title: 47_D0

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0


title: 46_D7

status: Public on Dec 31 2024

type: SRA

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7

library_source: transcriptomic

data_processing:
Human: Raw sequencing reads in the fastq files were mapped with STAR version 2.7.1a to the Gencode release 36 based on the GRCh38.p12 reference human genome with the corresponding GTF files.
Table counts was obtained with FeatureCounts function in the package subread, version 1.6.4
Assembly: GRCh38.p12
Supplementary files format and content: txt file containing the table counts obtained with FeatureCounts

molecule: total RNA

organism: Homo sapiens

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7

extract_protocol:
Quick-RNA microprep
NGS libraries with Globin/Ribosome depletion were prepared according to the manual Protocol for use with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) (New England Biolabs) (versión 1.0, 7/20) and Protocol for use with FFPE RNA, NEBNext rRNA Depletion for Illumina® (NEB #E6310) (New England Biolabs) (Version 3.1, 5/20)  Library Prep Kit for Illumina® (New England Biolabs) (Version 1.0, 4/17)

tag: tissue

value: peripheral blood

tag: disease state

tag: time

tag: batch


title: BL/6 LSKs w/o IL-33 1

city: Bern

first: Pascal

last: Naef

address: Murtenstrasse 35

country: Switzerland

institute: University of Bern

data_processing:
fastp was used to process the raw reads (removing reads containing adapter and poly-N sequences and low-quality reads) (at Novogene)
Clean reads were mapped using the Spliced Transcripts Alignment to a Reference (STAR) software (at Novogene)
Quantification (read counts) was done using FeatureCounts
Assembly: mm10
Supplementary files format and content: Csv file contains the raw reads for each sample (per row)

organism: Mus musculus

source_name: Lin-sca1+cKit+ (LSK)

growth_protocol: BL/6 mice were sacrificed and the long bones, hips, and spines were harvested, crushed, and AcK lysed. The single cells were purified for lin- cells (CD3-CD19-Gr1-Ter119-) by magnetic cell separation (MACS), and stained for the purification of ILC2s (lin-cKit-sca1+CD25+CD127+) LSKs (lin-cKit+sca1+). The ILC2s and LSKs were sorted using an ARIA III from BD.

extract_protocol:
LSKs were suspended in RLT lysis buffer (Quiagen) and sent to Novogene Europe on dry ice for RNA isolation.
RNA libraries for RNA-seq were prepared using NEBNext Ultra TM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Sorted ILC2s were cultured in IMDM 10% (5'000 cells per 100ul), supplemented with rmIL-2 (50U/ml) and rmIL-7 (50ng/ml), +/- rmIL-33. After 24h, the ILC2 conditioned supernatant (ILC2sn) was harvested from the wells and frozen at -80°
Sorted LSKs were cultred in IMDM 10% (25000 cells per 100ul), either with or without IL-33, or in ILC2sn (originating from ILC2s treated with or without rmIL-33)

tag: cell type

value: Lin-sca1+cKit+ (LSK)

tag: genotype

value: BL/6 WT

tag: treatment

value: 24h culture +SCF +Flt3L


title: MS21016-Islets-44% fat + fiber-pooled-rep1

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

country: USA

institute: The Jackson Laboratory

library_source: genomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were conducted using the Cell Ranger ATAC v2.0.0 for snATAC-Seq
Demuxlet software was used to separate cells originating from different strain genetic backgrounds in the pooled samples.
For quality control and filtering purposes, snATAC-Seq data, nuclei having a TSS enrichment <4, or <4,000 were removed.
Assembly: GRCm38
Supplementary files format and content: islet_snATAC.h5ad

molecule: genomic DNA

source_name: islets of Langerhans

extract_protocol:
Dissociation protocol for islets; after overnight incubation, cells were dissociated prior to loading on the 10X Chromium
version 1 10x ATAC-seq chemistry

treatment_protocol: Three inbred mouse strains, NZO/HlLTJ, CAST/EiJ, and C57BL/6J, were placed on control or high fat, high sugar diet starting at six weeks of age. Tissue was collected at sixteen weeks of age.

value: islets of Langerhans

tag: diet

value: 44% fat + fiber

tag: container id

tag: sequencing id


title: Caco-2.control.rep15

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
Library name: caco.ctrl.G09
cell lysate
caco.ctrl.G09

library_source: other

data_processing:
Reads were aligned using STAR alignment on Qiagen's online analysis portal RAP version 1.0
match score 1, mismatch cost 2, discard short reads (<15), insertion and deletion cost 3, length and similarity fraction 0.8
Raw counts were logCPM normalized and filtered for low abundance (4) and variance (15).
Normalized counts were analyzed for differential expression using DESeq2 and Limma.
Assembly: for human GRCh38.noalt.106, for rainbow trout USDA_OmykA_1.1.105
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

molecule: other

source_name: colon

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to extract of interest 24 hours after seeding at 35,000 cells per well

value: colon

tag: cell line

value: epithelial


title: MS21014-Islets-44% fat + fiber-pooled-rep1


title: MS21018-Islets-10% fat + fiber-pooled-rep1

value: 10% fat + fiber


title: 46_D0

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0


title: ST2-/- ILC2s w/o IL-33 3

extract_protocol:
BL/6 and ST2-/- mice were sacrificed and the long bones, hips, and spines were harvested, crushed, and AcK lysed. The single cells were purified for lin- cells (CD3-CD19-Gr1-Ter119-) by magnetic cell separation (MACS), and stained for the purification of ILC2s (lin-cKit-sca1+CD25+CD127+). The ILC2s were sorted using an ARIA III from BD.
ILC2s were suspended in RLT lysis buffer (Quiagen) and sent to Novogene Europe on dry ice for RNA isolation.
RNA libraries for RNA-seq were prepared using NEBNext Ultra TM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Sorted ILC2s were cultured in IMDM 10% (5'000 cells per 100ul), supplemented with rhIL-2 (50U/ml) and rhIL-7 (50ng/ml), as well as rhIL-33 for the IL-33 (10ng/ml) stimulated group.

tag: strain

value: 24h culture +rhIL-2, rhIL-7


title: MS21012-Islets-44% fat + fiber-pooled-rep1


title: 45D0

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0


title: Caco-2.control.rep13

description:
Library name: caco.ctrl.G01
cell lysate
caco.ctrl.G01


title: MS21008-Islets-44% fat + fiber-pooled-rep1


title: 44_D7

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19

source_name: Total RNA from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 7


title: ST2-/- ILC2s w/o IL-33 1


title: MS21006-Islets-44% fat + fiber-pooled-rep1


title: Caco-2.control.rep12

description:
Library name: caco.ctrl.F09
cell lysate
caco.ctrl.F09


title: Caco-2.control.rep10

description:
Library name: caco.ctrl.F01
cell lysate
caco.ctrl.F01


title: BL/6 ILC2s with IL-33 4

value: WT

value: 24h culture +rhIL-2, rhIL-7, rhIL-33


title: 42_D0


title: BL/6 ILC2s with IL-33 3


title: Caco-2.control.rep9

description:
Library name: caco.ctrl.E09
cell lysate
caco.ctrl.E09


title: 41_D7


title: MS20084-Islets-10% fat + fiber-pooled-rep1


title: Caco-2.control.rep14

description:
Library name: caco.ctrl.G05
cell lysate
caco.ctrl.G05


title: BL/6 ILC2s with IL-33 2


title: Caco-2.control.rep8

description:
Library name: caco.ctrl.E05
cell lysate
caco.ctrl.E05


title: 41_D0


title: Caco-2.control.rep7

description:
Library name: caco.ctrl.E01
cell lysate
caco.ctrl.E01


title: MS20081-Islets-44% fat + fiber-pooled-rep1


title: MS20085-Islets-44% fat + fiber-pooled-rep1


title: BL/6 ILC2s with IL-33 1


title: MS20080-Islets-10% fat + fiber-pooled-rep1


title: ST2-/- ILC2s w/o IL-33 2


title: BL/6 ILC2s w/o IL-33 3


title: 39_D0


title: 40D0


title: Caco-2.control.rep11

description:
Library name: caco.ctrl.F05
cell lysate
caco.ctrl.F05


title: 44_D0


title: Caco-2.control.rep6

description:
Library name: caco.ctrl.D09
cell lysate
caco.ctrl.D09


title: MS20068-Islets-10% fat + fiber-pooled-rep1


title: Caco-2.control.rep5

description:
Library name: caco.ctrl.D05
cell lysate
caco.ctrl.D05


title: MS20074-Islets-44% fat + fiber-pooled-rep1


title: BL/6 ILC2s w/o IL-33 2


title: 38_D0


title: MS20067-Islets-10% fat + fiber-pooled-rep1


title: Caco-2.control.rep4

description:
Library name: caco.ctrl.D01
cell lysate
caco.ctrl.D01


title: MS20048-Islets-10% fat + fiber-pooled-rep1


title: RAW264.7cells, LPS,biol rep 2

city: Jinan

first: Wenjun

last: Qi

address: Xingfu Temple Street

country: China

institute: Shandong First Medical University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus_musculus.GRCm38.V99
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: articulation

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: articulation

value: Macrophage

value: LPS alone

tag: condition

value: Rheumatoid arthritis


title: RAW264.7cells, LPS,biol rep 3


title: BL/6 ILC2s w/o IL-33 1


title: 37_D0


title: 36_D0


title: Caco-2.control.rep3

description:
Library name: caco.ctrl.C09
cell lysate
caco.ctrl.C09


title: Caco-2.control.rep1.

description:
Library name: caco.ctrl.C01
cell lysate
caco.ctrl.C01


title: MS20016-Islets-44% fat + fiber-pooled-rep1


title: 36_D7


title: Caco-2.control.rep2

description:
Library name: caco.ctrl.C05
cell lysate
caco.ctrl.C05


title: 35_D0


title: RAW264.7cells, LPS,biol rep 1


title: MS20009-Islets-10% fat + fiber-pooled-rep1


title: MS20047-Islets-10% fat + fiber-pooled-rep1


title: 34_D0


title: 33D7


title: RAW264.7cells, LPS, HPT,biol rep 2

value: LPS and Hydroprotopine


title: 34_D7

value: peripheral blood


title: 7852 Cre+; IkkβL/L Sensitization, replicate 3, scRNAseq

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Data was demultiplexed and counted using Cell Range
Cell Ranger output was analyzed using Seurat version 4.3
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Esophagus

extract_protocol:
Biopsies were briefly washed with DMEM/15%FBS, minced, digested with dispase (5000 caseinolytic Units) followed by trypsin (0.25%). Single cell suspensions were washed in PBS/2% BSA and checked for viability > 85%
10X Genomics NEXT GEM Kit V2, 10X genomics Library Construction kit

value: Esophagus

value: Cre+; IKKBL/L

value: Sensitization


title: 7558 Cre+; IkkβL/L EoE, replicate 3, scRNAseq

description: 10x Genomics

value: EoE


title: RAW264.7cells, LPS, HPT,biol rep 3


title: 33D0


title: Bone marrow-derived macrophage-WT-pIL4+LPS_rep2

city: Stanford

first: Andy

last: Chen

address: 240 Pasteur Rd

institute: Stanford University

description: WT-pIL4+LPS_2_CKDL230006644-1A_HW5C5DSX5_L3

data_processing:
Fastq files were aligned to a mm10 transcriptome index with STAR
The abundance of transcripts was quantified using Salmon
Transcript-level abundance estimates were imported and summarized using tximport v1.16.1
Differential expression was determined using the DESeq2 package v1.28.11 in Bioconductor v.3.11.
Assembly: mm10
Supplementary files format and content: Raw and normalized counts(.xls).

source_name: Bone marrow

growth_protocol: Wild type, 2-3 months old female C57Bl6 mice were purchased from Jackson laboratories. Mice were sacrificed and bone marrow was isolated form the tibiae and femora of the animals. Red blood cell lysis was carried out and cells were plated in differentiation media containing 10% FBS, Dulbecco’s Modified Eagle’s Medium (DMEM) and 20ng/ml mouse M-CSF (Peprotech). On the third day of differentiation, media was replaced with fresh differentiation media. Cytokine treatments sorting procedures were carried out on the 6th day of differentiation.

extract_protocol:
Total RNA was isolated with Trizol, followed by precipitation with isopropanol. RNA was washed with 75% Ethanol and pellet was dried and dissolved in nulcease-free water.
Approximately 20ng total RNA was used for library preparation with Ovation Ultralow RNA-seq V2 (Tecan) from two biological replicates. Libraries were generated according to the manufacturer’s instructions. Approximately 50ng amplified cDNA was subjected to Ovation Ultralow V2 library generation and manufacturer’s instructions were followed. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.

treatment_protocol: Macrophages were treated with either IL-4 (20ng/ml) or IFNG (20ng/ml) (Peprotech). For polarization we used 24 hours of IL-4 polarization and 3 hours of IFNG polarization in differentiation media that contained 10% FBS, 1% penicillin/streptomycin and M-CSF (20ng/ml). IL-4 priming was performed as follows: macrophages were polarized with IL-4 (20ng/ml) for 24 hours. Cell were washed three times with serum-free DMEM, then differentiation media was replaced, and cells were rested for an additional 24 hours. Repolarization was performed at this point for 3 hours with IFNG (20ng/ml). Macrophage polarization for cell cycle experiments used 3 hours of polarization with either IL-4 or IFNG (both at a 20ng/ml concentration).

value: Bone marrow-derived macrophage

value: Bone marrow

value: wild type

tag: agent

tag: Sex

value: female


title: D9_R2

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: Maryland

address: 733 N. Broadway

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University

description: Library name: EXR-KWITW1LPPFRACD9R2-BS

data_processing:
FASTQs were sequenced as paired-end but analyzed as single read. All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
RNA Isolation method was Trizol. RNA Isolation kit was Trizol + spin column.
Library construction kit was Other. Samples were multiplexed. Type of Starting Material was total RNA.

value: Plasma

value: Healthy Control

tag: anatomical location

value: Entire body system

tag: rna source

value: protein-lipid-RNA complex

tag: rna isolation kit

value: Trizol + spin column


title: 9_S9_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACD14-BS

tag: tissue


title: 12_S12_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ4R2-BS


title: 2_S2_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ8-BS


title: 10_S10_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD17-BS


title: 7320 Cre+; IkkβL/L Sensitization, replicate 1, scRNAseq

description: 10x Genomics


title: 32D0

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0

tag: disease state

tag: time


title: Bone marrow-derived macrophage-WT-pIL4+IL10_rep2

description: WT-pIL4+IL10_2_CKDL230006644-1A_HW5C5DSX5_L3

tag: cell type


title: 7849 Cre+; IkkβL/L Sensitization, replicate 2, scRNAseq

description: 10x Genomics

tag: genotype


title: 30_D7

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7

tag: batch


title: 7851 Cre+; IkkβL/L Vehicle, replicate 2, scRNAseq

description: 10x Genomics

tag: treatment

value: Vehicle


title: D12_R2

description: Library name: EXR-KWITW1LPPFRACD12R2-BS


title: Bone marrow-derived macrophage-WT-pIL4+LPS_rep1

description: WT-pIL4+LPS_1_CKDL230006644-1A_HW5C5DSX5_L3


title: Bone marrow-derived macrophage-WT-pIL4+IL10_rep1

description: WT-pIL4+IL10_1_CKDL230006644-1A_HW5C5DSX5_L3


title: 7469 Cre+; IkkβL/L Vehicle, replicate 1, scRNAseq

description: 10x Genomics


title: RAW264.7cells, LPS, HPT,biol rep 1

value: articulation

value: Macrophage

value: Rheumatoid arthritis


title: 30_D0

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0

value: peripheral blood


title: Bone marrow-derived macrophage-WT-pIL4+IFNG_rep2

description: WT-pIL4+IFNG_2_CKDL230006644-1A_HW5C5DSX5_L3


title: D19_R2

description: Library name: EXR-KWITW1LPPFRACD19R2-BS


title: 29_D7

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19


title: 3_S3_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ12-BS


title: Bone marrow-derived macrophage-WT-pIL4+IFNG_rep1

description: WT-pIL4+IFNG_1_CKDL230006644-1A_HW5C5DSX5_L3


title: 7414 Cre+; IkkβL/L, replicate 3, scRNAseq

description: 10x Genomics

value: Esophagus

value: Cre+; IKKBL/L

value: No treatment


title: 7798 Cre+; IkkβL/L, replicate 2, scRNAseq

description: 10x Genomics


title: 7_S7_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACD8-BS


title: 28_D7


title: 29_D0


title: Bone marrow-derived macrophage-WT-pIL4+DEX_rep2

description: WT-pIL4+DEX_2_CKDL230006644-1A_HW5C5DSX5_L3

value: Bone marrow-derived macrophage


title: Q17_R2

description: Library name: EXR-KWITW1LPPFRACQ17R2-BS


title: 28_D0


title: 7400 Cre+; IkkβL/L, replicate 1, scRNAseq

description: 10x Genomics


title: 8023 IkkβL/L EoE, replicate 3, scRNAseq

description: 10x Genomics

value: IkkBetaL/L

value: EoE


title: D6_R2

description: Library name: EXR-KWITW1LPPFRACD6R2-BS


title: 26_D7


title: Q15_R2

description: Library name: EXR-KWITW1LPPFRACQ15R2-BS


title: 4_S4_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ15-BS


title: 26_D0


title: 7_S7_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACD7-BS


title: Bone marrow-derived macrophage-WT-LPS_rep2

value: Bone marrow

value: wild type

value: LPS

value: female


title: 25D7


title: Bone marrow-derived macrophage-WT-LPS_rep1


title: 7872 IkkβL/L EoE, replicate 2, scRNAseq

description: 10x Genomics


title: 7559 IkkβL/L EoE, replicate 1, scRNAseq

description: 10x Genomics


title: 25D0


title: 11_S11_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD21-BS

value: Plasma

value: Healthy Control

value: Entire body system


title: 1_S1_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ4-BS

value: protein-lipid-RNA complex

value: Trizol + spin column


title: Bone marrow-derived macrophage-WT-IL4+LPS_rep2

description: WT-IL4+LPS_2_CKDL230006644-1A_HW5C5DSX5_L3


title: 7291 IkkβL/L Sensitization, replicate 1, scRNAseq

description: 10x Genomics

value: Sensitization


title: Bone marrow-derived macrophage-WT-pIL4+DEX_rep1

description: WT-pIL4+DEX_1_CKDL230006644-1A_HW5C5DSX5_L3


title: 1_S1_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ3-BS


title: Bone marrow-derived macrophage-WT-pIL4_rep2


title: 7467 IkkβL/L Vehicle, replicate 3, scRNAseq

description: 10x Genomics

value: Vehicle


title: Bone marrow-derived macrophage-WT-pIL4_rep1


title: 23_D0

value: peripheral blood


title: D5_R2

description: Library name: EXR-KWITW1LPPFRACD5R2-BS


title: 7881 IkkβL/L Vehicle, replicate 2, scRNAseq

description: 10x Genomics

value: Esophagus


title: Bone marrow-derived macrophage-WT-IL4+LPS_rep1

description: WT-IL4+LPS_1_CKDL230006644-1A_HW5C5DSX5_L3


title: 22_DO


title: 11_S11_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ2R2-BS


title: 8_S8_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACD12-BS


title: 7971 IkkβL/L Sensitization, replicate 3, scRNAseq

description: 10x Genomics


title: Brain3Pos

city: Oklahoma City

first: Willard

last: Freeman

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics and correlation analyses were performed in Strand NGS software package (Agilent)
Reads were aligned against the Mm10 build of the mouse genome (2014.11.26). Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 6bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. Reads were filtered based on the mapping status and only those reads that aligned normally (in the appropriate direction) were retained.
Normalization was performed with the DESeq algorithm
Transcripts with an average read count value >20 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue and those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable.
For statistical analysis of differential expression, a one-way ANOVA with the factor of TRAP fraction and a Benjamini-Hochberg Multiple Testing Correction followed by Student-Newman Keuls post hoc test were used. For those transcripts meeting this statistical criterion, a fold change >|1.25| cutoff was used to eliminate those genes which were statistically significant but unlikely to be biologically significant and orthogonally confirmable due to their very small magnitude of change.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains RPKM values for each sample.

source_name: Brain

extract_protocol:
RNA from the tissues of Tam-induced Cdh5(PAC)-cre/ERT2+; NuTRAP+ mice was isolated via the TRAP method (Input and Positive fractions). Tissue was minced into small pieces and homogenized in 100 ul ice-cold homogenization buffer (50 mM Tris, pH 7.4; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 1 mg/mL sodium heparin; 1 mM DTT) supplemented with 100 ug/mL cycloheximide (#C4859-1ML, Millipore Sigma), 200 units/mL RNaseOUT™ Recombinant Ribonuclease Inhibitor (#10777019; Thermofisher), and 1X cOmplete™, EDTA-free Protease Inhibitor Cocktail (#11836170001; Millipore Sigma) with a Kimble pellet pestle cordless motor with one pulse of 10 sec/each on ice. An additional 300 uL of homogenization buffer was added and homogenized with pellet pestle cordless motor with one pulse of 10 sec/each (on ice). Volume was taken up to 1.5 mL with homogenization buffer and centrifuged at 12,000 x g for 10 minutes at 4°C. After centrifugation, 100 uL of the supernatant was saved as input. The remaining supernatant was transferred to a 2 mL round-bottom tube and incubated with 5 ug/uL of anti-GFP antibody (ab290; Abcam) at 4°C with end-over-end rotation for one hour. Dynabeads™ Protein G for Immunoprecipitation (#10003D; Thermofisher) were washed three times in 1 mL ice-cold low-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 100mM KCl; 1% NP-40; 100μg/ml cycloheximide; 1mM DTT). After removal of the last wash, the homogenate/antibody mixture was transferred to the 2 mL round-bottom tube containing the washed Protein-G Dynabeads and incubated at 4°C with end-over-end rotation for an additional two hours. Magnetic beads were collected using a DynaMag-2 magnet and the unbound-ribosomes and associated RNA saved as the “negative” fraction. Beads were then washed three times with 1 mL of high-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 300mM KCl; 1% NP-40; 100μg/ml cycloheximide; 2mM DTT). Following the last wash, 350 uL of Buffer RLT (Qiagen) supplemented with 3.5 uL 2-β mercaptoethanol was added directly to the beads and incubated with mixing on a ThermoMixer (Eppendorf) for 10 minutes at room temperature. The beads were magnetically separated and the supernatant containing the target bead-bound ribosomes and associated RNA was transferred to a new tube. 350 uL of 100% ethanol was added to the tube (“positive” fraction) and then loaded onto an RNeasy MinElute column. RNA was isolated using RNeasy Mini Kit (#74104, Qiagen), according to manufacturer’s instructions. RNA was quantified with a Nanodrop 2000c spectrophotometer (Thermofisher Scientific) and its quality assessed by HSRNA screentape with a 2200 Tapestation analyzer (Agilent Technologies)
The NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs Inc., Ipswich, MA) was used on 100 ng of total RNA for the preparation of strand-specific sequencing libraries from each TRAP-isolated RNA sample (input, negative fraction, and positive fraction), according to manufacturer's instructions. Briefly, polyA containing mRNA was purified using oligo-dT attached magnetic beads. mRNA was chemically fragmented and cDNA synthesized. For strand-specificity, the incorporation of dUTP instead of dTTP in the second strand cDNA synthesis does not allow amplification past this dUTP with the polymerase. Following cDNA synthesis, each product underwent end repair process, the addition of a single ‘A’ base, and finally ligation of adapters. The cDNA products were further purified and enriched using PCR to make the final library for sequencing. Library sizing was performed with HS DNA ScreenTape (#5067-5582; Agilent Technologies) and libraries were quantified by Qubit dsDNA HS Assay Kit (ThermoFisher Scientific). The libraries for each sample were pooled at 4 nM concentration and sequenced using an Illumina NextSeq 6000 system (PE75bp) at the Oklahoma Medical Research Foundation Genomics Facility.

value: Brain

value: Cdh5(PAC)-cre/ERT2+; NuTRAP+

tag: fraction

value: Positive

tag: library prep_kit

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: 7713 IkkβL/L Sensitization, replicate 2, scRNAseq

description: 10x Genomics

value: IkkBetaL/L


title: Bone marrow-derived macrophage-WT-IL4+IFNG_rep2

description: WT-IL4+IFNG_2_CKDL230006644-1A_HW5C5DSX5_L3

value: Bone marrow-derived macrophage

value: Bone marrow

value: wild type


title: 21_D7


title: 10_S10_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACD20-BS

value: Plasma


title: Bone marrow-derived macrophage-WT-IL4+IFNG_rep1

description: WT-IL4+IFNG_1_CKDL230006644-1A_HW5C5DSX5_L3

value: female


title: Brain2Pos


title: Bone marrow-derived macrophage-WT-IL4+DEX_rep2

description: WT-IL4+DEX_2_CKDL230006644-1A_HW5C5DSX5_L3


title: 21_D0


title: Bone marrow-derived macrophage-WT-IL4+IL10_rep2

description: WT-IL4+IL10_2_CKDL230006644-1A_HW5C5DSX5_L3


title: Brain1Pos


title: 9_S9_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD13-BS

value: Healthy Control

value: Entire body system


title: 5_S5_L002_R1_001

description: Library name: EXR-KWITW1LPPFRAC18-BS

value: Trizol + spin column


title: 24_D0

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 at day 0


title: Brain3Input

value: Input


title: 20_D0


title: 7428 IkkβL/L, replicate 3, scRNAseq

description: 10x Genomics

value: No treatment


title: 22_D7

value: peripheral blood


title: Bone marrow-derived macrophage-WT-IL4+DEX_rep1

description: WT-IL4+DEX_1_CKDL230006644-1A_HW5C5DSX5_L3


title: Bone marrow-derived macrophage-WT-IL4+IL10_rep1

description: WT-IL4+IL10_1_CKDL230006644-1A_HW5C5DSX5_L3


title: D7_R2

description: Library name: EXR-KWITW1LPPFRACD7R2-BS

value: protein-lipid-RNA complex


title: Bone marrow-derived macrophage-WT-IL4_rep24h_rep1

description: WT-IL4_24h_1_CKDL230006644-1A_HW5C5DSX5_L3


title: D10_R2

description: Library name: EXR-KWITW1LPPFRACD10R2-BS


title: Brain2Input

value: Brain


title: 17_D0


title: Q16_R2

description: Library name: EXR-KWITW1LPPFRACQ16R2-BS


title: Bone marrow-derived macrophage-WT-IL10_rep2


title: Retina3Pos

source_name: Retina

value: Retina

value: Cdh5(PAC)-cre/ERT2+; NuTRAP+


title: 16_D0


title: 3_S3_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ10-BS


title: Bone marrow-derived macrophage-WT-IL10_rep1


title: Retina2Pos

value: Positive

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: Q13_R2

description: Library name: EXR-KWITW1LPPFRACQ13R2-BS


title: 6_S6_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACD3-BS


title: Bone marrow-derived macrophage-WT-IFNG_rep1

value: Bone marrow-derived macrophage

value: IFNG


title: Retina1Pos


title: 15_D0


title: 18_D0


title: 3_S3_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ11-BS


title: Bone marrow-derived macrophage-WT-IFNG_rep2

value: Bone marrow

value: wild type


title: 18_D7


title: Retina2Input


title: 14_D0


title: Bone marrow-derived macrophage-WT-DEX_rep2

value: DEX

value: female


title: Retina3Input


title: Bone marrow-derived macrophage-WT-IL4_rep24h_rep2

description: WT-IL4_24h_2_CKDL230006644-1A_HW5C5DSX5_L3


title: 14_D7

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 7


title: Bone marrow-derived macrophage-WT-DEX_rep1


title: Retina1Input


title: Q8_R2

description: Library name: EXR-KWITW1LPPFRACQ8R2-BS

value: Plasma

value: Healthy Control

value: Entire body system


title: Choroid3Pos

source_name: Choroid

value: Choroid


title: 6_S6_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACD2-BS

value: Trizol + spin column


title: 13_D0

value: peripheral blood


title: Bone marrow-derived macrophage-WT-CTR_rep2

value: CTR


title: Choroid2Pos


title: 11_S11_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ1R2-BS


title: Brain1Input

value: Brain

value: Input


title: 15_D7


title: Bone marrow-derived macrophage-WT-CTR_rep1


title: 5_S5_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ19-BS


title: 11_D0

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19 and SDRA at day 0


title: 9_D0


title: Choroid1Pos

value: Cdh5(PAC)-cre/ERT2+; NuTRAP+

value: Positive


title: Bone marrow-derived macrophage-KO-pIL4+LPS_rep1

description: KO-pIL4+LPS_1_CKDL230006644-1A_HW5C5DSX5_L3

value: Bone marrow-derived macrophage

value: STAT6 KO


title: Bone marrow-derived macrophage-KO-pIL4+LPS_rep2

description: KO-pIL4+LPS_2_CKDL230006644-1A_HW5C5DSX5_L3

value: Bone marrow


title: 7_D7

description: Total RNA from peripheral blood from adult patients with a positive RT-PCR for SARS-CoV-2 and COVID-19


title: Choroid3Input

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: Bone marrow-derived macrophage-KO-pIL4+IL10_rep2

description: KO-pIL4+IL10_2_CKDL230006644-1A_HW5C5DSX5_L3


title: Choroid2Input


title: Q14_R2

description: Library name: EXR-KWITW1LPPFRACQ14R2-BS

value: protein-lipid-RNA complex


title: D16_R2

description: Library name: EXR-KWITW1LPPFRACD16R2-BS


title: D3_R2

description: Library name: EXR-KWITW1LPPFRACD3R2-BS


title: 6_D7


title: 1227_WT_Pos

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics and correlation analyses were performed in Strand NGS software package (Agilent)
Reads were aligned against the Mm10 build of the mouse genome with RefSeq Genes and Transcripts (2013.04.01) annotation build. Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 6bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. Reads were filtered based on the mapping status and only those reads that aligned normally (in the appropriate direction) were retained.
Normalization was performed with the DESeq algorithm
Transcripts with an average read count value >50 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue and those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable
For statistical analysis of differential expression, a moderated T-test with Benjamini-Hochberg Multiple Testing Correction was used. For those transcripts meeting this statistical criterion, a fold change >|1.25| cutoff was used to eliminate those genes which were statistically significant but unlikely to be biologically significant and orthogonally confirmable due to their very small magnitude of change.
For statistical multiple comparison analysis of differential expression, 1-way ANOVA was performed, followed by Student-Newman-Keuls (SNK) pairwise post-hoc test T-test with Benjamini-Hochberg Multiple Testing Correction.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains RPKM values for each sample.

extract_protocol:
Mouse brain samples were rinsed in D-PBS, sliced into sagittal sections, placed into gentleMacs C-tubes, and processed for generation of single-cell suspensions using the Adult brain dissociation kit and gentleMacsTM Octodissociator system (#130-107-677 and #130-095-937, respectively, Miltenyi Biotech, San Diego, CA) (Chucair-Elliott et al., 2020; Ocanas et al., 2022). The single-cell suspensions were then immunostained for flow cytometric analysis of EGFP+ cell populations in the brain. The gating strategy of single cells was set to EGFP+/CD11b-/CD31+ for endothelial cells and EGFP+/CD11b+/CD31- for putative microglia. The antibodies used were anti-mouse CD11b: Vioblue (#130-113-810, clone REA592) and anti-CD31: APC (#130-111-355, clone REA784) (Milteny Biotec). Samples were analyzed with a MACSQuant Analyzer 10 Flow Cytometer (Miltenyi Biotec USA, Gaithersburg, MA) using MACSQuantify v2.13.0 software (Ocanas et al., 2022). A 488 nm (blue) laser with 525/50 and 585/40 filter combinations was used to gate on EGFP+cells within single cells (singlets) without auto-fluorescence interference, as previously performed for NuTRAP models (Chucair-Elliott et al., 2020; Ocanas et al., 2022). A 640 nm laser (red) with 655/730 nm filter and a 405 nm (violet) laser with 450/50 filter were used for detection of CD31 and CD11b, respectively. For cell sorting of endothelial cells, immunolabeled brain cell suspensions were loaded into the input chamber of a MACSQuant Tyto cartridge, to run through a MACSQuant Tyto Cell Sorter system (#130-103-931, Miltenyi Biotec) (Ocanas et al., 2022). A blue (488 nm) laser with B1 (525/50 nm) and B2 (585/40 nm) filter combinations was used to gate on eGFP+ cells without auto-fluorescence interference. Subsequent gating was based on CD31: APC fluorescence used a red (638 nm) laser and R1 (655-730 nm) filter and exclusion of CD11b: Vioblue fluorescence, using a violet (405 nm) laser and V1 (450/50) nm filter. After completion of the sort, the cells from the positive fraction chamber were collected in 0.5% BSA in D-PBS. The positive fraction chamber was washed twice using 450 µL of 0.5% BSA in D-PBS per wash and combined with the initial positive fraction collection. An aliquot of (10%) of the positive fraction was kept for analysis on the MACSQuant Analyzer 10 Flow Cytometer while the rest of the sorted sample was pelleted, along with an initial aliquot of input cell suspension (pre-sort) was resuspended in RNeasy Plus lysis buffer and subjected to RNA extraction using the AllPrep DNA/RNA Mini Kit (#80204, Qiagen), according to manufacturer’s instructions. RNA was quantified with a Nanodrop One spectrophotometer (Thermo Fisher Scientific) and its quality assessed by HSRNA ScreenTape with a 4150 TapeStation analyzer (Agilent Technologies, Santa Clara, CA).
The NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs Inc., Ipswich, MA) was used with 25 ng of total RNA for the preparation of strand-specific sequencing libraries from TRAP-isolated RNA samples (input and positive fraction) according to manufacturer's instructions (Chucair-Elliott et al., 2020). Briefly, polyA containing mRNA was purified using oligo-dT attached magnetic beads. mRNA was chemically fragmented and cDNA synthesized. For strand-specificity, the incorporation of dUTP instead of dTTP in the second strand cDNA synthesis does not allow amplification past this dUTP with the polymerase. Following cDNA synthesis, each product underwent end repair process, the addition of a single ‘A’ base, and finally ligation of adapters. The cDNA products were further purified and enriched using PCR to make the final library for sequencing. Library sizing was performed with HS RNA ScreenTape (#5067-5579; Agilent Technologies). The libraries for each sample from each mouse model were pooled at 2-4 nM concentration and sequenced in independent runs using an Illumina NovaSeq 6000 system (PE150bp) at the OMRF Clinical Genomics Facility.

value: Tie2-cre+; NuTRAP+


title: 7_D0


title: D18_R2

description: Library name: EXR-KWITW1LPPFRACD18R2-BS

value: Plasma


title: 12D0


title: Bone marrow-derived macrophage-KO-pIL4+IL10_rep1

description: KO-pIL4+IL10_1_CKDL230006644-1A_HW5C5DSX5_L3

value: female


title: Choroid1Input


title: 6_S6_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD1-BS

value: Healthy Control

value: Entire body system


title: 6_D0


title: 1223_WT_Pos


title: 5_D7


title: Bone marrow-derived macrophage-KO-pIL4+DEX_rep2

description: KO-pIL4+DEX_2_CKDL230006644-1A_HW5C5DSX5_L3


title: Bone marrow-derived macrophage-KO-pIL4+IFNG_rep1

description: KO-pIL4+IFNG_1_CKDL230006644-1A_HW5C5DSX5_L3


title: 2_S2_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ6-BS

value: Trizol + spin column


title: 2_S2_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ7-BS


title: 1222_WT_Pos


title: Bone marrow-derived macrophage-KO-pIL4+DEX_rep1

description: KO-pIL4+DEX_1_CKDL230006644-1A_HW5C5DSX5_L3


title: 5_D0

value: peripheral blood


title: 4_D7


title: 1227_WT_Input


title: Bone marrow-derived macrophage-KO-pIL4_rep2


title: Bone marrow-derived macrophage-KO-pIL4+IFNG_rep2

description: KO-pIL4+IFNG_2_CKDL230006644-1A_HW5C5DSX5_L3


title: 4_D0


title: 9_S9_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACD16-BS


title: Bone marrow-derived macrophage-KO-pIL4_rep1


title: 1222_WT_Input


title: 1D0


title: D4_R2

description: Library name: EXR-KWITW1LPPFRACD4R2-BS


title: 9_S9_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACD15-BS


title: D17_R2

description: Library name: EXR-KWITW1LPPFRACD17R2-BS


title: CTI 60

city: Morgantown

first: Pius

last: Joseph

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division/Toxicology and Molecular Biology Branch

institute: National Institute for Occupational Safety and Health (NIOSh)

data_processing:
Map reads to human genome version 38
normalize libraries usng DESeq2
remove any genes with counts less than 10
convert transcripts to genes using tximeta
identify differentially expressed genes using Deseq2
Supplementary_files_format_and_content: tar folder containing counts and meta data

extract_protocol:
Human blood samples collected were immediately mixed with RNALater (Invitrogen, Carlsbad, CA) and kept frozen until used for RNA isolation. Total RNA was isolated from 2ml blood sample (0.5 ml blood and 1.5 ml RNALater) each using Ribopure Blood Kit (ThermoFisher Scientific, Waltham, MA), including DNA treatment. The RNA extracted was quantified using a Nanodrop ND-1000 (ThermoFisher Scientific) and quality assessed via an Agilent 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA) using Agilent RNA 6000 Nano Reagents. Only RNA samples with an RNA Integrity Number (RIN) >8.0 were used to construct next generation sequence (NGS) libraries.
Immediately prior to NGS library synthesis, 1.4 mg total RNA per blood sample was used to deplete alpha and beta globin mRNA, using the GLOBINClear kit (ThermoFisher Scientific, Waltham, MA). 0.5mg globin-depleted RNA was then used as input for the Illumina TruSeq Stranded mRNA Kit to synthesize NGS libraries. Library synthesis was carried out using the default protocol in the Low Sample TruSeq Stranded mRNA Sample Preparation Guide with the following two modifications: fragmentation time was reduced to 3 minutes to achieve insert lengths ranging between 125 and 250 bp and the PCR amplification was reduced to 12 cycles. Individual cDNA libraries were quantified using a Qubit 3.0 Fluorometer (Invitrogen by ThermoFisher Scientific) and the dsDNA HS Assay Kit (Invitrogen by ThermoFisher Scientific). The average fragment size for each library was determined using an Agilent 2100 Bioanalyzer with High Sensitivity DNA Reagents.
Libraries were used in 2 x 125 basepair sequencing using the Illumina HiSeq 2500 (Illumina, San Diego, CA) in high output mode with v4 HiSeq Cluster and SBS Kits (Illumina).

tag: radiography

value: normal

tag: silica exposure time (years)

value: blood


title: CTI 58


title: Bone marrow-derived macrophage-KO-IL4+LPS_rep1

description: KO-IL4+LPS_1_CKDL230006644-1A_HW5C5DSX5_L3

tag: strain


title: 953_pos_Brain

extract_protocol:
The purification of endothelial RNA from retina, brain, and choroid tissues was achieved following an established protocol, with some modifications to facilitate the rupture of blood vessel structures and release the polysomes of endothelial cells (Chucair-Elliott et al., 2020; Heng et al., 2019b; Roh et al., 2017). Retina TRAP: Two retinae were pooled as a biological replicate and homogenized in ice-cold homogenization buffer (50 mM Tris, pH 7.4; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 1 mg/ml sodium heparin; 1 mM DTT) supplemented with 100 µg/ml cycloheximide (#C4859-1ML, Millipore Sigma), 0.5 mM spermidine (#05292-1ML-F, Millipore Sigma), 200 units/ml RNaseOUT Recombinant Ribonuclease Inhibitor (#10777019; Thermo Fisher), and 1X cOmplete, EDTA-free Protease Inhibitor Cocktail (#11836170001; Millipore Sigma), using a pellet pestle cordless motor (#749540-000; Kimble) (two pulses of 10 sec/each, on ice). Choroid TRAP: RPE-choroidal cells from two fellow eyes were collected in homogenization buffer by gently scraping with forceps. After passing homogenization volume to a tube, samples were homogenized with pellet pestle cordless motor with two pulses of 10 sec/each (on ice). Brain TRAP: Half a dissected brain was minced and homogenized in a 1.2ml glass dounce homogenizer. The homogenate was divided and distributed to two 1.5 ml RNAse-free tubes and further homogenized with pellet pestle cordless motor with two pulses of 10 sec/each (on ice). For each tissue sample, the homogenate was transferred to a 2 ml round-bottom tube and centrifuged at 12,000 x g for 10 minutes at 4°C. After centrifugation, 150 µl of the supernatant was saved as input. The remaining supernatant was transferred to a 2 ml round-bottom tube and incubated with 5 µg/µl of anti-GFP antibody (ab290; Abcam) at 4°C with end-over-end rotation overnight. Dynabeads Protein G for Immunoprecipitation (#10003D; Thermo Fisher) were washed three times in 1 ml ice-cold low-salt wash buffer (50 mM Tris, pH 7.5; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 100 μg/ml cycloheximide; 1mM DTT). After removal of the last wash, the homogenate/antibody mixture was transferred to the 2 ml round-bottom tube containing the washed Protein-G Dynabeads and incubated at 4°C overnight with end-over-end rotation. Magnetic beads were collected using a DynaMag-2 magnet. Beads were then washed three times with 1 ml of high-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 300mM KCl; 1% NP-40; 100μg/ml cycloheximide; 1mM DTT). Following the last wash, 350 µl of Buffer RLT (Qiagen) supplemented with 3.5 µl 2-β mercaptoethanol was added directly to the beads and incubated with mixing on a ThermoMixer (Eppendorf) for 10 minutes at room temperature. The beads were magnetically separated and the supernatant containing the target bead-bound ribosomes and associated RNA was transferred to a new tube. 350 µl of 100% ethanol was added to the tube (“positive” fraction: enriched in translatome associated to EGFP-tagged ribosomes) and then loaded onto a RNeasy MinElute column. RNA was isolated using RNeasy Mini Kit (#74104, Qiagen), according to manufacturer’s instructions. RNA was quantified with a Nanodrop One spectrophotometer (Thermo Fisher Scientific) and its quality assessed by HSRNA ScreenTape with a 4150 TapeStation analyzer (Agilent Technologies, Santa Clara, CA).
The NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs Inc., Ipswich, MA) was used with 25 ng of total RNA for the preparation of strand-specific sequencing libraries from TRAP-isolated RNA samples (input and positive fraction) according to manufacturer's instructions (Chucair-Elliott et al., 2020). Briefly, polyA containing mRNA was purified using oligo-dT attached magnetic beads. mRNA was chemically fragmented and cDNA synthesized. For strand-specificity, the incorporation of dUTP instead of dTTP in the second strand cDNA synthesis does not allow amplification past this dUTP with the polymerase. Following cDNA synthesis, each product underwent end repair process, the addition of a single ‘A’ base, and finally ligation of adapters. The cDNA products were further purified and enriched using PCR to make the final library for sequencing. Library sizing was performed with HS RNA ScreenTape (#5067-5579; Agilent Technologies). The libraries for each sample from each mouse model were pooled at 2-4 nM concentration and sequenced in independent runs using an Illumina NovaSeq 6000 system (PE150bp) at the OMRF Clinical Genomics Facility.

value: Brain


title: Bone marrow-derived macrophage-KO-IL4+LPS_rep2

description: KO-IL4+LPS_2_CKDL230006644-1A_HW5C5DSX5_L3

tag: agent


title: 960_pos_Brain


title: CTI 57


title: 4_S4_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ14-BS

tag: condition


title: Q9_R2

description: Library name: EXR-KWITW1LPPFRACQ9R2-BS

tag: anatomical location


title: Bone marrow-derived macrophage-KO-IL4+IL10_rep2

description: KO-IL4+IL10_2_CKDL230006644-1A_HW5C5DSX5_L3

tag: Sex


title: 960_input_Brain

value: Input


title: 1223_WT_Input


title: 4_S4_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ13-BS

tag: rna source

tag: rna isolation kit


title: Bone marrow-derived macrophage-KO-IL4+IFNG_rep2

description: KO-IL4+IFNG_2_CKDL230006644-1A_HW5C5DSX5_L3

tag: tissue


title: CTI 53


title: Bone marrow-derived macrophage-KO-IL4+IFNG_rep1

description: KO-IL4+IFNG_1_CKDL230006644-1A_HW5C5DSX5_L3


title: 953_input_Brain


title: 421_input_Brain


title: D1_R2

description: Library name: EXR-KWITW1LPPFRACD1R2-BS


title: D14_R2

description: Library name: EXR-KWITW1LPPFRACD14R2-BS


title: CTI 52


title: 421_pos_Brain

value: Positive


title: CTI 49


title: Bone marrow-derived macrophage-KO-IL4+DEX_rep2

description: KO-IL4+DEX_2_CKDL230006644-1A_HW5C5DSX5_L3

value: Bone marrow-derived macrophage


title: Bone marrow-derived macrophage-KO-IL4+DEX_rep1

description: KO-IL4+DEX_1_CKDL230006644-1A_HW5C5DSX5_L3

value: STAT6 KO


title: 8_S8_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD9-BS


title: 960_pos_Ret

value: Retina


title: 421_pos_Ret

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: Bone marrow-derived macrophage-KO-IL4_rep24h_rep2

description: KO-IL4_24h_2_CKDL230006644-1A_HW5C5DSX5_L3

value: Bone marrow


title: Bone marrow-derived macrophage-KO-IL4+IL10_rep1

description: KO-IL4+IL10_1_CKDL230006644-1A_HW5C5DSX5_L3


title: 953_pos_Ret

value: Tie2-cre+; NuTRAP+


title: CTI 48


title: 7_S7_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACD6-BS

value: Plasma


title: CTI 54


title: Q10_R2

description: Library name: EXR-KWITW1LPPFRACQ10R2-BS

value: protein-lipid-RNA complex


title: CTI 37


title: 953_input_Ret


title: Bone marrow-derived macrophage-KO-IL4_rep24h_rep1

description: KO-IL4_24h_1_CKDL230006644-1A_HW5C5DSX5_L3

value: female


title: 1_S1_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ2-BS

value: Healthy Control

value: Entire body system


title: CTI 33


title: 960_input_Ret


title: Bone marrow-derived macrophage-KO-CTR_rep2

value: CTR


title: 12_S12_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ7R2-BS

value: Trizol + spin column


title: CTI 41

value: normal

value: blood


title: 8_S8_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACD11-BS


title: CTI 32


title: 960_pos_Chor

value: Choroid


title: CTI 31


title: Bone marrow-derived macrophage-pIL4_rep2

library_source: genomic

data_processing:
Reads were trimmed for quality and adapter sequences using fastQC.
Trimmed reads were aligned to the mm10 reference genome using bowtie2.
Aligned reads were deduplicated using Picard.
Peakswere called using MACS2 from the paired endbed file (bedpe) using a false discovery thresh-old of 0.05 (-q 0.05).
Normalized bigwig files were created by normalizing the coverage track of the bedpe file by reads in peaks.
Assembly: mm10
Supplementary files format and content: Normalized bigwig files.

extract_protocol:
Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0).
DNA was quantified by Qubit and 10 ng DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 12 PCR cycles.

value: wild type


title: Q12_R2

description: Library name: EXR-KWITW1LPPFRACQ12R2-BS


title: Bone marrow-derived macrophage-pIL4_rep1

value: Bone marrow-derived macrophage


title: 421_pos_Chor

value: Positive


title: CTI 29


title: 953_pos_Chor


title: Bone marrow-derived macrophage-pIFNG_rep2

value: pIFNG


title: Bone marrow-derived macrophage-pIFNG_rep1


title: Q18_R2

description: Library name: EXR-KWITW1LPPFRAC18R2-BS


title: 2_S2_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ5-BS


title: CTI 28


title: CTI 27


title: D15_R2

description: Library name: EXR-KWITW1LPPFRACD15R2-BS


title: 960_input_Chor

value: Input

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: CTI 22


title: 953_input_Chor

value: Tie2-cre+; NuTRAP+


title: 421_input_Ret

value: Retina


title: Bone marrow-derived macrophage-IL4_rep2

value: Bone marrow


title: Q20_R2

description: Library name: EXR-KWITW1LPPFRACQ20R2-BS

value: Plasma

value: protein-lipid-RNA complex


title: Bone marrow-derived macrophage-IFNG_rep2

value: female

value: IFNG


title: D2_R2

description: Library name: EXR-KWITW1LPPFRACD2R2-BS

value: Healthy Control

value: Entire body system

value: Trizol + spin column


title: 421_input_Chor

value: Choroid


title: CTI 18

value: normal

value: blood


title: Bone marrow-derived macrophage-IL4_rep1

value: Bone marrow-derived macrophage

value: wild type


title: Bone marrow-derived macrophage-KO-CTR_rep1

value: STAT6 KO

value: CTR


title: Bone marrow-derived macrophage-IFNG_rep1


title: SAP

city: Hangzhou

first: Aikun

last: Fu

address: No. 866 Yuhangtang Road

institute: Zhejiang University

description: 10x Genomics

data_processing:
The Fastq files(10x Genomics) was processed by CellRanger and aligned to the mm10(provided by 10x Genomics) with default alignment parameters.
Seurat was then applied for further data analysis of clustering and dimensionally reduction. For filtering, cells with  less than 200 detected genes, as well as those with mitochondrial transcripts proportion higher than 20% were excluded.
Assembly: mm10
Supplementary files format and content: tsv

molecule: polyA RNA

source_name: ileum

extract_protocol:
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3)
The following cDNA amplification and library construction steps were performed according to the standard protocol.

value: ileum

value: T cells


title: 8_S8_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACD10-BS


title: Control

description: 10x Genomics


title: Bone marrow-derived macrophage-CTR_rep2

value: Bone marrow


title: 12_S12_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ5R2-BS

value: Plasma


title: CTI 9


title: CTI 7


title: Bone marrow-derived macrophage-CTR_rep1


title: 7_S7_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD5-BS


title: WT_UnStim_rep2

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description: B cells_female_BALB/c_unstimulated _Rep2

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
The reference genome (mm10) based alignment of clean reads were performed using STAR (v.2.6.1a) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts packgae by subread/2.0.1 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.

source_name: spleen

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina TruSeq mRNA for Sequencing.

treatment_protocol: Bead purified B cells (10M) from three 7-11week-old wild-type BALB/c mice were stimulated for 4 hours at 10M/ml with TLR9 agonist CpG (CpG ODN 1826, Hokkaido System Science) at 10µg/ml or left unstimulated.

value: spleen

value: Bead purified B cells

value: BALB/c

value: NoStim


title: WT_UnStim_rep3

description: B cells_male_BALB/c_unstimulated _Rep3

value: male


title: Treg-3

city: shanghai

first: Yali

address: 800 Xiangyin Road

institute: Second Military Medical University

description: Treg cells were collected at 3 days under Treg differentiation conditions

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome (GRCm38.p6) using Bowtie2
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-Seq by Expectation Maximization (RSEM).
Assembly: mm10
Supplementary files format and content: Excle file includes raw counts and FPKM values for each Sample

source_name: mouse spleen CD4+ T cells

extract_protocol:
Naivet, Th0, Th17 and Treg cells were collected at indicated times for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

value: mouse spleen CD4+ T cells

tag: cell line

value: Treg cells

value: Treg differentiation


title: CTI 5

value: normal

value: blood


title: 5_S5_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ20-BS

value: Healthy Control

value: Entire body system

value: Trizol + spin column


title: CTI 15


title: WT_UnStim_rep1

description: B cells_female_BALB/c_unstimulated _Rep1

value: female

tag: cell type


title: D20_R2

description: Library name: EXR-KWITW1LPPFRACD20R2-BS

value: protein-lipid-RNA complex


title: Treg-2

value: Treg cell

tag: genotype

value: wild type


title: CTI 2


title: WT_Stim_rep3

description: B cells_male_BALB/c_stimulated with TLR9 agonist (CpG) _Rep3

value: spleen

value: TLR9 agonists


title: TESC_89

source_name: blood_dust exposed without silicosis


title: TESC_87


title: Th17-3

description: Th17 cells were collected at 3 days under Th17 differentiation conditions

value: Th17 cells

value: Th17 differentiation


title: 1_S1_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ1-BS

value: Plasma


title: 10_S10_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACD19-BS


title: Th17-2

value: mouse spleen CD4+ T cells

value: Th17 cell


title: WT_Stim_rep1

description: B cells_female_BALB/c_stimulated with TLR9 agonist (CpG) _Rep1

value: Bead purified B cells

value: BALB/c


title: TESC_86

value: normal

value: blood


title: 10_S10_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACD18-BS

value: Healthy Control

value: Entire body system


title: TLR9KO_TLR779_stimNo.2

description: B cells_Tlr779_Tlr9-/-  MRL/lpr_unstimulated_Rep2

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols, using the Illumina TruSeq mRNA  for Sequencing.

treatment_protocol: Bead purified B cells (5M) from three Tlr779 Tlr9-/- and three Tlr7WT Tlr9-/- 5-7-week-old male MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated. Bead purified B cells (4M) from three Tlr997 Tlr7-/- and three Tlr9-/- Tlr7-/- 5-7-week-old female MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR9 agonist CpG (ODN 1826, Hokkaido System Science) at 10µg/ml or left unstimulated.

value: MRL/lpr (MRL.Faslpr)

value: B cells

value: StimNo


title: Q11_R2

description: Library name: EXR-KWITW1LPPFRACQ11R2-BS

value: protein-lipid-RNA complex

value: Trizol + spin column


title: Th0-1

description: Naïve t cells were stimulated with αCD3/CD28 for three days

value: Th0 cell

value: wild type

value: Stimulated with αCD3/CD28 for three days


title: Th0-3

value: Th0 cells


title: TESC_84


title: TESC_82


title: Naïvet-2

description: CD4+ T cells directly selected from the spleen

value: mouse spleen CD4+ T cells

value: Naive CD4+ T cells


title: 12_S12_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ6R2-BS

value: Plasma


title: 6_S6_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACD4-BS


title: TESC_83


title: TESC_80


title: Naïvet-1

value: Naive CD4+ T cell

value: CD4+ T cells directly selected from the spleen


title: TLR9KO_TLR779_stimNo.1

description: B cells_Tlr779_Tlr9-/-  MRL/lpr_unstimulated_Rep1

value: spleen

value: Bead purified B cells


title: TLR9KO_TLR779_stimTLR7.2

description: B cells_Tlr779_Tlr9-/-  MRL/lpr_stimulated with TLR7 agonist (CL097)_Rep2


title: WT_Stim_rep2

description: B cells_female_BALB/c_stimulated with TLR9 agonist (CpG) _Rep2

value: female

value: BALB/c

value: TLR9 agonists


title: TESC_79

value: normal

value: blood


title: 5_S5_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ17-BS

value: Healthy Control

value: Entire body system

value: Trizol + spin column


title: TLR9KO_TLR779_stimTLR7.1

description: B cells_Tlr779_Tlr9-/-  MRL/lpr_stimulated with TLR7 agonist (CL097)_Rep1

value: MRL/lpr (MRL.Faslpr)

value: B cells


title: TLR9KO_TLR779_stimNo.3

description: B cells_Tlr779_Tlr9-/-  MRL/lpr_unstimulated_Rep3

value: StimNo


title: 4_S4_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ16-BS


title: Q19_R2

description: Library name: EXR-KWITW1LPPFRACQ19R2-BS

value: protein-lipid-RNA complex


title: TLR9het_TLR7KO_stimTLR9.3

description: B cells_Tlr9+/-_Tlr7-/-  MRL/lpr_stimulated with TLR9 agonist (CpG)_Rep3


title: TESC_77


title: tumor,BG136 + anti-PD-1 antibodies, i.v. rep4

city: Yantai

first: Yuting

last: Xu

address: No. 198, Binhai East Road

institute: Bohai Rim Advanced Research Institute for Drug Discovery

data_processing:
Raw data (raw reads) were processed using Trimmomatic.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq (2012) R package functions estimateSizeFactors and nbinomTest.
Assembly: GRCm39
Supplementary files format and content: Excel spreadsheet file includes FPKM values for each sample

source_name: tumor

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following  the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: tumor

value: Colon adenocarcinoma cells

value: Wild type

value: Intravenous injection of BG136 and  anti-PD-1 antibodies


title: 11_S11_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ3R2-BS

value: Plasma


title: TESC_78


title: tumor,BG136 + anti-PD-1 antibodies, i.v. rep3


title: TESC_76


title: TLR9het_TLR7KO_stimTLR9.2

description: B cells_Tlr9+/-_Tlr7-/-  MRL/lpr_stimulated with TLR9 agonist (CpG)_Rep2

value: spleen

value: Bead purified B cells


title: tumor,BG136 + anti-PD-1 antibodies, i.v. rep2


title: D8_R2

description: Library name: EXR-KWITW1LPPFRACD8R2-BS


title: tumor,BG136 + anti-PD-1 antibodies, i.v. rep5


title: TESC_75


title: D11_R2

description: Library name: EXR-KWITW1LPPFRACD11R2-BS


title: tumor,BG136 + anti-PD-1 antibodies, i.v. rep1


title: TLR9het_TLR7KO_stimTLR9.1

description: B cells_Tlr9+/-_Tlr7-/-  MRL/lpr_stimulated with TLR9 agonist (CpG)_Rep1


title: TLR9KO_TLR779_stimTLR7.3

description: B cells_Tlr779_Tlr9-/-  MRL/lpr_stimulated with TLR7 agonist (CL097)_Rep3


title: TLR9het_TLR7KO_stimNo.2

description: B cells_Tlr9+/-_Tlr7-/- MRL/lpr_unstimulated _Rep2


title: tumor, anti-PD-1 antibodies, i.v. rep5

value: Intravenous injection of anti-PD-1 antibodies


title: tumor, anti-PD-1 antibodies, i.v. rep4


title: TESC_71

value: normal


title: 3_S3_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ9-BS


title: TESC_74

value: blood


title: TLR9het_TLR7KO_stimNo.3

description: B cells_Tlr9+/-_Tlr7-/- MRL/lpr_unstimulated _Rep3


title: D13_R2

description: Library name: EXR-KWITW1LPPFRACD13R2-BS

value: Healthy Control


title: TLR9het_TLR7KO_stimNo.1

description: B cells_Tlr9+/-_Tlr7-/- MRL/lpr_unstimulated _Rep1


title: tumor, anti-PD-1 antibodies, i.v. rep3


title: D21_R2

description: Library name: EXR-KWITW1LPPFRACD21R2-BS

value: Entire body system


title: TESC_68


title: tumor, anti-PD-1 antibodies, i.v. rep2


title: TLR997_TLR7KO_stimTLR9.3

description: B cells_Tlr997_Tlr7-/-  MRL/lpr_stimulated with TLR9 agonist (CpG)_Rep3


title: WT STING Control sgRNA

city: Philadelphia

first: Samuel

last: Chauvin

address: 518 Johnson Pavilion, 3610 Hamilton Walk

department: Medicine

institute: University of Pennsylvania Perelman School of Medicine

description: Library name: Sample 4

data_processing:
Reads were cleaned using cutadapt v3.0 (adapter sequence AGATCGGAAGAGC, minimum fragment length 30, minimum overlap 5, NextSeq quality cutoff 20).
The cleaned reads were pseudoaligned to known genes in GRCh38 release 85 using salmon (v1.3.0) with options libType IU, seqBias adjustment, gcBias adjustment, validateMappings, and numBootstraps 50.
Heatmaps used salmon TPM values.
We created abundance.h5 files from those output using the wasabi R package (v1.0.1).
Differential expression was calculated using the bootstrapped TPMs with sleuth (v0.30.0; R v4.0.3).
Assembly: GRCh38
Supplementary files format and content: Excel sheet with TPM values for each sample.

source_name: Jurkat T cells

growth_protocol: Jurkat T cells were culutred in R10 at 37˚C with 5% CO2.

extract_protocol:
RNA was isolated using the Qiagen Rneasy Mini kit with on-column Dnase treatment.
Libraries were prepared using the Illumina Stranded Total RNA prep with ribo-zero plus kit according to manufacturer's instructions.

treatment_protocol: Cells were treated with doxycycline (100 ng/mL) for 36 hours to induce expressio of either WT STING or STING N154S.

value: Jurkat T cells

value: WT STING Control sgRNA


title: tumor, anti-PD-1 antibodies, i.v. rep1


title: TLR997_TLR7KO_stimTLR9.2

description: B cells_Tlr997_Tlr7-/-  MRL/lpr_stimulated with TLR9 agonist (CpG)_Rep2

value: MRL/lpr (MRL.Faslpr)

value: B cells


title: TESC_67


title: STING N154S Control sgRNA

description: Library name: Sample 3

value: STING N154S Control sgRNA


title: TLR997_TLR7KO_stimTLR9.1

description: B cells_Tlr997_Tlr7-/-  MRL/lpr_stimulated with TLR9 agonist (CpG)_Rep1


title: WT STING ∆ArfGAP2

description: Library name: Sample 2

value: WT STING ArfGAP2 KO


title: TLR997_TLR7KO_stimNo.3

description: B cells_Tlr997_Tlr7-/- MRL/lpr_unstimulated _Rep3

value: StimNo


title: tumor, vehicle, i.v., rep5

value: tumor

value: Colon adenocarcinoma cells

value: Wild type

value: Intravenous injection of vehicle


title: tumor, vehicle, i.v., rep4


title: TESC_65


title: TESC_66


title: TLR997_TLR7KO_stimNo.2

description: B cells_Tlr997_Tlr7-/- MRL/lpr_unstimulated _Rep2

value: spleen

value: Bead purified B cells


title: TESC_63

value: normal


title: STING N154S ∆ArfGAP2

description: Library name: Sample 1

value: STING N154S ArfGAP2 KO


title: TLR997_TLR7KO_stimNo.1

description: B cells_Tlr997_Tlr7-/- MRL/lpr_unstimulated _Rep1


title: tumor, vehicle, i.v., rep3


title: tumor, vehicle, i.v., rep2


title: Day 15 GM23966 Control

city: Saint Louis

first: Kitra

last: Cates

state: MO

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

institute: Washington University in St. Louis

description: Library name: Day 15 GM23966 Control RNAseq

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custompython demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Quantitative CPM expression distances were analyzed by limma and graphically displayed using ComplexHeatmap. Gene function annotation was evaluated using Metascape.
Assembly: Ensembl_R76 h_sapien reference build
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted using the RNeasy plus micro kit (QIAGEN, USA) as instructed by the manufacturer.
RNA sample integrity was assessed on a 2100 Bioanalyzer (Agilent, USA) before proceeding to library preparation. mRNA was prepared for Illumina sequencing using SMARTer Ultra Low Input RNA Kit (Clontech, USA). cDNA libraries were sequenced on an Illumina NovaSeq 6000.

value: microRNA-induced neuron

value: miR-9/9*-124 + CTL for 15 days


title: tumor, vehicle, i.v., rep1


title: Day 15 GM23966 p53DD

description: Library name: Day 15 GM23966 p53DD RNAseq


title: Olfactory bulb_EAE_replicate 3

city: Hamburg

first: Charlotte

last: Schubert

address: Falkenried 94

department: Department of Neurology, University Hospital Hamburg - Eppendorf

country: Germany

institute: Institute of Neuroimmunology and Multiple Sclerosis Hamburg

description:
10x Genomics
Sample6_snRNA-seq_olfactory bulb_EAE_replicate 3

data_processing:
The Cell Ranger Software (version 5, 10X Genomics) was used for demultiplexing and alignment of sequencing reads to the mouse transcriptome. SnRNA-seq data were processed using the Seurat package (version 4.4.0, Satija Lab).
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Olfactory bulb

extract_protocol:
Olfactory bulb tissue was harvested and snap-frozen in –80°C until further analysis. For nuclei isolation olfactory bulb tissues were homogenized in EZ lysis buffer (Sigma Aldrich, NUC101) with a glass douncer ((Sigma-Aldrich, D9063). After 3-min incubation on ice cell suspension was then centrifuged by 500 × g for 4 min at 4°C. Nuclei were washed once with the EZ lysis buffer and twice in the nucleus incubation buffer (MgCl2 2 mM, KCl 25 mM, Glycerophosphate 65 mM, Sucrose 340 mM, glycerol 5%, ethylenediaminetetraacetic acid 1 mM, bovine serum albumin (BSA) 1%) and filtered through a 30 µm pre-separation filter (Miltenyi Biotech, 130-041-407). The nuclei suspensions were stained in nucleus incubation buffer for ten minutes with anti-HuC/D labeled to Alexa647 (1:300, rabbit, Abcam; Cat# ab237235, RRID: AB_2864321) and propidium iodide (PI) (1:1000, Thermo Fisher Scientific, Cat# P1304MP). PI-positive HuC/D positive nuclei were sorted in PBS containing 0.4% BSA using a BD Aria III cell sorter (BD Biosciences).
mRNA library preparation is performed according to the standard 10X Genomics protocol with the Chromium Next GEM Single Cell 3’GEM, Library & Gel Bead Kit v3.1 (Cat# 1000075, 10x Genomics). Briefly, gel bead emulsion (GEMs) was generated containing single nuclei and a master mix with reagents in the Chromium Controller followed by cell lysis and reverse transcription of RNA, cDNA amplification, enzymatic fragmentation, 5´adaptor attachment and sample indexing. On average around 25,000 nuclei were loaded on each channel of the Chromium instrument. To minimize batch effects, EAE and control samples were distributed evenly in the Chromium controller. Libraries were pooled and sequenced on an Illumina NovaSeq6000 platform (paired end sequencing, 2 x 100 bp read length, 500 million reads per sample).

value: Olfactory bulb

value: Neurons

tag: age

value: 10 weeks old

tag: disease state

value: Acute EAE (d15 p.i.)


title: TESC_62

value: blood


title: TESC_70


title: Day 15 F09-110 p53DD

description: Library name: Day 15 F09-110 p53DD RNAseq

tag: treatment


title: BG_IV_9

value: Intravenous injection of BG136


title: BG_IV_7


title: Olfactory bulb_Healthy_replicate 3

description:
10x Genomics
Sample5_snRNA-seq_olfactory bulb_healthy_replicate3

value: Healthy


title: Day 15 F09-110 Control

description: Library name: Day 15 F09-110 Control RNAseq


title: TESC_60


title: Olfactory bulb_EAE_replicate 2

description:
10x Genomics
Sample4_snRNAseq_olfactory bulb_EAE_replicate 2


title: TESC_59


title: Day 15 AG13369 p53DD

description: Library name: Day 15 AG13369 p53DD RNAseq


title: BG_IV_6

value: tumor


title: TESC_57


title: Day 15 AG13369 Control

description: Library name: Day 15 AG13369 Control RNAseq


title: BG_IV_4

value: Colon adenocarcinoma cells


title: Olfactory bulb_EAE_replicate 1

description:
10x Genomics
Sample2_snRNAseq_olfactory bulb_EAE_replicate 1


title: TESC_54


title: Day 15 AG08379 p53DD

description: Library name: Day 15 AG08379 p53DD RNAseq


title: BG_IV_2

value: Wild type


title: TESC_61


title: BG_IV_1


title: B16 tumor-infiltrating Piezo1KO CD4+ T cells, sample 2

city: beijing

first: qiuli

last: yang

address: beijing

institute: beijing normal university

data_processing:
mm10
fastp (version 0.19.7) Using fastp software to remove reads with adapters, reads containing N (N represents base information that cannot be determined) and low-quality reads (reads with Qphred<=5 and alkaline base accounting for more than 50% of the entire read length) Read count extraction was performed using featureCounts (version 1.5.0-p3).
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: Tab-limited text file includes FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Pre Kit following manufacturer’s protocols.

value: CD4+ T cell

value: lymphocyte

value: tumor microenviroment


title: Day 5 GM23966 p53DD

description: Library name: Day 5 GM23966 p53DD RNAseq


title: B16 tumor-infiltrating Piezo1KO CD4+ T cells, sample 1


title: TESC_47

value: normal


title: Day 5 GM23966 Control

description: Library name: Day 5 GM23966 Control RNAseq


title: Day 15 AG08379 Control

description: Library name: Day 15 AG08379 Control RNAseq


title: NC_IV_1 1

value: Intravenous injection of vehicle


title: B16 tumor-infiltrating WT CD4+ T cells, sample 2

value: WT


title: B16 tumor-infiltrating WT CD4+ T cells, sample 1


title: Day 5 F09-110 p53DD

description: Library name: Day 5 F09-110 p53DD RNAseq

value: microRNA-induced neuron

value: miR-9/9*-124 + p53DD for five days


title: TESC_50


title: Olfactory bulb_Healthy_replicate 1

description:
10x Genomics
Sample1_snRNAseq_olfactory bulb_healthy_replicate 1

value: Olfactory bulb

value: Neurons


title: NC_IV_1 2


title: NC_IV_7


title: TESC_44


title: Day 5 F09-110 Control

description: Library name: Day 5 F09-110 Control RNAseq

value: miR-9/9*-124 + CTL for five days


title: Olfactory bulb_Healthy_replicate 2

description:
10x Genomics
Sample3_snRNAseq_olfactory bulb_healthy_replicate2

value: 10 weeks old


title: TESC_45

value: blood


title: TESC_43


title: TESC_49


title: Day 5 AG13369 Control

description: Library name: Day 5 AG13369 Control RNAseq


title: Young PD-1, scRNA-seq

city: Kyoto

first: Hirotake

last: Tsukamoto

state: Sakyo-Ku

address: 53 Kawahara-cho Shogoin

department: Center for Cancer Immunotherapy and Immunobiology

country: Japan

institute: Kyoto University

description: 10x Genomics

data_processing:
The demultiplexing, barcorded processing, gene counting and aggregation were performed using the Cell Ranger software v7.0.0.
Assembly: mm10-2020-A
Supplementary files format and content: Tab separated value files and matrix files

source_name: lung

extract_protocol:
Single cells were harvested from the lung of tumor-beairng young or aged mice by dissociating with collagenase D and Dnase I, and then mononuclear cells were enriched by density gradient centrifugation. CD45+ immune cells were labeled with biotin-conjugated anti-CD45 Ab and isolated by EasySep Release Mouse Biotin Positive Selection Kit (STEMCELL TECHNOLOGIES). Magnetic particles bound to CD45+ cells were removed after the procedure. Viable cells were further separated by passing throuhg 40 microm cell strainer and using  Dead cell remover (Miltenyi Biotech) according to the manufacturer's insturction.
Library construction was performed according to the manufactures' instructions (single cell 3' v3 protocol, 10x Genomics). Briefly, CD45+ cells in the lung were resuspended in the master mix and loaded together with patitoning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Truseq Read1 sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropriated sized fragments were selected with SPRIselect reagent for subesquent library construction. During the library construction TruSeq Read2 sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: lung

value: immune cells

value: 2 month old

value: C57BL/6 Wild type

value: tumor inoculation / anti-PD-1 Ab injection


title: NC_IV_1

value: tumor

value: Colon adenocarcinoma cells

value: Wild type


title: Day 5 AG08379 Control

description: Library name: Day 5 AG08379 Control RNAseq


title: TESC_38

source_name: blood_dust exposed with silicosis

value: silicosis


title: TESC_35


title: Day 5 AG08379 p53DD

description: Library name: Day 5 AG08379 p53DD RNAseq


title: 22ko-th17

description: Th17 cells were collected at 3 days under Th17 differentiation conditions

extract_protocol:
Th17 cells were collected at indicated times for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

value: mouse spleen CD4+ T cells

value: 22ko-th17 cell

value: Setd2-CD4 cre

value: Naïve CD4+ T cells from Setd2-CD4 cre mice differentiated under Th17 polarizing condition for 3 days.


title: 24ko-th17

value: 24ko-th17 cell


title: TESC_40


title: P5 PBS3

city: Paris

first: Adrien

last: Dufour

address: 48, boulevard serurier

country: France

institute: INSERM

data_processing:
The pipeline used to do the preprocessing are available on GitHub repositories: https://github.com/Goultard59/indrops for whole transcriptome data and https://github.com/Goultard59/indrops-targeted for the targeted scRNA-seq data
Assembly: GRCm38.85 Mus musculus
Supplementary files format and content: microglia_info_experience.csv provides the metadata on whole transcriptome data
Supplementary files format and content: microglia_raw_counts.csv provides the processed whole gene expression matrix on the targeted gene panel
Supplementary files format and content: microglia_raw_counts_variable_feature.csv provides the processed whole gene expression matrix, restricted to the 2,000 most variable genes
Supplementary files format and content: microglia_metadata_targeted.csv provides the metadata on targeted data
Supplementary files format and content: microglia_raw_counts_targeted.csv provides the processed targeted gene expression matrix on the targeted gene panel
Supplementary files format and content: AR*_R2_dpBC.csv.gz provides the barcodes from demultiplexing
Supplementary files format and content: count_matrice_AR*.csv provides the count matrices for each targeted experiments

source_name: brain

extract_protocol:
MACS cell enrichment on dissociated tissue  (NTDK miltenyi)
InDrops like adaptated protocol

treatment_protocol: In brief, a 5µL volume of phosphate-buffered saline (PBS) containing 10µg/kg injection of recombinant mouse IL1B or of PBS alone (control) was injected intraperitoneally twice a day (morning and evening) on days postnatal P1 to P4 and once in the morning on day P5.

value: brain

tag: developemental stage

value: post natal day 5

value: CD11b positive

value: male

tag: biological replicate

tag: technical replicate

value: PBS

tag: expected cell_number


title: P5 PBS1

tag: strain


title: TESC_39

tag: radiography

tag: silica exposure time (years)

value: blood


title: P3 PBS2

value: post natal day 3

tag: Sex


title: P5 PBS2


title: F09-110 Fib B

description: Library name: F09-110 Fib B RNAseq

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custompython demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Quantitative CPM expression distances were analyzed by limma and graphically displayed using ComplexHeatmap. Gene function annotation was evaluated using Metascape.
Assembly: Ensembl_R76 h_sapien reference build
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: fibroblast

value: fibroblast

tag: batch

value: biological replicate 2


title: 13wt-th17

value: 13wt-th17 cell

value: wild type

value: Naïve CD4+ T cells from  WT mice differentiated under Th17 polarizing condition for 3 days.


title: 15wt-th17

value: mouse spleen CD4+ T cells

value: 14wt-th17 cell


title: F09-110 miN B

description: Library name: F09-110 miN B RNAseq

source_name: microRNA-induced neuron

value: microRNA-induced neuron


title: 24ko-treg

description: Treg cells were collected at 3 days under Treg differentiation conditions

extract_protocol:
Treg cells were collected at indicated times for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

value: 24ko-treg cell

value: Setd2-CD4 cre

value: Naïve CD4+ T cells from Setd2-CD4 cre mice differentiated under Treg polarizing condition for 3 days.


title: NC_IV_3

value: tumor

value: Colon adenocarcinoma cells

value: Wild type

value: Intravenous injection of vehicle


title: TESC_34

value: silicosis

value: blood


title: NC_IV_2


title: Aged PD-1, scRNA-seq

description: 10x Genomics

value: lung

value: immune cells

value: 18 month old

value: C57BL/6 Wild type

value: tumor inoculation / anti-PD-2 Ab injection


title: Day 5 AG13369 p53DD

description: Library name: Day 5 AG13369 p53DD RNAseq

value: miR-9/9*-124 + p53DD for five days


title: P3 PBS1

value: brain

value: post natal day 3

value: CD11b positive

value: male

value: PBS


title: 22ko-treg

value: mouse spleen CD4+ T cells

value: 22ko-treg cell

value: Setd2-CD4 cre

value: Naïve CD4+ T cells from Setd2-CD4 cre mice differentiated under Treg polarizing condition for 3 days.


title: TESC_42

value: normal


title: TESC_36

value: silicosis

value: blood


title: F09-110 miN A

description: Library name: F09-110 miN A RNAseq

value: microRNA-induced neuron

value: biological replicate 1


title: P3 PBS3


title: P1 PBS3

value: post natal day 1


title: TESC_33


title: 15wt-treg

value: 15wt-treg cell

value: wild type

value: Naïve CD4+ T cells from  WT mice differentiated under Treg polarizing condition for 3 days.


title: GM23966 miN B

description: Library name: GM23966 miN B RNAseq

value: biological replicate 2


title: P1 PBS2

value: brain

value: CD11b positive


title: Treg

value: Treg cel

value: Treg differentiation


title: TESC_30


title: GM23966 Fib B

description: Library name: GM23966 Fib B RNAseq

value: fibroblast


title: P5 IL1-2

value: post natal day 5

value: male


title: TESC_31


title: GM23966 miN A

description: Library name: GM23966 miN A RNAseq


title: P1 PBS1

value: PBS


title: TESC_29

value: silicosis


title: P5 IL1-3


title: GM23974 miN B

description: Library name: GM23974 miN B RNAseq


title: F09-110 Fib A

description: Library name: F09-110 Fib A RNAseq


title: TESC_26

value: blood


title: Th0

description: Naïve t cells were stimulated with αCD3/CD28 for three days

value: mouse spleen CD4+ T cells

value: Th0 cell

value: Stimulated with αCD3/CD28 for three days


title: GM23974 miN A

description: Library name: GM23974 miN A RNAseq

value: microRNA-induced neuron

value: biological replicate 1


title: Naïve t

description: CD4+ T cells directly selected from the spleen

value: Naive CD4+ T

value: wild type


title: P5 IL1-1

value: brain


title: P3 IL1-3

value: post natal day 3

value: CD11b positive


title: TESC_25


title: GM23974 Fib B

description: Library name: GM23974 Fib B RNAseq

value: biological replicate 2


title: KO12_48

extract_protocol:
Th0 cells were collected at indicated times for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

value: KO12-Th0 cell

value: Setd2-CD4 cre


title: P3 IL1-2

value: male


title: TESC_23

extract_protocol:
Human blood samples collected were immediately mixed with RNALater (Invitrogen, Carlsbad, CA) and kept frozen until used for RNA isolation. Total RNA was isolated from 2ml blood sample (0.5 ml blood and 1.5 ml RNALater) each using Ribopure Blood Kit (ThermoFisher Scientific, Waltham, MA), including DNA treatment. The RNA extracted was quantified using a Nanodrop ND-1000 (ThermoFisher Scientific) and quality assessed via an Agilent 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA) using Agilent RNA 6000 Nano Reagents. Only RNA samples with an RNA Integrity Number (RIN) >8.0 were used to construct next generation sequence (NGS) libraries.
Immediately prior to NGS library synthesis, 1.4 mg total RNA per blood sample was used to deplete alpha and beta globin mRNA, using the GLOBINClear kit (ThermoFisher Scientific, Waltham, MA). 0.5mg globin-depleted RNA was then used as input for the Illumina TruSeq Stranded mRNA Kit to synthesize NGS libraries. Library synthesis was carried out using the default protocol in the Low Sample TruSeq Stranded mRNA Sample Preparation Guide with the following two modifications: fragmentation time was reduced to 3 minutes to achieve insert lengths ranging between 125 and 250 bp and the PCR amplification was reduced to 12 cycles. Individual cDNA libraries were quantified using a Qubit 3.0 Fluorometer (Invitrogen by ThermoFisher Scientific) and the dsDNA HS Assay Kit (Invitrogen by ThermoFisher Scientific). The average fragment size for each library was determined using an Agilent 2100 Bioanalyzer with High Sensitivity DNA Reagents.
Libraries were used in 2 x 125 basepair sequencing using the Illumina HiSeq 2500 (Illumina, San Diego, CA) in high output mode with v4 HiSeq Cluster and SBS Kits (Illumina).


title: GM23966 Fib A

description: Library name: GM23966 Fib A RNAseq

value: fibroblast


title: Th17

value: Th17 cell

value: Th17 differentiation


title: TESC_28

value: silicosis

value: blood


title: GM23974 Fib A

description: Library name: GM23974 Fib A RNAseq


title: 13wt-treg

value: mouse spleen CD4+ T cells

value: 13wt-treg cell

value: Naïve CD4+ T cells from  WT mice differentiated under Treg polarizing condition for 3 days.


title: KO9_48

value: KO9-Th0 cell

value: Stimulated with αCD3/CD28 for three days


title: AG06858 miN B

description: Library name: AG06858 miN B RNAseq

value: microRNA-induced neuron


title: P3 IL1-1

value: brain

value: post natal day 3


title: WT6_48

value: WT6-Th0 cell

value: wild type


title: TESC_21


title: AG06858 miN A

description: Library name: AG06858 miN A RNAseq

value: biological replicate 1


title: P1 IL1-3

value: post natal day 1

value: CD11b positive

value: male


title: P1 IL1-2


title: TESC_17


title: AG06858 Fib B

description: Library name: AG06858 Fib B RNAseq

value: fibroblast

value: biological replicate 2


title: SIR-S29

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Adaptors were removed from sequencing read files from miRNA fractions using the clip_adaptors.pl module of mirdeep219. All sequence data were subjected to quality control by fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/commandline.html). Sequence read files from mRNA fractions were trimmed down to 50 bp to remove the poor-quality sequences at the ends. Sequence read files were further collapsed based on sequence identity and annotated for miRNA by mapping to miRbase version 2120 using the miraligner module of seqbuster. Reads passing QC standards were mapped to the GRCm38 mouse reference genome assembly using TopHat v2.0.13 (Bowtie v2.0.6) with supplied annotations at parameters (--min-anchor 8, --min-isoform-fraction 0.15). The raw count of mapped reads to genes was determined using the htseq-count utility (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html. Isomirs were identified using the R isomiRs library of the seqbuster package. Differential expression between groups of genes or miRNAs was assessed using DESEQ2.
Assembly: mm10
Supplementary files format and content: M1B_M54B_mRNAs_counts.xlsx : total gene counts
Supplementary files format and content: M1A_M54A_miRNAs_counts.xlsx : total expression counts
Supplementary files format and content: SIR_S3_to_S20_counts.xlsx : total expression counts
Supplementary files format and content: SIR_S23_S24_S29_S30_counts.xlsx : total expression counts
Supplementary files format and content: SIR_S33_S34_counts.xlsx : total expression counts

extract_protocol:
For RIP-seq analysis, the lungs of infected mice were perfused with formaldehyde to form crosslinks between miRNAs, MREs and individual proteins of bound RNA induced silencing complexes (RISCs). Crosslinked miRNA-mRNA-RISC complexes were immunoprecipitated by the addition of an antibody against AGO2, one component of RISC, and magnetic beads conjugated to protein A . Additional samples received either an antibody against IgG, as a negative control, or no antibody (labeled as 10% input), as a positive control. Protein-RNA complexes isolated from each sample were washed and eluted from the magnetic beads, crosslinks were reversed and protein components were digested. For SIR analysis, lungs from late-stage pulmonary adenocarcinoma animals infected with either adenoCre or adeno were formaldehyde crosslinked. Crosslinked miRNA-MRE complexes were isolated by the addition of a SIR probe followed by streptavidin beads. After extensive washing, complexes were eluted, crosslinks were reversed and the liberated miRNAs were sequenced. As positive controls, sequencing libraries were also generated from 10% of the starting input from each sample.
Sequencing libraries were constructed starting with the entire pellet of RIP or SIR RNA, using TruSeq Small RNA kits from Illumina (San Diego, CA), following manufacturer’s instructions. Two different gel fragments were isolated from each gel of RIP samples. The first fragment, containing miRNAs, corresponded to a size of 145 bps-160 bps, including ligated adapters. The second fragment of each gel, containing immunoprecipitated mRNA targets, corresponded to a size of 160 bps-500 bps, including ligated adapters. Only one gel fragment, containing miRNAs corresponding to a size of 145 bps-160 bps, including ligated adapters, was isolated from each SIR sample. Libraries were checked for quality and concentration using the DNA High-Sensitivity LabChip assay (Agilent Technologies, Santa Clara, CA) and quantitative PCR (KAPA Biosystems, Wilmington, MA), according to the manufacturers’ instructions.
RIP-seq libraries were pooled and sequenced on a MiSeq 50 base pair single-read flow cell using v2 reagents (Illumina, San Diego, CA). SIR libraries were also pooled and sequenced on either a HiSeq2500 high output 100 base pair paired-end flow cell using TruSeq SBS v3 reagents or on a NextSeq500 high output 75 base pair single-read flow cell using v2 reagents (Illumina, San Diego, CA).

treatment_protocol: We obtained two strains of mice: B6.129S4-Krastm4Tyj/J (stock #008179), referred to as K, and B6.129P2-Trp53tm1Brn/J (stock #008462), referred to as P. Both K and P mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and were interbred to create mice that were heterozygous for the KrasG12D allele and homozygous for the floxed Trp53 allele, referred to as KP. Male K and KP mice underwent one of three different experimental treatments at 6-7 weeks of age. The first treatment group of each mouse strain, referred to as early-stage tumor (ET) or late-stage tumor (LT), respectively, received intranasal administration of 5x106 PFU of adenovirusCre (Viral Vector Core, University of Iowa, Iowa City, IA).  The second group received 5x106 PFU of adenovirus (Viral Vector Core, University of Iowa, Iowa City, IA) while the third group was not infected. Collectively, K animals from the second and third groups are referred to early-stage normal (EN) and KP animals from the second and third groups are referred to late-stage normal (LN). Animals in the first two treatment groups were anesthetized with intraperitoneal injections of tribromoethanol (400 mg/kg body weight) prior to viral instillation. Animals in all three treatment groups were harvested 16 weeks later, at 22 weeks of age.

value: lung

value: uninfected


title: TESC_16

value: silicosis

value: blood


title: SIR-S30


title: RNA isolated from aged chondrocytes that were exposed to aged infrapatellar fat pad conditioned media, replicate 4

city: Boston

first: Gabrielle

last: Gilmer

state: MA

address: 149 13th Street

department: Pathology

description: male

data_processing:
Partek Flow was used bulk RNA sequencing as described in tutorial
Assembly: mm10
Supplementary files format and content: Gene counts post alignment; contains the chromosome, start, stop, length, strand, gene symbol, biotype, name and source

source_name: cartilage

growth_protocol: cultured in phenol red free low-glucose DMEM with 1% GlutaMAX and 1% PS

extract_protocol:
Qigen Rneasy  Kit
mm10; 40 million reads per sample with a directional library pre

treatment_protocol: see paper for details

value: cartilage

value: primary

value: chondrocyte

value: aged IFP


title: TESC_15


title: AG08379 miN B

description: Library name: AG08379 miN B RNAseq

value: microRNA-induced neuron


title: AG06858 Fib A

description: Library name: AG06858 Fib A RNAseq


title: SIR-S24

value: Cre


title: P1 IL1-1

value: brain


title: RNA isolated from aged chondrocytes that were exposed to aged infrapatellar fat pad conditioned media, replicate 3

description: male


title: TESC_13


title: TESC_14


title: AG08379 miN A

description: Library name: AG08379 miN A RNAseq

value: biological replicate 1


title: SIR-S23


title: RNA isolated from aged chondrocytes that were exposed to aged infrapatellar fat pad conditioned media, replicate 2

description: male


title: RNA isolated from aged chondrocytes that were exposed to aged infrapatellar fat pad conditioned media, replicate 1

description: male


title: TESC_12


title: AG08379 Fib B

description: Library name: AG08379 Fib B RNAseq