title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N707_S508]


title: 6289_6_6_GTCCGCA_S70

status: Public on May 16 2022

type: SRA

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

description:
A2780 WT carbo
A2780 wild type cell line + 6 M carboplatin
Total RNAseq
RNAseq_readscounts.txt

library_source: transcriptomic

data_processing:
RNA-seq: Data, as FASTQ file, were aligned with STAR to the human genome GRCh37.p13. HTSEQ with gencode.v19 annotation was used to count reads at exons of genes. Normalization of read counts was done using DEseq and DEseq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNAseq_readscounts.txt: Tab-delimited text file containing raw read counts (HTSeq).

molecule: total RNA

organism: Homo sapiens

growth_protocol: A2780 wt and its cisplatin resistant analogue A2780 cis cells were obtained from the ECACC (Sigma Aldrich ECACC 93112519 and Sigma Aldrich ECACC 93112517, respectively) and were maintained in RPMI medium containing 10% FBS (Gibco), 2 mM glutamine (L-Glutamine, Gibco), 100 IU penicillin and 100 μg/mL streptomycin (PenStrep, Gibco).

extract_protocol:
5x10^6 cells per condition per replicate were lysed using RLT buffer (Qiagen) and stored at -80°C. For the generation of total RNA libraries, total RNA was extracted using TRI Reagent (SIGMA), and mRNA was purified using Dynabeads mRNA DIRECT Purification Kit (Invitrogen), according to the manufacturers’ protocol.
Total RNA libraries were constructed using SENSE Total RNA-Seq Library Prep Kit for Illumina (LEXOGEN).

treatment_protocol: For experiments under serine/glycine deprivation conditions, cells were fed homemade medium (homemade RPMI with the same formulation as commercial RPMI from Gibco, supplemented with 10% dialyzed FBS (Gibco) and standard concentrations of penicillin-streptomycin and glutamine) with or without serine and/or glycine (Sigma Aldrich). Isogenic resistant A2780cis were obtained by chronically exposing parental cells to cisplatin.

tag: cell line

tag: cell type

value: ovarian cancer cells

tag: treatment

value: carbo


title: GBM [P12a]

type: genomic

city: BETHESDA

first: Zhichao

last: Wu

state: MD

address: BG 10 RM 4A31 MSC 1500, 10 CENTER DR

department: Center for Cancer Research

country: USA

institute: NIH/NCI

description: Tumor

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
R package minfi v1.40.0
Normalized (preprocessFunnorm) Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: GBM

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was bisulfite-converted with the EZ DNA Methylation Kitm (Zymo Research D5001)

tag: gender

value: Female

tag: age

tag: material

value: FFPE

tag: tissue

value: GBM


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N707_S506]

city: Edinburgh

first: Katrin

last: Ottersbach

address: 5 Little France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

description:
SLX-9712
processed data file: Kapeni_etal_rawcounts.txt
processed data file: Kapeni_etal_logcounts.txt

data_processing:
Single-cell RNA-seq reads were quantified using the GRCm38 transcriptome and Kallisto version 0.43.1.
Data were filtered to remove poor quality cells & genes with low abundances.
Normalised using Scater ComputeSumFactors.
Genome_build: Ensembl 87
Supplementary_files_format_and_content: Kapeni_etal_rawcounts.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: Kapeni_etal_logcounts.txt: Tab-delimited text file includes normalised expression measurements.

organism: Mus musculus

source_name: sympathoadrenal cells

extract_protocol:
Cells were sorted from freshly isolated mouse embryos; dissected tissues were treated with collagenase and then stained with cell surface markers and directly sorted into lysis buffer.
SmartSeq2

tag: genotype/variation

value: Wild-type

tag: developmental stage

value: aorta-gonads-mesonephros (AGM)

tag: cell type/region

value: Dorsal


title: GBM-F3T3-O [P14a]

description: Tumor

value: Male


title: GBM [P12b]

description: Tumor


title: 6289_5_5_CCGTCCC_S69


title: 6289_4_4_ATGTCAG_S68


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N707_S505]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N707_S507]


title: Ganglioglioma [P414]

description: Tumor

source_name: Ganglioglioma

value: Ganglioglioma


title: GBM [P11a1]

description: Tumor


title: GBM [P11a2]

description: Tumor


title: GBM [P1]

description: Tumor


title: GBM [F9]

description: Tumor


title: 6289_3_3_AGTTCCG_S67

description:
A2780 WT
A2780 wild type cell line
Total RNAseq
RNAseq_readscounts.txt


title: GBM [P045]

description: Tumor


title: GBM [F8]

description: Tumor


title: GBM [F6]

description: Tumor


title: Empty vector_in-vitro_2 [EV_2]

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

description:
s_2_BB
CD34 positive cells transduced with empty vector after five days culture in-vitro

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Reads whose AS (alignment score) was higher in the mouse compared to human were discarded. The reads were aligned to both GRCm38 sequence and GRCh38 sequences. Reads with a higher mapping quality to the mouse genome were excluded from the analysis.
Counting proceeded over genes annotated in Ensembl using htseq-count
Normalization was performed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file includes the normalized counts

source_name: CD34 positive  cells

growth_protocol: Samples 1-4: bone marrow samples from ETV6-NCOA2 patients were transplanted into NSGS mice. Samples 5-12: CD34 cord blood cells were retroviraly infected with ETV6-NCOA2 (NGFR) or ETV6-NCOA2 (NGFR)+NOTCH1-L1601PdP (GFP) and transplanted into NSGS mice. Samples 13-18: The cells were cultured for five days in-vitro (SCF, Flt3L, and TPO) , sorted for GFP positive, and sent for bulk RNA-sequencing.

extract_protocol:
CD34 positive cord blood cells were isolated using magnetic beads from fresh cord blood (For each biological replicate, three different cord blood samples were mixed). The cell were retrovirally infected with ETV6-NCOA2 or empty vector and cultured in IMDM supplemented with hSCF, hTPO, hFlt3L (100 ng/ml) for 5 days. The positive cells were sorted (GFP). ETV6-NCOA2 or ETV6-NCOA2+NOTCH1-L1601PdP were sorted (NGFR+/ GFP+NGFR+ respectively) from fresh bone marrow of engrafted NSGS mice. ETV6-NCOA2 patient derived xenografts were sorted with human CD45 from bone marrow of engrafted NSGS mice. We extracted RNA from the samples and performed bulk RNA-sequencing.
Inhouse poly A based RNA seq

treatment_protocol: Each CD34 biological replicate composed of three different cord blood units

tag: tissue/cell type

value: CD34 positive cells

tag: genotype/treatment

tag: sort

value: GFP+


title: Empty vector_in-vitro_3 [EV_3]

description:
s_3_BB
CD34 positive cells transduced with empty vector after five days culture in-vitro


title: GBM-F3T3-O [F7]

description: Tumor


title: GBM [I659]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N707_S503]


title: GBM [P11b]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N707_S504]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N706_S508]


title: GBM [F23]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N707_S502]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N706_S507]


title: GBM [F22]

description: Tumor


title: GBM-F3T3-O [P13]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N706_S517]


title: GBM [F3]

description: Tumor


title: 6289_1_1_CTTGTAA_S65


title: 6289_2_2_AGTCAAC_S66


title: ETV6-NCOA2_in-vitro_3 [EN2_in_vitro_3]

description:
s_3_EN2
CD34 positive cells transduced with ETV6-NCOA2 after five days culture in-vitro


title: GBM-F3T3-O [F4]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N706_S506]


title: ETV6-NCOA2_in-vitro_2 [EN2_in_vitro_2]

description:
s_2_EN2
CD34 positive cells transduced with ETV6-NCOA2 after five days culture in-vitro


title: GBM [F21]

description: Tumor


title: GBM [F5]

description: Tumor


title: GBM [F18]

description: Tumor


title: GBM [F2]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N706_S503]


title: ETV6-NCOA2_3 [EN2_1]

description:
s_C10UM_NGFR
CD34 positive cord bood cells transduced with ETV6-NCOA2, engrafted in NSGS mice

source_name: ETV6-NCOA2, engrafted in NSGS mice

value: CD34 positive cord bood cells

value: ETV6-NCOA2, engrafted in NSGS mice

value: NGFR+


title: Empty vector_in-vitro_1 [EV_1]

description:
s_1_BB
CD34 positive cells transduced with empty vector after five days culture in-vitro


title: GBM-F3T3-O [F16]

description: Tumor


title: GBM [F17]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N706_S504]


title: GBM-F3T3-O [F15]

description: Tumor


title: GBM [F13]

description: Tumor


title: ETV6-NCOA2_1 [EN2_2]

description:
s_C8R_L_NGFR
CD34 positive cord bood cells transduced with ETV6-NCOA2, engrafted in NSGS mice


title: GBM [F10]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N705_S517]


title: ETV6-NCOA2_2 [EN2_3]

description:
s_C10_R_T_NGFR
CD34 positive cord bood cells transduced with ETV6-NCOA2, engrafted in NSGS mice


title: GBM [F12]

description: Tumor


title: ETV6-NCOA2+NOTCH1-L1601PdP_4 [EN2+N_1]

description:
s_C8T_P4
CD34 positive cord bood cells transduced with ETV6-NCOA2+NOTCH1-L1601PdP, engrafted in NSGS mice

value: GFP+NGFR+


title: GBM [F1]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N706_S502]


title: ETV6-NCOA2_in-vitro_1 [EN2_in_vitro_1]

description:
s_1_EN2
CD34 positive cells transduced with ETV6-NCOA2 after five days culture in-vitro


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N705_S508]


title: GBM-F3T3-O [F11]

description: Tumor


title: GBM-F3T3-O [F20]

description: Tumor


title: GBM [F14]

description: Tumor


title: GBM [F19]

description: Tumor


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N705_S507]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N706_S505]


title: ETV6-NCOA2+NOTCH1-L1601PdP_2 [EN2+N_4]

description:
s_C8R_P3
CD34 positive cord bood cells transduced with ETV6-NCOA2+NOTCH1-L1601PdP, engrafted in NSGS mice


title: ETV6-NCOA2+NOTCH1-L1601PdP_3 [EN2+N_3]

description:
s_C8R_T_P4
CD34 positive cord bood cells transduced with ETV6-NCOA2+NOTCH1-L1601PdP, engrafted in NSGS mice


title: RNAseq_nonopt_3

city: Aurora

first: Olivia

last: Rissland

state: CO

address: 12801 East 17th Ave

department: BMG

institute: University Of CO Anschutz Medical Campus

data_processing:
Read 2 (reverse) reads were extracted with UMI-tools
Remaining rRNA-mapped reads were filtered out using Bowtie (version 1.2.2.) and SAMtools (version 1.12)
The remaining reads were aligned and mapped with STAR (version 2.6.0a)
The output .bam files were de-duplicated using UMI-tools and total transcript expression was calculated with Salmon (version 1.6.0). The transcriptome used was Gencode v26. Bigwig files were generated to visualize coverage across the genome.
bigWig files were generated using the genomicRanges R package
To look at our reporters specifically, we extracted the reads that did not map to the genome from the output .bam files. These reads were de-duplicated using UMI-tools and mapped to the reporter sequences using Bowtie (version 1.2.2)
Bedtools coverage was used to quantify reads across each reporter.
Assembly: hg38
Supplementary files format and content: bigwig files - coverage across genome
Supplementary files format and content: tab-delimited text files (.hist.coverage, generated with bedtools coverage) - coverage across reporters

growth_protocol: HEK293T cells were grown in DMEM with high glucose and pyruvate (Gibco), supplemented with 10% FBS (Gibco) in a humidified incubator maintained at 37°C with 5% CO2.

extract_protocol:
Cells were treated briefly with CHX, flash-frozen, then lysed. RNA-seq samples were rRNA-depleted and DNase-treated. Ribo-seq samples were footprinted to extract ribosome-protected fragments, rRNA-depleted, and ran out on a TBE-Urea PAGE gel to isolate 27-30 nt fragments (RPFs). The extracted RNA fragments were treated with PNK and cleaned.
RNA-seq samples were generated using KAPA RNA Hyperprep library kit protocol, with Illumina compatible IDT-UBI adapters (KAPA Dual-Indexed Adapter Kit [Roche]). Ribo-seq samples were generated using QIASeq miRNA Library preparation kit (Qiagen), with indexes supplied in QIAseq miRNA NGS 96 Index IL plate kit (Qiagen).

treatment_protocol: Cells were co-transfected with Ribo-seq firefly luciferase and Renilla luciferase reporters using lipofectamine, 24 hours prior to harvesting

value: Human embryonic kidney

tag: genotype

value: WT

value: transfected - SM-nonopt FLuc-GFP


title: RNAseq_opt_3

value: transfected - SM-opt FLuc-GFP


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N705_S505]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N705_S504]


title: ETV6-NCOA2+NOTCH1-L1601PdP_1 [EN2+N_5]

description:
s_C8R_T_P3
CD34 positive cord bood cells transduced with ETV6-NCOA2+NOTCH1-L1601PdP, engrafted in NSGS mice


title: RNAseq_opt_2


title: RNAseq_nonopt_2


title: RNAseq_nonopt_1


title: ETV6-NCOA2 patient derived xenograft_3 [EN2_PDX_2]

description:
EN2_CELL_LINE
Human patient engrafted in NSGS mice

source_name: Human patient engrafted in NSGS mice

value: Human patient engrafted in NSGS mice

value: human CD45


title: Riboseq_opt_3

data_processing:
Read 2 (reverse) reads were extracted with UMI-tools
Remaining rRNA-mapped reads were filtered out using Bowtie (version 1.2.2.) and SAMtools (version 1.12)
The remaining reads were aligned and mapped with STAR (version 2.6.0a)
The output .bam files were de-duplicated using UMI-tools and total transcript expression was calculated with Salmon (version 1.6.0). The transcriptome used was Gencode v26. Bigwig files were generated to visualize coverage across the genome.
bigWig files were generated using the genomicRanges R package
To look at our reporters specifically, we extracted the reads that did not map to the genome from the output .bam files. These reads were de-duplicated using UMI-tools and mapped to the reporter sequences using Bowtie (version 1.2.2)
Bedtools coverage was used to quantify reads across each reporter.
Assembly: hg38
Supplementary files format and content: bigwig files - coverage across genome
Supplementary files format and content: tab-delimited text files (.hist.coverage, generated with bedtools coverage) - coverage across reporters
Library strategy: Ribo-seq

molecule: polyA RNA


title: Riboseq_opt_1


title: ETV6-NCOA2 patient derived xenograft_1 [EN2_PDX_3]

description:
YFP_BM
Human patient engrafted in NSGS mice


title: ETV6-NCOA2 patient derived xenograft_2 [EN2_PDX_1]

description:
XENO_high
Human patient engrafted in NSGS mice


title: Riboseq_opt_2


title: ETV6-NCOA2+NOTCH1-L1601PdP_5 [EN2+N_2]

description:
s_C8R_P4
CD34 positive cord bood cells transduced with ETV6-NCOA2+NOTCH1-L1601PdP, engrafted in NSGS mice


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N705_S502]

description:
SLX-9712
processed data file: Kapeni_etal_rawcounts.txt
processed data file: Kapeni_etal_logcounts.txt

value: Wild-type


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N705_S506]

value: aorta-gonads-mesonephros (AGM)


title: Riboseq_nonopt_1


title: Riboseq_nonopt_3


title: ETV6-NCOA2 patient-derived xenograft_control

description: Human patient engrafted in NSGS mice

library_source: genomic

data_processing:
Reads were demultiplexed
Adapters were trimmed using the cutadapt tool
The reads were aligned uniquely to the human genome (hg19)
Bound regions were detected using MACS2 (version 2.0.10.20131216)
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files of MACS2 peaks (bed)

growth_protocol: Samples 1-2:  The cells were cultured for five days in-vitro (SCF, Flt3L, and TPO) , sorted for GFP positive. Sample 3: bone marrow samples from ETV6-NCOA2 patients were transplanted into NSGS mice.

extract_protocol:
CD34 positive cells were isolated using magnetic beads from fresh cord blood (For each biological replicate, at least three different cord blood samples were mixed). The cell were retrovirally infected with ETV6-NCOA2 or empty vector and cultured in IMDM supplemented with hSCF, hTPO, hFlt3L (100 ng/ml) for 5 days. The positive cells were sorted (GFP+). ETV6-NCOA2 patient derived xenografts were sorted from bone marrow of the sick mice (human CD45+). We extracted DNA from the samples and performed H3K27Ac ChIP sequencing.
In-house ChIP-Seq protocol, Libraries were evaluated by Qubit and BioAnalyzer. Sequencing libraries were constructed with barcodes to allow multiplexing of y samples on one lane.

value: ETV6-NCOA2 patient-derived xenograft

value: Expression of ETV6-NCOA2

tag: chip antibody


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N704_S517]

value: Dorsal


title: ETV6-NCOA2 patient-derived xenograft

description: Human patient engrafted in NSGS mice

value: H3K27Ac (Active motif cat:39133)


title: HEK293T Cells, shCtrl C, RNA-seq

city: Toronto

first: Alexander

middle: F

last: Palazzo

state: ON

address: 661 University Ave.

department: Biochemistry

country: Canada

institute: University of Toronto

data_processing:
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: “umi_tools extract -p "^(?P.{12})(?P.{4}).+$" --extract-method=regex”. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. Next, we used cutadapt to clip the 3’ adapter AAAAAAAAAACAAAAAAAAAA. After UMI extraction and adapter trimming, ribosomal and transfer RNAs were filtered by alignment using Bowtie2. The remaining reads were mapped to human transcriptome and alignments with mapping quality greater than two were retained. UMIs were used for deduplication and .ribo files are created using RiboPy.
Assembly: hg38
Supplementary files format and content: CSV file containing the RPKM value of detectable transcripts

source_name: kidney

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin at 37ºC and 5% CO2.

extract_protocol:
HEK293T cell line was obtained from ATCC and maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum. Cells were washed twice with 10 mL of ice-cold PBS and placed on ice. Lysis was carried out on plates using 400 μl volume (Tris HCl 20mM pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL Cycloheximide, 1% Triton-X). 5 μl of RNaseI (Invitrogen AM2249) was added to the lysates, followed by a 1 hr digestion at 4°C. Immediately following digestion, ribonucleoside vanadyl complex (NEB S1402S) (20 mM) was added to inhibit further digestion. Digested lysates (400 μl each) were loaded on a sucrose cushion (20mM TrisCl titrated to pH 7.4, 150mM NaCl, 5mM MgCl2, 1% TritonX-100, 34% sucrose, 1 mM DTT, 100 ug/ml cycloheximide) and centrifuged in a SW 41 Ti rotor (Beckman Coulter) at 38,000 rpm at 4°C for 2.5 hours to pellet ribosomes. 700 μl QIAzol Lysis Reagent (Qiagen) was used to resuspend the ribosome pellet, which was was transferred to a fresh 1.5 ml tube and frozen until further processing. To extract RNA, samples were thawed at room temperature and processed with the Qiagen miRNeasy Kit per manufacturer’s instructions. RNA was eluted in 20 μl nuclease-free water and size-selected by electrophoresis of 3 μg inputs in a Novex denaturing 15% polyacrylamide TBE-Urea gel. The 26-34 nt RNA fragments were excised, crushed with a pestle, and extracted in 310 μl gel extraction buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.25% w/v SDS) by incubating on dry ice for 30 minutes then overnight at room temperature. The gel-liquid mixture was passed through a Spin-X filter (Corning 8160) and the elution was precipitated with 1.5 μl Glycoblue (5 mM MgCl2, 75% ethanol). RNA was pelleted by centrifugation at 23,300 g at 4°C for 1 hour and resuspended in 10 μl nuclease-free water.
For ribosome profiling: 25 ng inputs of size-selected ribosome footprints were immediately processed for library preparation using the D-Plex Small RNA-Seq Kit (Diagenode) per manufacturer’s instructions, with some modifications. Approximately half of the resulting cDNA (14 μl) was amplified for 9 cycles. Following quantitation of the target libraries with Agilent HS DNA Kit and Bioanalyzer, the resulting libraries were pooled to equimolar concentrations and cleaned with AMPure 19 XP beads at 1.8x concentration (Beckman Coulter) and eluted in 30 μl TE. To enrich for ribosome footprints in the libraries, the entire elution was size selected in a 3% agarose precast gel (Sage Science) in the BluePippin system using a 172-206 nt range with tight settings. The resulting libraries were sequenced with NovaSeq SP SE 100 (Illumina). For RNA Sequencing: To extract RNA, samples were thawed at room temperature and processed with the Qiagen miRNeasy Kit per manufacturer’s instructions. RNA was eluted in 25 μl nuclease-free water and processed with the CATS RNA-seq Kit v2 per manufacturer’s instructions (Diagenode C05010045). Approximately half of the resulting cDNA (14 μl) was amplified for 11 cycles. PCR products were cleaned as outlined in the Diagenode protocol and the resulting libraries were sequenced with NovaSeq SP SE 100 (Illumina).

treatment_protocol: HEK293T were lentivral infected with either shCtrl or shPKM. Cells were collected 4 days post-infection.

value: kidney

value: embryonic kidney cells

value: shCtrl-treated


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N704_S508]


title: HEK293T Cells, shCtrl A, RNA-seq


title: HEK293T Cells, shCtrl Rep3, ribo-seq

description:
20201209-shRNA-scramble-control-3
ribosome footprints

data_processing:
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: “umi_tools extract -p "^(?P.{12})(?P.{4}).+$" --extract-method=regex”. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. Next, we used cutadapt to clip the 3’ adapter AAAAAAAAAACAAAAAAAAAA. After UMI extraction and adapter trimming, ribosomal and transfer RNAs were filtered by alignment using Bowtie2. The remaining reads were mapped to human transcriptome and alignments with mapping quality greater than two were retained. UMIs were used for deduplication and .ribo files are created using RiboPy.
Assembly: hg38
Supplementary files format and content: CSV file containing the RPKM value of detectable transcripts
Library strategy: Ribo-seq


title: RNAseq_opt_1


title: HEK293T Cells, shCtrl Rep2, ribo-seq

description:
20201209-shRNA-scramble-control-2
ribosome footprints


title: Empty vector CD34_control

description: CD34 positive cells transduced with empty vector after five days culture in-vitro

value: CD34 positive  cells

value: empty vector

value: GFP


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N705_S503]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N704_S507]


title: HEK293T Cells, shCtrl Rep1, ribo-seq

description:
20201209-shRNA-scramble-control-1
ribosome footprints

value: WT


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N704_S506]


title: HEK293T Cells, shPKM C, RNA-seq

value: PKM depletion

value: shPKM-treated


title: Riboseq_nonopt_2

value: Human embryonic kidney

value: transfected - SM-nonopt FLuc-GFP


title: HEK293T Cells, shPKM B, RNA-seq


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N704_S505]

value: Wild-type


title: ETV6-NCOA2 CD34_control

description: CD34 positive cells transduced with ETV6-NCOA2 after five days culture in-vitro


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N704_S504]

value: aorta-gonads-mesonephros (AGM)


title: HEK293T Cells, shPKM Rep1, ribo-seq

description:
20201209-shRNA-PKM-KD-1
ribosome footprints


title: Kasumi-1 ATAC rep 2

city: Portland

first: Theodore

middle: P

last: Braun

state: Oregon

address: 2720 S Moody Ave

institute: Oregon Health and Science University

description: ATAC-seq

data_processing:
Sequencing from ATAC-seq was aligned using Bowtie2
Peaks were called using gopeaks
Bigwigs are CPM normalized
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Kasumi-1 cells

growth_protocol: RPMI with 20% FBS, GlutaMAX, PenStrep

extract_protocol:
Samples were prepared according to published protocol Corces et al 2016
Samples were prepared according to published protocol Corces et al 2016


title: Kasumi-1 ATAC rep 1

description: ATAC-seq


title: Kasumi-1 ATAC rep 3

description: ATAC-seq


title: ETV6-NCOA2 CD34


title: sc-RNAseq of CD4conv and Treg cells in BM and spleen

city: New York

first: Michail

last: Schizas

address: 1275 York ave

institute: Memorial sloan Kettering

library_source: transcriptomic single cell

data_processing:
Alignment of fastq files
Gene quantification
Incorporate hashtag information
Filtering, normalization and log transformation
tSNE and clustering
Assembly: GRCm38
Supplementary files format and content: norm_df_all_samples.txt: cellXgene full table
Supplementary files format and content: norm_df.txt: cellXgene table for BM Treg cells
Supplementary files format and content: clusters.txt: clusters for BM Treg cells

source_name: T cell

extract_protocol: Single cell suspension from BM and spleen were prepared, enriched for CD4, sorted by gating on CD4+TCRb+GFP+ (Tregs) and CD4+TCRb+GFP- (CD4conv) and hashtagged.

treatment_protocol: The mice were not treated before the experiment (WT mice)

tag: strain

value: multiplexed sample:Spleen and bone marrow

value: multiplexed sample:Tregs and CD4 conv

value: 9 weeks


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N704_S503]

value: Dorsal


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N704_S502]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N703_S517]


title: METTL3_cyto_IP_rep2

city: Beijing

first: Yue

last: Huo

state: Beijing

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

country: China

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
Peaks were called with clipper software for eCLIP-seq.
Genome_build: Ensembl GRCh38.p5
Supplementary_files_format_and_content: peak files for eCLIP-seq

source_name: MGC-803 cell line

extract_protocol:
MGC-803 cells were UV-crosslinked and lysed then protein-RNA complexes were isolated with indicated antibodies. Then the RNA was purified for subsquential processes.
Libraries were prepared as described in "Van Nostrand, E. L. et al. Nat Methods, 2016, 13, 508-514" and sequenced by using Illumina Novaseq 6000 with pair end 150bp read length.

treatment_protocol: The lentiviruses for METTL3_wt or METTL3_cyto overexpression were used to infect MGC-803 cells. And the stable transfer cells were sreened with puromycin treatment.

value: MGC-803 cell line

tag: clip antibody

value: METTL3 (ab195352, abcam)

value: METTL3_cyto overexpression and treated with puromycin for 48 hours


title: METTL3_wt_IP_rep2

tag: cell line

value: METTL3_wt overexpression and treated with puromycin for 48 hours


title: METTL3_wt_Input_rep1


title: METTL3_wt_Input_rep2


title: GNAS_KO3-4h

city: San Francisco

first: Lihui

last: Duan

state: CA

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: UCSF

data_processing:
Sequences were aligned to the mm10 genome with STAR
HTseq was used to count the mapped reads of each gene .
DESeq2 was used for the gene differential expression analysis.
Assembly: mm10
Supplementary files format and content: csv table with raw gene counts for every gene and every sample

source_name: spleen

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

tag: cell type

value: follicular B cell CD21/35- CD23+

value: Gnas fl/fl Cd19 Cre +/-

tag: hours of_culture


title: Empty vector CD34

value: CD34 positive  cells

value: empty vector

value: GFP

value: H3K27Ac (Active motif cat:39133)


title: GNAS_KO2-4h


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N703_S507]

value: Wild-type


title: METTL3_cyto_Input_rep1

tag: treatment


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N703_S508]

value: aorta-gonads-mesonephros (AGM)


title: HEK293T Cells, shPKM Rep3, ribo-seq

description:
20201209-shRNA-PKM-KD-3
ribosome footprints

value: kidney

value: embryonic kidney cells

value: PKM depletion

value: shPKM-treated


title: METTL3_cyto_IP_rep1

value: MGC-803 cell line


title: GNAS_WT3-4h

value: Gnas +/+ Cd19 Cre +/-


title: HEK293T Cells, shPKM Rep2, ribo-seq

description:
20201209-shRNA-PKM-KD-2
ribosome footprints


title: H9-TSC

city: La Jolla

first: Robert

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Alignment and quantification with CellRanger v 6.0.1 count function with default parameters to human reference genome (GRCh38-2020-A)
Genome_build: human reference genome (GRCh38-2020-A)
Supplementary_files_format_and_content: Comma separated values text file containing the counts for all genes and all demultiplexed samples (one matrix per sample)

source_name: Trophoblast stem cell line

growth_protocol: Primed H9 hESC were cultured in StemFlex media on Geltrex-coated plates. Primed H9 hESC-derived TSC were cultured onto collagen IV-coated plates in TSC media containing: Advanced DMEM/F12, 1x N2, 1x B27, 1x Glutmax, 150μM 1-thioglycerol, 0.05% BSA, 1% Knockout serum replacement, 2µM CHIR99021, 0.5µM A83-01, 1µM SB431542, 5µM Y27632, 130µg/mL Valproic Acid sodium salt, 100ng/mL recombinant human FGF2, 50ng/mL recombinant human EGF, 50ng/mL recombinant human HGF, and 20ng/mL Noggin.

extract_protocol:
Chromium Next GEM Single Cell 3' reagent kit v3.3 from 10X Genomics was used to extract RNA from single cells.
Chromium Next GEM Single Cell 3' reagent kit v3.3 from 10X Genomics was used to rpepare the libraries from single cells

treatment_protocol: For TE differentiation, H9 hESC were treated with 10 ng/mL BMP4 and 2µM IWP2 in minimal media containing DMEM/F12, 1x ITS, 64μg/ml L-ascorbic acid, 543μg/ml NaHCO3, and 2% BSA. Media was changed every day and conversion into TE-like cells was confirmed based on surface EGFR expression of over 90% by flow cytometry at day 4. For Conversion into TSC, TE cells at day 4 were detached with TrypLE Express, re-plated onto collagen IV-coated plates and grown in TSC media.

tag: Stage

value: adapted to TSC media p6

value: primed-TSC


title: GNAS_WT2-4h

value: spleen


title: METTL3_wt_IP_rep1

value: METTL3 (ab195352, abcam)

value: METTL3_wt overexpression and treated with puromycin for 48 hours


title: H9_t12h

source_name: Differentiating embryonic stem cell line

value: treated with BMP4/IWP2 for 12h

value: intermediate differentiating stage


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N703_S505]

value: Dorsal


title: H9_t24h

value: treated with BMP4/IWP2 for 24h


title: H9_d4

value: treated with BMP4/IWP2 for 4 days (96h)

value: primed-TE


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N703_S504]

value: Wild-type

value: aorta-gonads-mesonephros (AGM)


title: H9_t0

source_name: Pluripotent embryonic stem cell line

value: pluripotent

value: undifferentiated primed hESC


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N703_S502]


title: HDF_TSC_p8_2

data_processing:
Quality control was performed using FastQC (v. 0.11.8) and multiQC (v. 1.6).
Reads were mapped to GRCh38.p10 (GENCODE release 26) using STAR (v. 2.7.3a) (PMID: 23104886; Dobin, 2012) and annotated using featureCounts (subread v.1.6.3, GENCODE release 26 primary assembly annotation) (PMID:24227677; Liao, 2014). The STAR parameters used were: --runMode alignReads --outSAMmode Full --outSAMattributes Standard --genomeLoad LoadAndKeep --clip3pAdapterSeq AGATCGGAAGAGC --clip3pAdapterMMp 1 -- outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3. The featureCounts parameters were: -s 2 -p -t exon -T 13 -g gene_id (PMID:24227677; Liao, 2014).
Ensembl genes without at least three samples with 10 or more reads were removed from analysis.
Normalization (VST normalization in DESeq2) and differential expression analysis were performed using the R (v. 3.6.3) package DEseq2 (v. 1.28.1), (Love 2014). BiomaRt (v. 2.42.1) was used to convert Ensembl gene ID’s to HUGO gene names.
Genome_build: GRCh38.p10 (GENCODE release 26)
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample post filtering
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Primed hESC and hiPSC (together hPSC) were cultured in StemFlex media on Geltrex-coated plates. Both primary and primed hPSC-derived TSC were cultured onto collagen IV-coated paltes in TSC media containing: Advanced DMEM/F12, 1x N2, 1x B27, 1x Glutmax, 150μM 1-thioglycerol, 0.05% BSA, 1% Knockout serum replacement, 2µM CHIR99021, 0.5µM A83-01, 1µM SB431542, 5µM Y27632, 130µg/mL Valproic Acid sodium salt, 100ng/mL recombinant human FGF2, 50ng/mL recombinant human EGF, 50ng/mL recombinant human HGF, and 20ng/mL Noggin.

extract_protocol:
Total RNA was extracted using the MirVana kit.
RNAseq libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit with Ribo-Zero Gold (Illumina).

treatment_protocol: For TE differentiation, hPSC were treated with 10 ng/mL BMP4 and  2µM IWP2 in minimal media containing DMEM/F12, 1x ITS, 64μg/ml L-ascorbic acid, 543μg/ml NaHCO3, and 2% BSA for 4 days. Media was changed every day and conversion into TE-like cells was confirmed based on surface EGFR expression of over 90% by flow cytometry at day 4. For Conversion into TSC, TE cells at day 4 were detached with TrypLE Express, re-plated onto collagen IV-coated plates and grown in TSC media.

value: adapted to TSC media p8


title: GNAS_KO1-4h

value: follicular B cell CD21/35- CD23+

value: Gnas fl/fl Cd19 Cre +/-


title: HDF_hiPSC_d0_1

source_name: Pluripotent induced pluripotent stem cell line

value: undifferentiated primed hiPSC


title: GNAS_KO2-0h

value: spleen


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N703_S503]


title: HDF_hiPSC_d0_2


title: H1_TSC_p7_2

value: adapted to TSC media p7

value: primed-TSC


title: GNAS_WT1-4h

value: Gnas +/+ Cd19 Cre +/-


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N703_S506]


title: HDF_TSC_p8_1


title: GNAS_WT3-0h


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N702_S517]


title: METTL3_cyto_Input_rep2

value: MGC-803 cell line

value: METTL3_cyto overexpression and treated with puromycin for 48 hours


title: GNAS_KO1-0h


title: H1_hESC_d0_2


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N702_S508]

value: Dorsal


title: miR-21βKO-2

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

data_processing:
The fold change was calculated from the normalized expression values, and statistical significance was calculated using the DEGseq2 software.
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_expression.xls contains the expression of genes in each samples.

source_name: islet

growth_protocol: Islets from WT and miR-21βKO mice:total of 3 mL collagenase P solution (0.4-0.8 mg/mL) (Roche, USA) was slowly injected into the common bile duct after occlusion of the distal end proximal to the duodenum. The distended pancreas was excised and digested with collagenase at 37 °C for 15 min. The collagenase digest was then subjected to histopaque 1077 gradient separation to facilitate the harvest of islets. Islets were finally filtered through 45 µm cell strainer and hand-picked using a micropipette under stereomicroscope.

extract_protocol:
Total RNA was prepared using TRIzol Reagent (Invitrogen).
DNase I was used to digest DNA in total RNA and rRNA was removed by hybridization of complementary DNA oligos to rRNA followed by degradation of the RNA:DNA hybrids using RNase H. Purified mRNA from previous steps was fragmented into small pieces and then used to prepare mRNA sequencing library. For quality control, libraries were validated using Agilent Technologies 2100 bio-analyzer. The final library was amplified via rolling circle amplification with phi29 DNA polymerase (Thermo Fisher Scientific, MA, USA), which could result in DNA nanoballs (DNB) that had more than 300 copies of one original molecule. DNBs were then loaded into the patterned nanoarray and pair end 150 bases reads were generated on a BGISEQ500 platform (BGI Shenzhen, China).

treatment_protocol: Islets from WT and miR-21βKO mice were cultured at ~50 islets/well on 48-well plate and pre-incubated for 1 h at 37°C in Krebs–Ringer bicarbonate (KRB) buffer containing 0.5% bovine serum albumin and 2.8 mM glucose. The buffer was then replaced with KRB buffer supplemented with 16.7 mM glucose, and incubated for another 20 min.


title: miR-21βKO-3


title: H1_hESC_d0_1


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N702_S507]


title: GNAS_WT1-0h


title: GPR174_KO3-1h


title: H1_TSC_p7_1


title: TSC_1049_3

source_name: Primary trophoblast stem cell line

value: primary TSC

value: undifferentiated primary hTSC


title: TSC_1049_2


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N702_S506]

value: Wild-type


title: miR-21βKO-1


title: WT3

value: WT


title: GPR174_KO2-1h


title: GNAS_WT2-0h


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N702_S505]

value: aorta-gonads-mesonephros (AGM)


title: GPR174_KO1-1h


title: TSC_1049_1


title: WT1


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N702_S504]


title: WT2


title: TSC_1048_3


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N702_S503]


title: GPR174_WT3-1h


title: TSC_1048_1


title: TSC_1048_2


title: P6 cerebellum, TcMAC21, rep4 [Mac4]

city: Worcester

first: Summer

middle: B

last: Thyme

state: MA

address: 55 N Lake Ave

institute: UMass Chan

description:
Mac4.so.bam
AM34

data_processing:
Reads were mapped to mouse genome mm39 modified by appending human chromosome 21, using the alignment tool STAR v.2.4.2a
Aligned reads were assembled with PsiCLASS v.1.0.2 to create gene and transcript models
DESeq2 was used to quantify the expression levels and determine the sets of differentially expressed genes
Assembly: mouse genome mm39 modified to include human chromosome 21
Supplementary files format and content: CSV file with normalized read counts (read counts normalized to the sample size) for each sample

source_name: Whole cerebellum

extract_protocol:
RNA from whole cerebella was extracted using QIAGEN RNeasy Kit
Libraries were constructed using NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770) according to manufacturer’s instructions

value: Whole cerebellum

tag: age

value: Postnatal day 6

value: TcMAC21, C57BL/6J (B6) x DBA/2J (D2)


title: GPR174_WT1-1h

tag: tissue

value: follicular B cell CD21/35- CD23+


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N702_S502]

source_name: sympathoadrenal cells

tag: genotype/variation


title: P6 cerebellum, euploid (TcMAC21 littermate), rep4 [Eu8]

description:
Eu8.so.bam
AM33

value: euploid, C57BL/6J (B6) x DBA/2J (D2)


title: GPR174_WT2-1h

value: spleen


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N701_S517]

tag: developmental stage


title: P6 cerebellum, euploid (Ts65Dn littermate), rep2 [Eu5]

description:
Eu5.so.bam
AM24

value: euploid, C57BL/6J x C3H/HeJ


title: H9_TSC_p5_2

value: adaptation  to TSC media p5

value: intermediate adaptation stage


title: P6 cerebellum, euploid (Ts65Dn littermate), rep4 [Eu7]

description:
Eu7.so.bam
AM28


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N701_S507]

tag: cell type/region


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N701_S506]


title: Costal chondrocytes sirt1 atc rep2

city: jerusalem

first: lital

last: zecharyahu

address: Campus Ein Kerem

institute: hebrew university

description: ablated Sirt1 levels (TG)

data_processing:
Prior to sequence analysis, quality control of RNA-Seq samples was performed on the raw single-end reads using Fastqx to remove low-quality reads (average score less than 30). Reads that were less than 20 bp were discarded. In addition, all reads were cut at the ends, leaving the sequence between 14-54 base pair, due to low-quality base readings
Reads were aligned to the Mus Musculus genome GRCm38 version with STAR, using standard presets except for intron size, which was set between 30 and 30000 bp (–alignIntronMin 30 and –alignIntronMax 30000). Greater than 10 million reads were mapped for each sample with uniquely mapping reads accounting for ∼90% of total mapped reads in each sample
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Uniquely mapping reads were count using HT-Seq
Assembly: GRCm38
Supplementary files format and content: fastq file for each sample

source_name: Costal chondrocytes

growth_protocol: Embryos were extracted from induced dams at day 17 of gestation.  Thoracic cages were dissected and tissue from the osteochondral junctions of the ribs  were cultured (passage 2). The isolated tissues were incubated with collagenase (cat# LS004177, Worthington Biochemical Corporation, NJ) solution (3 mg/mL in DMEM) at 37°C for 1h, following a wash step with PBS.  Next was an overnight incubation with 0.5 mg/mL collagenase in DMEM, at 37°C, followed by tissue filtration in a 40um mesh filter and cultured in growth media till induction with doxocycline (24h before harvest).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA was tested for quality EMBL guidelines using a Tapstation Analysis Software (A.02.02(SR1)) .
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ATC transgenic mice provided by (Prof. Veronique, CHOP research Institute, PA) were crossed with Lef1 flfl (provided by Prof. Hai-Hui Xue, University of Iowa) or Sirt1 flox (#008041) to generate cartilage specific Lef1-knockout mice (ATC Lef1fl/fl) or Sirt1 KO mice (ATC Sirt1 fl/fl). Notably, ATC transgenic mice express an Agc1 enhancer-driven, tetracycline-inducible Cre (ATC) transgene.

value: Costal chondrocytes

value: Embryos Day 17

value: flox sirt1

value: 2ug/ml doxocycline


title: P6 cerebellum, euploid (Ts65Dn littermate), rep3 [Eu6]

description:
Eu6.so.bam
AM25


title: Costal chondrocytes sirt1 atc rep1

description: ablated Sirt1 levels (TG)


title: H9_TSC_p5_3


title: H9_TSC_p5_1


title: H9_TSC_p4_3

value: adaptation  to TSC media p4


title: P6 cerebellum, Ts65Dn, rep3 [Ts3]

description:
Ts3.so.bam
AM22

value: Ts65Dn, C57BL/6J x C3H/HeJ


title: H9_TSC_p4_2


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N701_S505]

value: Wild-type

value: Dorsal


title: P6 cerebellum, Ts65Dn, rep2 [Ts2]

description:
Ts2.so.bam
AM21

value: Whole cerebellum


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N701_S504]

value: aorta-gonads-mesonephros (AGM)


title: Costal chondrocytes lef1 atc rep3

description: ablated Lef1 levels (TG)

value: atc lef1


title: P6 cerebellum, Ts65Dn, rep4 [Ts4]

description:
Ts4.so.bam
AM23

value: Postnatal day 6


title: Costal chondrocytes lef1 atc rep2

description: ablated Lef1 levels (TG)


title: GNAS_KO3-0h

value: follicular B cell CD21/35- CD23+

value: Gnas fl/fl Cd19 Cre +/-


title: H9_TSC_p4_1


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N701_S503]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N701_S508]


title: dorsal Ngfr+Pdgfrb- cells (Dorsal) [SLX-9712.N701_S502]


title: Costal chondrocytes lef1 atc rep1

description: ablated Lef1 levels (TG)


title: P6 cerebellum, euploid (Ts65Dn littermate), rep1 [Eu4]

description:
Eu4.so.bam
AM13

value: euploid, C57BL/6J x C3H/HeJ


title: H9_TSC_p3_3

value: adaptation  to TSC media p3


title: Costal chondrocytes lef1 flox rep3

description: normal Lef1 levels (WT)

value: flox lef1


title: P6 cerebellum, Ts65Dn, rep1 [Ts1]

description:
Ts1.so.bam
AM12


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N712_S517]

description:
SLX-9711
processed data file: Kapeni_etal_rawcounts.txt
processed data file: Kapeni_etal_logcounts.txt

source_name: haematopoietic stem and progenitor cells

value: HSC


title: Costal chondrocytes lef1 flox rep2

description: normal Lef1 levels (WT)

value: Costal chondrocytes

value: Embryos Day 17


title: P6 cerebellum, euploid (TcMAC21 littermate), rep3 [Eu3]

description:
Eu3.so.bam
AM10

value: euploid, C57BL/6J (B6) x DBA/2J (D2)


title: Costal chondrocytes lef1 flox rep1

description: normal Lef1 levels (WT)

value: 2ug/ml doxocycline


title: H9_TSC_p2_3

value: adaptation  to TSC media p2

value: intermediate adaptation stage


title: Mouse Embryonic Fibroblasts pole4 wt and Trp53 wt_3

city: London

first: Roberto

last: Bellelli

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCm38-release-89 transcriptome
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Assembly: GRCm38
Supplementary files format and content: Tab delimited text files containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

growth_protocol: cell were grown in 15% FBS and low oxygen concentrations (5%)

extract_protocol:
Total RNA was isolated using TRIzol (15596026) according to the manufacturer’s instructions.
Double stranded full-length cDNA was generated using the Ovation RNA-Seq System V2 (NuGen Technologies, Inc.). cDNA was quantified on a Qubit 3.0 fluorometer (Thermo Fisher Scientific, Inc.), and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument (Covaris, Inc.) at standard settings. The fragmented cDNA was then normalized to 100ng, which was used for sequencing library preparation using the Ovation Ultralow System V2 1-96 protocol (NuGen Technologies, Inc.). A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay (Agilent Technologies, Inc.). The libraries were then normalized to 4 nM, pooled and loaded onto a HiSeq4000 (Illumina, Inc.) to generate 100 bp paired-end reads.

value: Mouse embryonic Fibroblasts

value: pole4 wt and Trp53 wt

tag: environmental condition

value: low oxygen concentrations (5%)


title: H9_TSC_p3_1


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N712_S508]

data_processing:
Single-cell RNA-seq reads were quantified using the GRCm38 transcriptome and Kallisto version 0.43.1.
Data were filtered to remove poor quality cells & genes with low abundances.
Normalised using Scater ComputeSumFactors.
Genome_build: Ensembl 87
Supplementary_files_format_and_content: Kapeni_etal_rawcounts.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: Kapeni_etal_logcounts.txt: Tab-delimited text file includes normalised expression measurements.

value: Wild-type

value: aorta-gonads-mesonephros (AGM)


title: P6 cerebellum, TcMAC21, rep2 [Mac2]

description:
Mac2.so.bam
AM07

value: Whole cerebellum

value: Postnatal day 6

value: TcMAC21, C57BL/6J (B6) x DBA/2J (D2)


title: P6 cerebellum, euploid (TcMAC21 littermate), rep1 [Eu1]

description:
Eu1.so.bam
AM03


title: Mouse Embryonic Fibroblasts pole4 wt and Trp53 wt_1


title: H9_TSC_p3_2

value: adaptation  to TSC media p3


title: Mouse Embryonic Fibroblasts pole4 wt and Trp53 wt_2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N712_S504]


title: H9_TSC_p2_2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N712_S507]


title: P6 cerebellum, euploid (TcMAC21 littermate), rep2 [Eu2]

description:
Eu2.so.bam
AM08


title: P6 cerebellum, TcMAC21, rep3 [Mac3]

description:
Mac3.so.bam
AM09


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N712_S506]


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N712_S503]


title: Mouse Embryonic Fibroblasts pole4 wt and Trp53 null_3

value: pole4 wt and Trp53 null


title: H9_TSC_p1_3

value: adaptation  to TSC media p1


title: H9_TSC_p1_2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N712_S502]

value: HSC


title: P6 cerebellum, TcMAC21, rep1 [Mac1]

description:
Mac1.so.bam
AM02


title: Mouse Embryonic Fibroblasts pole4 wt and Trp53 null_2


title: Mouse Embryonic Fibroblasts pole4 wt and Trp53 null_1


title: H9_TSC_p0_3

value: adaptation  to TSC media p0


title: H_Hepal_6_3: Hepa 1-6_3

city: Miaoli County

first: Li-Rung

last: Huang

address: No.35, Keyan rd. Zhunan town

country: Taiwan

institute: National Health Research Institutes

data_processing:
Illumina's official basecalling program, the  bcl2fastq  conversion software v2.20, was used to convert BCL files from all Illumina sequencing platforms into FASTQ reads.
Both adaptor clipping and sequence quality trimming were performed using Trimmomatic  v0.36 with a sliding-window approach.
Raw reads with good quality were mapped to mouse reference genome (GRCm38.p6) by HISAT 2 (2.1.0)
Differential expression analysis was performed using  StringTie  (StringTie v2.1.4)  and  DEseq  (DEseq v1.39.0)  or  DEseq2  (DEseq2 v1.28.1)  with genome bias detection/correction and Welgene Biotech's in-house pipeline.
Genes with low expression level (< 0.3 TPM value) in either or both of the treated and control samples were excluded
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: The file comprises TPM values for 18 samples.

source_name: mouse hepatocellular carcinoma cell lines

growth_protocol: Cells were seeded at 5 x 10^6 in 10cm dish by using DMEM medium (Thermo Fisher Scientific) supplemented with 10% FBS, sodium pyruvate, glutamine, HEPES, NEAA and antibiotics. The samples were collected after 24h.

extract_protocol:
Total RNA was extracted from cell lines using RNeasy mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. The quality of RNA was assessed with the Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA ) to assure RIN≧7.
Agilent's SureSelect Strand-Specific RNA Library Preparation Kit was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

treatment_protocol: no treatment

tag: origin

value: mouse liver

value: Hepa 1-6

value: derived from the BW7756 hepatoma tumor that arose spontaneously in C57L/J mice


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N711_S517]


title: Mouse Embryonic Fibroblasts pole4 wt and Trp53 het_3

value: pole4 wt and Trp53 heterozygous


title: H_Hepal_6_2: Hepa 1-6_2

value: mouse hepatocellular carcinoma cell line


title: Mouse Embryonic Fibroblasts pole4 wt and Trp53 het_2

value: Mouse embryonic Fibroblasts


title: H9_TSC_p1_1

value: intermediate adaptation stage


title: H9_TSC_p0_2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N711_S506]

value: Wild-type


title: H9_TSC_p2_1

value: adaptation  to TSC media p2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N711_S508]

value: aorta-gonads-mesonephros (AGM)


title: Mouse Embryonic Fibroblasts pole4 wt and Trp53 het_1

value: pole4 wt and Trp53 heterogygous

value: low oxygen concentrations (5%)


title: H_8_C4_1: NHRI-8-C4_1

value: transposons carrying human AKT-Luc and NRASG12V


title: H9_TSC_p0_1


title: H_8_C4_2: NHRI-8-C4_2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N711_S505]


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N711_S504]


title: Mouse Embryonic Fibroblasts pole4 null and Trp53 wt_1

value: pole4 null and Trp53 wt


title: H_8_A4_3: NHRI-8-A4_3


title: Mouse Embryonic Fibroblasts pole4 null and Trp53 wt_2


title: Mouse Embryonic Fibroblasts pole4 null and Trp53 wt_3


title: H9_TSC_p6_1

value: adapted to TSC media p6

value: primed-TSC


title: H9_TSC_p6_2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N711_S502]

value: HSC


title: H_8_A4_2: NHRI-8-A4_2

value: mouse liver


title: H_Hepal_6_1: Hepa 1-6_1

value: Hepa 1-6


title: Mouse Embryonic Fibroblasts pole4 null and Trp53 null_3

value: pole4 null and Trp53 null


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N710_S517]


title: H_8_C4_3: NHRI-8-C4_3


title: H_8_A4_1: NHRI-8-A4_1


title: CTB_1stL_832

description: Data from GSE173323

source_name: Placenta

value: primary 1st trimester CTB

value: primary


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N710_S508]


title: CTB_1stL_831

description: Data from GSE173323


title: H9_TSC_p6_3


title: H_8_2: pool #8_2

value: pool #8

value: mouse hepatocellular carcinoma cell line


title: Mouse Embryonic Fibroblasts pole4 null and Trp53 null_2

value: Mouse embryonic Fibroblasts


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N710_S506]

value: Wild-type


title: H_8_3: pool #8_3


title: H_8_1: pool #8_1


title: Mouse Embryonic Fibroblasts pole4 null and Trp53 heterozygous_2

value: pole4 null and Trp53 heterozygous


title: CTB_1stL_822

description: Data from GSE173323


title: Mouse Embryonic Fibroblasts pole4 null and Trp53 null_1


title: H_1_F1_2: NHRI-1-F1_2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N711_S503]

value: aorta-gonads-mesonephros (AGM)


title: Mouse Embryonic Fibroblasts pole4 null and Trp53 heterozygous_3

value: low oxygen concentrations (5%)


title: Mouse Embryonic Fibroblasts pole4 null and Trp53 heterozygous_1


title: CTB_1stL_830

description: Data from GSE173323


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N710_S503]


title: CTB_1stL_825

description: Data from GSE173323


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N710_S505]


title: CTB_1stL_805

description: Data from GSE173323


title: H_1_F1_3: NHRI-1-F1_3

value: transposons carrying human AKT-Luc and NRASG12V


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N710_S504]


title: CTB_1stL_804

description: Data from GSE173323


title: CTB_1stL_793

description: Data from GSE173323


title: H_1_F1_1: NHRI-1-F1_1


title: RNA_striatum_HDACi-CFC_rep4

city: Lausanne

first: Johannes

last: Gräff

state: Vaud

address: Rte Cantonale

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description: Animals were i.p. injected with HDACi 1 hour before exposure to novel context + mild shock, then sacrificed 1 hour after context exposure

data_processing:
Truseq adapter sequences were trimmed from raw FASTQ files using bcl2fastq (v2.20.0, Illumina)
STAR (v2.6) was used to align FASTQ reads to the mouse mm10 reference genome with annotations downloaded from Ensembl release 93.
A custom R script was used to count reads mapping to the exonic regions of genes and to define transcript abundance. Reads were only considered if they overlap a single gene region
Differential expression and downstream analysis were performed using DEseq2 and custom R scripts.
Genome_build: mm10 (annotation: ensembl 93)
Supplementary_files_format_and_content: matrix of raw gene counts for all libraries

source_name: striatal hemisphere

growth_protocol: Ten-week-old C57BL/6J male mice were  allowed an acclimatization and handling period for two weeks before experimentation. All animals were housed in groups of 4-5 animals at 22-25° C on a 12-hour light-dark cycle with food and water ad libitum. Mice were randomly assigned a drug treatment, and experimental conditions were randomly split by cage so that all mice in one cage underwent the same fear conditioning protocol.

extract_protocol:
Single frozen hippocampal and striatal hemispheres from four biological replicates were isolated1 hour after CFC. Samples were homogenized and total RNA was isolated using Trizol Reagent (Life Technologies) according to the manufacturer’s protocol. RNA was further purified by an on-column DNAse digestion using the RNase-Free DNase Set (Qiagen, Cat# 79254) and two rounds of washes using the RNAeasy Mini Kit (Qiagen, Cat# 74106). Total RNA concentration was determined with the Nanodrop 1000 (v3.8.1, Thermo Fisher).
Libraries were prepared using the TruSeq Stranded mRNA Preparation Kit (Illumina) starting from 900ng of RNA. Libraries were quantified with the dsDNA HS Assay kit (Qubit, Cat# Q32851) and profile analysis was performed using the TapeStation (Agilent, TS4200) D500 Screen Tape System (Agilent, Cat#5067- 5588 and 5067-5589). Finally, libraries were multiplexed and sequenced across five lanes on the Illumina HiSeq 4000 (Illumina), yielding 100-bp, paired-end reads, at EPFL’s gene expression core facility.

treatment_protocol: The class I HDAC inhibitor, CI-994, was dissolved in 10% dimethyl sulfoxide (Sigma-Aldrich, D2438), 30% Kolliphor (Sigma-Aldrich, C5135), and 60% 0.9% saline (Braun, 395158). Vehicle (VEH) solution consisted of all of the above, without CI-994. One hour before contextual fear conditioning, each animal was interperitoneally (i.p.) injected with either 30mg/kg of CI-994 or a corresponding volume of VEH pre-heated to 37˚C on a thermomixer.  CFC consisted of a 3 min habituation to the conditioning chamber (TSE Systems GmbH) followed by two 1 s foot shocks (0.2mA) with an interval of 29 s and a final 15 s in the chamber. The context groups in all experiments were exposed to the conditioning chamber for the same amount of time with no shocks.

value: striatum

value: 12 weeks

value: HDACi-CFC


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N709_S508]

extract_protocol:
Cells were sorted from freshly isolated mouse embryos; dissected tissues were treated with collagenase and then stained with cell surface markers and directly sorted into lysis buffer.
SmartSeq2

value: HSC


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N710_S502]


title: RNA_striatum_HDACi-CFC_rep3


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N709_S505]


title: CTB_1stL_716

description: Data from GSE173323


title: H_1_3: pool #1_3

value: mouse liver

value: pool #1


title: RNA_striatum_HDACi-CFC_rep2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N709_S517]


title: H_1_2: pool #1_2


title: CTB_1stE_772


title: RNA_striatum_HDACi-CFC_rep1


title: CTB_1stL_788

description: Data from GSE173323


title: H_1_1: pool #1_1


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N709_S504]


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N709_S502]


title: CTB_1stE_771


title: CTB_1stE_770


title: RNA_striatum_HDACi-Context_rep4

description: Animals were i.p. injected with HDACi 1 hour before exposure to novel context, then sacrificed 1 hour after context exposure

value: HDACi-Context


title: CTB_1stE_761

value: primary 1st trimester CTB


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N708_S508]


title: RNA_striatum_HDACi-Context_rep3


title: RNA_striatum_HDACi-Context_rep1


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N708_S517]


title: CTB_1stE_750

value: primary


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N708_S507]


title: RNA_striatum_Veh-CFC_rep3

description: Animals were i.p. injected with vehicle 1 hour before exposure to novel context + mild shock, then sacrificed 1 hour after context exposure

value: Veh - CFC


title: Hyperglycemic PDX repl-3

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

data_processing:
Base calling and generation of FASTQ files were performed using standard CASAVA pipeline
RNA-seq quality was checked by running FastQC, and TrimGalore was used for adapter and quality trimming. RNA-seq reads were mapped against GRCm39 using STAR (v 2.7.0e) aligner with default parameters.
Differential gene expression analysis was performed using DESeq2.
Genome_build: GRCm39
Supplementary_files_format_and_content: Tab-delimited text files of normalized abundance measurements.

source_name: Orthotopic tumor from KPC K8484 cells

growth_protocol: Mice were maintained under pathogen-free conditions in the animal facility.

extract_protocol:
Total RNA was extracted using PureLink RNA isolation (Life Technologies, 12183025) and treated with DNase (Life Technologies, AM2222).
Strandspecific RNA-seq library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Ipswich, MA) according to the manufacturer's protocols.

treatment_protocol: Hyperglycemia was induced by allowing mice to drink high glucose content water (30% dextrose; abbreviated as D30)


title: Hyperglycemic PDX repl-2


title: CTB_1stE_738


title: Hyperglycemic PDX repl-4


title: Hyperglycemic PDX repl-1


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N708_S505]


title: RNA_striatum_HDACi-Context_rep2


title: Hyperglycemic PDX repl-5


title: Normoglycemic PDX repl-5


title: RNA_striatum_Veh-CFC_rep2


title: RNA_striatum_Veh-CFC_rep1


title: CTB_1stE_734


title: Normoglycemic PDX repl-3


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N708_S504]


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N708_S502]


title: CTB_1stE_717


title: CTB_1stE_732


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N708_S503]


title: RNA_striatum_Veh-CFC_rep4


title: Normoglycemic PDX repl-4


title: H9_BMP4_d4_3

value: treated with BMP4/IWP2 for 4 day

value: primed-TE


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N707_S507]

value: Wild-type


title: RNA_striatum_Veh-Context_rep4

description: Animals were i.p. injected with vehicle 1 hour before exposure to novel context, then sacrificed 1 hour after context exposure

value: Veh - Context


title: RNA_striatum_Veh-Context_rep1


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N707_S506]

value: aorta-gonads-mesonephros (AGM)


title: RNA_striatum_Veh-Context_rep3


title: mpkCCD cell-shGR1-Vehicle

city: Taipei

first: Ming-Jiun

last: Yu

address: No. 1 Jen-Ai Road Sec. 1, Rm 816

department: Biochemistry and Molecular Biology

institute: National Taiwan University

description: Vehicle condition (no vasopressin stimulation)

data_processing:
Illumina bcl2fastq v2.20 program was used for basecalling.
Sequence reads were aligned to GRCm39 genome by HISAT2 program.
Differential expression analysis was performed using cuffdiff (cufflinks v2.2.1) with genome bias detection/correction and Welgene Biotech's in-house pipeline.
Genes with low expression level (< 0.3 FPKM value) were excluded.
Transcripts with log2 (control/glucocorticoid knockdown) values < -1 or > 1 were considered differentially expressed.
Genome_build: GRCm39
Supplementary_files_format_and_content: xlsx. Files included every gene's FPKM, FPKM ratio between shctrl and shGR, q-value and p-value.

source_name: mpkCCD cell

growth_protocol: The mpkCCD cells were grown on 12-well transwell in DMEM/Ham's F-12 medium containing 2% fetal bovine serum (FBS) and supplements.

extract_protocol:
After PBS washes, cells were lysed in Trizol reagent. Total RNA was extracted with the RNA extraction kit (Cat. E1011-A, ZYMO Research, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To facilitate cell polarization, FBS and supplements, except dexamethasone, were removed from the medium in both control and glucocorticoid receptor knockdown cells under the vehicle conditions.

value: kidney collecting duct cell

tag: cell passages

value: Glucocorticoid receptor knockdown with small hairpin sequence 1 (shRNA TRCN0000238464)


title: Normoglycemic PDX repl-1


title: Normoglycemic PDX repl-2


title: H9_BMP4_d4_1


title: H9_BMP4_d4_2


title: mpkCCD cell-shGR2-Vehicle

value: Glucocorticoid receptor knockdown with small hairpin sequence 2 (shRNA TRCN0000238463)


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N707_S505]

city: Edinburgh

first: Katrin

last: Ottersbach

address: 5 Little France Drive

institute: University of Edinburgh


title: RNA_hippocampus_HDACi-CFC_rep4

source_name: hippocampal hemisphere

value: hippocampus

value: 12 weeks


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N707_S517]

value: HSC


title: mpkCCD cell-shCtrl-Vehicle

value: None-targeting knockdown control (shRNA TRCN0000208001)


title: RNA_striatum_Veh-Context_rep2

value: striatum


title: RNA_hippocampus_HDACi-CFC_rep2

value: HDACi-CFC


title: CTB_1stE_722

value: primary 1st trimester CTB


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N707_S503]


title: H9_BMP4_d3_2

value: treated with BMP4/IWP2 for 3 days

value: intermediate differentiating stage


title: RNA_hippocampus_HDACi-CFC_rep1


title: T8_2: NHRI-8-B4_2

data_processing:
Illumina's official basecalling program, the  bcl2fastq  conversion software v2.20, was used to convert BCL files from all Illumina sequencing platforms into FASTQ reads.
Both adaptor clipping and sequence quality trimming were performed using Trimmomatic  v0.36 with a sliding-window approach.
Raw reads with good quality were mapped to mouse reference genome (GRCm38.p6) by HISAT 2 (2.1.0)
Differential expression analysis was performed using  StringTie  (StringTie v2.1.4)  and  DEseq  (DEseq v1.39.0)  or  DEseq2  (DEseq2 v1.28.1)  with genome bias detection/correction and Welgene Biotech's in-house pipeline.
Genes with low expression level (< 0.3 TPM value) in either or both of the treated and control samples were excluded
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: The file comprises TPM values and ratio (NHRI-8-B4/NHRI-1-E4) for 6 samples.

value: mouse liver

tag: genotype

value: transposons carrying human AKT-Luc and NRASG12V

value: hepatocellular carcinoma


title: H9_BMP4_d3_1


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N707_S502]

value: Wild-type


title: T8_1: NHRI-8-B4_1


title: H9_BMP4_d2_3

value: treated with BMP4/IWP2 for 2 days


title: C1_3: NHRI-1-E4_3


title: RNA_hippocampus_HDACi-Context_rep4

value: HDACi-Context


title: RNA_hippocampus_HDACi-Context_rep3


title: H9_BMP4_d2_2


title: C1_2: NHRI-1-E4_2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N707_S504]

value: aorta-gonads-mesonephros (AGM)


title: RNA_hippocampus_HDACi-CFC_rep3


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N706_S507]


title: H9_BMP4_d3_3


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N706_S504]


title: RNA_hippocampus_HDACi-Context_rep2


title: H9_BMP4_d2_1


title: RNA_hippocampus_HDACi-Context_rep1


title: H9_BMP4_d1_3

value: treated with BMP4/IWP2 for 1 day


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N706_S503]


title: C1_1: NHRI-1-E4_1


title: VD

city: Shanghai

first: Yuanbin

last: Lin

address: 99 Shangda Road, Baoshan District, Shanghai

institute: Shanghai University

data_processing:
scRNA-seq, low-quality raw reads and adaptor sequences were first removed with fastQC and fastp
Subsequently, reads were mapped to the reference genome GRCh38 (ensembl version 92 gene annotation) with STAR
After that, expression matrix files were generated based on gene counts and UMI counts that were acquired by featureCounts software.
Genome_build: genome GRCh38 (ensembl version 92 gene annotation)
Supplementary_files_format_and_content: matrix.tsv (expression matrix file)

source_name: skin cell

extract_protocol:
GEXSCOPE® Tissue Dissociation Solution (Singleron)
GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies)
Single cell RNA sequencing

value: Whole skin cell

value: UV irradiated+VD


title: T8_3: NHRI-8-B4_3


title: H9_BMP4_d1_2


title: RNA_hippocampus_Veh-CFC_rep4

value: hippocampus

value: 12 weeks

value: Veh - CFC


title: RNA_hippocampus_Veh-CFC_rep3


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N706_S517]

value: HSC


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N704_S517]


title: H9_BMP4_d1_1


title: Control

value: nomal+saline


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N704_S507]


title: RNA_hippocampus_Veh-CFC_rep2


title: H9_hESC_d0_3

value: pluripotent

value: undifferentiated primed hESC


title: RNA_hippocampus_Veh-CFC_rep1


title: H9_hESC_d0_2


title: RNA_hippocampus_Veh-Context_rep4

value: Veh - Context


title: RNA_hippocampus_Veh-Context_rep3


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N703_S507]


title: Mut1_P46 Lepr-Cre;mTmG;Smo+/- (Rep 1)

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

data_processing:
Raw FASTQs from sorted, GFP-positive cells were aligned to mouse mm10 reference genome (GRCm38.93.dna/GRCm38.93.gtf) using Cell Ranger version 2.1.1. The reference was modified to include a eGFP sequence. Raw FASTQs from unsorted, whole backskin were aligned to mouse mm10 reference genome (GRCm38.84.dna/GRCm38.84.gtf) and Cell Ranger version 3.1.0. The reference was modified to include a GFP, tdTomato, and YFP sequences.
Quality control of all data sets was performed using Seurat version 3.2.2 and Scrublet version 0.2.1
Processed files were analyzed with Scrublet Seurat V3.2.2,  scanpy V1.6.0. and CellChat V0.0.1
Genome_build: mm10
Genome_build: GRCm38.93.dna and GRCm.38.84.dna; GRCm38.93.gtf and GRCm.38.84.gtf
Supplementary_files_format_and_content: tsv and mtx

source_name: Backskin

growth_protocol: N/A. Primary cells were used in this study.

extract_protocol:
Dorsal skin from P46 Lepr-Cre;mTmG;Smo (n=2 technical replicates) and Lepr-Cre;mTmG;Smo+/- (n=2 technical replicates)  female mice were isolated and processed into single cells as previously described in Guerrero-Juarez, CF, et al. Nat Commun. 2019 with minor modifications.
Dorsal skin from P50 Lepr-Cre;mTmG female mice were isolated and processed into single cells as previously described in Guerrero-Juarez, CF, et al. Nat Commun. 2019 with minor modifications. Viable, GFP-positive cells were physicially sorted via FACS.
Single cells were captured using the Chromium Platform (10X Genomics) and cDNA libraries were generated using Single Cell 3’ v2 (sorted GFP-positive cells) and v3 chemistries (unsorted, whole dorsal skin cells). Single cells were quantified using a hemocytometer. Cell capture, cDNA library preparation, quality control, and sequencing was performed at UC Irvine Genomic High Throughput Facility.
Single Cell 3’ v2 Chemistry - 10X Genomics

tag: Sex

value: female

value: Lepr-Cre;mTmG;Smo+/-

value: Backskin

value: dorsal skin cells

value: Unsorted cells


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N703_S517]

value: Wild-type

value: aorta-gonads-mesonephros (AGM)


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N703_S506]


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N704_S508]


title: sodh_glucose_rep2

city: Kurume

first: Hiroko

last: Sano

state: Fukuoka

address: 67 Asahi-machi

country: Japan

institute: Kurume University

data_processing:
RNA-seq reads were mapped to the FlyBase reference genome (Dmel Release 6.19) using Tophat2.
Transcript abundance and splice variant identification were determined using Cufflinks.
Differential expression analysis was performed using CuffDiff.
Genome_build: Dmel  6.19
Supplementary_files_format_and_content: diff file from Cuffdiff

organism: Drosophila melanogaster

source_name: whole larvae, third instar

extract_protocol:
Larvae were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Standard mRNA Library Prep Kit LT was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: sodh1, sodh2 mutant

tag: agent

value: glucose


title: Mut2_P46 Lepr-Cre;mTmG;Smo+/- (Rep 2)

treatment_protocol: N/A. Primary cells were used in this study.


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N704_S502]


title: sodh_glucose_rep1


title: RNA_hippocampus_Veh-Context_rep1

value: hippocampus

tag: strain


title: WT_3D-spheroids_24h_rep2

first: Veronique

last: Azuara

state: London

address: Institute of Reproductive and Developmental Biology, Hammersmith Hospital Campus

department: Metabolism, Digestion and Reproduction

institute: Imperial College London

data_processing:
Image analysis and base calling was carried out on HiSeq Control Software (by Genewiz)
Quality of sequenced reads was assessed using FastQC, and reads were trimmed for adaptor sequences and low quality reads (<15) using Trimmomatic-0.33
Quantification of transcripts was carried out with Kallisto v0.43.1 using reference mouse transcriptome mm10 (GRCm38, Ensembl v94)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with abundance measurements as an output from Kallisto quantification for each sample

source_name: Mouse Embryonic Stem Cells

growth_protocol: ESCs, 10%FBS/+LIF ; 3D spheroids, 15%FBS/-LIF, embedded into growth factor-reduced matrigel (Corning, 354230).

extract_protocol:
ESCs were collected using TrypLE (Gibco, 12604013) and lysed in RLT buffer. For collection of 3D spheroids, Cell Recovery Solution (Corning, 354253) was used to degrade the matrigel by gentle scraping and incubation on ice for 30 minutes. RNA extraction was carried out by RNeasy Mini Kit (Qiagen, 74106) according to the manufacturer instruction.
RNA-sequencing libraries were prepared using TruSeq Stranded mRNA library prep kit (Illumina, Cat# RS-122-2101) (by Genewiz)

treatment_protocol: Wild-type (WT) and Cidea knockout (KO) background

value: Wild type

tag: cell line

value: R1 mESC


title: WT_3D-spheroids_48h_rep2


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N704_S506]

value: HSC


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N702_S517]


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N703_S502]


title: sodh_fructose_rep3

value: fructose


title: WT_ESCs_rep2


title: UV

tag: cell type

value: Whole skin cell

value: UV irradiated+saline


title: sodh_glucose_rep3


title: WT_3D-spheroids_48h_rep1


title: H9_hESC_d0_1

source_name: Pluripotent embryonic stem cell line

value: pluripotent

value: undifferentiated primed hESC


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N702_S507]


title: RNA_hippocampus_Veh-Context_rep2

value: 12 weeks

value: Veh - Context


title: WT_3D-spheroids_24h_rep1


title: sodh_fructose_rep2


title: WT_ESCs_rep1


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N702_S503]


title: sodh_sorbitol_rep2

value: sorbitol


title: Cidea-KO_3D-spheroids_48h_rep2

value: Cidea -/-


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N701_S508]

value: Wild-type


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N701_S517]

value: aorta-gonads-mesonephros (AGM)


title: sodh_sorbitol_rep1

value: sodh1, sodh2 mutant


title: Cidea-KO_3D-spheroids_24h_rep2


title: sodh_starved_rep6


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N701_S507]


title: Cidea-KO_3D-spheroids_48h_rep1


title: sodh_starved_rep5


title: sodh_fructose_rep1


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N701_S504]


title: sodh_starved_rep3

description: sodh_sorbitol.diff, sodh_fructose.diff


title: Cidea-KO_ESCs_rep1


title: Cidea-KO_3D-spheroids_24h_rep1


title: sodh_starved_rep2

description: sodh_sorbitol.diff, sodh_fructose.diff


title: sodh_sorbitol_rep3


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N701_S503]


title: Sample 07670080C0030R (cancer immune panel)

type: RNA

city: Waltham

first: Uma

last: Saxena

address: 1000 Winter Street

institute: Glaxosmithkline

hyb_protocol: Hybridization of biotinylated reporter probes was carried out according to the manufacturer's protocol

scan_protocol: Scanning was perfomred on the nCounter Digital Analyzer at 555 FOV.

data_processing:
The nSolver Analysis Software (NanoString Technologies) was used for the extraction of raw mRNA data.
Raw data extracted from the RCC files using the Nanostring nSolver software
The normalization for raw nCounter counts of expressed genes was separately done for QC-passed samples in PanCancer immune and PanCancer pathway panel using the R-package “NanoStringNorm” (R version 4.0.3) with a set of parameters; CodeCount = ‘geo.mean’, Background = ‘mean.2sd’, SampleContent = ‘housekeeping.geo.mean’, round.values = TRUE, take.log = TRUE.

source_name: Synovial Sarcoma tumor

label_protocol: RNA was analyzed and labeling was performed per manufacturer’s instructions of the NanoString nCounter system, with 2 sets of Nanostring assays (nCounter PanCancer Immune Profiling Panel and nCounter PanCancer Pathway Panel)

extract_protocol: RNA was extracted using the High Pure FFPET RNA Isolation Kit (Roche). RNA extract was quantified (including assessment of RNA purity) using the Quant-iT RiboGreen RNA Reagent and Kit, and RNA quality was assessed using Agilent RNA Pico chip analysis.

treatment_protocol: Tumor biopsies were obtained prior to treatment with NY-ESO-1 TCR T cells or at the time of progression post treatment. Fresh biopsies were formalin fixed and paraffin embedded. For each sample, five 4-µm unstained slides were used for macrodissection and subsequent RNA extraction.

tag: subject id

tag: timepoint

value: At Progression

tag: responder status

value: Responder

tag: progression free survival in weeks

tag: progression free survival status

value: Progressed or Died


title: Sample 08950118C0005R (cancer immune panel)

value: Pre


title: Sample 07670091C0043R (cancer immune panel)

tag: sample note

value: Excluded from analysis:Week 8 after 2nd infusion


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N702_S502]

tag: genotype/variation

tag: developmental stage

tag: tissue

value: HSC


title: Cidea-KO_ESCs_rep2

value: R1 mESC


title: Sample 07670079C0028R (cancer immune panel)


title: sodh_starved_rep1

description: sodh_sorbitol.diff, sodh_fructose.diff


title: WT_sorbitol_rep3

value: wild type


title: Col-0, Leaves, JSC-1A, replicate 8

city: Gainesville

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

description:
P8J4JSC2
Not included in the processed data spreadsheets (only used Replicates 1-4 for analyses)

data_processing:
The overall quality of the RNASeq sequence data was first evaluated using FastQC.  Low-quality bases were trimmed from the reads using Trimmomatic (Bolger et al., 2014). STAR Aligner was used to map high-quality paired-end reads to TAIR10 genome. Gene expression values were calculated from these alignments using RSEM. The expected read counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were extracted for further analysis. A generalized linear regression model was built to perform the differential gene analysis using edgeR.  Prior to the differential expression analysis, hierarchical clustering and Principal Component Analysis (PCA) were conducted to identify potential outliers in the samples. The thresholds for calling significantly differentially expressed genes (DEG) were set at, FDR of 0.05, a fold change of greater than 2, and the average FPKM for at least one replicate of each comparison group being higher than 0. DEG lists were analyzed for overlaps using BioVenn. Processing and Analysis of the RNASeq data was performed at the UF ICBR Bioinformatics Core (https://biotech.ufl.edu/bioinformatics/;  RRID:SCR_019120).
Genome_build: TAIR10
Supplementary_files_format_and_content: .xls spreadsheets containing lists of genes,  FPKM values, and CPM values.

organism: Arabidopsis thaliana

source_name: plant grown in JSC-1A Lunar simulant, 20 day-old plants harvested and flash frozen in Liquid Nitrogen

growth_protocol: plants grown in 48-well microtiter plates, each growth well contained 900mg lunar regolith from one of three lunar sites: Apollo 11, Apollo 12 and Apollo 17. Controls of JSC-1A lunar simulant  present on the same plates

extract_protocol:
RNA extraction was performed using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s guidelines RNA concentration was determined on Qubit® 2.0 Fluorometer, RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
First, 50 ng of total RNA was used for mRNA isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490). Then followed by RNA library construction with the NEBNext Ultra II  Directional RNA Library Prep Kit (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Briefly, RNA was fragmented in NEBNext First Strand Synthesis Buffer via incubation at 94 °C for the desired time. This step was followed by first-strand cDNA synthesis using reverse transcriptase and random hexamer primer.  Synthesis of ds-cDNA was performed using the 2nd strand master mix provided in the kit, followed by end-repair and adaptor ligation.  At this point, Illumina adaptors were ligated to the sample.  Finally, each library (uniquely barcoded) was enriched by 12 cycles of amplification, and purified with Agencourt AMPure beads (Beckman Coulter, catalog # A63881). 48 barcoded libraries were sized on the Bioanalyzer and quantified with the Qubit® 2.0 Fluorometer. Finally, these 20 individual libraries were pooled in equimolar concentration. RNASeq libraries were constructed at the UF ICBR Gene Expression Core (https://biotech.ufl.edu/gene-expression-genotyping/, RRID:SCR_019145).
Sequencing was performed at the ICBR NextGen Sequencing Core (https://biotech.ufl.edu/next-gen-dna/, RRID:SCR_019152). Normalized libraries were submitted to the “Free Adapter Blocking Reagent” protocol (FAB, Cat# 20024145) in order to minimize the presence of adaptor-dimers and index hopping rates.  The library pool was diluted to 0.8 nM and sequenced on one S4 flow cell lane (2x150 cycles) of the Illumina NovaSeq6000. The instrument’s computer utilized the NovaSeq Control Software v1.6. Cluster and SBS consumables were v1.5. The final loading concentration of the library was 120 pM with 1% PhiX spike-in control. One lane generated 2.5-3 billion paired-end reads (~950Gb) with an average Q30%>= 92.5% and Cluster PF= 85.4%. FastQ files were generated using the BCL2fastQ function in the Illumina BaseSpace portal. One NovaSeq S4, 2x150 cycles lane resulted in an average of 50 Million demultiplexed, paired-end reads when sequencing a pool of 48 samples.

treatment_protocol: plants grown in Apollo lunar regolith for 20 days were compared to those grown in JSC-1A lunar simulant

tag: cultivar

value: Wild Type

value: Leaves

tag: organism part

value: All leaves from 20 day-old seedling

tag: age

value: 21 day-old plants, 16/8 hr light/ dark cycle

tag: biosource type

value: LN2 fixed_sample


title: sodh_starved_rep4

tag: genotype

tag: agent


title: Col-0, Leaves, JSC-1A, replicate 7

description:
P7J4JSC2
Not included in the processed data spreadsheets (only used Replicates 1-4 for analyses)


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N701_S506]

tag: cell type/region


title: SW403_IRS2_knockdown_bio_rep3

city: Tel Aviv

first: Dor

last: Simkin

address: 6 Weizmann st.

institute: Department of Oncology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel

data_processing:
Adaptors were identified and removed from the raw sequence reads using TagCleaner with parameters “--adapter-stringency 0.9, --mask-short-adapter-reads 35, --minimum-trimmed-read-length 35”.
Trimmed reads were aligned to the human reference genome UCSC hg19 (Gencode gene annotations) using STAR 2.6.1a with default parameters.
Mapping was followed by transcriptome-wide abundance quantification using Salmon in alignment-based mode.
To import and summarize Salmon’s transcript-level abundance estimates (TPM) into a count matrix that can be used as input to DESeq2 R package, we used tximport package with the argument countsFromAbundance = “lengthScaledTPM" which scales back TPM values into non-normailized raw counts.
Assembly: UCSC hg19.
Supplementary files format and content: ‘counts_mat’ is a csv file containing the raw count matrix.
Supplementary files format and content: ‘norm_counts’ is a csv file DESeq2 normalized counts.

growth_protocol: SW403 Colon adenocarcinoma cell lines, with and without IRS2 knockdown, were seeded in triplicate for 24h in DMEM supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using the High Pure RNA Isolation Kit (Roche, Mannheim, Germany). 1000ng of total RNA was used for the construction of sequencing libraries.
The libraries were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs® inc., USA). The double strand cDNA was subjected to end repair, A-base addition, adapter ligation and PCR amplification to create barcoded libraries.

treatment_protocol: No treatment was supplied.

tag: cell line

tag: cell type

value: Colon adenocarcinoma


title: Sample 07670061C0025R (cancer immune panel)

tag: subject id

tag: timepoint


title: SW403_IRS2_knockdown_bio_rep2


title: WT_sorbitol_rep2

value: sorbitol


title: SW403_IRS2_knockdown_bio_rep1


title: WT_sorbitol_rep1


title: Col-0, Leaves, JSC-1A, replicate 6

description:
P6J4JSC2
Not included in the processed data spreadsheets (only used Replicates 1-4 for analyses)


title: Sorted_P50 Lepr-Cre;mTmG

tag: Sex

value: female

value: Lepr-Cre;mTmG

value: Backskin

value: dorsal skin cells

value: Sorted GFP-positive cells


title: Col-0, Leaves, JSC-1A, replicate 5

description:
P5J4JSC2
Not included in the processed data spreadsheets (only used Replicates 1-4 for analyses)


title: SW403_IRS2_control_bio_rep3

value: WT


title: Sample 07670063C0024R (cancer immune panel)

value: Pre

tag: responder status

value: Non-responder

tag: progression free survival in weeks

tag: progression free survival status

value: Progressed or Died


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N701_S502]

tag: genotype/variation

value: Wild-type

tag: developmental stage

value: aorta-gonads-mesonephros (AGM)

value: HSC


title: Col-0, Leaves, Apollo 17 regolith, replicate 4

description:
P4L3162
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030

source_name: plant grown in A17 Lunar regolith, 20 day-old plants harvested and flash frozen in Liquid Nitrogen

tag: cultivar

value: Wild Type

tag: tissue

value: Leaves

value: All leaves from 20 day-old seedling


title: Sample 07670056C0013R (cancer immune panel)


title: WT_glucose_rep3

value: wild type

value: glucose


title: WT_glucose_rep2


title: SW403_IRS2_control_bio_rep2

value: Colon adenocarcinoma


title: Col-0, Leaves, Apollo 12 regolith, replicate 4

description:
P4L2109
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030

source_name: plant grown in A12 Lunar regolith, 20 day-old plants harvested and flash frozen in Liquid Nitrogen

tag: organism part

tag: age

value: 21 day-old plants, 16/8 hr light/ dark cycle

value: LN2 fixed_sample


title: Col-0, Leaves, Apollo 11 regolith, replicate 4

description:
P4L12078
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030

source_name: plant grown in A11 Lunar regolith, 20 day-old plants harvested and flash frozen in Liquid Nitrogen

tag: genotype

tag: biosource type


title: Sample 08950124C0004R (cancer immune panel)


title: Col-0, Leaves, JSC-1A, replicate 4

description:
P4J4JSC1
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030

value: 20 day-old plants, 16/8 hr light/ dark cycle


title: WT_starved_rep3

tag: agent


title: Sample 08950121C0004R (cancer immune panel)

tag: sample note

value: Excluded from analysis:Screening


title: Kasumi-1 IgG rep 2

city: Portland

first: Theodore

last: Braun

address: 2720 S Moody Ave

institute: Oregon Health and Science University

description: CUT&Tag

data_processing:
Library strategy: CUT&Tag
Sequencing from CUT&Tag was aligned using Bowtie2
Peaks were called using gopeaks
Bigwigs are CPM normalized
Annotations with ChIPSeeker
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: Kasumi-1 cells

extract_protocol:
Samples were prepared according to published protocol Kaya-Okur et al 2019
Libraries were prepared according to published protocol Kaya-Okur et al 2019

tag: antibody

value: IgG (CST, cat 2729, lot 9)

tag: cell line


title: Sample 08950118C0004R (cancer immune panel)

tag: subject id

tag: timepoint

value: Pre

value: Responder


title: Col-0, Leaves, Apollo 17 regolith, replicate 3

first: Robert

description:
P3L3161
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030


title: WT_starved_rep1


title: Col-0, Leaves, Apollo 12 regolith, replicate 3

description:
P3L2106
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030


title: WT_starved_rep2


title: Sample 08950117C0004R (cancer immune panel)


title: Kasumi-1 H3K27Ac rep 1

description: CUT&Tag


title: Sample 08950124C0005R (cancer immune panel)

tag: responder status

value: Non-responder

value: Progressed or Died


title: Kasumi-1 H3K27Ac rep 2

description: CUT&Tag


title: Kasumi-1 IgG rep 1

description: CUT&Tag


title: Col-0, Leaves, Apollo 11 regolith, replicate 3

description:
P3L12077
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030


title: WT_glucose_rep1


title: SW403_IRS2_control_bio_rep1

tag: cell type

value: WT


title: Sample 08950116C0004R (cancer immune panel)

tag: progression free survival in weeks

tag: progression free survival status


title: Col-0, Leaves, Apollo 17 regolith, replicate 2

description:
P2L3160
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030


title: Col-0, Leaves, Apollo 12 regolith, replicate 2

description:
P2L299
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030


title: Col-0, Leaves, JSC-1A, replicate 3

description:
P3J4JSC1
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030


title: Sample 08950114C0004R (cancer immune panel)


title: Col-0, Leaves, Apollo 11 regolith, replicate 2

description:
P2L12076
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030


title: Sample 08950109C0004R (cancer immune panel)


title: Sample 08950113C0004R (cancer immune panel)


title: Sample 07670076C0023R (cancer immune panel)

value: At Progression


title: Col-0, Leaves, JSC-1A, replicate 2

description:
P2J4JSC1
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030

value: Wild Type


title: Col-0, Leaves, Apollo 17 regolith, replicate 1

description:
P1L3159
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030

value: Leaves


title: Sample 07670067C0011R (cancer immune panel)

value: Excluded from analysis:Progression after 2nd infusion


title: Col-0, Leaves, Apollo 12 regolith, replicate 1

description:
P1L2105
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030

value: All leaves from 20 day-old seedling


title: Sample 07670062C0013R (cancer immune panel)


title: Col-0, Leaves, JSC-1A, replicate 1

description:
P1J4JSC1
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030  Ferl_Paul_Lunar-DiffExp-by-Morphology_20211030


title: Sample 07670059C0015R (cancer immune panel)


title: Sample 07670055C0013R (cancer immune panel)


title: Sample 07670058C0013R (cancer immune panel)


title: Experiment 2, CellPlex_Pool6_part3

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
The Mesocricetus auratus genome MesAur 2.0 was downloaded from https://www.ncbi.nlm.nih.gov/genome/11998. The GFF file was converted to GTF, the generic gene names (LOCxxx) replaced with mouse-derived official gene symbols for several key genes, and 3'-UTRs extended as described previously (doi: 10.1101/2021.10.02.462569). Then, the SARS-CoV-2 genome annotation was merged.
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
For single-cell RNA-sequencing data, fastq files were processed using a the mergend MesAur2.0/SARS-CoV-2 genome with the GTF file provided here by applying CellRanger 6.0.2 with standard parameters
For single-cell RNA-sequencing data, fastq files were processed using a merged Roborvski hamster/SARS-CoV-2 genome by applying CellRanger 6.0.2 with standard parameters
Assembly: MesAur 2.0
Assembly: SARS-CoV-2 MN908947
Supplementary files format and content: GTF file
Supplementary files format and content: tab-separated values
Supplementary files format and content: h5 matrix

organism: Mesocricetus auratus

source_name: multiplexed sample

growth_protocol:
Hamsters were vaccinated intramuscularly with either an experimental adenovirus vector vaccine containing the whole SARS-CoV-2 spike (5 _ 108 infectious units (IFU) per animal) (PMID: 34835096), or BNT162b2 (5 ug per animal) or intranasally with 1x105 pfu of the live-attenuated SARS-CoV-2 vaccine candidate sCPD9 (PMID: 34320400, PMID: 34851677). For the prime-boost experiment, immunity was boosted by a second vaccination with the respective vaccines at the same dose 21 days after primary vaccination. In, one group, animals were primed with BNT162b2 and boosted with sCPD9, all other groups received a homologues boost.
Hamsters were weighted daily and monitored for signs of disease twice-daily. Hamsters were selected randomly for all scheduled take-out time points (day 2 and 5).
Euthanasia prior analysis occurred by cervical dislocation exsanguination under anesthesia as previously described (PMID 32698441, 33271063). Peripheral blood was collected in EDTA-coated syringes and lung lobes were collected for follow-up analyses, in which the left lobe was used for histopathology, the right caudal lobe for single-cell analysis, the right cranial lobe for virological assessments and the right medial as backup to repeat virological analyses as needed.

extract_protocol:
Bulk and single-cell RNA-sequencing libraries were constructed using commercial kits:
10xGenomics Chromium v3.1 single cell 3' gene expression kit
For isolation of single cells, the caudal lobe of the right lung was removed and placed in storage medium (1× PBS, 0.5 % BSA) until further processing. Storage and isolation media contained 2 µg/mL ActinomycinD. Tissues and cells were always spun at 350 x g for 6 minutes at 4 °C. Mechanical dissociation of lung lobes was achieved by clapping motions with tweezers for 2 minutes in enzymatic digestion medium (3,4 mg/mL Collagenase Cls II (Merck), 1 mg/mL DNase I (PanReac AppliChem), in 2 mL Dispase medium per lung lobe (Corning), 50 Caseinolytic Units/mL followed by 30 minutes incubation at 37°C and 5 % CO2.
Further tissue dissociation was achieved by repeated pipetting of digested lung tissue with 5 mL pipettes and passing of cell suspension with plungers through 70 µm cell strainers. Cells were pelleted from suspension by centrifugation and resuspended in red blood cell lysis buffer (BioLegend). Lysis reaction was stopped and cells washed with excessive volumes of PBS/BSA. Cells were centrifuged, resuspended in low-BSA buffer (1× PBS, 0.04 % BSA) and counted via hemocytometer and trypan blue.
Then, 1,000,000 lung cells per sample were subjected to Cell Multiplexing Oligo (CMO) labeling according to the manufacturers’ instructions (3ʹ-CellPlex-Kit-Set-A, 10x Genomics). Labelled cells from 12 samples were pooled, filtered (40 µm) and counted. Pooled cells were adjusted to a final concentration of ~1,600 cells / μL and filtered with 40 µm FloMi filters (Merck) suitable for low volumes prior subjection to scRNA sequencing.
For Lung RNA Bulk sequencing the lobus medialis of the right lung lobe was removed carefully and homogenzied in Trizol reagent using a bead mill procedure (Speedmill, Analytic Jena), RNA was extracted according to the manufacturer’s instructions.

treatment_protocol: 21 days following primary vaccination or 14 days following booster vaccination, hamsters were infected intranasally as previously described (PMID 32698441, 33271063). Briefly, hamster received 1 x 105 pfu SARS-CoV-2 Variant Delta. [SARS-CoV-2, Human, 2021, Germany ex India, 20A/452R (B.1.617)] intranasally under anesthesia.

tag: first vaccination

value: Multiplexed sample (mixed treatments)

tag: second vaccination

tag: sampling timepoint


title: Col-0, Leaves, Apollo 11 regolith, replicate 1

description:
P1L12075
Ferl_Paul_Lunar-DiffExp-by-Apollo-Site_20211030

tag: cultivar

tag: tissue

tag: organism part


title: Experiment 2, CellPlex_Pool6_part2


title: Experiment 2, GEX_Pool6_part3


title: Sample 08950118C0005R (cancer pathways panel)


title: Experiment 2, GEX_Pool6_part1


title: Experiment 2, GEX_Pool6_part2


title: Experiment 2, CellPlex_Pool6_part1


title: Sample 07670080C0030R (cancer pathways panel)


title: Sample 07670064C0023R (cancer immune panel)


title: Sample 07670079C0028R (cancer pathways panel)


title: Sample 07670091C0043R (cancer pathways panel)

value: Excluded from analysis:Week 8 after 2nd infusion


title: Sample 07420001B0032R (cancer pathways panel)

value: Excluded from analysis:Screening for 2nd infusion


title: Experiment 2, GEX_Pool5_part3


title: Sample 07670063C0035R (cancer pathways panel)


title: Sample 07670061C0024R (cancer pathways panel)


title: Experiment 2, CellPlex_Pool5_part2


title: Experiment 2, GEX_Pool5_part2


title: Experiment 2, CellPlex_Pool5_part3


title: Sample 08950124C0004R (cancer pathways panel)


title: Experiment 2, GEX_Pool5_part1


title: Experiment 2, CellPlex_Pool5_part1


title: Sample 08950118C0004R (cancer pathways panel)


title: Sample 08950121C0004R (cancer pathways panel)


title: Sample 08950117C0004R (cancer pathways panel)


title: Sample 08950116C0004R (cancer pathways panel)


title: Experiment 2, GEX_Pool4_part2


title: Experiment 2, CellPlex_Pool4_part2


title: Sample 08950113C0004R (cancer pathways panel)


title: Experiment 2, CellPlex_Pool4_part1


title: Sample 08950114C0004R (cancer pathways panel)


title: Sample 08950109C0004R (cancer pathways panel)


title: Experiment 2, GEX_Pool4_part1