title: VAT ADSCs, CD26+CD142+

city: Jinan

first: Honglin

last: Guo

address: No. 324, Jingwu Road

department: Department of Pathology, Department of Endocrinology

institute: Shandong University, Shandong Provincial Hospital

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited xls file includes raw counts for each sample

source_name: Adipose-derived stem cells

extract_protocol:
Total RNA was extracted from sorted cells using TRIzol (Takara). Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol:
Isolation of SVF from mouse adipose tissue: The adipose tissue underwent dissociation with collagenase II (Sigma-Aldrich, #9001-12-1, 2mg/ml in a collagenase buffer consisting of Hanks’ Balanced Salt Solution (Sigma, #H1641), 2% BSA (Sigma, #A3059), and 100mM HEPES (Sigma, #27920) at a pH of 7.34)) for 15 minutes at 37°C with agitation. Subsequently, the cells were strained through a 70-μm strainer and centrifuged at 500x g for 5 minutes at room temperature. After discarding the supernatant, the pellets housing the SVF were treated with red blood cell lysis buffer (absin, #abs9101) for 5 minutes at room temperature before being neutralized in H-DMEM supplemented with 10% FBS. The cells were then harvested via centrifugation at 500x g for 5 minutes at room temperature and resuspended in PBS (absin, #abs970) for further experimentation.
FACS was performed on SVFs from SAT and VAT of 30 mice (12-14 weeks old). Cells were resuspended in 100μl PBS and stained with Zombie Aqua viability dye (Biolegend, #423102) for 20 minutes at room temperature protected from light. After washing, cells were incubated with anti-CD16/32 antibody (Biolegend, #101320) to block nonspecific binding, followed by staining with PE/Cy7-CD31 (Biolegend, #102524), PE/Cy7-CD45 (Biolegend, #103114), FITC anti-mouse CD26 (DPP-4) antibody (Biolegend, #137806, Clone: H194-112) and CD142 antibody (R&D, #AF3178) for 25 minutes at 4°C protected from light. After washing twice, cells were incubated with PE-conjugated secondary antibody (R&D, #F0107) for indirect CD142 staining. Cells were washed twice again and sorted on a Moflo Astrios EQ (100-μm nozzle). CD31+ and CD45+ cells were gated out to exclude endothelial and immune cells

value: Adipose-derived stem cells

value: Chow diet


title: J-Gammal cells, NUDT21 knockdown, replicate 2 [PAS-seq]

status: Public on Feb 01 2026

type: SRA

city: suzhou

first: yang

last: yang

address: zhongnan road

country: China

institute: soochow university

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
Filtering: Only read 2 was used to determine PAS sites. Raw reads were trimmed to remove adapters, low-quality bases with a score below 20, more than 3 consecutive "G"s at the end of the sequence, as well as "N"s and all subsequent sequences. Reads containing no less than 30% of the bases with a quality score below 20 were filtered out. Processed reads with a remaining length greater than 20 were retained.
Removing poly(A) tract: To remove poly(A) tract, we first search for at least 8 consecutive A's from the end of the reads. If more than 2 consecutive non-A bases are encountered, the poly(A) tract and all subsequent bases are removed, retaining only those reads with a length of 12 bases or more. Next, we scan for A's starting from the 5' end of the reads; if more than 9 consecutive A's are present, the poly(A) tract and all subsequent bases are removed, with reads of 12 bases or longer retained.
Alignment: These two sets of processed reads above are then simultaneously aligned to hg38 genome and Gencode.v45 using HISAT2. For reads that align successfully under both conditions, priority is given to the alignment result corresponding to the read with a poly(A) tract at the end.
Assembly: hg38
Supplementary files format and content: BigWig files containing read coverage normalized to CPM (read count per million)

molecule: total RNA

organism: Homo sapiens

source_name: J-Gammal

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01).
For each sample, 5 μg of total RNA was treated with RQ1 DNase (M6101,Promega, USA) to remove DNA, fragmented RNAs were used for PAS-seq library preparation. mRNAs were captured with mRNA Capture Beads kit （N401,Vazyme,Chian）. Fragmented mRNAs were used for directional PAS-seq library preparation by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (KK8544, Roche, USA). Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726, Roche, USA). After purification of ligation product and size fractioning to 300-500 bp, the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq Xplus system for 150 nt paired-end sequencing.

tag: cell line

value: J-Gammal

tag: cell type

value: T-ALL cells

tag: treatment

value: NUDT21 knockdown


title: J-Gammal cells, NUDT21 knockdown, replicate 1  [PAS-seq]

description: Library name: Sample 1


title: TRExRTA BCBL-1,WT, DOX, 48h, biol rep 3

city: Berkeley

first: Britt

last: Glaunsinger

state: California

address: RM 565, 1951 Oxford St

department: PMB

country: USA

institute: University of California, Berkeley

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AY_WT_DOX_48h

data_processing:
Data was preprocessed (PhiX removal, deduplication, N-remover, adaptor trimming, etc.) using the standard HTStream version 1.3.0 workflow
Human GRCh38.p13, KSHV BAC16, ERCC Spike-In genomes were concatenated and indexed using STAR version 2.7.1a
Preprocessed reads were aligned with STAR version 2.7.1a and counts tables were exported
Assembly: Human genome GRCh38.p13; KSHV BAC16 genome; ERCC Spike-In sequences
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: TRExRTA BCBL-1 cells

growth_protocol: Cells harbor latent KSHV and were maintained in RPMI 1640 media (Gibco) supplemented with 10% Tet-free fetal bovine serum, 1X GlutaMAX (Gibco), and 10 ug/mL hygromycin B in a humidified chamber at 37℃ and 5% CO2. TFIIB-2xStrep or TFIIB(D207A)-2xStrep expression constructs were integrated via transposon delivery, then selected for and maintained in 1 ug/mL puromycin.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and phenol-chloroform extraction
RNA libraries were prepared using KAPA RNA Hyperprep Kit with RiboErase (HMR) with KAPA Unique Dual Index Adaptors according to the manufacturer's protocols and include ERCC Spike-In mix for normalization

treatment_protocol: TFIIB-2xStrep or TFIIB(D207A)-2xStrep expressing TRExRTA BCBL-1 cells were treated with 660 ng/mL Superkiller TRAIL (Enzo) for 7 h or reactivated to lytic KSHV infection for 24 or 48 h by addition of 1 ug/mL doxycycline, which induces expression of the viral lytic transactivator RTA.

value: TRExRTA BCBL-1 cells

value: B cell lymphoma

tag: genotype

value: WT

value: DOX

tag: time

tag: replicate


title: TRExRTA BCBL-1,WT, Mock, 24h, biol rep 3

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AU_WT_Mock_24h

value: Mock


title: VAT ADSCs, CD26-CD142+, rep2

state: Shandong

organism: Mus musculus

tag: tissue

tag: diet


title: preMegE_G320D_rep2

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

library_source: genomic

data_processing:
Reads were aligned with Bowtie2 (version 2.4.1)
SAM files were converted to BAM files and PCR duplicate reads were filtered out using SAMtools (version 1.17)
Peak calling was performed using MACS2 (version 2.1.2)
Unique reads mapped to these regions were quantified using featuresCounts (version 2.0.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

molecule: genomic DNA

source_name: Bone marrow cells

extract_protocol:
ATAC-seq based protocol
Dual index Nextera

value: Bone marrow cells

value: preMegE


title: preMegE_G320D_rep1


title: SAT ADSCs, CD26-CD142+


title: J-Gammal cells, control, replicate 2

description: Library name: Sample 4

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 whole genome and GENCODE v29 using STAR 2.7.10a with parameters --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 1
Transcripts per million (TPM) were calculated using stringtie v2.1.7. Gene differential expression were calculated using DESeq2 v1.40.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts and expression values of each gene for each sample and differential expression values between treatment group and control group.

molecule: polyA RNA

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol.  FastPure Cell/Tissue Total RNA Isolation Kit V2(( Vazyme , RC112-01)  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: control


title: TRExRTA BCBL-1,D207A, DOX, 48h, biol rep 2

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AT_D207A_DOX_48h


title: EMPP_WT_rep3

value: EMPP


title: J-Gammal cells, control, replicate 1

description: Library name: Sample 3


title: J-Gammal cells, NUDT21 knockdown, replicate 2

description: Library name: Sample 2


title: TRExRTA BCBL-1,D207A, DOX, 24h, biol rep 2

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AS_D207A_DOX_24h


title: EMPP_WT_rep1


title: Jurkat, sgRNA3, TRAIL, No 4sU, biol rep 3

description:
Library name: Sample 24
Ribodepleted RNA, ERCC spike-in.

library_source: other

data_processing:
Data was preprocessed (PhiX removal, deduplication, N-remover, adaptor trimming, etc.) using the standard HTStream version 1.3.0 workflow
Human GRCh38.p13, ERCC Spike-In genomes were concatenated and indexed using STAR version 2.7.1a. Gencode annotation v43 were used.
Preprocessed reads were aligned with STAR version 2.7.1a and counts tables were exported for bulk RNA
Separately, the same genome and annotation was prepared for GRAND-SLAM analysis with gedi and mapped using GRAND-SLAM default parameters to generate a counts table for nascent transcripts by multiplying total counts by the nascent-to-total ratio MAP statistic.
Assembly: Human genome GRCh38.p13 + Gencode v43; ERCC Spike-In sequences (Invitrogen)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample bulk RNA
Supplementary files format and content: Tab-delimited text file includes raw counts and nascent RNA statistics from GRAND-SLAM for nascent RNA from 4sU-containing samples.

molecule: other

source_name: Jurkat

growth_protocol: Jurkat cells base-edited for at least 10 days with ABE8e base editor RNA and indicated sgRNA pools were maintained in RPMI 1640 media (Gibco) supplemented with 10% Tet-free fetal bovine serum, 1X GlutaMAX (Gibco), 1x Pen-Strep (Gibco) and 1 mM sodium pyruvate (Gibco)  in a humidified chamber at 37℃ and 5% CO2. Cells were kept at densities between 0.5-2x10^6 cells/mL.

extract_protocol:
6 h post-TRAIL treatment, total RNA was extracted in the dark using TRIzol (Invitrogen) and phenol-chloroform extraction. ERCC Spike-In (Invitrogen) and mixed 4sU unlabelled/labelled spike-in was added. RNA was then alkylated, DNase-treated, and cleaned. General protocol from Lexogen's SLAM-seq Anabolic labelling kit.
RNA libraries for SLAM-seq/RNA-seq were prepared using KAPA RNA Hyperprep Kit with RiboErase (HMR) with KAPA Unique Dual Index Adaptors according to the manufacturer's protocols and include ERCC Spike-In mix for normalization. Sequencing on NovaSeq X Plus 25B.

treatment_protocol: SLAM-sequencing was performed: Each Jurkat genotype/guide pool was treated with 250 ng/mL SUPERKILLER TRAIL ligand (Enzo) or mock diluant for 6 h. After 3h, 300 uM of 4-thiouridine (4sU)  was added to all samples to label nascent RNA synthesized before the harvesting endpoint (except those indicated No 4sU as a control).

value: Jurkat

value: Immortalized T cell lymphocyte

tag: genotype/sgrna/sgrna code

value: TRAIL

value: No 4sU


title: VAT ADSCs, CD26-CD142+, rep1

value: Adipose-derived stem cells

value: Chow diet


title: SAT ADSCs, CD26+CD142-


title: J-Gammal cells, NUDT21 knockdown, replicate 1

description: Library name: Sample 1

value: J-Gammal

value: T-ALL cells


title: EMPP_G320D_rep3


title: TRExRTA BCBL-1,D207A, TRAIL, 24h, biol rep 2

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AR_D207A_TRAIL_24h

value: TRExRTA BCBL-1 cells


title: EMPP_WT_rep2


title: EZH2_--_RA_6-rep2

city: Tianjin

first: xuejiao

last: lv

state: Tianjin

address: No.22 Qixiangtai Rd

institute: Tianjin Medical University

data_processing:
Library construction and sequencing were carried out by Novogene.
Assembly: mm10
Supplementary files format and content: bigwig for each sample

source_name: ESC

extract_protocol:
RNA was harvested using, 1 mg of total RNA was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using  oligo -dT beads

value: ESC

value: RA_6 hr


title: EMPP_G320D_rep2


title: Jurkat, sgRNA3, TRAIL, 4sU, biol rep 3

description:
Library name: Sample 22
Ribodepleted RNA, ERCC spike-in.


title: TRExRTA BCBL-1,WT, DOX, 48h, biol rep 2

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AO_WT_DOX_48h

value: B cell lymphoma

value: WT

value: DOX


title: Jurkat, sgRNA3, Mock,No  4sU, biol rep 3

description:
Library name: Sample 23
Ribodepleted RNA, ERCC spike-in.

value: Mock


title: TRExRTA BCBL-1,WT, DOX, 24h, biol rep 2

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AN_WT_DOX_24h


title: EZH2_--_RA_3-rep2

value: RA_3 hr


title: TRExRTA BCBL-1,WT, TRAIL, 24h, biol rep 2

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AM_WT_TRAIL_24h


title: EZH2_--_RA_3-rep1


title: TRExRTA BCBL-1,D207A, Mock, 24h, biol rep 2

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AP_D207A_Mock_24h


title: Jurkat, sgRNA3, Mock, 4sU, biol rep 3

description:
Library name: Sample 21
Ribodepleted RNA, ERCC spike-in.


title: EZH2_--_RA_6-rep1


title: BEMP_WT_rep3

value: Bone marrow cells

value: BEMP


title: EZH2_--_RA_0-rep2

value: RA_0 hr


title: TRExRTA BCBL-1,WT, Mock, 24h, biol rep 2

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AK_WT_Mock_24h


title: EZH2_--_RA_0-rep1


title: EMPP_G320D_rep1

value: EMPP


title: BEMP_WT_rep2


title: Jurkat, sgRNA2, TRAIL, 4sU, biol rep 3

description:
Library name: Sample 20
Ribodepleted RNA, ERCC spike-in.

value: Jurkat

value: Immortalized T cell lymphocyte

value: TFIIB D207G/D207G-#2/sgRNA2

value: TRAIL


title: TRExRTA BCBL-1,D207A, DOX, 48h, biol rep 1

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AJ_D207A_DOX_48h


title: Jurkat, sgRNA1, TRAIL, 4sU, biol rep 3

description:
Library name: Sample 18
Ribodepleted RNA, ERCC spike-in.

value: TFIIB D207G/D207G-#1/sgRNA1


title: BEMP_G320D_rep3


title: TRExRTA BCBL-1,D207A, DOX, 24h, biol rep 1

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AI_D207A_DOX_24h

value: TRExRTA BCBL-1 cells


title: Jurkat, sgRNA2, Mock, 4sU, biol rep 3

description:
Library name: Sample 19
Ribodepleted RNA, ERCC spike-in.


title: TRExRTA BCBL-1,D207A, TRAIL, 24h, biol rep 1

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AH_D207A_TRAIL_24h


title: Jurkat, sgRNA1, Mock, 4sU, biol rep 3

description:
Library name: Sample 17
Ribodepleted RNA, ERCC spike-in.


title: EZH2_FF_RA_6-rep2

value: ESC


title: TRExRTA BCBL-1,D207A, Mock, 24h, biol rep 1

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AF_D207A_Mock_24h


title: EZH2_FF_RA_6-rep1

value: RA_6 hr


title: Jurkat, sgRNA3, TRAIL, No 4sU, biol rep 2

description:
Library name: Sample 16
Ribodepleted RNA, ERCC spike-in.

value: No 4sU


title: EZH2_FF_RA_3-rep2


title: BEMP_G320D_rep2


title: BEMP_WT_rep1

value: WT


title: BEMP_G320D_rep1


title: TRExRTA BCBL-1,WT, DOX, 24h, biol rep 1

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AD_WT_DOX_24h

value: B cell lymphoma

value: DOX


title: TRExRTA BCBL-1,WT, DOX, 48h, biol rep 1

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AE_WT_DOX_48h


title: Jurkat, sgRNA3, TRAIL, 4sU, biol rep 2

description:
Library name: Sample 14
Ribodepleted RNA, ERCC spike-in.


title: EZH2_FF_RA_0-rep2


title: EZH2_FF_RA_3-rep1

value: RA_3 hr


title: tail_3dpa_exp2_1

type: other

city: BAR HARBOR

first: CGDS

last: Data

state: ME

address: 159 OLD BAR HARBOR RD

institute: MDI Biological Laboratory

data_processing: Xenium panel design, tissue histology, and processing were carried out according to the manufacturer’s instructions for preparing Xenium slides from fresh frozen tissues (10x Genomics, Protocol: CG000579), with the following modification: slides containing embryo samples were fixed in methanol for 2hrs at RT (rather than the 30min stated in the protocol). Samples were subjected to probe hybridization, ligation, and amplification steps, and stained with the Cell Segmentation Add-On Kit (10x Genomics Protocol: CG000749). Xenium slides were subsequently processed on a Xenium Analyzer instrument running Xenium Software (v.2.0.1.0) and Onboard Analysis Software (v.2.0.0.10), generating the output data bundle which included principal component analysis (PCA), K-means and graph-based clustering, differential gene expression analysis, and UMAP-based dimensionality reduction for downstream analyses.

organism: Ambystoma mexicanum

source_name: Ambystoma mexicanum, limb, unninjured

label_protocol: Gene expression was detected using a custom 10x Genomics Xenium in situ probe panel targeting 100 axolotl genes. The panel included cell-type markers, transcription factors and signalling pathway components selected to capture tail patterning, progenitor states and regeneration-associated signalling. Probes were designed and synthesized by 10x Genomics according to the manufacturer’s specifications.

growth_protocol: Ambystoma mexicanum (axolotl) embryos were maintained in 0.1× MMR (Marc’s Modified Ringer) supplemented with penicillin–streptomycin at 23 °C under a 12 h light/12 h dark cycle and staged according to external morphology; stage 28 embryos were collected for Xenium profiling. Juvenile animals used for tail regeneration experiments were approximately 3 cm in length and were kept in 0.1× Holtfreter’s solution at 23 °C with regular water changes and ad libitum feeding, and size-matched unamputated tails from these juveniles were collected as mature reference tissue.

extract_protocol: Tissues were processed for spatial transcriptomics on the 10x Genomics Xenium platform. Stage 28 embryos were fixed in 4% paraformaldehyde (PFA) in PBS at 4 °C overnight, washed in PBS, and infiltrated with 2% gelatin in PBS at 37 °C for 30 min under vacuum to improve tissue integrity and section adherence before embedding. For tail samples, unamputated and regenerating tails (3, 7, 10, 14 dpa) were dissected, carefully oriented and embedded in OCT compound in separate molds, then snap-frozen and stored at −80 °C until sectioning. All samples were cryosectioned at 20 µm thickness using a cryostat microtome and mounted on Xenium-compatible slides for in situ hybridization.

treatment_protocol: 3 cm axolotls were anaesthetized in 0.03% benzocaine in Holtfreter’s solution, and the tail was amputated at five myotomes posterior to the cloaca using a sterile #11 scalpel blade. Animals were allowed to recover in fresh Holtfreter’s at 23 °C, and regenerating tail stumps were harvested at 3, 7, 10 and 14 days post-amputation (dpa). Stage 28 embryos and unamputated tails from size-matched juveniles served as untreated developmental and mature controls.

tag: Sex

tag: strain

value: dd

value: Tail 5 myotome post amputation

tag: regeneration timepoint


title: EZH2_FF_RA_0-rep1

value: RA_0 hr


title: whole_embryo_exp2_1

hyb_protocol: 10x Genomics according to the manufacturer’s specifications

source_name: Ambystoma mexicanum, limb, 14dpa

value: embryo


title: TRExRTA BCBL-1,WT, TRAIL, 24h, biol rep 1

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AC_WT_TRAIL_24h


title: Jurkat, sgRNA3, Mock, 4sU, biol rep 2

description:
Library name: Sample 13
Ribodepleted RNA, ERCC spike-in.

value: Jurkat

value: Mock


title: whole_embryo_exp1_1

scan_protocol: 10x Genomics according to the manufacturer’s specifications

source_name: Ambystoma mexicanum, limb, 10dpa


title: ESC, KO-Ser5-rep2

data_processing:
ChIP-seq reads were aligned to the reference mouse genome assembly mm10 using Bowtie2 with default parameters. Low mapping quality reads (mapping quality < 20) and duplicates were discarded.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a BioRuptor sonicator (Diagenode).
The DNA Library of ChIP were prepared with a TruePrep DNA Library Prep Kit according to the manufacturer’s instructions (TD503, Vazyme).

value: EZH2 KO

tag: chip antibody


title: TRExRTA BCBL-1,WT, Mock, 24h, biol rep 1

description:
Ribodepleted RNA, ERCC spike-in. Note "WT" refers to cells expressing exogenous TFIIB-2xStrep, and "D207A" refers to cells expressing exogenous TFIIB(D207A)-2xStrep.
AA_WT_Mock_24h


title: Jurkat, sgRNA2, TRAIL, 4sU, biol rep 2

description:
Library name: Sample 12
Ribodepleted RNA, ERCC spike-in.

value: Immortalized T cell lymphocyte

value: TFIIB D207G/D207G-#2/sgRNA2

value: TRAIL


title: tail_mature_exp2_1

source_name: Ambystoma mexicanum, limb, 7dpa

value: mature


title: ESC, KO-Ser5-rep1

value: ESC


title: Jurkat, sgRNA2, Mock, 4sU, biol rep 2

description:
Library name: Sample 11
Ribodepleted RNA, ERCC spike-in.


title: tail_mature_exp1_4

source_name: Ambystoma mexicanum, limb, 5dpa


title: ESC, FF-Ser5-rep2


title: High expression assay time point 10 (120h, dox-treated)

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

institute: University of Edinburgh

description:
Library name: ADSLxL_TREATdox_T10
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).

data_processing:
NextSeq 2000 data: Demultiplexed reads were transferred to a Linux computer. Regions flanking the 30-nt barcodes were trimmed using Trimmomatic, and barcodes were counted using the Enrich2 pipeline.
PacBio Sequel II data: Reads were transferred to a Linux computer, aligned, and parsed to the template using the alignparse pipeline.
Supplementary files format and content: Barcode counts for each timepoint and condition, in TSV format.
Supplementary files format and content: Barcode variant table for each expression plasmid, in TSV format.

organism: Saccharomyces cerevisiae

source_name: Yeast Cell

growth_protocol: Yeast strains were grown in media containing a complete supplement mixture without histidine (Formedium) and yeast nitrogen base without amino acids (Formedium), supplemented with 2% glucose.

extract_protocol:
Plasmid DNA was isolated using a protocol combining a freeze-thaw cycle and zymolyase-mediated cell wall digestion, followed by purification with the QIAprep Spin Miniprep Kit (Qiagen).
Samples from each timepoint were prepared for next-generation sequencing using a single, 15-cycles PCR. Barcodes were amplified with primers containing overhangs that included sequencing primer, annealing sequences, unique indexes, and P5/P7 Illumina adapter sequences.

treatment_protocol: Doxycycline hyclate (10–20 µg/mL) was added at timepoint 0 under treatment conditions.

value: Yeast Cell

value: Doxycycline hyclate


title: ESC, FF-Ser5-rep1

value: WT


title: High expression assay time point 9 (108h, dox-treated)

description:
Library name: ADSLxL_TREATdox_T9
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Jurkat, sgRNA1, TRAIL, 4sU, biol rep 2

description:
Library name: Sample 10
Ribodepleted RNA, ERCC spike-in.

value: TFIIB D207G/D207G-#1/sgRNA1


title: tail_mature_exp1_3

source_name: Ambystoma mexicanum, limb, 3dpa


title: Jurkat, sgRNA1, Mock, 4sU, biol rep 2

description:
Library name: Sample 9
Ribodepleted RNA, ERCC spike-in.


title: High expression assay time point 8 (96h, dox-treated)

description:
Library name: ADSLxL_TREATdox_T8
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: ESC, EZH2-KO-ERK2


title: ESC, EZH2-FF-ERK2


title: Jurkat, sgRNA3, TRAIL, No 4sU, biol rep 1

description:
Library name: Sample 8
Ribodepleted RNA, ERCC spike-in.


title: tail_mature_exp1_1


title: Jurkat, sgRNA3, Mock, No 4sU, biol rep 1

description:
Library name: Sample 7
Ribodepleted RNA, ERCC spike-in.

value: No 4sU


title: High expression assay time point 5 (60h, dox-treated)

description:
Library name: ADSLxL_TREATdox_T5
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: High expression assay time point 6 (72h, dox-treated)

description:
Library name: ADSLxL_TREATdox_T6
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: tail_mature_exp1_2

value: dd


title: ESC, 0-H3K27me3-rep1


title: tail_10dpa_exp2_2

value: Tail 5 myotome post amputation

value: 10 dpa


title: ESC, 0-H3K27me3-rep2


title: Jurkat, sgRNA3, TRAIL, 4sU, biol rep 1

description:
Library name: Sample 6
Ribodepleted RNA, ERCC spike-in.


title: High expression assay time point 7 (84h, dox-treated)

description:
Library name: ADSLxL_TREATdox_T7
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: High expression assay time point 4 (48h, dox-treated)

description:
Library name: ADSLxL_TREATdox_T4
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Jurkat, sgRNA3, Mock, 4sU, biol rep 1

description:
Library name: Sample 5
Ribodepleted RNA, ERCC spike-in.


title: tail_10dpa_exp2_1


title: Jurkat, sgRNA2, TRAIL, 4sU, biol rep 1

description:
Library name: Sample 4
Ribodepleted RNA, ERCC spike-in.


title: Jurkat, sgRNA2, Mock, 4sU, biol rep 1

description:
Library name: Sample 3
Ribodepleted RNA, ERCC spike-in.


title: J-Gamma1 cells, input

description: Library name: Sample 2

data_processing:
Filtering: Raw reads were filtered using fastp（version 0.23.1）
Removing duplication: Deduplication is performed based on the UID sequence in the reads.
Mapping: Clean reads were mapped to hg38
Peak calling: MACS2 was used to call peak
Assembly: hg38
Supplementary files format and content: BigWig files containing read coverage normalized to CPM (read count per million); Peaks in tab file.

extract_protocol:
The samples were irradiated twice with 254 nm UV-C light on ice, with each irradiation dose of 400 mJ. Subsequently, the samples were lysed with lysis buffer on ice for 15 minutes. The lysate was further treated with 40 U of RNase I and incubated with rotation at 37°C for 5 minutes.
libraries were prepared for sequencing using eCLIP-seq library construction protocols

value: T-ALL cells

value: input


title: High expression assay time point 2 (24h, dox-treated)

description:
Library name: ADSLxL_TREATdox_T2
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: High expression assay time point 1 (12h, dox-treated)

description:
Library name: ADSLxL_TREATdox_T1
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: tail_7dpa_exp1_7

value: 7 dpa


title: tail_7dpa_exp1_8


title: J-Gamma1 cells, NUDT21 antibody

description: Library name: Sample 1

value: NUDT21 antibody


title: Jurkat, sgRNA1, TRAIL, 4sU, biol rep 1

description:
Library name: Sample 2
Ribodepleted RNA, ERCC spike-in.

value: Jurkat

value: Immortalized T cell lymphocyte


title: tail_7dpa_exp2_1


title: Jurkat, sgRNA1, Mock, 4sU, biol rep 1

description:
Library name: Sample 1 Note Must rename fastqz for G and H that was swapped
Ribodepleted RNA, ERCC spike-in.

value: Mock


title: High expression assay time point 10 (120h, dox-untreated)

description:
Library name: ADSLxL_NOTREATdox_T10
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: tail_7dpa_exp1_5


title: Jurkat, sgRNA3, Mock,No  4sU, biol rep 2

description:
Library name: Sample 15
Ribodepleted RNA, ERCC spike-in.


title: High expression assay time point 9 (108h, dox-untreated)

description:
Library name: ADSLxL_NOTREATdox_T9
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: tail_7dpa_exp1_6


title: High expression assay time point 3 (36h, dox-treated)

description:
Library name: ADSLxL_TREATdox_T3
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Jurkat, sgRNA3 (S3), Clone B (CB), Trail, No 4sU, biol rep 3

description:
Library name: Sample 30
Ribodepleted RNA, ERCC spike-in.

data_processing:
Data was preprocessed (PhiX removal, deduplication, N-remover, adaptor trimming, etc.) using the standard HTStream version 1.3.0 workflow
Human GRCh38.p13, ERCC Spike-In genomes were concatenated and indexed using STAR version 2.7.1a. Gencode annotation v43 were used.
Preprocessed reads were aligned with STAR version 2.7.1a and counts tables were exported for bulk RNA
Separately, the same genome and annotation was prepared for GRAND-SLAM analysis with gedi and mapped using GRAND-SLAM default parameters to generate a counts table for nascent transcripts by multiplying the total counts by the nascent-to-total MAP statistic.
Assembly: Human genome GRCh38.p13 + Gencode v43; ERCC Spike-In sequences (Invitrogen)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample bulk RNA
Supplementary files format and content: Tab-delimited text file includes raw counts and nascent RNA statistics from GRAND-SLAM for nascent RNA from 4sU-containing samples.

growth_protocol: Jurkat cells base-edited for 2 days with ABE8e base editor RNA and indicated sgRNA were single cell dilution cloned and validated by amplicon sequencing at the edit locus. Clonal populations were maintained in RPMI 1640 media (Gibco) supplemented with 10% Tet-free fetal bovine serum, 1X GlutaMAX (Gibco), 1x Pen-Strep (Gibco) and 1 mM sodium pyruvate (Gibco) in a humidified chamber at 37℃ and 5% CO2. Cells were kept at densities between 0.5-2x10^6 cells/mL.

treatment_protocol: SLAM-sequencing was performed: Each Jurkat clonal line (1 each for TFIIB-targeting D207G-#1/sgRNA1 and 1 for D207G-#2/sgRNA2; 2 for AAVS1-targeting control/sgRNA3) was treated with 250 ng/mL SUPERKILLER TRAIL ligand (Enzo) or mock diluant for 6 h. After 3h, 300 uM of 4-thiouridine (4sU)  was added to all samples to label nascent RNA synthesized before the harvesting endpoint (except those indicated No 4sU as a control).

tag: clonal line_id_for_sgrna_(ca,_cb,_etc.)

value: CB

value: TRAIL (T)


title: High expression assay time point 8 (96h, dox-untreated)

description:
Library name: ADSLxL_NOTREATdox_T8
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).

value: Yeast Cell


title: tail_7dpa_exp1_4


title: Jurkat, sgRNA3 (S3), Clone B (CB), No Trail, No 4sU, biol rep 3

description:
Library name: Sample 29
Ribodepleted RNA, ERCC spike-in.

value: No TRAIL (NoT)


title: tail_7dpa_exp1_3


title: Jurkat, sgRNA3 (S3), Clone B (CB), Trail, No 4sU, biol rep 2

description:
Library name: Sample 28
Ribodepleted RNA, ERCC spike-in.


title: High expression assay time point 7 (84h, dox-untreated)

description:
Library name: ADSLxL_NOTREATdox_T7
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Jurkat, sgRNA3 (S3), Clone B (CB), No Trail, No  4sU, biol rep 2

description:
Library name: Sample 27
Ribodepleted RNA, ERCC spike-in.


title: High expression assay time point 5 (60h, dox-untreated)

description:
Library name: ADSLxL_NOTREATdox_T5
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: tail_7dpa_exp1_2


title: High expression assay time point 6 (72h, dox-untreated)

description:
Library name: ADSLxL_NOTREATdox_T6
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: tail_7dpa_exp1_1


title: High expression assay time point 4 (48h, dox-untreated)

description:
Library name: ADSLxL_NOTREATdox_T4
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: PBMCs_healthy control_sample 9

type: RNA

city: Beijing

first: xuetian

last: shang

address: No.9 Beiguan Street, Tongzhou District

institute: Beijing Chest Hospital, Capital Medical University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: PBMCs_healthy control_sample 9

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted from PBMCs using the miRNeasy® Mini kit (QIAGEN, Germany) according to the protocols recommended by the manufacturer.

tag: cell

value: peripheral blood mononuclear cells


title: Jurkat, sgRNA3 (S3), Clone B (CB), No Trail, No  4sU, biol rep 1

description:
Library name: Sample 25
Ribodepleted RNA, ERCC spike-in.


title: PBMCs_healthy control_sample 10

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: PBMCs_healthy control_sample 10


title: Jurkat, sgRNA3 (S3), Clone B (CB), Trail, No 4sU, biol rep 1

description:
Library name: Sample 26
Ribodepleted RNA, ERCC spike-in.


title: tail_14dpa_exp2_1

value: 14 dpa


title: High expression assay time point 3 (36h, dox-untreated)

description:
Library name: ADSLxL_NOTREATdox_T3
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: PBMCs_healthy control_sample 6

source_name: PBMCs_healthy control_sample 6


title: Jurkat, sgRNA3 (S3), Clone C (CC), Trail, 4sU, biol rep 3

description:
Library name: Sample 24
Ribodepleted RNA, ERCC spike-in.

value: CC


title: tail_14dpa_exp1_5

value: dd


title: PBMCs_healthy control_sample 3

source_name: PBMCs_healthy control_sample 3


title: tail_14dpa_exp1_4

value: Tail 5 myotome post amputation


title: PBMCs_healthy control_sample 2

source_name: PBMCs_healthy control_sample 2


title: High expression assay time point 2 (24h, dox-untreated)

description:
Library name: ADSLxL_NOTREATdox_T2
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: PBMCs_healthy control_sample 8

source_name: PBMCs_healthy control_sample 8


title: Jurkat, sgRNA3 (S3), Clone C (CC), No Trail, 4sU, biol rep 3

description:
Library name: Sample 23
Ribodepleted RNA, ERCC spike-in.


title: Jurkat, sgRNA3 (S3), Clone B (CB), Trail, 4sU, biol rep 3

description:
Library name: Sample 22
Ribodepleted RNA, ERCC spike-in.


title: High expression assay time point 0

description:
Library name: ADSLxL_T0
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: PBMCs_healthy control_sample 7

source_name: PBMCs_healthy control_sample 7


title: Jurkat, sgRNA3 (S3), Clone B (CB), No Trail, 4sU, biol rep 3

description:
Library name: Sample 21
Ribodepleted RNA, ERCC spike-in.


title: Low expression assay time point 10 (120h, dox-treated)

description:
Library name: ADSLxS_TREATdox_T10
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).

value: Doxycycline hyclate


title: tail_14dpa_exp1_2


title: tail_14dpa_exp1_3


title: Jurkat, sgRNA2 (S2), Clone A (CA), No Trail, 4sU, biol rep 3

description:
Library name: Sample 19
Ribodepleted RNA, ERCC spike-in.

value: CA


title: Cell_3135

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

institute: Cancer Research UK Manchester Institute

description: PromethION P2 Solo (Oxford Nanopore)

data_processing:
The quality control of  sequencing run  was performed using MinionQC.R version 1.4.2.
Raw .pod5 files were obtained from MinKNOW 23.04.6 and the basecalling was performed using Guppy 6.5.7.
Fastq files were aligned to the reference genome and transcriptome using splice aware aligner minimap2 (version 2.26) with the argument " -a -x splice".  GRCm39 M33 mouse reference genome, transcriptome, and their corresponding GTF files were downloaded from GENCODE website.
The indexed sorted genome aligned bam files were merged to get one bam file per condition i.e AGM (HE-HSC), YSm (HE-LMP), YSb (HE-EMP). These were visualized in IGV  App 2.17.0.
The transcriptome aligned bam files were quantified using Salmon 1.10.2 in alignment mode using --ont argument. The quant.sf files were used by IsoformSwitchAnalyzer  2.01.07 where importIsoformExpression function was used to give TMM normalized abundance values.
Assembly: GRCm39 M33 gencode
Supplementary files format and content: RDS file having TMM normalized abundance for each sample.

extract_protocol:
10ng full-length purified amplified cDNA from a miniaturised Smart-seq2 cDNA preparation  was further amplified using 9 cycles of PCR (according to conditions in the Smart-seq2 pre-amplication step).
Re-amplified cDNA was purified using a 0.7x volume of AMPure XP reagent (Beckman Coulter). Purified amplification product was quantified by Qubit (ThermoFisher) and sized / quality checked by Fragment Analyzer (Agilent). 200fmol  was used as input for the Ligation sequencing amplicons - Native Barcoding Kit 24 V14 (SQK-NBD114.24) protocol (revision H) (Oxford Nanopore).  Sequencing was performed on a PromethION P2 Solo (Oxford Nanopore) using flow cell FLO-PRO114M

value: YSb

tag: sequencing run


title: PBMCs_healthy control_sample 4

source_name: PBMCs_healthy control_sample 4


title: Cell_2972

description: PromethION P2 Solo (Oxford Nanopore)


title: PBMCs_healthy control_sample 5

source_name: PBMCs_healthy control_sample 5


title: Jurkat, sgRNA2 (S2), Clone A (CA), Trail, 4sU, biol rep 3

description:
Library name: Sample 20
Ribodepleted RNA, ERCC spike-in.

source_name: Jurkat


title: tail_14dpa_exp1_1

source_name: Ambystoma mexicanum, limb, unninjured


title: PBMCs_healthy control_sample 1

source_name: PBMCs_healthy control_sample 1


title: Low expression assay time point 9 (108h, dox-treated)

description:
Library name: ADSLxS_TREATdox_T9
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Jurkat, sgRNA1 (S1), Clone A (CA), Trail, 4sU, biol rep 3

description:
Library name: Sample 18
Ribodepleted RNA, ERCC spike-in.


title: High expression assay time point 1 (12h, dox-untreated)

description:
Library name: ADSLxL_NOTREATdox_T1
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Low expression assay time point 8 (96h, dox-treated)

description:
Library name: ADSLxS_TREATdox_T8
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: PBMCs_TB patient_sample 9

source_name: peripheral blood mononuclear cells, MTB patient, sample 9


title: PBMCs_TB patient_sample 10

source_name: peripheral blood mononuclear cells, MTB patient, sample 10


title: PBMCs_TB patient_sample 7

source_name: peripheral blood mononuclear cells, MTB patient, sample 7


title: Jurkat, sgRNA1 (S1), Clone A (CA), No Trail, 4sU, biol rep 3

description:
Library name: Sample 17
Ribodepleted RNA, ERCC spike-in.


title: Low expression assay time point 7 (84h, dox-treated)

description:
Library name: ADSLxS_TREATdox_T7
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).

source_name: Yeast Cell


title: Cell_2095

description: PromethION P2 Solo (Oxford Nanopore)


title: PBMCs_TB patient_sample 5

source_name: peripheral blood mononuclear cells, MTB patient, sample 5


title: Low expression assay time point 6 (72h, dox-treated)

description:
Library name: ADSLxS_TREATdox_T6
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: PBMCs_TB patient_sample 6

source_name: peripheral blood mononuclear cells, MTB patient, sample 6


title: Cell_1731

description: PromethION P2 Solo (Oxford Nanopore)


title: Jurkat, sgRNA3 (S3), Clone B (CB), No Trail, 4sU, biol rep 2

description:
Library name: Sample 13
Ribodepleted RNA, ERCC spike-in.


title: PBMCs_TB patient_sample 8

source_name: peripheral blood mononuclear cells, MTB patient, sample 8


title: Low expression assay time point 2 (24h, dox-treated)

description:
Library name: ADSLxS_TREATdox_T2
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Jurkat, sgRNA3 (S3), Clone C (CC), No Trail, 4sU, biol rep 2

description:
Library name: Sample 15
Ribodepleted RNA, ERCC spike-in.


title: Cell_0313

description: PromethION P2 Solo (Oxford Nanopore)

value: AGM


title: Low expression assay time point 4 (48h, dox-treated)

description:
Library name: ADSLxS_TREATdox_T4
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


city: Yangzhou

first: Juan

last: Yang

address: 大学南路88号

department: College of Veterinary Medicine

institute: Yangzhou University

description:
Library name: pTr cells, JEV_48 hpi, small RNA-seq, replicate 2
JEV_infect_PTr_miRNA_read_counts.txt
Column name in JEV_infect_PTr_miRNA_read_counts.txt: Infected_48h_2

data_processing:
Small RNA-seq reads were trimmed with Trim Galore v0.6.5 to remove reads that contain low-quality bases and with length less than 18 bp or greater than 25 bp, and then aligned to the pig reference genome (Sscrofa11.1) using the mapper.pl function of miRDeep2 v0.1.3. MiRNA-level read counts were calculated by using the quantifier.pl of miRDeep2 v0.1.3.
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited table,miRNA-level read counts

organism: Sus scrofa

source_name: pTr

extract_protocol:
Total RNA was extracted using RNAiso Plus (TaKaRa, 9109) with DNase digestion.
Small RNA-seq libraries were construction by using UMI small RNA library sample preparation kit (BGI), and sequenced as 50 bp single-end reads with DNBSEQ platform (DNBSEQ Technology).

value: pTr

value: porcine trophectoderm cells

value: JEV 48 hours post-infected


title: Cell_2457

description: PromethION P2 Solo (Oxford Nanopore)

value: YSm


title: Jurkat, sgRNA2 (S2), Clone A (CA), Trail, 4sU, biol rep 2

description:
Library name: Sample 12
Ribodepleted RNA, ERCC spike-in.

value: Jurkat

value: Immortalized T cell lymphocyte


title: PBMCs_TB patient_sample 4

source_name: peripheral blood mononuclear cells, MTB patient, sample 4


title: Cell_2767

description: PromethION P2 Solo (Oxford Nanopore)


title: Jurkat, sgRNA3 (S3), Clone C (CC), Trail, 4sU, biol rep 2

description:
Library name: Sample 16
Ribodepleted RNA, ERCC spike-in.

value: TRAIL (T)


title: Low expression assay time point 3 (36h, dox-treated)

description:
Library name: ADSLxS_TREATdox_T3
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).

value: Yeast Cell


description:
Library name: pTr cells, JEV_48 hpi, small RNA-seq, replicate 1
JEV_infect_PTr_miRNA_read_counts.txt
Column name in JEV_infect_PTr_miRNA_read_counts.txt: Infected_48h_1


title: Cell_0112

description: PromethION P2 Solo (Oxford Nanopore)


title: Jurkat, sgRNA2 (S2), Clone A (CA), No Trail, 4sU, biol rep 2

description:
Library name: Sample 11
Ribodepleted RNA, ERCC spike-in.

value: No TRAIL (NoT)


title: Low expression assay time point 1 (12h, dox-treated)

description:
Library name: ADSLxS_TREATdox_T1
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: PBMCs_TB patient_sample 1

source_name: peripheral blood mononuclear cells, MTB patient, sample 1

value: peripheral blood mononuclear cells


title: Low expression assay time point 5 (60h, dox-treated)

description:
Library name: ADSLxS_TREATdox_T5
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Jurkat, sgRNA1 (S1), Clone A (CA), Trail, 4sU, biol rep 2

description:
Library name: Sample 10
Ribodepleted RNA, ERCC spike-in.


title: Low expression assay time point 10 (120h, dox-untreated)

description:
Library name: ADSLxS_NOTREATdox_T10
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


description:
Library name: pTr cells, JEV_mock, small RNA-seq, replicate 2
JEV_infect_PTr_miRNA_read_counts.txt
Column name in JEV_infect_PTr_miRNA_read_counts.txt: Mock_2

value: JEV mock-infected


title: Cell_0316

description: PromethION P2 Solo (Oxford Nanopore)


title: Jurkat, sgRNA3 (S3), Clone B (CB), Trail, 4sU, biol rep 2

description:
Library name: Sample 14
Ribodepleted RNA, ERCC spike-in.

value: CB


description:
Library name: pTr cells, JEV_mock, small RNA-seq, replicate 1
JEV_infect_PTr_miRNA_read_counts.txt
Column name in JEV_infect_PTr_miRNA_read_counts.txt: Mock_1


title: PBMCs_TB patient_sample 3

source_name: peripheral blood mononuclear cells, MTB patient, sample 3


title: Cell_2065

description: PromethION P2 Solo (Oxford Nanopore)


title: Low expression assay time point 9 (108h, dox-untreated)

description:
Library name: ADSLxS_NOTREATdox_T9
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Jurkat, sgRNA1 (S1), Clone A (CA), No Trail, 4sU, biol rep 2

description:
Library name: Sample 9
Ribodepleted RNA, ERCC spike-in.


title: Cell_0151

description: PromethION P2 Solo (Oxford Nanopore)


title: pTr cells, small RNA-seq, replicate 2

description:
Library name: pTr cells, small RNA-seq, replicate 2
pig_placenta_pTr_miRNA_read_counts.txt
Column name in pig_placenta_pTr_miRNA_read_counts.txt: pTr_2


title: Low expression assay time point 8 (96h, dox-untreated)

description:
Library name: ADSLxS_NOTREATdox_T8
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: pTr cells, small RNA-seq, replicate 1

description:
Library name: pTr cells, small RNA-seq, replicate 1
pig_placenta_pTr_miRNA_read_counts.txt
Column name in pig_placenta_pTr_miRNA_read_counts.txt: pTr_1


title: Cell_0294

description: PromethION P2 Solo (Oxford Nanopore)


description:
Library name: term placenta, small RNA-seq, replicate 2
pig_placenta_pTr_miRNA_read_counts.txt
Column name in pig_placenta_pTr_miRNA_read_counts.txt: placenta_2

source_name: term placenta

value: term placenta


title: Jurkat, sgRNA3 (S3), Clone C (CC), No Trail, 4sU, biol rep 1

description:
Library name: Sample 7
Ribodepleted RNA, ERCC spike-in.

value: CC


title: Low expression assay time point 6 (72h, dox-untreated)

description:
Library name: ADSLxS_NOTREATdox_T6
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Low expression assay time point 7 (84h, dox-untreated)

description:
Library name: ADSLxS_NOTREATdox_T7
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Jurkat, sgRNA3 (S3), Clone B (CB), Trail, 4sU, biol rep 1

description:
Library name: Sample 6
Ribodepleted RNA, ERCC spike-in.


title: Jurkat, sgRNA3 (S3), Clone C (CC), Trail, 4sU, biol rep 1

description:
Library name: Sample 8
Ribodepleted RNA, ERCC spike-in.


title: PBMCs_TB patient_sample 2

source_name: peripheral blood mononuclear cells, MTB patient, sample 2


description:
Library name: term placenta, small RNA-seq, replicate 1
pig_placenta_pTr_miRNA_read_counts.txt
Column name in pig_placenta_pTr_miRNA_read_counts.txt: placenta_1


title: Cell_0315

description: PromethION P2 Solo (Oxford Nanopore)


title: Cell_0303

description: PromethION P2 Solo (Oxford Nanopore)


title: Cell_0115

description: PromethION P2 Solo (Oxford Nanopore)


title: Low expression assay time point 5 (60h, dox-untreated)

description:
Library name: ADSLxS_NOTREATdox_T5
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


description:
Library name: pTr cells, JEV_48 hpi, RNA-seq, replicate 2
Column name in JEV_infect_PTr_merged_count.txt: PTr_48h_2.bam

data_processing:
RNA-seq reads were trimmed with Trim Galore v0.6.5., and then aligned to the pig reference genome (Sscrofa11.1) using STAR v2.7.3. Gene-level read counts were calculated by using the featureCount function of subread v2.0.0.
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited table, gene-level read counts

extract_protocol:
Total RNA was extracted using RNAiso Plus (TaKaRa, 9109) with DNase digestion.
RNA-seq libraries were construction by using DNBSEQ Eukaryotic Strand-specific mRNA library sample preparation kit (BGI), and sequenced as 150 bp paired-end reads with DNBSEQ platform (DNBSEQ Technology).


title: Cell_0299

description: PromethION P2 Solo (Oxford Nanopore)


description:
Library name: pTr cells, JEV_48 hpi, RNA-seq, replicate 1
Column name in JEV_infect_PTr_merged_count.txt: PTr_48h_1.bam


title: Cell_3114

description: PromethION P2 Solo (Oxford Nanopore)


title: Jurkat, sgRNA2 (S2), Clone A (CA), No Trail, 4sU, biol rep 1

description:
Library name: Sample 3
Ribodepleted RNA, ERCC spike-in.

value: CA


title: Cell_2988

description: PromethION P2 Solo (Oxford Nanopore)

value: YSb


description:
Library name: pTr cells, JEV_24 hpi, RNA-seq, replicate 1
Column name in JEV_infect_PTr_merged_count.txt: PTr_24h_1.bam

value: JEV 24 hours post-infected


title: Jurkat, sgRNA3 (S3), Clone B (CB), No Trail, 4sU, biol rep 1

description:
Library name: Sample 5
Ribodepleted RNA, ERCC spike-in.


title: Low expression assay time point 2 (24h, dox-untreated)

description:
Library name: ADSLxS_NOTREATdox_T2
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


description:
Library name: pTr cells, JEV_24 hpi, RNA-seq, replicate 2
Column name in JEV_infect_PTr_merged_count.txt: PTr_24h_2.bam

value: pTr


title: Jurkat, sgRNA2 (S2), Clone A (CA), Trail, 4sU, biol rep 1

description:
Library name: Sample 4
Ribodepleted RNA, ERCC spike-in.


title: Low expression assay time point 4 (48h, dox-untreated)

description:
Library name: ADSLxS_NOTREATdox_T4
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: Cell_3415

description: PromethION P2 Solo (Oxford Nanopore)


title: Jurkat, sgRNA1 (S1), Clone A (CA), Trail, 4sU, biol rep 1

description:
Library name: Sample 2
Ribodepleted RNA, ERCC spike-in.


description:
Library name: pTr cells JEV_mock, RNA-seq, replicate 2
Column name in JEV_infect_PTr_merged_count.txt: PTr_mock_2.bam

value: porcine trophectoderm cells


title: MDA-MB-468, shFAM83H-AS1_2, rep2

city: Guangzhou

first: Zhimei

last: Liang

state: Guangdong

address: No. 107, Yanjiang West Road, Yuexiu District

department: Medical Research Center

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

description:
Library name: MDA-MB-468, shFAM2b
Column name in cellseq_FPKMs_allSamples.xlsx: shFAM2b

data_processing:
Raw data (raw reads) of fastq format were processed through in-house Perl scripts.
Index of the reference genome was built using Bowtie2 v2.2.3.
Paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample.
Assembly: Assembly: hg38
Supplementary files format and content: Matrix files include FPKM values for each Sample

growth_protocol: MDA-MB-468 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Trizol (Invitrogen) according to the manufacturer’s instructions. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® （NR604-01/02）following the manufacturer’s recommendations.

treatment_protocol: Lentivirus containing shRNAs targeting FAM83H-AS1 were constructed by Genechem. MDA-MB-468 cells were transduced with 10 MOI lentiviral particles with HiTransG P. Following the infection, cells were selected using puromycin (1 μg/mL) to generate stable cell lines.

value: breast cancer cells

value: FAM83H-AS1 knockdown

value: 1 μg/mL puromycin


description:
Library name: pTr cells JEV_mock, RNA-seq, replicate 1
Column name in JEV_infect_PTr_merged_count.txt: PTr_mock_1.bam


title: Cell_2944

description: PromethION P2 Solo (Oxford Nanopore)


title: Jurkat, sgRNA1 (S1), Clone A (CA), No Trail, 4sU, biol rep 1

description:
Library name: Sample 1
Ribodepleted RNA, ERCC spike-in.

value: Jurkat

value: Immortalized T cell lymphocyte


title: Cell_3122

description: PromethION P2 Solo (Oxford Nanopore)

value: YSm


title: Low expression assay time point 3 (36h, dox-untreated)

description:
Library name: ADSLxS_NOTREATdox_T3
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).

value: Yeast Cell


title: Cell_3104

description: PromethION P2 Solo (Oxford Nanopore)


title: Dvma13_GAL10-AAC2_3

city: Syracuse

first: Nicholas

last: Brennan

state: New York

address: 766 Irving Ave

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, using Cutadapt-1.2.1 and low-quality (q < 25) sequence
Trimmed sequences were mapped to sacCer3 whole genome using Bowtie 2 and quantified to Saccharomyces Genome Database (SGD) annotation, using strict paired-end compatibility, with requirement of junction reads to match introns, minimum feature overlap of 95%, and minimum reads of 1.
Assembly: sacCer3
Supplementary files format and content: tab-delimited text files include normalized alignment counts per gene for each sample

source_name: Single-cell eukaryote (haploid)

growth_protocol: Cells were grown at 30°C in 1% yeast extract+2% peptone+2% galactose+2% raffinose

extract_protocol:
Total RNA was extracted using glass beads and phenol/chloroform/isoamyl alcohol (25:24:1). RNA was precipitated, and the quality and quantity of RNA was assessed with the Bioanalyzer. 1 mg RNA was used as input to the Illumina Stranded mRNA kit for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina Stranded mRNA prep kit following the manufacturers protocol.

tag: medium

value: Yeast extract+peptone+2% galactose+2% raffinose

value: Single-cell eukaryote (haploid)


title: Low expression assay time point 0

description:
Library name: ADSLxS_T0
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).


title: KO-FGO-1

city: Nanning

first: liu

last: shaoyuan

address: Guangxi province of china

institute: Guangxi university

description:
Library name: RNA_seq_11
Smart-seq2

data_processing:
RNA-seq was performed using biological replicates for all samples. Raw reads were removed adapters and low-quality fragments using Trim-galore (version 0.6.7) and mapped to the mouse genome (mm10) using HISAT2 (version 2.2.1) with default parameters. Uniquely mapped reads were subsequently assembled into transcripts guided by reference annotation (University of California at Santa Cruz [UCSC] gene models) using Cufflinks (version 2.2.1). At the same time for analysis Transposable element (TE) transcript’s count the software TEtranscripts (version 2.2.3) was used with default parameters. The level of expression of each gene was quantified as the fragments per kilobase of transcript per million mapped reads (FPKM) and was further normalized to the ERCC spike-in. Samples prepared in different batches were normalized to GV-stage oocyte samples from each batch. Only expressed genes (FPKM > 1 in at least one sample) were considered in all analyses, unless otherwise specified.
Assembly: mm10
Supplementary files format and content: ERCC_adjust_FPKM

source_name: oocyte

extract_protocol:
Sequencing libraries were constructed from 500 pg of amplified cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (TD503, Vazyme) according to the manufacturer's instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform using 150 bp paired-end reads.
Sequencing libraries were constructed from 500 pg of amplified cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (TD503, Vazyme) according to the manufacturer's instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform using 150 bp paired-end reads

value: oocyte


title: Dvma13_GAL10-AAC2_1


title: MDA-MB-468, shFAM83H-AS1_2, rep1

description:
Library name: MDA-MB-468, shFAM2a
Column name in cellseq_FPKMs_allSamples.xlsx: shFAM2a

tag: cell line


title: Low expression assay time point 1 (12h, dox-untreated)

description:
Library name: ADSLxS_NOTREATdox_T1
Sequencing (1x50) was performed on the NextSeq 2000 platform (Illumina Inc, #SY-415- 1002) using the NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811).

tag: cell type


title: MDA-MB-468, shFAM83H-AS1_2, rep3

description:
Library name: MDA-MB-468, shFAM2c
Column name in cellseq_FPKMs_allSamples.xlsx: shFAM2c

tag: treatment


title: KO-FGO-2

description:
Library name: RNA_seq_12
Smart-seq2


title: MDA-MB-468, shFAM83H-AS1_1, rep3

description:
Library name: MDA-MB-468, shFAM1c
Column name in cellseq_FPKMs_allSamples.xlsx: shFAM1c

tag: genotype


title: Dvma13_GAL10-AAC2_2


title: KO-GO-2

description:
Library name: RNA_seq_10
Smart-seq2


title: Cell_1867

description: PromethION P2 Solo (Oxford Nanopore)


title: MDA-MB-468, shFAM83H-AS1_1, rep2

description:
Library name: MDA-MB-468, shFAM1b
Column name in cellseq_FPKMs_allSamples.xlsx: shFAM1b


title: GAL10-AAC2_2


title: Cell_2953

description: PromethION P2 Solo (Oxford Nanopore)


title: Cell_2275

description: PromethION P2 Solo (Oxford Nanopore)


title: KO-NGO-1

description:
Library name: RNA_seq_7
Smart-seq2


title: KO-NGO-2

description:
Library name: RNA_seq_8
Smart-seq2


title: GAL10-AAC2_3


title: GAL10-AAC2_1


title: Cell_3477

description: PromethION P2 Solo (Oxford Nanopore)


title: Cell_3217

description: PromethION P2 Solo (Oxford Nanopore)


title: Dvma13_3


title: MDA-MB-468, shNC, rep2

description:
Library name: MDA-MB-468, shNCb
Column name in cellseq_FPKMs_allSamples.xlsx: shNCb

value: WT


title: MDA-MB-468, shNC, rep1

description:
Library name: MDA-MB-468, shNCa
Column name in cellseq_FPKMs_allSamples.xlsx: shNCa


title: WT-FGO-1

description:
Library name: RNA_seq_5
Smart-seq2


title: Dvma13_2


title: Adult pig central canal associated spinal cord cells, ex vivo expanded (Pig_3)

city: Ottawa

first: Sasi Kumar

last: Jagadeesan

state: ON

address: 1053 Carling Avenue,

department: Neuroscience

country: Canada

institute: Ottawa Hospital Research Institute

description:
Library name: Pig_577941
Adult pig central canal associated spinal cord cells, ex vivo expanded.

data_processing:
Raw FASTQ files were quality-checked with FastQC and summarized with MultiQC.
Adapters/low-quality bases were trimmed (e.g., fastp/Trim Galore; default stringency).
Transcript quantification was performed with Salmon (v1.x) in selective-alignment mode using species-specific reference transcriptomes (pig: ss11; rat: rn6).
Per-sample quantification files (quant.sf) were retained as processed data; downstream gene-level summarization (tximport to DESeq2) was used for analyses described in the manuscript
Quality and mapping summaries were inspected to confirm expected depth and consistency across samples.
Assembly: Pig: ss11; Rat: rn6.
Supplementary files format and content: Processed files are Salmon quant.sf (tab-delimited) containing transcript-level TPM and estimated counts. Reference transcriptomes: pig (ss11) and rat (rn6). Raw FASTQ files: Pig_577939_R1_001.fastq, Pig_577940_R1_001.fastq, Pig_577941_R1_001.fastq, Rat_577942_R1_001.fastq, Rat_577943_R1_001.fastq, Rat_577944_R1_001.fastq.
Supplementary files format and content: No alignment (BAM/SAM) files are deposited; quantitative transcript-level abundances are provided as the primary processed outputs.

source_name: Spinal cord

growth_protocol: Central canal–associated regions were microdissected from adult pig and rat spinal cords. Cells were expanded as adherent cultures on matrix-coated plates in serum-free neural progenitor medium (DMEM/F12 supplemented with N2/B27, heparin, EGF, and FGF2).

extract_protocol:
Total RNA was isolated from central canal–associated spinal cord cell cultures using a column-based kit with on-column DNase digestion (Qiagen RNeasy Plus). RNA integrity was assessed by Bioanalyzer/TapeStation and quantified by Qubit
Poly(A)+ RNA was enriched and strand-specific libraries were prepared using Illumina TruSeq Stranded mRNA reagents with unique sample barcodes. Libraries were sequenced on an Illumina NovaSeq 6000 (150 bp, single-end).

treatment_protocol: No experimental treatment was applied in culture.

value: Spinal cord

value: Central canal associated cells

value: wild-type


title: KO-GO-1

description:
Library name: RNA_seq_9
Smart-seq2


title: Adult pig central canal associated spinal cord cells, ex vivo expanded (Pig_1)

description:
Library name: Pig_577939
Adult pig central canal associated spinal cord cells, ex vivo expanded.


title: WT-GO-2

description:
Library name: RNA_seq_4
Smart-seq2


title: MDA-MB-468, shNC, rep3

description:
Library name: MDA-MB-468, shNCc
Column name in cellseq_FPKMs_allSamples.xlsx: shNCc


title: MDA-MB-468, shFAM83H-AS1_1, rep1

description:
Library name: MDA-MB-468, shFAM1a
Column name in cellseq_FPKMs_allSamples.xlsx: shFAM1a


title: Adult pig central canal associated spinal cord cells, ex vivo expanded (Pig_2)

description:
Library name: Pig_577940
Adult pig central canal associated spinal cord cells, ex vivo expanded.


title: WT-GO-1

description:
Library name: RNA_seq_3
Smart-seq2


title: Dvma13_1


title: WT-FGO-2

description:
Library name: RNA_seq_6
Smart-seq2


title: Adult rat central canal associated spinal cord cells, ex vivo expanded (Rat_3)

description:
Library name: Rat_577944
Adult rat central canal associated spinal cord cells, ex vivo expanded.

organism: Rattus norvegicus


title: circCAMSAP1 NAI, repeat2

city: Shanghai

first: Li

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: Library name: circCAMSAP1_NAI_rep2

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to  experimental barcodes.
Analyses by CIRCshapemapper v2 (https://github.com/YangLab/circSHAPEmapper)
Assembly: Target RNA sequence
Supplementary files format and content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.

source_name: cDNA

extract_protocol:
For in vitro SHAPE-MaP, RNA are purified. About 50-200 ng of RNAs were obtained under each treatment, and were then used for SHAPE-MaP reverse transcription by adding 1 μL (200 U/μL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for EPIC. Mn2+ was removed using RNAClean XP (Beckman Coulter) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase.
circSHAPE-MaP libraries were prepared from 1 ng of DNAs for circular (circSHAPE-MaP) RNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Library was prepared by KAPA Hyper Prep Kit .Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina NovaSeq.

treatment_protocol: For in vitro circSHAPE-MaP, circular RNAs were refolded in 3.3× folding buffer (333 mM HEPES, pH 8.0; 333 mM NaCl; 33 mM MgCl2). After refolding, RNAs were incubated with10x SHAPE Chemical in DMSO with the final concentration of NAI (EMD Millipore) at 100 mM for 10 minutes at 37°C.

value: cDNA

value: EPIC-1 NAI samples modified by NAI in DMSO


title: WT_2


title: circCAMSAP1 NAI, repeat1

description: Library name: circCAMSAP1_NAI_rep1


title: WT-NGO-2

description:
Library name: RNA_seq_2
Smart-seq2


title: circCAMSAP1 DC

description: Library name: circCAMSAP1_DC

value: EPIC-1 DC samples suspended in a denaturing buffer containing formamide and incubated at 95 °C prior to modification with NAI


title: WT_3


title: WT_1


title: circCAMSAP1 DMSO

description: Library name: circCAMSAP1_DMSO

value: EPIC-1 DMSO samples only treated with DMSO


title: Adult rat central canal associated spinal cord cells, ex vivo expanded (Rat_2)

description:
Library name: Rat_577943
Adult rat central canal associated spinal cord cells, ex vivo expanded.


title: WT-NGO-1

description:
Library name: RNA_seq_1
Smart-seq2


title: ChIPseq_Input_Gata2_G320D

description: Library name: Id19

data_processing:
Reads were aligned with Bowtie2 (version 2.4.1)
SAM files were converted to BAM files and PCR duplicate reads were filtered out using SAMtools (version 1.17)
Peak calling was performed using MACS2 (version 2.1.2)
Unique reads mapped to these regions were quantified using featuresCounts (version 2.0.1)
Assembly: hg19
Supplementary files format and content: tab-delimited text file including raw counts for each sample

extract_protocol:
ChIP-seq based protocol
NEBNext® Ultra™ II DNA Library Prep Kit


title: Low expression barcode-variant match

description:
Library name: ADSLxS_Barcode_Variant
a region of the plasmid containing the barcodes and ADSL variants was excised from the vector followed by BluePippin purification and sequenced using PacBio Sequel II.

organism: synthetic construct

source_name: Synthetic DNA

value: Synthetic DNA


title: PPL1-gamma1pedc dopamine neurons, Stromalin KD, 3rd instar larva, biol rep 3

city: Edmonton

first: Anna

last: Phan

state: AB

address: Z-1111 BioSci

department: Bioinformatics and Statistics Core

institute: UF Scripps Biomedical Research

description:
Library name: 283_5
Column name 283_5

data_processing:
Aligned using star version 2.5.2a aligner and gene abundance was estimated with python version 2.7.11, and htseq version 0.9.1.
Assembly: fly-ENSEMBL-bdgp6.r91 : D.melanogaster-ENSEMBL-BDGP6.r91 : downloaded March 29, 2018
Supplementary files format and content: Excel spreadsheet with raw gene counts, normalized gene counts, TPM counts, and KD vs WT analysis with DESeq2

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: Larvae were raised on standard fly food, raised at 25dC under 12h light:12h dark cycle. Brains were harvestsed 120h after egg layging.

extract_protocol:
Brains were dissected, dissociated, and GFP+ neurons where manually collected using a glass pipette. There were 25 neurons collected per sample.
NuGEN Ovation SoLo RNA-seq kit with SoLo AnyDeplete Probe Mix for Drosophila was used for library preparation.

treatment_protocol: GFP and RNAi targetting stromalin was expressed using the GAL4-UAS system in the PPL1-gamma1pedc neurons

value: Brain

value: Dopamine Neuron

value: KD


title: ChIPseq_GATA2_Gata2_G320D_rep2

description: Library name: Id18


title: PPL1-gamma1pedc dopamine neurons, Control, 3rd instar larva, biol rep 3

description:
Library name: 283_6
Column name 283_6


title: Painful diabetic peripheral neuropathy root ganglion, replicate 3

first: Zhenxuan

last: Gao

state: Chaoyang

address: No.2 yinghua east street

institute: Chinese Academy of  Medical Sciences & Peking Union Medical College

description: Library name: PDPN85

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastpand the low quality reads were removed to obtain the clean reads.The clean reads were mapped to the reference genome  using HISAT2. The read counts of each gene were obtained by HTSeq-count and then FPKM of each gene was calculated.
Assembly: mRatBN7.2
Supplementary files format and content: counts_all.csv include all samples mRNA count data
Supplementary files format and content: lnc-count. csv include all samples lnc-RNA data

source_name: dorsal root ganglion

growth_protocol: The animals were maintained under standard conditions of 12-h light/dark cycle and room temperature. Food and water were available ad libitum.

extract_protocol:
After confirmation of the PDPN model by behavioral and electrophysiological assessments, the rats were euthanized and the dorsal root ganglia (DRGs) from the L4–L6 spinal segments were rapidly dissected, snap-frozen in liquid nitrogen, and stored at –80 °C.Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with qualified purity, quantity and integrity were used for subsequent library construction. Ribo-off rRNA Depletion Kit（vazyme, Nanjing, China）was used to remove ribosomal RNA
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Animals were randomly divided into two groups: PDPN group and control group . After 12 h of fasting, rats of the PDPN group were treated with streptozotocin (STZ, Sigma-Aldrich, United States) injection at a dose of 45 mg/kg body weight dissolved in 0.05 mol/L citrate buffer, pH 4.5 at 4°C .The other group was treated with a single intra-peritoneal injection of an equal volume of citrate buffer without STZ as control. After STZ treatment for a week, the glucose meter was used to monitor random blood glucose levels of all the rats from tail vein blood draws.  Rats which exhibited blood glucose levels of 16.7 mM or higher were diagnosed with diabetes  and enrolled in this study. Rats were kept to establish the model of DPN for 8 weeks . All animals survived until the end of the experiments.

value: dorsal root ganglion

value: SD

value: STZ injection


title: ChIPseq_GATA2_Gata2_WT_rep2

description: Library name: Id16


title: Painful diabetic peripheral neuropathy root ganglion, replicate 2

description: Library name: PDPN80


title: Adult rat central canal associated spinal cord cells, ex vivo expanded (Rat_1)

description:
Library name: Rat_577942
Adult rat central canal associated spinal cord cells, ex vivo expanded.


title: L7_flower_buds_rep3

city: Kayseri

first: Saffet

last: Teber

address: Erciyes University Faculty of Agriculture, Köşk Mahallesi, Fuat Sezgin Caddesi No:12, Melikgazi/KAYSERİ

country: Turkey

institute: Erciyes University

description: Library name: L7_rep3

data_processing:
ACGT101-miR pipeline (LC Sciences, Houston, TX, USA).
Assembly: CDC Redberry genome v2.0
Supplementary files format and content: xlsx file contains both raw and normalized counts

organism: Lens culinaris

source_name: Flower buds

extract_protocol:
Total RNA was isolated from pooled samples using TRI Reagent (Sigma Life Science) and the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich), following the manufacturer’s protocols.
Small RNA libraries were prepared using the Illumina TruSeq Small RNA Preparation Kit according to the manufacturer’s protocol.

value: Flower buds


title: PPL1-gamma1pedc dopamine neurons, Control, 3rd instar larva, biol rep 2

description:
Library name: 283_4
Column name 283_4


title: ChIPseq_Input_Gata2_WT

description: Library name: Id15


title: High expression barcode-variant match

description:
Library name: ADSLxL_Barcode_Variant
a region of the plasmid containing the barcodes and ADSL variants was excised from the vector followed by BluePippin purification and sequenced using PacBio Sequel II.


title: Painful diabetic peripheral neuropathy root ganglion, replicate 1

description: Library name: PDPN73


title: PPL1-gamma1pedc dopamine neurons, Stromalin KD, 3rd instar larva, biol rep 2

description:
Library name: 283_3
Column name 283_3


title: ChIPseq_GATA2_Gata2_G320D_rep1

description: Library name: Id14


title: Painful diabetic peripheral neuropathy root ganglion, replicate 4

description: Library name: PDPN88


title: L7_flower_buds_rep1

description: Library name: L7_rep1


title: ChIPseq_GATA2_Gata2_WT_rep1

description: Library name: Id13


title: ChIPseq_LMO4_Gata2_G320D_rep2

description: Library name: Id11


title: PPL1-gamma1pedc dopamine neurons, Control, 3rd instar larva, biol rep 1

description:
Library name: 283_2
Column name 283_2


title: control dorsal root ganglion, replicate 5

description: Library name: CON98


title: control dorsal root ganglion, replicate 6

description: Library name: CON99


title: control dorsal root ganglion, replicate 4

description: Library name: CON97


title: L7_flower_buds_rep2

description: Library name: L7_rep2


title: L6_young_pods_rep3

description: Library name: L6_rep3

source_name: Young pods

value: Young pods


title: ChIPseq_LMO4_Gata2_WT_rep2

description: Library name: Id10


title: L6_young_pods_rep2

description: Library name: L6_rep2


title: PPL1-gamma1pedc dopamine neurons, Stromalin KD, 3rd instar larva, biol rep 1

description:
Library name: 283_1
Column name 283_1


title: control dorsal root ganglion, replicate 3

description: Library name: CON96


title: ChIPseq_LMO4_Gata2_G320D_rep1

description: Library name: Id8


title: L6_young_pods_rep1

description: Library name: L6_rep1


title: L5_flowers_rep2

description: Library name: L5_rep2

source_name: Flowers

value: Flowers


title: control dorsal root ganglion, replicate 2

description: Library name: CON95


title: ChIPseq_LMO4_Gata2_WT_rep1

description: Library name: Id7


title: control dorsal root ganglion, replicate 1

description: Library name: CON90


title: ChIPseq_LMO2_Gata2_G320D_rep2

description: Library name: Id5


title: L4_stem_rep3

description: Library name: L4_rep3

source_name: Stem

value: Stem


title: L5_flowers_rep1

description: Library name: L5_rep1


title: MDA-MB-231 cells treated by exosomes  derived from M2 macrophage SAMPLE 3

city: hangzhou

first: wei

last: pan

address: 杭州医学院滨康路587号

institute: hangzhou medical college

hyb_protocol: In the discovery genome-wide miRNA expression analysis, MDA-MB-231 cell suspension miRNA samples were hybridized individually and blind to operator for 42 hours onto Affymetrix GeneChip miRNA 4.0 Array (Applied Biosystems #902411; product datasheet), which contains probes for more than 4,603 human miRNAs (2,578 mature miRNAs and 2,025 pre-miRNAs) following manufacturer instructions.

scan_protocol: Images were scanned using an Affymetrix GeneChip Scanner 3,000 7G following the manufacturer's recommendations. Files generated by the Affymetrix GeneChip Command Console (AGCC) were processed with the Expression Console software to determine the data quality.

data_processing: Files generated by the Affymetrix GeneChip Command Console (AGCC) were processed with the Expression Console software to determine the data quality. Microarray raw data were analysed using Partek Genomic Suite v7.0 software applying the robust multi-array average (RMA) background correction model, which allows the relative comparison of miRNA abundance in different arrays.Only miRNAs with fluorescence detection values above 2.4 arbitrary units and a significant expression P-value below 0.05 compared to background were considered expressed in human serum samples

label: biotin

source_name: miRNA extracted from MDA-MB-231 cells treated by  Exosomes from M2 macrophage

label_protocol: standard Affymetrix protocol

growth_protocol: Cells were cultured at 37 °C and 5% CO2 in their preferred medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol: The total RNA of the samples was extracted by Trizol method. The extracted total RNA was checked by NanoDrop 2000 and Agilent Bioanalyzer 2100.

treatment_protocol: experimental group was treated with 400 ug/ml exosomes and cultured for 48 hours.

value: MDA-MB-231 cells

value: treated by exosomes from M2 macrophage


title: MDA-MB-231 cells treated  by  vehicleSAMPLE  3

address: 杭州医学院滨康路587号

source_name: miRNA extracted from MDA-MB-231 cells treated by  vehicle

value: treated by vehicle


title: MDA-MB-231 cells treated by vehicle SAMPLE 1

address: 杭州医学院滨康路587号


title: cardiac tissue of aged mice treated with MLN4924, Rep2

city: Columbus

first: Gang

last: Xin

state: OH

address: 460 W 12th Ave

department: MI&I

institute: The Ohio State University

description: Library name: D2

data_processing:
hisat2 v2.2.1
DESeq2 v1.42.1
clusterProfiler v4.10.0
GSEA desktop software v4.3.3
ssGSEA
Assembly: GRCm38
Supplementary files format and content: CSV containing raw counts

source_name: cardiac tissue

extract_protocol:
Total RNA was isolated from cardiac tissue of young and aged mice treated with vehicle, and aged mice treated with MLN4924 (n = 3 per group), and RNA quality was assessed using an Agilent 2100 Bioanalyzer. Poly(A)+ mRNA was purified using oligo(dT)-attached magnetic beads and fragmented into short pieces using a fragmentation buffer.
First-strand cDNA synthesis was performed using random hexamer primers, followed by second-strand cDNA synthesis. The resulting double-stranded cDNA underwent end repair, 3′ adenylation, and adaptor ligation. Libraries were amplified by PCR, purified with XP beads, eluted in EB buffer, and quality-checked on the Agilent 2100 Bioanalyzer. Double-stranded PCR products were heat-denatured and circularized using a splint oligonucleotide to generate single-stranded circular DNA (ssCir DNA), which served as the final library template. DNA nanoballs (DNBs), each containing >300 copies of a single ssCir DNA molecule, were produced by phi29 polymerase–mediated rolling circle amplification.

value: cardiac tissue

tag: age

value: aged


title: L4_stem_rep2

description: Library name: L4_rep2


title: ChIPseq_LMO2_Gata2_WT_rep2

first: Claus

institute: Weatheral Institute of Molecular Medicine

description: Library name: Id4


title: cardiac tissue of aged mice treated with MLN4924, Rep3

description: Library name: D3


title: ChIPseq_LMO2_Gata2_G320D_rep1

description: Library name: Id2


title: cardiac tissue of aged mice treated with MLN4924, Rep1

description: Library name: D1


title: L4_stem_rep1

description: Library name: L4_rep1


title: cardiac tissue of aged mice, Rep3

description: Library name: C3

value: vehicle


title: HFD-2

first: Yinkun

last: Fu

address: chongqing Rd

department: school of medicine

institute: shanghai jiaotong university

description: Library name: GFP-HFD-2

data_processing:
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
mm10
tab-delimited text file includes raw counts for each sample
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Liver

extract_protocol:
RNA were extracted from livers using  Trizol method.
1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 6 PCR The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Liver


title: HFD-1

description: Library name: GFP-HFD-1


title: MDA-MB-231 cells treated by  vehicle SAMPLE 2

address: 杭州医学院滨康路587号


title: L3_mature_leaves_rep3

description: Library name: L3_rep3

source_name: Mature leaves

value: Mature leaves


title: L3_mature_leaves_rep2

description: Library name: L3_rep2


title: MDA-MB-231 cells treated by exosomes  derived from M2 macrophage SAMPLE 1

address: 杭州医学院滨康路587号

source_name: miRNA extracted from MDA-MB-231 cells treated by Exosomes from M2 macrophage


title: ChIPseq_LMO2_Gata2_WT_rep1

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

description: Library name: Id1


title: MDA-MB-231 cells treated by exosomes  derived from M2 macrophage SAMPLE 2

address: 杭州医学院滨康路587号


title: L3_mature_leaves_rep1

description: Library name: L3_rep1


title: cardiac tissue of aged mice, Rep1

description: Library name: C1


title: ND-2

description: Library name: GFP-ND-2


title: ND-1

description: Library name: GFP-ND-1


title: L2_shoots_rep3

description: Library name: L2_rep3

source_name: Shoots

value: Shoots


title: HIV infected cells, DDX3i and SMACm combination

city: Amsterdam

first: Neeltje

last: Kootstra

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

description: SUPT1 cells infected with HIV-1 NL4-3 Ba-L (2 days), treated with DDX3i FH1321 (50uM) and SMACm AZD5582 (1uM) for 6 hours

data_processing: LightCycler 480 1.5.1.62 SP3 software (Roche, Basel, Switzerland) was used for analysis of relative copy numbers and melting curves. TATA-binding protein (TBP), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and hypoxanthine phosphoribosyltransferase 1 (HPRT1) were included as reference genes to correct for cDNA input.

label: SYBR green

label_protocol: cDNA was produced using the M-MLV Reverse Transcriptase kit (Promega, Madison, WI) and random hexamers (Promega). PCR arrays were using the 384 well plates Apoptosis and Survival Tier 1-4 from Bio-Rad (Hercules, CA, USA), where 384 primer pairs are lyophilized on the plate. 10 ng cDNA was used for qPCR with GoTaq® qPCR Master Mix (Promega, Madison, WI, USA) on the LightCycler 480 System (Roche, Basel, Switzerland). The following cycling conditions were used: denaturation: 95 °C for 2 min; amplification: 40 cycles of 95°C for 5 sec and 60°C for 30 sec, followed by a melting curve stage.

growth_protocol: SUPT1-CCR5 cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM; Thermo Fisher Scientific, Gibco) supplemented with 10% fetal calf serum (FCS; HyClone, Cytiva, Marlborough, MA, USA) and antibiotics (100U/ml penicillin and 100ug/ml streptomycin) (Invitrogen, Carlsbad, CA, USA) at 37°C in a humidified 10% CO2 incubator.

extract_protocol: RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturers’ instructions.

treatment_protocol: Cells were treated with the different compounds (alone or in combination or solvent (DMSO) control for 6 hours. Coumpounds: DDX3i FH1321 (50uM) and SMACm AZD5582 (1uM)

tag: disease state

value: T-cell non-Hodgkin lymphoma that has been engineered (transfection) to express CCR5


title: cardiac tissue of aged mice, Rep2

description: Library name: C2

tag: tissue


title: HIV infected cells, SMACm treated

description: SUPT1 cells infected with HIV-1 NL4-3 Ba-L (2 days), treated with SMACm AZD5582 (1uM) for 6 hours


title: AAV-TBG-Zrsr1_3

description: Library name: Zrsr1HFD-3

extract_protocol:
RNA were extracted from livers using  Trizol method.
1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).


title: AAV-TBG-Zrsr1_2

description: Library name: Zrsr1HFD-2


title: L2_shoots_rep2

description: Library name: L2_rep2


title: cardiac tissue of young mice, Rep3

description: Library name: A3

value: young


title: HIV infected cells, DDX3i treated

description: SUPT1 cells infected with HIV-1 NL4-3 Ba-L (2 days), treated with DDX3i FH1321 (50uM) for 6 hours


title: AAV-TBG-Zrsr1_1

description: Library name: Zrsr1HFD-1


title: L2_shoots_rep1

description: Library name: L2_rep1


title: cardiac tissue of young mice, Rep2

description: Library name: A2


title: cardiac tissue of young mice, Rep1

description: Library name: A1


title: HIV infected cells

description: SUPT1 cells infected with HIV-1 NL4-3 Ba-L (2 days), with DMSO for 6 hours (control condition only containing the solvent)


title: L1_roots_rep2

description: Library name: L1_rep2

source_name: Roots

value: Roots


title: L1_roots_rep3

description: Library name: L1_rep3