title: Reg5_antiPD1_p101_rep3

source_name: BNL-MEA tumor-bearing Balb/c mice treated with 5 mg regorafenib and anti-PD1 (p101)


title: Ssc 2 T2 CD4+

status: Public on Jan 27 2021

type: SRA

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

library_source: transcriptomic

data_processing:
Library strategy: TCR-seq
Raw paired-end reads were assembled using Paired-End reAd mergeR (PEAR)
As part of our protocol, both reads contain barcodes/UMIs.
Sample specific barcode correction was performed using the ‘umi_group_ec’ command from the Recover T Cell Receptor (RTCR) pipeline, allowing zero mismatches in the barcode seed sequence for UMI detection.
Barcode sequence reads having the same UMI were collapsed into consensus sequences using the RTCR pipeline to accurately recover TCRβ sequences
Barcode and UMI sequences for each sample are contained in the file Barcodes_GEOsubmission_pandit.txt which is available from the series record.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited file containing TCRβ sequences and counts after error correction and post-processing using the RTCR pipeline

molecule: total RNA

organism: Homo sapiens

source_name: CD4+ non-naive T-cells peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation on Ficoll-PlaqueTM Plus (GE Healthcare Life Sciences). pDCs, mDCs, B-cells and monocytes were first depleted by magnetic bead sorting using the autoMACs Pro Separator (Miltenyi Biotec) according to the manufacturer’s protocol. The remaining peripheral blood lymphocytes (PBLs) were resuspended in freezing medium (80% FCS, Sigma / 20% DMSO, Sigma) and stored in sterile cryovials in liquid nitrogen (-196°C) until further use. PBLs were thawed in RPMI 1640 (Thermo Fisher Scientific) supplemented with 20% FCS (Sigma), and washed with PBS. Cells were resuspended in FACS buffer (PBS supplemented with 1% BSA (Sigma-Aldrich) and 0.1% sodium azide (Sigma-Aldrich)) and stained using the following antibodies: CD3-AF700 (clone UCHT1, Biolegend), CD4-BV711 (clone OKT4, Sony Biotechnology), CD8-V500 (clone RPA-T8, BD), CD56-PE-CF594 (clone B159, BD), CD16-BV785 (clone 3G8, Sony Biotechnology), CD14-PerCP-Cy5.5 (clone HCD14, Biolegend), HLADR-BV421 (clone L243, Biolegend), CD45RO-PE-Cy7 (clone L243, BD), CD27- APC-eFluor780 (clone O323, eBioscience). Multiparametric flow cytometry sorting of CD4+ and CD8+ non-naive T-cells was performed on the BD FACSAria II (BD Biosciences). After sorting, cells were washed in PBS, lysed in TRIzol™ Reagent (Invitrogen), and stored at -20°C. RNA was isolated and using the RNeasy Mini Kit (Qiagen) by adding ethanol to the upper aqueous phase of processed TRIzol samples and transferring directly to the RNeasy spin columns.
cDNA was generated by RACE using a primer directed to the TCRβ constant region. Thirteen nucleotide long unique molecular identifiers (UMIs) were incorporated during cDNA synthesis. Subsequently, two-stage semi-nested PCR amplification was performed including a size selection/agarose gel purification step after the first PCR. To minimize cross-sample contamination, 5-nucleotide sample specific barcodes were introduced at two steps during the library preparation process. Resulting TCR amplicons were subjected to high-throughput sequencing using the Ovation Low Complexity Sequencing System kit from NuGEN (San Carlos) according to the manufacturer’s instructions, and the Illumina MiSeq system (San Diego), using indexed paired-end 300 cycle runs.

tag: cell type

value: CD4+ non-naive T-cells peripheral blood

tag: diagnosis

value: dcSSc

tag: subject id

value: Ssc 2

tag: timepoint

value: T2 (25 months from baseline)

tag: gender

value: male

tag: age


title: WT NP+IgE+ Bcell#43

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
HISAT2(version 2.1.0) with default parameters
StringTie(version 2.0)
Genome_build: mm10
Supplementary_files_format_and_content: Fasta files including read sequences of Ig mRNA, and tab-delimited text files include read counts for genes

organism: Mus musculus

extract_protocol:
We transferred IL-13 sufficient or deficient OT-2 TH2 into IgE reporter (Verigem) mice followed by immunization with NP-OVA. At 7 day post immunization, NP specific IgE producing B cells were sorted by flow cytometer.
For scRNA-seq analysis, the single-cells were sorted into each well of 96 well plates using FACS Aria III (BD). The single cells are lysed in a buffer that contains dNTPs and oligo(dT)-tailed oligonucleotides with a universal 5'-anchor sequence. RT is performed, which adds 2–5 untemplated nucleotides to the cDNA 3’ end. A template-switching oligo (TSO) is added, carrying 2 riboguanosines and a modified guanosine to produce a LNA as the last base at the 3’ end. After the first-strand reaction, the cDNA is amplified using a 25 of cycles. Next, Tn5 tagmentation is used to construct sequencing libraries from the amplified cDNA (Nextera XT DNA Library Preparation Kit, illumina). The sequencing was carried out using NovaSeq6000 equipment (SP type, 150PE, Illumina).

tag: strain

tag: tissue

value: spleen

value: 8 weeks

tag: genotype

value: IgE repoter (Verigem)


title: Reg5_p101_rep1

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: BNL-MEA tumor-bearing Balb/c mice treated with 5 mg regorafenib (p101)

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCm38) by STAR (v2.7.2a) and then gene-level read counts were generated based on the annotations of Gencode (vM19).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level read counts.

extract_protocol:
Total RNA was extracted from frozen snaps using an AllPrep DNA/RNA mini kit (Qiagen,  Hilden, Germany).
Libraries were constructed using Illumina TruSeq Stranded mRNA kit according to the manufacturers

value: BNL-MEA tumor-bearing Balb/c mice

tag: treatment

value: regorafenib 5 mg/kg/day

value: hepatocellular carcinoma

tag: batch


title: WT NP+IgE+ Bcell#47


title: WT NP+IgE+ Bcell#48


title: WT NP+IgE+ Bcell#49


title: antiPD1_p101_rep3

description: BNL-MEA tumor-bearing Balb/c mice treated with anti-PD1 (p101)


title: Reg5_antiPD1_p101_rep2

description: BNL-MEA tumor-bearing Balb/c mice treated with 5 mg regorafenib and anti-PD1 (p101)

value: regorafenib + anti-PD1


title: Macrophage M0 treated with regorafenib

description:
Macrophage M0 treated with regorafenib
M0_rego

source_name: Mouse bone marrow-derived macrophages

growth_protocol: Mouse bone marrow-derived macrophages were polarized with IFN-gamma + LPS or IL4 for 24 h to induce M1 or M2 phenotypes, respectively.

treatment_protocol: macrophages were treated with DMSO and regorafenib

value: regorafenib

value: macrophage

tag: subtype


title: Ssc 2 T2 CD8+

source_name: CD8+ non-naive T-cells peripheral blood

value: CD8+ non-naive T-cells peripheral blood


title: WT NP+IgE+ Bcell#39


title: Veh_p101_rep2

description: BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p101)

value: vehicle


title: Ssc 2 T1 CD8+

value: T1 (12 months from baseline)


title: WT NP+IgE+ Bcell#37


title: WT NP+IgE+ Bcell#41


title: WT NP+IgE+ Bcell#42


title: Ssc 1 T2 CD8+

value: Ssc 1

value: T2 (34 months from baseline)

value: female


title: Veh_p101_rep3

source_name: BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p101)


title: WT NP+IgE+ Bcell#46


title: Ssc 2 T1 CD4+

value: CD4+ non-naive T-cells peripheral blood

value: dcSSc

value: Ssc 2


title: WT NP+IgE+ Bcell#35

value: spleen

value: 8 weeks


title: DC101_p103_rep2

description: BNL-MEA tumor-bearing Balb/c mice treated with DC-101 (p103)

value: BNL-MEA tumor-bearing Balb/c mice


title: WT NP+IgE+ Bcell#36

value: IgE repoter (Verigem)


title: Ssc 2 T0 CD8+

value: T0 (0 months from baseline)

value: male


title: DC101_p103_rep1

source_name: BNL-MEA tumor-bearing Balb/c mice treated with DC-101 (p103)

value: hepatocellular carcinoma


title: WT NP+IgE+ Bcell#38


title: Reg5_p103_rep3

description: BNL-MEA tumor-bearing Balb/c mice treated with 5 mg regorafenib (p103)

value: regorafenib 5 mg/kg/day


title: Ssc 1 T2 CD4+


title: Veh_p101_rep1


title: WT NP+IgE+ Bcell#33


title: Ssc 2 T0 CD4+


title: Ssc 1 T0 CD8+

value: CD8+ non-naive T-cells peripheral blood


title: Ssc 1 T1 CD4+

value: T1 (19 months from baseline)


title: WT NP+IgE+ Bcell#34


title: Reg5_p103_rep2

source_name: BNL-MEA tumor-bearing Balb/c mice treated with 5 mg regorafenib (p103)


title: WT NP+IgE+ Bcell#40


title: DC101_p103_rep3


title: WT NP+IgE+ Bcell#32


title: Ssc 1 T0 CD4+


title: Reg5_p103_rep1


title: Ssc 1 T1 CD8+


title: EBW3

city: Caparica

first: Pedro

middle: M.

last: Costa

address: Campus de Caparica

department: Department of Life Sciences

country: Portugal

institute: NOVA School of Science and Technology, NOVA University of Lisbon

description: polyA RNA

data_processing:
Data quality was assessed with the FastQC quality-control tool for high throughput sequence data.
Reads were combined and assembled with Trinity v2.8.4
Coding regions within the assembled transcriptome were predicted using TransDecoder v5.5.0
Proboscis-specific transcripts were selected by mapping independently libraries to the assembled transcriptome with Kallisto v0.44.028
Supplementary_files_format_and_content: xlsx

organism: Eulalia viridis

source_name: Body wall

extract_protocol:
RNA was isolated from whole-tissue preserved in RNALaser using the Rneasy Protect Mini Kit (Qiagen) combined with on-column DNA digestion with the DNase-Free DNase Set (Qiagen).
Library preparation was done using Kapa Stranded mRNA Library Preparation Kit and the generated RNA fragments were sequenced in an Illumina HiSeq 4000 platform, using 150bp paired-end sequencing reads: 100M for samples ERP2 and EBW2, 20M for the remaining

value: Whole organ


title: Veh_p103_rep3

description: BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p103)

value: vehicle


title: WT NP+IgE+ Bcell#31


title: Veh_p103_rep4

source_name: BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p103)


title: EBW2

description: polyA RNA


title: WT NP+IgE+ Bcell#30


title: EBW1

description: polyA RNA


title: EPR1

description: polyA RNA

source_name: Proboscis


title: Veh_p103_rep1


title: Reg20_p112_rep1

description: BNL-MEA tumor-bearing Balb/c mice treated with 20 mg regorafenib (p112)

value: regorafenib 20 mg/kg/day


title: Reg20_p112_rep3

source_name: BNL-MEA tumor-bearing Balb/c mice treated with 20 mg regorafenib (p112)


title: WT NP+IgE+ Bcell#27


title: Reg20_p112_rep2


title: WT NP+IgE+ Bcell#29


title: WT NP+IgE+ Bcell#28


title: EPR3

description: polyA RNA


title: WT NP+IgE+ Bcell#26


title: Veh_p103_rep2


title: Hoxblinc-Tg-RNA-seq-2

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

country: China

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads were aligned to the mm9 genome assembly using Tophat, and ATAC-seq, ChIP-seq and 4C-seq reads were aligned to the mm9 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples and peaks for ATAC-seq, ChIP-seq and 4C-seq

source_name: Bone marrow Lin- Sca1+ Kit+ cells

growth_protocol: Total bone marrow cells were taken from WT and Hoxblinc-Tg mice, LSK cells were then sorted using Lin-, Sca1+ and Kit+ markers, and LK cells were sorted using Lin- and Kit+ markers.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I. ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3 antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745). ATAC-seq samples derived according to Nextera Tn5 Transposase kits.    4C seq library samples derived from two enzymes digestion BglII and NlaIII and ligation with T4 ligase.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to  TruSeq ChIP Library Preparation Kit (#IP-202-1012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from LSK cells without any treatment

tag: cell types

value: Mouse-derived Bone marrow cells

value: Bone marrow

value: Lin- Sca1+ Kit+ cells

tag: genotype/variation

value: Hoxblinc-Tg


title: Reg5_p112_rep3

description: BNL-MEA tumor-bearing Balb/c mice treated with 5 mg regorafenib (p112)


title: Reg5_p112_rep2

source_name: BNL-MEA tumor-bearing Balb/c mice treated with 5 mg regorafenib (p112)


title: WT NP+IgE+ Bcell#24

value: spleen


title: WT NP+IgE+ Bcell#23

value: 8 weeks


title: Hoxblinc-Tg-RNA-seq-1


title: Reg5_p112_rep1

value: BNL-MEA tumor-bearing Balb/c mice


title: scRNAseq of Blood HIV-specific CD8+ T-cells (with B-cell spike in) from HIVPosSmpl2

city: Stockholm

first: Marcus

last: Buggert

state: PA

address: C2:94; Karolinska Universitetssjukhuset Huddinge

department: Microbiology

country: Sweden

institute: Karolinska Institutet

data_processing:
basecalling and demultiplexing with cellranger/v4.0.0 mkfastq with bcl2fastq2/v2.20.0.422
generating barcode/feature matrices with cellranger/v4.0.0 count
generating clonotype data with cellranger/v4.0.0 vdj
Genome_build: hg38
Supplementary_files_format_and_content: cellranger count filtered output

source_name: lymphocytes

extract_protocol: Chromium Single-cell VDJ v1.1 kit (10X Genomics)

value: Blood

tag: disease state

value: HIVpos

value: HIV-specific memory CD8+ T-cells + B cells spike in

tag: antigen-specificity

value: HIV


title: WT-RNA-seq-1

value: WT


title: scRNAseq of TDL HIV-specific CD8+ T-cells from HIVPosSmpl2

value: TDL

value: HIV-specific memory CD8+ T-cells


title: EPR2

description: polyA RNA

value: Whole organ


title: WT NP+IgE+ Bcell#21

value: IgE repoter (Verigem)


title: WT NP+IgE+ Bcell#22


title: Veh_p112_rep3

description: BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p112)

value: vehicle

value: hepatocellular carcinoma


title: WT NP+IgE+ Bcell#25


title: WT NP+IgE+ Bcell#20


title: scRNAseq of TDL CMV-specific CD8+ T-cells (with B-cell spike in) from HIVPosSmpl2

value: CMV-specific memory CD8+ T-cells + B cells spike in

value: CMV


title: Veh_p112_rep2

source_name: BNL-MEA tumor-bearing Balb/c mice treated with vehicle (p112)


title: Veh_p112_rep4


title: scRNAseq of Blood CMV-specific CD8+ T-cells from HIVPosSmpl2

value: CMV-specific memory CD8+ T-cells


title: WT NP+IgE+ Bcell#18

value: spleen


title: Veh_p112_rep1


title: chondrocyte [S19]

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

description: processed data file: ATACseq_peaks_readCount.txt

library_source: genomic

data_processing:
Bulk Mars-Seq (3' end-RNA-seq):
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
Adapters and low quality bases were removed from the raw reads using cutadapt
The remaining reads (raw data submitted)  were aligned to the Mus musculus genome (mm9) using Bowtie
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes UCSC), which was modified to contain a window surrounding the 3' UTR. Duplicate reads were marked and filtered based on having the same UMI and mapping to the same gene, using a python script.
Genes were filtered out if their sum counts after UMI filter <=10 or  maximum value <= 5. Normalization and differential expression analysis was performed using the DESeq2 R-package. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 (after adjusment with fdrtools).
ATAC-seq:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14 following demultiplexing.
Adapters and low quality bases were removed from the raw reads using cutadapt
The remaining reads (raw data submitted)  were aligned to the Mus musculus genome (mm10) using Bowtie
Non-mitochondrial, unique aligned read-pairs with an inter-distance of <120 bp were selected for peak calling
peak calling was performed using MACS2. The number of reads per peak was calculated using bamtools.
A set of reproducible peaks ( shred in >=50% of the replicates of each condition) were obtained Peaks were merged and quantified using bedtools
read count was normalized using DESeq2.
Genome_build: mm9 (RNA-seq); mm10 (ATAC-seq)
Supplementary_files_format_and_content: text file with crude read count

molecule: genomic DNA

source_name: Col2a1+ScxGFP- FACS sorted forelimb from E13.5 forelimb

growth_protocol:
Bulk Mars-Seq (3' end-RNA-seq): For collcetion of cells by laser capture microdissection (LCM), E14.5 Col2a1-tdTomato-Scx-GFP mouse forelimbs were dissected, shortly fixated in 4% PFA, washed with PBS and cryo-embedded. Next, samples were cryo-sectioned and mounted on LCM slides (PET, Zeiss), washed with RNase-free water and EtOH (Arcturus dehydration component kit) according to an altered protocol of Pazin et al 2012. LCM (PALM MicroBeam C system, Zeiss) was calibrated for refined tissue cutting. Isolated cells were collected to LCM caps (Adhesive Cap 500 clear, Zeiss) and RNA was purified using RNeasy FFPE Kit (Qiagen).
ATAC-seq: For collection of cells by FACS, forelimbs were dissected and suspended in cold PBS. To extract cells from tissues, PBS was replaced with 1 ml heated 0.05% trypsin and collagenase type V (dissolved in DMEM, Sigma) and incubated for 15 min at 37˚C, gently agitated every 5 minutes. Tissues were then dissociated by vigorous pipetting using 1 ml tips. Next, 4 ml of DMEM supplemented with 10% FBS and 1% Pen-Strep was added and cell suspensions were filtered with 40 μm filter net. Finally, tubes were centrifuged at 1,000 rpm for 7 minutes, supernatant was removed and cells were resuspended in 1 ml of cold PBS and used immediately for FACS.

extract_protocol:
Bulk Mars-Seq (3' end-RNA-seq): RNA was purified using RNeasy FFPE Kit (Qiagen) according to manufacture guidelines (Protocol:Protocol: Purification of Total RNA from Microdissected FFPE Tissue Sections).
Bulk Mars-Seq (3' end-RNA-seq): Purified RNA was stored at -80C. For library preparation RNA was used for the bulk MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9, Keren-Shaul et al. 2019 Nature Protocols). MARS-seq libraries were sequenced using  Hiseq 2500 SR50 cycles kit (Illumina)
For ATAC-seq protocol we used a modified protocol of Buenrostro et al., 2015 Curr Protoc Mol Biol.

tag: strain background

value: A mixed background of C57BL/6 and B6.129 (ICR)

value: wild-type

value: chondrocyte


title: WT NP+IgE+ Bcell#19

value: 8 weeks


title: WT NP+IgE+ Bcell#15


title: scRNAseq of TDL HIV-specific CD8+ T-cells (with B-cell spike in) from HIVPosSmpl1

value: HIVpos

tag: cell type

value: HIV-specific memory CD8+ T-cells + B cells spike in


title: attachment [E5_TG]

source_name: Scx+Sox9+ FACS sorted humeral deltoid tuberosity and greater tuberosity from E13.5 forelimb

value: attachment


title: attachment [E4_TG]


title: WT NP+IgE+ Bcell#13


title: scRNAseq of Blood memory CD8+ T-cells from HUP222

value: Blood

value: HIVneg

value: Memory CD8+ T-cells


title: WT NP+IgE+ Bcell#11

value: IgE repoter (Verigem)


title: scRNAseq of TDL memory CD8+ T-cells from HUP213

value: TDL


title: tenocyte [E5_GFP]

source_name: Scx+ FACS sorted from humeral deltoid tuberosity and greater tuberosity from E13.5 forelimb

value: tenocyte


title: tenocyte [E7_GFP]


title: WT NP+IgE+ Bcell#10


title: scRNAseq of Blood memory CD8+ T-cells from HUP217


title: scRNAseq of TDL memory CD8+ T-cells from HUP217


title: attachment [E3_TG]


title: AB10331

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

data_processing:
library strategy: MARS-seq
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes mRNA molecule count values for each Sample
[metadata_s.txt]  Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

source_name: Bone marrow aspiration

growth_protocol:
(1)  Cells were cultured using an aseptic technique in RPMI medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum, 1mM sodium pyruvate, 2mM L-glutamine, 1% penicillin-streptomycin (ThermoFisher Scientific).
(2)  Bone marrow cells from a relapse refractory myeloma patient (penta-refractory, refractory to bortezomib and carfilzomib) were stained with magnetic CD138+ enrichment beads (Miltenyi). Cells were washed and re-suspended in RPMI 1640 medium (Gibco) supplemented with 15% FBS, 1% Glutamine and 1% penicillin-streptomycin (ThermoFisher Scientific).

extract_protocol:
After informed consent (in accordance with Helsinki declaration), bone marrow aspiration was placed in EDTA-containing tubes (Beckton Dickenson), diluted 1:1 with ice cold FACS buffer (EDTA pH8.0 2mM, BSA 0.5% in PBS), placed on ice and immediately transported to the lab.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

treatment_protocol:
(1)  The designed therapeutic treatment includes a quadruple regimen comprised of Daratumumab, Carfilzomib, Lenalidomide and Dexamethasone (DARA-KRD) (Methods; KYDAR Clinical Trial).
(2)  RPMI-8226 PPIA-/- cells were treated with CFZ, CsA and their combination, and were harvested 4- and 8-hours post treatment.

tag: organ

value: Bone marrow

tag: sample type

value: Bone marrow aspiration

value: Plasma cells

tag: selection marker

tag: growth protocol (2)

value: Ex vivo

tag: time point

value: Baseline

tag: replicate id

value: PRMM


title: attachment [E7_TG]

value: wild-type

tag: age


title: scRNAseq of Blood memory CD8+ T-cells from HUP213

tag: tissue


title: scRNAseq of Blood HIV-specific CD8+ T-cells (with B-cell spike in) from HIVPosSmpl1

value: HIV


title: AB10330


title: chondrocyte [S2]

source_name: Col2a1+ScxGFP- FACS sorted from E13.5 forelimb

value: A mixed background of C57BL/6 and B6.129 (ICR)

value: chondrocyte


title: WT NP+IgE+ Bcell#17

tag: strain

value: spleen

value: 8 weeks

tag: genotype


title: WT NP+IgE+ Bcell#16


title: tenocyte [E4_GFP]


title: scRNAseq of TDL memory CD8+ T-cells from HUP222

value: HIVneg


title: WT NP+IgE+ Bcell#9


title: WT NP+IgE+ Bcell#14


title: tenocyte [E3_GFP]


title: AB10329


title: AB10328

source_name: RPMI-8226 cell line

tag: cell line

value: PPIA-/- knockout

tag: growth protocol (1)

value: In vitro

tag: treatment (2)

value: CFZ+CSA


title: WT NP+IgE+ Bcell#6

value: IgE repoter (Verigem)


title: WT NP+IgE+ Bcell#12


title: AB10327


title: tenocyte [E1_GFP]

tag: genotype/variation

value: tenocyte


title: Meninges, Old

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

country: USA

institute: Washington University in Saint Louis

description: Dural endothelial (CD45-CD31+CD13-) and mural cells (CD34-CD13+CD31-) were sorted from 5 mice

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline. Fastq files from each run were specified using the --fastqs flag  The cellranger count pipeline, resulted in one count matrix for each of our sample conditions (brain old, brain young, meninges old, meninges young)
Genome_build: mm10
Supplementary_files_format_and_content: tar archive containing the raw UMI count matrices for each sample as well as matrices with cell barcodes and gene symbols.

source_name: Dural meninges

growth_protocol: not applicable

extract_protocol:
10x Genomics Chromium single cell preparation
NGS Illumina Next Seq

treatment_protocol: not applicable

value: Dural meninges

value: Endothelial and mural

value: 24 months

tag: Sex

value: Male


title: Meninges, Young

value: 2 months


title: WT NP+IgE+ Bcell#5


title: WT NP+IgE+ Bcell#3


title: WT NP+IgE+ Bcell#8


title: AB10324

value: Plasma cells

value: CFZ


title: WT NP+IgE+ Bcell#4


title: AB10323


title: AB10325

value: CSA


title: Brain, Old

description: Whole brain endothelial (CD45-CD31+CD13-) and mural cells (CD34-CD13+CD31-) were sorted from 5 mice

source_name: Whole brain

value: Whole brain


title: WT-RNA-seq-2

tag: cell types

value: Mouse-derived Bone marrow cells

value: Bone marrow

value: Lin- Sca1+ Kit+ cells

value: WT


title: Brain, Young

tag: cell type


title: Tcells, Old

description: T cells were FACS sorted from n=4 mice

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline. Fastq files from each run were specified using the --fastqs flag  The cellranger count pipeline, resulted in one count matrix for each of our sample conditions (old, young)
Genome_build: mm10
Supplementary_files_format_and_content: tar archive containing the raw UMI count matrices for each sample as well as matrices with cell barcodes and gene symbols.

source_name: Brain meninges

extract_protocol:
10x Genomics Chromium single cell preparation
NGS Illumina Nextseq

value: Brain meninges

value: T cells

value: 22 month

value: male


title: Myeloid cells, DN

description: Dural myeloid cells were sorted from 20 mice

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline. Fastq files from each run were specified using the --fastqs flag  The cellranger count pipeline, resulted in one count matrix for each of our sample conditions (A488 + (IV injection) A647+ (ICM injection, Double Positive, Double Negative)
Genome_build: mm10
Supplementary_files_format_and_content: tar archive containing the raw UMI count matrices for each sample as well as matrices with cell barcodes and gene symbols.

source_name: Dura

growth_protocol: Not applicable

treatment_protocol: Intracisternal and intravenous injections of Ovalbumin

value: Dura

value: Myeloid cells

tag: treatment

value: double negative


title: Tcells, Young

description: T cells were FACS sorted from n=4 mice

value: 3 month


title: AB10321

value: PPIA-/- knockout

value: In vitro

value: Control


title: WT NP+IgE+ Bcell#2

value: spleen

value: 8 weeks

value: IgE repoter (Verigem)


title: WT NP+IgE+ Bcell#1


title: AB10322

value: Plasma cells


title: AB10326

value: CSA


title: WT NP+IgE+ Bcell#7


title: Myeloid cells, DP

value: 2 months

value: Male

value: double positive


title: Myeloid cells, A647

value: OVA 647 positive only


title: Myeloid cells, A488

value: OVA-488 positive only


title: AB10320

value: CFZ+CSA


title: RNAseq_quadKO_3

city: Grand Rapids

first: Gerd

middle: P

last: Pfeifer

state: MI

address: 333 Bostwick Ave NE

department: Center for Epigenetics

institute: Van Andel Research Institute

data_processing:
Sequencing was performed with an Illumina NextSeq 500 machine and 75 bp single-end runs were performed.
Single-end RNAseq reads were trimmed using TrimGalore with defaut parameters.
Trimmed reads were aligned to the mouse genome mm9 with STAR (v2.5.1) , and gene count were performed using a STAR (v2.5.1)
The limma (v3.38.2) statistical package19 was used to call the differential expressed gene. Statistical significance for differentially expressed genes was q<0.05 with FC > 2.
Genome_build: mm9
Supplementary_files_format_and_content: Text file containing log2 CPM matrices from STAR-derived transcript abundance counts

source_name: Embryonic stem cells

growth_protocol: All ES cells were cultured cultured under feeder-free conditions on 0.1% gelatin-coated tissue culture plates in knockout DMEM supplemented with 15% fetal bovine serum, 1,000 U/ml LIF, 1x non-essential amino acids, 100 µM β-mercaptoethanol   and 2 mM L-glutamine.

extract_protocol:
Total RNA was extracted from whole cells with a PureLinkTM RNA Mini kit accoding to manufacturer’s instructions.
Total RNA integrity was verified with an Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified with a NanoDrop 8000 instrument (Thermo Fisher). RNA-seq libraries were prepared from total RNA with the KAPA RNA HyperPrep kit with RiboErase (KAPA Biosystems). Library size distributions were validated on the Bioanalyzer (Agilent Technologies).

value: Embryonic stem cells


title: E13.5 Zfp57-/- maternal-zygotic mutant (M-Z-) WGBS rep3

city: Shanghai

first: weijun

last: jiang

address: Haike Road, 230

institute: Shanghaitech University

data_processing:
RNA-Seq
Sequences are filtered by Seqtk.
Clean reads were mapped to mm10 whole genome using Hisat2(version:2.0.4) with parameters spliced mapping.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated using a protocol from Mortazavi et al., Nature Methods, 2008.
Supplementary_files_format_and_content: tab-delimited text files include FPKM and count values for each Sample
Bisulfite-Seq
Trim_galore v0.4.1 used for  triming off the  low-quality reads.
Filtered sequences were then aligned to the mm10 using Bismark (v0.15.0； bowtie v2.2.9).
Duplicates removed via the Bismark deduplication tool (deduplicate_bismark_alignment_output.pl).
Supplementary_files_format_and_content: bismark.cov

source_name: E13.5 total embryo

extract_protocol:
Live E13.5 embryo were flash frozen on liquid nitrogen, and genomic DNA was harvested using OMEGA TISSUE DNA Kit.
DNA (1 µg) was spiked with 1 ng unmethylated lamda DNA (Promega), fragmented, end-repaired, A-tailed, and adapter-ligated using Truseq DNA sample prep kit (Illumina). Then purified DNA was treated by EZ-DNA Methylation-Gold Kit(Cat#D5006, Zymo Research, USA). After amplified with PfuTurbo Cx Hotstart DNA Polymerase(Cat#600410, Agilent, USA), DNA was cleaned with VAHTSTM DNA Clean Beads(Cat#N411-03, Vazyme, China).

value: hybrid 129/DBA

value: total embryo

value: embryonic day 13.5

value: Zfp57-/- maternal-zygotic mutant (M-Z-)


title: E13.5 Zfp57-/- maternal-zygotic mutant (M-Z-) WGBS rep2


title: AB10318

value: PPIA-/- knockout

value: In vitro


title: E13.5 Zfp57-/- maternal-zygotic mutant (M-Z-) WGBS rep4


title: AB10319


title: AB10316

value: CFZ


title: RNAseq_Tet_TKO_3


title: AB10314

value: Control


title: RNAseq_Tet_TKO_2


title: E13.5 Zfp57 WT WGBS rep4

value: wild type


title: RNAseq_Tet_TKO_1


title: RNAseq_quadKO_1


title: RNAseq_quadKO_2


title: AB10315

value: Plasma cells


title: E13.5 Zfp57-/+ (M-Z+) WGBS rep3


title: E13.5 Zfp57-/+ (M-Z+) WGBS rep2


title: E13.5 Zfp57 WT WGBS rep3


title: LuCaP_93_Control_3

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LuCaP 93: control, sample: 1-6

data_processing:
Sequencing reads were mapped to the hg38 human and mm10 mouse genomes using STAR.v2.7.3a. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis using XenofiltR .
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.29
Gene level abundance was quantitated from the filtered human alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 93 PDX Control

growth_protocol: CB-17 SCID mice (Charles River) were implanted subcutaneously with LuCaP 93 tumor tissue.  Animals underwent rolling enrollment once tumors reached 100 mm3 and were randomized into one of two groups (Control vs. Treatment.)

extract_protocol:
RNA was isolated from flash frozen tissue from 6 xenografts of animals (3 animals treated with vehicle control, 3 animals treated with cabozantinib for 5 days) bearing LuCaP 93 tumors with RNA STAT-60 (Tel-Test).  The isolated RNA was then purified with Qiagen RNeasy Kit (Qiagen Inc.) according to the manufacturer’s protocol utilizing the optional DNase treatment in solution prior to purification.  RNA concentration, purity, and integrity was assessed by NanoDrop 2000 (Thermo Fisher Scientific Inc) and 2100 Bioanalyzer (Agilent Technologies).
RNA-Seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on an Illumina NovaSeq S1 100 flowcell generating 50 bp paired end reads.

treatment_protocol: Group 1 received control vehicle (10Vol% DMSO/10Vol% Cremophor EL/15Vol% PEG 400/15% HPCD in sterile water), by oral gavage, 200 uL, 4 times weekly for 8 weeks.  Group 2 received 30 mg/kg cabozantinib in vehicle (sterile water), by oral gavage, 100 uL, 5 times weekly for up to 7.5 weeks.  Tumor volumes and body weights were measured twice weekly once tumors were palpable.  Three mice per group were euthanized at 5 days post enrollment for early time point analysis and the remaining 14 mice per group were dosed for up to 7.5 weeks.  Tumor volumes (TV) were measured using Fowler Utlra-Cal calipers (calculated as LxHxWx0.5236).  Animals were euthanized after 7.5 weeks of follow up, when tumors exceeded 1,000 mm3, or when animals became otherwise compromised.  The tumors were then divided equally into paraffin blocks with the remainder flash frozen for subsequent molecular analyses.

tag: gender

value: male

tag: tumor type

value: LuCaP 93 PDX tumor

value: prostate cancer

tag: treatment group

value: control


title: LuCaP_93_Control_2

description: LuCaP 93: control, sample: 1-4


title: E13.5 Zfp57 WT WGBS rep1


title: RNAseq_DoubleKO_3


title: RNAseq_DoubleKO_2


title: E13.5 Zfp57-/- maternal-zygotic mutant (M-Z-) WGBS rep1


title: E13.5 Zfp57 WT WGBS rep2


title: E13.5 Zfp57-/+ (M-Z+) WGBS rep4


title: LuCaP_93_Control_1

description: LuCaP 93: control, sample: 1-2


title: RNAseq_DoubleKO_1


title: E13.5 Zfp57-/- maternal-zygotic mutant (M-Z-) mRNA-Seq rep6

extract_protocol:
Live E13.5 embryo were flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®(Cat#NR604-02, Vazyme, China)


title: E13.5 Zfp57-/- maternal-zygotic mutant (M-Z-) mRNA-Seq rep5


title: LuCaP_93_Cabozantinib_2

description: LuCaP 93: treated with Cabozantinib, sample: 3-4

source_name: LuCaP 93 PDX treated with Cabozantinib

value: Cabozantinib


title: LuCaP_93_Cabozantinib_1

description: LuCaP 93: treated with Cabozantinib, sample: 3-2


title: E13.5 Zfp57-/+ (M-Z+) WGBS rep1


title: LuCaP_93_Cabozantinib_3

description: LuCaP 93: treated with Cabozantinib, sample: 3-6


title: AB10317

tag: time point


title: RNAseq_DuxKO_3


title: E13.5 Zfp57-/- maternal-zygotic mutant (M-Z-) mRNA-Seq rep4


title: Smchd1KO2_rep2


title: RNAseq_DuxKO_2


title: E13.5 Zfp57-/- maternal-zygotic mutant (M-Z-) mRNA-Seq rep3


title: E13.5 Zfp57-/- maternal-zygotic mutant (M-Z-) mRNA-Seq rep1


title: Right Cranial Lung Male Day 7 VIDO# 89

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to NCBI MusPutFur1.0 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v2.0.0 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: MusPutFur1.0
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
Supplementary_files_format_and_content: normalizedCounts.csv: remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+3) CPM

organism: Mustela putorius furo

source_name: Right Cranial Lung

growth_protocol: in vivo

extract_protocol:
RNA was extracted from tissues using RNeasy Plus Mini Kit from QIAGEN
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded Total RNA - Globin kit.

treatment_protocol: Infected ferrets were infected intranasally with SARS-CoV-2 isolate /Canada/ON/VIDO-01-2020. The viral stock used was from the second passage and the sequence is available at GISAID – EPI_ISL_425177.

tag: donor

value: VIDO# 89

tag: day

value: Day 7

value: Male


title: Right Cranial Lung Male Day 7 VIDO# 90

value: VIDO# 90


title: E13.5 Zfp57-/- maternal-zygotic mutant (M-Z-) mRNA-Seq rep2

value: hybrid 129/DBA

tag: tissue

value: total embryo

tag: age

value: embryonic day 13.5


title: Smchd1KO3_rep2

value: Embryonic stem cells


title: Right Cranial Lung Male Day 7 VIDO# 85

value: VIDO# 85


title: Smchd1KO1_rep2


title: RNAseq_DuxKO_1


title: Right Cranial Lung Male Day 21 VIDO# 96

value: VIDO# 96

value: Day 21


title: Smchd1KO3_rep1


title: E13.5 Zfp57-/+ (M-Z+) mRNA-Seq rep6

tag: strain

tag: genotype


title: Right Cranial Lung Male Day 21 VIDO# 95

value: VIDO# 95


title: Right Cranial Lung Male Day 21 VIDO# 94

value: VIDO# 94


title: E13.5 Zfp57-/+ (M-Z+) mRNA-Seq rep5


title: Smchd1KO2_rep1


title: E13.5 Zfp57-/+ (M-Z+) mRNA-Seq rep4


title: E13.5 Zfp57-/+ (M-Z+) mRNA-Seq rep3


title: Smchd1KO1_rep1


title: RNAseq_WT_6 (WT3_rep2)


title: Right Cranial Lung Male Day 2 VIDO# 86

value: VIDO# 86

value: Day 2


title: E13.5 Zfp57-/+ (M-Z+) mRNA-Seq rep2


title: Right Cranial Lung Male Day 2 VIDO# 87

value: VIDO# 87


title: E13.5 Zfp57-/+ (M-Z+) mRNA-Seq rep1


title: RNAseq_WT_5 (WT2_rep2)


title: RNAseq_WT_4 (WT1_rep2)


title: Right Cranial Lung Male Day 14 VIDO# 93

value: VIDO# 93

value: Day 14


title: Right Cranial Lung Male Day 14 VIDO# 92

value: VIDO# 92


title: Meninges Young 2

description: RNA was isolated from the brains of 5 mice.

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 4.0.0. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: Dural Meninges

extract_protocol:
10x Genomics Chromium single-cell preparation
NGS Illumina Next Seq

value: 2 months

value: male

value: Dural Meninges


title: Right Cranial Lung Male Day 14 VIDO# 91

value: VIDO# 91

value: Male


title: RNAseq_WT_3 (WT3_rep1)

value: Embryonic stem cells


title: Meninges Old 2


title: RNAseq_WT_2 (WT2_rep1)


title: Meninges Old 1

value: 24 months


title: RNAseq_WT_1 (WT1_rep1)


title: Right Cranial Lung Female Day 7 VIDO# 68

value: VIDO# 68

value: Day 7

value: Female


title: Right Cranial Lung Male Day 2 VIDO# 88

value: VIDO# 88


title: Right Cranial Lung Female Day 21 VIDO# 78

value: VIDO# 78

value: Day 21


title: Meninges, young, CD31+

description: RNA was isolated from the brains of 10 mice.

value: Endothelial cells


title: Meninges, young, CD13+

value: Mural cells


title: Right Cranial Lung Female Day 7 VIDO# 67

value: VIDO# 67


title: WT-H3K4me3-ChIP-seq

source_name: Bone marrow Lin-  Kit+ cells

tag: antibody

tag: antibody vendor

value: Millipore

tag: antibody catalogy no

value: Mouse-derived Bone marrow cells

value: Bone marrow

value: Lin- Kit+ cells

value: WT


title: Meninges, old, CD13+

value: male

value: Dural Meninges


title: Hoxblinc-Tg-CBS73K-bait-4C-seq

data_processing:
Library strategy: 4C-seq
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads were aligned to the mm9 genome assembly using Tophat, and ATAC-seq, ChIP-seq and 4C-seq reads were aligned to the mm9 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples and peaks for ATAC-seq, ChIP-seq and 4C-seq

tag: genotype/variation

value: Hoxblinc-Tg


title: Hoxblinc-Tg-CBS43K-bait-4C-seq

tag: cell types


title: Hoxblinc-Tg-Hoxb13-bait-4C-seq

tag: cell type


title: Meninges, old, CD31+

value: 24 months


title: Hoxblinc-Tg-Hoxb4-bait-4C-seq


title: Right Cranial Lung Female Day 2 VIDO# 66

value: VIDO# 66

value: Day 2

tag: Sex

tag: treatment


title: Right Cranial Lung Female Day 21 VIDO# 76

value: VIDO# 76

value: Female


title: Meninges Young 1

value: 2 months

tag: gender


title: Right Cranial Lung Female Day 2 VIDO# 65

value: VIDO# 65


title: Right Cranial Lung Female Day 7 VIDO# 69

value: VIDO# 69

value: Day 7


title: Hoxblinc-Tg-H3K4me3-ChIP-seq

value: Millipore


title: Brain, old, CD31+

value: Endothelial cells

value: Whole brain


title: Right Cranial Lung Female Day 2 VIDO# 64

value: VIDO# 64


title: Brain, young, CD31+


title: Right Cranial Lung Female Day 14 VIDO# 75

value: VIDO# 75

value: Day 14


title: Brain, old, CD13+

value: Mural cells

value: male


title: Hoxblinc-Tg-ChIRP-seq-LSK

value: Bone marrow

value: Lin- Kit+ cells

value: Hoxblinc-Tg


title: Right Cranial Lung Female Day 14 VIDO# 74

value: VIDO# 74


title: WT-Hoxb4-bait-4C-seq

value: Mouse-derived Bone marrow cells

value: WT


title: Brain, young, CD13+

value: 2 months


title: Hoxblinc-Tg-ATAC-seq-2

source_name: Bone marrow Lin- Sca1+ Kit+ cells

value: Lin- Sca1+ Kit+ cells


title: WT-ChIRP-seq-LSK


title: Right Cranial Lung Female Day 21 VIDO# 77

value: VIDO# 77

value: Day 21

value: Female


title: Right Cranial Lung Female Control VIDO# 63

value: VIDO# 63

value: Control

value: PBS


title: Right Cranial Lung Female Control VIDO# 62

value: VIDO# 62


title: Hoxblinc-Tg-ATAC-seq-1


title: Hoxblinc-Tg-MLL-ChIP-seq-LSK


title: WT-ATAC-seq-1


title: Right Caudal Lung Male Day 7 VIDO# 90

source_name: Right Cauadal Lung

value: VIDO# 90

value: Day 7

value: Male


title: 654_V1_mouse_06272019_S29

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The Cell Ranger Single-Cell Software Suite (version 3.0, 10x Genomics) was used to align and quantify sequencing data against the provided mm10 mouse reference genome.
Downstream analyses, such as graph-based clustering, and differential expression analysis/visualization, was performed using the Loupe Cell Browser (version 3.1, 10x Genomics) and the Seurat package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text and matrix files

source_name: Spinal cord

extract_protocol:
Single cell RNA Seq was performed using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3’ gene expression (3’ GEX) V3 kit, and an input of ~10,000 viable cells from a debris-free suspension. Briefly, Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM R
-cleanup and amplified for 12 cycles followed by fragmentation of amplified cDNA, end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol.
Libraries were quantified using QuBit (Thermofisher) and Bioanalyzer (Agilent). Libraries were sequenced in paired end mode on a NovaSeq instrument (Illumina, San Diego, CA) targeting a depth of 50,000-100,000 reads per cell.

tag: group

value: spinal cord


title: WT-ATAC-seq-2

value: Bone marrow


title: Right Cranial Lung Female Control VIDO# 61

value: VIDO# 61


title: WT-MLL-ChIP-seq-LSK

value: Lin- Kit+ cells


title: WT-CBS73K-bait-4C-seq

value: Mouse-derived Bone marrow cells

value: WT


title: WT-Hoxb13-bait-4C-seq


title: Right Caudal Lung Male Day 7 VIDO# 89

value: VIDO# 89


title: WT-CBS43K-bait-4C-seq


title: 653_R1_mouse_06272019_S28


title: Right Cranial Lung Female Day 14 VIDO# 73

value: VIDO# 73

value: Day 14


title: Right Caudal Lung Male Day 21 VIDO# 96

value: VIDO# 96

value: Day 21


title: splenocytes WES

city: Heidelberg

first: Bernhard

last: Radlwimmer

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

country: Germany

institute: Deutsches Krebsforschungszentrum / German National Cancer Research Centre

description: control mouse splenocytes isolated from spleen

data_processing:
Whole exome sequencing paired end reads in fastq format were aligned using BWA (v0.7.15) to the mm10 reference genome with options: -M –T 0. Duplicates were marked using sambamba (0.6.6).
CNV analysis was performed using CNVkit (v0.9.6). Tumor WES samples (tNSC0-3, mGB0-2) were analysed with reference to the two normal WES samples, ctrlNSC and normal splenocytes. The mm10 genome .fasta was used to calculate accessibility as follows: access mm10.fa -s 10000 –o mm10_accessibility.bed. The S0276129 bedfile with Agilent capture array loci, lifted over to the mm10 genome, was used as the target regions. Regions were annotated using UCSC’s mm10 flat reference (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refFlat.txt.gz, accessed 21 November 2019).
Calling was performed with the batch command and the following options: batch TUMOR_SAMPLES --normal NORMAL_SAMPLES --targets S0276129_mm10.bed --fasta mm10.fa --access mm10_accessibility.bed --annotate refFlat.txt --drop-low-coverage. Copy number state segmentation was performed using the ‘cbs’ method as implemented in the R package DNAcopy (v1.54.0).
The results of the CNV calling were visualised using the R package circlize (v0.4.4)35in R v3.5.1. Regions overlapping annotated segmental duplications (downloaded from the UCSC Table Browser, accessed 25 January 2020) were removed before plotting due to potential issues with inferring copy number states in these repetitive regions.  For ease of visualisation, extreme values with CNVkit log2 copy ratio < -2 or > 2 were set to this minimum and maximum. The integer CNVkit segmented copy number states were smoothed using the rollarray command from zoo (v1.8-2) with the options width = 301, partial=TRUE.
Genome_build: mm10
Supplementary_files_format_and_content: GB_GEMMs_mGB_tNSC_CNVkit_results.txt.gz: table of output of CNV calling results, generated by CNVkit

source_name: control splenocytes

growth_protocol: Tlx-CreERT2/p53-floxed/pten-floxed (double knockout [DKO]) mice were described in Costa et al., Blood Advances 2019. To induce recombination of floxed alleles, 4-week-old mice were injected intraperitoneally with 1 mg tamoxifen (S5007 Sigma) in 5% ethanol and 95% oil (T5648 Sigma) for 5 consecutive days. Animal experiments were approved by the German responsible authority (Regierungspräsidium Karlsruhe) and performed in conformity with the German law for Animal Protection (animal license number: G-156/15, G-199/11). Control NSCs were isolated from the subventricular zone.

extract_protocol:
DNA and RNA were isolated using spin column preparation kits from cells cultured in vitro.
Genomic DNA was fragmented to a size range of 150-250 bp using the Covaris S220 instrument. The fragmented DNA was end repaired and adenylated. The SureSelect Adaptor was then ligated followed by a pre-amplification. After library preparation target regions were captured by hybridization of biotinylated baits (library probes from the Agilent SureSelect XT Mouse All Exon). Captured target sequences were then isolated using streptavidin coated magnetic beads. Subsequently the appropriate 8 bp single index tags were added during sequencing library amplification. All steps were done using Agilent SureSelect XT Reagent Kit. Final quality control was done using Qubit 3 fluorometer and Agilent Bioanalyzer 2100. The libraries were sequenced in paired-end mode (2 x 50 nt) on a NovaSeq6000 S2 Flowcell resulting in ~200 million distinct sequencing reads per library.

treatment_protocol: tNSCs were isolated from the subventricular zone (SVZ) of mice 2 weeks after the injection of either tamoxifen or oil. For mGB tumor cell isolation, glioma-bearing mice were euthanized with carbon dioxide; brains were minced and dissociated in Leibovitz-L15 (Life Technologies) containing 10 U/mL papain, 5 mM EDTA, and 200 U/mL DNAse. Cells were grown according in stem cell-maintaining conditions.

value: normal mouse splenocytes


title: tNSC3 WES

description: mouse glioblastoma cells isolated from transformed NSCs isolated from the subventricular zone, generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, third in vivo passage

source_name: tNSC line, after third in vivo passage

value: mouse glioblastoma cell line


title: Right Caudal Lung Male Day 21 VIDO# 95

value: VIDO# 95


title: tNSC2 WES

description: mouse glioblastoma cells isolated from transformed NSCs isolated from the subventricular zone, generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, second in vivo passage

source_name: tNSC line, after second in vivo passage


title: Right Caudal Lung Male Day 21 VIDO# 94

value: VIDO# 94


title: tNSC1 WES

description: mouse glioblastoma cells isolated from transformed NSCs isolated from the subventricular zone, generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, first in vivo passage

source_name: tNSC line, after first in vivo passage


title: Right Caudal Lung Male Day 7 VIDO# 85

value: VIDO# 85

value: Day 7


title: Right Caudal Lung Male Day 2 VIDO# 88

value: VIDO# 88

value: Day 2

value: Male


title: Right Caudal Lung Male Day 2 VIDO# 86

value: VIDO# 86


title: Right Caudal Lung Male Day 2 VIDO# 87

value: VIDO# 87


title: tNSC0 WES

description: mouse glioblastoma cells isolated from transformed NSCs isolated from the subventricular zone, generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, initial isolation

source_name: tNSC line, initial isolation


title: mGB1 WES

description: mouse glioblastoma cells from gross tumour generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, first in vivo passage

source_name: mGB line, after first in vivo passage


title: mGB2 WES

description: mouse glioblastoma cells from gross tumour generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, second in vivo passage

source_name: mGB line, after second in vivo passage


title: ctrlNSC WES

description: control mouse neural stem cells isolated from the subventricular zone

source_name: control neural stem cells isolated from SVZ

value: normal mouse neural stem cells


title: Right Caudal Lung Male Day 14 VIDO# 93

value: VIDO# 93


title: mGB0 WES

description: mouse glioblastoma cells isolated from gross tumour generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, initial isolation

source_name: mGB line, initial isolation


title: Time 40h, Rep 4

type: RNA

city: Frederick

first: Shivendra

middle: G

last: Tewari

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute

description: Gene expression data

hyb_protocol: The eight time course samples were hybridized (along with the manufacturer’s RNA spike-in controls) according to standard protocol to the 8 sectors of an Agilent 8x15K platform microarray (AMADID 037237) with separate microarray slides used for each biological replicate.

scan_protocol: Arrays were scanned with the Agilent G2600D SureScan microarray scanner using scan protocol AgilentHD_GX_1color. Agilent’s Feature Extraction Software was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data.

data_processing: Txt files from Agilent’s Feature Extraction Software were transferred to Partek Genomics Suite software (v7.0). Within Partek, the gProcessedSignal was imported and the intensity values were normalized using Quantile Normalization and Log Tranformation Base 2.0 after import.

organism: Plasmodium falciparum

source_name: FOS-treated NF54, Time 40, Rep 4

label_protocol: From 100 ng of total RNA, Cyanine-3 labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit One-Color (Agilent).

extract_protocol: For each data point, RNA was extracted from 50 µL of packed RBC culture with Trizol Reagent and the PureLink Mini Kit (Invitrogen/Thermo Fisher Scientific). 1ml Trizol was added to each sample, followed by high-speed disruption in tubes containing Lysing Matrix D (MP Biomedical) in a FastPrep 120 Instrument at speed 6 for 20 seconds. Homogenates were subsequently processed according to the PureLink Mini Kit manufacturer’s (Invitrogen/Thermo Fisher Scientific) protocol, including on-column DNase treatment.

treatment_protocol: Sub-lethal dose of fosmidomycin (1 uM) was added to control RPMI medium at 0 h of the experiment, which was determined using blood smears of the parasite cultures (described in the paper).

tag: protocol

value: Blood-stage NF54 P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and 1 uM fosmidomycin

tag: time

tag: replicate

value: Rep 4


title: siTfe3/Tfeb iron

city: Nagoya

first: Yohei

last: Kanamori

address: Furo-cho, Chikusa-ku

institute: Nagoya University

description: Gene expression data from RAW264 cells

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of Agilent 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 μm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Agilent Feature Extraction ver.12.0.3.1. Data were normalized to the median of samples using GeneSpring software version 14.9 (Agilent Technologies).

source_name: siTfe3/Tfeb, iron

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop 1000(Thermo Fisher Scientific).

extract_protocol: Total RNA was prepared using Sepasol(nacalai-tesque). Cleanup and concentration was performed by Rneasy MinElute Cleanup Kit.

treatment_protocol: RAW264 cells were transfected with siRNA targeting Tfe3/Tfeb or GFP. Forty-eight hours after transfection, cells were treated with or without 500 μM of FeCl3 for 24 hours.

value: BALB/c

tag: cell-type

value: RAW264 macrophages


title: siTfe3/Tfeb untreated

description: Gene expression data from RAW264 cells

source_name: siTfe3/Tfeb, untreated


title: siGFP untreated

description: Gene expression data from RAW264 cells

source_name: siGFP, untreated


title: Time 32h, Rep 4

description: Gene expression data

source_name: FOS-treated NF54, Time 32, Rep 4


title: Time 8h, Rep 4

description: Gene expression data

source_name: FOS-treated NF54, Time 8, Rep 4


title: Time 24h, Rep 4

description: Gene expression data

source_name: FOS-treated NF54, Time 24, Rep 4


title: Right Caudal Lung Male Day 14 VIDO# 92

source_name: Right Cauadal Lung

tag: donor

value: VIDO# 92

tag: day

value: Day 14


title: siGFP iron

description: Gene expression data from RAW264 cells

source_name: siGFP, iron

tag: strain


title: tNSC2 RNA-Seq

description:
mouse glioblastoma cells isolated from transformed NSCs isolated from the subventricular zone, generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, second in vivo passage
GB_GEMMs_mGB_tNSC_log-cpm_expression_Gencode_M2.csv.gz
GB_GEMMs_Idh1-Idh2_hotspots_SNV_calling_RNAseq.vcf

data_processing:
Reads were aligned to the mouse genome (mm10 build) with the Gencode reference transcriptome (M2) using STAR (v2.5.2a) with the following options: --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.05 --alignIntronMax 1 --outFilterMatchNminOverLread 0.95 --outFilterScoreMinOverLread 0.95 --outFilterMultimapNmax 10 --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outSAMunmapped Within --outSAMattributes Standard --alignIntronMin 21 --outFilterMatchNmin 16.
Overlapping read pairs were clipped using the clipOverlap tool in bamUtil (v1.0.9) 37. The raw counts matrix was generated using featureCounts (v1.5.3)38 using options -Q 255 -p -t exon against the M2 transcriptome. Aligned data were quality controlled using RSeQC (v2.6.4)39.
Gene expression values for each sample were quantified using limma-voom (v3.34.4)'s log-cpm metric.
Single nucleotide variants (SNVs) were called using BCFTools (v1.9) at the 3 hotspots (Idh1: R132 = 1:65170977-65170979; Idh2: R140 = 7:80099112-80099114; R172 = 7:80099016-80099018, mm10 coordinates). bcftools mpileup was used on the full set of samples for each data type, and consensus calling performed with bcftools call –c.
Genome_build: mm10
Supplementary_files_format_and_content: GB_GEMMs_mGB_tNSC_log-cpm_expression_Gencode_M2.csv.gz: limma-voom calculated log-cpm values of gene expression
Supplementary_files_format_and_content: GB_GEMMs_Idh1-Idh2_hotspots_SNV_calling_RNAseq.vcf - SNV calling results for Idh1/2 mutation hotspots

growth_protocol: Tlx-CreERT2/p53-floxed/pten-floxed (double knockout [DKO]) mice were described in Costa et al., Blood Advances 2019. To induce recombination of floxed alleles, 4-week-old mice were injected intraperitoneally with 1 mg tamoxifen (S5007 Sigma) in 5% ethanol and 95% oil (T5648 Sigma) for 5 consecutive days. Animal experiments were approved by the German responsible authority (Regierungspräsidium Karlsruhe) and performed in conformity with the German law for Animal Protection (animal license number: G-156/15, G-199/11).

extract_protocol:
DNA and RNA were isolated using Qiagen spin column preparation kits from cells cultured in vitro.
For RNA-seq: poly(A)-positive mRNA transcripts were isolated from the total RNA by binding to magnetic oligo(d)T beads (RNA purification beads). After elution from the beads and fragmentation, the mRNA was reverse transcribed during first and second strand synthesis yielding double-stranded cDNA. The ends of the cDNA molecules were end repaired and an adenosine overhang was added to all 3’ ends (A-tailing step) to facilitate the ligation of the adapter molecules. These adapters have individual dedicated index sequences and add the Illumina specific sequences that are needed for amplification, flow cell hybridization and sequencing. 8 bp single-index NEXTflex DNA barcodes (Bioo Scientific) were used. The final ligation product was amplified via PCR. Double-stranded cDNA sequencing libraries were further checked for quality and quantity using Qubit 3 fluorometer and Agilent Bioanalyzer 2100. The libraries were sequenced in paired-end mode (2 x 50 nt) on a NovaSeq6000 S2 Flowcell resulting in ~50 million distinct sequencing reads per library.

treatment_protocol: NSCs were isolated from the subventricular zone (SVZ) of mice 2 weeks after the injection of either tamoxifen or oil. For tumor cell isolation, glioma-bearing mice were euthanized with carbon dioxide; brains were minced and dissociated in Leibovitz-L15 (Life Technologies) containing 10 U/mL papain, 5 mM EDTA, and 200 U/mL DNAse. Cells were grown according in stem cell-maintaining conditions.

tag: tissue

value: mouse glioblastoma cell line


title: ctrlNSC RNA-Seq

description:
control mouse neural stem cells isolated from the subventricular zone
GB_GEMMs_mGB_tNSC_log-cpm_expression_Gencode_M2.csv.gz
GB_GEMMs_Idh1-Idh2_hotspots_SNV_calling_RNAseq.vcf


title: Right Caudal Lung Male Day 14 VIDO# 91

value: VIDO# 91


title: Right Caudal Lung Female Day 7 VIDO# 69

value: VIDO# 69

value: Female


title: Right Caudal Lung Female Day 21 VIDO# 77

value: VIDO# 77

value: Day 21


title: Right Caudal Lung Female Day 7 VIDO# 68

value: VIDO# 68

value: Day 7


title: tNSC3 RNA-Seq

description:
mouse glioblastoma cells isolated from transformed NSCs isolated from the subventricular zone, generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, third in vivo passage
GB_GEMMs_mGB_tNSC_log-cpm_expression_Gencode_M2.csv.gz
GB_GEMMs_Idh1-Idh2_hotspots_SNV_calling_RNAseq.vcf

source_name: tNSC line, after third in vivo passage


title: Time 32h, Rep 3

description: Gene expression data

source_name: FOS-treated NF54, Time 32, Rep 3

value: Rep 3


title: Time 48h, Rep 4

description: Gene expression data

source_name: FOS-treated NF54, Time 48, Rep 4


title: Right Caudal Lung Female Day 21 VIDO# 76

value: VIDO# 76


title: tNSC1 RNA-Seq

description:
mouse glioblastoma cells isolated from transformed NSCs isolated from the subventricular zone, generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, first in vivo passage
GB_GEMMs_mGB_tNSC_log-cpm_expression_Gencode_M2.csv.gz
GB_GEMMs_Idh1-Idh2_hotspots_SNV_calling_RNAseq.vcf

source_name: tNSC line, after first in vivo passage


title: tNSC0 RNA-Seq

description:
mouse glioblastoma cells isolated from transformed NSCs isolated from the subventricular zone, generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, initial isolation
GB_GEMMs_mGB_tNSC_log-cpm_expression_Gencode_M2.csv.gz
GB_GEMMs_Idh1-Idh2_hotspots_SNV_calling_RNAseq.vcf

source_name: tNSC line, initial isolation


title: Time 40h, Rep 3

description: Gene expression data

source_name: FOS-treated NF54, Time 40, Rep 3


title: Time 0h, Rep 4

description: Gene expression data

source_name: FOS-treated NF54, Time 0, Rep 4


title: Time 48h, Rep 3

description: Gene expression data

source_name: FOS-treated NF54, Time 48, Rep 3


title: mGB1 RNA-Seq

description:
mouse glioblastoma cells from gross tumour generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, first in vivo passage
GB_GEMMs_mGB_tNSC_log-cpm_expression_Gencode_M2.csv.gz
GB_GEMMs_Idh1-Idh2_hotspots_SNV_calling_RNAseq.vcf

source_name: mGB line, after first in vivo passage


title: Right Caudal Lung Female Day 2 VIDO# 66

value: VIDO# 66

value: Day 2


title: mGB2 RNA-Seq

description:
mouse glioblastoma cells from gross tumour generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, second in vivo passage
GB_GEMMs_mGB_tNSC_log-cpm_expression_Gencode_M2.csv.gz
GB_GEMMs_Idh1-Idh2_hotspots_SNV_calling_RNAseq.vcf

source_name: mGB line, after second in vivo passage


title: mGB0 RNA-Seq

description:
mouse glioblastoma cells isolated from gross tumour generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53, initial isolation
GB_GEMMs_mGB_tNSC_log-cpm_expression_Gencode_M2.csv.gz
GB_GEMMs_Idh1-Idh2_hotspots_SNV_calling_RNAseq.vcf

source_name: mGB line, initial isolation


title: Right Caudal Lung Female Day 2 VIDO# 65

value: VIDO# 65


title: C2C12(Myod1-/-) rep3

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

data_processing:
Illumina bcl2fastq software used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp software, clean data were generated with fastQC software, then mapped to GRCm38 whole genome using Hisat2/Tophat software.
After removal of genes or transcripts shorter than 100 bp, Fragments Per Kilobase Million (FPKM) were calculated using Stingie software. Expression of a gene was considered as 0 if the FPKM for the gene or transcript was less than 0.0001. Genes with zero expression in all samples were removed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel files including fpkm values for each sample

source_name: Myoblast cells

growth_protocol: Wild type and Myod1 knockout C2C12 cells were culture in Ndiff227 serum-free medium, cultured at 37°C in 5% CO2 for 6 days

extract_protocol:
Cells were collected with trypsinization and total RNA was extract with TRIzol using the protocol from the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols. 2-3 mg total RNA of each sample was used for library construction.

value: Satellite cells from the thigh muscle of a 2-month-old female C3H mouse

tag: genotype

value: Myod1 -/-


title: Time 16h, Rep 4

description: Gene expression data

source_name: FOS-treated NF54, Time 16, Rep 4

value: Blood-stage NF54 P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and 1 uM fosmidomycin

value: Rep 4


title: Right Caudal Lung Female Day 21 VIDO# 78

value: VIDO# 78


title: Time 24h, Rep 3

description: Gene expression data

source_name: FOS-treated NF54, Time 24, Rep 3


title: Time 8h, Rep 3

description: Gene expression data

source_name: FOS-treated NF54, Time 8, Rep 3


title: Right Caudal Lung Female Day 14 VIDO# 75

source_name: Right Cauadal Lung

value: VIDO# 75

value: Day 14


title: Time 16h, Rep 3

description: Gene expression data

source_name: FOS-treated NF54, Time 16, Rep 3


title: Right Caudal Lung Female Day 2 VIDO# 64

value: VIDO# 64

value: Female


title: Time 48h, Rep 2

description: Gene expression data

source_name: FOS-treated NF54, Time 48, Rep 2

value: Rep 2


title: C2C12(Myod1-/-) rep1


title: C2C12(Myod1-/-) rep2


title: Right Caudal Lung Female Day 14 VIDO# 74

value: VIDO# 74


title: Time 40h, Rep 2

description: Gene expression data

source_name: FOS-treated NF54, Time 40, Rep 2


title: Right Caudal Lung Female Day 14 VIDO# 73

value: VIDO# 73


title: C2C12(WT) rep2

value: Wild type


title: Time 32h, Rep 2

description: Gene expression data

source_name: FOS-treated NF54, Time 32, Rep 2


title: Stage47_Rep2

city: San Francisco

first: Arthur

middle: Jeremy

last: Willsey

state: CA

address: 675 Nelson Rising Lane, Mail Code 0518

department: Psychiatry

institute: UCSF

description:
xtrop_timecourse_rawcounts.csv
xtrop_timecourse_filtered_FQ_cpm.csv

data_processing:
Reads were aligned to the XenBase X. tropicalis v9.1 reference genome using STAR v2.7.3 with default parameters and  --quantmode GeneCounts to generate raw reads counts.
Read counts were converted to counts per million and filtered to keep only those with more than 1 cpm in at least 3 samples (replicate size).
Full quantile normalization was performed across samples within the two respective experiments (timecourse and small molecule treatments).
Please refer to XenBase JgiToXenbaseGenePage_9.1.txt file for the most up-to-date annotations for each gene ID.
Genome_build: XenBase X. tropicalis v9.1
Supplementary_files_format_and_content: rawcounts.csv, normcounts.csv, filtered_FQ_cpm.csv

organism: Xenopus tropicalis

source_name: Brain

growth_protocol: Standard X. tropicalis growth media

extract_protocol:
Trizol-based RNA extraction.
PolyA selection and stranded, low yield library preparation.

treatment_protocol: Treatment in drug at stage 30 onward. 5uM for cyclopamine, 10uM for beta-estradiol. No treatment for timecourse data.

value: wildtype

tag: developmetal stage

value: Stage 47

value: Brain


title: C2C12(WT) rep3


title: Time 24h, Rep 2

description: Gene expression data

source_name: FOS-treated NF54, Time 24, Rep 2


title: Stage47_Rep3


title: C2C12(WT) rep1


title: Right Caudal Lung Female Control VIDO# 63

value: VIDO# 63

value: Control

value: PBS


title: Stage46_Rep3

value: Stage 46


title: Right Caudal Lung Female Control VIDO# 61

value: VIDO# 61


title: Right Caudal Lung Female Control VIDO# 62

value: VIDO# 62


title: Stage47_Rep1


title: Time 16h, Rep 2

description: Gene expression data

source_name: FOS-treated NF54, Time 16, Rep 2

value: Blood-stage NF54 P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and 1 uM fosmidomycin


title: Nasal Turbinates Male Day 7 VIDO# 90

source_name: Nasal Turbinates

value: VIDO# 90

value: Day 7

value: Male


title: Th17 differentiation + FICZ 2

city: Ribeirão Preto

first: Paula

middle: Barbim

last: Donate

address: Bandeirantes avenue, 3900

country: Brazil

institute: University of São Paulo

description:
miRNA expression after 24 hours  + FICZ
Th17 + FICZ_2

hyb_protocol: Each labeled RNA sample was hybridized to an individual array on an 8×15K format Agilent mouse miRNA array slides, and each array contained probes for 567 mouse miRNAs and 10 mouse gamma herpes virus miRNAs. Hybridizations were performed in SureHyb chambers (Agilent) for 20 h at 55 ◦C, washed according to the manufacturer’s instructions and scanned.

scan_protocol: The oligo-miRNA array slides were scanned using a DNA microarray scanner (Agilent Technologies), and the hybridization signals were extracted using the Agilent Feature Extraction software version 10.5.

data_processing: The microarray numerical quantitative data were processed within R using the software package AgiMicroRna (Lopez-Romero, 2019) from Bioconductor (http://www.bioconductor.org).

source_name: Culture, Th17 differentiation, 24h, FICZ (100nM)

label_protocol: The total RNA samples (Th0, Th0 + FICZ, Th17, Th17 + FICZ) were Cy-3-labeled using the Agilent miRNA Complete Labeling and Hybridization Kit (Agilent Tech, Mississauga, ON, Canada). Briefly, 100 ng of total RNA was dephosphorylated by incubation with calf intestinal phosphatase at 37 ºC for 30 min, denatured in 100% DMSO at 100 ◦C for 5 minutes and labeled with perCp-Cy3 using T4 ligase at 16 ◦C for 1 h.

growth_protocol: Naïve T cells (CD4+CD44-CD62L+) were sorted and differentiate for Th17 as previously described. To purify our sample for the microarray, the IL-17 secretion assay kit (Miltenyi Biotec) was used to isolate the IL-17 producing cells by magnetic beads.

extract_protocol: The total RNA was isolated using the mirVana total RNA isolation kit (Ambion, NY, USA), according to the manufacturer’s instructions. RNA preparations were screened for purity and concentration in a Nanodrop Spectrophotometer (Thermo Scientific). RNA degradation was assessed by microfluidic electrophoresis using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only RNA samples that were free of proteins and phenol and featured an RNA Integrity Number (RIN) ≥ 9.0 were used.

treatment_protocol: Th17 cells were then cultivated in the presence of the same recombinant cocktail with IL-23 (20ng/ml) in the presence or absence of FICZ (Enzo Life Sciences; 100 nM) for 24hs. Th0 cells were used as control.

tag: strain background

value: Naïve T cells (CD4+CD44-CD62L+)

tag: culture condition

value: Th17 differentiation, 24h, FICZ (100nM)


title: Stage46_Rep1


title: Time 0h, Rep 2

description: Gene expression data

source_name: FOS-treated NF54, Time 0, Rep 2

value: Rep 2


title: Time 8h, Rep 2

description: Gene expression data

source_name: FOS-treated NF54, Time 8, Rep 2


title: Time 40h, Rep 1

description: Gene expression data

source_name: FOS-treated NF54, Time 40, Rep 1

value: Rep 1


title: Time 48h, Rep 1

description: Gene expression data

source_name: FOS-treated NF54, Time 48, Rep 1


title: Nasal Turbinates Male Day 7 VIDO# 89

value: VIDO# 89


title: Stage45_Rep3

value: wildtype

value: Stage 45


title: Nasal Turbinates Male Day 7 VIDO# 85

value: VIDO# 85


title: Time 32h, Rep 1

description: Gene expression data

source_name: FOS-treated NF54, Time 32, Rep 1


title: Th17 differentiation + FICZ 1

description:
miRNA expression after 24 hours + FICZ
Th17 + FICZ_1

tag: cell type


title: Nasal Turbinates Male Day 21 VIDO# 96

value: VIDO# 96

value: Day 21

tag: Sex


title: Stage45_Rep2

value: Brain


title: Th17 differentiation 2

description:
miRNA expression after 24 hours
Th17_2

source_name: Culture, Th17 differentiation, 24h

value: Th17 differentiation, 24h


title: Th17 differentiation 1

description:
miRNA expression after 24 hours
Th17_1


title: Time 24h, Rep 1

description: Gene expression data

source_name: FOS-treated NF54, Time 24, Rep 1


title: Control 2 + FICZ

description:
miRNA expression after 24 hours  + FICZ
Th0 + FICZ_2

source_name: Culture, Th0, 24h, FICZ (100nM)


title: Stage45_Rep1


title: Nasal Turbinates Male Day 21 VIDO# 95

value: VIDO# 95

tag: treatment


title: Stage46_Rep2

value: Stage 46


title: Stage44_Rep3

value: Stage 44


title: Control 1 + FICZ

description:
miRNA expression after 24 hours + FICZ
Th0 + FICZ_1


title: Stage44_Rep2


title: Nasal Turbinates Male Day 21 VIDO# 94

value: VIDO# 94


title: Time 16h, Rep 1

description: Gene expression data

source_name: FOS-treated NF54, Time 16, Rep 1

value: Blood-stage NF54 P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and 1 uM fosmidomycin


title: F8: CD8_TDL_TEMRA_rep3

data_processing:
Raw FASTQ files from RNAseq paired-end sequencing were aligned to the  hg38 reference genome using STAR2.5.2a
Counts were corrected/normalized using PORT(github.com/itmat/normalization)
Genes with differential  expression across samples (DEGs) were assessed using the R package DeSeq2
Differential genes were calculated using a FDR cutoff of 0.05 and Log2 fold change of 1 otherwise indicated
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with counts

source_name: Tumor Draining Lymph Node(TDL)

extract_protocol:
mRNA was extracted using RNeasy Plus Micro kit  (Qiagen) following manufacturer’s protocol and eluted in 14μl of RNAse free water.  mRNA quality was assessed on a 2200 TapeStation (Agilent Technologies) using  High Sensitivity RNA ScreenTape (Agilent Technologies).mRNA from each  biological replicate (5ng/sample) was converted into cDNA and amplified (9 cycles)  using the SMART-Seq V4 Ultra Low Input RNA Kit (Takara Bio).
10ng of cDNA  was used to prepare DNA libraries using Nextera XT DNA Library Prep Kit  (Illumina). Barcoded samples were pooled, diluted at 1.8pM, loaded onto a TG  NextSeq 500/550 High Output Kit v2 (150 cycles, 400M reads, Illumina) and  paired-end sequencing was performed on a NextSeq 550 (Illumina)

treatment_protocol: Sorted cells were centrifuged, resuspended in 350μl of RLT buffer (RNeasy Plus  Micro kit, Qiagen) in DNA LoBind tubes (Eppendorf), vortexed for 30s, flash-frozen  on dry ice and stored at -80oC

value: Tumor Draining Lymph Node(TDL)

value: Effector (RA+) CD8+ T cell


title: Time 8h, Rep 1

description: Gene expression data

source_name: FOS-treated NF54, Time 8, Rep 1


title: Time 0h, Rep 1

description: Gene expression data

source_name: FOS-treated NF54, Time 0, Rep 1


title: E8: CD8_TDL_TEMRA_rep2


title: Nasal Turbinates Male Day 2 VIDO# 88

value: VIDO# 88

value: Day 2

value: Male


title: D8: CD8_TDL_TEMRA_rep1


title: Stage44_Rep1

source_name: Brain

value: wildtype


title: Nasal Turbinates Male Day 2 VIDO# 87

value: VIDO# 87


title: Stage42_Rep3

value: Stage 42


title: Nasal Turbinates Male Day 2 VIDO# 86

value: VIDO# 86


title: F6: CD8_TDL_Naive_rep3

value: Naive CD8+ T cell


title: Telogen replicate8

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were pre-processed to remove the adapter sequences, low-quality reads and low-quality bases filtration towards 3’- end using cutadapt program v2.10
Filtered reads were mapped to Capra hircus reference assembly ARS1 using Hisat program v2.20 (release date 2/6/2020)
Genome_build: ARS1
Supplementary_files_format_and_content: Comma saparated file containing log2(FC) for every gene.

organism: Capra hircus

source_name: Skin

extract_protocol:
The skin samples containing Pashmina follicles were collected from the flanking region of each goat. The skin biopsies samples were snap-frozen in liquid nitrogen and shipped to the laboratory in RNA-later for processing.  Trizol method were used for RNA extraction. Illumina TruSeq RNA Sample Prep Kit was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Chanthangi Pashmina Goat

value: skin containing pashmina follicles

tag: age

value: 24 months

tag: growth stage

value: Telogen


title: Stage42_Rep2

value: Brain


title: Telogen replicate7


title: Telogen replicate6


title: Nasal Turbinates Male Day 14 VIDO# 93

value: VIDO# 93

value: Day 14


title: Nasal Turbinates Male Day 14 VIDO# 92

value: VIDO# 92


title: Telogen replicate5


title: Stage40_Rep3

value: Stage 40


title: E6: CD8_TDL_Naive_rep2

value: Tumor Draining Lymph Node(TDL)


title: D6: CD8_TDL_Naive_rep1


title: Stage42_Rep1


title: Control 2

description:
miRNA expression after 24 hours
Th0_2

source_name: Culture, Th0, 24h

value: Naïve T cells (CD4+CD44-CD62L+)


title: Nasal Turbinates Male Day 14 VIDO# 91

source_name: Nasal Turbinates

value: VIDO# 91

value: Male


title: F5: CD8_TDL_EM_rep3

value: Effector memory CD8+ T cell


title: Telogen replicate4


title: Telogen replicate9


title: Stage40_Rep2

value: wildtype


title: Nasal Turbinates Female Day 7 VIDO# 69

value: VIDO# 69

value: Day 7

value: Female


title: Stage40_Rep1


title: Nasal Turbinates Female Day 7 VIDO# 67

value: VIDO# 67


title: E5: CD8_TDL_EM_rep2


title: dmso_Rep3

description:
bEST_cyclo_xtrop_rawcounts.csv
bEST_cyclo_xtrop_FQ_normcounts.csv

value: dmso treatment

value: Stage 46


title: D5: CD8_TDL_EM_rep1


title: Telogen replicate2

value: Chanthangi Pashmina Goat

value: skin containing pashmina follicles

value: 24 months

value: Telogen


title: Control 1

description:
miRNA expression after 24 hours
Th0_1


title: dmso_Rep2

value: Brain


title: Nasal Turbinates Female Day 21 VIDO# 77

value: VIDO# 77

value: Day 21


title: Nasal Turbinates Female Day 21 VIDO# 78

value: VIDO# 78


title: D9: CD8_TDL_CXCR5pos_rep1

value: Tumor Draining Lymph Node(TDL)

value: CXCR5pos CD8+ T cell


title: E9: CD8_TDL_CXCR5pos_rep2


title: Anagen replicate10

value: Male

value: Anagen


title: dmso_Rep1


title: Nasal Turbinates Female Day 2 VIDO# 66

value: VIDO# 66

value: Day 2


title: Anagen replicate9


title: Nasal Turbinates Female Day 2 VIDO# 65

value: VIDO# 65

value: Female


title: Nasal Turbinates Female Day 21 VIDO# 76

value: VIDO# 76


title: Telogen replicate1

value: Chanthangi Pashmina Goat


title: cyclo_Rep3

value: cyclopamine treatment

value: Stage 46


title: Telogen replicate3

value: skin containing pashmina follicles

value: 24 months

value: Telogen


title: cyclo_Rep2

value: Brain


title: Nasal Turbinates Female Day 2 VIDO# 64

value: VIDO# 64


title: cyclo_Rep1


title: Anagen replicate6


title: Anagen replicate7


title: D7: CD8_TDL_CM_rep1

value: Tumor Draining Lymph Node(TDL)

value: Central memory CD8+ T cell


title: bEST_Rep3

value: beta-estradiol treatment


title: bEST_Rep2


title: Anagen replicate5

value: Male

value: Anagen


title: Nasal Turbinates Female Day 14 VIDO# 75

value: VIDO# 75

value: Day 14


title: Nasal Turbinates Female Day 14 VIDO# 74

value: VIDO# 74

value: Female


title: F9: CD8_TDL_CXCR5pos_rep3

value: CXCR5pos CD8+ T cell


title: C6: CD8_LN_Naive_rep3

source_name: Lymph Node(LN)

value: Lymph Node(LN)

value: Naive CD8+ T cell


title: F7: CD8_TDL_CM_rep3


title: Anagen replicate8

value: Chanthangi Pashmina Goat

value: skin containing pashmina follicles


title: E7: CD8_TDL_CM_rep2


title: B6: CD8_LN_Naive_rep2


title: Anagen replicate4

value: 24 months


title: Anagen replicate3


title: Nasal Turbinates Female Control VIDO# 63

value: VIDO# 63

value: Control

value: PBS


title: A6: CD8_LN_Naive_rep1


title: bEST_Rep1

value: Stage 46

value: Brain


title: Nasal Turbinates Female Control VIDO# 62

value: VIDO# 62


title: Anagen replicate2

value: Male

value: Anagen


title: B5: CD8_LN_EM_rep2

value: Effector memory CD8+ T cell


title: Anagen replicate1


title: Nasal Turbinates Female Control VIDO# 61

value: VIDO# 61


title: A5: CD8_LN_EM_rep1


title: C_10: CD8_LN_CXCR5pos_rep3


title: K13/4722

city: Gent

first: Mattias

last: Hofmans

address: C. Heymanslaan 10

department: Department of pediatrics

country: Belgium

institute: Ghent University Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 reference genome using STAR v2.4.2 using a 2-pass strategy for identification of novel transcripts
Known gene quantification was performed on gencode v25 during the first pass.
Differential expression analysis of known genes was performed in R with DESeq2 v1.14.1
Genome_build: hg38
Supplementary_files_format_and_content: normalizedCounts_Deseq2.txt

extract_protocol:
Mononuclear cell preparations were isolated from bone marrow or peripheral blood using Ficoll density gradient (Axis-shield). Next, Total RNA was extracted using the miRNeasy Mini Kit (Qiagen) in combination with on-column DNase I digestion (RNase-Free DNase set, Qiagen) according to manufacturer’s instructions. The quality of the extracted RNA was assessed using the RNA 6000 Nano and RNA 6000 PICO assays on an 2100 Bioanalyzer (Agilent).
Sequencing libraries were prepared using a TruSeq Stranded Total RNA Kit adapted for long fragments (+/- 550 bp) with the Ribo-Zero Gold rRNA Removal Kit (Illumina), according to the manufacturer’s instructions. Prepared libraries were run on a HiSeq3000 high-throughput sequencing system (Illumina) and paired end reads were generated (average of 52 million  reads per sample)

tag: disease state

tag: hemoglobin (%)

value: normal

tag: karyotype

tag: mutation

value: Normal

tag: platelets (x 10^9/l)

tag: Cause of death

tag: survival from diagnosis (os) (years)

tag: survival from hsct (efs) (years)


title: Fenoxaprop 4 (FOX)

city: Newcastle upon Tyne

first: Robert

last: Edwards

address: Agriculture Building, Newcastle University, King's Rd

department: School of  Natural and Environmental Sciences

country: United Kingdom

institute: Newcastle University

description:
salmon_counts-Fenoxaprop.txt
AlopecurusFEN4

data_processing:
A de novo transcriptome assembly was carried out with Trinity v2.8.5. using default parameters
Trimmomatic option
coding regions of the assembled transcripts were identified by TransDecoder v5.5.0 with the default parameters and the -single_best_only option to limit to a single ORF per transcript.
Differentially expressed genes (³1-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Transcript quantification was performed using salmon with the autodetect strandedness and validation mappings parameters.
Tximport was used to transform the salmon expression count data into the DESeq data set. Genes with a single count or not counts across all the samples were removed. Counts were transformed and normalized using the DESeq2 package in R Studio
Weight co-expression network analysis performed in WGCNA R package with normalized reads (log+1)
Genome_build: de novo assembly (Alopecurus_Trinity.fasta, Alopecurus_Trinity.fasta_mapping.gene_trans_map)
Supplementary_files_format_and_content: counts

organism: Alopecurus myosuroides

source_name: 7-days old seedlings of Fenoxaprop population

growth_protocol: Black-grass seeds were pre-germinated in petri-dishes on 4 layers of filter paper (Whatman No. 1, Sigma Aldrich, Gillingham, UK) wetted with 7 mL of sterile deionized water. Petri-dishes were maintained at 4°C in the dark for 7 days prior to transfer to a growth cabinet with a 16h/8h (light/dark) and 18°C/16°C temperature cycle. For each population, five seedlings were sown into 10 cm plastic pots (n=5), containing John Innes No.2 compost (Marshalls, Huntingdon, UK) mixed with osmocote fertilizer (Osmocote, Suffolk, UK) and propagated in the growth cabinet (Sanyo, MLR-351 SANYO Electric Co., Ltd., Osaka, Japan)

extract_protocol:
The aerial tissue from five 1-2 tiller black grass plants were used for RNA extraction. Total RNA was extracted from frozen tissues (n=5), using NucleoSpin RNA plant kits (Macherey-Nagel, Dueren, Germany) according to the manufacturer’s instructions
Libraries were prepared using the NEBNext Ultra™ RNA Library Prep Kit for Illumina  according to the manufacturer’s instructions. 1ug of the poly (A) mRNA was purified from the total RNA using Oligo d(T)25 paramagnetics beads and the mRNA Magnetic Isolation Module (NEB). Barcodes were incorporated by using NEBNext Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB)
RNA-seq. Run in NovaSeq 6000 (Illumina) along with NovaSeq 6000 SP cluster cartridge

treatment_protocol: Plants were not treated

tag: population

value: Fenoxaprop

tag: phenotype

value: Resistant to fenoxaprop-p-ethyl, derived from Rothamsted after repeated field-rate applications of fenoxaprop-ethyl during 6 years

tag: genotype

value: still remain unknown. derived from wild-type

tag: tissue

value: 7-days old seedlings

value: untreated


title: 5.input

first: Xiaolin

last: Qu

address: No.415, Fengyang Road

department: Department of neurosurgery

institute: Changzheng Hospital affliated to Naval Medical University

data_processing:
library strategy: meRIP-seq
m6A: Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC RN5)  by Hisat2 software (v2.0.4).
m6A: Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
input: Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome(UCSC RN5) with hisat2 software (v2.0.4).
input: Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: UCSC  RN5
Supplementary_files_format_and_content: excel format

organism: Rattus norvegicus

source_name: retina from TON rats

growth_protocol: The protocols for animal studies were approved by the Animal Ethics Committee of the Naval Medical University (Shanghai, China), Ethic Certificate No:81371382. All experiments were performed under the guidance of the National Institute of Health Guide for the Care and Use of Laboratory Animals. Male Sprague-Dawley (SD) rats (220-250 g, 7–8 weeks of age) were housed for at least 7 days in a temperature-regulated (22-25℃) and humidity-controlled (50% relative humidity) animal faculty with a 12-hour light/dark circle. During the experiments, all rats had free access to water and food, except that food was withheld overnight before surgery.

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions
m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library  Prep Kit (New England Biolabs, Inc., USA).
m6A: The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
input: RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
input: 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

treatment_protocol: In this study, the TON model was established by clamping the optic nerve of rats, as previously described (Jiang et al., 2013; Ibrahim et al., 2018; Oku et al., 2019). Briefly, adult male SD rats were intraperitoneally anesthetized with pentobarbital sodium (1%, 35 mg/kg body mass) and placed on an electric heating blanket to ensure the stabilization of body temperature at 37℃ (Zhou et al., 2019). After anesthesia, microsurgical instruments were used to cut the upper eyelid skin vertically under a microscope. The optic nerve was then exposed by cutting the bulbar conjunctiva and conducting the blunt separation of retrobulbar adipose tissue. To cause the injury, the optic nerve was directly clamped at 2 mm behind the eyeball for 10 s by forceps with a 40 g constant holding force. After injury, the surgical incision was sutured, chlortetracycline eye ointment was used for anti-infection. In the sham-operated group, rats received identical surgical procedure, but without clamping applied to the optic nerve. A total of 40 rats were assigned to TON model group and 36 to sham group.

tag: strain background

value: Sprague-Dawley (SD)

value: 7-8 weeks

tag: group

value: traumatic optic neuropathy (TON)

value: extracted retinal tissue


title: Fenoxaprop 5 (FOX)

description:
salmon_counts-Fenoxaprop.txt
AlopecurusFEN5

tag: treatment


title: K13/4716


title: K13/4721


title: B_10: CD8_LN_CXCR5pos_rep2

city: Stockholm

first: Marcus

last: Buggert

address: C2:94; Karolinska Universitetssjukhuset Huddinge

institute: Karolinska Institutet

value: Lymph Node(LN)

tag: cell type

value: CXCR5pos CD8+ T cell


title: 4.input

tag: age


title: 5.IP


title: 4.IP


title: A_10: CD8_LN_CXCR5pos_rep1


title: 6.input


title: Nasal Turbinates Female Day 14 VIDO# 73

tag: donor

value: VIDO# 73

tag: day

value: Day 14

tag: Sex

value: Female


title: C5: CD8_LN_EM_rep3

value: Effector memory CD8+ T cell


title: Fenoxaprop 3 (FOX)

description:
salmon_counts-Fenoxaprop.txt
AlopecurusFEN3


title: 6.IP


title: K17/3554

source_name: no_information_available (either Bone_Marrow_MNCs or Peripheral_Blood_MNCs)

tag: disease state

value: JMML

tag: hemoglobin (%)

tag: karyotype

tag: mutation

value: Relapse


title: 3.input

source_name: retina from control rats

value: control


title: C7: CD8_LN_CM_rep3

value: Central memory CD8+ T cell


title: Fenoxaprop 1 (FOX)

description:
salmon_counts-Fenoxaprop.txt
AlopecurusFEN1

value: Fenoxaprop

value: Resistant to fenoxaprop-p-ethyl, derived from Rothamsted after repeated field-rate applications of fenoxaprop-ethyl during 6 years

value: still remain unknown. derived from wild-type


title: Fenoxaprop 2 (FOX)

description:
salmon_counts-Fenoxaprop.txt
AlopecurusFEN2

value: 7-days old seedlings

value: untreated


title: K17/3553

tag: platelets (x 10^9/l)

tag: Cause of death

tag: survival from diagnosis (os) (years)

tag: survival from hsct (efs) (years)


title: 2.input

value: Sprague-Dawley (SD)

value: 7-8 weeks

tag: tissue


title: A7: CD8_LN_CM_rep1

value: Lymph Node(LN)


title: Rothamsted 5 (ROTH)

description:
salmon_counts-Rothamsted.txt
AlopecurusROTH5

source_name: 7-days old seedlings of Rothamsted population (isolated in Rothamsted, UK)

tag: population

value: Rothamsted

tag: phenotype

value: Sensitive to all herbicides

tag: genotype

value: wild-type


title: B7: CD8_LN_CM_rep2

tag: cell type


title: K17/3544

value: No event


title: 2.IP

tag: strain background

tag: age

tag: group

value: extracted retinal tissue


title: C8: CD8_LN_CD69neg_rep6

value: CD69pos CD8+ T cell


title: K17/3877

value: JMML

value: No data

value: Disease progression (acutisation, relapse after second HSCT)

value: Relapse


title: Rothamsted 3 (ROTH)

description:
salmon_counts-Rothamsted.txt
AlopecurusROTH3

tag: treatment


title: B8: CD8_LN_CD69neg_rep5


title: 1.input

value: control


title: Rothamsted 2 (ROTH)

description:
salmon_counts-Rothamsted.txt
AlopecurusROTH2


title: 1.IP


title: A8: CD8_LN_CD69neg_rep4


title: K17/3875

tag: disease state


title: K17/3552

tag: hemoglobin (%)