title: FACS sorted alveolar macrophages_RNA,SC2,8Dpi,rep2

description: Library name: LP47_121


title: APT140

status: Public on Feb 23 2026

type: SRA

city: Portland

first: Lisa

last: Coussens

state: OR

address: 3181 SW Sam Jackson Park Rd

country: USA

institute: Oregon Health and Science University

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38847

library_source: genomic

data_processing:
*library strategy: TCRseq
Combine paired-end sequences with PEAR (v.0.9.6)
Custom script extracts synthetic template sequences and determines normalization factors
Align reads to TCR reference sequences using MiXCR v 4.4.2
Normalize clonotype counts using normalization factors
Calculate summary statistics, e.g. clonality, shannon diversity, Jaccard index, etc.
Assembly: Mouse TCRb from RepSeq.IO library v2.1
Supplementary files format and content: tab-delimited text files containing clonotype information: raw and normalized counts and frequencies, sequence information for V, D, J, and CDR3, etc.

molecule: genomic DNA

organism: Mus musculus

source_name: mammary gland

growth_protocol: Mice were maintained in standard conditions

extract_protocol:
As described by Medler et al, Cancer Cell 2019
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run

treatment_protocol: 80-day-old MMTV-PyMT female littermates were randomized by initial tumor volume and fed either with PLX3397 (Pexidartinib) formulated in mouse chow or control chow until endpoints. PLX3397 was formulated so that the average dose per animal per day was 40 mg/kg. When PLX3397-treated MMTV-PyMT mice reached 85 days of age, they were then administered PTX (Breckenridge Pharmaceutical, Inc.) every 5 days by i.v. injection into the retroorbital plexus. PTX was given at 10 mg/kg of the animal per injection, diluted in PBS. At 87 days of age, mice were treated with aPD-1 (RMP1-14, BioXcell, Cat#BE0146) or Isotype control rat IgG2a (BioXcell, Cat# BE0089) at 1.0 mg/mouse for initial dose, then every 5 days at 0.5 mg/mouse for follow-up doses by i.p. injection. Primary tumor burden was determined by caliper measurements on live sedated mice every 5 days following initiation of PLX3397 treatment. At endpoints, mice were intraperitoneally injected with 50 mg/kg BrdU (Roche) for 90 min and prior to tissue collection, followed by were cardiac-perfusion with PBS containing 10 U/ml heparin (Sigma-Aldrich) to clear peripheral blood. Resected tissues were enzymatically and mechanistically digested to obtain single cell suspensions for susequent DNA extraction

tag: tissue

value: mammary gland

tag: cell line

tag: cell type

value: primary tumor

tag: genotype

value: MMTV-PyMT

tag: treatment

tag: time


title: APT136

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FTWT3

value: FVBN

value: WTNT


title: Whole-blood RNA-seq from AD(13_016_S02_08)

city: Barcelona

first: Ferran

last: Aguilar Parera

state: BARCELONA

address: Avinguda Diagonal 477, 11th floor, EF CLIF

country: Spain

institute: EF-CLIF

library_source: transcriptomic

data_processing:
The reads were aligned to the hg38 genome assembly and the transcriptome using STAR v2.5.3a and GENCODE 26 annotation
Gene expression was quantified using STAR (–quantMode GeneCounts) and VSN-transformed (variance stabilizing normalization)
Then a quantile normalization method was applied to normalize the nonbiological variability.
Using the HUGO Genome Nomenclature Committee (HGNC), which is a resource for approved human gene nomenclature, we included protein-coding genes, and among other gene locus types, immunoglobulin genes, and T cell receptor genes. Genes brought by sexual chromosomes and mitochondrial DNA were not included in the analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited file with expected counts (RSEM) for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
RNA was isolated from blood stored in Tempus tubes using the Tempus™ Spin RNA Isolation Kit (reference 4380204, Applied Biosystems). RNA quality was assessed using Agilent RNA 6000 Nano and Pico Chips (Agilent Technologies, Cat.# 5067-1511 and Cat.# 5067-151, respectively) and concentration via Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat.# Q32855).
Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina Inc., Cat.# 20020612) and TruSeq RNA CD Index Plate (Illumina Inc., Cat.# 20019792) following TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E). Briefly, starting from 500 ng of total RNA, rRNA and globin mRNA were depleted and remaining RNA was purified, fragmented and primed for cDNA synthesis. cDNA first strand was synthesized with SuperScript-II Reverse Transcriptase (Thermo Fisher Scientific, Cat.#18064-014) for 10 min at 25°C, 15 min at 42°C, 15 min at 70°C and pause at 4°C. cDNA second strand was synthesized with Illumina reagents at 16°C for 1 hour. Then, A-tailing and adaptor ligation were performed. Finally, enrichment of libraries was achieved by PCR (30 sec at 98°C; 15 cycles of 10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C; 5min at 72°C and pause at 4°C). Afterwards, libraries were visualized on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626), quantified using Qubit dsDNA HS DNA Kit (Thermo Fisher Scientific, Cat. # Q32854) and sequenced in a NovaSeq-6000 (Illumina Inc.) by at least 100 million paired-end 100nt reads.

value: Whole blood

value: AD


title: APT134

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FTWT1


title: APT133

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37850

value: PTX


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep7

city: Vienna

first: Sylvia

last: Knapp

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

description: Library name: LP47_119

data_processing:
BAM to FASTQ with Picard v.3.0.0 SAMtoFASTQ
Read mapping with STAR v.2.7.9a
Assembly: GRCmm39
Supplementary files format and content: raw counts (raw.tsv)
Supplementary files format and content: counts per million (cpm.tsv)

molecule: total RNA

source_name: Lung

extract_protocol:
RNA was isolated with the micro RNA kit (Qiagen), frozen with liquid nitrogen and stored at -80 for at least 1 week.
QuantSeq

treatment_protocol: Mouse lungs were infected with PBS, SC2 or IAV and FACS sorted on different timepoints after the infection (2, 4, 8, 28 Days post infection - Dpi)directly into RLT buffer + 2-Mercaptoethanol.

value: Lung

value: AM

value: WT

value: PBS

tag: batch

tag: time point_(dpi)


title: APT130

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37817

value: PLX+PTX


title: FACS sorted alveolar macrophages_RNA,SC2,8Dpi,rep1

description: Library name: LP47_120


title: APT131

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37590


title: APT132

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37849


title: Whole-blood RNA-seq from AD(13_016_S00_08)


title: Whole-blood RNA-seq from AD(13_014_S02_08)


title: Whole-blood RNA-seq from AD(13_014_S01_08)


title: FACS sorted alveolar macrophages_RNA,SC2,4Dpi,rep4

description: Library name: LP47_118


title: APT129

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37876


title: FACS sorted alveolar macrophages_RNA,SC2,4Dpi,rep3

description: Library name: LP47_117


title: APT128

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37582


title: APT127

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37869


title: Whole-blood RNA-seq from AD(13_014_S00_08)


title: FACS sorted alveolar macrophages_RNA,SC2,4Dpi,rep2

description: Library name: LP47_116


title: APT124

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37847


title: APT125

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37881


title: APT126

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37868


title: Whole-blood RNA-seq from AD(13_011_S02_08)


title: FACS sorted alveolar macrophages_RNA,SC2,4Dpi,rep1

description: Library name: LP47_115


title: APT123

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37826


title: Whole-blood RNA-seq from AD(13_011_S00_08)


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep6

description: Library name: LP47_114


title: APT121

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37759


title: Whole-blood RNA-seq from AD(13_005_S02_08)


title: APT122

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37828


title: APT119

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37584


title: FACS sorted alveolar macrophages_RNA,SC2,2Dpi,rep4

description: Library name: LP47_113


title: Whole-blood RNA-seq from AD(13_005_S00_08)


title: APT118

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37526


title: Whole-blood RNA-seq from pre-ACLF(13_003_S00_08)

value: pre-ACLF


title: Whole-blood RNA-seq from ACLF(13_001_S00_08)

value: ACLF


title: APT114

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32942

value: PLX


title: FACS sorted alveolar macrophages_RNA,SC2,2Dpi,rep2

description: Library name: LP47_111


title: FACS sorted alveolar macrophages_RNA,SC2,2Dpi,rep1

description: Library name: LP47_110


title: APT115

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32693


title: APT113

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32940


title: APT111

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32635


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep5

description: Library name: LP47_109


title: Whole-blood RNA-seq from ACLF(13_001_A01_08)


title: FACS sorted alveolar macrophages_RNA,SC2,2Dpi,rep3

description: Library name: LP47_112


title: APT109

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31506


title: APT116

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32696


title: APT117

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32697


title: APT120

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37785


title: Whole-blood RNA-seq from pre-ACLF(11027_A02)


title: APT107

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31632


title: Whole-blood RNA-seq from pre-ACLF(11020_S01)


title: APT108

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31634


title: FACS sorted alveolar macrophages_RNA,IAV,28Dpi,rep4

description: Library name: LP47_108

value: IAV


title: APT110

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32634

value: mammary gland


title: FACS sorted alveolar macrophages_RNA,IAV,28Dpi,rep2

description: Library name: LP47_106


title: APT112

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32667

value: primary tumor


title: APT106

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34663

value: MMTV-PyMT


title: Whole-blood RNA-seq from pre-ACLF(11020_S00)


title: APT105

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34662


title: APT104

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34659


title: FACS sorted alveolar macrophages_RNA,IAV,28Dpi,rep1

description: Library name: LP47_105


title: Whole-blood RNA-seq from pre-ACLF(11_I_018_S00_09)


title: Whole-blood RNA-seq from AD(111016_S00)


title: APT103

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34603


title: FACS sorted alveolar macrophages_RNA,IAV,28Dpi,rep3

description: Library name: LP47_107


title: APT102

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34515


title: Whole-blood RNA-seq from pre-ACLF(11_I_018_A01_09)


title: APT99

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34510


title: APT100

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34513


title: Whole-blood RNA-seq from AD(11_I_014_S00_09)


title: APT98

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34509


title: FACS sorted alveolar macrophages_RNA,IAV,8Dpi,rep3

description: Library name: LP47_102


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep4

description: Library name: LP47_104


title: APT97

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34508


title: Whole-blood RNA-seq from AD(11_I_011_S00_09)


title: Whole-blood RNA-seq from AD(11_I_008_S00_09)


title: APT94

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34431


title: FACS sorted alveolar macrophages_RNA,IAV,8Dpi,rep2

description: Library name: LP47_101


title: APT101

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34514


title: FACS sorted alveolar macrophages_RNA,IAV,8Dpi,rep1

description: Library name: LP47_100


title: Whole-blood RNA-seq from ACLF(11_035_S00_08)


title: APT92

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34001


title: FACS sorted alveolar macrophages_RNA,IAV,8Dpi,rep4

description: Library name: LP47_103


title: APT91

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34005


title: APT93

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34584


title: Whole-blood RNA-seq from ACLF(11_035_A02_08)


title: APT90

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34006


title: APT89

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33965


title: APT95

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34433


title: APT88

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33972


title: FACS sorted alveolar macrophages_RNA,IAV,4Dpi,rep4

description: Library name: LP47_98


title: FACS sorted alveolar macrophages_RNA,IAV,4Dpi,rep3

description: Library name: LP47_97


title: APT87

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34358


title: APT86

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34357


title: APT96

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34425


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep3

description: Library name: LP47_99


title: Whole-blood RNA-seq from AD(11_033_S02_08)


title: Whole-blood RNA-seq from AD(11_034_S00_08)


title: Whole-blood RNA-seq from AD(11_034_S02_08)


title: APT85

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34024


title: APT83

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33654


title: FACS sorted alveolar macrophages_RNA,IAV,4Dpi,rep2

description: Library name: LP47_96


title: FACS sorted alveolar macrophages_RNA,IAV,4Dpi,rep1

description: Library name: LP47_95


title: APT84

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33740


title: APT81

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33553


title: Whole-blood RNA-seq from AD(11_033_S00_08)


title: Whole-blood RNA-seq from AD(11_032_S02_08)


title: APT80

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31048


title: APT82

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33559


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep2

description: Library name: LP47_94


title: FACS sorted alveolar macrophages_RNA,IAV,2Dpi,rep3

description: Library name: LP47_92


title: APT79

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31047


title: APT78

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31046


title: Whole-blood RNA-seq from AD(11_032_S00_08)


title: FACS sorted alveolar macrophages_RNA,IAV,2Dpi,rep4

description: Library name: LP47_93


title: FACS sorted alveolar macrophages_RNA,IAV,2Dpi,rep2

description: Library name: LP47_91


title: Whole-blood RNA-seq from AD(11_031_S02_08)


title: APT76

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32152


title: APT77

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31044


title: APT75

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32149


title: Whole-blood RNA-seq from AD(11_031_S00_08)


title: APT74

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32021


title: APT73

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32019


title: Whole-blood RNA-seq from AD(11_028_S00_08)


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep1

description: Library name: LP47_89


title: APT71

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31705


title: APT69

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31679


title: APT70

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31680


title: Whole-blood RNA-seq from AD(11_024_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(11_027_A00_08)


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep11

description: Library name: LP47_87

value: Monocyte


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep12

description: Library name: LP47_88


title: APT67

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31045


title: APT68

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31644


title: FACS sorted alveolar macrophages_RNA,IAV,2Dpi,rep1

description: Library name: LP47_90


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep10

description: Library name: LP47_86


title: APT64

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32155


title: Whole-blood RNA-seq from pre-ACLF(11_027_S00_08)


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep9

description: Library name: LP47_85


title: APT72

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32018


title: APT65

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30893


title: Whole-blood RNA-seq from AD(11_024_S00_08)


title: APT63

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32067


title: APT62

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32063


title: FACS sorted lung monocytes_RNA,SC2,28Dpi,rep4

description: Library name: LP47_84


title: APT61

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31728


title: APT60

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30839


title: APT66

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30894


title: Whole-blood RNA-seq from ACLF(11_023_S00_08)


title: FACS sorted lung monocytes_RNA,SC2,28Dpi,rep3

description: Library name: LP47_83


title: APT59

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30746


title: FACS sorted lung monocytes_RNA,SC2,28Dpi,rep2

description: Library name: LP47_82


title: Whole-blood RNA-seq from ACLF(11_021_S00_08)


title: Whole-blood RNA-seq from ACLF(11_023_A02_08)


title: APT58

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30700


title: Whole-blood RNA-seq from ACLF(11_021_A01_08)


title: APT57

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30699


title: FACS sorted lung monocytes_RNA,SC2,28Dpi,rep1

description: Library name: LP47_81


title: APT56

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30698


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep8

description: Library name: LP47_80


title: Whole-blood RNA-seq from AD(11_013_S02_08)


title: Whole-blood RNA-seq from AD(11_013_S00_08)


title: APT53

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32670


title: APT55

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30838


title: APT54

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30835


title: APT52

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32661


title: APT50

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32625


title: APT51

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32639


title: Whole-blood RNA-seq from pre-ACLF(11_018_S00_08)


title: APT48

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31766


title: APT49

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31767


title: FACS sorted lung monocytes_RNA,SC2,8Dpi,rep2

description: Library name: LP47_77


title: APT47

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31722


title: FACS sorted lung monocytes_RNA,SC2,8Dpi,rep3

description: Library name: LP47_78


title: FACS sorted lung monocytes_RNA,SC2,8Dpi,rep1

description: Library name: LP47_76


title: APT46

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30885


title: FACS sorted lung monocytes_RNA,SC2,8Dpi,rep4

description: Library name: LP47_79


title: Whole-blood RNA-seq from pre-ACLF(11_012_A00_08)


title: APT45

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30884


title: Whole-blood RNA-seq from AD(11_011_S00_08)


title: APT44

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30881


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep7

description: Library name: LP47_75


title: Whole-blood RNA-seq from AD(11_006_S02_08)


title: APT43

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32560


title: Whole-blood RNA-seq from pre-ACLF(11_012_S00_08)


title: APT42

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32463


title: FACS sorted lung monocytes_RNA,SC2,4Dpi,rep4

description: Library name: LP47_74


title: APT41

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32461


title: APT40

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32459


title: FACS sorted lung monocytes_RNA,SC2,4Dpi,rep3

description: Library name: LP47_73


title: APT39

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32458


title: Whole-blood RNA-seq from AD(11_006_S01_08)


title: Whole-blood RNA-seq from AD(11_006_S00_08)


title: APT37

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32384


title: APT38

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32379


title: APT36

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32355


title: APT34

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31926


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep6

description: Library name: LP47_70


title: APT35

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31927


title: Whole-blood RNA-seq from ACLF(11_004_A01_08)


title: FACS sorted lung monocytes_RNA,SC2,4Dpi,rep1

description: Library name: LP47_71


title: Whole-blood RNA-seq from ACLF(11_004_S00_08)


title: FACS sorted lung monocytes_RNA,SC2,2Dpi,rep4

description: Library name: LP47_69


title: Whole-blood RNA-seq from ACLF(11_002_A01_08)


title: APT32

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31878


title: APT30

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33026

value: Untreated


title: APT29

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33023


title: FACS sorted lung monocytes_RNA,SC2,2Dpi,rep3

description: Library name: LP47_68


title: APT31

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31852


title: FACS sorted lung monocytes_RNA,SC2,4Dpi,rep2

description: Library name: LP47_72


title: APT28

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33022


title: APT33

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31879


title: APT27

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33021


title: Whole-blood RNA-seq from ACLF(11_002_S00_08)

value: Whole blood


title: Whole-blood RNA-seq from ACLF(10002_A01)


title: FACS sorted lung monocytes_RNA,SC2,2Dpi,rep2

description: Library name: LP47_67


title: APT26

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33020


title: APT25

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33008


title: Whole-blood RNA-seq from AD(10_053_S02_08)

value: AD


title: APT23

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30608


title: Whole-blood RNA-seq from ACLF(10002_S00)


title: APT24

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31727


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep5

description: Library name: LP47_65


title: FACS sorted lung monocytes_RNA,IAV,28Dpi,rep4

description: Library name: LP47_64


title: APT20

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30625


title: FACS sorted lung monocytes_RNA,SC2,2Dpi,rep1

description: Library name: LP47_66


title: Whole-blood RNA-seq from AD(10_050_S02_08)


title: FACS sorted lung monocytes_RNA,IAV,28Dpi,rep3

description: Library name: LP47_63


title: APT22

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30660


title: Whole-blood RNA-seq from AD(10_053_S00_08)


title: FACS sorted lung monocytes_RNA,IAV,28Dpi,rep2

description: Library name: LP47_62


title: APT19

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30623


title: APT18

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32848


title: Whole-blood RNA-seq from AD(10_050_S00_08)


title: APT17

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32844


title: APT16

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32849


title: Whole-blood RNA-seq from AD(10_047_S02_08)


title: APT21

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30828


title: APT15

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31982


title: FACS sorted lung monocytes_RNA,IAV,28Dpi,rep1

description: Library name: LP47_61


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep4

description: Library name: LP47_60


title: APT14

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31979


title: Whole-blood RNA-seq from AD(10_047_S00_08)


title: APT13

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31932


title: FACS sorted lung monocytes_RNA,IAV,8Dpi,rep4

description: Library name: LP47_59


title: APT12

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31408


title: Whole-blood RNA-seq from AD(10_046_S02_08)


title: APT10

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5693

value: FVBN

value: WTNT


title: FACS sorted lung monocytes_RNA,IAV,8Dpi,rep3

description: Library name: LP47_58

value: Lung


title: APT11

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31407


title: Whole-blood RNA-seq from AD(10_045_S02_08)


title: APT8

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5691


title: FACS sorted lung monocytes_RNA,IAV,8Dpi,rep2

description: Library name: LP47_57

value: WT


title: APT7

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5690


title: APT9

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5692


title: Whole-blood RNA-seq from AD(10_046_S00_08)


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep3

description: Library name: LP47_55

value: PBS


title: Whole-blood RNA-seq from AD(10_042_S02_08)


title: APT3

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5703


title: FACS sorted lung monocytes_RNA,IAV,4Dpi,rep4

description: Library name: LP47_54


title: APT1

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33330


title: APT5

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5705


title: APT2

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33324


title: APT4

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5704


title: Whole-blood RNA-seq from AD(10_045_S00_08)


title: FACS sorted lung monocytes_RNA,IAV,4Dpi,rep3

description: Library name: LP47_53


title: APLN36

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38855

source_name: lymph node

treatment_protocol: 80-day-old MMTV-PyMT female littermates were randomized by initial tumor volume and fed either with PLX3397 (Pexidartinib) formulated in mouse chow or control chow until endpoints. PLX3397 was formulated so that the average dose per animal per day was 40 mg/kg. When PLX3397-treated MMTV-PyMT mice reached 85 days of age, they were then administered PTX (Breckenridge Pharmaceutical, Inc.) every 5 days by i.v. injection into the retroorbital plexus. PTX was given at 10 mg/kg of the animal per injection, diluted in PBS. At 87 days of age, mice were treated with PD-1 (RMP1-14, BioXcell, Cat#BE0146) or Isotype control rat IgG2a (BioXcell, Cat# BE0089) at 1.0 mg/mouse for initial dose, then every 5 days at 0.5 mg/mouse for follow-up doses by i.p. injection. Primary tumor burden was determined by caliper measurements on live sedated mice every 5 days following initiation of PLX3397 treatment. At endpoints, mice were intraperitoneally injected with 50 mg/kg BrdU (Roche) for 90 min and prior to tissue collection, followed by were cardiac-perfusion with PBS containing 10 U/ml heparin (Sigma-Aldrich) to clear peripheral blood. Resected tissues were enzymatically and mechanistically digested to obtain single cell suspensions for susequent DNA extraction

value: lymph node

value: PTX


title: APT6

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5706


title: APLN37

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38856


title: Whole-blood RNA-seq from AD(10_040_S01_08)


title: APLN35

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38854


title: FACS sorted lung monocytes_RNA,IAV,4Dpi,rep1

description: Library name: LP47_51


title: APLN33

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38852

value: PLX+PTX


title: Whole-blood RNA-seq from AD(10_040_S00_08)


title: Whole-blood RNA-seq from AD(10_040_S02_08)


title: FACS sorted lung monocytes_RNA,IAV,8Dpi,rep1

description: Library name: LP47_56


title: FACS sorted lung monocytes_RNA,IAV,4Dpi,rep2

description: Library name: LP47_52


title: APLN34

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38853


title: APLN32

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38851


title: Whole-blood RNA-seq from AD(10_042_S00_08)


title: Whole-blood RNA-seq from AD(10_038_S02_08)


title: FACS sorted lung monocytes_RNA,IAV,2Dpi,rep4

description: Library name: LP47_49


title: APLN28

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38847


title: APLN29

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38848


title: Whole-blood RNA-seq from AD(10_038_S00_08)


title: Whole-blood RNA-seq from AD(10_037_S02_08)


title: APLN26

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38845


title: APLN25

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38844


title: FACS sorted lung monocytes_RNA,IAV,2Dpi,rep2

description: Library name: LP47_47


title: FACS sorted lung monocytes_RNA,IAV,2Dpi,rep3

description: Library name: LP47_48


title: Whole-blood RNA-seq from AD(10_037_S00_08)


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep2

description: Library name: LP47_50


title: Whole-blood RNA-seq from AD(10_036_S02_08)


title: APLN30

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38849


title: APLN31

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38850


title: APLN24

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38843


title: APLN23

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FLNW5


title: FACS sorted lung monocytes_RNA,IAV,2Dpi,rep1

description: Library name: LP47_46


title: APLN22

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FLNW4


title: APLN27

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38846


title: Whole-blood RNA-seq from AD(10_036_S00_08)


title: Whole-blood RNA-seq from ACLF(10_033_S00_08)

value: ACLF


title: APLN20

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FLNW2


title: APLN18

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37850


title: FACS sorted lung monocytes_RNA,PBS,0Dpi,rep1

description: Library name: LP47_45


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep12

description: Library name: LP47_44

value: Epithelial cell


title: APLN17

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37849


title: Whole-blood RNA-seq from ACLF(10_033_A01_08)


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep11

description: Library name: LP47_43


title: APLN21

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FLNW3


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep10

description: Library name: LP47_42


title: Whole-blood RNA-seq from AD(10_032_S02_08)


title: APLN15

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37589


title: APLN19

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FLNW1


title: Whole-blood RNA-seq from AD(10_032_S00_08)


title: APLN14

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37817


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep9

description: Library name: LP47_41


title: APLN12

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37582


title: Whole-blood RNA-seq from AD(10_031_S02_08)


title: APLN16

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37590


title: APLN11

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37592


title: Whole-blood RNA-seq from AD(10_031_S00_08)


title: FACS sorted epithelial cells_RNA,SC2,28Dpi,rep4

description: Library name: LP47_40


title: APLN10

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37869


title: Whole-blood RNA-seq from ACLF(10_028_S00_08)


title: FACS sorted epithelial cells_RNA,SC2,28Dpi,rep3

description: Library name: LP47_39


title: APLN8

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37881


title: APLN6

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37826


title: APLN13

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37876


title: APLN7

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37847


title: APLN5

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37828


title: FACS sorted epithelial cells_RNA,SC2,28Dpi,rep2

description: Library name: LP47_38


title: FACS sorted epithelial cells_RNA,SC2,28Dpi,rep1

description: Library name: LP47_37


title: APLN9

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37868


title: APLN4

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37759


title: Whole-blood RNA-seq from AD(10_027_S00_08)


title: APLN3

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37785


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep8

description: Library name: LP47_36


title: Whole-blood RNA-seq from pre-ACLF(10_024_S00_08)

value: pre-ACLF


title: Whole-blood RNA-seq from ACLF(10_028_A01_08)


title: APLN2

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37588


title: FACS sorted epithelial cells_RNA,SC2,8Dpi,rep3

description: Library name: LP47_34


title: Whole-blood RNA-seq from AD(10_022_S02_08)


title: APLN1

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37584


title: APL120

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38856

value: lung metastasis


title: APL118

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38854

value: MMTV-PyMT


title: FACS sorted epithelial cells_RNA,SC2,8Dpi,rep4

description: Library name: LP47_35


title: FACS sorted epithelial cells_RNA,SC2,8Dpi,rep2

description: Library name: LP47_33


title: APL117

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38853


title: APL116

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38852


title: APL119

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38855


title: APL114

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38850


title: Whole-blood RNA-seq from AD(10_022_S00_08)


title: APL115

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38851


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep7

description: Library name: LP47_31


title: Whole-blood RNA-seq from AD(10_021_S02_08)


title: Whole-blood RNA-seq from AD(10_022_S01_08)


title: APL113

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38849


title: APL112

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38848


title: Whole-blood RNA-seq from AD(10_021_S01_08)


title: Whole-blood RNA-seq from AD(10_021_S00_08)


title: APL109

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38845


title: FACS sorted epithelial cells_RNA,SC2,8Dpi,rep1

description: Library name: LP47_32


title: FACS sorted epithelial cells_RNA,SC2,4Dpi,rep4

description: Library name: LP47_30


title: APL110

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38846


title: FACS sorted epithelial cells_RNA,SC2,4Dpi,rep3

description: Library name: LP47_29


title: APL107

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FLWT5


title: APL111

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38847


title: APL106

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FLWT4


title: FACS sorted epithelial cells_RNA,SC2,4Dpi,rep2

description: Library name: LP47_28


title: Whole-blood RNA-seq from AD(10_020_S02_08)


title: APL105

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FLWT3


title: APL108

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38843


title: FACS sorted epithelial cells_RNA,SC2,2Dpi,rep4

description: Library name: LP47_25


title: APL103

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FLWT1


title: Whole-blood RNA-seq from ACLF(10_016_S00_08)


title: APL101

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37849


title: FACS sorted epithelial cells_RNA,SC2,4Dpi,rep1

description: Library name: LP47_27


title: APL104

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FLWT2


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep6

description: Library name: LP47_26


title: APL99

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37817


title: Whole-blood RNA-seq from AD(10_020_S00_08)


title: APL98

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37876


title: APL96

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37592


title: FACS sorted epithelial cells_RNA,SC2,2Dpi,rep2

description: Library name: LP47_23


title: APL97

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37582


title: APL102

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37850


title: Whole-blood RNA-seq from ACLF(10_016_A02_08)


title: Whole-blood RNA-seq from AD(10_015_S02_08)


title: Whole-blood RNA-seq from ACLF(10_014_S00_08)


title: FACS sorted epithelial cells_RNA,SC2,2Dpi,rep3

description: Library name: LP47_24


title: APL100

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37590


title: Whole-blood RNA-seq from AD(10_015_S00_08)


title: APL94

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37868


title: FACS sorted epithelial cells_RNA,SC2,2Dpi,rep1

description: Library name: LP47_22


title: Whole-blood RNA-seq from ACLF(10_014_A01_08)


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep5

description: Library name: LP47_21


title: Whole-blood RNA-seq from AD(10_013_S02_08)


title: APL95

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37869


title: APL93

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37881


title: Whole-blood RNA-seq from AD(10_013_S00_08)


title: APL89

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37759


title: Whole-blood RNA-seq from AD(10_012_S02_08)


title: FACS sorted epithelial cells_RNA,IAV,28Dpi,rep4

description: Library name: LP47_20

value: IAV


title: APL90

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37828


title: FACS sorted epithelial cells_RNA,IAV,28Dpi,rep3

description: Library name: LP47_19


title: APL87

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37588


title: APL86

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37584


title: APL85

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37526


title: FACS sorted epithelial cells_RNA,IAV,28Dpi,rep2

description: Library name: LP47_18


title: Whole-blood RNA-seq from AD(10_012_S00_08)


title: Whole-blood RNA-seq from ACLF(10_007_S00_08)


title: APL88

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37785


title: APL83

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32696

value: PLX


title: APL91

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37826


title: APL92

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37847


title: APL82

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32693


title: APL80

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32667


title: Whole-blood RNA-seq from ACLF(10_007_A01_08)

value: Whole blood


title: FACS sorted epithelial cells_RNA,IAV,8Dpi,rep4

description: Library name: LP47_15


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep4

description: Library name: LP47_16


title: APL81

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32942


title: FACS sorted epithelial cells_RNA,IAV,28Dpi,rep1

description: Library name: LP47_17


title: Whole-blood RNA-seq from AD(10_005_S02_08)

value: AD


title: APL79

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32635


title: APL84

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32697


title: APL77

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31634


title: Whole-blood RNA-seq from AD(09_008_S02_08)


title: APL78

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31506


title: Whole-blood RNA-seq from AD(10_005_S00_08)


title: APL76

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31632


title: FACS sorted epithelial cells_RNA,IAV,8Dpi,rep2

description: Library name: LP47_13


title: FACS sorted epithelial cells_RNA,IAV,8Dpi,rep3

description: Library name: LP47_14


title: FACS sorted epithelial cells_RNA,IAV,8Dpi,rep1

description: Library name: LP47_12


title: Whole-blood RNA-seq from AD(09_008_S00_08)


title: FACS sorted epithelial cells_RNA,IAV,4Dpi,rep4

description: Library name: LP47_10


title: APL74

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34662


title: APL70

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34514


title: APL75

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34663


title: APL72

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34603


title: Whole-blood RNA-seq from AD(09_006_S00_08)


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep3

description: Library name: LP47_11


title: APL71

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34515


title: APL69

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34510


title: APL68

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34509


title: FACS sorted epithelial cells_RNA,IAV,4Dpi,rep3

description: Library name: LP47_9


title: APL67

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34508


title: Whole-blood RNA-seq from AD(09_004_S02_08)


title: APL73

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34659


title: APL66

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34425


title: Whole-blood RNA-seq from AD(09_006_S02_08)


title: FACS sorted epithelial cells_RNA,IAV,4Dpi,rep2

description: Library name: LP47_8


title: Whole-blood RNA-seq from AD(09_004_S00_08)


title: FACS sorted epithelial cells_RNA,IAV,4Dpi,rep1

description: Library name: LP47_7


title: APL62

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34001


title: APL63

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34584


title: APL64

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34431


title: APL61

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34005


title: APL59

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33965


title: APL60

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34006


title: APL65

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34433


title: Whole-blood RNA-seq from ACLF(08002_A01)


title: Whole-blood RNA-seq from AD(08_026_S02_08)


title: APL57

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34358


title: FACS sorted epithelial cells_RNA,IAV,2Dpi,rep1

description: Library name: LP47_2


title: Whole-blood RNA-seq from ACLF(08002_S00)


title: FACS sorted epithelial cells_RNA,IAV,2Dpi,rep4

description: Library name: LP47_5


title: APL58

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33972


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep1

description: Library name: LP47_1


title: Whole-blood RNA-seq from pre-ACLF(08_019_A00_08)


title: FACS sorted epithelial cells_RNA,IAV,2Dpi,rep2

description: Library name: LP47_3


title: APL55

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34024


title: FACS sorted epithelial cells_RNA,IAV,2Dpi,rep3

description: Library name: LP47_4


title: Whole-blood RNA-seq from pre-ACLF(08010_S01)


title: FACS sorted epithelial cells_RNA,PBS,0Dpi,rep2

description: Library name: LP47_6


title: APL56

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34357


title: APL54

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33740


title: Whole-blood RNA-seq from AD(08_026_S00_08)


title: Whole-blood RNA-seq from AD(08_013_S02_08)


title: APL49

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32018


title: APL53

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33654


title: Whole-blood RNA-seq from pre-ACLF(08_019_S00_08)


title: APL52

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33559


title: APL47

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31644


title: Whole-blood RNA-seq from AD(08_013_S00_08)


title: APL51

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33553


title: mIg-5_Gingiva

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

description:
Library name: Reem_mig_Minus6_S18_R1_001.fastq.gz
Reem_mig_Minus6

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the mouse transcriptome and genome version GRCm39 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: GRCm39 with annotations from Ensembl release 106
Supplementary files format and content: raw_and_norm_counts.xlsx
Supplementary files format and content: Each row in the file contains a certain ensembl Gene ID, Symbol,  raw counts and DESEq2 normalized counts per sample. Missing values are denoted by “?” are for genes with a too low expression that were filtered out prior to normalization (sum of counts in all samples lower than 10).

source_name: Gingiva

growth_protocol: mice were breeded in SPF conditions, and their gingiva was extracted at the age of 8 weeks old

extract_protocol:
RNA was extracted using QIAGEN RNeasy Micro Kit according to the manufacturer's instructions.
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000 (Illumina), using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles

treatment_protocol: both groups are WT mice but the experiment group lacked maternal antibodies during their development

value: Gingiva

value: lack maternal antibodies


title: mIg-4_Gingiva

description:
Library name: Reem_mig_Minus5_S17_R1_001.fastq.gz
Reem_mig_Minus5


title: APL50

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32019

value: Lung


title: APL45

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30839


title: mIg-1_Gingiva

description:
Library name: Reem_mig_Minus1_S13_R1_001.fastq.gz
Reem_mig_Minus1

value: WT


title: APL48

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31680


title: Whole-blood RNA-seq from AD(08_011_S02_08)


title: Whole-blood RNA-seq from AD(08_013_S01_08)


title: APL41

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30838


title: mIg-3_Gingiva

description:
Library name: Reem_mig_Minus4_S16_R1_001.fastq.gz
Reem_mig_Minus4


title: APL46

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32155


title: APL43

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30746


title: mIg-2_Gingiva

description:
Library name: Reem_mig_Minus3_S15_R1_001.fastq.gz
Reem_mig_Minus3


title: APL39

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32670


title: APL44

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30748


title: APL38

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32625


title: APL37

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31767


title: Whole-blood RNA-seq from pre-ACLF(08_010_S00_08)


title: mIg+3_Gingiva

description:
Library name: Reem_mig_Plus5_S11_R1_001.fastq.gz
Reem_mig_Plus5

value: recived maternal antibbodies


title: mIg+4_Gingiva

description:
Library name: Reem_mig_Plus6_S12_R1_001.fastq.gz
Reem_mig_Plus6


title: APL42

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30698


title: APL33

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30881


title: mIg+1_Gingiva

description:
Library name: Reem_mig_Plus1_S7_R1_001.fastq.gz
Reem_mig_Plus1


title: APL34

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30884


title: Whole-blood RNA-seq from AD(08_011_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(08_010_A00_08)


title: Whole-blood RNA-seq from AD(08_008_S00_08)


title: APL36

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31722


title: Whole-blood RNA-seq from AD(08_008_S02_08)


title: APL40

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30747


title: mIg+2_Gingiva

description:
Library name: Reem_mig_Plus2_S8_R1_001.fastq.gz
Reem_mig_Plus2


title: APL29

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32384


title: APL35

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30399


title: APL28

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32355


title: GFPlo non-cardiomyocyte cells_MI 7d

city: Shanghai

first: Jialei

last: Zheng

state: 上海

address: 393 Middle Huaxia Road

country: China

institute: ShanghaiTech University

description:
Library name: GFPlo
GFP_002
10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data was precessed by Fastp firstly to trim primer sequence and low quality bases. And then we used SeekOne®Tools to precess sequence data and aligned to Mouse mm10 in order to obtain gene expression matrix.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
In p16-CreER;R26-mTmG mice subjected to MI surgery, cardiac P16-positive cells were lineage-traced by administering tamoxifen via oral gavage on day 5 post-MI. At day 7, the infarcted region of the heart was dissected, enzymatically digested by the Langendorff perfusion method. The resulting cell suspension was filtered through a 70-μm cell strainer and centrifuged at 50 g for 5 minutes to pellet and remove cardiomyocytes. The supernatant was collected and centrifuged at 500 g for 5 minutes to obtain a cell pellet depleted of cardiomyocytes. Erythrocytes were subsequently subjected to lysis, followed by fluorescence-activated cell sorting (FACS) to isolate distinct populations: GFPhi and GFPlo cell populations. After cell sorting, cell viability and number were assessed using the Countstar Rigel S2 fluorescence analyzer and AO/PI staining. Subsequently, cell debris and non-viable cells were removed using Miltenyi kits (130-109-398/130-090-101). The resulting live cells were washed twice with RPMI 1640 and resuspended at 1×10e6 cells/mL in 1×PBS containing 0.04% BSA.
scRNA-seq libraries were prepared according to the manufacturer's instructions of Beijing SeekGene BioSciences Co., Ltd (Beijing, China).  Single-cell RNA-Seq libraries were prepared using SeekOne®Digital Droplet Single Cell 3'library preparation kit (SeekGene). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeckOne®DD Chip S3. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip S3. After emulsion droplet generation reverse transcription were performed at 42℃ for 90 minutes and inactivated at 80℃ for 15 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired，A-tailed and ligated to sequencing adaptor. Finally the indexed PCR were performed to amplified the DNA representing 3' polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were cleanup with SPRl beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on illumina NovaSeq 6000 with PE150 read length.

value: heart

value: non-cardiomyocyte cells

value: MI

tag: sorted fraction

value: GFP⁻ non-cardiomyocyte cells


title: CD45+ Marchf8 sgRNA-2, scRNAseq

city: Detroit

first: Qing-Sheng

last: Mi

address: 1 Ford Place, 1D

institute: Henry Ford Health

description:
Library name: sample 2
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger-6.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
For isolation of CD45+ immnue cells, tumors from mice were  surgically removed from mice, minced into RPMI medium, and sorted using BD FACS
scRNA-seq libraries were generated using the 10X Genomics Chromium Single Cell 3′ Reagent Kit (v2 Chemistry) and Chromium Single Cell Controller as described in the manufacturer's  instructions. Briefly, FACS-sorted cells were loaded into each reaction for gel bead-in-emulsion (GEM) generation and cell barcoding. Reverse transcription of the GEM (GEM-RT) was performed using a Veriti™ 96-Well Fast Thermal Cycler (Applied Biosystems) at 53 °C for 45 min, 85 °C for 5 min, and a 4 °C hold. cDNA amplification was performed after GEM-RT cleanup with Dynabeads MyOne Silane (Thermo Fisher Scientific) using the same thermocycler (98 °C for 3 min, 98 °C for 15 s, 67 °C for 20 s, 72 °C for 1 min, followed by a 12 cycle repeat at 72 °C for 1 min and a 4 °C hold). Amplified cDNA was cleaned up with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA) that was followed by a library construction procedure, including fragmentation, end repair, adapter ligation, and library amplification. An Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) was used for library quality control. Libraries were sequenced on an Illumina HiSeq4000 using a paired-end flow cell: Read 1, 26 cycles; i7 index, 8 cycles; Read 2, 98 cycles.

value: tumor

value: CD45+ immnue cells

value: sgR-Marchf8-2 injected C57BL/6J mice


title: Whole-blood RNA-seq from ACLF(08_004_S00_08)

value: ACLF


title: APL32

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32463

value: lung metastasis

value: MMTV-PyMT


title: APL27

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31927


title: APL31

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32459


title: Whole-blood RNA-seq from AD(08_005_S02_08)

value: Whole blood


title: GFPhi non-cardiomyocyte cells _MI 7d

description:
Library name: GFPhi
GFP_001
10x Genomics

value: GFP⁺ non-cardiomyocyte cells


title: CD45+ scramble, scRNAseq

description:
Library name: sample 1
10X Genomics

value: mEERL/scr injected C57BL/6J mice


title: CD45+ Marchf8 sgRNA-3, scRNAseq

description:
Library name: sample 3
10X Genomics

value: sgR-Marchf8-3 injected C57BL/6J mice


title: Whole-blood RNA-seq from AD(08_005_S01_08)

value: AD


title: APL30

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
32458

value: Lung


title: APL25

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33028

value: Untreated


title: APL26

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31926


title: APL22

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33021


title: Whole-blood RNA-seq from AD(071003_S00)


title: Whole-blood RNA-seq from ACLF(08_004_A01_08)


title: APL24

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33026


title: APL23

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33022


title: Male, Young, Control, rep 6

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

description:
Library name: JLMale2
Male_Young_Control_6

data_processing:
Reads were mapped to mouse genome (GRCm39) with STAR (version 2.7.11b). Genes were counted via featureCounts (version 2.0.6).
Assembly: GRCm39
Supplementary files format and content: comma-separated values file includes gene counts for each sample

source_name: Liver

extract_protocol:
RNA was extracted with PureLink RNA Mini Kit.
Libraries were prepared with TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: Mice were housed at the University of Michigan Medical School (UM), the University of Texas (UT), and The Jackson Laboratory (TJL). Animals were fed ad libitum with the Purina 5LG6 diet, produced in the same commercial diet facility (TestDiet, Richmond, IN, USA). Compounds were administered through food until the animals were sacrificed.

value: Liver

tag: strain

tag: Sex

value: Male

tag: cohort

tag: site

value: JL

value: Control

tag: treatment abbreviation

tag: dose

tag: age group

value: Young

tag: age

value: 5 months

tag: age at_start_of_treatment

tag: replicate


title: Whole-blood RNA-seq from AD(08_005_S00_08)

tag: tissue


title: APL21

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33020

tag: cell line

tag: cell type

tag: genotype


title: APL20

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33008

tag: treatment

tag: time


title: Male, Young, Control, rep 4

description:
Library name: YC2
Male_Young_Control_4

value: UM

value: 4 months


title: Male, Young, Control, rep 5

description:
Library name: JLMale1
Male_Young_Control_5


title: Whole-blood RNA-seq from ACLF(04203S_000)

value: ACLF


title: Whole-blood RNA-seq from ACLF(04003_A01)


title: APL17

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30608

value: lung metastasis

value: MMTV-PyMT


title: APL16

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30828


title: APL18

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31725


title: APL14

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30623


title: APL15

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
30625


title: APL12

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31979


title: APL11

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31978


title: Whole-blood RNA-seq from AD(04_051_S00_08)

value: Whole blood


title: APL10

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31934


title: APL19

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31727


title: Male, Young, Control, rep 3

description:
Library name: YC13
Male_Young_Control_3


title: Whole-blood RNA-seq from ACLF(04_058_A02_08)


title: Whole-blood RNA-seq from AD(04_048_S00_08)


title: Male, Young, Control, rep 1

description:
Library name: YC05
Male_Young_Control_1

value: 6 months


title: Male, Old, Syringaresinol, rep 2

description:
Library name: UM78645
Male_Old_Syr_2

value: Syringaresinol

value: Syr

value: 300 ppm

value: Old

value: 22 months


title: Whole-blood RNA-seq from ACLF(04_058_A01_08)


title: Male, Old, Syringaresinol, rep 3

description:
Library name: UT11125
Male_Old_Syr_3

value: Liver

value: Male

value: UT


title: Whole-blood RNA-seq from AD(04_046_S00_08)

value: AD


title: APL13

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31982

value: Lung


title: APL9

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31932


title: Male, Young, Control, rep 2

description:
Library name: YC06
Male_Young_Control_2

value: UM

value: Control

value: Young


title: APL6

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5691

value: lung metastasis

value: FVBN

value: WTNT


title: APL8

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31931

value: MMTV-PyMT


title: Male, Old, Sulindac, rep 3

description:
Library name: UT10960
Male_Old_Sul_3

value: Sulindac

value: Sul

value: 5 ppm

value: 5 months


title: Whole-blood RNA-seq from AD(04_044_S00_08)

value: Whole blood


title: APL3

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5703


title: Whole-blood RNA-seq from AD(04_044_S02_08)


title: APL7

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
31407


title: APL5

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5690


title: APL4

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
f5704


title: Male, Old, Sulindac, rep 2

description:
Library name: UM79702
Male_Old_Sul_2

value: Liver

value: Old

value: 22 months


title: Male, Old, Syringaresinol, rep 1

description:
Library name: JL16328
Male_Old_Syr_1

value: Male

value: JL

value: Syringaresinol

value: Syr

value: 300 ppm


title: Whole-blood RNA-seq from AD(04_040_S02_08)

value: AD


title: Male, Old, Late-start Rapamycin, rep 3

description:
Library name: UT08510
Male_Old_Rapa_20hi_3

value: UT

value: Late-start Rapamycin

value: 42 ppm

value: 20 months


title: APB47

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38854

data_processing:
*library strategy: TCRseq
Combine paired-end sequences with PEAR (v.0.9.6)
Custom script extracts synthetic template sequences and determines normalization factors
Align reads to TCR reference sequences using MiXCR v 4.4.2
Normalize clonotype counts using normalization factors
Calculate summary statistics, e.g. clonality, shannon diversity, Jaccard index, etc.
Assembly: Mouse TCRb from RepSeq.IO library v2.1 (Full Library MD5: 2f4877a1b3b109f2be617d38e9935b4f)
Supplementary files format and content: tab-delimited text files containing clonotype information: raw and normalized counts and frequencies, sequence information for V, D, J, and CDR3, etc.

source_name: Blood

value: Blood

value: peripheral blood mononuclear cells

value: MMTV-PyMT

value: PTX


title: Male, Old, Sulindac, rep 1

description:
Library name: JL16234
Male_Old_Sul_1

value: Liver

value: Sulindac

value: Sul

value: 5 ppm

value: 5 months


title: Whole-blood RNA-seq from ACLF(04_038_S00_08)

value: Whole blood

value: ACLF


title: Male, Old, Late-start Rapamycin, rep 2

description:
Library name: UM58870
Male_Old_Rapa_20hi_2

value: Male

value: UM

value: Old

value: 22 months


title: Male, Old, Late-start Rapamycin, rep 1

description:
Library name: JL12763
Male_Old_Rapa_20hi_1

value: JL

value: Late-start Rapamycin

value: 42 ppm


title: APB49

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38856

value: Blood

value: peripheral blood mononuclear cells


title: Whole-blood RNA-seq from AD(04_040_S01_08)

value: AD


title: APL1

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33330

value: Lung

value: lung metastasis

value: MMTV-PyMT

value: Untreated


title: APB41

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38848


title: APB40

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38847


title: Male, Old, Rapamycin+Acarbose, rep 3

description:
Library name: UT10944
Male_Old_RaAc9_3

value: Liver

value: UT

value: Rapamycin+Acarbose

value: 9 months


title: Whole-blood RNA-seq from AD(04_040_S00_08)

value: Whole blood


title: APB44

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38851

value: PLX+PTX


title: APB39

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38846


title: APB45

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38852


title: APB42

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38849


title: APB48

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38855

value: PTX


title: Whole-blood RNA-seq from ACLF(04_038_A01_08)

value: ACLF


title: APB38

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38845


title: APB46

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38853


title: Male, Old, Rapamycin+Acarbose, rep 2

description:
Library name: UM78449
Male_Old_RaAc9_2

value: Male

value: UM

value: Old

value: 22 months


title: APB43

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38850

value: Blood

value: peripheral blood mononuclear cells


title: Whole-blood RNA-seq from AD(04_037_S00_08)

value: AD


title: APB37

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38844

value: MMTV-PyMT


title: Male, Old, Rapamycin+Acarbose, rep 1

description:
Library name: JL16321
Male_Old_RaAc9_1

value: JL


title: APB36

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
38843


title: Whole-blood RNA-seq from AD(04_025_S00_08)


title: Whole-blood RNA-seq from AD(04_020_S02_08)


title: Male, Old, Middle-start Rapamycin+Acarbose, rep 3

description:
Library name: UT11057
Male_Old_RaAc16_3

value: Liver

value: Middle-start Rapamycin+Acarbose

value: 16 months


title: shZuc_Ago3-IP

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description:
Library name: shZuc_Ago3-IP
Sequencing of Ago3 bound small RNAs

library_source: other

data_processing:
Illumina reads were processed by removing 3′ adapters with cutadapt {Martin, 2011 #646}, trimming 4 random nucleotides from each end and filtering for minimal length (>18 nt) and sequence complexity (bbduk, entropy = 0.35, entropy window = 18, k = 4) . Reads were first aligned to Drosophila rRNA precursor sequences and the mitochondrial genome using bowtie {Langmead, 2009 #656}. Remaining unmapped reads were mapped to the OSC_r1.01 genome using bowtie allowing for 1 mismatch. Alignments were separated into uniquely and all‑mapping fractions. For visualization, HOMER was used to generate tag directories (makeTagDirectory … -format bed -keepAll -single -fragLength given) and UCSC‑compatible tracks (makeUCSCfile … -fsize 1e20 -strand +/- -fragLength given -noadj -normLength 0) were generated per strand. Counts were normalized to 1M miRNAs and final BigWig tracks were created with bedGraphToBigWig (Kent Utilities), producing strand‑specific (sense and antisense) coverage profiles for genome browser display. For transposon histogram analysis, piRNA reads longer than 23 nucleotides were aligned to transposable element consensus sequences using bowtie (--best --strata -f -v 2 -a), permitting multiple mappings. Alignments were subsequently filtered to retain reads that mapped either uniquely or at most twice to a single transposon consensus, to account for long terminal repeat (LTR) redundancy. Reads mapping twice were assigned a fractional count of 0.5 to each location.
Assembly: OSC_r1.01
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense

molecule: other

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Flies were maintained at 25 °C. Germline knockdown was achieved by crossing UAS shRNA lines to the maternal triple driver MTD GAL4 line (#31777; Bloomington Drosophila Stock Center). All shRNA transgenes used in this study were integrated at attP2. Zucchini depletion was performed using TRiP.GL00111 (#35227; Bloomington) crossed to MTD GAL4. As a matched control, an shRNA against white (attP2) was crossed to MTD GAL4. Adult females were aged for 6 days and maintained on apple juice agar plates supplemented with yeast paste to standardize ovarian maturation prior to dissection.

extract_protocol:
Ovaries (600 µl packed volume per genotype) were dissected in ice-cold PBS and lysed in 1× RIPA buffer (50 mM Tris HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 1 mM EDTA, 0.1 mM Pefabloc). Homogenates were cleared by centrifugation and diluted with 3 ml IP dilution buffer (50 mM Tris HCl pH 7.5, 150 mM NaCl). Antibodies were coupled to M280 sheep anti-mouse IgG Dynabeads (Life Technologies). For Piwi and Aub immunoprecipitations, 150 µl antibody-coupled beads were incubated with 1.5 ml lysate; for Ago3, 300 µl beads were incubated with 3 ml lysate. Lysates were rotated at 4 °C overnight. Beads were collected and washed seven times with IP wash buffer (50 mM Tris HCl pH 7.5, 500 mM NaCl, 2 mM MgCl₂, 10% glycerol, 1% Empigen); for Piwi IPs, 150 mM NaCl was used. Bound RNA was isolated by acid phenol–chloroform extraction and ethanol precipitation. For visualization during cloning, 10% of the extracted RNA was labeled with [γ-³²P]-ATP. The recovered IP-derived small RNAs were used directly as input for the gel-based library preparation pipeline described above.
Small RNAs were isolated by resolving the mixture on a 12.5% polyacrylamide–urea gel and excising the region flanked by the spike-in signals. These spike-ins were ligated to conventional 4N adapters alongside the endogenous small RNA population. Following each ligation step, libraries were gel-purified, with band excision guided by the radioactive signal. After reverse transcription and PCR amplification, the spike-in sequences were removed from the library via restriction digestion. The libraries  were pooled at the final stage using PCR-introduced dual or single index barcodes.

value: ovary

value: fly carrying an shRNA against zuc crossed to MTD-Gal4


title: Whole-blood RNA-seq from AD(04_037_S02_08)

value: Whole blood


title: APB35

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FBUT4

value: Untreated


title: Male, Old, Middle-start Rapamycin+Acarbose, rep 1

description:
Library name: JL16325
Male_Old_RaAc16_1


title: shZuc_Aub-IP

description:
Library name: shZuc_Aub-IP
Sequencing of Aub bound small RNAs


title: Male, Old, PB125, rep 3

description:
Library name: UT10974
Male_Old_PB125_3

value: UT

value: 100 ppm

value: 5 months


title: APB34

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FBUT3


title: Whole-blood RNA-seq from AD(04_019_S02_08)


title: shZuc_total-sRNA

description:
Library name: shZuc_total-sRNA
Sequencing of total small-RNAs after depletion of 2s rRNA

extract_protocol:
Total RNA was extracted from ovariesusing TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Briefly, ovaries were lysed in TRIzol, followed by phase separation with chloroform. The aqueous phase was recovered, and RNA was precipitated with isopropanol, washed with 75% ethanol, and resuspended in nuclease-free water. RNA concentration and purity were assessed by NanoDrop spectrophotometry (A260/280 and A260/230 ratios). To enrich for small RNAs and deplete ribosomal RNA, 10 µg of total RNA was subjected to 2S rRNA depletion using a biotinylated antisense oligonucleotide (5'–Bio-AGTCTTACAACCCTCAACCATATGTAGTCCAAGCAGCACT–3') immobilized on MyOne Streptavidin C1 magnetic beads (Invitrogen). RNA was denatured at 80 °C for 2 min, hybridized to the bead-bound probe at 50 °C for 1 h with rotation, and the rRNA-depleted supernatant was recovered by magnetic separation and ethanol precipitation. The depleted RNA was resuspended in nuclease-free water and used directly for library preparation.
Small RNAs were isolated by resolving the mixture on a 12.5% polyacrylamide–urea gel and excising the region flanked by the spike-in signals. These spike-ins were ligated to conventional 4N adapters alongside the endogenous small RNA population. Following each ligation step, libraries were gel-purified, with band excision guided by the radioactive signal. After reverse transcription and PCR amplification, the spike-in sequences were removed from the library via restriction digestion. The libraries  were pooled at the final stage using PCR-introduced dual or single index barcodes.


title: Whole-blood RNA-seq from AD(04_025_S02_08)


title: APL2

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
33324

value: Lung

value: lung metastasis


title: Whole-blood RNA-seq from AD(04_020_S00_08)


title: Whole-blood RNA-seq from ACLF(04_017_S00_08)

value: ACLF


title: APB33

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FBUT2

value: Blood

value: peripheral blood mononuclear cells


title: APB30

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34433

value: MMTV-PyMT


title: shZuc_Piwi-IP

description:
Library name: shZuc_Piwi-IP
Sequencing of Piwi bound small RNAs


title: shWhite_Aub-IP

description:
Library name: shWhite_Aub-IP
Sequencing of Aub bound small RNAs

value: fly carrying an shRNA against white crossed to MTD-Gal4


title: Whole-blood RNA-seq from AD(04_019_S00_08)

value: AD


title: Male, Old, PB125, rep 2

description:
Library name: UM78883
Male_Old_PB125_2

value: Liver

value: Male

value: UM

value: Old

value: 22 months


title: Whole-blood RNA-seq from ACLF(04_017_A01_08)

value: Whole blood


title: shWhite_Ago3-IP

description:
Library name: shWhite_Ago3-IP
Sequencing of Ago3 bound small RNAs

value: ovary


title: Male, Old, Nicotinamide Riboside, rep 3

description:
Library name: UT09733
Male_Old_NR_3

value: UT

value: Nicotinamide Riboside

value: NR

value: 8 months


title: APB31

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34425


title: Male, Old, PB125, rep 1

description:
Library name: JL16253
Male_Old_PB125_1

value: JL

value: 100 ppm

value: 5 months


title: shWhite_Piwi-IP

description:
Library name: shWhite_Piwi-IP
Sequencing of Piwi bound small RNAs


title: APB32

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FBUT1

value: Blood

value: peripheral blood mononuclear cells

value: MMTV-PyMT

value: Untreated


title: shWhite_total-sRNA

description:
Library name: shWhite_total-sRNA
Sequencing of total small-RNAs after depletion of 2s rRNA

value: fly carrying an shRNA against white crossed to MTD-Gal4


title: Whole-blood RNA-seq from AD(04_014_S02_08)

value: AD


title: Male, Old, Nicotinamide Riboside, rep 2

description:
Library name: UM68656
Male_Old_NR_2

value: Liver

value: Male

value: UM

value: Old


title: APB28

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
39670


title: APB29

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
34508


title: APB27

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
39669


title: Male, Old, MitoQ, rep 3

description:
Library name: UT08509
Male_Old_MitoQ_3

value: UT

value: MitoQ

value: 22 months

value: 7 months