title: WT_DN4_GEX

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

data_processing:
5' single cell gene expression libraries were processed with cellranger (v3.1.0)
5' VDJ single cell libraries were processed with cellranger (6.0.1)
Assembly: mm10
Supplementary files format and content: UMI count matrix in matrixMarket format
Supplementary files format and content: cell-level metadata (cluster annotations) in TSV format
Supplementary files format and content: TCR clonotype and contig annotations in CSV format

source_name: DN4 thymocytes

extract_protocol:
DN cells (CD4-CD8-) were purified by negative selection (magnetic beads) from the thymus of  C57BL/6J and GSK3-KI mice with the following antibodies: anti-MHC class II (M5/114/15/2), anti-CD11b (M1/70), anti-CD4 (GK1.5), anti-CD8 (Tib105), and anti-kappa (187.1). B220- T cells; anti-MHC class II (M5/114/15/2), anti-CD11b (M1/70), and anti-B220 (RA3-6B2). Then DN Thymocyte subsets DN3 (CD44-CD25+)  and DN4 (CD44-CD25-)  were sorted out (BD FACS AriaIII high-speed cell sorter) with anti-CD4, anti-CD8,  anti-CD44, and antiCD25 (BioLegend Way, San Diego, CA).
5' end single cell gene expression and VDJ libraries were prepared following manufacturers guidelines (10x Genomics)

value: DN4 thymocytes


title: KO-ND - TEN_025_06 (GE)

status: Public on May 29 2025

type: SRA

city: Noda

first: Yoshikazu

last: Higami

state: Chiba

address: 2641, Ymazaki

department: Faculty of Pharmaceutical Science

country: Japan

institute: Tokyo University of Science

description: Library name: LAB_312_14_S6

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v10.1.1
Reads mapped to reference with gene and transcript annotation using ENSEMBLE
Assembly: mm10
Supplementary files format and content: Processed data file was provided as in matrix table and CLC files.
Supplementary files format and content: tab-delimited excel files include RPKM values, the result of pairwise using edgeR and the result of ANOVA analysis for each sample.

molecule: total RNA

organism: Mus musculus

source_name: epididymal white adipose tissue

extract_protocol:
RNA was harvested using TRIZOL (ThermoFisher/Invitrogen, 15596026 or 10296028) according to the manufacturer’s protocol.
Standard: 500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420). Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420).

tag: tissue

value: epididymal white adipose tissue

tag: genotype

value: Wwp1 Knockout mice

tag: treatment

value: Normal diet


title: CONTROL_TE57_143

type: RNA

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

data_processing: Data were quantified by relative threshold cycles (Crt) methods and normalized on miR-16-5p as per the manufacturer’s instructions (Thermo Fisher Scientific). To further compensate for variability, we added additional normalizers by selecting the two miRNAs most correlating with miR-16-5p, from the list of six miRNAs previously described as housekeeping (doi:10.1093/jnci/djv063). Normalization was performed using the following procedure: a scaling factor (SF) was calculated for each sample, by subtracting the average of the three normalizers to a constant value (K=19.079)(doi:10.1093/jnci/djv063). Data were then normalized using the formula: Crt normalized=miRNA Crt raw – SF. Normalization was skipped for Crt=40. Batch bias was investigated through analysis of the miRNAs expression distribution across centers (FC analysis, Wilcoxon Rank Sum test).

label: FAM

organism: Homo sapiens

source_name: plasma

label_protocol: Total RNA was reverse transcribed using the custom RT Primers and components supplied with the TaqMan MicroRNA Reverse Transcription Kit. The pre-amplified samples were assembled with TaqMan OpenArray Real-Time PCR Master Mix and loaded to OpenArray plates using the OpenArray Accufill System

growth_protocol: not applicable

extract_protocol: Plasma samples were thawed on ice, and RNA was extracted with the commercial miRNeasy mini-Kit (QIAgen™, Hilden, Germany) using the QIAcube™ robot, following the manufacturer´s instructions.

treatment_protocol: not applicable

tag: age

tag: gender

value: F

tag: smocking status

value: FORMER

tag: nodule density

value: part-solid

tag: nodule size

tag: molecule subtype

value: microRNA

tag: center

value: MUG


title: D1-OE1-3-input

city: Beijing

first: Liwen

last: Yang

address: Zhongguancun sourth no.12

department: Biotechnology Research Institute

country: China

data_processing:
RNA-seq: The fastq was used to remove adapter and filter out low-quality reads with more than 20% low-quality bases (quality <20), The clean reads were mapped to rice reference genome MSU7 by HISAT2. The gene expression level was calculated by featureCounts using default parameters. The DEseq package was used for identification and analysis of differential genes, and gene functional enrichment analysis was performed using agriGO v2.0 online software.
Assembly: MSU7
Supplementary files format and content: txt, narrowpeak
RNA m5C IP-seq:  The fastq was used to remove adapter and filter out low-quality reads with more than 20% low-quality bases (quality <20), The clean reads were mapped to rice reference genome MSU7 by the BWA with MEN algorithm.Then, MACS was introduced to locate enriched regions to call m5C peaks by comparing reads from the IP sample with the input sample.

organism: Oryza sativa

source_name: seedlings

growth_protocol:
RNA-seq: ZH11 and DRW1-OE plants were growth in rice paddies at Chinese Academy of Agricultural Sciences Langfang Experiment Station, China.
RNA m5C IP-seq:  ZH11 and DRW1-OE plants were growth in chamber at Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, China.

extract_protocol:
RNA-seq: Total RNA was extracted using a Plant RNA Kit (RP3302; Bioteke, Beijing, China), 1 μg total RNA was used for library construction.
RNA-seq: RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) following manufacturer's protocols
RNA m5C IP-seq:  Total RNA was extracted using a Plant RNA Kit (RP3302; Bioteke, Beijing, China), ~300 μg total RNA was used for library construction.
RNA m5C IP-seq:  RNA libraries for RNA m5C IP-seq were prepared using NEB Next® Ultra™ RNA Library Prep Kit (New England Biolabs) following manufacturer's protocols

value: seedlings

value: 3 weeks after germination


title: ZH11-1-input

institute: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences

value: WT


title: KI_DN4_GEX

country: USA

library_source: transcriptomic single cell

molecule: polyA RNA

tag: cell type

value: GSK3B Ser389Ala KI


title: Reascent, FosHi-MPP, replicate2, DNA methylation

city: Tianjin

first: Peng

last: Wu

address: 288 Nanjing Road

institute: IHCAMS

library_source: genomic

data_processing:
Reads quality control by Trimgalore and reads alignment by Bismark
Assembly: mm10
Supplementary files format and content: bedGraph

molecule: genomic DNA

source_name: Bone marrow

extract_protocol:
FACS-sorted Fos+ and Fos- MPPs from bone marrow
Genome-wide bisulfite sequencing library

treatment_protocol: hypoxia exposure

value: Bone marrow

tag: cell line

value: MPP

value: Hypoxia


title: WT-ND - TEN_025_04 (GE)

description: Library name: LAB_312_12_S4

value: Wild type


title: TUMOR_TE57_133

value: M

tag: histology

value: adenocarcinoma

tag: Stage

value: IIIA

value: solid

value: HUM


title: D1-OE2-1

source_name: grains

value: grains

value: 3 days after pollination


title: Reascent, FosHi-MPP, replicate1, DNA methylation


title: CONTROL_TE57_141

value: F

value: CURRENT

value: microRNA


title: Hypoxia12wNormoxia5w, FosHi-MPP, replicate2, DNA methylation


title: WT_DN3_GEX

source_name: DN3 thymocytes

value: DN3 thymocytes


title: CONTROL_TE57_140


title: D1-OE1-3


title: WT-ND - TEN_025_02 (GE)

description: Library name: LAB_312_10_S2

value: epididymal white adipose tissue

value: Normal diet


title: D1-OE1-2


title: CONTROL_TE57_131

value: FORMER

value: MUG


title: CONTROL_TE57_168


title: ZH11-2-input

value: seedlings

value: 3 weeks after germination

value: WT


title: D1-OE1-1


title: WT-ND - TEN_025_01 (GE)

description: Library name: LAB_312_09_S1

value: Wild type


title: Hypoxia12w, FosLow-MPP, replicate4, DNA methylation

value: Bone marrow

value: MPP

value: Hypoxia


title: ZH11-3

value: grains


title: CONTROL_TE57_138

value: M

value: HUM


title: Hypoxia12w, FosHi-MPP, replicate4, DNA methylation


title: ZH11-2

value: 3 days after pollination


title: CONTROL_TE57_128

value: F

value: CURRENT

value: part-solid

value: microRNA


title: D1-OE2-3


title: BENIGN_TE57_137

value: FORMER

value: solid


title: Hypoxia12w, FosHi-MPP, replicate3, DNA methylation


title: KI_DN3_GEX

value: DN3 thymocytes

value: GSK3B Ser389Ala KI


title: D1-OE2-2


title: CONTROL_TE57_139


title: Hypoxia12w, FosHi-MPP, replicate2, DNA methylation


title: CD45+ cells, wild-type strain

city: Verona

first: Gabriela

last: Constantin

state: Verona

address: Strada le Grazie 8

department: Department of Medicine, Division of General Pathology

institute: University of Verona

data_processing:
The libraries were processed with the 10X Genomics Cell Ranger (v.6.0.1) pipeline.
cellranger mkfastq with default parameters
cellranger count with default parameters
Genome_build: mm10 2020-A downloaded from 10x website as part of Cell Ranger
Supplementary_files_format_and_content: HDF5 file format with matrix, features and barcodes data slots

source_name: leukocytes

extract_protocol:
Mice were anesthetized and perfused through the left cardiac ventricle by injecting cold phosphate-buffered saline (PBS). For the dissection of the meninges, skull caps was remove to collect the dura mater layer, whereas the leptomeninges were gently peeled from the surface of the brain. Then, meninges were enzymatically digested with a collagenase/DNase I solution at 37°C for 25 minutes. Leukocytes were labeled with an anti CD45–BV480 antibody. The cells were re-suspended in PBS supplemented with 10 % FBS, and viable CD45HIGH cells were sorted on a FACSAria Fusion (Becton Dickinson). Both the 3xTg-AD and wild-type samples consisted of > 98% viable cells.  CD45HIGH cells were resuspended to a final concentration of 700 cells/µl.
cDNA sequencing libraries were prepared using the 10x Genomics Chromium Controller and the Chromium Single Cell 3′ NextGEM, Library and Gel Bead kit v3.1 (Pleasanton) following the manufacturer’s instructions. Briefly, 10,000 live cells were loaded onto the Chromium Controller to recover 4000 single-cell gel-bead emulsions (GEMs) per inlet, uniquely barcoded.
After cDNA synthesis, sequencing libraries were generated and final 10× library quality was assessed using the Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies) before sequencing on the Illumina NextSeq500 platform, generating 75 bp paired-end reads (28 bp read 1, 91 bp read 2) at a depth of 50,000 reads per cell, yielding a median per-library depth of 72,783 reads per cell.

tag: organ

value: meninges

tag: strain

tag: Sex

value: female


title: WT_DN3_TCR

value: WT


title: Hypoxia12wNormoxia5w, FosHi-MPP, replicate1, DNA methylation

tag: tissue

value: Bone marrow

value: MPP


title: Hypoxia12wNormoxia5w, FosHi-MPP, replicate3, DNA methylation

value: Hypoxia


title: Hypoxia12w, FosHi-MPP, replicate1, DNA methylation


title: CD45HIGH cells, AD strain

data_processing:
The libraries were processed with the 10X Genomics Cell Ranger (v. 6.0.1) pipeline.
cellranger mkfastq with default parameters
cellranger count with default parameters
Genome_build: mm10 2020-A downloaded from 10x website as part of Cell Ranger
Supplementary_files_format_and_content: HDF5 file format with matrix, features and barcodes data slots

extract_protocol:
Mice were anesthetized and perfused through the left cardiac ventricle by injecting cold phosphate-buffered saline (PBS). After removal of the meninges, the brain was homogenized using a gentleMACS Dissociator (Miltenyi Biotec) and enzymatically digested with a collagenase/DNase I solution at 37 °C for 45 minutes. Cells were passed through a 70-μm cell strainer into a new tube for Percoll gradient centrifugation. Then, cells were removed from the interphase and washed with PBS. Leukocytes were labeled with an anti CD45–BV480 antibody. The cells were re-suspended in PBS supplemented with 10 % FBS, and viable CD45HIGH cells were sorted on a FACSAria Fusion (Becton Dickinson). Both the 3xTg-AD and wild-type samples consisted of > 98% viable cells.  CD45HIGH cells were resuspended to a final concentration of 700 cells/µl.
cDNA sequencing libraries were prepared using the 10x Genomics Chromium Controller and the Chromium Single Cell 3′ NextGEM, Library and Gel Bead kit v3.1 (Pleasanton) following the manufacturer’s instructions. Briefly, 10,000 live cells were loaded onto the Chromium Controller to recover 4000 single-cell gel-bead emulsions (GEMs) per inlet, uniquely barcoded.
After cDNA synthesis, sequencing libraries were generated and final 10× library quality was assessed using the Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies) before sequencing on the Illumina NextSeq500 platform, generating 75 bp paired-end reads (28 bp read 1, 91 bp read 2) at a depth of 50,000 reads per cell, yielding a median per-library depth of 72,783 reads per cell.

value: brain


title: drw1-H3K27me3-2

first: Xiaofeng

last: Gu

address: Zhongguancun south street

institute: Chinese Academy of Agricultrual Sciences

data_processing:
Raw data were trimmed with fastp to remove adapters and low-quality bases. Bowtie2 was used to align reads to Nip-BRI . For broad peaks of H3K27me3, the parameter of peak calling using macs2 was “-q 0.05 --broad”. Peaks were annotated to the rice genome using the R package ChIPseeker.The deeptools and IGV were used to visualize the bigwig files.
Assembly: Nip-BRI http://www.elabcaas.cn/rice/downloads.html
Supplementary files format and content: bw
Library strategy: H3K27me3 cut&tag

source_name: Grain

growth_protocol: ZH11 and drw1 mutant were growth in rice paddies at Chinese Academy of Agricultural Sciences Langfang Experiment Station, China.

extract_protocol:
About 10000 nuclei were harvested and was used for library construction.
Libraries for H3K27me3 cut tag were prepared using HyperactiveUniversalCUT&TagAssayKitfor Illumina (Vazyme, TD903) following manufacturer's protocols

value: Grain

tag: genotype

value: drw1 mutant


title: CONTROL_TE57_125

value: F

value: MUG


title: CONTROL_TE57_132

value: CURRENT


title: Hypoxia4w, FosLow-MPP, replicate4, DNA methylation

tag: treatment


title: KI_DN4_TCR

value: DN4 thymocytes


title: Hypoxia12w, FosLow-MPP, replicate3, DNA methylation


title: CONTROL_TE57_130

tag: age

value: microRNA


title: Hypoxia12w, FosLow-MPP, replicate2, DNA methylation


title: AD strain

data_processing:
The libraries were processed with the 10X Genomics Cell Ranger (v. 3.0.0) pipeline.
cellranger mkfastq with `--ignore-dual-index`
cellranger count with default parameters
Genome_build: GRCm38.93
Supplementary_files_format_and_content: HDF5 file format with matrix, features and barcodes data slots

extract_protocol:
Mice were anesthetized and perfused through the left cardiac ventricle by injecting cold phosphate-buffered saline (PBS). The brain was homogenized using a gentleMACS Dissociator (Miltenyi Biotec) and enzymatically digested with a collagenase/DNase I solution at 37 °C for 45 minutes. Cells were passed through a 70-μm cell strainer into a new tube for Percoll gradient centrifugation. Then, cells were removed from the interphase and washed with PBS. Leukocytes were labeled with an anti CD45–BV480 antibody. The cells were re-suspended in PBS supplemented with 10 % FBS, and viable CD45HIGH cells were sorted on a FACSAria Fusion (Becton Dickinson). Both the 3xTg-AD and wild-type samples consisted of > 98% viable cells.  CD45HIGH cells were resuspended to a final concentration of 700 cells/µl.
cDNA sequencing libraries were prepared using the 10´ Genomics Chromium Controller and the Chromium Single Cell 3′ GEM, Library and Gel Bead kit v3 (Pleasanton) following the manufacturer’s instructions. Briefly, 10,000 live cells were loaded onto the Chromium Controller to recover 4000 single-cell gel-bead emulsions (GEMs) per inlet, uniquely barcoded.
After cDNA synthesis, sequencing libraries were generated and final 10× library quality was assessed using the Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies) before sequencing on the Illumina NextSeq500 platform, generating 75 bp paired-end reads (28 bp read 1, 91 bp read 2) at a depth of 50,000 reads per cell, yielding a median per-library depth of 72,783 reads per cell.

value: CD45HIGH cells


title: KI_DN3_TCR

value: DN3 thymocytes


title: CONTROL_TE57_129

tag: gender

value: M


title: Hypoxia12w, FosLow-MPP, replicate1, DNA methylation


title: WT_DN4_TCR


title: wild-type strain


title: daf-2 mutant, Day 1, Rep 3

city: Huddinge

first: Christian

middle: Günter

last: Riedel

state: Stockholm

address: Blickagången 16 (Neo Building, 6th floor)

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
The analysis of raw ATAC-seq and mRNA-seq data was conducted using Cactus v0.8.4 (Salignon et al, Genomics, 2024), using default parameters and the following custom parameters: species = 'worm', chromatin_state = 'iHMM.M1K16.worm_L3', use_input_control = true, diffbind__summits = 'TRUE', diffbind__design = 'FALSE', diffbind__edger_tagwise = 'FALSE', diffbind__min_count = 1, diffbind__background = 'FALSE', diffbind__library_size = 'DBA_LIBSIZE_FULL', diffbind__scale_control = 'FALSE', diffbind__score = 'DBA_SCORE_TMM_READS_FULL_CPM', split__peak_assignment = [ 'all', 'prom', 'distNC' , '3pUPR' ] and pwms_motifs = hughesCePWMSForHomerLO9.motif'. The latter custom motif file contained experimentally defined C. elegans TF binding motifs and was created by the Brunet lab and used in (Daugherty et al, Genome Research, 2017). Two replicates of a genomic DNA control, taken from the strain GR1373, were used in all analyses to remove peaks located in hotspot regions.
Assembly: ce11/WBcel235, Ensembl release 107
Supplementary files format and content: mrna_raw_counts.txt.gz: TSV file containing the raw count matrix. Counts estimated from Kallisto were rounded.
Supplementary files format and content: mrna_TPM.txt.gz: TSV file containing the Transcripts Per Million count matrix.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C. elegans were grown on the Escherichia coli strain OP-50 using standard methods (Stiernagle, 2006). In the case of RNAi experiments, animals were grown on the Escherichia coli strain HT115 transformed with L4440-based plasmids expressing double-stranded RNA targeting the genes of interest.

extract_protocol:
For each condition and timepoint, a minimum of 80 worms were collected in triplicate. Worms were washed twice with M9, resuspended in 100 µl Tri Reagent (Zymo Research, Cat. No.: R2050-1-200), and then immediately frozen in liquid nitrogen. RNA was extracted with the Direct-zolTM RNA MiniPrep kit (Zymo Research, Cat. No.: R2052) according to the manufacturer’s instructions, and RNA amount and quality were determined using a NanoDrop. mRNA was isolated and cDNA constructed by following the TruSeq RNA Library Preparation Kit v2 protocol (Illumina, Cat. No.: RS-122-2001/RS-122-2002).
mRNA-seq libraries were constructed using the TruSeq RNA Library Preparation Kit v2 (Illumina, Cat. No.: RS-122-2001/RS-122-2002) according to the manufacturer’s instructions.

treatment_protocol: C. elegans were synchronized at the L1 stage by bleaching and hedging in M9 and seeded onto plates pre-seeded with either OP-50 or RNAi bacteria (E. coli strain HT115 containing dsRNA-expressing plasmids that target a specific gene of interest). HT115 with the empty plasmid L4440 was used as the control. The RNAi clone targeting daf-16 was obtained from the Ahringer library (Kamath et al., Nature 2003), while the clone targeting lin-39 was obtained from the Vidal library (Reboul et al., Nature Genetics 2003). Plates were incubated at 15°C until the animals reached the late L4 stage. FUDR was added to a final concentration of 50 µM to prevent progeny production, and plates were shifted to 20°C (mRNA-seq) or 25°C (ATAC-seq) for the remainder of the assays. Worms were collected and harvested at indicated timepoints.

value: whole organism


title: CD45+ cells, AD strain

value: meninges

value: female


title: Hypoxia4w, FosLow-MPP, replicate1, DNA methylation

value: Bone marrow


title: ZH11-1

value: grains

value: 3 days after pollination

value: WT


title: daf-2 mutant, Day 1, Rep 2


title: CONTROL_TE57_126

tag: smocking status

value: FORMER

value: solid


title: Hypoxia4w, FosHi-MPP, replicate3, DNA methylation

value: MPP

value: Hypoxia


title: drw1-H3K27me3-3

value: Grain

value: drw1 mutant


title: CONTROL_TE57_124

value: F

value: CURRENT

value: microRNA

value: HUM


title: CONTROL_TE57_127

value: MUG


title: CD45HIGH cells, wild-type strain

value: brain


title: drw1-H3K27me3-1


title: TUMOR_TE57_120

value: adenocarcinoma

value: IIB

tag: nodule density


title: Hypoxia4w, FosLow-MPP, replicate3, DNA methylation

value: Bone marrow


title: ZH11-H3K27me3-3


title: Hypoxia4w, FosHi-MPP, replicate2, DNA methylation


title: CONTROL_TE57_12

value: M

tag: nodule size


title: CONTROL_TE57_123

tag: molecule subtype


title: Hypoxia4w, FosLow-MPP, replicate2, DNA methylation


title: KO-HFD - TEN_025_14 (GE)

description: Library name: LAB_312_22_S14

value: epididymal white adipose tissue

value: Wwp1 Knockout mice

value: High fat diet


title: ZH11-H3K27me3-2

value: WT


title: BENIGN_TE57_122

value: solid

tag: center


title: ZH11-6mA-IP2

data_processing:
Raw data were trimmed with fastp to remove adapters and low-quality bases. Bowtie2 was used to align reads to Nip-BRI . After alignment, 6mA-enriched regions were called with MASC2 with the cutoffs false discovery rate (FDR) <0.05 and FC >2. Peaks were annotated to the rice genome using the R package ChIPseeker.The deeptools and IGV were used to visualize the bigwig files.
Assembly: Nip-BRI http://www.elabcaas.cn/rice/downloads.html
Supplementary files format and content: bw
Library strategy: DNA 6mA IP-seq

source_name: grain

extract_protocol:
Genomic DNA was extracted from ZH11 and drw1 seeds at 3 DAP, treated with RNase A and sonicated to produce ~250 bp fragments. 5 μg genomic DNA was used for library construction.
Libraries for DNA 6mA IP-seq were prepared using Novogene DNA Library Prep Kit following manufacturer's protocols.

value: grain


title: ZH11-H3K27me3-1

value: Grain


title: drw1-6mA-IP2

value: drw1 mutant


title: Hypoxia2w, FosLow-MPP, replicate3, DNA methylation

value: MPP

tag: cell type

value: Hypoxia


title: CONTROL_TE57_119

value: CURRENT

value: microRNA


title: CONTROL_TE57_118

value: FORMER

value: MUG


title: Wild-Type, Day 1, Rep 2

value: whole organism


title: Wild-Type, Day 1, Rep 3


title: Wild-Type, Day 1, Rep 1


title: drw1-6mA-input2


title: ZH11-6mA-IP1


title: glp-4, Day 7, Rep 2

data_processing:
The analysis of raw ATAC-seq and mRNA-seq data was conducted using Cactus v0.8.4 (Salignon et al, Genomics, 2024), using default parameters and the following custom parameters: species = 'worm', chromatin_state = 'iHMM.M1K16.worm_L3', use_input_control = true, diffbind__summits = 'TRUE', diffbind__design = 'FALSE', diffbind__edger_tagwise = 'FALSE', diffbind__min_count = 1, diffbind__background = 'FALSE', diffbind__library_size = 'DBA_LIBSIZE_FULL', diffbind__scale_control = 'FALSE', diffbind__score = 'DBA_SCORE_TMM_READS_FULL_CPM', split__peak_assignment = [ 'all', 'prom', 'distNC' , '3pUPR' ] and pwms_motifs = hughesCePWMSForHomerLO9.motif'. The latter custom motif file contained experimentally defined C. elegans TF binding motifs and was created by the Brunet lab and used in (Daugherty et al, Genome Research, 2017). Two replicates of a genomic DNA control, taken from the strain GR1373, were used in all analyses to remove peaks located in hotspot regions.
Assembly: ce11/WBcel235, Ensembl release 107
Supplementary files format and content: *.bw: BigWig files.

extract_protocol:
ATAC-seq was conducted as described in (Daugherty et al., 2017), using duplicates for every condition. In brief, day 1 adults were washed off the plates with M9, washed in PBS, and frozen in liquid nitrogen. Nuclei were released by mechanical homogenization(Haenni et al., 2012), counted by measuring optical density, and then processed as described in (Buenrostro et al., 2013).
ATAC-seq libraries were constructed by following the protocol described in (Buenrostro et al., 2013). 10 ng of genomic DNA were used as the input control.


title: Hypoxia4w, FosHi-MPP, replicate1, DNA methylation

value: Bone marrow

tag: cell line


title: drw1-6mA-IP1


title: CONTROL_TE57_115

value: F


title: Hypoxia2w, FosLow-MPP, replicate2, DNA methylation


title: daf-2 mutant, Day 1, Rep 1


title: Hypoxia2w, FosHi-MPP, replicate4, DNA methylation


title: TUMOR_TE57_114

tag: histology

value: carcinoma planoepitheliale

value: IA


title: CONTROL_TE57_117


title: ZH11-6mA-input1


title: Hypoxia2w, FosHi-MPP, replicate3, DNA methylation


title: glp-4, Day 3, Rep 1


title: drw1-6mA-input1


title: ZH11-6mA-input2


title: glp-4, Day 7, Rep 1


title: Hypoxia2w, FosHi-MPP, replicate2, DNA methylation


title: drw1-ATAC-3

data_processing:
Raw data were trimmed with fastp to remove adapters and low-quality bases. Bowtie2 was used to align reads to Nip-BRI . For broad peaks of H3K27me3, the parameter of peak calling using macs2 was “-q 0.05 --nomodel --shift 100 --extsize 200 --keep-dup all”. Peaks were annotated to the rice genome using the R package ChIPseeker.The deeptools and IGV were used to visualize the bigwig files.
Assembly: Nip-BRI http://www.elabcaas.cn/rice/downloads.html
Supplementary files format and content: bw

source_name: Panicle

extract_protocol:
About 2,0000 nuclei were harvested and was used for library construction.
~2,0000 nuclei were collected in each 20 μl Tn5 transposase integration reaction for 30 min at 37°C. Subsequently, DNA fragments were purified using VAHTS DNA Clean Beads (Vazyme, N411), eluted in 15 μl elution buffer. Subsequently, the entirety of each sample was amplified applying NEB Next Master Mix and barcode primers for 15 PCR cycles. These amplified ATAC-seq libraries were purified and sequenced on an Illumina Novaseq6000 platform with150-bp paired-end reads.

value: Panicle


title: drw1-ATAC-2


title: Hypoxia2w, FosLow-MPP, replicate1, DNA methylation


title: CONTROL_TE57_113

value: M

value: HUM


title: glp-4, Day 1, Rep 1


title: CONTROL_TE57_116

value: solid


title: Hypoxia2w, FosHi-MPP, replicate1, DNA methylation


title: drw1-ATAC-1


title: dppil4 KD, ZT16, #3

city: Suwon-si

first: Eun Young

last: Kim

address: 164 Worldcup-ro

country: South Korea

institute: Ajou University School of Medicine

description: Library name: Td2_CG5808Ri_3

data_processing:
Reads were aligned to the Drosophila melanogaster (dm6) using STAR v2.6.0c. After alignment, the transcripts were assembled and quantified using RSEM v1.3.1.
Assembly: dm6
Supplementary files format and content: Excel file that include Read counts, FPTM, and TPM

organism: Drosophila melanogaster

source_name: Drosophila head including brain

extract_protocol:
Total RNA from fly heads were extracted using QIAzol reagent (QIAGEN)
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA)

value: Drosophila head including brain

value: dppil4 KD (UAS-dicer2/UAS-dppil4 RNAi;tim(UAS)-Gal4/+)


title: CONTROL_TE57_11


title: dppil4 KD, ZT16, #2

description: Library name: Td2_CG5808Ri_2


title: ZH11-ATAC-3

value: WT


title: glp-4, Day 3, Rep 2


title: CONTROL_TE57_108


title: Control, FosLow-MPP, replicate2, DNA methylation

value: MPP

value: Control


title: CONTROL_TE57_107

value: CURRENT

value: microRNA


title: dppil4 KD, ZT16, #1

description: Library name: Td2_CG5808Ri_1


title: ZH11-ATAC-2


title: ZH11-ATAC-1


title: Control, FosLow-MPP, replicate1, DNA methylation


title: Control, FosHi-MPP, replicate4, DNA methylation


title: Control, ZT16, #3

description: Library name: Td2_ZT16_3

value: Control (UAS-dicer2/+;tim(UAS)-Gal4/+)


title: CONTROL_TE57_112


title: glp-4, Day 1, Rep 2

value: whole organism


title: DRW1-OE2-Flag-2

data_processing:
Raw data were trimmed with fastp to remove adapters and low-quality bases. Bowtie2 was used to align reads to Nip-BRI . After alignment, 6mA-enriched regions were called with MASC2 with the cutoffs false discovery rate (FDR) <0.05 and FC >2. Peaks were annotated to the rice genome using the R package ChIPseeker.The deeptools and IGV were used to visualize the bigwig files.
Assembly: Nip-BRI http://www.elabcaas.cn/rice/downloads.html
Supplementary files format and content: bw
Library strategy: DRW1-Flag cut&tag

growth_protocol: ZH11 and DRW1-OE plants were growth in rice paddies at Chinese Academy of Agricultural Sciences Langfang Experiment Station, China.

extract_protocol:
About 10000 nuclei were harvested and was used for library construction.
Libraries forDRW1-Flag cut tag were prepared using HyperactiveUniversalCUT&TagAssayKitfor Illumina (Vazyme, TD903) following manufacturer's protocols

value: Grain


title: CONTROL_TE57_106

value: MUG


title: CONTROL_TE57_111


title: Control, FosHi-MPP, replicate3, DNA methylation

value: Bone marrow


title: CONTROL_TE57_105

value: F

value: FORMER


title: Control, FosLow-MPP, replicate4, DNA methylation


title: Control, ZT16, #1

description: Library name: Td2_ZT16_1


title: DRW1-OE2-Flag-1


title: DRW1-OE1-Flag-2


title: CONTROL_TE57_104

value: M


title: Control, FosLow-MPP, replicate3, DNA methylation


title: dppil4 KD, ZT8, #3

description: Library name: td2_5808_ZT8-5


title: TUMOR_TE57_103

value: carcinoma planoepitheliale

tag: Stage

value: IB


title: Control, FosHi-MPP, replicate1, DNA methylation


title: Control, FosHi-MPP, replicate2, DNA methylation


title: dppil4 KD, ZT8, #2

description: Library name: td2_5808_ZT8-3

value: Drosophila head including brain


title: BV-2, BHB_3

city: Shanghai

first: Mengqiu

last: Deng

state: None Selected

address: 415 Fengyang Road

department: Department of Anesthesiology,

institute: Second Affiliated Hospital of Naval Medical University

data_processing:
The quality of the raw reads was first assessed using FastQC (v0.11.5).
Trimmomatic was used to remove single end sequence adaptors and a sliding window approach was used to determine the average base quality. Trailing bases were trimmed if the average quality within a window fell below 20, and reads below 50bp after quality filtering were discarded.
After sequence filtering, the resulting high-quality reads were aligned to the mouse reference genome (GRCm38) using Hisat2
StringTie was used for gene expression quantification for each gene, which produced a gene expression matrix
Assembly: GRCm38
Supplementary files format and content: Excel file include raw counts for each Sample

extract_protocol:
Total RNA was extracted from the BV-2 cell samples of each experimental group according to the instructions of the TRIzol reagent kit.
The cDNA libraries were prepared using the SmartScribeTM Reverse Transcriptase Kit (TAKARA, Japan). Ampure XP Beads (Beckman Coulter, USA) were used to select 300-450 bp DNA fragments from the indexed libraries. The libraries were quantified using an Agilent 2100 Bioanalyzer and then combined at a concentration of 2 nM in a 1:1 ratio.

value: LPS+BHB


title: BV-2, BHB_2


title: ZH11-Flag-2

value: WT


title: ZH11-Flag-1


title: CONTROL_TE57_102

value: HUM


title: CONTROL_TE57_101


title: Control, ZT16, #2

description: Library name: Td2_ZT16_2


title: Control, ZT8, #3

description: Library name: td2_ZT8-5


title: BENIGN_TE57_100

value: solid


title: BV-2, BHB_1


title: Control, ZT8, #2

description: Library name: td2_ZT8-4


title: BV-2, Medium_3

value: LPS


title: drw1-3

data_processing:
The fastp was used to remove adapter and filter out low-quality reads with more than 20% low-quality bases (quality <20), The clean reads were mapped to rice reference genome Nip-BRI by HISAT2. The gene expression levels were computed using featureCounts with default parameters. Identification and analysis of differential genes were conducted using the DESeq package, and gene functional enrichment analysis was performed using agriGO v2.0 online software.
Assembly: Nip-BRI http://www.elabcaas.cn/rice/downloads.html
Supplementary files format and content: txt

extract_protocol:
Total RNA was extracted using a Plant RNA Kit (RP3302; Bioteke, Beijing, China), 1 μg total RNA was used for library construction.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) following manufacturer's protocols

value: drw1 mutant


title: drw1-2


title: BV-2, Medium_2


title: VGLL_20

type: genomic

city: Berlin

first: Simone

last: Schmid

address: Charitéplatz 1

department: Department of Neuropathology

country: Germany

institute: Charité-Universitätsmedizin Berlin

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k or 850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned on the iscan instument acording to standarad protocol

data_processing:
Standard R packages minfi, Rtsne, conumee
Average Beta and Detection P value

label: Cy3 and Cy5

source_name: Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from human tumor samples using Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) according to standard instructions


title: drw1-1


title: APR.Adipocyte.PBS.plus.RAD

city: Omaha

first: Rebecca

last: Oberley-Deegan

state: NE

address: 2051 S 86TH AVE

institute: University of Nebraska Medical Center

description: Library name: COHP_49474_1_UN_Whole_C1_KBMRS_L49278_HCLW7DSX5_CCGTAAGA_L002_R1_001.fastq

data_processing:
CLC Genomics Workbench v 11.0.1
Sequenc  reads were trimmed for adaptor sequence.low quality sequence using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: cvs file include RPKM values for each sample

source_name: primary adipocytes

growth_protocol: Primary mouse gonadal adipose tissue was harvested two months after radiation. Fat pads were digested with collagenase and incubated at 37 °C for 45 minutes, with manual swirling every 5 minutes. Once the fat was dissociated, 4x volume of cold HBSS (without Ca2+ & Mg 2+) was added and the tube was centrifuged at 450 g for 3 minutes at 4 °C. Mature adipocytes found in the floating fraction were removed and maintained in culture for 3 days.

extract_protocol:
Quick-RNA MiniPrep (Plus) from Zymo Research
Illumina Stranded RNA-seq livarary perparation protocol

treatment_protocol: Mice were pelvically irradiated  receiving 7.5 Gy for 5 days or sham irradiated.

value: primary adipocytes

value: radiation


title: DRW1-OE1-Flag-1

value: Grain


title: BV-2, Medium_1


title: ZH11-3


title: VGLL_19


title: AP.Adipocyte.PBS

description: Library name: COHP_49472_1_UN_Whole_C1_KBMRS_L49276_HCLW7DSX5_CGACGTTA_L002_R1_001.fastq

value: no radiation


title: BV-2, Control_3

value: PBS


title: dppil4 KD, ZT8, #1

description: Library name: td2_5808_ZT8-1

value: dppil4 KD (UAS-dicer2/UAS-dppil4 RNAi;tim(UAS)-Gal4/+)


title: ZH11-2


title: VGLL-Peripheral_3


title: Control S5

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
Sequencing data (fastq files) were uploaded to and analyzed on the Galaxy web platform (usegalaxy.eu) 13, as previously described 14.
Reads were mapped to the human reference genome (Gencode, release 42, hg38) with RNA STAR Galaxy Version 2.7.8a 15 with default parameters using the Gencode annotation file (Gencode, release 42, https://www.gencodegenes.org/human/releases.html).
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 2.0.1 16 with default parameters using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (version 2024.04.2+764, R version 4.4.1).
Differential gene expression was analyzed using the R package DESeq2 Version 1.44.0 18 with default parameters (Benjamini-Hochberg adjusted p-values).
Assembly: Gencode GRCh38.p13, all regions, release 42
Supplementary files format and content: xlsx, normalized reads (DESeq2)

source_name: Retinal control tissue

extract_protocol:
Paired retinoblastoma and adjacent retinal tissue samples were collected from seven enucleated retinoblastoma eyes. Histopathological evaluation by at least two experienced ophthal-mic pathologists confirmed the presence of retinoblastoma in all seven cases and adjacent retinal tissue in five cases. In the remaining two eyes, normal retinal tissue could not be iso-lated. For RNA sequencing, tumor and control tissue were carefully isolated before analysis using a macrodissection protocol 10 to remove unwanted tissue prior to analysis.
FFPE samples were shipped in tubes at room temperature to the sequencing provider (Gen-XPro, Frankfurt, Germany)

value: Retinal control tissue


title: ZH11-1


title: VGLL_18


title: Control S4


title: BV-2, Control_1


title: VGLL-Peripheral_2


title: Control S3


title: Orgs AK3 KO CC+B

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
Qualified libraries were sequenced with Illumina Novaseq 6000 platform.
ChIP-Seq reads were aligned to the reference genome GRCm38 using the hisat2 software, and only uniquely and non-duplicate mapped reads were used to perform the downstream analysis.
The reads coverage and depth were calculated by samtools software.
The BAM files were subjected to peak calling analysis using MACS2 to identify regions in the genome exhibiting significant enrichment of reads.
The identified peaks were further subjected to gene annotation analysis and visualization using the Chipseeker package and IGV software.
Assembly: mm10

source_name: Gastric Organoids

extract_protocol:
The gastric epithelial cells or organoids were digested by Tryple and EDTA then follow the manufacturer’s instructions (novoprotein,N259-YH01) .
Gastric epithelial cells or organoids were fixed in 1% formaldehyde and lysed with lysis buffer, followed by digestion with micrococcal nuclease.

value: Gastric Organoids

value: gastric epithelial cell

tag: chip antibody

value: Tamoxifen and BMP4 treatment


title: MOLM13_OE_BTG2_2

city: Farmington

first: Harshpreet

last: Chandok

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

data_processing:
Reads from Dorado were used to determine polyA tail length and aligned to the genome using Minimap2 (-ax splice -t 7 =B 3 =O 3,20 --junc-ed GENCODE v43 annotation)
Each read was then assigned to a unique gene with the primary alignments using IsoWant --data_type nanopore --gene_quantification unique_only --splice correction_strategy default_ont --no-secondary)
Reads assigned were then extracted to get polyA tail length tags and data was exported to R to test for differences in length using a Kolmogorov-Smirnov test at the gene level between Empty Vector control and BTG overexpression
Assembly: hg38
Supplementary files format and content: BTG2OE_vs_EV_results.csv

source_name: cell line

growth_protocol: MOLM13 cells were maintained in RPMI-1640 media suppleented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin in a humidified incubator at 5%CO2 at 37ºC

extract_protocol:
Total RNA was extracted with the Rneasy Plus Mini Kit (Qiagen) and QIAshredder folloiwng the manufacturer's protocol.
Poly(A) mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module using ~1µg of total RNA as input following the manufacturer's protocol. The NEXTflex Rapid Directional RNA-Seq Kit 2.0 (PerkinElmer) was used to generate cDNA libraries utilizing the NEXTflex RNA-Seq barcodes accoridng to the manufacturer's protocol. LIbraries were sequenced using a Nova-Seq X with 150bp paired end reads.

treatment_protocol: All cDNA constructs were cloned into a lentiviral fector (EF1α-IRES-Puromycin-T2A-ZsGreen) and spin infections were performed at 32ºC at 1500 RCF for 60min with 5µg/mL polybrene and lentiviral supernatants. Cells were collected 3 days after transduction and processed for RNA isolation and library preparation.

value: cell line

value: Acute Myeloid Leukemia

value: BTG2 OE

value: Lentiviral infection and overexpression


title: CONTROL_TE57_10

data_processing: Data were quantified by relative threshold cycles (Crt) methods and normalized on miR-16-5p as per the manufacturer’s instructions (Thermo Fisher Scientific). To further compensate for variability, we added additional normalizers by selecting the two miRNAs most correlating with miR-16-5p, from the list of six miRNAs previously described as housekeeping (doi:10.1093/jnci/djv063). Normalization was performed using the following procedure: a scaling factor (SF) was calculated for each sample, by subtracting the average of the three normalizers to a constant value (K=19.079)(doi:10.1093/jnci/djv063). Data were then normalized using the formula: Crt normalized=miRNA Crt raw – SF. Normalization was skipped for Crt=40. Batch bias was investigated through analysis of the miRNAs expression distribution across centers (FC analysis, Wilcoxon Rank Sum test).

extract_protocol: Plasma samples were thawed on ice, and RNA was extracted with the commercial miRNeasy mini-Kit (QIAgen™, Hilden, Germany) using the QIAcube™ robot, following the manufacturer´s instructions.

value: F

value: CURRENT

value: microRNA

value: MUG


title: Control, ZT8, #1

description: Library name: td2_ZT8-2

value: Drosophila head including brain

value: Control (UAS-dicer2/+;tim(UAS)-Gal4/+)


title: VGLL-Peripheral_1


title: MOLM13_OE_BTG2_1


title: Control S2


title: Orgs AK3 KO CC

value: Tamoxifen


title: VGLL_17


title: MOLM13_OE_Ctrl_2

value: WT


title: Orgs CON CC+B

value: BMP4 treatment


title: VGLL_16


title: MOLM13_OE_Ctrl_1


title: Control S1

value: Retinal control tissue


title: Retinoblastoma S7

source_name: Retinoblastoma

value: Retinoblastoma


title: Orgs CON CC

value: Gastric Organoids

value: gastric epithelial cell

value: No


title: Retinoblastoma S6


title: Retinoblastoma S5


title: si-4c1

city: Xianyang

first: Yanfang

state: Shaanxi

address: No. 22, Xinong Road, Yangling District

department: College of Veterinary Medicine

institute: Northwest A&F University

description: Library name: B4

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Sus_scrofa.Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Sus scrofa

source_name: Porcine 2cell-embryo

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

value: Porcine 2cell-embryo


title: Retinoblastoma S4


title: si-4c3

description: Library name: B6


title: VGLL_13


title: VGLL-Peripheral_4


title: KOTissue ZB

source_name: Stomach

value: Stomach

value: epithelial cell and stromal cell


title: Orgs CC+B


title: Retinoblastoma S3


title: CON Tissue ZB


title: si-4c2

description: Library name: B5


title: BV-2, Control_2

value: PBS


title: VGLL_15


title: Retinoblastoma S2


title: VGLL_12


title: Orgs CC


title: Retinoblastoma S1


title: VGLL_14


title: CON S1


title: IgG


title: si-2c3

description: Library name: B3

source_name: Porcine 4cell-embryo

value: Porcine 4cell-embryo


title: si-2c2

description: Library name: B2


title: VGLL_11


title: ALK3 KO S1


title: si-2c1

description: Library name: B1


title: con-4c3

description: Library name: A6

value: blank control


title: VGLL_8


title: VGLL_6


title: 20289:ND-55-M + cytokines

city: Worcester

first: Mason

last: Tarpley

state: MA

address: 368 Plantation Street Albert Sherman Center, AS7.2049

department: Diabetes Center of Excellence

institute: UMass Chan Medical School

data_processing:
Data were processesd using the DolphinNext RNA-Seq pipeline (V 1.6.0) and Gencode hg38v34 as the reference genome.
FastQC was used for quality control checks
Trimmer was used to remove adaper sequcnes from ends of reads.
Sequential_Mapping was used to map and remove rRNA and snRNA reads.
STAR was used to map the reads to the reference genome.
RSEM was used to estimate gene expression levels.
DEBRowser was used to generate lists of differentiatlly expressed genes.
Feature counts and Picard were used after genome mapping for additional quality control.
Assembly: hg38v34
Supplementary files format and content: rsem.out.genes.results

molecule: cytoplasmic RNA

source_name: pancreatic islet

growth_protocol: Samples labeled untreated or cytokine tereated were cultured in AIM_V medium for 48 hs.  The remaininng samples were ddissociated upon receipt.

extract_protocol:
RNA was released from fixed and stained islet cells by treatment with resuspension buffer and Proteinase K from the Ambion Recoverall kit at 50˚C for 3 hours.  Depending on cell number, RNA was purified and DNA removed on a Recoverall column or RNA-Clean XP beads.
Libraries were constructed using with the the NUGen Ovation FFPE or the Clontech SMARTER Pico kits.

treatment_protocol: Samples labeled cytokine-treated were cultured with IFNg, IL-1b, and TNFa in AIM-V medium for 48 hrs.

value: pancreatic islet

tag: disease state

value: non-diabetic

value: M

value: beta cells

value: cytokine treated


title: KPC-tumor-tissue_Cstf2_KD_scRNA-Seq_Rep1

city: Guangzhou

first: Zhou

last: yifan

state: 周一帆

address: 74 Zhongshan Second Road

institute: Sun Yat-sen University Cancer Center

description: 10 × Genomics

data_processing:
Samples were sequenced with an average depth of 50,000 reads per cell. The quality of cells was assessed based on three metrics including controlling the number of total UMI count per cell (library size) below 30,000, the number of detected genes > 200 and < 6,000 and the percentage of mitochondrial genes < 10%. Subsequently, Seurat (version 4.3.0) was employed to normalize the data to sequencing depth through a LogNormalize approach. Mitochondrial contamination and cell cycle effects were also regressed out. To identify a subset of significant principal components, the PCElbowPlot function of Seurat was utilized. For cell clustering and UMAP visualization, the FindClusters and RunUMAP functions were executed, respectively. The annotations of cell identity on each cluster were defined by the expression of known marker genes.
Assembly: mm10

source_name: KPC tumor tissue

extract_protocol:
Transfer the chopped pieces to a 50 ml centrifuge tube, add Collagenase Type  II and Collagenase Type IV, add 15 ul CaCl2 (100 mg/ml) solution and 1mg/ml DNase I . Mix well and place on a shaker at 37 ℃ for 20-30 min. After the digestion is complete, take it out and filter it through a 70um sieve and then a 40um sieve into a new 50 ml centrifuge tube, and immediately place the filtered supernatant on ice. Centrifuge at 400g for 4 min. And resuspend the pellet with 5 ml RBC Lysis buffer. 5 ml of 0.04% BSA was used to resuspend, and then determine the cell concentration using a Countess II FL Automated Cell Counter. According to the requirements of 10X GENOMICS on the machine, suck out the corresponding volume of cell suspension.
library preparation was performed on  10 × Genomics system.

value: KPC tumor tissue

value: Cstf2 KD


title: 18024_T1D_49_F_27yr

tag: Sex

value: F

value: no treatment


title: BENIGN_TE57_121

source_name: plasma

value: CURRENT

value: solid

value: microRNA

value: HUM


title: con-4c2

description: Library name: A5

tag: tissue

value: Porcine 2cell-embryo


title: KPC-tumor-tissue_Normal_scRNA-Seq_Rep2

description: 10 × Genomics

tag: genotype

value: WT


title: con-2c2

description: Library name: A2

value: Porcine 4cell-embryo

tag: treatment


title: VGLL_9


title: sperm3 [ncRNA-seq]

description: Library name: C3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the Sus_scrofa.Sscrofa11.1 reference genome using Tophat2 (2.0.4) package,remaining reads (unmapped reads) were still mapped to reference genome using tophat-fusion (2.1.0), which wassubsequently used to identify circRNA.CIRCExplorer2 (2.2.6, default) and CIRI (2.0.2, default) was used to denovo assemble the mapped reads to circularRNAs at first; Then, back-spliced junction reads were identified in unmapped reads by tophat-fusion andCIRCExplorer2 or CIRI. All samples were generated unique circular RNAs.We normalized the back-spliced reads (support for circRNA) by read length and number of mapped reads (spliced reads per billion mapping, denoted as SRPBM), which permits quantitative comparisons between back splicing from differentRNA-seq. We counted the total number of reads mapped to the reference genome in each sample and normalized the number of reads spanning the back-spliced junction to the total number of mapped reads (units in billion) and read length. The SRPBM value of each sample circRNA was calculated by the Perl script and used as the expressionabundance.SRPBM = number of circular reads/number of mapped reads (units in billion)/read length.circRNAs differential expression analysis was performed by edgeR(http://bioconductor.org/packages/release/bioc/html/edgeR.html) software between two different group and twodifferent samples. The circRNAs with the parameter of pvalue < 0.05 (pvalue was corrected using Benjamini &Hochberg method) and fold change > 2 or fold change < 0.5 were considered differentially expressed circRNAs.Differentially circRNA host coding genes were then subjected to enrichment analysis of GO functions and KEGGpathways.
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9).
We aligned reads of all samples to the Homo sapiens reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package. The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/ , version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml , version:gffcompare-0.9.8). First of all, transcripts that overlapped with known mRNAs, lncRNAs and transcripts shorter than 200bp werefiltered. Then we utilized CPC0.9-r2 (http://cpc2.cbi.pku.edu.cn, ) and CNCI2.0(https://github.com/www-bioinfo-org/CNCI#install-cnci) with default parameters to predict novel transcripts withcoding potential. All transcripts with CPC score < 0.5 and CNCI score < 0 were retained and considered asnovel lncRNAs.The remaining transcripts with class code (I, j, o, u, x) were considered as novel lncRNAs.After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs and lncRNA by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: Sus_scrofa.Sscrofa11.1
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Porcine sperm

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) with RIN number > 7.0. Approximately 5ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero Gold rRNA Removal Kit (Illumina, cat.MRZG12324, SanDiego, USA).
After removing ribosomal RNAs, the left RNAs were fragmented (NEBNext® Magnesium RNA Fragmentation Module, cat.E6150S, USA) into short fragments using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II ReverseTranscriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection (300-600bp) was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50bp.

value: Porcine sperm

value: without treatment


title: HS-IU_2044

city: Wenzhou

first: Tong

last: Yin

address: Luchengqu Guantanglu38-9

institute: Zhejiang Key Laboratory of Dairy Cattle Genetic Improvement and Milk Quality Researc

description: Library name: HS-IU_2044

data_processing:
we clipped adaptors for RNA reads and discarded short reads (< 36 bp) and reads with poor quality (< 20) applying the software package cutadapt V4.2. In the second step, we assessed the quality of the RNA reads for each sample using FastQC V0.12.1, and found that all samples past the per base sequence quality. Afterwards, the reference genome sequences and the annotation file according to bovine assembly ARS-UCD1.2 were provided to generate the genome index files using the software package STAR V2.7.11a. Finally, the RNA-seq reads were mapped to the reference genome based on the index and genome files generated in the previous step and the number of reads per gene were counted for each sample using the flag “--quantMode GeneCounts” with STAR. After combining the reads per gene for all samples, we identified 23,010 genes with nonzero RNA-seq reads.
Assembly: bovine assembly ARS-UCD1.2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Bos taurus

source_name: Whole Blood

extract_protocol:
Total RNA was isolated using the Zymo directZol Mini Prep kit by homogenizing 100 ul of RLT cell suspension in 900 ul TriZOL reagent supplemented with 20 ul 1-Thioglycerol. 200 ng of total RNA were captured on oligo-dT beads and reverse transcribed directly on the beads.
Libraries were prepared using the Lexogen SENSE mRNA-seq Library Prep Kit V2 (Lexogen, Greenland, NH, USA).

value: Whole Blood

tag: age

value: Calf

value: no heat stress

tag: batch


title: 20289:ND-55-M no cytokines

value: pancreatic islet

value: non-diabetic

value: M

value: beta cells


title: HS-IU_2043

description: Library name: HS-IU_2043


title: HS-IU_2041

description: Library name: HS-IU_2041


title: ADX_SA infection with stress, Day 2, triplicate sample 1

city: San Diego

first: Hung

last: Chan

state: CA

address: 9452 Medical Center Drive,ACTRI Bldg, L1W420

institute: UCSD

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow
Trimmed sequence reads were mapped to STAR using Partek Flow
Read count extraction and normalization were performed using Partek Flow
Assembly: mm10 for mouse; hg38 for human
Supplementary files format and content: tab-delimited text files with raw counts values for each sample

source_name: skin

extract_protocol:
ThermoFisher PureLink RNA Kit Illumina stranded mRNA or Illumina total RNA prep (ribodepletion)
transcriptomic

value: skin

value: mouse tissues

value: whole tissues

value: wildtype

value: Adrenalectomy with intradermal injection of SA plus restraint stress


title: sperm1 [ncRNA-seq]

description: Library name: C1


title: 20276:ND-25-M + cytokines

value: cytokine treated


title: con-2c3

description: Library name: A3

value: blank control


title: 14236_ND_61_F

value: F

value: no treatment


title: 20276:ND-25-M no cytokines


title: PN embryo3 [ncRNA-seq]

description: Library name: B3

source_name: Porcine embryo

value: Porcine embryo

value: without treatment


title: HS-IU_2052

description: Library name: HS-IU_2052

value: Whole Blood

value: Calf


title: VGLL_10


title: KPC-tumor-tissue_Normal_scRNA-Seq_Rep1

description: 10 × Genomics

value: KPC tumor tissue

value: WT


title: con-2c1

description: Library name: A1

value: Porcine 4cell-embryo


title: 16356_ND_59_M

value: pancreatic islet

value: non-diabetic

value: M

value: beta cells


title: 18065_T1D_28_F_15yr


title: HS-IU_2038

description: Library name: HS-IU_2038

value: no heat stress


title: con-4c1

description: Library name: A4

value: Porcine 2cell-embryo


title: ADX_SA infection with stress, Day 2, triplicate sample 3

value: skin

value: mouse tissues

value: whole tissues

value: wildtype

value: Adrenalectomy with intradermal injection of SA plus restraint stress


title: 16031_T1D_24_M_2y

value: no treatment


title: 16054_ND_63_M


title: ADX_SA infection with stress, Day 2, triplicate sample 2


title: sperm2 [ncRNA-seq]

description: Library name: C2

value: Porcine sperm

value: without treatment


title: KPC-tumor-tissue_Cstf2_KD_scRNA-Seq_Rep2

description: 10 × Genomics

value: KPC tumor tissue

value: Cstf2 KD


title: ADX_SA infection, Day 2, triplicate sample 3

value: Adrenalectomy with intradermal injection of SA


title: HS-IU_2048

description: Library name: HS-IU_2048

value: Whole Blood

value: Calf

value: heat stress


title: HS-IU_2037

description: Library name: HS-IU_2037


title: HS-IU_2039

description: Library name: HS-IU_2039


title: Sham_SA infection with stress, Day 2, triplicate sample 2

value: intradermal injection of SA with restraint stress


title: PN embryo2 [ncRNA-seq]

description: Library name: B2

value: Porcine embryo


title: HS-IU_2034

description: Library name: HS-IU_2034

value: no heat stress


title: HS-IU_2036

description: Library name: HS-IU_2036


title: ADX_SA infection, Day 2, triplicate sample 2

value: skin


title: 13281_ND_53_M

value: pancreatic islet

value: non-diabetic

value: M

value: beta cells


title: MII oocytes1 [ncRNA-seq]

description: Library name: A1

source_name: Porcine MII oocytes

value: Porcine MII oocytes


title: 17180_ND_44_F

value: F

value: no treatment


title: Sham_SA infection, Day 2, triplicate sample 3

value: mouse tissues

value: whole tissues

value: wildtype

value: intradermal injection of SA


title: PN embryo1 [ncRNA-seq]

description: Library name: B1

value: without treatment


title: ADX_SA infection, Day 2, triplicate sample 1

value: Adrenalectomy with intradermal injection of SA


title: 15309_ND_41_F


title: MII oocytes2 [ncRNA-seq]

description: Library name: A2


title: 16292_ND_49_M


title: Sham_SA infection with stress, Day 2, triplicate sample 3

value: intradermal injection of SA with restraint stress


title: Sham_SA infection with stress, Day 2, triplicate sample 1


title: MII oocytes3 [ncRNA-seq]

description: Library name: A3


title: 14289_ND_39_F


title: HS-IU_2031

description: Library name: HS-IU_2031

value: Whole Blood

value: Calf


title: 15290_ND_52_F


title: HS-IU_2032

description: Library name: HS-IU_2032

value: no heat stress


title: 15275_ND_38_M

value: pancreatic islet


title: sperm3

description: Library name: C3

data_processing:
The sequencing strategy was Single-end 50 bp for Illumina NovaSeq 6000 following the vendor’s recommended protocol.
Raw reads were subjected to an in-house program, ACGT101-miR (v4.2) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26nucleotide were mapped to Sus_scrofa.Sscrofa11.1 precursors in miRBase 22.1 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to Sus_scrofa.Sscrofa11.1 mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p- derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.1 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12), (2) number of base pairs in the stem region of the predicted hairpin (≥16), (3) cutoff of free energy (kCal/mol ≤-15), (4) length of hairpin (up and down stems + terminal loop ≥50), (5) length of hairpin loop (≤20), (6) number of nucleotides in one bulge in mature region (≤8), (7) number of biased errors in one bulge in mature region (≤4), (8) number of biased bulges in mature region (≤2), (9) number of errors in mature region (≤7), (10) number of base pairs in the mature region of the predicted hairpin (≥12), (11) percent of mature in stem (≥80)
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using Student t test. The significance threshold was set to be 0.01 and 0.05 in each test.
Assembly: Sus_scrofa.Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was isolated and purified following the manufacturer’s procedure. The RNA amount and purity of each sample was evaluated using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA fragment integrity was evaluated through Bioanalyzer 2100 (Agilent,CA,USA).
The obtained total RNA were denaturated at 70℃ for 2 min with DNA 3’ Adapters , and thenmixed with T4 RNA Ligase 2, truncated K227Q (NEB, M0351L, USA) at room temperature. The3’ adapter ligation reaction was performed at 16℃ more than 8 hours. The rest of 3’Adapters wereremoved by RTP at 37℃ for 30 min. The 5’ adapters and the products from last step were ligationwith T4 RNA Ligase 1 (NEB,M0204L,USA) at 37℃ for 60 min following withreverse-transcription reaction carried by SuperScript II Reverse Transcriptase(Thermo,18064014,USA) at 50℃ for 60 min, and at 80 ℃ for 10 min. The cDNA products wereamplified using Phusion® High-Fidelity DNA Polymerase (NEB,M0530L,USA). Specifically, thedenaturation temperature was 98℃ for 30 sec with an annealing temperature of 60℃ for 30 sec, and the extension was carried out for 15 sec at 72℃ for 10-16 cycles. The final 5 minute extensionwas then done at 72℃.The PCR products were purified and enriched through PAGE electrophoresis.

value: Porcine sperm


title: HS-IU_2029

description: Library name: HS-IU_2029


title: HS-IU_2030

description: Library name: HS-IU_2030


title: sperm2

description: Library name: C2


title: Sham_SA infection, Day 2, triplicate sample 2

value: skin


title: 16085_ND_37_F

value: non-diabetic

value: beta cells


title: PN embryo3

description: Library name: B3

value: Porcine embryo


title: sperm1

description: Library name: C1


title: HS-IU_2028

description: Library name: HS-IU_2028


title: mdFB, Adipocyte differentiation medium (ADM) with adrenaline, Day 2, triplicate sample 3

value: cell line

value: mouse dermal fibroblast

value: primary isolated mouse dermal fibroblast

value: Adipocyte differentiation medium + adrenaline


title: 18076_ND_33_F

value: F

value: no treatment


title: Sham_SA infection, Day 2, triplicate sample 1

value: mouse tissues

value: whole tissues

value: wildtype

value: intradermal injection of SA


title: mdFB, Adipocyte differentiation medium (ADM) with adrenaline, Day 2, triplicate sample 2


title: mdFB, Adipocyte differentiation medium (ADM) with adrenaline, Day 2, triplicate sample 1


title: HS-IU_2026

description: Library name: HS-IU_2026

value: Whole Blood

value: Calf

value: no heat stress


title: 16231_ND_32_M

value: pancreatic islet

value: M


title: MII oocytes3

description: Library name: A3

value: Porcine MII oocytes

value: without treatment


title: PN embryo1

description: Library name: B1

value: Porcine embryo


title: HS-IU_2027

description: Library name: HS-IU_2027


title: mdFB, Adipocyte differentiation medium (ADM), Day 2, triplicate, sample 3

value: cell line

value: mouse dermal fibroblast

value: Adipocyte differentiation medium


title: mdFB, Adipocyte differentiation medium (ADM), Day 2, triplicate, sample 2

value: primary isolated mouse dermal fibroblast


title: MII oocytes2

description: Library name: A2


title: 17346_ND_27_M

value: non-diabetic

value: beta cells

value: no treatment


title: 17262_ND_27_M


title: HS-IU_2020

description: Library name: HS-IU_2020


title: mdFB, Adipocyte differentiation medium (ADM), Day 2, triplicate sample 1

value: wildtype


title: HS-IU_2019

description: Library name: HS-IU_2019


title: 21024_HTO

library_source: other

data_processing:
Illumina fastq files were processed through the DolphinNext single-cell analysis pipeline, which extracts the cell barcodes, filters to remove cell barcodes with fewer than 500 reads, aligns the reads to the hg38 GENCODE v34 genome (tophat2 v2.0.12), and maps reads to genes and collapses duplicate UMIs for each transcript (ESAT v1.0). The resulting output matrix contains the number of observed unique transcripts for each gene for each cell.
Convert ESAT output to Seurat object and remove dead cells (percent.mt < 25)
Remove doublets with scDblFinder(v1.14.0)
Build UMAPs for individual samples (custom script using Seurat runUMAP function)
Identify cell types using custom script for clustifyR (v1.3.4) with human pancreatic cell reference data from Baron et al. 2016
Assembly: hg38 GENCODE v34
Supplementary files format and content: *umiCleanMerged.rds - Raw UMI count matrix.
Supplementary files format and content: *counts_n1000.txt - Matrix of raw counts of barcodes.
Library strategy: CITE-Seq

molecule: protein

source_name: Male, 51, non-diabetic, islet, mixed sample +/- cytokine treatment, hashtags

growth_protocol: Isolated human islets were grown in AIM-V medium

extract_protocol:
10x Chromium version 3' V3 or V3.1
10x Chromium 3' V3 or 3.1

treatment_protocol: IFNg, IL-1b, and TNFa were added to the +cytokine cultures for 48 hours

tag: gander

value: Male

value: mixed sample(untreated, cytokine treated)

tag: library type

value: HTO

tag: hto

value: TotalSeq™-A0251 anti-human Hashtag 1, TotalSeq™-A0252 anti-human Hashtag 2


title: 17192_ND_18_F

value: pancreatic islet

value: F


title: PN embryo2

description: Library name: B2


title: MII oocytes1

description: Library name: A1

value: Porcine MII oocytes


title: HS-IU_2017

description: Library name: HS-IU_2017

value: Whole Blood

value: Calf

value: no heat stress


title: mdFB, adrenaline, Day 2, triplicate sample 3

value: cell line

value: mouse dermal fibroblast

value: adrenaline


title: HS-IU_2018

description: Library name: HS-IU_2018


title: mdFB, adrenaline, Day 2, triplicate sample 2

value: primary isolated mouse dermal fibroblast


title: gene expression library of Cre+ CD8+ T cells, from MC38 tumors, biological replicate M6

city: Boston

first: Samuel

middle: Cyrus

last: Markson

address: 77 Ave Louis Pasteur

department: Immunology

institute: Harvard Medical School

description: Library name: M6_CrePos_GEX

data_processing:
cellranger v6.1.0
Assembly: mm10
Supplementary files format and content: counts matrix (loom format)

source_name: tumor

extract_protocol:
Single-cell suspension from sorted CD8+ T cells from subcutaneous MC38 tumor
Chromium 10’x 5’ v3 scRNA

value: tumor

value: female C57BL/6

value: CD8+ T cell

value: Cre+

value: subcutaneous MC38 tumor


title: 13254_ND_30_M

value: non-diabetic

value: M

value: beta cells

value: no treatment


title: mdFB, adrenaline, Day 2 triplicate sample 1

value: wildtype


title: V(D)J library of Cre+ CD8+ T cells, from MC38 tumors, biological replicate M6

description: Library name: M6_CrePos_TCR


title: 20276-plus-cyto_HTO

source_name: Male, 25, non-diabetic, islet, cytokine treated, hashtags

value: pancreatic islet

value: Male

value: cytokine treated

value: HTO

value: mHT06:Purified anti-human β2-microglobulin (clone 2M2) and HLA-A,B,C (clone W6/32) antibodies (Biolegend) conjugated to TATGCTGCCACGGTA, mHT08:Purified anti-human β2-microglobulin (clone 2M2) and HLA-A,B,C (clone W6/32) antibodies (Biolegend) conjugated to:TATAGAACGCCAGGC, mHT12 Purified anti-human β2-microglobulin (clone 2M2) and HLA-A,B,C (clone W6/32) antibodies (Biolegend) conjugated to:CTGCAAATATAACGG


title: HS-IU_2015

description: Library name: HS-IU_2015

value: Whole Blood

value: Calf

value: no heat stress


title: HS-IU_2016

description: Library name: HS-IU_2016


title: feature barcoding library of Cre+ CD8+ T cells, from MC38 tumors, biological replicate M6

description: Library name: M6_CrePos_CITE

value: tumor

value: female C57BL/6


title: mdFB, Control, Day 2, triplicate sample 3

value: cell line

value: mouse dermal fibroblast

value: primary isolated mouse dermal fibroblast

value: Control


title: HS-IU_2013

description: Library name: HS-IU_2013


title: 21024_ADT

source_name: Male, 51, non-diabetic, islet, mixed sample +/- cytokine treatment, antibody tags

value: non-diabetic

value: mixed sample(untreated, cytokine treated)

value: ADT

tag: adt

value: TotalSeq™-A0008 anti-human CD273  (B7-DC, PD-L2), TotalSeq™-A0022 anti-human CD137L (4-1BB Ligand), TotalSeq™-A0031 anti-human CD40, TotalSeq™-A0032 anti-human CD154, TotalSeq™-A0071 anti-human CD194 (CCR4), TotalSeq™-A0124 anti-human CD31 (PECAM1), TotalSeq™-A0129 anti-human CD140b (PDGFRβ), TotalSeq™-A0140 anti-human CD183 (CXCR3), TotalSeq™-A0143 anti-human CD196 (CCR6), TotalSeq™-A0145 anti-human CD103 (Integrin αE), TotalSeq™-A0151 anti-human CD152 (CTLA-4), TotalSeq™-A0152 anti-human CD223 (LAG-3), TotalSeq™-A0153 anti-human KLRG1 (MAFA-L), TotalSeq™-A0154 anti-human CD27, TotalSeq™-A0155 anti-human CD107a (LAMP-1), TotalSeq™-A0156 anti-human CD95 (Fas), TotalSeq™-A0158 anti-human CD134 (OX40), TotalSeq™-A0159 anti-human HLA-DR, TotalSeq™-A0169 anti-human CD366 (Tim-3), TotalSeq™-A0174 anti-human CD58 (LFA-3), TotalSeq™-A0176 anti-human CD39, TotalSeq™-A0177 anti-human CD178 (Fas-L), TotalSeq™-A0219 anti-human CD119 (IFN-γ R α chain), -TotalSeq™-A0360 anti-human CD357 (GITR), TotalSeq™-A0368 anti-human CD226 (DNAM-1), TotalSeq™-A0579 anti-human CD9, TotalSeq™-A0584 anti-human TCR Vα24-Jα18 (iNKT cell), TotalSeq™-A0597 anti-human CD209 (DC-SIGN), TotalSeq™-A0804 anti-human CD186 (CXCR6), TotalSeq™-B0005 anti-human CD80, TotalSeq™-B0006 anti-human CD86, TotalSeq™-B0007 anti-human CD274 (B7-H1, PD-L1), TotalSeq™-B0048 anti-human CD45, TotalSeq™-B0053 anti-human CD11c, TotalSeq™-B0085 anti-human CD25, TotalSeq™-B0088 anti-human CD279 (PD-1), TotalSeq™-B0100 anti-human CD20, TotalSeq™-B0139 anti-human TCR γ/δ, TotalSeq™-B0146 anti-human CD69, TotalSeq™-B0147 anti-human CD62L, TotalSeq™-B0148 anti-human CD197 (CCR7), TotalSeq™-B0161 anti-human CD11b, TotalSeq™-B0165 anti-human CD314 (NKG2D), TotalSeq™-B0168 anti-human CD57 Recombinant, TotalSeq™-B0171 anti-human CD278 (ICOS), TotalSeq™-B0224 anti-human TCR α/β, TotalSeq™-B0355 anti-human CD137 (4-1BB), TotalSeq™-B0386 anti-human CD28, TotalSeq™-B0390 anti-human CD127 (IL-7Rα), TotalSeq™-B0034 anti-human CD3, TotalSeq™-B0050 anti-human CD19, TotalSeq™-B0063 anti-human CD45RA, TotalSeq™-B0072 anti-human CD4, TotalSeq™-B0080 anti-human CD8a, TotalSeq™-B0081 anti-human CD14, TotalSeq™-B0083 anti-human CD16, TotalSeq™-B0084 anti-human CD56 (NCAM) Recombinant, TotalSeq™-B0089 anti-human TIGIT (VSTM3), TotalSeq™-B0087 anti-human CD45RO, TotalSeq™-B0159 anti-human HLA-DR, TotalSeq™-A0575 anti-human CD49a (ITGA1)


title: gene expression library of Cre+ CD8+ T cells, from MC38 tumors, biological replicate M5

description: Library name: M5_CrePos_GEX

value: CD8+ T cell

value: Cre+

value: subcutaneous MC38 tumor


title: V(D)J library of Cre+ CD8+ T cells, from MC38 tumors, biological replicate M5

description: Library name: M5_CrePos_TCR


title: mdFB, Control, Day 2, triplicate sample 1

source_name: cell line

value: wildtype


title: feature barcoding library of Cre+ CD8+ T cells, from MC38 tumors, biological replicate M5

description: Library name: M5_CrePos_CITE


title: 20276-no-cyto_ADT

source_name: Male, 25, non-diabetic, islet, untreated, antibody tags

value: pancreatic islet

value: Male

value: untreated

value: TotalSeq™-A0008 anti-human CD273  (B7-DC, PD-L2), TotalSeq™-A0022 anti-human CD137L (4-1BB Ligand), TotalSeq™-A0031 anti-human CD40, TotalSeq™-A0032 anti-human CD154, TotalSeq™-A0071 anti-human CD194 (CCR4), TotalSeq™-A0124 anti-human CD31 (PECAM1), TotalSeq™-A0129 anti-human CD140b (PDGFRβ), TotalSeq™-A0140 anti-human CD183 (CXCR3), TotalSeq™-A0143 anti-human CD196 (CCR6), TotalSeq™-A0145 anti-human CD103 (Integrin αE), TotalSeq™-A0151 anti-human CD152 (CTLA-4), TotalSeq™-A0152 anti-human CD223 (LAG-3), TotalSeq™-A0153 anti-human KLRG1 (MAFA-L), TotalSeq™-A0154 anti-human CD27, TotalSeq™-A0155 anti-human CD107a (LAMP-1), TotalSeq™-A0156 anti-human CD95 (Fas), TotalSeq™-A0158 anti-human CD134 (OX40), TotalSeq™-A0159 anti-human HLA-DR, TotalSeq™-A0169 anti-human CD366 (Tim-3), TotalSeq™-A0174 anti-human CD58 (LFA-3), TotalSeq™-A0176 anti-human CD39, TotalSeq™-A0177 anti-human CD178 (Fas-L), TotalSeq™-A0219 anti-human CD119 (IFN-γ R α chain), -TotalSeq™-A0360 anti-human CD357 (GITR), TotalSeq™-A0368 anti-human CD226 (DNAM-1), TotalSeq™-A0579 anti-human CD9, TotalSeq™-A0584 anti-human TCR Vα24-Jα18 (iNKT cell), TotalSeq™-A0597 anti-human CD209 (DC-SIGN), TotalSeq™-A0804 anti-human CD186 (CXCR6), TotalSeq™-B0005 anti-human CD80, TotalSeq™-B0006 anti-human CD86, TotalSeq™-B0007 anti-human CD274 (B7-H1, PD-L1), TotalSeq™-B0048 anti-human CD45, TotalSeq™-B0053 anti-human CD11c, TotalSeq™-B0085 anti-human CD25, TotalSeq™-B0088 anti-human CD279 (PD-1), TotalSeq™-B0100 anti-human CD20, TotalSeq™-B0139 anti-human TCR γ/δ, TotalSeq™-B0146 anti-human CD69, TotalSeq™-B0147 anti-human CD62L, TotalSeq™-B0148 anti-human CD197 (CCR7), TotalSeq™-B0161 anti-human CD11b, TotalSeq™-B0165 anti-human CD314 (NKG2D), TotalSeq™-B0168 anti-human CD57 Recombinant, TotalSeq™-B0171 anti-human CD278 (ICOS), TotalSeq™-B0224 anti-human TCR α/β, TotalSeq™-B0355 anti-human CD137 (4-1BB), TotalSeq™-B0386 anti-human CD28, TotalSeq™-B0390 anti-human CD127 (IL-7Rα), TotalSeq™-B0034 anti-human CD3, TotalSeq™-B0050 anti-human CD19, TotalSeq™-B0063 anti-human CD45RA, TotalSeq™-B0072 anti-human CD4, TotalSeq™-B0080 anti-human CD8a, TotalSeq™-B0081 anti-human CD14, TotalSeq™-B0083 anti-human CD16, TotalSeq™-B0084 anti-human CD56 (NCAM) Recombinant, TotalSeq™-B0089 anti-human TIGIT (VSTM3), TotalSeq™-B0087 anti-human CD45RO, TotalSeq™-B0159 anti-human HLA-DR


title: V(D)J library of Cre- CD8+ T cells, from MC38 tumors, biological replicate M4

description: Library name: M4_CreNeg_TCR

value: tumor

value: female C57BL/6

value: Cre-


title: gene expression library of Cre- CD8+ T cells, from MC38 tumors, biological replicate M4

description: Library name: M4_CreNeg_GEX


title: HS-IU_2009

description: Library name: HS-IU_2009

value: Whole Blood

value: Calf

value: no heat stress


title: HS-IU_2011

description: Library name: HS-IU_2011


title: mdFB, Control, Day 2, triplicate sample 2

value: cell line

value: mouse dermal fibroblast

value: primary isolated mouse dermal fibroblast

value: Control


title: 20276-plus-cyto_mRNA

source_name: Male, 25, non-diabetic, islet, cytokine treated

value: non-diabetic

value: cytokine treated

value: mRNA


title: 20276-no-cyto_mRNA

source_name: Male, 25, non-diabetic, islet, untreated

value: pancreatic islet


title: HS-IU_2012

description: Library name: HS-IU_2012


title: V(D)J library of Cre- CD8+ T cells, from MC38 tumors, biological replicate M3

description: Library name: M3_CreNeg_TCR

value: CD8+ T cell

value: subcutaneous MC38 tumor


title: HS-IU_2007

description: Library name: HS-IU_2007


title: 21024_mRNA

source_name: Male, 51, non-diabetic, islet, mixed sample +/- cytokine treatment

value: Male

value: mixed sample(untreated, cytokine treated)


title: SA

description: 10X Genomics

data_processing:
Cell Ranger (10X Genomics) with default parameters was used to perform sample demultiplexing ,barcode processing, alignment to the mm10 reference genome, and gene counting
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single-cell suspensions generated from mouse skin
10X Genomics 3’ V3.1

value: skin

value: whole tissues

value: wild-type

value: SA infection


title: HS-IU_2010

description: Library name: HS-IU_2010

value: Whole Blood

value: Calf

value: no heat stress


title: feature barcoding library of Cre- CD8+ T cells, from MC38 tumors, biological replicate M4

description: Library name: M4_CreNeg_CITE

value: tumor

value: female C57BL/6

value: Cre-


title: HS-IU_2008

description: Library name: HS-IU_2008


title: Stress

description: 10X Genomics

value: restraint stress


title: SA +SB

description: 10X Genomics

value: SA infection +restraint stress +SB


title: SA+Stress +SB

description: 10X Genomics

value: SA infection + SB


title: 20276-no-cyto_HTO

source_name: Male, 25, non-diabetic, islet, untreated, hashtags

value: pancreatic islet

value: non-diabetic

value: untreated

value: HTO

value: mHT05:Purified anti-human β2-microglobulin (clone 2M2) and HLA-A,B,C (clone W6/32) antibodies (Biolegend) conjugated to CTTTGTCTTTGTGAG, mHT09:Purified anti-human β2-microglobulin (clone 2M2) and HLA-A,B,C (clone W6/32) antibodies (Biolegend) conjugated to:TGCCTATGAAACAAG, mHT11 Purified anti-human β2-microglobulin (clone 2M2) and HLA-A,B,C (clone W6/32) antibodies (Biolegend) conjugated to:GCTTACCGAATTAAC


title: Sample 34NT Non tumor tissue

city: Lyon

first: Massimiliano

last: Cocca

address: 151 Cours Albert Thomas

country: France

institute: Université Claude Bernard Lyon 1, Inserm UMR 1350 - PaThLiv

data_processing:
Sequence reads were processed using an internal pipeline developed with the snakemake framework. Reads were trimmed using the fastp software and QC was carried on using fastp and FastQC softaware.
Trimmed sequence reads were aligned to GRCh38 using STAR aligner.
Raw gene expression counts were generated by STAR and RSEM using default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab delimited files including raw counts for each sample

source_name: Liver

extract_protocol:
RNA was extracted with the RNAeasy mini kit (Qiagen, #74104) and treated with the RNAse Free DNAse set (Qiagen, #79254) and controlled for quality on a Bioanalyzer (Agilent)
libraries were prepared using the TruSeq® Stranded RNA HT (w/Ribo-Zero™) kit to increases the depth of sequencing.

value: HBV-related HCC

value: Liver

tag: tissue type

value: Non tumor tissue


title: gene expression library of Cre- CD8+ T cells, from MC38 tumors, biological replicate M3

description: Library name: M3_CreNeg_GEX

tag: cell type

value: CD8+ T cell

value: subcutaneous MC38 tumor


title: Control

description: 10X Genomics

value: skin

value: whole tissues

value: wild-type

value: Control


title: V(D)J library of PD-1+ sorted Cre- CD8+ T cells, from MC38 tumors, biological replicate M2

description: Library name: M2_CreNeg_PD1Pos_TCR

value: tumor

tag: cell line

value: female C57BL/6

value: Cre-


title: HS-IU_1853

description: Library name: HS-IU_1853

value: Whole Blood

value: Dam

value: heat stress


title: HS-IU_2006

description: Library name: HS-IU_2006

value: Calf

value: no heat stress


title: S4 4W ANT KO-2

city: Beijing

description:
SMAD4-4W results_ant_con-ko.csv
AN-4

data_processing:
RNA-seq reads were aligned to the reference genome GRCm38 using the STAR software.
Then the differential expression analysis was effectuated employing DESeq2 software.
For functional enrichment analyses, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted, utilizing ClusterProfiler software.
Assembly: mm10

source_name: Stomach

extract_protocol:
Total RNA was isolated from mouse gastric epithelial cells from Ctrl, ALK3 KO or Smad4 KO mice at 2 week or 4 week after the administration of tamoxifen using TRIzol Reagent (Life Technologies) according to the manufacturer’s instructions.
The library were prepared for sequecing using NEBNext Ultra RNA library Prep Kit for Illumina.

treatment_protocol: Mice were crossed with the mice expressing cre-recombinase and treated with four consecutive daily doses of tamoxifen (Sigma, 100 mg/kg) in corn oil.

value: Stomach

value: tissue

value: epithelial cell and stromal cell

value: Smad4 knockout

value: Tamoxifen injection


title: V(D)J library of PD-1- sorted Cre- CD8+ T cells, from MC38 tumors, biological replicate M2

description: Library name: M2_CreNeg_PD1Neg_TCR

value: CD8+ T cell

value: subcutaneous MC38 tumor


title: feature barcoding library of Cre- CD8+ T cells, from MC38 tumors, biological replicate M3

description: Library name: M3_CreNeg_CITE


title: Sample 144NT Non tumor tissue

value: HBV-related HCC

value: Liver

value: Non tumor tissue


title: Sample 144T Tumor tissue

value: Tumor tissue


title: Sample 13T Tumor tissue


title: WT CP-2

description: 10X Genomics

data_processing:
Raw reads were aligned to the GRCm38/mm10 mouse genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers
Raw aligned features were loaded and processed using the Seurat package (v4.0.2)
Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes
Assembly: mm10

extract_protocol:
Gastric epithelial cell and stromal cell were isolated and digested with EDTA and Tryple, alive cells were sorted by flow cytometry. Single cell suspensions were captured using the 10X Genomics Chromium
ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000.

tag: strain

value: 8-10 weeks


title: Sample 13NT Non tumor tissue


title: gene expression library of PD-1- sorted Cre- CD8+ T cells, from MC38 tumors, biological replicate M2

description: Library name: M2_CreNeg_PD1Neg_GEX

value: tumor

value: female C57BL/6

value: Cre-


title: WT ANT-1

description: 10X Genomics


title: HS-IU_1837

description: Library name: HS-IU_1837

value: Whole Blood

value: Dam

value: heat stress


title: Sample 28T Tumor tissue


title: HS-IU_1863

description: Library name: HS-IU_1863


title: Sample 28NT Non tumor tissue


title: gene expression library of PD-1+ sorted Cre- CD8+ T cells, from MC38 tumors, biological replicate M2

description: Library name: M2_CreNeg_PD1Pos_GEX


title: V(D)J library of PD-1+ sorted Cre+ CD8+ T cells, from MC38 tumors, biological replicate M1

description: Library name: M1_CrePos_PD1Pos_TCR

value: Cre+


title: HS-IU_1835

description: Library name: HS-IU_1835


title: WT CP-1

description: 10X Genomics

value: Stomach

value: tissue

value: epithelial cell and stromal cell


title: S4 4W ANT KO-1

description:
SMAD4-4W results_ant_con-ko.csv
AN-3

value: Smad4 knockout

value: Tamoxifen injection


title: HS-IU_1830

description: Library name: HS-IU_1830


title: HS-IU_1844

description: Library name: HS-IU_1844


title: Sample 105T Tumor tissue

value: HBV-related HCC


title: S4 4W ANT CON-2

description:
SMAD4-4W results_ant_con-ko.csv
AN-2

value: wild type


title: HS-IU_1828

description: Library name: HS-IU_1828

value: no heat stress


title: S4 4W ANT CON-1

description:
SMAD4-4W results_ant_con-ko.csv
AN-1


title: Sample 141T Tumor tissue

value: Liver

value: Tumor tissue


title: V(D)J library of PD-1- sorted Cre+ CD8+ T cells, from MC38 tumors, biological replicate M1

description: Library name: M1_CrePos_PD1Neg_TCR

value: tumor

value: CD8+ T cell

value: subcutaneous MC38 tumor


title: Sample 141NT Non tumor tissue

value: Non tumor tissue


title: gene expression library of PD-1- sorted Cre+ CD8+ T cells, from MC38 tumors, biological replicate M1

description: Library name: M1_CrePos_PD1Neg_GEX

value: female C57BL/6


title: Sample 150T Tumor tissue


title: S4 4W CP KO-2

description:
SMAD4-4W results_cp_con-ko.csv
CP-4


title: S4 4W CP KO-1

description:
SMAD4-4W results_cp_con-ko.csv
CP-3


title: HS-IU_1823

description: Library name: HS-IU_1823

value: Whole Blood

value: Dam

value: heat stress


title: S4 4W CP CON-2

description:
SMAD4-4W results_cp_con-ko.csv
CP-2

value: Stomach

value: tissue


title: HS-IU_1811

description: Library name: HS-IU_1811


title: HS-IU_1821

description: Library name: HS-IU_1821


title: HS-IU_1817

description: Library name: HS-IU_1817


title: Sample 51T Tumor tissue


title: Sample 150NT Non tumor tissue


title: Sample 51NT Non tumor tissue


title: HS-IU_1808

description: Library name: HS-IU_1808


title: S4 2W ANT KO-2

description:
SMAD4-2W results_ant_con-ko.csv
C18S4-2W-ko-173-ant

value: epithelial cell and stromal cell

value: Smad4 knockout


title: plt3plt7_1, plt3 plt7 tomato double mutant Inflorescence meristems

city: Cold Spring Harbor

first: Zachary

last: Lippman

state: New York

address: 1 Bungtown Rd

department: Plant Biology

institute: Cold Spring Harbor Laboratory

description: Library name: 1885-1

data_processing:
Reads were trimmed with Trimmomatic (ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:1:FALSE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) and aligned to the cDNA annotation of reference genome sequence of tomato (SL4.0) using STAR v2.6.1.d. Normalization and quantification of individual transcript expression was done in R by calculating transcripts per million (TPM).
Assembly: Tomato Heinz SL4.00
Supplementary files format and content: csv file, include TPM values for each sample

organism: Solanum lycopersicum

source_name: Inflorescence meristems

growth_protocol: Inflorescence meristems were collected from n = 4 plants at 8 weeks old under stereoscope magnification.

extract_protocol:
TRIzol (Invitrogen) and a Direct-zol RNA Miniprep kit with on-column DNA digestion (Zymo Research)
TruSeq V2 RNA-Seq prep kit (Illumina)

value: Inflorescence meristems

value: plt3 plt7


title: plt3plt7_3, plt3 plt7 tomato double mutant Inflorescence meristems

description: Library name: 1885-3


title: plt3plt7_2, plt3 plt7 tomato double mutant Inflorescence meristems

description: Library name: 1885-2


title: plt3plt7_4, plt3 plt7 tomato double mutant Inflorescence meristems

description: Library name: 1885-4


title: HS-IU_1804

description: Library name: HS-IU_1804

source_name: Whole Blood

value: no info


title: gene expression library of PD-1+ sorted Cre+ CD8+ T cells, from MC38 tumors, biological replicate M1

description: Library name: M1_CrePos_PD1Pos_GEX

value: Cre+


title: Sample 34T Tumor tissue

value: HBV-related HCC

value: Liver

value: Tumor tissue


title: S4 2W ANT KO-1

description:
SMAD4-2W results_ant_con-ko.csv
C18S4-2W-ko-92-ant

value: Tamoxifen injection


title: Sample 105NT Non tumor tissue

value: Non tumor tissue


title: HS-IU_1800

description: Library name: HS-IU_1800


title: ej2j2_3,  ej2 j2 tomato double mutant Inflorescence meristems

description: Library name: 1883-3

value: ej2 j2


title: S4 2W ANT CON-1

description:
SMAD4-2W results_ant_con-ko.csv
C18S4-2W-con-71-ant

value: wild type


title: S4 4W CP CON-1

description:
SMAD4-4W results_cp_con-ko.csv
CP-1


title: Sample FS43_NT Normal liver tissue

value: control

value: Normal liver tissue


title: Sample FS12_NT Normal liver tissue


title: HS-IU_1749

description: Library name: HS-IU_1749

value: Whole Blood

value: Dam

value: no heat stress


title: HS-IU_1727

description: Library name: HS-IU_1727


title: ej2j2_1,  ej2 j2 tomato double mutant Inflorescence meristems

description: Library name: 1883-1


title: ej2j2_2,  ej2 j2 tomato double mutant Inflorescence meristems

description: Library name: 1883-2


title: Sample FS6_NT Normal liver tissue


title: S4 2W CP KO-2

description:
SMAD4-2W results_cp_con-ko.csv
C18S4-2W-ko-173-cp

value: Stomach

value: tissue

value: epithelial cell and stromal cell

value: Smad4 knockout


title: healthy control 3

city: Shah Alam, Selangor, Malaysia

first: Yang

last: Jun

state: selangor

address: setia alam

country: Malaysia

institute: UiTM

description:
Library name: Sample 6
sample6

data_processing:
High-quality clean data were obtained by processing fastq-format data with Trimmomatic (v0.30).
removing adapter sequences
discarding 5' or 3' end bases containing Ns or with quality values below 20
removing bases with an average quality score below 20 using a sliding window of 4 bp
eliminating reads shorter than 18 bp after trimming.
Assembly: hg38
Supplementary files format and content: CSV file include the known miRNA in each sequencing sample.
Supplementary files format and content: CSV file include the novel miRNA in each sequencing sample.

source_name: blood

growth_protocol: Fresh whole-blood samples (5 mL) were collected in EDTA-coated anticoagulant tubes from both HCs and patients with active TB (ATB).

extract_protocol:
Total RNA was extracted using the Total RNA Extraction Kit (Thermo Fisher Scientific Inc., MA, USA), following the manufacturer’s instructions. RNA quantity and quality were determined using the Nanodrop 2000 (Thermo Fisher Scientific, MA, USA) and Agilent 2100 Bioanalyzer systems (Agilent Technologies). Only samples with an RNA Integrity Number (RIN) above 7 were utilized to construct a high-quality total RNA sequencing (RNA-seq) library.
For library preparation, 1 μg of total RNA or 10 ng of small RNA was used. The 3’ SR Adaptor for Illumina was attached to the small RNA using a 3’ ligation enzyme. To prevent adaptor-dimer formation, excess 3’ SR Adaptor was hybridized with the SR RT Primer for Illumina. The 5’ SR Adaptor for Illumina was then attached to the small RNA using a 5' ligation enzyme, and first-strand cDNA was synthesized using ProtoScript II Reverse Transcriptase. Each sample was amplified by PCR using P5 and P7 primers, and the PCR products were purified using DNA clean beads. The purified products, ranging from 140 to 160 bp, were recovered and cleaned using PAGE, and validated with an Agilent 2100 Bioanalyzer. Libraries with different indexes were multiplexed, and the qualified libraries were sequenced on the Illumina MGI2000 System (MGI Tech Co., Ltd, China) using paired-end PE150.

treatment_protocol: Samples were immediately centrifuged at 4℃ and 3000×g for 15 minutes to separate the plasma, which was then stored at -80℃ until RNA extraction.

value: blood

value: serum

tag: subject status

value: healthy control

value: infect differentiation

tag: time


title: HS-IU_1721

description: Library name: HS-IU_1721

value: heat stress


title: S4 2W CP CON-2

description:
SMAD4-2W results_cp_con-ko.csv
C18S4-2W-con-72-cp

value: Tamoxifen injection


title: S4 2W CP CON-1

description:
SMAD4-2W results_cp_con-ko.csv
C18S4-2W-con-71-cp


title: HS-IU_1712

description: Library name: HS-IU_1712


title: HS-IU_1711

description: Library name: HS-IU_1711


title: healthy control 1

description:
Library name: Sample 4
sample4