title: iPSC neuron pre-capture [WTCHG_264983_203202]


title: iPSC neuron pre-capture [WTCHG_264983_204204]

status: Public on Mar 06 2021

type: SRA

city: Oxford

first: Alexandra

last: Pokhilko

address: John Radcliffe Hospital, Headington

department: Nuffield Department of Clinical Neurosciences

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
RNA-seq data were mapped to the hg38 assembly via STAR version 2.4.2.
Ribosomal rRNA was removed with the SortMeRNA version 2.1.
Read quality check with FastQC Version 0.10.1.
Read alignment quantification into gene counts with featureCount of Subread version 1.4.0.
We excluded libraries with less than 2000 expressed genes; low complexity, where the % of 200 most expressed features represented more than 50% of total number of counts.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Supplementary files of raw counts are tab-delimited text files.

molecule: total RNA

organism: Homo sapiens

source_name: Dermal fibroblasts differentiated into iPS cells

growth_protocol: The growth protocol is described in Volpato et al., Stem Cell Rep. 2018, p.897-911. PMID: 30245212. Briefly, confluent monolayer iPSCs were induced by dual-SMAD inhibition for 12 days followed by three weeks of progenitor expansion and differentiation. Independent inductions were seeded into 12-well culture dishes at a final plating density of 8.5 x 10e4 cells /cm2. Samples were collected at day 55 after final plating.

extract_protocol:
RNeasy Mini Kits (QIAGEN) targeted enrichment with Roche NimbleGen SeqCap.
Libraries were prepared following the Smart-Seq2 protocol. Libraries were pooled in 288- or 384-plexes and each pool sequenced on 1 lane of HiSeq4000 at 75bp paired end.

tag: library

value: pre-capture

tag: cell type

value: iPSC-derived neuron

tag: cell line

tag: lab

value: D

tag: batch


title: iPSC neuron pre-capture [WTCHG_264983_203227]

value: E


title: iPSC neuron pre-capture [WTCHG_264983_203228]


title: iPSC neuron pre-capture [WTCHG_264983_204229]


title: iPSC neuron pre-capture [WTCHG_264983_203204]


title: iPSC neuron pre-capture [WTCHG_264983_203203]


title: iPSC neuron pre-capture [WTCHG_264983_202231]


title: iPSC neuron pre-capture [WTCHG_264983_203229]


title: iPSC neuron pre-capture [WTCHG_264983_202232]


title: iPSC neuron pre-capture [WTCHG_264983_202230]


title: iPSC neuron pre-capture [WTCHG_264983_202228]


title: iPSC neuron pre-capture [WTCHG_264983_203226]


title: iPSC neuron pre-capture [WTCHG_264983_203225]


title: Msn2_cg_deletion_Msn4_cg_deletion_0.5M_KCl_rep2

city: Beijing

first: Yan

last: WU

state: Beijing

address: No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

department: Academy for Advanced Interdisciplinary Studies

country: China

institute: Peking University

data_processing:
Sequencing reads were trimmed and filtered by Trimmomatic.
Resulting sequences were aligned to yeast genome reference sacCer3 for S. cerevisiae (or CBS138 for C. glabrata) with Tophat.
Alignments to gene loci were quantified with Cufflinks or featureCounts.
Genome_build: sacCer3 for S.cerevisiae, CBS138 for C. glabrata
Supplementary_files_format_and_content: csv files containing FPKM or featureCounts from Cufflinks or featureCounts.

molecule: polyA RNA

organism: Nakaseomyces glabratus

source_name: yeast cells

growth_protocol: For steady-state experiments, overnight single-colony culture was diluted to OD600 = 0.25 with 10 mL media in a 50 mL centrifuge tube and cultured for another 4 hours. For transient stress experiments, overnight single-colony culture was diluted to OD600 = 0.5 with 10 mL media without stress in a 50 mL centrifuge tube and cultured for another 4 hours.

extract_protocol:
Cells were briefly centrifuged. The supernatant was quickly discarded and cells were flash-frozen in liquid nitrogen before RNA extraction. RNA extraction was performed with HiPure HP Plant RNA Mini Kit (Magen).
Libraries were prepared according to standard Illumina protocols. Sequencing was performed on Illumina HiSeq X Ten.

treatment_protocol: For steady-state experiments, cells from two 10 mL cultures were combined with no treatments. For transient stress experiments, after 4-hour culture, 5 mL cell culture was mixed with 5 mL media containing double the designated stress concentration (1M potassium chloride). The rest of the culture was mixed with 5 mL media without stress, used as the control group. Cells were then cultured by shaking under 30°C for around 15 min.

tag: strain

tag: genotype

tag: treatment

tag: replicate


title: Msn4_cg_deletion_control_rep2

value: control


title: iPSC neuron pre-capture [WTCHG_264983_203207]


title: Msn4_cg_deletion_0.5M_KCl_rep2


title: WT_cg_0.5M_KCl_rep2


title: Msn2_cg_deletion_Msn4_cg_deletion_control_rep2


title: WT_cg_control_rep2


title: iPSC neuron pre-capture [WTCHG_264983_202227]


title: iPSC neuron pre-capture [WTCHG_264983_202225]


title: iPSC neuron pre-capture [WTCHG_264983_202226]


title: Msn2_cg_deletion_0.5M_KCl_rep2


title: Msn2_cg_deletion_control_rep2


title: WT_cg_control_rep1


title: iPSC neuron pre-capture [WTCHG_264983_202207]


title: Msn4_cg_deletion_control_rep1


title: iPSC neuron pre-capture [WTCHG_264983_202208]


title: WT_cg_0.5M_KCl_rep1


title: iPSC neuron pre-capture [WTCHG_264983_202204]


title: iPSC neuron pre-capture [WTCHG_264983_202205]


title: iPSC neuron pre-capture [WTCHG_264983_202206]


title: iPSC neuron pre-capture [WTCHG_264983_202229]


title: iPSC neuron pre-capture [WTCHG_264983_202203]


title: Msn2_cg_deletion_control_rep1


title: iPSC neuron pre-capture [WTCHG_264983_202202]


title: Msn2_cg_deletion_0.5M_KCl_rep1


title: iPSC neuron pre-capture [WTCHG_264983_202201]


title: Endothelial 2H11 cells treated with BMP4 _rep3

city: Houston

first: GUOYU

last: YU

state: TX

address: 1515 Holcombe Blvd, Houston,

department: Translational Molecular Pathology

country: USA

institute: MD Anderson Cancer Center

data_processing:
Sequence quality was examined using the FastQC.
The raw sequences were trimmed off 5’, 3’-adaptor bases using cutadapt.
The trimmed sequences were aligned to reference genome using Hisat2 software.
The aligned reads were assembled to transcripts by StringTie and FPKMs were computed.
The differentially expression of the genes and transcripts were analyzed using Ballgown R package.
rMATS was used to analzye alternative splicing events.
Genome_build: GENCODE mouse GRCm38
Supplementary_files_format_and_content: Gene/transcript expression levels in FPKM

organism: Mus musculus

source_name: axillary lymph node/vascular epithelium

extract_protocol: Libraries were prepared according to Roche KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Briefly, polyA+ mRNAs were enriched by oligo (dT)  magnetic beads from the total RNA samples; RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific; The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute  quantification qPCR method; The barcoded libraries were mixed, denatured to single strands in NaOH, captured on Illumina flow cell, amplified in situ, and sequenced for 150 cycles for paired-ends on an Illumina HiSeq 4000 system.

treatment_protocol: Starve 2H11 cells and treat 2H11 cells with or without BMP4 for 48 hours

tag: tissue

value: axillary lymph node/vascular epithelium

value: BMP4 treated for 48 hours


title: Endothelial 2H11 untreated cells _rep3

value: untreated


title: iPSC neuron pre-capture [WTCHG_264983_201232]


title: Endothelial 2H11 untreated cells _rep2


title: iPSC neuron pre-capture [WTCHG_264983_201230]


title: Endothelial 2H11 cells treated with BMP4_rep1


title: iPSC neuron pre-capture [WTCHG_264983_201227]


title: Endothelial 2H11 cells treated with BMP4 _rep2


title: Endothelial 2H11 untreated cells _rep1


title: Msn4_cg_deletion_0.5M_KCl_rep1


title: WT_sc_0.05percent_glucose_rep2

organism: Saccharomyces cerevisiae


title: Msn2_cg_deletion_Msn4_cg_deletion_control_rep1


title: iPSC neuron pre-capture [WTCHG_264983_201226]


title: iPSC neuron pre-capture [WTCHG_264983_201231]


title: iPSC neuron pre-capture [WTCHG_264983_201225]


title: iPSC neuron pre-capture [WTCHG_264983_201208]


title: Msn2_cg_deletion_Msn4_cg_deletion_0.5M_KCl_rep1


title: iPSC neuron pre-capture [WTCHG_264983_201206]


title: iPSC neuron pre-capture [WTCHG_264983_201205]


title: WT_sc_0.5percent_glucose_rep2


title: iPSC neuron pre-capture [WTCHG_264983_201207]


title: WT_sc_0.5percent_glucose_rep1


title: WT_sc_0.1percent_glucose_rep2


title: WT_sc_0.1percent_glucose_rep1


title: WT_sc_0.05percent_glucose_rep1


title: iPSC neuron pre-capture [WTCHG_264983_201228]


title: iPSC neuron pre-capture [WTCHG_264983_201204]


title: iPSC neuron pre-capture [WTCHG_264983_201229]


title: WT_sc_0.01percent_glucose_rep1


title: iPSC neuron pre-capture [WTCHG_264983_201203]


title: WT_sc_control_rep2


title: iPSC neuron pre-capture [WTCHG_264983_201202]


title: iPSC neuron pre-capture [WTCHG_264983_201201]


title: WT_sc_0.5M_KCl_rep2


title: HUWE1-promoted XLID 5

city: Trondheim

first: Sarah

middle: Louise Fordyce

last: Martin

address: Erling Skjalgssons gt 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Norwegian University of Science and Technology

description: Epstein-Barr Virus transformed B-cell line

data_processing:
Illumina bcl2fastq 2.20.0.422 used for basecalling
Sequenced reads were mapped to GRCh38.84 whole genome using STAR v2.4.0 with parameters --chimSegmentMin 30 --runThreadN 12 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000
Counting was performed using HTSeq (Anders et a., 2015 Bioinformatics) v0.6.0 (htseq-count) using reverse stranded settings, counting exon features and reporting Ensembl Gene Ids.
Data normalization and differential expression analysis was performed using limma v3.32.10 (Ritchie et al., 2015 Nucleic Acids Research), in R v 3.4.1, filtering out genes with expression (total normalized read counts) less than the number of samples.
Genome_build: GRCh38.84
Supplementary_files_format_and_content: Count matrix output from HTSeq (details above), no normalization was performed on the provided Aprigliano_matrix.txt.
Supplementary_files_format_and_content: Aprigliano_norm_matrix.txt: logCPM voom normalized count matrix

source_name: lymphoblastoid cells

growth_protocol: lymphoblastoid cells were cultured in  RPMI 1640 (Sigma Aldrich) supplemented with  Penicillin-Streptomycin (1% v/v Gibco, Invitrogen) and Fetal Bovine Serum (FBS) (15% v/v, Sigma-Aldrich) at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted from the pellets using RNAEasy Mini Kit (Qiagen, #74104).
Lexogen SENSE mRNA library preparation kit (polyA stranded)

tag: disease

value: HUWE1-promoted XLID

value: periferial blood

value: HUWE1 duplication


title: HUWE1-promoted XLID 4

value: HUWE1 p.R2981H


title: Msn4_sc_deletion_0.5M_KCl_rep2


title: Msn2_sc_deletion_control_rep2


title: HUWE1-promoted XLID 3

value: HUWE1 p.R4187C


title: HUWE1-promoted XLID 2

value: HUWE1 p.G4310R


title: WT_sc_0.01percent_glucose_rep2


title: Msn2_sc_deletion_0.5M_KCl_rep2


title: WT_sc_0.5M_KCl_rep1


title: healthy individual 4

value: healty

value: periferial bloL

value: WT


title: WT_sc_control_rep1


title: HUWE1-promoted XLID 1


title: Msn4_sc_deletion_control_rep1


title: healthy individual 3


title: Msn4_sc_deletion_0.5M_KCl_rep1


title: healthy individual 2


title: Msn2_sc_deletion_0.5M_KCl_rep1


title: CTRL_3

city: WUHAN

first: Qiuyun

last: She

address: No.13, Qingnian Road

institute: Huazhong University of Science and Technology

data_processing:
Illumina HiSeq platform used for basecalling.
Raw image Data files obtained by Illumina HiSeq are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences，and the results are stored in FASTQ (.fq) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT was used to compare clean reads to reference genes. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: Homo_sapiens.GRCh38.99.chr
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human melanoma cell

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

value: Human cutaneous melanoma cell

value: affected ABCB6 control lentivirus


title: CTRL_2


title: Msn2_sc_deletion_control_rep1


title: Msn4_sc_deletion_control_rep2


title: CTRL_1


title: ShABCB6#2_2

value: affected ABCB6 knock-down lentivirus


title: ShABCB6#2_3


title: ShABCB6#2_1


title: W1

city: Durham

first: Han Kyu

last: Lee

state: NC

address: 213 Research Dr. PO box #3175

institute: Duke University Medical Center

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) and then the library preparations were sequenced on an Illumina platform and paired-end were generated.
Raw reads of FASTQ format were processed through fastq.
Mapping to reference genome (STAR)
Read counting (HTseq)
Differential expression (DESeq2)

extract_protocol:
Mouse brain cortex was removed on ice and then was stored at -80C after fast-freezing with liquid nitrogen. RNA isolation was performed by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols (prepared by Novogene)

value: brain cortex

value: WSB/EiJ

tag: Sex

value: male


title: W2


title: C2


title: W3


title: healthy individual 1


title: C3


title: ShABCB6#1_2


title: B3


title: S15 JianKangRen LJ.rma-dabg

type: RNA

first: LIngxiao

last: Wang

address: Tian Tan Xi Li No.4

institute: School of Stomology, Capital Medical University

description: Male，63 years old, HbA1c (glycated hemoglobin) 4.5%, non-smoking

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RMA using Affymetrix  default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: BMSCs from human jaw in non-T2 DM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: BMSCs from human jaw.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: BMSCs from human jaw

value: Male

tag: age

value: 63 years old

tag: hba1c (glycated hemoglobin)

tag: group

value: nnon-smoking


title: B2


title: B1


title: RUNX1_Het_Rep3

city: Philadelphia

first: Paul

last: Gadue

state: PA

address: 3501 Civic Center Blvd

department: Hematology

institute: University of Pennsylvania

data_processing:
Reads were trimmed using cutadapt and quality scores were assessed using FastQC
Reads were aligned to the Homo sapiens genome build hg19 using STAR
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression (RLE) using DESeq2 R library
Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC
Fold change, p-value and optional covariate correction were calculated with DESeq2
Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library
Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies
Differentially expressed genes passed a threshold of +/- 1.2 fold change and have a p-value < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

source_name: RUNX1_Het_iPSC-derived megakaryocytes

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Invitrogen) and processed as per manufacturer’s instructions.
SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara Bio) and run on HiSeq 2500 (Illumina)

tag: background strain

value: CHOPWT6 iPSC

value: iPSC-derived megakaryocytes


title: WangQing DM.rma-dabg

description: Female， 61 years old, HbA1c (glycated hemoglobin) 7.0-8.0%, non-smoking

source_name: BMSCs from human jaw in T2 DM

value: Female

value: 61 years old


title: CAG JianKangRen LJ.rma-dabg

description: Male，72 years old, HbA1c (glycated hemoglobin) 5.2%, non-smoking

value: 72 years old


title: RUNX1_Het_Rep2


title: ShABCB6#1_3


title: C1


title: RUNX1_Het_Rep1


title: ShABCB6#1_1


title: LL JianKangRen LJ.rma-dabg

description: Female， 60 years old, HbA1c (glycated hemoglobin) 5.0%, non-smoking

value: 60 years old


title: DM2.rma-dabg

description: Male，63 years old, HbA1c (glycated hemoglobin) 7.5%, non-smoking


title: ETV6_Homo_Rep3

source_name: ETV6_Homo_iPSC-derived megakaryocytes


title: DM1.rma-dabg

description: Male，72 years old, HbA1c (glycated hemoglobin) 7.6%, non-smoking

source_name: BMSCs from human jaw in  T2 DM

value: non-smoking


title: ETV6_Homo_Rep2


title: KP tumor cCD1, biological rep3

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description:
cDC1_KP_r3
Gene expression profile of cCD1 cells from the lungs of KP tumor-bearing mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 2.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using Bioconductor affy library and Brainarray custom CDF mogene20st_Mm_ENTREZG_22.0.0. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization. Batch correction using the ComBat function of the sva package has to be applied to remove some batch effect affecting healthy replicates 3 and 4 and tumor replicate 3 (batch 2), as compared to all other samples (batch 1).

label: biotin

source_name: KP lung tumor cCD1

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions

growth_protocol: Primary cDC1 isolated from lung tissues

extract_protocol: Lungs were digested using collagenase and the CD11c fraction was enriched by column separation. CD11c cells were labeled with specific antibodies to allow sorting of cDC1. Total RNA was extracted using TriPure (Roche) accordingly to manifacturer guidelines. Extraction was followed by Qiagen Rneasy column clean-up accordingly to manifacturer instructions.RNA was amplified using the Nugen protocol before hybridization.

treatment_protocol: Mice were injected with 100.000 KP cells in the tail vein. Lungs were harvested 28 days after challenge.

tag: mouse status

value: injected with the KP tumor cell line

value: lung

value: conventional Batf3'dependent cDC1


title: KP tumor cCD1, biological rep1

description:
cDC1_KP_r1
Gene expression profile of cCD1 cells from the lungs of KP tumor-bearing mice


title: 20 Gy 6 Days P7KP_6 Biological rep 7

first: Warren

last: Floyd

state: North Carolina

address: 450 Research Drive, LSRC Bldg, Room B324

department: Pharmacology and Molecular Cancer Biology

institute: Duke University

description: P7KP_6 Biological rep 7

data_processing:
FPKM
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: Excel file with FPKM values

growth_protocol: Cell Lines: 10% FBS, 1% PenStep, 1% L-Glut DMEM , split 1:10

extract_protocol:
Cell Lines were washed with PBS, then harvested in Trizol and purified using Direct-Zol RNA Minprep Plus Kit (Zymo), Tumors were snap frozen, then harvested in Trizol and purified using Direct-Zol RNA Miniprep Plus Kit (Zymo),
NEBNext UltraTM RNALibrary Prep Kit for Illumina, RNA libraries performed using standard protocol for this kit and illumina libraries

treatment_protocol: Tumor: 20 Gy to right lower extremity

value: 129S4/SVJaeJ- C57/Bl6 Mixed

value: Soft Tissue Sarcoma

tag: atrx status

value: wild-type

value: 20 Gy 6 Days


title: untreated control-muscle Normal Muscle rep1

description: Normal Muscle

value: Normal Muscle

value: untreated control-muscle


title: 20 Gy 6 Days P7KP_6 biological rep 8

description: P7KP_6 biological rep 8


title: untreated control P7KPNIR biological rep 4

description: P7KPNIR biological rep 3

value: untreated control


title: KP tumor cCD1, biological rep2

description:
cDC1_KP_r2
Gene expression profile of cCD1 cells from the lungs of KP tumor-bearing mice

tag: cell type


title: 20 Gy 4 Hours P7KP_4 biological rep 2

description: P7KP_4 biological rep 2

value: 20 Gy 4 Hours


title: untreated control-muscle Normal Muscle rep2

description: Normal Muscle


title: 20 Gy 4 Hours P7KP_4 biological rep 3

description: P7KP_4 biological rep 3


title: 20 Gy 4 Hours P7KPA_4 biological rep 3

description: P7KPA_4 biological rep 3

value: deleted


title: 20 Gy 3 Days P7KP_3 biological rep 2

description: P7KP_3 biological rep 2

value: 20 Gy 3 Days


title: untreated control P7KPANIR biological rep 4

description: P7KPANIR biological rep 4


title: untreated control P7KPNIR biological rep 3

description: P7KPNIR biological rep 3


title: healthy cCD1, biological rep2

description:
cDC1_healthy_r2
Gene expression profile of cCD1 cells from the lungs of healthy mice

source_name: healthy lungs cCD1

value: healthy control


title: ETV6_Homo_Rep1

value: CHOPWT6 iPSC

value: iPSC-derived megakaryocytes


title: 20 Gy 6 Days P7KP_6 biological rep 6

description: P7KP_6 biological rep 6


title: healthy cCD1, biological rep4

description:
cDC1_healthy_r4
Gene expression profile of cCD1 cells from the lungs of healthy mice


title: healthy cCD1, biological rep3

description:
cDC1_healthy_r3
Gene expression profile of cCD1 cells from the lungs of healthy mice


title: healthy cCD1, biological rep1

description:
cDC1_healthy_r1
Gene expression profile of cCD1 cells from the lungs of healthy mice


title: Spleen, MOTS-c3

city: Seoul

first: ByungSoo

last: Kong

address: Yeongundong 128

country: South Korea

institute: Seoul National University Hospital

description: MOTS-c 4

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing:
Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1
Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

source_name: MOTS-c-treated

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: 6-week-old NOD (female, n=56). NOD  mice had a week of stabilization before any experimental procedure. Mice were bred and housed in a specific pathogen-free environment in the animal facility at the Seoul National University Hospital (IACUC no. 17-0095-C1A1, 18-0144-S1A1)  were purchased from the Jackson laboratory (Bar Harbor, USA)

extract_protocol: For euthanasia, NOD mice aged 18 weeks were fasted overnight (16-18 hrs), weighed and random blood glucose were measured. Then, spleen and other tissues were isolated. Total RNA was purified using the RNeasy Mini Kit (Qiagen) as per manufacturer’s protocol. cDNA was synthesized by reverse transcription of 1 μg of total RNA using AMV Reverse Transcriptase (Promega) following manufacturer’s instructions.

treatment_protocol: NOD mice were treated with either vehicle (non-specific scrambled MOTS-c peptide) or MOTS-c (0.5 mg/kg/day; IP) daily in the morning up to 18 or 30 weeks of age.

tag: gender

value: Female

value: MOTS-c

value: Spleen


title: Spleen, MOTS-c2

description: MOTS-c 2


title: ETV6_Het_Rep3

source_name: ETV6_Het_iPSC-derived megakaryocytes


title: Spleen, MOTS-c1

description: MOTS-c 1


title: 20 Gy 6 Days P7KP_6 biological rep 5

description: P7KP_6 biological rep 5


title: Beclin 2 KO_B_2

first: Motao

last: Zhu

state: Texas

address: 6670 Bertner Ave

department: Center for Inflammation and Epigenetics

institute: Houston Methodist Research Institute

data_processing:
The original raw data from Illumina HiSeqTM are transformed to Sequenced Reads by base calling with the Illumina CASAVA v1.8 software.
The filtering process is as follows:(1) Discard reads with adaptor contamination. (2) Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%).(3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.
To compare gene expression levels under different conditions, a diagram of the distribution of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) and a violin plot are used. DESeq, an R package based on a negative binomial distribution that models the number of reads from RNA-seq experiments, was applied for analysis of differentially expressed genes (DEGs). The threshold for DEGs was set as padj < 0.05 when using biological replicates in the experiments.
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: Excel files include readcount for each sample and p values for DEGs

source_name: Primary splenic B cells

growth_protocol: Bone marrow progenitor cells were cultured in L929-cell conditioned medium medium for 5-6 days to obtain BMDMs. Other cells or tissues were direcly used for RNA extraction without culture procedure.

extract_protocol:
Total RNA was extracted from cells or homogenized tissues using TRIzol reagent (Invitrogen) or Direct-zol™ RNA MiniPrep Plus w/ TRI Reagent® (ZYMO Research, R2071) following the manufacturer’s protocol.
An RNA-seq library was prepared using Novogene’s protocol. Briefly, mRNA was enriched using oligo(dT) beads and then fragmented randomly in fragmentation buffer. Next, cDNA was synthesized from these fragments using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added along with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand via nick translation. The final cDNA library was sequenced using the Illumina HiSeq platform at Novogene.

treatment_protocol: BMDMs were stimulated by LPS (100 ng/ml) for 3 hours, followed by RNA extraction.

value: Primary splenic B cells

tag: stimulation

value: Beclin 2 KO


title: Spleen, Control2

description: Control 2

source_name: Vehicle-treated

value: Vehicle


title: ETV6_Het_Rep2


title: Spleen, Control3

description: Control 34


title: Spleen, Control1


title: Beclin 2 KO_B_1


title: parental wild type HFF, CMV infected 20hpi, ZAP-bound RNA from eCLIP experiment

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: ZAP-bound RNA

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al,., doi: 10.1038/s41587-019-0201-4)
Sequencing reads were aligned to the hg19 version of the human genome using standard parameter, using the Refseq gtf file downloaded from the UCSC genome browser.
Reads were then quantified using quasR (Gaidatzis et al, 2015) and the above mentioned gtf file, or the HCMV TB40/E annotation (accession number MF871618).
Differential expression and corresponding p-values were calculated using edgeR (McCarthy et al., doi: 10.1093/nar/gks042).
For 4sU sequencing, reads were mapped to a combined index of the human genome (Hg38 / Ensembl v90) and the HCMV genome (accession number KF297339.1) using STAR (v2.5.3a) with parameters --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --alignEndsType Extend5pOfReads12 --outSAMattributes nM MD NH.
We used GRAND-SLAM (v2.0.5d) (Jurges et al., doi: 10.1093/bioinformatics/bty256) to estimate the new-to-total RNA ratios.
We only used the parts of the reads that were sequenced by both mates in a read pair (parameter -double) for the estimation.
New RNA was computed by multiplying total RNA with the maximum a posteriori estimate of the new-to-total RNA ratio.
For further analyses, we removed all cellular genes that had less than 10 transcripts per million transcripts (TPM) in more than 6 (cellular genes) or 2 (viral genes) samples.
To remove artefacts due to imprecise quantification, we furthermore removed all viral genes with less than 100 new reads. Log2 fold changes were estimated using PsiLFC (Erhard, doi: 10.1093/bioinformatics/bty471) with uninformative prior (corresponding to no pseudocounts).
Normalization factors were computed from total RNA such that the median log2 foldchange was 0 and applied to both total and new RNA.
Paired-end sequencing reads from eCLIP experiments were trimmed using a custom python script that simultaneously identified the umi-molecular identifier (UMI) associated with each read.
Trimmed reads were then aligned to the HCMV genome (accession number EF999921.1) and the human genome (Hg38 / Ensembl v100) using Burrows–Wheeler Aligner (Li and Durbin, doi: 10.1093/bioinformatics/btp324) (v0.7.15-r1140).
Next, we removed PCR duplicates using the UMI-aware deduplication functionality in Picard’s MarkDuplicates, and the generated .bam files were then split by strand using 'samtools view -f/-F 16' and converted to .bw (bigwig format) using bamCoverage (Ramírez et al., doi: 10.1093/nar/gkw257).
Finally, ZAP binding sites were identified as peaks that were enriched relative to a size-matched input control. MACS2 (Zhang et al., doi: 10.1186/gb-2008-9-9-r137) (v2.2.7.1) callpeak was used with the parameters '-f BAM --keep-884 dup all --nomodel --extsize 50 --d-min 5 --scale-to small -B'.
Genome_build: hg19
Genome_build: HCMV MF871618
Genome_build: hg38
Genome_build: HCMV KF297339.1
Genome_build: HCMV EF999921.1
Supplementary_files_format_and_content: tab-separated values
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: bed narrowpeak

source_name: Primary human foreskin fibroblasts (HFF) cells

growth_protocol:
Primary human foreskin fibroblasts (HFF-1) cells (ATCC SCRC-1041) were maintained in DMEM (high glucose) supplemented with 15% FCS, 1% P/S and 1% non‐essential amino acids (NEAA). Cells were cultured at 37°C and 7.5% CO2.
Knockouts of ZAP (ZC3HAV1) were done using CRISPR/Cas9, with components transduced by lentiviruses

extract_protocol:
eCLIP
For  RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol. For eCLIP, cells were subjected to UV crosslinking at 254 nM before harvesting. Frozen cell pellets were lysed in 50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% (v/v) NP40, 0.5% NaDeoxycholate, 0.25 mM DTT, and complete EDTA-free protease inhibitor cocktail. Subsequent steps were performed as described in the eCLIP protocol, with the following modifications. Immunoprecipitates were washed two times in 1 ml CLIP lysis buffer, two times in IP wash buffer (50 mM Tris-HCl pH 7.4, 300 mM NaCl, 1 mM EDTA, 1% (v/v) NP40, 0.5% sodium deoxycholate, 0.25 mM DTT), followed by two washes in 50 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.5% (v/v) NP40. For immunoprecipitation reactions a commercial ZC3HAV1 antibody was used (Proteintech, 16820-1-AP).
eCLIP

treatment_protocol: Cells were subjected to CMV infection and 4sU treatment as indicated

tag: grna sequence forward

tag: grna sequence reverse

tag: grna name

tag: 4su treatment

tag: cmv infection

value: yes

tag: harvesting timepoint

value: 20 hpi


title: unirradiated contralateral matched unirradiated tumor - contralateral leg

tag: strain

value: 129S4/SVJaeJ- C57/Bl6 Mixed

tag: tissue

value: Soft Tissue Sarcoma

tag: treatment

value: unirradiated contralateral


title: Beclin 2 KO_T_2

source_name: Primary splenic T cells

value: Primary splenic T cells

tag: genotype


title: 20 Gy 6 Days P7KPA_6 biological rep 4

description: P7KPA_6 biological rep 4

value: deleted

value: 20 Gy 6 Days


title: WT_B_2

value: Wild type


title: WT_B_1


title: parental wild type HFF, CMV infected 20hpi, input for eCLIP experiment

description: Input RNA


title: WT_T_2


title: Beclin 2 KO_T_1


title: 1376_07pw [RNA-Seq]

city: Columbus

first: Dimitris

last: Tatakis

state: OH

address: 305 W. 12th ave

department: Periodontology

institute: The Ohio State University

description: Prewound side of Volunteer #7

data_processing:
IonTorrent software was used for base-calling.
The raw sequences were aligned to the human hg19   reference sequence by  Ion Torrent Suite alignment tool
Quality control was assessed by the StrandNGS program, which determined the pre- and post-alignment quality of the reads for each sample.
The aligned reads were normalized and quantified using the Quantile algorithm by the StrandNGS program.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and Quantile normalization values for all samples.

source_name: human gingival tissue sample

extract_protocol:
Two biopsies in the form of free gingival grafts (FGG) were harvested in the same appointment from each volunteer, one from each side of the palate.
cDNA libraries were constructed using Ion Ampliseq Transcriptome Human Gene Expression Kit  from Life Technologies (Cat# A26325) per the manufacturer's protocol, at the PrimBio Research Institute LLC (Exton, PA).  The amplified cDNA libraries were purified using Nucleic Acid binding beads, binding buffers and run on Agilent 2100 Bioanalyzer to determine the yield and size distribution of each library.For all the DNA libraries, further template amplification and enrichment were performed on the Ion Chef system followed by sequencing on an Ion Proton sequencer (PrimBio Research Institute LLC ,Exton, PA).

value: palatal gingival tissue

tag: disease

value: Heathy individual

tag: group

value: Prewound side


title: WT_T_1


title: ETV6_Het_Rep1

tag: background strain

value: CHOPWT6 iPSC

value: iPSC-derived megakaryocytes


title: 1380_09pw [RNA-Seq]

description: Prewound side of Volunteer #9


title: 1378_08pw [RNA-Seq]

description: Prewound side of Volunteer #8


title: Bortezomib

first: Andre

last: Catic

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Sequence reads were obtained from the Illumina Genome Analyzer Pipeline using Basespace sequence hub.
RNA-seq fastq files were processed with Cutadapt ver. 1.12 in order to trim for adaptor sequences then sequence reads were mapped to the human reference genome hg19 using TopHat2/Bowtie2 ver. 2.1.070 with default parameters.
Gene expression changes were quantified with Cufflinks and Cuffdiff ver. 2.1.171.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample and log2 (fold change Treated vs Control) values. The file also contains ERCC control FPKM data for each sample.

growth_protocol: MM.1S cells were obtained from ATCC (#CRL-2974) and cultured in RPMI medium at 37°C in a humidified atmosphere containing 5% CO2 following vendor's recommendations.

extract_protocol:
Total RNAs were extracted with Qiagen RNeasy Mini kit (Cat. #74106) following vendor's protocol. An additional step of on column DNase I digestion was performed during RNA extraction in order to eliminate potential traces of genomic DNA (RNase-Free DNase Set, Qiagen, Cat. #79254).
Kapa Biosystems Stranded RNA-seq Kit with RiboErase (HMR) (Cat. # KK8483) was used with 1 ug of total RNA for the construction of sequencing libraries according to recommended protocol. ERCC RNA Spike-In control Mix 1 (Life Technologies, Cat. #4456740) has been included during library prep to assess platform dynamic range and lower limit of detection. Desired library insert size was 200 bp. The size distribution of the final libraries were confirmed by electrophoretic analysis on an Agilent Bioanalyzer 2100 prior to sequencing. Libraries were sequenced on the Illumina Genome Analyzer following the manufacturer's protocols for RNA-seq with HiSeq2500 in Rapid Run Mode using the HiSeq Rapid SBS v2 flow cell.

treatment_protocol: Treatment was performed with 6 µM lactacystin (Cayman Chemical, # 70980) or 60 nM Bortezomib (Selleckchem,#PS-341) as proteasome inhibitors, or 0.1% (v/v) DMSO (mock) for six hours. For each condition, cells were treated in 25cm2 flasks with an average of 3-4 million cells per flask.

tag: cell line

value: MM.1S cells (ATCC #CRL-2974)

value: B lymphoblast

tag: disease source

value: IgAλ myeloma

tag: cell line source gender

value: Female

value: Bortezomib (60 nM)


title: Control for Bortezomib

tag: cell type


title: untreated control P7KPANIR  biological rep 3

description: P7KPANIR  biological rep 3

value: 129S4/SVJaeJ- C57/Bl6 Mixed

tag: atrx status

value: untreated control


title: WT_Rep1

source_name: WT_iPSC-derived megakaryocytes


title: 20 Gy 6 Days P7KP_6 biological rep 4

description: P7KP_6 biological rep 4

value: Soft Tissue Sarcoma

value: wild-type


title: 20 Gy 3 Days P7KPA_3 biological rep 2

description: P7KPA_3 biological rep 2

value: deleted

value: 20 Gy 3 Days


title: 20 Gy 6 Days P7KP_6 biological rep 3

description: P7KP_6 biological rep 3

value: 20 Gy 6 Days


title: 1384_11pw [RNA-Seq]

description: Prewound side of Volunteer #11

value: palatal gingival tissue


title: 20 Gy 6 Days P7KPA_6 biological rep 3

description: P7KPA_6 biological rep 3


title: 1372_04pw [RNA-Seq]

description: Prewound side of Volunteer #4

value: Heathy individual


title: Beclin 2 KO_Tumor_2

description: Beclin_2_KO_TumorvsWT_LN.DEG;Beclin_2_KO_TumorvsKO_LN.DEG

source_name: Lymphoma tissue

value: Lymphoma tissue

tag: stimulation

value: Beclin 2 KO


title: Lactacystin

value: Lactacystin (6 µM)


title: 1374_06pw [RNA-Seq]

description: Prewound side of Volunteer #6

value: Prewound side


title: WT_Rep3

value: CHOPWT6 iPSC

value: Wild type

value: iPSC-derived megakaryocytes


title: WT_Rep2


title: 20 Gy 6 Days P7KPA_6 biological rep 2

description: P7KPA_6 biological rep 2


title: Control for Lactacystin

value: MM.1S cells (ATCC #CRL-2974)

value: B lymphoblast

value: IgAλ myeloma

value: Female


title: 20 Gy 6 Days P7KP_6 biological rep 2

description: P7KP_6 biological rep 2

value: 129S4/SVJaeJ- C57/Bl6 Mixed

value: Soft Tissue Sarcoma

value: wild-type


title: Beclin 2 KO_Tumor_1


title: 1370_03pw [RNA-Seq]

description: Prewound side of Volunteer #3


title: Beclin 2 KO_LN_2

description: Beclin_2_KO_LNvsWT_LN.DEG;_Beclin_2_KO_TumorvsKO_LN.DEG

source_name: Lymph nodes

value: Lymph nodes


title: RNA-seq-h7.5.1-control, Huh7.5.1 cells, biological replicate 3

city: Shanghai

first: Menghuan

last: Zhang

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description:
TableS1_FPKM_RNAseq_count64
controlR3_FPKM & controlR3_count

data_processing:
discarding low-quality reads
trimming adapter sequence
removing ribosomal RNA(rRNA)
non-rRNA sequencing reads were aligned to human genomic reference (hg38) using HISAT2
The abundance of these transcripts in each sample was computed with StringTie and Ballgown
Genome_build: hg38
Supplementary_files_format_and_content: csv files report RPKM values for each Sample

source_name: Hepatoma cells

growth_protocol: cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Hyclone) supplemented with 10% fetal bovine serum (FBS) and 100 units/ml of penicillin-streptomycin (Gibco), in a humidified incubator supplemented with 5% CO2 at 37°C

extract_protocol:
For Ribo-seq, cellular RNA were extracted by mild lysis buffer and Lysates of a 10 cm dish reached 100% confluence were treated with 750 U RNase I for 45 minutes at room temperature. Samples were then transferred to an ultracentrifuge tube on a sucrose cushion (~34%) and centrifuged at 70,000 rpm at 4C for 4 hr.  For RNA-seq,total RNA of cells was extracted by Trizol according to manufacturer’s instructions, and then the RNA was poly-A-selected using NEBNext® Poly(A) mRNA Magnetic Isolation Module.
For Ribo-seq, Ribosome-protected fragments were purified using miRNeasy RNA isolation kit (QIAGEN, cat. No. 217004). RNA was size selected by running a polyacrylamide gel, and then dephosphorylated, linker ligated, and then subjected to RT-PCR, circularization, rRNA depletion, and 10-12 cycles of PCR. The enzymes used were T4 PNK (NEB, cat. No. M0201S), T4 RNA ligase 2, truncated (NEB, cat. No. M0242S), Universal miRNA Cloning Linker (NEB, cat. No. S1315S), Superscript III (Invitrogen, cat. No 18080-044), Circ Ligase (Epicentre, cat. No. CL4111K), NEBNext® High-Fidelity 2X PCR Master Mix (cat. No. M0541L). Resulting fragments were size selected from an 8% acrylamide non-denaturing gel and purified by incubation overnight with DNA gel extraction buffer (300 mM NaCl, 10 mM Tris (pH 8) and 1 mM EDTA).  For RNA-seq, Library preparation using Illumina TrueSeq mRNA sample preparation kit (Catalog IDs: RS-122-2001)

treatment_protocol: 2 µg/ml harringtonine for 120s, then 100µg/ml cycloheximide treatment.

value: Hepatoma cells

tag: passages

tag: infection

value: control

tag: sampling time

value: 72 hour post infection


title: RNA-seq-h7.5.1-control, Huh7.5.1 cells, biological replicate 2

description:
TableS1_FPKM_RNAseq_count64
controlR2_FPKM & controlR2_count


title: 20 Gy 3 Days P7KP_3 biological rep 1

description: P7KP_3 biological rep 1

value: 20 Gy 3 Days


title: 1366_01pw [RNA-Seq]

description: Prewound side of Volunteer #1

value: palatal gingival tissue

value: Heathy individual


title: untreated control P7KPANIR biological rep 2

description: P7KPANIR biological rep 2

value: deleted

value: untreated control


title: Beclin 2 KO_LN_1

value: Beclin 2 KO


title: WT_LN_2

description: Beclin_2_KO_LNvsWT_LN.DEG;_Beclin_2_KO_TumorvsWT_LN.DEG

value: Wild type


title: 20 Gy 3 Days P7KPA_3 biological rep 1

description: P7KPA_3 biological rep 1


title: 20 Gy 6 Days P7KP_6 biological rep 1

description: P7KP_6 biological rep 1

value: 20 Gy 6 Days


title: RNA-seq-h7.5.1-control, Huh7.5.1 cells, biological replicate 1

description:
TableS1_FPKM_RNAseq_count64
controlR1_FPKM & controlR1_count


title: WT_LN_1


title: 1379_09con [RNA-Seq]

description: control side of Volunteer #9

value: control side


title: RNA-seq-h7.5.1-HBV, Huh7.5.1 cells, biological replicate 2

description:
TableS1_FPKM_RNAseq_count64
HBVR2_FPKM & HBVR2_count

value: HBV


title: RNA-seq-h7.5.1-HBV, Huh7.5.1 cells, biological replicate 3

description:
TableS1_FPKM_RNAseq_count64
HBVR3_FPKM & HBVR3_count


title: 1377_08con [RNA-Seq]

description: control side of Volunteer #8


title: Beclin 2 KO_BMDM2

source_name: Primary bone marrow derived macophages

value: Primary bone marrow derived macophages

value: Stimulated by LPS (100 ng/ml) for 3 hours


title: untreated control P7KPNIR biological rep 2

description: P7KPNIR biological rep 2

value: 129S4/SVJaeJ- C57/Bl6 Mixed

value: Soft Tissue Sarcoma

value: wild-type


title: Beclin 2 KO_BMDM1


title: RNA-seq-h7.5.1-HBV, Huh7.5.1 cells, biological replicate 1

description:
TableS1_FPKM_RNAseq_count64
HBVR1_FPKM & HBVR1_count

value: Hepatoma cells


title: 1375_07con [RNA-Seq]

description: control side of Volunteer #7


title: 20 Gy 4 Hours P7KPA_4 biological rep 2

description: P7KPA_4 biological rep 2

value: 20 Gy 4 Hours


title: Ribo-seq-h7.5.1-control, Huh7.5.1 cells, biological replicate 3

description:
TableS2_FPKM_ribosome_count5
controlR3_FPKM & controlR3_count

data_processing:
Library strategy: Ribo-seq
discarding low-quality reads
trimming adapter sequence
removing ribosomal RNA(rRNA)
non-rRNA sequencing reads were aligned to human genomic reference (hg38) using HISAT2
The abundance of these transcripts in each sample was computed with StringTie and Ballgown
Genome_build: hg38
Supplementary_files_format_and_content: csv files report RPKM values for each Sample

value: control

value: 72 hour post infection


title: WT_BMDM2


title: 1368_02pw [RNA-Seq]

description: Prewound side of Volunteer #2

value: palatal gingival tissue

value: Heathy individual

value: Prewound side


title: 1373_06con [RNA-Seq]

description: control side of Volunteer #6


title: 20 Gy 4 Hours P7KPA_4 biological rep 1

description: P7KPA_4 biological rep 1

value: deleted


title: 1371_04con [RNA-Seq]

description: control side of Volunteer #4


title: Ribo-seq-h7.5.1-control, Huh7.5.1 cells, biological replicate 2

description:
TableS2_FPKM_ribosome_count5
controlR2_FPKM & controlR2_count


title: 1383_11con [RNA-Seq]

description: control side of Volunteer #11


title: Ribo-seq-h7.5.1-control, Huh7.5.1 cells, biological replicate 1

description:
TableS2_FPKM_ribosome_count5
controlR1_FPKM & controlR1_count


title: X5_GC

city: New York

first: Daylon

last: James

state: NY

address: 515 East 71st Street

institute: Weill Cornell Medicine

data_processing:
fastq files were processed using CellRangr count and individual libraries were aggregated using CellRangr aggr
Resultant features/barcodes file was imported into R Studio and used to generate a Seurat Object in Seurat
GSE146512_Ovary.scSeqsample.summary was utilized to alocate sample designations, source and other details
ManEtal_CellRangr_Aggregation.csv file was utilized to scaffold the CellRangr aggr function on individual sample preps
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered feature matrix and barcodes

source_name: human antral follicle derived cells

growth_protocol: cells were isolated from primary patient or xenograft derived ovarian follicles

extract_protocol:
cells were enzymatically separated and sorted by fluorescence activated cell sorting
RNA libraries were prepared for sequencing using version 3 10x Chromium library preparation kits; 10x Chromium version 3

value: granulosa cells

tag: source tissue

value: xenografted antral follicle

tag: follicle size


title: P8_GC

value: ovarian antral follicle

value: 2 mm


title: Ribo-seq-h7.5.1-HBV, Huh7.5.1 cells, biological replicate 3

description:
TableS2_FPKM_ribosome_count5
HBVR3_FPKM & HBVR3_count

value: HBV


title: 20 Gy 4 Hours P7KP_4 biological rep 1

description: P7KP_4 biological rep 1

tag: strain

tag: tissue


title: 1367_02con [RNA-Seq]

description: control side of Volunteer #2

value: control side


title: 1369_03con [RNA-Seq]

description: control side of Volunteer #3


title: P7_55

value: stromal cells

value: 3 mm


title: 1365_01con [RNA-Seq]

description: control side of Volunteer #1

extract_protocol:
Two biopsies in the form of free gingival grafts (FGG) were harvested in the same appointment from each volunteer, one from each side of the palate.One side is preqounded 5 days before harvesting.
cDNA libraries were constructed using Ion Ampliseq Transcriptome Human Gene Expression Kit  from Life Technologies (Cat# A26325) per the manufacturer's protocol, at the PrimBio Research Institute LLC (Exton, PA).  The amplified cDNA libraries were purified using Nucleic Acid binding beads, binding buffers and run on Agilent 2100 Bioanalyzer to determine the yield and size distribution of each library.For all the DNA libraries, further template amplification and enrichment were performed on the Ion Chef system followed by sequencing on an Ion Proton sequencer (PrimBio Research Institute LLC ,Exton, PA).


title: Ribo-seq-h7.5.1-HBV, Huh7.5.1 cells, biological replicate 2

description:
TableS2_FPKM_ribosome_count5
HBVR2_FPKM & HBVR2_count


title: untreated control P7KPNIR biological rep 1

description: P7KPNIR biological rep 1

value: 129S4/SVJaeJ- C57/Bl6 Mixed

value: Soft Tissue Sarcoma

value: wild-type

tag: treatment

value: untreated control


title: 20 Gy 6 Days P7KPA_6 biological rep 1

description: P7KPA_6 biological rep 1

value: 20 Gy 6 Days


title: Ribo-seq-h7.5.1-HBV, Huh7.5.1 cells, biological replicate 1

description:
TableS2_FPKM_ribosome_count5
HBVR1_FPKM & HBVR1_count

value: Hepatoma cells

value: 72 hour post infection


title: untreated control P7KPANIR biological rep 1

description: P7KPANIR biological rep 1


title: P6_55


title: 1384_11pw

description: Two biopsies in the form of free gingival grafts (FGG) were harvested in the same appointment from each volunteer, one from each side of the palate. One side is prewounded 5 days before harvesting.

data_processing:
IonTorrent software was used for base-calling.
The raw sequences were aligned to the human Hg19 build reference sequence by  Ion Torrent Suite alignment tool
Quality control was assessed by the StrandNGS program, which determined the pre- and post-alignment quality of the reads for each sample.
The aligned reads were normalized and quantified using the Quantile algorithm by the StrandNGS program.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and Quantile normalization values for all samples.

source_name: Prewound side of Volunteer #11

extract_protocol: libraries were constructed using Ion Ampliseq Transcriptome Human Gene Expression Kit (Cat#A26325; Thermo Fisher Scientific) per the manufacturer's protocol, at the PrimBio Research Institute LLC (Exton, PA, USA). Briefly, small RNA was enriched with the Total RNA-seq Kit v2 using manufactured recommended protocol.  5 ng small RNA was hybridized with Ion Adapters in a thermocycler for 10 minutes at 65⁰C and 5 minutes at 16⁰C.  Hybridized Small RNA was then incubated overnight at 16⁰C with ligation enzyme mix to ligate the Ion adapters.  The hybridized samples were then mixed with a reverse transcriptase master mix and incubated at 70⁰C for 10 minutes, snap cooled, and incubated 42⁰C for 30 minutes to generate cDNA libraries.  The purified cDNA libraries were then amplified by PCR using Platinum PCR Super-Mix High Fidelity and Ion Xpress RNA Barcode reverse and forward primers with the conditions as follows: Step 1: 94⁰C for 2 mins; Step 2: 94⁰C for 30 sec, 50⁰C for 30 sec, 68⁰C for 30 sec for 2 cycles; Step 3: 94⁰C for 30 sec, 62⁰C for 30 sec, 68⁰C for 30 sec for 14 cycles; Step 4: 68⁰C for 5 mins.

value: palatal gingival tissue

tag: disease state

value: Heathy individual


title: yvrE NoDMS

city: Cambridge

first: Gene-Wei

last: Li

state: MA

address: 31 Ames Street, 68-223A

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Library strategy: DMS-MaPseq
Built-in Illumina software was used for base calling.
Paired-end reads were filtered for quality and trimmed using FASTQC v.0.11.8 and TrimGalore 0.4.1, respectively. Processed reads were aligned to target sequences in the reference genome NC_000964.3 using Bowtie2 2.3.4.1 with the parameters ‘--local --no-unal --no-discordant --no-mixed -X 1000 -L 12’.
Mapped reads were converted to bit vectors and clustered by their mutational signatures using the DREEM algorithm with established parameters from Tomezsko et al., Nature, 2020.
Genome_build: NC_000964.3
Supplementary_files_format_and_content: Tab-delimited text files contain the population average mutational fractions for each sample. The per-base fractions of mismatches as well as mismatches and deletions were calculated from bit vectors.
Supplementary_files_format_and_content: Tab-delimited text files contain the DNA sequence and DMS signals for each sample. DMS signals were quantified as the mutation rates of the bases in the cluster K=1 following expectation-maximization (EM) clustering.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: planktonic cells

growth_protocol: BS168 cultures were grown to exponential phase (OD600≈0.2) in LB liquid media by back-diluting an overnight culture.

extract_protocol:
Thawed cell pellets were treated with lysozyme and total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate). Total RNA was extracted using hot acid-phenol:chloroform and isopropanol precipitation.
Libraries were prepared according to established protocols from Tomezsko et al., Nature, 2020 and Zubradt et al., Nature Methods, 2016. In brief, DNA was removed using TURBO DNase, RNA >200 nt was purified using an RNA Clean & Concentrator-5 Kit, ribosomal RNA was depleted using a MICROBExpress Bacterial mRNA Enrichment Kit, and RNA >200 nt was again purified in the same manner. For each sample, gene-specific reverse transcription was performed for ctc and yvrE using TGIRT-III. RNA was removed using RNase H and DNA was PCR amplified for 15-25 cycles. ~250 bp amplicons were purified by gel extraction and isopropanol precipitation. Samples with low DNA concentrations were reamplified for 7-20 additional cycles and purified in the same manner. Illumina adapters were added via PCR and libraries were sequenced on an Illumina MiSeq (2 x 250 nt reads) per the manufacturer’s instructions.

treatment_protocol: Two cultures were grown in parallel. After subjecting one of the two cultures to DMS (~5% final concentration) for 2 min, both cultures were treated with chilled stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), washed with chilled wash solution (30% β-mercaptoethanol), and frozen as cell pellets.

tag: genotype

value: untreated


title: untreated control WT_ctl biological rep 2

description: WT_ctl biological rep 2

value: Sarcoma Cell Line


title: 1380_09pw

source_name: Prewound side of Volunteer #9


title: yvrE DMS

value: treated with DMS for 2 min


title: P6_GC

value: granulosa cells

value: ovarian antral follicle


title: P5_GC

value: 5 mm


title: WT_BMDM1

value: Primary bone marrow derived macophages

value: Stimulated by LPS (100 ng/ml) for 3 hours

value: Wild type


title: 4 Gy 36 hours WT_IR biological rep 2

description: WT_IR biological rep 2

value: 4 Gy 36 hours


title: 1378_08pw

source_name: Prewound side of Volunteer #8


title: ISD 3 ug/ml 24 hours WT_ISD biological rep 2

description: WT_ISD biological rep 2

value: wild-type

value: ISD 3 ug/ml 24 hours


title: X3_GC

data_processing:
fastq files were processed using CellRangr count and individual libraries were aggregated using CellRangr aggr
Resultant features/barcodes file was imported into R Studio and used to generate a Seurat Object in Seurat
Ovary.scSeqsample.summary was utilized to alocate sample designations, source and other details
CellRangr Aggregation.csv file was utilized to scaffold the CellRangr aggr function on individual sample preps
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered feature matrix and barcodes

extract_protocol:
cells were enzymatically separated and sorted by fluorescence activated cell sorting
RNA libraries were prepared for sequencing using version 3 10x Chromium library preparation kits
10x Chromium version 3

value: xenografted antral follicle

value: 2 mm


title: 1376_07pw

source_name: Prewound side of Volunteer #7


title: ctc DMS


title: X3_39

value: stromal cells


title: 1374_06pw

source_name: Prewound side of Volunteer #6

value: palatal gingival tissue


title: 1372_04pw

source_name: Prewound side of Volunteer #4

value: Heathy individual


title: 1370_03pw

source_name: Prewound side of Volunteer #3


title: 4 Gy 36 hours KO_ISD  biological rep 2

description: KO_ISD  biological rep 2

value: knockout


title: untreated control KO_ISD  biological rep 2

description: KO_ISD  biological rep 2

value: Sarcoma Cell Line

value: untreated control


title: X4_GCNecLo

description: Lg-Nec-lo

value: granulosa cells

value: 3 mm


title: ISD 3 ug/ml 24 hours KO_ISD  biological rep 2

description: KO_ISD  biological rep 2


title: F.pr grown on fructose (sample2)

first: Chang Kyu

last: Yoon

state: Seoul

address: 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea

institute: Seoul National University

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.  For counting reads which mapped to each CDS, featureCounts was used. Retrieved counts were normalized and analyzed for identifying differentially expressed genes with DESeq2 .
Cleaned reads were mapped to the reference genome of F. prausnitzii A2-165, which is available in GenBank accession number PRJNA603249 using hisat2 with ‘--no-spliced-alignment’ parameter.
Genome_build: F. prausnitzii A2-165 (PRJNA603249)
Supplementary_files_format_and_content: DESeq2 normalized count excel file

organism: Faecalibacterium prausnitzii

growth_protocol: F. prausnitzii A2-165 cells cultured overnight were diluted 100-fold in 10 mL of fresh YCFA medium

extract_protocol:
After fixing the cells with the same volume of 100% methanol for 1 h at -20°C, total RNA was extracted using the phenol-chloroform extraction method; the isolated RNAs were further purified using the TaKaRa MiniBEST Universal RNA Extraction Kit (Takara Bio Inc.) according to the manufacturer’s instructions. One microgram of total RNA was processed to deplete the ribosomal RNA by using NEBNext rRNA Depletion Kit (Bacteria) (#E7850, NEB).
Sequencing libraries for RNA-seq were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (#E7770, NEB) following the manufacturer’s instructions. Sequencing was performed on an NextSeq 500 instrument (Illumina) by the manufacturer’s protocol that generated 76 bp paired-end reads for each sample.

treatment_protocol: Medium was treated with the indicated filter-sterilized carbon sources in 0.5% (w/v) final concentration and incubated at 37°C until OD600 reached 0.4 for galactose and glucose and 0.2 for fructose and NAG.

tag: cuture condition

value: YCFA medium + 0.5% fructose

value: Wild-type


title: 1368_02pw

source_name: Prewound side of Volunteer #2


title: X4_GCNecHi

description: Lg-Nec-hi


title: untreated control WT_ctl biological rep 1

description: WT_ctl biological rep 1


title: F.pr grown on fructose (sample1)

value: YCFA medium + 0.5%  fructose


title: 4 Gy 36 hours WT_IR biological rep 1

description: WT_IR biological rep 1


title: F.pr grown on NAG (sample1)

value: YCFA medium + 0.5%  NAG


title: 1366_01pw

source_name: Prewound side of Volunteer #1


title: ISD 3 ug/ml 24 hours WT_ISD biological rep 1

description: WT_ISD biological rep 1


title: F.pr grown on glucose (sample2)

value: YCFA medium + 0.5%  glucose


title: P4_GC

value: ovarian antral follicle

value: 4 mm


title: X4_GC

value: xenografted antral follicle


title: untreated control KO_ctl biological rep 1

description: KO_ctl biological rep 1


title: 1383_11con

source_name: control side of Volunteer #11


title: ctc NoDMS

value: wild-type

value: untreated


title: F.pr grown on glucose (sample1)

value: YCFA medium + 0.5% glucose


title: P4_Hem

value: hematopoietic cells


title: 1379_09con

source_name: control side of Volunteer #9

value: palatal gingival tissue

value: Heathy individual


title: X3_55

value: stromal cells

value: 2 mm


title: 4 Gy 36 hours KO_IR biological rep 1

description: KO_IR biological rep 1

value: Sarcoma Cell Line

value: knockout

value: 4 Gy 36 hours


title: F.pr grown on galactose (sample2)

value: YCFA medium + 0.5% galactose

value: Wild-type


title: P3_GC

value: granulosa cells

value: 3 mm


title: F.pr grown on NAG (sample2)

value: YCFA medium + 0.5%  NAG


title: P3_Hem

value: ovarian antral follicle


title: 1375_07con

source_name: control side of Volunteer #7


title: F.pr grown on galactose (sample1)


title: ISD 3 ug/ml 24 hours KO_ISD  biological rep 1

description: KO_ISD  biological rep 1

value: ISD 3 ug/ml 24 hours


title: P2_GC


title: 1377_08con

source_name: control side of Volunteer #8


title: NFb50 rep3

city: San Miguel de Tucumán

first: Mariana

last: Grillo-Puertas

state: Tucumán

address: Chacabuco 461

country: Argentina

institute: INSIBIO-CONICET

data_processing:
Sequences were trimmed, mapped and analyzed using CLC Genomics Workbench 7.5.1 (Qiagen) against the H. seropedicae SmR1 genome (NC_014323)
Reads were trimmed to minimum of 40 bp, 90% alignment to the reference sequence and 80% identity required for inclusion as a mapped read, number of hits equal to 1, number of additional bases down and upstream of the CDS equal to 50 bp
Genome_build: NC_014323
Supplementary_files_format_and_content: RPKM

organism: Herbaspirillum seropedicae

source_name: H. seropedicae NFb50 rep3

growth_protocol: H. seropedicae strain SmR1 was routinely grown at 30°C with 120 rpm in NFbHPN-malate medium supplemented with 80 µg ml-1 of streptomycin. NFbHPN contain 50 mM potassium phosphate buffer and was denoted here as NFb50 medium. Also, NFbHPN-malate was prepared with a reduced Pi concentration of 5 mM and defined as NFb5 medium

extract_protocol:
Bacterial samples were taken, and total RNA was isolated using TRI Reagent (Sigma) followed by chloroform extraction as recommended by the manufacturer. Samples were treated with DNaseI (Ambion) and the RNA was quantified with NanoDrop Spectrophotometer (THERMO Scientific) and gel electrophoresis. The ribosomal RNA was depleted using Ribo-Zero rRNA Removal Kit-Gram-Negative Bacteria (Illumina)
The whole transcriptome libraries were constructed using the Ion total RNA-seq Kit v2 (Thermo Fisher Scientific), barcode with Ion Xpress™ Barcode Adapters, following the manufacturer instructions. The libraries were amplified and enriched using the Ion PI Hi-QTM OT2 200 Kit, and sequenced with the Ion PI Hi-QTM Sequencing 200 kit on an Ion PITM Chip Kit v3

treatment_protocol: Three independent samples (biological replicates) of H. seropedicae SmR1 cells grown in NFb5 or NFb50 media after 9 h of growth were used to construct 6 sequencing libraries

value: H. seropedicae SmR1

tag: growth time

value: 9 h


title: B3: GL261 shPTEN_rep 3

city: Shenzhen

first: Ping

address: Gongchang Road

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastp (version 0.12.4) software was use to do reads filtering, including adapter removing, low quality base removing (lower than 20),et. al.
HISAT2 (version 2.1.0)software were used to do alignmnet with reference genome with bwa algorithm
Reads count mapping to each chromosome were calculated using HTSeq (0.10.0) software and FPKM was used to measure gene expression
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: GL261 shPTEN

extract_protocol:
Total RNA was extracted using Trizol reagent (invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quntity and purity were analyzed by Life Invitrogen Qubit® 3.0 and NanoDrop™.
RNA libraries were prepared for sequencing using standard illunima protocols

value: GL261 cells


title: NFb50 rep2

source_name: H. seropedicae NFb50 rep2


title: 1371_04con

source_name: control side of Volunteer #4

value: palatal gingival tissue


title: B2: GL261 shPTEN_rep 2


title: B1: GL261 shPTEN_rep 1


title: NFb50 rep1

source_name: H. seropedicae NFb50 rep1


title: A3: GL261 shNC_rep 2

source_name: GL261 shNC


title: 1369_03con

source_name: control side of Volunteer #3

value: Heathy individual


title: X2_GC

source_name: human antral follicle derived cells

value: xenografted antral follicle

value: 4 mm


title: X1_GC

value: 1 mm


title: 1367_02con

source_name: control side of Volunteer #2


title: NFb5 rep2

source_name: H. seropedicae NFb5 rep2


title: A2: GL261 shNC_rep 2


title: A1: GL261 shNC_rep 1


title: NFb5 rep1

source_name: H. seropedicae NFb5 rep1


title: X2_39

value: stromal cells


title: P1_GC

value: 2 mm


title: 1373_06con

source_name: control side of Volunteer #6


title: P2_Hem

value: hematopoietic cells


title: NFb5 rep3

source_name: H. seropedicae NFb5 rep3


title: H3K27Ac_24hpi_Rep2

status: Public on Mar 05 2021

city: Chicago

first: Mary

last: Hummel

state: IL

address: 303 E. Chicago Ave

institute: Northwestern University

description: ChIPseq

library_source: genomic

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using HOMER
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

organism: Human betaherpesvirus 5

growth_protocol: Kasumi-3 were grown in RPMI-1640 medium (ATCC 30-2001) supplemented with 20% fetal bovine serum (Corning) and 1,000 Units/ml Penicillin-Streptomycin (Gibco)

extract_protocol:
After fixation, cells were lysed and sonication with Covaris Focused-ultrasonicator at 10% Duty Cycle, 140 peak, 200 cycles per burst, 360 seconds. ChIP was performed by incubating the sonicated sample with either Rpb1 NTD (D8L4Y) Rabbit mAb #14958, Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173, or Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 (Cell Signaling Technologies) and the protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit.
Libraries were prepared with the KAPA HTP Library Preparation Kit multiplexed with NEXTflex DNA Barcodes (Bio Scientific) and size selected with AMPure XB beads (Beckman Coulter) to have fragments 250-450 bp in length. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequencing was performed with Illumina NextSeq technology (50bp single- end reads).

treatment_protocol: Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1. Extracellular virus was inactivated at 4 hours post infection. Cells were either collected and fixed  immediately (4hpi) or left in culture for additional 24 hours.

value: HCMV infected, 24 hr

tag: chip antibody

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies)

tag: cell line


title: H3K27me3_24hpi_Rep2

description: ChIPseq

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 (Cell Signaling Technologies)


title: Pol2_24hpi_Rep2

description: ChIPseq

value: Rpb1 NTD (D8L4Y) Rabbit mAb #14958 (Cell Signaling Technologies)


title: H3K27me3_24hpi_Rep1

description: ChIPseq


title: H3K27Ac_24hpi_Rep3

description: ChIPseq


title: input_24hpi_Rep1

description: ChIPseq


title: input_24hpi_Rep2

description: ChIPseq


title: input_24hpi_Rep3

description: ChIPseq


title: 24hr_K3_Unsorted_Rep2

description: RNA-seq

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: tab-delimited file with read counts per gene
Supplementary_files_format_and_content: bigWig files

source_name: Total RNA_infected K3 cells_24hpi

extract_protocol:
Infected Kasumi-3 cells were collected and lysed in Trizol. Total RNA was prepared using the Direct-zol RNA miniprep kit (Zymo Research) with an on-column DNase digestion step according to the manufacturer’s instructions.
RNA was rRNA depleted with Ribo-zero (Illumina) and RNA-seq libraries were prepared with TrueSeq Stranded mRNA (Illumina). RNA-seq libraries were sequenced on the Illumina NextSeq 500 Sequencing System (50 bp single-end reads, 50 million reads/sample)

treatment_protocol: Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1. Extracellular virus was inactivated at 4 hours post infection. At 4 hr post-infection, virus was inactivated and cells were either collected immediately (4hpi) or left in culture for additional 24 hours.

tag: rna type

value: total RNA


title: Pol2_24hpi_Rep1

description: ChIPseq


title: 1365_01con

source_name: control side of Volunteer #1


title: Pol2_24hpi_Rep3

description: ChIPseq


title: 24hr_K3_Unsorted_Rep3

description: RNA-seq


title: H3K27me3_24hpi_Rep3

description: ChIPseq


title: H3K27Ac_24hpi_Rep1

description: ChIPseq


title: RNA-gamma1-2h-R3.bam

city: Los Angeles

first: Quen

last: Cheng

state: CA

address: 611 Charles E Young Dr E

institute: UCLA

description: Mixed-timecourse-counts.txt

data_processing:
Samples were sequenced and base calls performed on Illumina NovaSeq 6000 (samples 50-60) and Illumina HiSeq 2500 (remaining samples)
Reads were trimmed of adapter sequences and low-quality reads (q<30), then mapped to mm10 genome with bowtie2 (ChIP) or STAR (RNA)
Aligned reads were filtered based on mapping score (MAPQ ≥ 30) by Samtools. For ChIP-seq, duplicated reads were removed using Picard MarkDuplicates.
For ChIP-seq, MACS2 version 2.1.0 was used to identify peaks for each sample using pooled input samples as control, FDR < 0.01, and extension size of average fragment length. These peaks were merged to generate a single reference peak file, and the number of reads that fell into each peak was counted using deeptools multiBigwigSummary with extension size of average fragment length
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq raw count tables are provided (unnormalized), generated by the featureCounts function in the Subread package.
Supplementary_files_format_and_content: ChIP-seq count tables are provided, normalized to sequencing depth by the multiBigWigSummary command from the deepTools package.

source_name: MLE12 cell line

growth_protocol: MLE-12 cells obtained from ATCC (Manassas, VA) were cultured in DMEM (Corning Inc., Corning, NY) supplemented with 10% FBS, 100 IU/ml penicillin, 100 𝜇g/ml streptomycin, 2 mM L-glutamine at 370C at 5% CO2.

extract_protocol:
STAT1 ChIP was performed on lysed and sonicated chromatin using rabbit anti-STAT1 (Cell Signaling Technologies, Danvers, MA; CST-9172). Total RNA was extracted by Trizol according to manufacturer's instructions.
Libraries were prepared according to manufacturer's instructions: ChIP-seq with NEBNext Ultra II DNA Library Prep Kit (New England Biolabs E7645), RNA-seq samples 50-60 with Illumina TruSeq mRNA kit (Illumina), and for remaining RNA-seq samples KAPA Stranded mRNA-seq Library Preparation kit (KAPA Biosystems)

treatment_protocol: Recombinant murine IFN-b (PBL Assay Science, Piscataway, NJ) and IFN-γ (BD Biosciences, San Jose, CA) were used for stimulation.

tag: replicate

tag: assay

value: mRNA-seq

tag: stimulus

value: IFN-gamma (1 ng/ml)

tag: timepoint

tag: column header


title: RNA-beta1-3h-R3.bam

description: Mixed-timecourse-counts.txt

value: IFN-Beta (1 U/ml)


title: RNA-gamma1-6h-R3.bam

description: Mixed-timecourse-counts.txt


title: RNA-mix-4h-R3.bam

description: Mixed-timecourse-counts.txt

value: IFN-Beta (1 U/ml) + IFN-gamma (1 ng/ml)


title: RNA-beta1-6h-R3.bam

description: Mixed-timecourse-counts.txt


title: RNA-mix-6h-R3.bam

description: Mixed-timecourse-counts.txt


title: RNA-beta1-2h-R3.bam

description: Mixed-timecourse-counts.txt


title: RNA-gamma100-12h.bam

description: RNAseq-timecourse-counts.txt

value: IFN-gamma (100 U/ml)


title: RNA-mix-2h-R3.bam

description: Mixed-timecourse-counts.txt


title: RNA-gamma1-4h-R3.bam

description: Mixed-timecourse-counts.txt


title: 24hr_K3_Unsorted_Rep1

description: RNA-seq


title: RNA-mix-3h-R3.bam

description: Mixed-timecourse-counts.txt


title: RNA-gamma1-3h-R3.bam

description: Mixed-timecourse-counts.txt


title: RNA-unstim-mixedtimecourse.bam

description: Mixed-timecourse-counts.txt


title: RNA-gamma100-8h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-gamma100-4h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-gamma100-2.bam

description: RNAseq-timecourse-counts.txt


title: RNA-gamma100-0.5h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-gamma100-0h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-gamma100-1h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta100-12h.bam

description: RNAseq-timecourse-counts.txt

value: IFN-Beta  (100 U/ml)


title: RNA-beta100-8h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta100-2h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta100-4h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta100-1h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta100-0.5h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-8h-R2.bam

description: RNAseq-timecourse-counts.txt

value: IFN-Beta (10 U/ml)


title: RNA-beta10-6h-R2.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-3h-R2.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-2h-R2.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-1h-R2.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-0.5h-R2.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-4h-R1.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-8h-R1.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-0.5h-R1.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-12h-R1.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-1h-R1.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-0h-R1.bam

description: RNAseq-timecourse-counts.txt


title: ChIP-beta10-chx-01.bam

description: CHXandLowBeta.csv

value: STAT1 ChIP-seq

value: IFN-Beta (10 U/ml) + cycloheximide


title: ChIP-beta10-chx-04.bam

description: CHXandLowBeta.csv


title: RNA-beta100-0h.bam

description: RNAseq-timecourse-counts.txt


title: RNA-beta10-12h-R2.bam

description: RNAseq-timecourse-counts.txt


title: ChIP-beta1-01-R1.bam

description: CHXandLowBeta.csv


title: ChIP-beta1-04-R1.bam

description: CHXandLowBeta.csv


title: ChIP-beta10-12-R1.bam


title: ChIP-beta10-08-R1.bam


title: ChIP-beta10-04-R2.bam


title: RNA-beta10-4h-R2.bam

description: RNAseq-timecourse-counts.txt


title: ChIP-beta10-005-R1.bam


title: ChIP-beta10-01-R1.bam


title: RNA-beta10-2h-R1.bam

description: RNAseq-timecourse-counts.txt


title: ChIP-beta10-005-R2.bam


title: RNA-beta10-0h-R2.bam

description: RNAseq-timecourse-counts.txt


title: ChIP-unstim-R1.bam


title: ChIP-beta10-02-R1.bam


title: ChIP-Input-R2.bam

value: pooled input

value: (not in count table)


title: ChIP-Input-R1.bam


title: sh-Nup210 # 4 replicate 1

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
[RNA-seq]  mRNA samples were pooled and sequenced on HiSeq2500 with Illumina TruSeq V4 chemistry. The samples have yields between 60 to 95 million reads. Pass filter reads with base call quality of Q30 or above are 94% or higher for all samples. Both reads of the samples were trimmed for adapters and low quality bases using Trimmomatic software. Total (primary) alignment with the reference genome (mm9) is above 87% with the STAR aligner. RNA mapping statistics are calculated using Picard software. The samples have less than 2% ribosomal reads. Percent coding bases are between 59-61% and there are 83-86% mRNA bases. Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples have above 77% non-duplicated reads.
[ChIP-seq]  ChIP samples were pooled and sequenced on Nextseq run using TrueSeq v2 chemistry single end sequencing. All the samples have percent of Q30 bases above 92%. All the samples have yields between 37  and 100 million pass filter reads. Samples were trimmed for adapters using trimmomatic software before the alignment. The trimmed reads were aligned with Mouse - mm10 reference using Bowtie2 alignment. Overall alignment percentage for the samples is 88%. Uniquel alignment is above 53%. There are 2 to 24% of unmapped reads. Library complexity is measured by uniquely aligned reads using picard’s markduplicate utility. All the samples have library complexity with percent non-duplicated reads ranging from 17 to 86%.
Genome_build: mouse mm10 for Chipseq, mm9_ensembl_ncbim37 for RNAseq
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample or peak in bed file.

growth_protocol: 4T1 cells are grown in DMEM containing 9% fetal bovine serum, 1% penicillin/streptomycin and1% L-glutamine.

extract_protocol:
[RNA-seq]  Total RNA was isolated from 4T1 cells using RNeasy mini kit (Qiagen) according to manufacturer's instructions
[ChIP-seq]  Chromatin was extracted from 4T1 cells using ChIP-IT Express Enzymatic Shearing kit (Active Motif) according to manufacturer's instructions.
[RNA-seq]   Library was prepared using TruSeq stranded mRNA library prep kit (Illumina).
[ChIP-seq]   Library was prepared using TruSeq ChIP library prep kit (Illumina).

tag: tumor type

value: Spontaneous mammary primary tumor

value: BALB/cJ

tag: mouse id

value: Jackson Laboratory # 000651

value: Nup210 shRNA knockdown biological replicate 1


title: Pharma_KT_Paclitaxel+Trametinib+Carbo_Tumors

city: Stanford

first: Chuan

address: 327 Campus Drive

institute: Stanford University

data_processing:
Each read is expected to contain an 8-nucleotide sgID region followed by a 23-nucleotide barcode (BC) region (AANNNNNTTNNNNNAANNNNNAT), and each of the 15 Ns represent random nucleotides with roughly equal representation of A, T, G and C.
The sgID region identifies the putative tumour suppressor gene being targeted, for which we require perfect match between the sequence in the forward read and one of the 15 sgIDs with known sequences.
We require the forward and reverse read to agree completely within the 23 nucleotide sequence to be further processed. Any “tumours” that are within a Hamming distance of two from a larger tumour is assigned as “spurious tumours”, which are likely to be resulting from sequencing or PCR error, and are removed from subsequent analysis.
The tumour size (number of neoplastic cells) is calculated by normalizing the number of reads to the three benchmarks “spike-in” cell lines (5x10^5 cells for each benchmark cell line) added to each sample prior to lysis of the lung and DNA extraction step.
Supplementary_files_format_and_content: Txt files showing the tumor sgRNA, barcode and tumor size for each identified tumor.

source_name: Paclitaxel+Trametinib+Carbo-treated tumors in the Cas9-negative KT mice experiment

growth_protocol: All experiments were performed in accordance with Stanford University Institutional Animal Care and Use Committee guidelines.

extract_protocol:
Genomic DNA was isolated from bulk tumour-bearing lung tissue from each mouse. Three cell lines with a defined sgID-BC added at 5x10^5 cell/sample were added to each mouse lung sample prior to lysis to enable the calculation of the absolute number of neoplastic cells in each tumour from the number of sgID-BC reads.
Q5 High-Fidelity 2x Master Mix was used to amplify the sgID-BC region from 32 µg of genomic DNA using unique dual-indexed primers.

treatment_protocol: Lung tumors were initiated using a pool of barcoded Lentiviral-sgRNA/Cre vectors delivered by intratracheal transduction of mice. 1.1 x 10^5 and 2.2 x 10^4 infectious particles in 60 μl of PBS were administered to each KT and KT;Cas9 mouse, respectively.

tag: mouse genotype

value: KT

tag: viral pool

value: Lenti-sgTSPool/Cre

tag: weeks after tumor initiation

value: tumour-bearing lung tissue

tag: cell type

value: Lung epithelial cell


title: sh-Ctrl replicate 1

tag: strain

tag: treatment

value: shRNA scramble control biological replicate 1


title: sh-Nup210 # 4 replicate 2

value: Nup210 shRNA knockdown biological replicate 2


title: ChIP-beta10-08-R2.bam


title: Pharma_Repeat_Palbociclib_Tumors

source_name: Palbociclib-treated tumors in the repeat experiment

tag: tissue


title: sh-Ctrl replicate 2

value: shRNA scramble control biological replicate 2


title: Pharma_Repeat_Untreated_Tumors

source_name: Untreated tumors in the repeat experiment


title: Pharma_Mapping_Paclitaxel+Trametinib+Carbo_Tumors

source_name: Paclitaxel+Trametinib+Carbo-treated tumors in the main pharmacogenomic mapping experiment


title: Pharma_KT_Untreated_Tumors

source_name: Untreated tumors in the Cas9-negative KT mice experiment


title: Pharma_Mapping_Paclitaxel_Tumors

source_name: Paclitaxel-treated tumors in the main pharmacogenomic mapping experiment


title: ChIP-beta10-12-R2.bam


title: Pharma_Mapping_Phenformin_Tumors

source_name: Phenformin-treated tumors in the main pharmacogenomic mapping experiment


title: Pharma_Mapping_Everolimus_Tumors

source_name: Everolimus-treated tumors in the main pharmacogenomic mapping experiment


title: Pharma_Mapping_Paclitaxel+Carbo_Tumors

source_name: Paclitaxel+Carbo-treated tumors in the main pharmacogenomic mapping experiment


title: Pharma_Mapping_Trametinib_Tumors

source_name: Trametinib-treated tumors in the main pharmacogenomic mapping experiment


title: Pharma_Mapping_Paclitaxel+Trametinib_Tumors

source_name: Paclitaxel+Trametinib-treated tumors in the main pharmacogenomic mapping experiment


title: ChIP-beta10-04-R1.bam


title: Pharma_Mapping_Untreated_Tumors

source_name: Untreated tumors in the main pharmacogenomic mapping experiment


title: Lyz2Cre:Hif1a Fl/Fl-IL10-3

city: Cleveland

first: Ernest

middle: R

last: Chan

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

description:
CB9_HIF1a-KO-IL10_3_S9
processed data file: genes.read_group_tracking_IL10.txt

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

source_name: Lyz2Cre:Hif1a Fl/Fl-IL10_BMDMs

extract_protocol:
Total RNA was isolated from indicated samples using the High Pure RNA Isolation Kit.
100bp single-end on pooled libraries; Illumina TruSeq Stranded Total RNA kit

tag: strain background

tag: genotype/variation

tag: age

value: Postnatal week 10

value: bone marrow

value: BMDMs

value: 10ng/ml IL10 for 18 hours


title: Lyz2Cre-IL10-2

description:
CB23_WILD-TYPE-IL10_2_S23
processed data file: genes.read_group_tracking_IL10.txt


title: Lyz2Cre-IL10-3

description:
CB24_WILD-TYPE-IL10_3_S24
processed data file: genes.read_group_tracking_IL10.txt


title: Lyz2Cre:Hif1a Fl/Fl-IL10-1

description:
CB7_HIF1a-KO-IL10_1_S7
processed data file: genes.read_group_tracking_IL10.txt


title: Lyz2Cre:Hif1a Fl/Fl-IL10-2

description:
CB8_HIF1a-KO-IL10_2_S8
processed data file: genes.read_group_tracking_IL10.txt


title: Lyz2Cre:Hif1a Fl/Fl-IL4-3

description:
CB12_HIF1a-KO-IL4_3_S12
processed data file: genes.read_group_tracking_IL4.txt

source_name: Lyz2Cre:Hif1a Fl/Fl-IL4_BMDMs

value: 10ng/ml IL4 for 18 hours


title: Lyz2Cre-IL10-1

description:
CB22_WILD-TYPE-IL10_1_S22
processed data file: genes.read_group_tracking_IL10.txt


title: Lyz2Cre:Hif1a Fl/Fl-IL4-2

description:
CB11_HIF1a-KO-IL4_2_S11
processed data file: genes.read_group_tracking_IL4.txt


title: Lyz2Cre-IL4-3

description:
CB27_WILD-TYPE-IL4_3_S27
processed data file: genes.read_group_tracking_IL4.txt


title: Lyz2Cre:Hif1a Fl/Fl-gamma-3

description:
CB6_HIF1a-KO-IFNg_3_S6
processed data file: genes.read_group_tracking_IFG.txt

source_name: Lyz2Cre:Hif1a Fl/Fl-gamma_BMDMs

value: 10ng/ml IFNgamma for 18 hours


title: Lyz2Cre:Hif1a Fl/Fl-gamma-2

description:
CB5_HIF1a-KO-IFNg_2_S5
processed data file: genes.read_group_tracking_IFG.txt


title: Lyz2Cre-IL4-1

description:
CB25_WILD-TYPE-IL4_1_S25
processed data file: genes.read_group_tracking_IL4.txt


title: Lyz2Cre-IFNgamma-1

description:
CB19_WILD-TYPE-IFNg_1_S19
processed data file: genes.read_group_tracking_IFG.txt


title: Pharma_Mapping_Palbociclib_Tumors

source_name: Palbociclib-treated tumors in the main pharmacogenomic mapping experiment


title: Lyz2Cre-IFNgamma-2

description:
CB20_WILD-TYPE-IFNg_2_S20
processed data file: genes.read_group_tracking_IFG.txt


title: Lyz2Cre:Hif1a Fl/Fl-gamma-1

description:
CB4_HIF1a-KO-IFNg_1_S4
processed data file: genes.read_group_tracking_IFG.txt


title: Lyz2Cre-LPS-3

description:
CB30_WILD-TYPE-LPS_3_S30
processed data file: genes.read_group_tracking_LPS.txt

value: 100ng/ml LPS for 18 hours


title: Lyz2Cre:Hif1a Fl/Fl-LPS-1

description:
CB13_HIF1a-KO-LPS_1_S13
processed data file: genes.read_group_tracking_LPS.txt

source_name: Lyz2Cre:Hif1a Fl/Fl-LPS_BMDMs


title: Lyz2Cre-LPS-1

description:
CB28_WILD-TYPE-LPS_1_S28
processed data file: genes.read_group_tracking_LPS.txt


title: Lyz2Cre:Hif1a Fl/Fl-Control-2

description:
CB2_HIF1a-KO-CONTROL_2_S2
processed data file: genes.read_group_tracking_Control.txt

source_name: Lyz2Cre:Hif1a Fl/Fl-Control_BMDMs

value: control


title: Lyz2Cre:Hif1a Fl/Fl-Control-1

description:
CB1_HIF1a-KO-CONTROL_1_S1
processed data file: genes.read_group_tracking_Control.txt


title: Lyz2Cre-IFNgamma-3

description:
CB21_WILD-TYPE-IFNg_3_S21
processed data file: genes.read_group_tracking_IFG.txt


title: Lyz2Cre:Hif1a Fl/Fl-LPS-3

description:
CB15_HIF1a-KO-LPS_3_S15
processed data file: genes.read_group_tracking_LPS.txt


title: Lyz2Cre:Hif1a Fl/Fl-LPS-2

description:
CB14_HIF1a-KO-LPS_2_S14
processed data file: genes.read_group_tracking_LPS.txt


title: Lyz2Cre-Control-3

description:
CB18_WILD-TYPE-CONTROL_3_S18
processed data file: genes.read_group_tracking_Control.txt


title: Lyz2Cre-LPS-2

description:
CB29_WILD-TYPE-LPS_2_S29
processed data file: genes.read_group_tracking_LPS.txt


title: Lyz2Cre-Control-1

description:
CB16_WILD-TYPE-CONTROL_1_S16
processed data file: genes.read_group_tracking_Control.txt


title: Lyz2Cre:Hif1a Fl/Fl-IL4-1

description:
CB10_HIF1a-KO-IL4_1_S10
processed data file: genes.read_group_tracking_IL4.txt


title: H69EZ_HLA+_rep 1

city: Boston

first: Michael

last: Tolstorukov

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Raw sequencing data were aligned to hg19 version of the human genome or mm10 version of the mouse genome with Star aligner (v. 2.6.1).
Viper RNA-seq processing pipeline (Cornwell et al., 2018; PMID: 29649993) was used to generate normalized expression values.
Genome_build: hg19; mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: H69EZ cell line

growth_protocol: RPP-A cells were derived from RPP cells after selection for adherent cell growth on tissue-culture treated plastic cell culture dishes.

extract_protocol:
RNA was isolated  the Qiagen RNeasy isolation kit (Cat# 8028). RNA libraries were prepared from 250 ng total RNA.
RNA libraries were constructed using the Illumina Exome Capture kit per manufacturer’s instructions. RNA-sequencing (RNA-seq) was performed per the standard protocols at the Dana-Farber Molecular Biology Core Facilities with Illumina NextSeq 500 instrument.

treatment_protocol: H69M cells were derived from H69 cells as in Canadas et al. 2014 (PMID 24284055). H69EZ cells were derived from H69 cells after transient (6 day) EZH2 inhibitor exposure, and continued routine culture without inhibitor, with selection for adherent populations on tissue-culture treated plastic cell culture dishes.

tag: mhc class i status

value: high

tag: sorted population

value: HLA-ABC high


title: H69EZ_HLA-_rep 1

value: low/neg

value: HLA-ABC low/neg


title: H69EZ_HLA-_rep 2


title: wildtype

first: Man-Wook

last: Hur

address: 134 ShinChon-Dong, SeoDaeMoon-Ku

department: Department of Biochemistry and Molecular Biology and the Institute of Genetic Sciences

institute: Yonsei University School of Medicine

description: C57BL/6 Kaiso WT mice testis genomic DNA bound by MBD2 protein

data_processing:
Raw reads of paired end sequences were aligned to mouse reference genome (mm10) with bowtie2 (v2.2.6) with default options.
MeDIPs (v1.16) was performed to gain RMS (relative methylation score) with the window size 100.
During MeDIPs process, “MEDIPS.meth” function was used with the following options, CNV=F, diff.method=”edgeR”, p.adj=”none”, while “MEDIPS.selectSig” was performed with default options.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files includes counts and RPKM values for each sample

source_name: Dr. Alan Clarke

extract_protocol:
gDNA (1 µg) was sheared using a Covaris LE220 sonicator (Covaris Inc., Woburn, MA) to obtain 200-400 bp fragments. The fragmented products were immunoprecipitated using a MethylMiner Methylated DNA Enrichment Kit (Invitrogen, CA), according to the manufacturer's recommended protocol. Briefly, methylated DNA was isolated from fragmented whole genomic DNA by inducing it to bind to the methyl-CpG binding domain of mouse MBD2 protein coupled to paramagnetic Dynabeads labeled with M-280 streptavidin, via a biotin linker. The methylated fragments were eluted as a single enriched population using a 2, 000 mM NaCl elution buffer.
The methylated dsDNA was end-repaired to the 3' end, Illumina adapters were ligated to the fragments, and a sample size was selected. The goal was to obtain 300-to 500-bp products. The size-selected products were PCR-amplified, and the final products were validated using an Agilent Bioanalyzer. Sequencing was performed using an Illumina HiSeq 2500

tag: phenotype

value: wildtype

tag: genotype

tag: background strain

value: testis


title: Kaiso knockout

description: C57BL/6 Kaiso WT mice testis isolated from C57BL/6 Kaiso knockout mice mice

value: generation 3 offspring, male sterile

value: Kaiso KO


title: Lyz2Cre-IL4-2

description:
CB26_WILD-TYPE-IL4_2_S26
processed data file: genes.read_group_tracking_IL4.txt


title: H69M_PDL1+_rep 2

source_name: H69M cell line

value: PD-L1 high


title: H69M_PDL1+_rep 1


title: Lyz2Cre:Hif1a Fl/Fl-Control-3

description:
CB3_HIF1a-KO-CONTROL_3_S3
processed data file: genes.read_group_tracking_Control.txt

value: Postnatal week 10


title: H69M_PDL1-_rep 1

value: PD-L1 low/neg


title: H69M_PDL1-_rep 3


title: H69M_rep 3


title: H69_rep 2

source_name: NCI_H69 cell line


title: H69M_rep 1


title: H69M_rep 2


title: Lyz2Cre-Control-2

description:
CB17_WILD-TYPE-CONTROL_2_S17
processed data file: genes.read_group_tracking_Control.txt

value: bone marrow

value: BMDMs


title: H69M_PDL1-_rep 2


title: H69_rep 3


title: H69M_PDL1+_rep 3


title: H69_rep 1


title: H69EZ_HLA+_rep 2


title: AdCa-1

city: Utrecht

first: Kadi

last: Lõhmussaar

state: -- Select State/Province --

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer's protocol including DNaseI treatment. The libraries were prepared by the Utrecht Sequencing Facility (USEQ) based on polyA enrichment.
Cervix_allmerged_single-end.xlsx

data_processing:
Single- or paired-end reads from Illumina sequencing were aligned to the human transcriptome genome by BWA (v0.5.9)
DESeq2 (v1.18.0) was used for read normalization and differential expression analysis.
Viral transcripts were detected by using VirusSeq-CLI, a wrapper around the VirusSeq pipeline.
Genome_build: GRCh37
Supplementary_files_format_and_content: The data are in xlsx format. The table contains unnormalized counts.

source_name: Cervical adenocarcinoma organoids (early passage)

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer's protocol including DNaseI treatment.
Libraries were prepared by the Utrecht Sequencing Facility (USEQ) based on polyA enrichment, and sequenced on an Illumina NextSeq500 using 75bp single-end or paired-end sequencing.

tag: origin

value: Pap brush

tag: type

value: tumor organoid line

value: single-end seq


title: SqCa-4 (early passage - single-end seq)

source_name: Cervical squamous cell carcinoma organoids (early passage)


title: SqCa-1.2p (early passage - paired-end seq)

description:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer's protocol including DNaseI treatment. The libraries were prepared by the Utrecht Sequencing Facility (USEQ) based on polyA enrichment.
Cervix_allmerged_PAIRED-end.xlsx

value: paired-end seq


title: SqCa-4 (late passage - single-end seq)

source_name: Cervical squamous cell carcinoma organoids (late passage)


title: SqCa-5 (early passage - single-end seq)


title: SqCa-7


title: SqCa-5 (late passage - single-end seq)


title: SqCa-6


title: SqCa-5p (early passage - paired-end seq)


title: SqCa-4p (early passage - paired-end seq)


title: SqCa-3p


title: C-SqCa-2p

source_name: Cervical CIN1 organoids (early passage)

value: cervical CIN1 organoid line


title: SqCa-1.2 (early passage - single-end seq)


title: SqCa-1.2 (late passage - single-end seq)


title: SqCa-1.1p


title: TT-2

source_name: Cervical squamous cell carcinoma primary tumor tissue (TT)

value: tumor tissue


title: TT-3


title: TT-1


title: EndoO3 (late passage)

source_name: Endocervical org. (late passage)

value: Endocervix

value: healthy organoid line


title: EndoO2 (late passage)


title: EndoO2 (early passage)

source_name: Endocervical org. (early passage)


title: EndoO3 (early passage)


title: EndoO1 (early passage)


title: EndoO1 (late passage)


title: EndoT3

source_name: Endocervix tissue

value: healthy tissue


title: EndoT2


title: EndoT1


title: EctoO2 (late passage)

source_name: Ectocervical org. (late passage)

value: Ectocervix


title: EctoO3 (late passage)


title: EctoO1 (late passage)


title: EctoO3 (early passage)

source_name: Ectocervical org. (early passage)


title: EctoO1 (early passage)


title: EctoO2 (early passage)


title: EctoT3 (also NT-3)

source_name: Ectocervix tissue (normal tissue = NT)


title: EctoT2 (also NT-2)


title: EctoT1 (also NT-1)


title: 665X_d42_young_cDNA190916_H9

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina NextSeq 500 platform.
Demultiplexed fastq reads were trimmed with trimgalore (v0.6.6, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), using default parameters.
Trimmed reads were mapped to Ensembl build GRCh38.87 using HISAT2 (v2.1.0) with the options --sp 1000,1000.
Aligned reads were quantified using featureCounts, as implemented in Rsubread (Subread v2.0.0).
Downstream analyses were performed using Bioconductor packages: scater and the SingleCellExperiment data infrastructure.
Genome_build: GRCh38
Supplementary_files_format_and_content: GEO_supporting_processed_data_file_raw_count_matrix.csv.gz - the Rsubread count matrix as a gzipped comma separated values file.

source_name: Haemagglutinin specific B cell

extract_protocol:
Index sorting of haemagluttin (HA) specific B cells was performed with samples from days 0 and 42. B cells were negatively selected magnetically from cryopreserved peripheral blood mononuclear cells, after 1 hour rest at 37C. Individual HA specific B cells were isolated using FACS and fluorescently labelled recombinant haemagglutinin. Sorts were performed into 96 well plates.
Single HA specific B cells were index sorted in RNA lysis buffer, and samples were processed using plate-based SMART-Seq (SMART-Seq HT kit, Takara-Clontech). cDNA libraries were generated using Nextera XT adaptors, following the Takara-Clontech HT kit instructions. After library creation, libraries were pooled for clean-up.
scRNASeq (SMART-Seq) of haemagglutinin specific B cell flow sorted from PBMC

tag: treament

value: trivalent influenza vaccination

tag: time

value: day 42

value: PBMC

tag: cell type_sorted

value: haemagglutinin specific B cell


title: 665X_d42_young_cDNA190916_H6

tag: cell type


title: 665X_d42_young_cDNA190916_H4


title: 665X_d42_young_cDNA190916_H12


title: 665X_d42_young_cDNA190916_H11


title: 665X_d42_young_cDNA190916_H10


title: 665X_d42_young_cDNA190916_H5


title: 665X_d42_young_cDNA190916_H1


title: 665X_d42_young_cDNA190916_H3


title: 665X_d42_young_cDNA190916_G9


title: 665X_d42_young_cDNA190916_G6


title: 665X_d42_young_cDNA190916_H2


title: 665X_d42_young_cDNA190916_G5


title: 665X_d42_young_cDNA190916_G1


title: 665X_d42_young_cDNA190916_G2


title: 665X_d42_young_cDNA190916_G11


title: 665X_d42_young_cDNA190916_G3


title: 665X_d42_young_cDNA190916_G12


title: 665X_d42_young_cDNA190916_G10


title: 665X_d42_young_cDNA190916_F9


title: 665X_d42_young_cDNA190916_F4


title: 665X_d42_young_cDNA190916_F6


title: 665X_d42_young_cDNA190916_F5


title: 665X_d42_young_cDNA190916_F10


title: 665X_d42_young_cDNA190916_F1


title: 665X_d42_young_cDNA190916_F12


title: 665X_d42_young_cDNA190916_F3


title: 665X_d42_young_cDNA190916_F11


title: 665X_d42_young_cDNA190916_F2


title: 665X_d42_young_cDNA190916_G4


title: 665X_d42_young_cDNA190916_E9


title: 665X_d42_young_cDNA190916_E11


title: 665X_d42_young_cDNA190916_E3


title: 665X_d42_young_cDNA190916_D6


title: 665X_d42_young_cDNA190916_E12


title: 665X_d42_young_cDNA190916_E1


title: 665X_d42_young_cDNA190916_E2


title: 665X_d42_young_cDNA190916_D5


title: 665X_d42_young_cDNA190916_D2


title: 665X_d42_young_cDNA190916_D4


title: 665X_d42_young_cDNA190916_D1


title: 665X_d42_young_cDNA190916_D12