title: Subject 62, endometrial tissue sample, Day P+7

description:
Library name: Sample 184
molecule: small RNA

source_name: endometrial tissue

value: endometrial tissue


title: CODE116

status: Public on May 22 2025

type: RNA

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Samples were hybridized for 16 hours at 65C

scan_protocol: Detection and scanning were performed by the nCounter SPRINT Profiler analysis system.

data_processing: Raw count data from nCounter

label: fluorescence microscope

molecule: total RNA

organism: Homo sapiens

source_name: CRC tumor

label_protocol: Sample RNA is hybridized with target-specific capture and reporter probes. This creates a library of unique target-probe complexes. Each target is labelled with a specific barcode, which can be detected and counted using an automated fluorescence microscope.

extract_protocol: RNA was extracted from FF tissue using RNA-Bee (Tel-Test inc., USA) and Trizol (ABP Biosciences, Rockville, USA) according to manufacturer’s protocol. Samples with a tumor percentage <30% were excluded. For FFPE tissue, three 10 µm-slides with flanking H&Es were prepared and tissue deparaffinisation was performed with Xylene. Subsequently, tumor tissue was macro-dissected to enrich for tumor tissue. RNA was extracted using the RNeasy FFPE kit (QIAGEN GmbH, Hilden, Germany) according to manufacturer’s instructions. RNA quantity and quality were measured using Tapestation (Agilent).

tag: tissue

value: FFPE


title: CODE717

description: RCC file not available for this record


title: Subject 62, paired blood sample, repeat 1, Day P+7

type: SRA

city: Zhubei City, Hsinchu County

first: An

last: Hsu

address: 7F-6, No. 66, Shengyi 5th Road

country: Taiwan

institute: INTI Labs

description:
Library name: Sample 185
molecule: small RNA

library_source: transcriptomic

data_processing:
Data were preprocessed by performing quality control on raw fastq data, including trimming adapter sequences, and removing low-quality reads using FastQC and Trimmomatic. After trimming low-quality (Q value < 20) ends from reads in addition to adapter removal, reads shorter than 17bps or longer than 55bps were discarded.
Alignment of processed reads to Human Genome Assembly GRCh38 (hg38) reference genome and a specific set of small RNA sequences from miRBase was performed by using aligners such as Bowtie.
Quantification of extracted reads from the data by mapping the aligned reads using samtools and obtained reference annotations using miRBase (total 2656 miRNAs).
Assembly: GRCh38
Supplementary files format and content: csv file include  raw read counts of miRNAs for each sample

source_name: blood

extract_protocol:
Small RNA was isolated from 200–600 μL of plasma with miRNeasy Serum/Plasma Advanced Kit (QIAGEN, Hilden, Germany, Cat. No. 217204) following the manufacturer’s protocol. For each sample, at least 10ng miRNA was used as input for the following library construction.
The miRNA sequencing library was constructed using the QIAseq miRNA Library Kit (QIAGEN, Germany, Cat. No. 331502).

value: blood

tag: treatment

value: Progestrone treatment


title: Subject 61, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 183
molecule: small RNA


title: Primary CRC tumor samples (FF), P2999

data_processing:
Prior to read trimming and alignment, the quality of raw data was assessed using FastQC (v.0.11.9). Trimming was performed on 12 and 11 bases for single-end and pair-end RNAseq data, respectively. To further enhance data quality, bases with a Phred score less than 20 were filtered using Cutadapt (v1.18). The reads were aligned to the reference genome (GRCh38) and gene counts were generated using the STAR (v.2.7.4.a) algorithm. To enable accurate downstream analyses, the count data was log2-transformed and quantile normalization was applied.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw gene count for each Sample

source_name: Primary colorectal cancer

extract_protocol:
For RNA extraction from FF tissue, we followed the manufacturer's protocol using RNA-B and Trizol. Exclusion criteria for samples were set as a tumor percentage of less than 30%. When working with FFPE tissue, we prepared three 10 µm slides that were subjected to H&E staining. De-paraffinisation of tissue was carried out using Xylene, followed by macro-dissection of the specimen to enrich for tumor tissue. RNA extraction was performed using the RNeasy FFPE kit (Qiagen, location) as per the manufacturer's instructions. To assess the quality and quantity of RNA, we used the NanoDrop2000 and Tapestation (Agilent).
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep following manufacturer’s protocol.

value: Primary colorectal cancer

tag: Sex

value: Female

tag: fixation

value: Fresh Frozen


title: CODE86


title: Subject 61, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 182
molecule: small RNA


title: LT biol rep2

city: Zhengzhou

first: Lei

last: Zhang

state: Henan

address: No. 7, Weiwu Road

department: Reproductive Medicine Center

country: China

institute: Henan Provincial People’s Hospital

data_processing:
Firstly, Fastp (version 0.18.0) was used to remove the adaptor sequence and low-quality bases to obtain clean reads.
Bowtie2 (version 2.2.8) was used to remove ribosome RNA (rRNA) reads.
Then, mapped reads were obtained by comparing clean reads to the reference genome through Hisat2 (version 2.4).
The FPKM value of gene expression (fragment per kilobase of transcript per million mapped reads) was calculated by StringTie (version 1.3.1).
DEseq2 analyzed the gene expression differences between samples. An FDR value (q value) of <0.05 and fold change (FC) of >2 were defined as differential expressions.
Assembly: Ensembl_release100 (GRCm39)
Supplementary files format and content: gene_expression_anno.xls including FPKM values for each sample

organism: Mus musculus

source_name: liver

growth_protocol: After in vitro fertilization (IVF) of fresh and vitrified oocytes, the zygotes were cultured in KSOM medium for 24 hours, and the cleaved embryos were used for embryo transfer. The cleaved embryos were transferred into the fallopian tubes of pseudopregnant female mice by operation. Twenty embryos were transplanted into each female mouse and raised normally until the offspring mice were born. The offspring mice were raised to adulthood (8W) after birth. The feeding environment was 12 h/12 h light/dark, the temperature was 25℃, and the humidity was 50%. The offspring were raised to adulthood (8 weeks old) after birth. The feeding, management, and use of mice complied with the ‘3Rs’ of animal ethics.

extract_protocol:
The offspring mice were raised to adulthood (8W) after birth. After being killed by cervical dislocation, the liver and kidney tissues were retrieved and thoroughly washed with normal saline to remove the blood. Then, the tissue block was cut 0.5 cm×0.5 cm in size with sterile RNase-free surgical scissors, ground into a powder after adding liquid nitrogen, and collected in a sterile RNase-free EP tube. After TRIzol was added and fully lysed, the total RNA in the tissues was obtained for sequencing according to the conventional RNA extraction steps.
The library was built according to standard Illumina protocols, which mainly include the steps of rRNA removal, mRNA isolation and fragmentation, cDNA double-strand synthesis and purification, cDNA terminal repair, 3’ end plus A, adaptor ligation, screening cDNA fragments of around 200 bp, PCR library enrichment and purification, etc.

treatment_protocol: We used the Cryotop method commonly used in ART for vitrification and thawing of oocytes in this study. The thawed oocytes were placed in KSOM at 37℃ and incubated at 100% humidity for 3 hours before IVF. In the control group, except for oocyte vitrification and thawing, the other treatments were the same as those in the vitrification group.

tag: strain

value: CD-1 (ICR)

value: liver

tag: developmental stage

value: adult offspring

value: derived from vitrified oocytes


title: Primary CRC tumor samples (FF), P2916


title: Subject 61, endometrial tissue sample, Day P+7

description:
Library name: Sample 181
molecule: small RNA


title: CODE645

description: RCC file not available for this record


title: CODE137


title: Subject 60, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 180
molecule: small RNA


title: Subject 60, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 179
molecule: small RNA


title: CODE810

description: RCC file not available for this record


title: CODE925

description: RCC file not available for this record


title: Primary CRC tumor samples (FF), P2887

value: Male


title: Subject 59, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 177
molecule: small RNA


title: Subject 59, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 176
molecule: small RNA


title: Primary CRC tumor samples (FF), P2840


title: Primary CRC tumor samples (FF), P2846


title: Subject 58, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 173
molecule: small RNA


title: Subject 58, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 174
molecule: small RNA


title: CODE201

description: RCC file not available for this record


title: Subject 57, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 170
molecule: small RNA


title: Subject 59, endometrial tissue sample, Day P+7

description:
Library name: Sample 175
molecule: small RNA


title: Primary CRC tumor samples (FF), P2802


title: Primary CRC tumor samples (FF), P2807


title: CODE841

description: RCC file not available for this record


title: P2886

source_name: stage III CRC tumor

value: FF

tag: Stage

value: III


title: P2999


title: Subject 56, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 168
molecule: small RNA


title: Subject 57, endometrial tissue sample, Day P+7

description:
Library name: Sample 169
molecule: small RNA


title: Subject 56, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 167
molecule: small RNA


title: Primary CRC tumor samples (FF), P2886


title: Subject 60, endometrial tissue sample, Day P+7

description:
Library name: Sample 178
molecule: small RNA


title: P2887


title: Primary CRC tumor samples (FF), P2798


title: P3039


title: Subject 55, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 165
molecule: small RNA


title: Subject 58, endometrial tissue sample, Day P+7

description:
Library name: Sample 172
molecule: small RNA


title: Subject 56, endometrial tissue sample, Day P+7

description:
Library name: Sample 166
molecule: small RNA


title: Subject 55, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 164
molecule: small RNA


title: Primary CRC tumor samples (FF), P2772


title: P2916


title: Subject 57, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 171
molecule: small RNA


title: Subject 55, endometrial tissue sample, Day P+7

description:
Library name: Sample 163
molecule: small RNA


title: Primary CRC tumor samples (FF), P2763


title: Subject 54, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 162
molecule: small RNA


title: Primary CRC tumor samples (FF), P2746


title: P3043


title: Subject 54, endometrial tissue sample, Day P+7

description:
Library name: Sample 160
molecule: small RNA


title: Subject 54, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 161
molecule: small RNA


title: Subject 53, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 159
molecule: small RNA


title: Primary CRC tumor samples (FF), P2731


title: Primary CRC tumor samples (FF), P2715


title: Subject 53, endometrial tissue sample, Day P+7

description:
Library name: Sample 157
molecule: small RNA


title: P2772


title: P2840


title: Subject 52, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 156
molecule: small RNA


title: Subject 52, endometrial tissue sample, Day P+7

description:
Library name: Sample 154
molecule: small RNA


title: Subject 52, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 155
molecule: small RNA


title: Subject 51, paired blood sample, repeat 2, Day P+7

description:
Library name: Sample 153
molecule: small RNA


title: Primary CRC tumor samples (FF), P2711


title: Subject 53, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 158
molecule: small RNA


title: P2807


title: Subject 51, endometrial tissue sample, Day P+7

description:
Library name: Sample 151
molecule: small RNA


title: P2802


title: Subject 51, paired blood sample, repeat 1, Day P+7

description:
Library name: Sample 152
molecule: small RNA


title: Primary CRC tumor samples (FF), P2700


title: Subject 50, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 150
molecule: small RNA


title: P2846


title: Subject 50, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 149
molecule: small RNA


title: P2798


title: Primary CRC tumor samples (FF), P2712


title: Primary CRC tumor samples (FF), P2694


title: Subject 50, endometrial tissue sample, Day P+6

description:
Library name: Sample 148
molecule: small RNA


title: Primary CRC tumor samples (FF), P2654


title: Subject 49, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 147
molecule: small RNA


title: Subject 49, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 146
molecule: small RNA


title: P2763


title: P2712


title: Subject 49, endometrial tissue sample, Day P+6

description:
Library name: Sample 145
molecule: small RNA


title: Primary CRC tumor samples (FF), P2621


title: Primary CRC tumor samples (FF), P251


title: Subject 48, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 144
molecule: small RNA


title: Subject 48, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 143
molecule: small RNA


title: Subject 48, endometrial tissue sample, Day P+6

description:
Library name: Sample 142
molecule: small RNA


title: Subject 47, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 141
molecule: small RNA


title: Primary CRC tumor samples (FF), P2519


title: P2700


title: P2711


title: Subject 47, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 140
molecule: small RNA


title: Primary CRC tumor samples (FF), P2518


title: Subject 47, endometrial tissue sample, Day P+6

description:
Library name: Sample 139
molecule: small RNA


title: Subject 46, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 137
molecule: small RNA


title: Primary CRC tumor samples (FF), P2486


title: P2746


title: Subject 46, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 138
molecule: small RNA


title: P2694


title: Primary CRC tumor samples (FF), P244


title: Subject 45, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 135
molecule: small RNA


title: P2621


title: Primary CRC tumor samples (FF), P2428


title: Subject 45, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 134
molecule: small RNA


title: Subject 44, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 131
molecule: small RNA


title: Subject 44, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 132
molecule: small RNA


title: Subject 45, endometrial tissue sample, Day P+6

description:
Library name: Sample 133
molecule: small RNA


title: Primary CRC tumor samples (FF), P237


title: P2654


title: Subject 44, endometrial tissue sample, Day P+6

description:
Library name: Sample 130
molecule: small RNA


title: P2519


title: Subject 43, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 129
molecule: small RNA


title: Primary CRC tumor samples (FF), P2361


title: Subject 43, endometrial tissue sample, Day P+6

description:
Library name: Sample 127
molecule: small RNA


title: Subject 43, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 128
molecule: small RNA


title: Primary CRC tumor samples (FF), P2326


title: Subject 42, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 126
molecule: small RNA


title: Subject 42, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 125
molecule: small RNA


title: Primary CRC tumor samples (FF), P2305


title: Subject 46, endometrial tissue sample, Day P+6

description:
Library name: Sample 136
molecule: small RNA


title: P2518


title: P2715


title: P2486


title: Subject 42, endometrial tissue sample, Day P+6

description:
Library name: Sample 124
molecule: small RNA


title: Subject 41, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 123
molecule: small RNA


title: Primary CRC tumor samples (FF), P2304


title: Subject 41, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 122
molecule: small RNA


title: P2731


title: Primary CRC tumor samples (FF), P2283


title: P2326


title: Primary CRC tumor samples (FF), P224


title: Subject 40, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 119
molecule: small RNA


title: Subject 41, endometrial tissue sample, Day P+6

description:
Library name: Sample 121
molecule: small RNA


title: Subject 40, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 120
molecule: small RNA


title: P2428


title: Primary CRC tumor samples (FF), P2236


title: Subject 40, endometrial tissue sample, Day P+6

description:
Library name: Sample 118
molecule: small RNA


title: Subject 39, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 117
molecule: small RNA


title: Subject 39, endometrial tissue sample, Day P+6

description:
Library name: Sample 115
molecule: small RNA


title: Primary CRC tumor samples (FF), P2197


title: P2361


title: Subject 38, paired blood sample, repeat 2, Day P+6

description:
Library name: Sample 114
molecule: small RNA


title: Subject 38, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 113
molecule: small RNA


title: P2304


title: Primary CRC tumor samples (FF), P2194


title: P2283


title: Subject 38, endometrial tissue sample, Day P+6

description:
Library name: Sample 112
molecule: small RNA


title: Primary CRC tumor samples (FF), P2173


title: Subject 37, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 111
molecule: small RNA


title: Subject 37, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 110
molecule: small RNA


title: Subject 37, endometrial tissue sample, Day P+5

description:
Library name: Sample 109
molecule: small RNA


title: P2046


title: P2099


title: Subject 36, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 108
molecule: small RNA


title: P2305


title: Subject 36, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 107
molecule: small RNA


title: Primary CRC tumor samples (FF), P2099


title: Primary CRC tumor samples (FF), P2060


title: Subject 36, endometrial tissue sample, Day P+5

description:
Library name: Sample 106
molecule: small RNA


title: Subject 35, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 105
molecule: small RNA


title: Subject 35, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 104
molecule: small RNA


title: Subject 39, paired blood sample, repeat 1, Day P+6

description:
Library name: Sample 116
molecule: small RNA


title: P2236


title: P2173


title: Primary CRC tumor samples (FF), P2037


title: P2194


title: P1962


title: Primary CRC tumor samples (FF), P1975


title: Subject 34, endometrial tissue sample, Day P+5

description:
Library name: Sample 100
molecule: small RNA


title: Subject 33, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 99
molecule: small RNA


title: Subject 34, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 101
molecule: small RNA


title: Subject 33, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 98
molecule: small RNA


title: Primary CRC tumor samples (FF), P2148


title: Primary CRC tumor samples (FF), P1962


title: P2037


title: P2060


title: Subject 33, endometrial tissue sample, Day P+5

description:
Library name: Sample 97
molecule: small RNA


title: Subject 32, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 96
molecule: small RNA


title: Subject 32, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 95
molecule: small RNA


title: Primary CRC tumor samples (FF), P1946


title: Primary CRC tumor samples (FF), P1928


title: Primary CRC tumor samples (FF), P2046


title: Primary CRC tumor samples (FF), P1903


title: Subject 35, endometrial tissue sample, Day P+5

description:
Library name: Sample 103
molecule: small RNA


title: Subject 31, endometrial tissue sample, Day P+5

description:
Library name: Sample 91
molecule: small RNA


title: P1975


title: Subject 32, endometrial tissue sample, Day P+5

description:
Library name: Sample 94
molecule: small RNA


title: Subject 34, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 102
molecule: small RNA


title: Subject 30, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 90
molecule: small RNA


title: Subject 31, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 92
molecule: small RNA


title: P1928


title: P1946


title: P1903


title: Primary CRC tumor samples (FF), P18


title: Subject 30, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 89
molecule: small RNA


title: Primary CRC tumor samples (FF), P187


title: Subject 29, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 87
molecule: small RNA


title: Subject 29, endometrial tissue sample, Day P+5

description:
Library name: Sample 85
molecule: small RNA


title: P1846


title: P2197


title: Primary CRC tumor samples (FF), P186


title: Subject 29, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 86
molecule: small RNA


title: Subject 28, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 84
molecule: small RNA


title: Subject 31, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 93
molecule: small RNA


title: Subject 28, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 83
molecule: small RNA


title: Subject 28, endometrial tissue sample, Day P+5

description:
Library name: Sample 82
molecule: small RNA


title: Subject 27, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 80
molecule: small RNA


title: Primary CRC tumor samples (FF), P1846


title: Primary CRC tumor samples (FF), P183


title: P2148


title: Subject 26, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 77
molecule: small RNA


title: Subject 27, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 81
molecule: small RNA


title: Primary CRC tumor samples (FF), P1816


title: Subject 27, endometrial tissue sample, Day P+5

description:
Library name: Sample 79
molecule: small RNA


title: Subject 26, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 78
molecule: small RNA


title: Primary CRC tumor samples (FF), P178


title: P524


title: Subject 25, paired blood sample, repeat 2, Day P+5

description:
Library name: Sample 75
molecule: small RNA


title: P404


title: Subject 25, paired blood sample, repeat 1, Day P+5

description:
Library name: Sample 74
molecule: small RNA


title: Subject 30, endometrial tissue sample, Day P+5

description:
Library name: Sample 88
molecule: small RNA


title: Subject 26, endometrial tissue sample, Day P+5

description:
Library name: Sample 76
molecule: small RNA


title: P1816


title: P341


title: Primary CRC tumor samples (FF), P1779


title: P309


title: Primary CRC tumor samples (FF), P184


title: Subject 24, endometrial tissue sample, Day P+4

description:
Library name: Sample 70
molecule: small RNA


title: Subject 23, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 69
molecule: small RNA


title: Primary CRC tumor samples (FF), P1706


title: Primary CRC tumor samples (FF), P1705


title: Subject 23, endometrial tissue sample, Day P+4

description:
Library name: Sample 67
molecule: small RNA


title: Subject 23, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 68
molecule: small RNA


title: Subject 22, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 66
molecule: small RNA


title: Primary CRC tumor samples (FF), P1650


title: P1754


title: P1779


title: Subject 25, endometrial tissue sample, Day P+5

description:
Library name: Sample 73
molecule: small RNA


title: Primary CRC tumor samples (FF), P1642


title: Subject 20, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 60
molecule: small RNA


title: Subject 21, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 62
molecule: small RNA


title: Subject 21, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 63
molecule: small RNA


title: Primary CRC tumor samples (FF), P1648


title: Subject 21, endometrial tissue sample, Day P+4

description:
Library name: Sample 61
molecule: small RNA


title: Subject 22, endometrial tissue sample, Day P+4

description:
Library name: Sample 64
molecule: small RNA


title: Primary CRC tumor samples (FF), P1754


title: P1648


title: Subject 24, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 72
molecule: small RNA


title: P1650


title: Subject 20, endometrial tissue sample, Day P+4

description:
Library name: Sample 58
molecule: small RNA


title: P1705


title: Subject 24, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 71
molecule: small RNA


title: Subject 20, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 59
molecule: small RNA


title: Subject 19, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 57
molecule: small RNA


title: P1706


title: Subject 22, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 65
molecule: small RNA


title: Primary CRC tumor samples (FF), P1576


title: Subject 19, endometrial tissue sample, Day P+4

description:
Library name: Sample 55
molecule: small RNA


title: P237


title: Primary CRC tumor samples (FF), P1637


title: Subject 19, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 56
molecule: small RNA


title: Primary CRC tumor samples (FF), P1533


title: Primary CRC tumor samples (FF), P1327


title: P1576


title: P547


title: Subject 18, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 54
molecule: small RNA


title: Subject 18, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 53
molecule: small RNA


title: Subject 18, endometrial tissue sample, Day P+4

description:
Library name: Sample 52
molecule: small RNA


title: Subject 17, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 51
molecule: small RNA


title: Primary CRC tumor samples (FF), P1306


title: P1642


title: Primary CRC tumor samples (FF), P1209


title: P1637


title: P1533


title: Primary CRC tumor samples (FF), P119


title: Subject 17, endometrial tissue sample, Day P+4

description:
Library name: Sample 49
molecule: small RNA


title: Subject 16, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 47
molecule: small RNA


title: Subject 16, endometrial tissue sample, Day P+4

description:
Library name: Sample 46
molecule: small RNA


title: Subject 17, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 50
molecule: small RNA


title: Subject 15, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 45
molecule: small RNA


title: P1306


title: P1327


title: Subject 15, endometrial tissue sample, Day P+4

description:
Library name: Sample 43
molecule: small RNA


title: Primary CRC tumor samples (FF), P1175


title: Primary CRC tumor samples (FF), P1173


title: P1098


title: P1175


title: Primary CRC tumor samples (FF), P1098


title: Subject 14, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 41
molecule: small RNA


title: Subject 14, endometrial tissue sample, Day P+4

description:
Library name: Sample 40
molecule: small RNA


title: P1209


title: Primary CRC tumor samples (FF), P1055


title: P1024


title: Subject 16, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 48
molecule: small RNA


title: Primary CRC tumor samples (FF), P1024


title: Primary CRC tumor samples (FF), P1015


title: P658


title: Primary CRC tumor samples (FF), P1186


title: Subject 13, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 39
molecule: small RNA


title: Subject 15, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 44
molecule: small RNA


title: P1055


title: WD8

city: Baltimore

first: Som

last: Dev

state: MD

address: 725 N, Wolfe St

department: Physiology, School of Medicine

country: USA

institute: Johns Hopkins University

description: Gene expression data from WD liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using third generation Affymetrixs Genechip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and ubjected to global scaling with an average target intensity of 350 to allow for direct comparison of hybridization values from different targets.

label: IVT  labelling

source_name: Human WD liver (Cirrhosis)

label_protocol: cRNA were prepared using IVT labelling kit (Affymetrixs) from cDNA and cDNA was synthesized from 2 ug total RNA (starting amount)

growth_protocol: WD patients underwent liver transplantation for acute or chronic liver failure. Control specimens were obtained from patients who underwent liver resections for other clinical reasons.

extract_protocol: Trizol extraction of total RNA followed by Rneasy cleanup procedure performed according to the manufacturer's instructions.

treatment_protocol: Liver sections were snap frozen in liquid nitrogen and stored, RNA was extracted

tag: disease state

value: Human WD liver (Cirrhosis)

value: Liver

tag: genotype

tag: age


title: Primary CRC tumor samples (FF), LM41

data_processing:
Prior to read trimming and alignment, the quality of raw data was assessed using FastQC (v.0.11.9). Trimming was performed on 12 and 11 bases for single-end and pair-end RNAseq data, respectively. To further enhance data quality, bases with a Phred score less than 20 were filtered using Cutadapt (v1.18). The reads were aligned to the reference genome (GRCh38) and gene counts were generated using the STAR (v.2.7.4.a) algorithm. To enable accurate downstream analyses, the count data was log2-transformed and quantile normalization was applied.
Assembly: GRCh38
Supplementary files format and content: Excel file includes raw gene count for each Sample


title: Subject 14, paired blood sample, repeat 2, Day P+4

description:
Library name: Sample 42
molecule: small RNA


title: Subject 13, endometrial tissue sample, Day P+4

description:
Library name: Sample 37
molecule: small RNA


title: P1186


title: Subject 12, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 36
molecule: small RNA


title: Primary CRC tumor samples (FF), LM40


title: WD5

description: Gene expression data from WD liver


title: WD7

description: Gene expression data from WD liver


title: P844


title: Subject 12, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 35
molecule: small RNA


title: WD6

description: Gene expression data from WD liver


title: WD4

description: Gene expression data from WD liver


title: P948


title: Subject 13, paired blood sample, repeat 1, Day P+4

description:
Library name: Sample 38
molecule: small RNA


title: Primary CRC tumor samples (FF), LM39


title: Subject 12, endometrial tissue sample, Day P+3

description:
Library name: Sample 34
molecule: small RNA


title: WD2

description: Gene expression data from WD liver


title: Primary CRC tumor samples (FF), LM38


title: Subject 11, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 33
molecule: small RNA


title: P848


title: Primary CRC tumor samples (FF), LM28


title: Primary CRC tumor samples (FF), CO164


title: Subject 11, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 32
molecule: small RNA


title: P651


title: Primary CRC tumor samples (FF), CO116


title: P641


title: Subject 11, endometrial tissue sample, Day P+3

description:
Library name: Sample 31
molecule: small RNA


title: WD3

description: Gene expression data from WD liver


title: P633


title: Subject 10, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 30
molecule: small RNA


title: Subject 10, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 29
molecule: small RNA


title: P588


title: Primary CRC tumor samples (FF), CO115


title: Primary CRC tumor samples (FF), LM29


title: NL6

description: Gene expression data from Control liver

source_name: Human liver (no liver abnormality)

value: Human liver (no liver abnormality)


title: NL5

description: Gene expression data from Control liver


title: P538


title: NL3

description: Gene expression data from Control liver


title: Subject 10, endometrial tissue sample, Day P+3

description:
Library name: Sample 28
molecule: small RNA

value: endometrial tissue


title: Schizosaccharomyces Pombe,H2BK119R,repeat3

city: nanjing

first: Guangchun

last: Lu

address: wenyuan road

institute: Nanjing Normal University

description:
Library name: Sample6
H2BK119R-3

data_processing:
First, the descending raw reads was quality-controlled using the fastp
clean reads were aligned to the ribosome database of this species using the short reads alignment tool bowtie2[2], the reads on the upper ribosomes were removed without mismatch allowed, and the retained unmapped reads was used for subsequent transcriptome analysis.
Using the HISAT2 software, a reference genome-based alignment analysis was performed.
Based on the alignment results of the HISAT2, we reconstructed the transcripts using the Stringtie and calculated the expression levels of all the genes in each sample using the RSEM
Input data for gene differential expression analysis are the reads count data obtained from gene expression level analysis and were analyzed using DESeq2[6] software
Assembly: Using the STRING protein interaction database (http://string-db.org).
Supplementary files format and content: Ensembl_release45
Supplementary files format and content: Each data column corresponds to the information of one sample, with a total of two tables, namely all gene expression and significant gene expression.

organism: Schizosaccharomyces pombe

source_name: whole cell

extract_protocol:
Total RNA was extracted using Trizol reagent kit.The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), reverse transcribed to cDNA, after PCR amplification, and then sequenced.
The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT),following manufacturer's protocols.

value: whole cell


title: NL7

description: Gene expression data from Control liver


title: P582


title: Primary CRC tumor samples (FF), CO163


title: P598


title: Schizosaccharomyces Pombe,H2BK119R,repeat2

description:
Library name: Sample5
H2BK119R-2


title: NL4

description: Gene expression data from Control liver


title: Subject 9, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 26
molecule: small RNA

value: blood


title: NL8

description: Gene expression data from Control liver


title: Schizosaccharomyces Pombe,H2BK119R,repeat1

description:
Library name: Sample4
H2BK119R-1


title: Subject 9, endometrial tissue sample, Day P+3

description:
Library name: Sample 25
molecule: small RNA

value: Progestrone treatment


title: P447


title: P434


title: Primary CRC tumor samples (FF), CO160

value: Primary colorectal cancer


title: Primary CRC tumor samples (FF), CO144


title: Subject 8, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 24
molecule: small RNA


title: Primary CRC tumor samples (FF), CO172


title: P568


title: Subject 9, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 27
molecule: small RNA


title: Subject 8, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 23
molecule: small RNA


title: Schizosaccharomyces Pombe,WT,repeat1

description:
Library name: Sample1
Wild type-1

value: WT


title: Schizosaccharomyces Pombe,WT,repeat2

description:
Library name: Sample2
Wild type-2


title: Subject 8, endometrial tissue sample, Day P+3

description:
Library name: Sample 22
molecule: small RNA


title: NL2

description: Gene expression data from Control liver

value: Female


title: P492


title: Primary CRC tumor samples (FF), CO162

value: Fresh Frozen


title: SchizosaccharomycesPombe, D67N ubp8Δ, repeat3

data_processing:
First, the descending raw reads was quality-controlled using the fastp
clean reads were aligned to the ribosome database of this species using the short reads alignment tool bowtie2[2], the reads on the upper ribosomes were removed without mismatch allowed, and the retained unmapped reads was used for subsequent transcriptome analysis.
Using the HISAT2 software, a reference genome-based alignment analysis was performed.
Based on the alignment results of the HISAT2, we reconstructed the transcripts using the Stringtie and calculated the expression levels of all the genes in each sample using the RSEM
Input data for gene differential expression analysis are the reads count data obtained from gene expression level analysis and were analyzed using DESeq2[6] software
Assembly: Using the STRING protein interaction database (http://string-db.org).
Supplementary files format and content: Ensembl_release45
Supplementary files format and content: Each Excel corresponds to the information of one sample, with a total of two tables, namely all gene expression and significant gene expression.

value: H2BD67N ubp8 knockdown


title: Subject 7, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 21
molecule: small RNA


title: Primary CRC tumor samples (FF), LM37


title: SchizosaccharomycesPombe, D67N ubp8Δ, repeat2


title: Subject 7, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 20
molecule: small RNA


title: Primary CRC tumor samples (FF), CO131


title: Primary CRC tumor samples (FF), CO154


title: SchizosaccharomycesPombe, D67N ubp8Δ, repeat1


title: P415


title: P408


title: NL1

description: Gene expression data from Control liver


title: Subject 7, endometrial tissue sample, Day P+3

description:
Library name: Sample 19
molecule: small RNA


title: P449


title: SchizosaccharomycesPombe, D67N, repeat3


title: Primary CRC tumor samples (FF), CO153


title: P374


title: Primary CRC tumor samples (FF), CO150


title: Primary CRC tumor samples (FF), CO134


title: Subject 6, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 18
molecule: small RNA


title: SchizosaccharomycesPombe, D67N, repeat2


title: Primary CRC tumor samples (FF), CO140


title: Subject 6, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 17
molecule: small RNA


title: SchizosaccharomycesPombe, D67N, repeat1


title: Primary CRC tumor samples (FF), CO128


title: P373


title: P316


title: SchizosaccharomycesPombe, D67H, repeat3


title: Subject 6, endometrial tissue sample, Day P+3

description:
Library name: Sample 16
molecule: small RNA


title: Subject 5, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 15
molecule: small RNA


title: Primary CRC tumor samples (FF), CO157


title: Primary CRC tumor samples (FF), CO123


title: Subject 5, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 14
molecule: small RNA


title: SchizosaccharomycesPombe, D67H, repeat2


title: SchizosaccharomycesPombe, D67H, repeat1


title: P244


title: P251


title: P184


title: P369


title: Subject 5, endometrial tissue sample, Day P+3

description:
Library name: Sample 13
molecule: small RNA


title: Primary CRC tumor samples (FF), CO129


title: Subject 4, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 12
molecule: small RNA


title: SchizosaccharomycesPombe, P102S, repeat3


title: SchizosaccharomycesPombe, P102S, repeat2


title: Healthy Rectum 32 yo M

city: La Jolla

first: Eunice

last: Choi

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the CellRanger pipeline (10x Genomics)
Samples were further processed using Seurat v4.1.1 (14). Low quality (e.g., dead) cells and potential doublets were filtered with the following parameters: <200 features, >10% mitochondrial features, >2500 features.
ADT and RNA assays were normalized using the standard Seurat workflow of ‘NormalizeData’,‘FindVariableFeatures’, and ‘ScaleData’, and ‘RunPCA’.
Cell types were assigned using SingleR v.1.4.1 (15) and verified with canonical protein markers.
Assembly: hg38
Supplementary files format and content: raw count matrices
Supplementary files format and content: genes
Supplementary files format and content: barcodes

source_name: Rectum

extract_protocol:
Four intestinal biopsies were obtained with endoscopic biopsy forceps from the ileum and rectum and collected in separate conical tubes with Hank’s buffered saline solution (HBSS, Corning). Intestinal biopsies were transferred into freezing buffer (10%(v/v) DMSO, 40%(v/v) complete RPMI, 50%(v/v) FBS) and stored at -80°C. Biopsies were recovered, incubated in HBSS on a shaker, then incubated twice in HBSS + 5 mM dithiothreitol (DTT, Thermo Fisher Scientific) for 10 minutes on a rocker at 37°C, followed by a final HBSS wash. Intestinal biopsies were mechanically dissociated, then placed into a conical tube containing 10 mL of digestion mixture [complete RPMI + 1.5 mg/mL Collagenase type VIII (Sigma-Aldrich) + 50 µg/mL DNase I (Roche)]. The biopsies were digested in a shaking incubator (225 rpm) for 20 minutes at 37°C. The reaction was stopped with phosphatebuffered saline (PBS) pre-cooled to 4°C, filtered, and resuspended in fresh complete RPMI. Samples were incubated with BD Pharmingen Human BD Fc Block for 10 minutes to block non-specific binding of the Fc receptor as described in the manufacturer's protocol. The 55-plex BD AbSeq antibody cocktail was generated using 2.6 uL of each antibody and brought to volume with BD buffer. Concurrently, samples were stained with anti-human CD45 and a live/dead stain, and incubated for 60 minutes on ice. CD45 + immune cells were sorted on a FACSAria2 and collected in complete RPMI media with 10% FBS. Blood was collected in BD Vacutainer CPT tube and centrifuged at 400 x g for 25 minutes. The buffy coat layer was removed, washed, and counted. Cells were resuspended in freezing buffer (10%(v/v) Dimethylsulfoxide (DMSO, Sigma Aldrich), 40%(v/v) complete RPMI [RPMI (Corning) +10%(v/v) fetal bovine serum (FBS, Life Technologies) +100 U/mL penicillin/100 µg/mL streptomycin (Life Technologies)], 50%(v/v) FBS), placed into a freezing container (Mr. Frosty), and stored at -80°C. Cells were recovered, washed, filtered, and labeled with anti-human CD45 (2D1) (Biolegend) for sorting. CD45 + immune cells were sorted on a FACSAria2 (BD Biosciences).
Cells were washed and resuspended in phosphate-buffered saline (PBS) + 0.04%(w/v) bovine serum albumin (UltraPure BSA, Thermo Fisher Scientific) per the manufacturer’s guidelines. Single-cell libraries were prepared according to the protocol for 10x Genomics for Single Cell 3’ Gene Expression. Approximately 20,000 sorted CD45 + cells resuspended at a final concentration of 4,000 cells/uL were loaded and partitioned into Gel Bead-in-EMulsions (GEMs). The 10x Genomics cDNA generation protocol was modified to include the BD AbSeq PCR1 primer. After PCR amplification, the fractions containing the AbSeq oligos were processed through a separate library construction workflow. This AbSeq protocol generates libraries directly after cDNA amplification, eliminating intermediate steps as described in the 10x Genomics protocol. The quality of the sample fragments was determined by the High Sensitivity D5000 and D1000 ScreenTape assay (Agilent Technologies). The scRNA and protein libraries were pooled at equimolar amounts for a final 10nM concentration and sequenced on a NovaSeq 6000 S4 flow cell (Illumina).

tag: disease

value: Healthy

value: Rectum

tag: gender

value: M


title: Subject 4, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 11
molecule: small RNA


title: P183

value: FF


title: Healthy PBMC 32 yo M

description: 10x genomics

source_name: PBMC

value: PBMC


title: Subject 4, endometrial tissue sample, Day P+3

description:
Library name: Sample 10
molecule: small RNA


title: P178

value: III


title: SchizosaccharomycesPombe, P102S, repeat1


title: Healthy Ileum 32 yo M

description: 10x genomics

source_name: Ileum

value: Ileum


title: SchizosaccharomycesPombe, P102L ubp8Δ, repeat3

value: H2BP102L ubp8 knockdown


title: P224


title: Subject 3, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 9
molecule: small RNA


title: SchizosaccharomycesPombe, P102L ubp8Δ, repeat2


title: P187


title: Healthy Rectum 41 yo M

description: 10x genomics


title: Subject 3, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 8
molecule: small RNA


title: Healthy PBMC 41 yo M

description: 10x genomics


title: Healthy Ileum 41 yo M

description: 10x genomics


title: P77


title: P18


title: Subject 3, endometrial tissue sample, Day P+3

description:
Library name: Sample 7
molecule: small RNA

value: endometrial tissue


title: SchizosaccharomycesPombe, P102L, repeat3

value: whole cell


title: Healthy Rectum 61 yo M

description: 10x genomics


title: Subject 2, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 6
molecule: small RNA

value: blood


title: SchizosaccharomycesPombe, P102L, repeat2


title: Subject 2, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 5
molecule: small RNA

value: Progestrone treatment


title: Healthy PBMC 61 yo M

description: 10x genomics


title: P602


title: Subject 2, endometrial tissue sample, Day P+3

description:
Library name: Sample 4
molecule: small RNA


title: SchizosaccharomycesPombe, P102L, repeat1


title: SchizosaccharomycesPombe, G52R, repeat3


title: P824


title: Healthy Ileum 61 yo M

description: 10x genomics


title: Subject 1, paired blood sample, repeat 2, Day P+3

description:
Library name: Sample 3
molecule: small RNA


title: Healthy Rectum 59 yo F

description: 10x genomics

value: F


title: P119


title: Subject 1, paired blood sample, repeat 1, Day P+3

description:
Library name: Sample 2
molecule: small RNA


title: SchizosaccharomycesPombe, G52R, repeat2


title: SchizosaccharomycesPombe, P102L ubp8Δ, repeat1


title: Healthy PBMC 59 yo F

description: 10x genomics


title: SchizosaccharomycesPombe, G52R, repeat1


title: P345


title: P79


title: Subject 1, endometrial tissue sample, Day P+3

description:
Library name: Sample 1
molecule: small RNA


title: P186


title: Healthy Ileum 59 yo F

description: 10x genomics


title: PBMC, vitamin D bolus, day 1, Individual 45

city: Olsztyn

first: Carsten

last: Carlberg

state: Warmia-Mazury

address: Tuwima 10

department: Food Technology

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description:
After 1 day of vitamin D bolus intake
d1_Ind45

data_processing:
Trimming of files using Trimmomatic v0.39
Read alignment using STAR v2.7.10b using default parameters
Quantification using FastQC v0.12.1 and featureCounts v2.0.3 using default parameters for reverse strand
Filtering for protein coding genes and read counts normalization via EdgeR v4.0.14 (TMM-normalized CPM)
Assembly: GRCh38.p14, Aligned to Ensembl annotation version 112, final annotation (via Biomart) to Ensembl version 112.38
Supplementary files format and content: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline)

growth_protocol: no in vitro culture

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: Before and after intake of 1000 IU/kg of vitamin D3

tag: individual

value: Individual 45

value: Healthy Individuals

tag: cell type

value: 80000 IU vitamin D3

tag: time

value: day 1


title: P68


title: SchizosaccharomycesPombe, G52E, repeat3


title: PBMC, vitamin D bolus, day 1, Individual 44

description:
After 1 day of vitamin D bolus intake
d1_Ind44

value: Individual 44


title: SchizosaccharomycesPombe, G52E, repeat1


title: P45


title: PBMC, vitamin D bolus, day 1, Individual 43

description:
After 1 day of vitamin D bolus intake
d1_Ind43

value: Individual 43


title: SchizosaccharomycesPombe, G52D ubp8Δ, repeat3

value: H2BG52D ubp8 knockdown


title: Healthy PBMC 23 yo M

description: 10x genomics

value: Healthy

value: M


title: Healthy Ileum 23 yo M

description: 10x genomics


title: P1015

value: FF

value: III


title: PBMC, vitamin D bolus, day 1, Individual 42

description:
After 1 day of vitamin D bolus intake
d1_Ind42

value: Individual 42

value: PBMC


title: SchizosaccharomycesPombe, G52D ubp8Δ, repeat2

value: whole cell


title: Healthy Rectum 33 yo F

description: 10x genomics

value: Rectum


title: PBMC, vitamin D bolus, day 1, Individual 41

description:
After 1 day of vitamin D bolus intake
d1_Ind41

value: Individual 41


title: P1173


title: P521


title: SchizosaccharomycesPombe, G52D ubp8Δ, repeat1


title: COL100.FFPE

value: FFPE

tag: cms (ssp)


title: Healthy Rectum 23 yo M

description: 10x genomics


title: Healthy Ileum 33 yo F

description: 10x genomics

value: Ileum

value: F


title: PBMC, vitamin D bolus, day 1, Individual 39

description:
After 1 day of vitamin D bolus intake
d1_Ind39

value: Individual 39

value: Healthy Individuals

value: 80000 IU vitamin D3


title: SchizosaccharomycesPombe, G52E, repeat2


title: SchizosaccharomycesPombe, G52D, repeat3


title: SchizosaccharomycesPombe, G52D, repeat2


title: COL100.FF


title: Healthy PBMC 36 yo M

description: 10x genomics


title: Healthy Rectum 36 yo M

description: 10x genomics


title: COL098.FFPE


title: PBMC, vitamin D bolus, day 1, Individual 37

description:
After 1 day of vitamin D bolus intake
d1_Ind37

value: Individual 37

value: day 1


title: SchizosaccharomycesPombe, G52D, repeat1


title: Healthy Ileum 36 yo M

description: 10x genomics

value: Healthy


title: COL098.FF


title: PBMC, vitamin D bolus, day 1, Individual 36

description:
After 1 day of vitamin D bolus intake
d1_Ind36

value: Individual 36


title: SchizosaccharomycesPombe, ZT, repeat6

value: WT


title: Disease Rectum 72 yo M

description: 10x genomics

value: Crohn's disease

value: M


title: SchizosaccharomycesPombe, ZT, repeat5


title: Healthy PBMC 33 yo F

description: 10x genomics

value: PBMC


title: PBMC, vitamin D bolus, day 1, Individual 40

description:
After 1 day of vitamin D bolus intake
d1_Ind40

value: Individual 40


title: COL097.FFPE


title: Disease PBMC 72 yo M

description: 10x genomics


title: SchizosaccharomycesPombe, ZT, repeat4

value: whole cell


title: PBMC, vitamin D bolus, day 1, Individual 34

description:
After 1 day of vitamin D bolus intake
d1_Ind34

value: Individual 34


title: COL097.FF

value: FF


title: COL096.FFPE

value: FFPE


title: Disease Ileum 72 yo M

description: 10x genomics

value: Ileum


title: SchizosaccharomycesPombe, ZT, repeat3


title: PBMC, vitamin D bolus, day 1, Individual 33

description:
After 1 day of vitamin D bolus intake
d1_Ind33

value: Individual 33


title: PBMC, vitamin D bolus, day 1, Individual 38

description:
After 1 day of vitamin D bolus intake
d1_Ind38

value: Individual 38

value: Healthy Individuals


title: COL096.FF


title: SchizosaccharomycesPombe, ZT, repeat2


title: PBMC, vitamin D bolus, day 1, Individual 32

description:
After 1 day of vitamin D bolus intake
d1_Ind32

value: Individual 32

value: 80000 IU vitamin D3


title: Disease PBMC 39 yo M

description: 10x genomics


title: PBMC, vitamin D bolus, day 1, Individual 31

description:
After 1 day of vitamin D bolus intake
d1_Ind31

value: Individual 31

value: day 1


title: COL095.FFPE


title: SchizosaccharomycesPombe, ZT, repeat1

value: WT


title: COL095.FF


title: PBMC, vitamin D bolus, day 1, Individual 30

description:
After 1 day of vitamin D bolus intake
d1_Ind30

value: Individual 30


title: SchizosaccharomycesPombe,R,rep 3


title: PBMC, vitamin D bolus, day 1, Individual 35

description:
After 1 day of vitamin D bolus intake
d1_Ind35

value: Individual 35


title: Disease Ileum 39 yo M

description: 10x genomics

value: Crohn's disease

value: M


title: Disease Rectum 39 yo M

description: 10x genomics

value: Rectum


title: COL094.FFPE


title: SchizosaccharomycesPombe,R,rep 2

value: whole cell


title: Disease Rectum 74 yo F

description: 10x genomics

value: F


title: SchizosaccharomycesPombe,R,rep 1


title: Disease PBMC 74 yo F

description: 10x genomics

value: PBMC


title: PBMC, vitamin D bolus, day 1, Individual 29

description:
After 1 day of vitamin D bolus intake
d1_Ind29

value: Individual 29


title: COL094.FF

value: FF


title: COL093.FFPE

value: FFPE


title: PBMC, vitamin D bolus, day 1, Individual 27

description:
After 1 day of vitamin D bolus intake
d1_Ind27

value: Individual 27

value: Healthy Individuals


title: SchizosaccharomycesPombe,Q,rep 2


title: Disease Rectum 26 yo F [CD10]

description: 10x genomics


title: COL093.FF


title: COL092.FF


title: SchizosaccharomycesPombe,Q,rep 1


title: PBMC, vitamin D bolus, day 1, Individual 26

description:
After 1 day of vitamin D bolus intake
d1_Ind26

value: Individual 26

value: 80000 IU vitamin D3


title: PBMC, vitamin D bolus, day 1, Individual 24

description:
After 1 day of vitamin D bolus intake
d1_Ind24

value: Individual 24

value: day 1


title: PBMC, vitamin D bolus, day 1, Individual 23

description:
After 1 day of vitamin D bolus intake
d1_Ind23

value: Individual 23


title: Disease Ileum 26 yo F [CD10]

description: 10x genomics

value: Ileum


title: Disease Rectum 26 yo F

description: 10x genomics

value: Crohn's disease


title: Disease Rectum 55 yo M

description: 10x genomics

value: M


title: SchizosaccharomycesPombe,A,rep 2


title: COL090.FFPE


title: SchizosaccharomycesPombe,WT,rep 3

value: WT


title: PBMC, vitamin D bolus, day 1, Individual 22

description:
After 1 day of vitamin D bolus intake
d1_Ind22

value: Individual 22


title: SchizosaccharomycesPombe,A,rep 3

value: whole cell


title: COL090.FF


title: Disease PBMC 55 yo M

description: 10x genomics

value: PBMC


title: SchizosaccharomycesPombe,Q,rep 3


title: PBMC, vitamin D bolus, day 1, Individual 25

description:
After 1 day of vitamin D bolus intake
d1_Ind25

value: Individual 25


title: PBMC, vitamin D bolus, day 1, Individual 28

description:
After 1 day of vitamin D bolus intake
d1_Ind28

value: Individual 28


title: SchizosaccharomycesPombe,WT,rep 2


title: Disease Ileum 26 yo F [CD8]

description: 10x genomics

value: F


title: COL085.FFPE

value: FFPE


title: Schizosaccharomyces Pombe,WT,repeat3

description:
Library name: Sample3
Wild type-3


title: Disease PBMC 26 yo F [CD8]

description: 10x genomics


title: COL091.FF

value: FF


title: Disease Ileum 74 yo F

description: 10x genomics


title: COL084.FFPE


title: PBMC, vitamin D bolus, day 1, Individual 21

description:
After 1 day of vitamin D bolus intake
d1_Ind21

value: Individual 21

value: Healthy Individuals


title: Disease Rectum 41 yo M

description: 10x genomics

value: Rectum


title: COL085.FF


title: SchizosaccharomycesPombe,A,rep 1


title: SchizosaccharomycesPombe,WT,rep 1


title: Disease PBMC 41 yo M

description: 10x genomics


title: PBMC, vitamin D bolus, day 1, Individual 18

description:
After 1 day of vitamin D bolus intake
d1_Ind18

value: Individual 18

value: 80000 IU vitamin D3

value: day 1


title: Human Tenon's fibroblasts (HTFs), day0

city: Taipei

first: Yueh-Chang

last: Lee

address: No.128, Sec. 2, Academia Rd.

department: Genomics Research Center

institute: Academia Sinica

description:
Library name: Sample 1
Column name in FullTable.xlsx: HTF4

data_processing:
Libraries for the cDNA samples were sequenced using the Illumina HiSeq sequencing platform yielding 24.8–32 million 150 bp paired end (PE) sequence reads per sample. PE FASTQ files received back from Genomics were analyzed using a customized bioinformatics workflow. Bioinformatics analyses were conducted with the DAVID functional annotation tool. A heatmap of differentially expressed genes in iRPCs and HTFs that showed a positive or negative change of at least 2‐fold was displayed. Data were log2 transformed and normalized to the mean. The heatmap was generated by Cluster3.0 and Java TreeView.
Assembly: Homo sapiens (human) genome assembly GRCh37 (hg19)
Supplementary files format and content: xlsx file includes raw counts and FPKM values for each Sample

source_name: Human Tenon's capsule

growth_protocol: Fibroblast lines were cultured in DMEM with 10% fetal bovine serum (FBS). HTFs from passages 3 to 10 were used for subsequent experiments.

extract_protocol:
We used Trizol LS Reagent (Thermo Fisher Scientific, Waltham, MA, USA) to extract Total RNA, following the manufacturer's instructions. To eliminate contaminating DNA, the RNA was treated with DNase I (Promega).
Total RNA samples from iRPCs and parental HTFs were submitted to the Genomics commercial sequencing facility for Bioanalyzer quality control analysis and Illumina Next Generation Sequencing. All submitted samples had an RNA integrity number (RIN) > 8. Stranded TruSeq cDNA libraries with poly dT enrichment were prepared from total RNA from each sample according to the manufacture’s protocol.

treatment_protocol: 1 ×10^6 HTFs (passage <10) were seeded into a 10-cm dish pre-coated with 40X Matrigel. On day 1, the medium was replaced with HTF medium (10% FBS and DMEM) containing RG108 (20 μM, MedChemExpress, Monmouth Junction, NJ, USA). On day 3, the medium was changed to iRPC medium (50% Neural basal with 0.075% BSA, 50% DMEM/F12/Glutamax, 1X N2, 1X B27 without vitamin A, and 0.1 mM nonessential amino acids, all from Life Technologies, Carlsbad, CA, USA) with RG108 (20 μM, Tocris Bioscience, Bristol, UK) and VPA (3 mM, Tocris Bioscience, Bristol, UK). On day 4, the medium was replaced with iRPC medium containing SU9516 (10 μM, R & D Systems, Minneapolis, MN, USA), forskolin (10 μM, Tocris Bioscience, Bristol, UK), Y-27632 (10 μM, LC Laboratories, Woburn, MA, USA), and vitamin C (10 μM, Sigma-Aldrich, Saint Louis, MO, USA). On day 5, the medium was adjusted to include only forskolin (10 μM), Y-27632 (10 μM), and vitamin C (10 μM). By day 6, the cells had developed a dome shape with bright nuclei and were prone to form clusters, indicating the formation of iRPCs.

value: Human Tenon's capsule

tag: cell line

value: fibroblasts


title: Disease Ileum 41 yo M

description: 10x genomics

value: Crohn's disease

tag: tissue

value: Ileum

value: M


title: Disease Rectum 40 yo M

description: 10x genomics


title: PBMC, vitamin D bolus, day 1, Individual 20

description:
After 1 day of vitamin D bolus intake
d1_Ind20

value: Individual 20

value: PBMC

tag: treatment


title: PBMC, vitamin D bolus, day 1, Individual 17

description:
After 1 day of vitamin D bolus intake
d1_Ind17

value: Individual 17


title: PBMC, vitamin D bolus, day 1, Individual 16

description:
After 1 day of vitamin D bolus intake
d1_Ind16

value: Individual 16


title: Patient3-I_CD8-TCRseq

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Library name: Sample 8

data_processing:
TCRβ data were aligned and quantified using MixCR (version 2.1.5).
Assembly: hg19
Supplementary files format and content: TCRseq: Tab-deliminted text files with counts and VDJ-CDR3 description for all clonotypes for each sample.
Library strategy: TCR-Seq

molecule: polyA RNA

source_name: Invaded Lymph Node

growth_protocol: Ex-vivo

extract_protocol:
Norgen
TCRs were enriched using specific primers, and sequencing libraries were prepared according to standard Illumina protocols.

value: Invaded Lymph Node


title: COL074.FFPE

value: FFPE


title: PBMC, vitamin D bolus, day 1, Individual 15

description:
After 1 day of vitamin D bolus intake
d1_Ind15

value: Individual 15


title: Patient3-NI_CD8-TCRseq

description: Library name: Sample 7

source_name: Non Invaded Lymph Node

value: Non Invaded Lymph Node


title: Disease PBMC 40 yo M

description: 10x genomics


title: Disease Ileum 40 yo M

description: 10x genomics


title: PBMC, vitamin D bolus, day 1, Individual 14

description:
After 1 day of vitamin D bolus intake
d1_Ind14

value: Individual 14

value: Healthy Individuals


title: COL073.FFPE


title: Patient2-T_CD8-TCRseq

description: Library name: Sample 6

source_name: Breast tumor

value: Breast tumor


title: PBMC, vitamin D bolus, day 1, Individual 13

description:
After 1 day of vitamin D bolus intake
d1_Ind13

value: Individual 13

value: 80000 IU vitamin D3

value: day 1


title: Disease Rectum 57 yo F

description: 10x genomics

value: Crohn's disease

value: Rectum

value: F


title: COL074.FF

value: FF


title: COL073.FF


title: COL072.FF


title: Disease PBMC 57 yo F

description: 10x genomics

value: PBMC


title: PBMC, vitamin D bolus, day 1, Individual 19

description:
After 1 day of vitamin D bolus intake
d1_Ind19

value: Individual 19


title: Patient2-I_CD8-TCRseq

description: Library name: Sample 5


title: Induced retinal progenitor cells (iRPCs), day6

description:
Library name: Sample 2
Column name in FullTable.xlsx: iRPC4

value: retinal progenitor-like cells


title: COL084.FF


title: COL075.FF


title: PBMC, vitamin D bolus, day 1, Individual 12

description:
After 1 day of vitamin D bolus intake
d1_Ind12

value: Individual 12


title: Patient3-T_CD8-TCRseq

description: Library name: Sample 9


title: COL069.FFPE

value: FFPE


title: PBMC, vitamin D bolus, day 1, Individual 11

description:
After 1 day of vitamin D bolus intake
d1_Ind11

value: Individual 11


title: LPB [1246]

city: Guelph

first: Samantha

last: Dixon

state: Ontario

address: 50 Stone Rd E

department: Animal Biosciences

country: Canada

institute: University of Guelph

description: Library name: Sample 16

data_processing:
RNA-Seq analysis was performed using the CLC genomics workbench software, version 12 (CLC Bio, Aarhus, Denmark). Quality control analysis, including guanine-cytosine (GC) content, ambiguous base content, Phred score, base coverage, nucleotide contributions and over-represented sequences parameters, was performed on fastq files Sequence reads were aligned to the annotated Oar_v3.1 ovine reference genome (release 95). Counts per gene were transformed using a Log10 transformation and normalized to reads per kilo base per million mapped reads (RPKM) values
Assembly: Oar_v3.1
Supplementary files format and content: DESeq log2FoldChange on a xlsx file format

organism: Ovis aries

source_name: Liver

extract_protocol:
A representative sample of tissue (30 mg) from the center of the right liver lobe was ground using a mortar and pestle with liquid nitrogen and homogenized using a hand-held homogenizer. Total RNA was extracted following the manufacturer’s instructions using Qiagen RNeasy Mini Prep Kit (Qiagen, Calif., USA).
The NEBNext Ultra RNA Library Prep kit for Illumina (New England Biolabs, Mass., USA) was used for library preparation with Poly-A selection, according to the manufacturer’s recommendations.

value: Liver

value: GIN-exposed


title: Patient1-T_CD8-TCRseq

description: Library name: Sample 3


title: PBMC, vitamin D bolus, day 1, Individual 10

description:
After 1 day of vitamin D bolus intake
d1_Ind10

value: Individual 10

value: Healthy Individuals


title: COL069.FF


title: Patient1-I_CD8-TCRseq

description: Library name: Sample 2

value: Invaded Lymph Node


title: Patient1-NI_CD8-TCRseq

description: Library name: Sample 1

value: Non Invaded Lymph Node


title: COL068.FF


title: PBMC, vitamin D bolus, day 1, Individual 09

description:
After 1 day of vitamin D bolus intake
d1_Ind09

value: Individual 09

value: 80000 IU vitamin D3

value: day 1


title: PBMC, vitamin D bolus, day 1, Individual 07

description:
After 1 day of vitamin D bolus intake
d1_Ind07

value: Individual 07


title: KO_CysF_female

city: New Haven

first: Lucie

last: Orliaguet

state: CT

address: 310 Cedar Street

institute: Yale University

description:
Library name: Sample 4
10x genomics

data_processing:
Sample demultiplexing, barcode processing, and single-cell 3’ counting was performed using the Cell Ranger Single-Cell Software Suite (10x Genomics). Cellranger count was used to align samples to the reference genome (mm10), quantify reads, and filter reads with a quality score below 30.
Assembly: mm10
Supplementary files format and content: barcodes and features in tabulation-separated values files and matrix files

source_name: subcutaneous adipose depots

extract_protocol:
Cth+/+ (WT) and Cth-/- mice were fed with control or cystine free diet for 4 days.Subcutaneous adipose depots were collected, with lymph nodes removed, pooled and digested. Isolated cells were subjected to droplet-based 3' end massively parallel single cell RNA sequencing using Chromium Single Cell 3’ Reagent Kits as per manufacturer’s instructions (10x Genomics).
The libraries were sequenced using a HiSeq3000 instrument (Illumina)

treatment_protocol: Control or cystine free diet for 4 days.

value: subcutaneous adipose depots

value: stromal vascular cells

value: Cth-/-

tag: diet

value: cysteine free diet

tag: Sex

value: female


title: P195, PBL, male, old

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

description: Library name: P195

data_processing:
Sequence information was extracted in FastQ format using Illumina’s bcl2fastq v.1.8.4
The reads were mapped to the human reference genome (GRCh38) with the Ensembl genome annotation (Ensembl 92 / Gencode 28) using the short-read aligner STAR (version 2.5.4b; parameters: --alignIntronMax 100000 --outSJfilterReads Unique --outSAMmultNmax 1 --outFilterMismatchNoverLmax 0.04) (PMID: 23104886)
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 1.5.0 (meta-feature mode, stranded mode “2”, Ensembl 92) (PMID: 24227677)
Assembly: GRCh38
Supplementary files format and content: Per sample, one text file with tab separated values in FeatureCount output format with Gene ID, genomic coordinates of exons and their length and direction as well as the number of reads mapping to that gene.

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from up to 1 million primary cultured PBL using the RNeasy kit (Qiagen) following the manufacturer’s instructions.
An amount of 800ng total RNA was introduced into library preparation using a TruSeq stranded mRNA sample preparation kit (Illumina).

value: peripheral blood

value: peripheral blood lymphocytes

value: male

tag: age group

value: old

tag: age [years]


title: WT_CysF_female

description:
Library name: Sample 2
10x genomics

value: Cth+/+


title: PBMC, vitamin D bolus, day 1, Individual 08

description:
After 1 day of vitamin D bolus intake
d1_Ind08

value: Individual 08

value: Healthy Individuals

value: PBMC


title: COL064.FF

source_name: CRC tumor

value: FF


title: COL064.FFPE

value: FFPE


title: P189, PBL, male, old

description: Library name: P189


title: PBMC, vitamin D bolus, day 1, Individual 06

description:
After 1 day of vitamin D bolus intake
d1_Ind06

value: Individual 06

value: 80000 IU vitamin D3

value: day 1


title: WT_CTRL_female

description:
Library name: Sample 1
10x genomics

value: subcutaneous adipose depots

value: stromal vascular cells

value: Control


title: COL058.FF


title: P188, PBL, male, old

description: Library name: P188


title: COL058.FFPE


title: Disease Ileum 57 yo F

description: 10x genomics

value: Crohn's disease

value: Ileum

value: F


title: Patient2-NI_CD8-TCRseq

description: Library name: Sample 4

value: Non Invaded Lymph Node


title: PBMC, vitamin D bolus, day 1, Individual 05

description:
After 1 day of vitamin D bolus intake
d1_Ind05

value: Individual 05


title: P187, PBL, male, old

description: Library name: P187

value: peripheral blood

value: peripheral blood lymphocytes

value: male

value: old


title: Healthy Spleen 1

city: Duarte

first: Nancy

middle: Danielle

last: Ebelt

address: 1500 E Duarte Rd

department: Immuno-Oncology

institute: Beckman Research Institute of City of Hope

hyb_protocol: Overnight hybridization at 65C for 18h

scan_protocol: hybridized samples were processed in the prep station and the data acquisition was performed by nCounter MAX/FLEX profiler (Nanostring)

data_processing: nCounter bulk RNA expression data were analyzed using nSolver Analysis Software (Version 4.0, R Version 3.3.2) with the nSolver Advanced Analysis Add-On (Nanostring).

label: barcode

source_name: Whole Spleen

label_protocol: The CodeSet hybridization was set up by mixing 8ul of total RNA (200ng); 10ul hybridization master mix containing 5ul of hybridization buffer, 3ul of Reporter CodeSet and 2ul of Reporter Plus CodeSet; and capture master mix (100052, Nanostring; Seattle, WA, USA) containing 2ul of Capture Probe Set and 1ul of Capture Plus Probe Set. The CodeSet of Mouse PanCancer Immune Profiling Panel with Panel Plus (20 additional genes, Supplemental Table 2) was used for this study (15000142, Nanostring).

growth_protocol: C57Bl/6 mice were implanted via tail vein with 80,000 C1498 cells

extract_protocol: two days after the final treatment (end of week 2), whole blood was extracted by retro-orbital blood draw and whole spleens were extracted, both were immediately placed in RNAlater solution

treatment_protocol: three days after implant, treatment with vehicle (DMSO in diluent) or 5-Azacytidine (5mg/kg) began thrice weekly for two weeks by intraperitoneal injection

value: untreated

tag: leukemia

value: no implanted cells

tag: animal id

value: Mouse 13

value: Whole Spleen


title: COL057.FFPE

value: FFPE


title: PBMC, vitamin D bolus, day 1, Individual 04

description:
After 1 day of vitamin D bolus intake
d1_Ind04

value: Individual 04

tag: disease state

value: Healthy Individuals

value: PBMC

value: 80000 IU vitamin D3

value: day 1


title: KO_CTRL_female

description:
Library name: Sample 3
10x genomics

value: subcutaneous adipose depots

value: stromal vascular cells

tag: genotype

value: Cth-/-

value: Control

value: female


title: P183, PBL, male, old

description: Library name: P183

value: peripheral blood

value: peripheral blood lymphocytes

value: male


title: DMSO Spleen 4

value: DMSO in diluent

value: C1498 implanted

value: Mouse 12


title: COL057.FF

value: FF


title: P182, PBL, male, old

description: Library name: P182

value: old


title: PBMC, vitamin D bolus, day 1, Individual 03

description:
After 1 day of vitamin D bolus intake
d1_Ind03

value: Individual 03

value: Healthy Individuals


title: PBMC, vitamin D bolus, day 1, Individual 02

description:
After 1 day of vitamin D bolus intake
d1_Ind02

value: Individual 02

value: PBMC

value: 80000 IU vitamin D3


title: DMSO Spleen 3

value: Mouse 11

value: Whole Spleen


title: P190, PBL, female, old

description: Library name: P190


title: COL055.FFPE

value: FFPE


title: PBMC, vitamin D bolus, day 1, Individual 01

description:
After 1 day of vitamin D bolus intake
d1_Ind01

value: Individual 01

value: day 1


title: PBMC, Control, day 0, Individual 45

description:
Before vitamin D bolus intake
d0_Ind45

value: Individual 45

value: control

value: day 0


title: COL054.FFPE


title: DMSO Spleen 2

value: DMSO in diluent

value: C1498 implanted

value: Mouse 10


title: P186, PBL, female, old

description: Library name: P186

value: peripheral blood

value: peripheral blood lymphocytes

value: female

value: old


title: DMSO Spleen 1

value: Mouse 9


title: P184, PBL, female, old

description: Library name: P184


title: P185, PBL, female, old

description: Library name: P185


title: COL054.FF

value: FF


title: Aza Spleen 7

value: 5mg/kg 5-Azacytidine

value: Mouse 7


title: COL051.FFPE

value: FFPE


title: COL051.FF


title: PBMC, Control, day 0, Individual 43

description:
Before vitamin D bolus intake
d0_Ind43

value: Individual 43

value: Healthy Individuals

value: PBMC


title: P167, PBL, female, old

description: Library name: P167


title: Aza Spleen 6

value: Mouse 6

value: Whole Spleen


title: PBMC, Control, day 0, Individual 42

description:
Before vitamin D bolus intake
d0_Ind42

value: Individual 42

value: control

value: day 0


title: P165, PBL, female, old

description: Library name: P165

value: peripheral blood


title: Aza Spleen 5

value: C1498 implanted

value: Mouse 5


title: PBMC, Control, day 0, Individual 41

description:
Before vitamin D bolus intake
d0_Ind41

value: Individual 41


title: COL050.FF


title: P181, PBL, male, young

description: Library name: P181

value: peripheral blood lymphocytes

value: male

value: young


title: COL050.FFPE


title: PBMC, Control, day 0, Individual 40

description:
Before vitamin D bolus intake
d0_Ind40

value: Individual 40


title: Aza Spleen 4

value: 5mg/kg 5-Azacytidine

value: Mouse 4


title: Aza Spleen 3

value: Mouse 3


title: Aza Spleen 8

value: Mouse 8


title: P171, PBL, male, young

description: Library name: P171


title: COL055.FF

value: FF


title: PBMC, Control, day 0, Individual 44

description:
Before vitamin D bolus intake
d0_Ind44

value: Individual 44

value: Healthy Individuals

value: PBMC


title: Aza Spleen 2

value: Mouse 2

value: Whole Spleen


title: COL046.FF


title: COL045.FFPE

value: FFPE


title: P170, PBL, male, young

description: Library name: P170

value: peripheral blood


title: PBMC, Control, day 0, Individual 39

description:
Before vitamin D bolus intake
d0_Ind39

value: Individual 39

value: control

value: day 0


title: P168, PBL, male, young

description: Library name: P168

value: peripheral blood lymphocytes

value: male

value: young


title: PBMC, Control, day 0, Individual 37

description:
Before vitamin D bolus intake
d0_Ind37

value: Individual 37


title: COL045.FF


title: PBMC, Control, day 0, Individual 38

description:
Before vitamin D bolus intake
d0_Ind38

value: Individual 38


title: Healthy Blood 1

source_name: Retro-orbital Blood Draw

value: untreated

value: no implanted cells

value: Mouse 13

value: Retro-orbital Blood Draw


title: PBMC, Control, day 0, Individual 36

description:
Before vitamin D bolus intake
d0_Ind36

value: Individual 36

value: Healthy Individuals

value: PBMC


title: DMSO Blood 4

value: DMSO in diluent

value: C1498 implanted

value: Mouse 12


title: P164, PBL, male, young

description: Library name: P164

value: peripheral blood


title: COL041.FF

value: FF


title: PBMC, Control, day 0, Individual 35

description:
Before vitamin D bolus intake
d0_Ind35

value: Individual 35

value: control

value: day 0


title: P175, PBL, female, young

description: Library name: P175

value: peripheral blood lymphocytes

value: female

value: young


title: P174, PBL, female, young

description: Library name: P174


title: COL040.FFPE

value: FFPE


title: PBMC, Control, day 0, Individual 34

description:
Before vitamin D bolus intake
d0_Ind34

value: Individual 34


title: PBMC, Control, day 0, Individual 33

description:
Before vitamin D bolus intake
d0_Ind33

value: Individual 33


title: P173, PBL, female, young

description: Library name: P173


title: COL040.FF


title: DMSO Blood 3

value: Mouse 11

value: Retro-orbital Blood Draw


title: DMSO Blood 2

value: Mouse 10


title: P172, PBL, female, young

description: Library name: P172


title: DMSO Blood 1

value: DMSO in diluent

value: Mouse 9


title: COL041.FFPE


title: COL034.FFPE


title: Aza Spleen 1

value: 5mg/kg 5-Azacytidine

value: C1498 implanted

value: Mouse 1

value: Whole Spleen


title: Aza Blood 7

value: Mouse 7


title: COL035.FF

value: FF


title: Aza Blood 8

value: Mouse 8


title: COL034.FF


title: P166, PBL, male, young

description: Library name: P166

value: peripheral blood

value: peripheral blood lymphocytes

value: male


title: P163, PBL, female, young

description: Library name: P163

value: female

value: young


title: P160, PBL, female, young

description: Library name: P160


title: PBMC, Control, day 0, Individual 29

description:
Before vitamin D bolus intake
d0_Ind29

value: Individual 29

value: Healthy Individuals

value: PBMC

value: control

value: day 0


title: PBMC, Control, day 0, Individual 30

description:
Before vitamin D bolus intake
d0_Ind30

value: Individual 30


title: Aza Blood 5

value: 5mg/kg 5-Azacytidine

value: C1498 implanted

value: Mouse 5

value: Retro-orbital Blood Draw


title: COL026.FF

value: FF


title: Aza Blood 6

value: Mouse 6


title: PBMC, Control, day 0, Individual 28

description:
Before vitamin D bolus intake
d0_Ind28

value: Individual 28


title: COL022.FFPE

value: FFPE


title: Aza Blood 3

value: Mouse 3


title: COL016.FFPE


title: Aza Blood 4

value: Mouse 4


title: PBMC, Control, day 0, Individual 32

description:
Before vitamin D bolus intake
d0_Ind32

value: Individual 32


title: PBMC, Control, day 0, Individual 31

description:
Before vitamin D bolus intake
d0_Ind31

value: Individual 31


title: PBMC, Control, day 0, Individual 27

description:
Before vitamin D bolus intake
d0_Ind27

value: Individual 27

value: Healthy Individuals


title: BMAT-MSCS, FA-3 TNFa, 18h

city: Ankara

first: Bihter

last: Muratoğlu

state: Ankara

address: Sihhiye

department: Stem Cell Sciences

country: Turkey

institute: Hacettepe University

description:
Library name: Sample_36
Column name in FPKM_All_Samples.csv: FA-TNFa_FPKM

data_processing:
Base calling was performed using bcl2fastq (v2.20) to convert raw Illumina sequencing signals into FASTQ files. These files were used as input for downstream analysis.
Quality control of raw RNA-seq reads was performed using FastQC (v0.11.9) to identify adapter contamination, sequence quality scores, and GC content distribution.
Reads were trimmed using Trimmomatic (v0.39) to remove adapters, low-quality bases (Phred score <20), sequences with unidentified bases (N >5), and reads shorter than 32 bases.
RNA-seq reads were aligned to the human reference genome GRCh38 by using STAR (v2.7.10b) (default parameters).
Normalized FPKM values were calculated for library size and gene length normalization  using Cuffdiff (v2.2.1) with default parameters, including a false discovery rate (FDR) threshold of ≤ 0.01.
Assembly: GRCh38
Supplementary files format and content: Processed data files are provided in CSV format.
Supplementary files format and content: FPKM_All_Samples.csv:  contains normalized FPKM values for each sample, representing FPKM mapped reads.

source_name: Bone marrow adipose tissue

growth_protocol: Cells were cultured in low-glucose Dulbecco’s Modified Eagle Medium (LG-DMEM) (Biowest) supplemented with penicillin-streptomycin (100 U/ml and 100 μg/ml, respectively), 1% L-Glutamine (Biowest),  and 10% FBS (Gibco) in a humidified incubator at 5% CO2 and 37°C.

extract_protocol:
RNA was harvested using the RNeasy Miniprep Kit (Qiagen #74104), with optional on-column DNase treatment, following the manufacturer’s instructions.
RNA libraries for RNA-seq were generated from 1 μg total RNA using the Illumina Stranded Total RNA Library Prep with Ribo-Zero Plus Kit (Illumina #20040529), following the manufacturer’s instructions.

treatment_protocol: BMAT-MSCs were seeded into 6-well plates at 1 × 10^6 cells per well. After seeding, the medium was supplemented with 100 nM Dexamethasone (DEX) (Sigma-Aldrich, #50-02-2), and the plates were incubated for 1 hour. After synchronization, cells were treated with 1.5 μM SR1, 100 nM FICZ, and 100ng/ml TNFa for 18h.

value: Bone marrow adipose tissue

value: primary cells

value: mesenchymal stem cells

value: FA-3 TNFa


title: BMAT-MSCS, FA-2 TNFa, 18h

description:
Library name: Sample_35
Column name in FPKM_All_Samples.csv: FA-TNFa_FPKM

value: FA-2 TNFa


title: Aza Blood 2

value: 5mg/kg 5-Azacytidine

value: C1498 implanted

value: Mouse 2


title: COL022.FF

data_processing: Raw count data from nCounter

value: FF


title: COL015.FF


title: BMAT-MSCS, FA-1 TNFa, 18h

description:
Library name: Sample_34
Column name in FPKM_All_Samples.csv: FA-TNFa_FPKM

value: FA-1 TNFa


title: PBMC, Control, day 0, Individual 26

description:
Before vitamin D bolus intake
d0_Ind26

value: Individual 26

value: PBMC

value: control

value: day 0


title: PBMC, Control, day 0, Individual 25

description:
Before vitamin D bolus intake
d0_Ind25

value: Individual 25


title: BMAT-MSCS, HD-2 TNFa, 18h

description:
Library name: Sample_32
Column name in FPKM_All_Samples.csv: HD-TNFa_FPKM

value: HD-2 TNFa


title: COL014.FFPE

value: FFPE


title: BMAT-MSCS, HD-1 TNFa, 18h

description:
Library name: Sample_31
Column name in FPKM_All_Samples.csv: HD-TNFa_FPKM

value: Bone marrow adipose tissue

value: HD-1 TNFa


title: PBMC, Control, day 0, Individual 24

description:
Before vitamin D bolus intake
d0_Ind24

value: Individual 24

value: Healthy Individuals


title: BMAT-MSCS, HD-3 TNFa, 18h

description:
Library name: Sample_33
Column name in FPKM_All_Samples.csv: HD-TNFa_FPKM

value: primary cells

value: mesenchymal stem cells

value: HD-3 TNFa


title: Aza Blood 1

value: 5mg/kg 5-Azacytidine

value: C1498 implanted

value: Mouse 1

value: Retro-orbital Blood Draw


title: Human kidney, normothermic perfusion, RBC, 48 hrs, Oxiris, donor 10

city: Leiden

first: Roan

middle: Hugo

last: van Scheppingen

address: Albinusdreef 2

institute: LUMC

description:
Library name: BC4
150bp_pe

data_processing:
Data was aligned to using hg38p14 using Rsubread (v2.18.0)
A count matrix was generated, genes were annotated using useMart(v2.60.1) and genes without gene name or starting with "MT" were excluded.
A DESeqDataSet was generated using DESeq2(v1.44.0).
Data was processed and analysed using R (v4.4.1). For full code and packages, see the Github repository
Assembly: HG38p14
Supplementary files format and content: norm_counts_all is a comma separated file containing the normalized counts for the gene names per sample
Supplementary files format and content: metadata is a comma separated file containing extra data per sample.

source_name: Kidney

extract_protocol:
RNA was isolated using the QIAGEN mini RNA isolation kit according to manufacturer's protocol, subsequently mRNA was enriched for poly-A tails using oligo(dT)-magnetic beads.
After enrichment, mRNA was fragmented using fragmentation buffer, followed by reverse transcription using random N5 primers to synthesize cDNA double strands. The synthesized double-stranded DNA was then end-repaired and 5' phosphorylated, with a protruding 'A' at the 3'end forming a blunt end, followed by ligation of a  bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation producs were PCR amplified using specific primers. The PCR products were denatrued to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and seuenced after passing the quality control. (BGI's DNB-seq protocol)

value: Kidney

value: Male

tag: donor type

value: DCD

tag: preservation

value: HMP

tag: dialysis filter

value: OXI


title: COL009.FFPE

value: FFPE


title: Human kidney, normothermic perfusion, RBC, 24 hrs, Oxiris, donor 10

description:
Library name: BC3
150bp_pe


title: PBMC, Control, day 0, Individual 23

description:
Before vitamin D bolus intake
d0_Ind23

tag: individual

value: Individual 23

tag: cell type

value: PBMC

value: control

value: day 0


title: Human kidney, normothermic perfusion, RBC, 6 hrs, Oxiris, donor 10

description:
Library name: BC2
150bp_pe

tag: time


title: PBMC, Control, day 0, Individual 22

description:
Before vitamin D bolus intake
d0_Ind22

value: Individual 22

value: Healthy Individuals


title: COL014.FF

value: FF

tag: cms (ssp)


title: BMAT-MSCS, FA-3 SR1, 18h

description:
Library name: Sample_30
Column name in FPKM_All_Samples.csv: FA-SR1_FPKM

tag: tissue

value: Bone marrow adipose tissue

tag: cell line

value: primary cells

value: mesenchymal stem cells

value: FA-3 SR1


title: COL009.FF


title: Human kidney, normothermic perfusion, RBC, 0 hrs, Oxiris, donor 10

description:
Library name: BC1
150bp_pe

value: Kidney


title: BMAT-MSCS, FA-2 SR1, 18h

description:
Library name: Sample_29
Column name in FPKM_All_Samples.csv: FA-SR1_FPKM

tag: treatment

value: FA-2 SR1


title: PBMC, Control, day 0, Individual 21

description:
Before vitamin D bolus intake
d0_Ind21

value: Individual 21


title: COL008.FFPE


title: BMAT-MSCS, FA-1 SR1, 18h

description:
Library name: Sample_28
Column name in FPKM_All_Samples.csv: FA-SR1_FPKM

value: FA-1 SR1


title: Human kidney, subnormothermic perfusion, cell-free, 96hrs, HF20, donor 19

description:
Library name: Kidney_5
100bp_pe

tag: Sex

value: Male

value: DBD

value: SCS


title: PBMC, Control, day 0, Individual 20

description:
Before vitamin D bolus intake
d0_Ind20

value: Individual 20

value: PBMC


title: Human kidney, subnormothermic perfusion, cell-free, 96hrs, HF20, donor 18

description:
Library name: Kidney_4
100bp_pe

value: DCD


title: COL008.FF


title: PBMC, Control, day 0, Individual 19

description:
Before vitamin D bolus intake
d0_Ind19

value: Individual 19

value: control

value: day 0


title: BMAT-MSCS, HD-2 SR1, 18h

description:
Library name: Sample_26
Column name in FPKM_All_Samples.csv: HD-SR1_FPKM

value: Bone marrow adipose tissue

value: HD-2 SR1


title: BMAT-MSCS, HD-3 SR1, 18h

description:
Library name: Sample_27
Column name in FPKM_All_Samples.csv: HD-SR1_FPKM

value: primary cells

value: mesenchymal stem cells

value: HD-3 SR1


title: Human kidney, subnormothermic perfusion, cell-free, 96hrs, HF20, donor 17

description:
Library name: Kidney_3
100bp_pe

value: Kidney

value: Female


title: PBMC, Control, day 0, Individual 18

description:
Before vitamin D bolus intake
d0_Ind18

value: Individual 18

value: Healthy Individuals


title: Human kidney, subnormothermic perfusion, cell-free, 96hrs, HF20, donor 15

description:
Library name: Kidney_1
100bp_pe

value: Male

value: DBD


title: Human kidney, subnormothermic perfusion, cell-free, 96hrs, HF20, donor 16

description:
Library name: Kidney_2
100bp_pe

value: HMP


title: PBMC, Control, day 0, Individual 17

description:
Before vitamin D bolus intake
d0_Ind17

value: Individual 17

value: PBMC


title: COL007.FF

value: FF


title: COL005.FFPE

value: FFPE


title: Human kidney, unperfused, donor 14

description:
Library name: Control_4
100bp_pe

value: DCD

value: SCS


title: PBMC, Control, day 0, Individual 16

description:
Before vitamin D bolus intake
d0_Ind16

value: Individual 16

value: control

value: day 0


title: PBMC, Control, day 0, Individual 15

description:
Before vitamin D bolus intake
d0_Ind15

value: Individual 15


title: BMAT-MSCS, FA-2 FICZ, 18h

description:
Library name: Sample_22
Column name in FPKM_All_Samples.csv: FA-FICZ_FPKM

value: Bone marrow adipose tissue

value: primary cells

value: mesenchymal stem cells

value: FA-2 FICZ


title: BMAT-MSCS, AML-1 FICZ, 18h

description:
Library name: Sample_24
Column name in FPKM_All_Samples.csv: AML-FICZ_FPKM

value: AML-1 FICZ


title: BMAT-MSCS, HD-1 SR1, 18h

description:
Library name: Sample_25
Column name in FPKM_All_Samples.csv: HD-SR1_FPKM

value: HD-1 SR1


title: Human kidney, unperfused, donor 12

description:
Library name: Control_2
100bp_pe

value: Kidney

value: Female


title: BMAT-MSCS, FA-3 FICZ, 18h

description:
Library name: Sample_23
Column name in FPKM_All_Samples.csv: FA-FICZ_FPKM

value: FA-3 FICZ


title: COL005.FF

value: FF


title: PBMC, Control, day 0, Individual 13

description:
Before vitamin D bolus intake
d0_Ind13

value: Individual 13

value: Healthy Individuals

value: PBMC


title: COL004.FFPE

value: FFPE


title: Human kidney, normothermic perfusion, RBC, 24 hrs, Oxiris, donor 9

description:
Library name: BB3
150bp_pe

value: DCD

value: HMP

value: OXI


title: BMAT-MSCS, HD-2 FICZ, 18h

description:
Library name: Sample_19
Column name in FPKM_All_Samples.csv: HD-FICZ_FPKM

value: Bone marrow adipose tissue

value: HD-2 FICZ


title: Human kidney, unperfused, donor 13

description:
Library name: Control_3
100bp_pe

value: SCS


title: PBMC, Control, day 0, Individual 11

description:
Before vitamin D bolus intake
d0_Ind11

value: Individual 11

value: control

value: day 0


title: Human kidney, normothermic perfusion, RBC, 6 hrs, Oxiris, donor 9

description:
Library name: BB2
150bp_pe

value: Kidney


title: BMAT-MSCS, HD-1 FICZ, 18h

description:
Library name: Sample_18
Column name in FPKM_All_Samples.csv: HD-FICZ_FPKM

value: primary cells

value: mesenchymal stem cells

value: HD-1 FICZ


title: COL007.FFPE


title: PBMC, Control, day 0, Individual 14

description:
Before vitamin D bolus intake
d0_Ind14

value: Individual 14


title: PBMC, Control, day 0, Individual 10

description:
Before vitamin D bolus intake
d0_Ind10

value: Individual 10

value: Healthy Individuals


title: PBMC, Control, day 0, Individual 09

description:
Before vitamin D bolus intake
d0_Ind09

value: Individual 09

value: PBMC


title: LM40.FFPE

source_name: tumor

value: CRC tumor

tag: tissue type

value: FFPE


title: BMAT-MSCS, AML-1 Control, 18h

description:
Library name: Sample_17
Column name in FPKM_All_Samples.csv: AML-Control_FPKM

value: Bone marrow adipose tissue

value: AML-1 Control


title: COL004.FF

value: FF


title: BMAT-MSCS, FA-1 FICZ, 18h

description:
Library name: Sample_21
Column name in FPKM_All_Samples.csv: FA-FICZ_FPKM

value: FA-1 FICZ


title: BMAT-MSCS, HD-3 FICZ, 18h

description:
Library name: Sample_20
Column name in FPKM_All_Samples.csv: HD-FICZ_FPKM

value: HD-3 FICZ


title: BMAT-MSCS, FA-2 Control, 18h

description:
Library name: Sample_15
Column name in FPKM_All_Samples.csv: FA-Control_FPKM

value: FA-2 Control


title: Human kidney, normothermic perfusion, RBC, 24 hrs, Oxiris, donor 8

description:
Library name: BA3
150bp_pe

value: Kidney

value: Male

value: DCD

value: HMP

value: OXI


title: Human kidney, normothermic perfusion, RBC, 6 hrs, Oxiris, donor 8

description:
Library name: BA2
150bp_pe


title: LM41.FFPE


title: Human kidney, unfperfused, donor 11

description:
Library name: Control_1
100bp_pe

value: SCS


title: BMAT-MSCS, FA-1 Control, 18h

description:
Library name: Sample_14
Column name in FPKM_All_Samples.csv: FA-Control_FPKM

value: primary cells

value: mesenchymal stem cells

value: FA-1 Control


title: COL003.FFPE


title: BMAT-MSCS, HD-3 Control, 18h

description:
Library name: Sample_13
Column name in FPKM_All_Samples.csv: HD-Control_FPKM

value: HD-3 Control


title: Human kidney, normothermic perfusion, RBC, 48 hrs, HF20, donor 7

description:
Library name: AG4
150bp_pe


title: PBMC, Control, day 0, Individual 12

description:
Before vitamin D bolus intake
d0_Ind12

value: Individual 12

value: Healthy Individuals

value: PBMC

value: control

value: day 0


title: Human kidney, normothermic perfusion, RBC, 0 hrs, Oxiris, donor 9

description:
Library name: BB1
150bp_pe

value: Female


title: COL003.FF

value: FF


title: PBMC, Control, day 0, Individual 05

description:
Before vitamin D bolus intake
d0_Ind05

value: Individual 05


title: Human kidney, normothermic perfusion, RBC, 48 hrs, Oxiris, donor 8

description:
Library name: BA4
150bp_pe

value: Kidney

value: Male


title: BMAT-MSCS, FA-3 Control, 18h

description:
Library name: Sample_16
Column name in FPKM_All_Samples.csv: FA-Control_FPKM

value: Bone marrow adipose tissue

value: FA-3 Control


title: LM39.FFPE

value: CRC tumor

value: FFPE


title: PBMC, Control, day 0, Individual 08

description:
Before vitamin D bolus intake
d0_Ind08

value: Individual 08


title: CO170.FFPE


title: BMAT-MSCS, HD-1 Control, 18h

description:
Library name: Sample_11
Column name in FPKM_All_Samples.csv: HD-Control_FPKM

value: primary cells

value: mesenchymal stem cells

value: HD-1 Control


title: CO164.FFPE


title: BMAT-MSCS, AML-1 TNFa, 18h

description:
Library name: Sample_10
Column name in FPKM_All_Samples.csv: AML-TNFa_FPKM

value: AML-1 TNFa


title: PBMC, Control, day 0, Individual 07

description:
Before vitamin D bolus intake
d0_Ind07

value: Individual 07

value: Healthy Individuals

value: PBMC


title: LM38.FFPE


title: CO162.FFPE


title: BMAT-MSCS, AML-1 SR1, 18h

description:
Library name: Sample_9
Column name in FPKM_All_Samples.csv: AML-SR1_FPKM

value: AML-1 SR1


title: LM37.FFPE


title: PBMC, Control, day 0, Individual 06

description:
Before vitamin D bolus intake
d0_Ind06

value: Individual 06

value: control

value: day 0


title: LM29.FFPE


title: LM28.FFPE


title: Human kidney, normothermic perfusion, RBC, 6 hrs, HF20, donor 7

description:
Library name: AG2
150bp_pe

value: Kidney

value: Male

value: DCD

value: SCS


title: Human kidney, normothermic perfusion, RBC, 24 hrs, HF20, donor 7

description:
Library name: AG3
150bp_pe


title: PBMC, Control, day 0, Individual 04

description:
Before vitamin D bolus intake
d0_Ind04

value: Individual 04


title: BMAT-MSCS, AML-2 TNFa, 18h

description:
Library name: Sample_8
Column name in FPKM_All_Samples.csv: AML-TNFa_FPKM

value: Bone marrow adipose tissue

value: AML-2 TNFa


title: BMAT-MSCS, HD-2 Control, 18h

description:
Library name: Sample_12
Column name in FPKM_All_Samples.csv: HD-Control_FPKM

value: primary cells

value: mesenchymal stem cells

value: HD-2 Control


title: Human kidney, normothermic perfusion, RBC, 0 hrs, HF20, donor 7

description:
Library name: AG1
150bp_pe


title: PBMC, Control, day 0, Individual 03

description:
Before vitamin D bolus intake
d0_Ind03

value: Individual 03


title: Ru corresponding to Rubus ulmifolius aqueous extract intake 3

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

institute: University of Lille

description: Gene expression after 20 days of gavage (D20)

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mus musculus Sure Print GE 4x44 v2 microarrays with oligonucleotide 45,220 probes (G2519F) 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 4x44 were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting

data_processing: The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hepatic tissues

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug 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).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Standard chow and water ad libitum (Diet A04C-10, Scientific Animal Food and Engineering, Augy, France)

extract_protocol: Total RNA was extracted from hepatic tissues using RNAspin columns (Macherey-Nagel). RNA quality was observed with Nanodrop and absorbance ratios A260/280 and A260/230 were found between 2.0 and 2.2. RNA quality was also examined by RNA ScreenTape Analysis (Agilent) and a minimal RNA integrity number (RIN) of 0.8 was required for all samples.

treatment_protocol: Mice were fed for 20 days with an aqueous extract of Artemisia campestris (Ar) or Rubus ulmifolius (Ru). The mice gavages consisted in a daily force-feeding of 500 µl of Ar or Ru solution (6mg/mL) besides the standard chow. The administrated dose was calculated to correspond to the concentration used as an infusion for moderate daily consumption. Controls underwent an equivalent force-feeding with water (Ctr).

value: liver

tag: gender

value: male

tag: age

value: 8 weeks of age at D0


title: Human kidney, normothermic perfusion, RBC, 48 hrs, HF20, donor 6

description:
Library name: AF4
150bp_pe