title: naa50_I2

status: Public on May 31 2022

type: SRA

city: Linfen

first: lin

middle: jin

last: feng

state: Shanxi

address: gongyuan 1 street

department: College of Life Sciences

country: China

institute: Shanxi Normal University

library_source: transcriptomic

data_processing:
Clean data were obtained by removing reads containing adapters, calls marked as N, and low-quality reads from the raw data
The high-quality reads were mapped to the Arabidopsis TAIR10 genome using Hisat2 v2.0.5
The expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced for each gene was calculated based on the length of the gene and read count mapped to the gene.
Genome_build: Arabidopsis TAIR10 genome
Supplementary_files_format_and_content: Readcount or FPKM expression matrix of each gene in the samples; the significance analysis list of each gene in all comparison combinations

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Closed buds_naa50

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen) from closed buds of wild-type and naa50-1 mutant plants.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: tissue

value: Closed buds


title: naa50_I3


title: WT_I2

source_name: Closed buds_WT

value: wild type


title: WT_I1


title: EED WT mESC Input

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

library_source: genomic

data_processing:
ChipSeq samples were aligned using Bowtie2 (v2.2.5)  allowing uniquely mapping reads only
Peak calling was performed with MACS2 (v2.1.1) and filtered at FDR < 5 (0.05)
Genome_build: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: murine embryonic stem cells

growth_protocol: Mouse embryonic stem cells V6.5 were cultured on irradiated mouse embryonic fibroblast (MEF) feeder layers in 0.1% gelatin-coated tissue culture flask. Cells were

extract_protocol:
For ChIP-Seq, 5×107 cells were used per immunoprecipitation according to previously described protocols (Lee et al., 2006). ChIP-Seq libraries were prepared with Illumina's ChIP-Seq sample prep kit (0801-0303).
NEBNext® DNA Library Prep Master Mix Set for Illumina

tag: strain

value: C57BL/6 (female) x 129/S (male)

tag: cell type

value: murine embryonic stem cells

tag: chip antibody


title: ChIP-seq of BRCA2 in EED WT mESC

value: homemade 028


title: naa50_I1


title: WT_I3


title: ChIP-seq of BRCA2 in EED KO mESC


title: ChIP-seq of BRCA2 in ZFP281 shRNA mESC


title: ChIP-seq of BRCA2 in Non T shRNA mESC


title: SP3

city: New York

first: Michael

middle: Lawrence

last: Miller

state: NY

address: One Gustave L. Levy Place

department: Fishberg Department of Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Normalization Factor: 1.05716

data_processing:
FASTQ files were aligned to rat reference genome (build Rn6) using TopHat2.
Reads mapping to genetic features (genes based on Ensembl Rnor_6.0 annotation) were counted using HTSeq.
Raw counts were divided by each sample's normalization factor (based on the trimmed mean of M-values performed with EdgeR).
Genes with averaged normalized counts less than 50 in all comparison groups were removed from the analysis.
Differentially expressed genes were identified with limma using the voom calculation and quantile normalization.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Absolute (pre-normalized) counts per gene

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Striatum

extract_protocol:
Cells, captured onto high-specificity LCM caps, were lysed in TRIzol then purified using gel-filtration columns
PolyA-tailed RNAs were reverse transcribed using Qiagen's REPLI-g Single Cell Kit then sequencing libraries were prepared using Qiagen's GeneRead Illumina library prep kit

value: Striatopallidal neuron


title: SP1

description: Normalization Factor: 1.140104


title: SN1

description: Normalization Factor: 1.047965

value: Striatomesencephalic neuron


title: SP2

description: Normalization Factor: 0.779751


title: SN2

description: Normalization Factor: 1.015341


title: K562 cells, Control 2, Day0

city: Nanning

first: Haiqun

last: Dong

address: Shuangyong road 20

department: Department of Hematology

institute: The First Affiliated Hospital of Guangxi Medical University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: Genome_build: hg38
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

organism: Homo sapiens

growth_protocol: RPMI 1640, 10% fetal bovine serum,1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: K562 cells were treated with 10 or 20 μM/L Lip-1 (selleck) for 24h.

tag: cell line

value: leukemia cells

value: WT

tag: treatment

value: without Lip-1 treatment


title: K562 cells, Control 1, Day0

description: A-C


title: K562 cells, Case 2, Day1

value: 10μM Lip-1 treatment for 24h


title: K562 cells, Control 4, Day0


title: EED KO mESC Input


title: K562 cells, Case 1, Day1

description: A-E

value: 20μM Lip-1 treatment for 24h


title: K562 cells, Control 3, Day0


title: Type II Metastasis_9

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 transcriptome using salmon v0.14.1
Transcript per million (TPM) were calculated by salmon v0.14.1, and log2 transformed with floor value of -9.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: high grade serous ovarian cancer

extract_protocol:
RNA was extracted from frozen tissues using the Qiagen RNeasy kit (QIAGEN) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: site

value: metastatic


title: Type II Primary_7

value: primary


title: Type II Primary_9


title: Type II Primary_6


title: Type II Primary_8


title: K562 cells, Case 4, Day1

description: B-E


title: Type II Primary_5


title: K562 cells, Case 3, Day1


title: Type II Metastasis_4


title: Type II Metastasis_6


title: Type II Primary_12


title: Type II Metastasis_2


title: Type II Primary_3


title: Type II Metastasis_12


title: Type II Metastasis_11


title: Type II Primary_2


title: Type II Metastasis_13


title: Type II Metastasis_7


title: Type II Primary_13


title: Type I Metastasis_8


title: Type I Metastasis_7


title: Type II Metastasis_10


title: Type II Primary_11


title: Type II Metastasis_8


title: Type II Metastasis_3


title: Type I Primary_6


title: Type II Primary_1


title: Type I Primary_9


title: Type I Primary_3


title: Type I Primary_4


title: Type I Metastasis_9


title: Type I Primary_8


title: Type I Primary_5


title: Type II Metastasis_5


title: Type II Primary_10


title: Type I Primary_18


title: Type I Primary_19


title: Type I Metastasis_5


title: Type I Metastasis_3


title: Type I Primary_2


title: Type I Primary_7


title: Type I Primary_16


title: Type I Metastasis_17


title: Type I Metastasis_6


title: Type I Metastasis_15


title: Type I Metastasis_18


title: Type I Primary_17


title: Type I Metastasis_16


title: Type I Primary_13


title: Type I Metastasis_13


title: Type I Primary_12


title: Type I Metastasis_12


title: Type I Metastasis_2


title: Type I Primary_11


title: Type I Metastasis_19


title: Type I Metastasis_11


title: Type I Metastasis_10


title: Type I Primary_10


title: Type I Primary_1


title: Type I Metastasis_1


title: Type I Primary_15


title: Type I Metastasis_14


title: Type I Primary_14


title: s_215121

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Lung biopsy

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) from freshly frozen lung tissue biopsies obtained from the LTRC.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

tag: diagnosis

value: RA-UIP


title: s_282634


title: s_284489


title: s_254200


title: s_201630


title: s_202617

value: CTL


title: s_258760


title: s_191307


title: s_228552


title: s_133583


title: s_152649


title: s_263234


title: s_298223


title: s_102021


title: s_059774


title: s_104702


title: s_133378


title: s_131648


title: s_137431


title: s_039545


title: s_116004


title: s_059846


title: s_111533


title: s_280263


title: s_186024


title: RNAseq_Sub3_GF_Control_rep2

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

description: technical replicate 2

data_processing:
The raw RNA-seq data were aligned to reference genome hg19 by using STAR (version 2.7.7a). Low quality reads were filtered using samtools (version 1.3.1) view option with MAPQ < 10 score. Duplicated reads and artifacts were removed using samtools -rmdup command, then bedtools (version 2.29.2) intersectBed option with hg19 consensus backlist. Transcript abundances were calculated using featureCounts from Rsubread (version 2.4.0). R package, edgeR (PMID: 27008025) with paired analysis was used for differential gene expression analysis with cutoffs cpm > 2 more than 4 samples. P-value < 0.05 was used to determine statistical significance for differentially expressed genes.
Transcript per million (TPM) values were calculated by using TPMCalculator (PMID: 30379987)
Genome_build: hg19

source_name: subcutaneous gluteofemoral ASC

growth_protocol: Adipose–derived stem cells were cultured in aMEM medium (Gibco) supplemented with 2.5% FBS, EGF and FGF.

extract_protocol:
Fat biospsies were collected and SVF were isolated by centrifugation. Total RNA was extracted using RNAeasy mini kit (QIAGEN)
RNA-seq libraries were prepared and sequenced using standard Illumina protocols for HiSeq 2500 instrument.

treatment_protocol: Overexpression of HOTAIR using lentivirus - Downregulation using siRNA

value: hASCs


title: RNAseq_Sub4_GF_Control_rep2

description: technical replicate 2


title: s_022562


title: s_149517


title: RNAseq_Sub4_GF_Control_rep1

description: technical replicate 1


title: RNAseq_Sub1_GF_Control_rep1

description: technical replicate 1


title: RNAseq_Sub4_GF_si_rep2

description: technical replicate 2


title: RNAseq_Sub3_GF_si_rep1

description: technical replicate 1


title: RNAseq_Sub3_GF_si_rep2

description: technical replicate 2


title: RNAseq_Sub2_GF_si_rep2

description: technical replicate 2


title: RNAseq_Sub1_GF_si_rep2

description: technical replicate 2


title: RNAseq_Sub3_GF_Control_rep1

description: technical replicate 1


title: RNAseq_Sub1_GF_si_rep1

description: technical replicate 1


title: RNAseq_Sub2_GF_Control_rep1

description: technical replicate 1


title: RNAseq_Sub2_ABD_Control_rep2

description: technical replicate 2

source_name: subcutaneous abdominal ASC


title: RNAseq_Sub4_ABD_Control_rep1

description: technical replicate 1


title: RNAseq_Sub2_GF_Control_rep2

description: technical replicate 2


title: RNAseq_Sub1_GF_Control_rep2

description: technical replicate 2


title: RNAseq_Sub4_GF_si_rep1

description: technical replicate 1


title: RNAseq_Sub1_ABD_Control_rep2

description: technical replicate 2


title: RNAseq_Sub4_ABD_OE_rep2

description: technical replicate 2


title: RNAseq_Sub4_ABD_Control_rep2

description: technical replicate 2


title: RNAseq_Sub2_ABD_OE_rep2

description: technical replicate 2


title: RNAseq_Sub3_ABD_Control_rep2

description: technical replicate 2


title: RNAseq_Sub2_GF_si_rep1

description: technical replicate 1


title: RNAseq_Sub1_ABD_OE_rep2

description: technical replicate 2


title: RNAseq_Sub3_ABD_Control_rep1

description: technical replicate 1


title: hs_Sub4_RNAPII_glut

data_processing:
Burrows-Wheeler Alignment (BWA) tool (v07.10)
BAM files were generated with SAMtools (v0.1.19)
To remove the artifacts from the predicted peaks, we used the blacklisted genomic regions of the Encyclopedia of DNA Elements (ENCODE)
“Peaks” were predicted and broadPeak were created using the Model-based Analysis of ChIP-Seq (MACS2) tool (v2.0.10)
Coverage (bigwig) files were created by bamCoverage in the deepTools program
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak and bigwig

extract_protocol:
Fat biospsies were collected and SVF were isolated by centrifugation. For ATAC-seq, nuclei were used for tagmentation using Nextera DNA Library Preparation Kit (Illumina).DNA was purified with MinElute PCR Purification Kit (Qiagen). For ChIP-seq, Lysates were clarified from sonicated nuclei and histone/CTCF or RNAPII-DNA complexes were isolated with antibody.
ATAC-seq, ChIP-seq and ChIRP-seq libraries were prepared and sequenced using standard Illumina protocols for HiSeq 2500 instrument.
ATAC-seq, ChIP-seq, ChIRP-seq

tag: method

value: ChIP-seq

tag: antibody

value: RNAPII


title: RNAseq_Sub2_ABD_Control_rep1

description: technical replicate 1


title: hs_Sub4_H3K4me3_glut


title: hs_Sub4_H3K9me3_abd


title: RNAseq_Sub1_ABD_Control_rep1

description: technical replicate 1


title: hs_Sub4_H3K4me2_glut


title: hs_Sub4_H3K4me2_abd


title: hs_Sub4_ATAC-seq_glut_rep2

value: ATAC-seq


title: RNAseq_Sub4_ABD_OE_rep1

description: technical replicate 1


title: RNAseq_Sub3_ABD_OE_rep2

description: technical replicate 2


title: RNAseq_Sub3_ABD_OE_rep1

description: technical replicate 1


title: hs_Sub4_ATAC-seq_abd_rep2


title: RNAseq_Sub2_ABD_OE_rep1

description: technical replicate 1


title: hs_Sub4_ATAC-seq_abd_rep1


title: hs_Sub3_RNAPII_glut


title: hs_Sub_ChIRP-seq_glut

value: ChIRP-seq


title: RNAseq_Sub1_ABD_OE_rep1

description: technical replicate 1


title: hs_Sub3_H3K9me3_glut


title: hs_Sub3_H3K4me3_glut


title: hs_Sub4_RNAPII_abd


title: hs_Sub3_H3K4me3_abd


title: hs_Sub4_H3K4me3_abd


title: hs_Sub4_H3K9me3_glut


title: hs_Sub3_H3K27me3_glut


title: hs_Sub4_H3K27me3_glut


title: hs_Sub3_H3K27ac_glut


title: hs_Sub3_H3K27me3_abd


title: hs_Sub3_H3K27ac_abd


title: hs_Sub4_H3K27me3_abd


title: hs_Sub4_ATAC-seq_glut_rep1


title: hs_Sub4_H3K27ac_abd


title: hs_Sub4_H3K27ac_glut


title: hs_Sub4_CTCF_abd

value: CTCF


title: hs_Sub4_CTCF_glut


title: hs_Sub3_CTCF_glut


title: hs_Sub3_RNAPII_abd


title: hs_Sub3_H3K9me3_abd


title: hs_Sub3_ATAC-seq_glut_rep1


title: hs_Sub3_ATAC-seq_abd_rep1


title: hs_Sub3_ATAC-seq_abd_rep2


title: hs_Sub3_H3K4me2_glut


title: hs_Sub3_H3K4me2_abd


title: hs_Sub2_H3K9me3_glut


title: hs_Sub2_H3K4me3_glut


title: hs_Sub3_CTCF_abd


title: hs_Sub2_H3K4me2_abd


title: hs_Sub3_ATAC-seq_glut_rep2


title: hs_Sub2_CTCF_glut


title: hs_Sub2_H3K27ac_glut


title: hs_Sub2_CTCF_abd


title: hs_Sub2_ATAC-seq_glut_rep2


title: hs_Sub2_ATAC-seq_abd_rep1


title: hs_Sub2_RNAPII_glut


title: hs_Sub2_RNAPII_abd


title: hs_Sub2_H3K9me3_abd


title: hs_Sub2_ATAC-seq_abd_rep2


title: hs_Sub1_H3K4me3_abd


title: hs_Sub1_H3K9me3_abd


title: hs_Sub1_H3K4me3_glut


title: hs_Sub1_H3K9me3_glut


title: hs_Sub1_H3K27ac_glut


title: hs_Sub1_H3K27me3_abd


title: hs_Sub1_CTCF_abd


title: hs_Sub1_H3K4me2_glut


title: hs_Sub2_H3K4me3_abd


title: hs_Sub2_H3K4me2_glut


title: hs_Sub1_H3K27me3_glut


title: hs_Sub2_H3K27me3_glut


title: hs_Sub2_H3K27me3_abd


title: hs_Sub2_H3K27ac_abd


title: hs_Sub1_ATAC-seq_abd_rep2


title: hs_Sub1_ATAC-seq_abd_rep1


title: hs_Sub1_ATAC-seq_glut_rep1


title: hs_Sub2_ATAC-seq_glut_rep1


title: hs_Sub1_RNAPII_glut


title: WR1

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Base calling was done with RTA3 implemeation software in the NovaSeq 6000 system
3' trimming for Illumina adapters was performed using cutadapt v1.18
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated files included normalized counts for each sample; paired end reads for each sample processed together e.g. BN1_1 and BN1_2 became BN1 in normalized_counts.txt

source_name: Arabidopsis leaves

growth_protocol: Arabidopsis thaliana plants were grown on peat pelllets for 4 weeks, 10 hour light/ 14 hour dark under cool white light 50 µmole photons s-1 m-2 .

extract_protocol:
Total RNA was extracted using Qiagen Plant Rneasy mini kit
Libraries were prepared according to Illumina's instructions (poly A enrichment)

treatment_protocol: Plants were illuminated for 10 min with 740 µmole photons s-1 m-2 white light (300-700nm)or 120 µmole photons s-1 m-2 red light (600-700nm)

tag: sample type

tag: repeat

value: red light

value: wild type

value: Leaves


title: hs_Sub1_RNAPII_abd


title: WR3

value: WT


title: WW2

value: white light


title: WN3

value: untreated


title: hs_Sub1_H3K27ac_abd


title: hs_Sub1_CTCF_glut


title: WN1


title: hs_Sub1_H3K4me2_abd


title: hs_Sub1_ATAC-seq_glut_rep2


title: WW3


title: FR2

value: rbohF

value: mutant


title: WR2


title: FW1


title: WW1


title: FR1


title: FN3


title: WN2


title: FW3


title: FN2


title: FW2


title: FR3


title: FN1


title: DW3

value: rbohD


title: DW2


title: DR1


title: BR2

value: phyB


title: DN3


title: DR2


title: DN2


title: BW3


title: BW2


title: DW1


title: DR3


title: BN2


title: BN1


title: DN1


title: BW1


title: BR3


title: BR1


title: BN3


title: allergy+asthma LL021

type: RNA

city: Munich

first: Ulrich

middle: M

last: Zissler

address: Biedersteiner Str. 29

department: Center of Allergy & Environment (ZAUM)

country: Germany

institute: Technical University of Munich & Helmholtz Center Munich

description:
allergy+asthma
induced sputum

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25µl 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 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Agilent.SingleColor.28004 microarray, Software GeneSpring 14.5; Threshold: 1.0, Logbase: 2; Normalization: Quantile; Baseline Transformation: None; Filtered on Expression (20.0-100.0); Filtered on Flags (Detected, Not Detected); T test unpaired , P<=:0.05, FC>=1.5

source_name: induced sputum

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 17 ng RNA using the One-Color Agilent Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, GER). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Induced sputum samples were processed and isolated cells were directly transferred into RNAcell protect reagent (Qiagen) and stored at -80°C until RNA extraction. Total RNA was extracted using RNeasy Mini Kit (Cat.-No. 74104, Qiagen, Hilden, Germany) with on-column DNase digestion (Cat.-No. 79254, DNase-Free DNase Set, Qiagen) for avoiding DNA contaminations {Zissler, 2016 #317}. RNA quantification was performed by ultraviolet–visible spectrophotometry (Nanodrop Technologies, Wilmington, DE, USA), for assessment of the RNA integrity by the RNA 6000 Nano Chip Kit with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: season

value: in season

tag: ait treatment

value: no


title: allergy+asthma LL066

description:
allergy+asthma
induced sputum


title: allergy+asthma JA035

description:
allergy+asthma
induced sputum

value: yes


title: allergic rhinitis JA033

description:
allergic rhinitis
induced sputum


title: allergic rhinitis JA022

description:
allergic rhinitis
induced sputum


title: allergic rhinitis JA015

description:
allergic rhinitis
induced sputum


title: allergic rhinitis JA014

description:
allergic rhinitis
induced sputum


title: allergic rhinitis LL015

description:
allergic rhinitis
induced sputum


title: allergy+asthma AM028

description:
allergy+asthma
induced sputum


title: allergy+asthma LL068

description:
allergy+asthma
induced sputum


title: allergic rhinitis JA031

description:
allergic rhinitis
induced sputum


title: healthy LL048

description:
healthy
induced sputum


title: allergy+asthma AM052

description:
allergy+asthma
induced sputum


title: allergic rhinitis JA021

description:
allergic rhinitis
induced sputum


title: allergy+asthma JA028

description:
allergy+asthma
induced sputum


title: allergy+asthma LL038

description:
allergy+asthma
induced sputum


title: allergic rhinitis LL060

description:
allergic rhinitis
induced sputum


title: allergy+asthma LL022

description:
allergy+asthma
induced sputum


title: allergic rhinitis JA025

description:
allergic rhinitis
induced sputum


title: allergic rhinitis JA026

description:
allergic rhinitis
induced sputum


title: allergy+asthma JA023

description:
allergy+asthma
induced sputum


title: allergic rhinitis LL011

description:
allergic rhinitis
induced sputum


title: F763, SPINAL, C, Stress, 7W

city: Baltimore

first: Evelina

last: Mocci

state: MD

address: 655 W Lombard S

department: PTSS

institute: SON

data_processing:
We used FastQC and Trimmomatic  tools for evaluating the quality of the sequences, next we used HISAT2  software to align the sequences to the reference Rattus norvegicus (Norway rat) genome assembly Rnor_6.0 (rn6) from Rat Genome Sequencing Consortium [GCA_000001895.4 GCF_000001895.5]. Finally, gene expression was estimated using HTSeq(18) which considers a gene as the union of all exons regardless of the isoform and excludes reads that overlap multiple genes
Genome_build: rn6
Supplementary_files_format_and_content: batch effect corrected expression data have been uploaded to https://nemoanalytics.org/p?s=2f41a962

source_name: spinal

extract_protocol:
RNA was extracted from 4 type of tissues, including blood, colon, spinal, and dorsal root ganglia (DRG) at one week (week 1) and seven weeks (week 7) after the induction of stress
Libraries were prepared with NEB Ultra II Directional Library Prep kits. Samples at week 1 were sequenced on Illumina HiSeq 4000 platform using a 150 bp paired-end run (2 ´ 150), while samples at week7 were run on Illumina NovaSeq 6000 using a 150 bp paired-end run as well

treatment_protocol:
treatment protocol for stress (SIH). During the two hours, rats were tilted at a 45-degree angle head up or head down in 15 min blocks alternating with 15 min blocks in the horizontal position. The day after the last restraint session was designated Day 1
Rats were restrained in Broome style rodent restrainers (4.8 cm diameter, 20 cm length) preventing movement for 2 hours per day for 4 consecutive days
treatment protocol for comorbid rats. Masseter muscle inflammation: One day prior to starting the stress protocol, CPH rats were briefly sedated with isoflurane, and CFA (SigmaAldrich, F5881; 150 mL per side, 1:1 in saline) was injected bilaterally into the masseter muscles. This protocol (CFA+stress) produces the comorbid pain condition. We previously reported that saline injection into the masseter muscle followed by stress was similar to stress alone and CFA injection without stress did not induce visceral hypersensitivity

tag: Sex

value: female

tag: time

value: spinal

tag: ID

tag: experimental group

value: SIH


title: allergy+asthma LL054

description:
allergy+asthma
induced sputum


title: allergy+asthma LL070

description:
allergy+asthma
induced sputum


title: F763, SC, LS, Stress, 7W

tag: tissue


title: allergic rhinitis LL024

description:
allergic rhinitis
induced sputum


title: F763, COLON, P, Stress, 7W

source_name: colon

value: colon


title: F762, SPINAL, TL, Stress, 7W


title: F763, SPINAL, TL, Stress, 7W


title: healthy LL045

description:
healthy
induced sputum


title: F762, SPINAL, C, Stress, 7W


title: allergic rhinitis LL044

description:
allergic rhinitis
induced sputum


title: allergy+asthma LL055

description:
allergy+asthma
induced sputum


title: F762, SC, LS, Stress, 7W


title: allergic rhinitis LL065

description:
allergic rhinitis
induced sputum


title: healthy LL037

description:
healthy
induced sputum


title: F763, DRG, Stress, 7W

source_name: DRG

value: DRG


title: allergic rhinitis LL058

description:
allergic rhinitis
induced sputum


title: healthy LL059

description:
healthy
induced sputum


title: allergy+asthma LL027

description:
allergy+asthma
induced sputum


title: F762, COLON, P, Stress, 7W


title: allergic rhinitis LL047

description:
allergic rhinitis
induced sputum


title: F762, DRG, Stress, 7W


title: healthy LL069

description:
healthy
induced sputum


title: healthy LL041

description:
healthy
induced sputum


title: F763, blood, Stress, 7W

source_name: blood

value: blood


title: F760, SPINAL, C, Stress, 7W


title: F760, SPINAL, TL, Stress, 7W


title: F760, COLON, P, Stress, 7W


title: healthy LL025

description:
healthy
induced sputum


title: F762, blood, Stress, 7W


title: F760, SC, LS, Stress, 7W


title: F760, DRG, Stress, 7W


title: F762, COLON, D, Stress, 7W


title: F759, SPINAL, TL, Naive, 7W

value: Naive


title: F759, DRG, Naive, 7W


title: F758, COLON, P, Naive, 7W


title: F760, COLON, D, Stress, 7W


title: F759, blood, Naive, 7W


title: F759, SPINAL, C, Naive, 7W


title: F758, DRG, Naive, 7W


title: F758, COLON, D, Naive, 7W


title: F759, COLON, P, Naive, 7W


title: F759, SC, LS, Naive, 7W


title: F757, COLON, P, Naive, 7W


title: F757, DRG, Naive, 7W


title: F757, SC, LS, Naive, 7W


title: F757, SPINAL, TL, Naive, 7W


title: allergy+asthma LL010

description:
allergy+asthma
induced sputum


title: F757, SPINAL, C, Naive, 7W


title: F757, COLON, D, Naive, 7W


title: F757, blood, Naive, 7W


title: healthy LL023

description:
healthy
induced sputum


title: F758, blood, Naive, 7W


title: F756, SPINAL, TL, Naive, 7W


title: F756, blood, Naive, 7W


title: F756, SC, LS, Naive, 7W


title: F756, COLON, P, Naive, 7W


title: F755, SPINAL, C, CPH, 7W

value: CPH


title: F755, SC, LS, CPH, 7W


title: F755, DRG, CPH, 7W


title: F754, DRG, CPH, 7W


title: F755, blood, CPH, 7W


title: F755, COLON, D, CPH, 7W


title: F754, SPINAL, C, CPH, 7W


title: F754, SC, LS, CPH, 7W


title: F756, SPINAL, C, Naive, 7W


title: F756, DRG, Naive, 7W


title: F754, COLON, P, CPH, 7W


title: F753, DRG, CPH, 7W


title: F753, COLON, D, CPH, 7W


title: F755, SPINAL, TL, CPH, 7W


title: F753, SPINAL, TL, CPH, 7W


title: F756, COLON, D, Naive, 7W


title: F752, SPINAL, TL, CPH, 7W


title: F754, blood, CPH, 7W


title: F753, COLON, P, CPH, 7W


title: F754, SPINAL, TL, CPH, 7W


title: F753, SC, LS, CPH, 7W


title: F753, SPINAL, C, CPH, 7W


title: F755, COLON, P, CPH, 7W


title: F754, COLON, D, CPH, 7W


title: F752, SPINAL, C, CPH, 7W


title: F753, blood, CPH, 7W


title: F763, COLON, D, Stress, 7W


title: F752, SC, LS, CPH, 7W


title: F752, blood, CPH, 7W


title: F752, COLON, P, CPH, 7W


title: F752, COLON, D, CPH, 7W


title: 1075-base_BLD_ADT

city: New Haven

first: Jun

last: Zhao

state: CT

address: 300 George Street

department: Pathology/Immunology

institute: Yale University

description:
1075_base_BLD_cite_matrix.mtx.gz
1075_base_BLD_cite_barcodes.tsv.gz
1075_base_BLD_cite_features.tsv.gz

library_source: other

data_processing:
Library strategy: CITE-seq
Raw sequencing reads were processed with cellranger v3.0.2 to generate the gene-barcode count matrix.
Count matrices from different samples were normalized, integrated and analyzed by Seurat v3.
Assembly: hg38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: protein

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated by Ficoll gradient with Sepmate. CSF cells were isolated by centrifuging whole CSF
Libraries were prepared using the 10X 3' V2 kit

tag: disease status

value: HIV

value: Blood

tag: cell type

value: Peripheral blood mononuclear cells

value: ART


title: 1075-base_BLD_GEX

library_source: transcriptomic single cell


title: 1075_base_CSF_ADT

description:
1075_base_CSF_cite_matrix.mtx.gz
1075_base_CSF_cite_barcodes.tsv.gz
1075_base_BLD_cite_features.tsv.gz

source_name: cerebrospinal fluid cells

value: CSF

value: cerebrospinal fluid cells


title: 1075_base_CSF_GEX

description:
1075_base_CSF_cite_matrix.mtx.gz
1075_base_CSF_cite_barcodes.tsv.gz
1075_base_CSF_cite_features.tsv.gz


title: SUPB15_nonadh-2_RNA-seq

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

description: Nonadherent leukemia cells in coculure with hTERT-BMSC

data_processing:
Bulk RNA-seq were mapped to the human genome using STAR. Gene expression was quantified using RSEM.
scRNA-seq was processed using Seurat R package.
Assembly: hg19
Supplementary files format and content: FPKM values for bulk RNA-seq and Seurat object in RDS file for scRNA-seq

source_name: cell line

growth_protocol: Cell lines and primary leukemia cells were grown in Minimum Essential Medium Eagle supplemented with 10% FBS, 50 U/ml penicillin, 50 ug/ml streptomycin and 2 mM L-glutamine in the presenc or in the absence of stromal cells including  hTERT-BMSC and BM-MSC.

extract_protocol:
The total RNAs from leukemia only, the Nonadh and Adh leukemia cells were isolated using Qiagen kit
Bulk RNA-seq library construction for cell lines were performed using the Illumina TruSeq Stranded Total RNA library preparation kit and bulk RNA-seq library construction for patient samples were performed using the low-input RNA library preparation kit (NuGen Ovation V2). scRNA-seq library construction were performed using Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x GENOMICS)

treatment_protocol: no treatment

value: leukemia

tag: leukemia cell state in coculture with msc

value: nonadh

tag: leukemia subtype

tag: cell line name or comp bio id

tag: cocultured cells

value: hTERT-BMSC


title: SUPB15_nonadh-3_RNA-seq


title: NALM6_scRNA-seq

description: leukemia only

value: only

value: DUX/ERG


title: Adh NALM6_BM-MSC_scRNA-seq

description: Adherent leukemia with BM-MSC

source_name: cell line and primary cells

value: leukemia and BM-MSC

value: adh

value: DUX/ERG and N/A

value: NALM6 and BM-MSC

value: BM-MSC


title: SUPB15_adh-1_RNA-seq

description: Adherent leukemia cells in coculure with hTERT-BMSC


title: 697_nonadh-1_RNA-seq


title: 697_adh-1_RNA-seq


title: SUPB15_adh-3_RNA-seq


title: SUPB15_nonadh-1_RNA-seq


title: Nonadh NALM6_scRNA-seq

description: Nonadherent leukemia cells in coculure with BM-MSC


title: SUPB15_only-3_RNA-seq

description: leukemia only


title: SUPB15_only-2_RNA-seq

description: leukemia only


title: 697_adh-3_RNA-seq


title: F752, DRG, CPH, 7W

value: female

value: DRG

value: CPH


title: SUPB15_adh-2_RNA-seq


title: 697_adh-2_RNA-seq


title: SUPB15_only-1_RNA-seq

description: leukemia only


title: 697_nonadh-3_RNA-seq


title: 697_nonadh-2_RNA-seq


title: 697_only-2_RNA-seq

description: leukemia only


title: 697_only-1_RNA-seq

description: leukemia only


title: NC-1

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (1.26.0).
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM values for each sample

source_name: AGS

growth_protocol: The human gastric cancer cell line AGS was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The gastric cancer cell line was cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 ℃ in 5% CO2.

extract_protocol:
Gastric cancer cells were grown in 6-well plates and transfected with NC siRNAs and the ILF2/ILF3-targeted siRNAs. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: AGS cells were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with NC siRNAs and the PRSS23-targeted siRNAs (final concentration, 50 nM) by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

tag: cell line

value: AGS

value: gastric cancer cell

tag: treatment

value: negative control siRNA


title: PRSS23-siRNA-2

value: PRSS23 siRNA#2


title: PRSS23-siRNA-1

value: PRSS23 siRNA#1


title: BM-MSC_scRNA-seq

description: BM-MSC only

source_name: primary cells


title: 697_only-3_RNA-seq

description: leukemia only

value: leukemia


title: NALM6_adh-3_RNA-seq

value: hTERT-BMSC


title: S. baicalensis_Root_RNAseq

city: Xi'an

first: Bo

last: Cao

state: Shaanxi

address: 620 West Chang'an Road, Changan District

institute: Shaanxi Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Scutellaria baicalensis Georgi whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, et al., Nat Biotech, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Scutellaria baicalensis

source_name: root

extract_protocol:
Total RNA was extracted from each collected tissues using CTAB RNA isolation method (Chang et al. 1993). Three replicates were sampled and mixed for RNA preparation. RNA samples were treated with RNase-free DNase (TaKaRa, Dalian, China) to eliminate genomic DNA contamination. Degradation of RNA was monitored on 1% agarose gels. Purity of RNA was checked using Nano Photometer spectrophotometer (Implen, CA, USA). The concentration of RNA was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). The integrity of RNA was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total of 16.5 μg RNA was equally pooled from the collected tissues for cDNA library preparation. Library quality assessment, assembling, clustering and sequencing were performed following the method of Chen et al. (Chen et al. 2014).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: plant

value: Scutellaria baicalensis Georgi

tag: genotype

value: WT

tag: collection time

value: in October

value: root


title: NALM6_adh-1_RNA-seq

value: adh

value: DUX/ERG


title: MHH-CALL2_nonadh-2_RNA-seq

value: nonadh

value: Hypodiploid


title: MHH-CALL2_adh-2_RNA-seq


title: NALM6_nonadh-1_RNA-seq


title: NALM6_nonadh-3_RNA-seq


title: NALM6_only-1_RNA-seq

description: leukemia only

value: only


title: MHH-CALL2_nonadh-3_RNA-seq


title: NALM6_only-3_RNA-seq

description: leukemia only


title: NALM6_adh-2_RNA-seq


title: MHH-CALL2_nonadh-1_RNA-seq


title: NALM6_only-2_RNA-seq

description: leukemia only


title: MHH-CALL2_adh-3_RNA-seq


title: MHH-CALL2_adh-1_RNA-seq


title: REH_adh-1_RNA-seq

value: REH


title: MHH-CALL2_only-2_RNA-seq

description: leukemia only


title: MHH-CALL2_only-3_RNA-seq

description: leukemia only


title: NALM6_nonadh-2_RNA-seq


title: REH_only-2_RNA-seq

description: leukemia only


title: REH_nonadh-1_RNA-seq


title: MHH-CALL2_only-1_RNA-seq

description: leukemia only


title: REH_nonadh-2_RNA-seq


title: REH_only-3_RNA-seq

description: leukemia only


title: REH_nonadh-3_RNA-seq


title: HIV-1_8 [DL5939]

city: Lund

first: Angelica

last: Palm

address: Baravägen 18

country: Sweden

institute: Lund University

description: Performed according to the Illumina HT-12 manufactures instructions

scan_protocol: Standard Illumina iScan N240 scanning protocol scan setting file: Direct Hyb

data_processing: The data were normalised using quantile normalisation with BASE

label: biotin

source_name: HIV-1 infected

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

extract_protocol: PAXgene Blood RNA kit, Qiagen

value: HIV-1 infected

value: Treatment naïve

tag: gender

value: Male

tag: age

value: Whole blood


title: HIV-2_5 [DL2224]

source_name: HIV-2 infected

value: HIV-2 infected


title: Negative 8 [DL5239]

source_name: HIV negative

value: HIV negative


title: HIV1+2_8 [DL5775]

source_name: HIV-1 and HIV-2 dual infected

value: HIV-1 and HIV-2 dual infected


title: HIV1+2_7 [DL4276]


title: HIV-2_4 [DL5390]


title: HIV-1_7 [DL3806]


title: REH_only-1_RNA-seq

description: leukemia only

value: leukemia


title: HIV1+2_5 [DL3203]


title: Negative 7 [DL6539]


title: Negative 5 [DL2431]


title: HIV-1_5 [DL5759]


title: HIV-2_7 [DL3111]


title: Negative 6 [DL3143]


title: HIV-2_6 [DL2671]


title: HIV-1_6 [DL3710]


title: HIV-2_2 [DL2386]


title: HIV1+2_6 [DL5211]


title: HIV-2_3 [DL3941]


title: HIV-1_2 [DL2066]


title: HIV1+2_4 [DL3185]


title: HIV-1_4 [DL3865]


title: HIV-1_3 [DL3065]


title: HIV1+2_3 [DL6887]


title: shNC_2

city: Guangzhou

first: Ruiqing

last: Yu

state: Guangdong

address: 56 Ling Yuan Xi Road

institute: Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Macrophage

extract_protocol:
Total RNA was extracted from RAW264.7 cells using 1ml RNAzol per sample and purified according to the manufacturer’s instructions.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: RAW264.7 cells

value: LPS-induced for 24 h

value: Contorl


title: shNC_1


title: shMettl3_1

value: Mettl3 Knockdon


title: shMettl3_2


title: HIV-1_1 [DL3860]


title: HIV1+2_2 [DL6697]


title: HIV1+2_1 [DL2381]


title: Negative 4 [DL3580]


title: Negative_3 [DL3483]


title: HIV-2_1 [DL4397]


title: RM249_V2_Live

city: San Francisco

first: Zev

last: Gartner

state: CA

address: 600 16th St. Room GH-N512E Box 2280

department: Pharmaceutical Chemistry

institute: University of California San Francisco

description:
Sample name: Set 17
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds

data_processing:
Cell Ranger (10x Genomics V5.0.0) was used to align sequences, filter data and count unique molecular identifiers (UMIs). Data were mapped to the human reference genome GRCh37 (hg19).
For samples in the same batch run across multiple 10X lanes, the cellranger aggr pipeline (10X Genomics V5.0.0) was used to normalize read depth across droplet microfluidic lanes
For MULTI-seq barcode library pre-processing, raw barcode FASTQs were converted to barcode UMI count matrices as described in McGinnis et al., 2019.
For multiplexed samples, barcode UMI count matrices were used to classify cells using the MULTI-seq classification suite. To classify cells that were identified as unlabeled by MULTI-seq, we used the SoupOrCell pipeline (Heaton et al., 2020) to assign cells to different individuals based on single nucleotide polymorphisms (SNPs).
Cell type identification and data integration was performed using the Seurat package (version 3.1.5) in R.
Assembly: hg19
Supplementary files format and content: RDS files containing: 1) matrix tables with raw gene counts for each cell, 2) matrix tables with raw MULTIseq barcode counts (for multiplexed samples) for each cell, 3) sample metadata tables listing samples and relevant information (e.g. reproductive history, BMI, etc.), 4) a processed, integrated Seurat object for all reduction mammoplasty samples.
RM.raw.counts.matrix.rds (RDS - gene counts matrix table)
KTB.raw.counts.matrix.rds (RDS - gene counts matrix table)
RM.barcode.counts_Batch3_Live.rds (RDS - barcode counts matrix table)
RM.barcode.counts_Batch3_Epithelial.rds (RDS - barcode counts matrix table)
RM.barcode.counts_Batch4_Live.rds (RDS - barcode counts matrix table)
RM.barcode.counts_Batch4_Epithelial.rds (RDS - barcode counts matrix table)
KTB.barcode.counts.rds (RDS - barcode counts matrix table)
RM.metadata.rds (RDS - metadata table)
KTB.metadata.rds (RDS - metadata table)
breast.data.rds (RDS - processed seurat object)

source_name: reduction mammoplasty sample

extract_protocol:
Tissue was dissociated mechanically and enzymatically, collected after serial filtration to obtain epithelial-enriched tissue fragments, and cryopreserved until use. The day of sorting, the 150 µm fraction, or total banked material for the KTB samples, was thawed and digested to single cells by trituration in trypsin followed by dispase. For multiplexed experiments, samples were labeled by LMO MULTIseq barcodes. Single cells were sorted using the indicated sort gates.
Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide v2 or 10X Chromium Single Cell 3' Reagent Kit User Guide v3. For multiplexed samples, library preparation was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C and a MULTI-seq library preparation protocol (McGinnis et al.).

value: breast

value: untreated

tag: 10x chemistry

tag: sort gate

value: Live

value: primary breast cells

tag: multi-seq reagent

tag: number of multiplexed samples

tag: sample type

value: Live/singlet sort gate


title: RM263_V2_Live

description:
Sample name: Set 13
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds

tag: tissue

tag: cell type


title: Negative_2 [DL3200]

tag: disease status


title: RM273_V2_Basal

description:
Sample name: Set 9
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds

value: Basal

value: Basal/myoepithelial sort gate


title: RM282_V2_Luminal

description:
Sample name: Set 11
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds

value: Luminal

value: Luminal sort gate


title: Negative_1 [DL2478]

value: Treatment naïve

value: Male

value: Whole blood


title: RM282_V2_Live

description:
Sample name: Set 10
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM273_V2_Luminal

description:
Sample name: Set 8
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM248_V2_Live

description:
Sample name: Set 16
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM222_V2_Live

description:
Sample name: Set 14
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM273_V2_Live

description:
Sample name: Set 7
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM234_V2_Live

description:
Sample name: Set 15
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM272_V2_Basal

description:
Sample name: Set 6
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM282_V2_Basal

description:
Sample name: Set 12
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM264_V2_Basal

description:
Sample name: Set 3
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM272_V2_Luminal

description:
Sample name: Set 5
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM264_V2_Luminal

description:
Sample name: Set 2
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM264_V2_Live

description:
Sample name: Set 1
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: RM272_V2_Live

description:
Sample name: Set 4
RM.raw.counts.matrix.rds
RM.metadata.rds
breast.data.rds


title: WT HSCs, B

city: Frederick

first: Kristbjorn

middle: Orri

last: Gudmundsson

address: 1050 Boyles St.

department: MCGP

institute: NCI

description: WT 2

data_processing:
The sample was quantified and sequenced on the Illumina HiSeq 2500 sequencer.
The HiSeq Real Time Analysis software (RTA 1.18) was used for processing image files, the Illumina CASAVA_v1.8.4 was used for demultiplex and converting binary base calls and qualities to fastq format.
The sequencing reads were trimmed for adapters and low-quality bases using Trimmomatic (version 0.30). The trimmed reads were aligned to mouse mm9 reference genome (NCBIM37 /UCSC mm9) and Ensembl annotation version 67 using TopHat_v2.0.8 software.
Quantification was carried out with RSEM using the transcriptome bam file created by STAR.
Differentially expressed genes (DEGs) were analyzed with Ingenuity Pathway Analysis (IPA) software (Ingenuity Systems, Inc., Redwood City, CA, USA) and Gene Set Enrichment Analysis (GSEA, Broad Institute, Cambridge, MA, USA).
Assembly: mm9
Supplementary files format and content: Normalized count matrix file

source_name: WT HSCs

extract_protocol: RNeasyTM Micro Kit (Qiagen, 74004) was used to generate high quality RNA

treatment_protocol: RNA was purified from pooled HSCs isolated from Mx1-Cre; Id2+/+ (N=14) or Mx1-Cre; Id2Fl/Fl mice (N=15) by flow cytometry with LSK FLT3- CD48- CD150+ markers, 2 weeks after pIpC treatment in 2 separate experiments.

value: HSCs

value: WT


title: ID2Δ/Δ HSCs, A

description: ID2KO 1

source_name: ID2Δ/Δ HSCs


title: Control blood rRNA removed RNA-seq N7

city: Wuhan

first: Yong

last: Wu

address: Gongnongbing road 89#

institute: Wuhan Mental Health Center

data_processing:
For rRNA removed library sequencing data, the raw sequencing reads were firstly processed to remove sequencing adapters and low-quality reads using Trimmomatic (version 0.39) with default parameters. For mRNA and lncRNA quantification, the clean reads were mapped to human reference genome, GRCh38 using hisat2 (version 2.2.1) and then sorted by samtools (version 0.11.0) with sort function by genome position. The featureCounts (version 2.0.1) was used to count reads mapped to specific meta-features (mRNA or lncRNA). Since the gene annotation file from GENCODE only contained part of lncRNAs, we downloaded the lncRNA annotation file from NONCODE database (http://www.noncode.org/) in addition, and combined all the lncRNAs from the two databases.  We quantified the circRNAs expression using the CIRIquant (version 1.1.1) process. Briefly, the clean reads were first mapped to human reference genome using bwa (version 0.7.17). The back splice junction reads were identified and quantified by CIRI2 (version 2.0.6) and CIRIquant respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: VstNormalized_matrix_of_mRNAlncRNAcircRNA_all_Samples.csv: csv file includes normalized values by DESeq2 vst method for each mRNA sample.

source_name: Blood

extract_protocol:
The total RNA was extracted from the blood using the PAXgene® Blood RNA Kit (QIAGEN, Hombrechtikon, Switzerland) according to the handbook’s instructions
For the rRNA removed library, a total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Ribosomal RNA was removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA). For the small RNA library, a total of 2 μg total RNA isolated from each sample using NEBNext® Multiplex Small RNA Library Prep Set For Illumina® (NEB, USA) according to the manufacturer’s instruction.

value: blood

tag: disease state

value: Control

tag: bmi

value: male


title: Control blood rRNA removed RNA-seq N5


title: ID2Δ/Δ HSCs, B

description: ID2KO 2


title: Control blood rRNA removed RNA-seq N3


title: Control blood rRNA removed RNA-seq N6


title: NA_FD4

city: Otsu

first: Noriko

last: Nishikura

state: Shiga

address: Seta Tsukinowa

department: Department of Anatomy and Cell Biology

country: Japan

institute: Shiga University of Medical Science

data_processing:
Single read Illumina next seq (FC 404-2005, 75 bp reads) was run on an Illumina NextSeq 500.
For trimming adaptor sequence, all FASTQ files were processed on a Galaxy server (https://usegalaxy.org/) with Trimmomatic (Galaxy version 0.36.3).
RNA STAR Gapped-read mapper for RNA-seq data (Galaxy version 2.5.2b-0) mapped each read on the reference rat genome (Rat Jul. 2014 (RGSC 6.0/rn6)).
The number of reads per gene was counted by a gene model (UCSC Main on Rat: RefGene genome) and the built-in HTseq-count tools.
Differential gene expression analysis was performed using DESeq2.
Genome_build: Rat Jul. 2014 (RGSC 6.0/rn6)
Supplementary_files_format_and_content: Tab-separated values (tsv) files include the number of reads per gene for each sample.  STAR_*.tsv files report raw counts of sequencing reads.  *STAR.counts_padj.tsv files report normalized abundance measurements output from DESeq.

source_name: nucleus accumbens

extract_protocol:
The prefrontal cortex and nucleus accumbens were dissected and collected from brain sections. Tissue samples were placed in TRIzol (Invitrogen) and homogenized with a stainless-steel ball (AS ONE), using a tissue disrupter (TAITEC µT-12) at 1800 revolutions per minute for 1 min. Total RNA was purified from the supernatant using DNase (Qiagen) and a MinElute Cleanup kit (Qiagen), according to the TRIzol protocol.
An RNA integrity number greater than 8.3 was used for the RNA-seq analysis. NEBNext® Poly(A) mRNA magnetic isolation module (NEB) and NEBNext® UltraTM RNA Library prep kit for Illumina® (NEB) were used for polyA enrichment and RNA library prep. Each sample, labeled with the NEBNext® Index primer for Illumina® (NEB), was pooled (0.05 nM each, total 20 samples).
Single read Illumina next seq (FC 404-2005, 75 bp reads) was run on an Illumina NextSeq 500.

tag: experimental perturbation

value: Rat fed low-iron diet during age 21-39 days old

tag: developmental stage

value: Sampling at 13 weeks old

tag: strain

value: nucleus accumbens


title: Control blood rRNA removed RNA-seq N1


title: Control blood rRNA removed RNA-seq N4


title: WT HSCs, A

description: WT 1

tag: genotype


title: Control blood rRNA removed RNA-seq N2


title: NA_FD3


title: NA_FD1


title: NA_C5

value: Rat fed standard AIN-93G diet during age 21-39 days old


title: NA_C3


title: NA_FD5


title: OUD blood rRNA removed RNA-seq H4

value: OUD


title: OUD blood rRNA removed RNA-seq H5


title: NA_FD2


title: NA_C1


title: FC_FD5

source_name: prefrontal cortex

value: prefrontal cortex


title: FC_FD4


title: OUD blood rRNA removed RNA-seq H7


title: 25729

type: genomic

city: Newcastle upon Tyne

first: Ed

last: Schwalbe

address: Ellison Place

department: Applied Sciences

country: United Kingdom

institute: Northumbria University

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridised to Ilumina Infinium MethylationEPIC Beadchips using standard Illumina protocol

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

data_processing: arrays were imported and quality control performed using minfi

label: Cy5 and Cy3

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted and purified from ALL samples using standard extraction protocols

tag: cohort

value: IGMYC

value: D

value: IG-MYC rearranged ALL - Heavy chain


title: OUD blood rRNA removed RNA-seq H6

tag: gender


title: 30675


title: NA_C2


title: NA_C4


title: OUD blood rRNA removed RNA-seq H1

tag: age


title: 30728


title: FC_FD2


title: OUD blood rRNA removed RNA-seq H2


title: FC_FD3


title: BMDE_Af_co_culture_rep2

city: Erlangen

first: David

last: Voehringer

address: Wasserturmstrasse 3-5

department: Department of Infection Biology

institute: University Clinic Erlangen

data_processing:
Conversion raw data to reads (bcl2fastq v2.17)
Trimmed of adapters and discarded reads < 60bp (cutadapt v1.18)
Determined read quality (fastqc v0.11.8)
Aligned to GRCm38 with GENCODE annotation M23 (STAR v2.6.1c). A.fumigatus genome ASM265 was added to catch and remove Af reads.
Quality check (RNAseQC v2.3.4)
Read counts for non overlapping exons were generated (samtools v1.8, subread v1.6.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Dietschmann_raw_counts.txt, Dietschmann_et_al_diff_expr_and_norm_counts.xlsx

source_name: bone marrow derived eosinophils (BMDE)

growth_protocol: Bone marrow derived eosinophils (BMDE) were generated based on a published protocol (Dyer et al. J Immunol. 2008). Briefly, mouse bone marrow cells from femurs and tibiae were subjected to RBC lysis and adjusted to 10^6/ml in bone marrow medium (BMM), containing 20% FCS, 1% non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin, 19.25 μM 2-mercaptoethanol (all Thermo Fisher Scientific, Waltham, MA) and 25 mM HEPES (Carl Roth, Karlsruhe, Germany) in RPMI 1640 (PAN-Biotech, Aidenbach, Germany). For the first four days recombinant mouse SCF and FLT3L (Peprotech, Rocky Hill, NJ) were added to the culture (both 100 ng/ml) and afterwards replaced by recombinant mouse IL-5 (R&D Systems, Minneapolis, MN) (10 ng/ml) until day 14, with medium including fresh cytokine exchanged by half every two days from day 4 on. On day 14 eosinophil culture purity was usually above 90%, assessed by expression of SIGLEC-F and measured via flow cytometry. Bone marrow cells of BALB/c mice were used for BMDE generation.

extract_protocol:
RNA was isolated with the total RNA isolation kit (Fluka, Sigma-Aldrich). 75 mM DTT was added to the lysis buffer to prevent RNA degradation. Samples were treated with RNAse free DNAse set (Qiagen) and RNA integrity was determined with a Bioanalyzer instrument (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Kit (Illumina, San Diego, CA) was used for cDNA library preparation. Libraries were 96 bp single-end sequenced on a HiSeq2500 platform (Illumina).
TruSeq Stranded mRNA Kit (Illumina)

treatment_protocol: Af conidia (ATCC 46645 WT strain) were pre-grown for 5.5h in RPMI 1640. The medium was removed and eosinophils were added at a conidia-eosinophil ratio of 2:1 and 10 ng/mL rmIL-5. After 6h co-cultivation RNA was isolated.

value: BALB/c

value: bone marrow derived eosinophils (BMDE)

tag: growth protocol

value: Co-culture BMDE and Aspergillus fumigatus


title: FC_C4


title: FC_C3


title: 30280_H


title: ONS-76_R_N_2

city: Marseille

first: MANON

last: CARRE

address: 27 boulevard Jean Moulin

department: Faculté de Pharmacie

country: France

institute: CRCM

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed using cutadapt version 1.10 in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20), reads shorter than 40 bases were discarded for further analysis.
Reads mapping to rRNA were discarded (this mapping was performed using bowtie version 2.2.8).
Reads were mapped onto the hg38 assembly of human genome using STAR version 2.5.3a.
Gene expression was quantified using htseq-count version 0.6.1p1 and gene annotations from Ensembl release 99.
Genome_build: hg38
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.

source_name: cerebellum

growth_protocol: ONS-76 cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum and 1% penicillin-streptomycin. Cells were maintained at 37°C and 5% CO2

extract_protocol:
RNAs were extracted with RNeasy Plus Mini kit (Qiagen), including genomic DNA purification columns, according to the protocol supplied by the manufacturer
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: To establish β-blocker resistant cell lines, ONS-76 cells were exposed to increasing doses of propranolol (from 10 to 200µM), carvedilol or nebivolol (from 2.5 to 20 µM), over 3 to 4 months.

value: Human medulloblastoma cell line

tag: cell line

tag: treatment

value: Treated with nebivolol

tag: treatment sensitivity

value: Resistant to nebivolol


title: BMDE_Af_co_culture_rep1


title: 4564_L

value: IG-MYC rearranged ALL - Light chain


title: FC_C2


title: CUT&RUNseq_H3K36me3_K27me3_MpPp_hermaphrodite_germline_rep1

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

description:
CRseq_rawCounts.matrix.txt
CRseq_zscores.matrix.txt

data_processing:
library strategy: Cut&Run
Libraries sequenced on the NovaSeq platform were sequenced and demultiplexed at the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries sequenced on the NextSeq platform were sequenced and demultiplexed at UC Santa Cruz.
Illumina reads longer than 50 bp were trimmed to 50 bp. 50 bp reads were mapped to the Bristol (N2) genome version WS220 using tophat2 (v2.1.1) with bowtie2 (2.3.5.1).
For RNA-seq samples, R1 and R2 reads were mapped 3 ways: as single-end reads allowing 1 mismatch (mm1), as single-end reads allowing 0 mismatches (mm0) and as paired-end reads allowing 1 mismatch using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25.   For CUT&RUN samples, R1 and R2 reads were mapped 2 ways: as single-end reads allowing 1 mismatch (mm1) and as single-end reads allowing 0 mismatches (mm0).  For all samples, reads per transcript or gene body were counted using htseq and a gtf file specifying transcript/gene body (union of all exons) or SNP locations per transcript/gene body.
To determine RPKM for all reads that mapped to a transcript or gene body,  only the first mate (R1) of paired-end Illumina reads that mapped allowing 1 mismatch was used. RPKM was calculated by first scaling total reads used to 1 million, then dividing by transcript length in kb (union of all exons).   To determine allele-specific transcript and gene body reads, both mates of paired-end reads were mapped as single-end reads from which only SNP-containing reads were used for further SNP analysis. Reads that emanated from the sperm allele (N2 background) were SNP-containing reads that mapped to the N2 genome when allowing 0 mismatches. Reads that emanated from the oocyte allele (CB4856 background) were SNP-containing reads that mapped to the N2 genome when allowing 1 mismatch but not 0 mismatches. RPSM (reads per SNP per million) was calculated by scaling total SNP-containing reads to 1 million, then dividing transcript or gene body SNP-containing reads (reads per million) by the number of SNP locations in the transcript or gene body (per SNP).  To perform differential gene expression analysis, reads that were mapped paired-end using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25 were used to calculate significantly misexpressed genes using the differential analysis program DESeq2 (1.22.2).
Assembly: ce10
Supplementary files format and content: RNAseq_rawCounts.matrix.txt and CRseq_rawCounts.matrix.txt  are matrices containing raw gene-level counts over exons annotated in a Ensembl ce10 (WS220) GTF file. Counts were generated using HTseq from 1) R1 and R2 reads mapped as pairs for downstream differential expression analysis, 2) from R1 reads mapped as single end reads for RPKM calculations or 3) R1 and R2 reads mapped as single end reads and filtered for reads overalpping SNPs between Bristol (N2) and Hawaii (CB4856) genomes. RNAseq_DEGs_RPKM_RSPM.matrix.txt is a matrix containing log2 fold changes and adjusted p values generated with DESeq as well as transcript reads per kilobase per million (RPKM) and gamete-specific transcript reads per SNP per million SNPs (RSPM). CRseq_zscores.matrix.txt is a matrix containing H3K27me3 and H3K36me3 zscores calculated over exons and gamete-specific zscores.

organism: Caenorhabditis elegans

source_name: distal half of hermaphrodite germline

growth_protocol: All strains were maintained on nematode growth medium (NGM) agar plates seeded with a lawn of Escherichia coli OP50 and maintained at 20˚C except for fem-2 containing strains, which were maintained at 15˚C. To generate females, fem-2 containing strains were raised at 25˚C until they developed to the L4 stage

extract_protocol:
For germline collections, worms were selected at the L4 stage and allowed to develop 1 day at 20˚C to reach the 1st day of adulthood. Worms were decapitated to extrude the germlines. The distal halves of the germlines were collected by cutting the germline at the bend and transferring to ice-cold TRIzol reagent to reach a total of 30-50 germlines. Biological replicates of germlines in TRIzol were stored at -80˚C for later use in RNA sequencing library preparation.  2-4 biological replicates were collected for each genotype.   For L1 collections, gravid mothers were allowed to lay eggs overnight at 20˚C. The next day, late-stage embryos along with some bacteria were transferred to 50 uL drops of S Basal on gelatin chrom alum-coated slides. After 2 hours at room temperature, newly hatched L1 larvae were transferred to ice-cold TRIzol. This process of transferring embryos to S basal, incubating 2 hours, and transferring newly hatched L1 larvae to TRizol was repeated throughout the day to reach a final collection of ~100 newly hatched larvae per replicate. Biological replicates of L1 larvae in TRIzol were stored at -80˚C for later use in RNA sequencing library preparation. 3 biological replicates were collected for each genotype.
Libraries were prepared according to manufacturer's instructions.  For transcript analysis, RNA was polyA-selected (NEB #E7490) and libraries prepared (NEB #E7530). For CUT&RUN library preparation, DNA associated with H3K27me3 and H3K36me3 was collected via CUT&RUN method (Skene and Henikoff 2017; Skene et al. 2018) and libraries prepared (Tecan Genomics #0344NB-32).

tag: mother genotype

value: fem-2(b245ts) (CB4856 background)

tag: father genotype

value: mes-3(bn35)/hT2-GFP; him-8(e1489) (N2 background)

tag: molecule subtype

value: DNA associated with H3K36me3


title: only_BMDE_rep2

tag: cell type

value: only BMDE


title: FC_C1

value: Rat fed standard AIN-93G diet during age 21-39 days old

value: Sampling at 13 weeks old

tag: tissue


title: only_BMDE_rep1


title: FC_C5

value: prefrontal cortex


title: 27424_L


title: 5892_H

value: R


title: CUT&RUNseq_H3K36me3_K27me3_MpPm_hermaphrodite_germline_rep1

value: mes-3(bn35); him-8(e1489) (N2 background)


title: 29785_L

value: D


title: CUT&RUNseq_H3K27me3_K27me3_MpPm_hermaphrodite_germline_rep1

value: DNA associated with H3K27me3


title: 4352_H

value: IG-MYC rearranged ALL - Heavy chain


title: 30279_H


title: ONS-76_R_C_3

value: Treated with carvedilol

value: Resistant to carvedilol


title: RNAseq_K27me3_MpPp_L1_larvae_rep2

description:
RNAseq_rawCounts.matrix.txt
RNAseq_DEGs_RPKM_RSPM.matrix.txt

data_processing:
Libraries sequenced on the NovaSeq platform were sequenced and demultiplexed at the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries sequenced on the NextSeq platform were sequenced and demultiplexed at UC Santa Cruz.
Illumina reads longer than 50 bp were trimmed to 50 bp. 50 bp reads were mapped to the Bristol (N2) genome version WS220 using tophat2 (v2.1.1) with bowtie2 (2.3.5.1).
For RNA-seq samples, R1 and R2 reads were mapped 3 ways: as single-end reads allowing 1 mismatch (mm1), as single-end reads allowing 0 mismatches (mm0) and as paired-end reads allowing 1 mismatch using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25.   For CUT&RUN samples, R1 and R2 reads were mapped 2 ways: as single-end reads allowing 1 mismatch (mm1) and as single-end reads allowing 0 mismatches (mm0).  For all samples, reads per transcript or gene body were counted using htseq and a gtf file specifying transcript/gene body (union of all exons) or SNP locations per transcript/gene body.
To determine RPKM for all reads that mapped to a transcript or gene body,  only the first mate (R1) of paired-end Illumina reads that mapped allowing 1 mismatch was used. RPKM was calculated by first scaling total reads used to 1 million, then dividing by transcript length in kb (union of all exons).   To determine allele-specific transcript and gene body reads, both mates of paired-end reads were mapped as single-end reads from which only SNP-containing reads were used for further SNP analysis. Reads that emanated from the sperm allele (N2 background) were SNP-containing reads that mapped to the N2 genome when allowing 0 mismatches. Reads that emanated from the oocyte allele (CB4856 background) were SNP-containing reads that mapped to the N2 genome when allowing 1 mismatch but not 0 mismatches. RPSM (reads per SNP per million) was calculated by scaling total SNP-containing reads to 1 million, then dividing transcript or gene body SNP-containing reads (reads per million) by the number of SNP locations in the transcript or gene body (per SNP).  To perform differential gene expression analysis, reads that were mapped paired-end using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25 were used to calculate significantly misexpressed genes using the differential analysis program DESeq2 (1.22.2).
Assembly: ce10
Supplementary files format and content: RNAseq_rawCounts.matrix.txt and CRseq_rawCounts.matrix.txt  are matrices containing raw gene-level counts over exons annotated in a Ensembl ce10 (WS220) GTF file. Counts were generated using HTseq from 1) R1 and R2 reads mapped as pairs for downstream differential expression analysis, 2) from R1 reads mapped as single end reads for RPKM calculations or 3) R1 and R2 reads mapped as single end reads and filtered for reads overalpping SNPs between Bristol (N2) and Hawaii (CB4856) genomes. RNAseq_DEGs_RPKM_RSPM.matrix.txt is a matrix containing log2 fold changes and adjusted p values generated with DESeq as well as transcript reads per kilobase per million (RPKM) and gamete-specific transcript reads per SNP per million SNPs (RSPM). CRseq_zscores.matrix.txt is a matrix containing H3K27me3 and H3K36me3 zscores calculated over exons and gamete-specific zscores.

source_name: mixed sex L1 larvae


title: 10787_H


title: ONS-76_R_C_2

value: Human medulloblastoma cell line


title: 26683_L


title: 30454_L


title: RNAseq_K27me3_MpPp_L1_larvae_rep1


title: 30452_L


title: RS-1

city: Jerusalem

first: Eli

last: Pikarsky

address: Ein Karem

department: The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University-Hadassah Medical School

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the mouse genome (GRCm38) using STAR  v2.4.2a
Counting proceeded over genes annotated in Ensembl release 83, using htseq-count (intersection-strict mode)
Normalization and differential expression was performed using DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed file include raw counts

source_name: Testis

extract_protocol:
Germ cells were sorted using Aria 3 from transgenic mice Stracre-GAG-tdTomato (C57BL/5) background. RNA was isolated using Qiagen mini kit (74104). Samples were treated with DNAse.
Libraries were constructed from fragmented DNA while performing end repair, A- base addition, adapter ligation and PCR amplification steps with SPRI beads cleanup in between steps. Indexed samples were pooled and sequenced in an Illumina HiSeq 2500 machine in a single read mode.


title: ONS-76_R_C_1


title: RNAseq_K27me3_MpPm_L1_larvae_rep3


title: RNAseq_K27me3_MpPm_L1_larvae_rep2


title: RS-2


title: ONS-76_R_N_1

value: Treated with nebivolol

value: Resistant to nebivolol


title: RNAseq_K27me3_MpPm_L1_larvae_rep1

value: fem-2(b245ts) (CB4856 background)


title: PD-3


title: 30609_H


title: ONS-76_R_P_3

value: Treated with propranolol

value: Resistant to propranolol


title: RNAseq_K27me3_MpPp_L1_larvae_rep3

value: mes-3(bn35)/hT2-GFP; him-8(e1489) (N2 background)


title: OUD blood rRNA removed RNA-seq H3

value: blood

tag: disease state

value: OUD

tag: bmi

value: male


title: TMT5_1week_rep4

city: Geneve

first: subashika

last: govindan

state: Geneve

address: chemins de mine 9

country: Switzerland

institute: HEPIA-HESO

data_processing:
The sequencing reads were demultiplexed using the BRB-seq Tools suite
Reads were aligned against human genome (hg38) using STAR and HTSeq for producing the count matrices.
Assembly: hg38
Supplementary files format and content: gene readcount file for all samples

source_name: minibrain

growth_protocol: Minibrains were grown for 4 months as described in "Mass Generation, Neuron Labeling, and 3D Imaging of Minibrains" (https://doi.org/10.3389/fbioe.2020.582650)

extract_protocol:
RNA was isolated from the treated and control minibrains according using RNA easy plus kit, Qiagen #74034 .
BRB-seq libraries (barcoded RNA seq library) was performed using MERCURIUS BRB-seq kit and following manufacturer manual (Alithea Genomics, #M1001)

treatment_protocol: 1µM, 2.5µM or 5µM TMT was added to the medium for experimental condition. 0µM was added to the medium for control condition

value: minibrains (derived from human induced neural stem cells derived from iPScs)


title: 30278_H


title: BMDE_Af_co_culture_rep3

value: BALB/c

value: bone marrow derived eosinophils (BMDE)

value: Co-culture BMDE and Aspergillus fumigatus


title: TMT5_1week_rep3


title: 30611_L

value: D

value: IG-MYC rearranged ALL - Light chain


title: only_BMDE_rep3

value: only BMDE


title: ONS-76_R_P_2

value: Human medulloblastoma cell line


title: TMT5_1week_rep1


title: PD-2


title: TMT5_72h_rep4


title: ONS-76_R_P_1


title: TMT5_72h_rep1


title: TMT5_72h_rep2


title: ONS-76_WT_3

value: untreated

value: Sensitive


title: ONS-76_WT_1


title: TMT5_24h_rep2


title: FC_FD1

tag: experimental perturbation

value: Rat fed low-iron diet during age 21-39 days old

tag: developmental stage

value: Sampling at 13 weeks old

value: prefrontal cortex


title: LZ-1

tag: strain


title: LZ-2


title: TMT2.5_1week_rep4


title: TMT5_24h_rep1


title: TMT2.5_1week_rep3


title: TMT2.5_1week_rep2


title: ONS-76_WT_2


title: PreL-2


title: PreL-3


title: TMT2.5_72h_rep4


title: TMT2.5_72h_rep2


title: TMT2.5_24h_rep3


title: TMT2.5_72h_rep3


title: TMT2.5_24h_rep2


title: PD-1


title: TMT1_1week_rep3


title: TMT5_24h_rep4


title: TMT2.5_24h_rep1


title: ONS-76_R_N_3

value: Treated with nebivolol

value: Resistant to nebivolol


title: PreL-1


title: Diff.Spg-3


title: LZ-3


title: TMT1_1week_rep2


title: Diff.Spg-2


title: TMT1_72h_rep2


title: TMT1_1week_rep1


title: TMT1_72h_rep3


title: Undiff.Spg-2


title: control_1week_rep4


title: TMT1_24h_rep1


title: TMT1_24h_rep2


title: Undiff.Spg-3


title: TMT1_72h_rep1


title: Diff.Spg-1


title: control_1week_rep2


title: control_72h_rep2


title: Undiff.Spg-1


title: Counts_1009s2

city: Lausanne

first: Rachel

last: Jeitziner Marcone

address: Rue du Bugnon 25a

institute: Swiss Institute of Bioinformatics

data_processing:
10X scRNA-seq: cellranger count (3.1.0); --chemistry SC3Pv3
Smart-seq2 scRNA-seq: After demultiplexing with bcl2fastq (bcl2fastq -p 56 --output-dir lane_$lane), SMART-seq2 based FASTQ files were trimmed with Trim Galore (v0.4.4) followed by alignment of the data to the mouse reference genome (mm10-GRCm38) using TopHat (v2.1.1) and bowtie2 (v2.2.6.0). PCR duplicates were removed using SAMtools (v0.1.18). Counting of fragments aligning per gene was done using the featurecounts function of the Subread package (v1.4.6-p5)
The raw gene expression matrix from both sequencing techniques were filtered and normalized using the Seurat R package. The following criteria were used: cells with >10 unique molecular identifier (UMI) counts; >200 genes; and <20% of mitochondrial gene expression in UMI counts. From the filtered cells, the gene expression matrices were normalized to the total UMI counts per cell and transformed to the natural log scale. Using the integration in Seurat R we merged the two datasets using  as anchors the 4000 most variable genes using the FindVariableGenes function.
Genome_build: mm10-GRCm38
Supplementary_files_format_and_content: tab-delimited normalized counts

source_name: small intestine

extract_protocol:
Small intestines from adult, male C57Bl/6 mice were harvested and digested with Liberase TL. Single, live, CD45neg, EpCAMneg, CD31neg, gp38+ cells were either sorted into 384-well plates (Smartseq2) or captured in an oil emulsion (10X Genomics). RNA was amplified, barcoded and sequenced.
Smartseq2: 0.0025 μl of a 1:40,000 diluted ERCC spike-in concentration stock was used, and all cDNA was amplified with 22 PCR cycles before QC control with a Bioanalyzer (Agilent Biosystems). The libraries were sequenced on a HiSeq2500 (Illumina) with single 50-bp reads (dual indexing reads). 10X Genomics libraries were prepared according to manufacturer's protocols and libraries were sequenced on a HiSeq4000 (Illumina).
scRNA-seq

value: small intestinal stromal cells

tag: genotype

value: wild type

value: small intestine


title: control_1week_rep1

value: minibrains (derived from human induced neural stem cells derived from iPScs)


title: control_72h_rep3


title: control_72h_rep1


title: Counts_1008s2


title: control_24h_rep3


title: control_24h_rep1


title: WT_Fibro_1_sample_C1


title: WT_Fibro_2


title: FT rep2

city: Ube-shi

first: Kensuke

last: Shibata

state: Yamaguchi

address: 1-1 Minami-Kogushi 1-chome

institute: Yamaguchi univeristy

description: Sample 8

data_processing:
Illumina RTA3 software used for basecalling.
Quality trimming and adapter clipping were performed using fastp v0.20.1 with parameters -3 -q 15 -n 0 -t 1 -l 50 -w 8.
Trimmed reads were mapped to transcripts in the reference Francisella tularensis subsp. novicida U112 chromosome (NZ_CP009633.1) using Bowtie2 aligner within RSEM v1.3.1 (Robinson et al., 2009). RSEM performed the estimation of the abundance of genes and isoforms and  generated raw counts.
The EdgeR v3.32.1 software program (Li et al., 2011) was used to normalize and detect the differentially expressed genes (DEGs).
Genome_build: NZ_CP009633.1
Supplementary_files_format_and_content: tab-delimited text file includes normalized count values for each sample.

organism: Francisella tularensis subsp. tularensis SCHU S4

source_name: Francisella tularensis SCHU4 wild-type replicate 2

growth_protocol: Francisella strains were cultured  to exponential phase at 37 °C in a  brain heart infusion broth (Becton, Dickinson and Company, Franklin Lakes, NJ) supplemented with cysteine.

extract_protocol:
After the culture of Francisella strains in the growth media, cell pellets were harvested using NucleoSpin RNA (Takara Bio, Cat#740955). After removal of rRNA using Illumina Ribo-Zero Plus rRNA Depletion Kit(Cat#20037135), TruSeq Stranded mRNA Library Prep Kit(Cat#20020595) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild-type


title: FT rep3

description: Sample 9

source_name: Francisella tularensis SCHU4 wild-type replicate 3


title: TMT1_24h_rep3


title: FT rep1

description: Sample 7

source_name: Francisella tularensis SCHU4 wild-type replicate 1


title: AB183_72H_R1

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Reads were mapped to the human genome (hg19 assembly) using Bowtie2 (v2.2.7) with default parameters but allowing 1 mismatch in the seed alignment (-N 1 option).
Mapped reads per gene were counted using the summarizeOverlaps function in the GenomicAlignments R package.
Non-expressed genes were removed (mean read count per gene over all samples >1) and trimmed mean of M-values normalization was performed using edgeR
Assembly: hg19
Supplementary files format and content: Provided is a rawcount-matrix containing counts per gene for all conditions (removed were not expressed features) and a differential expression analysis file containing the changes in gene expression between 0 hour treatment and 6 hour, 24 hour and 72 hour treamtent with CX5461. Both tables are in text-format (*.txt).

source_name: LS174T cells

growth_protocol: LS174T cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum and 1% penicillin/ streptomycin. The cells were maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were harvested according to the protocol of the Quiagen RNAeasy Mini Kit. Total RNA was isolated by using the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA libraries were generated with purified mRNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Libraries were size selected using Agentcourt AMPure XP beads, followed by amplification with 12 PCR cycles. The quality of the library was determined with the Fragment Analyzer (Advanced Analytical). Libraries were sequenced on the NextSeq500 platform (Illumina).

treatment_protocol: LS174T cells were incubated with 500 nM CX5461 (Selleckchem) for 6 hours, 24 hours or 72 hours.

value: adenocarcinoma of the colon

tag: cx-5361 treatment

value: treatment for 72 hours with 500 nM CX5461 (=72H)


title: AB183_24H_R2

value: treatment for 24 hours with 500 nM CX5461 (=24H)


title: AB183_6H_R2

value: treatment for 6 hours with 500 nM CX5461 (=6H)


title: AB183_72H_R2


title: AB183_6H_R1


title: AB183_24H_R1


title: AB183_0H_R3

value: none (=untreated = UT = 0H)


title: AB183_72H_R3


title: control_24h_rep4


title: AB183_0H_R2


title: Mx1-Cre; ID2Δ/Δ Hematopoietic Stem Cells

data_processing:
The number of cells captured ranges from 384 to 686 and mean reads per cell ranged from 218,801 to 550,748. Cells with extremely low number of UMI counts were filtered out. Median genes found per cell ranges from 2,687 to 3,274 and the total number of genes detected ranges from 14,556 to 15,256. All metrics are within the expected range for 10x Chromium single cell libraries.
The single-cell barcoded cDNA libraries were sequenced on NextSeq500 (Illumina) for two runs. The sequencing run was setup as a 26 cycles + 57 cycles in a non-symmetric run. The 10X Genomics Cellranger toolkit (v2.2.0) was used to perform de-multiplexing, allowing 1 mismatch in the barcodes, and alignment to the mm10 transcriptome and gene-barcode matrices. Pre-processing, removal of highly variable genes and contaminating immune cells, dimensionality reduction, and clustering analyses procedures were applied to each dataset
Cells that had feature counts <200, >2500, or >5% mitochondrial counts were removed.  Mean reads/cell, median genes/cell, and number of removed and analyzed cells for each dataset
Dimensionality reduction was performed via principal component analysis followed by clustering t-SNE visualization
Differentially expressed genes, which represented at least 25% of each cluster (p<0.05), were initially visualized using the Heatmap function then further analyzed using Loupe Cell Browser for gene set enrichment
Assembly: mm10
Supplementary files format and content: demultiplexed TAR file

organism: Mus

source_name: Murine Bone Marrow-Tibia, Fibula

extract_protocol:
RNeasyTM Micro Kit (Qiagen, 74004) was used to generate high quality RNA
10x Genomics Chromium

treatment_protocol:
5 Mx1-Cre; ID2Δ/Δ and 5 Mx1-Cre; ID2+/+ tibias and fibulas were harvested from mice 8 -12 weeks of age and HSCs were subsequently sorted with the immunophenotype LSK/FLT3-/CD150+ /CD48- followed by 10x genomics capture
1000 LSK/FLT3-/CD150+ /CD48-  cells from Mx1-Cre; ID2Δ/Δ were sorted from bone from 5 Mx1-Cre; Id2+/+and captured using 10x Genomics Chromium
5 Mx1-Cre; ID2Δ/Δ and 5 Mx1-Cre; ID2+/+ tibias and fibulas were harvested from mice 8 -12 weeks of age and HSCs were subsequently sorted with the immunophenotype LSK/FLT3-/CD150+ /CD48- followed by 10x genomics capture

value: Murine Bone Marrow-Tibia, Fibula

value: HSCs

tag: cells analyzed


title: Mx1-Cre; ID2+/+  Hematopoietic Stem Cells

treatment_protocol:
5 Mx1-Cre; ID2Δ/Δ and 5 Mx1-Cre; ID2+/+ tibias and fibulas were harvested from mice 8 -12 weeks of age and HSCs were subsequently sorted with the immunophenotype LSK/FLT3-/CD150+ /CD48- followed by 10x genomics capture
1000 LSK/FLT3-/CD150+ /CD48-  cells from Mx1-Cre; Id2+/+ were sorted from bone from 5 Mx1-Cre; Id2+/+and captured using 10x Genomics Chromium
5 Mx1-Cre; ID2Δ/Δ and 5 Mx1-Cre; ID2+/+ tibias and fibulas were harvested from mice 8 -12 weeks of age and HSCs were subsequently sorted with the immunophenotype LSK/FLT3-/CD150+ /CD48- followed by 10x genomics capture

value: WT


title: advanced gallbladder cancer [T22]

city: Zhengzhou

first: Sen

last: Yang

state: Henan

address: Weiwu Road 7

department: Department of Hepatobiliary and Pancreatic Surgery

institute: People's Hospital of Zhengzhou University, Henan Provincial People’s Hospital

data_processing:
We used Seqtk (https://github.com/lh3/seqtk) to filter raw reads, according to the following procedure: 1. removal of the ligation sequence; 2. removal of the bases whose 3'end quality Q is less than 20; 3. removal of reads with a length of less than 25 bp; 4. removal of the ribosome RNA reads from each species
Genome mapping was performed on the pre-processed reads using a spliced mapping algorithm from Hisat2 (version:2.0.4)
The spliced results of Stringtie (version 1.3.0) were compared with the reference annotations using gffcompare (version 0.9.8) for lncRNA prediction.
Assembly: GRCh38
Supplementary files format and content: gene_expression_anno  Excel file The fragment number and FPKM value of every  gene including all samples
Supplementary files format and content: lncrna_expression_anno Excel file The fragment number and FPKM value of every lncRNA  including all samples

source_name: gallbladder tumor

extract_protocol:
The TransZol Up Plus RNA Kit (Cat#ER501-01, Trans, Beijing, China) was used for total RNA extraction according to the manufacturer’s instructions.
The purified total RNA was subjected to rRNA removal, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3'end addition, connector ligation, and enrichment to build a sequencing library following the experimental instructions

tag: tissue type

value: advanced gallbladder cancer

value: gallbladder tumor


title: advanced gallbladder cancer [T27]


title: AB183_24H_R3


title: advanced gallbladder cancer [T32]


title: CUT&RUNseq_H3K27me3_K27me3_MpPp_hermaphrodite_germline_rep1

value: fem-2(b245ts) (CB4856 background)

value: mes-3(bn35)/hT2-GFP; him-8(e1489) (N2 background)

value: DNA associated with H3K27me3


title: AB183_6H_R3


title: early gallbladder cancer [T31]

value: early gallbladder cancer


title: AB183_0H_R1


title: early gallbladder cancer [T18]


title: early gallbladder cancer [T13]


title: advanced gallbladder cancer [T1]


title: advanced gallbladder cancer [T19]


title: early gallbladder cancer [T5]


title: 05_CO_56_HC

city: Copenhagen

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

data_processing:
Library strategy: BRB-Seq
Each BRB batch fastq file was demultiplexed using BRB-seq tool 1.6.0 Demultiplex function
To generate the count matrix, BRB-seq data was mapped by aligning reverse reads to human reference genome (GRCh38.105) by STAR(2.7.9a), then de-multiplexing by the forward read barcoding using BRB-seq tool 1.6.0.
Only expressed genes (mean count  > 1 across 80% samples) were included in the count matrix.
Assembly: human reference genome (GRCh38.105)
Supplementary files format and content: csv; The first column, gene_name, is the standard gene symbol (HGNC or MGI-approved gene symbols; if no official gene symbol exists, Havana clone-based name is used). The remaining columns contain the gene counts for each sample.

source_name: skin

extract_protocol:
Total RNA was extracted from tape 5 to 8 from each skin site (RNAqueous, Life technologies) followed by digestion with DNase I.
Multiplexed cDNA libraries were generated using the BRB-seq workflow (Alpern et al. Genome Biology 2019;20:71.)

tag: visit

tag: group

value: CO

value: HC

tag: gender

value: male

tag: scorad

value: arm

value: skin


title: 05_CO_53_HC


title: gallbladder adenoma [T30]

value: gallbladder adenoma


title: X732, blood, SIH, 1w

city: Baltimore

first: Evelina

last: Mocci

address: 655 W Lombard S

institute: SON

data_processing:
We used FastQC and Trimmomatic  tools for evaluating the quality of the sequences, next we used HISAT2  software to align the sequences to the reference Rattus norvegicus (Norway rat) genome assembly Rnor_6.0 (rn6) from Rat Genome Sequencing Consortium [GCA_000001895.4 GCF_000001895.5]. Finally, gene expression was estimated using HTSeq(18) which considers a gene as the union of all exons regardless of the isoform and excludes reads that overlap multiple genes
Genome_build: rn6
Supplementary_files_format_and_content: batch effect corrected expression data have been uploaded to https://nemoanalytics.org/p?s=2f41a962

source_name: blood

extract_protocol:
RNA was extracted from 4 type of tissues, including blood, colon, spinal, and dorsal root ganglia (DRG) at one week (week 1) and seven weeks (week 7) after the induction of stress
Libraries were prepared with NEB Ultra II Directional Library Prep kits. Samples at week 1 were sequenced on Illumina HiSeq 4000 platform using a 150 bp paired-end run (2 ´ 150), while samples at week7 were run on Illumina NovaSeq 6000 using a 150 bp paired-end run as well

tag: Sex

value: female

tag: time

value: blood

tag: ID

tag: experimental group

value: SIH


title: 05_CO_52_HC

tag: tissue


title: 05_CO_54_HC


title: X731, blood, SIH, 1w


title: 05_CO_48_HC


title: X725, blood, Naive, 1w

value: Naive


title: gallbladder adenoma [T11]


title: 05_CO_43_HC


title: gallbladder with chronic inflammation induced by gallstones [Y16]

source_name: gallbladder

value: gallbladder


title: 05_CO_42_HC


title: 05_CO_39_HC


title: 05_AD_25_NL

value: AD

value: NL


title: X720, blood, CPH, 1w

value: CPH


title: early gallbladder cancer [T12]

value: gallbladder tumor


title: 05_AD_25_LS

value: LS

value: leg


title: 6w.3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: 6 week mice PMN-MDSC

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Assembly: mm10
Supplementary files format and content: Prosessed files contains the raw counts for each gene

source_name: Ly6G+ spleen cells

extract_protocol:
Total RNA was extracted from cell pellets using the  Trizol (Invitrogen, Carlsbad, CA, USA)  per manufacturer’s instructions
First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments were amplified by PCR, and products were purified by Ampure XP Beads. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control

tag: cell type

value: Ly6G+ spleen cells

tag: replicate


title: 6w.1

description: 6 week mice PMN-MDSC


title: 6w.2

description: 6 week mice PMN-MDSC


title: 14d.3

description: 14d mice PMN-MDSC


title: 14d.2

description: 14d mice PMN-MDSC


title: gallbladder with chronic inflammation induced by gallstones [Y12]


title: RS-3


title: gallbladder with chronic inflammation induced by gallstones [Y8]


title: 14d.1

description: 14d mice PMN-MDSC


title: X719, blood, CPH, 1w


title: gallbladder adenoma [T24]


title: F742, Spinal, TL, Naive, 1w

source_name: spinal

value: spinal


title: normal gallbladder [N20]

value: normal gallbladder


title: X724, blood, SIH, 1w


title: 7d.3

description: 7d mice PMN-MDSC


title: gallbladder with chronic inflammation induced by gallstones [Y13]


title: 7d.2

description: 7d mice PMN-MDSC


title: X721, blood, CPH, 1w


title: 05_AD_22_LS

value: male

value: arm


title: normal gallbladder [N10]


title: normal gallbladder [N8]


title: 7d.1

description: 7d mice PMN-MDSC


title: F742, Spinal, C, Naive, 1w


title: F742, DRG, Naive, 1w

source_name: DRG

value: DRG


title: F742, COLON, D, Naive, 1w

source_name: colon

value: female

value: colon


title: 2d.3

description: 2d mice PMN-MDSC


title: 2d.1

description: 2d mice PMN-MDSC


title: 2d.2

description: 2d mice PMN-MDSC


title: 05_AD_15_LS

value: skin


title: F742, COLON, M, Naive, 1w

value: Naive


title: F742, COLON, P, Naive, 1w


title: 05_AD_16_NL


title: 05_AD_15_NL


title: F742, blood, Naive, 1w

value: blood


title: F742, Spinal, LS, Naive, 1w


title: 05_AD_13_LS

value: AD


title: 05_AD_22_NL

value: NL


title: AD_5

city: Ultimo

first: Alison

last: Ricafrente

state: New South Wales

address: 15 Broadway

department: School of Life Sciences

country: Australia

institute: University of Technology Sydney

data_processing:
Sequenced reads were trimmed for adaptor sequences, masked for low quality reads and reads < 18 nt long
Cleaned reads were mapped to mature miRNA sequences of Fasciola hepatica derived from miRBase version 21 repositorry [Fhepatica_v1] and other published miRNAs featured in Ricafrente et al. 2021 using Bowtie version 1.3.0
Cleaned reads were analysed for novel miRNAs using MiRDeep2 (version 2.0.1.2) facilitated by inputs including F.hepatica genome (PRJEB25283); and reference mature miRNAs from F.hepatica miRBase repository [Fhepatica_v1] and other published miRNAs featured in Ricafrente et al. 2021, Schistosoma japonicum miRBase respository (ASM15177v1), Schistosoma mansoni miRBase repository (WTSI5) and  Caenorhabditis elegans miRBase respository(WBcel235)
Combined read counts of known/published and novel Fasciola hepatica miRNAs were normalised to counts per million (CPM)
Genome_build: F.hepatica genome (PRJEB25283)
Supplementary_files_format_and_content: Format is txt file tab delimited and contains raw read counts of Fasciola hepatica miRNAs of interest.

organism: Fasciola hepatica

source_name: Adult

extract_protocol:
Total RNA was extracted from the three F. hepatica life stages in triplicate using the miRNeasy mini kit (Qiagen) according to the manufacturer’s instructions, in a final elution of 50µl RNase-free water
Total RNA of each sample was used to prepare the miRNA sequencing library. After the completed libraries were quantified with Agilent 2100 Bioanalyzer, the DNA fragments in the libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ and finally sequenced for 51 cycles on Illumina NextSeq 500 according to the manufacturer’s instruction.The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 51 cycles on Illumina NextSeq per the manufacturer’s instructions.

value: Italian isolate

tag: time point

value: hepatic infection

value: Total tissue homogenisation