title: caco2_ko_a_3

city: St. Louis

first: Vincent

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

data_processing:
Sequences were aligned and gene count tables were produced using STAR aligner. Gene count tables were processed and analyzed using the DESeq2 package with R. Prior to differential comparison, genes with fewer than 10 counts among all of the samples were excluded. Differentially expressed genes (DEG) were considered significant when padj<0.05, or as indicated in the Result section and within the Figure legends.  Gene ontology analysis was conducted using Metascape39 (https://metascape.org).   Gene set enrichment analysis of DEGs was performed using Gene Set Enrichment Analysis software40, GSEA v3.Broad Institute (http://software.broadinstitute.org/gsea/index.jsp).
Genome_build: mm10
Supplementary_files_format_and_content: gene_counts

extract_protocol:
Spheroid preparation: Approximately 1 cm segment of intestinal tissue was minced with scissors and digested in 2 mg/ml of Collagenase I (Thermo Fisher Scientific) at 37°C for 30-40 min, with vigorous pipetting every 5 min. Solution was filtered through 70 mm cell strainer, and crypts were collected by centrifugation and plated on the 24-well plates in 20 mL of Matrigel (Cornig). Following polymerization of the Matrigel for 10 min at 37°C, 50% L-WRN conditioned medium was added. Spheroids were maintained in the culture in the cycles of three days before dissociation with TrypLE express (Thermo Fisher Scientific) and re-plating. For TAM induced gene ablation, spheroids were cultured for 3 days in 50% L-WRN medium containing 250 nM Z-4-Hydroxytamoxifen (MilliporeSigma). After re-plating, spheroids were cultured in 50% L-WRN without Z-4-Hydroxytamoxifen. Crypt preparation: Approximately 5 cm of small intestinal tissue was dissected, longitudinally opened and extensively washed in PBS. Tissue was placed in 2 mM EDTA in PBS for 30 min on the rotator at 4C. Tissue fragments were placed in 10 mL of  0.1% BCS and pipetted up and down. The pipetting and 0.1% BCS solution exchange was repeated 6 times. Fractions 4-6 were collected and crypts were collected by centrifugation. Caco-2 preparation: shERWOOD UltramiR Lentiviral Inducible shRNA target gene set for gene Fgrf1op was purchased from Transomic technologies. Lentiviral packaging was performed in 293T packaging cell line (ATCC, CRL-3216) with Lipofectamine 2000 (Thermo Fisher Scientific) per manufacturer’s protocol. Cells were transfected with psPAX2 packaging plasmid (Addgene No. 11260), pCMV-VSV-G envelope plasmid (Addgene No. 8454) and pZIP-TRE3G-ZsGreen-Puro vector expressing either shRNA targeting Fgfr1op (ULTRA-3199095) or control pZIP-TRE3G-ZsGreen-Puro vector expressing non targeting shRNA (TLNSU4300) per manufacturer instructions. Transduction was conducted with 1 mL of supernatant containing polybrene at final concentration of 8 mg/mL in the 12 well plate, with centrifugation at 900g for 1.5 h. The medium was changed next day. Transfected cells were selected with puromycin added in culture 3 days post transduction. Deletion of Fgfr1op in stably transduced Caco2 cells was induced by adding doxycycline (2 mg/ml) in the cell culture medium. Cells were kept under induction for 3 days, and doxycycline (Sigma) containing medium was changed on day 2. Efficiency of Fgfr1op shRNA induction and Fgfr1op deletion was confirmed by visualizing the expression of ZsGreen reporter with Olympus BX51 microscope and Western blot, respectively
Sequencing of RNA isolated from enriched crypts: Total RNA was extracted using RNeasy Micro Kit (Qiagen) per manufacturer’s instructions. Samples were prepared according to library kit manufacturer’s protocol (SMARTer Low Input RNA Kit, Clontech Takara Bio), indexed, pooled, and sequenced on an Illumina NovaSeq 6000. Base calls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52. Sequencing of RNA isolated from spheroid lines: Total RNA was extracted using RNeasy Micro Kit (Qiagen) per manufacturer’s instructions. Samples were prepared according to library kit manufacturer’s protocol (Dynal mRNA Direct Invitrogen) and sequencing was conducted on an Illumina HiSeq. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. Reads were aligned and processed as described for crypt RNA-sequencing.

tag: time point

value: day 3 post-doxycycline


title: SMA mouse Smn1_Hetero Rep3

status: Public on Jun 17 2024

type: SRA

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

country: USA

institute: Salk Institute for Biological Studies

library_source: transcriptomic

data_processing:
Sequenced reads were quality-tested using FASTQC and adapters were trimmed using Cutadapt with parameters `-j 8 -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC`.
Paired reads after trimming were aligned to custom mouse transcriptome and quantified at transcript level using Kallisto with arguments `quant -b 30`.
The custom transcriptome index was built with `kallisto index` by merging the cDNA FASTA files of mm10 mouse transcriptomes and three genome-editing conditions of gene Smn1 (including cDNA, HITI and Gene-DUET).
Raw gene expression was estimated and summarized from transcript-level abundance with tximport. Differential gene expression was performed on the raw gene counts with DESeq2.
Assembly: custome genome including mm10 mouse genome and three genome-editing conditions of gene Smn1 (including cDNA, HITI and Gene-DUET)
Supplementary files format and content: tab-delimited text file including raw transcript-level expression estimated from Kallisto

molecule: total RNA

organism: Mus musculus

source_name: Spinal cord

extract_protocol:
RNA was extraxcted from the spinal cord at P14 by using Trizol and RNAeasy kit
RNA libraries for RNA-seq were prepared using TruSeq  mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: AAVs were delivered by intravenous injection into SMA mice at P0.5

tag: tissue

value: Spinal cord

tag: cell type

value: Whole tissue

tag: genotype

tag: treatment

value: No treatment


title: UM32, ROR2, replicate 3

city: Detroit

first: Simone

last: Benitz

address: 2799 W Grand Blvd

institute: Henry Ford Health System

data_processing:
Adapter trimming and removal of ribosomal and mitochondrial genome was carried out with fastq-mcf, cutadapt and Bowtie2, respectively. Reads were mapped to the hg19 genome using STAR and raw read counts were estimated with HTSeq (v0.11.2) and normalized with DESeq2.
Assembly: hg19
Supplementary files format and content: RawNormCounts_ROR2.txt

organism: Homo sapiens

growth_protocol: HPAF-II cells were cultured in Minimum Essential Medium containing 1% sodium pyruvate , 1% non-essential amino acids, 10% FBS and 0.5% Gentamicin. UM32 were cultivated in RPMI 1640 supplemented with 10% FBS and 0.5% Gentamicin.

extract_protocol:
For total RNA extraction, the RNeasy® Plus Mini Kit (74134, Qiagen) was used following manufacturer’s instructions. Genomic DNA was digested on column by using the RNase-Free DNase Set (79254, Qiagen).
Library preparation and sequencing was performed at MedGenome Inc.. RNA-seq library preparation was performed by using the Illumina TruSeq stranded mRNA kit.

tag: cell line

value: Pancreatic cancer cell line


title: caco2_ko_a_2


title: UM32, vector control, replicate 3


title: Female Myf5 low  2

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

data_processing:
Sequencing raw data (bcl) were demultiplexed and transformed in fastq files using cassava v1.8.2.
The fastq files were aligned against the reference genome by RNAstar v2.5.3a.
The raw sequencing counts per gene were generated using htseq_count v2.16.2 using Mus_musculus.GRCm38.93_proteinCoding_lincRNA.gtf
Assembly: GRCm38
Supplementary files format and content: htseq_summary_20220628.tsv
Supplementary files format and content: tab-separated file containing count data per gene (row) per cells derived from pool of mice (column)

molecule: polyA RNA

source_name: Skeletal muscle

extract_protocol:
RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical).
Libraries were quantified with the Quant-iT Picogreen (Invitrogen, 10545213) on a FilterMax F3 (Molecular Devices, F3). Size pattern was assessed with Fragment Analyzer-96 with the DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, DNF-474-0500).
Libraries (Average size: 295 bp) were pooled at an equimolar ratio and clustered at a concentration of 9 pM on a single read sequencing flow cell.

value: Skeletal muscle

value: Muscle stem cells

tag: strain

value: Low Myf5 expression

tag: Sex

value: female

tag: pool


title: Nfur Wildtype 6-Day Diapause RNAseq Rep16

city: Stanford

first: Anne

last: Brunet

state: California

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

description:
Nfur_Wildtype_6D_16
Nfur_KO_Readcounts.csv

data_processing:
read trimming with Trim Galore (version 0.4.5)
Genome Alignment using STAR (version 2.7.1a) No reference genome is available for the red-striped killifish, so the reads from red-striped killifish RNA-seq libraries were aligned to the genome of its close relative, lyretail killifish.
Keep only uniquely mapped reads using samtools (version 1.5) samtools view -q255
Readcounts obtained using feature counts function from Subread package (version 2.0.1)
Normalized expression using DESeq2 (version1.30.1)
Assembly: Genomes used: African Turqouise Killifish: GCA_001465895.2 ; Red-Striped & Lyretail Killifish: GCA_006937985.1 MPIBA_Aaus_1.0 scaffolds: 12,236 contigs: 30,782 N50: 119,465 L50: 1,783
Supplementary files format and content: Read counts files for each speacies from featurecount of Subread package

organism: Nothobranchius furzeri

source_name: Dissected Embryo (Whole Body)

growth_protocol: Animals were housed in automated circulating water system with pH maintained at 6-7.5 and conductivity maintained between 3500 and 4500μS/cm with a 10% system water exchange every day by reverse osmosis treated water. Adult fish were manually fed Otohime fish diet (Reed Mariculture, Otohime C1 [Ep1 for the South American killifish]) twice a day during weekdays and once a day during weekends.

extract_protocol:
For each stage in each species, roughly 8-30 embryos were carefully dissected in ice-cold PBS using biological-grade tweezers (Electron Microscopy Sciences, 72700-D) to carefully remove the chorion, the enveloping layer, and the yolk without damaging the embryo body. Freshly dissected embryos were then quickly rinsed with ice-cold PBS, and all the PBS was carefully removed. Embryo bodies were then snap-frozen in liquid nitrogen and stored at -80°C. We used 8-10 snap-frozen embryos for RNA-seq. Snap frozen embryos at -80°C were thawed on ice for 1 minute and washed with 200µl ice-cold PBS. The embryos were then dissociated and homogenized with ~25 Zirconia/Silicon 0.5mm glass beads (RPI, Research Products International Corp, 9834) using FastPrep® -24 homogenizer (MB Biomedicals, 116004500) for 20 seconds, followed by centrifugation (17000g for 3 minutes). After centrifugation, 10.5µl of the supernatant was used as input to the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara, 634890) for the cDNA synthesis followed by amplification with 12 cDNA amplification cycles. Amplified cDNA was validated with Agilent 2100 Bioanalyzer using Agilent’s High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626).
The DNA libraries were then generated using the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096). Library quality and concentration were assessed by the Agilent 2100 Bioanalyzer and Agilent’s High Sensitivity DNA Kit (Agilent Technologies, Cat. No. 5067-4626), followed by high throughput sequencing on Illumina HiSeq platform with 2 x 150bp paired end reads.

treatment_protocol: Synchronized killifish embryos for African turquoise and South American killifish were collected within a tight (~5 hour) breeding window. Most collected embryos were at the 1-2 cell stage upon collection. We monitored embryos every day post-collection to observe the visual markers of diapause and development as previously described (12). Briefly, we used Kupffer’s vesicle (KV), which is a transient embryonic organ present from early to middle somitogenesis as a marker to stage embryos that are about to reach diapause. KV-positive embryos reach the end of somitogenesis in 1-2 days and the loss of KV roughly coincides with the onset of heartbeat in killifish, followed by either diapause or continue development (12, 17). We counted the number of somites in KV-positive embryos and designated KV-positive embryos at 15-22 somites as our “pre-diapause (Pre-Dia) stage”. Embryo morphology for all the killifish species was similar at this stage. This mid-somitogenesis time point also coincides with the vertebrate phylotypic period (the period of the most conserved gene expression pattern during vertebrate development) with available gene expression and chromatin accessibility data from multiple other fish species

value: Dissected Embryo (Whole body)

tag: Stage

value: Diapause

tag: timing

value: 6-Day Diapause


title: SMA mouse Smn1_Hetero Rep1


title: Nfur Wildtype 6-Day Diapause RNAseq Rep13

description:
Nfur_Wildtype_6D_13
Nfur_KO_Readcounts.csv


title: caco2_wt_a_3

value: scramble


title: caco2_ko_a_1


title: HPAF-II, ROR2, replicate 3

source_name: HPAF-II

value: HPAF-II


title: caco2_wt_a_2


title: Nfur Wildtype 6-Day Diapause RNAseq Rep14

description:
Nfur_Wildtype_6D_14
Nfur_KO_Readcounts.csv


title: HPAF-II, ROR2, replicate 1


title: crypt_wt_d9_3

source_name: small intestinal crypts

value: wt

value: day 9 post tamoxifen


title: UM32, vector control, replicate 2


title: Matched_DB6 Metastasis ccRCC

city: Dallas

first: Divya

last: Bezwada

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Ends of sequences were trimmed with remaining adapter or quality scores <25.
Sequencing reads were aligned to the human reference genome (hg19) by STAR 2.7.3.a with default parameters in the 2-pass mod.
Counts for each gene were generated using htseq-count v0.6.1. DEGs were identified by DESeq2 v1.14.1.
Ends of sequences were trimmed with remaining adapter or quality scores <25. Sequence less than 35bp after trimming were removed.
The trimmed Fastq files were aligned to the GRCh38 using HiSAT272 and duplicates were marked with SAMBAMBA. Features (genes, transcripts and exons) were counted using featureCounts73. Differential expression analysis was performed using EdgeR74 and DESeq75. Genes with 0 values for all samples were trimmed from the processed data.
Assembly: hg19
Supplementary files format and content: Excel file includes log2CPM counts for each Sample

source_name: ccRCC Metastasis

extract_protocol:
RNA was isolated using Trizol (Thermo Fisher Scientific, Cat. No. 15596018) and an Rneasy Mini Kit (Qiagen, Cat. No. 74106). Total RNA was quantified using a Qubit fluorometer and the Invitrogen Qubit RNA High Sensitivity kit (Invitrogen, Cat. No. Q32852). Samples were diluted in ultrapure water prior to sequencing.
RNA-seq libraries were prepared using the NEBNext Ultra II directional RNA library prep kit with the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs, Cat. No. E7490L, E7760L) according to manufacturer’s instructions. Libraries were stranded using standard N.E.B indices according to manufacturer’s instructions (New England Biolabs, Cat. No. E7730L, E7335L, E7500L).

value: ccRCC Metastasis


title: crypt_wt_d9_2


title: Female Myf5 low  1


title: Nfur Wildtype 6-Day Diapause RNAseq Rep12

description:
Nfur_Wildtype_6D_12
Nfur_KO_Readcounts.csv


title: Matched_DB7 Primary Tumour ccRCC


title: crypt_wt_d9_1


title: UM32, vector control, replicate 1


title: Nfur Wildtype 6-Day Diapause RNAseq Rep9

description:
Nfur_Wildtype_6D_9
Nfur_KO_Readcounts.csv


title: Matched_DB7 Adjacent Kidney

source_name: ccRCC Primary Tumour

value: ccRCC Primary Tumour


title: Nfur Wildtype 6-Day Diapause RNAseq Rep4

description:
Nfur_Wildtype_6D_4
Nfur_KO_Readcounts.csv


title: HPAF-II, vector control, replicate 1


title: crypt_wt_d6_3

value: day 6 post tamoxifen


title: Nfur Wildtype 6-Day Diapause RNAseq Rep8

description:
Nfur_Wildtype_6D_8
Nfur_KO_Readcounts.csv


title: crypt_wt_d6_2


title: iSLK-RGB, ATAT1, IP

city: Nanjing

first: jing

last: zhou

address: longmian Street No.101

country: China

institute: Nanjing Medical University

data_processing:
The tRNA library was firstly adapted from the tRNAScan-SE library by appending CCA to tRNAs from the genomic tRNA database (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/). Isodecoders with identical scores were consolidated for ease of identity assignment, decreasing the number of reference genes and pseudogenes. Then, raw reads were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (at least 15 nt) were left by cutadapt software (v1.9.3). Then, trimmed reads from all samples were aligned using bowtie2 software to the aforementioned tRNA library with sensitive options. Mapped reads on each tRNA were counted using samtools. IP and Input raw expression data were normalized by TPM method, then IP/IgG was calculated as tRNA expression level base on normalized results. t-test was used to detect statistical differences in expression level of tRNA.
Assembly: hg19
Supplementary files format and content: excel format
Supplementary files format and content: Number of raw junction read
Library strategy: tRNA ac4C-seq

source_name: iSLK-RGB

extract_protocol:
The remaining RNA was size-selected for < 200 nt RNA fraction with the MirVana Isolation Kit (Invitrogen). The RNAs were then de-aminoacylated in 0.1 M Tris-HCl pH 9.0 and 1 mM EDTA for 30 min at 37°C.
tRNA libraries were constructed according to TruSeq Small RNA Preparation Kit (Illumina) instructions.

value: iSLK-RGB

value: endothelial cells

value: ATAT1 overexpression


title: caco2_wt_a_1

value: day 3 post-doxycycline


title: Nfur Wildtype 6-Day Diapause RNAseq Rep2

description:
Nfur_Wildtype_6D_2
Nfur_KO_Readcounts.csv


title: HPAF-II, vector control, replicate 3

value: Pancreatic cancer cell line


title: Matched_DB7 Metastasis ccRCC

source_name: Adjacent Kidney

value: Adjacent Kidney


title: crypt_wt_d6_1


title: Matched_DB6 Primary Tumour ccRCC


title: iSLK-RGB, pCDH, IP

value: pCDH (control for the ATAT1 overexpression)


title: Matched_DB5 Adjacent Kidney


title: Nfur Wildtype 6-Day Diapause RNAseq Rep5

description:
Nfur_Wildtype_6D_5
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: HPAF-II, ROR2, replicate 2


title: HPAF-II, vector control, replicate 2


title: Matched_DB6 Adjacent Kidney


title: Matched_DB5 Metastasis ccRCC


title: Nfur Wildtype 6-Day Diapause RNAseq Rep7

description:
Nfur_Wildtype_6D_7
Nfur_KO_Readcounts.csv

value: Diapause


title: Nfur Wildtype 6-Day Diapause RNAseq Rep6

description:
Nfur_Wildtype_6D_6
Nfur_KO_Readcounts.csv

value: 6-Day Diapause


title: Nfur Wildtype 6-Day Diapause RNAseq Rep3

description:
Nfur_Wildtype_6D_3
Nfur_KO_Readcounts.csv


title: iSLK-RGB, ATAT1, input

data_processing:
The tRNA library was firstly adapted from the tRNAScan-SE library by appending CCA to tRNAs from the genomic tRNA database (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/). Isodecoders with identical scores were consolidated for ease of identity assignment, decreasing the number of reference genes and pseudogenes. Then, raw reads were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (at least 15 nt) were left by cutadapt software (v1.9.3). Then, trimmed reads from all samples were aligned using bowtie2 software to the aforementioned tRNA library with sensitive options. Mapped reads on each tRNA were counted using samtools. IP and Input raw expression data were normalized by TPM method, then IP/IgG was calculated as tRNA expression level base on normalized results. t-test was used to detect statistical differences in expression level of tRNA.
Assembly: hg19
Supplementary files format and content: excel format
Supplementary files format and content: Number of raw junction read


title: crypt_ko_d9_2

value: Fgfr1op KO


title: Matched_DB5 Primary Tumour ccRCC


title: Nfur Wildtype 6-Day Diapause RNAseq Rep1

description:
Nfur_Wildtype_6D_1
Nfur_KO_Readcounts.csv


title: Matched_DB4 Adjacent_Arenal_Gland

source_name: Adjacent Arenal_Gland

value: Adjacent Arenal_Gland


title: iSLK-RGB, NAT10+/-, input


title: crypt_ko_d9_3


title: Matched_DB4 Primary Tumour ccRCC


title: iSLK-RGB, pCDH, input


title: Matched_DB4 Metastasis ccRCC


title: Matched_DB3 Metastasis ccRCC


title: iSLK-RGB, NAT10+/-, IP


title: Nfur REST-KO Development RNAseq Rep10

description:
Nfur_REST_Dev_10
Nfur_KO_Readcounts.csv

value: Development

value: Diapause-Escape


title: Nfur REST-KO Development RNAseq Rep11

description:
Nfur_REST_Dev_11
Nfur_KO_Readcounts.csv


title: crypt_ko_d9_1

value: day 9 post tamoxifen


title: Nfur REST-KO Development RNAseq Rep8

description:
Nfur_REST_Dev_8
Nfur_KO_Readcounts.csv


title: crypt_ko_d6_3


title: Nfur REST-KO Development RNAseq Rep9

description:
Nfur_REST_Dev_9
Nfur_KO_Readcounts.csv


title: crypt_ko_d6_2


title: iSLK-RGB, WT, IP

value: WT


title: iSLK-RGB, WT, input


title: Matched_DB3 Adjacent Kidney


title: crypt_ko_d6_1

value: day 6 post tamoxifen


title: Nfur REST-KO Development RNAseq Rep7

description:
Nfur_REST_Dev_7
Nfur_KO_Readcounts.csv


title: spheroid_wt_4

source_name: small intestinal spheroids

value: wt

value: day 3 post hydroxytamoxifen


title: Nfur REST-KO Development RNAseq Rep6

description:
Nfur_REST_Dev_6
Nfur_KO_Readcounts.csv


title: Matched_DB2 Primary Tumour ccRCC

value: ccRCC Metastasis


title: spheroid_wt_3


title: Nfur REST-KO Development RNAseq Rep5

description:
Nfur_REST_Dev_5
Nfur_KO_Readcounts.csv


title: VECTOR_IP

city: Xi’an

first: jie

last: Chu

address: 169 Changle West Road

institute: Air Force Medical University

library_source: genomic

data_processing:
The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. The clean reads were used for protein binding site analysis.
They were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters.
The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
The Homer（version 4.10）was used for motifs analysis. Finally,the csaw software was used for analysis of diffpeak.
Supplementary files format and content: hg38

molecule: genomic DNA

source_name: liver

extract_protocol:
Cells was fixed in 1% formaldehyde for 10 min at room temperature , after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）.

value: liver

value: LM3 cells

value: HCC

value: control


title: Matched_DB2 Adjacent Kidney

value: Adjacent Kidney


title: spheroid_wt_2


title: spheroid_wt_1


title: Matched_DB1 Metastasis ccRCC


title: spheroid_ko_4


title: Nfur REST-KO Development RNAseq Rep2

description:
Nfur_REST_Dev_2
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: VECTOR_Input


title: HA_OE_IP

value: ZNF706 overexpression


title: Matched_DB3 Primary Tumour ccRCC

value: ccRCC Primary Tumour


title: HA_OE_Input


title: MC3

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina NovaseqTM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)
To get high quality clean reads, reads were further filtered by Cutadapt,the parameters were as follows:1) removing reads containing adapters;2) removing reads containing more than 10% of unknown nucleotides (N);3) removing low quality reads containing more than 50% of low quality (Q-value≤5) bases. Then sequence quality was verified using FastQC.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: homo_sapiens GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 1ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
hen, sequencing library was constructed after the quality of RNA samples with RIN number > 7.0. RNA sequencing was performed on Illumina Novaseq™ 6000.

value: ZNF706 knockdown


title: Matched_DB2 Metastasis ccRCC


title: MC2


title: Nfur REST-KO Development RNAseq Rep1

description:
Nfur_REST_Dev_1
Nfur_KO_Readcounts.csv

value: Development


title: Nfur REST-KO Development RNAseq Rep4

description:
Nfur_REST_Dev_4
Nfur_KO_Readcounts.csv

value: Diapause-Escape


title: spheroid_ko_3

value: Fgfr1op KO


title: Matched_DB1 Primary Tumour ccRCC


title: Nfur REST-KO Development RNAseq Rep3

description:
Nfur_REST_Dev_3
Nfur_KO_Readcounts.csv


title: MC1

value: WT


title: Nfur REST-KO 6-Day Diapause RNAseq Rep10

description:
Nfur_REST_6D_10
Nfur_KO_Readcounts.csv

value: Diapause

value: 6-Day Diapause


title: spheroid_ko_2

value: day 3 post hydroxytamoxifen


title: VM18 Primary Tumour Papillary

source_name: Papillary RCC Primary Tumour

value: Papillary RCC Primary Tumour


title: Matched_DB1 Adjacent Kidney


title: MA3

value: liver


title: Nfur REST-KO 6-Day Diapause RNAseq Rep9

description:
Nfur_REST_6D_9
Nfur_KO_Readcounts.csv


title: spheroid_ko_1


title: VM31 Primary Tumour Papillary


title: Nfur REST-KO 6-Day Diapause RNAseq Rep8

description:
Nfur_REST_6D_8
Nfur_KO_Readcounts.csv


title: MA2

value: LM3 cells


title: VM22 Primary Tumour Papillary


title: wt3

description: small intestinal crypt-enriched cells day 6 post-tamoxifen

data_processing:
FASTQ files were aligned to the mm10 genome using CellRanger v6.0.1 (10x Genomics) to produce a count matrix of cells and UMI counts per gene.  Count matrices for all samples (3 Fgfr1op KO, 3 WT) were combined for downstream analysis.  To filter cells with uncharacteristically low library size or genes with low counts across all cells, we removed cells with log10 library size > 3.2, and genes with log10 mean expression across all cells > 3.5, corresponding to the tails of each distribution.  Cells with greater than 20% mitochondrial reads were removed; ribosomal genes and noncoding RNAs were also removed.  We then conducted library size and log-normalization in addition to scaling by a factor of 10000 in Seurat v4.0.1 .  We further removed doublets as computed by Scrublet , and all lymphocyte clusters.  The top 10 principal components of the gene expression data were used for Louvain clustering at resolution 0.4, and for a two-dimensional embedding of the data using the RunUMAP() function with default parameters.  To define markers for each cluster, we used the FindMarkers() function and specified “Wilcox” as the statistical test.  Genes were considered significantly differentially expressed at FDR P < 0.05.  Cell cycle signatures were obtained from Tirosh et al , and stem/TA signatures were obtained from Haber et al .  Signature scores were computed for single cells using the AddModuleScore() function in Seurat with default parameters.  Comparisons of signature scores between cells were computed using a two-sided Wilcoxon test.
Genome_build: mm10
Supplementary_files_format_and_content: .h5 files containing Cellranger-filtered matrices

extract_protocol:
Crypt preparation: Approximately 5 cm of small intestinal tissue was dissected, longitudinally opened and extensively washed in PBS. Tissue was placed in 2 mM EDTA in PBS for 30 min on the rotator at 4C. Tissue fragments were placed in 10 mL of  0.1% BCS and pipetted up and down. The pipetting and 0.1% BCS solution exchange was repeated 6 times. Fractions 4-6 were collected and crypts were collected by centrifugation. Cells were flow-sorted as live single cells for single cell sequencing with 10X Genomicx.
Single cells gene expression libraries were prepared by the McDonnell Genome Institute (MGI) at Washington University using the 3′ Single Cell v3 kit from 10x Genomics. Cells were partitioned into nanoliter Gel-bead-inEmulsions (GEMs) droplets. Each GEM underwent retro-transcriptase reaction to generate single-cell cDNA and received a unique 12-nt cell barcode and unique molecular identifier (UMI). GEM cDNA was amplified for 11 cycles before being purified using SPRIselect beads. For scRNAseq, 10 ml of purified cDNA was used to generate the library for RNA sequencing. Libraries were sequenced on a NovaSeq S4 (Illumina, 300 cycle kit) flow cell, targeting 50K read pairs per cell.

value: wt


title: Nfur REST-KO 6-Day Diapause RNAseq Rep5

description:
Nfur_REST_6D_5
Nfur_KO_Readcounts.csv


title: wt1


title: MA1

value: HCC

value: control


title: VM57 Primary Tumour Papillary


title: wt2


title: ko3


title: VM68 Primary Tumour Papillary


title: ko2


title: Nfur REST-KO 6-Day Diapause RNAseq Rep6

description:
Nfur_REST_6D_6
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: VM37 Primary Tumour Papillary


title: Nfur REST-KO 6-Day Diapause RNAseq Rep4

description:
Nfur_REST_6D_4
Nfur_KO_Readcounts.csv


title: P12-24h FGF1+ICI-B

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

data_processing:
Quality trim to a minimum of Q15
Map to the Human GRCh38 genome using GSNAP version 2014-12-17
sort and index using SAMTOOLS
split forward and reverse reads using SAMTOOLS
call FPKM using CUFFLINKS, applying anti-sense reads to sense genes, and sense reads to anti-sense genes
Assembly: GRCh38
Supplementary files format and content: Cufflinks files containing FPKM values

source_name: Breast cancer

growth_protocol: MCF7 and tamoxifen resistant MCF7 (TAMR) cells were purchased from ATCC and were maintained as suggested by the vendor in complete growth. UCD12 cells were developed by the University of Colorado Denver/Anschutz Medical Campus

extract_protocol:
RNA was collected using the RNEasy mini kit (Qiagen).
Swift directional mRNA prep
NovaSeq 6000 2x151

treatment_protocol: Cell lines were treated with 17b-estradiol (E2; 10 nM) or recombinant human FGF1 (5 ng/mL) for 24 hours in the presence or absence of fulvestrant (ICI 182 780; 100 nM) following an overnight starvation period in phenol red-free media containing 0.5% charcoal stripped fetal bovine serum.

value: Breast cancer

value: epithelial cell

value: tamoxifen sensitive

value: FGF1 + Fulvestrant


title: P12-24h FGF1+ICI-C


title: VM15 Primary Tumour Papillary


title: P12-24h FGF1+ICI-A


title: Nfur REST-KO 6-Day Diapause RNAseq Rep3

description:
Nfur_REST_6D_3
Nfur_KO_Readcounts.csv


title: VM62 Primary Tumour Papillary


title: PHF2 2_2

city: Barcelona

first: Samuel

last: Aguirre Infantes

state: Barcelona

address: Baldiri Reixac 15-21

department: Department of Structural and Molecular Biology

country: Spain

institute: IBMB-CSIC

data_processing:
Single-end reads were aligned to the mouse mm10 reference genome using Bowtie2 (v2.3.5.1) with default options.
SAMtools (v1.9) was used to filter out the low-quality alignments using the flag 3844.
The resulting BAM files were sorted and deepTools was used to generate input-subtracted and counts per million (CPM) normalized signal tracks (bamCompare -- operation subtract -- normalizeUsing CPM --scaleFactorsMethod None) in bigWig format.
Assembly: mm10
Supplementary files format and content: bigWig files include input-subtracted ChIP-Seq signal.

source_name: Neural Stem Cell

growth_protocol: Neural Stem Cells were extracted from E12.5 mice forebrain and disgregated. Then cultured in DMEM+Neurobasal media with supplements and growth factors to maintain the stem status.

extract_protocol:
1x 10^6NSCs were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.
The libraries were prepared and amplified to make DNA NanoBall (DNB)
Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)

treatment_protocol: Cells were infected with lentiviral shRNA either scramble (control) or against PHF2 (shPHF2)

tag: developmental stage

value: forebrain E12.5

value: Neural Stem Cell

tag: chip antibody

value: PHF2 (Cell Signaling, D45A2)


title: Nfur REST-KO 6-Day Diapause RNAseq Rep1

description:
Nfur_REST_6D_1
Nfur_KO_Readcounts.csv

value: Diapause


title: P12-24h E2+ICI-C

value: Estradiol + Fulvestrant


title: P12-24h FGF1-C


title: Nfur PPARG-KO Development RNAseq Rep11

description:
Nfur_PPARG_Dev_11
Nfur_KO_Readcounts.csv

value: Development

value: Diapause-Escape


title: ko1

value: Fgfr1op KO


title: Nfur REST-KO 6-Day Diapause RNAseq Rep2

description:
Nfur_REST_6D_2
Nfur_KO_Readcounts.csv

value: 6-Day Diapause


title: VM19 Primary Tumour Oncocytic

source_name: Oncocytic Tumor Primary Tumour

value: Oncocytic Tumor Primary Tumour


title: P12-24h E2+ICI-A


title: Nfur PPARG-KO Development RNAseq Rep12

description:
Nfur_PPARG_Dev_12
Nfur_KO_Readcounts.csv


title: P12-24h FGF1-A


title: VM43 Primary Tumour FH Def RCC

source_name: FH deficient RCC Primary Tumour

value: FH deficient RCC Primary Tumour


title: PHF2 NIH 1

value: fibroblast


title: PHF2 2_1


title: PHF2 input 2


title: VM64 Primary Tumour Oncocytic


title: P12-24h E2+ICI-B


title: Nfur PPARG-KO Development RNAseq Rep10

description:
Nfur_PPARG_Dev_10
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: PHF2 NIH 2


title: VM52 Primary Tumour FH Def RCC


title: P12-24h FGF1-B

value: Breast cancer


title: Nfur PPARG-KO Development RNAseq Rep9

description:
Nfur_PPARG_Dev_9
Nfur_KO_Readcounts.csv


title: VM29 Primary Tumour Oncocytic


title: Nfur PPARG-KO Development RNAseq Rep7

description:
Nfur_PPARG_Dev_7
Nfur_KO_Readcounts.csv


title: VM61 Primary Tumour Oncocytic


title: P12-24h ICI-C

value: epithelial cell

value: Fulvestrant


title: P12-24h ICI-A

value: tamoxifen sensitive


title: Nfur PPARG-KO Development RNAseq Rep6

description:
Nfur_PPARG_Dev_6
Nfur_KO_Readcounts.csv


title: PHF2 NIH input


title: Nfur PPARG-KO Development RNAseq Rep8

description:
Nfur_PPARG_Dev_8
Nfur_KO_Readcounts.csv


title: PHF2 2

value: forebrain E12.5


title: Nfur PPARG-KO Development RNAseq Rep5

description:
Nfur_PPARG_Dev_5
Nfur_KO_Readcounts.csv


title: VM16 Primary Tumour Chromophobe

source_name: Chromophobe RCC Primary Tumour

value: Chromophobe RCC Primary Tumour


title: PHF2 3

value: Neural Stem Cell

value: PHF2 (Cell Signaling, D45A2)


title: VM42 Primary Tumour Chromophobe


title: P12-24h E2-A

value: Estradiol


title: Nfur PPARG-KO Development RNAseq Rep3

description:
Nfur_PPARG_Dev_3
Nfur_KO_Readcounts.csv

value: Development


title: VM45 Primary Tumour Chromophobe


title: P12-24h ICI-B


title: shPHF2 K4me3 2

value: H3K4me3 (Abcam ab8580)

value: infected with shPHF2


title: VM65 Primary Tumour CCRCC

value: ccRCC Primary Tumour


title: P12-24h E2-C


title: PHF2 input


title: Nfur PPARG-KO Development RNAseq Rep4

description:
Nfur_PPARG_Dev_4
Nfur_KO_Readcounts.csv

value: Diapause-Escape


title: shPHF2 K4me3 1


title: shPHF2 input


title: P12-24h E2-B


title: P12-24h VC-B

value: Vehicle control


title: VM34 Primary Tumour CCRCC


title: P12-24h VC-C


title: VM50 Primary Tumour CCRCC


title: VM27 Primary Tumour Chromophobe


title: Nfur PPARG-KO Development RNAseq Rep2

description:
Nfur_PPARG_Dev_2
Nfur_KO_Readcounts.csv


title: Nfur PPARG-KO Development RNAseq Rep1

description:
Nfur_PPARG_Dev_1
Nfur_KO_Readcounts.csv


title: shPHF2 K9me3 2

value: H3K9me3 (Abcam ab8898)


title: shCT input

value: shCT

value: infected with shControl


title: VM67 Primary Tumour CCRCC


title: VM36 Primary Tumour CCRCC


title: shCT K4me3 1


title: Nfur PPARG-KO 6-Day Diapause RNAseq Rep4

description:
Nfur_PPARG_6D_4
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)

value: Diapause

value: 6-Day Diapause


title: VM41 Primary Tumour CCRCC


title: M7T-24h E2+ICI-C

value: Breast cancer

value: MCF7 (TAMR)

value: epithelial cell

value: tamoxifen resistant

value: Estradiol + Fulvestrant


title: M7T-24h FGF1+ICI-C

value: FGF1 + Fulvestrant


title: shPHF2 K9me3 1

value: forebrain E12.5

value: Neural Stem Cell


title: Nfur PPARG-KO 6-Day Diapause RNAseq Rep3

description:
Nfur_PPARG_6D_3
Nfur_KO_Readcounts.csv


title: P12-24h VC-A

value: tamoxifen sensitive


title: Nfur PPARAb-KO Development RNAseq Rep6

description:
Nfur_PPARAb_Dev_6
Nfur_KO_Readcounts.csv

value: Development

value: Diapause-Escape


title: M7T-24h E2+ICI-B


title: VM44 Primary Tumour CCRCC

value: ccRCC Primary Tumour


title: M7T-24h FGF1+ICI-B


title: M7T-24h FGF1+ICI-A


title: M7T-24h FGF1-C


title: Nfur PPARAb-KO Development RNAseq Rep10

description:
Nfur_PPARAb_Dev_10
Nfur_KO_Readcounts.csv


title: h- nmt41-GST-pab1-KanMx6 igo1::natMx6 cells, pab1 repression, igo1 mutant, minimal medium w/o nitrogen 4 hrs, rep 2

city: Salamanca

first: Sergio

last: Moreno

email: smo@usal.es, ibfg_smp@usal.es

state: Salamanca

address: Zacarias Gonzalez 2

department: IBFG

institute: Institute of Functional Biology and Genomics (IBFG) (CSIC)

description:
igo_pab_2_4
norm_counts_Deseq2_DE_igo1pab1_igo1_N4.txt
h- nmt41-GST-pab1-KanMx6 igo1::natMx6 cells, pab1 repression, igo1 mutant, minimal medium without nitrogen 4 hours, bio rep 2

data_processing:
Sequencing quality was check with FastQC (v 0.11.8, Babraham Bioinformatics).
Adaptors were trimmed using Trimmomatic (v 0.38) (Bolger et al. 2014) .
Alignment was performed with HISAT2 v 2.1.0 (CCB in John Hopkins University) (Kim et al. 2015)
Read counts were obtained with featureCounts (Subread package v 1.6.3, Walter+Eliza Hall Bioinformatics) (Liao et al.2014) .
Assembly: ASM294v2
Supplementary files format and content: tab-delimited text files include normalized counts after Deseq2 analysisis

organism: Schizosaccharomyces pombe

source_name: h- nmt41-GST-pab1-KanMx6 igo1::natMx6

growth_protocol: Wild type, igo1∆ and cells repressing pab1+ from the nmt41+ promoter were grown to mid-exponential phase in supplemented yeast extract medium (YES) and minimal medium with thiamine.

extract_protocol:
Cells were washed with cold DEPC-H2O and snap freeze. RNA extraction was carried out by disrupting the cells with cells with glass beads in TRIzol® Reagent (Invitrogen) and following the manufacturer’s instructions.
Library preparation using the Illumina TruSeq Stranded Total RNA and subsequent NGS sequencing was performed by Macrogen.

treatment_protocol: Cells were centrifuged and washed three times in MM-N with thiamine, and cultured in MM-N at 25ºC. 2x10 8 cells were harvested at 4 hours

value: h- nmt41-GST-pab1-KanMx6 igo1::natMx6

value: igo1 knockdown pab1 repression

value: Minimal medium without nitrogen after 4 hours


title: Nfur PPARAb-KO Development RNAseq Rep4

description:
Nfur_PPARAb_Dev_4
Nfur_KO_Readcounts.csv

source_name: Dissected Embryo (Whole Body)

value: Dissected Embryo (Whole body)


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium w/o nitrogen 4 hrs, rep 2

description:
igo_2_4_bis
norm_counts_Deseq2_DE_igo1pab1_igo1_N4.txt
h- igo1::kanMX6 cells, igo1 mutant, minimal medium without nitrogen 4 hours, bio rep 2

source_name: h- igo1::kanMX6

value: h- igo1::kanMX6

value: igo1 knockdown


title: Nfur PPARAb-KO Development RNAseq Rep3

description:
Nfur_PPARAb_Dev_3
Nfur_KO_Readcounts.csv


title: shCT K9me3 2

value: H3K9me3 (Abcam ab8898)

value: shCT

value: infected with shControl


title: Nfur PPARAb-KO Development RNAseq Rep9

description:
Nfur_PPARAb_Dev_9
Nfur_KO_Readcounts.csv


title: Nfur PPARG-KO 6-Day Diapause RNAseq Rep2

description:
Nfur_PPARG_6D_2
Nfur_KO_Readcounts.csv

value: Diapause

value: 6-Day Diapause


title: shCT K4me3 2

value: forebrain E12.5

value: H3K4me3 (Abcam ab8580)


title: h- igo1::kanMX6 cells, igo1 mutant, minimal medium w/o nitrogen 4 hrs, rep 1

description:
igo_1_4_bis
norm_counts_Deseq2_DE_igo1pab1_igo1_N4.txt
h- igo1::kanMX6 cells, igo1 mutant, minimal medium without nitrogen 4 hours, bio rep 1


title: M7T-24h ICI-C

value: Breast cancer

value: MCF7 (TAMR)

value: epithelial cell

value: tamoxifen resistant

value: Fulvestrant


title: VM49 Primary Tumour CCRCC

value: ccRCC Primary Tumour


title: VM26 Primary Tumour CCRCC


title: Nfur PPARAb-KO Development RNAseq Rep1

description:
Nfur_PPARAb_Dev_1
Nfur_KO_Readcounts.csv

value: Development

value: Diapause-Escape


title: VM35 Primary Tumour CCRCC


title: M7T-24h ICI-B


title: M7T-24h E2+ICI-A

value: Estradiol + Fulvestrant


title: M7T-24h FGF1-A


title: Nfur PPARAb-KO 6-Day Diapause RNAseq Rep5

description:
Nfur_PPARAb_6D_5
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: M7T-24h ICI-A


title: Nfur PPARAb-KO Development RNAseq Rep5

description:
Nfur_PPARAb_Dev_5
Nfur_KO_Readcounts.csv


title: VM58 Primary Tumour CCRCC


title: VM23 Primary Tumour CCRCC


title: VM30 Primary Tumour CCRCC


title: M7T-24h E2-B

value: Estradiol


title: Nfur PPARAb-KO 6-Day Diapause RNAseq Rep1

description:
Nfur_PPARAb_6D_1
Nfur_KO_Readcounts.csv


title: shCT K9me3 1

value: Neural Stem Cell

value: H3K9me3 (Abcam ab8898)

value: shCT


title: h- nmt41-GST-pab1-KanMx6 igo1::natMx6 cells, pab1 repression, igo1 mutant, minimal medium w/o nitrogen 4 hrs, rep 1

description:
igo_pab_1_4
norm_counts_Deseq2_DE_igo1pab1_igo1_N4.txt
h- nmt41-GST-pab1-KanMx6 igo1::natMx6 cells, pab1 repression, igo1 mutant, minimal medium without nitrogen 4 hours, bio rep 1

value: h- nmt41-GST-pab1-KanMx6 igo1::natMx6

value: igo1 knockdown pab1 repression

value: Minimal medium without nitrogen after 4 hours


title: VM46 Primary Tumour CCRCC


title: Dmel pupae 48h 3

city: Moscow

first: Aleksandra

middle: M

last: Ozerova

address: Skolkovo Innovation Center, Bolshoy Boulevard, 30, p.1

department: Life sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

description: pupae 48h 3

data_processing:
Low-quality nucleotides and reads were systematically eliminated using the fastp tool with the default parameters. Subsequently, the filtered reads were aligned to the respective reference genomes with the kallisto pseudomapping procedure and the BDGP6.46 and DvirRS2 assemblies as references for D. melanogaster and D. virilis, respectively.
Assembly: BDGP6.46 for D. melanogaster and DvirRS2 for D. virilis
Supplementary files format and content: {species}_vst_matrix.csv files contain comma-separated table witth normalized expression values for each sample and each replicate.

organism: Drosophila melanogaster

source_name: whole body

growth_protocol: The flies, spanning all developmental stages, were reared on the standard Drosophila wheat meal-yeast-sugar-agar medium and maintained at a constant temperature of 25°C.

extract_protocol:
The samples underwent a thorough rinsing process to remove any residual food and yeast, using the PBS buffer. Following this step, total RNA was extracted from the samples using RNAzol RT reagent (MRC, Cincinnati, OH, USA), following the manufacturer’s recommended protocols. RNA quality assessments were performed through gel electrophoresis, and the RNA samples were carefully stored in ethanol at -70°C, in preparation for subsequent experimental procedures.
Ribosomal RNA depletion was conducted using the NEBNext® Poly(A) mRNA Magnetic Isolation Module. Subsequently, RNA library preparation was carried out with the NEBNext® Ultra™ II Directional RNA Library Prep Kit, and the prepared libraries were sequenced on the Illumina HiSeq4000 platform.

value: whole body

tag: replicate

value: biol rep 3

tag: gender

value: unknown

value: pupae


title: M7T-24h FGF1-B

value: Breast cancer

value: MCF7 (TAMR)

value: epithelial cell

value: tamoxifen resistant


title: VM54 Primary Tumour CCRCC

value: ccRCC Primary Tumour


title: VM32 Primary Tumour CCRCC


title: Nfur FOXO3b-KO Development RNAseq Rep6

description:
Nfur_FOXO3b_Dev_6
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)

value: Development

value: Diapause-Escape


title: Dmel pupae 48h 1

description: pupae 48h 1

value: biol rep 1


title: VM14 Primary Tumour CCRCC


title: VM12 Primary Tumour CCRCC


title: h- 972 cells, wild type, minimal medium w/o nitrogen 4 hrs, rep 2

description:
wt_2_4
norm_counts_Deseq2_DE_wt_igo1pab1_N4.txt
h- 972 cells, wild type, minimal medium without nitrogen 4 hours, bio rep 2

value: WT


title: Nfur PPARAb-KO Development RNAseq Rep2

description:
Nfur_PPARAb_Dev_2
Nfur_KO_Readcounts.csv


title: M7P-24h FGF1+ICI-C

value: tamoxifen sensitive

value: FGF1 + Fulvestrant


title: VM10 Primary Tumour CCRCC


title: Dmel pupae 24h 2

description: pupae 24h 2

value: biol rep 2


title: Nfur PPARAb-KO 6-Day Diapause RNAseq Rep4

description:
Nfur_PPARAb_6D_4
Nfur_KO_Readcounts.csv

value: Diapause

value: 6-Day Diapause


title: M7T-24h E2-C

value: Estradiol


title: VM40 Primary Tumour CCRCC


title: VM47 Primary Tumour CCRCC


title: Dmel imago 5d 3

description: adults 5d 3

value: whole body

value: biol rep 3

value: male

value: imago


title: Dmel imago 5d 2

description: adults 5d 2


title: Nfur PPARAb-KO 6-Day Diapause RNAseq Rep2

description:
Nfur_PPARAb_6D_2
Nfur_KO_Readcounts.csv


title: h- 972 cells, wild type, minimal medium w/o nitrogen 4 hrs, rep 1

description:
wt_1_4
norm_counts_Deseq2_DE_wt_igo1pab1_N4.txt
h- 972 cells, wild type, minimal medium without nitrogen 4 hours, bio rep 1

value: Minimal medium without nitrogen after 4 hours


title: Dmel pupae 24h 1

description: pupae 24h 1

value: unknown

value: pupae


title: Nfur FOXO3b-KO 6-Day Diapause RNAseq Rep5

description:
Nfur_FOXO3b_6D_5
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: VM09 Primary Tumour CCRCC

value: ccRCC Primary Tumour


title: Dmel imago 5d 1

description: adults 5d 1

value: biol rep 1


title: M7T-24h E2-A

value: Breast cancer

value: MCF7 (TAMR)

value: epithelial cell

value: tamoxifen resistant


title: Nfur FOXO3b-KO 6-Day Diapause RNAseq Rep4

description:
Nfur_FOXO3b_6D_4
Nfur_KO_Readcounts.csv

value: Diapause


title: Dmel pupae P5 2

description: pupae P5 2

value: biol rep 2


title: Nfur FOXO3b-KO Development RNAseq Rep7

description:
Nfur_FOXO3b_Dev_7
Nfur_KO_Readcounts.csv

value: Development

value: Diapause-Escape


title: Dmel pupae 48h 2

description: pupae 48h 2

value: whole body


title: VM20 Primary Tumour CCRCC


title: M7T-24h VC-C

value: Vehicle control


title: M7P-24h E2+ICI-B

value: tamoxifen sensitive

value: Estradiol + Fulvestrant


title: M7P-24h E2+ICI-A


title: Nfur FOXO3b-KO 6-Day Diapause RNAseq Rep2

description:
Nfur_FOXO3b_6D_2
Nfur_KO_Readcounts.csv

value: 6-Day Diapause


title: Nfur FOXO3b-KO Development RNAseq Rep8

description:
Nfur_FOXO3b_Dev_8
Nfur_KO_Readcounts.csv


title: Nfur FOXO3b-KO Development RNAseq Rep5

description:
Nfur_FOXO3b_Dev_5
Nfur_KO_Readcounts.csv


title: M7T-24h VC-A


title: Dmel pupae 24h 3

description: pupae 24h 3

value: biol rep 3

value: unknown

value: pupae


title: Nfur FOXO3b-KO 6-Day Diapause RNAseq Rep14

description:
Nfur_FOXO3b_6D_14
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: M7T-24h VC-B

value: Breast cancer


title: M7P-24h FGF1+ICI-B

value: FGF1 + Fulvestrant


title: VM28 Metastasis CCRCC

source_name: ccRCC Metastasis

value: ccRCC Metastasis


title: M7P-24h FGF1-C

value: epithelial cell


title: Nfur FOXO3b-KO 6-Day Diapause RNAseq Rep1

description:
Nfur_FOXO3b_6D_1
Nfur_KO_Readcounts.csv

value: Diapause


title: M7P-24h FGF1+ICI-A


title: VM38 Primary Tumour CCRCC

source_name: ccRCC Primary Tumour

value: ccRCC Primary Tumour


title: Nfur FOXO3b-KO 6-Day Diapause RNAseq Rep8

description:
Nfur_FOXO3b_6D_8
Nfur_KO_Readcounts.csv


title: Nfur FOXO3a-KO Development RNAseq Rep8

description:
Nfur_FOXO3a_Dev_8
Nfur_KO_Readcounts.csv

value: Development


title: Dmel pupae P5 3

description: pupae P5 3


title: VM90_2 Metastasis CCRCC


title: VM60 Primary Tumour CCRCC


title: Dmel pupae P4 1

description: pupae P4 1

value: biol rep 1


title: Dmel pupae P4 2

description: pupae P4 2

value: whole body

value: biol rep 2


title: VM36 Metastasis CCRCC


title: M7P-24h FGF1-A

value: tamoxifen sensitive


title: M7P-24h E2+ICI-C

value: Estradiol + Fulvestrant


title: Nfur FOXO3b-KO 6-Day Diapause RNAseq Rep3

description:
Nfur_FOXO3b_6D_3
Nfur_KO_Readcounts.csv

value: 6-Day Diapause


title: Dmel pupae P5 1

description: pupae P5 1


title: VM66 Metastasis CCRCC


title: Nfur FOXO3a-KO Development RNAseq Rep7

description:
Nfur_FOXO3a_Dev_7
Nfur_KO_Readcounts.csv

value: Diapause-Escape


title: Dmel pupae P4 3

description: pupae P4 3

value: biol rep 3

value: unknown


title: Nfur FOXO3a-KO Development RNAseq Rep6

description:
Nfur_FOXO3a_Dev_6
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: Nfur FOXO3a-KO Development RNAseq Rep5

description:
Nfur_FOXO3a_Dev_5
Nfur_KO_Readcounts.csv


title: VM38_2 Metastasis CCRCC


title: M7P-24h FGF1-B

value: Breast cancer


title: Dmel pupae P3 3

description: pupae P3 3

value: pupae


title: Nfur FOXO3a-KO Development RNAseq Rep4

description:
Nfur_FOXO3a_Dev_4
Nfur_KO_Readcounts.csv


title: M7P-24h ICI-C

value: Fulvestrant


title: VM81_2 Metastasis CCRCC

value: ccRCC Metastasis


title: VM90_1 Metastasis CCRCC


title: VM54 Metastasis CCRCC


title: M7P-24h ICI-A

value: epithelial cell


title: Dmel pupae P3 2

description: pupae P3 2


title: M7P-24h ICI-B


title: M7P-24h E2-B

value: Estradiol


title: Nfur FOXO3a-KO Development RNAseq Rep2

description:
Nfur_FOXO3a_Dev_2
Nfur_KO_Readcounts.csv

value: Development


title: Dmel pupae P3 1

description: pupae P3 1

value: biol rep 1


title: Dmel pupae P2 2

description: pupae P2 2

value: whole body


title: VM92 Metastasis CCRCC


title: M7P-24h E2-A


title: Nfur FOXO3a-KO Development RNAseq Rep1

description:
Nfur_FOXO3a_Dev_1
Nfur_KO_Readcounts.csv


title: Dmel pupae P2 1

description: pupae P2 1


title: M7P-24h VC-C

value: Vehicle control


title: Dmel pupae P1 3

description: pupae P1 3


title: Nfur FOXO3a-KO 6-Day Diapause RNAseq Rep8

description:
Nfur_FOXO3a_6D_8
Nfur_KO_Readcounts.csv

value: Diapause


title: Dmel pupae P1 2

description: pupae P1 2

value: biol rep 2


title: M7P-24h E2-C

value: tamoxifen sensitive


title: Nfur FOXO3a-KO Development RNAseq Rep3

description:
Nfur_FOXO3a_Dev_3
Nfur_KO_Readcounts.csv

value: Diapause-Escape


title: VM38_1 Metastasis CCRCC


title: VM91_2 Metastasis CCRCC


title: Dmel pupae P2 3

description: pupae P2 3

value: biol rep 3


title: M7P-24h VC-B


title: Nfur FOXO3a-KO 6-Day Diapause RNAseq Rep6

description:
Nfur_FOXO3a_6D_6
Nfur_KO_Readcounts.csv

value: 6-Day Diapause


title: Dmel pupae P1 1

description: pupae P1 1

value: unknown


title: VM91_1 Metastasis CCRCC


title: M7P-24h VC-A

value: Breast cancer


title: Dmel larvae 3instar 3

description: larvae 3rd instar 1

value: larvae


title: Nfur FOXO3a-KO 6-Day Diapause RNAseq Rep5

description:
Nfur_FOXO3a_6D_5
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: VM83 Metastasis CCRCC

value: ccRCC Metastasis


title: HCT116-WT-3A

city: Guangzhou

first: wei

last: xiong

state: Guangdong

address: No.1023,South Shatai Road

department: Bioinformatics Section

institute: Southern Medical University

data_processing:
Illumina NovaSeq6000 reads were trimmed and clipped for quality control in trim_galore(0.6.6). Read quality was checked for each sample using FastQC v0.11.9
High-quality reads were then imported into HISAT2 (2.2.1) for alignment into BAM files.
StringTie2 (2.1.4) was used to assembe alignments into transcripts and quantitate  transcripts. Read counts were obtained from StringTie2.
Assembly: hg38 (GRCh.38.100)
Supplementary files format and content: Read counts for genes in each sample included in comma-separated values

source_name: HCT116 wild type

extract_protocol:
Genome editing using CRISPR/Cas9 was used to knockout the lncRNAs' DNA binding domains (DBDs). Before and after the knockout, RNA-sequencing was performed to examine gene expression (performed by HaploX Genomics Center, Shenzhen, China, https://www.haplox.cn/pc/home). Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The quality and purity of RNA were examined by a NanoDrop™ One/OneC spectrophotometer (Thermo Scientific, Waltham, MA, USA) and Life Invitrogen Qubit RNA BR (Broad-Range) Assay Kit. RNA integrity was analyzed using Agilent 4200 TapeStation system (Agilent, Santa Clara, CA, USA).
1 μg of total RNA per sample was prepared for library preparation. Firstly, Ribo-Zero rRNA Removal Reagent (H/M/R) (Illumina, USA) was used to remove rRNA. Then, Magmetic RNA Beads (Vazyme, China) was used to purify remaining RNA. Finally, library was constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) and VAHTS DNA Clean Beads (Vazyme, China) and Q5 Hot Start High-Fidelity 2X Master Mix and primer mix (NEB, USA) was used to amplify library.The concentration of constructed library was measured by Qubit®3.0 Fluorometer and Library molar concentration was measured by QuantStudio 3 qPCR, and Agilent 4200 was used to examine the distribution of segments in library. Finally, RNA-Seq was performed on an Illumina NovaSeq6000 platform according to the manufacturer’s instructions

value: Colon

value: cancer

value: wild type


title: VM65 Adjacent Kidney

source_name: Adjacent Kidney

value: Adjacent Kidney


title: Dmel larvae 2instar 2

description: larvae 2nd instar 1

value: whole body


title: Nfur FOXO3a-KO 6-Day Diapause RNAseq Rep3

description:
Nfur_FOXO3a_6D_3
Nfur_KO_Readcounts.csv


title: HCT116-WT-2A


title: Nfur FOXO3a-KO 6-Day Diapause RNAseq Rep2

description:
Nfur_FOXO3a_6D_2
Nfur_KO_Readcounts.csv


title: Nfur FOXO3a-KO 6-Day Diapause RNAseq Rep1

description:
Nfur_FOXO3a_6D_1
Nfur_KO_Readcounts.csv


title: HCT116-WT-1A


title: Dmel larvae 1instar 1

description: larvae 1st instar 1

value: biol rep 1


title: VM50 Adjacent Kidney


title: VM52 Adjacent Kidney


title: Dmel embryo 10h 3

description: embryo 10h 3

value: embryo


title: Nfur Control-KO Development RNAseq Rep18

description:
Nfur_Control_Dev_18
Nfur_KO_Readcounts.csv

value: Development


title: Dmel embryo 10h 2

description: embryo 10h 2

value: biol rep 2


title: VM18 Adjacent Kidney


title: HCT116-MSTRG-34636-7_KO-3A

source_name: MSTRG.34636.7 DBD knockout in HCT116

value: MSTRG.34636.7 DBD knockout in HCT116

value: knockout


title: Dmel embryo 10h 1

description: embryo 10h 1


title: HCT116-MSTRG-34636-7_KO-2A


title: VM43 Adjacent Kidney


title: VM90 Metastasis CCRCC


title: HCT116-MSTRG-34636-7_KO-1A


title: Nfur Control-KO Development RNAseq Rep16

description:
Nfur_Control_Dev_16
Nfur_KO_Readcounts.csv

value: Diapause-Escape


title: VM42 Adjacent Kidney


title: HCT116-3B_WT_S14


title: Nfur Control-KO Development RNAseq Rep15

description:
Nfur_Control_Dev_15
Nfur_KO_Readcounts.csv


title: VM67 Adjacent Kidney


title: IMR90, ICM, replicate 2, input

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str. 40

department: Institute of Pathology

country: Germany

institute: University Medical Center Göttingen

data_processing:
*library strategy: eCLIP
The data were analyzed via the eCLIP pipeline (https://github.com/YeoLab/eCLIP)
Assembly: hg38
Supplementary files format and content: bigWig separated by strandness
Supplementary files format and content: narrowPeaks

growth_protocol: Proliferating primary lung fibroblasts (IMR90) isolates (I79 and I83, passage 5; Coriell) were grown in MEM (M4655, Sigma-Aldrich) supplemented with 1x non-essential amino acids and 10% FBS under 5% CO2.

extract_protocol:
~20x10^6 IMR90 were UV-crosslinked (400 mJ/cm2 constant energy), lysed in iCLIP lysis buffer, and sonicated (on a BioRuptor Pico). Lysates were treated with RNase I (Ambion, AM2294) to fragment RNA, after which CTCF protein-RNA complexes were immunoprecipitated using the relevant antibody (anti-CTCF, Active Motif 61331). In parallel to the IP, an “input” library was generated for each replicate for which no antibody was used. Stringent washes were next performed, during which RNA was dephosphorylated with FastAP enzyme (Fermentas) and T4 PNK (NEB, M0201S). Subsequently, a 3’ RNA adaptor oligonucleotide was ligated onto the RNA using a T4 RNA ligase (NEB, M0242S). Protein-RNA complexes were separated on an SDS-polyacrylamide gel electrophoresis gel and transferred to nitrocellulose membranes, and RNA was isolated off the membrane. After precipitation, RNA was reverse-transcribed with AffinityScript reverse transcriptase (Agilent, 600107), free oligos were removed using ExoSap-IT (Thermo Fisher Scientific, 78201.1.ML), and a 3’ DNA adaptor was ligated onto the cDNA product.
Libraries were then amplified with 2x Q5 PCR mix (NEB)

tag: eclip antibody

value: primary lung fibroblasts

value: WT

value: ICM inducing senescence


title: Nfur Control-KO Development RNAseq Rep14

description:
Nfur_Control_Dev_14
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: HCT116-1B_WT_S12


title: IMR90, ICM, replicate 1, input


title: VM31 Adjacent Kidney


title: Nfur Control-KO Development RNAseq Rep13

description:
Nfur_Control_Dev_13
Nfur_KO_Readcounts.csv


title: IMR90, wild type, replicate 2, input


title: VM41 Adjacent Kidney


title: HCT116-MSTRG-4401-1_KO_S16

source_name: MSTRG.4401.1 DBD knockout in HCT116

value: MSTRG.4401.1 DBD knockout in HCT116


title: Nfur Control-KO Development RNAseq Rep12

description:
Nfur_Control_Dev_12
Nfur_KO_Readcounts.csv


title: Nfur Control-KO Development RNAseq Rep17

description:
Nfur_Control_Dev_17
Nfur_KO_Readcounts.csv


title: VM22 Adjacent Kidney


title: Nfur Control-KO Development RNAseq Rep11

description:
Nfur_Control_Dev_11
Nfur_KO_Readcounts.csv


title: VM26 Adjacent Kidney


title: Human rep 2

city: New York

first: Sumin

last: Jang

state: NY

institute: Columbia University

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode analysis and gene expression quantification was done using CellRanger v3.1.0
Assembly: mm10 and hg38
Supplementary files format and content: tab-delimited gene expression matrix (UMI)

extract_protocol:
Embryoid bodies were dissociated with papain and DNase I, followed by FACS to select GFP+ cells.
Library was prepared according to manufacturer's protocol (10X Genomics: single cell 3')

treatment_protocol: Prior to differentiation, human and mouse pluripotent stem cells were transduced with a lentivirus harboring unique 6bp barcode sequences downstream of CAGGS-driven GFP.

value: Human iPS

value: in vitro motor neuron differentiation


title: IMR90, wild type, replicate 1, input


title: Nfur Control-KO Development RNAseq Rep9

description:
Nfur_Control_Dev_9
Nfur_KO_Readcounts.csv


title: HCT116-MSTRG-4401-1_KO_S15

value: Colon

value: cancer


title: HCT116-MSTRG-4401-1_KO_S10


title: IMR90, ICM, replicate 2, eclip

value: CTCF(Active Motif 61331)


title: VM45 Adjacent Kidney

value: Adjacent Kidney


title: IMR90, ICM, replicate 1, eclip


title: IMR90, wild type, replicate 2, eclip


title: VM58 Adjacent Kidney


title: HCT116-MSTRG-2513-6_KO_S8

source_name: MSTRG.2513.6 DBD knockout in HCT116

value: MSTRG.2513.6 DBD knockout in HCT116


title: HCT116-2B_WT_S13

value: wild type


title: HCT116-MSTRG-2513-6_KO_S9


title: Nfur Control-KO Development RNAseq Rep6

description:
Nfur_Control_Dev_6
Nfur_KO_Readcounts.csv

value: Development


title: VM36 Adjacent Kidney


title: Nfur Control-KO Development RNAseq Rep5

description:
Nfur_Control_Dev_5
Nfur_KO_Readcounts.csv


title: N2, 96 hours, injured, rep4

first: Peter

last: Douglas

state: Tx

address: 6000 Harry Hines Blvd

department: Molecular Biology

data_processing:
raw reads were trimmed and mapped using CLC genomics workbench (v23) default settings. CLC was also used for statistical analysis to idenify DEGs and generate expression browsers.
Assembly: C. elegans (ce11)
Supplementary files format and content: Excel file containing RPKMs and statistical tests

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: N2 worms were maintained at 25 degrees on cdc-25.1 RNAi

extract_protocol:
Phenol-chloroform extraction
mRNA library preparation (poly A enrichment)

tag: RNAi

tag: temperature

value: Whole worm

value: 96 hours

value: injured

tag: biological replicate

value: Biol rep 4


title: VM68 Adjacent Kidney

tag: tissue


title: Nfur Control-KO Development RNAseq Rep4

description:
Nfur_Control_Dev_4
Nfur_KO_Readcounts.csv

value: Diapause-Escape


title: IMR90, wild type, replicate 1, eclip

tag: cell type

value: primary lung fibroblasts

tag: genotype

value: WT


title: N2, 96 hours, injured, rep3

tag: time point

tag: treatment

value: Biol rep 3


title: A549-3B_WT_S22

source_name: A549 wild type

value: Lung

tag: cell line


title: N2, 96 hours, injured, rep2

value: Biol rep 2


title: Nfur Control-KO Development RNAseq Rep8

description:
Nfur_Control_Dev_8
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)


title: A549-1B_WT_S20

value: cancer


title: A549-2B_WT_S21


title: VM35 Adjacent Kidney


title: VM66 Adjacent Kidney


title: Nfur Control-KO Development RNAseq Rep1

description:
Nfur_Control_Dev_1
Nfur_KO_Readcounts.csv


title: Nfur Control-KO Development RNAseq Rep3

description:
Nfur_Control_Dev_3
Nfur_KO_Readcounts.csv


title: VM10 Adjacent Kidney


title: N2, 96 hours, injured, rep1

value: Biol rep 1


title: VM49 Adjacent Kidney

value: Adjacent Kidney


title: Nfur Control-KO 6-Day Diapause RNAseq Rep11

description:
Nfur_Control_6D_11
Nfur_KO_Readcounts.csv

value: Diapause

value: 6-Day Diapause


title: A549-MSTRG-4401-1_KO_S24

source_name: MSTRG.4401.1 DBD knockout in A549

value: MSTRG.4401.1 DBD knockout in A549

value: knockout


title: Nfur Control-KO 6-Day Diapause RNAseq Rep12

description:
Nfur_Control_6D_12
Nfur_KO_Readcounts.csv


title: N2, 96 hours, control, rep4

value: Whole worm

value: 96 hours

value: control


title: VM13 Adjacent Kidney


title: A549-MSTRG-4401-1_KO_S23


title: N2, 96 hours, control, rep3


title: HCT116-MSTRG-2513-6_KO_S11

value: Colon

value: MSTRG.2513.6 DBD knockout in HCT116


title: Nfur Control-KO 6-Day Diapause RNAseq Rep10

description:
Nfur_Control_6D_10
Nfur_KO_Readcounts.csv


title: VM15 Adjacent Kidney


title: A549-MSTRG-2513-6_KO_S19

source_name: MSTRG.2513.6 DBD knockout in A549

value: MSTRG.2513.6 DBD knockout in A549


title: N2, 96 hours, control, rep1

value: WT


title: VM40 Adjacent Kidney


title: Nfur Control-KO 6-Day Diapause RNAseq Rep9

description:
Nfur_Control_6D_9
Nfur_KO_Readcounts.csv


title: A549-MSTRG-4401-1_KO_S25

value: Lung


title: N2, 48 hours, injured, rep4

value: 48 hours

value: injured

value: Biol rep 4


title: A549-MSTRG-2513-6_KO_S18

value: cancer


title: VM17 Adjacent Kidney

value: Adjacent Kidney


title: A549-MSTRG-2513-6_KO_S17


title: N2, 48 hours, injured, rep3

value: Biol rep 3


title: Nfur Control-KO 6-Day Diapause RNAseq Rep7

description:
Nfur_Control_6D_7
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)

value: Diapause

value: 6-Day Diapause


title: d7_post_nanoCAR_T_HTO

city: Ghent

first: Stijn

last: De Munter

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

description:
10x Genomics
WT: TotalSeq(tm)-C0258 anti-human Hashtag 8 Antibody (BioLegend)
Barcode Sequence: CTCCTCTGCAATTAC
hash.ID: Hashtag8
KO: TotalSeq(tm)-C0259 anti-human Hashtag 9 Antibody (BioLegend)
Barcode Sequence: CAGTAGTCACGGTCA
hash.ID: Hashtag9

data_processing:
The Cell Ranger pipeline (10x Genomics, version 6.0.0) was used to perform sample demultiplexing and generation of FASTQ files for read 1, read 2 and the i5, i7 sample index for the gene expression and hashtag libraries. Read 2 of the gene expression library was subsequently mapped to a combined reference genome of hg38 and mm10. The resulting count matrices were loaded into R and processed using the Seurat package (version 4.0.5).
Assembly: GRCh38.99
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
Mice were injected with 5x10e5 Raji cells. After seven days, nanoCAR T cells were injected intravenously. Mice were sacrificed seven days post CAR T cell injection. Bone marrow was isolated and processed to obtain a single cell suspension. . Single cell suspension was labelled with antibodies for human CD45, CD19 and hashtag antibodies. The suspension was sorted on a BD ARIA II device based on positivity for human CD45, human CD19 and eGFP. Sorted cells were pooled and resuspended in PBS + 0.04% BSA to obtain on average 1200 cells/µl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM) at the VIB Single Cell Core.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).

value: bone marrow

value: T cells

value: multiplexed sample:CD70 WT and CD70 KO


title: VM23 Adjacent Kidney


title: Nfur Control-KO 6-Day Diapause RNAseq Rep5

description:
Nfur_Control_6D_5
Nfur_KO_Readcounts.csv


title: VM39 Adjacent Kidney


title: Nfur Control-KO 6-Day Diapause RNAseq Rep6

description:
Nfur_Control_6D_6
Nfur_KO_Readcounts.csv


title: N2, 48 hours, injured, rep1

value: Whole worm

value: Biol rep 1


title: N2, 48 hours, injured, rep2

value: Biol rep 2


title: VM37 Adjacent Kidney


title: HIF1A-AS1 overexpression in PA-treated HUVECs-3

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Illumina PE150/SE50  software used for basecalling.
Compare the clean reads to the reference sequence useing Hisat2 software
Use Stringtie software to splice the reads into transcripts and quantify them
Quantitative expression levels of all detected and predicted samples
Genome_build: hg38
Supplementary_files_format_and_content: FPKM
Supplementary_files_format_and_content: reads count

source_name: human vascular endothelial cells

growth_protocol: Cells were cultured  in Dulbecco’s modified Eagle medium (Gibco, United States), which supplemented with 10% fetal bovine serum (Gibco, United States), 100 U/ml penicillin, and 100 μg/ml streptomycin. Then, incubating the cells at 37 °C in a humidified atmosphere (Thermo Fisher Scientific, MA, USA) with 5 % CO2.

extract_protocol:
Total RNA was extracted from HUVECs cells using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), accordance with the instructions of the kits used.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One replicate was PA treated for 24 hours.

value: treated with PA for 24 hours

tag: vector

value: PLVX-Puro 1.0, HIF1A-AS1


title: N2, 96 hours, control, rep2

value: WT

value: 96 hours

value: control


title: Nfur Control-KO 6-Day Diapause RNAseq Rep3

description:
Nfur_Control_6D_3
Nfur_KO_Readcounts.csv

data_processing:
read trimming with Trim Galore (version 0.4.5)
Genome Alignment using STAR (version 2.7.1a) No reference genome is available for the red-striped killifish, so the reads from red-striped killifish RNA-seq libraries were aligned to the genome of its close relative, lyretail killifish.
Keep only uniquely mapped reads using samtools (version 1.5) samtools view -q255
Readcounts obtained using feature counts function from Subread package (version 2.0.1)
Normalized expression using DESeq2 (version1.30.1)
Assembly: Genomes used: African Turqouise Killifish: GCA_001465895.2 ; Red-Striped & Lyretail Killifish: GCA_006937985.1 MPIBA_Aaus_1.0 scaffolds: 12,236 contigs: 30,782 N50: 119,465 L50: 1,783
Supplementary files format and content: Read counts files for each speacies from featurecount of Subread package

tag: Stage


title: HIF1A-AS1 overexpression in PA-treated HUVECs-2


title: Nfur Control-KO 6-Day Diapause RNAseq Rep2

description:
Nfur_Control_6D_2
Nfur_KO_Readcounts.csv

tag: timing


title: N2, 48 hours, control, rep4

value: 48 hours

value: Biol rep 4


title: VM64 Adjacent Kidney

data_processing:
Ends of sequences were trimmed with remaining adapter or quality scores <25.
Sequencing reads were aligned to the human reference genome (hg19) by STAR 2.7.3.a with default parameters in the 2-pass mod.
Counts for each gene were generated using htseq-count v0.6.1. DEGs were identified by DESeq2 v1.14.1.
Ends of sequences were trimmed with remaining adapter or quality scores <25. Sequence less than 35bp after trimming were removed.
The trimmed Fastq files were aligned to the GRCh38 using HiSAT272 and duplicates were marked with SAMBAMBA. Features (genes, transcripts and exons) were counted using featureCounts73. Differential expression analysis was performed using EdgeR74 and DESeq75. Genes with 0 values for all samples were trimmed from the processed data.
Assembly: hg19
Supplementary files format and content: Excel file includes log2CPM counts for each Sample

value: Adjacent Kidney


title: N2, 48 hours, control, rep3

value: Biol rep 3


title: VM32 Adjacent Kidney


title: N2, 48 hours, control, rep2


title: Nfur Control-KO 6-Day Diapause RNAseq Rep8

description:
Nfur_Control_6D_8
Nfur_KO_Readcounts.csv

value: Dissected Embryo (Whole body)

value: Diapause


title: N2, 48 hours, control, rep1


title: VM16 Adjacent Kidney


title: d7_post_nanoCAR_T_GEX

value: bone marrow


title: VM09 Adjacent Kidney


title: HIF1A-AS1 overexpression in PA-treated HUVECs-1


title: Nfur Control-KO 6-Day Diapause RNAseq Rep1

description:
Nfur_Control_6D_1
Nfur_KO_Readcounts.csv

value: 6-Day Diapause


title: N2, 8 hours, injured, rep3

value: 8 hours

value: injured


title: VM54 Adjacent Kidney


title: transfected blank plasmid to PA-treated HUVECs-2

value: blank plasmid


title: N2, 8 hours, injured, rep4

value: Whole worm


title: VM59 Adjacent Kidney


title: VM20 Adjacent Kidney


title: transfected blank plasmid to PA-treated HUVECs-1

value: treated with PA for 24 hours


title: PA-treated HUVECs-2


title: N2, 8 hours, injured, rep1

value: Biol rep 1


title: transfected blank plasmid to PA-treated HUVECs-3


title: VM25 Adjacent Kidney


title: N2, 8 hours, control, rep3

value: WT


title: VM62 Adjacent Kidney


title: HUVECs-2

value: untreated


title: N2, 8 hours, control, rep4

value: control


title: VM12 Adjacent Kidney


title: HUVECs-1


title: N2, 8 hours, control, rep1


title: VM63 Adjacent Kidney


title: HIF1A-AS1 overexpression in PA-treated HUVECs-3 [miRNA-Seq]

data_processing:
Illumina SE50  software used for basecalling.
Compare the clean reads to the miRBase Hisat2 software
Predicting novel miRNAs
Quantitative expression levels of all detected and predicted samples
Genome_build: hg38
Supplementary_files_format_and_content: provide the miRNA TPM express level and reads count sheet

extract_protocol:
Total RNA was extracted from HUVECs cells using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), accordance with the instructions of the kits used.
miRNA libraries were prepared for sequencing using Small RNA Sample Pre Kit

value: PLVX-Puro 1.0, HIF1A-AS1


title: VM81_1 Metastasis CCRCC

value: ccRCC Metastasis


title: PA-treated HUVECs-1


title: HUVECs-3


title: VM56 Adjacent Kidney

value: Adjacent Kidney


title: N2, 8 hours, injured, rep2

value: Biol rep 2


title: PMD216, cat-2, rep4

tag: age

value: Day 1 adults

value: Biol rep 4


title: PA-treated HUVECs-3


title: HIF1A-AS1 overexpression in PA-treated HUVECs-2 [miRNA-Seq]


title: HIF1A-AS1 overexpression in PA-treated HUVECs-1 [miRNA-Seq]


title: PMD216, cat-1, rep4


title: VM60 Adjacent Kidney


title: PMD216, EV, rep4

value: EV


title: PMD216, cat-2, rep3

value: Biol rep 3


title: N2, 8 hours, control, rep2

value: 8 hours


title: VM53 Adjacent Kidney


title: transfected blank plasmid to PA-treated HUVECs-3 [miRNA-Seq]

value: blank plasmid


title: PMD216, EV, rep3


title: VM51 Adjacent Kidney


title: VM29 Adjacent Kidney


title: PA-treated HUVECs-3 [miRNA-Seq]


title: GS_129_2

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

data_processing:
Illumina RTA version 2.11.3 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.2.1), with the GENCODE M23 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-3.4.
The gene expression levels were caluculated using HTSeq (version 0.13.5) and DESeq2 (v1.30.1) with GENCODE M23 annotation gtf file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RawCounts values for each Sample

source_name: testis

growth_protocol: GS cells established  from 10 day old mice of C57BL/6 and 129 strains.

extract_protocol:
GS cells were dissociated into single-cell suspension by trypsin. Total RNA samples were extracted by using TRIzol solution (Invitrogen) and purified by the RNeasy cleanup system (QIAGEN, Valencia, CA).
The library preparation was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina), according to the manufacturer’s instructions.

value: spermatogonia

value: wild-type

tag: strain

value: testis


title: PMD216, cat-2, rep2

value: Whole worm


title: VM47 Adjacent Kidney

extract_protocol:
RNA was isolated using Trizol (Thermo Fisher Scientific, Cat. No. 15596018) and an Rneasy Mini Kit (Qiagen, Cat. No. 74106). Total RNA was quantified using a Qubit fluorometer and the Invitrogen Qubit RNA High Sensitivity kit (Invitrogen, Cat. No. Q32852). Samples were diluted in ultrapure water prior to sequencing.
RNA-seq libraries were prepared using the NEBNext Ultra II directional RNA library prep kit with the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs, Cat. No. E7490L, E7760L) according to manufacturer’s instructions. Libraries were stranded using standard N.E.B indices according to manufacturer’s instructions (New England Biolabs, Cat. No. E7730L, E7335L, E7500L).


title: PA-treated HUVECs-2 [miRNA-Seq]

value: treated with PA for 24 hours


title: GS_129_1


title: PMD216, cat-1, rep2


title: PA-treated HUVECs-1 [miRNA-Seq]


title: HUVECs-3 [miRNA-Seq]

value: untreated


title: VM38 Adjacent Kidney


title: PMD216, cat-2, rep1

value: Biol rep 1


title: PMD216, cat-1, rep1


title: GS_B6_F0_1


title: PMD216, EV, rep2


title: GS_B6_F0_2


title: HUVECs-1 [miRNA-Seq]


title: PMD216, EV, rep1


title: PMD216, cat-1, rep3


title: transfected blank plasmid to PA-treated HUVECs-2 [miRNA-Seq]


title: Opa1cKO, scRNAseq

city: Ottawa

first: Ruth

last: Slack

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hippocampus

extract_protocol:
Freshly collected hippocampus was digested using papain in a shaking incubator at 37 °C for 10 minutes. After quencing the digestion with FBS, single cell suspension was centrifuged in 22% percoll. Cells were washed and re-suspended in sorting medium (DMEM:F12 and 1mM EDTA). Alive YFP-positive cells were sorted using a Beckman Coulter MoFlo platform, according to the presence of YFP signal and the absence of Propidium Iodide, using an Opa1-Flox negative mouse as WT control.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Neural stem cells and their progenies

value: hippocampus

value: 12 weeks old


title: transfected blank plasmid to PA-treated HUVECs-1 [miRNA-Seq]


title: WT, scRNAseq

description: 10x Genomics


title: HUVECs-2 [miRNA-Seq]


title: Spinal cord rep1

status: Public on Jun 16 2024

city: Monterrey

first: Raquel

last: Cuevas Diaz Duran

address: Av Morones Prieto No. 3000, Colonia Los Doctores

department: Escuela de Medicina y Ciencias de la Salud

country: Mexico

institute: Tecnologico de Monterrey

data_processing:
Basecalling was performed with CASAVA v1.7 from Illumina
The 100-bp paired-end reads were aligned to the reference genome mm10 (downloaded from GENCODE) using TopHat v2.1.0 with default parameters.
Mapped reads were assembled using Cufflinks v2.2.1 and FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were obtained for annotated genes and transcripts.
Read counts for annotated genes and transcripts were calculated using HTSeq-count
Genome_build: mm10

source_name: Spinal cord endothelial cells

extract_protocol:
RNA extraction and purification were performed using RNeasy Micro Kit (Qiagen)
RNA samples were poly-A selected and paired-end sequencing libraries were constructed using the TruSeq RNA Sample Prep Kit, as described in the TruSeq RNA Sample Preparation V2 Guide (Illumina). Samples were then sequenced using the Illumina HiSeq 2000 sequencer.

value: Homozygous Tie2GFP mice (Jax stock #003658)

value: Adult


title: Spinal cord rep2


title: Liver

source_name: Liver endothelial cells


title: Forebrain rep2

source_name: Forebrain endothelial cells


title: Forebrain rep1


title: Cerebellum rep2

source_name: Cerebellum endothelial cells


title: Cerebellum rep1


title: mst2-deg epe1-deg,+TN 120hr, H3K9me3

city: Waltham

first: Ajay

last: Larkin

state: MA

address: 415 South St

department: MCB

institute: Brandeis University

data_processing:
sequences were trimmed with Trimmomatic, aligned with BWA, and normalized by SES using Deeptools BamCompare to input
Assembly: ASM294v2.29
Supplementary files format and content: bedgraph files

source_name: mst2-deg epe1-deg,+TN 120hr, H3K9me3

growth_protocol: EMMC, grown to log phase at 32C

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cells were lysed with bead beating.
ChIPseq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina. 1Ng of DNA was used as starting material

treatment_protocol: +TN cultures were treated with 15mM thiamine and 500mM 1-napthaleneacetic acid

tag: chip antibody


title: mst2-deg epe1-deg,+TN 120hr, input

source_name: mst2-deg epe1-deg,+TN 120hr, input


title: mst2-deg epe1-deg,+TN 96hr, input

source_name: mst2-deg epe1-deg,+TN 96hr, input


title: mst2-deg epe1-deg,+TN 72hr, input

source_name: mst2-deg epe1-deg,+TN 72hr, input


title: mst2-deg epe1-deg,+TN 72hr, H3K9me3

source_name: mst2-deg epe1-deg,+TN 72hr, H3K9me3


title: mst2-deg epe1-deg,+TN 48hr, input

source_name: mst2-deg epe1-deg,+TN 48hr, input


title: mst2-deg epe1-deg,+TN 24hr, input

source_name: mst2-deg epe1-deg,+TN 24hr, input


title: mst2-deg epe1-deg,+TN 24hr, H3K9me3

source_name: mst2-deg epe1-deg,+TN 24hr, H3K9me3


title: mst2-deg epe1-deg,-TN, H3K9me3

source_name: mst2-deg epe1-deg,-TN, H3K9me3


title: mst2D epe1-deg red1D,+TN 96hr, H3K9me3

source_name: mst2D epe1-deg red1D,+TN 96hr, H3K9me3

value: ade6::ade6+-adh15prom-skp1-OsTIR1-natMX6-adh15prom-skp1-AtTIR1-2NLS nmt81-epe1-3xFLAG-AID mst2D red1D


title: Lung

source_name: Lung endothelial cells


title: mst2D epe1-deg red1D,+TN 120hr, input

source_name: mst2D epe1-deg red1D,+TN 120hr, input


title: mst2D epe1-deg red1D,+TN 72hr, H3K9me3

source_name: mst2D epe1-deg red1D,+TN 72hr, H3K9me3


title: mst2D epe1-deg red1D,+TN 48hr, input

source_name: mst2D epe1-deg red1D,+TN 48hr, input


title: mst2D epe1-deg red1D,+TN 72hr, input

source_name: mst2D epe1-deg red1D,+TN 72hr, input


title: mst2D epe1-deg red1D,+TN 24hr, H3K9me3

source_name: mst2D epe1-deg red1D,+TN 24hr, H3K9me3


title: mst2D epe1-deg red1D,-TN, input

source_name: mst2D epe1-deg red1D,-TN, input


title: mst2D epe1-deg,-TN, H3K9me3

source_name: mst2D epe1-deg,-TN, H3K9me3


title: mst2D epe1-deg red1D,+TN 48hr, H3K9me3

source_name: mst2D epe1-deg red1D,+TN 48hr, H3K9me3


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs +TN 24hrs, input


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs +TN 24hrs, H3K9me3


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs +TN 24hrs, H3K9me2


title: mst2D epe1-deg,+TN 120hrs -TN 48hrs, input


title: mst2-deg epe1-deg,+TN 96hr, H3K9me3

source_name: mst2-deg epe1-deg,+TN 96hr, H3K9me3


title: mst2D epe1-deg,+TN 120hrs -TN 48hrs, H3K9me3


title: mst2-deg epe1-deg,+TN 48hr, H3K9me3

source_name: mst2-deg epe1-deg,+TN 48hr, H3K9me3


title: mst2D epe1-deg,+TN 120hrs -TN 48hrs, H3K9me2


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs +TN 24hrs, memory exp rep3

description: memory.txt

data_processing:
sequences were trimmed with Trimmomatic, then aligned and quantified by STAR
downstream diff. expression quantification was performed with USEQ DRDS
Assembly: ASM294v2.29
Supplementary files format and content: txt files contain raw transcript count matricies

extract_protocol:
Hot phenol extraction followed by DNAse I treatment and Qiagen RNeasy Column Cleanup
RNAseq libraries were prepared by Novogene Corporation Inc.


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs +TN 24hrs, memory exp rep2

description: memory.txt


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs, input


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs, H3K9me3


title: mst2-deg epe1-deg,-TN, input

source_name: mst2-deg epe1-deg,-TN, input


title: mst2D epe1-deg red1D,+TN 96hr, input

source_name: mst2D epe1-deg red1D,+TN 96hr, input


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs, H3K9me2


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs +TN 24hrs, memory exp rep1

description: memory.txt


title: mst2D epe1-deg red1D,+TN 120hr, H3K9me3

source_name: mst2D epe1-deg red1D,+TN 120hr, H3K9me3


title: mst2D epe1-deg, +TN 120hrs, H3K9me2 rep1


title: mst2D epe1-deg,+TN 120hrs -TN 48hrs, memory exp rep3

description: memory.txt


title: mst2D epe1-deg,+TN 120hrs -TN 48hrs, memory exp rep2

description: memory.txt


title: mst2D epe1-deg red1D,+TN 24hr, input

source_name: mst2D epe1-deg red1D,+TN 24hr, input


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs, memory exp rep3

description: memory.txt


title: mst2D epe1-deg,+TN 120hrs -TN 48hrs, memory exp rep1

description: memory.txt


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs, memory exp rep1

description: memory.txt


title: mst2D epe1-deg, +TN 24hrs, H3K9me2 rep1

source_name: mst2D epe1-deg, +TN 24hrs, H3K9me2 rep1


title: mst2D epe1-deg,-TN, H3K9me2 rep1

source_name: mst2D epe1-deg,-TN, H3K9me2 rep1


title: mst2D epe1-deg, +TN 72hrs, H3K9me2 rep1

source_name: mst2D epe1-deg, +TN 72hrs, H3K9me2 rep1


title: mst2D epe1-deg, +TN 96hrs, H3K9me2 rep1

source_name: mst2D epe1-deg, +TN 96hrs, H3K9me2 rep1


title: mst2D epe1-deg,+TN 120hrs -TN 24hrs, memory exp rep2

description: memory.txt


title: mst2D epe1-deg, +TN 48hrs, H3K9me2 rep1

source_name: mst2D epe1-deg, +TN 48hrs, H3K9me2 rep1


title: mst2D epe1-deg,+TN 120hrs, memory exp rep3

description: memory.txt

value: +TN


title: mst2D epe1-deg,+TN 120hrs, memory exp rep2

description: memory.txt


title: mst2D epe1-deg,+TN 120hrs, memory exp rep1

description: memory.txt


title: mst2D epe1-deg,-TN, memory exp rep3

description: memory.txt

source_name: mst2D epe1-deg,-TN, memory exp rep3


title: DP bb 2

city: Denver

first: Philippa

last: Marrack

state: CO

address: 1400 Jackson St

department: Immunology & Genomic Medicine

institute: National Jewish Health

data_processing:
MKION VDJ sequence analysis v 1.0
Sequence reads were trimmed for short and long reads (>100nt, <800nt)
Out-of-frame sequences were recovered by repairing the TRAJ segment by mapping back to germline
Organize by clonotype and reformat columns into immunarch format
Assembly: mm9
Supplementary files format and content: Comma-separated text file including ranked TCR clonotype counts for each Sample
Library strategy: TCR-Seq

source_name: Tymus

extract_protocol:
Mice were euthanized, and axillary, brachial, inguinal, mesenteric, lumbar, and caudal lymph nodes were collected and filtered through a sterile 100µM filter. Cells were resuspended and washed 3x in BSS in a 15 ml conical tube. Cells were counted and resuspended in BSS supplemented with 1% BSA and anti-mouse CD16/CD32 (Clone: 2.4G2), as a pre-treatment reagent to block non-antigen-specific interactions of immunoglobulins to the FcγIII and FcγII, and possibly FcγI. Lymphocytes were stained with antibodies specific to TCRβ, CD45R, CD4, CD8, CD44, CD62L, and CD25 for 30 mins, washed 3x in BSS wash buffer. Cells were resuspended at 107/ml and fluorescently sorted for naïve lymphocytes on an iCyt Synergy.
RNA was isolated from purified naïve CD4 T cells using the RNeasy Kit (Invitrogen).  cDNA was made using the SuperScript VILO Kit (Invitrogen). For sequencing of TCR α-chains, a two-step PCR was done which added the machine oligonucleotides as well as barcodes for the sequencing runs. The first PCR included a reverse oligonucleotide in the constant region of the α-chain and a mixture of forward oligonucleotides that together cover all the different TCRα family members. The sequence or sequences for each TRAV family are as follows: TRAV01: GAGGGAACCTTTGCTCGGGTC; TRAV02: TATGAAGGGCAAGAAGTGAAC; TRAV03: CArGTCTTCAGTTGCTTATGA; TRAV04: TGCTCTGAGATGCAATTTTwC; TRAV05a: GGTGGAACAGCTCCCTTCCTC; TRAV05b: ATGGCTGCAGCTGGATGGGA; TRAV06a: GGACAAGGTCCACAGCTCCT; TRAV06b: GGAGAAGGTCCACAGCTCCTC; TRAV06c: GTCCAATATCCTGGAGAAGG; TRAV07: AGCAGAGCCCAGAATCCCTCA; TRAV08: AAAGAGCCAATGGGGAGAAG; TRAV08, GAATAGTCAACTAGCAGAAG; TRAV09: AGCTGAGATGCAAsTATTCCT; TRAV10: ACTTACACAGATACTGCyTCA; TRAV11: CACAGGCAAAGGTCTTGTGTC; TRAV12: GCTGAACTGCACCTATCAGA; TRAV13: TGGTTCTGCAGGAGGGGGArA; TRAV14: GTCCCCAATCTCTGACAGTCT; TRAV15: ACTGTTCATATrAGACAAGT; TRAV16: TGGAGAAGACAACGGTGACA; TRAV17: GTTATTCATACAGTGCAGCAC; TRAV18: ACCGCACGCTGCAGCTCCTCA; TRAV19: TACCCTGACAACAGCCCCACA; TRAV21: GTAGCCACGCCACAATCAGTG. The second PCR included just one forward oligonucleotide to add the machine oligonucleotide and a reverse oligonucleotide to add the barcode. For TCR β-chains, one PCR was done that contained a forward oligonucleotide priming all three TRBV13 family members at an identical region, the sequencing machine oligonucleotide CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGATGCTGAGGCTGATCCATTA, and a reverse oligonucleotide that primed the Cβ region and contained the machine oligonucleotide and the barcode, CCATCTCATCCCTGCGTGTCTCCGACTCAGCTAAGGTAACGATCTTGGGTGGAGTCACATTTCTC.

value: Tymus

value: preselection thymocyte

value: bb


title: CD4 ss 3

source_name: Peripheral lymph nodes

value: Peripheral lymph nodes

value: naive CD4 T cell

value: ss


title: mst2D epe1-deg,-TN, memory exp rep1

description: memory.txt

source_name: mst2D epe1-deg,-TN, memory exp rep1


title: CD4 fxs 3

value: fxs


title: E11.5-KO-1

city: Xiamen

first: wanshan

last: zheng

state: Fujian

address: Xiang'an Road

department: School of Medicine,

institute: Xiamen University

data_processing:
The raw reads were first aligned to the genome mm10  with STAR version 2.7.9a, and then gene counts were acquired from the number of uniquely and unambiguously aligned reads by Subread:featureCount (version 2.0.1). The variation analysis was conducted by DESeq2 to the DEGs and the corresponding adjusted p-values in the Benjamini and Hochberg correction. The DEGs were identified using the setting: |fold change| >2 for mice and >1.5 for cell samples with adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: placenta

growth_protocol: All mice used in this study were kept at C57BL6 background and maintained in a specific pathogen-free animal facility. For mating experiments, male and nulliparous female mice aged between 8 and 12 weeks old were cohoused

extract_protocol:
Total RNAs from placentas of conrtol or tfeb ko were extracted by TRIzol and  subjected to RNA-Seq. 1 μg of  total RNA was used for sequencing libraries.
MGIEasy Fast PCR-FREE FS Library Prep Set

treatment_protocol: The Tfeb-null mice (Tfeb-/-) mice were generated by GemPharmatech Co., Ltd. The placenta were harvested at E9.5 and E11.5.

value: placenta

value: KO


title: E11.5-KO-2


title: DP ff 7

value: ff


title: E11.5-wt-2

value: wt


title: CD4 fxs 2


title: CD4 fxs 1


title: CD4 ff 3


title: E9.5-KO-1


title: DP bb 1


title: CD4 bxs 2

value: bxs


title: CD4 bxf 3

value: bxf


title: E11.5-wt-1


title: CD4 ff 2


title: E9.5-wt-2


title: CD4 bxf 2


title: DP bb 3


title: E9.5-KO-3


title: E9.5-wt-3


title: E9.5-KO-2


title: CD4 bxs 3


title: CD4 bxf 1


title: CD4 bxs 1


title: E9.5-wt-1


title: CD4 bb 1


title: STZ+ SCD mice, 32w, batch 9, biological replication 3

city: Songpa-Gu

first: Byung-Kwan

last: Jeong

state: Seoul

address: 88, Olympic-ro 43-gil

department: Pathology

country: South Korea

institute: Asan Medical Center

data_processing:
Raw RNA-sequencing data obtained from mouse were mapped to mouse genome build mm10 (GRCm38) and those from human mapped to human genome build 38 (GRCh38) using STAR (version 020201).
Count matrices were generated using RSEM (v1.3.1)
Assembly: mm10
Supplementary files format and content: rawcounts_newsamples_mouse.txt: raw expected count generated by RNA-seq for each sample

source_name: Liver

growth_protocol: Mice were housed in climate-controlled, specific pathogen-free barrier facilities under a 12 h light-dark cycle and provided diet and water ad libitum. They were fed standard chow diet (SCD) (Teklad Global 18% Protein Rodent Diet 2018; Harlan Teklad, WI, USA), 18% fat or HFD (Research Diet (New Brunswick, NJ, USA) D12492, 60% fat) from 8 weeks of age.

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit (Qiagen, Hilden, Germany; 74104) in keeping with the manufacturer’s instructions.
The RNA sequencing library was prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswitch, MA, USA; E7760).

treatment_protocol: Vehicle (HyClone DPBS, Cytiva, Germany) or tirzepatide (109.5 nmol/kg, CPC, Hanzhou, China) dissolved in vehicle was administered via subcutaneous injection to ad libitum-fed STZ+HFD mice 1-2 hours prior to the onset of the dark cycle every 2 days for 10 to 11 weeks.

value: Liver

value: 32 weeks

tag: streptozotocin treatment

value: Treated

tag: diet

value: SCD

tag: Sex

value: Male

value: WT

tag: drug treatment

value: Untreated


title: Control SCD fed mice without STZ treatment, 32w, batch 9, biological replication 2


title: HFD fed mice without STZ treatment, 32w, batch 9, biological replication 3

value: HFD


title: mst2D epe1-deg,-TN, memory exp rep2

description: memory.txt

source_name: mst2D epe1-deg,-TN, memory exp rep2


title: STZ+ SCD mice, 32w, batch 9, biological replication 1


title: CD4 bb 3

value: Peripheral lymph nodes

value: naive CD4 T cell

value: bb


title: Control SCD fed mice without STZ treatment, 32w, batch 9, biological replication 4


title: STZ+HFD model, 52w, treated with tirzepatide (109.5 nmol/kg) for 11 weeks, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch8_STZHFD52w_Tirzepatide_11w_3

data_processing:
Raw RNA-sequencing data obtained from mouse were mapped to mouse genome build mm10 (GRCm38) and those from human mapped to human genome build 38 (GRCh38) using STAR (version 020201).
Count matrices were generated using RSEM (v1.3.1)
Assembly: mm10, human genome build 38 (GRCh38)
Supplementary files format and content: tab-delimited text files include raw expected count generated by RNA-seq for each sample

growth_protocol: Mice were housed in climate-controlled, specific pathogen-free barrier facilities under a 12 h light-dark cycle and provided diet and water ad libitum. They were fed standard chow diet (SCD) (Teklad Global 18% Protein Rodent Diet 2018; Harlan Teklad, WI, USA), 18% fat  or HFD (Research Diet (New Brunswick, NJ, USA) D12492, 60% fat) from 8 weeks of age.

value: 52 weeks

value: Tirzepatide


title: Control SCD fed mice without STZ treatment, 32w, batch 9, biological replication 3


title: HA-PKR w/o PACT fCLIP(HA) biol rep 2

city: Boston

first: Sun

last: Hur

address: 3 Blackfan St,

institute: Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine

data_processing:
Fastq files were trimmed by trimmomatic (v0.36), aligned to RNA45SN1 and RNA5SN1, and the leftover reads were mapped to human genome.
In order to normalize different sequencing depths among samples, all groups were normalized to 1M total non-rRNA reads mapped. They were named as "*PM.bedgraph" (per million bedgraph) individually.
The bedgraph files can be readily opened in IGV using Grch38.p14 human genome.
Assembly: Grch38.p14
Supplementary files format and content: PM (per million) bedgraph files: the alignment file of indivual groups after normalizing to 1M total non-rRNA reads mapped.

source_name: Mammary gland

extract_protocol:
RNA was phenol:chloroform extracted and isopropanol precipitated
cDNA library wa prepared using SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian using manufacturer's guidelines
CLIP-seq

value: Mammary gland

value: epithelial breast cancer


title: CD4 bb 2


title: HA-PKR w/ PACT fCLIP(HA) biol rep 2


title: HA-PKR w/ PACT fCLIP(HA) biol rep 1


title: A2780 cells, WT, treat wogonin_4

city: Minxiong Township

first: Wen

middle: Long

last: Huang

state: Chiayi County

address: No. 168. Section 1, Daxue Road

department: Biomedical Sciences

country: Taiwan

institute: CCU

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh37/hg19 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: UCSC GRCh37/hg19
Supplementary files format and content: Excel includes TPM values, RPKM values
Supplementary files format and content: Excel includes TPM values, fold change values, T test values for each sample

source_name: Ovarian cancer cell

growth_protocol: A2780 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were then treated with 10 ug/mL wogonin (Cayman, Cat. no. 14248) for 48 hours.

value: Ovarian cancer cell

value: ovarian adenocarcinoma

value: treat wogonin


title: STZ+ SCD mice, 32w, batch 9, biological replication 2

value: Liver

value: 32 weeks


title: A2780 cells, WT, treat wogonin_3


title: Control SCD fed mice without STZ treatment, 32w, batch 9, biological replication 1

value: SCD


title: STZ+HFD model, 52w, treated with tirzepatide (109.5 nmol/kg) for 11 weeks, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch8_STZHFD52w_Tirzepatide_11w_1

value: Treated

value: Male


title: A2780 cells, WT, treat DMSO_2

value: WT

value: treat DMSO


title: A2780 cells, WT, treat DMSO_1


title: HFD fed mice without STZ treatment, 32w, batch 9, biological replication 2

value: Untreated

value: HFD


title: HA-PKR w/o PACT fCLIP(HA) biol rep 1


title: STZ+HFD model, 52w, treated with tirzepatide (109.5 nmol/kg) for 11 weeks, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch8_STZHFD52w_Tirzepatide_11w_4


title: STZ+HFD model, 52w, treated with control vehicle for 11 weeks, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch8_STZHFD52w_Vehicle_11w_3

value: Vehicle


title: HA-PKR w/o PACT Input biol rep 2


title: DKO (HA-PKR) fCLIP (HA) biol rep 3