title: WholeBlood_HVTN087134520076_Day14

description: Whole blood gene expression of participant HVTN087134520076 on day 14 after treatment: VSVHIVGAG

value: black or african american


title: Total RNA from Stage5_tonsil_G2

status: Public on Jan 12 2022

type: SRA

city: Columbus

first: Christopher

last: OAKES

state: OH

address: 400 W. 12th Avenue, Wiseman Hall, Suite 455

country: USA

institute: The Ohio State University

library_source: transcriptomic

data_processing:
For fresh/frozen samples, alignment to human genome (hg38) was done using TopHat. Transcriptome assembly and analysis was performed using Cufflinks and expression was reported as FPKM
For FFPE-derived samples, low-quality reads (q<10), and adaptor sequences were eliminated from raw reads using bbduk version 37.64.  Samples were aligned to Ensemble Human reference GRCh37.97 using the RNA-Seq aligner STAR version 2.6.0c. Features were identified from Ensemble (grch37/release-97). Feature coverage counts were calculated using featureCounts, FPKMs values were generated based on overall alignment. Expression was normalized using DESeq2.
Genome_build: FFPE mapped to GRCh37.97 and fresh/frozen mapped to hg38
Supplementary_files_format_and_content: csv files include FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: tonsil

extract_protocol:
For fresh-frozen samples, total RNA was isolated using the Qiagen RNeasy Mini Kit (Qiagen). Total RNA was extracted from FFPE samples using the RNeasy FFPE kit (Qiagen).
For fresh-frozen samples, directional poly-A RNA sequencing libraries were prepared and sequenced as 42-bp paired-end reads on an Illumina NextSeq 500 instrument (Illumina) to a depth of 33.2-48.0 million read pairs. For FFPE samples, directional RNA sequencing libraries were prepared and sequenced as 150-bp paired-end reads to a depth of ~50 million read pairs per sample.

tag: disease state

value: Normal

tag: sample type

value: NKDI

tag: isolation type

value: fresh-frozen

tag: pdx-derived

value: No

tag: pdx treatment

tag: sorted population


title: Total RNA from Stage5_tonsil_G1


title: HP_b

type: RNA

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE

hyb_protocol: Samples (1.2 µg) were hybridized on SurePrint G3 Custom GE 8x60K microarrays (Agilent technologies, design n° 071137) at 65°C using Agilent's GE Hybridization kit. Washes were conducted as recommended by the manufacturer using Agilent's Gene Expression Wash Pack.

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides. Spot intensities and other quality control features were extracted with Agilent's Feature Extraction software version 10.7.3.1.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 071137_D_F_20141113) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The “gProcessedSignal” produced by Agilent Feature Extraction software served as probe-level raw expression values. An aggregated raw expression value was computed for each feature as the median of probe-level values. CDS expression values were quantile-normalized between all experiments (64 hybridizations data) using the R package ‘limma’ and this transformation was propagated to all other types of regions.

organism: Flavobacterium psychrophilum

source_name: Bacteria

label_protocol: 10 µg of DNase-treated RNA were converted into Cy3-labeled cDNA using Fairplay III Microarray labelling kit (Agilent technologies) with random priming and 50 µg/mL actinomycin D as described for strand-specific hybridization (Rasmussen et al., 2009).

extract_protocol: Total RNA was extracted as described in Rochat T. et al (2019) (PMID:30635380).

treatment_protocol: Adaptation to stress conditions. Starting cultures were diluted 500 times in TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) at 18°C until OD600nm of 0.8. Cultures were then split in three parts and hydrogen peroxide [HP] or lysozyme [LYSO] was added to one of them at a final concentration of 100 µM or 100 µg/mL, respectively. The third part was used as an unstressed control [CS1]. Cells were harvested from the three cultures 10 min after addition of the chemicals.

tag: strain

value: OSU THCO2-90

tag: stress

value: hydrogen peroxyde


title: WholeBlood_HVTN087134520123_Day3

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

description: Whole blood gene expression of participant HVTN087134520123 on day 3 after treatment: VSVHIVGAG

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) according the manufacturers protocol.

scan_protocol: Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth

data_processing: The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.

source_name: Peripheral Blood, PaxGene

label_protocol: Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer

treatment_protocol: Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: participant

tag: gender

value: female

tag: age

tag: race

value: other

tag: ethnicity

value: hispanic or latino

tag: group

tag: vaccinations received

value: DDDV

tag: treatment

value: VSVHIVGAG

tag: day

tag: tissue

value: whole blood


title: WholeBlood_HVTN087134520076_Day3

description: Whole blood gene expression of participant HVTN087134520076 on day 3 after treatment: VSVHIVGAG

value: male

value: not hispanic or latino


title: SGA-2_Hpa

city: Philadelphia

first: Paul

middle: Zhiping

last: Wang

state: pa

address: 3440 Market St

institute: Bioinformatics Core, IBI, UPen

description: processed data file: Methyl_HELP-Tag_Processeddata.xlsx

library_source: genomic

data_processing:
Library strategy: HELP
Raw sequence reads were quality checked, trimmed, and mapped to rn6 genome. Tag count was calculated and normalized as described in Greally JM. The HELP-Based DNA Methylation Assays. Methods Mol Biol. 2018;1708:191‐207. doi:10.1007/978-1-4939-7481-8_11.
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: Methyl_HELP-Tag_Processeddata.xlsx

molecule: genomic DNA

organism: Rattus norvegicus

extract_protocol:
Genomic DNA were isolated with phenol-chloroform-isoamyl alcohol (25:24:1), then followed by dialysis with 2x SSC.
Multiplexed libraries were created using the published protocol by Greally JM (The HELP-Based DNA Methylation Assays. Methods Mol Biol 2018;1708:191-207).
TruSeq-HELP Tagging

value: Pancreatic islets

value: 2 weeks

tag: condition

value: IUGR


title: SGA-3_Hpa


title: WholeBlood_HVTN087134520076_Day7

description: Whole blood gene expression of participant HVTN087134520076 on day 7 after treatment: VSVHIVGAG

value: black or african american


title: WholeBlood_HVTN087134520076_Day1

description: Whole blood gene expression of participant HVTN087134520076 on day 1 after treatment: VSVHIVGAG


title: HP_a


title: CS1_b

value: no


title: WholeBlood_HVTN087134520112_Day7

description: Whole blood gene expression of participant HVTN087134520112 on day 7 after treatment: VSVHIVGAG


title: Total RNA from Stage5_blood_G3

source_name: peripheral blood

tag: disease state

value: Normal

tag: sample type

value: NKDI

tag: isolation type

value: fresh-frozen


title: WholeBlood_HVTN087134520076_Day0

description: Whole blood gene expression of participant HVTN087134520076 on day 0 after treatment: VSVHIVGAG


title: CS1_a

value: OSU THCO2-90


title: FishWater_c

treatment_protocol: Expression of cells in water. Starting cultures were diluted 500 times in TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) until OD600nm of 1. Cultures were then diluted 100-times in 15 L dechlorinated water maintained at 10°C with vigorous aeration in aquarium containing 10 juveniles rainbow trout [FishWater] or no fish [Water]. Bacteria were harvested after 24 h of incubation by vacuum filtration of 1 L of water on TPP® Filtermax rapid bottle-top filter with 0.22 micron pore size. Cultures used for inoculation of aquarium water were harvested at OD600 of 1 using the same procedure of vacuum filtration.

tag: freshwater

value: fish water


title: SGA-1_MSP


title: NaCl_c

treatment_protocol: Adaptation to various growth conditions. Starting cultures performed in TYES broth were diluted 500 times in a same batch of TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) under various conditions. For cold temperature adaptation, cultures were incubated at 18°C [CS3], 4°C [Temp4C] or 10°C [Temp10C]. To test growth at high osmolarity, the salinity of the medium was adjusted by adding NaCl before cells inoculation to produce a final concentration of 0.75% [NaCl]. Iron depletion was obtained by adding 2,2-dipyridyl in the medium at a final concentration of 25µM [DIP]. For [NaCl] and [DIP], growth was performed at 18°C. Cells were harvested at OD600nm of 0.4, corresponding to exponential phase for all conditions.

tag: strain

tag: growth condition


title: SGA-2_MSP


title: Total RNA from Stage5_blood_G2

tag: pdx-derived

value: No

tag: pdx treatment

tag: sorted population


title: SGA-1_Hpa

tag: age


title: Control-3_MSP

value: Control


title: NaCl_a


title: Control-3_Hpa


title: Total RNA from Stage4B_tonsil_G3


title: WholeBlood_HVTN087134520033_Day3

description: Whole blood gene expression of participant HVTN087134520033 on day 3 after treatment: VSVHIVGAG

tag: participant

tag: gender

value: female

tag: race

tag: ethnicity

value: DDDV


title: Total RNA from Stage4B_tonsil_G2


title: Site#1_Legacy_3 [RNA-seq]

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then processed using the Hisat2 sequence alignment programs. Reads were mapped to the hg19 genome reference to identify transcripts.
Count value were calculated by featureCount
Normalized by DESeq2 with rlogTransformed
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include rlogTransformed values for each Sample.

source_name: hippocampal

extract_protocol:
Tissues [hippocampal  (flash frozen on dry ice, and DNA/RNA was harvested using Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA, USA). DNA and RNA quantity was assessed using a Qubit fluorometer, and the quality was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS‐122‐2001, RS‐122‐2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampal

value: Sprague Dawley


title: WholeBlood_HVTN087134520164_Day3

description: Whole blood gene expression of participant HVTN087134520164 on day 3 after treatment: VSVHIVGAG

value: other

value: hispanic or latino

tag: group

tag: vaccinations received

tag: treatment

value: VSVHIVGAG

tag: day

value: whole blood


title: Control-2_MSP

tag: tissue

value: Pancreatic islets

value: 2 weeks

tag: condition


title: DIP_c

value: iron depletion


title: Total RNA from Stage4B_tonsil_G1

tag: disease state

value: Normal

tag: sample type

value: NKDI

tag: isolation type


title: WholeBlood_HVTN087134520033_Day0

description: Whole blood gene expression of participant HVTN087134520033 on day 0 after treatment: VSVHIVGAG

value: black or african american

value: not hispanic or latino


title: WholeBlood_HVTN087134520033_Day1

description: Whole blood gene expression of participant HVTN087134520033 on day 1 after treatment: VSVHIVGAG


title: Control-2_Hpa


title: DIP_a

tag: strain

value: OSU THCO2-90

tag: growth condition


title: Total RNA from Stage4B_blood_G3

value: fresh-frozen

tag: pdx-derived

value: No

tag: pdx treatment

tag: sorted population


title: WholeBlood_HVTN087134520029_Day14

description: Whole blood gene expression of participant HVTN087134520029 on day 14 after treatment: VSVHIVGAG

tag: participant

tag: gender

value: male

tag: age

value: DDDV


title: Total RNA from Stage4B_blood_G2


title: Control-1_MSP

value: Control


title: Control-1_Hpa


title: Total RNA from Stage4B_blood_G1


title: Temp10C_c


title: 09CEB13BAC -1 [GLA-9_S12]

data_processing:
Low quality triming with sickle (options: -t sanger -x -n -q 20 -l 20)
Read mapping using bowtie2 version 2.2.6 (options: -N 1 -L,-0.2,-0.2)
Read counts on each allelic variant were obtained using HTSeq-count (version 0.6.1)
Differential expression analysis R library EdgeR" and associated "median ratio method" normalization procedure
EdgeR p-values were converted into q-values using R library "fdrtool"
Genome_build: In absence of whole genome sequences for the 15 strains, the cleaned reads were mapped against a repertoire of allelic variants for 23,815 genes aiming at accounting for the pangenome of B. cereus group. This repertoire was obtained by single-linkage clustering based on the results of an all-against-all blastn comparison (version 2.2.26, e-value cut-off 1e-5) [46] of 519,931 CDSs extracted from the 91 annotated complete genomes available at the time of analysis for B. cereus group in Genbank. Pairs of CDSs that aligned over at least 70% of the length of the shortest sequence and with at least 75% nucleotide sequence identity were grouped in the same cluster, which resulted in 23,815 clusters representing distinct genes.
Supplementary_files_format_and_content: csv file containing for each gene/sample raw data counts and rpkm

organism: Bacillus cereus

growth_protocol: Bacterial cultures were incubated in BHI medium at 30°C in microaerophilic condition (5% O2–15% CO2–80% N2) at pH 7 until entry into stationary growth phase. Samples were centrifuged at 12,000 g for 3 min at 4°C and placed immediately at -80°C until processing.

extract_protocol:
The bacterial pellets were re-suspended with 200 μl of 10 mM Tris-HCl at pH 8 + 4 μl of lysozyme at 50 mg/ml and incubated at 37°C. Total RNA was extracted with the HPRNA kit (High Pure RNA Isolation Kit; Roche). Remaining traces of DNA were removed by two steps of DNase treatment (TURBO-DNAse Free kit, Ambion). The RNA integrity was measured by the RIN (RNA Integrity Number) obtained using the capillary electrophoresis Bioanalyser® (Agilent). RIN was calculated with the total RNA ratio of the area of ribosomal bands to the total area and the height of the 16S and 23S peaks. The RIN of samples were between 7 and 10. The mRNA were purified with the RiboZero Kit (Illumina).
Directional and paired libraries were prepared with the Illumina scriptseq kit and the sequencing was performed on an Illumina Nextseq machine.

tag: replicate

tag: toxic

value: yes


title: Temp10C_a


title: Total RNA from Stage4A_tonsil_G3


title: WholeBlood_HVTN087134520029_Day7

description: Whole blood gene expression of participant HVTN087134520029 on day 7 after treatment: VSVHIVGAG

tag: race

tag: ethnicity

value: hispanic or latino

tag: group

tag: vaccinations received

tag: treatment


title: 14 SBCL 369 -1 [GLA-8_S11]

source_name: Bacteria_14 SBCL 369


title: WholeBlood_HVTN087134520029_Day0

description: Whole blood gene expression of participant HVTN087134520029 on day 0 after treatment: VSVHIVGAG

value: VSVHIVGAG

tag: day

tag: tissue


title: WholeBlood_HVTN087134520029_Day1

description: Whole blood gene expression of participant HVTN087134520029 on day 1 after treatment: VSVHIVGAG

value: whole blood


title: Temp4C_a

tag: strain


title: Total RNA from Stage4A_tonsil_G2

tag: disease state

tag: sample type

tag: isolation type


title: CS3_c

tag: growth condition


title: WholeBlood_HVTN087123520351_Day7

description: Whole blood gene expression of participant HVTN087123520351 on day 7 after treatment: VSVHIVGAG

tag: participant

value: white


title: CS3_a


title: 09CEB33BAC -1 [GLA-7_S10]


title: Total RNA from Stage4A_tonsil_G1

tag: pdx-derived

tag: pdx treatment

tag: sorted population


title: 09CEB14BAC -1 [GLA-6_S9]

tag: replicate

tag: toxic


title: TYESA-0.2_b

treatment_protocol: Expression in colonies on TYES agar. Starting cultures were performed in TYES at 18°C 200 rpm. These cultures were then diluted in 1% peptone water at final concentration of 1E4 cfu/mL and cells plated onto TYES plates containing various nutrient concentrations. After incubation for 4 days at 18°C, cells were harvested  from plates containing individual colonies. TYES-based agar (TYESA) plates contained standard nutrients concentration supplemented with 5% FCS [TYESA-FCS] and not supplemented [TYESA], or TYES nutrients diluted 2-times [TYESA-0.5] or 5-times [TYESA-0.2] without FCS supplementation.

tag: nutrient change

value: diluted 5-times

tag: blood

value: no


title: WholeBlood_HVTN087123520351_Day3

description: Whole blood gene expression of participant HVTN087123520351 on day 3 after treatment: VSVHIVGAG

tag: gender

tag: age

tag: race

tag: ethnicity

tag: group

tag: vaccinations received


title: Total RNA from Stage3_tonsil_G3

tag: disease state

value: Normal

tag: sample type


title: WholeBlood_HVTN087123520351_Day14

description: Whole blood gene expression of participant HVTN087123520351 on day 14 after treatment: VSVHIVGAG

tag: treatment

tag: day

tag: tissue


title: 10CEB13BAC -1 [GLA-5_S8]

tag: strain


title: Total RNA from Stage3_tonsil_G2

value: NKDI

tag: isolation type

tag: pdx-derived

tag: pdx treatment

tag: sorted population


title: 12CEB01BAC -1 [GLA-4_S7]

tag: replicate

tag: toxic


title: C64 -3 [GLA-45_S48]


title: WholeBlood_HVTN087123520351_Day1

description: Whole blood gene expression of participant HVTN087123520351 on day 1 after treatment: VSVHIVGAG

tag: participant

tag: gender

tag: age


title: TYESA-0.5_b

tag: nutrient change

value: diluted 2-times


title: TYESA-0.2_a

tag: blood


title: WholeBlood_HVTN087134520033_Day7

description: Whole blood gene expression of participant HVTN087134520033 on day 7 after treatment: VSVHIVGAG

value: female

tag: race

value: black or african american

tag: ethnicity

value: not hispanic or latino

tag: group

tag: vaccinations received


title: TYESA-0.5_a

value: OSU THCO2-90


title: WholeBlood_HVTN087123520347_Day3

description: Whole blood gene expression of participant HVTN087123520347 on day 3 after treatment: VSVHIVGAG

tag: treatment

tag: day

tag: tissue


title: WholeBlood_HVTN087123520347_Day1

description: Whole blood gene expression of participant HVTN087123520347 on day 1 after treatment: VSVHIVGAG


title: WholeBlood_HVTN087123520347_Day7

description: Whole blood gene expression of participant HVTN087123520347 on day 7 after treatment: VSVHIVGAG


title: WholeBlood_HVTN087123520347_Day14

description: Whole blood gene expression of participant HVTN087123520347 on day 14 after treatment: VSVHIVGAG


title: ADRIA I3 -3 [GLA-44_S47]

source_name: Bacteria_ADRIA I3

tag: strain

value: ADRIA I3


title: Total RNA from ENKTL1_PDX_KirNeg_03

source_name: Tumor

tag: disease state

value: Tumor

tag: sample type

value: ENKTL

tag: isolation type

value: fresh-frozen

tag: pdx-derived

value: Yes

tag: pdx treatment

value: human CD56/KIR-positive


title: TYESA-FCS_b

value: 5% FCS


title: TYESA_b

value: diluted 0-times


title: INRA 5 -3 [GLA-43_S46]

source_name: Bacteria_INRA 5

value: INRA 5

tag: replicate

tag: toxic


title: Total RNA from Stage3_tonsil_G1

value: No

tag: sorted population


title: I13 -3 [GLA-42_S45]

value: no


title: TYESA-FCS_a

tag: nutrient change


title: PF -3 [GLA-41_S44]

value: PF


title: TYESA_a


title: Total RNA from ENKTL1_PDX_KirPos_02


title: Total RNA from ENKTL1_PDX_KirNeg_01

value: human CD56/KIR-negative


title: Total RNA from ENKTL1_PDX_KirPos_03


title: 13CEB06BAC -3 [GLA-40_S43]

value: yes


title: Total RNA from ENKTL1_PDX_KirNeg_02


title: Total RNA from Stage5_blood_G1

value: Normal

value: NKDI


title: Total RNA from ENKTL1_PDX_KirPos_01


title: T2-FCS_b

treatment_protocol: Expression in cells grown in TYES broth supplemented with 5% fœtal calf serum.  Starting cultures performed in TYES were diluted 500 times in fresh TYES 5% FCS and cultures incubated at 18°C with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio). Cells were harvested at OD600nm of 1 [T2-FCS].

value: OSU THCO2-90

tag: fœtal calf serum


title: WholeBlood_HVTN087123520347_Day0

description: Whole blood gene expression of participant HVTN087123520347 on day 0 after treatment: VSVHIVGAG

tag: participant

tag: gender

value: female

tag: age

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

value: DDDV

value: VSVHIVGAG

value: whole blood


title: Total RNA from ENKTL1_PDX_5aza_08

value: Tumor

value: ENKTL

value: fresh-frozen

value: Yes

value: human CD56


title: 14 SBCL 102 -1 [GLA-3_S6]

source_name: Bacteria_14 SBCL 102


title: T2-FCS_a


title: WholeBlood_HVTN087123520339_Day7

description: Whole blood gene expression of participant HVTN087123520339 on day 7 after treatment: VSVHIVGAG

value: male

tag: group

tag: vaccinations received

tag: treatment

tag: day

tag: tissue


title: 12CEB31BAC -3 [GLA-39_S42]

tag: strain


title: 09CEB33BAC -3 [GLA-38_S41]


title: Total RNA from ENKTL1_PDX_5aza_05

tag: disease state

tag: sample type

tag: isolation type

tag: pdx-derived

tag: pdx treatment


title: Total RNA from ENKTL1_PDX_5aza_07

tag: sorted population


title: WholeBlood_HVTN087123520339_Day3

description: Whole blood gene expression of participant HVTN087123520339 on day 3 after treatment: VSVHIVGAG

tag: participant


title: 09CEB13BAC -3 [GLA-36_S39]

tag: replicate

tag: toxic


title: T5_a

treatment_protocol: Expression during the growth cycle. Cells were grown in Tryptone Yeast Extract Salts (TYES) broth at 18°C with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio). Five samples were harvested in the course of growth: Starting cultures were diluted 500 times in fresh TYES and cells were harvested at OD600nm of 0.4 ([T1], exponential phase), 1 and 1.2 ([T2] and [T3], transition phase), 1.3 and 1.7 ([T4] and [T5], early and late stationary phase, resp.).

tag: growth phase


title: WholeBlood_HVTN087123520339_Day14

description: Whole blood gene expression of participant HVTN087123520339 on day 14 after treatment: VSVHIVGAG

tag: gender

tag: age

tag: race

tag: ethnicity


title: WholeBlood_HVTN087123520339_Day1

description: Whole blood gene expression of participant HVTN087123520339 on day 1 after treatment: VSVHIVGAG

tag: group

tag: vaccinations received

tag: treatment

tag: day


title: WholeBlood_HVTN087123520339_Day0

description: Whole blood gene expression of participant HVTN087123520339 on day 0 after treatment: VSVHIVGAG

tag: tissue


title: WholeBlood_HVTN087123520225_Day14

description: Whole blood gene expression of participant HVTN087123520225 on day 14 after treatment: VSVHIVGAG


title: T5_c

tag: strain


title: Temp4C_c

tag: growth condition


title: T3_a


title: T4_a


title: T3_c


title: T4_c


title: 14 SBCL 369 -3 [GLA-35_S38]


title: 09CEB14BAC -3 [GLA-37_S40]


title: Total RNA from ENKTL1_PDX_Veh_07

tag: disease state

tag: sample type

tag: isolation type

tag: pdx-derived

tag: pdx treatment

value: Vehicle


title: WholeBlood_HVTN087123520225_Day7

description: Whole blood gene expression of participant HVTN087123520225 on day 7 after treatment: VSVHIVGAG

tag: participant


title: 14 SBCL 102 -3 [GLA-34_S37]

tag: replicate

tag: toxic

value: yes


title: Total RNA from ENKTL1_PDX_5aza_06

tag: sorted population


title: Total RNA from ENKTL1_PDX_Veh_08


title: Total RNA from ENKTL1_PDX_Veh_06


title: Total RNA from ENKTL1_PDX_5aza_04


title: T2_c

tag: growth phase

tag: fœtal calf serum

value: no


title: Global RNA-seq

description: Global RNA-seq of a pool of 18 total RNA samples extracted in different biological conditions

data_processing:
Adaptor removal with cutadapt (options: -a TGGAATTCTCGGGTGCCAAGG -n 5 -O 3 -m 10)
Low quality triming with sickle (options: -t sanger -x -n -q 20 -l 20)
Read mapping using bowtie2 version 2.2.4 (options: --phred33 --very-sensitive --score-min L,-0.2,-0.2)
Genome_build: F. psychrophilum OSU THCO2-90 complete genome sequence (ENA accession number LT670843)

growth_protocol: Flavobacterium psychrophilum OSU THCO2-90 was grown aerobically at 18°C in tryptone yeast extract salts (TYES) broth [0.4 % (w/v) tryptone, 0.04 % yeast extract, 0.05 % (w/v) MgSO4 7H2O, 0.02 % (w/v) CaCl2 2H2O, 0.05 % (w/v) D-glucose, pH 7.2] or on TYES agar. Medium was supplemented with 5% fetal calf serum (FCS) when specified. The sample corresponds to a pool of total RNA samples extracted in 18 different biological conditions as described below: seven samples from cells harvested in the course of growth in TYES broth with fetal calf serum (FCS), two samples from cells grown at low temperature, seven samples harvested under stress conditions (peroxide and disulfide stresses, oxygen limitation, sub-lethal concentration of antibiotics, high osmolarity, iron scarcity), one sample from cells grown without FCS and one sample from colonies grown on TYES agar.

extract_protocol:
Total RNA extraction was performed using hot phenol method. Bacterial cells were collected after addition of ½ volume of frozen killing buffer (20 mM Tris-HCl pH 7.5, 5 mM MgCl2, 20 mM NaN3) to the culture. Cell pellets were frozen in liquid nitrogen and stored at −80 °C. For extraction, the pellets were resuspended into lysis buffer (4M guanidine thiocyanate, 25 mM sodium acetate pH 5.2, 5 g L−1 N-laurylsarcosinate), immediately mixed to hot acid phenol v:v and incubated during 10 min at 65 °C. The aqueous phases were recovered by centrifugation after addition of 400 µL chloroform. The samples were extracted with acid phenol:chloroform:IAA (25:24:1, pH 4.5) and then chloroform. Total RNAs were ethanol precipitated and the pellets resuspended in RNase-free water. Fifty µg of RNA extracts were treated using TurboDNase I (Ambion) to remove residual genomic DNA, then purified using the RNA Clean-Up and Concentration Kit (Norgen Biotek). RNA concentration of the DNase-treated sample was measured using a NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Inc.) and RNA quality was assessed by capillary electrophoresis using RNA Nano chips with a Bioanalyzer Agilent 2100 (Agilent Technologies, Palo Alto, USA). The 18-condition RNA pool was obtained by mixing each of the extracts in equal quantity.
20 µg of the 18-condition RNA pool were processed using MICROBExpress (Ambion) according to manufacturer’s instructions to remove ribosomal RNAs. Efficient rRNA depletion was confirmed by Bioanalyzer 2100. Strand specific transcriptome RNA-Seq library was performed using the TruSeq SBS Kit v3 with no modification.

tag: pool


title: 10CEB13BAC -3 [GLA-32_S35]


title: Total RNA from ENKTL1_PDX_Veh_05


title: 12CEB01BAC -3 [GLA-33_S36]


title: WholeBlood_HVTN087123520225_Day0

description: Whole blood gene expression of participant HVTN087123520225 on day 0 after treatment: VSVHIVGAG

tag: gender

tag: age

tag: race

tag: ethnicity

tag: group

tag: vaccinations received

tag: treatment


title: 5'-end RNA-seq

description: 5'-end RNA-seq of a pool of 18 total RNA samples extracted in different biological conditions

data_processing:
Adaptor removal with cutadapt (options: -a TGGAATTCTCGGGTGCCAAGG -n 5 -O 3 -m 10)
Low quality triming with sickle (options: -t sanger -x -n -q 20 -l 20)
Read mapping using bowtie2 version 2.2.4 (options: --phred33 --very-sensitive --score-min L,-0.2,-0.2)
Non-unique mapped reads removal
Genome_build: F. psychrophilum OSU THCO2-90 complete genome sequence (ENA accession number LT670843)

extract_protocol:
Total RNA extraction was performed using hot phenol method. Bacterial cells were collected after addition of ½ volume of frozen killing buffer (20 mM Tris-HCl pH 7.5, 5 mM MgCl2, 20 mM NaN3) to the culture. Cell pellets were frozen in liquid nitrogen and stored at −80 °C. For extraction, the pellets were resuspended into lysis buffer (4M guanidine thiocyanate, 25 mM sodium acetate pH 5.2, 5 g L−1 N-laurylsarcosinate), immediately mixed to hot acid phenol v:v and incubated during 10 min at 65 °C. The aqueous phases were recovered by centrifugation after addition of 400 µL chloroform. The samples were extracted with acid phenol:chloroform:IAA (25:24:1, pH 4.5) and then chloroform. Total RNAs were ethanol precipitated and the pellets resuspended in RNase-free water. Fifty µg of RNA extracts were treated using TurboDNase I (Ambion) to remove residual genomic DNA, then purified using the RNA Clean-Up and Concentration Kit (Norgen Biotek). RNA concentration of the DNase-treated sample was measured using a NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Inc.) and RNA quality was assessed by capillary electrophoresis using RNA Nano chips with a Bioanalyzer Agilent 2100 (Agilent Technologies, Palo Alto, USA). The 18-condition RNA pool was obtained by mixing each of the extracts in equal quantity.
The preparation of the library started with 35 µg of the RNA pool. A first ligation was performed over-night at 16°C with a RNA adapter (5’-GCAUAGGGGUAAA-3’) using 4 units/µg of T4 RNA ligase (New England Biolabs). After phenol-chloroform RNA extraction and removal of non-ligated RNA adapters using a Micro Bio-spin column P-30 (Biorad), 30 µg of purified RNA sample was treated by 50 units of Tobacco Alkaline Phosphatase (TAP; Epicentre) at 37°C for 2h, then phenol-chloroform purified. The TAP-treated RNA sample was then used to prepare a strand-specific RNA-seq library using the TruSeq SBS Kit v3 – HS 50-cycles (FC-401-3002, Illumina) according to the manufacturer’s instructions except that the 5’-Illumina adapters were ligated before RNA fragmentation to specifically amplify 5’-ends of RNAs. Dimers of adapters were removed before sequencing by two sequential agarose gel extractions.

tag: strain


title: WholeBlood_HVTN087123520225_Day1

description: Whole blood gene expression of participant HVTN087123520225 on day 1 after treatment: VSVHIVGAG

tag: day

tag: tissue


title: WholeBlood_HVTN087123520175_Day14

description: Whole blood gene expression of participant HVTN087123520175 on day 14 after treatment: VSVHIVGAG

tag: participant


title: T2_a


title: WholeBlood_HVTN087123520175_Day3

description: Whole blood gene expression of participant HVTN087123520175 on day 3 after treatment: VSVHIVGAG


title: T1_a


title: 08CEB116BAC -3 [GLA-31_S34]

tag: replicate


title: T1_c


title: 08CEB116BAC -1 [GLA-2_S5]

tag: toxic


title: 120_Blood-Cau_III

city: Jena

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

description: C_auris_in_human-whole-blood_120min_donorC

data_processing:
quality controlled with FastQC (v0.11.8)
quality trimming of raw reads with Trimmomatic (v0.39)
rRNA depleted with SortMeRNA (v2.1b)
read alignment with HiSat2 (v2.1.0) against concatenated genomes
read counting with featureCounts (v1.34.0)
Genome_build: C. auris B8441 (s01-m01-r05)
Genome_build: H. sapiens genome GRCh38.p13 release 100.38
Supplementary_files_format_and_content: tab delimited text file with unnormalised C. auris read counts
Supplementary_files_format_and_content: tab delimited text file with unnormalised H. sapiens read counts
Supplementary_files_format_and_content: tab delimited text file with MRN normalised C. auris read counts
Supplementary_files_format_and_content: tab delimited text file with MRN normalised H. sapiens read counts

organism:
Homo sapiens
Candidozyma auris

source_name: fungal cells & whole blood

growth_protocol: Candida auris preculture was prepared by growth over night in YPD at 30°C

extract_protocol:
human RNA was isolated with PAXgene Blood RNA kit, fungal RNA was isolated with RiboPure RNA isolation kit yeast
After poly(A) filtering, mRNA was fragmented, and cDNA libraries were generated for each sample. 50 bp single sequence reads were produced using the Illumina HiSeq 2500 platform.

treatment_protocol: 1000000/ml of Candida auris were used for infection of freshly drawn human whole blood

value: fungal cells & whole blood

tag: fungal train

tag: sex (h. sapiens)

tag: time

value: 120 min

tag: donor

value: C


title: WholeBlood_HVTN087123520175_Day7

description: Whole blood gene expression of participant HVTN087123520175 on day 7 after treatment: VSVHIVGAG

tag: gender

value: white


title: Total RNA from ENKTL2

tag: disease state

tag: sample type

tag: isolation type

tag: pdx-derived

value: No

tag: pdx treatment

tag: sorted population


title: Total RNA from ENKTL1_PDX_Veh_04


title: C64 -2 [GLA-30_S33]

tag: strain


title: 60_Blood-Cau_III

description: C_auris_in_human-whole-blood_60min_donorC

value: 60 min


title: 240_Blood-Cau_III

description: C_auris_in_human-whole-blood_240min_donorC

value: 240 min


title: Total RNA from ENKTL8


title: ADRIA I3 -2 [GLA-29_S32]

value: ADRIA I3


title: 30_Blood-Cau_III

description: C_auris_in_human-whole-blood_30min_donorC

value: 30 min


title: 09CEB14BAC -2 [GLA-28_S31]


title: Total RNA from ENKTL1_BM

value: Tumor

value: ENKTL


title: 15_Blood-Cau_III

description: C_auris_in_human-whole-blood_15min_donorC

value: 15 min


title: WholeBlood_HVTN087123520175_Day1

description: Whole blood gene expression of participant HVTN087123520175 on day 1 after treatment: VSVHIVGAG

tag: age

tag: race

tag: ethnicity

value: not hispanic or latino

tag: group

tag: vaccinations received

value: DDDV

tag: treatment

value: VSVHIVGAG

tag: day

value: whole blood


title: WholeBlood_HVTN087123520169_Day3

description: Whole blood gene expression of participant HVTN087123520169 on day 3 after treatment: VSVHIVGAG

tag: participant

value: male

value: black or african american

tag: tissue


title: WholeBlood_HVTN087123520169_Day7

description: Whole blood gene expression of participant HVTN087123520169 on day 7 after treatment: VSVHIVGAG

tag: gender


title: WholeBlood_HVTN087123520175_Day0

description: Whole blood gene expression of participant HVTN087123520175 on day 0 after treatment: VSVHIVGAG


title: 09CEB13BAC -2 [GLA-27_S30]

tag: replicate

tag: toxic

value: yes


title: Total RNA from ENKTL1

tag: disease state

tag: sample type

tag: isolation type

value: fresh-frozen

value: human CD56


title: 0_Blood-Cau_III

description: C_auris_in_human-whole-blood_0min_donorC

value: fungal cells & whole blood

tag: fungal train

tag: sex (h. sapiens)

tag: time

value: 0 min

tag: donor

value: C


title: I13 -2 [GLA-26_S29]

tag: strain

value: no


title: 13CEB06BAC -2 [GLA-25_S28]


title: 240_Blood-Cau_II

description: C_auris_in_human-whole-blood_240min_donorB

value: 240 min

value: B


title: 120_Blood-Cau_II

description: C_auris_in_human-whole-blood_120min_donorB

value: 120 min


title: INRA 5 -2 [GLA-24_S27]

value: INRA 5


title: WholeBlood_HVTN087123520169_Day14

description: Whole blood gene expression of participant HVTN087123520169 on day 14 after treatment: VSVHIVGAG

tag: age

tag: race

tag: ethnicity

value: not hispanic or latino

tag: group


title: Total RNA from ENKTL1_SPL

value: Tumor

value: ENKTL

tag: pdx-derived

value: Yes

tag: pdx treatment

tag: sorted population


title: PF -2 [GLA-23_S26]

value: PF

tag: replicate


title: WholeBlood_HVTN087123520169_Day1

description: Whole blood gene expression of participant HVTN087123520169 on day 1 after treatment: VSVHIVGAG

tag: participant

tag: gender

value: male

value: black or african american

tag: vaccinations received

value: DDDV

tag: treatment

value: VSVHIVGAG

tag: day

tag: tissue

value: whole blood


title: Ewing_sarcoma_4

city: Bologna

first: Emanuela

last: Palmerini

address: via G.C.Pupilli, 1

country: Italy

institute: IRCCS Istituto Ortopedico Rizzoli

description: Snap-frozen tissue

data_processing:
After performing Fastqc quality check,paired end reads were aligned to human reference sequence GRCh37 by STAR alignment.
HTSeq-count  was used to calculate counts
DeSeq2  R package   was used to perform gene expression analysis
Genome_build: GRCh37

source_name: Ewing sarcoma primary tumor

extract_protocol:
Total RNA was extracted using Trizol reagent.
800 ng of total RNA was used as input for libraries preparation according to Illumina TruSeq Stranded Total RNA with RiboZero Gold kit.

tag: disease state

value: Ewing sarcoma


title: KO_siNC_rep2

city: Jiangsu suzhou

first: Jingfei

last: Zhu

state: CN

address: Chongwen Road 215123

country: China

institute: ISM

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mus musculus

source_name: immortalized macrophage cell lines

extract_protocol:
The cell samples were lysed in TRIzol and extract total RNA for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: lincRNA-EPS-/-

value: negative control


title: KO_siPKR_rep1

value: PKR knockdown


title: 12CEB31BAC -2 [GLA-22_S25]

tag: strain

tag: toxic

value: yes


title: KO_siPKR_rep2


title: KO_siNC_rep1


title: 30_Blood-Cau_II

description: C_auris_in_human-whole-blood_30min_donorB

value: fungal cells & whole blood

tag: fungal train

tag: sex (h. sapiens)

tag: time

value: 30 min

tag: donor

value: B


title: WholeBlood_HVTN087123520169_Day0

description: Whole blood gene expression of participant HVTN087123520169 on day 0 after treatment: VSVHIVGAG

tag: age

tag: race

tag: ethnicity

value: not hispanic or latino

tag: group


title: Ewing_sarcoma_3

description: Snap-frozen tissue


title: 09CEB33BAC -2 [GLA-21_S24]

tag: replicate


title: 15_Blood-Cau_II

description: C_auris_in_human-whole-blood_15min_donorB

value: 15 min


title: WT_siPKR_rep2

value: wild type


title: Ewing_sarcoma_2

description: Snap-frozen tissue


title: WT_siPKR_rep1


title: Ewing_sarcoma_1

description: Snap-frozen tissue


title: INRA 5 -1 [GLA-1_S4]

value: INRA 5

value: no


title: 60_Blood-Cau_II

description: C_auris_in_human-whole-blood_60min_donorB

value: male

value: 60 min


title: WT_siNC_rep2


title: 14 SBCL 369 -2 [GLA-20_S23]


title: 120_Blood-Cau_I

description: C_auris_in_human-whole-blood_120min_donorA

value: 120 min

value: A


title: CIC-DUX4_sarcoma_4

description: Snap-frozen tissue

source_name: CIC-DUX4 Sarcoma primary tumor

value: Capicua–double homeobox 4 (CIC-DUX4) rearranged sarcomas (CDSs)


title: 60_Blood-Cau_I

description: C_auris_in_human-whole-blood_60min_donorA


title: WT_siNC_rep1


title: CIC-DUX4_sarcoma_3

description: Snap-frozen tissue


title: 08CEB116BAC -2 [GLA-18_S21]


title: 14 SBCL 102 -2 [GLA-19_S22]


title: KO_VSV6h_rep2

value: lincRNA-EPS-/-

value: VSV infection


title: KO_Mock_rep2

value: untreated


title: 30_Blood-Cau_I

description: C_auris_in_human-whole-blood_30min_donorA


title: 15_Blood-Cau_I

description: C_auris_in_human-whole-blood_15min_donorA


title: CIC-DUX4_sarcoma_1

description: Snap-frozen tissue


title: 0_Blood-Cau_I

description: C_auris_in_human-whole-blood_0min_donorA

value: 0 min


title: 12CEB01BAC -2 [GLA-17_S20]

value: yes


title: CIC-DUX4_sarcoma_2

description: Snap-frozen tissue


title: C64 -1 [GLA-15_S18]


title: KO_Mock_rep1


title: 0_Blood-Cau_II

description: C_auris_in_human-whole-blood_0min_donorB

value: fungal cells & whole blood


title: 240_Blood-Cau_I

description: C_auris_in_human-whole-blood_240min_donorA

value: 240 min


title: ADRIA I3 -1 [GLA-14_S17]

value: ADRIA I3


title: PF -1 [GLA-13_S16]

value: PF


title: I13 -1 [GLA-12_S15]


title: WT_VSV6h_rep1

value: wild type


title: WT_VSV6h_rep2


title: WholeBlood_HVTN087123520225_Day3

description: Whole blood gene expression of participant HVTN087123520225 on day 3 after treatment: VSVHIVGAG

tag: participant

tag: gender

value: white

value: not hispanic or latino

tag: vaccinations received

value: DDDV

value: VSVHIVGAG

value: whole blood


title: WT_Mock_rep2

tag: treatment


title: Daudi

city: Vancouver BC

first: Christian

last: Steidl

state: British Columbia

address: 675, West 10th Ave

department: Department of Lymphoid Cancer Research

country: Canada

institute: BC Cancer

data_processing:
Whole-transcriptome RNA sequencing data was generated for 34 cell lines derived from lymphoma tumors: 11 from mantle cell lymphoma (MCL), 3 from Burkitt lymphoma, and 20 from diffuse large B-cell lymphoma (DLBCL; 14 of the germinal centre B-cell-like (GCB) subtype and 6 of the activated B-cell-like (ABC) subtype).
The STAR aligner (v2.5.3a_modified) was used to align reads to the GRCh38 reference and produce raw counts per gene.
Raw counts were read into R (v3.6.1) and normalized across all cell lines using a variance-stabilizing transformation in the DESeq2 package (v1.26.0).
Expression of CXCR4 between cell lines was visualized in R, and statistical comparisons between pathologies were performed using Student’s t-tests.
Genome_build: GRCh38

source_name: Cell line

extract_protocol: RNA sequencing data were generated using standard Illumina protocols at the British Columbia Cancer Research Centre from 34 lymphoma cell lines representing multiple pathologies. These datasets were generated at multiple timepoints.

tag: cell line

value: Daudi

tag: pathology

value: Burkitt’s Lymphoma


title: 13CEB06BAC -1 [GLA-11_S14]

tag: strain


title: WT_Mock_rep1

tag: genotype


title: 12CEB31BAC -1 [GLA-10_S13]

tag: toxic


title: Adult 7D Post MTZ ZF Hearts - 2

status: Public on Jan 11 2022

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

description:
Bulk RNA-Seq
AH5HWLBCXY_US.1623014_TGACCA_L002

data_processing:
Raw reads were aligned to Ensembl GRCz10 using Tophat (version 2.0.13).
Gene-level read counts were quantified using htseq-count using Ensembl GRCz10 gene annotations.
Genome_build: GRCz10
Supplementary_files_format_and_content: zebrafish_bulk_RNAseq_count_matrix.txt: Tab-delimited text file of counts.
Supplementary_files_format_and_content: zebrafish_bulk_RNAseq_0-3-7-DPI_reads_per_million.txt: Tab-delimited text file of normalized gene-level read counts for each cell.

organism: Danio rerio

source_name: Zebrafish heart

growth_protocol: Wild-type (AB; Zebrafish International Resource Center, Eugene, OR, USA), hsWnt8:GFP [Tg(hsp70l:Wnt8a-GFP)w34] and hsDKK1:GFP [Tg(hsp70l:DKK1b-GFP)w32] and vmhc:mCherry-NTR [Tg(vmhc:mCherry-Eco.NfsB)] were used and maintained using standard procedures in accordance with the Institutional Animal Care and Use Committee-approved protocols IACUC 2057-01 & 4364-02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C, pH of 7.5, conductivity of 800 µS, hardness of 140 ppm, alkalinity of 35 ppm, dissolved oxygen content of 7.8 mg/L, and a total gas pressure of 101%. The average nitrate level is 55 ppm, the average nitrite level is 0.05 ppm, and the average ammonium level is 0.01 ppm. Larval feed starting at 5 days post fertilization (dpf) is a rotifer polyculture supplemented with the Zeigler larval diet, at 12 dpf live artemia is added to the diet, and at 60-90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.

extract_protocol:
For young, 3-day-old zebrafish heart samples, we sequenced N=2 with about n=500 hearts pooled. For the adult heart samples, we sequenced N=2 hearts at UI, 3 and 7 dpi with each n=4-6 pooled hearts. A negative binomial test was performed to determine significantly changed genes. Around 20,000 genes were found.
RNA was isolated from young (3 days old), adult (~6 months old), and regenerating (3 and 7 dpi) zebrafish hearts as per manufacturers’ protocol (TRIzol, ThermoFisher). The libraries were sequenced together on an Illumina HiSeq 4000 (Illumina Inc., San Diego, CA).

treatment_protocol: All chemical ventricular cardiomyocyte (VCM) ablation were conducted on adult Zebrafish (~5-12 months old). For chemical mediated VCM ablation, fish were treated with 5 mM Metronidiazole (MTZ; Sigma) containing 0.1% dimethyl sulfoxide (DMSO) or vehicle control (0.1% DMSO) for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals, 7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 (prior to MTZ), 3, 7, 12 and 30 days post injury (dpi). Larval hearts (72 hpf) were isolated and pooled as previously described. 6 hearts, 3 males and 3 females, were isolated from Adult UI, 3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described. All cells per group were then pooled and sent for sequencing.

tag: tissue

value: Heart

value: Adult

value: MTZ

tag: time point

value: 7 day post injury


title: Adult 7D Post MTZ ZF Hearts - 1

description:
Bulk RNA-Seq
AH5HWLBCXY_US.1622940_TTAGGC_L002


title: Adult control ZF Hearts - 2

description:
Bulk RNA-Seq
AC89UAANXX_US.1601904_GCCAAT_L006

value: DMSO control

value: 0 day non-injured control


title: zebrafish day 7

data_processing:
Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings.
Monocle version 3 alpha was used for single cell RNA-seq data analysis and visualization. We kept cells with at least 200 expressed genes, and 1000 Unique Molecular Identifiers (UMIs), and less than 40% reads mapped to mitochondrial transcripts.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited file of normalized gene-level read counts for each cell

growth_protocol: Wild-type (AB; Zebrafish International Resource Center, Eugene, OR, USA), , hsWnt8:GFP [Tg(hsp70l:Wnt8a-GFP)w34] and hsDKK1:GFP [Tg(hsp70l:DKK1b-GFP)w32] [19] and vmhc:mCherry-NTR [Tg(vmhc:mCherry-Eco.NfsB)] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee-approved protocols IACUC 2057-01 & 4364-02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C, pH of 7.5, conductivity of 800 µS, hardness of 140 ppm, alkalinity of 35 ppm, dissolved oxygen content of 7.8 mg/L, and a total gas pressure of 101%. The average nitrate level is 55 ppm, the average nitrite level is 0.05 ppm, and the average ammonium level is 0.01 ppm. Larval feed starting at 5 days post fertilization (dpf) is a rotifer polyculture supplemented with the Zeigler larval diet, at 12 dpf live artemia is added to the diet, and at 60-90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.

extract_protocol:
Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total, 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart, 141 cells for 3 days post injury and 368 cells for 7 days post injury sample.
The captured cells then underwent lysis, reverse transcription, cDNA amplification, and library preparation with indexing per the manufacturer’s protocol (10X Genomics). The libraries were sequenced together on an Illumina HiSeq 4000 (Illumina Inc., San Diego, CA) using a high output 150 cycle kit with read lengths recommended by 10X Genomics.

treatment_protocol: All chemical ventricular cardiomyocyte (VCM) ablation were conducted on adult Zebrafish (~5-12 months old). For chemical mediated VCM ablation, fish were treated with 5 mM Metronidiazole (MTZ; Sigma) containing 0.1% dimethyl sulfoxide (DMSO) or vehicle control (0.1% DMSO) for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals, 7.5 mM MTZ was used.  Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 (prior to MTZ), 3, 7, 12 and 30 days post injury (dpi). Larval hearts (72 hpf) were isolated and pooled as previously described [68, 69]. 6 hearts, 3 males and 3 females, were isolated from Adult UI, 3 dpi and 7 dpi zebrafish.  Each group had 2 sets of samples of 3 hearts each for the digestion process.  Each set of 3 hearts were single celled as previously described [79].  All cells per group were then pooled and sent for sequencing.

value: heart

value: AB

tag: time

value: 7d post injury


title: Adult 3D Post MTZ ZF Hearts - 2

description:
Bulk RNA-Seq
AC89UAANXX_US.1601899_ACAGTG_L006

tag: age

value: 3 day post injury


title: Young day 3 heart - 2

description:
Bulk RNA-Seq
AC7N1CANXX_US.1555478_CGATGT_L004

value: Young


title: Adult 3D Post MTZ ZF Hearts - 1

description:
Bulk RNA-Seq
AC89UAANXX_US.1592737_ATCACG_L006


title: KO_VSV6h_rep1

value: lincRNA-EPS-/-

value: VSV infection


title: 10CEB13BAC -2 [GLA-16_S19]

value: yes


title: Young day 3 heart - 1

description:
Bulk RNA-Seq
AC7N1CANXX_US.1555441_ATCACG_L004


title: SK-N-MC_TCF7L1_c1_noDOX, 1 biologial Rep, 96h

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

description: Gene expression data

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Clariom D™ Arrays. Microarrays were washed and stained with Affymetrix GeneChip® 3000 Fluidics Station.

scan_protocol: Microarrays were scanned with Affymetrix GeneChip® 3000 Scanner.

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

label: Biotin

source_name: re-expression TCF7L1

label_protocol: Biotinylated cRNA were prepared using Affymetrix GeneChip® WT PLUS Reagent Kit according to its manufacture's instruction from 6 μg total RNA.

growth_protocol: 1.000.000 cells per flask/T75 flask were cultured for 96h with/without addtion of dox (1μg/ml).

extract_protocol: RNA was extracted by using RNA isolation kit from Macherey-Nagel.

treatment_protocol: Cells were treated with/without dox (1μg/ml) for 96h, with a refreshment after 48h.

tag: cell type

value: Ewing sarcoma


title: TC-71_Empty_noDOX, 1 biologial Rep, 96h

description: Gene expression data

source_name: Empty control


title: TC-71_TCF7L1_c6_noDOX, 1 biologial Rep, 96h

description: Gene expression data


title: TC-71_TCF7L1_c6_DOX, 1 biologial Rep, 96h

description: Gene expression data


title: SK-N-MC_TCF7L1_c1_DOX, 1 biologial Rep, 96h

description: Gene expression data


title: zebrafish day 3

value: 3d post injury


title: zebrafish day 0


title: TC-71_Empty_DOX, 1 biologial Rep, 96h

description: Gene expression data


title: SK-N-MC_Empty_DOX, 1 biologial Rep, 96h

description: Gene expression data


title: SK-N-MC_Empty_noDOX, 1 biologial Rep, 96h

description: Gene expression data


title: P9808_Piri_L

city: Zhejiang

first: Chong

last: Liu

address: NO.866 of Yuhang Tong Road

institute: Medical College of Zhejiang University

data_processing:
Six samples from two Glioma_CKO mice (one normal brain tissue, two tumor tissues per mouse) were performed Whole Exome Sequencing by Novegene. The insert size of library was tested by Agilent 2100. After the validation of library quality, sequencing was performed by Illumina HiSeq PE150. Raw data was filtered by removing reads with adaptor, reads with more than 10% undetermined bases and read with more than 50% low quality bases. Effective sequencing data was aligned by BWA and Samblaster and processed by Samblaster further. Somatic SNV was processed by muTect. Somatic INDEL was performed by Strelka. Somatic CNV was performed by freec (http://bioinfo-out.curie.fr/projects/freec/)
Genome_build: GRCm38
Supplementary_files_format_and_content: somatic.snv of each samples

molecule: polyA RNA

source_name: Brain

extract_protocol:
Six samples from two Glioma_CKO mice (one normal brain tissue, two tumor tissues per mouse) were performed Whole Exome Sequencing by Novegene. The insert size of library was tested by Agilent 2100. After the validation of library quality, sequencing was performed by Illumina HiSeq PE150. Raw data was filtered by removing reads with adaptor, reads with more than 10% undetermined bases and read with more than 50% low quality bases. Effective sequencing data was aligned by BWA and Samblaster and processed by Samblaster further. Somatic SNV was processed by muTect. Somatic INDEL was performed by Strelka. Somatic CNV was performed by freec (http://bioinfo-out.curie.fr/projects/freec/)
RNA libraries were prepared for sequencing using standard Illumina protocols.Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesize dusing random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on a Hiseq platform (Illumina)

value: brain

tag: disease state

value: tumor


title: P9808_OB_L


title: P9808_control

value: normal


title: P8772_OB_R_C


title: P8772_OB_R


title: Adult control ZF Hearts - 1

description:
Bulk RNA-Seq
AC89UAANXX_US.1601914_ACTTGA_L006

value: Heart

value: Adult


title: P8772_control


title: 1039L

data_processing:
Six paired OBs form three left naris mice were performed RNA-Seq by Shanghai Personal Biotechnology Co.,Ltd. The quality of library was confirmed by Agilent 2100 Bioanalyzer. After the validation of library quality, sequencing was performed by Illumina NextSeq500 PE150. Raw data was filtered by removing polluted reads with Cutadapt (Version 1.2.1) and quality control (not lower than Q20). Clean reads was aligned to the reference genome Mus_musculus.GRCm38.dna.primary_assembly.fa (38.86) in Ensembl by Tophat2. Quality of alignment was confirmed though insert length and sequence-based duplication by RseQC. Read counts were calculated by HTSeq 0.6.1p2 (http://www huber.embl.de/users/anders/HTSeq) and normalized by RPKM (Reads Per Kilo bases per Million reads). Differential gene expression analysis was performed by DESeq (version 1.18.0). The screening threshold was fold change >1.5 and P-value < 0.05.
Genome_build: GRCm38
Supplementary_files_format_and_content: rpkm expression of each sample

source_name: mouse 1039 left OB

extract_protocol:
OBs were lysed by the TRIzol Reagent.  Chloroform was added to samples and the tubes must be thoroughly vortexed. The tubes were centrifuged at 12,000 g for 15 min at 4°C. Upper aqueous phase was removed to a new tube and added with 250 μL isopropyl alcohol. After inverted a few times to mix, the samples were incubated for 10 min and centrifuged at 12,000 g for 10 min at 4°C. Supernatant was discarded by 1 mL pipet tip. After washing the RNA pellet with 950 μL 75% ethanol, the tubes were centrifuged at 7,500 g for 5 min at 4°C. The supernatant was discarded. The RNA pellet was dried and resuspended in RNase free water.
RNA libraries were prepared for sequencing using standard Illumina protocols.Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesize dusing random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on a Hiseq platform (Illumina)

treatment_protocol: ICR mice were anesthetic before surgery at p30. Then silica gel plug (No: 63-625), trimmed to 1~1.2 cm and tied with surgical suture (5-0(3/0) 60 cm×15, Hangzhou Huawei medical applicance co. LTD), was carefully plugged into the naris. After 60 days. Mice were perfused with PBS and then dissected for OBs.

value: olfactory bulb

tag: location

value: left OB

tag: mouse id


title: 1039R

source_name: mouse 1039 Right OB

value: right OB


title: 1038L

source_name: mouse 1038 left OB


title: 1037R

source_name: mouse 1037 Right OB


title: 1037L

source_name: mouse 1037 left OB


title: 1038R

source_name: mouse 1038 Right OB


title: S3

city: Hangzhou

first: zhaowei

last: cai

state: Zhejiang

address: Binwen road 548

department: Laboratory Animal Research Center

institute: zhejiang chinese medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequencing data were evaluated by FAST-QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), an online bioinformatics program used to characterize quality distributions of nucleotides, position-specific sequencing qualities, GC contents, the proportions of PCR duplication, and k-mer frequencies
Raw reads after quality control testing were then mapped to the reference mouse genome version 10 (mm10), using Hisat2 software
The normalized expression level of each gene was measured by Fragments Per Kilobase of exon per Million Reads (FPKM).
Genome_build: mm10

source_name: 3T3-L1_Smilax glabra flavonoids

extract_protocol:
3T3-L1 adipocytes were subjected to total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Sequencing libraries were prepared using a TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Differentiated 3T3-L1 adipocytes were treated with final concentration of 0.125 μg/mL Smilax glabra flavonoids and compared to untreated control

value: adipocytes

value: eight days after differentiation

value: 0.125 μg/mL Smilax glabra flavonoids


title: S2


title: S1


title: M2

value: none (untreated control)


title: M3


title: MII6 AMA

city: Leeds

first: Panagiotis

last: Ntostis

address: Clarendon Way

department: Medicine and Health

institute: University of Leeds

data_processing:
Paired-end read trimming was performed to remove adapters and poor quality sequence using Trim galore
Read mates were mapped to the Human reference genome (hg38) using the HISAT2 aligner version 2.0.4, with the following parameters -p 8 -k 1 --dta --rna-strandness FR --no-mixed --no-discordant.
Unmapped reads and incorrectly paired reads were removed and the remaining reads converted to bam format with the view function of samtools version 1.3.
Potential PCR duplicates were tagged using Picard MarkDuplicates version 2.1.1
StringTie was used to identify potential novel transcripts, using the UCSC hg38 annotation of the human genome as a guide.
We used both the Python script prepDE.py (https://ccb.jhu.edu/software/stringtie/dl/prepDE.py) and Rsubread's featureCounts function to count assigned reads to genomic features. Only uniquely mapped, non-duplicated and correctly paired-end reads were considered in this study.
The edgeR function calcNormFactors was used to normalize library sizes, based on the trimmed mean M value (TMM). The copies-per-million (cpm) threshold was set at 1 in at least half of the libraries to be included in the analysis. Differential gene expression (DGE) between successfully and non-successfully implanted blastocysts was tested statistically using the edgeR Exact test with FDR 0.05.
Genome_build: hg38

source_name: MII oocyte advanced maternal age

growth_protocol: Human oocytes donated for research.

extract_protocol:
Isolated oocytes were inserted separate into lysis buffer with RNase Inhibitor (Clontech, USA) and frozen at -80°C until required.
RNA libraries were prepared for sequencing using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) and Nextera XT DNA library preparation kit (Illumina), according to the manufacturer's instructions.

tag: developmental stage

value: Late oogenesis

value: Gamete

tag: maternal age

value: advanced maternal age (≥40 yo)


title: M1


title: MII4 AMA


title: MII3 AMA


title: MII5 AMA


title: MII2 AMA


title: MII1 AMA


title: GV5 AMA

source_name: GV oocyte young maternal age


title: GV3 AMA


title: GV4 AMA


title: GV2 AMA


title: GV1 AMA


title: MII3 YMA

source_name: MII oocyte young maternal age

value: young maternal age (<30 yo)


title: MII6 YMA


title: MII2 YMA


title: GV4 YMA


title: MII5 YMA


title: MII1 YMA


title: GV2 YMA


title: GV1 YMA


title: twin2_ADHD

type: genomic

city: Eiheiji-cho, Yoshida-gun

first: Shota

last: Nishitani

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

department: Research Center for Child Mental Development

country: Japan

institute: University of Fukui

description: monozygotic twin

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio Software v2.0.5

label: Cy5 and Cy3

source_name: ADHD

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from saliva samples (Oragene Discover OGR-500 kits) using prepIT®•L2P reagent (DNA Genotek) according to standard instructions

tag: sample type

value: saliva

tag: gender

value: female

tag: desease state

value: ADHD

tag: race

value: Japanese


title: Sample 266

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Well-barcode-RMT are extracted from the 9 first base pairs in the R2 fastq sequences. Unique-molecular-identifier are extracted from the subsequent 8 base pairs in the R2 sequences. R1 contains the genomic sequences.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: metadata_q.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

growth_protocol:
Human samples: Samples of tumor and adjacent normal lung tissues were obtained from treatment-naive surgical specimens of NSCLC patients undergoing resection at the Mount Sinai Medical Center (New York, NY) after obtaining informed consent in accordance with a protocol reviewed and approved by the Institutional Review Board at the Icahn School of Medicine at Mount Sinai
Mouse samples: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were euthanized and auricular LNs were disected. Lymph nodes were digested in IMDM containing 100µg/mL Liberase TL and 100µg/mL DNase I for 20 minutes at 37°C. In the last 5 minutes of incubation, EDTA was added at a final concentration of 10mM. Cells were collected, filtered through a 70µm cell strainer, washed with IMDM and maintained strictly at 4°C. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

treatment_protocol:
treatment protocol (1): Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
treatment protocol (2): mice were treated with depleting or neutralizing antibodies or their isotype controls: Anti-NK1.1 (200 µg/dose), anti-IFNγ (500 µg/dose), Mouse IgG2a Isotype control and Rat IgG1 Isotype control were injected 24 hours prior to immunization and on the day of immunization

tag: strain

value: C57BL/6, TCR-transgenic OT-II, and OVA-expressing B16 cell line

tag: organ

value: dLN

value: OT-II T cells

tag: selection marker

tag: co-culture conditions

value: day 17 post tumor injection

tag: patient id

tag: replicate id

tag: mouse age

value: 6-8 weeks


title: GV5 YMA

tag: cell type


title: Sample 268

value: tumor

value: Doublets of T cells and myeloid cells

tag: time point


title: Sample 264

value: T cells

value: TCRb+


title: Sample 263

value: cLN

value: day 10 post tumor injection


title: Sample 261

value: Myeloid cells


title: twin2_TD

description: monozygotic twin

source_name: TD

tag: age

value: TD


title: GV3 YMA

value: Late oogenesis

value: Gamete

value: young maternal age (<30 yo)


title: Sample 259


title: twin1_ADHD

description: monozygotic twin

value: saliva

value: male

value: ADHD

value: Japanese


title: Sample 258

value: C57BL/6, TCR-transgenic OT-II, and OVA-expressing B16 cell line

value: day 17 post tumor injection


title: Sample 257

value: 6-8 weeks


title: Sample 256

value: Doublets of T cells and myeloid cells


title: Sample 255

value: T cells


title: Sample 260

value: dLN

value: TCRb+


title: Sample 254

value: cLN


title: Sample 267


title: Sample 253

value: OT-II T cells


title: Sample 252


title: Sample 265


title: Sample 250


title: Sample 262

value: day 10 post tumor injection


title: Sample 248


title: Sample 245

value: tumor


title: Sample 244


title: Sample 247


title: Sample 242

value: Myeloid cells


title: Sample 243


title: twin1_TD

description: monozygotic twin

value: TD


title: Sample 241


title: Sample 240


title: Sample 239


title: Sample 238


title: Sample 237


title: Sample 251


title: Sample 236


title: Sample 249


title: Sample 235


title: Sample 232


title: Sample 230


title: Sample 231


title: Sample 228


title: Sample 226


title: Sample 234


title: Sample 223


title: Sample 221


title: Sample 227


title: Sample 222


title: Sample 224


title: Sample 217


title: Sample 218


title: Sample 216


title: Sample 219


title: Sample 215

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 10 days after tumor injection; intra-peritoneal injection with 250microgram of anti-PD-1 11 and 14 days after tumor injection


title: Sample 220


title: Sample 246


title: Sample 214


title: Sample 233


title: Sample 229


title: Sample 212

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 10 days after tumor injection; intra-peritoneal injection with 250microgram of isotype control 11 and 14 days after tumor injection


title: Sample 213


title: Sample 211


title: Sample 225


title: Sample 209


title: Sample 207


title: Sample 206


title: Sample 208


title: Sample 205


title: Sample 204


title: Sample 203


title: Sample 202


title: Sample 179

value: C57BL/6, TCR-transgenic SMARTA

value: LN

value: CD4+ SMARTA Tfh cells

value: Adoptive transfer of SMARTA CD4+ T cells; subcutaneous intra-footpad infection with rVSV 24 hours after transfer


title: Sample 177

value: CD4+ SMARTA T cells

value: Adoptive transfer of SMARTA CD4+ T cells

value: 6-8 weeks


title: Sample 180


title: Sample 178


title: Sample 181


title: Sample 176


title: Sample 175


title: Sample 174

value: C57BL/6, TCR-transgenic OT-II, and OVA-expressing B16 cell line

value: T cells

value: day 17 post tumor injection


title: Sample 173

value: Doublets of T cells and myeloid cells


title: Sample 170

value: in vitro

value: TCRb+

value: OVA + LPS T only

value: 20 hours


title: 5_1483co_IGF1

data_processing:
raw data was filtered by removing adapter with Cutadapt (Version 3.4) and quality control (not lower than 25).
Clean reads were aligned to the reference genome Mus_musculus.GRCm39.dna.primary_assembly.fa (39.103) from Ensembl by STAR (Version 2.7.9a).
Read counts were calculated by featureCounts (Version 2.0.1). The feature was selected as Exon, and only reads with mapping quality score greater than 25 were retained.
The batch effect was removed by sva (Version 3.63.0) for samples sequenced at different times.
Differential gene expression analysis was performed by DESeq2 (Version 1.28.1). The screening threshold was fold change > 1.5 and P-adj < 0.05.
Genome_build: GRCm39
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: glioma cells co-cultured with OB neurons after IGF-1 stimulation

growth_protocol: OBs were dissected from P2~3 mouse pups and digested in 10 mL papain solution (1x EBSS (Sigma, E7510), 0.5 mM EDTA, 10 mM HEPES, 26 mM NaHCO3, 22.5 mM D(+)-glucose, 0.16 mg/mL L-cycteine, 20 units/mL papain (Worthington Biochem, LS003126), 250 μg/mL DNase I (Sigma, DN-25) in dd-water) for 30min at 37°C. Papain solution was discarded and the tissue was triturated with 2 mL Diluted Trypsin Inhibitor Buffer (1x EBSS (Sigma, E7510), 10 mM HEPES, 26 mM NaHCO3, 1x ovomucoid (Worthington Biochem, LS003086), 250 μg/mL DNase I (Sigma, DN-25), 1 mg/mL BSA (equitech-bio, BAH62) in dd-water) by 1 mL pipette and was allowed to settle for 2 min. 1 mL upper cell suspension was carefully collected and additional 1 mL Diluted Trypsin Inhibitor Buffer was add to the tissue. The process was repeated until all Diluted Trypsin Inhibitor Buffer was consumed. Cell suspension was layered over the Standard Trypsin Inhibitor Buffer (1x EBSS (Sigma, E7510), 10 mM HEPES, 26 mM NaHCO3, 1x ovomucoid (Worthington Biochem, LS003086), 10 mg/mL BSA (equitech-bio, BAH62) in dd-water) and centrifuged at 1,200 rpm for 10 min. Supernatant was discarded and cells were resuspended with plating medium (25 mM D(+)-glucose, 2.5 mM NaHCO3, 0.1 mg/mL transferrin (Sigma, T-1147), 10% FBS (serapro, s601s), 2 mM L-glutamine, 0.25 mg/mL insulin (Sigma, I-6634), 1x pen/strep (Hydone, SV30010), 50 μg/mL gentamycin (Sigma, 46305) in neurobasal medium (Gibco, #12349015)) for cell culture. 24 h after initial plating, 80% medium was removed and replaced with 0ARAC medium (25 mM D(+)-glucose, 2.5 mM NaHCO3, 0.1 mg/mL transferrin (Sigma, T-1147), 5% FBS (serapro, s601s), 0.5 mM L-glutamine, 1x pen/strep (Hydone, SV30010), 50 μg/mL gentamycin (Sigma, 46305), 1x B27 (Gibco, 17504044) in neurobasal medium (Gibco, #12349015)). 48-72 h after initial plating, 50% medium was removed and replaced with 4ARAC medium (25 mM D(+)-glucose, 2.5 mM NaHCO3, 0.1 mg/mL transferrin (Sigma, T-1147), 5% FBS (serapro, s601s), 0.5 mM L-glutamine, 1x pen/strep (Hydone, SV30010), 50 μg/mL gentamycin (Sigma, 46305), 1x B27 (Gibco, 17504044), 4 μM AraC (MKbio, MS0237) in neurobasal medium (Gibco, #12349015)). Glioma cells were plating on OB neurons for co-culture on DIV7 with experiment medium (25 mM D(+)-glucose, 2.5 mM NaHCO3, 0.5 mM L-glutamine, 1x pen/strep (Hydone, SV30010), 50 μg/mL gentamycin (Sigma, 46305), 1x B27 minus insulin (Gibco, A1895601), in neurobasal medium (Gibco, #12349015)).

extract_protocol:
Glioma cells were seperated from neurons by FACS through tdTomato tag In the tuomor. RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Experiment group was incubated with 20 ng/mL IGF-1 overnight.

value: glioma

tag: tissue

value: brain

tag: genotype

tag: treatment

value: IGF-1 stimulation


title: 4_1483co_IGF1


title: 3_1483co_IGF1


title: 2_1483co

source_name: glioma cells co-cultured with OB neurons


title: Sample 210

value: dLN

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 10 days after tumor injection; intra-peritoneal injection with 250microgram of anti-PD-1 11 and 14 days after tumor injection


title: 1_1483co


title: LN_cells and Spleen NK_cells [HTO]

city: Leiden

first: Sumit

last: Kumar

address: Einthovenweg 20

department: CCB

country: Netherlands

institute: Leids Universitair Medisch Centrum  (LUMC)

description:
Processed data file: sample_feature_bc_matrix.h5
LN_cells_M1
LN_cells_M2
LN_cells_M3
LN_cells_M4
Spleen NK_cells_M1
Spleen NK_cells_M2
Spleen NK_cells_M3
Spleen NK_cells_M4

data_processing:
Cell Ranger software v6.0.1 (10x Genomics) using the multi pipeline
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: sample_feature_bc_matrix.h5

source_name: lymph nodes and spleen

extract_protocol:
Single cells were isolated from LN and spleen.
Single cell gene expression libraries were generated on the 10x Genomics Chromium platform using the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v2 and Chromium Next GEM Chip K Single Cell Kit

treatment_protocol: Mice were treated with TAK-981 or vehicle control

value: lymph nodes and spleen

value: immune cells

value: TAK-981 or vehicle control


title: LN_cells and Spleen NK_cells [GEX]


title: IL-4/IL-13+TNF L49682_M2_TNF_2_05_P23

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF

data_processing:
Bbasecalling: Basecalls were done with Illumina bcl2fastq version 2.19.1.
Read alignment: Fragments were aligned to the mouse reference genome mm10 using the aligner gsnap (2019-06-10) with Ensembl 98 splice sites as support (parameters: --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit -N 0  --action-if-cigar-error noprint).
Counts per feature: Uniquely mapped fragments were compared based on their overlap to Ensembl 98 gene annotations using featureCounts (v1.6.3) to create a table of counts per gene and cell (parameters:  -a EnsemblGene-98.mm10.TR.gtf -s 0 -p -o bfx1341.mm10.e98.txt -Q 1).
Samples were processed and analyzed in R (4.0.0) using Seurat (v3)
Genes from specific metabolic pathways were retrieved from KEGG
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells.

source_name: Bone marrow

growth_protocol: In the presence of M-CSF

extract_protocol:
Wild-type BMDMs were stimulated with 10ng/ml IL4, IL13 and TNF. Cells were scraped and stained for live/dead staining with LDFA. Single cells were flow-sorted into 384-well plates containing nuclease-free water with 0.2% Triton X-100 and 1 U murine RNase inhibitor, centrifuged, and frozen at −80°C. After thawing, the primer mix and 1 U murine RNase inhibitor was added to each well. The reverse transcription reaction was performed, cDNA was amplified and purified. The concentration of samples was measured using a plate reader (Infinite 200 PRO, Tecan).
Then, pre-amplified cDNA was used for library preparation (TruePrep DNA library preparation kit V2 for Illumina, Vazyme) in a 1-μL reaction volume. Illumina indices were added during the PCR reaction with 1 × KAPA Hifi HotStart Ready Mix and dual indexing primers. After PCR, the libraries were quantified with AccuBlue Broad Range kit, pooled in equimolar amounts, and purified twice with Sera-Mag SpeedBeads. The libraries were sequenced on the Novaseq 6000 Illumina platform to obtain 50 bp paired-end reads aiming at an average sequencing depth of 0.5 million reads per cell.
Single Cell RNA seq

treatment_protocol: 10ng/ml IL4, IL13 and/or TNF

value: BMDM


title: IL-4/IL-13+TNF L49667_M2_TNF_2_05_P08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49675_M2_TNF_2_05_P16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49674_M2_TNF_2_05_P15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49668_M2_TNF_2_05_P09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49681_M2_TNF_2_05_P22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49679_M2_TNF_2_05_P20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49678_M2_TNF_2_05_P19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49672_M2_TNF_2_05_P13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49670_M2_TNF_2_05_P11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49680_M2_TNF_2_05_P21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49666_M2_TNF_2_05_P07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: Sample 172

value: C57BL/6, TCR-transgenic OT-II, and OVA-expressing B16 cell line

value: 6-8 weeks


title: Sample 171

value: T cells


title: IL-4/IL-13+TNF L49669_M2_TNF_2_05_P10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49664_M2_TNF_2_05_P05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49659_M2_TNF_2_05_O24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49663_M2_TNF_2_05_P04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49658_M2_TNF_2_05_O23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49657_M2_TNF_2_05_O22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49656_M2_TNF_2_05_O21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49653_M2_TNF_2_05_O18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49654_M2_TNF_2_05_O19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49655_M2_TNF_2_05_O20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49677_M2_TNF_2_05_P18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49676_M2_TNF_2_05_P17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49673_M2_TNF_2_05_P14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49671_M2_TNF_2_05_P12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49644_M2_TNF_2_05_O09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49645_M2_TNF_2_05_O10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49652_M2_TNF_2_05_O17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49648_M2_TNF_2_05_O13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49646_M2_TNF_2_05_O11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49643_M2_TNF_2_05_O08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49642_M2_TNF_2_05_O07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49647_M2_TNF_2_05_O12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49651_M2_TNF_2_05_O16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49665_M2_TNF_2_05_P06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49637_M2_TNF_2_05_O02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49649_M2_TNF_2_05_O14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49635_M2_TNF_2_05_N24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49636_M2_TNF_2_05_O01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49634_M2_TNF_2_05_N23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49650_M2_TNF_2_05_O15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49633_M2_TNF_2_05_N22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49640_M2_TNF_2_05_O05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49631_M2_TNF_2_05_N20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49629_M2_TNF_2_05_N18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49632_M2_TNF_2_05_N21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49639_M2_TNF_2_05_O04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49628_M2_TNF_2_05_N17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49630_M2_TNF_2_05_N19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49627_M2_TNF_2_05_N16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49626_M2_TNF_2_05_N15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49625_M2_TNF_2_05_N14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49641_M2_TNF_2_05_O06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49638_M2_TNF_2_05_O03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49619_M2_TNF_2_05_N08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49621_M2_TNF_2_05_N10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49618_M2_TNF_2_05_N07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49617_M2_TNF_2_05_N06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49623_M2_TNF_2_05_N12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49622_M2_TNF_2_05_N11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49683_M2_TNF_2_05_P24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49616_M2_TNF_2_05_N05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49604_M2_TNF_2_05_M17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49606_M2_TNF_2_05_M19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49610_M2_TNF_2_05_M23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49603_M2_TNF_2_05_M16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49608_M2_TNF_2_05_M21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49612_M2_TNF_2_05_N01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49605_M2_TNF_2_05_M18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49609_M2_TNF_2_05_M22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49614_M2_TNF_2_05_N03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49624_M2_TNF_2_05_N13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49620_M2_TNF_2_05_N09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49615_M2_TNF_2_05_N04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49613_M2_TNF_2_05_N02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49602_M2_TNF_2_05_M15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49607_M2_TNF_2_05_M20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49600_M2_TNF_2_05_M13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49601_M2_TNF_2_05_M14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49599_M2_TNF_2_05_M12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49598_M2_TNF_2_05_M11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49597_M2_TNF_2_05_M10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49595_M2_TNF_2_05_M08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49596_M2_TNF_2_05_M09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49594_M2_TNF_2_05_M07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49593_M2_TNF_2_05_M06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49592_M2_TNF_2_05_M05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49591_M2_TNF_2_05_M04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49611_M2_TNF_2_05_M24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49590_M2_TNF_2_05_M03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49589_M2_TNF_2_05_M02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49586_M2_TNF_2_05_L23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49585_M2_TNF_2_05_L22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49588_M2_TNF_2_05_M01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49587_M2_TNF_2_05_L24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49582_M2_TNF_2_05_L19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49583_M2_TNF_2_05_L20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49581_M2_TNF_2_05_L18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 263L

city: torrance

first: Omid

last: Khorram

state: CA

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

description: Leiomyoma #263

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies), and adjusting batch effects in expression data using empirical Bayes methods. SE-LncRNAs and mRNAs that at least 2 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed SE-LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: Leiomyoma #263

label_protocol: An efficient and robust linear amplification method to produce fluorescently labeled target cRNA for sensitive detection of transcripts at even low copy numbers. Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from leiomyoma and matched myometrium using Trizol. RNA concentration and integrity was determined using a Nanodrop 2000c spectrophotometer and Agilent 2100 Bioanalyzer.

treatment_protocol: Portions of uterine leiomyomas and paired myometrium were obtained from patients who were not taking any hormonal medications for at least 3 months prior to surgery at Harbor-UCLA Medical Center.

value: African American

value: Wild Type


title: 214L

description: Leiomyoma #214

source_name: Leiomyoma #214


title: 280L

description: Leiomyoma #280

source_name: Leiomyoma #280

value: Caucasian

value: MED12 Mutant


title: IL-4/IL-13+TNF L49580_M2_TNF_2_05_L17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49579_M2_TNF_2_05_L16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 32M

description: Myometrium #32

source_name: Myometrium #32


title: 263M

description: Myometrium #263

source_name: Myometrium #263


title: 97L

description: Leiomyoma #97

source_name: Leiomyoma #97


title: 276L

description: Leiomyoma #276

source_name: Leiomyoma #276


title: IL-4/IL-13+TNF L49584_M2_TNF_2_05_L21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 97M

description: Myometrium #97

source_name: Myometrium #97


title: 276M

description: Myometrium #276

source_name: Myometrium #276


title: 214M

description: Myometrium #214

source_name: Myometrium #214


title: IL-4/IL-13+TNF L49578_M2_TNF_2_05_L15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49577_M2_TNF_2_05_L14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49576_M2_TNF_2_05_L13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 299L

description: Leiomyoma #299

source_name: Leiomyoma #299


title: 314L

description: Leiomyoma #314

source_name: Leiomyoma #314


title: Wilms tumor (seq)

city: Valencia

first: Jaime

last: Font de Mora Sain

state: Valencia

address: Avenida Fernando Abril Martorell, 106

department: Oncology

country: Spain

institute: Instituto de Investigación Sanitaria La Fe

data_processing:
Library strategy: DNA-Seq
Bioinformatic analysis was performed with BWA-MEM aligner, caller variant VarDict and annotation by Ensembl Variant Effect Predictor.
Quality metrics performed through Picard Pipeline (Broad Institute).
Genome_build: hg19
Supplementary_files_format_and_content: Variant Call Format (vcf)

source_name: FFPE-resected tumor

extract_protocol:
DNA was isolated from blood with RecoverAll kit (Invitrogen) and from paraffin-embedded tumor-selected section with QIAamp DNA Investigator Kit (QIAGEN). DNA quantification and integrity were assessed with Qubit and TapeStation.
Libraries were prepared with Agilent SureSelect customized panel (254 genes, 0.8 Mb, Agilent XT-HS). Sequencing by Illumina NextSeq at 2x150bp; Depth>1000X.

value: Wilms Tumor (Kidney)

value: untreated


title: Blood cells (seq)

source_name: Blood liquid biopsy

value: Germline (Blood cells)


title: 314M

description: Myometrium #314

source_name: Myometrium #314


title: 32L

description: Leiomyoma #32

source_name: Leiomyoma #32


title: IL-4/IL-13+TNF L49574_M2_TNF_2_05_L11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF

source_name: Bone marrow


title: IL-4/IL-13+TNF L49573_M2_TNF_2_05_L10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 280M

description: Myometrium #280

source_name: Myometrium #280


title: 147-Enroll

city: Hershey

first: Steven

last: Hicks

state: Pennsylvania

address: 500 University Drive

department: Pediatrics

institute: Penn State College of Medicine

data_processing:
Basecalling in Illumina BaseSpace
Adapter trimming with CUTADAPT in Partek Flow
Aligned to human genome with Bowtie2 in Partek Flow
Mature miRNAs quantified with miRBase v22
Raw counts were median normalized and mean-center scaled
Genome_build: hg38
Supplementary_files_format_and_content: csv file including normalized mature microRNA levels

source_name: Milk

extract_protocol:
Samples were spun for 20 min at 4 °C at 800 rpm to 130 separate lipid, skim, and cellular fractions. For each sample, 50 μl of the lipid fraction was used for RNA extraction. RNA purification was performed using a 134 Norgen Circulating and Exosomal RNA Purification Kit (Norgen Biotech; Ontario, Canada)
Illumina TruSeq Small RNA Prep protocol

value: Milk

tag: biologic sex

value: Female

tag: maternal age

value: White


title: 299M

description: Myometrium #299

source_name: Myometrium #299


title: 144-Enroll


title: IL-4/IL-13+TNF L49572_M2_TNF_2_05_L09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 143-Enroll

value: Asian


title: 142-Enroll


title: IL-4/IL-13+TNF L49569_M2_TNF_2_05_L06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49571_M2_TNF_2_05_L08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 138-Enroll


title: 141-Enroll


title: IL-4/IL-13+TNF L49568_M2_TNF_2_05_L05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49567_M2_TNF_2_05_L04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49570_M2_TNF_2_05_L07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 137-Enroll


title: IL-4/IL-13+TNF L49575_M2_TNF_2_05_L12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 146-Enroll


title: 135-Enroll


title: 134-Enroll

value: Black


title: IL-4/IL-13+TNF L49565_M2_TNF_2_05_L02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49564_M2_TNF_2_05_L01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49563_M2_TNF_2_05_K24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 129-Enroll


title: IL-4/IL-13+TNF L49562_M2_TNF_2_05_K23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 130-Enroll


title: 128-Enroll


title: IL-4/IL-13+TNF L49561_M2_TNF_2_05_K22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 125-Enroll


title: IL-4/IL-13+TNF L49560_M2_TNF_2_05_K21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 124-Enroll


title: IL-4/IL-13+TNF L49559_M2_TNF_2_05_K20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 120-Enroll


title: IL-4/IL-13+TNF L49558_M2_TNF_2_05_K19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 119-Enroll


title: 118-Enroll


title: 115-Enroll


title: IL-4/IL-13+TNF L49555_M2_TNF_2_05_K16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49566_M2_TNF_2_05_L03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 112-Enroll


title: 107-Enroll


title: IL-4/IL-13+TNF L49553_M2_TNF_2_05_K14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 106-Enroll


title: IL-4/IL-13+TNF L49556_M2_TNF_2_05_K17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49551_M2_TNF_2_05_K12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 104-Enroll

value: Other


title: 105-Enroll


title: 133-Enroll


title: IL-4/IL-13+TNF L49552_M2_TNF_2_05_K13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF

value: BMDM


title: 102-Enroll


title: 101-Enroll


title: 100-Enroll


title: IL-4/IL-13+TNF L49547_M2_TNF_2_05_K08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49550_M2_TNF_2_05_K11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 103-Enroll


title: IL-4/IL-13+TNF L49548_M2_TNF_2_05_K09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49549_M2_TNF_2_05_K10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 98-Enroll


title: IL-4/IL-13+TNF L49545_M2_TNF_2_05_K06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49546_M2_TNF_2_05_K07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49544_M2_TNF_2_05_K05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 97-Enroll


title: 96-Enroll


title: IL-4/IL-13+TNF L49543_M2_TNF_2_05_K04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49557_M2_TNF_2_05_K18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: 95-Enroll