title: HS-SY-II, H3K27ac, ChIP, untreated 1

data_processing:
H3K27ac ChIP-seq data was analysed using the Nextflow ChIP-seq (https://nf-co.re/chipseq/2.0.0) pipeline.
Assembly: hg38
Supplementary files format and content: narrowPeak


title: HS-SY-II, H3K27ac, ChIP, treated 4

status: Public on Aug 06 2025

type: SRA

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

country: USA

institute: Virginia Commonwealth University

description: Illumina NovaSeq 6000 or NextSeq 2000 platform

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: HS-SY-II

growth_protocol: DMEM with 10% FBS and 1 µg/mL penicillin and streptomycin

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. After quenching and cell lysis, chromatin was sonicated using the Bioruptor sonicator from Diagenode.
Approximately 0.1ng to 20ng ChIP DNA was fragmented to size range around 200bps using Covaris (shearing parameter 2 minutes in LV tubes using 15ul microTUBE-15 AFA Beads Screw-cap, Cat: #520145), and used for ChIP-seq library preparation by following the NEBNext Ultra II DNA library preparation Kit for Illumina (Cat. No: E7645L, New England Biolabs Inc, Ipswich, MA, USA). This kit utilizes a proprietary adapter attachment chemistry which minimizes bias and supports very low amount of input sample.

tag: cell line

value: HS-SY-II

tag: cell type

value: human synovial sarcoma cell line

tag: treatment


title: Vehicle_Oil_Cre+_3

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description: Library name: N153-21

library_source: transcriptomic

data_processing:
Read1(10bp of UMI + 9bp of cell barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore.
Reads were aligned to GRCm38 reference using HISAT2.
Uniquely mapped reads were counted by featureCounts and UMI duplication was ramoved by using UMI tools.
Assembly: GRCm38
Supplementary files format and content: compressed tab separated files(.tsv.gz)

molecule: total RNA

organism: Mus musculus

source_name: Brain

growth_protocol: Mice postnatal 8 days, 14 days, and 6-15 weeks old were bred under SPF conditions.

extract_protocol:
Brains were excised from mice transcardially perfused with PBS and 500 cells of CD11b+ CD45+ Ly6G- CD206- microglia were collected into 30uL of direct lysis buffer (TaKaRa #635013) by CytoFlex SRT(Beckman Coulter, Inc).
Libraries were prepared using 15uL out of 30uL lysate by CEL-Seq2(Hashimshony T et al.) method individually. 10nt of UMI followed by 9nt of cell barcode are in Read1 and 81nt of insert reads are in Read2.

treatment_protocol: Tamoxifen was dissolved in corn oil before injection. In 6- to 15-week-old mice, adult mice were induced by injecting 4 mg TAM per 200 µl oil intraperitoneally twice. In neonates, pups were intraperitoneally injected with 0.1 mg TAM per 10 µl oil at P1 and P3 or 0.2 mg TAM per 20 µl at P5 and P7. For functional inhibition of CDKN1A, postnatal mice were intraperitoneally injected with UC2288 (100 mg per kg body weight) in corn oil containing 2% DMSO. The BLZ945 was dissolved in 20% (2-hydroxypropyl)-β-cyclodextrin. A dose of 100 mg kg−1 bodyweight of BLZ945 was applied by oral gavage in adult mice for five consecutive days.

tag: tissue

value: Brain

value: Microglia

tag: genotype

value: Cx3cr1CreERT2(Litt) Hetero

value: Vehicle and Oil


title: HS-SY-II, H3K27ac, ChIP, treated 3


title: SYO-1, H3K27ac, ChIP, treated 2

data_processing:
SYO-1 H3K27ac ChIP-seq data were quality controlled at each processing step using FASTQC, alignment was performed using STAR v.2.7.9a using the UCSC’s hg38 genome assembly. Peaks were called with MACS23 and differential peaks were identified using DESeq2 v.1.42.1 using FDR correction for multiple testing.
Assembly: hg38
Supplementary files format and content: narrowPeak


title: SYO-1, H3K27ac, ChIP, treated 1


title: HS-SY-II, H3K27ac, ChIP, untreated 4

value: untreated


title: Vehicle_Oil_Cre+_4

description: Library name: N153-22


title: HS-SY-II, H3K27ac, ChIP, untreated 3


title: HS-SY-II, H3K27ac, ChIP, untreated 2


title: HS-SY-II, H3K27ac, ChIP, treated 2


title: Uninfected_rep3

city: shanghai

first: Xianwei

last: Wu

address: No.725 South Wanping Road

department: Institute of Respiratory Diseases

country: China

institute: Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine

description: Library name: SAMPLES 3

data_processing:
Quality-filtered RNA-seq reads were aligned to the mouse genome (GCF_000001635. 27_GRCm39) by Bowtie2 software
Each gene expression was obtained and normalized by software.
Differentially expressed genes (DEGs) were filtered with 2.0-fold cut-off and p < 0.05.
Assembly: The mouse genome, GCF_000001635.27_GRCm39
Supplementary files format and content: Tab-delimited text files include gene count values for each Sample

source_name: BMDMs

extract_protocol:
Total RNA was extracted by Trizol Reagent and the RNA quality was assessed using Qubit®3.0 Fluorometer (Life Technologies, CA, USA).
The mRNA polyA-based enrichment method was performed to establish RNA library. To establish an RNA library, the mRNA polyA-based enrichment method was performed.  RNA sequencing was performed by Illumina NovaSeq 6000 to generate 150-bp paired-end reads with about 40 million reads per sample (Sinotech Genomics).  Quality-filtered RNA-seq reads were aligned to the mouse genome (GCF_000001635.27_GRCm39) by using Hisat2 software.

treatment_protocol: Female C57BL/6J mice (6-8 weeks old) were infected  via intratracheal delivery with M. abscessus at 5 × 10^7 CFU in 40 mL of sterile PBS once. For infected WT mice on 7dpi and 35dpi, lung tissue was harvested, immediately frozen in liquid nitrogen and stored at -80°C.Per condition, four biological replicates were performed.  Three uninfected WT mice served as blank controls.

value: BMDMs

tag: strain

value: uninfected


title: Uninfected_rep2

description: Library name: SAMPLES 2


title: Inhibitor_TAM_Cre+_4

description: Library name: N153-17


title: SYO.1, Atac seq, untreated 2

data_processing:
The SYO-1 ATAC-seq data was quality controlled at each processing step using FASTQC, alignment was performed using STAR v.2.7.9a using the UCSC’s hg38 genome assembly. Peaks were called with MACS23 and differential peaks were identified using DESeq2 v.1.42.1 using FDR correction for multiple testing.
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: cell line

extract_protocol:
Nuclei were isolated using the ATAC Lysis Buffer of the Atac seq kit (Active Motif; #53150)
sequencing-ready Illumina-compatible ATAC-Seq libraries were produced using the Active Motif ATAC-Seq Kit (#53150)


title: Macrophages, sWAT infiltrating, obese individual 9

type: RNA

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

hyb_protocol: Labeled cDNAs were hybridized onto Clariom D Human Assay Microarrays, which include probe sets enabling transcriptome-wide gene- and exon-level expression profiling (Affymetrix, ThermoFisher Scientific).

scan_protocol: The arrays were scanned using the GeneChip 3000 system (Affymetrix).

data_processing: Transcript Analysis Console (TAC v4.0; Affymetrix, ThermoFisher) software was used for initial hybridization quality assessment and data inspection. All statistical analyses of microarray data were performed using R-based software environment. Quality control was done with the array QualityMetrics package. Background correction, probe set summarization and normalization were performed with the oligo package using the most up to date annotation in Bioconductor. Subsequent differential expression analysis was performed using the Limma package at the gene level taking the average of all probe sets for a particular gene and focusing on known genes (with assigned gene symbols).

label: biotin

source_name: macrophages from white adipose tissue

label_protocol: CD11b+ cell extracted RNA was reverse transcribed into cDNA and amplified and biotinylated by in vitro transcription (MultiScribe TaqMan Reverse Transcription Reagents; ThermoFisher Scientific, Waltham, MA, USA).

growth_protocol: The study was approved by the Ethical Committee of the Hospital Germans Trias i Pujol (Badalona, Spain) and follow the guidelines of Helsinki convention. Participants of both Cohorts 1 and 2 gave their written informed consent before clinical data collection.Two different cohorts of patients were enrolled in this study. All patients were evaluated by the same endocrinologist (S.P.) following the institutional protocol for bariatric surgery between October 2015 and September 2021, according to criteria for bariatric surgery formulated in Spanish Position Statement between Obesity, Endocrinology, Diabetes and Surgery Societies. For Cohort 1, 11 patients with obesity (BMI>35 kg/m2) and different metabolic status were enrolled, and vWAT and sWAT from the same patient were collected on occasion of bariatric surgery. For Cohort 2, 27 patients with or without severe obesity (BMI>35 kg/m2 or BMI<27 kg/m2, respectively) were enrolled; for individuals with obesity, they attended to bariatric surgery, while for normal-weight individuals on occasion of consultation/minor surgery. Then, vWAT and sWAT were collected during the surgical procedures. The inclusion criterion for individuals with obesity was exhibiting a BMI higher than 35 kg/m2. Exclusion criteria for all cohorts were having active infectious or inflammatory pathologies other than those related to obesity and treatment with immunosuppressant drugs, since these conditions could alter the results of the study.

extract_protocol: Total RNA was then extracted using affinity column-based methodology suitable for small amounts of biological material (NucleoSpin RNA XS; Mecherey-Nagel, Duren, Germany). RNA yield and purity were determined by spectrophotometry and RNA integrities were assessed with the Nano 6000 assay on Agilent's 2100 Bioanalyzer. Samples with RNA integrity number (RIN) values mostly above 6.7 were used as input for subsequent microarray gene expression profiling assays.

treatment_protocol: vWAT and sWAT samples (n = 36 in total) were obtained from these 11 patients from Cohort 1 during bariatric surgery. Fresh WAT collected during surgeries was transferred into two 50 mL tubes containing a 2% fetal bovine serum (FBS) in phosphate saline buffer (PBS) solution and placed on separate multiwell plate wells submerged in collagenase and Hank's Balanced Salt Solution (pH=7.1). The tissue was then minced into small pieces followed by several centrifugation and supernatant removal steps as previously published (19,20). CD11b+ cells were then labeled with anti-CD11b+ MicroBeads and magnetically separated from the unlabeled cells by a magnetic-activated cell sorting (MACS) Column supplied by Miltenyi Biotec (Miltenyi Biotec S.L Madrid). Briefly, the cell suspension was centrifuged at 300 x g for 10 min and the supernatant was completely discarded. Second, the pellet was resuspended in 82 µL of MACS buffer and 2 µL were diluted by adding 18 µl of MACS buffer and reserved at 4º C to evaluate percentage of CD11b+ cells. Then, 20 µL of CD11b+ MicroBeads were added to 80 µL of cell suspension, mixed and incubated for 15 min in ice. Next, the cells were washed by adding 2 mL of MACS buffer and centrifugated at 300 g for 10 minutes at 4ºC. Then the pellet was resuspended in 500 µL of MACS buffer and maintained in ice. Meanwhile, the separation column was prepared. For this, the LS column was placed in the magnetic field, on the MidiMACS™ Separator and rinsed with 3 mL of MACS buffer. Once the column reservoir was empty, the cell suspension was added into the column. When all the suspension passed, the column was washed by adding 3 mL of MACS buffer, twice. After that, the column was removed from the magnetic field, and placed onto a new 15 mL conical tube (collection tube). Then, 5 mL of MACS buffer was added and the fraction with the magnetically labeled cells was immediately flushed out applying the plunger supplied with the column. 20 µL of the eluted fraction was reserved in ice. Next, the CD11b+ fraction of cells was centrifuged at 300 g for 7 min at 4º C, 4 mL of the supernatant was discarded, and the pellet was resuspended in the remaining volume, which was transferred into 1.5 mL conical tube and centrifuged at 11000g for 5 min, the resulting pellet was used to perform RNA extraction. The reserved aliquots from sWAT and vWAT were labeled to quantify the viability and the number of infiltrated CD11b+ cells, respectively. For this purpose, 10 µL of cell sample were mixed with 48 µL of MACS Buffer, 2 µL of 7-AAD and 0.5 µL of CD11b+, the prepared mix was incubated in darkness for 10 min and then 10 µL of Counting beads were added. Isolated macrophages were detected by the flow cytometer FACSCanto II by BD Biosciences. The optic consists of an excitation source and a three-laser system: blue (488 nm, air-cooled, 20-mV solid state), red (633 nm, 17-mV HeNe) and violet (405 nm, 30-mV solid state) allowing measurement of 8 parameters (FSC, SSC and 6 fluorescence detectors) with carrousel acquisition option for tubes. For quantification analysis the FACSDiva software were used, and FlowJo Software (Tree Star Inc.) was used for the graphs and the gating strategy. Cells are being separated based on their size and fluorescence. Viability, percent, and concentration (cells/μL) of macrophage cells (CD11b+) in each tissue (vWAT and sWAT) was measured at the flow cytometer.

tag: gender

value: male

value: subcutaneous white adipose tissue (sWAT)

value: macrophages (CD11b+)

tag: health status

value: Obese

tag: individual

tag: batch


title: HS-SY-II, H3K27ac, ChIP, treated 1


title: SYO.1, Atac seq, untreated 1


title: SYO.1, Atac seq, treated 3


title: Inhibitor_TAM_Cre+_2

description: Library name: N153-15


title: SYO.1, Atac seq, treated 2


title: Vehicle_Oil_Cre+_2

description: Library name: N153-20


title: HS-SY-II, H3K27ac, ChIP, input


title: Vehicle_Oil_Cre+_1

description: Library name: N153-19


title: Inhibitor_TAM_Cre+_5

description: Library name: N153-18


title: Inhibitor_TAM_Cre-_1

description: Library name: N153-11


title: Vehicle_TAM_Cre+_4

description: Library name: N153-09

value: Vehicle and TAM


title: Inhibitor_TAM_Cre-_2

description: Library name: N153-12


title: SYO.1, Atac seq, untreated 3


title: Inhibitor_TAM_Cre+_3

description: Library name: N153-16


title: Vehicle_TAM_Cre+_3

description: Library name: N153-08


title: SYO-1, KDM2B (JHDM1B), ChIP, treated 3

data_processing:
KDM2B (JHDM1B) ChIP-seq data were quality controlled at each processing step using FASTQC, alignment was performed using STAR v.2.7.9a using the UCSC’s hg38 genome assembly. Peaks were called with MACS23 and differential peaks were identified using DESeq2 v.1.42.1 using FDR correction for multiple testing.
Assembly: hg38
Supplementary files format and content: narrowPeak


title: Inhibitor_TAM_Cre-_3

description: Library name: N153-13


title: SYO-1, KDM2B (JHDM1B), ChIP, treated 2


title: SYO.1, Atac seq, treated 1


title: SYO-1, KDM2B (JHDM1B), ChIP, untreated 2


title: SYO-1, KDM2B (JHDM1B), ChIP, untreated 3


title: SYO-1, KDM2B (JHDM1B), ChIP, input


title: SYO-1, KDM2B (JHDM1B), ChIP, untreated 1


title: Uninfected_rep1

description: Library name: SAMPLES 1


title: SYO.1, SS18::SSX, ChIP, untreated 1

data_processing:
SSX ChIP-seq data was quality controlled at each processing step using FASTQC, alignment was performed using STAR v.2.7.9a using the UCSC’s hg38 genome assembly. Peaks were called with MACS2 and differential peaks were identified using DESeq2 v.1.42.1 using FDR correction for multiple testing.
Assembly: hg38
Supplementary files format and content: narrowPeak


title: Inhibitor_TAM_Cre+_1

description: Library name: N153-14


title: SYO.1, SS18::SSX, ChIP, untreated 3


title: Vehicle_TAM_Cre-_4

description: Library name: N153-04


title: Vehicle_TAM_Cre+_1

description: Library name: N153-06


title: Postnatal_Jung_Tam_4

description: Library name: N107-19

value: Cx3cr1CreERT2(Jung) Hetero; Rosa26YFP Hetero

value: TAM


title: Vehicle_TAM_Cre-_2

description: Library name: N153-02


title: Postnatal_Jung_Tam_3

description: Library name: N107-18


title: SYO.1, SS18::SSX, ChIP, untreated 2


title: SYO.1, SS18::SSX, ChIP, treated 3


title: Vehicle_TAM_Cre-_1

description: Library name: N153-01


title: SYO.1, SS18::SSX, ChIP, treated 2


title: HS-SY-II, KDM2B (JHDM1B), ChIP, untreated 3


title: SYO.1, SS18::SSX, ChIP, input


title: SYO.1, SS18::SSX, ChIP, treated 1


title: Postnatal_Jung_Oil_4

description: Library name: N107-14

value: Oil


title: Vehicle_TAM_Cre-_5

description: Library name: N153-05


title: SYO-1, KDM2B (JHDM1B), ChIP, treated 1


title: Vehicle_TAM_Cre-_3

description: Library name: N153-03


title: HS-SY-II, KDM2B (JHDM1B), ChIP, treated 3

value: HS-SY-II


title: Vehicle_TAM_Cre+_2

description: Library name: N153-07


title: Postnatal_Jung_Tam_2

description: Library name: N107-17


title: HS-SY-II, KDM2B (JHDM1B), ChIP, untreated 2

value: human synovial sarcoma cell line


title: Postnatal_Jung_Oil_5

description: Library name: N107-15

value: Brain


title: HS-SY-II, KDM2B (JHDM1B), ChIP, untreated 1


title: Postnatal_Jung_Tam_1

description: Library name: N107-16

value: Microglia


title: HS-SY-II, KDM2B (JHDM1B), ChIP, treated 1


title: Postnatal_Jung_Oil_3

description: Library name: N107-13


title: HS-SY-II, KDM2B (JHDM1B), ChIP, treated 2


title: Postnatal_Jung_Oil_1

description: Library name: N107-11


title: HS-SY-II, SS18::SSX, ChIP, treated 3


title: Postnatal_Littman_Cre+_1

description: Library name: N107-06

value: Cx3cr1CreERT2(Litt) Hetero


title: Postnatal_Littman_Cre+_5

description: Library name: N107-10


title: HS-SY-II, SS18::SSX, ChIP, treated 2


title: HS-SY-II, KDM2B (JHDM1B), ChIP, input


title: Postnatal_Littman_Cre+_4

description: Library name: N107-09


title: HS-SY-II, SS18::SSX, ChIP, untreated 3


title: Postnatal_Littman_Cre+_3

description: Library name: N107-08


title: HS-SY-II, SS18::SSX, ChIP, untreated 2


title: Postnatal_Littman_Cre+_2

description: Library name: N107-07


title: HS-SY-II, SS18::SSX, ChIP, untreated 1


title: HS-SY-II, SS18::SSX, ChIP, treated 1


title: Postnatal_Littman_Cre-_5

description: Library name: N107-05


title: Postnatal_Littman_Cre-_1

description: Library name: N107-01


title: Postnatal_Littman_Cre-_4

description: Library name: N107-04


title: HS-SY-II, SMARCA4, ChIP, untreated3

data_processing:
SMARCA4 ChIP-seq data was quality controlled at each processing step using FASTQC, alignment was performed using STAR v.2.7.9a using the UCSC’s hg38 genome assembly. Peaks were called with MACS2 and differential peaks were identified using DESeq2 v.1.42.1 using FDR correction for multiple testing.
Assembly: hg38
Supplementary files format and content: narrowPeak


title: HS-SY-II, SMARCA4, ChIP, untreated2


title: Postnatal_Jung_Oil_2

description: Library name: N107-12


title: Postnatal_Littman_Cre-_3

description: Library name: N107-03


title: HS-SY-II, SMARCA4, ChIP, untreated1


title: HS-SY-II, SS18::SSX, ChIP, input


title: HS-SY-II, SMARCA4, ChIP, untreated4


title: HS-SY-II, SMARCA4, ChIP, untreated5


title: Adult_Jung_TAM_2

description: Library name: N160-16

value: Cx3cr1CreERT2(Jung) Hetero


title: Postnatal_Littman_Cre-_2

description: Library name: N107-02


title: Adult_Jung_TAM_1

description: Library name: N160-15


title: HS-SY-II, SMARCA4, ChIP, treated5


title: Adult_Jung_TAM_3

description: Library name: N160-17


title: Adult_Jung_Oil_4

description: Library name: N160-14


title: HS-SY-II, SMARCA4, ChIP, treated3


title: Adult_Littman_TAM_2

description: Library name: N160-09


title: Adult_Jung_Oil_3

description: Library name: N160-13


title: HS-SY-II, SMARCA4, ChIP, input


title: Adult_Jung_Oil_2

description: Library name: N160-12


title: Adult_Littman_TAM_3

description: Library name: N160-10


title: HS-SY-II, SMARCA4, ChIP, treated4


title: HS-SY-II, SMARCA4, ChIP, treated1


title: s26C_down30

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road, Oxford, OX3 7LD, UK

country: United Kingdom

institute: University of Oxford

description: Single-nuclei +10x Genomics

library_source: transcriptomic single cell

data_processing:
The fastq files were processed using the scflow pipeline workflows (https://github.com/Acribbs/scflow).
The downsized fastq files (down30 fastq files) were using Seqtk to downsize before processing in the scflow pipeline workflows.
The Kallisto BUS/ BUStools (v0.39.3) workflow1 was implemented to pseudo-align the reads, with a K-mer size of 31 base pairs.
The output was converted to single-cell experiment object and then to Seurat object (Seurat v4.0)
Doublets in the samples were detected using the R package scDblFinder and removed in the scflow pipeline with Seurat clustering.
For data integration, the VST method provided by Seurat for variable gene selection was used and Harmony v1.04 was then applied for batch correction.
Assembly: Human genome hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pseudocapsule

extract_protocol:
A petri dish, 50 ml centrifuge tube, scalpel and forceps were precooled on dry ice before tissue samples were removed from -80°C and placed in the petri dish. Typical sample sizes ranged from 100-500 mg.  Tissue was cut into thin slices and transferred to centrifuge tubes. If processing multiple samples, cut tissue could be stored at -80°C until use.  Sample tubes were transferred to wet ice, 4 ml of ice-cold CST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 1 mM CaCl, 21 mM MgCl2, 0.5% CHAPS (w/v), 0.01% BSA (w/v), 4 ul/ml SUPERaseIN, 4 ul/ml RNasein Plus, 1 cOmplete protease inhibitor tablet/10 ml) added and tubes placed on a rotator for 10 minutes at 4°C.  Samples were passed through 30 µm cell strainers (MACS SmartStrainer) into prechilled 15 ml collection tubes on ice. Sample tubes were rinsed with 2 ml ice cold PBS + 1% BSA, which was added to the cell strainer. Cell strainers were rinsed with an additional 2 ml ice cold PBS + 1% BSA and collection tubes centrifuged at 500g for 5 minutes at 4°C.  Supernatant was removed and pellet washed by resuspending in 10 ml ice cold PBS + 1% BSA, centrifugation at 500g for 5 minutes at 4°C, removal of supernatant and resuspension in 500 µl ice cold PBS + 1% BSA. A subsample of the nuclei preparation was incubated with DAPI (1 µg/ml) for 5 minutes, added to a haemocytometer and counted under a fluorescent microscope. Concentration of the nuclei was adjusted to ~1,000 cells/µl and used as input for analysis by 10X Chromium single cell gene expression.
Chromium single cell gene expression (10X Genomics) was performed using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G Single Cell Kit and Single Index Kit T Set A according to the manufacturer’s instructions starting with 20,000 nuclei as input. Resulting libraries were quantitated by TapeStation (Agilent), pooled at equimolar concentration and sequenced (Novogene (UK) Ltd or Genewiz GmbH) on an Illumina NovaSeq 6000 using a S4 Reagent Kit v1.5 to give ~30,000 reads/cell.
10X Genomics

tag: organ

value: Uterus

value: Pseudocapsule

tag: cycle phase

value: early-mid secretory

tag: hmb symptom

value: HMB

tag: disease

value: leiomyoma


title: s91C_down30

description: Single-nuclei +10x Genomics

value: mid secretory


title: Adult_Littman_Oil_3

description: Library name: N160-04


title: s91C

description: Single-nuclei +10x Genomics


title: Adult_Jung_TAM_4

description: Library name: N160-18


title: s28C_down30

description: Single-nuclei +10x Genomics


title: 4T1_KIRA6_Rep3

city: Zhuhai

first: Hong-Wei

last: Sun

address: 79 Kangning Road

department: The Affiliated Hospital of Beijing Institute of Technology (Zhuhai People's Hospital)

institute: Beijing Institute of Technology

description: Library name: 4T1_KIRA6_Rep3

data_processing:
Raw sequencing reads in FASTQ format were processed using Cutadapt (v1.9.1) to remove technical sequences and low-quality bases.
Clean reads were aligned to the reference genome using HISAT2 (v2.2.1), a splice-aware aligner.
Gene-level counts were quantified using HTSeq (v0.6.1). Reads overlapping exons were counted, and multi-mapping reads or reads overlapping multiple genes were excluded.
Differentially expressed genes were identified using DESeq2 (v1.34.0).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

growth_protocol: 4T1 cells were plated overnight in complete RPMI 1640 medium.

extract_protocol:
RNA was havested using TRIzol (Invitrogen) according to manufacturer's' instructions. 1 μg total RNA was used for library preparation.
For mRNA enrichment, poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA synthesis was carried out using reverse transcriptase, followed by second-strand cDNA synthesis. For strand-specific library construction, during the second-strand synthesis the standard dTTP was replaced with dUTP; subsequent treatment with USER enzyme selectively degrades the second strand prior to PCR amplification, thereby preserving strand information. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tail in a single reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers, and the PCR products were validated.

treatment_protocol: 4T1 cells were cultured with fresh culture medium with Vehicle or KIRA6 (1 μmol/L) for 4 hours before RNA sample collection with TRIzol.


title: s111E

description: Single-nuclei +10x Genomics

source_name: Endometrium

value: Endometrium

value: mid-late secretory


title: 4T1_KIRA6_Rep2

description: Library name: 4T1_KIRA6_Rep2


title: Adult_Jung_Oil_1

description: Library name: N160-11


title: Adult_Littman_TAM_1

description: Library name: N160-08


title: 4T1_KIRA6_Rep1

description: Library name: 4T1_KIRA6_Rep1


title: s91E

description: Single-nuclei +10x Genomics


title: s64C

description: Single-nuclei +10x Genomics

value: inactive

value: No


title: ATAC-Seq SW620-rep2

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

data_processing:
ATAC-seq: Raw fastq files were subjected to quality control using FastQC (v0.11.9) and Trim Galore (v0.6.0).
ATAC-seq: Reads were aligned with bowtie2 (v2.3.5.1) and samtools (v1.3.1, options: -Sb -q 20).
ATAC-seq: BAM files were deduplicated with picard (v2.25.7) MarkDuplicates
ATAC-seq: MACS2 (v2.2.7.1) subcommand callpeak was used for peak calling
Assembly: hg19, Sscrofa11
Supplementary files format and content: Peak file

value: Human colorectal cancer


title: Adult_Littman_Oil_1

description: Library name: N160-02

value: Oil


title: Adult_Littman_Oil_2

description: Library name: N160-03


title: BioX1

city: Huddinge

first: Lorenz

last: Wirth

state: Stockholms län

address: Alfred Nobels Allé 8

country: Sweden

institute: Karolinska Institutet

description:
Library name: ANON_BioX1_sample_filtered_feature_bc_matrix.h5
Patient C Pre and Post; Patient A Pre

data_processing:
Libraries were sequenced by SciLIfeLab (NGI; Stockholm, Sweden) using a NovaSeq XPlus sequencer and a 1.5B-100 flow cell (Illumina).
Count matrices were generated from FASTQ files using CellRanger v9.0.0 (10X Genomics) and downstream analysis was performed using the R package Seurat (v5.1.0). DeMuxMix (v1.6.0) was used for hashtag demultiplexing using the antibody derived tag (ADT) matrices as the hashtag oligo (HTO) counts, and Harmony (v1.2.3) was used with donor as a covariate to integrate the samples. Low quality cells and doublets were removed according to the number of detectable genes (number of genes < 200 or > 4000) and percentage of mitochondrial genes for each cell (≥15%). Differentially expressed genes for each cell cluster and between treatment conditions were identified using a non-parametric Wilcoxon rank-sum test, for a gene to be considered it had to be expressed in a minimum of at least 20% of cells in both treatment conditions.
Assembly: GRCh38
Supplementary files format and content: "BioX1" includes patient C (baseline and 1 year treatment) and patient A (baseline): "Anon_Patient_C_Pre", "Anon_Patient_C_Post", "Anon_Patient_A_Pre".  "BioX2" includes patient A (1 year treatment) and patient B (baseline and 1 year treatment): "Anon_Patient_A_Post", "Anon_Patient_B_Pre", "Anon_Patient_B_Post".

source_name: blood

extract_protocol:
Cryopreserved PBMCs isolated from n = 3 severe asthma patients before ("Pre") and after ("Post") mepolizumb treatment were thawed and FACS-sorted to isolate ILC2, Th2 and Tc2 cells. Sorted and hashtagged cells (Biolegend TotalSeq Hashtags) were combined for 10X scRNA-seq.
A 5 ’library was generated using Chromium GEM-X Single Cell 5' Kit (PN-1000695), Chromium GEM-X Single Cell 5' Chip Kit (PN-1000698), Library Construction Kit C (PN-1000694), Chromium GEM-X Single Cell 5' Feature Barcode Kit v3 (PN-1000703), and Dual Index Kits TT Set A (PN-1000215) and TN Set A (PN-1000250, all 10X Genomics). All steps were followed as listed in the manufacturer’s instructions (user guide CG000734 Revision A).

treatment_protocol: Patients diagnosed with severe asthma with underlying eosinophilic inflammation were assessed at baseline/before  and after  1 year of mepolizumab treatment .

value: blood

value: ILC2, Th2, and Tc2

value: Biologics-naive ("Pre") and after 1 year of mepolizumab (anti-IL-5) treatment ("Post")


title: s28C

description: Single-nuclei +10x Genomics


title: HS-SY-II, SMARCA4, ChIP, treated2

value: HS-SY-II

value: human synovial sarcoma cell line


title: s28E

description: Single-nuclei +10x Genomics

value: Uterus


title: s26C

description: Single-nuclei +10x Genomics

value: Pseudocapsule


title: 4T1_Veh_Rep2

description: Library name: 4T1_Veh_Rep2

value: Vehicle


title: NCM460-rep3

data_processing:
CUT&Tag: Raw fastq files were subjected to quality control using FastQC (v0.11.9) and Trim Galore (v0.6.0).
CUT&Tag: Reads were aligned with bowtie2 (v2.3.5.1) and samtools (v1.3.1, options: -Sb -q 20).
CUT&Tag: BAM files were deduplicated with picard (v2.25.7) MarkDuplicates
CUT&Tag: MACS2 (v2.2.7.1) subcommand callpeak was used for peak calling
Assembly: hg19, mm10, Sscrofa11
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Living cells with a 10 minutes’ incubation at room temperature
Cleavage Under Targets and Tagmentation (CUT&Tag) have been described in detail (KayaOkur et al. 2019; Wang et al. 2019) with some modifications. Briefly, cells were incubated with activated concanavalin A-coated magnetic beads (Smart-Lifesciences). The bead-bound cells were permeabilized and incubated first with BG4 primary antibody, followed by anti-Flag M2 antibody (Sigma-Aldrich), and lastly with rabbit antimouse IgG antibody. Diluted pA-Tn5 adapter complex was then added followed by the tagmentation reaction. Extracted DNA fragments were used for library preparation. More details of this experiment and data analysis are described in following.

value: Human normal colon mucosal epithelial cell

tag: chip antibody


title: NOVkoL1bPOLY

city: Chicago

first: Elspeth

last: Beauchamp

state: IL

address: 303 E Superior St

department: Medicine

institute: Northwestern University-Feinberg School of Medicine

description: Library name: NOVkoL1bPOLY

data_processing:
Raw FASTQ files were processed using the nf-core/rnaseq pipeline (v3.14.0) executed in Nextflow with the nu_genomicsprofile on the Northwestern University Quest HPC cluster. Satisfactory percent alignment (>60%) was derived from nf-core via MultiqC.
Lane-level reads were trimmed using Trim Galore! (v0.6.5), and aligned to the hg38 genome using STAR.
Transcript-level quantification was performed using Salmon. Count matrices were aggregated at the gene level for downstream analysis.
After quantification, differential expression analysis was carried out in R (v4.3.3) using DESeq2 (v1.42.1), with drug treatment or genotype as explanatory variables.
Assembly: hg38
Supplementary files format and content: gene counts from Salmon as csv files
Supplementary files format and content: differentially expression analysis as csv files

molecule: polyA RNA

growth_protocol: U937 cells (Cat#: CRL-1593.2; ATCC) were grown in RPMI 1640 medium (Gibco) supplemented with 10% FBS  at 37°C and 5% CO2 .

extract_protocol:
Following polysomal profiling, RNA from total/input and polysome associated fractions was isolated using Qiagen AllPrep RNA/Protein Kit, Cat#: 80404 according to manufacturers protocol.
RNA samples obtained from polysome profiling experiments were sent to Novogene Corporation for processing. RNA quantity, integrity, and purity were assessed using the Agilent 5400 Fragment Analyzer System. Samples with an RNA Integrity Number (RIN) above 6.0 qualified for library preparation. Messenger RNA (mRNA) was purified from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, first-strand cDNA synthesis was performed using random hexamer primers, followed by second-strand cDNA synthesis. Library preparation included end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The final libraries were assessed using a Qubit fluorometer and real-time PCR for quantification, as well as a Bioanalyzer for size distribution analysis. Quantified libraries were pooled and sequenced on Illumina platforms based on the effective library concentration and desired data output.
Quantified libraries were pooled and sequenced on the Illumina NovaSeq X Plus (25B flowcell), using a paired-end 150bp (PE150) sequencing strategy. The clustering of the index coded samples was performed according to the manufacturer’s instructions.

treatment_protocol: U937 cells were subjected to CRISPR/Cas9-mediated knockout of LARP1 using lentiviral transduction with sgRNA targeting LARP1 (Edit-R All-in-one sgRNA system, Horizon, Cat#: VSGH11936-247722211), followed by puromycin selection (10 ng/mL) and clonal expansion. Control cells were generated using non-targeting sgRNA (Edit-R All-in-one sgRNA system, Horizon, Cat#: GSGC11953). For pharmacological treatment, control U937 cells were treated with 500 nM Vistusertib (mTOR inhibitor - Chemietek, Cat#: CT-A2014), 500 nM Enitociclib (CDK9 inhibitor - MedChemExpress, Cat#: HY-103019B), or a combination of both for 4 hours. Following treatments, cells were treated with 100 μg/mL cycloheximide (Thermo Scientific Chemicals, Cat#: J66901.03) for 30 minutes, lysed, and subjected to polysome profiling using sucrose gradient ultracentrifugation to isolate monosomal and polysomal RNA fractions for RNA-seq.

value: pro-monocytic cell line

value: WT carrying CAS9 and LARP1-targeting sgRNA

value: No treatment


title: Adult_Littman_Oil_4

description: Library name: N160-05

value: Brain

value: Microglia

value: Cx3cr1CreERT2(Litt) Hetero


title: 4T1_Veh_Rep3

description: Library name: 4T1_Veh_Rep3


title: s26E

description: Single-nuclei +10x Genomics

value: Endometrium

value: early-mid secretory

value: HMB

value: leiomyoma


title: NOVkoL1aPOLY

description: Library name: NOVkoL1aPOLY


title: SM cells, PBS/NDV-WT/NDV-GP group, spleen (merged data)

city: Chongqing

first: shuai

last: yue

state: Chongqing

address: Gaotanyan street

institute: army medical university

description:
Library name: Sample 2
BD Rhapsody platform (3 spleen samples mixed by Sample Tags)

data_processing:
The output files produced from raw data were generated by Seven Bridges platform (https://velsera.com/bd-rhapsody/)
Assembly: Mouse mm10
Supplementary files format and content: Processed data files include a sparse gene expression matrix (matrix, mtx format), a cell barcode list (barcodes, tsv), and a gene/features annotation (features, tsv).

source_name: spleen

extract_protocol:
To obtain SM CD4 T cells in lung, lungs were mechanically minced and digested using with 1 mg/mL collagenase I (Sigma, c0130) and mashed through filters. Then, lymphocytes were enriched using Percoll (GE Healthcare, 17-0891-09) density gradient. To obtain SM CD4 T cells in spleen, cells were harvested by mashing the spleens through cell strainer (BD Falcon). Next, lymphocytes were stained with flow cytometry antibodies specicifc for CD4, Va2, CD45.1, and CD45.2 and SM cells were FACS-sorted.
The library preparation for single-cell RNA sequencing (scRNA-seq) using the BD Rhapsody platform according to manufacturer instructions. scRNA-seq begins with the capture of individual cells which employs microfluidic technology to isolate cells within nanowells. Once captured, each cell is lysed, and reverse transcription is performed to convert the RNA into complementary DNA (cDNA). During this process, unique molecular identifiers (UMIs) and cell barcodes are incorporated into each cDNA molecule, enabling accurate quantification and differentiation of transcripts from different cells. Following reverse transcription, the cDNA undergoes amplification through PCR to generate an adequate quantity of material for sequencing. The amplified cDNA is then processed to prepare sequencing libraries, which involves enzymatic fragmentation, adapter ligation, and purification steps to ensure that only the desired fragments are included in the final product. To confirm that the libraries meet the necessary standards for sequencing, quality and quantity assessments are conducted using methods such as bioanalyzer or Qubit. Finally, the libraries were sequenced using paired-end sequencing, with 150 nucleotides on each end, conducted in a single lane of a NovaSeq 6000 for each sample. Raw gene expression matrices were generated using the Cell Ranger pipeline (version 6.1.1), coupled with the mm10 genome annotation reference.

value: spleen

value: PBS/NDV-WT/NDV-GP


title: BioX2

description:
Library name: ANON_BioX2_sample_filtered_feature_bc_matrix.h5
Patient A Post; Patient B Pre and Post

value: blood

value: ILC2, Th2, and Tc2

value: Biologics-naive ("Pre") and after 1 year of mepolizumab (anti-IL-5) treatment ("Post")


title: NCM460-rep2


title: 4T1_Veh_Rep1

description: Library name: 4T1_Veh_Rep1

value: Vehicle


title: NOVcas9aPOLY

description: Library name: NOVcas9aPOLY

value: WT carrying CAS9 and non-targeting sgRNA


title: NCM460-rep1

value: Human normal colon mucosal epithelial cell


title: NOVkoL1bINP

description: Library name: NOVkoL1bINP

value: pro-monocytic cell line

value: WT carrying CAS9 and LARP1-targeting sgRNA


title: Ly108-CD39+ SM cells, NDV-GP group, spleen, Rep1

description:
Library name: Sample 15
SC39_1
S_GP39.bigwig

data_processing:
All samples are paired-end sequencing files and the quality was checked by fastqc tools. Adapter trimming and low-quality sequence removal were achieved by fastp tools (PMID: 30423086) and recheck data by fastqc tools. BWA-MEM tool was used to align the data to mm10 genome. After that, aligned data were further purified by cleaning mitochondria DNA, PCR duplicates, and mm10 genome blacklist. Genrich was used to call narrowpeak and bigwig, bam and bedgraph files were prepared for visualization.
Assembly: Mouse mm10
Supplementary files format and content: Processed data files are in bigWig format, representing genome-wide chromatin accessibility signal (normalized read coverage) for each sample; two replicates processed into one bigwig file, linked to the corresponding rep1 sample records

extract_protocol:
To obtain SM CD4 T cells in tumor, tumors were mechanically minced and digested using with 1 mg/mL collagenase I (Sigma, c0130) and mashed through filters. Then, lymphocytes were enriched using Percoll (GE Healthcare, 17-0891-09) density gradient. To obtain SM CD4 T cells in spleen, cells were harvested by mashing the spleens through cell strainer (BD Falcon). Next, lymphocytes were stained with flow cytometry antibodies specicifc for CD4, Va2, CD45.1, CD45.2, Ly108 and CD39, SM cells were FACS-sorted.
ATAC-seq library was prepared using Hyperactive ATAC-seq Library Prep Kit for Illumina (Vazyme, TD711). Briefly, sorted cells were lysed on ice and fragment DNA in waterbath at 37℃ for 30 min. ATAC DNA Extract Beads were used for DNA extraction of fragmented products and extracted DNA fragments were amplified in a PCR instrument. Finally, ATAC DNA Clean Beads were used for two-step fragment size selection of amplified products and quality and quantity assessments are conducted using methods such as bioanalyzer or Qubit. Finally, the libraries were sequenced using paired-end sequencing, with 150 nucleotides on each end, conducted in a single lane of a NovaSeq 6000 for each sample.

value: Ly108-CD39+ SM cells

value: NDV-GP


title: NOVcas9cPOLY

description: Library name: NOVcas9cPOLY

value: No treatment


title: NOVkoL1cPOLY

description: Library name: NOVkoL1cPOLY


title: Ly108-CD39+ SM cells, NDV-GP group, spleen, Rep2

description:
Library name: Sample 16
SC39_2
S_GP39.bigwig


title: SM cells, PBS/NDV-WT/NDV-GP group, lung (merged data)

description:
Library name: Sample 1
BD Rhapsody platform (3 lung samples mixed by Sample Tags)

source_name: lung

value: lung


title: NOVcas9bPOLY

description: Library name: NOVcas9bPOLY


title: NOVkoL1cINP

description: Library name: NOVkoL1cINP


title: ATAC-Seq SW620-rep1

value: Human colorectal cancer


title: NOVcas9bINP

description: Library name: NOVcas9bINP


title: NOVcas9cINP

description: Library name: NOVcas9cINP


title: Ly108+CD39- SM cells, NDV-GP group, spleen, Rep1

description:
Library name: Sample 13
SC108_1
S_GP108.bigwig

value: Ly108+CD39- SM cells


title: Ly108+CD39- SM cells, NDV-GP group, spleen, Rep2

description:
Library name: Sample 14
SC108_2
S_GP108.bigwig


title: NOVkoL1aINP

description: Library name: NOVkoL1aINP


title: NOVcas9aINP

description: Library name: NOVcas9aINP


title: Ly108+CD39- SM cells, NDV-WT group, spleen, Rep2

description:
Library name: Sample 12
SB_2
S_WT.bigwig

value: NDV-WT


title: A_Bpol26JUN

description: Library name: A_Bpol26JUN

value: 500 nM Vistusertib and 500 nM Enitociclib for 4 hrs


title: HT29-rep1


title: A_Bpol22JUN

description: Library name: A_Bpol22JUN


title: BAYpol27JUN

description: Library name: BAYpol27JUN

value: 500 nM Enitociclib for 4 hrs


title: HepG2-rep2

value: Human liver carcinoma cells


title: Ly108+CD39- SM cells, NDV-WT group, spleen, Rep1

description:
Library name: Sample 11
SB_1
S_WT.bigwig

value: spleen


title: BAYpol22JUN

description: Library name: BAYpol22JUN


title: BAYpol26JUN

description: Library name: BAYpol26JUN


title: Ly108+CD39- SM cells, PBS group, spleen, Rep2

description:
Library name: Sample 10
SA_2
S_PBS.bigwig

value: PBS


title: A_Bpol27JUN

description: Library name: A_Bpol27JUN


title: HepG2-rep1


title: AZDpol27JUN

description: Library name: AZDpol27JUN

value: 500 nM Vistusertib for 4 hrs


title: A549-rep3

value: Human lung carcinoma epithelial cell


title: AZDpol26JUN

description: Library name: AZDpol26JUN

value: WT carrying CAS9 and non-targeting sgRNA


title: HT29-rep3


title: Ly108+CD39- SM cells, PBS group, spleen, Rep1

description:
Library name: Sample 9
SA_1
S_PBS.bigwig


title: HT29-rep2


title: AZDpol22JUN

description: Library name: AZDpol22JUN

value: pro-monocytic cell line


title: A549-rep2


title: Ly108-CD39+ SM cells, NDV-GP group, tumor, Rep1

description:
Library name: Sample 7
TC39_1
T_GP39.bigwig

source_name: tumor

value: tumor


title: CTRLpol26JUN

description: Library name: CTRLpol26JUN

value: DMSO


title: CTRLpol22JUN

description: Library name: CTRLpol22JUN


title: Ly108-CD39+ SM cells, NDV-GP group, tumor, Rep2

description:
Library name: Sample 8
TC39_2
T_GP39.bigwig

value: Ly108-CD39+ SM cells

value: NDV-GP


title: A_Bin27JUN

description: Library name: A_Bin27JUN


title: CTRLpol27JUN

description: Library name: CTRLpol27JUN


title: Ly108+CD39- SM cells, NDV-GP group, tumor, Rep2

description:
Library name: Sample 6
TC108_2
T_GP108.bigwig


title: A_Bin26JUN

description: Library name: A_Bin26JUN


title: A_Bin22JUN

description: Library name: A_Bin22JUN


title: BAYin27JUN

description: Library name: BAYin27JUN


title: Ly108+CD39- SM cells, NDV-GP group, tumor, Rep1

description:
Library name: Sample 5
TC108_1
T_GP108.bigwig


title: SW620-rep1


title: Ly108+CD39- SM cells, NDV-WT group, tumor, Rep2

description:
Library name: Sample 4
TB_2
T_WT.bigwig


title: BAYin26JUN

description: Library name: BAYin26JUN


title: HCT116-rep3


title: HCT116-rep2


title: BAYin22JUN

description: Library name: BAYin22JUN


title: AZDin27JUN

description: Library name: AZDin27JUN


title: AZDin26JUN

description: Library name: AZDin26JUN


title: HCT116-rep1


title: A549-rep1


title: Ly108+CD39- SM cells, PBS group, tumor, Rep2

description:
Library name: Sample 2
TA_2
T_PBS.bigwig


title: CTRLin27JUN

description: Library name: CTRLin27JUN


title: 293T-rep3

value: Human embryonic kidney


title: CTRLin26JUN

description: Library name: CTRLin26JUN


title: Ly108+CD39- SM cells, PBS group, tumor, Rep1

description:
Library name: Sample 1
TA_1
T_PBS.bigwig


title: SW620-rep3

value: Human colorectal cancer


title: 293T-rep2


title: snRNA-Seq, MUX_33-1, Liver, TCF7L2 Flox and LKO, HTOs

city: Boston

first: Sudha

last: Biddinger

state: Massachusetts

address: 3 Blackfan Circle, 16th Floor (Endocrinology)

institute: Boston Children's Hospital

description:
Library name: MUX_33-1_HTOs
Mm_liver_TCF4-KO_08-1,Mm_liver_WT_04-1,Mm_liver_TCF4-KO_09-1,Mm_liver_WT_05-1,Mm_liver_TCF4-KO_10-1

library_source: other

data_processing:
10X genomics CellRanger Count (v6.1.2) was used to align FASTQs against the mouse genome (mm39)
Ambient RNA was removed with CellBender (v0.2.0)
Assembly: mm39
Supplementary files format and content: h5 files with barcode csvs

molecule: protein

source_name: Liver

extract_protocol: As per Habib, N. et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat. Methods 14, 955–958 (2017)

value: Liver

value: mixed samples (Tcf7l2 Flox/Flox, Tcf7l2LKO/LKO)


title: 293T-rep1


title: snRNA-Seq, MUX_32-2, Liver, TCF7L2 Flox and LKO, HTOs

description:
Library name: MUX_32-1_HTOs
Mm_liver_WT_01-2,Mm_liver_TCF4-KO_06-2,Mm_liver_WT_02-2,Mm_liver_TCF4-KO_07-2,Mm_liver_WT_03-2


title: INTS11 dTAG HEK293T 25uM U1 AMO/dTAG 4sU-seq Replicate 2

city: Irvine

first: Yongsheng

last: Shi

state: California

address: 811 Health Sciences Road, Medical Sciences B Room 262

department: Microbiology & Molecular Genetics

institute: UC Irvine

description: Library name: U1_AMO_25uM_dTAG2

data_processing:
We used trimGalore to remove adaptor sequences and low quality nucleotides. Trimmed reads were then mapped to the human genome (hg19)  using STAR (v2.7.3a) with the --alignEndsType EndToEnd parameter. The mapped reads (bam files) were used to generate bigwig files for visualization.
Assembly: hg19
Supplementary files format and content: bigwig

molecule: other

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and grown at 37˚C with 5% CO2

extract_protocol:
Total RNA was extracted from Trizol following the manufacturer's protocol
Total RNA was enriched for 4sU-labeled RNAs as described previously (PMID: 23963265). 4sU labeled RNAs were then used for library construction. Libraries were then prepared using ribosomal RNA depletion (RiboZero) and the Illumina TruSeq Total RNA kit.

value: INTS11 FKBP12 F36V

value: 25uM Non-targeting U1 AMO + dTAG


title: INTS11 dTAG HEK293T 25uM U1 AMO/dTAG 4sU-seq Replicate 1

description: Library name: U1_AMO_25uM_dTAG1


title: INTS11 dTAG HEK293T 25uM U1 AMO/DMSO 4sU-seq Replicate 3

description: Library name: U1_AMO_25uM_DMSO3

value: 25uM Non-targeting U1 AMO + DMSO


title: INTS11 dTAG HEK293T 25uM U1 AMO/DMSO 4sU-seq Replicate 2

description: Library name: U1_AMO_25uM_DMSO2


title: INTS11 dTAG HEK293T 25uM Control AMO/dTAG 4sU-seq Replicate 3

description: Library name: Control_AMO_25uM_dTAG3

value: 25uM Non-targeting Control AMO + dTAG


title: Ly108+CD39- SM cells, NDV-WT group, tumor, Rep1

description:
Library name: Sample 3
TB_1
T_WT.bigwig

value: Ly108+CD39- SM cells

value: NDV-WT


title: AZDin22JUN

description: Library name: AZDin22JUN

value: 500 nM Vistusertib for 4 hrs


title: snRNA-Seq, MUX_32-2, Liver, TCF7L2 Flox and LKO, GEX

description:
Library name: MUX_32-2_mRNA
Mm_liver_WT_01-2,Mm_liver_TCF4-KO_06-2,Mm_liver_WT_02-2,Mm_liver_TCF4-KO_07-2,Mm_liver_WT_03-2

molecule: nuclear RNA


title: ALS6 BA9+BA4+SC PM058 (ALS only)

city: New York

first: John

last: Tuddenham

state: NY

institute: Columbia University

description:
ALS6 BA9+BA4+SC
polyA RNA, HTO
F libraries are HTO

data_processing:
Fastq files were run through 10x Genomics Cellranger v3.1.0.
Assembly: hg38.91
Supplementary files format and content: Counts tables for all barcodes, filtered by CellRanger, in standard hdf5 output from CellRanger. For samples with cell hashing, HTO count library is also included.

extract_protocol:
CD45+ cells were isolated from autopsy tissue or surgical resections using a cold mechanical dissociation protocol, as described in our prior publication. (Olah,Menon, et al. 2020)
10x Genomics Chromium 3' v3 chemistry

tag: antibodies

value: TotalSeq-B anti-human Hashtag Antibody (7,8,9)


title: ALS7 BA9+BA4+SC PM062 (ALS only)

description:
ALS7 BA9+BA4+SC
polyA RNA, HTO
F libraries are HTO


title: ALS9 BA9+BA4+SC PM080 (ALS only)

description:
ALS9 BA9+BA4+SC
polyA RNA, HTO
F libraries are HTO

value: TotalSeq-B anti-human Hashtag Antibody (6,9,10)


title: INTS11 dTAG HEK293T 25uM Control AMO/dTAG 4sU-seq Replicate 2

description: Library name: Control_AMO_25uM_dTAG2


title: INTS11 dTAG HEK293T 25uM Control AMO/dTAG 4sU-seq Replicate 1

description: Library name: Control_AMO_25uM_dTAG1


title: snRNA-Seq, MUX_33-1, Liver, TCF7L2 Flox and LKO, GEX

description:
Library name: MUX_33-1_mRNA
Mm_liver_TCF4-KO_08-1,Mm_liver_WT_04-1,Mm_liver_TCF4-KO_09-1,Mm_liver_WT_05-1,Mm_liver_TCF4-KO_10-1


title: INTS11 dTAG HEK293T 25uM U1 AMO/DMSO 4sU-seq Replicate 1

description: Library name: U1_AMO_25uM_DMSO1


title: CTRLin22JUN

description: Library name: CTRLin22JUN

value: pro-monocytic cell line

value: WT carrying CAS9 and non-targeting sgRNA


title: ALS5 SC PM052 (ALS only)

description:
ALS5 SC
polyA RNA

source_name: SC

value: SC


title: INTS11 dTAG HEK293T 25uM U1 AMO/dTAG 4sU-seq Replicate 3

description: Library name: U1_AMO_25uM_dTAG3


title: INTS11 dTAG HEK293T 25uM Control AMO/DMSO 4sU-seq Replicate 3

description: Library name: Control_AMO_25uM_DMSO3

value: 25uM Non-targeting Control AMO + DMSO


title: HEK293T 25uM U1 AMO 4sU-seq Replicate 3

description: Library name: U1_25uM_AMO3

value: WT

value: U1 snRNA targeting AMO


title: ALS5 GM PM051 (ALS only)

description:
ALS5 GM
polyA RNA


title: INTS11 dTAG HEK293T 25uM Control AMO/DMSO 4sU-seq Replicate 1

description: Library name: Control_AMO_25uM_DMSO1


title: HEK293T 25uM U1 AMO 4sU-seq Replicate 2

description: Library name: U1_25uM_AMO2


title: BMDMs, LPS, rep 2

city: Los Angeles

first: Roberto

last: Spreafico

state: CA

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

description: Library name: Sample 7

data_processing:
nf-core/cutandrun pipeline v3.2.283
Assembly: GRCm38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: BMDM

extract_protocol:
H3K27me3 profiling was performed in BMDMs using CUT&RUN kit (Epicypher, #14-1048)
The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

value: BMDM

value: LPS


title: BMDMs, oxPAPC, rep 2

description: Library name: Sample 6

value: OxPAPC


title: ALS3 FN PM047 (ALS only)

description:
ALS3 FN
polyA RNA


title: BMDMs, NT, rep 2

description: Library name: Sample 5

value: NT


title: HEK293T 25uM U1 AMO 4sU-seq Replicate 1

description: Library name: U1_25uM_AMO1


title: HEK293T 25uM Control AMO 4sU-seq Replicate 2

description: Library name: Control_25uM_AMO2

value: 25uM Non-targeting Control AMO


title: HEK293T 25uM Control AMO 4sU-seq Replicate 3

description: Library name: Control_25uM_AMO3


title: BMDMs, LPS+oxPAPC, rep 2

description: Library name: Sample 8

value: LPS + OxPAPC


title: HEK293T 25uM Control AMO 4sU-seq Replicate 1

description: Library name: Control_25uM_AMO1


title: HEK293T PlaB 4sU-seq Replicate 3

description: Library name: PB_3

value: Pladienolide B


title: ALS3 GM PM046 (ALS only)

description:
ALS3 GM
polyA RNA

source_name: FN

value: FN


title: ALS3 GM PM045 (ALS only)

description:
ALS3 GM
polyA RNA


title: HEK293T PlaB 4sU-seq Replicate 2

description: Library name: PB_2


title: HEK293T OTS964 4sU-seq Replicate 3

description: Library name: OTS_3


title: INTS11 dTAG HEK293T 25uM Control AMO/DMSO 4sU-seq Replicate 2

description: Library name: Control_AMO_25uM_DMSO2

value: INTS11 FKBP12 F36V


title: ALS2 SC PM043 (ALS only)

description:
ALS2 SC
polyA RNA


title: BMDMs, oxPAPC, rep 1

description: Library name: Sample 2


title: HEK293T PlaB 4sU-seq Replicate 1

description: Library name: PB_1


title: BMDMs, LPS, rep 1

description: Library name: Sample 3


title: HEK293T OTS964 4sU-seq Replicate 1

description: Library name: OTS_1


title: ALS2 FN PM042 (ALS only)

description:
ALS2 FN
polyA RNA


title: BMDM, LPS+oxPAPC, 24h, rep 3

description: Library name: Sample 12

data_processing:
kallisto v0.46.2 with transcriptome GENCODE vM27 (GRCm39, Ensembl 104)
Assembly: GRCm39, Ensembl 104
Supplementary files format and content: Kallisto abundance.tsv output, renamed per sample

extract_protocol:
BMDMs (1 × 106) were treated as indicated and RNA was purified using Direct-zol RNA Miniprep (Zymo Research Corporation, Cat# R2053). Samples were submitted to Azenta Life Sciences for standard RNA-seq processing.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched  mRNAs  were fragmented for  15 minutes  at 94 °C.  Converted  the RNA  molecules  into complementary DNA (cDNA). cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto,  CA,  USA), and  quantified  by  using  Qubit  2.0  Fluorometer  (Invitrogen,  Carlsbad,  CA)  as  well  as  by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: LPS + oxPAPC

tag: time point


title: HEK293T DMSO 4sU-seq Replicate 2

description: Library name: DMSO_2

tag: cell line

value: DMSO


title: HEK293T DMSO 4sU-seq Replicate 3

description: Library name: DMSO_3


title: BMDMs, NT, rep 1

description: Library name: Sample 1

tag: cell type


title: HEK293T OTS964 4sU-seq Replicate 2

description: Library name: OTS_2

tag: treatment


title: HEK293T DMSO 4sU-seq Replicate 1

description: Library name: DMSO_1


title: ALS3 SC PM048 (ALS only)

description:
ALS3 SC
polyA RNA

tag: tissue


title: HEK293T U2AF2 shRNA 4sU-seq Replicate 3

description: Library name: U2AF2_shRNA3

tag: genotype

value: U2AF2 targeting shRNA


title: ALS2 GM PM040 (ALS only)

description:
ALS2 GM
polyA RNA


title: HEK293T U2AF2 shRNA 4sU-seq Replicate 2

description: Library name: U2AF2_shRNA2


title: BMDM, LPS+oxPAPC, 24h, rep 1

description: Library name: Sample 10


title: BMDM, LPS+oxPAPC, 24h, rep 2

description: Library name: Sample 11


title: ALS1 SC PM039 (ALS only)

description:
ALS1 SC
polyA RNA


title: HEK293T U2AF2 shRNA 4sU-seq Replicate 1

description: Library name: U2AF2_shRNA1


title: BMDMs, LPS+oxPAPC, rep 1

description: Library name: Sample 4


title: HEK293T U2AF1 shRNA 4sU-seq Replicate 3

description: Library name: U2AF1_shRNA3

value: U2AF1 targeting shRNA


title: HEK293T U2AF1 shRNA 4sU-seq Replicate 2

description: Library name: U2AF1_shRNA2


title: ALS1 FN PM038 (ALS only)

description:
ALS1 FN
polyA RNA


title: BMDM, LPS, 24h, rep 2

description: Library name: Sample 8


title: HEK293T U2AF1 shRNA 4sU-seq Replicate 1

description: Library name: U2AF1_shRNA1


title: HEK293T empty shRNA control vector 4sU-seq Replicate 3

description: Library name: pLKO_3

value: Empty shRNA vector


title: ALS1 GM PM037 (ALS only)

description:
ALS1 GM
polyA RNA


title: BMDM, LPS, 24h, rep 1

description: Library name: Sample 7


title: HEK293T empty shRNA control vector 4sU-seq Replicate 1

description: Library name: pLKO_1


title: ALS1 GM PM036 (ALS only)

description:
ALS1 GM
polyA RNA


title: ALS2 GM PM041 (ALS only)

description:
ALS2 GM
polyA RNA

value: SC


title: BMDM, LPS+oxPAPC, 3h, rep 3

description: Library name: Sample 6


title: HEK293T 50uM U2 AMO 4sU-seq Replicate 3

description: Library name: U2_50uM_AMO3

value: WT

value: U2 snRNA targeting AMO


title: ALS4 SC MA004 (ALS only)

description:
ALS4 SC
polyA RNA


title: HEK293T 50uM U2 AMO 4sU-seq Replicate 2

description: Library name: U2_50uM_AMO2


title: HEK293T 50uM U2 AMO 4sU-seq Replicate 1

description: Library name: U2_50uM_AMO1


title: HEK293T 50uM Control AMO 4sU-seq Replicate 2

description: Library name: Control_50uM_AMO2

value: 50uM Non-targeting Control AMO


title: HEK293T 50uM Control AMO 4sU-seq Replicate 3

description: Library name: Control_50uM_AMO3


title: ALS4 FN MA003 (ALS only)

description:
ALS4 FN
polyA RNA


title: BMDM, LPS+oxPAPC, 3h, rep 2

description: Library name: Sample 5

value: BMDM


title: BMDM, LPS+oxPAPC, 3h, rep 1

description: Library name: Sample 4


title: INTS11 dTAG HEK293T 25uM U1 AMO/dTAG mRNA-seq Replicate 3

description: Library name: U1_AMO_25uM_dTAG3

extract_protocol:
Total RNA was extracted from Trizol following the manufacturer's protocol
Total RNA was Dnase treated and purified by phenol/chloroform extraction. Libraries were then prepared using the Illumina TruSeq mRNA stranded kit (oligo dT-selected).

value: 25uM Non-targeting U1 AMO + dTAG


title: INTS11 dTAG HEK293T 25uM U1 AMO/dTAG mRNA-seq Replicate 2

description: Library name: U1_AMO_25uM_dTAG2


title: ALS4 GM MA002 (ALS only)

description:
ALS4 GM
polyA RNA


title: BMDM, LPS, 24h, rep 3

description: Library name: Sample 9

value: LPS


title: HEK293T 50uM Control AMO 4sU-seq Replicate 1

description: Library name: Control_50uM_AMO1


title: INTS11 dTAG HEK293T 25uM U1 AMO/dTAG mRNA-seq Replicate 1

description: Library name: U1_AMO_25uM_dTAG1


title: BMDM, LPS, 3h, rep 2

description: Library name: Sample 2


title: BMDM, LPS, 3h, rep 3

description: Library name: Sample 3


title: ALS4 GM MA001 (ALS only)

description:
ALS4 GM
polyA RNA


title: HEK293T empty shRNA control vector 4sU-seq Replicate 2

description: Library name: pLKO_2


title: INTS11 dTAG HEK293T 25uM U1 AMO/DMSO mRNA-seq Replicate 3

description: Library name: U1_AMO_25uM_DMSO3

value: 25uM Non-targeting U1 AMO + DMSO


title: INTS11 dTAG HEK293T 25uM U1 AMO/DMSO mRNA-seq Replicate 1

description: Library name: U1_AMO_25uM_DMSO1


title: INTS11 dTAG HEK293T 25uM Control AMO/dTAG mRNA-seq Replicate 3

description: Library name: Control_AMO_25uM_dTAG3

value: 25uM Non-targeting Control AMO + dTAG


title: BMDM, LPS, 3h, rep 1

description: Library name: Sample 1


title: mRNA_LG_3

city: URBANA

first: Ullas

middle: Valiya

last: Chembazhi

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: UIUC

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors were trimmed from the reads using trimmomatic V0.38.
Reads were mapped to the genome using STAR_2.6.1d.
Differential splicing analysis was performed using rMATs v4.0.2 (turbo).
FPKM/TPM values were calculated and compared between sets of samples using Cufflinks package.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Cuffdiff_genes.fpkm_tracking: Cuffdiff output as text file.
Supplementary_files_format_and_content: Olig8_splicing_recovery.xlsx: Splicing rescue calculations as Excel file.

source_name: myotubes

growth_protocol: Approximately 200,000 DM1 fibroblasts were plated to each well in 0.1% gelatin-coated of a 6-well plate with MEM media supplemented with 15% fetal bovine serum. After 1 d, cells were infected with MyoD-expressing lentivirus (lentivirus supernatant: DMEM = 1 : 9) and polybrene (8 µg/mL) for 1 d. The transduced cells were selected with selection DMEM media supplemented with 10% FBS and 2 µg/mL puromycin for 4 d. The selection media was replaced with complete growth MEM media and cells were allowed to recover until confluency. Cells further differentiated for 10 d in differentiation DMEM media containing 1% heat-inactivated horse serum, 10 µg/mL insulin, 10 µg/mL transferrin, and 3 µg/mL Dox.

extract_protocol:
RNA was isolated from myotubes using RNeasy Mini Kit (QIAGEN) with on-column DNase 1 treatment according to the recommended protocol.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

treatment_protocol: Cells were subjected to the respective treatments for 3 days.

value: Fibroblast-derived myotubes

tag: disease state

value: (8+LNA) Polyplex treated


title: FKDL202594953-1a-SI-NA-A4_S4

city: Hamburg

first: Michael

last: Spohn

address: Martinistr. 52

department: Bioinformatics Core

country: Germany

institute: UKE Hamburg

description:
Library name: 4 -/GFP_akut
10x Genomics

library_source: genomic single cell

data_processing:
The count tool of the Cell Ranger ATAC v1.2 software was employed to process the raw fastq files. Parameter force-cells was set to 5000.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files, bed files and matrix files

growth_protocol: T cells were isolated by negative selection from spleens of Irf4+/fl × CreERT2 (CD90.1+) and Irf4‑/fl × CreERT2 donor mice (CD90.2+) using the EasySepTM Mouse T cell Isolation Kit. 4×10e5 T cells from each donor cell population mixed to a 1:1 ratio in 200 μl of sterile PBS were transferred intravenously into CD45.1+ Rag1-/- mice. After 5 weeks, mice received i.p. 2mg per day of tamoxifen dissolved in corn oil on 5 consecutive days to activate the Cre recombinase. After further 5 weeks, mice were infected i.v. with 5-10×10e3 colony-forming units of a L. monocytogenes strain recombinant for ovalbumin.

extract_protocol:
Eight days later, spleen cells were isolated and CD90.1+ Irf4+/fl, CD90.1+ Irf4+/GFP, CD90.1- Irf4-/fl, and CD90.1- Irf4-/GFP CD4+ T cells were sorted. Similar numbers of each population were analyzed by ATAC seqencing using the Chromium Single Cell ATAC-Sequencing Kit (10x Genomics, Chromium Next GEM Chip H Single Cell Kit) according to the manufacturer’s protocols.
Libraries were constructed using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit (10x Genomics)

value: spleen

value: primary mouse CD4 T cells

value: Irf4-/- (GFP)


title: INTS11 dTAG HEK293T 25uM Control AMO/dTAG mRNA-seq Replicate 2

description: Library name: Control_AMO_25uM_dTAG2

value: INTS11 FKBP12 F36V


title: FKDL202594953-1a-SI-NA-A3_S3

description:
Library name: 3 -/flox_akut
10x Genomics


title: mRNA_LG_1


title: mRNA_3_GM5

value: Oligomer 8 treated


title: INTS11 dTAG HEK293T 25uM Control AMO/dTAG mRNA-seq Replicate 1

description: Library name: Control_AMO_25uM_dTAG1


title: INTS11 dTAG HEK293T 25uM Control AMO/DMSO mRNA-seq Replicate 2

description: Library name: Control_AMO_25uM_DMSO2

value: 25uM Non-targeting Control AMO + DMSO


title: HEK293T 25uM U1 AMO mRNA-seq Replicate 2

description: Library name: U1_25uM_AMO2

value: U1 snRNA targeting AMO


title: mRNA_2_GM5


title: HEK293T 25uM U1 AMO mRNA-seq Replicate 1

description: Library name: U1_25uM_AMO1

value: WT


title: FKDL202594953-1a-SI-NA-A2_S2

description:
Library name: 2 +/flox_akut
10x Genomics


title: INTS11 dTAG HEK293T 25uM Control AMO/DMSO mRNA-seq Replicate 3

description: Library name: Control_AMO_25uM_DMSO3


title: mRNA_1_GM5


title: FKDL202594953-1a-SI-NA-A1_S1

description:
Library name: 1 +/GFP_akut
10x Genomics

value: Irf4+/- (GFP)


title: INTS11 dTAG HEK293T 25uM U1 AMO/DMSO mRNA-seq Replicate 2

description: Library name: U1_AMO_25uM_DMSO2


title: P5_Setdb1_cKO_scRNAseq

city: Shanghai

first: Yunli

last: Xie

state: Shanghai

address: 131 Dong'an Road, Shanghai

department: Institutes of Brain Science

institute: Fudan University

description: Library name: sample2

data_processing:
Raw sequencing data (fastq files) were aligned to the reference genome mm10 (cellranger reference 2020-A, and Ensembl v98 gene annotation) using the Cell Ranger pipeline (v.7.1.0, 10x Genomics) with parameters: --include-introns=false. After alignment, filtering, barcode counting, and UMI counting we use feature-barcode matrices for downstream analysis.
Downstream analysis were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: P5_DG_ctr_matrix.mtx.gz
Supplementary files format and content: p5_mutant_matrix.mtx.gz

source_name: brain

extract_protocol:
Dentate gyri originating from WT and SETDB1 cKO mice at P5 were collected in PBS on ice. The dissected DG was then digested using the Neural Tissue dissociation kit (P) (Miltenyi Biotec) according to the manufacturer’s instructions. Approximately 20,000 cells were utilized as input for the 10X Genomics Chromium Controller, aiming for a targeted recovery of 10,000 cells per library.
The libraries were then prepared employing the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3, strictly adhering to the manufacturer’s instructions. Following the cDNA clean-up, the libraries were quantified using a BioAnalyzer then were sequenced on the Illumina NovaSeq 6000.

value: brain

value: mouse brain cells

value: postnatal day 5


title: mRNA_LG_2


title: HEK293T PlaB mRNA-seq Replicate 3

description: Library name: PB_3

value: Pladienolide B


title: P5_control_scRNAseq

description: Library name: sample1

value: wild type


title: HEK293T 25uM Control AMO mRNA-seq Replicate 1

description: Library name: Control_25uM_AMO1

value: 25uM Non-targeting Control AMO


title: HEK293T PlaB mRNA-seq Replicate 2

description: Library name: PB_2


title: mRNA_2_GM01653B

value: Fibroblast-derived myotubes

value: Healthy


title: mRNA_1_GM01653B


title: Geniad10

city: Camperdown

first: Søren

last: Madsen

state: NSW

address: D17 Charles Perkins Centre – School of L, The University of Sydney

country: Australia

institute: University of Sydney

description:
Library name: SAM24456463
Colname in processed data - same as title

data_processing:
bcl2fastq - demultiplexing
Quality of sequencing data was assessed with multiQC (Ewels et al, 2016). Gene expression levels were quantified with Kallisto (Bray et al, 2016) version 0.50.1 with the following flags: kallisto quant -b 100 --single -l 50 -s 20. Mouse index file was downloaded from (November 2023): https://github.com/pachterlab/kallisto-transcriptome-indices/releases. Transcript levels were estimated with the r package tximport (Soneson et al, 2015) and EdgeR (Robinson et al, 2010) was used to filter lowly expressed genes. No samples were excluded.
Assembly: mm10
Supplementary files format and content: tab-delimited file includes log(CPM) for individual samples

source_name: quadriceps muscles

extract_protocol:
combined TRIzol/chloroform/RNeasy kit (Invitogen/Sigma Aldrich/Qiagen) spin column protocol
KAPA mRNA HyperPrep Kit (Roche) was used for RNA sequencing library preparation following manufacturer's instructions with 500 ng of RNA as input

treatment_protocol: Animals are ~18-20 weeks old and have been fed standard rodent chow their whole life

value: quadriceps muscles

value: Chow


title: Geniad117

description:
Library name: SAM24456464
Colname in processed data - same as title


title: HEK293T OTS964 mRNA-seq Replicate 2

description: Library name: OTS_2


title: HEK293T OTS964 mRNA-seq Replicate 3

description: Library name: OTS_3


title: HEK293T PlaB mRNA-seq Replicate 1

description: Library name: PB_1


title: HEK293T DMSO mRNA-seq Replicate 3

description: Library name: DMSO_3

value: DMSO


title: HEK293T OTS964 mRNA-seq Replicate 1

description: Library name: OTS_1


title: Geniad446

description:
Library name: SAM24456462
Colname in processed data - same as title


title: mRNA_3_control


title: HEK293T 25uM Control AMO mRNA-seq Replicate 3

description: Library name: Control_25uM_AMO3


title: INTS11 dTAG HEK293T 25uM Control AMO/DMSO mRNA-seq Replicate 1

description: Library name: Control_AMO_25uM_DMSO1

value: INTS11 FKBP12 F36V


title: Geniad429

description:
Library name: SAM24456461
Colname in processed data - same as title


title: HEK293T DMSO mRNA-seq Replicate 1

description: Library name: DMSO_1


title: HEK293T DMSO mRNA-seq Replicate 2

description: Library name: DMSO_2


title: mRNA_1_control


title: HEK293T U2AF2 shRNA mRNA-seq Replicate 3

description: Library name: U2AF2_shRNA3

value: U2AF2 targeting shRNA


title: Geniad279

description:
Library name: SAM24456460
Colname in processed data - same as title


title: HEK293T 25uM Control AMO mRNA-seq Replicate 2

description: Library name: Control_25uM_AMO2


title: HEK293T U2AF2 shRNA mRNA-seq Replicate 2

description: Library name: U2AF2_shRNA2


title: Geniad43

description:
Library name: SAM24456459
Colname in processed data - same as title


title: HEK293T U2AF1 shRNA mRNA-seq Replicate 3

description: Library name: U2AF1_shRNA3

value: U2AF1 targeting shRNA


title: HEK293T U2AF1 shRNA mRNA-seq Replicate 2

description: Library name: U2AF1_shRNA2


title: HEK293T U2AF2 shRNA mRNA-seq Replicate 1

description: Library name: U2AF2_shRNA1


title: HEK293T U2AF1 shRNA mRNA-seq Replicate 1

description: Library name: U2AF1_shRNA1


title: Geniad126

description:
Library name: SAM24456458
Colname in processed data - same as title


title: HEK293T empty shRNA control vector mRNA-seq Replicate 3

description: Library name: pLKO_3

value: Empty shRNA vector


title: mRNA_2_control


title: Geniad260

description:
Library name: SAM24456456
Colname in processed data - same as title


title: HEK293T 50uM U2 AMO mRNA-seq Replicate 3

description: Library name: U2_50uM_AMO3

value: WT

value: U2 snRNA targeting AMO


title: Geniad48

description:
Library name: SAM24456455
Colname in processed data - same as title


title: HEK293T 50uM U2 AMO mRNA-seq Replicate 1

description: Library name: U2_50uM_AMO1


title: NOVA10_Blood_Phase_2_SD7

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profiling of PBMC  from influenza infected humans

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from PBMCs in Paxgene tubes according to manufacturer's instructions.RNA quality was assessed using Agilent Bioanalyzer.

treatment_protocol: PBMCs  collected from humans  and stored in Paxgene tubes  according to manufacturer's instructions.

value: influenza

value: PBMC

tag: study group

value: Vaccinated

tag: study date


title: HEK293T 50uM U2 AMO mRNA-seq Replicate 2

description: Library name: U2_50uM_AMO2


title: Geniad63

description:
Library name: SAM24456454
Colname in processed data - same as title


title: HEK293T 50uM Control AMO mRNA-seq Replicate 1

description: Library name: Control_50uM_AMO1

value: 50uM Non-targeting Control AMO


title: Geniad24

description:
Library name: SAM24456453
Colname in processed data - same as title


title: NOVA52_Blood_Phase_2_SD7

value: Unvaccinated


title: Geniad338

description:
Library name: SAM24456452
Colname in processed data - same as title


title: NOVA19_Blood_Phase_2_SD7


title: NALM-6 cells, albendazole-1

city: Guangzhou

first: Zhongjie

last: Huang

state: Guangdong

address: No. 253, Middle Industrial Avenue

institute: Zhuujiang hospital

description:
Library name: Sample4
Sample4_FPKM

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool,BMKCloud(www.biocloud.net) online platform.
Assembly: GRCH38
Supplementary files format and content: Tab-delimited txt file includes raw counts and FPKM values for each Sample

extract_protocol:
RNA was isolated from each group using TRIzol reagent(Accurate Biology). 1 μg of total RNA was used to construct sequencing libraries.
RNA libraries for RNA-seq were prepared using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology) following the manufacturer’s protocol

value: acute lymphoblastic leukemia

value: albendazole


title: NALM-6 cells, albendazole-3

description:
Library name: Sample6
Sample6_FPKM


title: NALM-6 cells, albendazole-2

description:
Library name: Sample5
Sample5_FPKM


title: Geniad49

description:
Library name: SAM24456457
Colname in processed data - same as title


title: HEK293T empty shRNA control vector mRNA-seq Replicate 2

description: Library name: pLKO_2


title: NOVA04_Blood_Phase_2_SD7


title: NALM-6 cells, DMSO-3

description:
Library name: Sample3
Sample3_FPKM


title: HEK293T empty shRNA control vector mRNA-seq Replicate 1

description: Library name: pLKO_1


title: NOVA18_Blood_Phase_2_SD7


title: NOVA30_Blood_Phase_2_SD7


title: NALM-6 cells, DMSO-2

description:
Library name: Sample2
Sample2_FPKM


title: Geniad97

description:
Library name: SAM24456451
Colname in processed data - same as title


title: NOVA41_Blood_Phase_2_SD7


title: Geniad81

description:
Library name: SAM24456450
Colname in processed data - same as title


title: HEK293T 50uM Control AMO mRNA-seq Replicate 3

description: Library name: Control_50uM_AMO3


title: NALM-6 cells, DMSO-1

description:
Library name: Sample1
Sample1_FPKM


title: NOVA17_Blood_Phase_2_SD7


title: Geniad281

description:
Library name: SAM24456449
Colname in processed data - same as title


title: HEK293T 50uM Control AMO mRNA-seq Replicate 2

description: Library name: Control_50uM_AMO2


title: SW480 KD-3-1 rep3

city: El Paso

first: Md Zahirul

last: Islam Khan

state: TX

address: 500 W University Ave

department: Biological Sciences

institute: University of Texas at El Paso

description:
Library name: SW480_KD_3_1.fq.gz, SW480_KD_3_2.fq.gz
SW480_KD_3
Sw480_Control_vs_MCM10-KD.txt

data_processing:
The data was processed using HISAT2, featureCounts, DESeq2
The sequenced reads were trimmed and mapped to GRCh38 genome
Read count were obtained using featureCounts and the differential expression of the genes were analyzed using DESeq2, Bioconductor R-package.
Assembly: GRCh38 genome
Supplementary files format and content: tab-delimited text file includes the raw counts for each sample
Supplementary files format and content: DESEq2 output file for Caco2_Control_vs_MCM10-KD and Sw480_Control_vs_MCM10-KD

growth_protocol: Caco-2 and SW480 cells were maintained in DMEM supplemented by 10% FBS and antibiotics (pencillin and streptomycin) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
ZYMO QuickRNA mini-prep kit was used for RNA extraction following the manufacturer's protocol
RNA-seq was performed at NOVOGENE

treatment_protocol: The cells were treated with siRNA targeting the gene MCM10 for 2 days prior to RNA isolation.

value: colorectal cancer cell


title: SW480 KD-2-1 rep2

description:
Library name: SW480_KD_2_1.fq.gz, SW480_KD_2_2.fq.gz
SW480_KD_2
Sw480_Control_vs_MCM10-KD.txt


title: SW480 WT-3-1 rep3

description:
Library name: SW480_C3_1.fq.gz, SW480_C3_2.fq.gz
SW480_C3
Sw480_Control_vs_MCM10-KD.txt


title: NOVA49_Blood_Phase_2_SD7


title: Geniad290

description:
Library name: SAM24456448
Colname in processed data - same as title

value: quadriceps muscles


title: SW480 WT- 2-1 rep2

description:
Library name: SW480_C2_1.fq.gz, SW480_C2_2.fq.gz
SW480_C2
Sw480_Control_vs_MCM10-KD.txt


title: Geniad87

description:
Library name: SAM24456447
Colname in processed data - same as title

value: Chow


title: Caco2 KD -3-1 rep3

description:
Library name: CaCo2_KD_3_1.fq.gz, CaCo2_KD_3_2.fq.gz
CaCo2_KD_3
Caco2_Control_vs_MCM10-KD.txt


title: NOVA29_Blood_Phase_2_SD7


title: NOVA23_Blood_Phase_2_SD7


title: Caco2 KD -2-1 rep2

description:
Library name: CaCo2_KD_2_1.fq.gz, CaCo2_KD_2_2.fq.gz
CaCo2_KD_2
Caco2_Control_vs_MCM10-KD.txt


title: Caco2 KD -1-1 rep1

description:
Library name: CaCo2_KD_1_1.fq.gz, CaCo2_KD_1_2.fq.gz
CaCo2_KD_1
Caco2_Control_vs_MCM10-KD.txt


title: Geniad287

description:
Library name: SAM24456446
Colname in processed data - same as title


title: NOVA50_Blood_Phase_2_SD7

description: Gene expression profiling of PBMC  from influenza infected humans


title: Caco2 WT-2-1 rep2

description:
Library name: CaCo2_C2_1.fq.gz, CaCo2_C2_2.fq.gz
CaCo2_C2
Caco2_Control_vs_MCM10-KD.txt


title: Caco2 WT-3-1 rep3

description:
Library name: CaCo2_C3_1.fq.gz, CaCo2_C3_2.fq.gz
CaCo2_C3
Caco2_Control_vs_MCM10-KD.txt


title: NOVA20_Blood_Phase_2_SD7


title: Geniad280

description:
Library name: SAM24456445
Colname in processed data - same as title


title: Caco2 WT-1 -1 rep1

description:
Library name: CaCo2_C1_1.fq.gz, CaCo2_C1_2.fq.gz
CaCo2_C1
Caco2_Control_vs_MCM10-KD.txt


title: Geniad206

description:
Library name: SAM24456444
Colname in processed data - same as title


title: NOVA65_Blood_Phase_2_SD7


title: Neuron, RNA, rep3

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Library name: CS_Neuron_RNA_rep3
R1: BC_Fwd, R2: UMI, R3: BC_Rev
Neuron_MPRA_results.tsv

data_processing:
Data was processed using MPRAflow and MPRAnalyze, as previously decribed (Achuach et al. 2019).
Assembly: hg38
Supplementary files format and content: tab-delimeted file

source_name: KOLF2.1J NGN2

extract_protocol:
Genomic DNA and total RNA was extracted using the Qiagen AllPrep DNA/RNA Mini kit
Sequencing libraries were generated as previously described (Gordon et al. 2020).

value: KOLF2.1J NGN2

value: Neuron


title: Geniad193

description:
Library name: SAM24456443
Colname in processed data - same as title


title: Neuron, RNA, rep2

description:
Library name: CS_Neuron_RNA_rep2
R1: BC_Fwd, R2: UMI, R3: BC_Rev
Neuron_MPRA_results.tsv


title: Neuron, RNA, rep1

description:
Library name: CS_Neuron_RNA_rep1
R1: BC_Fwd, R2: UMI, R3: BC_Rev
Neuron_MPRA_results.tsv


title: NOVA27_Blood_Phase_2_SD7


title: NOVA05_Blood_Phase_2_SD7


title: SW480 WT-1 -1 rep1

description:
Library name: SW480_C1_1.fq.gz, SW480_C1_2.fq.gz
SW480_C1
Sw480_Control_vs_MCM10-KD.txt


title: Neuron, DNA, rep3

description:
Library name: CS_Neuron_DNA_rep3
R1: BC_Fwd, R2: UMI, R3: BC_Rev
Neuron_MPRA_results.tsv


title: Geniad177

description:
Library name: SAM24456442
Colname in processed data - same as title


title: Neuron, DNA, rep1

description:
Library name: CS_Neuron_DNA_rep1
R1: BC_Fwd, R2: UMI, R3: BC_Rev
Neuron_MPRA_results.tsv


title: Geniad55

description:
Library name: SAM24456441
Colname in processed data - same as title


title: NPC, RNA, rep1

description:
Library name: CS_NPC_RNA_rep1
R1: BC_Fwd, R2: UMI, R3: BC_Rev
NPC_MPRA_results.tsv

value: Neuronal progenitor cell


title: NOVA16_Blood_Phase_2_SD7


title: NOVA01_Blood_Phase_2_SD7


title: NPC, RNA, rep2

description:
Library name: CS_NPC_RNA_rep2
R1: BC_Fwd, R2: UMI, R3: BC_Rev
NPC_MPRA_results.tsv


title: Geniad33

description:
Library name: SAM24456440
Colname in processed data - same as title


title: NPC, DNA, rep3

description:
Library name: CS_NPC_DNA_rep3
R1: BC_Fwd, R2: UMI, R3: BC_Rev
NPC_MPRA_results.tsv


title: Geniad452

description:
Library name: SAM24456439
Colname in processed data - same as title


title: NPC, DNA, rep2

description:
Library name: CS_NPC_DNA_rep2
R1: BC_Fwd, R2: UMI, R3: BC_Rev
NPC_MPRA_results.tsv


title: NOVA07_Blood_Phase_2_SD7

description: Gene expression profiling of PBMC  from influenza infected humans


title: NPC, DNA, rep1

description:
Library name: CS_NPC_DNA_rep1
R1: BC_Fwd, R2: UMI, R3: BC_Rev
NPC_MPRA_results.tsv


title: Geniad364

description:
Library name: SAM24456438
Colname in processed data - same as title


title: NOVA47_Blood_Phase_2_SD7


title: mRNA_3_GM01653B

value: Fibroblast-derived myotubes

value: Healthy


title: Geniad361

description:
Library name: SAM24456437
Colname in processed data - same as title


title: NOVA37_Blood_Phase_2_SD7


title: Neuron, DNA, rep2

description:
Library name: CS_Neuron_DNA_rep2
R1: BC_Fwd, R2: UMI, R3: BC_Rev
Neuron_MPRA_results.tsv


title: HEK, RNA, rep1

description:
Library name: CS_HEK_RNA_rep1
R1: BC_Fwd, R2: UMI, R3: BC_Rev
HEK293FT_MPRA_results.tsv

value: embryonic kidney


title: NOVA03_Blood_Phase_2_SD7


title: HEK, DNA, rep3

description:
Library name: CS_HEK_DNA_rep3
R1: BC_Fwd, R2: UMI, R3: BC_Rev
HEK293FT_MPRA_results.tsv


title: Geniad278

description:
Library name: SAM24456436
Colname in processed data - same as title


title: HEK, DNA, rep2

description:
Library name: CS_HEK_DNA_rep2
R1: BC_Fwd, R2: UMI, R3: BC_Rev
HEK293FT_MPRA_results.tsv


title: Geniad125

description:
Library name: SAM24456435
Colname in processed data - same as title


title: NPC, RNA, rep3

description:
Library name: CS_NPC_RNA_rep3
R1: BC_Fwd, R2: UMI, R3: BC_Rev
NPC_MPRA_results.tsv


title: HEK, DNA, rep1

description:
Library name: CS_HEK_DNA_rep1
R1: BC_Fwd, R2: UMI, R3: BC_Rev
HEK293FT_MPRA_results.tsv


title: chr1_12617218_F_rep4

description: Library name: EW143

data_processing:
Reads were trimmed using cutadpat for adapter removal (AGATCGGAAGAGC) and quality trimming (-m 30)
Reads were then aligned to hg38 with STAR [--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFileNamePrefix alignment/${sample}/ --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD]
Counts were generated for each annotated gene (GENCODE Human Release 42 (GRCh38.p13)) with htseq-count using the intersection-nonempty method and non-stranded counting.
Assembly: hg38
Supplementary files format and content: comma-delimited text file of raw counts
Supplementary files format and content: meta data csv

growth_protocol: NPCs were maintained in 2:1 DMEM:Ham's F12 supplemented with hFGF, hEGF, and heparin. NPCs were differentiated following the BrainPhys protocol from Bardy, et al. (doi:10.1073/pnas.1504393112)

extract_protocol:
Neurons were harvested for RNA isolation at day 14 of differentiation, following the Norgen Total RNA Purification kit (Norgen 37500) with the RNase-free DNase I kit (Norgen 25720)
100 ng total RNA per replicate was sent to Novogene for Eukaryotic mRNA library preparation with poly A enrichment. Samples were sequenced on a NovaSeq X Plus PE-150 flowcell, targeting 20 million reads per sample.

value: Neurons


title: chr1_12166839_F_rep2

description: Library name: EW142


title: Geniad343

description:
Library name: SAM24456434
Colname in processed data - same as title


title: chr11_124936086_F_rep4

description: Library name: EW141


title: HEK, RNA, rep3

description:
Library name: CS_HEK_RNA_rep3
R1: BC_Fwd, R2: UMI, R3: BC_Rev
HEK293FT_MPRA_results.tsv


title: chr1_12615462_F_rep4

description: Library name: EW144


title: chr11_124935297_F_rep4

description: Library name: EW140


title: NOVA36_Blood_Phase_2_SD7

value: influenza


title: NOVA02_Blood_Phase_2_SD7

value: PBMC


title: Geniad366

description:
Library name: SAM24456433
Colname in processed data - same as title


title: chr11_124740115_F_rep2

description: Library name: EW139


title: chr16_24175446_F_rep2

description: Library name: EW137


title: HEK, RNA, rep2

description:
Library name: CS_HEK_RNA_rep2
R1: BC_Fwd, R2: UMI, R3: BC_Rev
HEK293FT_MPRA_results.tsv


title: NOVA82_Blood_Phase_2_SD7


title: Geniad16

description:
Library name: SAM24456431
Colname in processed data - same as title


title: chr16_24174314_F_rep2

description: Library name: EW138


title: NOVA28_Blood_Phase_2_SD7

description: Gene expression profiling of PBMC  from influenza infected humans

value: Vaccinated


title: Geniad447

description:
Library name: SAM24456432
Colname in processed data - same as title


title: SafeHarbor_317_rep12

description: Library name: EW134


title: SafeHarbor_318_rep12

description: Library name: EW135


title: Geniad180

description:
Library name: SAM24456430
Colname in processed data - same as title


title: chr1_12615462_F_rep3

description: Library name: EW132


title: chr1_12617218_F_rep3

description: Library name: EW131


title: NOVA09_Blood_Phase_2_SD7


title: chr1_12166839_F_rep1

description: Library name: EW130


title: chr11_124936086_F_rep3

description: Library name: EW129


title: chr11_124935297_F_rep3

description: Library name: EW128


title: NOVA81_Blood_Phase_2_SD7


title: NOVA25_Blood_Phase_2_SD7_rehyb


title: chr11_124740115_F_rep1

description: Library name: EW127


title: chr16_23836300_F_rep2

description: Library name: EW136


title: Geniad450

description:
Library name: SAM24456429
Colname in processed data - same as title


title: NOVA22_Blood_Phase_2_SD7


title: NOVA57_Blood_Phase_2_SD7


title: NOVA75_Blood_Phase_2_SD7


title: Geniad174

description:
Library name: SAM24456428
Colname in processed data - same as title


title: Geniad337

description:
Library name: SAM24456425
Colname in processed data - same as title


title: Geniad282

description:
Library name: SAM24456427
Colname in processed data - same as title


title: chr16_24174314_F_rep1

description: Library name: EW126


title: NOVA61_Blood_Phase_2_SD7


title: chr1_230333042_F_rep2

description: Library name: EW120


title: chr19_13962808_F_rep4

description: Library name: EW117


title: chr19_13961888_F_rep4

description: Library name: EW116


title: chr19_13506161_F_rep2

description: Library name: EW115


title: NOVA51_Blood_Phase_2_SD7


title: chr16_24175446_F_rep1

description: Library name: EW125


title: chr1_230425617_F_rep2

description: Library name: EW118


title: Geniad348

description:
Library name: SAM24456426
Colname in processed data - same as title


title: chr16_23836300_F_rep1

description: Library name: EW124


title: chr20_6769491_F_rep2

description: Library name: EW114


title: NOVA62_Blood_Phase_2_SD7


title: SafeHarbor_318_rep11

description: Library name: EW123


title: SafeHarbor_317_rep11

description: Library name: EW122


title: SafeHarbor_318_rep10

description: Library name: EW111


title: chr20_6767865_F_rep2

description: Library name: EW112


title: NOVA56_Blood_Phase_2_SD7


title: SafeHarbor_317_rep10

description: Library name: EW110


title: Geniad289

description:
Library name: SAM24456424
Colname in processed data - same as title


title: chr1_230334708_F_rep2

description: Library name: EW119


title: Geniad295

description:
Library name: SAM24456423
Colname in processed data - same as title


title: NOVA15_Blood_Phase_2_SD7


title: Geniad256

description:
Library name: SAM24456420
Colname in processed data - same as title


title: Geniad17

description:
Library name: SAM24456422
Colname in processed data - same as title


title: chr20_6770358_F_rep2

description: Library name: EW113


title: chr19_13962808_F_rep3

description: Library name: EW105


title: chr19_13961888_F_rep3

description: Library name: EW104


title: NOVA45_Blood_Phase_2_SD7


title: Geniad45

description:
Library name: SAM24456421
Colname in processed data - same as title


title: Geniad433

description:
Library name: SAM24456417
Colname in processed data - same as title


title: NOVA40_Blood_Phase_2_SD7


title: Geniad27

description:
Library name: SAM24456419
Colname in processed data - same as title


title: chr1_230333042_F_rep1

description: Library name: EW108


title: chr20_6770358_F_rep1

description: Library name: EW101


title: chr20_6767865_F_rep1

description: Library name: EW100


title: Geniad431

description:
Library name: SAM24456418
Colname in processed data - same as title


title: SafeHarbor_318_rep9

description: Library name: EW99


title: chr1_230334708_F_rep1

description: Library name: EW107


title: Geniad453

description:
Library name: SAM24456413
Colname in processed data - same as title


title: NOVA66_Blood_Phase_2_SD7

description: Gene expression profiling of PBMC  from influenza infected humans


title: Geniad20

description:
Library name: SAM24456416
Colname in processed data - same as title


title: chr3_13281785_F_rep2

description: Library name: EW95


title: chr20_6769491_F_rep1

description: Library name: EW102


title: chr1_230425617_F_rep1

description: Library name: EW106


title: chr19_13506161_F_rep1

description: Library name: EW103


title: NOVA71_Blood_Phase_2_SD7


title: Geniad32

description:
Library name: SAM24456412
Colname in processed data - same as title


title: NOVA70_Blood_Phase_2_SD7


title: NOVA68_Blood_Phase_2_SD7


title: NOVA69_Blood_Phase_2_SD7


title: chr2_218272738_F_rep4

description: Library name: EW93


title: Geniad269

description:
Library name: SAM24456414
Colname in processed data - same as title


title: SafeHarbor_317_rep9

description: Library name: EW98


title: chr3_13281313_F_rep2

description: Library name: EW96


title: NOVA79_Blood_Phase_2_SD7


title: NOVA73_Blood_Phase_2_SD7


title: NOVA78_Blood_Phase_2_SD7


title: chr2_218272416_F_rep4

description: Library name: EW92


title: Geniad444

description:
Library name: SAM24456415
Colname in processed data - same as title


title: Geniad178

description:
Library name: SAM24456411
Colname in processed data - same as title


title: Geniad350

description:
Library name: SAM24456410
Colname in processed data - same as title


title: chr15 _67066587_F_rep2

description: Library name: EW89


title: chr3_13073695_F_rep2

description: Library name: EW94


title: chr15 _67065849_F_rep2

description: Library name: EW90


title: Geniad291

description:
Library name: SAM24456409
Colname in processed data - same as title


title: chr2_218292672_F_rep4

description: Library name: EW91


title: SafeHarbor_317_rep8

description: Library name: EW86


title: Geniad60

description:
Library name: SAM24456408
Colname in processed data - same as title


title: Geniad25

description:
Library name: SAM24456407
Colname in processed data - same as title


title: chr3_13073695_F_rep1

description: Library name: EW82


title: NOVA76_Blood_Phase_2_SD7


title: chr3_13281785_F_rep1

description: Library name: EW83


title: SafeHarbor_318_rep8

description: Library name: EW87


title: chr3_13281313_F_rep1

description: Library name: EW84


title: NOVA80_Blood_Phase_2_SD7


title: NOVA63_Blood_Phase_2_SD7


title: Geniad181

description:
Library name: SAM24456406
Colname in processed data - same as title


title: chr2_218272416_F_rep3

description: Library name: EW80


title: chr15 _67065849_F_rep1

description: Library name: EW78


title: NOVA31_Blood_Phase_2_SD7


title: NOVA77_Blood_Phase_2_SD7


title: Geniad189

description:
Library name: SAM24456404
Colname in processed data - same as title


title: NOVA12_Blood_Phase_2_SD7


title: Geniad120

description:
Library name: SAM24456403
Colname in processed data - same as title


title: SafeHarbor_317_rep7

description: Library name: EW74


title: NOVA08_Blood_Phase_2_SD7


title: chr2_218272738_F_rep3

description: Library name: EW81


title: Geniad263

description:
Library name: SAM24456402
Colname in processed data - same as title


title: chr19_13961888_F_rep2

description: Library name: EW68


title: NOVA48_Blood_Phase_2_SD7


title: chr2_218292672_F_rep3

description: Library name: EW79


title: chr19_13962808_F_rep2

description: Library name: EW69


title: Geniad253

description:
Library name: SAM24456405
Colname in processed data - same as title


title: Geniad438

description:
Library name: SAM24456400
Colname in processed data - same as title


title: chr16_73059122_F_rep2

description: Library name: EW66


title: chr15_67065032_F_rep2

description: Library name: EW88


title: chr15 _67066587_F_rep1

description: Library name: EW77


title: NOVA25_Blood_Phase_2_SD7


title: chr16_73057596_F_rep2

description: Library name: EW65


title: NOVA64_Blood_Phase_2_SD7


title: chr15_67065032_F_rep1

description: Library name: EW76


title: NOVA43_Blood_Phase_2_SD7


title: SafeHarbor_318_rep6

description: Library name: EW63


title: SafeHarbor_318_rep7

description: Library name: EW75


title: Geniad448

description:
Library name: SAM24456401
Colname in processed data - same as title


title: chr2_218292672_F_rep2

description: Library name: EW70


title: NOVA42_Blood_Phase_2_SD7

description: Gene expression profiling of PBMC  from influenza infected humans


title: SafeHarbor_317_rep6

description: Library name: EW62


title: Geniad57

description:
Library name: SAM24456396
Colname in processed data - same as title


title: chr16_73059616_F_rep2

description: Library name: EW64


title: chr2_218272738_F_rep2

description: Library name: EW72


title: Geniad432

description:
Library name: SAM24456398
Colname in processed data - same as title


title: chr2_218272416_F_rep2

description: Library name: EW71


title: Geniad284

description:
Library name: SAM24456399
Colname in processed data - same as title


title: NOVA32_Blood_Phase_2_SD7


title: NOVA11_Blood_Phase_2_SD7


title: chr19_14205870_F_rep2

description: Library name: EW67


title: NOVA33_Blood_Phase_2_SD7


title: chr2_218272416_F_rep1

description: Library name: EW59


title: Geniad183

description:
Library name: SAM24456397
Colname in processed data - same as title


title: chr19_13962808_F_rep1

description: Library name: EW57


title: Geniad11

description:
Library name: SAM24456395
Colname in processed data - same as title


title: chr2_218292672_F_rep1

description: Library name: EW58


title: chr19_13961888_F_rep1

description: Library name: EW56


title: NOVA21_Blood_Phase_2_SD7


title: chr2_218272738_F_rep1

description: Library name: EW60


title: Geniad190

description:
Library name: SAM24456394
Colname in processed data - same as title


title: chr19_14205870_F_rep1

description: Library name: EW55


title: chr16_73059122_F_rep1

description: Library name: EW54


title: NOVA59_Blood_Phase_2_SD7


title: Geniad169

description:
Library name: SAM24456393
Colname in processed data - same as title


title: Geniad179

description:
Library name: SAM24456392
Colname in processed data - same as title


title: NOVA34_Blood_Phase_2_SD7


title: chr16_73059616_F_rep1

description: Library name: EW52


title: SafeHarbor_318_rep5

description: Library name: EW51


title: chr14_105151525_F_rep2

description: Library name: EW48


title: NOVA46_Blood_Phase_2_SD7


title: NOVA60_Blood_Phase_2_SD7


title: SafeHarbor_317_rep5

description: Library name: EW50


title: chr11_124936086_F_rep2

description: Library name: EW45


title: chr11_124935297_F_rep2

description: Library name: EW44


title: chr14_105168266_F_rep2

description: Library name: EW46


title: Geniad378

description:
Library name: SAM24456390
Colname in processed data - same as title


title: NOVA20_Blood_Phase_2_SD5


title: Geniad268

description:
Library name: SAM24456388
Colname in processed data - same as title


title: chr11_82756421_F_rep2

description: Library name: EW41


title: chr11_82758310_F_rep2

description: Library name: EW42


title: chr11_124953964_F_rep2

description: Library name: EW43


title: Geniad187

description:
Library name: SAM24456391
Colname in processed data - same as title


title: Geniad95

description:
Library name: SAM24456389
Colname in processed data - same as title


title: Geniad288

description:
Library name: SAM24456387
Colname in processed data - same as title


title: NOVA69_Blood_Phase_2_SD5


title: chr16_73057596_F_rep1

description: Library name: EW53


title: NOVA70_Blood_Phase_2_SD5


title: NOVA42_Blood_Phase_2_SD5


title: chr11_83071905_F_rep2

description: Library name: EW40


title: NOVA79_Blood_Phase_2_SD5


title: chr14_105152528_F_rep2

description: Library name: EW47


title: Geniad14

description:
Library name: SAM24456386
Colname in processed data - same as title


title: SafeHarbor_317_rep4

description: Library name: EW38