title: Cultivated peanut 180930D_SY01_P1_D15_SAAS_147_191127


title: Cultivated peanut 180930D_SY01_P1_F15_SAAS_209_191127

status: Public on Feb 22 2022

type: genomic

city: Jinan

first: rz

last: Tian

state: Shandong

address: 202 North Industrial Road

country: China

institute: SAAS

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
As per manufacturer (Affymetrix)
Genotype Call (SNP call): 'ATCG' type or '---' (means NoCall)

label: biotin

molecule: genomic DNA

organism: Arachis hypogaea

source_name: Cultivated peanut

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Field collection or laboratory cultivation

extract_protocol: Unkown

tag: tissue

value: leaf


title: FB46_I

type: SRA

city: La Jolla

first: Caroline

middle: R

last: McKeown

state: CA

address: 10550 N. Torrey Pines Rd., DNC-216

department: Dorris Neuroscience Center

country: USA

institute: The Scripps Research Institute

library_source: transcriptomic

data_processing:
Reads were aligned using STAR v2.5.2a to the Xenbase 9.2 transcriptome with parameters outReadsUnmapped=Fastx, outFilterMismatchNmax=10, seedSearchStartLmax=30
Reads were counted using HTSeq v0.11.1 with parameters -m intersection-nonempty -s no -a 20 -t exon
Counts were normalized using the DESeq2 v1.22.2 package
Genome_build: Xenbase v9.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Xenopus laevis

source_name: stage 46 forebrain

extract_protocol:
Brain regions were collected from the appropriate stage and total RNA was extracted using the mirVana kit (Life Technologies, USA). DNase treatment was used to remove genomic DNA and was followed by clean-up using RNeasy mini kit (Qiagen, USA).
1µg of cDNA was sheared in microTube (Covaris) and then used for library preparation (KAPA Taq PCR kits). The next generation sequencing was done using HiSeq2000 platform (Illumina; RRID:SCR_020132)

value: forebrain

tag: Stage


title: Cultivated peanut 180930D_SY01_P1_D13_SAAS_142_191127


title: MB44_II

source_name: stage 44 midbrain

value: midbrain


title: MB44_I


title: Cultivated peanut 180930D_SY01_P1_D09_SAAS_121_191127


title: Cultivated peanut 180930D_SY01_P1_D05_SAAS_118_191127


title: Cultivated peanut 180930D_SY01_P1_D11_SAAS_130_191127


title: Cultivated peanut 180930D_SY01_P1_D21_SAAS_162_191127


title: Cultivated peanut 180930D_SY01_P1_D07_SAAS_120_191127


title: MB46_II

source_name: stage 46 midbrain


title: Cultivated peanut 180930D_SY01_P1_D03_SAAS_109_191127


title: Lut_cocul2

city: Tucson

first: David

last: Baltrus

state: AZ

address: 1140 E. South Campus Drive

institute: University of Arizona

data_processing:
Quality Control: QoRTs (Quality of RNA-seq Tool-Set)
Alignment: STAR v2.7.3
Subset: SAMtools
Quantification: featureCount, part of the subread package v2.0.1
Expression Analysis: DESeq2
Genome_build: fungal: PRJNA732082 (genome in submission)
Genome_build: bacterial: JQNL00000000.1
Supplementary_files_format_and_content: Output from featureCount

organism: Luteibacter mycovicinus

source_name: fungal and bacterial coculture

growth_protocol: Liquid M9 media with 2% glucose and 100 uM methionine shaking at 27C

extract_protocol:
Samples were ground in TRIzol, then chlorofom and ethanol were used to isolate nucleic acids. The samples were treated with DNAse and checked for quality and contamination.
From RNA samples from fungi-containing cultures, fungal rRNA was depleted twice and poly-A selected to acquire fungal transcripts. The remaining RNA from the coculture sample and the RNA from the axenic bacteria sample were depleted twice of bacterial rRNA. Sequencing libraries were prepared using RNA TruSeq library construction kits.

treatment_protocol: Organisms were grow axenically and in co-culture

value: mixed culture


title: SJOS001121_X8

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
align using bwa sampe
count genes using Hiseq count
covrt count to FPKM in R
Genome_build: GRCH37-lite

organism: Homo sapiens

source_name: osteosarcoma patient derived xenograft

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Snap frozen PDX samples were ground into fine powder on in liquid nitrogen and RNA was extracted with QIAGEN RNeasy kit. In both cases, genomic DNA was removed using gDNA eliminator columns. Quality control was performed with Agilent Bioanalyser.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599).

tag: cell line

value: OS-PDX


title: SJOS048101_C3

source_name: osteosarcoma cell line


title: Cultivated peanut 180930D_SY01_P1_B23_SAAS_107_191127


title: Cultivated peanut 180930D_SY01_P1_B19_SAAS_084_191127


title: SJOS048101_C1


title: SJOS001132_X1


title: SJOS048101_C2


title: Cultivated peanut 180930D_SY01_P1_B13_SAAS_072_191127


title: SJOS048100_C2


title: Cultivated peanut 180930D_SY01_P1_B21_SAAS_093_191127


title: Cultivated peanut 180930D_SY01_P1_B09_SAAS_038_191127


title: Lut_cocul1


title: Lut_axenic2

source_name: bacterial culture

value: pure culture


title: SJOS048100_C3


title: Cultivated peanut 180930D_SY01_P1_B17_SAAS_082_191127


title: Cultivated peanut 180930D_SY01_P1_B15_SAAS_080_191127


title: Cultivated peanut 180930D_SY01_P1_D01_SAAS_108_191127


title: Cultivated peanut 180930D_SY01_P1_B07_SAAS_035_191127


title: SJOS048100_C1


title: Lut_axenic3


title: SJOS048099_C2


title: Cultivated peanut 180930D_SY01_P1_B03_SAAS_032_191127


title: Cultivated peanut 180930D_SY01_P1_B11_SAAS_064_191127


title: Lut_cocul3


title: Cultivated peanut 180930D_SY01_P1_B01_SAAS_022_191127


title: Cultivated peanut 180930D_SY01_P1_B05_SAAS_034_191127


title: Pest_axenic3

molecule: polyA RNA

organism: Pestalotiopsis sp. 9143b

source_name: fungal culture


title: Cultivated peanut 180930C_SY01_P1_O16_SAAS_268_191127


title: Cultivated peanut 180930C_SY01_P1_O14_SAAS_267_191127


title: Pest_axenic2


title: SJOS048099_C3


title: SJNORM048098_C3


title: SJOS048099_C1


title: Pest_axenic1


title: SJNORM048098_C2


title: Cultivated peanut 180930C_SY01_P1_O08_SAAS_266_191127


title: Cultivated peanut 180930C_SY01_P1_O12_SAAS_266_191127


title: Pest_cocul3


title: Cultivated peanut 180930C_SY01_P1_O10_SAAS_265_191127


title: Cultivated peanut 180930C_SY01_P1_O06_SAAS_265_191127


title: Cultivated peanut 180930C_SY01_P1_O02_SAAS_263_191127


title: Pest_cocul2


title: SJNORM048098_C1


title: Lut_axenic1


title: Cultivated peanut 180930C_SY01_P1_O04_SAAS_264_191127


title: Cultivated peanut 180930C_SY01_P1_M24_SAAS_262_191127


title: Cultivated peanut 180930C_SY01_P1_M22_SAAS_261_191127


title: Cultivated peanut 180930C_SY01_P1_M20_SAAS_258_191127


title: Pest_cocul1


title: Cultivated peanut 180930C_SY01_P1_M18_SAAS_257_191127


title: Coinfection_5

city: Bangalore

first: Nagasuma

last: Chandra

state: Karnataka

address: C V Raman Road

department: Biochemistry

country: India

institute: IISC

data_processing:
Illumina Bcl2fastq was used for basecalling.
Sequence reads were trimmed for adapters using Trimgalore v0.6.6
Sequence alignment was performed with STAR v2.7.6 against hg38 genome, followed by counts quantification with RSEM.
Differential gene expression analysis is performed with DEseq2 and Limma
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole Blood

extract_protocol:
Whole blood was collected in Paxgene tubes and total RNA was isolated with Paxgene Blood RNA kit (Cat# 762164) according to manufacturer’s instructions. 1ug of total RNA was used for sequencing library preparation.
poly-A mRNA enrichment was performed with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) followed by library preparation with NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7760) using manufacturer directions.

tag: age

tag: Sex

value: F

tag: condition

value: Covid-19 Bacterial Coinfection

tag: batch

tag: sequencing id


title: Coinfection_4

value: M


title: Coinfection_3


title: Cultivated peanut 180930C_SY01_P1_M16_SAAS_254_191127


title: Coinfection_6


title: Cultivated peanut 180930C_SY01_P1_M12_SAAS_252_191127


title: Cultivated peanut 180930C_SY01_P1_M08_SAAS_250_191127


title: Coinfection_2


title: Cultivated peanut 180930C_SY01_P1_M14_SAAS_253_191127


title: Cultivated peanut 180930C_SY01_P1_M06_SAAS_249_191127


title: Coinfection_1


title: Cultivated peanut 180930C_SY01_P1_M10_SAAS_251_191127


title: Cultivated peanut 180930C_SY01_P1_M04_SAAS_248_191127


title: CHT7HA_3_ND12

city: East Lansing

first: Christoph

last: Benning

state: MI

address: 612 Wilson Rd, Plant Research Laboratories

institute: MSU-DOE Plant Research Laboratory

data_processing:
Base calling was done using Illumina Real Time Analysis (RTA) v2.7.7 and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
For each sample, raw reads from different lanes were merged using the cat command (Unix)
Reads were trimmed for adapter sequences with Trimmomatic 0.33 using the following script:  java -jar $TRIM/trimmomatic SE -phred33 $f1 ${f1%%.fastq.gz}"_trimmed_.fastq.gz" ILLUMINACLIP:$TRIM/adapters/TruSeq3-PE.fa:2:30:10
Trimmed reads were mapped to Creinhardtii_281_v5.6.transcript.fa.gz and calculated for read count and abundance (TPM) of each trasncript with Salmon 0.9.1 (Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. 2017. Nat Methods 14: 417-419.). For each sample, a quant.sf file was generated.
The raw transcript counts matrix (Gene_quant_all.csv) was constructed from the .sf files with R package tximport 1.16.1 (Soneson C, Love MI, Robinson MD. 2015. F1000Res 4: 1521.),
The normalized transcript counts matrix (Gene_quant_all_normailzed.csv) was calculated from the raw transcript counts matrix and sample table with R package DESeq2 1.28.1 (Love MI, Huber W, Anders S. 2014. Genome Biol 15: 550.). During this process, transcripts with a total read count <2 across all samples were discarded.
Genome_build: Creinhardtii_281_v5.6
Supplementary_files_format_and_content: Sample_quant.sf: the raw transcript count and abundance (TPM) of individual samples
Supplementary_files_format_and_content: Gene_quant_all.csv: a table containing raw transcript counts of all samples
Supplementary_files_format_and_content: Gene_quant_all_normailzed.csv: a table containing normalized transcript counts of all samples

organism: Chlamydomonas reinhardtii

source_name: Bioreactor-synchronized cell culture

growth_protocol: Cells were grown autotrophically in 330 mL of nitrogen containing high salt (HS+N) medium (Sueoka, N. 1960 Proc. Natl. Acad. Sci. USA 46, 83-91) in ePBR under 12 h light: 12 h dark cycles with a light intensity of 2,000 µmol m-2s-1, and 5% CO2 was pumped into the cell culture regularly (30 seconds/15 minutes). Cells were maintained in mid-log phase (OD750 = 0.3-0.4, 3 µg/mL of total chlorophyll at ZT6 ) by automatically diluted to the target OD940.

extract_protocol:
Total RNA was extracted with Rneasy® Plant Mini Kit (cat. 74903, Qiagen). The RNA concentration was measured with Qubit® RNA BR Assay and Fluorometer (Cat. Q10210 and Cat. Q32866, Thermo Fisher Scientific). The quality of RNA was determined with Agilent 2100 Bioanalyzer and Agilent RNA 6000 Pico Assay (Cat. G2939BA and Cat. 5067-1514, Agilent Technologies) to ensure an RNA Integrity Number (RIN) value ≥8 before submitting an average of 4.36 µg of total RNA (220 ng/µl) per sample for RNA sequencing.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit on a Perkin Elmer Sciclone G3 robot following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Advanced Analytical Fragment Analyzer High Sensitivity DNA assays.

treatment_protocol: N+ (ZT) samples: The cells culture was grown under the condition above for 7-8 days to be synchronized prior to sample harvesting at 0, 6, 10, 12 hours following the onset of light.  ND samples: At ZT23, the synchronized cells were pelleted at 3,000 g for 5 minutes and rinsed twice with 50 mL of N-free HS (HS-N) medium before being resuspended with 330 mL of HS-N medium. The N-deprived cells were then transferred to a clean ePBR vessel and grown under 2,000 µmol m-2s-1 of constant light with other growth conditions the same as the N+ cultures. Samples were harvested at 6, 12, and 36 hours following N deprivation.  NR samples: A sterile NH4Cl solution were added into N-deprived ePBR cultures at ND36 to bring the final concentration of NH4Cl to be the same as the HS+N medium. Samples were harvested at 6 and 12 hours following N resupply.

tag: strain

tag: timepoint

tag: treatment

value: ND


title: CHT7HA_3_ND36


title: CHT7HA_3_NR12

value: NR


title: CHT7HA_3_NR6


title: CHT7HA_2_NR12


title: CHT7HA_3_ND6


title: Cultivated peanut 180930C_SY01_P1_K22_SAAS_245_191127


title: Severe_7

value: Severe Covid-19


title: Severe_6


title: CHT7HA_2_NR6


title: CHT7HA_2_ND36


title: Cultivated peanut 180930C_SY01_P1_K16_SAAS_242_191127


title: Cultivated peanut 180930C_SY01_P1_K12_SAAS_240_191127


title: Cultivated peanut 180930C_SY01_P1_K18_SAAS_243_191127


title: Severe_5


title: CHT7HA_2_ND12


title: Severe_4


title: Cultivated peanut 180930C_SY01_P1_K14_SAAS_241_191127


title: Cultivated peanut 180930C_SY01_P1_K10_SAAS_239_191127


title: Cultivated peanut 180930C_SY01_P1_K06_SAAS_236_191127


title: Cultivated peanut 180930C_SY01_P1_M02_SAAS_247_191127


title: Severe_3


title: CHT7HA_2_ND6


title: Cultivated peanut 180930C_SY01_P1_K02_SAAS_188_191127


title: Cultivated peanut 180930C_SY01_P1_K20_SAAS_244_191127


title: Severe_2


title: CHT7HA_1_NR12


title: Severe_1


title: Cultivated peanut 180930C_SY01_P1_I18_SAAS_235_191127


title: Cultivated peanut 180930C_SY01_P1_I22_SAAS_237_191127


title: Cultivated peanut 180930C_SY01_P1_I24_SAAS_238_191127


title: Cultivated peanut 180930C_SY01_P1_I20_SAAS_236_191127


title: Moderate_10

value: Moderate Covid-19


title: CHT7HA_1_ND36


title: Cultivated peanut 180930C_SY01_P1_I12_SAAS_186_191127


title: Cultivated peanut 180930C_SY01_P1_K04_SAAS_235_191127


title: Moderate_8


title: Moderate_9


title: Cultivated peanut 180930C_SY01_P1_K08_SAAS_239_191127


title: CHT7HA_1_NR6


title: CHT7HA_1_ND6


title: Cultivated peanut 180930C_SY01_P1_I10_SAAS_185_191127


title: Moderate_7


title: Cultivated peanut 180930C_SY01_P1_I16_SAAS_188_191127


title: Cultivated peanut 180930C_SY01_P1_I08_SAAS_184_191127


title: Cultivated peanut 180930C_SY01_P1_I06_SAAS_183_191127


title: Moderate_6


title: CHT7HA_3_12

value: N+


title: CHT7HA_3_10


title: Moderate_5


title: Cultivated peanut 180930C_SY01_P1_G24_SAAS_180_191127


title: Cultivated peanut 180930C_SY01_P1_I14_SAAS_187_191127


title: CHT7HA_3_06


title: Moderate_4


title: Cultivated peanut 180930C_SY01_P1_G22_SAAS_179_191127


title: Cultivated peanut 180930C_SY01_P1_K24_SAAS_246_191127


title: Cultivated peanut 180930C_SY01_P1_G20_SAAS_178_191127


title: CHT7HA_3_00


title: Moderate_2


title: CHT7HA_2_12


title: CHT7HA_2_10


title: Moderate_3


title: Cultivated peanut 180930C_SY01_P1_G14_SAAS_174_191127


title: Cultivated peanut 180930C_SY01_P1_G18_SAAS_176_191127


title: CHT7HA_2_06


title: Cultivated peanut 180930C_SY01_P1_I02_SAAS_181_191127


title: CHT7HA_1_ND12


title: Ascites-PC5511

type: protein

city: Singapore

first: Johnny

middle: Chin-Ann

last: Ong

state: Singapore

address: 11 Hospital Drive

department: Division of Surgical Oncology

country: Singapore

institute: National Cancer Centre Singapore

hyb_protocol: Target analytes are detected using biotinylated antibodies and developed with streptavidin conjugated to horseradish-peroxidase.

scan_protocol: Scanning protocol was performed based on the manufacturer's instructions (R & D).

data_processing: All sample measurements were performed in duplicate. Array coordinates representing each analyte has been provided in the manufacturer's manual. The average signal for each pair of duplicate spots representing each analyte was generated based on the raw spot density in Microsoft Excel.  Signals were normalized using internal, positive and negative controls included on the array.

molecule: protein

source_name: Cell free ascites derived from patient with colorectal peritoneal carcinomatosis

label_protocol: According to the manufacturer's instructions (R & D). Briefly, cell free ascites is applied to the array that contains duplicate spots of capture antibodies representing each analyte. The array is spotted with 105 different antibodies to human cytokines.

extract_protocol: Ascitic fluids collected from recruited patients were subjected to centrifugation at 2,000 g for 10 minutes. The fluid component was then filter-sterilized using 0.22 µm filter. Concentration of proteins in all ascitic fluids was quantified with Bradford protein assay (Bio-Rad) and equal amount of proteins were incubated with the membrane array according to the manufacturer’s instructions.

tag: patient condition

value: colorectal peritoneal carcinomatosis

tag: histology

value: Colorectal

tag: sample type

value: Cell free ascites


title: Cultivated peanut 180930C_SY01_P1_I04_SAAS_182_191127

value: leaf


title: Ascites-PC124


title: Ascites-PC203

source_name: Cell free ascites derived from patient with benign serous cystadenofibroma

value: benign serous cystadenofibroma

value: Benign


title: Cultivated peanut 180930C_SY01_P1_G16_SAAS_175_191127


title: Moderate_1


title: Mild_9

value: Mild Covid-19


title: Mild_6


title: Ascites-PC099


title: Ascites-PC062


title: CHT7HA_1_06


title: CHT7HA_2_00


title: Mild_8


title: Cultivated peanut 180930C_SY01_P1_G12_SAAS_173_191127


title: Cultivated peanut 180930B_SY01_P1_O23_SAAS_131_191127


title: Mild_4


title: Cultivated peanut 180930B_SY01_P1_O21_SAAS_129_191127


title: CHT7HA_1_12


title: cht7_3_NR12


title: Cultivated peanut 180930B_SY01_P1_O19_SAAS_128_191127


title: Mild_3


title: Cultivated peanut 180930B_SY01_P1_O13_SAAS_125_191127


title: Mild_1


title: Mild_5


title: CHT7HA_1_00


title: Cultivated peanut 180930B_SY01_P1_O17_SAAS_127_191127


title: Mild_7


title: cht7_3_NR6


title: Cultivated peanut 180930B_SY01_P1_O07_SAAS_122_191127


title: PyMT - WT - R1

city: Milan

first: Salvatore

last: Pece

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology IRCCS,

data_processing:
Raw reads were processed with NF-CORE RNASeq pipeline (https://github.com/nf-core/rnaseq, version 3.1).
Gene counts were quantified using the Salmon pseudo-aligner.
Genome_build: GRCh38 and GRCm39 (GENCODE)
Supplementary_files_format_and_content: Tab-delimited text file with raw gene abundances for each sample

organism: Mus musculus

source_name: PyMT

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) from breast tumor cells and then purified using the RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Gold kit according to the manufacturer’s protocol

value: PyMT derived mouse breast tumor cells

value: PyMT

value: Control


title: PyMT - WT - R2


title: cht7_3_ND36


title: Mild_2


title: CHT7HA_1_10


title: Cultivated peanut 180930B_SY01_P1_O11_SAAS_124_191127


title: Cultivated peanut 180930B_SY01_P1_O03_SAAS_117_191127


title: cht7_2_NR12


title: cht7_2_NR6


title: HC_6

value: Healthy


title: non-fibrosis1

type: RNA

city: Shanghai

first: Tao

last: Le

address: LANXI ROAD 164

institute: Shanghai University of traditional Chinese Medicine

description: normal people liver tissue

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: normal people liver biopsy tissue1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Clinical Inpatients

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: After obtaining the liver biopsy tissue, it was frozen at - 80 ℃ and sent to the detection sequence

tag: disease state

value: normal

value: liver

value: pooled male and female


title: cht7_3_ND12

value: ND


title: non-fibrosis4

description: normal people liver tissue

source_name: normal people liver biopsy tissue4


title: PyMT - CDK12-KI - R1

value: PyMT-CDK12 derived mouse breast tumor cells

value: CDK12 Knock-In


title: non-fibrosis3

description: normal people liver tissue

source_name: normal people liver biopsy tissue3


title: Cultivated peanut 180930B_SY01_P1_O01_SAAS_116_191127

source_name: Cultivated peanut


title: fibrosis2

description: Liver tissue of patients with chronic liver disease

source_name: liver fibrosis people biopsy tissue2

value: liver fibrosis


title: non-fibrosis2

description: normal people liver tissue

source_name: normal people liver biopsy tissue2


title: fibrosis1

source_name: liver fibrosis people biopsy tissue1


title: fibrosis3

source_name: liver fibrosis people biopsy tissue3


title: fibrosis4

source_name: liver fibrosis people biopsy tissue4


title: HC_3

value: M


title: Cultivated peanut 180930B_SY01_P1_O15_SAAS_126_191127


title: HC_9


title: Cultivated peanut 180930B_SY01_P1_O05_SAAS_119_191127


title: HC_8

value: F


title: cht7_3_ND6


title: HC_2


title: HC_7


title: PyMT - CDK12-KI - R2


title: Asymptomatic_8

value: Asymptomatic Covid-19


title: Cultivated peanut 180930B_SY01_P1_O09_SAAS_123_191127

value: leaf


title: Cultivated peanut 180930B_SY01_P1_M15_SAAS_111_191127


title: cht7_2_ND36


title: HC_5


title: PAM-2-30_S89.17

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description:
Plasma activated medium_controls
organoid at passage 4

data_processing:
Sequenced reads were trimmed for adaptor sequence (Trimmomatic-0.36)
Paired-end reads were mapped against the mouse reference genome (GRCm38.p4/mm10) using the STAR_2.5.3a software to generate read alignments.
The annotation file Mus_musculus.GRCm38.90.gtf was obtained from the ftp.Ensembl.org server
Following transcript assembly, gene level counts were obtained using HTSeq-0.9.1
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: tab-delimited csv file includes counts per 20 millions of aligned reads values for each sample.

source_name: duodenum

growth_protocol: Sato's protocol (Nature, 2009) was followed for Crypt isolation of mouse small intestine epithelium. Amplication of small intestine organoids was performed over the course of time of 5 days and then organoids were frozen in order to constitute a biobank. Thawing frozen mouse intestinal organoids was then pe rformed and CAP treatements were delivered one day after initial seeding.

extract_protocol:
Total RNA was extracted with the MIRVANA MIRNA ISO KIT (Thermo Fisher scientific, Life technologies Europe, Bleiswijk, NL) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using Ovation® SoLo RNA-Seq Library Preparation Kit (NuGEN, TECAN genomics)
RNA-Seq 2x100 bases Paired-End

treatment_protocol: CAP application based on different timing of exposure and different applications (direct, indirect, PAM)

tag: development stage

value: adult stage

tag: cell type

value: stem cells

tag: genotype

value: wild type

value: CAP application (plasma activated medium)_ 30 minutes

value: epithelium


title: PAM-WT2-24_S94.22

description:
Plasma activated medium_controls
organoid at passage 14

value: CAP application (plasma activated medium)_ 24 hours

tag: tissue


title: Asymptomatic_7


title: I-WT2-24_S88.16

description:
Indirect_controls
organoid at passage 14

value: CAP application (indirect)_24 hours


title: Cultivated peanut 180930B_SY01_P1_M23_SAAS_115_191127


title: HC_4

value: Healthy


title: cht7_2_ND12


title: Cultivated peanut 180930B_SY01_P1_M21_SAAS_114_191127


title: cht7_2_ND6


title: PAM-2-24_S92.20


title: PAM-CD1-24_S93.21

description:
Plasma activated medium_controls
organoid at passage 12


title: cht7_1_ND36


title: Cultivated peanut 180930B_SY01_P1_M19_SAAS_113_191127


title: Cultivated peanut 180930B_SY01_P1_M17_SAAS_112_191127


title: PAM-WT2-30_S91.19


title: cht7_1_NR6

value: NR


title: HC_1


title: cht7_1_ND12

value: ND


title: Cultivated peanut 180930B_SY01_P1_M13_SAAS_110_191127


title: Asymptomatic_4


title: cht7_1_NR12


title: Cultivated peanut 180930B_SY01_P1_M11_SAAS_106_191127


title: cht7_1_ND6


title: Cultivated peanut 180930B_SY01_P1_M03_SAAS_100_191127


title: PAM-CD1-30_S90.18


title: Asymptomatic_6


title: I-CD1-24_S87.15

description:
Indirect_controls
organoid at passage 12


title: Cultivated peanut 180930B_SY01_P1_M09_SAAS_105_191127


title: Asymptomatic_5


title: cht7_3_12

value: N+


title: Cultivated peanut 180930B_SY01_P1_M07_SAAS_102_191127


title: I-2-24_S86.14

description:
Indirect_controls
organoid at passage 4


title: D-WT2-24_S82.10

description:
Direct_controls
organoid at passage 14

value: CAP application (direct)_24 hours


title: Asymptomatic_1


title: I-WT2-30_S85.13

value: CAP application (indirect)_30 minutes


title: cht7_3_06


title: cht7_3_10


title: cht7_2_10


title: Asymptomatic_3


title: Cultivated peanut 180930B_SY01_P1_M05_SAAS_101_191127


title: I-CD1-30_S84.12


title: Cultivated peanut 180930B_SY01_P1_M01_SAAS_099_191127


title: D-CD1-24_S81.9

description:
Direct_controls
organoid at passage 12


title: Asymptomatic_2


title: cht7_2_06


title: S389

city: Lille

first: Laurent

last: Dubuquoy

address: Faculté de Médecine - Pôle Recherche, place Verdun.

country: France

institute: Inserm

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto hg38 assembly of human genome using STAR 2.5.3a.
Quantification : Gene expression was quantified using HTSeq v0.6.1p1 (union mode) and Ensembl release 96 annotations.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values file containing raw read counts in each sample.

source_name: RNA extracted from microdissected hepatocyte from frozen human liver

extract_protocol:
Total RNA was isolated using the PicoPure RNA Extraction Kit (Excilone 0204, MDS Analytical Technologies), according to the manufacturer’s instructions.
Complementary DNA were generated and linearly amplified from 5 ng of total RNA using the Ovation RNA-seq system V2 (NuGEN technologies Inc., Leek, Netherlands), according to manufacturer's instructions. Amplified cDNA was then purified using Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France) in a 1.8:1 ratio of beads to sample and fragmented by sonication using a Covaris E220 instrument (with duty factor: 10 percent, peak incident power: 175 watts and cycles/burst: 200 for 120 seconds). RNA-Seq libraries were generated from 100 ng of fragmented ds-cDNA using Ovation Ultralow Library System v2 (NuGEN technologies Inc., Leek, Netherlands) according to manufacturer's instructions with only 6 PCR cycles for library amplification. The final libraries were checked for quality and quantified using capillary electrophoresis.

tag: disease

value: Control

tag: tissue/cell type


title: Cultivated peanut 180930B_SY01_P1_K23_SAAS_098_191127


title: cht7_3_00


title: Cultivated peanut 180930B_SY01_P1_K21_SAAS_097_191127


title: I-2-30_S83.11

description:
Indirect_controls
organoid at passage 4


title: cht7_2_12


title: S391

value: microdissected hepatocyte from frozen human liver


title: Cultivated peanut 180930B_SY01_P1_K19_SAAS_096_191127


title: S387


title: cht7_2_00


title: S395


title: D-2-24_S80.8

description:
Direct_controls
organoid at passage 4


title: cht7_1_12


title: D-CD1-30_S78.6

description:
Direct_controls
organoid at passage 12

value: CAP application (direct)_30 minutes


title: D-WT2-30_S79.7

description:
Direct_controls
organoid at passage 14


title: Cultivated peanut 180930B_SY01_P1_K17_SAAS_095_191127

value: leaf


title: Cultivated peanut 180930B_SY01_P1_K15_SAAS_094_191127


title: S390


title: cht7_1_10


title: D-2-30_S77.5

description:
Direct_controls
organoid at passage 4

value: adult stage


title: Cultivated peanut 180930B_SY01_P1_K13_SAAS_092_191127


title: cht7_1_06


title: S419

value: Alcoholic cirrhosis


title: C-2-20_S76.4

description:
controls
organoid at passage 4

value: stem cells

value: wild type


title: Cultivated peanut 180930B_SY01_P1_K11_SAAS_091_191127


title: cht7_1_00


title: Cultivated peanut 180930B_SY01_P1_K09_SAAS_089_191127


title: C-1-20_S75.3

description:
controls
organoid at passage 4

value: epithelium


title: Wild_type_3_NR12


title: S418


title: S431


title: S445


title: Wild_type_3_NR6


title: Cultivated peanut 180930B_SY01_P1_K07_SAAS_088_191127


title: C-CD1_S73.1

description:
controls
organoid at passage 12


title: Wild_type_3_ND36


title: Vav-cre; Dnmt3af/f male (8 wks) treated w/ two doses of IFNg, 24h apart, and sacrified 2h post the 2nd dose

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

description:
IFN_KM
M_IX-Dnmt3aKO_IFNg_Male-KIM-lib1_S1_L004
Vav-cre; Dnmt3af/f male (8 weeks) treated with two doses of IFNg, 24h apart, and sacrified for cell harvest 2h post the second dose

data_processing:
Single cell count: single cells were counted using Cellranger 3.1.0. Reads were further aligned to the Genome Reference Consortium Human genome, CRChg38. The aligned data were then annotated and UMI-collapsed using Cellranger (v3.1.0). Cells with more than 10% mitochondrial gene expression and with top 5% unique feature counts were excluded. Data reduction and cluster identification were performed using Seurat.
Alignment and UMI-collapse: Reference genome: the Genome Reference Consortium Human genome, CRChg38. Package: Cellranger 3.1.0
Cell exclusion: Cells with more than 10% mitochondrial gene expression and with top 5% unique feature counts were excluded
Principal component analysis: Data were reduced to 20 components.
Clustering identification: Reduction techniques: tSNE and UMAP
Genome_build: Reference genome: the Genome Reference Consortium house mouse genome, GRC38(mm10)
Supplementary_files_format_and_content: For each sample, three files are provided: barcodes.tsv.gz; features.tsv.gz; and matrix.mtx.gz

source_name: Mouse bone marrow progenitor cells

growth_protocol: 8 weeks old mice were caged with food and water ad libitum

extract_protocol:
17000 cells were used for construction of the scRNA library of each sample
Chromnium Single Cell 3’Reagent Kit v3 (10x Genomics) according to the manufacturer’s protocol

treatment_protocol: Two doses of mouse recombinant IFNg (10ug) or volume-equivalent PBS were retro-orbitally injected into mice with 24h apart. Mice were sacrificed for cell harvest 2h post-the second injection.

tag: genotype/variation

value: Vav-cre; Dnmt3af/f

value: bone marrow

tag: source

value: Lin-cKIT+EPCR+

tag: antibody used for sorting


title: Cultivated peanut 180930B_SY01_P1_K05_SAAS_087_191127


title: Vav-cre; Dnmt3af/f female (8 wks) treated w/ two doses of IFNg, 24h apart, and sacrified 2h post the 2nd dose

description:
IFN_KF
M_IX-Dnmt3aKO_IFNg_Female-KIF-lib1_S7_L004
Vav-cre; Dnmt3af/f female (8 weeks) treated with two doses of IFNg, 24h apart, and sacrified for cell harvest 2h post the second dose


title: Cultivated peanut 180930B_SY01_P1_K01_SAAS_083_191127


title: Wild_type_3_ND6


title: S420


title: Cultivated peanut 180930B_SY01_P1_K03_SAAS_086_191127


title: S430


title: S423


title: Wild_type_3_ND12


title: Vav-cre female (8 wks) treated w/ two doses of IFNg, 24h apart, and sacrified for cell harvest 2h post the 2nd dose

description:
IFN_VF
M_IX-VavCre_IFNg_Female-CIF-lib1_S6_L004
Vav-cre female (8 weeks) treated with two doses of IFNg, 24h apart, and sacrified for cell harvest 2h post the second dose

value: Vav-cre


title: Wild_type_2_NR12

value: NR


title: S422

value: Alcoholic hepatitis


title: S412


title: C-WT2_S74.2

description:
controls
organoid at passage 14


title: Wild_type_2_ND12

value: ND


title: Cultivated peanut 180930B_SY01_P1_I17_SAAS_077_191127


title: Cultivated peanut 180930B_SY01_P1_I23_SAAS_081_191127


title: S416


title: Cultivated peanut 180930B_SY01_P1_I15_SAAS_076_191127


title: Cultivated peanut 180930B_SY01_P1_I13_SAAS_075_191127


title: S421


title: Cultivated peanut 180930B_SY01_P1_I11_SAAS_074_191127


title: Vav-cre male (8 wks) treated w/ two doses of IFNg, 24h apart, and sacrified for cell harvest 2h post the 2nd dose

description:
IFN_VM
M_IX-VavCre_IFNg_Male-CIM-lib1_S2_L004
Vav-cre male (8 weeks) treated with two doses of IFNg, 24h apart, and sacrified for cell harvest 2h post the second dose


title: S443


title: Cultivated peanut 180930B_SY01_P1_I21_SAAS_079_191127


title: Wild_type_2_NR6


title: S410


title: AML_H3K4me3

city: Durham

first: Arum

last: Kim

state: NC

address: Medical Sciences Research Building III  3 Genome Ct

institute: Duke University

library_source: genomic

data_processing:
All reads were mapped to mouse genome (mm10) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools. We filter out reads with a mapping quality score < 20 for downstream analysis
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: BW

source_name: NUP98-NSD1+ AML cells

growth_protocol: The established murine AML cell lines were grown in the OptiMEM base medium supplemented with 15% of FBS, 50uM of beta-mercaptoethanol, 1% of penicillin and streptomycin, and murine stem cell factor (mSCF; added with 10% of supernatant from a mSCF-secreting CHO cell line).

extract_protocol:
Fixed cell pellets were sonicated in Bioruptor for 45 cycles at high setting to enrich the sonicated DNA to be ~300-500bp. Then these sonicated samples were incubated with indicated antibodies with either protein G or A beads overnight. Then, the beads were washed 4 times with distinct buffers (see our method) and eluted with elution buffer at 65 degree for 30 min. This eluted DNA were reverse crosslinked and treated with RNAse and protease K, then the final Chipped DNA are purified with PCR cleanup kit (Qiagen).
Libraries were prepared for deep sequencing using standard Illumina protocols.

treatment_protocol: For ChIP-seq experiments, cells were grown in medium and then fixed with 1% formaldehyde in PBS for 10 min at room temperature.

tag: cell line

value: NUP98-NSD1+ AML cells

tag: antibody

value: H3K4me3 (abcam 8580)


title: Cultivated peanut 180930B_SY01_P1_I07_SAAS_071_191127


title: Wild_type_1_ND36

source_name: Bioreactor-synchronized cell culture

tag: strain

tag: timepoint


title: Vav-cre female (8 wk) treated w/ 2 doses of IFNg, 24h apart, and sacrificed 2h post the 2nd dose

description: Vav-cre female (8 weeks) treated with two doses of IFNg, 24h apart, and sacrified for cell harvest 2h post the second dose


title: Vav-cre; Dnmt3af/f male (8 wks) treated w/ two doses of PBS, 24h apart, and sacrified 2h post the 2nd dose

description:
PBS_KM
M_IX-Dnmt3aKO_PBS_Male-KPM-lib1_S8_L004
Vav-cre; Dnmt3af/f male (8 weeks) treated with two doses of PBS, 24h apart, and sacrified for cell harvest 2h post the second dose


title: S415

value: microdissected hepatocyte from frozen human liver


title: Vav-cre; Dnmt3af/f female (8 wks) treated w/ two doses of PBS, 24h apart, and sacrified 2h post the 2nd dose

description:
PBS_KF
M_IX-Dnmt3aKO_PBS_Female-KPF-lib1_S5_L004
Vav-cre; Dnmt3af/f female (8 weeks) treated with two doses of PBS, 24h apart, and sacrified for cell harvest 2h post the second dose


title: Wild_type_1_ND6

tag: treatment


title: Vav-cre male (8 wk) treated w/ 2 doses of IFNg, 24h apart, and sacrificed 2h post the 2nd dose

description: Vav-cre male (8 weeks) treated with two doses of IFNg, 24h apart, and sacrified for cell harvest 2h post the second dose


title: Wild_type_2_ND36


title: AML_Kdm5b

value: Kdm5b (abcam ab50958)


title: Cultivated peanut 180930B_SY01_P1_I19_SAAS_078_191127

value: leaf


title: AML_INPUT

value: none (input)


title: Wild_type_3_12

value: N+


title: Vav-cre; Dnmt3af/f male (8 wk) treated w/ 2 doses of PBS, 24h apart, and sacrificed 2h post the 2nd dose

description: Vav-cre; Dnmt3af/f male (8 weeks) treated with two doses of PBS, 24h apart, and sacrified for cell harvest 2h post the second dose


title: Cultivated peanut 180930B_SY01_P1_I01_SAAS_068_191127


title: Vav-cre female (8 wks) treated w/ two doses of PBS, 24h apart, and sacrified for cell harvest 2h post the 2nd dose

description:
PBS_VF
M_IX-VavCre_PBS_Female-CPF-lib1_S9_L004
Vav-cre female (8 weeks) treated with two doses of PBS, 24h apart, and sacrified for cell harvest 2h post the second dose


title: Wild_type_2_ND6


title: Wild_type_3_06


title: Vav-cre; Dnmt3af/f female (8 wk) treated w/ 2 doses of IFNg, 24h apart, and sacrificed 2h post the 2nd dose

description: Vav-cre; Dnmt3af/f female (8 weeks) treated with two doses of IFNg, 24h apart, and sacrified for cell harvest 2h post the second dose


title: Vav-cre male (8 wks) treated w/ two doses of PBS, 24h apart, and sacrified for cell harvest 2h post the 2nd dose

description:
PBS_VM
M_IX-VavCre_PBS_Male-CPM-lib1_S3_L004
Vav-cre male (8 weeks) treated with two doses of PBS, 24h apart, and sacrified for cell harvest 2h post the second dose


title: Wild_type_1_NR6


title: sgPHF8-3-B

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the human genome using the splice-aware STAR aligner.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
Htseq package was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: hg19
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: Melanoma cell line

extract_protocol:
RNAeasy Mini Kit (Qiagen), according to the manufacturer's instructions.
RNA quality was defined on an Agilent 2100 Bioanalyzer, then processed with Ribo-Zero rRNA Removal Kit (Illumina) to remove rRNA, and further processed into sequencing libraries using the Illumina ScriptSeq Complete Gold kit following manufacturer’s protocol.

value: SKMEL-147 melanoma cell line

tag: guide

value: sgPHF8 3


title: sgPHF8-3-C


title: sgPHF8-3-A


title: Vav-cre; Dnmt3af/f male (8 wk) treated w/ 2 doses of IFNg, 24h apart, and sacrificed 2h post the 2nd dose

description: Vav-cre; Dnmt3af/f male (8 weeks) treated with two doses of IFNg, 24h apart, and sacrified for cell harvest 2h post the second dose


title: sgPHF8-1-C

value: sgPHF8 1


title: Wild_type_1_ND12


title: AML_NUP98-NSD1(Flag)

value: Flag (Sigma, M2; F1804)


title: Wild_type_1_NR12


title: Cultivated peanut 180930B_SY01_P1_I05_SAAS_070_191127


title: Cultivated peanut 180930B_SY01_P1_G17_SAAS_063_191127


title: Vav-cre; Dnmt3af/f female (8 wk) treated w/ 2 doses of PBS, 24h apart, and sacrificed 2h post the 2nd dose

description: Vav-cre; Dnmt3af/f female (8 weeks) treated with two doses of PBS, 24h apart, and sacrified for cell harvest 2h post the second dose


title: Dnmt3a-HET with IFNg exposure

description: gDNA extracted from 3x10^5 sorted CD45.2 donor derived bone marrow cells

data_processing:
Raw reads were trimmed using cutadapt (V2.4).
Trimmed erads were aligned using bismark (v0.19.0) with options --bowtie2 -X 1000 --score_min L,0,-0.6 -N 0 --multicore 2 -p 4
Duplicate alignments were removed with the deduplicate_bismark function in bismark
Positional methylation levels, methylated counts, and unmethylated counts were quantified using the bismark_methylation_extractor function in bismark
Genome_build: mm10
Supplementary_files_format_and_content: bismark coverage and methylation text file

source_name: sorted CD45.2 BM cells

growth_protocol: 1.5x10^5 donor bone marrow cells (CD45.2) were transplanted with 1.5x10^5 competitor bone marrow cells (WT, CD45.1/2) and 1.2x10^6 bone marrow cells (IFNgrKO; rtTa-M2 for the sample C, H, K or IFNgrKO; rtTA-M2;TetO-IFNg for the sample CI, HI, KI) into CD45.1 recipients. All recipients were fed with 1250 ppm doxycycline chow from week 5-24 post-transplant. All recipients were sacrificed 26-weeks post-transplant. 3x10^5 donor derived bone marrow cells (CD45.2) were sorted from the bone marrow samples that were pooled within each group.

extract_protocol:
gDNA was extracted from 3x10^5 donor derived bone marrow cells at the conclusion of the primary transplant using PureLink Genomic DNA mini Kit (Invitrogen)
250ng of gDNA of each sample, spiked in with lambda control was fragmented using Covaris. The fragmented DNA was then subjected to an overnight cytosine-to-thymine conversion using EZ DNA Methylation-Gold Kit. The CT converted samples were used for library construction with Accel-NGS Methyl-Seq DNA Library Prep Kit, indexed with Methyl-Seq Dual Indexing kit. The sequencing was performed on NovaSeqS4 300XP.

treatment_protocol: Recipients were fed with 1250 ppm doxycycline chow from week 5-24 post-transplant.

value: bone marrow

value: donor derived CD45.2 cells

value: Vav-Cre; Dnmt3af/WT

value: Doxycycline 1250ppm every other week from 5-24 post-transplant

tag: dox-induced inteferon gamma

value: Yes


title: Cultivated peanut 180930B_SY01_P1_G13_SAAS_060_191127


title: Wild_type_3_00


title: Cultivated peanut 180930B_SY01_P1_I03_SAAS_069_191127


title: sgScr-C

value: sgScrambled


title: Wild_type_2_12


title: Cultivated peanut 180930B_SY01_P1_I09_SAAS_073_191127


title: Cultivated peanut 180930B_SY01_P1_G23_SAAS_067_191127


title: sgScr-B


title: Vav-cre female (8 wk) treated w/ 2 doses of PBS, 24h apart, and sacrificed 2h post the 2nd dose

description: Vav-cre female (8 weeks) treated with two doses of PBS, 24h apart, and sacrified for cell harvest 2h post the second dose

value: Lin-cKIT+EPCR+


title: Wild_type_3_10


title: Vav-cre male (8 wk) treated w/ 2 doses of PBS, 24h apart, and sacrificed 2h post the 2nd dose

description: Vav-cre male (8 weeks) treated with two doses of PBS, 24h apart, and sacrified for cell harvest 2h post the second dose


title: Cultivated peanut 180930B_SY01_P1_G21_SAAS_066_191127


title: Wild_type_1_10


title: Dnmt3a-KO with IFNg exposure

value: Vav-Cre; Dnmt3af/f


title: Cultivated peanut 180930B_SY01_P1_G09_SAAS_058_191127


title: Wild_type_1_06


title: Cultivated peanut 180930B_SY01_P1_G19_SAAS_065_191127


title: Endosperm 26°C 72 hour rep3

city: Norwich

first: Xiaochao

last: Chen

address: Norwich Research Park, Colney Ln

department: Crop Genetics

country: United Kingdom

institute: John Innes Centre

description:
HT_3d_R3
TPM_DEG_endosperm

data_processing:
raw reads were trimmed using cutadapt-1.9.1
trimmed reads were mapped to Brassica oleracea reference genome using STAR-2.5.a
featureCounts was employed to count mapped reads
egdeR was used to calculate differentially expressed genes (DEG)
Supplementary_files_format_and_content: csv files including TPM values

organism: Brassica oleracea

source_name: Endosperm 26°C 72 hour rep3

growth_protocol: Brassica oleracea plants were grown in 21°C till bolting, then transferred to 16°C till bent-cotyledon stage.

extract_protocol:
endosperm/seed coat and embryo were dissected under microscope, then RNA was extracted using the ENZA Plant RNA kit (OmegaBio-tek).
For day7, day15, day18, day22 endosperm samples, library was constructed using Ovation RNA-seq system(Nugen, 0351 Arabidopsis); for all the other samples, library was constructed using standard Illumina protocols by Novogene (China).

treatment_protocol: at bent-cotyledon stage, plants were grown in eitehr 16°C or 26°C

value: Endosperm

tag: temperature


title: Dnmt3a-KO without IFNg exposure

value: No


title: Wild_type_2_10


title: Wild_type_1_00


title: Dnmt3a-HET without IFNg exposure


title: Wild_type_2_06


title: Cultivated peanut 180930B_SY01_P1_G15_SAAS_062_191127

value: leaf


title: Wild_type_2_00


title: sgPHF8-1-A


title: sgPHF8-1-B


title: Cultivated peanut 180930B_SY01_P1_G07_SAAS_056_191127


title: Endosperm 26°C 72 hour rep1

description:
HT_3d_R1
TPM_DEG_endosperm

source_name: Endosperm 26°C 72 hour rep1


title: Vav-cre control with IFNg exposure

value: Vav-cre Control


title: Wild_type_1_12

value: N+


title: Cultivated peanut 180930B_SY01_P1_G11_SAAS_059_191127


title: PHF8 ChIPseq-replicate B1

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Reads were aligned to the human genome (build hg19/GRCh37) with Bowtie 2 using local alignment.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
MACS was utilized to perform peak calling for each replicate.
Genome_build: hg19
Supplementary_files_format_and_content: BED files of peaks

extract_protocol:
SKMEL-147 cells were crosslinked with 1% PFA (in PBS 1X) for 10 min at RT. The reaction was quenched with 0.125 M glycine for 5 min at room temperature. After washing with PBS, cells were collected and the pellet was lysed in 50 mM Hepes pH7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Igepal CA-630, and 0.25% Triton X-100, freshly supplemented with 1X Protease Inhibitors Cocktail (Sigma-Aldrich). After centrifugation, isolated nuclei were washed once in 10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA, 1X Protease Inhibitors Cocktail then resuspended in ChIP buffer (10 mM Tris pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-Lauryl Sarcosine, 1X Protease Inhibitors Cocktail) prior sonication. After optimization for each cell line, sonication of SKMEL-147 nuclei was carried out for 30 cycles (30 seconds on, 30 seconds off), with high intensity at 4°C in a Bioruptor sonicator (Diagenode).  Under these conditions, chromatin fragments have an average size of 200 bp.
Thruplex kit was used according to manufacturer's instructions.

value: SKMEL-147 melanoma cell line

tag: chip antibody

value: anti-PHF8 antibody (Abcam, ab36068)


title: Vav-cre control without IFNg exposure

tag: cell type


title: SC27__FL002_DL4plusVCAM

city: vancouver

first: Peter

middle: W

last: Zandstra

address: 2222 Health Sciences Mall

department: sbme

country: Canada

institute: ubc

data_processing:
Illumina Casava1.6 software used for basecalling.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: fetal liver cells

extract_protocol: RNA libraries were prepared for sequencing. 10X Chromium was used to prepare single-cell cDNA librariesstandard Illumina protocols

treatment_protocol: Isolated fetal liver cells from decapitated E13.5 CD1 mouse embryos were subjected to TER-119 depletion by EasySep magnetic sorting (STEMCELL Technologies). Next, sorted HSPCs (Sca-1+ cKit+) cultured at 3.1 x10E3 HSPCs/cm2 (corresponding to 1000 cells/well) in DL4 (10 μg/mL) and VCAM-1 (2.32 μg/mL) coated 96-well plates

value: fetal liver

value: sorted HSPCs (Sca-1+ cKit+)

tag: age

value: E13.5 CD1 mouse embryos

tag: genotype

value: wild type


title: Control Input-replicate B


title: Endosperm 26°C 72 hour rep2

description:
HT_3d_R2
TPM_DEG_endosperm

source_name: Endosperm 26°C 72 hour rep2

tag: tissue


title: Cultivated peanut 180930B_SY01_P1_G08_SAAS_206_191127

data_processing:
As per manufacturer (Affymetrix)
Genotype Call (SNP call): 'ATCG' type or '---' (means NoCall)

source_name: Cultivated peanut

extract_protocol: Unkown


title: Endosperm 26°C 24 hour rep2

description:
HT_1d_R2
TPM_DEG_endosperm

source_name: Endosperm 26°C 24 hour rep2


title: PHF8 ChIPseq-replicate A


title: sgScr-A


title: PHF8 ChIPseq-replicate B2


title: SC27__FL001_DL4plusVCAM


title: Endosperm 26°C 1 hour rep3

description:
HT_1h_R3
TPM_DEG_endosperm

source_name: Endosperm 26°C 1 hour rep3


title: Cultivated peanut 180930B_SY01_P1_G10_SAAS_207_191127


title: 12wk_3

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description:
Endothelial cells with the surrounding cells, isolated by LMD from the ossification front of 12-week-old Tg(TIE2GFP)287Sato/J mice.
LMD protocol: Femurs from 4- and 12-week-old mice were snap frozen (unfixed) in dry ice-isopropanol-hexane cooling bath. For cryosectioning, type D knife for hard tissue was used. All surfaces including the knife were cleaned with RNaseZap before use. Cryosectioning was performed with Kawamoto’s films for LMD.  To minimise RNA degradation, 12 µm sections were mounted into the metal frame directly after cutting and transported in the evaporating phase of liquid nitrogen. Laser microdissection was performed using Leica LMD7 device with fluorescent lamp for endothelial cell identification. The samples were directly collected into the lysis buffer.

data_processing:
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

source_name: ossificationt front, 12-week-old mice

extract_protocol:
Total RNA was purified with PicoPure Kit (ARCTURUS) from LMD derived endothelial and perivascular cells of the OF.
For poly-A dependent cDNA synthesis and a first amplification step the Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) was used. After quality control (High sensitivity DNA Kit, Agilent) and concentration measurement (Qubit dsDNA HS Assay Kit, Invitrogen), up to 10 ng  of the purified cDNA was used for tagmentation and library completion with the Nextera XT DNA Sample Preparation Kit  (Illumina). For sequencing, Illumina NextSeq500 device was used generating 75 bp paired-end reads.

tag: donor

value: adult

tag: cells

value: endothelial cells and perivascular cells

tag: mouse origin

tag: organ

value: femur


title: Control Input-replicate A


title: 12wk_4


title: Cultivated peanut 180930B_SY01_P1_G06_SAAS_200_191127

city: Jinan

last: Tian

address: 202 North Industrial Road

institute: SAAS


title: Cultivated peanut 180930B_SY01_P1_G05_SAAS_054_191127


title: Cultivated peanut 180930B_SY01_P1_G03_SAAS_053_191127


title: H9_hESCs_TFIIIC

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

institute: University of Parma

data_processing:
ChIP-seq peak calling. Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using bowtie (Langmead et al., 2009) and aligning parameters of uniqueness (-S –m1 –v2 –t –q). P-values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10-8 and a false discovery rate (FDR) < 1%.
Genome_build: hg38

source_name: H9 hESCs

growth_protocol: Human H9 (WiCell) ES cells were grown feeder-free on the matrigel (Corning™ 354277)  coated 6-well plate in the maintenance media (StemCellTechnologie # 85850).  They were passaged with enzyme-free method (ReLeSR ,StemCellTechnologie #05872) once they become nearly confluent.  On the day of passaging, the media is supplemented with 10 µM Y27632 (Rho kinase inhibitor IV, EMD Chemicals).

extract_protocol:
Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen).
Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen).

tag: cell line

value: n house anti-GTF3C2 rabbit polyclonal


title: Endosperm 26°C 24 hour rep1

description:
HT_1d_R1
TPM_DEG_endosperm

source_name: Endosperm 26°C 24 hour rep1


title: 12wk_1


title: Endosperm 26°C 1 hour rep2

description:
HT_1h_R2
TPM_DEG_endosperm

source_name: Endosperm 26°C 1 hour rep2


title: Cultivated peanut 180930B_SY01_P1_G04_SAAS_199_191127

first: rz


title: Cultivated peanut 180930B_SY01_P1_G02_SAAS_196_191127


title: Cultivated peanut 180930B_SY01_P1_G01_SAAS_052_191127


title: Endosperm 26°C 24 hour rep3

description:
HT_1d_R3
TPM_DEG_endosperm

source_name: Endosperm 26°C 24 hour rep3


title: 4wk_5

description:
Endothelial cells with the surrounding cells, isolated by LMD from the ossification front of 4-week-old Tg(TIE2GFP)287Sato/J mice.
LMD protocol: Femurs from 4- and 12-week-old mice were snap frozen (unfixed) in dry ice-isopropanol-hexane cooling bath. For cryosectioning, type D knife for hard tissue was used. All surfaces including the knife were cleaned with RNaseZap before use. Cryosectioning was performed with Kawamoto’s films for LMD.  To minimise RNA degradation, 12 µm sections were mounted into the metal frame directly after cutting and transported in the evaporating phase of liquid nitrogen. Laser microdissection was performed using Leica LMD7 device with fluorescent lamp for endothelial cell identification. The samples were directly collected into the lysis buffer.

source_name: ossificationt front, 4-week-old mice

value: juveline


title: 12wk_2


title: Endosperm 26°C 1 hour rep1

description:
HT_1h_R1
TPM_DEG_endosperm

source_name: Endosperm 26°C 1 hour rep1


title: Cultivated peanut 180930B_SY01_P1_E24_SAAS_193_191127


title: Endosperm 16°C 72 hour rep3

description:
LT_3d_R3
TPM_DEG_endosperm

source_name: Endosperm 16°C 72 hour rep3


title: Plate_Q8_115

city: Ashburn

first: Scott

middle: M

last: Sternson

state: VA

address: 19700 Helix Dr.

institute: Janelia Research Campus, HHMI

description: a 96 well plate of single cells from LHA

data_processing:
The libraries were pooled and sequenced on an Illumina NextSeq 550 with 27 bases for read 1 and 125 bases for read 2.  Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings.
Sequencing adapters were trimmed from the reads with Cutadapt v2.1.0 (Martin, 2011) prior to alignment with STAR v2.7.5c (Dobin et al., 2013) to the Mus musculus  GRCm38.90 genome assembly from Ensembl (ensembl.org).
STAR alignment was performed with the following additional parameters: "--alignSJoverhangMin 8 --alignSJDBoverhangMin 8 --alignIntronMin 20 --alignIntronMax 150000 --outSAMmultNmax 20 --outSAMattributes NH HI NM MD CR CY UR UY --quantMode TranscriptomeSAM GeneCounts"
Gene counts were generated with the STARsolo v2.7.5c algorithm (github.com/alexdobin/STAR/) using the following additional parameters: “--soloType CB_UMI_Simple --soloCBwhitelist smartscrb_whitelist.txt --soloCBstart 2 --soloCBlen 8 --soloUMIstart 10 --soloUMIlen 10 -soloBarcodeReadLength 0 --soloCBmatchWLtype 1MM_multi_pseudocounts --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_Directional --soloUMIfiltering MultiGeneUMI --soloCellFilter None”.
Gene count filtering, variable gene selection, dimensionality reduction and clustering was performed with Seurat (v2.3.4) in R (v3.4.3).  Cell doublets/multiplets and low-quality cells were filtered based on the total number of detected genes (1,500-7,500), relative abundance of mitochondrial transcripts (percent.mito<0.055) and number of unique molecular identifiers (nUMI) per cell (<2× 105) respectively. Genes expressed in less than 3 cellswere also removed.
The filtered dataset was log-normalized and scaled, while regressing out the effects of latent variables including nUMI, and percent.mito. We performed principle component analysis (PCA) and used the first 31principle componentsfor downstream analysis. For clustering, we used the graph-based clustering approach implemented in Seurat, with the original Louvain algorithm and 10 iterations. Non-neuronal cells were identified and removed from the dataset before further analysis.
Genome_build: GRCm38.90
Supplementary_files_format_and_content: smartscrb_whitelist.txt = text file containing Smart-SCRB plate, well, and sequence for barcode RT primers.
Supplementary_files_format_and_content: merged_counts.txt = text file containing UMI counts for single cell RNA-seq
Supplementary_files_format_and_content: merged_sample_info.txt = text file containing sample metadata for single cell RNA-seq

source_name: lateral hypothalamic area

growth_protocol: All methods for animal care and use were conducted according to National Institutes ofHealth guidelines for animal research and approved by the Institutional Animal Care andUse Committee(IACUC)at Janelia Research Campus.

extract_protocol:
The dissected tissue sections were then subject to protease digestion, after which cells were dissociated and hand picked into PCR strip tubes containing 3 μl lysis buffer (0.2% TritonX-100 (Sigma) and 0.1 U/μl RNase inhibitor (Lucigen)) and cDNA libraries were prepared using the Smart-SCRB chemistry as described previously (Cembrowski et al., 2018; Xu et al., 2020).
600 pg cDNA from each pooled sample was used in a modified Nextera XT library preparation (Illumina) (Soumillon et al., 2014) using the P5NEXTPT5 primer and extending the tagmentation time to 15 m. The resulting libraries were purified according to the Nextera XT protocol (0.6x bead ratio) and quantified by qPCR using Kapa Library Quantification (Kapa Biosystems).

treatment_protocol: The manual sorting procedureto isolate non-fluorescent cell bodies from micro-dissected brain slices was similar to previously described (Hempel et al., 2007). Briefly, we sectioned 300 μm coronal slices from male Agrp-IRES-Cre ×Ai9mice (age 6-8 weeks) and used the tdTomoato fluorescence signal from AGRP neuron axon bundle terminal in the LHA to identify the boundaries of the LHA and then manually dissected with spring scissors.

value: lateral hypothalamic area

value: Agrp-IRES-Cre x Ai9

value: 6 to 8 weeks

tag: gender

value: male


title: H9_input

tag: antibody

value: input


title: Plate_Q8_107


title: Cultivated peanut 180930B_SY01_P1_E22_SAAS_192_191127

value: leaf


title: Endosperm 16°C 72 hour rep1

description:
LT_3d_R1
TPM_DEG_endosperm

source_name: Endosperm 16°C 72 hour rep1

value: Endosperm


title: Plate_Q7_120


title: 4wk_2


title: 4wk_3


title: 4wk_1


title: Endosperm 16°C 24 hour rep3

description:
LT_1d_R3
TPM_DEG_endosperm

source_name: Endosperm 16°C 24 hour rep3


title: Cultivated peanut 180930B_SY01_P1_E20_SAAS_270_191127


title: Cultivated peanut 180930B_SY01_P1_E21_SAAS_049_191127


title: Plate_Q7_114


title: Endosperm 16°C 24 hour rep1

description:
LT_1d_R1
TPM_DEG_endosperm

source_name: Endosperm 16°C 24 hour rep1


title: Plate_Q8_111


title: Endosperm 16°C 24 hour rep2

description:
LT_1d_R2
TPM_DEG_endosperm

source_name: Endosperm 16°C 24 hour rep2


title: Plate_Q7_106


title: Plate_Q7_110


title: Endosperm 16°C 1 hour rep3

description:
LT_1h_R3
TPM_DEG_endosperm

source_name: Endosperm 16°C 1 hour rep3


title: Cultivated peanut 180930B_SY01_P1_E19_SAAS_048_191127

source_name: Cultivated peanut


title: Cultivated peanut 180930B_SY01_P1_E18_SAAS_269_191127


title: 4wk_4


title: Endosperm 16°C 1 hour rep2

description:
LT_1h_R2
TPM_DEG_endosperm

source_name: Endosperm 16°C 1 hour rep2


title: Endosperm 16°C 72 hour rep2

description:
LT_3d_R2
TPM_DEG_endosperm

source_name: Endosperm 16°C 72 hour rep2


title: Cultivated peanut 180930B_SY01_P1_E17_SAAS_047_191127


title: Cultivated peanut 180930B_SY01_P1_E23_SAAS_051_191127


title: Plate_Q6_117


title: Plate_Q8_103


title: Endosperm 16°C 1 hour rep1

description:
LT_1h_R1
TPM_DEG_endosperm

source_name: Endosperm 16°C 1 hour rep1


title: Cultivated peanut 180930B_SY01_P1_E16_SAAS_270_191127


title: Embryo recovery day22 rep3

description:
D22HLEm3
TPM_DEG_embryo

source_name: Embryo recovery day22 rep3

value: Embryo

value: 26degreeC to 16degreeC


title: Cultivated peanut 180930B_SY01_P1_E15_SAAS_046_191127


title: Plate_Q6_113


title: Plate_Q6_109


title: Cultivated peanut 180930B_SY01_P1_E14_SAAS_269_191127


title: Plate_Q7_102


title: Embryo recovery day22 rep2

description:
D22HLEm2
TPM_DEG_embryo

source_name: Embryo recovery day22 rep2


title: Cultivated peanut 180930B_SY01_P1_E13_SAAS_045_191127


title: Plate_Q6_105


title: Cultivated peanut 180930B_SY01_P1_E12_SAAS_256_191127


title: Embryo recovery day22 rep1

description:
D22HLEm1
TPM_DEG_embryo

source_name: Embryo recovery day22 rep1


title: Embryo recovery day18 rep3

description:
D18HLEm3
TPM_DEG_embryo

source_name: Embryo recovery day18 rep3


title: Plate_Q5_116


title: Cultivated peanut 180930B_SY01_P1_E11_SAAS_044_191127


title: Embryo recovery day18 rep2

description:
D18HLEm2
TPM_DEG_embryo

source_name: Embryo recovery day18 rep2


title: Colo205_PC085_DMSO_24Hr

description: Gene expression data from Colo205 cell line which was co-treated with PAI-1 paracrine addicted (PPA) cell free ascites (PC085) and DMSO vehicle for 24 hours

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Microarray data was uploaded into the free programming software R (version 3.4.2) for processing and normalization.

source_name: Colo205 cell line co-treated with PAI-1 paracrine addicted (PPA) cell free ascites (PC085) and DMSO vehicle for 24 hours

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was isolated using Qiagen Mini Kit (Qiagen) following the manufacturer’s instructions. Gene expression profiling was performed using Affymetrix GeneChip Human Gene 2.0 ST Array.

tag: histology of cell line

value: Metastatic colorectal adenocarcinoma

tag: source of ascites

value: Patient diagnosed with peritoneal carcinomatosis of colorectal origin


title: Colo205_PC085_TM5441_24Hr

description: Gene expression data from Colo205 cell line which was co-treated with PAI-1 paracrine addicted (PPA) cell free ascites (PC085) and TM5441 inhibitor for 24 hours

source_name: Colo205 cell line co-treated with PAI-1 paracrine addicted (PPA) cell free ascites (PC085) and TM5441 inhibitor for 24 hours

tag: treatment


title: Colo205_PC249_TM5441_24Hr

description: Gene expression data from Colo205 cell line which was co-treated with co-activators predominant (CAP) cell free ascites (PC249) and TM5441 inhibitor for 24 hours

source_name: Colo205 cell line co-treated with co-activators predominant (CAP) cell free ascites (PC249) and TM5441 inhibitor for 24 hours


title: Embryo recovery day18 rep1

description:
D18HLEm1
TPM_DEG_embryo

source_name: Embryo recovery day18 rep1


title: Plate_Q5_108

source_name: lateral hypothalamic area


title: Cultivated peanut 180930B_SY01_P1_E10_SAAS_255_191127


title: Cultivated peanut 180930B_SY01_P1_E09_SAAS_043_191127


title: Plate_Q5_112


title: Colo205_PC249_DMSO_24Hr

description: Gene expression data from Colo205 cell line which was co-treated with co-activators predominant (CAP) cell free ascites (PC249) and DMSO vehicle for 24 hours

source_name: Colo205 cell line co-treated with co-activators predominant (CAP) cell free ascites (PC249) and DMSO vehicle for 24 hours


title: Embryo 26°C day22 rep3

description:
D22HTEm3
TPM_DEG_embryo

source_name: Embryo 26°C day22 rep3


title: Colo205_FBS_TM5441_24Hr

description: Gene expression data from Colo205 cell line which was co-treated with fetal bovine serum and TM5441 inhibitor for 24 hours

source_name: Colo205 cell line co-treated with fetal bovine serum and TM5441 inhibitor for 24 hours as control


title: Cultivated peanut 180930B_SY01_P1_E08_SAAS_260_191127

source_name: Cultivated peanut


title: Plate_Q5_104


title: Embryo 26°C day22 rep2

description:
D22HTEm2
TPM_DEG_embryo

source_name: Embryo 26°C day22 rep2


title: Plate_Q5_100


title: Embryo 26°C day22 rep1

description:
D22HTEm1
TPM_DEG_embryo

source_name: Embryo 26°C day22 rep1


title: Cultivated peanut 180930B_SY01_P1_E07_SAAS_042_191127


title: Plate_Q6_101


title: Embryo 26°C day18 rep3

description:
D18HTEm3
TPM_DEG_embryo

source_name: Embryo 26°C day18 rep3


title: Cultivated peanut 180930B_SY01_P1_E05_SAAS_041_191127


title: Embryo 26°C day18 rep2

description:
D18HTEm2
TPM_DEG_embryo

source_name: Embryo 26°C day18 rep2


title: SJAML062383_G1

city: Memphis

first: Jeffery

last: Klco

state: Tennessee

address: 262 Danny Thomas Place, D4047B

department: Pathology

institute: St Jude Children's Research Hospital

data_processing:
200207_A00239_0357_BH5MJ5DSXY v3.4.4 and bcl2fastq 2.20.0 to make basecalling
200207_A00239_0359_BH5MJ5DSXY v3.4.4 and bcl2fastq 2.20.0 to make basecalling
RNA reads were mapped using our in house pipeline Strongarm, which utilizes bwa 0.7.15 and STAR 2.3.0e
Reads from aligned bam files were assigned to genes and counted using HTSeq (v0.11.2) with the GENCODE human release 19 gene annotation.  Log2 CPM (counts per million) values were used for differential gene expression analysis. A cut-off of 10 CPM was used as the threshold to define "expressed" genes. We first determined the number of samples in the smallest group among all groups being compared as N. For a gene to be considered as expressed, we required that at least N samples should have >=10 CPM.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix txt file for log2 CPM(counts per million) values for genes defined as "expressed".
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cord blood

growth_protocol: Cells were cultured at 37℃, 5% CO2 in 1X Boitano media (StemSpan™ SFEM II, supplemented with 1X Pen/Strep, 100ng/mL of human IL-6, human Flt-3 Ligand, human SCF, human TPO, 1uM of StemRegenin1, and 35nM of UM171).

extract_protocol:
CD34 cells were washed with cold 1X PBS, flash frozen on dry ice bath. Total RNA was then extracted from the frozen cell pellets using the Quick-RNA™ Miniprep Kit from Zymo (cat#R1054) following manufacturer's protocol.  Following RNA extraction, 500ng of total RNA were submited for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment was performed.

value: hematopoietic cells

value: cord blood CD34+ cells

tag: disease state

value: normal control


title: SJAML062382_G1


title: Cultivated peanut 180930B_SY01_P1_E06_SAAS_259_191127


title: promastigotes stationary phase late passage (LP.1), rep 2

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome (Leishmania donovani)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g gene_id -s 1).
Count data were analyzed using R version 3.6.1 and the Bioconductor package DESeq2 version 1.24.0
The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model including the replicate effect as blocking factor was set in order to test for the differential expression
Genome_build: Leishmania donovani (NCBI, GCA_002243465.1)
Supplementary_files_format_and_content: Matrix from DESeq2

organism: Leishmania donovani

source_name: promastigote parasites

growth_protocol: Promastigotes, derived from splenic amastigotes, were serially passaged in M199 complete medium (M199, 10% FBS, 20 mM HEPES; 100 µM adenine, 2 mM L-glutamine, 10 µg/ml folic acid, 13.7 µM hemin, 4.2 mM NaHCO3, 1xRPMI1640 vitamins, 8 µM 6-biopterin, 100 units penicillin and 100 µg/ml streptomycin, pH 7.4) once stationary phase was reached for less than 5 passages (EP, early passage) or 20 passages (LP, late passage), incubation at 26°C.

extract_protocol:
Total RNA was extracted from EP.1 and LP.1 cultures at logarithmic and stationary (3 days) phases or from EP.1 metacyclic-enriched parasites. Promastigotes were centrifuged at 3000xg for 10 min at room temperature and re-suspended in the lysis buffer supplied with the Qiagen RNeasy Plus kit. The samples were stored at -80 °C and RNA extractions were performed according to the manufacturer’s instructions, including a DNase treatment.
RNA integrity was controlled using the Agilent Bioanalyzer. DNAse-treated RNA extracts were used for library preparation using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, California) according to the manufacturer’s instructions.   An initial poly(A) RNA isolation step (included in the Illumina protocol) was performed on total RNA to remove ribosomal RNA. Fragmentation was performed on the enriched fraction by divalent ions at high temperature. The fragmented RNA samples were randomly primed for reverse transcription followed by second-strand synthesis to create double-stranded cDNA fragments. No end repair step was necessary. An adenine was added to the 3'-end and specific Illumina adapters were ligated. Ligation products were submitted to PCR amplification. The obtained oriented libraries were controlled by Bioanalyzer DNA1000 Chips (Agilent, # 5067-1504) and quantified by spectrofluorimetry (Quant-iT™ High-Sensitivity DNA Assay Kit, #Q33120, Invitrogen).

tag: strain

value: promastigotes derived from hamster splenic amastigotes

tag: culture stage

value: stationary phase late passage


title: promastigotes stationary phase late passage (LP.1), rep 3

tag: cell type


title: Embryo 26°C day18 rep1

description:
D18HTEm1
TPM_DEG_embryo

source_name: Embryo 26°C day18 rep1

tag: temperature


title: promastigotes stationary phase late passage (LP.1), rep 1


title: Cultivated peanut 180930B_SY01_P1_E04_SAAS_190_191127


title: SJAML062381_G1


title: promastigotes log phase late passage (LP.1log), rep 3

value: log phase late passage


title: Cultivated peanut 180930B_SY01_P1_E03_SAAS_039_191127


title: Colo205_FBS_DMSO_24Hr

description: Gene expression data from Colo205 cell line which was co-treated with fetal bovine serum and DMSO vehicle for 24 hours

source_name: Colo205 cell line co-treated with fetal bovine serum and DMSO vehicle for 24 hours as control


title: SJAML062379_G1


title: Embryo 26°C day15 rep3

description:
D15HTEm3
TPM_DEG_embryo

source_name: Embryo 26°C day15 rep3


title: promastigotes log phase late passage (LP.1log), rep 2


title: SJAML062380_G1


title: Embryo 26°C day15 rep2

description:
D15HTEm2
TPM_DEG_embryo

source_name: Embryo 26°C day15 rep2


title: Cultivated peanut 180930B_SY01_P1_E01_SAAS_037_191127


title: Embryo 26°C day15 rep1

description:
D15HTEm1
TPM_DEG_embryo

source_name: Embryo 26°C day15 rep1


title: MPC-UBTF-WT 2

data_processing:
200207_A00239_0357_BH5MJ5DSXY v3.4.4 and bcl2fastq 2.20.0 to make basecalling
200207_A00239_0359_BH5MJ5DSXY v3.4.4 and bcl2fastq 2.20.0 to make basecalling
RNA reads were mapped using our in house pipeline Strongarm, which utilizes bwa 0.7.15 and STAR 2.3.0e
Reads from aligned bam files were assigned to genes and counted using HTSeq (v0.11.2) with the GENCODE human release 19 gene annotation.  Log2 CPM (counts per million) values were used for differential gene expression analysis. A cut-off of 10 CPM was used as the threshold to define "expressed" genes. We first determined the number of samples in the smallest group among all groups being compared as N. For a gene to be considered as expressed, we required that at least N samples should have >=10 CPM.
The batch effect among lots of cord blood CD34+ cells was corrected using the ComBat method available from R package SVA (v3.36.0)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix txt file for log2 CPM(counts per million) values for genes defined as "expressed".
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

tag: day

value: day 32

tag: expression vectors

value: UBTF-WT

tag: nha


title: Embryo 26°C day7 rep3

description:
D7HTEm3
TPM_DEG_embryo

source_name: Embryo 26°C day7 rep3

tag: tissue


title: MPC-UBTF-ITD54 2


title: Cultivated peanut 180930B_SY01_P1_C24_SAAS_172_191127


title: promastigotes stationary phase early passage (EP.1stat), rep 2

value: stationary phase early passage


title: Cultivated peanut 180930B_SY01_P1_C23_SAAS_033_191127


title: Cultivated peanut 180930B_SY01_P1_C22_SAAS_171_191127


title: MPC-UBTF-ITD54 1


title: metacyclic enriched promastigotes from early passage  (EP.1meta), rep 3

value: metacyclic enriched from early passage


title: Embryo 26°C day7 rep1

description:
D7HTEm1
TPM_DEG_embryo

source_name: Embryo 26°C day7 rep1


title: MPC-UBTF-WT 1


title: Cultivated peanut 180930B_SY01_P1_E02_SAAS_189_191127


title: MPC-nHA-UBTF-ITD54 4

value: nHA-tagged


title: Embryo 26°C day7 rep2

description:
D7HTEm2
TPM_DEG_embryo

source_name: Embryo 26°C day7 rep2


title: promastigotes log phase late passage (LP.1log), rep 1


title: Embryo 26°C day3 rep2

description:
D3HTEmR2
TPM_DEG_embryo

source_name: Embryo 26°C day3 rep2


title: Embryo 26°C day3 rep1

description:
D3HTEmR1
TPM_DEG_embryo

source_name: Embryo 26°C day3 rep1


title: metacyclic enriched promastigotes from early passage (EP.1meta), rep 2


title: Embryo 26°C day3 rep3

description:
D3HTEmR3
TPM_DEG_embryo

source_name: Embryo 26°C day3 rep3


title: Colo205_0.1% PC009 Ascites

description: Gene expression data from Colo-205 cells treated with 0.1% colorectal PC CFA medium for 24 hours

source_name: Colo205 cell line treated with 0.1% of PC009 cell free ascites for 24 hours

extract_protocol: Total RNA was isolated using Qiagen Mini Kit (Qiagen) following the manufacturer’s instructions. Gene expression profiling was performed using Affymetrix GeneChip Genome U133 Plus 2.0 array (Affymetrix).

value: 0.1% of PC009 cell free ascites


title: MPC-nHA-UBTF-ITD54 3


title: metacyclic enriched promastigotes from early passage (EP.1meta), rep 1


title: promastigotes log phase early passage (EP.1log), rep 3

value: log phase early passage


title: MPC-nHA-UBTF-ITD54 2


title: Embryo 26°C day1 rep3

description:
D1HTEmR3
TPM_DEG_embryo

source_name: Embryo 26°C day1 rep3

value: Embryo


title: MPC-nHA-UBTF-ITD54 1


title: Cultivated peanut 180930B_SY01_P1_C19_SAAS_030_191127

source_name: Cultivated peanut

value: leaf


title: promastigotes log phase early passage (EP.1log), rep 2


title: Cultivated peanut 180930B_SY01_P1_C18_SAAS_168_191127


title: promastigotes stationary phase early passage (EP.1stat), rep 3


title: Embryo 26°C day1 rep2

description:
D1HTEmR2
TPM_DEG_embryo

source_name: Embryo 26°C day1 rep2


title: promastigotes stationary phase early passage (EP.1stat), rep 1


title: Cultivated peanut 180930B_SY01_P1_C17_SAAS_029_191127


title: promastigotes log phase early passage (EP.1log), rep 1


title: Cultivated peanut 180930B_SY01_P1_C21_SAAS_031_191127


title: Cultivated peanut 180930B_SY01_P1_C16_SAAS_160_191127


title: MPC-nHA-UBTF-WT 3

source_name: cord blood


title: Embryo 26°C day1 rep1

description:
D1HTEmR1
TPM_DEG_embryo

source_name: Embryo 26°C day1 rep1


title: Cultivated peanut 180930B_SY01_P1_C20_SAAS_170_191127


title: Embryo 16°C day22 rep3

description:
D22LTEm3
TPM_DEG_embryo

source_name: Embryo 16°C day22 rep3


title: Cultivated peanut 180930B_SY01_P1_C15_SAAS_028_191127


title: Cultivated peanut 180930B_SY01_P1_C14_SAAS_159_191127


title: MPC-nHA-UBTF-WT 1


title: Embryo 16°C day22 rep1

description:
D22LTEm1
TPM_DEG_embryo

source_name: Embryo 16°C day22 rep1


title: Embryo 16°C day22 rep2

description:
D22LTEm2
TPM_DEG_embryo

source_name: Embryo 16°C day22 rep2


title: MPC-EMPTY 3

value: Empty


title: Cultivated peanut 180930B_SY01_P1_C12_SAAS_157_191127


title: MPC-EMPTY 2


title: Embryo 16°C day18 rep3

description:
D18LTEm3
TPM_DEG_embryo

source_name: Embryo 16°C day18 rep3


title: Cultivated peanut 180930B_SY01_P1_C13_SAAS_027_191127


title: MPC-EMPTY 1


title: Cultivated peanut 180930B_SY01_P1_C11_SAAS_026_191127


title: Embryo 16°C day18 rep1

description:
D18LTEm1
TPM_DEG_embryo

source_name: Embryo 16°C day18 rep1


title: MPC-nHA-UBTF-WT 4


title: Cultivated peanut 180930B_SY01_P1_C10_SAAS_156_191127


title: Embryo 16°C day15 rep3

description:
D15LTEm3
TPM_DEG_embryo

source_name: Embryo 16°C day15 rep3


title: U2OS_TERT-WT_dsRNA

city: Hangzhou

first: Jian

last: Mao

address: 2318 Yuhangtang Rd

institute: Hangzhou Normal University

description: double-stranded RNA (dsRNA)

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
To assess the expression levels of ERVs, RNA-seq clean reads were mapped to the hg38 genome using the STAR aligner software, allowing up to three mismatches and filtering out reads that mapped to > 500 positions in the genome. Mapped files were then processed using the makeTagDirectory script of HOMER with the -keepOne option.
The tag directories of the mapped files were analyzed using the analyzeRepeats.pl script of HOMER with the option ‘repeat’ and -noadj or -fpkm.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw counts for every ERV element and every sample.

source_name: osteosarcoma

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen). For dsRNA enrichment, total RNA was immunoprecipitated using the J2 dsRNA-specific antibody (English and Scientific Consulting Kft., 10010200). In brief, the product of 9 μg RNA was incubated in binding buffer (150 mM NaCl, 50 mM Tris pH 8.0, 1 mM EDTA, 1% NP-40) with 5 μg J2 antibody and 20 μl Magna ChIP™ Protein A+G Magnetic Beads (Millipore), rotating overnight at 4°C, followed by 5 washes in cold binding buffer. RNA was then extracted with TRIzol Reagent.
RNA libraries were prepared for sequencing using strand-specific Illumina protocols
Strand-specific RNA-Seq

treatment_protocol: U2OS cells were transfected with pcDNA3.1-TERT-WT or pcDNA3.1-TERT-K626A using Lipofectamine 3000 according to the manufacturer’s instructions for 48 h.


title: Cultivated peanut 180930B_SY01_P1_C09_SAAS_025_191127


title: Embryo 16°C day15 rep2

description:
D15LTEm2
TPM_DEG_embryo

source_name: Embryo 16°C day15 rep2


title: U2OS_TERT-K626A_rep3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 and paired-end clean reads were aligned to the reference genome using Hisat2.
HTSeq was used to count the reads numbers mapped to each gene.
Differential expression analyses of two groups were performed using the DESeq2 R package.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen). A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U2OS cells were transfected with pcDNA3.1-TERT-WT, pcDNA3.1-TERT-K626A or empty vector using Lipofectamine 3000 according to the manufacturer’s instructions for 48 h.


title: EnC-C_DMSO

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

description: Gene expression data from EnC-C PDCs treated with vehicle (DMSO).

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip (Human Clariom S Array). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (build.1.2.1.20) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: EnC-C, DMSO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: Endometrial cancer patient-derived cells (EnC-A, EnC-B, and EnC-C) were maintained in STEMPRO hESC SFM medium supplemented with 8 ng/mL bFGF, penicillin/streptomycin, 20 mmol/L Y27632, and 0.1 mmol/L 2-mercaptoethanol using ultra-low-attachment culture dish.

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: Cells were transfected with 100 microM N,N-diethylaminobenzaldehyde (DEAB) or control (DMSO) for 8 h.

value: EnC-C

value: Vehicle (DMSO)


title: EnC-C_DEAB

description: Gene expression data from EnC-C PDCs treated with ALDH inhibitor DEAB.

source_name: EnC-C, DEAB

value: ALDH inhibitor DEAB


title: EnC-A_DMSO

description: Gene expression data from EnC-A PDCs treated with vehicle (DMSO).

source_name: EnC-A, DMSO

value: EnC-A


title: MPC-nHA-UBTF-WT 2

value: hematopoietic cells

value: cord blood CD34+ cells


title: Cultivated peanut 180930B_SY01_P1_C07_SAAS_024_191127


title: EnC-A_DEAB

description: Gene expression data from EnC-A PDCs treated with ALDH inhibitor DEAB.

source_name: EnC-A, DEAB


title: Embryo 16°C day15 rep1

description:
D15LTEm1
TPM_DEG_embryo

source_name: Embryo 16°C day15 rep1


title: EnC-B_DEAB

description: Gene expression data from EnC-B PDCs treated with ALDH inhibitor DEAB.

source_name: EnC-B, DEAB

value: EnC-B


title: U2OS_TERT-K626A_rep2


title: EnC-A_estrogen+progesterone

description: Gene expression data from EnC-A PDCs treated with mixed estrogen and progesterone.

source_name: EnC-A, estrogen+progesterone

growth_protocol: Endometrial cancer patient-derived cells (EnC-A) were maintained in STEMPRO hESC SFM medium supplemented with 8 ng/mL bFGF, penicillin/streptomycin, 20 mmol/L Y27632, and 0.1 mmol/L 2-mercaptoethanol using ultra-low-attachment culture dish.

treatment_protocol: Cells were transfected with 10 nM 17beta-estradiol, 10 nM progesterone, mixed (10 nM each) 17beta-estradiol and progesterone, or control (ethanol) for 48 h.

value: estrogen+progesterone


title: Embryo 16°C day18 rep2

description:
D18LTEm2
TPM_DEG_embryo

source_name: Embryo 16°C day18 rep2


title: EnC-A_progesterone

description: Gene expression data from EnC-A PDCs treated with progesterone.

source_name: EnC-A, progesterone

value: progesterone


title: Embryo 16°C day7 rep3

description:
D7LTEm3
TPM_DEG_embryo

source_name: Embryo 16°C day7 rep3


title: Cultivated peanut 180930B_SY01_P1_C06_SAAS_154_191127

source_name: Cultivated peanut


title: U2OS_TERT-K626A_rep1


title: Embryo 16°C day7 rep2

description:
D7LTEm2
TPM_DEG_embryo

source_name: Embryo 16°C day7 rep2


title: Cultivated peanut 180930B_SY01_P1_C05_SAAS_023_191127


title: U2OS_TERT-WT_rep3


title: U2OS_TERT-K626A_dsRNA

description: double-stranded RNA (dsRNA)


title: EnC-B_DMSO

description: Gene expression data from EnC-B PDCs treated with vehicle (DMSO).

source_name: EnC-B, DMSO


title: Embryo 16°C day7 rep1

description:
D7LTEm1
TPM_DEG_embryo

source_name: Embryo 16°C day7 rep1


title: EnC-A_estrogen

description: Gene expression data from EnC-A PDCs treated with estrogen.

source_name: EnC-A, estrogen

value: estrogen


title: Cultivated peanut 180930B_SY01_P1_C04_SAAS_153_191127


title: Cultivated peanut 180930B_SY01_P1_C08_SAAS_155_191127


title: U2OS_TERT-WT_rep2

source_name: osteosarcoma


title: Embryo 16°C day3 rep3

description:
D3LTEmR3
TPM_DEG_embryo

source_name: Embryo 16°C day3 rep3


title: Cultivated peanut 180930B_SY01_P1_C03_SAAS_020_191127


title: EnC-A_ethanol

description: Gene expression data from EnC-A PDCs treated with vehicle (ethanol).

source_name: EnC-A, ethanol

value: ethanol


title: EnC-C_liver metastasis

description: Gene expression data from secondary EnC-C PDCs which were prepared from liver metastasis in xenograft mouse model.

source_name: EnC-C, liver metastasis

growth_protocol: Endometrial cancer patient-derived cells (EnC-C) were maintained in STEMPRO hESC SFM medium supplemented with 8 ng/mL bFGF, penicillin/streptomycin, 20 mmol/L Y27632, and 0.1 mmol/L 2-mercaptoethanol using ultra-low-attachment culture dish.

treatment_protocol: Cells were injected into the flank of immunodeficient mice and xenografted tumors were generated. When the xenografted tumors were further inoculated into the next immunodeficient mice, liver and lung metastases were developed. Secondary PDCs were cultured from the dissected metastatic tumors.


title: U2OS_TERT-WT_rep1


title: U2OS_Vector_rep3


title: Embryo 16°C day3 rep1

description:
D3LTEmR1
TPM_DEG_embryo

source_name: Embryo 16°C day3 rep1


title: U2OS_Vector_rep1


title: Cultivated peanut 180930B_SY01_P1_A24_SAAS_151_191127


title: EnC-C_lung metastasis

description: Gene expression data from secondary EnC-C PDCs which were prepared from lung metastasis in xenograft mouse model.

source_name: EnC-C, lung metastasis


title: U2OS_Vector_rep2


title: Cultivated peanut 180930B_SY01_P1_C01_SAAS_019_191127


title: Embryo 16°C day1 rep3

description:
D1LTEmR3
TPM_DEG_embryo

source_name: Embryo 16°C day1 rep3


title: EnC-C

description: Gene expression data from primary EnC-C PDCs which were established from patient.

source_name: EnC-C, parental


title: Embryo 16°C day3 rep2

description:
D3LTEmR2
TPM_DEG_embryo

source_name: Embryo 16°C day3 rep2


title: Embryo 16°C day1 rep2

description:
D1LTEmR2
TPM_DEG_embryo

source_name: Embryo 16°C day1 rep2


title: Cultivated peanut 180930B_SY01_P1_A23_SAAS_018_191127


title: kidney_sample_RNAseq_18

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

institute: Lunenfeld-Tanenbaum Research Institute

description: AllRPMforGEO.txt

data_processing:
The RNAseq data was processed with an in-house pipeline on computers with Mac OS X 10.11.5.
The quality was inspected with FastQC v0.11.5.
The data was trimmed to remove 15 nucleotides on the 5’ end of each read resulting in most reads having a length of 87.
The data was mapped to the reference human genome hg19 using Tophat (version 1.4.1) (-r = 100) 58, and bowtie (version 0.12.7) 59 with default parameters. These older versions were used to maintain compatibility with extensively tested in-house perl processing scripts (perl version 5.16.2) and R scripts (R version 3.4.3).
The mapped read files were converted to sam format with samtools (version 0.1.18) 60, and ambiguous reads were filtered out with an in-house script.
truRPM data (transcript union Reads Per Million reads) was calculated using in-house scripts, to represent overall transcript level normalized by total mapped reads.  This includes reads mapped onto exons and introns for coding genes.  An unrelated control sample was included in the processing pipeline to verify the integrity of the output.
Genome_build: hg19
Supplementary_files_format_and_content: AllRPMforGEO.txt: A txt file with RPM information for samples

source_name: kidney

extract_protocol:
RNA was extracted from formalin fixed paraffin embedded kidney biopsy blocks.  Ten 10 um thick cryomatrix-embedded kidney biopsy blocks were sectioned. Total RNA was extracted using RNeasy kit (QIAGEN). The yield and quality of total RNA was then assessed using Nanodrop (Thermo Fisher) and BioAnalyzer (Agilent), respectively.
cDNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2 (RS-122-2001) and then loaded as 2 indexed samples per lane on an Illumina HiSeq 2000.

tag: type

value: transplant


title: Embryo 16°C day1 rep1

description:
D1LTEmR1
TPM_DEG_embryo

source_name: Embryo 16°C day1 rep1


title: S72_16X

city: Parow

first: Gian

last: van der Spuy

address: Francie van Zijl Dr

department: Biomedical Sciences

country: South Africa

institute: Stellenbosch University

data_processing:
import into R and normalisation based on 3 reference genes using BioConductor packages readqPCR and normqPCR
statistical analysis using Stan via the brms package

extract_protocol:
Pre-alveolar macrophageplification protocol: cDNA were further subjected to either 16 or 20 pre-alveolar macrophageplification cycles using Fluidigm One Tube Prealveolar macrophagep Master Mix (Fluidigm PN 100-5580)
RNEasy® Micro Kit (Qiagen, Germany)

value: Peripheral blood

tag: pre_alveolar macrophageplification

tag: patient condition

value: Tuberculosis

value: monocyte


title: S71_20X

source_name: Peripheral blood_TDMT429_total RNA_myeloid-derived  suppressor cell

value: myeloid-derived  suppressor cell


title: S71_16X


title: S70_20X


title: Cultivated peanut 180930B_SY01_P1_A22_SAAS_150_191127

source_name: Cultivated peanut

value: leaf


title: S72_20X


title: kidney_sample_RNAseq_17

description: AllRPMforGEO.txt


title: Embryo 16°C day0 rep3

description:
D0LTEmR3
TPM_DEG_embryo

source_name: Embryo 16°C day0 rep3

value: Embryo


title: Cultivated peanut 180930B_SY01_P1_A21_SAAS_017_191127


title: S70_16X


title: Embryo 16°C day0 rep2

description:
D0LTEmR2
TPM_DEG_embryo

source_name: Embryo 16°C day0 rep2


title: Cultivated peanut 180930B_SY01_P1_C02_SAAS_152_191127


title: kidney_sample_RNAseq_15

description: AllRPMforGEO.txt


title: S69_20X

source_name: Peripheral blood_TDMT439_total RNA_myeloid-derived  suppressor cell


title: Cultivated peanut 180930B_SY01_P1_A20_SAAS_149_191127


title: Embryo 16°C day0 rep1

description:
D0LTEmR1
TPM_DEG_embryo

source_name: Embryo 16°C day0 rep1


title: kidney_sample_RNAseq_14

description: AllRPMforGEO.txt


title: Endosperm recovery day22 rep3

description:
D22HLEd3
TPM_DEG_endosperm

source_name: Endosperm recovery day22 rep3

value: Endosperm

value: 26degreeC to 16degreeC


title: Cultivated peanut 180930B_SY01_P1_A18_SAAS_148_191127


title: Cultivated peanut 180930B_SY01_P1_A19_SAAS_016_191127


title: S69_16X


title: kidney_sample_RNAseq_13

description: AllRPMforGEO.txt


title: Cultivated peanut 180930B_SY01_P1_A17_SAAS_015_191127


title: kidney_sample_RNAseq_12

description: AllRPMforGEO.txt


title: Endosperm recovery day22 rep2

description:
D22HLEd2
TPM_DEG_endosperm

source_name: Endosperm recovery day22 rep2


title: S68_16X

source_name: BAL Fluid_TBH70446489_total RNA_myeloid-derived  suppressor cell

value: BAL Fluid


title: kidney_sample_RNAseq_11

description: AllRPMforGEO.txt


title: Endosperm recovery day22 rep1

description:
D22HLEd1
TPM_DEG_endosperm

source_name: Endosperm recovery day22 rep1


title: kidney_sample_RNAseq_10

description: AllRPMforGEO.txt


title: kidney_sample_RNAseq_16

description: AllRPMforGEO.txt


title: S67_20X

source_name: BAL Fluid_TBH163527450_total RNA_alveolar macrophage

value: alveolar macrophage


title: Endosperm recovery day18 rep2

description:
D18HLEd2
TPM_DEG_endosperm

source_name: Endosperm recovery day18 rep2


title: Cultivated peanut 180930B_SY01_P1_A16_SAAS_141_191127


title: Endosperm recovery day18 rep3

description:
D18HLEd3
TPM_DEG_endosperm

source_name: Endosperm recovery day18 rep3


title: Cultivated peanut 180930B_SY01_P1_A15_SAAS_012_191127


title: S67_16X


title: Cultivated peanut 180930B_SY01_P1_A14_SAAS_140_191127


title: Endosperm recovery day18 rep1

description:
D18HLEd1
TPM_DEG_endosperm

source_name: Endosperm recovery day18 rep1


title: Endosperm 26°C day22 rep3

description:
D22HTEd3
TPM_DEG_endosperm

source_name: Endosperm 26°C day22 rep3


title: kidney_sample_RNAseq_8

description: AllRPMforGEO.txt

source_name: kidney


title: S66_20X

source_name: BAL Fluid_TBH163527450_total RNA_myeloid-derived  suppressor cell


title: kidney_sample_RNAseq_6

description: AllRPMforGEO.txt


title: Cultivated peanut 180930B_SY01_P1_A10_SAAS_138_191127


title: kidney_sample_RNAseq_7

description: AllRPMforGEO.txt


title: kidney_sample_RNAseq_4

description: AllRPMforGEO.txt


title: Cultivated peanut 180930B_SY01_P1_A09_SAAS_005_191127


title: S68_20X


title: Endosperm 26°C day22 rep2

description:
D22HTEd2
TPM_DEG_endosperm

source_name: Endosperm 26°C day22 rep2


title: Cultivated peanut 180930B_SY01_P1_A11_SAAS_008_191127

source_name: Cultivated peanut


title: Endosperm 26°C day18 rep2

description:
D18HTEd2
TPM_DEG_endosperm

source_name: Endosperm 26°C day18 rep2


title: Cultivated peanut 180930B_SY01_P1_A12_SAAS_139_191127


title: S65_16X

value: Other Lung Disease

value: TBHFungalInfection


title: S65_20X


title: S63_20X

value: TBHLeukaemiaTB


title: kidney_sample_RNAseq_3

description: AllRPMforGEO.txt


title: Endosperm 26°C day22 rep1

description:
D22HTEd1
TPM_DEG_endosperm

source_name: Endosperm 26°C day22 rep1


title: S64_20X

source_name: Peripheral blood_TBHFungalInfection_total RNA_myeloid-derived  suppressor cell


title: kidney_sample_RNAseq_5

description: AllRPMforGEO.txt


title: S66_16X


title: Endosperm 26°C day18 rep1

description:
D18HTEd1
TPM_DEG_endosperm

source_name: Endosperm 26°C day18 rep1


title: Cultivated peanut 180930B_SY01_P1_A08_SAAS_137_191127


title: S64_16X


title: kidney_sample_RNAseq_9

description: AllRPMforGEO.txt


title: Cultivated peanut 180930B_SY01_P1_A07_SAAS_004_191127


title: kidney_sample_RNAseq_2

description: AllRPMforGEO.txt


title: Endosperm 26°C day18 rep3

description:
D18HTEd3
TPM_DEG_endosperm

source_name: Endosperm 26°C day18 rep3


title: Cultivated peanut 180930B_SY01_P1_A13_SAAS_011_191127


title: S62_20X

source_name: Peripheral blood_TBHLeukaemiaTB_total RNA_myeloid-derived  suppressor cell


title: Cultivated peanut 180930B_SY01_P1_A04_SAAS_135_191127


title: Cultivated peanut 180930B_SY01_P1_A06_SAAS_136_191127


title: S63_16X


title: mutant rep3

city: Shanghai

first: Mingguang

last: Lei

address: No. 3888, Chenhua Road

institute: Shanghai Center for Plant Stress Biology

data_processing:
Basecalls performed using CASAVA version 1.4
low quality sequences were trimmed using the bbduk.sh script in the bbmap suite of tools
Clean reads were mapped to the TAIR10 genome using the STAR aligner v2.5.3a and gene abundances were estimated with StringTie v1.3.3b.
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma separated value text file with count data for each sample

organism: Arabidopsis thaliana

growth_protocol: Growth at 22 °C with 100 μmol·m-2·s-1 for 12 days

extract_protocol:
Whole seedlings were ground in liquid nitrogen, and RNA was harvested using RNeasy Plant Mini Kit, Qiagen, Germany.  The NEBNext Ultra II Directional RNA library Prep Kit for Illumina (New England Biolabs) was used for generating the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 1/2 MS with 1% sucrose and 1% agar.

value: seedling


title: S62_16X


title: WT rep3


title: Cultivated peanut 180930B_SY01_P1_A05_SAAS_003_191127

growth_protocol: Field collection or laboratory cultivation


title: Endosperm 26°C day15 rep3

description:
D15HTEd3
TPM_DEG_endosperm

data_processing:
raw reads were trimmed using cutadapt-1.9.1
trimmed reads were mapped to Brassica oleracea reference genome using STAR-2.5.a
featureCounts was employed to count mapped reads
egdeR was used to calculate differentially expressed genes (DEG)
Supplementary_files_format_and_content: csv files including TPM values

source_name: Endosperm 26°C day15 rep3

extract_protocol:
endosperm/seed coat and embryo were dissected under microscope, then RNA was extracted using the ENZA Plant RNA kit (OmegaBio-tek).
For day7, day15, day18, day22 endosperm samples, library was constructed using Ovation RNA-seq system(Nugen, 0351 Arabidopsis); for all the other samples, library was constructed using standard Illumina protocols by Novogene (China).


title: S58_20X

source_name: Peripheral blood_TDMT428_total RNA_myeloid-derived  suppressor cell


title: Endosperm 26°C day15 rep1

description:
D15HTEd1
TPM_DEG_endosperm

source_name: Endosperm 26°C day15 rep1