title: 221802-2

city: nice

first: Ilaria

last: Di Mauro

address: 28 avenue de valombrose

institute: CHU de Nice

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console Software (version 3.2.2). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using CHAs (version 4.0). Genomic Smoothing analysis was performed by CHAs
The CNV value is the logarithm base 2 of the sample signal divided by a reference value from the OncoScan_CNV.FFPE.na33.r2.REF_MODEL library. The allelic status is determined accordind the B-Allelic Frequency (BAF = B/(A+B) ; AA : BAF = 0, BB : BAF = 1, AB : BAF = 0,5) or the Allele Difference (Diff = A - B where each A and B allele are 0,5 units. AA : Diff = 1, AB : Diff = 0, BB : Diff = -1)

label: Biotin

source_name: chRCC

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from formol fixed-paraffin embedded fragments using Maxwell FFPE DNA LEV Kit (PROMEGA).

tag: disease state

value: chRCC


title: RNA-Seq_exp1 SGBS_day11_rep2

status: Public on Feb 01 2024

type: SRA

city: Heidelberg

first: Clarissa

last: Feuerstein-Akgoz

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

library_source: transcriptomic

data_processing:
Data were processed with the nf-core rnaseq pipeline. Default parameters were used unless mentioned otherwise.
Sequences were aligned to the human reference genome (hg19/GRCh37) by application of the software HISAT2, with --unstranded option.
Transcripts were assembled using StringTie and gene codes gene annotation v.29 lift 37.
Gene counts were generated with the Stringties prepDE.py script (setting: -eb).
Normalized counts per million (CPM) were used for statistical analyses performed by edgeR.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Raw count data in a comma-separated .csv file

molecule: total RNA

organism: Homo sapiens

source_name: SGBS cells at day 11 of adipocyte differentiation

growth_protocol: Human Simpson-Golabi-Behmel syndrome (SGBS) pre-adipocytes were grown to confluency in Dulbecco’s Modified Eagle’s Medium (DMEM)/F-12Nutrient Mixture (Ham) supplemented with 10 % fetal bovine serum  (FBS), 33 µM biotin, 17 µM pantothenate, 100 U/ml penicillin, 100 µg/ml streptomycin, 1ng/µl fibroblast growth factor (FGF) 1, and 90 µg/ml heparin. Three days post-confluency (day 0), SGBS cells were washed three times with PBS and stimulated to differentiate with serum-free growth medium, supplemented with 10 nM insulin, 200 pM triiodothyronine, 1 µM cortisol, 2 µM rosiglitazone/BRL49653, 500 µM 1-methyl-3-isobuthylxanthine (IBMX), 250 nM dexamethasone (Dex), and 0.01 mg/ml human transferrin. After 6 days, FGF-1, Heparin, IBMX, Dex, rosiglitazone were removed from the medium. Cells were harvested at day 0, 1, 7 and 11.

extract_protocol:
RNA was extracted using TRIzol reagent (Sigma Aldrich) and the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions, including an DNAse I digest (RNase-free DNAse set, Qiagen) and Proteinase K digest  (Puregene Proteinase K, Qiagen). RNA quality was checked by Agilent Bioanalyzer ( Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA).
Illumina TrueSeq Stranded total RNA Library Prep Kit

tag: cell type

value: SGBS

tag: day

tag: experiment

tag: replicate


title: Ribo_BAN-1

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: SacCer3
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribosome profiling

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: SC medium

extract_protocol:
The cells were filtered using 0.45µm MCE membrane and lysed in lysis buffer using the beads shocker.
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion by riboPOOL for Saccharomyces cerevisiae (siTOOLs), reverse transcription, cDNA circularization, and PCR amplification. For RNA-Seq, SEQuoia Express Stranded RNA Library Prep Kit (Bio-Rad).

tag: isolates

value: BAN

value: yeast cells

tag: genotype

value: Wild type


title: Promastigotes, treated with EPHB (biological rep2)

city: Karachi

first: Ishtiaq

middle: Ahmad

last: Khan

state: SIndh

address: University Road

department: Dr. Panjwani Center for Molecular Medicine and Drug Research

country: Pakistan

institute: University of Karachi

data_processing:
The quality of short reads was assessed with FastQC tool
The short reads were alinged with the reference Leishmania genome uisng the Tophat
The bam files were sorted, and read-count was performed using the featureCounts tool
The raw counts were normalized using the R package, and TPM were calculated for each sample
Group-wise comparison (Control v.s. Treated) was performed to find the differentially expressed genes
Assembly: ASM272v2
Supplementary files format and content: tab delimited text file containing TPM for each sample

organism: Leishmania major

source_name: Promastigotes

growth_protocol: The promastigotes were cultured on M199 medium (supplemented with L-glutamine, 10% heat-inactivated fetal bovine serum, 0.25% hemin, 40 mM NaHCO3, 100μM adenine, 40 mM HEPES, 100 U/mL penicillin and 100μg/mL streptomycin)

extract_protocol:
Total RNA was isolated using the RNeasy kit (QIAGEN, Germany)
The RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit
Paired-end libraries were prepared for performing 2 x 75 sequencing

treatment_protocol: Promastigotes (mid lg phase 1×107parasites/mL)were exposed for 24 hours to EPHB (3.22 µm)

value: Promastigotes

tag: treatment

value: EPHB


title: Ribo_BAN-2


title: Promastigotes, treated with EPHB (biological rep3)


title: 221310

type: genomic

country: France

molecule: genomic DNA


title: RNA-Seq_exp1 SGBS_day11_rep3

value: SGBS cells at day 11 of adipocyte differentiation


title: mESCs, INKDX2

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

library_source: genomic

data_processing:
Adapters were removed using cutadapt with parameters -e 0.2 -a GTTTTAGAGCTAGAAATAGCAAGTTAAAATA -m 18 and processed to contain only the sgRNA sequence
Processed reads were aligned to the sgRNA probe sequences using bowtie (v.0.12.9) with parameters -n 1 -l 19
The number of reads aligning to each probe and sample were computed in R.
Assembly: Genome-wide Mouse Lentiviral CRISPR gRNA Library v1
Supplementary files format and content: Count matrix by probe in excel format
Library strategy: CRISPR sgRNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: mES cells were grown on gelatin with ES medium (EM): Dulbecco's modified Eagle's medium (DMEM, high glucose, Life Technologies) supplemented with 15% foetal bovine serum (FBS) (Gibco), penicillin/streptomycin (100 U/mL), LIF (1000 U/ml), 0.1 mM non-essential amino acids, 1% glutamax, and 55 mM β-mercaptoethanol.

extract_protocol:
genomic DNA was extracting using QIAGEN Blood & Cell Culture DNA Midi Kit according to manufacturer's instructions.
The sequencing library preparation method is a two-step PCR protocol. The first round of PCR amplifies the region of 250-300 bp containing the sgRNA from the genomic DNA with custom primers. The PCR1 forward primer has only the part needed to bind to the flow cell (P5) and vector-specific sequence upstream of the sgRNA insert (about 40nt in length). The primer lacks the Illumina sequencing primer binding site. The PCR1 reverse primer contains the partial adaptor sequence of the NEBNext Multiplex. Oligo for single indexing for Illumina (the 3' region after the index) plus vector-specific sequence downstream of the sgRNA insert (about 25 nt in length). The second round of PCR adds at 3’ unique single indexes to each library. A 5ul aliquot of PCR1 is taken to perform the PCR2. The PCR2 forward primer is the P5 sequence and the PCR2 reverse primer is a NEBNext Multiplex Oligo for single indexing for Illumina. PCR2 amplicons are purified with magnetic beads. Libraries are sequenced as a pool with a custom sequencing primer to increase complexity in the first 20 nucleotides of the libraries. The sequencing primer are the 44 nt of the vector sequence immediatly upstream of the first nucleotide of the sgRNA where the sequence read begins.

treatment_protocol: Diapause was induced by INK128 treatment (100 nM, Sellekchem).

value: mouse embryonic stem cells

value: R26:rtTA | Col1a1:tetO-Cas9

value: INK + DOXY


title: RNA-Seq_exp1 SGBS_day11_rep1


title: Promastigotes, treated with EPHB (biological rep1)


title: mESCs, INKDX3


title: 223891


title: mESCs, INK3

value: INK


title: mESCs, INKDX1


title: RNA_CQC-2

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: SacCer3
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

value: CQC


title: Promastigotes, control (biological rep3)

value: Saline


title: RNA-Seq_exp1 SGBS_day27_rep3

source_name: SGBS cells at day 27 of adipocyte differentiation


title: mESCs, INK2


title: RNA-Seq_exp1 SGBS_day07_rep2

source_name: SGBS cells at day 7 of adipocyte differentiation


title: Ribo_AMH-2

value: AMH


title: Promastigotes, control (biological rep2)


title: RNA_CQC-1


title: RNA-Seq_exp1 SGBS_day07_rep1

value: SGBS cells at day 7 of adipocyte differentiation


title: Ribo_AMH-1


title: Promastigotes, control (biological rep1)


title: mESCs, CTRDX3

value: CTR + DOXY


title: RNA_CPI-2

value: CPI


title: RNA-Seq_exp1 SGBS_day07_rep3

value: SGBS


title: mESCs, CTRDX2


title: RNA_CMP-2

value: CMP


title: mESCs, CTR3

value: CTR


title: RNA-Seq_exp1 SGBS_day01_rep3

source_name: SGBS cells at day 1 of adipocyte differentiation


title: RNA_CMP-1

value: yeast cells

value: Wild type


title: RNA_CPI-1


title: RNA-Seq_exp1 SGBS_day00_rep3

source_name: SGBS cells at day 0 of adipocyte differentiation


title: mESCs, CTRDX1


title: RNA-Seq_exp1 SGBS_day01_rep1

value: SGBS cells at day 1 of adipocyte differentiation


title: mESCs, CTR1


title: RNA-Seq_exp1 SGBS_day00_rep2

value: SGBS cells at day 0 of adipocyte differentiation


title: RNA_BTT-1

value: BTT


title: RNA_BTT-2


title: FOXP4_KO1_2

city: Lianyungang

first: Yasong

last: Wang

state: Jiangsu

address: Jiangsu Ocean University, School of Pharmacy, 108 Tongguan South Road, Haizhou District, Lianyungang City, Jiangsu Province,

country: China

institute: Jiangsu Ocean University

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

growth_protocol: FOXP4_Con/KO HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics at a humidity of 5% CO2 and a concentration of 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: cell line

value: human embryonic kidney cells

value: FOXP4 knock down


title: RNA-Seq_exp1 SGBS_day00_rep1


title: RNA_BPL-2

value: BPL


title: mESCs, INK1

value: mouse embryonic stem cells

value: R26:rtTA | Col1a1:tetO-Cas9

value: INK


title: RNA-Seq_exp1 SGBS_day01_rep2


title: FOXP4_KO1_1


title: SGBS_day11_rep11 (RNA-Seq)

data_processing:
Data were processed with the nf-core rnaseq pipeline. Default parameters were used unless mentioned otherwise.
Sequences were aligned to the human reference genome (hg19/GRCh37) by application of the software HISAT2, with --unstranded option.
Transcripts were assembled using StringTie and gene codes gene annotation v.29 lift 37.
Gene counts were generated with the Stringties prepDE.py script (setting: -eb).
Normalized counts per million (CPM) were used for statistical analyses performed by edgeR.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: gene_count_matrix.csv (Raw gene count data in a comma-separated .csv file)
Supplementary_files_format_and_content: transcript_count_matrix.csv (Raw transcript count data in a comma-separated .csv file)
Supplementary_files_format_and_content: gene_logCPM_differential.txt (Log2CPM (LogCPM), mean (NormAve), standard error (SE_NormAve), log2 fold changes (logFC) and FDR values calculated with respect to SGBS at day 0 in a tab-delimited .txt file)

value: SGBS preadipocyte cell line

tag: time

value: day 11


title: FOXP4_Con_2.

value: Control


title: RNA_BPL-1


title: SGBS_day11_rep10 (RNA-Seq)


title: RNA_BED-2

value: BED


title: SGBS_day11_rep09 (RNA-Seq)


title: P4.DMSO

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

data_processing:
Data was processed using Laxy (https://laxy.io)
Alignment and mapping was performed using STAR v.2.5.2b and to the mouse reference genome GRCm38 or hg19 for human samples
Read counting was performed using FeatureCounts
Differential Gene expression analysis was performed using Degust.
Genome_build: GRCm38 and hg19
Supplementary_files_format_and_content: text file containing matrix of genes and read counts

molecule: polyA RNA

source_name: CD34+ Bone marrow

growth_protocol: Generation of Jak2V617F knockin mice is summarized here Mullally et al 2010. All animal experiments were approved by the AMREP (Alfred Medical Research and Education Precinct) Animal Ethics Committee. Bone marrow was isolated from Jak2VF (CD45.2) or WT (CD45.1) mice aged 6-12 weeks. Bone marrow cells were mixed at an ∼3:1 ratio (Jak2VF:WT) and injected into lethally irradiated C57BL/6-Ly5.1 (CD45.1 positive) recipient mice. Recipient mice received 950 Rads total body irradiation in equal divided doses, at least 3 hours apart within 24 hours of transplantation. All transplanted cells were injected by lateral tail vein. Chimerism was determined 5 weeks after injection. Mice were maintained on antibiotic (Neomycin) water for 3 weeks after transplantation. Human CD34+ cells were isolated from human bone marrow using a MiniMACS magnetic cell sorting system (Miltenyi Biotec) and maintained in StemSpan SFEM II (STEMCELL Technologies Inc.) supplemented with Penicillin/Streptomycin (10,000 µg/ml, Gibco), L-Glutamine (200 mM, Gibco) Human SCF (100 ng/ml, R&D systems), Human IL-3 (5 ng/ml, R&D systems) Epoetin alfa (3U/ml, EPREX) and Dexamethasone (2 µM, Sigma) for up to 14 days.

extract_protocol:
bone marrow cells were recovered by flushing both femurs with 1 mL of ice-cold PBS and Total RNA was extracted using TriZol method according to manufacturer's instructions.
MGIEasy V2 Library preparation was performed as per manufacturer's instructions.

treatment_protocol: Female C57Bl6 mice 6-8 weeks of age, were divided into five groups (n=6 mice per group) and were treated for 11 days with either vehicle or CTX-0391034 at 10, 30 or 100 mg/kg b.i.d. via oral gavage. A fifth group of mice was treated with CTX-0391034 100 mg/kg b.i.d. for 11 days and then drug was withdrawn for seven days. All groups were harvested 12 h after the final dose. Human CD34+ cells were treated with either DMSO or CTX-034 (1 microM) for 72 hours before harvesting for RNA-seq analysis.

tag: tissue

value: CD34+ Bone marrow

value: DMSO

tag: dose


title: RNA_BAN-2

value: BAN

value: yeast cells


title: SGBS_day07_rep11 (RNA-Seq)

value: day 7


title: FOXP4_Con_1


title: SGBS_day07_rep10 (RNA-Seq)


title: RNA_BAN-1

value: Wild type


title: P3.DMSO


title: RNA_BED-1


title: RNA_AMH-2

value: AMH


title: SGBS_day01_rep11 (RNA-Seq)

value: day 1


title: P3.034_CTX-034

value: 1uM concentration of drug


title: B6_mice Colitis tissue

type: RNA

city: Soochow

first: Qiaoming

last: Zhi

address: No.188 Shizi Road

institute: Soochow university

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

scan_protocol: The labeled cRNAs were hybridized onto the microarray.After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.

source_name: Mice of the colitis group 3.0% DSS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the mice colons using the TRIzol® reagent (Life Technologies, USA). Then the quantity and integrity of total RNAs were measured by the NanoDrop™ ND-2000 (Thermo Fisher Scientifc, Scotts Valley, CA, USA) and Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) respectively.

treatment_protocol: The large bowels were removed and cut open longitudinally along the main axis and flushed with saline. The masses, inflamed and normal colonic mucosa were cut and immediately placed in five volumes of RNAlater (Ambion, Austin, TX), then stored in liquid nitrogen for RNA extraction.

tag: strain

value: BALB/c

value: colonic mucosa

tag: Sex

value: male

tag: group

value: colitis


title: B5_mice Colitis tissue


title: B4_mice Colitis tissue


title: B3_mice Colitis tissue


title: D4_mice colitis associated cancer tissue

source_name: mice of the CAC group intraperitoneally injected with 12.5 mg/kg AOM

value: CAC


title: D6_mice colitis associated cancer tissue


title: P2.DMSO


title: KO2, mouse testis cells,repeat2

city: beijing

first: dingfeng

last: zou

state: 北京

address: Beijing, Dong Dan San Tiao 5

institute: Institute of Basic Medical Sciences  Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
The original RNA-seq reads used Trimmomatic (v0.39) to filter low-quality reads and trim the adaptor sequence.
Reads then were aligned to the mm10 reference genome using STAR (2.7.5c).
After comparing with the reference genome, use StringTie (v2.1.7) for gene quantification, and get the standardized gene level FPKM value. Use DEseq2 to analyze the difference of the gene count matrix. Use edgeR to perform difference analysis on the grouping of no duplicate samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample
Library strategy: Ribo-seq

source_name: mouse testis cells

extract_protocol:
About 1000 cells were collected in tubes and lysed in the lysis buffer, then treated with 1 μl RNase I 100 U μl−1and incubated at room temperature for 45 min with gentle mixing. The digested extracts were stopped by the addition of 10 μl SUPERase•In and were overlaid onto a 700 μl sucrose cushion of 1 M sucrose buffer for 4 h at 260,000g, 4 °C in MLA-150 rotor in Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris pH 7.5 and 1% SDS). RPFs were extracted from pellet buffer by using 1 ml TRIzol and 200 μl chloroform. The aqueous phase was precipitated by adding 750 μl isopropanol and 20 μg glycogen. Precipitation was carried out at −20 °C overnight, and RPFs were then pelleted by centrifugation for 40 min at 12,000 g, 4 °C. RPF was resuspended in 6 μl nuclease-free water and mixed with 6 μl Gel Loading Buffer II. RPFs from 26 to 34 nt were recovered and purified by TBE-urea gel.
The library was finally generated by RNA tailing, reverse transcription, PCR amplification, and AMPure XP bead purification using D-Plex Small RNA-seq Kit. Then, the qualified libraries were sequenced on the Illumina HiSeq-PE150 platform with paired-end 150 bp read length.

value: mouse testis cells

value: Ddx20 knockout


title: P4.034_CTX-034


title: D12_mice colitis associated cancer tissue


title: P2.034_CTX-034


title: SGBS_day01_rep09 (RNA-Seq)

value: SGBS preadipocyte cell line


title: D14_mice colitis associated cancer tissue


title: D13_mice colitis associated cancer tissue


title: SGBS_day01_rep10 (RNA-Seq)


title: P1.DMSO

value: CD34+ Bone marrow


title: SGBS_day07_rep09 (RNA-Seq)


title: KO1, mouse testis cells,repeat1


title: SGBS_day00_rep11 (RNA-Seq)

value: day 0


title: B2_mice Colitis tissue


title: Ctrl2, mouse testis cells,repeat2

value: control


title: RNA_AMH-1

value: yeast cells


title: A8_mice intestinal epithelial tissue

source_name: Mice of the NC group drank water


title: SGBS_day00_rep10 (RNA-Seq)


title: P1.034_CTX-0391034

value: 100 mg/kg b.i.d. of drug


title: 12Z,rhChemerin-3,biological replicate 3

status: Public on Jan 31 2024

city: Shenzhen

first: Ming

last: yu

address: 1068 Xueyuan Avenue, Shenzhen University Town

institute: Chinese Academy of Sciences

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2 . FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar.
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was www.oebiotech.com used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking listGene Set Enrichment Analysis (GSEA) was performed using GSEA software 8-9 . The analysis was www.oebiotech.com used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human endometrial

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: human endometrial

value: endometrial epithelial cells

value: rhChemerin


title: 12Z,rhChemerin-2,biological replicate 2


title: A6_mice intestinal epithelial tissue


title: A7_mice intestinal epithelial tissue


title: A5_mice intestinal epithelial tissue


title: 12Z,rhChemerin-1,biological replicate 1


title: A4_mice intestinal epithelial tissue


title: 12Z,NC-1,biological replicate 1

value: Non-treatment


title: 12Z,NC-2,biological replicate 2


title: Healthy control-3

city: Adelaide

first: Nick

last: Warnock

state: South Australia

address: UniSA Bradley Building, North Terrace

department: Centre for Cancer Biology

institute: SA Pathology

data_processing:
Adapters were trimmed using cutadapt version 4.1 and the following parameters: -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT --minimum-length=18 --error-rate 0.2 --overlap=5
Reads were aligned to the hg38 reference genome using STAR version 2.7.7a, producing gene counts for each sample
Assembly: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz using RefSeq annotations
Supplementary files format and content: <library_name>.hg38.ReadsPerGene.out.tab: tab-separated gene counts file for each sample
Supplementary files format and content: gene_counts.tsv: tab-separated file containing strand-specific gene counts for all samples

source_name: PBMCs

extract_protocol:
Total RNA was extracted from the peripheral blood mononuclear cells (PBMCs) of the patient and healthy controls using Blood RNA purification kit (Macherey-Nagel).
RNA libraries were prepared using an Illumina Stranded mRNA Prep kit according to the manufacturer's protocols

value: PBMCs


title: Healthy control-1


title: Healthy control-2


title: ARPE-19 cells,miR-NC,RNAseq, control-3

status: Public on Jan 26 2024

city: Hangzhou

first: hao

last: lei

state: Zhejiang province

address: No. 866, Yuhangtang Road, Xihu District, Hangzhou City, Zhejiang Province

department: biology

institute: zhejiang university

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the Grch38,(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: hg38
Supplementary files format and content: xlsx fromat; context:1. gene id 2. gene symbol 3. transcript id  4. GO enrich results 5. KEGG enrich results 6.  enzyme commission 7. description of gene 8. type of transcripts 9. FPKM value of samples 10. fold change of gene expression differential analysis 11.log2 Fold change 12.p value 13. q value 14. gene regulation 15. significance of differential gene expression analysis

source_name: Eye; Retina; Retinal pigmented epithelium

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: epithelial cell

value: miR-NC transfected


title: ARPE-19 cells,miR-NC,RNAseq, control-2

value: Eye; Retina; Retinal pigmented epithelium


title: ARPE-19 cells,miR-204-5p,RNAseq, over expressed-2

value: miR-204-5p transfected


title: ARPE-19 cells,miR-204-5p,RNAseq, over expressed-3


title: Ctrl1, mouse testis cells,repeat1

value: mouse testis cells


title: ARPE-19 cells,miR-NC,RNAseq, control-1


title: ARPE-19 cells,miR-204-5p,RNAseq, over expressed-1


title: MDA-MB-436_siRNACTRL_plate_biol rep2

status: Public on Jan 22 2024

city: New York

first: Alberto

last: Ciccia

state: NY

address: 1130 St. Nicholas avenue, ICRC Room 407B

country: USA

institute: The Trustees of Columbia University in the City of New York

description:
plateseq-counts.csv
CATTAACG

data_processing:
library strategy: pooled library amplification for transcriptome expression (PLATE-Seq),
Reads were then aligned to the Homo sapiens genome (hg38) using STAR aligner
Reads counting per gene was performed by using HTseq software. For Plate-seq data, count files were merged in a data matrix and processed together for downstream analysis. Next, genes were filtered retaining only those expressed at least in one sample.
Supplementary files format and content: truseq-counts.csv contains counts/gene
Supplementary files format and content: plateseq-counts.csv contains counts/gene

growth_protocol: DMEM supplemented with 10% (v/v) Fetalgro bovine growth serum, 100 U/ml of penicillin, and 100 μg/ml of streptomycin. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated using the RNeasy kit (#74104, Qiagen) according to the manufacturer’s instructions. For Plate-seq, cells were lysed in Buffer TLC (Qiagen) supplemented with 2-mercaptoethanol and processed for high-throughput mRNA sequencing in the PLATE-seq assay
RNA quality was assessed on an Agilent Bioanalyzer instrument using Agilent RNA 6000 Pico Reagents. RNA-seq libraries were prepared with the Illumina TruSeq Stranded Total RNA Sample Preparation kit. For Plate-seq, cells were lysed in Buffer TLC (Qiagen) supplemented with 2-mercaptoethanol and processed for high-throughput mRNA sequencing in the PLATE-seq assay
Final libraries were quantified with the KAPA Library Quantification Kit (Roche), pooled in equal amounts and sequenced (PE150) on an Illumina HiSeq4K sequencer. For Plate-seq, cells were lysed in Buffer TLC (Qiagen) supplemented with 2-mercaptoethanol and processed for high-throughput mRNA sequencing in the PLATE-seq assay

value: Breast, Adenocarcinoma


title: MDA-MB-436_SL1KO clone 3_plate_biol rep1

description:
plateseq-counts.csv
TCAAGGTT

value: SMARCAL1 knockout


title: MDA-MB-436_SL1KO clone 2_plate_biol rep1

description:
plateseq-counts.csv
TCAGTCTA


title: MDA-MB-436_siRNACTRL_plate_biol rep1

description:
plateseq-counts.csv
ACAAAGGA


title: MDA-MB-436_CTRL_plate_biol rep2

description:
plateseq-counts.csv
GATCCCAT

value: Control


title: MDA-MB-436_CTRL_plate_biol rep1

description:
plateseq-counts.csv
AACCCCGT


title: MDA-MB-436_SL1KO_clone 3_plate_biol rep2

description:
plateseq-counts.csv
GAGGGTGT


title: MDA-MB-436_SL1KO clone 1_plate_biol rep1

description:
plateseq-counts.csv
TACGCAAT


title: MDA-MB-436_siRNASMARCAL1_plate_biol rep1

description:
plateseq-counts.csv
GTTCTCTG


title: 12Z,NC-3,biological replicate 3


title: B16F10 KO_biol rep2

data_processing:
Fastq files aligned to the hg38 reference genome using the HISAT2
Uniquely aligned reads were retained, while duplicate reads and those in blacklist regions were filtered out
Peaks were called using MACS2 and annotated by the R package 'ChIPseeker'
bed file including the chromatin accessible peaks identified in MDA-MB-436* replicates
Assembly: hg38 reference genome or mm10

extract_protocol:
ATAC-seq was performed as previously described in Buoenrostro, J.D. et., Nature methods 2013 with the exception that 0.1% NP-40 was used for cell lysis instead of IGEPAL.
ATAC-Seq libraries were quantified with the KAPA Library Quantification kit (Roche)

value: Melanoma

value: Smarcal1 knockout


title: MDA-MB-436_SL1KO_clone 1_plate_biol rep2

description:
plateseq-counts.csv
CAGACATG


title: MDA-MB-436_SL1KO_clone 2_plate_biol rep2

description:
plateseq-counts.csv
ACGCATGG


title: B16F10 KO_biol rep3


title: B16F10 WT_biol rep2

value: Smarcal1 reconstitued


title: B16F10 WT_biol rep3


title: MDA-MB-436_siRNASMARCAL1_plate_biol rep2

description:
plateseq-counts.csv
CGTCTACT


title: B16F10 KO_biol rep1


title: cJun_Parental_biol rep3

description: TMF_5_cJun_P_436_Parental_500K_Native_kMet0uL__05_05_23__S5

data_processing:
Fastq files aligned to the hg38 reference genome using the Bowtie2
Uniquely aligned reads were retained, while duplicate reads and those in blacklist regions were filtered out
Peaks were called using SICER2 and annotated by the function “annotatePeaks.pl” using Homer
The de novo motif discovery analysis was performed by the function “findMotifsGenome.pl” of Homer (4.11)
Assembly: hg38 reference genome
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed using CUTANA ChIC / CUT&RUN Kit. For each CUT&RUN reaction, 500K permeabilized native cells were used.
5 ng DNA was used to prepare sequencing libraries with the CUTANA CUT&RUN Library Prep Kit.

tag: cut&run antibody

value: cJun

value: Parental


title: cJun_Parental_biol rep2

description: TMF_7_cJun_P_436_Parental_500K_Native_kMet0uL____S5


title: H3K27me3_Parental_biol rep2

description: TMF_3_H3K27me3_P_436_Parental_500K_Native_kMet2uL____S3


title: H3K4me3_Parental_biol rep2

description: TMF_2_H3K4me3_P_436_Parental_500K_Native_kMet2uL____S1


title: H3K4me3_Parental_biol rep3

description: TMF_2_H3K4me3_P_436_Parental_500K_Native_kMet2uL__05_05_23__S2


title: H3K4me3_Parental_biol rep1

description: TMF_26_H3K4me3_436_Parental_500K_Native_kMet2uL____S26


title: SMARCAL1_JUNKD_biol rep2

description: TMF_35_SMARCAL1_JD_436_JUN_Depleted_500K_Native_kMet0uL____S25

value: JUN knockdown


title: H3K27me3_Parental_biol rep3

description: TMF_3_H3K27me3_P_436_Parental_500K_Native_kMet2uL__05_05_23__S3


title: SMARCAL1_Parental_biol rep2

description: TMF_5_SMARCAL1_P_436_Parental_500K_Native_kMet0uL____S3


title: SMARCAL1_Parental_biol rep1

description: TMF_30_SMARCAL1_ab154226_436_Parental_500K_Native_kMet0uL____S30


title: SMARCAL1_JUNKD_biol rep3

description: TMF_14_SMARCAL1_JD_436_JUN_Depleted_500K_Native_kMet0uL__05_05_23__S14


title: SMARCAL1_Parental_biol rep3

description: TMF_4_SMARCAL1_P_436_Parental_500K_Native_kMet0uL__05_05_23__S4


title: IgG_JUNKD_biol rep2

description: TMF_31_IgG_JUN_Depleted_436_JUN_Depleted_500K_Native_kMet2uL____S31

value: IgG


title: IgG_Parental_biol rep1

description: TMF_25_N_IgG_Parental_436_Parental_500K_Native_kMet2uL____S25


title: IgG_Parental_biol rep2

description: TMF_1_IgG_Parental_436_Parental_500K_Native_kMet2uL____S1


title: MDA-MB-436_SL1KO clone_2_batch2_biol rep1

description:
KO-Rep1_S3_L004_R1_001
processed data file: MDA-MB-436_SL1KO clone_2_batch2_merged_rep.bed


title: MDA-MB-436_SL1KO clone 1_ biol rep3

description:
truseq-counts.csv
RHC10643

data_processing:
Reads were then aligned to the Homo sapiens genome (hg38) using STAR aligner
Reads counting per gene was performed by using HTseq software. For Plate-seq data, count files were merged in a data matrix and processed together for downstream analysis. Next, genes were filtered retaining only those expressed at least in one sample.
Supplementary files format and content: truseq-counts.csv contains counts/gene
Supplementary files format and content: plateseq-counts.csv contains counts/gene


title: MDA-MB-436_SL1KO clone_1_batch1_biol rep3

description:
p2572GLat1018_7_1
processed data file: MDA-MB-436_SL1KO clone_1_batch1_merged_rep.bed


title: IgG_JUNKD_biol rep3

description: TMF_11_IgG_JD_436_JUN_Depleted_500K_Native_kMet2uL__05_05_23__S11


title: IgG_Parental_biol rep3

description: TMF_1_IgG_P_436_Parental_500K_Native_kMet2uL__05_05_23__S1


title: B16F10 WT_biol rep1


title: MDA-MB-436_SL1KO clone_2_batch2_biol rep2

description:
KO-Rep2_S4_L004_R1_001
processed data file: MDA-MB-436_SL1KO clone_2_batch2_merged_rep.bed


title: MDA-MB-436_SL1KO_clone 1_biol rep1

description:
truseq-counts.csv
RHC10631


title: MDA-MB-436_SL1KO clone_1_batch1_ biol rep2

description:
p2572GLat1018_1_1
processed data file: MDA-MB-436_SL1KO clone_1_batch1_merged_rep.bed


title: MDA-MB-436_SL1KO_clone 1_ biol rep2

description:
truseq-counts.csv
RHC10637


title: MDA-MB-436_SL1KO clone_1_batch1_ biol rep1

description:
p2571GLatac19_4_1
processed data file: MDA-MB-436_SL1KO clone_1_batch1_merged_rep.bed


title: MDA-MB-436_CTRL_biol rep3

description:
truseq-counts.csv
RHC10640


title: H3K27me3_Parental_biol rep1

description: TMF_27_H3K27me3_436_Parental_500K_Native_kMet2uL____S27


title: MDA-MB-436_CTRL_batch1_biol rep3

description:
p2572GLat1018_4_1
processed data file: MDA-MB-436_CTRL_batch1_merged_rep.bed


title: MDA-MB-436_CTRL_batch1_biol rep2

description:
p2571GLatac19_7_1
processed data file: MDA-MB-436_CTRL_batch1_merged_rep.bed


title: MDA-MB-436_CTRL_biol rep1

description:
truseq-counts.csv
RHC10628


title: MDA-MB-436_CTRL_biol rep2

description:
truseq-counts.csv
RHC10634


title: MDA-MB-436_CTRL_batch1_biol rep1

description:
p2571GLatac19_1_1
processed data file: MDA-MB-436_CTRL_batch1_merged_rep.bed


title: T25

status: Public on Jan 15 2024

city: CHARLOTTESVILLE

first: Sara

middle: J

last: Adair

state: VA

address: 345 Crispell Dr.

department: Surgical Oncology

institute: University of Virginia

description: Murine orthotopic xenograft from human PDAC tumor

data_processing:
Raw read processing and gene expression quantification to FPKM values was performed by Novogene.
GC content was computed to detect potential AT/GC separation.
Raw reads were filtered to remove reads containing adaptor sequences, reads containing > 10% undetermined bases, and reads with > 50% of bases having a Qscore (quality value) ≤ 5.
High-quality reads were then aligned to the reference genome into BAM files using STAR v2.5 with the parameter "mismatch = 2.0".
FPKM counts were calculated using HTSeq v0.6.1 with the parameter "-m union".
Assembly: GRCh37/hg19
Supplementary files format and content: Gene-level fragments per kilobase per million mapped fragments (FPKM)

source_name: Pancreas

growth_protocol: Human PDACs were resected and orthotopically (intrapancreatically) implanted and propagated in immunocompromised mice.

extract_protocol:
Upon harvest, tumors were stored in Qiagen AllProtect at −80°C. Samples were processed using Qiagen Tissuelyser LT along with Qiagen AllPrep DNA/RNA extraction kit. Samples were quantified and quality control was performed before libraries were prepared.
Library preparation and sequencing was performed by Novogene with the Illumina PE150 platform at a read depth of 40 million reads (Novogene Corp., Chula Vista, CA).. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, followed by random fragmentation via addition of fragmentation buffer. Library construction was performed using the NEBNext® UltraTM RNA Library Prep Kit. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext® Adaptor with hairpin loop structure is ligated to prepare for hybridization. To preferentially select cDNA fragments of 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). The final library was then obtained by PCR amplification and purification of PCR products by AMPure XP beads.

value: Pancreas

value: Tumor

tag: pdx tumor_stage

value: PRIMARY

tag: pdx tumor_differentiation

value: Moderate

tag: f0 tumor_differentiation

tag: f0 tumor_stage


title: T26

tag: disease state

value: Poor


title: T24b


title: T17

value: MET


title: T19


title: T10


title: T14


title: T22


title: T11


title: T23


title: T12


title: T20


title: T7


title: T5b


title: T15b


title: T6


title: T9


title: T4


title: T16


title: T27


title: T2


title: T3


title: T1


title: Chronic EAE infiltrating, biol rep 3

status: Public on Jan 10 2024

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The barcoded processing and gene counting were made using the Cell Ranger software v7.1.0 [Zheng2017] and post-alignment processing and visualisation was performed using Seurat v4.3.0.1 [Stuart2019]. Data was normalised using Sctransform [Hafemeister2019].
The clustering was performed using SLM; ClustAssess was used for identifying stable clusters; the identification of markers was performed per cluster vs its complement.
The visualisation and community accessible overview were complied using ShinyCell [Ouyang2021]
Assembly: GRCm38 (Ensembl 93 from pre-built Cell Ranger reference 3.1.0)
Supplementary files format and content: count matrix containing raw gene expression (csv)

source_name: Spinal cord

extract_protocol:
Mice were perfused with aCSF, spinal cords were extracted and underwent mechanical dissociation in homogenization buffer. After myelin removal, live cells were isolated via FACS based on the RFP or YFP protein expression.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, the cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Spinal cord

value: Chronic EAE

tag: cell type

value: CNS infiltrating myeloid cells


title: BM_CR_123

status: Public on Jan 11 2024

first: Anna

last: Mathioudaki

state: None / N/A

address: Meyerhofstraße 1, 1

institute: EMBL Heidelberg

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Sample demultiplexing based on genotypes was performed using souporcell (https://www.nature.com/articles/s41592-020-0820-1)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow aspirates

extract_protocol:
Ficoll-processed primary BM samples were sorted into CD34+ and CD3+ fractions.
Library was performed according to the manufacter’s protocol CG000204 (single cell 3’ v2 protocol, 10x Genomics).

value: T cells & HSPCs

value: Bone marrow aspirates

tag: patient diagnosis

value: acute myeloid leukemia

value: complete remission (CR)


title: T21


title: Chronic EAE resident, biol rep 3

description: 10x Genomics

value: CNS resident myeloid cells

tag: genotype


title: T13


title: Chronic EAE infiltrating, biol rep 2

description: 10x Genomics


title: T8


title: Chronic EAE infiltrating, biol rep 1

description: 10x Genomics


title: Control resident, biol rep 3

description: 10x Genomics

value: Control


title: Peak EAE resident, biol rep 1

description: 10x Genomics

value: Peak EAE


title: Chronic EAE resident, biol rep 1

description: 10x Genomics


title: Peak EAE resident, biol rep 2

description: 10x Genomics


title: Chronic EAE resident, biol rep 2

description: 10x Genomics


title: Control resident, biol rep 1

description: 10x Genomics


title: Peak EAE infiltrating, biol rep 1

description: 10x Genomics


title: T18


title: Peak EAE infiltrating, biol rep 2

description: 10x Genomics


title: B097

status: Public on Jan 09 2024

city: Prague

first: Aneta

last: Prokopcova

address: Na Slupi 450/4

country: Czech Republic

institute: Institute of Rheumatology

data_processing:
Adaptor sequences were identified and removed from MPS data with the Cutadapt (v2.5) software. Only high-quality reads (Phred ≥ ten over at least 85% of the read length) with a length between 16 and 28 bp after adapter trimming were retained as potential miRNA reads. To assess the quality of raw and processed reads,  the FastQC software was employed. To prevent an increase in variance during the normalisation process, we randomly sampled 3,000,000 raw reads from each library using the seqtk toolkit before proceeding with miRNA alignment.
The Chimira tool, applied to FASTQ files, generated count-based miRNA expression data. Prior to mapping against miRBase, all sequences underwent adapter trimming, allowing up to two mismatches per sequence. The miRNAs accounted for 1.7 million reads per sample with a balanced distribution (SD = 0.061). Only samples with a total number of aligned miRNA reads exceeding 1,000,000 were included in the evaluation of differential expression, which was performed by the DESeq method. Subsequent analyses were conducted utilising R/Bioconductor packages.
DESeq provides an adaptive shrinkage estimator for log2 fold change, which is particularly useful for miRNAs with low read count and dispersion. Additionally, the DESeq algorithm calculated the base mean, which is essentially the average of the normalised count values divided by size factors and computed across all samples. To enhance the specificity of the analysis and reduce the potential for false positives, miRNAs with a base mean > 10 were retained for further investigation. This filtering step helps exclude miRNAs that may be too low in abundance or exhibit high variability, making them difficult to distinguish from random noise. In order to identify differentially expressed miRNAs while minimising false-positives, the following criteria were applied based on the results computed by DESeq: a) an adjusted p-value < 0.05; b) the base mean > 10; and c) the difference in shrunk log2 fold change (log2FC) > 0.5.
Supplementary files format and content: seq_raw.txt contains raw reads
Supplementary files format and content: seq_norm.txt contains normalized reads
Assembly: NA

extract_protocol:
ceramic beads, QIAzol Lysis Reagent
NEXTflex Small RNA-Seq Kit v3

value: PBMCs

tag: gender

value: male

tag: age

tag: crp

tag: diagnosis

value: r-axspa


title: B095

value: female

value: nr-axspa


title: B094

value: hc


title: B096


title: B091


title: B090


title: B089


title: B087


title: B092


title: B088


title: B085


title: B082


title: B084


title: B083


title: B086


title: B093


title: B079


title: Control resident, biol rep 2

description: 10x Genomics

tag: tissue


title: B076


title: B074


title: B077


title: B075


title: B072


title: B070


title: B068


title: B067


title: B069


title: B060


title: B063


title: B064


title: B062


title: B058


title: B080


title: B057


title: B056


title: B059


title: B054


title: B061


title: B053


title: B055


title: B052


title: B078


title: B051


title: B073


title: B049


title: B071


title: B066


title: B047


title: B065


title: B046


title: B048


title: B045


title: B044


title: B043


title: B040


title: B042


title: B037


title: B036


title: B038


title: B039


title: B041


title: B030


title: B034


title: B032


title: B029


title: B028


title: B027


title: B031


title: B026


title: B025


title: B024


title: B023


title: B022


title: B020


title: B019


title: B018


title: B050


title: B015


title: B016


title: B033


title: B014


title: B013


title: B017


title: B010


title: B012


title: B011


title: B007


title: B006


title: B005


title: B003


title: B035


title: B001


title: B008


title: ChIP-seq Input merged

status: Public on Jan 01 2024

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
ChIP-sequenced libraries were mapped separately to mouse mm10 genome and human hg19 (spike-in) using Bowtie 2 v2.3.4.1 with default parameters. ChIP-Rx spike-in normalization was performed by calculating spike-in normalization factor, by dividing the number of mapped reads from the spike-in of the smallest sample by the number of mapped reads from the spike-in of each sample. For each sample, this factor was multiplied by the number of reads that mapped to the mouse genome. All bam files for subsequent analysis were adjusted to this read count using. Samtools was used to manipulate the bam files (indexing and subsampling). To visualize read alignments on the Integrated Genome Browser v9.1.10, BAM files were converted to bigwig files using Deeptools with no further normalization and a bin size of 10 bases.
CUT&RUN libraries were mapped to the mouse mm10 genome using default parameters using Bowtie 2 v2.3.4.1. Samples were read-normalized with the number of reads in the smallest sample. BAM files were converted to bigwig files using Deeptools with no further normalization and a bin size of 10 bases.
Assembly: mm10

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
ChIP-seqCells were treated with 1% formaldehyde for 5 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using sonification. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used. CUT&RUN: cells were harvested using Accutase (Sigma) for cell detachement. Cells were counted and washed in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine). After washing, cells were coupled to ConA-coated magnetic beads (Polysciences Europe) and subsequently permeabilized and followed by addition of primary antibody in antibody binding buffer (wash buffer, 0.05% digitonin, 2 mM EDTA) over night at 4 °C. Cells were wased in Dig-Wash buffer (Wash buffer, 0.05% digitonin) and MNase (700ng/ml) was added to each sample for 1 hr at 4 °C. After washing with Dig-wash buffer and Low-salt Rinse buffer (20 mM HEPES pH 7.5, 0.5 mM Spermidinge, 0.05% digitonin) incubation buffer (3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.05% digitoin) was added for 30 min at 4°C. STOP buffer (170 mM NaCL, 20 mM EGTA, 0.05% digitonin, 20 ug/ml RMAse A, 25 ug/ml Glycogen was added to stop the MNase digestion. DNA fragments were released at 37 °C for 30 min and proteins digested for 1 h at 50 °C after adding 0.01 % SDS and 10 mg/ml Proteinase K followed by Phenol Chloroform extraction. Precipitated DNA was resuspended in 30 ul 0.1x TE buffer
ChIP-seq Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (150 bp) and eluted. DNA fragments were amplified by 11 to 16 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay. CUT&RUN: NEBnext Ultra II DNA Library Prep Kit (New England Biolabs) was used. Pre-PCR samples were purified using AmpureXP beads with a ratio of 1.75x. Then half of the eluted material was used with 12-16 PCR cycles. The libraries were cleaned using Agentcourt AMPure XP Beads (ratio 1.1x, Beckman Coulter), quality, quantity and fragment size assessed on the Fragment Analyzer (Agilent) using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent)

treatment_protocol: Treatment as indicated

value: Pancreas

tag: cell line

value: PDAC cell line

value: Dox-inducible shRNA targeting Ctr9

tag: antibody

tag: treatment

value: merged


title: B004


title: B002


title: 22Rv1, Input, replicate 2

status: Public on Dec 22 2023

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

library_source: other

data_processing:
3'-adapters were trimmed from reads using cutadapt (v2.7) [http://journal.embnet.org/index.php/embnetjournal/article/view/200], and reads shorter than 18 bp in length were removed. Reads were then mapped to a database of human repetitive elements and rRNA sequences compiled from Dfam and Genbank.
All non-repeat mapped reads were mapped to the human genome (hg38) using STAR (v2.6.0c). PCR duplicates were removed using umi_tools (v0.5.1) by utilizing UMI sequences from the read names and mapping positions. Peaks were identified within eCLIP samples using the peak caller CLIPper (https://github.com/YeoLab/clipper)
For each peak, IP versus input fold enrichment values were calculated as a ratio of counts of reads overlapping the peak region in the IP and the input samples
A p-value was calculated for each peak by the Yates’ Chi-Square test, or Fisher Exact Test
Peaks were annotated using transcript information from GENCODE. Enrichment of motifs in the e-CLIP peaks were determined with the HOMER suite
Assembly: GRCh38
Supplementary files format and content: bw

molecule: other

growth_protocol: Human prostate cancer cell line 22Rv1were grown in RPMI supplemented with 10% FBS and 1x Steptomycin-penicillin

extract_protocol:
Approximately 5 x107 22Rv1 cells per sample were grown and UV crosslinked at 400 mJoules/cm2 with 254 nm radiation, flash frozen, and stored until use at -80°C. Cells were lysed using 1mL of eCLIP lysis mix and subjected to one round of sonication for 5 minutes with 30 second ON/OFF (total 10 minutes) at 75% amplitude. Rabbit Anti-eIF3B/EF3S9 antibody was then pre-coupled to Anti-Rabbit IgG Dynabeads, added to lysate, and incubated overnight at 4°C. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder magnetically separated and washed with eCLIP high stringency wash buffers. IP and input samples were cut from the membrane at the relative band size to 75kDa above. RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed as previously described.
eCLIP studies were performed according to the single-end seCLIP protocol (PMID: 28766298). The eCLIP cDNA adapter contains a sequence of 10 random nucleotides at the 5¢ end. This random sequence serves as a unique molecular identifier (UMI) after sequencing primers are ligated to the 3¢ end of cDNA molecules. Therefore, eCLIP reads begin with the UMI and, in the first step of analysis, UMIs were pruned from read sequences using umi_tools (v0.5.1. UMI sequences were saved by incorporating them into the read names in the FASTQ files to be utilized in subsequent analysis steps
Single-end seCLIP protocol (PMID: 28766298)

value: human prostate carcinoma epithelial cell line

value: Input


title: peripheral B cells of a patient with newly-onset SLE

status: Public on Dec 31 2023

city: Shanghai

first: dai

last: dai

state: Shanghai

address: 上海市黄浦区山东中路仁济医院西院区

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The raw FASTQ data were processed with Cell Ranger (v3.1.1) by using GRCh37 annotation (v1.2.0). Output from Cell Ranger was loaded into R and used Seurat (v3.1.1) package for further analysis. A total of 5721 cells with <500 or >5000 expressed genes or a high percentage of mitochondrial genes (>10%) were removed. Next, the UMI counts in each cell were normalized and scaled. The top 1500 highly variable genes were used for dimensionality reduction using Principal Components Analysis. We selected the first 15 PC for clustering according to the result from the elbow method and used UMAP visualization with default parameters. For clustering, we first selected resolution parameter 0.8 which produced nine clusters. To obtain cluster-specific gene signatures, we identified differential expression analysis of each cluster against the others using wilcox with parameter (logfc. threshold 0.25, min.pct 0.1).
Assembly: hg19
Supplementary files format and content: tsv files contains barcode sequences correspond to column indices.
Supplementary files format and content: tsv files contains gene ID and name.
Supplementary files format and content: Market Exchange Format (MEX) file contains feature and barcode sequences corresponding to row and column indices respectively.

source_name: PBMC

extract_protocol:
FACS sorted CD19+ B cells from PBMCs of a patient with new-onset SLE were resuspended in PBS. The viability was confirmed to be >90%.
Single-cell suspensions were loaded on a 10x Genomics Chromium single-cell 5′ v2 chip to prepare the libraries according to the manufacturer’s protocol. The library quality was checked by Agilent 2100 Bioanalyzer and Qubit fluorometric quantitation. Samples were sequenced on an Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per cell.

value: PBMC

value: B cell


title: 22Rv1, eIF3B replicate 3


title: 22Rv1, Input, replicate 1


title: 22Rv1, eIF3B replicate 1


title: HGC27, RUNX3KO, rep2

status: Public on Dec 20 2023

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
Basecalls were performed using bcl2fastq.
Sequenced reads from RNA-seq experiments were aligned by using HISAT2 v2.1.0.
Read count extraction wqas performed using Htseq.
Assembly: hg19
Supplementary files format and content: tab-deliminated text file included raw counts for each sample

growth_protocol: MEM, 10% fetal bovine serum, 1x penicillin/streptmycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was extracted using the TRIzol reagent (Thermo Fisher Scientific) and the Direct-zol RNA MiniPrep Kit (Zymo Research) following the manufacturers’ protocols.
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

value: gastric cancer cell line

value: RUNX3 knock-out


title: B021


title: HGC27, wt, rep2

value: wildtype


title: control_943

city: La Plata

first: Guillermo

last: Giovambattista

state: Buenos Aires

address: Calle 60 y 118 S/N

department: Facultad de Ciencias Veterinarias

country: Argentina

institute: CONICET-UNLP

data_processing:
Raw data were filtered to remove low-quality and adapter sequences
nf-core/RNAseq project pipeline  was used to perform RNA-seq analysis
This workflow includes the following analyses: quality control of reads with FastQC, STAR software for alignment to reference genome and featureCounts software for counting reads. Reads not having in average 10 total reads in SG and CG were filtered to delete non-expressed genes and transcripts with low expression levels
To identify differentially expressed genes (DEG), the DESeq2 software in R was applied using the Benjamini and Hochberg method implemented in this package
Transcripts with an adjusted p value < 0.05 were considered to have DGE, as identified by the Ensembl database
Assembly: ARS-UCD1.2 version as the reference bovine genome
Supplementary files format and content: Count matrix. Content including Raw count matrix, filtered matrix average>10, Deseq2 analysis results
Supplementary files format and content: Calcaterra_et_al_biochemichal_determinations_and_productive_data.xlsx: Excel file contains measurements of different parameters in the samples (Osi, GSHpx and SOD activity, AC, Tbars) and milk production on day 30
Supplementary files format and content: metadata.docx

organism: Bos taurus

source_name: White blood cell

extract_protocol:
Blood extraction from jugular vein later preserved in RNAlater (Thermo Fisher Scientific, USA) and stored at -80 °C until processing by RNA-sequencing analysis
RNA extraction with assay and hemoglobin depletion. RNA quality was verified with an Agilent bioanalyzer (Agilent, CA, USA).
After quality control procedures, the samples were sequenced in a NovaSeq 6000 sequencing platform (Illumina Inc, CA, USA) and the paired-end 150b (PE150) strategy

tag: breed

value: Holstein

tag: Sex

value: Female

value: White blood cell

value: Control

tag: time

value: Day 7 after calving


title: control_985


title: HGC27. wt, rep1


title: control_821


title: control_1010


title: caso_952

value: mineral supplementation


title: caso_974


title: caso_988


title: control_3844


title: HGC27, RUNX3KO, rep1


title: control_3660


title: caso_1090


title: 22Rv1, Input, replicate 3


title: 22Rv1, eIF3B replicate 2


title: T28

value: Pancreas

value: Tumor

tag: pdx tumor_stage

value: PRIMARY

tag: pdx tumor_differentiation

value: Moderate

tag: f0 tumor_differentiation


title: COPD [DK21067B 04]

status: Public on Dec 18 2023

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

description:
DK21067B_04
3' RNA-seq

data_processing:
Removal of poly A tail and adapter sequences were performed using BBDuk (BBMap version 38.96) with the following settings (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20).
Trimmed reads were mapped to hg38 using STAR version 2.7.6a with the following settings (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts for each gene were obtained using HTSeq-count version 1.99.2 with the following settings (-m intersection-nonempty -s yes).
Assembly: hg38
Supplementary files format and content: xlsx files include raw counts for each sample.
Supplementary files format and content: xlsx files include RPM values for each sample.

extract_protocol:
RNA was harvested using ISOGEN reagent (Life Technologies, Carlsbad, CA, USA).
Purified total RNA (200 ng) was used for RNA library preparation, according to the instructions of the Quant Seq 3' mRNA-seq library preparation kit FWD of Illumina (Lexogen, Vienna, Austria). The RNA libraries were sequenced on an Illumina NextSeq 500 system with 75-nt-long reads.

tag: disease

value: Chronic Obstructive Pulmonary Disease

value: Male

tag: race

value: Asian


title: COPD [DK21067B 03]

description:
DK21067B_03
3' RNA-seq

value: PBMC


title: COPD [DK21067B 12]

description:
DK21067B_12
3' RNA-seq


title: COPD [DK21067B 11]

description:
DK21067B_11
3' RNA-seq


title: COPD [DK21067B 07]

description:
DK21067B_07
3' RNA-seq


title: COPD [DK21067B 10]

description:
DK21067B_10
3' RNA-seq


title: COPD [DK21067B 06]

description:
DK21067B_06
3' RNA-seq


title: COPD [DK21067B 09]

description:
DK21067B_09
3' RNA-seq


title: COPD [DK21067B 05]

description:
DK21067B_05
3' RNA-seq


title: caso_3466

tag: cell type


title: COPD [DK21067B 08]

description:
DK21067B_08
3' RNA-seq


title: COPD [DK21222 14]

description:
DK21222_14
3' RNA-seq


title: COPD [DK21222 15]

description:
DK21222_15
3' RNA-seq


title: COPD [DK21222 16]

description:
DK21222_16
3' RNA-seq


title: caso_1014


title: COPD [DK21222 10]

description:
DK21222_10
3' RNA-seq


title: COPD [DK21222 08]

description:
DK21222_08
3' RNA-seq


title: COPD [DK21222 12]

description:
DK21222_12
3' RNA-seq


title: COPD [DK21222 05]

description:
DK21222_05
3' RNA-seq


title: COPD [DK21222 01]

description:
DK21222_01
3' RNA-seq


title: COPD [DK21222 11]

description:
DK21222_11
3' RNA-seq


title: COPD [DK21222 03]

description:
DK21222_03
3' RNA-seq


title: COPD [DK21222 02]

description:
DK21222_02
3' RNA-seq


title: B009

value: PBMCs

tag: gender

value: male

value: nr-axspa


title: COPD [DK21222 09]

description:
DK21222_09
3' RNA-seq

tag: age


title: Healthy control [DK21222 19]

description:
DK21222_19
3' RNA-seq

value: Healthy


title: Healthy control [DK22269 12]

description:
DK22269_12
3' RNA-seq

value: Female


title: COPD [DK21222 04]

description:
DK21222_04
3' RNA-seq


title: Healthy control [DK21222 18]

description:
DK21222_18
3' RNA-seq


title: Healthy control [DK22269 14]

description:
DK22269_14
3' RNA-seq


title: COPD [DK21222 13]

description:
DK21222_13
3' RNA-seq


title: Healthy control [DK21222 17]

description:
DK21222_17
3' RNA-seq


title: Healthy control [DK22269 10]

description:
DK22269_10
3' RNA-seq


title: Healthy control [DK22269 04]

description:
DK22269_04
3' RNA-seq


title: Healthy control [DK22269 08]

description:
DK22269_08
3' RNA-seq


title: COPD [DK21222 07]

description:
DK21222_07
3' RNA-seq


title: Healthy control [DK22269 03]

description:
DK22269_03
3' RNA-seq


title: Healthy control [DK22269 02]

description:
DK22269_02
3' RNA-seq


title: Healthy control [DK22269 01]

description:
DK22269_01
3' RNA-seq


title: Healthy control [DK22269 09]

description:
DK22269_09
3' RNA-seq


title: Healthy control [DK20193B 09]

description:
DK20193B_09
3' RNA-seq


title: stem apex, rapid growth stage, cutting, Biological repeat 3

status: Public on Dec 08 2023

city: kunming

first: Shaojie

last: MA

state: yunnan

address: panlongqu

institute: Southwest Forestry University

data_processing:
Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, cDNA libraries were sequenced on Illumina high-throughput platform.
Populus yunnanensis Reference genome was pre-defined for the mapping RNA-seq reads with HISAT2，StringTie was applied to assemble the mapped reads.（--merge -F 0.1 -T 0.1）
Discovery of novel transcripts and genes was achieved by StringTie on base of Populus yunnanensis reference genome.  Excluding short transcripts(coding peptides with less than 50 amino acids) or those containing only one exons, 1,917 novel genes were discovered in this project.
Assembly: Populus yunnanensis reference genome (PRJNA886471)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Populus yunnanensis

source_name: stem apex

extract_protocol:
The cuttings of Populus yunnanensis were carried out in two ways: cutting and  inverted cutting.
The mRNA of two cuttings were collected at the primary and rapid growth stages respectively.

value: stem apex

tag: developmental stage

value: rapid growth stage

value: cutting


title: stem apex, rapid growth stage, cutting, Biological repeat 1


title: stem apex, rapid growth stage, inverted cutting, Biological repeat 3

value: inverted cutting


title: stem apex, primary stage, cutting, Biological repeat 3

value: primary stage


title: stem apex, rapid growth stage, inverted cutting, Biological repeat 2


title: stem apex, primary stage, cutting, Biological repeat 1


title: stem apex, primary stage, inverted cutting, Biological repeat 2


title: stem apex, primary stage, cutting, Biological repeat 2


title: stem apex, primary stage, inverted cutting, Biological repeat 3


title: COPD [DK21067B 02]

description:
DK21067B_02
3' RNA-seq


title: C4-2 cells, ATGL KO + S404A ATGL rep3

status: Public on Nov 22 2023

city: Houston

first: Daniel

middle: E.

last: Frigo

address: 1881 East Road - Unit 1907

institute: University of Texas MD Anderson Cancer Center

data_processing: BCL (raw output of Illumina HigSeq) files are processed using Illumina’s Consensus Assessment of sequence And Variation (CASAVA) tool for demultiplexing/conversion to FASTQ format.FASTQ files of RNA samples are processed using both STAR following the two-step alignment procedure.

growth_protocol: RPMI1640 no glucose supplemented with 5mM glucose and 5% dialyzed FBS

extract_protocol:
RNA was isolated and purified using RNEasy Plus Mini Kit (QIAGEN, Hilden, Germany).
Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNextR Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5L d(N6) 3L [N=A,C,G,T]) and fragmented based on manufacturerfs recommendations.
The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42.C. All remaining steps for library construction were used according to the NEBNextR Ultra. II Directional RNA Library Prep Kit for IlluminaR (New England BioLabs Inc., Massachusetts, USA).
Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 500bp with an insert size of about 350bp.

value: castration-resistant prostate cancer cells

tag: genotype

value: ATGL knockout with S404A ATGL addback


title: stem apex, primary stage, inverted cutting, Biological repeat 1

tag: tissue


title: C4-2 cells, ATGL KO + WT rep2

tag: cell line

value: ATGL knockout with wildtype ATGL addback


title: C4-2 cells, ATGL KO + S404A ATGL rep1


title: C4-2 cells, ATGL KO + S47A ATGL rep1

value: ATGL knockout with S47A ATGL addback


title: C4-2 cells, ATGL KO + S47A ATGL rep3


title: C4-2 cells, ATGL KO + S47A ATGL rep2


title: C4-2 cells, ATGL KO + WT rep3


title: C4-2 cells, ATGL KO + WT rep1


title: C4-2 cells, Scramble rep3

value: Scramble control


title: stem apex, rapid growth stage, cutting, Biological repeat 2


title: C4-2 cells, Scramble rep2


title: C4-2 cells, ATGL KO rep3

value: ATGL knockout


title: C4-2 cells, Scramble rep1


title: C4-2 cells, ATGL KO rep2


title: N_D3_2F_H9_1

status: Public on Oct 17 2023

city: Kyoto

first: Yasuhiro

last: Takashima

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.15
The sequenced reads were mapped to the hg38 human reference genome and the EGFP sequence using Tophat2 (version 2.1.1) with the human GENCODE (version 27) annotation gtf file.
The mapped reads with high mapping quality (MAPQ >= 20) were used for further analyses.
FPKM values were determined by Cufflinks version 2.2.1 package with the human GENCODE (version v27) annotation gtf file.
Genome_build: hg38
Supplementary_files_format_and_content: The tab-delimited text file include FPKM values for each sample.

source_name: 2F D3 naïve H9(PDGFRA positive)_1

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (QIAGEN)
To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

tag: analysis method

value: RNA-seq

value: 2F naive PSC


title: N_D3_4F_H9_1

source_name: 4F D3 naïve H9(PDGFRA positive)_1

value: 4F naive PSC


title: stem apex, rapid growth stage, inverted cutting, Biological repeat 1

tag: treatment


title: C4-2 cells, ATGL KO rep1


title: N_D3_4F_H9_2

source_name: 4F D3 naïve H9(PDGFRA positive)_2


title: N_D3_2F_H9_2

source_name: 2F D3 naïve H9(PDGFRA positive)_2


title: N_D3_7F_H9_4

source_name: 7F D3 naïve H9(PDGFRA positive)_4

value: 7F naive PSC


title: N_D0_H9_5

source_name: Naïve H9 (hESCs)_5

value: naive PSC


title: N_D0_H9_4

source_name: Naïve H9 (hESCs)_4


title: N_D3_G6_H9_3

source_name: GATA6 o/e D3 naïve H9(PDGFRA positive)_3

value: PDGFRA positive cells induced by GATA6 o/e from naive and primed PSCs


title: N_D3_G6_H9_4

source_name: GATA6 o/e D3 naïve H9(PDGFRA positive)_4


title: C4-2 cells, ATGL KO + S404A ATGL rep2


title: GATA6 o/e D3 primed H9(PDGFRA positive)_1

description:
P_D3_G6_H9_1
P_G6_D3_PRA_ex1

source_name: H9 ESCs

growth_protocol: Primed human PSCs were maintained on MEF under DMEM/F12 with 20% KSR, 1% NEAA, 4 ng/ml bFGF and 0.1 mM 2-ME. Naïve human PSCs were maintained on MEF with t2iLGo medium, which consists of N2B27 (Ndiff227) with 1 uM PD0325901, 1 uM CHIR99021, 10 ng/ml hLIF and 3 uM Go6983.  GATA6 was overexpressed in naïve and primed PSCs. PDGFRA+ cells were sorted at day 1 and 3. As another samples, 7 factors were added in naïve PSCs. PDGFRA positive cells were collected at day 3. 7 factors: 25 ng/ml FGF4, 1 ug/ml heparin sodium, 10 ug/ml recombinant human BMP4, 10 ng/ml recombinant human PDGF-AA, 1 uM XAV939, 3 uM A83-01, 0.1 uM retinoic acid, and 10 ng/ml recombinant human IL-6

value: H9 ESCs

value: PDGFRA+ cells at day 3 after GATA6 overexpression in primed PSCs


title: GATA6 o/e D3 primed H9(PDGFRA positive)_2

description:
P_D3_G6_H9_2
P_G6_D3_PRA_ex2


title: GATA6 o/e D1 primed H9(PDGFRA positive)_2

description:
P_D1_G6_H9_2
P_G6_D1_PRA_ex2

value: PDGFRA+ cells at day 1 after GATA6 overexpression in primed PSCs


title: GATA6 o/e D1 primed H9(PDGFRA positive)_1

description:
P_D1_G6_H9_1
P_G6_D1_PRA_ex1


title: Primed H9 (hESCs)_2

description:
P_D0_H9_2
P_ex2

value: conventional primed PSCs


title: N_D3_7F_H9_3

source_name: 7F D3 naïve H9(PDGFRA positive)_3


title: Primed H9 (hESCs)_1

description:
P_D0_H9_1
P_ex1


title: Naïve H1 (hESCs)_2

description:
N_D0_H1_2
N_H1_ex2

source_name: H1 ESCs

value: H1 ESCs

value: naive human PSCs


title: 7F D3 naïve H1(PDGFRA positive)_2

description:
N_D3_7F_H1_2
N_7F_D3_PRA_H1_ex2

value: PDGFRA+ cells at day 3 after growth factors (7F) treatment in naive H1 PSCs (primitive endoderm-like cells)


title: 7F D3 naïve AdiPS(PDGFRA positive)_2

description:
N_D3_7F_Adi_2
N_7F_D3_PRA_Adi_ex2

source_name: adipose-derived iPSCs

value: adipose-derived iPSCs

value: PDGFRA+ cells at day 3 after growth factors (7F) treatment in naive AdiPSCs (primitive endoderm-like cells)


title: 7F D3 naïve AdiPS(PDGFRA positive)_1

description:
N_D3_7F_Adi_1
N_7F_D3_PRA_Adi_ex1


title: Naïve AdiPS (hiPSCs)_1

description:
N_D0_Adi_1
N_Adi_ex1


title: GATA6 o/e D1 naïve H9(PDGFRA positive)_2

description:
N_D1_G6_H9_2
N_G6_D1_PRA_ex2

value: PDGFRA+ cells at day 1 after GATA6 overexpression in naive PSCs


title: GATA6 o/e D3 naïve H9(PDGFRA positive)_1

description:
N_D3_G6_H9_1
N_G6_D3_PRA_ex1

value: PDGFRA+ cells at day 3 after GATA6 overexpression in naive PSCs (primitive endoderm-like cells)


title: Naïve H9 (hESCs)_2

description:
N_D0_H9_2
N_ex2


title: Naïve AdiPS (hiPSCs)_2

description:
N_D0_Adi_2
N_Adi_ex2


title: 7F D3 naïve H9(PDGFRA positive)_2

description:
N_D3_7F_H9_2
N_7F_D3_PRA_H9_ex2

value: PDGFRA+ cells at day 3 after growth factors (7F) treatment in naive H9 PSCs (primitive endoderm-like cells)


title: GATA6 o/e D3 naïve H9(PDGFRA positive)_2

description:
N_D3_G6_H9_2
N_G6_D3_PRA_ex2


title: GATA6 overexpression  D1 naïve H9(PDGFRA+)_1

description:
N_D1_G6_H9_1
N_G6_D1_PRA_ex1


title: MAFLD liver 3

status: Public on Oct 01 2023

city: St. Louis

first: Joel

middle: D

last: Schilling

state: MO

address: 660 S. Euclid Ave

department: Internal Medicine

institute: Washington University School of Medicine

data_processing:
Read alignment and quantification: Cell Ranger count pipeline v3.0.2
Assembly: Human reference GRCh38
Supplementary files format and content: Tab-separated values files and matrix files of filtered feature-barcode matrix

source_name: liver

extract_protocol:
human liver tissue was digested and flow sorted for CD45 positive cells.  Single nuclear RNA seq was performed on these cells.
v2 Chromium Single Cell 3" library kit and Chromium instrument (10X genomics)

value: liver

value: CD45 cells

tag: disease state

value: Metabolic dysfunction-associated fatty liver disease (MAFLD)


title: Naïve H9 (hESCs)_1

description:
N_D0_H9_1
N_ex1


title: Isis D21 BhA4P 75I9

status: Public on Sep 14 2023

city: Hannover

first: Sylvia

last: Merkert

address: Carl-Neuberg-Str. 1

department: LEBAO

institute: Hannover Medical School

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (version 1.4.2) which is a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden. The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. The genome reference and annotation data were taken from GENCODE.org (Homo sapiens; GRCh38.p13; release 34).
Normalization and differential expression analysis was performed on the internal Galaxy (version 20.05) instance of the RCU Genomics, Hannover Medical School, Germany with DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled (“Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering” set “Yes”).
Assembly: GRCh38.p13; release 34
Supplementary files format and content: Tab-delimited text files include normalized espression values as a matrix table for all or a part of the samples (DESeq2 output)

source_name: Isis (MHHi007-A)

extract_protocol:
Cells were lysed with TRIzol and RNA harvested using the NucleoSpin RNA mini kit (Macherey-Nagel)
Library generation, quality control, and quantification:  500ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs). All steps were performed as recommended in user manualE7760 (Version 1.0_02-2017; NEB) except that all reactions were downscaled to 2/3 of initial volumes. Furthermore, one additional purification step was introduced at the end of the standard procedure, using 1x ‘Agencourt® AMPure® XP Beads’ (#A63881; Beckman Coulter, Inc.). cDNA libraries were barcoded by dual indexing approach, using ‘NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs’ (6440S; New England Biolabs). All generated cDNA libraries were amplified with 7 cycles of final pcr.  Fragment length distribution of individual libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).   Library denaturation and Sequencing run:  Equal molar amounts of 8 individually barcoded libraries were pooled for a common sequencing run. The library pools were denatured with NaOH and were finally diluted to 2pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina). 1.3 ml of each denatured pool was loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell for single reads (20024906; Illumina). Sequencing was performed with the following settings: Sequence reads 1 and 2 with 38 bases each; Index reads 1 and 2 with 8 bases each.

treatment_protocol: Trophoblast differentiation was induced with either BAP (BMP4, A83-01, and PD173074) or BhAhP (BMP4, high A83-01, high PD173074) for 9 or 21 days

value: Isis (MHHi007-A)

value: hiPSC derivative

value: 21 days BhAhP differentiation


title: MAFLD liver 1


title: MAFLD liver 2


title: Isis D9 BhA4P 75I3

value: 9 days BhAhP differentiation


title: Isis D21 BhA4P 73I11


title: 7F D3 naïve H1(PDGFRA positive)_1

description:
N_D3_7F_H1_1
N_7F_D3_PRA_H1_ex1


title: Naïve H9 (hESCs)_3

description:
N_D0_H9_3
N_ex3

value: H9 ESCs


title: Naïve H1 (hESCs)_1

description:
N_D0_H1_1
N_H1_ex1


title: Isis D9 BhA4P 73I7


title: Isis iPS RNA P40+18

value: hiPSC


title: Isis D9 BAP 98I3

value: 9 days BAP differentiation


title: 7F D3 naïve H9(PDGFRA positive)_1

description:
N_D3_7F_H9_1
N_7F_D3_PRA_H9_ex1


title: IMM19_698_scRNA-seq_B002-P1

status: Public on Aug 31 2023

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

data_processing:
For TEA-seq, demultiplexing of raw base call files into FASTQ files was performed using bcl2fastq2 (Illumina v2.20.0.422, parameters: --create-fastq-for-index-reads, --minimum-trimmed-read-length=8, --mask-short-adapter-reads=8, --ignore-missing-positions, -ignore-missing-filter, --ignore-missing-bcls, -r 24 -w 24 -p 80). The --use-bases-mask option was used to adjust the read lengths for each library type as follows: Y28n*,I10,I10n*,Y90n* for RNA, Y50n*,I8n*,n8Y16,Y50n* for ATAC, and Y28n*,I8n*,n*,Y90n* for ADT and cell hashing (HTO).
For TEA-seq, the RNA and ATAC assays were run through cellranger-arc count to align to the genome.  For scRNA-seq, the fastq files were run through cellranger count.
ADT and HTO count matrices were generated using BarCounter v1.0 (Swanson et al. 2022). The RNA count matrix, and ADT count matrix were then combined into a single Seurat object. Cells were filtered based on the following cutoffs: > 250 genes/cell, > 500 RNA UMIs/cell, < 10,000 ADT UMIs/cell, < 35% mitochondrial reads, < 20,000 RNA UMIs/cell. Normalization, feature selection and scaling were performed on the RNA matrix (SCTransform function, default settings), followed by PCA (RunPCA function, default settings). A UMAP projection was generated (RunUMAP, dims = 1:30) and clustering was performed (FindNeighbors, dims = 1:30; FindClusters, resolution = 0.5). We used the Seurat Multimodal Reference Dataset for PBMCs (available from the Satija lab (Hao et al. 2021)) to perform label transfer on the dataset using the functions described in the Seurat V4 Vignettes (FindTransferAnchors; TransferData). Two clusters were identified to be non-T cells and were excluded. Sample specific transcripts, AC105402.3 and MTRNR2L8, were identified and removed prior to further downstream RNA analysis.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: scRNA-seq files have suffix _labeled.h5 and are hdf5 format.  TEA-seq data comes in a few formats: hdf5 for RNA and ADT data, and tsv.gz for ATAC fragment data and csv.gz for ATAC metadata.

source_name: peripheral blood mononuclear cells

extract_protocol:
All samples were collected, processed to PBMCs using a Ficoll-based approach and frozen in FBS with 10% DMSO within 4 hours of blood draw. Cord and peripheral blood samples for follow-up studies were purchased from Bloodworks Northwest (Seattle, WA) through protocols approved by the Bloodworks Northwest and internal Allen Institute IRBs.
TEA-seq library preparation was performed as described previously (Swanson et al. 2021), with the addition of Cell Hashing (Stoeckius et al. 2018) to allow for sample multiplexing and limit well-to-well batch effects. In brief, samples were thawed and processed across three batches, with each batch containing a common PBMC control. Antibody staining for Cell Hashing and cell sorting was performed simultaneously on 2 x 106 cells from each sample. Each sample was incubated with uniquely barcoded TotalSeq-A antibody, anti-CD45 antibody and anti-CD3 antibody, then pooled by T cell proportion previously determined, targeting 800,000 T cells for each donor sample and 200,000 T cells for the control, and sorted on a BD FACSAria Fusion. T cells were sorted as live, single CD45+CD3+ cells. 2 x 106 sorted T cells were then used for the library preparation. A panel of 55 barcoded oligo-conjugated antibodies (BioLegend TotalSeq-A) was used for these studies (Supp Table 4). Individual ATAC, RNA, and ADT libraries were prepared, sequenced and processed as described previously.(Swanson et al. 2021)     Single cell RNA sequencing was performed on PBMCs was previously described. (Genge et al. 2021) In brief, scRNA-seq libraries were generated using a modified 10x genomics chromium 3’ single cell gene expression assay with Cell Hashing. 8 donors were pooled per library, with the addition of a common batch control sample in each library. Libraries were sequenced on a Illuminia Novaseq platform. scRNA-seq Analysis. Count matrices from each sample were merged into age-specific Seurat objects, followed by normalization, feature selection, scaling, PCA, UMAP embedding, and clustering. Label transfer from the T cell subset Seurat reference was performed as previously described on each age specific Seurat Object. Following label transfer, all objects were merged into a single object. Cells identified CD4 Naïve with a prediction score greater than 0.7 were taken into downstream analysis. We then averaged the expression on each cell in each age group (AverageExpression function, group.by = ‘age’) for the DEGs identified in our TEA-seq analysis.

value: peripheral blood mononuclear cells

tag: birth year

tag: Sex

value: Male

value: African American

value: Unknown


title: PB00015_scRNA-seq_B002

value: Caucasian


title: PB00006_scRNA-seq_B002

value: Female


title: PB00004_scRNA-seq_B002


title: Isis iPS RNA P40+30


title: PB00022_scRNA-seq_B002


title: IMM19_698_scRNA-seq_B002-P2


title: plasma exosomes, FOS, rep9 (lncRNA and mRNA)

status: Public on Aug 30 2023

city: Taiyuan City

first: Xinzhe

last: Du

state: Shanxi Province

address: Jiefang Road

institute: Shanxi Medical University

description:
0003SZ000019
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx

data_processing:
Transcriptome high throughput sequencing was performed by CloudSeq Biotech (Shanghai, China).
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyze LncRNAs .
the high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA was identified.
LncRNA target genes were predicted by the locations to nearby genes. And GO and KEGG Pathway analysis were performed on these target genes.
Assembly: hg19
Supplementary files format and content: Excel file includes FPKM and Count values for each Sample

source_name: Peripheral Blood

extract_protocol:
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
library construction protocol:  RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA). Library sequencing was performed on an illumina Novaseq 6000 instrument with 150bp paired end reads.

value: Peripheral Blood

tag: sample type

value: plasma exosome

value: schizophrenia


title: plasma exosomes, FOS, rep5 (lncRNA and mRNA)

description:
0003SZ000010
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, FOS, rep4 (lncRNA and mRNA)

description:
0003SZ000009
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, FOS, rep8 (lncRNA and mRNA)

description:
0003SZ000015
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, FOS, rep1 (lncRNA and mRNA)

description:
0003SZ000006
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, FOS, rep10 (lncRNA and mRNA)

description:
0003SZ010001
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, FOS, rep2 (lncRNA and mRNA)

description:
0003SZ000007
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: Isis D9 BAP 99I3


title: plasma exosomes, HC, rep8 (lncRNA and mRNA)

description:
0003CK000014
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx

value: healthy control


title: plasma exosomes, HC, rep9 (lncRNA and mRNA)

description:
0005ZC000001
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, FOS, rep6 (lncRNA and mRNA)

description:
0003SZ000011
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, HC, rep5 (lncRNA and mRNA)

description:
0003CK000011
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, HC, rep10 (lncRNA and mRNA)

description:
0005ZC000003
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, FOS, rep3 (lncRNA and mRNA)

description:
0003SZ000008
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, HC, rep7 (lncRNA and mRNA)

description:
0003CK000013
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, HC, rep4 (lncRNA and mRNA)

description:
0003CK000010
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, HC, rep2 (lncRNA and mRNA)

description:
0003CK000007
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, HC, rep3 (lncRNA and mRNA)

description:
0003CK000009
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, HC, rep6 (lncRNA and mRNA)

description:
0003CK000012
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, HC, rep1 (lncRNA and mRNA)

description:
0003CK000006
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: plasma exosomes, FOS, rep7 (lncRNA and mRNA)

description:
0003SZ000013
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: scRNAseq_post_transplant_BM_RX_3

status: Public on Aug 24 2023

city: Memphis

first: Kim

last: Nichols

state: TN

address: 262 Danny Thomas Pl

department: Oncology

institute: St. Jude Children's Research Hospital

description: 10x Genomics

data_processing:
Sequencing reads from 10X experiment were mapped to mouse reference genome (mm10) using cellranger-7.1.0 (transcriptome version: mm10-2020-A). Single cell counts matrices were then processed using Scanpy as described in the best practices workflow previously (https://www.sc-best-practices.org). For quality control, doublet cells were filtered out, and low-quality cells with excess outliers calculated as 3 MADs (Median absolute deviations) for no. of counts per barcode, no. of genes per barcode, and fraction of counts from mitochondrial genes. We performed SCRAN normalization followed by dimensionality reduction with top 40 PCs selected using elbow plot using UMAP and tSNE algorithms. We used the Leiden algorithm for finding clusters at resolution of 0.25,0.5, and 1 and selected 0.25 as final resolution with optimal number of clusters preserving distinct cell populations.
For cell type identification across 22 clusters, we used a combination of known gene markers for cell populations or top gene markers that distinguished each cluster from other clusters identified using rank_genes_groups function in Scanpy. We used two determine hematopoietic sub populations of cells, bloodspot (https://servers.binf.ku.dk/bloodspot) and mouse cell atlas (https://bis.zju.edu.cn/MCA/atlas2.html; accessed April 2023) along with literature mining for known cell markers. We also used hscScore and scCATCH tools to aid cell identification. Finally, two authors (MB, NO) independently identified these clusters and finalized annotations.
We next performed integration of all 6 replicates, 3 each for wild-type and mutant genotypes, using Harmony algorithm, re-clustered the populations and annotated using the iterative process described above. Integrated anndata file was used to preform cell composition analysis within each cluster using scCODA Bayesian model for labeled clusters and Milo algorithm for unlabeled clusters. We used edgeR algorithm to identify significant differentially expressed genes within each cluster. We performed gene set enrichment analysis using MSigDb v.7.5.1 Hallmark genesets using python package GSEApy.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone Marrow

extract_protocol: For each mouse, sort-purified CD45.1+ and CD45.2+ LSK and BM cells were washed three times with 1X Phosphate-Buffered Saline (PBS-, calcium-, and magnesium-free) containing 0.04% weight/volume BSA (Thermo Fisher Scientific, Waltham, Massachusetts) and manually counted. LSK and BM cells were mixed at a ratio 1:1 to have a total desired recovery target of 8,000-10,000 total cells and loaded onto a Chromium Next GEM Chip K (10X Genomics, Pleasanton, California) with Master Mix from Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index; 10X Genomics, Pleasanton, California), Single Cell VDJ 5' Gel Beads (10X Genomics, Pleasanton, California) and Partitioning Oil (10X Genomics, Pleasanton, California) following the manufacturer's protocol. Briefly, gel beads-in-emulsion (GEMs) were generated, lysed and 10x barcoded, and full-length cDNA from polyadenylated mRNA was produced. Next, GEMs were broken, pooled fractions were recovered, and cDNA was purified by Dynabeads MyOne SILANE (10X Genomics, Pleasanton, California). Barcoded, full-length cDNA was amplified via PCR, purified by SPRIselect Reagent (Beckman Coulter, Brea, California), and quantified using High Sensitivity D5000 ScreenTape with High Sensitivity D5000 Reagents at the Agilent 2200 TapeStation system and used for library preparation (10X Genomics, Pleasanton, California; Library Construction Kit, Dual Index Kit TT Set A). The High Sensitivity D1000 ScreenTape and the High Sensitivity D1000 Reagents were used to assess library’s quality at the Agilent 2200 TapeStation system. Libraries were sequenced on the NovaSeq 6000 (Illumina, San Diego, California) according to the manufacturer's recommendations.

tag: strain

value: Bone Marrow

value: LSK


title: scRNAseq_post_transplant_BM_RX_2

description: 10x Genomics


title: scRNAseq_post_transplant_BM_WT_3

description: 10x Genomics