title: SIR-S33

extract_protocol:
For RIP-seq analysis, the lungs of infected mice were perfused with formaldehyde to form crosslinks between miRNAs, MREs and individual proteins of bound RNA induced silencing complexes (RISCs). Crosslinked miRNA-mRNA-RISC complexes were immunoprecipitated by the addition of an antibody against AGO2, one component of RISC, and magnetic beads conjugated to protein A . Additional samples received either an antibody against IgG, as a negative control, or no antibody (labeled as 10% input), as a positive control. Protein-RNA complexes isolated from each sample were washed and eluted from the magnetic beads, crosslinks were reversed and protein components were digested. For SIR analysis, lungs from late-stage pulmonary adenocarcinoma animals infected with either adenoCre or adeno were formaldehyde crosslinked. Crosslinked miRNA-MRE complexes were isolated by the addition of a SIR probe followed by streptavidin beads. After extensive washing, complexes were eluted, crosslinks were reversed and the liberated miRNAs were sequenced. As positive controls, sequencing libraries were also generated from 10% of the starting input from each sample.
Sequencing libraries were constructed starting with the entire pellet of RIP or SIR RNA, using TruSeq Small RNA kits from Illumina (San Diego, CA), following manufacturer’s instructions. Two different gel fragments were isolated from each gel of RIP samples. The first fragment, containing miRNAs, corresponded to a size of 145 bps-160 bps, including ligated adapters. The second fragment of each gel, containing immunoprecipitated mRNA targets, corresponded to a size of 160 bps-500 bps, including ligated adapters. Only one gel fragment, containing miRNAs corresponding to a size of 145 bps-160 bps, including ligated adapters, was isolated from each SIR sample. Libraries were checked for quality and concentration using the DNA High-Sensitivity LabChip assay (Agilent Technologies, Santa Clara, CA) and quantitative PCR (KAPA Biosystems, Wilmington, MA), according to the manufacturers’ instructions.
RIP-seq libraries were pooled and sequenced on a MiSeq 50 base pair single-read flow cell using v2 reagents (Illumina, San Diego, CA). SIR libraries were also pooled and sequenced on either a HiSeq2500 high output 100 base pair paired-end flow cell using TruSeq SBS v3 reagents or on a NextSeq500 high output 75 base pair single-read flow cell using v2 reagents (Illumina, San Diego, CA).


title: WT_F17_biol_rep1

status: Public on Dec 31 2024

type: SRA

city: San Francisco

first: Kaveh

last: Ashrafi

state: CA

department: Physiology

country: USA

institute: UCSF

library_source: transcriptomic

data_processing:
Galaxy EC2 instance
FASTq groomer
TopHat2 ( paired end, mate-inner-distance: 150 bp, stdev 40 bp )
HTSeq-counts
Assembly: WS235
Supplementary files format and content: comma separated value, Raw_counts.csv

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole animal_L4_stage

growth_protocol: C. elegans were cultured from synchronized L1 stage animals in liquid culture until the L4 stage

extract_protocol:
C. elegans were extracted directly with trizol, total RNA purified using spin columns with on column DNAse digestion (Zymo Research)
Total RNA was converted into Illumina adapter ligated cDNA using Nextflex polyA beads in conjunction with the NextFlex Rapid Directional RNA-Seq Kit (Bioo Scientific/Perkin-Elmer)

treatment_protocol: 4 hr before harvest, liquid cultures were treated with either F17 or DMSO alone

tag: tissue

value: whole animal_L4_stage

tag: genotype

value: wild type

tag: treatment


title: WT_DMSO_biol_rep5

value: DMSO


title: liver, HSS100_5

city: Goyang

first: Hee-sung

last: Chae

state: Gyeonggi-do

address: Dongguk-ro 32

department: Department of pharmacy

country: South Korea

institute: Dongguk university

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.5.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each Sample

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA)according to the manufacturer’s instructions.
The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina), according to the manufacturer's protocol.

tag: strain

value: liver

value: High fat diet with Schisandrin C plus simvastatin100 mg/kg


title: liver, HST100_5

value: High fat diet with simvastatin100 mg/kg


title: WT_DMSO_biol_rep2


title: liver, HST100_1


title: WT_DMSO_biol_rep4


title: nhr131_DMSO_biol_rep5


title: liver, HST100_3


title: WT_DMSO_biol_rep3


title: WT_DMSO_biol_rep1


title: liver, HSC100_6

value: High fat diet with Schisandrin C100 mg/kg


title: Normal Cell 148

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: 75 read length

library_source: transcriptomic single cell

data_processing:
Alignment to reference genome GRCh38
Counting of reads per gene using FeatureCounts
Normalisation using DESeq2
Assembly: GRCh38
Supplementary files format and content: Counts_genocode_v26_AMarkiewicz_221018.txt
Supplementary files format and content: Normalized_AMarkiewicz_221103.txt

organism: Homo sapiens

source_name: blood

extract_protocol:
Cells picked by micromanipulation were transferred into 0.2 mL tube containing 2µL of Lysis Buffer (1.9 µL of 0.2% Triton + 0.1 uL of Recombinant Rnase Inhibitor) and stored in -80°C. The samples were prepared according to Smart-seq2 protocol (Picelli et al. 2014). The RNA quality was evaluated using multiplex PCR-based protocol described by Durst et al. (2017).
cDNA libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina, cat. No. FC-131-1024 and FC-131-1096) using protocol describe by Picelli et al. (2014). cDNA fragments were ligated to index adapters (Nextera XT Index Kit, cat. No. FC-131-1001 or IDT® for Illumina® DNA/RNA UD Indexes Set A, cat. No. 20027213, both from Illumina). PCR products were purified using Ampure XP beads (Beckman Coulter, cat. No. A63881). A size distribution of prepared libraries was verified by a 2100 Bioanalyzer Instrument (Agilent Technologies, cat. No. G2939BA) and Agilent High Sensitivity DNA Kit (Agilent Technologies, cat. No. 5067-4626) or 4150 TapeStation System (Agilent Technologies, cat. No. G2992AA) and High Sensitivity D5000 ScreenTape (Agilent Technologies, cat. No. NC1874887). Libraries were diluted to the concentration of 10 nM, pooled and PhiX Control v3 (Illumina, cat. No. FC-110-3001) in the final amount of 5 or 10% was added. RNA-Seq libraries were sequenced using MiniSeq System (Illumina, cat. No. SY-420-1001) and MiniSeq High Output Reagent Kit (Run 1 –  2x75 bp; Illumina, cat. No. FC-420-1001,) or HiSeq X Ten System (Illumina, cat. No. SY-412-1001) and HiSeq X Ten Reagent Kit v2.5 (Run 2 – 2x150 bp; Illumina, cat. No. FC-501-2501, Illumina; service in Macrogen, Korea).

value: blood

tag: disease

value: breast cancer

tag: cell type

value: normal cell

value: no modification


title: liver, HSC100_4


title: liver, HSC100_3


title: liver, HSC20_4

value: High fat diet with Schisandrin C20 mg/kg


title: Normal Cell 76

description: 75 read length


title: Normal Cell 143

description: 75 read length


title: liver, HSC20_3


title: Circulating Tumor Cell 31

description: 75 read length

value: circulating tumor cell


title: Circulating Tumor Cell 136

description: 75 read length


title: liver, HSC20_2


title: liver, H_11

value: High fat diet


title: Circulating Tumor Cell 30

description: 75 read length


title: liver, H_1


title: Circulating Tumor Cell 29

description: 75 read length


title: Circulating Tumor Cell 69

description: 75 read length


title: Circulating Tumor Cell 70

description: 75 read length


title: liver, N_11

value: Normal diet


title: liver, H_9


title: Circulating Tumor Cell 152

description: 75 read length


title: DD68 - AW78

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

country: Germany

institute: Biozentrum

description: FcgRIIb-/-

data_processing:
RNAseq reads were mapped to the reference genome of Mus musculus (GRcm39 version 104) using STAR aligner (version 2.0.2)
the sorted bam files were processed by feature Counts to obtain a count matrix. After quality control, a differential gene expression analysis was performed using edgeR (version 3.36), where a normalization method TMM was applied.  A threshold of p-value ≤0 .01 and log2 fold changes ≥1 or ≤ -1 were used to identify regulated genes
Assembly: RNAseq reads were mapped to the reference genome of Mus musculus (GRcm39 version 104) using STAR aligner (version 2.0.2)
Supplementary files format and content: tab-delimited text files include read counts

source_name: not applicable

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
The total RNA isolated from each sample served as input to prepare the sequencing libraries using the Illumina TruSeq Stranded messenger RNA LT Sample Prep Kit (Illumina) by the supplied protocol of the manufacturer

tag: cell line

value: not applicable

value: monocytes

value: FcgRIIb knockout

value: IVIg

tag: time

value: Day 3


title: liver, N_10

value: liver


title: liver, N_3


title: PBMCs from  Normal dog 3, Beagle

city: Jeongeup-si

first: Hanna

last: Suh

address: 30, Baekhak 1-gil, Jeongeup-si, Jeollabuk-do, Republic of Korea

institute: Korea institute of toxicology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Dog10K_Boxer_Tasha(NCBI) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: Dog10K_Boxer_Tasha
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Canis lupus familiaris

source_name: Normal

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

value: Normal

tag: breed

value: Beagle

value: peripheral blood mononuclear cells (PBMCs)


title: PBMCs from  Normal dog 1, Beagle


title: PBMCs from  Normal dog 2, Beagle


title: DD66 - AW52

description: FcgRIIb-/-


title: DD67 - AW54

description: FcgRIIb-/-


title: PBMCs from obese dog 5, Welsh Corgi

source_name: obese

value: obese

value: Welsh Corgi


title: DD65 - AW76

description: FcgRIIb-/-

value: PBS


title: DD64 - AW48

description: FcgRIIb-/-


title: PBMCs from obese dog 4, Labrador retrievers

value: Labrador retrievers


title: PBMCs from obese dog 2, Chihuahua

value: Chihuahua


title: DD74 - AW62

value: Dectin-1 knockout


title: PBMCs from obese dog 3, Labrador retrievers


title: DD73 - AW60


title: DD72 - AW58


title: DD63 - AW48

description: FcgRIIb-/-


title: DD71 - AW36


title: PBMCs from obese dog 1, Dachshunds

value: Dachshunds


title: DD61 - AW74

value: WT


title: DD70 - AW36

value: not applicable


title: DD69 - AW21

value: monocytes


title: DD59 - AW15


title: DD62 - AW76


title: DD60 - AW46


title: BY-2H_exp_3

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

description: Novogene

data_processing:
reads were quality filterred by rcorrector and trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Nicotiana tabacum v1 Edwards 2017
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Nicotiana tabacum

source_name: suspension cell culture

growth_protocol: Auxin autonomous tobacco cell line BY-2H (Nicotiana tabacum L. cv. Bright Yellow 2) was maintained in liquid Murashige and Skoog (MS). VBI-0 culture (Nicotiana tabacum cv. 'Virginia Bright Italia') were grown in modified Heller medium supplemented with 2,4-D and NAA. Auxin-autonomous VBI-2 cells were grown in modified Heller's medium without the supplemented auxins. All lines were cultivated in the dark, at 27°C, under continuous shaking (150 rpm; orbital diameter 30 mm) and sub-cultured every 14 days.

extract_protocol:
protocol from Plant Total RNA Mini Kit, QIAGEN
performed by sequencing service company (GATC Biotech or Novogene)

treatment_protocol: no treatments

tag: cultivar

value: Bright Yellow 2

tag: biological replicates

value: suspension cell culture

tag: life cycle_stage

value: exponential

tag: growth conditions

value: auxin free


title: D30 Immune cells from the knee joints

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

address: 7000 East Ave

department: BBTD

institute: LLNL

data_processing:
Cellranger mkfastq to generate FASTQ
Cellranger count to generate count matrix
Assembly: mm10
Supplementary files format and content: gene list (features.tsv) and cell barcodes (barcodes.tsv) as well as gene/barcode matrices (matrix.mtx) are provided for each experimental group.

source_name: Immune cells from the knee joints

extract_protocol:
10-week-old MRL/MpJ mice were subjected to anterior cruciate ligament injury using a non-invasive single dynamic tibial compressive overload model
Mice were euthanized and femur and tibia of injured and uninjured hindlimbs were dissected, and superficial tissue were thoroughly removed, taking care to maintain the integrity of the knee joint. Joint residing cells were liberated by first dissociating the two bones into 7.5 mL of 3% Collagenase 1 solution (Worthington Biochemical, Lakewood, NJ; CLS-1) and 100 µg/mL DNase I (Roche, Basel, Switzerland; 11284932001) in DMEM/F12 shaking at 37 °C for two 1-hour digests followed by PBS wash steps between digests. Cells released from the joint were filtered through a 70 μm nylon cell strainer prior to red blood cell (RBC) lysis using ammonium-chloride-potassium (ACK) lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA; A1049201). Separation of immune cells was performed using CD45 conjugated magnetic microbeads followed by Miltenyi Biotech MACS separation with LC columns for CD45+ cell enrichment.
Both immune (CD45+) and non-immune (CD45-) cell populations were independently sequenced using a Chromium Single Cell 3' Reagent Kit and Chomium instrument (10X Genomice, Pleasanton, CA). Library preparation was performed according to manufacturer’s protocol.

value: MRL/MpJ

tag: injury status

value: Injured joints

value: CD45+ cells

tag: time point

tag: age


title: BY-2H_exp_2

description: Novogene


title: BY-2H_stac_1

description: Novogene

value: stationary


title: BY-2H_stac_3

description: Novogene


title: DD57 - AW64

value: Day 3


title: BY-2H_stac_2

description: Novogene


title: DD58 - AW66

value: PBS


title: D7 Immune cells from the knee joints


title: D3 Immune cells from the knee joints


title: N1_S4_L006_R1_001

city: EAST LANSING

first: MARCELA

last: TABARES

state: MI

address: 567 WILSON RD

department: MMG

institute: MICHIGAN STATE UNIVERSITY

data_processing:
SPARTA pipeline https://sparta.readthedocs.io/en/latest/
raw data output file from SPARTA
raw data counts obtained in csv file were filtered base on the cuttoff parameters as follow: false discovery rate FDR< 0.05, log CPM>5, and a log2 FC<-1 (downregulated genes) or > 1 (upregulated genes) (Johnson et al., 2016).

organism: Trichlorobacter lovleyi

source_name: Exponential growth phase

growth_protocol: Anaerobic growth in liquid media without agitation

extract_protocol:
Total RNA extraction following manufacturer's recommendation for QIAGEN RNeasy kit (QIAGEN)
rRNA depletion used an Illumina TruSeq Total RNA Library Preparation kit with RiboZero Bacteria rRNA depletion beads. Libraries were quantified using Qubit and Advanced Analytical Fragment Analyzer High Sensitivity DNA NGS assays. The libraries were then pooled in equimolar amounts for multiplexed sequencing and the pool was quantified using the Kapa Biosystems Illumina Library Quantification qPCR kit.

treatment_protocol: Addition of sodium nitrite into the culture media

value: SZ

value: with nitrate


title: D0 Immune cells from the knee joints

value: Uninjured joints


title: F2_S2_L006_R1_001

value: without  nitrate


title: N3_S6_L006_R1_001


title: D1 Immune cells from the knee joints


title: F1_S1_L006_R1_001


title: BY-2H_exp_1

description: Novogene


title: F3_S3_L006_R1_001


title: D1 Stim B Cell rep 2

city: PHILADELPHIA

first: MONTSERRAT

last: ANGUERA

state: PA

address: 380 S. University Ave, Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania

description: XCI is skewed; Cast X chromosome will always be inactive

library_source: genomic

data_processing:
HiC-Pro v2.8.9 was used for allele-specific analysis, SNP files were downloaded from Sanger Institiute Mouse Genomes Project for each strain, SNP files were used to mask mm9 reference genome (UCSC Genome Browser), alignment to mask genome was performed using Bowtie2 and the custom SNP-masked index. Parameters for alignment were: (global parameters: --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end –reorder; local parameters: --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end –reorder). Unampped reads, non-uniquely mapped reads, PCR duplicates were filtered out
Raw cis contact matrices at 30kb were assembled, replicates for each condition were merged then balanced using Knight-Ruiz balancing. For each balanced matrix, simple scalar normalization, where a simple scalar size factor for each pixel was calculated based on genomic distance between pairs of bins.
For domain calling, 3DNetMod was used to identify TADs and subTADs on the balanced Hi-C matrices binned at 30kb resolution. Data was log transformed and chunked into 6Mb regions with 4Mb overlap between adjacent regions, and into 3Mb regions with 2Mb overlap. Sparse regions, where a chunked region contained zero counts for 1/3 of all pixels on the diagnal or contained consecutive zeros for more than 1500kb distance, were filtered out. High confidence domains were identified as consecutive gamma steps resulting in the same number of communitues (mean per 20 partitions) with a minimum plateu size of 16 and 8 for 6Mb and 3Mb chinked regions. 6Mb and 3Mb chunked regions were merged and domains smaller than or equal to 150kb were filtered out. Final unique boundary locations were made by merging redudent domains and colocalizing boundary locaitons. Domains were considered redundant if two domains were within =/- 60kb on both boundary edges. Boundary locations were colocalized to share a single consistent boundary if the gap between adjacent boundaries was less than 7.5% of the domain size of each of the boundaries or if boundaries were located within 60 kb of each other.
Assembly: C57BL/6NJ (accession #ERS076384) and CAST/EiJ (accession# ERS076381) genomes, assembled by Sanger Institute Mouse Genomes Project https://www.sanger.ac.uk/data/mouse-genomes-project/, mm9 (https://hgdownload.soe.ucsc.edu/downloads.html#mouse)
Supplementary files format and content: .gz files containing all valid pairs for either the whole genome or for each X allele (active X and inactive X) for all replicates and timepoints
Supplementary files format and content: .npz files of merged replicates containing balanced files for each X allele (active X and inactive X), and .txt files of merged replicates containing bias for each X allele at 30kb and 200kb resolution

molecule: genomic DNA

source_name: spleen

extract_protocol:
Arima HiC+ kit was used to prepare samples with no changes to protocol (Arima Genomics, San Diego, CA, USA), 2 million cells/replicate (n=2 mice per timepoint)
KAPA HyperPrep kit (07962312001, Roche) with modifications provided by Arima Genomics

treatment_protocol: in vitro stimulated cells were treated with 1uM CpG for 12hr and 24hrs before collection

tag: Sex

value: Female

value: spleen

value: CD23+ B Cell

value: F1 C57BL6/Cast; Xist+/-

value: 1uM CpG for 24hrs


title: N2_S5_L006_R1_001


title: R21047353-2nd-6-2nd-6 [nsf_1]

city: Shanghai

first: Yuxiaofei

last: Wang

address: 320 Yue-Yang Road

country: China

institute: University of Chinese academy of sciences

data_processing:
Read counts for each transcripts are generated using samtools idxstats (version 1.3.1);
batch are removed by ComBat-seq function in the R package sva
data was normalized to TPM format
Assembly: Schmidtea mediterranea transcriptome FASTA file can be downloaded from the foot of GSE72389
Supplementary files format and content: normalized counts(TPM) in csv files

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: tail

growth_protocol: Asexual S. mediterranea (strain CIW4) anamials were maintained at 20 °C as previously described (Newmark and Sanchez Alvarado, 2000). For all experiments, animals were starved for at least 7 days.

extract_protocol:
For small fragments of different regeneration time points and RNAi-treated planaria, total RNA was purified using TRIzol.
For each RNAi treated sample replicates, 2ug RNA was used to generate RNA libraries using VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme, NR605).

treatment_protocol: Animals were fed every 3 days for a total of two RNAi feeding and EGFP dsRNA was used for control.

tag: tissue

value: tail

value: 10dpf adult planarian

tag: strain background

value: nsf RNAi

value: 10dpf planarian after nsf RNAi


title: D0 Naive B Cell rep 1

tag: genotype

tag: treatment


title: Pancreatic tumor tissue3

type: RNA

city: Jinshan Distric

first: Jin

state: Shanghai

address: 2901 Caolang Road, Scientific Research Center, RM 319

department: Shanghai Public Health Clinical Center

institute: Fudan University

description: Gene expression data from  gastrointestinal tissue  lower than imatinib-resistant gastrointestinal stromal tumors

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Pancreatic tumor tissue

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: 4 Pancreatic tumorscame from obvious lesions during operation as well as its corresponding Pancreatic adjacent normal tissue

extract_protocol: Total RNA was extracted and purified using TRIzol reagent (Invitrogen) and an RNAsimple Total RNA Kit (Tiangen Biotech, Beijing, China) following the manufacturer’s instructions. Total RNA was quantified by a NanoDrop-2000 spectrophotometer (NanoDrop, USA) and assessed by an Agilent Bioanalyzer 2100 (CA, US) to inspect RNA integration.

treatment_protocol: The fresh samples were extremely quick intensive chilling in liquid nitrogen within 5 minutes of excision to avoid degradation. Then frozen specimens were storage at -80 °C refrigerator.

value: Pancreatic tumor tissue

tag: gender

value: female


title: Pancreatic tumor tissue2

value: male


title: Pancreatic tumor tissue1


title: Pancreatic adjacent normal tissue3

source_name: Pancreatic adjacent normal tissue

value: Pancreatic adjacent normal tissue


title: Pancreatic adjacent normal tissue4


title: D15 Immune cells from the knee joints

tag: strain

value: MRL/MpJ

value: Injured joints

tag: cell type

value: CD45+ cells


title: Pancreatic tumor tissue4


title: Pancreatic adjacent normal tissue2


title: R21047354-2nd-EGFP-10d-p-2nd-EGFP-10d-p [ctr_2]

value: EGFP RNAi

value: 10dpf planarian after EGFP RNAi


title: R21047356-2nd-6-p-2nd-6-p [nsf_2]


title: P5-PBS-5

city: Paris

first: Adrien

last: Dufour

address: 48, boulevard serurier

country: France

institute: INSERM

data_processing:
UMI Barcode read:  Read1
UMI barcode offset:  38 or 41bp (depending on barcode1 size) => cf D73
UMI barcode size:  6
Cell barcode read:  Read1
Cell barcode offset:  0
Cell barcode size:  38 to 41bp (barcode1 = [8 to 11bp], spacer w1=22bp, barcode2=8bp) => cf D73
cDNA read:  Read2
cDNA read offset:  0
cDNA read size:  50
Sample barcode read:  index2
Sample barcode offset:  0
Sample barcode size:  6
Data analysis protocol:  https://github.com/Goultard59/indrops
Genome_build: GRCm38.85 Mus musculus
Supplementary_files_format_and_content:  gene count matrix

source_name: brain

extract_protocol:
Tissue dissociation:  NTDK miltenyi
Cell enrichment:  MACS
Enrichment markers:  CD11B microbeads (Miltenyi 130-049-601)
Single cell isolation:  droplet-based cell isolation
Single cell entity:  whole cell
Single cell quality metric:  Cell encapsulation follows Poisson distribution (lambda 0.1) => flow rate control with syringe pump and Droplet size and bead loading control with droplet dye and laser detection + high speed camera (Phantom)
Single cell identifier:  bc*_1
Single cell isolation protocol:  droplet-based cell isolation
Nucleic acid library construction protocol:  inDrops like, adapted from Zilionis et al (Nature Protocols 2017), https://doi.org/10.1038/nprot.2016.154
Nucleic acid sequencing protocol:  Illumina PE sequencing
Library construction:  inDrops like, adapted from Zilionis et al (Nature Protocols 2017), https://doi.org/10.1038/nprot.2016.154
Input molecule:  polyadenylated RNA
Primer:  oligodT
Amplification method:  IVT (In vitro Transcription)
Amplification cycles:  12 to 17 cycles (Finale PCR to incorporate Illimuna index)
End bias:  3'
Library strand:  both (PE sequencing)
Spike in:  NO

treatment_protocol: In brief, a 5µL volume of phosphate-buffered saline (PBS) containing 10µg/kg injection of recombinant mouse IL1B or of PBS alone (control) was injected intraperitoneally twice a day (morning and evening) on days postnatal P1 to P4 and once in the morning on day P5.

tag: disease state

value: neonatal neuroinflammation mice model

tag: developmental stage

value: post natal day 5

value: brain

value: CD11b positive

tag: biological replicate

tag: technical replicate

value: PBS

tag: expected cell number


title: P5-PBS-6


title: P5-IL1B-6


title: D0 Naive B Cell rep 2

value: Female

value: spleen

value: CD23+ B Cell

value: F1 C57BL6/Cast; Xist+/-


title: P5-IL1B-5


title: R21047351-2nd-EGFP-10d-2nd-EGFP-10d [ctr_1]

value: tail

value: 10dpf adult planarian


title: Pancreatic adjacent normal tissue1

value: Pancreatic adjacent normal tissue

value: male


title: RNAseq shPhf6 d3_rep2

city: Birmingham

first: Maarten

last: Hoogenkamp

state: West Midlands

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description:
poly(A)+ RNA
processed data file: PUER_shPhf6_sig_FPKM.txt

data_processing:
RNAseq and ChIPseq reads were mapped to the mouse (mm10) or human (hg38) genome using HISAT2.
Transcripts were assembled using Cufflinks 2.0.0 based on the reference genome with quartile normalisation and effective length correction.
A combined gtf file was produced using Cuffmerge 2.1.1 and used for determination of differential gene expression using Cuffdiff 2.0.1.
ChIP-seq peaks were called using MACS2.
Genome_build: Human hg38 (GRCh38), Mouse mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig and tabular files containing FPKM values of all genes and significantly differentially expressed genes between PUER and shPHF6 in pairwise comparisons per day of differentiation.

source_name: myeloid progenitors

extract_protocol:
RNA extraction using columns; AmPure beads for the ChIP-Seq.
According to Illumina Sample Preparation Kit.

tag: cell line

value: shPhf6 PUER

value: 72h +100nM OHT


title: RTgill-W1.DMSO.conc8.rep3

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
Library name: rt.dmso.0.03.H10
cell lysate
rt.dmso.0.03.H10

library_source: other

data_processing:
Reads were aligned using STAR alignment on Qiagen's online analysis portal RAP version 1.0
match score 1, mismatch cost 2, discard short reads (<15), insertion and deletion cost 3, length and similarity fraction 0.8
Raw counts were logCPM normalized and filtered for low abundance (4) and variance (15).
Normalized counts were analyzed for differential expression using DESeq2 and Limma.
Assembly: for human GRCh38.noalt.106, for rainbow trout USDA_OmykA_1.1.105
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

molecule: other

organism: Oncorhynchus mykiss

source_name: gill

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to extract of interest 24 hours after seeding at 35,000 cells per well

value: gill

value: epithelial


title: RTgill-W1.DMSO.conc7.rep3

description:
Library name: rt.dmso.0.06.G10
cell lysate
rt.dmso.0.06.G10


title: RTgill-W1.DMSO.conc8.rep2

description:
Library name: rt.dmso.0.03.H06
cell lysate
rt.dmso.0.03.H06


title: RNAseq PUER d3_rep2

value: PUER


title: RNAseq shPhf6 d0_rep2


title: RTgill-W1.DMSO.conc7.rep1

description:
Library name: rt.dmso.0.06.G02
cell lysate
rt.dmso.0.06.G02


title: RNAseq PUER d1_rep2

value: 24h +100nM OHT


title: RNAseq shPhf6 d1_rep2


title: RTgill-W1.DMSO.conc7.rep2

description:
Library name: rt.dmso.0.06.G06
cell lysate
rt.dmso.0.06.G06


title: RNAseq PUER d3_rep1


title: RTgill-W1.DMSO.conc6.rep1

description:
Library name: rt.dmso.0.12.F02
cell lysate
rt.dmso.0.12.F02


title: RTgill-W1.DMSO.conc6.rep3

description:
Library name: rt.dmso.0.12.F10
cell lysate
rt.dmso.0.12.F10


title: RNAseq shPhf6 d3_rep1


title: RTgill-W1.DMSO.conc5.rep3

description:
Library name: rt.dmso.0.25.E10
cell lysate
rt.dmso.0.25.E10


title: RTgill-W1.DMSO.conc5.rep2

description:
Library name: rt.dmso.0.25.E06
cell lysate
rt.dmso.0.25.E06


title: RNAseq PUER d1_rep1


title: RNAseq shPhf6 d1_rep1


title: RNAseq PUER d0_rep1


title: RTgill-W1.DMSO.conc8.rep1

description:
Library name: rt.dmso.0.03.H02
cell lysate
rt.dmso.0.03.H02


title: RTgill-W1.DMSO.conc4.rep3

description:
Library name: rt.dmso.0.5.D10
cell lysate
rt.dmso.0.5.D10


title: PHF6 ChIPseq shPhf6

tag: chip antibody

value: PHF6 (Santa Cruz sc-365237)


title: RTgill-W1.DMSO.conc5.rep1

description:
Library name: rt.dmso.0.25.E02
cell lysate
rt.dmso.0.25.E02


title: RTgill-W1.DMSO.conc4.rep2

description:
Library name: rt.dmso.0.5.D06
cell lysate
rt.dmso.0.5.D06


title: PHF6 ChIPseq PUER


title: RTgill-W1.DMSO.conc4.rep1

description:
Library name: rt.dmso.0.5.D02
cell lysate
rt.dmso.0.5.D02


title: LDB1 ChIPseq shPhf6

value: LDB1 (Abcam ab96799)


title: RNAseq PUER d0_rep2

tag: time point


title: RTgill-W1.DMSO.conc3.rep3

description:
Library name: rt.dmso.1.C10
cell lysate
rt.dmso.1.C10


title: LDB1 ChIPseq PUER


title: TAL1 ChIPseq shPhf6

value: TAL1 (Santa Cruz sc-12984X)


title: RTgill-W1.DMSO.conc6.rep2

description:
Library name: rt.dmso.0.12.F06
cell lysate
rt.dmso.0.12.F06


title: TAL1 ChIPseq PUER


title: RTgill-W1.DMSO.conc2.rep3

description:
Library name: rt.dmso.2.B10
cell lysate
rt.dmso.2.B10


title: LMO2 ChIPseq shPhf6

value: LMO2 (R&D systems AF2726)


title: RTgill-W1.DMSO.conc2.rep2

description:
Library name: rt.dmso.2.B06
cell lysate
rt.dmso.2.B06


title: LMO2 ChIPseq PUER


title: RNAseq shPhf6 d0_rep1

description:
poly(A)+ RNA
processed data file: PUER_shPhf6_sig_FPKM.txt


title: RTgill-W1.DMSO.conc2.rep1

description:
Library name: rt.dmso.2.B02
cell lysate
rt.dmso.2.B02


title: PHF6 ChIPseq  WT FLK

source_name: Flk-1+ cells

value: ES cell derived Flk-1+ cells


title: RTgill-W1.DMSO.conc1.rep2

description:
Library name: rt.dmso.4.A06
cell lysate
rt.dmso.4.A06


title: RTgill-W1.DMSO.conc1.rep1

description:
Library name: rt.dmso.4.A02
cell lysate
rt.dmso.4.A02


title: mRNA-Seq, mutant 4

city: Augusta

first: Kai

last: Jiao

state: GA

address: 1462 Laney Walker Blvd.

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia at Augusta University

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw fastq files were pre-processed by trimming adapters (Trimmomatic-0.38)
Trimmed fastq files were aligned using mouse genome (mm10) reference (HISAT2)
PCR-duplicates were marked (Samtools) before quantification using BAM files (Samtools) in Partek Genomics Suite (PGS, Partek, USA) and FPKM normalization
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited Excel file containing FPKM values for genes for each sample

source_name: mouse cardiac nerual crest cells

growth_protocol: Male Wnt1-Cre2; Chd7 loxp/+mice crossed with femal Chd7 loxp/loxp; mTmG/mTmG female mice to obtain control (Wnt1-cre2; Chd7 +/+; mTmG) and mutant (Wnt1-cre2; Chd7 loxp/loxp; mTmG) embryos at E10.5

extract_protocol:
GFP+ cells from pharyngeal arch 3-6 of mouse embryos at E10.5 were isolated using FACS Aria II sorter.
the quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer.  The RNA Integrity Number (RIN) of all of our samples was 9.5 or above. The SureSelect Strand Specific mRNA library kit was used for library construction, as per the manufacturer’s instructions (Agilent). Library construction began with ribosome reduction using the NEBNext rRNA depletion kit. The resulting RNA was randomly fragmented with cations and heat, which was followed by first strand synthesis using random primers with inclusion of Actinomycin D (2.4ng/µL final concentration) and second strand cDNA production.

tag: cell types

value: mouse cardiac nerual crest cells

tag: Stage

tag: isolation

value: GFP+ cells from Wnt1Cre2; mtmg; chd7loxp/loxp embryos

tag: genotype/variation


title: mRNA-Seq, mutant 3


title: RTgill-W1.DCA.conc8.rep3

description:
Library name: rt.dca.0.25.H11
cell lysate
rt.dca.0.25.H11

tag: tissue


title: RTgill-W1.DCA.conc8.rep2

description:
Library name: rt.dca.0.25.H07
cell lysate
rt.dca.0.25.H07

tag: treatment


title: mRNA-Seq, control 4 (wt)

value: GFP+ cells from Wnt1Cre2; mtmg; chd7+/+ embryos

value: wild type


title: mRNA-Seq, mutant 1


title: RTgill-W1.DCA.conc8.rep1

description:
Library name: rt.dca.0.25.H03
cell lysate
rt.dca.0.25.H03


title: mRNA-Seq, control 2 (wt)


title: RTgill-W1.DCA.conc7.rep3

description:
Library name: rt.dca.0.5.G11
cell lysate
rt.dca.0.5.G11


title: RTgill-W1.DMSO.conc3.rep2

description:
Library name: rt.dmso.1.C06
cell lysate
rt.dmso.1.C06


title: RTgill-W1.DCA.conc7.rep2

description:
Library name: rt.dca.0.5.G07
cell lysate
rt.dca.0.5.G07


title: RTgill-W1.DCA.conc7.rep1

description:
Library name: rt.dca.0.5.G03
cell lysate
rt.dca.0.5.G03


title: RTgill-W1.DCA.conc6.rep3

description:
Library name: rt.dca.1.F11
cell lysate
rt.dca.1.F11


title: RTgill-W1.DMSO.conc3.rep1

description:
Library name: rt.dmso.1.C02
cell lysate
rt.dmso.1.C02


title: H3K27ac-ChIP seq, sample 2

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw sequence reads were aligned with Bowtie2 version 2.3.3.1 with parameters -x; -U; -S
Duplicates were removed from aligned reads using Picard MarkDuplicates version 2.9.2
Peaks were identified from the dedup alignments using MACS2 version 2.1.2 with parameters callpeak -t; -f BAM; -g mm; -n; -B; --call-summits
Genome_build: UCSC mm10
Supplementary_files_format_and_content: BED file of peaks identified for each sample from MACS2 callpeak

growth_protocol: Male Wnt1-Cre2 mice crossed with femal mTmG female mice.

extract_protocol:
GFP+ cells from pharyngeal arch 3-6 of mouse embryos at E10.5 were isolated using FACS Aria II sorter.
ChIP-Seq was performed using iDeal ChIP-Seq kit (diagenode). The library was prepared using the NEBNext ChIP-Seq Library Prep kit.

value: GFP+ cells from Wnt1Cre2; mtmg embryos

tag: antibody


title: Input, Sample 1

value: input


title: RTgill-W1.DMSO.conc1.rep3

description:
Library name: rt.dmso.4.A10
cell lysate
rt.dmso.4.A10


title: RTgill-W1.DCA.conc5.rep3

description:
Library name: rt.dca.1.9.E11
cell lysate
rt.dca.1.9.E11


title: H3K27ac-ChIP seq, sample 1


title: CHD7-ChIP seq, sample 2


title: CHD7-ChIP seq, sample 1


title: RTgill-W1.DCA.conc5.rep2

description:
Library name: rt.dca.1.9.E07
cell lysate
rt.dca.1.9.E07


title: 11TP

city: Balice

first: Ewelina

last: Semik-Gurgul

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

data_processing:
Raw sequencing reads were first subjected to quality control using FastQC software (Babraham Bioinformatics, UK)
Low quality reads (phred-quality set to 20 and a minimum read length of 36 was required to pass the filter) and fragments containing adapter sequences were filtered with the use of FlexBar software (Dodt et al., 2012)
The mapping procedure was utilized using STAR software v. 2.7.8 (Dobin et al., 2013), followed by counting of the reads to the Ensembl GTF annotation file of ARS-UCD1.2  assembly release 104 with the use of HTSeq-count software v. 1.99.2 (Anders et al., 2015)
The differential expression analysis was performed with the use of Deseq2 software with the log transformation method (Love et al., 2014)
Assembly: ARS-UCD1.2
Supplementary files format and content: Files containing gene counts for every gene and every sample created with htseq-count software

organism: Bos taurus

source_name: parenchyma tissue

extract_protocol:
RNA was isolated from tissue using using TRIzol reagent (Invitrogen, Carlsbad, California) in combination with a Direct-zol RNA kit (Zymo Research)
The RNA-seq was performed using Swift Rapid RNA Library Kit (Biosciences) with deplete rRNA (Ribo-off rRNA Depletion Kit (Vazyme)), according to the protocol. The libraries were ligated with different indexes,  pooled in one pool and sequenced in the 150 pair-end cycles on Illumina NovaSeq.

treatment_protocol: Three experimental groups: Control group (n= standard nutrition , estimated by Nutrient Requirement of Dairy Cattle (NRC, 2001); Restricted group (n=6) restriction of the daily ration of milk replacer (MR); and Unlimited group (n=6) administration of MR ad libitum 3x a day for 30 min. The collected material was transferred into tubes with RNAlater and stored at -80°C.

value: parenchyma tissue

tag: treatment/diet

value: Unlimited nutrition


title: mRNA-Seq, control 3 (wt)


title: RTgill-W1.DCA.conc5.rep1

description:
Library name: rt.dca.1.9.E03
cell lysate
rt.dca.1.9.E03

value: gill

tag: cell type


title: 15TP


title: RTgill-W1.DCA.conc4.rep2

description:
Library name: rt.dca.3.8.D07
cell lysate
rt.dca.3.8.D07

value: epithelial


title: RTgill-W1.DCA.conc4.rep3

description:
Library name: rt.dca.3.8.D11
cell lysate
rt.dca.3.8.D11


title: 6TP


title: 9TP


title: RTgill-W1.DCA.conc3.rep3

description:
Library name: rt.dca.7.5.C11
cell lysate
rt.dca.7.5.C11


title: mRNA-Seq, control 1 (wt)


title: RTgill-W1.DCA.conc3.rep2

description:
Library name: rt.dca.7.5.C07
cell lysate
rt.dca.7.5.C07


title: 3TP


title: Input, Sample 2


title: 16TP

value: Restricted nutrition


title: RTgill-W1.DCA.conc2.rep3

description:
Library name: rt.dca.15.B11
cell lysate
rt.dca.15.B11


title: RTgill-W1.DCA.conc3.rep1

description:
Library name: rt.dca.7.5.C03
cell lysate
rt.dca.7.5.C03


title: 13TP


title: RTgill-W1.DCA.conc6.rep2

description:
Library name: rt.dca.1.F07
cell lysate
rt.dca.1.F07


title: RTgill-W1.DCA.conc6.rep1

description:
Library name: rt.dca.1.F03
cell lysate
rt.dca.1.F03


title: 10TP


title: RTgill-W1.DCA.conc2.rep1

description:
Library name: rt.dca.15.B03
cell lysate
rt.dca.15.B03


title: 5TP


title: 8TP


title: RTgill-W1.DCA.conc2.rep2

description:
Library name: rt.dca.15.B07
cell lysate
rt.dca.15.B07


title: RTgill-W1.DCA.conc1.rep2

description:
Library name: rt.dca.30.A07
cell lysate
rt.dca.30.A07


title: 21TP

value: Control


title: RTgill-W1.DCA.conc1.rep3

description:
Library name: rt.dca.30.A11
cell lysate
rt.dca.30.A11


title: RTgill-W1.DCA.conc4.rep1

description:
Library name: rt.dca.3.8.D03
cell lysate
rt.dca.3.8.D03


title: 7TP


title: RTgill-W1.DCA.conc1.rep1

description:
Library name: rt.dca.30.A03
cell lysate
rt.dca.30.A03


title: 19TP


title: 18TP


title: RTgill-W1.control.rep24

description:
Library name: rt.ctrl.H09
cell lysate
rt.ctrl.H09


title: RTgill-W1.control.rep22

description:
Library name: rt.ctrl.H01
cell lysate
rt.ctrl.H01


title: RTgill-W1.control.rep23

description:
Library name: rt.ctrl.H05
cell lysate
rt.ctrl.H05


title: 11PPP

source_name: fat pad tissue

value: fat pad tissue


title: RTgill-W1.control.rep21

description:
Library name: rt.ctrl.G09
cell lysate
rt.ctrl.G09


title: 15PPP


title: RTgill-W1.control.rep20

description:
Library name: rt.ctrl.G05
cell lysate
rt.ctrl.G05


title: 9PPP


title: RTgill-W1.control.rep19

description:
Library name: rt.ctrl.G01
cell lysate
rt.ctrl.G01


title: RTgill-W1.control.rep18

description:
Library name: rt.ctrl.F09
cell lysate
rt.ctrl.F09


title: 6PPT


title: 7PPP


title: RTgill-W1.control.rep17

description:
Library name: rt.ctrl.F05
cell lysate
rt.ctrl.F05


title: 3PP


title: RTgill-W1.control.rep16

description:
Library name: rt.ctrl.F01
cell lysate
rt.ctrl.F01


title: 4PTP


title: 16PPP


title: RTgill-W1.control.rep13

description:
Library name: rt.ctrl.E01
cell lysate
rt.ctrl.E01


title: RTgill-W1.control.rep14

description:
Library name: rt.ctrl.E05
cell lysate
rt.ctrl.E05


title: 10PPP


title: 13PPP


title: RTgill-W1.control.rep12

description:
Library name: rt.ctrl.D09
cell lysate
rt.ctrl.D09


title: 2PAD


title: 5PPT


title: RTgill-W1.control.rep10

description:
Library name: rt.ctrl.D01
cell lysate
rt.ctrl.D01


title: RTgill-W1.control.rep11

description:
Library name: rt.ctrl.D05
cell lysate
rt.ctrl.D05


title: RTgill-W1.control.rep9

description:
Library name: rt.ctrl.C09
cell lysate
rt.ctrl.C09


title: 21PPP


title: D1 Stim B Cell rep 1

description: XCI is skewed; Cast X chromosome will always be inactive

tag: Sex

value: Female

value: spleen

value: CD23+ B Cell

tag: genotype

value: F1 C57BL6/Cast; Xist+/-

value: 1uM CpG for 24hrs


title: 2PAR


title: RTgill-W1.control.rep7

description:
Library name: rt.ctrl.C01
cell lysate
rt.ctrl.C01


title: 18PPP


title: 4PPP


title: 11w

source_name: liver tissue

value: liver tissue


title: 15w


title: 9w


title: RTgill-W1.control.rep3

description:
Library name: rt.ctrl.A09
cell lysate
rt.ctrl.A09


title: RTgill-W1.control.rep6

description:
Library name: rt.ctrl.B09
cell lysate
rt.ctrl.B09


title: RTgill-W1.control.rep5

description:
Library name: rt.ctrl.B05
cell lysate
rt.ctrl.B05


title: 7w


title: RTgill-W1.control.rep15

description:
Library name: rt.ctrl.E09
cell lysate
rt.ctrl.E09


title: 6w


title: 8PPP


title: RTgill-W1.control.rep2

description:
Library name: rt.ctrl.A05
cell lysate
rt.ctrl.A05


title: 16w


title: 13w


title: 10w


title: 8w


title: RTgill-W1.control.rep8

description:
Library name: rt.ctrl.C05
cell lysate
rt.ctrl.C05


title: 5w


title: 1PAR


title: RTgill-W1.control.rep4

description:
Library name: rt.ctrl.B01
cell lysate
rt.ctrl.B01


title: 4w


title: Batch 3 Biphenyl alone

city: Durham

first: Louis

middle: S

last: Tisa

state: NH

address: 46 College Rd

department: MCBS

institute: University of New Hampshire

data_processing:
Illumina Casava1.8.3 software used for basecalling.
Sequenced reads were trimmed for adapter sequence, and mapped to Frankia whole genome using CLC workstation
Genome_build: NC_014666 (EuI1c)
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample

organism: Pseudofrankia inefficax

source_name: culture

growth_protocol: 3 days growth at 30 C in MP growth medium with glucose as carbon source with or without 1.0 mM biphenyl or MP growth with 1 mM biphenyl as sole carbon spource.

extract_protocol:
Rneasy kit
Stable bacterial RNA removal via the Microbexppress kit.  RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Growth with biphenyl

tag: strain

tag: stress

value: Biphenyl sole C & E source

tag: temperature

tag: time

value: 3 days


title: 21w


title: Batch 2 Biphenyl alone


title: 18w


title: Batch 1 Biphenyl alone


title: 2w


title: Batch 3 Biphenyl Glucose

value: Biphenyl + Glucose


title: 1w


title: Batch 2 Biphenyl Glucose


title: RTgill-W1.control.rep1.

description:
Library name: rt.ctrl.A01
cell lysate
rt.ctrl.A01

tag: cell line


title: 3w


title: Mouse_T2_GFP

city: New York City

first: Benjamin

last: Chen

state: New York

address: 1468 Madison Avenue

department: Infectious Disease

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
10xGenomics CellRanger (v.6.21.) https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_in
Seurat v4.3 (https://satijalab.org/seurat/)
Analysis was conducted using Seurat (v4.3.0) as well as scCustomize (v1.1.1) in R (v4.2.0). Standard QC based on individual mitochondrial gene cutoffs (5%,10%, or 15%) and overall minimum of 200 and individual maximum of unique feature counts ranges were applied. Furthermore, cells with more than 5% of mouse gene UMIs were removed, likewise keeping cells with >95% human gene transcripts. DoubletFinder (v2.0.3) was used to identify potential technical doublets in the datasets, however due to the homogeneity of the cells in the datasets we chose not to remove those doublets but keep the distinction within the metadata.  To reduce batch and donor effects we avoided merging and integrating datasets from different mice or sequencing runs. We utilized the multimodal reference mapping workflow from Satija Lab which uses a K Nearest Neighbor approach to predict a likely CD4 T cell type that we used to annotate the cells in our dataset in relation to a comprehensive Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) derived reference map of 162,000 PBMCs using 228 antibodies in conjunction with scRNAseq expression data and added the predicted cell type data as meta data to the original datasets.  Datasets from the same mouse were merged and normalized using SCTransform, which utilizes regularized negative binomial regression approach. Principal component analysis (PCA) was performed identifying variable genes, Lenti-RG and HIV specific genes were manually removed. The number of principal components was chosen using the JackStraw and ElbowPlot function within Seurat (v4.3.0) and was individual for each dataset between 15 to 30. Non-linear dimensionality reduction analysis was used to produce unsupervised clustering using individual cluster resolutions based on clustree results (v0.5.0). Samples were visualized via Uniform Manifold Approximation and Projection (UMAP).  Differential gene expression analysis was conducted independent of cluster identity using the FindMarkers function of Seurat (v4.1.0) and Model-based analysis of single cell transcriptomics (MAST). Multiplicity correction was performed with the Benjamini-Hochberg method. These results were displayed with an false discovery rate cutoff (FDR) < 0.05 using EnhancedVolcano (v1.16.0). Lastly, we chose to merge, SCTransform, and integrate based on mutual-nearest-neighbor (MNN) using fastMNN within SeuratWrappers (v.0.3.1).

organism:
Homo sapiens
Mus musculus

source_name: Spleen

extract_protocol:
Spleen from infected mice were harvested and processed by homogenizing the spleen through 40um sterile filters. The cells were washed with 2mM EDTA containing PBS and treated with lysing buffer ACK (Life Technologies) to remove RBC. The remaining cells were stained with antibodies described in engraftment panel and flow sorted. Cells were sorted to enrich for GFP+ infected cells as described in results section. In 15 acutely infected cells, GFP+ HIV infected cells were pooled with dsRed+ and unmarked cells for 10x sample processing. 10d and 29d ART treated GFP+ latently infected cells were sorted into carrier wild type mouse B cells and processed for 10x sample processing. Unmarked and dsRed+ bystander cells were sorted separately and sequenced separately.
FACS sorting followed by Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v.3.1 (CG000204 Rev D) protocol

value: Spleen

value: UCB CD34+

value: CD4+ T-cells

value: 29 day ART


title: Batch 1 Biphenyl Glucose


title: Mouse_T1_GFP

description: 10x Genomics

value: 10 day ART


title: Batch 2 EuI1c Control


title: Library_8_High_Fuctose_Sample

city: Albuquerque

first: Christos

last: Argyropoulos

state: New Mexico

address: 1 University of New Mexico MSC 04-2785

department: Internal Medicine

institute: University of New Mexico

description:
Samples analyzed with and without polyadenylation of total RNA
Raw and Processed files bearing R10 in their file names, indicate libraries sequenced on R10 chemistry devices without a polyadenylation step and without a spike in control. Other libraries were sequenced with a ERCC spike in and a PAP step
Flow Cell Used: FLO-MIN106 and FLO-MIN111 (for the non PAP treated libraries, those with a R10 in their filename). There are two processed files for the PAP treated RNA sample in this run, one mapped against the coding and the non-coding RNAs from the mm39 build, and another one that enhanced this build with the ERCC spiked RNAs ("spike" in fliename). As the libraries that were not treated with PAP did not incorporate ERCC, they were mapped against the mm39 build (coding and non coding RNAs) without including the ERCC sequences

data_processing:
Custom bioinformatics workflow in python to identify the adaptors and classify reads as well formed (adapters present at both 5' and 3' end), naked (no adapters could be identified) , fusion (multiple adapters that did not conform to a well formed read) and partial (only one adapter either a 5' or 3' could be identified in the data)
Adapters were identified by blastn searches, and an adapter was considered to be present if at least 80% of its sequence was present in the read at an epsilon value of 0.001 or less. After mapping, adapters were trimmed from within python
Reorientation of the reads to identify those sequenced from the 3'->5' direction took place using the adapter orientation
PolyA trimming took place by custom regular expression matches using python's regex module
Inserts (defined as the part of the read surviving the trimming of adapters and polyA tails were mapped to the reference database using blastn. Identification required an e-value of 0.001 or less, and the top scoring alignment (smallest e-value) was assigned to each read
Assembly: a) Mmusculus.39.cDNAncRNA that included  all non-coding RNAs and cDNAs from the Genome Reference Consortium Mouse Build 39  b) Mmusculus.39.cDNAncRNA_spike that enhanced the mouse database with the sequences of the ERCC spike-in mix c) ERCC+10 microRNAs and d) ERCC + entire miRbase
Supplementary files format and content: Tab separated file which contains the counts for each RNA species identified, the type of RNA insert and the quality of the run
Supplementary files format and content: Each library was mapped to multiple databases to explore the false positives and negatives by each technique

source_name: Jejunum

growth_protocol: Mice were housed in humidity-, temperature-, and light/dark-controlled rooms and cared for by trained individuals according to the Institutional Animal Care and Use Committees (IACUC) approved-protocols at the University of Cincinnati and the University of New Mexico.

extract_protocol:
Synthetic RNA in water for the synthetic libraries.  Jejunal RNA was extracted using the TRI Reagent method (Molecular Research Center; Cincinnati, OH). RNA samples were stored at -80o C until needed for Illumina sequencing.
Library construction followed Nanopore's instruction for the SQKPCS109  kit, except for samples that included a poly-adenylation step. Those samples were subjected to a 15 PAP reaction, followed by cold inactivation of the PAP enzyme. Then the entire product was used as input to the SQKPCS109  protocol without an intermediate cleanup. Biological samples were subjected to a PAP step, except for those designated as "R10" : they were processed with the unmodified Nanopore protocol. Number of PCR cycles: biological samples subjected to the unmodified Nanopore protocol :10, Biological samples subjected to PALS-NS : 18, , Libraries 1-4 & Libraries 1-5 (up to 10 fold dilution) : 15, Library 5 100fold diluted 19, Library 5 1000 fold diluted 22
RNAseq with or without an optional polyadenylation step. Synthetic libraries were made under conditions of sham polyadenylation, in which all the re-agents for the reaction except the PAP enzyme were included in the mix. These sham polyadenylated samples were subjected to the same conditions (incubation and cold treatment) as their PAP counterparts.

treatment_protocol: Mice were fed either a carbohydrate control or 60% fructose diet (Envigo, Indianapolis, IN) for 5 weeks.  Mice were euthanized with an overdose of pentobarbital sodium and jejunum were harvested, cleaned of dietary material, snap frozen and stored at -80o C.

value: Jejunum

value: 60% Fructose diet


title: Batch 3 EuI1c Control

value: Control


title: Library_7_Control_Bio_Sample

value: Control diet


title: Batch 1 EuI1c Control


title: B Cell Stim Rep 3

data_processing:
For allele specific alignment: SNPsplit was used to identify SNPs that differ between the Castaneus and 129S1 or B6 genomes and to generate an mm10 genome in which all differential SNPs are N-masked. Spliced Transcripts Alignment to a Reference (STAR) was used to align reads to the N-Masked Genome and aligned reads were then separated into "Cast" and "129S1" or "B6" reads using SNPsplit.
Aligned reads were quantified using FeatureCounts (subread-2.0.0).
Diploid RPKM was calculated, genes are expressed if RPKM >1
Haploid gene expression of expressed genes was calculated in allele-specific reads per 10 million uniquely mapped (SRPM), genes considered expressed from inactive X if SRPM > 2
Binomial model of escape probablity calculated, 95% confidence interval was applied to genes passing RPKM and SRPM filters; if 95% confidence interval is > 0 gene was considered as escaping XCI
Assembly: 129S1/SvlmJ (accession# ERS076385) and CAST/EiJ (accession# ERS076381) genomes, assembled by Sanger Institute Mouse Genomes Project https://www.sanger.ac.uk/data/mouse-genomes-project/
Supplementary files format and content: .TXT files containing raw outputs generated by FeatureCounts (subread-2.0.0), 2/sample, allele-specific, whole genome
Supplementary files format and content: .CSV files containing final list of escape genes with processed read counts; columns contain gene name, mean diploid RPKM for naïve and stim, mean SRPM for each X allele in naïve and stim, and the Xi/Xa ratio of SRPM for naïve and stim

organism: Mus

extract_protocol:
phenol/chloroform isolation (TRIzol)
Illumina TruSeq Stranded Total RNA LT kit

treatment_protocol: in vitro stimulated cells were treated with 1uM CpG for 12hrs or 24hrs before collection

value: spleen

value: female

value: CD23+ B cells

value: F1 129S1/Cast; Xist+/-

value: in vitro CpG 24hrs


title: (stim2a;stim2b)-/- larvae - rep3

city: Warsaw

first: Shamba

middle: S.

last: Mondal

address: Księcia Trojdena 4

institute: International Institute of Molecular and Cell Biology

description: Thirty larvae were pooled together for one RNA sample

data_processing:
We utilized the SQuIRE (Yang et al., 2019) pipeline for analyzing the RNA-Seq data. Human genome hg38 and corresponding refseq gene annotations were downloaded from UCSC (https://genome.ucsc.edu/; (Haeussler et al., 2019) with SQuIRE. STAR version 2.5.3a (Dobin et al., 2013), StringTie version 1.3.3b (Pertea et al., 2015), and DESeq2 version 1.16.1 (Love et al., 2014) were used within the SQuIRE pipeline for alignment of reads, transcript assembly and quantification, and differential gene expression analysis respectively.
Differentially expressed genes with false discovery rate (FDR) < 0.05 were considered for further analysis.
Assembly: danRer11
Supplementary files format and content: tab separated text files with gene transcript abundance measurements for each sample
Supplementary files format and content: tab separated text files containing DESeq2 output for differential expression of genes between (stim2a;stim2b)+/+ and (stim2a;stim2b)-/- samples

organism: Danio rerio

source_name: whole zebrafish larvae

growth_protocol: Larvae were kept in E3 medium (2.48 mM NaCl, 0.164 mM CaCl2·2H2O, 0.09 mM KCl, and 0.428 mM MgCl2·6H2O) at 28.5C. Larvae were kept in the incubator with light-dark cycle (14h:10h) in the Petri dish (~50 larvae/dish).

extract_protocol:
Total RNA was was extracted from 5 dpf larvae using TRI Reagent (Invitrogen, Cat. No. AM9738). Thirty larvae were pooled together to obtain one RNA sample. Total RNA was digested by DNase I and purified using the RNA-Clean and Concentrator Kit (ZYMO Research, Irvine, CA, USA) as the manufacturer described. Quality of RNA was checked by measuring absorbance at 260, 280, and 230 nm and Bioanalyzer Nano RNA chip (Agilent, USA) analysis. Samples with 260/280 nm as well as 230/280 nm absorbance ratio>1.8 and RNA integrity number (RIN) values above eight were used for further processing.
RNA libraries were prepared from 1 ug of total RNA, for each sample, using KAPA Stranded RNA-seq kit (KK8401 from Roche). Breafly, mRNA was isolated with poliA beads from Illumina. The 1st and 2nd strands of DNA were synthetise and A tailing and ligation reactions were run. In ligation step the TruseqLT RNA adapter (Illumina) were used. The libraies were amplified runing 8 cycle of PCR.Quantity of each library were measure with Quantus device, then libraies were pooled in ratio 1:1 and concentration of the pool was confirmed with real-time PCR using KAPA Library Quantification kit (Roche). Libraries were sequence as pair-end (2 x 75 bp) on NextSeq 500 Illumina platform.

tag: age

value: 5 days post fertilization

value: whole larvae

value: untreated

tag: developmental stage

value: larvae


title: B Cell Stim Rep 2


title: (stim2a;stim2b)-/- larvae - rep2


title: Unirradiated Sample 1

city: Berkeley

first: Iswar

middle: Krishna

last: Hariharan

address: 515 LSA

department: Molecular and Cell Biology

institute: University of California Berkeley

description:
Library name: Unirradiated Sample 1
PE150

data_processing:
Sequences were aligned to Drosophila transcriptome v6.55 using kallisto-bustools v0.28.2 (kallisto v0.50.1, bustools v0.43.2) with default settings.
Assembly: Drosophila transcriptome v6.55
Supplementary files format and content: Files from kallisto-bustools output were cells_x_genes.barcodes.txt (cell barcode identities), cells_x_genes.genes (genes captured), and cells_x_genes.mtx (transcript counts for each gene in each cell). These files can be turned into a sparse matrix using read_count_output() in R using the ‘BUSpaRse’ package.

organism: Drosophila melanogaster

source_name: Drosophila Wing Discs, Late Wandering Third Instar Larvae, Unirradiated, Sample 1

growth_protocol: Drosophila were reared at 25°C on Bloomington style food with dry yeast supplement.

extract_protocol:
Larvae were dissected 4 hours after the end x-ray exposure (or non-exposure in the case of control samples) and wing discs from many larvae pooled together. Wing discs were dissociated using a trypsin enzymatic digest.
Single-cell suspensions were FACS sorted to remove dead cells and cell debris and libraries were constructed using 10x v3.1 next gem chips.

treatment_protocol: Irradiated larvae were exposed to 4000 rad over ~35-45 minutes

value: Late Wandering Third Instar Larvae

value: Wing imaginal disc

value: Epithelial, Myoblast

value: Oregon R (Wildtype)


title: B Cell Stim Rep 1

source_name: spleen


title: (stim2a;stim2b)+/+ larvae - rep2


title: (stim2a;stim2b)-/- larvae - rep1


title: (stim2a;stim2b)+/+ larvae - rep3


title: B Cell Naïve Rep 2


title: RNAs_NSCLCBM_BM3

city: Nanjing

first: Yang

last: Daolu

state: Jiangsu

address: 101 Longmian Road

institute: Nanjing Medical University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat.# 5188-5327, Agilent Technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.After the original data were normalized with the limma package in the software R, the differential genes were screened using Fold-change (fold of expression difference) and T-test (Student's t-test) statistical methods, and the selection conditions were as follows: 1) Fold Change (linear) =< 0.5 or Fold Change (linear) >= 2. 2) T-test p-value <0.05 or <0.01.

source_name: NSCLC tissue, Brain metastases

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent Technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100.

value: NSCLC brain metastatic tumor tissue

tag: gender

value: male


title: RNAs_NSCLCBM_BM2


title: Normal Cell 265

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

institute: University of Bergen

description: 150 read length

data_processing:
Alignment to reference genome GRCh38
Counting of reads per gene using FeatureCounts
Normalisation using DESeq2
Assembly: GRCh38
Supplementary files format and content: Counts_genocode_v26_AMarkiewicz_221018.txt
Supplementary files format and content: Normalized_AMarkiewicz_221103.txt

source_name: blood

extract_protocol:
Cells picked by micromanipulation were transferred into 0.2 mL tube containing 2µL of Lysis Buffer (1.9 µL of 0.2% Triton + 0.1 uL of Recombinant Rnase Inhibitor) and stored in -80°C. The samples were prepared according to Smart-seq2 protocol (Picelli et al. 2014). The RNA quality was evaluated using multiplex PCR-based protocol described by Durst et al. (2017).
cDNA libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina, cat. No. FC-131-1024 and FC-131-1096) using protocol describe by Picelli et al. (2014). cDNA fragments were ligated to index adapters (Nextera XT Index Kit, cat. No. FC-131-1001 or IDT® for Illumina® DNA/RNA UD Indexes Set A, cat. No. 20027213, both from Illumina). PCR products were purified using Ampure XP beads (Beckman Coulter, cat. No. A63881). A size distribution of prepared libraries was verified by a 2100 Bioanalyzer Instrument (Agilent Technologies, cat. No. G2939BA) and Agilent High Sensitivity DNA Kit (Agilent Technologies, cat. No. 5067-4626) or 4150 TapeStation System (Agilent Technologies, cat. No. G2992AA) and High Sensitivity D5000 ScreenTape (Agilent Technologies, cat. No. NC1874887). Libraries were diluted to the concentration of 10 nM, pooled and PhiX Control v3 (Illumina, cat. No. FC-110-3001) in the final amount of 5 or 10% was added. RNA-Seq libraries were sequenced using MiniSeq System (Illumina, cat. No. SY-420-1001) and MiniSeq High Output Reagent Kit (Run 1 –  2x75 bp; Illumina, cat. No. FC-420-1001,) or HiSeq X Ten System (Illumina, cat. No. SY-412-1001) and HiSeq X Ten Reagent Kit v2.5 (Run 2 – 2x150 bp; Illumina, cat. No. FC-501-2501, Illumina; service in Macrogen, Korea).

value: blood

tag: disease

value: breast cancer

value: normal cell

value: no modification


title: B Cell Naïve Rep 3

value: spleen

value: female

value: CD23+ B cells


title: Normal Cell 204

description: 150 read length


title: (stim2a;stim2b)+/+ larvae - rep1

value: 5 days post fertilization


title: B Cell Naïve Rep 1

value: F1 129S1/Cast; Xist+/-


title: Normal Cell 252

description: 150 read length


title: RNAs_NSCLCBM_BM1


title: hiPSC-CMs; treated with guide RNA to induce Gln3924Glu (Q3924E) mutation in Ryr2; rep 3

city: Charleston

first: Allison

last: Trouten

state: SC

address: 173 Ashley Ave Room BSB 642

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

description: Library name: QE_3

data_processing:
Raw fastq files were aligned using STAR 2.7.6a aligner
Differential expression analysis run using DEseq2 1.44.0
Heatmaps created using pheatmap (1.0.12)
Other plots made via ggplot2 3.5.1
Gene ontology assessment via enrichGO function via clusterprofiler package (4.12.2)
Assembly: hg38
Supplementary files format and content: Tab delimited CSV file includes normalized raw counts for each sample
Supplementary files format and content: Compressed fastq files include raw unaligned sequencing files

source_name: K3 stem cells

growth_protocol: K3 stem cells were obtained and maintained in Stemflex medium

extract_protocol:
Standard Trizol phenol chloroform extraction
Total RNA samples were sent to Novogene for library prep and sequencing (mRNA library preparation poly A enrichment)

treatment_protocol: Cardiogenic differentiation was induced by treating dissociated induced pluripotent stem cells (iPSCs) with CHIR99021 (a GSK3β inhibitor) for 24 h in RPMI/B-27 without insulin. After three days of CHIR99021 treatment, IWR1 (a Wnt signaling inhibitor) was added culture media for 48 h. Cells were then maintained in RPMI/B-27 media without insulin and switched to RPMI/B-27 medium containing insulin (B27(+) medium) when majority of the cells started beating.

value: K3 stem cells

value: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs)

value: Q3924E mutant

value: cardiogenic differentiation of stem cells to iCMs


title: hiPSC-CMs; treated with guide RNA to induce Glu3848Ala (E3848A) mutation in Ryr2, rep 3

description: Library name: EA_3

value: E3848A mutant


title: wild type 21 dpi sample 1

city: Chapel Hill

first: Yiran

last: Song

state: NC

address: 111 Mason Farm Road

institute: The University of North Carolina

data_processing:
RNA-seq raw data quality was checked by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-seq were aligned to the zebrafish reference genome using STAR(Dobin et al., 2013).
Gene expression was quantified as gene hit counts (reads per gene) using FeatureCounts(Liao et al., 2014).
Assembly: Danio rerio (zebrafish) genome assembly GRCz11 (danRer11)
Supplementary files format and content: txt data file include raw counts for each sample

source_name: Heart ventricle

extract_protocol:
Total RNA was isolated from zebrafish ventricles using Trizol (Invitrogen). Reverse transcription was performed using SuperScript IV VILO Master Mix (Invitrogen).
For RNA-seq, library preparation and Illumina RNA-seq were performed by Novogene.

value: Heart ventricle

value: wild type


title: RNAs_NSCLCBM_PT2

source_name: NSCLC tissue, Primary

value: NSCLC primary tumor tissue


title: RNAs_NSCLCBM_PT1


title: Normal Cell 209

description: 150 read length

value: blood


title: wild type 21 dpi sample 2


title: RNAs_NSCLCBM_PT3

value: male


title: hiPSC-CMs; no guide RNA; rep 3

description: Library name: WT_3


title: Normal Cell 256

description: 150 read length

value: breast cancer

value: normal cell


title: wild type 7 dpi sample 2


title: wild type 7 dpi sample 1


title: Normal Cell 49

description: 150 read length

value: no modification


title: Normal Cell 178

description: 150 read length


title: Circulating Tumor Cell 269

description: 150 read length

value: circulating tumor cell


title: wild type 0 dpi sample 2


title: Normal Cell 203

description: 150 read length


title: wild type 0 dpi sample 1


title: Circulating Tumor Cell 245

description: 150 read length


title: Circulating Tumor Cell 207

description: 150 read length


title: Circulating Tumor Cell 47

description: 150 read length


title: nr4a1 mutant 21 dpi sample 2

value: nr4a1 mutant


title: wild type 2 dpi sample 2


title: nr4a1 mutant 7 dpi sample 2


title: Circulating Tumor Cell 25

description: 150 read length


title: nr4a1 mutant 7 dpi sample 1


title: Circulating Tumor Cell 250

description: 150 read length


title: nr4a1 mutant 21 dpi sample 1


title: Circulating Tumor Cell 46

description: 150 read length


title: nr4a1 mutant 2 dpi sample 1


title: Circulating Tumor Cell 275

description: 150 read length


title: nr4a1 mutant 0 dpi sample 2


title: nr4a1 mutant 2 dpi sample 2


title: Circulating Tumor Cell 187

description: 150 read length


title: Circulating Tumor Cell 251

description: 150 read length


title: nr4a1 mutant 0 dpi sample 1


title: Circulating Tumor Cell 135

description: 150 read length


title: C57BL/6J mice, colon, obesity-resistant, Sample 3

city: Hangzhou

first: Fei

last: Yang

address: 866 Yu-hang-tang Road

institute: Zhejiang University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) .
After that, Ericscript (v0.5.5)  and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: Tab-delimited text file including fpkm expression quantities for each sample

source_name: colon

extract_protocol:
Total RNA was extracted from the colon using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) , and was used for the construction of sequencing libraries.
Bowtie2 (v2.2.5)  was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12) .

value: colon

tag: phenotype

value: obesity-resistant

value: WT

value: A high-fat diet


title: Circulating Tumor Cell 85

description: 150 read length

tag: tissue


title: wild type 2 dpi sample 1


title: YE 48h niol rep 3

city: Leiden

first: Ron

middle: P

last: Dirks

address: Sylviusweg 74

country: Netherlands

institute: Future Genomics Technologies BV

description:
FG2160_29
FG2160_YE24h-vs-YE48h_DESeq2.xlsx
FG2160_YE48h-vs-Ctrl48h_DESeq2.xlsx
FG2160_YEall-vs-Ctrlall_DESeq2.xlsx

data_processing:
Image analysis and base calling were done by the Illumina pipeline (Illumina Inc., San Diego, CA, USA)
Adapters were trimmed using BBMap v38.26 (Joint Genome Institute)
Reads were aligned against the Mitragyna speciosa reference genome using Hisat2 (version 2.2.1) (Kim et al., 2019)
The resulting files were filtered and secondary alignments were removed using SAMtools (version 1.9) (Li et al., 2009)
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.10.0) (Anders et al., 2014)
Differentially expressed genes were identified using DESeq2 (Love et al., 2014) and data were further processed using Microsoft Excel
Assembly: Mitragyna_speciosa_genome_v1.0_2020_Jul_27; Mitragyna_speciosa_genome_v1.0.03.gff3
Supplementary files format and content: Microsoft Office Excel file (.xlsx) with the following columns: gene_id; PFAMs; best_OG_desc; library names (with # aligned reads per library); baseMean; log2FoldChange; lfcSE; stat; pvalue; padj

organism: Mitragyna speciosa

source_name: plantlet

extract_protocol:
RNA was extracted using PureLink™ Plant RNA Reagent (Thermo Fisher Scientific). 1 ug of total RNA was used for the construction of sequencing libraries.
TruSeq Stranded mRNA Library Prep kit (Illumina)

value: plantlet

tag: treatment

value: 0.1 mg/ml yeast extract 48h


title: Circulating Tumor Cell 218

description: 150 read length


title: C57BL/6J mice, colon, obesity-resistant, Sample 2


title: Circulating Tumor Cell 84

description: 150 read length


title: YE 48h biol rep 2

description:
FG2160_28
FG2160_YE24h-vs-YE48h_DESeq2.xlsx
FG2160_YE48h-vs-Ctrl48h_DESeq2.xlsx
FG2160_YEall-vs-Ctrlall_DESeq2.xlsx


title: Circulating Tumor Cell 6

description: 150 read length


title: Q81Q27, IP_3

city: Toronto

first: Tiantian

last: Li

state: Ontario

address: 101 College St.

institute: University Health Network

data_processing:
Sequence reads were trimmed for adaptor sequence using cutadapt
Trimmed sequence reads were mapped to hg38 by using STAR
Read counts were generated by STAR and the differential analysis was done by DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts

growth_protocol: Fibroblasts: cultured in DMEM (Life Technologies #10370) with 15% (v/v) fetal bovine serum (FBS; Gibco #12484-028), 1X GlutaMAX (Life Technologies #35050) and 1x penicillin Streptomycin antibiotics. Cells were grown at 37°C with 5% CO2. Isogenic NPCs: DMEM/F12 (Thermo Fisher Cat No. A4192001) and NeuroBasal medium (Thermo Fisher Cat No. A3582901); 50µg/ml BSA (Thermo Fisher Cat No. B14); 1X PenStrep (Thermo Fisher Cat No. 15140122); 1X MEM NEAA (Thermo Fisher Cat No. 11140050); 1X N2 (Thermo Fisher Cat No. 17502001); 1X B27 without Vit A (Thermo Fisher Cat No. 12587010); 10µg/ml human LIF (Merck Millipore Cat No. LIF1010); 2µM SB431542 (Stem Cell Tech Cat No. 72232); 3µM CHIR99021 (Stem Cell Tech Cat No. 72052); 0.1µM Compound E (Stem Cell Tech Cat No. 73952)] supplemented with 10µM Y-27632 (Stem Cell Tech Cat No. 72304) on Geltrex (Thermo Fisher cat No. A1413301) coated plates. This is day 1 of differentiation. NPC+ medium was replaced on a daily basis till day 7. On day 7, the cells were passaged using Accutase (Thermo Fisher Cat No. A1110501), split at a ratio of 1:10 and plated in NPC- medium (NPC+ medium without Compound E) with 10µM Y-27632. Both fibroblasts and NPC cell lines were UV-crosslinked at 254-nm UV with an energy setting of 400mJoules/cm2 for 10 minutes.

extract_protocol:
Cells were lysed in cold CLIP lysis buffer (50mM Tris-HCl pH 7.4, 100mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1X protease inhibitor, and RNasin plus ribonuclease inhibitor). Followed by sonication in Bioruptor at “low” setting, 4°C for 5 min with 30 sec on and 30 sec off. 4 Units of DNase were added, and the tubes were incubated in a thermomixer at 37°C with shaking at 1200 rpm for 30 min. Next, the tubes were transferred on ice and immediately 50mM final concentration of EDTA was added. The tubes were centrifuged at 20,000xg at 4°C for 15 min to pellet debris. The supernatant was transferred to a new tube. The beads with EPR5526 (Abcam) antibody were rotated at 4°C for 1-2 hours and cell lysates were added to the prepared magnetic beads and the tubes were kept rotating at 4°C overnight. Next day, the tubes were placed in a magnetic rack and the cell lysate flowthrough was collected. The beads were washed 2x with cold high salt wash buffer (50mM Tris-HCl pH 7.4, 500mM NaCl, 1mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) and 1x with cold CLIP lysis buffer. 150uL of Proteinase K buffer (50mM Tris-HCl pH 7.4, 150mM NaCl, 1mM MgCl2, 0.05% NP-40, 1% sodium deoxycholate, and 1.2mg/mL Proteinase K) was added to the beads and incubated at 55°C for 30 min while shaking to digest proteins. After this reverse cross-linking step, the tubes were gently centrifuged using a table-top centrifuge and placed on a magnetic rack. The supernatants were transferred to new tubes and 600µL TRIzol reagent was added, and the tubes were incubated for 10 min at room temperature. The RNA was further purified using Direct-Zol RNA miniprep plus kit (Zymo Research, Cat. no. R2071). The purified RNA was eluted in RNases and DNase free water, and concentrations were estimated by nanodrop prior to library preparation.
RIP-Seq libraries were prepared by using SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; Takara, 634413) as per the manufacturer's instructions. Subsequently, the libraries were subjected to paired-end sequencing with a read length of 150 bp on the Illumina HiSeq X Ten platform, ensuring a minimum sequencing depth of 30 million reads per sample.

value: human mutated huntingtin cells

value: RIP IP

value: IP


title: ctrl 48h biol rep 2

description:
FG2160_25
FG2160_YE48h-vs-Ctrl48h_DESeq2.xlsx
FG2160_YEall-vs-Ctrlall_DESeq2.xlsx

value: control methyl jasmonate 48h


title: Q81Q27, IP_2


title: Q81Q27, IP_1


title: C57BL/6J mice, colon, obesity-prone, Sample 3

value: obesity-prone


title: Q81Q27, INPUT_3

value: RIP input

value: input control


title: C57BL/6J mice, colon, obesity-prone, Sample 2


title: Q81Q27, INPUT_2


title: YE 48h biol rep 4

description:
FG2160_23
FG2160_YE24h-vs-YE48h_DESeq2.xlsx
FG2160_YE48h-vs-Ctrl48h_DESeq2.xlsx
FG2160_YEall-vs-Ctrlall_DESeq2.xlsx


title: Q81Q27, INPUT_1


title: ctrl 48h biol rep 1

description:
FG2160_24
FG2160_YE48h-vs-Ctrl48h_DESeq2.xlsx
FG2160_YEall-vs-Ctrlall_DESeq2.xlsx


title: Q45Q19, IP_3


title: NT2-7_TCR

city: Munich

first: Klaus

last: Dornmair

address: Grosshaderner Strasse 9

department: Institute of Clinical Neuroimmunology

institute: University Hospital LMU Munich

description: 10x Genomics

data_processing:
Raw data obtained from sequencing was pre-processed and aligned to the human reference genome GRCh38-2020-A using Cell Ranger (10 Genomics, v6.0.2).
Pre-processed data were then further processed and analysed in JupyterLab (v3.2.1) using an R kernel (R v4.1.3and the R package Seurat (v4.1.1). In summary, data from GEX and CSP (=ADT) libraries were combined for each sample and quality-filtered to remove low-quality cells, doublets, and dead cells. Cells were kept if the contained >500 and <20,000 RNA molecules, >200 and <2,500 genes, and ≤7.5% mitochondrial RNA. Read counts from GEX and CSP assays were normalized by sample using the NormalizeData-function with normalization-method set to “LogNormalize” and “CLR”, respectively. .
CD8+ and CD4+ T-cell subsets were identified based on normalized CSP (=ADT) barcode read count data. Cells that were at ≥1.5-fold enriched in CD8A compared to CD4 were assigned the cell type CD8+ T cells. Conversely, cells that were at least 1.5-fold depleted in CD8A compared to CD4 were assigned the cell type CD4+ T cells. The remaining cells were assigned to CD8+ T cells if their normalized CD8A RNA count in the RNA assay was ≥0.8 and CD4 expression was <0.2, and to CD4+ T cells if the opposite was the case. Cells that could not be assigned to CD4+ T cells or CD8+ T cells and cells that expressed no TCR chain were categorized as ambiguous
Assembly: GRCh38-2020-A
Supplementary files format and content: Cellranger output files: mRNA+ADT_matrix.mtx.gz,  mRNA+ADT_barcodes.tsv.gz,  mRNA+ADT_features.tsv.gz
Supplementary files format and content: Cellranger output files: TCR_filtered_contig_annotations.csv, TCR_clonotypes.csv

source_name: cerebrospinal fluid cells

extract_protocol:
Single cells from CSF were labelled with barcoded antibodies targeting CD4 or CD8A (cell surface protein (CSP) staining with antibody-derived tags (ADT)) using the TotalSeq-C with 10x Feature Barcoding Technology (Biolegend) as described in 10x Genomics protocol CG000149 (Rev B).
Single-cell gene expression (GEX), T-cell receptor (TCR), and cell surface protein (CSP = antibody-derived tags (ADT)) libraries were prepared using the 10x Genomics platform according to protocol CG000208 (Rev F). All antibody-labelled CSF cells from each sample were used as input. Nuclease-free water was added to the barcode antibody-labelled cells to a final volume of 37.8 µL and the protocol was carried out with minor alterations: TE buffer (Affymetrix #J75793) was used instead of elution buffer EB. ThermoScientific 2x Phusion MasterMix with HF (#F-531) was used instead of the Amplification Master Mix at step 4.1 and 4.3.
OTHER: scRNAseq, CITE-seq, TCRseq

value: cerebrospinal fluid cells

value: primary cells

value: untreated

tag: library type

value: TCR


title: C57BL/6J mice, colon, obesity-prone, Sample 1

value: colon


title: set C 3rd leaf

description:
FG2160_22
FG2160_setA_vs_setC_DESeq2.xlsx

source_name: leaf

value: leaf


title: Q45Q19, IP_1


title: Q45Q19, IP_2


title: set C 2nd leaf

description:
FG2160_21
FG2160_setA_vs_setC_DESeq2.xlsx

value: WT


title: NT1-12_TCR

description: 10x Genomics


title: Q45Q19, INPUT_3


title: Q45Q19, INPUT_1


title: NT1-11_TCR

description: 10x Genomics


title: C57BL/6J mice, colon, obesity-resistant, Sample 1

value: obesity-resistant

value: A high-fat diet


title: set C 1st leaf

description:
FG2160_20
FG2160_setA_vs_setC_DESeq2.xlsx


title: Q45Q19, INPUT_2


title: Q30Q19, IP_2

value: human wild-type huntingtin cells


title: Q30Q19, IP_3


title: set A 3rd leaf

description:
FG2160_19
FG2160_setA_vs_setC_DESeq2.xlsx


title: NT1-10_TCR

description: 10x Genomics


title: set A 2nd leaf

description:
FG2160_18
FG2160_setA_vs_setC_DESeq2.xlsx


title: Q30Q19, INPUT_3


title: Q30Q19, IP_1


title: Q30Q19, INPUT_2


title: set A 1st leaf

description:
FG2160_17
FG2160_setA_vs_setC_DESeq2.xlsx


title: NT1-9_TCR

description: 10x Genomics


title: NT1-8_TCR

description: 10x Genomics


title: Q43Q19, IP_2

value: human mutated huntingtin cells


title: ctrl 24h biol rep 2

description:
FG2160_14
FG2160_YE24h-vs-Ctrl24h_DESeq2.xlsx
FG2160_YEall-vs-Ctrlall_DESeq2.xlsx

value: plantlet

value: control methyl jasmonate 24h


title: Q43Q19, IP_1

value: RIP IP

value: IP


title: Q43Q19, INPUT_2

value: RIP input


title: ctrl 24h biol rep 1

description:
FG2160_13
FG2160_YE24h-vs-Ctrl24h_DESeq2.xlsx
FG2160_YEall-vs-Ctrlall_DESeq2.xlsx


title: NT1-6_TCR

description: 10x Genomics


title: Q43Q19, INPUT_1

value: input control


title: NT1-5_TCR

description: 10x Genomics

value: cerebrospinal fluid cells


title: YE 48h biol rep 1

description:
FG2160_09
FG2160_YE24h-vs-YE48h_DESeq2.xlsx
FG2160_YE48h-vs-Ctrl48h_DESeq2.xlsx
FG2160_YEall-vs-Ctrlall_DESeq2.xlsx

value: 0.1 mg/ml yeast extract 48h


title: Q40Q18, IP_2


title: NT1-4_TCR

description: 10x Genomics

value: primary cells

value: untreated


title: Q40Q18, INPUT_2


title: YE 24h biol rep 2

description:
FG2160_08
FG2160_YE24h-vs-Ctrl24h_DESeq2.xlsx
FG2160_YE24h-vs-YE48h_DESeq2.xlsx
FG2160_YEall-vs-Ctrlall_DESeq2.xlsx

value: 0.1 mg/ml yeast extract 24h


title: YE 24h biol rep 1

description:
FG2160_07
FG2160_YE24h-vs-Ctrl24h_DESeq2.xlsx
FG2160_YE24h-vs-YE48h_DESeq2.xlsx
FG2160_YEall-vs-Ctrlall_DESeq2.xlsx


title: Q19Q17, IP_2


title: Q40Q18, INPUT_1


title: NT1-2_TCR

description: 10x Genomics

value: TCR


title: Q19Q17, INPUT_2


title: NT2-7_GEX

description: 10x Genomics

value: mRNA, ADT

tag: adt

value: TotalSeq-C0072 anti-human CD4 Antibody, TotalSeq-C0046 anti-human CD8 Antibody


title: Q19Q17, IP_1

tag: cell type


title: Porcine ileum apical out organoid, PEDV infected 3

city: Seoul

first: Jae Han

last: Park

address: 25, Nambusunhwan-ro 224-gil

institute: Seoul national university

data_processing:
Differentially expressed genes were subjected to gene enrichment analysis with the R package clusterProfiler
GSEA v3.0
Assembly: susScr2
Supplementary files format and content: tab-delimited text file include raw counts for each example

organism: Sus scrofa

source_name: Ileum

growth_protocol: The organoids were separated from Matrigel by incubating them with 5 mM EDTA on a shaking rotor for 30 mins at 4 ℃. For apical-out organoid culture, organoids were cultured in ultra-low attachment 24-well cell culture plate (Corning) for 3 days.

extract_protocol:
Total RNA was extracted and purified from organoids using the TRIzol reagent. 1.2ug of total RNA was used to construct sequencing library
Libraries were generated using the Illumina TruSeq strand mRNA sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

treatment_protocol: For apical-out organoids, 200 organoids were infected with PEDV DR13 for 1 h at 37 ℃. After 1 h, the medium containing virus was removed and differentiation medium was added.

value: Ileum

value: PEDV


title: Q30Q19, INPUT_1

value: human wild-type huntingtin cells


title: Q19Q17, INPUT_1


title: NT1-12_GEX

description: 10x Genomics


title: NT1-11_GEX

description: 10x Genomics


title: Porcine ileum apical out organoid, PEDV infected 2


title: PANC-1 cells, shControl for shSTN1, biol rep 2

city: Beijing

first: Chengqi

last: Yi

address: Yiheyuan Road

department: School of Life Sciences

institute: Peking University

data_processing:
Adaptor and low-quality reads were trimmed using cutadapt
FastQC was used for quality control of the sequencing data.
Reads were aligned to the human (GRCh38) reference genome using STAR (v2.7.2b)
Mapped reads were assigned to genes using featureCounts (v2.0.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for all samples

growth_protocol: PANC-1 were maintained in DMEM(CORNING), supplemented with 10% FBS(PAN) in a 37℃ incubator with 5 % (v/v) CO2.

extract_protocol:
Total RNA was isolated from cultured cells using Trizol (Invitrogen, 10296010).
After quality check, samples were sent to library preparation using the NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530L, NEB, USA).

value: human pancreatic cancer cell lines

value: WT


title: Q40Q18, IP_1

value: human mutated huntingtin cells

value: RIP IP


title: NT1-9_GEX

description: 10x Genomics


title: KO-HU-rep2

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
RNA-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the human genome (hg19) using Tophat v2.1.1 with default parameters. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) using Cufflinks v2.2.1. The RNA abundance of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments). Genes with FPKM < 1 in all samples were excluded, and for the remaining genes, all FPKM values smaller than 1 were set to 1 in subsequent analyses.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include FPKM values of all RNA-seq samples

source_name: DLD1 cell

growth_protocol: DLD1 cells were obtained from ATCC, CRISPR/Cas9 genomic editing for IRF3 deletion,  WT and IRF3 KO DLD1 cells  were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) at 37°C in 5% CO2 (v/v).

extract_protocol:
Cells were washed with ice-cold PBS, and then used for cDNA synthesis using the Smart-seq2 method (Picellietal., 2014). Briefly, the polyadenylated mRNAs were captured usingby the PolyT primers. After 3 min lysis at 72°C, the Smart-seq2 reverse transcription reactions were performed. After the first-strand reaction, the cDNA was amplified using a limited number of cycles (12∼14 cycles).
Sequencing libraries were constructed from 1 ng of amplified cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to the manufacturer's instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform in the 150 bp paired-end mode.

treatment_protocol: A total of 5*106 cells were treated with ddH2O or HU 1 mM for 24 hours and normal cultured for 5 days before collection.

value: DLD1 cell

value: Treated with HU to induce senescence


title: PANC-1 cells, shSTN1, biol rep 2

value: STN2 knockdown


title: PANC-1 cells, shSTN1, biol rep 3

value: STN3 knockdown


title: Porcine ileum apical out organoid, PEDV infected 1


title: Porcine ileum apical out organoid, MOCK infected 3

value: MOCK


title: PANC-1 cells, shControl for shSTN1, biol rep 1


title: PANC-1 cells, shSTN1, biol rep 1

value: STN1 knockdown


title: NT1-10_GEX

description: 10x Genomics

value: cerebrospinal fluid cells

value: primary cells

value: untreated


title: Porcine ileum apical out organoid, MOCK infected 1


title: NT1-6_GEX

description: 10x Genomics

value: mRNA, ADT

value: TotalSeq-C0072 anti-human CD4 Antibody, TotalSeq-C0046 anti-human CD8 Antibody


title: KO-woHU-rep1

value: Treated with ddH2O as control


title: KO-woHU-rep2


title: Porcine ileum apical out organoid, MOCK infected 2

value: Ileum


title: KO-HU-rep1


title: NT1-5_GEX

description: 10x Genomics


title: WT-woHU-rep2


title: PANC-1 cells, shControl for shSTN1, biol rep 3

value: human pancreatic cancer cell lines


title: WT-woHU-rep1


title: Porcine jejunum apical out organoid, PEDV infected 3

value: Jejunum

value: PEDV


title: NT1-8_GEX

description: 10x Genomics


title: Porcine jejunum apical out organoid, PEDV infected 1


title: NT1-2_GEX

description: 10x Genomics


title: NT1-4_GEX

description: 10x Genomics


title: WT-HU-rep1


title: Patient3 normal breast tissue

first: Shanliang

last: Zhong

address: Baiziting 42

institute: The Affiliated Cancer Hospital of Nanjing Medical University

data_processing:
Genome_build: hg38
Normalized read counts using DESeq2 in the statistical program R after removing the genes with a zero read count in 3 or more samples.
Matrix table with raw gene counts for every gene and every sample

source_name: breast

extract_protocol:
Total RNA was extracted and digested using RNase R.
Strand-specific RNA-seq libraries were prepared using the VAHTS Total RNAseq (H/M/R) Library Prep Kit for Illumina (Vazyme, Nanjing, China). Briefly, the digested RNA samples was fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. In the second-strand synthesis reaction, dTTP was replaced with dUTP. After cDNA synthesis, the double-stranded products were end repaired, a single ‘A’ base was added, and adaptors were ligated onto the cDNA products. Fragments of cDNA were captured using magnetic particles and treated with uracil DNA glycosylase to remove the second-strand cDNA. Purified first-strand cDNA was subjected to PCR amplification, followed by analysis of the libraries with a Bioanalyzer 4200 (Agilent, CA, USA); the cDNA was then sequenced on an Illumina HiSeq X Ten (X10) system (Illumina, CA, USA).

value: adjacent normal tissue

tag: Stage

value: III


title: Patient2 normal breast tissue


title: Patient1 normal breast tissue


title: Porcine jejunum apical out organoid, MOCK infected 2


title: Patient2 breast cancer tissue

value: breast tumors


title: Patient1 breast cancer tissue


title: Lung, Sort_Fib_3

city: Dearborn

first: Caymen

last: Novak

address: HPEC 1296, 4901 Evergreen Rd

department: Mechanical Engineering

institute: University of Michigan Dearborn

data_processing:
Reads were filtered using sequencying platform BGISEQ
HISAT was used to align the clean reads to the reference genome
Bowtie2 was used to align the clean reads to the reference genes
Reference species was Mus_musculus from NCBI, Reference genome version GCF_000001635.26_GRCm38.p6
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: excel file including raw counts for each sample

source_name: Lung

growth_protocol: Collagenase digestion of lung tissue followed by 2D or 3D culture in collagen hydrogels for 4 days followed by 2 days of culture in the same or opposite conditions.

extract_protocol:
TRIzol and Direct-zol RNA miniprep Plus Kit
HISAT was used to align clean reads to the reference genome

treatment_protocol: No chemical treatment was used

value: Lung

tag: disease state

value: Normal

tag: Sex

value: Male

value: Collagenase digestion, Pramagnetic bead sorted


title: Lung, Sort_Fib_4

tag: strain


title: PLL

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: PLL-NC

growth_protocol: Normal posterior longitudinal ligament were dissected during the surgery, all tissues were obtained with written informed consent signed by the donors voluntarily for research. Ligaments were further cut into pieces and cultured in DMEM supplemented with 20% fetal bovine serum, and cells of passage 3 were used for the experiments.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentivirus bearing hTERT or SV40 were transfected into the OPLL or PLL ligament cells. 5 days after the transfection, G418 or Puromycin was used for stably expressed cell selection.

value: Wild type primary cell

value: male

tag: origin

value: Posterior longitudinal ligament


title: WT-HU-rep2

value: DLD1 cell

value: Treated with HU to induce senescence


title: Porcine jejunum apical out organoid, PEDV infected 2

source_name: Jejunum


title: Lung, Sort_Fib_2


title: SV40-PLL-rep2

value: SV40 bearing lentivirus transfected


title: SV40-PLL-rep1


title: Porcine duodenum apical out organoid, PEDV infected 3

source_name: Duodenum

value: Duodenum


title: SV40-OPLL-rep2

value: Ossified Posterior longitudinal ligament


title: SV40-OPLL-rep1


title: OPLL

source_name: OPLL-NC


title: hTERT-OPLL

source_name: OPLL-A-hTERT

value: hTERT bearing lentivirus transfected


title: 6-6NaCl-rep1

first: Yuying

last: Ren

address: chenhua road,No 3888

institute: CAS center for excellence in Molecular plant Sciences

data_processing:
Paired-end reads were cleaned by Trimimomatic
Clean reads were mapped to the genome of Arabidopsis thaliana (TAIR 10) using HISAT2
The mapped reads on each gene were counted by htseq-count
The differentially expressed genes (DEGs) were identified using the R package edgeR (FDR (false discovery rate) < 0.05, log2FoldChange > 1.5)
Assembly: TAIR 10
Supplementary files format and content: Tab separated values file include RPKM values for each sample and logFC (log2 fold change) and FDR (false discovery rate) of differentially expressed genes analysis in indicated sample.

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Plants were grown in a growth chamber at 22 °C and under long day (16 h light/8 h dark) conditions for 8 days

extract_protocol:
Total RNAs were extracted from eight-day-old seedlings grown under the long-day condition using RNeasy Plant Mini Kit (Qiagen, Cat#74904) according to the manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 8-day-old seedings were transferred to 1/2 MS medium with or without NaCl for 24h, and then Cut off the root tip approximately 1 cm tissue

value: root


title: Porcine duodenum apical out organoid, PEDV infected 1

value: PEDV


title: Lung, 3D-3D_3

value: 3D culture 4 days, 3D culture 2 Days


title: 6-6NaCl-rep3


title: Porcine duodenum apical out organoid, MOCK infected 3

value: MOCK


title: 6-6NaCl-rep2


title: Lung, Sort_Fib_1

value: Lung


title: Lung, 3D-3D_2

value: Normal


title: Porcine duodenum apical out organoid, PEDV infected 2


title: Lung, 3D-3D_4

value: Male


title: hTERT-PLL

source_name: PLL-A-hTERT


title: Porcine jejunum apical out organoid, MOCK infected 1

value: Jejunum


title: Porcine duodenum apical out organoid, MOCK infected 2


title: 6-6MS-rep2


title: Lung, 3D-3D_1


title: Porcine duodenum apical out organoid, MOCK infected 1


title: 6-6MS-rep3


title: Patient3 breast cancer tissue

value: breast tumors

value: III


title: Lung, 3D-2D_4

value: 3D culture 4 days, 2D culture 2 Days


title: Porcine jejunum apical out organoid, MOCK infected 3