title: Brain Macrophages - Hashing Sample 3

city: New York

first: Elisa

last: Konofagou

state: NY

address: 630 West 168th Street, P&S 19th Fl. Rm. 418

department: Biomedical Engineering

institute: Columbia University

description:
7 samples combined, identifiable by genetic hashing
Raw files contain both GEX and HTO reads.

data_processing:
Base calling software:
Barcoded reads were processed and aligned to the GRCm38 genome with Ensemble transcriptome annotation (GRCm38.p6) using CellRanger with default parameters.
For the hashing study, the barcoded hashtag reads were processed and aligned to the relevant antibody codes with CellRanger's default parameters. The unfiltered matrix was then loaded into R for subsequent processing. Cells with no antibody reads were removed and then the genetic and hashtag matrices were merged, only keeping UMIs present in both. Seurat functions were used to demultiplex the data and assign hashtags to each cell.
Assembly: mm10-3.0.0
Supplementary files format and content: Processed files are in h5 matrix format after combining hashing and count matrices, feature filtering and counting and include UMI counts for each barcoded cell.

source_name: Brain macrophages

extract_protocol: At time of sacrifice, animals were transcardially perfused with 1xPBS until the liver demonstrated clearing. After perfusion, both hippocampi of each brain were extracted and combined prior to being homogenized, filtered and prepared for myelin removal. Then each sample was incubated with CD11B-PE. In the hashing study, each sample was simultaneously incubated with one of seven Biolegend TotalSeq anti-Mouse Antibodies. Samples were spun down after staining (in the case of the hashing study, they were also combined at this stage) and resuspended in 1mL of 10% FBS with Violet Live/Dead for 5min prior to being resuspended in 1xPBS with DNAse. Microglia were isolated with the BD Influx Cell Sorter. After selection, cells were resuspended at 1000 cells/uL of 10% FBS. Cells were then loaded onto a single channel of a 3' 10x Chromium chip for sequencing.

treatment_protocol: All mice (FUS+MB and Sham) were anesthetized with oxygen and 1-2\% isoflurane, placed on a stereotaxis with head immobilized and depilated to reduce acoustic impedance mismatch. In mice that were treated with FUS (FUS+MB and FUS Sham), a single-element, spherical-segment FUS transducer (center frequency: 1.5 MHz, focal depth: 60mm, radius: 30mm Imasonic, France)  was used to treat the bilateral hippocampus. In all mice treated with microbubbles (FUS+MB and MB Sham) lab-made microbubbles were diluted in sterile saline and then injected intraveneously. The transducer was not triggered for the treatment of MB Sham mice, but otherwise the treatment was identical to that of the FUS+MB mice. All FUS+MB and Sham mice were intraperitonealy injected with 0.2 mL of gadodiamide prior to undergoing a contrast-enhanced T1-weighted 2D FLASH MRI to confirm BBB opening.

tag: number of treatments (hashing)

value: 7 (yes)

tag: number animals/treatmet

tag: treatment

value: multiplexed sample:FUS+MB, MB, FUS, Naive

tag: time of sacrifice

value: multiplexed sample:1d, 3d


title: Preadipocyte rep1

status: Public on Jun 17 2023

type: SRA

city: Doha

first: Borbala

last: Mifsud

address: LAS Building, Education City

country: Qatar

institute: Hamad Bin Khalifa University

library_source: transcriptomic

data_processing:
tab-delimited text file including average RPKM per cell type and log2 fold change and adjusted p-values from differential expression analysis.
Assembly: mm9
Supplementary files format and content: tab-delimited text file including average RPKM per cell type and log2 fold change and adjusted p-values from differential expression analysis.

molecule: polyA RNA

organism: Mus musculus

source_name: epididymal fat pad

extract_protocol:
RNeasy Plus Micro Kits (Qiagen #74034) following manufacturer's protocol
TruSeq Stranded mRNA Kit (Illumina #20020595) following manufacturer's protocol

tag: tissue

value: epididymal fat pad

tag: cell type

value: Preadipocyte

tag: age

value: 3 months

tag: genotype


title: Brain Macrophages - Hashing Sample 2

country: USA

molecule: total RNA


title: 16A_M_532

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: strain


title: 16A_M_537


title: 16A_M_526


title: 16A_M_529


title: Brain Macrophages - MB 24h

description: 5 MB samples combined

value: MB


title: 16A_M_525


title: 16A_M_524


title: Brain Macrophages - Hashing Sample 1


title: 16A_M_522


title: 16A_M_527


title: Brain Macrophages - FUS+MB 24h

description: 5 FUS+MB samples combined

value: FUS+MB


title: 16A_M_519


title: 16A_M_533


title: 16A_M_520


title: Preadipocyte rep4


title: 16A_M_523


title: 16A_M_521


title: A549-TIMM13_si1-rep2

city: shanghai

first: xiaomeng

last: cheng

state: Shanghai

address: Jiangwan Campus of Fudan University, 2205 Songhu Road, Yangpu District, Shanghai, China

country: China

institute: Fudan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore with default settings
Trimmed sequence reads were mapped to hg38 using STAR with default settings
Read count extraction were performed using featurecounts with default settings
Assembly: hg38
Supplementary files format and content: Excel file includes normalized gene expression values (FPKMs) for each Sample

organism: Homo sapiens

source_name: lung cancer

extract_protocol:
We constructed the dUTP-based strand-specific RNA-seq library by RNA HyperPrep Kit (KAPA). 500 ng purified total RNA of each sample were processed for poly (A)-enrichment and fragmentation. Then 1st strand cDNA and 2st strand cDNA were synthesized from fragmented RNA, followed by A-tailing and adapter ligation. Finally, adapter ligated library DNA was amplified by PCR
Library concentration was determined by Qubit dsDNA HS Assay Kit (Invitrogen) according to manufacturers instructions

value: lung cancer

tag: cell line

value: epithelial-like cell

value: TIMM13 knockdown

tag: sirna

value: cell differentiation


title: A549-TIMM13_si2-rep2


title: A549-TIMM13_si1-rep1


title: A549-NonTarget-rep2

value: WT

value: control


title: A549-TIMM13_si2-rep1


title: A549-NonTarget-rep1


title: 16A_M_518


title: 16A_M_516


title: 16A_M_517


title: 16A_M_514


title: 16A_M_515


title: CHi-C D7 rep3

data_processing:
Reads were mapped to the mm9 genome and filtered using the HiCUP pipeline (v0.5.8).
Differential interactions were identified using GOTHiC, and those present in at least two of the replicates were compiled in the list of differential interactions.
Assembly: mm9
Supplementary files format and content: tab delimited file with the positions of the anchors of differential interactions.
Library strategy: promoter capture Hi-C

growth_protocol: 3T3-L1 cells were grown at 37°C and 5% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM high glucose, Sigma-Aldrich #D6546) supplemented with 10% calf serum, 2% glutamine (Sigma-Aldrich #G7513) and 1% Pen-Strep (Sigma-Aldrich #P0781).

extract_protocol:
30-40 million cells/sample were fixed with 2% formaldehyde (Agar Scientific #AGR1026) for 10 min at room temperature, prior to harvesting from the tissue culture flasks. Digestion of cross-linked chromatin with HindIII (NEB #R3104), labelling with biotin-14-dATP (Invitrogen #19524016) and DNA Polymerase I (Large Klenow Fragment; NEB #M0210) and ligation (with T4 DNA ligase; Invitrogen #15224025) were all performed on nuclei kept intact. Chromatin cross-linking was then reversed by incubation with proteinase K (Roche #03115879001) at 65°C overnight and the DNA was purified by phenol/chloroform extraction. Aliquots of the Hi-C libraries were used to verify efficiency of chromatin digestion and digestion using standard PCR and qPCR. Then, biotin from un-ligated DNA ends was removed using T4 DNA polymerase (NEB #M0203) and the DNA was sonicated  (Covaris E220) to an average size of around 400 base pairs. Sonicated DNA was end-repaired using DNA Polymerase I (Large Klenow Fragment; NEB #M0210), T4 DNA polymerase (NEB #M0203) and T4 DNA polynucleotide kinase (NEB #M0201), then dATP was added to the 3′ ends of the DNA using Klenow exo- (NEB #M0212). The DNA was then subjected to double-sided SPRI bead size selection (AMPure XP beads; Beckman Coulter #A63881) and biotin-marked ligation products were isolated using MyOne Streptavidin C1 Dynabeads (Invitrogen #65002). After adapter ligation (Illumina PE PCR 1.0 and PE PCR 2.0 primers), the bead-bound Hi-C DNA was amplified with seven PCR amplification cycles. Promoter capture Hi-C was performed using a custom-made RNA capture bait system (Agilent Technologies) consisting of 39,021 individual biotinylated RNAs targeting the ends of 22,225 promoter-containing mouse HindIII restriction fragments, as described (PMID: 25752748). After a post-capture PCR (four amplification cycles using Illumina’s PE PCR 1.0 and PE PCR 2.0 primers), the PCHi-C libraries were purified with AMPure XP beads (Beckman Coulter #A63881) and paired-end sequenced (HiSeq 1000, Illumina) at the Babraham Institute Sequencing Facility.
Illumina TruSeq paired-end

treatment_protocol: Cells were induced to differentiate two days post confluency (defined as day zero – D0) by addition of differentiation media: DMEM high glucose supplemented with 10% fetal bovine serum (Sigma-Aldrich #F7524), 1% Pen-Strep, 1 μg/ml insulin (Sigma-Aldrich #I9278), 390 ng/ml dexamethasone (Sigma-Aldrich #D4902), 1,115 μg/ml 3-Isobutyl-1-methylxanthine (Sigma-Aldrich #I5879) and 2 μM rosiglitazone (Sigma-Aldrich #R2408). Two days after the induction of differentiation, fresh differentiation media supplemented with 1 μg/ml insulin was added. From day four and onward, cells were maintained in differentiation media.

tag: time

value: day 7

value: adipogenic differentiation


title: CHi-C D7 rep2


title: CHi-C D7 rep1


title: 16A_M_512


title: 16A_M_191


title: 24d brl1-701 brl1 brl3 +bl repeat 2

city: Shanghai

first: Xiaolei

last: Liu

address: Chenhua Road 3888

institute: Chinese Academy of Sciences

data_processing:
the raw data is preprocessed by trimmomatic (version 0.36).
The clean reads were aligned to the TAIR 10 reference genome using hisat2 (version 2.1.0) with parameters "--rna-strandness RF -p 30 --dta”.
Reads_count matrix was produced by htseq-count (version 0.9.1).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each Sample

organism: Arabidopsis thaliana

source_name: Arabidopsis

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

tag: Stage

value: seedling

value: brl1-701 brl1 brl3

value: BL


title: CHi-C D0 rep3

value: day 0


title: CHi-C D0 rep2


title: 24d brl1-701 brl1 brl3 +bl repeat 1


title: 24d brl1-701 brl1 brl3 +bl repeat 3


title: CHi-C D0 rep1


title: 24d cpd+bl repeat 2

value: cpd


title: 16A_M_190


title: 16A_M_189


title: 24d cpd+bl repeat 3


title: 24d brl1-701 brl1 brl3 repeat 3


title: 16A_M_186


title: 24d brl1-701 brl1 brl3 repeat 1


title: 16A_M_188


title: 24d brl1-701 brl1 brl3 repeat 2


title: 16A_M_184


title: 16A_M_513


title: 24d cpd repeat 2


title: 16A_M_181


title: 16A_M_511


title: 7d brl1-701 brl1 brl3 +bl repeat 3

value: 7- -day-old


title: 7d brl1-701 brl1 brl3 +bl repeat 1


title: 24d cpd+bl repeat 1


title: 16A_M_179


title: 16A_M_178


title: 7d cpd+bl repeat 3


title: 7d cpd+bl repeat 2


title: 16A_M_177


title: 16A_M_176


title: 16A_M_175


title: 7d cpd+bl repeat 1


title: 7d brl1-701 brl1 brl3 +bl repeat 2


title: 16A_M_185


title: 16A_M_174


title: 7d brl1-701 brl1 brl3 repeat 1


title: 7d brl1-701 brl1 brl3 repeat 3


title: 7d brl1-701 brl1 brl3 repeat 2


title: 16A_M_172


title: 16A_M_171


title: 7d cpd repeat 3


title: 16A_M_173


title: 24d cpd repeat 1


title: 16A_M_183


title: 16A_M_180


title: 24d cpd repeat 3


title: 16A_M_187


title: 16A_M_169


title: 7d cpd repeat 1


title: 16A_M_170


title: 7d cpd repeat 2


title: 16A_M_168


title: 16A_M_167


title: 16A_M_165


title: R20291 Pxyl-DraRD54E Replicate 3

city: Iowa City

first: Anthony

last: Pannullo

state: IA

address: 30 N Dubuque St

department: Microbiology

institute: University of Iowa

data_processing:
QC done using FastQC through prokSeq pipleine
Alignment to reference genome done through Bowtie2 in prokSeq pipeline
RNA expression levels qunatified through FeatureCounts in prokSeq pipline
Differential gene expression determerined through DEseq2 in prokSeq pipeline
Assembly: Clostridioides difficile R20291 FN545816
Supplementary files format and content: .xlsx files include log2 fold change, gene annotation, and p-value

organism: Clostridioides difficile

source_name: Bacteria

growth_protocol: All cultures were grown in liquid TY (Tryptone-yeast extract) supplemented with either 0, 4 ug/mL daptomycin, or 1% xylose

extract_protocol:
RNA was extracted using the Quiagen RNeasy extraction kit, RIN of 8 and greater were used for this study
Library construction and subsequent sequencing was performed by SeqCenter (Pittsburgh, PA)

value: Bacteria

value: R20291, Pxyl-DraRD54E

value: 1% xylose


title: R20291 Pxyl-EV Replicate 3

value: R20291, Pxyl-EV


title: 16A_M_162


title: 16A_M_163


title: R20291 Pxyl-EV Replicate 2


title: 16A_M_164


title: R20291 Pxyl-EV Replicate 1


title: delta-draRS 4 ug/mL Daptomycin replicate 3

value: delta_draRS, R20291

value: 4ug/mL daptomycin


title: 16A_M_161


title: delta-draRS 4 ug/mL Daptomycin replicate 2


title: delta-draRS 4 ug/mL Daptomycin replicate 1


title: delta-draRS 0 ug/mL Daptomycin replicate 3

value: 0ug/mL daptomycin


title: delta-draRS 0 ug/mL Daptomycin replicate 2


title: 16A_M_158


title: 16A_M_157


title: 16A_M_159


title: 16A_M_155


title: WT 4 ug/mL Daptomycin replicate 3


title: delta-draRS 0 ug/mL Daptomycin replicate 1


title: 16A_M_160


title: 16A_M_154


title: 16A_M_156


title: WT 4 ug/mL Daptomycin replicate 2


title: R20291 Pxyl-DraRD54E Replicate 2


title: R20291 Pxyl-DraRD54E Replicate 1


title: 16A_M_153


title: 16A_M_152


title: WT 0 ug/mL Daptomycin replicate 2


title: WT 0 ug/mL Daptomycin replicate 3


title: 16A_M_151


title: WT 4 ug/mL Daptomycin replicate 1


title: 16A_M_150


title: 16A_M_148


title: 16A_M_147


title: 16A_M_149


title: WT 0 ug/mL Daptomycin replicate 1


title: Fractional CO2 laser,DAY7,biol rep 3

city: Changsha

first: Haoran

last: Guo

address: No.138 Tongzipo Road, Yuelu District, Changsha, China

institute: The Third xiangya Hospital

data_processing:
Quality control
Quality mapping
Gene-level quantification
Transcript-level quantification
Gene structure extension and novel transcripts identification
Assembly: mm10
Supplementary files format and content: tab-delimited text file include Counts values for each Sample
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

organism: Cavia porcellus

source_name: skin

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following  the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100  Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA  Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: skin

value: Fractional CO2 laser,DAY7


title: Fractional CO2 laser,DAY7,biol rep 2


title: Fractional CO2 laser,DAY7,biol rep 1


title: 16A_M_146


title: Control,DAY7,biol rep 3


title: 16A_M_145


title: 16A_M_144


title: Control,DAY7,biol rep 2


title: Control,DAY7,biol rep 1


title: 16A_M_143


title: Fractional CO2 laser,DAY5,biol rep 2

value: Fractional CO2 laser,DAY5


title: 16A_M_141


title: 16A_M_142


title: Fractional CO2 laser,DAY5,biol rep 3


title: 16A_M_140


title: Control,DAY5,biol rep 3


title: 16A_M_139


title: 16A_M_138


title: 16A_M_137


title: 16A_M_136


title: Fractional CO2 laser,DAY3,biol rep 3

value: Fractional CO2 laser,DAY3


title: 16A_M_135


title: Fractional CO2 laser,DAY3,biol rep 2


title: Control,DAY5,biol rep 2


title: Fractional CO2 laser,DAY3,biol rep 1


title: Control,DAY3,biol rep 2


title: 16A_M_133


title: Control,DAY3,biol rep 1


title: Fractional CO2 laser,DAY5,biol rep 1


title: 16A_M_134


title: 16A_M_132


title: 16A_M_131


title: Fractional CO2 laser,DAY1,biol rep 2

value: Fractional CO2 laser,DAY1


title: Ly6C low macrophage, SLC29A3/TLR7 deficient, replicate4

city: Tokyo

first: Takuma

last: Shibata

state: Tokyo-to

address: 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, 4th Building, 2nd Floor

department: The Institute of Medical Science

country: Japan

institute: The University of TOKYO

data_processing:
The sequencing reads were aligned to mm10_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: mm10
Supplementary files format and content: Comma-delimited text files include RPM values for each Sample.

source_name: Spleen

growth_protocol: Splenic macrophages were subjected to RNAseq analysis soon after FACS sorting.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kits (Qiagen). 1 ng of total RNA with RIN value of more than 7.3 was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using an Ion AmpliSeq Transcriptome Mouse Gene Expression kit (Thermo Fisher Scientific) according to the manufacturer's instructions.

treatment_protocol: No Treatment

value: Spleen

value: Ly6C low CD11b(+) Fcgr4(+) Ly6G(-) SiglecF(-) NK1.1(-)

value: macrophage

value: No Treatment


title: Fractional CO2 laser,DAY1,biol rep 1


title: Ly6C low macrophage, SLC29A3/TLR7 deficient, replicate3


title: Ly6C low macrophage, SLC29A3/TLR7 deficient, replicate2


title: Ly6C low macrophage, SLC29A3/TLR7 deficient, replicate1


title: Control,DAY1,biol rep 3


title: 16A_M_130


title: Control,DAY1,biol rep 2


title: Control,DAY5,biol rep 1


title: Ly6C low macrophage, SLC29A3 deficient, replicate4


title: Ly6C low macrophage, SLC29A3 deficient, replicate3


title: Ly6C low macrophage, SLC29A3 deficient, replicate2


title: Ly6C low macrophage, SLC29A3 deficient, replicate1


title: Ly6C low macrophage, Control, replicate4

value: wild-type


title: 16A_M_129


title: Control,DAY1,biol rep 1


title: Leaf.Head_Removal.DD.10d biol rep 3

city: Urbana

first: Gabriel

last: Beuchat

email: beuchat2@illinois.edu, beuchag@uw.edu

state: IL

address: 1201 W Gregory Dr

department: Plant Biology

institute: University of Illinois at Urbana Champaign

data_processing:
FASTQ files were filtered with FASTQC, and trimmed for quality with Trimmomatic.
Reads were aligned to the Sorghum genome v3.1.1 with the STAR aligner.
Fold Changes and DEG analysis were calculated in DESeq2 with Rstudio.
Signal-to-Noise ratio was calculated using values from the DESeq2 results.
GSEA was carried out a local copy of the software from the MSigDB, using the preranked method and the signal-to-noise values calculated in R.
TPM values were calculated in Rstudio.
Assembly: Sbicolor_454_v3.1.1.gene_exons.gtf
Supplementary files format and content: Excel files with TPM values for each library not removed after PCA, as well as the results calculated from DESeq and hierarchical clustering after filtering for DEGs.

organism: Sorghum bicolor

source_name: Leaf Number 2

extract_protocol:
Samples frozen in liquid nitrogen were ground by hand with mortars and pestles, and total RNA was extracted using TRIzol.
The cDNA libraries were prepared from 1 µg RNA using the KAPA mRNA Hyper Prep Kit with the KAPA Dual-indexed Adapter Kit for Illumina platforms.

value: Leaf Number 2

value: DD


title: 16A_M_128


title: Control,DAY3,biol rep 3


title: Fractional CO2 laser,DAY1,biol rep 3


title: Leaf.Head_Removal.DD.10d biol rep 4


title: Leaf.Head_Removal.DD.10d biol rep 2


title: Ly6C low macrophage, Control, replicate3


title: Leaf.Head_Removal.DD.10d biol rep 1


title: A549, shHES4-2

first: Jing

last: He

address: No. 160 Pujian Road

institute: Renji Hospital

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was extracted with TRIZOL from A549 cells
RNA libraries for RNA-seq were prepared using SMARTER RNA-Seq Library Prep Kit  following manufacturer's protocols

tag: shRNA


title: A549, shHES4-3


title: Leaf.Control.DD.10d biol rep 4


title: A549, shHES1-3


title: Leaf.Control.DD.10d biol rep 3


title: A549, shHES4-1


title: Leaf.Control.DD.10d biol rep 2


title: A549, shHES1-1


title: Ly6C high macrophage, SLC29A3/TLR7 deficient, replicate3

value: Ly6C high CD11b(+) Ly6G(-) SiglecF(-) NK1.1(-)


title: Ly6C high macrophage, SLC29A3/TLR7 deficient, replicate2


title: Leaf.Head_Removal.DD.3d biol rep 4


title: Ly6C high macrophage, SLC29A3/TLR7 deficient, replicate4


title: A549, shCtrl-3

value: shCtrl


title: A549, shHES1-2


title: Leaf.Head_Removal.DD.3d biol rep 2


title: Ly6C high macrophage, SLC29A3 deficient, replicate4


title: Leaf.Head_Removal.DD.3d biol rep 3


title: A549, shCtrl-1


title: Leaf.Head_Removal.DD.3d biol rep 1


title: Ly6C high macrophage, SLC29A3 deficient, replicate2


title: Ly6C low macrophage, Control, replicate1


title: Ly6C high macrophage, SLC29A3 deficient, replicate1


title: Leaf.Control.DD.3d biol rep 4


title: Ly6C high macrophage, SLC29A3 deficient, replicate3


title: Ly6C low macrophage, Control, replicate2


title: Leaf.Control.DD.3d biol rep 3


title: A549, shCtrl-2


title: Leaf.Control.DD.3d biol rep 1


title: Leaf.Control.DD.3d biol rep 2


title: A10

city: Nanjing

first: Minglong

last: Chen

state: Jiangsu

address: 300#, Guangzhou Road

department: Cardiology

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
fastp version 0.17.1
HISAT2 version 2.1.0
String Tie v1.3.4d
DESEQ2 1.18.1
R version 3.4.3
Genome_build: gencode v27
Supplementary_files_format_and_content: abundance measurements

source_name: plasma

extract_protocol:
Extraction of plasma，then total RNA was extracted using a miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
The strand-specific RNA-seq libraries were prepared using a NEBNext® Ultra™ I RNA Library Prep Kit for Illumina (NEB, MA, USA) following the manufacturer’s instructions.

value: plasma

tag: diagnosis

value: atrial fibrillation

tag: gender

value: male


title: A8

value: female


title: Leaf.Head_Removal.dd.10d biol rep 4

value: dd


title: Ly6C high macrophage, Control, replicate3


title: C5

value: healthy person


title: A7


title: A9


title: A11


title: Ly6C high macrophage, SLC29A3/TLR7 deficient, replicate1


title: Ly6C high macrophage, Control, replicate1


title: Leaf.Head_Removal.dd.10d biol rep 3


title: C4


title: Leaf.Head_Removal.dd.10d biol rep 2


title: Ly6C high macrophage, Control, replicate4


title: Leaf.Control.dd.10d biol rep 4


title: Leaf.Head_Removal.dd.10d biol rep 1


title: C2


title: C1


title: D2_2_GFP+_GFP

city: Basel

first: Rocio

last: Castellanos Rueda

state: --None--

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH

library_source: transcriptomic single cell

data_processing:
Identification of GFP-BC  and 10X barcode  using Biostrings R package
Synthetic
.csv file containing GFP-BC library identity

source_name: T cells

growth_protocol: Primary human PBMCs derived from healthy donors were activated with EBV Peptivator Consensus peptide pool in CTLm medium (RPMI-1640, P/S, human serum 5%) supplemented with IL-4 (400 IU/mL) and IL-7 (5 ng/mL). After 3 days, non-adhesive cells were engineered to integrate a GFP barcoded reporter gene into the CCR5 locus using CRISPR-Cas9/AAV genome editing and cultured further in CTLm with IL-4/7. GFP+ and GFP- cells were FACS-sorted 7 days later and rested for 3 additional days.

extract_protocol:
Single cell cDNA was done following the the Chromium Single Cell V(D)J Reagent Kits User Guide (CG000086 Rev M; 10x Genomics). Resulting cDNA was used to do a target amplification of GFP cDNA barcoded transcripts. Transcripts were sequenced on the Illumina NovaSeq platform.
GFP+ or GFP- T cells were extracted using Fluorescence Activated Cell Sorting (FACS).

treatment_protocol: not applicable

tag: sort

value: GFP+

value: T cells

value: Donor 2

value: EBV peptide stimulation and CRISPR Cas9 directed knock in of GFP in CCR5 locus


title: D1_1_GFP+_GFP

value: Donor 1


title: D2_1_GFP+_GFP


title: Ly6C high macrophage, Control, replicate2

value: Spleen

value: macrophage

value: No Treatment


title: D2_2_GFP-_VDJ

data_processing:
Allignment and transcript counting: cellranger Pipeline Version 3.1.7
vdj_GRCh38_alts_ensembl-5.0.0
.csv file containing filtered contig annotations

extract_protocol:
Single cell V(D)J enriched library preparation was done following the the Chromium Single Cell V(D)J Reagent Kits User Guide (CG000086 Rev M; 10x Genomics) and sequenced on the Illumina NovaSeq platform.
GFP+ or GFP- T cells were extracted using Fluorescence Activated Cell Sorting (FACS).

value: GFP-


title: Leaf.Control.dd.10d biol rep 3

value: Leaf Number 2


title: D1_2_GFP+_GFP


title: Leaf.Control.DD.10d biol rep 1

value: DD


title: Leaf.Control.dd.10d biol rep 2


title: Leaf.Control.dd.10d biol rep 1


title: Mature Sperm, EtOH, Cessation, PO_EM46

city: College Station

first: Michael

last: Golding

state: Texas

address: Veterinary Research Building, Bldg 1197, Rm 334, 588 Raymond Stotzer Pkwy

department: Veterinary Physiology & Pharmacology

institute: Texas A&M University

description: We only used Read1 as for small RNA reads, paired-end is not needed

data_processing:
Fast QC
Cutadapt
Fast QC
TESmall
count summaries
Supplementary files format and content: counts summaries

source_name: spermatozoa

extract_protocol: Roszkowski M, Mansuy IM. High Efficiency RNA Extraction From Sperm Cells Using Guanidinium Thiocyanate Supplemented With Tris(2-Carboxyethyl)Phosphine. Front Cell Dev Biol. 2021;9:648274. doi:10.3389/fcell.2021.648274

treatment_protocol: Control, EtOH

value: spermatozoa

value: EtOH-Cessation


title: Mature Sperm, EtOH, Cessation, PO_EM47


title: Leaf.Head_Removal.dd.3d biol rep 4


title: Mature Sperm, EtOH, Cessation, PO_M2112


title: Mature Sperm, EtOH, Cessation, PO_M2120


title: Leaf.Head_Removal.dd.3d biol rep 3


title: D2_1_GFP-_VDJ

data_processing:
Allignment and transcript counting: cellranger Pipeline Version 3.1.6
vdj_GRCh38_alts_ensembl-5.0.0
.csv file containing filtered contig annotations


title: D1_2_GFP-_VDJ

data_processing:
Allignment and transcript counting: cellranger Pipeline Version 3.1.3
vdj_GRCh38_alts_ensembl-5.0.0
.csv file containing filtered contig annotations


title: Mature Sperm, Control, Cessation, PO_CM24

value: Control-Cessation


title: D2_2_GFP+_VDJ

data_processing:
Allignment and transcript counting: cellranger Pipeline Version 3.1.5
vdj_GRCh38_alts_ensembl-5.0.0
.csv file containing filtered contig annotations


title: D2_1_GFP+_VDJ

data_processing:
Allignment and transcript counting: cellranger Pipeline Version 3.1.4
vdj_GRCh38_alts_ensembl-5.0.0
.csv file containing filtered contig annotations


title: Leaf.Head_Removal.dd.3d biol rep 2


title: C3

value: plasma

value: female


title: Mature Sperm, Control, Cessation, PO_CM23


title: Leaf.Head_Removal.dd.3d biol rep 1

value: dd


title: D1_1_GFP-_VDJ

data_processing:
Allignment and transcript counting: cellranger Pipeline Version 3.1.2
vdj_GRCh38_alts_ensembl-5.0.0
.csv file containing filtered contig annotations


title: D1_2_GFP+_VDJ

data_processing:
Allignment and transcript counting: cellranger Pipeline Version 3.1.1
vdj_GRCh38_alts_ensembl-5.0.0
.csv file containing filtered contig annotations

value: GFP+


title: Mature Sperm, Control, Cessation, PO_CM22


title: AtTPax7_Tpit

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.3.5 (--no-unal --no-mixed --no-discordant).
Duplicated reads removed using MarkDuplicates from Picard/2.17.3.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing RPKM) from deepTools/3.3.
Peaks were called using callpeak (-f BAMPE -p 1e-3/1e-5 -g mm) from MACS/2.1.1.
Assembly: mm10
Supplementary files format and content: Bigwig, unit: fragments per million over 10 bp bins

source_name: Cell line

growth_protocol: AtT-20 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) and antibiotics (penicillin, streptomycin).

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-500 bp were kept for library preparation.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation.

value: Cell line

value: Corticotrope


title: Leaf.Control.dd.3d biol rep 4


title: Mature Sperm, Control, Cessation, PO_CM21


title: Leaf.Control.dd.3d biol rep 2


title: AtTPax7_Q+GL+_Tpit

value: Pax7 Q+GL+


title: Leaf.Control.dd.3d biol rep 3


title: CAGEseq D7 rep4

data_processing:
Raw reads were mapped to the mm9 genome using TopHat with default settings
Assembly: mm9
Supplementary files format and content: bed files with the number of reads mapped at each position

extract_protocol:
RNeasy Plus Mini Kit (Qiagen #74134) following manufacturer's protocol
nAnT-iCAGE

value: day 7

value: adipogenic differentiation


title: AtTPax7_Q+GL+_H3K4me1


title: D2_2_GFP-_GEX

data_processing:
Allignment and transcript counting: cellranger v5.0.8
GRCh38 + GFP
10x format single cell gene expression matrices

extract_protocol:
Single cell gene expression library preparation was done following the the Chromium Single Cell V(D)J Reagent Kits User Guide (CG000086 Rev M; 10x Genomics) and sequenced on the Illumina NovaSeq platform.
GFP+ or GFP- T cells were extracted using Fluorescence Activated Cell Sorting (FACS).

value: T cells

value: Donor 2

value: EBV peptide stimulation and CRISPR Cas9 directed knock in of GFP in CCR5 locus


title: CAGEseq D7 rep3


title: Stem.Head_Removal.DD.10d biol rep 4

source_name: Stem Internode 4

value: Stem Internode 4


title: Leaf.Control.dd.3d biol rep 1

value: Leaf Number 2


title: CAGEseq D7 rep2


title: AtTPax7_Q+GL+_Brg1


title: D2_1_GFP-_GEX

data_processing:
Allignment and transcript counting: cellranger v5.0.7
GRCh38 + GFP
10x format single cell gene expression matrices

value: GFP-


title: CAGEseq D7 rep1


title: D2_1_GFP+_GEX

data_processing:
Allignment and transcript counting: cellranger v5.0.5
GRCh38 + GFP
10x format single cell gene expression matrices


title: AtTPax7_Q+GL+_Ash2


title: D2_2_GFP+_GEX

data_processing:
Allignment and transcript counting: cellranger v5.0.6
GRCh38 + GFP
10x format single cell gene expression matrices


title: CAGEseq D0 rep4

value: day 0


title: Stem.Head_Removal.DD.10d biol rep 3

data_processing:
FASTQ files were filtered with FASTQC, and trimmed for quality with Trimmomatic.
Reads were aligned to the Sorghum genome v3.1.1 with the STAR aligner.
Fold Changes and DEG analysis were calculated in DESeq2 with Rstudio.
Signal-to-Noise ratio was calculated using values from the DESeq2 results.
GSEA was carried out a local copy of the software from the MSigDB, using the preranked method and the signal-to-noise values calculated in R.
TPM values were calculated in Rstudio.
Assembly: Sbicolor_454_v3.1.1.gene_exons.gtf
Supplementary files format and content: Excel files with TPM values for each library not removed after PCA, as well as the results calculated from DESeq and hierarchical clustering after filtering for DEGs.

value: DD


title: Stem.Head_Removal.DD.10d biol rep 2


title: AtTPax7_Brg1


title: D1_2_GFP-_GEX

data_processing:
Allignment and transcript counting: cellranger v5.0.4
GRCh38 + GFP
10x format single cell gene expression matrices

value: Donor 1


title: CAGEseq D0 rep3


title: Stem.Head_Removal.DD.10d biol rep 1


title: D1_1_GFP-_GEX

data_processing:
Allignment and transcript counting: cellranger v5.0.3
GRCh38 + GFP
10x format single cell gene expression matrices


title: D1_1_GFP+_VDJ

data_processing:
Allignment and transcript counting: cellranger Pipeline Version 3.1.0
vdj_GRCh38_alts_ensembl-5.0.0
.csv file containing filtered contig annotations


title: AtTPax7_Ash2


title: D1_2_GFP+_GEX

data_processing:
Allignment and transcript counting: cellranger v5.0.2
GRCh38 + GFP
10x format single cell gene expression matrices


title: AtTPax7_465_Tpit


title: Stem.Control.DD.10d biol rep 4


title: CAGEseq D0 rep1


title: D1_1_GFP+_GEX

data_processing:
Allignment and transcript counting: cellranger v5.0.1
GRCh38 + GFP
10x format single cell gene expression matrices


title: Stem.Control.DD.10d biol rep 3


title: AtTPax7_465_H3K4me1


title: AtTPax7_Q-GL-_RNA_Rep2

data_processing:
Strand-specific RNA-seq paired-end reads were trimmed with trimmomatic and mapped with TopHat2 (--rg-library L --rg-platform ILLUMINA --rg-platform-unit X --rg-id run#many --no-novel-juncs --library-type fr-firststrand).
Gene expression was quantified with analyzeRepeats from HOMER.
Assembly: mm10
Supplementary files format and content: Gene expression, unit: FPKM.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Kit. Ribosomal depletion was performed on extracted RNA.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation.

value: Pax7 Q-GL-


title: AtTPax7_H3K4me1


title: Stem.Control.DD.10d biol rep 2


title: AtTPax7_Q-GL-_RNA_Rep1


title: AtTPax7_Q-GL+_RNA_Rep2

value: Pax7 Q-GL+


title: blood, ctrl,  4h, donor4

city: Schlieren

first: Marina

last: Bacac

address: Wagistrasse 10

department: Oncology Discovery

institute: Roche Glycart AG

data_processing:
RNA-seq reads were quantified using Kallisto v0.46.1 and human reference transcriptome from ENSEMBL r107.
Transcript-level estimates of counts and tpm were imported and summarized at the gene-level using tximport v1.26.1 from Bioconductor.
Assembly: GRCh38.p13
Supplementary files format and content: Supplementary file raw_count.csv provides estimated counts obtained from Kallisto, rounded to the smallest successive integer. Rows are ENSEMBL Gene IDs and columns are individual samples.
Supplementary files format and content: Supplementary file raw_tpm.csv provides tpm values obtained from Kallisto. Rows are ENSEMBL Gene IDs and columns are individual samples.

source_name: blood

extract_protocol:
At assay endpoints (4 and 20 hrs), blood was collected for neutrophil isolation using the MACSxpress whole blood neutrophil isolation kit (Miltenyi). Neutrophils were lysed with 350 µL of RTL buffer and frozen at -80°C prior the RNA extraction following manufacturer’s instructions (QIAGEN RNeasy Mini Kit).
The RNA concentration was quantified using a Nanodrop instrument and the quality of the preparations (RIN) was evaluated with an Agilent BioAnalyzer. Libraries were prepared using Illumina TruSeq Stranded mRNA kit following the recommended instructions and quantified using qPCR KAPA Library Quantification kit (KAPA Biosystems). The fragment size distribution was evaluated using an Agilent Tapestation. The libraries were sequenced in an Illumina NovaSeq 6000 instrument (R1:51, i7:8, i5:8, R2:51) with a targeted depth of 30 M paired reads per sample.

treatment_protocol: Whole blood from 4 donors was treated with 0.2 μg/mL CD20-TCB or DP47-TCB (untargeted-TCB).

value: blood

value: neutrophils

tag: donor

tag: timepoint


title: Stem.Head_Removal.DD.3d biol rep 4

tag: treatment


title: blood, treated,  4h, donor4

tag: tissue


title: AtTPax7_465_Ala459-461_Tpit

value: Cell line

tag: cell type

value: Corticotrope


title: blood, ctrl,  20h, donor4


title: blood, treated,  20h, donor4


title: AtTPax7_Q-GL+_RNA_Rep1


title: Stem.Head_Removal.DD.3d biol rep 3


title: AtTPax7_465_Ala459-461_H3K4me1


title: AtTPax7_Q+GL+_RNA_Rep2

value: Pax7 Q+GL+


title: Stem.Head_Removal.DD.3d biol rep 2


title: CAGEseq D0 rep2


title: AtTPax7_465_Ala459-461_Brg1


title: AtTPax7_Q+GL+_RNA_Rep1


title: blood, ctrl,  4h, donor3


title: blood, treated,  4h, donor3


title: AtTPax7_NoTag_RNA_Rep2


title: AtTPax7_465_Ala459-461_Ash2


title: Stem.Head_Removal.DD.3d biol rep 1


title: Stem.Control.DD.3d biol rep 4


title: AtTPax7_431_Tpit


title: AtTPax7_465_Ash2


title: blood, treated,  20h, donor3


title: AtTPax7_NoTag_RNA_Rep1


title: AtTPax7_465_Brg1


title: Stem.Control.DD.10d biol rep 1


title: AtTPax7_431_H3K4me1


title: blood, ctrl,  4h, donor2


title: AtTPax7_431_Brg1


title: Stem.Control.DD.3d biol rep 1


title: blood, treated,  4h, donor2


title: Stem.Control.DD.3d biol rep 2


title: AtTPax3_RNA_Rep2


title: Stem.Control.DD.3d biol rep 3


title: AtTPax7_431_Ash2


title: blood, ctrl,  20h, donor2


title: Stem.Head_Removal.dd.10d biol rep 3

value: dd


title: AtTPax3_H3K4me1


title: AtTPax3_RNA_Rep1


title: Stem.Head_Removal.dd.10d biol rep 4


title: blood, treated,  20h, donor2


title: AtTNeo_Brg1


title: AtTPax7_Q-GL-_Flag_Rep2


title: blood, ctrl,  20h, donor3


title: Stem.Head_Removal.dd.10d biol rep 2


title: AtTNeo_Ash2


title: AtTPax7_Q-GL-_Flag_Rep1


title: blood, ctrl,  4h, donor1


title: AtTPax7_Q-GL+_Flag_Rep2


title: AtTPax7_Q+GL+_ATAC

extract_protocol:
Nuclei from 50,000 cells were isolated and transposition was performed using Tagment DNA kit following Illumina’s recommendations.
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation.


title: Stem.Head_Removal.dd.10d biol rep 1


title: AtTPax7_465_RNA_Rep2


title: blood, ctrl,  20h, donor1


title: blood, treated,  4h, donor1


title: AtTPax7_465_RNA_Rep1


title: AtTPax7_465_ATAC_Rep2


title: Stem.Control.dd.10d biol rep 2


title: AtTPax7_Q+GL+_Flag_Rep2


title: HUVEC, treated,  6h, biol rep 3

source_name: HUVEC

extract_protocol:
At assay endpoint (6hrs), HUVECs were washed with PBS, lysed with 350 µL of RTL buffer, and frozen at -80°C prior the RNA extraction following manufacturer’s instructions (QIAGEN RNeasy Mini Kit).
The RNA concentration was quantified using a Nanodrop instrument and the quality of the preparations (RIN) was evaluated with an Agilent BioAnalyzer. Libraries were prepared using Illumina TruSeq Stranded mRNA kit following the recommended instructions and quantified using qPCR KAPA Library Quantification kit (KAPA Biosystems). The fragment size distribution was evaluated using an Agilent Tapestation. The libraries were sequenced in an Illumina NovaSeq6000 instrument (R1:51, i7:8, i5:8, R2:51) with a targeted depth of 30 Mio paired reads per sample.

treatment_protocol: HUVECs were incubated with superntants from T cell dependent cytotoxicity assay with CEA-TCB or DP47-TCB (untargeted-TCB) for 6 hrs.

value: HUVEC

value: endothelial cells

value: CEA-TCB


title: AtTPax7_431_ATAC


title: Stem.Control.dd.10d biol rep 4

value: Stem Internode 4


title: Stem.Control.dd.10d biol rep 3


title: blood, treated,  20h, donor1


title: AtTPax7_465_ATAC_Rep1


title: AtTPax7_Q-GL+_Flag_Rep1


title: AtTPax7_Q+GL+_Flag_Rep1


title: AtTPax7_Flag


title: AtTPax7_465_Flag_Rep2


title: AtTPax7_465_Flag_Rep1


title: Stem.Head_Removal.dd.3d biol rep 3


title: Stem.Head_Removal.dd.3d biol rep 4


title: HUVEC, treated,  6h, biol rep 1


title: AtTPax7_291_ATAC


title: AtTPax7_465_Ala459-461_Flag


title: HKO_3

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

description: Mice were fed with an MCD for 3 weeks.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.p6 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then   F  PKM   of each gene was calculated based on the length of the gene and reads count mapped   to this   gene.  F  PKM,   expected  number  of  Fragment  s  Per  Kilobase  of  transcript  sequence  per   Millions  base  pairs  sequenced  ,  considers  the  effect  of  sequencing  depth  and  gene  length   for the reads count at the same time, and is currently the most commonly used method for   estimating gene expression  levels (  Tr  apnell, Cole, et al., 2010  )
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: FPKM

source_name: liver

extract_protocol:
Livers were removed, flash frozen on liqid nitrogen, and total RNA was harvested using TriPure reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HuRflox/flox and HKO mice were fed with an MCD diet for 3 weeks, and sacrificed at 11 weeks old.

value: Liver

tag: age

value: 11 weeks

tag: genotypes

value: HuR HKO (HuRflox/flox Alb-Cre+/-)


title: HKO_1

description: Mice were fed with an MCD for 3 weeks.


title: HKO_2

description: Mice were fed with an MCD for 3 weeks.


title: AtTPax7_291_Flag

tag: genotype


title: Stem.Head_Removal.dd.3d biol rep 1


title: Stem.Head_Removal.dd.3d biol rep 2


title: HUVEC, ctrl,  6h, biol rep 2


title: HUVEC, treated,  6h, biol rep 2


title: AtTPax3_ATAC


title: HUVEC, ctrl,  6h, biol rep 1


title: Stem.Control.dd.10d biol rep 1


title: 769P_sh2_2

city: Dalian

first: Han

state: Liaoning

address: 9 West sec. Lvshun South Road

institute: Dalian Medical University

description: sample: 769P_sh2_2

data_processing:
Raw data(raw reads) of fastq format were firstly processed through perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built and paired-end clean reads were aligned to the reference genome using hisat2 v2.0.5.
FeatureCounts (v1.5.0-p3) was used to calculate FPKMs of coding genes in each sample . Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Limma package from R provides statistical routines for determining differential expression in digital transcript or gene expression data .
Assembly: human NCBI genome build 38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: cell line

growth_protocol: 769-P cells stably transfected with USP35 shRNA construct (inducible expression) were maintained at standard culture conditions (37°C, 5% CO2) in RPMI 1640 medium with 10% FBS, Sodium Pyruvate , Pen/Strep, and puromycin .

extract_protocol:
RNA was harvested using TRIzol and cleaned using RNAeasy Kit (Qiagen). 2  μg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 769-P cells were untreated (control) or treated with doxycycline (sh2) at 1 μg/ml for 4 days.

value: cell line

value: renal clear cell carcinoma

value: wild type with stable transfection of inducible shUSP35

value: doxycycline


title: 769P_sh2_1

description: sample: 769P_sh2_1


title: AtTPax3_Flag_Rep2


title: Stem.Control.dd.3d biol rep 3


title: Stem.Control.dd.3d biol rep 2


title: FF_2

description: Mice were fed with an MCD for 3 weeks.

tag: strain

value: HuR flox/flox


title: AtTPax7_431_Flag

tag: cell line


title: Stem.Control.dd.3d biol rep 4


title: Stem.Control.dd.3d biol rep 1


title: Clostridium sporogenes, no uric acid, replicate 3

status: Public on Jun 16 2023

city: Stanford

first: Dylan

last: Dodd

address: 269 Campus Drive

department: Pathology

institute: Stanford University

data_processing:
CLC Genomics Workbench v 21.0.4
Reads were trimmed using a quality score limit of 0.05 and ambiguous nucleotides (n = 2), and automatic read-through adapter trimming was performed.
Genomes were downloaded from NCBI in GenBank file format (.gbff) for each of the three bacteria (NCBI assembly accession numbers: GCF_010509075.1, Collinsella aerofaciens ATCC 25986; GCF_000144625.1, Lacrimispora saccharolyticum WM1; GCF_000155085.1, Clostridium sporogenes ATCC 15579).
Genomes were uploaded into CLC Genomics Workbench and converted to tracks.
RNAseq was performed using the genome track as the reference sequence and genes for the gene track. Mapping settings included: Mismatch cost, 2; Insertion cost, 3; Deletion cost, 3; Length fraction, 0.8; Similarity fraction, 0.8; maximum number of hits for a read, 10. Expression settings included: Strand setting, both; Library type setting, bulk; Expression value, TPM.
Statistical comparisons were made between organisms cultured with or without uric acid using multi-factorial statistics based on a negative binomial GLM as implemented in CLC Genomics Workbench (v.21.0.4).
The expression and CDS tracks were then exported as Excel files and expression and annotation tracks were merged in Excel using the VLOOKUP function based on the chromosome coordinates.
Assembly: NCBI assembly accession numbers: GCF_010509075.1, Collinsella aerofaciens ATCC 25986; GCF_000144625.1, Lacrimispora saccharolyticum WM1; GCF_000155085.1, Clostridium sporogenes ATCC 15579
Supplementary files format and content: tab-delimited text files include Chromosome, Region, Annotation, Locus Tag, Protein ID, Gene Name, reads, TPM, for each Sample

organism: Clostridium sporogenes ATCC 15579

growth_protocol: All growth experiments were performed anaerobically at 37 degrees Celsius. Three individual colonies were selected for each bacterium and were inoculated into separate overnight cultures in Mega medium. The following day, each culture was precultured in Mega medium, and after three hours diluted to an OD of 0.1 into two experimental cultures, one containing standard Mega medium and one with Mega medium containing 5 mM uric acid. Bacteria were allowed to grow until reaching an OD that was commensurate with approximately 50% uric acid degradation as determined by previous experiments.

extract_protocol:
Cells were then subjected to lysozyme digestion, Proteinase K digestion and mechanical disruption with a mixer mill (RETSCH MM400) at 4 °C, 25/s, for 30 min. RNA was then purified using RNeasy kit (Qiagen), followed by DNase digestion and second RNA purification step using the RNeasy kit (Qiagen).
Ribosomal RNA was removed with the Ribo-Zero Bacteria kit (Illumina). The RNA-seq libraries were prepared using a TruSeq Stranded mRNAseq Sample Prep kit with each sample individually ligated with unique adapters (Illumina). The libraries were quantitated by qPCR, pooled, and sequenced on one lane for 101 cycles from one end of the fragments on a NovaSeq 6000 using a NovaSeq SP reagent kit. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina) and adaptors were removed from the 3’ end of the reads. Read 1 aligns to the antisense strand and read 2 aligns to the sense strand.

treatment_protocol:
Cells were cultured in rich medium with or without supplemental uric acid (5 mM final concentration).
Cell cultures were combined with two volumes of RNAprotect (Qiagen) in an anaerobic chamber, mixed thoroughly and then allowed to sit for five minutes. Cells were then centrifuged (5,000 x g, 4 °C, 10 min) and the supernatant was decanted.

value: no uric acid


title: 769P_ctrl_1

description: sample: 769P_ctrl_1

value: untreated


title: Clostridium sporogenes, no uric acid, replicate 2


title: HUVEC, ctrl,  6h, biol rep 3


title: Clostridium sporogenes, no uric acid, replicate 1


title: Clostridium sporogenes, uric acid, replicate 2

value: uric acid


title: Clostridium sporogenes, uric acid, replicate 3


title: Clostridium sporogenes, uric acid, replicate 1


title: Clostridium saccharolyticum, no uric acid, replicate 3

organism: [Clostridium] saccharolyticum WM1


title: Clostridium saccharolyticum, uric acid, replicate 2


title: FF_3

description: Mice were fed with an MCD for 3 weeks.


title: 769P_ctrl_2

description: sample: 769P_ctrl_2


title: MP_Single_cell

city: Seoul

first: Joonyub

last: Lee

state: Seoul

address: 222, Banpo-daero, Seocho-gu

country: South Korea

institute: Seoul St. Mary's hospital

data_processing:
Sequenced data were aligned to GRCm38/mm10 and processd by using Cell Ranger (3.1.0)
The processed data were analyzed by using Seurat v3.0
Assembly: mm10
Supplementary files format and content: Virgin_barcodes.tsv.gz, MP_barcodes.tsv.gz
Supplementary files format and content: Virgin_features.tsv.gz, MP_features.tsv.gz
Supplementary files format and content: Virgin_matrix.mtx.gz, MP_matrix.mtx.gz

source_name: Pancreatic islets

extract_protocol:
Freshly collected islets from virgin and multipara mice. Isolated islets were incubated in RPMI + 10% FBS for 30 minutes (37℃, CO2: 4%) and underwent single cell dissociation by using 0.25% Trypsin (Hyclone, SH30042.01).
Chromium Single Cell 3' Reagent Kits (v3.1 Chemistry)

value: Pancreatic islets

value: Wild type (C57BL/6J )


title: Virgin_Single_cell


title: Liver cells from a humanized liver (one mouse)

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: Yale University

data_processing:
Raw sequencing reads were processed with Cell Ranger 3.1.0 using a human–mouse combined reference to generate a gene cell count matrix.
To distinguish human and mouse cells, we counted the number of human genes (nHuman) and mouse genes (nMouse) with non-zero expression in each cell and selected cells with nHuman >20x nMouse as human cells and cells with nMouse >10x nHuman as mouse cells. Human Cells <20x nMouse were named mixed cells and were excluded from the analysis.
The count matrix of human cells and human genes was used in the downstream analysis with Seurat 3.2. Specifically, this matrix was filtered, retaining cells with more than 500 and fewer than 5,000 genes and more than 1000 UMIs. We then log-transformed each entry of the matrix by computing log (CPM/100 + 1), where CPM stands for counts per million.
After normalization, we used adaptively thresholded low-rank approximation (ALRA) to impute the matrix and fill in the technical dropped-out values.
To visualize the cell subpopulations in two dimensions, we applied principal component analysis, followed by t-distributed stochastic neighbor embedding (t-SNE), a non-linear dimension reduction method for visualization.
Louvain clustering was then used to generate clusters that were overlaid on the t-SNE embedding to investigate cell subpopulations. Marker genes for each cluster of cells were identified using the Wilcoxon test with Seurat.
Assembly: hg19+mm10
Supplementary files format and content: "barcodes.tsv.gz" contains cell barcodes, "features.tsv.gz" contains metadata for genes, "matrix.mtx.gz" contains digital expression matrix

source_name: Liver tissue

growth_protocol: Standard mouse housing conditions, liver cell isolation from freshly isolated liver tissue

extract_protocol:
10X Genomics Next GEM Single Cell 3′
10X Genomics Chromium 3' v3.1, 11 cycles of cDNA amplification, 14 cycles of SIP amplification

treatment_protocol: No treatment of mice

value: BALB/c

value: humanized liver tissue with human hepatocytes and human NPCs

value: 18 weeks

value: MISTRG-Fah-/-


title: Clostridium saccharolyticum, uric acid, replicate 1


title: Clostridium saccharolyticum, uric acid, replicate 3


title: Pro2_N_47081

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

data_processing:
The quality of the raw RNA-seq data was assessed using FastQC, and poor-quality ends were trimmed (Trimgalore). High-quality sequences were aligned against the Macaca mulatta reference genome using STAR aligner v2.7.9, and counts were generated using featureCount. A list of differentially expressed genes (DEGs) were generated using DESeq2 based on the negative binomial distribution. The resulting DEGs between the groups were defined at cut-off criteria of |log2 fold-change|1.5 and p-value <0.05 adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate.
Supplementary files format and content: gene_count.txt

organism: Macaca mulatta

source_name: Lymph node

extract_protocol:
Lymph node cells obtained from vaccinated animals by LN biopsy. Cells sorting were performed and CD4+ memory and naïve population were collected. RNA was extracted from CD4+ memory and Naïve cells using QIAgen kit
Library construction was performed based on manufacturer’s recommendation for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio USA Inc., California, USA) followed by Nextera® XT DNA Library Prep Kit (Illumina, California, USA).
Final library size was about 450bp with an insert size of about 300bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for 40 M PE reads per sample (20M in each direction)

value: Lymph node

value: Lymph node cells

tag: cell subset

value: CD4+ naive

tag: adjuvant

value: MPLA

value: Week3 post protein2


title: Clostridium saccharolyticum, no uric acid, replicate 1


title: Clostridium saccharolyticum, no uric acid, replicate 2


title: Pro2_N_47466


title: Pro2_N_46354


title: Pro2_M_47161

value: CD4+ memory


title: Pro2_N_47161


title: Pro2_N_45721


title: Pro1_M_47466

value: Week2 post protein1


title: Pro1_N_46354


title: Pro1_M_46354


title: Pro1_N_47081


title: Pro2_M_46354


title: Pro2_M_47081


title: Pro2_M_46548


title: Pro2_M_45721


title: Pro1_M_45721


title: Pro2_M_47466


title: Pro2_N_46548


title: Pro1_N_47466


title: Pro1_M_47081


title: Pro1_N_46548


title: Pro1_N_47161


title: BL_N_47466

value: Baseline


title: Pro1_M_46548


title: Pro1_M_47161


title: BL_M_47466


title: BL_N_45721


title: Pro1_N_45721


title: BL_N_47081


title: BL_N_47161


title: BL_M_46354


title: BL_M_47081


title: BL_M_46548


title: BL_M_47161


title: 16A_M_3060

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 16A_M_3061


title: 16A_M_3057


title: 16A_M_3059


title: 16A_M_3058


title: 16A_M_3055


title: 16A_M_3056


title: 16A_M_3054


title: BL_N_46548


title: 16A_M_3053


title: 16A_M_3049


title: 16A_M_3046


title: 16A_M_3051


title: 16A_M_3052


title: 16A_M_3050


title: 16A_M_3048


title: 16A_M_3040


title: 16A_M_3041


title: 16A_M_3044


title: 16A_M_3043


title: 16A_M_3045


title: 16A_M_3039


title: 16A_M_3038


title: 16A_M_3036


title: 16A_M_3037


title: 16A_M_3034


title: 16A_M_3032


title: 16A_M_3030


title: 16A_M_3033


title: 16A_M_3031


title: 16A_M_3028


title: 16A_M_3029


title: 16A_M_3026


title: 16A_M_3025


title: 16A_M_3042


title: 16A_M_3021


title: 16A_M_3023


title: 16A_M_3019


title: 16A_M_3022


title: 16A_M_3024


title: 16A_M_3018


title: 16A_M_3035


title: 16A_M_3009


title: 16A_M_3017


title: 16A_M_3013


title: 16A_M_3015


title: 16A_M_3012


title: 16A_M_3010


title: 16A_M_3016


title: 16A_M_3014


title: 16A_M_3005


title: 16A_M_3003


title: 16A_M_3004


title: 16A_M_3027


title: 16A_M_3001


title: 16A_M_3020


title: 16A_M_3002


title: 16A_M_3011


title: 16A_M_2999


title: 16A_M_2867


title: 16A_M_2866


title: 16A_M_2870


title: 16A_M_2869


title: 16A_M_2868


title: 16A_M_2998


title: 16A_M_3007


title: 16A_M_2865


title: 16A_M_2862


title: 16A_M_2863


title: 16A_M_2864


title: 16A_M_3006


title: 16A_M_2853


title: 16A_M_2852


title: 16A_M_3000


title: 16A_M_2857


title: 16A_M_2855


title: 16A_M_2861


title: 16A_M_2856


title: 16A_M_2859


title: 16A_M_2854


title: 16A_M_2848


title: 16A_M_2850


title: 16A_M_2843


title: 16A_M_2841


title: 16A_M_2851


title: 16A_M_2842


title: 16A_M_2847


title: 16A_M_2839


title: 16A_M_2838


title: 16A_M_2837


title: 16A_M_2844


title: 16A_M_2846


title: 16A_M_2845


title: 16A_M_2860


title: 16A_M_2849


title: 16A_M_2840


title: 16A_M_2836


title: 16A_M_2835


title: 16A_M_2834


title: 16A_M_2830


title: 16A_M_2831


title: 16A_M_2827


title: 16A_M_2824


title: 16A_M_2832


title: 16A_M_2828


title: 16A_M_2833


title: 16A_M_2818


title: 16A_M_2825


title: 16A_M_2819


title: 16A_M_2820


title: 16A_M_2815


title: 16A_M_2823


title: 16A_M_2822


title: 16A_M_2821


title: 16A_M_2816


title: 16A_M_2817


title: 16A_M_2814


title: 16A_M_2813


title: 16A_M_2810


title: 16A_M_2809


title: 16A_M_2812


title: 16A_M_2858


title: 16A_M_2811


title: 16A_M_2826


title: 16A_M_2807


title: 16A_M_2808


title: 16A_M_2550


title: 16A_M_2548


title: 16A_M_2549


title: 16A_M_2546


title: 16A_M_2547


title: 16A_M_2544


title: 16A_M_2543


title: 16A_M_2542


title: 16A_M_2539


title: 16A_M_2545


title: 16A_M_2541


title: 16A_M_2540


title: 16A_M_2538


title: 16A_M_2536


title: 16A_M_2534


title: 16A_M_2535


title: 16A_M_2533


title: 16A_M_2531


title: 16A_M_2537


title: 16A_M_2532


title: 16A_M_2530


title: 16A_M_2529


title: 16A_M_2528


title: 16A_M_2526


title: 16A_M_2527


title: 16A_M_2524


title: 16A_M_2525


title: 16A_M_2523


title: 16A_M_2519


title: 16A_M_2520


title: 16A_M_2518


title: 16A_M_2517


title: 16A_M_2516


title: 16A_M_2513


title: 16A_M_2515


title: 16A_M_2514


title: 16A_M_2511


title: 16A_M_2512


title: 16A_M_2508


title: 16A_M_2506


title: 16A_M_2504


title: 16A_M_2503


title: 16A_M_2507


title: 16A_M_2522


title: 16A_M_2521


title: 16A_M_2500


title: 16A_M_2502


title: 16A_M_2501


title: 16A_M_2499


title: 16A_M_2490


title: 16A_M_2495


title: 16A_M_2496


title: 16A_M_2494


title: 16A_M_2493


title: 16A_M_2491


title: 16A_M_2510


title: 16A_M_2509


title: 16A_M_2505


title: 16A_M_2497


title: 16A_M_2489


title: 16A_M_2487


title: 16A_M_2488


title: 16A_M_2485


title: 16A_M_2484


title: 16A_M_2483


title: 16A_M_2481


title: 16A_M_2478


title: 16A_M_2498


title: 16A_M_2477


title: 16A_M_2476


title: 16A_M_2475


title: 16A_M_2479


title: 16A_M_2474


title: 16A_M_2480


title: 16A_M_2473


title: 16A_M_2468


title: 16A_M_2472


title: 16A_M_2467


title: 16A_M_2486


title: 16A_M_2471


title: 16A_M_2470


title: 16A_M_2466


title: 16A_M_2469


title: 16A_M_2463


title: 16A_M_2460


title: 16A_M_2465


title: 16A_M_2464


title: 16A_M_2458


title: 16A_M_2482


title: 16A_M_2459


title: 16A_M_2462


title: 16A_M_2457


title: 16A_M_2461


title: 16A_M_2455


title: 16A_M_2456


title: 16A_M_2451


title: 16A_M_2452


title: 16A_M_2450


title: 16A_M_2454


title: 16A_M_2453


title: 16A_M_2449


title: 16A_M_2447


title: 16A_M_2448


title: 16A_M_2439


title: 16A_M_2443


title: 16A_M_2442


title: 16A_M_2440


title: 16A_M_2441


title: 16A_M_2438


title: 16A_M_2437


title: 16A_M_2435


title: 16A_M_2436


title: 16A_M_2433


title: 16A_M_2430


title: 16A_M_2431


title: 16A_M_2429


title: 16A_M_2428


title: 16A_M_2427


title: 16A_M_2423


title: 16A_M_2424


title: 16A_M_2230


title: 16A_M_2229


title: 16A_M_2445


title: 16A_M_2426


title: 16A_M_2227


title: 16A_M_2446


title: 16A_M_2444


title: 16A_M_2225


title: 16A_M_2224


title: 16A_M_2223


title: 16A_M_2434


title: 16A_M_2220


title: 16A_M_2222


title: 16A_M_2221


title: 16A_M_2432


title: 16A_M_2218


title: 16A_M_2219


title: 16A_M_2217


title: 16A_M_2425


title: 16A_M_2215


title: 16A_M_2228


title: 16A_M_2214


title: 16A_M_2211


title: 16A_M_2210


title: 16A_M_2209


title: 16A_M_2208


title: 16A_M_2213


title: 16A_M_2207


title: 16A_M_2206


title: 16A_M_2226


title: 16A_M_2202


title: 16A_M_2204


title: 16A_M_2201


title: 16A_M_2200


title: 16A_M_2203


title: 16A_M_2199


title: 16A_M_2197


title: 16A_M_2198


title: 16A_M_2216


title: 16A_M_2193


title: 16A_M_2196


title: 16A_M_2194


title: 16A_M_2191


title: 16A_M_2212


title: 16A_M_2192


title: 16A_M_2195


title: 16A_M_2189


title: 16A_M_2205


title: 16A_M_2190


title: 16A_M_2187


title: 16A_M_2183


title: 16A_M_2186


title: 16A_M_2184


title: 16A_M_2185


title: 16A_M_2181


title: 16A_M_2182


title: 16A_M_2178


title: 16A_M_2177


title: 16A_M_2176


title: 16A_M_2180


title: 16A_M_2175


title: 16A_M_2174


title: 16A_M_2172


title: 16A_M_2173


title: 16A_M_2170


title: 16A_M_2169


title: 16A_M_2168


title: 16A_M_2171


title: 16A_M_2038


title: 16A_M_2188


title: 16A_M_2036


title: 16A_M_2167


title: 16A_M_2034


title: 16A_M_2035


title: 16A_M_2037


title: 16A_M_2031


title: 16A_M_2033


title: 16A_M_2032


title: 16A_M_2030


title: 16A_M_2027


title: 16A_M_2025


title: 16A_M_2026


title: 16A_M_2028


title: 16A_M_2024


title: 16A_M_2023


title: 16A_M_2020


title: 16A_M_2021


title: 16A_M_2018


title: 16A_M_2019


title: 16A_M_2017


title: 16A_M_2016


title: 16A_M_2015


title: 16A_M_2014


title: 16A_M_2013


title: 16A_M_2009


title: 16A_M_2010


title: 16A_M_2011


title: 16A_M_2012


title: 16A_M_2029


title: 16A_M_2007


title: 16A_M_2004


title: 16A_M_2005


title: 16A_M_2008


title: 16A_M_2006


title: 16A_M_2002


title: 16A_M_1999


title: 16A_M_2000


title: 16A_M_2001


title: 16A_M_2022


title: 16A_M_1997


title: 16A_M_1996


title: 16A_M_1994


title: 16A_M_1995


title: 16A_M_1993


title: 16A_M_1992


title: 16A_M_1990


title: 16A_M_1991


title: 16A_M_1989


title: 16A_M_1985


title: 16A_M_1986


title: 16A_M_1983


title: 16A_M_1984


title: 16A_M_1982


title: 16A_M_1981


title: 16A_M_2003


title: 16A_M_1980


title: 16A_M_1977


title: 16A_M_1979


title: 16A_M_1998


title: 16A_M_1976


title: 16A_M_1978


title: 16A_M_1907


title: 16A_M_1909


title: 16A_M_1908


title: 16A_M_1910


title: 16A_M_1906


title: 16A_M_1988


title: 16A_M_1905


title: 16A_M_1987


title: 16A_M_1902


title: 16A_M_1904


title: 16A_M_1903


title: 16A_M_1900


title: 16A_M_1899


title: 16A_M_1901


title: 16A_M_1896


title: 16A_M_1897


title: 16A_M_1898


title: 16A_M_1894


title: 16A_M_1893


title: 16A_M_1892


title: 16A_M_1975


title: 16A_M_1891


title: 16A_M_1887


title: 16A_M_1888


title: 16A_M_1885


title: 16A_M_1890


title: FF_1

description: Mice were fed with an MCD for 3 weeks.

value: Liver

value: 11 weeks

value: HuR flox/flox


title: 16A_M_1886


title: 16A_M_1884


title: 16A_M_1889


title: 16A_M_1882


title: 16A_M_1883


title: 16A_M_1881


title: 16A_M_1879


title: 16A_M_1880


title: 16A_M_1878


title: 16A_M_1876


title: 16A_M_1877


title: 16A_M_1872


title: 16A_M_1871


title: 16A_M_1875


title: 16A_M_1873


title: 16A_M_1870


title: 16A_M_1868


title: 16A_M_1867


title: 16A_M_1869


title: 16A_M_1864


title: 16A_M_1865


title: 16A_M_1861


title: 16A_M_1858


title: 16A_M_1860


title: 16A_M_1862


title: 16A_M_1866


title: 16A_M_1863


title: 16A_M_1856


title: 16A_M_1859


title: 16A_M_1874


title: 16A_M_1857


title: 16A_M_1855


title: AtTPax3_Flag_Rep1

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.3.5 (--no-unal --no-mixed --no-discordant).
Duplicated reads removed using MarkDuplicates from Picard/2.17.3.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing RPKM) from deepTools/3.3.
Peaks were called using callpeak (-f BAMPE -p 1e-3/1e-5 -g mm) from MACS/2.1.1.
Assembly: mm10
Supplementary files format and content: Bigwig, unit: fragments per million over 10 bp bins

value: Cell line

value: Corticotrope


title: 16A_M_1854


title: 16A_M_1849


title: 16A_M_1853


title: 16A_M_1852


title: 16A_M_1851


title: 16A_M_1850


title: 16A_M_1847


title: 16A_M_1848


title: 16A_M_1846


title: 16A_M_1845


title: 16A_M_1843


title: 16A_M_1842


title: 16A_M_1844


title: 16A_M_1837


title: 16A_M_1839


title: 16A_M_1841


title: 16A_M_1838


title: 16A_M_1840


title: 16A_M_1835


title: 16A_M_1836


title: 16A_M_1833


title: 16A_M_1831


title: 16A_M_1834


title: 16A_M_1828


title: 16A_M_1829


title: 16A_M_1830


title: 16A_M_1832


title: 16A_M_1826


title: 16A_M_1824


title: 16A_M_1825


title: 16A_M_1823


title: 16A_M_1821


title: 16A_M_1818


title: 16A_M_1820


title: 16A_M_1819


title: 16A_M_1817


title: 16A_M_1815


title: 16A_M_1814


title: 16A_M_1813


title: 16A_M_1807


title: 16A_M_1808


title: 16A_M_1811


title: 16A_M_1809


title: 16A_M_1827


title: 16A_M_1804


title: 16A_M_1806


title: 16A_M_1803


title: 16A_M_1802


title: 16A_M_1800


title: 16A_M_1822


title: 16A_M_1798


title: 16A_M_1801


title: 16A_M_1795


title: 16A_M_1797


title: 16A_M_1793


title: 16A_M_1794


title: 16A_M_1790


title: 16A_M_1816


title: 16A_M_1792


title: 16A_M_1796


title: 16A_M_1812


title: 16A_M_1791


title: 16A_M_1789


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