title: C55_B4_L1_8w_RepB_Replicate1


title: DREADDTranscriptomics_Control_45min_dHC_Rep_5

status: Public on Feb 02 2023

type: SRA

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

library_source: transcriptomic

data_processing:
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Assembly: GRCm38
Supplementary files format and content: .tar.gz zipped directories with kallisto output (pseudoaligned read counts and tpm measures of trancripts) containing .h5 and .tsv files

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Trizol
illumina TrueSeq

tag: tissue

value: brain

tag: brain region

value: hippocampus

tag: sub region

value: dHC

tag: animalid

tag: genotype

tag: replicate

tag: group

value: DREADDTranscriptomics

tag: virus

value: Control

tag: treatment

value: Clozapine

tag: timepoint

tag: stimulation frequency

tag: Sex

value: Male


title: DREADDTranscriptomics_hM3Dq_45min_dHC_Rep_4


title: DREADDTranscriptomics_Control_45min_vHC_Rep_3

value: vHC


title: C55_B2_L1_8w_RepB_Replicate1

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

data_processing:
Following quality controls , reads were mapped to the Mus musculus transcriptome (ENSEMBL version 101) using Salmon v 0.13.1 and RNA-seq data were analysed using Seurat packages (v 4.0.1) on R (v 4.0.3).
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of gene expression read counts matrix per gene/cell.

source_name: Murine Epidermal cells

extract_protocol:
Flow citometry was used to sort tomato positive epidermal cells.
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).

treatment_protocol: Lrig1-EGFP-ires-CreERT2 Rosa26-fl/STOP/fl-tdTomato mice received a single topical application of hydroxytamoxifen on tail skin prior wounding.

tag: strain

value: CBA C57BL/6 mixed

tag: cell type

value: Keratinocytes

tag: time

tag: plate

tag: population


title: C55_B3_L1_8w_RepB_Replicate1


title: bat_cb2_spln

city: Oakland

first: Ravi

last: Sachidanandam

state: CA

address: 2945 Webster St

country: USA

institute: Girihlet Inc.

description: From euthanized bat

data_processing:
Kallisto was used to determine transcript expression levels from reads. Kallisto uses pseudo-alignments and is relatively more accepting of errors/variants in reads31
kallisto version 0.44.0 was used to generate the processed files.
A custom reference database of RNA sequences was used, it is attached to this dataset (bat_master_rna.fa)
The reference rna database was indexed using the command: kallisto index -i bat_23 -k 23  bat_master_rna.fa
The processed files were generated using the following commands,
For Single end reads:
kallisto quant -i ref/bat_23 --single -t 30 -l 250 -s 60 -o outfile infile
For Paired-end reads;
kallisto quant -i ref/bat_23  -t 30  -o outfile infileR1 infileR2"
Genome_build: bat_master_rna.fa; a database of bat transcripts were assembled from a variety of sources, and the genes were names on the basis of mouse and/or human homologues
Supplementary_files_format_and_content: Expression values from Kallisto

organism: Chiroptera

source_name: Spleen_from euthanized bat

growth_protocol:
Two immortalized cell lines, derived from R. aegyptiacus bats, were used in the study, including R06EJ (fetus body) and RoNi/7 (adult bat kidney). The R06EJ cells were maintained in Dulbecco's modified Eagle's medium (DMEM)?F-12 GlutaMAX medium, and RoNi/7 cells were maintained in DMEM (Life Technologies, Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (HyClone, Thermo Fisher Scientific, Waltham, MA) and antibiotic-antimycotic (Life Technologies, Thermo Fisher Scientific, Waltham, MA) as previously described. Cells were seeded in 6-well plates (Corning) in the density assuring formation of 80-100% confluent monolayer in 24 hours. Cells either transfected by PolyI:C (using Trans-IT mRNA reagent [Mirrus Bio] per manufacturer?s recommendation), or infected with filoviruses at multiplicity of infection (MOI) of 2 plaque forming units (PFU) per cell as determined previously in Vero E6 cells. After one hour of adsorption, the inoculum was removed, cell monolayers washed three times with phosphate buffered saline (PBS), and two ml of fresh culture medium was added into each well. Cells transfected with PolyI:C were harvested after 6, 12 and 24 hours whereas cells infected with filoviruses were harvested after 8, 12 and 24 hours. Prior to harvesting, cell medium was removed, the monolayer washed twice with PBS, and lysed in 1 ml of TRIzol reagent. Productive filovirus infections in cell culture were confirmed by the presence of eGFP expression [15]. Active replication in the cells was also evidenced by expression of all viral genes (from sequencing data), including MARV, which could not be visualized and did not produce cytopathic effect at harvesting (Table 1)
Viruses:  Recombinant wild-type EBOV, strain Mayinga, was recovered from the full-length clone and support plasmids in HEK 293T cells and passaged twice in Vero E6 cells for amplification, as described previously29. Recombinant wild-type MARV, strain Uganda, was recovered similarly in BHK-21 cells as described previously30 and was also passaged twice in Vero E6 cells for amplification.
Bat experimental protocol: Adult Egyptian rousettes were obtained from a commercial source and quarantined for 30 days under ABSL-2 conditions. Animals were implanted with microchip transponders for animal ID and temperature data collection. For studies with EBOV and MARV, animals were transferred to the Galveston National Laboratory ABSL-4 facility. Animals were segregated into groups of three. Except for one MARV-infected male, all bats were female. Each group was housed in a separate cage for inoculation with the same virus. After acclimation to the facility, animals were anesthetized with isoflurane and infected subcutaneously in the scapular region with 105 focus forming units (FFU; titrated on Vero E6 cells) of EBOV or MARV. Every other day, animals were anesthetized by isoflurane, weighed, temperature was determined via transponder, and 100-150 µL of blood was collected from the propatagial vein. Nucleases in blood were inactivated in 1 mL of TRIzol reagent (Thermo-Fisher Scientific). Samples were then removed from ABSL-4 containment, and RNA was extracted. Droplet-digital RT-PCR (ddRT-PCR) with primers specific to the nucleoprotein (NP) gene was used to detect viremia. If fewer than 106 MARV RNA copies/mL viremia were detected in a MARV-inoculated bat, the animal was observed for additional 2 days to allow the animal to reach a higher viral RNA load. In 48-96 hours after first observation of viremia, the animal was euthanized under deep isoflurane sedation via cardiac exsanguination confirmed by bilateral open chest. All EBOV-inoculated bats were euthanized 48 hours after the first detection of viremia, independent of viral RNA load. Tissues were collected (listed in Table S1) and immediately homogenized in an appropriate volume of TRIzol reagent and stored at -80°C. Tissue sections were also homogenized in minimal essential media (MEM) supplemented with 10% fetal bovine serum and stored at -80°C. Additional tissue sections were fixed in 10% neutral buffered formalin for histopathology.
All animal procedures were performed in compliance with protocols approved by the Institutional Animal Care and Use Committee at the University of Texas Medical Branch at Galveston.

extract_protocol:
Tissues and PBMCs were also collected from three uninfected control animals. Given that the course of infection appears to be relatively short in these animals21, we sacrificed them shortly after onset of viremia in the infected animals to ensure adequate capture of changes in transcriptional dynamics. As such, animals were bled every other day, and viral loads were assessed via ddRT-PCR. In addition, animals were weighed, and temperature was determined with each bleed.
Total RNA was isolated from samples using Ambion's RNA isolation and purification kit. PolyA-tailed mRNA was selected using beads with oligo-deoxythymidine and then fragmented. cDNA was synthesized using random hexamers and ligated with bar-coded adaptors compatible with Illumina's NextSeq 500. A total of 88 samples, as 75 nucleotide-long single-end reads, were sequenced on the NextSeq

treatment_protocol: Myotis lucifugus bats infected with RV. For a separate rabies study, bats were inoculated at 104 , 50% tissue culture infectious dose (TCID50) with a Myotis lucgus RV variant in their deltoid muscle.  Bats were inoculated, maintained, and euthanized as described earlier [28].  Brain, lung, and spleen tissue were aseptically collected from control and RV-inoculated bats following euthanasia due to clinical RV infection or at the end of the study (Table 2). Tissues were placed in 800 µl Trizol (Ambion) and stored at -80 oC until further processing could occur.

tag: tissue/cell line

value: Spleen

value: From euthanized bat


title: C55_B12_L1_8w_RepB_Replicate1


title: bat_cb2_lvr

description: From euthanized bat

source_name: Liver_from euthanized bat

value: Liver


title: DREADDTranscriptomics_hM3Dq_45min_dHC_Rep_3

tag: tissue

tag: brain region


title: 20190822_208480731120_FFX S16 21626 B5_02

type: RNA

city: Boston

first: Sonu

last: Subudhi

state: MA

address: 100 Blossom St, Cox 7

department: Radiation Oncology

institute: Massachusetts General Hospital

description: RNA was extracted and Nanostring performed by the Center for Advanced Molecular Diagnostics (CAMD) at Brigham and Women's Hospital

data_processing: Nanostring raw data was normalized to housekeeping genes in nCounter Software (Default settings)

organism: Homo sapiens

source_name: Human Pancreatic Adenocarcinoma

extract_protocol: Total RNA extracted by the Center for Advanced Molecular Diagnostics (CAMD) at Brigham and Women's Hospital

tag: treatment group

value: FFX


title: 20190822_208480731120_FFX S16 29342 C18_03


title: 20190822_208480731120_FFX S16 24760 C11_04


title: bat_cb1_spln

description: From euthanized bat


title: DREADDTranscriptomics_hM3Dq_45min_vHC_Rep_4

tag: sub region

tag: animalid

tag: genotype


title: 20190822_208480731120_FFX S14 14444 B1_05


title: 20190822_208480731120_FFX S14 39606 C5_01


title: DREADDTranscriptomics_hM3Dq_45min_vHC_Rep_2

tag: replicate

tag: group

tag: virus


title: 20190822_208480731120_FFX Iosartan S16 22494 F5_08


title: C55_B10_L1_8w_RepB_Replicate1


title: bat_cb2_kdny

description: From euthanized bat

source_name: Kidney_from euthanized bat

value: Kidney

tag: treatment


title: bat_cb1_lvr

description: From euthanized bat


title: DREADDTranscriptomics_hM3Dq_45min_dHC_Rep_2

tag: timepoint

tag: stimulation frequency

tag: Sex


title: DREADDTranscriptomics_Control_45min_dHC_Rep_3


title: C55_A7_L1_8w_RepB_Replicate1

tag: strain

tag: cell type

tag: time


title: bat_cb1_kdny

description: From euthanized bat

tag: tissue/cell line


title: C55_A9_L1_8w_RepB_Replicate1

tag: plate

tag: population


title: DREADDTranscriptomics_Control_45min_vHC_Rep_2

tag: tissue

tag: brain region


title: DREADDTranscriptomics_Control_45min_dHC_Rep_2

tag: sub region

tag: animalid


title: DREADDTranscriptomics_hM3Dq_45min_vHC_Rep_3

tag: genotype

tag: replicate


title: 20190822_208480731120_FFX Iosartan S15 7950 H10_07

tag: treatment group


title: C55_B11_L1_8w_RepB_Replicate1


title: 20190814_208480351120_control C 67613_10

value: Untreated


title: C55_A6_L1_8w_RepB_Replicate1


title: 20190822_208480731120_FFX Iosartan S15 54377 C20_10


title: bat_brn_6

description: From euthanized bat infected with NAIVE

source_name: Brain_from euthanized bat infected with NAIVE

value: Brain

tag: treatment

value: infected with NAIVE


title: DREADDTranscriptomics_hM3Dq_45min_dHC_Rep_1

value: brain

value: hippocampus

tag: group

tag: virus

tag: timepoint


title: C55_A5_L1_8w_RepB_Replicate1

tag: strain


title: bat_ab11_tsts_nv_1

description: From euthanized bat infected with Marburg with Ebola GP

source_name: Testes_from euthanized bat infected with Marburg with Ebola GP

value: Testes

value: infected with Marburg with Ebola GP


title: 20190814_208480351120_control C 6245_11


title: bat_brn_9

description: From euthanized bat infected with NAIVE


title: 20190814_208480351120_control C23 71019_04


title: C55_A3_L1_8w_RepB_Replicate1

tag: cell type


title: 20190814_208480351120_control C19 55539_05


title: DREADDTranscriptomics_Control_45min_vHC_Rep_1

value: DREADDTranscriptomics

value: Control

value: Clozapine

tag: stimulation frequency

tag: Sex


title: DREADDTranscriptomics_Control_45min_dHC_Rep_1

value: dHC

value: Male


title: bat_ab11_smlint_nv_1

source_name: Small Intestine_from euthanized bat infected with Marburg with Ebola GP

tag: tissue/cell line

value: Small Intestine


title: 20190822_208480731120_FFX Iosartan S16 2542 L2_09


title: 20190814_208480351120_control C7 51443_01


title: C55_A2_L1_8w_RepB_Replicate1

value: CBA C57BL/6 mixed

value: Keratinocytes

tag: time

tag: plate

tag: population


title: bat_ab11_slvglnd_nv_1

source_name: Salivary gland_from euthanized bat infected with Marburg with Ebola GP

value: Salivary gland


title: bat_ab11_pbmc_nv_1

source_name: PBMC_from euthanized bat infected with Marburg with Ebola GP

value: PBMC


title: WT_5_M_RNA, batch B

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

data_processing:
FASTQ files were trimmed, filtered, and aligned using the cellranger pipeline from 10X genomics.
snRNA-seq profiles were clustered and visualized using Seurat and Bbrowser (BioTuring).
Assembly: mm39
Supplementary files format and content: raw cell by gene counts matrices generated by cellranger 10X pipeline

molecule: polyA RNA

source_name: Lin- CD11b+ brain cells

extract_protocol:
Brain was homogenized and then immune cells (Lin- CD11b+) were isolated via FACS.
scRNA libraries were constructed using commerically available reagents and protocols from 10X Genomics

tag: batch

value: B

value: Lin- CD11b+ brain cells

value: WT

value: male


title: 20190814_208480351120_control C6 28544_02

value: Untreated


title: C55_A11_L1_8w_RepB_Replicate1


title: WT_4_M_RNA, batch B


title: L5_9W_Rep3

data_processing:
After quality controls, raw reads were processed with Trim Galore! v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to perform quality and adapter trimming (parameters: --stringency 3 –q 20). Trimmed reads were next aligned to the mouse reference genome (UCSC mm10/GRCm38) using HiSat2 v2.2.01 with options -N 1 -L 20 -i S,1,0.5 -D 25 -R 5 --pen-noncansplice 20 --mp 1,0 --sp 3,0 and providing a list of known splice sites. Gene expression levels were quantified with featureCounts v1.6.12(options: -t exon -g gene_name ) using the GENCODE (https://www.gencodegenes.org ) release M20 annotation.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of gene expression read counts per gene/samples.

source_name: Mouse Epidermal Cells

extract_protocol:
Flow citometry was used to sort tomato positive epidermal cells.
Full length mini bulk RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, the Smart-Seq2 biotinylated Oligo(dT) was bound to Dynabeads MyOne Streptavidin T1 beads (Thermo-Fisher) and used to isolate mRNA from the cell lysate. Reverse transcription, amplification and library preparation were performed as for the single cell library preparation doubling the volumes.

treatment_protocol: Lrig1 and Lgr5 -EGFP-ires-CreERT2 Rosa26-fl/STOP/fl-tdTomato mice received a single topical application of hydroxytamoxifen on tail skin prior wounding.

tag: cell population


title: C55_A4_L1_8w_RepB_Replicate1


title: DREADDTranscriptomics_hM3Dq_45min_vHC_Rep_1

tag: tissue

value: brain

tag: brain region

value: hippocampus

tag: sub region

value: vHC

tag: animalid

tag: genotype


title: bat_ab11_lvr_nv_1

source_name: Liver_from euthanized bat infected with Marburg with Ebola GP

value: Liver

tag: treatment

value: infected with Marburg with Ebola GP


title: bat_ab11_spln_nv_1

source_name: Spleen_from euthanized bat infected with Marburg with Ebola GP

value: Spleen


title: WT_3_M_RNA, batch B


title: 20190814_208480351120_control C1 69209_07

tag: treatment group


title: bat_ab11_lrgint_nv_1

source_name: Large Intestine_from euthanized bat infected with Marburg with Ebola GP

value: Large Intestine


title: L5_9W_Rep2

tag: replicate


title: 5XFAD_4_M_RNA, batch B

tag: cell type


title: bat_ab11_lng_nv_1

source_name: Lung_from euthanized bat infected with Marburg with Ebola GP

value: Lung


title: 20190814_208480351120_contorl C16 10481_08


title: L5_9W_Rep1


title: bat_ab11_kdny_nv_2

source_name: Kidney_from euthanized bat infected with Marburg with Ebola GP

value: Kidney


title: 20181220_208264190420_72252_06

value: FFX


title: 5XFAD_2_M_RNA, batch A

value: A


title: 5XFAD_3_M_RNA, batch A


title: L5_8W_Rep2


title: bat_ab11_kdny_nv_1


title: 20181220_208264190420_69809_02


title: L5_8W_Rep1


title: 5XFAD_1_M_RNA, batch A


title: 20181220_208264190420_54769_12


title: 20190814_208480351120_control C5 52944_03


title: bat_ab10_smlint_nv_1

value: Small Intestine


title: 20181220_208264190420_46012_05


title: WT_1_M_RNA, batch A


title: L5_4W_Rep2


title: 20181220_208264190420_36128_04


title: bat_ab10_slvglnd_nv_1

value: Salivary gland


title: 20181220_208264190420_32144_01


title: L5_4W_Rep1


title: L5_8W_Rep3


title: GOT1-/- Th17 replicate 3

city: Baltimore

first: Jonathan

last: Powell

state: MD

address: 1650 Orleans Street

institute: Johns Hopkins University

data_processing:
The Sequenced Reads/raw reads often contain low quality reads or reads with adapters, which will affect the analysis quality and reliability. To avoid this, it's necessary to filter the raw reads and get the clean reads. The procedure of raw reads filtering is as follows:  (1) Remove reads containing adapters;  (2) Remove reads containing N > 10% (N represents base that could not be determined);  (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Mapping clean reads to the reference genome or the transcriptome is the basis for the next following analysis. For human and mice, the species with completed annotation, when only differential expression gene (quantification) analysis is needed, the raw data can map reads to the transcriptome directly. However, in studies on transcript structural variation, such as alternative splicing, variation, the fusion gene, the alignment should be carried out at the genomic level. STAR software is used to accomplish the mapping. The alignment by STAR precisely and effectively performs positioning junction reads for RNA sequencing data analysis.
Mapped regions can be classified as exon, intron, or intergenic region. Exon-mapped reads should be the most abundant type of read when the reference genome is well-annotated. Intron-reads may be derived from pre-mRNA contamination or intron-retention events from alternative splicing. Reads mapped to intergenic regions are mainly because of weak annotation of the reference genome.
The abundance of transcript reflects the gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.
The input data for differential gene expression analysis is read counts from gene expression level analysis. The differential gene expression analysis commonly contains three steps:  1) Read counts Normalization;  2) Model dependent p-value estimation;  3) FDR value estimation based on multiple hypothesis testing.
Cluster analysis is used to find genes with similar expression patterns under various experimental conditions. By clustering genes with similar  expression patterns, it is possible to discern unknown functions of previously characterized genes or functions of unknown genes. In hierarchical  clustering, areas of different colors denote different groups (clusters) of genes, and genes within each cluster may have similar functions or take  part in the same biological process.In addition to the FPKM cluster, the H-cluster are used to cluster the log2(fpkm+1). Genes within the same  cluster exhibit the same trends in expression levels under different conditions.  Tips:When the number of gene in heatmap.xls is between 50 ~30000, we will do analysis of cluster.
Assembly: GRCM38

source_name: in vitro differentiated Th17 cells

growth_protocol: Naïve CD4+ T cells (CD4+CD25-CD62L+CD44-) were FACS sorted on a FACSAria Fusion (BD Biosciences) from C57BL/6 wild-type or T cell specific GOT1-/- mice (6-10 weeks old male or female mice were used unless specified). 1 million cells were activated in 12-well plate coated with 5 µg mL-1 anti-mouse CD3 (clone 2C11, Bio X Cell) and soluble 2 µg mL-1 anti-mouse CD28 (clone 37.51, Bio X Cell)

extract_protocol:
2.5 ng mL-1 TGFβ, 10 ng mL-1 mouse IL-1β, 10 ng mL-1 mouse IL-6, 10 ng mL-1 mouse IL-23, 2 µg mL-1 anti-mouse IFNγ, and 2 µg mL-1 anti-mouse IL-4 for TH17. All cytokines were from PeproTech. All anti-cytokine antibodies were from Bio X Cell. TH17 cells were supplemented with fresh media on day 2. RNA from day 4 differentiated TH17 cells were extracted using RNeasy Micro Kit (QIAGEN) according to the manufacturer’s instructions.
Samples were then sent to Novogene for sequencing and analysis. RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on an Illumina Novaseq sequencer according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on the same machine and paired-end reads were generated.

tag: strain


title: bat_ab10_pbmc_nv_1

value: PBMC


title: bat_ab10_lvr_nv_1


title: L5_2W_Rep3


title: 20181220_208264190420_31082_11


title: GOT1-/- Th17 replicate 2


title: L5_2W_Rep2


title: GOT1-/- Th17 replicate 1


title: L5_2W_Rep1


title: bat_ab10_lng_nv_1


title: WT Th17 replicate 2


title: 20181220_208264190420_18816_03


title: WT Th17 replicate 3


title: bat_ab10_spln_nv_1


title: WT_2_M_RNA, batch A

value: Lin- CD11b+ brain cells

value: WT

tag: Sex


title: L5_4W_Rep3


title: 20181220_208264190420_18401_10


title: bat_ab10_kdny_nv_1

tag: tissue/cell line


title: WT Th17 replicate 1


title: 20181220_208264190420_15760_08


title: bat_ab09_tsts_nv_1

value: Testes


title: Aged, replicate 1, scATAC-seq

city: San Francisco

first: Susanna

last: Rosi

address: 2200 Island Dr

institute: Altos labs

description: 10x Genomics

library_source: genomic

data_processing:
Raw sequencing data were demultiplexed and converted to FASTQ files using the ‘bcl-convert’ command (Illumina, v3.9.3) and aligned to the mm10 reference genome (refdata-cellranger-arc-mm10-2020-A-2.0.0) using cellranger-atac count (v2.1.0).
Assembly: mm10
Supplementary files format and content: Tab-separated ATAC fragment files and corresponding tabix indexes generated by CellRanger.

molecule: genomic DNA

source_name: Hindlimb skeletal muscle

extract_protocol:
Young (3 months old) and aged (28-29 months old) Pax7CreER/+;Rosa26TdTomato/+  female mice were obtained from a breeding colony at UM. All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and the Institutional Animal Care and Committee and were in accordance with the U.S. National Institute of Health (NIH).
Mouse hindlimb muscles were extracted and placed into separate petri dishes containing ice-cold PBS. Using surgical scissors, muscle tissues were minced and placed into 20mL of digestion buffer (DMEM with Collagenase type II (0.2%) and Dispase II (2.5U/mL)) per mouse. Samples were placed on a shaker in a 37˚C incubator for 1.5 hours and mixed by pipette every 30 minutes. The enzymes were then inactivated by addition of 20mL 20% heat-inactivated fetal bovine serum (HI-FBS) in Ham’s F10 media. The solution was passed through a 70um cell strainers, centrifuged, washed in PBS containing 3% BSA, and nuclei isolation was performed according to 10x Demonstrated Protocol CG000375 Revision B starting at step 1.1c. Nuclei from two age-matched mice were pooled prior to sorting, at step 1.1n, and 7-AAD+ nuclei were sorted on a Sony MA900 or MoFlo Astrios 3. Sorted nuclei were then permeabilized according to the same protocol.
10,000 permeabilized nuclei were loaded onto the 10x Genomics Chromium single cell controller and single nuclei were captured into nanoliter-scale gel bead-in-emulsions (GEMs). Single nuclei ATAC library constructions were performed using the ATAC-seq Next GEM kit (10x Genomics). All libraries were submitted for 51x51bp paired-end sequencing on a NovaSeq 6000 with 50,000 targeted reads per cell.

value: Single nuclei

value: Hindlimb skeletal muscle

tag: age

value: 28-29 months


title: L5_1W_Rep2

tag: time


title: bat_ab09_spln_nv_1


title: bat_ab10_lrgint_nv_1


title: Young, replicate 2, scATAC-seq

description: 10x Genomics

value: 3 months


title: bat_ab09_smlint_nv_1

value: infected with Marburg with Ebola GP


title: 20181220_208264190420_9161_07


title: Young, replicate 1, scATAC-seq

description: 10x Genomics


title: L5_0W_Rep2


title: L5_1W_Rep1


title: 20181220_208264190420_4779_09


title: bat_ab09_slvglnd_nv_1


title: L5_0W_Rep3


title: L5_1W_Rep3


title: 20181220_207963871019_79416_11


title: 20181220_207963871019_74281_10


title: bat_ab09_pbmc_nv_2


title: Aged, replicate 2, Hi-C

description: Arima Genomics

data_processing:
Raw sequencing data were trimmed using Cutadapt (v2.6) and aligned as single-end reads to the mm10 reference genome using BWA 'aln' and 'samse'. Paired-end mates were then re-joined and duplicate reads from the same biological sample were removed.
Each chromosome was split into 5 kb bins and the number of interactions in each bin was counted.
The resulting contact maps were converted to .hic files using the 'pre' command in Juicer Tools (v1.22.01).
Assembly: mm10
Supplementary files format and content: Filtered pairwise contact maps at 5 kb resolution ready for conversion to .hic files using Juicer Tools.

extract_protocol:
Young (4 months) and aged (24-26 months) Pax7CreER/+;Rosa26TdTomato/+ female mice were obtained from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hr light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH).
In brief, hind limb muscles were harvested from mice using sterile surgical tools. Muscle tissue was minced and digested in 20 mL of a digestion solution (2.5 U/mL Dispase II and 0.2% [~5500 U/mL] Collagenase Type II in Dulbecco’s modified Eagle medium [DMEM]). Samples were incubated at 37°C for 60 min. Once the digestion was complete, 20 mL of F10 media containing 20% heat inactivated FBS was added into each sample to inactivate enzyme activity. The solution was then filtered through a 70 µm cell strainer into a new 50 mL conical tube and centrifuged at 350× g for 5 min. Subsequently, the protocol for crosslinking low input mammalian cells was followed, as written in the Arima-HiC kit workflow provided by Arima Genomics Inc (San Diego, CA). Briefly, the pellets were re-suspended in 1X PBS and 37% formaldehyde was added to obtain a final concentration of 2% formaldehyde. The samples were inverted and incubated at RT for 10 mins. Arima-Hi-C Stop Solution 1 was added to samples, and they incubated for an additional 5 mins. The samples were then placed on ice to incubate for 15 mins. Cells were pelleted by centrifugation for 5 min at 500 × g, the supernatant was discarded, and cells were resuspended in staining media (2% heat-inactivated FBS, 2 mM EDTA in Hank’s buffered salt solution) and antibody cocktail containing Sca-1:APC (1:400), CD45:APC (1:400), CD11b:APC (1:400), Ter119:APC (1:400), CD29/β1-integrin:PE (1:200), and CD184/CXCR-4: BIOTIN (1:100) and incubated for 30 min on ice in the dark. Cells and antibodies were diluted in 3 mL of staining solution, centrifuged at 350× g for 5 min, and supernatants discarded. Pellets were re-suspended in 200 µL staining solution containing PECy7:STREPTAVIDIN (1:100) and incubated on ice for 20 min in the dark. Again, samples were diluted in 3 mL staining solution, centrifuged, supernatants discarded, and pellets re-suspended in 200 μL staining buffer. Samples were filtered through 70 μm cell strainers before the FACS.
In situ Hi-C was performed using the Arima-HiC Protocol. Approximately 75,000-100,000 sorted muscle cells were crosslinked, permeabilized and chromatin digested as specified by the manufacturer in biological replicates. Restriction fragment ends were then labeled with biotinylated nucleotides and proximal DNA ligated, followed by reversal of cross-links. The DNA was then sheared using Diagenode’s Bioruptor sonicator for 4 cycles of 15 sec on, 90 sec off, then briefly centrifuged. An additional 4 cycles of sonication were performed after centrifugation. The resultant DNA was size-selected using AMPure XP beads followed by verification with the Arima Quality Control 2 assay. Biotinylated junctions were then magnetically isolated with streptavidin coated beads, followed by end-repair, A-tailing, sequencing adaptor ligation and PCR amplification. The resultant libraries were then size-selected using AMPure XP beads and sequenced with 150 bp paired-end reads at a depth of 750 million reads per library on an Illumina NovaSeq flow cell.

value: Muscle stem cells

value: 24-26 months


title: L5_0W_Rep1


title: Aged, replicate 1, Hi-C

description: Arima Genomics


title: L1_9W_Rep3


title: Young, replicate 2, Hi-C

description: Arima Genomics

value: 4 months


title: bat_ab09_pbmc_nv_1


title: L1_9W_Rep2


title: bat_ab09_lvr_nv_2

value: Liver


title: 20181220_207963871019_31389_12


title: 20181220_207963871019_47530_09


title: Young, replicate 1, Hi-C

description: Arima Genomics


title: L1_9W_Rep1


title: bat_ab09_lvr_nv_1


title: L1_8W_Rep3


title: bat_ab09_lrgint_nv_1

value: Large Intestine


title: L1_8W_Rep2


title: 20181220_207963871019_29565_03


title: 20181220_207963871019_72146_06


title: bat_ab09_kdny_nv_1

value: Kidney


title: bat_ab09_lng_nv_1

value: Lung


title: WT_4_F_RNA

library_source: transcriptomic single cell

data_processing:
FASTQ files were trimmed, filtered, and aligned using the cellranger arc pipeline from 10X genomics.
snRNA-seq profiles were clustered and visualized using Seurat.
snATAC-seq profiles were clustered and visualized using ArchR.
Assembly: mm10
Supplementary files format and content: Filtered cell by gene counts matrices (scRNA) and fragments files (scATAC) generated by 10X cellranger arc pipeline.

source_name: brain immune cells

extract_protocol:
Brain was homogenized and then immune cells (CD45+Ly6G-) were isolated via FACS.
Multi-ome (paired snRNA and snATAC) libraries were constructed using commercially available reagents and protocols from 10X Genomics.

treatment_protocol: 6-8 week old mice of each genotype were used for multi-omic analysis.

value: Smad4 F/F

value: F

value: 6-8 weeks

tag: molecule subtype

value: cDNA


title: WT_3_M_RNA

value: M


title: WT_3_M_ATAC

library_source: genomic single cell

value: transposed genomic DNA


title: WT_2_F_RNA


title: 20181220_207963871019_27659_01

source_name: Human Pancreatic Adenocarcinoma


title: L1_4W_Rep3


title: A. pleuropneumoniae whole genome, modQ knockout

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description:
Apleur_modQ_KO
modQ-ON_difference.RDS

data_processing:
For plasmid libraries, reads were base called in super-accuracy mode (dna_r9.4.1_450bps_sup_prom) with demultiplexing, using Guppy 6.0.7 and default parameters.
Read depth was downsampled to 400x per plasmid with ont_fast5_api v4.0.1 (https://github.com/nanoporetech/ont_fast5_api), first filtering for read quality with Filtong v0.2.1 (https://github.com/rrwick/Filtlong).
DNA modification motif discovery and classification was performed with Nanodisco v1.0.3, down-sampling read depth to 400x per plasmid, aligning reads to the pET15b vector containing the relevant mod insert.
For genomic DNA libraries of E. coli and A. pleuropneumoniae, reads were basecalled in high-accuracy mode (dna_r9.4.1_450bps_hac_prom) with demultiplexing, using Guppy 6.1.5 and default parameters, and downsampled to a read depth of 400x per sample.
DNA modification motif discovery and classification was performed with Nanodisco v1.0.3, aligning reads to the E. coli and A. pleuropneumoniae complete genomes.
Assembly: pET15b plasmid (EMD Millipore, catalog number: 69661),  E. Coli genome (ASM584v2),  A. pleuropneumoniae genome (57675_E01)
Supplementary files format and content: RDS objects containing methylation current difference values computed by Nanodisco
Library strategy: Transposase (DNA sequencing)

organism: Actinobacillus pleuropneumoniae

source_name: bacterial culture

growth_protocol: A. pleuropneumoniae isolates were grown on BBL™ blood agar base supplemented with thiamine HCl (0.0005%), NADH (0.0025%), oleic acid bovine albumin complex (5%) consisting of 4.75% bovine serum albumin (Fraction V) in normal saline (with the saline containing 5% NaOH and 0.06% oleic acid) and heat inactivated horse serum (1%) (termed BA/SN) or brain heart infusion (BHI, Oxoid) agar containing β-nicotinamide adenine dinucleotide, NAD (0.01%) at 37°C for 24 h. Escherichia coli strains (DH5α and BL21) were grown overnight in lysogeny broth (LB) supplemented with ampicillin at 100 µg/ml or chloramphenicol at 20 µg/ml as required at 37 °C in a shaker at 200 rpm. For mutant selection, A. pleuropneumoniae strains were grown overnight on BHI-NAD plates with 1 µg/ml of chloramphenicol. The Type III methyltransferase genes were cloned into the pET15b vector (Novagen).

extract_protocol:
Genomic DNA was isolated using the Sigma GenElute kit, or plasmid DNA isolated with the Qiagen miniprep kit.
Nanopore sequencing libraries were prepared from 400 ng of DNA per sample with the Rapid DNA Barcoding kit (RBK004) according to manufacturer’s instructions. A 500 ng pool of 6 indexed plasmid libraries was sequenced on 1 PromethION R9.4.1 flow cells (FLO-PRO002) on a PromethION 24 instrument running MinKNOW 22.03.4. For genomic DNA libraries of E. coli and A. pleuropneumoniae, a 500 ng pool of 10 indexed samples was sequenced on 1 PromethION R9.4.1 flow cells (FLO-PRO002) on a PromethION 24 instrument running MinKNOW 22.08.6.

value: bacterial culture

value: modQ knockout


title: 20181220_207963871019_8342_02


title: L1_4W_Rep2


title: WT_2_F_ATAC


title: A. pleuropneumoniae whole genome, modQ expression

description:
Apleur_modQ_ON
modQ-ON_difference.RDS

value: modQ expression


title: L1_4W_Rep1


title: 20181220_207963871019_5760_04


title: 20181220_207963871019_3557_08


title: WT_1_M_RNA


title: L1_2W_Rep3


title: A. pleuropneumoniae whole genome, modP2 knockout

description:
Apleur_modP2_KO
modP2-ON_difference.RDS

value: modP2 knockout


title: WT_1_M_ATAC


title: A. pleuropneumoniae whole genome, modP2 expression

description:
Apleur_modP2_ON
modP2-ON_difference.RDS

value: modP2 expression


title: L1_2W_Rep2


title: WT_4_F_ATAC


title: KO_4_F_RNA

value: Smad4 cKO


title: A. pleuropneumoniae whole genome, modP1 knockout

description:
Apleur_modP1_KO
modP1-ON_difference.RDS

value: modP1 knockout


title: KO_4_F_ATAC


title: L1_1W_Rep3


title: 20181220_207963871019_7467_07


title: KO_3_M_RNA


title: L1_1W_Rep2


title: L1_8W_Rep1


title: L1_1W_Rep1


title: KO_2_F_RNA


title: KO_3_M_ATAC


title: L1_0W_Rep3


title: NB/Monocyte + Etanercept  T23

city: HOUSTON

first: Leonid

last: Metelitsa

state: TX

address: 3639 Skyline Dr1102 Bates Ave., Ste. 1570

department: Pediatrics

institute: BAYLOR COLLEGE OF MEDICINE/Texas Children's Hospital

data_processing:
QC by FastQC (version 0.11.2)
Mapping and alignment by HISAT2 software (v2.1.0)
transcripts assembly by StringTie software (v1.3.5)
Reads unique to human or mouse genome are split by XenoFilteR
extracts coding genes by custom python scripts
Assembly: human genome: GRCh38 v.84; mouse genome: GRCm38 v.81
Supplementary files format and content: gtf files including FPKM and TPM matrices for each sample

organism: Homo sapiens/Mus musculus xenograft

source_name: PDX

growth_protocol: Total RNA from cell pellets was isolated using the RNeasy Micro Plus Kit (Qiagen). One-step cDNA synthesis and qRT-PCR was performed using the KAPA SYBR Fast One Step qRT-PCR kit (Roche) with the CFX96 Touch RT-PCR Detection System (BioRad). Snap-frozen tumor specimens (30mg) were incubated in RLT buffer (Qiagen) and homogenized using manual microtube homogenizers (BioMasher, Takara). The lysates were sheared using QiaShredder columns (Qiagen). Total RNA was isolated using the RNeasy Micro Plus Kit with gDNA elimination columns (Qiagen).

extract_protocol:
RNA was harvested using the RNeasy Micro Plus Kit (Qiagen)
RNA libraries were generated through polyA capture and reverse transcription of cDNA. Illumina PE150 technology was employed to sequence the sample (Novogene).

value: PDX

value: tumor

value: etanercept-treated

value: NB/Monocyte + Etanercept


title: NB/Monocyte + Etanercept  T24


title: NB/Monocyte + Etanercept  T27


title: KO_2_F_ATAC


title: L1_0W_Rep1


title: KO_1_M_RNA


title: NB/Monocyte + Etanercept  T21


title: NB/Monocyte + Etanercept  T22


title: A. pleuropneumoniae whole genome, modP1 expression

description:
Apleur_modP1_ON
modP1-ON_difference.RDS

value: modP1 expression


title: L1_0W_Rep2


title: siCtrl_Jun_replicate

city: Beijing

first: Siling

last: Fu

address: No. 7, Science Park Road

country: China

institute: National Institute of Biological Sciences, Beijing.

data_processing:
Paired-end reads were aligned to hg38 reference genome using Bowtie2 (V2.2.5) with options: -local-very-sensitive-local-no-unal–no-mixed-no-discordant–phred33 -I 10 -X 700.
Peaks were called using SEACR (V1.3) with the parameters: norm stringent. Peaks were annotated by ChIPseeker (V 3.13) and analyzed by deeptTools(V2.0)
Assembly: hg38
Library strategy: CUT&Tag

source_name: lung

extract_protocol:
Cultured human lung LECs (CC-2527,Lonza) treated with scramble or JUN siRNAs were harvested
Sequencing libraries were generated using a kit (TD902, Vazyme) according to manufacturer’s instructions.. The libraries were sequenced by Illumina Hiseq X10.

value: lung

value: lymphatic endothelial cells

value: siCtrl

tag: antibody

value: anti-c-JUN


title: NB/Monocyte + VEH  T18

value: CTL

value: NB/Monocyte + VEH


title: KO_1_M_ATAC

value: M

value: 6-8 weeks

value: transposed genomic DNA


title: siCtrl_IgG_replicate

value: anti-IgG


title: L1_2W_Rep1

tag: cell population


title: Tumor2 (Mouse 41884), scRNAseq

city: Paris

first: Isabelle

last: Janoueix-Lerosey

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

data_processing:
Alignment with cellranger v3.1.0, default options
Ambient RNA correction with SoupX v0.2.1
Doublet removal with Scrublet v0.2.1, default options
Remove RPL/RPS genes
Remove cells with more than 20% of reads mapping mitochondrial genes
Apply additional coverage based filters to remove low quality cells
Normalization and downstream analysis with Seurat v3.1.5
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts generated by cellranger and corresponding normalized counts generated by Seurat v3

source_name: Tumor2 (Mouse 41884)

growth_protocol: TH-MYCN mice used in this study have been previously described (Weiss et al.,1997). All analyzed mice were heterozygous for the transgene. Bearing tumor mice for the single-cell RNA-seq analysis (42369, 41884 and 42007) were studied at 62, 79 and 63 days, respectively

extract_protocol:
Mouse tumors were cut with scalpels in small fragments. Enzymatic dissociation was performed in GIBCO medium containing 150 µg/mL Liberase™ TL Research Grade (5401020001, Merk) and 150 µg/mL DNase (DN25, Sigma Aldrich), for 30 minutes at 37°C with 400 rpm agitation. Cell suspension was then filtered using a 70 µm cell strainer (130-098-462, Miltenyi Biotec). The cell suspension was washed twice with PBS. Viability was measured using Vi-cell XR Viability Analyzer (Beckman Coulter).
Single-cell RNA-seq was performed with the 10x Genomics Chromium Single Cell 3’ Kit (v3.1) according to the standard protocol

value: Neuroblastoma tumor


title: Tumor3 (Mouse 42007), scRNAseq

source_name: Tumor3 (Mouse 42007)


title: LECs, siJUN, Jun

data_processing:
Paired-end reads were aligned to hg38 reference genome using Bowtie2 (V2.2.5) with options: -local-very-sensitive-local-no-unal–no-mixed-no-discordant–phred33 -I 10 -X 700.
Peaks were called using SEACR (V1.3) with the parameters: norm stringent. Peaks were annotated by ChIPseeker (V 3.13) and analyzed by deeptTools(V2.0)
Assembly: hg38
Supplementary files format and content: bw
Library strategy: CUT&Tag

tag: tissue

value: siJUN


title: Tumor1 (Mouse 42369), scRNAseq

source_name: Tumor1 (Mouse 42369)


title: NB/Monocyte + VEH  T15

value: PDX


title: NB/Monocyte + VEH  T13

value: tumor


title: LECs, siJUN, IgG


title: NB/Monocyte + VEH  T12


title: LECs, siCtrl, Jun


title: CD4+CXCR5+PD1+FOXP3 and ICOS- cells

city: Montreal

first: Woong-Kyung

last: Suh

state: QC

address: 110 Pine avenue, SuhLab

country: Canada

institute: institut de Recherche Clinique de Montreal (IRCM)

description: Single Cell RNAseq

data_processing:
Genome_build: Mus musculus GRCm38.93
We added IRES-YFP-eCRE to the mm10 genome in order to account for the YFP and CRE expression
the alignement was performed using Cellranger V4.0
Supplementary_files_format_and_content: Control.txt and KO.txt: RNA expression Matrix
Supplementary_files_format_and_content: clusters.txt: Cluster identities of the cells
Supplementary_files_format_and_content: 28_12_2020.rdata: R Object (all processed data in it)

source_name: Splenocytes

extract_protocol:
Splenocytes from Foxp3YFP-creIcos+/+(ICOS WT) and Foxp3YFP-creIcosfl/fl(ICOS FC) male mice were isolated 6 dpi with NP-OVA/alum and stained with anti-CD4 alexa fluor 647 (GK1.5, BioLegend), anti-TCRβ PeCy7 (H57-597, BioLegend) and propidium iodide (ThermoFisher). Live (PI-) conventional (YFP-) and regulatory (YFP+) CD4+TCRβ+ T cells were sorted with a BD FACSAria (BD Biosciences) and mixed in a 1:10 ratio. A total of 13500 cells from ICOS WT and ICOS FC mice were sent for library preparation
Libraries were generated using the following components from 10x Genomics: Chromium Next GEM Chip G Single Cell kit, Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead kit v3.1, Chromium i7 Multiplex kit

tag: sorting markers

value: CD4+CXCR5+PD1+FOXP3 and ICOS- cells

value: Spleen


title: NB/Monocyte + VEH  T11


title: CD4+CXCR5+PD1+FOXP3 and ICOS+ cells

description: Single Cell RNAseq

value: CD4+CXCR5+PD1+FOXP3 and ICOS+ cells


title: LECs, siCtrl, IgG

value: lung


title: Wild type t8 rep 1 PzevIME1_re-used

status: Public on Feb 01 2023

city: DC

first: Zachory

last: Park

state: Washington DC

address: 37th and O Streets NW

department: Biology

institute: Georgetown University

data_processing:
Reads were mapped using BWA-MEM
Reads were counted using htseqcount
differential expression analysis was conducted with DESeq2
Assembly: SacCer3
Supplementary files format and content: excel file of log2 fold chages from wild type t=0 that were used to construct heat maps for the study

organism: Saccharomyces cerevisiae

extract_protocol:
RNA was harvested using the Qiagen Rneasy kit
Library construction and sequencing was conducted by Novogene Corporation

tag: cell line

value: Wild type

tag: condition

value: Sporulation

tag: overexpression


title: Wild type t2 rep 2 PzevIME1_re-used

tag: genotype


title: Wild type t0 rep 2 PzevIME1_re-used


title: Wild type t4 rep 1 PzevIME1_re-used


title: Wild type t6 rep 2 PzevIME1_re-used


title: Wild type t2 rep 1 PzevIME1_re-used


title: Wild type t8 rep 2 PzevIME1_re-used


title: Wild type t6 rep 1 PzevIME1_re-used


title: Wild type t2 rep 2_re-used


title: Wild type t0 rep 1 PzevIME1_re-used


title: Wild type t12 rep 2_re-used


title: Wild type t6 rep 2_re-used


title: Wild type t12rep 1 PzevIME1_re-used


title: Wild type t4 rep 2_re-used


title: Wild type t4 rep 1_re-used


title: Wild type t6 rep 1_re-used


title: Wild type t0 rep 1_re-used


title: Wild type t0 rep 2_re-used


title: WT t48 rep 2 PzevIME1 PzevRIM4

value: IME1 and RIM4


title: Wild type t12rep 1_re-used


title: Wild type t8 rep 1_re-used


title: Wild type t12 rep 2 PzevIME1_re-used


title: WT t24 rep 2 PzevIME1 PzevRIM4


title: Wild type t4 rep 2 PzevIME1_re-used


title: WT t12 rep 2 PzevIME1 PzevRIM4


title: WT t48 rep 1 PzevIME1 PzevRIM4


title: Wild type t8 rep 2_re-used


title: WT t0 rep 2 PzevIME1 PzevRIM4


title: WT t12 rep 1 PzevIME1 PzevRIM4


title: kfc1-- t12 rep 2 PzevIME1 PzevRIM4

value: kfc1 --


title: kfc1-- t48 rep 1 PzevIME1 PzevRIM4


title: kfc1-- t0 rep 2 PzevIME1 PzevRIM4


title: kfc1-- t48 rep 2 PzevIME1 PzevRIM4


title: kfc1-- t12 rep 2 PzevIME1


title: kfc1-- t0 rep 1 PzevIME1 PzevRIM4


title: kfc1-- t12 rep 1 PzevIME1 PzevRIM4


title: kfc1-- t4 rep 2 PzevIME1


title: kfc1-- t24 rep 2 PzevIME1 PzevRIM4


title: kfc1-- t12rep 1 PzevIME1


title: Wild type t2 rep 1_re-used


title: kfc1-- t0 rep 2 PzevIME1


title: kfc1-- t2 rep 2 PzevIME1


title: kfc1-- t24 rep 1 PzevIME1 PzevRIM4


title: kfc1-- t6 rep 2 PzevIME1


title: WT t24 rep 1 PzevIME1 PzevRIM4


title: kfc1-- t8 rep 1 PzevIME1


title: kfc1-- t4 rep 1 PzevIME1


title: kfc1-- t0 rep 1 PzevIME1


title: kfc1-- t6 rep 1 PzevIME1


title: kfc1-- t12 rep 2


title: kfc1-- t6 rep 2


title: kfc1-- t8 rep 2


title: kfc1-- t2 rep 2


title: WT t0 rep 1 PzevIME1 PzevRIM4


title: kfc1-- t8 rep 2 PzevIME1


title: kfc1-- t0 rep 2


title: kfc1-- t8 rep 1


title: kfc1-- t6 rep 1


title: kfc1-- t2 rep 1 PzevIME1


title: kfc1-- t4 rep 1


title: kfc1-- t2 rep 1


title: kfc1-- t12rep 1


title: kfc1-- t0 rep 1


title: kfc1-- t4 rep 2


title: kar4-- t4 rep 1 PzevIME1 PzevRIM4

value: kar4 --


title: kar4-- t4 rep 2 PzevIME1 PzevRIM4


title: kar4-- t8 rep 2 PzevIME1 PzevRIM4


title: kar4-- t8 rep 1 PzevIME1 PzevRIM4


title: kar4-- t0 rep 2 PzevIME1 PzevRIM4


title: kar4-- t0 rep 1 PzevIME1 PzevRIM4


title: kar4-- t12 rep 2 PzevIME1


title: kar4-- t2 rep 1 PzevIME1 PzevRIM4


title: kar4-- t2 rep 2 PzevIME1 PzevRIM4


title: kar4-- t6 rep 2 PzevIME1


title: kar4-- t4 rep 2 PzevIME1


title: kar4-- t6 rep 2 PzevIME1 PzevRIM4


title: kar4-- t2 rep 2 PzevIME1


title: kar4-- t8 rep 2 PzevIME1


title: kar4-- t6 rep 1 PzevIME1 PzevRIM4


title: kar4-- t12rep 1 PzevIME1 PzevRIM4


title: kar4-- t0 rep 2 PzevIME1


title: kar4-- t12rep 1 PzevIME1


title: kar4-- t8 rep 1 PzevIME1


title: kar4-- t6 rep 1 PzevIME1


title: kar4-- t4 rep 1 PzevIME1


title: kar4-- t12 rep 2 PzevIME1 PzevRIM4


title: kar4-- t0 rep 1 PzevIME1


title: kar4-- t12 rep 2


title: kar4-- t2 rep 1 PzevIME1


title: kar4-- t4 rep 2


title: kar4-- t8 rep 2


title: kar4-- t2 rep 2


title: kar4-- t0 rep 2


title: Wild type t8 rep 2 PzevIME1 PzevRIM4


title: Wild type t2 rep 2 PzevIME1 PzevRIM4


title: Wild type t6 rep 2 PzevIME1 PzevRIM4


title: kar4-- t0 rep 1


title: Wild type t12rep 1 PzevIME1 PzevRIM4


title: kar4-- t12rep 1


title: Wild type t4 rep 2 PzevIME1 PzevRIM4


title: Wild type t0 rep 2 PzevIME1 PzevRIM4


title: Wild type t12 rep 2 PzevIME1 PzevRIM4


title: Wild type t8 rep 1 PzevIME1 PzevRIM4


title: Wild type t2 rep 1 PzevIME1 PzevRIM4


title: Wild type t6 rep 1 PzevIME1 PzevRIM4


title: kar4-- t8 rep 1


title: kar4-- t6 rep 1


title: kar4-- t4 rep 1


title: Wild type t12 rep 2 PzevIME1


title: kar4-- t2 rep 1


title: Wild type t0 rep 1 PzevIME1 PzevRIM4


title: Wild type t4 rep 1 PzevIME1 PzevRIM4


title: Wild type t8 rep 2 PzevIME1


title: kar4-- t6 rep 2


title: Wild type t4 rep 2 PzevIME1


title: Wild type t6 rep 2 PzevIME1


title: Wild type t12rep 1 PzevIME1


title: Wild type t0 rep 2 PzevIME1


title: Wild type t6 rep 1 PzevIME1


title: Wild type t8 rep 1 PzevIME1


title: Wild type t4 rep 1 PzevIME1


title: Wild type t2 rep 1 PzevIME1


title: Wild type t0 rep 1 PzevIME1


title: Wild type t0 rep 2


title: Wild type t2 rep 2


title: Wild type t12 rep 2


title: Wild type t6 rep 1


title: Wild type t0 rep 1


title: Wild type t8 rep 1


title: 210acKO_Late_Rep2

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description:
210a_cKO_9M
YaoP_100118_deSeq2_counts.txt

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Genome Alignment - STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Genome_build: GRCm38 + gencode M17
Supplementary_files_format_and_content: Sample level raw gene counts

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. The RNA was treated by DNase I followed by Pheno-Chroloform extraction.
The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100 ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100-nt are generated for each sample and aligned to the organism specific reference genome.

value: heart

value: Fam210afl/fl, alphaMHCMCM/+

tag: time-points

value: ~10 weeks post tamoxifen injection.

tag: gender

value: Male


title: Wild type t12rep 1


title: Wild type t6 rep 2


title: Wild type t4 rep 2


title: Wild type t8 rep 2


title: Wild type t2 rep 2 PzevIME1


title: Ctrl_Early_Rep4

description:
Myh6Cre_30d_8M
YaoP_031119_deSeq2_counts.txt

value: alphaMHCMCM/+

value: ~5 weeks post tamoxifen injection.


title: Wild type t4 rep 1


title: 210acKO_Late_Rep1

description:
210a_cKO_7M
YaoP_100118_deSeq2_counts.txt


title: Wild type t2 rep 1


title: Ctrl_Early_Rep1

description:
Myh6Cre_30d_4M
YaoP_031119_deSeq2_counts.txt


title: Ctrl_Early_Rep3

description:
Myh6Cre_30d_6M
YaoP_031119_deSeq2_counts.txt


title: Ctrl_Early_Rep2

description:
Myh6Cre_30d_5M
YaoP_031119_deSeq2_counts.txt


title: 210acKO_Early_Rep2

description:
210acKO_30d_5M
YaoP_031119_deSeq2_counts.txt


title: Ctrl_Late_Rep2

description:
Myh6_Cre_9M
YaoP_100118_deSeq2_counts.txt


title: Ctrl_Late_Rep1

description:
Myh6_Cre_8M
YaoP_100118_deSeq2_counts.txt


title: 210acKO_Late_Rep3

description:
210a_cKO_10M
YaoP_100118_deSeq2_counts.txt


title: KRV_Day9, bio replicate 2

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description: 10x Genomics

data_processing:
Samples were sequenced on an Illumina NextSeq 550 to a depth of 20-25k raw paired-end reads per cell, with an average of 12.2k transcripts/cell and 1.4k non-zero genes/cell
The 16-base cell barcode and 10-base UMI from the R1 read were first appended to the corresponding R2 read name as a colon-delimited pair. For all further processing, the reads were treated as single-ended.
Reads with cell barcodes that were not in the 10X barcode dictionary, or had UMIs containing 'N', or had cell barcodes that were observed fewer than 500 times were discarded.
mRNA sequences (R2) were aligned to the rat genome (rn6) using tophat2 (v2.0.12) with default settings and RefSeq transcript annotations.
Gene transcripts were quantified using ESAT (https://github.com/garber-lab/ESAT), again using RefSeq transcript annotations. ESAT ignores reads that result from PCR duplication during the library preparation process using the UMI. If reads from the same cell barcode map to the same gene and have the same UMI, they are considered PCR duplicates, and only one is counted.
The output of ESAT is an array containing the observed transcript countsfor each gene for each cell. Each row of the counts matrix corresponds to one gene and each column corresponds to one cell from the sample.
Assembly: rn6
Supplementary files format and content: Processed data files are in the R language RDS format (*.rds). Files can be read using the readRDS() function in the R base language package.
Supplementary files format and content: Each file contains one matrix for the sample containing the transcript counts for each gene for each cell, with each row corresponding to a gene and each colum corresponding to a cell, labeled by its 16-base cell barcode.

organism: Rattus norvegicus

source_name: pancreas

extract_protocol:
Pancreatic islets were isolatedfrom euthanized animals over a time courseondays7, 9, and 11followingpIC+KRVtreatmentor day 11 followingpICcontrol(n=2 animalsper group)or day 11following PBS control(n=2 animals per group
10X Genomics single-cell library protocol.

value: pancreas

tag: cell type

value: islet cells

tag: treatment

value: poly I:C x3 + KRV

tag: post-treatment day


title: 210acKO_Early_Rep1

description:
210acKO_30d_4M
YaoP_031119_deSeq2_counts.txt

tag: strain


title: KRV_Day9, bio replicate 1

description: 10x Genomics


title: Ctrl_Late_Rep3

description:
Myh6_Cre_11M
YaoP_100118_deSeq2_counts.txt


title: 210acKO_Early_Rep4

description:
210acKO_30d_9M
YaoP_031119_deSeq2_counts.txt


title: KRV_Day7, bio replicate 2

description: 10x Genomics


title: KRV_Day11, bio replicate 2

description: 10x Genomics


title: pIC_Day11, bio replicate 2

description: 10x Genomics

value: poly I:C x3 only


title: KRV_Day7, bio replicate 1

description: 10x Genomics


title: KRV_Day11, bio replicate 1

description: 10x Genomics


title: pIC_Day11, bio replicate 1

description: 10x Genomics


title: 210acKO_Early_Rep3

description:
210acKO_30d_6M
YaoP_031119_deSeq2_counts.txt


title: OVA_HH_2

city: Indianapolis

first: Michelle

last: Chu

state: IN

address: 635 Barnhill Drive

institute: Indiana University

description: Nova_S2_165_Chrm_115_Tepper_6samples_Nov2023

data_processing:
CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Assembly: rn6
Supplementary files format and content: HDF5 file of filtered gene-barcode matrices

source_name: Lung

extract_protocol:
Whole lungs from normoxic and hypoxic (15% FiO2) rats sensitized with OVA (250ug) and challenged with either OVA or PBS were digested with collagenase A (1mg/ml) at 37C, processed into single cell suspensions, and RBCs were lysed with ACK lysing buffer. .
10x Genomics protocol for chromium single cell 3' reagent kits V3

treatment_protocol: Rat breeding pairs were acclimated to either hypoxic (15% FiO2) (CDH) or normoxic/room air (RA) conditions for 3 weeks. Pups born to the breeding pairs were then weaned and raised in the same conditions in which they were born. At 4-6 weeks of age, both hypoxic and normoxic animals received IP OVA (250ug in PBS) and pertussis toxin (50ng) followed by a booster 8-12 days later.  Both hypoxic and normoxic rats were then challenged with either intranasal OVA or a PBS vehicle control for 3 days.

value: Lung

value: Sprague Dawley

value: All lung cells

value: WT

value: Rats were concieved and grown in hypoxic (15% FiO2) conditions, sensitized to OVA, and challenged with OVA.


title: PBS_Day11, bio replicate 1

description: 10x Genomics

value: PBS only


title: OVA_RA_2

description: Nova_S2_165_Chrm_115_Tepper_6samples_Nov2020

value: Rats were concieved and grown in normoxic conditons, sensitized to OVA, and challenged with OVA.


title: PBS_RA_2

description: Nova_S2_121_Chrm_090_Tepper_6samples_Aug2020

value: Rats were concieved and grown in normoxic conditons, sensitized to OVA, and challenged with PBS.


title: PBS_HH_3

description: Nova_S2_121_Chrm_090_Tepper_6samples_Aug2024

value: Rats were concieved and grown in hypoxic (15% FiO2) conditions, sensitized to OVA, and challenged with PBS.


title: PBS_RA_1

description: Nova_S2_121_Chrm_090_Tepper_6samples_Aug2019


title: PBS_HH_2

description: Nova_S2_121_Chrm_090_Tepper_6samples_Aug2023


title: OVA_RA_1

description: Nova_S2_165_Chrm_115_Tepper_6samples_Nov2019


title: PBS_RA_3

description: Nova_S2_121_Chrm_090_Tepper_6samples_Aug2021


title: OVA_RA_3

description: Nova_S2_165_Chrm_115_Tepper_6samples_Nov2021


title: dog1, NaCl, 3

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

data_processing:
In our sequencing strategy read R1 of pooled libraries contains UMI, barcode, oligo(dT) and some low quality sequence after oligo(dT) run. We trim read R1 to keep only UMI and barcode. Our oligo(dT) primers has two parts of UMI split by barcode sequence - we move UMI sequences to be next to each other. For all of this we use single awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq file for read R2 of control and NaCl pools was demultiplexed into separate fastq files for each replica using BRBseqTools (v 1.6) Demultiplex with parameters -p UB -UMI 14 -n 1. Read R2 of each librarry was trimmed to remove potential contamination with poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes. Counts were used for differential gene expression analysis using DESeq2 R package.
Assembly: TAIR10
Supplementary files format and content: count text files

organism: Arabidopsis thaliana

source_name: seeds

growth_protocol: Freshly collected seeds (1 day after harvest) were imbibed at 4C on 1/2 MS medium agar plates or 1/2 MS + 100 mM NaCl agar plates for 72h. After that seeds were colected and frozen for RNA isolation.

extract_protocol:
Frozen seeds were ground and mixed with 0.6 ml of homogenization buffer (100 mM Tris pH 8.5, 5 mM EDTA, 100 mM NaCl, 0.5 % SDS, 1% b-mercaptoethanol). Then, 0.6 ml of chloroform was added, vortexed, and centrifuged for 10 min 14,000g. Supernatant was transfered to new tubes and 0.3 ml of phenol was added and vortexed. Then, 0.3 ml of chloroform was added, vortexed, and centrifuged for 10 min 14,000g at 4°C. 0.5 mL of supernatant was transferred to new tubes, mixed with 0.5 mL acidic phenol-chloroform-isoamyl alcohol, vortexed, and centrifuged for 10 min 14,000g at 4°C. Last step was repeated once more. Then, supernatant was mixed with 0.5 mL of chloroform, vortexed, and centrifuged for 10 min 14,000g at 4°C. Finally, the supernatant was mixed with 10% of the volume of 3M sodium acetate and 80% of the volume of pure isopropanol and incubated for 20 min at -80C. The RNA was pelleted by centrifugation for 30 min 14,000g at 4°C, the pellet was washed with 80% ethanol, dried and resuspended in pure water. DNase treatment of RNA samples was performed following the rigorous treatment from TURBO DNase protocol (ThermoFisher) with the following modifications: after adding DNase buffer to the RNA, the samples were mixed by pippeting up and down 10 times and centrifuged 10,000g for 2 min; and DNase incubation at 37C was 30 min plus 20 min. RNA quality was assessed using gel electrophoresis, NanoDrop, PCR and qPCR, before library construction.
500 ng of RNA was used in reverse transcription with 50 mM different barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled (control and NaCl pools) and pools were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 17 ul of water. 15 ul of recovered cDNA pool was mixed by pipetting with 15 ul of second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 uM dNTPs) and incubated overnight at 16°C. Reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 ul of water. 3 ul of recovered dsDNA sample was used for tagmentation using 3 ul 5x diluted B-loaded Tn5 enzyme (homemade) and 6 ul freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). Reactions were mixed by pipetting and incubated for 7 min at 55°C followed by 5 min at 80°C. Water was added up to 30 ul, samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 11 ul of water. Illumina indexing PCR was performed using 10 ul tagmented DNA in 50 ul reactions with Q5 2× PCR Master Mix (NEB) and 0.5 uM final concentration of primers. Libraries were Illumina Nova-seq sequenced to obtain two reads: R1 (contain barcode and UMI) and R2 (contain mRNA sequence).

treatment_protocol: Half-strength MS media pH 5.7 with 0.8 % plant agar was used. To half of the media 100 mM NaCl was added. Media was autoclaved and plates were prepared. Seeds were imbibed on those plates for 72h at 4C.

value: seeds

value: 1/2 MS + 100mM NaCl


title: dog1, NaCl, 2


title: dog1, NaCl, 1


title: dog1, NaCl, 4


title: Col0, NaCl, 3


title: Col0, NaCl, 4


title: Col0, NaCl, 2


title: PBS_Day11, bio replicate 2

description: 10x Genomics


title: Col0, NaCl, 1


title: OVA_HH_3

description: Nova_S2_165_Chrm_115_Tepper_6samples_Nov2024


title: dog1, control, 4


title: dog1, control, 1


title: PBS_HH_1

description: Nova_S2_121_Chrm_090_Tepper_6samples_Aug2022


title: OVA_HH_1

description: Nova_S2_165_Chrm_115_Tepper_6samples_Nov2022


title: dog1, control, 3


title: Col0, control, 3


title: dog1, control, 2


title: Col0, control, 1


title: IT1

city: East Lansing

first: Dae Kwan

last: Ko

state: MI

address: 612 Wilson Rd.  Plant Biology RM 122

department: Plant Research Laboratories

institute: Michigan State University

data_processing:
ChIP-seq analysis: The quality of raw ChIP-seq reads was evaluated using FastQC (version 0.11.5). Reads were cleaned for quality and adapters with Cutadapt (version 1.8.1) using a minimum base quality of 20 retaining reads with a minimum length of 30 nucleotides after trimming. Quality-filtered reads were aligned to the Col-0 reference genome (TAIR10) using Bowtie (version 1.1.2) with parameters “-n 2 -m 3 -k 1 --threads 7 --best --chunkmbs 256 -q”. Duplicated reads were removed using Samtools (version 1.8). Peak calling was performed using MACS2 (version 2.1.2) in individual samples with input samples pooled for DMSO-only and Tm treated samples and with a relaxed threshold of P-value (--pvalue=1e-2), as recommended by the IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr). Peaks across replicates with an IDR < 0.10 were retained for further analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_peaks.txt: Tab-delimited text files: peak coordinates, annotated genes and scores.

source_name: Whole seedlings

growth_protocol: Surface-sterilized seeds were plated on half-strength Linsmaier Skoog (LS) medium (Caisson Labs, Ontario, Canada) supplemented with 1% sucrose (Sigma-Aldrich, St. Louis, MO, USA), and 1.2% Agar (Acumedia, Lansing, MI, USA). Appropriate antibiotics was also added for screening of transgenic lines. After stratification in the dark at 4 °C for 2 days, plates were transferred to a controlled growth chamber with 80 μmol m−2 s−1 under 16 h light:8 h dark with temperature 22 °C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed in two biological replicates using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) according to manufacturer’s protocol.

treatment_protocol: 5-day-old seedlings were transferred to half-strength LS liquid buffer containing either 0.5 µg/mL Tm (Sigma-Aldrich, St. Louis, MO, USA) or DMSO alone as mock, and treated for 6 hours. After the incubation, the seedlings were transferred to 100x100 square petri dishes with grid (Fisher Scientific, Hampton, NH, USA) containing half-strength LS medium (Caisson Labs, Ontario, Canada) supplemented with 1% sucrose (Sigma-Aldrich, St. Louis, MO, USA), 1.2% Agar (Acumedia, Lansing, MI, USA).

value: pGBF2:GBF2-Ypet (Col-0)

value: Whole seedlings

value: Tunicamycin

tag: chip antibody


title: IT2


title: Col0, control, 4


title: GD2

value: DMSO

value: GFP (Millipore, ab290)


title: ID2


title: GT1


title: GT2


title: GD1


title: ID1


title: Col0, control, 2


title: Ctr_16_rep3

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: cell line, bronchial epithelial cells Beas-2B

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: Beas-2B cells were grown in BEGM media with BEGM SingleQuots (w/o Gentamycin/Amphotericin-B).

extract_protocol: Phenol-Chloroform Precipitation

treatment_protocol: Beas-2B were stimulated with S. pneumoniae strain D39 (Multiplicity of infection (MOI): 0.5 and 1) or LTA for 9 and 16 hours. After 9 and 16 h, RNA was harvested and isolated by Phenol-Chloroform precipitation.

tag: lta treatment

value: no

tag: infection

tag: time


title: LTA_9_rep3

value: yes


title: MOI1_16_rep2

value: Streptococcus pneumoniae MOI 1.0


title: MOI0.5_9_rep3

value: Streptococcus pneumoniae MOI 0.5


title: LTA_16_rep3


title: MOI0.5_16_rep3


title: Ctr_9_rep2


title: LTA_16_rep1


title: LTA_9_rep2


title: MOI1_9_rep1


title: MOI1_16_rep3


title: ds20181001-0693

city: Los Angeles

first: David

last: Cobrinik

address: 4546 Sunset Blvd

institute: Children's Hospital Los Angeles

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to grch38 using HISAT2
Transcript assembly and quantitation were performed using StringTie
Read count extraction was performed using tximport
Assembly: GRCh38

source_name: retinal organoid

extract_protocol:
Retinal organoids were cultured per published protocols (Kuwahara et al., 2015; Zhong et al., 2014) with small changes. At desired timepoints (54-55, 70-71, 76, 83-85, 98-99, 112-113, 126-127, 139-140, and 225 days in culture (DIC)), three organoids with bright and organized neuroepithelial layers when viewed with phase contrast microscopy were placed in 1 ml 10 u/ml papain at 37 o C for 10 min, followed by gentle pipetting with a 1000 ul tip to dissociate larger pieces every 5-10 min (at 37o C for an additional 20-30 min total) to obtain a mostly single-cell suspension. ~ 2 volumes of retina culture media (IMDM, 10% fetal bovine serum (FBS), 0.28 u/ml insulin, 55 uM β-mercaptoethanol, glutamine, penicillin-streptomycin] was added to halt dissociation. Cells were centrifuged at 300 x g for 10 min, resuspended for counting, then recentrifuged and resuspended at 10,000 cell/ul in PBS with 5% FBS and CD133-PE, CD44-FITC, and CD49b FITC antibodies. After 1 h at room temperature, samples were diluted in PBS + 5% FBS, centrifuged, and resuspended in PBS with 1% FBS and 10 ug/ml DAPI. Forward and side scatter and CD133+/CD44,CD49b-low gating was used to enrich for cone photoreceptors. Single cells were directly collected from FACS into 1.2 ul lysis buffer droplets on a parafilm-covered glass slide and transferred to low-adherence tubes for subsequent processing.
Full-length single cell cDNA transcripts were generated using SMART-SeqV4 chemistry from Clontech (now Takara Bio) at ~ 0.1x scale using a Mantis liquid handler. Library preparation was performed using the Nextera XT DNA Library Preparation Kit at reduced volume using Mantis liquid handler and otherwise as per the manufacturer instructions.

value: retinal organoid

value: human embryonic stem cell (H9)

tag: prep method

value: Zhong

tag: prep id

tag: age (dic)

tag: time group

tag: cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia, conesg = cone side group)

tag: reduced data cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia)

tag: final dataset

value: Y

tag: removal reason


title: ds20181001-0689

tag: tissue

tag: cell line


title: ds20181001-0688


title: ds20181001-0691


title: MOI0.5_16_rep2


title: ds20181001-0690

value: MG


title: Ctr_16_rep2


title: MOI0.5_9_rep2


title: ds20181001-0692


title: LTA_9_rep1


title: MOI0.5_9_rep1


title: Ctr_16_rep1


title: ds20181001-0687


title: MOI1_9_rep2


title: Ctr_9_rep1


title: MOI1_9_rep3


title: LTA_16_rep2


title: ds20181001-0686


title: ds20181001-0685


title: ds20181001-0684


title: ds20181001-0683


title: MOI0.5_16_rep1


title: Ctr_9_rep3


title: ds20181001-0681


title: ds20181001-0680


title: MOI1_16_rep1


title: ds20181001-0679

value: RPC/MG

value: cRPC


title: ds20181001-0675


title: ds20181001-0676


title: ds20181001-0677


title: ds20181001-0669


title: ds20181001-0678

value: ConeSG


title: ds20181001-0673


title: ds20181001-0668


title: ds20181001-0670


title: ds20181001-0674


title: ds20181001-0671


title: ds20181001-0672


title: ds20181001-0667


title: ds20181001-0664


title: ds20181001-0682


title: ds20181001-0666


title: ds20181001-0665


title: ds20181001-0662


title: ds20181001-0663


title: ds20181001-0661


title: ds20181001-0659


title: ds20181001-0657


title: ds20181001-0656


title: ds20181001-0654


title: ds20181001-0655


title: ds20181001-0660


title: ds20181001-0658


title: ds20181001-0653


title: ds20181001-0651


title: ds20181001-0652


title: ds20181001-0650


title: ds20181001-0648


title: ds20181001-0649


title: ds20181001-0646


title: ds20181001-0644


title: ds20181001-0645


title: ds20181001-0641


title: ds20181001-0639


title: ds20181001-0642


title: ds20181001-0640


title: ds20181001-0636

value: N


title: ds20181001-0637


title: ds20181001-0633


title: ds20181001-0630


title: ds20181001-0632


title: ds20181001-0627


title: ds20181001-0628


title: ds20181001-0634


title: ds20181001-0629


title: ds20181001-0625


title: ds20181001-0631


title: ds20181001-0623


title: ds20181001-0622


title: ds20181001-0624


title: ds20181001-0626


title: ds20181001-0620


title: ds20181001-0647


title: ds20181001-0621


title: ds20181001-0619


title: ds20181001-0618


title: ds20181001-0638


title: ds20181001-0643


title: ds20181001-0617


title: ds20181001-0616


title: ds20181001-0614


title: ds20181001-0635


title: ds20181001-0613


title: ds20181001-0611


title: ds20181001-0610


title: ds20181001-0608


title: ds20181001-0612


title: ds20181001-0609


title: ds20181001-0605


title: ds20181001-0604


title: ds20181001-0603


title: ds20181001-0602


title: ds20181001-0607


title: ds20181001-0606


title: ds20181001-0600


title: ds20181001-0601


title: ds20181001-0596


title: ds20181001-0597


title: ds20181001-0599


title: ds20181001-0594


title: ds20181001-0593


title: ds20181001-0590


title: ds20181001-0589


title: ds20181001-0591


title: ds20181001-0587


title: ds20181001-0586


title: ds20181001-0588


title: ds20181001-0583


title: ds20181001-0584


title: ds20181001-0580


title: ds20181001-0581


title: ds20181001-0582


title: ds20181001-0579


title: ds20181001-0577


title: ds20181001-0578


title: ds20181001-0598


title: ds20181001-0575


title: ds20181001-0572


title: ds20181001-0595


title: ds20181001-0571


title: ds20181001-0576


title: ds20181001-0574


title: ds20181001-0573


title: ds20181001-0568


title: ds20181001-0567


title: ds20181001-0570


title: ds20181001-0565


title: ds20181001-0564


title: ds20181001-0585


title: ds20181001-0562


title: ds20181001-0566


title: ds20181001-0563


title: ds20181001-0560


title: ds20181001-0559


title: ds20181001-0556


title: ds20181001-0557


title: ds20181001-0558


title: ds20181001-0554

value: Kuwahara


title: ds20181001-0553


title: ds20181001-0552


title: ds20181001-0550


title: ds20181001-0569


title: ds20181001-0549


title: ds20181001-0548


title: ds20181001-0547


title: ds20181001-0546


title: ds20181001-0544


title: ds20181001-0551


title: ds20181001-0539


title: ds20181001-0538


title: ds20181001-0540


title: ds20181001-0536


title: ds20181001-0561


title: ds20181001-0537


title: ds20181001-0534


title: ds20181001-0533


title: ds20181001-0532


title: ds20181001-0555


title: ds20181001-0529


title: ds20181001-0530


title: ds20181001-0531


title: ds20181001-0528


title: ds20181001-0526


title: ds20181001-0527


title: ds20181001-0525


title: ds20181001-0543


title: ds20181001-0524


title: ds20181001-0545


title: ds20181001-0541


title: ds20181001-0521


title: ds20181001-0523


title: ds20181001-0518


title: ds20181001-0520


title: ds20181001-0542


title: ds20181001-0519


title: ds20181001-0517


title: ds20181001-0522


title: ds20181001-0535


title: ds20181001-0516


title: ds20181001-0515


title: ds20181001-0514


title: ds20181001-0511


title: ds20181001-0513


title: ds20181001-0512


title: ds20181001-0510


title: ds20181001-0508


title: ds20181001-0507


title: ds20181001-0509


title: ds20181001-0504


title: ds20181001-0505


title: ds20181001-0506


title: ds20181001-0502


title: ds20181001-0501


title: ds20181001-0503


title: ds20181001-0499


title: ds20181001-0498


title: ds20181001-0497


title: ds20181001-0496


title: ds20181001-0494


title: ds20181001-0495


title: ds20181001-0493


title: ds20181001-0492


title: ds20181001-0490


title: ds20181001-0488


title: ds20181001-0489


title: ds20181001-0486


title: ds20181001-0491


title: ds20181001-0487


title: ds20181001-0485


title: ds20181001-0484


title: ds20181001-0480


title: ds20181001-0482


title: ds20181001-0481


title: ds20181001-0479


title: ds20181001-0500


title: ds20181001-0478


title: ds20181001-0473


title: ds20181001-0483


title: ds20181001-0474


title: ds20181001-0476


title: ds20181001-0472


title: ds20181001-0470


title: ds20181001-0468


title: ds20181001-0475


title: ds20181001-0467


title: ds20181001-0466


title: ds20181001-0471


title: ds20181001-0469


title: ds20181001-0463


title: ds20181001-0465


title: ds20181001-0464


title: ds20181001-0461


title: ds20181001-0459


title: ds20181001-0460


title: ds20181001-0462


title: ds20181001-0455


title: ds20181001-0458


title: ds20181001-0457


title: ds20181001-0453


title: ds20181001-0477


title: ds20181001-0454


title: ds20181001-0452


title: ds20181001-0451


title: ds20181001-0449


title: ds20181001-0447


title: ds20181001-0450


title: ds20181001-0448


title: ds20181001-0445


title: ds20181001-0446


title: ds20181001-0443


title: ds20181001-0444


title: ds20181001-0442


title: ds20181001-0440


title: ds20181001-0439


title: ds20181001-0435


title: ds20181001-0436


title: ds20181001-0437


title: ds20181001-0438


title: ds20181001-0427


title: ds20181001-0423


title: ds20181001-0411


title: ds20181001-0412


title: ds20181001-0410


title: ds20181001-0409


title: ds20181001-0407


title: ds20181001-0406


title: ds20181001-0456


title: ds20181001-0405


title: ds20181001-0408


title: ds20181001-0404


title: ds20181001-0403


title: ds20181001-0428


title: ds20181001-0434


title: ds20181001-0425


title: ds20181001-0426


title: ds20181001-0433


title: ds20181001-0400


title: ds20181001-0441


title: ds20181001-0430


title: ds20181001-0398


title: ds20181001-0399


title: ds20181001-0432


title: ds20181001-0431


title: ds20181001-0397


title: ds20181001-0424


title: ds20181001-0401


title: ds20181001-0402


title: ds20181001-0396


title: ds20181001-0395


title: ds20181001-0394


title: ds20181001-0391


title: ds20181001-0393


title: ds20181001-0392


title: ds20181001-0429


title: ds20181001-0422


title: ds20181001-0419


title: ds20181001-0390


title: ds20181001-0389


title: ds20181001-0420


title: ds20181001-0387


title: ds20181001-0388


title: ds20181001-0386


title: ds20181001-0331

value: iPSC


title: ds20181001-0421


title: ds20181001-0333


title: ds20181001-0385


title: ds20181001-0329


title: ds20181001-0330


title: ds20181001-0328


title: ds20181001-0415


title: ds20181001-0416


title: ds20181001-0418


title: ds20181001-0327


title: ds20181001-0332


title: ds20181001-0326


title: ds20181001-0324


title: ds20181001-0325


title: ds20181001-0413


title: ds20181001-0323


title: ds20181001-0320


title: ds20181001-0417


title: ds20181001-0318


title: ds20181001-0317


title: ds20181001-0321


title: ds20181001-0414


title: ds20181001-0319


title: ds20181001-0316


title: ds20181001-0312


title: ds20181001-0313


title: ds20181001-0315


title: ds20181001-0309


title: ds20181001-0311


title: ds20181001-0304


title: ds20181001-0308


title: ds20181001-0301


title: ds20181001-0307


title: ds20181001-0310


title: ds20181001-0305


title: ds20181001-0300


title: ds20181001-0303


title: ds20181001-0299


title: ds20181001-0296


title: ds20181001-0292


title: ds20181001-0298


title: ds20181001-0294


title: ds20181001-0302


title: ds20181001-0306


title: ds20181001-0295


title: ds20181001-0293


title: ds20181001-0290


title: ds20181001-0291


title: ds20181001-0286


title: ds20181001-0288


title: ds20181001-0297


title: ds20181001-0284


title: ds20181001-0282


title: ds20181001-0281


title: ds20181001-0283


title: ds20181001-0280


title: ds20181001-0289


title: ds20181001-0279


title: ds20181001-0277


title: ds20181001-0278


title: ds20181001-0287


title: ds20181001-0275


title: ds20181001-0285


title: ds20181001-0274


title: ds20181001-0273


title: ds20181001-0272


title: ds20181001-0265


title: ds20181001-0269


title: ds20181001-0270


title: ds20181001-0267


title: ds20181001-0271


title: ds20181001-0268


title: ds20181001-0266


title: ds20181001-0264


title: ds20181001-0262


title: ds20181001-0263


title: ds20181001-0259


title: ds20181001-0260


title: ds20181001-0261


title: ds20181001-0258


title: ds20181001-0276


title: ds20181001-0257


title: ds20181001-0256


title: ds20181001-0255


title: ds20181001-0253


title: ds20181001-0254


title: ds20181001-0252


title: ds20181001-0251


title: ds20181001-0250


title: ds20181001-0249


title: ds20181001-0248


title: ds20181001-0247


title: ds20181001-0245


title: ds20181001-0246


title: ds20181001-0242


title: ds20181001-0244


title: ds20181001-0243


title: ds20181001-0241


title: ds20181001-0240


title: ds20181001-0236


title: ds20181001-0234


title: ds20181001-0238


title: ds20181001-0237


title: ds20181001-0233


title: ds20181001-0232


title: ds20181001-0230


title: ds20181001-0229


title: ds20181001-0231


title: ds20181001-0239


title: ds20181001-0235


title: ds20181001-0228


title: ds20181001-0226


title: ds20181001-0224


title: ds20181001-0227


title: ds20181001-0225


title: ds20181001-0203


title: ds20181001-0204


title: ds20181001-0211


title: ds20181001-0201


title: ds20181001-0223


title: ds20181001-0206


title: ds20181001-0202


title: ds20181001-0199


title: ds20181001-0200


title: ds20181001-0221


title: ds20181001-0197


title: ds20181001-0222


title: ds20181001-0195


title: ds20181001-0215


title: ds20181001-0216


title: ds20181001-0214


title: ds20181001-0213


title: ds20181001-0217


title: ds20181001-0212


title: ds20181001-0193


title: ds20181001-0194


title: ds20181001-0210


title: ds20181001-0209


title: ds20181001-0189


title: ds20181001-0192


title: ds20181001-0191


title: ds20181001-0207


title: ds20181001-0208


title: ds20181001-0188


title: ds20181001-0196


title: ds20181001-0198


title: ds20181001-0205


title: ds20181001-0187


title: ds20181001-0219


title: ds20181001-0186


title: ds20181001-0185


title: ds20181001-0184


title: ds20181001-0182


title: ds20181001-0183


title: ds20181001-0190


title: ds20181001-0181


title: ds20181001-0178


title: ds20181001-0179


title: ds20181001-0177


title: ds20181001-0180


title: ds20181001-0172


title: ds20181001-0173


title: ds20181001-0175


title: ds20181001-0176


title: ds20181001-0169


title: ds20181001-0170


title: ds20181001-0168


title: ds20181001-0171


title: ds20181001-0165


title: ds20181001-0166


title: ds20181001-0164


title: ds20181001-0174


title: ds20181001-0163


title: ds20181001-0167


title: ds20181001-0161


title: ds20181001-0160


title: ds20181001-0220


title: ds20181001-0314


title: ds20181001-0156


title: ds20181001-0158


title: ds20181001-0159


title: ds20181001-0218


title: ds20181001-0154


title: ds20181001-0155


title: ds20181001-0150


title: ds20181001-0152


title: ds20181001-0151


title: ds20181001-0153


title: ds20181001-0147


title: ds20181001-0149


title: ds20181001-0148


title: ds20181001-0143


title: ds20181001-0142


title: ds20181001-0145


title: ds20181001-0162


title: ds20181001-0144


title: ds20181001-0146


title: ds20181001-0141


title: ds20181001-0139


title: ds20181001-0140


title: ds20181001-0138


title: ds20181001-0135


title: ds20181001-0136


title: ds20181001-0133


title: ds20181001-0137


title: ds20181001-0134


title: ds20181001-0132


title: ds20181001-0157


title: ds20181001-0131


title: ds20181001-0130


title: ds20181001-0129


title: ds20181001-0128


title: ds20181001-0126


title: ds20181001-0127


title: ds20181001-0124


title: ds20181001-0120


title: ds20181001-0119


title: ds20181001-0115


title: ds20181001-0114


title: ds20181001-0116


title: ds20181001-0121


title: ds20181001-0112


title: ds20181001-0118


title: ds20181001-0111


title: ds20181001-0110


title: ds20181001-0109


title: ds20181001-0113


title: ds20181001-0107


title: ds20181001-0108


title: ds20181001-0106


title: ds20181001-0125


title: ds20181001-0104


title: ds20181001-0123


title: ds20181001-0103


title: ds20181001-0122


title: ds20181001-0117


title: ds20181001-0105


title: ds20181001-0101


title: ds20181001-0100


title: ds20181001-0099


title: ds20181001-0097


title: ds20181001-0098


title: ds20181001-0095


title: ds20181001-0096


title: ds20181001-0092


title: ds20181001-0088


title: ds20181001-0090


title: ds20181001-0091


title: ds20181001-0084


title: ds20181001-0086


title: ds20181001-0087


title: ds20181001-0093


title: ds20181001-0081


title: ds20181001-0085


title: ds20181001-0089


title: ds20181001-0078


title: ds20181001-0080


title: ds20181001-0079


title: ds20181001-0083


title: ds20181001-0073


title: ds20181001-0077


title: ds20181001-0075


title: ds20181001-0074


title: ds20181001-0094


title: ds20181001-0082


title: ds20181001-0070


title: ds20181001-0076


title: ds20181001-0067


title: ds20181001-0069


title: ds20181001-0068


title: ds20181001-0065


title: ds20181001-0066


title: Neisseria elongata subsp. glycolytica in BSTSY+FBS early exponential

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

data_processing:
Reads adapter-trimmed and filtered using trimmomativ v0.39 (ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:80 SLIDINGWINDOW:4:15) and prinseq-lite v0.20.4 (-min_qual_mean 30 -min_len 25). PhiX contaminant sequences were removed using bbduk.sh of bbmap v38.90 (k=31 hdist=1), as well as further contaminants (human, animal, plant, fungi) removed against repeat-masked references (minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 qtrim=rl trimq=10 untrim). Reads were mapped against the reference genomes using bowtie2 v2.4.4, and index-sorted using samtools v1.9. Reads were counted using the bamCoverage program of deeptools v3.5.1 (Ramírez et al. 2016) in non-overlapping 1kb windows and the resulting bigwig file converted to human-readable format using the bigWigToWig of UCSC v391.
Genome_build: NZ_CP031252.1
Supplementary_files_format_and_content: Read counts in 1kb non-overlapping windows

organism: Neisseria elongata subsp. glycolytica ATCC 29315

source_name: bacterial cells

growth_protocol: Cells grown in modified PY medium 37°C 350 rpm

extract_protocol:
Cells were lysed using lysozyme and Proteinase K, DNA extracted using Phenol-Chloform and precipitated using ammonium acetate (2.5M final concentration), 2X 100% ice-cold Ethanol, and 5 ug/ml glycogen. RNA was degraded by incubation with 10 mg/ml RNase A for 30 min at 37°C, and DNA cleaned up using DNA Clean & Concentrator-5 (Zymo).
Enzymatic shearing; NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina, 150 bp PE sequenced on NovaSeq 6000 S4
WGS

tag: sample type

value: cells


title: ds20181001-0063


title: Neisseria elongata subsp. glycolytica in BSTSY+FBS late exponential


title: ds20181001-0062


title: ds20181001-0072


title: ds20181001-0058


title: ds20181001-0059


title: ds20181001-0071


title: ds20181001-0057


title: ds20181001-0060


title: ds20181001-0061


title: ds20181001-0056


title: ds20181001-0054


title: ds20181001-0055


title: Neisseria elongata subsp. glycolytica in BSTSY+FBS stationary


title: D54-Control-Week1-5

city: Chapel Hill

first: Jason

middle: L

last: Stein

state: NC

address: Neuroscience Research Building 8109C, 115 Mason Farm Rd

department: Genetics

institute: UNC Chapel Hill

description: primary human neural progenitor cells grown in differentiation media

hyb_protocol: GeneChip 3’ IVT Pico Kit (ThermoFisher 902789)

scan_protocol: Affymetrix GeneChip Scanner 3000 7G Plus

data_processing:
Data processed using the rma() function (Robust Multichip Average) using the oligo package in the R programming language.
Clariom_S_Human_HT.r1.pgf
Clariom_S_Human_HT.r1.mps

label: biotin

source_name: phNPCs, control, week 1

growth_protocol: phNPCs grown in differentation media. See methods of PMID: 36629315.

extract_protocol: miRNeasy Mini Kits (QIAGEN 217004) with the inclusion of an on-column DNase digestion (QIAGEN 79254)

treatment_protocol: 1 microgram/mL doxycycline

tag: cell type

value: phNPC

tag: expression

value: Control

tag: replicate

tag: timepoint


title: D54-Control-Week1-4

label_protocol: GeneChip 3’ IVT Pico Kit (ThermoFisher 902789)


title: D54-Control-Week1-3


title: ds20181001-0053


title: D54-4707-Week2-1

source_name: phNPCs, mir4707, week 2


title: D54-4707-Week2-3


title: ds20181001-0052


title: D54-4707-Week1-3

source_name: phNPCs, mir4707, week 1


title: ds20181001-0051


title: ds20181001-0049


title: D54-Control-Week2-1

source_name: phNPCs, control, week 2


title: ds20181001-0047


title: D54-Control-Week2-2


title: ds20181001-0048


title: D54-4707-Week1-6


title: ds20181001-0050


title: ds20181001-0046


title: ds20181001-0045


title: ds20181001-0044


title: D54-4707-Week1-1


title: D54-Control-Week1-6


title: D54-Control-Week2-5


title: ds20181001-0042


title: ds20181001-0040


title: D54-4707-Week1-5


title: D54-4707-Week1-2


title: D54-Control-Week2-4


title: D54-4707-Week2-4


title: ds20181001-0039


title: D54-4707-Week2-5


title: ds20181001-0038


title: D54-4707-Week2-2


title: ds20181001-0036


title: Covid-427, Exp8_sum, Cov.patient_8

city: Cambridgeshire

first: Veronika

last: Goriacha

address: 5 The Quay, St. Ives

country: United Kingdom

institute: HQ Science

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and gene counts) was performed using the differential gene expression (DGE) and differential transcript usage (DTU) pipeline (https://github.com/nanoporetech/pipeline-transcriptome-de). This pipeline uses snakemake, minimap2, salmon, edgeR, DEXSeq and stageR packages.
Assembly: GRCh38 (hg38): Homo_sapiens.GRCh38.cdna.all.fa - transcriptome fasta file
Assembly: GRCh38 (hg38): Homo_sapiens.GRCh38.102.gtf - annotation GFF/GTF file
Supplementary files format and content: results_dge.tsv - results of edgeR differential gene expression analysis.
Supplementary files format and content: all_gene_counts.tsv - the gene count table including all samples

source_name: Venous Human Blood

extract_protocol:
Freshly collected venous blood from ten COVID-19 patients (five male and five female) was sourced through Tissue Solutions Ltd. COVID-19 samples were obtained from hospitals in the United Kingdom according to NHS REC approved protocols (no. REC 19/WS/0164) and with approved consent forms for molecular and genetic analysis. Venous blood from ten healthy donors (five male and five female) was taken at the Radiation, Chemical and Environmental Hazards Directorate, UK Health Security Agency (Chilton, UK) with informed consent and the ethical approval of the West Midlands - Solihull Research Ethics Committee (no. REC 14/WM/1182).
WBCs were isolated from approximately 3-4 ml whole blood samples by a density gradient centrifugation using HetaSep (STEMCell technologies). RNA was extracted from WBC samples using the miRNAeasy Mini kit (Qiagen, Manchester, UK). The quantity of isolated RNA was determined by spectrophotometry with an ND-1000 NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA), and quality was assessed using a Tapestation 220 (Agilent Technologies, Santa Clara, CA, USA).
cDNA was prepared from 50 ng of whole blood RNA using strand-switching and VN primers. After the cDNA synthesis, selective PCR amplification was performed for full-length transcripts before specific adapters were added to start the sequencing. The samples were run in SpotON flow cells in a MinION sequencer.
According to the manufacturer's protocol, reverse transcription reactions were performed with 350 ng RNA using a High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City). Cycling conditions were as follows: 25°C for 10 min, 37°C for 120 min and 85°C for 5 min.
SQK-PCS109 kit

value: Venous Human Blood

value: Blood cells

tag: Sex

value: Female

tag: age

tag: condition

value: Covid-19 infected


title: Covid-428, Exp10_sum, Cov.patient_10


title: ds20181001-0037

value: retinal organoid

value: human embryonic stem cell (H9)

tag: prep method

tag: prep id


title: Covid-277, Exp7_sum, Cov.patient_7

value: Male


title: Covid-278, Exp9_sum, Cov.patient_9


title: ds20181001-0041

tag: age (dic)

tag: time group

value: Y


title: ds20181001-0035

tag: cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia, conesg = cone side group)

value: RPC/MG

tag: reduced data cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia)


title: Covid-425, Exp6_sum, Cov.patient_6


title: D54-4707-Week1-4


title: ds20181001-0043

value: cRPC

tag: final dataset

tag: removal reason


title: D54-4707-Week2-6


title: D54-Control-Week1-1


title: D54-Control-Week1-2


title: Covid-276, Exp5_sum, Cov.patient_5

tag: tissue


title: D54-Control-Week2-6


title: D54-Control-Week2-3


title: ds20181001-0033

tag: cell line


title: Covid-420, Exp4_sum, Cov.patient_4

tag: cell type


title: ds20181001-0032


title: ds20181001-0029


title: Control-P6, C10_sum, H.donor_10

value: Healthy


title: Covid-274-1, Exp1_sum, Cov.patient_1


title: Covid-279, Exp2_sum, Cov.patient_2


title: ds20181001-0102


title: ds20181001-0030


title: Control-H50, C9_sum, H.donor_9


title: ds20181001-0028


title: ds20181001-0026

value: ConeSG


title: ds20181001-0034

value: Kuwahara


title: ds20181001-0025


title: Control-P22, C8_sum, H.donor_8


title: Control-H48, C7_sum, H.donor_7


title: control-P1, C6_sum, H.donor_6


title: Control-H43, C5_sum, H.donor_5


title: ds20181001-0023

value: N


title: ds20181001-0024


title: ds20181001-0027


title: Control-H69, C4_sum, H.donor_4


title: ds20181001-0022


title: Covid-275-1, Exp3_sum, Cov.patient_3


title: Control-H20, C3_sum, H.donor_3


title: ds20181001-0020


title: ds20181001-0019

value: MG


title: Control-H19, C1_sum, H.donor_1


title: ds20181001-0031


title: ds20181001-0018


title: ds20181001-0017


title: ds20181001-0016


title: ds20181001-0014


title: ds20181001-0021


title: Control-H56, C2_sum, H.donor_2


title: ds20181001-0012


title: ds20181001-0011


title: ds20181001-0009


title: ds20181001-0013


title: ds20181001-0008