title: PGE2TL_D

data_processing:
STAR (v2.5) was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
DESeq2 R package (v2_1.6.3) was utilized to identify differentially expressed genes
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab delimited text file include sequence read counts of each sample

source_name: peripheral blood cDC1

growth_protocol: Human peripheral blood cDC1 were isolated from blood of healthy, voluntary donors after they gave written and informed consent. Blood was mixed with PBS and loaded on Pancoll to isolate peripheral blood mononuclear cells (PBMCs) via centrifugation. cDC1 were then sorted for CD3-CD141+CD370+ via FACS. Blood was drawn from voluntary donors at the Klinikum rechts der Isar, TUM in accordance with a protocol approved by the ethics committee at TUM (564/18S-AS).

extract_protocol:
RNA from human cDC1 was isolated using the NEB Monarch Total RNA Miniprep Kit.
Isolated mRNA from human cDC1 was fragmented and the first strand of cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library preparation. Following end repair, A-tailing, adapter ligation, size selection, amplification, and purification, the library was checked with Qubit and real-time PCR for quantification, as well as bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: 5x10e4 cDC1 were seeded in 200µl RPMI supplemented with the respective treatments for indicated periods of time.

value: D

value: peripheral blood

value: PGE2 (1microg/ml)  24h + poly I:C (10microg/ml) 4h


title: NO_AG, biol replicate 2, scRNAseq

status: Public on May 27 2023

type: SRA

city: New Haven

first: Martina

last: Damo

state: CT

address: 300 Cedar St

department: Immunobiology

country: USA

institute: Yale University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
All scRNAseq datasets were processed with CellRanger 3.1 using mm10 mouse genome indices from 10X
Libraries were further preprocessed using the scprep package, removing cells with library size lower than 1500 unique molecular identifiers (UMI) per cell and more than 15000 UMI per cell
Cells with high mitochondrial content (>85th percentile per sample) were removed, and genes not detected in any of the six samples were removed.
The resulting data matrix was then normalized by library size to 1000 counts per cell
Finally, the matrix was log-transformed.
Assembly: mm10
Supplementary files format and content: Gzipped CSV files, where rows are cells and columns are measures genes after pre-processing.

molecule: total RNA

organism: Mus musculus

source_name: Skin

extract_protocol:
Confirmed all experimental animals had expected phenotypes based on presence/absence of overt macroscopic skin pathology, and skin infiltration and functional properties of P14 CD8 T cells recovered from each moouse. Then prepared single-cell suspensions from 4-OH-Tam-treated skin area for sequencing.
Libraries were prepared by the Yale Center for Genome Analysis using Chromium Single Cell 5' Reagent Kit (10X Genomics), according to manufacurer's instructions

tag: tissue

value: Skin

tag: strain

value: NINJA

tag: age

value: 6-12 weeks old

tag: treatment


title: AG_CPI, biol replicate 1, scRNAseq

description: 10x Genomics


title: AG, biol replicate 1, scRNAseq

description: 10x Genomics

value: AG


title: NO_AG, biol replicate 1, scRNAseq

description: 10x Genomics


title: PGE2TL_C

city: Munich

first: Felix

middle: Archibald

last: Bayerl

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Molecular Immunology

country: Germany

institute: Technical Univerity of Munich

description: PGE2 treated cDC1 24h + poly I:C activation for 4h

library_source: transcriptomic

organism: Homo sapiens

tag: biological replicate

value: C


title: PGE2+EP1antagonist_cDC1_4h_C

description: PGE2 + EP1 antagonist treated cDC1 4h

data_processing:
Dropseq tools v1.12 was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
DESeq2 v1.14.1 R package was utilized to identify differentially expressed genes
Assembly: GRCm38.p6
Supplementary files format and content: tab delimited text file include sequence read counts of each sample

source_name: CD103+ cDC1

growth_protocol: In brief, bone marrow cells were isolated from murine femur and tibia by flushing the bones with RPMI using a syringe. After red blood cell lysis with hypotonic ACK buffer (ddH2O with 150mM ammonium chloride, 10mM potassium bicarbonate and 1um disodium EDTA) for 2 minutes at room temperature, 15x105 bone marrow cells/ml were incubated with GM-CSF (300pg/ml) and FLT3L (55ng/ml) in complete RPMI for 9 days. Cells were washed and reseeded in fresh medium with GM-CSF and FLT3L for 5 days. CD103+ cDC1 purified by cell sorting were used for functional assays

extract_protocol:
RNA from murine cDC1 was isolated using the NEB Monarch Total RNA Miniprep Kit.
As described previously (Macosko et al 2015), library construction for bulk 3’-sequencing of poly(A)-RNA was performed. In brief, Barcoded cDNA was produced from isolated RNA of each sample using a Maxima RT polymerase (Thermo Fisher), oligo-dT primers containing barcodes, and unique molecular identifiers (UMIs). Adaptor 5′ ends of the cDNAs were elongated using a template switch oligo (TSO). After pooling the samples, full-length cDNA was amplified using TSO site- and adaptor- specific primers. cDNA was supplemented with the Nextera XT kit (Illumina), 3′-end-fragments, as well as P5 and P7 Illumina overhangs. Barcoded cDNA libraries were sequenced using a NextSeq 500 system (Illumina). UMI tables were spawned for samples and genes using Drop-seq pipeline (https://github.com/broadinstitute/Drop-seq). We annotated reads using the GRCm38 reference genome (ENSEMBL annotation release 75). Using the DESeq2 R package (Love, Huber & Anders, 2014), differentially expressed genes were extracted. (DEGs, Log2 fold change of 1.5 and adjusted p-value (p.adj) <= 0.05).

treatment_protocol: 2x10e5 CD103+ cDC1 were seeded in 200ul RPMI supplemented with growth factors and the respective treatments for indicated periods of time.

value: bone marrow derived in vitro culture


title: PGE2+EP1antagonist_cDC1_4h_D

description: PGE2 + EP1 antagonist treated cDC1 4h


title: PGE2+EP1antagonist_cDC1_4h_B

description: PGE2 + EP1 antagonist treated cDC1 4h

value: B


title: PGE2TL_A

value: A


title: Ptgs1/Ptgs2-/-_BRAFV600E_CM_cDC1_4h_C

description: Ptgs1/Ptgs2-/- BRAFV600E CM treated cDC1 4h

value: Ptgs1/Ptgs2-/- BRAFV600E CM cDC1 4h


title: PGE2+EP1antagonist_cDC1_4h_A

description: PGE2 + EP1 antagonist treated cDC1 4h


title: TL_B

description: Untreated cDC1 24h + poly I:C activation for 4h

value: Untreated cDC1 24h + poly I:C (10microg/ml) 4h


title: Ptgs1/Ptgs2-/-_BRAFV600E_CM_cDC1_4h_D


title: TL_A


title: Dox_rep1

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

data_processing:
After obtaining raw RNA-Seq data, we first used Trimmomatic to perform sliding window trimming, cutting the average quality once within the 4-bp window falling below 20 and removing the trimmed read if it had a length less than 38. SortMeRNA (Kopylova et al., 2012) was used to filter ribosomal RNAs with default parameters. We mapped the filtered reads to the genome (genome version mm10) using STAR (Dobin et al., 2013) with parameters --outFilterScoreMinOverLread 0.1, --outFilterMatchNminOverLread 0.1, --outFilterMismatchNmax 4 and --outFilterMultimapNmax 8.
After obtaining the mapping files, we removed the duplicate reads using Picard (http://broadinstitute.github.io/picard/) with parameters MarkDuplicates and REMOVE_DUPLICATES = true. We calculated the gene read counts using FeatureCounts (Liao et al., 2014) and converted them to FPKM using the edgeR (Robinson et al., 2010) package in R language. The bigwig files of each RNA-Seq data set from the sense strand and antisense strand were obtained using bamCoverage from DeepTools with a parameter --binSize 1, --ignoreDuplicates, –minMappingQuality 255 and –normalizeUsing CPM.
For the analysis of relative gene abundance and reads signals, we constructed an in-house reference file by combing the genome assembly mm10 with drosophila genome sequence (dm6). The RNA-seq data were mapped to the in-house reference and the ratio of reads that mapped to spike-in was also calculated ((reads mapped to spike-in)/(total mappable reads)). The FPKM value of each gene and the bigwig file signals was further normalized by the corresponding ratio of spike-in. We constructed the new Exon and intron annotation files based on the RefSeq gene annotation downloaded from UCSC database. The SPI value and 3SS ratio were calculated as previously described (Herzel and Neugebauer, 2015).
Genome_build: mm10

source_name: mESC cell

growth_protocol: mESCs were cultured in 2i + LIF conditions at 37 °C in a 5% of CO2 incubator. Cells were negative for mycoplasma (tested every three months).

extract_protocol: Each RNA was extracted using Trizol reagent and coupled with Direct-zol RNA Miniprep kit according to the manufacturer’s instructions.

treatment_protocol: The cell fractionation was performed as previously described, with additional modifications. Briefly, 5 x 106 cells were gently trypsinized and collected by centrifugation. the cell pellets were rinsed twice with ice-cold 1 x PBS and then were lysed by ice-cold CE buffer (10 mM HEPES [pH 7.5], 0.1 % NP-40, 1 mM EDTA, 1 mM DTT, 60 mM KCl and 340 mM Sucrose) for 5 min on ice. The supernatant (cytoplasmic fraction) was collected by centrifugation. the nuclei pellets were gently rinsed with ice-cold 1 x PBS/1 mM EDTA then gently resuspended in ice-cold glycerol buffer (20 mM Tris-HCl [pH 7.5], 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT and 50% glycerol). Gently mix with equal volume of nuclei lysis buffer (10 mM HEPES [pH 7.5], 1.0% NP-40, 0.2 mM EDTA, 1 mM DTT, 7.5 mM MgCl2, 300 mM NaCl and 1 M urea) and incubated on ice for 3 min, then collect the supernatant (nucleoplasm fraction) by centrifugation. the chromatin pellets were gently rinsed twice with ice-cold 1 x PBS/1 mM EDTA and then dissolved with TRIzol reagents (Invitrogen) for extracting chromatin-associated RNA. The purified chromatin-associated RNA was used for RNA-seq library preparation. RNA-seq libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes. Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. The libraries were multiplexed and sequenced with 100 bp paired end (PE100) to a depth of approximately 30 million reads per library on an Illumina NovaSeq 6000.

tag: condition

value: control


title: Rpb9_degron_rep2

value: degradating Rpb9


title: TL_D


title: Dox_rep2


title: Rpb9_degron_rep1


title: PGE2_D

description: PGE2 treated cDC1 24h

value: PGE2 (1microg/ml) 24h


title: Control_BRAFV600E_CM_cDC1_4h_D

description: Control BRAFV600E CM treated cDC1 4h

value: Control BRAFV600E CM 4h


title: Ptgs1/Ptgs2-/-_BRAFV600E_CM_cDC1_4h_B


title: Control_BRAFV600E_CM_cDC1_4h_C

description: Control BRAFV600E CM treated cDC1 4h


title: DN+NaB-3

city: Chongqing

first: Hansen

last: Yang

state: Chongqing

address: No.1 Medical College Road

department: Department of Cell Biology and Genetics

country: China

institute: Chongqing Medical University

description: All.counts.txt

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCm_38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Renal cortex

growth_protocol: All mice were fed in SPF animal laboratory, and all samples were stored in liquid nitrogen before sequencing

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sample 9,10,11,12 were treated with Sodium butyrate (NaB)

value: Renal cortex

value: 12 weeks

tag: disease state

value: diabetic nephropathy

value: NaB


title: DN+NaB-4

description: All.counts.txt


title: DN+NaB-2

description: All.counts.txt


title: PGE2_C

description: PGE2 treated cDC1 24h

value: peripheral blood


title: DN+NaB-1

description: All.counts.txt


title: PGE2_B

description: PGE2 treated cDC1 24h


title: PGE2_A

description: PGE2 treated cDC1 24h


title: DN-4

description: All.counts.txt


title: PGE2TL_B

value: PGE2 (1microg/ml)  24h + poly I:C (10microg/ml) 4h


title: PGE2+EP3antagonist_cDC1_4h_C

description: PGE2 + EP3 antagonist treated cDC1 4h


title: TL_C


title: ctrl_D

description: Untreated cDC1 24h

value: D

value: none 24h


title: Ptgs1/Ptgs2-/-_BRAFV600E_CM_cDC1_4h_A

value: bone marrow derived in vitro culture


title: DN-3

description: All.counts.txt


title: Control_BRAFV600E_CM_cDC1_4h_B

description: Control BRAFV600E CM treated cDC1 4h

value: B


title: DN-2

description: All.counts.txt


title: Control_BRAFV600E_CM_cDC1_4h_A

description: Control BRAFV600E CM treated cDC1 4h

value: A


title: ctrl_A

description: Untreated cDC1 24h


title: PGE2_cDC1_4h_B

description: PGE2 treated cDC1 4h

value: PGE2 (100ng/ml) 4h


title: ctrl_B

description: Untreated cDC1 24h


title: DN-1

description: All.counts.txt


title: NC-4

description: All.counts.txt

value: normal control


title: PGE2_cDC1_4h_C

description: PGE2 treated cDC1 4h

value: C


title: NC-3

description: All.counts.txt


title: ctrl_C

description: Untreated cDC1 24h


title: CH_i35_rep2

data_processing:
After obtaining raw RNA-Seq data, we first used Trimmomatic to perform sliding window trimming, cutting the average quality once within the 4-bp window falling below 20 and removing the trimmed read if it had a length less than 38. SortMeRNA (Kopylova et al., 2012) was used to filter ribosomal RNAs with default parameters. We mapped the filtered reads to the genome (genome version hg38) using STAR (Dobin et al., 2013) with parameters --outFilterScoreMinOverLread 0.1, --outFilterMatchNminOverLread 0.1, --outFilterMismatchNmax 4 and --outFilterMultimapNmax 8.
After obtaining the mapping files, we removed the duplicate reads using Picard (http://broadinstitute.github.io/picard/) with parameters MarkDuplicates and REMOVE_DUPLICATES = true. We calculated the gene read counts using FeatureCounts (Liao et al., 2014) and converted them to FPKM using the edgeR (Robinson et al., 2010) package in R language. The bigwig files of each RNA-Seq data set from the sense strand and antisense strand were obtained using bamCoverage from DeepTools with a parameter --binSize 1, --ignoreDuplicates, –minMappingQuality 255 and –normalizeUsing CPM.
For the analysis of relative gene abundance and reads signals in different samples, we constructed an in-house reference file by combing the genome assembly hg38 with our in-house spike-in sequence ( transcribed EGFP and FireFly luciferase RNA ). The RNA-seq data of each fraction were mapped to the in-house reference and the ratio of reads that mapped to spike-in was also calculated ((reads mapped to spike-in)/(total mappable reads)). The FPKM value of each gene and the bigwig file signals was further normalized by the corresponding ratio of spike-in. We constructed the new Exon and intron annotation files based on the latest ReSeq gene annotation downloaded from UCSC. The SPI value and 3SS ratio were calculated as previously described (Herzel and Neugebauer, 2015).
Genome_build: hg38

source_name: HeLa S3 cell

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1 x penicillin-streptomycin, at 37 °C in a 5% of CO2 incubator. Cells were negative for mycoplasma (tested every three months).

tag: knock down

value: U2AF1 knock-down


title: PGE2_cDC1_4h_D

description: PGE2 treated cDC1 4h


title: Untreated_cDC1_4h_C

description: untreated control cDC1 4h

value: none 4h


title: Untreated_cDC1_4h_D

description: untreated control cDC1 4h


title: NC-2

description: All.counts.txt


title: CH_i35_rep1


title: NC-1

description: All.counts.txt


title: pcDNA-EtROP2-YFP-Flag-4

status: Public on May 26 2023

city: Nouzilly

first: Anne

last: SILVESTRE

department: Animal Health

country: France

institute: INRAE

data_processing:
Illumina NextSeq 500 sequencer was used to sequence libraries (75 bp single-ends reads). The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017). We used the RNA‐seq pipeline (v0.9.16), which is available online (https://github.com/sequana/sequana_rnaseq).
Reads were trimmed from adapters using Cutadapt (v2.10) and then mapped to the Gallus gallus genome assembly from Ensembl using STAR (v2.7.3a). FeatureCounts (v2.0.0) was used to produce the count matrix, assigning reads to features using annotation GRCg6a with strand‐specificity information.
Quality control statistics were summarized using MultiQC (v1.8). Statistical analysis on the count matrix was performed to identify differentially regulated genes, comparing cell expressed a parasite protein (EtROP2) versus empty vector samples.
Clustering of transcriptomic profiles was assessed using a principal component analysis (PCA). Differential expression testing was conducted using DESeq2 library (v1.24.0) scripts based on SARTools 1.7.0 (Varet et al, 2016) indicating the significance (Benjamini–Hochberg‐adjusted P‐values, false discovery rate FDR < 0.05) and the effect size (fold change) for each comparison.
Assembly: Gallus_gallus.GRCg6a

organism: Gallus gallus

source_name: cell line

extract_protocol:
RNA was harvested using NucleSpin RNA kit (Macherey-Nagel).
RNA preparation was used to construct strand‐specific single‐end cDNA libraries according to the manufacturers' instructions (TruSeq Stranded mRNA sample prep kit, Illumina)

value: cell line

tag: cell line

tag: cell type

value: lung epithelial cells

tag: transfected with


title: pcDNA-EtROP2-YFP-Flag-3


title: CH_iNC_rep1

value: control


title: Untreated_cDC1_4h_A

description: untreated control cDC1 4h


title: Untreated_cDC1_4h_B

description: untreated control cDC1 4h


title: PGE2_cDC1_4h_A

description: PGE2 treated cDC1 4h


title: pcDNA-EtROP2-YFP-Flag-2


title: pcDNA-EGFP-2

value: pcDNA-EGFP


title: pcDNA-EGFP-3


title: pcDNA-EtROP2-YFP-Flag-1


title: pcDNA-EGFP-1


title: Whole blood, B9, Arthritis, Day 2, replicate 2

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

data_processing:
The paired-end reads with strand-specific library (fr-firststrand) preparation of samples were aligned using HISAT2 (v2.2.1) against reference ensemble mouse genome GRCm39.
Alignment (BAM) files were further used for gene quantification using GENCODE gene annotation corresponds to GRCm39 genome. featureCounts from subread (v2.0.0) package is used for assigning high quality uniquely mapped reads to the gene features with paired-end and strand-specific parameters (-p -s 2 -B --minOverlap 10 -Q 30 --ignoreDup).
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RAW count values for each Sample

source_name: Whole blood

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen). 0.5 - 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq was performed with TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold (Illumina, San Diego, USA), following the manufacturer’s instructions.

value: Whole blood

value: Blood

tag: genotype

value: NMRI WT

value: Arthritis

tag: time

value: Day 2


title: Whole blood, B3, No arthritis, Day 2, replicate 1

value: No arthritis


title: Whole blood, A4, Arthritis, Day 2, replicate 1


title: Whole blood, A4, Arthritis, Day 2, replicate 2


title: Whole blood, B3, No arthritis, Day 2, replicate 2


title: Circadian Rhythm Disruption model PMN-MDSC-Rep1

city: Tianjin

first: Jie

last: Zhou

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Spleen

extract_protocol:
3×10^5 PMN-MDSCs from spleens of neonatal mice (PND7) were sorted and lysed in 500 μL Trizol (n=3)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pregnant mice (E10.5) were subjected to light intervention under different light schedule. The control dams were maintained in conventional 12 hours light: 12 hours dark (LD12/12). The circadian rhythm disruption (CRD) model mice were subjected to 8-hour phase advance every 2 days

tag: developmental stage

value: neonatal mice (PND7)

value: Spleen

value: primary cell

value: myeloid-derived suppressor cells

value: wild type

value: Circadian Rhythm Disruption model


title: Circadian Rhythm Disruption model PMN-MDSC-Rep3


title: Whole blood, B8, Arthritis, Day 2, replicate 2


title: Control PMN-MDSC-Rep3

value: Control group


title: Control PMN-MDSC-Rep2


title: CH_iNC_rep2


title: Circadian Rhythm Disruption model PMN-MDSC-Rep2


title: Control PMN-MDSC-Rep1


title: pcDNA-EGFP-4

value: cell line


title: Whole blood, B6, No arthritis, Day 2, replicate 2


title: Whole blood, B2, Arthritis, Day 2, replicate 1


title: Whole blood, B6, No arthritis, Day 2, replicate 1


title: Whole blood, B8, Arthritis, Day 2, replicate 1


title: Whole blood, A8, No arthritis, Day 2, replicate 2


title: Whole blood, A8, No arthritis, Day 2, replicate 1


title: Whole blood, B9, Arthritis, Day 2, replicate 1


title: Whole blood, A8, No arthritis, Day 10, replicate 2

value: Day 10


title: Whole blood, A3, No arthritis, Day 2, replicate 2


title: Whole blood, A3, No arthritis, Day 2, replicate 1


title: Whole blood, A8, No arthritis, Day 10, replicate 1


title: Whole blood, B9, Arthritis, Day 10, replicate 1


title: Whole blood, B8, Arthritis, Day 10, replicate 1


title: Whole blood, B2, Arthritis, Day 10, replicate 1


title: Whole blood, B2, Arthritis, Day 2, replicate 2


title: Whole blood, B9, Arthritis, Day 10, replicate 2


title: Whole blood, B8, Arthritis, Day 10, replicate 2


title: Whole blood, A4, Arthritis, Day 10, replicate 2


title: Whole blood, B7, No arthritis, Day 0, replicate 1

value: Day 0


title: Whole blood, B7, No arthritis, Day 0, replicate 2


title: Whole blood, B6, No arthritis, Day 10, replicate 2


title: Whole blood, A4, Arthritis, Day 10, replicate 1


title: Whole blood, A6, No arthritis, Day 0, replicate 2


title: Whole blood, A6, No arthritis, Day 0, replicate 1


title: Whole blood, B2, No arthritis, Day 0, replicate 2


title: Whole blood, B2, No arthritis, Day 0, replicate 1


title: MM-expr04-plate02-096

city: Seattle

first: Chengxiang

last: Qiu

state: WA

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

department: Genome Sciences

institute: University of Washington

description: sci-RNA-seq3 library

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

source_name: mouse embryos

growth_protocol: The mutants were generated through conventional gene editing tools and breeding or tetraploid aggregation and collected at the embryonic stage E13.5, calculated from the day of vaginal plug (noon= E0.5). Collection and whole embryo dissection was performed as previously described (Kraft et al. 2015). The embryos were immediately snap-frozen in liquid nitrogen. Each wildtype and mutant was collected consistent within the background strain (either all male or half male half female).

extract_protocol:
The snap frozen embryos were processed as previously described (Cao et al. 2019). Briefly, the frozen embryos were cut into small pieces with a blade and further dissected by resuspension in 1 ml ice cold cell lysis buffer (CLB) in a 6 cm dish. adding another 3ml CLB, the sample was strained (40 µm) into a 15 ml Falcon tube and centrifuged to a pellet (500g, 5 min). Resuspending the sample with another 1 ml CLB, the isolation of nuclei was ensured. Pelleting the isolated nuclei again (500g, 5 min) was followed by a washing step by fixation in 10 ml 4% Paraformaldehyde (PFA) for 15 minutes on ice. The fixed nuclei were pelleted (500g, 3 min) and washed twice in the nuclei suspension buffer (NSB) (500g, 5 min). The nuclei finally were resuspended in 500µl NSB and split into 2 tubes, each containing 250 µl sample. The tubes were flash frozen in liquid nitrogen, until further use for library preparation. The embryo preparation was preceded randomly for nuclei isolation in order to avoid batch effects.
The library preparation proceeded as previously described (Cao et al. 2019). In short, the fixed nuclei were permeabilized, sonicated and washed. Nuclei from each mouse embryo were then distributed into several individual wells into 4 96-well plates. We split samples into four batches (~25 samples randomly selected in each batch) for sci-RNA-seq3 processing. The ID of the reverse transcription well was linked to the respective embryo for downstream analysis. In a first step the nuclei were then mixed with oligo-dT primers and dNTP mix, denatured and placed on ice, afterwards they were proceeded for reverse transcription including a grading incubation step. After reverse transcription, the Nuclei from all wells were pooled with the nuclei dilution buffer, spun down and redistributed into 96-well plates containing the reaction mix for ligation. The ligation was proceeded for 3 h at 16 °C. Afterwards, nuclei again were pooled with nuclei suspension buffer, spun down and washed and filtered. Next, the nuclei were counted and recistributed for second strand synthesis, which was was carried out at 16 °C for 3h. Afterwards tagmentation mix was added to each well and  tagmentation was carried out for 5 minutes. Stopping the reaction, DNA binding buffer was added and the sample was incubated for another 5 minutes. Following an elution step  using AMPure XP beads and elution mix, the samples were PCR amplified. Finally after PCR amplification, the nuclei were pooled and purified using AMPure XP beads. The library was analyzed by electrophoresis and the concentration was calculated using Qubit (Invitrogen). The library was sequenced on the NovaSeq platform (Illumina) (read 1: 34 cycles, read 2: 52 cycles, index 1: 10 cycles, index 2: 10 cycles).

value: mouse embryo (E13.5)

value: C57BL/6, BALB/C, FVB, G4

value: multiplexed sample:WT and mutant


title: Whole blood, B2, Arthritis, Day 10, replicate 2

value: Whole blood

value: Blood

value: NMRI WT


title: MM-expr04-plate02-093

description: sci-RNA-seq3 library


title: EasySci-ATAC, mouse brain

city: New York

first: Junyue

last: Cao

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: EasySci-ATAC library

library_source: genomic single cell

data_processing:
EasySci-RNA data processing: A custom computational pipeline was developed to process the raw fastq files from the EasySci libraries. Similar to our previous studies10,11, the barcodes of each read pair were extracted. Both adaptor and barcode sequences were trimmed from the reads. Second, an extra trimming step is implemented using Trim Galore 60 with default settings to remove the poly(A) sequences and the low-quality base calls from the cDNA. Afterward, the paired-end sequences were aligned to the genome with the STAR aligner 61, and the PCR duplicates removed based on the UMI sequence and the alignment location. Finally, the reads are split into SAM files per cell, and the gene expression is counted using a custom script. At this level, the reads from the same cell originating from the short dT and the random hexamer RT primers were counted as independent cells. During the gene counting step, we assigned reads to genes if the aligned coordinates overlapped with the gene locations on the genome. If a read was ambiguous between genes and derived from the short dT RT primer, we assigned the read to the gene with the closest 3’ end; otherwise, the reads were labeled as ambiguous and not counted. If no gene was found during this step, we then searched for candidate genes 1000 bp upstream of the read or genes on the opposite strand. Reads without any overlapped genes were discarded.  We used a similar strategy to generate an exon count matrix across cells. Specifically, we counted the number of expressed exons based on the number of reads overlapping each exon. If one read overalpped with multiple exons, this read was split between the exons. Read overlapped with multiple genes were discarded, except if we can determine the exact gene based on the other paired-end read. For reads without overlapped genes, we checked if there are any overlapped exons on the opposite strand. Reads without any overlapped exons were discarded.    EasySci-ATAC data processing: Base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/v2.19.0.316 tolerating one mismatched base in barcodes (edit distance (ED) < 2). Downstream sequence processing were similar to sci-ATAC-seq69. Indexed Tn5 barcodes and ligation barcodes were extracted, corrected to its nearest barcode (edit distance (ED) < 2) and reads with uncorrected barcodes (ED >= 2) were removed. Tn5 adaptors were removed from 5’-end and clipped from 3’-end using trim_galore/0.4.1 60. Trimmed reads were mapped to the mouse genome (mm39) using STAR/v2.5.2b 61 with default settings. Aligned reads were filtered using samtools/v1.4.1 70 to retain reads mapped in proper pairs with quality score MAPQ > 30 and to keep only the primary aligment. Duplicates were removed by picard MarkDuplicates/v2.25.271  per PCR sample. Deduplicated bam files were converted to bedpe format using bedtools/v2.30.072, which were further converted to offset-adjusted (+4 bp for plus strand and -5 bp for minus) fragment files (.bed). Deduplicated reads were further split into constituent cellular indices by further demultiplexing reads using the Tn5 and ligation indexes. For each cell, we also created sparse matrices counting reads falling into promoter regions (±1 kb around TSS) for downstream analysis. To define peaks of accessibility, we used MACS2/v2.1.176. Nonduplicate ATAC-seq reads of cells from each main cell type were aggregated and peaks were called on each group separately with these parameters: --nomodel --extsize 200 --shift -100 -q 0.05. To correct for differences in read depth or the number of nuclei per cell type, we converted MACS2 peak scores (−log10(q-value)) to ‘score per million’77 and filtered peaks by choosing a score-per-million cut-off of 1.3. Peak summits were extended by 250bp on either side and then merged with bedtools/v2.30.0. Cells were determined to be accessible at a given peak if a read from a cell overlapped with the peak. The peak count matrix was generated by a custom python script with the HTseq package78.
Assembly: mouse reference genome (mm39)
Supplementary files format and content: Processed data files include a cell annotation csv file,  a gene annotation csv file,  and a gene count sparse matrix file for RNA data; a cell annotation csv file,  a peak annotation csv file,  a peak count sparse matrix file,  and a gene annotation csv file and a gene activity sparse matrix for ATAC data.

molecule: genomic DNA

source_name: Mouse brain

growth_protocol: The C57BL/6 WT mice and two AD models mutant mice were obtained from The Jackson Laboratory.  All animal procedures were in accordance with institutional, state, and government regulations and approved under the IACUC protocol 21049.

extract_protocol:
EasySci-RNA: Extracted mouse brains were snap-frozen in liquid nitrogen and stored at -80°C. For nuclei extraction, thawed samples were minced in 1 mL PBS (Genesee, 25-507) with 1% Diethyl Pyrocarbonate (DEPC) (VWR, 97062-652) using a blade on a 6 cm dish (Genesee, 25-260) on ice. After centrifuging for 5 minutes at 200g (4 °C), 1mL ice-cold EZ lysis buffer (Millipore Sigma, NUC101-1KT) +1% DEPC was added to the tissue (0.1g-0.5g) for nuclei extraction and kept on ice for 5 minutes. The nuclei suspension was homogenized through 40 µm cell strainers (VWR, 470236-276) with the rubber tips of syringes inside a 6-cm dish, centrifuged for 5 minutes at 500g, re-suspended in 500ul EZ lysis buffer + 0.1% SuperRnase Inhibitor (Thermo Fisher Scientific, AM2696). After repeated centrifugation for 5 minutes at 500g, the nuclei are fixed using 1mL ice-cold 0.1% Formaldehyde (Thermofisher, 28906) on ice for 10 minutes. The fixed nuclei are centrifuged for 3 minutes at 500g, resuspended in 500ul EZ buffer +  0.1% SuperRnase Inhibitor, centrifuged again for 5 minutes at 500g, and re-suspended in 500mL EZ buffer + 0.1% SuperRnase Inhibitor. After checking the nuclei morphology, the nuclei are re-suspended in 100uL nuclei suspension buffer (NSB) [Nuclei Buffer (10mM Tris-HCl, pH 7.5 (Thermo Fisher Scientific, 15567027); 10mM NaCl (Thermo Fisher Scientific, AM9759); 3mM MgCl2 (Thermo Fisher Scientific, AM9530G) in nuclease-free water (Ambion, AM 9937)) with 1% SuperRnase Inhibitor and 1% BSA (NEB, B9000S)] + 10% Dimethyl Sulfoxide (DMSO) (VWR, 97063-136) and slow frozen to -80C for storage.    EasySci-ATAC: Mouse brain samples were snap-frozen in liquid nitrogen and stored at -80°C. For nuclei extraction, thawed brain samples were minced in PBS using a blade, re-frozen and stored at -80°C, and processed in multiple batches. On the day of nuclei extraction, minced tissues were resuspended in 1 mL EZ-sci-ATAC Nuclei Buffer (EZ-sci-ATAC NB) [10 mM Tris-HCl pH 7.5 (VWR, 97062-936), 10 mM NaCl (VWR, 97062-858), 3 mM MgCl2 (VWR, 97062-848), 0.1% Tween-20 (Sigma, P9416-100ML), 1x cOmplete™, EDTA-free Protease Inhibitor Cocktail (Sigma, 11873580001)], centrifuged at 200g for 5 minutes, resuspended in EZ-sci-ATAC NB supplemented with 0.1% IGEPAL® CA-630 (VWR, IC0219859650), incubated on ice for 5 minutes, and homogenized through 40 µm cell strainers (Fisher, 22363547) with the rubber tips of syringes inside a 6-cm dish (Genesee, 25-260). The isolated nuclei were centrifuged for 5 minutes at 500g, washed with 1 mL EZ-sci-ATAC NB, and re-suspended in 1 mL EZ-sci-ATAC NB. Nuclei concentration was determined by 4',6-diamidino-2-phenylindole staining (DAPI, Invitrogen D1306) and adjusted to ~10,000 nuclei/µL. Extracted nuclei were slow-frozen in 10% final concentration of DMSO, placed in FreezeCell containers (Genesee, 27-802) and stored at -80°C.
EasySci-RNA: On the day of the library preparation, nuclei were thawed in a 37°C water bath and placed on ice immediately. After thawing, 500 μL NSB + Triton X-100 (Sigma Aldrich, 93443-100ML) is added, and the nuclei are sonicated for 12 seconds at low power. After filtering the nuclei through a 20 μm filter (PluriSelect 43-10020-70) the sample is pelletized for 5 minutes, 500 g at 4°C and resuspended in 100 μL of NSB. After nuclei counting the concentration is set to 20,000 nuclei/μL. For the reverse transcription reaction nuclei in 4 μL of NSB, 0.5 μL of 10 mM dNTP (Thermo Fisher Scientific, R0192), 1 μL 50 μM short-dT primer (100 μM, 5′-/5Phos/ACGACGCTCTTCCGATCTNNNNNNNN[10bp barcode]TTTTTTTTTTTTTTTT-3′, where “N” is any base; IDT) and 1μL 50 μM randomN primer (100 μM, 5'-/5Phos/ACGACGCTCTTCCGATCTNNNNNNNN[10bp barcode]NNNNNN-3', where "N" is any base; IDT) are distributed on every well of a 96-well plate and incubated at 55°C for 5 minutes. 3.5 μL of reverse transcription reaction mix [Maxima H Minus Reverse Transcriptase (105 μL) with Buffer (420 μL) (ThermoFisher, EP0753); 105 μL SuperRnase Inhibitor; 105 μL nuclease-free water] is added to each well and the following thermocycler program is used for the reaction: 4°C for 2 minutes, 10°C for 2 minutes, 20°C for 2 minutes, 30°C for 2 minutes, 40°C for 2 minutes, 50°C for 2 minutes, 55°C for 15 minutes. After the reverse transcription reaction, 10 μL NBB (Nuclear Buffer + 1% BSA + 0.1% Triton-X-100) is added to each well, the wells are pooled and moved into a 15 mL tube and centrifuged for 3 minutes, 1000 g at 4°C. Then the nuclei is resuspended in 1 mL NBB, moved into a 1.5 mL microcentrifuge tube, and centrifuged again for 3 minutes, 1000 g at 4°C. For the ligation reaction, the cells are resuspended in 950 μL NBB, and distributed into four PCR plates with 2.5 μL of the solution going into each well. Then 1 μL of the DNA ligation primer(100 μM, 5’-AATGATACGGCGACCACCGAGATCTACAC[10bp barcode]ACACTCTTTCCCTAC-3’, IDT) + adaptor (100 μM,5'-A*G*A*T*C*G*G*A*A*G*A*G*C*G*T*C*G*T*G*T*A*G*G*G*A*A*A*G*A*G*T*G*T*/3ddC/, IDT) complex (3.125 μM) is added with 1.5 μL of the ligation reaction mix [210 μL 10x T4 Ligation Buffer with 210 μL T4 DNA Ligase (NEB, M0202L); 21 μL SuperRnase Inhibitor; 189 μL nuclease free water] and the mixture is incubated for 30 minutes at room temperature with gentle shaking (300 rpm with Thermomixer, 50 rpm on Fisherbrand Nutating Mixer). After 30 minutes, 1 μL EDTA (18 mM) (VWR, 97062-656) is added to each well, and the wells are pooled into a 15 mL tube. After centrifuging the tube for 3 minutes, 1000 g at 4°C, the nuclei are resuspended in 1 mL NBB, centrifuged again for 3 minutes, 1000 g at 4°C, resuspended in 500 μL NBB and filtered through a 40 μM filter and centrifuged again for 3 minutes, 1000 g at 44°C and resuspended in 500 μL NBB for nuclei counting. After counting, 10,000 nuclei per well is distributed in 4 μL / well volume on a 96 well plate. The second-strand synthesis is performed by adding 1 μL enzyme-buffer mix [⅔ μL Second-Strand Synthesis buffer + ⅓ μL Second-Strand Synthesis Enzyme Mix (NEB, E7550S)] and incubating at 16°C for one hour, followed by 0.8X AMPure beads (Beckman Coulter, A63882) purification. For the tagmentation step, 6.6 μL of the tagmentase-buffer mix (Nextera N7 adaptor loaded Tn5 (provided by Illumina) or custom Tn5) is added and the solution is incubated at 55°C for 5 minutes. Next, 0.4 µL 1% SDS (ThermoFisher AM9820) and 0.4 µL BSA is added and incubated at 55°C for 15 minutes to stop the tagmentation reaction. Then, 2 μL 10% Tween-20 (Millipore Sigma, P9416-100ML) was added to quench the SDS. Following on, 1 μL of 10 μM universal P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC-3′, IDT), 1 μL of 10 μM indexed P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT) and 10 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541L) were added into each well. Amplification was carried out using the following program: 72°C for 5 minutes, 98°C for 30 seconds, 12-15 cycles of (98°C for 10 seconds, 66°C for 30 seconds, 72°C for 30 seconds) and a final 72°C for 5 minutes. Final PCR products were pooled and purified with 0.8X AMPure beads and the second round of 0.9X AMPure beads to remove primer dimers. Library concentrations were determined by Qubit and the libraries were visualized by electrophoresis on a 2% E-Gel™ EX Agarose Gels (ThermoFisher, G402002).    EasySci-ATAC: On the day of the library preparation, nuclei were thawed in a 37°C water bath and placed on ice immediately. Nuclei were washed once with EZ-sci-ATAC NB, filtered through pluriStrainer Mini 40 µm filters (Pluriselect, 43-10040-70), then concentrations were adjusted to 1000 nuclei/µL. Nuclei were mixed 1:1 ratio with 2X TD buffer [20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 20% Dimethylformamide (Fisher, AC327175000)] and dispensed 10 µL (5000 nuclei) into each well of four 96-well plates. 1 µL barcoded Tn5 was loaded into each well. Tagmentation reaction was performed at 55°C for 10 minutes with gentle shaking at 300 rpm and stopped by adding 11 µL of 2X Stop buffer [40 mM EDTA (VWR, 97062-656), 1 mM Spermidine (Sigma, S0266-1G)] to each well. Samples were pooled and washed twice by EZ-sci-ATAC NB, then resuspended in 2.2 mL EZ-sci-ATAC NB. 5 µL tagmented sample (~4400 nuclei) was distributed into each well of four 96-well plates. 2 µL indexed EZ-sci P5 ligation adapters and 3 µL ligation mix [1 µL nuclease-free water, 1 µL 10X T4 DNA ligase buffer, 1 µL T4 DNA ligase (NEB, M0202L)] were added to each well. Ligation was performed at room temperature for 30 minutes with medium-speed rocking (350g) and stopped by adding 2 µL of 18 mM EDTA to each well. After that, nuclei were pooled, washed twice by EZ-sci-ATAC NB, resuspended in 300 µL EZ-sci-ATAC NB and filtered through a pluriStrainer Mini 20 µm filter (Pluriselect, 43-10020-70). The filter was washed three times with 100 µL EZ-sci-ATAC NB for maximum recovery rate. Then, nuclei were diluted to 2000 nuclei/µL and 5 µL (10000 nuclei) was distributed into 8-well PCR strips. Proteinase K treatment was performed by mixing each well with 0.25 μL 18.9 mg/mL proteinase K (Sigma, 3115828001), 0.25 µL 1% SDS and 0.5 µL EB buffer, and plates were incubated at 65°C for 16 hours. Then, 2 μL 10% Tween-20 was added to each well to quench the SDS. Following on, 1 μL of 10 μM universal P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC-3′, IDT), 1 μL of 10 μM indexed P7 primer (5’-CAAGCAGAAGACGGCATACGAGAT[i7]GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’, IDT) and 10 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541L) were added into each well. Amplification was carried out using the following program: 72°C for 5 minutes, 98°C for 30 seconds, 11 cycles of (98°C for 10 seconds, 66°C for 30 seconds, 72°C for 30 seconds) and a final 72°C for 5 minutes. Final PCR products were pooled and purified by column purification using Zymo DNA Clean & Concentrator kit (Zymoresearch, D4014) followed by gel extraction using Zymoclean Gel DNA Recovery Kit (Zymoresearch, D4007) to remove adapter dimers. Library concentrations were determined by Qubit and the libraries were visualized by electrophoresis on a 2% E-Gel™ EX Agarose Gels (Invitrogen G402022).

value: brain

value: C57BL/6 background


title: EasySci-RNA, mouse brain

description: EasySci-RNA library


title: MM-expr04-plate02-095

description: sci-RNA-seq3 library


title: MM-expr04-plate02-094

description: sci-RNA-seq3 library


title: Whole blood, B3, No arthritis, Day 10, replicate 2

value: No arthritis


title: Whole blood, A3, No arthritis, Day 10, replicate 2


title: MM-expr04-plate02-092

description: sci-RNA-seq3 library


title: Whole blood, B8, No arthritis, Day 0, replicate 2


title: Whole blood, B6, No arthritis, Day 10, replicate 1


title: MM-expr04-plate02-090

description: sci-RNA-seq3 library


title: Whole blood, B8, No arthritis, Day 0, replicate 1


title: Whole blood, A3, No arthritis, Day 10, replicate 1


title: MM-expr04-plate02-091

description: sci-RNA-seq3 library


title: Whole blood, B3, No arthritis, Day 10, replicate 1


title: MM-expr04-plate02-089

description: sci-RNA-seq3 library


title: MM-expr04-plate02-084

description: sci-RNA-seq3 library


title: MM-expr04-plate02-083

description: sci-RNA-seq3 library


title: MM-expr04-plate02-088

description: sci-RNA-seq3 library


title: MM-expr04-plate02-086

description: sci-RNA-seq3 library


title: MM-expr04-plate02-085

description: sci-RNA-seq3 library


title: MM-expr04-plate02-087

description: sci-RNA-seq3 library


title: MM-expr04-plate02-081

description: sci-RNA-seq3 library


title: MM-expr04-plate02-082

description: sci-RNA-seq3 library


title: MM-expr04-plate02-077

description: sci-RNA-seq3 library


title: MM-expr04-plate02-079

description: sci-RNA-seq3 library


title: MM-expr04-plate02-072

description: sci-RNA-seq3 library


title: MM-expr04-plate02-080

description: sci-RNA-seq3 library


title: MM-expr04-plate02-076

description: sci-RNA-seq3 library


title: MM-expr04-plate02-074

description: sci-RNA-seq3 library


title: MM-expr04-plate02-075

description: sci-RNA-seq3 library


title: MM-expr04-plate02-071

description: sci-RNA-seq3 library


title: MM-expr04-plate02-069

description: sci-RNA-seq3 library


title: MM-expr04-plate02-063

description: sci-RNA-seq3 library


title: MM-expr04-plate02-060

description: sci-RNA-seq3 library


title: MM-expr04-plate02-064

description: sci-RNA-seq3 library


title: MM-expr04-plate02-061

description: sci-RNA-seq3 library


title: MM-expr04-plate02-070

description: sci-RNA-seq3 library


title: MM-expr04-plate02-066

description: sci-RNA-seq3 library


title: MM-expr04-plate02-067

description: sci-RNA-seq3 library


title: MM-expr04-plate02-065

description: sci-RNA-seq3 library


title: MM-expr04-plate02-059

description: sci-RNA-seq3 library


title: MM-expr04-plate02-058

description: sci-RNA-seq3 library


title: MM-expr04-plate02-056

description: sci-RNA-seq3 library


title: MM-expr04-plate02-078

description: sci-RNA-seq3 library


title: MM-expr04-plate02-054

description: sci-RNA-seq3 library


title: MM-expr04-plate02-053

description: sci-RNA-seq3 library


title: MM-expr04-plate02-055

description: sci-RNA-seq3 library


title: MM-expr04-plate02-051

description: sci-RNA-seq3 library


title: MM-expr04-plate02-052

description: sci-RNA-seq3 library


title: MM-expr04-plate02-062

description: sci-RNA-seq3 library


title: MM-expr04-plate02-050

description: sci-RNA-seq3 library


title: MM-expr04-plate02-049

description: sci-RNA-seq3 library


title: MM-expr04-plate02-046

description: sci-RNA-seq3 library


title: MM-expr04-plate02-043

description: sci-RNA-seq3 library


title: MM-expr04-plate02-048

description: sci-RNA-seq3 library


title: MM-expr04-plate02-047

description: sci-RNA-seq3 library


title: MM-expr04-plate02-044

description: sci-RNA-seq3 library


title: MM-expr04-plate02-042

description: sci-RNA-seq3 library


title: MM-expr04-plate02-038

description: sci-RNA-seq3 library


title: MM-expr04-plate02-040

description: sci-RNA-seq3 library


title: MM-expr04-plate02-041

description: sci-RNA-seq3 library


title: MM-expr04-plate02-039

description: sci-RNA-seq3 library


title: MM-expr04-plate02-036

description: sci-RNA-seq3 library


title: MM-expr04-plate02-035

description: sci-RNA-seq3 library


title: MM-expr04-plate02-031

description: sci-RNA-seq3 library


title: MM-expr04-plate02-033

description: sci-RNA-seq3 library


title: MM-expr04-plate02-034

description: sci-RNA-seq3 library


title: MM-expr04-plate02-032

description: sci-RNA-seq3 library


title: MM-expr04-plate02-030

description: sci-RNA-seq3 library


title: MM-expr04-plate02-029

description: sci-RNA-seq3 library


title: MM-expr04-plate02-073

description: sci-RNA-seq3 library


title: MM-expr04-plate02-028

description: sci-RNA-seq3 library


title: MM-expr04-plate02-027

description: sci-RNA-seq3 library


title: MM-expr04-plate02-026

description: sci-RNA-seq3 library


title: MM-expr04-plate02-025

description: sci-RNA-seq3 library


title: MM-expr04-plate02-037

description: sci-RNA-seq3 library


title: MM-expr04-plate02-024

description: sci-RNA-seq3 library


title: MM-expr04-plate02-022

description: sci-RNA-seq3 library


title: MM-expr04-plate02-023

description: sci-RNA-seq3 library


title: MM-expr04-plate02-018

description: sci-RNA-seq3 library


title: MM-expr04-plate02-016

description: sci-RNA-seq3 library


title: MM-expr04-plate02-017

description: sci-RNA-seq3 library


title: MM-expr04-plate02-015

description: sci-RNA-seq3 library


title: MM-expr04-plate02-020

description: sci-RNA-seq3 library


title: MM-expr04-plate02-021

description: sci-RNA-seq3 library


title: MM-expr04-plate02-012

description: sci-RNA-seq3 library


title: MM-expr04-plate02-013

description: sci-RNA-seq3 library


title: MM-expr04-plate02-011

description: sci-RNA-seq3 library


title: MM-expr04-plate02-010

description: sci-RNA-seq3 library


title: MM-expr04-plate02-006

description: sci-RNA-seq3 library


title: MM-expr04-plate02-005

description: sci-RNA-seq3 library


title: MM-expr04-plate02-008

description: sci-RNA-seq3 library


title: MM-expr04-plate02-009

description: sci-RNA-seq3 library


title: MM-expr04-plate02-004

description: sci-RNA-seq3 library


title: MM-expr04-plate02-007

description: sci-RNA-seq3 library


title: MM-expr04-plate02-003

description: sci-RNA-seq3 library


title: MM-expr04-plate02-001

description: sci-RNA-seq3 library


title: MM-expr04-plate02-002

description: sci-RNA-seq3 library


title: MM-expr04-plate02-019

description: sci-RNA-seq3 library


title: MM-expr04-plate02-045

description: sci-RNA-seq3 library


title: MM-expr04-plate02-014

description: sci-RNA-seq3 library


title: MM-expr04-plate01-093

description: sci-RNA-seq3 library


title: MM-expr04-plate01-094

description: sci-RNA-seq3 library


title: MM-expr04-plate01-095

description: sci-RNA-seq3 library


title: MM-expr04-plate01-089

description: sci-RNA-seq3 library


title: MM-expr04-plate01-090

description: sci-RNA-seq3 library


title: MM-expr04-plate01-092

description: sci-RNA-seq3 library


title: MM-expr04-plate01-088

description: sci-RNA-seq3 library


title: MM-expr04-plate01-085

description: sci-RNA-seq3 library


title: MM-expr04-plate01-086

description: sci-RNA-seq3 library


title: MM-expr04-plate01-087

description: sci-RNA-seq3 library


title: MM-expr04-plate01-091

description: sci-RNA-seq3 library


title: MM-expr04-plate01-079

description: sci-RNA-seq3 library


title: MM-expr04-plate01-082

description: sci-RNA-seq3 library


title: MM-expr04-plate01-081

description: sci-RNA-seq3 library


title: MM-expr04-plate01-077

description: sci-RNA-seq3 library


title: MM-expr04-plate01-075

description: sci-RNA-seq3 library


title: MM-expr04-plate01-096

description: sci-RNA-seq3 library


title: MM-expr04-plate01-076

description: sci-RNA-seq3 library


title: MM-expr04-plate01-074

description: sci-RNA-seq3 library


title: MM-expr04-plate01-072

description: sci-RNA-seq3 library


title: MM-expr04-plate02-057

description: sci-RNA-seq3 library


title: MM-expr04-plate02-068

description: sci-RNA-seq3 library


title: MM-expr04-plate01-080

description: sci-RNA-seq3 library


title: MM-expr04-plate01-071

description: sci-RNA-seq3 library


title: MM-expr04-plate01-069

description: sci-RNA-seq3 library


title: MM-expr04-plate01-070

description: sci-RNA-seq3 library


title: MM-expr04-plate01-083

description: sci-RNA-seq3 library


title: MM-expr04-plate01-084

description: sci-RNA-seq3 library


title: MM-expr04-plate01-067

description: sci-RNA-seq3 library


title: MM-expr04-plate01-078

description: sci-RNA-seq3 library


title: MM-expr04-plate01-061

description: sci-RNA-seq3 library


title: MM-expr04-plate01-066

description: sci-RNA-seq3 library


title: MM-expr04-plate01-059

description: sci-RNA-seq3 library


title: MM-expr04-plate01-060

description: sci-RNA-seq3 library


title: MM-expr04-plate01-063

description: sci-RNA-seq3 library


title: MM-expr04-plate01-065

description: sci-RNA-seq3 library


title: MM-expr04-plate01-062

description: sci-RNA-seq3 library


title: MM-expr04-plate01-055

description: sci-RNA-seq3 library


title: MM-expr04-plate01-057

description: sci-RNA-seq3 library


title: MM-expr04-plate01-064

description: sci-RNA-seq3 library


title: MM-expr04-plate01-056

description: sci-RNA-seq3 library


title: MM-expr04-plate01-073

description: sci-RNA-seq3 library


title: MM-expr04-plate01-053

description: sci-RNA-seq3 library


title: MM-expr04-plate01-054

description: sci-RNA-seq3 library


title: MM-expr04-plate01-051

description: sci-RNA-seq3 library


title: MM-expr04-plate01-052

description: sci-RNA-seq3 library


title: MM-expr04-plate01-042

description: sci-RNA-seq3 library


title: MM-expr04-plate01-048

description: sci-RNA-seq3 library


title: MM-expr04-plate01-046

description: sci-RNA-seq3 library


title: MM-expr04-plate01-045

description: sci-RNA-seq3 library


title: MM-expr04-plate01-047

description: sci-RNA-seq3 library


title: MM-expr04-plate01-044

description: sci-RNA-seq3 library


title: MM-expr04-plate01-043

description: sci-RNA-seq3 library


title: MM-expr04-plate01-041

description: sci-RNA-seq3 library


title: MM-expr04-plate01-068

description: sci-RNA-seq3 library


title: MM-expr04-plate01-050

description: sci-RNA-seq3 library


title: MM-expr04-plate01-049

description: sci-RNA-seq3 library


title: MM-expr04-plate01-040

description: sci-RNA-seq3 library


title: MM-expr04-plate01-039

description: sci-RNA-seq3 library


title: MM-expr04-plate01-028

description: sci-RNA-seq3 library


title: MM-expr04-plate01-027

description: sci-RNA-seq3 library


title: MM-expr04-plate01-037

description: sci-RNA-seq3 library


title: MM-expr04-plate01-032

description: sci-RNA-seq3 library


title: MM-expr04-plate01-030

description: sci-RNA-seq3 library


title: MM-expr04-plate01-058

description: sci-RNA-seq3 library


title: MM-expr04-plate01-029

description: sci-RNA-seq3 library


title: MM-expr04-plate01-035

description: sci-RNA-seq3 library


title: MM-expr04-plate01-036

description: sci-RNA-seq3 library


title: MM-expr04-plate01-038

description: sci-RNA-seq3 library


title: MM-expr04-plate01-031

description: sci-RNA-seq3 library


title: MM-expr04-plate01-033

description: sci-RNA-seq3 library


title: MM-expr04-plate01-034

description: sci-RNA-seq3 library


title: MM-expr04-plate01-022

description: sci-RNA-seq3 library


title: MM-expr04-plate01-021

description: sci-RNA-seq3 library


title: MM-expr04-plate01-019

description: sci-RNA-seq3 library


title: MM-expr04-plate01-020

description: sci-RNA-seq3 library


title: MM-expr04-plate01-026

description: sci-RNA-seq3 library


title: MM-expr04-plate01-025

description: sci-RNA-seq3 library


title: MM-expr04-plate01-023

description: sci-RNA-seq3 library


title: MM-expr04-plate01-015

description: sci-RNA-seq3 library


title: MM-expr04-plate01-017

description: sci-RNA-seq3 library


title: MM-expr04-plate01-016

description: sci-RNA-seq3 library


title: MM-expr04-plate01-014

description: sci-RNA-seq3 library


title: MM-expr04-plate01-018

description: sci-RNA-seq3 library


title: MM-expr04-plate01-013

description: sci-RNA-seq3 library


title: MM-expr04-plate01-012

description: sci-RNA-seq3 library


title: MM-expr04-plate01-009

description: sci-RNA-seq3 library


title: MM-expr04-plate01-011

description: sci-RNA-seq3 library


title: MM-expr04-plate01-010

description: sci-RNA-seq3 library


title: MM-expr04-plate01-008

description: sci-RNA-seq3 library


title: MM-expr04-plate01-006

description: sci-RNA-seq3 library


title: MM-expr04-plate01-024

description: sci-RNA-seq3 library


title: MM-expr04-plate01-005

description: sci-RNA-seq3 library


title: MM-expr04-plate01-003

description: sci-RNA-seq3 library


title: MM-expr04-plate01-004

description: sci-RNA-seq3 library


title: MM-expr04-plate01-002

description: sci-RNA-seq3 library


title: MM-expr04-plate01-001

description: sci-RNA-seq3 library


title: MM-expr03-plate03-096

description: sci-RNA-seq3 library


title: MM-expr03-plate03-094

description: sci-RNA-seq3 library


title: MM-expr03-plate03-093

description: sci-RNA-seq3 library


title: MM-expr04-plate01-007

description: sci-RNA-seq3 library


title: MM-expr03-plate03-092

description: sci-RNA-seq3 library


title: MM-expr03-plate03-091

description: sci-RNA-seq3 library


title: MM-expr03-plate03-087

description: sci-RNA-seq3 library


title: MM-expr03-plate03-082

description: sci-RNA-seq3 library


title: MM-expr03-plate03-090

description: sci-RNA-seq3 library


title: MM-expr03-plate03-085

description: sci-RNA-seq3 library


title: MM-expr03-plate03-086

description: sci-RNA-seq3 library


title: MM-expr03-plate03-083

description: sci-RNA-seq3 library


title: MM-expr03-plate03-081

description: sci-RNA-seq3 library


title: MM-expr03-plate03-084

description: sci-RNA-seq3 library


title: MM-expr03-plate03-088

description: sci-RNA-seq3 library


title: MM-expr03-plate03-089

description: sci-RNA-seq3 library


title: MM-expr03-plate03-080

description: sci-RNA-seq3 library


title: MM-expr03-plate03-078

description: sci-RNA-seq3 library


title: MM-expr03-plate03-079

description: sci-RNA-seq3 library


title: MM-expr03-plate03-095

description: sci-RNA-seq3 library


title: MM-expr03-plate03-077

description: sci-RNA-seq3 library


title: MM-expr03-plate03-076

description: sci-RNA-seq3 library


title: MM-expr03-plate03-075

description: sci-RNA-seq3 library


title: MM-expr03-plate03-057

description: sci-RNA-seq3 library


title: MM-expr03-plate03-059

description: sci-RNA-seq3 library


title: MM-expr03-plate03-054

description: sci-RNA-seq3 library


title: MM-expr03-plate03-066

description: sci-RNA-seq3 library


title: MM-expr03-plate03-056

description: sci-RNA-seq3 library


title: MM-expr03-plate03-062

description: sci-RNA-seq3 library


title: MM-expr03-plate03-065

description: sci-RNA-seq3 library


title: MM-expr03-plate03-064

description: sci-RNA-seq3 library


title: MM-expr03-plate03-073

description: sci-RNA-seq3 library


title: MM-expr03-plate03-070

description: sci-RNA-seq3 library


title: MM-expr03-plate03-060

description: sci-RNA-seq3 library


title: MM-expr03-plate03-074

description: sci-RNA-seq3 library


title: MM-expr03-plate03-058

description: sci-RNA-seq3 library


title: MM-expr03-plate03-067

description: sci-RNA-seq3 library


title: MM-expr03-plate03-069

description: sci-RNA-seq3 library


title: MM-expr03-plate03-053

description: sci-RNA-seq3 library


title: MM-expr03-plate03-061

description: sci-RNA-seq3 library


title: MM-expr03-plate03-063

description: sci-RNA-seq3 library


title: MM-expr03-plate03-055

description: sci-RNA-seq3 library


title: MM-expr03-plate03-072

description: sci-RNA-seq3 library


title: MM-expr03-plate03-049

description: sci-RNA-seq3 library


title: MM-expr03-plate03-052

description: sci-RNA-seq3 library


title: MM-expr03-plate03-050

description: sci-RNA-seq3 library


title: MM-expr03-plate03-051

description: sci-RNA-seq3 library


title: MM-expr03-plate03-071

description: sci-RNA-seq3 library


title: MM-expr03-plate03-048

description: sci-RNA-seq3 library


title: MM-expr03-plate03-047

description: sci-RNA-seq3 library


title: MM-expr03-plate03-068

description: sci-RNA-seq3 library


title: MM-expr03-plate03-046

description: sci-RNA-seq3 library


title: MM-expr03-plate03-021

description: sci-RNA-seq3 library


title: MM-expr03-plate03-024

description: sci-RNA-seq3 library


title: MM-expr03-plate03-027

description: sci-RNA-seq3 library


title: MM-expr03-plate03-025

description: sci-RNA-seq3 library


title: MM-expr03-plate03-019

description: sci-RNA-seq3 library


title: MM-expr03-plate03-029

description: sci-RNA-seq3 library


title: MM-expr03-plate03-020

description: sci-RNA-seq3 library


title: MM-expr03-plate03-026

description: sci-RNA-seq3 library


title: MM-expr03-plate03-028

description: sci-RNA-seq3 library


title: MM-expr03-plate03-017

description: sci-RNA-seq3 library


title: MM-expr03-plate03-018

description: sci-RNA-seq3 library


title: MM-expr03-plate03-032

description: sci-RNA-seq3 library


title: MM-expr03-plate03-035

description: sci-RNA-seq3 library


title: MM-expr03-plate03-034

description: sci-RNA-seq3 library


title: MM-expr03-plate03-040

description: sci-RNA-seq3 library


title: MM-expr03-plate03-031

description: sci-RNA-seq3 library


title: MM-expr03-plate03-033

description: sci-RNA-seq3 library


title: MM-expr03-plate03-038

description: sci-RNA-seq3 library


title: MM-expr03-plate03-041

description: sci-RNA-seq3 library


title: MM-expr03-plate03-042

description: sci-RNA-seq3 library


title: MM-expr03-plate03-036

description: sci-RNA-seq3 library


title: MM-expr03-plate03-043

description: sci-RNA-seq3 library


title: MM-expr03-plate03-037

description: sci-RNA-seq3 library


title: MM-expr03-plate03-044

description: sci-RNA-seq3 library


title: MM-expr03-plate03-039

description: sci-RNA-seq3 library


title: MM-expr03-plate03-016

description: sci-RNA-seq3 library


title: MM-expr03-plate03-030

description: sci-RNA-seq3 library


title: MM-expr03-plate03-045

description: sci-RNA-seq3 library


title: MM-expr03-plate03-023

description: sci-RNA-seq3 library


title: MM-expr03-plate03-022

description: sci-RNA-seq3 library


title: MM-expr03-plate03-010

description: sci-RNA-seq3 library


title: MM-expr03-plate03-009

description: sci-RNA-seq3 library


title: MM-expr03-plate03-015

description: sci-RNA-seq3 library


title: MM-expr03-plate02-095

description: sci-RNA-seq3 library


title: MM-expr03-plate02-088

description: sci-RNA-seq3 library


title: MM-expr03-plate03-013

description: sci-RNA-seq3 library


title: MM-expr03-plate02-090

description: sci-RNA-seq3 library


title: MM-expr03-plate02-092

description: sci-RNA-seq3 library


title: MM-expr03-plate03-003

description: sci-RNA-seq3 library


title: MM-expr03-plate03-011

description: sci-RNA-seq3 library


title: MM-expr03-plate03-001

description: sci-RNA-seq3 library


title: MM-expr03-plate03-006

description: sci-RNA-seq3 library


title: MM-expr03-plate03-012

description: sci-RNA-seq3 library


title: MM-expr03-plate03-014

description: sci-RNA-seq3 library


title: MM-expr03-plate02-091

description: sci-RNA-seq3 library


title: MM-expr03-plate03-002

description: sci-RNA-seq3 library


title: MM-expr03-plate03-004

description: sci-RNA-seq3 library


title: MM-expr03-plate02-089

description: sci-RNA-seq3 library


title: MM-expr03-plate02-093

description: sci-RNA-seq3 library


title: MM-expr03-plate02-094

description: sci-RNA-seq3 library


title: MM-expr03-plate02-086

description: sci-RNA-seq3 library


title: MM-expr03-plate02-084

description: sci-RNA-seq3 library


title: MM-expr03-plate02-085

description: sci-RNA-seq3 library


title: MM-expr03-plate02-082

description: sci-RNA-seq3 library


title: MM-expr03-plate02-087

description: sci-RNA-seq3 library


title: MM-expr03-plate02-083

description: sci-RNA-seq3 library


title: MM-expr03-plate03-005

description: sci-RNA-seq3 library


title: MM-expr03-plate02-096

description: sci-RNA-seq3 library


title: MM-expr03-plate03-007

description: sci-RNA-seq3 library


title: MM-expr03-plate03-008

description: sci-RNA-seq3 library


title: MM-expr03-plate02-080

description: sci-RNA-seq3 library


title: MM-expr03-plate02-079

description: sci-RNA-seq3 library


title: MM-expr03-plate02-077

description: sci-RNA-seq3 library


title: MM-expr03-plate02-076

description: sci-RNA-seq3 library


title: MM-expr03-plate02-075

description: sci-RNA-seq3 library


title: MM-expr03-plate02-074

description: sci-RNA-seq3 library


title: MM-expr03-plate02-072

description: sci-RNA-seq3 library


title: MM-expr03-plate02-068

description: sci-RNA-seq3 library


title: MM-expr03-plate02-070

description: sci-RNA-seq3 library


title: MM-expr03-plate02-069

description: sci-RNA-seq3 library


title: MM-expr03-plate02-073

description: sci-RNA-seq3 library


title: MM-expr03-plate02-067

description: sci-RNA-seq3 library


title: MM-expr03-plate02-064

description: sci-RNA-seq3 library


title: MM-expr03-plate02-066

description: sci-RNA-seq3 library


title: MM-expr03-plate02-065

description: sci-RNA-seq3 library


title: MM-expr03-plate02-062

description: sci-RNA-seq3 library


title: MM-expr03-plate02-060

description: sci-RNA-seq3 library


title: MM-expr03-plate02-063

description: sci-RNA-seq3 library


title: MM-expr03-plate02-061

description: sci-RNA-seq3 library


title: MM-expr03-plate02-059

description: sci-RNA-seq3 library


title: MM-expr03-plate02-057

description: sci-RNA-seq3 library


title: MM-expr03-plate02-058

description: sci-RNA-seq3 library


title: MM-expr03-plate02-056

description: sci-RNA-seq3 library


title: MM-expr03-plate02-054

description: sci-RNA-seq3 library


title: MM-expr03-plate02-081

description: sci-RNA-seq3 library


title: MM-expr03-plate02-053

description: sci-RNA-seq3 library


title: MM-expr03-plate02-052

description: sci-RNA-seq3 library


title: MM-expr03-plate02-078

description: sci-RNA-seq3 library


title: MM-expr03-plate02-055

description: sci-RNA-seq3 library


title: MM-expr03-plate02-071

description: sci-RNA-seq3 library


title: MM-expr03-plate02-051

description: sci-RNA-seq3 library


title: MM-expr03-plate02-048

description: sci-RNA-seq3 library


title: MM-expr03-plate02-049

description: sci-RNA-seq3 library


title: MM-expr03-plate02-045

description: sci-RNA-seq3 library


title: MM-expr03-plate02-046

description: sci-RNA-seq3 library


title: MM-expr03-plate02-050

description: sci-RNA-seq3 library


title: MM-expr03-plate02-037

description: sci-RNA-seq3 library


title: MM-expr03-plate02-040

description: sci-RNA-seq3 library


title: MM-expr03-plate02-038

description: sci-RNA-seq3 library


title: MM-expr03-plate02-047

description: sci-RNA-seq3 library


title: MM-expr03-plate02-036

description: sci-RNA-seq3 library


title: MM-expr03-plate02-039

description: sci-RNA-seq3 library


title: MM-expr03-plate02-043

description: sci-RNA-seq3 library


title: MM-expr03-plate02-044

description: sci-RNA-seq3 library


title: MM-expr03-plate02-041

description: sci-RNA-seq3 library


title: MM-expr03-plate02-035

description: sci-RNA-seq3 library


title: MM-expr03-plate02-034

description: sci-RNA-seq3 library


title: MM-expr03-plate02-033

description: sci-RNA-seq3 library


title: MM-expr03-plate02-032

description: sci-RNA-seq3 library


title: MM-expr03-plate02-030

description: sci-RNA-seq3 library


title: MM-expr03-plate02-031

description: sci-RNA-seq3 library


title: MM-expr03-plate02-026

description: sci-RNA-seq3 library


title: MM-expr03-plate02-027

description: sci-RNA-seq3 library


title: MM-expr03-plate02-025

description: sci-RNA-seq3 library


title: MM-expr03-plate02-023

description: sci-RNA-seq3 library


title: MM-expr03-plate02-024

description: sci-RNA-seq3 library


title: MM-expr03-plate02-042

description: sci-RNA-seq3 library


title: MM-expr03-plate02-022

description: sci-RNA-seq3 library


title: MM-expr03-plate02-021

description: sci-RNA-seq3 library


title: MM-expr03-plate02-020

description: sci-RNA-seq3 library


title: MM-expr03-plate02-017

description: sci-RNA-seq3 library


title: MM-expr03-plate02-019

description: sci-RNA-seq3 library


title: MM-expr03-plate02-018

description: sci-RNA-seq3 library


title: MM-expr03-plate02-016

description: sci-RNA-seq3 library


title: MM-expr03-plate02-008

description: sci-RNA-seq3 library


title: MM-expr03-plate02-006

description: sci-RNA-seq3 library


title: MM-expr03-plate02-015

description: sci-RNA-seq3 library


title: MM-expr03-plate02-010

description: sci-RNA-seq3 library


title: MM-expr03-plate02-014

description: sci-RNA-seq3 library


title: MM-expr03-plate02-012

description: sci-RNA-seq3 library


title: MM-expr03-plate02-011

description: sci-RNA-seq3 library


title: MM-expr03-plate02-002

description: sci-RNA-seq3 library


title: MM-expr03-plate02-004

description: sci-RNA-seq3 library


title: MM-expr03-plate02-005

description: sci-RNA-seq3 library


title: MM-expr03-plate02-003

description: sci-RNA-seq3 library


title: MM-expr03-plate02-007

description: sci-RNA-seq3 library


title: MM-expr03-plate02-001

description: sci-RNA-seq3 library


title: MM-expr03-plate02-028

description: sci-RNA-seq3 library


title: MM-expr03-plate01-095

description: sci-RNA-seq3 library


title: MM-expr03-plate01-093

description: sci-RNA-seq3 library


title: MM-expr03-plate01-091

description: sci-RNA-seq3 library


title: MM-expr03-plate01-096

description: sci-RNA-seq3 library


title: MM-expr03-plate01-094

description: sci-RNA-seq3 library


title: MM-expr03-plate01-090

description: sci-RNA-seq3 library


title: MM-expr03-plate01-092

description: sci-RNA-seq3 library


title: MM-expr03-plate01-089

description: sci-RNA-seq3 library


title: MM-expr03-plate01-086

description: sci-RNA-seq3 library


title: MM-expr03-plate01-084

description: sci-RNA-seq3 library


title: MM-expr03-plate02-013

description: sci-RNA-seq3 library


title: MM-expr03-plate01-088

description: sci-RNA-seq3 library


title: MM-expr03-plate01-085

description: sci-RNA-seq3 library


title: MM-expr03-plate01-083

description: sci-RNA-seq3 library


title: MM-expr03-plate01-081

description: sci-RNA-seq3 library


title: MM-expr03-plate02-009

description: sci-RNA-seq3 library


title: MM-expr03-plate01-087

description: sci-RNA-seq3 library


title: MM-expr03-plate01-076

description: sci-RNA-seq3 library


title: MM-expr03-plate01-071

description: sci-RNA-seq3 library


title: MM-expr03-plate01-072

description: sci-RNA-seq3 library


title: MM-expr03-plate01-074

description: sci-RNA-seq3 library


title: MM-expr03-plate01-077

description: sci-RNA-seq3 library


title: MM-expr03-plate01-079

description: sci-RNA-seq3 library


title: MM-expr03-plate01-073

description: sci-RNA-seq3 library


title: MM-expr03-plate01-080

description: sci-RNA-seq3 library


title: MM-expr03-plate01-075

description: sci-RNA-seq3 library


title: MM-expr03-plate01-070

description: sci-RNA-seq3 library


title: MM-expr03-plate01-068

description: sci-RNA-seq3 library


title: MM-expr03-plate01-078

description: sci-RNA-seq3 library


title: MM-expr03-plate01-063

description: sci-RNA-seq3 library


title: MM-expr03-plate01-060

description: sci-RNA-seq3 library


title: MM-expr03-plate01-069

description: sci-RNA-seq3 library


title: MM-expr03-plate01-066

description: sci-RNA-seq3 library


title: MM-expr03-plate01-057

description: sci-RNA-seq3 library


title: MM-expr03-plate01-065

description: sci-RNA-seq3 library


title: MM-expr03-plate01-067

description: sci-RNA-seq3 library


title: MM-expr03-plate01-056

description: sci-RNA-seq3 library


title: MM-expr03-plate01-064

description: sci-RNA-seq3 library


title: MM-expr03-plate01-062

description: sci-RNA-seq3 library


title: MM-expr03-plate01-059

description: sci-RNA-seq3 library


title: MM-expr03-plate01-054

description: sci-RNA-seq3 library


title: MM-expr03-plate01-061

description: sci-RNA-seq3 library


title: MM-expr03-plate01-053

description: sci-RNA-seq3 library


title: MM-expr03-plate01-082

description: sci-RNA-seq3 library


title: MM-expr03-plate01-052

description: sci-RNA-seq3 library


title: MM-expr03-plate01-058

description: sci-RNA-seq3 library


title: MM-expr03-plate01-051

description: sci-RNA-seq3 library


title: MM-expr03-plate01-050

description: sci-RNA-seq3 library


title: MM-expr03-plate01-048

description: sci-RNA-seq3 library


title: MM-expr03-plate01-049

description: sci-RNA-seq3 library


title: MM-expr03-plate01-047

description: sci-RNA-seq3 library


title: MM-expr03-plate01-043

description: sci-RNA-seq3 library


title: MM-expr03-plate01-046

description: sci-RNA-seq3 library


title: MM-expr03-plate01-055

description: sci-RNA-seq3 library


title: MM-expr03-plate01-041

description: sci-RNA-seq3 library


title: MM-expr03-plate01-036

description: sci-RNA-seq3 library


title: MM-expr03-plate01-038

description: sci-RNA-seq3 library


title: MM-expr03-plate01-035

description: sci-RNA-seq3 library


title: MM-expr03-plate01-045

description: sci-RNA-seq3 library


title: MM-expr03-plate01-032

description: sci-RNA-seq3 library


title: MM-expr03-plate01-042

description: sci-RNA-seq3 library


title: MM-expr03-plate01-031

description: sci-RNA-seq3 library


title: MM-expr03-plate01-037

description: sci-RNA-seq3 library


title: MM-expr03-plate01-034

description: sci-RNA-seq3 library


title: MM-expr03-plate01-030

description: sci-RNA-seq3 library


title: MM-expr03-plate01-040

description: sci-RNA-seq3 library


title: MM-expr03-plate01-029

description: sci-RNA-seq3 library


title: MM-expr03-plate01-028

description: sci-RNA-seq3 library


title: MM-expr03-plate01-044

description: sci-RNA-seq3 library


title: MM-expr03-plate01-027

description: sci-RNA-seq3 library


title: MM-expr03-plate01-026

description: sci-RNA-seq3 library


title: MM-expr03-plate01-024

description: sci-RNA-seq3 library


title: MM-expr03-plate01-039

description: sci-RNA-seq3 library


title: MM-expr03-plate01-025

description: sci-RNA-seq3 library


title: MM-expr03-plate01-023

description: sci-RNA-seq3 library


title: MM-expr03-plate01-022

description: sci-RNA-seq3 library


title: MM-expr03-plate02-029

description: sci-RNA-seq3 library


title: MM-expr03-plate01-021

description: sci-RNA-seq3 library


title: MM-expr03-plate01-020

description: sci-RNA-seq3 library


title: MM-expr03-plate01-033

description: sci-RNA-seq3 library


title: MM-expr03-plate01-019

description: sci-RNA-seq3 library


title: MM-expr03-plate01-018

description: sci-RNA-seq3 library


title: MM-expr03-plate01-017

description: sci-RNA-seq3 library


title: MM-expr03-plate01-016

description: sci-RNA-seq3 library


title: MM-expr03-plate01-015

description: sci-RNA-seq3 library


title: MM-expr03-plate01-014

description: sci-RNA-seq3 library


title: MM-expr03-plate01-009

description: sci-RNA-seq3 library


title: MM-expr03-plate01-011

description: sci-RNA-seq3 library


title: MM-expr03-plate01-008

description: sci-RNA-seq3 library


title: GBM-P45 [primary GBM]

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing:
FASTQ files were generated from raw sequencing data using Illumina BaseSpace and Illumina Local Run Manager Software.
FASTQ files were analyzed with HTG EdgeSeq parser software to generate raw counts for 2,083 miRs per sample.
Supplementary_files_format_and_content: Raw counts obtained by using HTG EdgeSeq parser software

source_name: GBM

extract_protocol:
Blood samples from NHD and cancer patients were obtained. All blood samples were collected in Streck tubes (Streck, La Vista, NE, USA) or EDTA tubes (BD vacutainers®, USA). Blood samples were processed and cryopreserved at -80°C. All plasma samples were analyzed by the HTG miR WTA.
Libraries were prepared according to Illumina instrument sequencing protocols. Probe-captured miR samples were amplified and indexed via polymerase chain reaction (PCR) using master mix (dNTP 10 mM, 5X Hemo Klentaq® Reaction buffer, Hemo Klentaq® DNA polymerase (New England Biolabs Inc., Ipswich, MA), forward, and reverse primers (HTG Molecular Diagnostics Inc., Tucson, AZ).  Following PCR, library cleanup was performed using Ampure® XP beads (Beckman Coulter Inc., Brea, CA, USA). The samples were mixed  and incubated with the beads at room temperature  for 5 min. The bead-bound libraries were then  washed twice with 80% ethanol. After washing, the samples were dried at RT for 2 min. The libraries were then  eluted off the beads with 10 mM Tris hydrochloride, pH 8.0.

treatment_protocol: Plasma samples were thawed, mixed, and analyzed using the HTG miRNA WTA following the manufactures’ recommendations.

tag: sample type

value: primary GBM


title: MM-expr03-plate01-012

description: sci-RNA-seq3 library


title: GBM-P44 [primary GBM]


title: MM-expr03-plate01-013

description: sci-RNA-seq3 library


title: MM-expr03-plate01-010

description: sci-RNA-seq3 library


title: GBM-P43 [primary GBM]


title: GBM-P41 [primary GBM]


title: GBM-P40 [primary GBM]


title: MM-expr03-plate01-005

description: sci-RNA-seq3 library


title: MM-expr03-plate01-007

description: sci-RNA-seq3 library


title: MM-expr03-plate01-006

description: sci-RNA-seq3 library


title: LNCaP-AI_siKMT5A #2,SDM + 10nM DHT_rep2

type: RNA

city: Newcastle upon Tyne

first: Kelly

last: Coffey

address: Framlington Place

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard scan protocol

data_processing: Array processing, background correction, normalisation and quality control checks were performed using the R package ‘Lumi’. Probe intensity values were converted to VSD (variance stabilized data) using variance stabilising transformation. The robust spline normalization (RSN) was used as an array normalisation method.

label: Biotin

source_name: LNCaP-AI,SDM + 10nM DHT,siKMT5A #2

label_protocol: Standard Illumina labelling protocol accompanying platform used

growth_protocol: LNCaP-AI cells were grown in RPMI 1640 media supplemented with L-Glutamine and dextran-coated charcoal stripped fetal bovine serum

extract_protocol: RNA was extracted with Trizol reagent, followed by DNase I treatment with Invitrogen DNA-free DNA removal kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser 2100.

treatment_protocol: LNCaP-AI cells were reverse transfected with 25nM siRNA targeting KMT5A in steroid depleted media for 72 hours followed by 24 hours stimulation with 10nM Dihydrotestosterone

tag: organ

value: Prostate

tag: Sex

value: Male


title: MM-expr03-plate01-004

description: sci-RNA-seq3 library


title: MM-expr03-plate01-003

description: sci-RNA-seq3 library


title: GBM-P42 [primary GBM]


title: LNCaP-AI_siKMT5A #2,SDM + 10nM DHT_rep4


title: LNCaP-AI_siKMT5A #1,SDM + 10nM DHT_rep4

source_name: LNCaP-AI,SDM + 10 nM DHT,siKMT5A #1


title: LNCaP-AI_Non-silencing, SDM + 10nM DHT_rep1

source_name: LNCaP-AI,SDM + 10 nM DHT,N/S


title: GBM-P37 [primary GBM]


title: GBM-P36 [primary GBM]


title: LNCaP-AI_siKMT5A #2,SDM + 10nM DHT_rep1


title: LNCaP-AI_siKMT5A #1,SDM_rep2

source_name: LNCaP-AI,SDM,siKMT5A #1


title: LNCaP-AI_siKMT5A #1,SDM + 10nM DHT_rep1


title: LNCaP-AI_siKMT5A #2,SDM_rep2

source_name: LNCaP-AI,SDM,siKMT5A #2


title: LNCaP-AI_Non-silencing, SDM_rep1

source_name: LNCaP-AI,SDM,N/S


title: GBM-P38 [primary GBM]


title: GBM-P33 [primary GBM]


title: GBM-P34 [primary GBM]


title: LNCaP-AI_Non-silencing, SDM_rep2


title: LNCaP-AI_Non-silencing, SDM + 10nM DHT_rep3


title: GBM-P32 [primary GBM]


title: LNCaP-AI_siKMT5A #2,SDM + 10nM DHT_rep3


title: GBM-P35 [primary GBM]


title: MM-expr02-plate02-092

description: sci-RNA-seq3 library


title: MM-expr02-plate02-094

description: sci-RNA-seq3 library


title: MM-expr03-plate01-002

description: sci-RNA-seq3 library


title: MM-expr02-plate02-095

description: sci-RNA-seq3 library


title: MM-expr02-plate02-096

description: sci-RNA-seq3 library


title: MM-expr03-plate01-001

description: sci-RNA-seq3 library


title: MM-expr02-plate02-091

description: sci-RNA-seq3 library


title: LNCaP-AI_siKMT5A #1,SDM + 10nM DHT_rep3


title: MM-expr02-plate02-089

description: sci-RNA-seq3 library


title: MM-expr02-plate02-093

description: sci-RNA-seq3 library


title: MM-expr02-plate02-088

description: sci-RNA-seq3 library


title: LNCaP-AI_Non-silencing, SDM + 10nM DHT_rep2


title: GBM-P30 [recurrent GBM]

value: recurrent GBM


title: MM-expr02-plate02-090

description: sci-RNA-seq3 library


title: MM-expr02-plate02-086

description: sci-RNA-seq3 library


title: MM-expr02-plate02-084

description: sci-RNA-seq3 library


title: MM-expr02-plate02-083

description: sci-RNA-seq3 library


title: GBM-P08 [recurrent GBM]


title: LNCaP-AI_siKMT5A #1,SDM + 10nM DHT_rep2


title: LNCaP-AI_siKMT5A #1,SDM_rep3


title: LNCaP-AI_Non-silencing, SDM_rep3


title: GBM-P01 [recurrent GBM]


title: GBM-P04 [recurrent GBM]


title: LNCaP-AI_siKMT5A #2,SDM_rep3


title: GBM-P29 [recurrent GBM]


title: MM-expr02-plate02-087

description: sci-RNA-seq3 library


title: LNCaP-AI_siKMT5A #2,SDM_rep4


title: GBM-P25 [primary GBM]


title: LNCaP-AI_Non-silencing, SDM + 10nM DHT_rep4


title: GBM-P23 [primary GBM]


title: GBM-P28 [recurrent GBM]


title: MM-expr02-plate02-077

description: sci-RNA-seq3 library


title: GBM-P26 [recurrent GBM]


title: GBM-P31 [primary GBM]


title: MM-expr02-plate02-085

description: sci-RNA-seq3 library


title: GBM-P39 [primary GBM]


title: GBM-P24 [recurrent GBM]


title: MM-expr02-plate02-075

description: sci-RNA-seq3 library


title: MM-expr02-plate02-076

description: sci-RNA-seq3 library


title: GBM-P09 [recurrent GBM]


title: MM-expr02-plate02-082

description: sci-RNA-seq3 library


title: GBM-P20 [recurrent GBM]


title: MM-expr02-plate02-081

description: sci-RNA-seq3 library


title: MM-expr02-plate02-080

description: sci-RNA-seq3 library


title: GBM-P27 [recurrent GBM]


title: MM-expr02-plate02-079

description: sci-RNA-seq3 library


title: MM-expr02-plate02-073

description: sci-RNA-seq3 library


title: MM-expr02-plate02-070

description: sci-RNA-seq3 library


title: MM-expr02-plate02-072

description: sci-RNA-seq3 library


title: MM-expr02-plate02-078

description: sci-RNA-seq3 library


title: GBM-P14 [primary GBM]


title: GBM-P13 [primary GBM]


title: MM-expr02-plate02-068

description: sci-RNA-seq3 library


title: GBM-P21 [primary GBM]


title: GBM-P22 [recurrent GBM]


title: MM-expr02-plate02-074

description: sci-RNA-seq3 library


title: GBM-P19 [primary GBM]


title: MM-expr02-plate02-065

description: sci-RNA-seq3 library


title: GBM-P18 [primary GBM]


title: GBM-P17 [primary GBM]


title: MM-expr02-plate02-071

description: sci-RNA-seq3 library


title: GBM-P05 [primary GBM]


title: GBM-P16 [primary GBM]


title: GBM-P06 [recurrent GBM]


title: GBM-P15 [primary GBM]


title: MM-expr02-plate02-061

description: sci-RNA-seq3 library


title: MM-expr02-plate02-060

description: sci-RNA-seq3 library


title: MM-expr02-plate02-057

description: sci-RNA-seq3 library


title: MM-expr02-plate02-069

description: sci-RNA-seq3 library


title: MM-expr02-plate02-064

description: sci-RNA-seq3 library


title: MM-expr02-plate02-055

description: sci-RNA-seq3 library


title: MM-expr02-plate02-067

description: sci-RNA-seq3 library


title: MM-expr02-plate02-066

description: sci-RNA-seq3 library


title: GBM-P11 [primary GBM]


title: GBM-P12 [primary GBM]


title: GBM-P03 [primary GBM]


title: MM-expr02-plate02-053

description: sci-RNA-seq3 library


title: MM-expr02-plate02-052

description: sci-RNA-seq3 library


title: GBM-P10 [primary GBM]


title: MM-expr02-plate02-063

description: sci-RNA-seq3 library


title: MM-expr02-plate02-059

description: sci-RNA-seq3 library


title: GBM-P02 [Normal - Cancer-free]

value: Normal - Cancer-free


title: MM-expr02-plate02-048

description: sci-RNA-seq3 library


title: MM-expr02-plate02-047

description: sci-RNA-seq3 library


title: MM-expr02-plate02-062

description: sci-RNA-seq3 library


title: MM-expr02-plate02-058

description: sci-RNA-seq3 library


title: GBM-P07 [primary GBM]


title: MM-expr02-plate02-056

description: sci-RNA-seq3 library


title: U2OS, IFNβ 20U/mL, 24h, Rep1

city: Dallas

first: John

last: Schoggins

state: TX

address: 6000 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

data_processing:
Raw data were first processed through fastp to remove low quality from raw data. Sequencing reads were then mapped to the human genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
DESeq2 was then used to determine genes that were differentially expressed after IFN treatment. P-values were adjusted using Benjamini-Hochberg method for controlling the False Discovery Rate (FDR). Level of gene expression was determined by using HTSeq v0.6.1 software to count the reads mapped to each gene. Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene was calculated based on gene length and read counts mapped to the corresponding gene.
Assembly: (GRCh38/hg38)
Supplementary files format and content: .txt - read counts
Supplementary files format and content: .txt - normalized read counts (fpkm)

source_name: U-2 OS

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen) following manufacturer instructions.
1 µg RNA per sample was used as input and mRNA was enriched using poly-T oligo-attached magnetic beads. Libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations.

value: U-2 OS

value: epithelial

value: IFNβ 20U/mL, 24h


title: U2OS, IFNβ 20U/mL, 24h, Rep2


title: U2OS, IFNβ 20U/mL, 6h, Rep3

value: IFNβ 20U/mL, 6h


title: U2OS, IFNβ 20U/mL, 24h, Rep3


title: U2OS, Mock, 0h, Rep1

value: Mock


title: U2OS, Mock, 0h, Rep3


title: U2OS, IFNβ 20U/mL, 6h, Rep2


title: LNCaP_RB_4xKO_50_48h_R1881

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome using STAR.v2.7.3a.
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LNCaP-RBL1/RBL2/RB1/TP53 quadruple knockout human prostate tumor cell line

extract_protocol:
Total RNA was isolated from cell line samples using the RNeasy Mini Kit (Qiagen, cat#74134) with DNase digestion.
RNA-seq libraries were constructed from total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with 10nM R1881. After 48 hours, RNA was harvested.

value: male

value: prostate cancer

tag: growth media

value: Cells were cultured in RPMI-1640, no phenol red (GIBCO, cat#11835030) with 10% FBS (GIBCO, cat#10437-02).

tag: timepoint

value: 48 hours


title: LNCaP_B72_DKO_MYC_48h_DMSO_2

source_name: LNCaP-RB1/TP53 double knockout MYC-overexpression human prostate tumor cell line

treatment_protocol: Cells were cultured for 48 hours in their normal growth media (10% FBS) with vehicle (DMSO). After 48 hours, RNA was harvested.


title: LNCaP_RB_4xKO_50_48h_DMSO


title: MM-expr02-plate02-054

description: sci-RNA-seq3 library

value: mouse embryo (E13.5)

tag: strain

value: C57BL/6, BALB/C, FVB, G4

value: multiplexed sample:WT and mutant


title: LNCaP_B72_DKO_MYC_48h_R1881_2


title: U2OS, Mock, 0h, Rep2

tag: treatment


title: MM-expr02-plate02-051

description: sci-RNA-seq3 library


title: U2OS, IFNβ 20U/mL, 6h, Rep1


title: MM-expr02-plate02-049

description: sci-RNA-seq3 library


title: LNCaP_B72_DKO_MYC_48h_R1881_1


title: LNCaP_B72_DKO_MYC_48h_DMSO_1


title: MM-expr02-plate02-046

description: sci-RNA-seq3 library


title: MM-expr02-plate02-045

description: sci-RNA-seq3 library


title: MM-expr02-plate02-050

description: sci-RNA-seq3 library


title: MM-expr02-plate02-040

description: sci-RNA-seq3 library


title: MM-expr02-plate02-044

description: sci-RNA-seq3 library


title: MM-expr02-plate02-039

description: sci-RNA-seq3 library


title: MM-expr02-plate02-037

description: sci-RNA-seq3 library


title: MM-expr02-plate02-043

description: sci-RNA-seq3 library


title: MM-expr02-plate02-042

description: sci-RNA-seq3 library


title: LNCaP_RBL2_KO_40_48h_R1881

source_name: LNCaP-RBL2 knockout human prostate tumor cell line


title: LNCaP_RBL2_KO_20_48h_DMSO


title: LNCaP_RB_4xKO_33_48h_R1881


title: LNCaP_RB_4xKO_33_48h_DMSO


title: LNCaP_RBL2_KO_40_48h_DMSO


title: MM-expr02-plate02-041

description: sci-RNA-seq3 library


title: LNCaP_RBL1_KO_32_48h_R1881

source_name: LNCaP-RBL1 knockout human prostate tumor cell line


title: LNCaP_RBL1_KO_32_48h_DMSO


title: MM-expr02-plate02-034

description: sci-RNA-seq3 library


title: LNCaP_RBL1_KO_17_48h_R1881


title: MM-expr02-plate02-035

description: sci-RNA-seq3 library


title: LNCaP_RBL2_KO_20_48h_R1881


title: MM-expr02-plate02-033

description: sci-RNA-seq3 library


title: MM-expr02-plate02-036

description: sci-RNA-seq3 library


title: MM-expr02-plate02-038

description: sci-RNA-seq3 library


title: MM-expr02-plate02-032

description: sci-RNA-seq3 library


title: MM-expr02-plate02-030

description: sci-RNA-seq3 library


title: MM-expr02-plate02-031

description: sci-RNA-seq3 library


title: LNCaP_RBL1_KO_17_48h_DMSO


title: MM-expr02-plate02-029

description: sci-RNA-seq3 library


title: leukocytes, DR group R_JS039

city: Shanghai

first: zhaoyu

last: xiang

state: Shanghai

address: No.85 Wujin Road

institute: Shanghai general hospital

description: leukocytes, DR group

data_processing:
The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).
Paired-end sequence files (fastq) were mapped to the reference genome (GRCh38.100) using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5).
The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM).
Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Assembly: GRCh38.100
Supplementary files format and content: Excel file contains the FPKM value and original read count for each Sample

source_name: Blood

growth_protocol: Blood samples were added with EDTA for anticoagulation, separated at 3000 RPM for 15min, and supernatant was obtained, preserved at -20°, and transported on dry ice.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ul of total RNA was used for the construction of sequencing libraries.
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.

tag: tissue

value: Blood

value: Leukocytes


title: leukocytes, DR group R_JS040

description: leukocytes, DR group


title: leukocytes, DR group R_JS038

description: leukocytes, DR group


title: leukocytes, DR group R_JS037

description: leukocytes, DR group


title: leukocytes, DR group R_JS035

description: leukocytes, DR group


title: leukocytes, DR group R_JS032

description: leukocytes, DR group


title: leukocytes, DR group R_JS041

description: leukocytes, DR group


title: leukocytes, DR group R_JS033

description: leukocytes, DR group


title: leukocytes, DR group R_JS034

description: leukocytes, DR group


title: MM-expr02-plate02-028

description: sci-RNA-seq3 library


title: MM-expr02-plate02-027

description: sci-RNA-seq3 library


title: leukocytes, DR group R_JS036

description: leukocytes, DR group


title: MM-expr02-plate02-025

description: sci-RNA-seq3 library


title: Nup133 KO ES cells (#319) day 3 technical replicate d

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

data_processing:
Illumina bcl2fastq 2.17.1.14 software was used for basecalling.
The analyses were performed using the Eoulsan pipeline version 2.0-alpha7, including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis: Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome from Ensembl version 81 using STAR (version 2.4.0k). Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression, Mus musculus GFF genome annotation version 81 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted and aggregated by genes using the HTSeq-count algorithm.
Assembly: mm10 version Ensembl 81
Supplementary files format and content: tab-delimited text files include transcripts counting for each Sample

source_name: Nup133 KO (merm #319)

growth_protocol: mESCs were grown at 37°C and 5% CO2 on Mitomycin-C inactivated feeder cells (DR4-mouse embryonic fibroblast) plated on 0.1% gelatin (Sigma-Aldrich) in serum/leukemia inhibitory factor (LIF, ESGRO, Millipore)-containing stem cell medium. Following trypsinization, feeders were removed by plating the resuspended cells in gelatin-free wells for 20 minutes. Feeder-free mESCs were  collected (day 0), or resuspended in N2B27 medium [Neurobasal, DMEM-F12, 7.5% BSA, N2 supplement, B27 supplement, Pen/Strep, L-glutamin, ß-mercaptoethanol] and plated at a density of 8500 cells/cm2 on gelatin-coated dishes. On day 2, cells were either collected (day 2 timepoint), or the medium was changed and supplemented with 1μM RA (all-trans-Retinoic acid, Sigma) for 24h before cell collection at day 3.

extract_protocol:
RNA extraction was performed using NucleoSpin RNAII isolation kit (Macherey-Nagel)
Library preparation and Illumina sequencing were performed at the Ecole normale superieure genomics core facility (Paris, France). Messenger (polyA+) RNAs were purified from 1 µg of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).

value: Nup133 KO (merm #319)

value: Embryonic stem cells

value: Nup133merm/merm, Sox1gfp/+, 42 Chr, XX +8 +12

value: day 3


title: Nup133 KO ES cells (#319) day 3 technical replicate c


title: MM-expr02-plate02-026

description: sci-RNA-seq3 library


title: BAT, WT-3

city: Daejeon

first: Anna

last: Park

state: Yuseong-gu

address: 125, Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Brown adipose tissue

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Wild type

value: Brown adipose tissue

tag: age


title: BAT, WT-2


title: BAT, Letmd1 KO-3

value: Letmd1 Knockout


title: BAT, WT-1


title: BAT, Letmd1 KO-1


title: BAT, Letmd1 KO-2


title: leukocytes, DR group R_JS031

description: leukocytes, DR group


title: Nup133 KO ES cells (#319) day 3 technical replicate a


title: Nup133 KO ES cells (#319) day 3 technical replicate b


title: MM-expr02-plate02-024

description: sci-RNA-seq3 library

source_name: mouse embryos


title: Nup133 KO ES cells (#319) day 2 technical replicate d

value: day 2


title: MM-expr02-plate02-023

description: sci-RNA-seq3 library


title: leukocytes, DR group R_JS029

description: leukocytes, DR group


title: leukocytes, DR group R_JS028

description: leukocytes, DR group


title: Nup133 KO ES cells (#319) day 2 technical replicate c


title: leukocytes, DR group R_JS026

description: leukocytes, DR group


title: MM-expr02-plate02-022

description: sci-RNA-seq3 library


title: MM-expr02-plate02-018

description: sci-RNA-seq3 library


title: MM-expr02-plate02-021

description: sci-RNA-seq3 library


title: MM-expr02-plate02-019

description: sci-RNA-seq3 library


title: MM-expr02-plate02-020

description: sci-RNA-seq3 library


title: Nup133 KO ES cells (#319) day 0 technical replicate a

value: day 0


title: Nup133 KO ES cells (#319) day 2 technical replicate a


title: Nup133 KO ES cells (#319) day 2 technical replicate b