0


title: BM from xenotransplanted mouse 7 collected at the end of the experiment Ampli-seq

value: GE


title: Fibroblasts from early-met lungs of mice treated with doxorubicin (Dox), biol rep 3


title: Muscle_Week13_NM2913_2

value: male


title: Muscle_Week6_NM2913_7


title: im-scWAT, D3, si-Mypt1

data_processing:
The libraries were sequenced on HiSeq 2500 (Illumina).
Fastp was used to filter out low-quality reads and adapters from fastq files of RNA-seq reads.
RNA-seq reads were aligned to the mouse mm9 genome by using STAR2.
RPKM tables of RNA-seq were calculated by using GFOLD with GENOCODE comprehensive gene annotation set M1 release.
Assembly: mm9
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample.

growth_protocol: Primary or immortalized preadipocytes derived from inguinal subcutaneous white adipose tissue (scWAT or im-scWAT) were cultured in the complete medium (DMEM/F12 containing 1.2 g/L NaHCO3 and 10% FBS)  at 37 °C.

extract_protocol:
Total RNA was extracted using ISOGEN (Nippongene) following manufacturer's protocol.
Libraries were prepared by TruSeq sample purification kit (Illumina) following manufacturer's protocol.

treatment_protocol: Preadipocytes were transfected with control siRNA or siRNA targeting Mypt1. Preadipocytes were cultured until confluent (day 0), and then treated with the culture medium containing  0.125 mM indomethacin, 5 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine, 0.5 μM rosiglitazone, 5 μg/mL insulin, and 1 nM T3) for 48 h (day 2), followed by treatment with only insulin, T3, and rosiglitazone for another 6 days, with medium replacement every 2 days (day 8).

value: im-scWAT cells

tag: day

value: Day 3


title: im-scWAT, D3, si-Ctr

value: si-Ctr


title: Fibroblasts from early-met lungs of mice treated with doxorubicin (Dox), biol rep 2


title: BM from xenotransplanted mouse 1 collected at the end of the experiment Ampli-seq

value: GE + MSCs


title: scWAT, D8, si-Mypt1

source_name: scWAT cells

value: scWAT cells

value: Day 8


title: Muscle_Week6_NM2913_6


title: Fibroblasts from early-met lungs of mice treated with doxorubicin (Dox), biol rep 1

value: Fibroblasts (CD45- EpCAM- PDGFRa+)

value: Doxorubicin


title: PB from xenotransplanted mouse 9 collected at 12 weeks Ampli-seq

source_name: Peripheral Blood (PB)

value: Peripheral Blood (PB)

value: 12 weeks


title: scWAT, D8,  si-Ctr


title: Fibroblasts from early-met lungs of mice treated with vehicle (Pbs), biol rep 4

value: Saline


title: Muscle_Week6_NM2913_4

value: Muscle

value: Week 6

value: female


title: Fibroblasts from early-met lungs of mice treated with vehicle (Pbs), biol rep 3


title: PB from xenotransplanted mouse 8 collected at 12 weeks Ampli-seq


title: Muscle_Week6_NM2913_3


title: Muscle_Week6_NM2913_2


title: PB from xenotransplanted mouse 7 collected at 12 weeks Ampli-seq


title: Liver tNET-seq A3

description: nascent RNA

data_processing:
Library strategy: NET-seq
Single-end tNET-seq reads were trimmed to 50-bp length using cutadapt (v 1.13).
Sequencing reads were aligned to the GRCm38 (Ensembl release 99) reference genome using STAR (v. 2.7.3a). To avoid alignment biases in favor of annotated genomic regions, the alignment was performed without providing transcriptome
The data was further processed using custom Python scripts (adapted from https://github.com/BradnerLab/netseq) to remove reads from reverse transcription mispring events, PCR duplicates and splicing intermediates.
Pol II density was calculated by recording the genomic position of the 5' end of each tNET-seq read, which corresponds to the 3' end of the nascent RNA. For this, bedtools (v. 2.29.2) genomecov with parameters -dz and -5 was used.
Assembly: GRCm38
Supplementary files format and content: per-base coverage files for both strands separately (pos/neg)

extract_protocol:
Isolation of chromatin-associated nascent RNA using cellular fractionation in the presence of alpha-amanitin, a potent inhibitor of RNA polymerase II.
Libraries were prepared according to the NET-seq protocol by Mayer and Churchman (2016).

value: liver

value: 18 months


title: PB from xenotransplanted mouse 6 collected at 12 weeks Ampli-seq

value: GE


title: Fibroblasts from early-met lungs of mice treated with vehicle (Pbs), biol rep 2


title: PB from xenotransplanted mouse 5 collected at 12 weeks Ampli-seq


title: PB from xenotransplanted mouse 10 collected at 12 weeks Ampli-seq


title: Muscle_Week6_NM2913_1

value: male


title: PB from xenotransplanted mouse 3 collected at 12 weeks Ampli-seq


title: Fibroblasts from early-met lungs of mice treated with vehicle (Pbs), biol rep 1


title: Muscle_Week11_NMF421_11

value: Nadk2 +/+

value: Week 11


title: Liver tNET-seq A2

description: nascent RNA


title: Liver tNET-seq A1

description: nascent RNA


title: Muscle_Week6_NM2913_5


title: Muscle_Week11_NMF421_10


title: PB from xenotransplanted mouse 2 collected at 12 weeks Ampli-seq

value: GE + MSCs


title: eyeball organization, Inac-rBc-PI-PLC-A1 protein, 24h rep3

value: eyeball organization from C57/B6 mouse

value: eyeball organization

value: WT

value: Inac-rBc-PI-PLC-A1 protein


title: Mouse Hypo Adlib 1

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: Mouse Hypo Adlib 1

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: hypothalamus

extract_protocol:
The brains were harvested, and the hypothalami dissected before being frozen on dry ice and stored at -80°C until use. Brain tissues were thawed on the day of library preparation and samples from the sample nutritional condition were pooled together to yield 2 ad libitum fed samples (prepared on separate days) and 1 fasted sample. Samples were homogenized using a dounce homogenizer in ice cold homogenate buffer. Homogenates were centrifuged at 900xg for 10 minutes and pellets were resuspended in homogenate buffer with 25% Optiprep solution. Suspensions were layered on top of 29% Optiprep solution and centrifuged for 20 minutes at 13,500xg. Pellets were removed and resuspended in 1 ml of wash buffer containing DRAQ5. Samples were passed through a 40um cell strainer prior to FACS sorting. Samples were FACS sorted with gating set according to size and granularity using the FSC and SSC to capture singlets and remove debris. Each sample was sorted into two tubes and sequencing libraries were generated from these samples.
Library construction was perfomed using 10X Genomics Chromium Single Cell 3’ Reagent kits (Version 3) according to the standardised protocol.

treatment_protocol: 12 mice (2 cohorts of 6) were chow fed ad libitum and 6 mice were fasted for 16 hours (overnight) prior to sample collection

value: hypothalamus

value: 6-8 weeks

value: C57Bl/6 WT

value: Male

value: ad libitum fed


title: scWAT, D0, si-Mypt1

value: scWAT cells

value: Day 0


title: Mouse Hypo Adlib 2

description: Mouse Hypo Adlib 2


title: Liver tNET-seq MA3

description: nascent RNA

value: liver

value: 12 months


title: scWAT, D0, si-Ctr

value: si-Ctr


title: Liver tNET-seq MA2

description: nascent RNA


title: Mouse Hypo Fasted 1

description: Mouse Hypo Fasted 1

value: 16 hour overnight fast


title: Liver tNET-seq MA1

description: nascent RNA


title: PB from xenotransplanted mouse 10 collected at 6 weeks Ampli-seq

value: Peripheral Blood (PB)

value: 6 weeks

value: GE


title: Mouse Hypo Adlib 4

description: Mouse Hypo Adlib 4


title: Muscle_Week11_NMF421_7

value: Nadk2 -/-

value: Muscle

value: Week 11

value: female


title: Muscle_Week11_NMF421_8

value: male


title: PB from xenotransplanted mouse 9 collected at 6 weeks Ampli-seq


title: Liver tNET-seq Y2

description: nascent RNA

value: 3 months


title: PB from xenotransplanted mouse 8 collected at 6 weeks Ampli-seq


title: Muscle_Week11_NMF421_6


title: Liver tNET-seq Y3

description: nascent RNA


title: Mouse Hypo Adlib 3

description: Mouse Hypo Adlib 3

value: hypothalamus

value: 6-8 weeks

value: C57Bl/6 WT

value: Male


title: Liver tNET-seq Y1

description: nascent RNA

value: liver


title: Muscle_Week11_NMF421_4

value: Nadk2 +/+


title: PB from xenotransplanted mouse 7 collected at 6 weeks Ampli-seq


title: Liver ChIP-seq input O2

data_processing:
ChIP-seq reads were aligned to the GRCm38 reference genome (Ensembl release 99) using Bowtie2 (v 2.4.1) by enabling soft clipping (--local)
Aligned reads were then filtered for high quality (MAPQ > 10). Reads arising from PCR duplicates and those aligned to the mitochondrial genome were removed using PicardTools (v 2.21.4) and samtools (v 1.10) in combination with grep, respectively.
ChIP-seq peaks were called on aligned and filtered BAM files using MACS2 (v. 2.2.7)
Aligned and filtered BAM files were converted to bigwig coverage tracks using Deeptools (v. 3.5.1) by extending the reads (--extendReads), counting in 10-bp bins (--binSize 10) and normalizing to 1x coverage (--normalizeUsing RPGC)
Assembly: GRCm38

extract_protocol:
Liver tissue was crosslinked with 1% formaldehyde, dounce homogenized and the crosslinking reaction was quenched with 0.125 M glycine. Cross-linked tissue was lysed, nuclei pellets washed and then sonicated. For immunoprecipitations, samples were incubated with the respective antibody overnight and purified using magnetic protein G Dynabeads. Crosslinks were reversed and DNA was purified using the Nucleospin Gel and PCR Clean up kit (Macherey-Nagel)
Libraries were prepared as described in Tessarz et al, 2014

value: 18 months


title: PB from xenotransplanted mouse 1 collected at 12 weeks Ampli-seq

value: 12 weeks

value: GE + MSCs


title: Muscle_Week11_NMF421_5


title: PB from xenotransplanted mouse 5 collected at 6 weeks Ampli-seq

value: Peripheral Blood (PB)

value: 6 weeks


title: Liver ChIP-seq input O1


title: PB from xenotransplanted mouse 6 collected at 6 weeks Ampli-seq

value: GE


title: PB from xenotransplanted mouse 2 collected at 6 weeks Ampli-seq


title: Muscle_Week11_NMF421_9

value: Nadk2 -/-

value: Muscle


title: Mouse Hypo Fasted 2

description: Mouse Hypo Fasted 2

value: 16 hour overnight fast


title: PB from xenotransplanted mouse 3 collected at 6 weeks Ampli-seq


title: Muscle_Week11_NMF421_3

value: Week 11

value: male


title: Muscle_Week5_NMF421_10

value: Week 5

value: female


title: Muscle_Week11_NMF421_1


title: Muscle_Week5_NMF421_9


title: PB from xenotransplanted mouse 1 collected at 6 weeks Ampli-seq


title: Liver ChIP-seq input Y1

value: 3 months


title: Liver ChIP-seq input Y2


title: Liver ChIP-seq Y2

value: SPT4 (Cell Signaling Technology, catalog number:64828, lot number:1)


title: BM from xenotransplanted mouse 14 collected at the end of the experiment Bar-seq

data_processing:
Barcode sequences were extracted with the TagDust software (v2.33)
Extracted barcode sequences were processed with an ad-hoc script to merge similar (erroneous) barcodes
Assembly: none
Supplementary files format and content: Tab-separated matrix with barcode counts
Library strategy: Bar-Seq

extract_protocol:
QIAamp DNA Micro Kit (QIAGEN)
Custom library construction protocol. PCR amplicons for each individual sample were generated by nested PCR starting from >50-100 ng of purified gDNA. The first PCR step was performed with GoTaq Hot Start Polymerase (Promega) according to manufacturer instruction using the following amplification protocol: 95°C x 5’, (95°C x 0.5’, 60°C x 0.5’, 72°C x 0.5’) x 20 cycles, 72°C x 5’. Forward primers were designed to bind donor template upstream the BAR sequence, while the reverse primers annealed outside the homology region, thus amplifying 328 bp of the on-target integrated cassette. Exclusively for targeted sequencing of the transfer vector plasmid and AAV library, the reverse primer annealed to the downstream homology region. The second PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to manufacturer instruction using 5 µl of the first-step PCR product and the following amplification protocol: 95°C x 5’, (95°C x 0.5’, 60°C x 0.5’, 72°C x 0.5’) x 20 cycles, 72°C x 5’. Second-step PCR primers were endowed with tails containing P5/P7 sequence, i5/i7 Illumina tag to allow multiplexed sequencing and R1/R2 primer complementary sequence. PCR library amplicons were separately purified using MinElute PCR Purification kit (QIAGEN) and AmpPure XP beads (Invitrogen).

value: Bone Marrow (BM)

value: End of Experiment


title: Muscle_Week5_NMF421_8

value: Nadk2 +/+


title: Liver ChIP-seq O1

value: liver

value: 18 months


title: BM from xenotransplanted mouse 12 collected at the end of the experiment Bar-seq

value: GE + MSCs


title: Muscle_Week5_NMF421_6


title: Muscle_Week11_NMF421_2


title: BM from xenotransplanted mouse 13 collected at the end of the experiment Bar-seq


title: BM from xenotransplanted mouse 11 collected at the end of the experiment Bar-seq


title: Liver ChIP-seq Y1


title: Liver ATAC-seq O4

data_processing:
Paired-end ATAC-seq reads were trimmed to remove Tn5 transposase adapter sequence using cutadapt (v 1.13)
Reads were then aligned to the GRCm38 reference genome (Ensembl release 99) using Bowtie2 (v 2.4.1) by enabling soft clipping (- -local) and the alignment of fragments up to 2 kb (-X 2000).
Aligned reads were filtered for high-quality (MAPQ > 10) and properly paired reads. PCR duplicates and mitochondrial reads were removed.
Peaks were called on aligned and filtered BAM files using MACS2 (v. 2.2.7) in paired-end mode.
A consensus peak set was defined (non-redundant peaks present in at least two samples regardless of condition).
Reads overlapping consensus peak regions were recorded using featureCounts from the R package Rsubread (v. 2.0.1)
Assembly: GRCm38
Supplementary files format and content: raw count table of counts in consensus peak regions

extract_protocol:
Nuclei from liver tissue were isolated using nuclei EZ lysis buffer from Sigma-Aldrich. DNA was tagmented following the Omni-ATAC protocol.
Libraries were prepared using Nextera PCR primers and the NEBNext High-Fidelity PCR Master Mix


title: Muscle_Week5_NMF421_7


title: BM from xenotransplanted mouse 10 collected at the end of the experiment Bar-seq


title: Liver ATAC-seq O3


title: Muscle_Week5_NMF421_4


title: Muscle_Week5_NMF421_5


title: Liver ATAC-seq O2


title: Liver ChIP-seq O2


title: BM from xenotransplanted mouse 8 collected at the end of the experiment Bar-seq


title: BM from xenotransplanted mouse 7 collected at the end of the experiment Bar-seq


title: Liver ATAC-seq O1


title: Muscle_Week5_NMF421_3


title: H3K27ac, Mac, GRLysMCre, replicate2

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

data_processing:
RNA-seq reads were aligned to mm10 genome using STAR aligner (Dobin A, et al., Bioinformatics 29:15-21) and default settings.
Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550)
ChIP-seq reads were aligned to mm10 genome using STAR aligner (Dobin A, et al., Bioinformatics 29:15-21) with the following parameters: --outSJfilterIntronMaxVsReadN 0 --alignIntronMax 1 --alignSJDBoverhangMin 200, with all other parameters set at default. Only one read per position and read length was kept.
H3K27ac peak calling was done using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with -style histone and peaks that were reproducible across all three replicates were kept before merging peak files of wt and ko data. Tag density at peak regions was quantified using HOMER and subjected to DESeq2 analysis for normalization, log transformation and statistical analysis of differential binding.
Assembly: GRCM38 (mm10)
Supplementary files format and content: Txt file containing raw counts and DEseq2 normalized and rlog transformed counts as well as p values, adjusted p values and logFC

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow derived macrophages (BMDMs) were isolated from bone by flushing out bone marrow of mice. After 4 days of culturing in macrophage differentiation medium containing DMEM (Sigma, D5671), 20% heat-inactivated FCS (Sigma, F7524), 30% cell-conditioned L929 medium and 1% Penicillin/Streptomycin, 1% sodium pyruvate (Sigma, S8636), 1% L-glutamine (Sigma, G7513), 1% amphotericin-b (Gibco, 15290-026), medium was changed, and cells were allowed to grow for a further 3 days.

extract_protocol:
20 million bone marrow derived macrophages were changed to Macrophage serum free medium (Gibco, 12065-0723) overnight before treatment with IL-4 (20ng/ml) and Dexamethasone (100nM) for 2 hours. Cells were washed twice with ice cold PBS then fixed for 15 minutes with 1% formaldehyde (ThermoScientific 28908) followed by quenching with 1M Glycine (Sigma, 33226) for 5 minutes at room temperature. After washing twice with ice cold PBS cells were homogenized with a Douncer (Active Motif, 40415) in  Fast IP buffer (150mM NaCl, 50mM Tris-HCl (pH7.5), 5mM EDTA, 0.5%v/v NP-40, 1%v/v Triton X-100) with protease inhibitors (Complete Tablets EDTA-free, EASYpack, Roche, 04693132001). Resulting nuclei were centrifuged at 12,000 RPM and resuspended in shearing buffer (1% SDS, 10mM EDTA pH 8, 50mM Tris pH8) and sheared in 1.5ml Bioruptor Microtubes (Diagenode, C30010016) in a Bioruptor (Diagenode). Resulting sheared chromatin was cleared by centrifugation for 10 minutes at 12,000 RPM, 4C before diluting 1/10
ChIP-seq libraries were constructed from 10 to 20 ng of genomic DNA according to the manufacturer's instructions (Illumina) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).

treatment_protocol: Bone marrow derived macrophages were treated with interleukin-4 (20ng/ml) and Dexamethasone (100nM) for 2 hours

value: bone marrow derived macrophages

value: LysMCre (GRflox)

value: 20ng/ml Interleukin-4 + 100nM Dexamethasone 2hrs

value: H3K27ac (Active Motif, #39685)


title: H3K27ac, Mac, GRLysMCre, replicate3


title: Liver ATAC-seq Y3


title: H3K27ac, Mac, GRLysMCre, replicate1


title: BM from xenotransplanted mouse 6 collected at the end of the experiment Bar-seq

value: GE


title: Muscle_Week5_NMF421_1

value: Nadk2 -/-

value: Muscle


title: Liver ATAC-seq Y2


title: H3K27ac, Mac, GRflox, replicate3

value: wildtype (GRflox)


title: Doub3

city: New York

first: Dingcheng

last: Gao

state: NY

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

description: Tri-PyMT cell line was derived from advanced tumor

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR, embedded algorism of Partek Flow software (Partek Inc)
Gene counts were normalized to counts per million and added 0.0001 with Partek Flow software (Partek Inc)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: Breast tumor

extract_protocol:
Tri-PyMT cells were cultured in growth medium with 10% FBS. RFP+, GFP+ and Double+ cells were sorted seperately by flow cytometry. Total RNA was using RNeasy plus kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mixed strain of FVB and C57BL6

value: MMTV-PyMT breast tumor

value: Sorted from culture of parental Tri-PyMT cells


title: BM from xenotransplanted mouse 2 collected at the end of the experiment Bar-seq

value: Bone Marrow (BM)


title: Liver ATAC-seq Y1

value: 3 months


title: Doub1

growth_protocol: Tri-PyMT cells were cultured in growth medium with 10% FBS.


title: Doub2


title: PB from xenotransplanted mouse 14 collected at 12 weeks Bar-seq

value: Peripheral Blood (PB)

value: 12 weeks


title: GFP3


title: PB from xenotransplanted mouse 13 collected at 12 weeks Bar-seq


title: PB from xenotransplanted mouse 12 collected at 12 weeks Bar-seq


title: H3K27ac, Mac, GRflox, replicate2


title: RNA, Mac, GRnull, il4dex, replicate2

source_name: Fetal liver derived macrophage

growth_protocol: ATMs were isolated from the stromal vascular fraction of epidydymal white adipose using MACS technology (anti-F4/80, Miltenyi, 130-110-443). For fetal liver derived macrophages fetal livers (day 14.5 post fertalization) were passed through a 70m cell strainer (Greiner Bio-one #542070) and seeded in 10cm plates with macrophage medium (DMEM, 30% L929 conditioned medium, 20% FCS, 1% L-glutamine, 1% sodium pyruvate, 1% Penicillin-Streptomycin, 1% Amphotericin-B) for 7 days before use. Cells were changed to Macrophage serum free medium (Gibco 12065-0723) with Penicillin/Streptomycin 1% and Amphotericin-B 1% overnight before treatment.

extract_protocol:
RNA was extracted using TRIzol
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA for preparation of cDNA libraries.

treatment_protocol: Fetal liver derived macrophages were treated with vehicle, Dexamethasone (100nM), Interleukin-4 (20ng/ml), or Interleukin-4 (20ng/ml)  and Dexamethasone (100nM) for 2 hours  and Dexamethasone (100nM)

value: fetal liver derived macrophage

value: GRnull


title: RNA, Mac, GRnull, il4dex, replicate1


title: Plate2-mh82-RNA

city: Chapel Hill

first: Julia

last: Rager

address: 135 Dauer Drive, CB 7431

institute: UNC

data_processing:
The counts of sequencing reads per mRNA within the FASTQ files were aligned to the ENSEMBLE mouse genome database (v98) and organized using the Bowtie algorithm within Tempo-SeqR script.
Count data were normalized by median signal intensity using algorithms enabled within the DESeq2 package, resulting in variance stabilized expression values.
Genome_build: ENSEMBLE database version 98
Supplementary_files_format_and_content: Count data are provided as a .csv, aligned to gene symbols, and represent count values prior to normalization

source_name: Heart tissue from CD-1 mice

extract_protocol:
Lung and heart tissue samples were collected immediately 4 h and 24 h postexposure  and stored at -80 degrees C until further analysis.  RNA molecules with 18 nucleotides or greater were extracted with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) and quantified with the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, Ma) and tested for quality based on RNA integrity scores produced by the QIiAxcel system (Qiagen).
Isolated RNA samples were analyzed using next generation sequencing technologies enabled through the BioSpyder TempO-Seq platform. mRNA-seq libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina, and then these libraries were pooled and sequenced (single-end 50 bp) on the Illumina Ultra-High-Throughput Sequencing System (Hiseq) 2500.

value: PeatSmolder

tag: treatment duration (hrs)

value: Heart

value: female


title: RNA, Mac, GRnull, il4, replicate2

value: 20ng/ml Interleukin-4 2hrs


title: GFP2


title: PB from xenotransplanted mouse 10 collected at 12 weeks Bar-seq

tag: time point

value: GE + MSCs


title: PB from xenotransplanted mouse 11 collected at 12 weeks Bar-seq

tag: treatment


title: Plate2-mh81-RNA


title: Plate2-mh79-RNA


title: Muscle_Week5_NMF421_2

data_processing:
Filtering of reads was perfomed using NGSQCToolkit/2.3 and custom perls scripts
Read alignment was done using bowtie2/2.2.0
Read count estimations were performed using rsem/1.2.12
Genome_build: We used the Mus musculus GRCm38v74 genome for this work
Supplementary_files_format_and_content: Read counts matrix from rsem

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Tissues 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).
Libraries were prepared using the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  Libraries were checked for quality and concentration using the D5000 ScreenTape assay (Agilent Technologies) and quantitative PCR (KAPA Biosystems), according to the manufacturers’ instructions.
Libraries were pooled and sequenced 70 bp single-end on the HiSeq 4000 (Illumina) using HiSeq 3000/4000 SBS Kit reagents (Illumina), targeting 30 million reads per sample.

value: Nadk2 -/-

value: Week 5

value: male


title: Plate2-mh78-RNA


title: RFP3

value: Mixed strain of FVB and C57BL6


title: Plate2-mh77-RNA


title: PB from xenotransplanted mouse 8 collected at 12 weeks Bar-seq


title: RNA, Mac, GRnull, dex, replicate2

value: 100nM Dexamethasone 2hrs


title: RNA, Mac, GRnull, il4, replicate1


title: H3K27ac, Mac, GRflox, replicate1

value: bone marrow derived macrophages

value: wildtype (GRflox)

value: 20ng/ml Interleukin-4 + 100nM Dexamethasone 2hrs

value: H3K27ac (Active Motif, #39685)


title: Plate2-mh76-RNA

value: RedOakSmolder


title: RFP1

value: MMTV-PyMT breast tumor

value: Sorted from culture of parental Tri-PyMT cells


title: PB from xenotransplanted mouse 7 collected at 12 weeks Bar-seq

value: Peripheral Blood (PB)

value: 12 weeks

value: GE


title: RNA, Mac, GRnull, veh, replicate2

value: fetal liver derived macrophage

value: GRnull

value: Vehicle 2hrs


title: RNA, Mac, GRnull, dex, replicate1


title: Plate2-mh80-RNA

value: PeatSmolder

value: Heart

value: female


title: Plate2-mh75-RNA


title: BM from xenotransplanted mouse 3 collected at the end of the experiment Bar-seq

value: Bone Marrow (BM)

value: End of Experiment


title: Plate2-mh73-RNA


title: PB from xenotransplanted mouse 6 collected at 12 weeks Bar-seq


title: RED_OAK_SM3-24hr_mouse_plasma_ATTCCT_S9_L002

data_processing:
Sequencing counts were processed through our published BCGSC miRNA profiling pipeline (publicly available at: https://github.com/bcgsc/mirna), aligned to the UCSC GRCm38/mm10, and annotated to miRBase 22.1.
Genome_build: miRBase 22.1
Supplementary_files_format_and_content: Count data are provided as a .csv, aligned to microRNA symbols, and represent count values prior to any normalization or batch effect correction algorithms.

source_name: Extracellular vesicles from circulating plasma of CD-1 mice

extract_protocol:
Blood was obtained by cardiac puncture 24 h post-exposure. Approximately 0.5 ml was collected per animal in microfuge tubes containing 17 ul of 4% sodium citrate. Complete blood count on citrate whole blood sample was performed and the blood sample was spun down and an aliquot of the citrated plasma was stored at -80 degrees C until further analysis.  Exosomes were extracted from plasma using the Invitrogen Total Exosome Isolate kit, and RNA molecules with 18 nucleotides or greater were extracted with the Invitrogen Total Exosome RNA and Protein Isolation Kit and tested for quality based on the LabChip Small RNA Chip (PerkinElmer).
Isolated RNA samples were analyzed using next generation sequencing technologies enabled through the Illumina HiSeq 4000 platform. mRNA-seq libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina, and then these libraries were pooled and sequenced (single-end 50 bp) on the Illumina Ultra-High-Throughput Sequencing System (HiSeq) 4000.

tag: sample collection post-exposure (hrs)

tag: individual mouse id

tag: sex (0=female, 1=male)

tag: sequencing batch date


title: PB from xenotransplanted mouse 5 collected at 12 weeks Bar-seq

tag: cell line


title: SALINE_SM1-24hr_mouse_plasma_CACGAT_S10_L002

value: Extracellular vesicles from circulating plasma

value: Saline


title: GFP1

value: Mixed strain of FVB and C57BL6


title: Plate2-mh74-RNA

value: RedOakSmolder


title: Plate2-mh72-RNA


title: RNA, Mac, wt, il4dex, replicate2

tag: cell type

tag: genotype

value: wildtype

value: 20ng/ml Interleukin-4 + 100nM Dexamethasone 2hrs


title: RED_OAK_SM1-24hr_mouse_plasma_ACTGAT_S7_L002

tag: strain

tag: tissue


title: RNA, Mac, GRnull, veh, replicate1


title: PB from xenotransplanted mouse 9 collected at 12 weeks Bar-seq

value: Peripheral Blood (PB)

value: GE + MSCs


title: RED_OAK_SM2-24hr_mouse_plasma_ATGAGC_S8_L002


title: PB from xenotransplanted mouse 3 collected at 12 weeks Bar-seq

value: 12 weeks

value: GE


title: RFP2

value: MMTV-PyMT breast tumor

value: Sorted from culture of parental Tri-PyMT cells


title: RNA, Mac, wt, il4dex, replicate1

value: fetal liver derived macrophage


title: PB from xenotransplanted mouse 1 collected at 12 weeks Bar-seq


title: Plate2-mh118-RNA

value: PeatFlame

value: Heart

tag: Sex


title: RNA, Mac, wt, il4, replicate2

value: 20ng/ml Interleukin-4 2hrs


title: Plate2-mh71-RNA

value: female


title: PEAT_SM3-24hr_mouse_plasma_CACCGG_S6_L002

value: Extracellular vesicles from circulating plasma

value: PeatSmolder


title: PB from xenotransplanted mouse 14 collected at 6 weeks Bar-seq

value: 6 weeks


title: Plate2-mh117-RNA


title: RNA, Mac, wt, dex, replicate2

value: 100nM Dexamethasone 2hrs


title: SALINE_SM2-24hr_mouse_plasma_CACTCA_S11_L002

value: Saline


title: RNA, Mac, wt, dex, replicate1

value: wildtype


title: Plate2-mh116-RNA


title: RNA, Mac, wt, veh, replicate2

value: Vehicle 2hrs


title: PEAT_SM1-24hr_mouse_plasma_CAAAAG_S4_L002


title: PB from xenotransplanted mouse 2 collected at 12 weeks Bar-seq

value: Peripheral Blood (PB)


title: Plate2-mh115-RNA


title: RNA, Mac, wt, veh, replicate1


title: RNA, ATM, GRLysMCre, replicate2

source_name: Adipose tissue macrophages

value: epidydymal white adipose

value: Adipose tissue macrophages

value: LysMCre (GRflox)


title: Plate2-mh114-RNA


title: 108_RNA-m108_ROF_24H_PLASMA_CTAGCT_S42_L004

value: RedOakFlame


title: 117_RNA-m117_PF_24H_PLASMA_TCGAAG_S51_L004


title: Plate2-mh113-RNA


title: PB from xenotransplanted mouse 11 collected at 6 weeks Bar-seq

value: GE + MSCs


title: PB from xenotransplanted mouse 10 collected at 6 weeks Bar-seq


title: PB from xenotransplanted mouse 12 collected at 6 weeks Bar-seq


title: RNA, ATM, GRLysMCre, replicate1


title: 116_RNA-m116_PF_24H_PLASMA_TCCCGA_S50_L004

value: PeatFlame


title: PB from xenotransplanted mouse 9 collected at 6 weeks Bar-seq


title: Plate2-mh112-RNA

value: Heart


title: SALINE_SM3-24hr_mouse_plasma_CAGGCG_S12_L002


title: RNA, Mac, wt, il4, replicate1

value: fetal liver derived macrophage

value: 20ng/ml Interleukin-4 2hrs


title: Plate2-mh111-RNA

value: female


title: RNA, ATM, GRflox, replicate2

value: wildtype (GRflox)


title: PB from xenotransplanted mouse 13 collected at 6 weeks Bar-seq

value: 6 weeks


title: 114_RNA-m114_PF_24H_PLASMA_TATAAT_S48_L004

value: Extracellular vesicles from circulating plasma


title: PEAT_SM2-24hr_mouse_plasma_CAACTA_S5_L002

value: PeatSmolder


title: RNA, ATM, GRflox, replicate1


title: PB from xenotransplanted mouse 7 collected at 6 weeks Bar-seq

value: GE


title: 104_RNA-m104_Sal_24H_PLASMA_CATGGC_S38_L004

value: Saline


title: PB from xenotransplanted mouse 6 collected at 6 weeks Bar-seq

value: Peripheral Blood (PB)


title: Plate2-mh109-RNA


title: Plate2-mh108-RNA


title: NYU2

city: Stony Brook

first: Jinyu

last: Li

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

data_processing:
Single Cell sequencing data were pre-processed by cellranger 6.0.1 from 10X Genomics using default settings.
Downstreaming analysis was performed by Seurat 3.0
Assembly: mm10, GRCh38
Supplementary files format and content: gzipped file format containing "filtered_feature_bc_matrix" folder contents from cellranger outputs

source_name: mammary gland

extract_protocol:
The tumors were digested both mechanically and enzymatically (Collagenase/Hyaluronidase, and DNaseI) and single cell suspensions of viable cells were prepared. mRNA from each individual cell was captured and tagged with barcodes using 10X Genomics microfluidic platform.
Barcoded cDNA library was prepared using the manufacturer's instructions, 10X Genomics.

value: FVB

tag: tissue of origin for tumor

value: Mammary gland

tag: genetic alteration

value: MMTV-PyMT


title: 107_RNA-m107_ROF_24H_PLASMA_CGGAAT_S41_L004

value: RedOakFlame


title: PB from xenotransplanted mouse 5 collected at 6 weeks Bar-seq


title: 80_RNA-m80_PS_24H_PLASMA_GAGTGG_S56_L004


title: PB from xenotransplanted mouse 3 collected at 6 weeks Bar-seq


title: NYU1


title: 76_RNA-m76_ROS_24H_PLASMA_CGTACG_S55_L004

value: RedOakSmolder


title: PB from xenotransplanted mouse 8 collected at 6 weeks Bar-seq

value: GE + MSCs


title: PB from xenotransplanted mouse 2 collected at 6 weeks Bar-seq


title: Plate2-mh107-RNA

value: Heart


title: Plate2-mh110-RNA


title: Plate2-mh106-RNA


title: β-actin knockout Mouse Embryonic Fibroblast

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Raw reads quality trimmed using trim-galore with default settings and assessed with fastqc
Surviving paired reads were then aligned against the mouse reference genome mm10 using bwa-mem
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
RPKM normalized bamCoverage files were produced using deeptools2
RPKM normalized bamCoverage files for two replicates of each condition were averaged and blacklisted regions were removed using deeptools2
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: bigwig files containing RPKM normalized ChIP-Seq signal for each sample and bigwig files of averaged replicates of each condition

source_name: mouse embryonic fibroblasts (MEFs)

growth_protocol: WT and KO mouse embryonic fibroblasts (MEFs) (from the lab of Dr. Christophe Ampe, University of Ghent, Belgium) were maintained and cultured with Dulbecco’s modified Eagle medium (DMEM) with high glucose, 10% fetal bovine serum (FBS) and 100 U/mL penicillin and 100 μg/mL streptomycin, in a humidified incubator with 5% CO2 at 37 °C.

extract_protocol:
Cells were crosslinked (two biological replicates per condition and input controls) using 1% formaldehyde (Sigma Cat. No. F8775) for 10 min followed by quenching with 0.125 M Glycine for 5 min and lysis with lysis buffer 1-LB1-(50 mM Hepes KOH pH 7.5, 10 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100). Nuclei were pelleted, collected and washed using lysis buffer 2-LB2- (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). This was followed by lysis using lysis buffer 3 LB3 (10 mM Tris-HCl pH 8; 100 mM NaCl, 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate, 0.5% N-laurylsarcosine). Chromatin was sheared using Qsonica Sonicator (4 cycles of 3 min at 70 % Amplitude), and then checked on 0.8% agarose gel. 100 μg of fragmented chromatin was mixed with 5 μg of H3K27ac-Anti-Histone H3 (acetyl K27) antibody-ChIP Grade (ab4729) - abcam). The protein-antibody immunocomplexes were recovered by the Pierce Protein A/G Magnetic Beads (Thermo-Scientific). Beads and attached immunocomplexes were washed twice using Low salt wash buffer (LS) (0.1% SDS; 2 mM EDTA, 1% Triton X-100, 20 mM Tris-HCl pH 8, 150 mM NaCl), and High Salt (HS) wash buffer (0.1% SDS, 2 mM EDTA, 1% Triton X-100, 20 mM Tris-HCl pH 8, 500 mM NaCl), respectively. The beads were resuspended in elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS). De-crosslinking was achieved by adding 8 µL 5 M NaCl and incubating at 65 °C overnight. RNase A (1 µL 10 mg/mL) was added for a 30 min incubation at 37 °C. Then, 4 µL 0.5 M EDTA, 8 µL 1 M Tris-HCl, and 1 µL 20 mg/mL proteinase K (0.2 mg/mL) were added for a 2-hour incubation at 42 °C to digest the chromatin. DNA was purified by QIAquick PCR purification kit (Qiagen, Germantown, MD, USA) for qPCR analysis and sequencing. Library preparation and sequencing was performed by Novogene Co., Ltd using standard illumina protocols.
Library preperation and sequencing was performed by Novogene. Co Ltd using standard illumina protocols

value: beta-actin knockout

value: mouse embryonic fibroblasts (MEFs)

value: BALB/c

tag: developmental stage

value: 10.5 day old embryos

tag: chip antibody


title: 118_RNA-m118_PF_24H_PLASMA_TCGGCA_S52_L004

value: PeatFlame


title: 111_RNA-m111_ROF_24H_PLASMA_GACGAC_S45_L004

value: Extracellular vesicles from circulating plasma


title: Plate2-mh105-RNA

tag: treatment duration (hrs)

value: female


title: β-actin knockout Mouse Embryonic Fibroblast, rep1

value: H3K27ac-Anti-Histone H3 (acetyl K27) antibody (ab4729)


title: β-actin knockout Mouse Embryonic Fibroblast, rep2


title: Plate2-mh104-RNA

value: Saline


title: PB from xenotransplanted mouse 1 collected at 6 weeks Bar-seq

value: Peripheral Blood (PB)

tag: time point

value: 6 weeks

value: GE


title: S1_END_seq_GM15851_paired-end

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

data_processing:
END-seq reads were aligned to hg19 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser

Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: ENDseq

source_name: v-ABL immortalyzed human lymphocytes - GM15851

growth_protocol: iPS cell culture was performed as previously described. Tissue culture-treated dishes were coated with human embryonic cell (hES cell)-qualified matrigel (Corning, ref 354277). Matrigel was removed and iPS cells were plated in Essential 8 Medium (E8; Thermo Fisher Scientific, cat. no. A1517001) and 10 μM ROCK inhibitor (RI; Y-27632; Selleckchem, cat. no. S1049). iPS cells were maintained in an incubator at 37 °C with 5% CO2 and fed every 1–2 days as needed. Cells were split using either accutase (Life Technologies, cat. no. A1110501) for enzymatic dissociation into single cells or EDTA (0.5 mM; Life Technologies, cat. no. 15575020) for routine passaging. Medium was supplemented with 10 μM RI to promote survival during passaging. As necessary, iPS cells were frozen in 90% ES cell-qualified fetal bovine serum (FBS) (Sigma Aldrich, cat. no. ES-009-B) and 10% DMSO (Mediatech, cat. no. 25-950-CQC), and then thawed rapidly at 37 °C, followed by removal of FBS/DMSO and plating in E8 + RI medium. Colon cancer cancer (KM12, SW837, SW48, SW620 and RKO). KM12, SW837, and SW48 cells were grown in RPMI1640 media (Gibco), SW620 was grown in Leibovitz’s L-15 (Gibco) media. RKO was grown in Dulbecco's Modified Eagle Medium (DMEM – Gibco). FRDA patient (GM15850) and an unaffected sibling (GM15851) lymphoblasts were grown in RPMI1640 media (Gibco) supplemented with 15% FBS, penicillin 100 μg ml−1 and streptomycin 100 μg ml−1. Cell lines were tested for mycoplama contamination. Cells were maintained at 37°C and 5% CO2.

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

treatment_protocol: shWRN induction was perfomed using doxycycline 2mg/mL for 48 hours. For G2 arrest, cells were treated with CDK1 inhibitor (RO3306) for 24 hours. For induction of replication stress, cells were treated with aphidicolin 600 nM for 24 hours. G1 arrest was performed using CDK4/6 inhibitor (palbociclib) for 24 hours. Disruption of triplex formation was performed by treatting cells with the polyamide PA1 1 mM for 48 hours. iPSC differentiation into neurons was performed through the treatment with doxycycline (CONCENTRATION)

tag: treatment

value: NT

tag: endseq type

value: WT


title: β-actin knockout Mouse Embryonic Fibroblast, rep3


title: 112_RNA-m112_ROF_24H_PLASMA_TAATCG_S46_L004

value: RedOakFlame

tag: sample collection post-exposure (hrs)

tag: individual mouse id


title: Wild Type Mouse Embryonic Fibroblast, rep2

value: Wild Type


title: Plate2-mh103-RNA

value: Heart


title: 75_RNA-m75_ROS_24H_PLASMA_GTTTCG_S54_L004

value: RedOakSmolder

tag: sex (0=female, 1=male)

tag: sequencing batch date


title: Plate2-mh102-RNA


title: Wild Type Mouse Embryonic Fibroblast, rep1

tag: cell type

value: mouse embryonic fibroblasts (MEFs)


title: Plate2-mh101-RNA


title: Plate2-m140-RNA

source_name: Lung tissue from CD-1 mice

value: LPS

value: Lung


title: 109_RNA-m109_ROF_24H_PLASMA_CTATAC_S43_L004


title: 82_RNA-m82_PS_24H_PLASMA_CAGGCG_S58_L004

value: PeatSmolder


title: Plate2-m139-RNA


title: NPC in SCI recovered at 5d rep 5

city: Boston

first: Timothy

middle: M

last: O'Shea

address: 44 Cummington Mall, ERB Room 521

department: Biomedical Engineering

institute: Boston University

description: NPC SCI 5d 5

data_processing:
The R1 and R2 FASTQ files from lanes 1 and 2 that were obtained directly from the Illumina NovaSeq S2 run were concatenated and cleaned-up using the Trimmomatic tool with default parameters in Galaxy.
Data was then aligned to the M. musculus (mm10) reference genome using the HISAT2 tool applying default parameters in Galaxy
Gene counts from the aligned datasets was performed using the featureCounts tool applying default parameters in Galaxy
Differential expressed gene (DEG) analysis on raw gene count data was conducted using Edge-R in Galaxy applying Benjamini and Hochberg p-value adjustment and TMM normalization
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample

source_name: NPC in SCI recovered at 5d

growth_protocol: mESCs were maintained and expanded on 0.1% gelatin-coated flasks (EmbryoMax™ 0.1% Gelatin Solution, Millipore Sigma, Cat# ES006B) in KnockOut™ DMEM media (Cat# 10829018, ThermoFisher Scientific) containing 15% Fetal bovine serum (FBS) (ES cell tested) (ThermoFisher Sci cat # 10439-016), MEM Non-Essential Amino Acids Solution (100X) (Cat# 11140050, ThermoFisher Scientific), 100X EmbryoMax® Nucelosides (EMD Millipore cat # ES-008-D), Beta-Mercaptoethanol (Sigma Aldrich M3148), Antibiotic-Antimycotic (100X) (Cat# 15240096, ThermoFisher Scientific) and Leukemia inhibitory factor (LIF) (1 million units/mL stock) (EMD Millipore cat # ESG1106). NPC lines were derived from mESCs using a standard 2-/4+ induction protocol followed by a neural expansion protocol. The 2- step of embryoid body (EB) formation involved removing LIF and FBS supplements from the cell media and changing media to a differentiation media consisting of Advanced DMEM/F12 (ThermoFisher Sci cat # 12634-010) supplemented with L-Glutamine (Thermofisher Scientific Cat#25-030-081) (2mM) and Knockout serum replacement (ThermoFisher Sci cat # 10828010) plus the other constituents described above for 2 days. Neural induction (4+) of embryoid bodies (EB) was performed by culturing isolated EB in differentiation media supplemented with retinoic acid (RA) (R2625-50MG, Sigma) (50nM) and purmorphamine (PUR) (sonic hedgehog (SHH) agonist) (SML0868-5MG, Sigma) (500nM) for 4 days. To propagate the neurally induced mESCs, the cells were grown in neural expansion media consisting of Advanced DMEM/F12 supplemented with B27 (no Vitamin A) (50X) (ThermoFisher Sci cat # 12587010) and growth factors EGF (Cat# AF-100-15-100UG, Peprotech) and FGF (Cat# 100-18B-100UG, Peprotech) (100ng/ml for each) for a period of 2-6 weeks resulting in a passagable line of adherent NPC. Samples at defined passages after neural induction (P) were collected for analysis.

extract_protocol:
SCI tissue or cell pellet samples were homogenized in supplemented homogenization buffer (50 mM Tris pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM Dithiothreitol (DTT), 1X Protease inhibitors, 200 U/ml RNAsin, 100 mg/ml Cyclohexamide, 1 mg/ml Heparin) using 2mL glass Dounce tissue grinders (D8938-1SET, Sigma). Tissue homogenates were centrifuged to remove tissue debris before being incubated with Anti-HA.11 Epitope Tag Antibody (Biolegend, Cat# 901515) for 4 hours in a microcentrifuge tube on a microtube rotator kept at 4°C. At the end of 4 hours, IP solutions were combined with Pierce A/G Magnetic Beads (Thermofisher, #PI88803) and incubated overnight on a microtube rotator at 4°C. On the second day, magnetic beads were washed three times with high salt solution (50 mM Tris pH 7.4, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM Dithiothreitol (DTT), 100 mg/ml Cyclohexamide). Unpurified RNA was collected from the magnetic beads by addition of RLT Plus buffer with BME and vigorous vortexing. RNA was then purified using RNeasy Plus Mini (for in vitro cell pellets) or Micro Kits (for spinal cord tissue) (QIAGEN Cat# 74134 and 74034). Total mRNA derived from the RiboTag IP was quantified using an automated electrophoresis bioanalyzer. RNA samples with RNA integrity numbers (RIN) greater than seven were processed for RNA-Sequencing. Sequencing was performed on poly-A selected libraries using Illumina NovaSeq S2 (housed in the UCLA Technology Center for Genomics & Bioinformatics) using pair end reads (2x50 – 50bp length) with an average of 50-100M reads per sample.
The workflow for library construciton involved poly(A) RNA selection, RNA fragmentation and double-stranded cDNA synthesis using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final library.

treatment_protocol: NPC were differentiated spontaneously (Spont) by lowering the EGF/FGF concentration in the neural expansion media from 100ng/ml to 1ng/ml for 4 days. CNTF (Cat# 450-13-100UG, Peprotech) and IGF-1 (Cat#100-11-100UG, Peprotech) differentiation involved adding 100ng/ml of the respective growth factor into the Spont media and culturing for 4 days. FBS differentiation involved adding FBS (Cat# 10437010, ThermoFisher Scientific) at 1, 5, 10 or 20% vol/vol to the Spont media and culturing for 4 days.

value: ES-derived neural progenitor cells

tag: genotype

value: RiboTag +


title: 74_RNA-m74_ROS_24H_PLASMA_GTGGCC_S53_L004

tag: strain

value: Extracellular vesicles from circulating plasma


title: NPC in SCI recovered at 5d rep 4

description: NPC SCI 5d 4


title: 105_RNA-m105_Sal_24H_PLASMA_CATTTT_S39_L004

tag: tissue

value: Saline


title: NPC in SCI recovered at 5d rep 3

description: NPC SCI 5d 3


title: Plate2-m138-RNA

tag: Sex

value: female


title: 106_RNA-m106_Sal_24H_PLASMA_CCAACA_S40_L004


title: 81_RNA-m81_PS_24H_PLASMA_GGTAGC_S57_L004


title: Plate2-m136-RNA

value: EucalyptusFlame


title: Plate1-m137-RNA


title: NPC in SCI recovered at 5d rep 2

description: NPC SCI 5d 2


title: NPC in double crush SCI recovered at 14 d rep 5

description: NPC dSCI 5


title: NPC in SCI recovered at 5d rep 1

description: NPC SCI 5d 1


title: 113_RNA-m113_PF_24H_PLASMA_TACAGC_S47_L004

value: PeatFlame


title: T12

type: RNA

city: Shijiazhuang

first: Zhan

last: Yang

state: Hebei

address: 215 Heping W Rd

institute: The Second Hospital of Hebei Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C. Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

data_processing: When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 2 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: prostate cancer

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA extraction was performed with the miRNeasy Mini Kit (217004; Qiagen) according to the manufacturer's instructions. The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Results were provided in Sample QC report.

treatment_protocol: Place a freshly dissected cross-section prostate tissue (5mm thick) on to a pre-labeled tissue base mold. Cover the entire tissue block with Surgipath FSC 22 Frozen Section Embedding Medium (Leica). Slowly place the base mold containing the tissue block into liquid nitrogen till the entire tissue block is submerged into liquid nitrogen to ensure tissue is frozen completely. Store the frozen tissue block at -80°C until ready for sectioning. Transfer the frozen tissue block to a cryotome cryostat (-20 °C) prior to sectioning and allow the temperature of the frozen tissue block to equilibrate to the temperature of the cryotome cryostat. Section the frozen tissue block into 8 μm using the cryotome.Place the tissue sections onto glass slides suitable for HE staining and  immunohistochemistry.The tissue specimens were confirmed by two experienced pathologists. Pathological grading was judged by Gleason points-scoring system, Gleason score ≥8 and Gleason score <8.

value: prostate cancer

tag: gender

value: male


title: P11

source_name: benign prostatic hyperplasia

value: benign prostatic hyperplasia


title: P3


title: Plate2-m135-RNA


title: T5


title: 115_RNA-m115_PF_24H_PLASMA_TCATTC_S49_L004


title: NPC in double crush SCI recovered at 14 d rep 4

description: NPC dSCI 4


title: Plate2-m134-RNA


title: NPC in double crush SCI recovered at 14 d rep 3

description: NPC dSCI 3


title: MaMel86b_1

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

institute: University Hospital Freiburg

hyb_protocol: Illumina

scan_protocol: Microarrays-based gene expression profiling of MaMel cell lines was performed with Illumina HumanHT-12 v4 BeadChips. Quantile normalization was performed using the Illumina BeadStudio software

data_processing: Raw files were qunatile normailzed and log2 transformed.

label: biotin

source_name: patient-derived melanoma cell line

label_protocol: Illumina

growth_protocol: The cell lines were maintained at 37 °C in a humidified atmosphere of 5% CO2 using RPMI-1640 medium supplemented with 10% FCS, 1% L-glutamine, and 1% penicillin-streptomycin

extract_protocol: Total RNA was isolated using the Universal RNA Purification Kit (Roboklon), according to the manufacturer’s instructions

tag: mutation

value: BRAF p.V600E

tag: cell line


title: 110_RNA-m110_ROF_24H_PLASMA_CTCAGA_S44_L004

value: RedOakFlame


title: MaMel86b_2


title: NPC in double crush SCI recovered at 14 d rep 2

description: NPC dSCI 2


title: Plate2-m133-RNA


title: MaMel86b_3


title: MP2

city: Nanjing

first: Cong

last: Xiang

state: JiangSu Province

address: 12 Xuefu Road, Pukou High-Tec District

institute: Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
The library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome ebsite directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with FPKM values for every sample and every gene
Supplementary_files_format_and_content: Matrix table with raw gene counts for every sample and every gene

source_name: Gastrocnemius muscle

growth_protocol: 0.2% doxycycline in drinking water was supplied at the age of 4 weeks

extract_protocol:
Gastrocnemius muscle were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.  preparations. A total amount of 3 µg RNA per sample was used as input material for the RNA sample  preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.

value: Gastrocnemius muscle

tag: age

value: Mck cre; Tg Glut1-Hk2-Pfkfb3


title: MP3


title: NPC in double crush SCI recovered at 14 d rep 1

description: NPC dSCI 1


title: Plate1-m131-RNA

tag: treatment duration (hrs)


title: MaMel19_1


title: NPC in uninjured Spinal cord recovered at 14 d rep 5

description: NPC uninjured SC 5


title: Plate2-m132-RNA


title: MaMel21_3


title: MP1


title: MaMel21_2


title: MaMel19_3


title: Plate2-m130-RNA

value: PineFlame


title: NPC in uninjured Spinal cord recovered at 14 d rep 4

description: NPC uninjured SC 4


title: Ctrl3

value: Mck cre


title: MaMel19_2


title: NPC in uninjured Spinal cord recovered at 14 d rep 3

description: NPC uninjured SC 3


title: Plate2-m129-RNA

value: Lung


title: Ctrl2


title: Plate2-m128-RNA


title: NPC in uninjured Spinal cord recovered at 14 d rep 2

description: NPC uninjured SC 2

value: ES-derived neural progenitor cells


title: Ctrl1


title: Plate2-m127-RNA


title: NPC in uninjured Spinal cord recovered at 14 d rep 1

description: NPC uninjured SC 1

value: RiboTag +


title: small preB_2

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 (mouse genome) assembly using the genome mappers STAR
Assembly: mm10

source_name: Bone Marrow

extract_protocol:
proB, largepreB, smallpreB (BM):  Erythroid, myeloid, T cells, NK cells and mature B lineage (Lin) cells were depleted from bone marrow cell suspensions, and Lin(–)cKitloCD19+CD43+ pro-B cells, Lin(–)CD19+CD43+BP1+ large preB cells, and Lin(–)CD19+CD43–CD25+ small preB cells were sorted by FACSAria (BD Biosciences).    ETP, DN2, DN3, preDP (Thymus):  Erythroid, myeloid, gdT, CD8+CD4+DP, CD8+T, CD4+T, NK and B lineage (Lin) cells were depleted from thymocyte cell suspensions, and Lin(–)CD44+cKit+CD25– ETP, Lin(–)CD44+cKit+CD25+ DN2, Lin(–)CD44–CD25+ DN3, and Lin(–)CD44–CD25– preDP cells were sorted by FACSAria (BD Biosciences).      smallDP, CD8+T, CD4+T (Thymus):  Erythroid, myeloid, NK and B lineage (Lin) cells were depleted from thymocyte cell suspensions, and CD8+CD4+ small DP, CD8+T, and CD4+T were sorted by FACSAria (BD Biosciences).    RNA was isolated using Trizol reagent and Direct-zol RNA prep kit (Zymo Research).
Illumina TruSeq RNA Sample Prep Kit (Illumina) or NEB Next Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB) were used for the construction of sequencing libraries.

value: WT


title: small preB_1


title: MaMel63a_3


title: NPC in SCI recovered at 14 d rep 5

description: NPC SCI 5

source_name: NPC in SCI recovered at 14 d


title: large preB_2


title: Plate2-m126-RNA


title: Input

first: Yuxi

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

institute: Nanjing University

data_processing:
Illumina bcl2fastq2-v 2.20.0.422 software was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.9.
Paired-end reads were aligned using Bowtie2 version 2.4.2 with options: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 8. Mapping results with MAPQ and kept unique reads for further analysis by Picard version 2.26.1.
File format conversion for the peak calling and visualization were performed with samtools (version 1.10) and bedtools (version 2.30.0).
For peak calling, parameters used were macs2 callpeak -t drlfile/blffile -c inputfile -g 1.37e9 -f BAMPE –n out_name -q 0.01.
Assembly: GRCz11

organism: Danio rerio

source_name: RFP+ hematopoietic progenitors

extract_protocol:
Blf-/-;drl 4KO embryos were injected with Drl-Flag and Blf-Flag mRNA. At 20 hpf,  zebrafish embryos were dissociated into single cells with Librase treatment, RFP+ hematopoietic progenitors were purified with FACS.
Enriched RFP+ hematopoietic progenitors were immobilized on Concanavalin A-coated paramagnetic beads and permeabilized with digitonin.   Cells were incubated overnight with the anti-FLAG antibody (F3165, Sigma).   Tethered cells were washed thoroughly to remove unbound antibody, and then with pA-Tn5 for 60 min.   Tn5 transposase mediated tagmentation was then initiated by the addition of MgCl2.   Cellular DNA was extracted using Phenol/Chloroform/IsoamyI alcohol and then precipitated. Tagmented DNA libraries were generated and sequenced on an Illumina NovaSeq 6000 platform.
CUT&Tag

tag: cut&tag antibody

tag: developmental stage

value: 20 hpf

value: RFP+ hematopoietic progenitors

value: blf-/-;drl 4KO with drl-Flag mRNA

value: Digested with Liberase and enriched by FACS


title: NPC in SCI recovered at 14 d rep 4

description: NPC SCI 4


title: large preB_1


title: blf-Flag_anti-Flag_rep2

value: anti-FLAG (Sigma, F3165)

value: blf-/-;drl 4KO with blf-Flag mRNA

tag: treatment


title: blf-Flag_anti-Flag_rep1


title: drl-Flag_anti-Flag_rep2


title: Plate2-m123-RNA

value: PineNeedlesFlame

value: female


title: NPC in SCI recovered at 14 d rep 3

description: NPC SCI 3


title: proB_2


title: NPC in SCI recovered at 14 d rep 2

description: NPC SCI 2


title: MaMel21_1

value: BRAF p.V600E


title: proB_1


title: drl-Flag_anti-Flag_rep1


title: Plate2-m122-RNA


title: NPC in SCI recovered at 14 d rep 1

description: NPC SCI 1


title: DN1c DN3_2

source_name: Thymus


title: MaMel63a_2


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag at 14 days after crush SCI rep 5

description: Astro SCI 5

value: mouse astrocytes


title: Plate2-m121-RNA


title: Tg_3

first: Hongji

address: Building 6, School of Pharmacy, Shanghai Jiao Tong University, No.800 Dongchuan Road, Minhang District, Shanghai

department: School of Pharmacy

institute: Shanghai Jiao Tong University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCz11
Supplementary files format and content: Table with raw gene counts for every gene and every sample

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Tg (drl:hoxa9;hsp70:meis1)

value: kidney


title: Plate1-m125-RNA

value: PineFlame


title: Tg_2


title: Plate2-m124-RNA

value: Lung


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag at 14 days after crush SCI rep 4

description: Astro SCI 4


title: MaMel63a_1


title: DDNS DN3_2


title: Tg_1


title: WT_3

value: AB


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag at 14 days after crush SCI rep 3

description: Astro SCI 3

value: RiboTag +


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag at 14 days after crush SCI rep 2

description: Astro SCI 2


title: Plate2-m118-RNA

value: PeatFlame


title: WT_2


title: DDNS DN3_1


title: WTDN3_3

value: WT


title: WTDN3_2


title: Plate2-m117-RNA


title: WT_1


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag at 14 days after crush SCI rep 1

description: Astro SCI 1


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag rep 9

description: Astro 9


title: Plate2-m116-RNA


title: hnf4ahnf4gCR_4

city: Durham

first: John

middle: F

last: Rawls

address: 213 Research Drive

institute: Duke University School of Medicine

data_processing:
Paired read files were concatenated in Galazy and trimmed using Trim Galore
Reads were mapped to the Danio rerio DanRer11 genome using RNAstar
Features counts was used to quanity the number of reads mapped per gene
DESeq was used to determine differential gene expression and statisical significance
Genome_build: DanRer11
Supplementary_files_format_and_content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar

source_name: dissected GI tract

extract_protocol:
larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit (Invitrogen) was used to extract total RNA
RNA libraries were prepared using standard Illumina protocols

value: dissected GI tract

tag: microbial status

value: Conventionally rasied

value: 6 dpf


title: Plate2-m115-RNA


title: WTDN3_1


title: DN1c DN3_1


title: CD4

value: CD4+ SP


title: Plate2-m120-RNA


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag rep 8

description: Astro 8


title: hnf4ahnf4gCR_3


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag rep 6

description: Astro 6


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag rep 7

description: Astro 7


title: Plate1-m113-RNA


title: Plate1-m119-RNA


title: hnf4ahnf4gCR_2


title: hnf4ahnf4gCR_1


title: Plate2-m114-RNA


title: CD8

value: CD8+ SP


title: hnf4gCR_4


title: Plate2-m111-RNA

value: RedOakFlame


title: smallDP

value: CD8+CD4+ smallDP


title: Plate2-m112-RNA

value: female


title: hnf4gCR_3


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag rep 5

description: Astro 5

value: mouse astrocytes


title: preDP

value: Lin(-)CD44-CD25- preDP


title: DN2


title: hnf4gCR_2


title: DN3


title: Plate2-m109-RNA


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag rep 3

description: Astro 3


title: hnf4gCR_1


title: Plate2-m108-RNA


title: WTCR_4

value: wild type


title: Tns3iKO 3 (KO3)

city: Paris

first: Carlos

last: Parras

address: 47 boulevard de l'hôpital

country: France

institute: Paris Brain Institute

data_processing:
All RNA-seq reads were aligned onto the mm10 reference genome using RNAstar, gene expression levels were quantified with featureCounts
RNA-seq reads were aligned onto the mm10 reference transcriptome using bowtie
The edgeR R-package was used to perform both data normalization and differential expression analyses
Assembly: mm10
Supplementary files format and content: genes were considered regulated when p-value < 0.05

source_name: O4+ cells

growth_protocol: in vivo Magnetic-activated cell sorting of O4+ cells from P12 Ctrl or Tns3-iKO mouse cortices using anti-O4 antibodies

extract_protocol:
RNAs were extracted from MACsorted O4+-cells from P12 Tns3iKO mice and their control littermates, using Nucleospin RNA kit (Macherey-Nagel, 740955)
RNA-seq libraries from control (n=5) and Tns3iKO (n=3) O4+-cells were prepared using TruSeq Stranded mRNA (Illumina 20020594)

treatment_protocol: Tamoxifen was injected subcutaneously at 20mg/ml concentration at postnatal stages P5 and P8 in Ctrl and Tns3iKO animals.

value: Cortex and Corpus callosum

value: Postnatal day 12


title: Plate1-m107-RNA

value: Lung


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag rep 1

description: Astro 1

value: RiboTag +


title: WTCR_3


title: NPC in media passed through pippette rep 5

description: NPC media 5

source_name: NPC in media passed through pippette

value: ES-derived neural progenitor cells


title: Tns3iKO 2 (KO2)


title: Plate2-m106-RNA

value: Saline


title: NPC in media passed through pippette rep 4

description: NPC media 4


title: Plate2-m110-RNA


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag rep 4

description: Astro 4


title: WTCR_1

value: dissected GI tract


title: Plate2-m104-RNA


title: Plate2-m105-RNA


title: Plate2-m103-RNA


title: hnf4gCV_4

value: Conventionalized with microbes at 3dpf


title: NPC in media passed through pippette rep 3

description: NPC media 3


title: hnf4gCV_3

value: 6 dpf


title: NPC in media passed through pippette rep 2

description: NPC media 2


title: Host Spinal cord astrocytes from 73.12 Gffap-Ribotag rep 2

description: Astro 2


title: NPC in media passed through pippette rep 1

description: NPC media 1


title: ETP

first: Katia

address: 13th street

value: Lin(-)CD44+cKit+CD25- ETP

value: WT


title: Control 5 (CT5)


title: Plate2-m102-RNA


title: Control 4 (CT4)


title: hnf4gCV_2


title: Control 2 (CT2)


title: NPC in DCH retained for 4 hours and then passed through pippette rep 4

description: NPC DCH t=4 hrs 4


title: NPC in DCH retained for 4 hours and then passed through pippette rep 5

description: NPC DCH t=4 hrs 5


title: Plate1-m101-RNA


title: hnf4gCV_1


title: Tns3iKO 1 (KO1)


title: WTCR_2

value: Conventionally rasied


title: WTCV_4


title: Control 1 (CT1)


title: Plate2-m100-RNA

value: EucalyptusSmolder


title: NPC in DCH retained for 4 hours and then passed through pippette rep 3

description: NPC DCH t=4 hrs 3


title: Plate2-m99-RNA

value: female


title: 14_ChIP_OPC_Input_5

description: Control for 12_ChIP_OPC_H3K4me3_5 & 13_ChIP_OPC_H3K27me3_5

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2
Data were filtered using SAMtools and PCR-derived duplicates removed by using PICARD MarkDuplicates
peaks were called using MACS (Model-based Analysis of ChIP-Seq)with options: keep-dup all, nolambda, broad, nomodel, extsize 75 -q 0.01 and filtered according to the following criteria: (i) length>=100bp and (ii) p-value<=5%
Assembly: mm10
Supplementary files format and content: narrowpeaks and broadpeaks files with in this order: chrom, chromStart, chromEnd, peak name, score, signalValue, pValue, qValue; bigwig

growth_protocol: in vivo Magnetic-activated cell sorting of O4+ cells from P7 or P12 WT mouse cortices using anti-O4 antibodies

extract_protocol:
Lysates were clarified from sonicated nuclei and Olig2-DNA and Histones-DNA complexes were isolated with corresponding antibodies.
The ChIP-seq libraries were prepared using TruSeq ChIP library preparation kit (Illumina ip-202-1012)

tag: chip antibody


title: NPC in DCH retained for 4 hours and then passed through pippette rep 2

description: NPC DCH t=4 hrs 2


title: WTCV_3


title: Control 3 (CT3)


title: Plate2-m97-RNA


title: NPC in DCH passed through pippette rep 5

description: NPC DCH 5

source_name: NPC in DCH passed through pippette


title: 13_ChIP_OPC_H3K27me3_5

description: H3K27me3 ChIP in OLglia

value: mouse anti-H3K27me3 antibody (Abcam, ab6002)


title: 12_ChIP_OPC_H3K4me3_5

description: H3K4me3 ChIP in OLglia

value: rabbit anti-H3K4me3 antibody (Active motif, 39060)


title: Plate2-m98-RNA


title: NPC in DCH retained for 4 hours and then passed through pippette rep 1

description: NPC DCH t=4 hrs 1


title: WTCV_1

value: wild type


title: 11_ChIP_OPC_Input_4

description: Control for 8_ChIP_OPC_H3K4me3_4 & 9_ChIP_OPC_H3K4me1_4 & 10_ChIP_OPC_H3K27me3_4

value: Cortex and Corpus callosum


title: Plate1-m95-RNA


title: hnf4gGF_3

value: Germfree


title: Plate2-m96-RNA

value: Lung


title: Plate2-m94-RNA

value: PineSmolder


title: NPC in DCH passed through pippette rep 3

description: NPC DCH 3

value: ES-derived neural progenitor cells

value: RiboTag +


title: 9_ChIP_OPC_H3K4me1_4

description: H3K4me1 ChIP in OLglia

value: Postnatal day 12

value: rabbit anti-H3K4me1 antibody (Ozyme, 5326T)


title: NPC in DCH passed through pippette rep 2

description: NPC DCH 2


title: 10_ChIP_OPC_H3K27me3_4

description: H3K27me3 ChIP in OLglia


title: NPC in DCH passed through pippette rep 4

description: NPC DCH 4


title: hnf4gGF_4

value: dissected GI tract

value: 6 dpf


title: Plate2-m93-RNA


title: hnf4gGF_1


title: 8_ChIP_OPC_H3K4me3_4

description: H3K4me3 ChIP in OLglia


title: hnf4gGF_2


title: NPC in DCH passed through pippette rep 1

description: NPC DCH 1


title: 7_ChIP_OPC_Input_3

description: Control for 5_ChIP_OPC_H3K4me3_3 & 6_ChIP_OPC_H3K27Ac_3


title: Plate2-m92-RNA


title: WTCV_2

value: Conventionalized with microbes at 3dpf


title: CNTF+5% FBS rep4

description: CNTF+5% FBS 4

source_name: CNTF+5% FBS rep4


title: WTGF_4


title: Plate2-m91-RNA


title: CNTF+5% FBS rep2

description: CNTF+5% FBS 2

source_name: CNTF+5% FBS rep2


title: WTGF_3


title: CNTF+5% FBS rep3

description: CNTF+5% FBS 3

source_name: CNTF+5% FBS rep3


title: Plate2-m90-RNA

source_name: Lung tissue from CD-1 mice


title: WTGF_2


title: 6_ChIP_OPC_H3K27Ac_3

description: H3K27Ac ChIP in OLglia

value: rabbit anti-H3K27Ac antibody (Active motif, 39034)


title: CNTF+5% FBS rep1

description: CNTF+5% FBS 1

source_name: CNTF+5% FBS rep1


title: 4_ChIP_OPC_Input_2

description: Control for 3_ChIP_OPC_Olig2_2

value: Postnatal day 7


title: 20%FBS rep 3

description: 20% FBS 3


title: 3_ChIP_OPC_Olig2_2

description: Olig2 ChIP in OPCs

value: mouse anti-Olig2 antibody (Millipore, MABN50)


title: 20%FBS rep 4

description: 20% FBS 4


title: Plate1-m87-RNA

value: PineNeedlesSmolder

value: female


title: 1_ChIP_OPC_Olig2_1

description: Olig2 ChIP in OPCs


title: Plate1-m88-RNA


title: 20%FBS rep 2

description: 20% FBS 2


title: Plate1-m86-RNA


title: Plate1-m84-RNA


title: 20%FBS rep 1

description: 20% FBS 1


title: Plate1-m85-RNA


title: 10%FBS rep 4

description: 10% FBS 4


title: IDG-SW3+TG-DTA-rep2

city: San Antonio

first: Katherine

middle: Vivian

last: Lillis

state: TX

address: 7703 Floyd Curl Dr

department: Endodontics

institute: UNIVERSITY OF TEXAS HLTH SCI CTR SAN ANTONIO

data_processing:
The base called files were converted to fastq, demultiplexed, and mm10 alignments and analysis was done with TopHat-Bowtie and DESeq programs.
Genome_build: mm10
Supplementary_files_format_and_content: read count

source_name: CellLine from Dmp1-GFP  bones +  SensoryNerve Deleted TG Preparations

extract_protocol: Total RNA was isolated from IDG-SW3 cells after 14 days culture in the presence of differentiation media (n=2 wells/condition) using the RNAeasy Kit (Qiagen, Valencia, CA) following the manufacturer’s recommendation. Total RNA was ribosomal RNA depleted using the NEBNext rRNA Depletion Kit. Libraries were built for the biological duplicates (6 libraries, n=2: IDG-SW3 [d1 and d2], IDG-SW3 +TG-cre [TGd1 and TGd2], and IDG-SW3 +TG-DTA [SNSd1 and SNSd2]). We used the Next Flex Rapid Directional RNA-Seq Kit to prepare libraries as described by the manufactuer with appropriate barcodes (Bioo Scientific).  The total RNA libraries were submitted to the U. Texas Health Science Center Gene Sequencing Facility at the Greehey Childrens Cancer Center, and the paired end libraries were sequenced on one lane with the Illumina Hi-Seq 2000.

treatment_protocol: The osteoblast cell line IDG-SW3 with a GFP expression under the Dmp1 promoter (Kerafast, Boston, MA) was cultured at the concentration of (~1x105/well) in collagen type-1 coated 24 well plated with the addition of ascorbic acid (50 μg/ml) and β-glycerolphosphate (4mM). Once cells reached 80% confluency, inserts of TG-cre or TG-DTA cultures were transferred to the plates and incubated for 14 days at 37ºC and 5% CO2 with media replaced every 2 days and new TG-cre or TG-DTA cultures were replaced every 7 days.

tag: osteoblast cell

tag: tg insert

value: Nav1.8 sensory nerve depleted TG


title: IDG-SW3+TG-cre-rep2

source_name: CellLine from Dmp1-GFP  bones + WT TG Preparations

value: Wildtype TG preparations