title: melanoma_K409_tumor_VDJ

description: total RNA

data_processing:
Library strategy: TCR-Seq
Cell Ranger analysis pipelines (version 3.0.2, 10X Genomics) were used to process the generated sequencing data.
Data was demultiplexed into FASTQ and aligned to the GRCh38 human reference genome and counted.
TCR library reads were assembled into single cell V(D)J sequences and annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: GEX samples have three files each: tsv file containing filtered cellular barcodes, tsv file containing filtered cellular genes, and mtx file containing filtered cellular matrix. VDJ samples have two files each; csv file containing clonotypes and csv file containing the sequence for each cell barcode.
Supplementary_files_format_and_content: VDJ samples have two files each: csv file containing clonotypes and csv file containing the sequence for each cell barcode.

value: Cutaneous primary tumor


title: AX2 24h rep1

status: Public on Apr 07 2020

type: SRA

city: London

first: Jonathan

last: Chubb

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

country: United Kingdom

institute: University College London

library_source: transcriptomic

data_processing:
Paired end reads were mapped to the Dictyostelium genome (version obtained from Gareth Bloomfield, masking the duplication on chromosome 2) using Tophat v2.0.9; library type parameter fr-firststrand, -p 4, -g 0
reads for each gene were counted with HtSeqCount v0.5.4p3. -m union -s reverse -a 0
Genome_build: dicty_2.7
Supplementary_files_format_and_content: tab-delimited text file with read counts for all samples

molecule: total RNA

organism: Dictyostelium discoideum

source_name: dedifferentiating cells

growth_protocol: Cells were grown on Klebsiella bacteria on SM agar and harvested before clearing of the bacterial lawn. Cells were washed free of bacteria before further processing

extract_protocol:
Cells were pelleted and flash frozen. Total RNA was extracted by SDS-based lysis, followed by phenol extraction and ethanol preciptiation to remove protein.
100 ng total RNA was used to prepare mRNA libraries using NEBNext mRNA isolation kit and NEBNext Ultra Directional RNA Library preparation kit. mRNA fragmentation used manufacturer recommended conditions for a 300bp insert size. Library amplification used 13 cycles of PCR. 75bp paired-end reads were generated using an Illumina NextSeq 500.

treatment_protocol: Cells were developed for 14 h on Whatman #50 filter paper in a humified chamber. Developed cells were disaggregated in KK2 + 20 mM EDTA then dedifferentiated in HL5 growth medium as a shaken suspension

tag: strain

tag: genotype

value: wild type

tag: replicate


title: WT rep3

type: RNA

city: Chongqing

first: Huakan

last: Zhao

state: State...

address: Xinqiao Street 183, Shapingba district

department: Clinical Medicine Research Center

country: China

institute: Xinqiao Hospital, Third Military Medical University

description: Control (3)

data_processing:
For the normalization in this study, we useed ACTB as the housekeeping gene. Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
Fold Change worksheet reports test/control (i.e., STIM1 KO/WT; Snail1+STIM1 dOE/Mock ratios.
Results were analyzed using 2^-ΔΔCt and 2^-ΔΔCt relative quantification methods. mRNAs that displayed threshold cycles (Ct) >35 were excluded from the analysis. ACTB was used as housekeeping gene. Data were analyzed with Statminer software (Integromics, Philadelphia, PA) and normalized against WT-group.

label: SYBR Green II

organism: Homo sapiens

source_name: SMMC7721 cell line

label_protocol: Reverse transcription was performed from 1μg total RNA using PrimeScript™ RT reagent Kit with gDNA Eraser (TAKARA).3 ng cDNA was added into each 20 μL reaction mix. MRNA expressions of selected genes were assessed by RT-quantitative PCR using TB Green® Premix Ex Taq™ II (TAKARA) on BioRad CFX386 (Bio-Rad, CA) with 40 cycles at 95 °C for 10 seconds, 59 °C for 20 seconds and 72 °C for 30 seconds.

growth_protocol: Cells  were cultured in DMEM supplemented with 10% (v/v) FBS at 37°C in 5% CO2.

extract_protocol: When the cells grow to 60~70% confluent, Total RNA was extracted by using Trizol (TAKARA, Japan).

treatment_protocol: STIM1 knockout(STIM1 KO)-SMMC7721 cells were constructed by CRISPR/Cas9.STIM1 KO+Snail1 OE-SMMC7721 cells were established via lentiviral Infection of Snail1 overexpression (Snail1 OE) in STIM1 KO-SMMC7721 cells.

tag: genotype/variation

value: SMMC7721 without any gene editing


title: melanoma_K409_tumor_GEX

city: San Francisco

first: Kelly

middle: Maria

last: Mahuron

state: CA

address: 513 Parnassus Avenue, HSW 1201B

country: USA

institute: UCSF

description: total RNA

data_processing:
Cell Ranger analysis pipelines (version 3.0.2, 10X Genomics) were used to process the generated sequencing data.
Data was demultiplexed into FASTQ and aligned to the GRCh38 human reference genome and counted.
TCR library reads were assembled into single cell V(D)J sequences and annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: GEX samples have three files each: tsv file containing filtered cellular barcodes, tsv file containing filtered cellular genes, and mtx file containing filtered cellular matrix. VDJ samples have two files each; csv file containing clonotypes and csv file containing the sequence for each cell barcode.
Supplementary_files_format_and_content: VDJ samples have two files each: csv file containing clonotypes and csv file containing the sequence for each cell barcode.

source_name: human melanoma

growth_protocol: Live cells were sort-purified using an BD FACSAria Fusion (BD Biosciences) from collagenase-digested human melanoma samples or from PBMCs isolated by Ficoll gradient.

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument.
Reverse transcription was performed and libraries were constructed according to the 10X Chromium Single Cell 5' Gene Expression and V(D)J Profiling Solution kit.

tag: tissue

value: melanoma

tag: tumor site

tag: treatment status

value: naive

tag: sort purification strategy

value: Cells were sort-purified as live, singlet, CD45+CD3+CD4-CD8+ and CD45+CD3+CD4+CD8- loaded into a single channel in a 60:40 ratio


title: AX2 8h rep1


title: melanoma_K409_LN_VDJ

description: total RNA

value: Involved regional lymph node


title: WT rep1

description: Control (1)


title: AX2 6h rep1


title: Control 1

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
BGI internal software used to remove adpators and low quality reads.
Mapped to Sus Scrofa (ss11.1) using HISAT
DEG assessed using DeSeq2 and NOIseq
Genome_build: ss11.1
Supplementary_files_format_and_content: text file with count data and FPKM for each sample.

organism: Sus scrofa

source_name: Intestinal tissue

growth_protocol: Piglets were followed from birth to 24-25 days of age and fed milk replacer (DI-9224, Arla Foods, Denmark), or the same product with added wheat.

extract_protocol:
Tissue was collected at euthanasia. Total RNA was extracted using miRNAeasy kits (Qiagen).
Standard BGI protocol.

tag: breed

value: Danish Landrace/Yorkshire

value: distal small intestine

tag: age


title: STIM1 KO+Snail1 OE  rep2

description: Testl (5)

value: STIM1 KO+Snail1 OE-SMMC7721 cells were established via lentiviral Infection of Snail1 overexpression in STIM1 KO-SMMC7721 cells


title: melanoma_K409_LN_GEX

description: total RNA


title: cRNA-seq HSV-1 8hpi R2

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

country: Germany

institute: Julius-Maximilians-Universität Würzburg

description: cRNA.tsv

data_processing:
3' sequencing adapter sequence were removed from the 50 nt long reads by computing a prefix-suffix sequence alignment (cRNA-seq only)
Barcode sequences (first 9 nt = 3 random bases followed by 4 bases of experiment specific barcodes followed by 2 random bases) were removed from all reads and stored for later use. (cRNA-seq only)
Bowtie 1.0 was used to align all reads to the human genome, Ensembl transcripts (v75), ribosomal rRNA, the HSV1 genome (JN555585, terminal repeats masked), the HSV1 transcripts as well as novel junctions identified in the 4sU data by ContextMap. Only reads aligning to at most 3 distinct genome positions with at most 2 mismatches were kept for further analyses.
Peaks were called by identifying significant enrichment in a sliding-window approach.
Genome_build: JN555585
Supplementary_files_format_and_content: FPKM

organism:
Homo sapiens
Human alphaherpesvirus 1 strain 17

source_name: human foreskin fibroblasts (HFF)

growth_protocol: Primary human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 15 were infected with HSV-1 strain 17 at an MOI of 10

extract_protocol:
Cells were lyzed using Trizol and total cellular RNA was isolated.
Sequencing libraries were prepared using the cRNA-seq and dRNA-seq inhouse protocols.

treatment_protocol: Cells were infected for 15 min using an MOI of 10. 15min after infection (time point 0h), cell culture media was replaced with fresh media. Cells were harvested prior to or at 8h p.i. cRNA-seq and dRNA-seq libraries were prepared.

tag: cell type

value: primary fibroblasts

tag: time post infection

value: HSV-1, 8 h p.i.

value: Replicate 2

tag: enrichment

value: 5' RNA ends enriched


title: AX2 4h rep2


title: AX2 4h rep1


title: melanoma_K409_blood_GEX

description: total RNA

value: PBMC

value: Cells were sort-purified as live, singlet, CD45+CD3+CD4-CD8+ and loaded into a single channel


title: cRNA-seq HSV-1 8hpi R1

description: cRNA.tsv

value: Replicate 1


title: melanoma_K383_LN_GEX

description: total RNA

value: Cells were sort-purified as live, singlet, CD45+CD3+CD4-CD8+, CD45+CD3+CD4+CD8-, and CD45+CD3- and loaded into a single channel in a 40:40:20 ratio


title: cRNA-seq HSV-1 4hpi R2

description: cRNA.tsv

value: HSV-1, 4 h p.i.


title: AX2 2h rep1

value: wild type


title: cRNA-seq HSV-1 4hpi R1

description: cRNA.tsv


title: Control 3


title: AX2 0h rep1


title: cRNA-seq HSV-1 2hpi R2

description: cRNA.tsv

value: HSV-1, 2 h p.i.


title: Hep3B stimulating status RNAseq rep1

city: Xi’an

first: Yi

last: Wu

state: Shaanxi

address: No.28, Xianning West Road

institute: Xi'an Jiaotong University

data_processing:
The raw data were subject to quality control with trimmmomatic/0.39 and sickle/1.33
Alignment to Genome using hisat2/2.1.0 for RNAseq, bismark/0.19.0(bowtie2/2.3.5.1) for GWBS
samtools/1.7 for file transformation or sorting
picard/2.9.2 for removing duplications of PCR
the counts were extracted using htseq/0.9.1 for RNAseq; bismark(bismark_methylation_extractor) for GWBS
Genome_build: GRCh38.p13 for human; GRCm38.p6 for mouse
Supplementary_files_format_and_content: ht.counts for RNAseq; cytosine_report results for GWBS

source_name: cell line

growth_protocol: Hep3B was obtained from ATCC and cultured using DMEM with 10% FBS

extract_protocol: RNA / DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hep3B cells with or without IL-6 and IL-1β treatment for 24 h;100ul turpentine was subcutaneously injected to the mouse every hind limb for 2 days.

value: liver

tag: treated

tag: cell line


title: Control 2


title: Hep3B resting status RNAseq rep2


title: Development 12h rep2

source_name: developing cells

growth_protocol: Before development, cells were grown in HL5 (Formedium, UK).

treatment_protocol: Cells were developed for the indicated time on Whatman #50 filter paper in a humidified chamber

tag: timepoint


title: cRNA-seq HSV-1 2hpi R1

description: cRNA.tsv


title: Hep3B resting status RNAseq rep1


title: bzpS- 2h

extract_protocol:
Cells were pelleted and flash frozen. Total RNA was extracted by SDS-based lysis, followed by phenol extraction and ethanol preciptiation to remove protein.
100 ng total RNA was used to prepare mRNA libraries using NEBNext mRNA isolation kit and NEBNext Ultra II Directional RNA Library preparation kit. mRNA fragmentation used manufacturer recommended conditions for a 300bp insert size. Library amplification used 13 cycles of PCR. 75bp paired-end reads were generated using an Illumina NextSeq 500.

value: bzpS-


title: ChIP_HL60_input_WT_rep2

city: Kyoto

first: Yotaro

last: Ochi

address: Yoshida-Konoe-cho

department: Department of Pathology and Tumor Biology

country: Japan

institute: Kyoto Univiersity

library_source: genomic

data_processing:
The sequencing reads were aligned to the reference genome (hg19 or mm9) using bowtie (v1.2.2) following trimming of adapters and read tails to a total length of 50 base pairs using cutadapt.
Duplicates and reads on blacklisted regions (ENCODE) were removed by Picard and bedtools, respectively.
Peaks were called using MACS (v2.1.1) for each replicate individually with a p value threshold of 1 x 10–3.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Peaks were called using MACS (v2.1.1) for each replicate individually with a p value threshold of 1 x 10–3.

molecule: genomic DNA

extract_protocol:
ChIP-seq experiments were performed using c-Kit+ HSPCs or HL-60 cell lines.
Cells were fixed in PBS with 1% formaldehyde (Thermo Fisher Scientific) for 10 min at room temperature with gentle mixing.  The reaction was stopped by adding glycine solution (10x) (Cell Signaling Technology) and incubating for 5 minutes at room temperature, and the cells were washed in cold PBS twice.  The cells were then processed with SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology) and Covaris E220 (Covaris) according to the manufacturer’s protocol.  The antibodies used for ChIP are as follows: STAG1 (Protein Tech, 14015-1-AP), STAG2 (Novus, NBP1-30472), SMC1 (Abcam, ab9262), CTCF (Cell Signaling Technology, D31H2), RUNX1 (Abcam, 23980), total Pol II (CST, D8L4Y), Ser5-P Pol II (Abcam, ab5408), H3K27ac (Cell Signaling Technology, D5E4), H3K27me3 (Cell Signaling Technology, C36B11), H3K4me1 (Cell Signaling Technology, D1A9), or H3K4me3 (Cell Signaling Technology, C42D8).  ChIP-seq libraries were constructed using ThruPLEX DNA-seq kit (Takara) according to the manufacturer’s protocol, and then subjected to sequencing using HiSeq 2500 or NovaSeq 6000 (Illumina).

value: WT


title: Development 8h rep2


title: Development 10h rep2


title: cRNA-seq HSV-1 1hpi R1

description: cRNA.tsv

value: HSV-1, 1 h p.i.


title: ChIP_HL60_STAG2_WT_rep2


title: Development 6h rep2


title: Development 4h rep2


title: Hep3B stimulating status RNAseq rep2


title: RP 8 h p.i. - Harringtonin - Rep 2

description:
Ribosome protected RNA fragments (29-30nt)
Library sequenced three times.
Human.B.tsv,HSV.B.tsv

data_processing:
3' sequencing adapter sequence were removed from the 50 nt long reads by computing a prefix-suffix sequence alignment
Barcode sequences (first 9 nt = 3 random bases followed by 4 bases of experiment specific barcodes followed by 2 random bases) were removed from all reads and stored for later use.
Bowtie 1.0 was used to align all reads to the human genome, Ensembl transcripts (v75), ribosomal rRNA, the HSV1 genome (JN555585, terminal repeats masked), the HSV1 transcripts as well as novel junctions identified in the 4sU data by ContextMap. Only reads aligning to at most 3 distinct genome positions with at most 2 mismatches were kept for further analyses.
At each alignment position a greedy algorithm successively discarded alignments such that no read sequence remained that has hamming distance 1 to any other read. The total number of unique sequences was taken as the conservative fragment count.
Mapped reads were further processed by Price 1.0.1, once with standard parameters for cellular ORFs, and once with -novelTranscripts to identify novel viral transcripts.
Genome_build: hg19, JN555585

source_name: Ribosome profiling

growth_protocol: Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 13 were infected at 60% confluency 24h after the last split.

extract_protocol:
Cells were snap frozen followed by cell lysis in presence of cycloheximide. Following removal of cell nuclei by centrifugation and stringent RNAse digest, ribosomes were pelleted through a sucrose cushion. Translated RNA fragments were recovered by size selection.
Translated RNA fragments were cloned following the protocol described by Stern-Ginossar N et al. Science 2012. rRNA depletion involved additional biotinylated oligos to improve depletion. To efficiently remove all biotinylated oligos complementary to specific rRNA sequences, two rounds of streptavidin depletion were performed. cDNA libraries were amplified by PCR and sequenced (HiSeq 50nt reads).

treatment_protocol: Cells were infected for 10 min with HSV-1 strain 17 at an MOI of 10 followed by PBS wash and media replacement. 500µM 4-thiouridine was added to the cell culture at the indicated time points.

value: human foreskin fibroblasts

value: 8 h p.i.

tag: infection with

value: Herpes simplex virus 1, strain 17

tag: barcode

value: NNNTTAANN


title: RP 4 h p.i. - Lactimidomycin - Rep 2

description:
Ribosome protected RNA fragments (29-30nt)
Human.B.tsv,HSV.B.tsv

value: 4 h p.i.

value: NNNAATAANN


title: RP 8 h p.i. - Lactimidomycin - Rep 2


title: ChIP_HL60_STAG2_WT_rep1

tag: genotype


title: Development 2h rep2

tag: strain

tag: replicate


title: Development 14h rep2


title: Development 0h rep2


title: RP 8 h p.i. - Lactimidomycin - Rep 1

description:
Ribosome protected RNA fragments (29-30nt)
Human.A.tsv,HSV.A.tsv

value: NNNCCGGNN


title: RP 2 h p.i. - Harringtonin - Rep 2

value: 2 h p.i.

value: NNNAATANN


title: Development 14h rep1


title: ChIP_HL60_STAG1_WT_rep2


title: ChIP_HL60_SMC1_WT_rep2


title: ChIP_HL60_STAG1_WT_rep1


title: Development 12h rep1


title: RP 8 h p.i. - Harringtonin - Rep 1

description:
Ribosome protected RNA fragments (29-30nt)
Library sequenced three times.
Human.A.tsv,HSV.A.tsv


title: RP 4 h p.i. - Lactimidomycin - Rep 1

value: NNNCAATNN


title: ChIP_HL60_SMC1_WT_rep1


title: cRNA-seq HSV-1 1hpi R2

description: cRNA.tsv

value: primary fibroblasts

value: Replicate 2

value: 5' RNA ends enriched


title: Development 8h rep1


title: ChIP_HL60_H3K4me3_WT_rep2


title: RP 2 h p.i. - Harringtonin - Rep 1


title: ChIP_HL60_input_WT_rep1


title: Development 6h rep1


title: Development 4h rep1


title: ChIP_HL60_H3K27ac_WT_rep2


title: Development 2h rep1


title: Development 0h rep1


title: ChIP_HL60_CTCF_WT_rep2


title: ChIP_HL60_CTCF_WT_rep1


title: ChIP_HL60_H3K27ac_WT_rep1


title: Development 10h rep1


title: Hi-C_HL60_KO_WT_2

data_processing:
The sequencing reads were processed using Juicer.
For comparative analysis, the valid interactions after filtering were randomly resampled and arranged in the number of the lowest sample.
Loops were called at 5kb and 10kb resolutions using HICCUPS.
Genome_build: hg19, mm10

extract_protocol:
Hi-C experiments were performed using WT-, SKO-, RKO-, or DKO-cells.
Briefly, two million cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Cells were permeabilized and chromatin was digested with MboI restriction enzyme, and the ends of restriction fragments were labeled with biotinylated nucleotides and ligated.  After crosslink reversal, DNA was purified and sheared with Covaris M220 (Covaris).  Then point ligation junctions were pulled down with streptavidin beads.  Then libraries were constructed with Nextera Mate Pair Sample Preparation Kit (Illumina) according to the manufacturer’s protocol, and subject to sequencing using NovaSeq (Illumina).


title: Hi-C_HL60_KO_RKO_2

value: RUNX1 KO


title: Hi-C_HL60_KO_SKO_1

value: STAG2 KO


title: Hi-C_HL60_KO_SKO_2


title: Bacteria 24h rep2

treatment_protocol: Cells were developed for 14 h on Whatman #50 filter paper in a humified chamber. Developed cells were disaggregated in KK2 + 20 mM EDTA. Cells were dedifferentiated in culture dishes containing live Klebsiella (OD600 = 2) in KK2


title: Bacteria 12h rep2


title: Hi-C_HL60_KO_DKO_2

value: STAG2/RUNX1 KO


title: Hi-C_HL60_KO_WT_1

value: WT


title: ChIP_HL60_H3K4me3_WT_rep1


title: Hi-C_HL60_KO_DKO_1


title: Hi-C_HL60_KO_RKO_1


title: Bacteria 8h rep2


title: Bacteria 5h rep2


title: Bacteria 4h rep2


title: Bacteria 3h rep2


title: RNA_HL60_KO_SKO_5

data_processing:
RNA-seq experiments were performed in two or more biological replicates.  The sequencing reads were aligned to the reference genome (hg19 or mm9) using STAR7 (v2.5.3).
Reads on each gene were counted with featureCounts (v1.5.3) from Subread package, and edgeR package in R was used to identify the differentially expressed genes with FDR threshold of 0.05 and to generate the multidimensional scaling (MDS) plot.
The analysis was performed in genes expressed at >1 count per million (CPM) in two or more samples, and generalized linear models were used to compare gene expression data.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Reads on each gene were counted with featureCounts (v1.5.3) from Subread package, and edgeR package in R was used.

extract_protocol:
RNA-seq experiments were performed using WT-, SKO-, RKO-, or DKO-cells.
RNA was extracted using RNeasy Mini Kit (QIAGEN) or NucleoSpin RNA XS (Macherey-Nagel).  Libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep kit for Illumina (New England BioLabs) and were subjected to sequencing using HiSeq 2500 or NovaSeq 6000 instrument (Illumina) with a 100-150 bp paired-end protocol.


title: RNA_HL60_KO_SKO_4


title: RNA_HL60_KO_WT_5


title: RNA_HL60_KO_WT_4


title: RNA_HL60_KO_RKO_5


title: Bacteria 1h rep2


title: RNA_HL60_KO_DKO_5


title: Bacteria 2h rep2


title: Bacteria 0.5h rep2


title: RNA_HL60_KO_RKO_4


title: CPEP9_TET_7 scATAC-seq

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

data_processing:
single cell ATAC data were mapped to hg38 using the Cell Ranger ATAC pipeline
SnapATAC (https://github.com/r3fang/SnapATAC) was used to combine multiple samples, i.e. the fragment.tsv files generated by Cell Ranger ATAC pipeline, and then clustering analysis was performed.
Genome_build: hg19
Supplementary_files_format_and_content: raw MEX format for called peaks (bar code, mtx file, peak file ) and fragment file

source_name: T1D Tetramer+

extract_protocol:
Nuclei were exteacted for ATAC-Seq.
For ATAC-Seq, nuclei were isolated from FACS purified tetramer+ beta cell-specific CD8 T cells and polyclonal Tem and naive CD8 T cells from T1D donors using the Low Cell Input Nuclei Isolation protocol from 10x Genomics. The transposition reaction was then performed on the bulk nuclei. The transposed nuclei were partitioned into nanoliter-scale barcoded Gel Beads-in-emulsion (GEMs) after running the loaded Chromium microfluidic Chip E on the Chromium Controller, and the transposed DNA was uniquely indexed and barcoded for each individual nucleus per manufacturer’s instructions (10x Genomics). Libraries were generated and sequenced using Illumina Hiseq system following the manufacturer's protocols. For each sample, the single cell ATAC data were mapped to hg38 using the Cell Ranger ATAC pipeline.  We then used SnapATAC (https://github.com/r3fang/SnapATAC) to combine multiple samples, i.e. the fragment.tsv files generated by Cell Ranger ATAC pipeline, and performed the clustering analysis.
scATAC-Seq, the libraries were paired-end (50bp+49bp) sequenced

tag: tissue

value: Tetramer+ T1D CD8 T cells


title: Bacteria/Buffer 0h rep2

treatment_protocol: Cells were developed for 14 h on Whatman #50 filter paper in a humified chamber. Developed cells were disaggregated in KK2 + 20 mM EDTA


title: RNA_HL60_KO_DKO_4


title: Bacteria 6h rep2


title: L58_1

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Graduate School of Medicine, Kyoto University

hyb_protocol: cRNA was hybridized to Clariom D Assay human array (Thermofisher), washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Transcriptome Analysis Console Software, and obtained normalized intensity values.

label: biotin

source_name: Peripheral blood, CD8+ sorted

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit (ThermoFisher) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.

tag: diagnosis

value: Non-small cell lung cancer

value: Blood

tag: treatment

value: Pre-treatment

tag: individual


title: L56_2

value: Post-treatment (nivolumab)


title: CPEP1_TET_1 scATAC-seq


title: L59_2


title: L60_2


title: L57_2


title: L54_2


title: Bacteria 1.5h rep2


title: L52_2


title: CPEP1_NAIVE_3 scATAC-seq

source_name: T1D Naive

value: Polyclonal Naive CD8 T cells


title: CPEP1_TEM_2 scATAC-seq

source_name: T1D Tem

value: Polyclonal TEM CD8 T cells


title: 740254: HIV Tetramer+ WGBS

data_processing:
Basecalling was performed using Illumina RealTimeAnalysis software
FASTQ sequences adapter trimmed (trimglore) and mapped to the hg19 and mm10 genome by BSMAP
CpGs were extracted by the methratio.py in the BSMAP package
Genome_build: mm10 (mouse WGBS), hg19 (human WGBS)
Supplementary_files_format_and_content: methylation ratio are in bed formats that contains methylation ratio for each CpG

source_name: HIV Tetramer+

extract_protocol:
DNA was extracted followed by bisulfite treatment for library prepration. Nuclei were exteacted for ATAC-Seq.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer.  The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols. For ATAC-Seq, nuclei were isolated from FACS purified tetramer+ beta cell-specific CD8 T cells and polyclonal Tem and naive CD8 T cells from T1D donors using the Low Cell Input Nuclei Isolation protocol from 10x Genomics. The transposition reaction was then performed on the bulk nuclei. The transposed nuclei were partitioned into nanoliter-scale barcoded Gel Beads-in-emulsion (GEMs) after running the loaded Chromium microfluidic Chip E on the Chromium Controller, and the transposed DNA was uniquely indexed and barcoded for each individual nucleus per manufacturer’s instructions (10x Genomics). Libraries were generated and sequenced using Illumina Hiseq system following the manufacturer's protocols. For each sample, the single cell ATAC data were mapped to hg38 using the Cell Ranger ATAC pipeline.  We then used SnapATAC (https://github.com/r3fang/SnapATAC) to combine multiple samples, i.e. the fragment.tsv files generated by Cell Ranger ATAC pipeline, and performed the clustering analysis.

value: Tetramer+ HAART CD8 T cells


title: 1302923: HIV Tetramer+ WGBS


title: Bacteria 12h rep1


title: L50_2


title: 2-736133: Healthy Donor TEM WGBS

source_name: Healthy Donor TEM


title: L53_2


title: Bacteria 8h rep1


title: 1302922: HIV Tetramer+ WGBS


title: 1302925: HIV Tetramer+ WGBS


title: Bacteria 24h rep1


title: 647760: Healthy Donor TEM WGBS


title: L49_2


title: Bacteria 6h rep1


title: L51_2


title: 383226: Healthy Donor TEM WGBS


title: D8

first: Amy

middle: Frances

last: Danson

state: Greater London

address: 2 Newark St

department: Centre for Genomics and Child Health

institute: The Blizard Institute

data_processing:
Raw FASTQ files were mapped to the reference hetGla2 using BISMARK (v0.16.3) and Bowtie2 (v2.2.8).
Reads that mapped outside of the targeted regions were discarded from analyses, and methylated and unmethylated counts for each CpG were calculated using the custom C++ program (https://bitbucket.org/lowelabq- mul/methylation-extractor). Those CpGs with a coverage < 50× were also discarded from analyses
Genome_build: hetGla2
Supplementary_files_format_and_content: csv file containing the fractional methylation level at each contig and position within included aDMP primers for each sample.

organism: Heterocephalus glaber

source_name: Skin

extract_protocol:
DNA was extracted from tissues using the PureLink™ Genomic DNA kit (Thermo Fisher, Cat. K182002), as per the manufacturer’s instructions. Tissues were digested overnight at 55 °C using 180 µl PK buffer and 20 µl PK enzyme from the kit. DNA concentration was quantified using a High Sensitivity DNA Qubit® assay (Life Technologies, Cat. Q32851).
DNA from tissues was diluted to a concentration of 11 ng/µl and 45 µl of each sample was used for generation of targeted bisulfite sequencing data by the Genome Centre Facility at the Blizard Institute, Queen Mary University of London. DNA was bisulfite converted in a 96 well plate format using the EZ-96 DNA Methylation™ Kit (Zymo, Cat. D5003). Target amplification was performed using the FastStart High Fidelity PCR System, dNTPack (Sigma-Aldrich, Cat. 4738284001) in the 48.48 layout on the Fluidigm® C1 system (Fluidigm®, USA), a microfluidics platform. Library preparation was performed using the same kit including 4 μl of Access Array Barcode Library Primer and 1 μl of PCR product diluted 1:100. Libraries were sequenced with Illumina MiSeq sequencing using v2 chemistry (150 bp, paired-end).

value: Skin

tag: age (weeks)

tag: individual id


title: Bacteria 5h rep1


title: 2-736134: Healthy Donor TCM WGBS

source_name: Healthy Donor TCM

value: Polyclonal TCM CD8 T cells


title: D9

source_name: Liver

value: Liver


title: D7


title: Bacteria 3h rep1

source_name: dedifferentiating cells


title: Bacteria 4h rep1


title: Kidney_H557

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

description:
SAMPLE1
Mouse 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Genome Studio 5.0
background subtraction, rank invariant normalization

label: Biotin

organism: Mus musculus

source_name: mouse kidney

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: N/A: adult mouse kidney and lung tissue

extract_protocol: RNA was extracted with Trizol reagent,Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Mice were healthy, or subjected to Unilateral Ureter Obstruction (UUO), or to intratracheal bleomycin injection.

value: BALB/C

tag: gender

value: female

tag: developmental stage

value: adult

tag: disease state

value: healthy kidney


title: D6


title: L46_2

tag: cell type


title: 383227: Healthy Donor TCM WGBS


title: Bacteria 2h rep1


title: 383225: Healthy Donor TSCM WGBS

source_name: Healthy Donor TSCM

value: Polyclonal TSCM CD8 T cells


title: D5


title: Bacteria 1.5h rep1


title: L45_2


title: 647762: Healthy Donor TSCM WGBS


title: Bacteria 1h rep1


title: Bacteria 0.5h rep1


title: D2


title: 647761: Healthy Donor TCM WGBS


title: D11


title: D12


title: D10


title: Undifferentiated rep2

source_name: undifferentiated cells

treatment_protocol: Cells were harvested from mid-log growth in HL5 growth medium


title: 2-736141: Healthy Donor TSCM WGBS


title: 1107220: T1D Tetramer+ WGBS


title: Bacteria/Buffer 0h rep1


title: 1179494: T1D Tetramer+ WGBS


title: D1


title: 1179493: T1D Tetramer+ WGBS


title: L47_2


title: L44_2


title: L42_2


title: L41_2


title: CPEP10_TET_10 scATAC-seq


title: L48_2


title: C8


title: C9


title: Media 14h rep2


title: 888378: T1D Tetramer+ WGBS


title: Undifferentiated rep1


title: L36_2


title: Media 12h rep2


title: 1237930: T1D Naïve WGBS

source_name: T1D Naïve

value: Polyclonal T1D Naive CD8 T cells


title: C6


title: Media 8h rep2


title: L35_2


title: C7


title: Media 18h rep2


title: C2


title: 1237931: T1D Naïve WGBS


title: Media 10h rep2


title: 1107219: T1D Tetramer+ WGBS

value: Tetramer+ T1D CD8 T cells


title: Media 6h rep2


title: 1142383: T1D Naïve WGBS


title: C12


title: C11


title: 1237933: Health Donor Naïve WGBS

source_name: Health Donor Naïve

value: Polyclonal Naive CD8 T cell HD


title: 1237932: Health Donor Naïve WGBS


title: C10


title: Media 1.5h rep2


title: B4


title: Media 2.5h rep2


title: C1


title: B9


title: 2-736139: HIV Naive WGBS

source_name: HIV Naive

value: HAART HIV TN CD8 T cells


title: 383224: Health Donor Naive WGBS

source_name: Health Donor Naive


title: 888379: HIV Naïve WGBS

source_name: HIV Naïve


title: 2-736140: HIV Naïve WGBS


title: 647759: Health Donor Naïve WGBS


title: NC-100_4

city: Solna

first: Toon

last: Verheyen

address: Tomtebodavägen 16

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: For the DNA nanocalipers, the numbers refer to the distance (in nm) between the ligand dimers on the surface of the DNA nanocalipers. NC-0, however, refers to only one ligand dimer on the surface of the DNA nanocaliper.

data_processing:
Samples were sequenced on the Illumina NovaSeq 6000 platform with S1 flow cell and 2x51 setup. The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+
Sequenced reads were trimmed for adaptor sequence and low quality bases using Trimmomatic (v. 0.35)  for paired-end reads using the following parameters: -phred33 ILLUMINACLIP:'./adapters/NexteraPE.fa':2:30:10 TRAILING:15 SLIDINGWINDOW:4:18 MINLEN:36.
Trimmed RNA-Seq reads were mapped to the GRCg38 genome using the STAR package (v. 2.2.1) using default settings
Count tables were generated for each mapped sample using htseq-count (v. 0.5.4p3). This was performed using default settings except for the following: --stranded= No. All genes with an RPKM value below 1 were discarded.
Differential expression analysis was tested using the DESeq2 (v. 1.24.0) R package using default settings.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files containing the count tables per sample generated by the htseq-count package

source_name: Human Glioma Cell Line

growth_protocol: For the U3013 cell line, a T25 flask was coated with 10 µg/ml of poly-L-ornithine (Sigma-Aldrich) and allowed to incubate for 3 h at room temperature. After 3 h, the flask was washed with twice with 1XDPBS (Gibco). The plate was then coated with 10 µg/ml laminin (Sigma-Aldrich) and allowed to incubate for 30 min at 37°C, 5% CO2. After incubation, most of the laminin was removed. The U3013 cell line was cultured in coated T25 flasks in GBM media  (For 50 ml: 25 ml Neurobasal media (Thermofisher Scientific), 25 ml DMEM/F-12, GlutaMAX suppl. (ThermoFisher Scientific), 10 ng/ml EGF (R&D Systems), 10 ng/ml bFGF (ThermoFisher Scientific), 1 ml B27 (ThermoFisher Scientific) and  0.5 ml N2 Supplement (ThermoFisher Scientific) supplemented with 1% penicillin/streptomycin. 1x10E6 U3013 cells were then added to the T25 flask. For the RNA-Seq experiment, 4,000 cells were plated in a 96-well plate format and allowed to attach for 24 hrs.

extract_protocol:
The cells were lysed according to the SMART-Seq2 protocol
The Smart-Seq2 protocol was used for the library construction with minor changes. After stimulation and lysis, rather then using 2 µl of the cell lysate, 5 µl was used and subsequent steps, ie. reverse transcription and PCR preamplification, were performed in twice the volume, 20 and 50 µl instead of 10 and 25 µl, to prevent any inhibitory effects from occurring. For the tagmentation step, 200 pg of cDNA was used for input. The final libraries for both experiments were prepared utilizing Illumina Paired-end  sequencing using the Nextera XT library prep kit (Illumina).  The library was sequenced on the HiSeq2500 platform with a 2x126 setup using  'HiSeq SBS Kit v4' chemistry

treatment_protocol: 4,000 cells were plated per well in a 96-well plate. The cells were treated with Ephrin-A5 DNA Nanocalipers in a total volume of 50 µl for 30 min at 37℃, 5% CO2. This was performed in duplicates which were pooled together after cell lysis.

tag: cell line


title: B5


title: NC-100_2


title: C5


title: B2


title: B3


title: L33_2

source_name: Peripheral blood, CD8+ sorted

value: Non-small cell lung cancer

value: Blood


title: Media 18h rep1

extract_protocol:
Cells were pelleted and flash frozen. Total RNA was extracted by SDS-based lysis, followed by phenol extraction and ethanol preciptiation to remove protein.
100 ng total RNA was used to prepare mRNA libraries using NEBNext mRNA isolation kit and NEBNext Ultra Directional RNA Library preparation kit. mRNA fragmentation used manufacturer recommended conditions for a 300bp insert size. Library amplification used 13 cycles of PCR. 75bp paired-end reads were generated using an Illumina NextSeq 500.

tag: timepoint


title: L32_2

value: Post-treatment (nivolumab)


title: B6


title: B12


title: L31_2


title: L25_2


title: L27_2


title: NC-100_3


title: B11


title: NC-100_1


title: Media 14h rep1


title: L23_2


title: Media 12h rep1


title: B10


title: Media 8h rep1


title: NC-40_2


title: NC-40_3


title: B1


title: L30_2


title: Media 10h rep1


title: A9


title: A8


title: NC-40_4


title: NC-14_4


title: Media 6h rep1


title: A7


title: A6


title: NC-40_1


title: NC-14_3


title: NC-14_2


title: A5


title: NC-14_1


title: Media 2.5h rep1


title: NC-0_4


title: A3


title: A4


title: Media 1.5h rep1


title: NC-0_3


title: A12


title: L21_2


title: NC-0_2


title: L22_2


title: L19_2


title: NC-0_1


title: Ecc15_delNH

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: nucleoside hydrolase mutant E. carotovora carotovora15 strain

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences using Cutadapt v1.2.1, and then mapped to Ecc15 contig sequences using TopHat v2.1.1 with parameters -r 100 --library-type fr-firststrand --mate-std-dev 100 --solexa-quals -p 24 --bowtie-n.
After the alignment, the number of reads mapped to gene features were counted using HTSeq v0.6.1.
Fragments per kilobase of transcript per million fragments mapped (FPKM) was estimated by normalizing the counts using the library size and gene length. The FPKM values were converted to log2-FPKM after adding one to the FPKM values. The log2-FPKM values for the samples were then normalized using the quantile normalization method (MATLAB R2019a).
Genome_build: Ecc15 contig sequences
Supplementary_files_format_and_content: tab-delimited text files including normalized FPKM values for each sample

organism: Pectobacterium carotovorum

source_name: E. carotovora carotovora15 strain

growth_protocol: Ecc15 and Ecc15_delNH were grown in the M9 medium.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) and treated with 2 U of TURBO DNase (Ambion) for 30 min at 37 °C. Finally, RNA was purified and concentrated with the RNeasy MiniElute kit (Qiagen).
cDNA libraries were generated with Ribo-Zero Bacteria TruseqTM Stranded Total RNA H/M/R Prep Kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: 1 mM uridine was treated to late-exponential phase (OD600=~1.5) at 30 °C.

value: nucleoside hydrolase mutant

value: 1 mM uridine to late-exponential phase (OD600=~1.5) at 30 °C


title: dRNA-seq HSV-1 8hpi control R2

description: dRNA.tsv

source_name: human foreskin fibroblasts (HFF)

value: primary fibroblasts

tag: time post infection

value: HSV-1, 8 h p.i.

value: Replicate 2

tag: enrichment

value: 5' RNA ends (selective)


title: Ecc15

description: wild type E. carotovora carotovora15 strain

tag: genotype

value: wild type


title: NC-Empty_2

value: NC-Empty


title: NC-Empty_3


title: dRNA-seq HSV-1 8hpi control R1

description: dRNA.tsv

value: Replicate 1


title: A10

value: Skin


title: dRNA-seq HSV-1 8hpi XRN1 R1

description: dRNA.tsv


title: L14_2


title: NC-Empty_1


title: NC-Empty_4


title: SB43 16h #2

status: Public on Apr 06 2020

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: Overnight TGFb inhibition

data_processing:
Alignment was performed in two step: first reads were aligned on genome build GRCh37.p13 with STAR, reads that were not aligned in this step were realigned with bowtie2. Raw counts over the ensembl annotation release 75 were obtained with htseq-count v 0.6.0.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Bedgraph files generated from BAM alignments

source_name: Keratinocyte-derived iPS (KiPS)

growth_protocol: hESCs (HES2, H9 and BG01) and hiPSCs (KiPS) were cultured in Feeder-free on pre-coated plates with 0.5% growth factor-reduced Matrigel (CORNING Cat. 356231) (vol/vol in PBS with MgCl2/CaCl2_Sigma-Aldrich D8662) in E8 medium (made in-house according to Chen et al., 2011) or in mTeSR (StemCell Technologies 05850) at 37°C, 5% CO2, 5% O2. Cells were passaged every 3-4 days at a split ratio of 1:8 following dissociation with EDTA solution (0,5 mM in PBS without MgCl2/CaCl2_Sigma-Aldrich D8662, pH 8.0, ThermoFisher). The human foreskin fibroblasts BJ (passage 12, ATCC, CRL-2522) were cultured in DMEM/F12 (Sigma-Aldrich D6421) with 10% fetal bovine serum (FBS; Sigma-Aldrich F7524) at 37°C, 5% CO2, 21% O2. H9 line (WA09) and HES2 were obtained from and used under authorisation from WiCell Research Institute. KiPS were kindly provided by Austin Smith's laboratory (Takashima et al., 2014). All cell lines were mycoplasma-negative (Mycoalert, Lonza).

extract_protocol:
Total RNA was isolated using Total RNA Purification Kit (Norgen Biotek Cat. 37500)
PolyA-selection from total RNA, fragmentation of RNA with RNAse III, adapters ligation, PCR amplification (Ion Total RNA-seq Kit v2)

treatment_protocol: Transcriptome analysis of human iPSCs treated for 4 hours with mTeSR after 16 hours of SB43 treatment. Keratinocytes-derived iPSCs were treated with the TGF-beta receptor inhibitor SB431542 overnight (KiPS SB43) and then TGF-beta signalling was re-induced treating cells with TGFB1 for 4 hours (KiPS TGFB1), 2 experimental replicates for each condition.

value: Keratinocyte-derived iPS (KiPS)


title: dRNA-seq HSV-1 8hpii XRN1 R2

description: dRNA.tsv


title: SB43 16h + TGFB1 4h #1

description: Overnight TGFb inhibition, and re-induction with TGFB1 for 4h

value: SB43 16h + TGFB1 4h


title: SB43 16h #1

description: Overnight TGFb inhibition


title: SB43 16h + TGFB1 4h #2


title: p16 papilloma (3)

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Ein-Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Faculty of Medicine

description: p16_expressing_versus_control_skin_papillomas.xlsx

data_processing:
Reads containing adapters and poly-A sequences were trimmed using Cutadapat.
Genome mapping was performed using Tophat2, and read counts summarized through HTSeq count
Normalization was performed on the counts using DESeq2
Genes found not to be expressed in sorted keratinocytes (series 1,2) were excluded from analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file with headers. The column ‘Expressed in sorted keratinocytes’ indicates whether the gene was found in sorted keratinocytes (series 1,2) and hence included in our final analysis. ‘Norm.’  columns are the values after DESeq2 normalization. Log2FoldChange, lfcSE, stat, pvalue, padj are the results of DESeq2 analysis.

source_name: Papilloma-derived cells

growth_protocol: 3-week-old K5-rtTA/tet-p16 and control tet-p16 mice received a single topical treatment of 50nmole DMBA. A week later dox was added to the drinking water and the mice began twice-weekly topical treatments with TPA. Mice were examined for 23 additional weeks and were sacrificed 10 days after the last TPA treatment.

extract_protocol:
Total RNA was extracted from whole papillomas using the Tissue RNA purification kit (Norgen Biotek)
Libraries were prepared using the CEL-Seq protocol, and sequenced on Illumina HiSeq 2500.

treatment_protocol: Whole papillomas were dissected.

value: Whole papillomas

tag: induction period

value: 27wks-age mice

tag: profiled cells

value: Papilloma-derived cells

tag: genotype/variation

value: Treatment (expressing P16)


title: L13_2

tag: diagnosis

value: Non-small cell lung cancer

tag: tissue

value: Blood

value: Post-treatment (nivolumab)


title: p16 papilloma (1)


title: p16 papilloma (2)


title: p16 keratinocytes GFP- (3) series II

data_processing:
Reads containing adapters and poly-A sequences were trimmed using Cutadapat.
Genome mapping was performed using Tophat2, and read counts summarized through HTSeq count
Normalization was performed on the counts using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file with headers. Columns E:Q are the raw count data for all conditions; Columns R:Y are the normalized counts for all conditions;  The basemean is calculated across all conditions; Following that are the comparisons of p16 GFP+ to Control GFP+ and of p16 GFP+ to p16 GFP- , performed by DESeq2.

source_name: Epidermal keratinocytes

growth_protocol: K5-rtTA/tet-GFP/tet-p16 and K5-rtTA/tet-GFP mice were treated with doxycycline at the age of 3 weeks for 6 months, and epidermal keratinocytes were isolated from their dorsal skin.

extract_protocol:
Total RNA was extracted using the Single Cell RNA Purification Kit (Norgen Biotek).
Libraries were prepared using the CEL-Seq protocol, and sequenced on Illumina HiSeq 2500.

treatment_protocol: Live cells were isolated from the dorsal skin of K5-rtTA/tet-GFP/tet-p16 and K5-rtTA/tet-GFP mice, and stained for CD140a, CD45 and CD31 to gate out fibroblasts, immune and endothelial cells, according to standard staining protocols. GFP expressing and non expressing cells, were isolated from K5-rtTA/tet-GFP/tet-p16 mice, and GFP expressing cells from K5-rtTA/tet-GFP. Cells were then sorted.  ~ 80,000 GFP expressing keratonicytes and 20,000 GFP- cells were pooled from three mice in each sample.

value: Dorsal skin

value: 6 months

value: Non GFP-expressing cells


title: p16 keratinocytes GFP- (5) series II


title: Cont papilloma (3)

value: Control


title: Cont papilloma (5)


title: p16 keratinocytes GFP- (4) series II


title: Cont papilloma (1)


title: p16 keratinocytes GFP- (1) series II


title: L12_2

tag: treatment

tag: individual


title: p16 keratinocytes GFP+ (4) series II

value: GFP-expressing cells


title: p16 keratinocytes GFP+ (2) series II


title: p16 keratinocytes GFP- (2) series II


title: p16 keratinocytes GFP+ (1) series II


title: p16 keratinocytes GFP+ (3) series II


title: L10_2


title: Control keratinocytes GFP+ (3) series II


title: Control keratinocytes GFP+ (4) series II


title: Control keratinocytes GFP+ (2) series II


title: Input ChIP-Seq

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

description: Lin- CD117+ Sca1- CD16/32+ CD34+

data_processing:
The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. 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. In addition, duplicate reads (“PCR duplicates”) are removed.
Peaks were called using MACS (v.2.1.0) with default values. Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist.
Genome_build: mm10
Supplementary_files_format_and_content: chip_for_home_Gfi1-Mut_all_peaks.bed

source_name: Bone Marrow

growth_protocol: Cells were harvested from bone marrow. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34). Cell sorting was performed on BD FACSAria II with a 100μm nozzle and subjected to flow cytrometric sorting of Lin- CD117+ Sca1- CD16/32+ CD34+ cells (GMP).

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.

value: Granulocyte Macrophage Progenitors

tag: strain

tag: library prep

value: ChIP Seq

tag: chip antibody


title: Gfi1 GMP ChIP-Seq (Gfi1 R412X-R412X mice)

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: 1142382: T1D Naïve WGBS

value: Polyclonal T1D Naive CD8 T cells


title: Control keratinocytes GFP+ (1) series II


title: wt6361

city: Minneapolis

first: Michael

last: Kyba

state: MN

address: 2231 6th St SE

institute: University of Minnesota

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Trimmomatics v0.33), then mapped to mm10 whole genome using salmon v0.6.0.
Read assignments were performed using salmon v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include salmon count assigned raw reads for each sample.

source_name: WT

extract_protocol:
RNA from whole muscle was extracted using an RNA extraction kit (Zymo) following manufacturer’s instructions. RNA from endothelial and FAPs, i.e. CD31+ and Pdgfrα+ cells, 75,000 cells were FACS sorted from hind limb muscle, and total RNA was extracted using RNeasy Mini Kit (Qiagen).
RNAseq libraries from whole muscle were prepared using 500 ng total RNA and KAPA mRNA Hyper Prep kit following manufacturer’s instructions. cDNA from RNA from FAPs and CD31 ositive cels was synthesized using NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification kit (New England Biolabs) and libraries we generated with Nextera XT DNA Library Preparation Kit (Illumina). 50 base paired-end sequencing was performed  50 base paired end sequencing was performed on an Illumina instrument at the University of Minnesota Genomics Center.

treatment_protocol: Mice were treated with  doxyxycline contaning chow.

tag: inducible gene

value: WT

tag: tissue type

value: Whole Muscle

tag: group name


title: wt6418


title: wt6363


title: Cont papilloma (2)

value: Whole papillomas


title: dux6420


title: dux6422


title: dux6364


title: dux6367


title: WT2


title: CeA_IP_rep1

city: Berkeley

first: Chenyan

last: Ma

address: 230E Li Ka Shing Center

institute: UC Berkeley

data_processing:
Sequenced reads were trimmed for adaptor sequences and index sequences
Alignment and abundance calculation were done using RSEM (RNA-Seq by Expectation-Maximization) software.
Gene expression analysis was performed with DESeq software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene ID and TPM values fore each sample; csv files includes p-values and fold changes averaged from two repeats between IP and input group, calculated by DESeq software .

source_name: brain CeA region

extract_protocol:
CeA was rapidly dissected on ice. For each repeat, tissues from 4-5 mice were pooled, homogenized, and immunoprecipitation with FLAG and HA antibodies
RNA libraries were prepared for sequencing using Illumina Nextera Library Prep Kits

treatment_protocol: Cre-inducible retrograde HSV expressing the large ribosomal subunit protein Rpl10a fused with FLAG/hemagglutinin (HA) tag (HSV-LSL-FlagHA-L10a) were injected into the LC and PB region of Gad2-Cre mice

tag: strain background

value: brain

tag: cell type

value: LC/PB projecting GABAergic neurons

tag: ip antibody

value: FLAG and HA antibodies


title: CeA_input_rep1


title: wt6365


title: Control keratinocytes GFP+ (2) Series I

data_processing:
Read data demultiplxing was done using the CELseq pipeline script https://github.com/yanailab/CEL-Seq-pipeline
Reads containing adapters and poly-A sequences were trimmed using Cutadapat.
Genome mapping was performed using Tophat2, and read counts summarized through HTSeq count
Data for each sample was pooled across three Celseq barcodes and normalization was performed on the counts using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: A tab-delimited text file with columns for general gene details, followed by normalized counts in each sample, mean counts for each condition and the log2 of the ratio between mean expression in p16 samples and mean expression in control sample, and finally the results of a DESeq2 analysis (stat, pvalue and padj). The first row is a header line.

source_name: control_epidermal kerainocytes

growth_protocol: K5-rtTA/tet-GFP/tet-p16 and K5-rtTA/tet-GFP mice were treated with doxycycline at the age of 3 weeks for 6 months, and GFP+ epidermal keratinocytes were isolated from their dorsal skin.

treatment_protocol: Live cells were isolated from the dorsal skin of K5-rtTA/tet-GFP/tet-p16 and K5-rtTA/tet-GFP mice, and stained for CD140a, CD45 and CD31 to gate out fibroblasts, immune and endothelial cells, according to standard staining protocols. GFP-expressing cells were then sorted.  ~ 80,000 GFP-expressing keratonicytes were pooled from three mice in each sample.

tag: strain a background

value: mixed (FVB, C57Bl and 129sv)

value: Epidermal keratinocytes


title: Control keratinocytes GFP+ (1) Series I

tag: induction period


title: p16 keratinocytes GFP+ (2) Series I

source_name: p16_epidermal kerainocytes

tag: profiled cells


title: p16 keratinocytes GFP+ (1) Series I

tag: genotype/variation


title: Control keratinocytes GFP+ (4) Series I


title: WT_GMP-CD11b+_Cell40

description:
WT CD11b+ GMP-P
061217_Cell40-F10

data_processing:
RNA reads were aligned to the reference mm9 mouse genome using Bowtie2.
Single-cell RNA-Seq data were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Genome_build: mm9
Supplementary_files_format_and_content: [exp.Ly6g-Cd11b.txt]  Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values
Supplementary_files_format_and_content: [groups.Ly6g-Cd11b.txt]  Group annotations assigned by cellHarmony

source_name: Bone marrow

extract_protocol:
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with fluorchome-conjugated antibodies for FACS-sorting, then cells were separated using the Fluidigm C1 system and lysed on chip for subsequent reverse transcription.
cDNA was made with the SMARTer mRNA-Seq Kit (Clontech) and libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina).

tag: genotype

value: Wild-type

value: Bone marrow derived CD11b+ GMP-P

tag: cdna synthesis

value: Fluidigm C1 protocol

tag: sequencing parameters

value: 150bp Paired-End, 150 million reads/96 cell library


title: WT_GMP-CD11b+_Cell47

description:
WT CD11b+ GMP-P
061217_Cell47-F12

value: Nextera XT DNA Library Preparation Kit (Illumina)


title: WT_GMP-CD11b+_Cell32

description:
WT CD11b+ GMP-P
061217_Cell32-H8


title: p16 keratinocytes GFP+ (3) Series I

growth_protocol: K5-rtTA/tet-GFP/tet-p16 and K5-rtTA/tet-GFP mice were treated with doxycycline at the age of 3 weeks for 6 months, and GFP-positive epidermal keratinocytes were isolated from their dorsal skins for RNA-Seq.

extract_protocol:
Total RNA was exrtacted using the Single Cell RNA Purification Kit (Norgen Biotek).
Libraries were prepared and sequenced using to Illumina's RNA sequencing protocol, by Illumina HiSeq 2500.

treatment_protocol: Live cells were isolated from dorsal skins of K5-rtTA/tet-GFP/tet-p16 and K5-rtTA/tet-GFP mice, and stained for CD140a, CD45 and CD31 to gate out fibroblasts, immune and endothelial cells, according to standard staining protocols. GFP-expressing cells were then sorted for RNA-Seq.  ~ 80,000 GFP-expressing keratonicytes were pooled from three mice in each sample.

tag: tissue

value: Dorsal skin

value: 6 months

value: GFP-expressing cells


title: WT_GMP-CD11b+_Cell46

description:
WT CD11b+ GMP-P
061217_Cell46-B12

tag: strain


title: WT_GMP-CD11b+_Cell24

description:
WT CD11b+ GMP-P
061217_Cell24-F6

tag: library prep


title: WT_GMP-CD11b+_Cell44

description:
WT CD11b+ GMP-P
061217_Cell44-F11


title: WT_GMP-CD11b+_Cell31

description:
WT CD11b+ GMP-P
061217_Cell31-F8


title: WT_GMP-CD11b+_Cell15

description:
WT CD11b+ GMP-P
061217_Cell15-E4


title: WT_GMP-CD11b+_Cell29

description:
WT CD11b+ GMP-P
061217_Cell29-B8


title: WT_GMP-CD11b+_Cell8

description:
WT CD11b+ GMP-P
061217_Cell8-D2


title: WT_GMP-CD11b+_Cell36

description:
WT CD11b+ GMP-P
061217_Cell36-E9


title: WT_GMP-CD11b+_Cell43

description:
WT CD11b+ GMP-P
061217_Cell43-D11


title: WT_GMP-CD11b+_Cell21

description:
WT CD11b+ GMP-P
061217_Cell21-E5


title: WT_GMP-CD11b+_Cell14

description:
WT CD11b+ GMP-P
061217_Cell14-H3


title: WT_GMP-CD11b+_Cell7

description:
WT CD11b+ GMP-P
061217_Cell7-C2


title: p16 keratinocytes GFP+ (4) Series I


title: WT_GMP-CD11b+_Cell41

description:
WT CD11b+ GMP-P
061217_Cell41-A11


title: WT_GMP-CD11b+_Cell42

description:
WT CD11b+ GMP-P
061217_Cell42-C11


title: WT_GMP-CD11b+_Cell13

description:
WT CD11b+ GMP-P
061217_Cell13-G3


title: WT_GMP-CD11b+_Cell6

description:
WT CD11b+ GMP-P
061217_Cell6-B2


title: WT_GMP-CD11b+_Cell39

description:
WT CD11b+ GMP-P
061217_Cell39-E10


title: WT_GMP-CD11b+_Cell20

description:
WT CD11b+ GMP-P
061217_Cell20-C5


title: WT_GMP-CD11b+_Cell12

description:
WT CD11b+ GMP-P
061217_Cell12-F3


title: WT_GMP-CD11b+_Cell25

description:
WT CD11b+ GMP-P
061217_Cell25-B7


title: WT_GMP-CD11b+_Cell11

description:
WT CD11b+ GMP-P
061217_Cell11-E3


title: WT_GMP-CD11b+_Cell26

description:
WT CD11b+ GMP-P
061217_Cell26-C7


title: WT_GMP-CD11b+_Cell22

description:
WT CD11b+ GMP-P
061217_Cell22-F5


title: WT_GMP-CD11b+_Cell4

description:
WT CD11b+ GMP-P
061217_Cell4-E1


title: WT_GMP-CD11b+_Cell19

description:
WT CD11b+ GMP-P
061217_Cell19-B5


title: WT_GMP-CD11b+_Cell35

description:
WT CD11b+ GMP-P
061217_Cell35-D9


title: WT_GMP-CD11b+_Cell5

description:
WT CD11b+ GMP-P
061217_Cell5-F1


title: Control keratinocytes GFP+ (3) Series I


title: WT_GMP-CD11b+_Cell17

description:
WT CD11b+ GMP-P
061217_Cell17-G4


title: WT_GMP-CD11b+_Cell9

description:
WT CD11b+ GMP-P
061217_Cell9-E2


title: WT_GMP-CD11b+_Cell1

description:
WT CD11b+ GMP-P
061217_Cell1-A1


title: WT_GMP-CD11b+_Cell48

description:
WT CD11b+ GMP-P
061217_Cell48-G12


title: WT_GMP-CD11b+_Cell2

description:
WT CD11b+ GMP-P
061217_Cell2-B1


title: WT_GMP-CD11b+_Cell3

description:
WT CD11b+ GMP-P
061217_Cell3-D1


title: WT_GMP-CD11b+_Cell27

description:
WT CD11b+ GMP-P
061217_Cell27-D7


title: WT_GMP-CD11b+_Cell33

description:
WT CD11b+ GMP-P
061217_Cell33-B9


title: WT_GMP-P-Ly6ghigh_Cell68

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell68-F7

value: Bone marrow derived CD11b+ Ly6g high GMP-P


title: WT_GMP-P-Ly6ghigh_Cell47

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell47-H1


title: WT_GMP-P-Ly6glow_Cell40

description:
WT Ly6g low GMP-P
WTLy6glow_cell40-F11

value: Bone marrow derived CD11b+ Ly6g low GMP-P


title: WT_GMP-P-Ly6ghigh_Cell82

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell82-A10


title: WT_GMP-P-Ly6ghigh_Cell61

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell61-D6


title: WT_GMP-P-Ly6ghigh_Cell89

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell89-E11


title: WT_GMP-P-Ly6glow_Cell32

description:
WT Ly6g low GMP-P
WTLy6glow_cell32-A10


title: WT_GMP-P-Ly6ghigh_Cell81

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell81-H9


title: WT_GMP-P-Ly6ghigh_Cell75

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell75-B9


title: WT_GMP-CD11b+_Cell18

description:
WT CD11b+ GMP-P
061217_Cell18-H4


title: WT_GMP-P-Ly6glow_Cell39

description:
WT Ly6g low GMP-P
WTLy6glow_cell39-D11


title: WT_GMP-P-Ly6ghigh_Cell53

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell53-F3


title: WT_GMP-P-Ly6ghigh_Cell74

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell74-E8


title: WT_GMP-P-Ly6ghigh_Cell46

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell46-F1


title: WT_GMP-CD11b+_Cell10

description:
WT CD11b+ GMP-P
061217_Cell10-H2


title: WT_GMP-P-Ly6ghigh_Cell73

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell73-D8


title: WT_GMP-P-Ly6glow_Cell38

description:
WT Ly6g low GMP-P
WTLy6glow_cell38-B11


title: WT_GMP-P-Ly6ghigh_Cell59

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell59-G5


title: WT_GMP-P-Ly6ghigh_Cell60

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell60-C6


title: WT_GMP-P-Ly6glow_Cell37

description:
WT Ly6g low GMP-P
WTLy6glow_cell37-A11


title: WT_GMP-P-Ly6ghigh_Cell65

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell65-C7


title: WT_GMP-P-Ly6glow_Cell30

description:
WT Ly6g low GMP-P
WTLy6glow_cell30-D9


title: WT_GMP-P-Ly6glow_Cell16

description:
WT Ly6g low GMP-P
WTLy6glow_cell16-C5


title: WT_GMP-P-Ly6glow_Cell24

description:
WT Ly6g low GMP-P
WTLy6glow_cell24-E6


title: WT_GMP-P-Ly6glow_Cell23

description:
WT Ly6g low GMP-P
WTLy6glow_cell23-D6


title: WT_GMP-P-Ly6ghigh_Cell66

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell66-D7


title: WT_GMP-P-Ly6ghigh_Cell52

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell52-C3


title: WT_GMP-P-Ly6ghigh_Cell44

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell44-C1


title: WT_GMP-P-Ly6ghigh_Cell51

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell51-A3


title: WT_GMP-P-Ly6glow_Cell8

description:
WT Ly6g low GMP-P
WTLy6glow_cell8-H2


title: WT_GMP-P-Ly6glow_Cell22

description:
WT Ly6g low GMP-P
WTLy6glow_cell22-A6


title: WT_GMP-P-Ly6glow_Cell43

description:
WT Ly6g low GMP-P
WTLy6glow_cell43-F12


title: WT_GMP-P-Ly6glow_Cell15

description:
WT Ly6g low GMP-P
WTLy6glow_cell15-B5


title: WT_GMP-P-Ly6glow_Cell29

description:
WT Ly6g low GMP-P
WTLy6glow_cell29-B9


title: WT_GMP-P-Ly6ghigh_Cell49

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell49-D2


title: WT_GMP-P-Ly6glow_Cell14

description:
WT Ly6g low GMP-P
WTLy6glow_cell14-A5


title: WT_GMP-P-Ly6glow_Cell21

description:
WT Ly6g low GMP-P
WTLy6glow_cell21-H5


title: WT_GMP-P-Ly6glow_Cell28

description:
WT Ly6g low GMP-P
WTLy6glow_cell28-G8


title: WT_GMP-P-Ly6glow_Cell35

description:
WT Ly6g low GMP-P
WTLy6glow_cell35-D10


title: WT_GMP-P-Ly6ghigh_Cell58

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell58-F5


title: WT_GMP-P-Ly6ghigh_Cell57

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell57-E5


title: WT_GMP-P-Ly6ghigh_Cell96

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell96-H12


title: WT_GMP-P-Ly6ghigh_Cell88

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell88-C11


title: WT_GMP-P-Ly6glow_Cell6

description:
WT Ly6g low GMP-P
WTLy6glow_cell6-F2


title: WT_GMP-P-Ly6glow_Cell27

description:
WT Ly6g low GMP-P
WTLy6glow_cell27-F8


title: WT_GMP-P-Ly6glow_Cell41

description:
WT Ly6g low GMP-P
WTLy6glow_cell41-H11


title: WT_GMP-P-Ly6glow_Cell34

description:
WT Ly6g low GMP-P
WTLy6glow_cell34-C10


title: WT_GMP-P-Ly6glow_Cell20

description:
WT Ly6g low GMP-P
WTLy6glow_cell20-G5


title: WT_GMP-P-Ly6glow_Cell5

description:
WT Ly6g low GMP-P
WTLy6glow_cell5-E2


title: WT_GMP-P-Ly6glow_Cell42

description:
WT Ly6g low GMP-P
WTLy6glow_cell42-B12


title: WT_GMP-P-Ly6glow_Cell36

description:
WT Ly6g low GMP-P
WTLy6glow_cell36-G10


title: WT_GMP-P-Ly6glow_Cell13

description:
WT Ly6g low GMP-P
WTLy6glow_cell13-G4


title: WT_GMP-P-Ly6ghigh_Cell87

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell87-A11


title: WT_GMP-P-Ly6ghigh_Cell50

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell50-F2


title: WT_GMP-P-Ly6ghigh_Cell94

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell94-D12


title: WT_GMP-P-Ly6glow_Cell25

description:
WT Ly6g low GMP-P
WTLy6glow_cell25-F6


title: WT_GMP-P-Ly6glow_Cell12

description:
WT Ly6g low GMP-P
WTLy6glow_cell12-D4


title: WT_GMP-P-Ly6glow_Cell19

description:
WT Ly6g low GMP-P
WTLy6glow_cell19-F5


title: WT_GMP-P-Ly6glow_Cell26

description:
WT Ly6g low GMP-P
WTLy6glow_cell26-G7


title: WT_GMP-P-Ly6ghigh_Cell72

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell72-C8


title: WT_GMP-P-Ly6ghigh_Cell79

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell79-F9


title: WT_GMP-P-Ly6glow_Cell18

description:
WT Ly6g low GMP-P
WTLy6glow_cell18-E5


title: WT_GMP-P-Ly6ghigh_Cell86

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell86-G10


title: WT_GMP-P-Ly6ghigh_Cell78

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell78-E9


title: WT_GMP-P-Ly6ghigh_Cell85

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell85-E10


title: WT_GMP-P-Ly6ghigh_Cell71

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell71-B8


title: WT_GMP-P-Ly6ghigh_Cell92

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell92-B12


title: WT_GMP-P-Ly6glow_Cell17

description:
WT Ly6g low GMP-P
WTLy6glow_cell17-D5


title: WT_GMP-P-Ly6glow_Cell33

description:
WT Ly6g low GMP-P
WTLy6glow_cell33-B10


title: WT_GMP-P-Ly6glow_Cell10

description:
WT Ly6g low GMP-P
WTLy6glow_cell10-H3


title: WT_GMP-P-Ly6ghigh_Cell63

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell63-G6


title: WT_GMP-P-Ly6ghigh_Cell70

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell70-A8


title: WT_GMP-P-Ly6ghigh_Cell56

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell56-B5


title: WT_GMP-P-Ly6glow_Cell9

description:
WT Ly6g low GMP-P
WTLy6glow_cell9-E3


title: SCN-12yrs-M-Cell96

description:
G_J25_P2Cell_96_USPD16100592-AK1585-AK416_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

data_processing:
RSEM version 1.3.0 was run using a GTF transcriptome referenced that contained both exon and intron regions (pre-mRNA sequences) for Ensembl version 72 (hg19). 96 single-cell libraries captured per donor or patient, with only 3 cells removed with less than 100,000 reads. Differential expression between each SCN patient and the combination of healthy donor was conducted in the software AltAnalyze, using an empirical Bayes moderated t-test p<0.05 (FDR corrected), a cell-level, to identify SCN impacted genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values
Supplementary_files_format_and_content: donors.Neutrophils-RSEM-TPMs: Donor annotations for individual cells

source_name: Peripheral blood neutrophils

extract_protocol:
De-identified clinical data and peripheral blood from healthy donors or neutropenic patients was obtained at Cincinnati Children’s Hospital Medical Center through informed consent under an approved institutional review board research protocol.  Human Neutrophils were enriched from whole blood using the EasySep™ Direct Human Neutrophil Isolation Kit (Stemcell Technologies) and sequenced using the Fluidigm C1 platform using the SMART-Seq v4 chemistry.
cDNA was made with the SMARTer mRNA-Seq Kit version 4 (Clontech) and libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina).

value: Peripheral blood neutrophils

value: Fluidigm C1 protocol (v4 chemistry)

value: 75bp Paired-End, 150 million reads/96 cell library

tag: age

value: 12 year old

tag: Sex

value: male

tag: disease

value: with Severe Congenital Neutropenia


title: WT_GMP-P-Ly6ghigh_Cell77

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell77-D9


title: SCN-12yrs-M-Cell95

description:
G_J25_P2Cell_95_USPD16100592-AK1584-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: WT_GMP-P-Ly6ghigh_Cell84

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell84-D10


title: WT_GMP-P-Ly6glow_Cell11

description:
WT Ly6g low GMP-P
WTLy6glow_cell11-C4


title: SCN-12yrs-M-Cell94

description:
G_J25_P2Cell_94_USPD16100592-AK1583-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: WT_GMP-P-Ly6glow_Cell1

description:
WT Ly6g low GMP-P
WTLy6glow_cell1-C1


title: WT_GMP-P-Ly6glow_Cell2

description:
WT Ly6g low GMP-P
WTLy6glow_cell2-F1


title: WT_GMP-P-Ly6ghigh_Cell64

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell64-H6


title: WT_GMP-P-Ly6ghigh_Cell55

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell55-E4


title: SCN-12yrs-M-Cell92

description:
G_J25_P2Cell_92_USPD16100592-AK1581-AK428_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

tag: Sex:


title: SCN-12yrs-M-Cell90

description:
G_J25_P2Cell_90_USPD16100592-AK205-AK391_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: WT_GMP-P-Ly6ghigh_Cell48

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell48-C2


title: SCN-12yrs-M-Cell91

description:
G_J25_P2Cell_91_USPD16100592-AK1579-AK400_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: WT_GMP-P-Ly6ghigh_Cell62

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell62-E6


title: SCN-12yrs-M-Cell88

description:
G_J25_P2Cell_88_USPD16100592-AK1584-AK416_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell93

description:
G_J25_P2Cell_93_USPD16100592-AK1582-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell87

description:
G_J25_P2Cell_87_USPD16100592-AK1583-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: WT_GMP-P-Ly6ghigh_Cell69

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell69-H7


title: SCN-12yrs-M-Cell89

description:
G_J25_P2Cell_89_USPD16100592-AK366-AK390_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: WT_GMP-P-Ly6ghigh_Cell83

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell83-B10


title: WT_GMP-P-Ly6glow_Cell3

description:
WT Ly6g low GMP-P
WTLy6glow_cell3-G1


title: WT_GMP-P-Ly6ghigh_Cell76

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell76-C9


title: WT_GMP-P-Ly6ghigh_Cell90

description:
WT Ly6g high GMP-P
WTLy6ghigh_cell90-H11


title: SCN-12yrs-M-Cell85

description:
G_J25_P2Cell_85_USPD16100592-AK1581-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell84

description:
G_J25_P2Cell_84_USPD16100592-AK1579-AK428_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell55

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_55

data_processing:
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with fluorchome-conjugated antibodies for FACS-sorting, then cells were separated using the Fluidigm C1 system and lysed on chip for subsequent reverse transcription.
Single-cell RNA-Seq data were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Genome_build: mm9
Supplementary_files_format_and_content: [exp.R412X-Irf8-all.txt]  Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values
Supplementary_files_format_and_content: [groups.R412X-Irf8-all.txt]  Group annotations assigned by cellHarmony

extract_protocol:
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with fluorchome-conjugated antibodies for FACS-sorting of Lineage- CD117+ Sca-1- CD34+ CD16/32high cells were separated using the Fluidigm C1 system and lysed on chip for subsequent reverse transcription.
cDNA was made with the SMARTer mRNA-Seq Kit (Clontech) and libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina).


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell69

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_69


title: SCN-12yrs-M-Cell83

description:
G_J25_P2Cell_83_USPD16100592-AK205-AK400_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell83

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_83


title: SCN-12yrs-M-Cell81

description:
G_J25_P2Cell_81_USPD16100592-AK1860-AK390_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell82

description:
G_J25_P2Cell_82_USPD16100592-AK366-AK391_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell90

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_90


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell89

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_89


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell54

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_54


title: SCN-12yrs-M-Cell79

description:
G_J25_P2Cell_79_USPD16100592-AK1582-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell78

description:
G_J25_P2Cell_78_USPD16100592-AK1581-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell77

description:
G_J25_P2Cell_77_USPD16100592-AK1579-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell61

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_61


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell82

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_82


title: SCN-12yrs-M-Cell68

description:
G_J25_P2Cell_68_USPD16100592-AK366-AK428_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell70

description:
G_J25_P2Cell_70_USPD16100592-AK1579-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell81

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_81


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell75

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_75


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell68

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_68


title: SCN-12yrs-M-Cell86

description:
G_J25_P2Cell_86_USPD16100592-AK1582-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell9

description:
G_J25_P1Cell_9_USPD16100592-AK1581-AK390_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell62

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_62


title: SCN-12yrs-M-Cell8

description:
G_J25_P1Cell_8_USPD16100592-AK1858-AK416_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell76

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_76


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell60

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_60


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell67

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_67


title: SCN-12yrs-M-Cell76

description:
G_J25_P1Cell_76_USPD16100592-AK205-AK428_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell75

description:
G_J25_P1Cell_75_USPD16100592-AK366-AK400_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell74

description:
G_J25_P1Cell_74_USPD16100592-AK1860-AK391_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell80

description:
G_J25_P2Cell_80_USPD16100592-AK1583-AK416_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell52

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_52


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell59

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_59


title: SCN-12yrs-M-Cell73

description:
G_J25_P1Cell_73_USPD16100592-AK1859-AK390_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell71

description:
G_J25_P1Cell_71_USPD16100592-AK1581-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell72

description:
G_J25_P1Cell_72_USPD16100592-AK1582-AK416_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: WT_GMP-P-Ly6glow_Cell7

description:
WT Ly6g low GMP-P
WTLy6glow_cell7-G2


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell66

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_66


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell53

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_53


title: SCN-12yrs-M-Cell7

description:
G_J25_P1Cell_7_USPD16100592-AK1586-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell51

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_51


title: SCN-12yrs-M-Cell67

description:
G_J25_P1Cell_67_USPD16100592-AK1860-AK400_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell57

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_57


title: SCN-12yrs-M-Cell65

description:
G_J25_P1Cell_65_USPD16100592-AK1858-AK390_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell69

description:
G_J25_P1Cell_69_USPD16100592-AK205-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell66

description:
G_J25_P1Cell_66_USPD16100592-AK1859-AK391_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell63

description:
G_J25_P1Cell_63_USPD16100592-AK1579-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell49

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_49


title: SCN-12yrs-M-Cell61

description:
G_J25_P1Cell_61_USPD16100592-AK366-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell62

description:
G_J25_P1Cell_62_USPD16100592-AK205-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell73

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_73


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell96

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_96


title: SCN-12yrs-M-Cell60

description:
G_J25_P1Cell_60_USPD16100592-AK1860-AK428_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell88

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_88


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell95

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_95


title: SCN-12yrs-M-Cell6

description:
G_J25_P1Cell_6_USPD16100592-AK1585-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell94

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_94


title: SCN-12yrs-M-Cell59

description:
G_J25_P1Cell_59_USPD16100592-AK1859-AK400_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell87

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_87


title: SCN-12yrs-M-Cell58

description:
G_J25_P1Cell_58_USPD16100592-AK1858-AK391_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell65

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_65


title: SCN-12yrs-M-Cell57

description:
G_J25_P1Cell_57_USPD16100592-AK1586-AK390_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell56

description:
G_J25_P1Cell_56_USPD16100592-AK1579-AK416_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell50

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_50


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell86

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_86


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell72

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_72


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell58

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_58


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell79

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_79


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell71

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_71


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell78

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_78


title: SCN-12yrs-M-Cell55

description:
G_J25_P1Cell_55_USPD16100592-AK205-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell85

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_85


title: SCN-12yrs-M-Cell50

description:
G_J25_P1Cell_50_USPD16100592-AK1586-AK391_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell93

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_93


title: SCN-12yrs-M-Cell51

description:
G_J25_P1Cell_51_USPD16100592-AK1858-AK400_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell52

description:
G_J25_P1Cell_52_USPD16100592-AK1859-AK428_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell53

description:
G_J25_P1Cell_53_USPD16100592-AK1860-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell56

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_56


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell92

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_92


title: SCN-12yrs-M-Cell5

description:
G_J25_P1Cell_5_USPD16100592-AK1584-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell63

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_63


title: SCN-12yrs-M-Cell49

description:
G_J25_P1Cell_49_USPD16100592-AK1585-AK390_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell64

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_64


title: SCN-12yrs-M-Cell48

description:
G_J25_P1Cell_48_USPD16100592-AK1586-AK416_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell70

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_70


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell77

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_77


title: SCN-12yrs-M-Cell46

description:
G_J25_P1Cell_46_USPD16100592-AK1584-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP-P-CD11b+_Cell84

description:
Gfi1-R412X-Irf8 CD11b+ GMP-P
Feb20_x_x_273_Cell_84


title: SCN-12yrs-M-Cell54

description:
G_J25_P1Cell_54_USPD16100592-AK366-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell47

description:
G_J25_P1Cell_47_USPD16100592-AK1585-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell45

description:
G_J25_P1Cell_45_USPD16100592-AK1583-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell40

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_40

value: Bone marrow derived GMP


title: SCN-12yrs-M-Cell44

description:
G_J25_P1Cell_44_USPD16100592-AK1582-AK428_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell43

description:
G_J25_P1Cell_43_USPD16100592-AK1581-AK400_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell41

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_41


title: SCN-12yrs-M-Cell42

description:
G_J25_P1Cell_42_USPD16100592-AK1579-AK391_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell32

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_32


title: Gfi1-R412X-Irf8_GMP_Cell39

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_39


title: SCN-12yrs-M-Cell41

description:
G_J25_P1Cell_41_USPD16100592-AK205-AK390_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell24

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_24


title: Gfi1-R412X-Irf8_GMP_Cell31

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_31


title: Gfi1-R412X-Irf8_GMP_Cell16

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_16


title: SCN-12yrs-M-Cell4

description:
G_J25_P1Cell_4_USPD16100592-AK1583-AK428_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell39

description:
G_J25_P1Cell_39_USPD16100592-AK366-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell38

description:
G_J25_P1Cell_38_USPD16100592-AK1860-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell23

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_23


title: Gfi1-R412X-Irf8_GMP_Cell38

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_38


title: SCN-12yrs-M-Cell37

description:
G_J25_P1Cell_37_USPD16100592-AK1859-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell40

description:
G_J25_P1Cell_40_USPD16100592-AK205-AK416_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell34

description:
G_J25_P1Cell_34_USPD16100592-AK1585-AK391_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell30

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_30


title: Gfi1-R412X-Irf8_GMP_Cell8

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_8


title: Gfi1-R412X-Irf8_GMP_Cell15

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_15


title: SCN-12yrs-M-Cell33

description:
G_J25_P1Cell_33_USPD16100592-AK1584-AK390_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell31

description:
G_J25_P1Cell_31_USPD16100592-AK1860-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell48

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_48


title: SCN-12yrs-M-Cell30

description:
G_J25_P1Cell_30_USPD16100592-AK1859-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell29

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_29


title: SCN-12yrs-M-Cell35

description:
G_J25_P1Cell_35_USPD16100592-AK1586-AK400_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell22

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_22


title: SCN-12yrs-M-Cell32

description:
G_J25_P1Cell_32_USPD16100592-AK366-AK416_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell36

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_36


title: SCN-12yrs-M-Cell3

description:
G_J25_P1Cell_3_USPD16100592-AK1582-AK400_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell28

description:
G_J25_P1Cell_28_USPD16100592-AK1586-AK428_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell37

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_37


title: Gfi1-R412X-Irf8_GMP_Cell7

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_7


title: SCN-12yrs-M-Cell26

description:
G_J25_P1Cell_26_USPD16100592-AK1584-AK391_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell25

description:
G_J25_P1Cell_25_USPD16100592-AK1583-AK390_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell29

description:
G_J25_P1Cell_29_USPD16100592-AK1858-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell14

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_14


title: Gfi1-R412X-Irf8_GMP_Cell13

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_13


title: Gfi1-R412X-Irf8_GMP_Cell6

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_6


title: Gfi1-R412X-Irf8_GMP_Cell27

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_27


title: SCN-12yrs-M-Cell27

description:
G_J25_P1Cell_27_USPD16100592-AK1585-AK400_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell35

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_35


title: SCN-12yrs-M-Cell36

description:
G_J25_P1Cell_36_USPD16100592-AK1858-AK428_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell21

description:
G_J25_P1Cell_21_USPD16100592-AK1586-AK402_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Gfi1-R412X-Irf8_GMP_Cell47

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_47


title: Gfi1-R412X-Irf8_GMP_Cell21

description:
Gfi1-R412X-Irf8 GMP
Feb20_x_x_272_Cell_21


title: SCN-12yrs-M-Cell22

description:
G_J25_P1Cell_22_USPD16100592-AK1858-AK403_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell23

description:
G_J25_P1Cell_23_USPD16100592-AK1859-AK417_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-12yrs-M-Cell2

description:
G_J25_P1Cell_2_USPD16100592-AK1581-AK391_H2W2YBBXX_L7_1
Neutrophils from a 12 year old male patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs