title: WT_Control_1

value: IMM

value: Wild type Immortalized Mouse bone-marrow derived Macrophages (IMM)


title: Tumor, CD45+NK1.1+ cells, with HET genotype

status: Public on May 27 2022

type: SRA

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

description:
CD45_barcodes.tsv.gz
CD45_features.tsv.gz
CD45_matrix.mtx.gz
CD45NK11_barcodes.tsv.gz
CD45NK11_features.tsv.gz
CD45NK11_matrix.mtx.gz

library_source: transcriptomic

data_processing:
Cellranger was executed with refdata-cellranger-mm10 transcriptome. Both, cellranger count for individual samples as well as cellranger aggr for NK1.1+ and all CD45+ samples was executed
Assembly: mm10
Supplementary files format and content: standard cellranger output

molecule: polyA RNA

organism: Mus musculus

source_name: hepatocellular carcinoma

extract_protocol:
FACS sorted cells from Hepatocellular carcinoma were processed according to 10x genomics protocol
The single-cell droplets were generated with chromium single-cell controller using Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, 1000121)

tag: genotype

value: HET

tag: tumor

value: T


title: Low Ca shoot2-mi6

city: Greensboro

first: Muhammad

last: Numan

state: North Carolina

address: 321 McIver Street

department: Biology

institute: University of North Carolina Greensboro

data_processing:
Assembly
annotation
Go terms
target identification
Supplementary_files_format_and_content: excel

molecule: total RNA

organism: Eragrostis tef

source_name: shoot

growth_protocol: Plants were grown in hydroponic solution with low calcium and optimum calcium

extract_protocol:
RNA was extracted and sequenced
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: 4 replicates  for each treatment

tag: treatment

value: low calcium


title: 16HBE14o cells, untreated_2

type: RNA

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

country: Germany

institute: Helmholtz Center for Infection Research

hyb_protocol: Hybridization was performed acording to Clariom S microarray manufacturer recommendations

scan_protocol: Scanning was performed acording to Clariom S microarray manufacturer recommendations

data_processing:
Data were processed with Transcriptome Analysis Console 4.0 (Thermo Fischer) using SST-RMA algorithm
SST-RMA normalized log2-transformed signal intensities from Transcriptome Analysis Console 4.0
Clariom_S_Human.r1.bgp

label: biotin

organism: Homo sapiens

source_name: 16HBE14o cell line

label_protocol: Labeling was performed acording to Clariom S microarray manufacturer recommendations

growth_protocol: Cells were cultivated in T75 flask in minimum essential medium with earle’s salt supplemented with 10 % fetal bovine serum, 200 mM L-Glutamine and  penicillin/streptomycin. Cells were incubated in a humidified incubator at 37 °C with 7.5% CO2. Upon 90% confluency, the cells were detached and harvested with Trypsin/EDTA 0.025%.

extract_protocol: Total RNA was isolated using RNeasy Mini plus Kit (Qiagen)

treatment_protocol: Cells were stimulated with either untreated medium and cigarette smoke extract (CSE) for 28h, or with CSE 24h followed by 4h medium (CSE cessation), Streptococcus pneumoniae (Sp) MOI 10 and MOI 20 for 4h, FCCP 50 µM for 4h, CSE for 24h followed by Sp MOI 10 and 20 for 4h as well as CSE for 24h followed by FCCP 50 µM.

tag: cell line

tag: cell type

value: bronchial epithelial cell

value: medium negative control


title: 16HBE14o cells, untreated_1


title: Low Ca shoot1-mi5


title: ML-DS1, ruxolitinib, rep2

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

data_processing:
Raw reads were trimmed and filtered by Novogene Company, Ltd. using in-house scripts, then mapped to human reference genome hg38 using HISAT2.
Gene expression values (FPKM) were calculated using the featureCounts package in R.
Assembly: hg38
Supplementary files format and content: Normalized read counts (FPKM) in tab-separated format

source_name: patient sample expanded via xenotransplantation

growth_protocol: Patient samples were maintained in StemSpan supplemental with a cytokine cocktail (FLT3-L, SCF, IL-6, IL-3, TPO) for the duration of the treatment (48 hours).

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Miniprep Kit with on-column DNase treatment (R1054).
Illumina sequencing libraries were prepared by Novogene Company, Ltd. using total cellular RNA, and sequenced on an Illumina NovaSeq platform (150 bp paired-end reads).

treatment_protocol: ML-DS patient samples were treated with DMSO (vehicle control), 350nM of the LSD1 inhibitor T-3775440, 1uM ruxolitinib, or the combination of T-3775440 and ruxolitinib for 48 hours.

tag: tissue

value: ruxolitinib

tag: time

value: 48 hours


title: ML-DS1, ruxolitinib, rep1

value: patient sample expanded via xenotransplantation


title: pDC_H3K27ac_KO3

city: Beijing

first: Zhimin

last: He

address: No. 1 Qinghuayuan Street

department: School of Medicine

country: China

institute: Tsinghua University

description: Cut & Tag

library_source: genomic

data_processing:
Base calling using bcl-convert
clean reads were generated using Trimmomatic software version:0.36, by setting ILLUMIACLIP:Adapter.fa:2:30:10, SLIDINGWINDOW:4:15, LEADING: 3, TRAILING:3, MINLEN:36.
reads aligne to the mm10 genome using bowtie2 version 2.1.0
peak calling using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig sorftware.

molecule: genomic DNA

source_name: bone marrow pDCs

extract_protocol:
Cut& Tag assay using Hyperactive In-Situ ChIP Library Prep Kit for Illumina, Vazyme, TD901, following the manuscfacturer's insutrction
Library were constructed with index from TruePrep Index Kit V2/v3 fro Illumina (Vazyme #TD202)

treatment_protocol: Hdac3fl/fl mice or Hdac3fl/fl CreERT2 mice were i.p. injected with tomaxifen for 5 days and waited for 7 days before bone marrow pDCs were sorted using FACS

value: HDAC3-KO pDCs

tag: strain

tag: chip antibody

value: H3K27ac Active Motif 39085


title: Low Ca Root3-mi3

source_name: root


title: ML-DS1, LSD1 inhibitor, rep2

value: LSD1 inhibitor


title: pDC_H3K27ac_KO2

description: Cut & Tag


title: ML-DS1, LSD1 inhibitor, rep1


title: Low Ca Root4-mi4


title: Low Ca Root2-mi2


title: pDC_H3K27ac_WT3

description: Cut & Tag

value: control pDCs


title: E9.5 mand, scRNA-seq

city: LOS ANGELES

first: Jimmy

last: Hu

state: CA

address: 650 Charles E Young DR S, CHS 73-041

institute: UCLA

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.0
Assembly: mm10 - GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mandibular arch epithelium and mesenchyme

extract_protocol:
E12.0 mandibular arches from K14Cre;R26mT/mG embryos were dissected in cold HBSS. Tissues were then pooled and incubated with 10 mg/ml Dispase II in HBSS supplemented with 10 µg/ml DNase at 37°C and swirled at 100 rpm for 32 minutes to enzymatically separate the epithelium from the mesenchyme. Epithelia were peeled off using forceps and dissociated in TrypLE at 37°C for 30 minutes, with gentle pipetting every 10 minutes. Cells were then centrifuged at 400 rcf for 5 minutes and resuspended in cold flow cytometry buffer (calcium free HBSS with 5% fetal bovine serum (FBS), 2 mM EDTA, and 10 mM HEPES). Undissociated cell clumps were sieved out using a 20 µm pluriStrainer. The resulting cell suspension was sorted using fluorescence-activated cell sorting (FACS) to isolate GFP+ single epithelial cells. To collect E9.5 mandibular cells, mandibular arches were dissected in cold HBSS, washed with DPBS without Ca2+/Mg2+, and directly incubated in TrypLE at 37°C for 19 minutes with shaking at 300 rpm. Tissues are gently pipetted up and down for 4 times at the 12th minute mark. Cells were then spun down at 250 rcf for 4 minutes at 4°C and resuspended in DPBS with 0.5% BSA. Undissociated cell clumps were sieved out using a 20 µm pluriStrainer. Cell numbers and viability of dissociated cells were analyzed using the Invitrogen Countess II FL.
Library was performed using 10x Genomics single cell 3’ V3 chemistry according to the manufacturer’s instructions. Briefly, dissociated cells were combined with barcoded Gel Beads and Partitioning Oil onto a Chromium Chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retro-transcribed to cDNA using primers containing the TruSeq Read 1 (R1) primer sequence, the 10x Barcode, and a Unique Molecular Identifier (UMI). The pooled barcoded cDNA was then cleaned up using Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected using SPRIselect for subsequent library construction. During the library construction, the TruSeq Read 2 (R2) primer sequence, the P5 and P7 paired-end construct primer sequences and a sample index were added via End Repair, A-tailing, Adaptor Ligation, and PCR.

value: epithelial and mesenchymal cells

tag: age


title: pDC_H3K27ac_KO1

description: Cut & Tag


title: E12.0 mand epi, scRNA-seq

description: 10x Genomics

source_name: mandibular arch epithelium

value: mandibular arch epithelium

value: epithelial cells


title: Low Ca Root1-mi1


title: pDC_H3K27ac_WT2

description: Cut & Tag


title: Control shoot4-mi16

value: optimum calcium


title: 10x_scRNA-seq_prEpiSCs

city: Guangzhou

first: Manqi

last: Chen

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

data_processing:
Raw sequencing reads were aligned to the GRCh38 human genome (Single Cell 3' v3 chemistry) following the Cell Ranger count pipeline (v.5.0.1).
Genome_build: hg38
Supplementary_files_format_and_content: processed tsv files contain barcodes of cells.
Supplementary_files_format_and_content: processed tsv files contain information of detected genes.
Supplementary_files_format_and_content: processed mtx files contain gene raw counts matrix.

source_name: Embryonic stem cells

growth_protocol: The prEpiSCs are cultured in the GIX medium which contains DMEM/F12 (Thermo Fisher Scientific, catalog. no. 21331020), Neurobasal medium (Thermo Fisher Scientific, catalog. no. 21103049), 2 mM L-glutamine (Thermo Fisher Scientific, catalog. no. 25030081), non-essential amino acids (Thermo Fisher Scientific, catalog. no. 11140050), 1% N2 supplement (Thermo Fisher Scientific, catalog. no. 17502048), 2% B27 supplement (Thermo Fisher Scientific, catalog. no. 12587010, minus vitamin A), 100 mg/ml Vitamin C (Sigma, catalog no. A4403), 50 ng/ml Bovine Albumin Fraction V (Thermo Scientific, cat. no. 15260-037), 20 ng/ml IL6 (PeproTech, catalog. no. AF-200-06), 20 ng/ml sIL-6R (PeproTech, catalog. no. 200-06R),5 ng/ml BMP4 (PeproTech, catalog. no. 120-05ET), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific, catalog. no. 21985023), 0.2 μM GSK112022 (Selleckchem, catalog. no. S2673), 2.5 μM XAV939 (Tocris, catalog. no. 3748), 1 μM Go6983 (Tocris, 2285) and Primocin (InvivoGen, catalog. no. ant-pm-2).To get ci8CLCs, Human prEpiSCs were cultured with the GIX medium plus the chemical cocktail (0.05 μM DZNep, 0.25 μM CBL0137, 0.5 μM AG14361, 1 μM GSK872, and 0.25 μM Ac-EVCD).The medium was changed every other day. The cells were treated with Accutase to dissociate into single cells, and then passaged onto new Matrigel- or feeder-coated plates every 3 - 4 days.

extract_protocol:
Total RNA was extracted from prEpiSCs and ci8CLCs using the Trizol kit (Thermo Fisher Scientific, catalog. no. 15596018) following the manufacturer’s instructions. PolyA(+) RNA was isolated for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: prEpiSCs are culturered in the GIX medium containing a chemical cocktail (0.05-0.1 μM GSK112022, 2.5 μM XAV939, 1 μM Go6983) without any other treatment. Ci8CLCs are cultured in the GIX mdium with the treatment of the chemical cocktail (0.05 μM DZNep, 0.25 μM CBL0137, 0.5 μM AG14361, 1 μM GSK872, and 0.25 μM Ac-EVCD)

value: Embryonic stem cells


title: pDC_H3K27ac_WT1

description: Cut & Tag


title: Control shoot3-mi15


title: Mouse_ileum_scRNA

first: Ye-guang

address: Tsinghua Road, Medical Building

department: School of life science

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
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: UMI counts

source_name: Mouse intestine

extract_protocol:
Ileum crypts were isolated and digested with Tryple, alive cells were sorted by flow cytometry. Single cell suspensions were captured using the 10X Genomics Chromium Single cell 3’ Solution according to the manufacturers protocol. Briefly, a single-cell suspension was mixed with RT-PCR master mix and loaded together with Single Cell 3’ Gel beads and partitioning Oil into a Single Cell 3’ Chip. About 5,000 cells were loaded into each reaction. RNA transcripts from single cell were uniquely barcoded and reverse-transcribed.
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.

value: intestine

value: wild type


title: Control Root4-mi12


title: Control Root3-mi11


title: Untreated C57BL/6 mouse TA [BMP_QUAD_WT_2]

city: Oxford

first: Thomas

middle: C

last: Roberts

address: Paediatrics, University of Oxford, Le Gros Clark Building, South Parks Road

country: United Kingdom

institute: University of Oxford

data_processing:
Base-calling was performed at sequencing core facility (WTCHG, Oxford, UK)
Reads were trimmed using Trim_galore and aligned to the mouse genome (GRCm38) using HISAT2
Reads were counted in known transcript features using htseq-count
Differential expression analysis was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix of all un-normalized raw counts data in text file

source_name: Untreated C57BL/6 mouse TA

growth_protocol: Mice were harvested at 11 weeks of age

extract_protocol:
Maxwell RNA extraction robot (Promega)
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Mice were injected IV at 5 weeks of age

tag: strain/genotype

value: C57BL/6 (wild-type)

value: Untreated

value: 11 weeks

value: quadricpes femoris


title: Control Root2-mi10


title: Untreated C57BL/6 mouse TA [BMP_QUAD_WT_1]


title: AAV-AR45-treated A100Q mouse TA [BMP_QUAD_A_2]

source_name: AAV-AR45-treated A100Q mouse TA

value: AR100Q (SBMA)


title: AAV-GFP-treated A100Q mouse TA [BMP_QUAD_B_1]

source_name: AAV-GFP-treated A100Q mouse TA


title: Control Root1-mi9


title: AAV-AR45-treated A100Q mouse TA [BMP_QUAD_A_1]


title: VSD sample 5

city: Fuzhou

first: Huaming

last: Wang

state: Fujian

address: No. 1 Xuefu North Road

institute: Fujian Medical University

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C). 1. Assemble the slides into an slide holder. 2. Place assembled slide holders into scanner carousel. 3. Verify scan settings for one-color scans. 4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: Amniotic Fluid

label_protocol: Each RNA sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated  from Amniotic Fluid using the TRIzol reagent (Invitrogen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: disease state

value: VSD

tag: tissue preparation

value: frozen tissue

value: amniotic fluid


title: Control shoot2-mi14


title: Control shoot1-mi13


title: control sample 4

value: healthy


title: Virus7_2

status: Public on May 26 2022

city: Seoul

first: Hyun Jik

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of otorhinolaryngology

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Mesocricetus auratus whole genome using Tophat
Read count extraction and Quantile nomalization were performed using edgeR.
Assembly: Mesocricetus auratus
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Mesocricetus auratus

source_name: The lung tissue with SARS-CoV-2 infection (7 days after infection)

extract_protocol:
Total RNA was isolated from cell lysate in the lungs of SARS-CoV-2-infected hamsters at indicated timepoints using TRIzol. cDNA was synthesized from 1 μg of RNA with random hexamer primers using Moloney murine leukemia virus reverse transcriptase.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol:
Infection protocol: Male Syrian golden hamsters aged 7 weeks (190–230 g) were used as a wild-type (WT) animal model. To induce viral infections, WT hamsters were inoculated with SARS-CoV-2 (2.5 x103 TCID50/ml in 30 μl of phosphate-buffered saline [PBS]) by intranasal delivery to induce acute viral lung infections.
The nasal cavities of Syrian golden hamsters (N=3 in each of four groups) were inoculated with recombinant IFN-λ (IFN-λ2: 5 μg, IFN-λ3: 5 μg with 30 μl of PBS) immediately after SARS-CoV-2 infection

value: Lung

value: SARS-CoV-2 infection

tag: Sex

value: male


title: Virus7_3


title: IFN7d_1

source_name: The lung tissue with SARS-CoV-2 infection and inoculation interferon-lambda (7 days after infection)


title: IFN7d_3


title: IFN7d_2


title: VSD sample 4


title: Virus7_1


title: VSD sample 2


title: control sample 1


title: IFN3d_2

source_name: The lung tissue with SARS-CoV-2 infection and inoculation interferon-lambda (3 days after infection)


title: control sample 2


title: control sample 3


title: IFN3d_1


title: Virus3_3

source_name: The lung tissue with SARS-CoV-2 infection (3 days after infection)


title: Virus3_1


title: Con1

source_name: The lung tissue without SARS-CoV-2 infection

value: uninfected


title: Con3


title: Con2


title: 633.2 KO Littermate pair 2_S28_L002

city: Giessen

first: Daniela

last: Fietz

address: Frankfurter Straße 98

department: Institute for Veterinary Anatomy,  Histology and Embryology

institute: Justus Liebig University Giessen

description: Sequencing run 2

data_processing:
Samples for sequencing runs 1 and 2 were run via the Illumina HiSeq 3000 and NextSeq 2000, and 80bp and 100bp reads were generated for each sample respectively. Reads were aligned with STAR (v2.5.2b and v2.7.9a)
Analysis was performed RNAseq processing pipeline RNAsik (v1.8.9 for sequencing run 1, and v1.5.4 for sequencing run 2)
Quality (QC) of fastq files was assessed with FastQC (v0.11.5 and 0.11.9), Picard (v2.26.3), and gathered by MultiQC (v 1.0 and v.1.10.1)
Single-end reads were mapped to the mouse genome (GRCm38) using the R package subread (v1.5.2 and v2.0.2). FeatureCounts was computed from R-subread. Count normalization with Limma/Voom and differential gene expression analyses were performed on Degust (v4.1.5)
Assembly: GRCm38 (Ensembl release 84)
Supplementary files format and content: Excel spreadsheet with raw gene counts for every gene and every sample

source_name: Testis

extract_protocol:
RNA was extracted from cell pellets using the Machery Nagel RNA NucleoSpin XS kit, according to manufacturers instructions
Libraries were sequenced on an Illumina HiSeq3000 using 80 bp reads to generate 30 to 40 million reads per sample

treatment_protocol: Embryonic testes were dissociated and sorted into GFP positive (germ cell) and GFP negative (somatic cell) populations by FACS.

value: Embryonic day 13.5

value: Testis

value: Germ cell

value: Inha x Oct4-GFP KO


title: 633.2 KO Littermate pair 2_S28_L001

description: Sequencing run 2


title: 1516.1 KO Littermate pair 1_S30_L001

description: Sequencing run 2


title: Virus3_2


title: VSD sample 1


title: IFN3d_3


title: 633.4 WT Littermate pair 2_S23_L002

description: Sequencing run 2

value: Inha x Oct4-GFP WT


title: VSD sample 3


title: 1516.5 WT Littermate pair 1_S25_L002

description: Sequencing run 2


title: 1516.5 WT Littermate pair 1_S25_L001

description: Sequencing run 2


title: Mammary ductal Carcinoma Pool 2

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

data_processing:
Sequenced reads were performed quality assessment using FastQC. Reads with phred score >30 were accepted
Adapters were removed using trimomatic in the default options
Paired-end reads for mRNA were mapped to the CamFam3.1 genome using STAR with default options
Counts for RefSeq genes were obtained using Featurecounts with the default settings
DESeq2 was used to normalize expression counts.
Assembly: CamFam3.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Canis lupus familiaris

source_name: Mammary ductal Carcinoma

extract_protocol:
RNA was extracted from tissue from mammary ductal carcinoma and adjacent non-tumor mammary tissue. A 50 mg sample of tissue was ground using Precellys®24-Dual homogenizer (Bertin Technologies, Rockville, Washington D.C., USA). Total RNA was extracted using TRIzol (Thermo Scientific, USA) according to the manufacturer's instructions.
The cDNA libraries were built with the TruSeqTM Stranded Total RNA Sample Preparation Kit v2 (Illumina)

tag: disease

value: mammary ductal carcinoma

tag: pool

value: Pool 2


title: Mammary ductal Carcinoma Pool 1

value: Pool 1


title: THLE-3 EtOH (F) I

city: Hannover

first: Britta

last: Skawran

address: Carl-Neuberg-Straße 1

institute: Hannover Medical School

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version 2.17.1.14 (Illumina).
The FASTQ files were adapter and quality trimmed using Trim Galore! (version 0.4.1) with default settings as described in the User Guide except for the setting of the quality cutoff (-q/--quality) which was set to a Phred score of 15 and the length cutoff (--length) which was set to 6bp. Trim Galore! used Cutadapt (version 1.9.1) as subroutine.
Trimmed FASTQ files were imported to StrandNGS software (version 3.3). To perform the alignment, a Small RNA Alignment experiment type was created according to the following settings: Build: Human hg19 (UCSC); Sequencing Platform: Illumina; Library layout: Directional Single End.  The alignment was conducted with following parameters: Number of mismatches allowed: 1; Minimum match length: 10; Maximum number of matches to be reported per read: 5; Ignore reads with more than 5 valid matches; Fixed Trimming was inactivated; Trim 3’ end with average quality less than 10.
For quantification and analysis, a Small RNA Analysis Experiment type was created, according to the following settings: Build: Human hg19 (UCSC); Transcript Annotation: RefSeq Transcripts (2015.10.05); Small RNA Annotation: SmallRNA SmallRNA (2012.01.15); Sequencing Platform: Illumina; Library layout: Directional Single End.  Quantification was performed using Quantile normalization algorithm (including partial reads). Normalized read counts were thresholded to 1. No baseline transformation was conducted.
Genome_build: Human hg19 (UCSC)
Supplementary_files_format_and_content: tab-delimited txt file containing microRNA annotations and normalized, log(base2) transformed count values.

extract_protocol:
Direct-zol RNA MiniPrep Kit (Zymo Research, Irvine, CA, USA)
500 ng of total RNA (including small RNA) per sample were utilized as input for cDNA library generation using ‘NEBNext® Multiplex Small RNA Library Prep Kit for Illumina® 96 rxns; Index Primers 1-48’ (E7560S; New England Biolabs). All steps were performed as recommended in user manualE7560 (Version 1.0_08-2016; NEB) except that all reactions were downscaled to 1/2 of initial volumes.  cDNA libraries were barcoded by single indexing approach, using contained ‘NEBNext Multiplex Oligos for Illumina (Index Primer 1 – 48). All generated cDNA libraries were amplified by 14 cycles of final pcr.   Fragment length distribution of individual libraries was monitored using ‘Bioanalyzer DNA 1000 Assay’ (5067-1504; Agilent Technologies). Quantification of libraries was additionally performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).  Equal molar amounts of twenty-eight differently barcoded smallRNA libraries in total were pooled for one sequencing run and were subjected to size selection. Mature miRNA libraries appeared as a peak at 147 bp (corresponding to a 21 nucleotide insert flanked by illumina adapters). Size selection using the BluePippin was performed as described in the ''Blue Pippin DNA Size Selection System Operations Manual Software v6.23 Cassette Definition Set 22" using the following settings and parameters: Cassette: '3% agarose'; Standards: 'Internal'; Programming Mode: 'Tight'; Target base pair value: '146'. 30 μl of sample were combined with 10 μl of DNA marker F and were loaded on one well of the 3% agarose cassette (Biozyme # BDQ3003). After elution, 45 μl of sample were reduced to 20µl (speedvac) and 1µl was subjected to a ‘Bioanalyzer DNA HS Assay’ (5067-4626; Agilent Technologies).  An aliquot of the pooled size-selected library was denatured with NaOH and finally diluted to 1.5pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina). 1.3 ml of denatured pool were loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell for 75bp single reads (#FC-404-2005; Illumina).

treatment_protocol: For HDAC inhibition, HCC cells (HLE, HLF, Huh7, HepG2, Hep3B) and normal liver cells (THLE-2, THLE-3) were treated with 2 µM suberoyl anilide hydroxamic acid (SAHA), 35 nM romidepsin (FK228), or ethanol vehicle control.

tag: stimulus

value: EtOH (F)

tag: replicates

value: I


title: THLE-2 EtOH (F) II

value: II


title: AAV-GFP-treated A100Q mouse TA [BMP_QUAD_B_2]

value: AR100Q (SBMA)

value: 11 weeks

value: quadricpes femoris


title: THLE-2 EtOH (F) I


title: Hep3B EtOH (F) II


title: Hep3B FK228 I


title: THLE-2 FK228 II


title: Hep3B EtOH (F) I


title: HepG2 FK228 II


title: THLE-3 EtOH (F) II


title: HepG2 EtOH (F) II


title: Adjacent Non-Tumor mammary tissue  Pool 1

source_name: Mammary tissue

value: Non-tumor Tissue


title: HepG2 FK228 I


title: THLE-3 FK228 II


title: THLE-2 FK228 I


title: THLE-3 FK228 I


title: HepG2 EtOH (F) I


title: Hep3B FK228 II


title: 20220520_alexander scheiter 20052022-1_12 s57-20 apc_12

city: Regensburg

first: Alexander

last: Scheiter

state: Bavaria

address: Franz-Josef-Strauss Allee 11

department: Institute of Pathology

institute: University of Regensburg

hyb_protocol: Nanostring hybridization protocol by manufacturer

scan_protocol: nCounter digital analyzer

data_processing: nsolver advanced analysis

label: nanostring reporter and capture probes

source_name: CCA sample

growth_protocol: cell lines revitalized and harvested after one passage in RPMI or DMEM medium

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: no treatment

tag: wnt pathway mutation status

value: APC mutation

value: CCA sample


title: 20220520_alexander scheiter 20052022-1_07 h12521-03-a5 apc_07

label_protocol: Nanostring hybridization protocol by manufacturer


title: 20220520_alexander scheiter 20052022-1_09 h12521-03-a5 apc_09


title: 20220520_alexander scheiter 20052022-1_10 s57-20 apc_10


title: 20220520_alexander scheiter 20052022-1_11 s57-20 apc_11


title: 633.4 WT Littermate pair 2_S23_L001

description: Sequencing run 2

value: Embryonic day 13.5

tag: genotype


title: Huh7 EtOH (F) II


title: 20220520_alexander scheiter 20052022-1_08 h12521-03-a5 apc_08


title: 20220520_alexander scheiter 20052022-1_05 h6236-02-1 apc_05


title: 20220520_alexander scheiter 20052022-1_06 h6236-02-1 apc_06


title: 20220520_alexander scheiter 20052022-1_02 h8873-10-3 ctnnb1_02

value: CTNNB1 mutation


title: HLF EtOH (F) II

source_name: HLF


title: HLF FK228 I


title: HLF FK228 II


title: 20220520_alexander scheiter 20052022 2_12 sg231 rnf43_12

source_name: SG231 CCA cell line

value: RNF43 mutation

tag: cell line

value: SG231 CCA cell line


title: Huh7 FK228 II


title: 20220520_alexander scheiter 20052022-1_04 h6236-02-1 apc_04


title: 20220520_alexander scheiter 20052022-1_03 h8873-10-3 ctnnb1_03


title: Adjacent Non-Tumor mammary tissue  Pool 2


title: HLE FK228 II

source_name: HLE


title: HLE EtOH (F) II


title: HLF EtOH (F) I


title: 20220520_alexander scheiter 20052022 2_10 sg231 rnf43_10


title: 20220520_alexander scheiter 20052022-1_01 h8873-10-3 ctnnb1_01


title: 20220520_alexander scheiter 20052022 2_11 sg231 rnf43_11


title: THLE-3 EtOH (S) I

value: EtOH (S)


title: THLE-2 SAHA II

value: SAHA


title: Huh7 EtOH (F) I


title: THLE-2 EtOH (S) II


title: THLE-2 SAHA I


title: Hep3B SAHA II


title: 20220520_alexander scheiter 20052022 2_08 h5967-21-3c none_08

value: WT for APC/CTNNB1/APC


title: 20220520_alexander scheiter 20052022 2_02 h9458-22 none_02


title: 20220520_alexander scheiter 20052022 2_03 h9458-22 none_03


title: 20220520_alexander scheiter 20052022 2_05 h25218-21-3b none_05


title: 20220520_alexander scheiter 20052022 2_09 h5967-21-3c none_09


title: 20220520_alexander scheiter 20052022 2_07 h5967-21-3c none_07


title: 20220520_alexander scheiter 20052022 2_04 h25218-21-3b none_04


title: 20220520_alexander scheiter 20052022 2_01 h9458-22 none_01


title: 20220520_alexander scheiter 20052022 2_06 h25218-21-3b none_06


title: Hep3B SAHA I


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_12 tkkk_12

source_name: TKKK CCA cell line

value: TKKK CCA cell line


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_10 tkkk_10


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_09 hucca1_09

source_name: HUCCA1 CCA cell line

value: HUCCA1 CCA cell line


title: control sample 5

value: healthy

value: frozen tissue

value: amniotic fluid


title: Hep3B EtOH (S) II

value: II


title: THLE-2 EtOH (S) I

value: I


title: HLE FK228 I


title: THLE-3 EtOH (S) II


title: Hep3B EtOH (S) I


title: HLE EtOH (F) I

value: EtOH (F)


title: THLE-3 SAHA II


title: THLE-3 SAHA I


title: HepG2 EtOH (S) II


title: HepG2 SAHA I


title: Huh7 EtOH (S) II


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_11 tkkk_11


title: HepG2 SAHA II


title: Huh7 SAHA I


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_08 hucca1_08


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_07 hucca1_07


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_04 cclp1_04

source_name: CCLP1 CCA cell line

value: CCLP1 CCA cell line


title: 855.2 GFPpos E15.5 WT_S29

description: Sequencing run 1

value: Embryonic day 15.5

value: Testis

tag: cell type

value: Germ cell

value: Inhba x Oct-GFP KO


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_06 cclp1_06

value: CTNNB1 mutation


title: HepG2 EtOH (S) I

value: EtOH (S)


title: 855.2 GFPpos E15.5 WT_S13

description: Sequencing run 1

tag: tissue


title: 1064.2 GFPpos E15.5 WT_S16

description: Sequencing run 1


title: 941.3 GFPpos E15.5 WT_S14

description: Sequencing run 1


title: 1064.2 GFPpos E15.5 WT_S32

description: Sequencing run 1


title: Huh7 SAHA II

value: SAHA


title: IL-1b 3h [07_Cells]

city: Baton Rouge

first: James

middle: Jason

last: Collier

state: LA

address: 6400 Perkins Road

department: Islet Biology

institute: Pennington Biomedical

data_processing:
conversion of SOLiD 5500 XSQ files to csfastq files used CLC Genomics Workbench V11.01
alignment of sequence tags back to the human or rat reference genome was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
filtering non-unique tags, and establishing counts per RefSeq gene was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
The raw data set was filtered to remove genes where the sum of counts was less than 10  across each group.  The dataset was normalized and differential expression calculated using DESeq2 (Bioconductor.org) version 1.4.5.  JMP Genomics version 6.0 was used for principal components analysis, heatmaps, and Venn diagrams.
Genome_build: human GRCh38
Genome_build: rat Rnor 6.0
Supplementary_files_format_and_content: tab delimited text raw and normalized counts

organism: Rattus norvegicus

source_name: Insulinoma Cell Line -832/13

growth_protocol: 832/13 rat insulinoma cells were cultured in T75 flasks using RPMI 1640 with 10% FBS. For experimental analysis, cells were split onto 12 well coated plates. Upon receipt, human islets were transferred to a 12 well tissue culture plate (~100 human Islets per well) for treatment.

extract_protocol:
RNA was extracted from cells using Trizol (Samples 1-8) and using a Qiagen Rneasy Kit (samples 9-16).
Libraries were prepared using the Applied Biosystems SOLiDSAGE kit, according to AB's instructions for the SOLiD 4 System (except a 1:100 of Adaptor B dilution was used).
SOLiD SAGE Kit with Barcoding Adaptor Module (#4452811) and SOLiD RNA Barcode Kit (#4427046)

treatment_protocol: Samples were either untreated (NT; no treatment: 1-4, and 9-12) or treated with 1ng/mL rat (samples 5-8) or human (samples 13-16) recombinant IL-1b for 3h in RPMI 1640 without FBS.

value: Insulinoma Cell Line -832/13

tag: agent

tag: time point


title: IL-1b 3h [08_Cells]


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_05 cclp1_05


title: 831.2 GFPpos E13.5 KO_S2

description: Sequencing run 1

value: Embryonic day 13.5

tag: strain


title: IL-1b 3h [06_Cells]


title: IL-1b 3h [05_Cells]


title: 831.2 GFPpos E13.5 KO_S18

description: Sequencing run 1

tag: age


title: HLF SAHA II


title: Huh7 EtOH (S) I


title: NT [04_Cells]


title: 696.6 GFPpos E13.5 KO_S17

description: Sequencing run 1


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_02 kku55_02

source_name: KKU55 CCA cell line

value: APC mutation

value: KKU55 CCA cell line


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_01 kku55_01


title: 928.1 GFPpos E13.5 KO_S20

description: Sequencing run 1

value: Inhba x Oct-GFP WT


title: 696.6 GFPpos E13.5 KO_S1

description: Sequencing run 1


title: NT [03_Cells]


title: 832.1 GFPpos E13.5 KO_S19

description: Sequencing run 1


title: 20220510_alex scheiter cca cell lines beta catenin 10 05 2022_03 kku55_03


title: HLF SAHA I


title: 928.1 GFPpos E13.5 KO_S4

description: Sequencing run 1


title: HLF EtOH (S) I


title: 900.2 GFPpos E13.5 WT_S23

description: Sequencing run 1


title: HLE SAHA II


title: NT [02_Cells]


title: 900.2 GFPpos E13.5 WT_S7

description: Sequencing run 1


title: 1516.1 KO Littermate pair 1_S30_L002

description: Sequencing run 2

value: Inha x Oct4-GFP KO


title: HLF EtOH (S) II

value: II


title: HLE EtOH (S) II


title: 941.3 GFPpos E15.5 WT_S30

description: Sequencing run 1


title: 876.4 GFPpos E13.5 WT_S6

description: Sequencing run 1


title: 876.4 GFPpos E13.5 WT_S22

description: Sequencing run 1


title: 803.2 GFPpos E13.5 WT_S8

description: Sequencing run 1


title: 803.2 GFPpos E13.5 WT_S24

description: Sequencing run 1


title: sCEPS

city: Suita

first: Yu

last: Yoshinaga

state: Osaka

address: 2-2 Yamadaoka

department: Ophthalmology

country: Japan

institute: Osaka University Graduate School of Medicine

description:
Sample 3
genes.fpkm_tracking.xlsx (as presented in the columns where the sample name is GA02647)

data_processing:
Illumina Casava1.8.2 software used for basecalling
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffdiff v2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample

source_name: Somatic stem cell-derived corneal epithelial cell sheet

extract_protocol:
Total RNA was obtained from iCEPS or sCEPS using the RNeasy total RNA kit and the QIAzol reagent (Qiagen, California, USA)
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, California, USA) according to the manufacturer’s instructions. Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.

treatment_protocol: Sample 2 and 4 were treated with rIFN-g (100 ng/ml) for 48 hours

tag: treatment

value: untreated


title: HLE EtOH (S) I

value: I


title: 832.1 GFPpos E13.5 KO_S3

description: Sequencing run 1


title: 892.2 GFPpos E15.5 KO_S26

description: Sequencing run 1


title: iCEPS with rIFN-g treatment

description:
Sample 2
genes.fpkm_tracking.xlsx (as presented in the columns where the sample name is GA02646)

source_name: iPSC-derived corneal epithelial cell sheet

value: iPSC-derived corneal epithelial cell (YZWJ14)

value: treated with rIFN-g (100 ng/ml) for 48 hours


title: 1052.4 GFPpos E15.5 KO_S12

description: Sequencing run 1

value: Embryonic day 15.5

value: Testis


title: iCEPS

description:
Sample 1
genes.fpkm_tracking.xlsx (as presented in the columns where the sample name is GA02645)


title: 1052.4 GFPpos E15.5 KO_S28

description: Sequencing run 1

value: Germ cell

value: Inhba x Oct-GFP KO


title: 1052.2 GFPpos E15.5 KO_S27

description: Sequencing run 1


title: NT [01_Cells]


title: sCEPS with rIFN-g treatment

description:
Sample 4
genes.fpkm_tracking.xlsx (as presented in the columns where the sample name is GA02648)

value: Somatic stem cell-derived corneal epithelial cell


title: 855.1 GFPpos E15.5 KO_S25

description: Sequencing run 1


title: HLE SAHA I

value: SAHA


title: xf60_adult_r2

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: lotr-1 mutant xf60, small RNA were treated with RppH before library prep

data_processing:
The raw sequence reads in FastQ format were cleaned from adapter sequences and size-selected for 18-30 base-long inserts (plus 8 random adapter bases) using cutadapt v.2.4 (http://cutadapt.readthedocs.org) with parameters ‘-a AGATCGGAAGAGCACACGTCT -m 26 -M 38’ followed by quality checks with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read alignment  to the C. elegans genome (Ensembl WBcel235/ce11 assembly) with concomitant trimming of the random adapter bases was performed using Bowtie v.1.2.2 (http://bowtie-bio.sourceforge.net) with parameters ‘-v 1 -M 1 -y --best --strata --trim5 4 --trim3 4 -S’ and the SAM alignment files were converted into sorted BAM files using Samtools v.1.9 (http://www.htslib.org).
WBcel235/ce11 gene annotation in GTF format was downloaded from Ensembl release 96 (ftp://ftp.ensembl.org/pub) and annotation for transposable elements (LINE, SINE, LTR, DNA and RC) in GTF format was downloaded from the UCSC Table Browser (http://genome-euro.ucsc.edu/cgi-bin/hgTables) RepeatMasker track and merged with the gene annotation GTF file using the Ensembl chromosome naming style.
22G-RNA read counts summarized per gene or transposon were computed using Subread featureCounts v.1.6.2 (http://bioinf.wehi.edu.au/featureCounts). 22G-RNA coverage tracks in bigWig format were produced using Bedtools v.2.27.1 and kentUtils v.385 (https://github.com/ucscGenomeBrowser/kent) using custom normalization based on the size factors computed by DESeq2 v.1.30.0 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: WBcel235/ce11
Supplementary_files_format_and_content: tab-delimited text file with summarized 22G-RNA read counts
Supplementary_files_format_and_content: normalized 22G-RNA coverage track in bigWig format

organism: Caenorhabditis elegans

source_name: gravid adult - whole animal

growth_protocol: Worms were synchronized by bleaching and overnight hatching in M9. L1 arrested worms were brought on OP50-seeded NGM plates. After 63 hours, gravid adult animals were washed off plates into fresh tubes with M9 buffer and frozen in dry ice.

extract_protocol:
For RNA extraction, worms were thawed and M9 was replaced with 250 µL of worm lysis buffer (0.2M NaCl, 0.1M Tris pH 8.5, 50 mM EDTA, 0.5% SDS), supplemented with 300 µg Proteinase K (Sigma-Aldrich, P2308). Subsequently, lysis was conducted for approximately 90 minutes at 65oC. Next, 3 volumes of TRIzol LS (Life Technologies, 10296-028) were added and subsequent isolation was as defined by the manufacturer’s instructions. Samples were enriched for small RNAs using a mirVana Kit (Life Technologies, AM1561). Samples were subsequently treated with RppH as described in Almeida et al. 2019 (https://doi.org/10.1016/j.mex.2019.01.009).  Then, 1 µg of RppH-treated RNA was loaded on a 15% TBE-urea gel and size-selected between 16- to 30-nt. Purified fraction was confirmed by Bioanalyzer sRNA chip (Agilent).
Small RNA library preparation was based on the NEBNext Multiplex sRNA Library Prep Set for Illumina (New England BioLabs) with slight modifications. To counteract ligation biases, the 3’ and 5' adapters contained 4 random bases at the 5’- and 3’-end, respectively, and were chemically synthesized by BioScientific. Adapter-ligated RNA was reverse-transcribed and PCR-amplified for 14 cycles using index primers. The PCR-amplified cDNA construct was purified using AMPure XP beads (Beckman Coulter). The purified PCR reaction was checked on the Bioanalyzer using High Sensitivity DNA chip (Agilent). Size selection of the sRNA library was done on LabChip XT instrument (Perkin Elmer) using DNA 300 assay kit. Only the fraction containing 140-165 bp was pooled in equal molar ratio. The resulting 10 nM pool was denatured to 10 pmol with 5% PhiX spike-in and sequenced as single-read on HiSeq 2500 (Illumina) in rapid mode for 51 cycles (plus 7 cycles index read)  using on-board cluster generation.

value: lotr-1(xf60) I


title: 1052.2 GFPpos E15.5 KO_S11

description: Sequencing run 1


title: xf61_adult_r3

description: lotr-1 mutant xf61, small RNA were treated with RppH before library prep

value: lotr-1(xf61) I


title: 995.1 GFPpos E15.5 WT_S31

description: Sequencing run 1


title: 855.1 GFPpos E15.5 KO_S9

description: Sequencing run 1


title: PBS3 IEL

city: New York

first: Roham

last: Parsa

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Raw fastq files were processed by using the mouse transcriptome with the kallisto (v0.46) software (Bray et al., 2016).
Analysis of transcript quantification was performed at the gene level by using the sleuth (v0.30) package for R (Pimentel et al., 2017)
We modeled batch effect and our experimental design using the sleuth_fit function and detected differentially expressed genes between all groups by the likelihood ratio test (LRT). To determine significantly expressed genes between group pairs, we used the wald-test function.
TCRa and TCRb CDR3 sequences were reconstructed in silico using MixCR software (Bolotin et al., 2015) and the extracted sequences were analyzed with the Immunarch package (v0.6.5) for R (10.5281/zenodo.3893991).
Genome_build: Gencode  M23 GRCm38
Supplementary_files_format_and_content: tab-delimited tsv files (Kallisto)

source_name: Small intestine epithelium

extract_protocol: For bulk RNAseq: Sorted cells (800 cells) were lysed in a guanidine thiocyanate buffer (TCL buffer, QIAGEN) supplemented with 1% b-mercaptoethanol.

value: Small intestine epithelium

tag: time

value: 10 days post treatment

tag: infection status

value: PBS control


title: PBS3 LP

source_name: Small intestine lamina propria

value: Small intestine lamina propria


title: PBS1 LP


title: 995.1 GFPpos E15.5 WT_S15

description: Sequencing run 1

source_name: Testis


title: PBS2 LP


title: 892.2 GFPpos E15.5 KO_S10

description: Sequencing run 1


title: N2_adult_r2

description: wild-type replicate 2, small RNA were treated with RppH before library prep

value: wild-type


title: N2_adult_r3

description: wild-type replicate 3, small RNA were treated with RppH before library prep


title: BaP Sperm, 1 (Bisulfite-seq)

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

institute: Woods Hole Oceanographic Institution

data_processing:
DNA methylation analysis was carried out following Bisulfite Analysis Toolkit (BAT). The details are provided in this website: https://www.bioinf.uni-leipzig.de/Software/BAT/. This contains 4 different modules - Mapping,  Calling, Analysis and DMRs
RNAseq - pre-processing using FASTQC
RNAseq - mapping the reads to the genome using Salmon
RNAseq - statistical analysis using DESeq2
Assembly: GRCz11
Supplementary files format and content: Text format - RNAseq data files contains read counts ; bigWig - DNA methylation calls of differentially methylated regions. (DMRs).

organism: Danio rerio

source_name: BaP Sperm

extract_protocol:
Both RNA and DNA were extracted using a Quick-DNA/RNA Miniprep Plus Kit (Zymo, Cat # D7005) following the manufacturer’s instructions
RNAseq libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Cat # R3000) according to the manufacturer’s instructions. RNA-Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of >50 million read pairs (150 bp paired-end sequencing) per sample.
DNA methylation profiling - Starting input genomic DNA (100 ng) was digested with 30 units of MspI (NEB). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor-ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™-5 (Cat#: D4003). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (Cat#: D5030). Preparative-scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™-5 (Cat#: D4003) for sequencing on an Illumina platform.

value: Sperm

value: Benzo[a]Pyrene


title: BaP Sperm, 3 (Bisulfite-seq)


title: BaP Sperm, 2 (Bisulfite-seq)


title: PBS1 IEL


title: AdV4 LP

value: mAdV-2 infection


title: BaP Sperm, 4 (Bisulfite-seq)


title: PBS2 IEL


title: Control Sperm, 3 (Bisulfite-seq)

source_name: Control Sperm

value: Control


title: AdV4 IEL


title: Control Sperm, 4 (Bisulfite-seq)


title: N2_adult_r1

description: wild-type replicate 1, small RNA were treated with RppH before library prep


title: Control Sperm, 2 (Bisulfite-seq)


title: Control Sperm, 1 (Bisulfite-seq)


title: hDup-MECP2 ASO-16wk rep3

city: Houston

first: Yingyao

last: Shao

state: TX

address: 1250 Moursund St., Suite 1350

institute: Baylor College of Medicine

data_processing:
Trimmomatic (v0.36)
STAR aligner (v2.6.0a) default besides --limitOutSJcollapsed 3000000
Genome_build: mm10
Supplementary_files_format_and_content: STAR gene counts - per gene with strandedness

source_name: Hippocampus

extract_protocol: none provided by the submitter

value: C57BL/6 x  FVB hybrid

value: Hippocampus

value: 25 weeks


title: hDup-MECP2 ASO-16wk rep2


title: xf58_adult_r1

description: lotr-1 mutant xf58, small RNA were treated with RppH before library prep

value: lotr-1(xf58) I


title: AdV 3 IEL


title: AdV 3 LP


title: BaP 10hpf, 3 (Bisulfite-seq)

value: 10hpf embryos


title: hDup-MECP2 ASO-16wk rep1


title: hDup-MECP2 ASO-12wk rep3

value: 21 weeks


title: BaP 10hpf, 4 (Bisulfite-seq)


title: BaP 10hpf, 2 (Bisulfite-seq)


title: AdV 2 LP


title: Cf.Bm.10hpf, 3 (Bisulfite-seq)

value: Control female x BaP male


title: Cf.Bm.10hpf, 4 (Bisulfite-seq)


title: AdV 2 IEL

extract_protocol:
For bulk RNAseq: Sorted cells (800 cells) were lysed in a guanidine thiocyanate buffer (TCL buffer, QIAGEN) supplemented with 1% b-mercaptoethanol.
RNA was isolated by solid-phase reversible immobilization bead cleanup using RNAClean XP beads (Agentcourt, A63987), reversibly transcribed, and amplified as described (Trombetta et al., 2014).
Uniquely barcoded libraries were prepared using the Nextera XT kit (Illumina) following the manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq500 for a total yield of 400M reads.


title: Cf.Bm.10hpf, 2 (Bisulfite-seq)


title: hDup-MECP2 ASO-12wk rep2


title: hDup-MECP2 ASO-12wk rep1


title: hDup-MECP2 ASO-8wk rep3

value: 17 weeks


title: Cm.Bf.10hpf, 2 (Bisulfite-seq)

value: Control male x BaP female


title: Cm.Bf.10hpf, 4 (Bisulfite-seq)


title: Cm.Bf.10hpf, 1 (Bisulfite-seq)


title: Control 10hpf, 4 (Bisulfite-seq)

source_name: Control 10hpf


title: Cf.Bm.10hpf, 1 (Bisulfite-seq)


title: BaP 10hpf, 1 (Bisulfite-seq)


title: hDup-MECP2 ASO-8wk rep2


title: Control 10hpf, 3 (Bisulfite-seq)


title: hDup-MECP2 ASO-8wk rep1


title: Patient_ENDPOP111_PTC

city: Bialystok

first: Iwona

last: Sidorkiewicz

address: Sklodowska-Curie Street 24a

department: Clinical Research Centre

country: Poland

institute: Medical University of Bialystok

hyb_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer’s recommendations (NanoString Technologies, USA). Briefly, 3 ng miRNA samples were prepared by ligating a specific miR-tag onto 3′ end of each mature miRNA followed by an overnight hybridization (65 °C) to nCounter Reporter and Capture probes. Subsequently, samples were placed into the nCounter Prep Station for automated sample purification and subsequent reporter capture.

scan_protocol: Each sample was scanned on the nCounter Digital Analyzer for data collection.

data_processing: nSolver 4.0 Analysis software (NanoString) was used for data analysis including normalization using the average geometric mean of the top 100 probes detected. The p-values were adjusted using the False Discovery Rate (FDR) correction for multiple comparisons, which was limited to 0.05

source_name: FFPE

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (nanostring technologies inc.) were conducted according to the manufacturer's protocol.

growth_protocol: not applicable

extract_protocol: miRNeasy FFPE kit (Qiagen, Germany) according to the manufacturer’s instructions

treatment_protocol: not applicable

tag: disease state

value: PTC

tag: tnm staging system

tag: tumor size

tag: lymph node metastasis


title: Patient_ENDPOP110_Control

value: control (normal thyroid)


title: hDup-MECP2 ASO-5wk rep3

value: 14 weeks


title: BaP eggs, 3 (Bisulfite-seq)

source_name: BaP eggs

value: Eggs


title: Control 10hpf, 2 (Bisulfite-seq)


title: Control 10hpf, 1 (Bisulfite-seq)


title: BaP eggs, 2 (Bisulfite-seq)


title: Patient_ENDPOP108_PTC


title: hDup-MECP2 ASO-5wk rep2


title: Patient_ENDPOP109_PTC

tag: multifocalization

tag: angioinvasion


title: BaP eggs, 1 (Bisulfite-seq)


title: BaP eggs, 4 (Bisulfite-seq)


title: Patient_ENDPOP112_PTC


title: Cm.Bf.10hpf, 3 (Bisulfite-seq)


title: Patient_ENDPOP107_PTC


title: control eggs, 4 (Bisulfite-seq)

source_name: control eggs


title: hDup-MECP2 ASO-5wk rep1

tag: genotype


title: hDup-MECP2 ASO-2wk rep3

value: 11 weeks


title: Patient_ENDPOP106_Control


title: hDup-MECP2 ASO-2wk rep2


title: control eggs, 2 (Bisulfite-seq)


title: control eggs, 1 (Bisulfite-seq)


title: Cm.Bf.10hpf, 3 (RNA-seq)


title: Cm.Bf.10hpf, 4 (RNA-seq)


title: hDup-MECP2 ASO-2wk rep1


title: control eggs, 3 (Bisulfite-seq)


title: Cm.Bf.10hpf, 2 (RNA-seq)


title: Cm.Bf.10hpf, 1 (RNA-seq)


title: Patient_ENDPOP105_PTC


title: Patient_ENDPOP104_Control


title: Huh7 FK228 I

tag: stimulus

tag: replicates

value: I


title: hDup-MECP2 ASO-1wk rep3

tag: tissue

value: 10 weeks


title: Cf.Bm.10hpf, 3 (RNA-seq)


title: hDup-MECP2 ASO-1wk rep2


title: Cf.Bm.10hpf, 4 (RNA-seq)


title: Control 10hpf, 4 (RNA-seq)

value: Control


title: Cf.Bm.10hpf, 2 (RNA-seq)


title: Control 10hpf, 3 (RNA-seq)


title: Patient_ENDPOP103_Control


title: hDup-MECP2 ASO-1wk rep1

value: C57BL/6 x  FVB hybrid


title: Control 10hpf, 2 (RNA-seq)


title: Patient_ENDPOP102_PTC


title: Control 10hpf, 1 (RNA-seq)


title: hDup-ctrl ASO rep3

value: Hippocampus

value: control ASO


title: control eggs, 4 (RNA-seq)


title: Patient_ENDPOP98_Control


title: hDup-ctrl ASO rep2


title: Patient_ENDPOP99_PTC


title: control eggs, 2 (RNA-seq)


title: control eggs, 3 (RNA-seq)


title: Patient_ENDPOP97_Control


title: hGFP-ctrl ASO rep3


title: hDup-ctrl ASO rep1


title: control eggs, 1 (RNA-seq)


title: Patient_ENDPOP96_PTC


title: Patient_ENDPOP100_PTC


title: hGFP-ctrl ASO rep2


title: Patient_ENDPOP95_Control


title: Patient_ENDPOP94_PTC


title: Patient_ENDPOP92_Control


title: HeLa_DL_2

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

description: RNAseq of HeLa cells treated with dye+light

data_processing:
Salmon 0.7.2 was used to align the reads to the transcriptome and extract counts, reads for genes were summed across isoforms
DEseq2 was used to analyzed the readcounts
Genome_build: HG19, Refseq transcript annotations
Supplementary_files_format_and_content: Counts per gene

source_name: HeLa 1211

growth_protocol: Cells are grown at 5% CO2 and O2 in complete media (DMEM or DMEM/F12 (RPE)) with 1% Penn/Strep and 500 mg/ml G418

extract_protocol:
Qiagen Rneasy Plus Mini Kit
PolyA selection followed by random priming, first and second strand synthesis, end-repair, and ligation to adpaters.  PCR was used to add barcodes to each sample.
mRNA sequencing, with pola selection, fragmentation and random priming, 2x150bp sequencing  --  Preformed by genewiz

treatment_protocol: Cells were treated with MG2I and 660 nm light for 5 minutes, and then recovered 24 hours.

tag: cell line

value: HeLa 1211

value: Cervical Cancer Epithelial Cells

tag: genotype/variation

value: treated with dye+light


title: HeLa_DL_3


title: HeLa_DL_1


title: Patient_ENDPOP93_PTC


title: HeLa_UT_3

description: RNAseq of untreated HeLa cells

value: untreated


title: Patient_ENDPOP91_PTC


title: HeLa_UT_2

description: RNAseq of untreated HeLa cells


title: hGFP-ctrl ASO rep1

tag: strain


title: Patient_ENDPOP90_Control


title: IDL Col-0 leaf, 6 days of darkness - Rep 1

city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

hyb_protocol: Hybridization was carried out at 45 °C for 16 h, and the arrays were washed and stained according to the protocol described in the Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays (P/N 703174 Rev.2, Affymetrix)

scan_protocol: The arrays were scanned using GeneAtlas Imaging Station (Affymetrix)

data_processing: Array data was read into R using the oligo package that retrieved the pd.aragene.1.1.st array information, which features (probeset) were annotated using Affymetrix online resources through the getNetAffx function. The technical quality of the arrays was assessed using the arrayQualityMetrics (Kauffmann et al., 2009) R package (data not shown). Next, the resulting microarray data was subjected to a variance stabilizing transformation (within-array normalization) and to cyclic-loess between-array normalization.

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf, leaf was individually darkened, 6 days darkening

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana ecotype Col-0 and PIF5 knockout were grown at 22 C under short day conditions (8 h light and 16 h dark) with 180 µmol m2 s-1 white light

extract_protocol: About 40 mg of frozen material was used for RNA isolation using a RNAeasy kit from QIAGEN (Hilden, Germany) and followed by a DNase treatment

treatment_protocol: Individually darkened leaves (IDL), one fully expanded leaf was covered on each side of the plant (total of 2 covered leaves/plant) with plastic mittens coated with aluminum foil while the rest of the rosette remained under normal light/dark cycle (Keech et al., 2007)

value: Col-0 WT

value: leaf

value: individually darkened leaves, darkened for 6 days


title: IDL Col-0 leaf, 3 days of darkness - Rep 3

source_name: Arabidopsis leaf, leaf was individually darkened, 3 days darkening

value: individually darkened leaves, darkened for 3 days


title: Patient_ENDPOP89_PTC

value: PTC


title: IDL Col-0 leaf, 3 days of darkness - Rep 1


title: IDL Col-0 leaf, 1 day of darkness - Rep 2

source_name: Arabidopsis leaf, leaf was individually darkened, 1 day darkening

value: individually darkened leaves, darkened for 1 day


title: IDL Col-0 leaf, 6 days of darkness - Rep 2


title: Col-0 leaf in light - Rep2

source_name: Arabidopsis leaf, in light (short day conditions)

value: control leaves grown in light


title: IDL Col-0 leaf, 1 day of darkness - Rep 1


title: IDL Col-0 leaf, 1 day of darkness - Rep 3


title: IDL Col-0 leaf, 6 days of darkness - Rep 3


title: HeLa_UT_1

description: RNAseq of untreated HeLa cells


title: IDL Col-0 leaf, 3 days of darkness - Rep 2


title: Patient_ENDPOP87_Control

value: control (normal thyroid)


title: Col-0 leaf in light - Rep1


title: IDL PIF5 leaf, 6 days of darkness - Rep 2

value: PIF5 knockout


title: RPE_DL_3

description: RNAseq of  RPE cells treated with dye+light

source_name: hTERT RPE

value: hTERT RPE

value: hTERT Retinal Pigment Epithelial cells


title: Patient_ENDPOP88_Control

value: Control


title: Patient_ENDPOP86_FTC

value: FTC


title: IDL PIF5 leaf, 12 days of darkness - Rep 2

source_name: Arabidopsis leaf, leaf was individually darkened, 12 days darkening

value: individually darkened leaves, darkened for 12 days


title: Col-0 leaf in light - Rep3


title: IDL PIF5 leaf, 6 days of darkness - Rep 1


title: IDL PIF5 leaf, 12 days of darkness - Rep 1


title: IDL PIF5 leaf, 1 day of darkness - Rep 3


title: IDL PIF5 leaf, 6 days of darkness - Rep 3


title: Patient_ENDPOP84_Control


title: RPE_DL_1


title: Patient_ENDPOP83_Control


title: IL-1b 3h [16_Islet]

source_name: Human Islet

tag: cell type

value: primary human islet tissue

tag: agent

tag: time point


title: IDL PIF5 leaf, 3 days of darkness - Rep 1

tag: treatment


title: IDL PIF5 leaf, 3 days of darkness - Rep 2


title: IDL PIF5 leaf, 1 day of darkness - Rep 2


title: IDL PIF5 leaf, 3 days of darkness - Rep 3


title: IDL PIF5 leaf, 1 day of darkness - Rep 1


title: PIF5 leaf in light - Rep2


title: PIF5 leaf in light - Rep3


title: IL-1b 3h [15_Islet]


title: RPE_UT_2

description: RNAseq of untreated RPE cells


title: RPE_DL_2

value: treated with dye+light


title: IL-1b 3h [14_Islet]


title: RPE_UT_1

description: RNAseq of untreated RPE cells

value: untreated


title: Patient_ENDPOP82_PTC

tag: disease state


title: IL-1b 3h [13_Islet]


title: NT [12_Islet]


title: Patient_ENDPOP81_PTC

tag: tnm staging system


title: RPE_UT_3

description: RNAseq of untreated RPE cells


title: NT [11_Islet]


title: NT [10_Islet]


title: BJ_DL_3

description: RNAseq of BJ5 cells treated with dye+light

value: hTERT  forskin fibroblasts


title: Patient_ENDPOP80_Control


title: BJ_DL_2


title: lotr1_sam117_r3

description: lotr-1 mutant sam117 replicate 3

data_processing:
The raw sequence reads in FastQ format were cleaned from adapter sequences and size-selected for 18-30 base-long inserts (plus 8 random adapter bases) using cutadapt v.2.4 (http://cutadapt.readthedocs.org) with parameters ‘-a TGGAATTCTCGGGTGCCAAGG -m 26 -M 38’, followed by quality checks with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and MultiQC (https://multiqc.info/).
Read alignment  to the C. elegans genome (Ensembl WBcel235/ce11 assembly) with concomitant trimming of the random adapter bases was performed using Bowtie v.1.2.2 (http://bowtie-bio.sourceforge.net) with parameters ‘-v 1 -M 1 -y --best --strata --trim5 4 --trim3 4 -S’ and the SAM alignment files were converted into sorted BAM files using Samtools v.1.9 (http://www.htslib.org).
WBcel235/ce11 gene annotation in GTF format was downloaded from Ensembl release 96 (ftp://ftp.ensembl.org/pub) and annotation for transposable elements (LINE, SINE, LTR, DNA and RC) in GTF format was downloaded from the UCSC Table Browser (http://genome-euro.ucsc.edu/cgi-bin/hgTables) RepeatMasker track and merged with the gene annotation GTF file using the Ensembl chromosome naming style.
22G-RNA read counts summarized per gene or transposon were computed using Subread featureCounts v.1.6.2 (http://bioinf.wehi.edu.au/featureCounts). 22G-RNA coverage tracks in bigWig format were produced using Bedtools v.2.27.1 and kentUtils v.385 (https://github.com/ucscGenomeBrowser/kent) using custom normalization based on the size factors computed by DESeq2 v.1.30.0 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: WBcel235/ce11
Supplementary_files_format_and_content: tab-delimited text file with summarized 22G-RNA read counts
Supplementary_files_format_and_content: normalized 22G-RNA coverage track in bigWig format

source_name: gravid adult - whole animal

growth_protocol: Worms were synchronized by bleaching and overnight hatching in M9 buffer. L1 arrested worms were brought on OP50-seeded NGM plates. After 65 hours, gravid adult animals were washed off plates into fresh tubes with M9 buffer. Worms were washed with M9 buffer three times followed by Ultrapure water three times. Liquid was removed and 50 ul of worms were transferred into a new tube.

extract_protocol:
For RNA extraction, 500 µl of Trizol LS (Life Technologies) was added to 50 µl of worms and frozen for 30 s in liquid nitrogen followed by thawing for 2 min at 37°C. Freeze-thaw cycles were repeated until worms were dissolved. Samples were centrifuged for 5 min at 14800g and supernatants were mixed 1:1 with cold 100% ethanol. RNA isolation was performed with Zymo Research Direct-zol RNA microprep kit (R2062) according to manufacturer’s protocol and 1 µg RNA of each sample was subsequently treated with RNA 5´ Pyrophosphohydrolase (RppH, NEB) as described in Almeida et al. 2019 (https://doi.org/10.1016/j.mex.2019.01.009).
NGS library prep was performed using the NEXTflex Small RNA-Seq Kit V3 following Step A to Step G of Bioo Scientific`s standard protocol (V19.01) with a ligation of the 3’ 4N Adenylated Adapter overnight at 20°C. Libraries were prepared with a starting amount of 580 ng RppH-treated RNA per sample, amplified in 16 PCR cycles, purified on an 8% TBE gel and size-selected in the range 144-163 bp. Purified libraries were profiled with a High Sensitivity DNA kit on a 2100 Bioanalyzer (Agilent), quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer (Life Technologies), pooled in equimolar ratio and sequenced on a NextSeq 500/550 Illumina sequencer.

value: lotr-1(sam117) I


title: NT [09_Islet]


title: BJ_DL_1


title: Patient_ENDPOP79_PTC

tag: tumor size


title: Patient_ENDPOP78_Control


title: N2_r2

description: wild-type replicate 2

value: wild-type


title: N2_r1

description: wild-type replicate 1


title: BJ_UT_3

description: RNAseq of untreated BJ5 cells


title: PIF5 leaf in light - Rep1

value: leaf


title: Patient_ENDPOP77_PTC

value: PTC

tag: lymph node metastasis


title: Patient_ENDPOP76_Control


title: BJ_UT_1

description: RNAseq of untreated BJ5 cells


title: Patient_ENDPOP75_PTC

tag: multifocalization


title: lotr1_sam117_r2

description: lotr-1 mutant sam117 replicate 2


title: A375 NECTIN1 KO3 - FBS

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to GRCh38 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with htseq-count. Raw counts  were used to normalize and quantify each transcripts
Genome_build: GRCh38
Supplementary_files_format_and_content: Read raw counts for each Sample ...

source_name: A375 human melanoma cell line

growth_protocol: Cells were grown in DMEM + 10% FBS.

extract_protocol:
Cells were washed with PBS, then total RNA was extracted with the RNeasy mini plus kit from Qiagen.
Total RNA was depleted of ribosomal RNA with the RiboZero gold kit (Epicentre). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a HiSeq Illumina sequencer with 2x100bp paired-end reads.

treatment_protocol: Cells were grown to ~60% confluence, rinsed with PBS and cultured for 12 hours in DMEM supplemented or not with 10% FBS.

value: human melanoma

value: NECTIN1 KO


title: N2_r3

description: wild-type replicate 3


title: lotr1_sam117_r1

description: lotr-1 mutant sam117 replicate 1


title: Patient_ENDPOP74_PTC


title: BJ_UT_2

description: RNAseq of untreated BJ5 cells


title: Patient_ENDPOP73_PTC

tag: angioinvasion


title: A375 NECTIN1 KO1 - FBS


title: A375 NECTIN1 KO4 - FBS


title: A375 WT4 - FBS


title: A375 NECTIN1 KO2 - FBS


title: A375 WT3 - FBS


title: Patient_ENDPOP71_FTC


title: Patient_ENDPOP70_Control

value: control (normal thyroid)


title: Patient_ENDPOP69_Control


title: A375 WT2 - FBS


title: Patient_ENDPOP72_Control


title: Patient_ENDPOP68_PTC


title: Patient_ENDPOP66_FTC


title: A375 WT1 - FBS


title: A375 WT4 + FBS


title: Patient_ENDPOP66_Control


title: Patient_ENDPOP65_PTC


title: A375 WT3 + FBS


title: Patient_ENDPOP85_PTC


title: Patient_ENDPOP63_Control


title: Patient_ENDPOP64_PTC


title: A375 WT2 + FBS


title: Patient_ENDPOP62_FTC


title: htf, umbilical cord blood sample 105

type: genomic

city: Maastricht

first: Rebekka

middle: Maria

last: Koeck

address: Maastricht UMC+

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Centre

description:
htf umbilical cord blood sample
3007

hyb_protocol: bisulphite converted DNA (EpiTect - Qiagen) was hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: The raw data were processed in R using the RnBeads package. SWAN normalisation was carried out before greedycut (p-value threshold 0.05) filtering was applied to remove poor quality sites and samples. Further filtering was carried out to remove sites (i) on the sex chromosomes, (iii) near single nucleotide polymorphisms, (iii) with missing values in 5% or more of the samples, (iv) sites not in a CpG context. Samples were also excluded if their predicted sex, predicted using the sEst package, did not match the recorded sex. The values presented are methylation beta values.

label: Cy5 and Cy3

source_name: umbilical cord blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from umbilical cord blood samples using the Gentra Puregene DNA purification kit (Qiagen Hilden, Germany) according to the manufacturer's instructions with modifications to the red blood cell lysis solution (8.5mL) and the centrifugation time 4 or 8 minutes instead of 2 and 5, respectively).

tag: culture medium

value: htf

tag: Sex

value: M

tag: maternal age

tag: gestational age

tag: pregnancy complication

value: no

tag: birthweight

tag: batch


title: g5, umbilical cord blood sample 100

description:
g5 umbilical cord blood sample
5023

value: F


title: A375 WT1 + FBS

tag: cell line


title: patient 10 - high-grade MDS

city: Athens

first: georgia

last: tsekoura

address: Zografou

country: Greece

institute: National and Kapodistrian University of Athens

description: test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/gr/analyze
For normalization purposes, the housekeeping gene  HPRT1 was used.
The web-based software package automatically performs all deltadeltaCt (ΔΔCt) based fold-change calculations from the raw Ct data.

label: Sybr Green

source_name: bone marrow

label_protocol: PCR assays were performed using the RT² Profiler™ PCR Array Human Autophagy (Qiagen) following the Manufacturer’s instructions. Reverse transcription was performed from 0,5 μg total RNA using the RT2 First Strand Kit (Qiagen). Quantitative real-time PCR were performed (CFX96, Biorad) with 40 cycles at 95 oC for 10 minutes, 95oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit

value: high-grade Myelodysplastic syndromes (MDS)

tag: tissue

value: bone marrow


title: g5, umbilical cord blood sample 106

description:
g5 umbilical cord blood sample
3117


title: g5, umbilical cord blood sample 102

description:
g5 umbilical cord blood sample
5131


title: htf, umbilical cord blood sample 98

description:
htf umbilical cord blood sample
3156


title: htf, umbilical cord blood sample 99

description:
htf umbilical cord blood sample
2008


title: patient 9 - high-grade MDS

description: test


title: htf, umbilical cord blood sample 104

description:
htf umbilical cord blood sample
2060

value: hyp


title: Patient_ENDPOP61_Control

value: Control


title: g5, umbilical cord blood sample 101

description:
g5 umbilical cord blood sample
3141


title: g5, umbilical cord blood sample 97

description:
g5 umbilical cord blood sample
3131


title: patient 8 - high-grade MDS

description: test


title: g5, umbilical cord blood sample 103

description:
g5 umbilical cord blood sample
3129


title: Patient_ENDPOP60_PTC


title: patient 7 - high-grade MDS

description: test


title: htf, umbilical cord blood sample 90

description:
htf umbilical cord blood sample
5165


title: g5, umbilical cord blood sample 87

description:
g5 umbilical cord blood sample
1057


title: htf, umbilical cord blood sample 85

description:
htf umbilical cord blood sample
3091


title: Patient_ENDPOP58_Control


title: htf, umbilical cord blood sample 84

description:
htf umbilical cord blood sample
2002


title: g5, umbilical cord blood sample 95

description:
g5 umbilical cord blood sample
3009


title: g5, umbilical cord blood sample 82

description:
g5 umbilical cord blood sample
5031


title: g5, umbilical cord blood sample 86

description:
g5 umbilical cord blood sample
3142


title: g5, umbilical cord blood sample 92

description:
g5 umbilical cord blood sample
3163

value: pree


title: Patient_ENDPOP59_PTC


title: g5, umbilical cord blood sample 83

description:
g5 umbilical cord blood sample
5109


title: g5, umbilical cord blood sample 88

description:
g5 umbilical cord blood sample
3095


title: htf, umbilical cord blood sample 94

description:
htf umbilical cord blood sample
3078


title: Patient_ENDPOP57_PTC


title: htf, umbilical cord blood sample 93

description:
htf umbilical cord blood sample
3021


title: g5, umbilical cord blood sample 91

description:
g5 umbilical cord blood sample
3023


title: g5, umbilical cord blood sample 96

description:
g5 umbilical cord blood sample
5020


title: htf, umbilical cord blood sample 81

description:
htf umbilical cord blood sample
5043


title: patient 6 - high-grade MDS

description: test


title: htf, umbilical cord blood sample 89

description:
htf umbilical cord blood sample
5003


title: patient 3 - low-grade MDS

description: test

value: low-grade Myelodysplastic syndromes (MDS)


title: g5, umbilical cord blood sample 78

description:
g5 umbilical cord blood sample
3012


title: Patient_ENDPOP55_PTMC

value: PTMC


title: patient 4 - low-grade MDS

description: test


title: Patient_ENDPOP54_Control


title: patient 2 - low-grade MDS

description: test


title: g5, umbilical cord blood sample 79

description:
g5 umbilical cord blood sample
4052


title: Patient_ENDPOP53_PTMC


title: patient 5 - low-grade MDS

description: test


title: Patient_ENDPOP56_Control


title: patient 1 - low-grade MDS

description: test


title: Patient_ENDPOP52_Control


title: Patient_ENDPOP51_PTC


title: control 2 - healthy

description: control

source_name: peripheral blood

value: healthy

value: peripheral blood


title: control 1 - healthy

description: control


title: Patient_ENDPOP50_PTC

value: PTC


title: g5, umbilical cord blood sample 77

description:
g5 umbilical cord blood sample
5106

value: diab


title: Patient_ENDPOP49_Control


title: g5, umbilical cord blood sample 73

description:
g5 umbilical cord blood sample
1040


title: htf, umbilical cord blood sample 76

description:
htf umbilical cord blood sample
3139


title: g5, umbilical cord blood sample 74

description:
g5 umbilical cord blood sample
5011


title: htf, umbilical cord blood sample 80

description:
htf umbilical cord blood sample
4002


title: Expt 2 M2 right tumor sgRNAs

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

description: CRISPR sgRNA

library_source: other

data_processing:
Publicly available 10X Genomics cellranger count pipeline was used to jointly process the sgRNA and gene expression libraries for each sample.
Counts matrices were loaded into Seurat for downstream processing.
Low quality barcodes were filtered out.
sgRNA counts matrix was filtered and used to assign sgRNAs to the majority of single cells.
Clustering was performed to identify cell types.
Assembly: mm10
Supplementary files format and content: Seurat object (Seurat v4) with relevant metadata (ie, sgRNA assignments and clusters).

molecule: other

organism: Mus

source_name: MC-38 tumor

growth_protocol: 1 million CD8+ T cells were injected into Rag1-/- mice on day 6. 9 days later, tumor infiltrating T cells were isolated for perturb-seq.

extract_protocol:
Direct capture perturb-seq was performed using the 10X Genomics 5' scRNA-seq kit and protocol with additional spike-in primer to capture sgRNAs in each single cell.
10X Genomics 5' scRNA-seq

value: MC-38 tumor

tag: cell type

value: CD8+ tumor infiltrating T cells

tag: independent experiment

tag: mouse id

tag: tumor

value: right tumor


title: Patient_ENDPOP48_Control

source_name: FFPE

tag: disease state

value: control (normal thyroid)


title: htf, umbilical cord blood sample 75

description:
htf umbilical cord blood sample
3034

value: htf

value: no


title: Patient_ENDPOP47_PTC

tag: tnm staging system

tag: tumor size

tag: lymph node metastasis


title: control 3 - healthy

description: control


title: Expt 2 M2 left tumor sgRNAs

description: CRISPR sgRNA

value: left tumor


title: g5, umbilical cord blood sample 70

description:
g5 umbilical cord blood sample
2036

tag: culture medium

value: M


title: g5, umbilical cord blood sample 65

description:
g5 umbilical cord blood sample
3033

tag: Sex

value: F


title: g5, umbilical cord blood sample 69

description:
g5 umbilical cord blood sample
5077

tag: maternal age


title: htf, umbilical cord blood sample 72

description:
htf umbilical cord blood sample
2025

tag: gestational age


title: Expt 2 M2 right tumor GEX

description: polyA RNA


title: Expt 2 M2 left tumor GEX

description: polyA RNA


title: g5, umbilical cord blood sample 67

description:
g5 umbilical cord blood sample
3065

tag: pregnancy complication


title: Patient_ENDPOP46_Control

value: Control


title: htf, umbilical cord blood sample 60

description:
htf umbilical cord blood sample
5073

tag: birthweight


title: g5, umbilical cord blood sample 63

description:
g5 umbilical cord blood sample
4001

tag: batch


title: htf, umbilical cord blood sample 58

description:
htf umbilical cord blood sample
4029


title: Patient_ENDPOP44_Control


title: g5, umbilical cord blood sample 68

description:
g5 umbilical cord blood sample
3122


title: g5, umbilical cord blood sample 64

description:
g5 umbilical cord blood sample
1118


title: Expt 2 M1 right tumor GEX

description: polyA RNA


title: Patient_ENDPOP45_PTC

tag: multifocalization

tag: angioinvasion


title: htf, umbilical cord blood sample 71

description:
htf umbilical cord blood sample
1001


title: Patient_ENDPOP43_PTC

tag: tissue


title: RES3

city: Nanning

first: Sanbao

last: Zhang

address: No.100,Daxue East Road

institute: Guangxi University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per Kilobase per Million Mapped Fragments (FPKM)were calculated using a protocol from Trapnell, C. et al, 2010.Spliced Reads per Billion Mapping (SRPBM)  calculated using a protocol from Li, et al. 2015 . In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include TPM values for each Sample …

organism: Sus scrofa

source_name: subcutaneous fat tissues

extract_protocol:
Fresh adipose tissues were collected and stored in liquid nitrogen at −80 ℃, and RNA was harvested using Trizol reagent(Invitrogen，Carlsbad，CA，USA). A total amount of 3 μg RNA per sample was used as an initial material for the RNA sample preparation. The library was prepared according to the method and process of lncRNA sample preparation kit (Illumina, NEB) and Small RNA Sample Preparation Kit (Illumina, RS-200-0048) at Annoroad Gene Technology Corporation (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: subcutaneous fat tissues

tag: diet

value: Resveratrol-supplemented Diet


title: Expt 2 M1 left tumor sgRNAs

description: CRISPR sgRNA

tag: cell type

tag: independent experiment

tag: mouse id


title: g5, umbilical cord blood sample 56

description:
g5 umbilical cord blood sample
2018


title: htf, umbilical cord blood sample 55

description:
htf umbilical cord blood sample
3126


title: Expt 2 M1 left tumor GEX

description: polyA RNA

tag: tumor


title: Expt 2 M1 right tumor sgRNAs

description: CRISPR sgRNA


title: RES2


title: htf, umbilical cord blood sample 66

description:
htf umbilical cord blood sample
5058


title: g5, umbilical cord blood sample 61

description:
g5 umbilical cord blood sample
3162

value: pree


title: g5, umbilical cord blood sample 59

description:
g5 umbilical cord blood sample
2034


title: htf, umbilical cord blood sample 53

description:
htf umbilical cord blood sample
1141


title: RES1


title: htf, umbilical cord blood sample 57

description:
htf umbilical cord blood sample
5019


title: Expt 1 M3 sgRNAs

description: CRISPR sgRNA

value: 2 tumors pooled


title: Control3

value: control


title: Patient_ENDPOP42_Control

tag: disease state


title: Expt 1 M3 GEX

description: polyA RNA


title: htf, umbilical cord blood sample 62

description:
htf umbilical cord blood sample
5178


title: Control2


title: Patient_ENDPOP40_Control


title: g5, umbilical cord blood sample 52

description:
g5 umbilical cord blood sample
4019


title: Expt 1 M2 sgRNAs Capture 2

description: CRISPR sgRNA


title: Control1


title: Expt 1 M2 GEX Capture 2

description: polyA RNA


title: Patient_ENDPOP38_Control


title: Patient_ENDPOP41_PTC

value: PTC

tag: tnm staging system

tag: tumor size

tag: lymph node metastasis


title: Patient_ENDPOP37_PTC


title: htf, umbilical cord blood sample 54

description:
htf umbilical cord blood sample
3036

tag: culture medium

tag: Sex

tag: maternal age


title: g5, umbilical cord blood sample 49

description:
g5 umbilical cord blood sample
4084

tag: gestational age

tag: pregnancy complication

tag: birthweight


title: htf, umbilical cord blood sample 47

description:
htf umbilical cord blood sample
2038

tag: batch


title: Expt 1 M2 GEX Capture 1

description: polyA RNA

tag: tissue


title: g5, umbilical cord blood sample 50

description:
g5 umbilical cord blood sample
3035

value: hyp


title: Patient_ENDPOP36_Control


title: Expt 1 M1 GEX

description: polyA RNA

value: MC-38 tumor


title: htf, umbilical cord blood sample 46

description:
htf umbilical cord blood sample
3062


title: Patient_ENDPOP39_PTC

tag: multifocalization

tag: angioinvasion


title: Expt 1 M1 sgRNAs

description: CRISPR sgRNA

tag: cell type

value: CD8+ tumor infiltrating T cells

tag: independent experiment


title: Ligamentum flavum.Control level (L2/3, L4/5)

city: Osaka

first: Akinobu

last: Suzuki

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Orthopaedic surgery

institute: Osaka Metropolitan University

description: Gene expression 16 weeks after surgery in rabbit ligamentum flavum obtained at control level.

hyb_protocol: 2.0ug of Cy3-labelled cDNA was filled up to 50 ul containing blocking agent and hybridization buffer, and hybridized to Rabbit Gene Expression Microarray (Agilent technologies), 4x44K for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 and 1 minute with 37°C GE Wash buffer 2, then dried immediately.

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3 (Agilent technologies) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.

organism: Oryctolagus cuniculus

source_name: Ligamentum flavum (L2/3, L4/5), 16weeks, control

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 20 ng total RNA using the SureTag Complete DNA Labeling Kit (Agilent technologies) according to the manufacturer's instructions.

extract_protocol: The total RNA from LF tissues was isolated using QIAzol Lysis Reagent and RNeasy Plus Universal Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturers’ protocol.

treatment_protocol: Eighteen-week-old male rabbits underwwent resection of the L3-4 supraspinal muscle and L2-3, L4-5 posterolateral fusion with instrumentation.

value: Ligamentum flavum

tag: gender

value: male

tag: age

value: 34 weeks old


title: Patient_ENDPOP35_PTMC

tag: disease state

value: PTMC

tag: tnm staging system


title: Ligamentum flavum.Fused level (L2/3, L4/5)

description: Gene expression 16 weeks after surgery in rabbit ligamentum flavum obtained at fused level.

source_name: Ligamentum flavum (L2/3, L4/5), 16weeks, fused


title: htf, umbilical cord blood sample 48

description:
htf umbilical cord blood sample
3169

value: htf


title: htf, umbilical cord blood sample 51

description:
htf umbilical cord blood sample
1058

value: no


title: Expt 1 M2 sgRNAs Capture 1

description: CRISPR sgRNA

tag: mouse id

tag: tumor


title: Patient_ENDPOP33_PTC

tag: tumor size

tag: lymph node metastasis


title: Ligamentum flavum.ISC level (L3/4)

description: Gene expression 16 weeks after surgery in rabbit ligamentum flavum obtained at ISC level.

source_name: Ligamentum flavum (L3/4), 16weeks, stress indused


title: Ligamentum flavum.Control level (L3/4)

source_name: Ligamentum flavum (L3/4), 16weeks, control


title: g5, umbilical cord blood sample 44

description:
g5 umbilical cord blood sample
4101

tag: culture medium

tag: Sex

value: M

tag: maternal age

tag: gestational age


title: in vitro TEX day 10 Arid1a-sgRNA replicate 4

data_processing:
Reads were trimmed and quality filtered using fastp.
Reads were aligned to mm10 or hg38 using hisat2
Aligned reads were de-duplicated using Picard
Mitochondrial reads and Y chromosome reads were removed
Peaks were called for each sample using MACS2, merged into a union peak set, and the peak by count matrix was loaded into DESeq2 for differential analysis
Assembly: mm10 or hg38
Supplementary files format and content: Genome tracks files were created by using the deduplicated reads, normalizing each sample using counts in TSS, and exported from R as bigwig files.

source_name: primary CD8 T cells

growth_protocol: Primary T cells were isolated from mouse spleen or human blood and cultured in media containing IL-2

extract_protocol:
Live CD8+ T cells were isolated by FACS and subjected to ATAC-seq
Omni ATAC-seq was performed as previously described (Corces et al Nature Methods 2017)

treatment_protocol: After activation, T cells were plated on chronic stimulation (anti-CD3 coated) plates to induce exhaustion

value: primary CD8 T cells

tag: days of_anti-cd3_stim

tag: sgrna

tag: sgrna delivery

value: retrovirus


title: in vitro TEX day 10 CTRL1 replicate 4

tag: cell type


title: Patient_ENDPOP32_PTC

tag: multifocalization

tag: angioinvasion

tag: tissue


title: Habenula_NS4

city: Seoul

first: Hyeijung

last: Yoo

address: Goryeodaero 73

department: Department of anatomy

institute: Korea University College of Medicine

hyb_protocol: Hybridization cocktails containing biotin-labeled DNA fragments for the target and hybridization controls were prepared. The target was then hybridized to the GeneChip Rat Gene 1.0 ST array (901172, Affymetrix) in a GeneChip Hybridization Oven 640 (Affymetrix) for 16 hours. Chips were washed and stained with streptavidin phycoerythrin conjugate using GeneChip Hybridization, Wash and Stain kit (900720, Affymetrix) on the GeneChip Fluidics Station 450 according to Affymetrix recommendations

scan_protocol: GeneChip arrays were scanned with the GeneChip Scanner 3000 7G (Affymetrix). Raw scanned images (.DAT) as well as processed DAT files (.CEL) were acquired using Affymetrix GeneChip Command Console software (AGCC).

data_processing: Raw data CEL files from Affymetrix were imported into GeneSpring Analysis software version GX12.1 (Agilent Technologies, Santa Clara, CA, USA). For the analysis of expression changes between stress and control samples, the files were pre-processed using the probe logarithmic intensity error, and replicas from each of the stress or control group arrays were binned using the grouping feature of the program. Normalized mean values for the two experimental groups were then generated for the experimental interpretation. Signal intensities from the chronic stress group were compared to those from the corresponding non-stress group to generate fold changes.

source_name: Habenula

label_protocol: Labeled using the GeneChip WT Terminal Labeling and Controls Kit (901525, Affymetrix), following the manufacturer’s instructions.

extract_protocol: Total RNA was extracted by using RNeasy Mini Kit (74104, Qiagen, Valencia, CA, USA) and double-amplified cDNA was synthesized using the Ambion WT Expression kit (4411973, Ambion)

treatment_protocol: In CRS group, the animals were exposed to restraint stress for 2 hours/day  for 2 weeks, and control non-stress group were kept in their home cages without any stressors. Restraint stress was induced using breathable plastic film envelopes (DC 200, DecapiCones, Braintree Scientific, Braintree, MA, USA)

tag: strain

value: Sprague-Dawley

value: habenula

tag: group

value: non-stress


title: Habenula_NS5


title: g5, umbilical cord blood sample 45

description:
g5 umbilical cord blood sample
2073

value: F

tag: pregnancy complication

value: diab

tag: birthweight

tag: batch


title: Patient_ENDPOP30_PTMC

tag: disease state

tag: tnm staging system

tag: tumor size

tag: lymph node metastasis


title: in vitro TEX day 10 CTRL1 replicate 3


title: g5, umbilical cord blood sample 43

description:
g5 umbilical cord blood sample
4082

tag: culture medium

tag: Sex

tag: maternal age

tag: gestational age


title: g5, umbilical cord blood sample 42

description:
g5 umbilical cord blood sample
3093


title: in vitro TEX day 10 Arid1a-sgRNA replicate 3

tag: cell type

tag: days of_anti-cd3_stim

tag: sgrna

tag: sgrna delivery


title: Patient_ENDPOP29_Control

value: Control

tag: tissue

value: control (normal thyroid)


title: Patient_ENDPOP34_Control


title: Habenula_NS1

tag: strain

tag: group


title: in vitro TEX day 10 Arid1a-sgRNA replicate 2


title: Patient_ENDPOP28_FTC

value: FTC

tag: multifocalization

tag: angioinvasion


title: in vitro TEX day 10 CTRL1 replicate 2


title: Habenula_CRS10

value: chronic stress


title: Habenula_CRS8


title: Patient_ENDPOP26_Control

tag: disease state


title: Patient_ENDPOP27_PTC

value: PTC

tag: tnm staging system


title: in vitro TEX day 6 Arid1a-sgRNA replicate 4


title: g5, umbilical cord blood sample 39

description:
g5 umbilical cord blood sample
2059

tag: pregnancy complication

tag: birthweight

tag: batch


title: g5, umbilical cord blood sample 37

description:
g5 umbilical cord blood sample
5104

tag: culture medium

tag: Sex

value: pree


title: Habenula_CRS7


title: in vitro TEX day 10 Arid1a-sgRNA replicate 1


title: SD_3

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

institute: Yangzhou University

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

source_name: liver

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

value: liver

tag: treatment

value: short-day

tag: time

value: Day 28


title: Patient_ENDPOP25_Control


title: Habenula_CRS12


title: SD_2


title: Habenula_NS3


title: Patient_ENDPOP31_Control


title: in vitro TEX day 6 CTRL1 replicate 4

tag: cell type

tag: days of_anti-cd3_stim


title: Patient_ENDPOP24_PTC

tag: tumor size

tag: lymph node metastasis


title: in vitro TEX day 6 Arid1a-sgRNA replicate 3

tag: sgrna

tag: sgrna delivery


title: SD_1

tag: strain

tag: tissue


title: in vitro TEX day 6 CTRL1 replicate 3


title: Patient_ENDPOP23_PTC

tag: disease state

tag: multifocalization

tag: angioinvasion


title: htf, umbilical cord blood sample 35

description:
htf umbilical cord blood sample
3084

value: htf

value: M

tag: maternal age

tag: gestational age

tag: pregnancy complication

value: no

tag: birthweight


title: g5, umbilical cord blood sample 34

description:
g5 umbilical cord blood sample
5024

tag: culture medium

tag: Sex

tag: batch


title: g5, umbilical cord blood sample 40

description:
g5 umbilical cord blood sample
5122


title: htf, umbilical cord blood sample 33

description:
htf umbilical cord blood sample
1056


title: in vitro TEX day 6 Arid1a-sgRNA replicate 2

tag: cell type

value: primary CD8 T cells

tag: days of_anti-cd3_stim

value: retrovirus


title: NLD_3

tag: treatment

value: normal LD cycle

tag: time


title: Patient_ENDPOP22_Control


title: in vitro TEX day 6 CTRL1 replicate 2

tag: sgrna

tag: sgrna delivery


title: Patient_ENDPOP21_PTC

tag: tnm staging system

tag: tumor size

tag: lymph node metastasis

tag: tissue


title: htf, umbilical cord blood sample 41

description:
htf umbilical cord blood sample
3092

value: F

tag: maternal age


title: NLD_1

tag: strain


title: in vitro TEX day 6 Arid1a-sgRNA replicate 1


title: g5, umbilical cord blood sample 30

description:
g5 umbilical cord blood sample
4023

tag: gestational age

tag: pregnancy complication


title: Patient_ENDPOP20_PTC

tag: disease state

tag: multifocalization

tag: angioinvasion


title: in vitro TEX day 6 CTRL1 replicate 1

tag: cell type


title: in vitro TEX day 10 replicate 3

tag: days of_anti-cd3_stim


title: in vitro TEX day 10 replicate 2


title: htf, umbilical cord blood sample 29

description:
htf umbilical cord blood sample
3080

tag: culture medium

tag: Sex

tag: birthweight

tag: batch


title: Patient_ENDPOP19_Control


title: Patient_ENDPOP18_Control


title: in vitro TEX day 10 replicate 1

tag: sgrna

tag: sgrna delivery


title: Patient_ENDPOP17_PTC

tag: tnm staging system

tag: tumor size

tag: lymph node metastasis


title: g5, umbilical cord blood sample 38

description:
g5 umbilical cord blood sample
1046

tag: maternal age


title: Patient_ENDPOP16_Control

tag: tissue


title: g5, umbilical cord blood sample 27

description:
g5 umbilical cord blood sample
3079

tag: gestational age

tag: pregnancy complication


title: in vitro TEX day 8 replicate 3


title: NLD_2

tag: strain

tag: treatment

tag: time


title: Patient_ENDPOP14_PTC

tag: disease state

tag: multifocalization

tag: angioinvasion


title: htf, umbilical cord blood sample 28

description:
htf umbilical cord blood sample
5101

tag: culture medium

tag: Sex

value: diab

tag: birthweight


title: in vitro TEX day 8 replicate 1

tag: cell type

tag: days of_anti-cd3_stim

tag: sgrna

tag: sgrna delivery


title: Patient_ENDPOP15_PTC

tag: tnm staging system

tag: tumor size

tag: lymph node metastasis


title: g5, umbilical cord blood sample 25

description:
g5 umbilical cord blood sample
3181

tag: maternal age

tag: gestational age

tag: pregnancy complication

value: hyp

tag: batch


title: in vitro TEX day 6 replicate 2


title: in vitro TEX day 6 replicate 3


title: htf, umbilical cord blood sample 24

description:
htf umbilical cord blood sample
3011


title: g5, umbilical cord blood sample 23

description:
g5 umbilical cord blood sample
4080


title: Patient_ENDPOP12_Control

tag: disease state

value: Control

tag: tissue

value: control (normal thyroid)


title: Patient_ENDPOP10_Control


title: Patient_ENDPOP11_PTC

tag: multifocalization

tag: angioinvasion


title: in vitro TEX day 4 replicate 3


title: htf, umbilical cord blood sample 22

description:
htf umbilical cord blood sample
5010

tag: culture medium

tag: Sex


title: in vitro TEX day 6 replicate 1

tag: cell type


title: htf, umbilical cord blood sample 26

description:
htf umbilical cord blood sample
3046

tag: birthweight


title: htf, umbilical cord blood sample 21

description:
htf umbilical cord blood sample
1140


title: Patient_ENDPOP08_Control


title: g5, umbilical cord blood sample 20

description:
g5 umbilical cord blood sample
3098


title: Patient_ENDPOP13_PTC

value: no data


title: htf, umbilical cord blood sample 19

description:
htf umbilical cord blood sample
5069


title: in vitro TEX day 4 replicate 1

tag: days of_anti-cd3_stim

tag: sgrna


title: in vitro TEX day 2 replicate 3

tag: sgrna delivery


title: in vitro TEX day 4 replicate 2


title: Patient_ENDPOP06_PTC

value: PTC

tag: tnm staging system

tag: tumor size


title: Patient_ENDPOP07_PTMC

value: PTMC

tag: lymph node metastasis


title: in vitro TEX day 8 replicate 2


title: Patient_ENDPOP07_Control


title: g5, umbilical cord blood sample 18

description:
g5 umbilical cord blood sample
3137

tag: maternal age

tag: gestational age


title: in vitro TEX day 2 replicate 1


title: in vitro TEX day 2 replicate 2


title: Patient_ENDPOP05_Control