title: AML, scRNA-seq

city: Houston

first: Hussein

middle: A.

last: Abbas

state: TX

address: 1400 Holcombe Blvd

department: Leukemia and Genomic Medicine

institute: MD Anderson Cancer Center

data_processing:
All prepared libraries were sequenced at the MD Anderson Cancer Center Advanced Technology Genomics Core
Demutiplex cellular barcodes, read alignment, and generation of gene read count matrix performed using Cell Ranger Single Cell Software Suite
Data were filtered using the following specifications: genes detected in fewer than 3 cells; cells with less than 200 genes detected; cells with more than 15% of mitochondria transcripts
Doublets were evaluated using DoubletFinder
Genome_build: GRCh38
Supplementary_files_format_and_content: RData files were generated using seurat package in Rstudio; Values represent counts of genes (row) detected in cells (column)
readCounts_AML.rda: RData file containing gene read counts for 60753 acute myeloid leukemia cells across 23207 genes collected from 22 (8 pre- and 14 post-treatment) BM aspirates from 8?relapsed/refractory AML patients treated with ICB-based therapy on NCT02397720 protocol.
readCounts_TME_NL.rda: RData file containing gene read counts for 52,641 tumor microenvironment cells (i.e. cells other than AML cells) from the 22?R/R AML and 13,633 bone marrow cells from 2 healthy donors.
meta_data_TME_NL.xls: meta information for cells in readCounts_TME_NL including cell type, original identity, # genes in the cell, etc.
metadata_AML_Cells.xls: meta information for cells in readCounts_AML.rda

source_name: Bone Marrow

extract_protocol:
cells were thawed then gently transferred to a 10 ml media and centrifuged (453 g for 5 min); the cell pellet was resuspended in 10 ml enriched media followed by incubation in 37 °C for 15 min. Then, cells were centrifuged and gently washed twice. Additionally, cells were passed through 35μm strainer and were stained with 0.4% Trypan blue.
10x Single Cell Immune Profiling Solution
scRNA-seq

treatment_protocol: Treatment consisted of azacitidine 75 mg/m2 days 1 to 7 administered intravenously (i.v.) over 60 to 90 min or subcutaneously, and nivolumab 3 mg/kg administered as a 60 to 90 min i.v. infusion on days 1 and 14 of each cycle. Each cycle consisted of 28 days and were repeated every 4 to 6 weeks, depending on count recovery

tag: sample type

value: AML

tag: disease state

value: relapsed/refractory acute myeloid leukemia (AML)

value: Bone marrow

value: AML cells


title: 6875 [E12/H1-PEC-CD2]

status: Public on Mar 10 2022

type: SRA

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

country: Germany

institute: BIH at Charité

library_source: transcriptomic

data_processing:
Fastq-files were quality checked with FastQC (Babraham Bioinformatics)
Trimming was done with Trimmomatic (v0.36) (settings: Nextera adaptors, ILLUMINACLIP:${ADAPTER}:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:3:20, MINLEN:36)
Reads were aligned to mm10 using TopHat and Bowtie 2
Counts per gene were calculated from the bam files by adding all counts mapped to the region of a corresponding gene (Rsamtools).
Raw data were filtered and normalized in R using the scater package.
Assembly: mm10
Supplementary files format and content: Raw counts - tab-deliminated file with reads summerized per gene.
Supplementary files format and content: Normalized data - tab-deliminated file with normelized and log2-transformed data

molecule: total RNA

organism: Mus musculus

source_name: CD4+ Tcells

growth_protocol: Wild-type female C57BL/6 mice (age 8-10 weeks) were purchased from Janvier Labs (Saint-Berthevin, France). All animals were maintained under specific pathogen-free (SPF) conditions and were fed standard chow ad libidum.

extract_protocol:
Capture and processing of single CD4+ T cells was performed using the Fluidigm C1 autoprep system. Sorted CD4+ T cells (50 cells/µl) were mixed with (ratio 6/4) C1 Cell Suspension Reagent (Fluidigm) and subsequently loaded onto a 5-10-μm-diameter C1 Integrated Fluidic Circuit (IFC; Fluidigm).
Reverse transcription and cDNA preamplification were performed using the SMARTer Ultra Low RNA kit (Clontech). Sequencing libraries were prepared using Nextera XT DNA Sample Preparation kit with 96 indices (Illumina), according to the protocol supplied by Fluidigm. Size distribution in final libraries was analyzed by Bioanalyzer High Sensitivity DNA assay (Agilent) and library concentrations were quantified by Qubit High Sensitivity DNA assay (ThermoFisher).

treatment_protocol: H. polygyrus was maintained by serial passage in C57BL/6 mice (H0099/13). Mice were infected with 225 third-stage infective (L3) H. polygyrus larvae via oral gavage in 200µL drinking water. For cure of infection, mice were treated on two consecutive days during the acute stage of infection (day 14-15) with 2mg pyrantel pamoate (Sigma, St. Louis, MO, USA) in 200µL drinking water via oral gavage. On indicated days, mice were sedated via isofluorane inhalation, followed by cervical dislocation. All animal experiments were performed in accordance with the National Animal Protection Guidelines and approved by the German Animal Ethics Committee for the Protection of Animals (LAGeSO, G0176/20).

tag: strain

tag: cell type

value: TH2 cells

tag: tissue

value: PEC

tag: genotype

value: wild type


title: 6874 [E11/G12-PEC-CD2]


title: Normal, scRNA-seq

country: USA

organism: Homo sapiens

source_name: Bone marrow

value: normal

value: relapsed/refractory acute myeloid leukemia (AML) AND healthy control

value: tumor microenvironment cells (ie, cells other than AML cells) AND healthy bone marrow cells


title: Bone marrow progenitor GATA1+ biorep 1, techrep 1

city: Stanford

first: Amy

last: Chen

state: CA

address: 279 Campus Drive West

institute: Stanford University

description:
BMprogenitor_countmatrix.csv
Bone marrow progenitor GATA1+ rep 1.1

library_source: genomic

data_processing:
Adapters were trimmed using cutadapt and reads were mapped using bowtie2 with max fragment length of 2000bp to hg19 (primary bone marrow samples) or hg38 (GM12878 and K562 samples).
Reads were filtered for non-mitochondrial reads, mapq > 20, and properly paired reads. We then removed duplicates using Picard tools
Peaks were called using macs2 with the following parameters on Tn5 insertion sites: --shift -75 --extsize 150 --nomodel --call-summits --nolambda -p 0.01 -B –SPMR
Genome_build: hg19 for bone marrow samples, hg38 for K562 and GM12878

molecule: genomic DNA

source_name: Ficoll-separated bone marrow mononuclear cells

growth_protocol: GM12878 and K562 cells were grown in RPMI 1640 with 15% FBS

extract_protocol: Transposed DNA fragments were purified using Qiagen minelute columns then PCR amplified with barcoded Nextera adapters to generate ATAC-seq libraries

treatment_protocol: Cells were fixed and stained with GATA1 antibody where applicable and sorted based on GATA1 levels. Cells were then transposed with Tn5 and reversal of crosslinks was performed at 37C overnight for fixed samples.

tag: facs sorting

value: Sorted for CD34+CD38+GATA1+ cells


title: 6873 [E10/G11-PEC-CD2]


title: K562 GATA1-high rep 2

description:
K562_countmatrix.csv
K562 GATA1-high rep 2

value: Sorted for highest 15% of GATA1 expression

tag: cell line


title: 6871 [E8/G9-PEC-CD2]


title: 6872 [E9/G10-PEC-CD2]


title: K562 GATA1-low rep 2

description:
K562_countmatrix.csv
K562 GATA1-low rep 2

value: Sorted for lowest 15% of GATA1 expression


title: 6870 [E7/G8-PEC-CD2]


title: 6869 [E6/G7-PEC-CD2]


title: 6868 [E5/G5-PEC-CD2]


title: 6867 [E4/G4-PEC-CD2]


title: SW480 KO rescue, Bru-seq rep2

city: Piscataway

first: Jia

last: Fei

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University - New Brunswick

description: nascent RNA

data_processing:
Library strategy: Bru-seq
Sequencing data were aligned to the hg19 genome by using Bowtie2, and all data were analyzed with HOMER.
Bru-seq Rep 1 samples were sequenced twice for more reads or coverage. Bam files from each sequencing runs were merged using samtools and normalized to 10million total reads.
Genome_build: hg19
Supplementary_files_format_and_content: TagDirectory, bw and bedgraph files were generated using HOMER.

source_name: SW480 NDF KO rescue by WT NDF

growth_protocol: Human Cells were maintained in DMEM with 10% FBS, 5% CO2, 37oC.

extract_protocol:
To stop the reaction, cells on the culture plate were quickly washed once with 10 mL 1x PBS. After complete removal of PBS, 3 mL TRIzol LS (ThermoFisher, Invitrogen, 10296010) was added directly to the cells. RNA was purified by using a standard isopropanol precipitation protocol. The 5-bromouridine-labeled RNAs were isolated as described (https://doi.org/10.1073/pnas.1219192110).
Bru-seq libraries were prepared using NEBNext multiplex small RNA library prep set for Illumina.

treatment_protocol: About 1.5 x 107 cells were seeded and maintained in a 15 cm dish about 16 h before the experiment. Cell culture media were then replaced with 15 mL fresh complete media containing 2 mM 5-bromouridine (MilliporeSigma, 850187). Cells were further incubated for 10 min in the incubator (37 °C, 5% CO2) to let the 5-bromouridine incorporate into the nascent RNA.

value: SW480 NDF KO rescue by WT NDF

tag: antibodies

value: BrdU antibody:BDB555627, BD Biosciences

tag: genotype/variation

value: NDF knockout rescue


title: K562 GATA1-low rep 1

description:
K562_countmatrix.csv
K562 GATA1-low rep 1


title: SW480 KO rescue, Bru-seq rep1

description: nascent RNA


title: 6866 [E3/G3-PEC-CD2]


title: 6880 [F5/H7-PEC-CD2]


title: Purigen 100 cells rep 2

description: GM12878 Purigen 100 rep 2

tag: experiment

value: Purigen 100 cells


title: Purigen 100 cells rep 1

description: GM12878 Purigen 100 rep 1


title: 6865 [E2/G2-PEC-CD2]


title: 6862 [D11/F8-PEC-CD2]


title: SW480 KO, Bru-seq rep2

description: nascent RNA

source_name: SW480 NDF Knockout

value: SW480 NDF Knockout

value: NDF knockout


title: SW480 KO, Bru-seq rep1

description: nascent RNA


title: 6863 [D12/F9-PEC-CD2]


title: 6864 [E1/G1-PEC-CD2]


title: 6861 [D10/F7-PEC-CD2]


title: Purigen 1K cells rep 2

description: GM12878 Purigen 1K rep 2

value: Purigen 1K cells


title: 6859 [D8/F5-PEC-CD2]


title: 6858 [D7/F4-PEC-CD2]


title: SW480 WT, Bru-seq rep2

description: nascent RNA

source_name: SW480 WT

value: SW480 WT

value: WT


title: SW480 NDF ChIP-seq rep2

data_processing:
Sequencing data were aligned to the hg19 genome by using Bowtie2, and all data were analyzed with HOMER.
Bru-seq Rep 1 samples were sequenced twice for more reads or coverage. Bam files from each sequencing runs were merged using samtools and normalized to 10million total reads.
Genome_build: hg19
Supplementary_files_format_and_content: TagDirectory, bw and bedgraph files were generated using HOMER.

extract_protocol: ChIP-seq libraries were prepared using NEBNext DNA library prep kit

treatment_protocol: For ChIP-seq, about 1.5 x 107 cells were crosslinked with 1% PFA for 10 min at 37 °C. Crosslinkings were stopped by adding Glycine. Crosslinked cells were sonicated and processed using a standard immunoprecipitation protocol.

value: hNDF_6 antibody (homemade)


title: Sw480 WT, Bru-seq rep1

description: nascent RNA


title: Purigen 1K cells rep 1

description: GM12878 Purigen 1K rep 1


title: Purigen 5K cells rep 2

description: GM12878 Purigen 5K rep 2

value: Purigen 5K cells


title: 6860 [D9/F6-PEC-CD2]

value: TH2 cells

value: PEC

value: wild type


title: SW480 NDF ChIP-seq rep1


title: 6856 [D5/E10-PEC-CD2]


title: K562 GATA1-high rep 1

description:
K562_countmatrix.csv
K562 GATA1-high rep 1


title: HeLa KO, negative control rep2

source_name: HeLa NDF knockout

treatment_protocol: About 1.5 x 107 wild-type and NDF knockout (KO) HeLa cells were seeded and maintained in a 15 cm dish about 16 h before the experiment. Cell culture media were then replaced with 15 mL fresh complete media containing 2 mM 5-bromouridine (MilliporeSigma, 850187). Cells were further incubated for 10 min in the incubator (37 °C, 5% CO2) to let the 5-bromouridine incorporate into the nascent RNA.

value: HeLa NDF knockout


title: 6857 [D6/F1-PEC-CD2]


title: 6855 [D4/E9-PEC-CD2]


title: Purigen 5K cells rep 1

description: GM12878 Purigen 5K rep 1


title: 6854 [D3/E8-PEC-CD2]


title: 6852 [D1/E5-PEC-CD2]


title: HeLa WT, negative control rep2

source_name: HeLa WT

value: HeLa WT


title: Purigen 25K cells rep 2

description: GM12878 Purigen 25K rep 2

value: Purigen 25K cells


title: HeLa KO, negative control rep1 more reads


title: 6851 [C12/E1-PEC-CD2]


title: Purigen 25K cells rep 1

description: GM12878 Purigen 25K rep 1


title: 6850 [C11/D12-PEC-CD2]


title: HeLa KO, negative control rep1


title: Qiagen 100 cells rep 2

description: GM12878 Qiagen 100 rep 2

value: Qiagen 100 cells


title: 6849 [C10/D11-PEC-CD2]


title: HeLa WT, negative control rep1 more reads

value: BrdU antibody:BDB555627, BD Biosciences


title: 6847 [C8/D9-PEC-CD2]


title: Qiagen 100 cells rep 1

description: GM12878 Qiagen 100 rep 1


title: 6844 [C5/D4-PEC-CD2]


title: 6845 [C6/D7-PEC-CD2]


title: 6846 [C7/D8-PEC-CD2]


title: HeLa WT, negative control rep1


title: 6843 [C4/D2-PEC-CD2]


title: Qiagen 1K cells rep 1

description: GM12878 Qiagen 1K rep 1

value: Qiagen 1K cells


title: Qiagen 5K cells rep 2

description: GM12878 Qiagen 5K rep 2

value: Qiagen 5K cells


title: HeLa KO, Bru-seq rep2


title: HeLa KO, Bru-seq rep1 more reads


title: 6840 [C1/C11-PEC-CD2]


title: HeLa KO, Bru-seq rep1


title: 6839 [B12/C10-PEC-CD2]


title: 6838 [B11/C8-PEC-CD2]


title: HeLa WT, Bru-seq rep2


title: 6853 [D2/E6-PEC-CD2]


title: Qiagen 25K cells rep 2

description: GM12878 Qiagen 25K rep 2

value: Qiagen 25K cells


title: 6836 [B9/C3-PEC-CD2]


title: 6837 [B10/C4-PEC-CD2]


title: 6834 [B7/B12-PEC-CD2]


title: 6848 [C9/D10-PEC-CD2]


title: HeLa WT, Bru-seq rep1 more reads


title: 6835 [B8/C2-PEC-CD2]


title: Qiagen 5K cells rep 1

description: GM12878 Qiagen 5K rep 1


title: GM12878 InTAC-seq rep 3

description:
Fixed_vs_live_countsmatrix.csv
GM12878 InTAC rep 3


title: Qiagen 1K cells rep 2

description: GM12878 Qiagen 1K rep 2


title: 6832 [B5/B10-PEC-CD2]


title: 6833 [B6/B11-PEC-CD2]


title: Col-0_3-OH-C10:0 rep3

city: Hangzhou

first: YAN

middle: BIN

last: WU

state: Zhejiang

address: 866 Yuhangtang Rd

department: College of Agriculture & Biotechnology

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads containing adapters, more than 10% of unknown nucleotides and more than 50% of low quality (Q-value≤20) bases were further filtered by fastp (v0.18.0).
Reads were mapped to ribosome RNA (rRNA) database using Bowtie2 (v2.2.8). The rRNA mapped reads were then removed.
Clean reads were mapped to the reference genome using HISAT (v2.2.4)
The mapped reads of each sample were assembled by using StringTie (v1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis Col-0 seedlings were grown under short-day conditions (i.e., 10 h light/14 h dark).

extract_protocol:
Total RNA was extracted with TRIzol Reagent kit (Thermo Fisher Scientific), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) according to the manufacturer’s protocol.
Library construction and RNA sequencing were performed on the HiSeq2500 platform (Illumina, San Diego, CA) by Gene Denovo Biotechnology.

treatment_protocol: Ten-day old seedlings were incubated overnight in water under light conditions. Thereafter, water was replaced with 5 mM 3-OH-C10:0 or dimethyl sulfoxide (DMSO), and samples were collected 8 h after replacement.

value: seedlings

tag: treatment

value: 5 microM 3-OH-C10:0

tag: age

value: Ten-day old

tag: ecotype

value: Columbia


title: 6831 [B4/B8-PEC-CD2]


title: GM12878 InTAC-seq rep 2

description:
Fixed_vs_live_countsmatrix.csv
GM12878 InTAC rep 2


title: 6842 [C3/D1-PEC-CD2]


title: 6841 [C2/C12-PEC-CD2]


title: Col-0_3-OH-C10:0 rep2


title: 6830 [B3/B7-PEC-CD2]


title: 6829 [B2/B6-PEC-CD2]


title: GM12878 InTAC-seq rep 1

description:
Fixed_vs_live_countsmatrix.csv
GM12878 InTAC rep 1


title: Col-0_3-OH-C10:0 rep1


title: 6828 [B1/B4-PEC-CD2]


title: 6825 [A10/A12-PEC-CD2]


title: 6826 [A11/B1-PEC-CD2]


title: GM12878 live ATAC-seq rep 3

description:
Fixed_vs_live_countsmatrix.csv
GM12878 live rep 3


title: Qiagen 25K cells rep 1

description: GM12878 Qiagen 25K rep 1


title: Col-0_DMSO rep2

value: dimethyl sulfoxide (DMSO)


title: 6823 [A8/A9-PEC-CD2]


title: HeLa WT, Bru-seq rep1

value: WT


title: 6824 [A9/A11-PEC-CD2]

value: TH2 cells


title: 6822 [A7/A8-PEC-CD2]

value: PEC


title: Col-0_DMSO rep1


title: 6821 [A6/A7-PEC-CD2]

value: wild type


title: AT_2C: Col-0 Infected (Alternaria brassicicola infected)

city: Kolkata

first: Sharmila

last: Chattopadhyay

state: West Bengal

address: 4, Raja S.C. Mullick Road,

country: India

institute: CSIR-Indian Institute of Chemical Biology, Kolkata

data_processing:
the data was trimmed using cutadapt initially to remove low quality bases and trim adapters using AGATCGGAAGAGCACACGTCT
Novel miRNAs of P.hexandrum were identified using miRDeep2 using miARma-Seq
Differential expression was obtained using DEGSeq
Target genes were identified using psrnatarget
Genome_build: Arabidopsis_thaliana.TAIR10 / NCBI_Assembly:GCA_000001735.1
Supplementary_files_format_and_content: miRNA sequences and mirdeep2 predicted scores

source_name: Arabidopsis thaliana Col-0

extract_protocol:
total RNA was isolated
NEBNext multiplex smallRNA library kit using manufacturer’s protocol

value: Leaf

tag: developmental stage

value: Mature


title: 6820 [A5/A6-PEC-CD2]


title: AT_2I: AtECS (enhanced GSH level) Infected (Alternaria brassicicola)


title: GM12878 live ATAC-seq rep 1

description:
Fixed_vs_live_countsmatrix.csv
GM12878 live rep 1


title: 6819 [A4/A4-PEC-CD2]


title: 6818 [A3/A3-PEC-CD2]


title: 6817 [A2/A2-PEC-CD2]


title: 6814 [H11/F10-siLP2]

value: siLP


title: 6816 [A1/A1-PEC-CD2]


title: 6827 [A12/B2-PEC-CD2]


title: AT_1C: Col-0 Control


title: Col-0_DMSO rep3


title: AT_1I: AtECS (enhanced GSH level) Control


title: Total RNA from brain without hypothalamus Room temperature mouse  [B19_S1] [re-used]

city: Genève

first: Noushin

last: Hadadi

address: 1 rue Michel-Servet

department: Physiology and Cellular Metabolism

country: Switzerland

institute: University of Geneva

data_processing:
The reads were mapped with STAR aligner v.2.5.3a to the UCSC Mus musculus mm10
reference. The average mapping rate is 80 %.
The transcriptome metrics were evaluated with the Picard tools v.1.141
The table of counts with the number of reads mapping to each gene feature of the UCSC Mus
Genome_build: musculus mm10 was prepared with HTSeq v0.6p1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole brain without hypothalamus

extract_protocol:
Trizol
TruSeq stranded mRNA kit
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina RNA Kits were used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 34 °C for 4 weeks

value: Whole brain without hypothalamus

value: 12 weeks

value: RT


title: Total RNA from brain without hypothalamus Room temperature mouse  [B20_S2] [re-used]


title: 6812 [H9/E5-siLP2]


title: 6813 [H10/D7-siLP2]


title: GM12878 live ATAC-seq rep 2

description:
Fixed_vs_live_countsmatrix.csv
GM12878 live rep 2


title: Total RNA from brain without hypothalamus Room temperature mouse  [B21_S3] [re-used]


title: 6811 [H8/C2-siLP2]


title: VAT CE rep3 [re-used]

source_name: VAT

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina RNA Kits were used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: VAT

value: week 11

value: CE


title: 39735_Hepa-KO50-5

city: Duarte

first: wei

last: chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to mm10 using Tophat2 with default settings
Gene expression level of Ensembl GRCm38 coding genes were quantified using HTSeq v0.6.1p1
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file gene expression counts

source_name: Liver

growth_protocol: Cells were grown and cultivated in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
RNA was extracted with the Quick-RNA Microprep kit (Zymo Research) and treated with DNase I.
RNA-seq libraries were constructed by using KAPA RNA HyperPrep kit with RiboErase, HMR (Roche)
ribosome depleted RNA sequencing

treatment_protocol: Hepa1-6 cells were transduced with lentiviral particles containing scramble vector or midnolin shRNA vector, and selected by puromycin treatment for 7-10 days. For isolation of single-cell-derived colony from puromycin selected cells, limiting dilution of cells was performed.

value: midnolin shRNA vector

tag: Stage

value: hepatoma from C57/L


title: 6809 [H6/F9-lung CD2]

value: lung


title: VAT CE rep1 [re-used]


title: 39733_Hepa-KO25-3


title: Total RNA from brain without hypothalamus 34 degree mouse  [B22_S4] [re-used]

value: WE


title: 39732_Hepa-Scr50-1

value: scramble vector


title: 6802 [G11/B10-siLP2]

value: TH2 cells


title: VAT RT rep2 [re-used]


title: 6807 [H4/F6-lung CD2]


title: VAT RT rep3 [re-used]


title: 6806 [H3/D5-lung CD2]


title: 6805 [H2/C3-lung CD2]


title: 6808 [H5/D8-lung CD2]


title: 6804 [H1/B2-lung CD2]


title: Hepa-wt

value: no treatment


title: 6801 [G10/C7-siLP2]

value: wild type


title: 6800 [G9/G4-siLP2]


title: VAT CE rep2 [re-used]


title: 6797 [G6/D9-lung CD2]


title: 39734_Hepa-KO50-2


title: 39731_Hepa-Scr25-2


title: Spleen RT rep3 [re-used]

source_name: Spleen

value: Spleen


title: Spleen RT rep2 [re-used]


title: 6799 [G8/B2-siLP2]


title: 6798 [G7/G11-lung CD2]


title: VAT RT rep1 [re-used]


title: testis sperm rep2

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

country: France

institute: UMR1078 - Université de Bretagne Occidentale

data_processing:
Sequencing was performed on an Illumina 2500
Quality control of sequencing reads was performed using FastQC.
Adapter removal was perfomed using Trim Galore 0.4.1
Reads were aligned using Bismark v0.16.1 and followed by methylation calling using the corresponding bismark functionality
The methylKit package  was used for data processing (outliers removal) and analysis
Genome_build: mouse genome GRcm38
Supplementary_files_format_and_content: methylation call after filtering (meth_DMS.csv), DMS and DMR with q value < 0.01, methylation difference above 25 % (with outliers removal)

source_name: spermatozoa

growth_protocol: Colonies were reproduced and maintained in the elite animal facility of CHU de Quebec Research Center

extract_protocol:
Spermatozoa were incubated in DNA lysis buffer (100mM Tris HCL (pH 8.5), 5mM EDTA, 0.2% SDS, 200mM NaCL, 100mM DTT, 300 μg/mL proteinase K) overnight at 55 °C. Spermatic genome extraction was performed following the standard phenol: chloroform protocol. Spermatic DNA was precipitated overnight at -20 °C, and washed twice with 70% ethanol. Finally, DNA was resuspended in 30 µL DNAse-free water.
libraries were prepared following Diagenode Premium RRBS kit (Diagenode, C02030032).

treatment_protocol: Untreated

value: Testicular spermatozoa

value: 10-12 weeks


title: testis sperm rep3


title: 6796 [G5/C8-lung CD2]


title: 6810 [H7/C8-siLP2]

value: siLP


title: 6795 [G4/D6-lung CD2]


title: cauda sperm rep3

value: Cauda spermatozoa


title: 6793 [G2/A3-lung CD2]


title: testis sperm rep1


title: Spleen RT rep1 [re-used]

value: RT


title: cauda sperm rep2


title: 6791 [F12/A6-siLP2]


title: Spleen CE rep3 [re-used]


title: 6790 [F11/A10-siLP2]


title: 6792 [G1/A2-lung CD2]


title: Spleen CE rep2 [re-used]


title: cauda sperm rep1


title: 6788 [F9/E4-siLP2]


title: corpus sperm rep2

value: Corpus spermatozoa


title: 6787 [F8/E1-siLP2]


title: 6784 [F5/H7-lung CD2]


title: Spleen CE rep1 [re-used]

value: week 11


title: corpus sperm rep1


title: SAT CE rep3 [re-used]

source_name: SAT

value: SAT

value: CE


title: corpus sperm rep3


title: SAT CE rep2 [re-used]


title: caput sperm rep3

value: Caput spermatozoa


title: 6786 [F7/E11-lung CD2]

value: lung


title: 6785 [F6/C9-lung CD2]


title: SAT CE rep1 [re-used]


title: 6781 [F2/H2-lung CD2]


title: 6783 [F4/C6-lung CD2]


title: 6794 [G3/C5-lung CD2]


title: caput sperm rep2


title: 6789 [F10/B7-siLP2]


title: caput sperm rep1


title: SAT RT rep3 [re-used]


title: 6778 [E11/E9-siLP2]


title: glh1null_WAGO9_rep1

city: Worcester

first: Siyuan

last: Dai

state: MA

address: 368 Plantation St.

department: RTI

institute: UMass Chan Medical School

description: IP small-RNA seq

data_processing:
cutadapt, trim 3' linkers
Bowtie2, mapping to C. elegans genome and transcriptome
Python, extract information from SAM files to csv files
WBcel235
Genome_build: WS262
Supplementary_files_format_and_content: csv

organism: Caenorhabditis elegans

source_name: C. elegans yound adults

growth_protocol: C. elegans were grown on NGM plates with OP50 E. coli

extract_protocol:
Worms were lysated and individual argonuates were immunoprecipitated by anti-FLAG antibody, and argonaute-bound small-RNAs were later extracted by Trizol.
Purified small-RNAs were pre-treated with PIR-1 and ligated with 3' and 5' linkers. cDNA were generated by reverse transcribed and further amplified by PCR. A size selection procedure on native PAGE were carried out.

treatment_protocol: untreated

value: untreated

tag: molecule type

value: small RNAs


title: glh1null_WAGO9_rep2

description: IP small-RNA seq


title: SAT RT rep1 [re-used]


title: glh1null_WAGO2_rep2

description: IP small-RNA seq


title: 6777 [E10/A7-siLP2]

value: TH2 cells


title: Liver RT rep1 [re-used]

value: Liver


title: glh1null_input_rep1

description: IP small-RNA seq


title: 6782 [F3/B5-lung CD2]

value: wild type


title: GM-CSF induced BMDMs_LPS

city: Qingdao

first: zhao

last: zhan

state: Shandong

address: No.23 HongKong East Road,Laoshan District

department: School of Medicine and Pharmacy

institute: Ocean University of China

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

source_name: macrophage

growth_protocol: GM-CSF stimulated for 7 days

extract_protocol:
The medium was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GSK-J4 for 2 days and/or LPS for 1 hour

value: bone marrow derived macrophage

value: LPS for 1 hour


title: 6776 [E9/D4-siLP2]

source_name: CD4+ Tcells


title: GM-CSF induced BMDMs_untreated

description: G


title: 6775 [E8/B1-siLP2]


title: glh1null_input_rep2

description: IP small-RNA seq


title: glh1null_WAGO1_rep1

description: IP small-RNA seq


title: GM-CSF induced BMDMs_G

value: GSK-J4 for 2 days


title: glh1null_CSR1_rep2

description: IP small-RNA seq


title: STARR_motif_modifications_DNA_input_rep2

first: Jesse

last: Engreitz

address: 240 Pasteur Drive, Room 3700

department: Department of Genetics

institute: Stanford University School of Medicine

description:
STARR-seq library transfected DNA
starr_seq_100x100_all_experimental_counts_file.txt

data_processing:
Library strategy: STARR-seq
Illumina bcl2fastq2-v2.20.0 used for basecalling.
STARR-seq: bowtie2 was used to align sequences to custom indices with options: --maxins 2000 -p 16 --no-discordant --no-mixed --fast
motif modification STARR-seq: bowtie2 was used to align sequences to custom indices with options: --maxins 2000 -p 16 --no-discordant --no-mixed --fast --score-min L,-0.7,-0.7
PRO-Seq: bowtie was used to align sequences to hg19 with options: --wrapper basic-0 -p 4, and reads were counted in gene bodies with a custom script.
ExP 1Kx1K barcode to promoter aligned reads were counted with a custom python script to associate ExP barcodes to promoter sequences.
ExP 1Kx1K DNA and RNA reads were demultiplexed with the Je-suite demultiplex version 2.0 and counted with a custom python script.
HS-STARR-seq DNA and RNA reads were counted with a custom python script.
Motif modification STARR-seq Promoter + barcode aligned reads were counted with a custom python script to associate motif_modification barcodes to promoter sequences and quality filtered.
Motif modification STARR-seq DNA and RNA reads were counted with a custom python script.
Assembly: hg19
Supplementary files format and content: tabular separated values - promoter and barcode read count
Supplementary files format and content: tab separated values - K562 ExP 1Kx1K DNA and RNA counts
Supplementary files format and content: tab separated values - Hybrid-selected K562 Enhancer regions STARR-seq DNA and RNA counts
Supplementary files format and content: tab separated values - Hybrid-selected Promoter regions STARR-seq DNA and RNA counts

source_name: transfected plasmid reporter

growth_protocol: We maintained cells at a density between 100,000 and 1,000,000 cells per ml in RPMI-1640 (Thermo Fisher Scientific) with 10% heat-inactivated FBS, 2 mM L-glutamine and 100 units per ml streptomycin and 100 mg ml−1 penicillin by diluting cells 1:8 in fresh medium every 3 days. Cell lines were regularly tested for mycoplasma.

extract_protocol:
STARR-seq: We extracted RNA using 3 RNAeasy columns per 25-million cells and isolated polyA+ mRNA using the Qiagen Oligotex mRNA kit.  Motif-modification STARR-seq: We extracted RNA using 3 RNAeasy columns per 50-million cell replicate and isolated polyA+ mRNA using the Poly(A)Purist MAG kit from Thermo Fisher Scientific.  PRO-Seq: We performed PRO-Seq essentially as described in Kwak H et al. Science 2013.
We performed reverse transcription using SuperScript IV, then performed a junction PCR using intron-spanning primers, then finally a sequence-ready PCR.

tag: library type

value: STARR-seq transcript DNA


title: 6780 [F1/H1-lung CD2]


title: GM-CSF induced BMDMs_G_LPS

value: GSK-J4 for 2 days and LPS for 1 hour


title: 6774 [E7/C11-lung CD2]


title: Liver RT rep2 [re-used]

value: RT


title: 6779 [E12/E12-siLP2]

value: siLP


title: 6773 [E6/B9-lung CD2]


title: Liver RT rep3 [re-used]

value: week 11


title: SAT RT rep2 [re-used]

value: SAT


title: STARR_motif_modifications_DNA_input_rep1


title: Liver CE rep2 [re-used]

value: CE


title: WT_WAGO9_rep2

description: IP small-RNA seq

value: wild-type


title: STARR_motif_modifications_rep4

description:
STARR-seq library reporter-derived mRNA
starr_seq_100x100_all_experimental_counts_file.txt

value: STARR-seq transcript RNA


title: 6772 [E5/F7-lung CD2]

value: lung


title: glh1null_CSR1_rep1

description: IP small-RNA seq

value: untreated

value: small RNAs


title: 6771 [E4/B6-lung CD2]

value: TH2 cells


title: Ileum CE rep3 [re-used]

source_name: Ileum

value: Ileum

value: wild type


title: Liver CE rep1 [re-used]

value: Liver


title: STARR_motif_modifications_rep2


title: Ileum CE rep1 [re-used]


title: WT_WAGO9_rep1

description: IP small-RNA seq


title: WT_WAGO2_rep2

description: IP small-RNA seq


title: 6768 [E1/G1-lung CD2]


title: 6769 [E2/G2-lung CD2]


title: WT_input_rep2

description: IP small-RNA seq


title: Liver CE rep3 [re-used]


title: HeLa_T4_rep3 [CTL_R3_T4]

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
RNA-seq read quality was evaluated using FastQC
Sequence reads were aligned to the human genome hg19 using STAR after removing reads which aligned to rRNA, tRNA and other abundant annotations. Gene quantification was determined in the STAR function using parameters "--quantMode GeneCounts".
Assembly: hg19
Supplementary files format and content: HeLa_raw_counts.txt is a tab-delimited file of raw RNA-Seq read counts per gene, per sample.

molecule: polyA RNA

source_name: HeLa

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% of foetal bovine serum in a 5% CO2 atmosphere at 37°C.

extract_protocol:
Nucleospin RNA kit (Macherey-Nagel)
Illumina TruSeq stranded mRNA

treatment_protocol: Biological replicates of HeLa cells were treated with 5 µM actinomycin D for 0, 1, 2 and 4h.

tag: timepoint

tag: replicate

value: HeLa


title: 6770 [E3/H4-lung CD2]

tag: strain

tag: cell type


title: STARR_motif_modifications_rep3


title: WT_input_rep1

description: IP small-RNA seq

tag: genotype


title: WT_WAGO1_rep1

description: IP small-RNA seq


title: Ileum CE rep2 [re-used]

tag: tissue


title: HeLa_T2_rep3 [CTL_R3_T2]

tag: cell line


title: 6765 [D10/G6-siLP2]


title: Ileum RT rep3 [re-used]


title: STARR_motif_modifications_rep1


title: 6767 [D12/D12-siLP2]


title: Ileum RT rep2 [re-used]


title: WT_CSR1_rep2

description: IP small-RNA seq


title: WT_CSR1_rep1

description: IP small-RNA seq


title: 6764 [D9/C4-siLP2]


title: HeLa_T1_rep3 [CTL_R3_T1]


title: 6766 [D11/D9-siLP2]


title: HeLa_T4_rep2 [CTL_R2_T4]


title: Hypothalamus CE rep2 [re-used]

source_name: Hypothalamus

value: Hypothalamus


title: Hypothalamus RT rep3 [re-used]


title: HeLa_T0_rep3 [CTL_R3_T0]


title: Hypothalamus RT rep2 [re-used]


title: 6763 [D8/A1-siLP2]


title: Ileum RT rep1 [re-used]


title: 6761 [D6/A9-lung CD2]


title: HeLa_T4_rep1 [CTL_R1_T4]


title: Hypothalamus CE rep1 [re-used]


title: 6762 [D7/B11-lung CD2]


title: 6759 [D4/A6-lung CD2]


title: 6760 [D5/E7-lung CD2]


title: HeLa_T2_rep2 [CTL_R2_T2]


title: HeLa_T1_rep2 [CTL_R2_T1]


title: HeLa_T2_rep1 [CTL_R1_T2]


title: Hypothalamus CE rep3 [re-used]


title: Brain RT rep3 [re-used]

source_name: Brain

value: Brain


title: Hypothalamus RT rep1 [re-used]

value: RT


title: Brain RT rep2 [re-used]


title: A/E9a;NRASG12D;Ifnar1-/- pano_rep3_RNAseq

city: Melbourne

first: Izabela

last: Todorovski

state: VIC

address: 305 Grattan Street

department: Cancer Research Division

country: Australia

institute: Peter MacCallum Centre

data_processing:
Sequencing files were demultiplexed (Bcl2fastq, v2.17.1.14) and QC was performed on FASTQ files using FASTQC (v0.11.6).
Sequencing reads were trimmed (cutadapt v2.1) and aligned to the mm10 mouse reference genome using HISAT2 (v2.1.0).
Read counting across genomic features was performed using FeatureCounts (Subread, v2.0.0)
Differential gene expression analysis was performed using Voom-Limma in R (v3.42.2)
Genome_build: mm10
Supplementary_files_format_and_content: Raw Counts

source_name: leukemia cells

extract_protocol:
Spleens were removed and leukemia cells sorted, RNA was isolated using Trizol reagent and the RNeasy MinElute kit (QIAGEN) according to the manufacturers instructions
mRNA libraries were generated using Illumina TruSeq RNA LibraryPrep Kit with 1 ug of total RNA.

value: spleen

value: leukemia cells

value: panobinostat


title: 6758 [D3/G4-lung CD2]


title: A/E9a;NRASG12D;Ifnar1-/- pano_rep2_RNAseq


title: HeLa_T0_rep1 [CTL_R1_T0]


title: HeLa_T1_rep1 [CTL_R1_T1]


title: 6757 [D2/F2-lung CD2]


title: Brain RT rep1 [re-used]

value: week 11


title: 6756 [D1/F1-lung CD2]


title: shA673-1c_T4_rep3 [CTL_R3_T4]

data_processing:
RNA-seq read quality was evaluated using FastQC
Sequence reads were aligned to the human genome hg19 using STAR. STAR quantMode was used to obtain raw read counts.
Assembly: hg19
Supplementary files format and content: A673_raw_counts.txt is a tab-delimited file of raw RNA-Seq read counts per gene, per sample.

source_name: shA673-1c (Ewing sarcoma)

growth_protocol: Cells were cultured in a 37°C, 5% CO2 humidified incubator in DMEM high glucose with 10% FBS, 1% Penn/Strep, 20 µg/ml Blasticidin and 200 µg/ml zeocyn

treatment_protocol: Biological replicates of shA673-1c cells were seeded in 6-well plates and treated with 5 µM ActD for 0, 1, 2 and 4h.

value: shA673-1c (Ewing sarcoma)


title: shA673-1c_T2_rep3 [CTL_R3_T2]


title: A/E9a;NRASG12D;Ifnar1-/- pano_rep1_RNAseq


title: A/E9a;NRASG12D;Ifnar1-/- vehicle_rep3_RNAseq

value: vehicle


title: HeLa_T0_rep2 [CTL_R2_T0]


title: Brain CE rep2 [re-used]

value: CE


title: Brain CE rep1 [re-used]


title: 6754 [C11/H8-siLP2]

value: siLP


title: shA673-1c_T1_rep3 [CTL_R3_T1]


title: BAT CE rep3 [re-used]

source_name: BAT

value: BAT


title: A/E9a;NRASG12D;Ifnar1-/- vehicle_rep2_RNAseq


title: 6753 [C10/E6-siLP2]

value: TH2 cells


title: BAT CE rep2 [re-used]


title: shA673-1c_T0_rep3 [CTL_R3_T0]


title: A/E9a;NRASG12D;Ifnar1-/- vehicle_rep1_RNAseq


title: A/E9a;NRASG12D_pano_rep3_RNAseq

extract_protocol:
Spleens were removed and leukemia cells sorted, RNA was isolated using Trizol reagent and the RNeasy MinElute kit (QIAGEN) according to the manufacturers instructions.
mRNA libraries were generated using Illumina TruSeq RNA LibraryPrep Kit with 1 ug of total RNA.


title: shA673-1c_T4_rep2 [CTL_R2_T4]


title: 6752 [C9/E3-siLP2]


title: 6751 [C8/H12-lung CD2]

value: lung


title: BAT CE rep1 [re-used]

value: wild type


title: A/E9a;NRASG12D_pano_rep2_RNAseq


title: BAT RT rep3 [re-used]


title: shA673-1c_T2_rep2 [CTL_R2_T2]


title: Brain CE rep3 [re-used]


title: A/E9a;NRASG12D_vehicle_rep3_RNAseq


title: shA673-1c_T0_rep2 [CTL_R2_T0]


title: 6755 [C12/C11-siLP2]


title: A/E9a;NRASG12D_vehicle_rep2_RNAseq


title: shA673-1c_T4_rep1 [CTL_R1_T4]


title: 6747 [C4/H5-lung CD2]


title: A/E9a;NRASG12D_vehicle_rep1_RNAseq


title: 6750 [C7/G10-lung CD2]


title: 6746 [C3/E4-lung CD2]


title: shA673-1c_T1_rep1 [CTL_R1_T1]


title: BAT RT rep1 [re-used]


title: Total RNA from BAT 34 degree mouse  [BA36_S12] [re-used]

source_name: Brown adipose tissue

value: Brown adipose tissue

value: 12 weeks

value: WE


title: shA673-1c_T0_rep1 [CTL_R1_T0]


title: shA673-1c_T2_rep1 [CTL_R1_T2]


title: 6744 [C1/E1-lung CD2]


title: BAT RT rep2 [re-used]


title: 6748 [C5/D7-lung CD2]


title: 6749 [C6/H8-lung CD2]


title: Total RNA from BAT 34 degree mouse  [BA35_S11] [re-used]


title: Total RNA from BAT 34 degree mouse  [BA34_S10] [re-used]


title: pDC_24hrs

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

data_processing:
The raw data from the sequencer was demultiplexed into reads along with cell and unique molecular identified  barcodes which were then aligned to GrCH38 human reference and quantified via CellRangerV3 from 10x Genomics.
For each condition, cells belonging to each donor were determined using Demuxlet (Kang et al.,  Nature Biotechnology 2018).
Further downstream analysis was done using Seurat (Stuart, Butler  et al.,Cell  2019). Doublets and ambiguous cells identified by Demuxlet were removed along with any cell with < 200 unique genes, any cell expressing > 20% mitochondrial genes and any gene not identified in at least 3 cells.
Clusters were identified using Seurat’s SCT transform analysis using 30 PCs with time point as an effect being removed using Harmony (Korsunsky et al., Nature Methods 2019).
Genome_build: Hg38 (10x’s reference: refdata-cellranger-GRCh38-3.0.0)

source_name: peripheral blood enriched for  pDCs

growth_protocol: PDCs were cultured in Advanced RPMI-1640 supplemented with 5% FCS

extract_protocol:
Fresh whole blood was drawn from three donors into sodium-heparin vacutainers. PBMCs were extracted over Ficoll. pDCs were isolated from PBMCs using Miltenyi Plasmacytoid Dendritic Cell Isolation Kit II, human or EasySep Human Plasmacytoid DC Enrichment Kit. pDC purity was determined by flow cytometry against BDCA2 and/or BDCA4. pDCs were counted, pooled at equal ratios from the 3 donors for each time condition, washed, resuspended in PBS/0.4% BSA at a final concentration of 1000 cells/ul
GEMs were generated using a 10x Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, following the manufacturer’s recommendations. Single cell libraries were assessed and quantitated using an Aglient High Sensitivity DNA chip. Libraries were loaded onto a High Output Cartridge v2 at 1.8pM and run on an Illumina NextSeq 500 sequencer.

treatment_protocol: Influenza virus H1N1 A/PR/8/34 at 0.4 HAU/mL

value: plasmacytoid dendritic cells

value: 24 hrs

value: influenza virus H1N1 A/PR/8/34 at 0.4 HAU/mL


title: Bonemarrow RT rep5 [re-used]

source_name: Bone marrow

value: Bone marrow

value: RT


title: Bonemarrow RT rep4 [re-used]

value: week 11


title: A/E9a;NRASG12D_pano_rep1_RNAseq

value: spleen

value: leukemia cells

value: panobinostat


title: Bonemarrow RT rep6 [re-used]


title: shA673-1c_T1_rep2 [CTL_R2_T1]

value: shA673-1c (Ewing sarcoma)


title: 6743 [B12/A11-siLP2]

extract_protocol:
Capture and processing of single CD4+ T cells was performed using the Fluidigm C1 autoprep system. Sorted CD4+ T cells (50 cells/µl) were mixed with (ratio 6/4) C1 Cell Suspension Reagent (Fluidigm) and subsequently loaded onto a 5-10-μm-diameter C1 Integrated Fluidic Circuit (IFC; Fluidigm).
Reverse transcription and cDNA preamplification were performed using the SMARTer Ultra Low RNA kit (Clontech). Sequencing libraries were prepared using Nextera XT DNA Sample Preparation kit with 96 indices (Illumina), according to the protocol supplied by Fluidigm. Size distribution in final libraries was analyzed by Bioanalyzer High Sensitivity DNA assay (Agilent) and library concentrations were quantified by Qubit High Sensitivity DNA assay (ThermoFisher).

value: siLP


title: Total RNA from BAT Room temperature mouse  [BA33_S9] [re-used]


title: 6742 [B11/D8-siLP2]

value: TH2 cells


title: Bonemarrow RT rep1 [re-used]


title: 6741 [B10/D6-siLP2]


title: pDC_baseline

source_name: peripheral blood enriched for pDCs

value: 0 hrs


title: Bonemarrow RT rep3 [re-used]

value: wild type


title: Bonemarrow CE rep5 [re-used]

value: CE


title: Bonemarrow CE rep6 [re-used]


title: Unstimulated human airway epithelium cells [Med_D4_6h]

city: Bilthoven

first: Alberto

last: Miranda-Bedate

state: Utrecht

address: Antonie van Leeuwenhoeklaan 9

department: Department of Immune Mechanisms (IMM)

country: Netherlands

institute: RIVM

data_processing:
Basecalling and demultiplexing was performed using bcl2fastq2 Conversion Software v2.20
RNAseq reads were aligned to the Homo sapiens reference genome (GRCh38) and the corresponding transcript annotations (Ensembl release 103 for Homo sapiens genome) using kallisto (v0.46.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_counts_HAE_all_samples.txt: Tab-delimited text file includes raw gene counts of all HAE samples used in this study

source_name: Bronchia/Trachea

growth_protocol: Primary human bronchial/tracheal epithelial cells from four healthy donors (Lonza, Basel, Switzerland, catalog#: CC-2540) were cultured in serum-free PneumaCult-Ex medium (STEMCELL, Vancouver, Canada) supplemented with 480 ng/ml hydrocortisone (STEMCELL) and 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma, Saint Louis, Missouri, USA) at 37°C and 5% CO2. ReagentPack Subculture Reagents (Lonza) were used to passage the cells. Before reaching passage 4, a total of 50,000 cells were seeded into 6.5 mm transwell plates with 0.4 μm pore polyester membrane inserts (Corning Inc., Corning, New York, USA) that were pre-coated with 30 μg/ml Collagen I Rat Tail Protein (ThermoFisher, Waltham, Massachusetts, USA) for 45 min at 37°C. After 2-4 days of submerged culture in complete PneumaCult-Ex medium (500 μl in basal and 100 μl in apical compartment) the cells confluently covered the membrane at which point the cells were airlifted. Meaning, medium was removed from the apical compartment and medium in the basal compartment was replaced with 500 μl serum-free PneumaCult-ALI medium (STEMCELL) supplemented with 480ng/ml hydrocortisone (STEMCELL), 4 μg/ml Heparin (STEMCELL), 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma), creating an air-liquid interface (ALI). These HAE air-liquid cultures were differentiated for 6-8 weeks towards a pseudostratified epithelial cell layer. PneumaCult-ALI medium in the basal compartment was refreshed every 2-3 days and after 2 weeks the apical surface was washed weekly with 200 μl PBS for 5 min at 37°C to remove excessive mucus.

extract_protocol:
The column-based miRNeasy RNA isolation kit (Qiagen) was used. RNA was isolated according to the manufacturer’s instructions with minor modifications (extra column-washing step with 80% ethanol before extracting the RNA with RNase-free water)
To determine RNA quality and integrity we used Lab-on-Chip analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples with an RNA integrity number above 8 were used.
The TruSeq Stranded mRNA Library Prep Kit from Illumina was used to construct libraries

treatment_protocol: Differentiated HAE air-liquid cells were stimulated with 3 strains of live B. pertussis at MOI 100 for 6 hours at the apical (air) side of the plate

value: human airway epithelium cells

tag: donor

tag: agent

value: Unstimulated

tag: b. pertussis strain

value: Mock

tag: b. pertussis year of isolation

tag: batch of sequencing


title: Bonemarrow CE rep4 [re-used]

tag: age

tag: treatment


title: Bonemarrow CE rep3 [re-used]


title: Total RNA from liver 34 degree mouse  [L28_S22] [re-used]

source_name: liver

value: liver

value: 12 weeks

value: WE


title: 6737 [B6/F8-lung CD2]

data_processing:
Fastq-files were quality checked with FastQC (Babraham Bioinformatics)
Trimming was done with Trimmomatic (v0.36) (settings: Nextera adaptors, ILLUMINACLIP:${ADAPTER}:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:3:20, MINLEN:36)
Reads were aligned to mm10 using TopHat and Bowtie 2
Counts per gene were calculated from the bam files by adding all counts mapped to the region of a corresponding gene (Rsamtools).
Raw data were filtered and normalized in R using the scater package.
Assembly: mm10
Supplementary files format and content: Raw counts - tab-deliminated file with reads summerized per gene.
Supplementary files format and content: Normalized data - tab-deliminated file with normelized and log2-transformed data

value: lung


title: Bonemarrow CE rep2 [re-used]

value: Bone marrow

value: week 11


title: Total RNA from liver Room temperature mouse  [L27_S21] [re-used]

value: RT


title: human airway epithelium cells stimulated with B. pertussis strain Bp2 [B4436_D3_6h]

value: B. pertussis


title: Unstimulated human airway epithelium cells [Med_D3_6h]


title: 6738 [B7/B10-lung CD2]


title: Bonemarrow CE rep1 [re-used]


title: 6735 [B4/F5-lung CD2]


title: Total RNA from BAT Room temperature mouse  [BA31_S7] [re-used]

value: Brown adipose tissue


title: Spinalcord RT rep5 [re-used]

source_name: spinal cord

value: spinal cord


title: Total RNA from BAT Room temperature mouse  [BA32_S8] [re-used]


title: human airway epithelium cells stimulated with B. pertussis strain Bp2 [B4436_D4_6h]


title: 6736 [B5/C7-lung CD2]

value: TH2 cells


title: human airway epithelium cells stimulated with B. pertussis strain Bp2 [B4436_D2_6h]


title: 6745 [C2/E2-lung CD2]


title: Total RNA from Iliver Room temperature mouse  [L26_S20] [re-used]


title: Total RNA from liver 34 degree mouse  [L30_S24] [re-used]


title: Spinalcord RT rep4 [re-used]


title: Total RNA from liver Room temperature mouse  [L25_S19] [re-used]


title: human airway epithelium cells stimulated with B. pertussis strain Bp1 [B4393_D4_6h]


title: human airway epithelium cells stimulated with B. pertussis strain Bp1 [B4393_D3_6h]


title: Total RNA from brain without hypothalamus 34 degree mouse  [B23_S5] [re-used]

source_name: Whole brain without hypothalamus

value: Whole brain without hypothalamus


title: 6732 [B1/D1-lung CD2]

source_name: CD4+ Tcells

value: wild type


title: human airway epithelium cells stimulated with B. pertussis strain Bp1 [B4393_D2_6h]


title: 6734 [B3/A4-lung CD2]


title: Spinalcord RT rep2 [re-used]


title: Unstimulated human airway epithelium cells [Med_D2_6h]


title: Total RNA from Ileum 34 degree mouse  [I18_S18] [re-used]

source_name: ileum

value: ileum


title: Total RNA from liver 34 degree mouse  [L29_S23] [re-used]


title: human airway epithelium cells stimulated with B. pertussis strain Bp3 [B1707_D4_6h]

value: human airway epithelium cells


title: Total RNA from brain without hypothalamus 34 degree mouse  [B24_S6] [re-used]


title: 6730 [A11/F7-siLP2]

value: siLP


title: Total RNA from Ileum 34 degree mouse  [I16_S16] [re-used]


title: human airway epithelium cells stimulated with B. pertussis strain Bp3 [B1707_D3_6h]


title: human airway epithelium cells stimulated with B. pertussis strain Bp3 [B1707_D2_6h]


title: Spinalcord RT rep1 [re-used]


title: Spinalcord CE rep5 [re-used]

value: CE


title: Spinalcord CE rep4 [re-used]


title: Total RNA from Ileum Room temperature mouse  [I15_S15] [re-used]


title: 6731 [A12/G10-siLP2]


title: 6729 [A10/C6-siLP2]


title: Total RNA from Ileum 34 degree mouse  [I17_S17] [re-used]


title: 6728 [A9/E2-siLP2]


title: 6733 [B2/D2-lung CD2]


title: Total RNA from Ileum Room temperature mouse  [I13_S13] [re-used]


title: Spinalcord CE rep1  [re-used]


title: 6727 [A8/B12-lung CD2]


title: Spinalcord CE rep2 [re-used]


title: 6725 [A6/E8-lung CD2]


title: CW02-48

city: New York

first: Li

last: Gan

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: ReadCount.xlsx

data_processing:
For samples 1-34, RNA-seq reads were mapped using the BlueBee genomics platform and the GENCODE GRCm38 mouse genome (Lexogen QuantSeq 2.2.3) as reference genome. For samples 35-58, RNA-seq read mapping was performed using the STAR program and same GENCODE GRCm38 mouse genome was used as reference. Total mapping rate is more than 95% and unique mapping rate is >90%. The read count table was generated with the RSEM program.
Counts were normalized with the trimmed mean normalization method.
Differential gene expression was calculated with R package edgeR and limma.
Genome_build: GRCm38

source_name: cortical tissue from IkbkbCA male mice

extract_protocol:
total RNA was extracted using Quick-RNA miniprep (R1055, Zymo Research).
cDNA libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530S, New England Biolabs)

tag: age (m)

tag: Sex

value: M

value: brain

value: ikbkbCA


title: Total RNA from Quadriceps 34 degree mouse  [Q12_S28] [re-used]

source_name: Quadriceps

value: Quadriceps

value: 12 weeks

value: WE


title: Spinalcord RT rep3 [re-used]

value: week 11

value: RT


title: 6724 [A5/A7-lung CD2]

value: lung


title: Total RNA from Quadriceps 34 degree mouse  [Q11_S27] [re-used]


title: Bonemarrow RT rep2 [re-used]

value: Bone marrow


title: CW02-45

description: ReadCount.xlsx


title: Total RNA from Quadriceps 34 degree mouse  [Q10_S26] [re-used]


title: 6723 [A4/E5-lung CD2]

value: TH2 cells


title: CW02-44

description: ReadCount.xlsx


title: Total RNA from Quadriceps Room temperature mouse  [Q9_S36] [re-used]


title: CW02-39

description: ReadCount.xlsx

value: F


title: 6722 [A3/H3-lung CD2]

value: wild type


title: Total RNA from Quadriceps Room temperature mouse  [Q7_S34] [re-used]


title: Total RNA from Quadriceps Room temperature mouse  [Q8_S35] [re-used]


title: CW02-37

description: ReadCount.xlsx

source_name: cortical tissue from IkbkbWT male mice

value: ikbkbWT


title: CW02-35

description: ReadCount.xlsx


title: Spinalcord CE rep3 [re-used]

value: spinal cord


title: Total RNA from Ileum Room temperature mouse  [I14_S14] [re-used]

value: ileum


title: Total RNA from Quadriceps 10 degree cold mouse  [Q6_S33] [re-used]

value: CE


title: 6739 [B8/G12-lung CD2]


title: CW02-34

description: ReadCount.xlsx

value: M


title: 6720 [A1/A1-lung CD2]


title: 6674 [E3/H11-lung CD1]


title: 6726 [A7/G9-lung CD2]


title: CW02-28

description: ReadCount.xlsx

source_name: cortical tissue from Ikbkb-/-; P301S+ male mice

value: brain


title: Total RNA from Quadriceps 10 degree cold mouse  [Q4_S31] [re-used]


title: Total RNA from Quadriceps Room temperature mouse  [Q3_S30] [re-used]


title: Total RNA from Quadriceps 10 degree cold mouse  [Q5_S32] [re-used]


title: CW02-33

description: ReadCount.xlsx


title: 6673 [E2/H8-lung CD1]


title: 6672 [E1/H7-lung CD1]


title: Total RNA from Quadriceps Room temperature mouse  [Q2_S29] [re-used]


title: 6671 [D12/H6-lung CD1]


title: CW02-11

description: ReadCount.xlsx


title: Total RNA from Quadriceps Room temperature mouse  [Q1_S25] [re-used]


title: 6670 [D11/H4-lung CD1]


title: 6721 [A2/C2-lung CD2]


title: CW02-29

description: ReadCount.xlsx

source_name: cortical tissue from Ikbkb+/+ ; P301S+ male mice


title: CW02-12

description: ReadCount.xlsx


title: miT7_1

city: Ningbo

first: cao

last: yuhao

state: Zhejiang Province

address: 818 Fenghua Road, Jiangbei District, Ningbo City, Zhejiang Province

institute: Medical School of Ningbo University

data_processing:
Raw data (raw reads) of FASTQ format was firstly processed through custom Perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing ploy-N, with 5' adapter contaminants, without 3' adapter or the insert tag, containing ploy A or T or G or C, and low-quality reads from raw data. The small RNA tags were mapped to the reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference. Differential expression analysis of day 0 and day 7 was performed using the DESeq R package (3.0.3). The P-values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 or 0.01 was set as the threshold for significantly differential expression by default
n the target gene candidates of differentially expressed miRNAs, gene ontology (GO) enrichment analysis was employed. GOseq based Wallenius non-central hypergeometric distribution, which could adjust for gene length bias, was implemented for GO enrichment analysis. The underlying functions of miRNAs were predicted through KEEG pathway enrichment. The statistical enrichment of the target gene candidates in KEGG pathways was tested using the KOBAS software
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: skin

extract_protocol:
Total RNA was extracted according to the manufacturer's instructions using TRIzol reagent (Invitrogen, USA). RNA integrity was assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies).
A total amount of 3μg total RNA per sample was used as input material for the small RNA library. Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA, and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded deoxyribonucleic acid (DNA) adaptor into a double-stranded DNA molecule. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA, and piRNA. After synthesis of the first-strand cDNA, PCR amplification is performed. DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors). At last, library quality was assessed on the Agilent Bioanalyzer 2100. The library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.

treatment_protocol: ine mice were randomly divided into three groups. After anesthesia with 1% pentobarbital sodium, a hole punch with a diameter of 8 mm was used to model the skin wound on the mouse back. The skin from the mouse back cut by the punch was collected as the skin samples of wound healing Day 0. After quick-frozen with liquid nitrogen, the skin samples were stored at -80 ⁰C immediately. The wounded mice were raised under normal conditions. On day 7, day 14, and day 21, the skin samples from wound edges of each group were collected and frozen in the same way.

value: skin

value: adult (6-month-old) female mice

value: Construction of a diabetic mouse model，After anesthesia with 1% pentobarbital sodium, a hole punch with a diameter of 8 mm was used to model the skin wound on the mouse back. The skin from the mouse back cut by the punch was collected as the skin samples of wound healing Day 0


title: miT7_3


title: pDC_6hrs

value: plasmacytoid dendritic cells

value: 6 hrs

value: influenza virus H1N1 A/PR/8/34 at 0.4 HAU/mL


title: miD7_2

value: On day 7, the skin samples from wound edges of each group were collected and frozen in the same way


title: 6668 [D9/H2-lung CD1]

first: Karsten

last: Jürchott

address: Luisenstraße

institute: BIH at Charité

value: lung


title: 6667 [D8/H1-lung CD1]

value: TH2 cells


title: miD7_3


title: 6665 [D6/G11-lung CD1]


title: CW02-05

description: ReadCount.xlsx


title: CW02-30

description: ReadCount.xlsx

source_name: cortical tissue from Ikbkb-/- male mice

value: ikbkb-/-


title: miD7_1


title: 6664 [D5/G10-lung CD1]

value: wild type


title: miD0_3

value: After anesthesia with 1% pentobarbital sodium, a hole punch with a diameter of 8 mm was used to model the skin wound on the mouse back. The skin from the mouse back cut by the punch was collected as the skin samples of wound healing Day 0


title: CW02-01

description: ReadCount.xlsx


title: CW02-19

description: ReadCount.xlsx


title: 6740 [B9/A3-siLP2]

value: siLP


title: miD0_2


title: CW02-27

description: ReadCount.xlsx


title: CW02-06

description: ReadCount.xlsx


title: 6663 [D4/G9-lung CD1]


title: CW02-02

description: ReadCount.xlsx


title: 6662 [D3/G7-lung CD1]


title: miD0_1


title: 6719 [H12/B12-lung CD1]


title: 6669 [D10/H3-lung CD1]


title: CW02-08

description: ReadCount.xlsx


title: miT7_2


title: 6661 [D2/G6-lung CD1]


title: Podo_C: Control sample of P.hexandrum

data_processing:
the data was trimmed using cutadapt initially to remove low quality bases and trim adapters using AGATCGGAAGAGCACACGTCT
Novel miRNAs of P.hexandrum were identified using miRDeep2 using miARma-Seq
Differential expression was obtained using a probablity value of > 0.8 from noiseq
Target genes were identified using psrnatarget

organism: Sinopodophyllum hexandrum

source_name: Mature leaf

extract_protocol:
total RNA was isolated
NEBNext multiplex smallRNA library kit using manufacturer’s protocol
Single ended sequencing on HiSeq 2500

value: Leaf

tag: developmental stage

value: Mature


title: CW02-25

description: ReadCount.xlsx

source_name: cortical tissue from Ikbkb+/+ male mice

value: M

value: ikbkb+/+


title: CW02-20

description: ReadCount.xlsx

value: brain


title: 6660 [D1/G4-lung CD1]


title: ISC 22 month (old) full length rep 2

city: Clayton

first: Monika

last: Mohenska

address: 15 Innovation Walk

institute: Monash University

data_processing:
Raw sequencing reads were assessed for overall quality using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequencing specific adaptors and low quality reads (Phred score of 3 consecutive bases below 15, minimum read length of 36nt) were filtered and hard trimmed using Trimmomatic [v 0.30]. Where RNA-sequencing reads were 100 nt length, a crop to a length of 50 bp was performed (Trimmomatic [v 0.30].
Sample reads were aligned to the mouse genome (GENCODE GRCm38 primary assembly) using STAR version 2.4.2a.
Transcript quantification was performed using featureCounts (exonic regions of GENCODE’s vM15 annotation version), and transcripts with more than 5 sequencing reads and 1 count per million of mapped reads in at least one sample were used for further analysis, previously library-size normalized using the TMM method.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: intestinal stem cell (ISC)

extract_protocol:
The isolated small intestine was flushed with PBS and opened longitudinally. The tissue was then scraped with a glass coverslip to remove villi, cut into 5-mm pieces and washed with PBS five times (20 inversions of the tube per wash). Following incubation for 30 min at 4°C in 4mM EDTA-PBS, intestinal crypts were released from small intestinal tissue fragments by mechanically pipetting with a 10ml pipette in PBS and repeating this step twice. After centrifugation (430xg for 5 min at 4°C), the pellet was resuspended in PBS and strained using a 70-μm cell strainer (BD Biosciences). Following centrifugation (430xg for 5 min at 4°C), the collected crypts were incubated for 30 minutes at 4°C in DMEM/F12 – 10% serum (Gibco), pelleted again by centrifugation (430xg for 5 min at 4°C) and then dissociated in TrypLE Express (Invitrogen) supplemented with 10 μM Rock inhibitor (Y-27632, Abcam) and 2.5µg/ml DNAse 1 (Sigma-Aldrich) for 4 minutes at 37°C. The dissociated cells were strained using a 70-μm cell strainer and were washed twice with PBS and collected by centrifugation at 4°C at 430xg for 5 minutes. Cellularized intestinal epithelial were labelled with antibodies and ISCs isolated by FACS (SM6 strategy, CD31-/CD45-/CD24med/CD166+/CD44high/GRP78low/EPHB2high/EPCAM+).
RNA was extracted with Qiagen’s RNeasy micro kit from 2-3*104 FACS isolated cells. For generation of sequencing libraries, 25ng of RNA (RIN value >8) were submitted to SPIA amplification (NuGen). Young (2 month) and old samples (22 month) used a full length (FL) transcript RNA sequencing approach were derived from the cells of a pool of 5 animals per condition and 2 replicates, using the HiSeq3000 platform. Each library was single-end with a 50-100nt read length. The targeted number of sequencing reads per sample was 30 million.

value: intestinal stem cell (ISC)

value: WT

value: 22 months

value: old


title: 6666 [D7/G12-lung CD1]

city: Berlin


title: 6659 [C12/G3-lung CD1]


title: Podo_T: Treated sample of P.hexandrum


title: CW02-15

description: ReadCount.xlsx


title: 6658 [C11/G1-lung CD1]


title: CW02-07

description: ReadCount.xlsx


title: ISC 2 month (young) full length rep 2

value: 2 months

value: young


title: CW_01_18

source_name: wildtype mouse primary Ikbkb-/- microglia

extract_protocol:
total RNA was extracted using Quick-RNA miniprep (R1055, Zymo Research).
cDNA library generation was done using the QuantSeq 3′ mRNA-Seq Library Prep Kit (FWD) for Illumina (K01596, Lexogen) following manufacturer’s instructions.

value: primary microglia


title: 6656 [C9/F10-lung CD1]

value: TH2 cells

value: lung


title: ISC 22 month (old) full length rep 1


title: 6657 [C10/F11-lung CD1]

value: wild type


title: ISC 2 month (young) full length rep 1


title: 6654 [C7/F8-lung CD1]


title: CW_01_17

value: ikbkb-/-


title: HEK293FT_TargetSeq_Sample_545

city: Shanghai

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
DNA deep sequencing read quality was evaluated by FastQC (v0.11.8) and low quality read sequences were trimmed.
BWA-MEM algorithm (0.7.17-r1188) was used to map clean reads to the targeted sequences.
Base substitution calling was performed by SAMtools (v1.9) mpileup function and indel calling was based on the CIGAR values of the SAM/BAM files.
Frequencies of base substitutions and indels are calculated according to reported CFBI (https://github.com/YangLab/CFBI, v1.0.0).
Assembly: hg19 for human samples
Supplementary files format and content: Excel for indel and base subtitution calculation results

source_name: HEK293FT cells

growth_protocol: 293FT (Thermo Fisher Scientific, R70007), U2OS (ATCC® HTB-96) and HeLa (ATCC® CCL-2™) cells were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination.

extract_protocol:
The genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) for subsequent sequencing analysis.
DNA libraries were prepared by using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina. After quantitated with Qubit High-Sensitivity DNA kit (Invitrogen), PCR products with different tags were pooled together for deep sequencing by using the Illumina HiSeq X10 (2×150) or NovaSeq 6000 (2×150) at Shanghai Institute Nutrition and Health, Big Data Center Omics Core, Shanghai, China.

treatment_protocol: For prime editing with pegRNA (spegRNA or apegRNA), 293FT, U2OS or Hela cells were seeded in a 24-well plate at a density of 1×105 per well and transfected with 250 μl serum-free Opti-MEM that contained 2.6 μl LIPOFECTAMINE LTX (Life, Invitrogen), 1.3 μl LIPOFECTAMINE plus (Life, Invitrogen), 0.9 μg PE2 expression vector, 0.3 μg pegRNA (spegRNA or apegRNA) expression vector with 0.1 μg nick-sgRNA expression vector. After 24 hrs, puromycin (ant-pr-1, InvivoGen) was added to the medium at the final concentration of 4 μg/ml.

tag: type

value: DNA


title: HEK293FT_TargetSeq_Sample_544


title: 6655 [C8/F9-lung CD1]

treatment_protocol: H. polygyrus was maintained by serial passage in C57BL/6 mice (H0099/13). Mice were infected with 225 third-stage infective (L3) H. polygyrus larvae via oral gavage in 200µL drinking water. For cure of infection, mice were treated on two consecutive days during the acute stage of infection (day 14-15) with 2mg pyrantel pamoate (Sigma, St. Louis, MO, USA) in 200µL drinking water via oral gavage. On indicated days, mice were sedated via isofluorane inhalation, followed by cervical dislocation. All animal experiments were performed in accordance with the National Animal Protection Guidelines and approved by the German Animal Ethics Committee for the Protection of Animals (LAGeSO, G0176/20).


title: CW_01_16


title: 6653 [C6/F7-lung CD1]


title: 6652 [C5/F6-lung CD1]


title: CW_01_14

source_name: wildtype mouse primary Ikbkb+/+ microglia


title: CW_01_15


title: HEK293FT_TargetSeq_Sample_543


title: HEK293FT_TargetSeq_Sample_542


title: CW_01_13


title: CW_01_12


title: HEK293FT_TargetSeq_Sample_540


title: 6651 [C4/F4-lung CD1]


title: 6648 [C1/E12-lung CD1]


title: 6649 [C2/F2-lung CD1]


title: HEK293FT_TargetSeq_Sample_539


title: CW_01_09

source_name: wildtype mouse primary IkbkbCA microglia

value: ikbkbCA


title: 6647 [B12/E11-lung CD1]


title: CW_01_08


title: HEK293FT_TargetSeq_Sample_538


title: 6646 [B11/E8-lung CD1]


title: 6650 [C3/F3-lung CD1]


title: 6644 [B9/E3-lung CD1]


title: 6645 [B10/E6-lung CD1]


title: HEK293FT_TargetSeq_Sample_534


title: CW_01_05

source_name: wildtype mouse primary IkbkbWT microglia

value: ikbkbWT


title: CW_01_04


title: HEK293FT_TargetSeq_Sample_541


title: CW_01_06


title: CW_01_11


title: 6641 [B6/D6-lung CD1]

source_name: CD4+ Tcells


title: CW_01_03


title: CW_01_02


title: HEK293FT_TargetSeq_Sample_536


title: CW_01_10


title: CW_01_07


title: 6642 [B7/D7-lung CD1]


title: HEK293FT_TargetSeq_Sample_533


title: HEK293FT_TargetSeq_Sample_535


title: HEK293FT_TargetSeq_Sample_532


title: 6643 [B8/E2-lung CD1]


title: 6639 [B4/D3-lung CD1]


title: HEK293FT_TargetSeq_Sample_537


title: HEK293FT_TargetSeq_Sample_529


title: CW_01_01


title: 6640 [B5/D4-lung CD1]


title: CW_01_25

source_name: adult microglia isolated from 11m old NTG male mice

value: M


title: 6638 [B3/D1-lung CD1]


title: HEK293FT_TargetSeq_Sample_530


title: HEK293FT_TargetSeq_Sample_527


title: 6636 [B1/C2-lung CD1]


title: CW_01_24


title: CW_01_26


title: 6635 [A12/C1-lung CD1]


title: 6633 [A10/B8-lung CD1]


title: CW_01_23


title: 6632 [A9/B6-lung CD1]


title: 6634 [A11/B9-lung CD1]


title: HEK293FT_TargetSeq_Sample_523


title: HEK293FT_TargetSeq_Sample_528


title: CW_01_30

source_name: adult microglia isolated from 11m old P301S+ male mice


title: HEK293FT_TargetSeq_Sample_522


title: HEK293FT_TargetSeq_Sample_525


title: HEK293FT_TargetSeq_Sample_526


title: HEK293FT_TargetSeq_Sample_531


title: 6630 [A7/B2-lung CD1]


title: MC11

source_name: wildtype mouse primary microglia treated with vehicle

value: vehicle


title: CW_01_22

value: brain


title: 6637 [B2/C3-lung CD1]


title: MC10


title: HEK293FT_TargetSeq_Sample_521


title: MC9


title: MC12


title: 6631 [A8/B5-lung CD1]


title: 6626 [A3/A6-lung CD1]


title: CW_01_21


title: MC3

source_name: wildtype mouse primary microglia treated with 2μg/ml full length  tau fibrils for 24 hours

value: 2μg/ml full length tau fibrils


title: 6625 [A2/A5-lung CD1]


title: 6629 [A6/A12-lung CD1]


title: HEK293FT_TargetSeq_Sample_519


title: HEK293FT_TargetSeq_Sample_515


title: HEK293FT_TargetSeq_Sample_520


title: 6627 [A4/A8-lung CD1]


title: HEK293FT_TargetSeq_Sample_518


title: MC2

value: WT


title: HEK293FT_TargetSeq_Sample_513


title: 6628 [A5/G8-lung CD1]


title: HEK293FT_TargetSeq_Sample_516


title: HEK293FT_TargetSeq_Sample_514


title: RNA-seq-D3(-SGC)

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 ensembl v79) transcriptome using rsem (version 1.3.1)
The gene expression level was calculated by using  RSEM
The RNA-seq data processing was performed as described45. To analyze the regular gene expression, the reads were aligned to the reference transcriptome by RSEM46 and bowtie2 (—bowtie2— bowtie2-sensitivity-level very_sensitive —no-bam-output —estimate -rspd) using the index built by RSEM with the mouse genome, mm10, and Ensembl gene annotation track v79
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: expression counts table

source_name: epiblast stem cell

growth_protocol: EpiSCs were cultured and maintained in N2B27 medium with Activin A (20ng/ml, PeproTech), bFGF (15ng/ml, PeproTech) and XAV939 (1uM, Selleck) on fetal bovine serum (FBS, NATOCOR)-coated dishes. For induction of BVSC double positive (BV+SC+) cells, the EpiSCs containing BVSC reporter were cultured in iCD1 medium which comprised of Vitamin C (50 μg/ml, Sigma), bFGF (10 ng/ml, PeproTech), LiCl (5 mM, Sigma), LIF (1000 U/ml, Millipore) and CHIR99021 (1 μM, synthesized in GIBH), with the addition of BMP4 (5-10 ng/ml,  R&D Systems), EPZ5676 (2.5 μM, Selleck ) and EPZ6438 (1 μM, TargetMol) for 3 days, and then in N2B27 medium with 2i (PD0325901, 1uM, synthesized in GIBH; CHIR99021, 3uM, synthesized in GIBH) and Vitamin C (50 μg/ml, Sigma) for another 3 days.  Fluorescence-activated cell sorting (FACS) was performed with a FACSAriaIII (BD) cell sorter for purifying BV+SC+ cells.

extract_protocol:
Genomic DNA and total RNA
Total RNAs were extracted as described above. The VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (VAHTS, #NR603) was used for RNA library preparation. In brief, 1 μg total RNAs were hybridized with the rRNA probe (H/M/R) and digested by RNase H to remove ribosomal RNAs. After DNase I digestion, the ribosomal-depleted RNAs were fragmented at 94°C for 8min. Then the first-strand and second-strand cDNAs were synthesized successively using the provided reagents. The cDNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411), followed by end repaired, dA-tailing, adapter ligation, and second strand cDNA digestion. After two-round of purification, the cDNAs was PCR-amplified and purified by VAHTS DNA Clean Beads. High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150 (pair-end sequencing, 150 bp reads).

value: epiblast stem cell


title: HEK293FT_TargetSeq_Sample_512


title: HEK293FT_TargetSeq_Sample_524


title: HEK293FT_TargetSeq_Sample_511


title: OA4

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

description:
osteoarthritic cartilage
single cell suspension from cartilage
barcode appendix in series record processed data files: _7

data_processing:
We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads to achieve clean data. Then the feature-barcode matrices were obtained by aligning reads to the mouse genome (GRCH38 ensembl: version 91) using CellRanger v3.1.0.
We applied the down sample analysis among samples sequenced according to the mapped barcoded reads per cell of each sample and finally achieved the aggregated matrix. A range of more than 250 expressed genes and a mitochondria UMI rate below 20% were implemented as cell quality filtering criteria and mitochondrial genes were removed in the expression table.
Seurat package (version: 4.0, https://satijalab.org/seurat/) was used for cell normalization reads. RPCA integration was performed,  dimention reduction was applied by UMAP methods.
mtx = GetAssayData(object, assay = 'RNA', slot = 'counts')
A matrix (mtx) with gene expression per cell data were exported by Matrix::writeMM function.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcode, feature, matrix

source_name: patients receiving total knee joint replacement surgery for OA at New York University Langone Orthopaedic Hospital

extract_protocol:
Articular cartilage obtained from non-arthritic and OA patients was finely minced under sterile conditions and digested with 0.25% Collagenase type II from Clostrudium histolyticum (Sigma-Aldrich) dissolved in DMEM at 37oC overnight. After enzymatic digestion, cells were pelleted by centrifugation, washed, filtered through 50uM cell strainer, and resuspended in 1ml PBS.
The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA) and sequenced the Illumina HiSeq 4,000 with read length of 150 bp by the NYU Genome Technology Center.

value: cartilage

tag: disease state

value: osteoarthritis


title: OA3

description:
osteoarthritic cartilage
single cell suspension from cartilage
barcode appendix in series record processed data files: _6


title: HEK293FT_TargetSeq_Sample_509


title: Input-EpiSC


title: OA2

description:
osteoarthritic cartilage
single cell suspension from cartilage
barcode appendix in series record processed data files: _5


title: MC4


title: CW_01_29


title: STARR_motif_modifications_promoter_bc

city: Stanford

description:
STARR-seq plasmid DNA barcode-promoter dictionary
starr_seq_100x100_all_experimental_counts_file.txt

source_name: transfected plasmid reporter

tag: library type

value: STARR-seq transcript DNA


title: HEK293FT_TargetSeq_Sample_507


title: HEK293FT_TargetSeq_Sample_517


title: 6624 [A1/A1-lung CD1]

tag: strain

tag: cell type


title: H3K79me2-EpiSC


title: RNA-seq-D3(+SGC)


title: K562_PROSeq

description:
PROSeq
GeneBody.PROseq.txt

data_processing:
Library strategy: PRO-seq
Illumina bcl2fastq2-v2.20.0 used for basecalling.
STARR-seq: bowtie2 was used to align sequences to custom indices with options: --maxins 2000 -p 16 --no-discordant --no-mixed --fast
motif modification STARR-seq: bowtie2 was used to align sequences to custom indices with options: --maxins 2000 -p 16 --no-discordant --no-mixed --fast --score-min L,-0.7,-0.7
PRO-Seq: bowtie was used to align sequences to hg19 with options: --wrapper basic-0 -p 4, and reads were counted in gene bodies with a custom script.
ExP 1Kx1K barcode to promoter aligned reads were counted with a custom python script to associate ExP barcodes to promoter sequences.
ExP 1Kx1K DNA and RNA reads were demultiplexed with the Je-suite demultiplex version 2.0 and counted with a custom python script.
HS-STARR-seq DNA and RNA reads were counted with a custom python script.
Motif modification STARR-seq Promoter + barcode aligned reads were counted with a custom python script to associate motif_modification barcodes to promoter sequences and quality filtered.
Motif modification STARR-seq DNA and RNA reads were counted with a custom python script.
Assembly: hg19
Supplementary files format and content: tabular separated values - promoter and barcode read count
Supplementary files format and content: tab separated values - K562 ExP 1Kx1K DNA and RNA counts
Supplementary files format and content: tab separated values - Hybrid-selected K562 Enhancer regions STARR-seq DNA and RNA counts
Supplementary files format and content: tab separated values - Hybrid-selected Promoter regions STARR-seq DNA and RNA counts

source_name: cDNA (from nascent RNA)

value: transcriptomic PRO-Seq


title: normal1

description:
normal human cartilage
single cell suspension from cartilage
barcode appendix in series record processed data files: _1

source_name: fresh osteochondral allografts discarded following donor plug harvesting during surgical osteochondral allograft implantation

tag: tissue

value: non-arthritic


title: Input-D3(+SGC)


title: Input-D3(-SGC)


title: HEK293FT_TargetSeq_Sample_510

tag: cell line


title: HEK293FT_TargetSeq_Sample_508


title: MC1

value: primary microglia

tag: genotype


title: H3K27me3-EpiSC


title: HEK293FT_TargetSeq_Sample_505


title: WT_Leukemia-bearing vehicle_pano_Gene_Expression

data_processing:
10X Genomics’ Cell Ranger Software (v3.1.0) was used to align reads to the mm10/GRCm38 reference genome, demultiplex cellular barcodes and quantify unique molecular identifiers (UMIs) and antibody capture (Hashtag oligos (HTOs) and Antibody Derived Tags (ADTs))
Inter-sample doublets and intra-sample doublets were removed using Seurat’s HTODemux function and the Scrublet python package (v0.2.1), respectively.
Counts with more than one median absolute derivation (MAD) above the median Scrublet score were retained.
The Seurat R package (v3.1.0) (64) was used to process gene expression and antibody count matrices within R studio (v3.6.1). Seurat’s SCTransform function was subsequently used to sctransform normalise RNA transcript counts for barcodes identified as cells by Cell Ranger. Transformation of counts with no covariates in the sctranform model was first performed, then Seurat’s CellCycleScoring function with cell cycle gene sets of mouse homologues was used to calculate cell cycle phase scores. Cell cycle phase scores and the percent of raw RNA counts belonging to mitochondrial genes for each cell were used to rerun sctransform normalisation and regress out of the model.
Centred log ratio (CLR) transformation was performed to normalise ADT counts.
Sctransform scaled RNA expression values for genes with residual variance greater than 1.3 in the sctransform model were used for Principle component analysis (PCA). The top 10 principle components were used to calculate a shared-nearest-neighbours (SNN) network with the FingNeighbors function with a cosine distance metric and 50 k-nearest neighbors. Cell populations were subsequently identified using the SNN network and the FindClusters function with the Louvain algorithm and a resolution parameter of 0.6. The top 10 principle components were also used to calculate Uniform Manifold Approximation and Projection (UMAP) values using the RunUMAP function with a cosine distance metric and 50 nearest neighbors as parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Raw Counts

source_name: dendritic cells

extract_protocol:
Spleens were removed and dendritic cells isolated. Pooled DC samples were loaded onto the 10x Chromium instrument (10x Genomics) to generate single-cell Gel Beads-in-Emulsion (GEMs) and capture/barcode cells.
10x Genomics Single Cell 3′ v3

value: spleen

tag: disease status

value: leukemia

value: vehicle, panobinostat


title: H3K79me2-EpiSC(-SGC)


title: H3K79me2-EpiSC(+SGC)


title: OA1

description:
osteoarthritic cartilage
single cell suspension from cartilage
barcode appendix in series record processed data files: _4


title: HEK293FT_TargetSeq_Sample_502

value: DNA


title: H3K27me3-D3(+SGC)


title: normal2

description:
normal human cartilage
single cell suspension from cartilage
barcode appendix in series record processed data files: _2


title: HEK293FT_TargetSeq_Sample_500


title: normal human cartilage, s3

data_processing:
RSEM v1.3.1 (rsem-calculate-expression function w/ STAR aligning), GRCh38
DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab separated text file of genes x 7 samples matrix

extract_protocol:
For RNA isolation, about 1g of cartilage was pulverized in liquid nitrogen and homogenized in Trizol at a concentration of 1g tissue per 10ml Trizol (Invitrogen), followed by incubation at 4oC with rotating for 2h. To remove debris, samples were mixed with 0.2 volumes of chloroform, vortexed for 20sec, and centrifuged at 14000 rpm for 20min at 4 oC. The aqueous phase was collected and gently mixed with an equal volume of isopropanol, followed by centrifugation at 14000 rpm for 20min at 4 oC. The resulting pellet was suspended in 350µl of RLT buffer and processed for cleanup using the RNeasy Mini Kit (Qiagen) in accordance with manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: HEK293FT_TargetSeq_Sample_504


title: IKKbKO_P301S+_2

description: mRNA expression in mouse cortical nuclei

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.3.1.0) (10x Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 8,000 or less than 300, and cells with high fraction of mitochondrial reads (> 5%).
Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
Seurat v3.0 (Butler et al., 2018) R package used for analysis.
Genome_build: mm10 genome

source_name: single nuclei from frozen mouse cortical tissue

extract_protocol:
Nuclei isolation adapted from Mathys et al. 2019
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: F

value: brain cortex


title: osteoarthritic cartilage, s5


title: normal human cartilage, s2


title: IKKbKO_P301S+_1


title: HEK293FT_TargetSeq_Sample_498


title: H3K27me3-D3(-SGC)


title: CF_M3_30

city: Bielefeld

first: Barbara

last: Kaltschmidt

address: Universitätsstr. 25

department: Molecular Neurobiology

institute: University of Bielefeld

description:
NCSCs from male donor III after 30 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells

data_processing:
Hisat2: Mapping to the reference genome GRCh38/hg19.
HTSeq: Quantification of gene expression.
DESeq2 R Package: Differential gene expression analysis.
Genome_build: GRCh38/hg19
Supplementary_files_format_and_content: genes.readcount.txt: Tab-delimited text file

source_name: NSCSs after 30 days of osteogenic differentiation on collagen type I fibers

growth_protocol: Isolation and growth protocol according to Stem Cells Dev. 2012 Mar 20;21(5):742-56. and Eur Cell Mater. 2011 Dec 17;22:403-19.

extract_protocol:
RNA isolation: NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany).
NEB Next Ultra Library Prep Kit (New England Biolabs, Frankfurt am Main, Germany).

treatment_protocol: Osteogenic differentiation on collagen type I fibers according to Nanomedicine. 2019 Apr;17:319-328.

value: Neural crest-derived stem cells

tag: gender

value: Male

tag: time point

value: 30 days of osteogenic differentiation

tag: donor

value: MIII


title: IKKbCA_P301S+_2


title: IKKbCtrl_P301S+_2


title: normal human cartilage, s1


title: osteoarthritic cartilage, s6


title: IKKbWT_P301S+_1


title: HEK293FT_TargetSeq_Sample_501

source_name: HEK293FT cells


title: osteoarthritic cartilage, s4


title: HEK293FT_TargetSeq_Sample_503


title: normal3

description:
normal human cartilage
single cell suspension from cartilage
barcode appendix in series record processed data files: _3


title: HEK293FT_TargetSeq_Sample_499


title: CF_M3_14

description:
NCSCs from male donor III after 14 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells

source_name: NSCSs after 14 days of osteogenic differentiation on collagen type I fibers

value: 14 days of osteogenic differentiation


title: HEK293FT_TargetSeq_Sample_506


title: IKKbCtrl_P301S+_1


title: CF_M2_30

description:
NCSCs from male donor II after 30 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells

value: MII


title: IKKbCA_P301S+_1


title: CF_M1_30

description:
NCSCs from male donor I after 30 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells

value: MI


title: osteoarthritic cartilage, s7

value: cartilage

value: osteoarthritis


title: HM8M

type: RNA

city: shanghai

first: Zhi

last: Pang

address: 180 fenglin road

department: Liver Cancer Institute,

institute: Zhongshan Hospital,Fudan University

description: This sample is the F1-generation of MUC1-CD-GFP mice with the MMTV-Her2/neu tg mice.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: The MUC1CD+ transgenic mice were  C57BL/6J backgroud, and the Her2/neu transgenic mice were FVB backgroud. Both the MUC1-CD and Her2 genes are driven under the mouse mammary tumor virus (MMTV) promoter to allow their expression in the mammary epithelium. To generate a MUC1CD+/Her2+ double transgenic mouse model, we crossed the parental strains. F1 generation mice were used for further analysis.

extract_protocol: Total RNA was harvested from six pairs of samples according to the Trizol manufacturer’s instructions (Thermo Scientific). Two replicates for MUC1WT/Her2+ and four for MUC1CD+/Her2+. Each pair included one tumor tissue and one normal adjacent tissue.

treatment_protocol: Tumors were measured with calipers three times per week and tumor volume in cubic millimeters was calculated using the formula volume = width2 × length/2. Mice were scarified when tumor volume reaches 1,500~2,000mm3.

tag: phenotype

value: Normal


title: IKKbWT_2

value: ikbkb+/+


title: CF_M1_14

description:
NCSCs from male donor I after 14 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells


title: CF_F2_30

description:
NCSCs from female donor II after 30 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells

value: Female

value: FII


title: CF_F3_14

description:
NCSCs from female donor III after 14 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells

value: FIII


title: CF_M2_14

description:
NCSCs from male donor II after 14 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells


title: monoculture_EV_2

data_processing:
Prinseq to remove first 5 nucleotides and low-complexity reads.
Mapped to the set of NCBI RefSeq rRNA sequences using STAR v. 2.5.2b. Mapping reads were discarded.
Mapped to the GRCh38.90 human transcriptome from Ensembl (cDNA + noncoding RNA) using Salmon v.0.8.2.
Reads that were likely PCR duplicates were removed using an in-house Python script that identified reads with matching Ovation SoLo barcodes that mapped within 38 bp of each other.
Re-mapped to the GRCh38.90 human transcriptome using Salmon v.0.8.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon output files (.sf) with estimated read counts and TPM per transcript

source_name: HUVEC

growth_protocol: Cells were amplified in a 37°C incubator with 5% CO2 in endothelial growth media-2 (EGM-2) with 5% FBS and 5 ng/ml rhFGF and without heparin. Cells between passages 2 and 8 were used for all experiments.

extract_protocol:
QIAGEN miRNeasy kit
NuGen Ovation SoLo Human RNA-Seq system

treatment_protocol: Twenty-four hours before initiating coculture, HUVEC cells were rinsed with DPBS and placed in EGM-2 media with 1% exosome-depleted FBS and 5 ng/ml rhFGF and without heparin, and MDA-MB-231 cells were rinsed with DPBS and placed in DMEM with 5% exosome-depleted FBS. To initiate coculture, MDA-MB-231 cells were treated with trypsin, rinsed twice in DPBS and resuspended in EGM-2 media with 1% exosome-depleted FBS and 5 ng/ml rhFGF and without heparin. HUVEC cells were rinsed twice in DPBS and placed in EGM-2 media with 1% exosome-depleted FBS and 5 ng/ml rhFGF and without heparin. MDA-MB-231 cells were added to plates of adherent HUVEC cells in a 1:1 ratio of near-confluent plates. EVs were purified by ultracentrifugation from the conditioned media after 48 hours.  To purify HUVEC cells and their EVs from mixed populations Dynabeads CD31 Endothelial Cell magnetic beads were used. Cells were purified according to manufacturer’s instructions. CD31+ EVs were purified by resuspending the ultracentrifugation EV pellet in Dynabeads Isolation buffer, adding to 50 µl of washed beads per T-175 of culture, incubating overnight at 4°C with rotation, washing twice with Isolation buffer, then resuspending beads with attached EVs in lysis buffer.

tag: treatment

value: monoculture

tag: compartment

value: extracellular vesicles


title: HM40T

value: Tumor


title: HM4M


title: ST_High Fat Diet 14 Weeks

city: Ann Arbor

first: Lindsey

last: Muir

state: MI

address: 1600 Huron Parkway

institute: University of Michigan

data_processing:
Raw spatial transcriptomics sequencing data were processed using the 10X Genomics SpaceRanger (version 1.0.0) pipeline
Processed spatial transcriptomics data is filtered by removing barcodes not associated with (not overlapping) the tissue
Raw single-cell RNA-sequencing data were processed using the 10X Genomics CellRanger (version 4.0.0) pipeline
Processed single-cell RNA-seq data is filtered by removing barcodes that correspond to background noise (free-floating mRNA from lysed or dead cells), as determined by a cell-calling heuristic in the 10X genomics software pipeline.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: Processed data files are in the Hierarchical Data Format (HDF5 or H5) which is a compressed binary format. The file contains a matrix stored in Compressed Sparse Column (CSC) format containing absolute transcript counts reported as unique molecular identifier (UMI) counts, as well as the features and spot-barcodes/cell-barcodes associated with the matrix rows and columns, respectively, which are stored as HDF5 groups
Supplementary_files_format_and_content: Tissue positions lists are also provided as CSV files supplementing the spatial transcriptomics data. These files contain a table with rows corresponding to tissue spots and columns specifying the tissue spot coordinates among other details. More information can be found here: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/output/images

source_name: epidydymal white adipose tissue

extract_protocol:
For spatial transcriptomics, extraction and library construction was performed according to manufacturer protocols with permeablization optimized for adipose tissue (10X genomics, fresh frozen tissue). Stromal vascular cells that were magnetically enriched for CD45 were used for single cell RNA-seq samples after isolation from enzymatically digested adipose tissue. Single cell RNA-seq samples underwent additional surface protein staining followed by extraction and processing through a standard single cell Chromium workflow.
spatial transcriptomics and scRNA-seq

treatment_protocol: Obese mice were fed 60% high-fat diet for the stated durations.

value: white adipose

tag: status

value: obese

tag: diet

value: High Fat

value: 14 Weeks


title: CF_F1_30

description:
NCSCs from female donor I after 30 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells

value: Neural crest-derived stem cells

value: 30 days of osteogenic differentiation

value: FI


title: IKKbWT_1

tag: age (m)

tag: Sex

value: F

value: brain cortex


title: HM40M

value: Normal


title: HM4T


title: HM32M


title: HM26T


title: HM24T


title: CF_F2_14

description:
NCSCs from female donor II after 14 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells

value: 14 days of osteogenic differentiation


title: IKKbCtrl_1

value: ikbkb+/+


title: HM24M


title: NEGATIVE_CONTROL_6

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

data_processing:
Base-calling was done with bcl2fastq2 conversion software (NovaSeq 6000)
Read alignment and counting was done using Rsubread package (v. 2.0) using in-built RefSeq gene annotation.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file rsubread_featureCounts.csv is tab delimited text file containing the genewise read counts for each sample.

growth_protocol: The HTR-8/Svneo cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 100 U/ml penicillin, 100 mg/ml streptomycin, 2 mM glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was isolated by using RNeasy Micro Kit
TruSeq® Stranded mRNA Sample Preparation, Illumina (15031047)

treatment_protocol: The transfection with siRNA was done either with 10 nM siRNA pair or 10 nM siRNA universal negative control and using approximately 100 000 cells and duoble transfection. The first transfection was done in suspension and the second transfection in adherent cells.

value: trophoblast

value: placenta

value: siRNA universal negative control


title: Gut, Clean, AdipQ, rep3

city: Hangzhou

first: Xiaotian

last: Tang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

description:
Adip--gfp-all-genes.txt
tpm-values-all-samples.txt

data_processing:
Tick transcript data was downloaded from the VectorBase (https://vectorbase.org/vectorbase/app/) and indexed using the kallisto-index.
The reads from the sequencer were pseudo-aligned with the index reference transcriptome using kallisto.
The counts generated were processed by DESeq2 in RStudio (https://rstudio.com).
Assembly: IscaW1
Supplementary files format and content: tab-delimited text files include baseMean, log2Foldchange, TPMs, etc. for each gene

organism: Ixodes scapularis

source_name: Gut

extract_protocol:
Tick gut was dissected, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gut

tag: condition

value: clean

value: Recombinant adiponectin


title: CF_F1_14

description:
NCSCs from female donor I after 14 days of osteogenic differentiation on collagen type I fibers.
inferior turbinate stem cells

value: Female


title: IKKbCtrl_2


title: ST_Normal Diet_rep1

tag: strain

value: white adipose

value: lean

value: Normal Diet


title: Gut, Clean, AdipQ, rep1


title: ST_High Fat Diet 8 Weeks

value: obese

value: High Fat

value: 8 Weeks