title: BMWAPLChIP_Input_rep3

description: aligned to mm9 genome


title: BMWAPLChIP_rep3

status: Public on Nov 07 2020

type: SRA

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: PCMM

country: USA

institute: Boston Children's Hospital

description: aligned to mm9 genome

library_source: genomic

data_processing:
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag
reads were quantified for specific loci using samtools version 1.8
bigwig files were produced using RseqQ package
Genome_build: mm9 genome
Supplementary_files_format_and_content: bigwig files contain peak information for samples

molecule: genomic DNA

organism: Mus musculus

source_name: B6 mouse BM pro-B  cell

growth_protocol:
Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days
RPMI1640+15% FBS

extract_protocol:
Crosslinked cells were treated with cell lysis buffer (5mM PIPES pH 8, 85mM KCl, 0.5% NP-40) and nuclei lysis buffer (50mM TrisCl pH 8.1, 10mM EDTA, 1% SDS) and subjected to sonication. IP and Input DNA were de-crosslinked at 65o overnight and purified via Qiagen PCR purification columns.
ChIP-Seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645)

treatment_protocol:
Purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)
3 uM STI-571 treated for 4 days

tag: genotype

value: RAG1 deficient


title: BMWAPLChIP_Input_rep1

description: aligned to mm9 genome

source_name: B6 mouse BM pro-B cell


title: BMWAPLChIP_rep1

description: aligned to mm9 genome


title: BMINVRad21ChIP_Input_rep1

description: aligned to mm9 genome

value: Igh Inversion,RAG1 deficient


title: BMINVRad21ChIP_rep2

description: aligned to mm9 genome


title: BMWTRad21ChIP_Input_rep3

description: aligned to mm9 genome


title: BMINVRad21ChIP_rep1

description: aligned to mm9 genome


title: BMWTRad21ChIP_rep3

description: aligned to mm9 genome


title: BMWTRad21ChIP_rep2

description: aligned to mm9 genome


title: BMWTRad21ChIP_Input_rep2

description: aligned to mm9 genome


title: v-Abl_proB_Wapl_degron_IAADox_GRO_rep1

description: aligned to mm9 genome

library_source: transcriptomic

molecule: total RNA

source_name: v-Abl transformed B6 pro-B cell line

extract_protocol:
Briefly, 10 million cells were permeabilized with permeabilization buffer (10 mM Tris-HCl, pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, one tablet of protease inhibitors per 50 ml and 4 units Rnase inhibitor per ml) and resuspended in 100 ul storage buffer (10 mM Tris-HCl, pHHH 8.0, 25% (vol/vol) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT). Permeabilized cells were subjected to nuclear run-on (2xRun-on mix: 5 mM Tris-Cl, PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, 10 units of RNase inhibitor, 1% sarkosyl) at 37o for 5 min, followed by Trizol-based RNA extraction.
Illumina adapters were ligated to RNA followed by cDNA generation with reverse transcriptase.  Libraries were PCR-amplified with Illumina primers and subjected to sequencing.
GRO-Seq

treatment_protocol:
3 uM STI 1 day, then 150 μM IAA, 3 uM STI-571 with 2 mg/mL Dox treated for 3 days
3 uM STI-571 treated for 4 days

value: Wapl degron, Emu-Bcl2, RAG1 deficient


title: BMWTRad211WAPL2ChIP_Input_rep

description: aligned to mm9 genome


title: v-Abl_proB_Wapl_degron_IAADox_GRO_rep3

description: aligned to mm9 genome


title: v-Abl_proB_Wapl_degron_IAADox_GRO_rep2

description: aligned to mm9 genome


title: BMWTRad21ChIP_rep1

description: aligned to mm9 genome


title: v-Abl_proB_Wapl_degron_NT_GRO_rep2

description: aligned to mm9 genome

treatment_protocol:
3 uM STI 4 days
3 uM STI-571 treated for 4 days


title: v-Abl_proB_Wapl_degron_NT_GRO_rep1

description: aligned to mm9 genome


title: v-Abl_proB_Wapl_degron_NT_GRO_rep3

description: aligned to mm9 genome


title: BM_proB_Igh_Inversion_GRO_rep4

description: aligned to mm9 genome


title: BM_proB_Igh_Inversion_GRO_rep3

description: aligned to mm9 genome


title: BM_proB_WT_GRO_rep4

description: aligned to mm9 genome


title: BM_proB_Igh_Inversion_GRO_rep1

description: aligned to mm9 genome


title: BM_proB_WT_GRO_rep3

description: aligned to mm9 genome


title: BMWAPLChIP_rep2

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_single igh_Untreated_rep3

description: aligned to mm9 genome

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9 genome
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: v-Abl transformed pro-B cell line

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
LAM-HTGTS V(D)J-Seq libraries were prepared using linear-amplification PCR-mediated HTGTS.
Linear-amplification PCR-mediated HTGTS

treatment_protocol:
RAG1/2 retrovirus infected, 3 uM STI-571 treated for 4 days
3 uM STI-571 treated for 4 days

value: Wapl-degron, OsTIR1, Single Igh, Emu-Bcl2, RAG1 deficient


title: BM_proB_WT_GRO_rep1

description: aligned to mm9 genome


title: BM_proB_WT_GRO_rep2

description: aligned to mm9 genome


title: BMINVRad21ChIP_Input_rep2

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_single igh_Untreated_rep2

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_single igh_Untreated_rep1

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_IAADox_rep3

description: aligned to mm9 genome

treatment_protocol:
RAG1/2 retrovirus infected, 3 uM STI 1 day, then 150 μM IAA, 3 uM STI-571 with 2 mg/mL Dox treated for 3 days
3 uM STI-571 treated for 4 days

value: Wapl-degron, OsTIR1, Emu-Bcl2, RAG1 deficient


title: JH1-4_Wapl-degron_IAADox_rep2

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_IAADox_pooled_rep1-3

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_IAADox_rep1

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_Untreated_rep3

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_Untreated_pooled_rep1-3

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_Untreated_rep1

description: aligned to mm9 genome


title: JH1-4_Primary_Untreated_rep3

description: aligned to mm9 genome

value: OsTIR1, Emu-Bcl2, RAG1 deficient


title: JH1-4_Wapl-degron_Untreated_rep2

description: aligned to mm9 genome


title: JH1-4_Primary_Untreated_rep1

description: aligned to mm9 genome


title: BM_proB_Igh_Inversion_GRO_rep2

description: aligned to mm9 genome


title: JH1-4_Primary_Untreated_rep2

description: aligned to mm9 genome


title: JH1-4_INV_BM_pooled_rep2/3

description: aligned to mm9 genome

source_name: INV primary BM pro-B cells

value: C57BL/6, Igh Inversion,RAG1 deficient


title: JH1-4_INV_BM_rep4

description: aligned to mm9 genome


title: JH1-4_INV_BM_rep3

description: aligned to mm9 genome


title: JH1-4_INV_BM_rep1

description: aligned to mm9 genome


title: JH1-4_INV_BM_rep2

description: aligned to mm9 genome


title: JH1-4_WT_BM_pooled_rep2/3

description: aligned to mm9 genome

source_name: WT primary BM pro-B cells

value: C57BL/6, RAG1 deficient


title: JH1-4_WT_BM_rep3

description: aligned to mm9 genome


title: JH1-4_WT_BM_rep2

description: aligned to mm9 genome


title: JH1-4_WT_BM_rep1

description: aligned to mm9 genome


title: HP423a

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

data_processing:
Low quality reads and and contaminants (e.g. sequence adapters) were removed using Trimmomatic (version 0.32)
Sequences were aligned to the GRCh38  genome using HiSat2 (version 2.1.0)
Transcript abundance level (Transcript count) was generated using HTSeq (version 0.9.1)
The transcript counts were further processed using R software environment for statistical computing and graphics (version 3.4.0)
The transcript counts were further processed using R software environment for statistical computing and graphics (version 3.4.0)
Differential expression was performed using edgeR R package using the negative binomial GLM approach
Genome_build: GRCh38
Supplementary_files_format_and_content: read count

organism: Homo sapiens

source_name: tibia

growth_protocol: Periosteal samples (5x10 mm) were obtained from the posterior areas of the maxilla and mandible of 16 to 30-year old healthy patients who underwent bimaxillary orthognathic surgery, after informed consent was obtained (Belgian registration number B322201731127). The tibial samples were harvested by orthopedic surgeons as described previously (Eyckmans and Luyten, 2006).

extract_protocol:
RNA was isolated from biological duplicates when a cumulative at PD~16 for RNA-seq analysis. 106 cells were rinsed twice in PBS and centrifuged at 260 RCF for 10 min. After removing the supernatant, the cell pellet was lysed by adding 350 μl RLT buffer (Qiagen) containing 1% β-mercaptoethanol (Sigma Aldrich) and homogenized by thoroughly pipetting up and down. Samples were directly placed on ice and frozen at -80 °C until further processing. The Qiagen RNeasy mini kit was used to isolate RNA according to the manufacturer’s instructions. cDNA was obtained by reverse transcription of 500 ng of total RNA, using the RevertAid H Minus First Strand cDNA Synthesis Kit, 1 mM oligo-dT20 and random hexamer primers (Thermo Fisher Scientific).
RNA-seq samples were obtained from 3 donors for the maxillary samples (HP417, HP421 and HP424), 4 donors for mandibular samples (HP418, HP422, HP425 and HP427) and 3 tibial donors (HP415, HP420 and HP423). RNA-seq samples were prepared from hPDCs at cumulative PD~16 in technical duplicates (A and B) and sequencing library was generated using the Illumina TruSeq Stranded mRNA Library Prep Kit. The resulting cDNA libraries were sequenced (50bp length) according to Illumina TruSeq Rapid v2 protocol on an Illumina HiSeq2500 sequencer.

tag: tissue

value: tibial periosteum-derived cells

value: wildtype

tag: age

tag: doubling time


title: HP423b


title: K562-Cas9 cancer chromatin modifiers, ATAC-seq library

city: New York

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
ATAC-seq K562: Cells demultiplexed and aligned based on cellular barcodes using the snATAC_mat.py script in a previously published sci-ATAC-seq pipeline (https://github.com/r3fang/snATAC)(Preissl et al., 2018) and using hg19 as reference genome. Briefly, reads were aligned using bowtie2 (Langmead B., 2012) -D 15 -R 2 -L 22 -i S,1,1.15 -p 5 -t -X2000 -e 75 --no-mixed --no-discordant and deduplicated using Picard(http://broadinstitute.github.io/picard). Unmapped reads, mitochondrial reads and reads overlapping ENCODE blacklist regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were filtered out. For downstream analyses, we required each cell to have at least 100 aligned sgRNA reads with >= 99% of the reads assigned to one sgRNA sequence for the chromatin modifier screen and >=90% of thereads assigned to one sgRNA sequence for the chromatin remodeling complex subunit screen.
sgRNA seq: sgRNA datasets were demultiplexed based on cellular barcodes using the snATAC_mat.py script in a previously published sci-ATAC-seq pipeline (https://github.com/r3fang/snATAC) (Preissl S. et al., 2018) . The processed sequences were aligned to a custom guide reference using bowtie (Langmead B. et al., 2009) using the command bowtie -v 1 -m 1. For the human-mouse experiment, we show data for cells with at least 20 mapped reads. Cells with over 90% of sgRNA reads that mapped exclusively to human or mouse sgRNAs were considered species-specific cells. Cells where one sgRNA represented at least 90% of the total reads were kept for further analyses. The remaining cells were considered collisions and/or the result of multiple infections. For downstream analysis of the K562 data, we required each cell to have at least 100 aligned sgRNA reads with ≥ 99% of the reads assigned to one sgRNA sequence for the chromatin modifier screen and >=90% of the reads assigned to one sgRNA sequence for the chromatin remodeling complex subunit screen.
Genome_build: hg19 and mm10

source_name: K562-Cas9 cells

growth_protocol: Cells grown under standard conditions. HEK293T and NIH3T3 were cultured in DMEM supplemented with 10% FBS and 1 ug/ml puromycin. K562-Cas9 cells were cultured in RPMI supplemented with 10% FBS and 1 ug/ml puromycin and 5 ug/ml blasticidin.

extract_protocol:
Cells were first fixed with glyoxal and nuclei were isolated using ATAC-seq lysis buffer.
Following cell fixation and lysis, nuclei are recovered and the open chromatin regions of the genomic DNA undergo barcoded tagmentation in a 96-well plate using a unique, easy-to purify transposase purified from Vibrio parahemolyticus. Next, the sgRNA is barcoded with the same barcode as the ATAC fragments, using in situ reverse transcription. The nuclei are pooled together and split again to a new 96-well plate and both the ATAC fragments and the sgRNA are tagged again with a well-specific barcode in two consecutive PCR steps. At the end of this process, every single cell contains a unique combination of barcodes that tag both the sgRNA and the ATAC fragments with the same barcode combination (“cell barcode”).

tag: cell line

value: K562 constitutively expressing Cas9

tag: treatment

value: Cells infected with pooled CRISPR library of 63 gRNAs targeting the most mutated chromatin modifiers in cancer patients and 3 non-targeting sgRNAs.

tag: library type

value: ATAC-seq library


title: K562-Cas9 chromatin remodeling complexes, ATAC-seq library

value: Cells infected with pooled CRISPR library of 252 gRNAs targeting chromatin remodelers complex subunits and 3 non-targeting sgRNAs.


title: HP420b


title: HP424b

source_name: maxilla

value: maxillary periosteum-derived cells


title: HP421a


title: HP424a


title: HP421b


title: HP415b


title: HP415a


title: HP420a


title: HP417a


title: HP425a

source_name: mandibular

value: mandibular periosteum-derived cells


title: IVF_fri33LH7E

city: Tartu

first: Viktorija

last: Kukushkina

address: Riia 23b

country: Estonia

institute: Estonian Genome Center, University of Tartu

data_processing:
Data quality was checked with fastQC v.0.11.3 before and after preprocessing step.
Adapter removal and trimming with Trimmomatic tool v. 0.32. Parameters:  PE, -phred33,ILLUMINACLIP:/gpfs/depoofs/a73038/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa:2:30:10:8:'true', LEADING:3, TRAILING:3, HEADCROP:11, SLIDINGWINDOW:4:30, MINLEN:36.
Low quality reads removal was made with fastq_quality_filter from Fastx toolkit v. 0.0.13. Parameters: -Q33, -q 30, -p 50
Good quality reads were mapped using TopHat v. 2.0.11. Parameters: --bowtie1, -p 12, --mate-inner-dist 300, --mate-std-dev 100, --library-type fr-firststrand. Bam files name sorted with picard-tools-1.102 SortSam script. Parameters: SO=queryname.
Raw read counts were counted with HTSeq-count v.0.6.1. Parameters: --format=bam, --stranded=reverse, --type=exon, --idattr=gene_id. Annotation GTF version: Ensembl v.75
Genome_build: hg19
Supplementary_files_format_and_content: Raw read count tab delimited matrix, edgeR CountsPerMillion comma delimited matrix.

source_name: Endometrium

extract_protocol:
Tissue samples were extracted with Pipelle® catheters under sterile conditions from 23-36-year-old  healthy and IVF women in with BMI of 19-29 Kg/m2, rinsed with PBS and processed immediately or frozen at -80 °C.
Up to 30 mg of the tissue was homogenized in the presence of QIAzol reagent (Qiagen) and processed using miRNeasy Mini kit (Qiagen), following manufacturer's protocol. miRNA content was decreased using Qiagen's MinElute protocol. Purified RNA quality was assigned with Bioanalyzer (Agilent Technologies).cDNA libraries were generated from ~1 μg of endometrial total RNA using Illumina TruSeq Stranded technology (Illumina), followed by cDNA quality control with Bioanalyzer

tag: gender

value: Female

value: Endometrium

tag: receptivity time-point

tag: country of origin

value: Spain

tag: tissue state

value: IVF

tag: sequencing batch


title: HP418a


title: HP417b


title: IVF_fri32LH7E


title: JH1-4_WT_BM_rep4

description: aligned to mm9 genome


title: HP427b


title: HP425b


title: IVF_fri28LH7E


title: IVF_fri31LH7E


title: IVF_fri29LH7E


title: IVF_fri27LH7E


title: K562-Cas9 chromatin remodeling complexes, sgRNA library

data_processing:
Library strategy: sgRNA-Seq
ATAC-seq K562: Cells demultiplexed and aligned based on cellular barcodes using the snATAC_mat.py script in a previously published sci-ATAC-seq pipeline (https://github.com/r3fang/snATAC)(Preissl et al., 2018) and using hg19 as reference genome. Briefly, reads were aligned using bowtie2 (Langmead B., 2012) -D 15 -R 2 -L 22 -i S,1,1.15 -p 5 -t -X2000 -e 75 --no-mixed --no-discordant and deduplicated using Picard(http://broadinstitute.github.io/picard). Unmapped reads, mitochondrial reads and reads overlapping ENCODE blacklist regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were filtered out. For downstream analyses, we required each cell to have at least 100 aligned sgRNA reads with >= 99% of the reads assigned to one sgRNA sequence for the chromatin modifier screen and >=90% of thereads assigned to one sgRNA sequence for the chromatin remodeling complex subunit screen.
sgRNA seq: sgRNA datasets were demultiplexed based on cellular barcodes using the snATAC_mat.py script in a previously published sci-ATAC-seq pipeline (https://github.com/r3fang/snATAC) (Preissl S. et al., 2018) . The processed sequences were aligned to a custom guide reference using bowtie (Langmead B. et al., 2009) using the command bowtie -v 1 -m 1. For the human-mouse experiment, we show data for cells with at least 20 mapped reads. Cells with over 90% of sgRNA reads that mapped exclusively to human or mouse sgRNAs were considered species-specific cells. Cells where one sgRNA represented at least 90% of the total reads were kept for further analyses. The remaining cells were considered collisions and/or the result of multiple infections. For downstream analysis of the K562 data, we required each cell to have at least 100 aligned sgRNA reads with ≥ 99% of the reads assigned to one sgRNA sequence for the chromatin modifier screen and >=90% of the reads assigned to one sgRNA sequence for the chromatin remodeling complex subunit screen.
Genome_build: hg19 and mm10

value: CRISPR sgRNA library


title: IVF_fri26LH7E


title: IVF_fri25LH7E


title: IVF_fri23LH7E


title: HP418b


title: IVF_fri19LH7E


title: IVF_fri20LH7E


title: IVF_fri30LH7E


title: IVF_fri17LH7E


title: HP427a


title: IVF_fri22LH7E


title: IVF_fri21LH7E


title: IVF_fri14LH7E


title: white blood cell in PDCM Group_3

type: RNA

city: jinan

first: sun

last: wei

address: HuaiYin District Jingwuweiqi Road

country: China

institute: Provincial Hospital affiliated to Shandong University

description: white blood cell in PDCM Group

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Microarray data were extracted and visualized using the Feature Extraction software 10.7(Agilent Technologies), and the resulting raw data were subjected to quantile normalization using the limma package in R. Data analysis was performed according to by Agilent Technologies at Sinotech Genomics Corporation. Differentially expressed circRNAs were identified using a fold change cutoff of 2 and a P value of 0.05.

source_name: PDCM

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: RNA from the three paired samples was extracted with RNeasy Mini Kit (Qiagen, Germany) per the manufacturer’s instructions. RNA from the other 44 samples was extracted using Sparkzol Reagent (SparkJade Science Co., Ltd., China), chloroform, and isopropanol precipitation.

treatment_protocol: Leukocytes were isolated from whole peripheral blood via centrifugation (1500g for 15 minutes at 4°C), after lysing red blood cells with Red Blood Lysis Buffer (Solarbio, China).

tag: cell type

value: white blood cell

tag: diagnosis

value: pediatric dilated cardiomyopathy


title: Healthy_30LH7E

value: Healthy


title: IVF_fri12LH7E


title: IVF_fri18LH7E


title: IVF_fri13LH7E


title: Healthy_29LH2E


title: white blood cell in PDCM Group_1

description: white blood cell in PDCM Group


title: Healthy_28LH2E


title: Healthy_27LH7E


title: Healthy_29LH7E


title: white blood cell in PDCM Group_2

description: white blood cell in PDCM Group


title: Rad011040

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: C4-HD tumors were grown in BALB/c mice.

hyb_protocol: cRNA was hybridized onto chips for 18 h at 45 degrees C.  GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

scan_protocol: Chips were scanned in an Affymetrix 3000 (7G) Confocal Scanner.

data_processing: Raw microarray data were normalized using GCRMA function from GeneSpring GX 7.3.1 (Agilent Technologies, Palo Alto, CA, USA) using Affymetrix default analysis settings.

label: biotin

source_name: 12 h MFP

label_protocol: This project used the Affymetrix Gene Chip Mouse Genome 430 2.0 (Affymetrix, #900497)  200 ng of total RNA was used as input.

growth_protocol: C4-HD tumors were grown in MPA-treated BALB/c mice.

extract_protocol: RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tumors using the RNeasy FFPE kit (Qiagen; #73504).

treatment_protocol: When tumors reached 50 mm2, MPA pellets were removed by surgery, and MFP (10 mg/kg/day) was inoculated sc  for 48 h. Saline-treated tumors growing in the presence of MPA were considered the control group.

value: 12 h MFP-treated tumors

value: Mammary carcinoma


title: DKO_rep4

first: Taiyi

middle: Diana

last: Kuo

state: NY

address: 1150 St Nicholas Ave., Ste. 237

department: Medicine

institute: Columbia University

data_processing:
For the analysis, 25 to 38 million read-pairs per sample were used. The reads were mapped to the mouse genome mm10 using STAR (v2.5.2b) algorithm with default settings.
FeatureCounts from the Subread (v1.5.2) package was used to assign concordantly aligned reads pairs to RefSeq genes.
A 25-bp minimum as overlapping bases in a fragment was specified for read assignment.
Raw read counts were used as input for DESeq2 (v1.14.1), which was further used to filter out genes with low counts, normalize the counts using library sizes, and perform statistical tests to find significant differential genes.
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts

source_name: FAC-sorted pancreatic beta cells

growth_protocol: Mice were fed a standard chow diet, and maintained on a 12h light cycle (lights on at 7am).

extract_protocol:
We purified the pancreatic islets (Kuo et al, JBC, 2016) and FAC-sorted the beta cells (Kuo et al, JCI Insight, 2019), as these beta cells were genetically labeled with RIP-Cre and ROSA26-tomato alleles.
RNA was isolated with Nucleospin RNA kit (Macherey-Nagel) with DNase I treatment.
Directional poly-A RNAseq libraries were prepared and sequenced as PE42 (42 bp paired-end reads) on Illumina Hiseq 2500 in high output mode.

treatment_protocol: We generated beta cell-specific single knockout of Foxo1 and Hnf4a, as well as double knockout of both Foxo1 and Hnf4a, by crossing floxed Foxo1 (Kuo et al, JBC, 2016) and/or floxed Hnf4a (Miura et al, JBC, 2006) to RIP-Cre mice (Kuo et al, JCI Insight, 2019).

value: pancreatic beta cells

tag: Sex

value: male

value: 6 to 8 month old

value: beta cell specific Foxo1 and Hnf4a double knockout


title: DKO_rep5


title: Rad011042

description: C4-HD tumors were grown in BALB/c mice.

source_name: 24 h MFP

value: 24h MFP-treated tumors


title: Healthy_26LH2E


title: Healthy_27LH2E


title: Rad011043

description: C4-HD tumors were grown in BALB/c mice.

source_name: 48h MFP

value: 48h MFP-treated tumors


title: Healthy_26LH7E


title: Healthy_28LH7E


title: Rad011037

description: C4-HD tumors were grown in BALB/c mice.

source_name: 6 h MFP

value: 6 h MFP-treated tumors


title: DKO_rep2


title: white blood cell in Control Group_3

description: white blood cell in Control Group

source_name: Healthy volunteers

value: healthy control


title: DKO_rep1


title: Rad011034

description: C4-HD tumors were grown in BALB/c mice.

source_name: MPA

value: Tumors growing in the presence of MPA


title: Healthy_24LH7E

value: Female

value: Endometrium

value: Spain


title: Rad011039

description: C4-HD tumors were grown in BALB/c mice.


title: HKO_rep5

value: beta cell specific Hnf4a knockout


title: Rad011041

description: C4-HD tumors were grown in BALB/c mice.


title: Rad011035

description: C4-HD tumors were grown in BALB/c mice.

source_name: no MPA

value: 48 h saline-treated tumors


title: Healthy_23LH7E

value: Healthy


title: Rad011038

description: C4-HD tumors were grown in BALB/c mice.


title: Rad011044

description: C4-HD tumors were grown in BALB/c mice.

source_name: 48 h MFP


title: Healthy_23LH2E


title: Rad011036

description: C4-HD tumors were grown in BALB/c mice.


title: Rad011033

description: C4-HD tumors were grown in BALB/c mice.


title: DKO_rep3


title: white blood cell in Control Group_1

description: white blood cell in Control Group

value: white blood cell


title: HKO_rep3


title: HKO_rep2


title: Healthy_21LH7E


title: Healthy_22LH2E


title: HKO_rep4


title: white blood cell in Control Group_2

description: white blood cell in Control Group


title: Healthy_21LH2E


title: Healthy_22LH7E


title: IKO_rep4

value: beta cell specific Foxo1 knockout


title: Healthy_18LH2E


title: Healthy_16LH7E


title: Healthy_16LH2E


title: IKO_rep3

value: pancreatic beta cells


title: WT_rep5

value: male

value: WT


title: IKO_rep2

value: 6 to 8 month old


title: IKO_rep5


title: Healthy_15LH7E


title: WT_rep4


title: Healthy_15LH2E


title: Healthy_14LH7E


title: IKO_rep1


title: HKO_rep1


title: WT_rep2


title: Healthy_14LH2E


title: WT_rep1


title: Healthy_18LH7E


title: Healthy_12LH7E


title: hypothalamus input DNA

city: Seoul

first: Sujeong

last: Lim

address: 369 Sangdo-ro, Dongjak-gu, Seoul, Republic of Korea

country: South Korea

institute: Soongsil University

data_processing:
Illumina HiSeq 2500 Software used for basecalling.
ChIP-seq reads were aligned to the mm10 genome assembly using BWA version 0.7.17 with BWA mem algorithm.
Data were filtered using the MarkDuplicate by picard.
Peaks were called using MACS2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bedGraph files

source_name: E15 hypothalamus

growth_protocol: Embryonic day 15 embryos were isolated from pregnant mom and the developing hypothalami were dissected out.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Without any special treatment, the dissected out hypothalami were dissolved to cells, followed by isolation of nuclei.

tag: strain

tag: genotype/variation

tag: developmental stage

value: Embryonic day 15

value: hypothalamus

tag: chip antibody


title: hypothalamus Nrf1 IP

tag: tissue

value: Home-made Nrf1 antibody


title: Healthy_11LH7E


title: H3K27ac ChIPseq 3M WT rep1

data_processing:
Reads were aligned to mouse genome mm10 using the Burrows-Wheeler Aligner (BWA) algorithm with default settings
These reads passed Illumina’s purity filter, and aligned with no more than 2 mismatches. Duplicate reads were removed, and only uniquely mapped reads with mapping quality greater or equal to 25 were subjected for further analysis.
Reads were extended to 200bp at their 3’ ends, and bigwig files were created for visualization using Active Motif software (Active Motif Inc., CA).
H3K27ac peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of p value = 1 x 10-7
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: FAC-sorted beta cells

extract_protocol:
We purified the pancreatic islets (Kuo et al, JBC, 2016) and FAC-sorted the beta cells with fluorescence (Kuo et al, JCI Insight, 2019), as these beta cells were genetically labeled with RIP-Cre and ROSA26-tomato alleles. We then performed H3K27ac ChIPseq using antibody purchased from Active Motif (39133, RRID:AB_2561016).
ChIP DNA libraries were prepared from ChIP DNA with the following steps: end-repair, dA-addition, adaptor ligation and PCR amplification.
The resulting ChIPseq DNA libraries were quantified with Bioanalyzer (Agilent), and sequenced on Illumina NextSeq 500 with 75-nt reads and single-end.

treatment_protocol: We generated mice lacking FoxO1 in pancreatic β cells using RIP-Cre transgenics to excise the floxed FoxO1 gene (Kuo et al, JCI Insight, 2019).

tag: genotype

tag: age

value: 3 month old

tag: pregnancy history

value: nulliparous

value: female

value: H3K27ac (Active Motif 39133, RRID:AB_2561016)


title: WT_rep3


title: Healthy_11LH2E

value: Female

value: Endometrium

value: Spain


title: Healthy_8LH2E

value: Healthy


title: H3K27ac ChIPseq 12M NP IKO_rep3

value: beta cell-specific FoxO1 knockout

value: 12 month old


title: H3K27ac ChIPseq 12M NP WT_rep2

value: pancreatic beta cells


title: IVF_NOTNV71LH8E

value: Estonia

value: IVF


title: H3K27ac ChIPseq 3M IKO rep1


title: IVF_NOTNV73LH8E


title: IVF_NOTNV78LH8E


title: H3K27ac ChIPseq 12M NP IKO_rep2


title: H3K27ac ChIPseq 12M NP WT_rep3

value: WT


title: IVF_NOTNV62LH8E


title: H3K27ac ChIPseq NGT_rep3

value: multiparous, i.e. 3 pregnancies


title: IVF_NOTNV64LH8E


title: H3K27ac ChIPseq DM_rep3


title: IVF_NOTNV59LH8E


title: IVF_NOTNV58LH8E


title: H3K27ac ChIPseq DM_rep2


title: H3K27ac ChIPseq DM_rep1


title: IVF_NOTNV44LH8E


title: IVF_NOTNV52LH8E


title: Healthy_12LH2E


title: H3K27ac ChIPseq NGT_rep1


title: hypothalamus Mll4 IP

value: Embryonic day 15

value: hypothalamus

value: Home-made Mll4 antibody


title: Healthy_8LH7E


title: IVF_NOTNV43LH8E


title: H3K27ac ChIPseq 12M NP IKO_rep1

value: nulliparous


title: IVF_NOTNV41LH8E


title: IVF_NOTNV39LH8E


title: IVF_NOTNV35LH8E


title: IVF_NOTNV33LH8E


title: H3K27ac ChIPseq 12M NP WT_rep1

value: female


title: IVF_NOTNV38LH8E


title: IVF_NOTNV36LH8E


title: IAADox_Wapl-degron_rep2

description: aligned to mm9 genome

data_processing:
Library strategy: Linear-amplification PCR-mediated HTGTS
Standard basecalling formats for Miseq reads
Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9 genome and AJ851868/mm9 hybrid genome
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paired end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library).

source_name: v-Abl transformed B6 pro-B cell line

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
LAM-HTGTS V(D)J-Seq libraries were prepared using linear-amplification PCR-mediated HTGTS.

value: Wapl-degron, OsTIR1, Single Igh, Emu-Bcl2, RAG1 deficient


title: IAADox_Wapl-degron_rep1

description: aligned to mm9 genome


title: H3K27ac ChIPseq NGT_rep2

value: H3K27ac (Active Motif 39133, RRID:AB_2561016)


title: IVF_NOTNV30LH8E

value: Female

value: Endometrium


title: IVF_NOTNV32LH8E


title: BM_PreB_Rep2

description: aligned to mm9 genome

source_name: BM Pre B cells from 129sv mice

treatment_protocol:
BM preB cells were isolated from WT 129 mice
3 uM STI-571 treated for 4 days


title: IVF_NOTNV29LH8E


title: BM_PreB_Rep1

description: aligned to mm9 genome


title: BM_PreB_Rep3

description: aligned to mm9 genome


title: IVF_NOTNV27LH8E


title: v-Abl_cycling_Rep4

description: aligned to mm9 genome

source_name: v-Abl transformed 129sv pro-B cell line

treatment_protocol:
RAG2 retrovirus infected, 3 uM STI 4 days
3 uM STI-571 treated for 4 days

value: Emu-Bcl2, RAG2 deficient


title: v-Abl_cycling_Rep3

description: aligned to mm9 genome


title: TP_20_REP_3 HFD

city: Irvine

first: Muntaha

middle: Fatima

last: Samad

state: CA

address: Campus Dr

department: CS

institute: UC Irvine

description:
Ten week high fat diet feeding
Brain homogenate
mouse_scn_high_fat.tsv

data_processing:
Trim using Trimmomatic.
Alignment to reference assembly mm10 using Tuxedo Tophat.
Read counting for each gene to get FPKM values using Tuxedo Cufflinks.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: FPKM value for each gene in tsv table format.

source_name: Suprachiasmatic nucleus

extract_protocol:
Suprachiasmatic nucleus (SCN) enriched region was dissected from the fresh brain and immediately snap frozen in liquid nitrogen. Total RNA was extracted using RNeasy Micro Kit (QIAGEN).
Library construction was performed according to the Illumina TruSeq mRNA stranded protocol.

value: Suprachiasmatic nucleus

value: Adult

tag: treatment

value: High-fat diet

tag: timepoint

value: TP 20


title: Untreated_Wapl-degron_rep1

description: aligned to mm9 genome

treatment_protocol:
RAG1/2 retrovirus infected, 3 uM STI 4 days
3 uM STI-571 treated for 4 days


title: Untreated_Wapl-degron_rep3

description: aligned to mm9 genome


title: v-Abl_cycling_Rep2

description: aligned to mm9 genome


title: TP_20_REP_2 HFD


title: TP_20_REP_1 HFD


title: v-Abl_cycling_Rep1

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_single Igh_INV_IAADox_rep3

description:
aligned to mm9 genome
The data in these processed data files are the pooled results of Samples JH1-4_Wapl-degron_single Igh_INV_IAADox_rep1-rep3:
v-Abl_IAADOX_Igh_INV_pooled_OFT.tlx.txt
v-Abl_IAADOX_Igh_INV_pooled_OFT.pos.bedgraph.gz
v-Abl_IAADOX_Igh_INV_pooled_OFT.neg.bedgraph.gz


title: Untreated_Wapl-degron_rep2

description: aligned to mm9 genome


title: TP_16_REP_2 HFD

value: TP 16


title: JH1-4_Wapl-degron_single Igh_INV_IAADox_rep2


title: JH1-4_Wapl-degron_single Igh_INV_IAADox_rep1


title: TP_12_REP_3 HFD

value: TP 12


title: plp-1(ok2155)-3

city: Chennai

first: Kuppuswamy

last: Subramaniam

state: Tamil Nadu

address: Room#301, Block-2

department: Department of Biotechnology

country: India

institute: Indian Institute of Technology Madras

description:
Expression_Profile.WBcel235_WS264.gene
Expression_Profile.WBcel235_WS264.transcript

data_processing:
Average base quality at each cycle was determined using FastQC v0.11.7
Trimmomatic 0.38 was used for trimming
HISAT2 version 2.1.0, Bowtie2 2.3.4.1 was used for mapping reads to C. elegans reference genome version WS264
StringTie version 1.3.4d was used for RNA-seq alignments into transcripts
Fold Change, nbinomWaldTest using DESeq2, and Hierarchical Clustering were used for differential gene expression analysis
Genome_build: Wormbase version WS264
Supplementary_files_format_and_content: xlsx format; mapped genes and expression profiles of transcripts

organism: Caenorhabditis elegans

source_name: Loss-of-function allele of the plp-1 gene

growth_protocol: Hermaphrodites were grown on OP50-seeded NGM plates

extract_protocol:
Total RNA was extracted using the Tri-reagent (Sigma-Aldrich) using manufacturer's protocols.
Libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) using manufacturer's protocols (TruSeq Stranded mRNA Sample Preparation Guide, Part #  15031047 Rev. E.)

treatment_protocol: Animals were grown at 20C till the plates became confluent, but not starved.

value: Mixed stage, includes embryos, larval stages and adults

tag: growth temperature

tag: medium


title: TP_12_REP_2 HFD


title: 3'CBE KO_Splenic_Nonproductive_Rep3

description: aligned to AJ851868/mm9 hybrid genome

source_name: Splenic B cells from 129sv mice

treatment_protocol:
Splenic B cells were isolated from chimeras by CD43-negative selection kit and then treated with LPS/aIgD-dextran for 96 hours; gRNA were extracted for HTGTS
3 uM STI-571 treated for 4 days

value: 3'CBEs deletion


title: Wild-type (control)-1

source_name: N2 strain


title: plp-1(ok2155)-2


title: Species mixing experiment, sgRNA library

organism:
Homo sapiens
Mus musculus

source_name: HEK293T and NIH3T3 cells

tag: cell line

value: Mixture of NIH3T3 and HEK293T

value: Cells infected with pooled CRISPR library of 20 non-targeting gRNAs (10 non-targeting for human genome and 10 non-targeting for mouse genome).

tag: library type

value: CRISPR sgRNA library


title: Wild-type (control)-2


title: Species mixing experiment, ATAC-seq library

value: ATAC-seq library


title: plp-1(ok2155)-1


title: TP_12_REP_1 HFD


title: TP_8_REP_2 HFD

value: TP 8


title: TP_8_REP_3 HFD


title: 3'CBE KO_Splenic_Nonproductive_Rep2

description: aligned to AJ851868/mm9 hybrid genome


title: TP_16_REP_3 HFD


title: WT_Splenic_Nonproductive_Rep1

description: aligned to AJ851868/mm9 hybrid genome

value: WT


title: Wild-type (control)-3


title: WT_Splenic_Nonproductive_Rep3

description: aligned to AJ851868/mm9 hybrid genome


title: TP_8_REP_1 HFD


title: 3‘CBE KO_Splenic_Nonproductive_Rep1

description: aligned to AJ851868/mm9 hybrid genome


title: TP_4_REP_3 HFD

value: TP 4


title: TP_4_REP_2 HFD


title: TP_16_REP_1 HFD


title: WT_Splenic_Nonproductive_Rep2

description: aligned to AJ851868/mm9 hybrid genome


title: 21-days toosendanin, rep4

city: Hangzhou

first: Lingqi

last: Yu

address: Yuhangtang Road No.388

institute: Zhejiang University

description: gene expression after 21-days toosendanin treatment

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete   Labeling and Hyb Kit (Agilent technologies, Santa Clara, CA, US) in   hybridization Oven (Agilent technologies, Santa Clara, CA, US )  according to the manufacturer’s instructions, hybridization

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent  technologies, Santa Clara, CA, US) and Feature Extraction software 10.7.1.1  (Agilent  technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: serum exosomes, 21-days toosendanin, replicate 4

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

growth_protocol: Male BALB/c mice were housed in an environmentally controlled room at 25 ± 1 °C with a relative humidity of 50 ± 10%, and a light-dark cycle of 12 h each. Food and tap water were provided ad libitum. Mice were allowed to acclimate for 3 days before the experiments were initiated.

extract_protocol: Total RNA along with miRNA was isolated with the Trizol reagent (Qiagen, Germany).

treatment_protocol: Twenty-four hours after last administration, serum was obtained. miRNAs were extracted and purified using the mirVana™ PARISTM Kit (Ambion, Inc., USA) and stored at -80°C for further microarray analysis.

value: serum

tag: gender

value: male

value: BALB/c


title: 21-days toosendanin, rep3

source_name: serum exosomes, 21-days toosendanin, replicate 3


title: elevated CO2, normal light, stationary, series C, rep 3

city: Seattle

first: Justin

last: Ashworth

address: 401 Terry Ave N

institute: Institute for Systems Biology

hyb_protocol: Array slides were hybridized according to the standard Agilent protocol for 8x60k custom array slides.

scan_protocol: Array slides were scanned using an Agilent slide scanner.

data_processing: Data were processed from Agilent files using the limma package in R, including background correction, loess (within-array) and 'Aquantile' (between-array) normalization.

organism: Thalassiosira pseudonana

source_name: T. pseudonana batch culture

label_protocol: Total RNA was amplified and labeled using the Agilent Quick-Amp labeling kit (two-color).

growth_protocol: 2L batch cultures of artificial seawater medium with reduced nitrate (100 uM) and 80 uM silicic acid were equilibrated to normal or elevated CO2 levels by bubbling with co2 enrich air, and then innoculated with Thalassiosira pseudonana cells at 2x10^5 cells/mL starting cell density. Cells were grown under constant light for approximately three days, after which cultures reached a stationary cell density (~2x10^6/cells/mL) and both free nitrate and silicic acid levels were exhausted (completely incorporated into cells).

extract_protocol: Cells (3x10^7 cells, volume dependent on cell culture density) were harvested by filtration, flash frozen, and then total RNA was extracted using the mirVANA extraction kit.

treatment_protocol: Cells were grown under normal (~400ppm) or elevated (~800ppm) CO2 levels. Experiments were also repeated twice each at normal and elevated light levels.

tag: light level

value: normal

tag: phase

value: mid-log phase

tag: co2 level

value: stationary

value: elevated


title: elevated CO2, normal light, exponential, series C, rep 2

value: exponential


title: elevated CO2, normal light, exponential, series C, rep 3


title: elevated CO2, normal light, stationary, series C, rep 1


title: elevated CO2, normal light, stationary, series C, rep 2


title: TP_0_REP_3 HFD

tag: strain

value: Suprachiasmatic nucleus

value: Adult

value: High-fat diet

value: TP 0


title: TP_20_REP_3 NC

description:
Ten week normal chow feeding
Brain homogenate
mouse_scn_control.tsv

value: Normal chow

value: TP 20


title: 9-days toosendanin, rep4

description: gene expression after 9-days toosendanin treatment

source_name: serum exosomes, 9-days toosendanin, replicate 4


title: TP_4_REP_1 HFD


title: TP_0_REP_1 HFD


title: 21-days toosendanin, rep1

source_name: serum exosomes, 21-days toosendanin, replicate 1


title: 9-days toosendanin, rep3

source_name: serum exosomes, 9-days toosendanin, replicate 3


title: 21-days toosendanin, rep2

source_name: serum exosomes, 21-days toosendanin, replicate 2


title: 9-days toosendanin, rep2

source_name: serum exosomes, 9-days toosendanin, replicate 2


title: elevated CO2, high light, stationary, series C, rep 2

value: high


title: normal CO2, normal light, stationary, series C, rep 1


title: elevated CO2, high light, exponential, series C, rep 3


title: elevated CO2, high light, stationary, series C, rep 3


title: normal CO2, normal light, exponential, series C, rep 3


title: normal CO2, normal light, exponential, series C, rep 1


title: normal CO2, normal light, stationary, series C, rep 2


title: normal CO2, normal light, stationary, series C, rep 3


title: elevated CO2, high light, exponential, series C, rep 1


title: normal CO2, normal light, exponential, series C, rep 2


title: elevated CO2, high light, exponential, series C, rep 2


title: normal CO2, high light, stationary, series C, rep 3


title: Healthy_24LH2E

source_name: Endometrium

value: Female

value: Endometrium

tag: receptivity time-point

tag: country of origin

value: Spain

tag: tissue state

value: Healthy

tag: sequencing batch


title: elevated CO2, high light, stationary, series C, rep 1


title: TP_20_REP_1 NC

tag: tissue

tag: age


title: TP_16_REP_3 NC

tag: treatment

value: TP 16


title: 3-days toosendanin, rep4

description: gene expression after 3-days toosendanin treatment

source_name: serum exosomes, 3-days toosendanin, replicate 4

value: serum

value: male

value: BALB/c


title: TP_16_REP_2 NC

tag: timepoint


title: 9-days toosendanin, rep1

source_name: serum exosomes, 9-days toosendanin, replicate 1


title: normal CO2, high light, exponential, series C, rep 3

value: normal

value: mid-log phase


title: normal CO2, high light, exponential, series C, rep 2

value: exponential


title: 3-days toosendanin, rep3

source_name: serum exosomes, 3-days toosendanin, replicate 3


title: TP_16_REP_1 NC

source_name: Suprachiasmatic nucleus

value: Suprachiasmatic nucleus

value: Adult


title: normal CO2, high light, exponential, series C, rep 1


title: elevated CO2, normal light, exponential, series C, rep 1

value: elevated


title: 3-days toosendanin, rep2

source_name: serum exosomes, 3-days toosendanin, replicate 2


title: D4_KO_Nanog_2

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

data_processing:
Paired-end reads for ATAC-seq and ChIP-seq were aligned to the mouse mm10 genome using Bowtie2 with the ‘‘-X 2000’’ options
The Picard was used to remove PCR duplicates and Samtools was used to remove low quality reads (MAPQ < 30)
The MACS2 software calls the ChIP-seq peak with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using deepTools

growth_protocol: ESCs were routinely cultivated on mitotically inactivated mouse embryonic fibroblasts (MEFs) in Knockout DMEM supplemented with 20% Knockout Serum Replacement, 1× Glutamine Max, 1× NEAA, 1× Pen/Strep, 0.1 mM 2-mercaptoethanol, 1000 U ml-1 LIF, 1 μM PD0325901 and 3 μM CHIR99021. MEFs were grown in DMEM high glucose supplemented with 15% FBS and 1× Pen/Strep.

extract_protocol: ChIP was performed as described previously (Liu et al., 2015)

treatment_protocol: The EpiLCs induction were performed by seeding 1.0×105 ESCs into a well of a 12-well plate coated with 16.7 mg/ml human plasma fibronectin in N2B27 medium containing 20 ng/ml Activin A, 12 ng/ml bFGF, and 20% KSR. The culture medium was changed every day.

tag: antibody

value: Nanog

tag: cell type

value: Embryonic Stem Cells (ESCs)

tag: time point

value: Atg7 KO


title: normal CO2, high light, stationary, series C, rep 2

value: high

value: stationary


title: normal CO2, high light, stationary, series C, rep 1


title: D4_KO_OTX2_2

tag: cell line


title: TP_12_REP_2 NC

value: Normal chow

value: TP 12


title: TP_12_REP_3 NC


title: D4_KO_OTX2_1


title: EHP1

city: Guangzhou

first: Hairuo

last: Lin

state: Guangdong

address: 1838 Guangzhou avenue north

department: Department of Cardiology

institute: Nanfang Hospital, Southern Medical University

data_processing:
Briefly, the ribosomal RNA was depleted from total RNA using the rRNA Removal Kit following manufacturer’s instruction. RNA was then fragmented into 250~300 bp fragments, and first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP). RNA was degraded using RNase H, and second strand cDNA was synthesised using DNA polymerase I and dNTPs (dATP, dUTP, dCTP and dGTP). After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing.
Raw data of FASTQ format were firstly processed through in-house perl scripts. Clean reads for each sample were first mapped to a reference genome with the software HISAT2. Reads alignment results were transferred to the program StringTie for transcript assembly. Quantification of the transcripts and genes was performed using StringTie software and Reads Per Kilobase of transcript per Million mapped reads (RPKM) was obtained. DEseq2 was used for differential expression analysis. The resulting P-values were adjusted using the Benjamini approach for controlling the false discovery rate.
Genes with RPKM > 500 & |log2 (Fold Change) | > 1 & padj < 0.05 were assigned as differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: heart

extract_protocol:
The heart sample from mice in sedentary group and EHP group were collected at the one week after the termination of swimming. For each sample, the whole cardiac tissue was isolated and treated with RNAlater (Qiagen, CA) RNA stabilization reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6 male mice (n=142, 8-10 weeks old and weighing 20-25 g) were provided by the Animal Center of Southern Medical University. The mice were divided into two groups, an exercise hypertrophic preconditioning (EHP; n=72) group and a sedentary control (Sed; n=70) group. The EHP group performed an endurance exercise protocol consisting of daily swimming training to induce physiological cardiac hypertrophy, according to a previously described protocol, with minor modifications. The swimming program started with 2 daily sessions of 15 minutes, and sessions were separated by at least 6 hours. The length of each session was then increased by 15 minutes every 2 days until they lasted 90 minutes; the program was conducted on 5 days/week, followed by 2 days of rest. The twice daily 90-minute swimming sessions were continued for the next 7 days. The protocol thus lasted for a total of 21 days. The mice were closely observed to avoid relative hypoxia. Mice in the Sed group were free to move around the cage. One week after the end of exercise training, all mice underwent either transverse aortic constriction (TAC) or a sham operation.

tag: Sex

value: heart

value: swimming 3w +sedentary1w

tag: rna population

value: lnc RNA


title: 3-days toosendanin, rep1

source_name: serum exosomes, 3-days toosendanin, replicate 1

value: serum

tag: gender

value: male

value: BALB/c


title: sedentary3

value: sedentary 4w


title: EHP2


title: D4_KO_H3K4me1_2


title: TP_12_REP_1 NC

value: Suprachiasmatic nucleus


title: TP_8_REP_3 NC

value: Adult

value: TP 8


title: EHP3


title: sedentary2


title: 21-days control, rep4

description: gene expression after 21-days vehicle control treatment

source_name: serum exosomes, 21-days control, replicate 4


title: D4_KO_H3K27ac_2


title: TP_8_REP_2 NC


title: sedentary1


title: D4_KO_H3K4me3_2


title: TP_8_REP_1 NC


title: D4_Ctr_Nanog_2

value: Nanog

value: Control


title: 21-days control, rep1

source_name: serum exosomes, 21-days control, replicate 1


title: 21-days control, rep2

source_name: serum exosomes, 21-days control, replicate 2


title: 21-days control, rep3

source_name: serum exosomes, 21-days control, replicate 3


title: TP_4_REP_3 NC

value: TP 4


title: D4_Ctr_OTX2_2

value: Embryonic Stem Cells (ESCs)


title: 9-days control, rep4

description: gene expression after 9-days vehicle control treatment

source_name: serum exosomes, 9-days control, replicate 4


title: control-11

city: Beijing

first: Yu

last: Fu

address: Yuanmingyuan West Road 2#,Haidian District

department: college of animal science and technology

institute: China agricultural university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus_musculus.GRCm38.99 whole genome using Bowtie v1.0.1 and HISAT2 (version:2.1.0), and two mismatches were allowed for 150 bp reads in each alignment.
Numbers of fragment reads per kilobase of exon region in a gene per million mapped reads (FPKM) analyzed by Cufflink (version: 2.2.1) were used as the value of normalized gene expression
Genome_build: Mus_musculus.GRCm38.99
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: The C2C12 myoblast cell line was cultured at subconfluent densities in growth medium, made up of  DMEM supplemented with 10% heat-inactivated fetal bovine serum  and 1% penicillin/streptomycin.

extract_protocol:
C2C12 cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#E7530L) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C2C12 cells were transfected with 4 μg of the negative control or TRPC1 overexpressed vectors using Lipofectamine 2000 in each well of a 6-well plate.

tag: genotype

value: control

value: myoblast cell line


title: control-8

tag: strain


title: D4_Ctr_OTX2_1


title: TP_0_REP_2 HFD

value: High-fat diet

value: TP 0


title: control-7


title: TP_4_REP_2 NC

value: Normal chow


title: D4_Ctr_H3K4me3_2


title: TP_4_REP_1 NC


title: TRPC1-OE34


title: 9-days control, rep3

source_name: serum exosomes, 9-days control, replicate 3


title: D4_Ctr_H3K4me1_2


title: 9-days control, rep1

source_name: serum exosomes, 9-days control, replicate 1


title: 9-days control, rep2

source_name: serum exosomes, 9-days control, replicate 2


title: TRPC1-OE33


title: TP_0_REP_3 NC


title: 3-days control, rep4

description: gene expression after 3-days vehicle control treatment

source_name: serum exosomes, 3-days control, replicate 4


title: TP_0_REP_2 NC


title: D4_Ctr_H3K27ac_2


title: TP_20_REP_2 NC

value: TP 20


title: TRPC1-OE32


title: TP_0_REP_1 NC


title: K562-Cas9 cancer chromatin modifiers, sgRNA library

source_name: K562-Cas9 cells

value: K562 constitutively expressing Cas9

value: Cells infected with pooled CRISPR library of 63 gRNAs targeting the most mutated chromatin modifiers in cancer patients and 3 non-targeting sgRNAs.

tag: library type

value: CRISPR sgRNA library


title: D2_Ctr_Nanog_2


title: 3-days control, rep3

source_name: serum exosomes, 3-days control, replicate 3

value: serum

value: male

value: BALB/c


title: 3-days control, rep2

source_name: serum exosomes, 3-days control, replicate 2


title: 3-days control, rep1

source_name: serum exosomes, 3-days control, replicate 1


title: YFP+_mut_rep2_scRNA-seq

status: Public on Nov 06 2020

city: Philadelphia

first: Ben

middle: Z.

last: Stanger

state: PA

address: 421 Curie Boulevard

institute: Perelman School of Medicine at the University of Pennsylvania

description: Treated with DDC

data_processing:
Library strategy: scRNA-Seq
10X Genomics CellRanger pipeline
Genome_build: mm10 with the added YFP sequence
Supplementary_files_format_and_content: UMI counts in h5 file

source_name: Smad4fl/fl;RosaYFP/YFP mice (injected with AAV8-TBG-Cre to lineage label hepatocytes) treated with DDC

growth_protocol: Male RosaYFP/YFP mice (Srinivas et al., 2001) and and Smad4fl/fl mice (Yang et al., 2002) were injected retro-orbitally at four weeks of age with 2.5x10^11 viral particles of AAV8-TBG-Cre virus obtained from the Penn Vector Core. One week following Cre injection, mice were treated with 0.1% DDC (3,5-diethoxycarbonyl-1,4-dihydrocollidine, Sigma-Aldrich) chow diet (Envigo) for 2-6 weeks.

extract_protocol:
Livers of control and DDC-treated mice were perfused with first 1X HBSS, followed by HBSS+ 1 mM EGTA, and HBSS + 5 mM CaCl2 with liberase. Following perfusion, livers were mechanically dissociated and incubated for 15 minutes in HBSS with CaCl2 and liberase at 37 degrees. Digests were filtered and cells isolated by FACS. After removing CD31, CD45, and CD11b cells, living cells were then sorted from the remaining cells (Bulk samples) or further sorted for YFP+ cells (YFP samples)
Following isolation of sorted cells, single cell libraries were generated by the Center for Applied Genomics at the Children’s Hospital of Philadelphia on a 10x Genomics chromium platform

treatment_protocol: AAV8-TBG-Cre labeled RosaYFP mice were treated with 0.1% DDC chow for 2, 3, 4, and 6 weeks to induce reprogramming. Following treatment, mice were sacrificed and cell isolated from the liver then sorted by FACS.

value: Week 4

value: Liver

tag: cell population

value: YFP+ cells


title: Bulk_mut_rep2_scRNA-seq

description: Treated with DDC

source_name: Smad4fl/fl;RosaYFP/YFP mice  (injected with AAV8-TBG-Cre to lineage label hepatocytes) treated with DDC

value: bulk (including YFP+ and YFP- cells)


title: YFP+_mut_rep1_scRNA-seq

description: Treated with DDC


title: YFP+_ctrl_rep2_scRNA-seq

description: Treated with DDC

source_name: Smad4fl/+;RosaYFP/YFP (injected with AAV8-TBG-Cre to lineage label hepatocytes) treated with DDC


title: Bulk_mut_rep1_scRNA-seq

description: Treated with DDC


title: Zmat3 knockout 1 input

city: Stanford

first: Kathryn

last: Bieging-Rolett

state: California

address: CCSR-South, Rm 1240, 269 Campus Drive

department: Radiation Oncology

institute: Stanford University School of Medicine

data_processing:
For each gene in Gencode v19, the transcript with the highest abundance in WT control (WT1, WT2, WT3) RNA-seq datasets was chosen as the representative transcript, and genes with representiative transcript with TPM < 1 were discarded.
Next, for all internal exons (excluding the first and last exons) the region from 500nt upstream to 500nt downstream (for introns less than 1000nt, the region was split with half assigned to the upstream exon and half to the downstream exon) was queried for the presence of significant peaks.
Finally, the number of peaks at each position was averaged over all events to obtain the final meta-exon value.
Genome_build: mm10
Supplementary_files_format_and_content: bw and bed

source_name: Mouse embryonic fibroblasts

extract_protocol:
20 million cells were UV crosslinked, lysed, sonicated, and treated with Rnase.  Then the sampels were immunoprecipitated with anti-Zmat3 antibodies.  After washes, samples were run on a NuPAGE gel, transferred to nitrocellulose membrane, and the region from 35 to 110 kDa was isolated and treated with Proteinase K. RNA was isolated with RNA clean and concentrator columns (Zymo).
Reverse transcription was performed with 120 U Superscript III (ThermoFisher) with InvAR17 primer (CAGACGTGTGCTCTTCCGA) at 55C for 20 min, followed by addition of 2.5 uL ExoSAP-IT and incubation at 37C for 15 min. After addition of 1 uL 0.5M ETDA, RNA was removed by addition of 3 uL 1M NaOH and incubation at 70C for 10 min. 3 uL of 1M HCl was added to normalize pH, and RNA was purified with MyOne Silane beads (ThermoFisher). Ligation of InvRand3Tr3 adapter (/5Phos/NNNNNNNNNNAGATCGGAAGAGCGTCGTGT/3SpC3/) to the 5’ end of cDNA was performed with T4 RNA Ligase plus the addition of 15 U 5’ Deadenylase (NEB). After RNA purification with MyOne Silane beads (ThermoFisher), PCR amplification (Q5 Master Mix, NEB) was performed with standard Illumina multiplexing indexes, and samples were sequenced on the HiSeq4000 platform.

treatment_protocol: Cas9+ MEFs were transduced with E1A and HrasV12 retroviruses and selected with hygromycin and blasticidin. Then the cells were transduced with lentiviruses containing one of three negative control sgRNAs, selected with Puromycin for 3 days, and then cultured for another 10 days.  In addition, one Zmat3 knockout MEF line (Janic et al Nature Medicine 2018) was also transduced with E1A and HrasG12V retroviruses as described above.

tag: sgrna

tag: sample type

value: Input

tag: rip antibody

value: none (input)


title: YFP+_ctrl_rep1_scRNA-seq

description: Treated with DDC

source_name: Smad4fl/+;RosaYFP/YFP  (injected with AAV8-TBG-Cre to lineage label hepatocytes) treated with DDC

tag: tissue


title: Bulk_ctrl_rep2_scRNA-seq

description: Treated with DDC


title: Bulk_ctrl_rep1_scRNA-seq

description: Treated with DDC


title: Control 2 input

value: sgNegative control SPA


title: Control 1 input

value: sgNegative control EV


title: Control 3 input

value: sgNegative control ACOCA


title: Zmat3 knockout 1

value: IP

value: anti-Zmat3 (Proteintech, 10504-1-AP)


title: Control 2


title: Control 1


title: Control 3


title: B_M microRNA

first: Rong

last: Liu

address: 185 East Lake Road

department: School of Basic Medical Sciences

institute: Wuhan University

description: male worms from BALB/c mice

data_processing:
Basecalls performed using illumina CASAVA version 1.8
Clean reads were obtained from initial Illumina (Solexa) data after removal of the low quality reads (more than half of the bases had a quality value less than 5), insert null reads, adaptor null reads, reads with ploy A tail, and reads shorter than 15 nt. The small RNAs with sizes ranging from 18 nt to 30 nt were used for further analyses. The clean reads were processed using Illumina’s Genome Analyzer Pipeline software and then subjected to a series of data filtration steps using mammalian miRNAs in miRBase 21.0 to obtain mappable sequences using the ACGT101-miR program. Reads that matched ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), repeat sequences, and other non-coding RNA (ncRNA) previously deposited in Rfam 8.0 and NCBI GenBank (http://www.ncbi.nlm.nih.gov/GenBank) were excluded. The 18–26 nt-long reads remaining in each library were mapped onto the draft S. japonicum genome sequences (ftp://down:lsbilifecenter.sgst.cn:2121/subjectData/schistosoma/sjr2 scaffold.fasta.zip and ftp://ftp.sanger.ac.uk/pub/pathogens/Schistosoma/mansoni/genome/sma v5.2.chr.fa) using ShortOligonucleotide Alignment Program (SOAP; http://soap.genomics.org.cn). Next, we aligned the predicted miRNAs to all known mature deuterostoma miRNA sequences in miRBase version 21.0 (http://microrna.sanger.ac.uk) to distinguish novel sequences. Other small RNAs were also analyzed to predict candidate new miRNAs using miRDeep2 software (https://www.mdc-berlin.de/8551903/en/). Secondary structure prediction of individual miRNAs was performed using MFOLD software (version 2.38, http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form).
The expression of miRNAs in four samples were normalized by TPM (transcript per million) with the normalization formula (Normalized expression = actual miRNAs reads counts/total clean reads counts ×10^6). The expression of the miRNAs in two samples was visualized by the fold change, which was calculated from the normalized expression, and ratio were generated using the formula (fold change = TPM of schistosome isolated from BALB/c-Scid mice/TPM of schistosome isolated from BALB/c mice).
Genome_build: S. japonicum (PRJEA34885)
Supplementary_files_format_and_content: tab-delimited .xls files include raw counts and TPM values for each Sample ...

organism: Schistosoma japonicum

source_name: Whole body

extract_protocol:
Worms were recovered by hepatic-portal perfusion with PBS solution at five weeks post infection. The worms were transferred into sterile RPMI 1640 and separated by sex under light microscopy, after which the worms were washed three times with sterile RPMI 1640. Schistosomes were homogenized in a glass homogenizer, and total RNA was isolated using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, USA).
Small RNA libraries were constructed using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® according to the manufacturer’s instructions (New England Biolabs, USA). Briefly, the assay began with 20 μg of total RNA from each sample, the small RNAs (<300 nt) extracted were 5' and 3' extended with adapters, and was transcribed into the first strand cDNA using random hexamer primer, and the products were amplified by PCR. The PCR products purified and size-selected by polyacrylamide gel electrophoresis (PAGE), quantified by Qubit2.0 and examined by Agilent 2100 for insert size,which was followed by quantification of the effective concentration of the constructed library by quantitative PCR. Small RNA sequencing was performed on an Illumina HiseqTM 2500/MiSeq platform (Illumina).

tag: host

value: BALB/c mouse

tag: worm sex

tag: Stage

value: five weeks post infection


title: S_F microRNA

description: female worms from SCID mice

value: SCID mouse

value: female


title: B_F microRNA

description: female worms from BALB/c mice


title: D2_KO_Nanog_2

tag: antibody

value: Nanog

tag: cell type

value: Embryonic Stem Cells (ESCs)

tag: treatment

value: Atg7 KO


title: LC3 [NV_3]

city: São Carlos

first: Mateus

middle: José

last: Sudano

state: SP

address: Rod. Washington Luis - Km 235

department: Department of Genetics and Evolution

country: Brazil

institute: Federal University of São Carlos

data_processing:
The quality filtering was performed by seqyClean v1.3.12. (https://bitbucket.org/izhbannikov/seqyclean/get/stable.zip) using a minimum of 26 Phred quality vector, and adaptor sequences from the Univec database (https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/) were used as guide to remove possible contaminants and minimum read length of 65 bases. Only high quality paired-end sequences were kept for further analyses
The reads were mapped with Tophat v.2.0.8 (KIM et al., 2013) and Bowtie2 v2.1.0 (LANGMEAD & SALZBERG, 2012) on the masked bovine genome assembly (Bos taurus UMD 3.1, NCBI). The isoforms were obtained with the package Cufflinks v.2.1.1 1 (TRAPNELL et al., 2012), with the annotation file (.gtf) as guide through the option -G (the RABT assembly) and specifically the PGR gene isoforms were searched.
The mapping file was sorted using SAMTools v 0.1.18 (LI et al., 2009) and read counts were obtained using the script from HTSeq-count v0.5.4p2 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
The differential expression analysis was performed with package DESEq v1.12.1 (ANDERS, 2010), from R/Bioconductor. Using the function “estimate Size Factors”, the normalized counts were obtained (baseMean values, which are the number of reads divided by the size factor or normalization constant). The standard deviation along the baseMean values was also calculated for each transcript. In order to avoid artifacts caused by low expression profiles and high expression variance, only transcripts that had an average of baseMean > 5 and the mean greater than the standard variation were analyzed. The method to test for differential expression was the negative binomial distribution, through the nbinom Test function on DESeq. The threshold for evaluating significance was obtained by applying a p-value of 0.05 FDR- Benjamini-Hochberg.
Supplementary_files_format_and_content: tab-delimited text files include LogFC, LogCPM, pvalue,  and FDR values for each Sample

organism: Bos taurus

source_name: bovines embryos presenting low cryosurvival

growth_protocol: standard medium for in vitro production of bovine embryos (SOFaaci)

extract_protocol:
Total RNA extraction and purification of each sample was performed using the PicoPure RNA Isolation kit (Life technologies, Foster City, CA, USA) according to manufacturer´s instructions. Genomic DNA contamination was removed by performing an on-column DNA digestion using RNase-free DNase (Qiagen, Mississauga, ON, Canada). RNA was eluted in 11 µL of elution buffer and the RNA concentration was checked using a Qubit® 3 fluorometer (Life technologies), RNA integrity was evaluated using a Bioanalyzer 2100 (Agilent Technologies, CA, USA) with the use of RICH Pico Chips (Agilent Technologies). All samples analyzed had a RNA concentration ≥ 10 ng/µL an RNA integrity number (RIN) ≥ 7.7, and was considered adequate.
The library preparation was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England, Biolabs, MA, EUA), according to manufacturer´s instructions

treatment_protocol: high vs low embryo cryosurvival afeter vitrification

tag: embryo origin

value: in vitro produced

tag: developmental stage

value: blastocyst

tag: sample group

value: low cryosurvival after vitrification


title: LC2 [NV_2]


title: LC1 [NV_1]


title: HC3 [V_3]

source_name: bovines embryos presenting high cryosurvival

value: high cryosurvival after vitrification


title: SET-2 OTX P/R 1

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

data_processing:
Sequencing reads were trimmed using the trimGalore software.
The reads were mapped using HISAT2 against the human genome build UCSC hg19
Quantified using StringTie against the Gencode gene model
Gene expression (FPKM) was quantile normalized using the R statistical system
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

source_name: Drug resistant sAML cell line

growth_protocol: SET-2 and SET-2-OTX P/R cells were cultured in 20% FBS containing RPMI1640 media.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Libraries were constructed following standard Illumina protocols for RNA sequencing.

treatment_protocol: Total RNA was isolated from exponential phase cultures with a kit from Ambion, Inc

value: leukemia blast cells

tag: cell line

value: SET-2 OTX P/R

value: untreated cells


title: SET-2 OTX P/R 2


title: SET-2 Parental 3

source_name: sAML cultured cell line

value: SET-2 Parental


title: HEL OTX P/R 1000 nM OTX015 1

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were kept
The mapped reads were quantified with Cufflinks 2.0 and the GENCODE gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

source_name: Drug resistant sAML cell line (BET inhibitor treated)

growth_protocol: HEL92.1.7 and HEL-OTX P/R  cells were cultured in 20% FBS containing RPMI1640 media.

treatment_protocol: HEL92.1.7 and HEL-OTX P/R cells were untreated or treated with 1000 nM of OTX015 for 8 hours.  Cells were harvested and total RNA was isolated with a kit from Ambion, Inc

value: HEL92.1.7 OTX P/R

value: 1000 nM OTX015 8 hours


title: SET-2 Parental 1


title: HEL92.1.7 1000 nM OTX015 2

source_name: sAML cultured cell line (BET inhibitor treated)

value: HEL92.1.7 parental


title: S_M microRNA

description: male worms from SCID mice

value: male

value: five weeks post infection


title: SET-2 Parental 2


title: HEL OTX P/R 1000 nM OTX015 2


title: HEL92.1.7 1000 nM OTX015 1


title: CEPD2ox_rep1

city: Nagoya

first: Yoshikatsu

last: Matsubayashi

state: Aichi

address: Chikusa

department: Graduate School of Science

country: Japan

institute: Nagoya University

description: Gene expression data from root tissues of CEPD2ox plants.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Arabidopsis Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: Data procession was performed with Expression Console Version 1.3 (Affymetrix).

organism: Arabidopsis thaliana

source_name: CEPD2ox 14d root

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Surface-sterilized seeds were sown on B5 medium (1% sucrose) solidified using 1.5% agar in 13 × 10 cm plastic plates (18 seeds × 3 rows/plate) and grown vertically at 22°C with continuous light at an intensity of 80 µmol·m–2·s–1. After 7 d, seedlings were transferred to modified Murashige-Skoog medium solidified using 1.5% agar in 13 × 10 cm plastic plates (12 seedlings/plate) and further grown vertically at 22°C with continuous light. Modified Murashige-Skoog medium for N-replete conditions contains 10 mM NH4Cl and 10 mM KNO3 as N and K sources, respectively, and half-strength concentrations of the other elements and 0.5% sucrose, adjusted to pH 5.7 with KOH.

extract_protocol: An RNeasy kit (Qiagen) was used to isolate total RNA from roots of WT (Col), CEPD1ox, CEPD2ox and CEPDL2ox plants grown on N-replete vertical plates for 14 d.

value: 14d root

tag: genotype


title: HEL OTX P/R  untreated 1

source_name: Drug resistant sAML cell line (no drug treatment)


title: CEPDL2ox_rep1

description: Gene expression data from root tissues of CEPDL2ox plants.

source_name: CEPDL2ox 14d root


title: HEL92.1.7 untreated 1

source_name: sAML cultured cell line (no drug treatment)


title: WT control_rep1

description: Gene expression data from root tissues of WT.

source_name: WT 14d root, control

value: Wild type


title: SWN-GFP_val1val2-2

city: guangzhou

first: Liang

middle: Bing

last: Yuan

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: Life of Science

institute: Sun Yat-Sen University

description: GFP_antibody (abcam, ab290)

data_processing:
bowtie2; samtools; picard to remove replicated; macs2
• Extract unique mapped no-duplicated reads; • Use MACS2 (gsize=1.35e8, bw=300, q=0.05, Do not Build shift model, extsize= 100) to call peaks;
Genome_build: Tair 10
Supplementary_files_format_and_content: bed files were generated using macs2

source_name: Young seedlings

growth_protocol: For seed germination, sterilized seeds were stratified for 3 days at 4℃ in darkness; seeds were then sown on Murashige and Skoog (MS) plates containing 1% sucrose and 0.6% agar. Seedlings were grown in growth rooms with 16-h light/8-h dark cycles at 22℃.

extract_protocol: ChIP-seq libraries were prepared for sequencing using standard illumina protocols

value: seedling

tag: age

value: 14 days old


title: CEPD1ox_rep1

description: Gene expression data from root tissues of CEPD1ox plants.

source_name: CEPD1ox 14d root


title: HEL OTX P/R  untreated 2


title: SWN-GFP-2

description: GFP_antibody (abcam, ab290)


title: SWN-GFP_val1val2-1

description: GFP_antibody (abcam, ab290)


title: SWN-GFP-input

description: input


title: HC2 [V_2]

value: in vitro produced


title: HEL92.1.7 untreated 2


title: SET-2 OTX P/R 3


title: HC1 [V_1]

value: blastocyst


title: val1val2-H3K27me3-1

description:
anti-H3K27me3 antibody, Millipore, 07-449
va1val2-H3K27me3-1.peaks.xls

data_processing:
tophat v2.1.1; cufflinks v2.2.1; cuffmerge; cuffdiff
• Extract unique mapped no-duplicated reads; • Use MACS2 (gsize=1.35e8, bw=300, q=0.05, Do not Build shift model, extsize= 100) to call peaks;
Genome_build: Tair 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample; bed files were generated using macs2

extract_protocol:
Total RNA was isolated from about 100 milligrams of 14-day-old seedlings using the RNAprep pure Plant Kit (Tiangen) according to supplier’s instruction.
For RNA-seq, DNA-free total RNA was used for the Illumina Tru-seq library preparation according to manufacturer’s instruction. For ChIP-seq, end repair, adapter ligation and amplification were performed using NEBNext Ultra II for DNA Library Prep (E7645S), and NEBNext® Multiplex Oligos for Illumina® (E7335L).

tag: ecotype


title: val1val2-H3K27me3-2

description:
anti-H3K27me3 antibody, Millipore, 07-449
va1val2-H3K27me3-2.peaks.xls


title: Col-0-1-input

value: wildtype


title: VAL2-GFP-val2-2

description:
GFP_antibody (abcam, ab290)
VAL2-GFP-val2-2.peaks.xls


title: VAL1-GFP-val1-1

description:
GFP_antibody (abcam, ab290)
VAL1-GFP-val1-1.xls


title: val1val2-1-input


title: VAL1-GFP-val1-2

description:
GFP_antibody (abcam, ab290)
VAL1-GFP-val1-2.xls


title: VAL1-GFP-val1-input


title: SWN-GFP_val1val2-input

description: input


title: VAL2-GFP-val2-input


title: SWN-GFP-1

description: GFP_antibody (abcam, ab290)


title: Col-0-H3K27me3-1

description:
anti-H3K27me3 antibody, Millipore, 07-449
Col-0-H3K27me3-1.peaks.xls


title: Adh -74 single cell RNA-seq

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
The raw fastq files were aligned to hg19 genome using tophat. The bam file acheived after alignment was used with cuffdiff to calculate FPKM of genes in every cell
Genome_build: hg19
Supplementary_files_format_and_content: Processed data is in text format. The processed data in every cell contains both both read-count and FPKM values for genes

molecule: polyA RNA

source_name: Non small Lung cancer cell

growth_protocol: Cells derived from lung cancer patient were grown as Tumor sphere (TS) and maintained in medium with DMEM/F12 (US Biomedical),  4mg/ml Bovine Serum Albumin (Sigma), Non-essential amino acids, sodium pyruvate (Life Technologies) and 20ng/ml Epidermal Growth Factor, 4 ng/ml bovine Fibroblast Growth Factor and Insulin –Transferrin Selenium (Sigma). Tumor sphere derived adherent (Adh) cells were grown in the same media as above, without EGF, bFGF, ITS and BSA.  For Adh cell media was supplemented with 10% fetal bovine serum.

extract_protocol:
The single-cells were captured using C1 96 (large size) IFC using Fluidigm-C1 system. Reverse transcription and cDNA amplification were processed using SMART-seq2 script automatically in C1-Fluidigm machine.
The harvested single cell cDNA was barcoded in 96 well plate using Nextera XT Library Prep kit (Ilumina). Uniquely barcoded libraries from single cells pooled together and sequenced using a HiSeq-Hi-output sequencer (Illumina).

value: Tumorosphere dreived Adherant

value: Adherant


title: Adh -75 single cell RNA-seq


title: Adh -73 single cell RNA-seq


title: Adh -70 single cell RNA-seq


title: Adh -68 single cell RNA-seq


title: Adh -69 single cell RNA-seq


title: Adh -71 single cell RNA-seq


title: Adh -72 single cell RNA-seq


title: Adh -67 single cell RNA-seq


title: Adh -66 single cell RNA-seq


title: Adh -65 single cell RNA-seq


title: Adh -64 single cell RNA-seq


title: Adh -63 single cell RNA-seq


title: Adh -62 single cell RNA-seq


title: Adh -61 single cell RNA-seq


title: Adh -60 single cell RNA-seq


title: VAL2-GFP-val2-1

description:
GFP_antibody (abcam, ab290)
VAL2-GFP-val2-1.peaks.xls


title: Adh -58 single cell RNA-seq


title: Adh -59 single cell RNA-seq


title: Adh -57 single cell RNA-seq


title: Adh -56 single cell RNA-seq


title: Adh -53 single cell RNA-seq


title: Adh -54 single cell RNA-seq


title: Adh -51 single cell RNA-seq


title: Adh -50 single cell RNA-seq


title: Adh -52 single cell RNA-seq


title: Adh -49 single cell RNA-seq


title: Adh -48 single cell RNA-seq


title: Adh -47 single cell RNA-seq


title: Adh -45 single cell RNA-seq


title: Adh -41 single cell RNA-seq


title: Adh -46 single cell RNA-seq


title: Adh -44 single cell RNA-seq


title: Adh -42 single cell RNA-seq


title: Adh -40 single cell RNA-seq


title: Adh -39 single cell RNA-seq


title: Adh -38 single cell RNA-seq


title: Adh -37 single cell RNA-seq


title: Adh -35 single cell RNA-seq


title: Adh -36 single cell RNA-seq


title: Adh -32 single cell RNA-seq


title: Adh -31 single cell RNA-seq


title: Adh -33 single cell RNA-seq


title: Adh -30 single cell RNA-seq


title: Adh -55 single cell RNA-seq


title: Adh -29 single cell RNA-seq


title: Adh -28 single cell RNA-seq


title: Adh -25 single cell RNA-seq


title: Adh -23 single cell RNA-seq


title: Adh -24 single cell RNA-seq


title: Adh -22 single cell RNA-seq


title: Adh -26 single cell RNA-seq


title: Adh -43 single cell RNA-seq


title: Adh -20 single cell RNA-seq


title: Adh -21 single cell RNA-seq


title: Adh -18 single cell RNA-seq


title: Adh -17 single cell RNA-seq


title: Adh -19 single cell RNA-seq


title: Adh -16 single cell RNA-seq


title: Adh -15 single cell RNA-seq


title: Adh -34 single cell RNA-seq


title: Adh -14 single cell RNA-seq


title: cc03-20covid1

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
Raw reads were aligned using Star aligner 2.6.1 (8)/RSEM 1.2.28
Genome_build: using a custom human GRCh38  transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein  5 coding and long non-coding RNA genes based on human GENCODE version 33 annotation with  SARS-Cov2 virus genome MT246667.1 https://www.ncbi.nlm.nih.gov/nuccore/MT246667.1.
Supplementary_files_format_and_content: count and TPM

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Organoid

extract_protocol:
Total RNA was extracted from mock and SARS-CoV-2 infected alveolar organoid cultures lysed in Trizol (Thermo Fisher Scientific) using the chloroform-iso-propanolethanol method.
Library construction was performed by the Cedars-Sinai Applied Genomics, Computation and Translational Core using the Lexogen RiboCop rRNA Depletion kit and Swift Biosciences RNA Library Sciences

value: lung organoid

tag: group

value: Infected


title: cc03-20covid2


title: Adh -13 single cell RNA-seq

tag: sample type


title: cc03-19covid


title: cc01-20covid2


title: Adh -12 single cell RNA-seq


title: cc01-20covid1


title: Adh -27 single cell RNA-seq


title: Adh -10 single cell RNA-seq


title: Adh -11 single cell RNA-seq


title: Adh -9 single cell RNA-seq


title: i44_DMSO_2_2

city: London

first: Matt

last: Lechner

state: Please Select

address: 72 Huntley Street

country: United Kingdom

institute: UCL

data_processing:
Basecalling was performed using Illumina FASTQ Generation v1.0.0
Quantification of expression was performed using the alignment-free tool salmon v0.11.2
Transcript level expression values were converted to gene level values using the R package tximport
TPM values were calculated in R as (count/lengths/1000)/(sum(count/lengths/1000)/1000000)
Genome_build: gencode.v28lift37.transcripts.fa
Supplementary_files_format_and_content: Comma separated matrix of TPM values for each gene (rows) in each sample (columns)

source_name: Nasopharyngeal carcinoma

growth_protocol: C666-1 cells were cultured in RPMI-1640 with 25 mM Hepes (Lonza, Berlin, Germany) supplemented with 10% heat-inactivated FCS (Gibco, Carlsbad, CA), 2 mM L-Glutamine, 100 units/ml penicillin (Gibco) and 0.1 mg/ml streptomycin (Gibco). Cells were maintained at 37°C, 5% CO2 and passaged every 7 days at a 1:2 ratio using accutase (Sigma, St. Louis, MO, USA). 75% of culture medium was replaced by fresh medium every 2 to 3 days.    C666-1 cells were seeded at a density of 1x106 /well in 6-well plates 2 days prior to compound addition.

extract_protocol:
DNA and RNA extraction was performed from separate wells using Quick-DNA Plus and Direct-zol RNA Plus Kit (Zymo Research, Irvine, CA, USA) according to the manufacturers’ instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lanreotide and octreotide acetate were dissolved in ddH2O to obtain a 10 mM stock solution. Belinostat and Pen-221 were dissolved in DMSO to obtain a 10 mM stock solution.    Medium was carefully aspirated from every well and replaced by 2 mL of fresh culture medium. Lanreotide and octreotide acetate were added at final concentration of 10 µM, Belinostat and Pen-221 at a final concentration of 5 µM and cells incubated for 24h and 72h at 37°C, 5% CO2.

value: DMSO

tag: timepoint


title: i42_untreated_2_2

value: untreated


title: Adh -7 single cell RNA-seq


title: Adh -6 single cell RNA-seq


title: Adh -8 single cell RNA-seq


title: i41_untreated_2_1


title: Adh -5 single cell RNA-seq


title: i39_untreated_72h


title: i38_Belinostat_72h

value: Belinostat


title: Adh -1 single cell RNA-seq


title: i35_Pen221_72h


title: TS-87 single cell RNA-seq

value: Tumorosphere - TS

value: Non adherant


title: Adh -4 single cell RNA-seq


title: Adh -3 single cell RNA-seq


title: TS-86 single cell RNA-seq


title: i32_DMSO_24h


title: TS-85 single cell RNA-seq


title: i31_untreated_24h


title: TS-84 single cell RNA-seq


title: i30_Belinostat_24h


title: TS-83 single cell RNA-seq


title: i43_DMSO_2_1


title: i40_DMSO_72h


title: TS-82 single cell RNA-seq


title: TS-81 single cell RNA-seq


title: TS-80 single cell RNA-seq


title: i29_Belinostat_24h


title: TS-79 single cell RNA-seq


title: i28_Belinostat_24h


title: i26_Pen221_24h


title: i37_Belinostat_72h


title: Adh -2 single cell RNA-seq


title: i36_Belinostat_72h


title: TS-78 single cell RNA-seq


title: i25_Pen221_24h


title: TS-77 single cell RNA-seq


title: i33_Pen221_72h


title: TS-76 single cell RNA-seq


title: i34_Pen221_72h


title: TS-73 single cell RNA-seq


title: TS-74 single cell RNA-seq


title: TS-72 single cell RNA-seq


title: TS-71 single cell RNA-seq


title: TS-70 single cell RNA-seq


title: i27_Pen221_24h


title: TS-68 single cell RNA-seq


title: TS-69 single cell RNA-seq


title: TS-67 single cell RNA-seq


title: TS-66 single cell RNA-seq


title: TS-65 single cell RNA-seq


title: TS-75 single cell RNA-seq


title: TS-64 single cell RNA-seq


title: TS-63 single cell RNA-seq


title: Conventional TB infection mouse 12

first: Kevin

last: Urdahl

state: Washington

address: 307 Westlake Ave N #500

department: Global Infectious Disease

institute: Seattle Children's Research Institute

hyb_protocol: standard Agilent protocol

scan_protocol: Agilent Technologies Scanner G2505C US93103711

data_processing: quantile normalized, duplicate probes averaged, log2 transformed

source_name: Whole blood

label_protocol: standard Agilent protocol

extract_protocol: none provided by the submitter

tag: infection group

value: HighDose

tag: day blood taken

tag: day cfu measured

tag: lung log10cfu


title: Late CFU measument ULD mouse 25

value: Late


title: Early CFU measument ULD mouse 29

value: Early


title: Late CFU measument ULD mouse 24


title: Early CFU measument ULD mouse 28


title: TS-62 single cell RNA-seq


title: TS-61 single cell RNA-seq


title: Early CFU measument ULD mouse 27


title: Early CFU measument ULD mouse 26


title: Conventional TB infection mouse 25


title: Early CFU measument ULD mouse 25


title: Early CFU measument ULD mouse 24


title: Late CFU measument ULD mouse 21


title: Early CFU measument ULD mouse 23


title: TS-60 single cell RNA-seq


title: TS-59 single cell RNA-seq


title: Col-0-H3K27me3-2

description:
anti-H3K27me3 antibody, Millipore, 07-449
Col-0-H3K27me3-2.peaks.xls

tag: tissue

value: seedling


title: TS-56 single cell RNA-seq

tag: cell type


title: TS-58 single cell RNA-seq


title: TS-55 single cell RNA-seq


title: TS-53 single cell RNA-seq


title: TS-54 single cell RNA-seq


title: Late CFU measument ULD mouse 22


title: TS-57 single cell RNA-seq


title: TS-52 single cell RNA-seq


title: Early CFU measument ULD mouse 22


title: Late CFU measument ULD mouse 19


title: Late CFU measument ULD mouse 20


title: Late CFU measument ULD mouse 18


title: Early CFU measument ULD mouse 21


title: TS-51 single cell RNA-seq


title: Early CFU measument ULD mouse 20


title: TS-50 single cell RNA-seq


title: Late CFU measument ULD mouse 17


title: Conventional TB infection mouse 13


title: TS-49 single cell RNA-seq


title: TS-48 single cell RNA-seq


title: Early CFU measument ULD mouse 18


title: TS-47 single cell RNA-seq


title: TS-46 single cell RNA-seq


title: TS-45 single cell RNA-seq


title: TS-44 single cell RNA-seq


title: Late CFU measument ULD mouse 16


title: Early CFU measument ULD mouse 19


title: TS-43 single cell RNA-seq


title: Early CFU measument ULD mouse 17


title: Early CFU measument ULD mouse 13


title: Early CFU measument ULD mouse 15


title: Early CFU measument ULD mouse 16


title: Early CFU measument ULD mouse 14


title: Early CFU measument ULD mouse 12


title: Early CFU measument ULD mouse 10


title: Con, DT 3 days, 4

first: Ruteja

middle: A

last: Barve

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University

description: wt_day3_4.CACCTCC.run_2891_s_8_withindex_sequence.txt_CACCTCC

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

source_name: Con_DT 3 days

growth_protocol: iDTR mice are cross-mated with adiponectin-Cre tp generate DTRADQ mice

extract_protocol:
Total RNA of femur whole bone marrow were extracted with Trizole and cleaned-up with RNeasy mini kiy (Qiagen)
Clontech SMARTer v1

treatment_protocol: 2 months old DTRADQ mice and their Cre negative littermate control were IP injected with Diphtheria Toxin (100ng/mouse) daily for indicated days

tag: strain background

tag: genotype/variation

value: DTR flox, No Cre

tag: treatment/time point

value: DT 3 days

value: whole bone marrow (femur)


title: TS-42 single cell RNA-seq


title: Early CFU measument ULD mouse 11


title: Early CFU measument ULD mouse 9


title: Early CFU measument ULD mouse 8


title: Con, DT 3 days, 3

description: wt_day3_3.CATCGCG.run_2891_s_8_withindex_sequence.txt_CATCGCG


title: Late CFU measument ULD mouse 23


title: Con, DT 3 days, 2

description: wt_day3_2.CCTAATC.run_2891_s_8_withindex_sequence.txt_CCTAATC


title: Con, DT 3 days, 1

description: wt_day3_1.TGATTAC.run_2891_s_8_withindex_sequence.txt_TGATTAC


title: TS-41 single cell RNA-seq


title: DTRADQ, DT 3 days, 3

description: dtr_day3_3.GTACGGC.run_2891_s_8_withindex_sequence.txt_GTACGGC

source_name: DTRADQ_DT 3 days

value: DTR flox, ADQ Cre+


title: TS-39 single cell RNA-seq


title: TS-40 single cell RNA-seq


title: DTRADQ, DT 3 days, 2

description: dtr_day3_2.TACATGG.run_2891_s_8_withindex_sequence.txt_TACATGG


title: Con, DT 2 days, 4

description: wt_day2_4.ATGACAG.run_2891_s_*_withindex_sequence.txt_ATGACAG

source_name: Con_DT 2 days

value: DT 2 days


title: Con, DT 2 days, 3

description: wt_day2_3.TACAGAC.run_2891_s_*_withindex_sequence.txt_TACAGAC


title: Con, DT 2 days, 2

description: wt_day2_2.TCCCAGC.run_2891_s_*_withindex_sequence.txt_TCCCAGC


title: Early CFU measument ULD mouse 7


title: DTRADQ, DT 3 days, 1

description: dtr_day3_1.CGGTGGC.run_2891_s_8_withindex_sequence.txt_CGGTGGC


title: DTRADQ, DT 3 days, 4

description: dtr_day3_4.GCCGTTT.run_2891_s_8_withindex_sequence.txt_GCCGTTT


title: TS-37 single cell RNA-seq


title: TS-36 single cell RNA-seq


title: Con, DT 2 days, 1

description: wt_day2_1.GCAACGC.run_2891_s_*_withindex_sequence.txt_GCAACGC


title: Early CFU measument ULD mouse 4


title: TS-38 single cell RNA-seq


title: DTRADQ, DT 2 days, 4

description: dtr_day2_4.CTCCCGA.run_2891_s_*_withindex_sequence.txt_CTCCCGA

source_name: DTRADQ_DT 2 days


title: DTRADQ, DT 2 days, 3

description: dtr_day2_3.CCGGACC.run_2891_s_*_withindex_sequence.txt_CCGGACC


title: Early CFU measument ULD mouse 6


title: TS-35 single cell RNA-seq


title: Con, DT 1 day, 4

description: wt_day1_4.GCTTAGA.run_2891_s_*_withindex_sequence.txt_GCTTAGA

source_name: Con_DT 1 day

value: DT 1 day


title: Con, DT 1 day, 3

description: wt_day1_3.GTCGATA.run_2891_s_*_withindex_sequence.txt_GTCGATA


title: Early CFU measument ULD mouse 5


title: DTRADQ, DT 2 days, 2

description: dtr_day2_2.TGTTTGT.run_2891_s_*_withindex_sequence.txt_TGTTTGT


title: DTRADQ, DT 2 days, 1

description: dtr_day2_1.GGTCCTC.run_2891_s_*_withindex_sequence.txt_GGTCCTC


title: Con, DT 1 day, 2

description: wt_day1_2.AGATACT.run_2891_s_*_withindex_sequence.txt_AGATACT


title: Early CFU measument ULD mouse 2


title: Early CFU measument ULD mouse 3


title: Con, DT 1 day, 1

description: wt_day1_1.GGGTCAA.run_2891_s_*_withindex_sequence.txt_GGGTCAA


title: TS-32 single cell RNA-seq


title: TS-31 single cell RNA-seq


title: TS-33 single cell RNA-seq


title: DTRADQ, DT 1 day, 4

description: dtr_day1_4.CAATATC.run_2891_s_*_withindex_sequence.txt_CAATATC

source_name: DTRADQ_DT 1 day


title: Early CFU measument ULD mouse 1


title: TS-30 single cell RNA-seq


title: Conventional TB infection mouse 10


title: TS-34 single cell RNA-seq


title: DTRADQ, DT 1 day, 2

description: dtr_day1_2.TCAACTG.run_2891_s_*_withindex_sequence.txt_TCAACTG


title: DTRADQ, DT 1 day, 3

description: dtr_day1_3.ACCCACT.run_2891_s_*_withindex_sequence.txt_ACCCACT


title: Con, No DT, 3

description: wt_con3.ACGTCTG.run_2891_s_*_withindex_sequence.txt_ACGTCTG

source_name: Con_No DT

value: No DT treatment


title: Con, No DT, 2

description: wt_con2.GCAGGGG.run_2891_s_*_withindex_sequence.txt_GCAGGGG


title: DTRADQ, DT 1 day, 1

description: dtr_day1_1.TTTAACT.run_2891_s_*_withindex_sequence.txt_TTTAACT


title: Conventional TB infection mouse 9


title: Conventional TB infection mouse 7


title: Con, No DT, 1

description: wt_con1.CAAGCCG.run_2891_s_*_withindex_sequence.txt_CAAGCCG


title: Conventional TB infection mouse 8