title: S-16_1h

description:
Library name: sample144
expression matrix (txt) and original file (fastq)


title: Parental_3

status: Public on Dec 11 2024

type: SRA

city: Wuhan

first: Zhiwen

last: FU

state: Hubei

address: 1277 Jianghan District, Wuhan, China

country: China

institute: Wuhan Union Hospital

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

tag: cell type

value: colorectal carcinoma cell


title: Cre_8week_1

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
clean reads were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data (by Novogene)
clean reads were mapped to the reference genome GRCm38 using HISAT2 (by Novogene)
HTSeq was used to count the read numbers mapped to each gene (by Novogene)
Assembly: mm38
Supplementary files format and content: Comma-separated text file containing raw count values for each sample

molecule: polyA RNA

source_name: pancreas

growth_protocol: Pancreatic fibroblasts were isolated from KPC and CRE mice of age 4,6,8,10 12 weeks by Nycodenz density gradient method. Fibroblast were further cultured in DMEM media supplemented with 15% FBS, 1% penicillin-streptomycin, and 1% Amphotericin B at 37°C .

extract_protocol:
Total RNA isolation from fibroblast was performed using the Direct-zol RNA Microprep Kit (Zymo Research)
RNA samples were analyzed together with Novogene Co Ltd. (Cambridge, UK). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) by Novogene.

tag: tissue

value: pancreas

value: murine pancreatic stellate cells

tag: genotype

tag: time

value: week 8


title: TEX_sgAcly_H3K9ac_rep2

city: La Jolla

first: Shixin

last: Ma

state: CA

address: 10010 N Torrey Pines Rd

department: IMPL-K

country: USA

institute: SALK Institute for biological studies

library_source: genomic

data_processing:
Sequence reads were aligned to mm10 using bowtie2
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: Cut&Run

molecule: genomic DNA

extract_protocol:
DNA extraction following Cut&Tag protocol
Library preparation following Cut& Tag protocol

value: sgAcly

value: Day 6

tag: treatment

value: in vitro exhaustion culture


title: Cre_10week_2

value: week 10


title: Cre_6week_1

value: week 6


title: S-16_0h

city: Xiamen

first: Xing

last: Xu

address: 422, Siming South Road

institute: Xiamen University

description:
Library name: sample143
expression matrix (txt) and original file (fastq)

library_source: transcriptomic single cell

data_processing:
The source code for the analysis of scBiopsy-seq is available on github (https://github.com/linl-linl/scBiopsy-seq).
Assembly: GRCh38,GRCh38.105, GRCm38 and GRCm38.102
Supplementary files format and content: matrix files

organism: Homo sapiens

source_name: colon

extract_protocol:
The capillary tip was filled with 1.5 μL of mixed solution (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP (AD101–12, TransGen Biotech, Beijing, China), 0.4 U·μL−1 Murine RNase Inhibitor (GMP4102PA-01, Vazyme Biotech Co., Ltd., Nanjing, China)), and then connected to the work electrode of the ultra-micro extraction instrument (Rayme Biotechnology Co., Ltd., Jiangsu, China). The counter electrode and the reference electrode were immersed in the culture medium within the confocal dish. The cells to be extracted were visualized by microscope and the preloaded capillary was gradually moved downward until it touched the cytoplasm of the selected cell. The tip of the capillary was then inserted into the cytoplasm, with a deformation observed in the selected cell. By setting the applied voltages and the duration of current application, a precisely controlled volume was extracted from the cell. After that, the capillary was retracted out of the cell, taken out of the extraction instrument and placed at -80°C for RNA storage.
Once it was required to undergo the RNA library construction, the capillary was connected to the work electrode again. The cellular contents within the capillary were injected into the top plate of the DMF device, enabling the subsequent RNA library processing on the DMF system. The lysis buffer (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP, 0.4 U·μL−1 Murine RNase Inhibitor and 0.2% Triton-X-100(A110694, Sangon Biotech, Shanghai, China) was introduced and mixed with the cellular contents at 72°C for 3 minutes for complete RNA release. Then the reverse transcription (RT) mix (1.7 μM biotinylated-TSO oligo, 5 × HiScript II RT buffer (Vazyme Biotech Co., Ltd., Nanjing, China), 1.7 U·μL−1 Murine RNase Inhibitor, 19 U·μL−1 HiScript II Reverse Transcriptase (R201, Vazyme Biotech Co., Ltd., Nanjing, China) and 0.05% Pluronic F68 (24040032, ThermoFisher, America)) was introduced to initiate the RT reaction at 42°C for 90 minutes, which was stopped by heat at 70°C for 15 min. After that, the PCR mix (2 × KAPA HiFi HotStart ReadyMix (KK2602, KAPA, America), 0.06 μM Biotinylated-ISPCR oligo and 0.05% Pluronic F68) was introduced to amplify the cDNAs (95°C 3 minutes, 25 cycles of 98°C 30 s, 65°C 45 s and 72°C 6 minutes, followed by a final step at 72˚C for 5 min). The products were recovered from the DMF device into a 200-μL eppendorf tube, purified with 0.6 × DNA clean beads (Vazyme Biotech Co., Ltd., Nanjing, China) and quantified by qubit 3.0. Then 1 ng of the products were utilized and processed by sequencing-ready library construction kits (TD503, Vazyme). The library was purified twice with 0.6 × DNA clean beads (N411, Vazyme Biotech Co., Ltd., Nanjing, China) and sequenced by Novaseq500 according to the manufacturer’s instructions.

treatment_protocol: The cellular contents of SW480 cells were extracted initially prior to the ARV771 treatment, designated as the sample at 0 h. Immediately thereafter 250 nM ARV771 was added to the culture medium, and the cells were extracted at 1 h and 4 h.

value: colon

value: colon cancer cell line

value: WT


title: TEX_sgscramble_H4ac_rep1

value: sgscramble


title: 10x_34_5FU

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

data_processing:
Raw sequencing fragments were trimmed using TrimGalore (0.4.3)
Alignment to the mouse reference genome (build mm10) was performed using Bismark (v0.23.1)
Differentially methylated sites were generated using methylKit (v1.22.0)
Assembly: mm10
Supplementary files format and content: DNA methylation level, text format
Library strategy: DNA-seq

source_name: blood

extract_protocol:
Qiagen DNA extraction kit
Reduced representation bisulfite sequencing(RRBS)

value: blood

value: HSC


title: Cre_12week_3

value: week 12


title: TEX_sgscramble_H3K9ac_rep1


title: PC, donor 3, scRNAseq VDJ

city: Erlangen

first: Ulrike

last: Steffen

address: Glueckstrasse 4a

department: Internal Medicine 3

institute: University Clinic Erlangen

description: VDJ sequencing

data_processing:
Reads were converted to FASTQ format using mkfastq from Cell Ranger 3.1.0 (10X Genomics). Reads were then aligned to the human reference genome provided by 10X Genomics (GEX: GRCh38-3.0.0; VDJ: vdj_GRCh38_alts_ensembl-3.1.0-3.1.0). Alignment was performed with the count or vdj command from Cell Ranger 3.1.0 (10X Genomics). Further QC filtering was performed in the R package Seurat (v.3.1.4) for samples individually. IgH-Annotation was imported from VDJ sequencing results and the 3 samples were merged for SCTransform normalization. The SCTransform normalization included the number of genes per cell and the sample identity as covariates. Standard dimensionality reduction (PCA) was used, with removal of ribosomal, mitochondrial, immunoglobulin and cell-cycle genes from VariableFeatures.
Assembly: hg38
Supplementary files format and content: tab separated values files and matrix files

source_name: bone marrow

extract_protocol:
Bone marrow cells were stained for viability with Zombie-Yellow™ Fixable Viability Kit (1:600) for 20 minutes at room temperature; and afterwards with anti-CD14-BV421, anti-CD16-BV421, anti-CD56-BV421, anti-CD38-APC, anti-CD45-FITC, and anti-CD138-PE/Cy7 (all Biolegend). After the staining, plasma cells (CD45+CD14-CD16-CD56-CD38++CD138++) were sorted on a FACS Aria machine.
At the output, 1600-3100 live cells were subjected to 10x Chromium Single Cell sequencing library generation with 10X Chromium 5’ GEX/VDJ kits according to the manufacturer’s instructions. GEX Library sequencing was performed on an Illumina HiSeq 2500 sequencer to a depth of about 50 million reads each. In all samples, the mean number of reads per cell was greater than 30000. VDJ Libraries were sequenced to a depth of about 30 million reads resulting in 1000 to 10000 read pairs per cell.

value: bone marrow

value: plasma cell


title: S-15_4h

description:
Library name: sample142
expression matrix (txt) and original file (fastq)

value: ARV771 treatment


title: PC, donor 4, scRNAseqVDJ

description: VDJ sequencing


title: Parental_1

value: colorectal carcinoma cell


title: TEX_sgAcly_H3K9ac_rep1


title: TEX_sgscramble_H3K9ac_rep2


title: S-15_1h

description:
Library name: sample141
expression matrix (txt) and original file (fastq)


title: Cre_10week_1

value: pancreas

value: murine pancreatic stellate cells


title: Cre_12week_1


title: S-15_0h

description:
Library name: sample140
expression matrix (txt) and original file (fastq)


title: S-14_4h

description:
Library name: sample139
expression matrix (txt) and original file (fastq)


title: TEX_sgAcly_H3K27ac_rep2

value: sgAcly

value: Day 6


title: PC, donor 4, scRNAseq 5'

description: 5' sequencing


title: PC, donor 2, scRNAseq VDJ

description: VDJ sequencing


title: Parental_2


title: TEX_sgAcly_H3K27ac_rep1

value: in vitro exhaustion culture


title: S-14_1h

description:
Library name: sample138
expression matrix (txt) and original file (fastq)


title: KPC_6week_4

value: week 6


title: Cre_12week_2


title: PC, donor 3, scRNAseq 5'

description: 5' sequencing


title: TEX_sgscramble_H3K27ac_rep2


title: S-14_0h

description:
Library name: sample137
expression matrix (txt) and original file (fastq)

value: colon


title: KPC_6week_3


title: S-13_4h

description:
Library name: sample136
expression matrix (txt) and original file (fastq)

value: colon cancer cell line


title: TEX_sgscramble_H3K27ac_rep1


title: KPC_6week_2


title: PC, donor 2, scRNAseq 5'

description: 5' sequencing


title: KPC_6week_1


title: LCMV-Cl13_TEXterm_H4ac_rep2

value: TEXterm

value: Day 21

value: LCMV Clone 13


title: KPC_8week_4

value: week 8


title: KPC_4week_2

value: week 4


title: LCMV-Cl13_TEXterm_H4ac_rep1


title: S-12_0h

description:
Library name: sample131
expression matrix (txt) and original file (fastq)

value: WT


title: LCMV-Cl13_TEXprog_H4ac_rep1

value: TEXprog


title: LCMV-Cl13_TEXprog_H4ac_rep2


title: LCMV-Cl13_TEXterm_H3K9ac_rep2


title: LCMV-Cl13_TEXterm_H3K9ac_rep1


title: S-11_4h

description:
Library name: sample130
expression matrix (txt) and original file (fastq)

value: ARV771 treatment


title: S-13_0h

description:
Library name: sample134
expression matrix (txt) and original file (fastq)


title: Pancreas, Tumor, input control rep2

first: Andrew

middle: M.

last: Lowy

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: UCSD Health

data_processing:
Processed using bcl2fastq
Aligned to hg19 using bowtie2 (v.2.0.5) using the option sensitive
Bigwig files were made using deeptools bamCompare, and normalizing to 1e6 reads
Assembly: hg19
Supplementary files format and content: bigwig, signal normalized by input control

source_name: Pancreas

extract_protocol:
Frozen tissue samples were homogenized using the Covaris CP02 cryoPREP Automated Dry Pulverizer. Homogenized tissue was fixed rotating at room temperature for eight minutes in 1% formaldehyde (ThermoFisher catalog #28906), diluted in PBS. Fixation was quenched with 1/20th volume of 2.5M glycine. All buffers after fixation and prior to wash buffer before elution included HALT protease inhibitor (Life Technologies catalog #78438) and 1mM sodium butyrate to inhibit histone deacetylase activity. Samples were pelleted and washed twice with cold PBS. Samples were then lysed rotating at 4°C with ChIP Lysis Buffer 1 (Boston BioProducts catalog # CHP-126) for ten minutes, then with Lysis Buffer 2 (Boston BioProducts catalog # CHP-127). Samples were then washed with Sonication Buffer (CHP-133). Samples were resuspended in sonication buffer and sonicated to an average size of 100-500 bp on the Covaris E220 focused ultrasonicator, in a volume of 750 µL sonication buffer. Following sonication, samples were collected and centrifuged at 20,000xg for 10 minutes at 4°C to pellet insoluble material. The supernatant was collected and diluted in one volume of ChIP Dilution Buffer (Boston BioProducts #CHP-143), and input controls were collected. Chromatin was immunoprecipitation overnight (12-16 hours) rotating at 4°C with anti-H3K27ac antibody (Abcam, catalog #4729) conjugated to protein G Dynabeads (Life Technologies, catalog #10004D). The following day, immunoprecipitated chromatin was washed twice with low salt wash buffer (Boston BioProducts #CHP-146), once with high salt wash buffer (Boston BioProducts #CHP-147), once with LiCl wash buffer (Boston BioProducts #CHP-149), and once with Tris- based wash buffer (Boston BioProducts #CHP-148). Chromatin was eluted with ChIP Elution Buffer (Boston BioProducts #CHP-153) for one hour at 65°C with agitation at regular intervals. Eluted chromatin was reverse crosslinked for 16 hours at 65°C. Chromatin was then diluted in one volume of TE buffer, then treated with RNAse (Fisher catalog # AM2286) for 2 hours at 37°C and proteinase K (Fisher catalog # AM2548) for 1 hour at 55°C. An equal volume of phenol/chloroform (Fisher, catalog #15593031) was added to each sample, and the aqueous phase was collected in a Phase Lock Gel tube (VWR catalog #10847-802). Each sample received 1 mL ethanol, 20 µL 5M NaCl, and 30 µg GlycoBlue (Fisher Scientific, catalog # AM9516), which were then mixed by inversion and stored at −20°C overnight. The following day, the samples were centrifuged at 20,000xg for 20 minutes to precipitate the purified DNA. Pellets were washed with 800 µL cold 80% ethanol and a second centrifugation at 20,000xg for 10 minutes. Pellets were briefly air dried and resuspend in 50 µL water.
Libraries were generated using the Swift Accel-NGS 2S Plus DNA library kit (Swift Biosciences catalog #21024). Samples were multiplexed six libraries per lane on an Illumina HiSeq 2500.

value: Pancreas

tag: chip antibody

value: none (input control)

tag: condition

value: Tumor


title: S-12_4h

description:
Library name: sample133
expression matrix (txt) and original file (fastq)


title: KPC_4week_1

value: pancreas

value: murine pancreatic stellate cells


title: Pancreas, Tumor, input control rep5


title: Pancreas, Tumor, input control rep7


title: Pancreas, Tumor, input control rep4


title: Pancreas, Tumor, input control rep3


title: Pancreas, Tumor, input control rep1


title: Pancreas, Tumor, input control rep6


title: KPC_8week_3


title: S-13_1h

description:
Library name: sample135
expression matrix (txt) and original file (fastq)


title: S-12_1h

description:
Library name: sample132
expression matrix (txt) and original file (fastq)


title: KPC_4week_3


title: S-11_1h

description:
Library name: sample129
expression matrix (txt) and original file (fastq)


title: LCMV-Cl13_TEXprog_H3K9ac_rep2


title: KPC_8week_2


title: Pancreas, Normal, input control rep6

value: Normal


title: KPC_8week_1


title: LCMV-Cl13_TEXprog_H3K9ac_rep1


title: Pancreas, Normal, input control rep5


title: S-10_4h

description:
Library name: sample127
expression matrix (txt) and original file (fastq)


title: Pancreas, Normal, input control rep4


title: S-11_0h

description:
Library name: sample128
expression matrix (txt) and original file (fastq)


title: S-10_1h

description:
Library name: sample126
expression matrix (txt) and original file (fastq)


title: LCMV-Cl13_TEXterm_H3K27ac_rep1


title: LCMV-Cl13_TEXterm_H3K27ac_rep2


title: KPC_12week_2

value: week 12


title: Pancreas, Normal, input control rep3


title: Pancreas, Normal, input control rep1


title: LCMV-Cl13_TEXprog_H3K27ac_rep2


title: TGS04_CD44_Low

city: Kanazawa

first: Masahiko

last: Kobayashi

address: Kakuma machi

department: Cancer Research Institute

country: Japan

institute: Kanazawa University

data_processing:
Fastq files were converted by CLC Genomics Workbench Version 12.0.2.
All genes are extracted based on the reference genome, and annotated transcripts are extracted.
The reads are categorized and assigned to the genes, and expression values for each gene and each transcript are calculated.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample

growth_protocol: Culture in DMEM/F12 medium including hEGF 20 ng/ml, hFGF 20 ng/ml and B27.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen). 1400–2400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA (Illumina) following manufacturer's protocols.

treatment_protocol: Cells were stained with APC anti-mouse/human CD44 Antibody (BioLegend), and CD44-high and CD44-low populations were collected by cell sorter.

tag: cell population

tag: disease

value: glioblastoma


title: S-10_0h

description:
Library name: sample125
expression matrix (txt) and original file (fastq)

value: colon

value: colon cancer cell line


title: KPC_12week_1


title: LCMV-Cl13_TEXprog_H3K27ac_rep1

value: Day 21


title: S-9_4h

description:
Library name: sample124
expression matrix (txt) and original file (fastq)


title: Pancreas, Normal, input control rep2


title: S-9_1h

description:
Library name: sample123
expression matrix (txt) and original file (fastq)


title: KPC_10week_3

value: week 10


title: KPC_10week_2


title: Pancreas, Tumor, H3K27ac rep7


title: KPC_10week_1


title: Pancreas, Tumor, H3K27ac rep6


title: TGS04_CD44_High


title: S-9_0h

description:
Library name: sample122
expression matrix (txt) and original file (fastq)


title: KGS10 spheres

growth_protocol: Culture in DMEM/F12 medium including hEGF 20 ng/ml, hFGF 20 ng/ml,and B27.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen). 615–2346 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA (Illumina) following manufacturer's protocols.

value: Wild type


title: Pancreas, Tumor, H3K27ac rep5


title: KPC_12week_3


title: Hepa1-6 cells, sgYthdf1 Replicate 3

city: Singapore

first: Muhammad

last: Idris

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB / A*STAR

data_processing:
Adaptor and poly-G trimming and low complexity filter was applied to raw sequencing reads using fastp (v0.23.2).
Sequencing reads were aligned mouse genome using STAR (v2.7.10a).
read counts were determined using salmon (v1.9.0) with seqBias, gcBias and posBias options applied.
Assembly: gencode vM26 (GRCm39)
Supplementary files format and content: tab-delimited file contains the raw read counts for each sample

source_name: Hepa 1-6

growth_protocol: Hepa 1-6 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
RNA was extracted using the Total RNA Extractor (Trizol) kit (B511311, Sangon Biotech, China).
To eliminate genomic DNA contamination, the total RNA samples underwent treatment with RNase-free DNase I.
1 μg of RNA was used as input material for library construction using VAHTSTM mRNA-seq V2 Library Prep Kit from Illumina.

treatment_protocol:
Ythdf1 knockout cell lines were generated using a Ythdf1-specific CRISPR/Cas9/EGFP plasmids, while Usp5 knockout cell lines were generated using a pLentiCRISPR-Usp5-sgRNA purchased from GeneChem (Shanghai, China).
The selection of single cell clones was performed by serial dilution in 96-well plates, followed by immunoblot analysis of YTHDF1 or USP5 to confirm knockout efficiency of multiple selected clones.

value: Hepa 1-6

tag: disease state

value: Liver Hepatoma

value: Ythdf1 knockout


title: S-8_4h

description:
Library name: sample121
expression matrix (txt) and original file (fastq)

value: WT

value: ARV771 treatment


title: S-8_1h

description:
Library name: sample120
expression matrix (txt) and original file (fastq)


title: KGS23 spheres


title: Hepa1-6 cells, sgYthdf1 Replicate 1


title: Hepa1-6 cells, sgUsp5 Replicate 2

value: Usp5 knockout


title: KGS04 spheres


title: Pancreas, Tumor, H3K27ac rep2

value: Pancreas

value: Tumor


title: Pancreas, Tumor, H3K27ac rep3


title: KGS22 spheres


title: S-7_0h

description:
Library name: sample116
expression matrix (txt) and original file (fastq)


title: S-7_4h

description:
Library name: sample118
expression matrix (txt) and original file (fastq)


title: Hepa1-6 cells, sgUsp5 Replicate 3


title: S-6_4h

description:
Library name: sample115
expression matrix (txt) and original file (fastq)


title: KGS03 spheres


title: Hepa1-6 cells, sgUsp5 Replicate 1


title: S-7_1h

description:
Library name: sample117
expression matrix (txt) and original file (fastq)


title: Pancreas, Normal, H3K27ac rep6


title: Pancreas, Tumor, H3K27ac rep1


title: Pancreas, Normal, H3K27ac rep5


title: Hepa1-6 cells, sgControl Replicate 3

value: Control


title: S-6_1h

description:
Library name: sample114
expression matrix (txt) and original file (fastq)


title: KGS22_TFE3CTRL_2_biol rep 2


title: KGS22_TFE3CTRL_1_biol rep 1


title: TGS04 spheres


title: Hepa1-6 cells, sgYthdf1 Replicate 2


title: Hepa1-6 cells, sgControl Replicate 2


title: S-8_0h

description:
Library name: sample119
expression matrix (txt) and original file (fastq)


title: Pancreas, Normal, H3K27ac rep4

value: Normal


title: S-6_0h

description:
Library name: sample113
expression matrix (txt) and original file (fastq)


title: Hepa1-6 cells, sgControl Replicate 1


title: TGS04_TFE3WT_2_biol rep 2

value: WT Control


title: Pancreas, Tumor, H3K27ac rep4


title: Pancreas, Normal, H3K27ac rep3


title: TGS04_TFE3WT_1_biol rep 1

value: glioblastoma


title: S-5_4h

description:
Library name: sample112
expression matrix (txt) and original file (fastq)

value: colon


title: S-5_1h

description:
Library name: sample111
expression matrix (txt) and original file (fastq)

value: colon cancer cell line


title: Midbrain, wt/wt, rep3

city: NY

first: Yoko

last: Tajima

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description: bulk RNA-seq

data_processing:
alignment with Olego
RNA abundance analysis (edgeR)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

extract_protocol:
Trizol and RNeasy Mini extraction
Illumina High-throughput TruSeq RNA Sample preparation: polyA selection

tag: strain background

value: brain

tag: tissue compartment

value: midbrain

tag: developmental stage


title: FELINE trial, patient P111, day 180, Letrozole alone

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

data_processing:
Pre-processing of the raw sequencing reads were performed using the Bioinformatics ExperT SYstem (BETSY).
10X data were preprocessed with CellRanger using the mRNA procedure recommended for nuclei sequencing.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing read counts

source_name: breast

extract_protocol:
RNA was extracted from single nuclei using the 10X Genomics Chromium Single Cell 3’ V3 Kit following manufacturer’s protocol.
snRNA-seq libraries were prepared using the 10X Genomics Chromium Single Cell 3’ V3 Kit following manufacturer’s protocol.

value: tumor

value: breast

tag: patient

tag: days treated

value: Letrozole alone

tag: response

value: Sustained response


title: Pancreas, Normal, H3K27ac rep2


title: S-5_0h

description:
Library name: sample110
expression matrix (txt) and original file (fastq)

tag: cell line

value: WT


title: TGS04_TFE3KO_2_biol rep 2

value: TFE3 knockout


title: S-4_4h

description:
Library name: sample109
expression matrix (txt) and original file (fastq)

tag: cell type

value: ARV771 treatment


title: Pancreas, Normal, H3K27ac rep1

tag: tissue

value: Pancreas


title: KGS22_TFE3OE_2_biol rep 2

tag: genotype

value: TFE3 overexpression


title: TGS04_TFE3KO_1_biol rep 1


title: FELINE trial, patient P111, day 0, Letrozole alone


title: S-4_1h

description:
Library name: sample108
expression matrix (txt) and original file (fastq)


title: Midbrain, wt/wt, rep2

description: bulk RNA-seq


title: Midbrain, wt/wt, rep4

description: bulk RNA-seq


title: FELINE trial, patient P111, day 14, Letrozole alone


title: FELINE trial, patient P110, day 180, Combination ribociclib

value: Combination ribociclib

value: Rebound disease


title: Midbrain, hu/hu, rep3

description: bulk RNA-seq


title: S-3_4h

description:
Library name: sample106
expression matrix (txt) and original file (fastq)


title: S-4_0h

description:
Library name: sample107
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P110, day 14, Combination ribociclib


title: Midbrain, wt/wt, rep1

description: bulk RNA-seq


title: Midbrain, hu/hu, rep2

description: bulk RNA-seq


title: Ravuconazole Infected 3 72h

city: Yokohama

first: Imad

last: Abugessaisa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

institute: RIKEN

description: Library name: Ravuconazole Infected 3 72h

data_processing:
LQ-ssCAGE Paired-End sequence data provide cDNA sequence as Read1 and Sample Barcode sequence as Read2. In order to demultiplex Sample Barcode sequence, house made script is used with Read1 and Read2 data (discarded). Analysis of LQ-ssCAGE tags is performed by Moirai workflow using Read1 cDNA read. The genome mapping software is STAR version 2.5.3. BAM format files are treated by samtools version 1.14. For counting LQ-ssCAGE tags, bedtools version 2.30.0 is used. LQ-ssCAGE tags per each sample stored as bed file ctss.bed
Assembly: ASM258982v1
Supplementary files format and content: cor_links.rds
Supplementary files format and content: CTSSs.rds
Supplementary files format and content: Enhancers.rds
Supplementary files format and content: RawCount.rds
Supplementary files format and content: stretches.rds
Supplementary files format and content: TSSs.rds

organism: Galleria mellonella

source_name: hemolymph

growth_protocol: G. mellonella larvae were obtained from the Forelshop (Tremelo, Belgium) and kept in the dark on wood shaving at room temperature until use. Within five days of receipt, larvae of approximately 300-500mg were selected for experimental use. The selected larvae were divided over Petri dishes containing 90mm Whatman filter paper and five larvae per dish.

extract_protocol:
RNA isolated at 6, 30, 72 and 168 hours post-infection. The contents of three larvae were pooled, flash-frozen with liquid nitrogen and mechanically crushed using a pestle and mortar. The resulting powder was suspended in RLT buffer (supplemented with 1% β-Mercaptoethanol), provided in the RNeasy Mini Kit (Qiagen, Germany). The samples were incubated at 57⁰C for 3 minutes before proceeding according to the manufacturer's instructions.
LQ-ssCAGE (low quantity single strand CAGE) started by Reverse Transcription (RT) of 200 ng of total RNA (*measured by the RNA provider) to generate 5’-end of the capped RNA/first-strand cDNA hybrids. The RNA/cDNA hybrids were cap-trapped and adapted with illumine sequencer-compatible barcode-tagged adaptors (PMID: 34382184). No PCR amplification was performed during the LQ-ssCAGE library preparation. The amount of resulting libraries were checked by qPCR using KAPA Library Quantification Kits (Kapa Biosystems).
LQ-ssCAGE library sequenced using Illumina HiSeq2500 platform in Rapid mode and 50 base read length.

treatment_protocol: An inoculum of M. mycetomatis strain MM55 was prepared following the method described by Kloezen et al . In short, the mycelium was harvested, transferred to RPMI-media supplemented with 0.35 g/L L-glutamine, 1.98 mM 4-morpholinepropanesulfonic acid (MOPS) and 100 mg/L chloramphenicol, sonicated for 30 seconds at 10 micron (Soniprep 150 plus, MSE, The United Kingdom) and incubated for two weeks at 37 ⁰C. Next, the mycelium was harvested using vacuum filtration (Nalgene, Abcoude, the Netherlands using a 22 micron filter (Whatman)). The fungal biomass was scrapped from the filter and the wet weight was measured, before resuspending the mycelium in phosphate-buffered saline (PBS). The obtained suspension was sonicated for 120 seconds at 10 micron, washed in PBS, and diluted to a final concentration of 4 mg per 40 µL. The larvae were infected using the prepared inoculum, by injection in the last left proleg using an insulin 29G U-100 needle (BD diagnostics, Sparsk, USA). After 4, 30 and 52 hours of the infection, larvae were treated with itraconazole or ravuconazole to a final concentration of 5.71 mg/kg, a clinically relevant dose of 400 mg based on an average human with a weight of 70 kg39. The course of the infection was monitored by infecting and treating separate groups consisting of 15 larvae per group, and survival was recorded daily for the duration of ten days. During all experiments, Pupa were removed from the equation, and non-infected larvae were included as control.

value: hemolymph

value: Ravuconazole

tag: infection

value: Infected

tag: time


title: Midbrain, hu/hu, rep4

description: bulk RNA-seq


title: Ravuconazole Infected 3 30h

description: Library name: Ravuconazole Infected 3 30h

tag: treatment


title: KGS22_TFE3OE_1_biol rep 1

value: glioblastoma


title: S-3_1h

description:
Library name: sample105
expression matrix (txt) and original file (fastq)

value: colon

value: colon cancer cell line


title: Midbrain, hu/hu, rep1

description: bulk RNA-seq

value: brain

value: midbrain


title: FELINE trial, patient P110, day 0, Combination ribociclib

value: tumor

value: breast


title: S-3_0h

description:
Library name: sample104
expression matrix (txt) and original file (fastq)

value: WT


title: FELINE trial, patient P105, day 180, Combination ribociclib

value: Partial response


title: S-2_4h

description:
Library name: sample103
expression matrix (txt) and original file (fastq)

value: ARV771 treatment


title: FELINE trial, patient P105, day 14, Combination ribociclib


title: Ravuconazole Infected 2 6h

description: Library name: Ravuconazole Infected 2 6h


title: FELINE trial, patient P105, day 0, Combination ribociclib


title: Ravuconazole Infected 3 6h

description: Library name: Ravuconazole Infected 3 6h


title: Ravuconazole Infected 2 30h

description: Library name: Ravuconazole Infected 2 30h


title: Ravuconazole Infected 2 72h

description: Library name: Ravuconazole Infected 2 72h


title: Cortex, wt/wt, rep1

description: bulk RNA-seq

value: cortex


title: FELINE trial, patient P100, day 180, Combination ribociclib


title: Ravuconazole Infected 3 168h

description: Library name: Ravuconazole Infected 3 168h


title: Cortex, hu/hu, rep4

description: bulk RNA-seq


title: Ravuconazole Infected 2 168h

description: Library name: Ravuconazole Infected 2 168h


title: S-2_1h

description:
Library name: sample102
expression matrix (txt) and original file (fastq)


title: Cortex, wt/wt, rep4

description: bulk RNA-seq


title: S-2_0h

description:
Library name: sample101
expression matrix (txt) and original file (fastq)


title: S-1_4h

description:
Library name: sample100
expression matrix (txt) and original file (fastq)


title: Cortex, hu/hu, rep3

description: bulk RNA-seq


title: FELINE trial, patient P100, day 0, Combination ribociclib


title: S-1_1h

description:
Library name: sample99
expression matrix (txt) and original file (fastq)


title: S-1_0h

description:
Library name: sample98
expression matrix (txt) and original file (fastq)


title: Ravuconazole Infected 1 72h

description: Library name: Ravuconazole Infected 1 72h


title: Cortex, wt/wt, rep3

description: bulk RNA-seq


title: Cortex, hu/hu, rep2

description: bulk RNA-seq


title: FELINE trial, patient P097, day 14, Letrozole alone

value: Letrozole alone

value: Stable disease


title: Cortex, wt/wt, rep2

description: bulk RNA-seq


title: Cortex, hu/hu, rep1

description: bulk RNA-seq


title: FELINE trial, patient P097, day 180, Letrozole alone


title: scBiopsy-seq_6h-6

description:
Library name: sample96
expression matrix (txt) and original file (fastq)

value: breast cancer cell


title: FELINE trial, patient P097, day 0, Letrozole alone


title: Ravuconazole Infected 1 30h

description: Library name: Ravuconazole Infected 1 30h

value: hemolymph


title: FELINE trial, patient P100, day 14, Combination ribociclib

value: Combination ribociclib


title: scBiopsy-seq_6h-5

description:
Library name: sample95
expression matrix (txt) and original file (fastq)


title: E18.5, Midbrain, wt/wt, rep6

description: bulk RNA-seq


title: Ravuconazole Infected 1 168h

description: Library name: Ravuconazole Infected 1 168h

value: Ravuconazole

value: Infected


title: FELINE trial, patient P096, day 180, Letrozole alone


title: Ravuconazole Control 3 72h

description: Library name: Ravuconazole Control 3 72h

value: Healthy


title: E18.5, Midbrain, wt/wt, rep5

description: bulk RNA-seq


title: scBiopsy-seq_6h-4

description:
Library name: sample94
expression matrix (txt) and original file (fastq)


title: Ravuconazole Control 3 6h

description: Library name: Ravuconazole Control 3 6h


title: Ravuconazole Infected 1 6h

description: Library name: Ravuconazole Infected 1 6h


title: E18.5, Midbrain, wt/wt, rep4

description: bulk RNA-seq


title: FELINE trial, patient P096, day 14, Letrozole alone


title: scBiopsy-seq_6h-7

description:
Library name: sample97
expression matrix (txt) and original file (fastq)


title: Ravuconazole Control 3 30h

description: Library name: Ravuconazole Control 3 30h


title: scBiopsy-seq_6h-3

description:
Library name: sample93
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P092, day 180, Letrozole alone


title: E18.5, Midbrain, wt/wt, rep2

description: bulk RNA-seq


title: Ravuconazole Control 3 168h

description: Library name: Ravuconazole Control 3 168h


title: FELINE trial, patient P096, day 0, Letrozole alone


title: FELINE trial, patient P092, day 14, Letrozole alone


title: scBiopsy-seq_6h-1

description:
Library name: sample91
expression matrix (txt) and original file (fastq)


title: Ravuconazole Control 2 72h

description: Library name: Ravuconazole Control 2 72h


title: E18.5, Midbrain, wt/wt, rep1

description: bulk RNA-seq


title: FELINE trial, patient P092, day 0, Letrozole alone


title: scBiopsy-seq_4h-6

description:
Library name: sample89
expression matrix (txt) and original file (fastq)


title: Ravuconazole Control 2 6h

description: Library name: Ravuconazole Control 2 6h


title: Ravuconazole Control 2 30h

description: Library name: Ravuconazole Control 2 30h


title: FELINE trial, patient P090, day 180, Letrozole alone


title: E18.5, Midbrain, hu/hu, rep5

description: bulk RNA-seq


title: FELINE trial, patient P090, day 14, Letrozole alone


title: Ravuconazole Control 2 168h

description: Library name: Ravuconazole Control 2 168h


title: E18.5, Midbrain, hu/hu, rep4

description: bulk RNA-seq


title: scBiopsy-seq_4h-5

description:
Library name: sample88
expression matrix (txt) and original file (fastq)


title: Ravuconazole Control 1 72h

description: Library name: Ravuconazole Control 1 72h


title: scBiopsy-seq_4h-2

description:
Library name: sample87
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P090, day 0, Letrozole alone


title: E18.5, Midbrain, wt/wt, rep3

description: bulk RNA-seq


title: E18.5, Midbrain, hu/hu, rep3

description: bulk RNA-seq


title: Ravuconazole Control 1 6h

description: Library name: Ravuconazole Control 1 6h


title: FELINE trial, patient P089, day 180, Letrozole alone

value: Progressive disease


title: scBiopsy-seq_6h-2

description:
Library name: sample92
expression matrix (txt) and original file (fastq)


title: scBiopsy-seq_1h-7

description:
Library name: sample85
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P089, day 14, Letrozole alone


title: E18.5, Midbrain, hu/hu, rep6

description: bulk RNA-seq

value: brain


title: scBiopsy-seq_4h-7

description:
Library name: sample90
expression matrix (txt) and original file (fastq)


title: Ravuconazole Control 1 168h

description: Library name: Ravuconazole Control 1 168h


title: FELINE trial, patient P085, day 180, Combination ribociclib


title: FELINE trial, patient P089, day 0, Letrozole alone


title: E18.5, Midbrain, hu/hu, rep1

description: bulk RNA-seq

value: midbrain


title: scBiopsy-seq_1h-4

description:
Library name: sample82
expression matrix (txt) and original file (fastq)


title: scBiopsy-seq_4h-1

description:
Library name: sample86
expression matrix (txt) and original file (fastq)


title: Itraconazole Infected 3 6h

description: Library name: Itraconazole Infected 3 6h

value: Itraconazole


title: scBiopsy-seq_1h-6

description:
Library name: sample84
expression matrix (txt) and original file (fastq)

value: breast


title: scBiopsy-seq_1h-5

description:
Library name: sample83
expression matrix (txt) and original file (fastq)

value: WT


title: scBiopsy-seq_1h-2

description:
Library name: sample80
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P085, day 14, Combination ribociclib

value: tumor

value: Partial response


title: Control 2

city: Jinan, Shandong

first: Shuai

last: Leng

address: 105 Jiefang Road

institute: Central Hospital Affiliated to Shandong First Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: mm10

source_name: aorta

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: aorta

value: VSMCs

value: Vascular smooth muscle cells

value: Control


title: FELINE trial, patient P083, day 180, Combination ribociclib


title: Itraconazole Infected 3 72h

description: Library name: Itraconazole Infected 3 72h

value: hemolymph


title: Control 3


title: Itraconazole Infected 3 168h

description: Library name: Itraconazole Infected 3 168h


title: Ravuconazole Control 1 30h

description: Library name: Ravuconazole Control 1 30h


title: scBiopsy-seq_1h-1

description:
Library name: sample79
expression matrix (txt) and original file (fastq)

value: breast cancer cell


title: E18.5, Midbrain, hu/hu, rep2

description: bulk RNA-seq


title: Itraconazole Infected 2 72h

description: Library name: Itraconazole Infected 2 72h


title: FELINE trial, patient P085, day 0, Combination ribociclib

value: Combination ribociclib


title: scBiopsy-seq_1h-3

description:
Library name: sample81
expression matrix (txt) and original file (fastq)


title: scRNA-seq-14

description:
Library name: sample78
expression matrix (txt) and original file (fastq)

value: colon

value: colon cancer cell line


title: siSirt6 2


title: FELINE trial, patient P083, day 0, Combination ribociclib


title: Control 1


title: FELINE trial, patient P083, day 14, Combination ribociclib


title: Itraconazole Infected 2 6h

description: Library name: Itraconazole Infected 2 6h

value: Infected


title: siSirt6 3


title: FELINE trial, patient P082, day 180, Letrozole alone

value: Letrozole alone

value: Progressive disease


title: Itraconazole Infected 2 30h

description: Library name: Itraconazole Infected 2 30h

value: Itraconazole


title: scRNA-seq-12

description:
Library name: sample76
expression matrix (txt) and original file (fastq)


title: Itraconazole Infected 2 168h

description: Library name: Itraconazole Infected 2 168h


title: WM4007-1, T4, treated, sample S1

city: Farmington

middle: H

last: Chuang

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

description: Flash frozen spatial transcriptome sequencing

data_processing:
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina)
FASTQ files were split into mouse and human counterparts with Xenome 1.0.1
Mouse sequencing reads were aligned to mm10-2020-A genome with Space Ranger count 1.3.1
Human sequencing reads were aligned to GRCh38-2020-A genome with Space Ranger count 1.3.1
Human and mouse gene count matrices were merged into one matrix
Assembly: GRCh38 (GENCODE v32/Ensembl 98) and mm10 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: WM4007 melanoma PDX

growth_protocol: Subcutaneously implanted solid tumor on NSG mice

extract_protocol:
OCT-embedded fresh frozen tissue was used. Five 10µm sections from each block were used for total RNA extraction (Qiagen), which was used for RNA integrity determination by RINe score using an Agilent Tapestation and High Sensitivity RNA ScreenTape. Blocks with RINe greater than 7 were optimized for ideal permeabilization time following the vendor protocol (10x Genomics, CG000238). Sections from four tissue blocks were placed on Visium Gene Expression slide for H&E staining and brightfield imaging via NanoZoomer SQ (Hamamatsu), block-specific tissue permeabilization, mRNA capture, and subsequent library generation per the manufacturer’s protocol (10x Genomics, CG000239).
Library concentration was quantified using a Tapestation High Sensitivity DNA ScreenTape (Agilent) and fluorometry (Thermofisher Qubit) and verified via KAPA qPCR. Libraries were pooled for sequencing on an Illumina NovaSeq 6000 using a 28-10-10-90 read configuration, targeting 100,000 read pairs per spot covered by tissue.

treatment_protocol: Either untreated, treated with phosphate-buffered saline with 5% DMSO, or treated with dual BRAF/MEK inhibitor dabrafenib/trametinib via chow (~5 g/day).

tag: sample

tag: alternative id

tag: time point

tag: day

tag: mouse id

tag: tumor volume_mm3

value: WM4007 melanoma PDX

tag: model

value: dabrafenib (150 mg/kg), trametinib (1.5 mg/kg)


title: FELINE trial, patient P082, day 14, Letrozole alone

value: tumor

value: breast

tag: patient


title: WM4007-1, T4, treated, sample S2


title: Itraconazole Infected 1 72h

description: Library name: Itraconazole Infected 1 72h


title: scRNA-seq-11

description:
Library name: sample75
expression matrix (txt) and original file (fastq)

value: WT


title: siSirt6 1

value: aorta

value: VSMCs


title: WM4007-1, T3, treated, sample S2


title: scRNA-seq-10

description:
Library name: sample74
expression matrix (txt) and original file (fastq)


title: WM4007-1, T3, treated, sample S1


title: Itraconazole Infected 1 6h

description: Library name: Itraconazole Infected 1 6h


title: FELINE trial, patient P079, day 180, Letrozole alone

tag: days treated

value: Stable disease


title: scRNA-seq-9

description:
Library name: sample73
expression matrix (txt) and original file (fastq)

source_name: uterus

value: uterus

value: HeLa

value: uterus cancer cells


title: Itraconazole Infected 1 30h

description: Library name: Itraconazole Infected 1 30h

value: hemolymph


title: scRNA-seq-13

description:
Library name: sample77
expression matrix (txt) and original file (fastq)

value: colon

value: colon cancer cell line


title: FELINE trial, patient P079, day 14, Letrozole alone

value: Letrozole alone

tag: response


title: WM4007-1, T2, treated, sample S2


title: scRNA-seq-8

description:
Library name: sample72
expression matrix (txt) and original file (fastq)

tag: cell line


title: WM4007-1, T2, treated, sample S1


title: Itraconazole Infected 1 168h

description: Library name: Itraconazole Infected 1 168h

value: Infected


title: scRNA-seq-7

description:
Library name: sample71
expression matrix (txt) and original file (fastq)

tag: cell type

value: breast cancer cell


title: Itraconazole Control 3 72h

description: Library name: Itraconazole Control 3 72h

tag: tissue

value: Itraconazole

value: Healthy


title: FELINE trial, patient P078, day 180, Combination ribociclib

value: tumor

value: Combination ribociclib


title: WM4007-1, T1, treated, sample S2

value: WM4007 melanoma PDX

value: dabrafenib (150 mg/kg), trametinib (1.5 mg/kg)


title: WM4007-1, T1, treated, sample S1


title: scRNA-seq-6

description:
Library name: sample70
expression matrix (txt) and original file (fastq)

value: breast

tag: genotype

value: WT


title: scRNA-seq-5

description:
Library name: sample69
expression matrix (txt) and original file (fastq)


title: Itraconazole Control 3 6h

description: Library name: Itraconazole Control 3 6h

tag: infection


title: Itraconazole Control 3 30h

description: Library name: Itraconazole Control 3 30h

tag: time


title: FELINE trial, patient P082, day 0, Letrozole alone

tag: treatment

value: Progressive disease


title: WM4007-1, T0, untreated, sample S2

tag: sample


title: FELINE trial, patient P078, day 0, Combination ribociclib

value: Stable disease


title: scRNA-seq-4

description:
Library name: sample68
expression matrix (txt) and original file (fastq)


title: WM4007-1, T0, untreated, sample S1

tag: alternative id


title: FELINE trial, patient P075, day 180, Combination ribociclib

value: Sustained response


title: Itraconazole Control 3 168h

description: Library name: Itraconazole Control 3 168h

value: hemolymph


title: WM4007-1, TC, vehicle, sample S2

description: Flash frozen spatial transcriptome sequencing

tag: time point

value: TC

value: phosphate-buffered saline with 5% DMSO


title: FELINE trial, patient P079, day 0, Letrozole alone

value: Letrozole alone


title: scRNA-seq-3

description:
Library name: sample67
expression matrix (txt) and original file (fastq)


title: Itraconazole Control 2 72h

description: Library name: Itraconazole Control 2 72h


title: FELINE trial, patient P075, day 14, Combination ribociclib


title: scRNA-seq-2

description:
Library name: sample66
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P075, day 0, Combination ribociclib


title: WM4007-1, TC, vehicle, sample S1

tag: day


title: Itraconazole Control 2 6h

description: Library name: Itraconazole Control 2 6h


title: scRNA-seq-1

description:
Library name: sample65
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P074, day 180, Combination ribociclib

value: Partial response


title: FELINE trial, patient P078, day 14, Combination ribociclib


title: WM4237-1, T4, treated, sample S2

source_name: WM4237-1 melanoma PDX

tag: mouse id

value: WM4237-1 melanoma PDX


title: scBiopsy-seq-18

description:
Library name: sample64
expression matrix (txt) and original file (fastq)

value: colon

value: colon cancer cell line


title: Itraconazole Control 2 168h

description: Library name: Itraconazole Control 2 168h

value: Itraconazole

value: Healthy


title: Itraconazole Control 2 30h

description: Library name: Itraconazole Control 2 30h


title: FELINE trial, patient P074, day 0, Combination ribociclib

value: tumor

value: Combination ribociclib


title: FELINE trial, patient P074, day 14, Combination ribociclib

value: breast


title: scBiopsy-seq-17

description:
Library name: sample63
expression matrix (txt) and original file (fastq)

value: WT


title: WM4237-1, T3, treated, sample S2

tag: tumor volume_mm3

value: dabrafenib (150 mg/kg), trametinib (1.5 mg/kg)


title: Itraconazole Control 1 72h

description: Library name: Itraconazole Control 1 72h


title: WM4237-1, T4, treated, sample S1

tag: model


title: WM4237-1, T3, treated, sample S1


title: scBiopsy-seq-16

description:
Library name: sample62
expression matrix (txt) and original file (fastq)


title: Itraconazole Control 1 6h

description: Library name: Itraconazole Control 1 6h


title: FELINE trial, patient P072, day 180, Combination ribociclib

tag: patient


title: scBiopsy-seq-15

description:
Library name: sample61
expression matrix (txt) and original file (fastq)


title: Itraconazole Control 1 30h

description: Library name: Itraconazole Control 1 30h


title: WM4237-1, T2, treated, sample S2


title: FELINE trial, patient P072, day 14, Combination ribociclib

tag: days treated


title: FELINE trial, patient P072, day 0, Combination ribociclib

tag: response


title: WM4237-1, T2, treated, sample S1


title: Itraconazole Control 1 168h

description: Library name: Itraconazole Control 1 168h


title: scBiopsy-seq-13

description:
Library name: sample59
expression matrix (txt) and original file (fastq)

value: uterus

tag: cell line

value: HeLa

value: uterus cancer cells


title: WM4237-1, T1, treated, sample S2


title: Control Infected 3 72h

description: Library name: Control Infected 3 72h

value: hemolymph

value: Control

value: Infected


title: scBiopsy-seq-14

description:
Library name: sample60
expression matrix (txt) and original file (fastq)

tag: cell type


title: scBiopsy-seq-12

description:
Library name: sample58
expression matrix (txt) and original file (fastq)

tag: tissue


title: Control Infected 3 6h

description: Library name: Control Infected 3 6h


title: FELINE trial, patient P068, day 14, Combination ribociclib

value: Stable disease


title: WM4237-1, T1, treated, sample S1

description: Flash frozen spatial transcriptome sequencing

value: WM4237-1 melanoma PDX


title: FELINE trial, patient P068, day 180, Combination ribociclib


title: FELINE trial, patient P068, day 0, Combination ribociclib


title: WM4237-1, T0, untreated, sample S2


title: scBiopsy-seq-11

description:
Library name: sample57
expression matrix (txt) and original file (fastq)

tag: genotype


title: scBiopsy-seq-10

description:
Library name: sample56
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P063, day 180, Letrozole alone

value: Letrozole alone


title: Control Infected 3 168h

description: Library name: Control Infected 3 168h

tag: infection


title: WM4237-1, T0, untreated, sample S1


title: Control Infected 2 72h

description: Library name: Control Infected 2 72h

tag: time


title: scBiopsy-seq-9

description:
Library name: sample55
expression matrix (txt) and original file (fastq)

tag: treatment


title: WM4237-1, TC, vehicle, sample S2

tag: sample

value: TC

value: phosphate-buffered saline with 5% DMSO


title: scBiopsy-seq-8

description:
Library name: sample54
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P063, day 14, Letrozole alone


title: Control Infected 3 30h

description: Library name: Control Infected 3 30h


title: WM4237-1, TC, vehicle, sample S1

tag: alternative id


title: Control Infected 2 6h

description: Library name: Control Infected 2 6h


title: Heart, P1, MerTK KO, MI

city: Chicago

first: Connor

last: Lantz

state: IL

address: 303 E. Chicago Ave. Ward 4-075

institute: Northwestern University

description: 10x Genomics

data_processing:
The raw FASTQ files were first aligned to the murine transcriptome (GRCm38; mm10) using CellRanger (10X Genomics, v4.0.0).
Aligned reads were then filtered for valid barcodes and UMIs to generate gene-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files

source_name: Heart

extract_protocol:
Mice were euthanized and hearts were extensively perfused with cold PBS to removal peripheral cells. Infarcted myocardium was excised, minced with fine scissors, and digested with Collagenase Type II and DNase at 37°C for 30 minutes with gentle shaking. Larger pieces were broken down through vigorous pipetting and filtered through a 40 µm cell strainer. After RBC lysis, samples underwent dead cell removal (StemCell Technologies) by Annexin V staining. Next, samples underwent a CD45-positive selection (StemCell Technologies) to enrich cardiac leukocytes. Enriched cells and flow-through cells were both counted and recombined at a ratio of 2 CD45+ cells for every 1 non-CD45+ cell. Combined single cell suspensions were diluted to target a recovery of 5,000 cells per sample.
The single cell RNA-sequencing libraries were prepared using the 10X Genomics Single Cell 3’ Gene Expression (v3 or v3.1 chemistry) pipeline.

value: Heart

tag: age

value: MerTK KO

value: MI


title: Control Infected 2 30h

description: Library name: Control Infected 2 30h


title: FELINE trial, patient P062, day 180, Letrozole alone

value: tumor

value: breast


title: scBiopsy-seq-6

description:
Library name: sample52
expression matrix (txt) and original file (fastq)

value: breast cancer cell

value: WT


title: scBiopsy-seq-7

description:
Library name: sample53
expression matrix (txt) and original file (fastq)


title: Heart, P1, MerTK KO, Sham

description: 10x Genomics

value: Sham


title: Control Infected 2 168h

description: Library name: Control Infected 2 168h


title: Heart, 8weeks, B6, MI

description: 10x Genomics

value: 8 weeks


title: FELINE trial, patient P062, day 14, Letrozole alone


title: scBiopsy-seq-5

description:
Library name: sample51
expression matrix (txt) and original file (fastq)


title: Control Infected 1 72h

description: Library name: Control Infected 1 72h

value: hemolymph


title: FELINE trial, patient P062, day 0, Letrozole alone


title: Heart, 8weeks, B6, Sham

description: 10x Genomics


title: FELINE trial, patient P063, day 0, Letrozole alone


title: Control Infected 1 6h

description: Library name: Control Infected 1 6h

value: Control


title: scBiopsy-seq-4

description:
Library name: sample50
expression matrix (txt) and original file (fastq)


title: scBiopsy-seq-3

description:
Library name: sample49
expression matrix (txt) and original file (fastq)


title: Control Infected 1 30h

description: Library name: Control Infected 1 30h

value: Infected


title: FELINE trial, patient P060, day 14, Letrozole alone

value: Stable disease


title: scBiopsy-seq-2

description:
Library name: sample48
expression matrix (txt) and original file (fastq)


title: Control Infected 1 168h

description: Library name: Control Infected 1 168h


title: FELINE trial, patient P060, day 0, Letrozole alone


title: Heart, P1, B6, MI, Rep1

description: 10x Genomics


title: Control Healthy 3 72h

description: Library name: Control Healthy 3 72h

value: Healthy


title: scBiopsy-seq-1

description:
Library name: sample47
expression matrix (txt) and original file (fastq)


title: Heart, P1, B6, Sham

description: 10x Genomics


title: lysis-buffer5

description:
Library name: sample25
expression matrix (txt) and original file (fastq)


title: Control Healthy 3 6h

description: Library name: Control Healthy 3 6h


title: lysis-buffer4

description:
Library name: sample24
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P059, day 0, Combination ribociclib

value: Combination ribociclib

value: Partial response


title: FELINE trial, patient P059, day 14, Combination ribociclib


title: Control Healthy 3 30h

description: Library name: Control Healthy 3 30h


title: lysis-buffer3

description:
Library name: sample23
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P058, day 180, Combination ribociclib

value: Sustained response


title: FELINE trial, patient P060, day 180, Letrozole alone

value: Letrozole alone


title: Control Healthy 3 168h

description: Library name: Control Healthy 3 168h


title: lysis-buffer2

description:
Library name: sample22
expression matrix (txt) and original file (fastq)


title: Control Healthy 2 72h

description: Library name: Control Healthy 2 72h


title: lysis-buffer1

description:
Library name: sample21
expression matrix (txt) and original file (fastq)


title: Control Healthy 2 6h

description: Library name: Control Healthy 2 6h


title: FELINE trial, patient P058, day 14, Combination ribociclib


title: FELINE trial, patient P059, day 180, Combination ribociclib


title: 60s-4

description:
Library name: sample20
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P058, day 0, Combination ribociclib


title: Control Healthy 2 30h

description: Library name: Control Healthy 2 30h


title: FELINE trial, patient P053, day 180, Combination ribociclib


title: Heart, P1, B6, MI, Rep2

description: 10x Genomics

value: Heart


title: media_sham_72h_exp2_5

type: RNA

city: Bethesda

first: Simone

last: Grant

state: MD

address: 4301 Jones Bridge Rd

department: PHA

institute: Uniformed Services University

scan_protocol: Evaluation of the expression of 798 unique miRNAs was evaluated with the nCounter MAX/FLEX Analysis System using the Nanostring nCounter® Human v3 miRNA Expression Panels (NanoString Technologies, Seattle, WA, USA). Samples were prepared and ran according to the manufacturer’s instructions to determine the mean copy of each miRNA probe of interest.  Housekeeping genes for normalization included: ribosomal protein L10, beta-actin, beta-2-microglobulin, glyceraldehyde 3-phosphate dehydrogenase, and ribosomal protein L19, as well as endogenous miRNAs and positive and negative controls. Raw data was analyzed by nSolver Software version 4.0 (NanoString Technologies).

data_processing: All samples passed quality control checks and  normalization was carried out using the geometric mean of the ligation factors. miRNA expression differences in sham and impact injury at the different time points were measured using t-tests, with the Benjamini-Hochberg’s False Discovery Rate (FDR) method for multiple comparison corrections. Expression data were log2 transformed for presentation.

label: not provided

source_name: Scaffold Triculture Media

growth_protocol: 3D human tricultures were fabricated following an earlier published protocol (6, 7). Human induced neural stem cell (hiNSCs)  , human primary astrocytes (Sciencell research laboratories, cat. no. 1800), and HMC3 (human microglial) cells were allowed to reach nearly 100% confluency at the day of triculture seeding. All cell types were collected and concentrated as described in the individual culture methods. Silk scaffolds freshly coated with poly-ornithine (PLO) (Sigma, cat.no. A004C) - and laminin  were placed in 96-well plates, and a vacuum manifold was used to remove excess liquid (45). Each scaffold was seeded with a 40L cell suspension containing 2:0.5:0.1 million neurons, astrocytes, and microglia, followed by 30 minutes of incubation at 37°C to allow cell adhesion to the scaffolds. To ensure efficient cell attachment, the freshly seeded scaffolds were submerged in 150L of Neuronal media (composed of NeuroBasal medium supplemented with 2% B-27, 1% Anti-Anti, 1% Glutamax, all from Invitrogen, and 1% astrocyte growth factors, Sciencell research laboratories) and incubated overnight in a tissue culture incubator (37°C, 5% CO2 in a humidified atmosphere). The following day, the cell-seeded scaffolds were transferred to new 96-well plates to remove the unattached cells, embedded with 100L of collagen type I solution (Corning or R&D systems, 3 mg/mL with a pH adjusted to 7.0-7.2 with NaOH), and incubated for 30 minutes at 37°C to allow the collagen gel to crosslink. Neuronal media (150L) was added to all scaffolds and incubated for 24h at 37°C. The following day, 3D tricultures were moved into 48-well plates with 1 ml of Neuronal media in each well. Half the media volume was changed every fourth day until the tissues were used for experiments (6-7 weeks).

extract_protocol: miRNA isolation and purification were performed on 1 mL of triculture media collected from sham and impact samples at 6, 24, 72 hours post-injury. Samples were immediately stored in -80 °C. Once all samples were collected, samples were thawed and miRNA purification was performed using the mirVANA miRNA isolation kit (AM1560, Ambion, Life Technologies). Briefly, miRNA homogenate additive and Acid-Phenol:Chloroform was added to the media and centrifuged at 10,000 x g for 5 minutes. The upper aqueous phase containing the RNA was then collected and transferred to a new tube. Total RNA purification followed by miRNA purification was carried out using the filter cartridges from the mirVANA miRNA isolation kit per the manufacturer’s instructions. miRNA was collected by eluting the filter cartridge with 100 μl of nuclease-free water.  miRNA samples were further concentrated for Nanostring analysis using the Oligo Clean and Concentrator Kit (D4060, Zymo Research) per the manufacturer’s instructions. The eluate, containing the miRNA was collected and the concentration was measured using the Quibit miRNA assay kit (Q32880, Molecular probes, Life Technology) per manufacturer’s instructions.

treatment_protocol: 3D brain-like tissues were placed on a flat weigh boat and subjected to contusion injury using a pneumatic cylinder with a 3 mm flat tip impactor at a velocity of 6 m/s, penetration depth 0.6 mm, and a dwell time duration of 200 ms (6). Sham tissues were handled similarly to the injured tissues but without receiving the contusion injury. Following injury or sham protocol, the tissues were incubated at 37 °C in 5% CO2 in a humidified atmosphere until the indicated time marks for imaging and/or media collection for miRNA analysis.

tag: injury

value: No injury (Sham)

tag: timepoint

value: 72 Hours Post-Injury

tag: molecule type

value: miRNA


title: media_sham_72h_exp2_4


title: media_sham_72h_exp2_2


title: media_sham_72h_exp2_6


title: media_sham_72h_exp2_3


title: media_sham_72h_exp2_1


title: FELINE trial, patient P053, day 14, Combination ribociclib

value: tumor

value: breast


title: 60s-3

description:
Library name: sample19
expression matrix (txt) and original file (fastq)

value: breast cancer cell

value: WT


title: 60s-2

description:
Library name: sample18
expression matrix (txt) and original file (fastq)


title: Control Healthy 1 72h

description: Library name: Control Healthy 1 72h

value: hemolymph


title: FELINE trial, patient P053, day 0, Combination ribociclib


title: 60s-1

description:
Library name: sample17
expression matrix (txt) and original file (fastq)


title: Control Healthy 1 6h

description: Library name: Control Healthy 1 6h

value: Control


title: FELINE trial, patient P051, day 180, Combination ribociclib


title: media_sham_72h_exp1_4


title: media_sham_72h_exp1_5


title: 30s-4

description:
Library name: sample16
expression matrix (txt) and original file (fastq)


title: media_sham_72h_exp1_3


title: Control Healthy 1 30h

description: Library name: Control Healthy 1 30h


title: Itraconazole Infected 3 30h

description: Library name: Itraconazole Infected 3 30h

value: Itraconazole

value: Infected


title: media_sham_72h_exp1_6


title: 30s-3

description:
Library name: sample15
expression matrix (txt) and original file (fastq)


title: 30s-2

description:
Library name: sample14
expression matrix (txt) and original file (fastq)


title: Control Healthy 2 168h

description: Library name: Control Healthy 2 168h

value: Healthy


title: Control Healthy 1 168h

description: Library name: Control Healthy 1 168h


title: FELINE trial, patient P051, day 0, Combination ribociclib

value: Combination ribociclib


title: media_sham_72h_exp1_2


title: FELINE trial, patient P049, day 14, Combination ribociclib

value: Stable disease


title: 20s-4

description:
Library name: sample12
expression matrix (txt) and original file (fastq)


title: PCMC, vehicle, rep3

city: PITTSBURGH

first: Jishnu

last: Das

state: PA

address: 5051 CENTRE AVE

department: Department of Immunology

institute: University of Pittsburgh

data_processing:
Kallisto (v0.46.1) for transcript abundances, followed by sleuth to generate normalized counts
Assembly: GRCm38/mm10
Supplementary files format and content: abundances.h5, abundances.tsv, containing counts associated with each of the samples
Supplementary files format and content: normalized_counts.csv, tpm_names.csv, normalized_counts_names.csv, normalized_tpm_names.csv, are comma seperated values file containing counts and tpm values

source_name: peritoneal mast cell cultures

extract_protocol:
/ix/djishnu/Swapnil/kaplanAnalysis
mRNA libraries were generated using Illumina Truseq Stranded mRNA Library Prep kit

value: peritoneal mast cell cultures


title: FELINE trial, patient P049, day 180, Combination ribociclib


title: PCMC, vehicle, rep4


title: FELINE trial, patient P049, day 0, Combination ribociclib


title: PCMC, vehicle, rep2


title: media_CCI_72h_exp2_6

value: Controlled Cortical Impact (CCI)


title: PCMC, vehicle, rep1


title: media_CCI_72h_exp2_4


title: media_CCI_72h_exp2_5


title: FELINE trial, patient P048, day 180, Combination ribociclib


title: 20s-3

description:
Library name: sample11
expression matrix (txt) and original file (fastq)


title: PCMC, 6 mM glutamate, rep4


title: FELINE trial, patient P051, day 14, Combination ribociclib

value: Partial response


title: 20s-2

description:
Library name: sample10
expression matrix (txt) and original file (fastq)


title: FELINE trial, patient P048, day 14, Combination ribociclib


title: media_CCI_72h_exp2_3


title: PCMC, 6 mM glutamate, rep3


title: FELINE trial, patient P048, day 0, Combination ribociclib


title: media_CCI_72h_exp2_2


title: media_sham_72h_exp1_1

value: No injury (Sham)


title: 10s-4

description:
Library name: sample8
expression matrix (txt) and original file (fastq)


title: 30s-1

description:
Library name: sample13
expression matrix (txt) and original file (fastq)


title: 10s-3

description:
Library name: sample7
expression matrix (txt) and original file (fastq)


title: PCMC, 6 mM glutamate, rep1


title: Hi-C_PS_A-myb-KO_rep2

city: Davis

first: Satoshi

last: Namekawa

address: One Shields Avenue

department: Department of Molecular and Cellular Biology

institute: University of California, Davis

data_processing:
Bases were called using Illumina's HiSeq Control Software.
Paired-end fastq files of Hi-C libraries were aligned to the Mus musculus mm10 genome via BWA (version 0.7.17) and processed using the Juicer package.
Matrices were balanced using cooler package (version 0.8.11).
Interaction frequency heat maps were generated and visualized using the HiCExplorer (version 3.6).
Chromatin loops were called using the HiCExplorer.
Topologically Associated Domains were detected from cool files using the HiCExplorer.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files specify each Hi-C contacts with duplicates removed.
Supplementary files format and content: .hic files contain contact matrices generated from unfiltered or >= MAPQ score 30 reads.

source_name: testis

extract_protocol:
Germ cells were isolated from mouse testis by STA-PUT method or MACS.
Hi-C library construction was performed using the Arima Hi-C kit according to the manufacturer’s instructions.

value: testis

tag: strain

value: adult

value: Pachyten spermatocytes


title: PCMC, 6 mM glutamate, rep2


title: 10s-2

description:
Library name: sample6
expression matrix (txt) and original file (fastq)

value: breast


title: Hi-C_PS_A-myb-KO_rep1


title: media_CCI_72h_exp2_1

value: 72 Hours Post-Injury

value: miRNA


title: PCMC, 1600 nM SYM2081, rep4


title: Hi-C_RS_Scml2-KO_rep2

value: Round spermatides


title: PCMC, 1600 nM SYM2081, rep3


title: 10s-1

description:
Library name: sample5
expression matrix (txt) and original file (fastq)

value: breast cancer cell

value: WT


title: Hi-C_RS_Scml2-KO_rep1


title: PCMC, 1600 nM SYM2081, rep2


title: media_CCI_72h_exp1_4


title: Hi-C_PS_Scml2-KO_rep2


title: 5s-4

description:
Library name: sample4
expression matrix (txt) and original file (fastq)


title: 5s-3

description:
Library name: sample3
expression matrix (txt) and original file (fastq)


title: 20s-1

description:
Library name: sample9
expression matrix (txt) and original file (fastq)


title: media_CCI_72h_exp1_3


title: PCMC, 1600 nM SYM2081, rep1


title: media_CCI_72h_exp1_6


title: media_CCI_72h_exp1_2


title: Hi-C_PS_Scml2-KO_rep1


title: Hi-C_RS_WT_rep2

value: wild type


title: smRNA_Control_D1Kyoto_TM6C_rep 3

city: Zurich

first: Madhav

last: Jagannathan

address: Otto Stern-Weg 3

department: Biology

country: Switzerland

institute: ETH Zurich

description: Library name: D1-TM6_sample3

library_source: other

data_processing:
The resulting raw reads were cleaned by removing adaptor sequences, low-quality-end trimming, and removal of low-quality reads using BBTools v 38.18 (Bushnell, B. BBMap. Available from: https://sourceforge.net/projects/bbmap/). The exact commands used for quality control can be found on the Methods in Microbiomics webpage (Sunagawa, S. Data Preprocessing — Methods in Microbiomics 0.0.1 documentation. Available from: https://methods-in-microbiomics.readthedocs.io/en/latest/preprocessing/preprocessing.html). The quality-controlled reads were aligned against BDGP6.32 using STAR aligner[90]. Transcript and transposon abundances were quantified using TetranscriptsDifferential gene expression analysis was performed using Bioconductor R package DESeq2 v 1.37.4. For small RNA-seq: Raw reads were trimmed for linker sequences, barcodes and the 4/6 random nucleotides before mapping to the D. melanogaster genome (dm6), using Bowtie (version.1.3.0, settings: -f -v 3 -a --best --strata --sam) with 0 mismatches allowed. Genome-mapping reads were crossreferenced with Flybase genome annotations (r6.40) using BEDTools to allow the removal of reads mapping to rRNA, tRNA, snRNA, snoRNA loci, and the mitochondrial genome. For TE mappings, all genome mappers were used allowing no mismatches. Reads mapping to multiple elements were assigned to the best match. Reads mapping equally well to multiple positions were randomly distributed. Libraries were normalized to 1 million sequenced microRNA reads. For calculation of piRNAs mapping to TEs, only antisense piRNAs were considered, and counts were normalized to TE length.
Assembly: For total RNA -seq: r6.40, For small RNA-seq: Dm6
Supplementary files format and content: For differential gene expression: tab delimited file containing raw reads for D1 mutants and controls  for differential gene expresson. For small RNA-seq: Bigwig (bw) files for three replicates. Each replicate has 4 files - antisense, sense, uniq_antisense, uniq_sense

molecule: other

organism: Drosophila melanogaster

source_name: Ovaries

growth_protocol: Drosophila melanogatser females (4 day old) of the correct genotypes: D1 mutant and control were selected for RNA extraction.

extract_protocol:
RNA-seq differential expression: rRNA-depleted libraries were prepared and sequenced by Novogene on a NovaSeq 6000 (Illumina) using paired-end 150 bp sequencing. For small RNA-seq:~5 ovaries were dissected per genotype and subjected to small RNA extraction as described in Baumgartner et al 2022
For RNA-seq differential expression: total mRNA  (rRNA -depleted) libraries. For Small RNA seq: Small RNA cloning was performed as previously described in Baumgartner et al 2022

treatment_protocol: ~5 ovaries were dissected per genotype

value: Ovaries

value: germline cell

value: Control


title: media_CCI_72h_exp1_1


title: media_CCI_72h_exp1_5


title: smRNA_Control_D1Kyoto_TM6C_rep 1

description: Library name: D1-TM6_sample1


title: media_sham_24h_exp2_6

value: 24 Hours Post-Injury


title: Hi-C_RS_WT_rep1


title: LX-2 cells, TGF-β (T)

city: JiNan

first: Tao

last: Li

address: No.44, West Wenhua Road

institute: Shandong University

description:
Library name: TGF-β (T)
DMSO_TGF_1

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRCh38.111 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Assembly: GRCh38.111
Supplementary files format and content: Raw_gene_counts_matrix.txt

growth_protocol: LX-2 cells were cultured in DMEM medium (C11995500, Gibco) containing 10% heat-inactivated fetal bovine serum (FBS, Cellmax), 100 units/mL penicillin, and 100 μg/mL streptomycin (Thermo Scientific, Cat. No. 15140122). Cells were cultured in a humidified 37 °C incubator with 5% CO2.

extract_protocol:
According to the manufacturer’s instruction, RNA of cells was isolated using AG RNAex Pro Reagent （AG21102， Accurate Biology）.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3 × 105 LX-2 cells were evenly distributed into 6-well plates and incubated overnight at 37 °C in 5% CO2. Upon starvation for 24 h in DMEM containing 0.5% FBS, the cells were treated only with TGF-β (20 ng/mL, HZ-1011, Proteintech) or cotreated with TGF-β (20 ng/mL) and indicated compounds (5 μM) for 24 h. After incubation, the cells were collected for RNA sequencing.


title: LX-2 cells, T+RVX-208

description:
Library name: T+RVX-208
RVX_208_TGF_2


title: LX-2 cells, T+BDS4

description:
Library name: T+BDS4
TGF_9d_1


title: Hi-C_PS_WT_rep1


title: 5s_1

last: Xu

address: 422, Siming South Road

institute: Xiamen University

description:
Library name: sample1
expression matrix (txt) and original file (fastq)

data_processing:
The source code for the analysis of scBiopsy-seq is available on github (https://github.com/linl-linl/scBiopsy-seq).
Assembly: GRCh38,GRCh38.105, GRCm38 and GRCm38.102
Supplementary files format and content: matrix files

extract_protocol:
The capillary tip was filled with 1.5 μL of mixed solution (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP (AD101–12, TransGen Biotech, Beijing, China), 0.4 U·μL−1 Murine RNase Inhibitor (GMP4102PA-01, Vazyme Biotech Co., Ltd., Nanjing, China)), and then connected to the work electrode of the ultra-micro extraction instrument (Rayme Biotechnology Co., Ltd., Jiangsu, China). The counter electrode and the reference electrode were immersed in the culture medium within the confocal dish. The cells to be extracted were visualized by microscope and the preloaded capillary was gradually moved downward until it touched the cytoplasm of the selected cell. The tip of the capillary was then inserted into the cytoplasm, with a deformation observed in the selected cell. By setting the applied voltages and the duration of current application, a precisely controlled volume was extracted from the cell. After that, the capillary was retracted out of the cell, taken out of the extraction instrument and placed at -80°C for RNA storage.
Once it was required to undergo the RNA library construction, the capillary was connected to the work electrode again. The cellular contents within the capillary were injected into the top plate of the DMF device, enabling the subsequent RNA library processing on the DMF system. The lysis buffer (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP, 0.4 U·μL−1 Murine RNase Inhibitor and 0.2% Triton-X-100(A110694, Sangon Biotech, Shanghai, China) was introduced and mixed with the cellular contents at 72°C for 3 minutes for complete RNA release. Then the reverse transcription (RT) mix (1.7 μM biotinylated-TSO oligo, 5 × HiScript II RT buffer (Vazyme Biotech Co., Ltd., Nanjing, China), 1.7 U·μL−1 Murine RNase Inhibitor, 19 U·μL−1 HiScript II Reverse Transcriptase (R201, Vazyme Biotech Co., Ltd., Nanjing, China) and 0.05% Pluronic F68 (24040032, ThermoFisher, America)) was introduced to initiate the RT reaction at 42°C for 90 minutes, which was stopped by heat at 70°C for 15 min. After that, the PCR mix (2 × KAPA HiFi HotStart ReadyMix (KK2602, KAPA, America), 0.06 μM Biotinylated-ISPCR oligo and 0.05% Pluronic F68) was introduced to amplify the cDNAs (95°C 3 minutes, 25 cycles of 98°C 30 s, 65°C 45 s and 72°C 6 minutes, followed by a final step at 72˚C for 5 min). The products were recovered from the DMF device into a 200-μL eppendorf tube, purified with 0.6 × DNA clean beads (Vazyme Biotech Co., Ltd., Nanjing, China) and quantified by qubit 3.0. Then 1 ng of the products were utilized and processed by sequencing-ready library construction kits (TD503, Vazyme). The library was purified twice with 0.6 × DNA clean beads (N411, Vazyme Biotech Co., Ltd., Nanjing, China) and sequenced by Novaseq500 according to the manufacturer’s instructions.


title: smRNA_D1_Mutant_D1 Kyoto_D1Bsc666_rep 2

description: Library name: D1-BSC66_sample2

value: D1 mutant


title: Hi-C_KIT_WT_rep2

value: 6-8 days

value: c-Kit+ spermatogonia


title: Hi-C_KIT_WT_rep1

value: testis


title: LX-2 cells, Control

description:
Library name: Control
Control_3


title: smRNA_D1_Mutant_D1 Kyoto_D1Bsc666_rep 1

description: Library name: D1-BSC66_sample1


title: ASCs from donor 6-passage 10

city: Tokyo

first: Toshiya

last: Tsubaki

address: 7-3-1 Hongo, Bunkyo-ku

institute: The University of Tokyo

description: Sample 15

data_processing:
The raw data were mapped to a reference genome from GENCODE (FASTA file: GRCh38.primary_assembly.genome.fa, GTF file: gencode.v41.annotation.gtf) using STAR (ver. 2.7.10a) after adapter sequences were removed using fastp (ver. 0.20.1). Expression levels were calculated using RSEM (ver. 1.3.3).
Assembly: GENCODE (FASTA file: GRCh38.primary_assembly.genome.fa, GTF file: gencode.v41.annotation.gtf)
Supplementary files format and content: tab-delimited text file includes rae read counts for each Sample

source_name: adipose

growth_protocol: ASCs were cultured in MSC NutriStem® XF Basal Medium (NutriStem, Sartorius Stedim Biotech, Lower Saxony, Germany) supplemented with 2% fetal bovine serum (FBS) and 0.1% penicillin-streptomycin at 37°C in an incubator with humidified 5% CO2.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s procedure.
Library preparation was performed using the Strand-specific library preparation method (dUTP method).

value: adipose

value: mesenchymal stem cells


title: media_sham_24h_exp2_2

value: No injury (Sham)


title: media_sham_24h_exp2_3


title: 5s-2

city: Xiamen

first: Xing

description:
Library name: sample2
expression matrix (txt) and original file (fastq)

value: breast


title: smRNA_Control_D1Kyoto_TM6C_rep 2

description: Library name: D1-TM6_sample2


title: Hi-C_THY1_WT_rep2

value: Thy1+ spermatogonia


title: ASCs from donor 6-passage 5

description: Sample 14


title: Control_D1Kyoto_TM6C_rep 2

description: Library name: C2_EKRN230063491-1A_HVVNJDSX7


title: Hi-C_THY1_WT_rep1


title: media_sham_24h_exp2_1

value: miRNA


title: Control_D1Kyoto_TM6C_rep 1

description: Library name: C1_EKRN230063490-1A_HVVNJDSX7


title: ASCs from donor 5-passage 10

description: Sample 13


title: smRNA_D1_Mutant_D1 Kyoto_D1Bsc666_rep 3

description: Library name: D1-BSC66_sample3


title: media_sham_24h_exp2_5


title: media_sham_24h_exp1_6


title: media_sham_24h_exp1_5


title: ASCs from donor 5-passage 5

description: Sample 12


title: D1_Mutant_D1Kyoto_D1Bsc666_rep 2

description: Library name: B2_EKRN230063488-1A_HVVNJDSX7


title: ASCs from donor 4-passage 10

description: Sample 11


title: GC, replicated 2, stRNA-seq

city: Nanjing

first: Zhennan

last: Tao

address: Nanjing

department: Department of Neurosurgery

institute: Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School

description:
Sample_2_stRNA-seq
Fresh frozen Spatial transcriptome sequencing

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: GBM centre

growth_protocol: GS2 and GC2 tumor pieces were implanted into the 4th mammary fat pads

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction

treatment_protocol: Once the implanted tumors were established, placebo or E2 (1 mg) pellet were implanted subcutaneously. To ensure that there was enough tumor mass remaining for the analysis, GS3 tumors were implanted in intact mice and treated with E2 only for 1 week, or with placebo for 2 weeks, while SC31 tumors were implanted in ovariectomized mice and were treated for 6 weeks. After the treatment periods, tumor samples were collected, and spatial transcriptomics was performed.

value: GBM centre

value: Glioma cells


title: GS, replicated 2, stRNA-seq

description:
Sample_1_stRNA-seq
Fresh frozen Spatial transcriptome sequencing

source_name: GBM surround

value: GBM surround


title: Hi-C_PS_WT_rep2

value: adult

value: Pachyten spermatocytes

value: wild type


title: media_sham_24h_exp1_4

value: 24 Hours Post-Injury


title: Whole rosette tissue, ref4-3, 21 day, RNA, rep3

city: West Lafayette

first: Joe

last: Ogas

state: Indiana

address: 175 S. University Street

department: Department of Biochemistry

institute: Purdue University

data_processing:
Short reads were trimmed for adapter, polyG and low quality sequences using fastp (v 0.23.2) (parameters: -g -x -q 5 -u 50 -n 15)
Trimmed reads were mapped to the TAIR10 reference gemome assembly using hisat2 (v 2.2.1)
The mapped SAM files were converted, sorted and indexed to BAM files using SAMtools (v 1.17)
The gene feature was counted in DESeq2 and limma packages in Bioconductor
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: Whole rosette tissue

growth_protocol: Plants used for RNA-sequencing were sown directly on soil pots. Seeds were cold-treated in dark at 4°C for three days before moving to a Percival AR75 growth chamber. Plants were grown under 16-hour light/8-hour dark photoperiod cycle at 150μE light (Phillip F32T8/TL941) with far-red supplements (soft white 25W incandescent light) at 22°C prior to sample collection. Samples for the following analyses were harvested 6 hours after the light was turned on.

extract_protocol:
Total RNA was extracted from 21-day-old shoot tissue of 5 plants that had not bolted and that were randomly selected from 5 individual pots using a RNeasy Plant Mini Kit (Qiagen; catalog no. 74904) following with the DNase I digestion and RNA clean up included in an RNA Clean & Concentrator kit (Zymo Research; catalog no. 1014). Three biological replicates were collected for each indicated genotype.
1 μg of total RNA of each sample was used for cDNA library construction. cDNA library construction was performed using an NEBNextUltraII Directional RNA Library Prep C (NEB; catalog no. E7760S) combined with an NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; catalog no. E7490S) according to the manufacturer’s manual.

value: Whole rosette tissue

tag: ecotype

tag: development stage


title: media_sham_24h_exp1_3


title: Whole rosette tissue, ref4-3, 21 day, RNA, rep2


title: Whole rosette tissue, ref4-3, 21 day, RNA, rep1


title: NOVA1-CLIP, wt/wt, P21, cerebellum, rep3

data_processing:
collapsing of exact sequences
stripping of degenerate linker (5nt; ends with a G)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambigous mapping on mm10)
collapsing of PCR duplicates
clustering of unique reads
Assembly: mm10
Supplementary files format and content: bedgraph

extract_protocol:
Brain tissue was UV irradiated and subjected to NOVA1-CLIP
Partial RNAse digestion, RNA linker ligation and PCR amplification. NOVA1 bound fragments were ligated to a degenerate 5'linker and a 3'linker.

tag: strain background

value: brain

tag: tissue compartment

value: cerebellum

tag: developmental stage


title: ASCs from donor 3-passage 15

description: Sample 9

tag: tissue

tag: cell type


title: ASCs from donor 3-passage 10

description: Sample 8


title: media_sham_24h_exp1_1


title: Whole rosette tissue, wild type, 21 day, RNA, rep3

tag: genotype

value: Wild type


title: media_CCI_24h_exp2_6

value: Controlled Cortical Impact (CCI)


title: ASCs from donor 4-passage 5

description: Sample 10

value: adipose

value: mesenchymal stem cells


title: D1_Mutant_D1Kyoto_D1Bsc666_rep 3

description: Library name: B3_EKRN230063489-1A_HVVNJDSX7

value: Ovaries

value: germline cell

value: D1 mutant


title: ASCs from donor 2-passage 15

description: Sample 6


title: media_CCI_24h_exp2_4

value: miRNA


title: media_CCI_24h_exp2_5


title: NOVA1-CLIP, hu/hu, P21, cerebellum, rep3


title: Whole rosette tissue, wild type, 21 day, RNA, rep1


title: NOVA1-CLIP, hu/hu, P21, cerebellum, rep2


title: media_sham_24h_exp1_2

value: No injury (Sham)


title: Whole rosette tissue, ref4-3, 21 day, H3K27me3 ChIP, rep2

description:
H3K27me3_ref4_merge_islands.bed
ChIP-seq_H3K27me3_genes_islands_overlap.bed
ChIP-seq_H3K27me3_counts_matrix.txt

data_processing:
Short reads were trimmed for adapter, polyG and low quality sequences using fastp (v 0.23.2) (parameters: -g -x -q 5 -u 50 -n 15)
Trimmed reads were mapped to the TAIR10 reference gemome assembly using Bowtie2 (v 2.2.1) in very-sensitive-end-to-end mode
The mapped SAM files were converted, sorted and indexed to BAM files using SAMtools (v 1.17)
The reads of individual biological replicate were merged into one BAM file using SAMtools (v 1.17)
The BAM files of individual replicate and the merged sample were converted to paired-end BED files using BEDTools
The enriched peaks were called by using epic2 (parameters: egf = 0.85, bin = 200, g = 1, and fdr = 0.05)
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample of H2A.Z-marked genes
Supplementary files format and content: tab-delimited text file includes raw counts for each sample of H3K27me3-marked genes
Supplementary files format and content: BED files includes the genomic regions as coordinates for H3K27me3 enriched regions
Supplementary files format and content: BED files includes the genomic regions as coordinates for H2A.Z enriched regions
Supplementary files format and content: BED files includes the genomic regions as coordinates and associated annotations for overlaps between genes and H3K27me3 enriched regions
Supplementary files format and content: BED files includes the genomic regions as coordinates and associated annotations for overlaps between genes and H2A.Z enriched regions

source_name: Whole Rosette tissue

growth_protocol: Plants used for ChIP-sequencing were sown directly on soil pots. Seeds were cold-treated in dark at 4°C for three days before moving to a Percival AR75 growth chamber. Plants were grown under 16-hour light/8-hour dark photoperiod cycle at 150μE light (Phillip F32T8/TL941) with far-red supplements (soft white 25W incandescent light) at 22°C prior to sample collection. Samples for the following analyses were harvested 6 hours after the light was turned on.

extract_protocol:
4 g of 21-day-old whole rosette tissue were collected for each biological replicate. Nuclear lysis buffer was replaced with 1.7 mL of ChIP Lysis Buffer (50 mM HEPES-NaOH (pH =7.4), 16.7 mM Tris-HCl (pH = 8), 1 mM EDTA (pH = 8), 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 0.1% Sodium deoxycholate, 1 cOmpleteTM mini tablet / 10 mL solution). The total chromatin samples were sonicated using Bioruptor Pico. Sheared chromatin samples were stored at -80 °C overnight prior to the immunoprecipitation. The following antibodies were used in the analysis: Anti-H3 (ab1791, Abcam) (1:200 dilution), Anti-H3K27me3 (07-449, Millipore) (1:100 dilution), and Anti-H2A.Z (1.5 µg for a 500 µL IP sample) (Deal et al., 2007). The QIAquick MinElute PCR purification kit was replaced with ChIP DNA Clean & Concentrator purification kit (D5205, Zymo research) for elution of the ChIP DNA. The eluted ChIP DNA was quantified us a Qubit 2.0 Fluorometer and used immediately in library construction.
0.5 ng eluted ChIP DNA was used for each library construction. ChIP DNA libraries were constructed using a NEBNext Ultra II DNA Library Prep Kit (NEB; catalog no. E7645L) according to the manufacturer’s manual. Illumina Multiplexing adapter was used for indexing. Pair-ended,150-bp sequencing was performed using an Illumina Novaseq S4 lane.

value: Whole Rosette tissue


title: ASCs from donor 2-passage 10

description: Sample 5


title: NOVA1-CLIP, wt/wt, P21, cerebellum, rep2

source_name: brain


title: media_CCI_24h_exp2_2


title: media_CCI_24h_exp2_3


title: ASCs from donor 2-passage 5

description: Sample 4


title: NOVA1-CLIP, wt/wt, P21, midbrain, rep3

value: midbrain


title: ASCs from donor 3-passage 5

description: Sample 7


title: ASCs from donor 1-passage 15

description: Sample 3


title: Whole rosette tissue, ref4-3, 21 day, H2A.Z, ChIP, rep2

description:
H2AZ_ref4_merge_islands.bed
ChIP-seq_H2AZ_genes_islands_overlap.bed
ChIP-seq_H2AZ_counts_matrix.txt


title: Whole rosette tissue, wild type, 21 day, RNA, rep2


title: NOVA1-CLIP, wt/wt, P21, midbrain, rep2


title: ASCs from donor 1-passage 10

description: Sample 2


title: Whole rosette tissue, ref4-3, 21 day, H2A.Z, ChIP, rep1


title: ASCs from donor 1-passage 5

description: Sample 1


title: NOVA1-CLIP, wt/wt, P21, midbrain, rep1


title: Whole rosette tissue, ref4-3, 21 day, input, ChIP, rep2


title: NOVA1-CLIP, hu/hu, P21, cerebellum, rep1


title: Control_D1Kyoto_TM6C_rep 3

description: Library name: C3_EKRN230063492-1A_HVVNJDSX7

value: Control


title: GC, replicated 3, scRNA-seq

description: 10X Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: GBM centre

value: Glioma cells


title: Whole rosette tissue, ref4-3, 21 day, input, ChIP, rep1


title: NOVA1-CLIP, hu/hu, P21, midbrain, rep3


title: media_CCI_24h_exp1_4

value: 24 Hours Post-Injury


title: media_CCI_24h_exp2_1


title: Whole rosette tissue, ref4-3, 21 day, H3K27me3 ChIP, rep1


title: NOVA1-CLIP, hu/hu, P21, midbrain, rep2

value: brain


title: media_CCI_24h_exp1_3


title: media_CCI_24h_exp1_6


title: Whole rosette tissue, wild type, 21 day, H3K27me3 ChIP, rep1

description:
H3K27me3_WT_merge_islands.bed
ChIP-seq_H3K27me3_genes_islands_overlap.bed
ChIP-seq_H3K27me3_counts_matrix.txt


title: NOVA1-CLIP, hu/hu, P21, midbrain, rep1


title: Whole rosette tissue, wild type, 21 day, H3K27me3 ChIP, rep2


title: NOVA1-CLIP, wt/wt, P21, cortex, rep3

value: cortex


title: media_CCI_24h_exp1_2


title: media_CCI_24h_exp1_5


title: Whole rosette tissue, wild type, 21 day, H2A.Z, ChIP, rep2

description:
H2AZ_WT_merge_islands.bed
ChIP-seq_H2AZ_genes_islands_overlap.bed
ChIP-seq_H2AZ_counts_matrix.txt

value: Wild type


title: NOVA1-CLIP, wt/wt, P21, cerebellum, rep1

value: cerebellum


title: media_CCI_24h_exp1_1

value: Controlled Cortical Impact (CCI)


title: NOVA1-CLIP, wt/wt, P21, cortex, rep2


title: GC, replicate 1, scRNA-seq

description: 10X Genomics


title: media_sham_6h_exp2_6

value: 6 Hours Post-Injury


title: Whole rosette tissue, wild type, 21 day, H2A.Z, ChIP, rep1


title: NOVA1-CLIP, wt/wt, P21, cortex, rep1


title: GS, replicate 1, scRNA-seq

description: 10X Genomics

value: GBM surround


title: GS, replicated 3, scRNA-seq

description: 10X Genomics


title: D1_Mutant_D1Kyoto_D1Bsc666_rep 1

description: Library name: B1_EKRN230063487-1A_HVVNJDSX7

value: Ovaries

value: germline cell


title: Whole rosette tissue, wild type, 21 day, input, ChIP, rep1


title: NOVA1-CLIP, hu/hu, P21, cortex, rep3


title: media_sham_6h_exp2_5

value: miRNA


title: GC, replicated 2, scRNA-seq

description: 10X Genomics


title: L-shFgf13+HG-PA+siPrkn rep3

city: wenzhou

first: jia

last: sun

address: wenzhou medical university

institute: wenzhou medical university

data_processing:
HISAT2 software (https://daehwankimlab.github.io/hisat2/, version: hisat2-2.0.4) was used to map reads to the genome (Homo sapiens Ensembl v101)
The mapped reads of each sample were assembled using StringTie.
 Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HRGEC

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HRGEC

value: Human renal glomerular endothelial cells

value: HG-PA-treated Fgf13 KD HRGEC transfected with siPrkn


title: L-shFgf13+HG-PA+siPrkn rep2

tag: treatment


title: NOVA1-CLIP, hu/hu, P21, cortex, rep2


title: GS, replicated 2, scRNA-seq

description: 10X Genomics


title: L-shFgf13+HG-PA+siPrkn rep1


title: media_sham_6h_exp2_3

value: No injury (Sham)