title: DMSO RS2 CD2

city: London

first: Arnulf

last: Hertweck

address: Gower Street

department: UCL Cancer Institute

country: United Kingdom

institute: University College London

data_processing:
Raw reads were ﬁltered for base quality using FastQC with default parameters and adapters sequences were removed with Trim Galore!
Transcript-level read abundances were created with kallisto using the GRCh38 reference transcriptome
Transcript level abundances were combined at the gene level with tximport and expression estimates were then modelled using DESeq2
Due to a repressive effect of NVP-2 on all pol II-transcribed genes, the data were normalised to the average of the following RNA pol I and pol III transcripts: RNA5S12, RNA5S11, RNA5S3, RNA5S1, RNA5S5, RNA5S10, RNA5S8, RNA5S17, RNA5S4, RNA5S6, RNA5S9, RNA5S14, RNA5S2, RNU6-7, RNA5S15, RN7SK, RNA5S16, RNU6-8, RNA5S7, RNA5S13, RNU6-1, RNU6-2, RNU6-9, RMRP, RN7SL2, RNA5-8SN3, RN7SL1, RPPH1, RNA5-8SN1, RNA5-8SN2, RN7SL3
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM count matrix normalised to RNA pol I and pol II transcripts; tab-delimited text file

source_name: Colonic CD4+ T cells

growth_protocol: CD4+ T cells were isolated from human colon biopsis of Crohn's disease and ulcerative colitis patients by fluorescence-activated cell sorting (FACS) or positive magnetic activated cell separation (MACS)

extract_protocol:
Total RNA was isolated with the RNeasy mini kit (Qiagen)
Libraries were prepared from 10 ng total RNA using the NuGEN Ovation SoLo RNA-Seq Library Preparation kit

treatment_protocol: In RS1 samples, CD4+ T cells isolated from colonic biopsies were stimulated for 3h with PMA (50ng/ml) + ionomycin (1 μM) +/- 1 μM NVP-2. In RS2 samples, CD4+ T cells were cultured in complete media containing IL-2 (1 IU/ml) on plate-bound anti-CD3 and anti-CD28 (2 mg/ml)  for 72 h. Cells were rested in complete media with IL-2 (1 IU/ml) for an additional 48 h then restimulated for 3h with PMA (50ng/ml) + ionomycin (1 μM) +/- 1 μM NVP-2.

tag: disease

value: Crohn's disease

value: DMSO

tag: stimulation

value: 72h plate-bound anti-CD3 and anti-CD28 (2 mg/ml) -> 48h rest -> 3h PMA + ionomycin

tag: stimulation time point

value: day 5


title: NVP2 RS2 CD2

status: Public on Jun 17 2022

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: treatment

value: 72h plate-bound anti-CD3 and anti-CD28 (2 mg/ml) -> 48h rest -> 3h PMA + ionomycin (+ NVP-2)


title: LM17

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were processed and normalised using RMA with Transcriptome analysis Console software

label: biotin

molecule: total RNA

source_name: human melanoma cell line

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Thermo Fisher Scientific).

extract_protocol: RNA was extracted with QIAGEN RNeasy Lipid Tissue Mini kit in accordance with the prescribed protocol provided with the kit.

tag: cell type

value: human melanoma cell line

tag: phenotype

value: S


title: Control_P9_5

city: Vestec

first: Šárka

last: Benešová

address: Prumyslova 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science

data_processing:
Raw reads were trimmed of Illumina sequencing adaptor and bases with reading quality lower than 20 using cutadapt v1.18 49. Reads shorter than 20 bp were filtered out.
Ribosomal RNA and reads mapping to UniVec database were filtered out using bowtie v1.2.2. with parameters -S -n 1 and SortMeRNA database
FASTQ files were mapped to the mouse genome using STAR [version 2.7.0c 48] GRCm38 primary assembly and annotation version M8
Count table was generated by Rsubread v2.0.1 package using default parameters without counting multi-mapping reads
Assembly: GRCm38.p6 (Ensembl)
Supplementary files format and content: Count_matrix_E14.5.txt.gz: Compressed tab seprated text file containing raw counts for control and Isl1 knockout samples of E14.5. Rows corresponds individual genes with ensembl ID and columns to samples.
Supplementary files format and content: Count_matrix_P9.txt.gz: Compressed tab separated text file containing raw counts for control and Isl1 knockout samples of P9. Rows corresponds individual genes with ensembl ID and columns to samples.

organism: Mus musculus

source_name: Pancreas

growth_protocol: Cre/loxP system was used to delete ISL1 from Neurod1+ pancreatic cells

extract_protocol:
The pancreata microdissected from E14.5 embryos were directly trypsinized and prepared for FACS. Briefly, tissue was dissociated using 0.05% trypsin/0.53 mM EDTA at 37oC for 5 min. Digestion was stop by the FACS buffer (2% FBS and 10 mM EGTA in PBS 46), and cells were then 1x washed by FACS buffer. The pancreata from P9-P10 pups were first perfused by 1mg/ml collagenase in Hank’s balanced salt solution, dissected, and incubated at 37oC for 10-12 min to release endocrine cells/islets. Digested pancreatic tissue was washed 3x by 1% FBS in Hank’s solution. To generate single cells, the tissue was further dissociated by trypsinization as described above. Finally, cell suspensions were filtered through 40 μm nylon mesh and immediately tdTomato+ cells were sorted using a flow cytometer (BD FACSAriaTM Fusion), through a 100 μm nozzle in 20 psi, operated with BD FACSDiva™ Software.
For RNA sequencing, 100 sorted cells were collected into individual wells of 96-well plate containing 5 μl of lysis buffer of NEB Next single-cell low input RNA library prep kit for Illumina (New England Biolabs #E6420).

tag: tissue

value: Pancreas

value: endocrine cells

tag: genotype

value: WT


title: LM16


title: K562_DMSO_RNAseq_rep3

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

country: USA

institute: Harvard University

data_processing:
Adapter contamination, polyA read through, and low quality tails were removed using bbduk (version 38.23) with the following parameters: ref=polyA.fa.gz,truseq_rna.fa.gz k=13 int=f ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20.
Read mapping was performed with STAR (version 2.6.0c)  with the following parameters: --genomeDir Homo_sapiens.GRCh38.dna.primary_assembly.fa --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD.
Reads aligned over annotated genes were quantified using HTSeq (version 0.11.2) using the following command: htseq = count -s yes.
Changes in expression calculated through DEseq2 are detailed in the tab-delimited text file: K562_EZH2_DMSO_Differential.txt, containing Transcript_ID in the first column and values for expression change as well as statistical significance in the subsequent columns.
Genome_build: hg38
Supplementary_files_format_and_content: The HTSeq raw count files for each individual sample are provided as well as a summary table, "K562_EZH2_DMSO_Differential.csv", describing the expression changes upon EZH2 inhibition.

source_name: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells, DMSO, 72 hours, Doxycycline 24 hours

growth_protocol: K562 cells were grown in RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
RNA was harvested using the RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).

treatment_protocol: Cells were seeded at 125,000 cell/mL and then treated with DMSO (0.1% v/v) or GSK343 (1µM) for 72 hours. For the final 24 hours of the drug treatment, doxycycline (1µg/mL) was added. Cells were then centrifigued and washed twice with cold PBS before being snap frozen.

tag: cell line

value: chronic myeloid leukemia

value: DMSO (0.1%) for 72 hours and induced with doxcycline (1µg/mL) for the final 24 hours of treatment


title: Control_P9_2


title: Control_P9_4


title: DMSO RS1 CD2

value: 3h PMA  + ionomomycin

value: day 0


title: DMSO US2 CD2

value: 72h plate-bound anti-CD3 and anti-CD28 (2 mg/ml) -> 48h rest -> Unstimulated


title: K562_DMSO_RNAseq_rep2

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells


title: NVP2 RS1 CD2

value: 3h PMA  + ionomomycin (+ NVP-2)


title: Control_P9_3


title: K562_DMSO_RNAseq_rep1


title: K562_DMSO_plus_dox_rep1_in_situ

library_source: genomic

data_processing:
The LIMe-Hi-C data were processed utilizing the CPU version of the JuiceMe (version 1.0.0) pipeline developed for analyzing bisulfite Hi-C reads using Juicertools (version 1.22.01). In situ Hi-C data were processed according to the SLURM version of Juicer pipeline (version 1.6) with Juicertools (version 1.22.01).
Reads were aligned to the hg38 reference genome containing no ALT contigs through bwa-meth (version 0.2.2).
To identify both GpC methylation and CpG methylation, the Biscuit pileup program (version 0.3.16) was utilized with the following parameters: -q 12, -N.
To obtain position specific information on GpC and CpG methylation, the Biscuit vcf2bed program was employed with the following parameters:"-k 3" and -t gch” or “-t hcg” to exclude GpCpG sites, in which methylation signal would be ambiguous.
The bedgraph files generated from the methylation analysis were converted to bigwig format utilizing the bedGraphToBigWig function (UCSC).
Genome_build: hg38
Supplementary_files_format_and_content: Hic files for LIMe-Hi-C experiments were generated using the JuiceMe (version 1.0.0) pipeline and Juicertools (version 1.22.01). Hic files for in situ Hi-C were generated using the Juicer (version 1.6) pipeline and Juicertools (version 1.22.01). Bigwig files f0r GpC and CpG methylation were generated using Biscuit (version 0.3.16) and the bedGraphToBigWig (UCSC) utility.

molecule: genomic DNA

source_name: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells, DMSO 72 hours

extract_protocol:
Cells were fixed in 1% formaldehyde, washed, snap frozen, and stored at -80ºC. Nuclei were lysed, and overnight digestion was performed using DpnII. Digested ends were filled in with biotinylated dATP and in situ ligation was performed. Samples were digested with Proteinase K for and crosslinks were reversed. DNA was purified through an ethanol precipitation and sheared to a size of 300-500 bp with sonication. DNA was size-selected with a double-SPRI magnetic bead purification. At this point, the DNA was split in half for bisulfite (LIMe) and traditional in situ Hi-C, if performed. For the traditional in situ Hi-C workflow, biotinylated fragments were isolated using T1 streptavidin beads, and on bead library preparation was performed on beads according to published precedent. The preparation of bisulfite (LIMe) Hi-C libraries was performed according to the Hi-Culfite protocol. DNA was bisulfite-converted with the EpiTect Fast Bisulfite Conversion Kit (Qiagen). Following bisulfite conversion, biotinylated fragments were purified using C1 streptavidin beads.
LIMe-Hi-C libraries were generated using the Accel-NGS-methyl-Seq Kit (Swift Biosciences) according to the manufacturers protocol with 8-10 cycles of amplification.
LIMe-Hi-C and in situ Hi-C

treatment_protocol: Cells were seeded at 125,000 cell/mL and then treated with DMSO (0.1% v/v) for 72 hours. For the final 24 hours of the treatment, doxycycline (1µg/mL) was added.

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells were treated with DMSO (0.1%) for 72 hours


title: K562_EZH2i_plus_dox_rep2

source_name: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells, EZH2i (GSK343 ) 72 hours, Doxycycline 24 hours

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells were treated with GSK343 (1µM) for 72 hours and induced with doxcycline (1µg/mL) for the final 24 hours of treatment.


title: DMSO RS2 CD1

value: Crohn's disease

value: DMSO

value: 72h plate-bound anti-CD3 and anti-CD28 (2 mg/ml) -> 48h rest -> 3h PMA + ionomycin


title: K562_EZH2i_plus_dox_rep3


title: Control_P9_1


title: ISL1CKO_E14.5_3

value: Isl1 knockout


title: DMSO US1 CD2

value: Unstimulated


title: LM16R

value: human melanoma cell line

value: Ra


title: ISL1CKO_E14.5_4

value: Pancreas

value: endocrine cells


title: ISL1CKO_E14.5_5


title: DMSO US2 CD1

value: day 5


title: TG8f_rep4

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: Organ homogenate, Lung

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

extract_protocol: Trizol, followed by column purification (PeqLAB kit)

treatment_protocol: The line was kept in SPF housing conditions. The generated Fra-2 tg/wt  female and male  mice were used for organ collection at the age of 8 weeks .The animals were euthanized in deep anesthesia. The left lung was fixed in 4% neutral buffered formalin for histology, while the right lung was snap-frozen in liquid nitrogen for molecular biology analysis.

value: transgene

tag: Sex

value: female

tag: age

value: 8 weeks

value: lung homogenate


title: DMSO RS1 CD1

value: 3h PMA  + ionomomycin

value: day 0


title: TG8m_rep4

value: male


title: WT8m_rep3

value: wild type


title: K562_EZH2i_plus_dox_rep1

value: chronic myeloid leukemia

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells were treated with GSK343 (1µM) for 72 hours and induced with doxcycline (1µg/mL) for the final 24 hours of treatment.


title: WT8f_rep4


title: NVP2 RS2 CD1

value: Crohn's disease

value: 72h plate-bound anti-CD3 and anti-CD28 (2 mg/ml) -> 48h rest -> 3h PMA + ionomycin (+ NVP-2)


title: WT8m_rep4


title: WT8f_rep3


title: TG8f_rep3


title: ISL1CKO_E14.5_1

value: Isl1 knockout


title: Control_E14.5_6

value: WT


title: K562_DNMT1i_plus_dox_rep3

source_name: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells, DNMT1i (GSK3482364 ) 72 hours, Doxycycline 24 hours

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells were treated with DNMT1i (10µM) for 72 hours and induced with doxcycline (1µg/mL) for the final 24 hours of treatment.


title: TG8m_rep3


title: K562_DNMT1i_plus_dox_rep2

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells


title: K562_DNMT1i_plus_dox_rep1


title: K562_DMSO_plus_dox_rep3

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells were treated with DMSO (0.1% v/v) for 72 hours and induced with doxcycline (1µg/mL) for the final 24 hours of treatment.


title: Control_E14.5_5

value: Pancreas

value: endocrine cells


title: K562_DMSO_plus_dox_rep2


title: NVP2 RS2 UC1

value: Ulcerative colitis

value: day 5


title: NVP2 RS1 UC1

value: 3h PMA  + ionomomycin (+NVP-2)


title: ISL1CKO_E14.5_2


title: DMSO US1 CD1

value: DMSO

value: Unstimulated

value: day 0


title: DMSO RS1 UC1

value: 3h PMA  + ionomomycin


title: WT8f_rep2

value: wild type

value: female

value: 8 weeks

value: lung homogenate


title: K562_DMSO_minus_dox_rep2

value: chronic myeloid leukemia

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells were treated with DMSO (0.1%) for 72 hours


title: TG8m_rep2

value: transgene

value: male


title: DMSO RS2 UC1

value: 72h plate-bound anti-CD3 and anti-CD28 (2 mg/ml) -> 48h rest -> 3h PMA + ionomycin


title: DMSO US2 UC1

value: 72h plate-bound anti-CD3 and anti-CD28 (2 mg/ml) -> 48h rest -> Unstimulated


title: WT8m_rep2


title: WT8f_rep1


title: Control_E14.5_4

value: Pancreas

value: endocrine cells

value: WT


title: TG8f_rep2


title: WT8m_rep1


title: Control_E14.5_3


title: K562_DMSO_plus_dox_rep1

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells were treated with DMSO (0.1% v/v) for 72 hours and induced with doxcycline (1µg/mL) for the final 24 hours of treatment.


title: K562_DMSO_minus_dox_rep3

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells


title: Control_E14.5_2


title: sample.ginkgo.11766984

status: Public on Jun 16 2022

city: Austin

first: Joshua

last: Urrutia

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_NAND_Circuit/1

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cell culture

extract_protocol:
Total RNA was extracted using Magjet RNA extraction kit (Thermo) according to manufacturer's instructions.
RNA quality was assessed using Tapestation (Agilent). KAPA RNA Hyperprep kit (Roche) was used for ribosomal RNA depletion and Illumina compatible library preparation.

tag: temperature

value: 37.0 celsius

tag: timepoint

value: 5.0 hour


title: sample.ginkgo.11766981

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_pJS007_LALT__backbone/1


title: sample.ginkgo.11767012

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_empty_landing_pads/1


title: sample.ginkgo.11766979

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_IcaR_Gate/1


title: Control_E14.5_1


title: DMSO US1 UC1

value: Ulcerative colitis

value: DMSO

value: Unstimulated

value: day 0


title: sample.ginkgo.11767006

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_pJS007_LALT__P3__PhlF/1


title: sample.ginkgo.11767004


title: sample.ginkgo.11767013

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_PhlF_Gate/1


title: sample.ginkgo.11767003


title: sample.ginkgo.11767018


title: sample.ginkgo.11766995

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_pTACmin/1


title: sample.ginkgo.11766987


title: TG8m_rep1

value: 8 weeks

value: lung homogenate


title: K562_DMSO_minus_dox_rep1

value: chronic myeloid leukemia

value: Flag-NLS-M.CviPI-Lamin-B1 K562 clonal cells were treated with DMSO (0.1%) for 72 hours


title: sample.ginkgo.11766998


title: TG8f_rep1

value: transgene

value: female


title: sample.ginkgo.11766989

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_pBADmin/1


title: sample.ginkgo.11767016


title: sample.ginkgo.11767005


title: sample.ginkgo.11767001


title: sample.ginkgo.11588606


title: sample.ginkgo.11766983


title: sample.ginkgo.11767008


title: sample.ginkgo.11766973


title: sample.ginkgo.11766996


title: sample.ginkgo.11766985


title: sample.ginkgo.11766990

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_pJS007_LALT__I1__IcaRA/1


title: sample.ginkgo.11767011


title: sample.ginkgo.11588579


title: sample.ginkgo.11588592


title: sample.ginkgo.11766994


title: sample.ginkgo.11588584


title: sample.ginkgo.11767010


title: sample.ginkgo.11766977

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/MG1655_WT/1


title: sample.ginkgo.11767017


title: sample.ginkgo.11767014


title: sample.ginkgo.11766982


title: sample.ginkgo.11766974


title: sample.ginkgo.11766986


title: sample.ginkgo.11588589


title: sample.ginkgo.11588599


title: sample.ginkgo.11588789

value: 18.0 hour


title: sample.ginkgo.11588752


title: sample.ginkgo.11588601


title: sample.ginkgo.11588582


title: sample.ginkgo.11588603


title: sample.ginkgo.11588604


title: sample.ginkgo.11588754


title: sample.ginkgo.11588793


title: sample.ginkgo.11588605


title: sample.ginkgo.11588580


title: sample.ginkgo.11588787


title: sample.ginkgo.11588602


title: sample.ginkgo.11588586


title: sample.ginkgo.11588583


title: sample.ginkgo.11588748


title: sample.ginkgo.11588590


title: sample.ginkgo.11588581


title: sample.ginkgo.11588600


title: sample.ginkgo.11588593


title: sample.ginkgo.11588585


title: sample.ginkgo.11588751


title: sample.ginkgo.11588588


title: sample.ginkgo.11588554


title: sample.ginkgo.11588810


title: sample.ginkgo.11588560


title: sample.ginkgo.11588587


title: sample.ginkgo.11588743


title: sample.ginkgo.11588591


title: sample.ginkgo.11588744


title: sample.ginkgo.11588607


title: sample.ginkgo.11588809


title: sample.ginkgo.11588562


title: sample.ginkgo.11588803


title: sample.ginkgo.11588788


title: sample.ginkgo.11588561


title: sample.ginkgo.11588802


title: sample.ginkgo.11588801


title: sample.ginkgo.11588545


title: sample.ginkgo.11588794


title: sample.ginkgo.11588594


title: sample.ginkgo.11588753


title: sample.ginkgo.11588549


title: sample.ginkgo.11588556


title: sample.ginkgo.11588745


title: sample.ginkgo.11588544


title: sample.ginkgo.11588553


title: sample.ginkgo.11588563


title: sample.ginkgo.11588555


title: sample.ginkgo.11588564


title: sample.ginkgo.11588565


title: sample.ginkgo.11588546


title: sample.ginkgo.11588808


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title: sample.ginkgo.11588558


title: sample.ginkgo.11588550


title: sample.ginkgo.11588741


title: sample.ginkgo.11588746


title: sample.ginkgo.11588557


title: sample.ginkgo.11588747


title: sample.ginkgo.11588541


title: sample.ginkgo.11588551


title: sample.ginkgo.11588539


title: sample.ginkgo.11588804


title: sample.ginkgo.11588800


title: sample.ginkgo.11588739


title: sample.ginkgo.11588805


title: sample.ginkgo.11588806


title: sample.ginkgo.11588540


title: sample.ginkgo.11588742


title: sample.ginkgo.11588798


title: sample.ginkgo.11588548


title: sample.ginkgo.11588799


title: sample.ginkgo.11588786


title: sample.ginkgo.11588777


title: sample.ginkgo.11588547


title: sample.ginkgo.11588542


title: sample.ginkgo.11588559


title: sample.ginkgo.11588776


title: sample.ginkgo.11588756


title: sample.ginkgo.11588738


title: sample.ginkgo.11588737


title: sample.ginkgo.11588731

value: 8.0 hour


title: sample.ginkgo.11588783


title: sample.ginkgo.11588735


title: sample.ginkgo.11588734


title: sample.ginkgo.11588552


title: sample.ginkgo.11588740


title: sample.ginkgo.11588733


title: sample.ginkgo.11588811


title: sample.ginkgo.11588796


title: sample.ginkgo.11588543


title: sample.ginkgo.11588778


title: sample.ginkgo.11588775


title: sample.ginkgo.11588755


title: sample.ginkgo.11588797


title: sample.ginkgo.11588615


title: sample.ginkgo.11588757


title: sample.ginkgo.11588795


title: sample.ginkgo.11588732


title: sample.ginkgo.11588678


title: sample.ginkgo.11588736


title: sample.ginkgo.11588695


title: sample.ginkgo.11588758


title: sample.ginkgo.11588616


title: sample.ginkgo.11588677


title: sample.ginkgo.11588638


title: sample.ginkgo.11588596


title: sample.ginkgo.11588675


title: sample.ginkgo.11588577


title: sample.ginkgo.11588597


title: sample.ginkgo.11588697


title: sample.ginkgo.11588635


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title: sample.ginkgo.11588696


title: sample.ginkgo.11588655


title: sample.ginkgo.11588595


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title: sample.ginkgo.11588657


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title: sample.ginkgo.11588572


title: sample.ginkgo.11588656


title: sample.ginkgo.11588571


title: sample.ginkgo.11588698


title: sample.ginkgo.11588636


title: sample.ginkgo.11588529


title: sample.ginkgo.11588578


title: sample.ginkgo.11588658


title: sample.ginkgo.11588637


title: sample.ginkgo.11588575


title: sample.ginkgo.11588676


title: sample.ginkgo.11588574


title: sample.ginkgo.11588532


title: sample.ginkgo.11588505


title: sample.ginkgo.11588468


title: sample.ginkgo.11588513


title: sample.ginkgo.11588477


title: sample.ginkgo.11588517


title: sample.ginkgo.11588501


title: sample.ginkgo.11588487


title: sample.ginkgo.11588519


title: sample.ginkgo.11588573


title: sample.ginkgo.11588470


title: sample.ginkgo.11588507


title: sample.ginkgo.11588528


title: sample.ginkgo.11588488


title: sample.ginkgo.11588485


title: sample.ginkgo.11588503


title: sample.ginkgo.11588476


title: sample.ginkgo.11588499


title: sample.ginkgo.11588464


title: sample.ginkgo.11588492


title: sample.ginkgo.11588481


title: sample.ginkgo.11588471


title: sample.ginkgo.11588509


title: sample.ginkgo.11588535


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title: sample.ginkgo.11588469


title: sample.ginkgo.11588482


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title: sample.ginkgo.11588533


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title: sample.ginkgo.11588479


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title: sample.ginkgo.11588462


title: sample.ginkgo.11588536


title: sample.ginkgo.11588500


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title: sample.ginkgo.11588504


title: sample.ginkgo.11588523


title: sample.ginkgo.11588502


title: sample.ginkgo.11588473


title: sample.ginkgo.11588480


title: sample.ginkgo.11588490


title: sample.ginkgo.11588466


title: sample.ginkgo.11588498


title: sample.ginkgo.11588483


title: sample.ginkgo.11588486


title: sample.ginkgo.11588495


title: sample.ginkgo.11588527


title: sample.ginkgo.11588484


title: sample.ginkgo.11588463


title: sample.ginkgo.11588515


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title: sample.ginkgo.11588510


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title: sample.ginkgo.11588537


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title: sample.ginkgo.11588436


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title: sample.ginkgo.11588446


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title: sample.ginkgo.11588431


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title: sample.ginkgo.11588444


title: sample.ginkgo.11588538


title: sample.ginkgo.11588449


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title: sample.ginkgo.11588456


title: sample.ginkgo.11588441


title: sample.ginkgo.11588439


title: sample.ginkgo.11588434


title: sample.ginkgo.11588451


title: sample.ginkgo.11588420


title: sample.ginkgo.11588429


title: sample.ginkgo.11588448


title: sample.ginkgo.11588415


title: sample.ginkgo.11588440


title: sample.ginkgo.11588459


title: sample.ginkgo.11588430


title: sample.ginkgo.11588414


title: sample.ginkgo.11588433


title: sample.ginkgo.11588454


title: sample.ginkgo.11588421


title: sample.ginkgo.11588427


title: sample.ginkgo.11588450


title: sample.ginkgo.11588438


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title: sample.ginkgo.11588437


title: sample.ginkgo.11588447


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title: sample.ginkgo.11588455


title: sample.ginkgo.11588435


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title: sample.ginkgo.11588404


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title: sample.ginkgo.11588460


title: sample.ginkgo.11588409


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title: sample.ginkgo.11588422


title: sample.ginkgo.11588453


title: sample.ginkgo.11588406


title: sample.ginkgo.11588417


title: sample.ginkgo.11588403


title: sample.ginkgo.11588402


title: sample.ginkgo.11588405


title: sample.ginkgo.11588398


title: sample.ginkgo.11588576


title: sample.ginkgo.11588396


title: sample.ginkgo.11588410


title: sample.ginkgo.11588400


title: sample.ginkgo.11588399


title: sample.ginkgo.11588397


title: sample.ginkgo.11588401


title: sample.ginkgo.11588407


title: sample.ginkgo.11588412


title: sample.ginkgo.11588408


title: sample.ginkgo.11588395


title: sample.ginkgo.11588730


title: sample.ginkgo.11588390


title: sample.ginkgo.11588364


title: sample.ginkgo.11588354


title: sample.ginkgo.11588349


title: sample.ginkgo.11588366


title: sample.ginkgo.11588358


title: sample.ginkgo.11588338


title: sample.ginkgo.11588728


title: sample.ginkgo.11588392


title: sample.ginkgo.11588340


title: sample.ginkgo.11588352


title: sample.ginkgo.11588361


title: sample.ginkgo.11588348


title: sample.ginkgo.11588334


title: sample.ginkgo.11588379


title: sample.ginkgo.11588369


title: sample.ginkgo.11588376


title: sample.ginkgo.11588359


title: sample.ginkgo.11588345


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title: sample.ginkgo.11588356


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title: sample.ginkgo.11588386


title: sample.ginkgo.11588332


title: sample.ginkgo.11588372


title: sample.ginkgo.11588782


title: sample.ginkgo.11588367


title: sample.ginkgo.11588363


title: sample.ginkgo.11588343


title: sample.ginkgo.11588347


title: sample.ginkgo.11588335


title: sample.ginkgo.11588394


title: sample.ginkgo.11588389


title: sample.ginkgo.11588344


title: sample.ginkgo.11588375


title: sample.ginkgo.11588727


title: sample.ginkgo.11588391


title: sample.ginkgo.11588780


title: sample.ginkgo.11588378


title: sample.ginkgo.11588362


title: sample.ginkgo.11588365


title: sample.ginkgo.11588387


title: sample.ginkgo.11588729


title: sample.ginkgo.11588381


title: sample.ginkgo.11588342


title: sample.ginkgo.11588337


title: sample.ginkgo.11588368


title: sample.ginkgo.11588374


title: sample.ginkgo.11588333


title: sample.ginkgo.11588388


title: sample.ginkgo.11588725


title: sample.ginkgo.11588353


title: sample.ginkgo.11588341


title: sample.ginkgo.11588377


title: sample.ginkgo.11588355


title: sample.ginkgo.11588726


title: sample.ginkgo.11588781


title: sample.ginkgo.11588350


title: sample.ginkgo.11588385


title: sample.ginkgo.11588779


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title: sample.ginkgo.11588360


title: sample.ginkgo.11588357


title: sample.ginkgo.11588393


title: sample.ginkgo.11588346


title: sample.ginkgo.11588689


title: sample.ginkgo.11588690


title: sample.ginkgo.11588383


title: sample.ginkgo.11588671


title: sample.ginkgo.11588336


title: sample.ginkgo.11588384


title: sample.ginkgo.11588785


title: sample.ginkgo.11588380


title: sample.ginkgo.11588672


title: sample.ginkgo.11588371


title: sample.ginkgo.11588351


title: sample.ginkgo.11588569


title: sample.ginkgo.11588720


title: sample.ginkgo.11588723


title: sample.ginkgo.11588370


title: sample.ginkgo.11588770


title: sample.ginkgo.11588567


title: sample.ginkgo.11588722


title: sample.ginkgo.11588685


title: sample.ginkgo.11588673


title: sample.ginkgo.11588667


title: sample.ginkgo.11588661


title: sample.ginkgo.11588774


title: sample.ginkgo.11588709


title: sample.ginkgo.11588687


title: sample.ginkgo.11588686


title: sample.ginkgo.11588700


title: sample.ginkgo.11588694


title: sample.ginkgo.11588716


title: sample.ginkgo.11588669


title: sample.ginkgo.11588566


title: sample.ginkgo.11588710


title: sample.ginkgo.11588718


title: sample.ginkgo.11588682


title: sample.ginkgo.11588692


title: sample.ginkgo.11588711


title: sample.ginkgo.11588665


title: sample.ginkgo.11588699


title: sample.ginkgo.11588714


title: sample.ginkgo.11588701


title: sample.ginkgo.11588719


title: sample.ginkgo.11588767


title: sample.ginkgo.11588712


title: sample.ginkgo.11588707


title: sample.ginkgo.11588704


title: sample.ginkgo.11588662


title: sample.ginkgo.11588772


title: sample.ginkgo.11588684


title: sample.ginkgo.11588773


title: sample.ginkgo.11588681


title: sample.ginkgo.11588679


title: sample.ginkgo.11588768


title: sample.ginkgo.11588771


title: sample.ginkgo.11588693


title: sample.ginkgo.11588691


title: sample.ginkgo.11588705


title: sample.ginkgo.11588674


title: sample.ginkgo.11588570


title: sample.ginkgo.11588683


title: sample.ginkgo.11588668


title: sample.ginkgo.11588713


title: sample.ginkgo.11588706


title: sample.ginkgo.11588721


title: sample.ginkgo.11588660


title: sample.ginkgo.11588702


title: sample.ginkgo.11588663


title: sample.ginkgo.11588680


title: sample.ginkgo.11588715


title: sample.ginkgo.11588568


title: sample.ginkgo.11588703


title: sample.ginkgo.11588717


title: sample.ginkgo.11588670


title: sample.ginkgo.11588708


title: sample.ginkgo.11588769


title: sample.ginkgo.11588688


title: sample.ginkgo.11588664


title: sample.ginkgo.11588651


title: sample.ginkgo.11588765


title: sample.ginkgo.11588649


title: sample.ginkgo.11588654


title: sample.ginkgo.11588650


title: sample.ginkgo.11588645


title: sample.ginkgo.11588648


title: sample.ginkgo.11588646


title: sample.ginkgo.11588666


title: sample.ginkgo.11588652


title: sample.ginkgo.11588766


title: sample.ginkgo.11588659


title: sample.ginkgo.11588764


title: sample.ginkgo.11588644


title: sample.ginkgo.11588791


title: sample.ginkgo.11588643


title: sample.ginkgo.11588763


title: sample.ginkgo.11588640


title: sample.ginkgo.11588641


title: sample.ginkgo.11588762


title: sample.ginkgo.11588633


title: sample.ginkgo.11588784


title: sample.ginkgo.11588628


title: sample.ginkgo.11588642


title: sample.ginkgo.11588761


title: sample.ginkgo.11588631


title: sample.ginkgo.11588623


title: sample.ginkgo.11588630


title: sample.ginkgo.11588629


title: sample.ginkgo.11588653


title: sample.ginkgo.11588647


title: sample.ginkgo.11588625


title: sample.ginkgo.11588626


title: sample.ginkgo.11588624


title: sample.ginkgo.11588750


title: sample.ginkgo.29774237.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"Cuminic Acid": [0.0001], "IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE

data_processing:
raw reads were trimmed and quality filtered with trimmomatic (v0.36)
trimmed reads were aligned with bwa (v0.7.17) the resulting sam files were sorted by PICARD tools (v2.18.15) function SortSam, and then AddOrReplaceGroups is run on the sorted sam
Gene-level quantification of counts was performed using the featureCounts function of Rsubread (v1.34.4)
Supplementary_files_format_and_content: QC_and_metadata.csv is a dataframe with sample IDs as the rownames and various metadata attributes as columns. raw_counts.csv is the quantified gene counts from every sample, rows are gene names and columns are sample IDs
Genome_build: https://hub.sd2e.org/user/sd2e/design/Bacillus0x20subtilis0x201680x20Marburg/1

organism: Bacillus subtilis subsp. subtilis str. 168

value: 30.0 celsius


title: sample.ginkgo.11588760


title: sample.ginkgo.11588759


title: sample.ginkgo.11588632


title: sample.ginkgo.11588634


title: sample.ginkgo.11588627


title: sample.ginkgo.29774238.experiment.ginkgo.41549


title: Spleen_male_cercariae_2

city: Rostock

first: Dirk

last: Koczan

address: Schillingallee 70

department: Institute for Immunology

institute: University of Rostock

description: Gene expression data of spleen infected by male cercariae

hyb_protocol: Hybridization was performed for 16 hours at 45 degrees celsius using the GeneChip Hybridization Oven 645 (Affymetrix, St. Clara, USA).

scan_protocol: Scanning was done using the GeneChip Scanner 3000/7G (Affymetrix, St. Clara, USA) with 0.7 micron resolution.

data_processing: Data were processed by SST-RMA (signal space transformation with robust multichip averaging) using TAC 4.0.2.15 (transcriptome analysis console; Applied Biosystems, Thermo Fisher Scientific Inc.)

source_name: excised spleen

label_protocol: 200 ng total RNA was labeled using WT-labeling protocol (Affymetrix/Thermofisher).

growth_protocol: Mice were sacrified 8 weeks after infection by cervical dislocation under isoflurane anesthesia and spleens were collected.

extract_protocol: The whole spleen together with an aliquot RLT Plus buffer (RNeasy Plus kit, Qiagen, Hilden) was homogenized in liquid nitrogen using mortar and pestle. After thawing the lysat was partly extracted with phenol/chloroform. Afterwards the RNA extraction of the supernant was done according to the RNeasy Plus protocol of Qiagen (Hilden).

treatment_protocol: Six-week-old female C57BL/6 mice were percutaneously exposed to 100 S. mansoni cercariae, either male only (M), female only (F), or both sexes (MF). Controls (naive) were left untreated.

tag: strain

value: Spleen

tag: parasite sex

value: male


title: Spleen_naive_1

description: Gene expression data of naive spleen


title: Spleen_male_cercariae_3


title: Spleen_male_female_cercariae_2

description: Gene expression data of spleen infected by male and female cercariae

value: pooled male and female


title: Spleen_male_cercariae_1


title: sample.ginkgo.29774234.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"Cuminic Acid": [0.0001], "IPTG": [0.001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: Spleen_female_cercariae_3

description: Gene expression data of spleen infected by female cercariae


title: sample.ginkgo.11588639

value: 37.0 celsius

value: 5.0 hour


title: Spleen_naive_2

description: Gene expression data of naive spleen


title: sample.ginkgo.29774231.experiment.ginkgo.41549


title: Spleen_female_cercariae_1


title: sample.ginkgo.29774236.experiment.ginkgo.41549


title: sample.ginkgo.29774235.experiment.ginkgo.41549


title: sample.ginkgo.29774229.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.29774227.experiment.ginkgo.41549


title: sample.ginkgo.11588621


title: sample.ginkgo.29774226.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11588622


title: sample.ginkgo.29774233.experiment.ginkgo.41549


title: sample.ginkgo.11588792


title: sample.ginkgo.29774224.experiment.ginkgo.41549


title: sample.ginkgo.11588620


title: sample.ginkgo.11588610


title: sample.ginkgo.29774223.experiment.ginkgo.41549


title: sample.ginkgo.29774232.experiment.ginkgo.41549


title: Spleen_male_female_cercariae_1


title: sample.ginkgo.11588611


title: sample.ginkgo.29774222.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"Cuminic Acid": [9.99995e-05], "IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11588614


title: sample.ginkgo.11588609


title: sample.ginkgo.29774220.experiment.ginkgo.41549


title: Spleen_female_cercariae_2


title: sample.ginkgo.29774219.experiment.ginkgo.41549


title: sample.ginkgo.29774218.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"IPTG": [0.001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767608


title: sample.ginkgo.11767598


title: sample.ginkgo.11767600


title: sample.ginkgo.11767594


title: sample.ginkgo.29774213.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767604


title: sample.ginkgo.29774214.experiment.ginkgo.41549


title: sample.ginkgo.29774217.experiment.ginkgo.41549


title: sample.ginkgo.11588790


title: sample.ginkgo.11767605


title: sample.ginkgo.29774211.experiment.ginkgo.41549


title: sample.ginkgo.11588749


title: sample.ginkgo.11588613


title: sample.ginkgo.29774215.experiment.ginkgo.41549


title: sample.ginkgo.29774228.experiment.ginkgo.41549


title: sample.ginkgo.29774225.experiment.ginkgo.41549


title: sample.ginkgo.11588612


title: sample.ginkgo.29774210.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.29774209.experiment.ginkgo.41549


title: sample.ginkgo.29774221.experiment.ginkgo.41549


title: sample.ginkgo.29774208.experiment.ginkgo.41549


title: sample.ginkgo.11588608


title: sample.ginkgo.11767602


title: sample.ginkgo.29774207.experiment.ginkgo.41549


title: sample.ginkgo.29774206.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Vanillic Acid": [0.001]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767606


title: sample.ginkgo.11767611


title: sample.ginkgo.11767609


title: sample.ginkgo.11588619


title: sample.ginkgo.29774203.experiment.ginkgo.41549


title: sample.ginkgo.29774216.experiment.ginkgo.41549


title: sample.ginkgo.29774202.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"RNA Later": ["Y"]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767603


title: sample.ginkgo.11767612


title: sample.ginkgo.11767596


title: sample.ginkgo.11767565


title: sample.ginkgo.29774200.experiment.ginkgo.41549


title: sample.ginkgo.29774212.experiment.ginkgo.41549


title: sample.ginkgo.11767557


title: sample.ginkgo.29774198.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [5.0] | {"Cuminic Acid": [0.0001], "IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767591


title: sample.ginkgo.11767610


title: sample.ginkgo.29774197.experiment.ginkgo.41549


title: sample.ginkgo.11767601


title: sample.ginkgo.29774195.experiment.ginkgo.41549


title: sample.ginkgo.11767571


title: sample.ginkgo.29774196.experiment.ginkgo.41549


title: sample.ginkgo.11767567


title: sample.ginkgo.29774194.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [5.0] | {"Cuminic Acid": [0.0001], "IPTG": [0.001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.29774193.experiment.ginkgo.41549


title: sample.ginkgo.29774205.experiment.ginkgo.41549


title: sample.ginkgo.11767599


title: sample.ginkgo.29774204.experiment.ginkgo.41549


title: sample.ginkgo.29774190.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [5.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767569


title: sample.ginkgo.11767564


title: sample.ginkgo.11767607


title: sample.ginkgo.29774189.experiment.ginkgo.41549


title: sample.ginkgo.29774187.experiment.ginkgo.41549


title: sample.ginkgo.29774186.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [5.0] | {"IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767597


title: sample.ginkgo.29774201.experiment.ginkgo.41549


title: sample.ginkgo.29774185.experiment.ginkgo.41549


title: sample.ginkgo.29774199.experiment.ginkgo.41549


title: sample.ginkgo.11767590


title: sample.ginkgo.11767584


title: sample.ginkgo.11767595


title: sample.ginkgo.11767559


title: sample.ginkgo.29774181.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [5.0] | {"Cuminic Acid": [9.99995e-05], "IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767585


title: sample.ginkgo.11767583


title: sample.ginkgo.29774180.experiment.ginkgo.41549


title: sample.ginkgo.11767580


title: sample.ginkgo.29774188.experiment.ginkgo.41549


title: sample.ginkgo.11767560


title: sample.ginkgo.11767561


title: sample.ginkgo.11767558


title: sample.ginkgo.11767568


title: sample.ginkgo.29774183.experiment.ginkgo.41549


title: sample.ginkgo.29774177.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [5.0] | {"IPTG": [0.001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.29774184.experiment.ginkgo.41549


title: sample.ginkgo.11767588


title: sample.ginkgo.29774230.experiment.ginkgo.41549


title: sample.ginkgo.29774192.experiment.ginkgo.41549


title: sample.ginkgo.29774182.experiment.ginkgo.41549


title: sample.ginkgo.29774191.experiment.ginkgo.41549


title: sample.ginkgo.11767552


title: sample.ginkgo.11767586


title: sample.ginkgo.11767576


title: sample.ginkgo.11767582


title: sample.ginkgo.11767579


title: sample.ginkgo.29774175.experiment.ginkgo.41549


title: sample.ginkgo.11767555


title: sample.ginkgo.29774178.experiment.ginkgo.41549


title: sample.ginkgo.29774174.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [5.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767577


title: sample.ginkgo.11767551


title: sample.ginkgo.11767593


title: sample.ginkgo.29774179.experiment.ginkgo.41549


title: sample.ginkgo.29774173.experiment.ginkgo.41549


title: sample.ginkgo.11767562


title: sample.ginkgo.29774169.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [5.0] | {"RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767587


title: sample.ginkgo.29774176.experiment.ginkgo.41549


title: sample.ginkgo.11767553


title: sample.ginkgo.11767554


title: sample.ginkgo.11767589


title: sample.ginkgo.29774163.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [5.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Vanillic Acid": [0.001]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.29774164.experiment.ginkgo.41549


title: sample.ginkgo.11767566


title: sample.ginkgo.29774172.experiment.ginkgo.41549


title: sample.ginkgo.11767570


title: sample.ginkgo.11767574


title: sample.ginkgo.29774170.experiment.ginkgo.41549


title: sample.ginkgo.11767563


title: sample.ginkgo.29774162.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [5.0] | {"RNA Later": ["Y"]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767575


title: sample.ginkgo.29774160.experiment.ginkgo.41549


title: sample.ginkgo.29774171.experiment.ginkgo.41549


title: sample.ginkgo.11767556


title: sample.ginkgo.11767581


title: sample.ginkgo.29774166.experiment.ginkgo.41549


title: sample.ginkgo.29774165.experiment.ginkgo.41549


title: sample.ginkgo.11767592


title: sample.ginkgo.11767537


title: sample.ginkgo.11767549


title: sample.ginkgo.11767578


title: sample.ginkgo.29774161.experiment.ginkgo.41549


title: sample.ginkgo.11767509


title: sample.ginkgo.29774168.experiment.ginkgo.41549


title: sample.ginkgo.11767573


title: sample.ginkgo.28034628.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Cuminic Acid": [0.0001], "IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE

value: 36.0 hour


title: sample.ginkgo.28034625.experiment.ginkgo.39011


title: sample.ginkgo.28034626.experiment.ginkgo.39011


title: sample.ginkgo.29774158.experiment.ginkgo.41549

description: Bacillus subtilis 168 Marburg | 30.0 | [0.0] | {"RNA Later": ["Y"]} | RNA_SEQ | NO_STANDARD_TYPE

value: 0.0 hour


title: sample.ginkgo.11767572


title: sample.ginkgo.29774167.experiment.ginkgo.41549


title: sample.ginkgo.11767545


title: sample.ginkgo.29774157.experiment.ginkgo.41549


title: sample.ginkgo.29774156.experiment.ginkgo.41549


title: sample.ginkgo.11767519


title: sample.ginkgo.29774159.experiment.ginkgo.41549


title: sample.ginkgo.29774155.experiment.ginkgo.41549


title: sample.ginkgo.11767542


title: sample.ginkgo.28034619.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767533


title: sample.ginkgo.28034627.experiment.ginkgo.39011


title: sample.ginkgo.11767503


title: sample.ginkgo.28034620.experiment.ginkgo.39011


title: sample.ginkgo.11767544


title: sample.ginkgo.11767526


title: sample.ginkgo.11767511


title: sample.ginkgo.11767493


title: sample.ginkgo.28034615.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Cuminic Acid": [0.0001], "IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28034616.experiment.ginkgo.39011


title: sample.ginkgo.11767488


title: sample.ginkgo.11767528


title: sample.ginkgo.28034624.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28034623.experiment.ginkgo.39011


title: sample.ginkgo.11767515


title: sample.ginkgo.28034622.experiment.ginkgo.39011


title: sample.ginkgo.11767543


title: sample.ginkgo.11767502


title: sample.ginkgo.11767547


title: sample.ginkgo.28034608.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767529


title: sample.ginkgo.28034621.experiment.ginkgo.39011


title: sample.ginkgo.28034618.experiment.ginkgo.39011


title: sample.ginkgo.11767513


title: sample.ginkgo.28034617.experiment.ginkgo.39011


title: sample.ginkgo.11767489


title: sample.ginkgo.11767550


title: sample.ginkgo.11767539


title: sample.ginkgo.28034614.experiment.ginkgo.39011


title: sample.ginkgo.11767482


title: sample.ginkgo.28034613.experiment.ginkgo.39011


title: sample.ginkgo.11767527


title: sample.ginkgo.28034605.experiment.ginkgo.39011


title: sample.ginkgo.28034603.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28034612.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"IPTG": [0.001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767536


title: sample.ginkgo.28034601.experiment.ginkgo.39011


title: sample.ginkgo.28034600.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Vanillic Acid": [0.001]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28034609.experiment.ginkgo.39011


title: sample.ginkgo.11767524


title: sample.ginkgo.11767514


title: sample.ginkgo.28034599.experiment.ginkgo.39011


title: sample.ginkgo.28034610.experiment.ginkgo.39011


title: sample.ginkgo.11767522


title: sample.ginkgo.11767517


title: sample.ginkgo.11767504


title: sample.ginkgo.11767546


title: sample.ginkgo.28034604.experiment.ginkgo.39011


title: sample.ginkgo.11767483


title: sample.ginkgo.28034611.experiment.ginkgo.39011


title: sample.ginkgo.28034606.experiment.ginkgo.39011


title: sample.ginkgo.28034602.experiment.ginkgo.39011


title: sample.ginkgo.11767510


title: sample.ginkgo.11767535


title: sample.ginkgo.28034593.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"RNA Later": ["Y"]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767518


title: sample.ginkgo.28034594.experiment.ginkgo.39011


title: sample.ginkgo.28034607.experiment.ginkgo.39011


title: sample.ginkgo.28034363.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Cuminic Acid": [0.0001], "IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE

value: 23.0 hour


title: sample.ginkgo.28034598.experiment.ginkgo.39011


title: sample.ginkgo.28034596.experiment.ginkgo.39011


title: sample.ginkgo.11767496


title: sample.ginkgo.11767532


title: sample.ginkgo.28034595.experiment.ginkgo.39011


title: sample.ginkgo.28034597.experiment.ginkgo.39011


title: sample.ginkgo.11767501


title: sample.ginkgo.11767486


title: sample.ginkgo.28034362.experiment.ginkgo.39011


title: sample.ginkgo.11767531


title: sample.ginkgo.28034359.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767505


title: sample.ginkgo.11767530


title: sample.ginkgo.28034360.experiment.ginkgo.39011


title: sample.ginkgo.11767508


title: sample.ginkgo.28034358.experiment.ginkgo.39011


title: sample.ginkgo.11767497


title: sample.ginkgo.28034364.experiment.ginkgo.39011


title: sample.ginkgo.11767487


title: sample.ginkgo.11767516


title: sample.ginkgo.11767491


title: sample.ginkgo.11767525


title: sample.ginkgo.28034355.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28034361.experiment.ginkgo.39011


title: sample.ginkgo.28034357.experiment.ginkgo.39011


title: sample.ginkgo.11767484


title: sample.ginkgo.11767538


title: sample.ginkgo.28034354.experiment.ginkgo.39011


title: sample.ginkgo.28034351.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Cuminic Acid": [0.0001], "IPTG": [0.001], "RNA Later": ["Y"], "Vanillic Acid": [0.001]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28034356.experiment.ginkgo.39011


title: sample.ginkgo.11767521


title: sample.ginkgo.11767506


title: sample.ginkgo.11767498


title: sample.ginkgo.11767499


title: sample.ginkgo.28034348.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"IPTG": [0.001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767520


title: sample.ginkgo.11767540


title: sample.ginkgo.28034346.experiment.ginkgo.39011


title: sample.ginkgo.28034353.experiment.ginkgo.39011


title: sample.ginkgo.11767485


title: sample.ginkgo.28034344.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28034352.experiment.ginkgo.39011


title: sample.ginkgo.28034343.experiment.ginkgo.39011


title: sample.ginkgo.11767492


title: sample.ginkgo.11767507


title: sample.ginkgo.11767494


title: sample.ginkgo.28034349.experiment.ginkgo.39011


title: sample.ginkgo.11767490


title: sample.ginkgo.11767523


title: sample.ginkgo.11767495


title: sample.ginkgo.11767541


title: sample.ginkgo.28034339.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"RNA Later": ["Y"], "Vanillic Acid": [0.001], "Xylose": [1.0]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28034340.experiment.ginkgo.39011


title: sample.ginkgo.28034350.experiment.ginkgo.39011


title: sample.ginkgo.11767500


title: sample.ginkgo.11767534


title: sample.ginkgo.28034341.experiment.ginkgo.39011


title: sample.ginkgo.28034337.experiment.ginkgo.39011


title: sample.ginkgo.28034336.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Cuminic Acid": [0.0001], "RNA Later": ["Y"], "Vanillic Acid": [0.001]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28034338.experiment.ginkgo.39011


title: sample.ginkgo.28034334.experiment.ginkgo.39011


title: sample.ginkgo.11767440

value: 6.5 hour


title: sample.ginkgo.11767450


title: sample.ginkgo.28034345.experiment.ginkgo.39011


title: sample.ginkgo.28034333.experiment.ginkgo.39011


title: sample.ginkgo.11767512


title: sample.ginkgo.28034332.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"RNA Later": ["Y"]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28034335.experiment.ginkgo.39011


title: sample.ginkgo.11767451


title: sample.ginkgo.28034331.experiment.ginkgo.39011


title: sample.ginkgo.11767548


title: sample.ginkgo.11767480


title: sample.ginkgo.28025131.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"RNA Later": ["Y"]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767468


title: sample.ginkgo.28025130.experiment.ginkgo.39011


title: sample.ginkgo.28025128.experiment.ginkgo.39011


title: sample.ginkgo.11767431


title: sample.ginkgo.28034342.experiment.ginkgo.39011


title: sample.ginkgo.28015443.experiment.ginkgo.39011

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767439


title: sample.ginkgo.11767458


title: sample.ginkgo.11767467


title: sample.ginkgo.28034330.experiment.ginkgo.39011


title: sample.ginkgo.11767453


title: sample.ginkgo.11767464


title: sample.ginkgo.28034329.experiment.ginkgo.39011


title: sample.ginkgo.28025129.experiment.ginkgo.39011


title: sample.ginkgo.11767470


title: sample.ginkgo.11767446


title: sample.ginkgo.11767478


title: sample.ginkgo.22175443.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Dextrose (D-Glucose)": [0.43], "Modified M9 Media": [1.074999], "Vanillic Acid": [0.001], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""], "e4739 (Ethanol for Molecular Biology 200 Proof)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.28015441.experiment.ginkgo.39011


title: sample.ginkgo.22175445.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Dextrose (D-Glucose)": [0.43], "Modified M9 Media": [1.075], "Xylose": [1.0], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767475


title: sample.ginkgo.28015440.experiment.ginkgo.39011


title: sample.ginkgo.28015442.experiment.ginkgo.39011


title: sample.ginkgo.11767476


title: sample.ginkgo.11767449


title: sample.ginkgo.11767473


title: sample.ginkgo.11767457


title: sample.ginkgo.22175439.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Dextrose (D-Glucose)": [0.43], "Modified M9 Media": [1.075], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.22175441.experiment.ginkgo.29422


title: sample.ginkgo.11767465


title: sample.ginkgo.22175440.experiment.ginkgo.29422


title: sample.ginkgo.22175438.experiment.ginkgo.29422


title: sample.ginkgo.11767471


title: sample.ginkgo.11767428


title: sample.ginkgo.22175442.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Dextrose (D-Glucose)": [0.430000001], "IPTG": [0.001], "Modified M9 Media": [1.075], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.22175437.experiment.ginkgo.29422


title: sample.ginkgo.11767463


title: sample.ginkgo.22175434.experiment.ginkgo.29422


title: sample.ginkgo.22175435.experiment.ginkgo.29422


title: sample.ginkgo.11767461


title: sample.ginkgo.22175433.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Cuminic Acid": [0.0001], "Dextrose (D-Glucose)": [0.43], "IPTG": [0.000999999], "Modified M9 Media": [1.075001], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""], "e4739 (Ethanol for Molecular Biology 200 Proof)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.22175431.experiment.ginkgo.29422


title: sample.ginkgo.11767447


title: sample.ginkgo.22175444.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Cuminic Acid": [0.0001], "Dextrose (D-Glucose)": [0.430000001], "Modified M9 Media": [1.075], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""], "e4739 (Ethanol for Molecular Biology 200 Proof)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767469


title: sample.ginkgo.11767462


title: sample.ginkgo.22175432.experiment.ginkgo.29422


title: sample.ginkgo.22175428.experiment.ginkgo.29422


title: sample.ginkgo.11767443


title: sample.ginkgo.22175429.experiment.ginkgo.29422


title: sample.ginkgo.22175430.experiment.ginkgo.29422


title: sample.ginkgo.11767438


title: sample.ginkgo.11767472


title: sample.ginkgo.22175427.experiment.ginkgo.29422


title: sample.ginkgo.11767481


title: sample.ginkgo.22175426.experiment.ginkgo.29422


title: sample.ginkgo.11767477


title: sample.ginkgo.22175425.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [36.0] | {"Dextrose (D-Glucose)": [0.43], "IPTG": [0.0009999], "Modified M9 Media": [1.075], "Vanillic Acid": [0.001], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""], "e4739 (Ethanol for Molecular Biology 200 Proof)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767444


title: sample.ginkgo.22175436.experiment.ginkgo.29422


title: sample.ginkgo.22175423.experiment.ginkgo.29422


title: sample.ginkgo.22175424.experiment.ginkgo.29422


title: sample.ginkgo.11767452


title: sample.ginkgo.22175421.experiment.ginkgo.29422


title: sample.ginkgo.11767448


title: sample.ginkgo.11767437


title: sample.ginkgo.11767435


title: sample.ginkgo.11767429


title: sample.ginkgo.11767456


title: sample.ginkgo.11767433


title: sample.ginkgo.22175419.experiment.ginkgo.29422


title: sample.ginkgo.22175422.experiment.ginkgo.29422


title: sample.ginkgo.22175418.experiment.ginkgo.29422


title: sample.ginkgo.22175420.experiment.ginkgo.29422


title: sample.ginkgo.11767430


title: sample.ginkgo.22175417.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [18.0] | {"Dextrose (D-Glucose)": [0.4], "Modified M9 Media": [1.0], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767434


title: sample.ginkgo.11767441


title: sample.ginkgo.11767445


title: sample.ginkgo.22175415.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Cuminic Acid": [0.0001], "Dextrose (D-Glucose)": [0.43], "IPTG": [0.000999999], "Modified M9 Media": [1.075001], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""], "e4739 (Ethanol for Molecular Biology 200 Proof)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767436


title: sample.ginkgo.22175414.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Dextrose (D-Glucose)": [0.43], "IPTG": [0.0009999], "Modified M9 Media": [1.075], "Vanillic Acid": [0.001], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""], "e4739 (Ethanol for Molecular Biology 200 Proof)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767427


title: sample.ginkgo.22175412.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Cuminic Acid": [0.0001], "Dextrose (D-Glucose)": [0.430000001], "Modified M9 Media": [1.075], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""], "e4739 (Ethanol for Molecular Biology 200 Proof)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.22175411.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Dextrose (D-Glucose)": [0.43], "Modified M9 Media": [1.074999], "Vanillic Acid": [0.001], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""], "e4739 (Ethanol for Molecular Biology 200 Proof)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.22175410.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Dextrose (D-Glucose)": [0.430000001], "IPTG": [0.001], "Modified M9 Media": [1.075], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767455


title: sample.ginkgo.11767459


title: sample.ginkgo.22175413.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Dextrose (D-Glucose)": [0.43], "Modified M9 Media": [1.075], "Xylose": [1.0], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.11767454


title: sample.ginkgo.11767460


title: sample.ginkgo.11767432


title: sample.ginkgo.11767426


title: sample.ginkgo.11767479


title: sample.ginkgo.11767474


title: sample.ginkgo.22175404.experiment.ginkgo.29422


title: sample.ginkgo.11767442


title: sample.ginkgo.11767419


title: sample.ginkgo.11767415


title: sample.ginkgo.11767466


title: sample.ginkgo.22175405.experiment.ginkgo.29422


title: sample.ginkgo.22175407.experiment.ginkgo.29422


title: sample.ginkgo.22175409.experiment.ginkgo.29422


title: sample.ginkgo.22175406.experiment.ginkgo.29422


title: sample.ginkgo.22175401.experiment.ginkgo.29422


title: sample.ginkgo.11767418


title: sample.ginkgo.22175402.experiment.ginkgo.29422


title: sample.ginkgo.22175416.experiment.ginkgo.29422

description: Bacillus subtilis 168 Marburg | 30.0 | [23.0] | {"Dextrose (D-Glucose)": [0.43], "Modified M9 Media": [1.075], "e1599 (Sterile Milli Q Water)": [""], "e3257 (1X LB)": [""], "e4070 (25% Glycerol w/v)": [""]} | RNA_SEQ | NO_STANDARD_TYPE


title: sample.ginkgo.22175400.experiment.ginkgo.29422


title: sample.ginkgo.22175403.experiment.ginkgo.29422


title: sample.ginkgo.22175399.experiment.ginkgo.29422


title: sample.ginkgo.22175408.experiment.ginkgo.29422


title: sample.ginkgo.11767417


title: sample.ginkgo.22175396.experiment.ginkgo.29422


title: sample.ginkgo.11767420


title: sample.ginkgo.22175398.experiment.ginkgo.29422


title: sample.ginkgo.11767425


title: sample.ginkgo.22175392.experiment.ginkgo.29422


title: sample.ginkgo.11767423


title: sample.ginkgo.22175393.experiment.ginkgo.29422


title: sample.ginkgo.11767421


title: sample.ginkgo.22175390.experiment.ginkgo.29422


title: sample.ginkgo.11767414


title: sample.ginkgo.11767363


title: sample.ginkgo.11767422


title: sample.ginkgo.11767424


title: sample.ginkgo.22175389.experiment.ginkgo.29422


title: sample.ginkgo.11767362


title: sample.ginkgo.22175386.experiment.ginkgo.29422


title: sample.ginkgo.22175397.experiment.ginkgo.29422


title: sample.ginkgo.11767390


title: sample.ginkgo.11767416


title: sample.ginkgo.11767413


title: sample.ginkgo.22175394.experiment.ginkgo.29422


title: sample.ginkgo.22175391.experiment.ginkgo.29422


title: sample.ginkgo.11767334


title: sample.ginkgo.22175395.experiment.ginkgo.29422


title: sample.ginkgo.11767411


title: sample.ginkgo.11767407


title: sample.ginkgo.11767359


title: sample.ginkgo.22175387.experiment.ginkgo.29422


title: sample.ginkgo.11767377


title: sample.ginkgo.22175388.experiment.ginkgo.29422


title: sample.ginkgo.11767343


title: Sample288

type: other

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: standard OLINK protocol

data_processing: log2 Normalized Protein Expression (NPX) values were provided by Proseek Multiplex OLINK Proteomics Platform

label: oligonucleotide-labeled antibody

molecule: other

source_name: blood

label_protocol: standard OLINK protocol

extract_protocol: serum

tag: asthma

tag: outcome

value: survived


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title: Sample58


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title: Sample55


title: Sample53


title: sample.ginkgo.11767232


title: sample.ginkgo.11767226


title: sample.ginkgo.11767215


title: Sample52


title: Sample54


title: Sample50


title: Sample51


title: sample.ginkgo.11767186


title: Sample48


title: Sample47


title: Sample49


title: sample.ginkgo.11767156


title: Sample46


title: sample.ginkgo.11767220


title: Sample45


title: Sample44


title: sample.ginkgo.11767214


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title: sample.ginkgo.11767172


title: sample.ginkgo.11767203


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title: sample.ginkgo.11767180


title: Sample41


title: sample.ginkgo.11767161


title: Sample40


title: sample.ginkgo.11767170


title: sample.ginkgo.11767140


title: Sample39


title: Sample36


title: sample.ginkgo.11767151


title: Sample43


title: sample.ginkgo.11767145


title: Sample38


title: Sample37


title: Sample34


title: Sample35


title: sample.ginkgo.11767154


title: sample.ginkgo.11767147


title: Sample33


title: sample.ginkgo.11767210


title: Sample32


title: sample.ginkgo.11767152


title: Sample42


title: sample.ginkgo.11767149


title: Sample31


title: Sample30


title: sample.ginkgo.11767144


title: Sample29


title: sample.ginkgo.11767138


title: Sample26


title: sample.ginkgo.11767143


title: Sample28


title: Sample25


title: sample.ginkgo.11767141


title: Sample22


title: Sample27


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title: sample.ginkgo.11767153


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title: Sample24


title: Sample23


title: Sample20


title: sample.ginkgo.11767133


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title: Sample19


title: Sample21


title: Sample16


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title: Sample15


title: sample.ginkgo.11767124


title: Sample14


title: sample.ginkgo.11767137


title: Sample13


title: sample.ginkgo.11767116


title: Sample17


title: sample.ginkgo.11767114


title: sample.ginkgo.11767110


title: Sample11


title: Sample12


title: sample.ginkgo.11767120


title: Sample9


title: Sample10


title: Sample7


title: sample.ginkgo.11767136


title: Sample6


title: sample.ginkgo.11767109


title: sample.ginkgo.11767132


title: sample.ginkgo.11767115


title: sample.ginkgo.11767128


title: sample.ginkgo.11767127


title: sample.ginkgo.11767123


title: Sample4


title: Sample3


title: sample.ginkgo.11767121


title: Sample5


title: Sample2


title: sample.ginkgo.11767129


title: Sample1


title: sample.ginkgo.11767118


title: HK2 ANXA2 knockdown rep3

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 16 --no-discordant --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue<=0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw counts or FPKM values for each sample.

source_name: kidney proximal tubule

growth_protocol: HK2 (ATCC® CRL-2190™) cells were cultured at 37 ˚C with 5% CO2 in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum, 100 µg/mL streptomycin, and 100 U/mL penicillin. Plasmid transfection of HK2 cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions.

extract_protocol:
HK2 cells were ground into fine powder before RNA extraction. Total RNA was extracted using TRIzol (Ambion)（Invitrogen, Carlsbad, CA, USA）. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The purified RNAs were then iron-fragmented at 95 ˚C followed by end repair and 5’ adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3’ adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at −80 ˚C until required for sequencing.
For each sample, 1 μg of the total RNA was used for RNA-sequencing (RNA-seq) library preparation. Polyadenylated RNAs were purified and concentrated using oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation.

value: kidney

tag: cell transformation method

value: human papillomavirus 16 (HPV-16) transformed

value: ANXA2 knockdown


title: sample.ginkgo.11767113


title: sample.ginkgo.11767135


title: HK2 ANXA2 knockdown rep2


title: SN_0_4

city: Belgrade

first: Stefan

last: Stanovčić

state: Serbia

address: Vojvode Stepe 444a

country: Serbia

institute: IMGGE

data_processing:
Raw FASTQ data were preprocessed using fastp to remove adapters, poly-N>10% sequences and low quality reads (Qscore of over 50% bases of the read <=5). Clean data served for calculating Q20, Q30 and GC content.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count reads mapped for each gene and expressed in FPKM (fragments per kilobase of exone model per million mapped reads). Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by Trimmed Mean- of M-values (TMM) through one scaling normalized factor. Differential expression analysis of two conditions was performed using EdgeR (without biological replicates) and DESeq2 (with three biological replicates per condition) R packages. The p-values were adjusted using Benjamini and Hochberg approach for controlling the false discovery rate. Genes with adjusted p-value < 0.005 and |log2(fold Change)| >1 found by EdgeR were assigned as differential expressed.
Assembly: RefSeq GCF_000328475.2 Genome assembly Umaydis521_2.0 (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000328475.2/)
Supplementary files format and content: Excel files including FPKM values for each sample in three comparisons: 1) Differential gene expression analysis between U.maydis control and U.maydis grown in supernatant of U.maydis cells treated with 0.4% H2O2 (SN_0_4vsControl_DEG_all), 2)Differential gene expression analysis  between U.maydis control and U.maydis grown in supernatant of U.maydis cells treated with 0.7% H2O2 (SN_0_7vsControl_DEG_all) and 3) Differential gene expression analysis between U.maydis grown in supernatant of U. maydis cells treated with 0.7% H2O2 and in supernatant of U. maydis cells treated with 0.4% H2O2 (SN_0_7vsSN_0_4_DEG_all)

organism: Mycosarcoma maydis

source_name: cultures

growth_protocol: Ustilago maydis wild type was grown for 16h in YEPS (1% (w/v) yeast extract, 2% (w/v) peptone, 2% (w/v) saccharose). The same amount of 2x107 cells of U.maydis wild type overnight culture was transfered to 10% YEPS (as control) as well as to cell-free supernatants of U.maydis wild type treated with H202 in two different concentrations (0.4% and 0.7%) (as two separate conditions).

extract_protocol:
Total RNA was extracted using GeneJET RNA Purification kit (ThermoScientific, Lithuania) according to the manufacturer recommendation for yeast total RNA isolation. DNA was removed from total RNA sampels using DNAfree DNase treatment and Removal Kit (Ambion). Purified RNA was analzyed by RNA 6000 Nano assay on Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). Samples were further processed by Novogene as follows: messenger RNA (mRNA) was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina NovaSeq 6000 platform using 150bp paired-end sequencing.

value: cultures

value: wild type R521


title: sample.ginkgo.11767122


title: HK2 ANXA2 knockdown rep1


title: SN_0_7

value: grown in supernatant of U.maydis cells treated with 0.7% H2O2


title: sample.ginkgo.11767131


title: sample.ginkgo.11767111


title: sample.ginkgo.11767125


title: HK2 WT rep3

value: wild type


title: HK2 WT rep2


title: sample.ginkgo.11767068


title: HK2 WT rep1


title: sample.ginkgo.11767117


title: sample.ginkgo.11767229

value: 18.0 hour


title: sample.ginkgo.11767134

value: 8.0 hour


title: Plate 9, 96 vagal neurons

city: Berlin

first: Carmen

last: Birchmeier

address: Robert-Roessle-Str. 10

institute: MDC

library_source: transcriptomic single cell

data_processing:
quality filtering with Drop-seq tools
trimming with Drop-seq tools
annotation of the reads with the cell barcode and UMI
mapping with STAR
quantification with Drop seq tools
Assembly: mm10
Supplementary files format and content: tsv of the Digital Gene Expression Matrix (counts)

source_name: vagal ganglia

extract_protocol:
We dissected the vagal ganglia from 15 VGlut2Cre;R26nGFP mice of either sex at P4, removed excess nerve, muscle and vascular tissue, and placed them in a 1.5 ml Eppendorf tube with warm F12/FHS (F12 with 10% fetal horse serum). Briefly, ganglia were digested in F12/FHS solution containing 0.125% collagenase, incubated at 37Co for 1 hour, washed 3x in PBS, and then incubated in PBS with 0.25% trypsin at 37Co for 15 minutes. Ganglia were dissociated using fire-polished Pasteur pipettes of decreasing diameter. The solution was transferred on top of a 2 ml BSA cushion (F12/FHS solution with 15% bovine serum albumin) and spun for 10 minutes at 900 RPM. The cell pellet was resuspended in 500 µl of HBSS without calcium or magnesium, strained twice through a 70 µm filter (Sysmex), and DAPI (Sigma) was added to a final concentration of 300 nM to label dead cells before sorting. We sorted GFP-positive / DAPI-negative cells into 96-well plates using ARIA Sorter III (BD) and BD FACSDiva software 8.0.1.
Libraries were constructed following the CEL-Seq2 protocol (doi: 10.1186/s13059-016-0938-8).

value: vagal ganglia

value: neuron


title: Plate 8, 96 vagal neurons


title: sample.ginkgo.11767045

value: 37.0 celsius

value: 5.0 hour


title: Plate E, 96 vagal neurons


title: Plate C, 96 vagal neurons


title: Control

value: grown in 10% YEPS


title: sample.ginkgo.11767035


title: Plate 4, 96 vagal neurons


title: Plate 7, 96 vagal neurons


title: sample.ginkgo.11767064

value: 6.5 hour


title: Sample8


title: Plate 3, 96 vagal neurons


title: sample.ginkgo.11767086


title: Plate 6, 96 vagal neurons


title: sample.ginkgo.11767037


title: sample.ginkgo.11767082


title: sample.ginkgo.11767025


title: sample.ginkgo.11767050


title: sample.ginkgo.11767056


title: Plate 14, 96 vagal neurons


title: Plate 3B, 96 vagal neurons


title: Plate 13, 96 vagal neurons


title: Plate 2, 96 vagal neurons


title: sample.ginkgo.11767057


title: Plate 10, 96 vagal neurons


title: sample.ginkgo.11767104


title: sample.ginkgo.11767076


title: Plate 5, 96 vagal neurons


title: sample.ginkgo.11767059


title: Plate 11, 96 vagal neurons


title: sample.ginkgo.11767091


title: sample.ginkgo.11767020


title: sample.ginkgo.11767049