title: SUM149/MUC1shRNA #2

status: Public on Mar 05 2020

city: Buffalo

first: Qiang

last: Hu

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.7.0).
The number of fragments in each known gene from GENCODE (version 25) was quantified using STAR QuantMode (GeneCounts) function.
The differential gene expression was analyzed by R/Bioconductor package DESeq2 (version 1.24.0).
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are raw counts for all the samples.

source_name: MUC1-C silenced Cells

growth_protocol: Human BT-549 TNBC (ATCC) cells were cultured in RPMI1640 medium (Corning Life Sciences, Corning, NY, USA) containing 10% heat-inactivated fetal bovine serum (FBS; GEMINI Bio-Products, West Sacramento, CA, USA), 100 mg/ml streptomycin, 100 U/ml penicillin and 10 mg/ml insulin. SUM149 TNBC cells were grown in Ham’s F-12 medium (Corning) supplemented with 10 mM HEPES, 5% FBS, 100 mg/ml streptomycin, 100 U/ml penicillin, 5 mg/ml insulin and 1 mg/ml hydrocortisone.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using Trizol reagent (Invitrogen).
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

tag: cell line

value: TNBC Breast Cancer Cell line (ER -ve, PR -ve, HER2/neu -ve)

value: shRNA against MUC1-C


title: SUM149/MUC1shRNA #3

type: SRA

state: NY

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: genotype


title: Ch_4_B

status: Public on Apr 21 2020

city: Houston

first: Benson

last: Otarigho

state: Texas

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Fq file dataset were uploaded into Galaxy Tool Version 2.11.40.2 that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Caenorhabditis elegans genome WS220
The htseq-count were further analyesd for the differentially expressed features from count tables using DESeq2
Genome_build: Caenorhabditis elegans genome WS220
Supplementary_files_format_and_content: tabular files include htseq-count/values for each Sample

organism: Caenorhabditis elegans

source_name: Whole organism

growth_protocol: Approximately 40 gravid animals were placed for 3 hours on 10-cm NGM plates (seeded with E. coli OP50) in order to have a synchronized population, which developed and grew to L4 larval stage at 20oC

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Purification of Total RNA was done using the TURBO DNase.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: Animals were washed off the plates with M9 and frozen in QIAzol by ethanol/dry ice and stored at -80 prior to RNA extraction.

tag: strain

value: Wild type (N2)

tag: tissue

value: Whole organism

tag: age

value: L4 stage

tag: treatment

value: 20µg/ml cholesterol


title: BT-549/CshRNA #3

source_name: MUC1-C +ve control cells

value: Control


title: BT-549/MUC1shRNA #3


title: SUM149/MUC1shRNA #1


title: BT-549/CshRNA #2


title: SUM149/CshRNA #1


title: BT-549/MUC1shRNA #2


title: SUM149/CshRNA #3


title: BT-549/CshRNA #1


title: SUM149/CshRNA #2


title: BT-549/MUC1shRNA #1


title: Embryo_D14A3S8

status: Public on Nov 26 2019

city: Kunming

first: Tianqing

last: Li

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

country: China

institute: Kunming University of Science and Technology

description: single cell total RNA

data_processing:
The sequencing qualities of 555 scRNA-seq profiles were examined with the FASTQC and MULTIQC (v 1.6)
The annotations of RefSeq genes were downloaded from UCSC Genome Browser. The RefSeq exons were used to build databases of exon and splice sites with the extract_exon.py and extract_splice_sites.py in the hisat2 package.
HISAT2 (v 2.1.0) was used to align the scRNA-seq profiles to the human genome.
The alignment results of HISAT2 in the SAM format were converted to BAM format and sorted with SAMTools (v 1.1).
Stringtie (v 1.3.4) was used to calculate the abundances of genes (in FPKM) annotated in GENCODE (v29) using the options of "-G gencode.v29.gtf -B -e –v".
Genome_build: hg38
Supplementary_files_format_and_content: 555-samples-fpkm.txt: Tab-delimited text file includes FPKM values for each sample.
Supplementary_files_format_and_content: 555sample_gene_count_matrix.txt: Tab-delimited text file includes gene counts for each sample.

source_name: embryo

growth_protocol: Embryo thawing and zona pellucida removal. Before embryos thawing, human embryo culture medium G-2 (10132, Vitrolife) was equilibrated in a 4-well plate (176740, Nunc) over night. First, 0.5ml G-2 medium was added into the well and 0.25 ml mineral oil (10029, Vitrolife) covered the G2 medium. Human blastocysts (day 5 or 6 post fertilization) were thawed using Kitazato Thawing Media Kit (VT102, Kitazato Corporation) by strictly following the manufacturer’s instructions. After cultured indrops of the equilibrated G-2 medium for 4 hours, embryos were transferred to acidic Tyrode’s solution (T1788, Sigma-Aldrich) to remove the zona pellucida. Embryos were washed in G-2 medium two times and then transferred to in vitro culture medium.   In vitro three-dimensional culture of human embryos. The embryos without zona pellucida were cultured in a low attachment 96-well plate (3474, Corning) with one embryo and 150µL extended medium each well. The embryo culture condition was the following: 37.2℃, 6% CO2 and saturated humidity. First, at day 6-8 post fertilization (d.p.f 6-8), the culture medium was modified in vitro culture medium 1 (mIVC1). At d.p.f 8, 50% of mIVC1 medium was replaced by modified in vitro culture medium 2 (mIVC2). At d.p.f 9, the embryos were transferred to new wells with the mIVC2 including 10% Matrigel (354234, Corning). After that, 50% culture medium was replaced by pre-equilibrated mIVC2 including 10% Matrigel every day.  The components of the mIVC1 and mIVC2 system are modifications of IVC1 and IVC2, which had been used to culture human attached embryos on the dish: mIVC1: Advanced DMEM/F12 (12634-010, Thermo Fischer Scientific) supplemented with 20% (vol/vol) DFBS (defined fetal bovine serum)(bs-0003, Biosera), 2 mM L-glutamine (25030, Thermo Fisher Scientific), 1X ITS-X (51500-056, Thermo Fisher Scientific), 8 nM β-estradiol (E8875, Sigma-Aldrich), 200 ng/ml progesterone (P0130, Sigma-Aldrich), 25 µM N-acetyl-L-cysteine (A7250, Sigma-Aldrich), 0.22% (vol/vol) sodium lactate (L7900， SigmaAldrich), 1 mM sodium pyruvate（P4562, Sigma-Aldrich） and 10µM Y27632 (S1049, Selleck). mIVC2: Advanced DMEM/F12 supplemented with 30% (vol/vol) KOSR (knockout serum replacement) (A3181501, Thermo Fischer Scientific), 2 mM L-glutamine, 1X ITS-X, 8 nM β-estradiol, 200 ng/ml progesterone, 25 µM N-acetyl-L-cysteine (A7250, Sigma-Aldrich), 0.22% (vol/vol) sodium lactate, 1 mM sodium pyruvate (P4562, Sigma-Aldrich) and 10µM Y27632 (S1049, Selleck).

extract_protocol:
Isolation of single cells. The embryos were washed in PBS for 3 times, washed in 0.25% trypsin (T4799; SigmaAldrich) 2 times, incubated with 0.25% trypsin for around 15 min at 37 °C, and terminated by DFBS. Embryo was dissociated into single cells by repeated pipetting and dispersed in 1% DFBS/PBS. A single cell was pipetted into a PCR tube. All operations above were performed under the Nikon SMZ645 microscopy.
The synthesis and amplification of full-length cDNAs were performed following Smart-seq2 protocol4. Briefly, single cells were washed in DPBS (Gibco 14190-144) and picked into lysis buffer using Pasteur pipettes under a dissecting microscope. Reversetranscription reactions and pre-amplification were performed using SuperScript II (Invitrogen 18064-014) and KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2601), respectively. The quality of the cDNAs were evaluated by Bioanalyzer 2100. Library construction and sequencing were performed by Annoroad Gene Technology (http://www.annoroad.com/) or BGI (https://www.bgi.com/). Sequencing was performed on Illumina X-ten platform or BGISEQ-500 sequencing platform (BGI, Shenzhen, China). Pair-end reads were got and the number of the reads were more than 7 M for every single cell

value: embryo invitro day 14

value: EVTs


title: Embryo_D14A3S7

description: single cell total RNA


title: rep1

status: Public on Dec 31 2019

city: Heidelberg

first: Ed

last: Hurt

address: Im Neuenheimer Feld 328

department: BZH

country: Germany

institute: Biochemie Zentrum Heidelberg

data_processing:
The reads were aligned to the Ct. genome (Ensembl, release39) assembly using HISAT2
HTseq_count performed directly on the resulting bam files.
GTF file generation:
The data quality assessment of raw sequence data was checked using FastQC. The reference genome of Chaetomium thermophilum was downloaded from the Ensemble genome browser and the raw reads were mapped to C.thermophilum reference genome using HISAT2 aligner.
Mapped reads further assembled separately using StringTie. Each assembled separate file was merged/union, thus reported as one in the combined.gtf output. The Gffcompare output reports various statistics related to the 'accuracy' of the input transcripts when compared to reference annotation data.
The accuracy is calculated at various levels such as nucleotide, exon, intron, transcript, the gene for each input file. GffCompare tracks a "class code" value showing the relationship between a transfrag and the closest reference transcript of combined.gtf evaluating transcript discovery accuracy.
Genome_build: Ensembl, release39, Chaetomium_thermophilum_var_thermophilum_dsm_1495.CTHT_3.0.dna.toplevel
Supplementary_files_format_and_content: htseq_count in tab-separated text format

molecule: polyA RNA

organism: Thermochaetoides thermophila

source_name: DSMZ, Braunschweig, Germany (No. 1495)

growth_protocol: Mycelium was grown in modified CCM medium in 250 ml baffled Erlenmeyer flasks at 52C for 6 h. (0.5g NaCl, 0.65g K2HPO4x3H2O, 0.5g MgSO4x7H2O, 0.01g Fe(III)-sulfatehydrate, 8g D glucose and 1g each of peptone and yeast extract per litre H2O, pH 7.0)

extract_protocol:
About 100mg mycelia from three independent biological replicates were used directly for total RNA-extraction using the SV total RNA isolation system (Promega).
The libraries were prepared with the NEBNext Ultra II Directional RNA Preparation Kit for Illumina in combination with NEBNext Poly A selection Module, plus the NEBNext Multiplex Oligos for Illumina.

value: DSMZ, Braunschweig, Germany (No. 1495)

value: wild type


title: rep3


title: rep2


title: Embryo_D14A3S5

description: single cell total RNA

value: CTBs


title: Embryo_D14A3S28

description: single cell total RNA


title: Embryo_D14A3S29

description: single cell total RNA

value: EPI


title: Embryo_D14A3S26

description: single cell total RNA


title: Embryo_D14A3S25

description: single cell total RNA


title: Embryo_D14A3S23

description: single cell total RNA


title: Embryo_D14A3S27

description: single cell total RNA


title: Embryo_D14A3S30

description: single cell total RNA


title: Embryo_D14A3S20

description: single cell total RNA


title: Embryo_D14A3S18

description: single cell total RNA

value: STBs


title: Embryo_D14A3S14

description: single cell total RNA


title: Embryo_D14A3S19

description: single cell total RNA


title: Embryo_D14A3B2

description: single cell total RNA


title: Embryo_D14A3B14

description: single cell total RNA


title: Embryo_D14A2S6

description: single cell total RNA


title: Embryo_D14A2S29

description: single cell total RNA


title: Embryo_D14A3B10

description: single cell total RNA


title: Embryo_D14A2S5

description: single cell total RNA


title: Embryo_D14A3B12

description: single cell total RNA


title: Embryo_D14A3B7

description: single cell total RNA


title: Embryo_D14A2S27

description: single cell total RNA


title: Embryo_D14A2S23

description: single cell total RNA


title: Embryo_D14A2S1

description: single cell total RNA


title: Embryo_D14A2S17

description: single cell total RNA


title: Embryo_D14A2S13

description: single cell total RNA


title: Embryo_D14A2S19

description: single cell total RNA


title: Embryo_D14A2B2

description: single cell total RNA


title: Embryo_D14A2B4

description: single cell total RNA


title: Embryo_D14A2B7

description: single cell total RNA


title: Embryo_D14A2S15

description: single cell total RNA


title: Embryo_D14A2S21

description: single cell total RNA


title: Embryo_D14A2B16

description: single cell total RNA


title: Embryo_D14A2B1

description: single cell total RNA


title: Embryo_D14A2B12

description: single cell total RNA


title: Embryo_D14A2B13

description: single cell total RNA


title: Embryo_D14A2S28

description: single cell total RNA


title: Embryo_D14A1S64

description: single cell total RNA


title: Embryo_D14A1S61

description: single cell total RNA


title: Embryo_D14A1S60

description: single cell total RNA


title: Embryo_D14A1S63

description: single cell total RNA


title: Embryo_D14A1S58

description: single cell total RNA


title: Embryo_D14A1S59

description: single cell total RNA


title: Embryo_D14A1S56

description: single cell total RNA


title: Embryo_D14A1S48

description: single cell total RNA


title: Embryo_D14A1S47

description: single cell total RNA


title: Embryo_D14A1S53

description: single cell total RNA


title: Embryo_D14A1S51

description: single cell total RNA


title: Embryo_D14A1S45

description: single cell total RNA


title: Embryo_D14A1S46

description: single cell total RNA


title: Embryo_D14A1S44

description: single cell total RNA


title: Embryo_D14A2B9

description: single cell total RNA


title: Embryo_D14A1S43

description: single cell total RNA


title: Embryo_D14A1S42

description: single cell total RNA


title: Embryo_D14A1S39

description: single cell total RNA


title: Embryo_D14A1S33

description: single cell total RNA


title: Embryo_D14A1S36

description: single cell total RNA


title: D150: Male 29 wkGA Lung

status: Public on Nov 23 2020

city: Cincinnati

first: LungMAPP

last: DCC

state: OH

address: 3333 Burnet Ave

institute: LungMAP DCC

data_processing:
Library strategy: snRNA-seq
Sequencing reads were demultiplexed (cellranger mkfastq) and processed (cellranger count) using the Cell Ranger software package v3.0.2 (10x Genomics). Reads were aligned to the human reference hg38 (Cell Ranger software package v3.0.2). Reads mapping to intronic and exon sequences were retained. Resulting UMI feature-barcode count matrices were loaded into Seurat (Stuart et al., 2019). All genes represented in >=3 nuclei and cells with 500-4000 detected genes were included for downstream processing. UMI counts were log-normalized and scaled by a factor of 10,000 using the NormalizeData function. Top 3000 variable features were identified using the FindVariableFeatures function and finally scaled using the ScaleData function. Barcode collisions were removed for individual datasets using DoubletFinder (McGinnis et al., 2019) with following parameters: pN =0.15 and pK = 0.005, anticipated collision rate = 10%. Clusters were assigned a doublet score (pANN) and classification as “doublet” or “singlet”; called doublets and cells with a pANN score > 0 were removed. UMI matrices for datasets were merged and corrected for batch effects due to experiment date, donor, and sex using the Harmony package (Korsunsky et al., 2019). UMAP coordinates and clustering were performed using the RunUMAP, FindNeighbors, and FindClusters functions in Seurat with principal components 1-23. 25-26, and 28. Clusters were annotated, and putative doublets as defined by expression of canonically mutually exclusive markers were excluded from analysis; remaining cells were re-clustered using the previously described parameters. Final cluster annotation was done using canonical markers. For genes of interest such as (e.g. ACE2, TMPRSS2), nuclei with at least one UMI for the gene were considered “expressing”. To analyze changes in percentage of nuclei expressing we performed One-way ANOVA (ANalysis Of VAriance) with post-hoc Tukey HSD (Honestly Significant Difference) using GraphPad Prism version 8.0.0 for Windows, GraphPad Software, San Diego, California USA, www.graphpad.com. Due to one potential outlier in the 30wkGA group (D062) we performed in addition a simple t-test comparing 3 yr to 30 yr groups. Differential gene expression analysis between ACE2+ and ACE2- AT2 cells we used FindAllMarkers with parameters logfc = 0, min.pct = 0, test.use = “wilcox”, verbose = TRUE. Cells were filtered using the following commonly used criteria: >500 expressed genes and <10% UMIs mapped to mitochondrial DNAs. In addition, cells with greater than or equal to 40,000 UMIs were excluded from the downstream analysis; this filtration criterion was selected based on the distribution of UMIs in single cells in individual donors. Seurat (version 3) (Stuart et al., 2019) was used to identify AT2 cells from individual aged donors. Nuclei from the 9 libraries generated in this study and cells from libraries for the 4 aged donors were integrated using the Seurat 3 standard integration pipeline (Stuart et al., 2019).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited separated value (tsv) file and .mtx

source_name: Biopsy from small airway

extract_protocol:
30 mg pulverized lung tissue was resuspended in 500 μl of nuclei permeabilization buffer (0.1% Triton X-100 (Sigma-Aldrich, T8787), 1X protease inhibitor, 1 mM DTT, and 0.2 U/μl RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS). Sample was incubated on a rotator for 5 minutes at 4°C and then centrifuged at 500 rcf for 5 minutes (4°C, run speed 3/3). Supernatant was removed and pellet was resuspended in 400 μl of sort buffer (1 mM EDTA 0.2 U/μl RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS) and stained with DRAQ7 (1:100; Cell Signaling, 7406). 75,000 nuclei were sorted using a SH800 sorter (Sony) into 50 μl of collection buffer consisting of 1 U/μl RNase inhibitor in 5% BSA; the FACS gating strategy sorted based on particle size and DRAQ7 fluorescence. Sorted nuclei were then centrifuged at 1000 rcf for 15 minutes (4°C, run speed 3/3) and supernatant was removed. Nuclei were resuspended in 35 μl of reaction buffer (0.2 U/μl RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS) and counted on a hemocytometer. 12,000 nuclei were loaded onto a Chromium controller (10x Genomics).
Droplet-based Chromium Single Cell 3’ solution (10x Genomics, v3 chemistry)(Zheng et al., 2017) was used to generate snRNA-seq libraries.   Libraries were generated using the Chromium Single Cell 3’ Library Construction Kit v3 (10x Genomics, 1000078) according to manufacturer specifications. CDNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter) was sued for size selection and clean-up steps. Final library concentration was assessed by Qubit dsDNA HS Assay Kit (Thermo-Fischer Scientific) and fragment size was checked using Tapestation High Sensitivity D1000 (Agilent) to ensure that fragment sizes were distributed normally about 500 bp.
Single-nucleus RNA-Seq libraries were sequenced using the NextSeq500 and a HiSeq4000 (Illumina) with these read lengths: 28 + 8 + 91 (Read1 + Index1 + Read2).

value: 29 wkGA

tag: Sex

value: M

tag: race

value: White

tag: clinpathdx

value: Normal lung growth; late canalicular/early saccular

tag: assessement of tissue quality

value: Very Good

tag: type of death

value: DCD

tag: Cause of death

value: Anencephaly


title: Embryo_D14A1S41

description: single cell total RNA


title: Embryo_D14A1S34

description: single cell total RNA


title: Embryo_D14A1S62

description: single cell total RNA


title: Embryo_D14A1S57

description: single cell total RNA


title: Pancreatic tumors, KRAS G12D intact (scRNAseq)

status: Public on Nov 11 2020

city: Stony Brook

first: Jinyu

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

data_processing:
*I1_001.fastq.gz: contains the 8 nt sample index.
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 150  nt RNA sequence.
Single Cell sequencing data were pre-processed by cellranger 3.0.1 from 10X Genomics using default settings.
Downstreaming analysis was performed by Seurat 3.0
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

organism: Mus musculus

source_name: mouse pancreas

growth_protocol: Tumor derived KRASG12D p53R172H/+ were cultured on gelatinzed plates in DMEM with 5% FBS supplemented with antibiotics and antimycotics. Syngeneic mice were injected with these cells and tumors were harvested when they were 1cm in size.

extract_protocol:
Pancreatic tumors for each sample set was pooled in from two mice. These tumors were digested both mechanically and enzymaticaly (collagenase Type II, DNaseI, Accutase) and a single cell suspension of viable cells was prepared. mRNA from each individual cell was captured and tagged with barcodes using 10X Genomics microfluidic platform.
Barcoded cDNA library was prepared using the manufacturer's instructions, 10X Genomics.

tag: tissue of origin for tumor

value: pancreas

tag: genetic alteration


title: Embryo_D14A1B27

description: single cell total RNA


title: Embryo_D14A1B28

description: single cell total RNA


title: Embryo_D14A1B25

description: single cell total RNA


title: Embryo_D14A1B26

description: single cell total RNA


title: Embryo_D14A1B24

description: single cell total RNA


title: Embryo_D14A1B19

description: single cell total RNA


title: Embryo_D14_2B3

description: single cell total RNA

value: embryo invitro day 13.5


title: Embryo_D14A1B17

description: single cell total RNA


title: Embryo_D14A1B18

description: single cell total RNA


title: Embryo_D14A1B21

description: single cell total RNA

value: Hypoblast


title: Embryo_D14_2S2

description: single cell total RNA


title: Embryo_D14A1B20

description: single cell total RNA

value: embryo invitro day 14


title: Embryo_D14_2B1

description: single cell total RNA

value: EVTs


title: Embryo_D14_3S9

description: single cell total RNA


title: Embryo_D14_3S10

description: single cell total RNA


title: Embryo_D14_3B6

description: single cell total RNA


title: Embryo_D14_3S16

description: single cell total RNA


title: Embryo_D14_1B5

description: single cell total RNA


title: Embryo_D14_1S2

description: single cell total RNA


title: Embryo_D14_1S10

description: single cell total RNA


title: Embryo_D14_1B1

description: single cell total RNA

value: embryo invitro day 12


title: Embryo_D14_1B2

description: single cell total RNA


title: Embryo_D14_2S1

description: single cell total RNA


title: Embryo_D12A4S27

description: single cell total RNA


title: Embryo_D12_2S1

description: single cell total RNA


title: Embryo_D12_1B3

description: single cell total RNA


title: Embryo_D14A1B22

description: single cell total RNA


title: Embryo_D12_2B2

description: single cell total RNA


title: Embryo_D12_1B4

description: single cell total RNA


title: Embryo_D12_2B9

description: single cell total RNA


title: Embryo_D12A5S6

description: single cell total RNA


title: Embryo_D14A1B23

description: single cell total RNA


title: Embryo_D12A5S5

description: single cell total RNA


title: Embryo_D12A5S30

description: single cell total RNA


title: Embryo_D12A5S4

description: single cell total RNA


title: Embryo_D12A5S24

description: single cell total RNA


title: Embryo_D12A5S18

description: single cell total RNA


title: Embryo_D14_3S15

description: single cell total RNA


title: Embryo_D12A5S25

description: single cell total RNA


title: Embryo_D12A5S1

description: single cell total RNA


title: Embryo_D12A5S19

description: single cell total RNA


title: Embryo_D14_3B5

description: single cell total RNA


title: Embryo_D12A5S17

description: single cell total RNA


title: Embryo_D12A5B9

description: single cell total RNA


title: Embryo_D12A5B6

description: single cell total RNA


title: Embryo_D12A5S16

description: single cell total RNA


title: Embryo_D12A5B5

description: single cell total RNA


title: Embryo_D12A4S7

description: single cell total RNA


title: Embryo_D12A4S30

description: single cell total RNA


title: Embryo_D12A5B15

description: single cell total RNA


title: Embryo_D12A4S9

description: single cell total RNA


title: Embryo_D12A5B11

description: single cell total RNA


title: Embryo_D12A4S21

description: single cell total RNA


title: Embryo_D12A4S12

description: single cell total RNA


title: Embryo_D12A4S29

description: single cell total RNA


title: Embryo_D12A4S26

description: single cell total RNA


title: Embryo_D12A4S22

description: single cell total RNA


title: Embryo_D12A5S20

description: single cell total RNA


title: Embryo_D12A4S2

description: single cell total RNA


title: Embryo_D12A4S16

description: single cell total RNA


title: Embryo_D12A4B5

description: single cell total RNA


title: Embryo_D12A4S17

description: single cell total RNA


title: Embryo_D12A4B8

description: single cell total RNA


title: Embryo_D12A3S9

description: single cell total RNA


title: Embryo_D12A3S8

description: single cell total RNA


title: Embryo_D12A3S6

description: single cell total RNA


title: Embryo_D12A3S7

description: single cell total RNA


title: Embryo_D12A5S13

description: single cell total RNA


title: Embryo_D12A3S5

description: single cell total RNA


title: Embryo_D12A3S4

description: single cell total RNA


title: Embryo_D12A3S31

description: single cell total RNA


title: Embryo_D12A3S32

description: single cell total RNA


title: Embryo_D12A3S3

description: single cell total RNA


title: Embryo_D12A3S30

description: single cell total RNA


title: Embryo_D12A3S29

description: single cell total RNA


title: Embryo_D12A3S2

description: single cell total RNA


title: Embryo_D12A3S23

description: single cell total RNA


title: Embryo_D12A3S26

description: single cell total RNA


title: Embryo_D12A3S27

description: single cell total RNA


title: Embryo_D12A3S25

description: single cell total RNA


title: Embryo_D12A4B9

description: single cell total RNA


title: Embryo_D12A3S24

description: single cell total RNA


title: Embryo_D12A4B16

description: single cell total RNA


title: Embryo_D12A4B15

description: single cell total RNA


title: Embryo_D12A3S19

description: single cell total RNA


title: Embryo_D12A3S1

description: single cell total RNA


title: Embryo_D12A3S12

description: single cell total RNA


title: Embryo_D12A3S17

description: single cell total RNA


title: Embryo_D12A3S13

description: single cell total RNA


title: Embryo_D12A3S16

description: single cell total RNA


title: Embryo_D12A3S18

description: single cell total RNA


title: Embryo_D12A3S20

description: single cell total RNA


title: Embryo_D12A3S22

description: single cell total RNA


title: Embryo_D12A3S14

description: single cell total RNA


title: Embryo_D12A3S21

description: single cell total RNA


title: Embryo_D12A3S15

description: single cell total RNA


title: Embryo_D12A3S11

description: single cell total RNA


title: Embryo_D12A3B8

description: single cell total RNA


title: Embryo_D12A3B9

description: single cell total RNA


title: Embryo_D12A3B7

description: single cell total RNA


title: Embryo_D12A3S10

description: single cell total RNA


title: Embryo_D12A3S28

description: single cell total RNA


title: Embryo_D12A3B6

description: single cell total RNA


title: Embryo_D12A3B5

description: single cell total RNA


title: Embryo_D12A3B4

description: single cell total RNA


title: Embryo_D12A3B3

description: single cell total RNA


title: Embryo_D12A3B2

description: single cell total RNA


title: Embryo_D12A3B14

description: single cell total RNA


title: Embryo_D12A3B15

description: single cell total RNA


title: Embryo_D12A3B16

description: single cell total RNA


title: Embryo_D12A3B13

description: single cell total RNA


title: Embryo_D12A3B11

description: single cell total RNA


title: Embryo_D12A3B12

description: single cell total RNA


title: Embryo_D12A3B10

description: single cell total RNA

value: embryo invitro day 10


title: Embryo_D10A6S8

description: single cell total RNA


title: Embryo_D10A6S7

description: single cell total RNA


title: Embryo_D10A6S5

description: single cell total RNA


title: Embryo_D10A6S1

description: single cell total RNA


title: Embryo_D10A6S14

description: single cell total RNA


title: Embryo_D10A6S10

description: single cell total RNA

value: CTBs


title: Embryo_D10A5S3

description: single cell total RNA


title: Embryo_D10A5B8

description: single cell total RNA


title: Embryo_D10A5S12

description: single cell total RNA


title: Embryo_D10A5S16

description: single cell total RNA


title: Embryo_D10A5B3

description: single cell total RNA


title: Embryo_D10A5B1

description: single cell total RNA


title: Embryo_D10A4S16

description: single cell total RNA


title: Embryo_D10A4S14

description: single cell total RNA


title: Embryo_D10A4S7

description: single cell total RNA


title: Embryo_D10A4S11

description: single cell total RNA


title: Embryo_D12A3B1

description: single cell total RNA


title: Embryo_D10A4B7

description: single cell total RNA


title: Embryo_D10A4B8

description: single cell total RNA


title: Embryo_D10A4B3

description: single cell total RNA


title: Embryo_D10A3S9

description: single cell total RNA


title: Embryo_D10A3S35

description: single cell total RNA


title: Embryo_D10A3S2

description: single cell total RNA


title: Embryo_D10A3S7

description: single cell total RNA


title: Embryo_D10A3S18

description: single cell total RNA


title: Embryo_D10A3S1

description: single cell total RNA


title: Embryo_D10A6S4

description: single cell total RNA

value: EPI


title: Embryo_D10A3S10

description: single cell total RNA

value: STBs


title: Embryo_D10A3B5

description: single cell total RNA


title: Embryo_D10A3B8

description: single cell total RNA


title: Embryo_D10A3B4

description: single cell total RNA


title: Embryo_D10A2S3

description: single cell total RNA


title: Embryo_D10A3B17

description: single cell total RNA


title: Embryo_D10A4S8

description: single cell total RNA


title: Embryo_D10A2S32

description: single cell total RNA


title: Embryo_D10A3B3

description: single cell total RNA


title: Embryo_D10A4S9

description: single cell total RNA


title: Embryo_D10A3B9

description: single cell total RNA


title: Embryo_D10A2S1

description: single cell total RNA


title: Embryo_D10A2S24

description: single cell total RNA


title: Embryo_D10A3B2

description: single cell total RNA


title: Embryo_D10A2S2

description: single cell total RNA


title: Embryo_D10A2S17

description: single cell total RNA


title: Embryo_D10A2B3

description: single cell total RNA


title: Embryo_D10A2B4

description: single cell total RNA


title: Embryo_D10A2B6

description: single cell total RNA


title: Embryo_D10A2B2

description: single cell total RNA


title: Embryo_D10A2B1

description: single cell total RNA


title: Embryo_D10A1S9

description: single cell total RNA


title: Embryo_D10A1S7

description: single cell total RNA


title: Embryo_D10A1S6

description: single cell total RNA


title: Embryo_D10A1S4

description: single cell total RNA


title: Embryo_D10A3B7

description: single cell total RNA


title: Embryo_D10A1S3

description: single cell total RNA


title: Embryo_D10A3B6

description: single cell total RNA


title: Embryo_D10A1S40

description: single cell total RNA


title: Embryo_D14A1S9

description: single cell total RNA

value: PSA-EPI


title: Embryo_D10A2S21

description: single cell total RNA


title: Embryo_D10A1S31

description: single cell total RNA


title: Embryo_D10A1S23

description: single cell total RNA


title: Embryo_D14A1S7

description: single cell total RNA


title: Embryo_D10A1S21

description: single cell total RNA


title: Embryo_D14A1S5

description: single cell total RNA


title: Embryo_D14A1S6

description: single cell total RNA


title: Embryo_D10A1S13

description: single cell total RNA


title: Embryo_D14A1S3

description: single cell total RNA


title: Embryo_D10A1S12

description: single cell total RNA


title: Embryo_D14A1S32

description: single cell total RNA


title: Embryo_D10A1S1

description: single cell total RNA


title: Embryo_D14A1S31

description: single cell total RNA


title: Embryo_D10A1S10

description: single cell total RNA


title: Embryo_D14A1S30

description: single cell total RNA


title: Embryo_D10A1S11

description: single cell total RNA


title: Embryo_D10A1B8

description: single cell total RNA


title: Embryo_D10A1B7

description: single cell total RNA


title: Embryo_D10A1B5

description: single cell total RNA


title: Embryo_D10A1S34

description: single cell total RNA


title: Embryo_D10A1B4

description: single cell total RNA


title: Embryo_D14A1S28

description: single cell total RNA


title: Embryo_D14A1S27

description: single cell total RNA


title: Embryo_D14A1S8

description: single cell total RNA


title: Embryo_D10A1S32

description: single cell total RNA


title: Embryo_D10A1S2

description: single cell total RNA


title: Embryo_D10A1B2

description: single cell total RNA


title: Embryo_D10A1B1

description: single cell total RNA


title: Embryo_D10A1B3

description: single cell total RNA


title: Embryo_D14A1S25

description: single cell total RNA


title: Embryo_D14A1S26

description: single cell total RNA


title: Embryo_D10A1B17

description: single cell total RNA


title: Embryo_D10A1B11

description: single cell total RNA


title: Embryo_D14A1S23

description: single cell total RNA


title: Embryo_D14A1S21

description: single cell total RNA


title: Embryo_D14A1S24

description: single cell total RNA


title: Embryo_D14A1S20

description: single cell total RNA


title: Embryo_D10A4S4

description: single cell total RNA

value: embryo invitro day 9


title: Embryo_D14A1S22

description: single cell total RNA


title: Embryo_D14A1S1

description: single cell total RNA


title: Embryo_D14A1S19

description: single cell total RNA


title: Embryo_D14A1S2

description: single cell total RNA


title: Embryo_D14A1S29

description: single cell total RNA


title: Embryo_D9A4S4

description: single cell total RNA

value: ICM


title: Embryo_D9A4S5

description: single cell total RNA


title: Embryo_D14A1S18

description: single cell total RNA


title: Embryo_D9A4S3

description: single cell total RNA


title: Embryo_D14A1S16

description: single cell total RNA


title: Embryo_D14A1S17

description: single cell total RNA


title: Embryo_D9A4S16

description: single cell total RNA


title: Embryo_D9A4S14

description: single cell total RNA


title: Embryo_D14A1S15

description: single cell total RNA


title: Embryo_D14A1S14

description: single cell total RNA


title: Embryo_D14A1S13

description: single cell total RNA


title: Embryo_D9A6S5

description: single cell total RNA


title: Embryo_D9A6S15

description: single cell total RNA


title: Embryo_D9A5S10

description: single cell total RNA


title: Embryo_D9A5S11

description: single cell total RNA


title: Embryo_D9A6S10

description: single cell total RNA


title: Embryo_D14A1B8

description: single cell total RNA


title: Embryo_D9A4B1

description: single cell total RNA


title: Embryo_D9A6S14

description: single cell total RNA


title: Embryo_D14A1B9

description: single cell total RNA


title: Embryo_D9A6S9

description: single cell total RNA


title: Embryo_D9A6B6

description: single cell total RNA


title: Embryo_D9A6B8

description: single cell total RNA


title: Embryo_D14A1B7

description: single cell total RNA


title: Embryo_D14A1S10

description: single cell total RNA


title: Embryo_D9A6B1

description: single cell total RNA


title: Embryo_D14A1B5

description: single cell total RNA


title: Embryo_D9A5S9

description: single cell total RNA


title: Embryo_D14A1S11

description: single cell total RNA


title: Embryo_D14A1B6

description: single cell total RNA


title: Embryo_D9A5S8

description: single cell total RNA


title: Embryo_D14A1B4

description: single cell total RNA


title: Embryo_D9A5S6

description: single cell total RNA


title: Embryo_D14A1S12

description: single cell total RNA


title: Embryo_D14A1B2

description: single cell total RNA


title: Embryo_D14A1B3

description: single cell total RNA


title: Embryo_D9A5S3

description: single cell total RNA


title: Embryo_D9A5B5

description: single cell total RNA


title: Embryo_D14A1B1

description: single cell total RNA


title: Embryo_D9A5S12

description: single cell total RNA


title: Embryo_D9A4S7

description: single cell total RNA


title: Embryo_D14A1B15

description: single cell total RNA


title: Embryo_D14A1B16

description: single cell total RNA


title: Embryo_D14A1B13

description: single cell total RNA


title: Embryo_D14A1B12

description: single cell total RNA


title: Embryo_D9A4S9

description: single cell total RNA


title: Embryo_D9A4S6

description: single cell total RNA


title: Embryo_D9A4B4

description: single cell total RNA


title: Embryo_D14A1B11

description: single cell total RNA


title: Embryo_D9A4B8

description: single cell total RNA


title: Embryo_D9A4S1

description: single cell total RNA


title: Embryo_D9A4S10

description: single cell total RNA


title: Embryo_D9A4B2

description: single cell total RNA


title: Embryo_D14A1B10

description: single cell total RNA


title: Embryo_D14A1B14

description: single cell total RNA


title: Embryo_D9A3S2

description: single cell total RNA


title: Embryo_D9A4B7

description: single cell total RNA


title: Embryo_D9A4S11

description: single cell total RNA


title: Embryo_D9A3S15

description: single cell total RNA


title: Embryo_D9A3S3

description: single cell total RNA


title: Embryo_D9A3S11

description: single cell total RNA


title: Embryo_D9A3S1

description: single cell total RNA


title: Embryo_D9A3B7

description: single cell total RNA


title: Embryo_D9A3B4

description: single cell total RNA


title: Embryo_D9A3B3

description: single cell total RNA


title: Embryo_D9A3B2

description: single cell total RNA


title: Embryo_D9A3B1

description: single cell total RNA


title: Embryo_D9A2S4

description: single cell total RNA


title: Embryo_D9A2S6

description: single cell total RNA


title: Embryo_D9A2S2

description: single cell total RNA


title: Embryo_D9A2B5

description: single cell total RNA


title: Embryo_D9A2B8

description: single cell total RNA


title: Embryo_D9A2S1

description: single cell total RNA


title: Embryo_D9A2S3

description: single cell total RNA


title: Embryo_D9A2B3

description: single cell total RNA


title: Embryo_D9A1S8

description: single cell total RNA


title: Embryo_D9A1S7

description: single cell total RNA


title: Embryo_D9A1S26

description: single cell total RNA


title: Embryo_D9A1S2

description: single cell total RNA


title: Embryo_D9A1S10

description: single cell total RNA


title: Embryo_D9A1S23

description: single cell total RNA


title: Embryo_D9A1S3

description: single cell total RNA


title: Embryo_D9A1S28

description: single cell total RNA


title: Embryo_D9A3S14

description: single cell total RNA


title: Embryo_D9A1S1

description: single cell total RNA


title: Embryo_D9A1B16

description: single cell total RNA


title: Embryo_D9A1B3

description: single cell total RNA


title: Embryo_D9A1B4

description: single cell total RNA


title: Embryo_D9A1B15

description: single cell total RNA


title: Embryo_D9A1B2

description: single cell total RNA


title: Embryo_D9A1B1

description: single cell total RNA

value: embryo invitro day 8


title: Embryo_D8A6S7

description: single cell total RNA


title: Embryo_D8A6S5

description: single cell total RNA


title: Embryo_D8A6S15

description: single cell total RNA


title: Embryo_D8A6B6

description: single cell total RNA


title: Embryo_D8A6B3

description: single cell total RNA


title: Embryo_D8A6B1

description: single cell total RNA


title: Embryo_D9A2B2

description: single cell total RNA


title: Embryo_D8A5S1

description: single cell total RNA


title: Embryo_D8A5S4

description: single cell total RNA


title: Embryo_D9A2B1

description: single cell total RNA


title: Embryo_D8A5B7

description: single cell total RNA


title: Embryo_D8A5B8

description: single cell total RNA


title: Embryo_D8A5S14

description: single cell total RNA


title: Embryo_D8A3S2

description: single cell total RNA


title: Embryo_D8A3S7

description: single cell total RNA


title: Embryo_D8A3B4

description: single cell total RNA


title: Embryo_D8A3S1

description: single cell total RNA


title: Embryo_D8A3S28

description: single cell total RNA


title: Embryo_D8A3B1

description: single cell total RNA


title: Embryo_D8A3S12

description: single cell total RNA


title: Embryo_D8A3S8

description: single cell total RNA


title: Embryo_D8A3S5

description: single cell total RNA


title: Embryo_D8A2S2

description: single cell total RNA


title: Embryo_D8A3B11

description: single cell total RNA


title: Embryo_D8A2S29

description: single cell total RNA


title: Embryo_D8A2S24

description: single cell total RNA


title: Embryo_D8A2S1

description: single cell total RNA


title: Embryo_D8A2S15

description: single cell total RNA


title: Embryo_D8A2S4

description: single cell total RNA


title: Embryo_D8A2S10

description: single cell total RNA


title: Embryo_D8A2S12

description: single cell total RNA


title: Embryo_D8A2B2

description: single cell total RNA


title: Embryo_D8A2B5

description: single cell total RNA


title: Embryo_D8A1S8

description: single cell total RNA


title: Embryo_D8A2B1

description: single cell total RNA


title: Embryo_D8A2S3

description: single cell total RNA


title: Embryo_D8A1S3

description: single cell total RNA


title: Embryo_D8A1S24

description: single cell total RNA


title: Embryo_D8A1S7

description: single cell total RNA


title: Embryo_D8A3S13

description: single cell total RNA


title: Embryo_D8A1S11

description: single cell total RNA


title: Embryo_D8A3B10

description: single cell total RNA


title: Embryo_D8A1B4

description: single cell total RNA


title: Embryo_D8A1S31

description: single cell total RNA


title: Embryo_D8A1B2

description: single cell total RNA


title: Embryo_D8A1B6

description: single cell total RNA


title: Embryo_D8_8S8

description: single cell total RNA


title: Embryo_D8_8S7

description: single cell total RNA


title: Embryo_D8A1B10

description: single cell total RNA


title: Embryo_D8_8S6

description: single cell total RNA


title: Embryo_D8_8S3

description: single cell total RNA


title: Embryo_D8_8S5

description: single cell total RNA


title: Embryo_D8_8S2

description: single cell total RNA


title: Embryo_D8_8S1

description: single cell total RNA


title: Embryo_D8_8B4

description: single cell total RNA


title: Embryo_D8_8B3

description: single cell total RNA


title: Embryo_D8_8B1

description: single cell total RNA

value: embryo invitro day 7


title: Embryo_D8_8B2

description: single cell total RNA


title: Embryo_D7N1S27

description: single cell total RNA


title: Embryo_D8A1S1

description: single cell total RNA


title: Embryo_D7N1S30

description: single cell total RNA


title: Embryo_D7N1S24

description: single cell total RNA


title: Embryo_D7N1S19

description: single cell total RNA


title: Embryo_D7N1S21

description: single cell total RNA


title: Embryo_D7N1S18

description: single cell total RNA


title: Embryo_D7N1S15

description: single cell total RNA


title: Embryo_D8A1B3

description: single cell total RNA


title: Embryo_D7N1B7

description: single cell total RNA


title: Embryo_D7N1S9

description: single cell total RNA


title: Embryo_D7N1B1

description: single cell total RNA


title: Embryo_D8_8S4

description: single cell total RNA


title: Embryo_D7A4S2

description: single cell total RNA


title: Embryo_D7A4S1

description: single cell total RNA


title: Embryo_D7A4S7

description: single cell total RNA


title: Embryo_D7A4S12

description: single cell total RNA


title: Embryo_D7A4S13

description: single cell total RNA


title: Embryo_D7A4S14

description: single cell total RNA


title: Embryo_D7A4S15

description: single cell total RNA


title: Embryo_D7A4B6

description: single cell total RNA


title: Embryo_D7A4B3

description: single cell total RNA


title: Embryo_D7A4B5

description: single cell total RNA


title: Embryo_D7A4B2

description: single cell total RNA


title: Embryo_D7A3S8

description: single cell total RNA


title: Embryo_D7A3S5

description: single cell total RNA


title: Embryo_D7A3S4

description: single cell total RNA


title: Embryo_D7N1B9

description: single cell total RNA


title: Embryo_D7A3S3

description: single cell total RNA


title: Embryo_D7A3S1

description: single cell total RNA


title: Embryo_D7N1B5

description: single cell total RNA


title: Embryo_D7A3S14

description: single cell total RNA


title: Embryo_D7A3S12

description: single cell total RNA


title: Embryo_D7A3B3

description: single cell total RNA


title: Embryo_D7A3B1

description: single cell total RNA


title: Embryo_D7A3S10

description: single cell total RNA


title: Embryo_D7N1S7

description: single cell total RNA


title: Embryo_D7A3B10

description: single cell total RNA


title: Embryo_D7A3B8

description: single cell total RNA


title: Embryo_D7A2S3

description: single cell total RNA


title: Embryo_D7A4B8

description: single cell total RNA


title: Embryo_D7A2S2

description: single cell total RNA


title: Embryo_D7A2S6

description: single cell total RNA


title: Embryo_D7A2S1

description: single cell total RNA


title: Embryo_D7A2S14

description: single cell total RNA


title: Embryo_D7A2B8

description: single cell total RNA


title: Embryo_D7A2S10

description: single cell total RNA


title: Embryo_D7A1S9

description: single cell total RNA


title: Embryo_D7A2B1

description: single cell total RNA


title: Embryo_D7A2B6

description: single cell total RNA


title: Embryo_D7A2B4

description: single cell total RNA


title: Embryo_D7A1S8

description: single cell total RNA


title: Embryo_D7A1S7

description: single cell total RNA


title: Embryo_D7A1S6

description: single cell total RNA


title: Embryo_D7A1S1

description: single cell total RNA


title: Embryo_D7A1S5

description: single cell total RNA


title: Embryo_D7A1S16

description: single cell total RNA


title: Embryo_D7A1S13

description: single cell total RNA


title: Embryo_D7A1S14

description: single cell total RNA


title: Embryo_D7A1S11

description: single cell total RNA


title: Embryo_D7A1B8

description: single cell total RNA


title: Embryo_D7A2S16

description: single cell total RNA


title: Embryo_D7A1B7

description: single cell total RNA


title: Embryo_D7A1B1

description: single cell total RNA

value: embryo invitro day 6


title: Embryo_D7A1B3

description: single cell total RNA


title: Embryo_D7A1S15

description: single cell total RNA


title: Embryo_D6N3S40

description: single cell total RNA


title: Embryo_D6N3S2

description: single cell total RNA


title: Embryo_D7A1B5

description: single cell total RNA


title: Embryo_D7A2B5

description: single cell total RNA


title: Embryo_D6N3S51

description: single cell total RNA


title: Embryo_D6N3S35

description: single cell total RNA


title: Embryo_D6N3S28

description: single cell total RNA


title: Embryo_D6N3S11

description: single cell total RNA


title: Embryo_D6N3B12

description: single cell total RNA


title: Embryo_D6N3S22

description: single cell total RNA


title: Embryo_D6N2S11

description: single cell total RNA


title: Embryo_D6N2B8

description: single cell total RNA


title: Embryo_D6N2S2

description: single cell total RNA


title: Embryo_D6N2B7

description: single cell total RNA


title: Embryo_D6N2B28

description: single cell total RNA


title: Embryo_D6N2B2

description: single cell total RNA


title: Embryo_D6N2B1

description: single cell total RNA


title: Embryo_D6N2B18

description: single cell total RNA


title: Embryo_D6N1S9

description: single cell total RNA


title: Embryo_D6N1S35

description: single cell total RNA


title: Embryo_D6N1S33

description: single cell total RNA


title: Embryo_D6N1S39

description: single cell total RNA


title: Embryo_D6N1S34

description: single cell total RNA


title: Embryo_D6N1S19

description: single cell total RNA


title: Embryo_D6N2B12

description: single cell total RNA


title: Embryo_D6N3B7

description: single cell total RNA


title: Embryo_D6N1B6

description: single cell total RNA


title: Embryo_D6N1S15

description: single cell total RNA


title: Embryo_D6A5B3

description: single cell total RNA


title: Embryo_D6N1B23

description: single cell total RNA


title: Embryo_D6A5B4

description: single cell total RNA


title: Embryo_D6N2S35

description: single cell total RNA


title: Embryo_D6A5S8

description: single cell total RNA


title: Embryo_D6A5S7

description: single cell total RNA


title: Embryo_D6A5S1

description: single cell total RNA


title: Embryo_D6A4B3

description: single cell total RNA


title: Embryo_D6A4B4

description: single cell total RNA


title: Embryo_D6A4S5

description: single cell total RNA


title: Embryo_D6A4S6

description: single cell total RNA


title: Embryo_D6A4S4

description: single cell total RNA


title: Embryo_D6N2B11

description: single cell total RNA


title: Embryo_D6N1S42

description: single cell total RNA


title: Embryo_D6A3B1

description: single cell total RNA


title: Embryo_D6A3S5

description: single cell total RNA


title: Embryo_D6N1S4

description: single cell total RNA


title: Embryo_D6A3S4

description: single cell total RNA


title: Embryo_D6A2B4

description: single cell total RNA


title: Embryo_D6A2B2

description: single cell total RNA


title: Embryo_D6A2B1

description: single cell total RNA


title: Embryo_D6A3S3

description: single cell total RNA


title: Embryo_D6A3S1

description: single cell total RNA


title: Embryo_D6A2S8

description: single cell total RNA


title: Embryo_D6A2S6

description: single cell total RNA


title: Embryo_D6A2S7

description: single cell total RNA


title: Embryo_D6A1B2

description: single cell total RNA


title: Embryo_D6A4S7

description: single cell total RNA


title: Embryo_D6A1S1

description: single cell total RNA


title: Embryo_D6A1S4

description: single cell total RNA


title: Embryo_D6A1B1

description: single cell total RNA


title: Embryo_D6A1S3

description: single cell total RNA


title: Embryo_D6A1S2

description: single cell total RNA


title: Pedsx3 PB Cell line

status: Public on Sep 10 2019

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

library_source: genomic

data_processing:
Sequencing reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. PRC duplicates reads are removed.
The 42 bp length of the reads is used for peak-calling. The peak caller used for ATAC-Seq is MACS2 (Zhang et al., Genome Biology 2008, 9:R137), using both PE reads from each aligned fragment.
To identify the density of transposition events along the genome, the genome is divided into 32 bp bins and the number of fragments in each bin is determined. For this purpose, reads are extended to 200 bp in order to smooth the data.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: Pediatric brain glioma

growth_protocol: Mice brains were electroporated at postnatal day 1-2 with Piggyback plasmids encoding for GFP (control) or tumor driver genes.

extract_protocol:
Brains were collected in PBS and tumors were microdissected, mechanically dissociated and further enzymatically digested to obtain a single cell suspension. Single cell suspension was grown in culture and FAC sorted for GFP+ cells. Sorted cells were frozen with 10% DMSO and submitted for ATACseq analysis.
Cells were lysed and nuclei isolated and transposition reaction was carried out with Tn5 Transposase. DNA was then isolated and library generated by PCR.

value: Brain

tag: disease state

value: Pediatric brain glioma

value: H3f3aK27M PdgfraD842V Trp53R270H


title: MADRK27M121418-scATACseq

description:
K27M-scATAC-2
10X single-cell ATAC-seq

data_processing:
Cell Ranger ATAC v1.0 from 10X company was used to do the demultiplexing, alignment and expression quantification with default parameter.
Genome_build: mm10 with transgene sequences integrated at insertion site.
Supplementary_files_format_and_content: peak-barcode matrices were stored in MTX files; BED files for peak location; TSV for cell barcodes and unique fragments.

growth_protocol: Mice brains were electroporated at postnatal day 1-2 with the MADR constructs and tumor growth developed during the next 3-5 months.

extract_protocol:
Brains were collected in PBS and tumors were microdissected, mechanically dissociated and further enzymatically digested to obtain a single cell suspension. Single cell suspensions were immediately processed for 10X single cell ATAC-seq.
scATAC sequencing library was prepared on the 10X Genomics Chromium platform following the manufacturer's protocol (10X Genomics 1000110). The isolated nuclei suspension was diluted and then incubated with transposition mix for a targeted nuclei recovery of 10,000 cells. GEMs were then captured on the chromium Chip E (10X Genomics 1000082). Following GEM incubation, clean up was performed using Dynabeads MyOne Silane beads (10X Genomics 2000048) and SPRIselect reagent (Beckman Coulter B23318). Finally, the library was amplified for a total of 10 SI PCR cycles.

value: postnatal day 251


title: Embryo_D6A3B2

description: single cell total RNA


title: MADRK27M113018-scATACseq

description:
K27M-scATAC-1
10X single-cell ATAC-seq

value: postnatal day 222


title: Macula-12mm-cd31-enriched-donor-6

status: Public on Oct 30 2019

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

institute: UNIVERSITY OF IOWA

description: Sample 9

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build hg19 (v3.0.0) with CellRanger (v3.0.1) using the CellRanger default human GTF and the following parameter: --expect-cells=8000.
Experiment 1:  Relates to donors 1-3 (Samples 1-6).  The six samples were collectively aggregated with the cellranger aggr function with the following parameter: --normalized=mapped.  Cells were then filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 300 (to remove cells with poor read quality) or greater than 6000 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-"). Aggregated reads were normalized and clustered in Seurat (v3.0.2) with the following commands: seurat_obj <- NormalizeData(seurat_obj, normalization.method = "LogNormalize", scale.factor = 10000); seurat_obj <- FindVariableFeatures(seurat_obj, selection.method = "mvp", nfeatures = 2000); all.genes <- rownames(seurat_obj); seurat_obj <- ScaleData(seurat_obj, features = all.genes); seurat_obj <- RunPCA(Seurat_obj, features = VariableFeatures(object = seurat_obj)); seurat_obj <- FindNeighbors(seurat_obj, dims = 1:14); seurat_obj <- FindClusters(seurat_obj, resolution = 0.175).
Experiment 2:   Relates to donors 4-7 (Samples 7-14).  Cells were filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 500 (to remove cells with poor read quality) or greater than 7000 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-"). For each of the eight libraries, reads were normalized with the Seurat (v3.0.2) NormalizeData function, and variable features were found with the following commands: donor_x_region <- NormalizeData(donor_x_region, normalization.method = "LogNormalize", scale.factor = 10000); donor_x_region <- FindVariableFeatures(donor_x_region, selection.method = "vst", nfeatures = 2000).  Integration anchors from the first 20 dimensions of the canonical correlation analysis were used to integrate data with the following commands: CD31.anchors <- FindIntegrationAnchors(object.list = c(donor_4_macula, donor_5_macula, donor_6_macula, donor_7_macula, donor_4_peripheral, donoro_5_peripehral, donor_6_peripheral, donor_7_peripheral), dims=1:20); CD31.combined <- IntegrateData(anchorset = CD31.anchors, dims = 1:20).  Data scaling, principal component analysis, and clustering were performed with the following commands: CD31.combined <- ScaleData(CD31.combined, verbose = FALSE); CD31.combined <- RunPCA(CD31.combined, npcs = 30, verbose = FALSE); CD31.combined <- RunUMAP(CD31.combined, reduction = "pca", dims = 1:20); CD31.combined <- FindNeighbors(CD31.combined, reduction = "pca", dims = 1:20); CD31.combined <- FindClusters(CD31.combined, resolution = 0.5).
Genome_build: hg19
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format. Log-normalized expression values (from GetAssayData(object = seurat_object) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values.

source_name: RPE-choroid

extract_protocol:
In experiment 2, a 12-mm macular centered and a 12-mm peripheral punch of RPE/choroid from the inferotemporal region were acquired from four human donors (Donors 4-7). After dissection away from the retina and sclera, the RPE/choroid was finely diced into small squares (approximately 1 mm x 1 mm) with a razor blade. The resulting suspension was dissociated in 450 units/mL of collagenase II (Gibco, Grand Island NY) reconstituted in Hank’s Balanced Salt Solution containing calcium chloride and magnesium chloride (Life technologies, Grand Island NY). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Single-cell RNA libraries were prepared for sequencing using standard 10X genomics protocols. Briefly, cryopreserved samples from donors 1-3 were thawed, and single cells were captured and barcoded using the Chromium System with the v3 single cell-reagent kit (10x Genomics, Pleasanton CA). Cryopreserved cells from donors 4-7 were rapidly thawed before pre-enrichment for endothelial cells. Cells were incubated for 15 minutes with anti-CD31 microbeads (Miltenyi Biotech, Bergisch Gladbach Germany) according to the manufacturer’s instructions before automated autoMACs magnetic separation (Miltenyi Biotech, Bergisch Gladbach Germany) of the CD31+ cell fraction. The positive cell fraction was passed two times through a 40 mm filter to remove aggregates before immediate single cell capturing and barcoding as described above. Sequencing was performed on pooled libraries using the Illumina HiSeq 4000 platform (San Diego, CA), generating 150 base pair paired-end reads.

tag: enrichment

tag: donor

value: RPE-choroid

tag: location

value: macula

tag: punch-size


title: Macula-12mm-cd31-enriched-donor-5

description: Sample 8


title: MADRK27M033018-input control

data_processing:
ChIP-seq reads were aligned to the mouse reference genome mm10 using bwa. BigWig tracks were generated for each sample.
H3K27me3 clustering was performed using ngs.plot (version 2.61) (Shen et al., 2014) for each  sample with mm10 mouse genome build. The list of genes associated with 7 clusters (Fig X) were imported to Seurat, and the expression for each cluster of genes was calculated using Seurat AddModuleScore.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: mice brains were electroporated at post natal day 1-2 with the MADR constructs and tumor growth developed during the next 3-5 months

extract_protocol:
Brains were collected in PBS and tumors where microdisected, mechanically dissociated and further enzimatically digested to obtain a single cell suspension. GFP+ tumoral cells were FACS sorted, growth in culture and fixed in formaldehide and pellet to submitted for ChIP-seq analysis
We completed the H3K27me3 ChIP reactions using 30 μg of mouse pediatric brain tumor chromatin and 4 μg of antibody (Active Motif, cat # 39155). The ChIP reactions also contained a drosophila chromatin spike in for the normalization of the sequencing data. We diluted a small fraction of the ChIP DNA and performed qPCR using positive control primer pairs that worked well in similar assays. For H3K27me3, the primer pair targeted to the promoter region of the active gene ACTB serves as a good negative control.

tag: strain

tag: post natal day

tag: genotype

tag: antibody


title: MADRK27M012618-input control


title: MADRK27M090617-input control


title: MADRK27M033018


title: MADRK27M090617


title: MADRK27M090617

data_processing:
The demultiplexed raw reads were aligned to the transcriptome using STAR (version 2.5.1) with default parameters, using a custom mm10 transcriptome reference from GENCODE M9 annotation, containing all protein coding and long non-coding RNA genes. Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts using Cell Ranger software version 1.3.0 (10X Genomics). The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.
Genome_build: mm10
Supplementary_files_format_and_content: csv files include gene expression for each cell with or without normalization.

source_name: brain

extract_protocol:
Brains were collected in PBS and tumors where microdisected, mechanically dissociated and further enzimatically digested to obtain a single cell suspension. GFP+ tumoral cells were FACS sorted and resuspended in neurobasal media to be processed for 10X single cell RNA-seq
Single-cell RNA-seq libraries were prepared per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, California). Cellular suspensions were loaded on a Chromium Controller instrument (10X Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-RT were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA). After RT, GEMs were harvested and the cDNAs were amplified, cleaned up with SPRIselect Reagent Kit.  Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA) with a custom sequencing setting (26bp for Read 1 and 98bp for Read 2), to obtain a sequencing depth of 100K~200K reads per cell.
10X single cell RNA-seq

tag: tissue

value: brain

tag: age

value: post natal day 150


title: Macula-12mm-cd31-enriched-donor-7

description: Sample 10


title: MADRK27M012618


title: MADRK27M033018

value: post natal days 149


title: Control GFP+ PB Cell line

description: NPC

source_name: Neural progenitor cells

value: Healthy

value: Nuclear GFP


title: Macula-12mm-cd31-enriched-donor-4

description: Sample 7


title: Sarkosyl 0.5min rep1

status: Public on Aug 01 2019

city: Coventry

first: Jie

last: Zhang

address: School of Life Sciences, Gibbet Hill Campus, The University of Warwick

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: processed data file:

data_processing:
Library strategy: PRO-seq
Reads were trimmed with cutadapt version 1.14 to remove the adaptor, command: cutadapt -a TGGAATTCTCGGGTGCCAAGG -m 20 -e 0.05
Trimmed reads were aligned to hg38 genome with Hisat2 version 2.1.0, command: hisat2 -p 4 -k 1 --no-unal
Sam file was modified by custom script Sam_enlong.pl to extand reads to theoretic length
The extanded sam file was transform to bam file and sort by samtools
Sorted bam file was further transformed into bedgraph files, the bedgraph with nascent RNA on plus strand from command: genomeCoverageBed -strand - -5 -bga -ibam; for minus strand reads:: genomeCoverageBed -strand + -5 -bga -ibam
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph, pausing time of peaks

source_name: HEK293 0.5min

growth_protocol: HEK293 cells were grown to 60% confluency at 37C and 5% CO2 in a 175cm2 flask in DMEM supplemented with 10% FBS. One day before permeabilization of cells, the culture medium was replaced with fresh medium.

extract_protocol:
Run on buffer is same with PRO-seq protocol (Mahat D B,2016), 37C for 0.5mins
total RNA was isolated using 500 ul TRIzol-LS for each sample according to the manufacturer's protocol (Invitrogen Life Technologies)

tag: cell line

tag: cell type

value: Human embryonic kidney cells

tag: run-on time

tag: sarkosyl run-on

value: Yes


title: Sarkosyl 0.5min rep2

description: processed data file:


title: Sarkosyl 8min rep2

description: processed data file:

source_name: HEK293 8min

extract_protocol:
Run on buffer is same with PRO-seq protocol (Mahat D B,2016), 37C for 8mins
total RNA was isolated using 500 ul TRIzol-LS for each sample according to the manufacturer's protocol (Invitrogen Life Technologies)


title: Sarkosyl 2min rep2

description: processed data file:

source_name: HEK293 2min

extract_protocol:
Run on buffer is same with PRO-seq protocol (Mahat D B,2016), 37C for 2mins
total RNA was isolated using 500 ul TRIzol-LS for each sample according to the manufacturer's protocol (Invitrogen Life Technologies)


title: Sarkosyl 8min rep1

description: processed data file:


title: Sarkosyl 32min rep1

description: processed data file:

source_name: HEK293 32min

extract_protocol:
Run on buffer is same with PRO-seq protocol (Mahat D B,2016), 37C for 32mins
total RNA was isolated using 500 ul TRIzol-LS for each sample according to the manufacturer's protocol (Invitrogen Life Technologies)


title: Sarkosyl 32min rep2

description: processed data file:


title: MADRK27M012618

value: post natal days 106


title: Sarkosyl 2min rep1

description: processed data file:


title: A549, CAGE library, replicate 2

status: Public on Jun 14 2019

city: Ipswich

first: Bo

last: Yan

state: MA

address: County Road

institute: New England Biolabs

description:
CAGE library, replicate 2
N07N08.mapq.gtf

data_processing:
adapter sequence was trimmed using trim_galore
The trimmed reads were mapped to the human genome using STAR
The number of reads starting at any position were counted using a customized script
Genome_build: gencode GRCh38.p5 Release 24
Supplementary_files_format_and_content: tab-delimited gtf file
Supplementary_files_format_and_content: number of reads starting at TSS

source_name: CAGE library, replicate 2

growth_protocol: Human lung carcinoma A549 cells (ATCC) were cultured in F12 media supplemented with L-glutamine.

extract_protocol:
Total RNA was purified using the RNeasy RNA purification kit (Qiagen).
NEB Small RNA library prep

value: A549 cancer cell


title: A549, Re-Cappable-seq control library, replicate 2

description:
Re-Cappable-seq control library, replicate 2
NegD4_i5.1.50nt.fastq


title: A549, Re-Cappable-seq enrich library, replicate 2

description:
Re-Cappable-seq enrich library, replicate 2
D3D4.tsscount.mapq.gtf


title: Marginal Zone Lymphoma patient MZL_021

status: Public on Jun 19 2019

type: RNA

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

hyb_protocol: According to affymetrix protocol

scan_protocol: According to affymetrix protocol

data_processing: Raw cel files were RMA normalized using the ExpressionFileCreator module of GenePattern31, and quality checked for batch effects by unsupervised clustering of the 3,000 most variably expressed genes across the dataset.

label: biotin

source_name: biopsy

label_protocol: According to affymetrix protocol

extract_protocol: Trizol or Qiagen RNA extraction kit

tag: diagnosis

value: Marginal Zone Lymphoma

value: tumor specimen


title: A549, Re-Cappable-seq control library, replicate 1

description:
Re-Cappable-seq control library, replicate 1
NegD3_i4.1.50nt.fastq


title: A549, CAGE library, replicate 1

description:
CAGE library, replicate 1
N07N08.mapq.gtf

source_name: CAGE library, replicate 1


title: Marginal Zone Lymphoma patient MZL_008


title: Marginal Zone Lymphoma patient MZL_016


title: Marginal Zone Lymphoma patient MZL_018


title: Marginal Zone Lymphoma patient MZL_013


title: Marginal Zone Lymphoma patient MZL_009


title: Marginal Zone Lymphoma patient MZL_014


title: Marginal Zone Lymphoma patient MZL_019


title: Marginal Zone Lymphoma patient MZL_005


title: Marginal Zone Lymphoma patient MZL_006


title: Marginal Zone Lymphoma patient MZL_023


title: Marginal Zone Lymphoma patient MZL_015


title: Marginal Zone Lymphoma patient MZL_007


title: Marginal Zone Lymphoma patient MZL_010


title: Marginal Zone Lymphoma patient MZL_017


title: A549, Re-Cappable-seq enrich library, replicate 1

description:
Re-Cappable-seq enrich library, replicate 1
D3D4.tsscount.mapq.gtf


title: Marginal Zone Lymphoma patient MZL_020


title: Marginal Zone Lymphoma patient MZL_012


title: Marginal Zone Lymphoma patient MZL_022


title: Marginal Zone Lymphoma patient MZL_004


title: A549, CIP treatment, Re-Cappable-seq control library, replicate 2

description:
CIP treatment, Re-Cappable-seq control library, replicate 2
NegD3D4.tsscount.gtf


title: A549, CIP treatment, Re-Cappable-seq enrich library, replicate 1

description:
CIP treatment, Re-Cappable-seq enrich library, replicate 1
D1D2.tsscount.gtf


title: A549, CIP treatment, Re-Cappable-seq enrich library, replicate 2

description:
CIP treatment, Re-Cappable-seq enrich library, replicate 2
D1D2.tsscount.gtf


title: A549, CIP treatment, Re-Cappable-seq control library, replicate 1

description:
CIP treatment, Re-Cappable-seq control library, replicate 1
NegD3D4.tsscount.gtf


title: Marginal Zone Lymphoma patient MZL_011


title: 416B_1_Sfpi1-Prom

status: Public on May 29 2019

city: Münster

first: Frank

last: Rosenbauer

address: Robert-Koch-Str. 43

department: Institute of Molecular Tumor Biology

institute: University Hospital Münster

data_processing:
Library strategy: 4C-seq
Base calling was performed with Illumina's CASAVA 1.7.
4C-seq reads were aligned against the mouse reference genome (mm10 /GRCm38.69) using BWA-mem (bwa v. 0.7.12;  default settings)
Aligned reads were mapped to a virtual restriction fragment library based on the chosen restriction enzyme sequences with the R/Bioconductor package Basic4Cseq.
Fragment data was RPM-normalized and filtered: Only uniquely aligned reads were kept for analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bed files were created with the R/Bioconductor package Basic4Cseq and include running median RPM values per valid fragment in the chosen near-cis region for the experiment's viewpoint.

source_name: myeloid progenitor cell line

growth_protocol: 416B cells were cultured under standard conditions using DMEM medium supplemented with 20% FCS.

extract_protocol: 4C-seq was performed as previously described (PMID: 22609568). For chromatin digestion NlaIII (NEB) and Csp6I (Thermo Scientific) were used as first and second restriction endonucleases. Inverse PCR was performed to amplify the specific viewpoint at the PU.1 promoter. Single-end sequencing was performed using the Illumina HiSeq2500 platform.

value: myeloid progenitor cell line

tag: 4c-seq viewpoint

value: PU.1 Promoter


title: 416B_2_Sfpi1-Prom


title: Marginal Zone Lymphoma patient MZL_003


title: T-cell_1_Sfpi1-Prom

source_name: Thymocytes

growth_protocol: Thymus of 1-2 BL6 (wt) mice was isolated and filtered in a 40 µm diameter cell strainer to prepare single cell suspension. After a centrifugation for 5 min at 1200 rpm 5 ml ACK buffer was applied. Incubation was done for 10 min at RT followed by inactivation using 10 ml 1x PBS buffer. Next, cells were washed in 1x PBS, counted after centrifugation.

value: Thymocytes


title: Marginal Zone Lymphoma patient MZL_002


title: T-cell_2_Sfpi1-Prom


title: Marginal Zone Lymphoma patient MZL_001


title: IPF_non-invasive_9

status: Public on May 17 2019

data_processing:
Tophat2 (2.0.7) was applied to align sequencing reads to the reference human genome (GRCh38).
The relative gene expression RPKM were estimated using SAMMate (2.7.4) and Ensembl database (Homo Sapiens.GRCh38.77).
Genome_build: GRCh28
Supplementary_files_format_and_content: excel table with gene expression in RPKM

source_name: Lung

growth_protocol: Human lung fibroblasts were isolated from surgical lung biopsies or lung transplant explants obtained from patients with IPF.

extract_protocol:
Totla RNA of each sample was isolated using the Absolutely RNA Microprep Kit (Aligent Technologies, Santa Clara, CA, USA) following the manufacture's recommendations.
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit. The workflow consists of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina HiSeq 3000 for 1x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: The tissues were minced, digested and cultured in DMEM supplemented with 15% FBS and Antibiotic-Antimycotic. The primary cells were used from four to six generation for further assays.

value: non-Invasive cells


title: IPF_non-invasive_10


title: IPF_non-invasive_8


title: IPF_non-invasive_6


title: IPF_non-invasive_7


title: IPF_non-invasive_4


title: BMM_1_Sfpi1-Prom

source_name: Bone Marrow-derived Macrophages

growth_protocol: Femurs of BL6 (wt) mice were isolated and flushed with 1x PBS. After centrifugation 250 µl ACK lysis buffer was applied. Incubation was done for 5 min at RT followed by inactivation using 1x PBS buffer. Once filtered in a 100 µm diameter cell strainer cells were counted and plated in 10 cm tissue-culture-treated dishes (1e6 cells each dish). After 7 days cultivation at 37°C and 5% CO2 in 10 ml DMEM supplemented with 1% Penicillin, 1% Streptomycin, 1% L-Glutamin, 20% FCS, 1:1000 M-CSF (10 ng/ml final) cells were harvested.

value: Bone Marrow-derived Macrophages


title: IPF_non-invasive_5


title: IPF_non-invasive_3


title: IPF_invasive_10

value: Invasive cells


title: IPF_invasive_5


title: IPF_invasive_8


title: IPF_invasive_6


title: IPF_invasive_4


title: IPF_invasive_9


title: IPF_invasive_3


title: Embryo_D6N1S1

description: single cell total RNA

source_name: embryo

extract_protocol:
Isolation of single cells. The embryos were washed in PBS for 3 times, washed in 0.25% trypsin (T4799; SigmaAldrich) 2 times, incubated with 0.25% trypsin for around 15 min at 37 °C, and terminated by DFBS. Embryo was dissociated into single cells by repeated pipetting and dispersed in 1% DFBS/PBS. A single cell was pipetted into a PCR tube. All operations above were performed under the Nikon SMZ645 microscopy.
The synthesis and amplification of full-length cDNAs were performed following Smart-seq2 protocol4. Briefly, single cells were washed in DPBS (Gibco 14190-144) and picked into lysis buffer using Pasteur pipettes under a dissecting microscope. Reversetranscription reactions and pre-amplification were performed using SuperScript II (Invitrogen 18064-014) and KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2601), respectively. The quality of the cDNAs were evaluated by Bioanalyzer 2100. Library construction and sequencing were performed by Annoroad Gene Technology (http://www.annoroad.com/) or BGI (https://www.bgi.com/). Sequencing was performed on Illumina X-ten platform or BGISEQ-500 sequencing platform (BGI, Shenzhen, China). Pair-end reads were got and the number of the reads were more than 7 M for every single cell

value: embryo invitro day 6

value: EPI


title: BMM_2_Sfpi1-Prom


title: IPF_invasive_1


title: Embryo_D6N1S3

description: single cell total RNA


title: ATACseq_stimulated_WT_rep1

status: Public on Mar 19 2019

data_processing:
ATAC-seq reads were trimmed for Nextera adapters sequences using Skewer version 0.2.2 with the following parameters: -m pe, -x CTGTCTCTTATA, -y CTGTCTCTTATA, -q 20.
ATAC-seq reads were aligned to the murine reference genome (NCBI build 38, mm10) using bowtie2 version 2.3.2.
ATAC-seq reads were filtered for primary, properly-paired alignments with a MAPQ ≥ 30 (view -f 3 -F 2308 -q 30) followed by duplicate removal with SAMtools version 1.4.
ATAC-seq replicates were merged, and analysed as one sample; peaks were determined by using MACS version 1.4 with a stringent p-value of 10-10.
Target regions were determined based on differential ATAC-seq peaks (unstimulated, stimulated WT); average count profiles for other samples were calculated for these target regions.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files were created with MACS 1.4 and represent the differential ATAC-seq peaks, including the MACS-specific score per identified peak region.
ATAC_wtU-wtCa_wtCa_spec_peaks.bed: differential peaks enriched for WT stimulated samples samples
ATAC_wtU-wtCa_wtU_spec_peaks.bed: differential peaks enriched for the WT unstimulated samples

source_name: HoxER-PU.1 WT neutrophils

growth_protocol: Progenitor cells were enriched from BM single cell suspensions of PU.1 WT or KO mice via density-gradient (Lymphocyte Separation Medium, Lonza) centrifugation (400g, 15 min, RT). Progenitors were prestimulated in RPMI (PAA) supplemented with 10 % FCS, 100 μg/ml Penicillin/Streptomycin, 2 mM L-glutamine and 10 ng/ml murine IL-3 (PeproTech), 20 ng/ml murine Il-6 (PeproTech) and 25 ng/ml murine SCF (PeproTech). Progenitor cells were immortalized by spin infection (4000 rpm, 1 h, RT) with a retrovirus expressing Hoxb8 fused to the estrogen receptor (HoxER) and by maintaining the cells in Opti-MEM® (Life Technologies) supplemented with 10 % FCS, 100 μg/ml Penicillin/Streptomycin, 10 ng/ml SCF, 30 µM 2-Mercaptoethanol and 2 µM β-Estradiol (Sigma). Differentiation into neutrophils was induced by withdrawal of Estradiol and addition of murine G-CSF (PeproTech) for 4 days.

extract_protocol:
5x104 HoxER-PU.1 WT and HoxER-PU.1 KO neutrophils were harvested after 2 hour stimulation with heat-inactivated C. albicans material (MOI=1) or treament for 2h with DMSO, 1h with TSA [100 nM] and 2h with Entinostat [5 µM]. All centrifugations steps were carried out at 500 g at 4°C in a fixed-angle centrifuge. Cells were washed once in 50 μl cold PBS and were lysed in 50 μl cold ATAC lysis buffer (10 mM NaCl, 10 mM Tris, pH 7.4, 3 mM MgCl2, 0.1 % Igepal CA 630) while centrifuging for 10 min. The supernatant was discarded, and the crude nuclei extract (pellet) was resuspended in 50 μl transposition mix composed of 2.5 μl Tn5 Transposase, 25 μl tagmentation buffer (Nextera Sample Prep Kit) and 22.5 μl H2O. The mixture was incubated for 30 min at 37°C in an Eppendorf Thermomixer at 300 rpm. The reaction was purified using the MinElute kit following instructions of Qiagen and eluted in 10 μl of prewarmed TE buffer.
The transposed DNA was amplified for 12 cycles using preactivated (1 min at 98°C before use) KAPA HiFi Hotstart Ready Mix and single-index primers following the Nextera Low Plex Pooling guidelines. To obtain PCR-amplifiable fragments, PCR was initiated with an elongation step to obtain amplifiable product since the transposase inserts adapters only to the 5' end of each fragment. PCR was run as followed: holding stage (5 min @70°C; 3 min @95°C) and cycling stage (20 sec @98°C, 30 sec @ 63°C, 15 sec @ 72°C). PCR amplified samples were purified using AMPure XP beads (Beckman Coulter) at a beads/sample ratio of 1.2x. Library quality control was performed with an Agilent High-Sensitivity DNA chip on a Bioanalyzer 2100. The Core Facility Genomic Muenster performed library quantification by qPCR (Kapa Library Quant Kit) and paired-end sequencing on an Illumina Nextseq 500.

value: HoxER-PU.1 WT neutrophils derived from immortalized progenitors

value: MRP8-Cre-ires/GFP (PU.1 WT)


title: ATACseq_stimulated_WT_rep2


title: ATACseq_stimulated_KO_rep2

source_name: HoxER-PU.1 KO neutrophils

value: HoxER-PU.1 KO neutrophils derived from immortalized progenitors

value: MRP8-Cre-ires/GFP:PU.1f/f (PU.1 KO)


title: JUNB_ChIPseq_unstimulated_KO_rep2

data_processing:
Basecalls were performed using Real-Time Analysis (RTA) version 2.4.11.
ChIP-Seq reads were aligned to the current mouse reference sequence (NCBI build 38, mm10) using bowtie2 version 2-2.2.6 and only uniquely mapped reads were used for downstream analysis.
ChIP-Seq replicates were merged and further analysed as one sample.
Peaks were called using MACS version 1.4 with a p-value of 1e-2.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files were created with MACS 1.4 and represent ChIP-seq peaks, including the MACS-specific score per identified peak region.

extract_protocol:
1-2x107 differentiated HoxER-PU.1 WT or HoxER-PU.1 KO neutrophils were harvested in a 50 ml Falcon tube and crosslinking was performed by adding 1 % formaldehyde followed by 10 min incubation at RT on a seesaw rocker SSL4 (Stuart). Fixation reaction was quenched by addition of glycine at a final concentration of 0.15 M and incubation for 5 min at RT while shaking. Cells were pelleted by centrifugation (290 g, 5 min, 4°C) and washed two times with ice-cold PBS. Cell pellets were resuspended in 1 ml ice-cold PBS, and cell suspensions were transferred to a 1.5 ml reaction tube. Cells were pelleted by centrifugation (850 g; 5 min, 4°C), were snap frozen in liquid nitrogen and stored at -80°C. Cell pellets were thawed on ice, were resuspended in 300 µl RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 140 mM NaCl, 1 % (v/v) Triton X-100, 0.1% (v/v) SDS, 0.1% (w/v) Na-DOC) and lysed for 10 min on ice. Cell lysates were transferred to 1.5 ml TPX hard plastic reaction tubes (Diagenode) and were sonicated using a Bioruptor (Diagenode). Sonication was performed for 40 minutes on high power settings with 15 sec on and 30 sec off, and cooling system was set to 4°C. Sheared chromatin was centrifuged (20000 g, 10 min, 4°C) and transferred to new reaction tubes. 15 µg of JUNB antibody (Cell Signaling, 3753S) or normal rabbit IgG (abcam, ab171870) were coupled to washed 75 µl Protein G Dynabeads (Thermo Fisher Scientific), then 300 µl binding/blocking buffer (0.5 % (w/v) BSA, 0.5 % (v/v) Tween-20 in PBS) was added, and the mixture was incubated for one hour at RT under rotation (Rotator SB3, Stuart). Afterwards, beads were washed once in 300 µl binding/blocking buffer, and 300 µl of chromatin was added directly to the beads. The mixtures were incubated overnight at 4°C under rotation. Beads were magnetically separated, resuspended in 180 µl ice-cold RIPA buffer and transferred to a well of a 96-well Twin tec microbiology PCR plate (Eppendorf). Beads were washed five times in ice-cold RIPA buffer, followed by two washing steps with ice-cold RIPA-500 (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 500 mM NaCl, 1 % (v/v) Triton X-100, 0.1% (v/v) SDS, 0.1% (w/v) Na-DOC) and LiCl buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 250 mM LiCl, 0.5 % (v/v) NP-40, 0.5 % (w/v) Na-DOC). After a final wash step with ice-cold TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0), ChIP DNA was eluted from the beads by adding 50 µl direct elution buffer (10 mM Tris-HCl, pH 8.0, 5 mM EDTA, pH 8.0, 300 mM NaCl, 0.5 % (v/v) SDS). RNase treatment was performed by incubation ChIP DNA with 2 µl RNase (Roche) for 30 min at 37°C. Next, 2.5 µl Proteinase K (Invitrogen) and 1 µl glycogen (Roche) were added, and the mixture was incubated for 2 h at 37°C. Decrosslinking was performed by incubating the mixture at 65°C overnight. After decrosslinking magnetic beads were discarded and the supernatant was transferred to a new well of a 96-well plate. ChIP DNA was purified by adding first the 0.4x volume of Agencourt AMPure XP beads (Beckman Coulter Genomics) to bind large DNA fragments. The supernatant was then transferred to a new well of 96-well plate. Then 1.2x volume of Agencourt AMPure XP beads were added, and the beads were washed two times with 80% ethanol. ChIP DNA was eluted from the beads by 35 µl 10 mM Tris-HCl (pH 8.0), and the DNA was transferred to a new well of 96 well plate. Plates were stored at -20°C until libraries were prepared.
ChIP-Seq libraries were prepared using the NEBNext® Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following the instructions of the supplier. The Core Facility Genomic Muenster performed library quantification by qPCR (Kapa Library Quant Kit) and single-end sequencing on an Illumina Nextseq 500.

tag: chip antibody

value: JUNB Cell Signaling (3753S)


title: JUNB_ChIPseq_unstimulated_KO_rep1


title: IgG_ChIPseq_unstimulated_KO_rep1

value: normal rabbit IgG (abcam, ab171870)


title: ATACseq_stimulated_KO_rep1


title: JUNB_ChIPseq_unstimulated_WT_rep1

value: MRP8-Cre-ires/GFP (PU.1WT)


title: IgG_ChIPseq_unstimulated_WT_rep1


title: JUNB_ChIPseq_unstimulated_WT_rep2


title: H3K27ac_ChIPseq_KO_unstimulated_rep2

data_processing:
Basecalls were performed using Real-Time Analysis (RTA) version 2.4.11.
ChIP-Seq reads were aligned to the current mouse reference sequence (NCBI build 38, mm10) using bowtie2 version 2.0.2 and only uniquely mapped reads were used for downstream analysis.
ChIP-Seq replicates with correlation values ≥0.9 as determined by DiffBind version 2.4.8 were merged and further analysed as one sample.
Peaks were called using MACS version 1.4 with a stringent p-value of 10-10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files were created with MACS 1.4 and represent ChIP-seq peaks, including the MACS-specific score per identified peak region.

extract_protocol:
1.5x107 HoxER-PU.1 WT and HoxER-PU.1 KO  neutrophils were harvested in a 50 ml Falcon tube. Cells were crosslinked with 1 % formaldehyde for 10 min at RT while shaking (seesaw rocker SSL4, Stuart). After crosslinking 5 ml 1 M HEPES (pH 7.5) was added and reaction was quenched by addition of 0.125 M glycine (5 min, RT, shaking). Cells were pelleted (1300 rpm, 8 min, 4°C) and washed two times with ice-cold PBS. Cell lysis was performed by swelling the pellet in ice-cold lysis buffer (10 mM Tris, pH 8.0, 10 mM NaCl, 0.2 % NP-40, 1:500 proteinase inhibitor cocktail (PIC, Sigma)) for 10 min on ice. Nuclei were pelleted by centrifugation (1800 rpm, 5 min, 4°C), and were dissolved in Non-SDS sonication buffer (10 mM Tris, pH 8.0, 1 mM EDTA, 0.5 M EGTA, 1:500 PIC). After incubation for 10 min on ice, chromatin was transferred to TPX hard plastic reaction tubes (1.5 ml or 15 ml, Diagenode) and was sonicated for 30 minutes sonication time on high power (30 sec on, 30 sec off, 0.5 sec pulse rate) using a Bioruptor (Diagenode) and a minichiller (Huber) for cooling. After sonication, chromatin was centrifuged (13200 rpm, 15 min, 4°C) to pellet cell debris and an aliquot (10% Input) was removed and was stored at -20°C for later usage. The chromatin was diluted 10x with ChIP dilution buffer (0.01 % SDS, 1.1 % Triton-X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl) in a 2 ml reaction tube. To preclear the chromatin, 40 μl Protein A/G Agarose beads (Santa Cruz) were added, and the mixture was incubated for 30 min at 4°C under constant rotation (Rotator SB3, Stuart). Beads were pelleted (1000 rpm, 1min, 4°C) and the supernatant was transferred to a new reaction tube. 10 µg H3K4me1 (Cell Signaling, 5326) or H3K27ac antibody (abcam, ab4729) were added to the chromatin, and the mixtures were incubated overnight at 4°C under rotation. Protein A/G agarose beads (Santa Cruz) were blocked for one hour at RT in 1ml PBS containing 1.5% fish skin gelatin (Sigma). After washing, beads were resuspended in the initial volume of ChIP dilution buffer. For precipitation, 200 µl protein A/G agarose beads were added to the chromatin/antibody mix, and the solution was incubated for one hour at 4°C under rotation. The beads were pelleted (1000 rpm, 1 min, 4°C) and were washed two times in 1 ml ChIP low salt immune complex wash buffer (0.1 % SDS, 1 % Triton-X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl) while rotation for 5 min at 4°. Then, beads were washed two times in 1 ml ChIP high salt immune complex wash buffer (0.1 % SDS, 1 % Triton-X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl) and two times in 1 ml ChIP LiCl immune complex wash buffer (0.25 M LiCl, 1 % NP-40, 1 % DOC, 1 mM EDTA, 10 mM Tris, pH 8.1). Afterwards, pelleted beads were washed two times in 1 ml TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0). DNA elution was performed by addition of 250 μl ChIP elution buffer (1 % SDS, 0.1 M NaHCO3) and incubation for 15 min at RT under rotation. The beads were pelleted (1000 rpm, 1 min, 4°C) and the supernatant was transferred to a new 1.5 ml Safe-Lock tube. The beads were conducted to a second elution step, and the two eluates were combined. Protein-DNA crosslinks of samples and inputs (10 %) were reversed by addition of 20 μl 5 M NaCl (overnight, 65°C). Next day, 2 μl (20 mg/ml) proteinase K (Invitrogen), 10 µl 0.5M EDTA and 20 µl Tris-HCl pH 6.5 were added and incubated 1h at 45°C. DNA was isolated by addition of one volume phenol/chloroform/isoamyl alcohol (Roth, 25:24:1) and subsequently centrifugation of the mixture (13200 rpm, 15 minutes, 4°C). The aqueous phase containing the DNA was transferred to a new tube, and 1 µl glycogen (20 mg/ml, Sigma) was added. The precipitated DNA was resuspended in 60 µl DNase and RNase free water (Gibco) and was stored at -20°C for further applications.
ChIP-Seq libraries were prepared using the NEBNext® Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following the instructions of the supplier. The Core Facility Genomic Muenster performed library quantification by qPCR (Kapa Library Quant Kit) and single-end sequencing on an Illumina Nextseq 500.

value: H3K27ac (abcam, ab4729)


title: IPF_non-invasive_1


title: IPF_invasive_7


title: H3K4me1_ChIPseq_KO_unstimulated_rep2

value: H3K4me1 (Cell Signaling, 5326)


title: H3K27ac_ChIPseq_KO_unstimulated_rep1


title: H3K4me1_ChIPseq_KO_unstimulated_rep1


title: H3K27ac_ChIPseq_WT_unstimulated_rep2


title: H3K4me1_ChIPseq_WT_unstimulated_rep2


title: H3K27ac_ChIPseq_WT_unstimulated_rep1


title: ATACseq_unstimulated_KO_rep1

data_processing:
Basecalls were performed using Real-Time Analysis (RTA) version 2.4.11.
ATAC-seq reads were trimmed for Nextera adapters sequences using Skewer version 0.2.2 with the following parameters: -m pe, -x CTGTCTCTTATA, -y CTGTCTCTTATA, -q 20.
ATAC-seq reads were aligned to the murine reference genome (NCBI build 38, mm10) using bowtie2 version 2.3.2.
ATAC-seq reads were filtered for primary, properly-paired alignments with a MAPQ ≥ 30 (view -f 3 -F 2308 -q 30) followed by duplicate removal with SAMtools version 1.4.
ATAC-seq replicates were merged, and analysed as one sample; peaks were determined by using MACS version 1.4 with a stringent p-value of 10-10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files were created with MACS 1.4 and represent ATAC-seq peaks, including the MACS-specific score per identified peak region.
ATAC_ffU_peaks.bed: unstimulated KO peaks

extract_protocol:
5x104 HoxER-PU.1 WT and HoxER-PU.1 KO neutrophils were harvested. All centrifugations steps were carried out at 500 g at 4°C in a fixed-angle centrifuge. Cells were washed once in 50 μl cold PBS and were lysed in 50 μl cold ATAC lysis buffer (10 mM NaCl, 10 mM Tris, pH 7.4, 3 mM MgCl2, 0.1 % Igepal CA 630) while centrifuging for 10 min. The supernatant was discarded, and the crude nuclei extract (pellet) was resuspended in 50 μl transposition mix composed of 2.5 μl Tn5 Transposase, 25 μl tagmentation buffer (Nextera Sample Prep Kit) and 22.5 μl H2O. The mixture was incubated for 30 min at 37°C in an Eppendorf Thermomixer at 300 rpm. The reaction was purified using the MinElute kit following instructions of Qiagen and eluted in 10 μl of prewarmed TE buffer.
The transposed DNA was amplified for 12 cycles using preactivated (1 min at 98°C before use) KAPA HiFi Hotstart Ready Mix and single-index primers following the Nextera Low Plex Pooling guidelines. To obtain PCR-amplifiable fragments, PCR was initiated with an elongation step to obtain amplifiable product since the transposase inserts adapters only to the 5' end of each fragment. PCR was run as followed: holding stage (5 min @70°C; 3 min @95°C) and cycling stage (20 sec @98°C, 30 sec @ 63°C, 15 sec @ 72°C). PCR amplified samples were purified using AMPure XP beads (Beckman Coulter) at a beads/sample ratio of 1.2x. Library quality control was performed with an Agilent High-Sensitivity DNA chip on a Bioanalyzer 2100. The Core Facility Genomic Muenster performed library quantification by qPCR (Kapa Library Quant Kit) and paired-end sequencing on an Illumina Nextseq 500.

value: HoxER-PU.1 KO neutrophils   derived from immortalized progenitors


title: H3K4me1_ChIPseq_WT_unstimulated_rep1


title: ATACseq_unstimulated_WT_rep2

data_processing:
Basecalls were performed using Real-Time Analysis (RTA) version 2.4.11.
ATAC-seq reads were trimmed for Nextera adapters sequences using Skewer version 0.2.2 with the following parameters: -m pe, -x CTGTCTCTTATA, -y CTGTCTCTTATA, -q 20.
ATAC-seq reads were aligned to the murine reference genome (NCBI build 38, mm10) using bowtie2 version 2.3.2.
ATAC-seq reads were filtered for primary, properly-paired alignments with a MAPQ ≥ 30 (view -f 3 -F 2308 -q 30) followed by duplicate removal with SAMtools version 1.4.
ATAC-seq replicates were merged, and analysed as one sample; peaks were determined by using MACS version 1.4 with a stringent p-value of 10-10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files were created with MACS 1.4 and represent ATAC-seq peaks, including the MACS-specific score per identified peak region.
ATAC_wtU_peaks.bed: unstimulated wildtype peaks


title: ATACseq_unstimulated_KO_rep2


title: ATACseq_unstimulated_WT_rep1


title: mRNAseq_KO_Ca_stimulated_rep2

data_processing:
Basecalls were performed using Real-Time Analysis (RTA) version 1.13.48.
mRNA-Seq reads were aligned to the current mouse reference sequence (NCBI build 38, mm10) using STAR version 2.3.1.
Differential gene expression was calculated using CuffDiff version 2.2.0. For normalisation, the classic reads per kilobase per million (RPKM) method was used. The default value of max bundle frags was elevated to 10 Mio.
For further analyses, only those genes were taken into consideration where the RPKM value of one condition in the differential analysis was at least one.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

extract_protocol:
1x107 HoxER-PU.1 WT and HoxER-PU.1 KO neutrophils were left unstimulated or were stimulated for 2 hours with Candida albicans heat-inactivated cell material. RNA was extracted with the RNeasy Mini Kit (Qiagen) and DNase I digestion was performed directly on the column by using the DNase I Kit (Qiagen). RNA concentration and quality were determined by using the Bioanalyzer (Agilent Technologies) with the Agilent RNA 6000 Nano Kit (Agilent Technologies).
Libraries were prepared using the NEBNExt® UltraTM Directional RNA Library Prep Kit for Illumina (New England Biolabs) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions. Briefly, 300 ng of total RNA was enriched for mRNA using NEBNExt Oligo d(T)25 beads and was fragmented to 200 nucleotides fragments. Next, two rounds of cDNA synthesis were performed to obtain double-stranded cDNA, which was purified using Agencourt AMPure XP Beads (Beckman Coulter Genomics). After the End Prep was completed, the NEBNext Adaptor for Illumina was ligated to the cDNA fragments. After another round of purification using the Agencourt AMPure XP Beads, adaptor-ligated DNA (library) was enriched with a PCR step. For pooling six libraries in one lane, NEBNext Index Primer # 2,4,5,6,7 and 12 were used in the PCR. Libraries were purified with Agencourt AMPure XP Beads and quality of libraries was determined on an Agilent Technologies 2100 Bioanalyzer by using the Agilent High sensitivity DNA Kit (2.2.1.2). The Core Facility Genomics of the Medical Faculty Muenster quantified, normalised and sequenced the libraries for 50 cycles on a HighScanSQ (Illumina).

treatment_protocol: HoxER-PU.1 WT or HoxER-PU.1 KO neutrophils were left unstimulated or were stimulated for 2 hours with Candida albicans heat-inactivated (15 min at 80°C) cell material in an multiplicity of infection of 1.


title: mRNAseq_KO_unstimulated_rep2


title: mRNAseq_KO_unstimulated_rep3


title: mRNAseq_WT_Ca_stimulated_rep3


title: mRNAseq_KO_Ca_stimulated_rep1


title: mRNAseq_KO_unstimulated_rep1


title: mRNAseq_WT_unstimulated_rep3


title: mRNAseq_WT_Ca_stimulated_rep2