title: Whole-blood RNA-seq from ACLF(33016_A02)


title: Whole-blood RNA-seq from AD(33_I_071_S00_09)

status: Public on Feb 23 2026

type: SRA

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.

tag: tissue

value: Whole blood

tag: genotype

value: AD

tag: time


title: Whole-blood RNA-seq from AD(33_I_065_S00_09)


title: Whole-blood RNA-seq from AD(33_I_082_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(33_I_078_S00_09)

value: pre-ACLF


title: Whole-blood RNA-seq from AD(33_I_077_S00_09)


title: Whole-blood RNA-seq from ACLF(33001_A01)

value: ACLF


title: Whole-blood RNA-seq from ACLF(33016_S00)


title: Whole-blood RNA-seq from pre-ACLF(33_I_060_S00_09)


title: Whole-blood RNA-seq from AD(33_I_052_S00_09)


title: Whole-blood RNA-seq from AD(40_I_027_S00_09)


title: Whole-blood RNA-seq from AD(33_I_057_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(33_I_043_S00_09)


title: Whole-blood RNA-seq from AD(33_I_045_S00_09)


title: Whole-blood RNA-seq from AD(33_I_032_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(33_I_016_S00_09)


title: Whole-blood RNA-seq from AD(33_I_015_S00_09)


title: Whole-blood RNA-seq from AD(33_I_010_S00_09)


title: Whole-blood RNA-seq from AD(33_I_014_S00_09)


title: Whole-blood RNA-seq from AD(33_I_002_S00_09)


title: Whole-blood RNA-seq from AD(33_I_050_S00_09)


title: Whole-blood RNA-seq from AD(32_I_011_S00_09)


title: Whole-blood RNA-seq from AD(33_I_001_S00_09)


title: Whole-blood RNA-seq from AD(32_I_013_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(33_I_040_S00_09)


title: Whole-blood RNA-seq from AD(32_I_006_S00_09)


title: Whole-blood RNA-seq from AD(32_I_002_S00_09)


title: Whole-blood RNA-seq from ACLF(302017_S01)


title: Whole-blood RNA-seq from pre-ACLF(31001_A01)


title: Whole-blood RNA-seq from ACLF(302017_S00)


title: Whole-blood RNA-seq from ACLF(302014_S01)


title: Whole-blood RNA-seq from pre-ACLF(31001_A00)


title: Whole-blood RNA-seq from ACLF(302007_S00)


title: Whole-blood RNA-seq from ACLF(302016_S00)


title: Whole-blood RNA-seq from ACLF(302005_S00)


title: Whole-blood RNA-seq from ACLF(302003_S00)


title: Whole-blood RNA-seq from ACLF(302009_S00)


title: Whole-blood RNA-seq from ACLF(302014_S00)


title: Whole-blood RNA-seq from ACLF(302001_S00)


title: Whole-blood RNA-seq from AD(301034_S01)


title: Whole-blood RNA-seq from AD(301036_S00)


title: Whole-blood RNA-seq from AD(301034_S00)


title: Whole-blood RNA-seq from AD(301057_S00)


title: Whole-blood RNA-seq from AD(301023_S01)


title: Whole-blood RNA-seq from AD(301019_S01)


title: Whole-blood RNA-seq from AD(301057_S01)


title: Whole-blood RNA-seq from AD(301017_S01)


title: Whole-blood RNA-seq from AD(301019_S00)


title: Whole-blood RNA-seq from AD(301017_S00)


title: Whole-blood RNA-seq from AD(301023_S00)


title: Whole-blood RNA-seq from AD(30_I_041_S00_09)


title: Whole-blood RNA-seq from AD(30_I_030_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(30_I_026_S00_09)


title: Whole-blood RNA-seq from AD(30_I_035_S00_09)


title: Whole-blood RNA-seq from AD(30_I_011_S00_09)


title: Whole-blood RNA-seq from AD(30_I_039_S00_09)


title: Whole-blood RNA-seq from AD(30_I_012_S00_09)


title: Whole-blood RNA-seq from AD(30_I_005_S00_09)


title: Whole-blood RNA-seq from AD(30_I_010_S00_09)


title: Whole-blood RNA-seq from ACLF(29_036_S00_08)


title: Whole-blood RNA-seq from AD(29_I_008_S00_09)


title: Whole-blood RNA-seq from AD(29_I_004_S00_09)


title: Whole-blood RNA-seq from ACLF(29_028_A02_08)


title: Whole-blood RNA-seq from ACLF(29_036_A01_08)


title: Whole-blood RNA-seq from AD(28_020_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(29_I_002_S00_09)


title: Whole-blood RNA-seq from AD(28_024_S00_08)


title: Whole-blood RNA-seq from ACLF(29_028_S00_08)


title: Whole-blood RNA-seq from AD(30_I_004_S00_09)


title: Whole-blood RNA-seq from AD(28_020_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(28_013_A00_08)


title: Whole-blood RNA-seq from AD(28_001_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(28_013_S00_08)


title: Whole-blood RNA-seq from AD(28_001_S01_08)


title: Whole-blood RNA-seq from AD(28_004_S00_08)


title: Whole-blood RNA-seq from ACLF(272006_S00)


title: Whole-blood RNA-seq from AD(28_001_S00_08)


title: Whole-blood RNA-seq from ACLF(272005_S01)


title: Whole-blood RNA-seq from AD(28_004_S02_08)


title: Whole-blood RNA-seq from ACLF(272005_S00)


title: Whole-blood RNA-seq from ACLF(272003_S00)


title: Whole-blood RNA-seq from AD(271004_S00)


title: Whole-blood RNA-seq from ACLF(272002_S01)


title: Whole-blood RNA-seq from pre-ACLF(27014_S01)


title: Whole-blood RNA-seq from AD(27_I_010_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(27014_S00)


title: Whole-blood RNA-seq from AD(27_I_025_S00_09)


title: Whole-blood RNA-seq from AD(27_I_031_S00_09)


title: Whole-blood RNA-seq from AD(27_I_011_S00_09)


title: Whole-blood RNA-seq from AD(27_I_020_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(27_I_019_S00_09)


title: Whole-blood RNA-seq from AD(27_I_012_S00_09)


title: Whole-blood RNA-seq from AD(27_I_006_S00_09)


title: Whole-blood RNA-seq from AD(27_075_S02_08)


title: Whole-blood RNA-seq from AD(271004_S01)


title: Whole-blood RNA-seq from AD(27_I_007_S00_09)


title: Whole-blood RNA-seq from AD(27_075_S00_08)


title: Whole-blood RNA-seq from ACLF(272002_S00)


title: Whole-blood RNA-seq from pre-ACLF(27_073_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(27_I_013_S00_09)


title: Whole-blood RNA-seq from ACLF(27_072_S00_08)


title: Whole-blood RNA-seq from ACLF(27_072_A01_08)


title: Whole-blood RNA-seq from AD(27_071_S02_08)


title: Whole-blood RNA-seq from AD(27_071_S00_08)


title: Whole-blood RNA-seq from AD(27_069_S00_08)


title: Whole-blood RNA-seq from ACLF(27_067_S00_08)


title: Whole-blood RNA-seq from AD(27_061_S00_08)


title: Whole-blood RNA-seq from AD(27_055_S02_08)


title: Whole-blood RNA-seq from AD(27_055_S01_08)


title: Whole-blood RNA-seq from ACLF(27_044_S00_08)


title: Whole-blood RNA-seq from AD(27_055_S00_08)


title: Whole-blood RNA-seq from AD(27_045_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(27_042_S00_08)


title: Whole-blood RNA-seq from AD(27_043_S00_08)


title: Whole-blood RNA-seq from AD(27_043_S02_08)


title: Whole-blood RNA-seq from AD(27_061_S02_08)


title: Whole-blood RNA-seq from ACLF(27_044_A01_08)


title: Whole-blood RNA-seq from AD(27_045_S00_08)


title: Whole-blood RNA-seq from AD(27_038_S00_08)


title: Whole-blood RNA-seq from ACLF(27_067_A01_08)


title: Whole-blood RNA-seq from AD(27_033_S00_08)


title: Whole-blood RNA-seq from AD(27_038_S02_08)


title: Whole-blood RNA-seq from AD(27_033_S02_08)


title: Whole-blood RNA-seq from AD(27_032_S00_08)


title: Whole-blood RNA-seq from AD(27_028_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(27_029_S00_08)


title: Whole-blood RNA-seq from AD(27_028_S00_08)


title: Whole-blood RNA-seq from AD(27_028_S01_08)


title: Whole-blood RNA-seq from AD(27_032_S02_08)


title: Whole-blood RNA-seq from AD(28_020_S01_08)


title: Whole-blood RNA-seq from AD(27_025_S00_08)


title: Whole-blood RNA-seq from ACLF(27_022_S00_08)


title: Whole-blood RNA-seq from ACLF(27_022_A01_08)


title: Whole-blood RNA-seq from AD(27_013_S01_08)


title: Whole-blood RNA-seq from AD(27_020_S02_08)


title: Whole-blood RNA-seq from AD(27_013_S02_08)


title: Whole-blood RNA-seq from AD(27_025_S02_08)


title: Whole-blood RNA-seq from AD(27_023_S00_08)


title: Whole-blood RNA-seq from AD(27_010_S00_08)


title: Whole-blood RNA-seq from AD(27_010_S02_08)


title: Whole-blood RNA-seq from AD(27_013_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(27_027_S00_08)


title: Whole-blood RNA-seq from AD(27_023_S02_08)


title: Whole-blood RNA-seq from AD(261005_S01)


title: Whole-blood RNA-seq from AD(26_I_011_S00_09)


title: Whole-blood RNA-seq from AD(26_I_005_S00_09)


title: Whole-blood RNA-seq from AD(26_I_010_S00_09)


title: Whole-blood RNA-seq from AD(26_I_006_S00_09)


title: Whole-blood RNA-seq from ACLF(27_001_A01_08)


title: Whole-blood RNA-seq from AD(26_I_012_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(26_I_004_S00_09)


title: Whole-blood RNA-seq from AD(26_I_007_S00_09)


title: Whole-blood RNA-seq from AD(26_I_001_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(26_I_004_A00_09)


title: Whole-blood RNA-seq from AD(26_I_003_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(25092_S01)


title: Whole-blood RNA-seq from pre-ACLF(25092_S00)


title: Whole-blood RNA-seq from pre-ACLF(25017_S00)


title: Whole-blood RNA-seq from ACLF(27_001_S00_08)


title: Whole-blood RNA-seq from ACLF(25024_S00)


title: Whole-blood RNA-seq from AD(25_099_S02_08)


title: Whole-blood RNA-seq from AD(25_099_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(25017_S02)


title: Whole-blood RNA-seq from AD(25_S00_022_08)


title: Whole-blood RNA-seq from AD(25_095_S02_08)


title: Whole-blood RNA-seq from AD(25_095_S01_08)


title: Whole-blood RNA-seq from AD(261007_S01)


title: Whole-blood RNA-seq from AD(25_090_S00_08)


title: Whole-blood RNA-seq from AD(25_083_S01_08)


title: Whole-blood RNA-seq from pre-ACLF(25_091_S00_08)


title: Whole-blood RNA-seq from AD(25_095_S00_08)


title: Whole-blood RNA-seq from AD(25_090_S02_08)


title: Whole-blood RNA-seq from AD(25_077_S02_08)


title: Whole-blood RNA-seq from AD(25_083_S02_08)


title: Whole-blood RNA-seq from ACLF(25_079_A02_08)


title: Whole-blood RNA-seq from AD(27_037_S00_08)


title: Whole-blood RNA-seq from AD(25_077_S00_08)


title: Whole-blood RNA-seq from ACLF(25024_S01)


title: Whole-blood RNA-seq from AD(25_081_S02_08)


title: Whole-blood RNA-seq from AD(25_081_S00_08)


title: Whole-blood RNA-seq from ACLF(25_079_S00_08)


title: Whole-blood RNA-seq from AD(25_075_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(25_071_S00_08)


title: Whole-blood RNA-seq from ACLF(25_070_S00_08)


title: Whole-blood RNA-seq from AD(25_075_S02_08)


title: Whole-blood RNA-seq from ACLF(25_070_A02_08)


title: Whole-blood RNA-seq from pre-ACLF(25_073_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(25_069_A00_08)


title: Whole-blood RNA-seq from AD(33_I_021_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(25_076_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(25_068_S00_08)


title: Whole-blood RNA-seq from AD(27_020_S00_08)


title: Whole-blood RNA-seq from AD(25_056_S02_08)


title: Whole-blood RNA-seq from AD(25_059_S02_08)


title: Whole-blood RNA-seq from AD(25_059_S00_08)


title: Whole-blood RNA-seq from AD(25_056_S00_08)


title: Whole-blood RNA-seq from ACLF(25_053_S00_08)


title: Whole-blood RNA-seq from ACLF(25_052_S00_08)


title: Whole-blood RNA-seq from ACLF(25_052_A01_08)


title: Whole-blood RNA-seq from ACLF(25_054_A01_08)


title: Whole-blood RNA-seq from pre-ACLF(25_051_S00_08)


title: Whole-blood RNA-seq from AD(25_043_S01_08)


title: Whole-blood RNA-seq from AD(25_043_S00_08)


title: Whole-blood RNA-seq from ACLF(25_054_S00_08)


title: Whole-blood RNA-seq from ACLF(25_041_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(25_042_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(25_051_A00_08)


title: Whole-blood RNA-seq from ACLF(25_047_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(25_042_A00_08)


title: Whole-blood RNA-seq from ACLF(25_047_A01_08)


title: Whole-blood RNA-seq from AD(25_039_S00_08)


title: Whole-blood RNA-seq from AD(25_037_S00_08)


title: Whole-blood RNA-seq from AD(25_036_S02_08)


title: Whole-blood RNA-seq from AD(25_036_S00_08)


title: Whole-blood RNA-seq from AD(25_031_S00_08)


title: Whole-blood RNA-seq from AD(25_030_S02_08)


title: Whole-blood RNA-seq from AD(25_025_S02_08)


title: Whole-blood RNA-seq from AD(25_032_S00_08)


title: Whole-blood RNA-seq from AD(25_025_S01_08)


title: Whole-blood RNA-seq from AD(25_030_S00_08)


title: Whole-blood RNA-seq from ACLF(25_023_S00_08)


title: Whole-blood RNA-seq from AD(25_022_S02_08)


title: Whole-blood RNA-seq from AD(25_025_S00_08)


title: Whole-blood RNA-seq from AD(25_022_S01_08)


title: Whole-blood RNA-seq from AD(25_031_S02_08)


title: Whole-blood RNA-seq from ACLF(25_014_S00_08)


title: Whole-blood RNA-seq from AD(25_013_S02_08)


title: Whole-blood RNA-seq from ACLF(25_023_A01_08)


title: Whole-blood RNA-seq from AD(25_013_S01_08)


title: Whole-blood RNA-seq from AD(25_013_S00_08)


title: Whole-blood RNA-seq from ACLF(25_014_A01_08)


title: Whole-blood RNA-seq from AD(25_011_S02_08)


title: Whole-blood RNA-seq from AD(25_011_S00_08)


title: Whole-blood RNA-seq from AD(25_012_S00_08)


title: Whole-blood RNA-seq from AD(25_012_S02_08)


title: Whole-blood RNA-seq from ACLF(25_019_S00_08)


title: Whole-blood RNA-seq from AD(25_010_S02_08)


title: Whole-blood RNA-seq from AD(25_010_S00_08)


title: Whole-blood RNA-seq from AD(25_083_S00_08)


title: Whole-blood RNA-seq from AD(25_009_S00_08)


title: Whole-blood RNA-seq from AD(25_007_S00_08)


title: Whole-blood RNA-seq from ACLF(25_004_S00_08)


title: Whole-blood RNA-seq from ACLF(25_004_A01_08)


title: Whole-blood RNA-seq from AD(25_003_S00_08)


title: Whole-blood RNA-seq from ACLF(25_008_A01_08)


title: Whole-blood RNA-seq from AD(25_001_S02_08)


title: Whole-blood RNA-seq from AD(25_007_S02_08)


title: Whole-blood RNA-seq from AD(25_001_S01_08)


title: Whole-blood RNA-seq from ACLF(25_020_S00_08)


title: Whole-blood RNA-seq from ACLF(25_041_A01_08)


title: Whole-blood RNA-seq from AD(25_001_S00_08)


title: Whole-blood RNA-seq from AD(241007_S01)


title: Whole-blood RNA-seq from pre-ACLF(25_048_S00_08)


title: Whole-blood RNA-seq from ACLF(24009_S00)


title: Whole-blood RNA-seq from AD(24_I_014_S00_09)


title: Whole-blood RNA-seq from AD(24_I_016_S00_09)


title: Whole-blood RNA-seq from AD(24_I_007_S00_09)


title: Whole-blood RNA-seq from AD(25_043_S02_08)


title: Whole-blood RNA-seq from AD(24_I_009_S00_09)


title: Whole-blood RNA-seq from AD(24_I_004_S00_09)


title: Whole-blood RNA-seq from ACLF(25_008_S00_08)


title: Whole-blood RNA-seq from ACLF(25_053_A01_08)


title: Whole-blood RNA-seq from AD(24_I_002_S00_09)


title: Whole-blood RNA-seq from ACLF(24009_A01)


title: Whole-blood RNA-seq from AD(24_I_001_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(24_005_S00_08)


title: TSLP-cDC2_1

city: Wuhan

first: Harris

last: Han

state: Hubei

address: No. 115, East Lake Road, Wuchang District

department: Medical Research Institute

country: China

institute: Wuhan University

description: Library name: Sample4

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.  The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the human reference genome using STAR software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor). The limma-voom method was utilized to perform differential expression analysis. Genome_build: hg38
Assembly: hg38
Supplementary files format and content: .csv files of count matrix

source_name: Spleen

extract_protocol:
Total RNAs were extracted from each sample using TRIzol Reagent (Invitrogen, cat. NO 15596026).
RNA-seq libraries were prepared by KC-DigitalTM Stranded mRNA-seq Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The library products corresponding to 200-500 bps were enriched, quantified, and finally sequenced on a Novaseq 6000 sequencer (Illumina) with a PE150 mode.

value: Spleen


title: Whole-blood RNA-seq from pre-ACLF(24_005_A00_08)


title: Whole-blood RNA-seq from AD(24_004_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(24_001_S00_08)


title: Whole-blood RNA-seq from AD(24_004_S00_08)


title: Whole-blood RNA-seq from ACLF(232004_S01)


title: Whole-blood RNA-seq from ACLF(232004_S00)


title: Whole-blood RNA-seq from ACLF(232001_S01)


title: Whole-blood RNA-seq from ACLF(232003_S00)


title: Whole-blood RNA-seq from ACLF(232001_S00)


title: Whole-blood RNA-seq from AD(231015_S00)


title: Whole-blood RNA-seq from AD(231008_S01)


title: Whole-blood RNA-seq from AD(231008_S00)


title: Whole-blood RNA-seq from AD(231019_S00)


title: Whole-blood RNA-seq from AD(231003_S01)


title: Whole-blood RNA-seq from pre-ACLF(23006_S01)


title: Whole-blood RNA-seq from AD(231003_S00)


title: Whole-blood RNA-seq from AD(231015_S01)


title: Whole-blood RNA-seq from AD(231019_S01)


title: Whole-blood RNA-seq from ACLF(23003_A01)


title: Whole-blood RNA-seq from pre-ACLF(23006_S00)


title: Whole-blood RNA-seq from ACLF(23003_S00)


title: Whole-blood RNA-seq from AD(231014_S00)


title: Whole-blood RNA-seq from AD(25_032_S02_08)


title: Whole-blood RNA-seq from AD(23_I_026_S00_09)


title: Whole-blood RNA-seq from AD(23_I_028_S00_09)


title: Whole-blood RNA-seq from AD(231014_S01)


title: Whole-blood RNA-seq from ACLF(232002_S00)


title: Whole-blood RNA-seq from AD(23_I_023_S00_09)


title: Whole-blood RNA-seq from AD(23_I_009_S00_09)


title: Whole-blood RNA-seq from AD(23_I_011_S00_09)


title: SHEP cells, hypoxia, rep1

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

country: USA

institute: University of Chicago

data_processing:
Trimmomatic (version 0.36) was used to process raw reads
reads were aligned to GRCh38 using STAR-aligner (version 2.6.1d)
Aligned reads were counted using featureCounts of subread (version 1.5.3), with the -exon flag
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

molecule: total RNA

source_name: SHEP

growth_protocol: Cells were grown in RPMI1640 medium (Life Technologies) supplemented with 10% heat-inactivated FBS, 2 mmol/L l-glutamine, and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated using TRIzol® reagent (Life Technologies) according to the manufacture’s protocol
Strand-specific RNA-SEQ libraries were prepared using an oligo-dT based RNA-SEQ library protocol (Illumina/NEB/Kapa provided).

treatment_protocol: Cells were grown at 1% O2 for 48 hours prior to RNA collection.

tag: cell line

value: SHEP

tag: cell type

value: neuroblastoma cell line, MYCN-non-amplified

value: WT

tag: treatment

value: hypoxia

value: Day 2


title: Whole-blood RNA-seq from AD(23_I_016_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(23_I_012_S00_09)


title: Whole-blood RNA-seq from AD(23_I_006_S00_09)


title: Whole-blood RNA-seq from ACLF(222007_S00)


title: Whole-blood RNA-seq from ACLF(25_020_A01_08)


title: Whole-blood RNA-seq from ACLF(222002_S01)


title: Whole-blood RNA-seq from AD(23_009_S00_08)


title: Whole-blood RNA-seq from ACLF(222004_S01)


title: NBLS cells, hypoxia, rep3

source_name: NBL-S

value: NBL-S

value: neuroblastoma celll line, MYCN-overexpressing


title: Whole-blood RNA-seq from ACLF(222006_S00)


title: Whole-blood RNA-seq from ACLF(222011_S00)


title: Whole-blood RNA-seq from ACLF(222004_S00)


title: Whole-blood RNA-seq from AD(23_009_S01_08)


title: Whole-blood RNA-seq from AD(23_I_017_S00_09)


title: Whole-blood RNA-seq from AD(221048_S00)


title: Whole-blood RNA-seq from pre-ACLF(25_069_S00_08)


title: Whole-blood RNA-seq from ACLF(222002_S00)


title: Whole-blood RNA-seq from AD(221008_S01)


title: Whole-blood RNA-seq from pre-ACLF(22024_S02)


title: Whole-blood RNA-seq from ACLF(22031_010)


title: Whole-blood RNA-seq from AD(221003_S01)


title: Whole-blood RNA-seq from AD(221008_S00)


title: Whole-blood RNA-seq from pre-ACLF(22006_010)


title: Whole-blood RNA-seq from pre-ACLF(22006_A00)


title: Whole-blood RNA-seq from ACLF(22031_S02)


title: Whole-blood RNA-seq from pre-ACLF(22024_S00)


title: Whole-blood RNA-seq from AD(22_I_041_S00_09)


title: Whole-blood RNA-seq from AD(22_I_045_S00_09)


title: Whole-blood RNA-seq from AD(22_I_037_S00_09)


title: Whole-blood RNA-seq from AD(22_I_039_S00_09)


title: Whole-blood RNA-seq from AD(22_I_032_S00_09)


title: Whole-blood RNA-seq from AD(22_I_046_S00_09)


title: Whole-blood RNA-seq from AD(22_I_030_S00_09)


title: Whole-blood RNA-seq from AD(22_I_029_S00_09)


title: Whole-blood RNA-seq from AD(22_I_025_S00_09)


title: Whole-blood RNA-seq from AD(22_I_026_S00_09)


title: Whole-blood RNA-seq from AD(22_I_015_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(22_I_017_A00_09)


title: Whole-blood RNA-seq from AD(22_I_004_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(22_I_017_S00_09)


title: Whole-blood RNA-seq from AD(22_I_021_S00_09)


title: Whole-blood RNA-seq from AD(22_I_005_S00_09)


title: Whole-blood RNA-seq from AD(22_I_024_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(22_045_01_08)


title: Whole-blood RNA-seq from pre-ACLF(22_I_002_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(22_033_01_08)


title: Whole-blood RNA-seq from AD(22_I_003_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(22_012_01_08)


title: Whole-blood RNA-seq from AD(21_005_S00_08)


title: Whole-blood RNA-seq from AD(21_010_S00_08)


title: Whole-blood RNA-seq from AD(21_010_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(22_003_A00_08)


title: Whole-blood RNA-seq from pre-ACLF(22_004_A00_08)


title: Whole-blood RNA-seq from pre-ACLF(22_004_01_08)


title: Whole-blood RNA-seq from pre-ACLF(20088_A01)


title: Whole-blood RNA-seq from AD(21_005_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(20055_S00)


title: Whole-blood RNA-seq from ACLF(20073_A01)


title: Whole-blood RNA-seq from AD(20054_S01)


title: Whole-blood RNA-seq from pre-ACLF(20055_S01)


title: Whole-blood RNA-seq from ACLF(20073_S00)


title: Whole-blood RNA-seq from AD(20054_S00)


title: Whole-blood RNA-seq from pre-ACLF(22_003_01_08)


title: Whole-blood RNA-seq from pre-ACLF(20050_S00)


title: Whole-blood RNA-seq from pre-ACLF(20088_S00)


title: Whole-blood RNA-seq from pre-ACLF(20041_S01)


title: Whole-blood RNA-seq from ACLF(20037_S02)


title: Whole-blood RNA-seq from pre-ACLF(20024_S01)


title: Whole-blood RNA-seq from ACLF(20034_S00)


title: Whole-blood RNA-seq from AD(20_093_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(20_I_002_S00_09)


title: Whole-blood RNA-seq from ACLF(20_084_S00_08)


title: Whole-blood RNA-seq from ACLF(20015_S00)


title: Whole-blood RNA-seq from ACLF(20015_A01)


title: Whole-blood RNA-seq from pre-ACLF(20024_S00)


title: Whole-blood RNA-seq from AD(20_075_S01_08)


title: Whole-blood RNA-seq from AD(20_093_S01_08)


title: Whole-blood RNA-seq from ACLF(20_084_A01_08)


title: Whole-blood RNA-seq from ACLF(20_072_S00_08)


title: Whole-blood RNA-seq from ACLF(20_072_A01_08)


title: Whole-blood RNA-seq from AD(20_075_S02_08)


title: Whole-blood RNA-seq from AD(20_060_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(20050_A01)


title: Whole-blood RNA-seq from AD(20_060_S01_08)


title: Whole-blood RNA-seq from AD(20_058_S02_08)


title: Whole-blood RNA-seq from AD(20_058_S00_08)


title: Whole-blood RNA-seq from AD(20_060_S00_08)


title: Whole-blood RNA-seq from ACLF(20037_A01)


title: Whole-blood RNA-seq from AD(20_058_S01_08)


title: Whole-blood RNA-seq from ACLF(20034_A01)


title: Whole-blood RNA-seq from AD(20_057_S02_08)


title: Whole-blood RNA-seq from AD(20_057_S01_08)


title: Whole-blood RNA-seq from pre-ACLF(20_053_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(20_053_A00_08)


title: Whole-blood RNA-seq from pre-ACLF(20_041_S00_08)


title: Whole-blood RNA-seq from AD(20_033_S02_08)


title: Whole-blood RNA-seq from ACLF(20_032_S00_08)


title: Whole-blood RNA-seq from AD(20_057_S00_08)


title: Whole-blood RNA-seq from AD(20_029_S02_08)


title: Whole-blood RNA-seq from AD(20_033_S00_08)


title: Whole-blood RNA-seq from AD(20_029_S00_08)


title: Whole-blood RNA-seq from ACLF(20_032_A01_08)


title: Whole-blood RNA-seq from AD(20_029_S01_08)


title: Whole-blood RNA-seq from AD(20_022_S02_08)


title: Whole-blood RNA-seq from AD(20_022_S00_08)


title: Whole-blood RNA-seq from AD(20_023_S01_08)


title: Whole-blood RNA-seq from pre-ACLF(20_028_S00_08)


title: Whole-blood RNA-seq from AD(20_022_S01_08)


title: Whole-blood RNA-seq from AD(20_018_S00_08)


title: Whole-blood RNA-seq from AD(20_023_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(20_010_S00_08)


title: Whole-blood RNA-seq from AD(20_018_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(20_010_A00_08)


title: Whole-blood RNA-seq from AD(20_013_S00_08)


title: Whole-blood RNA-seq from AD(20_023_S02_08)


title: Whole-blood RNA-seq from AD(18_001_S02_08)


title: Whole-blood RNA-seq from pre-ACLF(20_041_A00_08)


title: Whole-blood RNA-seq from AD(18_001_S00_08)


title: Whole-blood RNA-seq from HS(17K029)

value: HS


title: Whole-blood RNA-seq from HS(17K042)


title: Whole-blood RNA-seq from HS(17K032)


title: Whole-blood RNA-seq from HS(17K003)


title: Whole-blood RNA-seq from HS(17K008)


title: Whole-blood RNA-seq from HS(17K013)


title: Whole-blood RNA-seq from HS(17K004)


title: Whole-blood RNA-seq from ACLF(172019_S01)


title: Whole-blood RNA-seq from ACLF(172020_S01)


title: Whole-blood RNA-seq from HS(17K007)


title: Whole-blood RNA-seq from ACLF(172018_A01)


title: Whole-blood RNA-seq from ACLF(172018_A00)


title: Whole-blood RNA-seq from ACLF(172019_S00)


title: Whole-blood RNA-seq from ACLF(172016_S01)


title: Whole-blood RNA-seq from ACLF(172017_S00)


title: Whole-blood RNA-seq from ACLF(172016_S00)


title: Whole-blood RNA-seq from ACLF(172013_S01)


title: Whole-blood RNA-seq from ACLF(172012_S01)


title: Whole-blood RNA-seq from ACLF(172017_S01)


title: Whole-blood RNA-seq from ACLF(172012_S00)


title: Whole-blood RNA-seq from ACLF(172010_S00)


title: Whole-blood RNA-seq from ACLF(172013_S00)


title: Whole-blood RNA-seq from ACLF(172009_S01)


title: Whole-blood RNA-seq from ACLF(172014_S00)


title: Whole-blood RNA-seq from AD(20_013_S02_08)


title: Whole-blood RNA-seq from ACLF(172020_S00)


title: Whole-blood RNA-seq from ACLF(172010_S01)


title: Whole-blood RNA-seq from ACLF(172008_S01)


title: Whole-blood RNA-seq from ACLF(172009_S00)


title: Whole-blood RNA-seq from ACLF(172008_S00)


title: Whole-blood RNA-seq from AD(20_075_S00_08)


title: Whole-blood RNA-seq from ACLF(172007_S01)


title: Whole-blood RNA-seq from ACLF(172014_S01)


title: Whole-blood RNA-seq from ACLF(172007_S00)


title: Whole-blood RNA-seq from ACLF(172002_S01)


title: Whole-blood RNA-seq from ACLF(172003_S01)


title: Whole-blood RNA-seq from ACLF(172003_S00)


title: Whole-blood RNA-seq from AD(171108_S01)


title: Whole-blood RNA-seq from AD(171112_S00)


title: Whole-blood RNA-seq from AD(171112_S01)


title: Whole-blood RNA-seq from AD(171104_S01)


title: Whole-blood RNA-seq from AD(171108_S00)


title: Whole-blood RNA-seq from AD(171102_S01)


title: Whole-blood RNA-seq from AD(171091_S01)


title: Whole-blood RNA-seq from ACLF(172004_S00)


title: Whole-blood RNA-seq from AD(171099_S00)


title: Whole-blood RNA-seq from AD(171091_S00)


title: Whole-blood RNA-seq from AD(171090_S01)


title: Whole-blood RNA-seq from AD(171090_S00)


title: Whole-blood RNA-seq from AD(171104_S00)


title: Whole-blood RNA-seq from AD(171087_S01)


title: Whole-blood RNA-seq from AD(171087_S00)


title: Whole-blood RNA-seq from AD(171055_S01)


title: Whole-blood RNA-seq from AD(171080_S01)


title: Whole-blood RNA-seq from AD(171065_S00)


title: Whole-blood RNA-seq from AD(171065_S01)


title: Whole-blood RNA-seq from AD(171051_S01)


title: Whole-blood RNA-seq from AD(171066_S01)


title: Whole-blood RNA-seq from AD(171080_S00)


title: Whole-blood RNA-seq from AD(171039_S01)


title: Whole-blood RNA-seq from AD(171045_S01)


title: Whole-blood RNA-seq from AD(171044_S01)


title: Whole-blood RNA-seq from AD(171045_S00)


title: Whole-blood RNA-seq from AD(171044_S00)


title: Whole-blood RNA-seq from AD(171043_S01)


title: Whole-blood RNA-seq from AD(171031_S01)


title: Whole-blood RNA-seq from AD(171036_S01)


title: Whole-blood RNA-seq from AD(171029_S01)


title: Whole-blood RNA-seq from AD(171026_S01)


title: Whole-blood RNA-seq from AD(171032_S00)


title: Whole-blood RNA-seq from AD(171037_S01)


title: Whole-blood RNA-seq from AD(171039_S00)


title: C2 rep1

city: Columbia

first: Andrew

last: Kelleher

state: MO

address: 1030 Hitt Street

department: Ob, Gyn Womens Health

institute: University of Missouri

description: Library name: C2

library_source: transcriptomic single cell

data_processing:
Cell Ranger v9.0.0 (mkfastq) and aligned to the bovine reference genome ARS-UCD1.3
cellranger count with parameter --chemistry=ARC-v1
Assembly: ARS-UCD1.3.113
Supplementary files format and content: The base call files were demultiplexed, processed to generate FASTQ files with Cell Ranger v9.0.0 (10X Genomics) command mkfastq, and then aligned to the mouse reference genome (ARS-UCD1.3.113), followed by filtering and barcode and unique molecular identifier (UMI) counting to generate count matrices for each sample.

molecule: nuclear RNA

organism: Bos taurus

source_name: Differentiated Trophoblast stem cells

growth_protocol: These cells either cultured on MEFs in LCDM condition ( the undifferentiated TSC) or on collagen IV coated plate in forskolin and ROCK inhibitor containing media.

extract_protocol:
nuclei were extracted from snap frozen cells using Miltenyi tissue dissociator
Isolated nuclei (0.7–1.2 million nuclei/mL, 200 µL) were submitted to the University of Missouri Genomics Technology Core. Nuclei concentration and viability were assessed using acridine orange/propidium iodide staining and a Cellometer K2 (Nexcelom). Approximately 10,000 nuclei per sample were processed following the 10x Genomics Chromium Next GEM Single Cell Gene Expression protocol. Libraries were generated by cDNA synthesis, fragmentation, end repair, A-tailing, adapter ligation, barcoding, and clean-up as recommended by the manufacturer. The resulting libraries were quantified, size-assessed, pooled, and sequenced on an Illumina NovaSeq X+ instrument, targeting 50,000 reads per nucleus with a sequencing configuration of 28 bp on Read 1 and 100 bp on Read 2. Raw sequencing data were then delivered for downstream analysis.Single-nuclei RNA-seq analysis.

treatment_protocol: those cells were differentiated as mentioned above for 10 days.

value: Blastocyst-derived Trohoblast stem cells


title: Whole-blood RNA-seq from AD(171024_S01)


title: Whole-blood RNA-seq from AD(171013_S01)


title: Whole-blood RNA-seq from AD(171026_S00)


title: Whole-blood RNA-seq from AD(171021_S00)


title: B4 rep1

description: Library name: B4


title: Whole-blood RNA-seq from AD(171013_S00)


title: Whole-blood RNA-seq from AD(171031_S00)


title: Whole-blood RNA-seq from AD(171009_S01)


title: Whole-blood RNA-seq from AD(171002_S01)


title: Phf2 KO PHF2 binding sites

city: Nagakute

first: Taku

last: Fukushima

state: Aichi

country: Japan

institute: Aichi Medical University

description: Library name: KO_PHF2

library_source: genomic

data_processing:
Illumina NovaSeq X Plus (paired-end reads of 150 bp)
Following end repair of immunoprecipitated DNA, adenine (A) was added to the 3'-terminus of the DNA fragments, and full-length libraries for Illumina sequencing were ligated.
PCR amplification was performed using P5 and P7 oligonucleotide primers, and the PCR products constituting the final library construction were purified using AMPure XP.
The sequence reads were mapped to the mm10 genome by Bowtie2 and Peaks were called by MACS2 using Galaxy web tool.
Assembly: mm10
Supplementary files format and content: bigwig files were generated using Galaxy web tool
Supplementary files format and content: peak text files were generated using MACS2 callpeak
Library strategy: CUT&Run

molecule: genomic DNA

organism: Mus musculus

source_name: skeletal muscle

growth_protocol: Mice were housed under a 12-hour light/dark cycle at 23 °C with free access to food (MF feed, Oriental Yeast) and water.

extract_protocol:
The samples were stained at 4℃ for overnight with antibody.
NEBNext® Ultra ll DNA Library Prep Kit for Illumina

treatment_protocol: The gastroceiumus muscle was performed on gastrocnemius muscles from 4-week-old male mice according to the CUT&RUN Assay kit protocol (86652, CST).

value: skeletal muscle

value: gastroceiumus muscle

value: KO

value: Phf2 flox/flox;Acta1 Cre+

tag: batch

value: 4 week old C57BL/6


title: Whole-blood RNA-seq from AD(171009_S00)

value: Whole blood

value: AD


title: Phf2 KO IgG binding sites

description: Library name: KO_IgG


title: C1 rep1

description: Library name: C1


title: Whole-blood RNA-seq from AD(171002_S00)


title: Phf2 Ctrl IgG binding sites

description: Library name: Ctrl_IgG

value: Ctrl

value: Phf2 flox/flox;Acta1 Cre-


title: Whole-blood RNA-seq from AD(171001_S01)


title: RNAseq_PRC1cKO_P7GO_rep1

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

institute: UC Davis

description: Library name: Sample 3

data_processing:
Reads length: 150bp
Raw RNA-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.10) with the parameter ‘--paired’
Trimmed reads were aligned to the mouse (GRCm38/mm10) genome using HISAT2 77 (version 2.2.1) with default parameters. All unmapped reads, non-uniquely mapped reads, and reads with low mapping quality (MAPQ < 30) were filtered out by samtools 78 (version 1.16.1) with the parameter '-q 30' before being subjected to downstream analyses.
Raw read counts for each gene were generated using the featureCounts79 part of the Subread package (version 2.0.3) based on mouse gene annotations (gencode.vM25.annotation.gtf, GRCm38/mm10).
DESeq280 (version 1.44.0) was used for differential gene expression analyses with cutoffs FoldChange > 1.5  and Padj values < 0.05.
The TPM values of each gene were generated using RSEM (version 1.3.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: ovary

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, Cat # 74034) according to the manufacturer's instructions.
Library preparation was performed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420S) according to the manufacturer’s instructions.  Prepared RNA-seq libraries were sequenced on the HiSeq 4000 system (Illumina) with paired-ended 150-bp reads.

value: ovary

value: primary cells

value: P7 growing oocytes

value: Ring1-/-; Ring1F/-; Ddx4-Cre


title: RNAseq_PRC1cKO_P7GO_rep2

description: Library name: Sample 4


title: Whole-blood RNA-seq from HS(17_K_034_S00_09)


title: RNAseq_PRC1ctrl_P7GO_rep2

description: Library name: Sample 2

value: Ring1-/-; Rnf2F/+; Ddx4-Cre


title: Whole-blood RNA-seq from AD(171001_S00)


title: RNAseq_PRC1ctrl_P7GO_rep1

description: Library name: Sample 1


title: PRC1cKO_CT_P7GO_H3K27me3_rep1

description: Library name: Sample 23

data_processing:
For CUT&Tag data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html).
Raw paired-end reads were trimmed by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.10)
Trimmed reads were aligned with the mouse genome (GRCm38/mm10) using Bowtie2 83 (version 2.4.5) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. D. melanogaster DNA delivered by Drosophila S2 cells was used as spike-in DNA for CUT&Tag. For mapping D. melanogaster spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates from all mapped bam files were removed using the ‘MarkDuplicates’ command in Picard tools (version 3.0.0) (https://broadinstitute.github.io/picard/ ).
To compare replicates, Pearson correlation coefficients were calculated and plotted by ‘multiBamSummary bins’ and ‘plot correlation’ commands from deepTools 84 (version 3.5.5). Biological replicates were pooled using the ‘merge’ command in samtools for visualization and other analyses after confirming reproducibility (Pearson correlation coefficient > 0.85). Spike-in normalization was implemented using the exogenous scaling factor computed from the dm6 mapping files (scale factors = 10,000 / aligned spike-in reads).
Spike-in normalized genome coverage tracks with 1 bp resolution in BigWig format were generated using ‘bamCoverage’ from deepTools with the parameters ‘--binSize 1 --extendReads --samFlagInclude 64 --normalizeUsing RPKM --scaleFactor $scale_factor’. Track views were visualized and exported from Integrative Genomics Viewer 85 (version 2.14.1).
Assembly: mm10
Supplementary files format and content: bigWig, spike-in normalized tracks
Supplementary files format and content: bed, peaks
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag libraries of oocytes were prepared as previously described32,33 with some modifications (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ) using CUTANA™ pAG-Tn5 (Epicypher, 15-1017). To perform quantitative spike-in CUT&Tag, Drosophila S2 cells were added to mouse oocytes at a fixed ratio (e.g. 2000 S2 cells to 1000 mouse oocytes) at the beginning of each reaction.
CUT&Tag libraries were prepared using NEBNext HiFi 2x PCR Master mix (NEB, M0541L) according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ).

tag: antibody

tag: reads length


title: Phf2 Ctrl PHF2 binding sites

description: Library name: Ctrl_PHF2


title: PRC1ctrl_CT_P7GO_H3K27me3_rep1

description: Library name: Sample 21


title: Whole-blood RNA-seq from HS(17_K_021_S00_09)


title: PRC1ctrl_CT_P7GO_H3K27me3_rep2

description: Library name: Sample 22


title: PRC1cKO_CT_P7GO_H3K27me3_rep2

description: Library name: Sample 24


title: p258h_D21_naive_ATAC

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

description:
Library name: p258h
ATAC for sample young naïve mice

library_source: genomic single cell

data_processing:
scRNA-seq.  Libraries were sequenced on the Illumina NovaSeq X Plus platform (Illumina, San Diego, CA). Raw sequencing data were processed using the BD Rhapsody Analysis Pipeline (v2.2.1) on VELSERA cloud platform, aligned to the GRCm39 reference genome ( scATAC-seq Sequencing data was processed using BD Rhapsody Sequence Analysis Pipeline v2.2.1 ATAC Large Input  on the Seven Bridges Genomics (SBG, now VELSERA) cloud platform (San Francisco, CA). the output files were generated for secondary analysis and visualization. Spatial Transcriptomic The single nuclei whole transcriptome (snWT) seq data was uploaded to the BD Rhapsody SBG for gene expression analysis, and the RSEC_MolsPerCell_MEX.zip output files folder, along with the Trekker seq data,  were uploaded to the LatchBio cloud platform for the CurioTrekker v1.1.0 spatial single cell seq pipeline  analysis.
Assembly: GRCm39
Supplementary files format and content: CITE-Seq pipeline output: MEX.tar.gz files with matrix.mtx, barcodes.tsv, features.tsv; ATAC-seq pipeline output: 1. MEX.tar.gz files with matrix.mtx, barcodes.tsv, features.tsv. 2 peak.bed files, 3 fragment.bed files.;  Spatial Transcriptomics: 1. spatial positions: coordinates.csv. 2  Curio Trekker output: matrix.mtx, barcodes.tsv, features.tsv. 3. Curio Trekker output: anndata files for the final pipeline output

source_name: Lung

extract_protocol:
Lung immune and epithelial cells were isolated using a modified enzymatic digestion protocol from a previous study with minimal modification (17). Mice were euthanized and lungs were perfused and lavaged with digestion buffer composed of RPMI-1640 supplemented with elastase (Worthington), dispase II (Sigma-Aldrich), and DNase I (Sigma-Aldrich). Lung tissues were then excised, minced into small fragments, and further digested in RPMI-1640 containing liberase (Sigma-Aldrich) and DNase I at 37°C for 30 minutes. Following enzymatic digestion, single-cell suspensions were obtained by passing the mixture through a 100 μm cell strainer and red blood cells were lysed using ACK lysis buffer. To enrich for specific cell subsets, cells were stained with surface markers targeting CD11b⁺, EpCAM⁺, and CD11c⁺ populations using a customized innate immune panel. CD3⁺ T cells were enriched following FACS protocol. Cells were sorted using a FACSAria cell sorter (BD Biosciences) after staining with oligo antibodies (Table S2). CD11b⁺, EpCAM⁺, CD11c⁺, CD3⁺ cells and the non-sorted fraction at a 1:1:1:1:6 ratio and resuspended in cold PBS supplemented with 1% BSA (Miltenyi Biotec) and 0.5 U/μL RNase inhibitor (Sigma-Aldrich) for scRNA-seq. CD11b⁺, EpCAM⁺, CD11c⁺ and the non-sorted fraction at a 1:1:1:7 ratio and resuspended in BD OMICS Guard™ buffer (BD Biosciences, Cat. 570911).Spatial transcriptomics Lung tissues from C57BL/6 mice were freshly harvested, embedded in optimal cutting temperature (OCT) compound, and immediately snap-frozen in liquid nitrogen. Samples were stored at −80 °C until sectioning.
scRNA-seq analysis To simultaneously assess whole-transcriptome and targeted surface protein expression at the single-cell level, BD Rhapsody™ single-cell multi-omics technology was employed. Mouse lung cells were thawed and resuspended in FACS buffer prior to dextramer-based flow cytometric sorting for antigen-specific T cells. Sorted cells were collected into staining buffer at a concentration of 200–800 cells/μL in ~600 μL per sample. Approximately half of the collected cells were loaded onto the BD Rhapsody Cartridge (BD Biosciences, Cat. #633733) using the associated BD Rhapsody Cartridge Reagent Kit (Cat. #633731). Cells were captured in microwell arrays with barcoded beads, followed by cell lysis, bead retrieval, cDNA synthesis, template switching, and Klenow extension. Full-length cDNA containing unique molecular identifiers (UMIs) and cell barcodes was PCR-amplified. Whole-transcriptome was prepared using the BD Rhapsody Whole Transcriptome Amplification Kit (Cat. #633801) following the manufacturer’s instructions. scATAC-seq analysis Cryopreserved cells stored in BD OMICS-Guard™ buffer (Cat. #570911) for less than 48 hours were centrifuged at 800 × g for 5 minutes to remove the preservation buffer. Without additional washing, cells were resuspended in BD sample buffer at ~800 cells/μL for downstream ATAC-seq processing. Splint beads were prepared using a custom splint oligonucleotide specific to V3 capture beads provided by BD Biosciences. Nuclei were isolated following a modified protocol (62). Briefly, cell pellets were lysed and resuspended in Nuclei Buffer using a wide-bore pipette, aiming for a concentration of 10,000 nuclei/μL. In situ tagmentation was performed by incubating the nuclei with a Tagmentase mix that targets accessible chromatin regions, generating DNA fragments with preloaded adapter sequences. An aliquot of tagmented nuclei was stained with DyeCycle™ Green (1 mM) and counted using the BD Rhapsody™ Scanner. Single-nucleus capture, cell lysis, and genomic DNA processing were performed according to the BD Rhapsody manufacturer’s protocol. DNA fragments were captured via splint-oligo-bonded TSO (template-switch oligo) strands. Ligase was used to ligate the bead-bound oligos to the tagmented DNA, followed by gap filling and extension using a specific enzyme mix. Final denaturation removed DNA templates from beads, and Illumina-compatible adapters and sample indices were introduced during amplification. Libraries were prepared with the following sequencing parameters: Read 1: 50 cycles, Read 2: 50 cycles, Index 1: 8 cycles, and Index 2: 60 cycles. Sequencing data were analyzed using the BD Rhapsody ATAC Large Input pipeline (v2.2.1) on VELSERA cloud platform. Processed output files were used for secondary analysis and visualization using the Signac package (v1.14.0). In brief, fragment files were imported and used to create a Seurat object with a chromatin assay via the CreateChromatinAssay function. Spatial transcriptomics Lung tissues from C57BL/6 mice were freshly harvested, embedded in optimal cutting temperature (OCT) compound, and immediately snap-frozen in liquid nitrogen. Samples were stored at −80 °C until sectioning. Spatially resolved single-nucleus transcriptomic profiling was performed using the Curio Trekker Single-Cell Spatial Mapping Kit (Cat. Nos. SK017 and SK020; Takara Bio). Briefly, 25 μm cryosections of mouse lung tissue were placed onto Trekker 10 × 10 mm glass tiles, each embedded with a monolayer of uniquely DNA-barcoded microparticles (beads). Upon exposure to ultraviolet (UV) light, the spatial DNA barcodes were photocleaved and internalized into the overlying tissue. Following UV exposure and barcode incorporation, the tissue was dissociated from the tile into single-nucleus suspensions. These spatially tagged nuclei were then loaded onto the BD Rhapsody™ Single-Cell system (BD Biosciences) for single-nucleus capture and transcriptomic profiling.

value: Lung

value: NAÏVE

tag: library type

value: ATAC


title: Whole-blood RNA-seq from HS(17_K_005_S00_09)

value: HS


title: Whole-blood RNA-seq from HS(17_K_035_S00_09)


title: Whole-blood RNA-seq from HS(17_K_022_S00_09)


title: Whole-blood RNA-seq from ACLF(172002_S00)

value: ACLF


title: Whole-blood RNA-seq from HS(17_K_006_S00_09)


title: Whole-blood RNA-seq from HS(17_K_025_S00_09)


title: Whole-blood RNA-seq from HS(17_K_002_S00_09)


title: p258f_D21_IMM_ATAC

description:
Library name: p258f
ATAC for sample 21 days after vaccinations


title: Whole-blood RNA-seq from HS(17_K_031_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(17_I_113_S00_09)

value: pre-ACLF


title: Whole-blood RNA-seq from AD(171102_S00)


title: p258e_3M_IMM_ATAC

description:
Library name: p258e
ATAC for sample 3 months after vaccinations


title: Whole-blood RNA-seq from AD(17_I_107_S00_09)


title: p258d_D21_naive_ADT

description:
Library name: p258dAb
the Ab sequence of 4 months naive mice

library_source: other

data_processing:
scRNA-seq.  Libraries were sequenced on the Illumina NovaSeq X Plus platform (Illumina, San Diego, CA). Raw sequencing data were processed using the BD Rhapsody Analysis Pipeline (v2.2.1) on VELSERA cloud platform, aligned to the GRCm39 reference genome ( scATAC-seq Sequencing data was processed using BD Rhapsody Sequence Analysis Pipeline v2.2.1 ATAC Large Input  on the Seven Bridges Genomics (SBG, now VELSERA) cloud platform (San Francisco, CA). the output files were generated for secondary analysis and visualization. Spatial Transcriptomic The single nuclei whole transcriptome (snWT) seq data was uploaded to the BD Rhapsody SBG for gene expression analysis, and the RSEC_MolsPerCell_MEX.zip output files folder, along with the Trekker seq data,  were uploaded to the LatchBio cloud platform for the CurioTrekker v1.1.0 spatial single cell seq pipeline  analysis.
Assembly: GRCm39
Supplementary files format and content: CITE-Seq pipeline output: MEX.tar.gz files with matrix.mtx, barcodes.tsv, features.tsv; ATAC-seq pipeline output: 1. MEX.tar.gz files with matrix.mtx, barcodes.tsv, features.tsv. 2 peak.bed files, 3 fragment.bed files.;  Spatial Transcriptomics: 1. spatial positions: coordinates.csv. 2  Curio Trekker output: matrix.mtx, barcodes.tsv, features.tsv. 3. Curio Trekker output: anndata files for the final pipeline output
Library strategy: CITE-seq

molecule: protein

value: ADT


title: p258g_3M_naive_ATAC

description:
Library name: p258g
ATAC for sample old naive mice


title: Whole-blood RNA-seq from AD(17_I_103_S00_09)


title: p258d_D21_naive_GEX

description:
Library name: p258dWT
the gene expression of 4 months naive mice

value: mRNA


title: p258c_3M_naive_ADT

description:
Library name: p258cAb
the Ab sequence of 7 months naive mice


title: Whole-blood RNA-seq from pre-ACLF(17_I_105_S00_09)

value: Whole blood


title: Whole-blood RNA-seq from AD(17_I_098_S00_09)

value: AD


title: p258c_3M_naive_GEX

description:
Library name: p258cWT
the gene expression of 7 months naive mice


title: p258b_D21_IMM_ADT

description:
Library name: p258bAb
the Ab sequence of sample 3 months post vaccinations


title: Whole-blood RNA-seq from AD(17_I_094_S00_09)


title: Whole-blood RNA-seq from AD(17_I_092_S00_09)


title: p258b_D21_IMM_GEX

description:
Library name: p258bWT
the gene expression of sample 21 days post vaccinations


title: Whole-blood RNA-seq from pre-ACLF(17_I_082_A00_09)


title: p258a_3M_IMM_ADT

description:
Library name: p258aAb
the Ab sequence of sample 3 months post vaccinations


title: Whole-blood RNA-seq from AD(17_I_078_S00_09)


title: Whole-blood RNA-seq from pre-ACLF(17_I_070_S00_09)


title: p258a_3M_IMM_GEX

description:
Library name: p258aWT
the gene expression of sample 3 months post vaccinations


title: Whole-blood RNA-seq from pre-ACLF(17_I_082_S00_09)


title: Phf2 Ctrl input_2

description: Library name: Ctrl_input_2

value: skeletal muscle

value: gastroceiumus muscle

value: Ctrl

value: 4 week old C57BL/6


title: Phf2 KO input

description: Library name: CKO_input

value: CKO

value: Phf2 flox/flox;Acta1 Cre+


title: Whole-blood RNA-seq from pre-ACLF(17_I_067_S00_09)


title: Phf2 KO H3K9me2 binding sites

description: Library name: CKO_H3K9


title: Whole-blood RNA-seq from AD(17_I_066_S00_09)


title: Phf2 Ctrl input_1

description: Library name: Ctrl_input_1

value: Phf2 flox/flox;Acta1 Cre-


title: Wild type H3K4me3 binding sites

description: Library name: H3K4me3


title: Whole-blood RNA-seq from pre-ACLF(17_I_067_A00_09)


title: Whole-blood RNA-seq from AD(17_I_051_S00_09)


title: Donor 23 ADT

description: Library name: Sample 2-2

data_processing:
Raw FASTQ files were processed with Cell Ranger (v7.1.0) using the cellranger count pipeline.  Gene expression reads were aligned to the GRCh38 human reference genome (10x Genomics,  refdata-gex-GRCh38-2024-A), with intronic regions included (--include-introns=true). Antibody-derived tag (ADT) counts were quantified simultaneously using a custom feature reference CSV  provided by the feature–barcode matrix contained unique molecular identifier (UMI) counts for both genes and  ADTs per cell. Filtered feature-barcode matrices were imported into R (v4.3.0), and individual Seurat objects (v4.3.0) were generated for each sample. RNA and ADT counts were stored as separate assays. Quality control (QC) filtering removed cells with fewer than 500 or more than 6,000 detected genes, fewer than 2,000 total transcripts, or >10% mitochondrial gene content. Doublets were identified and removed using scDblFinder (v1.14.0, default parameters). Post-QC, gene expression data were log-normalized and clustered using the first 30 principal components at a resolution of 0.5 to identify major immune cell populations. Clusters corresponding to DCs were extracted for detailed subclustering. Subclusters were manually annotated based on the expression of canonical DC markers. To correct for background signal from ambient antibodies, ADT counts were re-normalized using the Denoised and Scaled by Background (dsb) method (v2.0.0), which models and subtracts technical noise using empty droplets and isotype controls. The resulting denoised “ADTNormalized” assay was used for all downstream protein-level analyses.
Assembly: GRCh38
Supplementary files format and content: Seurat objects stored in .rds format
Library strategy: CITE-seq

source_name: spleen

extract_protocol:
200 million splenocytes were resuspended in PBS containing 2% FBS and 2 mM EDTA, followed by incubation with Human TruStain FcX for 10 minutes. Cells were then labeled with a biotinylated lineage antibody cocktail (anti-CD3 [Cat# 100243], anti-CD19 [Cat# 302204], and anti-CD335 [Cat# 331906], all from BioLegend) for 15 minutes at 4˚ C. Following magnetic separation using the EasySep™ Release Human Biotin Positive Selection Kit (STEMCELL Technologies, Cat# 17663), the unlabeled fraction was collected and subjected to LIVE/DEAD Fixable Aqua Dead Cell Staining Dye (Invitrogen, Cat# L34966) for 10 minutes. The cells were then stained with PE -anti-Lin (CD3/CD19/NKp46), PE-anti-CD89, FITC-anti-CD11c, APC-anti-HLA-DR, and FITC- anti-CD66b, purified anti-CADM1 antibodies for 30 minutes at 4˚ C. The target population (Lin [CD3/CD19/CD56]⁻CD89⁻CD66b⁻CD88⁻HLA-DR⁺) was isolated using a MA900 Multi- Application Cell Sorter (SONY). Purified cells were blocked using antibody staining buffer, which contained human TruStain FcX (BioLegend), and then stained with FITC-anti-chicken, PE-anti- SIGLEC6, and APC-anti-AXL for 30 min at 4°C. After washing three times, cells were then incubated with Biolegend TotalSeq_B_Universal_Cocktail_v1 (Cat# 399904) and custom antibodies purchased from the Biolegend TOTALseq catalogue for 30 min at 4°C. Stained cells were washed three times and encapsulated for CITE-seq.
Single-cell suspensions were loaded onto the 10x Chromium platform, followed by 5′ gene expression library, immune repertoire library, and cell surface protein library.

value: spleen

value: splenocytes


title: Whole-blood RNA-seq from AD(17_I_055_S00_09)


title: Whole-blood RNA-seq from AD(17_I_038_S00_09)


title: Donor 6 RNA

description: Library name: Sample 1-1


title: Whole-blood RNA-seq from AD(17_I_043_S00_09)


title: Donor 6 ADT

description: Library name: Sample 1-2


title: Whole-blood RNA-seq from AD(17_I_036_S00_09)


title: SC1_DMSO_replicate_3

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description: Library name: SC1_dmso_3

data_processing:
Next Gen Sequencing was performed on DNBSEQ-T7 with PE150 (paired-end, 150 bp) at an approximate depth of 22-23 million reads per sample.
The initial RNA-seq data was processed using SOAPnuke (version 1.5.6, Chen et al. Gigascience. 2018) to remove low-quality reads, adapter sequences, and PCR duplicates.The filter reads were aligned to the reference human genome (GRCh38) using the aligner Hisat2 (version 2.2.1, Kim et al. Nat Methods. 2015). Gene-level expression values, including raw read counts, FPKM (fragments per kilobase of transcript per million fragments mapped), and TPM (transcripts per million reads), were quantified using RSEM (version 1.2.28, Li et al. BMC Bioinformatics. 2011). The raw read counts were normalized and differential expression between two groups (Bryostatin treated, n=3; or DMSO treated, n=3) were calculated using DESeq2 (version 1.40.2, Love et al. Genome Biol. 2014).
Assembly: GRCh38
Supplementary files format and content: excel file includes raw read counts, FPKM and TPM values for each sample

extract_protocol:
RNA was extracted using RNeasy Mini kit (Qiagen). Sample QC was performed with Tapestation to identify samples with RIN>7. 200ng qualified RNA from each sample was processed for library preparation.
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. Thevenriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded cDNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and pair end 150 bases reads were generated.

value: B cell lymphoma

value: DMSO


title: SC1_DMSO_replicate_2

description: Library name: SC1_dmso_2


title: Phf2 Ctrl H3K9me2 binding sites

description: Library name: Ctrl_H3K9


title: Whole-blood RNA-seq from AD(17_I_047_S00_09)


title: SC1_DMSO_replicate_1

description: Library name: SC1_dmso_1


title: SC1_bryostatin_1nM_replicate_3

description: Library name: SC1_bryo1nM_3

value: bryostatin


title: SC1_bryostatin_1nM_replicate_1

description: Library name: SC1_bryo1nM_1


title: Whole-blood RNA-seq from AD(17_I_030_S00_09)


title: Whole-blood RNA-seq from AD(17_I_016_S00_09)


title: Whole-blood RNA-seq from AD(17_I_024_S00_09)


title: Donor 23 RNA

description: Library name: Sample 2-1


title: Whole-blood RNA-seq from ACLF(162008_S01)

value: ACLF


title: Whole-blood RNA-seq from pre-ACLF(17_I_006_500_09)

value: pre-ACLF


title: SC1_bryostatin_1nM_replicate_2

description: Library name: SC1_bryo1nM_2


title: Whole-blood RNA-seq from AD(17_I_037_S00_09)


title: Mammary gland epithelial organoids, Torin 12 days, 2

city: Québec

first: Étienne

last: Audet-Walsh

state: Québec

address: 2705 boulevard Laurier

country: Canada

institute: CRCHU de Québec

description:
Library name: GM_Org_Torin D12-2
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Torin_J12_2

data_processing:
Timming : trim_galore/cutadapt
QC : FastQC & MultiQC
Pseudoalignement : Kallisto
Normalization : tximport/DESeq2
Assembly: GRCm39 (vM34)
Supplementary files format and content: Comma separated values, with genes on rows and sample on columns. Values are normalized counts.

source_name: Mammary gland

growth_protocol: Mammary gland were extracted, and epithelial cells were purified following protocols described in Lacouture et al. (2021). Organoids were formed using Matrigel droplets and cultured in EpiCult-B mouse medium for 18 days before collect and RNA extraction. During the first 24h of culture, medium was supplemented with 5% FBS. After 12 days in culture, 10 μL of Matrigel was added on each droplet to maintain their structure.

extract_protocol:
Total RNA was isolated and purified using NEB Monarch Total RNA Miniprep Kit.
Library was constructed using NEBNext Ultra II Directionnal RNA library prep kit for Illumina.

treatment_protocol: Organoids were treated with either Torin (100nM) or DMSO (1:1,000 ) during 6 days (D6) or 12 days (D12) before collect (D18).

value: Mammary gland

value: Epithelial cells

value: Wild Type

value: Torin

value: 12 days


title: Whole-blood RNA-seq from ACLF(162007_S00)

value: Whole blood


title: Mammary gland epithelial organoids, Torin 12 days, 1

description:
Library name: GM_Org_Torin D12-1
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Torin_J12_1


title: Whole-blood RNA-seq from AD(17_I_029_S00_09)

value: AD


title: Mammary gland epithelial organoids, Torin 6 days, 3

description:
Library name: GM_Org_Torin D6-3
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Torin_J6_3

value: 6 days


title: Whole-blood RNA-seq from ACLF(162006_S00)


title: Mammary gland epithelial organoids, Torin 12 days, 3

description:
Library name: GM_Org_Torin D12-3
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Torin_J12_3


title: Mammary gland epithelial organoids, Torin 6 days, 2

description:
Library name: GM_Org_Torin D6-2
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Torin_J6_2


title: Whole-blood RNA-seq from ACLF(162005_S01)


title: Mammary gland epithelial organoids, Torin 6 days, 1

description:
Library name: GM_Org_Torin D6-1
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Torin_J6_1


title: Whole-blood RNA-seq from ACLF(162005_S00)


title: Mammary gland epithelial organoids, DMSO 12 days, 2

description:
Library name: GM_Org_Ctrl D12-2
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Ctrl_J12_2


title: Whole-blood RNA-seq from ACLF(162008_S00)


title: Whole-blood RNA-seq from ACLF(162001_S00)


title: Whole-blood RNA-seq from AD(161073_S01)


title: Whole-blood RNA-seq from AD(161073_S00)


title: Whole-blood RNA-seq from AD(161040_S01)


title: Mammary gland epithelial organoids, DMSO 12 days, 3

description:
Library name: GM_Org_Ctrl D12-3
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Ctrl_J12_3


title: Whole-blood RNA-seq from ACLF(162002_S00)


title: Mammary gland epithelial organoids, DMSO 6 days, 3

description:
Library name: GM_Org_Ctrl D6-3
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Ctrl_J6_3


title: Whole-blood RNA-seq from AD(161029_S00)


title: Mammary gland epithelial organoids, DMSO 6 days, 1

description:
Library name: GM_Org_Ctrl D6-1
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Ctrl_J6_1


title: Mammary gland epithelial organoids, DMSO 12 days, 1

description:
Library name: GM_Org_Ctrl D12-1
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Ctrl_J12_1


title: siErk3_Palmitic_(2)

city: Warsaw

first: Grzegorz

last: Sumara

address: L Pasteur 3

country: Poland

institute: Nencki Institute of Experimental Biology PAS

description: Library name: ANG_F92_0014_P01_V11

data_processing:
Transcriptomic data analysis was done as follows: FASTQ files were aligned to mm10 mouse reference genome with STAR program (Dobin et al., 2013), reads were counted to genes using feature Counts algorithm (Liao et al., 2014). Gene counts were normalized with FPKM method and differential analysis was performed by DESeq2 (Love et al., 2014). Genes were considered to be differentially expressed (DE) with adjusted p value < 0.05(Yu et al., 2012).
In order to examine gene expression patterns, cluster analysis was performed in cultures after transfection with the respective viral constructs, in R software using the Mfuzz Clustering package.
Adapter and quality trimming (Trim Galore!), Mapping of reads to a reference genome (STAR-Salmon)
Sort and index alignments (SAMtools)
Counting reads mapped to genomic genes (FeatureCounts)
Differential analysis of gene expression (DeSeq2, R, pvalue<0.05)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples
Supplementary files format and content: coma-separated value text file includes FPKM log2+1 read counts for all Samples (result from DeSeq2)

growth_protocol: C2C12 myoblasts were maintained in growth medium (DMEM high glucose) supplemented with 10% fetal bovine serum, 1% penicillin–streptomycin, and 1% L-glutamine at 37°C and 5% CO₂. Medium was replaced every two days, and cultures were kept below 70% confluency to prevent premature fusion and preserve the myoblast population. Myogenic differentiation was induced by switching to differentiation medium (DMEM high glucose supplemented with 2% horse serum, 1% L-glutamine, and 1% penicillin–streptomycin).

extract_protocol:
Total RNA was isolated from cells using TRIzol (Invitrogen) following the manufacturer’s instructions. RNA quality and integrity were evaluated on an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit, and only high-quality samples were taken for further analysis.
Strand-specific, poly(A)-selected libraries were generated from 500 ng of total RNA using the KAPA Stranded mRNA Sample Preparation Kit. Briefly, mRNA was captured with poly-T–coated magnetic beads, fragmented, and converted into first-strand cDNA. Second-strand synthesis produced double-stranded cDNA, which was subsequently A-tailed and ligated to sequencing adapters (NEB). Adapter uracils were removed with USER enzyme prior to PCR amplification. Library size distribution (~300 bp) was assessed using the Agilent High Sensitivity DNA kit, and concentrations were measured using the QuantiFluor dsDNA system (Promega). Libraries were sequenced on an Illumina NovaSeq 6000 platform in 2 × 151 bp paired-end mode.

treatment_protocol: Undifferentiated C2C12 myoblasts at full confluence were transfected with siRNAs using DharmaFECT Duo (Dharmacon). siRNAs and transfection reagent were diluted separately in Opti-MEM, mixed, and incubated for 30 min at room temperature before being added directly to the cells in differentiation medium. Reagent amounts were normalized to cell growth area, corresponding to 2.1 μL/cm² DharmaFECT Duo and 1.25 nM/cm² siRNA. All siRNAs were used as SMARTpool reagents (Dharmacon). Cells were used for downstream experiments after six days of differentiation, unless stated otherwise. For experiments employing palmitic acid treatment, differentiated myotubes were incubated for 16 h in serum-free medium containing 0.5 mM palmitic acid conjugated to BSA, while control cells were treated with the corresponding BSA vehicle.

value: skeletal muscle


title: Whole-blood RNA-seq from AD(161001_S00)


title: siMk5_Palmitic_(1)

description: Library name: ANG_F92_0016_P01_V11


title: siMk5_Palmitic_(3)

description: Library name: ANG_F92_0018_P01_V11


title: siErk3_Palmitic_(3)

description: Library name: ANG_F92_0015_P01_V11


title: Whole-blood RNA-seq from AD(161001_S01)


title: siMk5_Palmitic_(2)

description: Library name: ANG_F92_0017_P01_V11


title: Whole-blood RNA-seq from AD(16_I_055_S00_09)


title: Whole-blood RNA-seq from AD(161012_S00)


title: Whole-blood RNA-seq from AD(16_I_084_S00_09)


title: siNTC_Palmitic_(2)

description: Library name: ANG_F92_0011_P01_V11


title: Whole-blood RNA-seq from AD(161040_S00)


title: Mammary gland epithelial organoids, DMSO 6 days, 2

description:
Library name: GM_Org_Ctrl D6-2
Column name in DESeq2_normalized_counts_Torin_treatments.csv : AL196_org_GM_ARN_Ctrl_J6_2


title: Whole-blood RNA-seq from AD(16_I_032_S00_09)


title: Whole-blood RNA-seq from AD(16_I_016_S00_09)


title: siErk3_Palmitic_(1)

description: Library name: ANG_F92_0013_P01_V11


title: siNTC_Palmitic_(1)

description: Library name: ANG_F92_0010_P01_V11


title: siMk5_BSA_(3)

description: Library name: ANG_F92_0009_P01_V11


title: siNTC_Palmitic_(3)

description: Library name: ANG_F92_0012_P01_V11


title: siMk5_BSA_(1)

description: Library name: ANG_F92_0007_P01_V11


title: Whole-blood RNA-seq from AD(16_I_037_S00_09)


title: siMk5_BSA_(2)

description: Library name: ANG_F92_0008_P01_V11


title: Whole-blood RNA-seq from pre-ACLF(16_I_007_S00_09)


title: Whole-blood RNA-seq from AD(16_I_003_S00_09)


title: siErk3_BSA_(3)

description: Library name: ANG_F92_0006_P01_V11


title: Whole-blood RNA-seq from AD(16_I_015_S00_09)


title: siErk3_BSA_(2)

description: Library name: ANG_F92_0005_P01_V11


title: Whole-blood RNA-seq from ACLF(16_057_A01_08)


title: Whole-blood RNA-seq from AD(16_053_S00_08)


title: siNTC_BSA_(2)

description: Library name: ANG_F92_0002_P01_V11


title: Whole-blood RNA-seq from AD(16_I_004_S00_09)


title: Whole-blood RNA-seq from ACLF(16_057_S00_08)


title: siNTC_BSA_(3)

description: Library name: ANG_F92_0003_P01_V11


title: siNTC_BSA_(1)

description: Library name: ANG_F92_0001_P01_V11


title: siErk3_BSA_(1)

description: Library name: ANG_F92_0004_P01_V11


title: Whole-blood RNA-seq from AD(16_053_S02_08)


title: FACS sorted lung pooled from 3 mice_ CCR2KO_0Dpi_PBS_rep2

city: Vienna

first: Sylvia

last: Knapp

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

description:
Library name: LP_16
10x Genomics, Flex single-cell RNA-seq with cell fixation

data_processing:
Chromium Mouse Transcriptome Probe Set v1.0.1
CellRanger v8.0.1
Assembly: mm10-2020-A
Supplementary files format and content: Cell Ranger output files: barcode.tsv.gz, feature.tsv.gz, matrix.mtx.gz

molecule: other

extract_protocol:
Lungs were processed and were FACS sorted (100 000CD45+, 100 000CD45-, 10000Epi) into PBS-BSA, spun down and fixed in 10x Fixation buffer for 22h, resuspended according to 10x 16plex flex scRNAseq protocol in Quenching buffer+ Enhancer+ Glycerol and frozen at -80°C for at least 1-4 weeks.
10x Genomics Fixed RNA Profiling

treatment_protocol: Mouse lungs were infected with PBS or SC2 and harvested on 1 Day post infection

value: Lung

value: FACS sorted cells

value: Pooled lung cells

value: PBS


title: Whole-blood RNA-seq from ACLF(16_042_S00_08)


title: Whole-blood RNA-seq from ACLF(16_044_S00_08)


title: Whole-blood RNA-seq from ACLF(16_042_A01_08)


title: FACS sorted lung pooled from 3 mice_ B6_0Dpi_PBS_rep2

description:
Library name: LP_15
10x Genomics, Flex single-cell RNA-seq with cell fixation


title: Whole-blood RNA-seq from ACLF(16_044_A01_08)


title: FACS sorted lung pooled from 3 mice_ B6_0Dpi_PBS_rep1

description:
Library name: LP_13
10x Genomics, Flex single-cell RNA-seq with cell fixation


title: FACS sorted lung pooled from 3 mice_ CCR2KO_0Dpi_PBS_rep1

description:
Library name: LP_14
10x Genomics, Flex single-cell RNA-seq with cell fixation


title: Whole-blood RNA-seq from ACLF(16_011_S00_08)


title: FACS sorted lung pooled from 3 mice_ CCR2KO_1Dpi_SC2_rep2

description:
Library name: LP_12
10x Genomics, Flex single-cell RNA-seq with cell fixation


title: Whole-blood RNA-seq from ACLF(16_029_S00_08)


title: FACS sorted lung pooled from 3 mice_ CCR2KO_1Dpi_SC2_rep1

description:
Library name: LP_10
10x Genomics, Flex single-cell RNA-seq with cell fixation


title: Whole-blood RNA-seq from ACLF(152010_S01)


title: Whole-blood RNA-seq from ACLF(16_011_A02_08)


title: FACS sorted lung pooled from 3 mice_ B6_1Dpi_SC2_rep2

description:
Library name: LP_11
10x Genomics, Flex single-cell RNA-seq with cell fixation


title: FACS sorted monocyte derived AM_RNA,SC2,28Dpi,rep3

description: Library name: LP47_175

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)

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: MoAM

value: WT

tag: time point_(dpi)


title: FACS sorted lung pooled from 3 mice_ B6_1Dpi_SC2_rep1

description:
Library name: LP_9
10x Genomics, Flex single-cell RNA-seq with cell fixation


title: FACS sorted monocyte derived AM_RNA,SC2,28Dpi,rep4

description: Library name: LP47_176


title: FACS sorted monocyte derived AM_RNA,SC2,28Dpi,rep2

description: Library name: LP47_174


title: Whole-blood RNA-seq from ACLF(152009_S01)

value: ACLF


title: FACS sorted monocyte derived AM_RNA,IAV,28Dpi,rep4

description: Library name: LP47_172

value: IAV


title: Whole-blood RNA-seq from ACLF(152010_S00)


title: Whole-blood RNA-seq from ACLF(152005_S00)


title: FACS sorted monocyte derived AM_RNA,SC2,28Dpi,rep1

description: Library name: LP47_173


title: Whole-blood RNA-seq from ACLF(152006_S00)


title: Whole-blood RNA-seq from ACLF(152015_S00)


title: FACS sorted monocyte derived AM_RNA,IAV,28Dpi,rep1

description: Library name: LP47_169


title: Whole-blood RNA-seq from ACLF(152006_S01)


title: FACS sorted monocyte derived AM_RNA,IAV,28Dpi,rep3

description: Library name: LP47_171


title: FACS sorted monocyte derived AM_RNA,IAV,28Dpi,rep2

description: Library name: LP47_170


title: FACS sorted monocyte derived AM_RNA,SC2,8Dpi,rep4

description: Library name: LP47_168


title: Whole-blood RNA-seq from AD(15_I_016_S00_09)


title: Whole-blood RNA-seq from ACLF(152004_S00)


title: Whole-blood RNA-seq from AD(15_I_014_S00_09)


title: Whole-blood RNA-seq from AD(15_I_007_S00_09)


title: FACS sorted monocyte derived AM_RNA,IAV,8Dpi,rep4

description: Library name: LP47_164


title: FACS sorted monocyte derived AM_RNA,IAV,8Dpi,rep3

description: Library name: LP47_163


title: FACS sorted monocyte derived AM_RNA,SC2,8Dpi,rep2

description: Library name: LP47_166


title: FACS sorted monocyte derived AM_RNA,SC2,8Dpi,rep3

description: Library name: LP47_167


title: Whole-blood RNA-seq from ACLF(152009_S00)


title: Whole-blood RNA-seq from AD(15_I_011_S00_09)


title: BMDM, WT, dTAG, 2

first: Wiktor

last: Antczak

address: Trojdena 4

institute: IIMCB

description:
Library name: Sample 59
cDNA seq

data_processing:
Basecalled nanopore reads were mapped to a transcriptome reference. The poly(A) tail lengths for each read were estimated using the Nanopolish 0.13.2 polya function
Assembly: gencode.vM35
Supplementary files format and content: tab separated value files with information on transcripts with the predited lengths of the poly(A) tails

source_name: BMDM

extract_protocol:
total RNA was extracted from tissue or cells using TRIzol
For library preparation, 3.5-5 µg of total mRNA was mixed with 50-200 ng oligo-(dT)25-enriched mRNA from Saccharomyces cerevisiae yeast and standards with predefined poly(A) lengths and processed with a Direct RNA Sequencing Kit (catalog no. SQK-RNA002, Oxford Nanopore Technologies) according to the manufacturer’s instructions.

value: BMDM


title: BMDM, WT, dTAG, 1

description:
Library name: Sample 58
cDNA seq


title: Whole-blood RNA-seq from AD(15_027_S00_08)


title: FACS sorted monocyte derived AM_RNA,IAV,8Dpi,rep1

description: Library name: LP47_161


title: BMDM, WT, DMSO, 1

description:
Library name: Sample 55
cDNA seq


title: FACS sorted monocyte derived AM_RNA,SC2,8Dpi,rep1

description: Library name: LP47_165


title: BMDM, WT, dTAG, 3

description:
Library name: Sample 60
cDNA seq


title: BMDM, TENT5A, dTAG, 3

description:
Library name: Sample 54
cDNA seq


title: Whole-blood RNA-seq from ACLF(152001_S00)


title: BMDM, TENT5A, dTAG, 2

description:
Library name: Sample 53
cDNA seq


title: Whole-blood RNA-seq from AD(15_027_S02_08)


title: FACS sorted monocyte derived AM_RNA,SC2,4Dpi,rep3

description: Library name: LP47_159


title: BMDM, WT, DMSO, 3

description:
Library name: Sample 57
cDNA seq


title: Whole-blood RNA-seq from ACLF(15_020_S00_08)


title: Whole-blood RNA-seq from pre-ACLF(15_016_A00_08)

value: pre-ACLF


title: FACS sorted monocyte derived AM_RNA,IAV,8Dpi,rep2

description: Library name: LP47_162


title: BMDM, WT, DMSO, 2

description:
Library name: Sample 56
cDNA seq


title: FACS sorted monocyte derived AM_RNA,SC2,4Dpi,rep4

description: Library name: LP47_160


title: Whole-blood RNA-seq from ACLF(15_020_A01_08)


title: Whole-blood RNA-seq from AD(15_004_S02_08)


title: BMDM, TENT5A, DMSO, 1

description:
Library name: Sample 49
cDNA seq


title: Whole-blood RNA-seq from pre-ACLF(15_016_S00_08)


title: BMDM, TENT4B, dTAG, 3

description:
Library name: Sample 48
cDNA seq


title: BMDM, TENT4B, dTAG, 2

description:
Library name: Sample 47
cDNA seq


title: BMDM, TENT5A, dTAG, 1

description:
Library name: Sample 52
cDNA seq


title: FACS sorted monocyte derived AM_RNA,IAV,4Dpi,rep4

description: Library name: LP47_156


title: BMDM, TENT5A, DMSO, 3

description:
Library name: Sample 51
cDNA seq


title: FACS sorted monocyte derived AM_RNA,SC2,4Dpi,rep2

description: Library name: LP47_158


title: FACS sorted monocyte derived AM_RNA,SC2,4Dpi,rep1

description: Library name: LP47_157


title: BMDM, TENT4B, DMSO, 2

description:
Library name: Sample 44
cDNA seq


title: BMDM, TENT4B, DMSO, 3

description:
Library name: Sample 45
cDNA seq


title: Whole-blood RNA-seq from AD(14_I_053_S00_09)


title: Whole-blood RNA-seq from AD(15_004_S00_08)


title: BMDM, TENT5A, DMSO, 2

description:
Library name: Sample 50
cDNA seq


title: FACS sorted monocyte derived AM_RNA,IAV,4Dpi,rep2

description: Library name: LP47_154


title: Whole-blood RNA-seq from AD(14_I_042_S00_09)


title: FACS sorted monocyte derived AM_RNA,IAV,4Dpi,rep3

description: Library name: LP47_155


title: BMDM, TENT4B, dTAG, 1

description:
Library name: Sample 46
cDNA seq


title: FACS sorted monocyte derived AM_RNA,IAV,4Dpi,rep1

description: Library name: LP47_153


title: BMDM, RNASEL, dTAG, 3

description:
Library name: Sample 42
cDNA seq


title: Whole-blood RNA-seq from AD(14_I_041_S00_09)


title: Whole-blood RNA-seq from AD(14_I_048_S00_09)


title: FACS sorted monocyte derived AM_RNA,SC2,2Dpi,rep4

description: Library name: LP47_152


title: BMDM, TENT4B, DMSO, 1

description:
Library name: Sample 43
cDNA seq


title: BMDM, RNASEL, dTAG, 2

description:
Library name: Sample 41
cDNA seq


title: BMDM, RNASEL, DMSO, 3

description:
Library name: Sample 39
cDNA seq


title: BMDM, RNASEL, dTAG, 1

description:
Library name: Sample 40
cDNA seq


title: BMDM, RNASEL, DMSO, 2

description:
Library name: Sample 38
cDNA seq


title: BMDM, PAN2, dTAG, 2

description:
Library name: Sample 35
cDNA seq


title: FACS sorted monocyte derived AM_RNA,SC2,2Dpi,rep2

description: Library name: LP47_150


title: BMDM, RNASEL, DMSO, 1

description:
Library name: Sample 37
cDNA seq


title: Whole-blood RNA-seq from AD(14_I_040_S00_09)


title: BMDM, PAN2, dTAG, 3

description:
Library name: Sample 36
cDNA seq


title: BMDM, PAN2, DMSO, 3

description:
Library name: Sample 33
cDNA seq


title: BMDM, PAN2, dTAG, 1

description:
Library name: Sample 34
cDNA seq


title: Whole-blood RNA-seq from AD(14_I_032_S00_09)


title: FACS sorted monocyte derived AM_RNA,SC2,2Dpi,rep1

description: Library name: LP47_149


title: Whole-blood RNA-seq from AD(14_I_010_S00_09)


title: FACS sorted monocyte derived AM_RNA,IAV,2Dpi,rep4

description: Library name: LP47_148


title: BMDM, PAN2, DMSO, 2

description:
Library name: Sample 32
cDNA seq


title: FACS sorted monocyte derived AM_RNA,SC2,2Dpi,rep3

description: Library name: LP47_151


title: Whole-blood RNA-seq from AD(14_I_022_S00_09)


title: BMDM, PAN2, DMSO, 1

description:
Library name: Sample 31
cDNA seq


title: BMDM, DCP2, dTAG, 2

description:
Library name: Sample 29
cDNA seq


title: Whole-blood RNA-seq from AD(14_033_S01_08)


title: Whole-blood RNA-seq from AD(14_033_S00_08)


title: BMDM, DCP2, dTAG, 1

description:
Library name: Sample 28
cDNA seq


title: BMDM, DCP2, dTAG, 3

description:
Library name: Sample 30
cDNA seq


title: BMDM, DCP2, DMSO, 3

description:
Library name: Sample 27
cDNA seq


title: BMDM, DCP2, DMSO, 1

description:
Library name: Sample 25
cDNA seq


title: FACS sorted monocyte derived AM_RNA,IAV,2Dpi,rep2

description: Library name: LP47_146


title: FACS sorted monocyte derived AM_RNA,IAV,2Dpi,rep3

description: Library name: LP47_147


title: Whole-blood RNA-seq from ACLF(14_028_S00_08)


title: Whole-blood RNA-seq from AD(14_033_S02_08)


title: BMDM, CNOT1, dTAG, 3

description:
Library name: Sample 24
cDNA seq


title: FACS sorted monocyte derived AM_RNA,IAV,2Dpi,rep1

description: Library name: LP47_145


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep11

description: Library name: LP47_143


title: BMDM, DCP2, DMSO, 2

description:
Library name: Sample 26
cDNA seq


title: BMDM, CNOT1, DMSO, 3

description:
Library name: Sample 21
cDNA seq


title: BMDM, CNOT1, dTAG, 1

description:
Library name: Sample 22
cDNA seq


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep12

description: Library name: LP47_144


title: Whole-blood RNA-seq from ACLF(14_022_A02_08)


title: BMDM, CNOT1, DMSO, 1

description:
Library name: Sample 19
cDNA seq


title: Whole-blood RNA-seq from ACLF(14_022_S00_08)


title: BMDM, CNOT1, dTAG, 2

description:
Library name: Sample 23
cDNA seq


title: liver, CNOT1, DMSO, DRS, 2

description:
Library name: Sample 16
DRS

source_name: liver

value: liver


title: liver, CNOT1, dTAG, DRS, 2

description:
Library name: Sample 18
DRS


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep10

description: Library name: LP47_142


title: BMDM, CNOT1, DMSO, 2

description:
Library name: Sample 20
cDNA seq


title: liver, CNOT1, dTAG, DRS, 1

description:
Library name: Sample 17
DRS


title: Whole-blood RNA-seq from AD(14_017_S02_08)


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep9

description: Library name: LP47_141


title: Whole-blood RNA-seq from AD(14_011_S02_08)


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep7

description: Library name: LP47_139


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep8

description: Library name: LP47_140


title: liver, WT, dTAG 24h, 3

description:
Library name: Sample 12
cDNA seq


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep6

description: Library name: LP47_138


title: Whole-blood RNA-seq from AD(14_011_S00_08)


title: Whole-blood RNA-seq from AD(14_017_S00_08)


title: Whole-blood RNA-seq from ACLF(14_010_S00_08)


title: liver, CNOT1, DMSO, DRS, 1

description:
Library name: Sample 15
DRS


title: liver, WT, DRS, 1

description:
Library name: Sample 13
DRS


title: liver, WT, dTAG 24h, 1

description:
Library name: Sample 10
cDNA seq


title: liver, WT, dTAG 24h, 2

description:
Library name: Sample 11
cDNA seq


title: liver, WT, DRS, 2

description:
Library name: Sample 14
DRS


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep5

description: Library name: LP47_137


title: liver, CNOT1, dTAG 24h, 3

description:
Library name: Sample 6
cDNA seq


title: liver, CNOT1, DMSO, 2

description:
Library name: Sample 8
cDNA seq


title: Whole-blood RNA-seq from ACLF(14_010_A02_08)


title: liver, CNOT1, DMSO, 3

description:
Library name: Sample 9
cDNA seq


title: Whole-blood RNA-seq from AD(14_007_S02_08)


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep3

description: Library name: LP47_135


title: Whole-blood RNA-seq from AD(14_007_S00_08)


title: liver, CNOT1, dTAG 24h, 1

description:
Library name: Sample 4
cDNA seq


title: liver, CNOT1, dTAG 2h, 3

description:
Library name: Sample 3
cDNA seq


title: liver, CNOT1, dTAG 24h, 2

description:
Library name: Sample 5
cDNA seq


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep4

description: Library name: LP47_136


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep2

description: Library name: LP47_134


title: liver, CNOT1, DMSO, 1

description:
Library name: Sample 7
cDNA seq


title: FACS sorted monocyte derived AM_RNA,PBS,0Dpi,rep1

description: Library name: LP47_133


title: Whole-blood RNA-seq from AD(14_002_S02_08)


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep12

description: Library name: LP47_132

value: AM


title: liver, CNOT1, dTAG 2h, 2

description:
Library name: Sample 2
cDNA seq


title: Whole-blood RNA-seq from AD(14_002_S01_08)


title: HEK293-FITR parental, iCLIP size-matched input, rep3

city: Glasgow

first: Louisa

last: Iselin

state: Lanarkshire

address: 464 Bearsden Road

country: United Kingdom

institute: University of Glasgow

description: Library name: SMI_M3P_MOCK_rep3

data_processing:
Basecalling was done on the Illumina NextSeq sequencer with the Illumina Real Time Analysis software version 2.11.3
Sequenced reads were demultiplexed (Je Suite) and adapters trimmed (Cutadapt).
Reads were aligned to a combined human (GRCh38) and SINV (pT7-SVwt) genome annotation using STAR.
Crosslink position and counts were extracted using Bedtools.
HTSeq-clip was used to generate a sliding window annotation of the human and SINV genome (50nt window, 20nt step size) and calculate the frequency of crosslink truncation sites within each window.
DEW-Seq was then used to calculate the differential enrichment of each window relative to size matched input control samples, with a cut-off of 2 log2 fold change and 0.01 adjusted p-value.
Assembly: GRCh38 (ENSEMBL Release 106), pT7-SVwt
Supplementary files format and content: A count matrix derived from HTSeq-clip displaying signal within each 50nt sliding window across the genome. Each column represents a single sample. This matrix is used as input to DEW-Seq for identifying binding sites.

growth_protocol: One 10cm dish of cells were seeded per line (10x10^6 cells) and treated with 1ug/ml Doxycycline for 24 hours.

extract_protocol:
Cells were washed with PBS 1x, and UV irradiated with 300 mJ/cm2 at 254 nm. Cells were then lysed in 1 ml RIPA buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.5% wt/vol Na deoxycholate and 0.2 mM AEBSF).
Libraries were constructed using iCLIP2 procotol (https://doi.org/10.1016/j.ymeth.2019.10.003)

value: HEK293 Flp-In Trex


title: HEK293-FITR parental, iCLIP size-matched input, rep1

description: Library name: SMI_M3P_MOCK_rep1


title: HEK293-FITR MATR3-GFP S188D, iCLIP immunoprecipiated for MATR3-GFP, rep3

description: Library name: IP_M3D_MOCK_rep3

source_name: HEK293-FITR MATR3-GFP S188D

value: HEK293-FITR MATR3-GFP S188D


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep10

description: Library name: LP47_130


title: Whole-blood RNA-seq from AD(14_002_S00_08)

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

value: Whole blood

value: AD


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep11

description: Library name: LP47_131


title: liver, CNOT1, dTAG 2h, 1

description:
Library name: Sample 1
cDNA seq


title: HEK293-FITR parental, iCLIP size-matched input, rep2

description: Library name: SMI_M3P_MOCK_rep2


title: Whole-blood RNA-seq from ACLF(132002_A00)


title: HEK293-FITR MATR3-GFP S188D, iCLIP immunoprecipiated for MATR3-GFP, rep1

description: Library name: IP_M3D_MOCK_rep1


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep9

description: Library name: LP47_129


title: Whole-blood RNA-seq from AD(131016_S01)


title: HEK293-FITR MATR3-GFP S188A, iCLIP immunoprecipiated for MATR3-GFP, rep3

description: Library name: IP_M3A_MOCK_rep3

source_name: HEK293-FITR MATR3-GFP S188A

value: HEK293-FITR MATR3-GFP S188A


title: HEK293-FITR MATR3-GFP S188A, iCLIP immunoprecipiated for MATR3-GFP, rep1

description: Library name: IP_M3A_MOCK_rep1


title: Whole-blood RNA-seq from AD(131016_S00)


title: HEK293-FITR MATR3-GFP S188D, iCLIP immunoprecipiated for MATR3-GFP, rep2

description: Library name: IP_M3D_MOCK_rep2


title: HEK293-FITR MATR3-GFP WT, iCLIP immunoprecipiated for MATR3-GFP, rep2

description: Library name: IP_M3WT_MOCK_rep2

source_name: HEK293-FITR MATR3-GFP

value: HEK293-FITR MATR3-GFP


title: FACS sorted alveolar macrophages_RNA,SC2,28Dpi,rep3

description: Library name: LP47_127

value: Lung


title: Whole-blood RNA-seq from AD(131006_S01)


title: HEK293-FITR MATR3-GFP WT, iCLIP immunoprecipiated for MATR3-GFP, rep3

description: Library name: IP_M3WT_MOCK_rep3


title: HEK293-FITR MATR3-GFP WT, iCLIP immunoprecipiated for MATR3-GFP, rep1

description: Library name: IP_M3WT_MOCK_rep1


title: Whole-blood RNA-seq from AD(131006_S00)


title: FACS sorted alveolar macrophages_RNA,SC2,28Dpi,rep2

description: Library name: LP47_126


title: APT145

city: Portland

first: Lisa

last: Coussens

state: OR

address: 3181 SW Sam Jackson Park Rd

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
38856

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.

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

value: mammary gland

value: primary tumor

value: MMTV-PyMT

value: PTX


title: HEK293-FITR MATR3-GFP S188A, iCLIP immunoprecipiated for MATR3-GFP, rep2

description: Library name: IP_M3A_MOCK_rep2


title: NMDA-24

city: Houston

first: Kamryn

last: Gerner-Mauro

state: Texas

address: 1 Baylor Plz

institute: Baylor College of Medicine

description:
Library name: NMDA-24
10x genomics

data_processing:
Raw sequencing data were handled using the 10X Genomics Cellranger software (https://www.10xgenomics.com/)
Assembly: mouse mm10
Supplementary files format and content: features.tsv.gz, barcodes.tsv.gz, and matrix.mtx.gz are outputs of Cellranger and can be opened with Seurat (R program)

source_name: retina

extract_protocol:
Fluorescence activated cell sorting Retinae were dissected in ice-cold PBS and dissociated in 10 units Papain/60 units216 DNAse (500μL/30μL respectively for 3-6 retinae) for 25-30 min in a shaking water bath at 37oC. Dissociated retinae were triturated 10 times with a polished pipette and EBSS-Ovomucoid-DNAse was added to stop digestion. The cell suspension was filtered using a 40μm strainer and centrifuged at 900 RPM for 8-10 min. For single cell analysis, cell pellets were resuspended and kept in DNAse/Ovomucoid/Neurobasal (1:1:10 respectively) during cell sorting. Cell sorting was performed using the Aria III cell sorter (BD Biosciences). Tomato positive and negative cells were sorted using an 80-micron nozzle, captured in chilled tubes and resuspended in 0.04% ultrapure BSA in 0.1M PBS. Fresh cell suspensions were immediately subjected to the scRNA-seq protocol.
FACS sorted TdTomato+ cells were counted and diluted in 1X PBS with 0.04 % BSA (Sigma Cat# SRE0036) before being loaded onto the 10X Genomics Chromium instrument. The scRNA-seq libraries were generated using the 10X Chromium Single Cell 3’ v2 reagent kit according to the manufacturer’s instructions and were sequenced on an Illumina Nextseq500.

value: retina

value: muller glia

value: Glast-CreERT2+/tg; ROSA26R-Ai9+/ki

value: NMDA


title: Whole-blood RNA-seq from ACLF(13002_S00)

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: ACLF


title: Noinjury

description:
Library name: Noinjury
10x genomics

value: no treatment


title: FACS sorted alveolar macrophages_RNA,SC2,28Dpi,rep4

description: Library name: LP47_128

value: AM

value: WT


title: FACS sorted alveolar macrophages_RNA,SC2,28Dpi,rep1

description: Library name: LP47_125


title: APT144

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


title: APT143

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


title: Whole-blood RNA-seq from ACLF(13002_A02)

value: Whole blood


title: APT142

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(13_I_019_S00_09)

value: AD


title: FACS sorted alveolar macrophages_RNA,SC2,8Dpi,rep4

description: Library name: LP47_123


title: APT139

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 alveolar macrophages_RNA,SC2,8Dpi,rep3

description: Library name: LP47_122


title: APT141

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


title: APT138

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FTWT5

value: FVBN

value: WTNT


title: Whole-blood RNA-seq from AD(13_I_018_S00_09)


title: APT137

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FTWT4


title: Whole-blood RNA-seq from pre-ACLF(13_I_015_S00_09)

value: pre-ACLF


title: FACS sorted alveolar macrophages_RNA,PBS,0Dpi,rep8

description: Library name: LP47_124

value: Lung

value: PBS


title: APT135

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FTWT2

value: mammary gland

value: primary tumor