title: RSB163-370 [Cilengitide]

value: Cilengitide


title: T. ni, fat body, TSA, rep1 [22044R-01-07_S77]

status: Public on Oct 19 2023

type: SRA

city: Carlisle

first: Dana

middle: J.

last: Somers

state: PA

department: Biology

country: USA

institute: Dickinson College

description:
Tni_raw_counts.txt
Tni_normalized_counts.txt

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence with Trimmomatic (v0.39) using the following parameters: LEADING:5, TRAILING:5, MAXINFO:36:0.2, MINLEN:50.
T. ni reads were aligned to the T. ni Cornell-1 isolate genome (obtained from the T. ni Genome Database on 2022-05-25) and S. exigua reads were aligned to the S. exigua TB_SE_WUR_2020 isolate genome (WGS JACEFF01 obtained from the NCBI Genome Database on 2022-06-06) using HISAT2 (v2.2.1) with the default parameters.
featureCounts implemented in the Rsubread package (v2.12.2) was used to calculate read counts for each gene using the appropriate species-specific annotations.
Low-count genes (mean counts-per-million [CPM] across all samples > 10) were filtered and read counts were normalized using the trimmed mean of M-values (TMM) normalization method.
Assembly: T. ni Cornell-1 isolate (tn1)
Assembly: S. exigua TB_SE_WUR_2020 isolate (GCA_022117675.1)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TMM-normalized CPM values for each sample

molecule: total RNA

organism: Trichoplusia ni

source_name: fat body

growth_protocol: Larvae were raised in 5 ml wells on a standard artificial diet (AD) appropriate for each species with antibiotics at 25°C and 50% humidity. Larvae developed in individual wells and were collected at approximately day 10.

extract_protocol:
Larvae from each experiment group were dissected to isolate fat body tissue. To obtain sufficient tissue, fat bodies from 3 – 5 individual larvae were pooled per replicate.
Total RNA was extracted from the tissue twice using Buffer A (50 mM sodium acetate pH 5.2, 10 mM EDTA, 1 % SDS) saturated phenol heated to 65 °C, followed by phenol/chloroform (1:1) extraction. Extracts were ethanol precipitated, resuspended in ddH2O and ethanol precipitated again.
Poly(A) selection was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) following the manufacturer’s protocols. RNA-seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocols.

treatment_protocol: For dietary treatments, the HDAC inhibitors SFN (70 mM) and TSA (330 µM) were solubilized in ethanol and aliquots were added to each well to cover the surface of the AD. The EtOH was fully evaporated for 8h at 20°C.

tag: tissue

value: fat body

tag: genotype

value: WT

tag: treatment

value: TSA


title: T. ni, fat body, TSA, rep4 [22044R-02-03_S30]


title: T. ni, fat body, TSA, rep2 [22044R-01-08_S78]


title: RSB163-114 [Choline Chloride]

city: Boston

first: Zhiyun

last: Wei

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
FastQ files were trimmed of adapter sequences using Cutadapt with the following parameters: cutadapt -u 1 -a TGGAATTCTCGGGTGCCAAGG -m 15.
Trimmed reads were aligned to miRBase 21 (hg38) by using Bowtie.
Assembly: hg38
Supplementary files format and content: tab-delimited Excel files include read count for each Sample

organism: Homo sapiens

growth_protocol: Induced pluripotent stem cell (iPSC) lines were retrieved and differentiated into neurons with NGN2 expression, as previously reported. Briefly, iPSCs were plated in mTeSR1 media at a density of 9.5x104 cells/cm2 on Matrigel (Corning #354234)-coated plates. Cells were then transduced with the following virus: pTet-O-NGN2-puro (Addgene #52047): 0.1 μL per 5x104 cells; Tet-O-FUW-eGFP (Addgene #30130): 0.05μL per 5x104 cells; Fudelta GW-rtTA (Addgene #19780): 0.11 μL per 5x104 cells. Transduced cells were dissociated with Accutase (StemCell Technologies) and plated onto Matrigel-coated plates in mTeSR1 (StemCell Technologies) at 5x104/cm2 (Day 0). On day 1, media was changed to KSR media (Knockout DMEM, 15% KOSR, 1x MEM-NEAA, 55 μM beta-mercaptoethanol, 1x GlutaMAX; Gibco) with doxycycline (2 μg/ml, Sigma-Aldrich). Doxycyline was maintained in the media for the remainder of the differentiation. On day 2, the media was changed to 1:1 KSR: N2B media with puromycin (5 μg/ml, Gibco), where N2B was composed of DMEM/F12, 1x GlutaMAX, 1x N2 supplement B (StemCell Technologies) and 0.3% dextrose (Sigma-Aldrich). Puromycin was maintained in the media throughout the differentiation. On day 3, the media was changed to N2B media + 1:100 B-27 supplement (GIBCO) and puromycin (10 μg/ml). From day 4 on, cells were cultured in NBM media (Neurobasal medium, 0.5x MEM-NEAA, 1x GlutaMAX, 0.3% dextrose) + 1:50 B-27 + BDNF, GDNF, CNTF (10 ng/ml each, Peprotech). After day 4, half of the media was replaced by fresh media twice per week. Cells were stocked on day 4 at 1~2x106 cells in 200 μL freezing media (50% day 4 media + 40% FBS + 10% DMSO) per cryovial in -80oC overnight, followed by liquid nitrogen storage. Twenty-five 96-well plates (Corning) were coated with Matrigel solution (0.2 mg/mL in DMEM/F12) at 60 μL per well for 1.5 hours at 37oC. Then, the Matrigel solution was completely removed, and 100 μL PBS (Gibco) was added per well using electronic 12-channel pipettes in speed 3 (e12c-pip; Eppendorf). The plates were temporality incubated at 37oC. Frozen day 4 iPSC-iNs were thawed in 500 μL pre-warmed resuspension media per vial, which was composed of NBM, 1:100 B27, and 1:1000 ROCKi (StemCell Technologies), and were kept in a warm metal bath to facilitate the thawing. Multiple vials were pooled into one 50 mL conical tube, then pre-warmed resuspension media were added drop-wisely to reach the volume of 40 mL. After gently mixing by reverting the tube, viable cell concentration was counted with trypan blue (Bio-Rad). The cells were spun down (220 g, 5 min, room temperature) and resuspended in day 4 media at 1x105 cells/mL. Then, PBS was completely removed from the plates, and 100 μL cell suspension was added per well, using e12c-pip at speed 3. The cells were incubated at 37oC after shaking the plates for even distribution (day 4). To reduce evaporation during incubation, plates were kept in plastic containers lined with sterile wet paper towels. On day 5, an additional 100 μL pre-warmed day 4 medium was added per well using e12c-pip in speed 1. On days 7/10/14/18, 95 μL conditioned medium was removed, and 100 μL pre-warmed day 4 medium was added per well, both using e12c-pip.

extract_protocol:
On day 20, four 10x photos were taken per well automatically using the ImageXpress Micro Confocal microscope (Molecular Devices). Then, the media in the plates was removed with approximately 20 μL media left, using a 24-channel stainless steel manifold (Drummond #3-000-101) linked with a vacuum at a low speed. With the help of Multidrop™ Combi Reagent Dispenser (Thermo Scientific) and the standard cassette (speed: low), 250 μL ice-cold DPBS (Wisent) was added per well. The DPBS was removed with approximately 20 μL liquid left, using another 24-channel stainless steel manifold linked with the vacuum at a low speed. The residual DPBS was completely removed using a mechanic 12-channel pipette. Next, 45 μL lysing solution was added per well using another Multidrop™ Combi Reagent Dispenser with the small cassette (speed: low), where the lysing solution is composed of single-cell lysis buffer (Takara #635013): 1x RNase Inhibitor Murine (NEB): nuclease-free water (Exiqon) = 19:1:190. Thorough lysis was achieved by shaking the plates on a shaker for 5 min at room temperature. The lysis samples were transferred from four 96-well plates to each 384-square-well plate using the 96-well module-coupled VPrep liquid handler (Agilent) with 30 μL tips (twice without changing tips). After sealing, the 384-square-well plates were spun down at 4000 rpm for 5 min, and 10 μL supernatant was aliquoted to a 384-well plate (Eppendorf) using the 384-well module-coupled VPrep liquid handler. The plates were finally sealed with the PlateLoc Heat Sealer (Agilent) and stored at -20oC.
To avoid RNA purification, we used RealSeq-T technology (RealSeq Biosciences) following manufacturer recommendations. In summary, cell lysates were incubated at 70C for 5 minutes on RealSeq hybridization buffer (100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl2, 1mM DTT, pH 7.9) with 1x RealSeq biotinylated DNA probes to target all miRNAs in miRbase 21. After 2 hours of incubation at 37C, 10 μL of RealSeq Beads were added, and miRNAs were captured using a 384-well Magnet Plate (Alpaqua, MA). Following three washes with RealSeq Wash buffer, miRNA was eluted from beads in 10uL of RNase-free water. All the miRNA elusion was input to prepare sequencing libraries with RealSeq-Biofluids following manufacturer instructions (RealSeq Biosciences). In summary, a single adapter and circularization approach was used. Libraries were barcoded with dual indexes and sequenced with a NextSeq 550 (Illumina, CA).

treatment_protocol: On day 19, half (three 384-well plates) of the Selleck bioactive compound library (N=1902 compounds) were pin transferred (V&P Scientific) to twelve NGN2-iN plates using the Seiko Compound Transfer Robot at 200 nL per well (final concentration at 10 μM). Positive control (Forskolin) and negative control (DMSO) were also pin transferred to the wells without library compound. The other half (three and a quarter 384-well plates) of the compound library were added to the remaining thirteen 96-well plates after one day delay (on day 20), using the identical protocol due to the time consumption.

tag: cell line

tag: cell type

value: Human NGN2-driven iPSC-derived neurons

value: Choline Chloride


title: RSB163-278 [Chlorzoxazone]

value: Chlorzoxazone


title: T. ni, fat body, SFN, rep4 [22044R-02-02_S29]

value: SFN


title: T. ni, fat body, SFN, rep3 [22044R-01-06_S76]


title: RSB163-110 [Chlorpropamide]

value: Chlorpropamide


title: T. ni, fat body, SFN, rep2 [22044R-01-05_S75]


title: T. ni, fat body, SFN, rep1 [22044R-01-04_S74]


title: RSB163-291 [Chlorocresol]

value: Chlorocresol


title: T. ni, fat body, TSA, rep3 [22044R-01-09_S79]


title: RSB163-317 [Cetrimonium Bromide (CTAB)]

value: Cetrimonium Bromide (CTAB)


title: RSB163-361 [CGI1746]


title: T. ni, fat body, control, rep3 [22044R-02-01_S28]

value: EtOH


title: T. ni, fat body, control, rep2 [22044R-01-03_S73]


title: RSB163-314 [Cepharanthine]

value: Cepharanthine


title: RSB163-267 [Carprofen]

value: Carprofen


title: RSB163-322 [Bromfenac Sodium]

value: Bromfenac Sodium


title: T. ni, fat body, control, rep1 [22044R-01-01_S0]


title: HOM 2 BAT

city: Madrid

first: Silvia

last: Corrochano

address: Calle del Prof Martín Lagos

department: Neurología

country: Spain

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR (v2.5)
HTSeq v0.6.1 was used to count the read mapped to each gene. For normalisation, the FPKM (fragments per kilobase per million mapped fragments) of each gene was then calculated
Differential expression analysis between genotypes was performed using the DESeq2 R package (2_1.6.3)
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each samples and the results of the differential expression analysis

organism: Mus musculus

extract_protocol:
RNA was extracted from frontal brain, lumbar spinal cord, BAT, iWAT, TA muscle and liver of wild type and homozygous FUSΔ14/Δ14 male mice at 9-weeks of age. Quality and quantity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. Total number of reads was 30 million per sample.

value: BAT


title: HOM 3 BAT


title: RSB163-36 [Brinzolamide]

value: Brinzolamide


title: HOM 1 BAT


title: RSB163-60 [Carbimazole]

value: Carbimazole


title: RSB163-161 [Brimonidine Tartrate]

value: Brimonidine Tartrate


title: WT 3 BAT

source_name: Wild type

value: Wild type


title: HOM 4 BAT


title: WT 2 BAT


title: RSB163-12 [Biotin (Vitamin B7)]

value: Biotin (Vitamin B7)


title: RSB163-358 [BMN 673]

value: Human NGN2-driven iPSC-derived neurons

value: BMN 673


title: RSB163-279 [Bezafibrate]

value: Bezafibrate


title: RSB163-223 [Diphemanil Methylsulfate]

value: Diphemanil Methylsulfate


title: RSB163-198 [Betulinic acid]

value: Betulinic acid


title: RSB163-35 [Betahistine 2HCl]

value: Betahistine 2HCl


title: RSB163-105 [Benzoic Acid]

value: Benzoic Acid


title: RSB163-315 [Bergapten]

value: Bergapten


title: RSB163-45 [Azlocillin sodium salt]

value: Azlocillin sodium salt


title: RSB163-292 [Benzocaine]

value: Benzocaine


title: RSB163-59 [Bisacodyl]

value: Bisacodyl


title: RSB163-298 [Azaperone]

value: Azaperone


title: RSB163-273 [Bacitracin]

value: Bacitracin


title: HOM 3 Liver

value: Liver


title: HOM 1 Liver


title: HOM 2 iWAT

value: iWAT


title: HOM 4 Liver


title: HOM 4 iWAT


title: HOM 1 iWAT


title: WT 3 iWAT

value: Wild type


title: WT 1 BAT

value: BAT


title: WT 4 BAT


title: WT 1 iWAT


title: HOM 3 iWAT


title: RSB163-46 [Azacyclonol]

value: Human NGN2-driven iPSC-derived neurons

value: Azacyclonol


title: WT 2 iWAT


title: WT 4 Liver


title: RSB163-30 [Benztropine mesylate]

value: Benztropine mesylate


title: WT 4 iWAT


title: WT 3 Liver


title: RSB163-356 [AZD3514]


title: RSB163-23 [Articaine HCl]

value: Articaine HCl


title: HOM 2 Liver


title: RSB163-133 [Azaguanine-8]


title: RSB163-272 [Amprolium HCl]

value: Amprolium HCl


title: RSB163-138 [Antazoline HCl]

value: Antazoline HCl


title: WT 1 Liver


title: HOM 4 Tibialis anterior

value: Tibialis anterior


title: RSB163-32 [Ampicillin sodium]

value: Ampicillin sodium


title: RSB163-207 [Ampiroxicam]

value: Ampiroxicam


title: HOM 3 Tibialis anterior


title: HOM 2 Tibialis anterior


title: RSB163-196 [Amidopyrine]

value: Amidopyrine


title: HOM 1 Tibialis anterior


title: WT 4 Tibialis anterior


title: RSB163-40 [Adrenalone HCl]

value: Adrenalone HCl


title: RSB163-137 [Aminothiazole]

value: Aminothiazole


title: RSB163-153 [Alizapride HCl]

value: Alizapride HCl


title: WT 2 Tibialis anterior


title: WT 3 Tibialis anterior


title: RSB163-222 [Aclidinium Bromide]

value: Aclidinium Bromide


title: RSB163-213 [Avanafil]

value: Avanafil


title: WT 2 Liver

value: Liver

value: Wild type


title: HOM 4 Spinal cord


title: WT 1 Tibialis anterior


title: HOM 3 Spinal cord

value: Spinal cord


title: RSB163-206 [Acebutolol HCl]

value: Human NGN2-driven iPSC-derived neurons

value: Acebutolol HCl


title: HOM 2 Spinal cord


title: RSB163-338 [(R)-Nepicastat HCl]

value: (R)-Nepicastat HCl


title: HOM 1 Spinal cord


title: RSB163-42 [(+,-)-Octopamine HCl]

value: (+,-)-Octopamine HCl


title: RSB163-275 [Amfenac Sodium Monohydrate]

value: Amfenac Sodium Monohydrate


title: WT 4 Spinal cord


title: RSB163-367 [(+)-Bicuculline]

value: (+)-Bicuculline


title: WT 3 Spinal cord


title: RSB163-39 [Amitriptyline HCl]

value: Amitriptyline HCl


title: RSB241-304 [VU 0364770]


title: WT 2 Spinal cord


title: HOM 4 Brain

value: Frontal cortex


title: RSB241-336 [T0070907]


title: RSB241-269 [Pitavastatin Calcium]

value: Pitavastatin Calcium


title: WT 1 Spinal cord


title: RSB241-290 [MRS 2578]


title: HOM 2 Brain


title: HOM 3 Brain


title: RSB241-208 [CI994 (Tacedinaline)]

value: CI994 (Tacedinaline)


title: RSB241-113 [PF-573228]


title: RSB241-334 [TG100713]


title: HOM 1 Brain


title: RSB241-350 [Pyridoxine HCl]

value: Pyridoxine HCl


title: RSB241-342 [2-Thiouracil]


title: WT 2 Brain


title: WT 3 Brain


title: RSB241-348 [Pidotimod]

value: Pidotimod


title: WT 4 Brain


title: WT 1 Brain


title: RSB241-226 [AM251]


title: RSB241-308 [Vanillin]

value: Vanillin


title: RSB241-285 [L-(+)-Rhamnose Monohydrate]

value: L-(+)-Rhamnose Monohydrate


title: RSB241-218 [Sitaxentan sodium]

value: Sitaxentan sodium


title: RSB241-125 [Pioglitazone HCl]

value: Pioglitazone HCl


title: MPTP+Curcumin3

city: haikou

first: benchi

last: cai

address: xiuyin road

country: China

institute: hainan general hospital

data_processing:
RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.  PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq
Assembly: mm10
Supplementary files format and content: FPKM3 of each gene was calculated by HTSeq-count.
Supplementary files format and content: The read counts of each gene were obtained by HTSeq-count.

source_name: Brian

growth_protocol: The mice were housed in a standard environment with unlimited access to food and water

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: The mice were then randomly divided into three groups: control, MPTP, and MPTP + Curcumin. To induce Parkinson's disease in the mouse model, MPTP (Sigma-Aldrich, United States) was administered through intraperitoneal injections at a dose of 20 mg/kg in saline, along with probenecid (250 mg/kg in tris-HCl buffer) every 3.5 days for a total of 10 doses over a period of 5 weeks. Starting from day 1 of the experiment, curcumin (Macklin, Shanghai, China) was administered daily via gavage at a dose of 60 mg/kg for 7 weeks in the MPTP + Curcumin group.

value: Brian

value: MPTP+curcumin


title: MPTP+Curcumin2


title: MPTP+Curcumin1


title: MPTP3

value: MPTP


title: RSB241-127 [Captopril]

value: Human NGN2-driven iPSC-derived neurons

value: Captopril


title: RSB241-79 [Rufinamide]

value: Rufinamide


title: RSB241-147 [Argatroban]

value: Argatroban


title: control3


title: MPTP1


title: MPTP2


title: RSB241-206 [Torin 2]

value: Torin 2


title: control2


title: MT2_Mmi_dCas9_ChIP

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
Raw read pairs were trimmed by Trimgalore (v0.6.6)(https://github.com/FelixKrueger/TrimGalore) with the option “--paired”, and aligned to mm10 by bowtie2 (v2.4.2) with the options “-p 6 --no-unal --no-mixed --no-discordant -I 0, -X 1000”.
PCR duplicates were removed using Picard (v2.18.22)(http://broadinstitute.github.io/picard/), and Macs2 (v2.1.4) was used to call peaks with the option “-f BAMPE -g mm -B -q 0.0001 --nolambda --nomodel”.
Bigwig files were generated using deeptools (v2.0.0) bamCoverage function with the options --binSize 25 --normalizeUsing RPKM --scalFactor 1”.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: ESCs were cultured in DMEM (high glucose, no glutamine) medium supplemented with 15% Fetal Bovine Serum, 100U/ml Pen-streptomycin, 2mM GlutaMax, 1mM sodium pyruvate, 0.1mM non-essential amino acids, 0.084mM 2-mercaptoethanol, 1000 units/ml LIF, 0.5µM PD0325901, and 3µM ChIR99021.

extract_protocol:
Cells were fixed in culture medium at room temperature for 10 min with final 1% formaldehyde, and fixation was quenched by final 0.14M glycine at room temperature for 5 min. After cell lysis, sonication was performed using Fisher Scientific Sonic Dismembrator.
About 1ng DNA was used for library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

value: embryonic stem cell

tag: chip-seq antibody


title: RSB241-210 [Pifithrin-?]

value: Pifithrin-?


title: MT2_Mmi_HA_ChIP

value: HA


title: CITEseq_IgG_day28_rep1

city: Nagasaki

first: Katsuyuki

last: Yui

state: Nagasaki

address: 長崎市坂本１丁目12番4号

country: Japan

institute: Nagasaki University

description:
10x Genomics - Chromium Single Cell 5' v2 workflow with Feature Barcode technology
scRNAseq_IgG_day28_barcodes.tsv.gz
scRNAseq_IgG_day28_features.tsv.gz
scRNAseq_IgG_day28_matrix.mtx.gz

library_source: other

data_processing:
Data was analyzed using Seurat v4.2.0. Cells with greater than 3% mitochondrial RNA were excluded. Cells with < 1,500, <1,500, <1,000 and <1,000, or > 5,000, >5,000, >4,000 and >3,000 detected genes were also excluded for each dataset (IgG-treated Day 7, and anti-IL-27-treated Days 7, 14, and 28), respectively.
Assembly: mm10-2020-A
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: spleen

extract_protocol:
CD4+ T cells were prepared from spleen using mouse CD4+ T cell Isolation Kit (Miltenyi Biotech) and AutoMACS cell separator (Miltenyi Biotech) according to manufacturer’s instructions. Enriched CD4+ T cells, which included PbT-II cells, were incubated with a panel of TotalSeqTM -C antibodies (BioLegend) and surface antibody markers in PBS + 1% BSA: TotalSeq™-C0238 Rat IgG2a for isotype control (clone RTK2758), TotalSeq™-C0078 anti-CD49d (clone R1-2), TotalSeq™-C0198 anti-CD127 (clone A7R34), and TotalSeq™-C0250 anti-KLRG1, as well as anti-CD4 (clone GK1.5), anti- TCR β chain (clone H57-597), anti-TCR anti-CD45.1 (clone A20), and 7AAD. Stained CD4+ T cells were washed using the recommended Cell Wash Protocol 1 in preparation for 10X Single Cell RNA sequencing (Chromium Next GEM Single Cell 5' v2 protocol). PbT-II cells (CD4+CD45.1+TCR+) were sorted using FACSAria II cell sorter (BD Biosciences). FACS-sorted cells were collected in PBS + 1%BSA after washing, and resulted in >99% purity and >98% viability in all samples.
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index; 10X Genomics) according to the manufacturer’s instructions. Libraries were quantified using Bioanalyzer High Sensitivity Chip (Agilent). Gene expression libraries and cell surface protein libraries were pooled for library construction and sequencing was performed using MGISeq-2000RS.

value: spleen

value: CD4+ T cells

value: IgG

tag: library type

value: cell surface protein library

tag: antibodies/tags

value: Anti-IgG2a/TotalSeq-C0238 ; Anti-CD127/TotalSeq-C0198 ; Anti KLRG1/TotalSeq-C0250 ; Anti CD49d/TotalSeq-C0078


title: RSB241-236 [JNJ-1661010]


title: CTR_HA_ChIP


title: RSB241-157 [Trimebutine]

value: Trimebutine


title: CTR_dCas9_ChIP


title: MT2Mmi_E2CRNA_rep2

data_processing:
Raw RNA-seq read pairs were trimmed by Trimgalore (v0.6.6)(https://github.com/FelixKrueger/TrimGalore) with the option “--paired --clip_R2 5”, and aligned to mm10 by STAR (v2.7.9) with the options “--outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outSAMattributes NH HI NM MD XS AS --alignIntronMax 1000000 --alignMatesGapMax 1000000 --limitBAMsortRAM 30000000000 --outFilterType BySJout”.
Uniquely aligned read pairs were  identified by sambamba (v0.6.8) with the option “-F “mapping_quality >=255”
Bigwig files were generated using deeptools (v2.0.0) bamCoverage function with the options --binSize 25 --normalizeUsing RPKM --scalFactor 1”
Assembly: mm10
Supplementary files format and content: Bigwig

source_name: Early 2-cell embryo

growth_protocol: Embryos were cultured in KSOM (Millipore) at 37 °C under 5% CO2 with air

extract_protocol:
Embryos were suspended in 7 μl RRI water (199 μl ultrapure H2O with 1 μl RNase inhibitor). Then, 6 μl shearing master mix (1 μl 10X lysis mix, 1 μl Smart scN6, 4 μl scRT Buffer) was added and incubated at 85°C for 6 min and immediately put on ice for 2 min.
The total RNA‐seq libraries were generated using the SMART‐Seq Stranded Kit (Takara) following the manufacturer's protocol.

treatment_protocol: About 6 pl dCas9-KRAB mRNA and sgRNA mixes were injected into cytoplasm of zygotes between 2-4 hpi using a Piezo impact-driven micromanipulator (Eppendorf). For all micro-injection experiments, sgRNAs were injected at 60ng/µl: 10ng/µl for each MT2_Mm sgRNA or 60ng/µl for the non-targeting control sgRNA.  For embryos used for total RNA-seq analyses, dCas9-KRAB mRNA was injected at 100ng/µl.

value: Early 2-cell embryo

value: dCas9-KRAB mRNA + MT2_Mm sgRNA


title: RSB241-344 [Moguisteine]

value: Moguisteine


title: MT2Mmi_E2CRNA_rep1


title: RSB241-301 [Nifedipine]

value: Human NGN2-driven iPSC-derived neurons

value: Nifedipine


title: CTRi_E2CRNA_rep2

value: dCas9-KRAB mRNA + control sgRNA


title: control1

value: Brian


title: RSB241-59 [Tropicamide]

value: Tropicamide


title: RSB163-144 [Cysteamine HCl]

value: Cysteamine HCl


title: CTRi_E2CRNA_rep1


title: RSB241-141 [Doripenem Hydrate]

value: Doripenem Hydrate


title: RSB241-318 [Atovaquone]

value: Atovaquone


title: RSB241-294 [MK-801 (Dizocilpine)]

value: MK-801 (Dizocilpine)


title: MT2Mmi_8CRNA_rep2

source_name: 8-cell embryo

value: 8-cell embryo


title: MT2Mmi_8CRNA_rep1


title: RSB241-165 [Sumatriptan Succinate]

value: Sumatriptan Succinate


title: RSB241-282 [Medetomidine HCl]

value: Medetomidine HCl


title: CTRi_8CRNA_rep1


title: RSB241-151 [Clevidipine Butyrate]

value: Clevidipine Butyrate


title: CTRi_8CRNA_rep2


title: MT2Mmi_4CRNA_rep2

source_name: 4-cell embryo

value: 4-cell embryo


title: MT2Mmi_4CRNA_rep1


title: CTRi_4CRNA_rep2


title: RSB241-330 [WHI-P154]


title: RSB241-83 [Sulbactam]

value: Sulbactam


title: RSB241-70 [Nitrendipine]

value: Nitrendipine


title: CTRi_4CRNA_rep1


title: RSB241-87 [Pranoprofen]

value: Pranoprofen


title: RSB241-159 [Detomidine HCl]

value: Human NGN2-driven iPSC-derived neurons

value: Detomidine HCl


title: MT2Mmi_L2CRNA_rep2

source_name: Late 2-cell embryo

value: Late 2-cell embryo

value: dCas9-KRAB mRNA + MT2_Mm sgRNA


title: MT2Mmi_L2CRNA_rep3


title: MT2Mmi_L2CRNA_rep1


title: RSB241-276 [Azelnidipine]

value: Azelnidipine


title: RSB241-214 [Amoxicillin]

value: Amoxicillin


title: CTRi_L2CRNA_rep2

value: dCas9-KRAB mRNA + control sgRNA


title: RSB241-320 [Etravirine (TMC125)]

value: Etravirine (TMC125)


title: RSB241-134 [Lonidamine]

value: Lonidamine


title: RSB241-86 [VU 0361737]


title: RSB241-46 [Tolbutamide]

value: Tolbutamide


title: Noninj_L2CRNA_rep1

value: Non-injected


title: CTRi_L2CRNA_rep1


title: RSB241-53 [Valsartan]

value: Valsartan


title: RSB241-117 [Formoterol Hemifumarate]

value: Formoterol Hemifumarate


title: RSB241-150 [WZ811]


title: RSB241-235 [Lubiprostone]

value: Lubiprostone


title: RNAseq, Lphn3 Exon31 KO, rep2

city: Stanford

first: Shuai

last: Wang

state: CA

address: 265 Campus Drive

institute: Stanford University

description:
SW6
normalized_counts.csv
Lphn3E31KO_vs_ctrl.csv

data_processing:
STAR (2.7.10b) for alignment
HTSeq (2.0.4) for read count
DEseq2 (3.17) for read count normalization and differential gene expression analysis
Assembly: GRCm38/mm10
Supplementary files format and content: normalized_counts.csv: normalized read count for all samples
Supplementary files format and content: Lphn3KO_vs_ctrl.csv: DEG analysis of Lphn3 KO group compared to control group
Supplementary files format and content: Lphn3E31KO_vs_ctrl.csv: DEG analysis of Lphn3 Exon31 KO group compared to control group

source_name: neuron

growth_protocol: Neonatal P0 mice pups of CAG-cas9 mice (JAX #024858) were dissected in ice cold HBS to obtain hippocampi, which were digested in 1% v/v papain suspension (Worthington) and 0.1 U/µl DNaseI (Worthington) DNaseI for 15min at 37˚C. Hippocampi from 2 pups were washing with calcium-free 1xHBS  (pH7.3) and dissociated using gentle pipetting in plating medium (MEM containing 5% FBS, 0.6% glucose, 2% Gem21 NeuroPlex™ Supplement, 2 mM GlutaMAX™), filtered through 70 µm cell strainer, and seeded onto Corning® Matrigel®-coated 12 mm cover glasses in one 24-well plate, and maintained at 37˚C 5% CO2. 16 hr post seeding (DIV1), 90% media were replaced by maintenance medium (Neurobasal A with 2% Gem21 NeuroPlex™ Supplement, 2 mM GlutaMAX™). At DIV 3, 50% of medium were replaced with fresh maintenance medium supplemented 4 µM Ara-C (Cytosine β-D-arabinofuranoside hydrochloride), and lentivirus expressing gRNA. At DIV7, 10, and 13, 30% media were replaced with fresh maintenance medium, before analyzing at DIV14.

extract_protocol:
Total RNA from cultured neurons were extracted by TRIzol®
0.1-0.2µg of total RNA was subject to library synthesis using Illumina Stranded mRNA Prep

treatment_protocol: Neurons were infected with lentiviruese expressing indicated gRNA at DIV3

value: neuron

value: lentivirus expressing Lphn3 Exon31 KO gRNA


title: RNAseq, Lphn3 Exon31 KO, rep1

description:
SW5
normalized_counts.csv
Lphn3E31KO_vs_ctrl.csv


title: RSB241-153 [Cilazapril Monohydrate]

value: Cilazapril Monohydrate


title: RNAseq, Lphn3 KO, rep3

description:
SW3
normalized_counts.csv
Lphn3KO_vs_ctrl.csv

value: lentivirus expressing Lphn3 KO gRNA


title: CTRi_L2CRNA_rep3


title: RNAseq, Lphn3 KO, rep1

description:
SW9
normalized_counts.csv
Lphn3KO_vs_ctrl.csv


title: RSB241-95 [Lacidipine]

value: Human NGN2-driven iPSC-derived neurons

value: Lacidipine


title: RNAseq, control, rep3

description:
SW7
normalized_counts.csv

value: lentivirus expressing control gRNA


title: RSB241-278 [Alverine Citrate]

value: Alverine Citrate


title: RNAseq, control, rep1

description:
SW1
normalized_counts.csv


title: Noninj_L2CRNA_rep2

value: Late 2-cell embryo


title: RSB241-229 [Zolmitriptan]

value: Zolmitriptan


title: RSB241-277 [Gramine]

value: Gramine


title: RNAseq, Lphn3 Exon31 KO, rep3

description:
SW11
normalized_counts.csv
Lphn3E31KO_vs_ctrl.csv


title: RSB241-93 [Adenine HCl]

value: Adenine HCl


title: RSB241-69 [PFI-1 (PF-6405761)]


title: ADC106 cells 497 mimic transfected day 3, 2

city: West Lafayette

first: Jason

middle: A

last: Hanna

state: IN

address: 201 S. University St. Hans219

department: Biological Sciences

institute: Purdue University

data_processing:
Raw reads were cleaned (adpater trimming, quality-trimming, removal of reads less than 50bp) was performed using Fastp toolkit (version 0.19.5).
Quality trimmed reads were mapped against the indexed mouse (GRCm38) reference genome using STAR aligner (v2.5.4b).
STAR derived mapping files (BAM) and annotation (GTF) file were fed into the using featureCounts program from Subread package (version 1.6.1).
Differential expression analysis was performed with R-package edgeR (v3.32.1).
Assembly: GRCm38
Supplementary files format and content: Tab delimited text file containing raw counts for each sample.

source_name: angiosarcoma tumor

growth_protocol: ADC106 cells were were maintained in DMEM with 10% FBS, 1× antibiotic‐antimycotic penicillin, streptomycin, and amphotericin B (PSA) and incubated at 37 °C in 5% CO2.

extract_protocol:
Total RNA was prepared using the Quick-RNA Miniprep Kit (Zymo)
Novagene PolyA enrichment mRNA library prep

treatment_protocol: ADC106 cells were transfected with 12.5 nM NC or miR-497 mimic and RNA was extracted 3 days post transfection

value: angiosarcoma tumor

value: angiosarcoma

value: miR-497 overexpression

value: microRNA mimic transfected (miR-497)


title: RSB241-242 [Fosaprepitant dimeglumine salt]

value: Fosaprepitant dimeglumine salt


title: RSB241-300 [IEM 1754 dihydrobroMide]

value: IEM 1754 dihydrobroMide


title: RSB241-146 [Tempol]

value: Tempol


title: ADC106 cells NC mimic transfected day 3,2

value: WT

value: microRNA mimic transfected (NC)


title: RNAseq, control, rep2

description:
SW2
normalized_counts.csv

value: neuron


title: RNAseq, Lphn3 KO, rep2

description:
SW10
normalized_counts.csv
Lphn3KO_vs_ctrl.csv

value: lentivirus expressing Lphn3 KO gRNA


title: ADC106 cells NC mimic transfected day 3,1


title: ADC106 cells 497 mimic transfected day 3, 3


title: RSB241-228 [RG108]

value: Human NGN2-driven iPSC-derived neurons


title: ADC106 cells NC mimic transfected day 3,3


title: RSB241-268 [Baricitinib (LY3009104, INCB028050)]

value: Baricitinib (LY3009104, INCB028050)


title: RSB241-284 [Diclofenac Diethylamine]

value: Diclofenac Diethylamine


title: CD8+ T cell, 2-DG treated, TCF1 Reporter eGFP+, replicate 2

city: New York

first: Vivek

last: Mittal

state: NY

address: 525 East 68th Street, W412

department: Cardiothoracic Surgery

institute: Weill Cornell Medicine

description: 2x100 cycles

data_processing:
Raw reads in BCL format were converted to FASTQ and demultiplexed with bcl2fastq 2.20 (Illumina)
RNA reads were aligned and mapped to mouse genome GRCm39 by STAR v2.7.10b
Sequencing and mapping quality was evaluated using FastQC v0.12.1
Raw read counts per gene were extracted using HTSeq-count v2.0.1
Assembly: mouse reference genome GRCm39
Supplementary files format and content: Count files generated by HTSeq-count

source_name: CD8+ T cell

growth_protocol: HKP1-ova-GFP cells for co-culture with T cells were cultured in DMEM supplemented with 10% FBS, 100 U/mL penicillin with 100μg/mL streptomycin, and 2mM L-glutamine and stored in a humidified incubator at 37℃, 5% CO2. OT-I+ CD8+ T cells expressing a TCF1 eGFP reporter were cultured on plates coated with 2µg/mL each of anti-CD3ε and anti-CD28  in complete T cell media (Advanced RPMI (RPMI-1640 with non-essential amino acids and 110mg/L sodium pyruvate) supplemented with 10% FBS, 100 U/mL penicillin with 100μg/mL streptomycin, 2mM GlutaMAX, 10mM HEPES, and 50μM β-mercaptoethanol) with 50U/mL mouse IL-2 in a humidified incubator at 37℃, 5% CO2 prior to drug treatment and co-culture. T cells and tumor cells were co-cultured in complete T cell media with 50U/mL mouse IL-2 and drug treatments in a humidified incubator at 37℃, 5% CO2.

extract_protocol:
RNA in RLT lysis buffer supplemented with β-mercaptoethanol was thawed from -80℃ and subsequently isolated using RNeasy Plus Micro Kits with gDNA elimination via gDNA eliminator spin column as per the manufacturer’s protocols (Qiagen).
Illumina Stranded mRNA Prep as per the manufacturer's protocols.

treatment_protocol: OT-I+ CD8+ T cells expressing a TCF1 eGFP reporter were isolated by negative selection from the spleen of a 7 week old female transgenic OT-I+ Tcf7GFP+ mouse on the C57Bl/6 background. T cells were activated on plates coated with 2µg/mL each of anti-CD3ε and anti-CD28 in complete T cell media supplemented with 50U/mL of mouse IL-2. After 24 hours, T cells were treated with equal volumes of DMSO vehicle control, 3μM glucose 6-phosphate dehydrogenase agonist AG1, 25μM glucose 6-phosphate dehydrogenase inhibitor G6PDi-1, or 2mM hexokinase inhibitor 2-DG, and maintained on anti-CD3ε and anti-CD28 coated plates in complete T cell media supplemented with 50U/mL of mouse IL-2 for an additional 24 hours. T cells were subsequently harvested, washed with PBS, counted, and co-cultured with HKP1-ova-GFP mouse lung cancer cells at a 5:1 T cell:tumor cell ratio (400,000 T cells with 80,000 tumor cells in each well of a 12 well plate) in complete T cell media supplemented with 50U/mL of mouse IL-2 with continuing drug treatment. Co-cultures were counted and passed to a 5:1 T cell:tumor cell ratio (400,000 T cells with 80,000 tumor cells in each well of a 12 well plate) every other day with continuing drug treatment. At day 6 post-initial-stimulation, co-cultures were harvested and single-cell suspensions made by filtered through 40μm filters and centrifuged for 5 minutes at 1500 rpm. Cell pellets were washed once with FACS Buffer, centrifuged for 5 minutes at 1500 rpm, and resuspended in FACS Buffer. Samples were subsequently stained with antibodies for CD8β-PerCP-Cy5.5 and Thy1.2-AlexaFluor 647 in the presence of anti-mouse CD16/32 for 30 minutes on ice in the dark, washed with FACS Buffer, and resuspended in FACS Buffer. Samples were dyed with DAPI at 0.2μg/mL, and sorted on a Becton-Dickinson FACS Aria II sorter for DAPI- CD8β+ Thy1.2+ TCF1 Reporter eGFP+ or DAPI- CD8β+ Thy1.2+ TCF1 Reporter eGFP- cells. Activated CD8+ OT-I+ T cells from mice without TCF1 eGFP reporter were used as a gating control. Cells were sorted into Complete T cell Media, centrifuged for 5 minutes at 1500 rpm, washed with PBS, and resuspended into RLT lysis buffer supplemented with β-mercaptoethanol, and frozen at -80℃ until RNA extraction.

value: 2mM 2-DG

tag: reporter status

value: TCF1 Reporter eGFP+

value: CD8+ T cell

tag: Sex

value: female

tag: timepoint

value: day 6 post initial stimulation

tag: mouse genotype

value: OT-I+ Thy1.2+/+ Tcf7GFP+/+


title: RSB241-264 [Cathepsin Inhibitor 1]

value: Cathepsin Inhibitor 1


title: CD8+ T cell, G6PDi-1 treated, TCF1 Reporter eGFP-, replicate 1

description: 2x100 cycles

value: 25μM G6PDi-1

value: TCF1 Reporter eGFP-


title: CD8+ T cell, 2-DG treated, TCF1 Reporter eGFP+, replicate 1

description: 2x100 cycles


title: RSB241-62 [Acesulfame Potassium]

value: Acesulfame Potassium


title: RSB241-52 [Camostat Mesilate]

value: Camostat Mesilate


title: CD8+ T cell, AG1 treated, TCF1 Reporter eGFP-, replicate 2

description: 2x100 cycles

value: 3μM AG1


title: RSB241-161 [Omeprazole]

value: Omeprazole


title: CD8+ T cell, G6PDi-1 treated, TCF1 Reporter eGFP+, replicate 1

description: 2x100 cycles


title: RSB241-299 [Acetylcholine Chloride]

value: Acetylcholine Chloride


title: RSB241-65 [Irinotecan]

value: Human NGN2-driven iPSC-derived neurons

value: Irinotecan


title: CD8+ T cell, G6PDi-1 treated, TCF1 Reporter eGFP+, replicate 2

description: 2x100 cycles


title: RSB241-280 [Azilsartan Medoxomil]

value: Azilsartan Medoxomil


title: CD8+ T cell, G6PDi-1 treated, TCF1 Reporter eGFP-, replicate 2

description: 2x100 cycles


title: RSB241-183 [Levosulpiride]

value: Levosulpiride


title: CD8+ T cell, AG1 treated, TCF1 Reporter eGFP-, replicate 1

description: 2x100 cycles


title: RSB241-230 [OC000459]


title: RSB241-54 [Prucalopride]

value: Prucalopride


title: CD8+ T cell, AG1 treated, TCF1 Reporter eGFP+, replicate 1

description: 2x100 cycles

value: TCF1 Reporter eGFP+

value: CD8+ T cell


title: CD8+ T cell, DMSO treated, TCF1 Reporter eGFP-, replicate 2

description: 2x100 cycles

value: DMSO

value: female

value: day 6 post initial stimulation


title: RSB241-111 [Flupirtine maleate]

value: Flupirtine maleate


title: CD8+ T cell, DMSO treated, TCF1 Reporter eGFP+, replicate 2

description: 2x100 cycles

value: OT-I+ Thy1.2+/+ Tcf7GFP+/+


title: CD8+ T cell, DMSO treated, TCF1 Reporter eGFP-, replicate 1

description: 2x100 cycles

value: TCF1 Reporter eGFP-


title: RSB241-158 [ML161]


title: RSB241-199 [Pyridostigmine Bromide]

value: Pyridostigmine Bromide


title: CD8+ T cell, DMSO treated, TCF1 Reporter eGFP+, replicate 1

description: 2x100 cycles


title: RSB241-255 [Cyclosporin A]

value: Cyclosporin A


title: dentate gyrus, running 12 day, rep16 KO

city: Udine

first: Simone

last: Scalabrin

state: UD

address: via Jacopo Linussio 51

country: Italy

institute: IGA Technology Services

data_processing:
Base calling and demultiplexing. Processing raw data for both format conversion and demultiplexing by Bcl2Fastq 2.20 version of the Illumina pipeline.
Adapters masking. Adapter sequences are masked with Cutadapt v1.11 from raw fastq data using the following parameters: --anywhere (on both adapter sequences) --overlap 5 --times 2 --minimumlength 35 --mask-adapter.
Trimming. Removing lower quality bases and adapters by ERNE software.
Alignments on the reference genome. Aligning reads on reference genome with STAR (default parameters).
Execute transcripts count. Assembling and quantitation of full-length transcripts representing multiple spliced variants for each gene locus by Stringtie (default parameters).
Read count per gene. htseq-count7 to preprocess RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.
Samples pairwise comparisons. DESeq2 to perform comparisons between expression levels of genes and transcripts by fitting a Generalized Linear Model (GLM) for each gene.
Assembly: mm10-ucsc
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: dentate gyrus

extract_protocol:
Twelve-month-old p16 WT and p16 KO mice, sedentary, 12 days runner (for RNA-seq) or subjected to a further 7 days of running (protocol 12d RUN + 21d + 7d RUN in Fig 5A), were sacrificed by rapid decapitation. Bilateral dentate gyrus was dissected under a stereomicroscope according to the procedure described by Hagihara et al. (2009), immediately homogenized in Trizol Reagent (Invitrogen, San Diego, CA, USA), and total RNA extraction was performed as described previously (Farioli-Vecchioli et al., 2012). Extracted RNA was quantified and assessed for purity using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara CA). RNAs were subsequently employed for Transcriptome sequencing and/or for real-time PCR experiments.
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand)

value: dentate gyrus

tag: strain

tag: age

value: one-year-old

value: male

value: running 12 days


title: RSB241-347 [Gastrodin]

value: Human NGN2-driven iPSC-derived neurons

value: Gastrodin


title: dentate gyrus, running 12 day, rep14 KO


title: CD8+ T cell, AG1 treated, TCF1 Reporter eGFP+, replicate 2

description: 2x100 cycles

value: 3μM AG1


title: dentate gyrus, running 12 day, rep15 KO


title: dentate gyrus, running 12 day, rep13 KO


title: RSB241-181 [Rasagiline Mesylate]

value: Rasagiline Mesylate


title: RSB241-260 [BI-D1870]


title: RSB241-136 [Fostamatinib (R788)]

value: Fostamatinib (R788)


title: RSB241-279 [Gynostemma Extract]

value: Gynostemma Extract


title: dentate gyrus, running 12 day, rep10 WT


title: RSB241-51 [Nizatidine]

value: Nizatidine


title: dentate gyrus, running 12 day, rep12 WT


title: dentate gyrus, running 12 day, rep9 WT


title: RSB241-145 [Orphenadrine Citrate]

value: Orphenadrine Citrate


title: dentate gyrus, sedentary, rep7 KO

value: sedentary


title: dentate gyrus, sedentary, rep8 KO


title: dentate gyrus, running 12 day, rep11 WT


title: ADC106 cells 497 mimic transfected day 3, 1

value: angiosarcoma tumor

value: angiosarcoma

value: miR-497 overexpression

value: microRNA mimic transfected (miR-497)


title: RSB241-283 [Kinetin]

value: Kinetin


title: RSB241-343 [Xanthone]

value: Xanthone


title: RSB241-261 [Glyburide]

value: Glyburide


title: RSB241-88 [SB742457]


title: RSB241-189 [Dextrose]

value: Dextrose


title: dentate gyrus, sedentary, rep5 KO

value: dentate gyrus

value: one-year-old

value: male


title: dentate gyrus, sedentary, rep6 KO


title: dentate gyrus, sedentary, rep4 WT


title: RSB241-47 [TAK-700 (Orteronel)]

value: Human NGN2-driven iPSC-derived neurons

value: TAK-700 (Orteronel)


title: dentate gyrus, sedentary, rep3 WT


title: dentate gyrus, sedentary, rep2 WT


title: RSB241-97 [BX-795]


title: RSB241-126 [Ki16198]


title: RSB241-311 [Nobiletin]

value: Nobiletin


title: RSB241-144 [Flavopiridol HCl]

value: Flavopiridol HCl


title: dentate gyrus, sedentary, rep1 WT


title: Repetitve administration of Bleomycin (fibrosis)

city: Research Triangle Park

first: Stavros

last: Garantziotis

state: NC

address: 111 TW Alexander Drive, Room 109

department: DIR

institute: NIH/NIEHS

description: 2 weeks after last dose, fibrotic (Bleomycin lungs were harvested from 3 mice, enzymatically digested and GFP+ collected by FACS for scRNA Seq

library_source: transcriptomic single cell

data_processing:
Base calling and generation of FASTQ files performed using RTA and cell ranger v3.0.1
scRNA-Seq processing completed using cell ranger v3.0.1 with Gencode M17 mm10 transcriptome filtered according to 10X recommendations.
Downstream processing completed with Seurat v3.
Assembly: mm10

source_name: Mouse lung fibroblasts

growth_protocol: Organoid cultures were prepared by combining AEC2 tomato+ cells and GFP+ fibroblasts from normal or fibrogenic mice in a ratio of 10:1 in matrigel. Cell suspensions were cultured for 2 weeks on transwell inserts in MTEC+ media.

extract_protocol:
Lungs were harvested on day 14 post-exposure (3 mice per group) and enzymatically digested with a cocktail including collagenase Type 1, elastase, DNase1, and Dispase. After red blood cell lysis and filtering, Pdgfra-GFP+ cells were sorted using FACS (BD Aria II). Organoids were dissoicated first in Accutase, followed by 0.25% trypsin digestion to generate single cell suspensions for scRNA library prep.
The mRNA reverse transcription and cDNA generation and amplification were carried out followed by the construction of single cell gene expression libraries according to the protocols provided by manufacturers.

treatment_protocol: Mice were dosed once with either PBS (50 ul, OP) or Bleomycin (2 U/Kg, OP)

value: PDGFRa-EGFP

value: GFP+ mice were dosed once weekly for three weeks with Bleomycin (1, 1, and 0.5 U/Kg) by oropharyngeal aspiration, 50 ul volume

value: GFP+ fibrogenic fibroblasts


title: RSB241-142 [PF-00562271]


title: TCR_Library

first: Peter

last: Sage

address: 221 Longwood Ave

department: Medicine/Renal

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD4 T cells

extract_protocol:
Live CD4+CD19-CXCR5+GITR- cells were sorted based on VFP and TdTomato expression into Tfh-Prog (VFP-TdTomato-), Tfh-Trans (VFP+TdTomato-), Tfh-Full (VFP+TdTomato+) and Tfh-Ex (VFP-TdTomato+). Conventional T cells (CD4+CD19-CXCR5-GITR-) were also sorted as a control. Cells were stained with TotalSeq-C Hashtags (Biolegened) and pooled in a single sample before loading.
Cells were resuspended in 0.4% BSA in PBS at a concentration of 2,000 cells per μl, then loaded onto a single lane (Chromium chip K, 10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 5′kit V2, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol. 5’ mRNA library was sequenced to an average of 50,000 reads per cell, V(D)J library and HTO (Cell Hashing antibodies) library sequenced to an average of 5,000 reads per cell, all using Illumina Novaseq.

value: CD4 T cells

value: Mouse CD4 T  cell

value: 6-8 weeks


title: RSB241-194 [Sirtinol]

value: Sirtinol


title: RSB241-295 [Azacitidine]

value: Azacitidine


title: GEX_HTO_Library


title: Alveolosphere fibrogenic PDGFRa fibroblasts

description: Tomato+ AEC2 and GFP+ fibrogenic PDGFRa+ fibroblasts were prepared from the lungs of 3 pooled  mice each cell type (for fibroblasts, 2 weeks after dosing), mixed 10:1 in matrigel and cultured for 2 weeks

source_name: Dissociated organoid cultures

value: AEC2 donor SpcCreER, tomato+. Fibroblast donor PDGFRa-EGF

value: AEC2 donors induced with tamoxifen (2X 1 mg/Kg ip). Fibroblast donors dosed by oropharyngeal aspiration 2U/Kg bleomycin, harvested at day 14

value: Spc+ alveolar type 2 epithelial cells and GFP+ PDGFRa+ fibroblasts


title: RSB241-211 [Almorexant HCl]

value: Almorexant HCl


title: RSB241-109 [Etodolac]

value: Etodolac


title: RSB241-212 [Rivaroxaban]

value: Human NGN2-driven iPSC-derived neurons

value: Rivaroxaban


title: Ileum_A53T

city: Wuerzburg

first: Rhonda

last: McFleder

address: Josef-schneider-strasse 11

country: Germany

institute: Neurologische Klinik und Poliklinik des Universitaetsklinikum Wuerzburg

data_processing:
Chromium single cell 3´ v2. Data were demultiplexed using the CellRanger software v. 6.1.2. The reads were aligned to the mm10 reference genome using the STAR aligner.
Assembly: mm10
Supplementary files format and content: matrix.h5; gene barcode matrices and feature barcode matrix
Supplementary files format and content: info.h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis

source_name: Ileum

extract_protocol:
Tissue was digested in with Accutase (Merck) at 37 °C for 30 min and triturated through 70 μm cell strainers which were rinsed with 10% FCS in PBS. Cells were purified by a linear 40% Percoll (GE Healthcare) centrifugation step at 650 xg without brakes for 25 min and the supernatant were discarded. Mononuclear cells were resuspended in FACS buffer (1% BSA and 0.1% sodium azide in PBS) and stained for live cells, CD45, CD11c, CD8, and CD4. Cells from similar organs and treatment were pooled from five mice and single cell libraries prepared.
Single cells were encapsulated in droplets using 10X Genomics GemCode Technology kit v2 and processed following manufacturer's specifications. Chromium single cell 3´ v2 (10XGenomics)

value: Ileum

value: CD4, CD8, CD11c


title: Brain_A53T

source_name: Brain

value: Brain


title: RSB241-163 [Pizotifen Malate]

value: Pizotifen Malate


title: Brain_EV

value: EV


title: RSB241-297 [Ranitidine]

value: Ranitidine


title: RSB241-64 [A-205804]


title: Spleen_A53T

source_name: Spleen

value: Spleen


title: RSB241-217 [Rosuvastatin Calcium]

value: Rosuvastatin Calcium


title: RSB241-198 [MPEP]

value: MPEP


title: Ileum_EV


title: Repetitve administration of PBS (control)

description: 2 weeks after last dose, control (PBS) lungs were harvested from 3 mice, enzymatically digested and GFP+ collected by FACS for scRNA Seq

value: PDGFRa-EGFP

value: GFP+ mice were dosed once weekly for three weeks with PBS by oropharyngeal aspiration, 50 ul per dose

value: GFP+ normal fibroblasts


title: semimembranosus muscles, IVS_diosmin_rep2

city: Nanjing

first: Zhiguang

last: Shi

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 v2.1.0 with default parameters
Read counts were calculated using Htseq-count with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each Sample

source_name: semimembranosus muscles, IVS_diosmin

growth_protocol: Semimembranosus collection:8-week-old C57BL/6 mice were anesthetized with gas. A groin incision was made to separate the left external iliac vein and ligated over a 30-gauge needle to achieve the stenosis.

extract_protocol:
Samples were collected and flash-frozen in liquid nitrogen and, then treated by Trizol in -80℃ until RNA extraction. Extracting total RNA from tissues by Trizol. 1.5% agarose gels were used to monitor the RNA degradation and contamination. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). The next RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Library preparation for RNA sequencing. A total amount of 1μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5X).First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with sizeselected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 System.

treatment_protocol: IVS group:  Intragastric administration of normal saline per day; IVS/diosmin group:  Intragastric administration of 40 mg/kg diosmin solution per day.

value: Semimembranosus

value: 8 weeks

value: Iliac vein stenosis/diosmin


title: Spleen_EV


title: RSB241-41 [TW-37]

value: Human NGN2-driven iPSC-derived neurons


title: Alveolosphere normal PDGFRa fibroblasts

description: Tomato+ AEC2 and GFP+ normal PDGFRa+ fibroblasts were prepared from the lungs of 3 pooled  mice each cell type (for fibroblasts, 2 weeks after dosing), mixed 10:1 in matrigel and cultured for 2 weeks

value: AEC2 donor SpcCreER, tomato+. Fibroblast donor PDGFRa-EGF

value: AEC2 donors induced with tamoxifen (2X 1 mg/Kg ip). Fibroblast donors dosed by oropharyngeal aspirationPBS, harvested at day 14

value: Spc+ alveolar type 2 epithelial cells and GFP+ PDGFRa+ fibroblasts


title: RSB241-101 [Cilnidipine]

value: Cilnidipine


title: CD8+ T cell, PKM2 knockout, anti-PD-1 treated, Early timepoint, replicate 3 [P5T_Het]

description: 2x100 cycles

data_processing:
Raw reads in BCL format were converted to FASTQ and demultiplexed with bcl2fastq 2.19 (Illumina)
Adaptors were trimmed with cutadapt v1.18
RNA reads were aligned and mapped to mouse genome GRCm38 (mm10) by STAR v2.5.2
Transcriptome reconstruction was performed by Cufflinks v2.1.1, and abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Raw read counts per gene were extracted using HTSeq-count v0.11.2
Assembly: mouse reference genome GRCm38 (mm10)
Supplementary files format and content: FPKM for protein coding genes in .txt file- fpkm.genes.ensembl_id.protein_coding.txt
Supplementary files format and content: Raw read counts per gene in .txt file- raw_counts_genes.txt

source_name: Tumor-bearing lung

growth_protocol: HKP1-ova-GFP cells for tumor generation were cultured in DMEM supplemented with 10% FBS, 100 U/mL penicillin with 100μg/mL streptomycin, and 2mM L-glutamine and stored in a humidified incubator at 37℃, 5% CO2. CD8+ T cells were cultured on plates coated with 2µg/mL each of anti-CD3ε and anti-CD28  in complete T cell media (Advanced RPMI (RPMI-1640 with non-essential amino acids and 110mg/L sodium pyruvate) supplemented with 10% FBS, 100 U/mL penicillin with 100μg/mL streptomycin, 2mM GlutaMAX, 10mM HEPES, and 50μM β-mercaptoethanol) with 50U/mL mouse IL-2 in a humidified incubator at 37℃, 5% CO2 prior to adoptive transfers into lymphodepleted C57BL/6 mice bearing HKP1-ova-GFP orthotopic lung tumors.

extract_protocol:
RNA in RLT lysis buffer supplemented with β-mercaptoethanol was thawed from -80℃ and subsequently isolated using RNeasy Micro Kits (Qiagen) with on-column DNA digestion as per the manufacturer’s protocols.
SMART-Seq v4 Ultra Low Input RNA plus Nextera XT DNA Sample preparation kit as per the manufacturer's protocols.

treatment_protocol: OT-I+ CD8+ T cells were isolated by negative selection from spleens from 6-8 week old female OT-I+ Thy1.1+/+ or OT-I+ Thy1.1+/- mice on the C57Bl/6 background. T cells were activated on plates coated with 2µg/mL each of anti-CD3ε and anti-CD28 in complete T cell media supplemented with 50U/mL of mouse IL-2. After 24 hours, T cells were electroporated with CRISPR/Cas9 RNPs with guide RNA duplexes formed with ATTO-conjugated tracrRNA and crRNA for non-targeting control (Thy1.1+/+) or crRNA for PKM2 (Thy1.1+/-), rested for 2 hours with IL-2, sorted for ATTO+ cells by flow cytometry, and replated on anti-CD3ε and anti-CD28 coated plates in complete T cell media supplemented with 50U/mL of mouse IL-2 for an additional 24 hours. T cells were subsequently harvested, washed twice with PBS, counted and mixed at a 1:1 PKM2 wildtype:PKM2 knockout ratio, resuspended at 20e6 cells/mL in sterile PBS, and 1e6 cells transferred retro-orbitally into irradiated HKP1-ova-GFP tumor-bearing recipient C57BL/6 mice. Mice were subsequently treated with either IgG or anti-PD-1 on days 3 and 7 post-transfer, with tissue harvest for the early timepoint happening on day 5 post-transfer, and for the late timepoint on day 9 post-transfer. At specified time points, mice were euthanized and perfused with PBS. Lungs were then dissected, diced, and ground through a 140μm wire mesh into Complete T Cell Media. Single-cell suspensions were subsequently filtered through 70μm filters and centrifuged for 5 minutes at 1500 rpm. Cell pellets were resuspended in 1mL ACK Lysing Buffer for one minute for red blood cell lysis, neutralized with 9mL Complete T Cell Media, and centrifuged for 5 minutes at 1500 rpm. Cell pellets were washed once with FACS Buffer, centrifuged for 5 minutes at 1500 rpm, and resuspended in FACS Buffer. Samples were subsequently blocked with anti-mouse CD16/32 for 15 minutes at room temperature, incubated with primary antibodies for CD8α, Thy1.1, Thy1.2, CD44, and CD62L for 30 minutes on ice in the dark, washed with FACS Buffer, stained with DAPI for 10 minutes at 0.2μg/mL, washed with FACS Buffer, and resuspended in FACS Buffer. Samples were sorted on a Becton-Dickinson FACS Aria II sorter. DAPI- CD8α+ Thy1.1+ Thy1.2- and and DAPI- CD8α+ Thy1.1+ Thy1.2+ were sorted into Complete T cell Media, centrifuged for 5 minutes at 1500 rpm, washed with PBS, and resuspended into RLT lysis buffer supplemented with β-mercaptoethanol, and frozen at -80℃ until RNA extraction.

value: Tumor-bearing lung

value: day 5 post ACT

value: OT-I+ Thy1.1+/- CD8+ T cell

value: PKM2 knockout

value: female


title: RSB241-244 [Purmorphamine]

value: Purmorphamine


title: CD8+ T cell, PKM2 knockout, anti-PD-1 treated, Early timepoint, replicate 2 [P3T_Het]

description: 2x100 cycles


title: semimembranosus muscles, IVS_diosmin_rep1


title: RSB241-118 [S-Ruxolitinib (INCB018424)]

value: S-Ruxolitinib (INCB018424)


title: CD8+ T cell, PKM2 knockout, anti-PD-1 treated, Early timepoint, replicate 1 [P1T_Het]

description: 2x100 cycles


title: RSB241-176 [GW4064]


title: CD8+ T cell, PKM2 wildtype, anti-PD-1 treated, Early timepoint, replicate 3 [P5T_Homo]

description: 2x100 cycles

value: OT-I+ Thy1.1+/+ CD8+ T cell

value: PKM2 wildtype


title: semimembranosus muscles, IVS_rep1

source_name: semimembranosus muscles, IVS

value: Semimembranosus

value: Iliac vein stenosis


title: CD8+ T cell, PKM2 wildtype, anti-PD-1 treated, Early timepoint, replicate 2 [P3T_Homo]

description: 2x100 cycles


title: RSB241-202 [Ciproxifan]

value: Ciproxifan


title: semimembranosus muscles, IVS_rep2

value: 8 weeks


title: RSB241-251 [Esculin]

value: Human NGN2-driven iPSC-derived neurons

value: Esculin


title: RSB241-115 [Benidipine HCl]

value: Benidipine HCl


title: RSB241-179 [Temocapril HCl]

value: Temocapril HCl


title: CD8+ T cell, PKM2 wildtype, anti-PD-1 treated, Early timepoint, replicate 1 [P1T_Homo]

description: 2x100 cycles

value: Tumor-bearing lung


title: RSB241-346 [Nadifloxacin]

value: Nadifloxacin


title: RSB241-40 [Apocynin]

value: Apocynin


title: RSB241-314 [Foscarnet Sodium]

value: Foscarnet Sodium


title: RSB241-258 [SAR131675]


title: RSB241-205 [Prilocaine]

value: Prilocaine


title: RSB241-190 [TAK-715]


title: CD8+ T cell, PKM2 knockout, IgG treated, Early timepoint, replicate 2 [I3T_Het]

description: 2x100 cycles

value: day 5 post ACT

value: OT-I+ Thy1.1+/- CD8+ T cell

value: PKM2 knockout

value: IgG

value: female


title: CD8+ T cell, PKM2 knockout, IgG treated, Early timepoint, replicate 3 [I5T_Het]

description: 2x100 cycles


title: RSB241-339 [Troxerutin]

value: Troxerutin


title: RSB241-329 [Metoprolol Tartrate]

value: Metoprolol Tartrate


title: RSB241-319 [Silymarin]

value: Silymarin


title: RSB241-85 [Tolfenamic Acid]

value: Human NGN2-driven iPSC-derived neurons

value: Tolfenamic Acid


title: RSB241-42 [Guanosine]

value: Guanosine


title: RSB241-209 [CGS 21680 HCl]

value: CGS 21680 HCl


title: CD8+ T cell, PKM2 wildtype, IgG treated, Early timepoint, replicate 3 [I5T_Homo]

description: 2x100 cycles

value: Tumor-bearing lung

value: OT-I+ Thy1.1+/+ CD8+ T cell

value: PKM2 wildtype


title: RSB241-326 [VUF 10166]


title: CD8+ T cell, PKM2 knockout, IgG treated, Early timepoint, replicate 1 [I1T_Het]

description: 2x100 cycles


title: CD8+ T cell, PKM2 wildtype, IgG treated, Early timepoint, replicate 2 [I3T_Homo]

description: 2x100 cycles


title: RSB241-164 [Resminostat]

value: Resminostat


title: CD8+ T cell, PKM2 knockout, anti-PD-1 treated, Late timepoint, replicate 3 [P9T_Het]

description: 2x100 cycles

value: day 9 post ACT


title: RPE-KO-16H

type: RNA

city: Fukushima

first: Miwako

middle: Kato

last: Homma

department: Biomolecular Sciences

institute: Fukushima Medcial University Sch Medicine

hyb_protocol: Hybridization was performed with a hybridization kit (MicroDiagnostic) in hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an  GenePix 4000B scanner (Molecular Devices).

data_processing:
The signals were converted into primary expression ratios (ratio of cyanine-5 intensity of each sample to cyanine-3 intensity of the human common reference RNA). Each ratio was normalized through multiplication using normalization factors and Gene Pix Pro 3.0 software (Molecular Devices).
The primary expression ratio was converted to log2 values (designated as log ratios). Spots that exhibited fluorescence intensities below the detection limit were assigned a log ratio value of 0 and were not included in the signal calculations of the averages and subtracted log ratios. The data were processed using Microsoft Excel software (Microsoft, Redmond, WA, USA) and the MDI gene expression analysis software package (MicroDiagnostic).

source_name: CK2-knockout RPE cells

label_protocol: 5 μg of total RNA were labeled using SuperScript II (Invitrogen) and cyanine 5-dUTP (PerkinElmer) for samples or cyanine 3-dUTP (PerkinElmer) for human common reference RNA with a labeling kit (MicroDiagnostic)

growth_protocol: DMEM supplemented with 10% fetal bovine serum, no antibiotics included. Cells were maintained at 37 °C in a humidified 5% CO2 incubator.

extract_protocol: Total RNA was extracted from cells using ISOGEN (Nippon Gene, Tokyo, Japan) .

treatment_protocol: Logarithmically growing cells were starved in 0.1% FBS for 48 h to obtain G0 cells, and then cultured in fresh media containing 10% FBS for an additional 3h, 6h or 16 h to obtain cell. populations enriched in early or late G1 of the cell cycle, respectively. Microarray with synthetic polynucleotides (80-mers) representing 14,400 human transcripts (MicroDiagnostic, Tokyo, Japan).

value: RPE-KO

value: stimulated for 16H

source_name: Total RNA extracted from 22 cell lines

value: cancer cell lines


title: RPE-WT-24H

source_name: RPE cells

value: RPE-WT

value: stimulated for 24H


title: RSB241-63 [Triamcinolone]

value: Triamcinolone


title: RPE-WT-16H


title: CD8+ T cell, PKM2 knockout, anti-PD-1 treated, Late timepoint, replicate 2 [P8T_Het]

description: 2x100 cycles

value: OT-I+ Thy1.1+/- CD8+ T cell

value: PKM2 knockout

value: female


title: RSB241-331 [Diltiazem HCl]

value: Human NGN2-driven iPSC-derived neurons

value: Diltiazem HCl


title: RSB241-281 [Indole-3-carbinol]


title: RPE-KO-6H

value: stimulated for 6H


title: RPE-WT-6H


title: CD8+ T cell, PKM2 wildtype, IgG treated, Early timepoint, replicate 1 [I1T_Homo]

description: 2x100 cycles

value: Tumor-bearing lung

value: day 5 post ACT

value: IgG


title: RPE-KO-G0

value: serum starved (G0)


title: RSB241-351 [Naringin Dihydrochalcone]

value: Naringin Dihydrochalcone


title: RSB241-341 [Vanillylacetone]

value: Vanillylacetone


title: CD8+ T cell, PKM2 wildtype, anti-PD-1 treated, Late timepoint, replicate 3 [P9T_Homo]

description: 2x100 cycles

value: day 9 post ACT

value: OT-I+ Thy1.1+/+ CD8+ T cell

value: PKM2 wildtype


title: RSB241-167 [Tianeptine sodium]

value: Tianeptine sodium


title: S. exigua, fat body, TSA, rep3 [22044R-01-18_S88]

description:
Sexi_raw_counts.txt
Sexi_normalized_counts.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence with Trimmomatic (v0.39) using the following parameters: LEADING:5, TRAILING:5, MAXINFO:36:0.2, MINLEN:50.
T. ni reads were aligned to the T. ni Cornell-1 isolate genome (obtained from the T. ni Genome Database on 2022-05-25) and S. exigua reads were aligned to the S. exigua TB_SE_WUR_2020 isolate genome (WGS JACEFF01 obtained from the NCBI Genome Database on 2022-06-06) using HISAT2 (v2.2.1) with the default parameters.
featureCounts implemented in the Rsubread package (v2.12.2) was used to calculate read counts for each gene using the appropriate species-specific annotations.
Low-count genes (mean counts-per-million [CPM] across all samples > 10) were filtered and read counts were normalized using the trimmed mean of M-values (TMM) normalization method.
Assembly: T. ni Cornell-1 isolate (tn1)
Assembly: S. exigua TB_SE_WUR_2020 isolate (GCA_022117675.1)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TMM-normalized CPM values for each sample

organism: Spodoptera exigua

source_name: fat body

extract_protocol:
Larvae from each experiment group were dissected to isolate fat body tissue. To obtain sufficient tissue, fat bodies from 3 – 5 individual larvae were pooled per replicate.
Total RNA was extracted from the tissue twice using Buffer A (50 mM sodium acetate pH 5.2, 10 mM EDTA, 1 % SDS) saturated phenol heated to 65 °C, followed by phenol/chloroform (1:1) extraction. Extracts were ethanol precipitated, resuspended in ddH2O and ethanol precipitated again.
Poly(A) selection was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) following the manufacturer’s protocols. RNA-seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocols.

value: fat body

value: WT

value: TSA


title: RSB241-160 [HC-030031]

data_processing:
FastQ files were trimmed of adapter sequences using Cutadapt with the following parameters: cutadapt -u 1 -a TGGAATTCTCGGGTGCCAAGG -m 15.
Trimmed reads were aligned to miRBase 21 (hg38) by using Bowtie.
Assembly: hg38
Supplementary files format and content: tab-delimited Excel files include read count for each Sample

extract_protocol:
On day 20, four 10x photos were taken per well automatically using the ImageXpress Micro Confocal microscope (Molecular Devices). Then, the media in the plates was removed with approximately 20 μL media left, using a 24-channel stainless steel manifold (Drummond #3-000-101) linked with a vacuum at a low speed. With the help of Multidrop™ Combi Reagent Dispenser (Thermo Scientific) and the standard cassette (speed: low), 250 μL ice-cold DPBS (Wisent) was added per well. The DPBS was removed with approximately 20 μL liquid left, using another 24-channel stainless steel manifold linked with the vacuum at a low speed. The residual DPBS was completely removed using a mechanic 12-channel pipette. Next, 45 μL lysing solution was added per well using another Multidrop™ Combi Reagent Dispenser with the small cassette (speed: low), where the lysing solution is composed of single-cell lysis buffer (Takara #635013): 1x RNase Inhibitor Murine (NEB): nuclease-free water (Exiqon) = 19:1:190. Thorough lysis was achieved by shaking the plates on a shaker for 5 min at room temperature. The lysis samples were transferred from four 96-well plates to each 384-square-well plate using the 96-well module-coupled VPrep liquid handler (Agilent) with 30 μL tips (twice without changing tips). After sealing, the 384-square-well plates were spun down at 4000 rpm for 5 min, and 10 μL supernatant was aliquoted to a 384-well plate (Eppendorf) using the 384-well module-coupled VPrep liquid handler. The plates were finally sealed with the PlateLoc Heat Sealer (Agilent) and stored at -20oC.
To avoid RNA purification, we used RealSeq-T technology (RealSeq Biosciences) following manufacturer recommendations. In summary, cell lysates were incubated at 70C for 5 minutes on RealSeq hybridization buffer (100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl2, 1mM DTT, pH 7.9) with 1x RealSeq biotinylated DNA probes to target all miRNAs in miRbase 21. After 2 hours of incubation at 37C, 10 μL of RealSeq Beads were added, and miRNAs were captured using a 384-well Magnet Plate (Alpaqua, MA). Following three washes with RealSeq Wash buffer, miRNA was eluted from beads in 10uL of RNase-free water. All the miRNA elusion was input to prepare sequencing libraries with RealSeq-Biofluids following manufacturer instructions (RealSeq Biosciences). In summary, a single adapter and circularization approach was used. Libraries were barcoded with dual indexes and sequenced with a NextSeq 550 (Illumina, CA).


title: S. exigua, fat body, TSA, rep2 [22044R-01-17_S87]


title: CD8+ T cell, PKM2 wildtype, anti-PD-1 treated, Late timepoint, replicate 2 [P8T_Homo]

description: 2x100 cycles

value: female


title: RSB241-237 [Mesalamine]

value: Human NGN2-driven iPSC-derived neurons

value: Mesalamine


title: RSB241-94 [ZM 306416]


title: CD8+ T cell, PKM2 knockout, anti-PD-1 treated, Late timepoint, replicate 1 [P7T_Het]

description: 2x100 cycles

value: OT-I+ Thy1.1+/- CD8+ T cell

value: PKM2 knockout


title: RPE-WT-G0

value: RPE-WT

value: cancer cell lines


title: RSB241-178 [IOX2]


title: S. exigua, fat body, SFN, rep3 [22044R-01-15_S85]

value: SFN


title: RSB241-156 [GW9662]


title: CD8+ T cell, PKM2 knockout, IgG treated, Late timepoint, replicate 3 [I12T_Het]

description: 2x100 cycles

value: Tumor-bearing lung

value: IgG


title: RSB241-207 [Allopurinol]

value: Allopurinol


title: RSB241-316 [Beclomethasone dipropionate]

value: Beclomethasone dipropionate


title: CD8+ T cell, PKM2 wildtype, anti-PD-1 treated, Late timepoint, replicate 1 [P7T_Homo]

description: 2x100 cycles

value: day 9 post ACT

value: OT-I+ Thy1.1+/+ CD8+ T cell

value: PKM2 wildtype


title: RSB241-105 [Costunolide]

value: Costunolide


title: RSB241-175 [Org 27569]


title: S. exigua, fat body, SFN, rep2 [22044R-01-14_S84]

value: fat body

value: WT


title: RPE-KO-24H

value: RPE-KO

value: stimulated for 24H


title: RSB241-223 [Aliskiren Hemifumarate]

value: Human NGN2-driven iPSC-derived neurons

value: Aliskiren Hemifumarate


title: CD8+ T cell, PKM2 knockout, IgG treated, Late timepoint, replicate 1 [I8T_Het]

description: 2x100 cycles

value: OT-I+ Thy1.1+/- CD8+ T cell

value: PKM2 knockout

value: female


title: RSB241-119 [Urapidil HCl]

value: Urapidil HCl


title: S. exigua, fat body, control, rep3 [22044R-01-12_S82]

value: EtOH


title: RSB241-192 [Pifithrin-? (PFT?)]

value: Pifithrin-? (PFT?)


title: TG0072A_Gut

type: genomic

first: Michael

last: Corley

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

description: TGW/Gut

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Illumina Infinium HumanMethylationEPIC protocol. Scanned using Illumina HiScan System.

data_processing: IDAT Data loaded into R using The Chip Analysis Methylation Pipeline (ChAMP) and normalized using BMIQ method.

label: Cy5 and Cy3

source_name: Sigmoid Biopsy from TGW

label_protocol: Illumina Infinium protocol. Cy5 and Cy3

extract_protocol: Genomic DNA was extracted from FACS sorted cells in RLT buffer using the Qiagen Allprep Universal DNA/RNA kit according to manufacturer's instructions. DNA was bisulfite converted using the Zymo EZ DNA methylation kit.

tag: condition

value: TGW

tag: disease state

value: HIV-

value: Sigmoid


title: CD8+ T cell, PKM2 knockout, IgG treated, Late timepoint, replicate 2 [I9T_Het]

description: 2x100 cycles

value: Tumor-bearing lung

value: day 9 post ACT

value: IgG


title: CD8+ T cell, PKM2 wildtype, IgG treated, Late timepoint, replicate 3 [I12T_Homo]

description: 2x100 cycles

value: OT-I+ Thy1.1+/+ CD8+ T cell

value: PKM2 wildtype


title: RSB241-78 [Phenytoin sodium]

value: Phenytoin sodium


title: RSB241-182 [Icotinib]

value: Human NGN2-driven iPSC-derived neurons

value: Icotinib


title: RSB241-114 [Cobicistat (GS-9350)]

value: Cobicistat (GS-9350)


title: S. exigua, fat body, control, rep2 [22044R-01-11_S81]

value: fat body

value: WT


title: CD8+ T cell, PKM2 wildtype, IgG treated, Late timepoint, replicate 2 [I9T_Homo]

description: 2x100 cycles

value: female


title: RSB241-36 [Palmatine chloride]

value: Palmatine chloride


title: CD8+ T cell, PKM2 wildtype, IgG treated, Late timepoint, replicate 1 [I8T_Homo]

description: 2x100 cycles


title: TG0071A_Gut

description: TGW/Gut


title: RSB241-220 [Daunorubicin HCl]

value: Daunorubicin HCl


title: S. exigua, fat body, TSA, rep1 [22044R-01-16_S86]

value: TSA


title: S. exigua, fat body, SFN, rep1 [22044R-01-13_S83]

value: SFN


title: S. exigua, fat body, control, rep1 [22044R-01-10_S80]

value: EtOH


title: RSB241-44 [Inosine]

value: Inosine


title: SiScd1-4_L2_2

city: Hangzhou

first: Hua

last: Yu

address: No.18 Shilongshan Road

institute: Westlake University

data_processing:
The RNA-seq raw data in fastq format were first processed to obtain clean data using fastp v0.23.2 software with the default parameters to trim reads containing adapters, to filter low quality reads and reads containing N bases.
Then the clean data were aligned to the GRCm39 (UCSC) genome assemblies using STAR v.2.7.10a software with default parameters.
The uniquely mapped read pairs were counted using featureCounts v2.0.1 software.
Assembly: mm39
Supplementary files format and content: xlsx, gene expression level

source_name: embryo

growth_protocol: Embryos were cultured in BSA-free KSOM medium covered with minor oil from zygote stage to 4.5dpc blastocyst stage.

extract_protocol:
Embryo were lysied firstly and cDNA was made with Superscript II reverse transcriptase.
The cDNA was amplified with KAPA Hifi HotStart using ~12 cycles. Sequencing libraries were constructed from 1 ng of preamplified cDNA using a DNA library preparation kit (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme). Libraries were sequenced on a HiSeq PE150 according to the manufacturer’s instructions.

treatment_protocol: Scd1 were inhibited/ knocked down at zygote stage and cultured until 4.5dpc blastocyst stage.

value: Scd1 knock down


title: gal80Δ, midlog+16h, fructose+palatinose, C

city: Edinburgh

middle: S

last: Swain

address: CH Waddington Building, Mayfield Road

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

data_processing:
The data processing pipeline is written in Nextflow and the repository is available at: https://git.ecdf.ed.ac.uk/s1856140/rnaseq-paired-end
Run FastQC v0.11.9 to produce a quality control report for the input data for every sample
Cut sequencing adapters from 3' end of gene with Cutadapt v1.18
Align reads to genome with HISAT2 v2.1.0
Turn unsorted aligned SAM files into sorted indexed compressed BAM files with SAMtools v1.11
Make bedgraphs showing coverage of aligned reads with BEDTools v2.30.0.
Run featureCounts (in Subread v2.0.0) to count aligned reads to genes for all processed samples
Run multiQC v1.13 to collate single quality control report across all samples.
Assembly: R64-1-1
Supplementary files format and content: CSV file that includes the counts per million reads (CPM) of each gene in each sample in a tidy format.

organism: Saccharomyces cerevisiae

growth_protocol: (1) FY4 (Brachmann et al, Yeast, 1998) cells were pre-cultured in media supplemented with 2% (w/v) sodium pyruvate in a 30C shaking incubator at 180 rpm for 40 hours, and diluted 6-fold with fresh media 6 hours before the experiment. (2) When the experiment began, the cells were washed twice with minimal (Delft) media without carbon sources and then inoculated into 250 mL flasks with 25 mL minimal (Delft) media supplemented with desired concentrations of fructose and palatinose. The volume of inoculated cells was calculated such that the initial OD was 0.05, and then the volume of each culture was topped up to 26 mL. (3) The cultures were then incubated in a 30C shaking incubator at 180 rpm.

extract_protocol:
For each sample, we harvested x mL of cells, such that the value of OD*x is around 4, by centrifuging the cells at 3500 rpm for 3 minutes at 4C. The supernatant was then removed and the cell pellets were stored in -80C. (2) We followed a column-based protocol on protocol.io to extract RNA: dx.doi.org/10.17504/protocols.io.beetjben, starting from Step 16 without using the deep well plate. Sample quality control was performed on the Fragment Analyser Automated Capillary Electrophoresis System (Agilent Technologies Inc, #5300) with the Standard Sensitivity RNA Analysis Kit (#DNF-471-0500) for quality, and on the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, #Q32866) with the Qubit RNA broad range assay kit (#10210) for quantification. The Qubit dsDNA HS assay kit (#Q32854) was used to quantify DNA contamination.
Libraries were generated from 400 ng of each total RNA sample with the QuantSeq 3' mRNA Library Prep Kit REV for Illumina (Lexogen Inc, #016) according to the manufacturer's protocol. A Custom Sequencing Primer (CSP Version 5, included in the kit) was used for Read 1. The libraries were then quantified by fluorometry with the Qubit dsDNA High Sensitivity assay, followed by assessment of quality and fragment size with the Agilent Fragment Analyser with the SS NGS Fragment 1--6000bp kit (#DNF-473-33). Sequencing was  performed  on  the  NextSeq 2000 platform (Illumina  Inc, #20038897) using NextSeq 1000/2000 P2 Reagents (100 Cycles) v3 (#20046811).

value: deleted gal80

value: 0.1% fructose + 0.9% palatinose

tag: time

value: mid-log + 16 h


title: gal80Δ, midlog+16h, fructose+palatinose, B


title: RSB241-296 [StemRegenin 1 (SR1)]

last: Wei

value: StemRegenin 1 (SR1)


title: SiScd1-3_L2_1


title: RSB241-96 [GNF-2]

value: Human NGN2-driven iPSC-derived neurons


title: RSB241-313 [Orotic acid (6-Carboxyuracil)]

value: Orotic acid (6-Carboxyuracil)


title: RSB241-185 [Flunixin Meglumin]

value: Flunixin Meglumin


title: SiScd1-1_L2_1


title: gal80Δ, midlog+16h, fructose+palatinose, A


title: RSB241-143 [Mosapride Citrate]

value: Mosapride Citrate


title: RSB241-135 [Lidocaine]

value: Lidocaine


title: gal80Δ, midlog+16h, fructose, C

value: 0.1% fructose


title: RSB241-266 [SB269970 HCl]


title: NC KO rep2

value: negative NC knockdown


title: RSB241-315 [Rutin]

value: Rutin


title: RSB241-110 [Phenacetin]

value: Phenacetin


title: RSB241-195 [Candesartan]

value: Candesartan


title: CAY_rep2

value: Scd1 inhibition


title: NC KO rep1


title: RSB241-305 [Myricitrin]

value: Myricitrin


title: gal80Δ, midlog+16h, fructose, A


title: CAY_rep1


title: WT, midlog+16h, fructose+palatinose, C

value: wildtype


title: WT, midlog+16h, fructose+palatinose, B


title: RSB241-99 [Benazepril HCl]

value: Benazepril HCl


title: RSB241-67 [Bleomycin Sulfate]

value: Bleomycin Sulfate


title: RSB241-332 [Alogliptin]

value: Alogliptin


title: WT embryo rep1

value: DMSO treated


title: WT embryo rep2


title: RSB241-81 [Enalapril Maleate]

value: Human NGN2-driven iPSC-derived neurons

value: Enalapril Maleate


title: RSB241-155 [Adiphenine HCl]

value: Adiphenine HCl


title: RSB241-215 [PD128907 HCl]


title: gal80Δ, midlog+16h, fructose, B

value: deleted gal80

value: mid-log + 16 h


title: WT, midlog+16h, fructose, C

value: 0.1% fructose


title: WT, midlog+16h, fructose+palatinose, A

value: 0.1% fructose + 0.9% palatinose


title: plp4h, biol rep 3, injury

city: Irapuato

first: Alfredo

last: Herrera Estrella

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: LANGEBIO

country: Mexico

institute: CINVESTAV

data_processing:
Non-barcoded sequencing reads were trimmed to remove the first ten bases from the start of the read.
Trimmed sequence reads were mapped to a new version of Trichoderma atroviride assembled genome (accession number: JAEAGS000000000) using HISAT2 (V. 2.2.1). Then, reads overlapping each gene model were counted using HTseq (V 2.0.2).
Gene expression analysis was performed using the edgeR package in R.
Assembly: JAEAGS000000000
Supplementary files format and content: The text file, raw_counts.txt, contains a raw count (CPM) matrix.
Supplementary files format and content: Text files contain raw count (CPM) values for each sample.

organism: Trichoderma atroviride

source_name: Mycelium

growth_protocol: All strains were propagated in potato dextrose agar (PDA; Difco) at 27 °C in complete darkness, before and after injury.

extract_protocol:
Harvested mycelium was immediately frozen with liquid nitrogen. Then, total RNA was extracted with Trizol.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Library Prep Set following the manufacturer's protocols.

treatment_protocol: 36 h old vegetative mycelium (grown in PDA) was damaged using a sterile scalpel to generate injury squares of 0.5 cm x 0.5 cm. Then, damaged mycelium was harvested after 90 min and 4 h (injury), or 0 h (undamaged mycelium or control).

tag: tissue

value: Mycelium

tag: background strain

value: 4 hours

value: injury


title: RSB241-271 [Suprofen]

first: Zhiyun

tag: treatment

value: Suprofen


title: RSB241-103 [Mercaptopurine (6-MP)]

tag: cell line

value: Mercaptopurine (6-MP)


title: HP4HA1_replicate_1

city: Athens

first: Wentao

last: Li

state: GA

address: 500 D. W Brooks Drive

department: Environmental Health Science

institute: University of Georgia

data_processing:
adaptor trimming and deduplication
alignment
reads filtering
strand separation
gene coverage count
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: tXR-seq

source_name: liver

growth_protocol: HepG2 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS at 37 °C in a 5% CO2 humidified chamber.

extract_protocol:
Cells were lysed gently and small molecular weight DNA, consisting mostly of excision products separated from chromosomal high molecular weight DNA by centrifugation.
Briefly, the excision products were captured by TFIIH/XPG IP and treated with carbonate-bicarbonate buffer (pH 9.6) to convert the AFB1-N7-dG to the ring-opened AFB1-FAPY-dG adducts. Following adaptor ligation, the adaptor-ligated excision products were further purified by IP with anti-aflatoxin monoclonal antibody. Then sulfolobus DNA polymerase IV was used to bypass the AFB1-FAPY-dG adduct during the primer extension step of tXR-seq. After purification of the primer extension products, Kapa Hotstart Readymix was used for amplifying the library.

treatment_protocol: For aflatoxin treatment, an AFB1 stock solution (4 mM) was added to the HepG2 cell culture medium in a cell culture flask, resulting in a final concentration of 40 µM. The cells were cultured for 4 hours, with gentle shaking every 30 minutes to ensure cell suspension in the medium.

value: liver

tag: cell type

value: Human hepatoma cell

tag: genotype

value: WT


title: RSB241-154 [Dapivirine (TMC120)]

city: Boston

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

value: Dapivirine (TMC120)


title: HP4HA2_replicate_2


title: TG0073A_Gut

description: TGW/Gut

value: TGW

value: HIV-

value: Sigmoid


title: plpc, biol rep 3, injury, barcode 94

description:
plpc-3r
plpc-3 and plpc-3r belong to the same library, each tagged with distinct barcodes

value: 0 h

value: control


title: RSB241-66 [Equol]

value: Human NGN2-driven iPSC-derived neurons

value: Equol


title: WT, midlog+16h, fructose, B

value: wildtype

value: 0.1% fructose

value: mid-log + 16 h


title: RSB241-259 [Divalproex Sodium]

value: Divalproex Sodium


title: RPE_KO_Input [0414]

data_processing:
Basecalls conversion was performed using bcl2fastq v1.8.4 for Hiseq2500 output.
ChIP-seq reads quality was assessed with FastQC version 0.1.1.7
ChIP-seq reads were mapped to the UCSC hg38 genome using Bowtie version 1.2.3 with "-n2 -m1" option. Only uniquely mapping reads with at most two mismatches were retained.
Mapped reads were used to make Bigwig files with parse2wig+ command of SROMPA+ v1.17.0 (  )
Peaks calling and visualization were performed also using DROMPA+, with PC SHARP command.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: RPE-CK3 deficient

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min for PolII, H3K4me3, H3K27ac, or PolIISer2P ChIP, and with di-succinimidyly-glutarate for 45 min, followed by 10 min fixation with 1% formaldehyde for CK2a ChIP. Fixation was performed at room temperature and terminated by incubation with 125 mM glycine for 10 min. Fixed chromatin was sonicated in lysis buffer containing 20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% Triton X-100, 1% NP-40, 1% sodium cholate, 0.1% SDS, using a Branson Sonifier 250D to generate DNA fragments with a mean length of 300-1000 bp.
Input and ChIP DNA was processed and sequenced according to the manufacturer’s instructions. Briefly, DNA was sheared to an average size of ~150 bp with ultrasonication (Covaris), end-repaired, ligated to sequencing adapters, amplified, size-selected, and DNA was then sequenced to generate single-end 65-bp reads using the Illumina HiSeq-2500  systems.

treatment_protocol: Logarithmically growing cells were starved in 0.1% FBS for 48 h, and then cultured in fresh media containing 10% FBS for an additional 6 or 15-16 h to obtain cell populations enriched in early G1 or late G1 of the cell cycle, respecitvely.

value: RPE-CK3 deficient

value: Retinal Pigment Epithelial

tag: chip antibody

value: Early G1


title: gal80Δ, midlog+10h, fructose+palatinose, C

value: deleted gal80

value: 0.1% fructose + 0.9% palatinose

value: mid-log + 10 h


title: plp90m, biol rep 3, injury

value: Mycelium

value: 90 minutes

value: injury


title: gal80Δ, midlog+10h, fructose+palatinose, B


title: plpc, biol rep 3, injury, barcode 93

description:
plpc-3
plpc-3 and plpc-3r belong to the same library, each tagged with distinct barcodes

value: 0 h


title: RPE-KO_CK2 [0414]

source_name: RPE-CK2 deficient

value: RPE-CK2 deficient


title: lox4h, biol rep 3, injury, barcode 92

description:
lox4h-3r
lox4h-3 and lox4h-3r belong to the same library, each tagged with distinct barcodes

value: 4 hours


title: RSB241-180 [PF-4981517]

value: Human NGN2-driven iPSC-derived neurons


title: gal80Δ, midlog+10h, fructose, C


title: RSB241-184 [Salubrinal]

value: Salubrinal


title: RPE_Input [0420]

source_name: RPE

value: RPE


title: gal80Δ, midlog+10h, fructose+palatinose, A


title: gal80Δ, midlog+10h, fructose, B

value: 0.1% fructose


title: lox4h, biol rep 3, injury, barcode 91

description:
lox4h-3
lox4h-3 and lox4h-3r belong to the same library, each tagged with distinct barcodes


title: RPE_Pol II [0420]

value: Pol II(CMA601), kindly provided by Dr. H Kimura (TITech)


title: RPE_Pol II-Ser2P [0420]

value: Pol II-Ser2P(CMA602), kindly provided by Dr. H Kimura (TITech)


title: WT, midlog+16h, fructose, A

value: wildtype

value: mid-log + 16 h


title: RSB241-171 [Calcifediol]

value: Calcifediol


title: RSB241-250 [Azilsartan]

value: Azilsartan


title: RSB241-74 [Naphazoline HCl]

value: Naphazoline HCl


title: lox90m, biol rep 3, injury, barcode 90

description:
lox90m-3r
lox90m-3 and lox90m-3 belong to the same library, each tagged with distinct barcodes

value: Mycelium


title: RPE_H3K27ac1 [0420]

value: Retinal Pigment Epithelial

value: H3K27ac1(CMA309), kindly provided by Dr. H Kimura (TITech)

value: Early G1


title: lox90m, biol rep 3, injury, barcode 89

description:
lox90m-3
lox90m-3 and lox90m-3 belong to the same library, each tagged with distinct barcodes

value: 90 minutes

value: injury


title: gal80Δ, midlog+10h, fructose, A

value: deleted gal80

value: mid-log + 10 h


title: WT, midlog+10h, fructose+palatinose, C

value: 0.1% fructose + 0.9% palatinose


title: RSB241-312 [Dexmedetomidine]

value: Human NGN2-driven iPSC-derived neurons

value: Dexmedetomidine


title: wt4h, biol rep 3, injury

value: 4 hours

value: WT


title: RPE_H3K4me3 [0420]

value: RPE

value: H3K4me3(CMA304), kindly provided by Dr. H Kimura (TITech)


title: RPE_Input [0414]


title: RSB241-323 [Atracurium Besylate]

value: Atracurium Besylate


title: WT, midlog+10h, fructose+palatinose, B

value: wildtype


title: wt90m, biol rep 3, injury

value: Mycelium


title: WT, midlog+10h, fructose+palatinose, A


title: RSB241-307 [Naringin]

value: Naringin


title: RPE_CK2 Early [0414]

value: Retinal Pigment Epithelial


title: wtc, biol rep 3, control

value: 0 h

value: control


title: RPE_KO_Input [0127]

value: RPE-CK3 deficient

value: Late G1


title: WT, midlog+10h, fructose, C

value: 0.1% fructose

value: mid-log + 10 h


title: RSB241-61 [Phenindione]

value: Human NGN2-driven iPSC-derived neurons

value: Phenindione


title: plp4h, biol rep 2, injury

value: 4 hours

value: injury


title: RPE_Input [0404]

value: RPE


title: WT, midlog+10h, fructose, B


title: RSB241-186 [Evacetrapib (LY2484595)]

value: Evacetrapib (LY2484595)


title: plp90m, biol rep 2, injury

value: 90 minutes


title: RSB241-169 [Alfacalcidol]

value: Alfacalcidol


title: gal80Δ, midlog, fructose+palatinose, C

value: deleted gal80

value: 0.1% fructose + 0.9% palatinose

value: mid-log


title: loxc, biol rep 3, injury

value: Mycelium

value: 0 h


title: plpc, biol rep 2, control

value: control


title: gal80Δ, midlog, fructose+palatinose, B


title: RPE_Pol II [0404]

value: Retinal Pigment Epithelial

value: Pol II(CMA601), kindly provided by Dr. H Kimura (TITech)

value: Late G1


title: RSB241-232 [TPCA-1]

value: Human NGN2-driven iPSC-derived neurons


title: lox4h, biol rep 2, injury


title: lox90m, biol rep 2, injury


title: RSB241-322 [ML130 (Nodinitib-1)]

value: ML130 (Nodinitib-1)


title: gal80Δ, midlog, fructose+palatinose, A


title: RSB241-84 [PF-562271]


title: RPE_H3K4me3 [0404]

value: H3K4me3(CMA304), kindly provided by Dr. H Kimura (TITech)


title: wt4h, biol rep 2, injury

value: 4 hours

value: WT

value: injury


title: gal80Δ, midlog, fructose, C

value: 0.1% fructose


title: RSB241-253 [Chlorogenic Acid]

value: Chlorogenic Acid


title: wt90m, biol rep 2, injury

value: 90 minutes


title: WT, midlog+10h, fructose, A

value: wildtype

value: mid-log + 10 h


title: RSB241-256 [Bosentan Hydrate]

value: Bosentan Hydrate


title: gal80Δ, midlog, fructose, B

value: deleted gal80

value: mid-log


title: RPE_Pol II-Ser2P [0404]

value: RPE

value: Retinal Pigment Epithelial

value: Pol II-Ser2P(CMA602), kindly provided by Dr. H Kimura (TITech)


title: RPE-KO_CK2 [0127]

value: RPE-CK2 deficient

value: Late G1


title: wtc, biol rep 2, control

value: Mycelium

value: 0 h

value: control


title: RSB241-124 [JNJ-7777120]

value: Human NGN2-driven iPSC-derived neurons


title: RPE_CK2 Late [0127]


title: plp4h, biol rep 1, injury

value: 4 hours

value: injury


title: RSB241-162 [BMY 7378]


title: RSB241-139 [Rigosertib (ON-01910)]

value: Rigosertib (ON-01910)


title: RPE_H3K27ac1 [0404]

value: H3K27ac1(CMA309), kindly provided by Dr. H Kimura (TITech)


title: SD rats 3 (S3), DON implant, 2 week

city: Guangzhou

first: Rongjie

last: Wu

address: Yuexiu District, 106, Zhongshan Road

institute: Guangdong Pronvincial People's Hospital

description:
1DON_2W_3
Gene expression.csv

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC (v0.11.2).
Clean reads were aligned to the referance genome using STAR(2.5.3a).
The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using StringTie (v1.3.1c).
Differentially expression genes(DEGs) were determined by DEGseq2(v1.16.1).
Assembly: rn6
Supplementary files format and content: Gene expression.csv contain FPKM value for each sample

organism: Rattus norvegicus

source_name: spinal cord

extract_protocol:
Total RNA was isolated from each sample using RNAiso Plus (TARAKA).
Libraries were constructed using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China), and sequencing was carried out using the Illumina Novaseq 6000 instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: spinal cord

value: Sprague-Dawley

value: DON implant


title: SD rats 2 (S2), DON implant, 2 week

description:
1DON_2W_2
Gene expression.csv


title: WT, midlog, fructose+palatinose, B

value: wildtype

value: 0.1% fructose + 0.9% palatinose

value: mid-log


title: plpc, biol rep 1, control


title: plp90m, biol rep 1, injury

value: 90 minutes


title: WT, midlog, fructose+palatinose, C


title: WT, midlog, fructose+palatinose, A


title: RSB241-82 [PJ34]


title: RPE_Input [0127]

value: RPE

value: Retinal Pigment Epithelial


title: SD rats 3 (S3), A-DON implant, 2 week

description:
2DON_APT2W_3
Gene expression.csv

value: A-DON implant


title: lox4h, biol rep 1, injury

value: Mycelium


title: lox90m, biol rep 1, injury


title: WT, midlog, fructose, C

value: 0.1% fructose


title: SD rats 2 (S2), A-DON implant, 2 week

description:
2DON_APT2W_2
Gene expression.csv


title: gal80Δ, midlog, fructose, A

value: deleted gal80


title: WT, midlog, fructose, B


title: RSB241-247 [Fesoterodine Fumarate]

value: Human NGN2-driven iPSC-derived neurons

value: Fesoterodine Fumarate


title: SD rats 1 (S1), A-DON implant, 2 week

description:
2DON_APT2W_1
Gene expression.csv


title: loxc, biol rep 1, control

value: 0 h

value: control


title: RSB241-243 [VX-765]


title: wt4h, biol rep 1, injury

value: 4 hours

value: WT

value: injury