title: DLBCL [Sample_187]

status: Public on May 31 2023

type: genomic

city: Firenze

first: Stefania

last: Nobili

address: viale Pieraccini 6

department: Health Sciences

country: Italy

institute: University of Florence

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions. The arrays were then washed using Affymetrix Fluidics Stations.

scan_protocol: The arrays were scanned using the Gene Chip Scanner 3000.

data_processing:
Files of .CEL type were imported in the Axiom Analysis Suite (Thermo Fisher Scientific. Axiom Genotyping Solution - Data Analysis Guide. Tech. Rep. 2011) and processed using the Axiom UKB WCSG array type to evaluate sample and SNP quality. In case of more than one probeset interrogating the same SNP, the best probeset was chosen according to the “BestProbeSet” variable and then, according to Axiom Analysis Suite metrics, SNPs quality was checked. In particular, monomorphic SNPs and SNPs with a call rate <95% were filtered. Fisher’s Linear Discriminant (FLD), Homozygous Ratio Offset (HomRO) and Heterozygous Strength Offset (HetSO) thresholds were also considered. Default cut-offs were used.
AxiomGT1_intensity.txt: Tab-delmited text file includes signal intensity of both alleles.
AxiomGT1_genotype_calls3.txt: Tab-delmited text file includes Genotype Calls (SNP calls): AA, AB, BB, No Call.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer (Affymetrix).

growth_protocol: Not applicable.

extract_protocol: Puregene Blood Core Kit (Qiagen).

treatment_protocol: All patients were treated with the R-CHOP 21 protocol.

tag: diagnosis

value: Diffuse large B-cell lymphoma (DLBCL)

tag: Stage

tag: treatment

value: Yes

tag: progression

value: No

tag: dead

tag: gender

value: Female

tag: age

value: Adult

tag: tissue

value: Blood


title: DLBCL [Sample_186]


title: DLBCL [Sample_185]

value: Male


title: DLBCL [Sample_184]


title: DLBCL [Sample_182]


title: DLBCL [Sample_181]


title: DLBCL [Sample_183]


title: lir12 mutant larvae

type: SRA

city: Cleveland

first: Takuya

last: Sakaguchi

address: 9500 Euclid Ave.

country: USA

institute: Cleveland Clinic Foundation

description: Whole body of 20 larvae at 5 dpf.

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Zv9 whole genome using bowtie
Assembly: Zv9
Supplementary files format and content: csv file includes FPKM values for wt and lri12 mutant larvae

molecule: total RNA

organism: Danio rerio

source_name: Whole body of 20 larvae

growth_protocol: Embryos were cultured at 28.5C and homogenized at 5 dpf.

extract_protocol:
Total RNA was isloated by the Rneasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole body of 20 larvae

value: 5 dpf

tag: genotype

value: lri12 mutant


title: WT siblings

description: Whole body of 20 larvae at 5 dpf.

value: Wild-type


title: DLBCL [Sample_179]


title: DLBCL [Sample_180]


title: DLBCL [Sample_176]


title: DLBCL [Sample_174]


title: DLBCL [Sample_175]


title: DLBCL [Sample_173]


title: DLBCL [Sample_170]


title: DLBCL [Sample_171]


title: DLBCL [Sample_172]


title: DLBCL [Sample_168]


title: DLBCL [Sample_169]


title: DLBCL [Sample_167]


title: DLBCL [Sample_166]


title: DLBCL [Sample_164]


title: DLBCL [Sample_165]


title: DLBCL [Sample_162]


title: DLBCL [Sample_161]


title: DLBCL [Sample_158]


title: DLBCL [Sample_155]


title: DLBCL [Sample_178]


title: DLBCL [Sample_156]


title: DLBCL [Sample_160]


title: DLBCL [Sample_177]


title: DLBCL [Sample_154]


title: DLBCL [Sample_157]


title: DLBCL [Sample_151]


title: DLBCL [Sample_152]


title: DLBCL [Sample_149]


title: DLBCL [Sample_148]


title: DLBCL [Sample_150]


title: DLBCL [Sample_153]


title: DLBCL [Sample_144]


title: DLBCL [Sample_147]


title: DLBCL [Sample_146]


title: DLBCL [Sample_142]


title: DLBCL [Sample_140]


title: DLBCL [Sample_141]


title: DLBCL [Sample_143]


title: DLBCL [Sample_145]


title: DLBCL [Sample_138]


title: DLBCL [Sample_163]


title: DLBCL [Sample_137]


title: DLBCL [Sample_136]


title: DLBCL [Sample_134]


title: DLBCL [Sample_133]


title: DLBCL [Sample_159]


title: DLBCL [Sample_132]


title: DLBCL [Sample_135]


title: DLBCL [Sample_130]


title: DLBCL [Sample_131]


title: DLBCL [Sample_129]


title: DLBCL [Sample_128]


title: DLBCL [Sample_127]


title: DLBCL [Sample_125]


title: DLBCL [Sample_124]


title: DLBCL [Sample_123]


title: DLBCL [Sample_122]


title: DLBCL [Sample_121]


title: DLBCL [Sample_120]


title: DLBCL [Sample_112]


title: DLBCL [Sample_118]


title: DLBCL [Sample_119]


title: DLBCL [Sample_109]


title: DLBCL [Sample_108]


title: DLBCL [Sample_116]


title: DLBCL [Sample_117]


title: DLBCL [Sample_115]


title: DLBCL [Sample_104]


title: DLBCL [Sample_105]


title: DLBCL [Sample_103]


title: DLBCL [Sample_114]


title: DLBCL [Sample_113]


title: DLBCL [Sample_111]


title: DLBCL [Sample_110]


title: DLBCL [Sample_099]


title: DLBCL [Sample_107]


title: DLBCL [Sample_106]


title: Tumor290

city: Baltimore

first: Thiago

last: Vidotto

state: MD

address: 1550 Orleans St

institute: Johns Hopkins

hyb_protocol: Resuspended DNA samples were dispensed in BeadChips.

scan_protocol: Illumina HiScan was used to scan BeadChips WITH standard Illumina recommendations.

data_processing:
Subset quantile Within-Array Normalization (SWAN) normalization using minfi
MATRIX_PROCESSED FILE CONTENT: SWAN-normalized beta values

label: Cy5 and Cy3

source_name: Primary prostate tumor

label_protocol: C and G nucleotides were labeled with biotin.

extract_protocol: DNA was extracted from FFPE material using the Qiagen AllPrep FFPE DNA/RNA Kit (Qiagen). DNA concentrations were quantified with the Qubit fluorometer, using a Quant-iT dsDNA High Sensitivity Assay Kit (Invitrogen)

value: Primary prostate tumor

tag: race

value: WH


title: Tumor289


title: DLBCL [Sample_102]


title: DLBCL [Sample_101]


title: DLBCL [Sample_100]


title: DLBCL [Sample_098]


title: DLBCL [Sample_126]


title: DLBCL [Sample_097]


title: DLBCL [Sample_090]


title: DLBCL [Sample_094]


title: DLBCL [Sample_093]


title: Tumor284


title: Tumor287


title: Tumor286


title: DLBCL [Sample_087]


title: Tumor281


title: DLBCL [Sample_091]


title: Tumor285


title: DLBCL [Sample_089]


title: DLBCL [Sample_085]


title: DLBCL [Sample_084]


title: DLBCL [Sample_096]


title: Tumor283


title: Tumor282


title: DLBCL [Sample_092]


title: Tumor288


title: Tumor280


title: DLBCL [Sample_095]


title: DLBCL [Sample_086]


title: Tumor279


title: DLBCL [Sample_088]


title: DLBCL [Sample_083]


title: Tumor278


title: DLBCL [Sample_080]


title: Tumor277


title: DLBCL [Sample_082]


title: Tumor273


title: DLBCL [Sample_081]


title: DLBCL [Sample_078]


title: Tumor276


title: Tumor275


title: Tumor272


title: DLBCL [Sample_079]


title: Tumor274


title: Tumor271


title: DLBCL [Sample_076]


title: DLBCL [Sample_075]


title: Tumor270


title: Tumor269


title: Tumor267


title: Tumor268


title: DLBCL [Sample_074]


title: DLBCL [Sample_073]


title: DLBCL [Sample_070]


title: DLBCL [Sample_069]


title: Tumor264


title: Tumor266


title: DLBCL [Sample_071]


title: Tumor265


title: DLBCL [Sample_072]


title: Tumor262


title: DLBCL [Sample_077]


title: Tumor263


title: Tumor261


title: DLBCL [Sample_066]


title: DLBCL [Sample_067]


title: DLBCL [Sample_068]


title: DLBCL [Sample_064]


title: Tumor260


title: DLBCL [Sample_065]


title: DLBCL [Sample_063]


title: Tumor258


title: DLBCL [Sample_062]


title: Tumor256


title: DLBCL [Sample_060]


title: DLBCL [Sample_061]


title: Tumor255


title: DLBCL [Sample_059]


title: Tumor254


title: Tumor257


title: Tumor253


title: DLBCL [Sample_058]


title: Tumor252


title: DLBCL [Sample_056]


title: Tumor251


title: DLBCL [Sample_057]


title: Tumor249


title: DLBCL [Sample_055]


title: Tumor250


title: Tumor259


title: DLBCL [Sample_052]


title: DLBCL [Sample_053]


title: Tumor248


title: DLBCL [Sample_051]


title: DLBCL [Sample_049]


title: DLBCL [Sample_048]


title: DLBCL [Sample_050]


title: Tumor243


title: Tumor244


title: Tumor246


title: Tumor247


title: Tumor245


title: Tumor242


title: DLBCL [Sample_045]


title: DLBCL [Sample_046]


title: DLBCL [Sample_044]


title: DLBCL [Sample_047]


title: Tumor241


title: DLBCL [Sample_043]


title: DLBCL [Sample_054]


title: Tumor235


title: Tumor237


title: Tumor239


title: Tumor236


title: DLBCL [Sample_042]


title: Tumor234


title: Tumor240


title: Tumor238


title: Tumor233

value: BL


title: DLBCL [Sample_039]


title: DLBCL [Sample_041]


title: DLBCL [Sample_038]


title: DLBCL [Sample_040]


title: DLBCL [Sample_034]


title: Tumor232


title: Tumor230


title: Tumor229


title: Tumor231


title: DLBCL [Sample_033]


title: DLBCL [Sample_036]


title: DLBCL [Sample_035]


title: DLBCL [Sample_032]


title: Tumor227


title: Tumor228


title: Tumor226


title: Tumor224


title: Tumor225


title: DLBCL [Sample_030]


title: DLBCL [Sample_029]


title: Tumor221


title: DLBCL [Sample_026]


title: DLBCL [Sample_025]


title: DLBCL [Sample_031]


title: Tumor223


title: DLBCL [Sample_028]


title: Tumor219


title: DLBCL [Sample_037]


title: Tumor220


title: DLBCL [Sample_023]


title: DLBCL [Sample_022]


title: Tumor218


title: Tumor216


title: Tumor217


title: DLBCL [Sample_016]


title: DLBCL [Sample_020]


title: DLBCL [Sample_021]


title: DLBCL [Sample_017]


title: Tumor215


title: Tumor214


title: DLBCL [Sample_019]


title: DLBCL [Sample_018]


title: Tumor222


title: Tumor213


title: DLBCL [Sample_015]


title: DLBCL [Sample_027]


title: Tumor211


title: Tumor210


title: DLBCL [Sample_014]


title: Tumor209


title: DLBCL [Sample_011]


title: DLBCL [Sample_012]


title: DLBCL [Sample_010]


title: Tumor206


title: Tumor207


title: DLBCL [Sample_008]


title: DLBCL [Sample_007]


title: DLBCL [Sample_005]


title: DLBCL [Sample_006]


title: Tumor212


title: DLBCL [Sample_004]


title: Tumor204


title: Tumor203


title: Tumor202


title: Tumor198


title: DLBCL [Sample_002]


title: Tumor197


title: DLBCL [Sample_001]


title: Tumor208


title: Normal30

source_name: Benign adjacent prostate

value: Benign adjacent prostate


title: Tumor196


title: DLBCL [Sample_013]


title: Tumor205


title: DLBCL [Sample_009]


title: Tumor194


title: Tumor193


title: 10870-CovR - output - 4 - biol rep 2

city: Houston

first: William

middle: Charles

last: Shropshire

state: TX

address: 1901 East Road

institute: The University of Texas MD Anderson Cancer Center

library_source: genomic

data_processing:
Raw sequencing reads (~30-35M reads per replicate/input sample) were quality filtered, trimmed, and mapped to the reference genome MGAS10870 using CLC Genomics Workbench (v 21, Qiagen).  Peaks representing potential CovR binding were identified using the Transcription Factor ChIP-seq module of CLC Genomics Workbench. Peak shape scores and RPKL values were plotted against each other and peaks manually inspected to identify a reliable threshold for statistically significant enrichment of DNA.  Peaks with a peak shape score >30 and RPKL >500 in at least two of the samples were called as statistically significant. A gene was associated with an enriched DNA region if the peak center was within 200 bps of the promoter or the open reading frame of the gene.
Supplementary files format and content: Each worksheet contains ChIP-seq data for that sample

organism: Streptococcus pyogenes

source_name: bacteria

extract_protocol: Three biological replicates of strains MGAS10870, M3-CovS-T284A, and 10870-ΔcovR (control), respectively, were chromatin immunoprecipitated using polyclonal antibody directed against the N-terminal part of CovR. Briefly, GAS strains were grown in 40 ml THY medium to mid-exponential phase (OD~0.45), proteins were cross-linked to DNA with 1% formaldehyde, cells harvested by centrifugation, and flash-frozen and stored at -80° C. The fixed cell pellets were resuspended in 1ml ice cold lysis buffer, and the lysates were sonicated for 15 cycles (30s on/30s off) at 4° C in 1.5 ml Bioruptor tubes (Diagenode) in a Diagenode Bioruptor Plus machine set at high power, to shear DNA to fragments of 200 and 400 bp length.  The cleared supernatant was collected to use for chromatin-immunoprecipitation (950μl) or input DNA (50μl), respectively. CovR-bound DNA fragments were immunoprecipitated over night at 4°C using Dynabeads protein G (Invitrogen) pre-coated with anti-CovRND antibody.  After several washing steps, the complex was eluted with 50μl elution buffer to obtain the ChIP DNA (output) samples. Proteins and RNA in both input and ChIP samples were degraded using RNaseA and proteinase K, crosslinking was reversed by incubation at 65° C overnight, and the DNA was purified using SPRI beads (AMPure XP, Beckman Coulter) on a magnetic stand. The DNA concentration was determined on a Qubit machine 4.0 (Invitrogen) following the Qubit manual for high-sensitive DNA, and DNA fragment size distribution was assessed using Agilent D1000 Screen Tape on an Agilent 2200 TapeStation system. ChIP sequencing was performed in the Advanced Technology Genomics Core (ATGC) Facility at MD Anderson Cancer Center] with Illumina compatible indexed libraries prepared from 2-10ng of sheared ChIP or input DNA.   Equimolar quantities of the indexed libraries were multiplexed with 8 libraries per pool and sequenced on an Illumina NextSeq500 sequencer using the high output 75nt single read flow cell format.

tag: cell type

value: bacteria

tag: strain

value: CovR knockout

tag: chip antibody

value: anti-CovR-ND


title: 10870-CovR - input - 10 - input DNA

value: input


title: MGAS10870-CovS-T284A - input - 15 - input DNA

value: hyperphosphoyrlated CovR


title: Tumor201


title: 10870-CovR - output - 3 - biol rep 1


title: Tumor200


title: MGAS10870-CovS-T284A - output - 5 - biol rep 3


title: Tumor199


title: DLBCL [Sample_003]

value: Diffuse large B-cell lymphoma (DLBCL)

value: Yes

value: No


title: Tumor191


title: Tumor190


title: MGAS10870-CovS-T284A - output - 1 - biol rep 1


title: Tumor189


title: Tumor188


title: MGAS10870 - output - 3 - biol rep 1

value: WT


title: Tumor187


title: MGAS10870 - output - 4 - biol rep 2


title: Tumor185


title: Tumor186


title: Tumor184


title: Tumor195


title: WL_TXCON_R_1

city: yangzhou

first: zhenxiang

last: zhou

state: jiangsu

address: 48 Wenhui Dong Lu

department: agricultural college

country: China

institute: Yangzhou University

description:
TXCON_R_1
WL_AllSamplesFPKMValue.xlsx

data_processing:
Fastp V0.20
1. Remove the Adapter sequence;  2. Reads with low quality (mass value less than 15) whose base number exceeded 40% of the Read length ratio were removed;  3. Reads with more than 5 bases of "N" were removed;  4. From the 5 'end of Reads (i.e., the beginning of Reads), sliding window quality filtering was carried out, and the sliding window whose average base quality was lower than the threshold value (20) was cut out (sliding window size 4);  5. Reads less than 36 in length were removed after filtering.
Using Hisat2 software, select the reference genome and annotation file of barley in NCBI or ENSEMBL and find the comparison with default parameters. Then evaluate the comparison of reads (read segments) obtained by sequencing.
The number of reads for each gene is calculated by using featureCounts v1.5.0, including the SAM recounts produced by Hisat and the GTF recounts of the genome. Then the FPKM value of the gene is calculated using the formula to represent its expression, depending on the length of the exon.
Assembly: Morex v1.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Hordeum vulgare

source_name: root

extract_protocol:
After qualified RNA samples were detected, magnetic beads with Oligo(dT) were used to enrich mRNA of eukaryotes
mRNA was divided into fragments by fragmentation buffer. cDNA was synthesized by six-base random hexamers based on mRNA template. Buffer solution, dNTPs, and DNA polymerase I and RNaseH were then added to synthesize the two-strand cDNA, which was then purified using AMPure XP beads. The purified double-stranded cDNA was first end-repaired with A tail and connected with sequencing connectors, and then AMPure XPbeads were used for segment size selection. After that, USER enzyme was used to degrade the second strand of cDNA containing U, so that the final sequencing information came from the first strand cDNA, thus preserving the strand orientation of mRNA. Finally, PCR products were amplified and purified by AMPure XP beads to obtain chain specific cDNA libraries.

value: root

tag: varity

value: Waterlogging stress was carried out on barley seedlings with three leaves at one stage

tag: time

value: 0 hour


title: WL_TXCON_L_2

description:
TXCON_L_2
WL_AllSamplesFPKMValue.xlsx

source_name: leaf

value: leaf


title: Tumor183

value: Primary prostate tumor


title: WL_TXCON_L_1

description:
TXCON_L_1
WL_AllSamplesFPKMValue.xlsx


title: Tumor192


title: Tumor182


title: MGAS10870-CovS-T284A - output - 2 - biol rep 2


title: WL_TX72h_R_1

description:
TX72h_R_1
WL_AllSamplesFPKMValue.xlsx

value: 72 hours


title: Tumor179

value: BL


title: WL_TX72h_L_2

description:
TX72h_L_2
WL_AllSamplesFPKMValue.xlsx


title: MGAS10870 - input - 5 - input DNA


title: WL_TX2w_R_2

description:
TX2w_R_2
WL_AllSamplesFPKMValue.xlsx

value: two weeks


title: Tumor177


title: MGAS10870 - output - 5 - biol rep 3

value: bacteria


title: WL_TX2w_R_1

description:
TX2w_R_1
WL_AllSamplesFPKMValue.xlsx


title: WL_TX72h_L_1

description:
TX72h_L_1
WL_AllSamplesFPKMValue.xlsx


title: Tumor178


title: Tumor176


title: WL_TX2w_L_2

description:
TX2w_L_2
WL_AllSamplesFPKMValue.xlsx


title: Tumor175


title: Tumor173


title: WL_TX1h_R_2

description:
TX1h_R_2
WL_AllSamplesFPKMValue.xlsx

value: 1 hour


title: WL_TX2w_L_1

description:
TX2w_L_1
WL_AllSamplesFPKMValue.xlsx


title: WL_TX1h_R_1

description:
TX1h_R_1
WL_AllSamplesFPKMValue.xlsx


title: WL_TX72h_R_2

description:
TX72h_R_2
WL_AllSamplesFPKMValue.xlsx


title: Tumor181


title: Tumor172


title: Tumor180


title: Tumor171


title: Tumor170


title: WL_TX1h_L_1

description:
TX1h_L_1
WL_AllSamplesFPKMValue.xlsx


title: WL_NNCON_R_2

description:
NNCON_R_2
WL_AllSamplesFPKMValue.xlsx

value: Nasonijo


title: WL_NNCON_R_1

description:
NNCON_R_1
WL_AllSamplesFPKMValue.xlsx


title: Tumor167

value: WH


title: Tumor168


title: Tumor164


title: Tumor165


title: WL_NNCON_L_1

description:
NNCON_L_1
WL_AllSamplesFPKMValue.xlsx


title: Tumor174


title: WL_NN72h_L_2

description:
NN72h_L_2
WL_AllSamplesFPKMValue.xlsx


title: WL_NN72h_R_1

description:
NN72h_R_1
WL_AllSamplesFPKMValue.xlsx


title: WL_NN72h_L_1

description:
NN72h_L_1
WL_AllSamplesFPKMValue.xlsx


title: Tumor162


title: WL_NN2w_R_2

description:
NN2w_R_2
WL_AllSamplesFPKMValue.xlsx


title: Tumor161


title: Tumor160


title: WL_NNCON_L_2

description:
NNCON_L_2
WL_AllSamplesFPKMValue.xlsx


title: Tumor169


title: Tumor158


title: WL_NN2w_L_1

description:
NN2w_L_1
WL_AllSamplesFPKMValue.xlsx


title: Tumor159


title: WL_NN72h_R_2

description:
NN72h_R_2
WL_AllSamplesFPKMValue.xlsx


title: WL_NN2w_L_2

description:
NN2w_L_2
WL_AllSamplesFPKMValue.xlsx


title: WL_TX1h_L_2

description:
TX1h_L_2
WL_AllSamplesFPKMValue.xlsx


title: WL_NN1h_R_2

description:
NN1h_R_2
WL_AllSamplesFPKMValue.xlsx


title: Tumor157


title: WL_NN1h_R_1

description:
NN1h_R_1
WL_AllSamplesFPKMValue.xlsx


title: Tumor156


title: Tumor166


title: Tumor163


title: Tumor152


title: Salt_TXCON_R_1

description:
TXCON_R_1
Salt_AllSamplesFPKMValue.xlsx

value: Salt stress was carried out on barley seedlings with three leaves at one stage


title: Tumor155


title: Salt_TXCON_R_2

description:
TXCON_R_2
Salt_AllSamplesFPKMValue.xlsx


title: Tumor151


title: WL_NN1h_L_2

description:
NN1h_L_2
WL_AllSamplesFPKMValue.xlsx


title: Tumor154


title: WL_NN1h_L_1

description:
NN1h_L_1
WL_AllSamplesFPKMValue.xlsx


title: Tumor153


title: Tumor150


title: Tumor149


title: Salt_TX24h_R_2

description:
TX24h_R_2
Salt_AllSamplesFPKMValue.xlsx

value: 24 hours


title: WL_NN2w_R_1

description:
NN2w_R_1
WL_AllSamplesFPKMValue.xlsx


title: Salt_TXCON_L_1

description:
TXCON_L_1
Salt_AllSamplesFPKMValue.xlsx


title: Salt_TX24h_R_1

description:
TX24h_R_1
Salt_AllSamplesFPKMValue.xlsx


title: Tumor148


title: Tumor147


title: Salt_TX24h_L_2

description:
TX24h_L_2
Salt_AllSamplesFPKMValue.xlsx


title: Salt_TX10D_R_1

description:
TX10D_R_1
Salt_AllSamplesFPKMValue.xlsx

value: 10 days


title: Salt_TX24h_L_1

description:
TX24h_L_1
Salt_AllSamplesFPKMValue.xlsx


title: Tumor144


title: Salt_TX10D_L_2

description:
TX10D_L_2
Salt_AllSamplesFPKMValue.xlsx


title: Tumor143


title: Tumor146


title: Salt_TX10D_L_1

description:
TX10D_L_1
Salt_AllSamplesFPKMValue.xlsx


title: Tumor145


title: Salt_TX10D_R_2

description:
TX10D_R_2
Salt_AllSamplesFPKMValue.xlsx


title: Salt_TXCON_L_2

description:
TXCON_L_2
Salt_AllSamplesFPKMValue.xlsx


title: Tumor140


title: Salt_TX1h_R_2

description:
TX1h_R_2
Salt_AllSamplesFPKMValue.xlsx


title: WL_TXCON_R_2

description:
TXCON_R_2
WL_AllSamplesFPKMValue.xlsx


title: Tumor142


title: Salt_TX1h_L_2

description:
TX1h_L_2
Salt_AllSamplesFPKMValue.xlsx


title: Tumor138


title: Tumor136


title: Tumor134


title: Tumor133


title: Salt_NNCON_L_1

description:
NNCON_L_1
Salt_AllSamplesFPKMValue.xlsx


title: Salt_NN24h_R_2

description:
NN24h_R_2
Salt_AllSamplesFPKMValue.xlsx


title: Tumor131


title: Salt_NN10D_R_2

description:
NN10D_R_2
Salt_AllSamplesFPKMValue.xlsx


title: Salt_TX1h_R_1

description:
TX1h_R_1
Salt_AllSamplesFPKMValue.xlsx


title: Tumor139


title: Salt_TX1h_L_1

description:
TX1h_L_1
Salt_AllSamplesFPKMValue.xlsx


title: Salt_NNCON_R_2

description:
NNCON_R_2
Salt_AllSamplesFPKMValue.xlsx


title: Salt_NNCON_L_2

description:
NNCON_L_2
Salt_AllSamplesFPKMValue.xlsx


title: Salt_NNCON_R_1

description:
NNCON_R_1
Salt_AllSamplesFPKMValue.xlsx


title: Tumor125


title: Salt_NN10D_L_1

description:
NN10D_L_1
Salt_AllSamplesFPKMValue.xlsx


title: Tumor135


title: Tumor130


title: Tumor124


title: Salt_NN24h_R_1

description:
NN24h_R_1
Salt_AllSamplesFPKMValue.xlsx


title: Tumor132


title: Salt_NN1h_L_2

description:
NN1h_L_2
Salt_AllSamplesFPKMValue.xlsx


title: Salt_NN24h_L_1

description:
NN24h_L_1
Salt_AllSamplesFPKMValue.xlsx


title: Salt_NN1h_L_1

description:
NN1h_L_1
Salt_AllSamplesFPKMValue.xlsx


title: 18_M4_24_NoRad

city: Belfast

first: Thomas

last: Cahill

address: 19 Chlorine Gardens

country: United Kingdom

institute: Queens university Belfast

data_processing:
Sequence quality was assessed with FastQC to identify over-represented sequences and low quality reads
Low quality reads and over-represented sequences were removed with Cutadapt
The STAR aligner was utilised to align the RNA-Seq reads to the zebrafish genome (GRCz11)
HTSeq was used to determine the number of reads per transcript
DESeq2 was used for determination of differentially expressed genes
Assembly: zebrafish genome (GRCz11)

source_name: Muscle

extract_protocol:
Total mRNA was extracted from liver tissue of the zebrafish using Qiagen’s miRNeasy Mini kit (Qiagen, Hilden, Germany).
To prepare mRNA seq kit (poly A capture, KAPA RNA hyper)(Illumina, San Diego, CA, USA);  was utilized; 100ng of total input muscle RNA was used in accordance with the manufacturer’s protocol.
High through-put RNA sequencing (RNAseq) was performed at the Queens University Belfast, Genomics Core Technology Unit on an Illumina Next SEQ 2000 instruments with the mRNA library sequenced to a minimum depth of 50 million reads using forward stranded  PE50 strategy.

treatment_protocol: A melatonin group (28.5- melatonin) received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group (18.5-Ctrl) received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group (18.5-mel) was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin. A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.

value: Muscle

tag: condition

value: Torpor

tag: radiation (cgy)

tag: temperature (c)

tag: melatonin (um)


title: Tumor141


title: Salt_NN1h_R_1

description:
NN1h_R_1
Salt_AllSamplesFPKMValue.xlsx

value: root

tag: treatment


title: Tumor129


title: Tumor128


title: Salt_NN10D_R_1

description:
NN10D_R_1
Salt_AllSamplesFPKMValue.xlsx


title: 18_F1_24_Rad

value: Torpor+radiation


title: 18_M1_24_Rad


title: Tumor118


title: Tumor127


title: Tumor117


title: Salt_NN10D_L_2

description:
NN10D_L_2
Salt_AllSamplesFPKMValue.xlsx


title: Tumor126


title: Salt_NN1h_R_2

description:
NN1h_R_2
Salt_AllSamplesFPKMValue.xlsx


title: Tumor137


title: Salt_NN24h_L_2

description:
NN24h_L_2
Salt_AllSamplesFPKMValue.xlsx


title: Tumor113


title: Tumor115


title: Tumor112


title: Tumor114


title: ll8

city: Jouy-en-Josas

first: Sandrine

last: Le Guillou

address: Domaine de Vilvert Bat.440

department: Animal Genetics

country: France

institute: INRAE

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
After adapters cleaning and filtering for their size (17-28 nt) with Cutadapt, the RNA-seq data were analysed using miRDeep2 software, with bovine reference genome bosTau8 and miRBase release 22 (all species). The quantification results generated by the quantifier.pl miRDeep2 module were filtered with a custom perl script parse_miRDeep2_outputs.pl
Assembly: bosTau8

organism: Bos taurus

source_name: whole milk

extract_protocol: Small RNA-Seq librairies were generated from NA to 200ng of total RNA (or from --- ng of purified small RNA fraction) using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer's instructions. The protocol takes advantage of the natural structure common to most microRNA molecules that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3' RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5' RNA adapter. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 15 sec at 72oC] x 13 cycles; 10 min at 72oC) to create cDNA constructs. Amplified cDNA constructs of 140 to 160 nt were selectively isolated by acrylamide gel purification followed by ethanol precipitation.  The final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: breed

value: Holstein

tag: group

value: After 5 days of feed restriction trial of moderate intensity


title: Tumor123

value: Primary prostate tumor


title: Tumor122


title: Tumor121


title: Tumor110


title: 18_M3_24_NoRad


title: Tumor108


title: Tumor120


title: Tumor106


title: Tumor119


title: 28.5_F3_Ctrl_NoRad

value: Control


title: 18_M2_24_Rad


title: Tumor116


title: ll2


title: 28.5_F7_Ctrl_NoRad


title: 28.5_F1_Ctrl_Rad

value: Radiation


title: ll1


title: lg8

source_name: milk fat globules


title: 28.5_F2_Ctrl_Rad


title: Tumor102

value: BL


title: 28.5_F7_Ctrl_Rad


title: Tumor111


title: ll7


title: ll5


title: Tumor109


title: ll6


title: Tumor107


title: ll3


title: Tumor100


title: ll4


title: Tumor99


title: Tumor103


title: Tumor105


title: lg6


title: lg2


title: lg3


title: Tumor101


title: lg5


title: Tumor95


title: Tumor96


title: lg1


title: Tumor98


title: lg4


title: lc5

source_name: exfoliated mammary epithelial cells in milk


title: Tumor104


title: Tumor92


title: lc8


title: lg7


title: lc7


title: Tumor88


title: lc2


title: Tumor94


title: Tumor87


title: lc1


title: lc6


title: Tumor93


title: Tumor91


title: lc4


title: lc3


title: Tumor90


title: Tumor89


title: Tumor97


title: cl8

value: After 5 days of feed restriction trial of high intensity


title: Tumor85


title: Tumor84


title: cl6


title: cl7


title: Tumor86


title: cl4


title: cg4


title: Tumor83


title: Tumor82


title: cl2


title: cl3


title: Tumor80


title: cl1


title: cg8


title: Tumor81


title: Tumor79


title: Tumor78


title: cg7


title: cg6


title: ce8

source_name: milk extracellular vesicles


title: Tumor71


title: Tumor77


title: cg5


title: Tumor76


title: Tumor75


title: ce6


title: Tumor74


title: cg3


title: cg2


title: cg1


title: Tumor68


title: ce7


title: Tumor73


title: Tumor72


title: Tumor70


title: ce1


title: cl5


title: ce2


title: Tumor69


title: ce5


title: Tumor65


title: Tumor67


title: ce4


title: Tumor66


title: ce3


title: Tumor64


title: Tumor63


title: LL5

value: Before initiation of feed restriction trial of moderate intensity


title: LL6


title: LL7


title: Tumor59


title: Tumor61


title: Tumor60


title: Tumor58


title: LL2


title: LL3


title: Tumor56


title: LL4


title: LL1


title: LG8


title: Tumor57


title: Tumor55


title: Tumor53


title: LG7


title: Tumor54


title: LG6


title: Tumor52


title: Tumor62


title: LL8


title: LG4


title: LG3


title: Tumor51


title: LG5


title: Tumor50


title: LG2


title: Tumor49


title: LC8


title: Tumor48


title: Tumor47


title: Tumor46


title: Tumor45


title: Tumor44


title: LC4


title: LC5


title: LC6


title: LC7


title: LC3


title: LC2


title: CL8

value: Before initiation of feed restriction trial of high intensity


title: LC1


title: CL6


title: CL7


title: Tumor39

value: WH


title: CL5


title: Tumor38


title: Tumor42


title: Tumor40


title: Tumor41


title: Tumor37


title: Tumor35


title: LG1


title: Tumor36


title: Tumor33


title: CL3


title: Tumor32


title: Tumor43


title: Tumor31


title: Tumor30


title: CG7


title: Tumor29


title: Tumor28


title: CG5


title: Tumor27


title: CG4


title: CL4


title: Tumor26


title: CG2


title: CG3


title: CG1


title: Tumor23


title: CL2


title: CE6


title: Tumor24


title: CE7


title: CL1


title: Tumor21


title: Tumor19


title: CG8


title: Tumor34


title: CG6


title: Tumor18


title: Tumor20


title: CE2


title: CE1


title: Tumor16


title: Tumor25


title: Tumor17


title: Tumor22


title: Tumor15


title: CE8


title: Tumor14


title: Tumor13


title: Tumor11


title: HS-PSS/3xFLAG-PRRX1A/3xHA-TOP2A, Doxycycline negative, replicate 1

city: Okayama

first: Takeshi

last: Takarada

country: Japan

institute: Okayama University

data_processing:
Fastp (version 0.23.2) was used to remove adapters and filter raw reads of < 60 bases in addition to leading and trailing bases with a read quality of less than 30.
Filtered reads were mapped to hg19 using HISAT2 (v2.2.1).
Raw counts for each gene were based on sense-strand data obtained using featureCounts software from the Subread package.
Assembly: hg19
Supplementary files format and content: Tab-delimited txt file represents feature counts

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
Sequencing libraries were KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) and SeqCap Adapter Kit (Set A or Set B, Roche) following manufacture`s instruction. The initial amount of total RNA was 1000 ng.

treatment_protocol: HS-PSS/3xHA-TOP2A, HS-PSS/3xFLAG-PRRX1A or HS-PSS/3xFLAG-PRRX1A/3xHA-TOP2A cells were treated with 1 mg/ml doxycycline, and then total RNA samples were extracted.

value: MPNST cell

tag: cell line

value: HS-PSS

value: Doxycycline negative


title: Tumor10


title: Tumor12


title: CE4


title: HS-PSS/3xFLAG-PRRX1A/3xHA-TOP2A, Doxycycline positive, replicate 2

value: Doxycycline positive


title: HS-PSS/3xFLAG-PRRX1A/3xHA-TOP2A, Doxycycline positive, replicate 1


title: CE5


title: neural stem cell, siSCR

city: shanghai

first: Ximing

last: Nian

state: Shanghai

address: Chongqing Nanlu 227

institute: Shanghai Jiao Tong University

data_processing:
RNA from NSCs following treatments with scrambled or Chd4 siRNAs were subjected to 50-bp single-end sequencing with a BGISEQ-500 sequencer
At least 20 million clean reads of sequencing depth were obtained for each sample
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes fpk, tpm, read_count values for each Sample

organism: Mus musculus

source_name: neural stem cell

extract_protocol:
Total RNA fraction was extracted using Eastep®Super Total RNA Extraction Kit (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: neural stem cell

value: control

value: transfection with scrambled  siRNA


title: Tumor9


title: HS-PSS/3xFLAG-PRRX1A/3xHA-TOP2A, Doxycycline negative, replicate 2


title: 3xHA-TOP2A, Doxycycline positive, replicate 2


title: 3xHA-TOP2A, Doxycycline positive, replicate 1


title: Tumor8


title: 3xFLAG-PRRX1A, Doxycycline positive, replicate 2


title: 3xHA-TOP2A, Doxycycline negative, replicate 2


title: Tumor5


title: CE3

value: Holstein


title: Tumor6


title: Tumor7


title: 3xHA-TOP2A, Doxycycline negative, replicate 1


title: neural stem cell, siChd4

value: Chd4 knockdown

value: transfection with Chd4  siRNA


title: Tumor3

value: Primary prostate tumor


title: 3xFLAG-PRRX1A, Doxycycline positive, replicate 1


title: Tumor4


title: 3xFLAG-PRRX1A, Doxycycline negative, replicate 1


title: 3xFLAG-PRRX1A, Doxycycline negative, replicate 2


title: Tumor2


title: Normal29

value: Benign adjacent prostate


title: Normal26

value: BL


title: Normal25


title: Tumor1


title: Normal24


title: Normal23


title: Normal22


title: Normal20


title: Normal21


title: Normal19


title: Normal18


title: PTC3

city: Changsha

first: Pei

last: Chen

state: Hunan

address: Xiangya Road No.88

institute: Xiangya Hospital, Central South University of China

data_processing:
Sequencing based on DNBSEQ platform of MGI
Filter out low quality, splice contamination, and reads with too much unknown base N content
The clean reads were aligned to the reference gene sequences using Bowtie2, after which the expression levels of the genes and transcripts were calculated using RSEM
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values, gene ID, gene symbol, chromosome start and end points for each sample

source_name: thyroid

extract_protocol:
RNA was harvested using TRIZOL (Invitrogen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: thyroid

tag: patient diagnosis

value: papillary thyroid cancer

value: primary tumor


title: P2-LNM

source_name: lymph node

tag: tissue

value: lymph node

value: lymph node metastasis of papillary thyroid cancer


title: PTC2


title: P3-LNM


title: Normal17


title: Normal27

value: WH


title: P1-LNM


title: PTC1


title: Normal16


title: Normal28


title: Normal15


title: Normal14


title: Normal12


title: Normal13


title: Normal8


title: Normal9


title: Mut pga rep3

city: Wuhan

first: Qiuhong

last: Zhang

address: No. 1, Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Data filtering and quality control were performed by Trimmomatic and FastQC to remove reads with an average quality score below Q20.
Mapping of high-quality sequences based on the Burrows-Wheeler method to the A. pleuropneumoniae 4074 genome (NZ_CP029003.1).
The RPKM (Reads per Kilobase per Million Reads) value was used as the index of gene expression.
Assembly: Actinobacillus pleuropneumoniae serovar 1 str. 4074 (NZ_CP029003.1)/ASM17849v2
Supplementary files format and content: reads counts and RPKM values for each sample

source_name: Bacterial culture

growth_protocol: Strains WT and Δpga were cultured to mid-log phase at 37°C  with shaking (WT_PK) or in static status (WT_BF, Δpga).

extract_protocol:
Total RNA was isolated from strains WT and Δpga cultured to mid-log phase supplemented with shaking or in static status. Total RNA was extracted using Trizol lysis according to the protocol recommended by the manufacturer (Total RNA Extraction Kit, Tianmo Biotech, Beijing, China), with three replicates per condition group.
Illumina PE RNA libraries for RNA-seq were prepared using IlluminaTruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol: Cultured with shaking or in static status

value: Bacterial culture

value: serovar 1 str. 4074

tag: genotype

value: pgaABCD operon deletion mutant

value: cultured in microplates in static status


title: Normal11

tag: race


title: Normal10


title: Normal6


title: Normal7


title: Mut pga rep2

organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074


title: Mut pga rep1


title: Normal aortic valve tissue 1

type: RNA

city: Shanghai

first: Guokun

last: Wang

address: 168 Changhai Road

institute: Changhai Hospital

description:
978364
Expression data from normal aortic valve tissues.

hyb_protocol: The microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, following fragmentation and biotin labeling, the 2nd cycle cDNAs were hybridized onto the microarray. After washing and staining, the arrays were scanned.

scan_protocol: Scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded separately.

source_name: Normal aortic valve tissue

label_protocol: The sample labeling was performed based on the manufacturer’s standard protocol. Briefly, total RNAs were transcribed to double strand cDNAs and then synthesized cRNAs. Next, 2nd cycle cDNAs were synthesized from cRNAs, followed by fragmentation and biotin labeling.

extract_protocol: Total RNA was extracted using RNAiso (TaKaRa, Dalian, China).

treatment_protocol: The collected aortic valve tissues were washed in RNase-free PBS, and stored in liquid nitrogen.

value: Normal aortic valves

tag: gender

value: Male

tag: age

value: 58 years


title: OE19 gastric cancer cell line grown in 2D condition (replicate 3)

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Hybridization was performed according to manufacturer’s standard protocols.

scan_protocol: Gene microarrays were scanned with the Gene Chip System 3000 scanner

data_processing: Raw CEL files were imported in R and pre-processed using the robust multi-array average method implemented in the oligo Bioconductor package

label: Biotin

source_name: OE19 gastric cancer cell line

label_protocol: RNA was labeled and processed according to manufacturer’s recommended protocols.

growth_protocol: HER2+ gastrospheres were cultured in 3D conditions for 7 days as described in Jiang J, Oncogene, 2012. HER2+ GC cells were cultured in 2D conditions in RPMI 1640 with 10% FBS

extract_protocol: Total RNA from HER2+ GC OE19 and N87 cells was extracted using Qiazol (Qiagen).


title: OE19 gastric cancer cell line grown in 3D condition (replicate 1)


title: Calcified aortic valve tissue 2

description:
978288
Expression data from calcified aortic valve tissues.

source_name: Calcified aortic valve tissue

value: Calcified aortic valves

value: 63 years


title: OE19 gastric cancer cell line grown in 2D condition (replicate 1)


title: OE19 gastric cancer cell line grown in 2D condition (replicate 2)


title: Normal aortic valve tissue 2

description:
Normal
Expression data from normal aortic valve tissues.

value: 56 years


title: OE19 gastric cancer cell line grown in 3D condition (replicate 2)


title: WT_BF rep2

tag: strain

value: wild type


title: Calcified aortic valve tissue 1

description:
595700
Expression data from calcified aortic valve tissues.

value: 61 years


title: WT_PK rep3

value: cultured in bottles with shaking


title: Normal5

value: Benign adjacent prostate

value: BL


title: N87 gastric cancer cell line grown in 2D condition (replicate 3)

source_name: N87 gastric cancer cell line


title: Normal4

source_name: Benign adjacent prostate


title: WT_PK rep2


title: N87 gastric cancer cell line grown in 3D condition (replicate 1)


title: Normal3


title: OE19 gastric cancer cell line grown in 3D condition (replicate 3)


title: WT_BF rep1


title: N87 gastric cancer cell line grown in 2D condition (replicate 1)


title: WT_PK rep1


title: Microbiota of Stool from patient MC11 [GM9]

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM9

data_processing:
demultiplexing from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
quality check qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
quality trimming, pair merging and ASV table creation (SALIVA) qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 10 --p-trim-left-r 0 --p-trunc-len-f 268 --p-trunc-len-r 194 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 10
quality trimming, pair merging and ASV table creation (STOOL) qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 261 --p-trunc-len-r 185 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 10
taxonomic assignment (RDP) qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
R phyloseq package (see https://github.com/matteoramazzotti/papers)
Assembly: NA
Supplementary files format and content: feature_table_stool.csv: CSV text file containing the abundance table of stool samples
Supplementary files format and content: taxonomy_stool.tsv: TSV text file containing the complete taxonomic classification of the reference sequence (rows of stool feature tables)
Supplementary files format and content: feature_table_saliva.csv: CSV text file containing the abundance table of saliva samples
Supplementary files format and content: taxonomy_saliva.tsv: TSV containing the complete taxonomic classification of the reference sequence (rows of saliva feature tables)
Supplementary files format and content: dna_sequences_stool.fasta: fasta file containing the reference sequences used for taxonomy classification of stool samples
Supplementary files format and content: dna_sequences_saliva.fasta: fasta file containing the reference sequences used for taxonomy classification of saliva samples
Library strategy: paired-end (2x300) amplicon sequencing

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Stool

tag: patient id

tag: time point

value: Untreated


title: WT_BF rep3

value: Bacterial culture


title: Normal1

value: WH


title: N87 gastric cancer cell line grown in 3D condition (replicate 2)


title: N87 gastric cancer cell line grown in 2D condition (replicate 2)


title: Microbiota of Stool from patient MC9 [GM7]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM7

tag: condition


title: N87 gastric cancer cell line grown in 3D condition (replicate 3)


title: Microbiota of Stool from patient MC10 [GM8]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM8


title: Microbiota of Stool from patient MC7 [GM6]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM6


title: Microbiota of Stool from patient MC45 [GM47]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM47

value: Placebo


title: Microbiota of Stool from patient MC45 [GM46]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM46


title: Microbiota of Stool from patient MC6 [GM5]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM5


title: Dec [DL12-2]

city: Hangzhou

first: Hengfu

last: Yin

state: Zhejiang

address: Daqiao 73

institute: Research Institute of Subtropical Forestry, Chinese Academy of Forestry

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to Camellia japonica using HISAT2 v2.1.0
Read count extraction and normalization were performed using StringTie V1.3.6
Assembly: Camellia japonica
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Camellia azalea

source_name: young leaf

extract_protocol:
The total RNA extractions were used RNAprep Pure Plant Kit (for Polysaccharides and Polyphenolics-rich; Cat. DP441, Tiangen, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: young leaf


title: Nov [DL11-2]


title: Dec [DL12-3]


title: Nov [DL11-1]


title: Oct [DL10-1]


title: Dec [DL12-1]


title: Oct [DL10-3]


title: Nov [DL11-3]


title: Microbiota of Stool from patient MC39 [GM44]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM44

value: Treated


title: Microbiota of Stool from patient MC45 [GM48]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM48


title: Sep [DL9-1]


title: Oct [DL10-2]


title: Microbiota of Stool from patient MC23 [GM42]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM42


title: Sep [DL9-2]


title: Aug [DL8-2]


title: Microbiota of Stool from patient MC39 [GM45]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM45


title: Microbiota of Stool from patient MC23 [GM40]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM40


title: Microbiota of Stool from patient MC39 [GM43]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM43


title: Aug [DL8-3]


title: Microbiota of Stool from patient MC23 [GM41]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM41


title: Aug [DL8-1]


title: Microbiota of Stool from patient MC5 [GM4]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM4


title: Jul [DL7-3]


title: Jul [DL7-2]


title: Jul [DL7-1]


title: Microbiota of Stool from patient MC15 [GM37]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM37


title: Microbiota of Stool from patient MC14 [GM34]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM34


title: Microbiota of Stool from patient MC14 [GM36]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM36


title: Microbiota of Stool from patient MC15 [GM38]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM38


title: Sep [DL9-3]


title: Jun [DL6-1]


title: Jun [DL6-3]


title: Jun [DL6-2]


title: May [DL5-2]


title: Microbiota of Stool from patient MC14 [GM35]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM35


title: Microbiota of Stool from patient MC15 [GM39]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM39


title: May [DL5-1]


title: May [DL5-3]


title: Microbiota of Stool from patient MC8 [GM31]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM31


title: Microbiota of Stool from patient MC8 [GM32]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM32


title: Apr [DL4-3]


title: Microbiota of Stool from patient MC56 [GM30]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM30


title: Apr [DL4-2]


title: Microbiota of Stool from patient MC50 [GM28]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM28


title: Microbiota of Stool from patient MC47 [GM27]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM27


title: Microbiota of Stool from patient MC52 [GM29]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM29


title: Apr [DL4-1]


title: Microbiota of Stool from patient MC3 [GM3]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM3


title: Microbiota of Stool from patient MC40 [GM26]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM26


title: Microbiota of Stool from patient MC8 [GM33]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM33


title: Mar [DL3-3]


title: Microbiota of Stool from patient MC36 [GM24]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM24


title: Mar [DL3-2]


title: Mar [DL3-1]


title: Jan [DL1-3]


title: Microbiota of Stool from patient MC34 [GM22]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM22


title: Feb [DL2-3]


title: Jan [DL1-2]


title: Microbiota of Stool from patient MC37 [GM25]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM25


title: Feb [DL2-2]


title: Feb [DL2-1]


title: Microbiota of Stool from patient MC28 [GM19]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM19


title: Microbiota of Stool from patient MC22 [GM17]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM17


title: FB-3 [E43]

organism: Camellia japonica

source_name: flower bud

value: flower bud


title: FB-2 [E42]


title: Microbiota of Stool from patient MC35 [GM23]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM23


title: Microbiota of Stool from patient MC21 [GM16]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM16


title: FB-2 [E40]


title: Microbiota of Stool from patient MC30 [GM21]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM21


title: Jan [DL1-1]


title: Microbiota of Stool from patient MC29 [GM20]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM20


title: FB-3 [E45]


title: Microbiota of Stool from patient MC2 [GM2]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM2


title: FB-3 [E44]


title: Microbiota of Stool from patient MC17 [GM13]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM13


title: Microbiota of Stool from patient MC12 [GM10]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM10


title: Microbiota of Stool from patient MC25 [GM18]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM18


title: FB-2 [E41]


title: FB-1 [E39]


title: Microbiota of Stool from patient MC20 [GM15]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM15


title: Microbiota of Stool from patient Healthy_33 [FL9]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
FL9

value: Healthy


title: Nov [E33]


title: Nov [E31]


title: Nov [E32]


title: FB-1 [E37]


title: Microbiota of Stool from patient MC18 [GM14]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM14


title: FB-1 [E38]


title: Microbiota of Stool from patient MC16 [GM12]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM12


title: Dec [E36]


title: Microbiota of Stool from patient Healthy_35 [FL15]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
FL15


title: Microbiota of Stool from patient Healthy_34 [FL11]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
FL11


title: Microbiota of Stool from patient MC13 [GM11]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM11


title: Dec [E34]


title: Z.Y.W. INAD

city: Huzhou

first: yongxue

last: lv

address: No. 2 East Street

institute: Huzhou Maternity & Child Health Care Hospital

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Chromosome Analysis Suite software (Affymetrix GeneChip Convert Console, Santa Clara, USA) and Chromosome Analysis Suite Version 2.0.0.. Log2 ratio and B Allele Frequency (BAF) values were plotted along chromosomal coordinates, allowing the detection of both copy number changes and copy neutral regions of homozygosity (ROH). The size threshold for CNVs analysis was set at > 50 kb for gains, > 25 kb for losses, and > 10 Mb for loss of heterozygosity. Data interpretation followed the ACMG guideline.

source_name: peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total genomic DNA was isolated by using QIAamp® DNA Blood Mini Kit (Qiagen GmbH, Germany) according to the manufacturer’s protocol.

tag: disease state

value: INAD


title: Microbiota of Stool from patient MC1 [GM1]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
GM1


title: Microbiota of Stool from patient Healthy_30 [FL1]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
FL1


title: Dec [E35]


title: Microbiota of Stool from patient Healthy_29 [EN48]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN48


title: Microbiota of Stool from patient Healthy_32 [FL5]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
FL5


title: Microbiota of Stool from patient Healthy_28 [EN47]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN47


title: Oct [E30]


title: Microbiota of Stool from patient Healthy_31 [FL3]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
FL3


title: Aug [E23]


title: Microbiota of Stool from patient Healthy_26 [EN44]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN44


title: Aug [E22]


title: Jul [E21]


title: Jul [E20]


title: Sep [E26]


title: Sep [E27]


title: Oct [E28]


title: Microbiota of Stool from patient Healthy_27 [EN46]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN46


title: Sep [E25]


title: Normal2


title: Aug [E24]


title: Jun [E17]


title: Microbiota of Stool from patient Healthy_19 [EN29]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN29


title: Oct [E29]


title: Microbiota of Stool from patient Healthy_25 [EN43]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN43


title: Microbiota of Stool from patient Healthy_18 [EN28]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN28


title: May [E15]


title: Microbiota of Saliva from patient Healthy_10 [GM99]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM99

source_name: Saliva

value: Saliva


title: May [E13]


title: Microbiota of Stool from patient Healthy_24 [EN41]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN41


title: Microbiota of Stool from patient Healthy_23 [EN40]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN40


title: Microbiota of Stool from patient Healthy_21 [EN34]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN34


title: Microbiota of Saliva from patient Healthy_9 [GM98]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM98


title: Jul [E19]


title: Microbiota of Stool from patient Healthy_22 [EN38]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN38


title: Microbiota of Stool from patient Healthy_20 [EN30]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN30


title: Jun [E18]


title: Apr [E11]


title: Apr [E10]


title: Microbiota of Saliva from patient Healthy_6 [GM95]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM95


title: Mar [E8]


title: Microbiota of Saliva from patient Healthy_5 [GM94]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM94


title: Jun [E16]


title: May [E14]


title: Microbiota of Stool from patient Healthy_17 [EN13]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN13


title: Microbiota of Stool from patient Healthy_16 [EN11]

description:
16s rRNA v3-v4 sequencing of human Stool
feature_table_stool.csv
EN11


title: Microbiota of Saliva from patient Healthy_8 [GM97]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM97


title: Microbiota of Saliva from patient Healthy_7 [GM96]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM96


title: Apr [E12]


title: Microbiota of Saliva from patient Healthy_2 [GM91]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM91


title: Feb [E5]


title: Mar [E7]


title: Microbiota of Saliva from patient MC58 [GM89]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM89


title: Jan [E1]


title: Microbiota of Saliva from patient Healthy_3 [GM92]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM92


title: Feb [E6]


title: Microbiota of Saliva from patient MC54 [GM85]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM85


title: Microbiota of Saliva from patient MC56 [GM87]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM87


title: Mar [E9]


title: Jan [E3]


title: Microbiota of Saliva from patient MC54 [GM84]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM84


title: Microbiota of Saliva from patient MC52 [GM82]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM82


title: Feb [E4]


title: Microbiota of Saliva from patient MC48 [GM80]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM80


title: Microbiota of Saliva from patient MC54 [GM83]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM83


title: Microbiota of Saliva from patient MC57 [GM88]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM88


title: Jan [E2]


title: Microbiota of Saliva from patient MC48 [GM78]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM78


title: Microbiota of Saliva from patient MC48 [GM79]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM79


title: Microbiota of Saliva from patient Healthy_4 [GM93]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM93


title: Microbiota of Saliva from patient MC47 [GM77]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM77


title: Microbiota of Saliva from patient MC39 [GM72]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM72


title: Microbiota of Saliva from patient MC49 [GM81]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM81


title: Microbiota of Saliva from patient MC45 [GM76]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM76


title: Microbiota of Saliva from patient MC42 [GM75]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM75


title: Microbiota of Saliva from patient MC36 [GM71]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM71


title: Microbiota of Saliva from patient Healthy_1 [GM90]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM90


title: Microbiota of Saliva from patient MC39 [GM73]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM73


title: Microbiota of Saliva from patient MC55 [GM86]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM86


title: Microbiota of Saliva from patient MC32 [GM69]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM69


title: Microbiota of Saliva from patient MC29 [GM67]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM67


title: Microbiota of Saliva from patient MC31 [GM68]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM68


title: Microbiota of Saliva from patient MC33 [GM70]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM70


title: Microbiota of Saliva from patient MC26 [GM65]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM65


title: Microbiota of Saliva from patient MC25 [GM64]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM64


title: Microbiota of Saliva from patient MC24 [GM63]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM63


title: Microbiota of Saliva from patient MC23 [GM62]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM62


title: Microbiota of Saliva from patient MC22 [GM61]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM61


title: Microbiota of Saliva from patient MC20 [GM59]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM59


title: Microbiota of Saliva from patient MC16 [GM56]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM56


title: Microbiota of Saliva from patient MC19 [GM58]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM58


title: Microbiota of Saliva from patient MC12 [GM54]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM54


title: Microbiota of Saliva from patient MC18 [GM57]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM57


title: Microbiota of Saliva from patient MC9 [GM53]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM53


title: Microbiota of Saliva from patient MC13 [GM55]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM55


title: Microbiota of Saliva from patient MC4 [GM51]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM51


title: Microbiota of Saliva from patient MC3 [GM50]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM50


title: Microbiota of Saliva from patient MC2 [GM49]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM49


title: Microbiota of Saliva from patient MC37 [GM136]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM136


title: Microbiota of Saliva from patient MC37 [GM135]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM135


title: Microbiota of Saliva from patient MC35 [GM132]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM132


title: Microbiota of Saliva from patient MC35 [GM134]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM134


title: Microbiota of Saliva from patient MC34 [GM130]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM130


title: Microbiota of Saliva from patient MC34 [GM131]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM131


title: Microbiota of Saliva from patient MC27 [GM66]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM66


title: Microbiota of Saliva from patient MC34 [GM129]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM129


title: Microbiota of Saliva from patient MC21 [GM60]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM60


title: Microbiota of Saliva from patient MC30 [GM127]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM127


title: Microbiota of Saliva from patient MC28 [GM125]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM125


title: Microbiota of Saliva from patient MC28 [GM124]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM124


title: Microbiota of Saliva from patient MC30 [GM126]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM126


title: Microbiota of Saliva from patient MC28 [GM123]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM123


title: Microbiota of Saliva from patient MC23 [GM121]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM121


title: Microbiota of Saliva from patient MC7 [GM52]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM52


title: Microbiota of Saliva from patient MC15 [GM117]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM117


title: Microbiota of Saliva from patient MC17 [GM118]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM118


title: Microbiota of Saliva from patient MC15 [GM116]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM116


title: Microbiota of Saliva from patient MC14 [GM114]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM114


title: Microbiota of Saliva from patient MC15 [GM115]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM115


title: Microbiota of Saliva from patient MC37 [GM137]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM137


title: Microbiota of Saliva from patient MC35 [GM133]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM133


title: Microbiota of Saliva from patient MC14 [GM112]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM112


title: Microbiota of Saliva from patient MC53 [GM111]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM111


title: Microbiota of Saliva from patient MC50 [GM109]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM109


title: Microbiota of Saliva from patient MC43 [GM106]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM106


title: Microbiota of Saliva from patient MC46 [GM108]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM108


title: Microbiota of Saliva from patient MC41 [GM105]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM105


title: Microbiota of Saliva from patient MC30 [GM128]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM128


title: Microbiota of Saliva from patient MC44 [GM107]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM107


title: Microbiota of Saliva from patient MC11 [GM103]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM103


title: Microbiota of Saliva from patient MC23 [GM122]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM122


title: Microbiota of Saliva from patient Healthy_15 [FL4]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
FL4


title: Microbiota of Saliva from patient Healthy_14 [FL12]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
FL12


title: Microbiota of Saliva from patient MC5 [GM101]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM101


title: Microbiota of Saliva from patient Healthy_12 [FL2]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
FL2


title: Microbiota of Saliva from patient Healthy_11 [GM100]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM100


title: Microbiota of Saliva from patient Healthy_13 [FL10]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
FL10


title: Microbiota of Saliva from patient MC17 [GM120]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM120


title: tt7-7, replicate 2

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

data_processing:
adaptor removal and low-quality trimming of raw reads with Cutadapt, clean reads  quality assessed with FastQC
reads mapped to Arabidopsis thaliana genome using HISAT2
gene counts obtained with Htseq-count and used for differential expression analysis using DESeq2
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Arabidopsis thaliana

source_name: seeds

extract_protocol:
Seed total RNA extraction was performed according to Oñate-Sánchez and Vicente-Carbajosa (2008). DNA removal was performed with DNAse kit (E.Z.N.A).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: accession

value: 8 days after polinization


title: Microbiota of Saliva from patient MC14 [GM113]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM113


title: tt7-7, replicate 1


title: wild type Col-0, replicate 3


title: wild type Col-0, replicate 1


title: Microbiota of Saliva from patient MC51 [GM110]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM110


title: PCV2b cells, Mock, rep3

city: Saint-Hyacinthe

first: Yaima

last: Burgher Pulgaron

state: Québec

address: 3200 Sicotte

country: Canada

institute: Faculté de médecine vétérinaire, Université de Montréal

data_processing:
Raw sequencing data was imported in FASTQ format into CLC Genomics Workbench (version 22.0.1, Qiagen, CA, USA)
Reads were trimmed for quality and adaptors using the CLC Genomics Workbench software
Trimmed reads were mapped to Sus scrofa rRNA 12S, 16S and 18S.
After removing the rRNA mapped reads the remaining unmapped reads were mapped to the reference genome (Sscrofa11.1).
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Sus scrofa

source_name: continuous cell line

growth_protocol: iPAM 3D4/21 cells were maintained in RPMI 1640  supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total cellular RNA was extracted from infected and mock-infected iPAM 3D4/21 cells and purified with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
The cDNA libraries were constructed using Lexogen’s QuantSeqTM 3’ mRNA-Seq Kit (Lexogen GmbH, Vienna, Austria) according to the manufacturer’s recommendations.

treatment_protocol: The cells were infected with PCV2, SwIV H1N1 or co-infected with both virus for 24 hours

value: continuous cell line

value: iPAM 3D4/21

tag: cell type

value: Porcine alveolar macrophages

tag: infection

value: Mock


title: Microbiota of Saliva from patient MC40 [GM104]

city: Firenze

institute: University of Florence

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM104


title: PCV2b cells, Mock, rep2


title: PCV2b cells, PCV2b, rep3

value: PCV2b infection


title: PCV2b cells, Mock, rep1


title: Microbiota of Saliva from patient MC10 [GM102]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table_saliva.csv
GM102


title: PCV2b cells, H1N1, rep3

value: SwIV H1N1 infection


title: PCV2b cells, PCV2b, rep1


title: PCV2b cells, PCV2b, rep2


title: PCV2b cells, H1N1, rep1


title: PCV2b cells, H1N1, rep2


title: PCV2b cells, PCV2b/H1N1, rep2

value: PCV2b and SwIV H1N1 co-infection


title: NPTr cells, PCV2b, rep3

growth_protocol: NPTr cells were maintained in EMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total cellular RNA was extracted from infected and mock-infected NPTr cells and purified with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
The cDNA libraries were constructed using Lexogen’s QuantSeqTM 3’ mRNA-Seq Kit (Lexogen GmbH, Vienna, Austria) according to the manufacturer’s recommendations.

value: NPTr

value: tracheal epithelial cells


title: NPTr cells, PCV2b, rep1


title: NPTr cells, PCV2b, rep2


title: PCV2b cells, PCV2b/H1N1, rep1


title: NPTr cells, Mock, rep3


title: tt7-7, replicate 3


title: wild type Col-0, replicate 2


title: NPTr cells, PCV2b/H1N1, rep3


title: NPTr cells, PCV2b/H1N1, rep2


title: NPTr cells, PCV2b/H1N1, rep1


title: NPTr cells, Mock, rep1


title: NPTr cells, H1N1, rep2


title: NPTr cells, H1N1, rep1


title: MB231_Z3

city: Pittsburgh

first: Shivendra

middle: V.

last: Singh

state: PA

address: 5117 Centre Avenue, UPMC HCC Research Pavilion Suite 2.32A

institute: University of Pittsburgh

data_processing:
hisat2 software was for mapping analysis. The fragments per kilobase per million mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq2 (1.20.0). Genes with an adjusted P-value ≤ 0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: FPKM represents summary of gene expression level analysis by FPKM; DEG represents differential gene expression analysis

source_name: breast cancer cells

growth_protocol: The MDA-MB-231 cells were plated in 10-cm dish at a density of 1×106 cells/dish in triplicate and incubated overnight for attachment.

extract_protocol:
The cells were harvested by trypsin treatment and total RNA was extracted using the RNeasy mini kit (Qiagen, Germantown, MD).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cells were treated with vecicle consisting of DMSO (final concentration - 0.02%) and water (final concentration - 0.1%) or 2 µM of BITC and/or 1 µM of ZA for 24 hours prior to RNA isolation and RNA-Seq analysis.

tag: treatment

value: Cells were treated with 1 microM of ZA for 24 hours.


title: MB231_BZ2

value: Cells were treated with 2 microM of BITC and 1 microM of ZA for 24 hours.


title: MB231_BZ1


title: MB231_BZ3


title: MB231_Z2


title: NPTr cells, Mock, rep2


title: MB231_C3

value: Cells were treated with vehicle for 24 hours.


title: MB231_B3

value: Cells were treated with 2 microM of BITC for 24 hours.


title: MB231_C2


title: MB231_B2


title: MB231_Z1


title: Caco-2/HT29 coculture, control, rep 2

city: Cleveland

first: Douglas

last: Brubaker

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve University

library_source: transcriptomic single cell

data_processing:
Raw sequence data (.bcl files) were converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger mkfastq command. Subsequent UMI and cell barcode de-convolution along with mapping to respective genome were performed using 10X Genomics’ cellranger software package to generate the final digital gene expression matrices and cloupe files.
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: colorectal carcinoma

growth_protocol: The intestinal epithelial Transwell system was established by human colon carcinoma cell lines Caco-2 (passage no. 8) and HT29 (passage no. 13) (ATTC, United States) at 1x105 cells/ cm2 on permeable polyester membrane Transwell inserts. The cells were cultured in DMEM medium with Glutamax (Gibco, United States), supplemented with 10% (v/v) FBS, and incubated in a humidified atmosphere (5% CO2, 37 °C) for 21 days to reach the full differentiation stage.

extract_protocol:
On day 23, cells were trypsinized to be harvested from the Transwell.
Following fast thaw in 37C water bath, cell viability was checked using Thermo Fisher Countess II FL with NucBlue staining. Following cell viability counting, all samples below 70% viability were subjected to dead cell removal via annexin bead conjugation to improve quality. Single cell RNA libraries were generated using the Chromium Single Cell 3’ kit (10X Genomics, CA, USA). The cells were counted and loaded onto the Chromium Controller. Loading was performed to target capture of ~3,000 GEMs per sample for downstream analysis, and samples were processed through the Chromium Controller following the standard manufacturer’s specifications. AThe sequencing libraries were evaluated for quality on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Pooled libraries were quantified using qPCR (Applied Biosystems, Carlsbad, CA, USA) prior to loading onto an Illumina sequencing platform. The samples were sequenced at a configuration compatible with the recommended guidelines as outlined by 10X Genomics.

treatment_protocol: Induction of barrier dysfunction in Caco-2 and HT29 cell monolayers was induced in the apical chamber by 1 ng/ml Escherichia coli O111:B4 lipopolysaccharides (LPS) stimulation on day 22 for 24 hours.

value: colorectal carcinoma

value: Caco-2, HT29

value: control


title: Caco-2/HT29 coculture, control, rep 1


title: MB231_C1


title: Caco-2/HT29 coculture, LPS-treated, rep 1

value: LPS-treated


title: NPTr cells, H1N1, rep3

value: continuous cell line


title: Inner ear organoid d40 SOX2nT+

city: Indianapolis

first: Tsubasa

last: Saeki

state: IN

address: 980 W Walnut St

department: Otolaryngology-Head and Neck Surgery

institute: Indiana University School of Medicine

description: 10x Genomics

data_processing:
Illumina's Real Time Analysis software was used to generate a BCL file, which was subsequently de-multiplexed and converted to a FASTQ file by the bcl2fastq Conversion Software (Illumina).
The Cell Ranger pipeline was used to process the FASTQ file as follows: De-multiplexed reads were mapped to the GRCh38/hg38 human reference genome with the STAR (Spliced Transcripts Alignment to a Reference) aligner, mapped reads were grouped by cell barcode, and single-cell gene expression was quantified using unique molecular identifiers (UMIs).
The resulting filtered gene-barcode (count) matrix was used as input for downstream analysis.
Assembly: GRCh38/hg38

source_name: Inner ear organoids

growth_protocol: hESCs were dissociated and distributed at 3,500 cells per well onto low-adhesion 96-well U-bottom plates in 100 μl of E8 flex media + Normocin (E8fn) containing 20 μM Y-27632 following by addition of 100 μl of E8fn. Following a 48-h incubation, the aggregates were transferred to a new low-adhesion 96-well U-bottom plate in 100 μl of E6 medium containing 4 ng/ml FGF-2, 10 μM SB-431542, and 500 pg/ml BMP-4, and 2% growth factor reduced Matrigel (differentiation day 0 (d0)). On d3, 25 μl of E6 containing 50 ng/ml FGF-2 and 200 nM LDN-193189 was added in each well. On d7, the aggregates were re-transferred into a 96-well U-bottom plate with E6 medium containing 40 ng/ml FGF-2, 200 nM LDN, and 3 μM CHIR-99021. On d8, the medium was partially changed with the same medium as d7. On d11, aggregates were washed and transferred into a 100-mm dish with Organoid Maturation Medium (OMM) containing a 50:50 mixture of Advanced DMEM:F12 and Neurobasal Medium supplemented with 0.5× N2 Supplement, 0.5× B27 without Vitamin A , 1× GlutaMAX, 0.1 mM β-mercaptoethanol, and 1X 100 Normocin supplemented with 1% Matrigel and 3 μM CHIR-99021. The medium was changed with OMM supplemented with 3 μM CHIR-99021 on d13 and d15. After changing the medium with OMM on d18, the medium was changed with OMM twice per week. Aggregates were transferred into new dishes every 1–3 weeks. The culture was maintained up to d60 for scRNA-seq.

extract_protocol:
D20 and d30 aggregates were washed with 0.5 mM EDTA in DPBS, followed by incubation with 1.1 mM EDTA and TrypLE in DPBS at 37°C for 60 min. While incubation, the samples were mechanically dissociated on low-cell-binding 24-well plates and gently pipetted with P1000 tips. After confirming most SOX2ntdTomato-positive cells become single cells, they were filtered sequentially through a 100-µm and a 40-µm cell strainer and then transferred into 2-ml tubes. After spinning down at 100 × g for 5 min, resuspend the cells with fluorescence-activated cell sorting (FACS) buffer which consists of 2% fetal bovine serum in 1X DPBS and collected into a 5-ml round-bottom polypropylene tube . D40, d50, and d60 aggregates were dissected to remove cartilage-like tissues and obvious non-epithelial tissues in OMM in a 60-mm dish with Style 5 tweezers under a fluorescence stereomicroscope. The dissected aggregates were kept in the incubator in OMM on low-cell-binding 6-well plates until dissociation. After dissociation with Accutase, SOX2ntdTomato-positive populations were collected with BD SORP Aria or BD FACSAria Fusion. Single-cell suspension after FACS was centrifuged and resuspended with FACS buffer.
The single-cell gene expression analysis was conducted using a 10X Chromium single-cell system (10X Genomics). Approximately 10,000 cells per sample were loaded on a single cell master mix with lysis buffer and reverse transcription reagents, according to the Chromium Single Cell 3' Reagent Kits V3 User Guide, CG000183 Rev A (10X Genomics). Along with the single-cell gel beads and partitioning oil, the single-cell master mixture containing the single-cell suspension was dispensed onto a Single Cell Chip B in separate wells, and the chip was loaded to the Chromium Controller for gel bead-in emulsion (GEM) generation and barcoding, followed by cDNA synthesis and library preparation. At each step, the quality of cDNA and library was examined by Bioanalyzer and Qubit. The resulting library was sequenced in a custom program for 28b plus 91b paired-end sequencing on an Illumina NovaSeq 6000 sequencer. Over 27K reads per cell were generated and 93% of the sequencing reads reached Q30 (99.9% base call accuracy).?

value: Inner ear organoids

tag: facs isolation_strategy

value: SOX2nT positive

value: WA25 human ESCs

tag: developmental stage

value: day 40


title: Inner ear organoid d20 SOX2nT+

description: 10x Genomics

tag: cell line

value: day 20


title: Inner ear organoid d60 SOX2nT+

description: 10x Genomics

tag: tissue

value: day 60


title: Inner ear organoid d30 SOX2nT+

description: 10x Genomics

value: day 30


title: MB231_B1


title: UK022 DMSO H3K4me3

city: Lexington

first: Jinpeng

last: Liu

state: Kentucky

address: 800 Rose St

institute: Markey Cancer Center

data_processing:
The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
The tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 200 bp. The genome is divided into 32-nt bins and the number of fragments in each bin is determined.
ChIP-seq reads were aligned to the hg38 genome assembly.
Peaks were called using SICER 1.1 (default cutoff is FDR 1e-7 with gap parameter of 600 bp). Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist.
Standard normalization was performed for the H3K27ac and H3K4me3 ChIPs, and spike-in normalization of Drosophila chromatin was performed for the H3K27me3 ChIP.

source_name: lung tumoroids

growth_protocol: Patient derived tumoroids were grown in Matrigel plus cocktail media

extract_protocol:
Matrigel was dissolved by Dispase and the cell pellets were collected and fixed.
Library was constructed by Active Motif using standard Illumina protocols.

treatment_protocol: Patient derived tumoroids were treated with 5uM EPZ6438 for 9 days followed by 2 days of EPZ6438 + 20 ng/mL IFNy

value: lung tumoroids

value: malignant epithelial lung

tag: chip antibody

value: H3K4me3 Active Motif

tag: genotype

value: WT

value: DMSO .05%


title: UK022 IFN H3K27ac

value: H3K27ac Active Motif

value: IFNy 20 ng/mL


title: UK022 IFN + EPZ H3K4me3

value: IFNy 20 ng/mL + EPZ6438 5uM


title: UK022 Pooled_Input

value: pooled


title: UK022 EPZ H3K4me3

value: EPZ6438 5uM


title: UK022 IFN H3Kme3


title: UK022 EPZ H3K27ac


title: UK022 DMSO H3K27ac


title: UK022 IFN + EPZ H3K27me3

value: H3K27me3 Active Motif


title: UK022 IFN H3K27me


title: UK022 EPZ H3K27me3


title: Inner ear organoid d50 SOX2nT+

description: 10x Genomics

value: Inner ear organoids

value: SOX2nT positive

value: day 50


title: JB_100 [RNA-seq]

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv

data_processing:
Sequenced strand unspecific paired-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.18) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -q --dta -k 5
Secondary alignments were filtered out using samtools (v 1.10).
Mapped reads were summarized using featureCounts (v 2.0.0) with parameterst -p -s 0 -T 6 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.96)
Differential gene expression was assessed using R/edgeR (v 4.0.3) using TMM normalization.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Comma-separated text files including FPKM, log2 fold change and false discovery rate values for each sample.

source_name: primary neuroblastoma tumor

extract_protocol:
500 ng of total RNA were depleted of ribosomal RNA using the RiboMinus kit (Life Technologies) according to the instructions of the manufacturer. Depleted RNA was then fragmented by addition of 5 fragmentation buffer (200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and heating at 94 °C for 3 min in a thermocycler followed by ethanol precipitation with ammonium acetate and GlycoBlue (Life Technologies) as carrier.
Fragmented RNA was then reverse transcribed using random hexamer and Superscript III (Life Technologies). The second strand was synthesized using the TargetAmp kit (Epicentre) according to the instructions of the manufacturer. The final steps of library preparation, e.g. blunt end repair, adapter ligation, adapter fill-in and amplification were done according to Meyer and Kircher (2010, PMID: 20516186). The barcoded libraries were purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. A pool of up to 10 libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 2x100 bp was performed with an IlluminaHighScan-SQ sequencer at the sequencing core facility of the IZKF Leipzig (Faculty of Medicine, University Leipzig) using version 3 chemistry and flowcell according to the instructions of the manufacturer.

value: primary neuroblastoma tumor

tag: tumor stage

tag: mycn status

value: not amplified


title: JB_98 [RNA-seq]


title: JB_99 [RNA-seq]


title: JB_97 [RNA-seq]


title: UK022 DMSO H3K27me3


title: UK022 IFN + EPZ H3K27ac


title: JB_95 [RNA-seq]


title: JB_93 [RNA-seq]

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_s123_s4_protein_coding.csv
DE_s1_s4_protein_coding.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv
DE_17_unbalanced_MNA_protein_coding.csv

value: amplified


title: JB_94 [RNA-seq]


title: JB_96 [RNA-seq]


title: Suspension Cultured Pancreas Exocrine - Hu1113 5% Matrigel

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
Illumina NovaSeq6000
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg19 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Suspension Cultured Pancreas Exocrine

growth_protocol: After islet removal, primary adult human pancreas tissue was dissociated into single cells, counted, and cryopreserved. Cryopreserved samples were thawed and plated in suspension culture medium. On D1 and D4, medium was refreshed. On D7 of each culture, cells were collected in RLT buffer with beta-mercaptoethanol for subsequent extraction.

extract_protocol: RNA was extracted using the RNeasy Micro Kit (Qiagen, Valencia, CA) to obtain 0.5-1 ug total RNA from each sample.

treatment_protocol: On D1, a subset of the cells from each donor was resuspended in suspension culture medium supplemented with 5% Matrigel (treatment).

value: Pancreas

value: Primary adult human pancreas cells

value: 5percent Matrigel


title: Suspension Cultured Pancreas Exocrine - Hu1135 No Addition

value: 0percent Matrigel


title: Suspension Cultured Pancreas Exocrine - Hu1113 No Addition


title: Suspension Cultured Pancreas Exocrine - Hu1135 5% Matrigel


title: Suspension Cultured Pancreas Exocrine - Hu1072 5% Matrigel


title: JB_92 [RNA-seq]


title: JB_91 [RNA-seq]

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_s123_s4_protein_coding.csv
DE_s1_s4_protein_coding.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv


title: JB_90 [RNA-seq]


title: JB_89 [RNA-seq]


title: JB_88 [RNA-seq]


title: JB_87 [RNA-seq]

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_s123_s4_protein_coding.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv
DE_17_unbalanced_MNA_protein_coding.csv


title: Suspension Cultured Pancreas Exocrine - Hu1072 No Addition


title: JB_86 [RNA-seq]

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_s123_s4_protein_coding.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv


title: JB_82 [RNA-seq]


title: JB_85 [RNA-seq]


title: JB_84 [RNA-seq]


title: JB_81 [RNA-seq]


title: JB_77 [RNA-seq]


title: JB_83 [RNA-seq]


title: JB_73 [RNA-seq]


title: JB_72 [RNA-seq]


title: JB_76 [RNA-seq]


title: JB_80 [RNA-seq]


title: JB_74 [RNA-seq]


title: Lesional lichenoid irAE patient 2, TCR

city: New Haven

first: Nikhil

last: Joshi

state: CT

address: 300 Cedar St, PO Box 208011

department: Immunobiology

institute: Yale University

description: cDNA enriched for T cell receptor RNA using V(D)J enrichment kit (10X Genomics)

data_processing:
Quality control, alignment, and gene quantification were performed using CellRanger 3.1 (10X Genomics).
Assembly: GRCh38-2020-A
Supplementary files format and content: h5
Supplementary files format and content: csv

source_name: skin

extract_protocol:
4 mm punch biopsy specimens were incubated in 1% Dispase II (Sigma-Aldrich) in RPMI (Gibco) with 10% FBS for 45 minutes at 37°C, followed by mincing with scalpel, incubation in 0.05% Liberase TL (Sigma Aldrich) in RPMI with 10% fetal bovine serum and 0.008% DNase I (Thermo) for 45 minutes at 37°C, and straining through 40μM mesh. If cryopreservation of sample was necessary (one patient sample), the cell pellet was resuspended in chilled RPMI with 40% FBS, to which was added an equivalent volume of chilled RPMI containing 40% FBS and 30% DMSO. Cells were stored overnight at -80°C. To thaw, the cryovial was placed in a water bath at 37°C for 2m, after which cells were serially diluted 1:1 with warmed RPMI with 10% FBS for a total of 5 dilutions. Viability and cell concentration was assessed using Trypan blue and a hemocytometer. Cells were pelleted and resuspended in phosphate buffered saline with 0.04% bovine serum albumin.
From single cell suspensions, libraries were constructed by the Yale Center for Genome Analysis using the Chromium Controller (10X Genomics) with 5’ chemistry v2 and V(D)J amplification according to manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000.

value: skin

tag: skin condition

value: lesional skin

value: all


title: Lesional lichenoid irAE patient 1, TCR

value: lichenoid cutaneous immune-related adverse events


title: JB_79 [RNA-seq]


title: Lesional lichenoid irAE patient 2, transcriptome


title: JB_75 [RNA-seq]


title: GUR-017M

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 11.0 using default settings.

data_processing: Data was extracted from the TIFF files using Agilent FE 11.  The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2)[23]. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval, and to the square root of the number of probes in the interval.

source_name: Prostate carcinoma

label_protocol: DNAs from frozen tissue were treated with DNAse 1 prior to Klenow-based labeling. High molecular weight templates were digested for 30 minutes. In each case 1 ul of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols [22]. All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to CGH arrays (Agilent Technologies, Santa Clara, CA).

growth_protocol: Fresh tumor samples from prostate cancer patient derived tumor xenograftswere flash-frozen and maintaned at -80 degrees C.

extract_protocol: Biopsies were minced in the presence of NST buffer and DAPI according to published protocols (Holley et al, 2012). Nuclei were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Aria III cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm. DNA content and cell cycle were analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA).DNAs were extracted using Qiagen micro kits (Qiagen Valencia, CA).

tag: tissue source

value: Patient derived xenograft

tag: tissue type

value: frozen tissue

tag: flow sort content

value: Human tumor and mouse host

source_name: Reference pooled 46XX

tag: sample type

value: Normal female genome


title: PRJ-88T


title: TMA-027


title: Lesional lichenoid irAE patient 1, transcriptome

tag: disease state


title: JB_71 [RNA-seq]


title: Nonlesional lichenoid irAE patient 2, TCR

value: nonlesional skin


title: JB_78 [RNA-seq]


title: JB_70 [RNA-seq]


title: Nonlesional lichenoid irAE patient 2, transcriptome


title: Nonlesional lichenoid irAE patient 1, TCR


title: JB_68 [RNA-seq]


title: JB_69 [RNA-seq]


title: Nonlesional lichenoid irAE patient 1, transcriptome


title: Healthy control skin patient 2, TCR

value: healthy


title: Healthy control skin patient 2, transcriptome


title: Healthy control skin patient 1, TCR


title: Healthy control skin patient 1, transcriptome