title: Z3_WT

city: Saskatoon

first: Brian

last: Eames

state: Saskatchewan

address: 107 Wiggins Road

department: Anatomy and Cell Biology

institute: University of Saskatchewan

data_processing:
The paired-end Illumina reads were trimmed using Trimmomatic v0.36 (Bolger et al. 2014).
Mapped to the Danio rerio Zv9 fom Ensembl.
TMM normalization (Robinson and Oshlack 2010) was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts.
Assembly: Danio_rerio_Ensembl_Zv9
Supplementary files format and content: Comma-delimited text file includes counts for wildtype samples

organism: Danio rerio

source_name: laser-captured cartilage (without perichondrium) from cranial base in occipital region

growth_protocol: standard conditions (EM-filled dishes at 28.5C)

extract_protocol:
RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit (ThermoFisher Scientific; Cat# KIT0204) according to the manufacturer’s instructions and DNase treatment was done using RNase-Free DNase (Qiagen; Cat#79254). RNA was amplified one round using MessageAmp II aRNA Kit (ThermoFisher Scientific; Cat# AM1751). The RNA integrity was evaluated on the observation of a signature electropherogram pattern (Bioanalyzer). A minimum of 5-10 ng of amplified RNA was used per sample for the construction of each library.
RNA-seq libraries were prepared by the National Research Council (NRC, Saskatoon) using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute, Prime, Fragment step using5 µl amplified mRNA (the minimum amount was 5-10 ng mRNA as determined using Quant-iT RiboGreen RNA Assay Kit (Invitrogen)). The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer (Agilent Technologies Inc.).

value: cartilage

value: wild type


title: BAB15420 Proband

status: Public on Dec 18 2023

type: genomic

city: Houston

first: Christopher

last: Grochowski

state: Texas

address: 1 Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 12.0)

data_processing: Agilent Feature Extraction Software (version 12.0) was used for background subtraction and normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole Blood Extracted Genomic DNA

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: Sex

value: Male

tag: sample type

value: Reference Sample


title: LX-2 cells, TGF-b1

status: Public on Dec 17 2023

type: SRA

city: Guangzhou

first: lu

last: gan

state: Guangdong

address: 132 Outer Ring East Road, Panyu District

country: China

institute: School of Pharmaceutical Sciences, Sun Yat-sen University

library_source: transcriptomic

data_processing:
sequence reads were mapped to the reference human-genome assembly with BWA and Bowtie software. Subsequently, the Cufflinks package was used for transcript assembly, quantification of normalized gene and isoform expression in RPKM or FPKM, and testing for differential expression (Cuffdiff). A transcript was considered to be expressed in each dataset if in at least one experimental condition the normalized FPKM>1.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text fles include RPKl values for each Sample

molecule: total RNA

source_name: LX-2 cell

growth_protocol: LX-2 cells were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco)

extract_protocol:
TRIeasy™ Total RNA Extraction Reagent TRIeasy™ was used to extract purified total RNA from LX-2 cells according to the manufacturer’s instructions.
Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA)

tag: cell line

value: LX-2 cell

tag: treatment


title: LX-2 cells, TGF-b1+10 μM DP


title: BAB15428 Proband


title: BAB15418 Proband


title: Z6_WT

country: Canada

tag: tissue

tag: age

tag: genotype


title: RNASEH1_shRNA1_rep1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: Ribominus RNA-seq

data_processing:
First filtered by using Trimmomatic v0.38; Next removed rRNA by bowtie v1.1.2.
Analyses by HISAT2, TopHat-Fusion v2.0.12, CLEAR and custom python script.
Genome_build: GRCh38/hg38 human reference genome with the GENCODE gene annotation (v28).
Supplementary_files_format_and_content: bw files include the read depths.
Supplementary_files_format_and_content: bb files include position of ciRNAs.

extract_protocol:
Total RNAs from cultured cells were extracted with Trizol Reagent (Life Technologies) according to the manufacturer’s protocol. RNAs were further treated with DNase I (Ambion, DNA-free kit) and cDNAs were reverse transcribed with PrimeScript II RTase (TAKARA) at 42 ℃ for 2hr, and then applied for qPCR analysis using the SYBR Green Realtime PCR Master Mix (TOYOBO).
For RNA-seq samples from PA1 cells treated with scramble or RNase H1 shRNAs, ribo minus RNA libraries were prepared using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit according to the manufacturer’s protocol with slight modifications in the step for synthesizing first strand cDNA, which used PrimeScript enzyme mix (TAKARA) for reverse transcription at 42 ℃ for 2 hr. All libraries were size-selected with AmpureXP beads (Agencourt) and quantified using Agilent Bio analyzer 2100 and Qubit high-sensitivity dsDNA assay.

treatment_protocol: PA1 cells were cultured using standard protocols from ATCC. PA1 cells were maintained in MEMα supplemented with 10% FBS, 1% Glutamine and 0.1% penicillin/streptomycin. We maintained cell lines at 37 ℃ in a 5% CO2 cell culture incubator and tested all cell lines routinely for Mycoplasma contamination.

tag: shRNA


title: BAB15740 Proband


title: Z1_WT


title: HIT-scISOseq Run3, scRNAseq

first: Zhuoxing

last: Shi

state: GD

address: #7 Jinsui Road, Tianhe District

department: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: HIT-scISOseq

library_source: transcriptomic single cell

data_processing:
HIT-scISOseq analysis software kit scISA-Tools (https://github.com/shizhuoxing/scISA-Tools) for Full-Length Non-Concatemer (FLNC) reads identification, cell barcode and UMI extraction and correction.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and fasta files

molecule: polyA RNA

organism: Mus musculus

source_name: preimplantation embryos

extract_protocol:
Tthe same amplification procedure as SCAN-seq，except for changing the reverse transcription primer with a 10x gel bead for each reaction for the embryonic samples.
Each pre-amplification product was purified by 0.6X Ampure XP beads (Beckman, Cat. A63882). The concentration was measured using Qubit™ dsDNA HS and BR Assay Kits (Invitrogen, Cat. Q32854). The PCR product from about 60 blastomeres which were confirmed of effective amplification were pooled together in proportion to the number of amplified cycles. We took 100ng of the pooled cDNA to build PacBio sequencing library following the protocol of HIT-scISOseq and sequenced for one cell with HiFi mode.

value: preimplantation embryos

tag: strain

value: DBA/2J x C57BL/6J

tag: cell type


title: BAB14547 Proband


title: HIT-scISOseq Run1, scRNAseq

description: HIT-scISOseq


title: TB-K05

type: RNA

city: Osakasayama City

first: Takashi

last: Kurosaki

address: 377-2 Ohno-higashi

country: Japan

institute: kindai university

description: Pancancer IO 360 panel

hyb_protocol: Hybridation was performed as per manufacturer's protocol.

scan_protocol: Scanned with nCounter SPRINT Profiler

data_processing: Data was normalised using the nSolver software, version 4.0.

label: Nanostring barcoding

source_name: advanced NSCLC

label_protocol: RNA were directly tagged with a capture probe and a reporter probe. This process was carried out according to the manufacturer's protocol.

extract_protocol: Tumor tissue was microdissected to avoid contamination from nontumor tissue before extraction of intratumoral RNA with the use of an AllPrep DNA/RNA FFPE Kit (Qiagen). The extracted RNA was measured with a NanoDrop system (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer system (Agilent Technologies).

value: NSCLC tumor

tag: gender

tag: smoking

value: current or former

tag: ecog ps

tag: pd-l1 tps

tag: histology

value: Adeno


title: TB-K03

description: Pancancer IO 360 panel

value: Sq


title: ENS, Plate 3 71

city: Storrs

first: Bin

last: Feng

state: CT

address: 4S2 67 N Eagleville Road

department: Biomedical Engineering

institute: University of Connecticut

description:
Lib_2_well_95_S191
S121_P2_matrix.mtx

data_processing:
Quality control, adapter trimming, sequence alignment, and gene expression quantification were made for upsteam analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: distal colon

extract_protocol:
We harvested ~30 mm of the VGLUT2-tdTomato mouse distal and gently dissected out the longitudinal and muscular layers containing the myenteric plexus, enzymatically dissociate into individual cells, and culture overnight. Under a fluorescent microscope, each tdTomato-positive neuron will be manually pipetted into a single tube containing 5 µL lysis mix.
cDNA library was generated using a library preparation kit (PWSCR96, SeqWell, MA). Briefly, In the first barcoding step, a unique i7-barcoded adapter is inserted into each of the 96 cDNA samples in segregated reactions. Next, the i7-barcoded cDNA samples are pooled into a single tube. In the second barcoding step, a single i5-barcoded adapter is inserted into each pool of cDNA samples. Finally, each 96-plex library is amplified in a single PCR reaction using universal library primers.

value: distal colon

value: neuron cell


title: ENS, Plate 3 64

description:
Lib_2_well_84_S180
S121_P2_matrix.mtx


title: ENS, Plate 3 68

description:
Lib_2_well_9_S105
S121_P2_matrix.mtx


title: ENS, Plate 3 62

description:
Lib_2_well_82_S178
S121_P2_matrix.mtx


title: ENS, Plate 3 66

description:
Lib_2_well_86_S182
S121_P2_matrix.mtx


title: ENS, Plate 3 72

description:
Lib_2_well_96_S192
S121_P2_matrix.mtx


title: ENS, Plate 3 61

description:
Lib_2_well_81_S177
S121_P2_matrix.mtx


title: ENS, Plate 3 70

description:
Lib_2_well_94_S190
S121_P2_matrix.mtx


title: LX-2 cells, DMSO

value: DMSO


title: ENS, Plate 3 57

description:
Lib_2_well_76_S172
S121_P2_matrix.mtx


title: ENS, Plate 3 67

description:
Lib_2_well_89_S185
S121_P2_matrix.mtx


title: ENS, Plate 3 58

description:
Lib_2_well_78_S174
S121_P2_matrix.mtx


title: ENS, Plate 3 65

description:
Lib_2_well_85_S181
S121_P2_matrix.mtx


title: BAB15705 Proband


title: BAB15702 Proband


title: ENS, Plate 3 63

description:
Lib_2_well_83_S179
S121_P2_matrix.mtx


title: ENS, Plate 3 69

description:
Lib_2_well_92_S188
S121_P2_matrix.mtx


title: ENS, Plate 3 52

description:
Lib_2_well_70_S166
S121_P2_matrix.mtx


title: ENS, Plate 3 60

description:
Lib_2_well_80_S176
S121_P2_matrix.mtx


title: ENS, Plate 3 49

description:
Lib_2_well_67_S163
S121_P2_matrix.mtx


title: ENS, Plate 3 46

description:
Lib_2_well_63_S159
S121_P2_matrix.mtx


title: ENS, Plate 3 50

description:
Lib_2_well_68_S164
S121_P2_matrix.mtx


title: ENS, Plate 3 51

description:
Lib_2_well_7_S103
S121_P2_matrix.mtx


title: ENS, Plate 3 59

description:
Lib_2_well_79_S175
S121_P2_matrix.mtx


title: ENS, Plate 3 48

description:
Lib_2_well_65_S161
S121_P2_matrix.mtx


title: ENS, Plate 3 47

description:
Lib_2_well_64_S160
S121_P2_matrix.mtx


title: ENS, Plate 3 42

description:
Lib_2_well_58_S154
S121_P2_matrix.mtx


title: ENS, Plate 3 38

description:
Lib_2_well_51_S147
S121_P2_matrix.mtx


title: ENS, Plate 3 43

description:
Lib_2_well_59_S155
S121_P2_matrix.mtx


title: ENS, Plate 3 37

description:
Lib_2_well_50_S146
S121_P2_matrix.mtx


title: ENS, Plate 3 55

description:
Lib_2_well_73_S169
S121_P2_matrix.mtx


title: ENS, Plate 3 53

description:
Lib_2_well_71_S167
S121_P2_matrix.mtx


title: ENS, Plate 3 44

description:
Lib_2_well_6_S102
S121_P2_matrix.mtx


title: ENS, Plate 3 41

description:
Lib_2_well_57_S153
S121_P2_matrix.mtx


title: ENS, Plate 3 35

description:
Lib_2_well_49_S145
S121_P2_matrix.mtx


title: ENS, Plate 3 54

description:
Lib_2_well_72_S168
S121_P2_matrix.mtx


title: ENS, Plate 3 40

description:
Lib_2_well_56_S152
S121_P2_matrix.mtx


title: ENS, Plate 3 34

description:
Lib_2_well_48_S144
S121_P2_matrix.mtx


title: ENS, Plate 3 33

description:
Lib_2_well_47_S143
S121_P2_matrix.mtx


title: ENS, Plate 3 24

description:
Lib_2_well_36_S132
S121_P2_matrix.mtx


title: ENS, Plate 3 39

description:
Lib_2_well_52_S148
S121_P2_matrix.mtx


title: ENS, Plate 3 21

description:
Lib_2_well_33_S129
S121_P2_matrix.mtx


title: ENS, Plate 3 32

description:
Lib_2_well_46_S142
S121_P2_matrix.mtx


title: ENS, Plate 3 20

description:
Lib_2_well_32_S128
S121_P2_matrix.mtx


title: ENS, Plate 3 22

description:
Lib_2_well_34_S130
S121_P2_matrix.mtx


title: ENS, Plate 3 31

description:
Lib_2_well_45_S141
S121_P2_matrix.mtx


title: ENS, Plate 3 18

description:
Lib_2_well_3_S99
S121_P2_matrix.mtx


title: ENS, Plate 3 30

description:
Lib_2_well_44_S140
S121_P2_matrix.mtx


title: ENS, Plate 3 19

description:
Lib_2_well_31_S127
S121_P2_matrix.mtx


title: ENS, Plate 3 29

description:
Lib_2_well_43_S139
S121_P2_matrix.mtx


title: ENS, Plate 3 45

description:
Lib_2_well_61_S157
S121_P2_matrix.mtx


title: ENS, Plate 3 36

description:
Lib_2_well_5_S101
S121_P2_matrix.mtx


title: ENS, Plate 3 28

description:
Lib_2_well_4_S100
S121_P2_matrix.mtx


title: ENS, Plate 3 14

description:
Lib_2_well_26_S122
S121_P2_matrix.mtx


title: ENS, Plate 3 26

description:
Lib_2_well_38_S134
S121_P2_matrix.mtx


title: ENS, Plate 3 27

description:
Lib_2_well_39_S135
S121_P2_matrix.mtx


title: ENS, Plate 3 23

description:
Lib_2_well_35_S131
S121_P2_matrix.mtx


title: ENS, Plate 3 15

description:
Lib_2_well_27_S123
S121_P2_matrix.mtx


title: ENS, Plate 3 56

description:
Lib_2_well_74_S170
S121_P2_matrix.mtx


title: ENS, Plate 3 16

description:
Lib_2_well_28_S124
S121_P2_matrix.mtx


title: ENS, Plate 3 13

description:
Lib_2_well_25_S121
S121_P2_matrix.mtx


title: ENS, Plate 3 10

description:
Lib_2_well_20_S116
S121_P2_matrix.mtx


title: ENS, Plate 3 12

description:
Lib_2_well_23_S119
S121_P2_matrix.mtx


title: ENS, Plate 3 11

description:
Lib_2_well_21_S117
S121_P2_matrix.mtx


title: ENS, Plate 3 25

description:
Lib_2_well_37_S133
S121_P2_matrix.mtx


title: ENS, Plate 3 7

description:
Lib_2_well_18_S114
S121_P2_matrix.mtx


title: ENS, Plate 3 6

description:
Lib_2_well_17_S113
S121_P2_matrix.mtx


title: ENS, Plate 3 3

description:
Lib_2_well_14_S110
S121_P2_matrix.mtx


title: ENS, Plate 3 1

description:
Lib_2_well_1_S97
S121_P2_matrix.mtx


title: ENS, Plate 3 4

description:
Lib_2_well_15_S111
S121_P2_matrix.mtx


title: ENS, Plate 3 5

description:
Lib_2_well_16_S112
S121_P2_matrix.mtx


title: ENS, Plate 3 9

description:
Lib_2_well_2_S98
S121_P2_matrix.mtx


title: ENS, Plate 3 8

description:
Lib_2_well_19_S115
S121_P2_matrix.mtx


title: ENS, Plate 2 66

description:
Lib_1_well_96_S96
S35_P2_matrix.mtx


title: ENS, Plate 3 17

description:
Lib_2_well_29_S125
S121_P2_matrix.mtx


title: ENS, Plate 3 2

description:
Lib_2_well_11_S107
S121_P2_matrix.mtx


title: ENS, Plate 2 64

description:
Lib_1_well_94_S94
S35_P2_matrix.mtx


title: ENS, Plate 2 65

description:
Lib_1_well_95_S95
S35_P2_matrix.mtx


title: ENS, Plate 2 63

description:
Lib_1_well_93_S93
S35_P2_matrix.mtx


title: ENS, Plate 2 62

description:
Lib_1_well_91_S91
S35_P2_matrix.mtx


title: ENS, Plate 2 60

description:
Lib_1_well_87_S87
S35_P2_matrix.mtx


title: ENS, Plate 2 61

description:
Lib_1_well_89_S89
S35_P2_matrix.mtx


title: ENS, Plate 2 57

description:
Lib_1_well_84_S84
S35_P2_matrix.mtx


title: MTX23

city: MILANO

first: VALENTINA

last: VAIRA

address: VIA FRANCESCO SFORZA 35

department: PATHOPHISIOLOGY AND TRANSPLANTATION

country: Italy

institute: UNIVERSITY OF MILANO

description:
genomic DNA from brain metastasis
brain metastasis from non small cell lung cancer

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and precipitated.The DNA was subsequently hybridized to probes on the Illumina Epic BeadChips using standard Illumina protocol.

scan_protocol: Scanning was conducted using the NextSeq 550 System (Illumina).

data_processing: none provided

label: Cy5 and Cy3

source_name: brain metastasis

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from frozen samples was extracted with the DNAeasy Blood and Tissue Kit (Qiagen), according to the manufacturer’s instruction and quantified using the Qubit dsDNA BR Assay kit.

tag: metastatic site

value: NSCLC SCC

value: brain metastasis

tag: disease state

value: tumor


title: ENS, Plate 2 59

description:
Lib_1_well_86_S86
S35_P2_matrix.mtx


title: MTX22

value: NSCLC ADCA


title: ENS, Plate 2 58

description:
Lib_1_well_85_S85
S35_P2_matrix.mtx


title: MTX21


title: MTX6


title: ENS, Plate 2 54

description:
Lib_1_well_81_S81
S35_P2_matrix.mtx


title: MTX20


title: ENS, Plate 2 56

description:
Lib_1_well_83_S83
S35_P2_matrix.mtx


title: ENS, Plate 2 55

description:
Lib_1_well_82_S82
S35_P2_matrix.mtx


title: MTX19

description:
genomic DNA from brain metastasis
brain metastasis from colon cancer

value: COLON ADK


title: ENS, Plate 2 53

description:
Lib_1_well_80_S80
S35_P2_matrix.mtx


title: MTX18

description:
genomic DNA from brain metastasis
brain metastasis from prostate cancer

value: PROSTATE ADCA


title: ENS, Plate 2 52

description:
Lib_1_well_8_S8
S35_P2_matrix.mtx


title: ENS, Plate 2 49

description:
Lib_1_well_76_S76
S35_P2_matrix.mtx


title: MTX16

description:
genomic DNA from brain metastasis
brain metastasis from serous carcinoma

value: SEROUS CA


title: MTX17

value: NSCLC G3


title: MTX15


title: ENS, Plate 2 48

description:
Lib_1_well_70_S70
S35_P2_matrix.mtx


title: ENS, Plate 2 50

description:
Lib_1_well_77_S77
S35_P2_matrix.mtx


title: MTX14


title: MTX5


title: MTX7


title: ENS, Plate 2 44

description:
Lib_1_well_67_S67
S35_P2_matrix.mtx


title: ENS, Plate 2 42

description:
Lib_1_well_64_S64
S35_P2_matrix.mtx


title: MTX2

description:
genomic DNA from brain metastasis
brain metastasis from melanoma

value: MELANOMA


title: ENS, Plate 2 45

description:
Lib_1_well_68_S68
S35_P2_matrix.mtx


title: MTX1


title: MTX4


title: MTX3


title: ENS, Plate 2 41

description:
Lib_1_well_63_S63
S35_P2_matrix.mtx


title: ENS, Plate 2 43

description:
Lib_1_well_65_S65
S35_P2_matrix.mtx


title: MTX13

description:
genomic DNA from brain metastasis
brain metastasis from breast ductal invasive carcinoma

value: BREAST DUCT invasive ca


title: MTX12


title: ENS, Plate 2 38

description:
Lib_1_well_60_S60
S35_P2_matrix.mtx


title: ENS, Plate 2 40

description:
Lib_1_well_62_S62
S35_P2_matrix.mtx


title: ENS, Plate 2 36

description:
Lib_1_well_55_S55
S35_P2_matrix.mtx


title: ENS, Plate 2 37

description:
Lib_1_well_57_S57
S35_P2_matrix.mtx


title: ENS, Plate 2 46

description:
Lib_1_well_69_S69
S35_P2_matrix.mtx


title: ENS, Plate 2 39

description:
Lib_1_well_61_S61
S35_P2_matrix.mtx


title: MTX9


title: ENS, Plate 2 47

description:
Lib_1_well_7_S7
S35_P2_matrix.mtx


title: ENS, Plate 2 51

description:
Lib_1_well_79_S79
S35_P2_matrix.mtx


title: MTX11


title: ENS, Plate 2 35

description:
Lib_1_well_53_S53
S35_P2_matrix.mtx


title: ENS, Plate 2 33

description:
Lib_1_well_51_S51
S35_P2_matrix.mtx


title: MTX10


title: ENS, Plate 2 34

description:
Lib_1_well_52_S52
S35_P2_matrix.mtx


title: ENS, Plate 2 29

description:
Lib_1_well_45_S45
S35_P2_matrix.mtx


title: ENS, Plate 2 32

description:
Lib_1_well_48_S48
S35_P2_matrix.mtx


title: ENS, Plate 2 30

description:
Lib_1_well_46_S46
S35_P2_matrix.mtx


title: Hypoxic neuroblasts, rep 3

city: Seville

first: Ricardo

last: Pardal

address: Avda. Manuel Siurot, s/n

department: Medical Physiology and Biophysics

country: Spain

institute: University of Seville

description: 500pg of total RNA converted to cDNA

hyb_protocol: Following fragmentation, 3.8 ug of cDNA were hybridized for 16 hr at 45C on GeneChip® Rat gene 2.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Scanner 3000 7G by Affymetrix®.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0 using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Rattus norvegicus

source_name: 3d hypoxic carotid body

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500 pg total RNA.

growth_protocol: Rats were maintained either at ambient air (normoxia) or inside hypoxic chambers (hypoxia) for 3 days, with humidity, CO2 and temperature controlled.

extract_protocol: Total RNA was extracted with RNAeasy kit, according to the manufacturer's instructions.

treatment_protocol: Carotid bodies were dissected and enzymatically dispersed. Cells were stained with HNK-1 antibody and both neuroblasts (HNK-1+) and glomus cells (HNK-1-) were sorted by flow cytometry into lysis buffer. See Sobrino et al., EMBO Rep 2018 for details about this protocol.

value: mixed bilateral carotid bodies

value: Wistar

value: 9-11 weeks


title: Hypoxic neuroblasts, rep 4

description: 500pg of total RNA converted to cDNA


title: MTX8

description:
genomic DNA from brain metastasis
brain metastasis from multiple mieloma

value: MULTIPLE MYELOMA


title: Hypoxic glomus cells, rep 3

description: 500pg of total RNA converted to cDNA


title: ENS, Plate 2 28

description:
Lib_1_well_44_S44
S35_P2_matrix.mtx

value: distal colon


title: Hypoxic glomus cells, rep 4

description: 500pg of total RNA converted to cDNA


title: ENS, Plate 2 24

description:
Lib_1_well_38_S38
S35_P2_matrix.mtx

value: neuron cell


title: ENS, Plate 2 26

description:
Lib_1_well_41_S41
S35_P2_matrix.mtx


title: Hypoxic neuroblasts, rep 1

description: 500pg of total RNA converted to cDNA


title: ENS, Plate 2 23

description:
Lib_1_well_37_S37
S35_P2_matrix.mtx


title: ENS, Plate 2 31

description:
Lib_1_well_47_S47
S35_P2_matrix.mtx


title: ENS, Plate 2 27

description:
Lib_1_well_42_S42
S35_P2_matrix.mtx


title: ENS, Plate 2 22

description:
Lib_1_well_36_S36
S35_P2_matrix.mtx


title: ENS, Plate 2 25

description:
Lib_1_well_40_S40
S35_P2_matrix.mtx


title: Hypoxic neuroblasts, rep 2

description: 500pg of total RNA converted to cDNA


title: Hypoxic glomus cells, rep 2

description: 500pg of total RNA converted to cDNA


title: Hypoxic glomus cells, rep1

description: 500pg of total RNA converted to cDNA


title: ENS, Plate 2 19

description:
Lib_1_well_31_S31
S35_P2_matrix.mtx


title: Normoxic neuroblasts, rep 4

description: 500pg of total RNA converted to cDNA

source_name: Normoxic carotid body


title: Normoxic neuroblasts, rep 3

description: 500pg of total RNA converted to cDNA


title: Normoxic glomus cells, rep 4

description: 500pg of total RNA converted to cDNA


title: Normoxic neuroblasts, rep 2

description: 500pg of total RNA converted to cDNA


title: Normoxic neuroblasts, rep 1

description: 500pg of total RNA converted to cDNA


title: ENS, Plate 2 21

description:
Lib_1_well_35_S35
S35_P2_matrix.mtx


title: ENS, Plate 2 20

description:
Lib_1_well_34_S34
S35_P2_matrix.mtx


title: Normoxic glomus cells, rep 3

description: 500pg of total RNA converted to cDNA


title: Normoxic glomus cells, rep 1

description: 500pg of total RNA converted to cDNA


title: JMat-baseline-ZF77_S16

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed using cutadapter
QIIME2.0 microbiome pipeline
OTU tables after rarefaction
Assembly: hg38
Supplementary files format and content: tab-delimited taxon dataset
Library strategy: 16S RNA amplicon sequencing

organism: gut metagenome

source_name: fecal

extract_protocol:
DNA was isolated using a Zymo Research Quick-DNA Fecal/Soil Microbe Miniprep Kit (catalog D6010)
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: host

value: Macaca mulatta

value: gut microbiome

tag: seq target

value: 16s rRNA

value: WT

value: Ad-lib


title: JMat-baseline-ZJ51_S21


title: ENS, Plate 2 18

description:
Lib_1_well_3_S3
S35_P2_matrix.mtx


title: Jmat-C6D8-MRI_S134


title: JMat-baseline-ZJ55_S19


title: JMat-baseline-ZE26_S3

value: PRF


title: ENS, Plate 2 13

description:
Lib_1_well_23_S23
S35_P2_matrix.mtx


title: ENS, Plate 2 16

description:
Lib_1_well_27_S27
S35_P2_matrix.mtx


title: JMat-baseline-T75_S5


title: ENS, Plate 2 15

description:
Lib_1_well_26_S26
S35_P2_matrix.mtx


title: JMat-baseline-ZF36_S12


title: JMat-baseline-ZA64_S18


title: ENS, Plate 2 17

description:
Lib_1_well_28_S28
S35_P2_matrix.mtx


title: JMat-baseline-ZA49_S23


title: ENS, Plate 2 10

description:
Lib_1_well_20_S20
S35_P2_matrix.mtx


title: ENS, Plate 2 12

description:
Lib_1_well_22_S22
S35_P2_matrix.mtx


title: ENS, Plate 2 11

description:
Lib_1_well_21_S21
S35_P2_matrix.mtx


title: JMat-baseline-T19_S6


title: JMat-baseline-RQ6683_S13


title: ENS, Plate 2 9

description:
Lib_1_well_2_S2
S35_P2_matrix.mtx


title: JMat-baseline-RQ2937_S20


title: ENS, Plate 2 14

description:
Lib_1_well_25_S25
S35_P2_matrix.mtx


title: ENS, Plate 2 8

description:
Lib_1_well_18_S18
S35_P2_matrix.mtx


title: ENS, Plate 2 7

description:
Lib_1_well_16_S16
S35_P2_matrix.mtx


title: ENS, Plate 2 5

description:
Lib_1_well_13_S13
S35_P2_matrix.mtx


title: ENS, Plate 2 6

description:
Lib_1_well_14_S14
S35_P2_matrix.mtx


title: JMat-baseline-MTR_S11


title: JMat-baseline-MLB_S4


title: JMat-baseline-MRI_S17


title: JMat-baseline-M1423_S1


title: Normoxic glomus cells, rep 2

description: 500pg of total RNA converted to cDNA


title: ENS, Plate 2 4

description:
Lib_1_well_12_S12
S35_P2_matrix.mtx


title: ENS, Plate 2 2

description:
Lib_1_well_10_S10
S35_P2_matrix.mtx


title: JMat-baseline-DF11_S10


title: JMat-baseline-DF46_S7


title: JMat-baseline-RQ6709_S15


title: JMat-baseline-DE76A_S8


title: ENS, Plate 1 65

description:
ENS-95_S122
S10_P1_matrix.mtx


title: ENS, Plate 1 64

description:
ENS-93_S120
S10_P1_matrix.mtx


title: ENS, Plate 1 66

description:
ENS-9_S36
S10_P1_matrix.mtx


title: JMat-baseline-DCJT_S14


title: ENS, Plate 1 62

description:
ENS-8_S35
S10_P1_matrix.mtx


title: JMat-baseline-99R1062_S22


title: ENS, Plate 1 63

description:
ENS-91_S118
S10_P1_matrix.mtx


title: JMat-ZJ55-1Day-PostABX_S117


title: ENS, Plate 1 61

description:
ENS-87_S114
S10_P1_matrix.mtx


title: JMat-C6D8-ZJ55_S136


title: ENS, Plate 1 60

description:
ENS-83_S110
S10_P1_matrix.mtx


title: JMat-C6D8-ZJ51_S138


title: JMat-C6D8-ZF77_S133


title: JMat-baseline-M1352_S2


title: ENS, Plate 2 3

description:
Lib_1_well_11_S11
S35_P2_matrix.mtx


title: ENS, Plate 1 58

description:
ENS-7_S34
S10_P1_matrix.mtx


title: ENS, Plate 2 1

description:
Lib_1_well_1_S1
S35_P2_matrix.mtx


title: ENS, Plate 1 57

description:
ENS-78_S105
S10_P1_matrix.mtx


title: ENS, Plate 1 56

description:
ENS-76_S103
S10_P1_matrix.mtx


title: JMat-C6D8-ZE26_S120


title: JMat-C6D8-ZF36_S129


title: ENS, Plate 1 55

description:
ENS-74_S101
S10_P1_matrix.mtx


title: JMat-baseline-DCGG_S9


title: JMat-C6D8-T75_S122


title: ENS, Plate 1 54

description:
ENS-73_S100
S10_P1_matrix.mtx


title: ENS, Plate 1 59

description:
ENS-81_S108
S10_P1_matrix.mtx


title: ENS, Plate 1 53

description:
ENS-72_S99
S10_P1_matrix.mtx


title: JMat-C6D8-ZA64_S135


title: JMat-C6D8-T19_S123


title: ENS, Plate 1 52

description:
ENS-71_S98
S10_P1_matrix.mtx


title: JMat-C6D8-RQ6683_S130


title: JMat-C6D8-RQ2937_S137


title: JMat-C6D8-RQ6709_S132


title: ENS, Plate 1 50

description:
ENS-69_S96
S10_P1_matrix.mtx


title: ENS, Plate 1 51

description:
ENS-70_S97
S10_P1_matrix.mtx


title: ENS, Plate 1 49

description:
ENS-68_S95
S10_P1_matrix.mtx


title: JMat-C6D8-MTR_S128


title: ENS, Plate 1 48

description:
ENS-67_S94
S10_P1_matrix.mtx


title: JMat-C6D8-MLB_S121


title: JMat-C6D8-M1423_S118


title: ENS, Plate 1 46

description:
ENS-64_S91
S10_P1_matrix.mtx


title: JMat-C6D8-M1352_S119


title: ENS, Plate 1 47

description:
ENS-65_S92
S10_P1_matrix.mtx


title: JMat-C6D8-ZA49_S140


title: ENS, Plate 1 45

description:
ENS-62_S89
S10_P1_matrix.mtx


title: JMat-C6D8-DF46_S124


title: JMat-C6D8-DF11_S127


title: ENS, Plate 1 43

description:
ENS-60_S87
S10_P1_matrix.mtx


title: JMat-C6D8-DE76A_S125


title: ENS, Plate 1 44

description:
ENS-61_S88
S10_P1_matrix.mtx


title: ENS, Plate 1 41

description:
ENS-59_S86
S10_P1_matrix.mtx


title: JMat-C6D8-DCJT_S131


title: ENS, Plate 1 42

description:
ENS-5_S32
S10_P1_matrix.mtx


title: JMat-C6D8-DCGG_S126


title: JMat-C6D4-ZF36_S93


title: JMat-C6D8-99R1062_S139


title: ENS, Plate 1 38

description:
ENS-56_S83
S10_P1_matrix.mtx


title: JMat-C6D4-ZE26_S84


title: ENS, Plate 1 39

description:
ENS-57_S84
S10_P1_matrix.mtx


title: ENS, Plate 1 37

description:
ENS-55_S82
S10_P1_matrix.mtx


title: JMat-C6D4-T75_S86


title: JMat-C6D4-T19_S87


title: JMat-C6D4-MTR_S92


title: ENS, Plate 1 34

description:
ENS-49_S76
S10_P1_matrix.mtx


title: ENS, Plate 1 31

description:
ENS-45_S72
S10_P1_matrix.mtx


title: ENS, Plate 1 33

description:
ENS-48_S75
S10_P1_matrix.mtx


title: ENS, Plate 1 32

description:
ENS-47_S74
S10_P1_matrix.mtx


title: JMat-C6D4-M1352_S83


title: JMat-C6D4-MLB_S85


title: ENS, Plate 1 29

description:
ENS-42_S69
S10_P1_matrix.mtx


title: JMat-C6D4-DF11_S91


title: ENS, Plate 1 30

description:
ENS-44_S71
S10_P1_matrix.mtx


title: ENS, Plate 1 40

description:
ENS-58_S85
S10_P1_matrix.mtx


title: JMat-C6D4-DF46_S88


title: JMat-C6D4-DCGG_S90


title: JMat-C6D4-DE76A_S89


title: ENS, Plate 1 28

description:
ENS-41_S68
S10_P1_matrix.mtx


title: ENS, Plate 1 36

description:
ENS-52_S79
S10_P1_matrix.mtx


title: ENS, Plate 1 35

description:
ENS-4_S31
S10_P1_matrix.mtx


title: ENS, Plate 1 26

description:
ENS-3_S30
S10_P1_matrix.mtx


title: JMat-C6D2-T75_S62


title: ENS, Plate 1 27

description:
ENS-40_S67
S10_P1_matrix.mtx


title: JMat-C6D2-ZE26_S60


title: ENS, Plate 1 24

description:
ENS-37_S64
S10_P1_matrix.mtx


title: JMat-C6D4-M1423_S82


title: JMat-C6D2-T19_S63


title: ENS, Plate 1 25

description:
ENS-39_S66
S10_P1_matrix.mtx


title: ENS, Plate 1 23

description:
ENS-36_S63
S10_P1_matrix.mtx


title: JMat-C6D2-MTR_S68


title: JMat-C6D2-MLB_S61


title: ENS, Plate 1 22

description:
ENS-35_S62
S10_P1_matrix.mtx


title: ENS, Plate 1 21

description:
ENS-34_S61
S10_P1_matrix.mtx


title: JMat-C6D2-M1423_S58


title: JMat-C6D2-ZF36_S69


title: JMat-C6D2-M1352_S59


title: ENS, Plate 1 20

description:
ENS-33_S60
S10_P1_matrix.mtx


title: JMat-C6D2-DF46_S64


title: ENS, Plate 1 18

description:
ENS-2_S29
S10_P1_matrix.mtx


title: ENS, Plate 1 17

description:
ENS-28_S55
S10_P1_matrix.mtx


title: JMat-C6D2-DF11_S67


title: ENS, Plate 1 19

description:
ENS-30_S57
S10_P1_matrix.mtx


title: JMat-C6D2-DE76A_S65


title: JMat-C6D2-DCGG_S66


title: JMat-C6D1-ZJ55_S41


title: ENS, Plate 1 14

description:
ENS-23_S50
S10_P1_matrix.mtx


title: ENS, Plate 1 16

description:
ENS-26_S53
S10_P1_matrix.mtx


title: JMat-C6D1-ZF77_S38


title: ENS, Plate 1 13

description:
ENS-22_S49
S10_P1_matrix.mtx


title: ENS, Plate 1 15

description:
ENS-24_S51
S10_P1_matrix.mtx


title: ENS, Plate 1 12

description:
ENS-21_S48
S10_P1_matrix.mtx


title: JMat-C6D1-ZJ51_S43


title: JMat-C6D1-ZA64_S40


title: JMat-C6D1-RQ6709_S37


title: ENS, Plate 1 9

description:
ENS-19_S46
S10_P1_matrix.mtx


title: ENS, Plate 1 10

description:
ENS-1_S28
S10_P1_matrix.mtx


title: ENS, Plate 1 11

description:
ENS-20_S47
S10_P1_matrix.mtx


title: JMat-C6D1-RQ6683_S35


title: ENS, Plate 1 8

description:
ENS-18_S45
S10_P1_matrix.mtx


title: JMat-C6D1-RQ2937_S42


title: ENS, Plate 1 7

description:
ENS-17_S44
S10_P1_matrix.mtx


title: ENS, Plate 1 6

description:
ENS-16_S43
S10_P1_matrix.mtx


title: JMat-C6D1-MRI_S39


title: JMat-C6D1-DCJT_S36


title: ENS, Plate 1 5

description:
ENS-14_S41
S10_P1_matrix.mtx


title: JMat-C3D8-ZJ55_S112


title: ENS, Plate 1 2

description:
ENS-11_S38
S10_P1_matrix.mtx


title: ENS, Plate 1 3

description:
ENS-12_S39
S10_P1_matrix.mtx


title: JMat-C6D1-ZA49_S45


title: ENS, Plate 1 4

description:
ENS-13_S40
S10_P1_matrix.mtx


title: JMat-C3D8-ZF77_S109


title: JMat-C3D8-ZJ51_S114


title: JMat-C6D1-99R1062_S44


title: JMat-C3D8-ZF36_S105


title: JMat-C3D8-ZE26_S96


title: brown adipose tissue from Hrd1 flox/flox; Ucp1-Cre B6 mouse, rep2

city: Ann Arbor

first: You

last: Lu

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

data_processing:
Base calling and de-multiplexing: BCL Convert Conversion Software v4.0 (Illumina)
Data QC: FastQC v0.11.8
Read alignment: STAR v2.7.8a
Count estimate: RSEM v1.3.3
Assembly: GRCh38 (ENSEMBL 109) for human HEK293T cells, GRCm38 (ENSEMBL 102) for mouse BAT samples
Supplementary files format and content: Tab-delimited text files include estimated counts by gene for each sample

source_name: brown adipose tissue

growth_protocol: All HEK293T cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1%  penicillin/streptomycin at 37°C in 5% CO2 in a humidified incubator. Brown adipose tissue (BAT) was collected from 12-week-old mice.

extract_protocol:
Total RNA was extracted from snap-frozen samples using TRIzol.
Libraries were generated following a standard polyA-enrichment RNA-seq library creation stratedgy.

value: brown adipose tissue

value: HRD1 KO


title: JMat-C3D8-ZA64_S111


title: ENS, Plate 1 1

description:
ENS-10_S37
S10_P1_matrix.mtx


title: JMat-C3D8-ZA49_S116


title: JMat-C3D8-T75_S98


title: brown adipose tissue from Sel1l flox/flox; Ucp1-Cre B6 mouse, rep2

value: SEL1L KO


title: brown adipose tissue from wild type B6 mouse, rep3


title: brown adipose tissue from wild type B6 mouse, rep2


title: brown adipose tissue from Sel1l flox/flox; Ucp1-Cre B6 mouse, rep3


title: JMat-C3D8-T19_S99


title: brown adipose tissue from Sel1l flox/flox; Ucp1-Cre B6 mouse, rep1


title: JMat-C3D8-RQ6709_S108


title: JMat-C3D8-RQ6683_S106


title: brown adipose tissue from Hrd1 flox/flox; Ucp1-Cre B6 mouse, rep1


title: brown adipose tissue from wild type B6 mouse, rep1


title: JMat-C3D8-MTR_S104


title: JMat-C3D8-RQ2937_S113


title: JMat-C3D8-MRI_S110


title: run2_mouse16-pBA_NAc

city: Biberach an der Riss

first: Gregorio

last: Alanis-Lobato

address: Birkendorfer Str 65

department: Global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma

data_processing:
Sequencing reads were mapped to the Mus musculus reference genome (mm10) using STAR v2.5.2b allowing for soft clipping of adapter sequences. An average of 20 million reads per sample was obtained, from which approximately 10 million reads were assigned to genomic features. Transcript quantification was conducted with RSEM v1.3.0 and featureCounts v1.5.1. QC, and downstream bioinformatic analyses were conducted with R v4.1.2 and Bioconductor v3.12 tools.
Assembly: mm10
Supplementary files format and content: intBA-NAc_pBA-NAc_Glu_neurons_mmu_Pryce_SE.rds: R data storage file (rds) with a SummarizedExperiment object containing all sample metadata, gene metadata, raw and normalized gene expression matrices

source_name: Posterior basal amygdala

extract_protocol:
At 29 days post-surgery, mice were deeply anaesthetized and then perfused with PBS at RT for 4 min to rinse blood from the brain. The brain was removed and placed in a cryo-mold (E6032-1CS, Sigma-Aldrich) with an embedding medium (Tissue-TEK OCT Compound). The cryo-mold was then placed on powdered dry ice for 10 min, wrapped in aluminium foil, placed in a plastic bag and stored at -80°C, prior to laser capture microdissection. Frozen brains were processed using RNA- and RNAse-free conditions throughout. Using a cryostat set at -17 to -20°C, coronal sections that included the NAc at +1.6 to +0.5 were cut at 40 µm, mounted on microscope slides (SuperFrost, Epredia) and processed to estimate the CTB injection site. Then, coronal sections that included the BA at -1.6 to -2.0 and -2.3 to -2.6 were cut at 10 µm and mounted (3 sections per slide) on RNAse-free PET membrane slides (50102, Molecular Machines & Industries, MMI). Sections then underwent fixation and dehydration using the following steps: 70% ETOH at -20°C for 120 s, dipping in/out ddH20 ice-cold for 60 s, dipping in/out 70% ETOH ice-cold for 60 s, 95% ETOH ice-cold for 45 s, 100% ETOH at RT for 120 s, 3x washing in xylene at RT, xylene at RT for 120 s. Slides/sections were placed on their edge in a covered dark box at RT for 10 min or until completely dried, and then in a capped 50 ml Falcon tube for either immediate cell collection or stored at -80°C for 7 days maximum. Tissue labelled with CTB-555 was collected from coronal sections at bregma AP -1.6 to -2.0 and -2.3 to -2.6 using a laser capture microdissection system (CellCut, MMI). Fluorescence settings were optimized for visualization of CTB-555+ tissue (channel TRITC). The membrane slide was positioned and using 40x magnification, BA tissue areas that were CTB-555+ were each encircled at Ø = 35 µm using the MMI CellTools software. There were 40-60 such areas per BA hemisphere and these were encircled for both hemispheres for each of the 3 sections on the membrane slide. A MMI Universal UV laser (355 nm, 2 µJ, 4 kHz frequency with 500 pico-s Pulse-Duration) at 40-50% laser power was activated (velocity = 54 µm/sec, focus = 27 µm) and the designated tissue areas were cut out and collected on the adhesive cap of an MMI Isolation tube (0.5 ml). The procedure was conducted with 2 membrane slides (6 sections) and isolation tubes per BA region and mouse,  giving a total of 500-510 CTB-555+ tissue samples per BA region and mouse. Following tissue collection, tissue lysis was conducted by adding QIAzol® (100 µl/tube) to the tube, triturating the tissue on the cap with 20 µl volumes and returning this volume to the tube; the tube was closed, inverted for 15 min at RT, and vortexed for 1 min, inverted for 5 min and centrifuged for 5 sec. The tube was then sealed with Parafilm and frozen at -80°C until RNA isolation. Lysate aliquots (2-3 x 100 µl per sample) from the same BA sample were pooled, and, if required, QIAzol was added to give a final lysis volume of 300 µL. Samples were transferred to 2mL PhaseLock tubes (QuantaBio). A half volume of chloroform:isoamyl alcohol (24:1 v:v) was added prior to shaking, 3 min RT incubation and centrifugation at 4°C. The aqueous phase was then transferred to a 1.5mL Eppendorf tube and mixed with a 1.5 volume of isopropanol (Sigma). After thorough pipette mixing, the isopropanol mixture was applied to an RNeasy MinElute spin column and total RNA was extracted using the miRNeasy Micro Kit (Qiagen) with a DNase treatment. Samples were eluted in 14 µL nuclease-free water. RNA samples were assessed both quantitatively and qualitatively using the High Sensitivity Total RNA 15nt Analysis DNF-472 Kit on a 48-channel Fragment Analyzer (Agilent). Total RNA yield was 1.14 ± 0.20 ng; RNA integrity could often not be computed due to low input.
Up to 1.5 ng of total RNA was used for cDNA synthesis, conducted with the SMART-Seq® v4 Ultra Low Input RNA kit (Takara Bio). Depending on the input amount, 12-15 amplification cycles were conducted. After clean-up, up to 10 ng of cDNA was used to generate the final sequencing libraries with the tagmentation-based DNA Prep Kit (#20018705) and the IDT® DNA/RNA UD Indexes Set A (#20026121), both Illumina®. The index PCR was performed with 9 or 10 cycles depending on cDNA amount, while the final library was eluted in 30 µL EB Buffer. Low input mRNA libraries were then quantified using the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Library molarity averaged at 21 nM. Libraries were also assessed for size distribution and adapter dimer presence (<0.5%) by the High Sensitivity NGS Fragment DNF-474 Kit on a 48-channel Fragment Analyzer (Agilent). All sequencing libraries were then normalized on the MicroLab STAR (Hamilton), pooled and spiked-in with PhiX Control v3 (Illumina). The library pools were subsequently clustered on an SP Flow Cell and sequenced on a NovaSeq 6000 Sequencing System (Illumina) with dual index, paired-end reads at 2 x 100 bp length (Read parameters: Rd1: 101, Rd2: 10, Rd3: 10, Rd4: 101), reaching an average depth of 26 million Pass-Filter reads per sample (18.2% CV).

treatment_protocol: BL/6 mice were bilaterally infused in the NAc with 300 nL of 1 mg/mL CTB-555. These mice were also the controls in an experiment that investigated chronic social stress effects on the BA-NAc transcriptome and were handled for 15 days but were otherwise unmanipulated.

value: Posterior basal amygdala

value: Glutamatergic neuron

tag: group

value: Control

value: CTB-555 infusion in NAc


title: run2_mouse15-pBA_NAc

tag: treatment


title: JMat-C3D8-MLB_S97

tag: tissue


title: run2_mouse13-pBA_NAc


title: run2_mouse8-pBA_NAc


title: JMat-C3D8-M1423_S94


title: JMat-C3D8-M1352_S95


title: JMat-C3D8-DF11_S103


title: run1_mouse14-pBA_NAc


title: run1_mouse13-pBA_NAc


title: JMat-C3D8-DF46_S100


title: JMat-C3D8-DE76A_S101


title: run1_mouse5-pBA_NAc


title: JMat-C3D8-DCGG_S102


title: run1_mouse3-pBA_NAc


title: JMat-C3D4-ZF36_S81


title: JMat-C3D8-DCJT_S107


title: run1_mouse6-pBA_NAc


title: JMat-C3D8-99R1062_S115


title: JMat-C3D4-ZE26_S72


title: run2_mouse15-intBA_NAc

source_name: Intermediate basal amygdala

value: Intermediate basal amygdala


title: run1_mouse4-pBA_NAc


title: run2_mouse16-intBA_NAc


title: JMat-C3D4-T19_S75


title: JMat-C3D4-T75_S74


title: run2_mouse9-pBA_NAc


title: JMat-C3D4-MTR_S80


title: JMat-C3D4-MLB_S73


title: run2_mouse7-pBA_NAc


title: run2_mouse13-intBA_NAc


title: run2_mouse8-intBA_NAc


title: JMat-C3D4-M1423_S70


title: run2_mouse7-intBA_NAc


title: run2_mouse6-intBA_NAc


title: JMat-C3D4-DF46_S76


title: JMat-C3D4-M1352_S71


title: run1_mouse6-intBA_NAc


title: JMat-C3D4-DF11_S79


title: JMat-C3D4-DCGG_S78


title: JMat-C3D2-ZF36_S57


title: run2_mouse14-intBA_NAc


title: JMat-C3D4-DE76A_S77


title: run1_mouse4-intBA_NAc


title: JMat-C3D2-T75_S50


title: run1_mouse5-intBA_NAc


title: run2_mouse9-intBA_NAc


title: run1_mouse3-intBA_NAc


title: JMat-C3D2-ZE26_S48


title: human_study participant_36, acute

city: Nedlands

first: Jonatan

last: Leffler

state: WA

address: 15 Hospital Ave

country: Australia

institute: Telethon Kids Institute

data_processing:
The paired-end raw reads were mapped to the GRCh38 human genome build using the STAR aligner
Gene counts were computed using featureCounts based on GENCODEv31 gene annotation
Processed data was adjusted using RUVseq6 (k=4)
Assembly: GRCh38
Supplementary files format and content: raw_counts.csv
Supplementary files format and content: processed_data.csv

source_name: peripheral blood mononuclear cells

extract_protocol:
Plasmacytoid dendritic cells (500 cells per tube) were sorted directly into PCR tubes each containing 2 µL of 1 mg/mL BSA (Ambion® Thermo Fisher Scientific) lysis buffer with 4 U/µL of recombinant RNase inhibitor (Takara Bio) and 1 µL of 10 mM dNTP mix, then stored at -80 °C
cDNA libraries were prepared using the SMART-seq2 protocol with the following modifications: (i) change in lysis buffer and cell collection as already described; (ii) addition of 20 μM TSO; (iii) use of 200 pg cDNA with 1/5 reaction of Nextera XT kit (Illumina)
All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq X system with 28-29 samples per lane.

value: peripheral blood mononuclear cells

tag: cell isolation

value: flow cytometry isolated cells

value: plasmacytoid dendritic cells

tag: wheeze vs_ctrl

value: acute

tag: wheeze phenotype

value: persistent

tag: Sex

value: F


title: JMat-C3D2-T19_S51

value: Macaca mulatta

value: gut microbiome

value: 16s rRNA

tag: genotype

value: WT


title: human_study participant_38, control

tag: cell type

value: control

value: M


title: human_study participant_37, acute

value: multiple


title: human_study participant_35, acute


title: JMat-C3D2-MTR_S56

value: PRF


title: human_study participant_34, control


title: JMat-C3D2-M1423_S46


title: JMat-C3D2-MLB_S49


title: run1_mouse14-intBA_NAc

tag: strain

value: Glutamatergic neuron

value: Control


title: human_study participant_33, acute

value: few


title: Neonatal, spleen-4

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

institute: Nihon University

data_processing:
Raw fastq files were precessed using fastqAnalysis script (Tipton, C. M. et al. Nat. Immunol. 16, 755–765 (2015)).
The output files were then analyzed with IMGT/High V-QUEST.
Assembly: mm10
Supplementary files format and content: IMGT/High V-QUEST output file
Library strategy: BCR-seq

source_name: Spleen

extract_protocol:
RNA was extracted using Nucleospin RNA XS kit.
BCR sequence library were prepared using SMARTer Mouse BCR IgG H/K/L Profiling Kit.

value: Spleen

tag: cell subtype

value: B cell

value: DOX


title: Neonatal, spleen-1


title: Neonatal, spleen-3


title: Neonatal, peritoneal cavity-4

source_name: Peritoneal cavity

value: Peritoneal cavity


title: Neonatal, spleen-2


title: JMat-C3D2-M1352_S47


title: Neonatal, peritoneal cavity-3


title: Neonatal, peritoneal cavity-2


title: JMat-C3D2-DF46_S52


title: human_study participant_32, acute

value: peripheral blood mononuclear cells

value: flow cytometry isolated cells

value: plasmacytoid dendritic cells

value: acute


title: Neonatal, peritoneal cavity-1


title: human_study participant_31, acute

value: F


title: JMat-C3D2-DF11_S55

value: Macaca mulatta

value: gut microbiome

value: 16s rRNA

value: WT


title: Neonatal, bone marrow IgM-4

source_name: Bone marrow

value: Bone marrow

value: palsmablast


title: human_study participant_30, acute

value: persistent


title: Neonatal, bone marrow IgM-3


title: Neonatal, bone marrow IgM-2


title: JMat-C3D2-DE76A_S53

value: PRF


title: Neonatal, bone marrow IgM-1


title: Neonatal, bone marrow B1-4


title: JMat-C3D2-DCGG_S54


title: Neonatal, bone marrow B1-3


title: human_study participant_28, control

value: control


title: JMat-C3D1-ZJ55_S30

value: Ad-lib


title: Embryo, spleen-5

value: Spleen

value: B cell

value: DOX


title: human_study participant_27, acute

value: peripheral blood mononuclear cells

value: flow cytometry isolated cells

value: M


title: JMat-C3D1-ZJ51_S32


title: JMat-C3D1-ZF77_S27


title: human_study participant_25, control

value: plasmacytoid dendritic cells

value: F


title: Embryo, spleen-3


title: Embryo, spleen-2


title: Embryo, spleen-4


title: Embryo, peritoneal cavity-5

value: Peritoneal cavity


title: human_study participant_24, acute

value: acute

value: few


title: Embryo, spleen-1


title: human_study participant_29, acute

value: multiple


title: JMat-C3D1-ZA49_S34

value: Macaca mulatta

value: gut microbiome

value: 16s rRNA

value: WT


title: Embryo, peritoneal cavity-4


title: human_study participant_23, control

value: control


title: Embryo, peritoneal cavity-3


title: Embryo, peritoneal cavity-1


title: Embryo, peritoneal cavity-2


title: Embryo, bone marrow IgM-5

value: Bone marrow

value: palsmablast


title: JMat-C3D1-RQ6683_S24

value: Ad-lib


title: Neonatal, bone marrow B1-2

value: B cell

value: DOX


title: Embryo, bone marrow IgM-4


title: Embryo, bone marrow IgM-3


title: Neonatal, bone marrow B1-1


title: JMat-C3D1-RQ2937_S31


title: human_study participant_26, acute

value: peripheral blood mononuclear cells

value: flow cytometry isolated cells


title: JMat-C3D1-ZA64_S29


title: JMat-C3D1-MRI_S28


title: JMat-C3D1-DCJT_S25


title: Embryo, bone marrow B1-4


title: Embryo, bone marrow IgM-1


title: human_study participant_19, control

value: plasmacytoid dendritic cells

value: M


title: Embryo, bone marrow IgM-2


title: JMat-C3D1-RQ6709_S26


title: human_study participant_18, acute

value: acute


title: JMat-C3D1-99R1062_S33


title: Adult, spleen-5

value: Spleen


title: Embryo, bone marrow B1-2


title: Embryo, bone marrow B1-1


title: human_study participant_22, acute

value: few


title: Adult, spleen-4


title: human_study participant_16, acute

value: multiple


title: Adult, spleen-2


title: NO10C

city: hangzhou

first: Rui

last: Zhu

address: yucai bei road

institute: xiaoshan hospital

data_processing:
Data filtering  The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification  Bowtie2[2] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) [3]. The heatmap was drawn by pheatmap (v1.0.8) [4] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) [8].
Assembly: hmmscan
Supplementary files format and content: tab-delimited text file includes raw counts for each example
Supplementary files format and content: tab-delimited text file includes RPKM values for each example

source_name: human,adipose

extract_protocol:
Total RNA was extracted from the BAT using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The total RNA from each sample was treated with Ribo-Zero_x005F_x0002_ Magnetic Kit (Epocentre) to deplete any ribosomal RNA. The retrieved RNA was fragmented by adding First Strand Mas_x0002_ter Mix (Invitrogen). First-strand cDNA was generated using random primers reverse transcription, followed by second-strand cDNA synthesis in which the RNA template was removed and dTTP was replaced by dUTP. The incorporation of dUTP prevents the second strand of cDNA from being amplified in the subse_x0002_quent process because the polymerase cannot cross the dUTP site on the template during extension. The double-stranded cDNA product was then ligated with an "A" base and a linker.
Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. PCR The PCR reaction system and program are configured and set up to amplify the product. Library QC The corresponding library quality control protocol will be selected depending upon product requirements. Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).
RNA-seq, miRNA-seq, ncRNA-seq

value: human,adipose


title: human_study participant_15, control

value: F


title: NO10B

source_name: human,para-cancer tissue

value: human,para-cancer tissue


title: Adult, spleen-1


title: Adult, spleen-3


title: Adult, peritoneal cavity-4

value: Peritoneal cavity


title: human_study participant_21, acute


title: Adult, peritoneal cavity-5


title: human_study participant_17, control

value: control


title: human_study participant_14, acute


title: Embryo, bone marrow B1-3

value: Bone marrow


title: Adult, peritoneal cavity-2


title: Adult, peritoneal cavity-3


title: human_study participant_13, control


title: Adult, bone marrow IgM-5

value: palsmablast


title: NO9C


title: human_study participant_20, acute

value: persistent


title: NO9B


title: Adult, bone marrow IgM-4

value: DOX


title: NO10A

source_name: human,Colorectal Cancer tissue

value: human,Colorectal Cancer tissue


title: human_study participant_11, acute

value: peripheral blood mononuclear cells

value: flow cytometry isolated cells


title: human_study participant_12, control

value: plasmacytoid dendritic cells

value: M


title: NO8C


title: NO9A


title: Adult, bone marrow B1-5

value: B cell


title: human_study participant_10, acute

value: acute


title: Adult, bone marrow IgM-2


title: Adult, bone marrow IgM-1


title: NO8B


title: NO8A


title: human_study participant_9, acute

value: few


title: human_study participant_8, acute

value: multiple


title: Adult, bone marrow B1-3


title: 6. CD4+ EM T-cell stable COPD

city: Szeged

first: Gabor

middle: Janos

last: Dr. Szebeni

state: Csongrád

address: Temesvári krt. 62.

country: Hungary

institute: Biological Research Centre

description: 3x40 ng pool

data_processing:
Geometric normalization was performed by GenXPro Gmbh
Differential expression of mRNA in relation to healhy controls
Assembly: not relevant
Supplementary files format and content: Microsoft Excel and Supplementary Table 3 of our publication: doi: 10.3389/fimmu.2023.1297577

source_name: CD4+ effector memory T-cells

growth_protocol: The cells were FACS sorted from human PBMC

extract_protocol:
Full methods is published: doi: 10.3389/fimmu.2023.1297577
The 3′ mRNA-Seq was performed as a service by GenxPro Gmbh.

treatment_protocol: There was no treatment

value: CD4+ effector memory T-cells

tag: cell line

value: wt


title: human_study participant_7, control


title: 7. CD4+ EM T-cell COPD with exacerbation

description: 4x100 ng pool


title: 8. CD4+ EM T-cell NSCLC

description: 5x200 ng pool


title: 5. CD4+ EM T-cell contol

description: 3x60 ng pool


title: 1. CD4+ CM T-cell contol

description: 3x150 ng pool

source_name: CD4+ central memory T-cells

value: CD4+ central memory T-cells


title: 3. CD4+ CM T-cell COPD with exacerbation

description: 4x200 ng pool


title: Adult, bone marrow IgM-3


title: 4. CD4+ CM T-cell NSCLC

description: 5x200 ng pool


title: human_study participant_5, acute

value: F


title: NO7A


title: NO7B

value: human,para-cancer tissue


title: NO6C

value: human,adipose


title: cMSC.MG.2

city: Hiroshima

first: Masashi

last: Kuwabara

address: 1-2-3 Kasumi, Minami-ku

department: Neurosurgery

institute: Graduate School of Biomedical and Health Sciences, Hiroshima University

data_processing:
miRNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). Quality and quantity of extracted miRNA was assessed by QuantiFluor RNA System (Promega) and Agilent Small RNA kit of BioAnalyzer 2100 System (Agilent Technologies) according to the manufacturer’s instruction. miRNA-seq library was prepared using QIAseq miRNA Library Kit (Qiagen) following the manufacturer’s instruction. In brief, a pre-adenylated DNA adapter is ligated to the 3’ ends of all miRNAs. An RNA adapter is ligated to the 5’ end of mature miRNAs. After that reverse-transcription (RT) was performed using the RT primer which contains Unique Molecular Indices (UMIs). Finally, the library was amplified by sample specific indexed primers. The libraries were sequenced on a NextSeq 500 sequencer (Illumina) to generate 75 nt single reads. Duplicated reads were removed from raw reads using seqkit (ver. 0.10.1), and adapter sequence was trimmed with cutadapt (ver. 1.16). Trimmed reads were mapped to the human genomes (genome assemblies used was GRCh38.p13 using STAR (ver. 2.7.2b) with the following parameters: --alignEndsType EndToEnd --outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --outReadsUnmapped None --outSAMtype BAM Unsorted --outFilterMultimapNmax 10 --outSAMunmapped Within --outFilterScoreMinOverLread 0 -- outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000 --alignIntronMax 1. Reads mapped to miRNA genes were quantified using featureCounts of the Subread package (ver. 1.6.1) with the following parameters: -s 1 -O -M -p -C -B -T. Differential gene expression analysis and GO analysis were performed using DESeq2 (ver. 1.18.1) and clusterProfiler (ver. 3.6.0), respectively.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include CPM (FPKM, peak) values for each sample.

source_name: Cranial bone

extract_protocol:
Passage 3 human cranial bone-derived mesenchymal stem cells (hcMSCs) cultured in normal gravity and microgravity environments were collected and centrifuged at 1,750 rpm for 5 min. Total RNA was eluted using the NucleoSpin™ RNA mini kit (MACHEREY-NAGEL GmbH & Co. KG, Duren, Germany), following the manufacturer’s protocol. RNA was also extracted from human bone marrow-derived mesenchymal stem cells for their comparison with hcMSCs.
The quality and quantity of extracted miRNA was assessed using QuantiFluor RNA System (Promega) and Agilent Small RNA kit of BioAnalyzer 2100 System (Agilent Technologies), according to the manufacturer’s instruction. miRNA library was prepared using QIAseq miRNA Library Kit (Qiagen) following the manufacturer’s instruction. The libraries were sequenced on a NextSeq 500 sequencer (Illumina) to generate 75 nt single reads. Duplicated reads were removed from raw reads using seqkit (ver. 0.10.1), and adapter sequence was trimmed with cutadapt (ver. 1.16). Trimmed reads were mapped to the human genomes (genome assemblies used was GRCh38.p13) using STAR (ver. 2.7.2b). Differential gene expression analysis and GO analysis were performed using DESeq2 (ver. 1.18.1) and clusterProfiler (ver. 3.6.0), respectively.

value: Cranial bone

value: mesenchymal stem cell


title: cMSC.MG.3


title: Adult, bone marrow B1-2

value: Bone marrow

value: DOX


title: cMSC.MG.1


title: human_study participant_4, control

value: peripheral blood mononuclear cells

value: flow cytometry isolated cells

value: control


title: NO7C


title: NO6B


title: cMSC.1G.1


title: human_study participant_3, control

value: plasmacytoid dendritic cells


title: human_study participant_2, acute

value: acute


title: cMSC.1G.2


title: human_study participant_6, control

value: M


title: bMSC.3


title: 2. CD4+ CM T-cell stable COPD

description: 3x100 ng pool


title: NO5C


title: bMSC.2


title: NO5B


title: Srebp1a_ff_Myeloid_biol_rep_4

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

description: 3 days after injury

data_processing:
Reads were aligned to the mm10 mouse genome using STAR.
Aligned read files were analyzed using HOMER.  Differentially expressed genes were analyzed using svaseq and DESeq2.
bedGraph files were generated using HOMER.
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: muscle

extract_protocol:
Total RNA was extracted using Rneasy column (Qiagen) according to the manufacturer's protocol.
Poly-A mRNA was extracted from total RNA by using an NEBNext Poly(A) mRNA magnetic Isolation module (NEB), after which RNA-seq libraries were prepared using a NEBNext UltraII RNA Library Prep kit for Illumina (NEB) according to the manufacturer’s protocol.

value: muscle

value: CD45+CD11b+ cells

value: CTX injury


title: bMSC.1


title: Orf8_input_N2

city: Philadelphia

first: Erica

last: Korb

state: PENNSYLVANIA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Fastq files were aligned by Bowtie2
IGVtools was used to generate TDF files
NGSplot was used to generate genome-wide analysis plots
Genome_build: hg38
Supplementary_files_format_and_content: bam files aligned by bowtie2

source_name: HEK cells

extract_protocol:
Strep tagged Orf8 transfected cells fixed and used for ChIP
ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: transfection

value: Transfected with Orf8

tag: antibody


title: human_study participant_1, acute

value: few

value: F


title: Orf8_input_N1


title: Orf8_IP_N1

value: Streptactin:MagStrep type3 XT beads, iba-lifesciences 2-4090-002


title: Orf8_IP_N2


title: Srebp1a_ff_Myeloid_biol_rep_3

description: 3 days after injury


title: NO4C

value: human,adipose


title: NO6A

value: human,Colorectal Cancer tissue


title: NO5A


title: Control_input

value: Transfected with GFP


title: Control_IP


title: cMSC.1G.3

value: Cranial bone

value: mesenchymal stem cell


title: Srebp1a_ff_Myeloid_biol_rep_2

description: 3 days after injury


title: NO4B

value: human,para-cancer tissue


title: NO4A


title: SI ANpm1 Rep4

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Small Intestine

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

treatment_protocol: Induction of genetic recombination was performed by 2 x 2mg intraperitoneal injection of Tamoxifen 24 hrs apart. Tissues at the noted distances along the intestine were harvested after 4 days.

value: Female

value: Small Intestine

value: VilCreER Apc f/f Npm1 f/f

tag: time

value: Day 4


title: LysM_Cre_Srebp1a_ff_Myeloid_biol_rep_6

description: 3 days after injury

value: muscle


title: SI AKNpm1 Rep4

value: Male

value: VilCreER Apc f/f KRasG12D/+ Npm1 f/f


title: SI ANpm1 Rep2


title: SI ANpm1 Rep3


title: Srebp1a_ff_Myeloid_biol_rep_1

description: 3 days after injury

value: CD45+CD11b+ cells

value: CTX injury


title: NO3C


title: SI ANpm1 Rep1


title: LysM_Cre_Srebp1a_ff_Myeloid_biol_rep_5

description: 3 days after injury


title: SI AKNpm1 Rep2


title: SI AKNpm1 Rep3


title: LysM_Cre_Srebp1a_ff_Myeloid_biol_rep_4

description: 3 days after injury


title: SI AKNpm1 Rep1


title: SI AK (Npm control) Rep4

value: VilCreER Apc f/f KRasG12D/+


title: LysM_Cre_Srebp1a_ff_Myeloid_biol_rep_3

description: 3 days after injury


title: SI AK (Npm control) Rep3


title: ZH11-UM-3

city: wuhan

first: zhu

last: bo

state: beijing

address: shi zi shan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing:
Raw reads of all sequencing data were trimmed using fastp (v0.20.1)
RNA-seq Clean read was then matched to the MSU7.0 rice reference genome using hisat2 software. FeatureCounts were used for quantitative analysis and the differentially expressed genes (Fold change > 2,q < 0.01) were calculated by DESeq2.
Supplementary files format and content: RNA-seq count file

organism: Oryza sativa Japonica Group

source_name: Unicellular microspores

extract_protocol:
Rice sperms, meiocytes and unicellular microspores were isolated from anthers of Cas9-free transgenic plants and tissue culture-regenerated wild type plants. For sperm isolation, mature anthers were soaked in 45% (w/v) sucrose and then transferred into 15% (w/v) sucrose to release sperm pairs. For isolation of meiocytes, panicles of about 5 cm length were chosen and middle parts of the panicles were collected. Intact anthers were carefully selected using dissecting needles, placed onto an RNAase-free slide, and suspended in a PBS solution containing 1% proteinase inhibitors. The outer wall of anthers was then removed by capillary to release meiocytes. For isolation of unicellular microspores, panicles of about 8 cm length were harvested and the middle parts of the panicles were collected. Anthers were dissected out and make a hole with a capillary tube in the same solution as used for meiocyte isolation. Squeeze gently from the opposite side of the hole to release unicellular microspore. All isolated cells were collected by a micromanipulator system (Eppendorf, TransferMan® 4r).Rice eggs and unicellular zygotes were isolated from ovules before and after fertilization of Cas9-free transgenic plants and tissue culture-regenerated wild type (Zhou et al., 2019; Zhou et al., 2021). Briefly, ovaries of non-pollinated and pollinated florets (about 6.5 h after pollination) were manually collected in RNAase-free water under a dissection microscope. The collected ovules were transferred to a solution containing 0.53 M mannitol and 1% proteinases inhibitors to release eggs or zygotes. All isolated cells were stained by FDA (Fluoresceinc diacetate, Sangon, 596-09-8) and collected by a micromanipulator system (Eppendorf, TransferMan® 4r).
For RNA-seq library construction, mRNA isolated from different types of cells were reverse transcribed and amplified by utilizing SMART-Seq® v4 Ultra® Low Input RNA Kit (TAKARA, Cat. No.634889). cDNAs were sheared into 200-400 bp DNA fragments followed by purification using Agencourt AMPure Beads (Beckman Coulter, USA A63881). The rest steps were performed using the Truseq ChIP DNA library preparation kit (Illumina. IP-202-1012). About 3000 sperm cells and 400 meiocytes were used to construct the transcriptome libraries. Fifty cells of egg or unicellular zygote were used for each replicate of the transcriptome library construction.

value: Unicellular microspores

value: wild type


title: NO3A

value: human,Colorectal Cancer tissue


title: LysM_Cre_Srebp1a_ff_Myeloid_biol_rep_2

description: 3 days after injury


title: SI AK (Npm control) Rep2


title: LysM_Cre_Srebp1a_ff_Myeloid_biol_rep_1

description: 3 days after injury


title: ZH11-UM-2


title: NO2A


title: NO2B


title: ZH11-UM-1


title: Wild-type plants under drought conditions, input_DNA, K4 rep 3

city: Harbin

first: Baofeng

last: Zhang

address: Hexing Road 26#, Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the P. trichocarpa genome v.3.0 genome using Bowtie2 v2.3.5 with parameter (-N 1). Only uniquely mapping reads were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 50 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off p-value <=1e-05
bigWig files were generated using the Deeptools v3.5.1. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2.1.0 with default settings.
Assembly: P. trichocarpa genome v.3.0
Supplementary files format and content: bigWig (Six IP DNA biological replicates, and six input DNA biological replicates), narrowPeak (Peak file with input as control)

organism: Populus trichocarpa

source_name: xylem

growth_protocol: Wild-type plants were grown in a walk-in growth chamber (21 to 25°C, 16-h-light/8-h-dark cycle, and 60 to 80% humidit).

extract_protocol:
Xylem tissue was cross-linked in 1% formaldehyde and used to isolate nuclei and chromatin. The chromatin was sheared into 200- to 1000-bp fragments, subjected to immunoprecipitation using Anti-H3K4me3 antibody (Abcam, ab8580), and collected with protein G magnetic beads (Invitrogen). Precipitated chromatin was de-cross-linked to release the ChIP-DNA.
Libraries were prepared using a library preparation kit (New England Biolabs) according to the manufacturer’s instructions. 20 ng of DNA was used as starting material for input and ip samples. DNA fragments around 200 bp in length were selected and amplified 9 cycles on the thermocycler.  Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: All plants were equally well watered prior to drought treatment. For treatment group, watering was withheld for 5 days (D5), while the control group was continuously watered (D0).

value: xylem

tag: chip antibody


title: Wild-type plants under drought conditions, input_DNA, K4 rep 2


title: SI Apc (Npm control) Rep3

value: VilCreER Apc f/f


title: Wild-type plants under drought conditions, input_DNA, K4 rep1


title: NO3B


title: GC3 [miRNA]

city: wuxi

first: fangmei

last: an

state: jiangsu

address: NO 299,QingYang Road

institute: Wuxi Public Hospital

description: processed data file: N-GC.all.miRNA.txt

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the human reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM/COUNT values for each Sample ...

source_name: gastric mucosa_GC

extract_protocol: Gastric mucosa specimens were collected from CSG(N), CAG(CAG+IM1), Dys, and GC patients through biopsy during their endoscopy procedures at the Wuxi People's Hospital between October and December 2019. Three samples were collected for each group, and 12 total samples were kept in RNAlater (AM7020, Thermo Fisher Scientific) for the miRNA, lncRNA and mRNA microarray analysis.

tag: source

value: Gastric Cancer (GC)

value: gastric mucosa


title: GC2 [miRNA]

description: processed data file: N-GC.all.miRNA.txt


title: NO1C

value: human,adipose


title: NO1A


title: NO1B

value: human,para-cancer tissue


title: Wild-type plants under well-watered conditions, input_DNA, K4 rep 3


title: GC1 [miRNA]

description: processed data file: N-GC.all.miRNA.txt


title: Dys3 [miRNA]

description: processed data file: N-Dys.all.miRNA.txt

source_name: gastric mucosa_Dys

value: Dysplasia


title: Wild-type plants under well-watered conditions, input_DNA, K4 rep 2


title: HEK293T cell culture, HRD1 knockout, rep2

value: Human embryonic kidney

value: HRD1 KO


title: Liver bcatMyc Npm1 Rep4

source_name: Liver

value: Male

value: Liver

value: AAV8 Cre bcatenin/+ ROSA DM-lsl-Myc hom Npm1 f/f

value: Day 4


title: SI AK (Npm control) Rep1

value: Small Intestine

value: VilCreER Apc f/f KRasG12D/+


title: Liver bcatMyc Npm1 Rep3


title: NO2C


title: Dys2 [miRNA]


title: HEK293T cell culture, HRD1 knockout, rep1


title: SI Apc (Npm control) Rep1


title: HEK293T cell culture, SEL1L knockout, rep3

value: SEL1L KO


title: Wild-type plants under drought conditions, IP_DNA, K4 rep 3

value: Anti-H3K4me3 (Abcam, ab8580)


title: Dys1 [miRNA]


title: CAG+IM3 [miRNA]

description: processed data file: N-CAG+IM.all.miRNA.txt

source_name: gastric mucosa_CAG+IM

value: Chronic Atrophic Gastritis (CAG) + Intestinal Metaplasia (IM)


title: SI Apc (Npm control) Rep4

value: Female

value: VilCreER Apc f/f


title: SI Apc (Npm control) Rep2


title: Wild-type plants under well-watered conditions, input_DNA, K4 rep1

value: xylem


title: Liver bcatMyc Npm1 Rep2


title: Wild-type plants under drought conditions, IP_DNA, K4 rep 2


title: HEK293T cell culture, SEL1L knockout, rep1


title: Liver bcatMyc Npm1 Rep1


title: HEK293T cell culture, SEL1L knockout, rep2


title: Liver bcatMyc Rep4

value: AAV8 Cre bcatenin/+ ROSA DM-lsl-Myc hom


title: CAG+IM2 [miRNA]

value: gastric mucosa


title: Wild-type plants under drought conditions, IP_DNA, K4 rep 1


title: Wild-type plants under well-watered conditions, IP_DNA, K4 rep 3


title: CAG+IM1 [miRNA]


title: HEK293T cell culture, HRD1 knockout, rep3


title: Liver bcatMyc Rep3


title: HEK293T cell culture, wild type, rep3

value: WT


title: N3 [miRNA]

source_name: gastric mucosa_chronic superficial gastritis

value: chronic superficial gastritis


title: HEK293T cell culture, wild type, rep2

value: Human embryonic kidney


title: HEK293T cell culture, wild type, rep1


title: Liver bcatMyc Rep2

value: Male


title: Liver bcatMyc Rep1

value: Liver


title: Wild-type plants under well-watered conditions, IP_DNA, K4 rep 2


title: Wild-type plants under well-watered conditions, IP_DNA, K4 rep 1


title: N1 [miRNA]


title: N2 [miRNA]


title: Skin normal 95

status: Public on Dec 16 2023

city: Hanoi

first: Tham

middle: H

last: Hoang

address: Floor 9th, 458 Minh Khai

country: Viet Nam

institute: Vingroup Big Data Institute

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-95

hyb_protocol: RA1 resuspended DNA was loaded onto Infinium Asian Screening Array-24 v1.0 BeadChip . After incubation 16 - 24 hours at 48˚C, single-base extension and allele-specific staining was performed on a Te-flow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining the Beadchip was coated with XC4, dried for 1 hour and scanned by IScan Software (Illumina).

data_processing: Genomic DNA extracted from saliva was genotyped using ASA-24 v1.0 Beadchip (Illumina).

label: Cy3, Cy5

source_name: Saliva

label_protocol: 250ng of genomic DNA was whole-genome amplified in an overnight reaction at 37˚C using amplification master mix (MA1, MA2 and MSM). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from saliva was performed using MagMAX DNA Multi-Sample Ultra 2.0 Kit on KingFisher™ Flex Purification System.

tag: gender

value: M


title: Skin normal 88

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-88


title: Skin normal 96

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-96


title: Skin normal 91

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-91

value: F


title: Skin normal 89

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-89


title: Skin normal 94

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-94


title: Skin normal 93

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-93


title: Skin normal 92

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-92


title: Skin normal 90

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-90


title: Skin normal 87

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-87


title: Skin normal 86

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-86


title: Skin normal 83

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-83


title: Skin normal 85

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-85


title: Skin normal 82

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-82


title: Skin normal 79

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-79


title: Skin normal 81

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-81


title: Skin normal 80

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-80


title: Skin normal 78

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-78


title: TSC.RNA_rep2

city: guangzhou

first: Wenjuan

last: Li

state: 广东

address: UCAS

department: GIBH

institute: UCAS

data_processing:
Data were aligned to the hg38 assembly using STAR (v2.7.3a) and RSEM (v1.2.18).
Genome_build: hg38
Supplementary_files_format_and_content: Text files include raw count, TPM values and FPKM values

source_name: TSC

growth_protocol: Cell culture: human naïve PSC were plated at a density of 100000 cells per well onextracellular matrix (ECM; Geltrex™)-coated 6-well plates and cultured with TE medium. TE medium was refreshed every two days. Cells were collected for RNA-seq on day 5. For human TSC cells, cells cultured in TS-1 medium for five or six days were plated on Collagen IV coated 6-well plates and cultured with TSC medium. Cells cultured in TSC medium became morphologically stable after 2-3 passages. For shRNA experiments, cells were infected with lentiviruses generated from HEK293T cells using Lipofectamine 3000 (Invitrogen, L3000015) following the manufacturer’s instructions.

extract_protocol: Bulk RNA-seq library preparation and sequencing were performed by BGI, China.

value: H9 human naive pluripotent stem cell derived TSC

tag: treatment

value: untreated(wild type)


title: TELC-D5.RNA_rep1

value: H9 human naive pluripotent stem cell derived TE


title: TELC-D5.RNA_rep2


title: Skin normal 77

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-77


title: Skin normal 75

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-75


title: 4CL.H3K27ac_rep3

description:
4CL.H3K27ac.3rep.narrowPeak
4CL.H3K27ac.3rep.CPM.bw

data_processing:
Raw sequence data were trimmed to remove both poor quality calls and adapters using fastp (v0.20.1) with the settings "--length_required=10 --n_base_limit=5".
Trimmed data were first aligned to the hg38 assembly using Bowtie2 (v2.2.5) with the settings “--very-sensitive.”
Low quality mapped reads were removed using Samtools with the settings “-q 30.”
Duplicated reads were collapsed using Picard (v1.9.0).
Peaks were called using MACS2 (v2.1.0) with the settings “-B, --nomodel, --keep-dup 1, -g hs, --call-summits, -q 1e-05”.
Assembly: hg38
Supplementary files format and content: BigWig files were generated from replicates merged file using deeptools(v3.1.3) bamCoverage tool with --normalizeUsing CPM options.
Library strategy: CUT&Tag

source_name: Not applicable

growth_protocol: Briefly, primed PSCs were dissociated into single cells with a 1:1 mixture of 0.5 mM EDTA and TrypLE Express (Gibco) and plated at a density of 100,000 to 150,000 cell/well of 6-well plate on feeders in mTeSRTM1 medium supplemented with 10 µM Y-27632 (Axon, 1683). Twenty-four hours later, the medium was switched to 4CL medium, which was refreshed daily. Cells were passaged as single cells (1:5 to 1:8) every 3 to 4 days.

extract_protocol:
For CUT&Tag library construction, Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD902-01) was used.
For CUT&Tag library construction, Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD902-01) was used. In brief, 100,000 cells were incubated with Concanavalin A-coated magnetic beads and then primary antibodies were added to incubate overnight at 4°C. Tubes were placed on a magnetic rack to remove the supernatants. Secondary antibodies were added and samples were incubated at room temperature for one hour. After placing the tubes on the magnetic rack and removing the supernatants, hyperactive pG-Tn5/pA-Tn5 transposon (incubated at room temperature for one hour) were added. Tagmentation was performed for 1 hour and DNA was extracted using phenol–chloroform–isoamyl alcohol. Purified DNA fragments were amplified by PCR for 15-20 cycles and the PCR products were purified following the kit’s instructions.

tag: tissue

value: Not applicable

value: Human ESC cultured in 4CL medium


title: Skin normal 74

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-74


title: Skin normal 84

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-84


title: Skin normal 76

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-76


title: 4CL.H3K27ac_rep2


title: 4CL.TEAD4_rep2

growth_protocol: Human naïve PSCs were dissociated into single cells with a 1:1 mixture of 0.5 mM EDTA and TrypLE Express and plated at a density of 100,000 cell/well of 6-well plate on Geltrex in TE induction medium (1:1 mix of Neurobasal medium (Gibco) and DMEM/F12 (HyClone) supplemented with N2 (Gibco) and B27 (Gibco), penicillin-streptomycin (HyClone), Glutamax (Gibco), β-mercaptoethanol (Sigma), 1 µM PD0325901 (Axon) and 1 µM A83-01 (Selleck)) for five days. TELCs at day 5 were used for downstream analysis throughout this study. For generating expandable TSCs, TELCs at day 5 were dissociated into single cells with TrypLE and plated on Geltrex-coated six-well plates at a 1:4-1:8 split ratio in TSC medium (DMEM/F12 supplemented with N2 and B27, penicillin-streptomycin, Glutamax, β-mercaptoethanol, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF (PeproTech), 0.5 µM A83-01 (Selleck), 1 µM SB431542 (Selleck), 2 µM CHIR99021 (Axon), 0.8 mM VPA (Vetec) and 5 µM Y-27632 (Axon)) supplemented with 10 µM Y-27632.

value: Human 4CL naive ESC


title: Skin normal 73

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-73


title: Skin normal 71

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-71


title: Skin normal 68

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-68


title: 4CL.H3K27ac_rep1


title: Skin normal 72

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-72


title: Skin normal 69

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-69


title: Skin normal 70

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-70


title: Skin normal 67

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-67


title: TELC-D5.TFAP2C_rep2

value: Human ESC derived-TELC-D5


title: TELC-D5.GATA3_rep1


title: TELC-D5.GATA3_rep2


title: 4CL.TEAD4_rep1


title: Skin normal 66

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-66


title: TELC-D5.TFAP2C_rep1


title: Skin normal 65

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-65


title: TELC-D5.YAP_rep2


title: Skin normal 64

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-64


title: TELC-D5.YAP_rep1


title: TSC.RNA_rep1


title: Skin normal 63

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-63


title: Skin normal 61

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-61


title: TSC.VGLL1_rep2

value: Human ESC derived-TSC


title: Skin normal 60

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-60


title: TSC.H3K27ac_rep3


title: TSC.H3K27ac_rep2


title: Skin normal 59

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-59


title: TSC.VGLL1_rep1


title: Skin normal 57

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-57


title: Skin normal 58

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-58


title: WT_TELC-D5.TEAD4_rep2


title: C68_TELC-D5.TEAD4_rep1

value: VGLL1 knockout


title: C68_TELC-D5.H3K27ac_rep2


title: WT_TELC-D5.H3K27ac_rep2


title: C68_TELC-D5.TEAD4_rep2


title: Skin normal 53

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-53


title: Skin normal 55

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-55


title: Skin normal 54

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-54


title: Skin normal 56

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-56


title: WT_TELC-D5.H3K27ac_rep1


title: C68_TELC-D5.H3K27ac_rep1


title: Skin normal 52

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-52


title: C68_TELC-D5.ATAC_rep2

data_processing:
Raw sequence data were trimmed to remove both poor quality calls and adapters using fastp (v0.20.1) with the settings "--length_required=10 --n_base_limit=5".
Trimmed data were first aligned to the hg38 assembly using Bowtie2 (v2.2.5) with the settings “--very-sensitive.”
Low quality mapped reads were removed using Samtools with the settings “-q 30.”
Duplicated reads were collapsed using Picard (v1.9.0).
Peaks were called using MACS2 (v2.1.0) with the settings “-B, --nomodel, --keep-dup 1, -g hs, --call-summits, -q 1e-05”.
Assembly: hg38
Supplementary files format and content: BigWig files were generated from replicates merged file using deeptools(v3.1.3) bamCoverage tool with --normalizeUsing CPM options.

extract_protocol:
For ATAC-seq library preparation, 50,000 cells were washed once with cold PBS and resuspended in lysis buffer (10 mM Tris-HCl (pH 7.4) 10 mM NaCl, 3 mM MgCl2, and 0.1% (v/v) IGEPAL CA-630 (Sigma)).
For ATAC-seq library preparation, 50,000 cells were washed once with cold PBS and resuspended in 50 ml of lysis buffer (10 mM Tris-HCl (pH 7.4) 10 mM NaCl, 3 mM MgCl2, and 0.1% (v/v) IGEPAL CA-630 (Sigma)). The suspension was then centrifuged at 500 g for 10minutes at 4°C, followed by the addition of 50 ml of the transposition reaction mixture of the TruePrep DNA Library Prep Kit (Vazyme, TD502). Samples were then incubated at 37°C for 30minutes. Transposition reactions were cleaned up using the MinElute PCR Purification Kit (Qiagen, 28004). ATAC-seq libraries were subjected to five cycles for preamplification and amplified by PCR for an appropriate number of cycles. Amplified libraries were purified using the QIAquick PCR Purification Kit (Qiagen, 28104). Library concentration was measured using the VAHTSTM Library Quantification Kit (Vazyme, NQ101).


title: Skin normal 50

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-50


title: C68_TELC-D5.ATAC_rep1


title: Skin normal 62

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-62


title: Skin normal 49

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-49


title: TSC.H3K27ac_rep1


title: Skin normal 47

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-47


title: Skin normal 48

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-48


title: WT_TELC-D5.ATAC_rep1


title: WT_TELC-D5.ATAC_rep2


title: TELC-D5.TEAD4-/--C171_rep2

data_processing:
For bulk RNA-seq, reads were trimmed of adapters and low-quality reads were removed by fastp62 (v0.21.0) (https://github.com/OpenGene/fastp) with the default option.
Trimmed data were aligned to the Ensembl v76 (hg38) transcript annotations using STAR63 (v2.7.3a) with the settings “--outSAMtype BAM Unsorted, --quantMode TranscriptomeSAM, --outSAMheaderHD\@HD VN:1.4 SO:unsorted.”
Gene counts were calculated using RSEM (v1.2.18) with the settings “--paired-end.”
After removing the genes with zero count in all samples, DEG was determined using DESeq264 (v1.24) in R (v3.6.0).
Assembly: hg38
Supplementary files format and content: Text files include raw count, TPM values and FPKM values

extract_protocol:
Total RNA was isolated using RNAzol (MRC) based on the manufacturer’s instructions.
Bulk RNA-seq library preparation and sequencing were performed at Berry Genomics (Beijing, China).

value: TEAD4 knockout


title: Skin normal 44

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-44


title: Skin normal 45

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-45


title: Skin normal 51

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-51


title: WT_TELC-D5.TEAD4_rep1


title: Skin normal 46

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-46


title: Skin normal 43

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-43


title: TELC-D5.TEAD4-/--C132_rep2


title: TELC-D5.TEAD4-/--C132_rep1


title: TELC-D5.VGLL1-/--C68_rep2


title: Skin normal 38

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-38


title: Skin normal 40

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-40


title: Skin normal 41

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-41


title: TELC-D5.WT_rep2


title: TELC-D5.TEAD4-/--C171_rep1


title: Skin normal 37

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-37


title: TELC-D5.WT_rep1


title: TELC-D5.VGLL1-/--C45_rep2


title: Skin normal 36

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-36


title: Skin normal 39

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-39


title: TSC.shVGLL1-4_rep2

value: VGLL1 knockdown


title: TSC.shVGLL1-4_rep1


title: Skin normal 35

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-35


title: TELC-D5.VGLL1-/--C45_rep1


title: Skin normal 34

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-34


title: TSC.shVGLL1-2_rep2


title: TELC-D5.VGLL1-/--C68_rep1


title: Skin normal 42

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-42


title: Skin normal 32

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-32


title: TSC.shLuc_rep2

value: Luciferase knockdown (control)


title: TSC.shLuc_rep1


title: TSC.shVGLL1-2_rep1


title: Skin normal 29

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-29


title: Skin normal 31

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-31


title: TELC-D5.shTEAD4-2_rep2

value: TEAD4 knockdown


title: Skin normal 30

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-30


title: TELC-D5.shTEAD4-3_rep1


title: Skin normal 27

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-27


title: Skin normal 28

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-28


title: TELC-D5.shTEAD4-3_rep2


title: Skin normal 25

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-25


title: Skin normal 26

description:
Genomic DNA extracted from saliva was genotyped usingInfinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-26


title: TELC-D5.shTEAD4-2_rep1


title: TELC-D5.shLuc_rep2


title: TELC-D5.shVGLL1-2_rep1


title: TELC-D5.shVGLL1-4_rep1


title: TELC-D5.shVGLL1-2_rep2