title: WBCs, BDB1P03091


title: WBCs, BDB1P03084

status: Public on Feb 01 2022

type: genomic

city: Lebanon

first: Ji-Qing

last: Chen

state: New Hampshire

address: 1 Medical Center Drive, Williamson level 6

department: Epidemiology

country: USA

institute: Dartmouth College

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R studio
Matrix_Processed.csv  represents SeSAMe Processed Average Beta values.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: White blood cell

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: non-muscle-invasive bladder cancer (NMIBC)

tag: gender

value: male

tag: age

tag: ten year-recurrence or death

value: Yes

tag: cell type

value: White blood cell


title: WBCs, BDB1P03085

value: female

value: No


title: WBCs, BDB1P03082


title: WBCs, BDB1P03073


title: WBCs, BDB1P03076


title: WBCs, BDB1P03078


title: WBCs, BDB1P03070


title: WBCs, BDB1P03067


title: WBCs, BDB1P03075


title: WBCs, BDB1P03065


title: WBCs, BDB1P03071


title: WBCs, BDB1P03079


title: WBCs, A00000FC7


title: WBCs, BDB1P03063


title: WBCs, BDB1P03072


title: WBCs, BDB1P03068


title: WBCs, BDB1P03064


title: WBCs, BDB1P03061


title: WBCs, BDB1P03060


title: WBCs, BDB1P03057


title: WBCs, BDB1P03056


title: WBCs, BDB1P03054


title: WBCs, BDB1P03052


title: WBCs, BDB1P03058


title: WBCs, BDB1P03055


title: WBCs, BDB1P03059


title: WBCs, BDB1P03048


title: WBCs, BDB1P03049


title: WBCs, BDB1P03047


title: WBCs, BDB1P03046


title: WBCs, BDB1P03051


title: WBCs, BDB1P03045


title: WBCs, BDB1P03044


title: WBCs, BDB1P03041


title: WBCs, BDB1P03050


title: WBCs, BDB1P03039


title: WBCs, BDB1P03038


title: WBCs, BDB1P03043


title: WBCs, BDB1P03036


title: WBCs, BDB1P03034


title: WBCs, BDB1P03037


title: WBCs, BDB1P03035


title: WBCs, BDB1P03033


title: WBCs, BDB1P03031


title: WBCs, BDB1P03030


title: WBCs, BDB1P03029


title: WBCs, BDB1P03028


title: WBCs, BDB1P03026


title: WBCs, BDB1P03025


title: WBCs, BDB1P03024


title: WBCs, BDB1P03022


title: WBCs, BDB1P03023


title: WBCs, BDB1P03027


title: WBCs, BDB1P03020


title: WBCs, BDB1P03019


title: WBCs, BDB1P03018


title: WBCs, BDB1P03011


title: WBCs, BDB1P03013


title: WBCs, BDB1P03042


title: WBCs, BDB1P03005


title: WBCs, BDB1P03016


title: WBCs, BDB1P03001


title: WBCs, BDB1P03012


title: WBCs, BDB1P03010


title: WBCs, BDB1P02095


title: WBCs, BDB1P03008


title: WBCs, BDB1P02090


title: WBCs, BDB1P02096


title: WBCs, BDB1P02088


title: WBCs, BDB1P02089


title: WBCs, BDB1P02085


title: WBCs, BDB1P02087


title: WBCs, BDB1P02086


title: WBCs, BDB1P02083


title: WBCs, BDB1P02084


title: WBCs, BDB1P02081


title: WBCs, BDB1P02077


title: WBCs, BDB1P02072


title: WBCs, BDB1P02074


title: WBCs, BDB1P02078


title: WBCs, BDB1P03014


title: WBCs, BDB1P02070


title: WBCs, BDB1P02067


title: WBCs, BDB1P02063


title: WBCs, BDB1P02061


title: WBCs, BDB1P02069


title: WBCs, BDB1P02059


title: WBCs, BDB1P02064


title: WBCs, BDB1P02058


title: WBCs, BDB1P02060


title: WBCs, BDB1P02068


title: WBCs, BDB1P02057


title: WBCs, BDB1P02055


title: WBCs, BDB1P02052


title: WBCs, BDB1P02047


title: WBCs, BDB1P02050


title: WBCs, BDB1P02080


title: WBCs, BDB1P02048


title: WBCs, BDB1P02049


title: WBCs, BDB1P02053


title: WBCs, BDB1P02071


title: WBCs, BDB1P02051


title: WBCs, BDB1P02076


title: WBCs, BDB1P02044


title: WBCs, BDB1P02043


title: WBCs, BDB1P02035


title: WBCs, BDB1P02042


title: WBCs, BDB1P02037


title: WBCs, BDB1P02031


title: WBCs, BDB1P02032


title: WBCs, BDB1P02030


title: WBCs, BDB1P02029


title: WBCs, BDB1P02024


title: WBCs, BDB1P02025


title: WBCs, BDB1P02020


title: WBCs, BDB1P02021


title: WBCs, BDB1P02017


title: WBCs, BDB1P02014


title: WBCs, BDB1P02016


title: WBCs, BDB1P02041


title: WBCs, BDB1P02011


title: WBCs, BDB1P02018


title: WBCs, BDB1P02007


title: WBCs, BDB1P02010


title: WBCs, BDB1P02013


title: WBCs, BDB1P02039


title: WBCs, BDB1P02012


title: WBCs, BDB1P02009


title: WBCs, BDB1P02006


title: WBCs, BDB1P02033


title: WBCs, BDB1P02004


title: WBCs, BDB1P02005


title: WBCs, BDB1P02027


title: WBCs, BDB1P02046


title: WBCs, BDB1P02003


title: WBCs, BDB1P02026


title: WBCs, BDB1P02001


title: WBCs, BDB1P02002


title: WBCs, BDB1P02028


title: WBCs, BDB1P02022


title: WBCs, BDB1P04096


title: WBCs, BDB1P04094


title: WBCs, BDB1P04095


title: WBCs, BDB1P02015


title: WBCs, BDB1P04092


title: WBCs, BDB1P04091


title: WBCs, BDB1P04090


title: WBCs, BDB1P04088


title: WBCs, BDB1P04085


title: WBCs, BDB1P04084


title: WBCs, BDB1P04081


title: WBCs, BDB1P04087


title: WBCs, BDB1P04080


title: WBCs, BDB1P04078


title: WBCs, BDB1P04077


title: WBCs, BDB1P04071


title: WBCs, BDB1P04075


title: WBCs, BDB1P04072


title: WBCs, BDB1P04069


title: WBCs, BDB1P04062


title: WBCs, BDB1P04056


title: WBCs, BDB1P04054


title: WBCs, BDB1P04055


title: WBCs, BDB1P04068


title: WBCs, BDB1P04064


title: WBCs, BDB1P04057


title: WBCs, BDB1P04061


title: WBCs, BDB1P04048


title: WBCs, BDB1P04049


title: WBCs, BDB1P04051


title: WBCs, BDB1P04053


title: WBCs, BDB1P04089


title: WBCs, BDB1P04052


title: WBCs, BDB1P04086


title: WBCs, BDB1P04042


title: WBCs, BDB1P04046


title: WBCs, BDB1P04045


title: WBCs, BDB1P04041


title: WBCs, BDB1P04044


title: WBCs, BDB1P04043


title: WBCs, BDB1P04035


title: WBCs, BDB1P04076


title: WBCs, BDB1P04040


title: WBCs, BDB1P04034


title: WBCs, BDB1P04036


title: WBCs, BDB1P04039


title: WBCs, BDB1P04037


title: WBCs, BDB1P04031


title: WBCs, BDB1P04033


title: WBCs, BDB1P04030


title: WBCs, BDB1P04067


title: WBCs, BDB1P04027


title: WBCs, BDB1P04028


title: WBCs, BDB1P04025


title: WBCs, BDB1P04047


title: WBCs, BDB1P04029


title: WBCs, BDB1P04024


title: WBCs, BDB1P04019


title: WBCs, BDB1P04022


title: WBCs, BDB1P04021


title: WBCs, BDB1P04017


title: WBCs, BDB1P04038


title: WBCs, BDB1P04018


title: WBCs, BDB1P04016


title: WBCs, BDB1P04014


title: WBCs, BDB1P04013


title: WBCs, BDB1P04009


title: WBCs, BDB1P04011


title: WBCs, BDB1P04006


title: WBCs, BDB1P04032


title: WBCs, BDB1P04004


title: WBCs, BDB1P04003


title: WBCs, BDB1P04010


title: WBCs, BDB1P04001


title: WBCs, BDB1P04002


title: WBCs, BDB1P04026


title: WBCs, BDB1P01091


title: WBCs, BDB1P01096


title: WBCs, BDB1P01092


title: WBCs, BDB1P01094


title: WBCs, BDB1P01086


title: WBCs, BDB1P01088


title: WBCs, BDB1P01087


title: WBCs, BDB1P01082


title: WBCs, BDB1P01081


title: WBCs, BDB1P01080


title: WBCs, BDB1P04015


title: WBCs, BDB1P01078


title: WBCs, BDB1P01077


title: WBCs, BDB1P01074


title: WBCs, BDB1P01073


title: WBCs, BDB1P01071


title: WBCs, BDB1P01069


title: WBCs, BDB1P01070


title: WBCs, BDB1P01090


title: WBCs, BDB1P01068


title: WBCs, BDB1P01089


title: WBCs, BDB1P01065


title: WBCs, BDB1P01066


title: WBCs, BDB1P01085


title: WBCs, BDB1P01084


title: WBCs, BDB1P01064


title: WBCs, BDB1P01058


title: WBCs, BDB1P01060


title: WBCs, BDB1P01059


title: WBCs, BDB1P01062


title: WBCs, BDB1P01061


title: WBCs, BDB1P01054


title: WBCs, BDB1P01051


title: WBCs, BDB1P01053


title: WBCs, BDB1P01050


title: WBCs, BDB1P01076


title: WBCs, BDB1P01075


title: WBCs, BDB1P01048


title: WBCs, BDB1P01049


title: WBCs, BDB1P01041


title: WBCs, BDB1P01042


title: WBCs, BDB1P01045


title: WBCs, BDB1P01067


title: WBCs, BDB1P01043


title: WBCs, BDB1P04008


title: WBCs, BDB1P01044


title: WBCs, BDB1P01039


title: WBCs, BDB1P01063


title: WBCs, BDB1P01057


title: WBCs, BDB1P01035


title: WBCs, BDB1P01038


title: WBCs, BDB1P01040


title: WBCs, BDB1P01018


title: WBCs, BDB1P01031


title: WBCs, BDB1P01016


title: WBCs, BDB1P01024


title: WBCs, BDB1P01027


title: WBCs, BDB1P01032


title: WBCs, BDB1P01023


title: WBCs, BDB1P01034


title: WBCs, BDB1P01028


title: WBCs, BDB1P01030


title: WBCs, BDB1P01015


title: WBCs, BDB1P01025


title: WBCs, BDB1P01013


title: WBCs, BDB1P01014


title: WBCs, BDB1P01022


title: WBCs, BDB1P01009


title: WBCs, BDB1P01003


title: WBCs, BDB1P01019


title: WBCs, BDB1P01021


title: WBCs, BDB1P01020


title: WBCs, BDB1P01017


title: WBCs, BDB1P01010


title: WBCs, BDB1P01012


title: WBCs, BDB1P01011


title: WBCs, BDB1P01006


title: WBCs, BDB1P01002


title: WBCs, BDB1P01001


title: WBCs, BDB1P01005


title: RPI11 A188xB73 Seedling RNA-seq

status: Public on Jan 27 2022

type: SRA

city: Athens

first: Brad

last: Nelms

state: GA

address: 120 E Green St

institute: University of Georgia

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Multiplexed libraries were sequenced with paired-end sequencing. The first read of each read pair contained exclusively barcoding information: a 6 nt sample barcode and a 10 bp unique molecular identifier (UMI). Paired-end reads were demultiplexed based on the sample barcodes, requiring a perfect match to one of the barcode sequences. The UMIs were extracted and appended to the read 2 sequence identifiers. The submitted fastq files are demultiplexed files for read2, with the UMI from read 1 appended to the sequence identifiers.
Prior to alignment, reads were trimmed and filtered using Fastp with parameters -y -x -3 -f 6. Reads were then aligned to the AGPv4 genome assembly using HiSat2.
For transcript counting, reads mapping to the same gene with a similar UMI were collapsed using the UMI-tools dedup function.
Genome_build: AgpV4
Supplementary_files_format_and_content: csv file containing transcript counts for each each gene and sample

molecule: polyA RNA

organism: Zea mays

source_name: Whole A188xB73 (HiII) seedling

growth_protocol: An F1 hybrid of Maize (Zea mays) lines A188 and B73 or inbred line B73 were grown in a greenhouse at Stanford, CA with a 14-h day / 10-h night light cycle

extract_protocol:
Whole V3 maize seedlings (roots and shoots) were removed from the ground, rinsed to remove dirt, and then frozen. Seedlings were ground to a powder with a mortal and pestil after freezing with liquid N2. Total RNA was then isolated using the Qiagen RNeasy Plant mini kit.
Library protocol based on CelSeq2 (Hashimshony, et al. 2016). Read 1 contained a 10 bp unique molecular identifier (UMI) followed by a 6 bp sample barcode. Read 2 contained transcript sequence. Deposited files are read 2 with the UMI appended to the fastq entry headers, all samples have been demultiplexed using the 6 bp sample barcodes.

tag: tissue

value: seedling

tag: genotype

value: A188 x B73 hybrid ("HiII")


title: RPI10 B73 Seedling RNA-seq

source_name: Whole B73 seedling

value: B73 inbred


title: RPI10 A188xB73 Seedling RNA-seq


title: GFP2_input

status: Public on Jan 31 2022

city: Basel

first: Emanuela

last: Kerschbamer

state: Basel Stadt

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

library_source: genomic

data_processing:
ChIP-seq reads were aligned on the human genome reference assembly GRCh38 using BWA (version 0.7.15) (Li and Durbin 2009). Aligned reads were filtered to discard unmapped, multiply mapped, PCR duplicates reads (Picard tools MarkDuplicates version: 2.3.0, Picard Toolkit.” 2019. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/) along with low quality alignments (samtools view -q 1, samtools version 1.7) (Li et al. 2009).
Peak calling was performed with MACS2 (version 2.1.0) using a minimum FDR threshold 0.00001. The same settings with the addition of the --broad option were used for H3K27me3 and H3K36me3 marks (Zhang et al. 2008). Peaks localized to blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/) or unplaced contigs were filtered out. Narrow peaks (for H3K27ac, H3K4me1, H3K4me2, H3K4me3 histone marks) closer than 350 bp were merged into a single peak.
Genome_build: GRCh38
Supplementary_files_format_and_content: narrowPeak files for H3K4me1, H3K4me2, H3K4me3 and H3K27ac; broadPeak files for H3K27me3 and H3K36me3

source_name: Neural progenitor cells control

growth_protocol: Human iPSC-derived NPC lines were cultured on poly-L-ornithine hydrobromide/laminin - coated plates in hiNPC medium (70% v/v DMEM completed with 30% v/v HAM F12 , 2% v/v B27, 1% v/v Penicillin-Streptomycin solution, 1% v/v L-Glutamine and supplemented with EGF, bFGF and Heparin). Semi-confluent monolayers of hiNPCs were maintained in 5% CO2, 37°C humidified incubator.

extract_protocol:
Chromatin immunoprecipitation was performed using the protocol described by (33); with minor modifications. Sonication of the samples was accomplished using a Bioruptor sonicator. Sheared-chromatin was diluted 10 fold in ChIP dilution buffer, supplemented with protease inhibitor. 50 μl of sheared chromatin was removed and stored at 4°C as control aliquot (INPUT).  Each sample was incubated overnight with antibodies (20 ug/ChIP) of interest. The following primary antibodies were used: H3K27me3 (07-449, Millipore), H3K4me3 (AB8580, Abcam), H3K36me3 (Ab9050, Abcam), H3K4me2 (AB7766, Abcam), H3K4me1 (AB8895, Abcam) and H3K27ac (AB4729, Abcam). Chromatin–Antibody complexes were then precipitated, washed eluted. DNA isolation was performed by phenol:chloroform:isoamyl alcohol, precipitated with NaCl, supplemented with glycogen, washed with EtOH and then treated with RNase I. Finally, DNA was purified with MinElute Kit.
Libraries were prepared according to NEBNext UltraII DNA Library preparation kit (Illumina).

treatment_protocol: Human iPSC-derived NPC line GM8330-8 (Sheridan et al., 2011), Sh1-CHD8, Sh2-CHD8, Sh4-CHD8 and Sh-GFP lines, were previously generated by lentiviral delivery of shRNAs targeting CHD8 and GFP coding sequences respectively (Sugathan et al., 2014).

value: iPSC-derived neural progenitor cells

value: GFPsh (knock-down treatment)

tag: chip antibody


title: GFP_input


title: CHD8sh1_input

source_name: Neural progenitor cells CHD8 KD

value: CHD8sh1 (knock-down treatment)


title: RING1AB_DKO-proseq-rep1

status: Public on Jan 25 2022

city: boston

first: Danesh

last: Moazed

state: MA

address: 240 longwood avenue

department: cell biology

institute: Harvard medical school

description:
PRO-seq
nascent RNA

data_processing:
Library strategy: PRO-seq
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were mapped to the human genome (GRCh37/hg19) with Kallisto (version 1.15.0).
Transcript abundances were normalized with Transcripts Per Million (TPM) mapped reads.
Differentially expressed genes were identified by DESeq2 ((v1.18.1)) with fold change>2 and Benjamini–Hochberg false discovery rate adjusted P < 0.05.
deeptool (v/3.0.2) was used to generate bigwig files for visualization in IGV tool
Genome_build: hg19

molecule: total RNA

extract_protocol:
For PRO-seq, total nascent RNA with biotin labeled was isolated from human cells.
For PRO-seq, two μg of total RNA was used to start RNA-seq library construction. Nascent RNA was isolated and further reverse transcribed to cDNA. The resulting cDNA was ligated with adapters, amplified by PCR, and further cleaned to obtain the final library. Libraries were sequenced on an Illumina Hiseq machine to obtain 150 bp paired-end reads.

tag: cell line

tag: sirna

value: siNC

tag: knockout

value: RING1A/B double knockout

tag: medium

value: DMEM

tag: antibody


title: siRING1AB-proseq-rep-1

description:
PRO-seq
nascent RNA


title: CHD8sh4_input

value: CHD8sh4 (knock-down treatment)


title: siRING1AB-proseq-rep-2

description:
PRO-seq
nascent RNA


title: siCtrl-for-RING1AB_KD_DKO-proseq-rep-1

data_processing:
library strategy: PRO-seq
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were mapped to the human genome (GRCh37/hg19) with Kallisto (version 1.15.0).
Transcript abundances were normalized with Transcripts Per Million (TPM) mapped reads.
Differentially expressed genes were identified by DESeq2 ((v1.18.1)) with fold change>2 and Benjamini–Hochberg false discovery rate adjusted P < 0.05.
deeptool (v/3.0.2) was used to generate bigwig files for visualization in IGV tool
Genome_build: hg19
Supplementary_files_format_and_content: bw

value: siControl

tag: molecule subtype

value: nascent RNA


title: Single cell RNA-seq cABMR 1

status: Public on Jan 12 2022

city: Wuhan

first: Yan

last: Xiong

address: donghu road

country: China

institute: Zhongnan Hospital of Wuhan University

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Genome_build: grch38
Supplementary_files_format_and_content: tsv files

source_name: PBMCs

extract_protocol:
The specimens were centrifuged at 400g for 5 min at 4℃, and the supernatant was discarded. Red blood cell lysate (SolarBio, R1010, China) was added and placed on ice for 15 min, followed by centrifugation at 400g at 4℃ for 10min, to precipitate PBMCs. The supernatant was discarded and the PBMCs were resuspended by phosphate buffered saline to obtain a single-cell suspension.
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies)

value: Peripheral blood

tag: subject status

value: chronic antibody-mediated rejection (cABMR) after renal transplantation patient


title: CHD8sh2_input

value: CHD8sh2 (knock-down treatment)


title: siCtrl-for-RING1AB_KD_DKO-proseq-rep-2


title: RPI11 B73 Seedling RNA-seq


title: Single cell RNA-seq cABMR 2


title: RING1AB_DKO-proseq-rep2

description:
PRO-seq
nascent RNA


title: WBCs, BDB1P01026

value: non-muscle-invasive bladder cancer (NMIBC)

value: male

value: Yes

value: White blood cell


title: Single cell RNA-seq control 1

value: control patient


title: Single cell RNA-seq control 2


title: Cd_only_1

status: Public on Nov 28 2021

city: Houston

first: Michael

last: Lorenz

state: TX

address: 6431 Fannin

institute: UTHealth Houston

data_processing:
Base-calling was performed by Axeq Technologies.
Adapters were trimmed using Trimmomatic v0.39, with additional removal of bases below a read quality of 3 at the start and end of the read and total removal of reads less than 36 bp after trimming.
Reads were mapped to a concatenated mouse-Candida transcriptome using Salmon v1.1.0 with --gcBias and --seqBias flags. Transcriptome files were generated from concatenated genome files using GffRead v0.11.6.
Genome_build: Concatenated genome files were generated from fungal genomes concatenated to the GRCm38.p6 Mus musculus reference genome (Ensembl release 98). All fungal genomes were obtained from the Candida Genome Database (http://candidagenome.org/) using current versions as of January 16, 2020, 11:57 am.
Supplementary_files_format_and_content: Salmon output files (.quant.sf). These contain gene name, length, and effective length (modeled based on factors affecting the probablility of sampling fragments from this transcript), TPM (transcripts per million, a normalized measure of abundance) and estimated number of mapped reads. For more information, see https://salmon.readthedocs.io/en/latest/file_formats.html.

organism: Candida dubliniensis

source_name: Whole cell

growth_protocol: Candida cultures were grown overnight in YPD medium at 30 °C then diluted back into YPD medium at 30 °C to allow return to exponential phase. Cultures were then washed twice in phosphate buffered saline followed by dilution into Iscove's Modified Dulbecco's Medium supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Candida-only cultures were scraped to detach fungal cells and pelleted by centrifugation, followed by resuspension in ice cold water and centrifugation again. For Candida-macrophage co-cultures, medium was aspirated and ice cold water was added to lyse macrophages. Wells were then scraped and samples were pelleted by centrifugation, resuspended again in ice-cold water followed by further centrifugation. Fungal cell walls were digested with zymolyase at 37 °C, followed by RNA extraction using the SV Total RNA Isolation System (Promega).
Libraries were constructed using the TruSeq Stranded RNA library preparation protocol. Sequencing was carried out using the HiSeq2000 platform (Illumina) to obtain 15-58 million 2 x 100 paired-end reads. All library preparation and sequencing was performed by Axeq Technologies.

treatment_protocol: Candida cultures were incubated for 1 hr at 37 °C, 5% CO2 in the presence or absence of primary murine bone marrow derived macrophages after which time the vast majority of fungal cells had been taken up by phagocytosis.

tag: sample type

value: C. dubliniensis CD36

tag: condition

value: only


title: Le_mac_2

organism:
Mus musculus
Lodderomyces elongisporus

value: L. elongisporus ATCC 6260 + M. musculus

value: macrophage


title: Ct_mac_2

organism:
Candida tropicalis
Mus musculus

value: C. tropicalis MYA-3404 + M. musculus


title: Le_mac_1


title: Ca_only_1

organism: Candida albicans

value: C. albicans SC5314


title: Ct_mac_1


title: Cd_only_2


title: Ca_only_2


title: Cl_mac_2

organism:
Mus musculus
Clavispora lusitaniae

value: C. lusitaniae ATCC 42720 + M. musculus


title: Cp_mac_1

organism:
Candida parapsilosis
Mus musculus

value: C. parapsilosis CDC317 + M. musculus


title: Cl_mac_1


title: Cp_mac_2


title: Cp_only_2

organism: Candida parapsilosis

value: C. parapsilosis CDC317


title: Cl_only_1

organism: Clavispora lusitaniae

value: C. lusitaniae ATCC 42720


title: UV_3

data_processing:
Base-calling was performed by Macrogen, Inc. using Illumina Real Time Analysis RTA software followed by fastq file generation with the Illumina package bcl2fastq.
Adapters were trimmed using Trimmomatic v0.39, with additional removal of bases below a read quality of 3 at the start and end of the read and total removal of reads less than 36 bp after trimming.
Reads were aligned to a concatenated mouse-Candida reference genome using STAR v2.7.3a with the flag --quantMode TranscriptomeSAM
Transcript quantification was performed using RSEM v1.3.1
Genome_build: A concatenated reference genome was made, with Mus musculus (GRCm38, Ensembl release 98), C. albicans, C. lusitaniae, C. parapsilosis and C. tropicalis genomes (fungal genomes from http://candidagenome.org/)
Supplementary_files_format_and_content: RSEM output file (.genes.results) containing gene level expression estimates as described in http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html#output.

organism: Mus musculus

source_name: Murine bone marrow-derived macrophage

growth_protocol: Murine bone marrow-derived macrophages were obtained from female C57BL/6 mice by differentiation in vitro using 10 ng/ml M-CSF for seven days. Non-adherent cells were removed by washing, followed by scraping after incubation in PBS at 4 °C. Macrophages were incubated overnight with or without 100 U/ml IFN-gamma.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Micro kit and RNA integrity was confirmed using the Agilent Bioanalyzer.
Libraries were prepared using the TruSeq Stranded RNA library preparation kit (Illumina). Sequencing was performed using the NovaSeq 6000 platform.

treatment_protocol: Non-IFN-gamma treated macrophages were  stimulated with medium only, live Candida (C. albicans, C. lusitaniae, C. parapsilosis, C. tropicalis) or UV-killed C. albicans (all in a 3:1 Candida:macrophage ratio). IFN-gamma pretreated macrophages were stimulated with 100 ng/ml LPS.

tag: treatment

value: UV-killed C. albicans

tag: mouse of origin

tag: strain


title: Ct_only_2

organism: Candida tropicalis

value: C. tropicalis MYA-3404


title: LPS_2

value: LPS/IFN-gamma


title: Cp_only_1


title: Ctrop_4

value: C. tropicalis


title: Ct_only_1


title: Cl_only_2


title: UV_1


title: Cpara_4

value: C. parapsilosis


title: LPS_3


title: UV_2


title: Cpara_2


title: Clus_3

value: C. lusitaniae


title: Ctrop_1


title: sample 89, RRMS - alemtuzumab 12

status: Public on Dec 14 2021

type: RNA

city: Rostock

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description: Gene expression data for a patient with RRMS treated with alemtuzumab. Please note that this is the only sample for which the amount of RNA was not sufficient for the measurement of microRNAs in our related study (Hecker et al. EBioMedicine 2022;80:104052, PMID: 35561450).

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Thermo Fisher Scientific.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.2 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.
Exon-level processed data are available on the series record.

label: Biotin

source_name: B cells from the peripheral blood

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Twenty ml of peripheral blood were taken from MS patients during regular clinical visits as well as from healthy donors at the Rostock University Medical Center.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll density gradient separation (Histopaque-1077, Sigma-Aldrich). Untouched B cells were then enriched from the PBMC by negative selection using the Pan B Cell Isolation Kit (Miltenyi Biotec). Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) in combination with the RNase-free DNase set (Qiagen).

treatment_protocol: The patients were treated with different therapies according to the approved labels and the guidelines and recommendations of the German Society of Neurology.

tag: subject identifier

tag: group

value: RRMS patient

tag: therapy

value: alemtuzumab

tag: Sex

value: female

tag: age (years)

tag: disease duration (years)

tag: edss score

tag: relapses in previous year


title: Cpara_1


title: Clus_1


title: LPS_1


title: Calb_1

value: C. albicans


title: Clus_5


title: Ctrop_3


title: Calb_3


title: BMDM_3

value: Medium


title: Le_only_2

organism: Lodderomyces elongisporus

value: L. elongisporus ATCC 6260

value: only


title: BMDM_1


title: Calb_2


title: BMDM_2


title: Le_only_1


title: Cd_mac_1

organism:
Mus musculus
Candida dubliniensis

value: C. dubliniensis CD36 + M. musculus

value: macrophage


title: Ca_mac_2

organism:
Candida albicans
Mus musculus

value: C. albicans SC5314 + M. musculus


title: Cd_mac_2


title: Ca_mac_1


title: B_Input_4h_LipidA_IBRD9_ChIPseq

status: Public on Nov 26 2021

city: San Diego

first: Diana

middle: C.

last: Hargreaves

state: CA

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

description: ChIP-seq of Input 4h Lipid A IBRD9-treated BMDMs for dataset B

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq and ChIP-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate normalized bedGraphs for the UCSC Genome Browser. ChIP-seq peaks for BRD9, BRD4, BRD2, IRF9, STAT1, and STAT2 were found by using the findPeaks program in HOMER with the default parameters for option "-style factor" using the appropriate ChIP input experiments as background. For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file Columns: (1) chrom (2) chromStart (3) chromEnd (4) dataValue.  DESeq Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-18) normalized Log2 read count for experiment (19,20,21) Log2 fold change, p-value, adjusted p-value BI9564 vs vehicle (22,23,24) Log2 fold change, p-value, adjusted p-value of dBRD9 vs vehicle (25,26,27) Log2 fold change, p-value, adjusted p-value of IBRD9 vs vehicle (28,29,30) Log2 fold change, p-value, adjusted p-value of JQ1 vs vehicle

source_name: C57BL/6, Bone-marrow derived macrophages (BMDMs)

growth_protocol: Bone marrow was harvested from the femurs and tibias of 8 to 12 week-old C57BL/6 mice. Bones were crushed and bone marrow progenitors were isolated and cultured in RPMI-1640 supplemented with 30% M-CSF, 20% fetal bovine serum (FBS), 10mM HEPES, 1mM sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin on petri dishes. On day 6, BMDMs were lifted using cold PBS and replated onto tissue-culture treated dishes in half-M-CSF media and half Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS. RAW 264.7 cell line was cultured in DMEM supplemented with 10% FBS.

extract_protocol:
RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). For ChIP-Seq, 15 million BMDMs were collected and cross-linked first in 3mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E229 sonicator for 10 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against BRD9, BRD4, IRF9, STAT1, or STAT2. The next day, the antibody bound DNA was incubated with Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% sodium dodecyl sulfate). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions. RNA-Seq libraries were prepared using either Illumina TruSeq RNA Library Prep Kit v2 or Illumina TruSeq Stranded mRNA Kit following the manufacturer's instructions.
ChIP-Seq and strand-specific polyA+ RNA-seq

treatment_protocol: On day 7, BMDMs were pre-treated overnight with 500 nM JQ1 (Tocris 4499); 3 uM dBRD9 (Tocris 6606); 3 uM BI9564 (Tocris 5590); and 10 uM I-BRD9 (Tocris 5591). On day 8, BMDMs were treated with vehicle or 100ng/ml Lipid A.

value: IBRD9 and Lipid A for 4h

tag: cell type

value: Bone-marrow derived macrophages (BMDMs)

tag: shRNA

tag: chip antibody source


title: B_Input_4h_LipidA_BI9564_ChIPseq

description: ChIP-seq of Input 4h Lipid A BI9564-treated BMDMs for dataset B

value: Bi9564 and Lipid A for 4h


title: B_Input_4h_LipidA_dBRD9_ChIPseq

description: ChIP-seq of Input 4h Lipid A dBRD9-treated BMDMs for dataset B

value: dBRD9 and Lipid A for 4h


title: B_Input_4h_LipidA_ChIPseq

description: ChIP-seq of Input 4h Lipid A BMDMs for dataset B

value: Lipid A for 4h


title: B_BRD4_4h_LipidA_IBRD9_ChIPseq

description: ChIPseq of BRD4 4h Lipid A IBRD9-treated BMDMs


title: B_BRD4_4h_LipidA_dBRD9_ChIPseq

description: ChIPseq of BRD4 4h Lipid A dBRD9-treated BMDMs


title: B_BRD4_4h_LipidA_ChIPseq

description: ChIPseq of BRD4 4h Lipid A BMDMs


title: B_BRD4_4h_LipidA_BI9564_ChIPseq

description: ChIPseq of BRD4 4h Lipid A BI9564-treated BMDMs


title: A_Input_4h_LipidA_JQ1_ChIPseq

description: ChIP-seq of Input 4h Lipid A JQ1-treated BMDMs for dataset A

value: JQ1 and Lipid A for 4h


title: A_Input_4h_LipidA_IBRD9_ChIPseq

description: ChIP-seq of Input 4h Lipid A IBRD9-treated BMDMs for dataset A


title: A_Input_0h_ChIPseq

description: ChIP-seq of Input 0h in BMDMs for for dataset A


title: A_STAT2_4h_LipidA_JQ1_ChIPseq

description: ChIPseq of STAT2 4h Lipid A JQ1-treated BMDMs

value: Cell Signaling 72604S


title: A_Input_4h_LipidA_dBRD9_ChIPseq

description: ChIP-seq of Input 4h Lipid A dBRD9-treated BMDMs for dataset A


title: A_STAT2_4h_LipidA_dBRD9_ChIPseq

description: ChIPseq of STAT2 4h Lipid A dBRD9-treated BMDMs


title: A_STAT2_4h_LipidA_IBRD9_ChIPseq

description: ChIPseq of STAT2 4h Lipid A IBRD9-treated BMDMs


title: A_Input_4h_LipidA_ChIPseq

description: ChIP-seq of Input 4h Lipid A BMDMs for dataset A


title: A_IRF9_4h_LipidA_dBRD9_ChIPseq

description: ChIPseq of IRF9 4h Lipid A dBRD9-treated BMDMs

value: EMD Millipore MABS1920


title: A_IRF9_4h_LipidA_veh_ChIPseq

description: ChIPseq of IRF9 4h Lipid A BMDMs


title: A_STAT2_0h_ChIPseq

description: ChIP-seq of STAT2 0h in BMDMs


title: A_IRF9_4h_LipidA_JQ1_ChIPseq

description: ChIPseq of IRF9 4h Lipid A JQ1-treated BMDMs


title: A_STAT2_4h_LipidA_veh_ChIPseq

description: ChIPseq of STAT2 4h Lipid A BMDMs


title: A_STAT1_4h_LipidA_IBRD9_ChIPseq

description: ChIPseq of STAT1 4h Lipid A IBRD9-treated BMDMs

value: Cell Signaling 91728


title: A_STAT1_4h_LipidA_dBRD9_ChIPseq

description: ChIPseq of STAT1 4h Lipid A dBRD9-treated BMDMs


title: A_IRF9_0h_ChIPseq

description: ChIP-seq of IRF9 0h in BMDMs


title: A_IRF9_4h_LipidA_IBRD9_ChIPseq

description: ChIPseq of IRF9 4h Lipid A IBRD9-treated BMDMs


title: A_STAT1_4h_LipidA_veh_ChIPseq

description: ChIPseq of STAT1 4h Lipid A BMDMs


title: A_BRD9_4h_LipidA_ChIPseq

description: ChIP-seq of BRD9 4h Lipid in BMDMs

value: Active Motif 61537


title: A_STAT1_0h_ChIPseq

description: ChIP-seq of STAT1 0h in BMDMs


title: A_BRD9_0h_ChIPseq

description: ChIP-seq of BRD9 0h in BMDMs


title: RAW_BRD2_4h_LipidA_ChIPseq

description: ChIP-seq of BRD2 4h Lipid in RAW 264.7

tag: cell line

value: Cell Signaling 5848S


title: RAW_Input_0h_ChIPseq

description: Input ChIP-seq of 0h in RAW 264.7


title: RAW_BRD4_4h_LipidA_ChIPseq

description: ChIP-seq of BRD4 4h Lipid in RAW 264.7


title: RAW_BRD9_4h_LipidA_ChIPseq

description: ChIP-seq of BRD9 4h Lipid in RAW 264.7


title: RAW_BRD2_0h_ChIPseq

description: ChIP-seq of BRD2 0h in RAW 264.7


title: RAW_BRD9_0h_ChIPseq

description: ChIP-seq of BRD9 0h in RAW 264.7


title: A_STAT1_4h_LipidA_JQ1_ChIPseq

description: ChIPseq of STAT1 4h Lipid A JQ1-treated BMDMs


title: 4h_LipidA_JQ1_rep2_RNAseq

description:
RNA-seq of 4h Lipid A JQ1-treated BMDMs replicate 2
DESeq_4h_Vehicle_BI9564_dBRD9_JQ1.txt


title: RAW_Input_4h_LipidA_ChIPseq

description: Input ChIP-seq of 4h in RAW 264.7


title: 4h_LipidA_JQ1_rep1_RNAseq

description:
RNA-seq of 4h Lipid A JQ1-treated BMDMs replicate 1
DESeq_4h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 1h_LipidA_JQ1_rep2_RNAseq

description:
RNA-seq of 1h Lipid A JQ1-treated BMDMs replicate 2
DESeq_1h_Vehicle_BI9564_dBRD9_JQ1.txt

value: JQ1 and Lipid A for 1h


title: 0h_JQ1_rep2_RNAseq

description:
RNA-seq of 0h JQ1-treated BMDMs replicate 2
DESeq_0h_Vehicle_BI9564_dBRD9_JQ1.txt

value: JQ1 overnight pretreatment


title: 1h_LipidA_JQ1_rep1_RNAseq

description:
RNA-seq of 1h Lipid A JQ1-treated BMDMs replicate 1
DESeq_1h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 4h_LipidA_IBRD9_rep1_RNAseq

description:
RNA-seq of 4h Lipid A IBRD9-treated BMDMs replicate 1
DESeq_4h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 0h_JQ1_rep1_RNAseq

description:
RNA-seq of 0h JQ1-treated BMDMs replicate 1
DESeq_0h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 0h_IBRD9_rep2_RNAseq

description:
RNA-seq of 0h IBRD9-treated BMDMs replicate 2
DESeq_0h_Vehicle_BI9564_dBRD9_JQ1.txt

value: IBRD9 overnight pretreatment


title: 1h_LipidA_dBRD9_rep1_RNAseq

description:
RNA-seq of 1h Lipid A dBRD9-treated BMDMs replicate 1
DESeq_1h_Vehicle_BI9564_dBRD9_JQ1.txt

value: dBRD9 and Lipid A for 1h


title: 1h_LipidA_dBRD9_rep2_RNAseq

description:
RNA-seq of 1h Lipid A dBRD9-treated BMDMs replicate 2
DESeq_1h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 0h_dBRD9_rep2_RNAseq

description:
RNA-seq of 0h dBRD9-treated BMDMs replicate 2
DESeq_0h_Vehicle_BI9564_dBRD9_JQ1.txt

value: dBRD9 overnight pretreatment


title: 4h_LipidA_dBRD9_rep2_RNAseq

description:
RNA-seq of 4h Lipid A dBRD9-treated BMDMs replicate 2
DESeq_4h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 0h_IBRD9_rep1_RNAseq

description:
RNA-seq of 0h IBRD9-treated BMDMs replicate 1
DESeq_0h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 0h_dBRD9_rep1_RNAseq

description:
RNA-seq of 0h dBRD9-treated BMDMs replicate 1
DESeq_0h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 1h_LipidA_IBRD9_rep1_RNAseq

description:
RNA-seq of 1h Lipid A IBRD9-treated BMDMs replicate 1
DESeq_1h_Vehicle_BI9564_dBRD9_JQ1.txt

value: IBRD9 and Lipid A for 1h


title: 4h_LipidA_dBRD9_rep1_RNAseq

description:
RNA-seq of 4h Lipid A dBRD9-treated BMDMs replicate 1
DESeq_4h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 1h_LipidA_BI9564_rep2_RNAseq

description:
RNA-seq of 1h Lipid A BI9564-treated BMDMs replicate 2
DESeq_1h_Vehicle_BI9564_dBRD9_JQ1.txt

value: Bi9564 and Lipid A for 1h


title: 4h_LipidA_BI9564_rep1_RNAseq

description:
RNA-seq of 4h Lipid A BI9564-treated BMDMs replicate 1
DESeq_4h_Vehicle_BI9564_dBRD9_JQ1.txt

value: Bone-marrow derived macrophages (BMDMs)


title: 4h_LipidA_BI9564_rep2_RNAseq

description:
RNA-seq of 4h Lipid A BI9564-treated BMDMs replicate 2
DESeq_4h_Vehicle_BI9564_dBRD9_JQ1.txt

value: Bi9564 and Lipid A for 4h


title: RAW_BRD4_0h_ChIPseq

description: ChIP-seq of BRD4 0h in RAW 264.7


title: 1h_LipidA_BI9564_rep1_RNAseq

description:
RNA-seq of 1h Lipid A BI9564-treated BMDMs replicate 1
DESeq_1h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 0h_BI9564_rep2_RNAseq

description:
RNA-seq of 0h BI9564-treated BMDMs replicate 2
DESeq_0h_Vehicle_BI9564_dBRD9_JQ1.txt

value: BI9564 overnight pretreatment


title: 4h_LipidA_Vehicle_rep2_RNAseq

description:
RNA-seq of 4h Lipid A vehicle-treated BMDMs replicate 2
DESeq_4h_Vehicle_BI9564_dBRD9_JQ1.txt

value: Lipid A for 4h


title: 4h_LipidA_IBRD9_rep2_RNAseq

description:
RNA-seq of 4h Lipid A IBRD9-treated BMDMs replicate 2
DESeq_4h_Vehicle_BI9564_dBRD9_JQ1.txt

value: IBRD9 and Lipid A for 4h


title: 1h_LipidA_IBRD9_rep2_RNAseq

description:
RNA-seq of 1h Lipid A IBRD9-treated BMDMs replicate 2
DESeq_1h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 4h_LipidA_Vehicle_rep1_RNAseq

description:
RNA-seq of 4h Lipid A vehicle-treated BMDMs replicate 1
DESeq_4h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 1h_LipidA_Vehicle_rep2_RNAseq

description:
RNA-seq of 1h Lipid A vehicle-treated BMDMs replicate 2
DESeq_1h_Vehicle_BI9564_dBRD9_JQ1.txt

value: Lipid A for 1h


title: 1h_LipidA_Vehicle_rep1_RNAseq

description:
RNA-seq of 1h Lipid A vehicle-treated BMDMs replicate 1
DESeq_1h_Vehicle_BI9564_dBRD9_JQ1.txt


title: 0h_Vehicle_rep2_RNAseq

description:
RNA-seq of 0h vehicle-treated BMDMs replicate 2
DESeq_0h_Vehicle_BI9564_dBRD9_JQ1.txt

value: Vehicle (DMSO)


title: 0h_Vehicle_rep1_RNAseq

description:
RNA-seq of 0h vehicle-treated BMDMs replicate 1
DESeq_0h_Vehicle_BI9564_dBRD9_JQ1.txt


title: E_Input_4h_LipidA_BI9564_ChIPseq

description: ChIPseq of Input for 4h Lipid A BI9564-treated BMDMs for dataset E

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq and ChIP-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate normalized bedGraphs for the UCSC Genome Browser. ChIP-seq peaks for BRD9, BRD4, BRD2, IRF9, STAT1, and STAT2 were found by using the findPeaks program in HOMER with the default parameters for option "-style factor" using the appropriate ChIP input experiments as background. For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file Columns: (1) chrom (2) chromStart (3) chromEnd (4) dataValue. DESeq Tab delimited text file: for DESeq_0hIFNa_Vehicle.txt: Columns: bedGraph file Columns: (1) chrom (2) chromStart (3) chromEnd (4) dataValue. DESeq Tab delimited text file: for DESeq_0hIFNa_Vehicle.txt: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-12) normalized Log2 read count for experiment (13) Log2 fold change (14) p-value, adjusted (15) p-value; for DESeq_4hIFNa_Vehicle_dBRD9_IBRD9_JQ1.txt bedGraph file Columns: (1) chrom (2) chromStart (3) chromEnd (4) dataValue. DESeq Tab delimited text file: for DESeq_0hIFNa_Vehicle.txt: Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-16) normalized Log2 read count for experiment (17,18,19) Log2 fold change, p-value, adjusted p-value dBRD9 4h IFNa vs vehicle 4h IFNa (20,21,22) Log2 fold change, p-value, adjusted p-value of IBRD9 4h IFNa vs vehicle 4h IFNa (23,24,25) Log2 fold change, p-value, adjusted p-value of JQ1 4h IFNa vs vehicle 4h IFNa


title: E_Input_4h_LipidA_ChIPseq

description: ChIPseq of Input for 4h Lipid A vehicle-trated BMDMs for dataset E


title: E_STAT2_4h_LipidA_BI9564_ChIPseq

description: ChIPseq of STAT2 4h Lipid A BI9564-treated BMDMs

value: Cell Signaling 72604S


title: D_BRD9_4h_LipidA_IBRD9_ChIPseq

description: ChIPseq of BRD9 4h Lipid A IBRD9-treated BMDMs

value: Active Motif 61537


title: D_Input_4h_LipidA_IBRD9_ChIPseq

description: ChIPseq of Input for 4h Lipid A IBRD9-treated BMDMs for dataset D


title: E_IRF9_4h_LipidA_BI9564_ChIPseq

description: ChIPseq of IRF9 4h Lipid A BI9564-treated BMDMs

value: EMD Millipore MABS1920


title: E_STAT1_4h_LipidA_BI9564_ChIPseq

description: ChIPseq of STAT1 4h Lipid A BI9564-treated BMDMs

value: Cell Signaling 91728


title: D_Input_4h_LipidA_ChIPseq

description: ChIPseq of Input for 4h Lipid A vehicle-trated BMDMs for dataset D


title: E_IRF9_4h_LipidA_ChIPseq

description: ChIPseq of IRF9 4h Lipid A vehicle-treated BMDMs


title: E_STAT1_4h_LipidA_ChIPseq

description: ChIPseq of STAT1 4h Lipid A vehicle-treated BMDMs


title: D_BRD9_4h_LipidA_dBRD9_ChIPseq

description: ChIPseq of BRD9 4h Lipid A dBRD9-treated BMDMs

value: dBRD9 and Lipid A for 4h


title: D_Input_4h_LipidA_BI9564_ChIPseq

description: ChIPseq of Input for 4h Lipid A BI9564-treated BMDMs for dataset D


title: D_Input_4h_LipidA_dBRD9_ChIPseq

description: ChIPseq of Input for 4h Lipid A dBRD9-treated BMDMs for dataset D


title: 0h_BI9564_rep1_RNAseq

description:
RNA-seq of 0h BI9564-treated BMDMs replicate 1
DESeq_0h_Vehicle_BI9564_dBRD9_JQ1.txt


title: D_BRD9_4h_LipidA_BI9564_ChIPseq

description: ChIPseq of BRD9 4h Lipid A BI9564-treated BMDMs


title: D_BRD9_4h_LipidA_ChIPseq

description: ChIPseq of BRD9 4h Lipid A vehicle-treated BMDMs


title: C_Input_4h_LipidA_ChIPseq

description: ChIPseq of Input of 4h Lipid A vehicle-treated BMDMs for dataset C


title: C_Input_4h_LipidA_JQ1_ChIPseq

description: ChIPseq of Input of 4h Lipid A JQ1-treated BMDMs for dataset C

value: JQ1 and Lipid A for 4h


title: D_BRD9_0h_Vehicle_ChIPseq

description: ChIPseq of BRD9 0h vehicle-treated BMDMs


title: E_STAT2_4h_LipidA_ChIPseq

description: ChIPseq of STAT2 4h Lipid A vehicle-treated BMDMs


title: C_BRD4_4h_LipidA_JQ1_ChIPseq

description: ChIPseq of BRD4 4h Lipid A JQ1-treated BMDMs


title: C_Input_0h_Vehicle_ChIPseq

description: ChIPseq of Input of 0h vehicle-treated BMDMs for dataset C


title: C_BRD4_0h_Vehicle_ChIPseq

description: ChIPseq of BRD4 0h vehicle-trated BMDMs


title: 4h_JQ1_rep1_IFNa_RNAseq

description:
RNA-seq of 4h IFNa JQ1-treated BMDMs replicate 1
DESeq_4hIFNa_Vehicle_dBRD9_IBRD9_JQ1.txt

value: JQ1 and IFNa for 4h


title: D_BRD9_4h_LipidA_JQ1_ChIPseq

description: ChIPseq of BRD9 4h Lipid A JQ1-treated BMDMs


title: 4h_JQ1_rep2_IFNa_RNAseq

description:
RNA-seq of 4h IFNa JQ1-treated BMDMs replicate 2
DESeq_4hIFNa_Vehicle_dBRD9_IBRD9_JQ1.txt


title: D_Input_0h_Vehicle_ChIPseq

description: ChIPseq of Input of 0h vehicle-treated BMDMs for dataset D


title: 4h_IBRD9_rep1_IFNa_RNAseq

description:
RNA-seq of 4h IFNa IBRD9-treated BMDMs replicate 1
DESeq_4hIFNa_Vehicle_dBRD9_IBRD9_JQ1.txt

value: IBRD9 and IFNa for 4h


title: 0h_Vehicle_rep1_IFNa_RNAseq

description:
RNA-seq of 0h vehicle-treated BMDMs replicate 1
DESeq_0hIFNa_Vehicle.txt


title: 0h_Vehicle_rep2_IFNa_RNAseq

description:
RNA-seq of 0h vehicle-treated BMDMs replicate 2
DESeq_0hIFNa_Vehicle.txt


title: 4h_dBRD9_rep1_IFNa_RNAseq

description:
RNA-seq of 4h IFNa dBRD9-treated BMDMs replicate 1
DESeq_4hIFNa_Vehicle_dBRD9_IBRD9_JQ1.txt

value: dBRD9 and IFNa for 4h


title: 4h_IBRD9_rep2_IFNa_RNAseq

description:
RNA-seq of 4h IFNa IBRD9-treated BMDMs replicate 2
DESeq_4hIFNa_Vehicle_dBRD9_IBRD9_JQ1.txt


title: CD4N_Gestalt_Expt_2_phase1 Gt015

status: Public on Nov 02 2021

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Human MethylationEPIC Beadchips using standard Illumina protocol.

scan_protocol: Illumina iScan System as per manufacturer’s protocol

data_processing:
GenomeStudion 2011.1 (Model M Version 1.9.0 Illumina, Inc. CA)
noob-BMIQ normalized β

label: Cy5 and Cy95

source_name: Naïve CD4

extract_protocol: DNA was isolated from 1 – 2 million cells using DNAQuik DNA Extraction protocol (Reprocell, Beltsville, MD)

tag: donor id

tag: age

value: M


title: BN_Gestalt_Expt_2_phase1 Gt015

label: Cy5 and Cy100

source_name: Naïve B


title: NK_Gestalt_Expt_2_phase1 Gt014

label: Cy5 and Cy91

source_name: Natural Killer cells


title: PBMC_Gestalt_Expt_2_phase1 Gt015

label: Cy5 and Cy92

source_name: Peripheral blood


title: NK_Gestalt_Expt_2_phase1 Gt011

label: Cy5 and Cy82

value: F


title: D_Input_4h_LipidA_JQ1_ChIPseq

description: ChIPseq of Input 4h Lipid A JQ1-treated BMDMs for dataset D

tag: treatment

value: Bone-marrow derived macrophages (BMDMs)


title: BN_Gestalt_Expt_2_phase1 Gt011

label: Cy5 and Cy80


title: NK_Gestalt_Expt_2_phase1 Gt013

label: Cy5 and Cy71


title: PBMC_Gestalt_Expt_2_phase1 Gt014

label: Cy5 and Cy84


title: PBMC_Gestalt_Expt_3_phase1 Gt016

label: Cy5 and Cy104


title: Mono_Gestalt_Expt_3_phase1 Gt015

label: Cy5 and Cy102

source_name: Monocytes


title: CD8N_Gestalt_Expt_2_phase1 Gt015

label: Cy5 and Cy98

source_name: Naïve CD8


title: PBMC_Gestalt_Expt_2_phase1 Gt011

label: Cy5 and Cy73


title: Mono_Gestalt_Expt_2_phase1 Gt013

label: Cy5 and Cy70


title: CD4N_Gestalt_Expt_2_phase1 Gt013

label: Cy5 and Cy63


title: 4h_Vehicle_rep1_IFNa_RNAseq

description:
RNAseq of 4h IFNa vehicle-treated BMDMs replicate 1
DESeq_0hIFNa_Vehicle.txt
DESeq_4hIFNa_Vehicle_dBRD9_IBRD9_JQ1.txt

value: Vehicle (DMSO) and IFNa for 4h


title: BN_Gestalt_Expt_2_phase1 Gt014

label: Cy5 and Cy89


title: C_BRD4_4h_LipidA_ChIPseq

description: ChIPseq of BRD4 4h Lipid A vehicle-trated BMDMs

value: Lipid A for 4h


title: CD8N_Gestalt_Expt_2_phase1 Gt001

label: Cy5 and Cy61


title: BN_Gestalt_Expt_2_phase1 Gt001

label: Cy5 and Cy83


title: NK_Gestalt_Expt_2_phase1 Gt005

label: Cy5 and Cy51


title: CD8N_Gestalt_Expt_2_phase1 Gt011

label: Cy5 and Cy78


title: CD4N_Gestalt_Expt_2_phase1 Gt011

label: Cy5 and Cy75


title: Mono_Gestalt_Expt_2_phase1 Gt005

label: Cy5 and Cy49


title: Mono_Gestalt_Expt_2_phase1 Gt011

label: Cy5 and Cy81


title: 4h_dBRD9_rep2_IFNa_RNAseq

description:
RNA-seq of 4h IFNa dBRD9-treated BMDMs replicate 2
DESeq_4hIFNa_Vehicle_dBRD9_IBRD9_JQ1.txt


title: Mono_Gestalt_Expt_2_phase1 Gt014

label: Cy5 and Cy90


title: BN_Gestalt_Expt_2_phase1 Gt013

label: Cy5 and Cy68


title: NK_Gestalt_Expt_2_phase1 Gt004

label: Cy5 and Cy40


title: 4h_Vehicle_rep2_IFNa_RNAseq

description:
RNAseq of 4h IFNa vehicle-treated BMDMs replicate 2
DESeq_0hIFNa_Vehicle.txt
DESeq_4hIFNa_Vehicle_dBRD9_IBRD9_JQ1.txt


title: NK_Gestalt_Expt_3_phase1 Gt015

label: Cy5 and Cy103


title: CD4N_Gestalt_Expt_2_phase1 Gt004

label: Cy5 and Cy32


title: PBMC_Gestalt_Expt_2_phase1 Gt013

label: Cy5 and Cy60


title: PBMC_Gestalt_Expt_2_phase1 Gt007

label: Cy5 and Cy52


title: Mono_Gestalt_Expt_2_phase1 Gt007

label: Cy5 and Cy58


title: CD4N_Gestalt_Expt_2_phase1 Gt007

label: Cy5 and Cy54


title: CD8N_Gestalt_Expt_2_phase1 Gt007

label: Cy5 and Cy56


title: NK_Gestalt_Expt_2_phase1 Gt007

label: Cy5 and Cy59


title: CD8N_Gestalt_Expt_2_phase1 Gt003

label: Cy5 and Cy25


title: CD4N_Gestalt_Expt_2_phase1 Gt003

label: Cy5 and Cy12


title: Mono_Gestalt_Expt_2_phase1 Gt003

label: Cy5 and Cy27


title: CD8N_Gestalt_Expt_2_phase1 Gt005

label: Cy5 and Cy46


title: Mono_Gestalt_Expt_4_phase1 Gt026

label: Cy5 and Cy3


title: BN_Gestalt_Expt_2_phase1 Gt005

label: Cy5 and Cy48


title: Mono_Gestalt_Expt_2_phase1 Gt004

label: Cy5 and Cy38


title: PBMC_Gestalt_Expt_2_phase1 Gt005

label: Cy5 and Cy41


title: CD8N_Gestalt_Expt_2_phase1 Gt013

label: Cy5 and Cy66


title: BN_Gestalt_Expt_4_phase1 Gt026


title: CD8N_Gestalt_Expt_2_phase1 Gt004

label: Cy5 and Cy35


title: BN_Gestalt_Expt_2_phase1 Gt004

label: Cy5 and Cy37


title: BN_Gestalt_Expt_4_phase1 Gt033


title: PBMC_Gestalt_Expt_2_phase1 Gt004

label: Cy5 and Cy30


title: NK_Gestalt_Expt_2_phase1 Gt003

label: Cy5 and Cy29


title: Granulo_Gestalt_Expt_4_phase1 Gt035

source_name: Granulocytes


title: Granulo_Gestalt_Expt_4_phase1 Gt026

label: Cy5 and Cy4


title: BN_Gestalt_Expt_2_phase1 Gt003

label: Cy5 and Cy26


title: CD4N_Gestalt_Expt_2_phase1 Gt001

label: Cy5 and Cy28


title: CD4N_Gestalt_Expt_4_phase1 Gt035


title: CD4N_Gestalt_Expt_4_phase1 Gt026


title: CD4N_Gestalt_Expt_2_phase1 Gt005

label: Cy5 and Cy43


title: Mono_Gestalt_Expt_4_phase1 Gt033


title: PBMC_Gestalt_Expt_4_phase1 Gt026


title: CD4N_Gestalt_Expt_4_phase1 Gt032


title: PBMC_Gestalt_Expt_4_phase1 Gt032


title: BN_Gestalt_Expt_4_phase1 Gt029


title: NK_Gestalt_Expt_4_phase1 Gt029


title: CD8N_Gestalt_Expt_4_phase1 Gt033


title: Mono_Gestalt_Expt_2_phase1 Gt002


title: PBMC_Gestalt_Expt_2_phase1 Gt003


title: CD4N_Gestalt_Expt_4_phase1 Gt033


title: PBMC_Gestalt_Expt_4_phase1 Gt033


title: Mono_Gestalt_Expt_4_phase1 Gt035


title: BN_Gestalt_Expt_4_phase1 Gt035


title: PBMC_Gestalt_Expt_4_phase1 Gt035


title: BN_Gestalt_Expt_2_phase1 Gt002


title: Mono_Gestalt_Expt_4_phase1 Gt032


title: NK_Gestalt_Expt_4_phase1 Gt032


title: NK_Gestalt_Expt_2_phase1 Gt002


title: CD8N_Gestalt_Expt_3_phase1 Gt030


title: BN_Gestalt_Expt_4_phase1 Gt032


title: CD4N_Gestalt_Expt_3_phase1 Gt030


title: PBMC_Gestalt_Expt_3_phase1 Gt030


title: Granulo_Gestalt_Expt_3_phase1 Gt027


title: PBMC_Gestalt_Expt_4_phase1 Gt029


title: BN_Gestalt_Expt_3_phase1 Gt027


title: CD4N_Gestalt_Expt_4_phase1 Gt029


title: Mono_Gestalt_Expt_3_phase1 Gt030


title: BN_Gestalt_Expt_3_phase1 Gt030


title: Granulo_Gestalt_Expt_4_phase1 Gt029


title: CD8N_Gestalt_Expt_2_phase1 Gt002


title: Mono_Gestalt_Expt_3_phase1 Gt027


title: Granulo_Gestalt_Expt_4_phase1 Gt032


title: Mono_Gestalt_Expt_4_phase1 Gt029


title: CD8N_Gestalt_Expt_3_phase1 Gt027


title: CD4N_Gestalt_Expt_3_phase1 Gt027


title: BN_Gestalt_Expt_3_phase1 Gt024


title: Mono_Gestalt_Expt_3_phase1 Gt024


title: PBMC_Gestalt_Expt_3_phase1 Gt027


title: CD8N_Gestalt_Expt_3_phase1 Gt022


title: Granulo_Gestalt_Expt_3_phase1 Gt024


title: PBMC_Gestalt_Expt_3_phase1 Gt022


title: NK_Gestalt_Expt_3_phase1 Gt022


title: CD8N_Gestalt_Expt_3_phase1 Gt024


title: NK_Gestalt_Expt_3_phase1 Gt030


title: Granulo_Gestalt_Expt_3_phase1 Gt022


title: NK_Gestalt_Expt_3_phase1 Gt024


title: CD4N_Gestalt_Expt_3_phase1 Gt022


title: Granulo_Gestalt_Expt_3_phase1 Gt018


title: Mono_Gestalt_Expt_3_phase1 Gt022


title: BN_Gestalt_Expt_3_phase1 Gt018


title: Mono_Gestalt_Expt_3_phase1 Gt018


title: CD8N_Gestalt_Expt_3_phase1 Gt018


title: NK_Gestalt_Expt_3_phase1 Gt018


title: CD4N_Gestalt_Expt_3_phase1 Gt018


title: PBMC_Gestalt_Expt_3_phase1 Gt018


title: CD4N_Gestalt_Expt_3_phase1 Gt024


title: PBMC_Gestalt_Expt_3_phase1 Gt024


title: Granulo_Gestalt_Expt_3_phase1 Gt025


title: BN_Gestalt_Expt_3_phase1 Gt025


title: Mono_Gestalt_Expt_3_phase1 Gt025


title: CD4N_Gestalt_Expt_3_phase1 Gt025


title: PBMC_Gestalt_Expt_3_phase1 Gt025


title: Granulo_Gestalt_Expt_3_phase1 Gt020


title: BN_Gestalt_Expt_3_phase1 Gt022


title: Mono_Gestalt_Expt_3_phase1 Gt020


title: BN_Gestalt_Expt_3_phase1 Gt020


title: CD8N_Gestalt_Expt_3_phase1 Gt020


title: PBMC_Gestalt_Expt_2_phase1 Gt002


title: PBMC_Gestalt_Expt_3_phase1 Gt020


title: NK_Gestalt_Expt_3_phase1 Gt020


title: CD4N_Gestalt_Expt_3_phase1 Gt020


title: Mono_Gestalt_Expt_3_phase1 Gt017


title: BN_Gestalt_Expt_3_phase1 Gt017


title: CD8N_Gestalt_Expt_3_phase1 Gt017


title: CD8N_Gestalt_Expt_3_phase1 Gt025


title: CD4N_Gestalt_Expt_3_phase1 Gt017


title: CD4N_Gestalt_Expt_2_phase1 Gt002


title: NK_Gestalt_Expt_3_phase1 Gt025


title: Mono_Gestalt_Expt_3_phase1 Gt016


title: BN_Gestalt_Expt_3_phase1 Gt016


title: PBMC_Gestalt_Expt_3_phase1 Gt017


title: CD4N_Gestalt_Expt_3_phase1 Gt016


title: PBMC_Gestalt_Expt_2_phase1 Gt001


title: NK_Gestalt_Expt_3_phase1 Gt016


title: NK_Gestalt_Expt_2_phase1 Gt001


title: Mono_Gestalt_Expt_2_phase1 Gt001


title: CD8N_Gestalt_Expt_3_phase1 Gt016


title: WB_Gestalt_Expt_4_phase1 Gt033

source_name: Whole Blood


title: WB_Gestalt_Expt_5_phase1 Gt030


title: WB_Gestalt_Expt_4_phase1 Gt035


title: WB_Gestalt_Expt_5_phase1 Gt032


title: WB_Gestalt_Expt_5_phase1 Gt029


title: WB_Gestalt_Expt_5_phase1 Gt027


title: WB_Gestalt_Expt_4_phase1 Gt026


title: NK_Gestalt_Expt_3_phase1 Gt017


title: WB_Gestalt_Expt_4_phase1 Gt024


title: WB_Gestalt_Expt_4_phase1 Gt025


title: WB_Gestalt_Expt_4_phase1 Gt022


title: WB_Gestalt_Expt_4_phase1 Gt020


title: WB_Gestalt_Expt_1_phase1 Gt018


title: WB_Gestalt_Expt_1_phase1 Gt015


title: WB_Gestalt_Expt_1_phase1 Gt016


title: WB_Gestalt_Expt_1_phase1 Gt014


title: WB_Gestalt_Expt_1_phase1 Gt013


title: WB_Gestalt_Expt_4_phase1 Gt005


title: WB_Gestalt_Expt_1_phase1 Gt011


title: WB_Gestalt_Expt_4_phase1 Gt002


title: WB_Gestalt_Expt_1_phase1 Gt017


title: WB_Gestalt_Expt_4_phase1 Gt004


title: WB_Gestalt_Expt_4_phase1 Gt003


title: WB_Gestalt_Expt_1_phase1 Gt007


title: Lane1_RPI2_95s

status: Public on Oct 26 2021

description: Pollen scRNA-seq

data_processing:
Basecalls performed using CASAVA version 1.4
Multiplexed libraries were sequenced with paired-end sequencing. The first read of each read pair contained exclusively barcoding information: a 6 nt sample barcode and a 10 bp unique molecular identifier (UMI). Paired-end reads were demultiplexed based on the sample barcodes, requiring a perfect match to one of the barcode sequences. The UMIs were extracted and appended to the read 2 sequence identifiers. The submitted fastq files are demultiplexed files for read2, with the UMI from read 1 appended to the sequence identifiers.
Prior to alignment, reads were trimmed and filtered using Fastp with parameters -y -x -3 -f 6. Reads were then aligned to the AGPv4 genome assembly using HiSat2. During read alignment, all SNPs that differ between B73 and A188 inbreds were masked. After alignment, SNPsplit was used to analyze the previously masked SNP positions and split the reads into four categories: those matching the A188 genome, those matching the B73 genome, those lacking SNPs that could separate the two alleles (“unassigned” reads), and those with conflicting SNPs (“conflicting” reads).
For transcript counting, reads mapping to the same gene with a similar UMI were collapsed using the UMI-tools dedup function. In cases in which multiple reads were associated with a single transcript, the allele calls for these reads were pooled as follows: if all reads were “unassigned”, then the transcript was labeled as “unassigned”; if all reads were assigned to only one of the two alleles (i.e. only A188 or only B73) or were unassigned, then the transcript was assigned to that allele (e.g. if there were three reads associated with a transcript, including two unassigned reads and one assigned to A188, then the transcript was assigned to A188); if any read was “conflicting” or if there were both A188 and B73-assigned reads, then the transcript was labeled as “conflicting”.
Genome_build: AgpV4
Supplementary_files_format_and_content: csv file containing allele-specific transcript counts for each each gene and sample. There are 4 columes per sample, separated based on allele calls. Columns ending “_g1” are counts of transcripts matching the B73 allele, “_g2” are transcripts matching the A188 allele, “_un” are transcripts that cannot be assigned to a parental allele, and “_cf” are transcripts with conflicting allele assignments

source_name: Isolated maize pollen precursor

growth_protocol: An F1 hybrid of Maize (Zea mays) inbred lines A188 and B73 was grown in a greenhouse at Stanford, CA with a 14-h day / 10-h night light cycle

extract_protocol:
Maize anthers were dissected and pollen precursors were released by cutting the anther in half and gently pressing on the anther. For meiotic cells, the anther was fixed for 2 hours in ice cold 3:1 ethanol:acedic acid prior to cell release. Pollen precursors were then picked up manually using blunted syringe needles, and placed on the cap of an 8-tube PCR strip.
Library protocol based on CelSeq2. Read 1 contained a 10 bp unique molecular identifier (Uninucleate Microspore (UM)I) followed by a 6 bp sample barcode. Read 2 contained transcript sequence. Deposited files are read 2 with the Uninucleate Microspore (UM)I appended to the fastq entry headers, all samples have been demultiplexed using the 6 bp sample barcodes.

tag: tissue

value: anther

value: pollen precursor cell

tag: Stage

value: Prophase I, Pachytene


title: Lane1_RPI6_95s

description: Pollen scRNA-seq

value: Mature Pollen


title: Lane1_RPI3_96s

description: Pollen scRNA-seq

value: Uninucleate Microspore (UM)


title: Lane1_RPI4_95s

description: Pollen scRNA-seq


title: Lane1_RPI3_95s

description: Pollen scRNA-seq


title: Lane1_RPI6_94s

description: Pollen scRNA-seq


title: Lane1_RPI1_96s

description: Pollen scRNA-seq


title: Lane1_RPI4_96s

description: Pollen scRNA-seq


title: Lane1_RPI5_96s

description: Pollen scRNA-seq

value: Prophase I, Zygotene


title: Lane1_RPI4_9s

description: Pollen scRNA-seq

value: Prophase I, Leptotene with central nucleolus


title: Lane1_RPI2_9s

description: Pollen scRNA-seq


title: Lane1_RPI3_9s

description: Pollen scRNA-seq

value: Tetrad


title: Lane1_RPI5_9s

description: Pollen scRNA-seq

value: Prophase I, Interphase


title: Lane1_RPI6_96s

description: Pollen scRNA-seq


title: Lane1_RPI1_9s

description: Pollen scRNA-seq

value: Uninucleate Microspore (UM), Early


title: Lane1_RPI6_9s

description: Pollen scRNA-seq


title: Lane1_RPI1_95s

description: Pollen scRNA-seq


title: Lane1_RPI5_95s

description: Pollen scRNA-seq


title: Lane1_RPI2_96s

description: Pollen scRNA-seq


title: Lane1_RPI5_94s

description: Pollen scRNA-seq


title: Lane1_RPI4_94s

description: Pollen scRNA-seq


title: Lane1_RPI2_94s

description: Pollen scRNA-seq


title: Lane1_RPI3_94s

description: Pollen scRNA-seq


title: Lane1_RPI1_94s

description: Pollen scRNA-seq


title: Lane1_RPI3_93s

description: Pollen scRNA-seq


title: WB_Gestalt_Expt_4_phase1 Gt001


title: Lane1_RPI4_93s

description: Pollen scRNA-seq


title: Lane1_RPI2_93s

description: Pollen scRNA-seq


title: Lane1_RPI5_93s

description: Pollen scRNA-seq


title: Lane1_RPI6_93s

description: Pollen scRNA-seq


title: Lane1_RPI1_93s

description: Pollen scRNA-seq


title: Lane1_RPI5_92s

description: Pollen scRNA-seq


title: Lane1_RPI6_92s

description: Pollen scRNA-seq


title: Lane1_RPI6_91s

description: Pollen scRNA-seq


title: Lane1_RPI5_91s

description: Pollen scRNA-seq


title: Lane1_RPI4_92s

description: Pollen scRNA-seq


title: Lane1_RPI4_91s

description: Pollen scRNA-seq


title: Lane1_RPI3_92s

description: Pollen scRNA-seq


title: Lane1_RPI2_92s

description: Pollen scRNA-seq


title: Lane1_RPI1_92s

description: Pollen scRNA-seq


title: Lane1_RPI2_91s

description: Pollen scRNA-seq


title: Lane1_RPI3_91s

description: Pollen scRNA-seq


title: Lane1_RPI6_90s

description: Pollen scRNA-seq


title: Lane1_RPI1_91s

description: Pollen scRNA-seq


title: Lane1_RPI3_90s

description: Pollen scRNA-seq


title: Lane1_RPI6_8s

description: Pollen scRNA-seq


title: Lane1_RPI5_90s

description: Pollen scRNA-seq


title: Lane1_RPI4_90s

description: Pollen scRNA-seq


title: Lane1_RPI4_8s

description: Pollen scRNA-seq


title: Lane1_RPI1_90s

description: Pollen scRNA-seq


title: Lane1_RPI3_8s

description: Pollen scRNA-seq


title: Lane1_RPI2_8s

description: Pollen scRNA-seq


title: Lane1_RPI5_89s

description: Pollen scRNA-seq


title: Lane1_RPI2_90s

description: Pollen scRNA-seq


title: Lane1_RPI6_89s

description: Pollen scRNA-seq


title: Lane1_RPI4_89s

description: Pollen scRNA-seq


title: Lane1_RPI1_8s

description: Pollen scRNA-seq

value: Uninucleate Microspore (UM), Middle


title: Lane1_RPI3_89s

description: Pollen scRNA-seq


title: Lane1_RPI2_89s

description: Pollen scRNA-seq


title: Lane1_RPI1_89s

description: Pollen scRNA-seq


title: Lane1_RPI6_88s

description: Pollen scRNA-seq


title: Lane1_RPI3_87s

description: Pollen scRNA-seq

value: Binucleate Microspore (BM)


title: Lane1_RPI2_88s

description: Pollen scRNA-seq


title: Lane1_RPI3_88s

description: Pollen scRNA-seq


title: Lane1_RPI2_86s

description: Pollen scRNA-seq


title: Lane1_RPI6_84s

description: Pollen scRNA-seq


title: Lane1_RPI5_83s

description: Pollen scRNA-seq

value: Prophase I, Prezygotene


title: Lane1_RPI3_83s

description: Pollen scRNA-seq


title: Lane1_RPI1_83s

description: Pollen scRNA-seq


title: Lane1_RPI6_82s

description: Pollen scRNA-seq


title: Lane1_RPI5_82s

description: Pollen scRNA-seq


title: Lane1_RPI6_87s

description: Pollen scRNA-seq


title: Lane1_RPI4_88s

description: Pollen scRNA-seq


title: Lane1_RPI4_82s

description: Pollen scRNA-seq


title: Lane1_RPI2_87s

description: Pollen scRNA-seq


title: Lane1_RPI4_87s

description: Pollen scRNA-seq


title: Lane1_RPI4_86s

description: Pollen scRNA-seq


title: Lane1_RPI2_82s

description: Pollen scRNA-seq


title: Lane1_RPI5_81s

description: Pollen scRNA-seq


title: Lane1_RPI3_85s

description: Pollen scRNA-seq


title: Lane1_RPI4_85s

description: Pollen scRNA-seq


title: Lane1_RPI4_84s

description: Pollen scRNA-seq


title: Lane1_RPI6_85s

description: Pollen scRNA-seq


title: Lane1_RPI3_86s

description: Pollen scRNA-seq


title: Lane1_RPI2_81s

description: Pollen scRNA-seq


title: Lane1_RPI3_81s

description: Pollen scRNA-seq


title: Lane1_RPI3_84s

description: Pollen scRNA-seq


title: Lane1_RPI2_84s

description: Pollen scRNA-seq


title: Lane1_RPI2_85s

description: Pollen scRNA-seq


title: Lane1_RPI6_83s

description: Pollen scRNA-seq


title: Lane1_RPI4_83s

description: Pollen scRNA-seq


title: Lane1_RPI6_86s

description: Pollen scRNA-seq


title: Lane1_RPI3_7s

description: Pollen scRNA-seq


title: Lane1_RPI3_82s

description: Pollen scRNA-seq


title: Lane1_RPI1_82s

description: Pollen scRNA-seq


title: Lane1_RPI2_7s

description: Pollen scRNA-seq


title: Lane1_RPI6_81s

description: Pollen scRNA-seq


title: Lane1_RPI1_7s

description: Pollen scRNA-seq


title: Lane1_RPI2_83s

description: Pollen scRNA-seq


title: Lane1_RPI6_80s

description: Pollen scRNA-seq


title: Lane1_RPI4_80s

description: Pollen scRNA-seq


title: Lane1_RPI5_80s

description: Pollen scRNA-seq


title: Lane1_RPI4_81s

description: Pollen scRNA-seq


title: Lane1_RPI3_80s

description: Pollen scRNA-seq


title: Lane1_RPI2_80s

description: Pollen scRNA-seq


title: Lane1_RPI6_79s

description: Pollen scRNA-seq


title: Lane1_RPI6_78s

description: Pollen scRNA-seq


title: Lane1_RPI3_79s

description: Pollen scRNA-seq


title: Lane1_RPI2_79s

description: Pollen scRNA-seq


title: Lane1_RPI5_78s

description: Pollen scRNA-seq


title: Lane1_RPI4_78s

description: Pollen scRNA-seq


title: Lane1_RPI3_78s

description: Pollen scRNA-seq


title: Lane1_RPI6_7s

description: Pollen scRNA-seq


title: Lane1_RPI4_7s

description: Pollen scRNA-seq


title: Lane1_RPI5_79s

description: Pollen scRNA-seq


title: Lane1_RPI4_77s

description: Pollen scRNA-seq


title: Lane1_RPI2_77s

description: Pollen scRNA-seq


title: Lane1_RPI1_79s

description: Pollen scRNA-seq


title: Lane1_RPI4_79s

description: Pollen scRNA-seq


title: Lane1_RPI1_81s

description: Pollen scRNA-seq


title: Lane1_RPI6_76s

description: Pollen scRNA-seq


title: Lane1_RPI2_78s

description: Pollen scRNA-seq


title: Lane1_RPI4_76s

description: Pollen scRNA-seq


title: Lane1_RPI5_75s

description: Pollen scRNA-seq


title: Lane1_RPI4_75s

description: Pollen scRNA-seq


title: Lane1_RPI3_75s

description: Pollen scRNA-seq


title: Lane1_RPI1_80s

description: Pollen scRNA-seq


title: Lane1_RPI1_78s

description: Pollen scRNA-seq


title: Lane1_RPI4_74s

description: Pollen scRNA-seq


title: Lane1_RPI5_77s

description: Pollen scRNA-seq


title: Lane1_RPI3_77s

description: Pollen scRNA-seq


title: Lane1_RPI5_76s

description: Pollen scRNA-seq


title: Lane1_RPI6_77s

description: Pollen scRNA-seq


title: Lane1_RPI2_76s

description: Pollen scRNA-seq


title: Lane1_RPI1_76s

description: Pollen scRNA-seq


title: Lane1_RPI3_76s

description: Pollen scRNA-seq


title: Lane1_RPI6_75s

description: Pollen scRNA-seq


title: Lane1_RPI1_75s

description: Pollen scRNA-seq


title: Lane1_RPI6_74s

description: Pollen scRNA-seq


title: Lane1_RPI6_6s

description: Pollen scRNA-seq


title: Lane1_RPI3_73s

description: Pollen scRNA-seq


title: Lane1_RPI4_6s

description: Pollen scRNA-seq


title: Lane1_RPI3_74s

description: Pollen scRNA-seq


title: Lane1_RPI2_74s

description: Pollen scRNA-seq


title: Lane1_RPI5_74s

description: Pollen scRNA-seq


title: Lane1_RPI1_6s

description: Pollen scRNA-seq


title: Lane1_RPI5_68s

description: Pollen scRNA-seq

value: Meiosis, M1


title: Lane1_RPI1_77s

description: Pollen scRNA-seq


title: Lane1_RPI1_74s

description: Pollen scRNA-seq


title: Lane1_RPI6_73s

description: Pollen scRNA-seq


title: Lane1_RPI5_73s

description: Pollen scRNA-seq


title: Lane1_RPI4_73s

description: Pollen scRNA-seq


title: Lane1_RPI2_68s

description: Pollen scRNA-seq


title: Lane1_RPI2_73s

description: Pollen scRNA-seq


title: Lane1_RPI2_67s

description: Pollen scRNA-seq


title: Lane1_RPI2_75s

description: Pollen scRNA-seq


title: Lane1_RPI1_73s

description: Pollen scRNA-seq


title: Lane1_RPI3_6s

description: Pollen scRNA-seq


title: Lane1_RPI6_68s

description: Pollen scRNA-seq


title: Lane1_RPI4_68s

description: Pollen scRNA-seq

value: Uninucleate Microspore (UM), Late


title: Lane1_RPI2_6s

description: Pollen scRNA-seq


title: Lane1_RPI1_68s

description: Pollen scRNA-seq


title: Lane1_RPI5_66s

description: Pollen scRNA-seq


title: Lane1_RPI6_67s

description: Pollen scRNA-seq


title: Lane1_RPI4_67s

description: Pollen scRNA-seq


title: Lane1_RPI3_67s

description: Pollen scRNA-seq


title: Lane1_RPI5_67s

description: Pollen scRNA-seq


title: Lane1_RPI4_65s

description: Pollen scRNA-seq


title: Lane1_RPI3_68s

description: Pollen scRNA-seq


title: Lane1_RPI6_66s

description: Pollen scRNA-seq


title: Lane1_RPI1_66s

description: Pollen scRNA-seq


title: Lane1_RPI2_66s

description: Pollen scRNA-seq


title: Lane1_RPI6_65s

description: Pollen scRNA-seq


title: Lane1_RPI5_65s

description: Pollen scRNA-seq


title: Lane1_RPI3_65s

description: Pollen scRNA-seq


title: Lane1_RPI6_64s

description: Pollen scRNA-seq


title: Lane1_RPI5_64s

description: Pollen scRNA-seq


title: Lane1_RPI2_65s

description: Pollen scRNA-seq


title: Lane1_RPI2_64s

description: Pollen scRNA-seq


title: Lane1_RPI6_63s

description: Pollen scRNA-seq


title: Lane1_RPI4_63s

description: Pollen scRNA-seq


title: Lane1_RPI1_67s

description: Pollen scRNA-seq


title: Lane1_RPI3_63s

description: Pollen scRNA-seq


title: Lane1_RPI4_64s

description: Pollen scRNA-seq


title: Lane1_RPI3_64s

description: Pollen scRNA-seq


title: Lane1_RPI3_66s

description: Pollen scRNA-seq


title: Lane1_RPI1_64s

description: Pollen scRNA-seq


title: Lane1_RPI4_66s

description: Pollen scRNA-seq


title: Lane1_RPI1_65s

description: Pollen scRNA-seq


title: Lane1_RPI1_62s

description: Pollen scRNA-seq


title: Lane1_RPI3_62s

description: Pollen scRNA-seq


title: Lane1_RPI2_63s

description: Pollen scRNA-seq


title: Lane1_RPI5_63s

description: Pollen scRNA-seq


title: Lane1_RPI4_62s

description: Pollen scRNA-seq


title: Lane1_RPI1_63s

description: Pollen scRNA-seq


title: Lane1_RPI5_62s

description: Pollen scRNA-seq


title: Lane1_RPI6_62s

description: Pollen scRNA-seq


title: Lane1_RPI6_60s

description: Pollen scRNA-seq


title: Lane1_RPI2_60s

description: Pollen scRNA-seq


title: Lane1_RPI6_61s

description: Pollen scRNA-seq


title: Lane1_RPI3_61s

description: Pollen scRNA-seq


title: Lane1_RPI6_5s

description: Pollen scRNA-seq


title: Lane1_RPI4_60s

description: Pollen scRNA-seq


title: Lane1_RPI2_61s

description: Pollen scRNA-seq


title: Lane1_RPI1_60s

description: Pollen scRNA-seq


title: Lane1_RPI2_62s

description: Pollen scRNA-seq


title: Lane1_RPI4_5s

description: Pollen scRNA-seq


title: Lane1_RPI3_5s

description: Pollen scRNA-seq


title: Lane1_RPI2_5s

description: Pollen scRNA-seq


title: Lane1_RPI6_59s

description: Pollen scRNA-seq


title: Lane1_RPI5_59s

description: Pollen scRNA-seq


title: Lane1_RPI5_61s

description: Pollen scRNA-seq


title: Lane2_RPI1_36s

description: Pollen scRNA-seq


title: Lane2_RPI1_34s

description: Pollen scRNA-seq


title: Lane1_RPI4_61s

description: Pollen scRNA-seq


title: Lane1_RPI1_61s

description: Pollen scRNA-seq


title: Lane1_RPI3_60s

description: Pollen scRNA-seq


title: Lane1_RPI1_5s

description: Pollen scRNA-seq


title: Lane1_RPI5_5s

description: Pollen scRNA-seq

value: Prophase I, Leptotene with peripheral nucleolus


title: Lane1_RPI4_59s

description: Pollen scRNA-seq


title: Lane1_RPI5_60s

description: Pollen scRNA-seq


title: Lane1_RPI3_59s

description: Pollen scRNA-seq


title: Lane1_RPI1_59s

description: Pollen scRNA-seq


title: Lane2_RPI1_33s

description: Pollen scRNA-seq


title: Lane1_RPI6_58s

description: Pollen scRNA-seq


title: Lane1_RPI5_58s

description: Pollen scRNA-seq


title: Lane2_RPI1_37s

description: Pollen scRNA-seq


title: Lane2_RPI1_31s

description: Pollen scRNA-seq


title: Lane1_RPI4_58s

description: Pollen scRNA-seq


title: Lane2_RPI1_30s

description: Pollen scRNA-seq


title: Lane2_RPI1_2s

description: Pollen scRNA-seq


title: Lane1_RPI3_58s

description: Pollen scRNA-seq


title: Lane1_RPI2_58s

description: Pollen scRNA-seq


title: Lane1_RPI1_58s

description: Pollen scRNA-seq


title: Lane2_RPI1_35s

description: Pollen scRNA-seq


title: Lane1_RPI6_57s

description: Pollen scRNA-seq


title: Lane1_RPI5_57s

description: Pollen scRNA-seq


title: Lane2_RPI1_27s

description: Pollen scRNA-seq


title: Lane2_RPI1_26s

description: Pollen scRNA-seq


title: Lane1_RPI3_57s

description: Pollen scRNA-seq


title: Lane2_RPI1_25s

description: Pollen scRNA-seq


title: Lane1_RPI4_57s

description: Pollen scRNA-seq


title: Lane2_RPI1_24s

description: Pollen scRNA-seq


title: Lane2_RPI1_23s

description: Pollen scRNA-seq


title: Lane2_RPI1_32s

description: Pollen scRNA-seq


title: Lane2_RPI1_20s

description: Pollen scRNA-seq


title: Lane2_RPI1_21s

description: Pollen scRNA-seq


title: Lane2_RPI1_1s

description: Pollen scRNA-seq


title: Lane2_RPI1_22s

description: Pollen scRNA-seq


title: Lane2_RPI1_19s

description: Pollen scRNA-seq


title: Lane2_RPI1_29s

description: Pollen scRNA-seq


title: Lane2_RPI1_17s

description: Pollen scRNA-seq


title: Lane2_RPI1_28s

description: Pollen scRNA-seq


title: Lane2_RPI1_16s

description: Pollen scRNA-seq


title: Lane1_RPI5_55s

description: Pollen scRNA-seq


title: Lane1_RPI5_56s

description: Pollen scRNA-seq


title: Lane2_RPI1_15s

description: Pollen scRNA-seq


title: Lane1_RPI3_56s

description: Pollen scRNA-seq


title: Lane1_RPI6_55s

description: Pollen scRNA-seq


title: Lane1_RPI4_55s

description: Pollen scRNA-seq


title: Lane1_RPI2_57s

description: Pollen scRNA-seq


title: Lane1_RPI6_56s

description: Pollen scRNA-seq


title: Lane1_RPI1_56s

description: Pollen scRNA-seq


title: Lane1_RPI1_57s

description: Pollen scRNA-seq


title: Lane1_RPI4_56s

description: Pollen scRNA-seq


title: Lane1_RPI2_55s

description: Pollen scRNA-seq


title: Lane1_RPI3_55s

description: Pollen scRNA-seq


title: Lane2_RPI1_13s

description: Pollen scRNA-seq


title: Lane1_RPI1_55s

description: Pollen scRNA-seq


title: Lane2_RPI1_12s

description: Pollen scRNA-seq


title: Lane2_RPI1_11s

description: Pollen scRNA-seq


title: Lane2_RPI1_10s

description: Pollen scRNA-seq


title: Lane1_RPI2_56s

description: Pollen scRNA-seq


title: Lane2_RPI1_18s

description: Pollen scRNA-seq


title: Lane1_RPI6_4s

description: Pollen scRNA-seq


title: Lane1_RPI4_4s

description: Pollen scRNA-seq


title: Lane1_RPI3_4s

description: Pollen scRNA-seq


title: Lane1_RPI5_4s

description: Pollen scRNA-seq


title: Lane1_RPI2_4s

description: Pollen scRNA-seq


title: Lane3_RPI2_9s

description: Pollen scRNA-seq


title: Lane3_RPI2_96s

description: Pollen scRNA-seq


title: Lane3_RPI2_95s

description: Pollen scRNA-seq


title: Lane1_RPI6_46s

description: Pollen scRNA-seq


title: Lane1_RPI5_46s

description: Pollen scRNA-seq


title: Lane1_RPI1_46s

description: Pollen scRNA-seq


title: Lane1_RPI4_46s

description: Pollen scRNA-seq


title: Lane1_RPI5_41s

description: Pollen scRNA-seq


title: Lane1_RPI6_41s

description: Pollen scRNA-seq


title: Lane1_RPI2_46s

description: Pollen scRNA-seq


title: Lane2_RPI1_14s

description: Pollen scRNA-seq


title: Lane1_RPI4_41s

description: Pollen scRNA-seq


title: Lane1_RPI1_4s

description: Pollen scRNA-seq


title: Lane1_RPI3_46s

description: Pollen scRNA-seq


title: Lane3_RPI2_85s

description: Pollen scRNA-seq


title: Lane3_RPI2_94s

description: Pollen scRNA-seq


title: Lane3_RPI2_91s

description: Pollen scRNA-seq


title: Lane3_RPI2_86s

description: Pollen scRNA-seq


title: Lane3_RPI2_87s

description: Pollen scRNA-seq


title: Lane3_RPI2_83s

description: Pollen scRNA-seq


title: Lane3_RPI2_88s

description: Pollen scRNA-seq


title: Lane3_RPI2_92s

description: Pollen scRNA-seq


title: Lane3_RPI2_84s

description: Pollen scRNA-seq


title: Lane3_RPI2_8s

description: Pollen scRNA-seq


title: Lane3_RPI2_90s

description: Pollen scRNA-seq


title: Lane1_RPI2_41s

description: Pollen scRNA-seq


title: Lane3_RPI2_93s

description: Pollen scRNA-seq


title: Lane3_RPI2_89s

description: Pollen scRNA-seq


title: Lane1_RPI1_41s

description: Pollen scRNA-seq


title: Lane1_RPI6_40s

description: Pollen scRNA-seq


title: Lane1_RPI3_41s

description: Pollen scRNA-seq


title: Lane3_RPI2_82s

description: Pollen scRNA-seq


title: Lane3_RPI2_81s

description: Pollen scRNA-seq


title: Lane3_RPI2_80s

description: Pollen scRNA-seq


title: Lane1_RPI3_40s

description: Pollen scRNA-seq


title: Lane1_RPI4_40s

description: Pollen scRNA-seq


title: Lane1_RPI5_40s

description: Pollen scRNA-seq


title: Lane3_RPI2_79s

description: Pollen scRNA-seq


title: Lane3_RPI2_7s

description: Pollen scRNA-seq


title: Lane3_RPI2_78s

description: Pollen scRNA-seq


title: Lane1_RPI2_40s

description: Pollen scRNA-seq


title: Lane1_RPI1_40s

description: Pollen scRNA-seq

value: Dyad


title: Lane3_RPI2_77s

description: Pollen scRNA-seq

value: anther


title: Lane1_RPI6_3s

description: Pollen scRNA-seq

value: pollen precursor cell


title: Lane1_RPI3_3s

description: Pollen scRNA-seq

value: Prophase I, Pachytene


title: Lane3_RPI2_76s

description: Pollen scRNA-seq


title: Lane3_RPI2_74s

description: Pollen scRNA-seq


title: Lane3_RPI2_70s

description: Pollen scRNA-seq


title: Lane1_RPI2_3s

description: Pollen scRNA-seq


title: Lane3_RPI2_72s

description: Pollen scRNA-seq


title: Lane3_RPI2_69s

description: Pollen scRNA-seq


title: Lane1_RPI6_39s

description: Pollen scRNA-seq


title: Lane1_RPI4_3s

description: Pollen scRNA-seq


title: Lane3_RPI2_6s

description: Pollen scRNA-seq


title: Lane3_RPI2_71s

description: Pollen scRNA-seq


title: Lane1_RPI5_3s

description: Pollen scRNA-seq


title: Lane1_RPI4_39s

description: Pollen scRNA-seq


title: Lane1_RPI1_3s

description: Pollen scRNA-seq


title: Lane1_RPI3_39s

description: Pollen scRNA-seq


title: Lane3_RPI2_75s

description: Pollen scRNA-seq


title: Lane3_RPI2_73s

description: Pollen scRNA-seq


title: Lane3_RPI2_68s

description: Pollen scRNA-seq


title: Lane3_RPI2_67s

description: Pollen scRNA-seq


title: Lane1_RPI5_39s

description: Pollen scRNA-seq


title: Lane3_RPI2_65s

description: Pollen scRNA-seq


title: Lane1_RPI2_39s

description: Pollen scRNA-seq


title: Lane1_RPI5_38s

description: Pollen scRNA-seq


title: Lane1_RPI6_38s

description: Pollen scRNA-seq


title: Lane1_RPI1_39s

description: Pollen scRNA-seq


title: Lane3_RPI2_66s

description: Pollen scRNA-seq


title: Lane3_RPI2_64s

description: Pollen scRNA-seq


title: Lane1_RPI4_38s

description: Pollen scRNA-seq


title: Lane1_RPI3_38s

description: Pollen scRNA-seq


title: Lane3_RPI2_63s

description: Pollen scRNA-seq


title: Lane3_RPI2_62s

description: Pollen scRNA-seq


title: Lane1_RPI2_38s

description: Pollen scRNA-seq


title: Lane3_RPI2_5s

description: Pollen scRNA-seq


title: Lane3_RPI2_61s

description: Pollen scRNA-seq


title: Lane1_RPI3_37s

description: Pollen scRNA-seq


title: Lane1_RPI5_37s

description: Pollen scRNA-seq


title: Lane3_RPI2_60s

description: Pollen scRNA-seq


title: Lane3_RPI2_59s

description: Pollen scRNA-seq


title: Lane1_RPI4_37s

description: Pollen scRNA-seq


title: Lane3_RPI2_58s

description: Pollen scRNA-seq


title: Lane1_RPI6_37s

description: Pollen scRNA-seq


title: Lane3_RPI2_56s

description: Pollen scRNA-seq


title: Lane1_RPI1_38s

description: Pollen scRNA-seq


title: Lane1_RPI1_37s

description: Pollen scRNA-seq


title: Lane3_RPI2_57s

description: Pollen scRNA-seq


title: Lane3_RPI2_55s

description: Pollen scRNA-seq


title: Lane1_RPI5_36s

description: Pollen scRNA-seq


title: Lane3_RPI2_54s

description: Pollen scRNA-seq


title: Lane3_RPI2_52s

description: Pollen scRNA-seq


title: Lane3_RPI2_50s

description: Pollen scRNA-seq


title: Lane1_RPI2_36s

description: Pollen scRNA-seq


title: Lane1_RPI3_36s

description: Pollen scRNA-seq


title: Lane1_RPI4_36s

description: Pollen scRNA-seq


title: Lane1_RPI2_37s

description: Pollen scRNA-seq


title: Lane3_RPI2_4s

description: Pollen scRNA-seq


title: Lane1_RPI1_36s

description: Pollen scRNA-seq


title: Lane1_RPI6_36s

description: Pollen scRNA-seq


title: Lane1_RPI5_35s

description: Pollen scRNA-seq


title: Lane3_RPI2_49s

description: Pollen scRNA-seq


title: Lane3_RPI2_48s

description: Pollen scRNA-seq


title: Lane3_RPI2_53s

description: Pollen scRNA-seq


title: Lane3_RPI2_47s

description: Pollen scRNA-seq


title: Lane1_RPI6_35s

description: Pollen scRNA-seq


title: Lane1_RPI4_35s

description: Pollen scRNA-seq


title: Lane3_RPI2_45s

description: Pollen scRNA-seq


title: Lane3_RPI2_44s

description: Pollen scRNA-seq


title: Lane3_RPI2_46s

description: Pollen scRNA-seq


title: Lane1_RPI3_35s

description: Pollen scRNA-seq


title: Lane1_RPI2_35s

description: Pollen scRNA-seq


title: Lane1_RPI1_35s

description: Pollen scRNA-seq


title: Lane3_RPI2_43s

description: Pollen scRNA-seq


title: Lane3_RPI2_42s

description: Pollen scRNA-seq


title: Lane3_RPI2_41s

description: Pollen scRNA-seq


title: Lane3_RPI2_40s

description: Pollen scRNA-seq


title: Lane1_RPI4_34s

description: Pollen scRNA-seq


title: Lane1_RPI6_34s

description: Pollen scRNA-seq


title: Lane1_RPI2_59s

description: Pollen scRNA-seq


title: Lane1_RPI5_34s

description: Pollen scRNA-seq


title: Lane1_RPI1_34s

description: Pollen scRNA-seq


title: Lane1_RPI2_34s

description: Pollen scRNA-seq


title: Lane3_RPI2_38s

description: Pollen scRNA-seq


title: Lane1_RPI5_33s

description: Pollen scRNA-seq


title: Lane3_RPI2_37s

description: Pollen scRNA-seq


title: Lane1_RPI6_33s

description: Pollen scRNA-seq


title: Lane3_RPI2_39s

description: Pollen scRNA-seq


title: Lane3_RPI2_36s

description: Pollen scRNA-seq


title: Lane1_RPI3_33s

description: Pollen scRNA-seq


title: Lane3_RPI2_34s

description: Pollen scRNA-seq


title: Lane3_RPI2_35s

description: Pollen scRNA-seq


title: Lane3_RPI2_31s

description: Pollen scRNA-seq


title: Lane1_RPI1_33s

description: Pollen scRNA-seq


title: Lane1_RPI2_33s

description: Pollen scRNA-seq


title: Lane3_RPI2_30s

description: Pollen scRNA-seq


title: Lane3_RPI2_2s

description: Pollen scRNA-seq


title: Lane3_RPI2_32s

description: Pollen scRNA-seq


title: Lane1_RPI3_32s

description: Pollen scRNA-seq


title: Lane1_RPI5_32s

description: Pollen scRNA-seq


title: Lane1_RPI2_32s

description: Pollen scRNA-seq


title: Lane1_RPI3_34s

description: Pollen scRNA-seq


title: Lane3_RPI2_29s

description: Pollen scRNA-seq


title: Lane1_RPI3_31s

description: Pollen scRNA-seq


title: Lane3_RPI2_27s

description: Pollen scRNA-seq


title: Lane1_RPI5_31s

description: Pollen scRNA-seq


title: Lane3_RPI2_28s

description: Pollen scRNA-seq


title: Lane3_RPI2_3s

description: Pollen scRNA-seq


title: Lane3_RPI2_26s

description: Pollen scRNA-seq


title: Lane3_RPI2_24s

description: Pollen scRNA-seq


title: Lane1_RPI2_31s

description: Pollen scRNA-seq


title: Lane1_RPI3_30s

description: Pollen scRNA-seq


title: Lane1_RPI5_30s

description: Pollen scRNA-seq


title: Lane1_RPI1_31s

description: Pollen scRNA-seq


title: Lane3_RPI2_25s

description: Pollen scRNA-seq


title: Lane3_RPI2_23s

description: Pollen scRNA-seq


title: Lane3_RPI2_33s

description: Pollen scRNA-seq


title: Lane1_RPI2_30s

description: Pollen scRNA-seq


title: Lane1_RPI1_30s

description: Pollen scRNA-seq


title: Lane3_RPI2_22s

description: Pollen scRNA-seq


title: Lane3_RPI2_21s

description: Pollen scRNA-seq


title: Lane1_RPI4_2s

description: Pollen scRNA-seq


title: Lane1_RPI5_2s

description: Pollen scRNA-seq


title: Lane3_RPI2_20s

description: Pollen scRNA-seq


title: Lane1_RPI3_2s

description: Pollen scRNA-seq


title: Lane3_RPI2_17s

description: Pollen scRNA-seq


title: Lane1_RPI4_33s

description: Pollen scRNA-seq


title: Lane3_RPI2_18s

description: Pollen scRNA-seq


title: Lane1_RPI2_2s

description: Pollen scRNA-seq


title: Lane1_RPI1_2s

description: Pollen scRNA-seq


title: Lane1_RPI5_29s

description: Pollen scRNA-seq


title: Lane3_RPI2_16s

description: Pollen scRNA-seq


title: Lane3_RPI2_19s

description: Pollen scRNA-seq


title: Lane3_RPI2_15s

description: Pollen scRNA-seq


title: Lane3_RPI2_14s

description: Pollen scRNA-seq


title: Lane1_RPI3_29s

description: Pollen scRNA-seq


title: Lane3_RPI2_13s

description: Pollen scRNA-seq


title: Lane1_RPI2_29s

description: Pollen scRNA-seq


title: Lane3_RPI2_11s

description: Pollen scRNA-seq


title: Lane3_RPI2_12s

description: Pollen scRNA-seq


title: Lane1_RPI1_29s

description: Pollen scRNA-seq


title: Lane3_RPI2_10s

description: Pollen scRNA-seq


title: Lane1_RPI3_28s

description: Pollen scRNA-seq


title: Lane1_RPI2_28s

description: Pollen scRNA-seq


title: Lane1_RPI6_2s

description: Pollen scRNA-seq


title: Lane3_RPI2_1s

description: Pollen scRNA-seq


title: Lane2_RPI1_9s

description: Pollen scRNA-seq


title: Lane2_RPI1_95s

description: Pollen scRNA-seq


title: Lane1_RPI1_28s

description: Pollen scRNA-seq


title: Lane1_RPI6_27s

description: Pollen scRNA-seq


title: Lane2_RPI1_96s

description: Pollen scRNA-seq


title: Lane2_RPI1_94s

description: Pollen scRNA-seq


title: Lane1_RPI3_27s

description: Pollen scRNA-seq


title: Lane1_RPI2_27s

description: Pollen scRNA-seq


title: Lane2_RPI1_92s

description: Pollen scRNA-seq


title: Lane1_RPI1_27s

description: Pollen scRNA-seq


title: Lane2_RPI1_91s

description: Pollen scRNA-seq


title: Lane1_RPI5_28s

description: Pollen scRNA-seq


title: Lane2_RPI1_90s

description: Pollen scRNA-seq


title: Lane1_RPI5_26s

description: Pollen scRNA-seq


title: Lane1_RPI6_26s

description: Pollen scRNA-seq


title: Lane2_RPI1_8s

description: Pollen scRNA-seq


title: Lane2_RPI1_89s

description: Pollen scRNA-seq


title: Lane1_RPI4_26s

description: Pollen scRNA-seq


title: Lane1_RPI2_26s

description: Pollen scRNA-seq


title: Lane1_RPI3_26s

description: Pollen scRNA-seq


title: Lane1_RPI5_27s

description: Pollen scRNA-seq


title: Lane1_RPI4_25s

description: Pollen scRNA-seq


title: Lane1_RPI6_25s

description: Pollen scRNA-seq


title: Lane1_RPI3_25s

description: Pollen scRNA-seq


title: Lane1_RPI5_25s

description: Pollen scRNA-seq


title: Lane2_RPI1_86s

description: Pollen scRNA-seq


title: Lane2_RPI1_85s

description: Pollen scRNA-seq


title: Lane1_RPI3_24s

description: Pollen scRNA-seq


title: Lane2_RPI1_83s

description: Pollen scRNA-seq


title: Lane1_RPI1_25s

description: Pollen scRNA-seq


title: Lane1_RPI1_26s

description: Pollen scRNA-seq


title: Lane1_RPI2_25s

description: Pollen scRNA-seq


title: Lane2_RPI1_80s

description: Pollen scRNA-seq


title: Lane2_RPI1_81s

description: Pollen scRNA-seq


title: Lane1_RPI6_24s

description: Pollen scRNA-seq


title: Lane2_RPI1_78s

description: Pollen scRNA-seq


title: Lane2_RPI1_7s

description: Pollen scRNA-seq


title: Lane2_RPI1_84s

description: Pollen scRNA-seq


title: Lane2_RPI1_77s

description: Pollen scRNA-seq


title: Lane2_RPI1_93s

description: Pollen scRNA-seq


title: Lane2_RPI1_87s

description: Pollen scRNA-seq


title: Lane2_RPI1_76s

description: Pollen scRNA-seq


title: Lane1_RPI3_23s

description: Pollen scRNA-seq


title: Lane1_RPI1_24s

description: Pollen scRNA-seq


title: Lane2_RPI1_88s

description: Pollen scRNA-seq


title: Lane1_RPI6_23s

description: Pollen scRNA-seq


title: Lane2_RPI1_82s

description: Pollen scRNA-seq


title: Lane2_RPI1_79s

description: Pollen scRNA-seq


title: Lane1_RPI2_24s

description: Pollen scRNA-seq


title: Lane2_RPI1_75s

description: Pollen scRNA-seq


title: Lane1_RPI1_32s

description: Pollen scRNA-seq


title: Lane1_RPI2_23s

description: Pollen scRNA-seq


title: Lane2_RPI1_72s

description: Pollen scRNA-seq


title: Lane1_RPI4_22s

description: Pollen scRNA-seq


title: Lane1_RPI2_22s

description: Pollen scRNA-seq


title: Lane1_RPI6_21s

description: Pollen scRNA-seq


title: Lane2_RPI1_70s

description: Pollen scRNA-seq


title: Lane1_RPI3_22s

description: Pollen scRNA-seq


title: Lane2_RPI1_68s

description: Pollen scRNA-seq


title: Lane2_RPI1_73s

description: Pollen scRNA-seq


title: Lane2_RPI1_69s

description: Pollen scRNA-seq


title: Lane1_RPI2_21s

description: Pollen scRNA-seq


title: Lane2_RPI1_6s

description: Pollen scRNA-seq


title: Lane2_RPI1_66s

description: Pollen scRNA-seq


title: Lane2_RPI1_65s

description: Pollen scRNA-seq


title: Lane1_RPI3_21s

description: Pollen scRNA-seq


title: Lane2_RPI1_67s

description: Pollen scRNA-seq


title: Lane1_RPI1_21s

description: Pollen scRNA-seq


title: Lane2_RPI1_64s

description: Pollen scRNA-seq


title: Lane1_RPI6_20s

description: Pollen scRNA-seq


title: Lane2_RPI1_63s

description: Pollen scRNA-seq


title: Lane2_RPI1_62s

description: Pollen scRNA-seq


title: Lane2_RPI1_74s

description: Pollen scRNA-seq


title: Lane1_RPI1_23s

description: Pollen scRNA-seq


title: Lane2_RPI1_61s

description: Pollen scRNA-seq


title: Lane1_RPI5_20s

description: Pollen scRNA-seq


title: Lane1_RPI6_22s

description: Pollen scRNA-seq


title: Lane2_RPI1_60s

description: Pollen scRNA-seq


title: Lane2_RPI1_71s

description: Pollen scRNA-seq


title: Lane1_RPI1_22s

description: Pollen scRNA-seq


title: Lane1_RPI4_21s

description: Pollen scRNA-seq


title: Lane2_RPI1_5s

description: Pollen scRNA-seq


title: Lane2_RPI1_59s

description: Pollen scRNA-seq


title: Lane2_RPI1_53s

description: Pollen scRNA-seq


title: Lane2_RPI1_55s

description: Pollen scRNA-seq


title: Lane2_RPI1_58s

description: Pollen scRNA-seq


title: Lane1_RPI1_20s

description: Pollen scRNA-seq


title: Lane1_RPI6_1s

description: Pollen scRNA-seq


title: Lane2_RPI1_57s

description: Pollen scRNA-seq


title: Lane1_RPI2_20s

description: Pollen scRNA-seq


title: Lane2_RPI1_4s

description: Pollen scRNA-seq


title: Lane2_RPI1_52s

description: Pollen scRNA-seq


title: Lane1_RPI5_1s

description: Pollen scRNA-seq


title: Lane2_RPI1_51s

description: Pollen scRNA-seq


title: Lane2_RPI1_54s

description: Pollen scRNA-seq


title: Lane2_RPI1_50s

description: Pollen scRNA-seq


title: Lane1_RPI4_1s

description: Pollen scRNA-seq


title: Lane1_RPI4_20s

description: Pollen scRNA-seq


title: Lane2_RPI1_48s

description: Pollen scRNA-seq


title: Lane2_RPI1_49s

description: Pollen scRNA-seq


title: Lane1_RPI3_1s

description: Pollen scRNA-seq


title: Lane2_RPI1_47s

description: Pollen scRNA-seq


title: Lane2_RPI1_46s

description: Pollen scRNA-seq


title: Lane1_RPI2_1s

description: Pollen scRNA-seq


title: Lane2_RPI1_45s

description: Pollen scRNA-seq


title: Lane2_RPI1_44s

description: Pollen scRNA-seq


title: Lane1_RPI1_1s

description: Pollen scRNA-seq


title: Lane2_RPI1_43s

description: Pollen scRNA-seq


title: Lane2_RPI1_42s

description: Pollen scRNA-seq


title: Lane2_RPI1_56s

description: Pollen scRNA-seq


title: Lane1_RPI6_19s

description: Pollen scRNA-seq


title: Lane2_RPI1_41s

description: Pollen scRNA-seq


title: Lane1_RPI3_20s

description: Pollen scRNA-seq


title: Lane2_RPI1_38s

description: Pollen scRNA-seq


title: Lane2_RPI1_39s

description: Pollen scRNA-seq


title: Lane1_RPI5_19s

description: Pollen scRNA-seq


title: Lane2_RPI1_3s

description: Pollen scRNA-seq


title: Lane1_RPI5_18s

description: Pollen scRNA-seq


title: Lane1_RPI2_18s

description: Pollen scRNA-seq


title: Lane1_RPI2_19s

description: Pollen scRNA-seq


title: Lane2_RPI1_40s

description: Pollen scRNA-seq


title: Lane1_RPI4_19s

description: Pollen scRNA-seq


title: Lane1_RPI1_18s

description: Pollen scRNA-seq


title: Lane1_RPI1_17s

description: Pollen scRNA-seq


title: Lane1_RPI3_17s

description: Pollen scRNA-seq


title: Lane1_RPI2_17s

description: Pollen scRNA-seq


title: Lane1_RPI2_16s

description: Pollen scRNA-seq


title: Lane1_RPI4_17s

description: Pollen scRNA-seq


title: Lane1_RPI6_17s

description: Pollen scRNA-seq


title: Lane1_RPI5_15s

description: Pollen scRNA-seq


title: Lane1_RPI5_17s

description: Pollen scRNA-seq


title: Lane1_RPI6_16s

description: Pollen scRNA-seq


title: Lane1_RPI6_15s

description: Pollen scRNA-seq


title: Lane1_RPI1_19s

description: Pollen scRNA-seq


title: Lane1_RPI1_16s

description: Pollen scRNA-seq


title: Lane1_RPI3_15s

description: Pollen scRNA-seq


title: Lane1_RPI3_19s

description: Pollen scRNA-seq


title: Lane1_RPI3_18s

description: Pollen scRNA-seq


title: Lane1_RPI6_18s

description: Pollen scRNA-seq


title: Lane1_RPI2_15s

description: Pollen scRNA-seq


title: Lane1_RPI1_15s

description: Pollen scRNA-seq


title: Lane1_RPI4_18s

description: Pollen scRNA-seq


title: Lane1_RPI4_14s

description: Pollen scRNA-seq


title: Lane1_RPI6_14s

description: Pollen scRNA-seq


title: Lane1_RPI5_14s

description: Pollen scRNA-seq


title: Lane1_RPI1_14s

description: Pollen scRNA-seq


title: Lane1_RPI6_13s

description: Pollen scRNA-seq


title: Lane1_RPI3_16s

description: Pollen scRNA-seq


title: Lane1_RPI2_14s

description: Pollen scRNA-seq


title: Lane1_RPI5_13s

description: Pollen scRNA-seq


title: Lane1_RPI4_13s

description: Pollen scRNA-seq


title: Lane1_RPI3_14s

description: Pollen scRNA-seq


title: Lane1_RPI5_12s

description: Pollen scRNA-seq


title: Lane1_RPI1_13s

description: Pollen scRNA-seq


title: Lane1_RPI3_11s

description: Pollen scRNA-seq


title: Lane1_RPI3_12s

description: Pollen scRNA-seq


title: Lane1_RPI3_13s

description: Pollen scRNA-seq


title: Lane1_RPI1_11s

description: Pollen scRNA-seq


title: Lane1_RPI5_10s

description: Pollen scRNA-seq


title: Lane1_RPI4_12s

description: Pollen scRNA-seq


title: Lane1_RPI2_13s

description: Pollen scRNA-seq


title: Lane1_RPI6_10s

description: Pollen scRNA-seq


title: Lane1_RPI2_12s

description: Pollen scRNA-seq


title: Lane1_RPI1_10s

description: Pollen scRNA-seq


title: Lane1_RPI6_12s

description: Pollen scRNA-seq


title: Lane1_RPI6_11s

description: Pollen scRNA-seq


title: Lane1_RPI1_12s

description: Pollen scRNA-seq


title: Lane1_RPI5_11s

description: Pollen scRNA-seq


title: Lane1_RPI2_11s

description: Pollen scRNA-seq


title: AOCS18.5_18B_FPos_3

status: Public on Sep 03 2021

city: Melbourne

first: Elizabeth

middle: Louise

last: Christie

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
bcl2fastq (v2.20.0.422) was used to demultiplex the sequencing data and convert base call (BCL) files into FASTQ files
Initial QC on the raw FASTQ files were done using FastQC (v0.11.8)
Reads were trimmed for low quality, adapters, N content and poly-A tails using fastq-mcf (v1.05)
Contamination was checked using FastQ Screen (v0.11.4)
Reads were mapped to the human reference GRCh37.92 using the STAR two pass method (v2.6.0b)
Mapped reads were sorted using Picard Tools (v2.17.3)
Additional QC after mapping was performed using Picard Tools CollectRnaSeqMetrics (v2.17.3) and RSeQC (v 2.6.4)
Counts were generated on the ensemble release GRCh37.92 GTF annotation using HTSeq (v0.10.0). Counts were done on the exons only using the “intersection-nonempty” mode
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts, gene by sample matrix

source_name: HGSOC cell

growth_protocol: Cells were seeded (5x10^5-1.5x10^6 cells/plate) in 10cm plates with exponentially growing cells collected 48-72hrs after seeding (approximately 70-80% confluency).

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) with on-column DNase digestion. 1ug of RNA was submitted for sequencing.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using standard Illumina protocols

treatment_protocol: Cell lines were grown in RPMI 1640 (GIBCO, USA) media supplemented with 10% HyClone Fetal Bovine Serum (GE Healthcare, USA) and 1% Penicillin-Streptomycin-Glutamine (GIBCO). Cells were cultured in a humidified atmosphere at 37°C containing 5% CO2.

tag: slc25a40-abcb1 fusion status

value: Fusion Positive


title: AOCS18.5_18B_FPos_2


title: Lane1_RPI4_11s

description: Pollen scRNA-seq


title: Lane1_RPI3_10s

description: Pollen scRNA-seq


title: Lane1_RPI4_10s

description: Pollen scRNA-seq


title: Lane1_RPI2_10s

description: Pollen scRNA-seq


title: AOCS18.5_13_FPos_3


title: AOCS18.5_15B_FPos_3


title: AOCS18.5_18B_FPos_1


title: AOCS18.5_15B_FPos_1


title: AOCS18.5_15B_FPos_2


title: AOCS18.5_13_FPos_2


title: AOCS18.5_9_FPos_3


title: AOCS18.5_13_FPos_1


title: AOCS18.5_9_FPos_1


title: AOCS18.5_8_FPos_2


title: AOCS18.5_8_FPos_3


title: AOCS18.5_8_FPos_1


title: AOCS18.5_F_FNeg_1

value: Fusion Negative


title: AOCS18.5_F_FNeg_2


title: AOCS18.5_E_FNeg_1


title: AOCS18.5_E_FNeg_2


title: AOCS18.5_D_FNeg_3


title: AOCS18.5_E_FNeg_3


title: AOCS18.5_B_FNeg_2


title: AOCS18.5_F_FNeg_3


title: AOCS18.5_C_FNeg_2


title: AOCS18.5_D_FNeg_2


title: AOCS18.5_9_FPos_2


title: AOCS18.5_C_FNeg_3