title: UC249

description: 3'-biased mRNA

data_processing:
Bases were called and samples demultiplexed with an Illumina 1.8+ pipeline.
Pipeline rnaseq v1.3 https://zenodo.org/record/2610144
Alignment with STAR v2.6.1d
Feature counting with FeatureCounts from the subread package v1.6.4
for more details, see pipeline documentation
Genome_build: GRCh37
Supplementary_files_format_and_content: Comma-separated values of raw feature counts results

source_name: Whole Blood

value: UC

tag: sequencing plate number (used for batch correction)


title: H929 cells, control, bio rep3

status: Public on Jan 22 2024

type: SRA

city: Boston

first: Jiye

last: Liu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: transcriptomic

data_processing:
The RNA-Seq data were processed following the VIPER pipeline
Raw reads were aligned to the human genome (hg38) by STAR
the differential gene expression analysis was performed by limma.
The differentially expressed genes (DEGs) were defined by the log of transformed fold change greater than 1 (log2(fold change)>1) and adjusted p value less than 0.05
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample …

molecule: total RNA

organism: Homo sapiens

growth_protocol: H929 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
1ug of RNA was used to make the libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: No treatment

tag: cell line

tag: cell type

value: myeloma derived cell line

tag: genotype

value: wildtype

tag: treatment


title: CT-3

city: Chuo-ku, Kobe City, Hyogo

first: Kana

last: Uchiyama

address: 7-5-1 Kusunoki-cho

department: Department of Internal Medicine Division of Diabetes and Endocrinology

country: Japan

institute: Kobe University Graduate School of Medicine

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCm38 (mm10) whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: gastrocnemius muscle

growth_protocol: Mice were maintained on a 12-hour light/dark cycle and allowed free access to food and water.

extract_protocol:
Total RNA was extracted from the cells with the use of an RNeasy Mini Kit (Qiagen) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The mice were subjected to restraint using 50 mL tubes for 3 hours every 4 days.

tag: tissue

value: gastrocnemius muscle

value: muscle

value: wild type

value: Control_Day 4


title: lib A baseline

library_source: genomic

data_processing:
The sequence reads were trimmed to remove a constant portion of the sgRNA sequences and mapped to the GeCKO v2 genome-wide CRISPR library with MAGeCK “count” module, which computes read counts for each sgRNA. We used MAGeCK “test” module to identify CD38 expression regulators, for which targeting sgRNA were significantly enriched in the sorted cell populations compared to the control unsorted populations grown in parallel.
Assembly: hg19
Supplementary files format and content: The read count files returned from the MAGeCK
Library strategy: CRISPR screening

molecule: genomic DNA

extract_protocol:
We extracted genomic DNA from each froup population by DNeasy Blood & Tissue Kits (Qiagen)
1 step PCR to construct the barcode-indexed sequencing library for each sample


title: shNC_DMSO_1

city: Guangzhou

first: Mei

last: Song

address: Zhongshan No.2 Road 1th, Nonglin Street

country: China

institute: Sun Yat-sen University

data_processing:
Base-calling was performed with the BGISEQ-500 software.
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were alignment to the reference genome, GRCh38.p13 using HISAT2 (v2.1.0).
Bowtie2 (2.3.4.3) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: FPKM, TPM and read_count values for each sample and each gene

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (#RC112-01, Vazyme), according to manufacturer’s instructions.
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads, then fragmented. Then cDNA were sythesized, added A and adaptor ligation, and put into PCR system. Finally, PCR products were circularized and single-stranded circle DNA molecules were replicated via rolling cycle amplificationa to generate a DNA nanoball (DNB), which were then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: WT

value: DMSO


title: GL53_340_Plate3_e22_Gfi1_HE_S148

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

library_source: transcriptomic single cell

data_processing:
Raw data was aligned to the reference mouse genome using STAR aligner tool (v2.7.3)
Gene counts were extracted from BAM files using HTSeq software (v0.9.1)
Python (v3.7.3) and scanpy (v1.4.4) for data pre-processing
As QC, cells with less than 2,500 expressed genes and less than 50,000 counts were discarded, and no more than 5% mitochondrial gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated value file: scRNAseq_Cell_annotation.txt: cell sample metadata table. For each cell (row, 860 in total): cell full name, corresponding plate/well, embryo developmental stage, cell population, batch name, FACS index data for (in this order) DLL4, NOTCH2, CKIT, GFI1, CD41, NOTCH1, CD31, JAG1 and CD45. Additionally, for those cells passing the QC, UMAP coordinates and annotated cluster (Louvain method, see publication for details) are included.
Supplementary files format and content: Tab-separated value file: scRNAseq_Raw_counts.txt: full-length RNAseq (SMART-Seq2).Raw expression levels for each gene (46,170 rows) in each single cell (860 columns) as calculated using HTseq. This data is prior to conducting any QC.
Supplementary files format and content: Tab-separated value file: scRNAseq_Norm_counts_filtered.txt. Normalized expression levels after QC. Matrix comprises 30,362 rows (genes) per 775 columns (cells). Counts were normalized per cell with pp.normalize_total function from scanpy (target sum of 1e4) and values logarithmize with pp.log1p scanpy function.

source_name: AGM

growth_protocol: E10.5 and E11.5 AGMs were prepared for flow sorting

extract_protocol:
Single cells were sorted into well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol. Briefly, cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher).
Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems).

treatment_protocol: no treatments, only FACS staining

value: Hemogenic endothelium cells

value: AGM

tag: strain

value: CD1/Gf1+ (Thambyrajah et al 2015)

tag: age

value: 6-8 weeks old

tag: developmental stage

tag: population

tag: batch


title: UC248

city: Kiel

first: Florian

last: Uellendahl-Werth

address: Rosalind-Franklin-Straße 12

department: Institute of Clinical Molecular Biology (IKMB)

country: Germany

institute: Christian-Albrechts Universität zu Kiel

description: 3'-biased mRNA

extract_protocol:
PAXgene Blood RNA Kit; Pellets from PAXgene Blood RNA Tubes are washed, resuspended, and incubated in optimized buffers together with proteinase K to digest proteins. Lysates are applied to a PAXgene 96 Filter Plate and centrifuged to remove residual cell debris. Ethanol is added to the flow-through to adjust binding conditions, and the lysates are applied to a PAXgene 96 RNA Plate. RNA is selectively bound to the PAXgene 96 RNA membrane as contaminants pass through. Residual DNA is removed through a DNase I digestion on the PAXgene 96 membrane. Remaining contaminants are removed in three efficient wash steps and RNA is eluted in Buffer BR5. (from manufacturer’s guide)
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit with 50 ng RNA input. Optional “Globin Block Module” used in all samples. Poly(A) RNA is reverse transcribed with poly(T)-Primers. RNA is digested and the second strand is synthesized by random priming. cDNA is purified. Illumina adapters are added. The PCR was run with 15 cycles.

tag: disease


title: ST2flox/floxMx1Cre, leukemia stem cells_2, Day 21

city: Charleston

first: Sophie

last: Paczesny

state: South Carolina

address: 86 Jonathan Lucas Street

department: Microbiology & Immunology

institute: Medical University of South Carolina

data_processing:
Reads were aligned to mouse genome assembly mm10 by STAR and quantified to annotation model (Partek E/M) using mm10
Differential expression analysis comparing ST2f/f MxCre- to ST2f/f Mx1Cre+ MLL-AF9eGFP LSCs were performed by DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Bone Marrow

extract_protocol:
RNA was havested with a Promega Maxwell RSC 16 using the Maxwell RSC simplyRNA Cells kit (Cat# AS1390)
RNA libraries for RNA-seq were prepared using the New England Biolabs NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# 7490L) and Ultra II Directional RNA Library Prep Kit for Illumina (Cat# 7760L) according to the manufacturer’s instructions

treatment_protocol: ST2 deletion in leukemia stem cells was induced by 7-doses of polyinosinic:polycytidylic acid (pIpC) injection post-AML challenge.

value: Bone Marrow

value: Leukemia stem cells

value: ST2 knockout

value: no treatment


title: ST2flox/flox, leukemia stem cells_2, Day 21


title: ST2flox/floxMx1Cre, leukemia stem cells_3, Day 21


title: ST2flox/flox, leukemia stem cells_4, Day 21


title: ST2flox/floxMx1Cre, leukemia stem cells_1, Day 21


title: ST2flox/flox, leukemia stem cells_1, Day 21


title: UC247

description: 3'-biased mRNA

value: UC


title: GL53_339_Plate3_d22_Gfi1_HE_S147


title: ST2flox/floxMx1Cre, leukemia stem cells_4, Day 21


title: UC246

description: 3'-biased mRNA


title: ST2flox/flox, leukemia stem cells_3, Day 21


title: GL53_338_Plate3_c22_Gfi1_HE_S146


title: con-2

first: Zhiliang

last: Jing

address: Nr. 1023–1063 Sha tai South Road

institute: Southern Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: subcutaneous tumor

extract_protocol:
Total RNA was extracted from cell by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: subcutaneous tumor

value: colon carcinoma

value: control

value: BALB/c


title: GL53_336_Plate3_d21_Gfi1_HE_S144


title: UC244

description: 3'-biased mRNA


title: con-3


title: con-1


title: IFN-2

value: IFN-gamma stimulation


title: UC243

description: 3'-biased mRNA


title: GL53_337_Plate3_b22_Gfi1_HE_S145


title: UC245

description: 3'-biased mRNA


title: KSP5D24 reanalysis

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

description: re-analysis of GSE165355

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to mouse genome annotation mm11 using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Assembly: ENSMBL mm11 release-104, Genome: Musmusculus.GRCm39.104
Supplementary files format and content: txt matrix with log2 normalized values per sample.

source_name: lung

extract_protocol:
Whole lung RNA was extracted using Rneasy Midi kit from Qiagen. Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
The RNA sequencing library was generated from 500 ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher) for mRNA purification followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs).
The libraries were treated with Illumina Free Adapter Blocking and  were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (300 cycles, paired end run 2x 150 bp) with an average of 6 x107 reads per RNA sample.

treatment_protocol: Lungs were collected from mice

value: lung

value: INF


title: KSP5D23 reanalysis

description: re-analysis of GSE165355


title: GL53_335_Plate3_c21_Gfi1_HE_S143


title: KSP5D25 reanalysis

description: re-analysis of GSE165355


title: KSP5D22 reanalysis

description: re-analysis of GSE165355


title: UC242

description: 3'-biased mRNA


title: UC241

description: 3'-biased mRNA


title: IFN-3

value: WT


title: GL53_334_Plate3_b21_Gfi1_HE_S142

value: Hemogenic endothelium cells


title: KSP5B64 reanalysis

description: re-analysis of GSE165355


title: KSP5B63 reanalysis

description: re-analysis of GSE165355


title: KSP5D21 reanalysis

description: re-analysis of GSE165355


title: GL53_333_Plate3_a21_Gfi1_HE_S141

value: AGM


title: KSP5B65 reanalysis

description: re-analysis of GSE165355


title: UC240

description: 3'-biased mRNA


title: IFN-1


title: GL53_332_Plate3_o20_Gfi1_neg_IAHC_S140

description:
SMART-Seq2
Not included in final analysis

value: Hematopoietic cells

value: CD1/Gf1+ (Thambyrajah et al 2015)


title: KSP5B62 reanalysis

description: re-analysis of GSE165355


title: KSP5B61 reanalysis

description: re-analysis of GSE165355


title: UC239

description: 3'-biased mRNA


title: KSP3D25 reanalysis

description: re-analysis of GSE165355


title: KSP3D24 reanalysis

description: re-analysis of GSE165355


title: GL53_330_Plate3_l20_Gfi1_neg_IAHC_S138

value: 6-8 weeks old


title: GL53_329_Plate3_k20_Gfi1_neg_IAHC_S137


title: KSP3D23 reanalysis

description: re-analysis of GSE165355


title: GL53_328_Plate3_j20_Gfi1_pos_IAHC_S136


title: UC238

description: 3'-biased mRNA


title: KSP3D22 reanalysis

description: re-analysis of GSE165355


title: KSP3D21 reanalysis

description: re-analysis of GSE165355


title: UC237

description: 3'-biased mRNA


title: UC236

description: 3'-biased mRNA


title: KSP3B63 reanalysis

description: re-analysis of GSE165355


title: GL53_331_Plate3_m20_Gfi1_neg_IAHC_S139


title: KSP3B64 reanalysis

description: re-analysis of GSE165355


title: KSP3B65 reanalysis

description: re-analysis of GSE165355


title: KSP3B62 reanalysis

description: re-analysis of GSE165355


title: GL53_326_Plate3_h20_Gfi1_pos_IAHC_S134


title: GL53_327_Plate3_i20_Gfi1_pos_IAHC_S135


title: KSMD25 reanalysis

description: re-analysis of GSE165355

value: MOCK


title: UC233

description: 3'-biased mRNA


title: KSMD24 reanalysis

description: re-analysis of GSE165355


title: UC234

description: 3'-biased mRNA


title: KSMD22 reanalysis

description: re-analysis of GSE165355


title: GL53_325_Plate3_g20_Gfi1_pos_IAHC_S133


title: UC232

description: 3'-biased mRNA


title: KSMD21 reanalysis

description: re-analysis of GSE165355


title: KSMB65 reanalysis

description: re-analysis of GSE165355


title: GL53_324_Plate3_h19_Gfi1_pos_IAHC_S132


title: UC231

description: 3'-biased mRNA


title: UC235

description: 3'-biased mRNA


title: KSMB64 reanalysis

description: re-analysis of GSE165355


title: KSMB63 reanalysis

description: re-analysis of GSE165355


title: GL53_323_Plate3_g19_Gfi1_pos_IAHC_S131


title: GL53_322_Plate3_f19_Gfi1_pos_IAHC_S130


title: UC229

description: 3'-biased mRNA


title: KSP3B61 reanalysis

description: re-analysis of GSE165355


title: UC230

description: 3'-biased mRNA


title: KSMB61 reanalysis

description: re-analysis of GSE165355


title: UC227

description: 3'-biased mRNA


title: HTO

city: Bunkyo-ku, Tokyo

first: YUKI

last: YONEMOTO

address: 1-5-45 Yushima

institute: Tokyo Medical And Dental University

description:
10xGenomics
Tcells-totalseqC

library_source: other

data_processing:
The Cell Ranger software v.7.0.1 (10x Genomics) was used to perform barcode counting and unique molecular identifier counting after filtering and alignment to the mouse / mm10 reference genome to generate the feature-barcode matrix and determine clusters.
Assembly: mm10
Supplementary files format and content: CellRanger output files: GEX_barcodes.tsv.gz, GEX_features.tsv.gz, GEX_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: TCR_filtered_contig_annotations.csv

molecule: protein

source_name: T cells

extract_protocol:
SI-IELs or SP cells were collected and pooled from young (6-week-old) or old C57BL/6 mice (80-week-old), the cells from 3 young mice and 3 old mice were mixed and pooled as young SP, young IEL, old SP and old IEL. CD45+ cells were enriched from each group using CD45 microbeads (Miltenyi Biotec), followed by cell hashing with TotalSeq-C anti-mouse hashtag antibodies (hashtag1-young IEL, hashtag2-old IEL, hashtag3-young SP, hashtag4-old SP). After the Fc blocking, cells were stained with anti-CD3e-FITC mAbs and anti-CD4-APC mAbs, and the CD3+ cells and CD3+CD4+ cells were sorted from each group by FACSMelody. Dead cells removal was performed with 7-AAD. To enrich CD4+ cells, which are rare population in young IEL, CD3+ cells and CD3+CD4+ cells were mixed as 1:1 in young and old IEL.
Cell suspension (6,000 cells each) was loaded in a 10x Chromium microfluidics system based on the manufacturer’s guidelines. One set of libraries were obtained from the 10x loaded samples: a 5’ gene expression messenger RNA library and a single-cell TCR library, using primers for amplification as per the manufacturer’s instructions. Library were pooled together and run separate lanes of 150 base-paired, paired-end, flow cell using the Illumina Novaseq6000.

value: T cells


title: GEX

description:
10xGenomics
Tcells-GEX


title: KSMD23 reanalysis

description: re-analysis of GSE165355


title: KSMB62 reanalysis

description: re-analysis of GSE165355


title: Young SP_scRNAseq

description:
10xGenomics
Hashtag_3

source_name: spleen

value: spleen

tag: Sex

value: male

value: 6 weeks old


title: Old IEL_scRNAseq

description:
10xGenomics
Hashtag_2

source_name: small intestine

value: small intestine

value: 80 weeks old


title: TCR

description:
10xGenomics
Tcells-TCR


title: Old SP_scRNAseq

description:
10xGenomics
Hashtag_4


title: UC228

description: 3'-biased mRNA

value: UC


title: GL53_321_Plate3_e19_Gfi1_HE_S129


title: UC226

description: 3'-biased mRNA


title: GL53_319_Plate3_c19_Gfi1_HE_S127


title: UC224

description: 3'-biased mRNA


title: young IEL_scRNAseq

description:
10xGenomics
Hashtag_1


title: GL53_316_Plate3_o18_Gfi1_neg_IAHC_S124


title: GL53_318_Plate3_b19_Gfi1_HE_S126


title: WGA purified sample, Differentiated HOXB8 cells [small RNA]

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St.

department: Yale Stem Cell Center

institute: Yale University

data_processing:
Fastq files were processed using a modified pipeline based on miRDeep2.
Fastq files were first converted to fasta files. Illumina adaptor sequences were removed from the reads. Reads shorter than 16 nt were removed.
Reads were mapped to RNAcentral databased release 20. Unmapped reads were then mapped to mouse genome assembly mm10.
Reads were then used to calculate reads per million mapped reads.
For sequences whose total read counts across all samples were fewer than 100, they were not included in the final processed file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPM values for each sequence and each sample

source_name: HOXB8 cell line

growth_protocol: Bone marrow neutrophils were freshly isolated from wildtype mice. HOXB8 cells were cultured in RPMI medium (Thermo Fisher) with 10% FBS (Thermo Fisher) and 1% penicillin-streptomycin and glutamine (Thermo Fisher), supplemented with 1 μM β-estradiol (Sigma) and 100 ng/ml recombinant murine SCF (Peprotech).

extract_protocol:
RNA was harvested using TRIzol. For input samples, small RNAs less than 300 nt were purified on an acrylamide gel. For biotin samples, RNAs were reacted with DBCO-PEG4-biotin and purified using streptavidin beads. For WGA samples, RNAs were purified using WGA beads. For PNG samples, purfiied RNAs were digested with PNGase F.
Small RNA libraries were prepared according to procedures in Illumina TruSeq small RNA library kit.

treatment_protocol: For differentiation of HOXB8 cells, cells were washed three times with PBS, and cultured in differentiation medium (same as growth medium but without β-estradiol). Cells were labeled with Ac4ManNAz at a final concentration of 100 μM in the culture medium supplemented with Gal and GalNAc at 10 μM and 100 μM, respectively. Treatment was performed for 36 hours.

value: HOXB8 cell line

value: Differentiated


title: Input sample, Differentiated HOXB8 cells [small RNA]


title: Biotin purified sample, Differentiated HOXB8 cells [small RNA]


title: WGA purfiied sample, primary neutrophils [small RNA]

source_name: Bone marrow neutrophils

value: Bone marrow neutrophils


title: GL53_315_Plate3_n18_Gfi1_neg_IAHC_S123


title: WGA purified sample, HOXB8 cells [small RNA]

value: Undifferentiated


title: Biotin purified sample, HOXB8 cells [small RNA]


title: Input sample, HOXB8 cells [small RNA]


title: psi

city: Beijing

first: Wen

last: Zhang

address: 38 Xueyuan Rd

institute: Peking University

description: one sample from OFC of the brains treated with psilocybin

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: brain

extract_protocol:
Single nuclei were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
single nucleus RNA-seq; RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: brain

value: psilocybin


title: UC220

description: 3'-biased mRNA


title: GL53_313_Plate3_l18_Gfi1_neg_IAHC_S121

value: Hematopoietic cells

value: AGM


title: Input sample, primary neutrophils [small RNA]


title: UC225

description: 3'-biased mRNA


title: GL53_312_Plate3_l17_Gfi1_neg_IAHC_S120

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: 6-8 weeks old


title: GL53_317_Plate3_a19_Gfi1_HE_S125

value: Hemogenic endothelium cells


title: Biotin purfied and PNGase digested sample, Differentiated HOXB8 cells [small RNA]


title: GL53_311_Plate3_k17_Gfi1_pos_IAHC_S119


title: GL53_320_Plate3_d19_Gfi1_HE_S128


title: UC217

description: 3'-biased mRNA


title: GL53_310_Plate3_j17_Gfi1_pos_IAHC_S118


title: UC223

description: 3'-biased mRNA


title: GL53_309_Plate3_i17_Gfi1_pos_IAHC_S117


title: GL53_314_Plate3_m18_Gfi1_neg_IAHC_S122


title: UC222

description: 3'-biased mRNA


title: UC216

description: 3'-biased mRNA


title: UC221

description: 3'-biased mRNA


title: Classical mono_03

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

institute: Institute of Science Tokyo

data_processing:
Single-end Fastq files (R1: reverse complement of 5prime region of cDNA) of sample Miyake18 were processed as follows.
Adapter trimming of sequencing data was performed by using cutadapt 4.1, and trimmed reads were mapped to reference RNA (build GRCm38 release-101) by using bowtie2-2.4.5 by the following parameters: -p 8 -N 1 -L 16 –very-sensitive-local –seed 656565 –nofw.
Then, read counts of each gene in each samples were counted by using awk, sort, and uniq -c commands.
Resulted gene-expression count data was summarized by same Gene Symbol and all of the expression table was full-outer joined by Gene Symbol by using dplyr-1.0.7 package.
Supplementary files format and content: GRCm38 release-101
Supplementary files format and content: Tab-separated count values

source_name: skin

extract_protocol:
On day 5 post-challenge, mice ears were cut into small pieces by razors, followed by tissue dissociation by using Multi Tissue Dissociation Kit 1 and gentleMACS Octo Dissociator with Heaters according to the protocol for the program named 37C_WSDK_2. Cells were then subjected to FACS sorting and four Mo-Mac subpopulations (Ly6ChiPD-L2lo, Ly6ChiPD-L2hi, Ly6CloPD-L2hi and Ly6CloPD-L2lo) were isolated.
Total RNA was lysed from 5,000-80,000 isolated Mo-Mac cells by using lithium dodecyl sulfate-based lysis/storage buffer. mRNA was isolated from total RNA by Dynabeads M-270 streptavidin with biotin-oligo (dT)25 (Thermo Fisher Scientific). First- and second-strand cDNA synthesis was performed by Superscript reverse transcriptase IV (Thermo Fisher Scientific) and Kapa HiFi DNA polymerase (Roche). Whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs, catalog #: E7805). Ligated products were purified and performed the barcoding PCR. Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer (Illumina) and NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles) (Illumina).

treatment_protocol: IgE-CAI was elicited as described previously (Egawa et al. Immunity 2013). In brief, mice were sensitized with intravenous injection of 300 μg of anti-TNP IgE, and on the following day challenged with an intradermal injection of 10 μg TNP12-conjugated ovalbumin (OVA) and control OVA into the right and left ear, respectively.

value: skin

value: BALB/c

value: monocytes and macrophages

value: WT

tag: cell subtype

value: Classical mono


title: Resident-like_03

value: Resident-like


title: Late CMDM_02

value: Late CMDM


title: UC219

description: 3'-biased mRNA

value: UC


title: Classical mono_01


title: Late CMDM_03


title: GL53_308_Plate3_h17_Gfi1_pos_IAHC_S116


title: Early CMDM_01

value: Early CMDM


title: Early CMDM_03


title: UC218

description: 3'-biased mRNA


title: Late CMDM_01


title: GL53_307_Plate3_g17_Gfi1_pos_IAHC_S115


title: Early CMDM_02


title: UC215

description: 3'-biased mRNA


title: Classical mono_02


title: Resident-like_01


title: Resident-like_02


title: sal

description: one sample from OFC of the brain from mice treated with saline

value: saline


title: UC214

description: 3'-biased mRNA


title: Colon tissue, DSS, Day 8 rep3

city: Huai'an

first: Honggang

last: Wang

state: Jiangsu

address: No.1 Huanghe West Road

institute: The Affiliated Huai’an No.1 People’s Hospital of Nanjing Medical University

data_processing:
Trimmomatic,v0.33
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this  step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing  ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence  duplication level of the clean data were calculated. All the downstream analyses were based on clean  data with high quality
STAR v2.5.2b
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw  sequences were transformed into clean reads after data processing. These clean reads were then  mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were  further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map  with reference genome.
DESeq2, padj<0.05
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes counts for each Sample

source_name: Colon

extract_protocol: Total RNA was extracted from inflammatory colonic tissue. For sequencing, a 1 cm section of colon tissue was sampled from a site approximately 2 cm from the anus.

value: Colon

value: DSS


title: GL53_306_Plate3_f17_Gfi1_pos_IAHC_S114

value: Hematopoietic cells


title: Colon tissue, DSS, Day 8 rep4


title: Colon tissue, DSS, Day 8 rep2


title: Colon tissue, Control, Day 0 rep3

value: CON

value: Water


title: GL53_305_Plate3_e17_Gfi1_HE_S113

value: AGM

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: 6-8 weeks old


title: Colon tissue, DSS, Day 8 rep1


title: Colon tissue, Control, Day 0 rep4


title: GL53_304_Plate3_d17_Gfi1_HE_S112

value: Hemogenic endothelium cells


title: UC211

description: 3'-biased mRNA


title: GL53_301_Plate3_a17_Gfi1_HE_S109


title: Colon tissue, Control, Day 0 rep2


title: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, transduced with AAV-hSyn-V5-SATB2, 1h bic, rep2

city: Innsbruck

first: Nico

last: Wahl

address: Innrain 66

department: Institute for Neuroscience

country: Austria

institute: Medical University Innsbruck

data_processing:
Pair-end fastq files were mapped using STAR v2.7.6a. Resulting bamfiles were sorted and indexed using samtools v1.11 followed by bigWig generation using deeptools v3.3.3. Next, bamfiles were used to generate a count matrix using featureCounts subread v2.0.1.
Count data was normalized using RUVseq and further processed using DeSeq2, RRHO was generated using normalized count data after RUVseq
Assembly: mm10
Supplementary files format and content: txt

source_name: Cortex

growth_protocol: Corical tissue was dissected at P0-P1, dissociated with Papain and titurated. Cells were plated in serum-containing medium (MEM, 1% horse serum, 0.1% Pen/Strep, 0.1 % sodium piruvate). After 2h, MEM was excahnged with serum-free feeding medium (Neurobasal-A Medium, containing B-27, 0.1% Pen/Strep and 2 mM Glutamine.  Cells were treated with 5µM cytosine arabinoside on DIV3 to inhibit glial cell proliferation.  At DIV4, one third of the medium was replaced by fresh serum-free feeding medium and cells were transduced with AAV at a MOI of 33000. Neurons were cultured for 14 days in 5% CO2 at 37°C.

extract_protocol:
Cells were lysed in Trizol and total RNA was extracted using the Purelink RNA Micro Kit according to the manufacturers protocol. Quantification was carried out using Qubit and RNA integrity was analyzed on a Agilent Tapestation.
Libraries were prepared by Novogene

treatment_protocol: Cortical neurons were treated with AAV MOI 33000 on DIV4. 20 µM NBQX for 16 h on DIV13. After silencing, neurons were stimulated with 50 µM biccuculine for 1h on DIV14 and then collected.

value: Cortex

value: DIV14 primary cortical cultures

value: Satb2 flx/flx::Nes-Cre

value: 1h bicucculine, AAV-hSyn-V5-SATB2


title: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, transduced with AAV-hSyn-V5-SATB2, 1h bic, rep4


title: UC210

description: 3'-biased mRNA


title: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, transduced with AAV-hSyn-V5-SATB2, 1h bic, rep3


title: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, transduced with AAV-hSyn-GFP, 1h bic, rep4

value: 1h bicucculine, AAV-hSyn-GFP


title: UC208

description: 3'-biased mRNA

value: UC


title: UC207

description: 3'-biased mRNA


title: UC213

description: 3'-biased mRNA


title: GL53_299_Plate3_c16_Gfi1_HE_S107


title: UC209

description: 3'-biased mRNA


title: UC212

description: 3'-biased mRNA


title: UC206

description: 3'-biased mRNA


title: Colon tissue, Control, Day 0 rep1


title: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, transduced with AAV-hSyn-GFP, 1h bic, rep1


title: Satb2 flx/flx DIV14 primary cortical cultures, transduced with AAV-hSyn-GFP, 1h bic, rep4

value: Satb2 flx/flx


title: GL53_302_Plate3_b17_Gfi1_HE_S110


title: GL53_297_Plate3_a16_Gfi1_HE_S105


title: GL53_303_Plate3_c17_Gfi1_HE_S111


title: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, transduced with AAV-hSyn-V5-SATB2, 1h bic, rep1


title: Satb2 flx/flx DIV14 primary cortical cultures, transduced with AAV-hSyn-GFP, 1h bic, rep1


title: GL53_298_Plate3_b16_Gfi1_HE_S106


title: Satb2 flx/flx DIV14 primary cortical cultures, transduced with AAV-hSyn-GFP, 1h bic, rep2


title: UC205

description: 3'-biased mRNA


title: GL53_300_Plate3_d16_Gfi1_HE_S108


title: UC204

description: 3'-biased mRNA


title: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, transduced with AAV-hSyn-GFP, 1h bic, rep2


title: GL53_296_Plate3_o15_Gfi1_neg_IAHC_S104


title: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, transduced with AAV-hSyn-GFP, 1h bic, rep3


title: UC203

description: 3'-biased mRNA


title: GL53_295_Plate3_n15_Gfi1_neg_IAHC_S103


title: UC202

description: 3'-biased mRNA


title: GL53_294_Plate3_m15_Gfi1_neg_IAHC_S102


title: K4-Mg-48hr

city: Research Triangle Park

first: Paula

last: Stein

state: NC

address: 111 T.W. A;exander Dr.

department: Reproductive and Developmental Biology Laboratory

institute: NIEHS

description: rescue.counts.tsv.gz

data_processing:
Adapter and low-quality tails were removed from sequenced reads using Cutadapt v3.7
Reads were allignmened to the reference genome using STAR v2.6.0c
RNA counts were quantified using uniquely mapped reads only with feature Counts v1.6.3
Assembly: mm10 with GENECODE GRCm38vM17
Supplementary files format and content: compressed gene x sample count matrix.

source_name: morula

extract_protocol:
RNA was sequenced from eggs or embryos from the 1-cell to the blastocyst stage. Four biological replicates at each stage for each group were sequenced. Each biological replicate consisted of five eggs or embryos. Following collection as described, eggs and embryos were washed in sterile PBS and snap-frozen on dry ice. RNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, Japan), and cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter). RNA quality and yield were measured using the Agilent 2100 Bioanalyzer (Agilent Technologies).
Library preparation was carried out on 100-150 pg amplified cDNA using the Illumina DNA Prep (Illumina, San Diego, CA). Sequencing was performed on a NovaSeq 6000 Sequencing System (Illumina).

value: morula

value: Trpm7 -/-

value: 10 mM MgSO4


title: K4-24hr

description: rescue.counts.tsv.gz

source_name: 8-cell embryo

value: 8-cell embryo


title: K4-48hr

description: rescue.counts.tsv.gz


title: K3-Mg-48hr

description: rescue.counts.tsv.gz


title: K3-Mg-24hr

description: rescue.counts.tsv.gz


title: K3-48hr

description: rescue.counts.tsv.gz


title: GL53_293_Plate3_l15_Gfi1_neg_IAHC_S101

value: Hematopoietic cells


title: UC201

description: 3'-biased mRNA

source_name: Whole Blood


title: UC200

description: 3'-biased mRNA


title: K3-24hr

description: rescue.counts.tsv.gz


title: GL53_292_Plate3_k15_Gfi1_pos_IAHC_S100


title: K2-Mg-24hr

description: rescue.counts.tsv.gz


title: K2-48hr

description: rescue.counts.tsv.gz


title: UC199

description: 3'-biased mRNA


title: GL53_291_Plate3_j15_Gfi1_pos_IAHC_S99


title: UC198

description: 3'-biased mRNA


title: K4-Mg-24hr

description: rescue.counts.tsv.gz


title: GL53_290_Plate3_i15_Gfi1_pos_IAHC_S98


title: UC197

description: 3'-biased mRNA


title: K2-24hr

description: rescue.counts.tsv.gz


title: K1-Mg-48hr

description: rescue.counts.tsv.gz


title: K1-Mg-24hr

description: rescue.counts.tsv.gz


title: GL53_289_Plate3_h15_Gfi1_pos_IAHC_S97


title: K1-48hr

description: rescue.counts.tsv.gz


title: UC196

description: 3'-biased mRNA


title: C4-48hr

description: rescue.counts.tsv.gz


title: GL53_288_Plate3_k14_Gfi1_pos_IAHC_S288


title: UC195

description: 3'-biased mRNA


title: C3-48hr

description: rescue.counts.tsv.gz


title: K2-Mg-48hr

description: rescue.counts.tsv.gz


title: C2-24hr

description: rescue.counts.tsv.gz


title: C3-24hr

description: rescue.counts.tsv.gz


title: C1-48hr

description: rescue.counts.tsv.gz


title: UC194

description: 3'-biased mRNA


title: UC192

description: 3'-biased mRNA


title: Satb2 flx/flx DIV14 primary cortical cultures, transduced with AAV-hSyn-GFP, 1h bic, rep3


title: UC193

description: 3'-biased mRNA


title: INS5_rep3

city: Tokyo

first: Stéphane

last: Poulain

address: Fw-203, 4-6-1, Komaba, Meguro-ku

department: Institute of Industrial Science

institute: The University of Tokyo

description:
INS5_rep3
exp_table_genes.csv

data_processing:
Basecalls were performed with Illumina CASAVA.
Demultiplexing, filtering, mapping and molecule assembly were performed with a dedicated Nextflow pipeline (see https://gitlab.com/mcfrith/cagescan-pipeline and https://github.com/oist/plessy_CAGEscan_Nextflow).
Tagdust v2.33 was used to demultiplex samples and filter out sequencing reads originating from ribosomal RNA or oligo-artifacts.
Remaining reads for each sample were then grouped based on their UMI sequences, assembled into contigs, and aligned on the human genome (hg38) with LAST (https://gitlab.com/mcfrith/last) to build transcript models.
Resulting .BED12 files were processed with the CAGEr package (Haberle et al., Nucleic Acids Research, 2015; doi: 10.1093/nar/gkv054) to call CAGE peaks and generate gene expression tables.
Assembly: hg38
Supplementary files format and content: BED12 files, one RNA molecule per line; the score indicates how many read pairs were used to assemble the molecule.
Supplementary files format and content: Coma-separated values (.csv) file including raw read counts for specific genes in each Sample.

source_name: PXB-cells (PhoenixBio, Japan)

growth_protocol: Primary human hepatocytes were maintained in chemically defined William's Medium E supplemented with 2% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was harvested using Trizol reagent and 500 ng of total RNA from each sample were used for the construction of the sequencing libraries.
NanoCAGE sequencing libraries were prepared according to the protocol described by Poulain et al., Methods in Molecular Biology, 2017 (doi: 10.1007/978-1-4939-6716-2_4).

treatment_protocol:
Microenvironmental differentiation was induced by condition-specific treatment after 2 days of culture initiation by exposure to differential oxygenation and perfusion-induced shear stress.
Cells were cultured for 5 days after start of treatment, purified by negative selection via MACS immunomagnetic separation, and then analyzed for RNA-seq.

value: PXB-cells (PhoenixBio, Japan)

value: primary human hepatocytes isolated from uPA/SCID chimeric mice with humanized liver

tag: culture condition

value: dynamic PDMS tissue culture with perfusion-derived mechanical stimulation (hemodynamic shear stress)

tag: oxygenation

value: bottom membrane (high)

tag: oxygen tension_(%)

tag: culture type

value: Coculture with human sinusoidal endothelial cells (hLSECs)

value: TCGCGT


title: INS5_rep2

description:
INS5_rep2
exp_table_genes.csv

tag: cell line

value: TATAGC


title: GL53_286_Plate3_i14_Gfi1_pos_IAHC_S286

source_name: AGM

tag: cell type

value: AGM

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: 6-8 weeks old


title: C2-48hr

description: rescue.counts.tsv.gz

tag: genotype


title: C1-24hr

description: rescue.counts.tsv.gz


title: GL53_284_Plate3_g14_Gfi1_pos_IAHC_S284


title: INS5_rep1

description:
INS5_rep1
exp_table_genes.csv

value: GCTGCA


title: UC191

description: 3'-biased mRNA

data_processing:
Bases were called and samples demultiplexed with an Illumina 1.8+ pipeline.
Pipeline rnaseq v1.3 https://zenodo.org/record/2610144
Alignment with STAR v2.6.1d
Feature counting with FeatureCounts from the subread package v1.6.4
for more details, see pipeline documentation
Genome_build: GRCh37
Supplementary_files_format_and_content: Comma-separated values of raw feature counts results

value: UC

tag: sequencing plate number (used for batch correction)


title: GL53_287_Plate3_j14_Gfi1_pos_IAHC_S287

tag: tissue


title: C4-24hr

description: rescue.counts.tsv.gz


title: K-6-4

description: development.counts.tsv.gz

value: morula


title: K-6-3

description: development.counts.tsv.gz

value: Trpm7 -/-


title: UC189

description: 3'-biased mRNA


title: UC190

description: 3'-biased mRNA


title: K1-24hr

description: rescue.counts.tsv.gz


title: GL53_282_Plate3_d14_Gfi1_HE_S282

value: Hemogenic endothelium cells

tag: strain


title: INS10_rep3

description:
INS10_rep3
exp_table_genes.csv

value: GAGCGT


title: K-6-2

description: development.counts.tsv.gz


title: GL53_285_Plate3_h14_Gfi1_pos_IAHC_S285

value: Hematopoietic cells

tag: age


title: K-6-1

description: development.counts.tsv.gz


title: GL53_280_Plate3_b14_Gfi1_HE_S280

tag: developmental stage


title: UC188

description: 3'-biased mRNA


title: INS10_rep2

description:
INS10_rep2
exp_table_genes.csv

value: PXB-cells (PhoenixBio, Japan)

value: CTGAGC


title: GL53_279_Plate3_a14_Gfi1_HE_S279

tag: population


title: UC187

description: 3'-biased mRNA


title: INS10_rep1

description:
INS10_rep1
exp_table_genes.csv

value: primary human hepatocytes isolated from uPA/SCID chimeric mice with humanized liver

value: dynamic PDMS tissue culture with perfusion-derived mechanical stimulation (hemodynamic shear stress)

value: CACTCT


title: CO5_rep3

description:
CO5_rep3
exp_table_genes.csv

value: static tissue culture using oxygen-permeable polydimethylsiloxane (PDMS) bottom membrane

value: bottom membrane (high)

value: Coculture with human sinusoidal endothelial cells (hLSECs)

value: ATCGCA


title: GL53_283_Plate3_f14_Gfi1_pos_IAHC_S283

value: AGM

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: 6-8 weeks old

tag: batch


title: K-5-4

description: development.counts.tsv.gz

value: 8-cell embryo


title: GL53_278_Plate3_o13_Gfi1_neg_IAHC_S278


title: UC186

description: 3'-biased mRNA

tag: disease

value: UC


title: CO5_rep2

description:
CO5_rep2
exp_table_genes.csv

value: AGTAGC


title: GL53_281_Plate3_c14_Gfi1_HE_S281

value: Hemogenic endothelium cells


title: UC185

description: 3'-biased mRNA


title: K-5-3

description: development.counts.tsv.gz

value: Trpm7 -/-


title: K-5-2

description: development.counts.tsv.gz


title: GL53_276_Plate3_o12_Gfi1_neg_IAHC_S276

value: Hematopoietic cells


title: CO5_rep1

description:
CO5_rep1
exp_table_genes.csv

value: PXB-cells (PhoenixBio, Japan)

value: TCGATA


title: GL53_275_Plate3_n12_Gfi1_neg_IAHC_S275


title: CO10_rep3

description:
CO10_rep3
exp_table_genes.csv

value: primary human hepatocytes isolated from uPA/SCID chimeric mice with humanized liver

value: GTATGA


title: CO10_rep2

description:
CO10_rep2
exp_table_genes.csv

value: static tissue culture using oxygen-permeable polydimethylsiloxane (PDMS) bottom membrane

value: GCTCTC


title: UC184

description: 3'-biased mRNA


title: K-5-1

description: development.counts.tsv.gz


title: GL53_277_Plate3_m13_Gfi1_neg_IAHC_S277


title: GL53_274_Plate3_l12_Gfi1_neg_IAHC_S274


title: CO10_rep1

description:
CO10_rep1
exp_table_genes.csv

value: bottom membrane (high)

value: Coculture with human sinusoidal endothelial cells (hLSECs)

value: GAGATA


title: K-4-3

description: development.counts.tsv.gz

source_name: 4-cell embryo

value: 4-cell embryo


title: UC183

description: 3'-biased mRNA


title: UC181

description: 3'-biased mRNA


title: K-4-2

description: development.counts.tsv.gz


title: M5_rep3

description:
M5_rep3
exp_table_genes.csv

value: Monoculture

value: CGATGA


title: UC180

description: 3'-biased mRNA

value: UC


title: K-4-1

description: development.counts.tsv.gz


title: GL53_272_Plate3_j12_Gfi1_pos_IAHC_S272

value: AGM

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: 6-8 weeks old


title: M5_rep2

description:
M5_rep2
exp_table_genes.csv

value: CACGTG


title: K-3-3

description: development.counts.tsv.gz

source_name: 2-cell embryo

value: 2-cell embryo

value: Trpm7 -/-


title: UC178

description: 3'-biased mRNA


title: GL53_270_Plate3_h12_Gfi1_pos_IAHC_S270

value: Hematopoietic cells


title: K-3-4

description: development.counts.tsv.gz


title: UC182

description: 3'-biased mRNA


title: UC179

description: 3'-biased mRNA


title: UC177

description: 3'-biased mRNA


title: M5_rep1

description:
M5_rep1
exp_table_genes.csv

value: PXB-cells (PhoenixBio, Japan)

value: primary human hepatocytes isolated from uPA/SCID chimeric mice with humanized liver

value: ATCATA


title: GL53_271_Plate3_i12_Gfi1_pos_IAHC_S271


title: K-4-4

description: development.counts.tsv.gz


title: GL53_268_Plate3_f12_Gfi1_pos_IAHC_S268


title: GL53_273_Plate3_k12_Gfi1_pos_IAHC_S273


title: GL53_269_Plate3_g12_Gfi1_pos_IAHC_S269


title: UC176

description: 3'-biased mRNA


title: M10_rep2

description:
M10_rep2
exp_table_genes.csv

value: static tissue culture using oxygen-permeable polydimethylsiloxane (PDMS) bottom membrane

value: bottom membrane (high)

value: TCGAGC


title: M10_rep3

description:
M10_rep3
exp_table_genes.csv

value: ACATGA


title: K-3-1

description: development.counts.tsv.gz


title: K-2-3

description: development.counts.tsv.gz

source_name: 1-cell embryo

value: 1-cell embryo


title: K-2-4

description: development.counts.tsv.gz


title: K-3-2

description: development.counts.tsv.gz


title: GL53_267_Plate3_e12_Gfi1_HE_S267

value: Hemogenic endothelium cells


title: UC175

description: 3'-biased mRNA

value: UC


title: K-2-2

description: development.counts.tsv.gz


title: UC174

description: 3'-biased mRNA


title: TCPS_rep2

description:
TCPS_rep2
exp_table_genes.csv

value: standard TCPS dishes cultures [control]

value: culture medium (low)

value: Monoculture

value: CTGACG


title: GL53_266_Plate3_d12_Gfi1_HE_S266

value: AGM

value: CD1/Gf1+ (Thambyrajah et al 2015)

value: 6-8 weeks old


title: UC173

description: 3'-biased mRNA


title: GL53_265_Plate3_c12_Gfi1_HE_S265


title: UC172

description: 3'-biased mRNA


title: GL53_263_Plate3_c11_Gfi1_HE_S263


title: K-1-7

description: development.counts.tsv.gz

source_name: MII egg

value: MII egg

value: Trpm7 -/-


title: K-1-6

description: development.counts.tsv.gz


title: GL53_264_Plate3_d11_Gfi1_HE_S264


title: TCPS_rep3

description:
TCPS_rep3
exp_table_genes.csv

value: PXB-cells (PhoenixBio, Japan)

value: primary human hepatocytes isolated from uPA/SCID chimeric mice with humanized liver

value: GAGTGA


title: PXB_rep2

description:
PXB_rep2
exp_table_genes.csv

value: fresh non-cultured cells [control]

value: fresh isolate, not cultured

value: ATCGTG


title: K-2-1

description: development.counts.tsv.gz

value: 1-cell embryo


title: PXB_rep1

description:
PXB_rep1
exp_table_genes.csv

value: ACAGAT


title: M10_rep1

description:
M10_rep1
exp_table_genes.csv

value: static tissue culture using oxygen-permeable polydimethylsiloxane (PDMS) bottom membrane

value: bottom membrane (high)

value: GTATAC


title: UC170

description: 3'-biased mRNA

value: UC


title: PXB_rep3

description:
PXB_rep3
exp_table_genes.csv

value: CACGAT


title: GL53_262_Plate3_b11_Gfi1_HE_S262

value: Hemogenic endothelium cells

value: AGM

value: CD1/Gf1+ (Thambyrajah et al 2015)


title: UC168

description: 3'-biased mRNA


title: K-1-2

description: development.counts.tsv.gz

value: MII egg

value: Trpm7 -/-


title: K-1-1

description: development.counts.tsv.gz


title: GL53_260_Plate3_o10_Gfi1_neg_IAHC_S260

value: Hematopoietic cells

value: 6-8 weeks old


title: GL53_261_Plate3_a11_Gfi1_HE_S261


title: UC167

description: 3'-biased mRNA


title: atprmt5-2 mutant, buds, sRNA purified from AGO1-IP, replicate 3, 23bp

city: Perpignan

first: Jacinthe

last: Azevedo Favory

address: 58 avenue Paul Alduy

country: France

institute: CNRS

description: small RNA seq (18-30 nt-long)

data_processing:
reads were trimmed using Trimmomatic v0.36 (Bolger et al., 2014)
Trimmed reads were divided according to their size (21, 22, 23 and 24 nt-long small RNAs)
reads were mapped against TAIR10 genome with bowtie2 and custom parameters for small sequences (-D 5 -R 2 -N 1 -L 5)
Only unique mapped reads were kept using samtools v1.9 with option ‘-q 10’ (Li et al., 2009)
libraries (21, 22, 23, 24nt) were mapped against Arabidopsis thaliana mature miRNA from Mirdatabase with bowtie2
Assembly: TAIR10
Supplementary files format and content: raw counts RPM values for each sample and for each smallRNA size

molecule: other

organism: Arabidopsis thaliana

source_name: closed buds

growth_protocol: plants cultivated on soil, in growth chambers, under long-day period (16h/8h) with VegeLED lights (100 mE), 60% hygrometry

extract_protocol:
trizol extraction
Illumina TrueSeq small RNA library prep

value: closed buds

tag: treatment

value: no


title: atprmt5-2 mutant, buds, sRNA purified from AGO1-IP, replicate 3, 24bp

description: small RNA seq (18-30 nt-long)


title: UC166

description: 3'-biased mRNA


title: C-7-3

description: development.counts.tsv.gz

source_name: blastocyst

value: blastocyst


title: atprmt5-2 mutant, buds, sRNA purified from AGO1-IP, replicate 3, 22bp

description: small RNA seq (18-30 nt-long)


title: C-7-6

description: development.counts.tsv.gz


title: TCPS_rep1

description:
TCPS_rep1
exp_table_genes.csv

value: PXB-cells (PhoenixBio, Japan)

value: primary human hepatocytes isolated from uPA/SCID chimeric mice with humanized liver

value: standard TCPS dishes cultures [control]

value: culture medium (low)

value: Monoculture

value: CACTGA


title: UC171

description: 3'-biased mRNA

value: UC


title: GL53_258_Plate3_m10_Gfi1_neg_IAHC_S258


title: atprmt5-2 mutant, buds, sRNA purified from AGO1-IP, replicate 3, 21bp

description: small RNA seq (18-30 nt-long)


title: C-7-2

description: development.counts.tsv.gz


title: UC165

description: 3'-biased mRNA


title: UC169

description: 3'-biased mRNA


title: GL53_257_Plate3_l10_Gfi1_neg_IAHC_S257


title: UC164

description: 3'-biased mRNA


title: GL53_256_Plate3_k10_Gfi1_pos_IAHC_S256


title: C-7-1

description: development.counts.tsv.gz


title: atprmt5-6 mutant,  buds, sRNA purified from AGO1-IP, replicate 3, 23bp

description: small RNA seq (18-30 nt-long)


title: UC163

description: 3'-biased mRNA


title: C-6-6

description: development.counts.tsv.gz

value: morula


title: GL53_255_Plate3_j10_Gfi1_pos_IAHC_S255

value: AGM


title: GL53_259_Plate3_n10_Gfi1_neg_IAHC_S259

value: CD1/Gf1+ (Thambyrajah et al 2015)


title: atprmt5-6 mutant,  buds, sRNA purified from AGO1-IP, replicate 3, 22bp

description: small RNA seq (18-30 nt-long)


title: UC162

description: 3'-biased mRNA


title: C-6-5

description: development.counts.tsv.gz


title: atprmt5-6 mutant,  buds, sRNA purified from AGO1-IP, replicate 3, 21bp

description: small RNA seq (18-30 nt-long)


title: UC161

description: 3'-biased mRNA


title: GL53_254_Plate3_i10_Gfi1_pos_IAHC_S254


title: GL53_253_Plate3_h10_Gfi1_pos_IAHC_S253


title: wild type, buds, sRNA purified from AGO1-IP, replicate 3, 24bp

description: small RNA seq (18-30 nt-long)


title: C-6-1

description: development.counts.tsv.gz


title: GL53_252_Plate3_i9_Gfi1_pos_IAHC_S252


title: C-6-3

description: development.counts.tsv.gz


title: UC160

description: 3'-biased mRNA


title: wild type, buds, sRNA purified from AGO1-IP, replicate 3, 23bp

description: small RNA seq (18-30 nt-long)


title: GL53_251_Plate3_h9_Gfi1_pos_IAHC_S251


title: UC158

description: 3'-biased mRNA


title: UC159

description: 3'-biased mRNA


title: GL53_250_Plate3_g9_Gfi1_pos_IAHC_S250


title: wild type, buds, sRNA purified from AGO1-IP, replicate 3, 21bp

description: small RNA seq (18-30 nt-long)


title: wild type, buds, sRNA purified from AGO1-IP, replicate 3, 22bp

description: small RNA seq (18-30 nt-long)


title: UC157

description: 3'-biased mRNA


title: GL53_249_Plate3_f9_Gfi1_HE_S249

value: Hemogenic endothelium cells


title: C-5-2

description: development.counts.tsv.gz

value: 8-cell embryo


title: C-5-4

description: development.counts.tsv.gz


title: C-5-1

description: development.counts.tsv.gz


title: atprmt5-2 mutant, buds, sRNA purified from AGO1-IP, replicate 1, 24bp

description: small RNA seq (18-30 nt-long)


title: atprmt5-6 mutant,  buds, sRNA purified from AGO1-IP, replicate 3, 24bp

description: small RNA seq (18-30 nt-long)


title: GL53_248_Plate3_e9_Gfi1_HE_S248


title: UC155

description: 3'-biased mRNA


title: C-4-5

description: development.counts.tsv.gz

value: 4-cell embryo


title: UC156

description: 3'-biased mRNA


title: atprmt5-2 mutant, buds, sRNA purified from AGO1-IP, replicate 1, 23bp

description: small RNA seq (18-30 nt-long)


title: GL53_247_Plate3_d9_Gfi1_HE_S247

value: 6-8 weeks old


title: GL53_246_Plate3_c9_Gfi1_HE_S246


title: UC153

description: 3'-biased mRNA


title: atprmt5-2 mutant, buds, sRNA purified from AGO1-IP, replicate 1, 21bp

description: small RNA seq (18-30 nt-long)

value: closed buds


title: GL53_245_Plate3_b9_Gfi1_HE_S245


title: C-4-3

description: development.counts.tsv.gz


title: atprmt5-6 mutant,  buds, sRNA purified from AGO1-IP, replicate 1, 24bp

description: small RNA seq (18-30 nt-long)

value: no


title: C-5-3

description: development.counts.tsv.gz


title: C-4-2

description: development.counts.tsv.gz


title: C-4-1

description: development.counts.tsv.gz


title: atprmt5-6 mutant,  buds, sRNA purified from AGO1-IP, replicate 1, 23bp

description: small RNA seq (18-30 nt-long)


title: GL53_244_Plate3_a9_Gfi1_HE_S244


title: UC152

description: 3'-biased mRNA


title: C-3-4

description: development.counts.tsv.gz

value: 2-cell embryo


title: UC151

description: 3'-biased mRNA


title: GL53_243_Plate3_p8_Gfi1_neg_IAHC_S243

value: Hematopoietic cells


title: GL53_242_Plate3_o8_Gfi1_neg_IAHC_S242


title: atprmt5-6 mutant,  buds, sRNA purified from AGO1-IP, replicate 1, 22bp

description: small RNA seq (18-30 nt-long)


title: UC150

description: 3'-biased mRNA


title: C-3-3

description: development.counts.tsv.gz


title: atprmt5-2 mutant, buds, sRNA purified from AGO1-IP, replicate 1, 22bp

description: small RNA seq (18-30 nt-long)


title: C-3-2

description: development.counts.tsv.gz


title: atprmt5-6 mutant,  buds, sRNA purified from AGO1-IP, replicate 1, 21bp

description: small RNA seq (18-30 nt-long)


title: UC149

description: 3'-biased mRNA


title: wild type, buds, sRNA purified from AGO1-IP, replicate 1, 24bp

description: small RNA seq (18-30 nt-long)


title: GL53_241_Plate3_n8_Gfi1_neg_IAHC_S241


title: UC148

description: 3'-biased mRNA


title: UC154

description: 3'-biased mRNA


title: UC147

description: 3'-biased mRNA


title: C-3-1

description: development.counts.tsv.gz


title: GL53_240_Plate3_p7_Gfi1_neg_IAHC_S240


title: wild type, buds, sRNA purified from AGO1-IP, replicate 1, 23bp

description: small RNA seq (18-30 nt-long)


title: wild type, buds, sRNA purified from AGO1-IP, replicate 1, 22bp

description: small RNA seq (18-30 nt-long)


title: C-2-4

description: development.counts.tsv.gz

value: 1-cell embryo


title: C-2-3

description: development.counts.tsv.gz


title: GL53_238_Plate3_k7_Gfi1_pos_IAHC_S238


title: wild type, buds, sRNA purified from AGO1-IP, replicate 1, 21bp

description: small RNA seq (18-30 nt-long)


title: UC145

description: 3'-biased mRNA


title: GL53_237_Plate3_j7_Gfi1_pos_IAHC_S237


title: C-2-2

description: development.counts.tsv.gz


title: C-2-1

description: development.counts.tsv.gz


title: GL53_236_Plate3_i7_Gfi1_pos_IAHC_S236


title: UC144

description: 3'-biased mRNA


title: atprmt5-2 mutant, buds, total sRNA fraction, replicate 2, 23bp

description: small RNA seq (18-30 nt-long)


title: UC143

description: 3'-biased mRNA


title: C-1-5

description: development.counts.tsv.gz

value: MII egg


title: GL53_235_Plate3_h7_Gfi1_pos_IAHC_S235


title: C-1-3

description: development.counts.tsv.gz


title: atprmt5-2 mutant, buds, total sRNA fraction, replicate 2, 21bp

description: small RNA seq (18-30 nt-long)


title: UC141

description: 3'-biased mRNA


title: C-1-2

description: development.counts.tsv.gz


title: atprmt5-2 mutant, buds, total sRNA fraction, replicate 2, 22bp

description: small RNA seq (18-30 nt-long)


title: UC146

description: 3'-biased mRNA


title: atprmt5-6 mutant, buds, total sRNA fraction, replicate 2, 24 bp

description: small RNA seq (18-30 nt-long)


title: GL53_233_Plate3_f7_Gfi1_HE_S233


title: UC142

description: 3'-biased mRNA


title: UC139

description: 3'-biased mRNA


title: GL53_234_Plate3_g7_Gfi1_pos_IAHC_S234


title: GL53_231_Plate3_d7_Gfi1_HE_S231


title: UC140

description: 3'-biased mRNA


title: GL53_232_Plate3_e7_Gfi1_HE_S232


title: C-1-1

description: development.counts.tsv.gz


title: UC138

description: 3'-biased mRNA


title: GL53_230_Plate3_c7_Gfi1_HE_S230


title: atprmt5-6 mutant, buds, total sRNA fraction, replicate 2, 23 bp

description: small RNA seq (18-30 nt-long)


title: atprmt5-6 mutant, buds, total sRNA fraction, replicate 2, 22 bp

description: small RNA seq (18-30 nt-long)


title: atprmt5-6 mutant, buds, total sRNA fraction, replicate 2, 21 bp

description: small RNA seq (18-30 nt-long)


title: UC137

description: 3'-biased mRNA


title: wild type, buds, total sRNA, replicate 2, 24bp

description: small RNA seq (18-30 nt-long)


title: GL53_229_Plate3_b7_Gfi1_HE_S229


title: UC136

description: 3'-biased mRNA


title: GL78_383_WN-S3-P5_C22_AGM_E11-5_SP_47-48_Gfi1_HE__S377


title: GL78_382_WN-S3-P5_C17_AGM_E11-5_SP_47-48_Gfi1_HE__S376


title: GL53_228_Plate3_d6_Gfi1_HE_S228


title: wild type, buds, total sRNA, replicate 2, 23bp

description: small RNA seq (18-30 nt-long)


title: UC135

description: 3'-biased mRNA


title: GL53_227_Plate3_c6_Gfi1_HE_S227


title: Multiplexed sublibraries 2 and 6

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

description:
Parse Biosciences
These raw fastq files of sublibrary 2 and 6 contain uniquely barcoded cells from all eight samples (1,2,7,8,5,11,17, and 21). Samples details are provided in the sample manifest file.

data_processing:
Each sublibrary contains uniquely barcoded cells from all samples.  Raw sequencing data for sub library-2 and sub library-6 were preprocessed and combined using Parse Biosciences’ split-pipe pipeline (v0.9.6p). Expression matrices were imported into Seurat for downstream analyses.
Assembly: GRCm39
Supplementary files format and content: text

source_name: left hippocampus

extract_protocol:
Wild type (C57BL/6J) and db/db male mice were fed a standard purified diet AIN-93M, for 8 wks. Mice were sacrificed at 18 weeks of age and hippocampus was dissected from left hemisphere and then stored at -80 degree celcius. Hippocampal nuclei was isolated and fixed using Parse biosciences nuclei isolation and fixation protocol.
Barcoded single cell libraries were prepared from fixed single cell suspensions using Evercode Whole Transcriptome Mega kit (Parse Biosciences) following the manufacturer’s instructions.  Individual transcriptomes from all samples were uniquely labeled by passing fixed nuclei through four rounds of barcoding. In each round, pooled cells are randomly distributed into different wells, and transcripts are labeled with well-specific barcodes. Using next-generation sequencing, cells from individual samples are identified using the first well (first barcode) placement. Each sublibrary contains uniquely barcoded cells from all samples.  At the end of library prep, cells are distributed into 16 different sublibraries. The cDNA and library fragment size distribution were verified on a Bioanalyzer 2100 and TapeStation, respectively. The libraries were quantified by fluorometry on a Qubit instrument and by qPCR with a Kapa Library Quant kit prior to sequencing. The libraries were sequenced with paired-end 100 bp reads.  The sequencing generated approximately 35,000 reads per cell.

value: left hippocampus

value: 4.5 months

value: All hippocampal cells

tag: Sex

value: Male


title: wild type, buds, total sRNA, replicate 2, 22bp

description: small RNA seq (18-30 nt-long)


title: GL78_380_WN-S3-P5_C14_AGM_E11-5_SP_47-48_Gfi1_HE__S374


title: GL78_381_WN-S3-P5_A15_AGM_E11-5_SP_47-48_Gfi1_HE__S375


title: GL78_379_WN-S3-P5_B14_AGM_E11-5_SP_47-48_Gfi1_HE__S373


title: UC133

description: 3'-biased mRNA

value: UC


title: GL53_226_Plate3_b6_Gfi1_HE_S226

value: AGM


title: GL53_225_Plate3_a6_Gfi1_HE_S225

value: CD1/Gf1+ (Thambyrajah et al 2015)


title: atprmt5-2 mutant, buds, total sRNA fraction, replicate 1, 24bp

description: small RNA seq (18-30 nt-long)


title: GL78_384_WN-S3-P5_D23_AGM_E11-5_SP_47-48_Gfi1_HE__S378

value: Hemogenic endothelium cells


title: UC132

description: 3'-biased mRNA


title: GL53_224_Plate3_m5_Gfi1_neg_IAHC_S224


title: atprmt5-2 mutant, buds, total sRNA fraction, replicate 1, 22bp

description: small RNA seq (18-30 nt-long)


title: GL78_376_WN-S3-P5_C9_AGM_E11-5_SP_47-48_Gfi1_HE__S370


title: UC130

description: 3'-biased mRNA


title: GL78_378_WN-S3-P5_B13_AGM_E11-5_SP_47-48_Gfi1_HE__S372


title: atprmt5-2 mutant, buds, total sRNA fraction, replicate 1, 23bp

description: small RNA seq (18-30 nt-long)


title: UC134

description: 3'-biased mRNA


title: atprmt5-2 mutant, buds, total sRNA fraction, replicate 1, 21bp

description: small RNA seq (18-30 nt-long)


title: GL53_222_Plate3_k5_Gfi1_pos_IAHC_S222


title: UC129

description: 3'-biased mRNA


title: GL53_223_Plate3_l5_Gfi1_neg_IAHC_S223


title: GL53_221_Plate3_j5_Gfi1_pos_IAHC_S221


title: wild type, buds, total sRNA, replicate 2, 21bp

description: small RNA seq (18-30 nt-long)


title: UC128

description: 3'-biased mRNA


title: GL78_373_WN-S3-P5_E2_AGM_E11-5_SP_47-48_Gfi1_HE__S367


title: GL78_374_WN-S3-P5_C3_AGM_E11-5_SP_47-48_Gfi1_HE__S368


title: GL53_220_Plate3_i5_Gfi1_pos_IAHC_S220


title: GL53_219_Plate3_h5_Gfi1_pos_IAHC_S219


title: UC127

description: 3'-biased mRNA


title: atprmt5-6 mutant, buds, total sRNA fraction, replicate 1, 23 bp

description: small RNA seq (18-30 nt-long)


title: atprmt5-6 mutant, buds, total sRNA fraction, replicate 1, 24 bp

description: small RNA seq (18-30 nt-long)


title: GL78_372_WN-S3-P5_D2_AGM_E11-5_SP_47-48_Gfi1_HE__S366


title: atprmt5-6 mutant, buds, total sRNA fraction, replicate 1, 22 bp

description: small RNA seq (18-30 nt-long)


title: UC131

description: 3'-biased mRNA


title: GL53_218_Plate3_g5_Gfi1_pos_IAHC_S218


title: GL78_371_WN-S3-P5_E1_AGM_E11-5_SP_47-48_Gfi1_HE__S365


title: GL78_375_WN-S3-P5_B4_AGM_E11-5_SP_47-48_Gfi1_HE__S369


title: GL53_217_Plate3_f5_Gfi1_HE_S217


title: atprmt5-6 mutant, buds, total sRNA fraction, replicate 1, 21 bp

description: small RNA seq (18-30 nt-long)


title: UC125

description: 3'-biased mRNA


title: wild type, buds, total sRNA fraction, replicate 1, 24 bp

description: small RNA seq (18-30 nt-long)


title: GL78_370_WN-S3-P5_A3_AGM_E11-5_SP_47-48_Gfi1_HE__S364


title: UC124

description: 3'-biased mRNA


title: GL78_369_WN-S3-P5_A1_AGM_E11-5_SP_47-48_Gfi1_HE__S363


title: GL78_368_WN-S2-P2_F2_AGM_E11-5_SP_48-49_Gfi1_HE__S362


title: UC123

description: 3'-biased mRNA


title: wild type, buds, total sRNA fraction, replicate 1, 22 bp

description: small RNA seq (18-30 nt-long)


title: GL53_215_Plate3_g4_Gfi1_pos_IAHC_S215


title: GL78_367_WN-S2-P2_J2_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S361


title: UC122

description: 3'-biased mRNA


title: wild type, buds, total sRNA fraction, replicate 1, 23 bp

description: small RNA seq (18-30 nt-long)


title: GL53_214_Plate3_f4_Gfi1_HE_S214


title: wild type, buds, total sRNA fraction, replicate 1, 21 bp

description: small RNA seq (18-30 nt-long)


title: UC121

description: 3'-biased mRNA


title: UC126

description: 3'-biased mRNA


title: UC120

description: 3'-biased mRNA


title: GL78_365_WN-S2-P2_N2_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S359


title: GL78_366_WN-S2-P2_K2_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S360


title: GL78_364_WN-S2-P2_O2_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S358


title: UC119

description: 3'-biased mRNA


title: GL53_211_Plate3_c4_Gfi1_HE_S211


title: GL78_363_WN-S2-P2_B3_AGM_E11-5_SP_48-49_Gfi1_HE__S357


title: GL53_212_Plate3_d4_Gfi1_HE_S212


title: UC118

description: 3'-biased mRNA


title: GL53_216_Plate3_h4_Gfi1_pos_IAHC_S216


title: UC117

description: 3'-biased mRNA


title: GL53_210_Plate3_b4_Gfi1_HE_S210


title: GL78_362_WN-S2-P2_D3_AGM_E11-5_SP_48-49_Gfi1_HE__S356


title: GL53_209_Plate3_a4_Gfi1_HE_S209


title: UC116

description: 3'-biased mRNA


title: GL53_208_Plate3_o3_Gfi1_neg_IAHC_S208


title: GL78_361_WN-S2-P2_F3_AGM_E11-5_SP_48-49_Gfi1_HE__S355


title: UC115

description: 3'-biased mRNA


title: GL78_360_WN-S2-P2_G3_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S354


title: GL53_213_Plate3_e4_Gfi1_HE_S213


title: GL53_207_Plate3_n3_Gfi1_neg_IAHC_S207


title: GL53_206_Plate3_l3_Gfi1_neg_IAHC_S206


title: GL78_359_WN-S2-P2_H3_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S353


title: UC113

description: 3'-biased mRNA


title: GL78_358_WN-S2-P2_I3_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S352


title: GL53_239_Plate3_o7_Gfi1_neg_IAHC_S239


title: UC112

description: 3'-biased mRNA


title: GL78_357_WN-S2-P2_J3_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S351


title: GL53_204_Plate3_k2_Gfi1_pos_IAHC_S204


title: GL78_356_WN-S2-P2_K3_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S350


title: MDA-MB231 treated with Manassantin rep3

type: RNA

city: Durham

first: Jen-Tsan

last: Chi

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® ____________ arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: The data were analyzed with Agilent 2100 Bioanalyzer G2939A

label: biotin

source_name: MDA-MB231 treated with Manassantin

growth_protocol: MDA-MB231 cells grew in the control full DMEM media supplement with 10% FBS and Penicillin/Streptomycin

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: MDA-MB231 were treated for 24 hours with the DMSO or indicated compounds


title: MDA-MB231 treated with Rotenone rep2

source_name: MDA-MB231 treated with Rotenone

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® ____________ arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450


title: MDA-MB231 treated with Digoxin rep3

source_name: MDA-MB231 treated with Digoxin


title: UC110

description: 3'-biased mRNA


title: GL53_203_Plate3_j2_Gfi1_pos_IAHC_S203


title: GL78_355_WN-S2-P2_M3_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S349


title: MDA-MB231 treated with Digoxin rep2


title: GL53_202_Plate3_i2_Gfi1_pos_IAHC_S202


title: UC114

description: 3'-biased mRNA


title: UC109

description: 3'-biased mRNA


title: MDA-MB231 treated with Manassantin rep1


title: GL78_354_WN-S2-P2_E4_AGM_E11-5_SP_48-49_Gfi1_HE__S348


title: GL53_201_Plate3_g2_Gfi1_pos_IAHC_S201


title: UC108

description: 3'-biased mRNA


title: MDA-MB231 treated with Rotenone rep3


title: GL53_205_Plate3_k3_Gfi1_pos_IAHC_S205


title: GL78_353_WN-S2-P2_G4_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S347


title: GL53_200_Plate3_f2_Gfi1_HE_S200


title: UC111

description: 3'-biased mRNA


title: MDA-MB231 treated with Digoxin rep1


title: UC107

description: 3'-biased mRNA


title: GL53_199_Plate3_d2_Gfi1_HE_S199


title: MDA-MB231 treated with DMSO rep1

source_name: MDA-MB231 treated with DMSO


title: atprmt5-2 mutant, buds, total sRNA fraction, replicate 2, 24bp

description: small RNA seq (18-30 nt-long)


title: MDA-MB231 treated with Manassantin rep2


title: MDA-MB231 treated with Rotenone rep1


title: GL53_198_Plate3_c2_Gfi1_HE_S198


title: GL78_351_WN-S2-P2_I4_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S345


title: GL78_349_WN-S2-P2_K4_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S343


title: GL78_348_WN-S2-P2_M4_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S342


title: MDA-MB231 treated with DMSO rep2


title: GL78_350_WN-S2-P2_J4_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S344


title: GL53_196_Plate3_a2_Gfi1_HE_S196


title: GL53_195_Plate3_p1_Gfi1_neg_IAHC_S195


title: GL78_352_WN-S2-P2_H4_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S346


title: Gametocyte, gSNF2 KO-3

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 3) by HISAT2. The SAM files were then sorted using samtools to produce BAM files.
Using the BAM files, number of reads mapped on each gene was counted by featureCounts.
Assembly: PlasmoDB, version 3
Supplementary files format and content: text read counts

organism: Plasmodium berghei

source_name: Gametocyte

growth_protocol: Balb/c mice were infected with P. berghei ANKA strain. Sulfadiazine was added to their drinking water in order to deplete asexual blood-stage parasites. Parasites were harvested after drug treatment for 2 days,.

extract_protocol:
Gametocytes enriched blood were subjected to erythrocyte lysis in 0.84% NH4Cl. Residual cells were lysed in and total RNA was extracted by Isogen 2 (Nippon gene) according to manufacturer protocols.
Libraries were prepared using the RNA Hyperprep kit (KAPA Biosystems), and sequencing was performed with an Illumina NEXTseq sequencer.

treatment_protocol: Balb/c mice were infected with P. berghei ANKA strain. Sulfadiazine was added to their drinking water in order to deplete asexual blood-stage parasites. Parasites were harvested after drug treatment for 2 days.

tag: Stage

value: gametocyte

value: ANKA

value: PFG knockout


title: UC102

description: 3'-biased mRNA


title: GL53_194_Plate3_o1_Gfi1_neg_IAHC_S194

first: Anna

last: Bigas

address: Dr. Aiguader 88

institute: Institut Hospital del Mar d'Investigacions Mèdiques

data_processing:
Raw data was aligned to the reference mouse genome using STAR aligner tool (v2.7.3)
Gene counts were extracted from BAM files using HTSeq software (v0.9.1)
Python (v3.7.3) and scanpy (v1.4.4) for data pre-processing
As QC, cells with less than 2,500 expressed genes and less than 50,000 counts were discarded, and no more than 5% mitochondrial gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated value file: scRNAseq_Cell_annotation.txt: cell sample metadata table. For each cell (row, 860 in total): cell full name, corresponding plate/well, embryo developmental stage, cell population, batch name, FACS index data for (in this order) DLL4, NOTCH2, CKIT, GFI1, CD41, NOTCH1, CD31, JAG1 and CD45. Additionally, for those cells passing the QC, UMAP coordinates and annotated cluster (Louvain method, see publication for details) are included.
Supplementary files format and content: Tab-separated value file: scRNAseq_Raw_counts.txt: full-length RNAseq (SMART-Seq2).Raw expression levels for each gene (46,170 rows) in each single cell (860 columns) as calculated using HTseq. This data is prior to conducting any QC.
Supplementary files format and content: Tab-separated value file: scRNAseq_Norm_counts_filtered.txt. Normalized expression levels after QC. Matrix comprises 30,362 rows (genes) per 775 columns (cells). Counts were normalized per cell with pp.normalize_total function from scanpy (target sum of 1e4) and values logarithmize with pp.log1p scanpy function.

extract_protocol:
Single cells were sorted into well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol. Briefly, cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher).
Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems).

value: 6-8 weeks old


title: Gametocyte, gSNF2 KO-2


title: GL78_347_WN-S2-P2_O4_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S341


title: UC101

first: Florian

last: Uellendahl-Werth

address: Rosalind-Franklin-Straße 12

institute: Christian-Albrechts Universität zu Kiel

description: 3'-biased mRNA

extract_protocol:
PAXgene Blood RNA Kit; Pellets from PAXgene Blood RNA Tubes are washed, resuspended, and incubated in optimized buffers together with proteinase K to digest proteins. Lysates are applied to a PAXgene 96 Filter Plate and centrifuged to remove residual cell debris. Ethanol is added to the flow-through to adjust binding conditions, and the lysates are applied to a PAXgene 96 RNA Plate. RNA is selectively bound to the PAXgene 96 RNA membrane as contaminants pass through. Residual DNA is removed through a DNase I digestion on the PAXgene 96 membrane. Remaining contaminants are removed in three efficient wash steps and RNA is eluted in Buffer BR5. (from manufacturer’s guide)
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit with 50 ng RNA input. Optional “Globin Block Module” used in all samples. Poly(A) RNA is reverse transcribed with poly(T)-Primers. RNA is digested and the second strand is synthesized by random priming. cDNA is purified. Illumina adapters are added. The PCR was run with 15 cycles.


title: GL53_193_Plate3_n1_Gfi1_neg_IAHC_S193


title: GL78_346_WN-S2-P2_A5_AGM_E11-5_SP_48-49_Gfi1_HE__S340


title: UC106

description: 3'-biased mRNA


title: Gametocyte, gSNF2 KO-1


title: MDA-MB231 treated with DMSO rep3


title: GL53_197_Plate3_b2_Gfi1_HE_S197


title: UC104

description: 3'-biased mRNA


title: UC105

description: 3'-biased mRNA


title: GL78_345_WN-S2-P2_F5_AGM_E11-5_SP_48-49_Gfi1_HE__S339


title: GL53_192_Plate1_e04_Gfi1_neg_IAHC_S384


title: AP2-FG_ChIP_PFG(-)_2_Input

data_processing:
Sequence data were mapped onto P. berghei genome sequence (PlasmoDB, version 3) using BOWTIE2 software in default settings. Mapping data were analyzed using MACS2 peak-calling algorithm using approximately 0.3 × 107 reads or 0.5 × 107 reads. Conditions for peak calling were FDR < 0.01
Assembly: PlasmoDB, version 3
Supplementary files format and content: peak call

extract_protocol:
Blood was filtered with Plasmodipur to remove lymphocytes and fixed with 1% formaldehyde for 60 min at 30C with shaking. After erythrocyte lysis in 0.85% NH4Cl, residual cells were subjected to ChIP-seq. Cells were sonicated with Bioruptor in the following condition: total of 20 times at 30 s in middle power in the cell lysis solution containing 1% sodium dodecyl sulfate. The supernatant was subjected to immunoprecipitation with anti-GFP antibodies using Dynabeads protein A.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

value: parasites expressing GFP-fused AP2-FG PFG-KO

tag: chip antibody


title: GL78_344_WN-S2-P2_G5_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S338


title: GL53_191_Plate1_e09_Gfi1_neg_IAHC_S383


title: AP2-FG_ChIP_PFG(-)_2_IP

value: GFP


title: UC099

description: 3'-biased mRNA


title: GL78_343_WN-S2-P2_I5_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S337

value: Hematopoietic cells


title: AP2-FG_ChIP_PFG(-)_1_Input


title: GL53_190_Plate1_e12_Gfi1_neg_IAHC_S382


title: UC098

description: 3'-biased mRNA


title: GL78_342_WN-S2-P2_J5_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S336


title: UC103

description: 3'-biased mRNA


title: AP2-FG_ChIP_PFG(-)_1_IP


title: GL78_341_WN-S2-P2_L5_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S335


title: UC097

description: 3'-biased mRNA


title: GL53_189_Plate1_e17_Gfi1_neg_IAHC_S381


title: GL53_188_Plate1_e20_Gfi1_neg_IAHC_S380


title: GL78_340_WN-S2-P2_C6_AGM_E11-5_SP_48-49_Gfi1_HE__S334


title: PFG_ChIP_AP2-FG(-)_input2

value: parasites expressing GFP-fused PFG AP2-FG-KO


title: GL53_187_Plate4_g5_Gfi1_pos_IAHC_S379


title: PFG_ChIP_AP2-FG(-)_IP2


title: UC100

description: 3'-biased mRNA


title: PFG_ChIP_AP2-FG(-)_input1


title: UC093

description: 3'-biased mRNA


title: UC094

description: 3'-biased mRNA


title: GL53_186_Plate4_g4_Gfi1_pos_IAHC_S378


title: GL78_339_WN-S2-P2_G6_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S333


title: GL78_338_WN-S2-P2_H6_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S332


title: GL53_185_Plate4_g3_Gfi1_pos_IAHC_S377


title: UC092

description: 3'-biased mRNA


title: GL78_337_WN-S2-P2_K6_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S331


title: GL53_184_Plate4_g2_Gfi1_pos_IAHC_S376


title: PFG_ChIP_2_Input

value: parasites expressing GFP-fused PFG


title: UC091

description: 3'-biased mRNA


title: UC095

description: 3'-biased mRNA


title: UC096

description: 3'-biased mRNA


title: GL53_183_Plate4_g1_Gfi1_pos_IAHC_S375


title: PFG_ChIP_1_Input


title: PFG_ChIP_2_IP


title: GL78_336_WN-S2-P2_L6_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S330


title: UC090

description: 3'-biased mRNA


title: GL53_182_Plate4_a7_Gfi1_HE_S374


title: GL78_334_WN-S2-P2_P6_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S328


title: PFG_ChIP_1_IP


title: GL78_335_WN-S2-P2_O6_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S329


title: UC089

description: 3'-biased mRNA


title: UC088

description: 3'-biased mRNA


title: UC087

description: 3'-biased mRNA


title: GL53_180_Plate4_j11_Gfi1_pos_IAHC_S372


title: PFG_ChIP_AP2-FG(-)_IP1


title: GL53_179_Plate4_l12_Gfi1_neg_IAHC_S371


title: GL78_332_WN-S2-P2_K7_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S326


title: GL53_181_Plate4_a6_Gfi1_HE_S373


title: GL78_333_WN-S2-P2_P7_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S327


title: GL78_331_WN-S2-P2_L7_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S325


title: UC086

description: 3'-biased mRNA


title: GL53_178_Plate4_c10_Gfi1_pos_IAHC_S370


title: GL53_177_Plate4_j9_Gfi1_pos_IAHC_S369


title: GL78_330_WN-S2-P2_M7_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S324


title: GL78_329_WN-S2-P2_G7_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S323


title: GL78_328_WN-S2-P2_H7_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S322


title: UC085

description: 3'-biased mRNA


title: UC084

description: 3'-biased mRNA


title: GL78_327_WN-S2-P2_I7_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S321


title: UC082

description: 3'-biased mRNA


title: GL53_174_Plate4_l8_Gfi1_neg_IAHC_S366


title: UC083

description: 3'-biased mRNA


title: IEL-cd27cd28-old

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: Not used in this paper.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: SI IEL

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: SI-IELs and SP cells were collected from each week-old C57BL/6 mice, stained with anti- CD3e-PerCP-Cy5.5 and anti-CD4-PE-Cy7, and then sorted by the FACS Melody as the CD4 (CD3+CD4+) fractions. More than 98% purity of each fraction was confirmed by analysing post-sorted cells with the FACS Canto II. RNA samples were extracted from cells using RNesy mini kit (Qiagen).

value: 89 weeks old

value: T cell


title: SP-cd4-old

description: Used in this paper.

source_name: spleen


title: SP-cd4-young

description: Used in this paper.

value: 5 weeks old


title: GL78_325_WN-S2-P2_C8_AGM_E11-5_SP_48-49_Gfi1_HE__S319

city: Barcelona


title: GL53_172_Plate4_l3_Gfi1_neg_IAHC_S364


title: GL53_173_Plate4_l4_Gfi1_neg_IAHC_S365


title: UC079

city: Kiel

description: 3'-biased mRNA

source_name: Whole Blood


title: UC081

description: 3'-biased mRNA


title: GL78_326_WN-S2-P2_B7_AGM_E11-5_SP_48-49_Gfi1_HE__S320


title: UC080

description: 3'-biased mRNA


title: GL53_171_Plate4_l2_Gfi1_neg_IAHC_S363


title: GL53_170_Plate4_l1_Gfi1_neg_IAHC_S362


title: UC078

description: 3'-biased mRNA


title: GL78_323_WN-S2-P2_F8_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S317


title: GL78_322_WN-S2-P2_G8_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S316


title: UC077

description: 3'-biased mRNA


title: T2DM218C

city: Copenhagen

first: Malene

middle: Maag

last: Kristensen

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

description: Sample name = 96

data_processing:
Non-normalized data: Background filtered Cq-values.
Normalized data: All data was normalised to the average of assays detected in all samples (dCq = global mean Cq – assay Cq (sample)).
Fold-change data: 2^dCq

label: SYBR green

source_name: skeletal muscle, T2DM, 4 months post-surgery

label_protocol: 30 ng RNA was reverse transcribed in 30 μl reactions using the miRCURY LNA Universal RT microRNA PCR, Polyadenylation and cDNA synthesis kit (Exiqon). cDNA was diluted 100x and assayed in 10 ul PCR reactions according to the protocol; each microRNA was assayed once by qPCR on the microRNA Ready-to-Use PCR, Human Panel I using ExiLENT SYBR® Green master mix. Negative controls excluding template from the reverse transcription reaction was performed and profiled like the samples. The amplification was performed in a LightCycler® 480 Real-Time PCR System (Roche) in 384-well plates.

growth_protocol: 16 severely obese patients without type 2 diabetes mellitus (OB) and nine severely obese patients with type 2 diabetes mellitus (T2DM) were elected for Roux-en-Y gastric bypass surgery. We examined the participants after a diet-induced weight loss (B) and approximately 4 months post-surgery (C).

extract_protocol: Total RNA was extracted from approximately 20 mg of muscle tissue using Trizol (Invitrogen).

treatment_protocol: We sampled skeletal muscle biopsies from vastus lateralis with a Bergstrom needle using suction and local anaesthesia (1% lidocaine) at both visits (B and C). Biopsies were snap-frozen in liquid nitrogen and stored at -80°C subsequently.

tag: phenotype

value: obese

tag: disease status

value: type 2 diabetes mellitus

value: skeletal muscle (vastus lateralis)

value: Roux-en-Y gastric bypass surgery

tag: timepoint

value: 4 months post-surgery

tag: individual identifier


title: UC076

description: 3'-biased mRNA

value: UC


title: GL53_169_Plate4_l19_Gfi1_neg_IAHC_S361

source_name: AGM

tag: cell type

value: AGM

value: CD1/Gf1+ (Thambyrajah et al 2015)


title: GL53_175_Plate4_l9_Gfi1_neg_IAHC_S367

value: 6-8 weeks old


title: IEL-others-old

description: Not used in this paper.

value: Male


title: T2DM218B

description: Sample name = 95

source_name: skeletal muscle, T2DM, diet-induced weight loss before surgery

value: before surgery, after diet-induced weight loss


title: GL53_168_Plate3_k23_Gfi1_neg_IAHC_S360

value: Hematopoietic cells


title: GL78_321_WN-S2-P2_H8_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S315


title: IEL-cd4-old

description: Used in this paper.


title: UC075

description: 3'-biased mRNA

tag: sequencing plate number (used for batch correction)


title: GL78_324_WN-S2-P2_D8_AGM_E11-5_SP_48-49_Gfi1_HE__S318

value: Hemogenic endothelium cells

tag: tissue


title: GL78_320_WN-S2-P2_I8_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S314

tag: strain


title: GL53_167_Plate3_j23_Gfi1_pos_IAHC_S359

tag: age


title: IEL-cd4-young

description: Used in this paper.


title: UC074

description: 3'-biased mRNA


title: GL78_319_WN-S2-P2_J8_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S313

tag: developmental stage


title: T2DM212B

description: Sample name = 91


title: T2DM212C

description: Sample name = 92


title: T2DM210C

description: Sample name = 88


title: GL53_166_Plate3_i23_Gfi1_pos_IAHC_S358

tag: population


title: GL78_318_WN-S2-P2_K8_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S312

tag: batch


title: T2DM210B

description: Sample name = 87


title: T2DM208C

description: Sample name = 85


title: UC072

description: 3'-biased mRNA

tag: disease


title: GL53_164_Plate3_g23_Gfi1_pos_IAHC_S356


title: T2DM208B

description: Sample name = 84

tag: treatment


title: GL53_165_Plate3_h23_Gfi1_pos_IAHC_S357


title: GL53_176_Plate4_l11_Gfi1_neg_IAHC_S368


title: GL78_316_WN-S2-P2_P8_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S310


title: GL53_163_Plate3_f23_Gfi1_pos_IAHC_S355


title: UC071

description: 3'-biased mRNA


title: UC070

description: 3'-biased mRNA


title: GL78_315_WN-S2-P2_C9_AGM_E11-5_SP_48-49_Gfi1_HE__S309


title: T2DM207C

description: Sample name = 81


title: GL53_162_Plate3_e23_Gfi1_HE_S354


title: GL78_314_WN-S2-P2_D9_AGM_E11-5_SP_48-49_Gfi1_HE__S308


title: T2DM207B

description: Sample name = 80


title: UC069

description: 3'-biased mRNA


title: UC073

description: 3'-biased mRNA


title: GL53_161_Plate3_d23_Gfi1_HE_S353


title: T2DM204C

description: Sample name = 78


title: T2DM204B

description: Sample name = 77


title: GL53_160_Plate3_c23_Gfi1_HE_S352


title: GL78_317_WN-S2-P2_L8_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S311


title: UC068

description: 3'-biased mRNA


title: UC067

description: 3'-biased mRNA


title: GL53_159_Plate3_b23_Gfi1_HE_S351


title: GL53_158_Plate3_a23_Gfi1_HE_S350


title: UC066

description: 3'-biased mRNA


title: T2DM203C

description: Sample name = 74


title: T2DM203B

description: Sample name = 73


title: GL78_311_WN-S2-P2_G9_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S305


title: UC065

description: 3'-biased mRNA


title: GL78_310_WN-S2-P2_H9_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S304


title: GL53_157_Plate3_p22_Gfi1_neg_IAHC_S349


title: UC064

description: 3'-biased mRNA


title: GL78_309_WN-S2-P2_I9_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S303


title: GL78_313_WN-S2-P2_E9_AGM_E11-5_SP_48-49_Gfi1_HE__S307


title: GL53_156_Plate3_p21_Gfi1_neg_IAHC_S348


title: T2DM202C

description: Sample name = 71


title: UC063

description: 3'-biased mRNA


title: GL78_308_WN-S2-P2_J9_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S302


title: UC062

description: 3'-biased mRNA


title: GL78_312_WN-S2-P2_F9_AGM_E11-5_SP_48-49_Gfi1_HE__S306


title: GL53_155_Plate3_o21_Gfi1_neg_IAHC_S347


title: GL78_306_WN-S2-P2_L9_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S300


title: GL53_154_Plate3_n21_Gfi1_neg_IAHC_S346


title: UC061

description: 3'-biased mRNA


title: T2DM202B

description: Sample name = 70


title: GL78_305_WN-S2-P2_M9_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S299


title: GL53_153_Plate3_m21_Gfi1_neg_IAHC_S345


title: T2DM201C

description: Sample name = 67


title: T2DM201B

description: Sample name = 66


title: GL78_304_WN-S2-P2_G10_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S298


title: GL53_152_Plate3_l21_Gfi1_neg_IAHC_S344


title: UC059

description: 3'-biased mRNA


title: GL53_151_Plate3_k21_Gfi1_neg_IAHC_S343


title: GL78_303_WN-S2-P2_H10_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S297


title: OB130C

description: Sample name = 60

source_name: skeletal muscle, OB, 4 months post-surgery

value: without type 2 diabetes mellitus


title: OB135C

description: Sample name = 64


title: OB130B

description: Sample name = 59

source_name: skeletal muscle, OB, diet-induced weight loss before surgery


title: OB135B

description: Sample name = 63


title: GL53_150_Plate3_j21_Gfi1_pos_IAHC_S342


title: UC057

description: 3'-biased mRNA


title: UC058

description: 3'-biased mRNA


title: GL53_149_Plate3_i21_Gfi1_pos_IAHC_S341


title: GL78_302_WN-S2-P2_I10_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S296


title: GL78_301_WN-S2-P2_J10_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S295


title: GL53_148_Plate3_h21_Gfi1_pos_IAHC_S340


title: UC056

description: 3'-biased mRNA


title: UC060

description: 3'-biased mRNA


title: GL78_299_WN-S2-P2_L10_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S293


title: GL78_300_WN-S2-P2_K10_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S294


title: UC055

description: 3'-biased mRNA


title: GL78_298_WN-S2-P2_M10_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S292


title: GL53_147_Plate3_g21_Gfi1_pos_IAHC_S339


title: GL53_146_Plate3_f21_Gfi1_pos_IAHC_S338


title: UC054

description: 3'-biased mRNA


title: GL78_297_WN-S2-P2_F11_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S291


title: GL53_145_Plate3_e21_Gfi1_HE_S337


title: GL53_144_Plate3_f20_Gfi1_pos_IAHC_S336


title: UC052

description: 3'-biased mRNA


title: GL78_296_WN-S2-P2_H11_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S290


title: OB123B

description: Sample name = 50


title: OB122C

description: Sample name = 49


title: OB123C

description: Sample name = 51


title: OB127B

description: Sample name = 56


title: GL53_143_Plate3_e20_Gfi1_HE_S335


title: OB117C

description: Sample name = 42


title: UC050

description: 3'-biased mRNA


title: UC051

description: 3'-biased mRNA


title: OB122B

description: Sample name = 48


title: GL78_295_WN-S2-P2_I11_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S289


title: GL78_294_WN-S2-P2_J11_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S288


title: OB117B

description: Sample name = 41


title: GL53_142_Plate3_d20_Gfi1_HE_S334


title: UC053

description: 3'-biased mRNA


title: UC048

description: 3'-biased mRNA


title: UC049

description: 3'-biased mRNA


title: GL53_141_Plate3_c20_Gfi1_HE_S333


title: GL53_140_Plate3_b20_Gfi1_HE_S332


title: GL78_292_WN-S2-P2_M11_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S286


title: GL78_293_WN-S2-P2_K11_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S287


title: OB116C

description: Sample name = 38


title: OB116B

description: Sample name = 37


title: GL53_139_Plate3_a20_Gfi1_HE_S331


title: GL78_291_WN-S2-P2_N11_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S285


title: OB114C

description: Sample name = 35


title: UC046

description: 3'-biased mRNA


title: GL78_290_WN-S2-P2_A12_AGM_E11-5_SP_48-49_Gfi1_HE__S284


title: OB113B

description: Sample name = 30


title: GL53_138_Plate3_o19_Gfi1_neg_IAHC_S330


title: OB114B

description: Sample name = 34


title: OB113C

description: Sample name = 31


title: OB112C

description: Sample name = 27


title: UC045

description: 3'-biased mRNA


title: GL53_137_Plate3_n19_Gfi1_neg_IAHC_S329


title: GL78_289_WN-S2-P2_E12_AGM_E11-5_SP_48-49_Gfi1_HE__S283


title: UC044

description: 3'-biased mRNA


title: GL78_288_WN-S2-P2_G12_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S282


title: UC043

description: 3'-biased mRNA


title: GL78_287_WN-S2-P2_H12_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S281


title: GL53_135_Plate3_k19_Gfi1_neg_IAHC_S327


title: UC047

description: 3'-biased mRNA


title: UC042

description: 3'-biased mRNA


title: GL78_286_WN-S2-P2_I12_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S280


title: GL53_134_Plate3_j19_Gfi1_pos_IAHC_S326


title: UC041

description: 3'-biased mRNA


title: GL78_285_WN-S2-P2_K12_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S279


title: GL53_133_Plate3_i19_Gfi1_pos_IAHC_S325


title: OB109B

description: Sample name = 22


title: UC040

description: 3'-biased mRNA


title: OB107C

description: Sample name = 20


title: UC039

description: 3'-biased mRNA


title: GL78_283_WN-S2-P2_P12_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S277


title: GL78_284_WN-S2-P2_O12_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S278


title: GL53_136_Plate3_l19_Gfi1_neg_IAHC_S328


title: GL53_131_Plate3_j18_Gfi1_pos_IAHC_S323


title: OB109C

description: Sample name = 23


title: GL53_130_Plate3_i18_Gfi1_pos_IAHC_S322


title: GL78_282_WN-S2-P2_H13_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S276


title: GL78_281_WN-S2-P2_I13_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S275


title: OB106C

description: Sample name = 16


title: GL53_129_Plate3_h18_Gfi1_pos_IAHC_S321


title: OB106B

description: Sample name = 15


title: OB112B

description: Sample name = 26


title: OB104C

description: Sample name = 13


title: OB107B

description: Sample name = 19


title: UC037

description: 3'-biased mRNA


title: UC036

description: 3'-biased mRNA


title: GL53_128_Plate3_g18_Gfi1_pos_IAHC_S320


title: GL78_280_WN-S2-P2_J13_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S274


title: GL78_279_WN-S2-P2_K13_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S273


title: UC035

description: 3'-biased mRNA


title: GL53_127_Plate3_f18_Gfi1_pos_IAHC_S319


title: GL53_132_Plate3_k18_Gfi1_pos_IAHC_S324


title: UC034

description: 3'-biased mRNA


title: UC038

description: 3'-biased mRNA


title: UC033

description: 3'-biased mRNA


title: GL78_277_WN-S2-P2_M13_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S271


title: GL53_125_Plate3_d18_Gfi1_HE_S317


title: OB104B

description: Sample name = 12


title: OB103C

description: Sample name = 9


title: UC032

description: 3'-biased mRNA


title: GL53_124_Plate3_c18_Gfi1_HE_S316


title: Bovine Peripheral Blood Mesenchynmal Stromal Cells

city: Ithaca

first: Gerlinde

middle: R.

last: Van de Walle

state: NY

address: 235 Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

description: 10X Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation using cellranger v6.1.1
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Tab separated values and matrices

organism: Bos taurus

source_name: peripheral blood

growth_protocol: DMEM (low glucose) supplemented with 30% FBS, 1X P/S and 1X L-glutamine

extract_protocol:
Tissue was collected from one healthy first-lactation Holstein-Frisian cow and cultured until MSC colonies were visible.
According to manufacturer instructions, single cell 3' v3.1 protocol (10X Genomics)

value: peripheral blood

tag: cell line

value: PB-MSC

value: MSC

tag: genotype

value: WT


title: OB102C

description: Sample name = 5

value: obese


title: UC031

description: 3'-biased mRNA


title: GL53_123_Plate3_b18_Gfi1_HE_S315


title: OB102B

description: Sample name = 4

value: skeletal muscle (vastus lateralis)


title: GL78_275_WN-S2-P2_C13_AGM_E11-5_SP_48-49_Gfi1_HE__S269


title: GL78_274_WN-S2-P2_C14_AGM_E11-5_SP_48-49_Gfi1_HE__S268


title: GL53_122_Plate3_o17_Gfi1_neg_IAHC_S314


title: UC029

description: 3'-biased mRNA


title: Bovine Adipose Tissue Mesenchymal Stromal Cells

description: 10X Genomics

source_name: adipose

value: adipose

value: AT-MSC


title: GL78_273_WN-S2-P2_F14_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S267


title: GL78_278_WN-S2-P2_L13_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S272


title: GL53_121_Plate3_m17_Gfi1_neg_IAHC_S313


title: OB103B

description: Sample name = 8

value: Roux-en-Y gastric bypass surgery


title: UC028

description: 3'-biased mRNA

value: UC


title: GL53_126_Plate3_e18_Gfi1_HE_S318

value: AGM

value: CD1/Gf1+ (Thambyrajah et al 2015)


title: GL78_272_WN-S2-P2_G14_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S266

value: 6-8 weeks old


title: GL78_276_WN-S2-P2_P13_AGM_E11-5_SP_48-49_Gfi1_neg_IAHC__S270


title: GL53_120_Plate3_p16_Gfi1_neg_IAHC_S312


title: GL78_271_WN-S2-P2_H14_AGM_E11-5_SP_48-49_Gfi1_pos_IAHC__S265


title: UC027

description: 3'-biased mRNA