title: Control Sample number 132

description:
Saliva Sample from Control
CONTROL132

value: Control Sample number 132


title: Control Sample number 119

status: Public on May 31 2025

type: genomic

city: London

first: Laurence

middle: Bruce

last: Lovat

address: 43-45 Foley Street

department: Division of Surgery & Interventional Science

country: United Kingdom

institute: University College London

description:
Saliva Sample from Control
CONTROL119

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

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

data_processing:
raw .idat files were read via the minfi package in the R programming environment, data was normalised using Functional Normalisation in R
Average Beta value and detection P-values
Summarisd and normalised beta intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Saliva samples were collected using the Oragene DNA OG/600 saliva collection kit (DNAGenotek, Ottawa, Canada). All participants were required to fast for a minimum of one hour prior to sample collection.

tag: disease

value: Control Sample number 119

tag: age

tag: Sex

value: Male


title: Control Sample number 129

description:
Saliva Sample from Control
CONTROL129

value: Control Sample number 129


title: Control Sample number 127

description:
Saliva Sample from Control
CONTROL127

value: Control Sample number 127


title: D2_D04_RNAseq

type: SRA

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: 2i_release_NMTSeq_RNAseq_filtered_normalized.txt

library_source: transcriptomic

data_processing:
All sequencing was carried out on HiSeq instrument. RNA-seq libraries were pooled as 96-plex or 192-plex pools and sequenced using 75-bp paired-end reads.
scRNA-seq alignments were performed using Hisat 2 as described previously (Clark et al. Nature Communications, 2018).
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-delimited file with Ensembl Gene IDs, quantified values show number of reads per gene per sample

molecule: polyA RNA

organism: Mus musculus

growth_protocol: E14 mESC were cultured in 2i+LIF media consisting out of N2B27 medium, composed out of DMEM/F12 (Life Technologies, 12634010) and Neurobasal (Life Technologies, 21103049) in a volume/volume (v/v) ratio 1:1, 0.1 mM 2-mercaptoethanol, 2 mM L-Glutamine, 1:200 v/v N2 (Life Technologies, 17502048) and 1:100 v/v B27 supplement (Life Technologies, 17504044), supplemented with 3 µM CHIR99021, 1 µM PD0325901 and 20 ng/ml of leukemia inhibitory factor (LIF)  (all Department of Biochemistry, University of Cambridge). mESCs were cultured on tissue culture plastic pre-coated with 0.1 % gelatine in H2O. Cultures were passaged when approaching confluence (every 2 days). All cells were cultured in a humidified incubator at 37 °C in 5 % CO2 and 20 % O2. mESCs were subject to routine mycoplasma testing using the MycoAlert testing kit (Lonza) and tested negative. For induction for 2i-relase experiment, the cell been rinsed with PBS before the culture media was changed to serum + LIF medium consisting of DMEM (Life Technologies, 10566-016), containing 15% Fetal Bovine Serum (FBS) (Gibco, 10270106), 1x non-essential amino acids (NEAA) (Life Technologies, 11140050), 0.1 mM 2-mercaptoethanol (Life Technologies, 31350-010), 2 mM L-Glutamine (Life Technologies, 25030-024), supplemented with 20 ng/ml of LIF (Department of Biochemistry, University of Cambridge).

extract_protocol:
0h, 24h, and 48h after induction of 2i-release  the cells been dissociated into single cells using accutase before flow sorting  (BD Influx) into 96-well plate containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL CA-630 (Sigma)). Samples were incubated for 15 min at 37 °C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at −80 °C before processing.
All downstream library preparation steps been performed as previously described by Clark et al. (Clark et al. Nature Communications, 2018).

tag: strain

tag: cell type

value: embryonic stem cell


title: Control Sample number 118

description:
Saliva Sample from Control
CONTROL118

value: Control Sample number 118

value: Female


title: D2_D12_RNAseq


title: Control Sample number 117

description:
Saliva Sample from Control
CONTROL117

value: Control Sample number 117


title: Control Sample number 116

description:
Saliva Sample from Control
CONTROL116

value: Control Sample number 116


title: D2_D02_RNAseq


title: D2_C12_RNAseq


title: Control Sample number 114

description:
Saliva Sample from Control
CONTROL114

value: Control Sample number 114


title: D2_D08_RNAseq


title: D2_C11_RNAseq


title: D2_D01_RNAseq


title: Control Sample number 113

description:
Saliva Sample from Control
CONTROL113

value: Control Sample number 113


title: Control Sample number 111

description:
Saliva Sample from Control
CONTROL111

value: Control Sample number 111


title: Control Sample number 109

description:
Saliva Sample from Control
CONTROL109

value: Control Sample number 109


title: Control Sample number 120

description:
Saliva Sample from Control
CONTROL120

value: Control Sample number 120


title: D2_C08_RNAseq


title: Control Sample number 110

description:
Saliva Sample from Control
CONTROL110

value: Control Sample number 110


title: D2_C10_RNAseq


title: D2_C07_RNAseq


title: D2_C06_RNAseq


title: Control Sample number 108

description:
Saliva Sample from Control
CONTROL108

value: Control Sample number 108


title: Control Sample number 112

description:
Saliva Sample from Control
CONTROL112

value: Control Sample number 112


title: D2_D05_RNAseq


title: D2_C05_RNAseq


title: Control Sample number 107

description:
Saliva Sample from Control
CONTROL107

value: Control Sample number 107


title: D2_D03_RNAseq


title: Control Sample number 115

description:
Saliva Sample from Control
CONTROL115

value: Control Sample number 115


title: D2_C04_RNAseq


title: Control Sample number 106

description:
Saliva Sample from Control
CONTROL106

value: Control Sample number 106


title: Control Sample number 105

description:
Saliva Sample from Control
CONTROL105

value: Control Sample number 105


title: Control Sample number 104

description:
Saliva Sample from Control
CONTROL104

value: Control Sample number 104

value: Male


title: Control Sample number 103

description:
Saliva Sample from Control
CONTROL103

value: Control Sample number 103

value: Female


title: D2_C01_RNAseq

value: embryonic stem cell


title: D2_C02_RNAseq


title: Control Sample number 102

description:
Saliva Sample from Control
CONTROL102

value: Control Sample number 102


title: D2_B11_RNAseq


title: Control Sample number 100

description:
Saliva Sample from Control
CONTROL100

value: Control Sample number 100


title: D2_B07_RNAseq


title: D2_B08_RNAseq


title: D2_B06_RNAseq


title: Control Sample number 99

description:
Saliva Sample from Control
CONTROL099

value: Control Sample number 99


title: D2_B05_RNAseq


title: Control Sample number 95

description:
Saliva Sample from Control
CONTROL095

value: Control Sample number 95


title: Control Sample number 96

description:
Saliva Sample from Control
CONTROL096

value: Control Sample number 96


title: D2_C03_RNAseq


title: D2_C09_RNAseq


title: D2_B03_RNAseq


title: Control Sample number 93

description:
Saliva Sample from Control
CONTROL093

value: Control Sample number 93


title: Control Sample number 190

description:
Saliva Sample from Control
CONTROL190

value: Control Sample number 190


title: Control Sample number 94

description:
Saliva Sample from Control
CONTROL094

value: Control Sample number 94


title: Control Sample number 92

description:
Saliva Sample from Control
CONTROL092

value: Control Sample number 92


title: D2_B02_RNAseq


title: D2_B12_RNAseq


title: Control Sample number 101

description:
Saliva Sample from Control
CONTROL101

value: Control Sample number 101


title: Control Sample number 91

description:
Saliva Sample from Control
CONTROL091

value: Control Sample number 91


title: D2_B01_RNAseq


title: D2_B10_RNAseq


title: D2_B09_RNAseq


title: Control Sample number 98

description:
Saliva Sample from Control
CONTROL098

value: Control Sample number 98


title: D2_A12_RNAseq


title: D2_A10_RNAseq


title: Control Sample number 89

description:
Saliva Sample from Control
CONTROL089

value: Control Sample number 89


title: Control Sample number 90

description:
Saliva Sample from Control
CONTROL090

value: Control Sample number 90


title: D2_A09_RNAseq


title: Control Sample number 86

description:
Saliva Sample from Control
CONTROL086

value: Control Sample number 86


title: D2_A08_RNAseq


title: Control Sample number 85

description:
Saliva Sample from Control
CONTROL085

value: Control Sample number 85

value: Male


title: D2_B04_RNAseq

value: embryonic stem cell


title: D2_A06_RNAseq


title: Control Sample number 84

description:
Saliva Sample from Control
CONTROL084

value: Control Sample number 84


title: Control Sample number 82

description:
Saliva Sample from Control
CONTROL082

value: Control Sample number 82

value: Female


title: Control Sample number 83

description:
Saliva Sample from Control
CONTROL083

value: Control Sample number 83


title: Control Sample number 81

description:
Saliva Sample from Control
CONTROL081

value: Control Sample number 81


title: D2_A04_RNAseq


title: D2_A03_RNAseq


title: D2_A05_RNAseq


title: D2_A02_RNAseq


title: D2_A11_RNAseq


title: Control Sample number 79

description:
Saliva Sample from Control
CONTROL079

value: Control Sample number 79


title: Control Sample number 78

description:
Saliva Sample from Control
CONTROL078

value: Control Sample number 78


title: D1_H12_RNAseq


title: D2_A01_RNAseq


title: Control Sample number 80

description:
Saliva Sample from Control
CONTROL080

value: Control Sample number 80


title: Control Sample number 88

description:
Saliva Sample from Control
CONTROL088

value: Control Sample number 88


title: Control Sample number 77

description:
Saliva Sample from Control
CONTROL077

value: Control Sample number 77


title: D1_H11_RNAseq


title: Control Sample number 87

description:
Saliva Sample from Control
CONTROL087

value: Control Sample number 87


title: Control Sample number 75

description:
Saliva Sample from Control
CONTROL075

value: Control Sample number 75


title: Control Sample number 76

description:
Saliva Sample from Control
CONTROL076

value: Control Sample number 76


title: D1_H09_RNAseq


title: D2_A07_RNAseq


title: Control Sample number 74

description:
Saliva Sample from Control
CONTROL074

value: Control Sample number 74


title: D1_H10_RNAseq


title: D1_H08_RNAseq


title: D1_H07_RNAseq


title: Control Sample number 73

description:
Saliva Sample from Control
CONTROL073

value: Control Sample number 73


title: Control Sample number 72

description:
Saliva Sample from Control
CONTROL072

value: Control Sample number 72

value: Male


title: D1_H06_RNAseq

value: embryonic stem cell


title: Control Sample number 71

description:
Saliva Sample from Control
CONTROL071

value: Control Sample number 71


title: D1_H05_RNAseq


title: Control Sample number 70

description:
Saliva Sample from Control
CONTROL070

value: Control Sample number 70


title: D1_H04_RNAseq


title: D1_H02_RNAseq


title: Control Sample number 69

description:
Saliva Sample from Control
CONTROL069

value: Control Sample number 69

value: Female


title: Control Sample number 68

description:
Saliva Sample from Control
CONTROL068

value: Control Sample number 68


title: D1_H01_RNAseq


title: D1_H03_RNAseq


title: Control Sample number 67

description:
Saliva Sample from Control
CONTROL067

value: Control Sample number 67


title: Control Sample number 65

description:
Saliva Sample from Control
CONTROL065

value: Control Sample number 65


title: Control Sample number 66

description:
Saliva Sample from Control
CONTROL066

value: Control Sample number 66


title: D1_G12_RNAseq


title: D1_G11_RNAseq


title: D1_G09_RNAseq


title: Control Sample number 63

description:
Saliva Sample from Control
CONTROL063

value: Control Sample number 63


title: Control Sample number 64

description:
Saliva Sample from Control
CONTROL064

value: Control Sample number 64


title: D1_G10_RNAseq


title: Control Sample number 62

description:
Saliva Sample from Control
CONTROL062

value: Control Sample number 62


title: D1_G07_RNAseq


title: Control Sample number 60

description:
Saliva Sample from Control
CONTROL060

value: Control Sample number 60


title: Control Sample number 61

description:
Saliva Sample from Control
CONTROL061

value: Control Sample number 61


title: D1_G04_RNAseq


title: D1_G06_RNAseq


title: Control Sample number 59

description:
Saliva Sample from Control
CONTROL059

value: Control Sample number 59


title: Control Sample number 58

description:
Saliva Sample from Control
CONTROL058

value: Control Sample number 58


title: D1_G03_RNAseq


title: Control Sample number 56

description:
Saliva Sample from Control
CONTROL056

value: Control Sample number 56


title: Control Sample number 57

description:
Saliva Sample from Control
CONTROL057

value: Control Sample number 57


title: Control Sample number 55

description:
Saliva Sample from Control
CONTROL055

value: Control Sample number 55


title: D1_G02_RNAseq

value: embryonic stem cell


title: D1_G01_RNAseq


title: Control Sample number 54

description:
Saliva Sample from Control
CONTROL054

value: Control Sample number 54

value: Male


title: D1_F12_RNAseq


title: D1_F11_RNAseq


title: Control Sample number 53

description:
Saliva Sample from Control
CONTROL053

value: Control Sample number 53


title: Control Sample number 52

description:
Saliva Sample from Control
CONTROL052

value: Control Sample number 52


title: D1_F08_RNAseq


title: Control Sample number 51

description:
Saliva Sample from Control
CONTROL051

value: Control Sample number 51


title: D1_G08_RNAseq


title: D1_F09_RNAseq


title: Control Sample number 50

description:
Saliva Sample from Control
CONTROL050

value: Control Sample number 50

value: Female


title: D1_G05_RNAseq


title: Control Sample number 49

description:
Saliva Sample from Control
CONTROL049

value: Control Sample number 49


title: D1_F07_RNAseq


title: D1_F06_RNAseq


title: Control Sample number 48

description:
Saliva Sample from Control
CONTROL048

value: Control Sample number 48


title: Control Sample number 46

description:
Saliva Sample from Control
CONTROL046

value: Control Sample number 46


title: D1_F03_RNAseq


title: Control Sample number 47

description:
Saliva Sample from Control
CONTROL047

value: Control Sample number 47


title: Control Sample number 45

description:
Saliva Sample from Control
CONTROL045

value: Control Sample number 45


title: D1_F02_RNAseq


title: D1_F05_RNAseq


title: D1_F04_RNAseq


title: Control Sample number 43

description:
Saliva Sample from Control
CONTROL043

value: Control Sample number 43


title: Control Sample number 42

description:
Saliva Sample from Control
CONTROL042

value: Control Sample number 42


title: D1_E12_RNAseq


title: D1_F01_RNAseq


title: D1_F10_RNAseq


title: D1_E11_RNAseq


title: Control Sample number 41

description:
Saliva Sample from Control
CONTROL041

value: Control Sample number 41


title: Control Sample number 40

description:
Saliva Sample from Control
CONTROL040

value: Control Sample number 40


title: Control Sample number 39

description:
Saliva Sample from Control
CONTROL039

value: Control Sample number 39


title: D1_E08_RNAseq

value: embryonic stem cell


title: Control Sample number 38

description:
Saliva Sample from Control
CONTROL038

value: Control Sample number 38


title: D1_E07_RNAseq


title: D1_E09_RNAseq


title: Control Sample number 37

description:
Saliva Sample from Control
CONTROL037

value: Control Sample number 37


title: D1_E06_RNAseq


title: D1_E04_RNAseq


title: Control Sample number 35

description:
Saliva Sample from Control
CONTROL035

value: Control Sample number 35

value: Male


title: D1_E05_RNAseq


title: Control Sample number 34

description:
Saliva Sample from Control
CONTROL034

value: Control Sample number 34


title: Control Sample number 36

description:
Saliva Sample from Control
CONTROL036

value: Control Sample number 36

value: Female


title: D1_E03_RNAseq


title: D1_E02_RNAseq


title: Control Sample number 44

description:
Saliva Sample from Control
CONTROL044

value: Control Sample number 44


title: Control Sample number 31

description:
Saliva Sample from Control
CONTROL031

value: Control Sample number 31


title: D1_E01_RNAseq


title: Control Sample number 32

description:
Saliva Sample from Control
CONTROL032

value: Control Sample number 32


title: Control Sample number 33

description:
Saliva Sample from Control
CONTROL033

value: Control Sample number 33


title: D1_E10_RNAseq


title: D1_D12_RNAseq


title: D1_D11_RNAseq


title: Control Sample number 29

description:
Saliva Sample from Control
CONTROL029

value: Control Sample number 29


title: Control Sample number 28

description:
Saliva Sample from Control
CONTROL028

value: Control Sample number 28


title: D1_D10_RNAseq


title: Control Sample number 27

description:
Saliva Sample from Control
CONTROL027

value: Control Sample number 27


title: D1_D09_RNAseq


title: D1_D08_RNAseq


title: Control Sample number 26

description:
Saliva Sample from Control
CONTROL026

value: Control Sample number 26


title: Control Sample number 24

description:
Saliva Sample from Control
CONTROL024

value: Control Sample number 24


title: Control Sample number 25

description:
Saliva Sample from Control
CONTROL025

value: Control Sample number 25


title: D1_D07_RNAseq

value: embryonic stem cell


title: D1_D06_RNAseq


title: D1_D05_RNAseq


title: Control Sample number 23

description:
Saliva Sample from Control
CONTROL023

value: Control Sample number 23


title: D1_D04_RNAseq


title: Control Sample number 22

description:
Saliva Sample from Control
CONTROL022

value: Control Sample number 22


title: Control Sample number 21

description:
Saliva Sample from Control
CONTROL021

value: Control Sample number 21


title: Control Sample number 20

description:
Saliva Sample from Control
CONTROL020

value: Control Sample number 20


title: D1_D02_RNAseq


title: D1_D03_RNAseq


title: D1_D01_RNAseq


title: Control Sample number 30

description:
Saliva Sample from Control
CONTROL030

value: Control Sample number 30

value: Male


title: Control Sample number 19

description:
Saliva Sample from Control
CONTROL019

value: Control Sample number 19

value: Female


title: D1_C12_RNAseq


title: Control Sample number 17

description:
Saliva Sample from Control
CONTROL017

value: Control Sample number 17


title: Control Sample number 18

description:
Saliva Sample from Control
CONTROL018

value: Control Sample number 18


title: D1_C11_RNAseq


title: D1_C10_RNAseq


title: Control Sample number 15

description:
Saliva Sample from Control
CONTROL015

value: Control Sample number 15


title: D1_C09_RNAseq


title: Control Sample number 16

description:
Saliva Sample from Control
CONTROL016

value: Control Sample number 16


title: D1_C08_RNAseq


title: Control Sample number 13

description:
Saliva Sample from Control
CONTROL013

value: Control Sample number 13


title: D1_C07_RNAseq


title: D1_C06_RNAseq


title: D1_C05_RNAseq


title: Control Sample number 11

description:
Saliva Sample from Control
CONTROL011

value: Control Sample number 11


title: D1_C04_RNAseq


title: Control Sample number 10

description:
Saliva Sample from Control
CONTROL010

value: Control Sample number 10


title: Control Sample number 9

description:
Saliva Sample from Control
CONTROL009

value: Control Sample number 9


title: D1_C03_RNAseq

value: embryonic stem cell


title: Control Sample number 8

description:
Saliva Sample from Control
CONTROL008

value: Control Sample number 8


title: D1_C02_RNAseq


title: D1_C01_RNAseq


title: Control Sample number 7

description:
Saliva Sample from Control
CONTROL007

value: Control Sample number 7


title: Control Sample number 12

description:
Saliva Sample from Control
CONTROL012

value: Control Sample number 12


title: D1_B12_RNAseq


title: Control Sample number 6

description:
Saliva Sample from Control
CONTROL006

value: Control Sample number 6


title: Control Sample number 5

description:
Saliva Sample from Control
CONTROL005

value: Control Sample number 5


title: Control Sample number 14

description:
Saliva Sample from Control
CONTROL014

value: Control Sample number 14


title: Control Sample number 4

description:
Saliva Sample from Control
CONTROL004

value: Control Sample number 4


title: Control Sample number 3

description:
Saliva Sample from Control
CONTROL003

value: Control Sample number 3

value: Female


title: D1_B10_RNAseq


title: Control Sample number 97

description:
Saliva Sample from Control
CONTROL097

value: Control Sample number 97

value: Male


title: D1_B09_RNAseq


title: Control Sample number 2

description:
Saliva Sample from Control
CONTROL002

value: Control Sample number 2


title: Control Sample number 1

description:
Saliva Sample from Control
CONTROL001

value: Control Sample number 1


title: D1_B07_RNAseq


title: Control 32

description: Saliva Sample from Control

data_processing:
raw .idat files were read via the minfi package in the R programming environment, data was normalised using Functional Normalisation in R
Average Beta value and detection P-values

source_name: Control

tag: tissue

value: saliva

tag: disease subtype

value: Control


title: D1_B05_RNAseq


title: Control 31

description: Saliva Sample from Control


title: D1_B06_RNAseq


title: D1_B04_RNAseq


title: Control 30

description: Saliva Sample from Control


title: D1_B03_RNAseq


title: Control 29

description: Saliva Sample from Control


title: Control 28

description: Saliva Sample from Control


title: D1_B02_RNAseq


title: D1_B01_RNAseq


title: Control 27

description: Saliva Sample from Control


title: D1_B11_RNAseq


title: D1_A12_RNAseq


title: Control 26

description: Saliva Sample from Control


title: D1_B08_RNAseq


title: D1_A11_RNAseq


title: D1_A10_RNAseq


title: Control 25

description: Saliva Sample from Control


title: D1_A09_RNAseq


title: Control 24

description: Saliva Sample from Control


title: D1_A06_RNAseq


title: Control 23

description: Saliva Sample from Control


title: D1_A07_RNAseq


title: D1_A05_RNAseq


title: Control 22

description: Saliva Sample from Control


title: D1_A08_RNAseq


title: Control 21

description: Saliva Sample from Control


title: yeast, SUL2 mutant group, biol rep 3

city: Cheng

first: Ma

last: Meng

address: University of Electronic Science and Technology Shahe Campus

country: China

institute: University of Electronic Science and Technology of China

description: Library name: SUL2-3A

data_processing:
SOAPnuke v1.5.6
Sequence reads for adaptor sequence/low-quality sequence/unknown base ('N' base) using SOAPnuke software. Low-Quality limit (base quality less than or equal to 15):20%, unknown base limit: 5%.
Clean sequence reads analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com)
The clean data were aligned to the reference genome using HISAT2 (v2.1.0) and  aligned to the gene set using Bowtie2.
Expression level of gene was calculated by RSEM (v1.3.1). The differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: R64
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Saccharomycotina

source_name: yeast

growth_protocol: The yeast strains were cultivated in YPD complete medium containing 2% glucose, 2% peptone, 1% yeast extract

extract_protocol:
RNA was harvested following the Microbial RNA BGI-NGS-TQ-RNA-002 protocol of Beijing Genomics institution
RNA libriaries for RNA-seq were prepared following the BGI-NGS-JK-RNA-001 protocol of Beijing Genomics institution

value: yeast

tag: cell line

value: Saccharomyces cerevisiae

tag: genotype

value: SUL2 knockdown

tag: treatment


title: yeast, SUL2 mutant group, biol rep 1

description: Library name: SUL2-1A


title: D1_A02_RNAseq

value: embryonic stem cell


title: yeast, E427 mutant group, biol rep 3

description: Library name: E427-3A

value: E427 mutant


title: D1_A04_RNAseq


title: yeast, SUL2 mutant group, biol rep 2

description: Library name: SUL2-2A


title: D1_A03_RNAseq


title: Control 20

description: Saliva Sample from Control


title: yeast,  E427mutant group, biol rep 2

description: Library name: E427-2A


title: D1_A01_RNAseq


title: Control 19

description: Saliva Sample from Control


title: D0_H11_RNAseq


title: yeast, E427 mutant group, biol rep 1

description: Library name: E427-1A


title: Control 18

description: Saliva Sample from Control


title: D0_H10_RNAseq


title: D0_H08_RNAseq


title: Control 17

description: Saliva Sample from Control


title: yeast,WT, biol rep 2

description: Library name: WT1-2

value: WT


title: D0_H12_RNAseq


title: D0_H06_RNAseq


title: yeast,WT, biol rep 1

description: Library name: WT1-1


title: Control 16

description: Saliva Sample from Control


title: yeast, SUL1 mutant group, biol rep 3

description: Library name: SUL1-3

value: SUL1 knockdown


title: D0_H04_RNAseq


title: D0_H03_RNAseq


title: Control 15

description: Saliva Sample from Control


title: yeast,  SUL1mutant group, biol rep 2

description: Library name: SUL1-2


title: Control 14

description: Saliva Sample from Control


title: D0_H02_RNAseq


title: yeast, SUL1 mutant group, biol rep 1

description: Library name: SUL1-1


title: D0_H01_RNAseq


title: Control 13

description: Saliva Sample from Control


title: D0_G12_RNAseq


title: D0_G10_RNAseq


title: Control 12

description: Saliva Sample from Control


title: D0_G09_RNAseq


title: Control 11

description: Saliva Sample from Control


title: D0_H09_RNAseq


title: D0_G08_RNAseq


title: D0_G07_RNAseq


title: Control 10

description: Saliva Sample from Control


title: D0_G06_RNAseq


title: D0_H05_RNAseq


title: 20220816_30102681520922-01_BT122-SPS_12

type: RNA

city: Taipei

first: Huang-chun

last: Lien

address: Chung-San S. Rd.

country: Taiwan

institute: National Taiwan University

hyb_protocol: According to manufacturer's protocol (Nanostring)

scan_protocol: Analyzed in the nCounter SPRINT Profiler

data_processing: RCC format files containing the raw data were analyzed via the NanoString nCounter nSolver4.0 software (MAN-C0019-08) with the NanoString Advanced Analysis 2.0 plugin (MAN-10030-03) following the NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04).

label: fluorescent barcode

source_name: primary breast cancer

extract_protocol: RNA was extracted using the miRNeasyFFPE Kit (Qiagen, Valencia, CA) following manufacturer’s protocol. Ten 5-μm FFPE slides were used for each tumor sample, and macrodissectionwas performed, when needed, to avoid normal tissue contamination. A minimum of 150 ng of total RNA was analyzed at the nCounter platform using the Breast Cancer 360 Panel.

value: primary breast cancer

tag: cancer subtype

value: SPS


title: D0_G05_RNAseq


title: D0_G04_RNAseq


title: 20220816_30102681520922-01_BT95-IDC_10

label_protocol: According to manufacturer's protocol (Nanostring)

value: IDC


title: D0_G03_RNAseq


title: D0_G11_RNAseq


title: D0_F12_RNAseq


title: Control 07

description: Saliva Sample from Control

value: Female


title: D0_F11_RNAseq


title: Control 06

description: Saliva Sample from Control


title: 20220816_30102681520922-01_BT91-IDC_07


title: D0_F10_RNAseq


title: 20220816_30102681520922-01_BT91-SPS_08


title: D0_F09_RNAseq


title: 20220816_30102681520922-01_BT42-SPS_05


title: 20220816_30102681520922-01_BT122-IDC_11


title: D0_F08_RNAseq


title: D0_F07_RNAseq


title: Control 05

description: Saliva Sample from Control


title: D0_F06_RNAseq


title: Control 04

description: Saliva Sample from Control


title: D0_H07_RNAseq


title: 20220816_30102681520922-01_BT15-SPS_04


title: 20220816_30102681520922-01_BT95-SPS_09


title: 20220816_30102681520922-01_BT42-IDC_06


title: D0_F04_RNAseq


title: D0_F05_RNAseq


title: Control 09

description: Saliva Sample from Control


title: Control 03

description: Saliva Sample from Control


title: D0_G02_RNAseq


title: Control 08

description: Saliva Sample from Control


title: D0_G01_RNAseq


title: D0_F03_RNAseq


title: D0_F02_RNAseq


title: Control 02

description: Saliva Sample from Control


title: 20220816_30102681520922-01_BT5-SPS_02


title: D0_F01_RNAseq


title: D0_E11_RNAseq


title: NonDysplasticBarrets 35

description: Saliva Sample from Control

source_name: Control (non-dysplastic Barrett's)

value: Non-dysplastic Barrett's Oesophageus


title: D0_E09_RNAseq


title: D0_E08_RNAseq


title: NonDysplasticBarrets 34

description: Saliva Sample from Control

value: Male


title: 20220816_30102681520922-01_BT5-IDC_01


title: TS2

city: Évora

first: Mariana

middle: Cardoso

last: Patanita

address: Pólo da Mitra, Ed. Santos Júnior, s.108

country: Portugal

institute: University of Évora

description: Library name: TS2_2019-N0007NR

data_processing:
The analysis of the generated sequence raw data was carried out using Qiagen CLC Genomics Workbench 12.0.3. Generated Fastq files were analysed using FastQC tool (v. 0.11.9) for quality control.
Bioinformatic analysis started with trimming of raw sequences to generate only high-quality data.
High-quality sequencing reads were mapped against the grapevine reference genome, GCA_000003745.2 Vitis vinifera 12X.
A generalized linear model approach influenced by the multi-factorial EdgeR method was used for differential expression analysis. This model corrects for differences in library size between samples and the effects of confounding factors. Genes were filtered out by a false discovery rate (FDR) of ≤ 0.05 and a fold change of ≥ 2.0 or ≤ -2.0, and were considered differentially expressed with a q-value adjusted, using the Bonferroni correction method, > 0 and < 0.05.
Assembly: GCA_000003745.2 Vitis vinifera 12X
Supplementary files format and content: Excel files that include log2FoldChange and associated p-adjusted values for each sample and for six comparisons.

organism: Vitis vinifera

source_name: woody plant tissue

extract_protocol:
Total RNA was extracted from plant material powder, according to the method of Landi & Romanazzi (2011), with some modifications, and was stored at -80°C.
The cDNA library construction was carried out using a Stranded mRNA Library Preparation Kit and the generated DNA fragments were sequenced in the lllumina Novaseq platform, using 150 bp paired-end sequencing reads.

value: woody plant tissue

value: cv. Trincadeira

value: asymptomatic


title: D0_E07_RNAseq


title: TS1

description: Library name: TS1_2019-N0006NR


title: NonDysplasticBarrets 33

description: Saliva Sample from Control

value: saliva


title: D0_E06_RNAseq


title: 20220816_30102681520922-01_BT15-IDC_03


title: TD3

description: Library name: TD3_M2020-N1514

value: symptomatic


title: NonDysplasticBarrets 32

description: Saliva Sample from Control


title: NonDysplasticBarrets 31

description: Saliva Sample from Control


title: D0_E02_RNAseq


title: D0_E03_RNAseq


title: D0_E01_RNAseq


title: TD2

description: Library name: TD2_2019-N0009NR


title: D0_D12_RNAseq


title: NonDysplasticBarrets 30

description: Saliva Sample from Control


title: Control 01

description: Saliva Sample from Control

value: Control


title: D0_E12_RNAseq


title: D0_E05_RNAseq


title: D0_E10_RNAseq


title: D0_D11_RNAseq


title: ABS3

description: Library name: ABS3_M2020-N1513

value: cv. Alicante Bouschet


title: D0_D10_RNAseq

value: embryonic stem cell


title: NonDysplasticBarrets 29

description: Saliva Sample from Control


title: D0_D09_RNAseq


title: TS3

description: Library name: TS3_M2020-N1515


title: D0_D08_RNAseq


title: D0_E04_RNAseq


title: ABS1

description: Library name: ABS1_2019-N0002NR


title: D0_D05_RNAseq


title: NonDysplasticBarrets 27

description: Saliva Sample from Control


title: D0_D06_RNAseq


title: ABD3

description: Library name: ABD3_M2020-N1512


title: NonDysplasticBarrets 26

description: Saliva Sample from Control


title: D0_D03_RNAseq


title: TD1

description: Library name: TD1_2019-N0008NR


title: D0_D04_RNAseq


title: D0_D02_RNAseq


title: NonDysplasticBarrets 25

description: Saliva Sample from Control


title: D0_D01_RNAseq


title: ABD2

description: Library name: ABD2_2019-N0005NR


title: NonDysplasticBarrets 24

description: Saliva Sample from Control


title: D0_C12_RNAseq


title: ABD1

description: Library name: ABD1_2019-N0004NR


title: macrophage cells cultured in vitro with M-CSF, VLDLRB3A

city: shantou

first: xiaoqiang

last: xiao

state: Guangdong

address: North dongxia road

institute: Joint Shantou International Eye Center,Shantou University and the Chinese University of Hong Kong

data_processing:
Clean data was mapped to the reference geneomic database with HISAT
reference gene was obtained by mapping the clean data with Bowtie2
Assembly: GCF_000001635.26_GRCm38.p6  GCF_000001635.26_GRCm38.p6
Supplementary files format and content: core_table_gene.txt, gene_expression.txt, rna_expression.txt

source_name: bone

extract_protocol:
Total RNA were extracted by TRIzol reagent
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
BGISEQ-500/RNA Sequencing/Pair-end 150 by BGI (Beijing Genomics Institute)

treatment_protocol: Bone macrophages derived from Wild type (WT),VLDLR Knockout (VLDLR-/-,KO) and ROBO4 knockout (ROBO4-/-,KO) mice ,respectively were cultured in vitro with 20ng/ml M-CSF for 14 days.

value: bone

value: macrophage

value: VLDLR knockout

value: M-CSF(Sigma)


title: D0_C11_RNAseq


title: NonDysplasticBarrets 23

description: Saliva Sample from Control


title: D0_C10_RNAseq


title: macrophage cells cultured in vitro with M-CSF, VLDLRB2A

description: core_table_gene.txt, gene_expression.txt, rna_expression.txt


title: NonDysplasticBarrets 28

description: Saliva Sample from Control


title: ABS2

description: Library name: ABS2_2019-N0003NR


title: D0_C08_RNAseq


title: NonDysplasticBarrets 22

description: Saliva Sample from Control


title: D0_D07_RNAseq


title: D0_C07_RNAseq


title: macrophage cells cultured in vitro with M-CSF, VLDLRB1A


title: D0_C06_RNAseq


title: NonDysplasticBarrets 21

description: Saliva Sample from Control


title: macrophage cells cultured in vitro with M-CSF, VLDLR3BA


title: D0_C04_RNAseq


title: NonDysplasticBarrets 20

description: Saliva Sample from Control


title: D0_C03_RNAseq


title: macrophage cells cultured in vitro with M-CSF, VLDLR2BA


title: D0_C02_RNAseq


title: NonDysplasticBarrets 19

description: Saliva Sample from Control


title: D0_C01_RNAseq


title: macrophage cells cultured in vitro with M-CSF, RB4B3A

value: ROBO4 knockout


title: D0_B12_RNAseq


title: D0_C09_RNAseq


title: NonDysplasticBarrets 18

description: Saliva Sample from Control


title: macrophage cells cultured in vitro with M-CSF, RB4B2A


title: D0_B11_RNAseq


title: NonDysplasticBarrets 17

description: Saliva Sample from Control


title: D0_B09_RNAseq


title: NonDysplasticBarrets 16

description: Saliva Sample from Control


title: D0_B10_RNAseq


title: D0_B07_RNAseq


title: macrophage cells cultured in vitro with M-CSF, RB42BA


title: macrophage cells cultured in vitro with M-CSF, RB4B1A


title: D0_B08_RNAseq


title: D0_B06_RNAseq


title: macrophage cells cultured in vitro with M-CSF, RB41BA


title: NonDysplasticBarrets 15

description: Saliva Sample from Control


title: D0_C05_RNAseq


title: NonDysplasticBarrets 14

description: Saliva Sample from Control


title: D0_B05_RNAseq


title: D0_B03_RNAseq


title: D0_B04_RNAseq


title: macrophage cells cultured in vitro with M-CSF, C573BA

value: WT


title: D0_B01_RNAseq


title: NonDysplasticBarrets 13

description: Saliva Sample from Control


title: D0_A12_RNAseq


title: macrophage cells cultured in vitro with M-CSF, C571BA


title: D0_A11_RNAseq


title: macrophage cells cultured in vitro with M-CSF, C572BA


title: D0_A10_RNAseq


title: macrophage cells cultured in vitro with M-CSF, C57B3A


title: NonDysplasticBarrets 11

description: Saliva Sample from Control


title: NonDysplasticBarrets 10

description: Saliva Sample from Control


title: D0_A09_RNAseq


title: D0_A08_RNAseq


title: D0_A07_RNAseq


title: D0_A06_RNAseq


title: D0_A04_RNAseq


title: D0_A05_RNAseq


title: NonDysplasticBarrets 09

description: Saliva Sample from Control


title: NonDysplasticBarrets 08

description: Saliva Sample from Control


title: D0_A03_RNAseq


title: D0_A02_RNAseq


title: NonDysplasticBarrets 07

description: Saliva Sample from Control

value: Female


title: D0_A01_RNAseq


title: D0_B02_RNAseq


title: NonDysplasticBarrets 12

description: Saliva Sample from Control

value: Non-dysplastic Barrett's Oesophageus


title: GFRA1_shRNA2_1

city: Kunming

first: Weipeng

last: Liu

state: Yunnan

address: Jiao ling road

department: Institute of Medical Biology

institute: Chinese Academy of Medical Sciences

description:
Library name: Sample-7
GFRA1 knockdown

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp  (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4  and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts  for each Sample

source_name: cervical tissue

growth_protocol: Cells were cultivated in Dulbecco’s Modified Eagle Medium, enriched with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using the BGISEQ-500 platform (MGI Tech; China).

value: cervical tissue

value: human cervical squamous cells

value: GFRA1 knockdown

tag: batch


title: GFRA1_shRNA2_2

description:
Library name: Sample-8
GFRA1 knockdown


title: NonDysplasticBarrets 06

description: Saliva Sample from Control

value: Male


title: GFRA1_shRNA1_3

description:
Library name: Sample-6
GFRA1 knockdown


title: GFRA1_shRNA2_3

description:
Library name: Sample-9
GFRA1 knockdown


title: NonDysplasticBarrets 05

description: Saliva Sample from Control

value: saliva


title: macrophage cells cultured in vitro with M-CSF, C57B1A


title: GFRA1_shRNA1_2

description:
Library name: Sample-5
GFRA1 knockdown


title: NonDysplasticBarrets 03

description: Saliva Sample from Control


title: NonDysplasticBarrets 04

description: Saliva Sample from Control


title: D2_H08

library_source: genomic

data_processing:
All sequencing was carried out on HiSeq instrument. BS-seq libraries were sequenced in 96-plex pools using 125-bp paired-end reads. RNA-seq libraries were pooled as 96-plex or 192-plex pools and sequenced using 75-bp paired-end reads.
Alignments of the single-cell bisulfite sequencing were performed using Bismark as well as subsequent CpG methylation and GpC accessibility calling.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

extract_protocol:
0h, 24h, and 48h after induction of 2i-release  the cells been dissociated into single cells using accutase before flow sorting  (BD Influx) into 96-well plate containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL CA-630 (Sigma)). Samples were incubated for 15 min at 37 °C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at −80 °C before processing.
E14 mESC were cultured in 2i+LIF media. For induction for 2i-relase experiment, the cell been rinsed with PBS before the culture media was changed to serum + LIF medium. 0h, 24h, and 48h after induction of 2i-release single cells were distracted and sc-NMT sequencing was performed.


title: D2_H10


title: D2_H11


title: D2_H07


title: D2_H06


title: D2_H12


title: GFRA1_shRNA1_1

description:
Library name: Sample-4
GFRA1 knockdown


title: D2_H05


title: D2_H09


title: NonDysplasticBarrets 02

description: Saliva Sample from Control


title: D2_H04


title: Ctrl 3

description:
Library name: Sample-3
Negative control

value: Negative control


title: D2_H03


title: D2_H02


title: Ctrl 1

description:
Library name: Sample-1
Negative control


title: D2_H01


title: NonDysplasticBarrets 01

description: Saliva Sample from Control


title: D2_G12


title: D2_G11


title: D2_G10


title: InvastiveOesophageal 22

description: Saliva Sample from Cancer

source_name: Cancer sample (Invasive Esophageal Carcinoma )

value: Invasive Esophageal Carcinoma


title: InvastiveOesophageal 23

description: Saliva Sample from Cancer


title: InvastiveOesophageal 21

description: Saliva Sample from Cancer


title: D2_G08


title: mouse pulmonary microvascular endothelial cells, Co-cultured with the ATP repleted TCMK-1 cells after ATP depletion, OD3

city: Hangzhou

first: Yuxian

last: Kuai

state: Zhejiang

address: No. 88 Jiefang Road, Shangcheng District

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

description: Library name: sample6

data_processing:
Reads mapping: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Expression analysis: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Enrichment analysis: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
GSEA(Gene Set EnrichmentAnalysis): GSEA is a computational approach to determine if a predefined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independently.
Assembly: grcm38_p6
Supplementary files format and content: .gz

extract_protocol:
RNA extraction and detection Reagent kit: InvitrogenTRIzol reagent Operation steps: 1. Homogenization treatment Take the sample in a 2ml grinding tube and thoroughly grind it using a grinder at 60Hz for 60 seconds. Then take 2-4 samples each time, add 1ml TRIzol reagent to the ground powder and mix immediately (the sample needs to be kept at low temperature before adding TRIzol). After adding all the samples to TRIzol, wet beat at 55Hz for 30 seconds and incubate at room temperature for 5 minutes to facilitate complete separation of nuclear protein bodies in the homogenized sample. Centrifuge at 12000rpm for 5 minutes and take the supernatant (a 1.5ml centrifuge tube can be prepared during centrifugation to hold the supernatant). 2. Phase separation Add 0.2ml chloroform to the supernatant, shake the tube vigorously for 30 seconds, and incubate at room temperature for 2-3 minutes. Centrifuge at 4 ° C and 12000rpm for 15 minutes (during centrifugation, prepare a 1.5ml centrifuge tube and write the sample name and number). The mixture separates into a red lower layer (phenol chloroform phase), an intermediate phase, and an upper colorless aqueous phase. RNA exists in the aqueous phase. 3. RNA precipitation Transfer 400 μ l of aqueous phase to a 1.5ml final tube, add 500 μ l of isopropanol, invert and mix well (about 30 times). Incubate the sample at room temperature for 10 minutes. Centrifuge at 4 ° C and 12000rpm for 10 minutes. 4. RNA washing Discard the supernatant and add 1ml of 75% ethanol to wash the precipitate (try to resuspend the precipitate as much as possible). Centrifuge at 4 ° C and 12000rpm for 5 minutes. 5. Dissolve RNA again At the end of the process, briefly centrifuge and extract ethanol, then add an appropriate amount of RNase free water-soluble sample directly. Do not vacuum centrifuge RNA. It is important not to let the RNA precipitate completely dry, as this will greatly reduce its solubility.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: cell line

value: Co-cultured with the ATP repleted TCMK-1 cells after ATP depletion (IR)


title: mouse pulmonary microvascular endothelial cells, Co-cultured with the ATP repleted TCMK-1 cells after ATP depletion, OD2

description: Library name: sample5


title: mouse pulmonary microvascular endothelial cells, Co-cultured with the ATP repleted TCMK-1 cells after ATP depletion, OD1

description: Library name: sample4


title: InvastiveOesophageal 20

description: Saliva Sample from Cancer


title: InvastiveOesophageal 19

description: Saliva Sample from Cancer


title: Ctrl 2

description:
Library name: Sample-2
Negative control


title: mouse pulmonary microvascular endothelial cells, Co-cultured with untreated TCMK-1 cells, C3

description: Library name: sample3

value: Co-cultured with untreated TCMK-1 cells (Control)


title: mouse pulmonary microvascular endothelial cells, Co-cultured with untreated TCMK-1 cells, C2

description: Library name: sample2


title: D2_G02

value: embryonic stem cell


title: D2_G05


title: D2_G04


title: mouse pulmonary microvascular endothelial cells, Co-cultured with untreated TCMK-1 cells, C1

description: Library name: sample1


title: D2_G07


title: D2_G01


title: D2_G03


title: D2_F12


title: InvastiveOesophageal 17

description: Saliva Sample from Cancer


title: InvastiveOesophageal 18

description: Saliva Sample from Cancer


title: InvastiveOesophageal 16

description: Saliva Sample from Cancer


title: D2_F11


title: D2_F10


title: D2_G09


title: D2_F09


title: Rdh10 KO eye RNA-seq, rep3

city: La Jolla

first: Gregg

last: Duester

state: CA

address: 10901 North Torrey Pines Road

department: Center for Cardiovascular and Muscular Diseases

country: USA

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: Rdh10_KO_eye_rep3

data_processing:
Reads were aligned to the mouse mm10 reference genome using TopHat splice-aware aligner; transcript abundance was calculated using Expectation-Maximization approach; fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: mm10
Supplementary files format and content: Tab-delimited normalized gene expression (FPKM)

source_name: Embryonic craniofacial

extract_protocol:
Total RNA was extracted from E10 face tissue (three pools of three of wild-type and  Rdh10-/- facial embryonic tissue).
RNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit with the PolyA selection module.

value: Embryonic craniofacial

value: Rdh10 KO


title: Rdh10 KO eye RNA-seq, rep2

description: Library name: Rdh10_KO_eye_rep2


title: D2_F08


title: Rdh10 KO eye RNA-seq, rep1

description: Library name: Rdh10_KO_eye_rep1


title: D2_F07


title: InvastiveOesophageal 15

description: Saliva Sample from Cancer


title: InvastiveOesophageal 14

description: Saliva Sample from Cancer


title: D2_F06


title: D2_G06


title: InvastiveOesophageal 12

description: Saliva Sample from Cancer


title: WT eye RNA-seq, rep3

description: Library name: WT_eye_rep3


title: D2_F03


title: WT eye RNA-seq, rep2

description: Library name: WT_eye_rep2


title: InvastiveOesophageal 10

description: Saliva Sample from Cancer


title: InvastiveOesophageal 13

description: Saliva Sample from Cancer


title: WT eye RNA-seq, rep1

description: Library name: WT_eye_rep1


title: D2_E11


title: D2_F04


title: D2_F01


title: D2_E09


title: D2_E10


title: InvastiveOesophageal 11

description: Saliva Sample from Cancer


title: D2_F02


title: D2_E12


title: VGat-cre-3 vGATCre mouse

city: Shanghai

first: Peijun

last: Ju

state: 上海市 - Shanghai Shi

address: Room 306, Research Building Humin Road 3210

institute: Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine

description: Library name: VGat-cre-3

library_source: transcriptomic single cell

data_processing:
R (v4.0.2) package Seurat (v2.3.4) for cell type and DEG analysis.   ClusterProfiler (v3.14.3) for gene ontology analysis. R package DoubletFinder(v2.0.3)  for doublet estimation.
Assembly: GRCm38 (Ensembl release 92)
Supplementary files format and content: Processed data file represents normalized expression values processed from raw UMI counts output by Cell Ranger.

molecule: nuclear RNA

source_name: brain

extract_protocol:
Two mice from EB2-flox and EB2-vGATCre group respectively were anesthetized with isoflurane and rapidly decapitated. Brains were extracted and transferred into ice-cold Hibernate A/B27 medium. The PFC was removed from slices and isolated intact nucleus suspension. The nucleus was isolated and purified as previously described with some modifications. Briefly, the frozen tissue was homogenized in NLB buffer containing 25mM Sucrose, 10 mM Tris-HCl, 3 mM MgAc2，0.1% Triton X-100 (Sigma-Aldrich), 0.1mM EDTA, 0.2 U/μL RNase Inhibitor(Takara). Various concentrations of sucrose were used to purify the nuclei. Nuclei counts were determined by PI staining. Finally, the concentration was adjusted to 1000 nuclei/μL for snRNA-Seq.
Single-nucleus RNA-seq libraries were constructed using the 10X Genomics Chromium Controller and Chromium Single Cell 3’ v3 Reagent Kit according to the manufacturer’s standard protocol. Briefly, nuclei were isolated, loaded into microfluidic chips to generate Gel Bead-In-Emulsions (GEMs), followed by reverse transcription, cDNA amplification, fragmentation, A-tailing, adaptor ligation, and index PCR. Final libraries were quantified using Qubit and size-checked with a Bioanalyzer.

value: brain

value: nuclei


title: D2_F05


title: D2_E08


title: VGat-cre-4 vGATCre mouse

description: Library name: VGat-cre-4


title: InvastiveOesophageal 09

description: Saliva Sample from Cancer


title: InvastiveOesophageal 08

description: Saliva Sample from Cancer


title: VGat-cre-1 vGATCre mouse

description: Library name: VGat-cre-1


title: D2_E05


title: VGat-cre-2 vGATCre mouse

description: Library name: VGat-cre-2


title: D2_E04


title: InvastiveOesophageal 07

description: Saliva Sample from Cancer


title: D2_E03


title: InvastiveOesophageal 06

description: Saliva Sample from Cancer

value: Female


title: EB2-4 flox mouse

description: Library name: EB2-4


title: D2_E02


title: D2_E07


title: D2_E01


title: EB2-3 flox mouse

description: Library name: EB2-3


title: D2_D12


title: D2_D11


title: EB2-2 flox mouse

description: Library name: EB2-2


title: InvastiveOesophageal 05

description: Saliva Sample from Cancer


title: InvastiveOesophageal 04

description: Saliva Sample from Cancer


title: D2_D09


title: D2_D10


title: D2_E06


title: InvastiveOesophageal 03

description: Saliva Sample from Cancer


title: D2_D08


title: MC38COM3

city: Wuhan

first: Chunya

last: Li

address: No. 1095 Jiefang Dadao, Hubei Province, Jiaokou District, Wuhan City

department: Tongji Hospital

institute: Huazhong University of Science and Technology

description:
Library name: sample12
MC38COM3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic bench work (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic bench work (parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic bench work
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols.

value: mouse colorectal cancer cell

value: Nintedanib (3uM,24h) + irradiation (8Gy,24h)


title: EB2-1 flox mouse

description: Library name: EB2-1


title: InvastiveOesophageal 02

description: Saliva Sample from Cancer


title: MC38COM2

description:
Library name: sample11
MC38COM2


title: D2_D04


title: D2_D06


title: D2_D05


title: D2_D07


title: InvastiveOesophageal 01

description: Saliva Sample from Cancer


title: MC38COM1

description:
Library name: sample10
MC38COM1


title: D2_D03


title: D2_D02


title: Intramucosal 25

description: Saliva Sample from Cancer

source_name: Cancer sample (intramucosal adenocarcinoma)

value: Intramucosal adenocarcinoma


title: MC38RT3

description:
Library name: sample9
MC38RT3

value: irradiation (8Gy,24h)


title: Intramucosal 24

description: Saliva Sample from Cancer

value: Male


title: D2_D01


title: D2_C11


title: MC38RT1

description:
Library name: sample7
MC38RT1


title: D2_C12


title: Intramucosal 22

description: Saliva Sample from Cancer

value: saliva


title: MC38RT2

description:
Library name: sample8
MC38RT2


title: MC38Ni3

description:
Library name: sample6
MC38Ni3

value: Nintedanib (3uM,24h)


title: D2_C10


title: D2_C09


title: D2_C06


title: Intramucosal 23

description: Saliva Sample from Cancer


title: MC38Ni2

description:
Library name: sample5
MC38Ni2


title: D2_C05


title: D2_C07


title: D2_C04


title: Intramucosal 20

description: Saliva Sample from Cancer


title: Intramucosal 21

description: Saliva Sample from Cancer


title: D2_C03


title: D2_C01


title: D2_C02


title: D2_B12


title: MC38CON3

description:
Library name: sample3
MC38CON3

value: Control


title: MC38Ni1

description:
Library name: sample4
MC38Ni1


title: Intramucosal 18

description: Saliva Sample from Cancer


title: Intramucosal 19

description: Saliva Sample from Cancer


title: MC38CON2

description:
Library name: sample2
MC38CON2


title: D2_C08


title: D2_B10


title: D2_B09


title: MC38CON1

description:
Library name: sample1
MC38CON1


title: D2_B11


title: D2_B08


title: Intramucosal 16

description: Saliva Sample from Cancer


title: Intramucosal 15

description: Saliva Sample from Cancer


title: mus skin,MV+12.5% a-KB ,rep6

city: KUNMING

first: LU

last: KeJin

state: YUNNAN

address: keyi Road NO.53#

institute: Yunnan Characteristic Plant Extraction Laboratory

description:
Library name: GB25-6-4
Raw data_Counts.txt:GB25-6-4_count

data_processing:
Using Seqtk for filtration, the main steps are as follows: 1. Remove the linker sequence contained in reads; 2. Remove the bases with 3'-terminal mass q less than 20, that is, the base error rate is less than 0.01, where q =-Q=-10logerror_ratio；; 3. Remove the reads； with the length less than 25; 4. Remove ribosome RNA reads from the species.
The spliced mapping algorithm of Hisat2(version:2.0.4) is applied to Genome mapping of pretreated reads, and the default parameters are adopted.
Stringtie(version:1.3.0) was used to count the Fragments of each gene after Hisat2 alignment, and then normalized by TMM(trimmed mean of M values). Finally, the FPKM value of each gene was calculated by perl script.
Assembly: The purified Total RNA was subjected to the steps of mRNA separation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, terminal repair, 3'-terminal A addition, linker connection, enrichment and so on to complete the construction of mRNA sequencing library. Using Qubit 2.0 fluorescence quantitative instrument (Thermo Fisher Scientific) to detect the library concentration, and Agilent 4200 Tape Station (Agilent Technologies) to detect the library fragment distribution.
Supplementary files format and content: CSV files include FPKM values for each sample

growth_protocol: Female Balb/C mice (6-8 weeks of age, weight range at 17 ± 1 g) were obtained from the Animal Center, Kunming Medical University (Kunming City, Yunnan, China). The mice were maintained at a constant temperature of 20-22 °C, with a 12-hour light/12-hour dark cycle and free access to food and water.

extract_protocol:
Total RNA was extracted by mjzol animal RNA isolation kit (major ivd) and purified by RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set(QIAGEN). The integrity of RNA was detected by Agilent 2100 Bioanalyzer/Agilent 4200 Tape Station (Agilent Technologies), and the total amount and purity of RNA were determined by using Qubit 2.0 fluorescence quantitative instrument (Thermo Fisher Scientific) and NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific).
Similar to NGS library preparation, scRNA library preparation was also performed by DNA fragmentation, end repair, A-tailing, adaptor ligation and sample index PCR. The post ligation cleanup cDNA was amplified using the following program: 98 °C for 45s, followed by 15 cycles of 98 °C for 20 s, 67 °C for 30 s and 72 °C for 20s. 1 µl of sample (1:10 dilution) was added to an Agilent Bioanalyzer High Sensitivity chip(Agilent, 5067-4626) to determine the average fragment size. Library concentration was determined using the Qubit dsDNA HS Assay Kit(Thermo, Q32854)

treatment_protocol: After one week of acclimation, the mice were shaved and treated with a depilatory cream. All mice were randomly divided into four groups with 6 mice in each group: 1) control group; 2) photoaging model group; 3) photoaging mice with 7.5%α-KB treatment for 10 weeks; 4) photoaging mice with 12.5% α-KB treatment for 10 weeks. The photoaging model group mice were placed in a metal box with compartments, and the dorsal skin was irradiated with Sigma SUV-1000 sunlight simulator at a vertical distance of about 30 cm from the back 3 times a week for a total of 4 weeks to establish a photoaging animal model. The dose of irradiated with UVA + UVB was 2 minimal erythema dose (MED) (UVA 6.72 J/ cm2; UVB 0.36 J/ cm2) for the first two weeks and the exposure time was 2 min. The dose of irradiated with UVA + UVB was 4 MED (UVA 13.44 J/ cm2; UVB 0.72 J/ cm2) for the last two weeks and the exposure time was 4 min.

tag: gender

value: female


title: D2_B07


title: D2_B04


title: Intramucosal 14

description: Saliva Sample from Cancer


title: mus skin,MV+12.5% a-KB ,rep5

description:
Library name: GB25-5-4
Raw data_Counts.txt:GB25-5-4_count


title: D2_B03


title: Intramucosal 13

description: Saliva Sample from Cancer


title: D2_B02


title: D2_B01


title: mus skin,MV+12.5% a-KB ,rep3

description:
Library name: GB25-3-4
Raw data_Counts.txt:GB25-3-4_count


title: D2_A12


title: Intramucosal 12

description: Saliva Sample from Cancer


title: D2_A10


title: D2_A11


title: Intramucosal 17

description: Saliva Sample from Cancer


title: Intramucosal 11

description: Saliva Sample from Cancer


title: Intramucosal 10

description: Saliva Sample from Cancer


title: D2_A08


title: D2_B05


title: D2_B06


title: mus skin,MV+7.5% a-KB ,rep6

description:
Library name: GB15-6-4
Raw data_Counts.txt:GB15-6-4_count


title: mus skin,MV+7.5% a-KB ,rep5

description:
Library name: GB15-5-4
Raw data_Counts.txt:GB15-5-4_count


title: D2_A06


title: mus skin,MV+7.5% a-KB ,rep4

description:
Library name: GB15-4-4
Raw data_Counts.txt:GB15-4-4_count


title: Intramucosal 07

description: Saliva Sample from Cancer


title: D2_A04


title: D2_A05


title: D2_A03


title: D2_A02


title: D2_A01


title: mus skin,MV+7.5% a-KB ,rep3

description:
Library name: GB15-3-4
Raw data_Counts.txt:GB15-3-4_count


title: Intramucosal 06

description: Saliva Sample from Cancer


title: mus skin,MV+12.5% a-KB ,rep2

description:
Library name: GB25-2-4
Raw data_Counts.txt:GB25-2-4_count


title: D1_H11


title: mus skin,MV+7.5% a-KB ,rep2

description:
Library name: GB15-2-4
Raw data_Counts.txt:GB15-2-4_count


title: Intramucosal 05

description: Saliva Sample from Cancer


title: mus skin,MV+12.5% a-KB ,rep1

description:
Library name: GB25-1-4
Raw data_Counts.txt:GB25-1-4_count


title: mus skin,MV+7.5% a-KB ,rep1

description:
Library name: GB15-1-4
Raw data_Counts.txt:GB15-1-4_count


title: D2_A07


title: mus skin,MV+12.5% a-KB ,rep4

description:
Library name: GB25-4-4
Raw data_Counts.txt:GB25-4-4_count


title: D1_H09


title: D1_H08


title: Intramucosal 09

description: Saliva Sample from Cancer


title: Intramucosal 04

description: Saliva Sample from Cancer


title: Intramucosal 08

description: Saliva Sample from Cancer


title: D1_H07


title: D2_A09


title: D1_H06


title: mus skin,MV,rep6

description:
Library name: GJ4B-6-4
Raw data_Counts.txt:GJ4B-6-4_count

source_name: skin,MV

value: skin,MV


title: D1_H05


title: Intramucosal 02

description: Saliva Sample from Cancer


title: D1_H03


title: mus skin,MV,rep5

description:
Library name: GJ4B-5-4
Raw data_Counts.txt:GJ4B-5-4_count


title: mus skin,MV,rep4

description:
Library name: GJ4B-4-4
Raw data_Counts.txt:GJ4B-4-4_count


title: D1_H12


title: Intramucosal 01

description: Saliva Sample from Cancer


title: D1_H02


title: D1_H10


title: mus skin,MV,rep3

description:
Library name: GJ4B-3-4
Raw data_Counts.txt:GJ4B-3-4_count


title: D1_G12


title: D1_G11


title: D1_G10


title: Ovarian tissue, Treatment, Cisplatin, 5 times injection

city: Padang

first: Roza

last: Silvia

state: Sumatera Barat

address: Limau Manis, Pauh

department: Department of Histology

country: Indonesia

institute: Universitas Andalas

data_processing:
Filtering was performed using fastp. Reads quality check was performed using fastqc and MultiQC.
Filtered reads from each sample were merged and were subsequently mapped against reference genome using hisat2.
The mapped reads were used for de novo assembly using Trinity. Redundant assembled-transcript sequences were removed using bbtools (dedupe.sh).
The quality of the assembled-transcript sequences were assessed using rnaQuast.
Assembly: NC_051336.1 Rattus norvegicus strain BN/NHsdMcwi
Supplementary files format and content: tab-separated values file include raw counts for each samples

organism: Rattus norvegicus

source_name: Ovarian Tissue

extract_protocol:
mRNA were extracted using Quick-RNA Miniprep Kit® (R1055) in accordance with the manufacturer’s instructions (Zymo Research).
mRNA libraries were prepared using Invitrogen™ Collibri™ Stranded RNA Library Prep Kit protocol.

treatment_protocol: Serial injections of  Cisplatin (3 mg/kg body weight, intraperitoneal, once a week) were performed either three- or five-time to induce mild- or severe-POI rat models, while control group was injected with NaCl 0.9%. Intraovarian injection of PRP (processed from the donor rats’ blood) was conducted on one mild- and severe-POI group a week after last injection of cisplatin, through laparotomic procedure. Post-operative infection was controlled with antibiotics (for the first three days).

value: Ovarian Tissue

tag: model

value: POI-Ovarian model

value: Sprague Dawley rat models

value: Cisplatin 5 times


title: D1_G09

value: embryonic stem cell


title: mus skin,MV,rep1

description:
Library name: GJ4B-1-4
Raw data_Counts.txt:GJ4B-1-4_count


title: D1_G08


title: Intramucosal 03

description: Saliva Sample from Cancer


title: Ovarian tissue, Treatment, Cisplatin, 3 times injection

value: Cisplatin 3 times


title: mus skin,Control,rep6

description:
Library name: GN4B-6-4
Raw data_Counts.txt:GN4B-6-4_count

source_name: skin,control

value: skin,control


title: D1_G07


title: oocyte,HS+Lasp2,MII

city: Guiyang

first: Qingwei

last: Wang

state: Guizhou

address: No. 515, Jiaxiu South Road, Huaxi District, Guiyang City

department: College of Animal Science

institute: Guizhou University

description:
Library name: HS_Lasp2
Column name in raw counts All Samples.txt:HS_Lasp2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Sus scrofa Ensembl V111
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: oocyte

growth_protocol: Oocytes with compact cumulus cell layers were selected for IVM in TCM-199 medium, enriched with 10% porcine follicular fluid, 0.6 mmol/L cysteine, 10 IU/mL PMSG and HCG, 1% ITS, 10 ng/mL EGF, 0.2 mmol/L sodium pyruvate, and 0.5% penicillin-streptomycin. Subsequently, 50–80 GV oocytes were cultured for 26–28 h to metaphase I (MI) stage and for 44–48 h to MII stage in 500 μL TCM-199 covered with mineral oil at 38.5 °C and 5% CO2.

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTM Reverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina Novaseq 6000 at the following the vendor's recommended protocol.

treatment_protocol: The HS treatment procedure was based on a previous study 25. Briefly, GV oocytes were cultured at 41.5 °C for 24 hours for heat stress treatment, and then cultured at 38.5 °C until MII stage for subsequent analysis. During heat stress, L -Asp (Sigma - Aldrich, St. Louis, MO, USA) was dissolved in water to 50 mmol/L as a stock solution, and then further diluted with the maturation medium to final concentrations of 0.5 mmol/L, 1.0 mmol/L, or 1.5 mmol/L, respectively.

value: oocyte

value: Porcine oocyte

value: WT

value: Heat stress +Lasp

value: MII


title: oocyte,HS+Lasp3,MII

description:
Library name: HS_Lasp3
Column name in raw counts All Samples.txt:HS_Lasp3


title: mus skin,Control,rep5

description:
Library name: GN4B-5-4
Raw data_Counts.txt:GN4B-5-4_count


title: mus skin,Control,rep4

description:
Library name: GN4B-4-4
Raw data_Counts.txt:GN4B-4-4_count


title: oocyte,HS2,MII

description:
Library name: HS2
Column name in raw counts All Samples.txt:HS2

value: Heat stress


title: oocyte,HS+Lasp1,MII

description:
Library name: HS_Lasp1
Column name in raw counts All Samples.txt:HS_Lasp1


title: D1_H01


title: Ovarian tissue, Control, NaCl 0.9%, 5 times injection


title: D1_H04


title: oocyte,HS3,MII

description:
Library name: HS3
Column name in raw counts All Samples.txt:HS3


title: Ovarian tissue, Treatment, Cisplatin, PRP, 5 times injection

value: Cisplatin 5 times and PRP


title: mus skin,MV,rep2

description:
Library name: GJ4B-2-4
Raw data_Counts.txt:GJ4B-2-4_count


title: mus skin,Control,rep3

description:
Library name: GN4B-3-4
Raw data_Counts.txt:GN4B-3-4_count


title: D1_G05


title: 1815_d10

first: Robert

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

description:
Library name: Sample7
10x genomics

data_processing:
Data was mapped using the STARsolo function of STAR (v.2.7.10a) (Dobin, 2013). STARsolo performed error correction and demultiplexing of cell barcodes using user-input whitelist (3M-3pgex-may-2023.txt for version 4), mapped reads to the reference genome (GRCh38, version 32, Ensembl 98), deduplicated and error corrected UMIs, quantified per-cell gene expression, and spliced and unspliced reads similar to Velocyto. The following are the CellRanger mimicking commands used: --outFilterScoreMin 30 --readFilesCommand zcat --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter EmptyDrops_CR --soloUMIlen 12 --soloType CB_UMI_Simple --soloCBwhitelist 3M-february-2018.txt --clipAdapterType CellRanger4 --outFileNamePrefix name --outSAMattributes All --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --soloCBlen 16 --soloCBstart 1 --soloUMIstart 17 --soloFeatures Gene GeneFull SJ Velocyto.
Assembly: GRCh38, version 32, Ensembl 98
Supplementary files format and content: barcodes.tsv:  tab-separated values for cell barcodes
Supplementary files format and content: features.tsv:  tab-separated values list of gene IDs
Supplementary files format and content: matrix.mtx:  gene expression count data in Matrix Market Exchange Format

source_name: Basal Plate placenta

growth_protocol: All tissue samples were processed within 2 hours of sample collection. Tissues were minced and subjected to sequential digestion with Trypsin and DNase, followed by Percoll gradient separation as previously described (PMID: 28167044). For trophoblast stem cell derivation, the CTBs were MACS-purified with with either a PE-conjugated anti-ITGA6 antibody (Biolegend #313612) or an APC-conjugated anti-EGFR antibody (Biolegend #352906). MACS-purified CTB were then plated for TSC derivation as previously described (PMID: 34540826 and PMID: 37164912 ) and cultured with modified TSC media (PMID: 34454392). Cells were collected at specified time points.

extract_protocol:
Single cell suspensions were washed, filtered for cell debris, counted, and stained with a viability marker to ensure correct loading concentration and a high percentage of live cells. Cell suspensions were then loaded onto the 10x Genomics Controller for GEM generation.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: hTSCs were derived as explained in PMID: 34791028, PMID: 3454082.

value: Basal Plate placenta

tag: gestational age_(weeksdays)


title: oocyte,HS1,MII

description:
Library name: HS1
Column name in raw counts All Samples.txt:HS1


title: D1_G04


title: mus skin,Control,rep2

description:
Library name: GN4B-2-4
Raw data_Counts.txt:GN4B-2-4_count

value: female


title: Ovarian tissue, Treatment, Cisplatin, PRP, 3 times injection

value: Cisplatin 3 times and PRP


title: oocyte, control3,MII

description:
Library name: Control3
Column name in raw counts All Samples.txt:Control3

value: Control


title: 1816_d4

description:
Library name: Sample6
10x genomics

source_name: whole placenta

value: whole placenta


title: mus skin,Control,rep1

description:
Library name: GN4B-1-4
Raw data_Counts.txt:GN4B-1-4_count


title: 1815_d4

description:
Library name: Sample5
10x genomics


title: oocyte, control2,MII

description:
Library name: Control2
Column name in raw counts All Samples.txt:Control2


title: D1_G02


title: oocyte, control1,MII

description:
Library name: Control1
Column name in raw counts All Samples.txt:Control1


title: 1816_d10

description:
Library name: Sample8
10x genomics

source_name: chorionic plate placenta

value: chorionic plate placenta


title: D1_G03


title: C1KO-4 heart P14

city: Xi'an

first: Shaozhou

last: Ma

address: No. 76, Yanta West Road, Yanta District, Xi 'an City, Shaanxi Province

institute: Xi’an Jiaotong University

description:
Library name: C1KO-4 heart P14
Column C1KO-3 in Cend1_LSD1_seq count.xlsx

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: mm10
Supplementary files format and content: Excel file of readcount value for each sample

source_name: heart

extract_protocol:
Total RNA was extracted from heart ventricles using TRIzol reagent (Sigma)
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA,Catalog #: E7530L)

value: heart


title: D1_G06

value: embryonic stem cell


title: C1KO-1 heart P14

description:
Library name: C1KO-1 heart P14
Column C1KO-1 in Cend1_LSD1_seq count.xlsx


title: D1_G01


title: 1816_d1

description:
Library name: Sample4
10x genomics


title: atlantic control rep2

city: Sainte-Anne-de-Bellevue

first: Juan Carlos

last: Camargo-Tavares

state: Quebec

address: 21111 Lakeshore Road

country: Canada

institute: McGill University

description:
atlantic_TMM.txt
atlantic_annotation.txt

data_processing:
Reads were trimmed and quality filtered with Trimmomatic v0.39 and then cleaned of viral sequences with custom pipeline.
De novo transcriptomes for each species were assembled by generating a de novo and a reference guided assemblies with Trinity and merging them with EvidentialGene.
Transcrpts were mapped
TMM files were generated with DESeq2 using a Trinity pipeline.
Assembly: Acaule: GenBank Biosample SAMN23440999; Atlantic: ATL_v2.0_asm.fasta https://doi.org/10.1016/j.molp.2022.01.003
Supplementary files format and content: There are two files per species: a TMM file with each colum representing each sample (2 conditions 3 replicates), and a annotation file pointing to respective reference genome gene and location. If there is no annotation

organism: Solanum tuberosum

source_name: shoot

extract_protocol:
Total RNA was extracted from shoot frozen samples using RNeasy Plant Mini Kit (Qiagen), according to the manufacturer’s instructions.
mRNA Stranded

value: shoot

value: control


title: C1KO-3 heart P14

description:
Library name: C1KO-3 heart P14
Column C1KO-2 in Cend1_LSD1_seq count.xlsx


title: D1_F12


title: 1815_d1

description:
Library name: Sample3
10x genomics


title: 1816_d0

description:
Library name: Sample2
10x genomics


title: atlantic control rep3


title: D1_F11


title: 1815_d0

description:
Library name: Sample1
10x genomics


title: atlantic freeze rep3

value: freeze


title: D1_F10


title: CTL-1 heart P14

description:
Library name: CTL-1 heart P14
Column WT-5 in Cend1_LSD1_seq count.xlsx


title: CTL-3 heart P14

description:
Library name: CTL-3 heart P14
Column WT-6 in Cend1_LSD1_seq count.xlsx


title: D1_F09


title: atlantic freeze rep2


title: Participants 549, intervention, 12 months

city: Puncak Alam

first: Kalavathy

last: Ramasamy

state: Selangor

address: UiTM Cawangan Selangor Kampus Puncak Alam Bandar Puncak Alam

department: Faculty of Pharmacy

country: Malaysia

institute: Universiti Teknologi MARA (UiTM)

description: Library name: t549

data_processing:
Raw sequencing reads were assessed for quality using FastQC. Adapter sequences and low-quality bases (Phred score <20) were trimmed using Cutadapt. High-quality reads were aligned to the human reference genome (GRCh38) using HISAT2 with default parameters. Gene expression levels were quantified using StringTie, and raw count matrices were generated. Normalization was performed using  Trimmed Mean of M-values (TMM). Differential expression analysis was conducted using DESeq2, and significantly differentially expressed genes (adjusted p-value <0.05) were identified.
Assembly: hg38
Supplementary files format and content: excel file that include raw counts for each samples.

extract_protocol:
RNA was prepared using the NucleoSpin RNA Mini Kit (Macherey-Nagel, Düren, Germany) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNAsynthesis using either dUTP for directional library or dTTP for non-directional library

value: Whole blood

tag: diagnosis

value: Cognitive frailty

value: male


title: Participants 549, intervention, 6 months

description: Library name: p549


title: EVP_TAC_5

city: Beijing

first: li

middle: guo

last: qi

state: Chaoyang

address: Anzhen number 2 road

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Library name: EVP_TAC_5

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

growth_protocol: Pressure-overloaded HF was induced by TAC in C57BL/6 mice, aged 8–10 weeks. After 4 weeks of TAC, the surviving mice were randomly divided into three groups (each of 15 mice), and the test drugs were administrated orally in drinking water.

extract_protocol: The 7nAchR agonist group was administered encenicline (EVP-6124) at a dosage of 2 mg/kg/day (Cat# M7227, AbMole, Texas, USA), and the acetylcholinesterase inhibitor group was administered donepezil at a dosage of 5 mg/kg/day (Cat# M8888, AbMole, Texas, USA).As EVP-6124 was tested at 1 mg/kg, which was found to be the most effective dose to enhance memory consolidation in rats8. We converted the rat dose to mouse dose according to the following equation9: Mouse equivalent dose = Rat does (1 mg/kg) × Km ratio (6/2), the mouse equivalent dose is 2 mg/kg. The dosage of donepezil treatment was selected as previous report10. Control mice received an equal volume of physiological saline.

treatment_protocol: WT mice that underwent TAC for 4 weeks were randomised into three treatment groups administered saline, donepezil (5 mg/kg/day), or EVP-6124 (2 mg/kg/day)

value: WT

value: encenicline

value: TAC 8Weeks


title: Participants 549, intervention, baseline

description: Library name: b549


title: atlantic freeze rep1


title: CTL-4 heart P14

description:
Library name: CTL-4 heart P14
Column WT-8 in Cend1_LSD1_seq count.xlsx


title: D1_F08

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs


title: EVP_TAC_4

description: Library name: EVP_TAC_4


title: Participants 509, intervention, 12 months

description: Library name: t509


title: D1_F07


title: EVP_TAC_3

description: Library name: EVP_TAC_3


title: Participants 509, intervention, 6 months

description: Library name: p509


title: atlantic control rep1


title: D1_F05


title: EVP_TAC_1

description: Library name: EVP_TAC_1

value: donepezil


title: EVP_TAC_2

description: Library name: EVP_TAC_2


title: Participants 482, intervention, 12 months

description: Library name: t482

value: female


title: Participants 509, intervention, baseline

description: Library name: b509


title: primary cultured cell of post treatment brain tumor treated with NUPR1v.1 siRNA 48hr 3

city: Seoul

first: Sun Ha

last: Paek

address: 101, Daehak-ro, Jongno-gu

department: Neurosurgery

country: South Korea

institute: Seoul National University College of Medicine

description: Gene expression of GBM-37 primary cells treated with NUPR1v.1 siRNA

hyb_protocol: Hybridization were performed using Agilent’s LowInput QuickAmp Labeling Kit (Agilent)

scan_protocol: The acquired hybridization images were then analyzed by Agilent DNA microarray Scanner and the data quantification was performed using Agilent Feature Extraction software 10.7

data_processing: Normalization process of all data and selection of fold-changed genes were carried out using GeneSpringGX 7.3.1

source_name: NUPR1v.1 siRNA treated primary cultured cell from post-treatment tumor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1650ng of RNA and labeled cRNA target was then quantified using ND-1000 spectrophotometer

extract_protocol: Total RNA was extracted from GBM primary cells (< 5 passages) using a TRIzol reagent following manufacturer's instructions and its quantity and quality were assessed using Nanodrop

treatment_protocol: Control siRNA or NUPR1a siRNA was transfected and treated for 48 hours.

tag: transfection

value: brain


title: Dol_TAC_5

description: Library name: Dol_TAC_5


title: D1_F04


title: Participants 482, intervention, 6 months

description: Library name: p482


title: D1_F03


title: primary cultured cell of post treatment brain tumor treated with NUPR1v.1 siRNA 48hr 2


title: D1_F02


title: Dol_TAC_4

description: Library name: Dol_TAC_4


title: primary cultured cell of post treatment brain tumor treated with control siRNA 3

description: Gene expression of GBM-37 primary cells treated with control siRNA

source_name: control siRNA treated primary cultured cell from post-treatment tumor

value: control siRNA


title: primary cultured cell of post treatment brain tumor treated with NUPR1v.1 siRNA 48hr 1


title: primary cultured cell of post treatment brain tumor treated with control siRNA 2


title: Participants 482, intervention, baseline

description: Library name: b482


title: D1_F06


title: Dol_TAC_3

description: Library name: Dol_TAC_3


title: D1_F01


title: D1_E12


title: Dol_TAC_2

description: Library name: Dol_TAC_2


title: D1_E11


title: Participants 479, intervention, 6 months

description: Library name: p479


title: Participants 479, intervention, 12 months

description: Library name: t479


title: Dol_TAC_1

description: Library name: Dol_TAC_1

value: physiological saline


title: Participants 464,control, 12 months

description: Library name: t464


title: Day10, CD133-positive, NS/PCs

city: Fukuoka

first: Takumi

last: Nakagawa

address: 3-1-1, Maidashi

country: Japan

institute: Kyushu University

description:
Library name: CD133_1
CD133

data_processing:
The sgRNA library was sequenced with Illumina HiSeq2500 for 50 bp single-end reads. MAGeCK (v0.5.9.4) was applied to trim the adapters of reads and count reads of each sgRNA. The reads of each sgRNA were trimmed and the number of each sgRNA reads in “Day 0”, “CD133”, and “CD24” samples were counted by “mageck count”. The sgRNAs whose reads were not detected in any groups were removed. The enrichment changes of each sgRNA between ‘Day0 and CD133’, and ‘Day0 and CD24’ was calculated by the “mageck mle”. From the result of “mageck mle”, the beta score in the “gene_summary” file was used as an enrichment value. The beta score difference between 'Day 0 vs CD133' and 'Day 0 vs CD24’ was calculated as the difference in enrichment value between CD24 and CD133. The threshold for enrichment was determined by the CutoffCalling function of the MAGeCKFlute (v1.14.0).
Assembly: For reads count, "all_library.txt" was used as reference.
Supplementary files format and content: all_library.txt.gz: the list of sgRNA sequences and their target genes. This file is an edited version of  Brunello Library Target Genes which is deposited in addgene #73179 (https://media.addgene.org/cms/filer_public/8b/4c/8b4c89d9-eac1-44b2-bb2f-8fea95672705/broadgpp-brunello-library-contents.txt).
Supplementary files format and content: sgRNA_count_summary.txt.gz: This file contains normalized counts of library targets.
Supplementary files format and content: enrichment_value_summary.txt.gz: This file contains the enrichment values calculated by "mageck mle".

growth_protocol: AF22 was seeded on 0.1 mg/mL poly-L-ornithine and 4 mg/mL laminin-coated plates in maintenance medium: DMEM/F12 containing N2 supplement, 1× Antibiotic-Antimycotic Mixed Stock Solution, 1 µL/mL B27, 1 µL/mL Glutamax, 10 ng/mL basic fibroblast growth factor, and 10 ng/mL epidermal growth factor (EGF), with daily media changes. For differentiation, AF22 was cultured in the differentiation medium: DMEM/F1- containing N2 supplement, 1× Antibiotic-Antimycotic Mixed Stock Solution, 10 µL/mL B27, and 10 µL/mL Glutamax. Half of the medium was changed every 2 days.

extract_protocol:
The collected cells were treated with 0.5 mg/mL proteinase K (Promega) in lysis buffer (50 mM Tris–HCl, pH 8.0, 50 mM EDTA, and 1% SDS) at 55 °C overnight. Subsequently, the lysates were treated with 300 µg/mL RNase A (Nacalai Tesque) at 37 °C for 30 min. Genomic DNAs were then extracted using the phenol-chloroform extraction method and precipitated with ethanol.
The integrated lentivirus genome encoding sgRNA was amplified by PCR using Q5 Hot Start High-Fidelity 2X Master Mix (NEB). The P5 and P7 primers were designed according to the manufacturer's protocol (addgene #73179). The PCR cycling condition included an initial 1 min at 95 °C, followed by 30 s at 95 °C, 30 s at 53 °C and 30 s at 72 °C for 28 cycles, and a final 10 min extension at 72 °C. The PCR products were fractionated by electrophoresis using a 2 % agarose gel and subsequently purified using FastGen Gel/PCR Extraction Kit (NIPPON Genetic). The obtained products were further purified using AMPure XP beads (Beckman Coulter) to remove undesirable large fragments and remaining primers according to the manufacturer's protocol (addgene #73179). The quality of the sgRNA library was assessed by Tapestation using an HS D1000 Kit (Agilent).

treatment_protocol: We used the human CRISPR knockout pooled library (Brunello, Addgene #73179) consisting of 76,441 unique sgRNAs targeting 19,114 human genes and 1,000 non-targeting controls. A total of 1.98 × 108 AF22 in a maintenance medium were transduced with pooled lentiviral library encoding Cas9, puromycin-resistance gene, and sgRNAs at a multiplicity of infection of 0.5. The next day, the cells were subjected to the puromycin-desistance selection (0.5 µg/mL of puromycin) for 2 days. Then the selected cells were dissociated by TrypLE and 8.8 × 106 cells were replated onto new dishes. The remaining cells were collected for the NGS library (“Day 0” sample). The replated cells were cultured in a differentiation medium for 10 days and were dissociated by Accutase solution for fluorescence-activated cell sorting (FACS). The dissociated cells were suspended by the FACS buffer (0.5% bovine serum albumin, 2 mM EDTA in PBS) and incubated with PE-conjugated anti-CD133 (1: 50) and FITC-conjugated anti-CD24 (1:5) antibodies at 4 °C for 10 min. Then the cells were washed once with a FACS buffer and collected based on the intensities of CD133-signal (undifferentiated NS/PCs) and CD24-signal (differentiating neurons) separately on a FACS Aria II (BD Biosciences). The genomic DNA was extracted from the collected cells.

value: Human iPS cell-derived NS/PC line


title: Day10, CD24-positive, neurons

description:
Library name: CD24_1
CD24


title: Participants 479, intervention, baseline

description: Library name: b479


title: D1_E10


title: Participants 464,control, 6 months

description: Library name: p464


title: D1_E09


title: T24 cells, Caba-780- 2

first: wen

last: liu

address: New temple Road num 1

institute: Tangdu Hospital of Air Force Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package
Assembly: hg38
Supplementary files format and content: RPKM values for each Sample

source_name: cell line

growth_protocol: T24 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using chloroform, isopropanol and washed with ethanol
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for illumina following manufacturer's protocols.

treatment_protocol: T24 cells were treated with 3.84μM Caba-780 for 24 hours,then collected cells and dissolved in Trizol

value: cell line

value: bladder cancer


title: T24 cells, Caba-780- 3


title: PBS_TAC_4

description: Library name: PBS_TAC_4

value: heart


title: D1_E08

value: embryonic stem cell


title: T24 cells, Caba-780- 1


title: Participants 464,control, baseline

description: Library name: b464


title: PBS_TAC_3

description: Library name: PBS_TAC_3


title: D1_E07


title: Participants 379, intervention, 12 months

description: Library name: t379


title: PBS_TAC_2

description: Library name: PBS_TAC_2


title: T24 cells, Control 3


title: PBS_TAC_5

description: Library name: PBS_TAC_5


title: PBS_TAC_1

description: Library name: PBS_TAC_1


title: primary cultured cell of post treatment brain tumor treated with control siRNA 1


title: Day0

description:
Library name: D0_1
Day0


title: Participants 379, intervention, 6 months

description: Library name: p379


title: D1_E06


title: T24 cells, Control 2