title: TrueLeaf_batch_11_Litva

value: Litva


title: TrueLeaf_batch_11_Si-0

status: Public on Aug 09 2023

type: SRA

city: Beijing

first: Wenwen

last: Liu

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
Quality control was conducted using fastp version 0.20.0.
Read mapping was performed using the aligner HISAT2 v2.1.0.
The read counts mapped to each gene were quantified using featureCounts.
Potential batch effects were corrected using the ComBat-seq function in the sva software package.
Transcript per million (TPM) gene expression was calculated by normalizing gene length and library size followed by TMM normalization.
Assembly: TAIR10 Arabidopsis Col-0 reference genome
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
Supplementary files format and content: Matrix table with TPM value for every gene and every sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: True leaf

growth_protocol: The plants were grown on MS plates containing 1% sucrose under long-day condition (16-h light at 22°C and 8-h dark at 18°C) after surface-sterilization followed by 7-day stratification of the seeds.

extract_protocol:
flash frozen in liquid nitrogen, and RNA was extracted using an RNeasy Plant Mini Kit (Qiagen), followed by on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: True leaf

tag: developmental stage

value: 15 DAS (days after sowing)

tag: batch

tag: genotype


title: TrueLeaf_batch_11_Ob-0


title: TrueLeaf_batch_11_Kyoto

value: Kyoto


title: TrueLeaf_batch_11_Ber

value: Ber


title: TrueLeaf_batch_10_Col-0


title: TrueLeaf_batch_10_Stw-0


title: TrueLeaf_batch_10_Rd-0


title: TrueLeaf_batch_10_Pog-0


title: TrueLeaf_batch_01_Kil-0_F1

value: Col-0 x Kil-0 F1


title: TrueLeaf_batch_11_ICE119


title: TrueLeaf_batch_09_Col-0


title: TrueLeaf_batch_10_Sha

value: Sha


title: TrueLeaf_batch_10_Mer-6


title: TrueLeaf_batch_10_Old-1


title: TrueLeaf_batch_09_Pt-0


title: TrueLeaf_batch_09_Lm-2


title: TrueLeaf_batch_09_Ler-1


title: TrueLeaf_batch_09_Kro-0


title: TrueLeaf_batch_11_Le-0


title: TrueLeaf_batch_09_Jl-3


title: TrueLeaf_batch_09_Ha-0


title: TrueLeaf_batch_09_Dr-0


title: TrueLeaf_batch_08_ICE29


title: TrueLeaf_batch_09_HR-5


title: TrueLeaf_batch_08_Knox-18


title: TrueLeaf_batch_09_Kar-1


title: TrueLeaf_batch_09_Fei-0


title: TrueLeaf_batch_08_Tottarp-2


title: TrueLeaf_batch_08_Hovdala-2


title: TrueLeaf_batch_10_Pu2-7


title: TrueLeaf_batch_08_El-0


title: TrueLeaf_batch_08_Bla-1


title: TrueLeaf_batch_08_Cerv-1


title: TrueLeaf_batch_10_Hn-0


title: TrueLeaf_batch_08_Da1-12


title: TrueLeaf_batch_07_Col-0


title: TrueLeaf_batch_07_Tscha-1


title: TrueLeaf_batch_07_TDr-1


title: TrueLeaf_batch_07_Sp-0


title: TrueLeaf_batch_07_No-0


title: TrueLeaf_batch_07_Bch-1


title: TrueLeaf_batch_07_Je-0


title: TrueLeaf_batch_07_Baa-1


title: TrueLeaf_batch_06_Col-0


title: TrueLeaf_batch_08_Col-0


title: TrueLeaf_batch_06_Pna-17


title: TrueLeaf_batch_08_ICE150


title: TrueLeaf_batch_06_Nw-0


title: TrueLeaf_batch_06_Koch-1


title: TrueLeaf_batch_05_Col-0


title: TrueLeaf_batch_06_Rou-0


title: TrueLeaf_batch_06_Nok-3


title: TrueLeaf_batch_06_Pla-0


title: TrueLeaf_batch_05_Zal-1


title: TrueLeaf_batch_05_Wl-0


title: TrueLeaf_batch_05_Ws-2


title: TrueLeaf_batch_05_Rubezhnoe-1


title: TrueLeaf_batch_07_ICE163


title: TrueLeaf_batch_05_Ak-1


title: TrueLeaf_batch_07_Bl-1


title: TrueLeaf_batch_04_TueWa1-2


title: TrueLeaf_batch_05_RRS-7


title: TrueLeaf_batch_05_Ey15-2


title: TrueLeaf_batch_04_Er-0


title: TrueLeaf_batch_04_Pro-0


title: TrueLeaf_batch_04_Chat-1


title: TrueLeaf_batch_04_Kl-5


title: TrueLeaf_batch_06_ICE102


title: TrueLeaf_batch_04_Ka-0


title: TrueLeaf_batch_04_HKT2.4


title: TrueLeaf_batch_04_Me-0


title: TrueLeaf_batch_04_Vind-1


title: TrueLeaf_batch_03_Col-0


title: TrueLeaf_batch_03_Ta-0


title: TrueLeaf_batch_05_Yeg-1


title: TrueLeaf_batch_03_Van-0


title: TrueLeaf_batch_03_Ven-1


title: TrueLeaf_batch_03_Vie-0


title: TrueLeaf_batch_04_Ga-0


title: TrueLeaf_batch_03_TueV-13


title: TrueLeaf_batch_04_Col-0


title: TrueLeaf_batch_05_Bay-0


title: TrueLeaf_batch_06_Nemrut-1


title: TrueLeaf_batch_02_Col-0


title: TrueLeaf_batch_03_Tu-0


title: TrueLeaf_batch_02_Ra-0


title: TrueLeaf_batch_02_Wei-0


title: TrueLeaf_batch_02_Kin-0


title: TrueLeaf_batch_02_Com-1


title: TrueLeaf_batch_02_Per-1


title: TrueLeaf_batch_02_Uod-1


title: TrueLeaf_batch_02_C24


title: TrueLeaf_batch_02_Abd-0


title: TrueLeaf_batch_01_Col-0


title: TrueLeaf_batch_01_Kil-0


title: TrueLeaf_batch_01_Bs-1


title: TrueLeaf_batch_01_Gel-1


title: TrueLeaf_batch_05_Westkar-4


title: TrueLeaf_batch_01_Bor-4


title: ShootApex_batch_11_Ts-1_F1

source_name: Shoot apex

value: Shoot apex

value: 6 DAS (days after sowing)

value: Col-0 x Ts-1 F1


title: TrueLeaf_batch_01_Gu-0


title: ShootApex_batch_11_Ob-0_F1

value: Col-0 x Ob-0 F1


title: ShootApex_batch_11_Si-0_F1

value: Col-0 x Si-0 F1


title: ShootApex_batch_11_Pu2-23_F1

value: Col-0 x Pu2-23 F1


title: TrueLeaf_batch_03_Uk-1


title: TrueLeaf_batch_03_Tuescha9


title: ShootApex_batch_11_Le-0_F1

value: Col-0 x Le-0 F1


title: ShootApex_batch_11_Kyoto_F1

value: Col-0 x Kyoto F1


title: ShootApex_batch_11_Ber_F1

value: Col-0 x Ber F1


title: ShootApex_batch_11_ICE119_F1

value: Col-0 x ICE119 F1


title: ShootApex_batch_10_Sha_F1

value: Col-0 x Sha F1


title: ShootApex_batch_10_Stw-0_F1

value: Col-0 x Stw-0 F1


title: ShootApex_batch_10_Pog-0_F1

value: Col-0 x Pog-0 F1


title: ShootApex_batch_10_Pu2-7_F1

value: Col-0 x Pu2-7 F1


title: ShootApex_batch_10_Rd-0_F1

value: Col-0 x Rd-0 F1


title: ShootApex_batch_10_Old-1_F1

value: Col-0 x Old-1 F1


title: ShootApex_batch_10_Mer-6_F1

value: Col-0 x Mer-6 F1


title: TrueLeaf_batch_01_Is-0

value: True leaf

value: 15 DAS (days after sowing)


title: TrueLeaf_batch_01_La-0


title: ShootApex_batch_09_HR-5_F1

value: Shoot apex

value: 6 DAS (days after sowing)

value: Col-0 x HR-5 F1


title: ShootApex_batch_09_Ler-1_F1

value: Col-0 x Ler-1 F1


title: ShootApex_batch_09_Kro-0_F1

value: Col-0 x Kro-0 F1


title: ShootApex_batch_09_Lm-2_F1

value: Col-0 x Lm-2 F1


title: ShootApex_batch_09_Kar-1_F1

value: Col-0 x Kar-1 F1


title: ShootApex_batch_09_Jl-3_F1

value: Col-0 x Jl-3 F1


title: ShootApex_batch_10_Hn-0_F1

value: Col-0 x Hn-0 F1


title: ShootApex_batch_11_Litva_F1

value: Col-0 x Litva F1


title: ShootApex_batch_09_Fei-0_F1

value: Col-0 x Fei-0 F1


title: Control_Mus_Oocyte_2

city: Nanjing

first: Yilong

last: Miao

address: Weigang No.1

institute: Nanjing Agricultural University

data_processing:
uses the filtering software SOAPnuke V1.5.2 developed by BGI independently for filtering
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Bowtie2 V2.2.5 with -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RSEM) were calculated using a protocol from Li, B et al., BMC Bioinformatics, 2011. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RESM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: mouse oocyte

extract_protocol:
RNA contents in 100 oocytes from each group were extracted, and RNA quality was assessed by using Agilent bioanalyzer 2100. Transcriptome library was prepared following NEB Next Ultra RNA library Prep Kit. After mixing libraries based on the set concentration and the standard volume, Illumina Hi Seq platform was applied for sequencing and biological information analyzing.
RNA libraries were prepared for sequencing using standard illumina protocols

tag: strain

value: ICR

tag: cell type

value: mouse oocyte

value: WT

tag: treatment

value: control


title: ShootApex_batch_09_Ha-0_F1

value: Col-0 x Ha-0 F1


title: BBP_Mus_Oocyte_2

value: Benzyl butyl phthalate (BBP)


title: ShootApex_batch_08_Knox-18_F1

value: Shoot apex

value: Col-0 x Knox-18 F1


title: ShootApex_batch_08_ICE29_F1

value: 6 DAS (days after sowing)

value: Col-0 x ICE29 F1


title: ShootApex_batch_08_ICE150_F1

value: Col-0 x ICE150 F1


title: ShootApex_batch_08_Hovdala-2_F1

value: Col-0 x Hovdala-2 F1


title: ShootApex_batch_09_Pt-0_F1

value: Col-0 x Pt-0 F1


title: ShootApex_batch_08_El-0_F1

value: Col-0 x El-0 F1


title: HEK293T cells, non-N-glycosylated SIDT1_2

first: Tingting

last: Yang

state: Jiangsu

address: No. 163 Xianlin Road

institute: Nanjing University

data_processing:
PCR products corresponding to 200-500 base pairs were enriched, quantified, and finally sequenced on a DNBSEQ-T7 sequencer (PE150, MGI)
Reads were mapped to the Cyprinus carpio genome using STAR (version 2.5.3a) with default parameters
The mapped reads were analyzed by feature Counts (Subread-1.5.1; Bioconductor)
Differential expression genes were estimated by the edgeR package (version 3.12.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 50 units/mL penicillin and 100 µg/mL streptomycin.Cells were then transfected with empty vector pcDNA3.1(+), wild-type SIDT1, and non-N-glycosylated SIDT1. Total RNA was extracted using a Trizol reagent (Invitrogen, USA) and was used for stranded RNA sequencing library preparation using a KCTM Stranded mRNA Library Prep Kit for Illumina® following the manufacturer's instruction. 1.3 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using KCTM Stranded mRNA Library Prep Kit following manufacturer's protocols.

tag: cell line

value: human embryonic kidney

value: non-N-glycosylated SIDT1 overexpression


title: HEK293T cells, non-N-glycosylated SIDT1_3

extract_protocol:
Total RNA was extracted using a Trizol reagent (Invitrogen, USA) and was used for stranded RNA sequencing library preparation using a KCTM Stranded mRNA Library Prep Kit for Illumina® following the manufacturer's instruction. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KCTM Stranded mRNA Library Prep Kit  following manufacturer's protocols.


title: ShootApex_batch_08_Da1-12_F1

value: Col-0 x Da1-12 F1


title: ShootApex_batch_08_Cerv-1_F1

value: Col-0 x Cerv-1 F1


title: HEK293T cells, wild-type SIDT1_2

value: wild-type SIDT1 overexpression


title: HEK293T cells, non-N-glycosylated SIDT1_1


title: HEK293T cells, wild-type SIDT1_1


title: ShootApex_batch_07_TDr-1_F1

value: Col-0 x TDr-1 F1


title: HEK293T cells, Control_2

value: WT


title: ShootApex_batch_08_Bla-1_F1

value: Col-0 x Bla-1 F1


title: ShootApex_batch_09_Dr-0_F1

value: Col-0 x Dr-0 F1


title: ShootApex_batch_07_Tscha-1_F1

value: Shoot apex

value: Col-0 x Tscha-1 F1


title: ShootApex_batch_08_Tottarp-2_F1

value: 6 DAS (days after sowing)

value: Col-0 x Tottarp-2 F1


title: HEK293T cells, Control_3


title: ShootApex_batch_07_No-0_F1

value: Col-0 x No-0 F1


title: ShootApex_batch_07_Je-0_F1

value: Col-0 x Je-0 F1


title: Control_Mus_Oocyte_1

value: ICR

value: mouse oocyte

value: control


title: ShootApex_batch_07_ICE163_F1

value: Col-0 x ICE163 F1


title: BBP_Mus_Oocyte_1

value: Benzyl butyl phthalate (BBP)


title: HEK293T cells, Control_1

value: human embryonic kidney


title: ShootApex_batch_07_Sp-0_F1

value: Col-0 x Sp-0 F1


title: Tumor organoid, alectinib resistant [FA34OA]

city: Hong Kong

first: Hoi-Hin

last: Kwok

address: Sassoon Road

institute: The University of Hong Kong

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequenced scRNA-seq samples were processed through Cellranger pipelines (v4.0.0). Cellranger count was used to align reads to human reference genome (GRCh38-3.0.0, from 10x Genomics) and to generate single cell feature counts for single library. Seurat (3.2.1) package was used for multiple library data integration and downstream analysis including singlet filtration, dimensional reduction, data scaling, clustering and markers identification.
Assembly: GRCh38-3.0.0, from 10x Genomics
Supplementary files format and content: Tab-separated values files, barcode files, and matrix files

source_name: Non-small cell lung cancer, Metastatic pleural effusion, Female, Stage IV

growth_protocol: The tumor organoids were cultured in Cultrex growth factor reduced basement membrane extract in PneumaCult™-Ex Plus Medium and then incubated at 37°C and 5% CO2.

extract_protocol:
The prepared cell suspension is coated with a bead and a cell with a cell barcode in a droplet using a microfluidic chip, and a droplet containing the cell is collected, in the droplet. The cells are lysed so that the mRNA in the cells is connected to the cell barcode on the bead to form single cell GEMs (Gel Bead-in-Emulsions).
RT reaction is carried out in the droplets, followed by demulsification to construct a  cDNA library. The cell barcode on the library sequence can distinguish which cell the target sequence is from, and the sample index on the sequence can distinguish which sample  the target sequence is from.

treatment_protocol: TKI sensitive tumor organoids TS485TOS and FA34OS were cultured in usual condition. Crizotinib treatment for TS485TOC and FA34OC. Alectinib treatment for TS485TOA and FA34OA.

tag: Sex

value: Female

tag: disease

value: Non-small cell lung cancer

tag: Stage

value: IV

value: Tumor organoid

value: Adenocarcinoma

value: Metastatic pleural effusion


title: Tumor organoid, crizotinib resistant [FA34OC]

description: 10X Genomics


title: Tumor organoid, TKI sensitive [FA34OS]

description: 10X Genomics

source_name: Non-small cell lung cancer, Female, Stage IV


title: Tumor organoid, crizotinib resistant [TS485TOC]

description: 10X Genomics

source_name: Non-small cell lung cancer, Resected primary tumor,  Male, Stage IIA

value: Male

value: IIA

value: Resected primary tumor


title: HEK293T cells, wild-type SIDT1_3

value: wild-type SIDT1 overexpression


title: ShootApex_batch_07_Bch-1_F1

value: Shoot apex

value: 6 DAS (days after sowing)

value: Col-0 x Bch-1 F1


title: Tumor organoid, TKI sensitive [TS485TOS]

description: 10X Genomics

source_name: Non-small cell lung cancer, Male, Stage IIA


title: ShootApex_batch_07_Baa-1_F1

value: Col-0 x Baa-1 F1


title: ShootApex_batch_06_Pla-0_F1

value: Col-0 x Pla-0 F1


title: Spn delta spxB (2)

city: Giessen

first: Mobarak

last: Abu Mraheil

state: Hessen

address: Schubertstrasse 81

department: Institute for Medical Microbiology

country: Germany

institute: Justus-Liebig University Giessen

data_processing:
The sequenced reads were image-processed, basecalled, and demultiplexed
All reads obtained were aligned to Streptococcus pneumoniae strain D39 (NCBI GCF_023635025.1_ASM2363502v1) using STAR (Dobin et al., 2013)
Aligned reads were sorted by position using samtools (Li et al., 2009)
Read counts per gene or transcript were calculated for each library using the subread function featureCounts (Liao et al., 2014)
Differential gene expression analyses were performed with the R-package DESeq2
Assembly: Streptococcus pneumoniae strain D39 (NCBI GCF_023635025.1_ASM2363502v1)
Supplementary files format and content: Tab-seperated text-file includes counts for each sample

organism: Streptococcus pneumoniae

source_name: bacteria

extract_protocol:
S. pneumoniae cultures (OD600nm 1.0) were aliquoted to 0.5 ml and treated with 1.0 ml RNA protect (Qiagen) for 5 min at RT. Bacterial cells were then collected by centrifugation at 13.000 rpm for 5 min and stored at -80°C.  RNA was isolated using the miRNAse kit (Qiagen), and the protocol was modified as follows. The collected bacterial pellets were thawed and washed with SET buffer [50 mM NaCl, 5 mM EDTA, and 30 mM Tris-HCl (pH 7.0)]. Subsequently, cells were centrifuged at 16.000 g for 3 min, and pellets were resuspended in Tris-HCl (pH 6.5) containing 40 U of SUPERase, 0.2 mg of proteinase K (Ambion), 50 mg/ml lysozyme (Sigma), and 25 U of mutanolysin (Sigma). After incubation for 30 min at 37 °C and 350 rpm, QIAzole (Qiagen) was added for 3 min at RT. Then, 0.2 volume chloroform was added followed by incubation for 3 min at RT. After centrifugation (16.000 x g at 4°C for 15 min)Tthe upper aqueous phase containing the RNA was transferred to a new collection tube. 1.5 volume ethanol (100%) was added to the sample and mixed. The aqueous phase and ethanol were transferred to miRNeasy Kit column (Qiagen) and treated according to the user’s manual.
Total RNA was depleted of ribosomal RNA with NEBNext® rRNA Depletion Kit v2 (Bacteria) (New England Biolabs, Ipswich, MA, USA) and Agencourt RNAClean XP beads (Beckman Coulter, Pasadena, CA, USA). Fragmentation and library preparation was then performed according to the manufacturer’s instructions using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina. To facilitate multiplex sequencing, NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (New England Biolabs, Ipswich, MA, USA) was used to barcode the reads.  Libraries were further purified with Agencourt AMPure XP Reagent (Beckman Coulter, Pasadena, CA, USA).

value: bacteria

value: spxB knockdown


title: Spn delta spxB (1)


title: ShootApex_batch_06_Pna-17_F1

value: Col-0 x Pna-17 F1


title: Spn delta lctO (2)

value: lcto knockdown


title: ShootApex_batch_06_Rou-0_F1

value: Col-0 x Rou-0 F1


title: Spn delta lctO (1)


title: ShootApex_batch_06_Nw-0_F1

value: Col-0 x Nw-0 F1


title: Spn delta lctO delta spxB (3)

value: lctO and spxB knockdown


title: Spn delta lctO delta spxB (1)


title: ShootApex_batch_06_ICE102_F1

value: Col-0 x ICE102 F1


title: ShootApex_batch_06_Nok-3_F1

value: Col-0 x Nok-3 F1


title: ShootApex_batch_06_Nemrut-1_F1

value: Col-0 x Nemrut-1 F1


title: ShootApex_batch_06_Koch-1_F1

value: Col-0 x Koch-1 F1


title: Spn wt (1)

value: WT


title: ShootApex_batch_05_Yeg-1_F1

value: Shoot apex

value: Col-0 x Yeg-1 F1


title: ShootApex_batch_05_Ws-2_F1

value: 6 DAS (days after sowing)

value: Col-0 x Ws-2 F1


title: ShootApex_batch_05_Zal-1_F1

value: Col-0 x Zal-1 F1


title: B6 female_H11

type: genomic

city: MINNEAPOLIS

first: Maureen

last: Cetera

state: MN

address: 515 Delaware St SE, Moos room 5-143

country: USA

institute: University of Minnesota-Twin Cities

hyb_protocol: Microarray experiment performed by: Applied Biosystems Axiom Genotyping Services

data_processing: primary data description Genotype Call (SNP call): nucleotide nucleotide and NoCall 0 0

label: biotin

molecule: genomic DNA

source_name: mouse ear punch/tail clip

extract_protocol: DNA was extracted from ear punches or tail clips using the Qiagen DNeasy Blood and Tissue kit. We sent high molecular weight DNA to FisherScientific for genotyping array service using the Affymetrix Mouse Diversity Array.

tag: fur phenotype


title: Spn wt (3)

value: bacteria


title: ShootApex_batch_07_Bl-1_F1

value: Col-0 x Bl-1 F1


title: B6 male

scan_protocol: Microarray experiment performed by: Applied Biosystems Axiom Genotyping Services


title: Spn wt (2)


title: B6 female_H10

label_protocol: Microarray experiment performed by: Applied Biosystems Axiom Genotyping Services


title: ShootApex_batch_05_Wl-0_F1

value: Col-0 x Wl-0 F1


title: 105802F4LLLLRR_H09


title: ShootApex_batch_05_Westkar-4_F1

value: Col-0 x Westkar-4 F1


title: 105801F4RRRRLL_H08


title: ShootApex_batch_05_Rubezhnoe-1_F1

value: Col-0 x Rubezhnoe-1 F1


title: 1031-1blkF3RRRRLLL_H07


title: ShootApex_batch_05_RRS-7_F1

value: Col-0 x RRS-7 F1


title: ShootApex_batch_05_Bay-0_F1

value: Col-0 x Bay-0 F1


title: Spn delta lctO delta spxB (2)

value: lctO and spxB knockdown


title: original brother


title: ShootApex_batch_05_Ey15-2_F1

value: Col-0 x Ey15-2 F1


title: ShootApex_batch_05_Ak-1_F1

value: Col-0 x Ak-1 F1


title: ShootApex_batch_04_Chat-1_F1

value: Col-0 x Chat-1 F1


title: ShootApex_batch_04_Pro-0_F1

value: Col-0 x Pro-0 F1


title: Tumor organoid, alectinib resistant [TS485TOA]

description: 10X Genomics

value: Male

value: Non-small cell lung cancer

value: IIA

value: Tumor organoid

value: Adenocarcinoma

value: Resected primary tumor


title: 10390-1LLLLR


title: 12150-1LLLLRRR


title: 12151-1RRRLL


title: ShootApex_batch_04_Kl-5_F1

value: Shoot apex

value: 6 DAS (days after sowing)

value: Col-0 x Kl-5 F1


title: ShootApex_batch_04_Er-0_F1

value: Col-0 x Er-0 F1


title: 12130-1RRLLL


title: 12130-2RRRLL


title: 12120-4LLLLRRR


title: ShootApex_batch_04_HKT2.4_F1

value: Col-0 x HKT2.4 F1


title: 12120-5LLLR


title: ShootApex_batch_04_TueWa1-2_F1

value: Col-0 x TueWa1-2 F1


title: 12120-3RRLBrn


title: ShootApex_batch_04_Me-0_F1

value: Col-0 x Me-0 F1


title: ShootApex_batch_04_Vind-1_F1

value: Col-0 x Vind-1 F1


title: ShootApex_batch_04_Ka-0_F1

value: Col-0 x Ka-0 F1


title: 12120-1RRRRLLLL


title: 12120-2RRR


title: ShootApex_batch_04_Ga-0_F1

value: Col-0 x Ga-0 F1


title: original stud_H06


title: ShootApex_batch_03_Ta-0_F1

value: Col-0 x Ta-0 F1


title: ShootApex_batch_03_Vie-0_F1

value: Col-0 x Vie-0 F1


title: 12100-5LLLRR


title: 12100-4RRRLL


title: ShootApex_batch_03_Van-0_F1

value: Col-0 x Van-0 F1


title: 10720-1LRRRR


title: 10720-2LLLLR


title: 12100-3RRLLLL


title: ShootApex_batch_03_Ven-1_F1

value: Col-0 x Ven-1 F1


title: ShootApex_batch_03_Tuescha9_F1

value: Col-0 x Tuescha9 F1


title: ShootApex_batch_03_Tu-0_F1

value: Col-0 x Tu-0 F1


title: ShootApex_batch_03_TueV-13_F1

value: Col-0 x TueV-13 F1


title: 12090-1LLRRR


title: 12100-1RRL


title: ShootApex_batch_03_Uk-1_F1

value: Shoot apex

value: Col-0 x Uk-1 F1


title: 12100-2RRRRLLL


title: ShootApex_batch_02_Wei-0_F1

value: 6 DAS (days after sowing)

value: Col-0 x Wei-0 F1


title: 12070-6LLRRBrn


title: 12070-4RRR


title: 12070-5RRRRLLL


title: ShootApex_batch_02_Uod-1_F1

value: Col-0 x Uod-1 F1


title: ShootApex_batch_02_Ra-0_F1

value: Col-0 x Ra-0 F1


title: 12070-3LLLLRRRR


title: ShootApex_batch_02_Per-1_F1

value: Col-0 x Per-1 F1


title: 12070-2LLLLRRR


title: 12070-1LLLR


title: 10370-5LLLRRRR


title: ShootApex_batch_02_Com-1_F1

value: Col-0 x Com-1 F1


title: ShootApex_batch_02_C24_F1

value: Col-0 x C24 F1


title: 10370-3LLRRRR


title: ShootApex_batch_02_Kin-0_F1

value: Col-0 x Kin-0 F1


title: ShootApex_batch_02_Abd-0_F1

value: Col-0 x Abd-0 F1


title: 10370-2LLLRRR


title: 105802F4LLLLRR_E12


title: 105801F4RRRRLL_E11


title: ShootApex_batch_01_Kil-0_F1

value: Col-0 x Kil-0 F1


title: 10370-1RRLLLL


title: ShootApex_batch_01_Gu-0_F1

value: Col-0 x Gu-0 F1


title: 1031-1blkF3RRRRLLL_E10


title: ShootApex_batch_01_Bor-4_F1

value: Col-0 x Bor-4 F1


title: original stud_E09


title: 11762-TGN4LLLLRRR


title: ShootApex_batch_01_Is-0_F1

value: Col-0 x Is-0 F1


title: 11762-TGN3LLLRRRR


title: 11762-TGN2RRLBrn


title: ShootApex_batch_11_Col-0


title: ShootApex_batch_11_Ts-1


title: 11760-TGN11RRRRLLL


title: 11762-TGN1RRR


title: ShootApex_batch_01_La-0_F1

value: Col-0 x La-0 F1


title: ShootApex_batch_11_Si-0


title: ShootApex_batch_01_Bs-1_F1

value: Col-0 x Bs-1 F1


title: ShootApex_batch_11_Le-0

value: Shoot apex


title: ShootApex_batch_11_Litva

value: Litva


title: ShootApex_batch_11_Ob-0

value: 6 DAS (days after sowing)


title: ShootApex_batch_11_Pu2-23


title: ShootApex_batch_11_Kyoto

value: Kyoto


title: ShootApex_batch_01_Gel-1_F1

value: Col-0 x Gel-1 F1


title: ShootApex_batch_11_Ber

value: Ber


title: ShootApex_batch_11_ICE119


title: ShootApex_batch_10_Stw-0


title: ShootApex_batch_10_Col-0


title: ShootApex_batch_10_Sha

value: Sha


title: 11611-TGN11RRRRL


title: 11611-TGN9LLLRR


title: 11611-TGN14RRRRL


title: 11760-TGN9RRRRLLL


title: 11760-TGN7RRRRLLL


title: 11760-TGN6LLLLRRR


title: 11611-TGN13LLLRR


title: 11760-TGN10LLLLRRR


title: 11611-TGN12LLLLR


title: 11611-TGN10LLLRR


title: 11760-TGN8RRL


title: 11611-TGN8RRRLL


title: 11611-TGN7LLLLR


title: ShootApex_batch_10_Rd-0


title: ShootApex_batch_10_Pog-0


title: ShootApex_batch_10_Pu2-7


title: 11610-TGN18RRRLL


title: 11610-TGN16LLRR


title: 11610-TGN17LLLRR


title: ShootApex_batch_10_Mer-6


title: ShootApex_batch_10_Hn-0


title: ShootApex_batch_09_Col-0


title: 11610-TGN15LLLR


title: ShootApex_batch_09_Pt-0


title: 11610-TGN14LLLRR


title: ShootApex_batch_09_Lm-2


title: ShootApex_batch_09_Ler-1


title: 11610-TGN13RRRLL


title: 11610-TGN12LLRR


title: 11610-TGN11LLLL


title: ShootApex_batch_09_Kro-0


title: 11762-TGP4LLLRRR


title: ShootApex_batch_10_Old-1


title: ShootApex_batch_09_HR-5


title: 11761-TGP5


title: 11762-TGP3LLLLRRRR


title: 11762-TGP1LLLBrn


title: 11761-TGP6


title: ShootApex_batch_09_Jl-3


title: ShootApex_batch_09_Kar-1


title: ShootApex_batch_09_Dr-0


title: 11761-TGP4


title: ShootApex_batch_08_Col-0


title: ShootApex_batch_09_Fei-0


title: 11761-TGP2


title: 11761-TGP1


title: 11761-TGP3


title: 11760-TGP4RRRLL


title: ShootApex_batch_08_Tottarp-2


title: ShootApex_batch_08_El-0


title: ShootApex_batch_08_Knox-18


title: 11762-TGP2RRL


title: ShootApex_batch_08_Hovdala-2


title: ShootApex_batch_08_Da1-12


title: 11760-TGP3LLLRRR


title: ShootApex_batch_08_ICE150


title: 11760-TGP2LLLRR


title: ShootApex_batch_09_Ha-0


title: 11611-TGP5LLLRR brn


title: 11611-TGP4RRL


title: 11760-TGP1LLLRRR


title: ShootApex_batch_07_Col-0


title: ShootApex_batch_08_Bla-1


title: ShootApex_batch_08_ICE29


title: ShootApex_batch_07_Sp-0


title: ShootApex_batch_08_Cerv-1


title: 11611-TGP1LLLRR brn


title: ShootApex_batch_07_TDr-1


title: ShootApex_batch_07_No-0


title: 11611-TGP2LLLRR


title: ShootApex_batch_07_Je-0


title: 11610-TGP9RRLLL


title: 11610-TGP10RRRLLL


title: ShootApex_batch_07_ICE163


title: 11610-TGP7LLLLRRR


title: 11611-TGP6RRRLL


title: ShootApex_batch_07_Bl-1


title: ShootApex_batch_06_Col-0


title: 11610-TGP8RRRRL


title: ShootApex_batch_07_Bch-1


title: 11610-TGP3LLLR


title: 11610-TGP6RRRLLL


title: 11610-TGP4LLLL


title: ShootApex_batch_07_Baa-1


title: 11611-TGP3RRR


title: 11610-TGP2LLLRR


title: ShootApex_batch_07_Tscha-1


title: 11610-TGP1LLLRR Brn


title: ShootApex_batch_06_Rou-0


title: ShootApex_batch_06_Nw-0


title: 200053740003_R06C02

city: Baltimore

first: Yuba

middle: R

last: Bhandari

state: MD

address: 1650 Orleans Street

institute: The Johns Hopkins University School of Medicine

description:
LESION: adenoma at baseline
AGE: age (years)
IS_FEMALE: 1=F, 0=M
ADEN_GRADE: grading score adenoma
ADEN_SIZE: size (mm)
ADEN_LEFT: adenoma located at left colon
ADEN_3PLUS: 3 or more adenomas in patient
ADEN_LT_1CM: adenoma larger than 1 cm
ADEN_HAS_HGD: adenoma has high grade dysplasia

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
Data belonging to both 450K and EPIC platform was normalized using "preprocessFunnorm" subroutine from "Minfi" package version 1.42.0.
450k_matrix.txt: methylation β-values (ratio of the methylated probe intensity and the overall intensity)

label: Cy3, Cy5

source_name: FFPE sample

label_protocol: not provided

extract_protocol: DNA was extracted from 2-3 slices (10 µm) from the FFPE samples (Qiagen), quantified using PicoGreen and checked for quality using the Illumina FFPE QC Kit. The DNA was then subjected to bisulfite conversion (EZ DNA methylation kit, Zymo Research) and controlled by two in-house qPCRs. Next, 250 ng DNA was subjected to Illumina’s FFPE restoration protocol. Data were processed in two batches: the first batch was profiled on Illumina Infinium 450K beadchips, the second batch was run on Infinium EPIC (850K) beadchips.

tag: patientid

tag: lesion

tag: age

tag: bmi

value: colon polyp


title: 200053740003_R05C02


title: ShootApex_batch_06_ICE102


title: 200053740003_R03C02


title: ShootApex_batch_06_Nok-3


title: 200053740003_R02C02


title: 11610-TGP5LLRRRR


title: ShootApex_batch_06_Nemrut-1


title: ShootApex_batch_06_Koch-1


title: ShootApex_batch_05_Col-0


title: ShootApex_batch_05_Zal-1


title: ShootApex_batch_06_Pna-17


title: ShootApex_batch_05_Yeg-1


title: ShootApex_batch_06_Pla-0


title: ShootApex_batch_05_Ws-2


title: 200053740003_R05C01


title: 200053740003_R02C01


title: ShootApex_batch_05_Westkar-4


title: 200053740003_R06C01


title: 200053740003_R04C01


title: 200053740003_R03C01


title: 200053740091_R06C02


title: ShootApex_batch_05_Wl-0


title: ShootApex_batch_05_RRS-7


title: ShootApex_batch_05_Rubezhnoe-1


title: 200053740091_R04C02


title: 200053740003_R04C02


title: ShootApex_batch_05_Bay-0


title: ShootApex_batch_05_Ak-1


title: 200053740091_R01C02


title: 200053740091_R05C01


title: ShootApex_batch_04_Chat-1


title: ShootApex_batch_04_Pro-0


title: 200053740091_R04C01


title: ShootApex_batch_04_Col-0


title: 200053740091_R02C01


title: 200053740003_R01C02


title: 200053740091_R03C01


title: 200053740091_R01C01


title: ShootApex_batch_04_TueWa1-2


title: ShootApex_batch_04_Er-0


title: 200053740089_R06C02


title: ShootApex_batch_04_Kl-5


title: ShootApex_batch_04_Ka-0


title: 200053740091_R05C02


title: 200053740089_R04C02


title: ShootApex_batch_04_Me-0


title: 200053740089_R01C02


title: ShootApex_batch_05_Ey15-2


title: ShootApex_batch_04_HKT2.4


title: 200053740089_R06C01


title: ShootApex_batch_04_Vind-1


title: 200053740089_R05C01


title: ShootApex_batch_04_Ga-0


title: ShootApex_batch_03_Col-0


title: 200053740089_R04C01


title: ShootApex_batch_03_Ta-0


title: ShootApex_batch_03_Vie-0


title: 200053740089_R02C01


title: ShootApex_batch_03_Ven-1


title: 200053740089_R03C01


title: ShootApex_batch_03_Van-0


title: 10011071005_R05C02


title: ShootApex_batch_03_Tuescha9


title: 200053740089_R03C02


title: 200053740089_R02C02


title: ShootApex_batch_03_TueV-13


title: 10011071005_R03C02


title: ShootApex_batch_03_Tu-0


title: D2 primary oviductal muscle cell Pbrm1 KO1

city: Bethesda

first: qiliang

last: Xin

address: 50 South Dr

department: NIDDK

institute: NIH

data_processing:
removing adapter sequences with cutadapt
aligning the reads with hisat2 against Mus musculus genome sequence
using featurecounts to estimate the number of gene reads
using a R script to perform differential expression analysis
Assembly: GRCm38.p5
Supplementary files format and content: featurecounts output  and fastq files

source_name: primary oviductal muscle cell

growth_protocol: The mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Oviduct isolated from 8-12 weeks aged control and knockout mice.

extract_protocol:
Oviduct were isolated and cut into small pieces (1-2 mm) and incubated (30-45 min) in rotation at 37 ℃ in pre-warmed DMEM/F12 (1:1) (Gibco), 12 mM HEPES (Gibco), 1% penicillin/streptomycin (Gibco), 2 mg/ml trypsin (Sigma), 400 U/ml collagenase type I (Invitrogen), and 5 U/ml dispase (Invitrogen). The digested cells were passed through a 70-mm filter to obtain a homogenous population of smooth muscle cells. Cells were plated in 100 mm dishes, containing DMEM and Ham F-12 media (1:1) (Gibco) with 12% charcoal-stripped fetal bovine serum (FBS) and antibiotics (penicillin-streptomycin, Thermo Fisher, 100 µg/mL). After 4 h, the medium was replaced with DMEM/F-12 (1:1) containing 10% FBS. 2 h later, the cells were gently washed twice with PBS and samples were prepared for RNA-seq. total RNA was isolated using a RNeasy Micro Kit.
The libraries were constructed by using a Universal RNA-Seq Library Preparation Kit (TECAN) per the manufacturer’s protocol in which double-strand cDNA was generated using a mixture of random and poly(T) priming, followed by fragmentation of double-stranded cDNA, end repair, adaptor ligation, strand selection, targeted transcript depletion with AnyDeplete, and PCR amplification to produce the final library.

treatment_protocol: Mate with stud male for pregrancy.

value: primary oviductal muscle cell

value: Pbrm1 cKO

value: Day 2 of pregrancy

tag: time

value: Day 2


title: ShootApex_batch_03_Uk-1

tag: tissue


title: 10011071005_R02C02


title: ShootApex_batch_02_Wei-0

tag: developmental stage


title: ShootApex_batch_02_Col-0

tag: batch


title: ShootApex_batch_02_Uod-1

tag: genotype


title: 10011071005_R01C02


title: D2 primary oviductal muscle cell WT3

value: WT


title: ShootApex_batch_02_Ra-0


title: D2 primary oviductal muscle cell WT2


title: ShootApex_batch_02_Kin-0


title: 10011071005_R06C01


title: D2 primary oviductal muscle cell WT1


title: D2 primary oviductal muscle cell Pbrm1 KO3


title: 10011071005_R04C01


title: ShootApex_batch_02_C24


title: ShootApex_batch_01_Col-0


title: ShootApex_batch_02_Com-1


title: ShootApex_batch_01_Bs-1


title: D2 primary oviductal muscle cell Pbrm1 KO2


title: miRNA-Seq - AsPC-1 cells, remove thapsigargin treatment, 4 days, rep2

city: Wuhan

first: Jingfeng

last: Li

address: Xiao hong shan zhong qu

department: Wuhan Institute of Virology

institute: University of Chinese Academy of Sciences

data_processing:
The libraries were sequenced using a MGISEQ-2000 platform (MGI Tech, Shenzhen, China). Raw data (raw reads) of the fastq format were first processed using SOAPnuke (v1.5.6).
For mRNA, lncRNA and circRNA sequencing, clean reads were obtained by removing adapter-containing reads, poly-N-containing reads, and low-quality reads from the raw data and followed by mapping to the Homo sapiens genome sequence (GCF_000001405.39_GRCh38.p13) using HISAT2 (version 2.1.0).
For miRNA sequencing, clean reads were obtained by removing low-quality reads, tag with 5’ adapter pollution, tag without 5’ adapter, tag without insert fragment, tag containing poly-A and tag less than 15 nt, the miRNA reads were aligned to known mature human microRNA sequences using Bowtie (v 2.0.6).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM, TPM and Reads count values for each Sample

growth_protocol: AsPC-1 cells were cultured in RPMI1640 medium supplemented with heat-inactivated 10% fetal bovine serum, 1.5 g/L sodium bicarbonate, 4.5 g/L glucose, 3 g/L HEPES, 1 mmol/L sodium pyruvate, 1% GlutaMAXTM-1, 1% antibiotic penicillin–streptomycin solution in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme) as instructed.
Sequencing libraries of total RNA were generated using MGIEasy RNA Library Prep Kit (MGI Tech) following manufacturer’s instructions, and the sequencing libraries of miRNA were generated using MGIEasy Small RNA Library Prep Kit (MGI Tech).

treatment_protocol: To develop persistent ER stress cell model, AsPC-1 cells were cultured in their media containing 30 nM Tg for more than 14 days and maintained under the same condition, these cells were designated as AsPC-1-Tg. The AsPC-1-Tg cells were cultured in the media removal Tg for more than 4 days were designated as AsPC-1-Tg -RE.

value: pancreatic ductal adenocarcinoma cells

value: remove thapsigargin treatment

value: 4 days


title: 10011071005_R03C01


title: 10011071005_R04C02


title: miRNA-Seq - AsPC-1 cells, 30 nM thapsigargin, 14 days, rep3

value: 30 nM thapsigargin

value: 14 days


title: ShootApex_batch_01_Bor-4

value: Shoot apex


title: ShootApex_batch_01_Kil-0

value: 6 DAS (days after sowing)


title: ShootApex_batch_01_Is-0


title: ShootApex_batch_02_Per-1


title: ShootApex_batch_01_Gu-0


title: 10011071005_R01C01


title: 10011071005_R02C01


title: 3999834088_R06C02


title: ShootApex_batch_01_La-0


title: 3999834088_R04C02


title: miRNA-Seq - AsPC-1 cells, remove thapsigargin treatment, 4 days, rep1


title: miRNA-Seq - AsPC-1 cells, No treatment, rep3

value: No treatment

value: 0 day


title: miRNA-Seq - AsPC-1 cells, remove thapsigargin treatment, 4 days, rep3


title: miRNA-Seq - AsPC-1 cells, 30 nM thapsigargin, 14 days, rep1


title: Heart, A6, Aging

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
Left ventricular  samples were homogenized as described previously by using the Direct-zol RNA Miniprep Kit including on-column DNase treatment (Zymo Research, Irvine, CA, USA). RNA was reverse transcribed to cDNA using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Heart

tag: condition

value: rat model of advanced aging

value: control


title: Heart, A10, Aging


title: miRNA-Seq - AsPC-1 cells, 30 nM thapsigargin, 14 days, rep2

tag: cell type


title: ShootApex_batch_02_Abd-0


title: Heart, A5, Aging

tag: treatment


title: miRNA-Seq - AsPC-1 cells, No treatment, rep2

tag: cell line


title: Heart, A2, Aging


title: Heart, A4, Aging


title: 3999834088_R02C02

value: colon polyp


title: ShootApex_batch_01_Gel-1


title: Heart, A1, Aging


title: miRNA-Seq - AsPC-1 cells, No treatment, rep1


title: Heart, Y7, Young

value: Young


title: 3999834088_R01C02


title: RNA-Seq - AsPC-1 cells, remove thapsigargin treatment, 4 days, rep3


title: Heart, Y6, Young


title: 3999834088_R06C01


title: Heart, Y5, Young


title: 3999834088_R05C01


title: RNA-Seq - AsPC-1 cells, remove thapsigargin treatment, 4 days, rep2


title: Heart, Y4, Young


title: 3999834088_R04C01


title: RNA-Seq - AsPC-1 cells, remove thapsigargin treatment, 4 days, rep1


title: Heart, Y1, Young


title: 3999834088_R03C02


title: RNA-Seq - AsPC-1 cells, 30 nM thapsigargin, 14 days, rep3


title: 3999834088_R01C01


title: RFID 933000320045785 (low), snATAC-seq

city: La Jolla

first: Jessica

middle: Lu

last: Zhou

state: California

address: 9500 Gilman Drive

institute: University of California San Diego

description: Single cell open chromatin sites from amygdala

library_source: genomic

data_processing:
Sequencing reads were aligned to the Ensembl Rattus norvegicus v98 Rnor_6.0 genome assembly using the 10X Cell Ranger Pipeline
Assembly: Rnor_6.0/rn6
Supplementary files format and content: Tab-separated values files and matrix files, and additional Cell Ranger output files.
Supplementary files format and content: signac.rds: Integrated Signac object that contains all of the snATAC-seq data across all 12 of the snATAC-seq samples.

source_name: Amygdala

growth_protocol: Male Heterogenous Stock (HS) rats were trained to self-administer drugs in short access conditions (2 h/day for for 10 days for cocaine) followed by long access conditions (6 h /day for cocaine) for 14 days to develop escalation of drug intake. Rats are also tested for motivation with progressive ratio sessions and for compulsivity with shock-paired sessions. Rats are classified as having low or high addiction index based on different behavioral measures. Brain punches of amygdala tissues were collected after 4 weeks of abstinence.

extract_protocol:
Brain tissues were extracted and snap-frozen. Cryosections of approximately 500 microns were used to dissect amygdala punches with a cryostat using a –20°C frozen stage. Single nuclei were isolated after tissue homogenization and iodixanol gradient purificaiton.
following the manifacturer's manual for Chromium™ Single Cell ATAC v1 Library kit (10x Genomics)

tag: strain

value: Heterogenous Stock (HS)

tag: Sex

value: Male

value: Amygdala

value: cocaine

value: low addition


title: RFID 933000320047174 (naïve), snATAC-seq

value: naive


title: RNA-Seq - AsPC-1 cells, 30 nM thapsigargin, 14 days, rep2

value: pancreatic ductal adenocarcinoma cells

value: WT

value: 30 nM thapsigargin


title: RFID 933000320046611 (low), snATAC-seq


title: 3999834088_R02C01


title: RFID 933000320187092 (high), snATAC-seq

value: high addition


title: 3999834051_R06C02


title: RFID 933000320047019 (high), snATAC-seq


title: RNA-Seq - AsPC-1 cells, 30 nM thapsigargin, 14 days, rep1

value: 14 days


title: RFID 933000320047161 (naïve), snATAC-seq


title: RFID 933000120138414 (low), snATAC-seq


title: RFID 933000120138730 (high), snATAC-seq


title: RFID 933000320047651 (naïve), snATAC-seq


title: 3999834051_R05C02


title: Heart, Y3, Young


title: RFID 933000320187130 (naïve), snATAC-seq


title: RNA-Seq - AsPC-1 cells, No treatment, rep2

value: No treatment

value: 0 day


title: RFID 933000320047166 (low), snATAC-seq


title: RNA-Seq - AsPC-1 cells, No treatment, rep3


title: 3999834051_R03C02


title: RFID 933000320186811 (high), snATAC-seq


title: 3999834051_R04C02


title: RFID 933000320046549 (naïve), snRNA-seq

description: Single cell RNA transcripts from amygdala

data_processing:
Sequencing reads were aligned to the Ensembl Rattus norvegicus v98 Rnor_6.0 genome assembly using the 10X Cell Ranger Pipeline
Assembly: Rnor_6.0/rn6
Supplementary files format and content: Tab-separated values files and matrix files, and additional Cell Ranger output files.
Supplementary files format and content: seurat.rds: Integrated Seurat object that contains all of the snRNA-seq data across all 19 of the snRNA-seq samples.

extract_protocol:
Brain tissues were extracted and snap-frozen. Cryosections of approximately 500 microns were used to dissect amygdala punches with a cryostat using a –20°C frozen stage. Single nuclei were isolated after tissue homogenization and iodixanol gradient purificaiton.
following the manifacture's manual for Chromium™ Single Cell 3’ v3 Library kit (10x Genomics)


title: RFID 933000120138730 (high), snRNA-seq


title: RFID 933000120138414 (low), snRNA-seq


title: 3999834051_R02C02


title: RFID 933000320045674 (high), snRNA-seq


title: Apo E4 heterozygous for synaptojanin, below injury site, sample 23bE4het

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Downsampling of reads to ensure each sample has the same number of reads and to prevent distortion of upper quartile normaliztion by read imbalances
Alignment to rat reference genome 'GRCm38.p6' using ensemble gene annotation and STAR 2.5.4b
Calculation of differentially expressed genes using Cuffdiff 1.3.0
Assembly: GRCm38.p6
Supplementary files format and content: Differentiallly expressed genes (p-value <= 0.01)
Supplementary files format and content: All differentially expressed genes with a cuffdiff test status 'OK'

source_name: Spinal cord

extract_protocol:
TRIzol reagent (ThermoFisher)
TruSeq RNA Sample Prep Kit v2 protocol (Illumina)
random primed

value: Spinal cord

tag: location

value: below injury site

value: Apo E4 heterozygous for synaptojanin

value: spinal cord injury


title: RFID 933000320047104 (low), snRNA-seq

value: Heterogenous Stock (HS)


title: RFID 933000320046625 (naïve), snRNA-seq

value: Male


title: 3999834051_R01C02

value: colon polyp


title: Apo E4 heterozygous for synaptojanin, below injury site, sample 22bE4het


title: Apo E4 homozygous for synaptojanin, below injury site, sample 21bE4ho

value: Apo E4 homozygous for synaptojanin


title: RFID 933000320046621 (naïve), snRNA-seq

value: Amygdala


title: 3999834051_R04C01


title: 3999834051_R06C01


title: RFID 933000320186801 (naïve), snRNA-seq

value: naive


title: Apo E4 homozygous for synaptojanin, below injury site, sample 20bE4ho


title: RFID 933000320047132 (low), snRNA-seq

value: cocaine

value: low addition


title: Apo E4 homozygous for synaptojanin, below injury site, sample 19bE4ho


title: RFID 933000320047225 (high), snRNA-seq


title: RFID 933000320046609 (high), snRNA-seq


title: Apo E4 heterozygous for synaptojanin, below injury site, sample 24bE4het


title: 3999834051_R03C01


title: RFID 933000320186802 (high), snRNA-seq


title: 3999834051_R02C01


title: 3999834051_R01C01


title: RFID 933000120138609 (low), snRNA-seq


title: RFID 933000320046077 (naïve), snRNA-seq


title: RFID 933000320046084 (naïve), snRNA-seq


title: RFID 933000120138586 (naïve), snRNA-seq


title: Sample: 82 [CHC SVR post HCC]

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

country: Japan

institute: Kanazawa University

hyb_protocol: Converted DNA (500 ng ) was hybridized to an Infinium HumanMethylation450 BeadChip (Illumina Inc.) and scanned using HiScanSQ (Illumina Inc.).

scan_protocol: HiScanSQ (Illumina Inc.)

data_processing: Data preprocessing and methylation-level extraction were performed using GenomeStudio Software (Illumina Inc.).

source_name: liver

label_protocol: Bisulfite conversion of genomic DNA was performed using EZ DNA Methylation-Gold Kit (Zymo Research, Irving, CA).

extract_protocol: DNA was extracted from frozen tissue samples with DNA NucleoSpin® Tissue (Macherey-Nagel, Düren, Germany), according to the manufacturer’s instructions.

value: liver

value: CHC SVR post HCC


title: Apo E4 heterozygous for synaptojanin, above injury site, sample 11aE4het

value: above injury site


title: RNA-Seq - AsPC-1 cells, No treatment, rep1

value: pancreatic ductal adenocarcinoma cells

value: WT

value: No treatment


title: RFID 933000120138592 (low), snRNA-seq


title: Apo E4 heterozygous for synaptojanin, above injury site, sample 10aE4het

value: Spinal cord


title: Sample: 81 [CHC SVR post HCC]


title: RFID 933000320047328 (high), snRNA-seq

value: high addition


title: RFID 933000320047001 (low), snRNA-seq


title: Apo E4 homozygous for synaptojanin, above injury site, sample 9aE4ho

value: spinal cord injury


title: Sample: 80 [CHC SVR post HCC]


title: Sample: 79 [CHC SVR post HCC]


title: Apo E4 homozygous for synaptojanin, above injury site, sample 8aE4ho


title: ATAC-seq DE replicate 5

city: Stanford

first: Aaron

middle: F

last: Straight

state: CA

address: 279 Campus Drive, B409A

department: Biochemistry

institute: Stanford University

description: DE-ATAC.bw

library_source: other

data_processing:
Demultiplexed fastq files from the ChAR-seq data were processed using a custom Snakemake pipeline (https://github.com/straightlab/charseq-pipelines), outputting pairs files containing the RNA and DNA coordinates of each RNA(cDNA)-DNA chimeric read and relevant annotations for each RNA-DNA contact.
RNA-seq data was processed using a Snakemake pipeline mirroring the ChAR-seq pipeline, but all of the operations related to the DNA-side of the reads were skipped. In brief, demultiplexed fastq files were deduplicated, sequencing adapters were removed, paired mates were merged as described for ChAR-seq reads. Reads that aligned to a rRNA sequence by Bowtie2 were filtered out using Picard. Reads were aligned to hg38 using STAR and were annotated with tagtools using the Gencode V29 gene models. Reads with low mapping scores (STAR Q < 255), reads which could not be attributed to a single known gene or a single locus, and reads that overlapped with a locus on the ENCODE black were discarded.
For ATAC-seq data Illumina Nextera Adapters were removed using a custom Python script. Reads were aligned to the hg38 using Bowtie2. Duplicates were removed with Picard. Mitochondrial reads or reads with Bowtie2 MAPQ score < 30 were removed using SAMtools. All replicates were similar, so their alignment files were merged to increase library complexity (>100 million mapped reads per cell type) and produce a single bigwig file per cell type used to display the ATAC-seq tracks, and a single bam file to determine ATAC-seq peaks. ATAC-seq peaks were identified in each cell line using HMMRATAC v1.2.10.
Assembly: hg38
Supplementary files format and content: bed

molecule: other

source_name: embryo

growth_protocol: Human H9 ES cells were grown on matrigel in mTeSR1 medium in 5%C02 at 37°C

extract_protocol:
Cell extraction is described in detail in Limouse, C. et al in RNA-Chromatin Interactions: Methods Mol Biol. 2020;2161:115-142. doi:10.1007/978-1-0716-0680-3_10.
Library preparation is described in detail in Limouse, C. et al in RNA-Chromatin Interactions: Methods Mol Biol. 2020;2161:115-142. doi:10.1007/978-1-0716-0680-3_10.

treatment_protocol: Cells were defferentiated into Definitive Endoderm by treatment with 10 µM Y27632 on day 0, and their media was replaced on day 1 with DE induction Media A (Gibco Cat# A3062601), and on day 2 with DE induction Media B (Gibco Cat# A3062601). On day 3, cells were harvested for ChAR-seq.

value: embryo

value: embryonic stem cell

value: DE wild type

value: endodermal differentiation


title: ATAC-seq DE replicate 4

description: DE-ATAC.bw


title: ATAC-seq DE replicate 3

description: DE-ATAC.bw


title: Sample: 77 [CHC SVR post HCC]


title: Apo E4 homozygous for synaptojanin, above injury site, sample 7aE4ho

value: Apo E4 homozygous for synaptojanin


title: Translated RNA from HTT-deleted MEF replicate 3

city: La Tronche

first: Julia

last: Schaeffer

address: Chemin Fortuné Ferrini

country: France

institute: Grenoble Institut Neurosciences

data_processing:
RNA-sequencing: RNA-sequencing analysis was performed on an Illumina NovaSeq 6000 platform, with paired-end reading (2x150bp).
Adapter trimming: Adapters were trimmed by Genewiz before data processing.
Quality control: FastQC control was performed by Genewiz. Mean quality score was > 35 for all samples. The percentage of bases with a quality score ≥ 30 was > 92% for all samples. Read depth was > 19M reads for all samples.
Read alignment: Fastq files were processed for alignment and read count. The mouse genome (Mus_musculus.GRCm38.dna.toplevel.fa) was indexed using STAR (version 2.7.2b), using 149bp overhangs and gene annotation (Mus_musculus.GRCm38.97.chr.gtf). Reads were aligned to the genome using STAR. The percentage of uniquely mapped reads was > 88% for all samples.
Read count: Reads were counted with HTSeq-count (version 0.11.1).
Differential gene expression analysis: Differential gene expression analysis was performed separately for the transcriptome and for the translatome using edgeR. Read counts were first normalized using RUVSeq with the RUVr method based on the residuals from the GLM fit after upper quartile normalization (number of residuals k=2).
Assembly: Mus musculus (house mouse) genome assembly GRCm38 (mm10)
Supplementary files format and content: Raw count data files for each samples (HTSeq-count files, .txt)

source_name: Mouse embryonic fibroblasts

growth_protocol: Primary cultures of MEF were prepared from E13.5 embryos according to Durkin et al., 2013. MEF were maintained at 37°C 5% CO2 in 10 cm dishes in cell culture medium: Dulbecco’s Modified Eagle Medium (DMEM, 31966047), high glucose, GlutaMAX Supplement, Thermo Fisher Scientific, 10% decomplemented fetal bovine serum (FBS, Eurobio Scientific, CVFSVF00- 01, 56°C for 30min), 1% penicillin-streptomycin (ThermoFisher Scientific, 15140122), 1% L- Glutamine (Thermo Fisher Scientific, 25-005-CI). Cells were passed when reaching confluency. Replicates were considered independent when originating from different primary cultures or from independent cell passages.

extract_protocol:
After cell transduction, cells were processed for ribosome purification. A fraction (1/15) of the cell suspension was kept for total RNA analysis (transcriptome), pelleted and resuspended in 1ml TRIzol Reagent (Invitrogen, 15596-026). After ribosome purification, the ribosome pellet was washed twice with ice-cold H2O, resuspended in 1ml TRIzol Reagent and homogenized very well by vortexing. Total RNA and ribosome-associated RNA was extracted with Trizol/chloroform extraction and isopropanol precipitation as per the manufacturer’s instructions. After washing once with 75% ethanol and drying, the RNA pellet was resuspended in 50μl H2O. 8μl RNA was treated with DNase I (Sigma-Aldrich,AMPD1) as per the manufacturer’s instructions. The final RNA concentration was determined using the Nanodrop (ThermoFisher Scientific, Nanodrop One).
Quality control was performed by Genewiz using RNA Screentape on Agilent TapeStation. All samples had a RNA quality number (RQN) > 9. Library preparation was performed by Genewiz. Libraries (stranded, reverse) were prepared with NEBNext Ultra II Directional RNA Library preparation kit with 250ng RNA as starting amount.

treatment_protocol: MEF were transduced with a lentiviral vector encoding the Cre recombinase (LV-Cre-GFP, Addgene #86805) or a control lentiviral vector (H2B-eGFP, Addgene #25999). After 1 day in culture, medium was replaced. Cells were kept for 7 days after transduction before harvesting.

value: Primary cultures of MEF

value: HTT-floxed (HTTfl/fl)

tag: rna source

value: Ribosome-associated RNA

value: HTT-deleted

tag: lentiviral transduction

value: Cre recombinase lentivirus


title: Translated RNA from control MEF replicate 3

value: Control

value: Control lentivirus


title: Total RNA from HTT-deleted MEF replicate 3

value: Total cellular RNA


title: Sample: 75 [CHC SVR post HCC]

value: liver

value: CHC SVR post HCC


title: ATAC-seq DE replicate 1

description: DE-ATAC.bw


title: ATAC-seq ES replicate 2

description: ES-ATAC.bw

value: ES wild type


title: ATAC-seq ES replicate 5

description: ES-ATAC.bw


title: ATAC-seq DE replicate 2

description: DE-ATAC.bw


title: ATAC-seq ES replicate 4

description: ES-ATAC.bw


title: DU145_ESS2shRNA

type: RNA

city: Minato

first: Sayuri

last: Takahashi

state: Tokyo

address: 4-6-1, Shiroganedai

department: The Institute of Medical Science

institute: The University of Tokyo

description: Gene expression in sh-ESS2 transduced DU145 cells

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: DU145, ESS2 shRNA

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cell were grown and maintained in a 37oC incubator with 5% CO2. RPMI1640 mefdium with 10%FBS penicillin/streptmycin.

extract_protocol: RNA was extracted according to the manufacturer's protocol, purified using RNeasy kit (Qiagen)

tag: knockdown

value: ESS2 shRNA


title: ATAC-seq ES replicate 3

description: ES-ATAC.bw

value: embryo


title: ATAC-seq ES replicate 1

description: ES-ATAC.bw

value: embryonic stem cell


title: Sample: 74 [CHC SVR post HCC]


title: PC3_control

description: Gene expression in sh-luc transduced PC3 cells

source_name: PC3, luciferase shRNA control

value: luciferase shRNA control


title: Total RNA from control MEF replicate 3


title: RNA-seq DE replicate 4

description:
DE_rna.negativeStrand.bw
DE_rna.positiveStrand.bw

value: DE wild type

value: endodermal differentiation


title: Apo E4 heterozygous for synaptojanin, above injury site, sample 12aE4het

value: Spinal cord

value: above injury site

value: Apo E4 heterozygous for synaptojanin

value: spinal cord injury


title: PC3_ESS2shRNA

description: Gene expression in sh-ESS2 transduced PC3 cells

source_name: PC3, ESS2 shRNA


title: DU145_control

description: Gene expression in sh-luc transduced DU145 cells

source_name: DU145, luciferase shRNA control


title: Translated RNA from HTT-deleted MEF replicate 2

value: Primary cultures of MEF

value: HTT-floxed (HTTfl/fl)

value: Ribosome-associated RNA

value: HTT-deleted

value: Cre recombinase lentivirus


title: Sample: 73 [CHC SVR post HCC]

value: liver

value: CHC SVR post HCC


title: RNA-seq DE replicate 3


title: Sample: 78 [CHC SVR post HCC]


title: RNA-seq DE replicate 1


title: Sample: 72 [CHC SVR post HCC]


title: RNA-seq DE replicate 2


title: Translated RNA from control MEF replicate 2

value: Control

value: Control lentivirus


title: Sample: 76 [CHC SVR post HCC]


title: Sample: 71 [CHC SVR post HCC]


title: Total RNA from HTT-deleted MEF replicate 2

value: Total cellular RNA


title: Total RNA from control MEF replicate 2


title: RNA-seq ES replicate 4

description:
ES_rna.negativeStrand.bw
ES_rna.positiveStrand.bw

value: embryo

value: embryonic stem cell

value: ES wild type


title: Sample: 70 [CHC SVR post HCC]


title: Translated RNA from HTT-deleted MEF replicate 1


title: Sample: 69 [CHC SVR post HCC]


title: Sample: 68 [CHC SVR post HCC]


title: RNA-seq ES replicate 2


title: RNA-seq ES replicate 3


title: Sample: 67 [CHC SVR post HCC]


title: Total RNA from HTT-deleted MEF replicate 1


title: RNA-seq ES replicate 1


title: Sample: 66 [CHC SVR post HCC]


title: Sample: 65 [CHC SVR post HCC]


title: Translated RNA from control MEF replicate 1


title: Total RNA from control MEF replicate 1


title: S23

city: London

first: Konstantinos

last: Theofilatos

address: 125 Coldharbour Lane

country: United Kingdom

institute: King's CollegeLondon

data_processing:
Galaxy Web Server
Adapters were filtered using the Trimmomatic tool
Quality control was done using the FastQC tool
Mapping was performed using the HISAT2 tool
Quantification and calculation of FPKM values was performed using the HTSeq-count tool
Filtering for lncRNAs was done using the Biomart tool
Assembly: hg19
Supplementary files format and content: Excel file including the raw count of reads per sample and the FPKM normalized expression values of alllncRNAs

source_name: Platelets

extract_protocol:
For isolation of total RNA, the miRNeasy Mini kit (Quagen, cat. No. 217004) was used according to the manufacturer's protocol
Ribosomal RNA depletion was performed using the Ribozero HMR kit (Illumina). The rRNA-depleted RNA was purified by 2x RNAClean XP beads (Beckman Coulter) and eluted in 45µL of nuclease-free water. 5µL of purified rRNA-depleted RNA was mixed with 4µL of NEBNext First Strand Synthesis Reaction Buffer and 1µL of random primers. The reaction was incubated at 94°C for 12min for fragmentation. Subsequently, to perform first strand cDNA synthesis, 8µL of NEBNext Strand Specificity Reagent and 2µL of NEBNext First Strand Synthesis Enzyme Mix was added to the reaction and the reaction was incubated at 25°C for 10 mins, 42°C for 30 mins, 70°C for 15 mins. Second strand reaction was then performed by adding 8µL of NEBNext Second Strand Synthesis Reaction Buffer with dUTP Mix (10X), 4µL of NEBNext Second Strand Synthesis Enzyme Mix, and 48µL of nuclease-free water. The reaction was incubated at 16°C for 1h. The cDNA was purified by 1.8x SPRIselect Beads (Beckman Coulter) and eluted in 50µL of nuclease-free water. Subsequently, endprep reaction was performed by adding 7µL of NEBNext Ultra II End Prep Reaction Buffer and 3µL of NEBNext Ultra II End Prep Enzyme Mix into 50µL purified cDNA. Endprep reaction was incubated at 20°C for 30 mins and 65°C for 20 mins. The adaptor ligation reaction was then performed by adding 1µL of NEBNext Ligation Enhancer, 30µL of NEBNext Ultra II Ligation Master Mix, and 2.5µL of NEBNext Adaptor, diluted to 0.5µM in Adaptor Dilution Buffer. The mix was incubated at 20°C for 15min. 3µL of USER Enzymer (New England Biolabs) was then added to the ligation product and the reaction was incubated at 37°C for 15min. The ligated product was purified by SPRIselect Beads (Beckman Coulter) and eluted in 15µL of nuclease-free water. PCR was carried out by adding 25µL of NEBNext Ultra II Q5 Master Mix, 5µL of i5 Primer, and 5µL of i7 Primer into 15µL of purified ligated product. PCR was performed at 98°C for 30s, 15 cycles of 98°C for 10s and 65°C for 75s, and a final extension at 65°C for 5min.  The final library was then purified by SPRIselect Beads.

value: Platelets

value: Healthy Donor


title: S22


title: Sample: 64 [CHC SVR post HCC]


title: S21


title: S20


title: Sample: 63 [CHC SVR post HCC]


title: Sample: 62 [CHC SVR post HCC]


title: Se_lowSe3

city: zhengzhou

first: jinke

last: hu

state: henan

address: Zhengzhou City, Henan Province

institute: zhengzhou

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the (http://mascotton.njau.edu.cn/info/1054/1118.htm) TM-1 reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: TM-1
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Medicago sativa

source_name: leaves

extract_protocol:
Total RNA was isolated and purified from plant leaf tissue under the two treatments (control and 100 mg/kg selenium) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Approximately 10 μ g of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, using divalent cations, the poly (A) - or poly (A) + RNA fractions were fragmented into small pieces under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to the final cDNA library according to the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp ( ± 50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following of the merchant's recommended protocol.
The paired-end libraries was 300 bp ( ± 50 bp)

value: treated with 100 mg/kg selenium


title: Se_lowSe2


title: LU99_MRTX1719_1uM_Day5_1

city: San Diego

first: Lars

last: Engstrom

address: 3545 Cray Court

institute: Mirati Therapeutics

data_processing:
The reads were trimmed and low-quality reads were removed using Trimgalore v0.6.3_dev
Trimmed fastq sequences were aligned to the human reference genome (GRCh38) usingSTARalignerv2.7.1a
Alignment QC and read mapping statistic were obtained from Picard v2.20.3
Raw gene counts were used for quality control and transformed to Log2CPM (Counts Per Million) for downstream differential expression analysis.  Lowly expressed genes with mean of Log2(CPM) less than -2 were eliminated prior to differential expression analysis
Assembly: GRCh38
Supplementary files format and content: comma-separated text file contains raw counts for each sample

molecule: polyA RNA

growth_protocol: LU99 cells were cultured as recommended by repository. Control and drug treated cells were collected at indicated timepoints with ~70% confluency.

extract_protocol:
Cells were rinsed with ice-cold PBS and cell pellets were snap frozen.  Total RNA was extracted from frozen cell samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany)
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: LU99 cells were treated with DMSO or MRTX1719 (1uM) for 3 or 5 days

value: Non-Small Cell Lung Cancer

value: 5 days


title: LU99_MRTX1719_1uM_Day5_2


title: Sample: 61 [CHC SVR post HCC]


title: Se_lowSe1


title: ospipt6-KO, root, 2

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

description: Gene expression in root tissues

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryza sativa

source_name: Rice seedlings

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

extract_protocol: RNA was prepared using the Maxwell RSC RNA kit (Promega) following the manufacturer's recommendations.

treatment_protocol: Shoot and root tissues from 28 day-old wild-type and ospipt6-KO seedlings grown under phosphate-sufficient conditions

value: root


title: ospipt6-KO, root, 3

description: Gene expression in root tissues


title: Sample: 60 [CHC SVR post HCC]


title: ospipt6-KO, root, 1

description: Gene expression in root tissues


title: Se_CK3

value: Untreated control


title: Sample: 59 [CHC SVR post HCC]


title: Sample: 58 [CHC SVR post HCC]


title: LU99_DMSO_Day5_1

value: DMSO


title: LU99_MRTX1719_1uM_Day3_2

value: 3 days


title: LU99_DMSO_Day5_2


title: WT, root, 2

description: Gene expression in root tissues

value: shoot

value: WT


title: Se_CK1


title: Sample: 57 [CHC SVR post HCC]

value: liver

value: CHC SVR post HCC


title: LU99_MRTX1719_1uM_Day3_1


title: Sample: 56 [CHC SVR post HCC]


title: p7l15D_3

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

data_processing:
Galaxy platform
Adaptors were removed with Trimmomatic (Bolger et al., 2014)
Sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Transcript abundances were calculated using Salmon (Patro et al. 2017) and AtRTD2-QUASI as reference transcriptome (Zhang et al. 2017).
The generated files were uploaded into the 3D RNA-Seq app (https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq; Calixto et al. 2018; Guo et al. 2021) and transcript per million reads (TPMs) were calculated using the implemented lengthScaledTPM method. Low expressed transcripts and genes were filtered based on analyzing the data mean-variance trend.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited file includes TPM values for each sample

source_name: whole plants

growth_protocol: Seeds were sown on 1/2 MS medium containing 1% (w/v) sucrose and 0.8% (w/v) agar, incubated at 4°C for 2 d, and transferred to a climate chamber under a 16-h-light/8-h-dark cycle with a light intensity of 100 μE m-2 s-1 at 22°C. For drought treatments, 7-d-old seedlings were transferred to pots containing same amounts of soil and grown for further 2 weeks under normal growth conditions. Three-week-old plants were subjected to drought conditions by withholding water for indicated time periods.

extract_protocol:
For RNA isolation, plant material was harvested, frozen in liquid nitrogen and crushed in a TissueLyser (Retsch, model: MM400). Total RNA was extracted with the Direct-zol RNA Kit (Zymo Research, Irvine, USA) according to the manufacturer’s protocol. RNA samples were quantified with a Nanodrop spectrophotometer (ThermoFisher Scientific, Langenselbold, Germany) and RNA integrity and quality was assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA). Isolated RNA was stored at −80 °C until further use.
Illumina Tru-Seq

treatment_protocol: drought treamtent under long-day conditions

value: pp7l-2 mutant

tag: ecotype

tag: time point


title: ospipt6-KO, shoot, 2

description: Gene expression in shoot tissues


title: ospipt6-KO, shoot, 1

description: Gene expression in shoot tissues


title: LU99_DMSO_Day3_2

tag: time


title: p7l15D_2


title: Sample: 55 [CHC SVR post HCC]

tag: tissue


title: ospipt6-KO, shoot, 3

description: Gene expression in shoot tissues


title: LU99_DMSO_Day3_1


title: p7l15D_1


title: p7l12D_2


title: Sample: 54 [CHC SVRpost]

value: CHC SVRpost


title: WT, root, 1

description: Gene expression in root tissues


title: WT, root, 3

description: Gene expression in root tissues


title: WT, shoot, 3

description: Gene expression in shoot tissues


title: p7l12D_1


title: reticulocytes, HbSS samp25

city: Chicago

first: Xu

last: Zhang

state: Illinois

address: 820 South Wood St

institute: University of Illinois at Chicago

description:
reticulocytes, HbSS
samp25

data_processing:
Sequences were trimmed using Trimmomatic-0.35. Sequencing data were mapped to human reference genome version GRCh37 annotated by Gencode version 24, using STAR_2.5.1b. Counts of genes were obtained using subread-1.5.0-p1.
Assembly: Human NCBI genome build 37
Supplementary files format and content: Tab-delimited text file with raw counts for autosomal protein-coding genes for each sample.

source_name: reticulocytes

extract_protocol:
Whole blood (8-16 mL) was collected using ACD as an anticoagulatent. Plasma and platelets were isolated by gentle centrifugation at 400 g. Blood was further layered on ficoll-histopaque (density 1.077 g/mL) for separation of mononuclear cells and lymphocytes. The lower layer of packed erythrocytes were transferred to a clean tube and preferentially lysed with 4 volumes of 0.144 M ammonium chloride, 1 mM ammonium bicarbonate solution. Granulocytes were separated by centrifugation and the supernatant containing reticulocyte RNA was precipitated by acid titration to pH 5.1. Precipitated RNA was preserved in Trizol and stored at -80ºC
Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Human/Mouse/Rat. Strand-specific libraries were constructed for 100 or 125 bp paired-end sequencing to 30-45 million read pairs per sample

value: reticulocytes

value: HbSS


title: WT, shoot, 2

description: Gene expression in shoot tissues


title: p7l12D_3


title: Sample: 51 [CHC SVRpost]


title: Se_CK2


title: WT, shoot, 1

description: Gene expression in shoot tissues


title: Sample: 53 [CHC SVRpost]


title: Sample: 52 [CHC SVRpost]


title: Central amygdala, snATAC-seq

description: Single Cell Multiome ATAC

data_processing:
Sequencing reads were aligned to the Ensembl Rattus norvegicus v98 Rnor_6.0 genome assembly using the 10X Cell Ranger ARC software.
Assembly: Rnor_6.0/rn6
Supplementary files format and content: Tar archives containing selected outputs from Cell Ranger ARC, including matrix files and TSV files.

source_name: Central amygdala

extract_protocol:
For nuclei isolation, brain punches from 3 rats for each region were pooled and homogenized in homogenization buffer (0.26 M sucrose, 0.03 M KCl, 0.01 M MgCl2, 0.02 M Tricine-KOH pH 7.8, 0.001 M DTT, 0.5 mM spermidine, 0.15 mM Spermine, 0.3% NP40) using with 1ml glass Dounce homogenizers. The homogenate was filtered with a 70-um strainer filter (SP Bel-Art, cat no 136800070) and centrifuged for 5 minutes at 350 RCF. The nuclei were purified with an iodixanol gradient (Sigma-Aldrich # 92339-11-2) by layering a 25% Iodixanol-nuclei mixture on top of 30% and 40% Iodixanol solutions. After centrifugation at 4oC 3,000 RCF for 20 minutes, nuclei were collected from the 30-40% interface. Nuclei were washed in ATAC-RSB-Tween buffer (0.01 M Tris-HCl pH 7.5, 0.01 M NaCl, 0.003 M MgCl2, 0.1% Tween-20) and then resuspended in 1X nuclei buffer (10X genomics, PN 2000207).
snATAC-seq library was performed using the Chromium Next GEM Single Cell Multiome Reagent Kit A (# 1000282) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide (10X Genomics). After the transposition reaction, nuclei were encapsulated and barcoded. Next-generation sequencing libraries were constructed following the User Guide.
10X Genomics Multiome ATAC + Gene Expression

value: Central amygdala


title: reticulocytes, HbSS samp23

description:
reticulocytes, HbSS
samp23


title: Sample: 50 [CHC SVRpost]


title: Basolateral amygdala, snATAC-seq

description: Single Cell Multiome ATAC

source_name: Basolateral amygdala

value: Basolateral amygdala


title: reticulocytes, HbSS samp21

description:
reticulocytes, HbSS
samp21


title: p7l9D_3


title: reticulocytes, HbAA samp10

description:
reticulocytes, HbAA
samp10

value: HbAA


title: reticulocytes, HbSS samp24

description:
reticulocytes, HbSS
samp24


title: Sample: 49 [CHC SVRpost]


title: Sample: 48 [CHC SVRpost]


title: p7l9D_1


title: Basolateral amygdala, snRNA-seq

description: Single Cell Multiome Gene Expression

extract_protocol:
For nuclei isolation, brain punches from 3 rats for each region were pooled and homogenized in homogenization buffer (0.26 M sucrose, 0.03 M KCl, 0.01 M MgCl2, 0.02 M Tricine-KOH pH 7.8, 0.001 M DTT, 0.5 mM spermidine, 0.15 mM Spermine, 0.3% NP40) using with 1ml glass Dounce homogenizers. The homogenate was filtered with a 70-um strainer filter (SP Bel-Art, cat no 136800070) and centrifuged for 5 minutes at 350 RCF. The nuclei were purified with an iodixanol gradient (Sigma-Aldrich # 92339-11-2) by layering a 25% Iodixanol-nuclei mixture on top of 30% and 40% Iodixanol solutions. After centrifugation at 4oC 3,000 RCF for 20 minutes, nuclei were collected from the 30-40% interface. Nuclei were washed in ATAC-RSB-Tween buffer (0.01 M Tris-HCl pH 7.5, 0.01 M NaCl, 0.003 M MgCl2, 0.1% Tween-20) and then resuspended in 1X nuclei buffer (10X genomics, PN 2000207).
snRNA-seq library was performed using the Chromium Next GEM Single Cell Multiome Reagent Kit A (# 1000282) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide (10X Genomics). After the transposition reaction, nuclei were encapsulated and barcoded. Next-generation sequencing libraries were constructed following the User Guide.
10X Genomics Multiome ATAC + Gene Expression


title: p7l6D_3


title: reticulocytes, HbSS samp22

description:
reticulocytes, HbSS
samp22


title: reticulocytes, HbAA samp08

description:
reticulocytes, HbAA
samp08


title: Sample: 47 [CHC SVRpost]


title: p7l6D_1


title: Sample: 46 [CHC SVRpost]


title: reticulocytes, HbAA samp07

description:
reticulocytes, HbAA
samp07


title: Liver, Vehicle injections (NASH Diet), S24

city: Hamilton

first: Dongdong

last: Wang

state: Ontario

address: 1200 Main Street West

department: Department of Medicine

country: Canada

institute: McMaster University

description: Data can be used by nSolver Software

hyb_protocol: Hyb protocol from NanoString Technologies, Inc.

scan_protocol: Scan protocol from NanoString Technologies, Inc.

data_processing: Gene expression data was normalized and log-transformed prior to differential gene expression analysis and pathway signature score computation using NanoString Technologies’ nSolver 4.0 software (version 4.0.70) and the embedded PLAGE algorithm.

label: Nanostring label

source_name: Liver

label_protocol: Label protocol from NanoString Technologies, Inc.

extract_protocol: Liver tissue (~15 mg) was lysed in 1 mL TRIzol reagent (Invitrogen) using ceramic beads and a Precellys 24 homogenizer (Bertin Technologies). Samples were spun down for 10 mins at 12 000 g at 4 ºC. 200 µL of chloroform was added and shaken vigorously before spinning samples again at same settings. Supernatant was placed in new tubes and an equal amount of 70% ethanol was added then vortexed. Solutions were loaded onto RNeasy columns and manufacturer’s instructions were followed including a DNAse I digestion step (Qiagen).

treatment_protocol: At 8 weeks of age, mice were moved into specific-pathogen free (SPF) microisolators in a room maintained at ~29 ºC and fed a high-fat, high-fructose diet (NASH Diet; ND; 40% fat from mostly palm, 20% fructose, 0.02% cholesterol). Due to fructose being supplemented in the diet, diet was changed every few weeks. 16 weeks later, mice were grouped by matching body weight and adiposity randomly and placed on respective interventional arms. Adiposity was assessed based on time-domain NMR using a Bruker Minispec LF90II. Control mice were continued on diet alone, vehicle-treated mice (Vehicle) were given subcutaneous saline injections every second day 1-2 hrs before the dark cycle, bempedoic acid-treated mice (BemA) had the drug supplemented in the diet at a dose of 10 mg/kg, liraglutide-treated mice (Lira) were given subcutaneous injections of Victoza diluted in saline to a dose of 70 µg/kg every second day 1-2 hrs before the dark cycle, and combination-treated mice (Lira+BemA) were given subcutaneous injections of Victoza diluted in saline to a dose of 70 µg/kg every second day 1-2 hrs before the dark cycle with bempedoic acid supplemented in the diet at a dose of 10 mg/kg.

tag: diet

value: NASH diet

value: Saline

value: mouse liver


title: Sample: 45 [CHC SVRpost]


title: p7l9D_2


title: reticulocytes, HbAA samp06

description:
reticulocytes, HbAA
samp06


title: Central amygdala, snRNA-seq

description: Single Cell Multiome Gene Expression


title: p7l0D_3


title: Liver, Control (NASH Diet), S23

description: Data can be used by nSolver Software


title: Liver, Control (NASH Diet), S22

description: Data can be used by nSolver Software


title: Liver, Control (NASH Diet), S21

description: Data can be used by nSolver Software


title: Liver, Control (NASH Diet), S20

description: Data can be used by nSolver Software


title: Sample: 44 [CHC SVRpost]


title: Sample: 43 [CHC SVRpost]


title: p7l0D_2


title: Liver, Control (NASH Diet), S19

description: Data can be used by nSolver Software


title: Hi-C naive

city: New Haven

first: In-Hyun

last: Park

state: CT

address: 10 AMISTAD ST # 201B

department: Genetics

institute: Yale University

data_processing:
Mapping, quality control, detection of valid interaction pairs of HiC reads were performed by HiC-Pro software (v2.9.0) with DpnII restriction sites in hg19 genome and “GATCGATC” ligation site (Servant et al., 2015).
Subsequent analyses were implemented by using HOMER suite (v4.11.1) (Heinz et al., 2010).
Assembly: hg19
Supplementary files format and content: Tab-separated file of all valid Hi-C read pairs

growth_protocol: hPSCs at the primed state were grown feeder-free on Matrigel-coated plates using the mTeSR1 media condition. Naïve iPSCs were cultured in 5iLA media on MEFs, as reported previously (Theunissen et al., 2014).

extract_protocol: Hi-C 2.0 was performed as described previously (Belaghzal et al., 2017). Briefly, 10 cm plates of naïve and primed hESCs were crosslinked and aliquoted into 5.5×106 cell aliquots. Each aliquot was separately treated as a Hi-C sample. Each sample underwent plasma membrane lysis and removal of the cytoplasm before nuclear semi-permeabilization. Next, semi-permeable crosslinked nuclei were digested with the DpnII restriction enzyme. The sticky ends were filled in with dNTPs and biotinylated dCTP before blunt-end ligation. After ligation, cross-linking was reversed, nuclei were broken down, and correctly sized biotinylated DNA was purified out of the larger DNA pool. Illumina sequencing primers were added to these biotinylated fragments, which were subsequently amplified.

value: Embryonic stem cell

value: 5iLA naive culture medium


title: Hi-C primed

value: Primed culture medium


title: reticulocytes, HbAA samp09

description:
reticulocytes, HbAA
samp09


title: Liver, Control (NASH Diet), S18

description: Data can be used by nSolver Software


title: p7l0D_1


title: Sample: 41 [CHC SVRpost]


title: Col15D_3

value: wild type


title: p7l6D_2


title: D3.5_2_XAV_NANOGNeg

first: Sivakamasundari

last: Vijayakumar

address: 265 Campus Drive, Lokey Stem Cell Building, Rm G3105

department: Institute for Stem Cell Biology and Regenerative Medicine

data_processing:
skewer (v0.2.2)  was used to trim adaptor sequences - skewer x -AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG; skewer y- AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTANNNNNNNNGATCTCGGTGGTCGCCGTATCATT
using Salmon (v1.7.0) trimmed reads were mapped to GRCh38 reference cDNA and ncRNA sequences from ensemble (release 95) (http://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/)
read counts were quantifed using Salmon (v1.7.0)
counts were normalized using DESeq2 R package
Assembly: GRCh38
Supplementary files format and content: mapped raw counts text file for all samples ("All_samples_rawcounts.csv")

source_name: hPSC

growth_protocol: hPGCLC differentiation protocol

extract_protocol:
Cells were dissociated with acutase and washed twice in wash buffer (0.04% Bovine Serum Albumin in Ca2+/Mg2+-free PBS), filtered using 40um strainer and counted on the Countess II automated cell counter (Thermo Fisher).
Library construction by Truseq; 8bp dual indices
RNA seq libraries were prepared by Truseq and seqeunced on HiSeq4000, 2x150bp, paired-end

treatment_protocol: untreated or XAV939 or CHIR99021 or Base media

value: hPSC

value: differentiated hPSC

tag: replicate

value: XAV


title: Sample: 42 [CHC SVRpost]

value: liver


title: Col15D_2

tag: genotype


title: Liver, Control (NASH Diet), S17

description: Data can be used by nSolver Software


title: Liver, Control (NASH Diet), S16

description: Data can be used by nSolver Software


title: Sample: 40 [CHC SVRpost]

tag: condition

value: CHC SVRpost


title: Sample: 39 [CHC SVRpost]


title: Col15D_1


title: D3.5_1_XAV_NANOGNeg

tag: cell type


title: Sample: 38 [CHC SVRpost]


title: Col12D_2


title: Liver, Lira injections (NASH Diet), S15

description: Data can be used by nSolver Software

tag: treatment

value: Liraglutide (70 µg/kg)


title: D3.5_2_XAV_NANOGPos

tag: cell line


title: Sample: 37 [CHC SVRpost]


title: D3.5_3_Base_Media_NANOGNeg


title: Liver, Lira injections (NASH Diet), S13

description: Data can be used by nSolver Software


title: Liver, Lira injections (NASH Diet), S14

description: Data can be used by nSolver Software


title: D3.5_1_XAV_NANOGPos


title: Liver, Lira injections (NASH Diet), S12

description: Data can be used by nSolver Software


title: Sample: 36 [CHC SVRpost]


title: D3.5_3_XAV_NANOGNeg


title: Col9D_3


title: Col12D_1


title: D3.5_2_Base_Media_NANOGNeg


title: Sample: 35 [CHC SVRpost]


title: D3.5_1_Base_Media_NANOGNeg


title: Col9D_2


title: Liver, Lira injections (NASH Diet), S11

description: Data can be used by nSolver Software


title: D3.5_3_XAV_NANOGPos


title: Sample: 34 [CHC SVRpost]


title: Sample: 33 [CHC SVRpre]

value: CHC SVRpre


title: Col9D_1


title: D3.5_3_Base_Media_NANOGPos


title: Col6D_3


title: Liver, BemA 10mg/kg diet + Lira injections, S9

description: Data can be used by nSolver Software

value: Bempedoic acid (10 mg/kg) + Liraglutide (70 µg/kg)


title: Col12D_3


title: Liver, BemA 10mg/kg diet + Lira injections, S8

description: Data can be used by nSolver Software


title: D3.5_2_Base_Media_NANOGPos


title: Sample: 32 [CHC SVRpre]


title: Col6D_1


title: Col0D_3


title: Sample: 30 [CHC SVRpre]


title: D3.5_3_CHIR

value: CHIR


title: Sample: 29 [CHC SVRpre]


title: D3.5_2_CHIR


title: Liver, BemA 10mg/kg diet + Lira injections, S6

description: Data can be used by nSolver Software


title: Liver, Bem A 10mg/kg, S4

description: Data can be used by nSolver Software

value: Bempedoic acid (10 mg/kg)


title: Liver, Bem A 10mg/kg, S5

description: Data can be used by nSolver Software

value: NASH diet


title: Col0D_1


title: Liver, BemA 10mg/kg diet + Lira injections, S10

description: Data can be used by nSolver Software


title: D3.5_1_CHIR


title: Sample: 28 [CHC SVRpre]


title: Sample: 27 [CHC SVRpre]


title: D3.5_3_XAV


title: Ls174 cells, Treatment 2

city: Larissa

first: Antonis

last: Giakountis

address: Biopolis-Mezourlo

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

data_processing:
HISAT2-BOWTIE2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to GRCh37/hg19 using hisat2 (parameters -un, --add-chrname). Hisat2 unaligned reads were mapped with BOWTIE2 (parameters --local –very-sensitive-local). Hisat2 and Bowtie2 aligned reads were merged.
Read count extraction and normalization were performed using the metaseqR2 Bioconductor package
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Ls174 and HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (MRC). 1 ug of total RNA was used for the construction of sequencing libraries.
3’ RNA libraries for RNA-seq were prepared using the 3’mRNA Quant Library Prep kit protocol of Ion Torrent following manufacturer's protocols.

treatment_protocol: 3x10^5 treated Ls174 and HepG2 cells were cultured with 0.7 mg/ml extract from Hypnea musciformis for 24 hr

value: Colon cancer cells

value: WT

value: Treatment with microalgea extract at IC50 concentration

value: 24 hrs


title: Liver, BemA 10mg/kg diet + Lira injections, S7

description: Data can be used by nSolver Software

value: mouse liver


title: Liver, Bem A 10mg/kg, S3

description: Data can be used by nSolver Software


title: Liver, Bem A 10mg/kg, S2

description: Data can be used by nSolver Software


title: Col0D_2

value: wild type


title: Ls174 cells, Treatment 1


title: Sample: 31 [CHC SVRpre]


title: Ls174 cells, Treatment 3


title: Sample: 25 [CHC SVRpre]


title: Sample: 24 [CHC SVRpre]


title: Sample: 26 [CHC SVRpre]


title: Liver, Bem A 10mg/kg, S1

description: Data can be used by nSolver Software


title: D3.5_1_Base_Media_NANOGPos

value: hPSC


title: D3.5_3_Base_Media

value: differentiated hPSC


title: Sample: 23 [CHC SVRpre]


title: Donor 891, TurboCAR.15.3

city: South San Francisco

first: Regina

middle: Junhui

last: Lin

address: 210 E Grand Ave

institute: Allogene Therapeutics, Inc.

description: Nanostring nCounter Human CAR T Characterization panel

hyb_protocol: Hybridization with probes was performed as per manufacturer's protocol: https://nanostring.com/wp-content/uploads/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf

scan_protocol: Data was acquired on the Nanostring nCounter instrument

data_processing: Genes that fell below the threshold (i.e. when 100% of the samples have a raw data count of 20 or less) were removed from analysis. Raw data counts above the threshold were normalized using the nSolver software.

label: Barcoded fluorescent reporters

source_name: TurboCAR.15.3, cytokine-untreated

label_protocol: Barcoded fluorescent reporters

growth_protocol: TurboCAR.15 T cells were generated by expansion in IL-2 as per standard protocol. To mimic the aggregate of cytokine signaling received by TurboCAR.15 T cells, unmodified CAR T cells were expanded in either IL-2 alone (100 U/ml), or a combination of IL-2 (100 U/ml) and IL-15 (10 ng/ml). At the end of expansion, CAR+ T cells were FACS-sorted and cultured for an additional 2 days to enrich for Turbodomain- or cytokine-induced gene signatures before Nanostring gene expression profiling and analysis.

extract_protocol: Total RNA from 2E5 cells per sample was extracted as per manufacturer's protocol: https://nanostring.com/wp-content/uploads/MAN-10051-05-Preparing-RNA-and-Lysates-from-Fresh-Frozen-Samples.pdf

treatment_protocol: During the final 2 days of culture, control CAR T cells were cultured without cytokines, 100 U/ml IL2, or 10 ng/ml IL15; TurboCAR.15 T cells were cultured without cytokines.

tag: individual

value: Donor 891

tag: car status

value: Cytokine-untreated

tag: cell number


title: Ls174 cells, Control 2

value: no treatment


title: Ls174 cells, Control 1


title: Ls174 cells, Control 3


title: D3.5_1_Base_Media


title: Sample: 22 [CHC SVRpre]

source_name: liver

extract_protocol: DNA was extracted from frozen tissue samples with DNA NucleoSpin® Tissue (Macherey-Nagel, Düren, Germany), according to the manufacturer’s instructions.

value: liver


title: D3.5_2_Base_Media


title: HEPG2 cells, Treatment 3

value: Liver hepatocellular carcinoma cells


title: Sample: 21 [CHC SVRpre]

value: CHC SVRpre


title: D3.5_1_XAV

value: XAV


title: D2.5_3_XAV


title: D3.5_2_XAV


title: HEPG2 cells, Treatment 1


title: D2.5_2_XAV


title: HEPG2 cells, Treatment 2


title: Donor 891, CAR + IL2

source_name: Unmodified CAR, IL2-treated

value: Unmodified CAR


title: Sample: 20 [CHC SVRpre]


title: Donor 891, CAR + no cytokines

source_name: Unmodified CAR, cytokine-untreated


title: Donor 891, CAR + IL15

source_name: Unmodified CAR, IL15-treated


title: HEPG2 cells, Control 3


title: D2.5_3_CHIR

value: CHIR


title: Sample: 18 [CHC SVRpre]


title: Donor 891, TurboCAR.15.1

source_name: TurboCAR.15.1, cytokine-untreated


title: Donor 177, TurboCAR.15.3

value: Donor 177


title: HEPG2 cells, Control 2

value: WT


title: D2.5_2_CHIR


title: Donor 177, TurboCAR.15.1


title: Sample: 16 [CHC SVRpre]


title: Donor 177, CAR + IL15


title: D2.5_1_CHIR


title: HEPG2 cells, Control 1


title: BMDM KIKO, LPS 60 min sample 36

city: Madrid

first: Ana

last: Cuenda

state: Madrid

address: C. Darwin, 3

department: DEPARTMENT OF IMMUNOLOGY AND ONCOLOGY

country: Spain

institute: National Biotechnology Centre (CNB-CSIC)

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_36_SAM

data_processing:
The RSEM package (version 1.2.31) in conjunction with the STAR alignment algorithm (version 2.5.2a) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser 15 on February 19, 2016. Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.2.3). Genes with a false discover rate <0.05 were judged to be differentially expressed.
Supplementary files format and content: tab-delimited text includes raw counts for each Sample
Supplementary files format and content: tab-delimited text includes edger analysis for paired Samples

source_name: Bone marrow

growth_protocol: Bone marrow derived macrophages were

extract_protocol:
RNA was isolated from 1 x 10xe6 BMDM from WT or p38γ/δKIKO male mice using the RNeasy kit (QIAGEN).
Biological replicate libraries were prepared using the TruSeq RNA library prep kit (Illumina)

treatment_protocol: Lipopolysacharide 100 ng/ml

value: Bone marrow

value: BMDM

value: Bone marrow derived macrophages

value: p38g knock in/p38d knock out

value: Lipopolysacharide 100 ng/ml

value: 60 minutes


title: D2.5_3_Base_Media

value: hPSC

value: differentiated hPSC


title: Donor 177, CAR + IL2


title: Sample: 15 [CHC SVRpre]

data_processing: Data preprocessing and methylation-level extraction were performed using GenomeStudio Software (Illumina Inc.).


title: BMDM KIKO, LPS 60 min sample 35

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_35_SAM


title: D2.5_2_Base_Media


title: D2.5_1_XAV


title: BMDM KIKO, LPS 60 min sample 34

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_34_SAM


title: Sample: 14 [CHC SVRpre]


title: Sample: 19 [CHC SVRpre]


title: Sample: 13 [CHC SVRpre]


title: D2.5_1_Base_Media


title: BMDM KIKO, LPS 60 min sample 33

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_33_SAM


title: Sample: 17 [CHC SVRpre]


title: Sample: 12 [CHC SVRpre]


title: Sample: 11 [CHC SVRpre]


title: BMDM KIKO, LPS 60 min sample 32

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_32_SAM


title: BMDM KIKO, LPS 60 min sample 31

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_31_SAM


title: D1.5_2_CHIR


title: Sample: 10 [Control]

value: Control


title: D1.5_1_CHIR


title: D1.5_3_XAV


title: BMDM WT, LPS 60 min sample 30

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_30_SAM


title: BMDM WT, LPS 60 min sample 29

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_29_SAM


title: Sample: 9 [Control]

value: liver


title: Donor 177, CAR + no cytokines

value: Cytokine-untreated


title: D1.5_2_XAV


title: BMDM WT, LPS 60 min sample 28

description:
data_raw_excel.txt
logFC_time.txt
Sample_MP_28_SAM


title: Sample: 8 [Control]


title: Two-Donor-SSNseq-CAR-T-ex-vivo-5P, TCR-derived cDNA

city: Houston

first: Pawel

last: Mazur

state: Texas

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

description:
10x Genomics
Sample 6-3
Exp6_filtered_contig_annotations.csv.gz

data_processing:
Gene expressing reads were aligned to the GRCh38 genome (human) using the 10x Genomics Cell Ranger, with the pipeline cellranger count or multi. Small RNA counts were retrieved through cellranger count using the pattern containing group barcodes and sequences derived from constant regions of corresponding small RNAs.
Assembly: GRCh38
Supplementary files format and content: T cell receptor V(D)J output: filtered_contig_annotations.csv.gz

source_name: Human CAR T cells

extract_protocol:
Lentiviral barcoded human primary CAR T cells were pooled and loaded into a Chromium Controller (10x Genomics).
10x Chromium Next GEM Single Cell 3' Reagent Kits v3.1 or 5' Reagent Kits V2 (with Feature Barcoding technology for CRISPR Screening) was used to construct the mRNA, small RNA and/or TCR libraries, according to the manufacturer’s protocol (CG000316_RevD or CG000510 Rev B).

value: Human CAR T cells

tag: fraction

value: other


title: Control sample

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

institute: Osaka Metropolitan University Graduate School of Medicine

description: Gene expression data from urinary bladder of Control male rats

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Rat array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

source_name: urinary bladder, control epithelium

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: TRIzol® Reagent was performed according to the manufacturer's instructions.

treatment_protocol: Male 10-week-old F344 rats were treated with 0 (Control) or 200 ppm dimethylarsinic acid (DMA) in drinking water for 2 years.

value: urinary bladder

tag: strain

value: F344 rats

tag: age

value: 114 weeks

tag: gender

value: male