title: PRAISE-seq-HuCCT1-Input3

description: Library name: PRAISE-seq-HuCCT1-Input3

data_processing:
To identify Ψ modification sites, the PRAISE sequencing data from HEK293T and HuCCT1 cells, together with  sequencing data  were analyzed using BASAL. Analysis was conducted with parameters ‘-M T:-’. Candidate Ψ sites were further filtered based on the following stringent criteria: (i) deletion rate > 5% in treated samples; (ii) frequency of the ‘convert-to’ bases (deletions in this case) > 3 in treated samples; (iii) deletion rate < 1% in control samples; (iv) sequencing depth > 10 in both treated and control samples; (v) the deletion rates in treated samples were > 1.5-fold of the deletion rates in control samples or met statistical significance (FDR < 0.05), and the candidate sites were detected in all biological replicates.
Assembly: hg38


title: IFNg Ax 50 sample10

status: Public on Jun 30 2026

type: SRA

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior St

department: Pulmonary and Critical Care

country: USA

institute: Northwestern University

description: Library name: IFNg_Ax_50_sample10

library_source: transcriptomic single cell

data_processing:
Data was processed using Cell Ranger 3.1.0 (10x Genomics), reads were mapped to GRCh38.84 reference genome (10x Genomics Cell Ranger Human 1.2.0 GRCh38 reference). Data was processed using Scanpy 1.10.4, and multisample integration was performed with scvi-tools 1.3.0. The scVI model was constructed on 2000 HVGs with the hyperparameters n_layers = 2, dropout_rate = 0.2, and n_latent = 10, and were trained using the settings max_epochs = 400, check_val_every_n_epoch = 2, and early_stopping = True. Default hyperparameters and settings were used otherwise. An initial round of Leiden clustering using the function sc.tl.leiden was performed on the integrated BAL object with a resolution of 1. Clusters characterized by low number of detected genes and transcripts and high percentage of mitochondrial genes were removed.
Assembly: GRCh38.84
Supplementary files format and content: Tab-separated values file and matrix file

molecule: total RNA

organism: Homo sapiens

source_name: lung

extract_protocol:
BALF samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 rcf for 10 min at 4°C, followed by hypotonic erythrocyte lysis using 1 ml of PharmLyse solution (BD) for 2 min, followed by another wash with 10 ml of 0.5% BSA in PBS and centrifugation. Cell pellet was resuspended in 0.5% BSA in PBS at the final concentration 1000 cells/ul. Cell concentration and viability were determined using K2 Cellometer (Nexcelom) with AO/PI reagent and cells were loaded on 10x Genomics Chip A with Chromium Single Cell 3′ V2 gel beads and reagents (10x Genomics) aiming to capture 5,000–7,000 cells per library.
Libraries were prepared according to the manufacturer’s protocol (10x Genomics, CG000052_RevB). BAL sample processing for scRNA-seq using “FACS” protocol: BAL fluid samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 relative centrifugal force (rcf) for 10 min at 4 °C, followed by hypotonic lysis of red blood cells with 2 ml of PharmLyse (BD Biosciences) reagent for 2 min. Lysis was stopped by adding 13 ml of MACS buffer (Miltenyi Biotech). Cells were pelleted again and resuspended in 100 μl of a 1:10 dilution of Human TruStain FcX (BioLegend) in MACS buffer and a 10-μl aliquot was taken for counting using a K2 Cellometer (Nexcelom) with Acridine orange (AO)/Propidium iodide (PI) reagent. The cell suspension volume was adjusted so the concentration of cells was always < 5 × 107 cells/ ml and the fluorophore-conjugated antibody cocktail was added in a 1:1 ratio.

tag: tissue

value: lung

tag: agent

value: IFNg Auxora 50 nM

tag: batch


title: seedlings_C1_pifq_ZT1_R2

city: York

first: Gina

last: Vong

address: Wentworth Way

department: Biology

country: United Kingdom

institute: University of York

description: Library name: P84

library_source: transcriptomic

data_processing:
fastq files were merged across lanes
Illumina adaptors were trimmed with Trim_Galore/0.6.10-GCCcore-11.3.0 --clip_R1 12 --clip_R2 12
Reads were mapped using Salmon/1.10.0-GCC-11.3.0
quantified reads were processed into abundance, counts and length tables using tximport v.1.34.0 in R v.4.5
Assembly: AtRTD3
Supplementary files format and content: Salmon quant output for each sample.
Supplementary files format and content: abundance_table_salmon.txt, counts_table_salmon.txt and length_table_salmon.txt are tab separated tables containing gene expression data for TPM, counts and read leangths respectively. Each row is a gene and each column is a sample.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seeds were surface sterilised and plated on 1xMS plates with 1% sucrose and 3% agar, in clusters of ~50 seeds. We stratified 3 genotypes of Arabidopsis thaliana (col-0, elf3-1, pifq) seeds at 4C for 3 days. To initiate germination, we exposed all plates to 24h continuous light with blue, red, far-red LEDs at 1:1:1 ratio. We grew the seedlings (on plates) in Snijders (Tilburg, Netherlands) MC1750 growth chamber at 22C and 60% room humidity under 4 light regimes: a) linear dawn; b) extreme dawn; c) 8h photoperiod control; d) 7h photoperiod control. After 7 days of growth, the seedlings were sampled every 30 mins from ZT-0.5 to ZT3 (i.e. 8 timepoints) for 2 replicates of  RNA-seq transcriptome analysis.

extract_protocol:
RNA was extracted using the Omega BioTek EZNA Plant RNA kit, following their protocols
NEBNext Ultra II Directional Library Prep Kit for Illumina, with NEBNext ploy(A) magnetic isolation

treatment_protocol: a) linear dawn (T1): blue, red and far red lights with a 1:1:1 ratio which increased in irradiance stepwise every 10 minutes, for 2h until a maximum PAR of 27.8 umol m-2 s-1. The maximum was sustained for a further 6h before lights turned off. b) extreme dawn (T2): using the same blue, red, far red light settings as the linear dawn treatment, but increasing the slope of the red channel and starting that 0.5h later than the other channels. This resulted in a <1 ratio initially (red relative to the other channels) but increasing as time progressed until the maximum PAR of 27.8 umol m-2 s-1. At the maximum, the B:R:FR ratio was 1:1:1 and was sustained for a further 6h before lights turned off. c) 8h control (C1): on/off square wave 8h photoperiod, with B:R:FR ratios at 1:1:1 d) 7h contro (C2)l: on/off square wave 7h photoperiod, with B:R:FR ratios at 1:1:1

value: seedling

tag: genotype

value: pifq

tag: treatment


title: PRAISE-seq-HuCCT1-Input2

city: Shanghai, P.R. China

first: weiying

last: meng

address: 1239 Siping Road, Shanghai, P.R. China

country: China

institute: Tongji University

description: Library name: PRAISE-seq-HuCCT1-Input2

source_name: cell line

extract_protocol:
PRAISE-seq Pre-mRNA purification:Ribosomal RNA was depleted using the Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme, N406) according to the manufacturer's protocol. Sulfite/bisulfite treatment:The 85% sulfite/15% bisulfite solution was prepared freshly by adding 2.58 g of potassium sulfite (Aladdin, P112413) and 0.3 g sodium bisulfite (Oxoid, 10019018) to 8 ml of RNase-free water and the solution was vortexed to clear (pH value is ~7.5). The 100 mM hydroquinone was prepared freshly by adding 11.01 mg of hydroquinone (Oxioid, 10011317) to 1 ml of RNase-free water. For sulfite/bisulfite treatment, 5 µl of RNA fragments was dissolved in 50 µl sulfite/bisulfite solution, which is a 100:1 mixture of 85% sulfite/15% bisulfite solution and 100 mM hydroquinone, and subjected to heat incubation at 70 °C for 5 h. The reaction mixture was purified by passing it through Spin Column (Sangon, B518688). Desulfonation:Purified RNA was transferred to a new 1.5 ml nuclease-free tube and adjusted to 100 μl with RNase-free water, then incubated with an equal volume of 1 M Tris–HCl (pH 9.0) at 75 °C for 30 min. The reaction was then immediately stopped by chilling on ice and ethanol precipitation. Add a coprecipitant (Takara, 9094) to aid in precipitation during the settling process. After ethanol precipitation, the RNA was resuspended in 10 µl of RNase-free water, and the concentration of RNA was quantified by Qubit RNA HS Assay Kit (Invitrogen, Q33231). Take 50 ng RNA (~1 µl) as ‘treated’ sample for subsequent library construction.
Library construction:‘Treated’ RNA sample and ‘untreated’ RNA sample were subjected to library construction. For first-strand cDNA synthesis, Maxima H minus Reverse Transcriptase (Thermo Fisher, K1651) was used. Second, we used RNase H to remove mRNA (Thermo Fisher, EN0201) and finally, for second-strand cDNA synthesis, VATHS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme, NR606) was used. Twelve cycles were used for untreated and treated RNA in the second round of PCR. High-throughput sequencing was performed on the Illumina xplus system.

value: cell line

tag: cell line

tag: cell type


title: IFNg Ax 50 sample9

description: Library name: IFNg_Ax_50_sample9


title: CDAA-WT-02

city: Bethesda

first: Yaron

last: Rotman

state: MD

address: 10 Center Drive, 10/10N248C

department: Liver Diseases Branch

institute: NIDDK

data_processing:
Transcriptomic analysis was performed using Partek Flow software (version 10.0).
Raw data were quality checked and trimmed (Phred score <30), then aligned to the mus musculus (mm10) reference genome using STAR (version 2.7.3a).
Transcripts were quantified and annotated using Ensembl (release 100).
Differential gene expression was examined using DESeq2 (version 1.14.1) R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA samples were extracted from 25-100 mg mouse liver tissues using TRIzol Reagent followed by purification process using RNeasy mini-Kit (QIAGEN, 74106) and RNase-free DNase set (QIAGEN, 79256).
Sequencing libraries were constructed from 1 µg total RNA using “Protocol for use with NEBNext® Globin & rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina”.

treatment_protocol: 8-10 week-old WT and Hsd17b13-KO mice were fed with CDAA-HFD for 12 weeks

value: liver

value: Wildtype

value: CDAA-HFD


title: seedlings_C1_pifq_ZT0.5_R2

description: Library name: P83


title: IFNg Ax 50 sample7

description: Library name: IFNg_Ax_50_sample7


title: seedlings_C1_pifq_ZT0_R2

description: Library name: P82


title: CDAA-WT-01


title: IFNg sample12

description: Library name: IFNg_sample12

value: IFNg


title: PRAISE-seq-HuCCT1-BS3

description: Library name: PRAISE-seq-HuCCT1-BS3


title: seedlings_C1_pifq_ZT-0.5_R2

description: Library name: P81


title: TMAO_3

city: Jinan, Shandong

first: Shuai

last: Leng

address: 105 Jiefang Road

institute: Central Hospital Affiliated to Shandong First Medical University

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

source_name: aorta

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

value: aorta

value: Vascular smooth muscle cells

value: TMAO


title: PRAISE-seq-HuCCT1-BS2

description: Library name: PRAISE-seq-HuCCT1-BS2


title: IFNg sample11

description: Library name: IFNg_sample11


title: seedlings_T2_pifq_ZT3_R2

description: Library name: P78


title: IFNg sample10

description: Library name: IFNg_sample10


title: PRAISE-seq-HuCCT1-BS1

description: Library name: PRAISE-seq-HuCCT1-BS1


title: seedlings_T2_pifq_ZT2.5_R2

description: Library name: P77


title: TMAO_1


title: IFNg sample9

description: Library name: IFNg_sample9


title: PRAISE-seq-HEK293T-BSPUS-TKO3

description: Library name: PRAISE-seq-HEK293T-BSPUS-TKO3


title: seedlings_T2_pifq_ZT2_R2

description: Library name: P76


title: PRAISE-seq-HEK293T-BSPUS-TKO2

description: Library name: PRAISE-seq-HEK293T-BSPUS-TKO2


title: Control_3

value: Control


title: IFNg sample7

description: Library name: IFNg_sample7


title: seedlings_T2_pifq_ZT1.5_R2

description: Library name: P75


title: Control_2


title: PRAISE-seq-HEK293T-BSPUS-TKO1

description: Library name: PRAISE-seq-HEK293T-BSPUS-TKO1


title: Anti CD3 28 Ax 500nM sample12

description: Library name: Anti_CD3_28_Ax_500nM_sample12

value: Anti CD3/28 Auxora 500 nM


title: seedlings_T2_pifq_ZT1_R2

description: Library name: P74


title: Control_1


title: Anti CD3 28 Ax 500nM sample11

description: Library name: Anti_CD3_28_Ax_500nM_sample11


title: seedlings_T2_pifq_ZT0.5_R2

description: Library name: P73


title: AR0382 ATACseq replicate 2

city: Ann Arbor

first: Ajay

last: Larkin

state: MI

address: 1150 W Medical Center Dr

department: Microbiology & Immunology

institute: University of Michigan

description:
Library name: AR0382_ATACseq_2
subsampled to match read depth of sample 1

library_source: genomic

data_processing:
quality control with FastQC
alignment with BWA
bedgraph coverage files were created using Deeptools bamcoverage
Assembly: B8441.v3
Supplementary files format and content: bedgraph files showing binned ATACseq read coverage

molecule: genomic DNA

organism: Candidozyma auris

source_name: yeast cell

extract_protocol:
Logarithmically-growing cells were harvested via centrifugation. Pellet was incubated in buffer 1 (100mM Tris pH 9.4, 10mM DTT) at 30°C for 5 minutes, then washed and digested in buffer 2 (DPBS, 1 M sorbitol, 1.5 U zymolase [Zymo E100])).
Tagmentation of spheroplasts and library construction were performed according to the ActiveMotif ATAC-seq kit (#53150).

tag: strain

value: yeast cell


title: PRAISE-seq-HEK293T-PUS-TKO2

description: Library name: PRAISE-seq-HEK293T-PUS-TKO2


title: seedlings_T2_pifq_ZT0_R2

description: Library name: P72


title: PRAISE-seq-HEK293T-PUS-TKO1

description: Library name: PRAISE-seq-HEK293T-PUS-TKO1


title: Anti CD3 28 Ax 500nM sample9

description: Library name: Anti_CD3_28_Ax_500nM_sample9


title: WT, RNA-seq, Replicate 2

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

country: Germany

institute: Albert-Ludwigs-University Freiburg

description:
Library name: Sample5
Total RNA extracted from WT strain biological replicate 2, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.1 (cutadapt parameters: -q 20 --trim-n -m 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) (HRIBO 1.8.1)
rRNA filtering was done using samtools 1.9 (HRIBO 1.8.1)
Coverage files were created using HRIBO 1.8.1
Assembly: ASM744v1
Supplementary files format and content: bigwig format files containing per million normalized read coverage for each sample

organism: Escherichia coli CFT073

source_name: bacteria

growth_protocol: E. coli UPEC CFT073 was cultivated in LB rich medium until early exponential phase. Cells corresponding to 40 OD600 equivalent units were harvested by fast chilling, without the use of antibiotics

extract_protocol:
Total RNA was extracted using hot phenol (hot phenol; Roth) and ribosome footprints were extracted using hot phenol-chloroform-isoamyl alcohol (25:24:1; Roth)
Total RNA was first DNase I digested, rRNA-depleted, fragmented then subjected to cDNA library preparation. Size selected RNA for Riboseq samples were directly subjected to cDNA library. First, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase (cycle numbers are indicated in Table 2). The TruSeq barcode sequences, which are part of the 5' and 3' TruSeq sequencing adapters. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.

treatment_protocol: No antibiotic treatment was applied during growth or during the experiment

value: bacteria

value: WT

value: no treatment


title: seedlings_T2_pifq_ZT-0.5_R3

description: Library name: P71


title: PRAISE-seq-HEK293T-BSCtrl2

description: Library name: PRAISE-seq-HEK293T-BSCtrl2


title: PRAISE-seq-HEK293T-BSCtrl1

description: Library name: PRAISE-seq-HEK293T-BSCtrl1


title: WT, RNA-seq, Replicate 3

description:
Library name: Sample6
Total RNA extracted from WT strain biological replicate 3, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation


title: HEP3B, NAT10-K290V, IP, Rep 3

first: Daniel

last: Arango

state: IL

address: 303 E Superior St, Office 7-119

description: Library name: SN10

data_processing:
Raw reads were pre-processed to remove low quality bases, adapter sequences, and a stretch of at least 10 consecutive guanine nucleotides at the 3’ end using cutadapt/4.2.
The UMI was extracted using UMI-tools/1.1.5.
Reads were aligned to the human genome using STAR/2.7.9a in local alignment mode.
All alignments were deduplicated using UMI-tools and R1 was extracted using samtools/1.6.
Alignments were converted to bigwig files normalized by RPKM using Deeptools/3.5.1. Bigwig files were visualized using Integrative Genomics Viewer/2.19.1.
Assembly: GRCh38
Supplementary files format and content: Bigwig files with R1 extracted, normalized by RPKM.

source_name: Liver

growth_protocol: HEP3B cells were maintained in DMEM supplemented with 10% fetal bovine albumin (FBS) and 1% Penicillin/Streptomycin. All cells were grown in an incubator condition of 37oC and 5% CO2 and passaged every 3 days.

extract_protocol:
For cellular lysis, pellets were resuspended in 1 mL cold lysis buffer [50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% (vol/vol) Igepal CA-630, 0.1% (vol/vol) SDS and 0.5% (wt/vol) sodium deoxycholate, and 5.5 µL 200× protease inhibitor cocktail III], Lysates were sonicated in a Bioruptor sonicator (30s on/30s off at 4°C for 5 min). 5 µL Turbo DNase and 10 µL diluted RNase I (1:25 dilution in iced cold 1× PBS) were added to each lysate and then immediately incubated in a Thermomixer at 37°C and 1,200 rpm for 5 min. RNAse digestion was stopped by adding 11 µL murine RNase inhibitor. Lysis were cleared by centrifugation at 15000 ×g, 4°C for 15 min and 1 mL of each supernatant was collected for further use.
NAT10 was immunoprecipitated with anti-NAT10 antibody (10 µg per sample, rabbit polyclonal) conjugated to M-280 sheep anti-rabbit IgG magnetic beads. To identify the NAT10 bound RNAs, a 3’ Illumina adapter was ligated on-beads followed by separation of the complexes via SDS-PAGE. The NAT10-RNA complexes were excised out of the membranes, followed by proteinase K digestion and RNA isolation using the RNA Clean and Concentrator Kit (Zymo Research, R1018). Reverse transcription was performed using a specific primer aligning to the 3’ Illumina adapter. Following cDNA purification, the other Illumina adapter, which contained a ten nucleotide UMI, was ligated to the 3’ end of the cDNA. Final libraries were generated by performing PCR using Q5® High-Fidelity 2X Master Mix (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs) as primers. Libraries were gel purified and quality was verified on a TapeStation 4200 System (Agilent) before sequencing.  To process size-matched input (SMInput) samples, an aliquot of cell lysates was collected before the immunoprecipitation was carried out. Inputs were separated using SDS-PAGE and a region that matches NAT10’s molecular weight was excised out of the membranes, followed by proteinase K digestion and RNA isolation using the RNA Clean and Concentrator Kit (Zymo Research, R1018). A 3’ Illumina adapter was ligated followed reverse transcription using a specific primer aligning to the 3’ Illumina adapter. Following cDNA purification, the other Illumina adapter, which contained a ten nucleotide UMI, was ligated to the 3’ end of the cDNA. Final libraries were generated by performing PCR using Q5® High-Fidelity 2X Master Mix (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs) as primers. Libraries were gel purified, and quality was verified on a TapeStation 4200 System (Agilent) before sequencing.

treatment_protocol: HEP3B cells expressing NAT10-FKBP  were transduced with single mutants in the Helicase domain (K290A or E389L) or vector control (YFP) for 24 h, released from transduction by replacing with fresh DMEM for 24 h, and then selected using 5 µg/ml Blasticidin-S HCl for 5 days. Blasticidin selected transduced cells with parental control and NAT10-FKBP cells were then treated with 100 nM dTAGV1. Cell were crosslinked at 400,000 µJ/cm2 UV254nm . Cells were scraped out and washed by centrifugation at 300 ×g with cold PBS twice. Pellets were flash-frozen in liquid nitrogen and stored at -80°C until further use.

value: Liver

value: Hepatocellular Carcinoma

value: IP

value: Replicate 3


title: Anti CD3 28 Ax 50nM sample10

description: Library name: Anti_CD3_28_Ax_50nM_sample10

value: lung

value: Anti CD3/28 Auxora 50 nM


title: seedlings_T2_pifq_ZT2_R1

description: Library name: P66

value: seedling

value: pifq


title: seedlings_T2_pifq_ZT3_R1

description: Library name: P68


title: PRAISE-seq-HEK293T-PUS-TKO3

description: Library name: PRAISE-seq-HEK293T-PUS-TKO3

value: cell line


title: Anti CD3 28 Ax 50nM sample12

description: Library name: Anti_CD3_28_Ax_50nM_sample12


title: HEP3B, NAT10-E389L, IP, Rep 3

description: Library name: SN9


title: WT, Ribo-seq, Replicate 2

description:
Library name: Sample2
RNA purified from WT ribosome footpints replicate 2, size selected and subjected to cDNA library preparation

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.1 (cutadapt parameters: -q 20 --trim-n -m 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) (HRIBO 1.8.1)
rRNA filtering was done using samtools 1.9 (HRIBO 1.8.1)
Coverage files were created using HRIBO 1.8.1
Assembly: ASM744v1
Supplementary files format and content: bigwig format files containing per million normalized read coverage for each sample
Library strategy: Ribo-Seq


title: Anti CD3 28 Ax 50nM sample9

description: Library name: Anti_CD3_28_Ax_50nM_sample9


title: seedlings_T2_pifq_ZT1.5_R1

description: Library name: P65


title: WT, Ribo-seq, Replicate 3

description:
Library name: Sample3
RNA purified from WT ribosome footpints replicate 3, size selected and subjected to cDNA library preparation


title: HEP3B, YFP, IP, Rep 3

description: Library name: SN8

value: YFP


title: WT, Ribo-seq, Replicate 1

description:
Library name: Sample1
RNA purified from WT ribosome footpints replicate 1, size selected and subjected to cDNA library preparation


title: Anti CD3 28 Ax 50nM sample8

description: Library name: Anti_CD3_28_Ax_50nM_sample8


title: WT, RNA-seq, Replicate 1

description:
Library name: Sample4
Total RNA extracted from WT strain biological replicate 1, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation


title: seedlings_T2_pifq_ZT1_R1

description: Library name: P64


title: RBE cell, sgKCNQ3_3

city: Bengbu

first: Shuoshuo

last: Ma

state: Anhui

address: NO. 287, Changhuai Road, Longzihu district, Bengbu 233000, Anhui, China;

institute: The First Affiliated Hospital of Bengbu Medical College

description:
Library name: sgKCNQ3_3
fpkm_sgKCNQ3_3,tpm_sgKCNQ3_3,read_count_sgKCNQ3_3

data_processing:
The raw sequencing data were filtered using SOAPnuke to obtain clean data by removing: (1) reads containing adapters (adapter contamination); (2) reads with unknown bases (N) exceeding 0.1% of the total read length; and (3) low-quality reads, defined as reads in which the proportion of bases with a quality value below 15 accounted for more than 20% of the total read length.
Assembly: GRCh38.p13
Supplementary files format and content: csv file including Reads count, tpm, fpkm for each sample.

extract_protocol:
Total RNA was extracted using chloroform.
mRNA with poly(A) tails was enriched using Oligo(dT)-conjugated magnetic beads. The obtained RNA was fragmented with fragmentation buffer, and reverse transcription was performed using random N6 primers, followed by second-strand synthesis to generate double-stranded cDNA. The double-stranded cDNA was end-repaired, 5'-phosphorylated, and a single adenine (A) overhang was added at the 3' ends. Bubble-shaped adapters with a protruding thymine (T) at the 3' ends were then ligated. The ligation products were amplified by PCR using specific primers. The PCR products were thermally denatured into single strands, and a bridging primer was used to circularize the single-stranded DNA to form a single-stranded circular DNA library. The constructed library was quality-checked and subjected to sequencing upon passing the quality assessment.

value: RBE

value: Cholangiocarcinoma cells


title: HEP3B, NAT10-WT, IP, Rep 3

description: Library name: SN7


title: seedlings_T2_pifq_ZT2.5_R1

description: Library name: P67


title: daf-16(mu86);daf-2(e1370);htz-1(bon101), the first day of young adult, rep 1

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1/99

institute: DZNE, German Center for Neurodegenerative Diseases

description: Library name: Sample6

data_processing:
Sequencing was executed in PE75 on a NextSeq 2000 System (Illumina) with a NextSeq 2000 P4 XLEAP-SBS™ Reagent Kit (300 Cycles) chemistry.
Raw sequencing data were demultiplexed using bcl2fastq2 v2.20 and aligned against C. elegans reference genome (Ensembl release 109) using Kallisto v048.0.
Assembly: WBcel235
Supplementary files format and content: csv file includes normalized counts for each sample.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Nematodes were grown on OP-50-1 E. coli at 20℃.

extract_protocol:
Young adult worms were collected and dissolved in 1ml Trizol (Invitrogen). Total RNA was extracted using miRNeasy Micro Kit (Qiagen).
Libraries were prepared using SMART-Seq2 protocol (Picelli et al., 2014).

value: whole animal


title: fiaj1_untreated_rep2

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

description: Library name: Part1_fiaj1_rep_2

data_processing:
Quality control, trimming and mapping of the FASTQ files was performed using the atacseq pipeline (version 2.1.2), distributed by nf-core [doi: 10.5281/zenodo.2634132].  The pipeline was configured so that each constituent component was under version control and executed within a Singularity container [https://sylabs.io].  The following command was used to execute the pipeline:  nextflow run nf-core/atacseq -r 2.1.2 --input batch2_samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config config.txt --read_length 50 --trim_nextseq 20 --mito_name MT --blacklist blacklist/ENCFF356LFX.bed.chr_deleted.txt --aligner bowtie2 --deseq2_vst --outdir results -bg  These parameters generally adhere to the defaults set by the nf-core atacseq pipeline, except that Bowtie2 (version 2.4.4) was used as the aligner for the pipeline. Reads were mapped to the human reference genome (GRCh38 / release 102), but reads mapping to the mitochondrial chromosome or regions blacklisted by the ENCODE project were removed [https://www.encodeproject.org/files/ENCFF356LFX/]. The specified read trimming parameters (--trim_nextseq 20) were sequencing platform-specific, to account for the Illumina colour chemistry in which high quality calls for guanine nucleotides may actually reflect no signal on a flowcell. The pipeline was also passed a sample list detailing the forward and reverse FASTQ file pairings, along with the sample identities and how technical and biological replicates should be grouped together.
The nf-core atacseq pipeline used the software MACS2 (version 2.2.7.1) to identify peaks i.e genomic regions with a localised high abundance of mapped reads. MACS2 was run using the default settings for the atacseq pipeline. Peaks present in at least 2 of any of the biological replicates were considered as “consensus peaks” and retained. Since the start and end positions of peaks rarely match to the exact base position between samples, overlapping peak regions from different biological replicates were merged together.
The number of reads mapping to each peak was quantitated using the genome browser and analysis software SeqMonk (version 1.48.1) [https://www.bioinformatics.babraham.ac.uk/projects/seqmonk]. To achieve this, BAM files of the aligned reads generated by the nf-core atacseq pipeline were imported into SeqMonk, along with a text-format list detailing ATAC-seq peak genomic locations. By using the “Feature Probe Generator” and “Read Count Quantitation” SeqMonk functions, an “Annotated Probe Report” was created listing the deduplicated raw read counts for each peak. A separate file was also created using this method, but instead it reported the log2-transformed normalised data (counts per million reads) for each peak. A minimum threshold of -2 (log2-transformed counts per million reads) in any of the datasets was applied to remove consensus peaks with low count values.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed data files list the coordinates of the peak regions and the identity of the nearest gene (to within 2kb).  The files also provide the log2-transformed read count (per million reads) mapping to each peak, as quantitated by the genome browser and analysis software SeqMonk.

growth_protocol: All cell lines were cultured under atmospheric oxygen, 5% CO2 and at 37 degrees C in Essential 8 (E8) medium (Thermo Fisher A1517001) on TC-treated 6 well plates (Corning 3506) coated with rh-VTN (Thermo Fisher A14700) at 10 mcg/ well in PBS without calcium or magnesium. For CHR lines culture plates were coated with rhL521 (Gibco A29249) at 5mcg per well of a 6 well plate in DPBS with calcium and magnesium (Gibco 14040133) and cells were cultured in Stemflex (ThermoFisher, A3349401) supplemented with 3mcM IWP2 (Cayman Chemicals 13951) for at least 8 passages before the experiment was carried out.

extract_protocol:
ATAC-seq was performed using the Active Motif ATAC-seq kit (Active Motif 53150). Briefly, adherent cells were treated with Accutase to produce a single cell suspension. 100,000 cells per sample were pelleted, washed once in ice-cold PBS, resuspended in ATAC Lysis Buffer and then combined with Tagmentation Master Mix. The reaction was then incubated for 30min at 37°C with 800rpm agitation. Immediately after, the tagmented DNA was column-purified, eluted in a 35μL volume and PCR-amplified for 10 cycles with indexing primers to generate sequencing libraries. Library quality control was carried out with the Bioanalyzer High-Sensitivity DNA analysis kit (Agilent 5067-4626). Libraries were sequenced as paired end 50bp reads, on the Illumina NovaSeq platform at the Cancer Research UK Cambridge Institute Genomics Core Facility. Two biological replicates were collected from independent experiments.
Sequencing libraries were prepared from 100,000 cells per sample using the Active Motif ATAC-seq kit, following tagmentation of accessible chromatin regions for 30 minutes at 37°C, column purification of tagmented DNA, and PCR amplification for 10 cycles with indexing primers. Library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit.

value: human pluripotent stem cells


title: Anti CD3 28 Ax 50nM sample7

description: Library name: Anti_CD3_28_Ax_50nM_sample7


title: daf-2(e1370);htz-1(bon101), the first day of young adult, rep 1

description: Library name: Sample5


title: H3K9me2_ab1220_HeLa_Rep1

city: Berlin

first: Konrad

middle: Jakub

last: Chudzik

address: Hannoversche Str. 28

institute: MDC-BIMSB

description: Library name: H3K9me2_ab1220_HeLa_Rep1

data_processing:
Sequencing adapters were trimmed using Trim Galore (v0.6.4) with the options --paired --nextera. Trimmed reads were aligned to the mouse genome (mm10) for rod cells or the human genome (hg38) for HeLa cells using Bowtie2 (v2.3.5.1) with --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 2000. Aligned reads were filtered for mapped, paired-end reads (MAPQ ≥ 20) using samtools (v1.10) with view -f 2 -q 20 and then sorted. ENCODE blacklisted regions were removed using bedtools (v2.29.2) with intersect -v.
Normalized coverage tracks (bigWig) were generated with deepTools2 (v3.4.1) using a bin size of 10 bp, read extension (-e), and CPM normalization, ignoring chrX and chrY. For merged tracks, FASTQ files were concatenated from biological replicates. To visualize enrichment relative to matched IgG controls, log2 ratio tracks were generated using deepTools bigwigCompare (v3.4.1). Analogous 20 kb binned subtraction bedGraphs were used as input for domain calling.
Domain calling was performed as previously described (Kefalopoulou et al., 2025) with minor changes in parameters. Specifically, 20 kb binned log2 matrices were binarized: bins above a signal threshold were considered positive (within domain) and below as negative. Adjacent segments separated by gaps ≤200 kb were merged, and regions smaller than 100 kb were removed. To evaluate biological replicate consistency, consensus domains were defined using bedtools intersect (v2.29.2). Consensus regions were used for all subsequent downstream analyses.
To characterize signal distribution across distinct chromatin environments, the genome was segmented into four categories based on the presence or absence of LMNB1 and ab1220 consensus domains: LMNB1+/ab1220+, LMNB1+/ab1220−, LMNB1−/ab1220+, and LMNB1−/ab1220−, using bedtools intersect and subtract (v2.29.2).
Assembly: mm10/hg38
Supplementary files format and content: bigWig (.bw): per-replicate CPM-normalized coverage tracks (10 bp bins, chrX/Y excluded), generated from blacklist-filtered alignments with deepTools2. Merged log2 ratio bigWigs (vs matched IgG, replicate-pooled) are provided as series-level supplementary files for visualization.
Supplementary files format and content: bedGraph (.bedgraph): per-replicate log2 ratio of signal vs matched IgG control, binned at 20 kb. Used as input for domain calling.
Supplementary files format and content: BED (.bed): per-replicate domain calls from the binarized 20 kb log2 bedGraphs (".bedgraph.bed"). Series-level supplementary BEDs include consensus domains per condition (intersection of biological replicates) and four genome-segmentation tracks (LMNB1+/ab1220+, LMNB1+/ab1220−, LMNB1−/ab1220+, LMNB1−/ab1220−)
Library strategy: CUT&Tag

source_name: HeLa

growth_protocol: All mice were housed in a centrally controlled environment with a 12 h light and 12 h dark cycle, temperature of 20-22.2°C, and humidity of 30–50%. All mice had access to food and water ad libitum. Bedding, food and water were routinely changed. All experiments involving animals were carried out following institutional guidelines as approved by LaGeSo Berlin and following the Directive 2010/63/EU of the European Parliament on the protection of animals used for scientific purposes. Biological replicates represent samples collected independently from different animals.  HeLa cells were cultured in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin at 37°C and 5% CO₂, and routinely tested for Mycoplasma contamination. Biological replicates represent HeLa cells grown independently from separate cryovials.

extract_protocol:
HeLa cells were collected using TrypLE (Gibco, 12604021) and following centrifugation (5 min, 300g, RT), resuspended in CUT&Tag wash buffer (20 mM HEPES pH 7.5 (Jena Bioscience, BU10675), 150 mM NaCl (Invitrogen, AM9760G), 0.5 mM spermidine (Sigma, S0266), 10 mM sodium butyrate (Sigma Aldrich, B5887), 1 mM PMSF (Thermo Scientific, 36978), Protease Inhibitor Cocktail (Roche, 04693132001)) and quantified using EVE automatic cell counter (NanoEntek). For sampling rod cells, retinas from 2-month-old NRL-GFP mice were dissociated using the Papain Dissociation System (Worthington, #130-094-802). Four retinas from two mice were used for one biological replicate. Briefly, retinas were dissociated in papain solution for 60 min at 37°C, while shaking at 700 rpm. Afterwards, retinas were triturated with a 1 ml micropipette and transferred to a new tube containing a mix of EBSS, DNase and albumin-ovomucoid inhibitor. Cell suspensions were triturated again with a glass Pasteur pipette ten times until tissue fragments were no longer visible. Finally, 250 µl of EBSS/albumin-ovomucoid inhibitor was added, and the single-cell suspension was cleared of cell clumps by filtration (pluriStrainer Mini 70 μm). FACS sorting of single cells was performed on the BD FACS Aria II or Aria III Cell Sorter System with sample and plate cooling at 4°C. Forward-side scatter gating was used to eliminate debris and identify intact cells, and GFP intensity was used to specifically isolate rod cells. Single cells were sorted into 15 ml falcons pre-coated with BSA and containing 5 ml of wash buffer for approximately 1 h. After sorting, rod cells were quantified using a haemocytometer. For each CUT&Tag reaction, 11 μl Concanavalin A beads (BioMag, 86057) were equilibrated twice with 100 μl and then concentrated in 11 μl of binding buffer (20 mM HEPES pH 7.5, 10 mM KCl (Invitrogen, AM9640G), 1 mM CaCl₂ (Merck, 102382), 1 mM MnCl₂ (Thermo, J63150.AD)). 100,000 cells were then bound to the beads by incubating for 10 min at RT with rotation. Beads were subsequently separated on a magnet and resuspended in 100 μl CUT&Tag Antibody buffer (Wash buffer with 0.05% Digitonin (Millipore, 30410) and 2 mM EDTA (Invitrogen, 15575-038)). Subsequently, 1 μl of primary antibody or IgG control was added and incubated on a rotator overnight (15 h) or for 48 h at 4°C. After magnetic separation, beads were resuspended in 100 μl of Dig-wash buffer containing 1 μl of matching secondary antibody (Abcam, ab46540 for mouse; Antibodies-online, ABIN101961 for rabbit) and incubated for 1 h at 4°C with rotation. Following three washes with CUT&Tag Dig-wash buffer (Wash buffer with 0.05% Digitonin), beads were resuspended in 100 μl CUT&Tag Dig-300 buffer (20 mM HEPES-KOH, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 10 mM Sodium butyrate, 1 mM PMSF) with a 1:250 dilution of homemade 3xFLAG-pA-Tn5 preloaded with Mosaic-end adapters. After incubation for 1 h at 4°C with rotation, beads were washed four times with Dig-300 buffer and resuspended in 50 μl Tagmentation buffer (Dig-300 buffer with 10 mM MgCl₂ (Invitrogen, AM9530G)). Homemade spike-in-AmpR was added to the tagmentation buffer at a final concentration of 33.6 fM (Li et al., 2021). Tagmentation was performed for 1 h at 37°C and subsequently stopped by adding 2.25 μl EDTA, 2.75 μl 10% SDS (Invitrogen, 15553-035) and 0.5 μl Proteinase K (Invitrogen, 25530049). DNA fragments were solubilized for 16 h at 55°C followed by 30 min at 70°C to inactivate residual Proteinase K. DNA fragments were finally purified and eluted with 25 μl of elution buffer (Zymo, D5205).
NGS libraries were generated by PCR amplifying the CUT&Tag DNA fragments with barcoded i5 and i7 primers (Buenrostro et al., 2015) as described previously (Gjaltema et al. 2022). Briefly, DNA fragments with Nextera barcoded HPLC grade primers were loaded with NEBNext HiFi 2x PCR Master Mix (New England BioLabs, M0541S) into a thermocycler for 5 min at 72 °C, 30 sec at 98 °C, 10 sec at 98 °C, 10 sec at 63 °C (14 Cycles for steps 3-4) and 1 min at 72°C. Following PCR, 1x volume of Ampure XP beads (Beckman Coulter) were mixed with the NGS libraries and incubated at RT for 10 minutes. After magnetic separation, the beads were washed three times on the magnet with 80% ethanol, and the libraries were eluted with Tris-HCL, pH 8.0 (Roth, 9090.3). The quality of the purified NGS libraries was assessed with the D5000 tapestation (Agilent Technologies).

value: HeLa

value: cervical adenocarcinoma epithelial cells

value: wild-type

tag: time

tag: chip antibody

value: H3K9me2 (ab1220, Abcam)

tag: strain background

value: human cervical adenocarcinoma (ATCC CCL-2)


title: HEP3B, Control, IP, Rep 3

description: Library name: SN6

value: Liver

value: Hepatocellular Carcinoma

value: Parental

value: IP


title: seedlings_T2_pifq_ZT0.5_R1

description: Library name: P63

value: seedling


title: seedlings_T2_pifq_ZT0_R1

description: Library name: P62

value: pifq


title: RBE cell, sgKCNQ3_2

description:
Library name: sgKCNQ3_2
fpkm_sgKCNQ3_2,tpm_sgKCNQ3_2,read_count_sgKCNQ3_2

value: cell line


title: RBE cell, sgKCNQ3_1

description:
Library name: sgKCNQ3_1
fpkm_sgKCNQ3_1,tpm_sgKCNQ3_1,read_count_sgKCNQ3_1


title: HEP3B, NAT10-K290V, Input, Rep 3

description: Library name: SN5

value: Input

value: Replicate 3


title: Anti CD3 28 sample12

description: Library name: Anti_CD3_28_sample12

value: lung

value: Anti CD3/28


title: burb1_untreated_rep1

description: Library name: Part1_burb1_rep_1

value: human pluripotent stem cells


title: Anti CD3 28 sample10

description: Library name: Anti_CD3_28_sample10


title: seedlings_T2_pifq_ZT-0.5_R1

description: Library name: P61


title: CDAA-KO-04

value: liver

value: CDAA-HFD


title: HEP3B, NAT10-E389L, Input, Rep 3

description: Library name: SN4


title: Anti CD3 28 sample9

description: Library name: Anti_CD3_28_sample9


title: seedlings_T1_pifq_ZT3_R2

description: Library name: P58


title: RBE cell, NC_3

description:
Library name: NC_3
fpkm_NC_3,tpm_NC_3,read_count_NC_3

value: RBE

value: Cholangiocarcinoma cells


title: RBE cell, NC_2

description:
Library name: NC_2
fpkm_NC_2,tpm_NC_2,read_count_NC_2


title: Anti CD3 28 sample8

description: Library name: Anti_CD3_28_sample8


title: HEP3B, YFP, Input, Rep 3

description: Library name: SN3

value: YFP


title: seedlings_T1_pifq_ZT2.5_R2

description: Library name: P57


title: RBE cell, NC_1

description:
Library name: NC_1
fpkm_NC_1,tpm_NC_1,read_count_NC_1


title: HEP3B, NAT10-WT, Input, Rep 3

description: Library name: SN2

value: Liver


title: Anti CD3 28 sample7

description: Library name: Anti_CD3_28_sample7


title: seedlings_T1_pifq_ZT2_R2

description: Library name: P56


title: T-NC, shNC, THP-1 cells, biol rep 3

city: Nanning

first: Huan

last: Peng

address: 59, Xiangzhu street

institute: Maternal and Child Health hospital of Guangxi Zhuang Autonomous Region

description:
Library name: Sample 6
TPM and FPKM in all samples

data_processing:
The raw sequencing data was quality assessed using FastQC. Quality trimming was performed with Trimmomatic to obtain relatively accurate and valid data. Subsequently, the RNA-seq data was subjected to further analysis. StringTie and known gene models were used to estimate gene expression levels. The vegan package in R software was used to conduct principal component analysis (PCA). DESeq2 was employed for differentially expressed gene (DEG) analysis, and the results of the differential expression analysis were visualized. Significantly DEGs were selected using the thresholds: qValue ≤ 0.05 and |log2FoldChange| ≥ 1. Gene Ontology (GO) enrichment analysis was conducted using topGO, and KEGG pathway as well as KOG classification enrichment analyses were performed using clusterProfiler.
Assembly: Human
Supplementary files format and content: TPM and FPKM values for each samples

extract_protocol:
RNA from shNC and shGOT1 cells was extracted using TRIzol reagent. Amplified cDNA was sequentially converted into short-read sequencing libraries.
First, mRNA was enriched from total RNA using oligo(dT) beads. The purified mRNA was then randomly fragmented using divalent cations. Using the fragmented RNA as a template, double-stranded cDNA was synthesized with random oligonucleotides as primers. The purified double-stranded cDNA underwent end repair and poly(A) tailing, followed by adaptor ligation. The ligation product was purified and size-selected to obtain cDNA fragments of the desired size. Subsequently, PCR amplification was performed, and the PCR product was purified again to finally obtain the sequencing library.

value: tumor cells

value: wt


title: HEP3B, Control, Input, Rep 3

description: Library name: SN1

value: Hepatocellular Carcinoma

value: Parental


title: Auxora 500nM sample12

description: Library name: Auxora_500nM_sample12

value: Auxora 500 nM


title: T-NC, shNC, THP-1 cells, biol rep 2

description:
Library name: Sample 5
TPM and FPKM in all samples


title: seedlings_T1_pifq_ZT1.5_R2

description: Library name: P55

value: seedling

value: pifq


title: Auxora 500nM sample10

description: Library name: Auxora_500nM_sample10


title: T-NC, shNC, THP-1 cells, biol rep 1

description:
Library name: Sample 4
TPM and FPKM in all samples


title: seedlings_T1_pifq_ZT1_R2

description: Library name: P54


title: Hep3B_H537A_rep2_NaCNBH3

description: Library name: M32

data_processing:
Raw reads were pre-processed to remove low quality bases, adapter sequences, and a stretch of at least 10 consecutive guanine nucleotides at the 3’ end using cutadapt/4.2.
The UMI was extracted using UMI-tools/1.1.5.
Reads were aligned to the human genome using STAR/2.7.9a in local alignment mode.
All alignments were deduplicated using UMI-tools and nucleotide counts of aligned reads were extracted via samtools/1.6 mpileup. Read counts were extracted with https://github.com/IARCbioinfo/mpileup2readcounts.
We appended strand information to each site. We then filtered: 1) read depth per position must be >=30 2) dominant mismatch nucleotide per position must have at least 5 reads and a mismatch frequency of 0.001 or 0.01. We then identified significantly decreased sites in each sample vs NAT10-WT. Statistics and plots were performed in R/.
Assembly: GRCh38
Supplementary files format and content: BED files containing raw nucleotide counts per position

extract_protocol:
Total RNA isolation was performed using Trizol Reagent (ThermoFisher Scientific) according to the manufacturer's protocol. Total RNA was then DNase treated with DNase I (NEB) and reconstituted in nuclease-free water.
Total RNA was dephosphorylated followed by a 3' adapter ligation. The 3' adapter contains a spacer that impedes the self-ligation of RNA. The ligated RNA was fragmented, treated with NaCNBH3, dephosphorylated, and repurified. Reverse transcription was performed using the Induro enzyme in a dNTP cocktail contianing 2-amino-dATP. cDNA was then ligated to an adapter containing unique molecular identifiers (UMI) of ten randomized nucleotides.Final libraries were PCR amplified using Q5® High-Fidelity 2X Master Mix (NEB) and NEBNext® Multiplex Oligos for Illumina®. The primers aligned perfectly to the 5’ adapter and the second 3’ adapter. Each sample was assigned a different indexed primer.

treatment_protocol: NAT10-FKBP cells were transduced with single mutants in the Helicase domain (E389L. K290A) or the acetyltransferase domain (G641E, H537A), NAT10-WT, or a control plasmid for 24 h, released from transduction by replacing with fresh DMEM for 24 h, and then selected using 5 µg/ml Blasticidin-S HCl for 5 days. Blasticidin selected transduced cells with parental control and NAT10-FKBP cells were then treated with 100 nM dTAGV1 for 24 hrs.

value: Hepatocellular carcinoma


title: Auxora 500nM sample9

description: Library name: Auxora_500nM_sample9

value: lung


title: Hep3B_E389L_rep2_NaCNBH3

description: Library name: M31


title: seedlings_T1_pifq_ZT0.5_R2

description: Library name: P53


title: T-91, shGOT1, THP-1 cells, biol rep 3

description:
Library name: Sample 3
TPM and FPKM in all samples

value: GOT1 knockdown


title: Hep3B_K290A_rep2_NaCNBH3

description: Library name: M30


title: Auxora 500nM sample8

description: Library name: Auxora_500nM_sample8


title: Auxora 500nM sample7

description: Library name: Auxora_500nM_sample7


title: Hep3B_G641E_rep2_NaCNBH3

description: Library name: M29


title: seedlings_T1_pifq_ZT-0.5_R2

description: Library name: P51


title: T-91, shGOT1, THP-1 cells, biol rep 2

description:
Library name: Sample 2
TPM and FPKM in all samples


title: T-91, shGOT1, THP-1 cells, biol rep 1

description:
Library name: Sample 1
TPM and FPKM in all samples


title: Auxora 50nM sample12

description: Library name: Auxora_50nM_sample12

value: Auxora 50 nM


title: seedlings_T1_pifq_ZT0_R2

description: Library name: P52


title: human cExNK cells, Day 14, replicate 3

city: Shanghai

first: Hongye

last: Wang

address: 1239 Siping Road, Yangpu District, Shanghai

description:
Library name: Sample 14
Column name in raw_counts.csv: M-3

data_processing:
The initial paired-end reads underwent trimming and quality control using Trimmomatic, applying the parameters (SLIDINGWINDOW:4:15 MINLEN:75).
The resulting clean reads were individually aligned to the reference genome in orientation mode using hisat2 software with default settings. The quality of these data was assessed using qualimap_v2.21.
Clean reads were aligned to the ribosome database of human genome (hg38) using the alignment tool bowtie2 to evaluate the proportion of rRNA in the sample. Using featurecount to count each gene reads.
To identify DEGs (differential expression genes) between the two different samples, the expression level for each gene was calculated using the fragments per kilobase of exon per million mapped reads (FRKM) method.
DEGs between PBNK and ExNK, Scramble and MS177, Scramble and Taz/GSK126 samples were analyzed with R statistical package edgeR and genes with an adjusted p-adjust < 0.05 were identified as DEGs.
Assembly: hg38
Supplementary files format and content: csv files include raw counts for each sample

source_name: human peripheral blood

growth_protocol: PBNK cells are freshly isolated from human peripheral blood monocyte cells (PBMC) using the NK Cell Isolation Kit (Miltenyi) according to the manufacturer's instructions. Cell purity, defined as the percentage of CD56⁺CD3⁻ cells, was determined by flow cytometry. Only preparations with a purity exceeding 90% were used for mRNA-seq.  Freshly purified PBNK were pre-activated with rhIL-12 (10ng/mL), rhIL-15 (100ng/mL), and rhIL-18 (50ng/mL) for 16- 24 hours to generate cytokine induced memory-like NK cells (CIML NK) , then harvested, washed, and allowed to differentiate for about 3-5 days supported with low-dose rhIL-15 (1 ng/ml). mExNK cells are NK cells that expanded with our protocol. Briefly, CD3-depleted PBMCs (dT-PBMC, with a residual T cell percentage ≤1%) were isolated from the PBMCs using Dynabeads™ CD3 (Thermo) in accordance with the manufacturer's protocol. Then dT-PBMCs were placed in anti-CD16a antibody (T&L) immobilization plate containing HIPP-T009 medium (Bioengine) supplemented with 5% UltraGRO™-Advanced Serum Replacement (Helios), 500U/mL rhIL-2 (PeproTech), 50ng/mL rhIL-15 (T&L), 50ng/mL rhIL-18 (T&L) and 4µM ADAM inhibitor (MCE) at 37℃ in a humidified atmosphere containing 5% CO2. After 2 days, fresh medium with 500U/mL rhIL-2 (PeproTech), 50ng/mL rhIL-15 (T&L) and 1μg/mL Urebumab (MCE) were added. From day 4, medium containing 500IU/mL rhIL-2 (PeproTech), 50ng/mL rhIL-15 (T&L) and 50ng/mL rhIL-21 (T&L) was replenished as necessary during the NK expansion process. After 14 days, expanded memory-like NK cells were tested, only expansion with the viability≥80%，purity≥97% were collected for preparation of mRNA-seq. cExNK cells s are NK cells that expanded with NK cell Activation/Expansion Kit (Miltenyi) by using the NKp46/CD2 coupling microbeads as described per manufacturer’s instructions. The expansion medium was HIPP-T009 medium (Bioengine) supplemented with 5% UltraGRO™-Advanced Serum Replacement (Helios), 500U/mL rhIL-2 (PeproTech). After 14 days, this conventional expanded NK cells (cExNK) were  collected for preparation of mRNA-seq.

extract_protocol:
Total RNA was extracted by TRIzol Reagent (Thermo)
Total RNA was constructed library using using VAHTS Universal V10 RNA-seq Library Prep Kit for MGI (Vazyme, NRM606). The libraries were size-selected for cDNA fragments of 200–300 bp on 2% Low Range Ultra Agarose and then subjected to PCR amplification using Phusion DNA polymerase (NEB) for 15 PCR cycles. Following quantification using TBS380, the paired-end libraries were sequenced

treatment_protocol: No treatment

value: human peripheral blood

value: natural killer cells

value: WT

value: NO treatment


title: seedlings_T1_pifq_ZT3_R1

description: Library name: P48


title: Hep3B_NAT10(-)_rep2_NaCNBH3

description: Library name: M27


title: Hep3B_NAT10-WT_rep2_NaCNBH3

description: Library name: M28


title: Auxora 50nM sample11

description: Library name: Auxora_50nM_sample11


title: human cExNK cells, Day 14, replicate 2

description:
Library name: Sample 13
Column name in raw_counts.csv: M-2


title: seedlings_T1_pifq_ZT2.5_R1

description: Library name: P47


title: CDAA-WT-03

value: liver

value: Wildtype

value: CDAA-HFD


title: seedlings_T1_pifq_ZT2_R1

description: Library name: P46


title: human cExNK cells, Day 14, replicate 1

description:
Library name: Sample 12
Column name in raw_counts.csv: M-1


title: Hep3B_FKBP_rep2_NaCNBH3

description: Library name: M26

value: Liver

value: FKBP


title: Hep3B_Wildtype_rep2_NaCNBH3

description: Library name: M25


title: Auxora 50nM sample10

description: Library name: Auxora_50nM_sample10


title: seedlings_T1_pifq_ZT1.5_R1

description: Library name: P45


title: human mExNK cells, Day 14, replicate 4

description:
Library name: Sample 11
Column name in raw_counts.csv: E-4


title: Auxora 50nM sample9

description: Library name: Auxora_50nM_sample9


title: Hep3B_H537A_rep2_Mock

description: Library name: M24

value: Mock


title: PRAISE-seq-HuCCT1-Input1

description: Library name: PRAISE-seq-HuCCT1-Input1

value: cell line


title: Auxora 50nM sample8

description: Library name: Auxora_50nM_sample8


title: seedlings_T1_pifq_ZT1_R1

description: Library name: P44

value: seedling


title: human mExNK cells, Day 14, replicate 3

description:
Library name: Sample 10
Column name in raw_counts.csv: E-3


title: Hep3B_E389L_rep2_Mock

description: Library name: M23


title: DMSO sample12

description: Library name: DMSO_sample12

value: DMSO


title: seedlings_T1_pifq_ZT0.5_R1

description: Library name: P43

value: pifq


title: human mExNK cells, Day 14, replicate 2

description:
Library name: Sample 9
Column name in raw_counts.csv: E-2


title: Hep3B_K290A_rep2_Mock

description: Library name: M22

value: Hepatocellular carcinoma


title: DMSO sample11

description: Library name: DMSO_sample11

value: lung


title: seedlings_T1_pifq_ZT0_R1

description: Library name: P42


title: human mExNK cells, Day 14, replicate 1

description:
Library name: Sample 8
Column name in raw_counts.csv: E-1


title: TMAO_2

value: aorta

value: Vascular smooth muscle cells

value: TMAO


title: DMSO sample10

description: Library name: DMSO_sample10


title: human CIML NK cells, Day 5, replicate 4

description:
Library name: Sample 7
Column name in raw_counts.csv: C-4

value: human peripheral blood

value: natural killer cells

value: WT


title: seedlings_T1_pifq_ZT-0.5_R1

description: Library name: P41


title: Hep3B_NAT10-WT_rep2_Mock

description: Library name: M20


title: seedlings_C2_pifq_ZT3_R2

description: Library name: P38


title: Hep3B_G641E_rep2_Mock

description: Library name: M21


title: DMSO sample8

description: Library name: DMSO_sample8


title: Hep3B_NAT10(-)_rep2_Mock

description: Library name: M19


title: DMSO sample7

description: Library name: DMSO_sample7


title: IFNg Ax 500 sample6

description: Library name: IFNg_Ax_500_sample6

value: IFNg Auxora 500 nM


title: human CIML NK cells, Day 5, replicate 2

description:
Library name: Sample 5
Column name in raw_counts.csv: C-2

value: NO treatment


title: Hep3B_FKBP_rep2_Mock

description: Library name: M18

value: Liver


title: seedlings_C2_pifq_ZT2_R3

description: Library name: P36


title: human CIML NK cells, Day 5, replicate 1

description:
Library name: Sample 4
Column name in raw_counts.csv: C-1


title: seedlings_C2_pifq_ZT2.5_R2

description: Library name: P37


title: Hep3B_Wildtype_rep2_Mock

description: Library name: M17

value: Wildtype


title: IFNg Ax 500 sample4

description: Library name: IFNg_Ax_500_sample4


title: Hep3B_H537A_rep1_NaCNBH3

description: Library name: M16


title: H82, FB23-2, rep3

city: Yiwu

first: Yixuan

last: Yu

address: 1575 Chouzhou North Road, Futian Street

institute: The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine

description: Library name: H82-FB23-2-3

data_processing:
RNA-seq data processing typically involves quality control, adapter trimming, alignment to a reference genome, quantification of gene expression, and differential expression analysis.
Assembly: hg38
Supplementary files format and content: txt file include count value for each samples

extract_protocol:
Total RNA was isolated using the TRIzol reagent.
Using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit for Illumina

value: Small Cell Lung Carcinoma (SCLC), classic type


title: IFNg Ax 500 sample3

description: Library name: IFNg_Ax_500_sample3


title: seedlings_C2_pifq_ZT0_R2

description: Library name: P32


title: H82, FB23-2, rep2

description: Library name: H82-FB23-2-2

value: cell line


title: Hep3B_E389L_rep1_NaCNBH3

description: Library name: M15


title: H82, FB23-2, rep1

description: Library name: H82-FB23-2-1


title: Female, DCT(early), replicate 3

city: Baltimore

first: Hyun Jun

last: Jung

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Two technical repliates of each biological replicate were concatenated into one replicate for further downstream data processing.
Counts and were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 using salmon (0.14.10).
Assembly: Gencode (GRCm38.p6)
Supplementary files format and content: tab-delimited text files include raw gene counts for each gene

source_name: Kidney

growth_protocol: Mice were fed with a normal diet with free access to water.

extract_protocol:
Microdissection of the tubules were performed at 9-11 am. The microdissected tubules were washed in PBS three times and lyzed in Trizon solution. Total RNA was extracted using Direct-zol RNA Microprep kit (ZYMO RESEARCH).
For library preparation, cDNA was synthesized using SMART-Seq HT Kit (Clontech) and Nextera XT DNA Library Preparation Kit (Illumina).

value: Kidney

value: distal convoluted tubule cell

value: C57BL/6-Tg (Pvalb-tdTomato)15Gfng/J


title: Hep3B_K290A_rep1_NaCNBH3

description: Library name: M14

value: Hepatocellular carcinoma


title: IFNg Ax 500 sample1

description: Library name: IFNg_Ax_500_sample1

data_processing:
Data was processed using Cell Ranger 3.1.0 (10x Genomics), reads were mapped to GRCh38.84 reference genome (10x Genomics Cell Ranger Human 1.2.0 GRCh38 reference). Data was processed using Scanpy 1.10.4, and multisample integration was performed with scvi-tools 1.3.0. The scVI model was constructed on 2000 HVGs with the hyperparameters n_layers = 2, dropout_rate = 0.2, and n_latent = 10, and were trained using the settings max_epochs = 400, check_val_every_n_epoch = 2, and early_stopping = True. Default hyperparameters and settings were used otherwise. An initial round of Leiden clustering using the function sc.tl.leiden was performed on the integrated BAL object with a resolution of 1. Clusters characterized by low number of detected genes and transcripts and high percentage of mitochondrial genes were removed.
Assembly: GRCh38.84
Supplementary files format and content: Tab-separated values file and matrix file

extract_protocol:
BALF samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 rcf for 10 min at 4°C, followed by hypotonic erythrocyte lysis using 1 ml of PharmLyse solution (BD) for 2 min, followed by another wash with 10 ml of 0.5% BSA in PBS and centrifugation. Cell pellet was resuspended in 0.5% BSA in PBS at the final concentration 1000 cells/ul. Cell concentration and viability were determined using K2 Cellometer (Nexcelom) with AO/PI reagent and cells were loaded on 10x Genomics Chip A with Chromium Single Cell 3′ V2 gel beads and reagents (10x Genomics) aiming to capture 5,000–7,000 cells per library.
Libraries were prepared according to the manufacturer’s protocol (10x Genomics, CG000052_RevB). BAL sample processing for scRNA-seq using “FACS” protocol: BAL fluid samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 relative centrifugal force (rcf) for 10 min at 4 °C, followed by hypotonic lysis of red blood cells with 2 ml of PharmLyse (BD Biosciences) reagent for 2 min. Lysis was stopped by adding 13 ml of MACS buffer (Miltenyi Biotech). Cells were pelleted again and resuspended in 100 μl of a 1:10 dilution of Human TruStain FcX (BioLegend) in MACS buffer and a 10-μl aliquot was taken for counting using a K2 Cellometer (Nexcelom) with Acridine orange (AO)/Propidium iodide (PI) reagent. The cell suspension volume was adjusted so the concentration of cells was always < 5 × 107 cells/ ml and the fluorophore-conjugated antibody cocktail was added in a 1:1 ratio.

value: lung


title: H82, DMSO, control3

description: Library name: H82-DMSO3

value: DMSO


title: Hep3B_G641E_rep1_NaCNBH3

description: Library name: M13


title: seedlings_C2_pifq_ZT2_R1

description: Library name: P26

data_processing:
fastq files were merged across lanes
Illumina adaptors were trimmed with Trim_Galore/0.6.10-GCCcore-11.3.0 --clip_R1 12 --clip_R2 12
Reads were mapped using Salmon/1.10.0-GCC-11.3.0
quantified reads were processed into abundance, counts and length tables using tximport v.1.34.0 in R v.4.5
Assembly: AtRTD3
Supplementary files format and content: Salmon quant output for each sample.
Supplementary files format and content: abundance_table_salmon.txt, counts_table_salmon.txt and length_table_salmon.txt are tab separated tables containing gene expression data for TPM, counts and read leangths respectively. Each row is a gene and each column is a sample.

extract_protocol:
RNA was extracted using the Omega BioTek EZNA Plant RNA kit, following their protocols
NEBNext Ultra II Directional Library Prep Kit for Illumina, with NEBNext ploy(A) magnetic isolation

value: seedling

value: pifq


title: IFNg Ax 50 sample6

description: Library name: IFNg_Ax_50_sample6

value: IFNg Auxora 50 nM


title: Hep3B_NAT10-WT_rep1_NaCNBH3

description: Library name: M12


title: Anti CD3 28 Ax 500nM sample10

description: Library name: Anti_CD3_28_Ax_500nM_sample10

value: Anti CD3/28 Auxora 500 nM


title: H82, DMSO, control2

description: Library name: H82-DMSO2


title: IFNg Ax 50 sample5

description: Library name: IFNg_Ax_50_sample5


title: seedlings_C2_pifq_ZT1_R1

description: Library name: P24


title: human CIML NK cells, Day 5, replicate 3

description:
Library name: Sample 6
Column name in raw_counts.csv: C-3

value: human peripheral blood

value: natural killer cells

value: WT


title: Hep3B_NAT10(-)_rep1_NaCNBH3

description: Library name: M11

value: Liver


title: seedlings_C2_pifq_ZT0.5_R1

description: Library name: P23


title: H69, FB23-2, rep3

description: Library name: 3-H69-FB23-2


title: seedlings_C2_pifq_ZT0_R1

description: Library name: P22


title: Anti CD3 28 Ax 500nM sample7

description: Library name: Anti_CD3_28_Ax_500nM_sample7


title: H69, FB23-2, rep2

description: Library name: 2-H69-FB23-2


title: IFNg Ax 50 sample2

description: Library name: IFNg_Ax_50_sample2


title: IFNg Ax 50 sample1

description: Library name: IFNg_Ax_50_sample1


title: seedlings_C2_pifq_ZT-0.5_R1

description: Library name: P21


title: H69, FB23-2, rep1

description: Library name: 1-H69-FB23-2


title: IFNg sample6

description: Library name: IFNg_sample6

value: IFNg


title: seedlings_C1_pifq_ZT3_R3

description: Library name: P18


title: H69, CS2, rep2

description: Library name: 2-H69-CS2

value: Small Cell Lung Carcinoma (SCLC), classic type


title: seedlings_C1_pifq_ZT2_R3

description: Library name: P16


title: Hep3B_K290A_rep1_Mock

description: Library name: M6

value: Mock


title: Hep3B_E389L_rep1_Mock

description: Library name: M7


title: IFNg sample4

description: Library name: IFNg_sample4


title: IFNg sample5

description: Library name: IFNg_sample5


title: H69, CS2, rep1

description: Library name: 1-H69-CS2

value: cell line


title: IFNg sample3

description: Library name: IFNg_sample3


title: seedlings_C1_pifq_ZT-0.5_R3

description: Library name: P11


title: seedlings_C1_pifq_ZT3_R1

description: Library name: P08


title: H69, DMSO, control2

description: Library name: 2-H69-DMSO


title: Anti CD3 28 Ax 500nM sample6

description: Library name: Anti_CD3_28_Ax_500nM_sample6


title: seedlings_C1_pifq_ZT2.5_R1

description: Library name: P07


title: Hep3B_FKBP_rep1_Mock

description: Library name: M2

value: FKBP


title: IFNg sample1

description: Library name: IFNg_sample1


title: Anti CD3 28 Ax 500nM sample4

description: Library name: Anti_CD3_28_Ax_500nM_sample4


title: seedlings_C1_pifq_ZT2_R1

description: Library name: P06


title: Stage 21 gonad, male, rep2

city: Dos Hermanas

first: Iván

last: Barberá Aura

address: Avenida Rectora Rosario Valpuesta 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo (CABD)

description:
Library name: male_21_rep2
10x genomics

data_processing:
The demultiplexing, barcoded processing, alignment to genome and transcriptome, gene counting and aggregation was performed using the Cell Ranger software (v7.0.2)
Assembly: UM_NZW_1.0 (GCA_009806435.2)
Supplementary files format and content: Barcode, feature tsv files and matrix files from filtered CellRanger output.

organism: Oryctolagus cuniculus

source_name: Embryonic gonad

growth_protocol: Pregnant New Zealand White rabbits at the stages 13-21 dpc were obtained from Charles River (France branch). For 24 and 28 dpc, fetal ovaries were obtained from New Zealand rabbits bred at the SAJ rabbit facility (Jouy-en-Josas, France).

extract_protocol:
Pregnant New Zealand White rabbits at the stages 13-21 dpc were obtained from Charles River (France branch). Dissected gonads were dissociated into single-cells by incubating them with 0.05% Trypsin-EDTA (Gibco cat#25300-054) in addition to 1/10 portion of 5% BSA (Sigma-Aldrich cat#A7030-50G) /DPBS for 7-10 minutes at 37ºC. Dissociation was facilitated by pipetting gently every 2-3 minutes. Residual connective tissue, which appeared as whitish clumps at the end of the dissociation process, was discarded. Trypsin activity was halted by adding 2 portions of 5% BSA/DPBS. Cell suspension was passed through a 40 µm FlowMi cell strainer (Fisher Scientific cat#15342931) to remove cell clumps and debris. Filtrated cells were collected by centrifugation at 250-300g for 5 minutes at 4°C. The cell pellet was resuspended in DPBS for counting and viability check using 50% v/v trypan blue staining (Sigma Aldrich cat#T8154-20ML) under a light microscope. Only samples with ≥ 80% were used for downstream single-cell library preparation. Finally cells were fixed with 98% methanol added drop by drop and stored in -80°C freezer. For ovaries collected at 24 and 28 dpc, gonads were obtained from New Zealand rabbits bred at the SAJ rabbit facility (Jouy-en-Josas, France). The two gonads from the same fetus were pooled per stage in 500 µl of Trypsin-EDTA 0.05% at 37°C for 30 min. Dissociation was facilitated by gently pipetting every 5 minutes. Tryspin activity was stopped by adding SVF for a final 2% concentration. The cell suspension was passed through a 70 µm filter, then a 40 µm FlowMi Cell Strainer (Sigma-Aldrich cat #BAH136800040) to remove cell clumps and debris. The filtrated cells were collected by centrifugation at 300g for 10 minutes. The cell pellet was resuspended in 500 µL (24 dpc) or 1 mL (28 dpc) of DMEM/F12-SVF 2%. To determine whether the obtained cells were suitable for downstream analysis (cell viability > 80%), cell viability was evaluated using trypan blue staining with a haemocytometer r (TC20, Bio-Rad cat#1450102). The cell concentration was then adjusted to around 1000 cells/μl before loading onto the single-cell chip.
For the data from gonads at the stages 13-21 dpc, fixed cells were equilibrated to 4ºC on ice for at least 5 minutes. Subsequently, the cells were pelleted at 1,000g for 5 minutes at 4℃. The cells were rehydrated and gently washed with rehydration buffer (0.04% BSA, 1mM DTT (Life Technologies cat#707265ML), 0.4U/µl RNaseIn (Life Technologies cat#AM2682), 0.2U/µl SuperaseIn (Life Technologies cat#AM2696), in DPBS), using wide-bore tips (Corning Axygen Cat#T- 205-WB-C-R-S). Cell number and quality after rehydration were assessed using 50% v/v trypan blue staining. Cell suspensions were adjusted to a final concentration of 700-1,200 cells/µl. Single-cell libraries were generated using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics), according to manufacturer’s instructions, targeting 10,000 cells per reaction. Two libraries were prepared for each developmental stage and sex, except for female gonads at stage 15, for which only one library was prepared. Libraries were sequenced to a minimum depth of 200 million reads per library using the paired-end sequencing format: Read 1, 28 cycles; I7 index, 10 cycles; I5 index, 10 cycles; Read 2, 90 cycles.  For the data from ovaries at 24 and 28 dpc, Gel-Bead in Emulsions (GEMs) were generated using a Chromium 10X Single Cell System (10X Genomics) and cDNA libraries were prepared using the Chromium Next GEM Single Cell 5' Reagent v2 (10X Genomics). Two libraries were prepared for each developmental stage. The I2BC High-throughput Sequencing Platform (https://www.i2bc.paris-saclay.fr/sequencing/ng-sequencing/; Université Paris-Saclay, Gif-sur-Yvette, France) provided the facilities and expertise for library preparation and sequencing (Paired-end 28-64 bp, Illumina NextSeq500).

value: Embryonic gonad

tag: Sex

value: male

value: Stage 21


title: Anti CD3 28 Ax 500nM sample3

first: Alexander

last: Misharin

address: 303 E Superior St

description: Library name: Anti_CD3_28_Ax_500nM_sample3

value: lung


title: Hep3B_H537A_rep1_Mock

description: Library name: M8

value: Hepatocellular carcinoma


title: Stage 21 gonad, male, rep1

description:
Library name: male_21_rep1
10x genomics


title: H69, CS2, rep3

description: Library name: 3-H69-CS2


title: A549 cells, siATF6, 16h Glucose deprivation (biological replicate 3)

city: L'Hospitalet de Llobregat

first: Cristina

last: Muñoz-Pinedo

state: Barcelona

address: Hospital Duran i Reynals, 3a planta - Avinguda de la Gran Via, 199

department: ONCOBELL

institute: Institut d'Investigació Biomédica de Bellvitge

description:
Library name: Sample 12 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_16h6

data_processing:
Reads were trimmed using fastp and aligned to the human genome (GRCh38) with STAR using ENCODE parameters.
Gene quantification was performed with RSEM.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung carcinoma

growth_protocol: A549 cells were cultured in pyruvate-free high-glucose DMEM (25mM Glc) supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine and incubated at 37°C in a 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using the PureLink RNA Mini Kit (Invitrogen), following the manufacturer’s instructions. 2.5 ug of total RNA was used for construction of sequencing libraries. Total RNA quality was assessed prior to library preparation to ensure suitability for sequencing (OD 260/280 ≥ 2.00; OD 260/230 ≥ 2.00).
Libraries were prepared using a poly(A) enrichment, non-stranded protocol and sequenced on an Illumina platform (paired-end, 150 bp), yielding approximately 50 million reads per sample, with ≥80% of bases at Q30.

treatment_protocol:
Glucose deprivation experiments were performed by seeding 300,000 cells per well in 6-well plates. 48h later (see below transfetion protocol) they were washed twice with FBS-pyruvate-and glucose-free DMEM media and incubated with glucose-free DMEM (0mM), while the control cells were supplemented with 25mM Glucose. Both conditions were supplemented with 10% dialysed FBS (dFBS) and 2mM L-glutamine.
For siRNA transfections, cells were seeded in 6-well plates, trypsinised and transfected while plated with a transfection mixture of unsupplemented media with 1μL/mL DharmaFECT and either non-targeting (NT, siControl) siRNA or specific siRNAs (ATF4 and ATF6) at a final concentration of 100nM. 24h later, cells were trypsinised, plated in two wells and incubated for 24h before treatment.

value: Lung carcinoma

value: Human lung adenocarcinoma

value: ATF6 siRNA

value: Glucose deprivation (0mM)

value: 16 hours


title: seedlings_C1_pifq_ZT1_R3

first: Gina

last: Vong

address: Wentworth Way

description: Library name: P14

value: seedling

value: pifq


title: Anti CD3 28 Ax 500nM sample2

city: Chicago

description: Library name: Anti_CD3_28_Ax_500nM_sample2

value: Anti CD3/28 Auxora 500 nM


title: seedlings_C1_pifq_ZT1_R1

city: York

description: Library name: P04


title: A549 cells, siATF6, 16h Glucose deprivation (biological replicate 2)

description:
Library name: Sample 12 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_16h6


title: Anti CD3 28 Ax 50nM sample5

description: Library name: Anti_CD3_28_Ax_50nM_sample5

value: Anti CD3/28 Auxora 50 nM


title: seedlings_C1_pifq_ZT0.5_R1

description: Library name: P03


title: A549 cells, siATF6, 16h Glucose deprivation (biological replicate 1)

description:
Library name: Sample 12 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_16h6


title: Anti CD3 28 Ax 50nM sample4

description: Library name: Anti_CD3_28_Ax_50nM_sample4


title: Stage 15 gonad, male, rep2

description:
Library name: male_15_rep2
10x genomics

value: WT

value: Stage 15


title: Anti CD3 28 Ax 50nM sample2

description: Library name: Anti_CD3_28_Ax_50nM_sample2


title: seedlings_C1_pifq_ZT1.5_R1

description: Library name: P05


title: seedlings_C1_pifq_ZT-0.5_R1

description: Library name: P01


title: Stage 15 gonad, male, rep1

description:
Library name: male_15_rep1
10x genomics


title: Vehicle_1_MouseMyo_ATACSeq

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description: Library name: Vehicle_1_MouseMyometrium_ATACSeq

data_processing:
Adapters were removed, reads were trimmed and aligned using the encode atac-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline)
bedgraphs were generated from aligned files using bamCoverage (part of Deeptools)
Assembly: GRCm38/mm10
Supplementary files format and content: bedgraph

source_name: Myometrium

growth_protocol: Female C57BL/6 mice were naturally bred, with gestational day 1 established as the morning of vaginal plug detection. Mice were maintained in a pathogen-free, humidity-controlled, 12h light, 12h dark cycle facility with free access to food and water.

extract_protocol:
Omni ATAC-seq protocol (Corces, et al. 2007)
Omni ATAC-seq protocol (Corces, et al. 2007)

treatment_protocol: Pregnant C57BL/6 mice were randomly divided into 4 groups: Vehicle, IL1A, BSCI, and IL1A+BSCI. On gestational day (GD)16.5, All mice were anesthetized and, using guided ultrasound, the amniotic sac injected with either saline (vehicle, 20µl) or IL-1α (400ng in 20 µl). These mice also received tail-vein injections of the vehicle (saline) or BSCI (10 mg/kg/day) at GD15.5 and 16.5 to form the four treatment groups. Myometrial tissues were collected on GD 17.5, 24 hours following IL-1α administration.

value: Myometrium

value: Vehicle (20 ul saline)


title: Stage 21 gonad, female, rep2

description:
Library name: female_21_rep2
10x genomics

value: Embryonic gonad

value: female


title: A549 cells, siATF6, 16h Control (biological replicate 3)

description:
Library name: Sample 11 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_16h3

value: Control


title: A549 cells, siATF6, 16h Control (biological replicate 2)

description:
Library name: Sample 11 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_16h3


title: Anti CD3 28 Ax 50nM sample1

institute: Northwestern University

description: Library name: Anti_CD3_28_Ax_50nM_sample1

value: lung


title: seedlings_C1_elf3_ZT-0.5_R2

institute: University of York

description: Library name: E01


title: Stage 15 gonad, female, rep1

description:
Library name: female_15_rep1
10x genomics


title: A549 cells, siATF6, 16h Control (biological replicate 1)

description:
Library name: Sample 11 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_16h3

value: Lung carcinoma


title: Stage 21 gonad, female, rep1

description:
Library name: female_21_rep1
10x genomics

value: Stage 21


title: seedlings_C2_pifq_ZT0.5_R2

description: Library name: P34


title: seedlings_T2_col-0_ZT3_R2

description: Library name: C78


title: Anti CD3 28 sample6

description: Library name: Anti_CD3_28_sample6

value: Anti CD3/28


title: Stage 13 gonad, male, rep2

description:
Library name: male_13_rep2
10x genomics

value: male

value: Stage 13


title: IFNg Ax 500 sample2

description: Library name: IFNg_Ax_500_sample2

value: IFNg Auxora 500 nM


title: seedlings_C1_pifq_ZT0_R1

description: Library name: P02

value: seedling

value: pifq


title: A549 cells, siATF4, 16h Glucose deprivation (biological replicate 3)

description:
Library name: Sample 10 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_16h5

value: Human lung adenocarcinoma

value: ATF4 siRNA

value: Glucose deprivation (0mM)

value: 16 hours


title: Anti CD3 28 sample5

description: Library name: Anti_CD3_28_sample5


title: seedlings_C2_pifq_ZT3_R1

description: Library name: P28


title: seedlings_C2_pifq_ZT2.5_R1

description: Library name: P27


title: seedlings_T2_col-0_ZT2.5_R2

description: Library name: C77


title: Stage 13 gonad, male, rep1

description:
Library name: male_13_rep1
10x genomics

value: WT


title: A549 cells, siATF4, 16h Glucose deprivation (biological replicate 2)

description:
Library name: Sample 10 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_16h5


title: Anti CD3 28 sample3

description: Library name: Anti_CD3_28_sample3


title: seedlings_T2_col-0_ZT2_R2

description: Library name: C76


title: H82, DMSO, control1

description: Library name: H82-DMSO1

value: cell line

value: Small Cell Lung Carcinoma (SCLC), classic type

value: DMSO


title: Stage 13 gonad, female, rep2

description:
Library name: female_13_rep2
10x genomics

value: Embryonic gonad

value: female


title: Anti CD3 28 sample2

description: Library name: Anti_CD3_28_sample2

value: lung


title: A549 cells, siATF4, 16h Glucose deprivation (biological replicate 1)

description:
Library name: Sample 10 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_16h5

value: Lung carcinoma


title: seedlings_T2_col-0_ZT1.5_R2

description: Library name: C75


title: IFNg Ax 50 sample3

description: Library name: IFNg_Ax_50_sample3

value: IFNg Auxora 50 nM


title: Anti CD3 28 sample1

description: Library name: Anti_CD3_28_sample1

value: Anti CD3/28


title: A549 cells, siATF4, 16h Control (biological replicate 3)

description:
Library name: Sample 9 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_16h2

value: Control


title: Stage 13 gonad, female, rep1

description:
Library name: female_13_rep1
10x genomics

value: Stage 13


title: seedlings_T2_col-0_ZT1_R2

description: Library name: C74

value: seedling


title: Hep3B_FKBP_rep1_NaCNBH3

description: Library name: M10

value: Liver

value: Hepatocellular carcinoma

value: FKBP


title: Hep3B_Wildtype_rep1_NaCNBH3

description: Library name: M9

value: Wildtype


title: Auxora 500nM sample6

description: Library name: Auxora_500nM_sample6

value: Auxora 500 nM


title: A549 cells, siATF4, 16h Control (biological replicate 2)

description:
Library name: Sample 9 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_16h2

value: Human lung adenocarcinoma

value: ATF4 siRNA

value: 16 hours


title: Acute hypoxia spleen Ter-119+ erythroid cells 4

type: RNA

city: Yerevan

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Yerevan

address: Khorenatsi 1

department: Research and Development

country: Armenia

institute: PerikLab

hyb_protocol: 100 ng of total RNA per sample was hybridized with the NanoString nCounter Mouse Immunology v1 panel for 20 h at 65 C according to the manufacturer protocols.

scan_protocol: Automated counting was performed on the NanoString nCounter SPRINT Profiler.

data_processing: We performed QC on the raw RCC data and normalized gene expression using the positive controls and 15 housekeeping genes (median-of-ratios), followed by background thresholding.

source_name: Spleen

growth_protocol: Adult male F1 (CBA x C57BL/6) mice (3-5 months) were maintained under standard conditions. Acute blood loss was induced under isoflurane anaesthesia by withdrawing 0.5-0.8 mL of blood from the retro-orbital sinus; acute hypoxia was induced in a hypobaric chamber at -46 kPa (altitude >4500 m) for 16 h; control (Normal) mice were kept under standard conditions. Spleens were harvested on day 3.

extract_protocol: Splenocytes were prepared by homogenisation and Ficoll-Urografin density-gradient centrifugation. Ter-119+ erythroid cells were enriched by positive magnetic selection with biotinylated anti-mouse Ter-119 (BioLegend 113803) and MojoSort Streptavidin Nanobeads (BioLegend 480015). Total RNA was isolated from 500,000 cells with the Total RNA Purification Plus Kit (Norgen Biotek).

tag: condition

value: Acute hypoxia


title: seedlings_T2_col-0_ZT0.5_R2

description: Library name: C73


title: seedlings_T2_col-0_ZT0_R2

description: Library name: C72


title: A549 cells, siATF4, 16h Control (biological replicate 1)

description:
Library name: Sample 9 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_16h2


title: Auxora 500nM sample5

description: Library name: Auxora_500nM_sample5


title: Acute hypoxia spleen Ter-119+ erythroid cells 3


title: Auxora 500nM sample4

description: Library name: Auxora_500nM_sample4


title: Acute hypoxia spleen Ter-119+ erythroid cells 2


title: A549 cells, siControl (NT), 16h Glucose deprivation (biological replicate 3)

description:
Library name: Sample 8 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_16h4

value: WT (siControl)

value: Glucose deprivation (0mM)


title: seedlings_T2_col-0_ZT-0.5_R2

description: Library name: C71


title: Auxora 500nM sample3

description: Library name: Auxora_500nM_sample3

value: lung


title: A549 cells, siControl (NT), 16h Glucose deprivation (biological replicate 2)

description:
Library name: Sample 8 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_16h4

value: Lung carcinoma


title: Acute hypoxia spleen Ter-119+ erythroid cells 1


title: seedlings_T2_col-0_ZT3_R1

description: Library name: C68


title: Auxora 500nM sample1

description: Library name: Auxora_500nM_sample1


title: A549 cells, siControl (NT), 16h Glucose deprivation (biological replicate 1)

description:
Library name: Sample 8 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_16h4


title: Acute blood loss spleen Ter-119+ erythroid cells 4

value: Acute blood loss


title: A549 cells, siControl (NT), 16h Control (biological replicate 3)

description:
Library name: Sample 7 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_16h1

value: Control


title: Auxora 50nM sample6

description: Library name: Auxora_50nM_sample6

value: Auxora 50 nM


title: seedlings_T2_col-0_ZT2_R1

description: Library name: C66

value: seedling


title: Acute blood loss spleen Ter-119+ erythroid cells 3


title: Acute blood loss spleen Ter-119+ erythroid cells 2


title: A549 cells, siControl (NT), 16h Control (biological replicate 2)

description:
Library name: Sample 7 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_16h1


title: Auxora 50nM sample4

description: Library name: Auxora_50nM_sample4


title: A549 cells, siControl (NT), 16h Control (biological replicate 1)

description:
Library name: Sample 7 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_16h1


title: Auxora 50nM sample3

description: Library name: Auxora_50nM_sample3


title: seedlings_T2_col-0_ZT1_R1

description: Library name: C64


title: Acute blood loss spleen Ter-119+ erythroid cells 1


title: Normal spleen Ter-119+ erythroid cells 4

value: Normal (homeostatic)


title: A549 cells, siATF6, 6h Glucose deprivation (biological replicate 3)

description:
Library name: Sample 6 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_6h6

value: ATF6 siRNA

value: 6 hours


title: seedlings_T2_col-0_ZT0.5_R1

description: Library name: C63


title: A549 cells, siATF6, 6h Glucose deprivation (biological replicate 2)

description:
Library name: Sample 6 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_6h6


title: Normal spleen Ter-119+ erythroid cells 3


title: Auxora 50nM sample1

description: Library name: Auxora_50nM_sample1


title: seedlings_T2_col-0_ZT0_R1

description: Library name: C62


title: Normal spleen Ter-119+ erythroid cells 2


title: seedlings_T2_col-0_ZT-0.5_R1

description: Library name: C61


title: DMSO sample5

description: Library name: DMSO_sample5

value: DMSO


title: DMSO sample4

description: Library name: DMSO_sample4


title: Normal spleen Ter-119+ erythroid cells 1


title: seedlings_T1_col-0_ZT3_R2

description: Library name: C58


title: DMSO sample3

description: Library name: DMSO_sample3


title: seedlings_T1_col-0_ZT2_R2

description: Library name: C56


title: ASM372_2

city: ATHENS

first: Aaron

middle: P

state: GA

address: 120 EAST GREEN STREET

department: Microbiology

institute: University of Georgia

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina)
Library preparations were sequenced on an Illumina platform and 125 bp/150 bp paired-end reads were generated.
Paired-end clean reads were aligned to the reference genome using HISAT2.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.14.1)
Assembly: C. albicans reference genome (Assembly A21)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Candida albicans SC5314

source_name: cells cultured in YPED

growth_protocol: C. albicans cells were culturered in YPED at 30°C for 4 hours

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy mini kit (Cat#74104) following manufacturer's instructions.
Library was constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA), following manufacturer's instructions.

value: bcr1 TDH3-HGC1 mutant

tag: culture condition

value: YPED, 30°C-4HRS


title: A549 cells, siATF6, 6h Control (biological replicate 3)

description:
Library name: Sample 5 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_6h3

value: Human lung adenocarcinoma


title: A549 cells, siATF6, 6h Control (biological replicate 1)

description:
Library name: Sample 5 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_6h3


title: seedlings_T1_col-0_ZT1.5_R2

description: Library name: C55


title: ASM372_1


title: A549 cells, siATF4, 6h Glucose deprivation (biological replicate 3)

description:
Library name: Sample 4 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_6h5

value: ATF4 siRNA


title: DMSO sample1

description: Library name: DMSO_sample1

source_name: lung


title: seedlings_T1_col-0_ZT1_R2

description: Library name: C54

source_name: seedling


title: A549 cells, siATF4, 6h Glucose deprivation (biological replicate 2)

description:
Library name: Sample 4 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_6h5


title: Tumor_P16_Post_infusion_VDJ

city: Philadelphia

first: Nelson

last: Freeburg

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

description: Library name: Tumor_P16_Post_infusion_VDJ

data_processing:
FASTQ files aligned and preprocessed using 10x Genomics CellRanger Multi v8.0.1 pipeline
For Single-cell, single-nucleus gene expression: Ambient RNA contamination removed using CellBender Remove-Background (CellBender v0.3.0).
For single-cell, single-nucleus gene expression, cellbender-adjusted counts imported intor seurat. Genes and cells were filtered for quality and expression thresholds, and data were lognormalized. Cells were annotated manually based on marker gene expression.
For bulk RNA sequencing, Fastq files were trimmed with umi_tools (v1.1.6) to extract UMIs. Cutadapt (v5.2) was used to trim nonbiological sequences from reads. Reads were aligned using the STAR aligner (v2.7.9a). Reads were deduplicated based on UMI identity using umi_tools (v1.1.6) and counted using FeatureCounts (v2.1.1). Normalized counts are in transcripts per milliion (TPM). Raw counts are also provided.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression data is in .h5 format and contains CellBender-processed gene expression counts.
Supplementary files format and content: Processed V(D)J data is the output of CellRanger and in .csv format. It contains cell barcode and TCR A a B chain sequence as DNA and protein.
Supplementary files format and content: Supplementary .rds files contain Seurat objects for single-cell CSF, single-cell Infusion product, and single-nucleus tumor samples
Library strategy: TCR-Seq

source_name: Glioblastoma tumor

extract_protocol:
Tumors (single-nucleus): Single cell supsensions produced by tumor sample dissociation with gentleMACS Octo Dissociator and filtered through 75 uM strainer before single nucleus prep with CHAPS; Cerebrospinal and infusion product: Cells or nucei input directly into 10x genomics single cell library preparation protocol. Tumors (Bulk RNAseq from FFPE). Malignant cell-enriched regions were extracted from slides using laser-capture microdissection. RNA was extracted using a Qiagen RNA FFPE kit.
Chromium GEM-X Single Cell 5' Kit v3 with Chromium Single Cell Human TCR Amplification kit (single-cell, single-nucleus). SMART-Seq® Total RNA Pico Input with UMIs (ZapR™ Mammalian) (Bulk RNA sequencing)

treatment_protocol: 5e6, 1e7 or 2.5e7 bivalent CAR T cells targeting EGFR and IL13RA2 administered intracerebroventricularly

value: Glioblastoma tumor

value: Primary cells

value: GBM tumor cells

value: EGFR amplified

value: 5e6 bivalent CAR T cells (EGFR, IL13RA2)


title: ASM331_3

value: bcr1 mutant


title: ASM331_2


title: A549 cells, siATF4, 6h Glucose deprivation (biological replicate 1)

description:
Library name: Sample 4 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_6h5

value: Lung carcinoma

value: Glucose deprivation (0mM)


title: Tumor_P16_Post_infusion_GEX

description: Library name: Tumor_P16_Post_infusion_GEX

data_processing:
FASTQ files aligned and preprocessed using 10x Genomics CellRanger Multi v8.0.1 pipeline
For Single-cell, single-nucleus gene expression: Ambient RNA contamination removed using CellBender Remove-Background (CellBender v0.3.0).
For single-cell, single-nucleus gene expression, cellbender-adjusted counts imported intor seurat. Genes and cells were filtered for quality and expression thresholds, and data were lognormalized. Cells were annotated manually based on marker gene expression.
For bulk RNA sequencing, Fastq files were trimmed with umi_tools (v1.1.6) to extract UMIs. Cutadapt (v5.2) was used to trim nonbiological sequences from reads. Reads were aligned using the STAR aligner (v2.7.9a). Reads were deduplicated based on UMI identity using umi_tools (v1.1.6) and counted using FeatureCounts (v2.1.1). Normalized counts are in transcripts per milliion (TPM). Raw counts are also provided.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression data is in .h5 format and contains CellBender-processed gene expression counts.
Supplementary files format and content: Processed V(D)J data is the output of CellRanger and in .csv format. It contains cell barcode and TCR A a B chain sequence as DNA and protein.
Supplementary files format and content: Supplementary .rds files contain Seurat objects for single-cell CSF, single-cell Infusion product, and single-nucleus tumor samples


title: ASM331_1


title: seedlings_T1_col-0_ZT0_R2

description: Library name: C52

value: seedling


title: Tumor_P14_Post_infusion_VDJ

description: Library name: Tumor_P14_Post_infusion_VDJ

value: Copy number gain, EGFRvIII


title: A549 cells, siATF4, 6h Control (biological replicate 3)

description:
Library name: Sample 3 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_6h2

value: Control


title: seedlings_T2_col-0_ZT2.5_R1

description: Library name: C67


title: seedlings_T1_col-0_ZT-0.5_R2

description: Library name: C51


title: ASM363_3


title: A549 cells, siATF4, 6h Control (biological replicate 2)

description:
Library name: Sample 3 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_6h2

value: 6 hours


title: Tumor_P14_Post_infusion_GEX

description: Library name: Tumor_P14_Post_infusion_GEX


title: ASM363_2


title: A549 cells, siATF4, 6h Control (biological replicate 1)

description:
Library name: Sample 3 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_6h2


title: Tumor_P13_Post_infusion_VDJ

description: Library name: Tumor_P13_Post_infusion_VDJ


title: seedlings_T1_col-0_ZT2.5_R1

description: Library name: C47


title: Auxora 50nM sample2

description: Library name: Auxora_50nM_sample2

value: lung

value: Auxora 50 nM


title: ASM363_1

value: YPED, 30°C-4HRS


title: A549 cells, siATF6, 6h Glucose deprivation (biological replicate 1)

description:
Library name: Sample 6 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_6h6

value: Human lung adenocarcinoma

value: ATF6 siRNA


title: A549 cells, siControl (NT), 6h Glucose deprivation (biological replicate 3)

description:
Library name: Sample 2 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_6h4

value: WT (siControl)


title: Tumor_P13_Pre_infusion_VDJ

description: Library name: Tumor_P13_Pre_infusion_VDJ

value: Glioblastoma tumor

value: Primary cells

value: Pre-treatment


title: seedlings_T1_col-0_ZT2_R1

description: Library name: C46


title: ASM1_3

value: SC5314 WT


title: Tumor_P13_Post_infusion_GEX

description: Library name: Tumor_P13_Post_infusion_GEX

value: GBM tumor cells

value: 5e6 bivalent CAR T cells (EGFR, IL13RA2)


title: A549 cells, siControl (NT), 6h Glucose deprivation (biological replicate 2)

description:
Library name: Sample 2 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_6h4

value: Lung carcinoma

value: Glucose deprivation (0mM)


title: seedlings_T1_col-0_ZT1.5_R1

description: Library name: C45

value: seedling


title: ASM1_2


title: A549 cells, siATF6, 6h Control (biological replicate 2)

description:
Library name: Sample 5 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_6h3

value: Control


title: ASM372_3

value: bcr1 TDH3-HGC1 mutant


title: A549 cells, siControl (NT), 6h Glucose deprivation (biological replicate 1)

description:
Library name: Sample 2 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_6h4

value: 6 hours


title: Tumor_P13_Pre_infusion_GEX

description: Library name: Tumor_P13_Pre_infusion_GEX

value: Copy number gain, EGFRvIII


title: seedlings_T1_col-0_ZT1_R1

description: Library name: C44


title: ASM1_1

value: YPED, 30°C-4HRS


title: A549 cells, siControl (NT), 6h Control (biological replicate 3)

description:
Library name: Sample 1 (biol rep 3)
Column name in RSEM_RawCounts.txt: A549n3_6h1

value: Human lung adenocarcinoma


title: DMSO sample2

description: Library name: DMSO_sample2

value: lung

value: DMSO


title: IP_P14_VDJ

description: Library name: IP_P14_VDJ

source_name: CAR T cells

value: CAR T cells

value: Normal