title: Acy_12_2

city: kunming

first: Meichen

last: Zhu

state: Yunnan

address: kunmingshi

department: School of Life Sciences

institute: yunnandaxue

data_processing:
The data from high-throughput sequencing were analyzed using the Majorbio tools, a free online platform for data analysis (www.majorbio.com).
Assembly: HiSat2 and StringTie
Supplementary files format and content: xls file includes tpm value for each sample

organism: Orbilia oligospora ATCC 24927

source_name: Fungal hyphae cells

growth_protocol: The wild-type and  mutant strains were cultured on potato dextrose agar (PDA) medium at 28°C.

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: synonymn

value: Arthrobotrys oligospora

value: Fungal hyphae cells

value: AoAcy deletion mutant

value: Trap induction with nematode extract


title: C1FN01_03_RNA

status: Public on Aug 13 2022

type: SRA

city: Urbana

first: Dr. Gregory

last: Underhill

address: 1406 West Green Street

country: USA

institute: University of Illinois at Urbana Champaign

library_source: transcriptomic

data_processing:
https://www.encodeproject.org/data-standards/rna-seq/small-rnas/
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for entrez geneids for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Primary Human HSCs

growth_protocol: HSCs were cultured on the cellular microarrays with defined ECM and stiffness composition in DMEM, 10% FBS, 1%Pen-Strep, 1% L-Glutamine for 72 hours

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

tag: cell line

value: Primary Human HSCs

tag: cell type

value: Hepatic Stellate Cells

tag: substrate stiffness

tag: ecm compositions

value: Collagen 1, Fibronectin

tag: time

value: 72 hours


title: Acy_12_3

country: China

tag: genotype

tag: treatment


title: lib28549

city: Seattle

first: Naresh

last: Doni Jayavelu

state: WA

address: 1201 9th AVE

department: Systems Immunology/Bioinformatics

institute: Benaroya Research Institute at Virginia Mason

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts_MUPPITS2_nasal_samples.csv is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
RNA quality was assessed using RNA electrophoresis (Agilent). All samples had RIN values ≥7. Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina)

tag: source tissue

value: Nasal Lavage

tag: flowcell id

value: CCHDTANXX

tag: visit

value: Randomization

tag: study id

tag: fastq total reads

tag: percent aligned

tag: aligned counts in millions

tag: median cv coverage

value: Placebo

tag: time in study in years

tag: status

value: Discontinued Study

tag: exacerbation number


title: AO_12_3

tag: strain

tag: synonymn

tag: cell type

value: wild type


title: AO_12_2

tag: time


title: C1FN01_02_RNA

tag: cell line

tag: substrate stiffness

tag: ecm compositions


title: AO_12_1

tag: genotype

tag: treatment


title: ChrX.3 male, day 6 IAV infection, rep3 [CM13]

city: Burlington

first: SABIKUNNAHAR

last: SABIKUNNAHAR

state: Vermont

address: 318 Rowell, 106 Carrigan Dr

department: Biomedical and Health Sciences

institute: The University of Vermont

data_processing:
Demultiplexed sequencing data was received from the sequencing facilities and quality control of the sequencing data was done using FastQC
Genomic alignment and transcript quantification from RNA-seq data was performed using Salmon tool
Differential gene expression analysis was done using Deseq2 in R studio
Assembly: Gencode.vM26
Supplementary files format and content: tab-delimited text files include TPM count values for each Sample

organism: Mus musculus

source_name: whole lung

extract_protocol:
RNA was extracted using Direct- zol RNA Microprep Kit
cDNA libraries were synthesized using SMARTer Stranded Total RNA- Seq Kit v2 - Pico Input Mammalian

treatment_protocol: mice were administered intranasally with PR8 influenza A virus in 0.05 ml of PBS

tag: Sex

value: male

tag: tissue

value: whole lung

value: B6.ChrX.3PWD (ChrX.3)

value: day 6 post-infection with IAV


title: ChrX.3 male, day 6 IAV infection, rep2 [CM12]


title: ChrX.3 male, day 6 IAV infection, rep4 [CM14]


title: FNLN25_03_RNA

value: Fibronectin, Laminin


title: Acy_0_2

value: Arthrobotrys oligospora

value: Fungal hyphae cells

value: AoAcy deletion mutant

value: no treatment


title: ChrX.3 male, day 6 IAV infection, rep1 [CM10]


title: AO_0_3


title: AO_0_2


title: ChrX.3 female, day 6 IAV infection, rep4 [CF19]

value: female


title: C4TC01_01_RNA

value: Primary Human HSCs

value: Hepatic Stellate Cells

value: Collagen 4, Tenascin C

value: 72 hours


title: FNLN25_02_RNA


title: FNLN25_01_RNA


title: AO_0_1


title: ChrX.3 female, day 6 IAV infection, rep3 [CF18]


title: C4TC25_03_RNA


title: C_0_3

value: AoPkaC1 deletion mutant


title: C_0_2


title: C_0_1


title: Acy_12_1

value: Trap induction with nematode extract


title: Acy_0_3


title: C1FN01_01_RNA

value: Collagen 1, Fibronectin


title: C4TC25_02_RNA


title: A_0_3

value: wild type


title: RUNX1-IT1 Silencer3 (SiS3)

city: Chongqing

first: Junfeng

last: Zhang

address: Gaotan Yanzheng Street, Shapingba District

institute: First Affiliated Hospital of Army Medical University

data_processing:
Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
Obtained clean reads were mapped to the hg38 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM

growth_protocol: Pancreatic cancer cell line PANC-1 cells were used for our research.

extract_protocol:
Total RNA was extracted from the samples using the TRIzol method. The total RNA extracted from the samples was tested by a NanoDrop 2000 and denaturing gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PANC-1 cells were transfected with RUNX1-IT1 Smart Silencer and control Smart Silencer, and sh-RUNX1 and control lentiviral vectors.

value: Pancreatic cancer cell line


title: Acy_0_1


title: RUNX1-IT1 Silencer2（SiS2）


title: ChrX.3 female, day 6 IAV infection, rep1 [CF16]

value: whole lung

value: B6.ChrX.3PWD (ChrX.3)


title: C4TC25_01_RNA


title: A_0_2


title: B6 male, day 6 IAV infection, rep4 [B6M4]

value: male

value: day 6 post-infection with IAV


title: A_0_1

value: Arthrobotrys oligospora

value: Fungal hyphae cells


title: ChrX.3 female, day 6 IAV infection, rep2 [CF17]


title: control Silencer3（NSiN3）


title: C1FN25_02_RNA


title: B6 male, day 6 IAV infection, rep3 [B6M3]


title: B6 male, day 6 IAV infection, rep2 [B6M2]


title: C1FN25_01_RNA


title: C_12_3


title: B6 male, day 6 IAV infection, rep1 [B6M1]


title: control Silencer1（NSiN1）


title: C_12_2


title: sh-RUNX1-2 (s3)


title: B6 female, day 6 IAV infection, rep4 [B6F9]


title: RUNX1-IT1 Silencer1（SiS1）


title: sh-RUNX1-1 (s2)


title: A_12_3


title: C1FN25_03_RNA


title: B6 female, day 6 IAV infection, rep3 [B6F8]


title: B6 female, day 6 IAV infection, rep1 [B6F5]


title: B6 female, day 6 IAV infection, rep2 [B6F7]


title: sh-NC3 (nc3)


title: sh-NC2 (nc2)


title: A_12_2


title: A_12_1


title: sh-NC1（nc1）


title: Acinar192 (NOMe-seq)

status: Public on Aug 12 2022

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description: single-cell NOMe-seq

library_source: genomic

data_processing:
read trimming and adapter removal
Bisulfite-aware read mapping
quantification of CpG and GpC methylation
Assembly: GRCm38 (mm10)
Supplementary files format and content: gzip-compressed tab-separated files produced by Bismark with the following columns: chromosome, start position, end position, methylation percentage, number of methylated cytosines, number of unmethylated cytosines.
Library strategy: NOMe-seq

molecule: genomic DNA

source_name: exocrine pancreas

extract_protocol:
Primary pancreatic acinar cells were isolated by digestive dissociation of pancreatic tissue and subsequent density gradient centrifugation. After cultivation as 3D matrigel embedded organoids for 9 days, the cells were harvested and subjected to the scNMT-seq protocol. For more information on the generation of pancreatic organoids, see the following papers (Wollny et al., 2016; Krieger et al., 2021).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the epigenomic portion of this multi-omic data set, i.e. DNA methylation and chromatin accessibility assessed with single-cell NOMe-seq.
Single-cell NOMe-seq

value: exocrine pancreas

value: acinar cell

tag: culture condition

value: 9 days as 3D organoids


title: Acinar189 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar191 (NOMe-seq)

description: single-cell NOMe-seq


title: control Silencer2（NSiN2）


title: Acinar190 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar179 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar180 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar178 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar187 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar177 (NOMe-seq)

description: single-cell NOMe-seq


title: C_12_1


title: Acinar188 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar168 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar175 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar176 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar167 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar166 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar165 (NOMe-seq)

description: single-cell NOMe-seq


title: Pterygium2

type: RNA

city: Beijing

first: lvzhen

last: Huang

state: (State)

address: Xizhimen South Street 11, Xi Cheng District

institute: Peking university people‘s hospital

hyb_protocol: GeneChip® Expression Wash, Stain, and Scan were performed following protocol from GeneChip® Hybridization Wash and Stain Kit (Affymetrix, USA, 900720)

scan_protocol: GeneChips were scanned using GeneChip®Scanner 3000 7G

data_processing: Probe cell intensity data (CEL) from microarrays are analyzed and normalized by Signal Space Transformation Robust Multichip Analysis (SST-RMA) algorithm in the Affymetrix® Expression Console™ software (v1.4). The normalized data were then subjected to R package limma (v3.42.2) to identify differentially expressed genes (DEGs)

label: biotin

source_name: Conjunctiva

label_protocol: cDNA was synthesized, amplified, fragmented, and labeled for hybridization using the GeneChip® WT PLUS Reagent Kit (Affymetrix, USA, 902280) from 2 ugs isolated RNA following the manufacturer's protocols.

extract_protocol: The total RNA of the tissues was isolated using TRIzol™ Reagent(Invitrogen, USA, 15596026) according to the manufacturer's protocol

tag: gender

tag: age

value: Conjunctiva

tag: type

value: disease


title: Acinar164 (NOMe-seq)

description: single-cell NOMe-seq


title: Pterygium1


title: Acinar156 (NOMe-seq)

description: single-cell NOMe-seq


title: Conjunctiva1

value: control


title: Conjunctiva2


title: Acinar154 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar153 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar152 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar151 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar142 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar143 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar144 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar129 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar131 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar132 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar130 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar140 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar128 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar127 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar119 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar118 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar117 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar116 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar163 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar141 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar115 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar108 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar155 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar106 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar105 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar107 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar120 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar139 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar103 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar104 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar96 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar95 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar93 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar91 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar92 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar83 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar72 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar81 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar80 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar68 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar82 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar84 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar71 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar70 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar67 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar59 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar60 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar57 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar58 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar55 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar46 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar45 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar44 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar43 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar35 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar36 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar94 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar33 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar69 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar31 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar20 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar7 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar19 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar22 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar8 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar185 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar186 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar183 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar181 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar56 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar184 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar182 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar48 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar174 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar34 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar173 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar170 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar172 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar162 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar171 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar161 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar159 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar169 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar21 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar157 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar158 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar160 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar149 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar148 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar150 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar146 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar138 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar147 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar145 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar137 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar135 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar136 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar133 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar134 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar126 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar122 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar123 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar121 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar111 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar114 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar113 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar102 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar98 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar109 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar112 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar101 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar110 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar90 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar99 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar124 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar87 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar100 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar97 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar76 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar89 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar88 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar73 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar78 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar64 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar65 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar75 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar74 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar85 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar77 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar125 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar63 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar66 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar62 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar61 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar54 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar53 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar51 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar86 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar52 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar49 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar50 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar42 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar41 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar40 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar38 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar37 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar30 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar29 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar18 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar27 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar28 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar16 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar13 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar14 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar15 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar5 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar2 (NOMe-seq)

description: single-cell NOMe-seq


title: Acinar4 (NOMe-seq)

description: single-cell NOMe-seq


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-12H]

first: Chengxiang

last: Qiu

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: sci-RNA-seq3 library

library_source: transcriptomic single cell

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

molecule: polyA RNA

extract_protocol: We performed a simplified version of sci-RNA-seq3, further optimized for “tiny” samples (Martin et al. 2021). Briefly, to each tube, 100ul of a hypotonic, PBS-based lysis buffer was added with DEPC as an RNase inhibitor. The resulting nuclei were then fixed with 4 volumes of a mix of methanol and dithiobis (succinimidyl propionate) (DSP). After rehydrating and washing the nuclei carefully in a sucrose/PBS/triton/MgCl2 buffer (SPBSTM), the nuclei were distributed to two 96-well plates for reverse transcription, allocating 8 wells per embryo. After reverse transcription, nuclei were pooled, washed in SPBSTM and redistributed to a fresh plate for ligation of the second index primer with T4 DNA ligase. Nuclei were then again pooled, washed, and redistributed to three final plates for second strand synthesis, extraction, tagmentation, and PCR to add the third index plus a plate index. Products were pooled by PCR plate, size-selected and sequenced on two Illumina NextSeq runs (termed “NextSeq-1" and “NextSeq-2”).

tag: developmental stage

value: ETiX mouse embryoids (Day6 and Day8) and natural mouse embryos (E7.5, E8, E8.5, E8.75. and E9)


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-12G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-12E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-12F]

description: sci-RNA-seq3 library


title: Acinar39 (NOMe-seq)

description: single-cell NOMe-seq


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-12D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-12B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-11H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-12C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-12A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-11F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-11G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-11D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-11E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-11B]

description: sci-RNA-seq3 library


title: Acinar17 (NOMe-seq)

description: single-cell NOMe-seq


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-11A]

description: sci-RNA-seq3 library


title: Acinar6 (NOMe-seq)

description: single-cell NOMe-seq


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-10G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-10F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-10D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-10C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-10B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-10A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-09F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-09G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-09H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-09E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-09C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-09D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-09A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-08G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-11C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-08H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-08F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-10H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-08C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-07H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-08A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-08B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-08D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-07G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-07F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-08E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-10E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-07E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-07B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-07C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-07D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-06H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-07A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-06F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-06E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-06C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-06D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-06B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-09B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-05H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-06A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-05G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-05C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-05F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-05E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-05D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-05B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-05A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-04H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-04F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-04G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-04E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-04A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-04C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-04B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-04D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-03H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-03C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-06G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-03E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-03F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-03B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-02G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-02F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-03A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-02E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-02C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-02B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-01H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-01F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-01E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-01G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-01D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-01C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-01B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-03G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-12H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-01A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-03D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-12G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-12E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-12F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-12D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-12C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-02H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-12B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-02D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-11H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-11G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-12A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-11F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-10H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PC-02A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-11D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-11A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-11E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-11B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-11C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-10G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-10E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-10D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-10B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-10C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-09H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-09F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-09G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-09D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-09E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-09B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-08G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-08H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-08F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-09A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-08D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-08E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-08B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-08A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-07H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-07E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-07G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-07F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-07D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-10F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-07C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-10A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-06H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-07A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-06F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-09C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-06G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-06C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-06A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-05H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-06D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-08C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-05G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-05F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-05E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-05C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-05D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-05B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-05A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-04H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-07B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-04F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-04D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-06E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-04B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-04A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-03H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-03E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-04C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-03F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-06B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-03D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-03B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-03C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-03A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-02F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-02G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-02H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-02E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-02A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-02D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-02C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-04G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-01E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-01H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-01G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-04E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-01F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-01D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-01A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-01C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-12F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-12E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-12C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-12D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-12G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-12H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-01B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-11G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-12B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-11H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-03G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PB-02B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-11E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-11B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-11C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-11D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-11A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-10G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-10H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-10F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-10E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-10C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-10B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-10A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-09H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-11F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-12A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-08E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-08G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-09E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-09A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-08C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-08B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-09C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-08D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-09F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-09G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-09D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-08F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-07F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-07H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-08A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-10D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-07D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-07C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-07B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-07G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-07A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-06G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-06H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-06F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-09B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-06E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-06D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-06C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-08H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-05E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-05F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-06B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-05G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-05H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-05B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-05D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-04D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-06A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-04H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-04E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-04G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-07E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-04F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-03H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-05A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-03G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-04A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-04B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-03F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-05C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-03C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-03D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-03B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-03A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-04C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-03E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-02H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-02F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-02G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-02E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-02A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-01H]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-02C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-02D]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-01F]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-01G]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-01C]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-02B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-01E]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-01B]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-01A]

description: sci-RNA-seq3 library


title: sci-RNA-seq3 with ETiX mouse embryoids and natural mouse embryos [NextSeq2_PA-01D]

description: sci-RNA-seq3 library


title: Origin mapping of the chromosome II rearrangement, pre-meiotic S phase, replicate 2, dye-swap 2

type: genomic

city: Bordeaux

first: Pei-Yun Jenny

last: Wu

address: 1 Rue Camille Saint Saens

country: France

institute: Institute of Biochemistry and Cellular Genetics

description: Ratio of S phase to unreplicated DNA

hyb_protocol: Labeled samples from before and after S phase entry were added to hybridization buffer (50 mM MES pH 6.7, 500 mM NaCl, 6 mM EDTA, 0.5% Sarcosine, 30% Formamide, 1.5 ng/µl herring sperm DNA, 0.8 µg/µl yeast tRNA, 0.05µg/µl Cot1 DNA). Samples were incubated in an Agilent hybridization oven at 42ºC for 18-21 hours, and washes were performed for 5 min at room temperature (wash 1: 6xSSPE, 0.005% N-Lauroylsarcosine (twice), wash 2: 0.06x SSPE)

scan_protocol: Slides were scanned using an Agilent G2505C scanner.

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1)
Ratio of S phase to unreplicated DNA. The ratios of S phase vs. unreplicated DNA (G2 or G1 block); the values not log-based. Values > 2 have been removed. The averaging and baseline correction that is part of the protocol for origin identification and efficiency determination described in the manuscript has not yet been applied here. For datasets that have been subjected to this processing and for which replicate experiments have been averaged, please see the associated Analyzed_data.txt file.

organism: Schizosaccharomyces pombe

source_name: Nitrogen starvation, meiosis, unreplicated

label_protocol: 2 μg of purified genomic DNA per sample was incubated for 5 min at 95 °C with 300 μg/mL of Random Primer (Invitrogen, Waltham, MA, USA , 481907011). This was followed by the addition of 2 µL Klenow (M0212S, New England BioLabs, Ipswich, MA, USA) and a nucleotide mix (0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.1 mM dTTP, 0.4 mM aha-dUTP)and incubation for two hours at 37 °C. aha-dUTP-labeled DNA was then purified using the PureLink PCR purification kit (K310001, ThermoFisher, Waltham, MA, USA ) and ethanol precipitated using 75 mM sodium acetate and 0.1 μg/μL glycogen for 30 min at −20 °C. DNA was then washed with 70% ethanol, air dried, and resuspended in 80 μL 0.1 M sodium bicarbonate (pH 8.7). Each sample was then divided in two, and each half was incubated for 90 min in the dark with either Cy3 or Cy5 (GE Healthcare, Chicago, IL, USA) for dye swap. The dye coupling reaction was stopped by the addition of 15 μL of 4 M hydroxylamine. DNA was then purified using the PureLink PCR purification kit (K310001, ThermoFisher, Waltham, MA, USA).

growth_protocol: Cells were grown to exponential phase in EMM6S at 25ºC, starved of nitrogen for 16 hours, then returned to nitrogen-rich conditions at 34ºC.

extract_protocol: Genomic DNA extraction was performed as in Hoffman and Winston, Gene, 1987, and samples were purified using the Qiagen Genomic Tip-20.

treatment_protocol: Cells were treated with 12 mM hydroxyurea (HU) at the time of nitrogen refeeding and shift to 34ºC. Cells were harvested just prior to addition of a nitrogen source as well as during S phase, 4 h after refeeding.

value: Chromosome II Inversion

tag: time point

value: Unreplicated (Time 0)

source_name: Nitrogen starvation, pre-meiotic S phase

value: S phase


title: Origin mapping of the chromosome II rearrangement, pre-meiotic S phase, replicate 2, dye-swap 1

description: Ratio of S phase to unreplicated DNA

tag: strain


title: Origin mapping of the control strain for the chromosome I rearrangement, pre-meiotic S phase, replicate 1, dye-swap 1

description: Ratio of S phase to unreplicated DNA

value: Chromosome I control


title: Origin mapping of the control strain for the chromosome I rearrangement, pre-meiotic S phase, replicate 2, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome II rearrangement, post-quiescence, replicate 2, dye-swap 2

description: Ratio of S phase to unreplicated DNA

source_name: Quiescent cells, nitrogen starvation, unreplicated

value: Chromosome II control

source_name: Quiescent cells, S phase


title: Origin mapping of the chromosome II rearrangement, post-quiescence, replicate 2, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome I rearrangement, post-quiescence, replicate 2, dye-swap 2

description: Ratio of S phase to unreplicated DNA

value: Chromosome I Inversion


title: Origin mapping of the control strain for the chromosome I rearrangement, pre-meiotic S phase, replicate 1, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome I rearrangement, pre-meiotic S phase, replicate 2, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome II rearrangement, pre-meiotic S phase, replicate 1, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome I rearrangement, pre-meiotic S phase, replicate 2, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome II rearrangement, pre-meiotic S phase, replicate 2, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome II rearrangement, pre-meiotic S phase, replicate 1, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome II rearrangement, pre-meiotic S phase, replicate 2, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome II rearrangement, pre-meiotic S phase, replicate 1, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome II rearrangement, post-quiescence, replicate 1, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome II rearrangement, post-quiescence, replicate 2, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome I rearrangement, pre-meiotic S phase, replicate 1, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome I rearrangement, post-quiescence, replicate 1, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome II rearrangement, pre-meiotic S phase, replicate 1, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome I rearrangement, pre-meiotic S phase, replicate 2, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome I rearrangement, pre-meiotic S phase, replicate 1, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome II rearrangement, post-quiescence, replicate 1, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome I rearrangement, post-quiescence, replicate 2, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome I rearrangement, post-quiescence, replicate 1, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome II rearrangement, post-quiescence, replicate 2, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome II rearrangement, post-quiescence, replicate 1, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome I rearrangement, post-quiescence, replicate 2, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the chromosome II rearrangement, post-quiescence, replicate 1, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: ADS patients_1

city: Kunming

first: Xin

last: Shi

address: Dianmian Road No.374

institute: The Second Affiliated Hospital of Kunming Medical University, Kunming

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
The fragments per kilobase of exon model per mapped reads (FPKM) were calculted
Assembly: mm9
Supplementary files format and content: tab-delimited text files include readcount values for each sample

source_name: whole blood

extract_protocol:
According to the manufacturer’s instructions, the total RNA was extracted from each WB sample employing TRIzol reagent (Invitrogen, Carlsbad, CA, United States).The temperature was maintained at −80°C, while the RNA quality was measured by the Agilent 2,100 TapeStation (Agilent Technologies, United States) Biochip Analysis System. Eventually, samples were selected with RNA integrity values > 7.0 to construct cDNA libraries.
The Illumina® NEBNext® Ultra™ Directed RNA Library  Preparation Kit is utilized to construct Illumina True-Seq  strand lncRNA libraries.

value: whole blood


title: ADS patients_2


title: ADS patients_3


title: non-degenerative lumbar adult volunteers_2


title: non-degenerative lumbar adult volunteers_1


title: non-degenerative lumbar adult volunteers_3


title: Origin mapping of the control strain for the chromosome I rearrangement, post-quiescence, replicate 2, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: primary OBs, Het, day 21, replicate 4

city: Bethesda

first: Sergey

last: Leikin

state: Maryland

department: NICHD

institute: National Institutes of Health

data_processing:
Cutadapt v2.5 trimming of reads (switches: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --overlap 6 -q 20 -j 8 --minimum-length 25)
STAR v2.73a two-pass alignment of trimmed reads against GENCODE mouse M16 (mm10) reference genome
Subread featureCounts v1.6.4 quantitation of reads against GENCODE mouse M23 comprehensive GTF gene annotations (optional switches: -p -J -O –extraAttributes gene_name)
Assembly: mm10
Supplementary files format and content: *.csv (unnormalized gene counts)

source_name: primary OBs, Het, day 21

extract_protocol:
RNA was extracted as described in Gorrell et al, Adv Sci, 2022
libraries for RNA-seq were prepared using TrueSeq library preparation kit (Illumina) and sequenced by the Molecular Genomics Core of NICHD/NIH

value: parietal osteoblasts

value: Het G610C

value: osteogenic differentiation

value: Day 21


title: primary OBs, Het, day 14, replicate 3

source_name: primary OBs, Het, day 14

value: Day 14


title: primary OBs, Het, day 8, replicate 4

source_name: primary OBs, Het, day 8

value: Day 8


title: primary OBs, Het, day 21, replicate 2


title: primary OBs, Het, day 8, replicate 3


title: primary OBs, Het, day 14, replicate 4


title: primary OBs, Het, day 8, replicate 2


title: primary OBs, Het, day 14, replicate 1


title: primary OBs, WT, day 14, replicate 4

source_name: primary OBs, WT, day 14

value: WT


title: primary OBs, Het, day 8, replicate 1


title: primary OBs, Het, day 21, replicate 1


title: primary OBs, WT, day 8, replicate 4

source_name: primary OBs, WT, day 8


title: Origin mapping of the control strain for the chromosome I rearrangement, post-quiescence, replicate 1, dye-swap 1

description: Ratio of S phase to unreplicated DNA


title: Origin mapping of the control strain for the chromosome I rearrangement, post-quiescence, replicate 1, dye-swap 2

description: Ratio of S phase to unreplicated DNA


title: primary OBs, WT, day 14, replicate 3


title: primary OBs, WT, day 21, replicate 3

source_name: primary OBs, WT, day 21


title: primary OBs, WT, day 8, replicate 3


title: primary OBs, WT, day 21, replicate 2


title: primary OBs, WT, day 14, replicate 2


title: primary OBs, Het, day 21, replicate 3


title: primary OBs, Het, day 14, replicate 2


title: IL4-3-SP

city: New Haven

first: Vishwa Deep

last: Dixit

state: CT

address: 310 Cedar St

department: Comparative Medicine

institute: Yale University

data_processing:
Basecalls performed using CASAVA bcl2fastq_1.8.4.
Raw reads were mapped to the GENCODE vM9 mouse reference genome using the STAR aligner with the following options: --outFilterMultimapNmax 15 --outFilterMismatchNmax 6  --outSAMstrandField All --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM.
Raw counts and fragments per kilobase per million reads mapped (FPKMs) were calculated using RSEM.
Genome_build: GENCODE vM9
Supplementary_files_format_and_content: Table of FPKM values for each gene in each sample.
Supplementary_files_format_and_content: Table of raw counts for each gene in each sample.

source_name: Peritoneal macrophage

growth_protocol: 3% thioglycollate was injected once 4 days before peritoneal cell collection. IL-4c were injected twice, the second injection was done 2 days after the first injection, and peritoneal cells were collected 2 days after the second injection. IL-4 (5ug, Peprotech) and IL-4 antibody (25ug, BioXcell) were incubated as 1:5 ratio in PBS for 1-2 min right before each injection.

extract_protocol:
RNA STAT-60 was directly added to collect cells in culure plates. Following phase separation with chloroform, RNA was extracted and purified using RNeasy Plus micro kit (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peritoneal cells were isolated by injection 7ml of PBS into peritoneum, and 3x10^6 of isolated cells were seeded on 24 well plate. After 2 hour, cells were washed with PBS for three times to keep only attached peritoneal macrophages. The peritoneal macrophages were either non-treated or SPARC (20ug/ml) treated for 24 hours.

value: Peritoneal macrophage

tag: injection

value: IL-4 complex IP

value: SPARC


title: IL4-2-SP

tag: cell type


title: primary OBs, WT, day 21, replicate 1

tag: time


title: IL4-3-No

value: No treatment


title: primary OBs, WT, day 8, replicate 2


title: primary OBs, WT, day 8, replicate 1


title: primary OBs, WT, day 14, replicate 1


title: primary OBs, WT, day 21, replicate 4


title: IL4-2-No


title: IL4-1-SP


title: TG-3-SP

value: Thioglycollate IP


title: TG-2-SP


title: IL4-1-No


title: TG-1-SP


title: TG-1-No


title: LTR18A MPRA K562 RNA [K562_run2]

city: St. Louis

first: Alan

middle: Y

last: Du

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University at St. Louis School of Medicine

data_processing:
library strategy: MPRA
Fastq reads (from read 1 only) were filtered to only include reads which contain barcodes that fully matched a synthesized barcode from the library design. The number of reads for each barcode was then counted.
Barcodes for the same associated element were added together to get element-level counts and then normalized to total read depth (counts per million, CPM). Elements with fewer than 5 counts in any sample (DNA or RNA) were filtered out.
Expression of an element was calculated as RNA CPM/DNA CPM. Expression was normalized to the average of Basal construct transfection replicates. Finally, enrichment score was calculated as the log2 of normalized expression.
Assembly: hg19
Supplementary files format and content: TXT file of barcode counts

growth_protocol: K562 cells were grown in RPMI1640 with L-glutamine supplemented with 10% FBS and 1% penicillin/streptomycin. HepG2 cells were grown in DMEM (with high glucose and L-glutamine, without sodium pyruvate) supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA was extracted from cell cultures using PureLink RNA Mini Kit with on-column DNase treatment followed by DNase I treatment using TURBO DNA-free kit. DNA was taken directly from the MPRA library used for transfections.
Barcodes were amplified from the MPRA library (DNA) or from cDNA after first strand cDNA synthesis of extracted RNA. Amplified barcodes were then ligated to Illumina adapters for pooled sequencing.

tag: cell line

value: LTR18A MPRA K562 RNA


title: LTR18A MPRA K562 RNA [K562_run4]


title: LTR18A MPRA K562 RNA [K562_run1]


title: LTR18A MPRA K562 RNA [K562_run3]


title: LTR18A MPRA HepG2 RNA [HepG2_run1]

value: LTR18A MPRA HepG2 RNA


title: LTR18A MPRA HepG2 RNA [HepG2_run4]


title: LTR18A MPRA HepG2 RNA [HepG2_run3]


title: HAM8, scRNAseq

city: Tokyo

first: Yukie

last: Tanaka

address: 1-5-45 Yushima, Bunkyo-ku

country: Japan

institute: Tokyo Medical and Dental University

description: BD Rhapsody

data_processing:
FASTQ sequence data files were processed on Seven Bridges Genomics online platform (https://www.sevenbridges.com) by running the BD Rhapsody Targeted Analysis Pipeline with V(D)J processing incorporated. After identifying the cell barcode and the unique molecular index (UMI), recursive substitution error correction (RSEC) counts as the final molecular counts by removing the effect of UMI errors were calculated.Quality control for removing dead cells was adopted using the putative cell detection function in the Seven Bridge pipeline as the first step, and then we excluded cell based on the distribution of gene and transcript counts as the following quality criteria: less than 25 expressed genes and less than 50 detected transcripts. RSEC counts were used for downstream analysis with SeqGeq version 1.7.0 (BD Biosciences) and R version 4.0.2. After RSEC data files were concatenated together, the plug-in Lex-BDSMK was run to separate the sample tags, then the plug-in VDJ Explorer to identify individual TCR CDR3 sequences. Consequently, a total of 11,029 TCR paired with mRNA expression were successfully assembled from the three patients’ data.
Supplementary files format and content: csv format files includes UMI count values for each cell for each sample

source_name: peripheral blood

extract_protocol:
Thawed PBMCs were reacted with LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, CD3mAb, CD8 mAb, and Tax301-309/HLA-A*24:02 tetramer reagents, and live HTLV-1 Tax301-309-CTLs were sorted by FACSAriaIII Fusion, centrifuged, and resuspended in cold sample buffer, respectively. Following viability confirmation (>92%), each cell sample was independently loaded on a Rhapsody Cartridge for single-cell capture and cDNA library preparation using the BD Rhapsody Express System (BD Biosciences). In the process, estimated 543 cells (HAM-1), 13,057 cells (HAM-7), and 2,053 cells (HAM-8) were captured by cell capture beads, respectively.
Following single-cell capture, we performed cDNA library construction for VDJ TCR, sample tags, and the targeted mRNA (259 different genes) with Human T-Cell Expression Panel, according to the manufacturer's protocols.

value: peripheral blood

value: CD8+ T cells

tag: subject status

value: HAM patient


title: HAM1, scRNAseq

description: BD Rhapsody


title: HAM7, scRNA-seq

description: BD Rhapsody


title: LNCaP-DMSO_3

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

country: Italy

institute: Catholic University of the Sacred Heart rome

data_processing:
Adapter trimming from raw 3′READS performed using Cutadapt.
The trimmed reads were aligned to hg19 using bowtie2.
Reads with a mapping quality score (MAPQ) ≥10 were kept for further analysis.
Reads with ≥2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads.
pAs within 24 nt of each other were clustered.
pAs with less than 5 PASS reads in all the samples were first trimmed.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file with raw isoform abundance, change of APA isoform abundance and significance score (APA), and RPM, gene expression log2FC and significance score (GE) for every sample.

source_name: LNCaP prostate cancer cell line

growth_protocol: LNCaP cells were maintained in RPMI 1640 (Euroclone) supplemented with 10% fetal bovine serum (GIBCO), 4500 mg/L glucose (Sigma-Aldrich), 10 mM Hepes (Eurocolone), 1mM sodium pyruvate (Euroclone), 100 U/mL penicillin (Euroclone) and 100 μg/mL streptomycin (Euroclone).

extract_protocol: TRIZOL. Poly(A)+ RNA in 0.115 g of total RNA was captured using 12 L of oligo(dT)25 magnetic beads (NEB) in 200 L 1_ binding buffer (10 mM Tris-Cl, pH 7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III (NEB) in 30 L RNase III buffer (10 mM Tris-Cl, pH 8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5_ adapter (5_-CCUUGGCACCCGAGAAUUCCANNNN, Sigma) in the presence of 1 mM ATP, 0.1 L of SuperaseIn (Life Technologies), and 0.25 L of T4 RNA ligase 1 (NEB) in a 5 L reaction at 22C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 L of Dynabeads MyOne Streptavidin C1 (Life Technologies). After washing with washing buffer (10 mM Tris-Cl, pH 7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/L of RNase H (Epicentre) at 37C for 30 min in 30 L of RNase H buffer (50 mM Tris-Cl, pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5_ adenylated 3_ adapter (5_-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 L T4 RNA ligase 2 (truncated KQ version, NEB) at 22C for 1 h in a 5 L reaction containing 15% PEG 8000 (NEB) and 0.2 L of SuperaseIn (Life Technologies). The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase (Promega), followed by PCR amplification using Phusion high-fidelity DNA polymerase (NEB) and bar-coded PCR primers for 1218 cycles (12 cycles for 15 g input RNA, 13 cycles for 5 g input, 15 cycles for 1 g input, and 18 cycles for inputs <1 g). Both RT primer (5_-GTTCAGAGTTCTACAGTCCGACGATC) and PCR primers with indexes were described previously in Hoque et al. (2013). PCR products were size-selected twice with AMPure XP beads (Beckman Coulter), using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer (Agilent). The library concentrations were further measured by qPCR using primers corresponding to 5_ and 3_ end regions of cDNAs.

treatment_protocol: for Enzalutamide treatment LNCaP cells were grown in charcoal-stripped serum, followed by treatment with DMSO or Enzalutamide for 24 hours.

value: LNCaP

value: prostate cancer

value: treated with DMSO for 24 hours


title: LNCaP-Enz_2

value: treated with Enzalutamide for 24 hours


title: scRNAseq_patient_5_tumor

city: New York

first: John

last: Grout

state: NY

address: 50 east 98th, apt. 11a4

institute: Mount Sinai School of Medicine

data_processing:
Cell Ranger 3 for demultiplexing, alignment and cell counting.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw feature-barcode matrices, containing UMI counts in Market Exchange Format. Also contains tsv files with feature and barcode sequences to row and column indices, respectively.

extract_protocol:
Stromal cells were sorted using a combination of positive and negative gating. CD45 and EpCAM were used to remove immune and epithelial/tumor cells respecitvely while CD29 and PDPN were used to positively select for stromal cells.
Library preparation was done according to 10X genomics protocols and their correponding verions as listed below.
ssRNA-seq

treatment_protocol: The non-involved adjacent lung and tumor tissue were diced by scissors then enzymatically digested with collagenase and Dnase. Digested tissue was agitated with repeated passes through a syringe and strained through a 70 miron strainer. The single cell suspension was resuspended in PBS until cell sorting.

tag: tissue type

value: Tumor

tag: disease

value: NSCLC

value: sorted stromal cells


title: LNCaP-DMSO_2

tag: treatment


title: scRNAseq_patient_13_tumor


title: scRNAseq_patient_13_adjacent

value: Adjacent


title: LNCaP-Enz_3


title: LNCaP-DMSO_1


title: scRNAseq_patient_9_tumor


title: TG-3-No

value: Peritoneal macrophage


title: LNCaP-Enz_1


title: TG-2-No


title: scRNAseq_patient_5_adjacent


title: scRNAseq_patient_1_adjacent


title: scRNAseq_patient_3_tumor


title: scRNAseq_patient_1_tumor


title: LTR18A MPRA HepG2 RNA [HepG2_run2]

tag: genotype


title: scRNAseq_patient_8_adjacent


title: scRNAseq_patient_12_tumor


title: scRNAseq_patient_7_tumor


title: scRNAseq_patient_10_tumor


title: scRNAseq_patient_7_adjacent


title: scRNAseq_patient_10_adjacent


title: scRNAseq_patient_8_tumor


title: scRNAseq_patient_2_tumor


title: scRNAseq_patient_2_adjacent


title: scRNAseq_patient_4_tumor


title: scRNAseq_patient_14_tumor


title: scRNAseq_patient_4_adjacent


title: scRNAseq_patient_15_tumor


title: scRNAseq_patient_15_adjacent


title: scRNAseq_patient_14_adjacent


title: scRNAseq_patient_11_adjacent


title: scRNAseq_patient_11_tumor


title: MLL3_ASXL2_RK

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: ASXL2 R639K/R641K mutant cells

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cells were maintained with either DMEM (Gibco, Gaithersburg, MD) or ATCC-formulated RPMI-1640 medium  containing 10% FBS (Sigma)

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were treated with different concentrations of CARM1 inhibitor or EZH2 inhibitor for 24 hours, with DMSO as negative control

value: breast cancer cell line

tag: passages

value: Low passages (6-10)

tag: chip antibody

value: anti-MLL3 homemade antibody

value: ASXL2 mutant


title: UTX_ASXL2_KO

description: ASXL2 knockout cells

value: anti-UTX homemade antibody

value: ASXL2 knockout


title: MLL3_ASXL2_RF

description: ASXL2 R639F/R641F mutant cells


title: MLL3_DMSO (MLL3 control)

description: CAL51 cells treated with DMSO

value: wild type


title: MLL3_CARMi

description: CAL51 cells treated with CARM1 inhibitor


title: UTX_ASXL2_WT

description: normal cells


title: scRNAseq_patient_6_tumor


title: MLL3_CARM1KO_R2

description: CARM1 knockout cells

value: CARM1 knockout


title: MLL3_ASXL2KO_R1

description: ASXL2 knockout cells


title: MLL3_WT_R2

description: normal cells


title: ASXL2_RF_Rep1

description: ASXL2 R639F/R641F mutant cells


title: ASXL2_RF_Rep2

description: ASXL2 R639F/R641F mutant cells


title: ASXL2_RK_Rep1

description: ASXL2 R639K/R641K mutant cells


title: CARM1KO_Rep2

description: CARM1 knockout cells


title: CARM1WT_Rep2

description: normal cells


title: CARM1WT_Rep1

description: normal cells


title: CARM1KO_Rep1

description: CARM1 knockout cells


title: ASXL2WT_Rep2

description: normal cells


title: ASXL2KO_Rep1

description: ASXL2 knockout cells


title: MLL3_ASXL2KO_R2

description: ASXL2 knockout cells


title: ASXL2WT_Rep1

description: normal cells


title: ASXL1WT_Rep1

description: normal cells


title: MLL3_WT_R1

description: normal cells


title: MLL3_CARM1KO_R1

description: CARM1 knockout cells


title: ASXL2KO_Rep2

description: ASXL2 knockout cells


title: HC#3_single_cell_RNAseq_with_feature_barcoding

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

data_processing:
Raw data were processed with the Cell Ranger pipeline (v.3.1.0).
Sequencing reads were aligned using STAR aligner
The cellranger-vdj pipeline was applied for single cell V(D)J BCR data
Genome_build: GRCh38

source_name: total B cells from a AA healthy donor, anti-DNA(-)/anti-Sm(-)/anti-SSA(-)/RD(-)

extract_protocol:
Single cells and beads containing barcoded DNA oligos were captured into oil droplets by 10xChromium controller using 10xGenomics 5' VDJ reagent kits. Individual cells were lyzed immediately, mRNA were released, and reverse transcription was performed by plyT primers according to 10xGenomics 5' VDJ standard protocol. Single-stranded cDNA was then captured in the each oil droplet by the barcoded DNA oligos carried by the beads.
Barcoded single cell cDNA were pooled and preamplified, 5' biased transcriptome libraries and BCR libraries were constructed according to the standard protocol of 10xGenomics 5' VDJ reagent kits.

value: African Am

tag: gender

value: Female

tag: tissue

value: heparinized blood

value: PBMC B cells


title: HC#2_single_cell_VDJseq(BCR)


title: HC#2_single_cell_RNAseq_with_feature_barcoding


title: ASXL1KO_Rep1

description: ASXL1 knockout cells

value: ASXL1 knockout


title: HC#3_single_cell_VDJseq(BCR)


title: ASXL1WT_Rep2

description: normal cells


title: ASXL2_RK_Rep2

description: ASXL2 R639K/R641K mutant cells


title: HC#1_T1_single_cell_RNAseq

data_processing:
Raw data were processed with the Cell Ranger pipeline (v.2.1.1).
Sequencing reads were aligned using STAR aligner
The cellranger-vdj pipeline was applied for single cell V(D)J BCR data
Genome_build: GRCh38

source_name: T1 B cells from a AA healthy donor, anti-DNA(-)/anti-Sm(-)/anti-SSA(-)/RD(-)

value: Male

value: PBMC Transitional Stage 1 (T1) B cells


title: SLE#2_single_cell_RNAseq

source_name: total B cells from an AA SLE, anti-DNA(+)/anti-Sm(+)/anti-SSA(-)/RD(+)


title: SLE#3_single_cell_RNAseq

source_name: total B cells from an AA SLE, anti-DNA(+)/anti-Sm(+)/anti-SSA(+)/RD(+)


title: SLE#1_single_cell_RNAseq


title: HC#1_single_cell_RNAseq


title: SLE#2_T1_single_cell_RNAseq

source_name: T1 B cells from an AA SLE, anti-DNA(+)/anti-Sm(+)/anti-SSA(-)/RD(+)


title: ASXL1KO_Rep2

description: ASXL1 knockout cells


title: Case 36

city: LOS ANGELES

first: Neal

last: Yuan

state: CA

address: 8700 Beverly Blvd, Davis 1015

institute: Cedars-Sinai

data_processing: We excluded any miRNA if greater than 80% of samples failed to meet manufacturer quality scores, a sign of either very low miRNA levels and/or failed amplification. We normalized miRNA expression data by subtracting the cycle threshold (Ct) from the global mean across the Ct’s of all miRNAs for that patient, a widely accepted normalization method (see D’haene Methods Mol Biol 2012). Lastly, we excluded any patients if greater than 80% of their samples failed to meet quality scores.

label: EVAGREEN

source_name: platelet poor plasma

extract_protocol: miRNeasy Serum Plasma Kit

tag: condition

value: Type 1 MI


title: Case 32


title: Case 31


title: Case 33


title: Case 30


title: Case 29


title: Case 28


title: Case 27


title: Case 26


title: Case 25


title: Case 19


title: Case 18


title: Case 22


title: Case 16


title: Case 21


title: Case 23


title: Case 24


title: Case 35


title: Case 34


title: Case 15


title: Case 17


title: Case 14


title: Case 13


title: Case 11


title: Case 12


title: Case 10


title: Case 9


title: Case 8


title: Case 6


title: Case 7


title: Case 3


title: Case 20


title: Case 1


title: Case 2


title: Case 4


title: Control 81

value: control


title: Control 78


title: Control 76


title: Control 79


title: Control 75


title: Control 77


title: Control 73


title: Control 68


title: Control 71


title: Control 69


title: Control 80


title: Control 72


title: Control 64


title: Control 66


title: Case 5


title: Control 67


title: Control 63


title: Control 65


title: Control 62


title: Control 70


title: Control 61


title: Control 58


title: Control 57


title: Control 59


title: Control 56


title: Control 74


title: Control 55


title: Control 52


title: Control 53


title: Control 47


title: Control 50


title: Control 46


title: Control 43


title: Control 44


title: Control 45


title: Control 60


title: Control 37


title: Control 41


title: Control 42


title: Control 40


title: Control 36


title: Control 35


title: Control 38


title: Control 34


title: Control 39


title: Control 54


title: Control 33


title: Control 31


title: Control 30


title: Control 51


title: Control 32


title: Control 49


title: Control 29


title: Control 27


title: Control 28


title: Control 26


title: Control 25


title: Control 24


title: Control 23


title: Control 18


title: Control 22


title: Control 16


title: Control 17


title: Control 15


title: Control 13


title: Control 20


title: Control 19


title: Control 12


title: Control 10


title: Control 9


title: Control 2


title: Control 7


title: Control 11


title: Control 8


title: Control 4


title: Control 3


title: Control 21


title: Control 6