title: FLAG_ctr_1_8_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
F_517_1:8_II_GTACTGACTCTCGCGC


title: PZH 2

status: Public on Mar 01 2021

type: SRA

city: Shanghai

first: Jinhang

last: Zhu

address: Huashan Road 1954

country: China

institute: Shanghai Jiao Tong University

description: processed data file: circRNAs.SRPBM.txt

library_source: transcriptomic

data_processing:
TrimGalore were trimmed for paired-end adaptor sequence.
Sequenced reads were mapped to mm10 whole genome using STAR software.
CIRI and CIRCexplorer software were used as the identified circRNA for subsequent analysis. CircBase and circ2Trait disease database was used to annotate the identification of circRNAs.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: circRNAs.SRPBM.txt: Tab-delimited text file includes SRPBM values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol:
Control group (CCl4-induced): mice received 10% carbon tetrachloride (CCl4, 10 μl/10 g bodyweight) for 8 weeks (two times a week) injection to induce liver fibrosis.
Treatment group (PZH-treated): mice were injected by CCl4, and administered with PZH (25 mg/ml, once daily, weeks 2-8) dissolved by double distilled water under sonication. Six mice of each group were killed for collecting liver samples at 8th week for RNA-seq.

extract_protocol:
RNA from each hepatic fibrosis tissue sample was extracted using Trizol reagent (Invitrogen, CA, USA) and Illumina Hiseq 4000 was used for the construction of circRNA sequencing libraries.
RNA libraries were prepared for sequencing according to Illumina's instructions accompanying the TruSeqTM RNA sample prep Kit.

treatment_protocol: PZH medication.

tag: strain

tag: tissue

value: Liver

tag: disease

value: carbon tetrachloride (CCl4)-induced liver fibrosis

tag: treatment

value: Pien Tze Huang (PZH)


title: Inguinal adipose tissue, male sucrose (MS8128)

city: Downers Grove

first: Erin

middle: J

last: Stephenson

state: IL

address: 555 31st street

country: USA

institute: Midwestern University

description: RNAseq performed by Novagene

data_processing:
Novogene transformed raw image data files to sequenced reads using CASAVA(1.8) base recognition and Qphred scores were used to determine the error rate distribution along reads. GC-content was used to detect potential AT/GC separation. To get clean reads, raw reads were filtered to remove reads containing adaptors, remove reads containing N>10%, and ensure the Qscore of over 50% of the read was <=5.
Novogene parsed alignments using Tophat and aligned paired-end clean reads to the reference genome using STAR (v2.5). HTSeq v0.6.1 was used to count the read numbers mapped to each gene
Investigators used DESeq2 (v1.24.0) to normalize counts and identify differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: matrixData_sucrose-iWAT.csv reports read counts

source_name: dorsolumbar-inguinal adipose tissue

growth_protocol: Temperature (~22 deg C) and humidity controlled rooms, ventilated cages with corn-cobb bedding

extract_protocol:
Total RNA was isolated using TRI reagent and purified using columns from a PureLink RNA isolation kit.
Total RNA samples were sent to Novogene where mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and NEB cDNA libraries were prepared. To construct libraries, first strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3'ends of DNA fragments, NEBNext Adaptor with hairpin look structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150-200 bp length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). The final library was constructed by PCR amplification and purification of PCR products by AMPure XP beads. Library quality was first determined by Qubit2.0 and the insert size was detected using Agilent 2100. Q-PCR was used to accurately quantify the library effective concentration (>2nM).

treatment_protocol: Beginning at 10 weeks of age, mice were either maintained on regular chow and plain drinking water, or began receiving drinking water supplemented with 10%w/v sucrose for 12 weeks. Mice were given an intraperitoneal injection of 0.9% saline prepared using 99% deuterium oxide 7 hours before tissues were collected

value: C57BL6/J x C57BL6/N

tag: Sex

value: male

tag: diet

value: chow diet (Envigo #7912)

tag: drinking water

value: 10%w/v sucrose in water ad libitum

tag: treatment duration

value: 12 weeks

tag: age

value: 22 weeks

value: dorsolumbar-inguinal adipose tissue


title: FLAG_ctr_1_8_I

city: Planegg-Martinsried

first: Martina

last: Peritore

state: Bayern

address: Am Klopferspitz 18

country: Germany

institute: MPIB

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
F_517_1:8_GGCTCTGACGCTCATT

library_source: genomic

data_processing:
Sequecing reads were mapped to the S. cerevisiae genome using Bowtie2  (version 2.2.9) with default parameters
Multiple mapping reads were filtered with SAMtools.
Genome_build: LYZE00000000.1, sacCer3
Supplementary_files_format_and_content: All files were generated with R. Bed files contain aligned reads, bedGraph files represent read coverage

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Cells

growth_protocol: Cells were grown in YP-media containing 2% raffinose at 30°C. Exponentially  growing cells (OD600 0.5-0.7) were synchronized in M phase with 5 μg/ml  nocodazole for 2-3 hours. Cell cycle arrest was assessed via microscopy and  DNA content measured by flow cytometry.

extract_protocol:
Cells were mechanically lysed and chromatin was sheared by sonication to  fragments of 200-500 bp. 40% of the chromatin extract was used for  immunoprecipitation, the purified complexes were treated with proteinase K and crosslinks reversed. DNA was purified by phenol-chloroform extraction and ethanol  precipitation.
Strand-specific ChIP-seq libraries were prepared starting from 1-3 ng of DNA using Accel-NGS® 1S Plus Library Kit following manufacturer instructions and 10-12 cycles were used for library amplification. Clean-up steps were performed with SPRIselect beads.

treatment_protocol: Site-specific DSBs were introduced  inducing the HO endonuclease or the AsiSI restriction enzyme via the galactose  promoter, adding galactose to the cultures to a final concentration of 2%. Cells  were crosslinked at the indicated time points with 1% formaldehyde for 16  minutes at room temperature and the reaction quenched with glycine (final concentration 400 mM). Cells were harvested by centrifugation (3500xg at  4°C), washed with cold PBS and the pellet flash frozen in liquid nitrogen.

tag: chip antibody

value: anti-FLAG beads (RRID:AB_2637089)

tag: genome used for alignment


title: Inguinal adipose tissue, male sucrose (MS8124)

description: RNAseq performed by Novagene


title: FLAG_H3flag_1_0_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
F_43_10h_GGCTCTGATCTCGCGC


title: Inguinal adipose tissue, male sucrose (MS8060)

description: RNAseq performed by Novagene


title: Inguinal adipose tissue, female sucrose (FS8371)

description: RNAseq performed by Novagene

value: female


title: Inguinal adipose tissue, female sucrose (FS8322)

description: RNAseq performed by Novagene


title: Inguinal adipose tissue, female sucrose (FS8158)

description: RNAseq performed by Novagene


title: FLAG_ctr_1_6_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
F_517_1:6_II_GTACTGACTCCGCGAA


title: Inguinal adipose tissue, female sucrose (FS8153)

description: RNAseq performed by Novagene


title: PZH 1

description: processed data file: circRNAs.SRPBM.txt


title: FLAG_ctr_1_6_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
F_517_1:6_I_TAATCTTAGAATTCGT


title: FLAG_ctr_1_4_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
F_517_1:4_I_TAATCTTAATTCAGAA


title: Inguinal adipose tissue, female sucrose (FS8120)

description: RNAseq performed by Novagene


title: FLAG_H3flag_1_0_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
F_43_10h_I_CAGGACGTCGCTCATT


title: FLAG_ctr_1_2_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
F_517_1:2_I_TAATCTTAGAGATTCC


title: FLAG_ctr_1_2_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
F_517_1:2_CCTATCCTAGCGATAG


title: Inguinal adipose tissue, male control (MC8205)

description: RNAseq performed by Novagene

value: Water ad libitum


title: Inguinal adipose tissue, female sucrose (FS8386)

description: RNAseq performed by Novagene


title: Inguinal adipose tissue, male control (MC8338)

description: RNAseq performed by Novagene


title: Inguinal adipose tissue, male control (MC8149)

description: RNAseq performed by Novagene


title: FLAG_ctr_1_1_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
F_517_1:1_I_TAATCTTACGCTCATT


title: Inguinal adipose tissue, female sucrose (FS8388)

description: RNAseq performed by Novagene


title: FLAG_ctr_1_0_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
F_517_10h_II_GTACTGACAGCGATAG


title: FLAG_ctr_1_1_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
F_517_1:1_CCTATCCTTCTCGCGC


title: FLAG_ctr_1_6_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
F_517_1:6_GGCTCTGATCCGGAGA


title: Inguinal adipose tissue, male control (MC8146)

description: RNAseq performed by Novagene


title: Inguinal adipose tissue, male control (MC8138)

description: RNAseq performed by Novagene


title: FLAG_ctr_1_0_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
F_517_10h_I_TAATCTTATAATGCGC


title: FLAG_ctr_1_4_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
F_517_1:4_GGCTCTGAATTACTCG


title: FLAG_ctr_1_0_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
F_517_10h_GGCTCTGAGAGATTCC


title: FLAG_ctr_1_2_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
F_517_1:2_II_GTACTGACTAATGCGC


title: Inguinal adipose tissue, male control (MC8088)

description: RNAseq performed by Novagene


title: FLAG_ctr_0_1_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
F_517_0h_II_GTACTGACGAATTCGT


title: FLAG_ctr_1_4_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
F_517_1:4_II_GTACTGACCGGCTATG


title: Inguinal adipose tissue, female sucrose (FS8242)

description: RNAseq performed by Novagene


title: FLAG_ctr_1_1_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
F_517_1:1_II_GTACTGACCTGAAGCT


title: Inguinal adipose tissue, male control (MC8084)

description: RNAseq performed by Novagene


title: FLAG_ctr_0_1_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
F_517_0h_CCTATCCTTCCGCGAA


title: Inguinal adipose tissue, female control (FC8381)

description: RNAseq performed by Novagene


title: FLAG_ctr_0_1_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
F_517_0h_I_TAATCTTATCCGGAGA


title: Inguinal adipose tissue, female control (FC8431)

description: RNAseq performed by Novagene


title: Inguinal adipose tissue, female control (FC8364)

description: RNAseq performed by Novagene


title: Inguinal adipose tissue, female control (FC8363)

description: RNAseq performed by Novagene


title: AsiSI_RPA_2_4h

value: anti-RFA antibody (Cat# AS07-214, Agrisera)


title: AsiSI_RPA_2_2h


title: Inguinal adipose tissue, female control (FC8350)

description: RNAseq performed by Novagene


title: Inguinal adipose tissue, male control (MC8195)

description: RNAseq performed by Novagene


title: Inguinal adipose tissue, female control (FC8103)

description: RNAseq performed by Novagene


title: AsiSI_RPA_1_6h


title: AsiSI_RPA_1_0h


title: AsiSI_IN_7_6h

description:
.bed files used to determine AsiSI cutting efficiency
IN_WT_6h_GGCTCTGAGAGATTCC


title: AsiSI_RPA_1_4h


title: AsiSI_RPA_2_6h


title: AsiSI_RPA_1_2h


title: OT-2:pex cDC1 rep 1

city: Seoul

first: Moah

last: Sohn

address: 50 YONSEI-RO, SEODAEMUN-GU

country: South Korea

institute: Yonsei University

description: [76] Normalized_FPKM.txt

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using HISAT2 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie 1.3.4d software in default options.
The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: OT-2 cells

extract_protocol:
For T cell isolation, splenic cells from OT-1 and OT-2 mice were enriched by excluding cells expressing CD11b, CD19, CD49b, MHCII, F4/80, B220, and CD4 (for OT-1) or CD8 (for OT-2) using biotinylated antibodies and anti-biotin Dynabeads (ThermoFisher Scientific). Purified T cells were labeled with 0.5 mM CFSE or CTV (Thermo Fisher Scientific) according to the manufacturer’s protocol. For the antigen presentation assay, CFSE or CTV labeled T cells and OVA-laden peritoneal APCs were co-cultured in the 96-well plates (SPL). The Number of T cells used for each well was fixed at 25,000 cells, and OVA laden APCs and T cells were mixed at the ratio of 1:10.
Reverse transcription of mRNA and generation of cDNA libraries were carried out with SMARTer Ultra low input RNA library kit and sequencing with Illumina NovaSeq

treatment_protocol: For sample 113 and 114, 1 ug/ml of IL-2 was supplemented.

value: Spleen

value: post natal week 11

tag: treatement

value: co-culuted with OVA-laden peritoneal cDC1s for 3 days


title: OT-2:pex cDC2 rep 2

description: [80] Normalized_FPKM.txt

value: co-culuted with OVA-laden peritoneal cDC2s for 3 days


title: AsiSI_IN_6_0h

description:
.bed files used to determine AsiSI cutting efficiency
IN_WT_0h__AGGCGAAGCGCTCATT


title: AsiSI_IN_6_6h

description:
.bed files used to determine AsiSI cutting efficiency
IN_WT_6h__AGGCGAAGGAATTCGT


title: OT-2:pex cDC1 rep 2

description: [87] Normalized_FPKM.txt


title: AsiSI_IN_5_0h

description:
.bed files used to determine AsiSI cutting efficiency
IN_958_0h_CAGGACGTATTCAGAA


title: E14.5 rep2

city: Chicago

first: Xiaochang

last: Zhang

address: 920 E 58th St, CLSC 507A

department: Human Genetics

institute: The University of Chicago

description:
processed data file:
count.mtx, cell_names.csv (E14_2.2), gene_names.csv
Zhang-XZ-12_S7

data_processing:
Libraries were pooled and sequenced in two runs on Illumina NextSeq
Sequencing reads were trimmed and processed using Drop-Seq tools (2.0.0) to obtain a unique molecular identified (UMI) count matrix.
We used the Seurat package (3.1.5) in R (4.0.2) and filtered out cells with gene counts over 6,000 or below 500, or had over 10% mitochondrial gene counts. This resulted in a data matrix of 21,862 genes and 10,261 cells.
The count matrix was then normalized by the library size, log-transformed and scaled, following the workflow in Seurat tutorial.
Genome_build: mm10
Supplementary_files_format_and_content: Unique molecular identified (UMI) count by cell matrices

source_name: Embryonic mouse (CD-1) dorsal forebrain

growth_protocol: CD1 timed pregnant mice were ordered from Charles River

extract_protocol:
Dorsal cortical tissues from E10.5-E18.5 embryos were dissected and dissociated with papain. Single cell collection and library preparation followed the Drop-Seq protocol v3.1
Drop-Seq tools v3.1

tag: developmental stage

value: dorsal forebrain


title: AsiSI_IN_5_6h

description:
.bed files used to determine AsiSI cutting efficiency
IN_958_6h_CAGGACGTTAATGCGC


title: OT-1:pex cDC2 + IL-2 1ug/ml rep 1

description: [113] Normalized_FPKM.txt

source_name: OT-1 cells

value: co-culuted with OVA-laden peritoneal cDC2s for 3 days with 1 ug/ml of IL-2


title: E18.5

description:
processed data file:
count.mtx, cell_names.csv (E18_1, E18_2), gene_names.csv
S5_L0001234
Zhang-XZ-6_S6


title: AsiSI_RPA_2_0h


title: AsiSI_IN_4_6h

description:
.bed files used to determine AsiSI cutting efficiency
IN_958_6h_TATAGCCTGAGATTCC


title: Inguinal adipose tissue, female control (FC8111)

description: RNAseq performed by Novagene

value: C57BL6/J x C57BL6/N


title: E16.5

description:
processed data file:
count.mtx, cell_names.csv (E16_1, E16_2), gene_names.csv
Zhang-XZ-5_S5


title: Inguinal adipose tissue, female control (FC8091)

description: RNAseq performed by Novagene


title: AsiSI_IN_4_0h

description:
.bed files used to determine AsiSI cutting efficiency
IN_958_0h_TATAGCCTATTACTCG


title: OT-1:pex cDC2 rep 1

description: [69] Normalized_FPKM.txt


title: AsiSI_IN_3_6h

description:
.bed files used to determine AsiSI cutting efficiency
IN_1_6h_TATAGCCTTAATGCGC


title: OT-1:pex cDC1 rep 2

description: [71] Normalized_FPKM.txt


title: AsiSI_IN_7_0h

description:
.bed files used to determine AsiSI cutting efficiency
IN_WT_0h_GGCTCTGAATTACTCG


title: E14.5

description:
processed data file:
count.mtx, cell_names.csv (E14_1, E14_2), gene_names.csv
S3_L0001234
Zhang-XZ-3_S3


title: OT-1:pex cDC1 rep 1

description: [68] Normalized_FPKM.txt


title: AsiSI_IN_3_0h

description:
.bed files used to determine AsiSI cutting efficiency
IN_1_0h_TATAGCCTATTCAGAA


title: E12.5

description:
processed data file:
count.mtx, cell_names.csv (E12_1, E12_2), gene_names.csv
S2_L0001234
Zhang-XZ-2_S2


title: OT-1:pex cDC2 + IL-2 1ug/ml rep 2

description: [114] Normalized_FPKM.txt


title: E10.5

description:
processed data file:
count.mtx, cell_names.csv (E10_1, E10_2), gene_names.csv
S1_L0001234
Zhang-XZ-1_S1


title: OT-1:pex total cDC rep 2

description: [70] Normalized_FPKM.txt

value: co-culuted with OVA-laden peritoneal total cDCs for 3 days


title: AsiSI_IN_2_6h_2


title: AsiSI_IN_2_6h_1

description:
.bed files used to determine AsiSI cutting efficiency
IN_6h_AGGCGAAGAGCGATAG


title: OT-2:pex cDC2 rep 1

description: [77] Normalized_FPKM.txt


title: IP118/PY115 NTS (5745)

city: Hørsholm

first: Jens Christian

last: Nielsen

address: Hørsholm Kongevej

country: Denmark

institute: Gubra

data_processing:
bcl2fastq v 2.20.0.422 (basecalling)
STAR v2.5.2a (alignment)
Genome_build: GRCm38_89
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Nucleus of the solitary tract, brainstem

extract_protocol:
NucleoSpin Plus RNA columns (Macherey-Nagel)
Illumina TruSeq Stranded mRNA Library kit for NeoPrep (Illumina)

treatment_protocol: IP injection and sacrifice 4 hours later.  Brains were snap-frozen and sectioned to 10um.  Laser capture microsopy was utilized to isolate 4 mm^2 from each brain region per animal (PVN, NTS, ARC)

value: Brain

tag: tissue region


title: OT-1:pex total cDC rep 1

description: [67] Normalized_FPKM.txt


title: OT-1:pex cDC2 rep 2

description: [72] .txt


title: IP118/PY115 NTS (5744)

value: Nucleus of the solitary tract, brainstem


title: AsiSI_IN_2_2h


title: OT-2:pex total cDC rep 1

description: [75] Normalized_FPKM.txt


title: AsiSI_IN_2_0h_2


title: E15.5

description:
processed data file:
count.mtx, cell_names.csv (E15_1, E15_2), gene_names.csv
S4_L0001234
Zhang-XZ-4_S4


title: Vehicle NTS (5742)

value: Vehicle


title: Sample 3

city: Guangzhou

first: Yingfeng

last: Zheng

address: Jinsui Road No.7

department: Zhongshan Ophthalmic Centre

institute: Sun Yat-sen University

description: single-cell RNA

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software (v3.0.2).
Genome_build: GRCh38/macFas5/mm10.
Supplementary_files_format_and_content: Filtered feature-barcode matrices containing cellular barcodes in MEX format

source_name: central corneal epithelial cells

extract_protocol:
Human, monkey and mouse single cell suspensions in 0.4% BSA-PBS were processed for single-cell sequencing using the Chromium Single Cell 3’ Reagent Version 1 Kit and Chromium Controller (10xGenomics, CA, USA).
In each experiment, 20,000 cells per reaction were loaded for Gel Bead-in-Emulsion (GEM) generation in the GemCode instrument, followed by cell lysis, barcoded reverse transcription of RNA, cDNA amplification, shearing, adaptor and sample index attachment.
scRNA-Seq

treatment_protocol: The injury experiment was performed under in vivo condition for mouse and monkey eyes, and under ex vivo condition for human donor eyes. To mimic central corneal injury, an excimer laser (Allegretto Wave Eye-Q) was used to make a wounding by removing a small portion of the central epithelium and anterior stroma. The full thickness of the limbal epithelium and a layer of stroma beneath were excised to exclude the potential influence of limbal cells. Normal central corneas from contralateral eyes from the same donors without laser injury and limbal excision were used as uninjured controls.

value: central corneal epithelium

value: 24 hours after surgical injury


title: AsiSI_IN_2_0h_1

description:
.bed files used to determine AsiSI cutting efficiency
IN_0h_AGGCGAAGCGGCTATG


title: AsiSI_IN_2_4h


title: Vehicle NTS (5743)


title: Sample 4

description: single-cell RNA


title: Sample 1

description: single-cell RNA

value: Normal


title: Sample 2

description: single-cell RNA


title: IP118/PY115 NTS (5741)


title: IP118/PY115 NTS (5740)


title: AsiSI_IN_1_6h_1

description:
.bed files used to determine AsiSI cutting efficiency
IN__6h__GGCTCTGATCCGCGAA


title: muscle tissue, BI42

city: Évora

first: André

middle: Filipe Barreto

last: Albuquerque

address: Rua Ramalho Ortigao, 15

country: Portugal

institute: Universidade de Évora

data_processing:
Obtained sequence reads were trimmed for three consecutive times for Ilumina adapters, poli-A and poli-T tails using Trim Galore (version 0.5.0) while removing resulting low quality nucleotides (Phred Score, Q<20) and short length reads (<40).
Reads were aligned to the reference pig genome version Sscrofa11.1 (Ensembl release 94) using HISAT2 version 2.1.0
Generated SAM files were then converted to BAM with Samtools version 1.9
HTSeq-count version 0.11.1 was used to count and merge reads based on overlapping paired-end reads
Gcount files were run with the R package DESeq2 with a filtering of a minimum 50 reads per group. Genes were considered as differentially expressed when presenting a false discovery rate (FDR) lower than 0.05
Genome_build: reference pig genome version Sscrofa11.1 (Ensembl release 94)
Supplementary_files_format_and_content: csv file includes normalized abundance measurements, log2FoldChange and associated p-adjusted values

organism: Sus scrofa

source_name: muscle tissue

extract_protocol:
Muscle tissue samples were collected at slaughter. Total RNA was obtained through extraction following Ambion RiboPure Kit with Trizol and was stored at -80°C
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Bisaro

value: longissimus lumborum

tag: carcass weight


title: Vehicle NTS (5738)


title: Vehicle NTS (5739)


title: AsiSI_IN_1_4h


title: muscle tissue, BI36


title: muscle tissue, BI34


title: AsiSI_IN_1_2h


title: IP118/PY115 NTS (5737)


title: AsiSI_IN_1_0h_2


title: IP118/PY115 NTS (5736)


title: Vehicle NTS (5735)


title: muscle tissue, AL52

value: Alentejano


title: muscle tissue, BI25


title: AsiSI_IN_1_0h_1

description:
.bed files used to determine AsiSI cutting efficiency
IN__0h__GGCTCTGACTGAAGCT


title: muscle tissue, AL63


title: muscle tissue, AL49


title: IP118/PY115 NTS (5733)


title: AsiSI_H3_FLAG_2_4h

value: anti-FLAG beads (RRID:AB_2637089)


title: AsiSI_H3_FLAG_2_6h


title: Vehicle NTS (5734)


title: AsiSI_H3_FLAG_2_2h


title: muscle tissue, AL46


title: IP118/PY115 NTS (5732)


title: muscle tissue, AL44


title: AsiSI_IN_1_6h_2


title: muscle tissue, BI37


title: Vehicle NTS (5731)


title: AsiSI_H3_FLAG_1_6h


title: EXP_192: genomic DNA from lung adenocarcinoma 79

type: genomic

city: Taichung

first: Wei-Chung

last: Cheng

address: No. 91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

description: normal cervical sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio™ software

label: Cy3, Cy5

organism: Homo sapiens

source_name: genomic DNA from lung adenocarcinoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: lung adenocarcinoma

value: PR

tag: gender

value: Female

tag: Stage

tag: smoking

value: Never-smoker


title: AsiSI_H3_FLAG_1_4h

tag: strain


title: IP118/PY115 NTS (5729)

tag: treatment

tag: tissue


title: EXP_182: genomic DNA from lung adenocarcinoma 77

description: normal cervical sample


title: EXP_189: genomic DNA from lung adenocarcinoma 78

description: normal cervical sample


title: IP118/PY115 NTS (5728)


title: AsiSI_H3_FLAG_1_2h


title: Vehicle NTS (5727)


title: EXP_181: genomic DNA from lung adenocarcinoma 76

description: normal cervical sample


title: EXP_166: genomic DNA from lung adenocarcinoma 75

description: normal cervical sample

value: WT


title: AsiSI_H3_FLAG_1_0h


title: EXP_160: genomic DNA from lung adenocarcinoma 73

description: normal cervical sample


title: Vehicle NTS (5726)


title: EXP_165: genomic DNA from lung adenocarcinoma 74

description: normal cervical sample

value: Male


title: AsiSI_H3_2_4h

value: anti-H3 antibody (RRID:AB_2687473)


title: AsiSI_H3_2_6h


title: AsiSI_H3_2_2h


title: AsiSI_H3_2_0h


title: EXP_158: genomic DNA from lung adenocarcinoma 72

description: normal cervical sample

value: PD

value: smoker


title: Vehicle PVN (5555)

source_name: Paraventricular Nucleus, hypothelamus

value: Vehicle

value: Brain

value: Paraventricular Nucleus, hypothalamus


title: EXP_157: genomic DNA from lung adenocarcinoma 71

description: normal cervical sample


title: Vehicle Arc (5556)

source_name: Arcuate nucelus, hypothalamus

value: Arcuate nucelus, hypothalamus


title: AsiSI_H3_1_6h


title: EXP_153: genomic DNA from lung adenocarcinoma 70

description: normal cervical sample


title: AsiSI_H3_1_4h


title: Vehicle NTS (5730)

value: Nucleus of the solitary tract, brainstem


title: Vehicle PVN (5553)


title: Vehicle PVN (5554)


title: EXP_152: genomic DNA from lung adenocarcinoma 69

description: normal cervical sample


title: AsiSI_H3_1_2h


title: AsiSI_H3_FLAG_2_0h


title: EXP_151: genomic DNA from lung adenocarcinoma 68

description: normal cervical sample


title: IP118/PY115 Arc (5527)


title: IP118/PY115 Arc (5528)


title: Vehicle Arc (5557)


title: AsiSI_H2B_FLAG_2_6h


title: EXP_149: genomic DNA from lung adenocarcinoma 67

description: normal cervical sample

value: SD


title: IP118/PY115 Arc (5524)


title: AsiSI_H3_1_0h


title: EXP_142: genomic DNA from lung adenocarcinoma 66

description: normal cervical sample


title: Vehicle Arc (5522)


title: AsiSI_H2B_FLAG_2_2h


title: IP118/PY115 Arc (5523)


title: EXP_133: genomic DNA from lung adenocarcinoma 63

description: normal cervical sample


title: EXP_141: genomic DNA from lung adenocarcinoma 65

description: normal cervical sample


title: AsiSI_H2B_FLAG_2_4h


title: IP118/PY115 Arc (5520)


title: Vehicle Arc (5521)


title: AsiSI_H2B_FLAG_1_6h


title: EXP_126: genomic DNA from lung adenocarcinoma 62

description: normal cervical sample


title: IP118/PY115 Arc (5519)


title: EXP_121: genomic DNA from lung adenocarcinoma 61

description: normal cervical sample


title: AsiSI_H2B_FLAG_2_0h


title: EXP_118: genomic DNA from lung adenocarcinoma 60

description: normal cervical sample


title: Vehicle Arc (5517)


title: AsiSI_H2B_FLAG_1_0h


title: AsiSI_H2B_FLAG_1_2h


title: IP118/PY115 Arc (5516)


title: EXP_114: genomic DNA from lung adenocarcinoma 59

description: normal cervical sample


title: AsiSI_gH2A_2_6h

value: anti-H2A phospho Ser129 antibody (RRID:AB_492642)


title: EXP_134: genomic DNA from lung adenocarcinoma 64

description: normal cervical sample


title: AsiSI_gH2A_2_4h


title: Vehicle Arc (5514)


title: EXP_113: genomic DNA from lung adenocarcinoma 58

description: normal cervical sample


title: Vehicle Arc (5513)


title: EXP_106: genomic DNA from lung adenocarcinoma 56

description: normal cervical sample


title: AsiSI_gH2A_2_0h


title: EXP_110: genomic DNA from lung adenocarcinoma 57

description: normal cervical sample


title: IP118/PY115 Arc (5512)


title: IP118/PY115 Arc (5515)


title: AsiSI_H2B_FLAG_1_4h

value: anti-FLAG beads (RRID:AB_2637089)


title: AsiSI_gH2A_1_6h


title: EXP_105: genomic DNA from lung adenocarcinoma 55

description: normal cervical sample

value: lung adenocarcinoma


title: Vehicle Arc (5510)


title: AsiSI_gH2A_1_2h


title: EXP_97: genomic DNA from lung adenocarcinoma 53

description: normal cervical sample

value: PR


title: AsiSI_gH2A_1_4h


title: Vehicle Arc (5509)


title: AsiSI_gH2A_1_0h


title: EXP_92: genomic DNA from lung adenocarcinoma 51

description: normal cervical sample


title: IP118/PY115 PVN (5484)


title: EXP_93: genomic DNA from lung adenocarcinoma 52

description: normal cervical sample

value: Female


title: arp8_mut2_H2Az_6h

value: anti-H2A.Z antibody (RRID:AB_2793289)


title: IP118/PY115 PVN (5483)


title: arp8_mut2_H2Az_0h


title: EXP_89: genomic DNA from lung adenocarcinoma 50

description: normal cervical sample

value: Never-smoker


title: EXP_88: genomic DNA from lung adenocarcinoma 49

description: normal cervical sample

value: Male


title: AsiSI_gH2A_2_2h


title: EXP_86: genomic DNA from lung adenocarcinoma 48

description: normal cervical sample

value: WT


title: Vehicle PVN (5481)


title: Vehicle PVN (5482)


title: arp8_mut1_H2Az_6h


title: arp8_mut1_H2Az_0h


title: IP118/PY115 PVN (5479)


title: EXP_98: genomic DNA from lung adenocarcinoma 54

description: normal cervical sample

value: PD


title: arp8_ctr_H2Az_6h


title: IP118/PY115 PVN (5480)


title: IP118/PY115 Arc (5511)


title: EXP_85: genomic DNA from lung adenocarcinoma 47

description: normal cervical sample


title: arp8_ctr_H2Az_0h


title: EXP_84: genomic DNA from lung adenocarcinoma 46

description: normal cervical sample


title: EXP_79: genomic DNA from lung adenocarcinoma 44

description: normal cervical sample

value: smoker


title: EXP_81: genomic DNA from lung adenocarcinoma 45

description: normal cervical sample


title: IP118/PY115 PVN (5476)


title: Vehicle PVN (5477)

value: Vehicle


title: spo11Y135F_Pif1-Myc_ChIPseq_5h_replicate_1

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Reads were aligned to the Saccer2 version (SGD June 2008) of the S. cerevisiae S288C genome, using Bowtie, allowing for 2 mismatches. Reads that matched more than once in the genome or matching to mitochondrial or ribosomal DNA were eliminated from further analysis.
Aligned and extended paired-end reads were then normalized using a custom script as follows: for normalization, for the negative spo11Y135F control, the top and bottom outliers of the distribution (Q3+1.5IQR and Q1-1.5IQR, respectively) were removed. The average read number per position (coverage) of the remaining reads of the control was then normalized to 1 (scaled control). Similarly, top and bottom outliers of the distribution were removed from the average read number in the samples. Average coverage for the remaining reads was then calculated for the sample and control at the same positions. This was used to compute the sample/ control ratio. Then all reads of the sample were scaled using this ratio (scaled sample).
Both scaled sample and control were converted to big wig format, and the scaled control was substracted from the scaled sample, producing the "Pif1-Myc normalized spo11Y135F" files.
Signal smoothing was performed on the normalized control-subtracted bigwig files using a custom script employing fast Fourier transform convolution with a sliding window of either 200 or 2000 bp. The script is available upon request.
Genome_build: Saccer2
Supplementary_files_format_and_content: bigwile format files

source_name: SK1 meiotic cells t=5h (pCUP1-IME1-synchronized meiosis)

growth_protocol: For synchronous meiosis, cells were grown in "semi-YPD" then transferred to sporulation medium and induced to undergo meiosis upon Cu++ addition after two hours. Cells were collected after five hours in sporulation medium.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the Illumina TruSeq procedure.

treatment_protocol: 1. 109 cells were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold PBS, and chromatin immunoprecipitation was performed as described (Sanchez et al Methods Mol Biol. 2021;2153:295-306).

tag: genotype

value: c-Myc monoclonal antibody (9E10, Santa Cruz)


title: EXP_77: genomic DNA from lung adenocarcinoma 43

description: normal cervical sample


title: Pif1-Myc_ChIPseq_5h_replicate_2


title: EXP_76: genomic DNA from lung adenocarcinoma 42

description: normal cervical sample


title: Vehicle PVN (5473)

value: Brain

value: Paraventricular Nucleus, hypothalamus


title: Pif1-Myc_ChIPseq_5h_replicate_1


title: spo11Y135F_Pif1-Myc_ChIPseq_5h_replicate_2


title: IP118/PY115 PVN (5472)


title: IP118/PY115 PVN (5475)


title: IP118/PY115 PVN (5471)


title: EXP_75: genomic DNA from lung adenocarcinoma 41

description: normal cervical sample


title: EXP_73: genomic DNA from lung adenocarcinoma 40

description: normal cervical sample


title: EXP_69: genomic DNA from lung adenocarcinoma 39

description: normal cervical sample


title: Vehicle PVN (5470)


title: EXP_68: genomic DNA from lung adenocarcinoma 38

description: normal cervical sample


title: rpl11b∆ [DY135Ffx]

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description: Biological replicate of DY183Ffx. Wig files composed of combination of two biological replicates (DY135Ffx and DY183Ffx).

data_processing:
Multiple sequencing lanes were pooled together to create a single fastq file.
Base calling and demultiplexing was performed at the NIDDK DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD for samples run on theHiseq2500. Demultiplexing was performed using CutAdapt for samples run on the HiSeq3000.
Reads were aligned to a library of RNA genes and those not matching were retained.
Samples sequenced on the HiSeq3000 had PCR duplicates removed according to McGlincy and Ingolia, 2017.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files. Trimming of consecutive 3'As was not performed for 40S samples.
Replicates for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome). 26-45 nt 5' end aligned for 40S profiling and 25-34 nt 5' end aligned for 80S profiling.

source_name: rpl11b∆_whole cells

growth_protocol: Cells were grown to an OD of ~1.5 for 40S profiling or ~0.6 for 80S profiling and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, Rnase I treated, and separated over sucrose gradients to isolate either the 40S peak (40S profiling) or the monosome peak (80S profiling). RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription (rRNA was subtracted using Ribo-Zero after ligation for 40S profiling). cDNAs were then circularized and PCR amplified. (Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos for 80S profiling).
40S ribosome profiling; 80S ribosome profiling

treatment_protocol: Cells were cross-linked with formaldehyde for 1h, spun down, resuspended in lysis buffer, and beaded into liquid nitrogen for 40S profiling. Cells were rapidly vacuum filtered and flash frozen for 80S profiling. Samples were lysed in a freezer mill with lysis buffer.

tag: molecule subtype

value: 40S Ribosome-protected RNA 15-80 nt


title: IP118/PY115 PVN (5468)


title: EXP_66: genomic DNA from lung adenocarcinoma 37

description: normal cervical sample


title: tma64∆/tma22∆ [DY137Ffx]

description: Biological replicate of DY185Ffx. Wig files composed of combination of two biological replicates (DY137Ffx and DY185Ffx).

source_name: tma64∆/tma22∆_whole cells


title: WT [DY134Ffx]

description: Biological replicate of DY182Ffx. Wig files composed of combination of two biological replicates (DY134Ffx and DY182Ffx).

source_name: WT_whole cells


title: tma64∆/tma20∆ [DY136Ffx]

description: Biological replicate of DY184Ffx. Wig files composed of combination of two biological replicates (DY136Ffx and DY184Ffx).

source_name: tma64∆/tma20∆_whole cells


title: IP118/PY115 PVN (5467)


title: Vehicle PVN (5466)


title: EXP_65: genomic DNA from lung adenocarcinoma 36

description: normal cervical sample


title: H11

type: RNA

city: Jakarta Barat

first: Velma

last: Herwanto

state: DKI Jakarta

address: Perum. Sunrise Garden, Jalan Surya Mutiara III blok V no. 30

country: Indonesia

institute: Faculty of Medicine, Universitas Tarumanagara

hyb_protocol: One hundred nanograms of RNA from samples with RIN ≥7.0 was used for setting up the hybridization reaction. A standard nCounter Prep Station was set up on the workstation for post-hybridization processing.

scan_protocol: Sample cartridge was removed, sealed and loaded into the Digital Analyzer to be scanned. Data resolution was set to high (280 images per sample).

data_processing: nCounter data files (RCC files) were imported into the nSolver™ analysis software v4.0 (NanoString Technologies) for quality control and raw mRNA abundance frequencies analysis. Quality control was performed with the built-in negative and positive controls following recommendations by NanoString Technologies.

source_name: peripheral blood mononuclear cells

label_protocol: The TagSet consists of fluorescently-labeled specific Reporter Tags and a biotinylated universal Capture Tag. The universal Capture Tag enables hybridized complexes to be captured on the imaging surface.

extract_protocol: Total RNA was extracted using PAXgene Blood RNA Kit (QIAGEN) following the manufacturer's protocol

tag: code

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: healthy


title: Vehicle PVN (5465)


title: EXP_64: genomic DNA from lung adenocarcinoma 35

description: normal cervical sample

tag: age


title: bEnd3 Medium rep4

city: Martinsried

first: Gurumoorthy

last: Krishnamoorthy

institute: MPI Biochemie

data_processing:
BCL raw data were converted to FASTQ data and demultiplexed by bcl2fastq Conversion Software (20-40 million reads per sample)
Pseudoalignment and quantification were performed with kallisto (v0.46.1, Bray 2016 Nat Biotechnol; Mus musculus genome assembly version mm10/GRCm38 was used for building an index)
Gene-level abundance estimates were generated with tximport (v1.14.2) by transcripts-to-genes mapping based on the Ensembl v96 Mus musculus transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: Transcript-level abundances (as estimated counts and TPM) for each sample (kallisto output abundance.tsv files)
Supplementary_files_format_and_content: Matrix table with gene-level estimated counts

source_name: bEnd3 brain endothelial cells

growth_protocol: 3x10^5 bEnd3 cells were seeded in DMEM containing 10% FCS and cultured overnight prior to treatment

extract_protocol:
Total RNA was isolated using NucleoSpin RNA purification Mini kit (Macherey Nagel, Cat# 740955.250)
Libraries were prepared from 1 microgram of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7765, NEB) with NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB)

treatment_protocol: 5 uM corticosterone for 24 hours; collected cells were washed in PBS and the cell pellets were snap-frozen in liquid nitrogen

tag: cell type

value: brain endothelial cells

value: culture medium

tag: cell line


title: H10


title: H8


title: bEnd3 Medium rep3


title: EXP_62: genomic DNA from lung adenocarcinoma 34

description: normal cervical sample

value: lung adenocarcinoma


title: H7


title: EXP_60: genomic DNA from lung adenocarcinoma 32

description: normal cervical sample

value: PR


title: bEnd3 Medium rep2


title: EXP_61: genomic DNA from lung adenocarcinoma 33

description: normal cervical sample


title: H6


title: EXP_59: genomic DNA from lung adenocarcinoma 31

description: normal cervical sample


title: bEnd3 Medium rep1


title: EXP_58: genomic DNA from lung adenocarcinoma 30

description: normal cervical sample

value: Female


title: bEnd3 CORT rep4

value: 5 uM corticosterone for 24 hours


title: EXP_54: genomic DNA from lung adenocarcinoma 29

description: normal cervical sample

value: SD


title: H4


title: H3


title: bEnd3 CORT rep2


title: bEnd3 CORT rep3


title: EXP_50: genomic DNA from lung adenocarcinoma 27

description: normal cervical sample

value: Never-smoker


title: H1


title: bEnd3 CORT rep1


title: EXP_49: genomic DNA from lung adenocarcinoma 26

description: normal cervical sample

value: Male


title: P31

value: Prosthetic endocarditis, acute on chronic renal failure, AF

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: CVD, epilepsy, asbestosis, post AVR, CABG, aortic aneurism repair, hypercholesterolemia

value: #NULL!

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)

value: Staph. aureus (tip, tissue, aortic graft)

tag: culture_blood (0=negative, 1=positive, 99=not performed)

value: Staph. aureus

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: EXP_47: genomic DNA from lung adenocarcinoma 25

description: normal cervical sample

tag: tissue

tag: age

tag: gender

tag: Stage

tag: smoking


title: ERa_veh_CR_rep3

city: Boston

first: Bruno

last: Gegenhuber

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

data_processing:
Paired-end reads were trimmed to remove low-quality basecalls and adapters (cutadapt -q 30). Trimmed reads were aligned to mm10 using Bowtie2 with the following flags: --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 --minins 10 --maxins 700. After alignment, duplicate reads were removed using Picard MarkDuplicates. Read pairs with MAPQ < 40 (samtools view) and fragment length > 120 bp were removed (deeptools alignmentSieve). Read pairs aligning to the mitochondrial DNA or incomplete assemblies were also removed (samtools view). Peaks were called using MACS2 callpeak (q < 0.01). Filtered BAM files were normalized by coverage (bamCoverage -bs 1 --normalizeUsing CPM) to generate bigwig tracks.
Genome_build: mm10

source_name: Limbic system

growth_protocol: Animals were injected subcutaneously with 5 ug estradiol benzoate or vehicle (corn oil).

extract_protocol: Tissue was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer and mixed 1:1 with 50% OptiPrep solution (Millipore Sigma) prepared in Dilution Buffer (150 mM KCl, 30 mM MgCl2, 120 mM Tricine-KOH, pH 7.8). The homogenate was underlaid with 5 ml of 30% and 40% OptiPrep solution, respectively, and centrifuged at 10,000xg for 18 min at 4°C in an ultracentrifuge. ~2 ml of nuclei solution were removed from the 30 - 40% OptiPrep. interface by direct tube puncture. Following nuclei isolation, 0.4% IGEPAL CA-630 was added to improve binding to concanavalin A magnetic beads.  Takara SMARTer ThruPlex DNA-seq Kit

treatment_protocol: 10-12 week-old C57/BL6 males were gonadectomized to clear circulating hormones. 3 weeks post-gonadectomy, males were treated for 4 hr prior to nuclei isolation.

value: Brain

tag: Sex

tag: developmental stage

value: Adult


title: EXP_46: genomic DNA from lung adenocarcinoma 24

description: normal cervical sample

value: PD


title: EXP_42: genomic DNA from lung adenocarcinoma 23

description: normal cervical sample


title: P30

tag: code

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Biliary sepsis, viral gastroenteritis

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Thyroid nodule, endomteriosis, hyponatremia, GORD

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

value: Rhinovirus (PCR)


title: H5

tag: code

tag: age

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: healthy


title: ERa_EB_CR_rep3

tag: tissue

tag: developmental stage


title: CIA_ES-62

city: Glasgow

first: Margaret

middle: M

last: Harnett

address: 120 University Place

department: Infection, Immunity & inflammation

country: United Kingdom

institute: University of Glasgow

description: methylation profile

data_processing:
Data processing was performed by the commercial Active Motif Reduced Representation Bisulfite Sequencing (RRBS) single base pair resolution DNA methylation and bioinformatic service, which can provide further detail and custom script on request.
Briefly, Illumina adapter sequences were trimmed from the single-end 75 bp sequencing reads generated by Illumina NextSeq 500 sequencing before trimming of bases added during library generation to facilitate sequencing, using a custom script.
The resulting reads were then mapped to the genome using RRBSMAP (Xi et al. 2012  RRBSMAP: a fast, accurate and use- friendly alignment tool for reduced representation bisulphite sequencing. Bioinformatics 28:430) using default settings (12bp seed length, max number of mismatches = 0.08 x read length) retaining only unique alignments. Any PCR duplicates based on a randomized 6-mer barcode were removed and alignment information for the remaining reads stored in the resulting BAM files.
Genome_build: mm10
Supplementary_files_format_and_content: CpG_Gene_Score.txt. Methylation percentages for the Promoter 3K, Promoter 2K, Transcription Start Site (1000bp upstream to 1000bp downstream of TSS), 1st Exon-Intron and Gene Body (start of 5' UTR to end of 3' UTR) regions generated by GBSA 2.0 software ( Benoukraf et al. 2013 GBSA: a comprehensive software for analysing whole genome bisulphite sequencing data Nucl. Acids Res. 41:e55). Tab-dlineated txt files
Supplementary_files_format_and_content: Methratio.txt. Detailed representation of the methylation data at single base pair resolution generated by the RRBSMAP software. Tab-delineated txt file.

source_name: synovial fibroblasts

growth_protocol: Following digestion of joint tissue with collagenase IV, explant SFs representative of the treatment cohorts were pooled and cultured for 3 passages and then the cells were stored frozen in liquid nitrogen.

extract_protocol:
Genomic DNA (gDNA) was extracted from cells using the Quick-gDNA MiniPrep kit (Zymo Research D3024) following manufacturer’s instructions at Active Motif.
Library production was by the Ovation RRBS Methyl-Seq System (Tecan 0353-32) following manufacturer’s instructions. Digested  gDNA (TaqaI [NEB R0149] and MspI [NEB R0106]) was randomly ligated, and then after fragment end repair, bisulfite converted using the EpiTect Fast DNA Bisulfite Kit (Qiagen 59824). Following amplification by the Ovation RRBS Methyl-Seq System protocol, libraries were quantified using the Agilent 2200 TapeStation System and KAPA Library Quant Kit ABI Prism qPCR Mix (Roche KK4835). Libraries were sequenced using an Illumina NextSeq 500 at SE75.

tag: strain

tag: agent

value: CIA, treated with ES-62 at day-2, day 0 and day 21

tag: group

value: Suppressed Inflammation/Joint damage


title: P29

value: Sepsis, collection post Whipple procedure

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Hypercholesterolemia, cholecystectomy

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: creatinine

tag: billirubin

tag: crp

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)

tag: culture_blood (0=negative, 1=positive, 99=not performed)

value: E. coli

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: P27

tag: code

tag: age

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Abscess on the leg, pyoderma gangrenosum

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: IBD, anaemia, AKI

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet


title: Naïve

description: methylation profile

tag: strain

tag: agent

value: no CIA induction

tag: group

value: Healthy


title: CIA

description: methylation profile

value: CIA

value: Inflammation/Joint damage


title: EXP_41: genomic DNA from lung adenocarcinoma 22

description: normal cervical sample

tag: tissue

value: lung adenocarcinoma

value: PR

tag: age

tag: gender

value: Male

tag: Stage

tag: smoking

value: smoker


title: EXP_52: genomic DNA from lung adenocarcinoma 28

description: normal cervical sample

value: PD

value: WT

value: Female

value: Never-smoker


title: OT-2:pex total cDC rep 2

description: [86] Normalized_FPKM.txt

source_name: OT-2 cells

value: Spleen

value: post natal week 11

tag: treatement

value: co-culuted with OVA-laden peritoneal total cDCs for 3 days


title: LP_ab_P3: LP ab T cells high prot 3

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

institute: Seoul National University

description: polyA RNA-seq

data_processing:
Sequencing reads were aligned to the mm10 mouse transcriptome (GRCm38 ensembl; cDNA and ncRNA) and quantified by Kallisto (v0.45.0) with a k-mer index 25 and 60 bootstrapping (Bray et al., 2016).
The expression of transcript was calculated in TPM (transcript per million). When multiple transcripts match to the same gene, the expression of the gene is calculated by summing the TPM of all matched transcripts. TPM’s of 3–4 biological replicates were averaged for each sample.
Statistical analyses for differentially expressed genes were performed by Sleuth Pimentel et al., 2017).
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a tab-delimited file including transcript identifiers, length, expected count, and TPM

source_name: Lamina propria alphabeta T cells

growth_protocol: Female C57BL/6J animals aged 7-12 weeks were maintained under specific-pathogen free conditions and were euthanized by cervical dislocation at ZT8.

extract_protocol:
RNA was isolated from sorted T-cells using RNEasy Plus Micro Kit (Qiagen). RNA was isolated from epithelial cells using DirectZol RNA Miniprep Plus Kit with on-column DNAse digestion according to the manufacturer’s instructions (Zymo).
Library preparation for sorted T-cells performed using SMART-seq2 protocol. Sequencing libraries for epithelial cells were constructed using Illumina TruSeq Library Prep Kit and sequenced on Illumina NextSeq 500 (38 x 38 bp paired-end run).

treatment_protocol: Animals were fed Envigo high carb (TD170403) or high protein (TD170405) diet for 5 days.

value: Wildtype C57BL/6J

tag: Sex

value: female

tag: diet

value: High protein diet

tag: surface marker

tag: cell type

value: Lamina propria alphabeta T cells


title: EXP_38: genomic DNA from lung adenocarcinoma 20

description: normal cervical sample


title: H2

tag: code

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: healthy


title: P26

value: Urosepsis

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: MS, OSA, CVI, recurrent UTI

value: #NULL!

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: creatinine

tag: billirubin

tag: crp

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)

tag: culture_blood (0=negative, 1=positive, 99=not performed)

value: E. coli

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: LP_ab_P4: LP ab T cells high prot 4

description: polyA RNA-seq

tag: strain

tag: Sex

tag: diet

tag: surface marker

tag: cell type


title: LP_ab_P2: LP ab T cells high prot 2

description: polyA RNA-seq


title: EXP_37: genomic DNA from lung adenocarcinoma 19

description: normal cervical sample

tag: tissue

value: lung adenocarcinoma

tag: age

tag: gender

tag: Stage

tag: smoking


title: P25

tag: code

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Ascending cholangitis due to choledocholythiasis

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Extensive diverticular disease, Iron deficiency anaemia, chronic kidney failure

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp


title: LP_ab_P1: LP ab T cells high prot 1

description: polyA RNA-seq

tag: strain

tag: Sex

tag: diet

tag: surface marker

tag: cell type


title: EXP_34: genomic DNA from lung adenocarcinoma 18

description: normal cervical sample

tag: tissue

value: PR

tag: age

tag: gender

value: Male

tag: Stage

tag: smoking

value: smoker


title: P24

tag: code

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Diverticulitis with septic shock, ishemic hepatitis

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Cholecystectomy

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)

tag: culture_blood (0=negative, 1=positive, 99=not performed)

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: P23

tag: code

tag: age

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Pneumonia

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: DM on metformin, HTN, epilepsy, peripheral neuropathy, OSA

tag: vassopressor (0=no, 1=yes)

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

value: Bordetella pertussis serology


title: EXP_33: genomic DNA from lung adenocarcinoma 17

description: normal cervical sample

tag: tissue

value: PD

tag: age

tag: gender

tag: Stage

tag: smoking

value: Never-smoker


title: EXP_26: genomic DNA from lung adenocarcinoma 16

description: normal cervical sample


title: P28

tag: code

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Pneumonia CAP and upper respiratory tract infection

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

value: Gout, dyslipidemia

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)

value: Rhinovirus (PCR)

tag: culture_blood (0=negative, 1=positive, 99=not performed)

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: P21

tag: code

tag: age

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Septic shock, enterocolitis, epilepsy, hypoalbuminemia, , psoriasis

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Cerebral abscess, schizophrenia, epilepsy, rhabdomyolysis, cholecystectomy

tag: vassopressor (0=no, 1=yes)

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

value: #NULL!


title: EXP_39: genomic DNA from lung adenocarcinoma 21

description: normal cervical sample

tag: tissue

value: lung adenocarcinoma

value: SD

value: WT

tag: age

tag: gender

value: Female

tag: Stage

tag: smoking


title: P19

tag: code

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Sepsis, ischemic colitis

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

value: IHD, CABG, HTN, hypercholesterolemia, hernia repair

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)

tag: culture_blood (0=negative, 1=positive, 99=not performed)

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: P20

tag: code

tag: age

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Septic shock,Urosepsis, pyelonephritis

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Depression

tag: vassopressor (0=no, 1=yes)

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

value: E. coli


title: D1-Cre-flTrkB-RT_no_stereotypy rep1

city: Baltimore

first: yang

last: song

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner
Reads counts were calculated for each sample.
Differential expression of genes were computed between spinner, non spinner and cre samples
Genome_build: M. musculus (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include counts per million reads (CPM) for each sample

extract_protocol:
Polyribosome immunoprecipitation with HA-coupled magnetic beads (Invitrogen: 100.03D; Covance: MMS-101R). RNA extraction with RNeasy Micro kit (Qiagen: 74004).
D1-Cre-flTrkB-RT IP RNA-seq libraries were prepared in biological triplicates from dorsal striatum tissue using the NEBNext Ultra kit (New England BioLabs)

tag: strain background

tag: genotype/variation

tag: age

tag: tissue

value: Dorsal Striatum

tag: cell type

value: D1-medium spiny neuron (enriched)

tag: polyribosome ip tag

value: RiboTag (HA)


title: D1-Cre-flTrkB-RT_no_stereotypy rep3


title: D1-Cre-flTrkB-RT_no_stereotypy rep2


title: LP_ab_C1: LP ab T cells high carb 1

description: polyA RNA-seq

tag: strain

value: Wildtype C57BL/6J

tag: Sex

value: female

tag: diet

value: High carbohydrate diet

tag: surface marker

value: Lamina propria alphabeta T cells


title: P17

tag: code

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Infective endocarditis, acute limb ishemia + splenic infarc due to septic emboli

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Typhoid

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: procalcitonin

value: #NULL!

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)

tag: culture_blood (0=negative, 1=positive, 99=not performed)

value: Streptococcus sangunis

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: EXP_21: genomic DNA from lung adenocarcinoma 14

description: normal cervical sample

tag: tissue

value: lung adenocarcinoma

value: SD

tag: age

tag: gender

value: Female

tag: Stage

tag: smoking

value: Never-smoker


title: EXP_20: genomic DNA from lung adenocarcinoma 13

description: normal cervical sample

value: PR

value: Male

value: smoker


title: D1-Cre-flTrkB-RT_stereotypy rep3

tag: strain background

tag: genotype/variation

value: Dorsal Striatum

tag: cell type

value: D1-medium spiny neuron (enriched)

tag: polyribosome ip tag


title: IEL_ab_P4: IEL ab T cells high prot 4

description: polyA RNA-seq

source_name: Intraepithelial alphabeta T cells

tag: strain

value: Wildtype C57BL/6J

tag: Sex

tag: diet

value: High protein diet

tag: surface marker

value: Intraepithelial alphabeta T cells


title: D1-Cre-flTrkB-RT_stereotypy rep2

value: RiboTag (HA)


title: LP_ab_C4: LP ab T cells high carb 4

description: polyA RNA-seq

value: female

value: High carbohydrate diet

value: Lamina propria alphabeta T cells


title: IEL_ab_P2: IEL ab T cells high prot 2

description: polyA RNA-seq


title: EXP_19: genomic DNA from lung adenocarcinoma 12

description: normal cervical sample

value: PD

value: WT


title: IEL_ab_P3: IEL ab T cells high prot 3

description: polyA RNA-seq


title: P14

tag: code

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: CCF + NSTEMI, pneumonia,DVT lower limb, pulmonary edema, UTI, acute on chronic AKI

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: OSA, recurrent UTI, gout, CCF cardio

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

tag: procalcitonin

value: #NULL!

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)


title: P22

tag: code

tag: age

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Seizure from epilepsy, pneumonia (viral?), rapid AF

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

value: Rhinovirus (PCR)

tag: culture_blood (0=negative, 1=positive, 99=not performed)

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: D1-Cre-flTrkB-RT_stereotypy rep1

tag: strain background

tag: genotype/variation

tag: age

tag: tissue

tag: cell type

tag: polyribosome ip tag


title: EXP_18: genomic DNA from lung adenocarcinoma 11

description: normal cervical sample

value: lung adenocarcinoma

value: PR

tag: gender

value: Female

tag: Stage

tag: smoking

value: smoker


title: P13

tag: code

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: UTI, pneumonia, immunosuppressed (on prednison and MTX)

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: HTN, AVR, hypercholesterolemia, IHD, RA

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)

value: E. coli


title: LP_ab_C3: LP ab T cells high carb 3

description: polyA RNA-seq

tag: strain

value: Wildtype C57BL/6J

tag: Sex

value: female

tag: diet

tag: surface marker

tag: cell type


title: LP_ab_C2: LP ab T cells high carb 2

description: polyA RNA-seq

value: High carbohydrate diet

value: Lamina propria alphabeta T cells


title: EXP_25: genomic DNA from lung adenocarcinoma 15

description: normal cervical sample

tag: tissue

value: PD

value: WT

tag: age

tag: gender

value: Male

tag: Stage

tag: smoking


title: IEL_ab_P1: IEL ab T cells high prot 1

description: polyA RNA-seq

value: High protein diet

value: Intraepithelial alphabeta T cells


title: D1-Cre-RT-rep3

tag: strain background

tag: genotype/variation

value: control (D1-Cre-RT)

value: Dorsal Striatum

value: D1-medium spiny neuron (enriched)

tag: polyribosome ip tag

value: RiboTag (HA)


title: EXP_15: genomic DNA from lung adenocarcinoma 10

description: normal cervical sample

value: lung adenocarcinoma

value: smoker


title: IEL_ab_C4: IEL ab T cells high carb 4

description: polyA RNA-seq


title: EXP_14: genomic DNA from lung adenocarcinoma 9

description: normal cervical sample

value: Female

value: Never-smoker


title: P12

tag: code

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Pneumonia

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Lymphoma on chemo, gout, HTN, hypercholesterolemia, barrett oesophagus

value: #NULL!

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

tag: culture_blood (0=negative, 1=positive, 99=not performed)

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: IEL_ab_C3: IEL ab T cells high carb 3

description: polyA RNA-seq

tag: strain

value: Wildtype C57BL/6J

tag: Sex

value: female

tag: diet

value: High carbohydrate diet

tag: surface marker

tag: cell type


title: P11

tag: code

tag: age

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Sepsis, bilateral pleural effusion, delirium, chest pain, AF, vit D deficiency

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Lower respiratory tract infection, AF, vitamin D deficiency, IHD, OA

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)


title: EXP_11: genomic DNA from lung adenocarcinoma 8

description: normal cervical sample

tag: tissue

value: PR

tag: age

tag: gender

value: Male

tag: Stage

tag: smoking


title: D1-Cre-RT-rep1

tag: strain background

tag: genotype/variation

value: control (D1-Cre-RT)

value: Dorsal Striatum

tag: cell type

tag: polyribosome ip tag


title: EXP_9: genomic DNA from lung adenocarcinoma 7

description: normal cervical sample


title: P16

tag: code

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Sepsis, pneumonia

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Coarctasio aorta, GORD, smoker

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

tag: culture_blood (0=negative, 1=positive, 99=not performed)

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: IEL_ab_C2: IEL ab T cells high carb 2

description: polyA RNA-seq

tag: strain

tag: Sex

tag: diet

tag: surface marker

tag: cell type

value: Intraepithelial alphabeta T cells


title: IEL_ab_C1: IEL ab T cells high carb 1

description: polyA RNA-seq


title: EXP_8: genomic DNA from lung adenocarcinoma 6

description: normal cervical sample

tag: tissue

value: lung adenocarcinoma

value: PD

value: WT

tag: age

tag: gender

tag: Stage

tag: smoking


title: EXP_7: genomic DNA from lung adenocarcinoma 5

description: normal cervical sample

value: SD

value: smoker


title: EXP_6: genomic DNA from lung adenocarcinoma 4

description: normal cervical sample

value: Female

value: Never-smoker


title: LP_gd_P3: LP gd T cells high prot 3

description: polyA RNA-seq

source_name: Lamina propria gammadelta T cells

value: Wildtype C57BL/6J

value: female

value: High protein diet

value: Lamina propria gammadelta T cells


title: EXP_4: genomic DNA from lung adenocarcinoma 3

description: normal cervical sample

value: PR

value: Male


title: EXP_2: genomic DNA from lung adenocarcinoma 2

description: normal cervical sample


title: LP_gd_P2: LP gd T cells high prot 2

description: polyA RNA-seq


title: LP_gd_C3: LP gd T cells high carb 3

description: polyA RNA-seq

value: High carbohydrate diet


title: P6

tag: code

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Vomitng, CKD, cholelithiasis

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: on CAPD, IgA nephropathy, HTN, depression, GORD

value: #NULL!

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)


title: P8

tag: code

tag: age

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Aspiration pneumonia, pleural effusion

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Myasthenia gravis, HTN

tag: vassopressor (0=no, 1=yes)

tag: creatinine

tag: billirubin

tag: crp

tag: culture_blood (0=negative, 1=positive, 99=not performed)

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: P5

tag: code

tag: age

value: Sepsis, cellulitis and abscess lower limb, URTI, ARF, hypercalcemia

value: HTN, MS, depression, hypothyroidism, GORD, endometrial hyperplasia

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)


title: LP_gd_C2: LP gd T cells high carb 2

description: polyA RNA-seq

tag: strain

tag: Sex

tag: diet

tag: surface marker

tag: cell type


title: D1-Cre-RT-rep2

tag: strain background

tag: genotype/variation

value: control (D1-Cre-RT)

tag: age

tag: tissue

value: Dorsal Striatum

value: D1-medium spiny neuron (enriched)

tag: polyribosome ip tag

value: RiboTag (HA)


title: EXP_1: genomic DNA from lung adenocarcinoma 1

description: normal cervical sample

value: lung adenocarcinoma

value: PD

value: WT

tag: gender

value: Female

tag: Stage

tag: smoking

value: Never-smoker


title: P4

tag: code

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Celluitis lower limb

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: AF. Parkinson, peripheral neuropathy

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

tag: culture_blood (0=negative, 1=positive, 99=not performed)

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: LP_gd_C1: LP gd T cells high carb 1

description: polyA RNA-seq

tag: strain

value: Wildtype C57BL/6J

tag: Sex

value: female

tag: diet

value: High carbohydrate diet

tag: surface marker

tag: cell type

value: Lamina propria gammadelta T cells


title: P10

tag: code

tag: age

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Sepsis, celulitis

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: AKI suspected ATN, HTN, dyslipidemia

value: #NULL!

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)

value: Streptococcus pyogenes


title: P9

tag: code

tag: age

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Sepsis, urosepsis, DM

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

value: Fibromyalgia, HTN, dyslipidemia

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

value: E. coli

tag: culture_blood (0=negative, 1=positive, 99=not performed)

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: IEL_gd_P4: IEL gd T cells high prot 4

description: polyA RNA-seq

source_name: Intraepithelial gammadelta T cells

tag: strain

tag: diet

value: High protein diet

tag: surface marker

tag: cell type

value: Intraepithelial gammadelta T cells


title: IEL_gd_P3: IEL gd T cells high prot 3

description: polyA RNA-seq

tag: Sex


title: P1

tag: code

tag: age

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Sepsis, pulmonary edema, drowsy, psoas abscess, NSTEMI, DM

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: Benzodiazepine and methadone +, smoking, hepatitis C, acute liver injury

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)

value: P. aeuroginosa


title: P2

tag: code

tag: age

tag: Sex

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Sepsis, hepatic abscess, urosepsis

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

value: DM on metformin, HTN, hypercholesterolemia, adrenal lesion, hiatus hernia

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

value: K. pneumoniae (urine), S. haemolyticus (liver)

tag: culture_blood (0=negative, 1=positive, 99=not performed)

value: Streptococcus, Parvimonas micra

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: P7

tag: code

tag: age

value: Acute tonsilitis

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: icu_admit (0=no, 1=yes)

tag: los

tag: mortal_inhosp (0=no, 1=yes)

tag: mortal_28d (0=no, 1=yes)

tag: readmit_28d (0=no, 1=yes)

tag: hb

tag: leukocyte

tag: procalcitonin

tag: lactate

tag: culture_from_infection_source  (0=negative, 1=positive, 99=not performed)


title: LP_gd_P1: LP gd T cells high prot 1

description: polyA RNA-seq

tag: strain

value: Wildtype C57BL/6J

tag: Sex

value: female

tag: diet

tag: surface marker

tag: cell type

value: Lamina propria gammadelta T cells


title: OCExo-BLK SeraExo#3

city: Hong Kong SAR

first: Jin

last: Liu

address: 7 Baptist University Road, Kowloon Tong

department: TMBJ

institute: Hong Kong Baptist University

description:
Osteoclast-exosome blockage
SAMPLE 6

data_processing:
The normalization and all the data analysis was performed using the manufacturer's qPCR analysis templates https://systembio.com/wp-content/uploads/Mouse_miRNome_v14_2.xls
For the normalization it uses the Spike-in control RNA.
Target miRNA signals were normalized to the average Spike-in control RNA signals; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_control average)]
All deltadeltaCt based fold-change were calculated from the uploaded raw threshold cycle data automatically by the templates.

label: SYBR Green

source_name: Serum exosomes

label_protocol: Reverse transcription was performed using the Mouse Complete SeraMir Exosome RNA Amplification and Profiling Kit (System Biosciences) according to the manufacturer's instructions. Real-time qPCR was performed (Applied Biosystems ViiA7) using standard run conditions (40 cycles at 95oC for 15 seconds and 60oC for 60 seconds.)

growth_protocol: The mice with osteoclast-exosome blockage and control mice with intact osteoclast-exosome at 2w after ACLT.

extract_protocol: Exosomal RNA was extracted with the SeraMir Exosome RNA Column Purification Kit (System Biosciences) according to the manufacturer's instructions.

treatment_protocol: The exosomes were isolated from serum of OCExo-BLK or OCExo-Intact mice.

tag: sample type

value: Exosomes


title: OCExo-BLK SeraExo#2

description:
Osteoclast-exosome blockage
SAMPLE 5


title: IEL_gd_P1: IEL gd T cells high prot 1

description: polyA RNA-seq


title: IEL_gd_C4: IEL gd T cells high carb 4

description: polyA RNA-seq

value: High carbohydrate diet


title: OCExo-BLK SeraExo#1

description:
Osteoclast-exosome blockage
SAMPLE 4


title: P3

tag: code

tag: age

tag: diagnosis_category (0 = healthy controls, 1=sepsis, 2=uncomplicated infection)

value: Sepsis, celulitis, dysphagia, abdominal pain, DM

tag: source_infection (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: source_infection_2 (0=unknown, 1=respiratory tract, 2=urinary tract, 3=abdominal/liver/biliary tract, 4=skin and soft tissue, 5=ent, 6= intracranial, 7=cardiovascular, 8=bone/joint, 9=pelvic)

tag: diabetes (0=no, 1=yes)

tag: chronic_kidney (0=no, 1=yes)

tag: respiratory_disease (0=no, 1=yes)

tag: cardiovascular (0=no, 1=yes)

tag: malignancy (0=no, 1=yes)

value: DM on insulin and metformin

tag: vassopressor (0=no, 1=yes)

tag: rhesus (0=no, 1=yes)

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: platelet

tag: creatinine

tag: billirubin

tag: crp

value: #NULL!

tag: culture_blood (0=negative, 1=positive, 99=not performed)

tag: etiology (1=bacterial, 2=viral, 3=coinfection, 4=not defined)

tag: sofa_admit_cat (0= <2; 1=≥2)


title: OCExo-Intact SeraExo#3

description:
Osteoclast-exosome intact
SAMPLE 3

tag: sample type


title: D707rna_D502rna

city: Cambridge

first: Pierre

last: Larraufie

address: Box 289, Addenbrooke's Site

department: WT-MRC Institute of Metabolic Science

institute: Metabolic Research Laboratories and MRC Metabolic Diseases Unit

data_processing:
data was demultiplexed using the Casava pipeline
data was mapped to the mouse genome GRCm38 using STAR v2.5.1 and raw counts generated simultaneously
Supplementary_files_format_and_content: Dye_Guca2a_raw_count.csv  is a csv file of number of counts for ensembl gene ids of each biological sample

source_name: Jejunum

growth_protocol: mice were grown on a 12h dark/light cycle with ad libitum access to water and standard chow

extract_protocol:
epithelium was single-cell digested and FACS sorted for GFP positive and neagative cells (excludin dead cells (DAPI pos), debris (Draq5 neg) and immune cells (CD45 pos)). RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer
10ng of RNA was used for library contruction using the SMARTer stranded total RNAseq kit v2 pico kit (Takara)
RNAseq SE-50 on an Illumina HiSEQ 4000

tag: strain

tag: tissue

value: Jejunum

tag: genotype/variation

value: GFP positive


title: D709rna_D502rna

source_name: Ileum

value: Ileum


title: D712rna_D502rna

source_name: Colon

value: Colon

value: GFP negative


title: D708rna_D502rna


title: IEL_gd_C3: IEL gd T cells high carb 3

description: polyA RNA-seq

tag: Sex

tag: diet

tag: surface marker

tag: cell type

value: Intraepithelial gammadelta T cells


title: D711rna_D502rna


title: IEL_gd_P2: IEL gd T cells high prot 2

description: polyA RNA-seq

value: High protein diet


title: IEL_gd_C2: IEL gd T cells high carb 2

description: polyA RNA-seq


title: D706rna_D502rna

source_name: Duodenum

value: Duodenum


title: IEL_gd_C1: IEL gd T cells high carb 1

description: polyA RNA-seq


title: OCExo-Intact SeraExo#2

description:
Osteoclast-exosome intact
SAMPLE 2


title: OCExo-Intact SeraExo#1

description:
Osteoclast-exosome intact
SAMPLE 1


title: D710rna_D502rna


title: D705rna_D502rna


title: IEC_P4: IEC high prot 4

description: polyA RNA-seq

source_name: Intestinal epithelial cells

value: Intestinal epithelial cells


title: OCExoInhib SeraExo#3

description:
OCExoInhib treatment
SAMPLE 6

data_processing:
The normalization and all the data analysis was performed using the manufacturer's qPCR analysis templates https://systembio.com/wp-content/uploads/Mouse_miRNome_v14_2.xls
For the normalization it uses the Spike-in control RNA.
Target miRNA signals were normalized to the average Spike-in control RNA signals; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_control average)]
All deltadeltaCt based fold-change were calculated from the uploaded raw threshold cycle data automatically by the templates.
Fold Change worksheet reports test/control (i.e., OCExoInhib/Vehicle) ratios.

growth_protocol: The mice with OCExoInhib treatment and control mice with vehicle treatment at 2w after ACLT.

treatment_protocol: The exosomes were isolated from serum of OCExoInhib-treated mice or Vehicle-treated mice.


title: D704rna_D502rna


title: IEC_P3: IEC high prot 3

description: polyA RNA-seq

value: Wildtype C57BL/6J


title: D703rna_D502rna


title: D702rna_D502rna


title: IEC_P2: IEC high prot 2

description: polyA RNA-seq

value: female


title: IEC_P1: IEC high prot 1

description: polyA RNA-seq


title: OCExoInhib SeraExo#1

description:
OCExoInhib treatment
SAMPLE 4


title: Vehicle SeraExo#3

description:
Vehicle treatment
SAMPLE 3


title: D701rna_D502rna


title: Vehicle SeraExo#2

description:
Vehicle treatment
SAMPLE 2


title: D712rna_D501rna


title: IEC_C4: IEC high carb 4

description: polyA RNA-seq


title: D711rna_D501rna


title: OCExoInhib SeraExo#2

description:
OCExoInhib treatment
SAMPLE 5