title: Stimulated KO CD4 T cells + Niacin_rep3 [St-NA_ko_rep3]

city: Duarte

first: Anastasia

middle: I

last: Kousa

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (version 0.38, default parameters).
Trimmed reads were then mapped to GRCm38.p5 whole genome using STAR (version 2.7.0e) with default parameters for paired end reads.
featureCounts (version 1.6.3) was used to quantify the gene counts with default options for paired-end reads.
Genome_build: GRCm38.p5 (mm10)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Stimulated KO CD4 T cells + Niacin

growth_protocol: CD45+CD3+CD4+CD8- T cells were FACS-sorted and cultured in vitro with either IL-2 alone (unstimulated), or with anti-CD3/CD28 (stimulated), and/or with niacin (+ Niacin)

extract_protocol:
RNA was isolated using TRIzol and total RNA was amplified using SMART-seq V4 Low Input RNA Kit
Amplified cDNA was used to prepare Illumina HiSeq libraries with the Kapa DNA library preparation chemistry. Samples were barcoded and run on Hiseq 2500 1T, in a 50bp/50bp paired-end run using the TruSeq SBS Kit v3

treatment_protocol: T cells were treated with 30IU/ml of IL-2, anti-CD3/CD28 +/- 5mM Niacin for 72 hours prior to RNA extraction

tag: strain background

value: spleen

value: T cell

tag: in vitro treatment

value: treated with anti-CD3/CD28, IL-2 and 5mM niacin


title: HG001-rep2

status: Public on Dec 11 2021

type: SRA

city: Singapore

first: Kelvin

last: Chong

address: 60 Nanyang Drive

department: SCELSE

country: Singapore

institute: Nanyang Technological University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Demultiplexed sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to respective bacterial genome using BWA (version 0.7.15-r1140) with default parameters.
Reads were counted with predicted open reading frames to each reference genome using HTSeq (version 0.6.1)  and subjected to differential analysis using EdgeR (3.36.0)
Genome_build: HG001 (GCA_000013425.1) and UTI89 (GCA_000013265.1)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

molecule: total RNA

organism: Staphylococcus aureus

extract_protocol:
Macrocolonies were excised and subjected to RNA extraction in Trizol and mechanical lysis. Dnase treatment was performed and remaining RNA was depleted of ribosomal RNA before subjected to first and second strand synthesis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

value: Wild type

tag: background

value: Single species


title: HG001-rep1


title: Stimulated KO CD4 T cells + Niacin_rep2 [St-NA_ko_rep2]

state: CA

country: USA

organism: Mus musculus

tag: tissue

tag: cell type


title: Stimulated KO CD4 T cells_rep3 [St_ko_rep3]

source_name: Stimulated KO CD4 T cells

value: treated with anti-CD3/CD28 and IL-2


title: IVF-treat-59

city: Jinan

first: Lianbao

last: Cao

state: shandong province

address: Wenhuaxi road

department: Medical department

country: China

institute: Shandong Univerisity

description:
IVF-embryo.txt
Tm3

data_processing:
the useful Perlscript was used to filter the original data
Removed the contaminated reads for adapters
Removed the low quality reads
Removed the reads which contained N base more than 5% for total bases
If either one of the PE Reads had high Ns bases, we will remove both ends of the reads
Genome_build: Reference gene and genome annotation files downloaded from the  UCSC(ttp://hgdownload.soe.ucsc.edu/goldenPath/galGal4), using Bowtie2 v2.2.3 to build  the reference genome library, and then the clean data were mapped to the reference  genome by TopHat v2.0.12
Supplementary_files_format_and_content: abundance measurements

source_name: Morula stage embryo

growth_protocol: The germinal vesicle (GV) staged oocytes were isolated and cultured in 6-hr pre-equilibrated oil-covered M16 medium (Cat# M7292, Sigma) and placed in 37°C, 5% CO2 and 95% relative humidity under normal atmosphere. Sixteen hours later, the in vitro-matured oocytes with the first polar body were defined as metaphase II (MII) oocyte.Fertilization was carried out for 6 hr and 20–40 inseminated oocytes were transferred into 40-μL droplets of pre-equilibrated G1 media (Cat.10127, Vitrolife) under mineral oil at 37 °C. Two-cell staged embryos were scored 24 hr later and all non-inseminated oocytes were removed from the droplet. The early embryos prior to morula formation were transferred to G2 medium (Cat.10132, Vitrolife) 72 hr later until reaching the blastocyst stage.

extract_protocol: The synthesis of full-length cDNA and preparation of the sequencing libraries was performed using the Smart-seq2 method

treatment_protocol: The small molecule were addedd in the culture medium(M16,G1/G2)

value: in vitro cultured morula stage embryo

tag: agent

value: VCD


title: IVF-treat-58

description:
IVF-embryo.txt
Tm2


title: Genomic DNA of HD02 MCSs

type: genomic

city: Tours

first: Benjamin

last: Roux

address: 2 boulevard Tonnelle

country: France

institute: CHRU Tours

description: Normal MSCs

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: ChAMP 2.10.2 was used to compute beta-values after BMIQ normalization

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: standard Illumina protocol

growth_protocol: In vitro amplification of MSCs for two passages after isolation from bone marrow. Medium: alpha-MEM, 10% FBS, 1% L-glutamine, 10ng/mL rh-FGF2

extract_protocol: Genomic DNA was extracted from MSCs samples using Qiagen  Kit according to standard instructions

treatment_protocol: No treatment applied

tag: age

value: unknown

tag: gender


title: Genomic DNA of HD04 MCSs

description: Normal MSCs

value: M


title: IVF-treat-60

description:
IVF-embryo.txt
Tm4


title: IVF-PBS-56

description:
IVF-embryo.txt
Cm4

value: PBS


title: IVF-treat-57

description:
IVF-embryo.txt
Tm1


title: Stimulated KO CD4 T cells_rep1 [St_ko_rep1]


title: IVF-PBSt-55

description:
IVF-embryo.txt
Cm3


title: IVF-PBS-53

description:
IVF-embryo.txt
Cm1


title: IVF-PBS-54

description:
IVF-embryo.txt
Cm2


title: Stimulated WT CD4 T cells_rep2 [St_wt_rep2]

source_name: Stimulated WT CD4 T cells

value: wild type


title: Stimulated KO CD4 T cells_rep2 [St_ko_rep2]


title: Stimulated WT CD4 T cells + Niacin_rep1 [St-NA_wt_rep1]

source_name: Stimulated WT CD4 T cells + Niacin


title: Stimulated WT CD4 T cells_rep1 [St_wt_rep1]


title: IVF-treat-52

description:
IVF-embryo.txt
T2d

source_name: 2-cell stage embryo

value: in vitro cultured 2-cell stage embryo


title: IVF-treat-51

description:
IVF-embryo.txt
T2c


title: Genomic DNA of HD03 MCSs

description: Normal MSCs


title: s9

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
Illumina bcl2fastq conversion software used for basecalling.
reads were aligned using the STAR (2.5.2b) software.
raw read counts were obtained using htseq-count (HTSeq-0.6.1p12)
Genome_build: GRCh38.rel77
Supplementary_files_format_and_content: tab-delimited text files of raw count values for each Sample

source_name: Placenta

extract_protocol:
Total RNA from the whole placental viili was isolated using RNeasy Mini Kit (#74104) from Qiagen per the manufacturer’s protocol with on column DNase digestion.  RNA concentrations were quantified using a NanoDrop Spectrophotometer at a  wavelength of 260nm. Integrity of the total RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
Sequencing libraries were prepared using the NuGEN Universal Plus Stranded (fr-secondstrand) mRNA Sample Preparation Kit

tag: tissue type

value: Normal

tag: prior miscarriage

value: no

tag: gestation days


title: R19


title: Genomic DNA of HD07 MCSs

description: Normal MSCs


title: Unstimulated KO CD4 T cells + Niacin_rep2 [Un-NA_ko_rep2]

source_name: Unstimulated KO CD4 T cells + Niacin

value: treated with 5mM niacin


title: R2


title: IVF-treat-49

description:
IVF-embryo.txt
T2a


title: R13


title: s6


title: Genomic DNA of HD01 MCSs (did not pass QC)

description: Normal MSCs


title: IVF-PBS-48

description:
IVF-embryo.txt
C2d


title: R7


title: R9


title: Unstimulated KO CD4 T cells_rep3 [Un_ko_rep3]

source_name: Unstimulated KO CD4 T cells

value: untreated


title: Stimulated WT CD4 T cells + Niacin_rep3 [St-NA_wt_rep3]

value: spleen


title: R3


title: IVF-PBS-47

description:
IVF-embryo.txt
C2c


title: UTI89-rep1

organism: Escherichia coli


title: s14


title: IVF-PBS-46

description:
IVF-embryo.txt
C2b


title: Stimulated WT CD4 T cells_rep3 [St_wt_rep3]

value: T cell


title: Unstimulated KO CD4 T cells_rep1 [Un_ko_rep1]


title: IVF-PBS-45

description:
IVF-embryo.txt
C2a


title: s8


title: Retina 4

city: Guangzhou

first: Kangxin

last: Jin

state: Guangdong Province

address: 7 Jinsui Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

data_processing:
Raw reads were processed using the 10x Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) with the mm10 as the reference. Cell Ranger can cluster the single cells, identify the marker genes of each cluster, and export a matrix with UMI values of each gene in a single cell. In total 468,282,957 reads were mapped and 3,237 cells were detected with a sequencing saturation of 86.2%. The R software package Seurat (https://satijalab.org/seurat, version 2.2) was used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: RGC_Matrix_all_cells.csv
Supplementary_files_format_and_content: barcodes.tsv
Supplementary_files_format_and_content: filtered_gene_bc_matrices_h5.h5
Supplementary_files_format_and_content: genes.tsv

source_name: Retina

extract_protocol:
Retinae were dissociated into single cells. GFP+ cells were enriched by FACS sorting. The number and viability of sorted retinal cells were quantified using the Countess II (ThermoFisher AMQAX1000). Next, single cell libraries were generated with the Chromium Single Cell 3’ V2 Chemistry Library Kit, Gel Bead & Multiplex Kit and Chip Kit from 10X Genomics.
To generate the libraries, Enzymatic Fragmentation, End Repair and A-tailing Double Sided Size Selection were used to incorporate the barcodes and index read sequences. The libraries were qualified by bioanalyzer (Agilent Technologies) and quantified by a Qubit® dsDNA High Sensitivity Assay Kit (Invitrogen), then sequenced on Illumina Xten platform in 150 Paired-end configuration.

value: Retinal ganglion cells

value: 3 months


title: Retina 3


title: Genomic DNA of HD09 MCSs

description: Normal MSCs


title: IVF-treat-50

description:
IVF-embryo.txt
T2b


title: Unstimulated WT CD4 T cells + Niacin_rep2 [Un-NA_wt_rep2]

source_name: Unstimulated WT CD4 T cells + Niacin


title: Retina 2


title: IVM-treat-28

description:
IVM-MII oocyte.txt
T4

source_name: MII stage oocyte

value: In vitro matured MII staged oocyte


title: UTI89-rep2

value: Wild type

value: Single species


title: Unstimulated KO CD4 T cells_rep2 [Un_ko_rep2]


title: s12


title: IVM-treat-27

description:
IVM-MII oocyte.txt
T3

value: VCD


title: Unstimulated WT CD4 T cells + Niacin_rep1 [Un-NA_wt_rep1]


title: s10


title: s5


title: Unstimulated WT CD4 T cells_rep3 [Un_wt_rep3]

source_name: Unstimulated WT CD4 T cells


title: IVM-treat-30

description:
IVM-MII oocyte.txt
T5


title: IVM-treat-26

description:
IVM-MII oocyte.txt
T2


title: Unstimulated WT CD4 T cells + Niacin_rep3 [Un-NA_wt_rep3]


title: Unstimulated WT CD4 T cells_rep2 [Un_wt_rep2]


title: Unstimulated WT CD4 T cells_rep1 [Un_wt_rep1]


title: R17


title: T1_cd138M

city: Limoges

first: Melissa

last: Ferrad

address: rue Pr. Descottes

department: UMR CNRS 7276, INSERM U1262, Equipe Labellisée LIGUE 2018, Université de Limoges

institute: Université de Limoges

data_processing:
Trimming was done with fastp (version: 0.20.1, parameters: --length_required 25 --detect_adapter_for_pe --cut_front --cut_tail --cut_window_size 6 --cut_mean_quality 10 --unqualified_percent_limit 40 --n_base_limit 7 --average_qual 0 --overrepresentation_analysis)
Abundance estimation was performed with Salmon (version: 1.5.2, parameters: --numBootstraps 100 --threads 8 --gcBias --validateMappings --seqBias --posBias --libType A) on mouse genome (mm10).
The differential gene expression analysis is done with DESeq2 for the 3 comparisons
Genome_build: mm10
Supplementary_files_format_and_content: Deseq2 normalized count

source_name: B-cell lymphoma

growth_protocol: homozygous iMycCα mice – Mice exhibiting obvious tumors or presenting signs of illness were sacrificed. B-cell Lymphoma are characterized by flow cytometry analysis (B220, CD19, CD43, CD117, CD138, IgM, IgD)

extract_protocol:
B-cell lymphoma are freshly isolated, and Total RNA from lymphoma cells (purified with B220-coupled beads from Miltenyi Biotech) RNA was harvested using Trizol reagent.
RNA-seq paired-end libraries were prepared according to the Illumina protocol with some adjustments, using the TruSeq Stranded Total RNA Gold library prep Kit (Illumina, San Diego, USA). Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche, Basel, Switzerland). Libraries quality was assessed by the HS NGS kit on the Fragment Analyzer (Agilent Technologies, Santa Clara, USA). Libraries were equimolarly pooled and RNA sequencing was then performed on one S4 lane of the Illumina NovaSeq 6000 instrument (Illumina, San Diego, USA), using the NovaSeq 6000 S4 v1.5 Reagent Kit (300 cycles), and a paired-end 2 x 150 pb strategy.

treatment_protocol: cells were not treated

value: cmyc-ki-c[alpha] homozygous

tag: tumor type

value: spleen tumor


title: R11


title: T1_cd138P_cmycM


title: R20


title: IVM-PBS-24

description:
IVM-MII oocyte.txt
C3

value: PBS


title: T2_cd138M


title: mc3b

value: Miscarriage

value: yes


title: FLM_G_2

city: Brookings

first: Natalie

middle: W

last: Thiex

state: SD

address: 1390 College Ave

department: Biology & Microbiology

institute: South Dakota State University

data_processing:
Fastq files were generated and multiplexed with bcl2fastq
Raw sequence reads were checked for their quality using FastQC
Sequence reads were trimmed for adapters, length of at least 20 nucleotides, Phred score quality of >= 20 using cutadapt and prinseq respectively
Cleaned sequence reads were aligned to the Mus musculus genome using Hisat2 and Gene expression levels in FPKM were quantified using Stringtie
Differential gene expression analysis was performed using DESeq2
Genome_build: Ensembl build v.mm10/GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and read count values for each Sample

source_name: fetal liver (gestational day 15-19)

growth_protocol: Fetal livers and bone marrow were isolated from C57BL/6J mice (The Jackson Laboratory, Bar Harbor, ME). FLM cell cultures were generated by isolating livers from gestational day 15-19 mouse fetuses in accordance with South Dakota State University Institutional Animal Use and Care Committee. Liver tissue was mechanically dissociated using sterile fine-pointed forceps and a single-cell suspension was created by passing the tissue through a 1 ml pipette tip (Fejer et al., 2013).  Cells were plated at 8x106 cells per 10 cm2 non-tissue culture treated dishes. Growth and differentiation medium for FLM-M consisted of 20% fetal bovine serum (FBS) and 30% L-cell supernatant, a source of M-CSF (Stanley et al., 1976; Waheed and Shadduck, 1979) and 50% Dulbecco’s modified growth medium containing 4.5 g/L glucose, 110 mg/L sodium pyruvate, 584 mg/L L-glutamine, 1 IU/ml penicillin and 100 μg/ml streptomycin. Growth medium for FLM-G consisted of high glucose Dulbecco’s modified growth medium containing 30 ng/ml recombinant mouse GM-CSF, 10% FBS, and 4.5 g/L glucose, 110 mg/L sodium pyruvate, 584 mg/L L-glutamine, 1 IU/ml penicillin and 100 μg/ml streptomycin. All cells were cultured for at least 8 weeks before experiments were conducted.

extract_protocol:
One day prior to harvesting RNA, FLM-M, FLM-G and BMM cells were plated in triplicate at 2.5 x 10^5 cells per well in a non-tissue culture treated six-well plate. Cells were harvested using trypsin and total RNA was purified using Genejet RNA purification kit per manufacturer's instructions (ThermoFisher Scientific Waltham, MA). Genomic DNA remaining in the RNA was removed using TURBO DNA-free kit (ThermoFisher Scientific Waltham, MA).
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq2500 using a HiSeq SBS sequencing kit version 4.

value: fetal liver macrophages (FLM_G)


title: FLM_G_3


title: mc3a


title: IVM-PBS-23

description:
IVM-MII oocyte.txt
C2


title: DLD1 parental cells, H3K27me3 IP ChIPSeq

city: Shanghai

first: Baoyu

last: He

address: No. 25, Lane 2200, Xietu Road

institute: Renji Hospital

library_source: genomic

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality control:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
The reads that passed the prefiltering step were aligned with the Bowtie2 v2.4.2 software to the human genome (hg19). Peak calling was performed with MACS2. Homer software was used to annotate ChIP-seq peaks, and getDifferentialPeaks was used to find differential peaks between DLD1 parental cells and DLD1 p85β K477A/R478A mutant cells.
Genome_build: hg19
Supplementary_files_format_and_content: peak bigwig files

source_name: DLD1 parental cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-H3K27me3 antibody.
ChIP was performed using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003) following the manufacturer’s instructions. Chromatin was sonicated and immunoprecipitated with anti-H3K27me3 antibody. Purified ChIP DNA was verified on agarose gel to ensure proper fragmentation and then sent to the Sequencing. Sequencing was performed at RiboBio Inc，Guangzhou on an lllumina nova machine. Raw reads (Paired-end, 150bp) were aligned to human reference genome hg19 using bowtie2 (v2.4.2), allowing up to one mismatch. Peak calling was performed using model-based analysis of ChIP–seq (MACS, v2.2.7) with a cutoff of P ≤ 1 × 10-8.

value: colon

tag: cell line

value: parental

tag: chip antibdy

value: H3K27me3 (Cell Signaling Technology, Cat# 9733, RRID:AB_2616029)


title: T3_cd138M


title: FLM_G_1


title: Peripheral_blood_cells_Con_rep1

city: Beijing

first: Weijie

last: LI

address: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China

description:
Peripheral_blood_cells_Con_rep1
C4

data_processing:
Sequencing: RNA-seq reads
Read alignment: HISAT2
Transcript compilation: StringTie
Expression estimation: StringTie
Differential expression: Ballgown
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: gene_count_matrix.csv with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: transcript_count_matrix.csv with raw transcrip counts for every transcript and every sample
Supplementary_files_format_and_content: gene_fpkm_all_samples
Supplementary_files_format_and_content: transcript_fpkm_all_samples

organism: Rattus norvegicus

source_name: Peripheral blood cells

extract_protocol:
Peripheral blood mononuclear cells were collected after 8 hours stored in liquid nitrogen for microarray detection. Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.

treatment_protocol: Briefly, male Lewis rats were injected intradermally at the base of tail with 10mg/mL M tuberculosis H37 Ra (Difco, BD company, New Jersey, US) suspended in liquid paraffin (Freund's complete adjuvant, CFA). From the day of primary immunization, male Lewis rats were kept in the artificial climate box (production license no. RXZ-380A-LED) for 2 hours daily with certain wind velocity (6m/s), temperature (37℃) and humidity (90%) for a period of 15 days.  In AIA_H_BHGZD treatment group, the dosage selection for BHGZD was 21.4 g/kg, nearly equivalent two times of the daily dosage of RA patients in clinics.

value: Lewis

value: Peripheral blood cells

tag: group

value: Normal control


title: IVM-treat-25

description:
IVM-MII oocyte.txt
T1


title: mc4


title: IVM-PBS-29

description:
IVM-MII oocyte.txt
C4


title: T5_cd138P_cmycM


title: FLM_M_3

value: fetal liver macrophages (FLM_M)


title: UTI-89 mixed with HG001-rep3

description: Mixed_UTI89_raw_counts.txt, Mixed_HG001_raw_counts.txt

organism:
Escherichia coli
Staphylococcus aureus

value: Multiple species


title: T3_cd138P_cmycP


title: IVM-PBS-21

description:
IVM-MII oocyte.txt
C1

value: In vitro matured MII staged oocyte


title: FLM_M_2


title: mc10

value: no


title: UTI-89 mixed with HG001-rep2

value: Wild type


title: Retina 1

value: Retinal ganglion cells

value: 3 months


title: T2_cd138P_cmycP

value: cmyc-ki-c[alpha] homozygous

value: spleen tumor


title: T1_cd138P_cmycP


title: FLM_M_1


title: UTI-89 mixed with HG001-rep1


title: T4_cd138P_cmycP


title: mc6

value: Miscarriage


title: BMM_3

source_name: bone marrow

value: bone marrow macrophages (BMM)


title: mc9


title: BMM_2


title: mc8


title: T3_cd138P_cmycM


title: mc2


title: T2_cd138P_cmycM


title: BMM_1


title: Whole cell lysate High-Small-RNA-Seq

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

description: AF357425 overexpression

data_processing:
sRNAbench tool is used to process the raw FASTQ files
Bowtie aligner was used to align reads to various reference genome and databases, such as GRCm38, mirbase small database, and RNAcentral
The expression of multiple classes of smallRNA are quantified in the single assignment based approach where reads mapping to multiple loci are assigned to the locus that have the highest expression.
RPM (Read per million) normalized counts are further generated that are used for downstream analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV file of RPM counts

source_name: Ear

growth_protocol: Fibroblasts were isolated from ear-clippings of C57BL/6 mice. Cells were expanded using culture media (DMEM with 10% heat-inactivated fetal calf serum and 1% PenStrep).

extract_protocol:
After transfection, RNA from whole cell lysates was isolated by standard TRIzol-chloroform extraction
Small RNA library

treatment_protocol: Cells were cultured for 48 hours with KN93 to synchronize the cell cycle and subsequently transfected with gapmers against AF357425 (snoRNA inhibition) or 3rd Generation Antisense against AF357425 (snoRNA overexpression) for 24 hours

value: Primary ear fibroblasts


title: MefGal4UASGsk3CA_BL5255_n3_larva

status: Public on Dec 10 2021

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA version 1.7
Sequences derived from total RNA paired-end 100-bp sequences were mapped to the dm5 genome using the STAR aligner.
Transcript-level data were counted with HTSEQ
Genome_build: dm5
Supplementary_files_format_and_content: txt

organism: Drosophila melanogaster

source_name: Drosophila body wall skeletal muscles

extract_protocol:
RNA was isolated from total cell lysates with the RNeasy Plus Mini kit (Qiagen)
RNA was prepared for RNA-seq with the TruSeq stranded mRNA library preparation kit (Illumina)
total RNA, paired 100 bp

treatment_protocol: RNAi treated skeletal muscle


title: MefGal4UASGsk3CA_BL5255_n2_larva


title: MefGal4Deaf1RNAi_BL32512_n2_larva


title: MefGal4Deaf1RNAi_BL32512_n1_larva


title: MefGal4Deaf1RNAi_BL32512_n3_larva


title: Whole cell lysate Low-Small-RNA-Seq

description: AF357425 inhibition


title: MefGal4HMS17_n3_larva


title: MefGal4UASGsk3CA_BL5255_n1_larva


title: MefGal4HMS17_n1_larva


title: MefGal4_n2_larva


title: MefGal4UASDeaf1_n1_larva


title: MefGal4_n1_larva


title: MefGal4UASDeaf1_n2_larva


title: MefGal4_n3_larva


title: T4_cd138P_cmycM


title: MefGal4UASDeaf1_n3_larva


title: MefGal4HMS17_n2_larva


title: Stimulated WT CD4 T cells + Niacin_rep2 [St-NA_wt_rep2]

tag: strain background

value: wild type

value: spleen

value: T cell

value: treated with anti-CD3/CD28, IL-2 and 5mM niacin


title: aged_3

type: RNA

city: Grand Forks

first: Alexei

last: Tulin

state: North Dakota

address: 501 N Columbia Rd Stop 9061

department: Epigenetics Department

institute: University of North Dakota

hyb_protocol: Target hybridization was performed on GeneChip Drosophila Genome 2.0 arrays (Affymetrix Inc., Santa Clara CA, USA) according to the manufacturer’s procedures in the GeneChip® Hybridization Oven 645, followed by washing and staining in the GeneChip® Fluidics Station 450.

scan_protocol: Data were acquired with GeneChip® Scanner 3000 7G (Affymetrix, Inc., Santa Clara, CA, USA).

data_processing:
Data analysis was performed using Partek Genomics Suite v6.5 to apply the GCRMA normalization algorithm.
processed_data.txt: Each probe is shown on a separate line. Column A corresponds to the gene symbols associated with the probe. Column B corresponds to Flybase IDs associated with the probe. Column C corresponds to the probe ID. Column D to I corresponds to the log2 scale of the fluorescence intensity recorded for each probe for 3 days-old biological replicates 1-3 and 45 days-old biological replicates 1-3.

label: biotin

source_name: mix of 100 female flies and 100 male flies_aged

label_protocol: All protocols were conducted as described in the NuGEN Ovation User Guide and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 100ng of total RNA were converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated an RNA priming region.  Second-strand cDNA synthesis was followed by ribo-SPIA linear amplification of each transcript using an isothermal reaction with RNase, RNA primer and DNA polymerase (Ovation RNA Amplification System V2, NuGEN Inc., San Carlos CA, USA), and the resulting cDNA was assessed by Bioanalyzer, fragmented and biotinylated (Encore Biotin Module, NuGEN Inc., San Carlos CA), followed by the addition of 3.75ug of labeled cDNA to Affymetrix hybridization cocktails.

growth_protocol: For each biological replicates 250 virgin females and 250 virgin males were cultured in 10 bottles (50 flies per bottle) containing 10ml of fly food and fresh yeast. The flies were cultured in a 20C degree incubator with standard day/night cycle and 50% humidity. Flies were transfered to fresh bottle every three days. To purify total RNA, 100 males and 100 females were used among 3 days-old flies and then among 45 days-old flies.

extract_protocol: Total RNA was purified using the RNeasy Mini kit (Qiagen, Valencia, CA) after isolation using TRIzol reagent (Life Technologies, Inc., Grand Island, NY). The purification was performed with whole organism.

value: 45 days-old

tag: Sex

value: mixed

value: Whole organism


title: Bone marrow cells - SNP array (928975-4)

city: Houston

first: Yuya

last: Sasaki

state: TX

address: 1515 Holcombe Blvd

institute: M.D. Anderson Cancer Center

hyb_protocol: According to the hybridazation protocol in manufacture's Reference Guide

scan_protocol: According to the scan protocol in manufacture's  Reference Guide

data_processing:
The raw data retrieved from an Illumina Omni2.5-8 SNP array was processed using GenomeStudio 2.0.
The raw log R ratio was used for ASCAT (allele-specific copy number analysis of tumors) algorithm to identify allele-specific copy-number alterations.
The log R ratio (LRR)

source_name: Bone marrow cells

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted from bone marrow or peripheral blood samples using a QIAamp DNA Mini kit (QIAGEN, Hilden, Germany).

treatment_protocol: Samples were either bone marrow aspirate or peripheral blood obtained from previously untreated patients.

tag: disease state

value: Ph-positive ALL

tag: treatment

value: bone marrow

value: leukemic cell

value: Male

tag: outcome

value: Complete Response


title: Bone marrow cells - SNP array (855377-5)

tag: tissue

value: Female


title: Bone marrow cells - SNP array (966152-2)

tag: cell type


title: Bone marrow cells - SNP array (877105-4)


title: Bone marrow cells - SNP array (962070-10)


title: Bone marrow cells - SNP array (890197-8)


title: Bone marrow cells - SNP array (921072-9)


title: Bone marrow cells - SNP array (973506-4)


title: Bone marrow cells - SNP array (992302-3)


title: Bone marrow cells - SNP array (939833-6)


title: Bone marrow cells - SNP array (833261-7)


title: Bone marrow cells - SNP array (984677-4)


title: Bone marrow cells - SNP array (923355-6)


title: Bone marrow cells - SNP array (838028-2)


title: Bone marrow cells - SNP array (934267-2)


title: Stimulated KO CD4 T cells + Niacin_rep1 [St-NA_ko_rep1]

source_name: Stimulated KO CD4 T cells + Niacin

tag: genotype

tag: in vitro treatment


title: Bone marrow cells - SNP array (814440-6)


title: young_1

source_name: mix of 100 female flies and 100 male flies_young

tag: age

value: 3 days-old


title: young_2


title: aged_1


title: young_3


title: aged_2


title: Bone marrow cells - SNP array (766053-7)


title: Bone marrow cells - SNP array (835209-2)


title: Bone marrow cells - SNP array (924362-4)


title: Bone marrow cells - SNP array (921120-4)


title: Bone marrow cells - SNP array (813733-9)


title: Bone marrow cells - SNP array (760777-6)


title: Bone marrow cells - SNP array (805345-5)


title: Bone marrow cells - SNP array (729567-3)


title: Bone marrow cells - SNP array (242032-17)

value: Early Death


title: Bone marrow cells - SNP array (241830-5)


title: Bone marrow cells - SNP array (242199-8)


title: Bone marrow cells - SNP array (752316-6)


title: Bone marrow cells - SNP array (322781-8)


title: Bone marrow cells - SNP array (653954-14)


title: Bone marrow cells - SNP array (783510-16)


title: Bone marrow cells - SNP array (277327-3)


title: Bone marrow cells - SNP array (321826-5)


title: Bone marrow cells - SNP array (318817-9)


title: Bone marrow cells - SNP array (362025-4)


title: Bone marrow cells - SNP array (241753-9)


title: Bone marrow cells - SNP array (497062-4)


title: Bone marrow cells - SNP array (640560-4)


title: Bone marrow cells - SNP array (742316-6)


title: Bone marrow cells - SNP array (241561-6)


title: Bone marrow cells - SNP array (241537-11)


title: Bone marrow cells - SNP array (338863-4)


title: Bone marrow cells - SNP array (241163-7)


title: Bone marrow cells - SNP array (241237-12)


title: Bone marrow cells - SNP array (502310-6)


title: Bone marrow cells - SNP array (240630-24)


title: Bone marrow cells - SNP array (241047-6)


title: Bone marrow cells - SNP array (240615-19)


title: Bone marrow cells - SNP array (240736-5)


title: Bone marrow cells - SNP array (240598-4)


title: Bone marrow cells - SNP array (240516-8)


title: Bone marrow cells - SNP array (240462-2)


title: Bone marrow cells - SNP array (240197-7)


title: Bone marrow cells - SNP array (235735-2)


title: Bone marrow cells - SNP array (235894-23)


title: Bone marrow cells - SNP array (237407-26)


title: Bone marrow cells - SNP array (238493-17)


title: Bone marrow cells - SNP array (1222650-5)


title: Bone marrow cells - SNP array (1241281-14)


title: Bone marrow cells - SNP array (236365-32)


title: Bone marrow cells - SNP array (237705-14)


title: Bone marrow cells - SNP array (1247996-9)


title: Bone marrow cells - SNP array (1149317-5)


title: Bone marrow cells - SNP array (1146473-5)


title: Bone marrow cells - SNP array (1214391-9)


title: Bone marrow cells - SNP array (239348-3)


title: Bone marrow cells - SNP array (1157117-9)


title: Bone marrow cells - SNP array (237595-10)


title: Bone marrow cells - SNP array (1187886-16)


title: Bone marrow cells - SNP array (1146245-4)


title: Unstimulated KO CD4 T cells + Niacin_rep3 [Un-NA_ko_rep3]

source_name: Unstimulated KO CD4 T cells + Niacin

value: treated with 5mM niacin


title: Bone marrow cells - SNP array (1012121-11)


title: Bone marrow cells - SNP array (1009724-4)


title: Bone marrow cells - SNP array (1023797-4)


title: Bone marrow cells - SNP array (1050752-5)


title: Bone marrow cells - SNP array (1065340-6)


title: Bone marrow cells - SNP array (1035563-6)


title: Bone marrow cells - SNP array (240093-10)


title: Bone marrow cells - SNP array (239041-3)


title: Bone marrow cells - SNP array (1137050-10)


title: IAV-infected srsf5−/− HEK293 cells

city: Bei jing

first: zhimin

last: jiang

address: No.2 Yuanmingyuan West Road, Haidian District, Beijing

department: college of Veterinary medicine

institute: China agriculture university

description: FLAG empty vector

data_processing:
Reads mapping to the reference genome. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the  reference genome using BWA mem (v 0.7.12).
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling
software to identify regions of IP enrichment over background.
The interaction between transcript factor or chromatin histone modification and DNA were not random,  while they show some specific sequence preference. Homer (Heinz et al., 2010) was used to detect the  denovo sequence motif and the matched known motifs.
Peak related genes can be confirmed by PeakAnnotator, and then Gene Ontology (GO) enrichment analysis of  performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq  R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were  considered significantly enriched by peak related genes.
Genome_build: Homo sapiens GRCh38.p13 and the M gene of influenza virus : A/Puerto Rico/8/34 ( CY033578, influenza research database)
Supplementary_files_format_and_content: peaks

source_name: SRSF5 knockout 293T cells

extract_protocol:
1 mL Tri-reagent (Sigma) was added to each sample, and RNA was harvested according to the manufacturer’s instructions. RNA was eluted from beads and examined by  RNA-seq
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Two 10-cm2 dishes (107 cells per dish) of A549 cells were infected with PR8 virus for 12h. Cells were lysed with RIP lysis buffer (50mM HEPES, 150mM KCl, 2mM EDTA, 1mM NaF, 0.5% NP40, 0.5mM dithiothreitol (DTT), 1× protease inhibitor cocktail and 25U RNasin) for 30min at 4 °C. Cell lysates were centrifuged at 12,000 r.p.m. for 15min at 4 °C and the supernatants were subjected to RIP. A 50μl aliquot of cell supernatant was saved as input, and the remaining samples were each incubated with 5μg anti-Flag antibody (Abcam, ab205606) or IgG antibody (ABclonal Biotechnology, AC005)and 40μl protein A/G beads for 10h at 4 °C under gentle shaking. After IP, the beads were pelleted and washed four times with RIP wash buffer (50mM Tris pH7.4, 150mM NaCl, 1mM MgCl2 and 0.05% NP40), resuspended in 250ml of DNase digestion buffer (40mM Tris pH8.0, 10mM MgSO4 and 1mM CaCl2) and treated with 25U RNasin (Promega) and 2U DNase I (NEB) at 37 °C for 20min. Beads were then washed and resuspended in 100μl RIP wash buffer, 10% of each sample was removed for immunoblot analysis. Samples were treated with 4U proteinase K at 55 °C for 30min. The input and immunoprecipitated RNAs were isolated by 1ml of TRIzol reagent (Sigma), and vRNAs were analysed by RNA-seq.

tag: condition

value: The SRSF5 knockout 293T cells were transfected with FLAG-tagged SRSF5 constructs and infected with PR8 (MOI = 2) for 12 hr.

tag: expressing

value: expressing Flag-SRSF5 protein


title: THP-1 cells , NI2

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

institute: Institut Pasteur

data_processing:
Basecalls performed using CASAVA version 1.9
Adapters removal with cutadapt software version 1.15
Trimming of the reads using Sickle, with a quality threshold of 20 (-q 20). Reads shorter than 36 nucleotides were removed
The remaining reads were aligned to the Human genome sequence build GRCh38 with STAR assembler and we kept only uniquely mapped reads
Reads count with featureCounts programm (from the Subreads package). We used --primary option and stranded counts (option -s 1)
Differential analysis performed with Sartools version 1.3.0 (DESeq2 methods and "median" option to compute size factors).
Genome_build: GRCh38
Supplementary_files_format_and_content: columns of the TSV result file are tabular separated. This analysis file contains reads count and normalized reads count (norm. ...) for each sample (column 1 to 13). In columns 14 to the end, there are different calculations like fold change, log2 fold change, P-value, adjusted p-value for the comparison between the two conditions (rsmY versus Wt).

source_name: human THP-1 cells, non infected

growth_protocol: Legionella strains were grown in liquid BYE medium until post-exponential phase (OD 4.2). Human monocyte derived macrophages (THP-1) were cultivated in RPMI 1640+GlutaMAX

extract_protocol:
RNA of THP-1 cells was  extracted using the miRNeasy®Mini kit (Qiagen) and  libraries were constructed according to the manufactures instruction
TruSeq stranded mRNA (Illumina)

treatment_protocol: For Lp-EV purification, Bacterial cells were harvested by centrifugation at 5.000xg, 4°C for 15 min and the supernatant was twice passed through a 0.2µm PES membrane Stericup® Quick Release (Millipore) and re-centrifuged for 15min at 15.000xg, 4°C. The supernatant was treated with RNaseA/T1 (Thermo Scientific) at a final concentration of 2µg/ml RNaseA for 1h at 37°C followed by centrifugation at 150.000xg for 2h at 4°C to pellet the MVs. The MV-pellet was washed, re-centrifuged and resuspended in PBS. THP-1 cells were incubated for 3h with purified Lp-EVs or not at an MOI of 10 according to flow cytometry quantification.

value: human THP-1 cells

value: human monocyte derived macrophages

value: control


title: THP-1 cells , NI3


title: OVCAR5 SpiD7 2h rep2

city: Omaha

first: Amarnath

last: Natarajan

state: NE

address: 986805 Nebraska Medical Center

institute: University of Nebraska Medical Center

data_processing:
Total RNA from each sample was analyzed using the Illumina (Illumina Inc., San Diego, CA) TruSeq V2 RNA sequencing library kit and the HiSeq 2500 following recommended procedures.
Adaptor sequences and low quality (Phred score: 20) ends were trimmed from sequences using the Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Resulting fastq files were aligned to the human genome (GRCm38/HG38) using the software TopHat (v2.0.8) (http://ccb.jhu.edu/software/tophat/index/shtml/).
The software Cufflinks (v2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/) was used to estimate the expression values and Cuffdiff (V2.1.1) was used to determine differential expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample plus gene, log2 fold change, pvalue and qvalue

source_name: OVCAR5 cells

growth_protocol: OVCAR5 cells (2 million) were cultured in DMEM high glucose medium supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C, 5%CO2

extract_protocol:
The cells were washed with PBS post-treatment andRNA was harvested using 2 mL of Trizol. RNA purification steps were performed using the Direct-zol Miniprep Plus kit (Zymo Research, #R2070). TruSeq V2 RNA sequencing library kit from Illumina was used to generate sequencing libraries with 1 µg of total RNA from each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OVCAR5 cells were treated with 10 µM of SpiD7 for 2, 6 and 12 h

value: Ovary

value: ovarian cancer cell

value: SpiD7 treated (2h treatment)


title: OVCAR5 SpiD7 6h

value: SpiD7 treated (6h treatment)


title: THP-1 cells , NI1


title: OVCAR5 DMSO rep2

value: DMSO treated


title: OVCAR5 DMSO rep1


title: Bone marrow cells - SNP array (1003312-3)

value: Ph-positive ALL

value: bone marrow

value: leukemic cell


title: OVCAR5 SpiD7 2h rep1


title: OVCAR5 SpiD7 12h

value: SpiD7 treated (12h treatment)


title: NSCLC 40

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

country: Japan

institute: National Cancer Center

data_processing:
The prepared RNA-seq libraries underwent next-generation sequencing of 120 bp from both ends (paired-end reads) with a HiSeq2500 platform.
For expression profiling with the RNA-seq data, paired-end reads were aligned to the hg38 human genome assembly using TopHat2 (https://ccb.jhu.edu/software/tophat/index.shtml).
Genome_build: hg38
Supplementary_files_format_and_content: The expression level of each RefSeq gene was calculated from the mapped read counts using Cufflinks (http://cufflinks.cbcb.umd.edu).

source_name: adenocarcinoma

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

tag: histology

value: adenocarcinoma

tag: pathological stage

value: IB

tag: brinkman index

tag: egfr gene status


title: NSCLC 42

source_name: squamous cell carcinoma

value: squamous cell carcinoma

value: IIB

value: not evaluated


title: NSCLC 35

value: female


title: NSCLC 46


title: NSCLC 37


title: NSCLC 38

source_name: adenosquamous cell carcinoma

value: adenosquamous cell carcinoma

value: IIIA


title: NSCLC 41


title: NSCLC 45


title: NSCLC 43


title: THP-1 cells , wt1

source_name: human THP-1 cells, Lpwt-EVs

tag: cell line

value: human THP-1 cells

value: human monocyte derived macrophages

value: experiment wt Lp-Evs


title: NSCLC 33


title: NSCLC 29


title: NSCLC 31

value: IIIB


title: NSCLC 39

value: exon21 L858R


title: NSCLC 30


title: NSCLC 36


title: NSCLC 32


title: NSCLC 34


title: NSCLC 44


title: NSCLC 28

source_name: LCNEC

value: LCNEC


title: NSCLC 23


title: NSCLC 24

value: IVA


title: NSCLC 26

value: exon19 deletions


title: NSCLC 22

value: male


title: NSCLC 25


title: NSCLC 21


title: NSCLC 27

value: adenocarcinoma


title: NSCLC 20


title: NSCLC 19


title: NSCLC 17


title: NSCLC 16


title: NSCLC 18


title: NSCLC 15


title: NSCLC 12


title: NSCLC 8

value: IB


title: NSCLC 1


title: NSCLC 9


title: NSCLC 2


title: NSCLC 10

value: IIA


title: NSCLC 14

source_name: pleomorphic carcinoma

value: pleomorphic carcinoma

value: IIB


title: NSCLC 4

value: female

value: squamous cell carcinoma


title: NSCLC 5

value: not evaluated


title: NSCLC 3

source_name: non-small cell carcinoma

value: non-small cell carcinoma

value: IIIA


title: NSCLC 6


title: NSCLC 11


title: NSCLC 7


title: Rat_Thop1_1

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

institute: Nankai University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: Rattus_norvegicus_Ensemble_103
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: embryonic stem cells

extract_protocol:
Cell samples were collected and RNA was harvested using Trizol reagent. NEB Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: embryonic stem cells

tag: genotype/variation


title: Rat_Thop1_2


title: Rat_Thop1_3


title: GE_GW16_RNA-seq

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

data_processing:
RNA-seq
Cell ranger 2.1.1 was used to perform quality control and read counting of Ensemble genes with default parameter (v2.1.1) by mapping to the hg19 human genome.
Poor quality cells after the gene-cell data matrix was generated by cell ranger software using the Seurat package (v2.1.1) in Bioconductor.
The data were natural log transformed and normalized for scaling the sequencing depth to a total of 1e4 molecules per cell, followed by regressing-out the number of UMI using Seurat package.
Genome_build: hg19
Supplementary_files_format_and_content: mtx

source_name: human embryonic ganglionic emiences

extract_protocol: The human ganglionic eminences at GW09, GW11, GW13, GW16 were dissected regardless of regions, while the GW18 sample was regionally dissected.and cut into small pieces and dissociated into single-cell suspensions by using a papain-based dissociation protocol (hibernate E medium with 1 mg/ml papain (Sigma) at 37℃ on a thermo cycler with 500g for 15-20 min). Single cells were suspended in 0.04% BSA/PBS at the proper concentration to generate cDNA libraries with Single Cell 3’ Reagent Kits, according to the manufacturer’s protocol. Briefly, after the cDNA amplification, enzymatic fragmentation and size selection were performed to optimize the cDNA size. P5, P7, an index sample, and R2 (read 2 primer sequence) were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used in Illumina bridge amplification of the cDNA (http://10xgenomics.com). Finally, the library was processed on the Illumina platform for sequencing with 150bp pair-end reads.

value: human embryonic ganglionic eminences

tag: development stage

value: gestational week GW16


title: GE_GW12_RNA-seq

value: gestational week GW12-1


title: GE_GW13_RNA-seq

value: gestational week GW13


title: GE_GW18_RNA-seq

data_processing:
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
RNA-seq
Cell ranger 2.1.1 was used to perform quality control and read counting of Ensemble genes with default parameter (v2.1.1) by mapping to the hg19 human genome.
Poor quality cells after the gene-cell data matrix was generated by cell ranger software using the Seurat package (v2.1.1) in Bioconductor.
The data were natural log transformed and normalized for scaling the sequencing depth to a total of 10e4 molecules per cell, followed by regressing-out the number of UMI using Seurat package.
ATAC-seq
Illumina Casava 1.8 software used for basecalling
Reads were aligned to human reference genome hg19 by bowtie2
Genome_build: hg19
Supplementary_files_format_and_content: csv and bw

source_name: human embryonic ganglionic eminences

extract_protocol: The human ganglionic eminence at GW18 was dissected and cut into small pieces and dissociated into single-cell suspensions by using a papain-based dissociation protocol (hibernate E medium with 1 mg/ml papain (Sigma) at 37℃ on a thermo cycler with 500g for 15-20 min). Single cells were suspended in 0.04% BSA/PBS at the proper concentration to generate cDNA libraries with Single Cell 3’ Reagent Kits, according to the manufacturer’s protocol. Briefly, after the cDNA amplification, enzymatic fragmentation and size selection were performed to optimize the cDNA size. P5, P7, an index sample, and R2 (read 2 primer sequence) were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used in Illumina bridge amplification of the cDNA (http://10xgenomics.com). Finally, the library was processed on the Illumina platform for sequencing with 150bp pair-end reads.  Besides, the ganglionic eminence cells at GW18 also carried out ATAC-Seq experiments.

tag: developmental stage

value: gestational week (GW) 18


title: GE-GW18-2-LGE-RNA-seq

data_processing:
RNA-seq
Cell ranger 2.1.1 was used to perform quality control and read counting of Ensemble genes with default parameter (v2.1.1) by mapping to the hg19 human genome.
Poor quality cells after the gene-cell data matrix was generated by cell ranger software using the Seurat package (v2.1.1) in Bioconductor.
The data were natural log transformed and normalized for scaling the sequencing depth to a total of 1e4 molecules per cell, followed by regressing-out the number of UMI using Seurat package.
Genome_build: hg19
Supplementary_files_format_and_content: txt

extract_protocol: The human ganglionic eminences at GW09, GW12, GW13, GW16,were dissected regardless of regions, while the GW18 sample was regionally dissected.and cut into small pieces and dissociated into single-cell suspensions by using a papain-based dissociation protocol (hibernate E medium with 1 mg/ml papain (Sigma) at 37℃ on a thermo cycler with 500g for 15-20 min). Single cells were suspended in 0.04% BSA/PBS at the proper concentration to generate cDNA libraries with Single Cell 3’ Reagent Kits, according to the manufacturer’s protocol. Briefly, after the cDNA amplification, enzymatic fragmentation and size selection were performed to optimize the cDNA size. P5, P7, an index sample, and R2 (read 2 primer sequence) were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used in Illumina bridge amplification of the cDNA (http://10xgenomics.com). Finally, the library was processed on the Illumina platform for sequencing with 150bp pair-end reads.

value: human embryonic ganglionic emiences


title: GE-GW18-2-MGE-RNA-seq


title: GE-GW12-2-Lane1-RNA-seq

value: gestational week (GW) 12


title: GE-GW12-2-Lane2-RNA-seq


title: GE-GW12-2-Lane3_RNA-seq


title: GE_GW09_RNA-seq

value: gestational week GW09


title: ribo_wt_base3_ip

city: Columbus

first: Federica

last: Accornero

state: OH

address: 473 W 12th Ave.

institute: Ohio State University Medical Center

data_processing:
Library strategy: RiboTag-seq
Sequencing alignment, hisat2 v2.2.0.
Read count matrix formation, htseq v2.0.
Peak calling, exomePeak2 v1.2. FDR <0.05 and peak enrichment > 4.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: htseq read counts (.txt).
Supplementary_files_format_and_content: exomePeak2 output (.xlsx).

source_name: mouse plantaris tissue

extract_protocol:
Trizol isolation after sample collection (either total RNA or IP RNA).
m6A samples were constructed using NEB Illumina kit. m6A samples were used for meRIP-seq analysis.
ribo samples were constructed using the DNBseq preparation method (BGI). ribo samples were used for Ribotag-seq analysis.

treatment_protocol: Muscle overload (mo) was attained using bilateral synergistic ablation of the soleus and gastrocnemius.

value: METTL3 wildtype control

value: plantaris

tag: muscle state

value: normal

tag: rna isolation

value: Ribotag IP RNA


title: ribo_wt_base3_input

tag: tissue

value: total RNA


title: ribo_wt_base2_ip

tag: genotype


title: ribo_wt_base1_ip


title: ribo_ko_base2_ip

value: HSA-driven METTL3 knockout


title: ribo_ko_base3_ip


title: ribo_ko_base1_ip


title: ribo_wt_base1_input


title: ribo_ko_base3_input


title: ribo_ko_base2_input


title: ribo_wt_base2_input


title: Rat_WT

tag: cell type

value: WT


title: GE-GW18-2-CGE-RNA-seq


title: ribo_ko_base1_input


title: Sample208.Mouse.204634420002_R05C01

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Lung species=Mouse

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

source_name: Lung

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: age

tag: Sex

value: Male

tag: samplename

value: Control

tag: group

tag: durationtreatment

tag: mouse strain


title: Sample207.Mouse.204634420002_R04C01

tag: condition

value: Treated (+Dox)


title: Sample205.Mouse.204634420002_R02C01

value: Female


title: Sample206.Mouse.204634420002_R03C01


title: Sample204.Mouse.204634420002_R01C01


title: Sample203.Mouse.204634420003_R06C02


title: Sample189.Mouse.204854860008_R04C02

description: genomic DNA methylation from tissue=Muscle species=Mouse

source_name: Muscle


title: Sample190.Mouse.204854860008_R05C02


title: Sample200.Mouse.204634420003_R03C02


title: Sample192.Mouse.204634420003_R01C01


title: Sample201.Mouse.204634420003_R04C02


title: Sample188.Mouse.204854860008_R03C02


title: Sample191.Mouse.204854860008_R06C02


title: Sample209.Mouse.204634420002_R06C01


title: Sample186.Mouse.204854860008_R01C02


title: Sample187.Mouse.204854860008_R02C02


title: Sample177.Mouse.204854860032_R04C02

description: genomic DNA methylation from tissue=Skin species=Mouse

source_name: Skin


title: Sample175.Mouse.204854860032_R02C02


title: Sample184.Mouse.204854860008_R05C01


title: Sample174.Mouse.204854860032_R01C02


title: Sample172.Mouse.204854860032_R05C01


title: Sample176.Mouse.204854860032_R03C02


title: Sample171.Mouse.204854860032_R04C01


title: Sample170.Mouse.204854860032_R03C01


title: Sample169.Mouse.204854860032_R02C01


title: Sample202.Mouse.204634420003_R05C02


title: Sample193.Mouse.204634420003_R02C01


title: Sample173.Mouse.204854860032_R06C01


title: Sample160.Mouse.204551090083_R05C01

description: genomic DNA methylation from tissue=Kidney species=Mouse

source_name: Kidney


title: Sample168.Mouse.204854860032_R01C01


title: Sample185.Mouse.204854860008_R06C01


title: Sample161.Mouse.204551090083_R06C01


title: Sample157.Mouse.204551090083_R02C01


title: Sample158.Mouse.204551090083_R03C01


title: Sample143.Mouse.204551090082_R06C02

description: genomic DNA methylation from tissue=Spleen species=Mouse

source_name: Spleen


title: Sample153.Mouse.204551090084_R04C02


title: Sample159.Mouse.204551090083_R04C01


title: Sample155.Mouse.204551090084_R06C02


title: Sample152.Mouse.204551090084_R03C02


title: Sample154.Mouse.204551090084_R05C02


title: Sample156.Mouse.204551090083_R01C01


title: Sample142.Mouse.204551090082_R05C02


title: Sample145.Mouse.204551090084_R02C01


title: NSCLC 13

tag: gender

value: male

tag: histology

value: squamous cell carcinoma

tag: pathological stage

value: IIIA

tag: brinkman index

tag: egfr gene status

value: not evaluated


title: Sample141.Mouse.204551090082_R04C02


title: Sample139.Mouse.204551090082_R02C02


title: Sample129.Mouse.204551090031_R04C02

description: genomic DNA methylation from tissue=Liver species=Mouse

source_name: Liver


title: Sample137.Mouse.204551090082_R06C01


title: Sample125.Mouse.204551090031_R06C01


title: Sample123.Mouse.204551090031_R04C01


title: Sample136.Mouse.204551090082_R05C01


title: Sample124.Mouse.204551090031_R05C01


title: Sample122.Mouse.204551090031_R03C01


title: Sample121.Mouse.204551090031_R02C01


title: Sample119.Mouse.204529320124_R06C02


title: Sample120.Mouse.204551090031_R01C01


title: Sample118.Mouse.204529320124_R05C02


title: Sample117.Mouse.204529320124_R04C02


title: Sample113.Mouse.204529320124_R06C01


title: Sample115.Mouse.204529320124_R02C02


title: Sample110.Mouse.204529320124_R03C01


title: Sample116.Mouse.204529320124_R03C02


title: Sample114.Mouse.204529320124_R01C02


title: Sample106.Mouse.204549720005_R05C02


title: Sample105.Mouse.204549720005_R04C02


title: Sample109.Mouse.204529320124_R02C01


title: Sample102.Mouse.204549720005_R06C01


title: Sample126.Mouse.204551090031_R01C02


title: Sample104.Mouse.204549720005_R02C02


title: Sample103.Mouse.204549720005_R01C02


title: Sample111.Mouse.204529320124_R04C01


title: Sample108.Mouse.204529320124_R01C01


title: Sample127.Mouse.204551090031_R02C02


title: Sample98.Mouse.204549720005_R02C01


title: Sample97.Mouse.204549720005_R01C01


title: Sample95.Mouse.204549720013_R05C02


title: Sample96.Mouse.204549720013_R06C02


title: Sample94.Mouse.204549720013_R04C02


title: Sample93.Mouse.204549720013_R03C02


title: Sample92.Mouse.204549720013_R02C02


title: Sample112.Mouse.204529320124_R05C01


title: Sample91.Mouse.204549720013_R01C02


title: Sample107.Mouse.204549720005_R06C02


title: Sample90.Mouse.204549720013_R06C01


title: Sample101.Mouse.204549720005_R05C01


title: Sample99.Mouse.204549720005_R03C01


title: Sample82.Mouse.204549720015_R04C02


title: Sample78.Mouse.204549720015_R06C01


title: Sample83.Mouse.204549720015_R05C02


title: Sample89.Mouse.204549720013_R05C01


title: Sample79.Mouse.204549720015_R01C02


title: Sample87.Mouse.204549720013_R03C01


title: Sample100.Mouse.204549720005_R04C01


title: Sample86.Mouse.204549720013_R02C01


title: Sample88.Mouse.204549720013_R04C01


title: Sample77.Mouse.204549720015_R05C01


title: Sample85.Mouse.204549720013_R01C01


title: Sample80.Mouse.204549720015_R02C02


title: Sample70.Mouse.204549720014_R04C02


title: Sample69.Mouse.204549720014_R03C02


title: Sample68.Mouse.204549720014_R02C02


title: Sample67.Mouse.204549720014_R01C02


title: Sample66.Mouse.204549720014_R06C01


title: Sample65.Mouse.204549720014_R05C01


title: Sample64.Mouse.204549720014_R04C01


title: Sample62.Mouse.204549720014_R02C01


title: Sample61.Mouse.204549720014_R01C01


title: Sample84.Mouse.204549720015_R06C02


title: Sample59.Mouse.204529320025_R05C02


title: Sample75.Mouse.204549720015_R03C01


title: Sample60.Mouse.204529320025_R06C02


title: Sample81.Mouse.204549720015_R03C02


title: Sample58.Mouse.204529320025_R04C02


title: Sample74.Mouse.204549720015_R02C01


title: Sample53.Mouse.204529320025_R05C01


title: Sample55.Mouse.204529320025_R01C02


title: Sample48.Mouse.204529320028_R06C02


title: Sample43.Mouse.204529320028_R01C02


title: Sample56.Mouse.204529320025_R02C02


title: Sample50.Mouse.204529320025_R02C01


title: Sample41.Mouse.204529320028_R05C01


title: Sample45.Mouse.204529320028_R03C02


title: Sample40.Mouse.204529320028_R04C01


title: Sample51.Mouse.204529320025_R03C01


title: Sample49.Mouse.204529320025_R01C01


title: Sample57.Mouse.204529320025_R03C02


title: Sample44.Mouse.204529320028_R02C02


title: Sample46.Mouse.204529320028_R04C02


title: Sample42.Mouse.204529320028_R06C01


title: Sample47.Mouse.204529320028_R05C02


title: Sample39.Mouse.204529320028_R03C01


title: Sample35.Mouse.204529320077_R05C02


title: Sample37.Mouse.204529320028_R01C01


title: Sample36.Mouse.204529320077_R06C02


title: Sample34.Mouse.204529320077_R04C02


title: Sample32.Mouse.204529320077_R02C02


title: Sample33.Mouse.204529320077_R03C02


title: Sample31.Mouse.204529320077_R01C02


title: Sample52.Mouse.204529320025_R04C01


title: Sample30.Mouse.204529320077_R06C01


title: Sample29.Mouse.204529320077_R05C01


title: Sample38.Mouse.204529320028_R02C01


title: Sample18.Mouse.204529320074_R06C01


title: Sample19.Mouse.204529320074_R01C02


title: Sample23.Mouse.204529320074_R05C02


title: Sample21.Mouse.204529320074_R03C02


title: Sample28.Mouse.204529320077_R04C01


title: Sample24.Mouse.204529320074_R06C02


title: Sample22.Mouse.204529320074_R04C02


title: Sample25.Mouse.204529320077_R01C01


title: Sample15.Mouse.204529320074_R03C01


title: Sample17.Mouse.204529320074_R05C01


title: Sample27.Mouse.204529320077_R03C01


title: Sample20.Mouse.204529320074_R02C02


title: Sample12.Mouse.204529320080_R06C02


title: Sample10.Mouse.204529320080_R04C02


title: Sample11.Mouse.204529320080_R05C02


title: Sample9.Mouse.204529320080_R03C02


title: Sample8.Mouse.204529320080_R02C02


title: Sample7.Mouse.204529320080_R01C02


title: Sample6.Mouse.204529320080_R06C01


title: Sample5.Mouse.204529320080_R05C01


title: Sample4.Mouse.204529320080_R04C01


title: Sample3.Mouse.204529320080_R03C01


title: Sample2.Mouse.204529320080_R02C01


title: Sample26.Mouse.204529320077_R02C01


title: Sample13.Mouse.204529320074_R01C01


title: Sample16.Mouse.204529320074_R04C01


title: Sample1.Mouse.204529320080_R01C01


title: HCT50HD6-SUR

city: Barcelona

first: Fernando

last: Salvador Gómez

address: Balmes 89, 3º 7

country: Spain

institute: SOLTI

description: A minimum of roughly 100 ng of total RNA was used to measure the expression of 540 genes and the five housekeeping genes (nCounter platform, Nanostring Technologies, Seattle, WA, USA). Data were log2 transformed and normalized using the housekeeping genes.

hyb_protocol: NOT PROVIDED

scan_protocol: NOT PROVIDED

data_processing: Data were normalized using 5 housekeeping genes (ACTB, MRPL19, PSMC4, RPLP0, and SF3A1), and log2 transformed

label: NOT PROVIDED

source_name: Breast tumor

label_protocol: NOT PROVIDED

extract_protocol: At baseline, a section of the formalin-fixed paraffin-embedded (FFPE) breast tissue was examined with haematoxylin and eosin (H&E) staining to confirm the presence of invasive tumor cells and to determine the minimum tumor surface area. For samples obtained at Cycle 2 Day 1, those without invasive tumor cells were also profiled. For RNA purification (High Pure FFPET RNA isolation kit, Roche, Indianapolis, IN, USA), at least 1–5 10 μm FFPE slides were used for each tumor specimen, and macrodissection was performed (when needed) to avoid contamination with normal breast tissues. A minimum of roughly 100 ng of total RNA was used to measure the expression of 540 genes and the five housekeeping genes (nCounter platform, Nanostring Technologies, Seattle, WA, USA).

tag: cellularity

value: N/A; no information

tag: tumor infiltrating lymphocytes (tils)

tag: pcrb

tag: er

tag: pr


title: TNOV9YGI-2W

tag: age


title: G0SD5Q8E-SUR


title: L84E9CY0-SCR

value: No

value: Positive

value: Negative


title: KG4Z3F5Y-SCR


title: KG4Z3F5Y-2W


title: ZCFTKN47-SUR


title: Z4L9CAMF-2W


title: 6G69A8TO-2W


title: 7WDDMP1Z-SUR


title: 0DZPJAVE-SUR


title: V90RW11S-2W


title: 8FKRMT1P-SUR


title: 0DZPJAVE-2W


title: 8U7P2ISX-2W


title: 6HXE01UJ-SUR


title: ZCFTKN47-2W


title: AV0X5XMI-2W


title: AV0X5XMI-SUR


title: Q37JN3NW-2W


title: UTRSAKYW-SUR


title: 1Q2LAXZY-2W


title: 6G69A8TO-SUR


title: XSFXJYSH-SUR


title: UTRSAKYW-2W


title: Patient Robust LVEF improvement-3

city: Bonn

first: Mohammed Rabiul

last: Hosen

state: NRW

address: Venusberg-Campus 1

department: Internal Medicine-II

country: Germany

institute: University of Bonn

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package:RQ manager
The amplification curves were analyzed with the Program RQ manager Version 1.2.1 (Applied Biosystems) to calculate CT values, using the same threshold across all respective plasma samples
ΔΔCT values were calculated by normalizing to RNU6B, which was the most stably expressed endogenous control RNA across the plasma samples.
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., Control/Test) ratios.

label: FAM

source_name: Circulating plasma-derived EV-RNA

label_protocol: MicroRNA arrays were performed using the TaqMan Array Human MicroRNA Card A v2.0 (Applied Biosystems  #4398965) in a 7900 HT fast real-time PCR instrument (Applied Biosystems). Total RNA (500 ng) from the plasma of patients with robust LVEF improvement (n=3) and no LVEF improvement (n=3) were converted into cDNA by use of the TaqMan MicroRNA Reverse Transcription Kit and specific Megaplex RT Primers (Applied Biosystems, #4399966). Subsequently, preamplification was performed using 2.5 µL of the RT product, Megaplex PreAmp Primers (Applied Biosystems, #4399233), and the TaqMan PreAmp Master Mix (Applied Biosystems, #4488593). 9 µl of the preamplification product mixture was used for the final amplification with the MicroRNA Array Card and TaqMan Universal Master Mix II.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: cell type

value: TAVR patients

tag: activation agent

value: Test

tag: time


title: Patient Robust LVEF improvement-2

description: Test


title: HCT50HD6-2W


title: XSFXJYSH-2W


title: Patient Robust LVEF improvement-1

description: Test


title: p0_rep2_rhx_10_input

city: Madison

first: Brent

last: Anderson

state: WI

address: 1550 Linden Dr.

department: Bacteriology

institute: University of Wisconsin-Madison

data_processing:
Adapters were removed with CutAdapt (--quality-base=33 -a AGATCGGAAGAGC -a CGGAAGAGCACAC -a GGGGGGGGGGGGGGG -n 3 -m 20 --match-read-wildcards -o)
Reads were aligned with bowtie2 (-U -q --end-to-end --very-sensitive -p 6 --phred33)
Aligned reads were filtered with samtools and made into a sampling object with a custom python script (bootstrap_sam_file.py, command "parse")
Read counts at 10bp resolution were bootstrapped with a custom python script (bootstrap_sam_file.py, command "sample")
PurR ChIP enrichment was calculated in R by determining the median and SD of the bootstraps at 10bp resolution. The median cpm for ChIP samples were divided by the median cpm for corresponding input samples. The input for rep3 was used to calculate enrichment for rep1. Infinite values (coming from regions with no reads, such as ribosomal operons) were excluded in the final dataset.
Peaks were manually called as all locations with greater than 2-fold enrichment over input
Genome_build: CP020102 concatenated with CP020103 (Bacillus subtilis NCIB3610 genome concatenated with the megaplasmid pBS32)
Supplementary_files_format_and_content: "cpm" files show the mean read counts per million in 10bp intervals across the genome as well as the standard deviation of that mean across 2 replicates (input) or 3 replicates (chip)
Supplementary_files_format_and_content: "log2_enrichment" files show the mean log2 enrichment of chip samples relative to input samples in 10bp intervals across the genome, as well as the standard deviation of that mean across 3 replicates
Supplementary_files_format_and_content: The files are in both txt and Rdata formats

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: bacteria

growth_protocol: Bacterial cultures were grown to OD ~ 0.5 at 37 C at 250 RPM shaking. The media used is described in the SAMPLES section.

extract_protocol:
Culture was crosslinked with formaldehyde and incubated at 37 C for 7-8 min. Crosslinked samples were held on ice for at least 30 min, centrifuged at 5,000 xg for 15 min, washed twice with ice-cold 25 mL 1X PBS, and resuspended in 1 mL ice-cold Solution A (20% sucrose, 10 mM Tris pH 8, 10 mM EDTA, 50 mM NaCl). Samples treated with lysozyme and sonicated to shear gDNA. A PurR polyclonal antibody was incubated with the sample before being pulled down with Dynabeads Protein A.
This protocol closely followed that of Bonocora and Wade (2015). Briefly, the ends of immunoprecipitated DNA were blunted and 5' phosphorylated with a blunt enzyme mix. Then, A-tails were added to the 3' ends with Klenow fragment (exo-). Adapters were ligated on with a Quick Ligase. The samples were reverse crosslinked and protein was degraded by incubation with proteinase K. DNA was purified with SPRI Sera-Mag SpeedBead clean-up. Input samples were treated the same, except they were first treated with RNase A and proteinase K, followed by a SPRI clean-up, blunting/5' phosphorylation, A-tailing, and ligation. Two successive SPRI clean-ups were used at the end to avoid adapter carryover. qPCR was used to determine the number of cycles for final library amplification.

treatment_protocol: As delineated in the SAMPLES section, cultures were treated with the drug arginine hydroxamate for 10 min.

tag: genotype

value: (p)ppGpp-null

tag: growth medium

tag: treatment

value: treated with arginine hydroxamate for 10 min

tag: chip antibody

value: none (input DNA)


title: p0_rep3_rhx_10_input


title: DA465RN0-SUR


title: DA465RN0-2W


title: 6NG1D6S9-2W


title: ODY1DV9D-2W


title: TM14IE05-SUR


title: TM14IE05-2W


title: Patient no LVEF improvement-3

description: Control


title: BF0XCR0I-SUR


title: Patient no LVEF improvement-1

description: Control


title: p0_rep2_rhx_00_input

value: untreated


title: SS9ZB4OA-2W


title: Patient no LVEF improvement-2

description: Control

value: Control


title: p0_rep1_rhx_10_chip

value: PurR polyclonal, anti-rabbit


title: p0_rep3_rhx_00_chip


title: UMNXPI4D-2W


title: p0_rep2_rhx_00_chip


title: 01BXNEBL-SUR


title: 31RJISH4-SUR


title: p0_rep1_rhx_00_chip


title: 74NRA1RC-2W


title: wt_rep3_rhx_10_input

value: wild type


title: 74NRA1RC-SCR


title: p0_rep2_rhx_10_chip


title: p0_rep3_rhx_10_chip


title: p0_rep3_rhx_00_input


title: 9Z1TKP77-SUR


title: wt_rep2_rhx_10_input


title: 4ZS39E9D-2W


title: PFPX382J-2W


title: wt_rep1_rhx_10_chip


title: wt_rep2_rhx_00_chip


title: wt_rep1_rhx_00_chip


title: wt_rep2_rhx_10_chip


title: DA465RN0-SCR


title: XSFXJYSH-SCR

value: Yes


title: TM14IE05-SCR


title: wt_rep3_rhx_00_chip


title: wt_rep2_rhx_00_input


title: 35ZT0755-SUR


title: 35ZT0755-SCR


title: wt_rep3_acgu_input


title: wt_rep2_acgu_input


title: wt_rep3_acgu_chip


title: wt_rep2_acgu_chip


title: K3RVM5DF-SUR


title: K3RVM5DF-SCR


title: UTRSAKYW-SCR


title: 35ZT0755-2W


title: wt_rep1_acgu_chip


title: 30PYG3WL-2W


title: 30PYG3WL-SCR


title: wt_rep3_rhx_00_input


title: Z4L9CAMF-SCR


title: mRNA-Seq P18 Sp ko replicate 2

city: beijing

first: shuntai

last: yu

state: beijing

address: 7 Science Park Road ZGC Life Science Park, Beijing

department: transgenic animal center

institute: NIBS

data_processing:
Basecalls performed using CASAVA version 1.9.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR v2.6.1a with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). 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: GRCm38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include RPKM (for single-end sequencing samples) or FPKM (for paired-end sequencing samples) values for each Sample.

molecule: polyA RNA

source_name: spermatocytes

growth_protocol: Mice were bred and maintained under a controlled temperature (22-25ºC) with a 12 h-light/12 h-dark cycle (light on from 7 am to 7 pm).

extract_protocol:
Total RNA of testes was extracted using Trizol reagent (15596026; Invitrogen). Poly(A) mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L).
Libraries for mRNA abundance examination were prepared by using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

tag: strain

tag: Sex

value: Male

value: Spermatocytes


title: wt_rep3_rhx_10_chip


title: mRNA-Seq P18 Sp ko replicate 3


title: K3RVM5DF-2W


title: mRNA-Seq P18 Sp ko replicate 1


title: RCZ5D4VH-SUR


title: mRNA-Seq P18 Sp het replicate 2


title: mRNA-Seq P18 Sp het replicate 1


title: RCZ5D4VH-2W


title: mRNA-Seq P14 ko replicate 3

source_name: testicular cells

value: Testicular cells


title: mRNA-Seq P14 ko replicate 1


title: mRNA-Seq P14 ko replicate 2


title: mRNA-Seq P18 Sp het replicate 3


title: 2Z12INVQ-2W

value: N/A; no information


title: 2Z12INVQ-SCR

value: No


title: L84E9CY0-2W


title: I5G6G8WD-SUR


title: RCZ5D4VH-SCR


title: mRNA-Seq P14 het replicate 3


title: mRNA-Seq P14 het replicate 2


title: I5G6G8WD-2W


title: I5G6G8WD-SCR


title: mRNA-Seq P14 het replicate 1


title: N_Ctrl3

city: Wuhan

first: Han

last: Wang

state: Hubei

address: 1095 Jiefang Avenue

department: Department of Gastroenterology,

institute: Tongji Hospital, Tongji Medical College,

data_processing:
Sequencing libraries were generated using NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) and sequenced on an Illumina platform. Paired-end reads were then generated and evaluated for quality control.
Clean raw data with high quality were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
For quantification, FeatureCouts was used to count the read numbers mapped of each gene. Differential expression analysis between two groups (three biological replicates per condition) was performed using DESeq2 R package.
Genome_build: mm9
Supplementary_files_format_and_content: text file named readcount_genename lists gene expression of every gene of 6 samples

source_name: Spleen lymphocytes

extract_protocol:
RNA was extracted from cultured naïve CD4+ t cells and purified by RNeasy kits (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Naïve CD4+ T cells were seeded in 96-well U-bottom with CD3/CD28 beads, IL-2, anti-IFNγ antibody, anti-IL-4 antibody, and NETs/Vehicle for 72h.

value: Naive CD4+ T cells

value: Vehicle


title: N_Ctrl2


title: KG4Z3F5Y-SUR


title: N_NETs3

value: NETs


title: N_Ctrl1


title: N50SBJ07-SUR


title: XHOGUOOX-SUR


title: N_NETs2


title: I4I5IDSJ-SUR


title: UI1LY9M8-SUR


title: N_NETs1


title: U6GIK59G-SUR


title: Old adult CBA/CaJ mouse AN-3

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out using Partek Flow. Alignment was conducted with TopHat2 using mouse genome (mm10) and the default option set
Aligned reads were quantified to annotation model (Partek E/M) using mm10 and RefSeq transcripts 83 (2017-11-01) with the settings: a) strict paired-end compatibility, b) require junction reads to match introns, c) min read overlap with feature 100% of read length, d) min reads 10
Gene counts were analyzed using DESeq2 to determine normalized expression measures and signficant differences (p-adjusted) for all pairwise comparisons among the postnatal samples
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of normalized counts and comparison measures

source_name: Isolated auditory nerves

extract_protocol:
Microdissections were performed to isolate the auditory nerve from mouse cochlear structures. Two cochleas from each mouse were pooled for individual samples. Total RNA was purified from each sample using the miRNeasy Mini Kit per the manufacturer’s instructions. Quality of each total RNA isolation was assessed using the Agilent 2100 Bioanalyzer and low-quality samples showing degradation or contamination were excluded.
RNA libraries were prepared for sequencing using standard Illumina protocols using Illumina's TruSeq RNA Library Prep Kit

value: Auditory nerve cells

tag: tissue

value: Isolated auditory nerves

value: CBA/CaJ


title: Old adult CBA/CaJ mouse AN-2


title: 9Z1TKP77-2W


title: H4FB6U67-SCR

value: Negative


title: Young adult CBA/CaJ mouse AN-2

value: 2 mo


title: UI1LY9M8-2W


title: mouse-cerebellum granule cell-WT-RIP-Ythdf2-rep1

city: Shenzhen

first: Lixin

last: Yang

address: 1088 Xueyuan Avenue, Shenzhen

department: brain institute

institute: Southern Universith of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: Cerebellum

extract_protocol:
Cerebellum were dissected and dissociated with trypsin, then cells were treated following the manual of the EZ-Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore) with minor modifications. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
100 ng RNA of input and elutes after RIP were used to generate the library using the TruSeq Stranded RNA Sample Preparation Kit (Illumina).

value: mouse-cerebellum granule cell

tag: antibody

value: Wildtype

value: Cerebellum

value: post natal day 8


title: Young adult CBA/CaJ mouse AN-1


title: UI1LY9M8-SCR

tag: cellularity


title: mouse-cerebellum granule cell-WT-RIP-Ythdf2-rep2


title: PNH73SPD-2W

tag: tumor infiltrating lymphocytes (tils)


title: 11RLNSX4-SUR

tag: pcrb


title: mouse-cerebellum granule cell-WT-RIP-Ythdf1-rep2


title: U6GIK59G-SCR

tag: er


title: U6GIK59G-2W

tag: pr


title: mouse-cerebellum granule cell-WT-RIP-Ythdf1-rep1

tag: age


title: mouse-cerebellum granule cell-WT-RIP-Input-rep2

tag: cell type


title: Old adult CBA/CaJ mouse AN-1


title: 9Z1TKP77-SCR


title: 7-AE1_dKO_NaCl_1_10-AE1_dKO_NaCl_2

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: KAPA RNA Stranded PolyA

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Ensembl version 98
Expression values were also computed using RSEM version 1.2.28 based on Ensembl version 98 transcript annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

source_name: alveolar epithelial cell type 1

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from polyA-enriched mRNA using the KAPA Stranded mRNA-Seq Kit and were further amplified for sequencing.

treatment_protocol: LPS inhalation (5ml of 2mg/ml). The primary lung ECs were freshly isolated using Liberase and DNase-I digestion. The cells were sorted directly into Trizol (Ambion, #15596018)

value: Stat1/Stat2 dKO

value: 6 to 12 weeks

value: Male

value: Lung

value: alveolar epithelial


title: mouse-cerebellum granule cell-WT-RIP-Input-rep1


title: 9-Bronc_dKO_NaCl_1_12-Bronc_dKO_NaCl_2

description: KAPA RNA Stranded PolyA

source_name: Bronchiolar epithelial cells

value: bronchiolar epithelial


title: 6-Bronc_dKO_LPS_2

description: KAPA RNA Stranded PolyA


title: OBIA1NKL-2W

value: N/A; no information


title: OBIA1NKL-SCR

value: No


title: Young adult CBA/CaJ mouse AN-3

value: Auditory nerve cells


title: 5-AE2_dKO_LPS_2

description: KAPA RNA Stranded PolyA

source_name: alveolar epithelial cell type 2


title: 203712390027_R08C01

city: Rochester

first: Julie

last: Cunningham

state: MN

address: 200 First Street SW

department: Department of Laboratory Medicine and Pathology

institute: Mayo Clinic

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data were normalized separately for the two platforms, and batch correction across the two platforms were performed via COMBAT

label: Cy3, Cy5

source_name: Fresh Frozen Tumor

extract_protocol: genomic DNA extraction

tag: gender

value: Female

tag: histology

value: Ovarian Clear Cell Carcinoma (OCCC)

tag: batch

value: epic


title: 203715540037_R08C01


title: 203715540065_R08C01


title: 203715540106_R08C01


title: 203711910041_R08C01


title: 9X9YV08N-2W


title: 8-AE2_dKO_NaCl_1

description: KAPA RNA Stranded PolyA

tag: genotype


title: 4-AE1_dKO_LPS_2

description: KAPA RNA Stranded PolyA


title: 203711910032_R08C01


title: 3-Bronc_dKO_LPS_1

description: KAPA RNA Stranded PolyA


title: 203711910057_R08C01


title: 6G69A8TO-SCR

value: Negative


title: 9X9YV08N-SCR


title: 203715540065_R07C01


title: 203715540106_R07C01


title: 203711910057_R07C01


title: 203712390027_R07C01


title: 203712390023_R07C01


title: 8U7P2ISX-SCR


title: 6HXE01UJ-SCR

value: Yes


title: 2-AE2_dKO_LPS_1

description: KAPA RNA Stranded PolyA


title: 203711910041_R07C01


title: ZW7924M3-SUR


title: ZW7924M3-2W


title: 18-Bronc_Nlrc5KO_NaCl_1

description: KAPA RNA Stranded PolyA

value: Nlrc5 KO


title: 203711910032_R07C01


title: 17-AE2_Nlrc5KO_NaCl_1

description: KAPA RNA Stranded PolyA


title: 203711910031_R07C01


title: 203715540107_R07C01


title: 203715540107_R06C01


title: 16-AE1_Nlrc5KO_NaCl_1

description: KAPA RNA Stranded PolyA


title: 203715540066_R06C01


title: 203715540106_R06C01


title: 203715540037_R06C01


title: 1-AE1_dKO_LPS_1

description: KAPA RNA Stranded PolyA


title: 203712390023_R06C01


title: 15-Bronc_Nlrc5KO_LPS_1

description: KAPA RNA Stranded PolyA


title: IHBUBOHT-SUR


title: 203711910057_R06C01


title: 203711910041_R06C01


title: 203711910031_R06C01


title: 13-AE1_Nlrc5KO_LPS_1

description: KAPA RNA Stranded PolyA


title: 203715540107_R05C01


title: 14-AE2_Nlrc5KO_LPS_1

description: KAPA RNA Stranded PolyA


title: IHBUBOHT-SCR


title: 203715550048_R05C01


title: 203715540037_R05C01


title: 11-AE2_dKO_NaCl_2

description: KAPA RNA Stranded PolyA


title: BR0ZPNRL-SUR


title: 203712390027_R05C01


title: BR0ZPNRL-2W


title: BR0ZPNRL-SCR


title: CYZZMN25-2W


title: L80A Input DNA_2

city: Münster

first: Dong

last: Han

address: Röntgenstraße 20

department: Cell and developmental biology

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
The sequencing data were uploaded to the Galaxy web platform, and we used the public server at usegalaxy.org to analyze the data
Sequence reads were aligned to the mm10 mouse reference genome using Map with Bowtie for Illumina with default parameters except suppress all alignments for a read if more than 1 reportable alignments exist.
Peak calling was performed using MACS  with the following parameters: do not build the shifting model, shift size 100.
The Wig files generated before were converted into bigWig files for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: mouse embryonic stem cells

growth_protocol: ESCs were culture on gelatin-coated dishes in ESCs medium: Konckout DMEM medium supplemented with 10% KSR, 10% FCS, 1% Glutamax, 1% NEAA, 1% penicillin-streptomycin, 1% b-mercaptoethanol, and 20 ng/ml human recombinant LIF.

extract_protocol:
Cells were lysed in lysis buffer 1 (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM 0.5 M EDTA, 10% glycerol, 0.5% IGEPAL CA630, 0.25% Triton X-100) containing protease inhibitor cocktail (Sigma) for 30 min at 4°C and washed in lysis buffer 2 (10 mM Tris-HCl [pH 8.0], 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). Chromatin was sheared using Diagenode Bioruptor (high power, 40 cycles of 30 s on and 30 s off) equipped with a water-cooling system (4°C) in 1 mL of sonication buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 0.5% SDS) per 1 ´ 107 cells.
ChIP seq sequencing libraries were prepared according to the instruction of KAPA Hyper Prep Kit (Roche).

value: Mixture of C57BL/6, C3H and CD7

value: mouse embryonic stem cells


title: 203715550048_R04C01


title: H3K9me3_ChIPSeq_L80A Oct4_ESCs_2

value: Mixture of C57BL/6, C3H and CD9

value: Rabbit anti-H3K9me3 (ab8898, Abcam)


title: 203715540107_R04C01


title: WT Input DNA_2

value: Mixture of C57BL/6, C3H and CD6


title: IHBUBOHT-2W


title: CYZZMN25-SCR


title: 203715540106_R04C01


title: 203711910032_R05C01


title: 203715540065_R04C01


title: TNOV9YGI-SCR


title: H3K9me3_ChIPSeq_WT Oct4_ESCs_2


title: PNH73SPD-SUR


title: 203711910041_R04C01


title: 203712390027_R04C01


title: H3K9me3_ChIPSeq_WT Oct4_ESCs_1


title: 203712390023_R05C01


title: 203711910031_R04C01


title: H3K36me3_ChIPSeq_L80A Oct4_ESCs_2

value: Mixture of C57BL/6, C3H and CD5

value: Rabbit-anti H3K36me3 (ab9050, Abcam)


title: 8MSZOEE2-2W


title: ZW7924M3-SCR


title: H3K36me3_ChIPSeq_L80A Oct4_ESCs_1

value: Mixture of C57BL/6, C3H and CD4


title: 203715550048_R03C01


title: 203715540107_R03C01


title: 203715540106_R03C01


title: H3K9me3_ChIPSeq_L80A Oct4_ESCs_1

value: Mixture of C57BL/6, C3H and CD8


title: 203715540066_R03C01


title: H3K36me3_ChIPSeq_WT Oct4_ESCs_2

value: Mixture of C57BL/6, C3H and CD3


title: 8MSZOEE2-SCR

value: No


title: 203715540066_R04C01

value: Female


title: 203712390027_R03C01

value: Ovarian Clear Cell Carcinoma (OCCC)


title: 203715540037_R03C01

value: epic


title: 203715540037_R04C01


title: 203711910041_R03C01


title: X3WD0D4U-SUR

value: N/A; no information


title: 203711910032_R04C01


title: X3WD0D4U-SCR

value: Negative


title: X3WD0D4U-2W


title: 203715540106_R02C01


title: V90RW11S-SUR


title: 203715540066_R02C01


title: 203715540107_R02C01


title: Input DNA for L80A_Oct4_ChIPSeq_1

value: Mixture of C57BL/6, C3H and CD1

value: L80A Oct4

value: none (input)


title: 203715540065_R02C01


title: Input DNA for WT_Oct4_ChIPSeq_2

value: mouse embryonic stem cells

value: WT


title: V90RW11S-SCR


title: H3K36me3_ChIPSeq_WT Oct4_ESCs_1

value: Mixture of C57BL/6, C3H and CD2


title: 203715540037_R02C01


title: Input DNA for WT_Oct4_ChIPSeq_1


title: L80A_Oct4_ChIPSeq_2

value: goat anti-Oct4 (sc-8628, Santa Cruz)


title: 203711910032_R02C01


title: Q37JN3NW-SCR


title: 203711910057_R03C01


title: Input DNA for L80A_Oct4_ChIPSeq_2


title: Q37JN3NW-SUR


title: 203715550048_R01C01


title: 203715540107_R01C01


title: WT_Oct4_ChIPSeq_2


title: 203711910031_R03C01


title: 203715540037_R01C01


title: A0FPLC73-SCR


title: 203711910032_R01C01


title: 203711910031_R01C01


title: 203715550003_R08C01


title: 203715550002_R08C01


title: RORcKO 2

city: Boston

first: Eunha

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Immunology

institute: Harvard Medical School

data_processing:
The basecall files were demultiplexed through the Harvard BPF Genomics Core’s pipeline, and the resulting fastq files
Quantification of gene expression was done by a lightweight alignment tool, Salmon (Patro, Rob, et al. “Salmon provides fast and bias-aware quantification of transcript expression.” Nature Methods (2017)) with kmer 31
Genome_build: GRCm38
Supplementary_files_format_and_content: Salmon quantification files (Patro, Rob, et al. “Salmon provides fast and bias-aware quantification of transcript expression.” Nature Methods (2017))

source_name: RORcKO

growth_protocol: 200,000 FACS-sorted naïve CD4 T cells (CD4+ CD8a- CD25- CD44low CD62Lhigh) from C57BL/6J mice were seeded on multiwell plates pre-coated with hamster anti-rat IgG. T cells then activated and expanded by soluble anti-CD3e (145-2C11, 0.25 μg/ml) and anti-CD28(37.51, 1 μg/ml) in Th17 polarizing condition (10 ng/ml mouse IL-6, 0.3 ng/ml human TGFβ1) in RPMI media supplemented with 55 mM β-mercaptoethanol, 1xGlutaMax and 10% fetal bovine serum for 3 days.

extract_protocol:
Qiagen RNeasy Plus Mini Kit according to the manufacture’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3-OxoLCA, isoLCA or DMSO (vehicle) was added to culture 18 hours after TCR activation at 10 μM final concentration.

value: In vitro differenciated Th17

tag: tissue origin

value: Spleen and lymphnodes originated naïve CD4 T cells


title: RORcKO 3


title: 203712390027_R02C01


title: LH9LYY87-SUR


title: LH9LYY87-2W


title: LH9LYY87-SCR


title: RORcKO 1


title: Wildtype isoLCA 3

source_name: WT isoLCA

tag: treatment

value: isolithocholic acid (isoLCA)


title: 203715550001_R08C01


title: A0FPLC73-2W


title: 7WDDMP1Z-2W


title: 203715540119_R08C01


title: 203715540052_R08C01


title: Wildtype isoLCA 1

tag: strain


title: 203715540065_R01C01


title: 203717910020_R07C01


title: 7WDDMP1Z-SCR


title: 203715550016_R07C01


title: Wildtype isoLCA 2


title: Wildtype 3-oxoLCA 3

source_name: WT 3-oxoLCA

value: 3-oxo-lithocholic acid (3-oxoLCA)


title: 203715550092_R07C01


title: 203715550003_R07C01


title: Y5UCJFBJ-SUR


title: Y5UCJFBJ-2W


title: Wildtype 3-oxoLCA 2


title: PNH73SPD-SCR

value: No


title: 203715540097_R08C01

value: Female


title: 203715540097_R07C01

value: Ovarian Clear Cell Carcinoma (OCCC)


title: 203715540057_R08C01

value: epic


title: 203715540119_R07C01


title: Y5UCJFBJ-SCR


title: Wildtype DMSO3

source_name: WT DMSO

value: DMSO (vehicle)


title: 203715540074_R07C01


title: Wildtype 3-oxoLCA 1


title: 203715540051_R07C01


title: 203715540057_R07C01


title: 203715550016_R06C01


title: 203715550092_R06C01


title: Wildtype DMSO2


title: 203715540052_R07C01


title: 203715550003_R06C01


title: 203715550002_R06C01


title: C51Y6OVJ-2W

source_name: Breast tumor

value: N/A; no information


title: C51Y6OVJ-SCR

value: Negative


title: H3UZRJ4L-2W


title: 203715550001_R06C01


title: Epcam_hi_LPS_rep2

description: KAPA RNA Stranded PolyA

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Ensembl version 98
Expression values were also computed using RSEM version 1.2.28 based on Ensembl version 98 transcript annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

value: 6 to 12 weeks

tag: Sex

value: Male

value: Lung

value: bronchiolar epithelial


title: 203715550002_R07C01


title: Epcam_hi_LPS_rep3

description: KAPA RNA Stranded PolyA

tag: tissue


title: 203715550001_R07C01


title: H3UZRJ4L-SCR


title: 66GZTW15-SUR


title: 203715540097_R06C01


title: 203715540052_R06C01


title: 203715540057_R06C01


title: Wildtype DMSO1


title: Epcam_hi_Control_rep3

description: KAPA RNA Stranded PolyA


title: Epcam_hi_LPS_rep_1

description: KAPA RNA Stranded PolyA


title: M6BTDBK8-SUR


title: M6BTDBK8-SCR


title: Epcam_hi_Control_rep2

description: KAPA RNA Stranded PolyA


title: 203715540074_R06C01


title: Epcam_hi_Control_rep1

description: KAPA RNA Stranded PolyA


title: 203715540051_R06C01


title: 203715550016_R05C01


title: 203717910020_R05C01


title: 203715550092_R05C01


title: AE2_LPS_rep3

description: KAPA RNA Stranded PolyA

value: alveolar epithelial


title: 203715550002_R05C01


title: C51Y6OVJ-SUR


title: QKDMBP7H-SUR


title: 203715550001_R05C01


title: 203715540119_R06C01


title: 203715540119_R05C01


title: AE2_LPS_rep2

description: KAPA RNA Stranded PolyA


title: 203715550003_R05C01


title: QKDMBP7H-2W


title: QKDMBP7H-SCR


title: AE2_LPS_rep1

description: KAPA RNA Stranded PolyA


title: ST70L5DZ-SUR


title: 203715540074_R05C01


title: AE2_Control_rep3

description: KAPA RNA Stranded PolyA


title: 203715540052_R05C01


title: 203715550003_R04C01


title: AE2_Control_rep2

description: KAPA RNA Stranded PolyA


title: 203715550092_R04C01


title: ST70L5DZ-2W


title: AE2_Control_rep1

description: KAPA RNA Stranded PolyA


title: 203715550001_R04C01


title: ST70L5DZ-SCR


title: AE1_LPS_rep3

description: KAPA RNA Stranded PolyA


title: 66GZTW15-SCR


title: 203715550002_R04C01


title: AE1_LPS_rep_2

description: KAPA RNA Stranded PolyA


title: 203715540119_R04C01


title: 203715540097_R04C01


title: GQAYGK8I-SUR


title: 203715540074_R04C01


title: 203715540057_R04C01


title: KJ189SGD-SCR


title: AE1_Control_rep3

description: KAPA RNA Stranded PolyA


title: T103E9MR-SUR


title: AE1_LPS_rep1

description: KAPA RNA Stranded PolyA


title: 203717910020_R04C01


title: 203715540097_R05C01


title: 203715540051_R04C01


title: 203715540057_R05C01


title: 203717910020_R03C01


title: 6NG1D6S9-SUR