title: WAPL/PDS5A/PDS5B RNAi R1

first: Michiel

middle: Johannes

last: Thiecke

state: Cambridgeshire

address: Babraham Hall

department: Nuclear dynamics

institute: Babraham research institute

description: PCHiC

data_processing:
QC: FastQC & FastQscreen
Pre-processing: HiCUP
Processing: ChiCAGO
Genome_build: GRCh37
Supplementary_files_format_and_content: .Rds serialized R objects

source_name: HeLa RNAi

growth_protocol: Cells were cultured at 37 degrees C in suspension in DMEM supplemented with 10% FCS, glutamate and penicillin-streptavidin

extract_protocol:
HindIII-based Hi-C libraries were captured using SureSelect target enrichment system, using a custom-designed RNA bait library and paired-end blockers. Promoter-based ligated products were isolated and amplified
PCHiC libraries were constructed using HindIII as described in (Schoenfelder et al. 2018 and Wutz et al. 2017).
PCHiC

treatment_protocol: SCC1 and CTCF depleted cells were treated with Auxin, G1 and G2 cells were synchronised with thymidine, Mitotic cells were synchronised with nocodazole, RNAi samples were treated simultaneously with appropriate shRNAs for WAPL, PDS5A and PDS5B

value: Kyoto

tag: type

value: Triple RNAi

tag: treatment

value: treatment


title: WAPL/PDS5A/PDS5B RNAi R2

status: Public on Jul 13 2020

type: SRA

city: Cambridge

country: United Kingdom

description: PCHiC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: strain


title: female hypoxia cervical cord replicate 3 [FHV_S33]

city: Madison

first: Andrea

middle: C

last: Ewald

state: WI

address: 2015 Linden Dr

department: Comparative Biomedical Sciences

country: USA

institute: University of Wisconsin - Madison

library_source: transcriptomic

data_processing:
Base calls made using Illumina 1.9 Software
Alignment made using Tophat v2.1
Raw counts generated using htseq-count --stranded reverse option
Filtered and normalized using EdgeR
GLM applied to count data and tagwise LRT performed using EdgeR
Differential expression calculated using decideTestDGE(lrt) in EdgeR
Genome_build: rn6
Supplementary_files_format_and_content: tab delimited txt files with raw counts

molecule: total RNA

organism: Rattus norvegicus

source_name: female hypoxia cervical cord

growth_protocol: Pregnant dams were exposed to intermittent normoxia or intermittent hypoxia from G10-G21. Pups were born under normal housing conditions and allowed to grow to 8 weeks.

extract_protocol:
Microglia were immunomagentically isolated using Miltenyi anti-cd11b antibody. Microglia were lysed in trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Intermittent exposures consisted of 8 hours of exposure per day, with 15 cycles per hour. Normoxia exposures consisted of room air (21%/21% O2), while hypoxia exposures consisted of alternating 10.5%/21% O2. After G21 exposure, mothers were allowed to birth under normal housing conditions. Offspring were grown to 8 weeks under normal housing conditions.

value: sprague dawley

tag: Sex

value: female

tag: air treatment

value: hypoxia

tag: tissue

value: C3-C6 spinal cord

tag: cell type

value: C3-C6 spinal cord microglia


title: female hypoxia cervical cord replicate 2 [FHV_S32]


title: female hypoxia cervical cord replicate 4 [FHV_S34]


title: female hypoxia cervical cord replicate 5 [FHV_S35]


title: female hypoxia cervical cord replicate 1 [FHV_S31]


title: Synchronised Mitosis R2

description: PCHiC

source_name: HeLa synchronised mitosis

value: nocodazole


title: Fig1-U1IAA-4

city: La Jolla

first: Rea

last: Lardelli

state: CA

address: 9500 Gilman Dr

department: Biology

institute: UCSD

description: nascent RNA

data_processing:
Demultiplexing: reads were demultiplexed based on the presence of a gene-specific primer at the beginning of R2, and a random-mer was extracted off of the beginning of R1.
Read trimming: reads were trimmed at the 3' end
tail counting: non-pcr duplicate reads were counted by summing reads with the same sequence that did not have the same randommer sequence as any other read.
Genome_build: analysis was done on raw reads without genome mapping
Supplementary_files_format_and_content: Processed files contain trimmed sequence, total read count and unique read count

extract_protocol:
For crosslinking IPs, cells were crosslinked with 0.2% formaldehyde and cells were lysed in RIPA lysis buffer (50 mM Tris-HCl pH 7.5, 1% Nonidet P-40, 0.5% sodium deoxycholate, 0.05% SDS, 1 mM EDTA, 150 mM NaCl, 2 µg/ml aprotinin and leupeptin, 1 mM PMSF) and sonicated 3x for 20 seconds. Lysates were precleared for 1 hr at 4˚C with protein A sepharose and then IPs were carried out with antibodies listed in metasheet at room temperature for 90 minutes before 6x washes in denaturating RIPA buffer and then 3 washes with NET2 before on-bead ligation of AG10/11. Ligated RNA was reverse crosslinked with 70˚C incubation for 45 minutes and then extracted with TRIzol per manufacturer's recommendation. For nascent RNA and total RNA librariers, 2.5 µg of RNA was ligated and then extracted with phenol/chlorofom/isoamyl alcohol. For nascent RNA, Click-iT nascent RNA capture kit (Invitrogen) was used on 1.25 µg of RNA according to manufacturer's protocol with the exception of using Superscript III reverse transcriptase (Invitrogen) for cDNA synthesis.
RNA adapters containing bar-codes and 10-11 nucleotide randomers were ligated to the 3’ ends of total and eluted RNA with T4 RNA ligase (NEB) at 16°C for 16 hours. cDNA was generated from AR-17 primer with Superscript III (Life Technologies). 3’ ends were amplified by Q5 High-Fidelity DNA Polymerase (NEB) first, using snRNA gene-specific primers and AR-17 and then with primers D50x and D70x (Illumina). Libraries were purified on AMPure XP magnetic beads (Beckman), and validated by 2200 Tape Station Instrument (Agilent). Libraries were pooled at 4 nM, denatured with NaOH and diluted in HT1 buffer (Illumina) to 7 pM before sequencing with MiSeq Reagent Kit V2 Nano configuration (Illumina).

treatment_protocol: cells were treated either with 1 ng/ml doxycycline or 500 µM indol-3-acetic acid for 48 hr prior to harvest and in the case of siRNA depletions, cells were transfected with 20 nM siRNA with SilentFect (BioRad)

tag: treatment (dox or iaa)

value: IAA

tag: target gene

tag: ip antibody

tag: adapter


title: female normoxia cervical cord replicate 5 [FNV_S25]

source_name: female normoxia cervical cord

value: normoxia


title: female normoxia cervical cord replicate 4 [FNV_S24]


title: female normoxia cervical cord replicate 2 [FNV_S22]


title: MSC001_control

type: RNA

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

description:
MSC001
Mesenchymal stromal cells derived from a healthy pediatric control.

hyb_protocol: Following fragmentation, 10 ug of labeled cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. After sample hybridization, GeneChips were stained using phycoerythrin-conjugated streptavidin in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000.

data_processing: The CEL files for these samples were read into R using the affy package and normalized at probe-level with vsnrma (Huber et al., Bioinformatics 2002). To identify differentially expressed probesets, Limma R Package (version 3.26.9) was used in R 3.0.1. Principal component analyses were performed in Partek Genomic Suite 6.6.

label: biotin

source_name: Control-MSCs

label_protocol: 100 ng total RNA was used as input for synthesis of two-stranded cDNA. Biotinylated cRNA was synthesized and amplified by in vitro transcription (IVT) of the second-stranded cDNA template using T7 RNA polymerase, according to the standard Affymetrix protocol (GeneChipTM 3' IVT PLUS Reagent Kit, user guide, Affymetrix).

growth_protocol: Bone marrow (BM) aspirates were collected from children with newly diagnosed BCP-ALL (day0‑leukemic‑MSCs), after 79 days of induction and consolidation treatment (day79-remission-MSCs), Relapsed BCP-ALL (Relapse-MSCs) or from children with healthy bone marrow (control-MSCs). MSCs were isolated from these aspirates as described previously. Briefly, BM aspirates were seeded in MSC expansion medium (DMEM low glucose medium (Life Technologies), 15% FCS (Integro), fungizone (Invitrogen), gentamycin (Invitrogen), freshly supplemented with 0.1 mM ascorbic acid (Sigma-Aldrich) and 1 ng/ml basic fibroblast growth factor (bFGF; Serotec, Kidlington, UK)). Non-adherent cells were removed after 24 hours. After a maximum of 10 days, MSC colonies were harvested using trypsin (Thermo Scientific). Cells were further expanded for one or two additional passages in order to isolate RNA and freeze cells in liquid nitrogen for future experiments. MSCs were negative for the hematopoietic markers (CD14, CD34, CD45; BD Biosciences, San Jose, CA, USA), and positive for the mesenchymal markers (CD13, CD29, CD54, CD73, and CD166; BD Biosciences) as detected by flow cytometry (BD Accuri C6 Plus). Multi-lineage potential was confirmed for adipocyte (Oil Red O staining), osteocyte (Alizarin Red S staining), and chondrocyte (Col2a/Thionine/Alcian Blue staining) differentiation.

extract_protocol: Total RNA was isolated out of mesenchymal stromal cells using Trizol reagent (Invitrogen, Bleiswijk, Netherlands). Quality of RNA was checked using an Agilent 2100 Bio-analyzer.

treatment_protocol: No treatment protocol was applied.

tag: age

value: Child

value: Mesenchymal stromal cells (MSCs)

tag: disease stage

value: Healthy

tag: bcp-all subtype

value: Control


title: male hypoxia cervical cord replicate 5 [MHV_S15]

source_name: male hypoxia cervical cord

value: male


title: Synchronised G2 R2

description: PCHiC

source_name: HeLa synchronised interphase

value: 6h release after thymidine

value: contol (interphase)


title: MSC009_Day0_leukemic

description:
MSC009
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: Newly diagnosed BCP-ALL

value: B-other


title: MSC007 _Day0_leukemic

description:
MSC007
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: female normoxia cervical cord replicate 1 [FNV_S21]

value: sprague dawley


title: MSC008 _Day0_leukemic

description:
MSC008
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MSC010_Day79_remission

description:
MSC010
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).

value: Remission BCP-ALL


title: Synchronised G2 R1

description: PCHiC

value: Kyoto


title: male hypoxia cervical cord replicate 2 [MHV_S12]

value: hypoxia

value: C3-C6 spinal cord


title: male hypoxia cervical cord replicate 1 [MHV_S11]

value: C3-C6 spinal cord microglia


title: male hypoxia cervical cord replicate 3 [MHV_S13]


title: Synchronised G1 R1

description: PCHiC

value: 15h release after thymidine


title: Synchronised G1 R2

description: PCHiC


title: male hypoxia cervical cord replicate 4 [MHV_S14]


title: male normoxia cervical cord replicate 2 [MNV_S2]

source_name: male normoxia cervical cord

value: normoxia


title: Synchronised Mitosis R1

description: PCHiC

value: nocodazole

value: treatment


title: female normoxia cervical cord replicate 3 [FNV_S23]

value: female


title: male normoxia cervical cord replicate 5 [MNV_S5]


title: CTCF control R1

description: PCHiC

source_name: HeLa CTCF SCC1 AID

value: -Auxin

value: control (AID)


title: CTCF depleted R2

description: PCHiC

value: +Auxin


title: female hypoxia medulla replicate 3 [FHV_B33]

source_name: female hypoxia medulla

value: medulla

value: Medulla microglia


title: female normoxia medulla replicate 5 [FNV_B25]

source_name: female normoxia medulla


title: CTCF depleted R1

description: PCHiC


title: female normoxia medulla replicate 4 [FNV_B24]


title: female hypoxia medulla replicate 5 [FHV_B35]


title: SCC1 depleted R1

description: PCHiC

source_name: HeLa SCC1 AID


title: male normoxia cervical cord replicate 3 [MNV_S3]

value: male


title: SCC1 depleted R2

description: PCHiC


title: female hypoxia medulla replicate 4 [FHV_B34]

value: sprague dawley


title: male normoxia cervical cord replicate 1 [MNV_S1]


title: female hypoxia medulla replicate 1 [FHV_B31]


title: CTCF control R2

description: PCHiC


title: female normoxia medulla replicate 1 [FNV_B21]


title: female normoxia medulla replicate 2 [FNV_B22]


title: female hypoxia medulla replicate 2 [FHV_B32]


title: male normoxia cervical cord replicate 4 [MNV_S4]


title: male hypoxia medulla replicate 5 [MHV_B15]

source_name: male hypoxia medulla


title: male hypoxia medulla replicate 3 [MHV_B13]


title: SCC1 control R2

description: PCHiC


title: SCC1 control R1

description: PCHiC


title: SCC1 depleted R3 TR2

description:
nascent RNA
Technical replicate 2

data_processing:
Slamdunk v0.2.4
Deseq
Genome_build: GRCh37
Supplementary_files_format_and_content: .tsv

extract_protocol:
Cells were snap-frozen and extracted total RNA was subjected to alkylation by iodoacetamide for 15 minutes at room temperature. Alkylation was stopped by addition of dithiothreitol and alkylated RNA purified by ethanol precipitation
3’ end mRNA sequencing libraries were generated from 500 ng of alkylated RNA using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina. Single-read sequencing was performed for 100 cycles on a HiSeq2500 sequencer (Illumina)
SLAM-seq

treatment_protocol: HeLa SCC1-AID cells were synchronized in G1 as for PCHiC. SCC1 degradation was induced by addition of auxin. Newly synthesized RNA was labelled by addition of 4-Thiouridine at a final concentration of 100 µM for 60 minutes


title: male hypoxia medulla replicate 1 [MHV_B11]


title: male hypoxia medulla replicate 4 [MHV_B14]


title: SCC1 depleted R3 TR1

description:
nascent RNA
Technical replicate 1


title: male normoxia medulla replicate 3 [MNV_B3]

source_name: male normoxia medulla


title: female normoxia medulla replicate 3 [FNV_B23]


title: Fig1-U5dox-1

description: nascent RNA

value: dox


title: male normoxia medulla replicate 5 [MNV_B5]


title: male normoxia medulla replicate 1 [MNV_B1]


title: CH2

city: Beijing

first: Ying

last: Zhang

address: Haidian District, Yuanmingyuan West Road 2

country: China

institute: China Agricultural University

data_processing:
Illumina Hiseq 4000 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then aligned to the chicken reference genome (Gallus gallus 4.75) using Tophat2 (version 2.0.9) software
Fragments per kilo base of exon model per million mapped reads (FPKM) were calculated using the Cufflink (version 2.1.1) program, Differential expression analysis comparing TC and CH was performed with the Cuffdiff
Genome_build: Gallus gallus 4.75 (ftp://ftp.ensembl.org/pub/release-75/fasta/gallus_gallus/dna/)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Gallus gallus

source_name: Chorioallantoic membrane (CAM) of embryos

extract_protocol:
Chorioallantoic membrane tissues were removed, frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina HiSeq RNA Sample Prep Kit (Cat.#RS-122-2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: chicken type

value: Chahua

tag: embryo

value: Chorioallantoic membrane

value: 11-day of embryo


title: TC3

value: Tibetan


title: male normoxia medulla replicate 4 [MNV_B4]


title: SCC1 depleted BR2 TR1

description:
nascent RNA
Technical replicate 1

value: Kyoto


title: CH3


title: SCC1 depleted BR2 TR2

description:
nascent RNA
Technical replicate 2


title: SCC1 control BR3 TR2

description:
nascent RNA
Technical replicate 2


title: SCC1 depleted BR1 TR1

description:
nascent RNA
Technical replicate 1


title: SCC1 depleted BR1 TR2

description:
nascent RNA
Technical replicate 2


title: male normoxia medulla replicate 2 [MNV_B2]

value: normoxia


title: SCC1 control BR3 TR1

description:
nascent RNA
Technical replicate 1


title: TC2


title: male hypoxia medulla replicate 2 [MHV_B12]

value: hypoxia


title: CH1


title: SCC1 control BR2 TR2

description:
nascent RNA
Technical replicate 2


title: SCC1 control BR2 TR1

description:
nascent RNA
Technical replicate 1


title: SCC1 control BR1 TR2

description:
nascent RNA
Technical replicate 2


title: SCC1 control BR1 TR1

description:
nascent RNA
Technical replicate 1


title: TC1


title: CLL_PT2_CD19pos_scRNAseq

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Fastqs were demultiplexed usiing CellRanger mkfastq (v3.0.2)
Sequencing reads were aligned to hg38 using CellRanger count (v.3.0.2). Single-cells were called using the default parameters from this step.
Genome_build: hg38
Supplementary_files_format_and_content: barcodes, gene names and Raw expression counts from 10x CellRanger count

growth_protocol: Cryopreserved cells were thawed in RPMI with 10% FBS and washed in media. CD19 positive and negative fractions were flow cytometry sorted / enriched using magnetic beads prior to 10x scRNA-seq.

extract_protocol: 10x Genomics 5' scRNA-seq including human VDJ enrichment

tag: subject status

value: chronic lymphocytic leukemia patient

tag: subject id

value: Patient 2

value: Peripherial blood mononuclear cells

tag: enrichment

value: CD19 positive


title: ScRNA-seq of airway epithelial tracheal cultures with acute IL-13 stimulation [Acute_stim_91497]

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

description: RNA-seq from 1,050 cells from ALI cultures taken from two tracheal donors stimulated with either IL-13 or BSA (control)

data_processing:
We trimmed and culled raw demultiplexed cDNA reads in FASTQ files using Cutadapt, trimming poly A tails and 5’ and 3’ ends with q < 20 and removing any reads shorter than 25 base pairs. We then aligned trimmed reads to the hg38 human genome with GSNAP, setting “max-mismatches=0.05” and accounting for both known Ensembl splice sites and SNPs. We quantified gene expression using HTSeq with “stranded=yes”, “mode=intersection-nonempty”, and “t=gene” and then summed the number of unique molecular identifiers (UMIs) for each gene across runs for each cell to obtain a UMI count matrix that we used for all downstream analysis.
Although samples comprising multiple cells were removed during the cell selection stage, to safeguard against undetected doublets, we removed 34 outlier cells expressing > 46,000 UMIs (chip 91497 cells) or > 28,500 UMIs (chip 94576 cells) from the acute stimulation dataset and 10 outlier cells expressing > 60,000 UMIs from the chronic stimulation dataset. For the acute dataset, we also removed 11 cells for which the percentage of reads that mapped to genes was < 50%. Prior to downstream analysis, we removed select mitochondrial and ribosomal genes (those beginning with MTAT, MT-, MTCO, MTCY, MTERF, MTND, MTRF, MTRN, MRPL, MRPS, RPL, RPS) and very lowly expressed genes (those genes not expressed in at least 0.5% of cells). Finally, we removed 446 cells expressing fewer than 2,500 UMIs from the acute dataset and three cells expressing fewer than 2,000 UMIs from the chronic dataset. The final QCed acute dataset contained 1,894 cells with a mean of 8,736 UMIs and 3,159 genes per cell and the final QCed chronic dataset contained 789 cells with a mean of 12,970 UMIs and 4,580 genes per cell.
For the acute simulation dataset, we accounted for differences in coverage across cells by dividing each cell’s UMI count by the sum of all the cell’s UMIs, multiplying by 10,000, and then taking the natural log. For input into dimensionality reduction and clustering analyses and for plotting relative expression in heat maps and dot plots, we also fitted normalized expression of each gene to a set of predictors that included the sum of the UMI counts per cell and the identity of the originating donor and chip, and then mean centered (subtracted from each gene count the average expression of that gene) and scaled (divided each centered gene count by that gene’s standard deviation) the residuals.
Due to batch-based differences in expression between the two donors in the chronic stimulation dataset, we reduced the dimensionality of variation in that dataset using canonical correlation analysis (CCA), which identifies the strongest components of gene correlation structure that are shared across datasets (Seurat’s RunMultiCCA function). After normalizing and scaling datasets for the two donors separately, we carried out CCA based on the 3,350 genes contained within the union of the top 2,000 most informative genes from each donor. Correlated expression across donors based on the top three CCA dimensions was then projected into a common subspace using Seurat’s AlignSubspace function, allowing us to identify and visualize universal populations of cells, rather than those driven by donor-specific variation. We removed 33 cells that were not well explained by these shared components (i.e., any gene for which variance explained by CCA was < 2-fold that explained by PCA).
R1 reads: barcodes: first 11 bp; UMIs: next 10 bp; five Ts
Genome_build: hg38
Supplementary_files_format_and_content: "expressionMatrix" text files contain expression count tables that include all samples in the original fastq files. All sample names include the sequencing barcode (after the underscore)
Supplementary_files_format_and_content: "raw" text files contain raw counts for samples and genes that have gone through QC filtering.
Supplementary_files_format_and_content: "norm" text files contain log-normalized counts for samples and genes that have gone through QC filtering. These are the data used for analysis in the study
Supplementary_files_format_and_content: "metadata" text files don't contain counts, but rather important variables associated with each sample
Supplementary_files_format_and_content: "seurat" files contain Seurat objects which contains raw counts, normalized counts, scaled counts, metadata, and dimentionality reduction coordinates for samples and genes that have gone through QC filtering. These are the data used for analysis in the study
Supplementary_files_format_and_content: chip91497_expressionMatrix.txt: Acute stimulation dataset: Full expression count table with gene symbols for chip 91497 (the sequencing barcode is embedded in sample names after the underscore)
Supplementary_files_format_and_content: chip94576_expressionMatrix.txt: Acute stimulation dataset: Full expression count table with gene symbols for chip 94576 (the sequencing barcode is embedded in sample names after the underscore)
Supplementary_files_format_and_content: chip97570_expressionMatrix.txt: Chronic stimulation dataset: Full expression count table with gene symbols for chip 97570 (the sequencing barcode is embedded in sample names after the underscore)
Supplementary_files_format_and_content: IL13_acute_raw_matrix.txt: Acute stimulation dataset: Raw count table including filtered samples and genes used in analysis (combining chips 91497 and 94576)
Supplementary_files_format_and_content: IL13_acute_norm_matrix.txt: Acute stimulation dataset: Normalized count table including filtered samples and genes used in analysis (combining chips 91497 and 94576)
Supplementary_files_format_and_content: IL13_acute_metadata.txt: Acute stimulation dataset: Metadata for samples included in the filtered dataset used in analysis, including treatment, donor identity, sequencing chip, and cluster assignment (combining chips 91497 and 94576)
Supplementary_files_format_and_content: IL13_acute_seurat.rda: Acute stimulation dataset: R object file that includes the Seurat dataset used for analysis. This object contains the raw, normalized, and scaled expression data as well as associated metadata (combining chips 91497 and 94576)
Supplementary_files_format_and_content: IL13_chronic_raw_matrix.txt: Chronic stimulation dataset: Raw count table including filtered samples and genes used in analysis
Supplementary_files_format_and_content: IL13_chronic_norm_matrix.txt: Chronic stimulation dataset: Normalized count table including filtered samples and genes used in analysis
Supplementary_files_format_and_content: IL13_chronic_metadata.txt: Chronic stimulation dataset: Metadata for samples included in the filtered dataset used in analysis, including treatment, donor identity, sequencing chip, and cluster assignment
Supplementary_files_format_and_content: IL13_chronic_seurat.rda: Chronic stimulation dataset: R object file that includes the Seurat dataset used for analysis. This object contains the raw, normalized, and scaled expression data as well as associated metadata

source_name: Human epithelial tracheal ALI cultures

growth_protocol: Primary basal HTECs from the two donors were isolated and expanded for 2 passages on NIH 3T3 fibroblast feeders using F-medium (67.5% DMEM-F, 25% Ham’s F-12, 7.5% FBS, 1.5 mM L-glutamine, 25 ng/mL hydrocortisone, 12 5 ng/mL EGF, 8.6 ng/mL cholera toxin, 24 μg/mL Adenine, 0.1% insulin, 75 U/mL pen/strep) with ROCK1 Inhibitor (RI, 10 μM) and antibiotics (1.25 μg/mL amphotericin B, 2 μg/mL fluconazole, 50 μg/mL gentamicin). Passage 2 cell suspensions were harvested by trypsinization, treated with DNase (12.5 mg/ml) in HBSS for 5min at 37C, and seeded onto bovine collagen-coated 6.5 mm transwell inserts (2x10^4 cells/insert for acute stimulation, 1x10^4 cells/insert for chronic stimulation) in ALI expansion medium (50% BEBM, 50% DMEM-C, 0.5 mg/mL BSA, 80 μM ethanolamine, 10 ng/mL hEGF, 0.4 μM MgSO4, 0.3 μM MgCl2, 1 μM CaCl2, 30 ng/mL retinoic acid, 0.8X insulin*, 0.5X transferrin*, 1X hydrocortisone*, 1X epinephrine*, 1X bovine pituitary extract*, 1X gentamicin/amphotericin* (*relative to BEGM Bullet Kit aliquot) with RI. RI was removed after 24 hours and confluent monolayers were airlifted 6 (acute stimulation) or 7 (chronic stimulation) days post seed and differentiated using complete PneumaCult ALI media made as per manufacturer’s instructions.

extract_protocol:
Replicate mature stimulated ALI cultures were washed with warm PBS/DTT (10 mM) for 5 minutes at 37°C, followed by a warm PBS wash of both chambers. Cultures were then harvested from the filter to single cell suspensions using apical dissociation solution (Accutase with 5 mM EDTA and 5 mM EGTA) for 30 minutes at 37°C with occasional manual agitation5. Single cell suspensions were diluted, centrifuged, and washed once with PBS/DTT and twice with PBS before sorting for live singlets. Cells from both donors and treatments were dispensed into each of two 5,184-nanowell version 1 microchips (91497 and 94576) using the ICELL8 platform (Takara Bio USA, Inc.), after which non-doublet cells were selected for library preparation and sequencing.
Library preparation was carried out using ICELL8 single-cell poly-(A)+ transcriptome amplification hands-on workflow (with Triton X-100 for cell lysis), protocol D07-000040-003 rev4. For the acute IL-13 experiment, libraries were generated for a total of 2,385 selected cells (plus positive and negative controls), after which they were sequenced as 100 base pair single-end reads on an Illumina HiSeq 2500 (Illumina, Inc., San Diego, CA), with cells from each of the two microchips sequenced across three flow cell lanes.

treatment_protocol: Starting at day 21 post-airlift, paired cultures for each donor were stimulated with IL-13 or BSA for 48 hours, after which cells were harvested on day 23.

value: Airway epithelial


title: ScRNA-seq of airway epithelial tracheal cultures with chronic IL-13 stimulation [Chronic_stim_97570]

description: RNA-seq from 802 cells (756 Qced cells in the processed data files) from ALI cultures taken from two tracheal donors stimulated with either IL-13 or BSA (control)

extract_protocol:
Replicate mature stimulated ALI cultures were washed with warm PBS/DTT (10 mM) for 5 minutes at 37°C, followed by a warm PBS wash of both chambers. Cultures were then harvested from the filter to single cell suspensions using apical dissociation solution (Accutase with 5 mM EDTA and 5 mM EGTA) for 30 minutes at 37°C with occasional manual agitation5. Single cell suspensions were diluted, centrifuged, and washed once with PBS/DTT and twice with PBS before sorting for live singlets. Cells from both donors and treatments were dispensed into a single version 2 microchip (97570) using the ICELL8 platform (Takara Bio USA, Inc.), after which non-doublet cells were selected for library preparation and sequencing.
Library preparation was carried out using ICELL8 single-cell poly-(A)+ transcriptome amplification hands-on workflow (with Triton X-100 for cell lysis), protocol D07-000040-003 rev4. For the acute IL-13 experiment, libraries were generated for a total of 802 selected cells (plus positive and negative controls), after which they were sequenced as 100 base pair single-end reads on an Illumina HiSeq 2500 (Illumina, Inc., San Diego, CA), with cells from a single microchip sequenced across three flow cell lanes.

treatment_protocol: Starting at day 11 post-airlift, paired cultures for each donor were stimulated with IL-13 or BSA for 11 days, after which cells were harvested on day 22.


title: Patient50_tumor [R50B]

city: Singapore

first: Caroline G.

last: Lee

address: MD7, Level 2, 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

hyb_protocol: Fragmentation was done on 1ug of cRNA using 5μl 10 × Blocking Agent and 1μlof 25 × Fragmentation Buffer. The mixture was heated at 60 °C for 30 min and then added with 25μl 2 × GE Hybridization buffer. 50ul of hybridization solution was added into the gasket slide, which is then assembled to the microarray slide. Incubation of the slides was carried out in an Agilent Hybridization Oven at 65°C for 17 hours.

scan_protocol: The scanning was performed using Agilent DNA Microarray Scanner (part number G2505C) after washing and fixing the hybridized arrays.

data_processing: The acquired array images was analyzed by Agilent Feature Extraction software (version 11.0.1.1). GeneSpring GX v12.1 software package (Agilent Technologies) was then used for quantile normalization and data processing. LncRNAs and mRNAs that have flags in Present or Marginal in at least 49 out of 100 samples were used for subsequent analysis.

label_protocol: RNA samples were labeled according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Pure mRNA was first obtained from the total RNA by removing rRNA using mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre. Amplification and transcription of samples into fluorescent cRNA without 3’bias was then carried out using a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). Purification of labeled cRNAs was performed by RNeasy Mini kit (Qiagen), followed by measurement of concentration and specific activity of the labeled cRNAs (pmol Cy3/μgcRNA) using NanoDrop ND-1000.

extract_protocol: The frozen tissues were added with RLT buffer (Qiagen, Germany) with 1% β-mercaptoethanol and then homogenized by gentleMACS dissociator (Miltenyi Biotec). RNeasy mini kit (Qiagen, Germany) was used to extract the total RNA following the manufacturer’s protocol.

tag: gender

value: M

value: Liver

tag: tissue type

value: Tumor


title: Patient59_tumor [R59B]


title: Patient59_adjacent non-tumor [R59A]

source_name: Adjacent non-tumor_liver

value: Adjacent non-tumor


title: CLL_PT1_CD19pos_scRNAseq

value: Patient 1


title: Patient52_adjacent non-tumor [R52A]

value: F


title: CLL_PT2_CD19neg_scRNAseq

value: CD19 negative


title: Patient52_tumor [R52B]


title: Patient50_adjacent non-tumor  [R50A]


title: Patient49_adjacent non-tumor [R49A]


title: Patient46_tumor [R46B]


title: Patient44_tumor [R44B]


title: Patient49_tumor [R49B]


title: CLL_PT1_CD19neg_scRNAseq


title: Patient47_tumor [R47B]


title: Patient43_tumor [R43B]


title: Patient47_adjacent non-tumor [R47A]


title: Patient44_adjacent non-tumor [R44A]


title: Patient45_tumor [R45B]


title: Patient45_adjacent non-tumor [R45A]


title: Patient41_tumor [R41B]


title: Patient46_adjacent non-tumor  [R46A]


title: Patient41_adjacent non-tumor [R41A]


title: NUP98-KDM5A_AML H3K27me3 ChIP

city: Chapel Hill

first: Yiran

last: Guo

state: North Carolina

address: 450 West Drive

department: GMB

institute: UNC

data_processing:
All reads were mapped to mouse genome (mm10) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools. We filter out reads with a mapping quality score < 20 for downstream analysis.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

organism: Mus musculus

source_name: murine acute myeloid leukemia (AML) cells

growth_protocol: The murine AML cells transformed by FLAG-tagged NUP98-KDM5A (N5A) was maintained in OptiMEM base medium (Invitrogen) complemented with 10% FBS (Invitrogen), 1% antibiotics, 50 μM β-mercaptoethanol and stem-cell factor (SCF; supernatant of SCF-producer cells).

extract_protocol:
Fixed cell pellets were sonicated in Bioruptor for 45 cycles at high setting to enrich the sonicated DNA to be ~300-500bp. Then these sonicated samples were incubated with indicated antibodies with either protein G or A beads overnight. Then, the beads were washed 4 times with distinct buffers (see our method) and eluted with elution buffer at 65 degree for 30 min. This eluted DNA were reverse crosslinked and treated with RNase and protease K, then the final Chipped DNA are purified with PCR cleanup kit (Qiagen).
The ChIP DNA library was prepared following the instructions of Illumina’s ChIP-seq prep product manual. ChIP-seq libraries were sequenced on Illumina Genome Analyzer for sequencing.

treatment_protocol: For ChIP-seq experiments, GFP or 3XHA3XFLAG-tagged wildtype or mutant NUP98-HOXA9/FUS-HOXA9 HEK293 cells were grown in DMEM medium and fixed with 1% formaldehyde in PBS for 10 min at room temperature. For Hexanediol treatment, all of growth medium was removed, and cells were incubated with 10% hexanediol in PBS for 1 min. Then, formaldehyde was added directly to make up the final concentration formaldehyde to be 1%, and incubated at room temperature for 10 min.

value: AML cells transformed with FLAG-tagged NUP98-KDM5A

tag: chip antibody

value: rabbit anti-H3K27me3 (Millipore #07-449)


title: Patient42_tumor [R42B]

tag: tissue


title: Patient42_adjacent non-tumor [R42A]


title: NUP98-KDM5A_AML N5A ChIP replicate 2

tag: cell type

value: mouse anti-FLAG antibody (Sigma #f1804 M2)


title: NUP98-KDM5A_AML H3K4me3 ChIP

value: rabbit anti-H3K4me3 (Abcam ab8580)


title: NUP98-KDM5A_AML N5A ChIP replicate 1


title: Patient40_adjacent non-tumor [R40A]


title: Patient38_tumor [R38B]


title: Patient40_tumor [R40B]


title: Patient43_adjacent non-tumor  [R43A]


title: Patient39_adjacent non-tumor [R39A]


title: Patient39_tumor [R39B]


title: ScRNA-seq of airway epithelial tracheal cultures with acute IL-13 stimulation [Acute_stim_94576]

description: RNA-seq from 1,335 cells from ALI cultures taken from two tracheal donors stimulated with either IL-13 or BSA (control)


title: CvD3_mRNAseq_run342

city: Bloomington

first: Malcolm

last: Winkler

state: IN

address: 1001 E. Third Street

institute: Indiana University

description:
ΔcvfD mutant
rRNA depleted (mRNA-seq)
processed data file: counts_table.txt

data_processing:
Adapters and low quality bases were trimmed using Trimmomatic (version 0.17).
Trimmed reads were mapped on the Streptococcus pneumoniae D39 using Bowtie2 version 2.0.0-beta7.
Read counts for genes and intergenic regions were determined with custom perl scripts.
Genome_build: Streptococcus pneumoniae D39 (RefSeq NC_008533) genome and D39 plasmid pDP1 sequence (RefSeq NC_005022.1).
Supplementary_files_format_and_content: counts_table.txt: Processed data file is a tab-delimited text file indicating the number of reads associated with a gene or intergenic region. Intergenic regions are given by molecule,strand,begin-end and are 100 bps long.

organism: Streptococcus pneumoniae D39

growth_protocol: Strains were grown in Difco Brain Heart Infusion Broth at 37oC in atmosphere of 5% CO2 to an OD620 of 0.1.

extract_protocol:
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals).
Library was generated by removing DNA by DNase treatment, depleting rRNA with Ribo-Zero rRNA removal kit for gram-positive bacteria and subsequently utilizing the ScriptSeqTM v2 RNA-Seq Library Preparation kit (Epicenter).

tag: strain

tag: genotype/variation

value: <delta>cvfD mutant


title: NUP98-KDM5A_AML Input


title: Patient37_adjacent non-tumor [R37A]


title: WR2_mRNAseq_run342

description:
rRNA depleted (mRNA-seq)
processed data file: counts_table.txt

value: Wildtype parent


title: CvD1_mRNAseq_run342


title: CvD2_mRNAseq_run342


title: Patient35_tumor [R35B]


title: Patient36_tumor [R36B]


title: WR1_mRNAseq_run342


title: Patient34_tumor [R34B]


title: WR3_mRNAseq_run342


title: Patient33_adjacent non-tumor [R34A]


title: si-rrp6-B

city: San Francisco

first: Jordan

middle: Emily

last: Burke

address: N374 Genentech Hall, 600 16th Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description:
si_rrp6-B_S60_L008
processed data file: small_RNA-seq.csv

data_processing:
ATMT insertional sequencing:
Illumina adaptor and T-DNA sequence removed with custom scripts
Reads were aligned to the  genome with bowtie v 1.1.2
Aligned reads per gene were counted with HTseq-count
QuantSeq and RNA-seq:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the  genome with STAR 2.5.3a
Analysis performed using custom read counting scripts and DESeq2
small RNA-seq:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the  genome with bowtie v 1.1.2
Analysis performed using custom read counting scripts and DESeq2
Genome_build: C. neoformans CNA3
Supplementary_files_format_and_content: CSV

organism: Cryptococcus neoformans

source_name: yeast

growth_protocol: Samples were inoculated from saturated starter cultures in YPAD at 30C until reaching OD 1.0 then harvested by centrifugation at 2000xg for 5 minutes.

extract_protocol:
genomic DNA: Cells were lyophilized then powdered by bead beating with 0.5 mm zirconia-silica beads. Genomic DNA was extracted as described in Chun and Madhani, Methods Enzym. 2010.
PolyA mRNA, small RNA: Cells were lyophilized then powdered by bead beating with 0.5 mm zirconia-silica beads. RNA was then extracted using Trizol and chloroform.
ATMT insertional sequencing: 20 μg of genomic DNA was sonicated for 10 min (30 sec on, 1 min rest) at 4°C. DNA was re-purified with phenol/chloroform/isoamyl alcohol (25:24:1, Sigma), washed with chloroform and precipitated with 3 volumes ethanol. Linear PCR originating in the T-DNA:NAT insertion was performed with Accuprime Taq High Fidelity polymerase (Thermo Fisher) using the JEBPN-Biotin2 primer. First strand DNA was then purified over M280 Dynabeads (Thermo Fisher) according to the manufacturer’s instructions. Purified linearized DNA was ligated to the JEBPN-DNA linker using Circligase II (Epicentre) according to the manufacturer’s instructions. Finally, DNA was amplified by nested PCR with JEBPN-SA-II and JEBPN_index-SA-I (Table S6) with various indexes using Accuprime Taq High Fidelity polymerase (Thermo Fisher).
RNA-seq: NEBNext Ultra II Directional library prep kit for Illumina according to manufacturer's instructions.
small RNA-seq: Lexogen Small RNA-seq library prep kit according to manufacturer's instructions.
QuantSeq: Lexogen QuantSeq 3' mRNA library prep kit according to manufacturer's instructions.

tag: library strategy

value: small RNA-seq

tag: molecule subtype

value: small RNA


title: Patient35_adjacent non-tumor [R35A]

tag: age


title: Patient36_adjacent non-tumor [R36A]


title: si_WT-B

description:
si_WT-B_S102
processed data file: small_RNA-seq.csv


title: si_WT-A

description:
si_WT-A_S101
processed data file: small_RNA-seq.csv


title: Patient32_tumor [R32B]


title: si-rrp6-A

description:
si_rrp6-A_S59_L008
processed data file: small_RNA-seq.csv


title: Patient33_tumor [R33B]


title: si-rdp1-B

description:
si_rdp1-B_S112
processed data file: small_RNA-seq.csv


title: Patient31_adjacent non-tumor [R31A]


title: si-rdp1-A

description:
si_rdp1-A_S111
processed data file: small_RNA-seq.csv


title: si-rde5-B

description:
si_rde5-B_S106
processed data file: small_RNA-seq.csv


title: Patient32_adjacent non-tumor [R32A]


title: Patient29_adjacent non-tumor [R29A]


title: Patient30_tumor [R30B]


title: Patient28_adjacent non-tumor  [R28A]


title: Patient31_tumor [R31B]


title: Patient27_adjacent non-tumor [R27A]


title: Patient33_adjacent non-tumor [R33A]


title: Patient29_tumor [R29B]


title: Patient28_tumor [R28B]


title: si-rde5-A

description:
si_rde5-A_S105
processed data file: small_RNA-seq.csv


title: Patient27_tumor [R27B]


title: Patient26_tumor [R26B]


title: Patient26_adjacent non-tumor  [R26A]


title: Patient30_adjacent non-tumor [R30A]


title: Patient24_tumor [R24B]


title: si-rde4-B

description:
si_rde4-B_S108
processed data file: small_RNA-seq.csv


title: Patient24_adjacent non-tumor [R24A]


title: Meal-fed_WIS_replicate_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's Mouse Ref-8v2 Expression Bead Chips (Illumina, San Diego, CA).The arrays were rinsed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.53 μm using the Illumina iScan scanner.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.

source_name: Meal-fed WIS

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: Male C57BL/6J mice were obtained from the Jackson Laboratory (Bar Harbor, ME) at 6 weeks of age. Animal husbandry, environmental factors, and diets are described in our recent publication (Mitchell et al., 2018). Starting at 5 mo of age, mice were fed either an open source diet (NIA diet) low in sucrose and fat (7.6% energy from sucrose, 17.7% from fat, 3.418 kcal/g) or a sucrose-rich diet (WIS diet) composed of purified ingredients (46% energy from sucrose, 24.4% from fat, 3.927kcal/g) for the remainder of their lives. The proportion of sucrose was 3.9% and 28.5% per gram of food for the NIA and WIS diet, respectively. Within each diet group (NIA or WIS), mice were divided into three feeding regimens: AL, 30% CR, and meal-fed (MF). The MF group takes into account the difference in energy densities between the NIA and WIS diets, with mice on MF-NIA diet consuming the same number of calories as the AL-WIS and MF-WIS diet groups. The AL-NIA group consumed the highest amount of calories of all groups. Both diets were repelleted for mouse chow. Food consumption and bodyweight were measured every two weeks and food allotments for CR and MF groups were adjusted accordingly. CR and MF mice underwent a stepdown procedure over two weeks in order to achieve their target daily allotments. At 14 mo of age (when bodyweight and average food consumption had plateaued), MF and CR mice had their food allotment fixed for the remainder of the study. MF and CR mice were given their food in a once daily allotment at 3:00 pm ± 1 hour.  AL and MF mice received food in the hopper, CR mice were fed on the floor of the cage. All animal protocols were approved by the Animal Care and Use Committee (352-TGB-2018) of the National Institute on Aging, National Institutes of Health.

extract_protocol: RNA was extracted from livers of mice using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. RNA quantity and integrity was evaluated by Nanodrop and Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

value: male

value: liver

tag: diet

value: Meal-fed WIS


title: Patient23_tumor [R23B]

value: M

value: Liver


title: Patient22_tumor [R22B]

value: Tumor


title: Meal-fed_WIS_replicate_4


title: Meal-fed_WIS_replicate_2


title: Patient23_adjacent non-tumor [R23A]

value: Adjacent non-tumor


title: si-rde3-A

description:
si_rde3-A_S115
processed data file: small_RNA-seq.csv


title: si-rde3-B

description:
si_rde3-B_S116
processed data file: small_RNA-seq.csv


title: si-rde4-A

description:
si_rde4-A_S107
processed data file: small_RNA-seq.csv


title: Patient22_adjacent non-tumor [R22A]


title: si-rde2-A

description:
si_rde2-A_S113
processed data file: small_RNA-seq.csv


title: si-rde1-B

description:
si_rde1-B_S110
processed data file: small_RNA-seq.csv


title: si-rde2-B

description:
si_rde2-B_S114
processed data file: small_RNA-seq.csv


title: si-ezh2-A

description:
si_ezh2-A_S117
processed data file: small_RNA-seq.csv


title: CR_WIS_replicate_10

value: Caloric restriction WIS


title: si-ezh2-B

description:
si_ezh2-B_S118
processed data file: small_RNA-seq.csv


title: Patient37_tumor [R37B]


title: CR_WIS_replicate_9


title: CR_WIS_replicate_6


title: si-clr4-B

description:
si_clr4-B_S120
processed data file: small_RNA-seq.csv


title: Patient20_adjacent non-tumor [R20A]

value: F


title: Patient18_adjacent non-tumor  [R18A]


title: CR_WIS_replicate_5


title: Patient21_adjacent non-tumor  [R21A]


title: Patient20_tumor [R20B]


title: si-rde1-A

description:
si_rde1-A_S109
processed data file: small_RNA-seq.csv


title: Patient19_tumor [R19B]


title: CR_WIS_replicate_3


title: CR_WIS_replicate_8


title: CR_WIS_replicate_4


title: Patient17_adjacent non-tumor [R17A]


title: CR_WIS_replicate_1


title: Patient19_adjacent non-tumor [R19A]


title: CR_WIS_replicate_2


title: Meal-fed_WIS_replicate_1


title: Patient17_tumor [R17B]


title: si-clr4-A

description:
si_clr4-A_S119
processed data file: small_RNA-seq.csv


title: Patient38_adjacent non-tumor [R38A]


title: si_ago1-A

description:
si_ago1-A_S103
processed data file: small_RNA-seq.csv


title: si-ago1-B

description:
si_ago1-B_S104
processed data file: small_RNA-seq.csv


title: R_WT-B

description:
PE_rrp6-B_S30
processed data file: NEBNext.csv

molecule: polyA RNA

value: RNA-seq


title: R_WT-A

description:
PE_rrp6-A_S29
processed data file: NEBNext.csv


title: R_rrp6-A

description:
PE_WT-A_S7
processed data file: NEBNext.csv


title: R_rrp6-B

description:
PE_WT-B_S8
processed data file: NEBNext.csv


title: QS_WT-B

description:
QS_WT-B_S20_L003
processed data file: QuantSeq.csv

value: QuantSeq


title: Ad lib_WIS_replicate_3

source_name: Ad lib_WIS

value: Ad libitum WIS


title: QS_WT-A

description:
QS_WT-A_S19_L003
processed data file: QuantSeq.csv


title: Ad lib_WIS_replicate_5


title: Ad lib_WIS_replicate_6


title: Ad lib_WIS_replicate_2


title: Ad lib_WIS_replicate_1


title: Meal-fed_NIA_replicate_4

value: Meal-fed NIA


title: Ad lib_WIS_replicate_4


title: Patient14_tumor [R14B]


title: Meal-fed_NIA_replicate_5


title: Patient14_adjacent non-tumor [R14A]


title: Patient15_tumor [R15B]


title: Meal-fed_NIA_replicate_6


title: Patient16_tumor [R16B]


title: Patient13_adjacent non-tumor [R13A]


title: Meal-fed_NIA_replicate_3


title: QS-rdp1-B

description:
QS_rdp1-B_S30_L003
processed data file: QuantSeq.csv


title: Patient13_tumor [R13B]


title: Patient15_adjacent non-tumor  [R15A]


title: Patient16_adjacent non-tumor [R16A]


title: Patient12_tumor [R12B]


title: CR_WIS_replicate_7


title: Patient12_adjacent non-tumor  [R12A]


title: QS-rdp1-A

description:
QS_rdp1-A_S29_L003
processed data file: QuantSeq.csv


title: Meal-fed_NIA_replicate_2


title: Meal-fed_NIA_replicate_1


title: Patient11_tumor [R11B]


title: QS-rde5-A

description:
QS_rde5-A_S23_L003
processed data file: QuantSeq.csv


title: QS-rde4-B

description:
QS_rde4-B_S26_L003
processed data file: QuantSeq.csv


title: QS-rde4-A

description:
QS_rde4-A_S25_L003
processed data file: QuantSeq.csv


title: QS-rde3-B

description:
QS_rde3-B_S34_L003
processed data file: QuantSeq.csv


title: CR_NIA_replicate_9

value: Caloric restriction NIA


title: QS-rde5-B

description:
QS_rde5-B_S24_L003
processed data file: QuantSeq.csv


title: QS-rde2-B

description:
QS_rde2-B_S32_L003
processed data file: QuantSeq.csv


title: QS-rde2-A

description:
QS_rde2-A_S31_L003
processed data file: QuantSeq.csv


title: Patient18_tumor [R18B]


title: QS-rde1-B

description:
QS_rde1-B_S28_L003
processed data file: QuantSeq.csv


title: Patient10_tumor [R10B]


title: DR2_2

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned using the Agilent DNA microarray scanner G2505C, and raw intensity data were extracted using the feature extraction software.

data_processing: The background adjustment and normalization of microarray data were processed using the Limma package in the R computing environment (http://www.bioconductor.org/). The distribution of probe intensities from eight microarrays was analyzed using the plotDensities function. Frequency densities before and after normalization were plotted against log2-based intensities. Genes exhibiting >4-fold enhanced transcription levels in two independent experiments were considered to show significantly increased expression.

organism: Glycine max

source_name: DR2 rep2

label_protocol: The probes were labeled using the Agilent Low RNA Input Linear Amplification Kit PLUS, following the manufacturer’s protocol (http://www.agilent.com). Total RNA (500 ng) was used to generate labeled cRNA by incorporating cyanine CTP.

growth_protocol: Certified quality soybean seed (Glycine max L. cv. Daepoong) was obtained from the Korea Seed and Variety Service. The seeds were sown in potting soil at 1.5-cm depth in a 50-well plate with one seed per well (35 mm W × 35 mm L × 45 mm D), and incubated in a growth chamber at 28°C and 50–60% relative humidity under a 16-h light (8,000 lux)/8-h dark photoperiod.

extract_protocol: Two independent biological replicates of microarray experiments were performed using soybean plants treated with or without water deprivation. Total RNA was isolated from soybean leaves as described previously (Chae et al., 2017),

treatment_protocol: Water was supplied from a watering tray located beneath the plate. The seedlings were grown for 7 d, then exposed to drought stress by withdrawing the watering tray for 4 d. After the drought treatment, leaves were collected and frozen in liquid nitrogen.

value: leaves

tag: cultivar

value: Daepoong

tag: treatment

value: Second drought stress proceeded for 4 days (DR2)


title: Patient10_adjacent non-tumor [R10A]


title: QS-rde3-A

description:
QS_rde3-A_S33_L003
processed data file: QuantSeq.csv


title: CR_NIA_replicate_8

value: male


title: CR_NIA_replicate_7

value: liver


title: CR_NIA_replicate_4


title: Patient9_tumor [R09B]


title: Patient9_adjacent non-tumor  [R09A]


title: CR_NIA_replicate_3


title: Patient7_tumor [R07B]


title: CR_NIA_replicate_2


title: Patient6_tumor [R06B]


title: CR_NIA_replicate_6


title: DR2_1

source_name: DR2 rep1


title: Patient6_adjacent non-tumor [R06A]


title: CR_NIA_replicate_1


title: WT2_2

source_name: WT2 rep2

value: DR1 plants were re-watered for 1 day (WT2)


title: QS-rde1-A

description:
QS_rde1-A_S27_L003
processed data file: QuantSeq.csv


title: CR_NIA_replicate_5


title: Patient7_adjacent non-tumor [R07A]

value: M


title: Patient21_tumor [R21B]

value: Liver


title: Patient5_tumor [R05B]

value: Tumor


title: Patient11_adjacent non-tumor [R11A]

value: Adjacent non-tumor


title: DR1_2

source_name: DR1 rep2

value: Leaves drought-treated 4 hours (DR1)


title: QS-clr4-B

description:
QS_clr4-B_S38_L003
processed data file: QuantSeq.csv


title: QS-ezh2-A

description:
QS_ezh2-A_S35_L003
processed data file: QuantSeq.csv


title: QS-clr4-A

description:
QS_clr4-A_S37_L003
processed data file: QuantSeq.csv


title: QS-ezh2-B

description:
QS_ezh2-B_S36_L003
processed data file: QuantSeq.csv


title: QS-ago1-B

description:
QS_ago1-B_S22_L003
processed data file: QuantSeq.csv


title: Patient5_adjacent non-tumor  [R05A]


title: WT2_1

source_name: WT2 rep1


title: TW03EV

city: Guangzhou

first: Jiang

last: Li

state: Guangdong

address: Dongfengdong Road NO.651, Yuexiu District

institute: State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.13 with parameters -p 8 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 -G hg19
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Counts and RPKMs for each Sample

source_name: nasopharyngeal carcinomas

growth_protocol: TW03 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37 °C in 5% CO2.

extract_protocol:
Total RNA from TW03-EV and TW03-Gal-9 cells were isolated using TRIzol reagent, and dissolved in RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: cell line

value: nasopharyngeal carcinomas cell line TW03

tag: genotype

value: control


title: Ad lib_NIA_replicate_4

source_name: Ad lib_NIA

value: Ad libitum NIA


title: Patient4_tumor [R04B]

value: F


title: ATMT_insertions_NATR

description:
JEBPN03_YPADBackground_index30_CCGGTG_L007
processed data file: Insertional_results.csv

tag: selection media

value: SC +NAT

value: ATMT insertional sequencing


title: SC-RNASeq_YC1_S2_L002

city: Los Angeles

first: Shuo

last: Chen

state: California

address: 2250 Alcazar Street, Clinical Science Annex, Room 103, CLINICAL SCIENCE ANNEX ROOM 103

institute: Center for Craniofacial Molecular Biology, University of Southern California

description: total RNA

data_processing:
Raw read counts were analyzed using the Seurat R 3.4.1 package
Standard Seurat log-normalization, variable gene seletction, and principal component analysis were performed using the LogNormalize, FindVaiableGenes, ScaleData, and RunPCA functions.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Incisor

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Mandibles were carefully dissected under a stereomicroscope. The surrounding jaw bones were removed by scalpel and the proximal region was then severed. Dental pulp with dental epithelium was isolated, cut into pieces, collected in cold PBS, and digested with 2mg/ml collagenase type I.
Single Cell 3ʹ Gene Expression libraries comprise standard Illumina paired-end  constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at  the start of TruSeq Read 1, while 8 bp sample index sequences are incorporated as  the i7 index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer  sites used in paired-end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x  Barcodes and 12 bp UMI. Sequencing these libraries produce a standard Illumina BCL  data output folder.

tag: Stage

value: 4-week old

value: dental mesenchyme


title: Patient4_adjacent non-tumor [R04A]

tag: gender


title: glob-micropylar-Input replicate 2

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
Basecalls performed using RTA version 1.12.4.2 for HiSeq 2000 and RTA3 version 3.4.4 for NovaSeq 6000
Sequenced reads passing Illumina quality filter were aligned to the Phaseolus vulgaris genome (v2.1) using Bowtie v0.12.7 with parameters -v 3 -5 0 -3 0 -m 1 --best --strata
Reads were filtered to remove PCR duplicates using samtools (v.0.1.18).
Peaks were identified using MACS2 with default parameters and a q-value threshold of 0.01.
Genome_build: Phaseolus vulgaris v2.1 (Phytozome)
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2

organism: Phaseolus coccineus

source_name: Scarlet runner bean seeds containing globular stage embryos

growth_protocol: Scarlet runner bean plants (Hammond's Dwarf Red Flower) were grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22C. Flowers were hand-pollinated and tagged (Chen et. al., Plant embryogenesis: Methods and protocols, 2020)

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp. Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 10 ug of an antibody raised against the peptide PNSPTTSVNQTYFQ corresponding to the amino acids 176-190 of Scarlet Runner Bean WOX9-like protein (GenBank No. ACL11801). Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.

treatment_protocol: Six days after hand pollination, seeds with length between 1.6mm and 2.5mm were harvested and only micropylar half seeds containing globular-stage embryos were collected and crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes. Tissues were rinsed twice with deionized water and stored at -80C until use.

value: Hammond's Dwarf Red Flower

tag: developmental stage

value: globular stage

value: micropylar half seeds

tag: antibody


title: WT1_1

source_name: WT1 rep1

tag: tissue

value: leaves

value: Daepoong

value: Leaves of well-watered (WT1)


title: glob-micropylar-WOX9-like-ChIP replicate 2

value: anti-peptide PcWOX9-like


title: Ad lib_NIA_replicate_5

value: male

value: liver


title: DR1_1

source_name: DR1 rep1

value: Leaves drought-treated 4 hours (DR1)


title: SC-RNASeq_YC1_S2_L001

description: total RNA


title: ATMT_insertions_URA_NATR

description:
JEBPN03_EarlyHits_index8_TCAAGT_L007
processed data file: Insertional_results.csv

value: SC -Ura +NAT


title: Ad lib_NIA_replicate_3

value: Ad libitum NIA


title: Ad lib_NIA_replicate_1


title: Patient3_tumor [R03B]

value: M

value: Liver

tag: tissue type

value: Tumor


title: WT1_2

source_name: WT1 rep2


title: TW03Gal-9

value: nasopharyngeal carcinomas cell line TW03

value: stable expression of Galectin-9


title: Patient2_tumor [R02B]


title: Patient1_tumor [R01B]

value: F


title: Caco2-TET2

status: Public on Jul 12 2020

city: guangzhou

first: Li

last: Changpeng

address: kai yuan road

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: hg38
Supplementary_files_format_and_content: TPM

source_name: Colorectal Adenocarcinoma cell Caco2-TET2

extract_protocol:
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: Colorectal Adenocarcinoma cell Caco2

tag: cell type

value: Epithelial

value: transfected with TET2 lentivirus


title: sw620-TET2CD

source_name: Colorectal Adenocarcinoma cell sw620-TET2CD

value: Colorectal Adenocarcinoma cell sw620

value: transfected with TET2CD lentivirus


title: Caco2-vector

source_name: Colorectal Adenocarcinoma cell Caco2-vector

value: transfected with vector control lentivirus


title: Patient3_adjacent non-tumor [R03A]

source_name: Adjacent non-tumor_liver

value: Adjacent non-tumor


title: sw620-TET2

source_name: Colorectal Adenocarcinoma cell sw620-TET2


title: Patient2_adjacent non-tumor  [R02A]


title: sw480-TET2

source_name: Colorectal Adenocarcinoma cell sw480-TET2

value: Colorectal Adenocarcinoma cell sw480


title: Ad lib_NIA_replicate_2

tag: strain

value: male

value: liver


title: Patient1_adjacent non-tumor [R01A]


title: Caco2-TET2CD

source_name: Colorectal Adenocarcinoma cell Caco2-TET2CD


title: sw480-vector

source_name: Colorectal Adenocarcinoma cell sw480-vector


title: sw620-vector

source_name: Colorectal Adenocarcinoma cell sw620-vector


title: sw480-TET2CD

source_name: Colorectal Adenocarcinoma cell sw480-TET2CD


title: Phase2_1%input-rep2

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

country: Japan

institute: Tokai University School of Medicine

data_processing:
ChIP-seq data were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC-genome browser (http://genome.ucsc.edu) (Speir et al., 2016).  ChIP peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”.  Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr).  Only reproducible high quality peaks, with a normalized peak score ≥ 15, were considered for further analysis.
RNA-sequenced reads were trimmed with Trimmomatic (v.033; http://www.usadellab.org/cms/?page=trimmomatic) (Bolger et al., 2014) for removal of adapter –and low quality sequences (settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).  Resulting reads were then mapped onto the mouse genome build NCBI37/mm9 with STAR (v2.4.0) (Dobin et al., 2013) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) (Li and Dewey, 2011) according to the settings in the ENCODE long-rna-seq-pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/DAC/STAR_RSEM.sh) with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build NCBI37/mm9 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf.  The resulting bam-files were used to create HOMER (Heinz et al., 2010) tag directories (makeTagDirectory with –keepAll setting).  For analysis of statistical significance among differentially expressed genes the raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) (Robinson et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include BED-files  All genomic coordinates are relative to mm10 mouse assembly.

source_name: BM derived Phase2 cells

growth_protocol: For in vitro differentiation of pro-T cells, bone marrow hematopoietic progenitors were used for input. Bone marrow (BM) was removed from the femurs and tibiae of 2-3 month-old mice. Suspensions of BM cells were prepared and stained for lineage markers using biotin-conjugated lineage antibodies (CD11b, CD11c, Gr1, TER-119, NK1.1, CD19, CD3e), then incubated with streptavidin-coated magnetic beads (Miltenyi Biotec), and passed through a magnetic column (Miltenyi Biotec).  Then, hematopoietic progenitors were cultured on OP9-DLL1 or OP9-DLL4 monolayers using OP9 medium (α-MEM, 20% FBS, 50 μM β-mercaptoethanol, Pen-Step-Glutamine) supplemented with 10 ng/ml of IL-7 (Pepro Tech Inc) and 10 ng/ml of Flt3L (Pepro Tech Inc).  On day 7, cultured cells were disaggregated, filtered through 40-m nylon mesh, and re-cultured on new OP9 monolayers with medium containing 5 ng/ml of IL-7 and 5 ng/ml of Flt3L. In cultures that were continued for longer times, cells were passaged onto fresh OP9-DLL1 monolayers at day 10 and maintained up to day 15 in 1 ng/ml each of IL-7 and Flt3L.

extract_protocol: ChIP-seq; Five to ten million of Phase1 or Phase2 cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%.  The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco).  Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power.  Five g of anti-Rbpj mAbs (a mixture of 2.5 g of 5313 (CST) and 2.5 g of ab180588 (Abcam)) were pre-bound to Dynabeads anti-Rabbit Ig (Invitrogen) and then added to the diluted chromatin complexes in parallel aliquots. The samples were incubated overnight at 4 °C, then washed and eluted for 6 h at 65 °C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 g/ml proteinase K). Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator. ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

value: Cultured on OP9DL1


title: Phase2_Rbpj_ChIP-rep1

tag: chip (antibody)

value: anti-Rbpj mAbs (a mixture of 2.5 mg of 5313 (CST) and 2.5 mg of ab180588 (Abcam))


title: Phase2_Rbpj_ChIP-rep2


title: Phase1_Rbpj_ChIP-rep2

source_name: BM derived Phase1 cells


title: Phase2_1%input-rep1


title: Phase1_Rbpj_ChIP-rep1


title: Phase1_1%input-rep2


title: Phase1_sgNotch1+2_DLL4_RNA-rep2

extract_protocol: RNA-seq; Total RNA was isolated from 200,000 cells using an RNAeasy MicroKit (Qiagen).  Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer’s instructions.  Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

value: Cultured on OP9DL4


title: Phase1_sgNotch2_DLL4_RNA-rep2


title: Phase1_sgNotch1_DLL4_RNA-rep2


title: Phase1_sgNotch2_DLL4_RNA-rep1


title: Phase1_sgNotch1+2_DLL4_RNA-rep1


title: Phase1_sgNotch1_DLL4_RNA-rep1


title: Phase1_1%input-rep1


title: Phase1_sgCont_DLL4_RNA-rep2


title: Phase1_sgCont_DLL4_RNA-rep1


title: Phase2_sgNotch1+2_DLL1_RNA-rep1


title: Phase2_sgNotch1+3_DLL1_RNA-rep2


title: Phase2_sgNotch1+3_DLL1_RNA-rep1


title: Phase2_sgNotch3_DLL1_RNA-rep2


title: Phase2_sgNotch1+2_DLL1_RNA-rep2


title: Phase2_sgNotch2_DLL1_RNA-rep2


title: Phase2_sgNotch1_DLL1_RNA-rep1


title: Phase2_sgNotch2_DLL1_RNA-rep1


title: Phase2_sgNotch3_DLL1_RNA-rep1


title: Phase2_sgCont_DLL1_RNA-rep2


title: Phase1_sgNotch1+3_DLL1_RNA-rep2


title: Phase2_sgNotch1_DLL1_RNA-rep2


title: Phase2_sgCont_DLL1_RNA-rep1


title: Phase1_sgNotch1+3_DLL1_RNA-rep1


title: Phase1_sgCont_DLL1_RNA-rep2


title: Phase1_sgNotch2_DLL1_RNA-rep2


title: Phase1_sgNotch1_DLL1_RNA-rep1


title: Phase1_sgNotch3_DLL1_RNA-rep1


title: Phase1_sgCont_DLL1_RNA-rep1


title: Phase1_sgNotch1_DLL1_RNA-rep2


title: Phase1_sgNotch2_DLL1_RNA-rep1


title: Phase1_sgNotch3_DLL1_RNA-rep2


title: HTA_EVminus_1

city: Boston

first: Zhiyun

last: Wei

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
The reads were quality controlled with FastQC, trimmed with Trimmomatic, aligned with HiSat2 to hg38 or mm10, and quantified with HTSeq-count using the Galaxy platform.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: xlsx format; reads count

source_name: Human transformed astrocytes (HTAs)

extract_protocol:
RNA was  isolated using the Total RNA Purification Kit with on-column DNase treatment (Norgen Biotek, Canada).
The libraries were prepared and sequenced on Illumina HiSeq X with PE150 mode to produce approximately 20 M reads per sample by Novogene Co., Ltd.

treatment_protocol: Human transformed astrocytes (HTAs), mouse transgenic EGFRVIII; CDKN2-/-; PTENlox/lox astrocytes (EC), and mouse transgenic EGFRVIII; CDKN2-/-; PTEN-/- astrocytes (ECP) were treated with either 10X complete  glioblastoma conditioned medium (10x EV(+) CM) or the one with extracellular vesicles depleted (10X EV(-) CM).

value: 10X complete  glioblastoma conditioned medium with extracellular vesicles depleted (10x EV(-) CM)


title: HTA_EVminus_2


title: SK-N-SH at TCDD, biological rep1

first: Tuan

last: Xu

state: Beijing

address: 18 Shuangqing Road

department: Research Center for Eco-Environmental Sciences

institute: Chinese Academy of Sciences

description: Expression profiling of TCDD-treated SK-N-SH

hyb_protocol: Then sample was hybridized to a GeneChip® Human Transcriptome Array 2.0 (HTA 2.0, Affymetrix) with 44699 annotated genes for 16-18 hr at 45°C.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

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: human neuroblastoma cell line, exposure, 24 h

label_protocol: fter fragmentation of 2nd-cycle single-stranded cDNA, sample was labeled with biotin by terminal deoxynucleotidyl transferase (TdT).

growth_protocol: SK-N-SH cells were routinely grown in in Dulbecco's modified Eagle's medium (DMEM, DMEM, Gibco, Life Technologies) supplemented with 10% Fetal Bovine Serum Australia Source (FBS, Corning) and the mix of 100 U/ml penicillin with 100 μg/ml streptomycin (1% P/S; DMEM, Gibco, Life Technologies). Cells were grown at 37 °C in a 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted from cell samples using Trizol/Chloroform method, and then purified with magnetic beads of Agencourt Ampure (Beckman Coulter, Brea, CA, USA).

treatment_protocol: Cells were seeded in culture dish at appropriate density for 24-36 hr. At 70% confluency, cells were exposed to TCDD. TCDD was purchased from Wellington Laboratories Inc. (Ontario, Canada) and dissolved in dimethyl sulfoxide (DMSO). TCDD was employed at the low concentration of 10-10 M. DMSO was present at 0.1% or lower for all treatments.

value: brain

value: SK-N-SH


title: HTA_EVplus_1

value: 10X complete  glioblastoma conditioned medium (10x EV(+) CM)


title: Pf3D7_+6h JIB-04 Z_rep 4

city: Dallas

first: Elisabeth

last: Martinez

state: Texas

address: 6000 Harry  Hines Blvd.

department: Department of Pharmacology

institute: UT Southwestern Medical Center

data_processing:
The RNAseq was run on an Illumina NextSeq 500 and the software used for base calling was RTA v2.20.
Raw reads were processed (McDermott Center Bioinformatics Core, UT Southwestern) and aligned (STAR aligner) to the P. falciparum 3D7 transcriptome (PlasmoDB v. 34)
Differential expression analysis was performed using EdgeR (Bioconductor) with a 0.1 RPKM cutoff
Genome_build: PlasmoDB Plasmodium falciparum 3D7 release 34
Supplementary_files_format_and_content: .txt: tab-delimited tables of RPKM normalized read counts

organism: Plasmodium falciparum

source_name: Pf3D7_+6h JIB-04 Z

growth_protocol: Parasites were cultured in standard RPMI medium supplemented with 5% Albumax I, 12 µg/ml hypoxanthine, 23 mM NaHCO3 and 2% human O+ red blood cells. Culturing occurred in 250 ml tissue culture ﬂasks placed in a humidified incubator with a gas composition of 3% O2, 4% CO2 and 93% N2 at 37°C.

extract_protocol:
RNA was isolated according to Trizol LS instructions and precipitated in the presence of linear acrylamide (Amresco).
Samples were prepared from 2 µg of RNA using the Illumina Single-stranded mRNA library kit according to manufacturers’ directions.  RNA and library quality were validated on an Agilent 2100 Bioanalyzer prior to sequencing on an Illumina NextSeq 500.

treatment_protocol: 3D7 parasites were tightly synchronized to a 3-hour window using Percoll-sorbitol gradients. Parasites were seeded into 6-well plates at 4% parasitemia and 2% hematocrit. At 29 hpi, drug was added to each well with a final DMSO concentration of 0.04%.  Four independent replicates were performed for each treatment. One set of cultures was harvested immediately corresponding to 0h treatment and the remaining cultures were harvested after a 6h incubation.  Parasite culture was passed through a Plasmodipur filter (EuroProxima) to remove residual white blood cells.  Parasite pellets were immediately lysed in Trizol LS Reagent (ThermoFisher Scientific) and subsequently snap frozen in liquid nitrogen.

value: red blood cell stage (35hpi +/- 2h)

tag: treated with

value: 4.5 uM JIB-04 Z for 6hrs


title: Pf3D7_+6h JIB-04 Z_rep 3


title: HTA_EVplus_2


title: Phase1_sgNotch1+2_DLL1_RNA-rep2


title: Pf3D7_+6h JIB-04 E_rep 4

source_name: Pf3D7_+6h JIB-04 E

value: 4.5 uM JIB-04 E for 6hrs


title: SK-N-SH at TCDD, biological rep2


title: Pf3D7_+6h JIB-04 E_rep 3


title: Pf3D7_+6h JIB-04 Z_rep 2


title: Pf3D7_+6h JIB-04 Z_rep 1


title: SK-N-SH at DMSO, biological rep2


title: Pf3D7_+6h JIB-04 E_rep 2


title: Pf3D7_+6h vehicle_rep 4

source_name: Pf3D7_+6h vehicle

value: vehicle for 6hrs


title: Pf3D7_+6h vehicle_rep 3


title: Pf3D7_+6h vehicle_rep 2


title: Pf3D7_+6h JIB-04 E_rep 1


title: Dnr7_ant-5x

city: Zurich

first: Jan

last: Krützfeldt

state: Zurich

address: Rämistrasse 100

department: Division of Endocrinology, Diabetes and Clinical Nutrition

country: Switzerland

institute: University Hospital Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the gene annotation as provided by ENCODE release 91.
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Genome_build: Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26
Supplementary_files_format_and_content: tab-delimited text files include identifiers and raw counts

source_name: human myotubes

growth_protocol: Primary human myoblasts were cultured on collagen-coated plates in 1:1 v/v DMEM and Ham´s F-10 Nutrient Mix (Gibco) containing 20% FBS, 5 ng/mL Recombinant Human FGF-2 (Gibco) and 1% penicillin/streptomycin (P/S, Gibco). Differentiation was initiated when myoblasts reached subconfluency by changing the media to DMEM containing 2% horse serum (Gibco) and 1% P/S.

extract_protocol:
Cells were collected and RNA was extracted using TRIzol Reagent (Invitrogen) according to manufacturer´s instruction.
Illumina TruSeq Stranded mRNA Library Prep kit (Cat# 20020594) was used with 500 ng of total RNA for the construction of sequencing libraries. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Primary myoblasts were transfected with miRNA inhibitors (24 nM antagomirs, Sigma) or control antagomirs using Lipofectamine RNAiMAX (Invitrogen). In case of the combination of multiple antagomirs, the total concentration per well was always kept constant at 24 nM. Antagomirs against the let-7 family consisted of a 1:1 mixture of antagomirs directed against let7a-5p and let7c-5p. Twenty-four hours after transfection differentiation was induced for two days before cells were collected.

tag: individual

value: myogenic progenitor cells


title: Dnr5_ant-5x


title: ECP_EVminus_1

source_name: Mouse transgenic EGFRVIII; CDKN2-/-; PTEN-/- astrocytes (ECP)


title: Pf3D7_+6h vehicle_rep 1


title: Phase1_sgNotch1+2_DLL1_RNA-rep1


title: Dnr4_ant-5x


title: Pf3D7_0h_rep 4

value: red blood cell stage (29hpi +/- 2h)

value: none (starting culture at 0h)


title: Dnr7_ant-miR-221


title: SK-N-SH at DMSO, biological rep1


title: Treatment with Enterococcus EME343 rep 4

city: Jout-en-Josas

first: Elliot

last: Mathieu

address: Domaine de Vilvert

department: MICALIS

country: France

institute: INRAE

description: 6 hours incubation of BEAS-2B cells with Streptococcus EMS321 for the treatment/ 6 hours incubation BEAS-2B cells non treated for the control

hyb_protocol: Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50oC for 18h on the Agilent Whole Human 4x44K microarrays (Agilent Technologies Inc., Ref#G2519F)

scan_protocol: Each array was scanned at 10µm with a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with QuantArray software (Perkin Elmer).

data_processing: The signal intensity of all spots was quantified and normalized (Global LOWESS) using ImaGene version 9.0 (BioDiscovery). Statistical analysis was done with MultiExperiment Viewer (MeV) version 4.8 (TM4 microarray software suite, J. Craig Venter Institute).

source_name: Control rep 4

label_protocol: Poly A mRNA were reverse transcribed from 10 µg of total RNA with SuperScript III (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences) before cDNA purification with PCR Purification Kit (Qiagen).

extract_protocol: Total RNA was extracted by TRIzol Reagent (Invitrogen, Ref #15596-026) following manufacturer's protocol and with PhaseLock tubes (Quantabio, Ref #2302830) for nucleic acids separation. Purification was achieved with RNeasy (QIAGEN, RNeasy mini kit, Ref #74104). Quality was assessed by Bioanalyzer (Agilent Technologies). RIN over 8.0 were considered good quality RNA for reverse transcription.

treatment_protocol: BEAS-2B cells were incubated for 6 hours with one of the 7 following bacterial strains: Streptococcus EMS321, Streptococcus EMS383, Streptococcus EMS3101, Enterococcus EME126, Enterococcus EME141, Enterococcus EME343 and Enterococcus EME394.

value: BEAS-2B cells

value: Bronchial epithelial cells

value: RPMI

source_name: Enterococcus EME343 rep 2

value: Enterococcus EME343


title: Treatment with Enterococcus EME394 rep 4

source_name: Enterococcus EME394 rep 4

value: Enterococcus EME394


title: Treatment with Enterococcus EME394 rep 2

source_name: Enterococcus EME394 rep 2

source_name: Control rep 2


title: ECP_EVminus_2


title: Treatment with Enterococcus EME394 rep 1

source_name: Enterococcus EME394 rep 1

source_name: Control rep 1


title: Undifferentiated single colony (No.8) derived from C6 glioma

city: Seoul

first: Jinsoo

last: Oh

address: Yonsei-ro, Shinchon-dong, Seodaemoon-gu

department: Neurosurgery

institute: Yonsei University

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: undifferentiated single colony (No.8) derived from C6 glioma

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: cells were cultured in DMEM containing 10% FBS and P/S.

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

treatment_protocol: Cells were treated with CHIR99021 (20uM) and forskolin (100uM) for 35 days

value: glioma cells


title: Treatment with Enterococcus EME343 rep 2


title: Treatment with Enterococcus EME394 rep 3

source_name: Control rep 3

source_name: Enterococcus EME394 rep 3


title: ECP_EVplus_2


title: Treatment with Enterococcus EME343 rep 1

source_name: Enterococcus EME343 rep 1


title: small molecule induced C6 glioma (SMiG)

description: Gene expression data from C6 glioma treated with forskolin, rapamycin, and I-BET151.

label: biotin-labeled with TdT (terminal deoxynucleotidyl transferase)

source_name: C6 glioma treated with small molecule (Forskolin, rapamycin, I-BET151)


title: Treatment with Enterococcus EME141 rep 3

source_name: Enterococcus EME141 rep 4

value: Enterococcus EME141


title: Undifferentiated C6 glioma (C6)

description: Gene expression data from undifferentiated C6 glioma

source_name: Undifferentiated C6 glioma


title: Treatment with Enterococcus EME141 rep 2

source_name: Enterococcus EME141 rep 3


title: Undifferentiated single colony (No.4) derived from C6 glioma

source_name: undifferentiated single colony (No.4) derived from C6 glioma


title: Treatment with Enterococcus EME141 rep 4

source_name: Control rep 7

source_name: Enterococcus EME141 rep 7


title: EC_EVminus_2

source_name: Mouse transgenic EGFRVIII; CDKN2-/-; PTENlox/lox astrocytes (EC)

value: 10X complete  glioblastoma conditioned medium with extracellular vesicles depleted (10x EV(-) CM)


title: Pf3D7_0h_rep 3


title: Dnr4_ant-miR-221

source_name: human myotubes


title: Pf3D7_0h_rep 2


title: ECP_EVplus_1

source_name: Mouse transgenic EGFRVIII; CDKN2-/-; PTEN-/- astrocytes (ECP)


title: EC_EVminus_1


title: Dnr7_ant-miR-199


title: Pf3D7_0h_rep 1


title: EC_EVplus_2


title: Treatment with Enterococcus EME141 rep 1

source_name: Enterococcus EME141 rep 2

source_name: Control rep 2


title: Input-DNA

city: Shanghai

first: liang

last: yu

address: No. 555, Zuchongzhi Road,Zhang Jiang Hi-Tech Park

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the Pseudomonas aeruginosa PAO1 genome assembly using BBTools version 37.48
Peaks were called using MACS software (version 1.4.2) with the following setting: band width = 300 , Model Fold = [5, 50], pvalue cutoff = 5.00e-02.
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: peak text files

organism: Pseudomonas aeruginosa

source_name: P.aeruginosa cells

growth_protocol: The ΔdsbRS::dsbR-Flag was cultured in LB medium supplemented with tetracycline until the mid-log phase (OD = 0.6, Optical Density).

extract_protocol:
The bactria was treated with 1% formaldehyde for 10 min at 37℃. Crosslinking was stopped by addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl), and then resuspended in 500 µl IP buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail (Roche)) and the DNA was sonicated (JY92-IIDN Ultrasonic Homogenizer) to sizes of 100–300 bp (15% total output, 1-second on, 2-second off, for 30 min on ice). Insoluble cellular debris was removed by centrifugation and the supernatant used as input sample in IP experiments.
DNA fragments (150–250 bp) were selected for library construction and sequencing libraries prepared using the NEXTflex™ ChIP-Seq Kit (Bioo Scientific). The libraries were sequenced using the HiSeq XTen (Illumina). ChIP-seq reads were mapped to the P. aeruginosa MPAO1 genomes, using TopHat (Version 2.0.0) with two mismatches allowed (13).

treatment_protocol: Untreated

tag: chip antibody

value: input


title: Dnr4_ant-miR-199


title: EC_EVplus_1

value: 10X complete  glioblastoma conditioned medium (10x EV(+) CM)


title: Dnr7_ant-miR-125b


title: QS-ago1-A

description:
QS_ago1-A_S21_L003
processed data file: QuantSeq.csv

source_name: yeast

tag: genotype/variation

tag: library strategy

value: QuantSeq


title: DsbR_ChIP-Seq_3

value: anti-Flag


title: DsbR_ChIP-Seq_2


title: Treatment with Enterococcus EME126 rep 2

source_name: Enterococcus EME126 rep 2

tag: cell line

tag: treatment

value: Enterococcus EME126


title: Treatment with Enterococcus EME126 rep 3

source_name: Control rep 3

source_name: Enterococcus EME126 rep 3


title: Dnr5_ant-miR-125b


title: Treatment with Enterococcus EME126 rep 4

source_name: Control rep 4

source_name: Enterococcus EME126 rep 4


title: Ama_KD_Rep5

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. We used STAR aligner to align the reads against Drosophila melanogaster genome version BDGP6 (From Ensembl) and corresponding gene modle is extracted from Ensembl version 90.
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Digital Gene Expression (DGE) data obtained from an aligned library is done using the Dropseq program DigitalExpression (integrated in Drop-seq_tools-1.13). Number of cells that were extracted from aligned BAM file is based on knee plot which extracts the number of reads per cell, then plot the cumulative distribution of reads and select the “knee” of the distribution.
Genome_build: BDGP6
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell

organism: Drosophila melanogaster

source_name: Ama_KD_adult muscle precursors

growth_protocol: Flies were kept at 25 °C in vials containing standard cornmeal- agar medium.

extract_protocol:
Third instar larva were collected, wing discs were dissected, pouch was manually removed using a microblade. Tissue was dissociated into single-cell suspension using a combination of Trypsin and Collagenase. Then  Drop-seq was performed on the single cell suspension. Libraries were made and sequenced.
Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol)

value: wandering third instar larva (25C)

value: Wing discs (notum and hinge, pouch was removed)

value: adult muscle precursors associated with the wing discs and epithelial cells of the presumptive hinge and notum


title: DsbR_ChIP-Seq_1

tag: genotype


title: Ama_KD_Rep4


title: Treatment with Enterococcus EME126 rep 1

source_name: Enterococcus EME126 rep 1

source_name: Control rep 1


title: Ama_KD_Rep1


title: Dnr7_ant-miR-29a

value: myogenic progenitor cells


title: RNAseq of mature seeds of Medicago truncatula NF13157(hsfa9-2)_rep3

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Genome mapping against Mt4.0 was performed using HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts), HISAT2: Version: v2.0.4, Website: http://www.ccb.jhu.edu/software/hisat
Clean reads were mapped to the reference genome Mt4.0 using Bowtie2 to calculate gene expression level with RSEM
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Medicago truncatula

source_name: Medicago truncatula NF13157(hsfa9-2)

growth_protocol: Plants were grown in a culture room in trays containing a sterile mix of vermiculite at 20°C/19°C, with a 16 h light photoperiod at 200 μmol photons m -²s-².

extract_protocol:
Total RNAs were extracted from the frozen grinded seeds lots using the NucleoSpin Extract II, Total RNA Purification kit (Macherey-Nagel, GmbH & Co. KG, Germany) following manufacturer’s instructions
Samples were sent to BGI, Hong Kong, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 24M reads of 50bp per sample

treatment_protocol: After harvest, pods were dried at 43% RH and seeds were stored at 20°C until extraction

value: seed

tag: Stage

value: mature


title: Dnr4_ant-miR-125b


title: RNAseq of mature seeds of Medicago truncatula NF13157 (hsfa9-2)_rep2

source_name: Medicago truncatula NF13157 (hsfa9-2)


title: Treatment with Streptococcus EMS3101 rep 4

source_name: Control rep 9

value: BEAS-2B cells

value: Bronchial epithelial cells

value: RPMI

source_name: Streptococcus EMS3101 rep 9

value: Streptococcus EMS3101


title: Dnr5_ant-miR-29a

source_name: human myotubes


title: Wild type_Rep7

source_name: Wild type_adult muscle precursors


title: Treatment with Streptococcus EMS3101 rep 3

source_name: Streptococcus EMS3101 rep 3


title: Wild type_Rep8


title: Treatment with Streptococcus EMS3101 rep 2

source_name: Streptococcus EMS3101 rep 2

source_name: Control rep 2


title: RNAseq of mature seeds of Medicago truncatula NF10440 (hsfa9-1)_rep3

source_name: Medicago truncatula NF10440 (hsfa9-1)


title: RNAseq of mature seeds of Medicago truncatula NF13157 (hsfa9-2)_rep1


title: Dnr4_ant-miR-29a


title: Dnr5_ant-let7


title: RNAseq of mature seeds of Medicago truncatula NF10440 (hsfa9-1)_rep2


title: Dnr7_ant-let7


title: Wild type_Rep6


title: RNAseq of mature seeds of Medicago truncatula NF10440 (hsfa9-1)_rep1


title: Treatment with Streptococcus EMS3101 rep 1

source_name: Streptococcus EMS3101 rep 1


title: Wild type_Rep5


title: Treatment with Streptococcus EMS383 rep 4

source_name: Streptococcus EMS383 rep 5

value: Streptococcus EMS383


title: Dnr4_ant-let7


title: Wild type_Rep3


title: Dnr5_ant-miR-199


title: Treatment with Streptococcus EMS383 rep 1

source_name: Streptococcus EMS383 rep 1


title: Wild type_Rep4


title: Dnr7_ant-CTR

value: antagomir-control


title: Treatment with Streptococcus EMS383 rep 3

source_name: Control rep 3

source_name: Streptococcus EMS383 rep 4


title: RNAseq of mature seeds of Medicago truncatula R108_rep3

source_name: Medicago truncatula R108


title: Wild type_Rep1


title: RNAseq of mature seeds of Medicago truncatula R108_rep2


title: Wild type_Rep2


title: RNAseq of mature seeds of Medicago truncatula R108_rep1


title: Dnr4_ant-CTR


title: Dnr5_ant-CTR


title: Treatment with Streptococcus EMS321 rep 3

source_name: Streptococcus EMS321 rep 4

value: Streptococcus EMS321


title: Treatment with Streptococcus EMS321 rep 4

source_name: Control rep 4

source_name: Streptococcus EMS321 rep 5


title: Treatment with Streptococcus EMS383 rep 2

source_name: Streptococcus EMS383 rep 2


title: Treatment with Streptococcus EMS321 rep 2

source_name: Streptococcus EMS321 rep 2


title: F33

status: Public on Jul 11 2020

first: Rhonda

middle: D

last: Kineman

state: Illinois

address: 1819 West Polk St

department: Medicine

description:
Kd_FvsC_F_DEG.txt
Kd_I_FvsC_F_DEG.txt
C_FvsC_M_DEG.txt

data_processing:
Illumina CASAVA used for base recognition (Base Calling)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse reference genome sequence (GRCm38/mm10) using STAR v2.5
HTSeq v0.6.1 to count the read numbers mapped of each gene and then, FPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads mapped to the gene (Mortazavi et al., 2008).
Differential expression analysis between groups was done using the DESeq2 R package (2_1.6.3) (Anders and Huber, 2010). The resulting p-values were adjusted using the Benajamini and Hochberg´s method to control the False Discovery Rate (FDR). Genes with an adjusted p-value <0.05 were considered as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: All processed data files are a matrix table with the information of all genes in rows.  Column A: gene ID. Column B-G: normalized readcounts of group A of samples (e.g. Kd_M samples). Column H-M: normalized readcounts of group B of samples (e.g. C_M samples). Column N: log2FoldChange: the result performed by DESeq2 R/EdgeR R package. Column O: pvalue. Column P: padj, corrected pvalue. Column Q: gene name. Column R: name of chromosome in which the gene is located. Column S: Strand, the chain information of the gene. Column T: the start position of the gene at the chromosome. Column U: the end position of the gene at the chromosome. Column V: gene length. Column W: gene type. Column X:  gene function description. Column Y-AJ: readcounts of all samples. Column AK-AV:  fpkm of all samples.

source_name: Liver

growth_protocol: All Ghrfl/fl mice were housed in a specific pathogen-free barrier facility maintained at 22-24C with a 12h light/12h dark cycle and were fed standard chow diet.

extract_protocol:
Livers were weighed and snap-frozen in liquid nitrogen and stored at -80C.  Total RNA from male and female livers (6 mice/sex), from GHR-intact controls, aHepGHRkd and aHepGHRkd+2.0*1011 AAV8-TBGp-rIGF1 mice were extracted using Rneasy Plus Mini Kit (Cat# 74134; Qiagen). Total RNA was quality checked (RIN>7) using the Agilent Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq (RNA libraries and analysis performed by Novogene (https://en.novogene.com/).

treatment_protocol: aHepGHRkd were generated by treating 10-12 week-old male and female Ghrfl/fl littermates with a single lateral tail vein injection of 1.5*1011 genome copies (GC) of an adeno-associated virus serotype 8 (AAV8) vector bearing a hepatocyte-specific thyroxine-binding globulin promoter (TBGp) driving a Cre recombinase transgene [AAV8-TBGp-Cre; Cat # 107787-AAV8, AAV.TBG.PI.Cre.rBG (AAV8), Addgene, Watertown, MA, diluted in 100ul sterile PBS)]. To reconstitute hepatocyte IGF1 expression in aHepGHRkd, a  subset of mice were co-injected with AAV8-TBGp-Cre (1.5*1011 GC) + AAV8-TBGp-rIGF1 (2.0*1011 or 1.0*1011 GC AAV8.TBG.PI.ratIGF1.WPRE.bGH).  Injection of an AAV8-TBGp-Null (Cat # 105536-AAV8, pAAV8.TBG.PI.Null.bGH, Addgene) was used to generate control mice and to equalize the total amount of AAV8 injected in each mouse (3.5*1011 GC).

tag: Sex

value: Female

value: Hepatocyte

value: Control (C )

tag: age of aav-injection

value: 10-12 weeks-old

tag: experiment duration

value: 8 months after AAV-injection

tag: diet

value: Chow diet (Teklad LM-485)


title: F35

description:
Kd_I_FvsC_F_DEG.txt
Kd_I_FvsKd_F_DEG.txt
Kd_I_FvsKd_I_M_DEG.txt

value: aHepGHRkd + rIGF1 2.0 (Kd_I)


title: F34

description:
Kd_FvsC_F_DEG.txt
Kd_I_FvsKd_F_DEG.txt
Kd_FvsKd_M_DEG.txt

value: aHepGHRkd (Kd)


title: Treatment with Streptococcus EMS321 rep 1

source_name: Streptococcus EMS321 rep 1


title: F32


title: F30


title: F31


title: F28