title: OB4_HB_2D, Day 0

value: Bone

value: Osteoprogenitor cells

tag: Sex

value: F

value: Healthy

value: Iliac crest

value: 0 month

tag: time


title: Patient11 20006-Nivo

status: Public on Jan 09 2024

type: RNA

city: Bangalore

first: Nandini

middle: Pal

last: Basak

state: Karnataka

address: Hosur road

department: R&D

country: India

institute: Farcast Biosciences

hyb_protocol: Manufacturer's protocol was followed

scan_protocol: Digital analyser is used for the scanning of  catridge.

data_processing: nSolver software was used to normalise the data against the selected 5 specific housekeeping genes DNAJC14, GUSB, NRDE2, TFRC, UBB.

molecule: total RNA

organism: Homo sapiens

source_name: HNSCC

growth_protocol: Ex vivo culture for 72 hours

extract_protocol: RNA was extracted from FFPE blocks.

treatment_protocol: Samples were either untreated (Control), Nivolumab treated (Nivo) or Nivolumab+Ipilimumab treated (N+I)

tag: gender

value: Female

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

value: Primary

tag: therapy

value: Radiotherapy

tag: cancer grade

tag: cancer stage

value: IVA

tag: cohort

tag: treatment in culture

value: Nivolumab


title: RNAseq_HFD_Ing_WT_rep4

type: SRA

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

description: White Adipose Tissue (WAT)

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to mm10 whole genome using BWA-MEM 0.7.15 with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
Transcripts per Million of library size (TPM) were calculated using StringTie version 1.3.3 with parameters -e -v -p 32 -G knownGene_UCSC_mm10.gtf
The expression level of all genes was estimated by DESeq2 1.40.1 in RStudio 2023.03.1+446
Assembly: GRCm38/mm10 assembly
Supplementary files format and content: tab-delimited text files include cov, FPKM, and TPM values for each Sample (*.gtf)
Supplementary files format and content: Matrix table with TPM values for every transcript and every sample (*.csv)

organism: Mus musculus

source_name: Inguinal (iWAT)

growth_protocol: Mixed genetic background dNT mice were generated as described (Fütterer, et al., 2005; doi:10.1172/JCI24177) and backcrossed more than 10 times on a C57BL/6 background.

extract_protocol:
Total RNA was purified with the Split RNA Extraction Kit (Lexogen, Austria). Triplicate RNA probes from wild-type and Dido1_dNT mutant were sequenced.
RNA libraries for epididymal WAT were prepared by the servicio de genomica at the Parque Cientifico de Madrid using standard Illumina protocols. RNA libraries for inguinal WAT were prepared by BGI Genomics (China).

treatment_protocol: Mice were maintained at 22º on a normal diet (ND) (SAFE150) composed of 12.6% fat, on a 12/12-h light/dark cycle with ad libitum access to food and water. A control diet (CD) / high fat diet (HFD) pair, was used as recommended by manufacturer. CD (Ssniff E15748) composed of 4.1% fat. HFD (Ssniff E15744) composed of 45% fat was used to induce obesity.

tag: tissue

value: Inguinal (iWAT)

tag: genotype

value: wild type

tag: strain


title: OB15_CA_2D, Day 0

city: Bern

first: Daniel

middle: Walter

last: Hanhart

state: Bern

address: Murtenstrasse 24

department: Department for BioMedical Research (DBMR)

country: Switzerland

institute: UroGenus

data_processing:
Sequencing reads were analyzed using the rnaseq pipeline from nf-core (version 3.7)
Adapter sequences were removed with trimgalore (version 0.6.7)
Alignment to the reference genome (GRCh38) was performed using STAR (version 2.7.10a)
Transcript quantification was done using Salmon (version 1.5.2)
The count matrix was loaded into R (version 4.1.2) with the tximport (version 1.20.0) package.
Assembly: GRCh38
Supplementary files format and content: File containing raw counts.

molecule: polyA RNA

source_name: Bone

extract_protocol:
For RNA extraction from cultured cells, 300,000 cells from the cell suspension used for differentiation were pelleted, washed in PBS and resuspended in 1 ml of TriPure. Differentiated OPC were gently washed twice with PBS and harvested with 1 ml of TriPure. RNA was then extracted according to the manufacturer’s instructions. Genomic DNA was eliminated by using the RNeasy MinElute Cleanup kit (Qiagen). RNA integrity of the samples from cultured cells was checked with the Qubit RNA IQ Assay kit (Thermo Fischer Scientific), that of tissue samples was assessed by using the RNA 6000 Nano kit and following manufacturer’s instructions (Agilent)
Specimens were prepared for RNA sequencing using the “NEBNext Ultra II Directional RNA Library Prep Kit for Illumina” (NEB #E7760S/L). For batch_3, library was prepared using the Illumina TruSeq v2 mRNA protocol. The mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used.

tag: cell type

value: M

tag: type

value: Callus

tag: fracture site

value: Femur

tag: age patient

tag: age fracture

value: 1 month

tag: batch

value: Day 0


title: RNAseq_HFD_Ing_WT_rep3

description: White Adipose Tissue (WAT)


title: RNAseq_HFD_Ing_WT_rep2

description: White Adipose Tissue (WAT)


title: Patient10 10108-Nivo

tag: gender

value: Male

tag: age (years)

value: Tongue

value: III


title: 32 Hippo Grp3

city: Morgantown

first: James

last: Walton

state: West Virginia

address: 108 Biomedical Road

department: Neuroscience

country: USA

institute: West Virginia University

description: Whole brain RNA stabilized in RNAlater, brain regions dissected, extracted with Trizol, quality analyzed with Agilent 2100 Bioanalyzer, samples were then assayed using the nanoString nCounter Mouse Neuroinflammation Panel V1. NOTE: each mouse has 3 brain regions as individual samples, so other characteristics are listed three times - pay attention to the "mouse number" when using characteristic data that are repeated.  Outliers (based on the raw data) were excluded from normalization and further analysis.

hyb_protocol: NanoString protocol

scan_protocol: NanoString protocol

data_processing: [nanostring protocol]  Verified samples (n=5 from each experimental condition) were processed following NanoString recommended protocol on their PrepStation and analyzed with their Digital Analyzer on nCounter cartridges for the nCounter mouse Neuroinflammation Panel V1. Following Analyzer scanning the raw data were transferred and normalized with the NanoString nSolver Analysis v3 software platform, employing: Negative Background Subtraction, Positive Control Normalization, and CodeSet Content Normalization using geometric mean values. The processed expression values were then exported and further analyzed using the Partek GS v6.6 (Partek Inc.) platform, where they underwent quantile normalization.

source_name: whole brain

extract_protocol: After preservation in RNAlater, brains were dissected and RNA was extracted from the hypothalamus, the hippocampus, and brainstem using Trizol according to manufacturer’s instructions. Samples were then coded to mask the groups and sent to the Johns Hopkins Genetic Resources Core Facility for further processing and analyses. RNA quality of each sample was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies)

treatment_protocol:
[tumor induction protocol]  Each mouse received an orthotopic injection into the 4th and 9th inguinal mammary glands. Half of the mice (n=16) were injected with mycoplasma-free murine non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL), the remainder (n=16) were injected with vehicle only (DMEM 0.1 mL). Injections occurred from ZT5-ZT7 (i.e., 5–7 h after lights on). The 67NR cell line is a non-metastatic mammary carcinoma cell line that was isolated from a single spontaneous Balb/cfC3H mammary tumor and obtained from Barbara Ann Karmanos Cancer Institute (Detroit, MI). Following injection, mice were returned to their home cages for recovery.
[tissue collection protocol]  On the 25th day after injection, half of the mice in each group were euthanized for tissue collection at one of two timepoints; mid-dark (ZT19, n=16), or mid-light (ZT7, n=16). Mice were transcardially perfused with ice cold 1X phosphate-buffered saline and decapitated. Adequate perfusion was confirmed based on clearance of blood from the liver. To preserve RNA integrity, brains were rapidly collected into RNAlater (Thermo Fisher) and stored in -80 °C overnight for later processing. 67NR-injected mice were verified to have mammary tumors, and vehicle injected mice were verified to be mammary tumor free.

tag: mouse #

tag: mammary tumor status

value: Vehicle

value: brain

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

value: Balb/C

tag: animal source

value: Charles River Labs

tag: Sex

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: RNAseq_HFD_Ing_WT_rep1

description: White Adipose Tissue (WAT)

tag: tissue

value: Inguinal (iWAT)

tag: genotype

value: wild type

tag: strain


title: 32 BS Grp3

tag: mouse #

tag: mammary tumor status

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)


title: 32 Hy Grp3

description:
Whole brain RNA stabilized in RNAlater, brain regions dissected, extracted with Trizol, quality analyzed with Agilent 2100 Bioanalyzer, samples were then assayed using the nanoString nCounter Mouse Neuroinflammation Panel V1. NOTE: each mouse has 3 brain regions as individual samples, so other characteristics are listed three times - pay attention to the "mouse number" when using characteristic data that are repeated.  Outliers (based on the raw data) were excluded from normalization and further analysis.
Outlier sample.

value: Hypothalamus

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: animal source

tag: Sex

tag: age at collection

tag: tumor cell type


title: Patient8 10093-Nivo

tag: gender

value: Male

tag: age (years)

tag: site

value: Supra Glottis

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

tag: cohort

tag: treatment in culture

value: Nivolumab


title: Patient9 10100-Nivo

value: Tongue

value: II


title: Patient7 10091-Nivo

value: IVB


title: PC9-BrM4-2

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

country: Japan

institute: Kanazawa Medical University Hospital

data_processing:
The fastq files were generated using bcl2fastq software.
Sequenced reads were mapped to hg38 using HISAT2 (v2.1.0) with default parameter.
Reads Per Kilobase of exon per Megabase of library size (RPKM)  and Transcripts per Million (TPM) were calcurated by StringTie (v1.3.4d) with default parameter.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary files format and content: Matrix table with TPMs for every gene and every sample

source_name: Human lung cancer cells

extract_protocol:
Total RNAs of cancer cells were extracted with TRIzol reagent (Thermo Fisher Scientific) according to manufacturer instructions.
The libraries were created using TruSeq Stranded mRNA according to manufacturer instructions.

tag: cell line

tag: cell type

value: Human lung cancer cells

tag: treatment

value: cultured in a conventional manner


title: RNAseq_MEF_Dido1_MUT_rep2

data_processing:
Sequenced reads were mapped to mm10 whole genome using BWA-MEM 0.7.15 with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
Transcripts per Million of library size (TPM) were calculated using StringTie version 1.3.3 with parameters -e -v -p 32 -G knownGene_UCSC_mm10.gtf
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cov, FPKM, and TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with TPM values for every transcript and every sample

source_name: Mouse Embryonic Fibroblast (MEF)

growth_protocol: Animals were maintained on a normal diet (ND) at 22ºC on a 12/12-h light/dark cycles with ad libitum access to food and water.

extract_protocol:
Total RNA was performed with a SPLIT RNA extraction kit (Lexogen, Austria). Triplicate RNA probes from wild-type and Dido1_dNT mutant were sequenced.
RNA libraries for epididymal WAT were prepared by the servicio de genomica at the Parque Cientifico de Madrid using standard Illumina protocols. RNA libraries for cells differentiated into adipocytes were prepared by BGI Genomics (China).

treatment_protocol: A high fat diet (HFD), made of 45% fat, 20% proteins and 35% carbohydrates (energy 4615 Kcal/kg; Ssniff E15744) was used to induce obesity in mice. MEF cells were from Trachana et al., 2007 (DOI 10.1073/pnas.0611132104) and differentiated precisely following the protocol described in Aune et al., 2013 (DOI 10.3791/50191).

tag: strain

tag: tissue

value: MEF differentiated into adipocytes

tag: source

value: cell culture

tag: wild type

value: Dido1_dNT mutant


title: PC9-AMG-1


title: Patient12 20012-Nivo

value: Buccal Mucosa

value: Local Recurrent

value: Prior treatment:CT/RT

value: IVA


title: RNAseq_MEF_Dido1_MUT_rep1


title: Patient6 10078-Nivo

value: Male

value: Lip


title: Patient5 10041-Nivo

value: Primary


title: PC9-BrM4-1


title: Patient4 10036-Nivo

value: Female

value: Hard Palate

value: Naive


title: RNAseq_MEF_Dido1_WT_rep3

value: wild type


title: PC9-2


title: 30 Hippo Grp4

tag: mouse #

tag: mammary tumor status

value: Vehicle

value: brain

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

value: Balb/C

tag: animal source

value: Charles River Labs

tag: Sex

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: 30 BS Grp4

tag: mouse #

tag: mammary tumor status

tag: tissue

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

tag: strain


title: 30 Hy Grp4

value: Hypothalamus

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)


title: PC9-AMG-2

tag: cell line

tag: cell type

value: Human lung cancer cells

tag: treatment

value: cultured in a conventional manner


title: Patient3 10035-Nivo

tag: gender

value: Female

tag: age (years)

tag: site

value: Larynx

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: IVb

tag: cohort

tag: treatment in culture

value: Nivolumab


title: 29 Hy Grp2

tag: mouse #

tag: mammary tumor status

value: Tumor

tag: tissue

value: brain

tag: brain region

tag: time of day of tissue collection

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: strain

value: Balb/C

tag: animal source

tag: Sex

tag: age at collection

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: PC9-1

tag: cell line

tag: cell type

tag: treatment


title: RNAseq_MEF_Dido1_WT_rep2

tag: tissue

value: MEF differentiated into adipocytes

tag: source

value: cell culture

tag: wild type

value: wild type


title: 29 BS Grp2

tag: mouse #

tag: mammary tumor status

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

value: Charles River Labs

value: female

value: 13 weeks

value: Teklad #2018

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

value: mid day


title: 29 Hippo Grp2

value: Hippocampus

tag: animal source

tag: Sex

tag: age at collection

tag: tumor cell type

tag: food

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: RNAseq_MEF_Dido1_WT_rep1

tag: tissue

tag: source

tag: wild type


title: RNAseq_MEF_Dido1_MUT_rep3

value: Dido1_dNT mutant


title: Patient1 20194-Nivo

tag: gender

value: Female

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: II

tag: cohort

tag: treatment in culture

value: Nivolumab


title: Cortex_20w

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

data_processing:
Sequence reads from QuantSeq 3’ mRNA-Seq were aligned in Mus musculus mm10 reference genome indexes using Bowtie2 for assembling transcripts.
Abundance of transcript as read counts was estimated using coverage in Bedtools. Read count data were normalized using TMM+CPM method in EdgeR package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Cortex

extract_protocol:
Total RNA was extracted from the hippocampus and cortex of mice exposed to UPM (3, 5, and 7 days and 3, 8, 12, 16, and 20 weeks) using TRIzol reagent, according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA). RNAs obtained from mice in the same experimental group was pooled. RNA quality was assessed using the Agilent TapeStation 4000 system (Agilent Technologies, Amstelveen, Netherlands). RNA was quantified  using a NanoDrop-2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Only samples with RNA integrity > 7.0 were included in QuantSeq Analysis.
A  cDNA library was constructed using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. Briefly , total RNA was hybridized with an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end to synthesize the first strand of cDNA by reverse transcription. The second strand of cDNA was synthesized using a random primer containing an Illumina-compatible linker sequence at its 5’ end. The cDNA library was then amplified to add the complete adapter sequences required for cluster generation. Finally, high-throughput sequencing was performed by a single-end 75-base pair sequencing using a NextSeq 550 (Illumina, Inc., USA ).

value: Cortex

tag: Sex

value: male

tag: strain

tag: treatment

value: UPM

tag: time

value: 20 weeks


title: 28 Hy Grp3

tag: mouse #

tag: mammary tumor status

value: Vehicle

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

value: Balb/C

tag: animal source

value: Charles River Labs

value: female

tag: age at collection

tag: tumor cell type

tag: food

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: 28 Hippo Grp3

tag: mouse #

tag: mammary tumor status

tag: tissue

tag: brain region

value: Hippocampus

tag: strain

tag: Sex

value: 13 weeks

value: Teklad #2018

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

value: mid day


title: Cortex_16w

tag: treatment

tag: time

value: 16 weeks


title: Patient31 L0042-Control

tag: gender

value: Female

tag: age (years)

tag: site

value: Tongue

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: II

tag: cohort

tag: treatment in culture

value: Control


title: Cortex_12w

value: Cortex

value: male

value: UPM

value: 12 weeks


title: M. purpureus cells pretreated with taurine, Sample1, Day1

city: Changzhou

first: Xia

last: Yi

address: Gehu Middle Road #21

country: China

institute: Changzhou University

data_processing:
The raw data was filtered with SOAPnuke.
Trinity (v2.0.6) was used to assemble the clean reads and BUSCO to assess the assembly quality.
Clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5) and the expression level of genes was calculated by RSEM (v1.2.8)
Differential gene analysis was performed using DESeq under the conditions of Fold Change ≥ 2 and Adjusted Pvalue ≤ 0.001. Using the pheatmap function on the differential gene set to draw a heatmap of differential gene clusters. According to the GO and KEGG annotation results and official classifications, the differentially expressed genes were functionally classified, and the phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) in R software was used for KEGG enrichment analysis, and the TermFinder package was used for GO Enrichment analysis (https://metacpan.org/pod/GO::TermFinder). With a Q value of  ≤ 0.05 as the threshold, candidate genes that met this condition was defined as being significantly enriched.
Assembly: ASM2599979v1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Monascus purpureus

source_name: M. purpureus MP2022

growth_protocol: M. purpureus cells were cultured in fermentation medium at 25 oC 150 rpm.

extract_protocol:
RNA was harvested using TRlzol Reagent (Life technologies, California, USA). 0.1-1.0 μg of total RNA was used for the construction of sequencing libraries.
mRNA Library Preparation (DNBSEQ) for Denovo Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: M. purpureus cells were cultured in fermentation medium at 25 oC 150 rpm adding the certain concentration of taurine.

tag: cell line

value: M. purpureus MP2022

tag: cell type

value: M. purpureus MP2022 cells

tag: genotype

value: WT

value: Pretreated with Taurine


title: 28 BS Grp3

tag: mouse #

tag: mammary tumor status

value: Vehicle

tag: tissue

value: brain

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

value: Balb/C

tag: animal source

value: Charles River Labs

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: Patient30 L0041-Control

tag: gender

value: Female

tag: age (years)

tag: site

value: RMT

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: III

tag: cohort

tag: treatment in culture

value: Control


title: M. purpureus cells pretreated with taurine, Sample2, Day1

tag: cell line

value: M. purpureus MP2022

tag: cell type

value: M. purpureus MP2022 cells

tag: genotype

value: WT

tag: treatment

value: Pretreated with Taurine

tag: time


title: Cortex_8w

tag: tissue

value: Cortex

tag: Sex

value: male

tag: strain

value: UPM

value: 8 weeks


title: Patient29 K0038-Control

tag: gender

value: Lip

value: II


title: 23 Hy Grp1

tag: mouse #

tag: mammary tumor status

value: Tumor

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

value: Balb/C

tag: animal source

value: Charles River Labs

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: 23 Hippo Grp1

tag: mouse #

tag: mammary tumor status

tag: tissue

tag: brain region

value: Hippocampus

tag: strain

tag: Sex


title: M. purpureus cells, Control2, day1

tag: cell line

value: M. purpureus MP2022

tag: cell type

value: M. purpureus MP2022 cells

tag: genotype

value: WT

tag: treatment

value: Untreated with Taurine

tag: time


title: M. purpureus cells, Control3, day1


title: HBL1_p50_CST_ChIP

city: Cold Spring Harbor

first: Christopher

middle: R.

last: Vakoc

state: NY

address: 1 Bungtown road

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
Sequencing reads were mapped to the human genome (hg38) using Bowtie2 (2.4.4). Duplicate read removal and sorting was performed using SAMtools (1.14). Peaks were called using MACS2 (2.2.7.1) broad peak (H3K27ac) or narrow peak (p50, OCT2, option using FDR cut off 5%. Big wig files were generated using DeepTools (3.5.1).
Assembly: hg38
Supplementary files format and content: peaks

molecule: genomic DNA

source_name: Blood

extract_protocol: For each ChIP, 20 million cells were used. Cells were cross-linked with 1% formaldehyde for 10 min at room temperature with agitation and quenched with 0.125 M glycine for 5 min at room temperature. After washing twice with PBS, cells were incubated in 1 ml cell lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2% NP-40 with protease inhibitor) for 15 min on ice. Nuclei were isolated by centrifugation at 600×g for 30 s, resuspended in 1 ml nuclear lysis buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS with protease inhibitor) and sonicated using a Bioruptor Pico (Diagenode) (30s on/off, 10 cycles). In all cases, the chromatin was centrifuged at maximum speed in a tabletop centrifuge for 15 min at 4 °C. The supernatant was mixed with 7 ml IP dilution buffer (20 mM Tris-HCl (pH 8.0), 2 mM EDTA, 150  mM NaCl, 1% Triton X-100), and incubated with the 2.5 µg of the indicated antibody for 2 h. Protein A/G magnetic beads (25 µl, Dynabeads, Thermo Fisher Scientific) were washed twice with PBS and added to the antibody–chromatin mixture at 4 °C overnight. The beads were washed once with IP wash 1 buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (20 mM Tris-HCl (pH 8.0), 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP wash 2 buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and twice with TE (pH 8.0). Chromatin DNA was eluted, and cross-linking was reversed in 200 µl nuclear extraction buffer with 12 µl of 5 M NaCl and 1 µg /mL RNase A at 65 °C overnight. The beads were then discarded. The DNA-containing supernatant was treated with 4 µg /mL proteinase K at 56 °C for 20 min and purified using the QIAquick PCR purification kit (QIAGEN) in 60 μl water.

value: Blood

value: Tumor Cells

value: Genomic DNA

tag: antibody


title: Patient2 20200-Nivo

tag: gender

value: Female

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: IVa

tag: cohort

tag: treatment in culture

value: Nivolumab


title: Cortex_3w

tag: tissue

value: Cortex

value: male

tag: strain

value: UPM

value: 3 weeks


title: Cortex_7d

tag: Sex

value: 7 days


title: 23 BS Grp1

tag: mouse #

tag: mammary tumor status

value: Tumor

value: brain

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

value: Balb/C

tag: animal source

value: Charles River Labs

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: M. purpureus cells pretreated with taurine, Sample3, Day1

tag: cell line

value: M. purpureus MP2022

tag: cell type

value: M. purpureus MP2022 cells

tag: genotype

value: WT

tag: treatment

value: Pretreated with Taurine

tag: time


title: Cortex_5d

tag: tissue

value: Cortex

tag: Sex

value: male

tag: strain

value: UPM

value: 5 days


title: 22 Hy Grp4

tag: mouse #

tag: mammary tumor status

value: Vehicle

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: animal source


title: Cortex_3d

value: 3 days


title: 22 Hippo Grp4

value: Hippocampus

value: Balb/C

value: Charles River Labs

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

tag: food

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: Cortex_Con

tag: tissue

tag: Sex

tag: strain

tag: treatment

value: control

tag: time


title: Patient28 K0037-Control

tag: gender

value: Female

tag: age (years)

tag: site

value: Mouth

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: IVA

tag: cohort

tag: treatment in culture

value: Control


title: 22 BS Grp4

tag: mouse #

tag: mammary tumor status

value: Vehicle

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: animal source

tag: age at collection

tag: tumor cell type

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]


title: Patient26 10002-Control

tag: gender

tag: age (years)

tag: site

value: Alveolus

tag: sample type

tag: therapy

value: Neoadjuvant CT/RT

tag: cancer grade

tag: cancer stage

tag: cohort

tag: treatment in culture


title: Patient25 10001-Control

value: Buccal Mucosa


title: Patient27 10006-Control

value: Male

value: Tongue


title: Patient23 20113-Control

value: II


title: Patient24 20114-Control

value: Submindibular region

value: IV


title: Hippocampus_20w

source_name: Hippocampus

tag: tissue

value: Hippocampus

tag: Sex

value: male

tag: strain

tag: treatment

value: UPM

tag: time

value: 20 weeks


title: Hippocampus_16w

value: 16 weeks


title: M. purpureus cells, Control1, day1

tag: cell line

value: M. purpureus MP2022

tag: cell type

value: M. purpureus MP2022 cells

tag: genotype

value: WT

value: Untreated with Taurine


title: Hippocampus_12w

value: 12 weeks


title: 19 BS Grp1

tag: mouse #

tag: mammary tumor status

value: Tumor

value: brain

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

value: Balb/C

tag: animal source

value: Charles River Labs

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: Hippocampus_8w

tag: tissue

value: Hippocampus

tag: Sex

value: male

tag: strain

tag: treatment

value: UPM

tag: time

value: 8 weeks


title: tick infested mice 5_3rd infestation

city: Chapel Hill

first: Shailesh

middle: Kumar

last: Choudhary

state: NC

address: 3300 Thurston Bldg., CB#7280

department: Medicine

institute: University of North Carolina at Chapel Hill

hyb_protocol: Hybridization was performed per the manufacturer’s instructions for Gene Expression Panels with Panel Plus/CodeSet with CodeSet Plus. Briefly, Hybridization was set up with 5 mcL of sample (100 ng of RNA), which was added to 10 mcL of hybridization master mix (5 mcL of hybridization buffer + 3 mcL of Reporter CodeSet + 2 mcL of Reporter Plus) + 3 mcL of Capture Maser Mix. The total hybridization volume was 18uL per sample. Each cartridge was hybridized for 18 hours on a thermal cycler set to 65℃ with a lid heated to 70℃.

scan_protocol: Cartridges were then analyzed on the nCounter Pro Analysis System

data_processing: Nanostring Data was analyzed by ROSALIND (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes, and p-values were calculated using criteria provided by Nanostring.

label: NanoString

source_name: skin

label_protocol: none provided

extract_protocol: Total RNA was extracted from the skin biopsies using the RNeasy Plus kit (Quick RNA miniprep plus kit from Zymo, USA).

tag: time course

value: 3rd sensitization

value: tick infestation


title: Patient22 20085-Control

tag: gender

value: Female

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: III

tag: cohort

tag: treatment in culture

value: Control


title: tick infested mice 3_3rd infestation


title: tick infested mice 4_3rd infestation


title: 13 Hy Grp2

tag: mouse #

tag: mammary tumor status

value: Tumor

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

value: Balb/C

tag: animal source

value: Charles River Labs

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

tag: food

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280


title: tick infested mice 6_3rd infestation

tag: time course

tag: treatment


title: tick infested mice 2_3rd infestation


title: Patient20 20057-Control

tag: gender

tag: age (years)

tag: site

tag: sample type

tag: therapy

tag: cancer grade

tag: cancer stage

tag: cohort

tag: treatment in culture


title: Hippocampus_3w

tag: tissue

value: Hippocampus

tag: Sex

value: male

tag: strain

value: UPM

tag: time

value: 3 weeks


title: Patient21 20074-Control

value: Male

value: Alveolus

value: IVa


title: Patient19 20047-Control

value: Buccal Mucosa

value: Primary

value: Naive

value: III


title: 19 Hy Grp1

tag: mouse #

tag: mammary tumor status

value: Tumor

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: animal source

tag: age at collection

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/230


title: 13 Hippo Grp2

tag: mouse #

tag: mammary tumor status

tag: tissue

value: Hippocampus

value: Mid Day (ZT7, 12:00 h)

tag: strain

value: Balb/C

value: Charles River Labs

tag: Sex

value: female

value: 13 weeks

tag: bioanalyzer total rna 260/280


title: Hippocampus_7d

value: male

tag: treatment

value: UPM

tag: time

value: 7 days


title: 19 Hippo Grp1

value: Tumor

tag: brain region

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)


title: Hippocampus_5d

value: 5 days


title: control mice 6_3rd infestation

tag: time course

value: 3rd sensitization

value: control infestation


title: control mice 5_3rd infestation


title: control mice 4_3rd infestation


title: Hippocampus_3d

value: 3 days


title: 13 BS Grp2

tag: mouse #

value: brain

value: Brain Stem

tag: animal source

tag: age at collection

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

value: Teklad #2018

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/230


title: Patient18 20043-Control

tag: gender

value: Male

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: IVb

tag: cohort

tag: treatment in culture

value: Control


title: tick infested mice 1_3rd infestation

tag: time course

tag: treatment

value: tick infestation


title: control mice 3_3rd infestation


title: 12 Hippo Grp3

tag: mouse #

tag: mammary tumor status

value: Vehicle

tag: tissue

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

value: Balb/C

tag: animal source

value: Charles River Labs

tag: Sex

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

value: mid day

tag: bioanalyzer total rna 260/280


title: 12 BS Grp3

tag: mouse #

value: brain

value: Brain Stem

tag: food

value: Teklad #2018

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/230


title: Patient15 20023-Control

tag: gender

value: Female

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

value: Primary

tag: therapy

tag: cancer grade

tag: cancer stage

value: III

tag: cohort

tag: treatment in culture


title: Hippocampus_Con

tag: tissue

tag: Sex

value: male

tag: strain

tag: treatment

value: control

tag: time


title: control mice 2_3rd infestation

tag: time course

value: 3rd sensitization

value: control infestation


title: Patient17 20026-Control

value: Male

value: GBS

value: Naive

value: Control


title: CV Day 32-2

data_processing:
The fastq files were generated using bcl2fastq software.
Sequenced reads were mapped to hg38 using HISAT2 (v2.1.0) with default parameter.
Reads Per Kilobase of exon per Megabase of library size (RPKM)  and Transcripts per Million (TPM) were calcurated by StringTie (v1.3.4d) with default parameter.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse astrocyte

extract_protocol:
Total RNAs of astrocytes were extracted with TRIzol reagent (Thermo Fisher Scientific) according to manufacturer instructions.
The libraries were constructed using  NEB Ultra II directional RNA Library Prep Kit for Illumina according to manufacturer instructions.

tag: cell type

value: mouse astrocyte

tag: treatment/time point

value: CV Day 32


title: 11 Hy Grp1

tag: mouse #

tag: mammary tumor status

value: Tumor

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

value: Balb/C

tag: animal source

value: Charles River Labs

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: CV Day 32-1

tag: cell type

tag: treatment/time point


title: Patient14 20019-Control

tag: gender

value: Male

tag: age (years)

tag: site

value: Oral Cavity

tag: sample type

value: Primary

tag: therapy

tag: cancer grade

tag: cancer stage

value: III

tag: cohort

tag: treatment in culture


title: Patient13 20015-Control

value: Female

value: Naive

value: II

value: Control


title: Patient12 20012-Control

value: Buccal Mucosa

value: Local Recurrent

value: Prior treatment:CT/RT

value: IVA


title: tick infested mice 6_2nd infestation

tag: time course

value: 2nd sensitization

tag: treatment

value: tick infestation


title: 12 Hy Grp3

tag: mouse #

tag: mammary tumor status

value: Vehicle

tag: tissue

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

value: Balb/C

tag: animal source

value: Charles River Labs

tag: Sex

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

tag: food

value: Teklad #2018

tag: light cycle

tag: time of day of tumor injection


title: 11 Hippo Grp1

tag: mouse #

tag: mammary tumor status

value: Tumor

tag: tissue

value: Hippocampus

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

value: mid day

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: tick infested mice 5_2nd infestation

tag: time course

tag: treatment


title: MGS Day 32-2

tag: cell type

value: mouse astrocyte

tag: treatment/time point

value: MGS Day 32


title: 11 BS Grp1

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source


title: Patient16 20025-Control

tag: gender

value: Male

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: III

tag: cohort

tag: treatment in culture

value: Control


title: MGS Day 32-1

tag: cell type

tag: treatment/time point


title: 10 Hy Grp4

tag: mouse #

tag: mammary tumor status

value: Vehicle

tag: tissue

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

value: Balb/C

value: Charles River Labs

tag: Sex

value: female

tag: age at collection

tag: tumor cell type

tag: food

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: tick infested mice 4_2nd infestation

tag: time course

value: 2nd sensitization

tag: treatment

value: tick infestation


title: CV Day 5-2

tag: cell type

value: mouse astrocyte

tag: treatment/time point

value: CV Day 5


title: 10 Hippo Grp4

tag: mouse #

tag: mammary tumor status

tag: tissue

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

value: 13 weeks

value: Teklad #2018

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

value: mid day


title: Patient11 20006-Control

tag: gender

value: Female

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

value: Primary

tag: therapy

value: Radiotherapy

tag: cancer grade

tag: cancer stage

value: IVA

tag: cohort

tag: treatment in culture

value: Control


title: 10 BS Grp4

tag: mouse #

tag: mammary tumor status

value: Vehicle

tag: tissue

value: brain

value: Brain Stem

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

value: Balb/C

value: Charles River Labs

tag: Sex

tag: age at collection

tag: tumor cell type

tag: food

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: MGS Day 5-2

tag: cell type

value: mouse astrocyte

tag: treatment/time point

value: MGS Day 5


title: control mice 1_3rd infestation

tag: time course

value: 3rd sensitization

tag: treatment

value: control infestation


title: Patient9 10100-Control

tag: gender

value: Male

tag: age (years)

tag: site

value: Tongue

tag: sample type

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: II

tag: cohort

tag: treatment in culture


title: Patient8 10093-Control

value: Supra Glottis

value: Primary

value: III


title: tick infested mice 2_2nd infestation

value: 2nd sensitization

value: tick infestation


title: tick infested mice 1_2nd infestation


title: 9 Hy Grp2

tag: mouse #

tag: mammary tumor status

value: Tumor

tag: tissue

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

tag: Sex

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day


title: Patient7 10091-Control

tag: gender

value: Male

tag: age (years)

tag: site

value: Tongue

tag: sample type

tag: therapy

tag: cancer grade

tag: cancer stage

value: IVB

tag: cohort

tag: treatment in culture

value: Control


title: MGS Day 5-1

tag: cell type

value: mouse astrocyte

tag: treatment/time point

value: MGS Day 5


title: control mice 5_2nd infestation

tag: time course

value: 2nd sensitization

tag: treatment

value: control infestation


title: 9 Hippo Grp2

tag: mouse #

tag: mammary tumor status

value: Tumor

tag: tissue

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

value: Balb/C

tag: animal source

value: Charles River Labs

tag: Sex

tag: age at collection

tag: tumor cell type

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: 8 Hy Grp3

tag: mouse #

tag: mammary tumor status

value: Vehicle

tag: tissue

value: brain

value: Hypothalamus

value: Mid Dark (ZT19, 00:00 h)

value: female

value: 13 weeks

tag: food

tag: light cycle

tag: time of day of tumor injection


title: HBL1 Cas9 cells, sgPOU2F2_9 rep1

data_processing: Raw reads were aligned to the human transcriptome (GRCh38-release 108) using Kallisto (v 0.46.1). For differential gene expression analysis, read counts were analyzed using DESeq2 (v. 1.40.2), comparing knockout samples of NFKBIZ  and POU2F2 to control sgROSA with 5 different guides as biological replicates for the the NFKBIZ knockout, 3 different guides for POU2F2 knockout and 2 different guides for sgROSA.  A technical replicate was also used for each sample, and the two technical replicates were combined in the transcript quantification step in Kallisto.  The differential expression gene analysis was performed using a gene expression cutoff of >2 TPM.  Significantly down or up-regulated genes were determined  using a cut of p.adj <0.1 in DESeq2.

source_name: Human diffuse large B-cell lymphoma

growth_protocol: For knockout experiments, cells were collected 6 days after infection with sgRNA for HBL1 Cas9 cells.

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher Scientific) according to the manufacturer’s protocol and resuspended in RNase-free water. Poly(A) RNA was selected and fragmented with NEBNext Poly(A) mRNA Magnetic isolation module (NEB, E7350).
The library was prepared using the NEBNext Ultra II RNA Library Prep kit for Illumina (NEB, E7770) with 2 µg RNA according to the manufacturer’s protocol.
RNA-seq libraries were pooled and analysed by single-end 76 bp sequencing using the NextSeq (Illumina) system.

value: Human diffuse large B-cell lymphoma

tag: cell line

value: HBL1 cells

tag: sgrna


title: HBL1 Cas9 cells, sgPOU2F2_9 rep2


title: 9 BS Grp2

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

value: Teklad #2018

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

value: mid day


title: control mice 4_2nd infestation

tag: time course

value: 2nd sensitization

tag: treatment

value: control infestation


title: HBL1 Cas9 cells, sgPOU2F2_8 rep2


title: Patient5 10041-Control

tag: gender

value: Male

tag: age (years)

tag: site

value: Tongue

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: II

tag: cohort

tag: treatment in culture

value: Control


title: Patient10 10108-Control

value: Radiotherapy

value: III


title: Patient4 10036-Control

value: Female

value: Hard Palate


title: tick infested mice 3_2nd infestation

value: tick infestation


title: control mice 3_2nd infestation


title: CV Day 5-1

tag: cell type

value: mouse astrocyte

tag: treatment/time point

value: CV Day 5


title: 8 BS Grp3

tag: mouse #

tag: mammary tumor status

value: Vehicle

tag: tissue

value: brain

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: strain

value: Balb/C

tag: animal source

value: Charles River Labs

tag: Sex

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: Patient3 10035-Control

tag: gender

tag: age (years)

tag: site

value: Larynx

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: IVb

tag: cohort

tag: treatment in culture

value: Control


title: control mice 2_2nd infestation

tag: time course

value: 2nd sensitization

tag: treatment

value: control infestation


title: 8 Hippo Grp3

tag: mouse #

tag: mammary tumor status

value: Vehicle

tag: tissue

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

tag: Sex

tag: age at collection

tag: tumor cell type

tag: food

value: mid day


title: control mice 6_2nd infestation

tag: time course

tag: treatment


title: HBL1 Cas9 cells, sgPOU2F2_5 rep2

tag: tissue

value: Human diffuse large B-cell lymphoma

tag: cell line

value: HBL1 cells

tag: sgrna


title: HBL1 Cas9 cells, sgPOU2F2_5 rep1


title: Patient2 20200-Control

tag: gender

value: Female

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

tag: therapy

tag: cancer grade

tag: cancer stage

value: IVa

tag: cohort

tag: treatment in culture


title: Patient6 10078-Control

value: Male

value: Lip

value: Local Recurrent

value: Prior treatment:CT/RT

value: IVA


title: tick infested mice 6_1st infestation

value: 1st sensitization

value: tick infestation


title: Patient1 20194-Control

value: Primary

value: Naive

value: II

value: Control


title: tick infested mice 5_1st infestation


title: 7 Hippo Grp1

tag: mouse #

tag: mammary tumor status

value: Tumor

value: brain

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

value: Balb/C

tag: animal source

value: Charles River Labs

tag: Sex

value: female

tag: age at collection

value: 13 weeks

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: HBL1 Cas9 cells, sgPOU2F2_8 rep1

tag: tissue

value: Human diffuse large B-cell lymphoma

tag: cell line

value: HBL1 cells

tag: sgrna


title: Patient14-L0042

tag: gender

value: Female

tag: age (years)

tag: site

value: Tongue

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

tag: cohort


title: 7 Hy Grp1

tag: mouse #

tag: mammary tumor status

value: Tumor

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

tag: Sex

tag: age at collection

tag: tumor cell type

tag: food


title: HBL1 Cas9 cells, sgNFKBIZ_9 rep2

tag: tissue

tag: cell line

tag: sgrna


title: 7 BS Grp1

tag: mouse #

tag: mammary tumor status

tag: brain region

value: Brain Stem

value: Mid Dark (ZT19, 00:00 h)

value: Balb/C

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: HBL1 Cas9 cells, sgNFKBIZ_8 rep2


title: HBL1 Cas9 cells, sgNFKBIZ_9 rep1


title: tick infested mice 4_1st infestation

tag: time course

value: 1st sensitization

tag: treatment

value: tick infestation


title: HBL1 Cas9 cells, sgNFKBIZ_8 rep1


title: tick infested mice 3_1st infestation


title: Patient13-L0041

tag: gender

tag: age (years)

tag: site

value: RMT

tag: sample type

tag: therapy

tag: cancer grade

tag: cancer stage

value: III

tag: cohort


title: 6 Hippo Grp4

tag: mouse #

tag: mammary tumor status

value: Vehicle

tag: tissue

value: Hippocampus

tag: time of day of tissue collection

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

value: Charles River Labs

tag: Sex

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

tag: food

value: Teklad #2018

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

value: mid day


title: Patient12-K0038

tag: gender

value: Female

tag: age (years)

tag: site

value: Lip

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: II

tag: cohort


title: Patient11-K0037

value: Mouth

value: IVA


title: 6 Hy Grp4

tag: mouse #

tag: mammary tumor status

tag: tissue

value: brain

tag: brain region

value: Hypothalamus

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

value: Balb/C

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: 6 BS Grp4

value: Vehicle

value: Brain Stem

value: Mid Day (ZT7, 12:00 h)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

tag: Sex

tag: age at collection

tag: tumor cell type

tag: food


title: control mice 1_2nd infestation

tag: time course

value: 2nd sensitization

tag: treatment

value: control infestation


title: tick infested mice 2_1st infestation

value: 1st sensitization

value: tick infestation


title: HBL1 Cas9 cells, sgNFKBIZ_106 rep2

tag: tissue

value: Human diffuse large B-cell lymphoma

tag: cell line

value: HBL1 cells

tag: sgrna


title: Patient10-10006

tag: gender

value: Male

tag: age (years)

tag: site

value: Tongue

tag: sample type

value: Primary

tag: therapy

tag: cancer grade

tag: cancer stage

tag: cohort


title: 5 Hy Grp2

tag: mouse #

tag: mammary tumor status

value: Tumor

tag: brain region

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

value: Charles River Labs

tag: Sex

value: female

value: 13 weeks

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: HBL1 Cas9 cells, sgNFKBIZ_106 rep1

tag: tissue

tag: cell line

tag: sgrna


title: tick infested mice 1_1st infestation

tag: time course

tag: treatment


title: 5 Hippo Grp2

tag: mouse #

tag: mammary tumor status

value: brain

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

value: Balb/C

tag: age at collection

tag: tumor cell type

tag: food


title: control mice 6_1st infestation

value: 1st sensitization

value: control infestation


title: Patient9-10001

tag: gender

value: Female

tag: age (years)

tag: site

value: Buccal Mucosa

tag: sample type

tag: therapy

tag: cancer grade

tag: cancer stage

value: IVA

tag: cohort


title: HBL1 Cas9 cells, sgNFKBIZ_104 rep2

tag: tissue

value: Human diffuse large B-cell lymphoma

tag: cell line

value: HBL1 cells

tag: sgrna


title: control mice 5_1st infestation

tag: time course

tag: treatment


title: Patient8-20025

value: Male

value: Primary

value: Naive

value: III


title: 5 BS Grp2

tag: mouse #

tag: mammary tumor status

value: Tumor

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

value: Charles River Labs

tag: Sex

value: female

value: 13 weeks

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: HBL1 Cas9 cells, sgNFKBIZ_104 rep1

tag: tissue

tag: cell line

tag: sgrna


title: HBL1 Cas9 cells, sgNFKBIZ_103 rep2


title: 4 Hippo Grp3

tag: mouse #

tag: mammary tumor status

value: Vehicle

value: brain

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

value: Balb/C

tag: age at collection

tag: tumor cell type

tag: food

value: mid day


title: Patient7-20019

tag: gender

value: Male

tag: age (years)

tag: site

value: Oral Cavity

tag: sample type

value: Primary

tag: therapy

tag: cancer grade

tag: cancer stage

tag: cohort


title: HBL1 Cas9 cells, sgROSA_2 rep2

tag: tissue

value: Human diffuse large B-cell lymphoma

tag: cell line

value: HBL1 cells

tag: sgrna


title: 4 Hy Grp3

tag: mouse #

tag: mammary tumor status

tag: brain region

value: Hypothalamus

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

value: Charles River Labs

tag: Sex

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: HBL1 Cas9 cells, sgNFKBIZ_103 rep1

tag: tissue

tag: cell line

tag: sgrna


title: 1.5% DMS treated lncRNA Panda + ASO2 replicate 3

city: Boston

first: Gabriel

middle: A

last: Romero Agosto

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

library_source: other

data_processing:
Data was processed using the DREEM software (https://github.com/rouskinlab/DREEM) .
Assembly: For PANDA the NCBI Reference Sequence is NR_109836.1. For the RRE the GenBank accession number is MN989412.1
Supplementary files format and content: The filw format is a .csv file that can be opened as a data table using excell. It provides the number of mutations per position of the entire population of RNA molecules that aligned to the referecne sequence.
Library strategy: DMS-MaPseq

molecule: other

organism: synthetic construct

source_name: Human olido-dt cDNA

extract_protocol:
All RNA was acquired from in-vitro transcription of PCR amplified cDNA or gene-blockes.
The libraies for the HIV-1 RRE were prepared using the NEBnext RNA library prep kit. The libraries for the lncRNA PANDA were prepared using the Broad range RNA Xgen kit form IDT. The reverse transcriptase was changed to the Induro RT from NEB for the purposes of our experiment.

value: Brain

tag: cell type

tag: treatment

value: 1.5%DMS + ASO2


title: 1.5% DMS treated lncRNA Panda + ASO2 replicate 2


title: HBL1 Cas9 cells, sgROSA_1 rep2


title: Patient5-10091

tag: gender

tag: age (years)

tag: site

value: Tongue

tag: sample type

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: IVB

tag: cohort


title: control mice 1_1st infestation

tag: time course

value: 1st sensitization

value: control infestation


title: control mice 2_1st infestation


title: Patient4-10041

value: II


title: control mice 4_1st infestation


title: control mice 3_1st infestation


title: 1.5% DMS treated lncRNA Panda + ASO2


title: Patient2-10035

value: Female

value: Larynx

value: IVb


title: Patient3-10036

value: Hard Palate


title: HBL1 Cas9 cells, sgROSA_1 rep1


title: 3 Hippo Grp1

tag: mouse #

tag: mammary tumor status

value: Tumor

value: brain

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

value: Mid Dark (ZT19, 00:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

value: Balb/C

tag: animal source

tag: Sex

value: female

tag: age at collection

value: 13 weeks

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]


title: 3 Hy Grp1

tag: mouse #

tag: mammary tumor status

tag: tissue

tag: brain region

value: Hypothalamus

value: Charles River Labs

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: 3 BS Grp1

value: Brain Stem

tag: time of day of tissue collection

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)


title: AlphaToxin_NonClonal_U2OS_lib4

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description:
combined-non-clonal.csv
lib3160_R1

data_processing:
Sequences were pre-processed (Trimmomatic v. 0.33) to remove Illumina adaptor sequences, filter out sequences < 40 bp and crop longer sequences to 50 bp.
Sequences were then aligned to human genome hg38 (Bowtie v. 2.1.0). Sequences that did not map to unique sites or showed significant mismatch or error (edit distance >2 over 50bp) were excluded from further analysis
Finally, reads were mapped and filtered to a known PiggyBac consensus insertion site (TTAA) at their start.
Common insertion sites (CIS) were identified using the Poisson Regression Insertion Model (PRIM) published by Bergemann et al 2012
The PRIM model was run using a p-value cutoff of 0.01 and Bonferroni correction on both selected, unselected, and in silico-generated libraries based on known TTAA sites in the genome, using window sizes of 10 kb, 25 kb, 50 kb, 75 kb, and 100 kb. CIS in experimental libraries that were also found in unselected or in silico generated libraries were excluded
Assembly: hg38
Supplementary files format and content: processed clonal data contain chromosome,mappingStart,mappingEnd,width,strand,libid,cpm,annotation,geneStart,geneEnd,geneLength,geneId,geneSymbol,normCpm,cpmRank
Supplementary files format and content: processed non clonal data contain CIS summary information and BED tracks

growth_protocol: U2OS cells were co-transfected with piggyBac plasmid pPB-SB-CMV-puro-SD3 and p-hyPBASE using Fugene 6 transfection reagent (Promega, Madison WI, USA). For each library, between 107 - 108 cells were transfected, cultured with the addition of 3 µg/ml puromycin (Gibco) for one week to select cells that had incorporated the transposon, and then used for screens of alpha-toxin resistance with minimal further expansion. Un-mutagenized U2OS cells were treated with alpha-toxin under the same conditions to confirm that no resistance was seen in the absence of transposon mutagenesis.

extract_protocol:
genomic DNA (gDNA) was isolated from 5-10 X 106 cells
4 mg of gDNA were digested with BfaI or CviQI (New England Biolabs, Ipswich MA, USA) and purified (QIAquick PCR purification kits, Qiagen, Hilden, Germany) then ligated with barcoded P7-side adaptors using T4 DNA Ligase (New England BioLabs). Ligated gDNA fragments were then combined and amplified by nested PCR. The first round of PCR used primers corresponding to transposon sequence (KS15) and the P7-side adaptor (LP1). A second round of PCR (primers P2A and LP22) added the full Illumina P5 and P7 sequences. Sequencing was performed by the BRI Genomics platform using a HiScan or HiSeq platform (Illumina, San Diego CA, USA) with a custom sequencing primer (Rd1SeqP.ipdC) to generate 50 or 100 bp single end reads.
described in Bruchez et al 2020

treatment_protocol: Cells were treated twice with alpha-toxin (500 ng/ml) for 48h to ensure the selection of only highly resistant cells.

tag: cell line

tag: genotype

value: mutagenized U2OS cells

tag: treatment

value: alpha-toxin


title: 1.5% DMS treated lncRNA Panda + ASO1 replicate 3

value: Brain

tag: cell type

value: 1.5%DMS + ASO1


title: PC9-AMG_in_MGS-2

data_processing:
Sequenced reads were mapped to hg38 using HISAT2 (v2.1.0) with default parameter.
Reads Per Kilobase of exon per Megabase of library size (RPKM)  and Transcripts per Million (TPM) were calcurated by StringTie (v1.3.4d) with default parameter.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary files format and content: Matrix table with TPMs for every gene and every sample

value: Human lung cancer cells

value: cultured in MGS


title: 4 BS Grp3

value: Vehicle

value: brain

value: Mid Dark (ZT19, 00:00 h)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

tag: Sex

tag: age at collection

tag: tumor cell type

tag: food

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]


title: Patient6-10100

tag: gender

value: Male

tag: age (years)

tag: site

value: Tongue

tag: sample type

value: Primary

tag: therapy

value: Naive

tag: cancer grade

tag: cancer stage

value: II

tag: cohort


title: AlphaToxin_NonClonal_U2OS_lib3-2

description:
combined-non-clonal.csv
lib3159_R1

tag: cell line

tag: genotype

tag: treatment


title: 2 Hippo Grp4

tag: mouse #

tag: mammary tumor status

tag: tissue

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

value: Balb/C

tag: animal source

tag: Sex

value: female

tag: age at collection

value: 13 weeks

value: Teklad #2018

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

value: mid day

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: 1.5% DMS treated lncRNA Panda + ASO1 replicate 2

value: Brain

tag: cell line

tag: cell type

tag: treatment

value: 1.5%DMS + ASO1


title: HBL1 Cas9 cells, sgROSA_2 rep1

tag: tissue

value: Human diffuse large B-cell lymphoma

value: HBL1 cells

tag: sgrna


title: PC9-AMG_in_MGS-1

value: Human lung cancer cells

value: cultured in MGS


title: 2 BS Grp4

tag: mouse #

tag: mammary tumor status

value: Vehicle

value: brain

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

tag: body mass (g)

value: Charles River Labs

tag: tumor cell type

tag: food

tag: light cycle

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]


title: 1.5% DMS treated lncRNA Panda + ASO1

value: 1.5% DMS + ASO1


title: AlphaToxin_NonClonal_U2OS_lib2-2

description:
combined-non-clonal.csv
lib3158_R1

tag: genotype

value: mutagenized U2OS cells

value: alpha-toxin


title: PC9-BrM4_in_MGS-2


title: 2 Hy Grp4

value: Hypothalamus

value: Mid Day (ZT7, 12:00 h)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

value: Balb/C

tag: animal source

tag: Sex

value: female

tag: age at collection

value: 13 weeks

tag: bioanalyzer total rna 260/280

tag: bioanalyzer total rna 260/230


title: AlphaToxin_NonClonal_U2OS_lib3-1

description:
combined-non-clonal.csv
lib2876_R1

tag: cell line

tag: treatment


title: 1.5% DMS treated lncRNA Panda

tag: tissue

value: Brain

tag: cell type


title: 1 Hippo Grp2

tag: mouse #

tag: mammary tumor status

value: Tumor

tag: brain region

value: Hippocampus

tag: time of day of tissue collection

tag: body mass (g)

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

value: mid day

tag: bioanalyzer total rna [ng/ul]


title: AlphaToxin_NonClonal_U2OS_lib1-1

description:
combined-non-clonal.csv
lib2870_R1

tag: genotype


title: untreated lncRNA PANDA

value: untreated


title: 1 Hy Grp2

value: brain

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

tag: animal source

value: Charles River Labs

tag: Sex

tag: age at collection

tag: bioanalyzer total rna 260/280


title: IL1b d6 #3

status: Public on Jan 08 2024

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
Sequencing data was trimmed, aligned and normalized (reads per million mapped reads) using default settings via Partek bioinformatics software.
Assembly: GRCm38
Supplementary files format and content: Xlsx file includes RPKM values for each Sample

source_name: Colon

growth_protocol: Mice grown under SPF conditions

extract_protocol:
RNA from frozen colonic tissues was extracted using Qiagen RNeasy Universal kit. Integrity of the isolated RNA was analysed using the Agilent TS HS RNA Kit and TapeStation 4200
1000ng of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB, #E7490L). RNA sequencing libraries were produced by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L). Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 250nM of each library was pooled together and diluted to 4nM according to the NextSeq manufacturer’s instructions. 1.6pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced with the Illumina NextSeq 550 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

treatment_protocol: WT and IL-1b-/- C57BL/6 mice were orally infected with 10^7 CFU of Salmonella typhimurium SL1334. Colonic tissues were removed at 2 and 6 days post infection and RNA was exptracted and sequenced.

tag: tissue

value: Colon

tag: treatment

value: Salmonella infection


title: Patient1-10002

tag: gender

value: Female

tag: age (years)

tag: site

value: Alveolus

tag: sample type

value: Primary

tag: therapy

value: Neoadjuvant CT/RT

tag: cancer grade

tag: cancer stage

value: IVA

tag: cohort


title: AlphaToxin_NonClonal_U2OS_lib2-1

description:
combined-non-clonal.csv
lib2871_R1

tag: cell line

tag: genotype

value: mutagenized U2OS cells

value: alpha-toxin


title: IL1b d6 #5


title: 1.5% DMS treated lncRNA Panda replicate 2

value: Brain

tag: cell type


title: PC9_in_MGS-1

value: Human lung cancer cells

value: cultured in MGS


title: PC9_in_MGS-2


title: IL1b d6 #2


title: IL1b d6 #4


title: PC9-BrM4_in_MGS-1


title: 1 BS Grp2

tag: mouse #

tag: mammary tumor status

value: Tumor

tag: brain region

value: Brain Stem

tag: time of day of tissue collection

value: Mid Day (ZT7, 12:00 h)

tag: body mass (g)

tag: spleen mass (g)

tag: m4 tumor mass (g)

tag: m4 tumor dimensions (mm)

tag: m9 tumor mass (g)

tag: m9 tumor dimensions (mm)

tag: strain

value: Balb/C

tag: animal source

value: female

value: 13 weeks

tag: tumor cell type

value: non-metastatic 67NR cells (1.0 x 10^5 cells in DMEM, volume 0.1 mL)

tag: food

value: Teklad #2018

tag: light cycle

value: 14:10 Light:Dark; lights on zeitgeber time (ZT) 0, 05:00 h; lights off ZT14, 19:00 h

tag: time of day of tumor injection

tag: bioanalyzer total rna [ng/ul]

tag: bioanalyzer total rna 260/230


title: AlphaToxin_NonClonal_U2OS_lib1-2

description:
combined-non-clonal.csv
lib3157_R1

tag: cell line

tag: genotype

tag: treatment


title: IL1b d2 #4

tag: tissue

value: Colon

value: Salmonella infection


title: WT d6 #3

value: WT


title: WT d2 #4


title: Kidney, LPS, sample2

city: Chicago

first: Michihiro

last: Takahama

state: Illinois

department: Pritzker School of Molecular Engineering

institute: University of Chicago

data_processing:
The output data of each sequencing run (Illumina BCL files) were demultiplexed into FASTQ files using Bcl2Fastq v2.19.1.
The Space ranger software (v1.2.0, 10X Genomics) was used to process, align, and summarize the FASTQ files against a GRCm39 mouse reference genome.
Raw UMI count spot matrices, spot coordinates, and images were imported into python using Scanpy v1.9.1. Raw UMI counts were log10 normalized and clustered using a Louvain algorithm (resolution = 0.35).
Differential expression between control and LPS-treated samples was performed using Scanpy’s rank_genes_groups function using a Wilcoxon rank-sum test.
Spatially resolved counts of differentially expressed genes were overlayed with corresponding grey-scale H&E images and visualized using seaborn v0.11.2.
Assembly: GRCm39
Supplementary files format and content: CTRL_1_filtered_feature_bc_matrix.h5: filtered feature-barcode matrices from space ranger
Supplementary files format and content: CTRL_2_filtered_feature_bc_matrix.h5: filtered feature-barcode matrices from space ranger
Supplementary files format and content: LPS_1_filtered_feature_bc_matrix.h5: filtered feature-barcode matrices from space ranger
Supplementary files format and content: LPS_2_filtered_feature_bc_matrix.h5: filtered feature-barcode matrices from space ranger
Library strategy: Spatial transcriptomics

source_name: Kidney

extract_protocol:
In brief, sections were fixed in 100% methanol and stained with hematoxylin and eosin (H&E) reagents. H&E-stained sections were imaged using a CRi Panoramic MIDI Whole Slide Scanner with 20X magnification. Sections were then permeabilized with 0.1% pepsin in 0.01M HCl for 14 min at 37°C and processed for in-tissue reverse transcription followed by on-slide second strand synthesis.
Samples were processed to generate spatial transcriptomics sequencing libraries according to the manufacturer’s instructions.

treatment_protocol: Mouse kidneys were dissected from LPS-injected (5 mg/kg, 24 hours) or control mice without transcardial perfusion and frozen in Optimal Cutting Temperature (OCT) media. 10 µm frozen tissue sections were cut with a CM1850 Cryostat (Leica) and mounted onto a Visium Spatial Gene Expression library preparation slide (10X Genomics).

value: Kidney

value: Wild-type (C57BL/6J)

value: LPS (5 mg/kg, 24 hours)


title: IL1b d2 #5


title: Kidney, LPS, sample1


title: IL1b d2 #3


title: WT d2 #2


title: WT d6 #2


title: IL1b d2 #2


title: IL1b d6 #1


title: IL1b d2 #1


title: WT d2 #1


title: WT d6 #1


title: Kidney, Untreated, sample1

value: Untreated


title: Kidney, Untreated, sample2


title: WT d2 #3


title: Thymus, LPS_antiTNF_d0.7, m294

description:
experiment10
counts_LPS_KO2.txt

data_processing:
We used the RNA-seq pipeline in the bcbio-nextgen project version 1.1.5 (https://bcbio-nextgen.readthedocs.io/en/latest/).
Reads were aligned to the mouse mm10 transcriptomes with RapMap.
Transcripts were counted with fasttagcount in umis (https://github.com/vals/umis).
Quality control metrics were compiled with a combination of FastQC (http:bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (https://github.com/ewels/MultiQC).
Assembly: mm10
Supplementary files format and content: counts_LPS_timecourse.txt: counts matrix from experiment1
Supplementary files format and content: counts_CLP.txt: counts matrix from experiment2
Supplementary files format and content: counts_Cytokine_combo.txt: counts matrix from experiment3
Supplementary files format and content: counts_Cytokine_combo2.txt: counts matrix from experiment4
Supplementary files format and content: counts_LPS_LPA.txt: counts matrix from experiment5
Supplementary files format and content: counts_LPS_antiPla2g5.txt: counts matrix from experiment6
Supplementary files format and content: counts_LPS_Plasma.txt: counts matrix from experiment7
Supplementary files format and content: counts_LPS_DEX.txt: counts matrix from experiment8
Supplementary files format and content: counts_LPS_KO.txt: counts matrix from experiment9
Supplementary files format and content: counts_LPS_KO2.txt: counts matrix from experiment10

source_name: Thymus

extract_protocol:
Whole-tissue RNA extraction was performed as described previously (Surya et al., 2020). Briefly, tissues stored in RNA-preserving solution were thawed and transferred to 2 mL tubes containing 700-1500 µL (depending on tissue) of PureZOL (Bio-Rad, 7326890) or homemade Trizol-like solution (38% phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate, 5% glycerol). Tissues were lysed by adding 2.8-mm ceramic beads (OMNI International, 19-646) and running 1-3 cycles of 5-45 s at 3500 rpm on the PowerLyzer 24 (QIAGEN). For liver, brain, and small intestine samples, tissues were lysed with 3-5 mL using M tubes (Miltenyi biotec, 130-096-335) and running 1-4 cycles of the RNA_02.01 program on the gentleMACS Octo Dissociator (Miltenyi biotec). Next, lysates were processed in deep 96-well plates (USA Scientific 1896-2000) by adding chloroform for phase separation by centrifugation, followed by precipitation of total RNA in the aqueous phase using magnetic beads coated with silane (Dynabeads MyOne Silane; TermoFisher Scientific 37002D), buffer RLT (QIAGEN 79216), and ethanol. Genomic DNA contamination was removed by on-bead DNase I (ThermoFisher Scientific AM2239) treatment at 37 °C for 20 min. After washing steps with 80% ethanol, RNA was eluted from beads. This RNA extraction protocol was performed on the Bravo Automated Liquid Handling Platform (Agilent). Sample concentrations were measured using a Nanodrop One (Termo Scientific). RNA quality was confirmed using a Tapestation 4200 (Agilent Technologies).
For each tissue sample, full-length cDNA was synthesized in 20 µl final reaction volume containing the following: (1) 10 µl of 10 ng/µl RNA; (2) 1 µl containing 2 pmoles of a custom RT primer biotinylated in 5’ and containing sequences from 5’ to 3’ for the Illumina read 1 primer, a 6-bp sample barcode (up to 384), a 10-bp unique molecular identifier (UMI), and an anchored oligo(dT)30 for priming; and (3) 9 µl of RT mix containing 4 µl of 5X RT buffer, 1 µl of 10 mM dNTPs, 2 pmoles of template switching oligo (TSO), and 0.25 µl of Maxima H Minus Reverse Trascriptase (Thermo Scientific, EP0753). First, barcoded RT primers were added to RNA, which were then denatured at 72°C for 1 min and snap cooled on ice. Second, the RT mix was added, and plates were incubated at 42°C for 120 min. For each library, double stranded cDNA from up to 384 samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research, D4013), and residual RT primers were removed using exonuclease I (New England Biolabs, M0293). Full-length cDNAs were amplified with 5 to 8 cycles of single-primer PCR using the Advantage 2 PCR Kit (clontech 639206) and cleaned up using SPRIselect magnetic beads (Beckman Coulter B23318). cDNA was quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific 32851) and 50 ng of cDNA per pool of samples was tagmented using the Tagment DNA Enzyme I (Illumina 20034197) and amplified using the NEBNext Ultra II Q5 Master Mix (NEW ENGLAND BioLabs M0544L). Libraries were gel purified using 2% E-Gel EX Agarose Gels (ThermoFisher Scientific G402002), quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851) and a Tapestation 4200 (Agilent Technologies), and sequenced on the NextSeq 550 platform (Illumina).

value: Thymus

value: IL18 KO


title: Thymus, LPS_antiTNF_d0.7, m293

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_antiTNF_d0.7, m291

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_antiTNF_d0.7, m290

description:
experiment10
counts_LPS_KO2.txt

value: IL1b KO


title: Thymus, LPS_antiTNF_d0.7, m288

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_antiTNF_d0.7, m287

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_antiTNF_d0.7, m292

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_antiTNF_d0.7, m286

description:
experiment10
counts_LPS_KO2.txt

value: IFNg KO


title: Thymus, LPS_antiTNF_d0.7, m285

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_antiTNF_d0.7, m284

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_d0.7, m282

description:
experiment10
counts_LPS_KO2.txt

value: STAT1 KO


title: Thymus, LPS_antiTNF_d0.7, m283

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_antiTNF_d0.7, m289

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_d0.7, m281

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_d0.7, m280

description:
experiment10
counts_LPS_KO2.txt


title: Spleen, LPS_antiTNF_d0.7, m294

description:
experiment10
counts_LPS_KO2.txt

source_name: Spleen

value: Spleen


title: Thymus, LPS_d0.7, m276

description:
experiment10
counts_LPS_KO2.txt

value: Wild type


title: Thymus, LPS_d0.7, m278

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_d0.7, m277

description:
experiment10
counts_LPS_KO2.txt


title: TH_m289

description:
experiment10
counts_LPS_KO2.txt


title: TH_m288

description:
experiment10
counts_LPS_KO2.txt


title: Spleen, LPS_antiTNF_d0.7, m292

description:
experiment10
counts_LPS_KO2.txt


title: Spleen, LPS_antiTNF_d0.7, m293

description:
experiment10
counts_LPS_KO2.txt


title: Spleen, LPS_antiTNF_d0.7, m291

description:
experiment10
counts_LPS_KO2.txt


title: TH_m291

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_d0.7, m279

description:
experiment10
counts_LPS_KO2.txt


title: TH_m293

description:
experiment10
counts_LPS_KO2.txt


title: TH_m287

description:
experiment10
counts_LPS_KO2.txt


title: TH_m292

description:
experiment10
counts_LPS_KO2.txt


title: Thymus, LPS_d0.7, m275

description:
experiment10
counts_LPS_KO2.txt


title: TH_m284

description:
experiment10
counts_LPS_KO2.txt


title: TH_m286

description:
experiment10
counts_LPS_KO2.txt


title: TH_m285

description:
experiment10
counts_LPS_KO2.txt


title: TH_m283

description:
experiment10
counts_LPS_KO2.txt


title: TH_m281

description:
experiment10
counts_LPS_KO2.txt


title: TH_m279

description:
experiment10
counts_LPS_KO2.txt


title: TH_m278

description:
experiment10
counts_LPS_KO2.txt

source_name: Lung


title: TH_m277

description:
experiment10
counts_LPS_KO2.txt


title: TH_m276

description:
experiment10
counts_LPS_KO2.txt


title: TH_m294

description:
experiment10
counts_LPS_KO2.txt


title: SP_m293

description:
experiment10
counts_LPS_KO2.txt


title: TH_m275

description:
experiment10
counts_LPS_KO2.txt


title: SP_m294

description:
experiment10
counts_LPS_KO2.txt


title: SP_m292

description:
experiment10
counts_LPS_KO2.txt


title: SP_m289

description:
experiment10
counts_LPS_KO2.txt


title: SP_m291

description:
experiment10
counts_LPS_KO2.txt


title: SP_m288

description:
experiment10
counts_LPS_KO2.txt


title: SP_m286

description:
experiment10
counts_LPS_KO2.txt


title: SP_m287

description:
experiment10
counts_LPS_KO2.txt


title: SP_m277

description:
experiment10
counts_LPS_KO2.txt

source_name: Liver


title: SP_m282

description:
experiment10
counts_LPS_KO2.txt


title: SP_m278

description:
experiment10
counts_LPS_KO2.txt


title: SP_m276

description:
experiment10
counts_LPS_KO2.txt


title: SP_m283

description:
experiment10
counts_LPS_KO2.txt


title: SP_m285

description:
experiment10
counts_LPS_KO2.txt


title: SP_m284

description:
experiment10
counts_LPS_KO2.txt


title: LU_m291

description:
experiment10
counts_LPS_KO2.txt

value: Lung


title: TH_m282

description:
experiment10
counts_LPS_KO2.txt


title: LU_m292

description:
experiment10
counts_LPS_KO2.txt


title: SP_m279

description:
experiment10
counts_LPS_KO2.txt


title: LU_m288

description:
experiment10
counts_LPS_KO2.txt


title: LU_m293

description:
experiment10
counts_LPS_KO2.txt


title: LU_m285

description:
experiment10
counts_LPS_KO2.txt


title: SP_m275

description:
experiment10
counts_LPS_KO2.txt


title: LU_m284

description:
experiment10
counts_LPS_KO2.txt


title: LU_m287

description:
experiment10
counts_LPS_KO2.txt


title: LU_m279

description:
experiment10
counts_LPS_KO2.txt


title: SP_m281

description:
experiment10
counts_LPS_KO2.txt


title: LU_m282

description:
experiment10
counts_LPS_KO2.txt


title: LU_m281

description:
experiment10
counts_LPS_KO2.txt


title: LU_m283

description:
experiment10
counts_LPS_KO2.txt


title: LU_m280

description:
experiment10
counts_LPS_KO2.txt


title: LU_m277

description:
experiment10
counts_LPS_KO2.txt


title: LU_m289

description:
experiment10
counts_LPS_KO2.txt


title: LI_m289

description:
experiment10
counts_LPS_KO2.txt

value: Liver


title: LI_m291

description:
experiment10
counts_LPS_KO2.txt


title: LI_m292

description:
experiment10
counts_LPS_KO2.txt


title: LI_m294

description:
experiment10
counts_LPS_KO2.txt


title: LI_m293

description:
experiment10
counts_LPS_KO2.txt


title: LU_m275

description:
experiment10
counts_LPS_KO2.txt


title: LI_m287

description:
experiment10
counts_LPS_KO2.txt


title: LI_m286

description:
experiment10
counts_LPS_KO2.txt


title: LI_m288

description:
experiment10
counts_LPS_KO2.txt


title: LI_m284

description:
experiment10
counts_LPS_KO2.txt


title: LI_m278

description:
experiment10
counts_LPS_KO2.txt

source_name: Inguinal lymph node


title: LI_m283

description:
experiment10
counts_LPS_KO2.txt


title: LI_m279

description:
experiment10
counts_LPS_KO2.txt


title: LI_m276

description:
experiment10
counts_LPS_KO2.txt


title: LI_m281

description:
experiment10
counts_LPS_KO2.txt


title: LI_m275

description:
experiment10
counts_LPS_KO2.txt


title: LI_m277

description:
experiment10
counts_LPS_KO2.txt


title: KI_m294

description:
experiment10
counts_LPS_KO2.txt


title: LI_m282

description:
experiment10
counts_LPS_KO2.txt


title: LU_m276

description:
experiment10
counts_LPS_KO2.txt


title: KI_m292

description:
experiment10
counts_LPS_KO2.txt


title: KI_m291

description:
experiment10
counts_LPS_KO2.txt


title: KI_m288

description:
experiment10
counts_LPS_KO2.txt


title: KI_m286

description:
experiment10
counts_LPS_KO2.txt


title: KI_m289

description:
experiment10
counts_LPS_KO2.txt


title: KI_m287

description:
experiment10
counts_LPS_KO2.txt


title: LI_m285

description:
experiment10
counts_LPS_KO2.txt


title: KI_m285

description:
experiment10
counts_LPS_KO2.txt


title: KI_m284

description:
experiment10
counts_LPS_KO2.txt


title: KI_m283

description:
experiment10
counts_LPS_KO2.txt


title: KI_m277

description:
experiment10
counts_LPS_KO2.txt

source_name: Heart


title: KI_m279

description:
experiment10
counts_LPS_KO2.txt


title: KI_m278

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m293

description:
experiment10
counts_LPS_KO2.txt

value: Inguinal lymph node


title: KI_m282

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m292

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m290

description:
experiment10
counts_LPS_KO2.txt


title: KI_m293

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m289

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m287

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m291

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m288

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m285

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m282

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m283

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m284

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m280

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m281

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m276

description:
experiment10
counts_LPS_KO2.txt


title: KI_m276

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m279

description:
experiment10
counts_LPS_KO2.txt


title: HE_m285

description:
experiment10
counts_LPS_KO2.txt

value: Heart


title: HE_m293

description:
experiment10
counts_LPS_KO2.txt


title: HE_m292

description:
experiment10
counts_LPS_KO2.txt


title: HE_m286

description:
experiment10
counts_LPS_KO2.txt


title: HE_m291

description:
experiment10
counts_LPS_KO2.txt


title: HE_m287

description:
experiment10
counts_LPS_KO2.txt


title: HE_m294

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m277

description:
experiment10
counts_LPS_KO2.txt


title: iLN_m275

description:
experiment10
counts_LPS_KO2.txt


title: KI_m281

description:
experiment10
counts_LPS_KO2.txt


title: KI_m275

description:
experiment10
counts_LPS_KO2.txt


title: HE_m289

description:
experiment10
counts_LPS_KO2.txt


title: HE_m282

description:
experiment10
counts_LPS_KO2.txt


title: HE_m288

description:
experiment10
counts_LPS_KO2.txt


title: HE_m280

description:
experiment10
counts_LPS_KO2.txt


title: CO_m294

description:
experiment10
counts_LPS_KO2.txt

source_name: Bone marrow

value: Colon


title: HE_m281

description:
experiment10
counts_LPS_KO2.txt


title: HE_m283

description:
experiment10
counts_LPS_KO2.txt


title: HE_m279

description:
experiment10
counts_LPS_KO2.txt


title: HE_m278

description:
experiment10
counts_LPS_KO2.txt


title: CO_m292

description:
experiment10
counts_LPS_KO2.txt


title: CO_m291

description:
experiment10
counts_LPS_KO2.txt


title: HE_m276

description:
experiment10
counts_LPS_KO2.txt


title: CO_m290

description:
experiment10
counts_LPS_KO2.txt


title: HE_m275

description:
experiment10
counts_LPS_KO2.txt


title: CO_m293

description:
experiment10
counts_LPS_KO2.txt


title: CO_m289

description:
experiment10
counts_LPS_KO2.txt


title: CO_m288

description:
experiment10
counts_LPS_KO2.txt


title: HE_m284

description:
experiment10
counts_LPS_KO2.txt


title: CO_m286

description:
experiment10
counts_LPS_KO2.txt


title: CO_m282

description:
experiment10
counts_LPS_KO2.txt


title: CO_m284

description:
experiment10
counts_LPS_KO2.txt


title: CO_m278

description:
experiment9
counts_LPS_KO.txt


title: CO_m283

description:
experiment10
counts_LPS_KO2.txt


title: CO_m279

description:
experiment10
counts_LPS_KO2.txt


title: CO_m280

description:
experiment10
counts_LPS_KO2.txt


title: CO_m277

description:
experiment9
counts_LPS_KO.txt


title: CO_m285

description:
experiment10
counts_LPS_KO2.txt


title: BM_m294

description:
experiment9
counts_LPS_KO.txt

value: Bone marrow


title: CO_m276

description:
experiment9
counts_LPS_KO.txt


title: BM_m292

description:
experiment9
counts_LPS_KO.txt


title: BM_m291

description:
experiment9
counts_LPS_KO.txt


title: BM_m288

description:
experiment9
counts_LPS_KO.txt


title: HE_m277

description:
experiment10
counts_LPS_KO2.txt


title: BM_m287

description:
experiment9
counts_LPS_KO.txt


title: BM_m289

description:
experiment9
counts_LPS_KO.txt


title: BM_m293

description:
experiment9
counts_LPS_KO.txt


title: BM_m285

description:
experiment9
counts_LPS_KO.txt


title: BM_m281

description:
experiment9
counts_LPS_KO.txt


title: BM_m283

description:
experiment9
counts_LPS_KO.txt


title: BM_m279

description:
experiment9
counts_LPS_KO.txt


title: BM_m278

description:
experiment9
counts_LPS_KO.txt


title: CO_m287

description:
experiment10
counts_LPS_KO2.txt


title: CO_m281

description:
experiment10
counts_LPS_KO2.txt


title: BM_m277

description:
experiment9
counts_LPS_KO.txt


title: TH_m271

description:
experiment9
counts_LPS_KO.txt

value: IRF1 KO


title: BM_m276

description:
experiment9
counts_LPS_KO.txt


title: CO_m275

description:
experiment9
counts_LPS_KO.txt


title: BM_m286

description:
experiment9
counts_LPS_KO.txt


title: BM_m280

description:
experiment9
counts_LPS_KO.txt


title: BM_m275

description:
experiment9
counts_LPS_KO.txt


title: TH_m265

description:
experiment9
counts_LPS_KO.txt

value: TNF KO


title: TH_m263

description:
experiment9
counts_LPS_KO.txt


title: TH_m264

description:
experiment9
counts_LPS_KO.txt


title: TH_m262

description:
experiment9
counts_LPS_KO.txt


title: TH_m261

description:
experiment9
counts_LPS_KO.txt


title: TH_m260

description:
experiment9
counts_LPS_KO.txt


title: TH_m258

description:
experiment9
counts_LPS_KO.txt


title: SP_m274

description:
experiment9
counts_LPS_KO.txt


title: SP_m273

description:
experiment9
counts_LPS_KO.txt


title: BM_m284

description:
experiment9
counts_LPS_KO.txt


title: SP_m272

description:
experiment9
counts_LPS_KO.txt


title: TH_m273

description:
experiment9
counts_LPS_KO.txt


title: SP_m264

description:
experiment9
counts_LPS_KO.txt