title: Bird_Blue-042_MG-protein_Day0

description:
ES73_Blue-042_MG-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: High protein diet


title: Input_DIP_rep1

status: Public on Aug 29 2024

type: SRA

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: Input DNA, replicate 1

library_source: genomic

data_processing:
Sample demultiplexing was performed using Illumina's bcl2fastq Conversion Software v.1.8.4 and read quality was checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequence reads were aligned to the Xenopus tropicalis genome assembly version 7.1 (https://ftp.xenbase.org/pub/Genomics/JGI/Xentr7.1) using weighted multi-mapping strategy employing bowtie2 v.2.2.7 (http://bowtie-bio.sourceforge.net/bowtie2) with default parameters.
Normalized bigWig coverage tracks were generated from the mapped reads extended to average fragment size using deepTools bamCoverage v.2.5.1 (https://deeptools.readthedocs.io/) with parameters “--normalizeUsing RPKM --extendReads 250”.
Assembly: Xenopus tropicalis v.7.1 (JGI7.1)
Supplementary files format and content: bigWig coverage tracks with RPKM normalization
Library strategy: DIP-seq

molecule: genomic DNA

organism: Xenopus tropicalis

source_name: blastula stage 9 embryos

extract_protocol:
Genomic DNA from stage 9 Xenopus tropicalis embryos was extracted using the DNeasy Blood and Tissue kit (Qiagen). 15 µg DNA was sheared to around 200 bp using a Covaris S2/E210 focused ultrasonicator. 5 pg of 5mC, 5hmC, 5fC or control unmodified amplicon were spiked in and the samples were brought to 450 μl with nuclease-free water. 5% sample was kept aside as input control. DNA was denatured for 10 min at 95°C and cooled immediately on ice. Samples were incubated in IP buffer (100 mM Na-Phosphate pH 7, 1.4 M NaCl, 0.5% Triton X-100) and 3 µg antibody overnight at 4°C with overhead shaking. Antibodies used: 5mC (MAb-5MECYT-100, Diagnode), 5hmC (39791, Active Motif), 5fC (61227, Active Motif), 5caC (61229, Active Motif) and IgG (ab46540, Abcam). Dynabeads Protein G (10004D, Thermo Scientific) were pre-washed with 0.1% BSA, PBS and resuspended in IP buffer. 40 μl Dynabeads per sample were added and the samples were incubated at 4°C for 2 h with overhead shaking. Dynabeads were collected in a magnetic rack, washed 3x in IP buffer, resuspended in Proteinase K digestion buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS) and Proteinase K (0.3 mg/ml final concentration) was added. Samples were incubated for 3 h at 50°C and DNA was purified with phenol/chloroform followed by ethanol precipitation.
Library preparation was performed with Swift Bioschiences's Accel-NGS 1S Plus DNA Library Kit following Accel-NGS 1S Plus DNA Library Kit Reference Guide (15-0300, 08/15). Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies). All samples were pooled in equimolar ratio and sequenced on 4 HiSeq 2500 Rapid Flowcells, SR mode with 59 cycles plus 2x8 cycles for dual index reads.

tag: tissue

value: blastula stage 9 embryos

tag: dip antibody


title: Bird_Blue-039_Control-lipid_Day21

city: Fayetteville

first: Carson

middle: Len

last: Stacy

state: AR

address: 850 W. Dickson St. Rm 601

department: Biological Sciences

country: USA

institute: University of Arkansas

description:
ES72_Blue-039_Control-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

library_source: transcriptomic

data_processing:
nf-core rnaseq version 3.10.1 pipeline was utilized with Nextflow version 22.10.3 [parameters: -profile singularity  --featurecounts_group_type transcript_biotype --skip_markduplicates --aligner star_rsem --pseudo_aligner salmon]
Adapter trimming performed with TrimGalore! v 0.6.7 [parameters: nf-core default]
Mapping to genome performed with STAR v 2.7.10a  [parameters: nf-core default]
Counts estimated from genes with RSEM v 1.3.1 [parameters: --strandedness reverse]
Differential expression was performed in EdgeR using expected counts and the quasi-liklihood (QL) framework with Benjamini-Hochberg FDR correction. Genes with less than 0.5 count per million (CPM) in more than 12 samples were excluded from the analysis.
Assembly: serCan2020
Supplementary files format and content: All files are tab delimited text files. One file is the STAR-RSEM gene count output (serinus_canaria_rsem.merged.gene_counts.tsv) and the other is the STAR-RSEM gene tpm values (serinus_canaria_rsem.merged.gene_tpm.tsv)

molecule: polyA RNA

organism: Serinus canaria

source_name: Whole blood

growth_protocol: Canaries were housed individually in cages and provided with either a high protein (n = 20) or high lipid (n = 22) diet for 17 days prior to inoculation and throughout the experiment. On day 0, birds were inoculated in the palpebral conjunctiva of both eyes with either 0.025 mL of MG suspended in Frey’s media or with a sham of Frey’s media alone.

extract_protocol:
Zymo Direct-zol RNA Miniprep with TRI Reagent phase separation
NEXTflex™ Rapid Directional RNA-Seq Kit 2.0

treatment_protocol: RNAlater was added to blood samples immediately upon collection. Samples were stored at 20°C for 24 hr then at -80°C until extraction. Canary RNA was extracted from whole blood on days 0, 14, and 21 post infection

value: Whole blood

tag: subject

tag: time

value: Day 21

tag: disease

value: Unexposed

tag: treatment

value: high lipid diet


title: NMP_037, POST, TP [259_S203]

city: Innsbruck

first: Theresa

last: Hautz

address: Anichstr. 45

department: Department of Visceral, Transplant and Thoracic Surgery

country: Austria

institute: Medical University of Innsbruck

data_processing:
Adapters were trimmed using BBDuk according to recommendations (Lexogen, Austria) and quality checked using FastQC.
Reads were mapped to the human reference genome (GRCh38/hg38) using the splice aware aligner STAR (v2.7.1a). Note, since  the specific 3'  sequencing libraries used here, only forward reads were mapped and all reverse reads were discarded since provide only limited information.
Read counts for NCBI Gene/Refseq annotation were detrmined using featureCounts (v2.0.0)
Differentially expressed genes were determined using DESeq2 based on raw counts and a negative binomial distribution
Data were normalized using DESeq2 and log-transformed (rlog).
Assembly: hg38
Supplementary files format and content: tab delimited txt file include raw counts for each sample (raw_counts.txt)
Supplementary files format and content: tab delimited txt file include log2 transformed normalized counts adding a pseudocount of 1 (DESeq2) for each sample (log2_normalized_counts_1.txt)

molecule: total RNA

organism: Homo sapiens

source_name: liver

extract_protocol:
Cryopreserved liver biopsies were homogenized using the ULTRA Turrax IKA T10 basic. Total RNA was extracted according to the Rneasy Micro Kit (Qiagen, Netherlands). RNA integrity was determined using a 2100 Bioanalyzer and RNA 6000 Nano LabChip kits (Agilent Technology, USA).
QuantSeq 3'protocol (Lexogen, Austria) according to manufacturers's recommendations

treatment_protocol: Grafts were flushed with 2000 ml histidin-tryptophan-ketoglutarate, surgically prepared for NMP and connected to the OrganOc metra® device.

value: liver

tag: transplantation

value: yes

value: POST

value: normothermic machine perfusion


title: NMP_048, POST, TP [267_S208]


title: 5caC_DIP_rep3

description: 5caC DIP, replicate 3


title: Bird_Blue-039_Control-lipid_Day14

description:
ES71_Blue-039_Control-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 14


title: Bird_Blue-039_Control-lipid_Day0

description:
ES70_Blue-039_Control-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 0


title: NMP_036, POST, TP [258_S202]


title: NMP_034, POST, TP [257_S201]


title: HaCaT cells, WT, rep1

city: ZÜRICH

first: Luca

last: Ferrarese

state: Zürich

address: Otto-Stern-Weg 7, HPL F23.2

department: Institute of Molecular Health Sciences (IMHS)

country: Switzerland

institute: ETH Zürich

data_processing:
The raw reads were first cleaned by removing adapter sequences and poly-x sequences (> 9 nt used for detection) using fastp (Version 0.20.0) [fastp].
Sequence pseudo alignment of the resulting high-quality reads to the Human reference genome (build GRCh38.p13) and quantification of gene level expression (gene model definition from GENCODE release 37) was carried out using Kallisto (Version 0.46.1) [Kallisto].
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: HaCaT cells

growth_protocol: Low-passage HaCaT keratinocytes (Boukamp et al., 1988) were cultured in high-glucose Dulbecco’s Modified Eagle Medium® (DMEM, Thermo Fisher Scientific, Waltham, MA) supplemented with 10% FBS (Life Technologies, Carlsbad, CA) under standard conditions at 37°C with 5% CO2.

extract_protocol:
Cells were lysed in RB lysis buffer, and stored at -80°C until further use. RNA extraction was performed using the Mini Total Tissue RNA kit (IBI Scientific, Dubuque, IO), including a DNase digestion step.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA (Illumina, Inc, California, USA) following manufacturer's protocols.

tag: cell line

value: HaCaT cells

tag: cell type

value: Keratinocyte

tag: genotype

value: WT


title: Bird_164_Control-protein_Day21

description:
ES6_164_Control-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-037_MG-protein_Day14

description:
ES68_Blue-037_MG-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Exposed


title: 5caC_DIP_rep1

description: 5caC DIP, replicate 1


title: 5caC_DIP_rep2

description: 5caC DIP, replicate 2


title: Bird_Blue-043_MG-lipid_Day0

description:
ES76_Blue-043_MG-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_SEM19-1481_MG-lipid_Day21

description:
ES64_SEM19-1481_MG-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: 5fC_DIP_rep3

description: 5fC DIP, replicate 3


title: NMP_032, POST, TP [256_S200]


title: 5fC_DIP_rep2

description: 5fC DIP, replicate 2


title: Bird_Blue-035_MG-protein_Day21

description:
ES63_Blue-035_MG-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_106_NA_Day0

description:
ES65_106_NA_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_617_Control-protein_Day14

description:
ES66_617_Control-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_029, POST, TP [255_S199]


title: Bird_Blue-035_MG-protein_Day14

description:
ES62_Blue-035_MG-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: 5fC_DIP_rep1

description: 5fC DIP, replicate 1


title: NMP_028, POST, TP [254_S198]


title: Bird_Blue-035_MG-protein_Day0

description:
ES61_Blue-035_MG-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_164_Control-protein_Day14

description:
ES5_164_Control-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: 5hmC_DIP_rep3

description: 5hmC DIP, replicate 3


title: Bird_Blue-037_MG-protein_Day21

description:
ES69_Blue-037_MG-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-032_MG-protein_Day14

description:
ES59_Blue-032_MG-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-032_MG-protein_Day21

description:
ES60_Blue-032_MG-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_026, POST, TP [252_S196]


title: 5hmC_DIP_rep2

description: 5hmC DIP, replicate 2


title: Bird_Blue-032_MG-protein_Day0

description:
ES58_Blue-032_MG-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-037_MG-protein_Day0

description:
ES67_Blue-037_MG-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-031_MG-lipid_Day0

description:
ES57_Blue-031_MG-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: 5hmC_DIP_rep1

description: 5hmC DIP, replicate 1


title: Bird_Blue-050_Control-lipid_Day21

description:
ES56_Blue-050_Control-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_022, POST, TP [250_S194]


title: Bird_SEM19-74_MG-protein_Day21

description:
ES55_SEM19-74_MG-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: 5mC_DIP_rep3

description: 5mC DIP, replicate 3


title: NMP_019, POST, TP [249_S193]


title: TAMs_rep2

type: RNA

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

country: China

institute: West China Hospital

description: circRNA expression profile of TAMs

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

scan_protocol: Raw images were obtained using Agilent Scanner G5761A (Agilent).

data_processing: Raw data were extracted using Feature Extraction (Agilent), followed by normalization using the quantile algorithm, Genespring (Agilent). Limma package in R (v.3.2.2) was employed to compare the differential expressions of circRNAs and mRNAs between matched profiles, followed by false discovery rate (FDR) correction using Benjamini and Hochberg’s approach.

source_name: macrophages

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA of macrophages and HCC cells was extracted and purified using a RNeasy Maxi kit (Qiagen) according to the manufacturer’s instructions. EVs-derived RNA extraction was performed using exoRNeasy Maxi kit (Qiagen) according to the manufacturer’s instructions. The purity, concentration and integrity were analyzed using NanoDrop ND-2000 (Thermo) and Agilent Bioanalyzer 2100 system (Agilent).

value: tumor-associated macrophages

tag: intervention

value: from human HCC tissues


title: Bird_SEM19-74_MG-protein_Day14

description:
ES54_SEM19-74_MG-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: High protein diet


title: Bird_SEM19-74_MG-protein_Day0

description:
ES53_SEM19-74_MG-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Whole blood


title: NMP_017, POST, TP [248_S192]


title: Bird_SEM19-1481_MG-lipid_Day14

description:
ES52_SEM19-1481_MG-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-024_Control-protein_Day21

description:
ES51_Blue-024_Control-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 21


title: Bird_Blue-024_Control-protein_Day14

description:
ES50_Blue-024_Control-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Unexposed


title: 5mC_DIP_rep2

description: 5mC DIP, replicate 2

value: blastula stage 9 embryos


title: NMP_016, POST, TP [247_S191]

value: liver


title: NMP_027, POST, TP [253_S197]

value: yes


title: 5mC_DIP_rep1

description: 5mC DIP, replicate 1


title: Bird_164_Control-protein_Day0

description:
ES4_164_Control-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: C,RRV,TCR,S6

first: Scott

last: Handley

state: MO

address: 660 S Euclid Ave

institute: Washington University in St.Louis

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing,barcode processing,gene counting and aggregation were made using Cell Ranger software v2.1.1 (https://bioinformatics-core-shared-training.github.io/UnivCambridge_ScRnaSeq_Nov2021/Markdowns/03_CellRanger.html)
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Popliteal lymph node

extract_protocol:
For the RRV and LCMV samples, cells from the popliteal draining lymph node of infected mice were pooled. For the naive sample, cells were pooled from uninfected wild type and P14 transgenic mouse draining lymph nodes. A portion of each sample was enriched for transgenic CD8+ T cells by magnetic bead negative selection and fluorescence-activated cell sorted for the CD45.2 congenic marker and added to the bulk sample at a 1:4 ratio.
Approximately 20,000 cells per sample were subjected to gel bead-in-emulsion (GEM) generation, reverse transcription, and construction of libraries for sequencing according to the protocol provided in the Chromium Single Cell 5' Reagent Kit v2 with TCR enrichment manual (10X Genomics). Briefly, cDNA was prepared after GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13 cycles before clean-up using SPRI select beads (Beckman Coulter, B23318). Samples were then run on a Bioanalyzer to determine cDNA concentrations. Gene expression libraries (GEX libraries) were prepared as recommended by the 10x Genomics Chromium Single Cell 5' Reagent Kit v2 with TCR enrichment user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Single Cell 5' Reagent Kit v2 with TCR enrichment, Chromium Next GEM Chip G Single Cell Kit, and Dual Index Kit TT Set A were used.  The concentration of each library was determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow according to manufacturer protocol. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

value: Popliteal lymph node

tag: developmental age

tag: strain

value: B6 and B6;D2-TCR LCMV (adoptive transfer)

value: CD45.1 and CD45.2 respectively

value: 1x10^3 FFU RRV-gp33 via footpad


title: Bird_Blue-024_Control-protein_Day0

description:
ES49_Blue-024_Control-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 0


title: NMP_023, POST, TP [251_S195]

value: POST

value: normothermic machine perfusion


title: NMP_013, POST, TP [245_S189]


title: NMP_014, POST, TP [246_S190]


title: Bird_Blue-45_MG-protein_Day14

description:
ES48_Blue-45_MG-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 14

value: Exposed


title: Bird_Blue-45_MG-protein_Day0

description:
ES47_Blue-45_MG-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-015_MG-lipid_Day14

description:
ES45_Blue-015_MG-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: high lipid diet


title: A,Naïve,TCR,S2

description: 10x Genomics

value: B6 and B6;D2-TCR LCMV

value: Uninfected


title: NMP_012, POST, TP [244_S188]


title: Bird_Blue-013_Control-protein_Day21

description:
ES43_Blue-013_Control-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Whole blood

value: Day 21

value: High protein diet


title: Bird_Blue-015_MG-lipid_Day0

description:
ES44_Blue-015_MG-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Unexposed


title: NMP_011, POST, TP [243_S187]

value: liver

value: yes


title: Bird_Blue-013_Control-protein_Day0

description:
ES41_Blue-013_Control-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-013_Control-protein_Day14

description:
ES42_Blue-013_Control-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_LD19-239_MG-lipid_Day14

description:
ES39_LD19-239_MG-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Htr2b ko mice3, HFD

city: Buk-gu, Gwangju

first: Suhyeon

last: Park

state: Gwangju

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호

country: South Korea

institute: GIST

data_processing:
kallisto
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes estimated counts for each sample

source_name: Quadriceps

growth_protocol: 8 weeks aged wild type and Htr2b KO mice were fed 60 HFD for 12 weeks.

extract_protocol:
RNA was harvested usging pure total RNA Extraction kit (INfusiontech, RPG1010).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Sample Prep Kit following manufacturer's protocols.

value: Quadriceps

value: skeletal muscle cells

value: Htr2b knockout

value: HFD


title: NMP_008, POST, TP [240_S185]

value: POST


title: Htr2b ko mice4, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: NMP_010, POST, TP [242_S186]

value: normothermic machine perfusion


title: Htr2b ko mice2, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: NMP_007, POST, TP [239_S184]


title: Bird_LD19-239_MG-lipid_Day21

description:
ES40_LD19-239_MG-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_AR17-21_MG-lipid_Day21

description:
ES38_AR17-21_MG-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_48_Control-lipid_Day21

description:
ES3_48_Control-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Htr2b ko mice1, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: B,LCMV,TCR,S4

description: 10x Genomics

value: Popliteal lymph node

value: B6 and B6;D2-TCR LCMV (adoptive transfer)

value: CD45.1 and CD45.2 respectively

value: 1x10^3 PFU LCMV Armstrong via footpad


title: Bird_AR17-21_MG-lipid_Day14

description:
ES37_AR17-21_MG-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 14

value: Exposed

value: high lipid diet


title: Bird_AR17-21_MG-lipid_Day0

description:
ES36_AR17-21_MG-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Whole blood

value: Day 0


title: NMP_002, POST, TP [235_S183]

value: liver


title: Bird_101-LS_MG-lipid_Day21

description:
ES35_101-LS_MG-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 21


title: Bird_Blue-015_MG-lipid_Day21

description:
ES46_Blue-015_MG-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: wild type mice4, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호

value: Quadriceps

value: WT


title: wild type mice3, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호

value: skeletal muscle cells


title: NMP_001, POST, TP [234_S182]

value: yes


title: Bird_101-LS_MG-lipid_Day0

description:
ES33_101-LS_MG-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Unexposed


title: wild type mice2, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호

value: HFD


title: Bird_Blue-055_NA_Day14

description:
ES32_Blue-055_NA_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_049, 24H, NTP [232_S180]

value: no

value: normothermic machine perfusion


title: wild type mice1, HFD

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: Bird_Blue-098_Control-lipid_Day21

description:
ES30_Blue-098_Control-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-055_NA_Day0

description:
ES31_Blue-055_NA_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_045, 24H, TP [228_S178]


title: Bird_619_MG-lipid_Day21

description:
ES27_619_MG-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_48_Control-lipid_Day14

description:
ES2_48_Control-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_619_MG-lipid_Day14

description:
ES26_619_MG-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_038, 24H, TP [223_S174]


title: Lens epithelium, replicate 2, scRNAseq

city: Stony Brook

first: David

last: McKinnon

state: New York

address: Nichols Rd

institute: Stony Brook University

description: 10x Genomics

data_processing:
Demultiplexing, alignment and gene count analysis were performed using CellRanger (10x Genomics)
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Lens epithelium

extract_protocol:
Lenses were dissected from 4 to 8 P2 wild-type C57BL/6N mouse pups, cleaned of the ciliary body and tunica vasculosa using fine forceps and then by digestion in 0.05% trypsin-EDTA for 10 minutes at 37°C and 5% CO2. Transferred to ice-cold Tyrode’s solution for 10 minutes then the lens capsule with the adhering epithelial monolayer was peeled off the remaining fiber cell mass using fine forceps and transferred to a tube containing 100 µL of Ca2+Mg2+-free DPBS on ice. 100 µL of 0.1% Collagenase/Dispase Blend was added, incubated at 37°C for 5 minutes. 1 mL of 0.5% trypsin-EDTA was added. Trypsinization was monitored until the majority of cells were present as single cells. MEM supplemented with 10% fetal bovine serum was added, and cells centrifuged for 5 minutes at 230 rcf. The cell pellet was washed at 4°C in DPBS containing 0.04% RNase-free BSA. Final pellet was resuspended in DPBS/0.04% RNAse-free BSA to a cell density of 1500 to 2500 cells per microliter, filtered using a 20-µm cell mini-strainer.
scRNA-seq libraries were generated using the Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Cells, gel beads, and partitioning oil were loaded onto a Chromium Next GEM Chip G, for a target recovery of 10,000 cells per sample. The chip was processed in a Chromium Controller. After reverse transcription using a GEM–reverse transcription (RT) incubation protocol on a PCR cycler, GEMs were broken using Recovery Agent, and the cDNA was purified with DynaBeads MyOne Silane beads, amplified with PCR for 11 cycles, and further purified with SPRIselect magnetic beads. After fragmentation, end repair, A-tailing, and size selection purification, the cDNA was ligated with adaptors and purified again with SPRISselect beads. Libraries were amplified using PCR with sample index oligonucleotides from the Chromium i7 Multiplex Kit, for a total of 10 or 11 PCR cycles. The final PCR products were subjected to double-sided size selection with SPRISselect beads (0.6× and 0.8×).

value: Lens epithelium

value: wild-type

tag: age


title: Bird_Blue-098_Control-lipid_Day14

description:
ES29_Blue-098_Control-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 14


title: Bird_Blue-010_Control-lipid_Day21

description:
ES24_Blue-010_Control-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_Blue-098_Control-lipid_Day0

description:
ES28_Blue-098_Control-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_036, 24H, TP [221_S173]


title: Bird_619_MG-lipid_Day0

description:
ES25_619_MG-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_034, 24H, TP [220_S172]


title: Bird_Blue-010_Control-lipid_Day0

description:
ES23_Blue-010_Control-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_618_Control-lipid_Day21

description:
ES22_618_Control-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_618_Control-lipid_Day0

description:
ES20_618_Control-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_101-LS_MG-lipid_Day14

description:
ES34_101-LS_MG-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Exposed


title: Microglia, invitro, WT, 6h, rep1

city: Hannover

first: Ulrich

last: Kalinke

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Institute for Experimental Infection Research

institute: Twincore, Centre for Experimental and Clinical Infection Research

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control of the sequenced raw FASTQ-files was performed with FastQC software (version 0.11.9) and mapped to Ensembl mouse genome reference version GRCm38 (mm10) using STAR (version 2.5.4b). Gene abundance was also determined by STAR. Differential expression analysis was performed using DESeq2 package in R environment (version 1.26.0).
Assembly: mm10
Supplementary files format and content: Matrix table with raw counts for every gene and there corresponding Ensembl ID

source_name: Brain

extract_protocol:
The RNA from microglia culture was isolated using Direct-zol RNA Miniprep Plus Kit following manufactures instruction. RNA quality and concentrations were accessed using Bioanalyzer RNA kit and samples with RIN value >8.0 were selected for further processing.
RNA libraries for RNA-seq were prepared using NEBNext Low input RNA library Prep Kit for Illumina (NEB, E6420) following manufacturer's protocols.

value: Brain

value: Microglia

value: Wild type

value: infected


title: Microglia, invitro, WT, 6h, rep2


title: Microglia, invitro, WT, 6h, rep3


title: Lens epithelium, replicate 1, scRNAseq

description: 10x Genomics


title: Bird_615_Control-protein_Day14

description:
ES18_615_Control-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Whole blood

value: High protein diet


title: Microglia, invitro, WT, 4h, rep2


title: NMP_033, 24H, NTP [219_S171]

value: liver


title: Bird_618_Control-lipid_Day14

description:
ES21_618_Control-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: high lipid diet


title: Bird_615_Control-protein_Day0

description:
ES17_615_Control-protein_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 0


title: Microglia, invitro, WT, 4h, rep1


title: NMP_026, 24H, TP [214_S167]

value: yes


title: Bird_615_Control-protein_Day21

description:
ES19_615_Control-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 21

value: Unexposed


title: Microglia, invitro, WT, 2h, rep3


title: Bird_48_Control-lipid_Day0

description:
ES1_48_Control-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_039, 24H, TP [224_S175]

value: normothermic machine perfusion


title: NMP_028, 24H, TP [216_S169]


title: Bird_601_Control-protein_Day21

description:
ES16_601_Control-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Microglia, invitro, WT, 2h, rep1


title: NMP_027, 24H, TP [215_S168]


title: Bird_209_MG-lipid_Day14

description:
ES13_209_MG-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_601_Control-protein_Day14

description:
ES15_601_Control-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_024, 24H, NTP [213_S166]

value: no


title: Bird_209_MG-lipid_Day21

description:
ES14_209_MG-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_172_Control-protein_Day21

description:
ES11_172_Control-protein_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Microglia, invitro, WT, 2h, rep2


title: Microglia, invitro, KO, 8h, rep3

value: Mavs-/-


title: Bird_172_Control-protein_Day14

description:
ES10_172_Control-protein_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Day 14


title: Microglia, invitro, WT, 4h, rep3


title: Bird_625_Control-lipid_Day14

description:
ES104_625_Control-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_032, 24H, TP [218_S170]


title: Bird_625_Control-lipid_Day21

description:
ES105_625_Control-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_023, 24H, TP [212_S165]


title: Bird_SEM19-140_Control-lipid_Day21

description:
ES102_SEM19-140_Control-lipid_21
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Microglia, invitro, KO, 8h, rep2


title: NMP_022, 24H, TP [211_S164]


title: Microglia, invitro, KO, 8h, rep1


title: NMP_021, 24H, NTP [210_S163]


title: Bird_SEM19-140_Control-lipid_Day14

description:
ES101_SEM19-140_Control-lipid_14
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_209_MG-lipid_Day0

description:
ES12_209_MG-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: Bird_SEM19-140_Control-lipid_Day0

description:
ES100_SEM19-140_Control-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv


title: NMP_020, 24H, NTP [209_S162]


title: Microglia, invitro, KO, 6h, rep3


title: NMP_019, 24H, TP [208_S161]


title: 190 PV/N 22000479 epithelium

city: Jefferson

first: Elijah

middle: F

last: Edmondson

state: MD

address: 4310 Mountville Rd

institute: Frederick National Laboratory for Cancer Research

description: FFPE (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

data_processing:
Raw data was evaluated in R (version 4.1.2). ROI segment and probe quality control (QC) was performed according to NanoString’s Whole Transcriptome Atlas Normalization guidelines. ROI QC was performed using the GeomxTools (V3.2.0) package. ROIs were flagged using the following settings: raw reads threshold 1000 reads, percent trimmed 80%, percent stitched 80%, percent aligned reads 80%, percent sequencing saturation 50%, negative probe count geomean 1, no template PCR control count > 60, minimum nuclei 20, and minimum surface area of 1000 µm². Of the 190 AOIs, one was flagged for a low negative probe count and low sequencing alignment. Probe QC was performed with default settings excluding probes from target count calculation in all segments if (geomean probe in all segments)/(geomean probes within target) ≤ 0.1 and if it fails Grubbs’ outlier test in ≥20% of the segments. The limit of quantification (LOQ) was calculated using two SDs of the geomean of the negative probes. Quartile 3 count (Q3) normalization was performed to account for technical effects between AOIs. Gene filtering was used to filter and select only genes detected in at least 10% of AOIs. Following QC, the resulting gene expression matrix consisted of 189 AOIs that passed QC and a total of 14,882 genes. Q3-normalised expression data was exported from the DSP Analysis Suite. Dimension-reduction of the expression matrix was performed using t-Distributed Stochastic Neighbor Embedding by R package Rtsne (V.0.16), umap (V.0.2.10.0), and visualized using ggplot2 (V.3.4.3).
Sequences were aligned to mm10 genome using Space Ranger default settings
Assembly: mm10
Supplementary files format and content: Mm_R_NGS_WTA_v1.0.pkc
Library strategy: Spatial Transcriptomics

source_name: uterus

extract_protocol:
Slides were processed within 5 days after the microtomy for the NanoString GeoMx DSP RNA assay following the GeoMx NGS Slide Preparation User Manual (NanoString, MAN-10 115-04). After 30 min baking at 60oC, dewaxing, heat-induced epitope retrieval (ER2 for 20 min at 100oC) and proteinase K treatment (1 mg/mL proteinase K in 1X phosphate-buffered saline (PBS) at 37°C for 15 min) was performed on Leica Biosystems BOND RX according to the FFPE RNA Slide Preparation Protocol. Slides were hybridized with the GeoMx Whole Transcriptome Atlas Mouse RNA for Illumina Panel (GMX[1]RNA-NGSMsWTA) overnight at 37oC, followed by a series of stringent washes and morphology staining: Syto 13 for nuclei, pancytokeratin- AF532 to visualize epithelial cells and smooth muscle actin (aSMA-AF647) to visualize stroma. The staining was visualized on the GeoMx DSP instrument using a 20X objective on FITC, CY3, Texas Red and CY5 channels. A total of 190 regions of interest (ROI) were selected from 13 mouse uterus sections (6 Thra1 PV/+ and 7 wild-type mice), which included endometrial mucosa, glands, and stroma; a minimum of 5 ROIs were taken per category per mouse. Annotations were selected by a board-certified veterinary pathologist based on morphology and marker staining using HALO (Indica Labs). ROI masks were imported to the GeoMx and used to guide UV light cleavage of the barcode linkers of the prebound RNA probes in each area of illumination, and the cleaved probes were deposited in DSP collection plates.
Library construction and sequencing (NextSeq2000) was performed according to Nanostring’s Guidelines at the Genomics Core (OSTR, CCR). Processed data was uploaded to the DSP analysis suite for visualization and quality control while detailed data analysis was performed using an R-package from Nanostring.

value: uterus

value: Uterus epithelium

value: PV/N


title: 189 PV/N 22000479 epithelium


title: 188 N/N 23002886 stroma

value: Uterus stroma

value: N/N


title: 191 PV/N 22000479 epithelium


title: NMP_018, 24H, NTP [207_S160]


title: 186 N/N 23000283 stroma


title: Microglia, invitro, KO, 6h, rep1

value: Brain

value: Microglia

value: infected


title: 187 N/N 23002886 epithelium


title: Bird_625_Control-lipid_Day0

description:
ES103_625_Control-lipid_0
serinus_canaria_rsem.merged.gene_counts.tsv
serinus_canaria_rsem.merged.gene_tpm.tsv

value: Whole blood

value: high lipid diet


title: 185 N/N 22002823 epithelium


title: Microglia, invitro, KO, 4h, rep3


title: Microglia, invitro, KO, 6h, rep2


title: 183 N/N 22002823 stroma


title: 182 N/N 22002823 stroma


title: NMP_016, 24H, TP [205_S158]

value: liver

value: yes


title: NMP_015, 24H, NTP [204_S157]


title: 184 N/N 22002823 stroma


title: Microglia, invitro, KO, 4h, rep2


title: Microglia, invitro, KO, 4h, rep1


title: 180 N/N 23000283 stroma


title: Microglia, invitro, KO, 2h, rep3


title: 179 N/N 22002823 epithelium


title: 178 N/N 22002823 epithelium


title: NMP_013, 24H, TP [202_S155]


title: 177 N/N 22002823 epithelium


title: Microglia, invitro, KO, 2h, rep2


title: NMP_017, 24H, TP [206_S159]


title: NMP_010, 24H, TP [199_S154]


title: Microglia, invitro, KO, 2h, rep1


title: 175 N/N 23000283 epithelium


title: 174 N/N 23000283 epithelium


title: 173 N/N 22000478 stroma


title: Microglia, invitro, KO, mock, rep3

value: mock


title: Microglia, invitro, KO, mock, rep2


title: 168 N/N 22000478 epithelium


title: 167 N/N 22000478 epithelium


title: 181 N/N 23000283 stroma


title: NMP_014, 24H, TP [203_S156]

value: normothermic machine perfusion


title: NMP_007, 24H, TP [196_S152]


title: 170 N/N 22000478 stroma


title: NMP_005, 24H, TP [194_S151]


title: NMP_003, 24H, NTP [192_S150]

value: no


title: 172 N/N 22000478 stroma


title: Microglia, invitro, KO, mock, rep1

value: Mavs-/-


title: 169 N/N 22000478 epithelium


title: 165 N/N 22000478 epithelium


title: 166 N/N 22000478 epithelium


title: NMP_002, 24H, TP [191_S149]


title: PTEN KO MycCap Tumors, IgG + MKC8866

city: Oslo

first: Fahri

last: Saatcioglu

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

description: Singleron GEXSCOPE

data_processing:
The sequencing reads were aligned to mouse reference Grcm38 genome and Singleron Celescope tool (https://github.com/singleron-RD/CeleScope) were used to generate the gene expression matrices.
Assembly: Grcm38
Supplementary files format and content: Matrix Count Files

source_name: Prostate Cancer

growth_protocol: Myc-CaP cells were purchased from ATCC and cultured in DMEM supplemented with 10% fetal bovine serum (FBS), penicillin and streptomycin. Cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Freshly dissected tumor samples were washed with PBS and transferred into GEXSCOPE Tissue Preservation Solution (Singleron), and stored on ice. Six tumor samples from each group were pooled for scRNA-seq. The tissue samples were then washed with Hanks balanced salt solution three times and minced into small pieces which were digested with Tissue Dissociation Solution (Singleron) at 37 °C for 15 min with agitation. After digestion, cells were passed through a 40 μm strainer to remove cell debris and centrifuged at 300 × g for 5 min. The supernatant was removed and cell pellet was resuspended in 1 ml PBS, followed by red blood cell lysis using RBC lysis buffer. Next, cells were centrifuged at 500 × g for 5 min and resuspended in PBS.
The single cell suspension was adjusted to a concentration of 1 × 105 / ml for library preparation. This was loaded onto microfluidics chips (GEXSCOPE Single Cell RNA-seq Kit, Singleron Biotechnologies) and GEXSCOPE 3´SD scRNAseq libraries were prepared according to manufacturer instructions (Singleron Biotechnologies).

treatment_protocol: PTEN knock-out (KO) Myc-CaP cell lines were generated by CRISPR Cas9 system using a guide RNA (gRNA) (5’-GCTAACGATCTCTTTGATGA-3’) targeting PTEN. 0.5 million Myc-CaP PTEN KO cells were injected into both hind flanks of FVB mice.  When the tumors were palpable, mice were randomized and either treated with vehicle (0.5% w/v hydroxypropyl-methylcellulose dissolved in water plus 0.2% v/v Tween-80, adjusted to pH 4.0) or MKC8866 (150 mg/kg) by oral gavage every other day. After 3 days of initial MKC8866 treatment, mice were treated weekly with either 10 mg/kg of PD-1 (ichorbio # ICH1132UL) or IgG isotype control (ichorbio # ICH2244UL) antibodies by intraperitoneal injection (IP). Tumors were harvested at the end of the experiment.

value: Prostate Cancer

value: Myc-CaP

value: Mouse Prostate Cancer Cell Line Xenograft

value: PTEN KO

value: IgG + MKC8866


title: PTEN KO MycCap Tumors, anti-PD1  + MKC8866

description: Singleron GEXSCOPE

value: anti-PD1  + MKC8866


title: 164 N/N 22000478 epithelium

value: uterus

value: Uterus epithelium

value: N/N


title: 176 N/N 22002823 epithelium


title: 163 N/N 22000478 epithelium


title: NMP_008, 24H, TP [197_S153]


title: 162 N/N 22000478 epithelium


title: 161 N/N 22000478 epithelium


title: 171 N/N 22000478 stroma

value: Uterus stroma


title: PTEN KO MycCap Tumors, anti-PD1 + Vehicle

description: Singleron GEXSCOPE

value: anti-PD1 + Vehicle


title: 160 N/N 23000283 stroma


title: PTEN KO MycCap Tumors, IgG + Vehicle

description: Singleron GEXSCOPE

value: IgG + Vehicle


title: NMP_049, 12H, NTP [188_S146]

value: liver


title: 158 N/N 23000283 epithelium


title: NMP_048, 12H, TP [231_S179]

value: yes


title: 157 PV/N 22000479 stroma

value: PV/N


title: 154 PV/N 22000479 stroma


title: NMP_044, 12H, TP [185_S144]

value: normothermic machine perfusion


title: 156 PV/N 22000479 epithelium


title: C5aR1-/-, biological replicate 7

city: Boston

first: Markus

last: Bosmann

state: MA

address: 72 E Concord Street

department: Pulmonary Centre, Department of Medicine

institute: Boston University

data_processing:
The FASTQ reads were aligned to the Mus musculus reference genome (Gencode version M32; GRCm39) using STAR aligned (version 2.7.10b).
The aligned reads were indexed and sorted using samtools (version 1.12) and quantified with the featureCounts function of the subread (version 2.0.3) software.
Exploratory data analysis and differential expression analysis were performed using DESeq2 (version 1.38.3) using the counts data, after excluding the Gencode suffix from the Ensembl IDs of the mouse genes. False Discovery Rate was set to 0.05
Assembly: Mus musculus: GRCm39; Gencode version M32
Supplementary files format and content: tab-delimited text file includes raw counts as input matrix to DESeq2 (this file excludes the Gencode suffix): Nippo_C5ar1KO_rawCounts.txt

source_name: Neutrophils

extract_protocol:
RNA was extracted using QIAGEN RNAeasy Plus micro kit.
RNA libraries were constructed following the ultra-low input protocol and paired-end sequencing (150 bp) was performed by Novogene (Sacramento, CA, USA)

value: Neutrophils

tag: Sex

value: male

value: Infection with Nippostrongylus brasiliensis


title: C5aR1-/-, biological replicate 8


title: 155 PV/N 22000479 stroma


title: C5aR1-/-, biological replicate 9


title: C5aR1-/-, biological replicate 6


title: NMP_001, 24H, TP [190_S148]


title: NMP_050, 12H, TP [189_S147]


title: NMP_040, 12H, TP [183_S143]


title: C5aR1-/-, biological replicate 5


title: 149 N/N 22002827 epithelium


title: NMP_037, 12H, TP [182_S142]


title: 150 N/N 22002827 epithelium


title: NMP_035, 12H, NTP [181_S141]

value: no


title: 148 N/N 22002827 stroma


title: 159 N/N 23000283 epithelium


title: 151 N/N 22002827 stroma


title: C5aR1-/-, biological replicate 4


title: 147 N/N 22002827 epithelium


title: C5aR1-/-, biological replicate 3


title: 145 PV/N 22000487 epithelium


title: C5aR1-/-, biological replicate 2


title: 144 N/N 22002827 epithelium


title: NMP_031, 12H, NTP [179_S139]


title: 152 PV/N 22000479 epithelium


title: 153 PV/N 22000479 epithelium


title: NMP_045, 12H, TP [186_S145]


title: C5aR1-/-, biological replicate 1


title: 142 PV/N 22000487 epithelium


title: NMP_032, 12H, TP [180_S140]


title: 143 PV/N 22000487 stroma


title: NMP_029, 12H, TP [178_S138]


title: wild type, biological replicate 8

value: wild type


title: 140 PV/N 22000487 epithelium


title: 141 PV/N 22000487 stroma


title: 139 N/N 22000480 epithelium


title: NMP_028, 12H, TP [177_S137]


title: wild type, biological replicate 7


title: wild type, biological replicate 6


title: NMP_026, 12H, TP [176_S136]


title: 136 N/N 22000480 stroma


title: 137 N/N 22000480 epithelium


title: 138 N/N 22000480 stroma


title: 146 PV/N 22000487 stroma


title: NMP_024, 12H, NTP [175_S135]


title: 135 N/N 22000480 epithelium


title: 134 N/N 22002827 epithelium


title: NMP_023, 12H, TP [174_S134]


title: 133 N/N 22002827 stroma


title: NMP_021, 12H, NTP [173_S133]


title: wild type, biological replicate 4


title: 132 N/N 22002827 epithelium


title: wild type, biological replicate 3


title: 131 PV/N 22000485 epithelium


title: 130 PV/N 22000485 stroma


title: 128 N/N 22000480 epithelium


title: 129 PV/N 22000485 epithelium


title: NMP_020, 12H, NTP [172_S132]


title: wild type, biological replicate 2


title: NMP_018, 12H, NTP [170_S130]


title: 126 PV/N 22000481 stroma


title: 127 PV/N 22000485 stroma


title: NMP_019, 12H, TP [171_S131]


title: wild type, biological replicate 1


title: 124 PV/N 22000481 stroma


title: 123 PV/N 22000481 epithelium


title: 125 PV/N 22000481 epithelium


title: NMP_017, 12H, TP [169_S129]


title: PCdNK_B (replicate 3)

city: Leeds

first: Mihaela

last: Lorger

address: Becket street

department: School of Medicine

country: United Kingdom

institute: University of Leeds

data_processing:
Raw mRNA-seq fastq reads were quality checked and filtered using an in-house perl script, discarding reads with adaptor contamination, low quality (Q < 5 constituting more than 50 percent of the read), and over 10% uncertain nucleotides (N > 10%). Filtered paired-end reads were aligned to the mouse reference genome (Ensembl GRCm38.p6) using STAR (v2.6.1d). Alignments were assembled to transcripts using Stringtie v1.3.3b, and gene expression was quantified using featureCounts v1.5.0-p3. Differential gene expression analysis was performed on raw gene expression counts using the DESeq2 R package (v1.26.0). Genes were tested for differential expression by pairwise comparisons between the four experimental groups, each with three biological replicates. Differentially expressed genes were also identified between the CD8H group versus the three other groups. P-values were adjusted by Benjamini-Hochberg correction, and genes with p-value ≤ 0.05 and False Discovery Rate (FDR) ≤ 0.05 were identified as differentially expressed. Differentially expressed genes were hierarchically clustered by z-score log2 (FPKM + 1) values and visualised as a heatmaps using the pheatmap R package.
Assembly: Ensembl GRCm38.p6
Supplementary files format and content: Excel file called fpkm contains fpkm values for individual genes for all samples. Excle file called readcounts contains read counts for individual genes for all samples.

source_name: Intracranial tumor

extract_protocol:
RNA was isolated from dissociated tumor tissue using the RNAqueous Total RNA Isolation Kit (Ambion)
Sequencing library generation, mRNA-seq and data analysis were performed by Novogene. A total amount of 2 μg RNA/sample was used as the input material. Messenger RNA was purified from total RNA using poly-A oligo-attached magnetic beads.  After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. End repair, A-tailing, adaptor ligation, size selection, amplification and purification were performed.

value: Intracranial tumor

value: B16-OVA derived

value: Murine melanoma

value: WT

value: anti-PD-1/anti-CTLA-4; anti-Asialo-GM2


title: wild type, biological replicate 5


title: PCdNK_B (replicate 2)


title: 121 PV/N 22000481 epithelium

value: uterus

value: Uterus epithelium


title: 122 PV/N 22000481 epithelium


title: 120 N/N 22008613 stroma

value: Uterus stroma

value: N/N


title: NMP_014, 12H, TP [167_S127]

value: liver

value: yes


title: NMP_015, 12H, NTP [168_S128]

value: normothermic machine perfusion


title: 119 N/N 22008613 epithelium


title: PCdNK_B (replicate 1)


title: 117 PV/N 22000481 epithelium

value: PV/N


title: 116 N/N 22008613 epithelium


title: PCcd8H_B (replicate 3)


title: 118 PV/N 22000481 stroma


title: NMP_011, 12H, TP [165_S125]


title: NMP_012, 12H, TP [166_S126]


title: PCcd8H_B (replicate 2)


title: NMP_010, 12H, TP [164_S124]


title: 112 PV/N 22000481 epithelium


title: NMP_007, 12H, TP [162_S123]


title: PCcd8H_B (replicate 1)


title: 113 N/N 22008613 stroma


title: 114 PV/N 22000481 epithelium


title: PCcd8L_B (replicate 1)


title: 111 PV/N 22000481 stroma


title: 110 PV/N 22000481 stroma


title: PCcd8L_B (replicate 2)


title: 109 PV/N 22000481 stroma


title: IgG_B (replicate 3)

value: IgG


title: PCcd8L_B (replicate 3)


title: 106 PV/N 22000481 epithelium


title: 108 N/N 22008613 epithelium


title: IgG_B (replicate 2)


title: NMP_050, 6H, TP [158_S120]


title: NMP_001, 12H, TP [159_S121]


title: 105 PV/N 22002828 stroma


title: 115 PV/N 22000481 epithelium


title: NMP_049, 6H, NTP [157_S119]


title: 102 PV/N 22002828 epithelium


title: NMP_048, 6H, TP [156_S118]


title: 101 PV/N 22002828 stroma


title: 182_Mc1r LKO

city: Helsinki

first: Bishwa

middle: Raj

last: Ghimire

address: Tukholmankatu 8

department: Institute for Molecular Medicine Finland

country: Finland

institute: University of Helsinki

data_processing:
Primary data analyses were done using FIMM-RNASeq (version 3.0.0) data analysis workflow. In the workflow, sequence reads were trimmed for adaptor sequence/ low-quality sequence using Trimgalore (version 0.6.6). Quality filter passed sequences were mapped to GRCm38 (release 102) from Ensembl using STAR (version 2.7.6a). Gene count files were generated using Subread (version 2.0.1)
Assembly: GRCm38
Supplementary files format and content: TXT

source_name: Liver

extract_protocol:
Total RNA was extracted using Direct-zol RNA miniprep (Zymo Research, CA, USA). Individual sample concentration was 50 ng/ uL
Individual libraries had a concentratrion of at least 1-5 nM and 10 uLvolume. RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Preparation, Ligation, Kit (Illumina) according to the manufacturere's protocol

treatment_protocol: All the mice (WT and KO) were kept in cholesterol-rich western diet for 12-weeks

value: Liver

value: Mc1r LKO

value: Western diet fed


title: 100 N/N 23000134 epithelium


title: NMP_003, 12H, NTP [160_S122]

value: no


title: IgG_B (replicate 1)

value: Intracranial tumor

value: B16-OVA derived


title: NMP_046, 6H, NTP [155_S117]


title: 99 PV/N 22002828 epithelium


title: NMP_045, 6H, TP [154_S116]


title: 103 PV/N 22002828 epithelium


title: 157_Mc1r LKO


title: 156_Mc1r LKO


title: NMP_044, 6H, TP [153_S115]


title: NMP_043, 6H, NTP [152_S114]


title: 96 PV/N 22000479 stroma


title: 94 PV/N 22000479 epithelium


title: 92 PV/N 22000479 epithelium


title: 93 PV/N 22000479 epithelium


title: 95 PV/N 22000479 stroma


title: NMP_039, 6H, TP [148_S113]


title: 104 PV/N 22002828 stroma


title: 90 N/N 23002886 epithelium


title: 181_Control

value: Control


title: 91 N/N 23002886 stroma


title: 193_Control


title: 89 N/N 23002886 epithelium


title: NMP_037, 6H, TP [147_S112]


title: 88 N/N 22002823 stroma


title: 159_Control


title: 86 N/N 22002823 stroma


title: 154_Control


title: 98 N/N 23000134 stroma


title: 85 N/N 22002823 epithelium


title: 84 N/N 22002823 epithelium


title: 141_Mc1r LKO


title: NMP_035, 6H, NTP [145_S110]


title: 107 PV/N 22000481 epithelium


title: 83 N/N 22002823 epithelium


title: NMP_034, 6H, TP [144_S109]


title: RNAseq_Sciatic nerve crush_KO2

city: Columbus

first: Ilaria

last: Palmisano

state: Ohio

address: 460 West 12th Avenue

institute: Ohio State University

description: RNAseq_Sciatic nerve crush_KO2

data_processing:
The raw reads were mapped to mm10 with HISAT2. The raw counts were obtained with featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts

molecule: nuclear RNA

source_name: DRG

extract_protocol:
Neuronal nuclei,  expressing nuclear membrane GFP, were immunoisolated via beads bound to anti-GFP.
Isolated neuronal nuclei were directly resuspended in RLT buffer. RNA was extracted with RNeasy Micro kit (Qiagen) and DNase on column digestion following manufacturer’s guidelines. RNA quality was assessed with Agilent 2100 Bioanalyzer (Agilent). RNA was treated with NEBNext rRNA Depletion Kit and libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, according to the recommended manufacturer protocol. After ligation, the NEBNext Multiplex Oligos for Illumina adapter sequences were ligated to each sample to allow for sequencing multiplexing.

treatment_protocol: Neuronal nuclei were isolated from mouse sciatic dorsal root ganglia 3 days after sciatic nerve crush (SNC) or sham  or in naïve conditions from WT (INTACT-AdvillinCre)  and Rad21 KO (INTACT-Scc1flox/flox-AdvillinCre) mice, 14 days after tamoxifen injection.

value: DRG

value: DRG neuronal nuclei

value: INTACT-Scc1flox-AdvillinCre (RAD21 KO)

value: tamoxifen


title: 81 N/N 22000478 stroma

value: uterus

value: Uterus stroma

value: N/N


title: 82 N/N 22000478 epithelium

value: Uterus epithelium


title: RNAseq_Sciatic nerve crush_KO3

description: RNAseq_Sciatic nerve crush_KO3


title: RNAseq_Sciatic nerve crush_KO1

description: RNAseq_Sciatic nerve crush_KO1


title: 80 N/N 22000478 stroma


title: 79 N/N 22000478 epithelium


title: NMP_031, 6H, NTP [142_S107]

value: liver

value: normothermic machine perfusion


title: 78 N/N 22000478 epithelium


title: NMP_032, 6H, TP [143_S108]

value: yes


title: NMP_030, 6H, NTP [141_S106]


title: 77 N/N 22000478 epithelium


title: 76 N/N 22000478 epithelium


title: NMP_036, 6H, TP [146_S111]


title: RNAseq_Sham_KO2


title: 87 N/N 22002823 stroma


title: 75 PV/N 22000479 epithelium

value: PV/N


title: 74 PV/N 22000479 stroma


title: RNAseq_Sham_KO1


title: 73 PV/N 22000479 epithelium


title: NMP_028, 6H, TP [139_S104]


title: NMP_029, 6H, TP [140_S105]


title: 72 PV/N 22000479 epithelium


title: 71 PV/N 22000479 epithelium


title: 70 PV/N 22000479 epithelium


title: RNAseq_Sciatic nerve crush_WT2

description: RNAseq_Sciatic nerve crush_WT2

value: INTACT-AdvillinCre (WT)


title: NMP_024, 6H, NTP [137_S102]

value: no


title: RNAseq_Sciatic nerve crush_WT1

description: RNAseq_Sciatic nerve crush_WT1


title: NMP_023, 6H, TP [136_S101]


title: 69 PV/N 22000479 stroma


title: RNAseq_Sham_KO3


title: 67 N/N 22002827 epithelium


title: 66 N/N 23000283 epithelium


title: 64 N/N 22002827 epithelium


title: NMP_022, 6H, TP [135_S100]


title: 68 N/N 23000283 epithelium


title: 63 N/N 22002827 stroma


title: 65 N/N 22002827 stroma


title: RNAseq_Sham_WT3


title: 62 N/N 22002827 epithelium


title: RNAseq_Sham_WT2


title: RNAseq_Sham_WT1


title: 60 PV/N 22000487 epithelium


title: NMP_021, 6H, NTP [134_S99]


title: 61 N/N 22002827 epithelium


title: RNAseq_nave_KO3


title: NMP_026, 6H, TP [138_S103]


title: 59 PV/N 22000487 stroma


title: 58 PV/N 22000487 epithelium


title: NMP_019, 6H, TP [132_S97]


title: RNAseq_nave_KO2


title: 57 PV/N 22000487 stroma


title: NMP_018, 6H, NTP [131_S96]


title: 55 N/N 22000480 stroma


title: NMP_016, 6H, TP [129_S94]


title: 51 PV/N 22000485 epithelium


title: NMP_017, 6H, TP [130_S95]


title: 53 PV/N 22000485 epithelium


title: RNAseq_nave_WT2


title: RNAseq_nave_WT3


title: 52 PV/N 22000485 stroma


title: RNAseq_nave_KO1


title: NMP_015, 6H, NTP [128_S93]


title: NMP_020, 6H, NTP [133_S98]


title: 50 N/N 22002827 epithelium


title: 49 N/N 22000480 epithelium


title: 48 N/N 22002827 stroma


title: RNAseq_nave_WT1


title: 47 N/N 22002827 epithelium


title: NMP_013, 6H, TP [126_S91]


title: 44 N/N 22000480 epithelium


title: NMP_012, 6H, TP [125_S90]


title: 45 N/N 22000480 stroma


title: 46 N/N 22000480 epithelium


title: H3K27ac_Sciatic nerve crush_WT2

data_processing:
We followed CUT&Tag Data Processing and Analysis Tutorial (https://www.protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-e6nvw93x7gmk/v1) to process H3K27ac.
QC and trim: TrimGalore
Mapping: Bowtie2
Assembly: mm10
Supplementary files format and content: .bigWig
Library strategy: CUT&tag

extract_protocol:
Neuronal nuclei were isolated via nuclear sorting after NeuN A488 labelling.
Sorted nuclei were pelleted by centrifugation, resuspended in wash buffer (20mM HEPES pH 7.5, 150 mM NaCl, 0.5mM spermidine, and EDTA-free protease inhibitors), and bound to 3.5 microliters Concanavalin A beads (Statech Scientific) in binding buffer (20mM HEPES-KOH pH 7.5, 10mM KCl, 1mM CaCl2 and 1mM MnCl2). Nuclei-bound beads were incubated with 1:100 anti H3K27ac (ab4729, Abcam) antibodies for 2 hours at r.t. and then o.n. at 4°C in antibody buffer (20mM HEPES pH 7.5, 150 mM NaCl, 0.5mM spermidine, 0.1% BSA, and EDTA-free protease inhibitors). After incubation with 1:100 guinea pig anti-rabbit secondary antibodies (ABIN101961, Antibodies online) for 1 h and washing, nuclei were incubated with 1:20 CUTANA pAG-Tn5 pre-loaded adaptor complex (Stratech) in 300-wash buffer (20mM HEPES pH 7.5, 300 mM NaCl, 0.5mM spermidine, and EDTA-free protease inhibitors) for 2 hours at r.t.. Tagmentation was initiated by adding 10mM MgCl2 and carried out at 37°C for 1 h. Tagmented DNA was released by resuspending the beads in 0.1% SDS in 1M TAPS pH8.5. Libraries were generated with 11-12 cycles-PCR using NEBnext PCR mix (New England Biolabs).

treatment_protocol: Neuronal nuclei were isolated from mouse sciatic dorsal root ganglia 3 days after sciatic nerve crush (SNC) or sham  conditions from WT (INTACT-AdvillinCre)  and Rad21 KO (INTACT-Scc1flox/flox-AdvillinCre) mice, 14 days after tamoxifen injection.

tag: antibody

value: Sciatic nerve crush


title: 56 PV/N 22000487 epithelium


title: H3K27ac_Sciatic nerve crush_WT1


title: NMP_010, 6H, TP [123_S89]


title: 43 PV/N 22000481 stroma


title: 54 PV/N 22000485 stroma


title: H3K27ac_Sham_WT3

value: Sham


title: NMP_008, 6H, TP [121_S88]


title: NMP_014, 6H, TP [127_S92]


title: 41 PV/N 22000481 epithelium


title: 39 PV/N 22000481 stroma


title: 38 PV/N 22000481 epithelium


title: H3K27ac_Sham_WT2


title: H3K27ac_Sham_WT1


title: 37 PV/N 22000481 stroma


title: 36 PV/N 22000481 epithelium


title: NMP_007, 6H, TP [120_S87]


title: NMP_005, 6H, TP [118_S86]


title: PromoterHIC_Sciatic nerve crush_KO3

description: PromoterHIC_Sciatic nerve crush_KO3

data_processing:
For Hi-C data processing, we used Juicer to generate two hic files (MAPQ > 0 and MAPQ >= 30).
For promoter capture Hi-C data processing, we followed Arima Capture Hi-C V1.4 pipeline (https://github.com/ArimaGenomics/CHiC).
Assembly: mm10
Supplementary files format and content: .hic
Supplementary files format and content: .Rds serialized R objects
Library strategy: promoter capture Hi-C

extract_protocol:
Neuronal nuclei,  expressing nuclear membrane GFP, were immunoisolated via beads bound to anti-GFP.
Nuclei were crosslinked with 2% formaldehyde for 10 min at room temperature.  Nuclei were processed for Hi-C using ARIMA Hi-C Genomics kits (A510008). Briefly, chromatin was digested with multiple enzymes, and purified proximity-ligated DNA was sheared using Bioruptor to obtain an average size of 400 bp. After DNA size selection of 200-600 bp, biotin enrichment, end-repair and adapter ligation, Hi-C libraries were prepared starting from 30-65 ng of DNA and 10 PCR cycles, using Swift Biosciences Accel-NGS 2S Plus DNA library kit (21024) and KAPA Library amplification kit (KK2620) or Arima Library preparation module (A303010). In the case of capture Hi-C, precapture Hi-C libraries were prepared starting from 30 ng of DNA and 14 PCR cycles, using KAPA Library amplification kit (KK2620) or Arima Library preparation module (A303010). After preclearing, hybridization and capture were performed using Arima Mouse Promoter Panel (A302020) starting from 1microg of precapture libraries.  Promoter Hi-C libraries were amplified with 13 cycles


title: 35 PV/N 22000481 epithelium


title: NMP_003, 6H, NTP [116_S85]


title: 34 PV/N 22000481 stroma


title: H3K27ac_Sciatic nerve crush_WT3


title: PromoterHIC_Sciatic nerve crush_KO2

description: PromoterHIC_Sciatic nerve crush_KO2


title: NMP_002, 6H, TP [115_S84]


title: 33 PV/N 22000481 epithelium


title: 42 PV/N 22000481 epithelium


title: PromoterHIC_Sciatic nerve crush_KO1

description: PromoterHIC_Sciatic nerve crush_KO1


title: 32 PV/N 22000481 epithelium


title: 31 N/N 22008613 stroma


title: 40 PV/N 22000481 epithelium


title: 30 N/N 22008613 epithelium


title: PromoterHIC_Sham_KO3


title: 29 N/N 22008613 epithelium


title: 28 N/N 22008613 stroma


title: 27 N/N 22008613 epithelium


title: 26 N/N 22008613 epithelium


title: PromoterHIC_Sham_KO2


title: 25 PV/N 22002828 stroma


title: NMP_048, 1H, TP [97_S81]


title: 23 PV/N 22002828 epithelium


title: NMP_050, 1H, TP [99_S82]


title: 24 PV/N 22002828 stroma


title: PromoterHIC_Sciatic nerve crush_WT3

description: PromoterHIC_Sciatic nerve crush_WT3


title: NMP_046, 1H, NTP [95_S80]


title: 22 N/N 23000134 epithelium


title: PromoterHIC_Sham_KO1


title: NMP_043, 1H, NTP [92_S78]


title: 21 N/N 23000134 stroma


title: PromoterHIC_Sciatic nerve crush_WT1

description: PromoterHIC_Sciatic nerve crush_WT1


title: NMP_001, 6H, TP [114_S83]


title: 18 PV/N 22002828 epithelium


title: 20 N/N 23000134 epithelium


title: PromoterHIC_Sham_WT3


title: 17 PV/N 22001713 stroma


title: NMP_040, 1H, TP [89_S77]


title: 19 N/N 23000134 epithelium


title: NMP_039, 1H, TP [88_S76]


title: PromoterHIC_Sham_WT2


title: 15 N/N 22002823 epithelium


title: 16 PV/N 22001713 epithelium


title: NMP_044, 1H, TP [93_S79]


title: 14 PV/N 22000479 epithelium


title: NMP_038, 1H, TP [87_S75]


title: PromoterHIC_Sham_WT1


title: 13 PV/N 22000479 stroma


title: 12 PV/N 22000479 stroma


title: NMP_037, 1H, TP [86_S74]


title: 11 PV/N 22000479 stroma


title: PromoterHIC_Sciatic nerve crush_WT2

description: PromoterHIC_Sciatic nerve crush_WT2


title: NMP_036, 1H, TP [85_S73]


title: NMP_035, 1H, NTP [84_S72]


title: HIC_Sciatic nerve crush_KO1

description: HIC_Sciatic nerve crush_KO1

data_processing:
For Hi-C data processing, we used Juicer to generate two hic files (MAPQ > 0 and MAPQ >= 30).
For promoter capture Hi-C data processing, we followed Arima Capture Hi-C V1.4 pipeline (https://github.com/ArimaGenomics/CHiC).
Assembly: mm10
Supplementary files format and content: .hic
Supplementary files format and content: .Rds serialized R objects


title: 8 PV/N 22000479 stroma


title: NMP_034, 1H, TP [83_S71]


title: 6 PV/N 22000479 epithelium


title: 5 PV/N 22000479 epithelium


title: HIC_Sham_KO3


title: NMP_032, 1H, TP [81_S70]


title: 7 PV/N 22000479 epithelium


title: 4 PV/N 22000479 epithelium


title: HIC_Sham_KO2


title: NMP_031, 1H, NTP [80_S69]


title: 2 PV/N 22000479 epithelium


title: HIC_Sciatic nerve crush_KO3

description: HIC_Sciatic nerve crush_KO3


title: 3 PV/N 22000479 epithelium


title: 10 PV/N 22000479 stroma


title: HIC_Sham_KO1


title: 9 PV/N 22000479 stroma


title: HIC_Sciatic nerve crush_KO2

description: HIC_Sciatic nerve crush_KO2


title: H9 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 5

city: Heidelberg

first: Rachel

middle: B

last: Gilmore

state: BW

address: Im Neuenheimer Feld 366

department: Institute for Human Genetics

institute: Heidelberg University

data_processing:
For hESC-derived neurons, .fastq.gz files from flow cell lanes were concatenated using pigz v2.2.3.
Quality of reads were checked using fastqc v0.11.7 and then MultiQC v1.10.1; equal distribution of reads across the gene body was verified using geneBody_coverage.py v3.0.1 from RSeQC on indexed BAM files (.bai) generated from sorted BAM files using samtools v1.9
Reads were aligned to the genome using HISAT2 v2.2.1 (using options --fr --no-discordant --avoid-pseudogene --no-mixed) and STAR v2.7.1a (using options --readFilesCommand zcat, --outFilterType BySJout, --outFilterMultimapNmax 1, --alignSJoverhangMin 8, --alignSJDBoverhangMin 2, --outFilterMismatchNoverReadLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMtype BAM SortedByCoordinate, --outWigType bedGraph)
For samples aligned using HISAT2, resulting SAM files were converted to sorted BAM files using samtools v1.9
Sorted BAM files were used to extract read counts using featureCounts from subread v2.0 (with options -s 2)
Assembly: hg38, gencodev25
Supplementary files format and content: Resultant read counts from featureCounts for STAR aligned reads as a text file (.txt) in tab-delimited format for ESCs and hESC-derived inducible neurons.
Supplementary files format and content: Resultant read counts from featureCounts for STAR aligned reads as a text file (.txt) in tab-delimited format for hESC-derived inducible neurons for both smDEL and lgDEL analyses.
Supplementary files format and content: Resultant read counts from featureCounts for HISAT2 aligned reads as a text file (.txt) in tab-delimited format for hESC-derived inducible neurons for both smDEL and lgDEl analyses.

growth_protocol: Human embryonic stem cells were maintained in mTeSR™ Plus (STEMCELL Technologies, Catalog #100-0276) on Matrigel™ hESC-Qualified Matrix (Corning™, Catalog #354277) coated 6-well plates in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
For hESCs, RNA was harvested using the miRNeasy® Mini Kit (QIAGEN, Catalog #1038703) following manufacturer's protocol with minor modifications, including homogenization with QIAshredder (QIAGEN, Catalog #1011711), addtional chloroform extration step, and on-column DNase treatment using RNase-Free DNase Set (QIAGEN, Catalog #79254). For hESC-derived neurons, RNA was harvested using the Direct-zol RNA Miniprep kit (Zymo Research, Cat No. R2050) following manufacturer's protocols. For both hESCs and hESC-derived neurons, 1 ug of RNA was used for the construction of sequencing libraries.
For hESCs, RNA libraries for RNA-seq were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (NEB, Catalog #E7760L) following manufacturer's protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490). For hESC-derived neurons, RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Cat No. 20020594 ) following manufacturer's protocols.

treatment_protocol: hESCs were differentiated into iNeurons following the published protocol by Fernandopulle et al (2020) with minor modifications. In brief, when hESCs reached 70-80% confluency, they were singularized using Accuatse (Millipore, SCR005), collected in mTeSR™ Plus media, transferred to a Falcon tube, and pelleted at 1.2X1000 rpm for 3 min. The cell pellet was resuspended, cells were counted using a hemocytometer, and cells were plated for differentiation in modified Induction Media (IM) supplemented with freshly added Doxycycline Hydrochloride (Fisher Scientific, BP2653-5) and ROCK inhibitor Y-27632 (Tocris, 1254) at final concentrations of 2uM and 10uM respectively (day 0 of differentiation). Media was changed using IM plus freshly added supplements for 3 more days before singularizing and replating for terminal differentiation with modified Cortical Neuron Media (CM) on day 4. Cells were plated at 1 million cells per PDL/laminin-coated well in a 6-well plate or 7 million cells per PDL/laminin-coated 10cm dish. CM was supplemented with 10uM ROCK inhibitor. Complete media change with CM was performed on day 5. Neurons were collected for RNA extraction on day 11.

value: hESC-derived neurons

value: lgDEL-NGN

value: inducible neuron differentiation

value: F


title: NMP_029, 1H, TP [78_S67]

data_processing:
Adapters were trimmed using BBDuk according to recommendations (Lexogen, Austria) and quality checked using FastQC.
Reads were mapped to the human reference genome (GRCh38/hg38) using the splice aware aligner STAR (v2.7.1a). Note, since  the specific 3'  sequencing libraries used here, only forward reads were mapped and all reverse reads were discarded since provide only limited information.
Read counts for NCBI Gene/Refseq annotation were detrmined using featureCounts (v2.0.0)
Differentially expressed genes were determined using DESeq2 based on raw counts and a negative binomial distribution
Data were normalized using DESeq2 and log-transformed (rlog).
Assembly: hg38
Supplementary files format and content: tab delimited txt file include raw counts for each sample (raw_counts.txt)
Supplementary files format and content: tab delimited txt file include log2 transformed normalized counts adding a pseudocount of 1 (DESeq2) for each sample (log2_normalized_counts_1.txt)


title: H9 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 4


title: H9 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 3


title: NMP_028, 1H, TP [77_S66]


title: H9 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 6


title: HIC_Sciatic nerve crush_WT2

description: HIC_Sciatic nerve crush_WT2

value: DRG

value: DRG neuronal nuclei

value: tamoxifen


title: H9 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 2


title: H9 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 1


title: HIC_Sciatic nerve crush_WT1

description: HIC_Sciatic nerve crush_WT1


title: NMP_027, 1H, TP [76_S65]


title: H9 neurons, delSNORD116 (smDEL) + NGN, biol rep 5

value: smDEL-NGN


title: RNAseq_Sciatic nerve crush_WT3

description: RNAseq_Sciatic nerve crush_WT3


title: H9 neurons, delSNORD116 (smDEL) + NGN, biol rep 4


title: H9 neurons, delSNORD116 (smDEL) + NGN, biol rep 3


title: HIC_Sham_WT2


title: NMP_026, 1H, TP [75_S64]


title: NMP_030, 1H, NTP [79_S68]


title: HIC_Sciatic nerve crush_WT3

description: HIC_Sciatic nerve crush_WT3


title: NMP_024, 1H, NTP [74_S63]


title: HIC_Sham_WT1


title: H9 neurons, wild type (WT) + NGN, biol rep 6

value: WT-NGN


title: H9 neurons, wild type (WT) + NGN, biol rep 4


title: H9 neurons, wild type (WT) + NGN, biol rep 5


title: H9 neurons, wild type (WT) + NGN, biol rep 3


title: NMP_023, 1H, TP [73_S62]

value: liver


title: H9 neurons, wild type (WT) + NGN, biol rep 1


title: HIC_nave_KO2

value: INTACT-Scc1flox-AdvillinCre (RAD21 KO)


title: NMP_022, 1H, TP [72_S61]

value: yes

value: normothermic machine perfusion


title: NMP_021, 1H, NTP [71_S60]


title: HIC_nave_WT2

value: INTACT-AdvillinCre (WT)


title: HIC_nave_KO1


title: H9 neurons, wild type (WT) + NGN, biol rep 2


title: CT2 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 5


title: CT2 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 3


title: NMP_020, 1H, NTP [70_S59]

value: no


title: H9 neurons, delSNORD116 (smDEL) + NGN, biol rep 1


title: HIC_Sham_WT3


title: CT2 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 4


title: NMP_019, 1H, TP [69_S58]


title: CT2 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 6


title: HIC_nave_WT1


title: H9 neurons, delSNORD116 (smDEL) + NGN, biol rep 2


title: Retina, EAU, biol rep2

city: Oxford

first: Kanmin

last: Xue

address: Nuffield Department of Clinical Neurosciences, Level 6, West Wing, John Radcliffe Hospital

institute: University of Oxford

description:
10X Genomics
features.tsv

data_processing:
For initial data processing, Illumina’s bcl2fastq and cellranger mkfastq demultiplexes were used to convert the raw base call (BCL) files generated by Illumina sequencers into FASTQ files. Cellranger was used to perform alignment, filtering, barcode counting, and UMI counting from FASTQ files. This generated feature-barcode matrices for each sample, which was used for downstream analyses.
Assembly: GRCm38
Supplementary files format and content: Tab separated values files containing features and barcodes
Supplementary files format and content: Matrix file

source_name: Retina

extract_protocol:
The retinas were carefully dissected out and placed into Hanks’ Balanced Salt Solution (HBSS) containing 10 mM HEPES on ice for transport. After all retinas were collected, they were dissociated using the Worthington Papain Dissociation system. Retinas were placed in a solution of 20 U/ml papain, 0.005% DNase I with 1 mM L-cysteine and 5 mM EDTA in Earle’s Balanced Salt Solution (EBSS), for 10 minutes at 37°C with frequent, gentle agitation. Samples were then diluted by addition of 500 μl of EBSS to inactivate the papain and centrifuged at 300 x g for 5 min at room temperature. Pellets were resuspended in 525 μl of a solution containing 1 mg/ml ovomucoid and BSA and 100 U/ml DNase I in EBSS. The resulting suspension was carefully layered over 500 μl ovomucoid/BSA solution and centrifuged at 70 x g for 6 min. Supernatant was discarded and cells were resuspended in a solution of PBS containing 0.04% BSA.
scRNAseq transcriptome processing was performed using the Chromium 10X system involving GEM generation, post GEM-generation clean-up, cDNA amplification and DNA quantification. Chromium Single Cell Reagent Kits solution (10X SC RNA CITE-TSC, 10X SC RNA 5pr v2.0 Chemistry) was used to deliver a scalable microfluidic platform for digital scRNA-seq by profiling 500-10,000 individual cells per sample. A pool of ~3,500,000 10x Barcodes were sampled separately to index each cell's transcriptome. Libraries were generated and sequenced from the cDNAs and 10x Barcodes were used to associate individual reads back to the individual partitions. The library was sequenced using the Illumina NovaSeq platform.

value: Retina

value: Female

value: 6-8 weeks

value: EAU


title: CT2 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 2

value: hESC-derived neurons

value: lgDEL-NGN

value: inducible neuron differentiation


title: CT2 neurons, delPWSIC-IPW (lgDEL) + NGN, biol rep 1

value: F


title: NMP_018, 1H, NTP [68_S57]

extract_protocol:
Cryopreserved liver biopsies were homogenized using the ULTRA Turrax IKA T10 basic. Total RNA was extracted according to the Rneasy Micro Kit (Qiagen, Netherlands). RNA integrity was determined using a 2100 Bioanalyzer and RNA 6000 Nano LabChip kits (Agilent Technology, USA).
QuantSeq 3'protocol (Lexogen, Austria) according to manufacturers's recommendations


title: CT2 neurons, delSNORD116 (smDEL) + NGN, biol rep 6


title: Retina, EAU, biol rep1

description:
10X Genomics
features.tsv


title: CT2 neurons, delSNORD116 (smDEL) + NGN, biol rep 5


title: NMP_017, 1H, TP [67_S56]


title: CT2 neurons, delSNORD116 (smDEL) + NGN, biol rep 4


title: Retina, healthy, biol rep1

description:
10X Genomics
features.tsv

value: Healthy


title: CT2 neurons, delSNORD116 (smDEL) + NGN, biol rep 3

value: smDEL-NGN


title: CT2 neurons, delSNORD116 (smDEL) + NGN, biol rep 2


title: NMP_016, 1H, TP [66_S55]


title: NMP_015, 1H, NTP [65_S54]


title: MycCap Tumors, IRE1A KO2, scRNA

description: Singleron GEXSCOPE

data_processing:
The sequencing reads were aligned to mouse reference Grcm38 genome and Singleron Celescope tool (https://github.com/singleron-RD/CeleScope) were used to generate the gene expression matrices.
Assembly: Grcm38
Supplementary files format and content: mtx

treatment_protocol: IRE1α knock-out (KO) Myc-CaP cell lines were generated by CRISPR Cas9 system using a guide RNA (gRNA) (5’-GCTTGCATGCTGTTAGCAAG-3’) targeting IRE1α.

value: Prostate Cancer

value: Myc-CaP

value: Mouse Prostate Cancer Cell Line Xenograft

value: KO


title: CT2 neurons, delSNORD116 (smDEL) + NGN, biol rep 1


title: CT2 neurons, wild type (WT) + NGN, biol rep 6

value: WT-NGN


title: CT2 neurons, wild type (WT) + NGN, biol rep 4


title: NMP_014, 1H, TP [64_S53]

value: liver

value: yes

value: normothermic machine perfusion


title: MycCap Tumors, IRE1A KO3, rep3

data_processing:
RNA-Seq data was processed through nf-core rnaseq pipeline (version 3.6). Briefly, reads were trimmed using Trimgalore (version 0.6.7) and then mapped to Grcm38 using STAR RNA-Seq aligner (version 2.6.1d). The reads were then quantified via Salmon (version 1.5.2) using Ensemble as a reference transcript database.
Assembly: Grcm38
Supplementary files format and content: tab delimitted file containing raw reads
Supplementary files format and content: tab delimited file containing normalized length scaled reads

extract_protocol:
RNA was isolated from the cells grown in vitro or the tumor samples using Trizol and purified using RNeasy columns (Qiagen).  On column DNAse treatment was performed.
TruSeq stranded RNA-seq libraries were prepared according to manufacturer instructions (Illumina)

value: Mouse Prostate Cancer Cell Line Xenografted Tumor

value: IRE1A KO


title: CT2 neurons, wild type (WT) + NGN, biol rep 5


title: NMP_013, 1H, TP [63_S52]


title: MycCap Tumors, IRE1A KO3, rep2


title: CT2 neurons, wild type (WT) + NGN, biol rep 1


title: CT2 neurons, wild type (WT) + NGN, biol rep 2


title: MycCap Tumors, IRE1A KO3, rep1


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep3)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

data_processing:
alignment to mm10 reference genome with HISAT2 (v2.1.0) using default parameters
transcript assembly with StringTie (v1.3.4d)
generation of coverage (bigWig) files with bamCoverage2 (v3.1.3) of deepTools using -binsize 1 --normalizeUsing RPKM parameters
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: mouse alveolar macrophage

growth_protocol: We applied primary mouse alveolar macrophages from C57BL6 background control and EGR2 myeloid specific conditional knock out mice.

extract_protocol:
The mice were euthanised by isoflurane inhalation then the cellular component were isolated through bronchoalveolar lavage. We sorted the CD45+ and F4/80+ alveolar macrophages and isolated total RNA using TriReagent.
Libraries were prepared with the TruSeq ChIP library systems (Illumina) according to the manufacturer protocol.

treatment_protocol: The mice were intranasally treated with 300 μg zymosan in 40 μl PBS+2 mM NaN3 for 6 hours and 24 hours or just with 40 μl PBS+2 mM NaN3 as vehicle control.

value: alveolar macrophage

value: EGR2 knock-out

value: 300 microgram zymosan

tag: time point


title: NMP_011, 1H, TP [61_S50]

tag: tissue


title: CT2 neurons, wild type (WT) + NGN, biol rep 3

value: hESC-derived neurons

value: inducible neuron differentiation


title: MycCap Tumors, IRE1A KO2, rep3


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep1)


title: NMP_010, 1H, TP [60_S49]


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep4)


title: RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep4)

value: wild type


title: RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep3)


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep2)


title: RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep2)


title: RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep1)


title: MycCap Tumors, IRE1A KO2, rep2


title: MycCap Tumors, IRE1A KO2, rep1


title: MycCap Tumors, WildType, rep4, scRNA

description: Singleron GEXSCOPE

value: WT


title: MycCap Tumors, IRE1A KO1, rep3

value: Prostate Cancer


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep3)


title: NMP_003, 1H, NTP [53_S45]

value: no


title: MycCap Tumors, IRE1A KO1, rep2

value: Myc-CaP


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep1)


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep2)


title: RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep4)


title: NMP_005, 1H, TP [55_S46]


title: MycCap Tumors, IRE1A KO1, rep1


title: RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep2)


title: RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep3)


title: NMP_002, 1H, TP [52_S44]


title: MycCap Tumors, WildType, rep4


title: RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep1)


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages (vehicle control, rep3)

value: vehicle control


title: NMP_008, 1H, TP [58_S48]


title: MycCap Tumors, WildType, rep3


title: NMP_001, 1H, TP [51_S43]


title: NMP_050, PRE, TP [50_S42]

value: PRE


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages (vehicle control, rep2)


title: NMP_007, 1H, TP [57_S47]

value: liver


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages (vehicle control, rep1)


title: MycCap Tumors, WildType, rep2


title: RNA-seq in wild type mouse alveolar macrophages (vehicle control, rep3)


title: NMP_049, PRE, NTP [49_S41]


title: RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep4)


title: MycCap Tumors, WildType, rep1


title: RNA-seq in wild type mouse alveolar macrophages (vehicle control, rep2)


title: RNA-seq in wild type mouse alveolar macrophages (vehicle control, rep1)


title: NMP_048, PRE, TP [48_S40]

value: yes


title: ATAC-seq in EGR2 knock-out mouse alveolar macrophages (rep3)

data_processing:
alignment to mm10 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile using -fsize 1e50 -norm parameters
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

growth_protocol: We applied primary mouse alveolar macrophages from C57BL6 background control and EGR2 myeloid-specific conditional knock out mice.

extract_protocol:
The mice were euthanised by isoflurane inhalation then we isolated the cells from bronchoalveolar lavage. We sorted the CD45+ and F4/80+ alveolar macrophages.
Libraries were prepared with the TruSeq ChIP library systems (Illumina) according to the manufacturer protocol.

treatment_protocol: We did not apply any treatment.

tag: organ

value: lung


title: NMP_046, PRE, NTP [46_S39]

value: normothermic machine perfusion


title: MycCap Cells, IRE1A KO3, rep2

value: Mouse Prostate Cancer Cell Line

value: IRE1A KO


title: ATAC-seq in EGR2 knock-out mouse alveolar macrophages (rep2)

value: EGR2 knock-out

value: alveolar macrophage


title: NMP_045, PRE, TP [45_S38]


title: MycCap Cells, IRE1A KO3, rep1


title: ATAC-seq in EGR2 knock-out mouse alveolar macrophages (rep1)


title: ATAC-seq in wild type mouse alveolar macrophages (rep3)


title: MycCap Cells, IRE1A KO2, rep2


title: ATAC-seq in wild type mouse alveolar macrophages (rep1)


title: MycCap Cells, IRE1A KO2, rep1


title: NMP_043, PRE, NTP [43_S36]


title: NMP_044, PRE, TP [44_S37]


title: NMP_042, PRE, NTP [42_S35]


title: MycCap Cells, WildType, rep2


title: NMP_040, PRE, TP [40_S34]


title: meninges_sd_rep7

city: Cambridge

first: Stacey

middle: L

last: Kigar

address: Puddicombe Way

institute: University of Cambridge

description: leptomeninges + dura

hyb_protocol: A hybridization cocktail containing fragmented and labeled cRNAs was hybridized to Affymetrix Mouse Gene 2.0 ST GeneChips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols described by the manufacturer. Probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

scan_protocol: Affymetrix Gene ChIP Scanner 3000

data_processing:
CEL files generated by the Affymetrix GCOS program were RMA-normalized with the Affymetrix Expression Consol program. The limma package in R was used to test for differential expression between CSD vs HC conditions.
DOI: 10.18129/B9.bioc.pd.mogene.2.0.st

label: biotin

source_name: meninges, chronic social defeat

label_protocol: 300 ng of total RNA per sample was used following the recommended protocol from Affymetrix

growth_protocol: mice were purchased from Jackson Labs and given 1 week to acclimate in our facility. They were then moved into reverse light-cycle housing and given 1 week to acclimate before being randomly assigned to either HC or CSD conditions

extract_protocol: leptomeninges surrounding brain (excluding choroid plexus) + dura from dorsal and ventral skull were collected for each mouse then stored in Trizol at -80. Samples were triturated with syringe needles and total RNA extracted with an miRNeasy kit (Qiagen).

treatment_protocol: mice in the CSD stress group underwent 14 consecutive days of stress. 2 h after the final stressor, mice were perfused with PBS, and the skull was collected.

value: male

tag: weight at setup (g)

tag: weight at dissection (g)

value: meninges

tag: age (days)


title: NMP_039, PRE, TP [39_S33]

first: Theresa

last: Hautz

institute: Medical University of Innsbruck

tag: time

tag: treatment


title: MycCap Cells, IRE1A KO1, rep1

tag: cell line


title: meninges_sd_rep6

description: leptomeninges + dura


title: meninges_sd_rep5

description: leptomeninges + dura


title: meninges_sd_rep4

description: leptomeninges + dura


title: meninges_sd_rep3

description: leptomeninges + dura


title: NMP_038, PRE, TP [38_S32]

tag: transplantation


title: total VisCtx RNA, Light condition, ZT18, biorep3

city: Rehovot

first: Daniella

last: Apelblat

address: Hertzl

department: Neuroscience

country: Israel

institute: Weizmann Institute of Science

description:
Light18_rep3
normalized_counts.xls, column 57

data_processing:
Data processing was performed using UTAP: User-friendly Transcriptome Analysis Pipeline (Kohen et al., 2019).
Reads were trimmed using CutAdapt (Martin 2011) [parameters: -a ADAPTER1 -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25].
Reads were mapped to genome mm10 using STAR (Dobin et al. 2013) v2.5.2b [parameters: –alignEndsType EndToEnd –outFilterMismatchNoverLmax 0.05 –twopassMode Basic].
Reads were counted using STAR, and count normalization and differential expression was done with DESeq2 (Love et al., 2014).
Assembly: mm10
Supplementary files format and content: excel file including DESeq2-normalized counts for each sample

source_name: visual cortex

extract_protocol:
this is an example, put the relevant info!!! ::: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the MARS-Seq protocol, in the Nancy and Stephen Grand Israel National Center for Personalized Medicine (INCPM)

value: visual cortex

tag: condition

value: Light condition

tag: genotype


title: NMP_037, PRE, TP [37_S31]

city: Innsbruck

address: Anichstr. 45

source_name: liver


title: MycCap Cells, IRE1A KO1, rep2

value: Prostate Cancer

tag: cell type


title: BE2C_PUS7sh#33-1

city: Birmingham

first: Han-Fei

last: Ding

state: Alabama

address: WTI 602D, 1824 6th Avenue South

department: Pathology

institute: University of Alabama at Birmingham

description: RNA expression value

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized from CEL files using R/Bioconductor and gcRMA algorithm (http://homer.ucsd.edu/homer/basicTutorial/affymetrix.html).

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit.

growth_protocol: BE(2)-C  cells were cultured in DME/F-12 1:1 (HyClone SH30023) supplemented with 10% FBS (Fisher Scientific, FB12999102).

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

treatment_protocol: BE(2)-C cells were infected with lentiviruses expressing shRNA to GFP (GFPsh) or human PUS7 (PUS7sh#33) for 6 days

tag: tumor cell line

value: Neuroblastoma


title: BE2C_PUS7sh#33-2

description: RNA expression value


title: BE2C_GFPsh-2

description: RNA expression value


title: ATAC-seq in wild type mouse alveolar macrophages (rep2)

value: wild type

tag: strain


title: BE2C_GFPsh-1

description: RNA expression value


title: BE2C_GFPsh-3

description: RNA expression value


title: total VisCtx RNA, Light condition, ZT18, biorep2

description:
Light18_rep2
normalized_counts.xls, column 56

value: WT


title: meninges_sd_rep1

description: leptomeninges + dura

tag: Sex


title: BE2C_PUS7sh#33-3

description: RNA expression value


title: meninges_hc_rep7

description: leptomeninges + dura

source_name: meninges, home cage


title: meninges_hc_rep6

description: leptomeninges + dura


title: meninges_hc_rep5

description: leptomeninges + dura


title: NMP_035, PRE, NTP [35_S30]

value: no

value: PRE


title: total VisCtx RNA, Light condition, ZT15, biorep4

description:
Light15_rep4
normalized_counts.xls, column 54


title: NMP_032, PRE, TP [32_S28]

value: liver

value: yes


title: meninges_hc_rep2

description: leptomeninges + dura


title: meninges_hc_rep3

description: leptomeninges + dura


title: NMP_034, PRE, TP [34_S29]

value: normothermic machine perfusion


title: meninges_hc_rep4

description: leptomeninges + dura


title: total VisCtx RNA, Light condition, ZT18, biorep1

description:
Light18_rep1
normalized_counts.xls, column 55


title: meninges_sd_rep2

description: leptomeninges + dura


title: meninges_hc_rep1

description: leptomeninges + dura


title: total VisCtx RNA, Light condition, ZT15, biorep3

description:
Light15_rep3
normalized_counts.xls, column 53


title: NMP_031, PRE, NTP [31_S27]


title: MycCap Cells, WildType, rep1

value: Myc-CaP

value: Mouse Prostate Cancer Cell Line


title: EtEC81_1_21d

city: Beijing

first: Haiyue

last: Yu

address: Yuanmingyuanxilu No.2

institute: Chinese Academy of Agricultural Sciences

data_processing:
The raw reads were filtered using ht2-filter in the HTQC package (1.92.1) with default parameters to remove low-quality reads. The filtered reads were compared to the reference maize genome (Zea mays RefGen_V4) using TopHat (2.0.11) to remove host genome sequences. The mapped reads were assembled, and fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks.
Assembly: Zea mays RefGen_V4
Supplementary files format and content: FPKM

organism: Zea mays

source_name: leaves

extract_protocol:
RNA was extracted using Trizol reagent
mRNA was purified from total RNA using poly-T  oligo-attached magnetic beads. Fragmentation was carried out using  divalent cations under elevated temperature in First Strand Synthesis  Reaction Buffer(5X). 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. Remaining overhangs were converted  into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments  of preferentially 370~420 bp in length, the library fragments were  purified with AMPure XP system.

value: leaves


title: EtEC81_3_21d


title: ZmEIP_3_21d

value: ZmEIP


title: total VisCtx RNA, Light condition, ZT15, biorep1

description:
Light15_rep1
normalized_counts.xls, column 51


title: NMP_030, PRE, NTP [30_S26]


title: ZmEIP_2_21d


title: NMP_029, PRE, TP [29_S25]


title: total VisCtx RNA, Light condition, ZT13, biorep4

description:
Light13_rep4
normalized_counts.xls, column 50


title: NMP_028, PRE, TP [28_S24]


title: ZmEIP_1_21d


title: GFP_3_21d

value: GFP


title: total VisCtx RNA, Light condition, ZT13, biorep3

description:
Light13_rep3
normalized_counts.xls, column 49


title: GFP_1_21d


title: GFP_2_21d


title: NMP_027, PRE, TP [27_S23]


title: EGFR_vIII_T2_KO_WWZA-B2

city: San Francisco

first: Zhenyi

last: An

department: Neurology

institute: UCSF

data_processing:
RNA STAR-Feature count-DESeq2
Assembly: hg38
Supplementary files format and content: txt files include DESeq2 file comparing mRNA expression of EGFR+EGFRvIII TLR2 KO cells to EGFR+EGFRvIII control cells.

extract_protocol:
RNA was extracted using Quick-RNA MiniPrep kit according to the manufacturer’s instructions (ZYMO Research).
Library was constructed by Functional Genomics Laboratory at UC Berkeley.

value: EGFR+vIII TLR2 KO


title: total VisCtx RNA, Light condition, ZT13, biorep2

description:
Light13_rep2
normalized_counts.xls, column 48

value: visual cortex


title: NMP_026, PRE, TP [26_S22]


title: total VisCtx RNA, Light condition, ZT13, biorep1

description:
Light13_rep1
normalized_counts.xls, column 47

value: Light condition


title: total VisCtx RNA, Light condition, ZT15, biorep2

description:
Light15_rep2
normalized_counts.xls, column 52


title: EGFR_vIII_T2_KO_WWZA-B3


title: EGFR_vIII_T2_KO_WWZA-B1


title: NMP_024, PRE, NTP [24_S20]


title: EtEC81_2_21d


title: total VisCtx RNA, Light condition, ZT11.5, biorep4

description:
Light11.5_rep4
normalized_counts.xls, column 46


title: total VisCtx RNA, Light condition, ZT11.5, biorep3

description:
Light11.5_rep3
normalized_counts.xls, column 45


title: total VisCtx RNA, Light condition, ZT11.5, biorep2

description:
Light11.5_rep2
normalized_counts.xls, column 44


title: EGFR_vIII_WWZA-A3

value: EGFR+vIII


title: NMP_023, PRE, TP [23_S19]


title: EGFR_vIII_WWZA-A2


title: NMP_022, PRE, TP [22_S18]


title: total VisCtx RNA, Light condition, ZT11.5, biorep1

description:
Light11.5_rep1
normalized_counts.xls, column 43


title: EGFR_vIII_WWZA-A1


title: NMP_025, PRE, NTP [25_S21]


title: total VisCtx RNA, Light condition, ZT7.5, biorep4

description:
Light7.5_rep4
normalized_counts.xls, column 42


title: NMP_020, PRE, NTP [20_S16]