title: Rat kidney cortex, DEFND, 56 weeks, rat O15, ATAC, sample aliquot 1

description:
Library name: RAGE24-O15-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.

value: 56 weeks


title: Y007_PSI_CA

status: Public on Apr 12 2026

type: SRA

city: Hangzhou

first: Li

last: Li

state: Zhejiang

address: Shilongshan ST #18, Xihu District

country: China

institute: Westlake University

description:
Library name: Y007_PSI_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing

library_source: other

data_processing:
In the spatio-DARLIN amplicon library, Read 1 (85 bp) contains the spatial barcode, while Read 2 (350 bp) captures the 5′ primer, array sequence, and 3′ primer of three target arrays (CA, TA, RA). To extract the array sequences, Cutadapt was used to sequentially trim Read 2: first removing the 3′ primer from the end of the read (right trimming), and then trimming the 5′ primer from the start (left trimming). Reads that did not contain identifiable primer sequences were discarded.
Then the paired Read 1 was processed with BSTMatrix (v2.4.f.1) to extract spatial barcodes and assign spot coordinates.
Subsequent spot-level quality control included: (i) filtering spots with fewer than 10 reads, (ii) denoising array sequences by correcting single-base errors within a Hamming distance of 1, and (iii) removing ambiguous spots (spots do not have a dominant lineage barcode) using the calculate_read_fraction_per_clone_cell function from the MosaicLineage Python package (https://github.com/ShouWenWang-Lab/MosaicLineage), with parameters read_fraction_per_clone_cell_cutoff = 0.2 and mode = "max".
Finally, UMI counts for each array were aggregated across spots belonging to the same cell mask, based on the cell segmentation results from the spatial transcriptomics preprocessing step.
Assembly: >CA
Assembly: CGCCGGACTGCACGACAGTCGACGATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATACGATACGCGCACGCTATGGAGTCGAGAGCGCGCTCGTCGACTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGAGTCGAGACGCTGACGATATGGAGTCGATACGTAGCACGCAGACGATGGGAGCT
Assembly: >TA
Assembly: TCGCCGGAGTCGAGACGCTGACGATATGGAGTCGACACGACTCGCGCATACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGAGCGCGCTCGTCGACTATGGA
Assembly: >RA
Assembly: GCGCCGGCGAGCGCTATGAGCGACTATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGTCGAGACGCTGACGATATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGAGAGCGCGCTCGTCGACTATGGA
Supplementary files format and content: barcodes.tsv.gz: list of segmented cell IDs
Supplementary files format and content: barcodes_pos.tsv.gz: list of spatial coordinates of segmented cell IDs
Supplementary files format and content: features.tsv.gz: list of clone barcodes
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: features_allele.tsv.gz: list of clone barcodes and mutation details
Library strategy: Spatial Transcriptomics

molecule: other

organism: Mus musculus

source_name: Intestine (proximal)

extract_protocol:
Firstly, we did perfusion on the mice with approximately 20 mL of precooled phosphate buffered saline (PBS) to remove blood, then excised the small intestine and rinsed the intestinal lumen with precooled PBS to remove its contents. Small intestine tissues were carefully cleaned from adipose tissue and divided into three segments equal in length named PSI (Proximal small intestine), MSI (Middle small intestine) and DSI (Distal small intestine). Each segment was cut longitudinally, starting from the most distal portion with the luminal side facing upward, the small intestine was rolled resulting in a Swiss-roll with the distal SI in the center and the proximal SI in the outer portion of the roll. The fresh tissue was then embedded in Optimal Cutting Temperature compound (OCT, Sakura Tissue-TEK) on dry ice and stored at -80 °C.
The BMKMANU S3000 RNA-seq was performed with the BMKMANU S3000 Gene Expression kit (BMKMANU, ST03010). In brief, OCT blocks were cut with a pre-cooled cryostat at 10 μm thickness, and sections were transferred to fit the 6.8*6.8 mm2 oligo-barcoded capture areas on the BMK S3000 slide. The experimental slide with small intestine tissue was fixed and stained with hematoxylin and eosin (H&E) and imaged. Sequence libraries were then processed according to manufacturer’s instructions. After cDNA amplification, cDNA quality inspection was performed using Agilent 2100. Before performing the complete protocol, Tissue Optimization (BMKMANU, ST03003) was performed according to manufacturer’s instructions, and the fluorescent footprint was imaged using a fluorescence microscope. About thirty minutes was selected as optimal permeabilization time. In parallel, we used unfragmented cDNA as starting material and a nested PCR approach to perform targeted amplification with KAPA HiFi HotStart ReadyMix (Roche Applied Science, 07958935001). We amplified each of the three target arrays individually by performing three separate PCR reactions for each sample. We first amplified the CA-, TA-, and RA-array libraries for 9 cycles using a 1/5th of the purified cDNA, the P5_PR1 primer, and either the NGS_CA_R1, NGS_TA_R1, or NGS_RA_R1 primer. The three PCR products were purified, and each was subject to a second PCR with 9 cycles, again using the P5_PR1 primer and either the NGS_CA_R2, NGS_TA_R2, or NGS_RA_R2 primer. Each of the resulting PCR products was further purified and used to perform an indexing PCR for 9 cycles using the primers included in this kit (New England Biosciences, E6609S). We used 0.8X SPRI SELECT REAGENT beads (Beckman Coulter, B23318) to purify the PCR product from each step once except the final indexing PCR product (0.8X, twice purification). The final indexing libraries were pooled and quantified with VAHTS Library Quantification Kit for Illumina (Vazyme, NQ101), and sequenced on an Illumina NovaSeq 6000 using NovaSeq 6000 SP kits (Read 1: 85 cycles; i7 Index: 8 cycles; Read 2: 350 cycles; Illumina, MS-102-2003) with 10% PhiX sequencing control v3 (Illumina, FC-110-3001).

treatment_protocol: To label adult mice, doxycycline (ABCONE, D48978) was administered via drinking water for one week (2 mg/mL, supplemented with 10 mg/mL sucrose) and three intraperitoneal injections (50 μg/g) every other day during the same week.

tag: tissue

value: Intestine (proximal)

tag: age

value: 8 weeks

tag: strain

tag: locus

tag: treatment

value: Dox induction for 1 week

tag: time after_dox_induction

value: 1 week


title: Rat kidney cortex, DEFND, 30 weeks, rat L12, RNA

city: Philadelphia

first: Hanzhi

last: Wang

address: 422 Curie Blvd

country: USA

institute: University of Pennsylvania

description:
Library name: RAGE24-L12-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.

library_source: transcriptomic single cell

data_processing:
Basecalls and sample demultiplexing were performed withh bcl-convert v4.3.6 (for Oracle 8) to generate Fastq files.
ATAC libraries were aligned to rat reference genome with cellranger-atac-2.1.0 to generate fragment maps. Gene expression libraries were mapped to the same rat reference genome and counted with cellranger-8.0.1, and then aggregated without normalization using cellranger-8.0.1. The result aggregated gene expression object was processed with Seurat v4.
Assembly: Rat reference genome GRCr8 supplemented with mitochonrial genome from mRatBN7.2 Assembly.
Supplementary files format and content: Cell Ranger ATAC outputs: [library_id]_filtered_peak_bc_matrix.h5, fragments.tsv.gz, fragments.tsv.gz.tbi
Supplementary files format and content: Cell Ranger individual library outputs: [library_id]_filtered_feature_bc_matrix.h5
Supplementary files format and content: Cell Ranger aggr output filtered feature-barcode matrices HDF5 file of scRNA libraries: RAGE24_single_cell_gex_aggr_filtered_feature_bc_matrix.h5
Supplementary files format and content: RAGE24_single_cell_gex_aggr_annotated_seurat_obj.rds (doublet-filtered, SC-Transformed and annotated Seurat object of aggregated RNA libraries. The file can be loaded into R)
Supplementary files format and content: feature_reference.csv (Cell Ranger aggr feature reference csv file)
Supplementary files format and content: aggregation.csv (cellranger aggr)
Supplementary files format and content: RAGE24_single_cell_gex_aggr_cell_annotation.csv (cell-type-annotated cell barcode information of aggregated gene expression libraries. This was exported from the Seurat object.)

molecule: polyA RNA

organism: Rattus norvegicus

source_name: kidney cortex flash frozen

extract_protocol:
Rat kidneys were dissected immediately following euthanasia and flash-frozen in liquid nitrogen. For each preparation, approximately ~35 mg of frozen tissue was processed. Tissues were mechanically dissociated using a gentleMACS™ Tissue Dissociator and nuclei were released by lysis under standard nuclei isolation conditions. Isolated nuclei were either processed using the standard 10x Genomics Chromium Multiome workflow (RNA + ATAC) or subjected to lithium diiodosalicylate pretreatment following the DEFND-seq protocol (Olsen et al. Nature Methods, 2025) to achieve nucleosome depletion.
Final nuclei suspensions were loaded onto the 10x Genomics Chromium platform for droplet-based single-cell library preparation according to the manufacturer’s protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide-Rev F). Libraries were generated following standard 10x Multiome (scRNA + scATAC) chemistry and sequenced on Illumina platforms.

value: kidney cortex flash frozen

tag: library type

value: RNA

value: 30 weeks

tag: Sex

value: male

tag: library construction

value: DEFND


title: Rat kidney cortex, DEFND, 30 weeks, rat J10, RNA

description:
Library name: RAGE24-J10-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: atacseq_tg, old_sirt6_tg_28

city: Ramat-Gan

first: Haim

middle: Yosef

last: Cohen

address: Max & Anna Webb

country: Israel

institute: Bar-Ilan University

description: Library name: Sample28

library_source: genomic

data_processing:
Adapters were trimmed using the cutadapt tool. Following adapter removal, reads that were shorter than 25 nucleotides were discarded (cutadapt option –m 25).An additional 3 bases were trimmed from the end of the read.
The reads were aligned uniquely to the M. musculus GRCm38 reference genome using bowtie (version 2.0.0). Reads that were mapped to the mitochondrial chromosome were excluded. Duplicate reads were excluded using Picard tools. Fragments that were longer than 120 nucleotides were excluded from the analysis.
Open regions were detected using MACS371. Merged peaks were conducted using Bedtools intersect. Peak annotation was performed using ChIPseeker. Additional analysis used csaw and EdgeR packages in R. Peaks were annotated with genes, defined as the closest gene to the peak.
Differentially accessible peaks were identified using DESeq2. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Assembly: mm10
Supplementary files format and content: csv file of normalized counts for each sample

molecule: genomic DNA

source_name: Liver

extract_protocol: ATAC-Seq Kit from active motif (cat: 53150)

value: Liver

value: old

tag: genotype

value: SIRT6 tg


title: Vector

city: Beijing

first: Jinchen

last: Xu

address: Tiantan xili

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

description: Library name: Sample 1

library_source: transcriptomic

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with Tophat2 software. Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs
Assembly: NC_002645.1
Supplementary files format and content: Gene Expression Profiling  Column A: gene_id, the id of the gene. Column B ~ E: count, the count of mapped reads. Column F ~ I: logCPM by edgeR. Column J ~ Q: annotation of the genes.

molecule: total RNA

organism: Human coronavirus 229E

extract_protocol:
Total RNA was extracted using Trizol reagent
Ribosome profiling was performed by CloudSeq Inc. (Shanghai, China) following the GenSeq Ribo Profile Kit manual (GenSeq, Inc.). Briefly, cycloheximide-treated Huh7 cells were lysed with lysis buffer and digested with nuclease. Ribosome footprints were purified by size-exclusion chromatography, and ribosome-protected fragments were size-selected by polyacrylamide gel electrophoresis (PAGE), followed by rRNA depletion. Purified RNA fragments were end-repaired, ligated with 3' adapters and reverse-transcribed to cDNA. The cDNA products were purified by PAGE, circularized, and amplified by PCR. The resulting libraries were purified and sequenced on a NovaSeq platform (Illumina).

tag: cell line


title: Rat kidney cortex, DEFND, 30 weeks, rat H08, RNA

description:
Library name: RAGE24-H08-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: hnRNPC1

description: Library name: Sample 2


title: Rat kidney cortex, DEFND, 30 weeks, rat I09, ATAC

description:
Library name: RAGE24-I09-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.

library_source: genomic single cell

value: ATAC


title: atacseq_tg, old_sirt6_tg_26

description: Library name: Sample26


title: Rat kidney cortex, DEFND, 30 weeks, rat H08, ATAC

description:
Library name: RAGE24-H08-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.


title: Rat kidney cortex, DEFND, 30 weeks, rat J10, ATAC

description:
Library name: RAGE24-J10-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.


title: Rat kidney cortex, DEFND, 30 weeks, rat G07, RNA

description:
Library name: RAGE24-G07-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: KMT5B_Uninduced_R3

city: New Haven

first: Huanyao

last: Gao

state: Connecticut

address: 300 George St., Suite 901

department: Department of Psychiatry

institute: Yale University

description: Library name: 23PE263

data_processing:
Raw fastq files were quality-checked by FastQC, then mapped to human genome reference hg38 (STAR). GRNA targeted-loci for each sample were extracted (SAMtools). Variation/small insertion/deletion at site of interest and mutation efficiency at corresponding loci was called (CrispRVariants R package), after excluding possible germline variants from Cas9-non-induced samples.
Assembly: GRCh38
Supplementary files format and content: sgRNA target region extracted bam files

organism: Homo sapiens

source_name: iPSC derived cell

growth_protocol: The H1 hESC line with iCas9 (NIHhESC-10-0043), generously provided by the Huangfu Lab, was used to assess the editing efficiency of the gRNAs77,145 and conduct the mitochondrial pooled and arrayed experiments. NPCs were generated using the dual SMAD inhibition approach per the STEMdiff SMADi Neural Induction Kit protocol (STEMCell Technologies, #08581). To validate gene KO, NPCs were transduced with LV particles carrying four gRNAs per target gene. After 48 h of selection with 1 µg/mL puromycin, Cas9 expression was induced by adding dox at 2 µg/mL for 72 h. Following induction, cells were collected for bulk RNA-seq.

extract_protocol:
Total RNA was extracted using TRIzol™ reagent (Invitrogen).
PolyA RNA-seq library preparation and sequencing were conducted at the Yale Center for Genomic Analysis (YCGA)

value: iPSC derived cell

tag: cell type

value: NPC

value: WT

value: DMSO

tag: batch


title: Rat kidney cortex, DEFND, 30 weeks, rat G07, ATAC

description:
Library name: RAGE24-G07-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.


title: Rat kidney cortex, DEFND, 30 weeks, rat I09, RNA

description:
Library name: RAGE24-I09-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: atacseq_tg, old_sirt6_tg_25

description: Library name: Sample25


title: NRXN1_Induced_R1

description: Library name: 23PE107


title: Rat kidney cortex, DEFND, 16 weeks, rat F06, RNA

description:
Library name: RAGE24-F06-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.

value: 16 weeks


title: atacseq_tg, old_sirt6_tg_23

description: Library name: Sample23


title: KMT5B_Uninduced_R1

description: Library name: 23PE261


title: KMT5B_Uninduced_R2

description: Library name: 23PE262


title: Rat kidney cortex, DEFND, 16 weeks, rat F06, ATAC

description:
Library name: RAGE24-F06-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.


title: atacseq_tg, old_sirt6_tg_24

description: Library name: Sample24


title: atacseq_tg, old_sirt6_tg_27

description: Library name: Sample27


title: KMT5B_Induced_R3

description: Library name: 23PE275


title: Rat kidney cortex, DEFND, 16 weeks, rat D04, RNA

description:
Library name: RAGE24-D04-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: Rat kidney cortex, Multiome, 16 weeks, rat C03, RNA

description:
Library name: RAGE24-C03-KYC-LN-01-Multiome-RNA
Gene expression (3'mRNA) part of 10X Genomics single cell multiome.

value: Multiome


title: Rat kidney cortex, DEFND, 16 weeks, rat E05, RNA

description:
Library name: RAGE24-E05-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: atacseq_tg, old_wt_22

description: Library name: Sample22


title: Rat kidney cortex, DEFND, 16 weeks, rat D04, ATAC

description:
Library name: RAGE24-D04-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.


title: Rat kidney cortex, DEFND, 16 weeks, rat E05, ATAC

description:
Library name: RAGE24-E05-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.


title: Rat kidney cortex, Multiome, 16 weeks, rat C03, ATAC

description:
Library name: RAGE24-C03-KYC-LN-01-Multiome-ATAC
ATAC part of 10X Genomics single cell multiome.


title: atacseq_tg, old_wt_21

description: Library name: Sample21


title: Rat kidney cortex, DEFND, 16 weeks, rat C03, RNA

description:
Library name: RAGE24-C03-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: atacseq_tg, old_wt_20

description: Library name: Sample20


title: Rat kidney cortex, DEFND, 16 weeks, rat B02, RNA

description:
Library name: RAGE24-B02-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: atacseq_tg, old_wt_19

description: Library name: Sample19


title: KMT5B_Induced_R2

description: Library name: 23PE274


title: B_KES29 deltapurR::Spc/MNY224_rep3

city: Chicago

first: Mee-Ngan

middle: F.

last: Yap

state: IL

address: 320 E Superior St

department: Microbiology-Immunology

institute: Northwestern University Feinberg School of Medicine

description: Library name: ALS36

data_processing:
Quality control and adapter trimming was performed with bcl2fastq 2.20.0.445.  Read mapping was performed with HISAT2 2.2.0.  Read quantification was performed using Subread’s featureCounts 2.0.1 functionality.  Mapping statistics can be found in the ‘alignment.tsv’ file.  Raw, quantified counts are available in the “hisat2_counts.tsv” file.  Read counts loaded into R 4.0.2 and were normalized using edgeR’s 1.14.5 Trimmed Mean of M values (TMM) algorithm.  Subsequent values were then converted to counts per million (cpm).  Differential expression analysis was performed using edgeR’s exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1.
Assembly: GenBank accession CP000255.1
Supplementary files format and content: Tab separated values (tsv) file showing read couts (cpm) of every locus

organism: Staphylococcus aureus

source_name: whole cell

growth_protocol: S. aureus cells were grown in TSB or RMPI-1640-1% casamino acids until mid-log phase (OD600~ 0.8) at 37ºC.

extract_protocol:
Bacterial cells were disrupted by Lysing Matrix B beads on a MP Biomedical FastPrep 24 instrument for 2 cycles of 40M/s.  Cell lysates were extracted with acidic phenol-chloroform (pH 4.7) at least 2-3 times before subjected to ethanol precipitation. Crude RNAs were further cleaned up using the Qiagen RNeasy mini columns. Final total RNA were digested with Turbo DNase I to remove genomic DNA contamination
Ribo-Zero rRNA depletion and cDNA libraries was performed by SeqCenter (formely MiGS) using Illumina kit.

treatment_protocol: No special treatment

value: whole cell

value: ermB-proficient deltapurR

value: RMPI+1% Cas


title: KMT5B_Induced_R1

description: Library name: 23PE273


title: atacseq_tg, old_wt_18

description: Library name: Sample18


title: B_JE2 deltarae1::Spc/MNY205_rep3

description: Library name: ALS33

value: ermB-minus deltarae1


title: Rat kidney cortex, DEFND, 16 weeks, rat C03, ATAC

description:
Library name: RAGE24-C03-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.

value: kidney cortex flash frozen


title: CHD8_Uninduced_R1

description: Library name: 23PE114


title: CHD8_Uninduced_R2

description: Library name: 23PE115


title: B_JE2 deltapurR::Spc/MNY221_rep3

description: Library name: ALS35

value: ermB-minus deltapurR


title: atacseq_tg, old_wt_17

description: Library name: Sample17


title: B_ermBL-ermB/KES29_rep3

description: Library name: ALS32

value: ermB-proficient


title: B_KES29 deltarae1::Spc/MNY212_rep3

description: Library name: ALS34

value: ermB-proficient deltarae1


title: Rat kidney cortex, DEFND, 16 weeks, rat B02, ATAC

description:
Library name: RAGE24-B02-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.

value: male

value: DEFND


title: CHD8_Uninduced_R3

description: Library name: 23PE116


title: atacseq_tg, old_wt_15

description: Library name: Sample15

value: Liver

value: old


title: B_KES29 deltarae1::Spc/MNY212_rep2

description: Library name: ALS28


title: atacseq_tg, old_wt_16

description: Library name: Sample16


title: B_wt/JE2_rep3

description: Library name: ALS31

value: parental, ermB-minus


title: B_JE2 deltapurR::Spc/MNY221_rep2

description: Library name: ALS29


title: B_KES29 deltapurR::Spc/MNY224_Rep2

description: Library name: ALS30


title: B_JE2 deltarae1::Spc/MNY205_rep2

description: Library name: ALS27


title: CHD8_Induced_R2

description: Library name: 23CS189

value: iPSC derived cell

value: NPC


title: B_ermBL-ermB/KES29_rep2

description: Library name: ALS26


title: atacseq_tg, young_sirt6_tg_14

description: Library name: Sample14

value: young

value: SIRT6 tg


title: CHD8_Induced_R3

description: Library name: 23CS190

value: DMSO


title: CHD8_Induced_R1

description: Library name: 23CS188


title: B_wt/JE2_rep2

description: Library name: ALS25

value: whole cell


title: ASH1L_Uninduced_R3

description: Library name: 24CS120

value: WT


title: B_JE2 deltapurR::Spc/MNY221_rep1

description: Library name: ALS23

value: RMPI+1% Cas


title: atacseq_tg, young_sirt6_tg_13

description: Library name: Sample13


title: atacseq_tg, young_sirt6_tg_12

description: Library name: Sample12


title: ASH1L_Uninduced_R1

description: Library name: 24CS118


title: B_KES29 deltapurR::Spc/MNY224_rep1

description: Library name: ALS24

value: ermB-proficient deltapurR


title: atacseq_tg, young_sirt6_tg_10

description: Library name: Sample10


title: A_JE2 deltarae1::Spc/MNY205_rep3

description: Library name: ALS15

value: ermB-minus deltarae1

value: TSB


title: A_KES29 deltapurR::Spc/MNY224_rep3

description: Library name: ALS18


title: ASH1L_Uninduced_R2

description: Library name: 24CS119


title: atacseq_tg, young_wt_8

description: Library name: Sample8


title: B_wt/JE2_rep1

description: Library name: ALS19


title: B_KES29 deltarae1::Spc/MNY212_rep1

description: Library name: ALS22

value: ermB-proficient deltarae1


title: ASH1L_Induced_R3

description: Library name: 24CS074


title: ASH1L_Induced_R2

description: Library name: 24CS073


title: A_JE2 deltapurR::Spc/MNY221_rep3

description: Library name: ALS17

value: ermB-minus deltapurR


title: A_wt/JE2_rep3

description: Library name: ALS13


title: atacseq_tg, young_sirt6_tg_11

description: Library name: Sample11


title: B_ermBL-ermB/KES29_rep1

description: Library name: ALS20

value: ermB-proficient


title: A_KES29 deltarae1::Spc/MNY212_rep3

description: Library name: ALS16


title: atacseq_tg, young_sirt6_tg_9

description: Library name: Sample9

value: Liver


title: A_KES29 deltapurR::Spc/MNY224_Rep2

description: Library name: ALS12


title: atacseq_tg, young_wt_7

description: Library name: Sample7


title: A_JE2 deltapurR::Spc/MNY221_rep2

description: Library name: ALS11


title: ASH1L_Induced_R1

description: Library name: 24CS070


title: Day77_WT_R3

description:
Library name: 23PE481
PCR amplified transfected sgRNA

data_processing:
Fragments amplified by PCR were sequenced on NovaSeq 6000 sequencer pair end at 150bp with ~10 million reads per sample. Flanking sequence on both side of gRNAs were trimmed using BBDuk, and reads were then mapped to gRNA reference sequences and counted using MAGeCK package150. Raw counts for each gRNA were normalized to counts of scrambled gRNA. Abundance of each gRNA-target genes were then calculated by sum of all gRNAs targeting that gene after excluding gRNAs with low KO-efficiency (<5%)
Assembly: GRCh38
Supplementary files format and content: sgRNA count, text file

growth_protocol: H1-hESC-iCas9 cells were transduced with a pooled gRNA library containing four gRNAs per target gene, with 20% of the library comprising non-targeting gRNAs. Following selection with 1 µg/mL puromycin, the established cell line was used to generate cortical organoids following a well-established protocol151 with slight modifications. In brief, embryoid bodies (EBs) were generated using AggreWell plates (Stemcell Technologies) according to the manufacturer’s instructions. Once formed, EBs were transferred to ultralow-attachment 10 cm plates (Corning) for further culture. Patterning was initiated using StemFlex base media (A3349401, Gibco) supplemented with 100 nM LDN193189 (x) and 10 µM SB431542 (x). The media was refreshed daily. Organoids were cultured on an orbital shaker at 53 rpm for the duration of the protocol. On Day 6, the patterning media was replaced with growth media; Neurobasal A medium (10888022, Gibco), 1× GlutaMAX (35050061, Gibco), and 1× B27 (12587010, Gibco), supplemented with 20 ng/mL FGF (PeproTech) and 20 ng/mL EGF (PeproTech). On Day 14, Cas9 expression was induced by treating the organoids with 2 µg/mL doxycycline (Sigma-Aldrich) for 72 hours. From Day 25, FGF and EGF were replaced with 20 ng/mL BDNF (PeproTech) and 20 ng/mL NT-3 (PeproTech). Media changes were performed every other day. Starting from Day 42, organoids were maintained in growth media without additional supplements. Media was refreshed 2–3 times per week. The organoids were maintained in culture for ~80 days, at which point five organoids from three biological replicates were collected for DNA extraction

extract_protocol:
DNA extraction using the DNeasy Blood & Tissue Kit (#69504, Qiagen)
Extracted DNA was subjected to PCR amplicon sequencing with unique molecular identifiers (UMIs) using a three-step PCR protocol. In the first step (PCR-1), UMI-containing primers (5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTACGTGACGTAGAAAGTAATAATTTCTTGGGT-3’) and (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTN(25252525)NNNNNNNNNACTCGGTGCCACTTTTTCAA-3’) were used for 4 cycles. PCR-2 utilized adaptor primers (5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’) for 22 cycles. PCR-3, performed by the sequencing facility, added sample-specific indexing in 7 additional cycles. The prepared libraries were sequenced on a NovaSeq platform with paired-end 150 bp reads, generating 10 million reads per sample at the Yale Center for Genomic Analysis (YCGA)

value: Forebrain oragnoid, day77

value: Uninduced


title: A_ermBL-ermB/KES29_rep3

description: Library name: ALS14


title: atacseq_tg, young_wt_5

description: Library name: Sample5


title: Day77_WT_R2

description:
Library name: 23PE480
PCR amplified transfected sgRNA

value: iPSC derived cell


title: A_JE2 deltarae1::Spc/MNY205_rep2

description: Library name: ALS9


title: A_ermBL-ermB/KES29_rep2

description: Library name: ALS8


title: A_KES29 deltarae1::Spc/MNY212_rep2

description: Library name: ALS10


title: Day77_WT_R1

description:
Library name: 23PE479
PCR amplified transfected sgRNA


title: A_wt/JE2_rep2

description: Library name: ALS7

value: parental, ermB-minus


title: atacseq_tg, young_wt_4

description: Library name: Sample4

value: young


title: Day77_KO_R3

description:
Library name: 23PE475
PCR amplified transfected sgRNA

value: Pooled 15genes KO


title: A_JE2 deltarae1::Spc/MNY205_rep1

description: Library name: ALS3


title: Day77_KO_R2

description:
Library name: 23PE474
PCR amplified transfected sgRNA


title: A_KES29 deltapurR::Spc/MNY224_rep1

description: Library name: ALS6


title: atacseq_tg, young_wt_6

description: Library name: Sample6


title: atacseq_tg, young_wt_3

description: Library name: Sample3


title: A_JE2 deltapurR::Spc/MNY221_rep1

description: Library name: ALS5


title: A_ermBL-ermB/KES29_rep1

description: Library name: ALS2


title: A_wt/JE2_rep1

description: Library name: ALS1


title: B_JE2 deltarae1::Spc/MNY205_rep1

description: Library name: ALS21


title: atacseq_tg, young_wt_2

description: Library name: Sample2


title: A_KES29 deltarae1::Spc/MNY212_rep1

description: Library name: ALS4


title: atacseq_tg, young_wt_1

description: Library name: Sample1


title: TAg Tumor rep7 (RIP)

city: Suita

first: Shotaro

last: Tatekawa

state: Osaka

address: 2-2(D10), Yamadaoka, Suita-city

department: Departments of Radiation Oncology,

country: Japan

institute: The University of Osaka Graduate School of Medicine

description:
Library name: C07_2
C07; Peak files name

data_processing:
Sequence reads were quality-checked using FastQC to confirm acceptable quality standards.
The mm10 reference genome was used for all analyses.
Read alignment was performed using STAR with default settings, and peak calling was conducted using MACS2 with the following parameters: q-value < 0.01, --nomodel --keep-dup 5.
For gene expression analysis, read counts were quantified using RSEM with control mapping files.
Assembly: mm10
Supplementary files format and content: Peak files were output in narrowpeak, bed, and bdg formats.
Supplementary files format and content: Read count data (raw counts) for each sample were compiled into tab-delimited files.

extract_protocol:
Total RNA extraction was carried out using ISOGEN (NIPPON GENE, Tokyo, Japan), and the isolated RNA was fragmented to approximately 100 nt using ZnCl₂ (FUJIFILM Wako Pure Chemical, Osaka, Japan). RNA fragmentation was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Tokyo, Japan). About 1/20 of the fragmented RNA was reserved as the input control for subsequent RNA sequencing analysis. The remaining RNA was treated with an anti-m6A antibody (#202 003, Synaptic Systems GmbH, Göttingen, Germany) at 4 °C for 2 hours, followed by mixing with pre-washed Pierce™ Protein A/G Magnetic Beads (#10004D, Thermo-Fisher Scientific) in immunoprecipitation buffer at 4 °C for another 2 hours. The mixture underwent magnetic separation. m6A-containing RNA was eluted from the complex using 6.7 mM N6-methyladenosine 5'-monophosphate sodium salt (#M2780, Sigma-Aldrich) at 4 °C for 2 hours, and the methylated RNA was subsequently purified for MeRIP-seq analysis using the RNeasy Mini Kit (QIAGEN, Tokyo, Japan).
RNA libraries were prepared following the manufacturer's protocol with the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA), with the exception of utilizing oligo-dT beads.

treatment_protocol: TAg/Mettl3-depleted mice were generated by administering tamoxifen (2 mg/30 g body weight) to TAg/Mettl3 mice to deplete the transgenic Mettl3. Other mice received no drug treatment.

value: Tumor cell

value: TAg


title: TAg Tumor rep7 (input)

description:
Library name: C07
C07; Column name in genes_counts_matrix.csv


title: old_sirt6_tg_28

description: Library name: Sample28

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt, resulting reads shorter than 30bp were discarded.
Reads were mapped to the M. musculus reference genome GRCm38 using STAR
supplied with gene annotations downloaded from Ensembl (and with EndToEnd option and outFilterMismatchNoverLmax was set to 0.04).
Reads with the same UMI were removed using the PICARD MarkDuplicate tool using the BARCODE_TAG parameter.
Expression levels for each gene were quantified using htseq-count [1], using the gtf above.
Differentially expressed genes were identified using DESeq2 [5] with the betaPrior, cooksCutoff and independentFiltering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg
Assembly: mm10
Supplementary files format and content: csv file of normalized counts for each sample

extract_protocol:
Trizol extraction (Phenol/chlorophorm)
RNA-seq libraries were prepared at the Crown Genomics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science using the INCPM-mRNA-seq. Briefly, the polyA fraction (mRNA) was purified from 500 ng of total input RNA, followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation, and PCR amplification were performed. Libraries were quantified by Qubit (Thermo Fisher Scientific) and TapeStation (Agilent)

value: old

value: SIRT6 tg


title: Day77_KO_R1

description:
Library name: 23PE473
PCR amplified transfected sgRNA


title: D0_WT_R2

description:
Library name: NB23CS164
PCR amplified transfected sgRNA

value: Embroynic stem cell


title: TAg Tumor rep6 (RIP)

description:
Library name: C06_2
C06; Peak files name


title: TAg Tumor rep6 (input)

description:
Library name: C06
C06; Column name in genes_counts_matrix.csv


title: old_sirt6_tg_27

description: Library name: Sample27


title: D0_WT_R1

description:
Library name: NB23CS163
PCR amplified transfected sgRNA


title: TAg Tumor rep5 (RIP)

description:
Library name: C05_2
C05; Peak files name


title: old_sirt6_tg_26

description: Library name: Sample26


title: CAL27-788-PBS-2

city: Shanghai

first: Zhichao

last: Ai

state: Shanghai

address: 371 Lishizhen Road

department: Oncology

institute: China Innovation Center of Roche (CICoR)

description:
Library name: CAL27-788-PBS-2
CAL27_WT_PBS

data_processing:
Reads were mapped to the mm10 genome using STAR with the options: “—runMode alignReads –outFilterMismatchNmax 2.” Uniquely mapped read pairs were counted over annotated genes using feature Counts with the options: “-T 18 -s 2 -Q 255.” Differential expression was then analysed with DESeq2
Assembly: GRCh38/GRCm38
Supplementary files format and content: Matrix files

growth_protocol: All cell lines were passed and cultured at 37°C with 5% CO2 in appropriate media. The cells in their exponential growth phase were harvested and used for cellular and in vivo assays.

extract_protocol:
After RNA isolation, oly-A selected mRNA libraries were sequenced on Illumina HiSeq4000 yielding 20-30x106 150 b.p. paired end reads per sample. Total RNAs were extracted using RNeasy mini kit (Qiagen) according to the manufacturer’s instruction.
Libraries were generated using the QIAseq 1-Step Amplicon Library Kit. mRNA was enriched via poly-A selection, followed by cDNA synthesis, adapter ligation, and PCR amplification.

value: cancer cells

value: WT

value: PBS


title: TAg Tumor rep4 (input)

description:
Library name: C04
C04; Column name in genes_counts_matrix.csv


title: old_sirt6_tg_25

description: Library name: Sample25


title: TAg Tumor rep5 (input)

description:
Library name: C05
C05; Column name in genes_counts_matrix.csv


title: D0_WT_R3

description:
Library name: NB23CS165A
PCR amplified transfected sgRNA


title: TAg Tumor rep4 (RIP)

description:
Library name: C04_2
C04; Peak files name


title: old_sirt6_tg_24

description: Library name: Sample24


title: CAL27-788-IFNB-2

description:
Library name: CAL27-788-IFNB-2
CAL27_WT_IFNB

value: IFNB


title: CAL27-788-PBS-1

description:
Library name: CAL27-788-PBS-1
CAL27_WT_PBS


title: TAg Tumor rep3 (input)

description:
Library name: C03
C03; Column name in genes_counts_matrix.csv


title: CAL27-788-IFNB-1

description:
Library name: CAL27-788-IFNB-1
CAL27_WT_IFNB


title: CAL27-788-Adar-N173S-2-PBS-2

description:
Library name: CAL27-788-Adar-N173S-2-PBS-2
CAL27_N173S_PBS


title: old_wt_22

description: Library name: Sample22


title: old_sirt6_tg_23

description: Library name: Sample23


title: TAg Tumor rep2 (RIP)

description:
Library name: C02_2
C02; Peak files name


title: L126_Brain_s3

description:
Library name: L126_Brain_s3
Fresh frozen Spatial transcriptome sequencing

data_processing:
Sequences from FASTQ files [R1] were parsed to extract spatial barcode and spatial coordinates using BSTMatrix (v2.4.f.1) pipeline with default settings.
Sequences from FASTQ files [R2] were aligned to mm10 genome to generate gene expression count matrix (spots by genes) using BMTMatrix with default settings.
Cellpose (v2.2.2) was used to segment nuclei from ssDNA-stained images (19954 × 20000 pixels). To approximate whole-cell boundaries, we utilized Cellpose’s flow-field–based mask estimation, specifying a target diameter of 35 pixels (~11.9 μm) to generate cell masks. The gene UMI counts of spots in the same cell mask were summed to generate a cell-level count matrix (cells by genes).
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of segmented cell IDs
Supplementary files format and content: barcodes_pos.tsv.gz: list of spatial coordinates of segmented cell IDs
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: he_roi_small.png: tissue HE image
Supplementary files format and content: Seurat_tidy_HQ.qs: final processed Seurat object in QS format
Supplementary files format and content: FL.tif: ssDNA staining
Supplementary files format and content: HE.tif: HE staining
Supplementary files format and content: HE.txt: encoded spots position
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Firstly, we did perfusion on the mice with approximately 20 mL of precooled phosphate buffered saline (PBS) to remove blood, then excised the small intestine and rinsed the intestinal lumen with precooled PBS to remove its contents. Small intestine tissues were carefully cleaned from adipose tissue and divided into three segments equal in length named PSI (Proximal small intestine), MSI (Middle small intestine) and DSI (Distal small intestine). Each segment was cut longitudinally, starting from the most distal portion with the luminal side facing upward, the small intestine was rolled resulting in a Swiss-roll with the distal SI in the center and the proximal SI in the outer portion of the roll. The fresh tissue was then embedded in Optimal Cutting Temperature compound (OCT, Sakura Tissue-TEK) on dry ice and stored at -80 °C.
The BMKMANU S3000 RNA-seq was performed with the BMKMANU S3000 Gene Expression kit (BMKMANU, ST03010). In brief, OCT blocks were cut with a pre-cooled cryostat at 10 μm thickness, and sections were transferred to fit the 6.8*6.8 mm2 oligo-barcoded capture areas on the BMK S3000 slide. The experimental slide with small intestine tissue was fixed and stained with hematoxylin and eosin (H&E) and imaged. Sequence libraries were then processed according to manufacturer’s instructions. After cDNA amplification, cDNA quality inspection was performed using Agilent 2100. Before performing the complete protocol, Tissue Optimization (BMKMANU, ST03003) was performed according to manufacturer’s instructions, and the fluorescent footprint was imaged using a fluorescence microscope. About thirty minutes was selected as optimal permeabilization time.

treatment_protocol: To label adult mice, doxycycline (ABCONE, D48978) was administered via drinking water for one week (2 mg/mL, supplemented with 10 mg/mL sucrose) and three intraperitoneal injections (50 μg/g) every other day during the same week. To label embryonic-stage mice, pregnant dams were anesthetized and injected a single dose of doxycycline (50 μg/g) through the retro-orbital route.

value: Brain

value: 7 weeks

value: Dox at E10


title: old_wt_21

description: Library name: Sample21

value: Liver


title: L126_Brain_s2

description:
Library name: L126_Brain_s2
Fresh frozen Spatial transcriptome sequencing


title: L126_Brain_s1

description:
Library name: L126_Brain_s1
Fresh frozen Spatial transcriptome sequencing


title: TAg Tumor rep2 (input)

description:
Library name: C02
C02; Column name in genes_counts_matrix.csv


title: Y195_MSI_s3

description:
Library name: Y195_MSI_s3
Fresh frozen Spatial transcriptome sequencing

source_name: Intestine (middle)

value: Intestine (middle)

value: 8 weeks

value: Dox induction for 1 week

value: 1 week


title: TAg Tumor rep3 (RIP)

description:
Library name: C03_2
C03; Peak files name

value: Tumor cell


title: old_wt_20

description: Library name: Sample20


title: Y195_MSI_s2

description:
Library name: Y195_MSI_s2
Fresh frozen Spatial transcriptome sequencing


title: old_wt_19

description: Library name: Sample19


title: CAL27-788-Adar-N173S-2-IFNB-2

description:
Library name: CAL27-788-Adar-N173S-2-IFNB-2
CAL27_N173S_IFNB


title: TAg Tumor rep1 (RIP)

description:
Library name: C01_2
C01; Peak files name

value: TAg


title: old_wt_18

description: Library name: Sample18

value: old


title: CAL27-788-Adar-N173S-2-IFNB-1

description:
Library name: CAL27-788-Adar-N173S-2-IFNB-1
CAL27_N173S_IFNB


title: Y195_MSI_s1

description:
Library name: Y195_MSI_s1
Fresh frozen Spatial transcriptome sequencing


title: TAg Tumor rep1 (input)

description:
Library name: C01
C01; Column name in genes_counts_matrix.csv


title: Y195_DSI

description:
Library name: Y195_DSI
Fresh frozen Spatial transcriptome sequencing

source_name: Intestine (distal)

value: Intestine (distal)


title: CAL27-788-Adar-N173S-2-PBS-1

description:
Library name: CAL27-788-Adar-N173S-2-PBS-1
CAL27_N173S_PBS


title: L0927_Brain

description:
Library name: L0927_Brain
Fresh frozen Spatial transcriptome sequencing


title: TAg/Mettl3 Tumor rep3 (RIP)

description:
Library name: B14_2
B14; Peak files name


title: OE33-788-Adar-N173S-41-PBS-2

description:
Library name: OE33-788-Adar-N173S-41-PBS-2
OE33_N173S_PBS


title: Y195_DSI_TA

description:
Library name: Y195_DSI_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing

value: Tigre


title: Y003_PSI, 3 weeks after Dox induction

description:
Library name: Y003_PSI
Fresh frozen Spatial transcriptome sequencing

value: Intestine (proximal)

value: 4 weeks

value: 3 weeks


title: old_wt_17

description: Library name: Sample17

value: WT


title: TAg/Mettl3 Tumor rep3 (input)

description:
Library name: B14
B14; Column name in genes_counts_matrix.csv


title: Y195_PSI

description:
Library name: Y195_PSI
Fresh frozen Spatial transcriptome sequencing


title: OE33-788-IFNB-1

description:
Library name: OE33-788-IFNB-1
OE33_WT_IFNB

value: cancer cells

value: IFNB


title: TAg/Mettl3 Tumor rep2 (input)

description:
Library name: B13
B13; Column name in genes_counts_matrix.csv


title: OE33-788-IFNB-2

description:
Library name: OE33-788-IFNB-2
OE33_WT_IFNB


title: old_wt_15

description: Library name: Sample15


title: TAg/Mettl3 Tumor rep2 (RIP)

description:
Library name: B13_2
B13; Peak files name


title: OE33-788-Adar-N173S-41-PBS-1

description:
Library name: OE33-788-Adar-N173S-41-PBS-1
OE33_N173S_PBS

value: PBS


title: OE33-788-PBS-2

description:
Library name: OE33-788-PBS-2
OE33_WT_PBS


title: Y007_PSI, 1 week after Dox induction

description:
Library name: Y007_PSI
Fresh frozen Spatial transcriptome sequencing


title: TAg/Mettl3 Liver rep3 (RIP)

description:
Library name: B12_2
B12; Peak files name

value: Liver


title: Y004_PSI, 2 weeks after Dox induction

description:
Library name: Y004_PSI
Fresh frozen Spatial transcriptome sequencing

value: 2 weeks


title: old_wt_16

description: Library name: Sample16


title: TAg/Mettl3 Liver rep3 (input)

description:
Library name: B12
B12; Column name in genes_counts_matrix.csv


title: Fungal_mouse_48h_rep3_1

city: Wuhan

first: Hao

last: Cui

address: Wuhan University, 299 Bayi Road, Wuchang District, Wuhan, Hubei, P.R. China

institute: Wuhan University

description: Library name: Fungal_O572-01-L18_good_1

data_processing:
1.2 Data analysis  The sequences were further processed with a bioinformatic pipeline tool, BMKCloud(www.biocloud.net) online platform.  1.2.1 Quality control  Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.  1.2.2 lncRNA analysis  The transcriptome was assembled using the StringTie based on the reads mapped to the reference genome ..The assembled transcripts were annotated using the gffcompare program .The unknowntranscripts were used to screen for putative lncRNAs. Four computational approaches include CPC2/CNCI/Pfam/CPAT were combined to sort non-protein codingRNA candidates from putative protein-coding RNAs in the unknown transcripts.Putative protein-coding RNAs were filtered out using aminimum length and exon number threshold . Transcripts with lengths more than 200 nt and have more than two exons were selected as lncRNA candidates and further screened using CPC2/CNCI/Pfam/CPAT that have the power to distinguish the protein-coding genes from the non-coding genes. As well as the different types of lncRNAs include lincRNA,introniclncRNA, anti-sense lncRNA ,sense lncRNA were selected using cuffcompare.  1.2.3 Quantification of gene expression levels  StringTie (1.3.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample . Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Assembly: Candida genome from Candida genome database
Supplementary files format and content: txt_all_mrna_counts
Supplementary files format and content: txt_all_mrna_fpkm
Supplementary files format and content: txt_all_lncrna_counts
Supplementary files format and content: txt_all_lncrna_fpkm

organism: Candida albicans

source_name: kidney

extract_protocol:
24 h and 48 h after intravenous injection of Candida albicans into mice, the kidneys were harvested, and RNA was extracted from them. Candida albicans cultured in vitro was used as the control group.
1.1 Sample collection and preparation  1.1.1 RNA quantification and qualification  RNA degradation and contamination, especially DNA contamination, was monitored on 1.5% agarose gels.RNA concentration and purity was mesured using the advanced molecular biology equipment to ensure the use of qualified samples for transcriptome sequencing.  1.1.2 Library preparation for lncRNA-Seq  A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer （ 5X）. First strand cDNA was synthesized using random hexamer primer and Reverse Transcriptase. Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select insert fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP Beads (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR.  1.1.3 Clustering and sequencing  The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS(Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced onan Illumina platform and paired-end reads were generated.

value: kidney


title: OE33-788-PBS-1

description:
Library name: OE33-788-PBS-1
OE33_WT_PBS


title: young_sirt6_tg_12

description: Library name: Sample12

value: young

value: SIRT6 tg


title: young_sirt6_tg_14

description: Library name: Sample14


title: TAg/Mettl3-depleted Liver rep4 (RIP)

description:
Library name: B11_2
B11; Peak files name

value: Tamoxifen


title: Fungal_mouse_48h_rep1_1

description: Library name: Fungal_O572-01-L16_good_1


title: OE33-788-Adar-N173S-41-IFNB-2

description:
Library name: OE33-788-Adar-N173S-41-IFNB-2
OE33_N173S_IFNB


title: L0927_Brain_CA

description:
Library name: L0927_Brain_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing

data_processing:
In the spatio-DARLIN amplicon library, Read 1 (85 bp) contains the spatial barcode, while Read 2 (350 bp) captures the 5′ primer, array sequence, and 3′ primer of three target arrays (CA, TA, RA). To extract the array sequences, Cutadapt was used to sequentially trim Read 2: first removing the 3′ primer from the end of the read (right trimming), and then trimming the 5′ primer from the start (left trimming). Reads that did not contain identifiable primer sequences were discarded.
Then the paired Read 1 was processed with BSTMatrix (v2.4.f.1) to extract spatial barcodes and assign spot coordinates.
Subsequent spot-level quality control included: (i) filtering spots with fewer than 10 reads, (ii) denoising array sequences by correcting single-base errors within a Hamming distance of 1, and (iii) removing ambiguous spots (spots do not have a dominant lineage barcode) using the calculate_read_fraction_per_clone_cell function from the MosaicLineage Python package (https://github.com/ShouWenWang-Lab/MosaicLineage), with parameters read_fraction_per_clone_cell_cutoff = 0.2 and mode = "max".
Finally, UMI counts for each array were aggregated across spots belonging to the same cell mask, based on the cell segmentation results from the spatial transcriptomics preprocessing step.
Supplementary files format and content: barcodes.tsv.gz: list of segmented cell IDs
Supplementary files format and content: barcodes_pos.tsv.gz: list of spatial coordinates of segmented cell IDs
Supplementary files format and content: features.tsv.gz: list of clone barcodes
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: features_allele.tsv.gz: list of clone barcodes and mutation details
Assembly: >CA
Assembly: CGCCGGACTGCACGACAGTCGACGATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATACGATACGCGCACGCTATGGAGTCGAGAGCGCGCTCGTCGACTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGAGTCGAGACGCTGACGATATGGAGTCGATACGTAGCACGCAGACGATGGGAGCT
Assembly: >TA
Assembly: TCGCCGGAGTCGAGACGCTGACGATATGGAGTCGACACGACTCGCGCATACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGAGCGCGCTCGTCGACTATGGA
Assembly: >RA
Assembly: GCGCCGGCGAGCGCTATGAGCGACTATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGTCGAGACGCTGACGATATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGAGAGCGCGCTCGTCGACTATGGA
Library strategy: Spatial Transcriptomics

value: Brain

value: 7 weeks

value: Dox induction for 12h at E10

value: 8 weeks


title: young_sirt6_tg_11

description: Library name: Sample11


title: TAg/Mettl3-depleted Liver rep4 (input)

description:
Library name: B11
B11; Column name in genes_counts_matrix.csv


title: young_sirt6_tg_13

description: Library name: Sample13


title: OE33-788-Adar-N173S-41-IFNB-1

description:
Library name: OE33-788-Adar-N173S-41-IFNB-1
OE33_N173S_IFNB


title: Fungal_mouse_24h_rep3_1

description: Library name: Fungal_O572-01-L15_good_1


title: Fungal_mouse_48h_rep2_1

description: Library name: Fungal_O572-01-L17_good_1


title: young_sirt6_tg_10

description: Library name: Sample10


title: TAg/Mettl3-depleted Liver rep3 (RIP)

description:
Library name: B10_2
B10; Peak files name


title: Fungal_mouse_24h_rep2_1

description: Library name: Fungal_O572-01-L14_good_1


title: OE21-788-PBS-2

description:
Library name: OE21-788-PBS-2
OE21_WT_PBS


title: OE21-788-PBS-1

description:
Library name: OE21-788-PBS-1
OE21_WT_PBS


title: Fungal_mouse_24h_rep1_1

description: Library name: Fungal_O572-01-L13_good_1


title: young_wt_8

description: Library name: Sample8


title: young_sirt6_tg_9

description: Library name: Sample9


title: Fungal_conctrol_0h_rep3_1

description: Library name: Fungal_O572-01-L03_good_1


title: TAg/Mettl3-depleted Liver rep3 (input)

description:
Library name: B10
B10; Column name in genes_counts_matrix.csv


title: TAg/Mettl3-depleted Tumor rep4 (input)

description:
Library name: B9
B9; Column name in genes_counts_matrix.csv

value: Tumor cell


title: young_wt_7

description: Library name: Sample7


title: Fungal_conctrol_0h_rep2_1

description: Library name: Fungal_O572-01-L02_good_1


title: OE21-788-IFNB-1

description:
Library name: OE21-788-IFNB-1
OE21_WT_IFNB


title: OE21-788-IFNB-2

description:
Library name: OE21-788-IFNB-2
OE21_WT_IFNB


title: young_wt_6

description: Library name: Sample6


title: OE21-788-Adar-N173S-2-PBS-2

description:
Library name: OE21-788-Adar-N173S-2-PBS-2
OE21_N173S_PBS


title: young_wt_5

description: Library name: Sample5


title: Fungal_ume6_rep3

description: Library name: C9

data_processing:
2 Data Analysis  2.1 Quality control  Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N 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.  2.2 Reads mapping to the reference genome  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. 2.3 Quantification of gene expression level  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: Candida genome from Candida genome database
Supplementary files format and content: gene_counts.xlsx
Supplementary files format and content: gene_fpkm.xlsx

source_name: strain

extract_protocol:
Total RNA was obtained from the Relov deletion mutant, ume6 deletion mutant, and wild-type strain under hyphal induction conditions.
1.1 Sample Quality Control RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).  1.2 Library preparation for Transcriptome sequencing  Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, 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. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.  1 1.3 Clustering and sequencing (Novogene Experimental Department)  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: strain


title: OE21-788-Adar-N173S-2-PBS-1

description:
Library name: OE21-788-Adar-N173S-2-PBS-1
OE21_N173S_PBS


title: young_wt_4

description: Library name: Sample4


title: TAg/Mettl3-depleted Liver rep2 (RIP)

description:
Library name: B8_2
B8; Peak files name


title: TAg/Mettl3-depleted Liver rep2 (input)

description:
Library name: B8
B8; Column name in genes_counts_matrix.csv


title: TAg/Mettl3-depleted Tumor rep4 (RIP)

description:
Library name: B9_2
B9; Peak files name


title: young_wt_3

description: Library name: Sample3


title: TAg/Mettl3-depleted Tumor rep3 (input)

description:
Library name: B7
B7; Column name in genes_counts_matrix.csv


title: OE21-788-Adar-N173S-2-IFNB-2

description:
Library name: OE21-788-Adar-N173S-2-IFNB-2
OE21_N173S_IFNB


title: TAg/Mettl3-depleted Tumor rep3 (RIP)

description:
Library name: B7_2
B7; Peak files name


title: OE21-788-Adar-N173S-2-IFNB-1

description:
Library name: OE21-788-Adar-N173S-2-IFNB-1
OE21_N173S_IFNB


title: Fungal_ume6_rep1

description: Library name: C7


title: Fungal_ume6_rep2

description: Library name: C8


title: Fungal_conctrol_0h_rep1_1

description: Library name: Fungal_O572-01-L01_good_1


title: TAg/Mettl3-depleted Tumor rep2 (RIP)

description:
Library name: B6_2
B6; Peak files name


title: HGC27-788-PBS-2

description:
Library name: HGC27-788-PBS-2
HGC27_WT_PBS


title: Fungal_relov_rep2

description: Library name: C5


title: HGC27-788-PBS-1

description:
Library name: HGC27-788-PBS-1
HGC27_WT_PBS


title: TAg/Mettl3-depleted Tumor rep2 (input)

description:
Library name: B6
B6; Column name in genes_counts_matrix.csv


title: Fungal_relov_rep3

description: Library name: C6


title: young_wt_2

description: Library name: Sample2


title: KO-MI/R3

city: wenzhou

first: jia

last: sun

address: 109 Xueyuan West Road, Lucheng District,

institute: The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM and  count values for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: heart

value: Prkn ECKO

value: MI/R


title: Fungal_relov_rep1

description: Library name: C4


title: TAg/Mettl3 Liver rep2 (input)

description:
Library name: B5
B5; Column name in genes_counts_matrix.csv


title: Fungal_WT_rep3

description: Library name: C3


title: HGC27-788-IFNB-1

description:
Library name: HGC27-788-IFNB-1
HGC27_WT_IFNB

value: cancer cells

value: WT

value: IFNB


title: Fungal_WT_rep2

description: Library name: C2


title: TAg/Mettl3 Liver rep1 (RIP)

description:
Library name: B4_2
B4; Peak files name

value: Liver


title: KO-MI/R1


title: HGC27-788-Adar-N173S-21-PBS-2

description:
Library name: HGC27-788-Adar-N173S-21-PBS-2
HGC27_N173S_PBS

value: PBS


title: HGC27-788-IFNB-2

description:
Library name: HGC27-788-IFNB-2
HGC27_WT_IFNB


title: KO-MI/R2


title: TAg/Mettl3 Liver rep1 (input)

description:
Library name: B4
B4; Column name in genes_counts_matrix.csv


title: HGC27-788-Adar-N173S-21-PBS-1

description:
Library name: HGC27-788-Adar-N173S-21-PBS-1
HGC27_N173S_PBS


title: KO-Sham4

value: Sham


title: TAg/Mettl3 Liver rep2 (RIP)

description:
Library name: B5_2
B5; Peak files name


title: Fungal_WT_rep1

description: Library name: C1


title: TAg/Mettl3 Tumor rep1 (RIP)

description:
Library name: B3_2
B3; Peak files name


title: KO-MI/R4


title: HGC27-788-Adar-N173S-21-IFNB-2

description:
Library name: HGC27-788-Adar-N173S-21-IFNB-2
HGC27_N173S_IFNB


title: KO-Sham3


title: GPR56 KD-LNCaP cells, with testosterone treatment (PTsiRNA_III)

city: Gurugram

first: Gargi

last: Bagchi

state: HARYANA

address: Amity University Haryana. Amity Education Valley Gurugram (Manesar), Haryana 122 413

country: India

institute: Amity University Haryana

description: Library name: sample 12

data_processing:
Quality control of RNA-seq reads was performed using FASTQC, and low-quality or low-complexity reads were removed using Cutadapt. Trimmed reads were aligned to the human reference genome (GRCh38) using STAR, and uniquely mapped reads were retained for downstream analysis. Gene expression levels were quantified using RSEM.
Assembly: Quality control of RNA-seq reads was performed using FASTQC, and low-quality or low-complexity reads were removed using Cutadapt. Trimmed reads were aligned to the human reference genome (GRCh38) using STAR, and uniquely mapped reads were retained for downstream analysis. Gene expression levels were quantified using RSEM.
Supplementary files format and content: csv file include FPKM Values for each sample

source_name: prostate cancer cells

growth_protocol: LNCaP cells were cultured at 37 °C in RPMI 1640 medium (HiMedia, India) supplemented with 10% fetal bovine serum (FBS; Gibco, USA; 26140079) and 1% streptomycin (10 mg/mL)

extract_protocol:
Total RNA was isolated, and RNA concentration was measured using a NanoDrop 1000. RNA integrity was assessed using an Agilent 2100 BioAnalyzer, and all samples used for RNA-seq had RIN values between 8 and 10. Prior to library preparation, all RNA samples underwent DNase treatment.
Sequencing was performed on an Illumina HiSeq 2500 platform using the V4 chemistry to generate single-end reads. Each experimental group consisted of three biological replicates, with matched replicates in the corresponding control group.

value: prostate cancer cells

value: LNCaP


title: young_wt_1

description: Library name: Sample1

value: young


title: TAg/Mettl3 Tumor rep1 (input)

description:
Library name: B3
B3; Column name in genes_counts_matrix.csv


title: KO-Sham2


title: fCLIP of hnRNPC in HeLa S3 cells arrested by proTAME (Low-Density sucore gradient fraction, RNase High)

city: Tel Aviv

first: Daniel

last: Benhalevy

address: Chaim Levanon St 55

institute: Tel Aviv University

description: Library name: fCLIP_hnRNPC_LD_rep2_RNaseHigh

data_processing:
Adapter trimming using cutadapt. Demultiplexing: bcl2fastq. Alignment: STAR aligner (to GRCh38)
Differential expression and binding using DESeq2, and PARalyzer
Assembly: GRCh38
Supplementary files format and content: proTAME_RNAseq_merged_counts_Inputs.txt, proTAME_RNAseq_merged_counts_Inputs_protein_coding.txt (generated for both replicates, linked to the rep1 records)
Supplementary files format and content: groups.csv

source_name: HeLa S3

growth_protocol: HeLa and HeLa S3 cultured in DMEM + 10% FBS at 37°C.

extract_protocol:
Cell extract was sampled for RNA-seq and loaded over a density gradinet. Endogenous hnRNPC was immunoprecipitated for low- and highdensity fractions, and beads were treated with RNaseI, followed by dephosphorylation of the RNA fragment (CIP), 3' ligation using using T4 Rnl2(1–249)K227Q, and phosphorylation (T4 PNK). Flluorescent RNA-protein complex was separated by SDS-PAGE and excised. After proteinase K treatment, RNA was extracted and 5' end labelled with T4 RNA ligase. Following small RNA cDNA library preparation was performed. See Anastasakis et al., PMID:33503264.
For fCLIP: Ligation products were reverse transcribed and amplified by PCR. For RNA-seq: RiboEX extraction; Ribo-Zero Gold depletion; TruSeq Stranded Total RNA Library Prep Gold.

treatment_protocol: Treatment: proTAME 12 µM; 254nm UV crosslinking.

value: HeLa S3

value: proTAME metaphase arrest, 254nm UV, sucrose gradient, RNaseI (0.15 U/µL)


title: TAg/Mettl3-depleted Liver rep1 (RIP)

description:
Library name: B2_2
B2; Peak files name

value: Tamoxifen


title: GPR56 KD-LNCaP cells, with testosterone treatment (PTsiRNA_II)

description: Library name: sample 11


title: HGC27-788-Adar-N173S-21-IFNB-1

description:
Library name: HGC27-788-Adar-N173S-21-IFNB-1
HGC27_N173S_IFNB


title: GPR56 KD-LNCaP cells, with testosterone treatment (PTsiRNA_I)

description: Library name: sample 10


title: fCLIP of hnRNPC in HeLa S3 cells arrested by proTAME (Low-Density sucore gradient fraction, RNase Low)

description: Library name: fCLIP_hnRNPC_LD_rep1_RNaseLow

value: proTAME metaphase arrest, 254nm UV, sucrose gradient, RNaseI (0.015 U/µL)


title: TAg/Mettl3-depleted Liver rep1 (input)

description:
Library name: B2
B2; Column name in genes_counts_matrix.csv


title: KO-Sham1


title: GPR56 KD-LNCaP cells, with no testosterone treatment (mTsiRNA_III)

description: Library name: sample 9


title: TAg/Mettl3-depleted Tumor rep1 (RIP)

description:
Library name: B1_2
B1; Peak files name

value: Tumor cell


title: WT-MI/R4

value: heart


title: fCLIP of hnRNPC in HeLa S3 cells arrested by proTAME (High-Density sucore gradient fraction, RNase High)

description: Library name: fCLIP_hnRNPC_HD_rep2_RNaseHigh


title: GPR56 KD-LNCaP cells, with no testosterone treatment (mTsiRNA_II)

description: Library name: sample 8


title: fCLIP of hnRNPC in HeLa S3 cells arrested by proTAME (High-Density sucore gradient fraction, RNase Low)

description: Library name: fCLIP_hnRNPC_HD_rep1_RNaseLow


title: TAg/Mettl3-depleted Tumor rep1 (input)

description:
Library name: B1
B1; Column name in genes_counts_matrix.csv


title: WT-MI/R2


title: GPR56 KD-LNCaP cells, with no testosterone treatment (mTsiRNA_I)

description: Library name: sample 7


title: Pt-02 pre-treatment

city: Houston

first: Sanghoon

last: Lee

state: TX

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

description: Library name: 237690

data_processing:
Raw RNA-seq data were processed using an in-house RNA-seq analysis pipeline, which included STAR aligner for aligning reads to the hg19 human reference genome. HTSeq-count (v0.11.0) tool was applied to aligned RNA-seq BAM files to count for each gene how many aligned reads overlap with its exons.
Assembly: hg19
Supplementary files format and content: gene count matrix

source_name: Pt-02 pre-treatment

extract_protocol:
Total RNA was extracted from patients' frozen tissues using the Qiagen RNeasy Mini Kit (Qiagen Inc.) according to the manufacturer’s instructions.
Library preparation was conducted with the SureSelect XT Low Input Reagent Kit (Agilent Technologies) using indexes 1-96 and automated on the Sciclone G3 NGSx Workstation (PerkinElmer, Inc.).

value: ovarian cancer

value: Abema/Ful


title: WT-Sham4


title: WT-LNCaP cells, with testosterone treatment (PT_II)

description: Library name: sample 5


title: Kras/Mettl3 Tumor rep3 (input)

description:
Library name: AR3
AR3; Column name in genes_counts_matrix.csv


title: Pt-13 pre-treatment

description: Library name: 237694

source_name: Pt-13 pre-treatment


title: WT-LNCaP cells, with testosterone treatment (PT_I)

description: Library name: sample 4


title: WT-MI/R1

value: MI/R


title: WT-LNCaP cells, with testosterone treatment (PT_III)

description: Library name: sample 6

value: WT


title: Kras/Mettl3 Tumor rep2 (input)

description:
Library name: AR2
AR2; Column name in genes_counts_matrix.csv


title: WT-Sham2


title: WT-LNCaP cells, with no testosterone treatment (Mt_III)

description: Library name: sample 3


title: WT-MI/R3


title: Kras/Mettl3 Tumor rep2 (RIP)

description:
Library name: AR2_2
AR2; Peak files name


title: Pt-13 post-treatment

description: Library name: 237700

source_name: Pt-13 post-treatment


title: Kras/Mettl3 Tumor rep3 (RIP)

description:
Library name: AR3_2
AR3; Peak files name


title: WT-Sham3


title: Kras/Mettl3 Tumor rep1 (RIP)

description:
Library name: AR1_2
AR1; Peak files name


title: WT-LNCaP cells, with no testosterone treatment (Mt_II)

description: Library name: sample 2


title: Pt-09 pre-treatment

description: Library name: 237691

source_name: Pt-09 pre-treatment


title: Pt-09 post-treatment

description: Library name: 237697

source_name: Pt-09 post-treatment


title: WT-Sham1


title: Kras/Mettl3 Tumor rep1 (input)

description:
Library name: AR1
AR1; Column name in genes_counts_matrix.csv


title: Pt-02 post-treatment

description: Library name: 237696

source_name: Pt-02 post-treatment


title: WT-LNCaP cells, with no testosterone treatment (Mt_I)

description: Library name: sample 1


title: rmt5∆ Rep2

status: Public on Apr 11 2026

city: Buffalo

first: John

middle: C.

last: Panepinto

state: NY

address: 955 Main Street Suite 5240

department: Microbiology and Immunology

institute: University at Buffalo

description:
Sample name:
23

data_processing:
Adapter sequences were trimmed and quality filtering performed using Cutadapt (-q 20 -m 1 -a AGATCGGAAGAG -A AGATCGGAAGAG).
Trimmed reads were then checked for quality using FastQC.
Reads were mapped to the genome using STAR aligner (--runThreadN 6 --runMode alignReads).
Transcipt counts were quantified usin RSEM. (-p 12)
Differential expression was determined using DeSeq2 in R.
Genome_build: FungiDB-54_CneoformansH99
Supplementary_files_format_and_content: rsem counts

organism: Cryptococcus neoformans

source_name: Mid Log Culture

growth_protocol: Cells were grown to midlog stage in YPD at 37 ˚C.

extract_protocol:
RNA was extracted using RNeasy kit  from QIAGEN, and Dnase treated using the QIAGEN on-column RNase free DNase kit.
Library prep was performed using NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: Indicated samples (FLUC) were treated with 3.75 µg/ml fluconazole for 3 hours.

value: rmt5 delta

tag: growth phase

value: Mid Log Culture

value: untreated


title: NT-UnStim-rep1

type: RNA

first: Irene

middle: M

last: Min

address: 6565 Fannin Street

department: Radiology

institute: Houston Methodist Research Institute

hyb_protocol: RNA was quantified using Nanodrop and quality controlled using an Agilent Bioanalyzer following manufacturer's instructions. 100 ng of total RNA from all the samples were used as input for the NanoString nCounter¬Æ CAR-T Characterization panel.

scan_protocol: following manufacturer's instructions

data_processing: After passing internal quality control process, the calculated background was subtracted from raw gene expression data. The data are normalized to positive control and housekeeping genes.

source_name: healthy donor 5

growth_protocol: Primary T cells were isolated via MACS separation using CD4 and CD8 microbeads. T cells were cultured in TexMACS medium with 5% human AB serum, 12.5 ng/ml IL7, and 12.5 ng/ml IL15s. T cells were activated using Dynabeads Human T-Expander CD3/CD28 (ThermoFisher, #11141D) and transduced twice with the ICCR lentivirus on day 1 and day 2 after activation. Nontransduced T cells (NT) were maintained as the same way as ICAM1-specific chimeric costimulatory receptor (ICCR)-T cells. T cells were maintained at a 1 million cell/ml density for 10 days before being cryopreserved in a 1:2 mixture of T cell growth medium: CryoStor CS10 (STEMCELL Technologies, # 07930).

extract_protocol: Total RNA was purified from T cells using RNeasy Mini Kit according to manufacturer's instructions. RNA concentration and quality were analyzed using nanodrop and agilent bioanalyzing total RNA pico series II. Reverse transcription (RT) was done for cDNA synthesis from 100 ng of RNA using reverse transcriptase according to the manufacturer's instructions.

treatment_protocol: ICCR-T cells and NT cells were stimulated with target tumor cells every 2-3 days or left unstimulated for 13-14 days of culture in TexMACS medium with 5% human AB serum, IL7 (12.5 ng/ml), and IL15 (12.5 ng/ml). T cells (both ICCR-T and NT) generated from healthy donor 5 T cells were stimulated by 8505C ATC cells. ATC patient RM-derived T cells (both ICCR-T and NT) were stimulated by autologous RM-ATC cells.

tag: stimulated

value: unstimulated


title: gis2∆ FLUC Rep2

description:
Sample name:
21

value: gis2 delta

value: treated with fluconazole


title: NT-UnStim-rep2

source_name: RM-ATC patient donor


title: H99 Rep2

description:
Sample name:
18

value: Wildtype


title: Panel-Std

source_name: panel std


title: rmt1∆rmt5∆ Rep1

description:
Sample name:
17

value: rmt1 deltarmt5 delta


title: rmt1∆rmt5∆ Rep2

description:
Sample name:
24


title: rmt1∆ Rep2

description:
Sample name:
22

value: rmt1 delta


title: H99 FLUC Rep2

description:
Sample name:
20


title: ICCRT-UnStim-rep1


title: NT-Stim-rep1

value: stimulated by 8505C ATC


title: gis2∆ Rep2

description:
Sample name:
19


title: rmt1∆ Rep1

description:
Sample name:
15


title: gis2∆ Rep1

description:
Sample name:
12


title: H99 Rep1

description:
Sample name:
11


title: NT-Stim-rep2

value: stimulated by RM ATC


title: rmt5∆ Rep1

description:
Sample name:
16


title: gis2∆ FLUC Rep1

description:
Sample name:
14


title: ICCRT-Stim-rep2


title: H99 FLUC Rep1

description:
Sample name:
13


title: beta actin_KO_replicate 3

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: abu dhabi

address: NYUAD Saadiyat Island

country: United Arab Emirates

institute: Biology

description: Library name: Sample 9

data_processing:
ATAC-seq preprocessing. Raw sequencing reads were processed to remove low-quality bases and adapter contamination using Trimmomatic v0.64, with quality control performed via FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Trimming parameters included: trimmomatic_adapter.fa:2:30:10, TRAILING:3, LEADING:3, SLIDINGWINDOW:4:15, and MINLEN:36. High-quality paired-end reads were subsequently aligned to the mouse reference genome (GRCm38) using BWA-MEM v0.65. Resulting alignments were cleaned, sorted, and deduplicated (removal of PCR and optical duplicates) using Picard Tools (http://broadinstitute.github.io/picard). To visualize chromatin accessibility, BigWig coverage tracks were generated from the cleaned BAM files using deepTools (bamCoverage) with the following parameters: --binSize 10, --extendReads, --ignoreDuplicates, and --normalizeUsing RPKM. ENCODE blacklisted regions were excluded. Replicate BigWig files were averaged using the bigwigCompare tool with the --operation mean option. Aggregated signal over genomic regions of interest was calculated and visualized using the computeMatrix function in deepTools.
Assembly: mm10
Supplementary files format and content: bigwig files
Supplementary files format and content: .txt files

source_name: mouse Embryonic stem cells

extract_protocol:
cell lysis and nuclei preparation following  Zymo-Seq ATAC Library Kit Catalog Number: D5458
ATAC protocol following Zymo-Seq ATAC Library Kit Catalog Number: D5458

value: mouse Embryonic stem cells


title: ICCRT-Stim-rep1


title: beta actin_KO_replicate 1

description: Library name: Sample 11


title: beta actin_NLS_replicate 1

description: Library name: Sample 7


title: ICCRT-UnStim-rep2


title: beta actin_KO_replicate 4

description: Library name: Sample 8


title: ICCRT-Stim-rep3


title: beta actin_KO_replicate 2

description: Library name: Sample 10


title: beta actin_NLS_replicate 3

description: Library name: Sample 5


title: beta actin_NLS_replicate 2

description: Library name: Sample 6


title: beta actin_WT_replicate 3

description: Library name: Sample 2


title: B cells,dmso,biol rep 2

first: Fang

last: Yue

address: No. 866 Yuhangtang Road

institute: Zhejiang University

description:
Library name: sample2
Column name in FPKMs_allSamples.txt:A1-2

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT22.
FPKM3 of each gene was calculated by HTSeq-count4.
Assembly: GRCm39
Supplementary files format and content: tab-delimited tex file include FPKM values for each Sample

source_name: B cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent(Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instruction.

value: B cells

value: DMSO


title: B cells,len,biol rep 2

description:
Library name: sample5
Column name in FPKMs_allSamples.txt:A3-2

value: lenvatinib


title: B cells,len,biol rep 3

description:
Library name: sample6
Column name in FPKMs_allSamples.txt:A3-3


title: B cells,dmso,biol rep 3

description:
Library name: sample3
Column name in FPKMs_allSamples.txt:A1-3


title: colon,len,biol rep 2

description:
Library name: sample5
Column name in FPKMs_allSamples.txt:lenv2

source_name: colon

value: colon


title: B cells,dmso,biol rep 1

description:
Library name: sample1
Column name in FPKMs_allSamples.txt:A1-1


title: colon,len,biol rep 1

description:
Library name: sample4
Column name in FPKMs_allSamples.txt:lenv1


title: colon,dmso,biol rep 3

description:
Library name: sample3
Column name in FPKMs_allSamples.txt:ctrt3

value: dmso


title: colon,len,biol rep 3

description:
Library name: sample6
Column name in FPKMs_allSamples.txt:lenv3


title: B cells,len,biol rep 1

description:
Library name: sample4
Column name in FPKMs_allSamples.txt:A3-1


title: beta actin_WT_replicate 2

description: Library name: Sample 3


title: colon,dmso,biol rep 2

description:
Library name: sample2
Column name in FPKMs_allSamples.txt:ctrt2


title: colon,dmso,biol rep 1

description:
Library name: sample1
Column name in FPKMs_allSamples.txt:ctrtl


title: CTD_PP2A_WT_rep2

city: San Francisco

first: Rongze

middle: Olivia

last: Lu

state: CA

address: 1450 3rd St, 4th floor

department: Department of Neurological Surgery

institute: University of California, San Francisco

description:
Library name: CTD_rep2
Column name in FPKM_CTD.txt: CTD_CTL_2

data_processing:
Trimmed sequence reads were mapped to mm39 using RSEM v.1.2.28. Gene expression was quantified as fragments per kilobase of transcript per million (FPKM).
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: CTD

extract_protocol:
Total RNA was isolated using the PureLink™RNA Mini Kit (Invitrogen, 12183025)
Poly(A) enrichment was performed. mRNA was isolated from total RNA using thePoly(A) Purist-MAG kit, libraries were prepared according to manufacturer’s instructions for the NEBNext Ultra IIDirectional RNA kit

value: CTD

value: Medulloblastoma group 3 syngeneic mouse model

value: WT

value: control


title: CTD_PP2A_KO_rep3

description:
Library name: CTD_KO_rep3
Column name in FPKM_CTD.txt: CTD_KO_3

value: PP2Ac KO


title: CTD_PP2A_KO_rep2

description:
Library name: CTD_KO_rep2
Column name in FPKM_CTD.txt: CTD_KO_2


title: CTD_PP2A_KO_rep1

description:
Library name: CTD_KO_rep1
Column name in FPKM_CTD.txt: CTD_KO_1


title: CTD_PP2A_WT_rep3

description:
Library name: CTD_rep3
Column name in FPKM_CTD.txt: CTD_CTL_3


title: SJ_PP2A_WT_rep3

description:
Library name: SJ_CTL_rep3
Column name in FPKM_All_samples.txt: SJ_CTL_3

data_processing:
Trimmed sequence reads were mapped to hg38/mm39 using RSEM v.1.2.28. Gene expression was quantified as fragments per kilobase of transcript per million (FPKM).
Assembly: hg38 and mm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
Supplementary files format and content: csv files include FPKM values for each sample


title: SJ_PP2A_KO_rep2

description:
Library name: SJ_KO_rep2
Column name in FPKM_All_samples.txt: SJ_KO_2


title: SJ_PP2A_KO_rep3

description:
Library name: SJ_KO_rep3
Column name in FPKM_All_samples.txt: SJ_KO_3


title: beta actin_WT_replicate 1

description: Library name: Sample 4


title: SJ_PP2A_KO_rep1

description:
Library name: SJ_KO_rep1
Column name in FPKM_All_samples.txt: SJ_KO_1


title: SJ_PP2A_WT_rep2

description:
Library name: SJ_CTL_rep2
Column name in FPKM_All_samples.txt: SJ_CTL_2


title: CTD_PP2A_WT_rep1

description:
Library name: CTD_rep1
Column name in FPKM_CTD.txt: CTD_CTL_1


title: beta actin_WT_replicate 4

description: Library name: Sample 1


title: SJ_PP2A_WT_rep1

description:
Library name: SJ_CTL_rep1
Column name in FPKM_All_samples.txt: SJ_CTL_1


title: [bEnd.3][Norrin][replicate4]

city: Minneapolis

first: Ha-Neul

last: Jo

state: Minnesota

address: 2001 6th St SE, Lions research building. Room 310

department: Ophthalmology and Visual Neuroscience

institute: University of Minnesota

description: Library name: BEND3-plus-Norrin-4

data_processing:
Data were processed using the DNASTAR Lasergene (version 15) Seqman NGen RNA-Seq module. Differential gene expression analysis, gene ontology analysis, and statistical tests were performed in the DNA STAR Lasergene (version 15) Arraystar module.
Assembly: mouse genome 38p12
Supplementary files format and content: Processed data were exported from the DNASTAR Arraystar module in xlsm format. The exported table contains the number of reads per gene, RPKM values, and the RPKM fold change between groups.

source_name: Brain endothelial cell

growth_protocol: bEnd.3 cells (mouse brain endothelial cells) were cultured and maintained in high glucose DMEM, 10 % FBS, 1 % penicillin/streptomycin

extract_protocol:
Trizol (Invitrogen, 15596026) was used to extract total RNA. DNA was digested (Turbo DNAse free, Invitrogen™ AM1907), and RNA was ribodepleted (Ribozero RNA removal kit, Illumina). The samples RNA integrity values were >8.
Libraries were made using the TakaraBio SMARTer Pico Mammalian kit. Novaseq 150PE was carried out, generating approximately 45 million reads per sample.

treatment_protocol: 24 hrs after seeding, cells were either non-treated or treated with R+D norrin (R+D Systems, 3014‐NR-025, 200 ng/ml) for 24 hr before harvest for RNA extraction.

value: Brain endothelial cell

value: Norrin 200 ng/ml


title: [bEnd.3][Norrin][replicate3]

description: Library name: BEND3-plus-Norrin-3


city: South San Francisco

first: Mitchell

last: Rezzonico

address: 1 DNA Way

institute: Genentech

description: Library name: ENU5994B6G38_E7_neuro2238_S85_R1_001_2367730839

data_processing:
RNA-seq reads were aligned to the mouse reference genome GRCm38 using GSNAP 74. Only uniquely mapping reads were carried forward to downstream analysis. Sample quality was further assessed on a per-plate basis based on total read counts, percentage of reads mapping to the reference genome, and percentage of reads mapping to exons. Reads predominantly mapped to transcript 3’ ends, as expected from the library preparation method.
Assembly: GRCm38

source_name: Whole brain

growth_protocol: Founder C57BL/6NCrl males were treated with 3 x 100 mg/kg ENU (Sigma) and mutations bred to homozygosity in three generations. Generation 3 mice were collected usually between 8-12 weeks old, and an ear notch for DNA and brain samples were collected. Typically, 12 siblings from each pedigree were screened.

extract_protocol:
To homogenize the tissue, RNAlater was removed, and a 5 mm stainless steel bead (Qiagen) and 1.6 mL of Qiazol (Qiagen) was added. The tissue was homogenized using a Tissue Lyser II (Qiagen) for at least 30 minutes until a homogenous solution was confirmed. 400 µL of the homogenate solution was transferred into a new tube and allowed to sit for 5 minutes before adding 100 µL of chloroform (Sigma). The homogenate-chloroform mixture was shaken vigorously, allowed to stand for 2 minutes before centrifugation for 5 minutes at 4°C and 1000 x g. The top clear layer was removed and stored at -80 °C. For RNA extraction, 120 µL was transferred into a QIAgen S-block and processed on the QIAcube using the RNeasy 96 QIAcube HT Kit.
cDNA fragment libraries were constructed using the SMART-Seq® v4 3’ DE Kit (Takara Bio) following manufacturer’s recommendations, with minor modifications. Total RNA samples were processed in batches of 1152, distributed across twelve 96-well plates. For each sample, 4 ng total RNA was used as input for cDNA synthesis, then amplified for 8 cycles, with each sample in a row receiving a unique in-line index. Amplified cDNAs within a row were then combined into a 12-plex pool, cleaned up with Ampure XP beads (Beckman Coulter) and quantified using the Qubit HS DNA assay kit (Thermo Fisher Scientific). For each of the 96 cDNA pools generated from 12 plates, 400 pg were carried into Nextera XT library preparations (Illumina Inc.), each assigned with one of the 96 unique combinations of Forward and Reverse HT Index Primers included in the SMART-Seq® v4 3’ DE kit. After Ampure XP clean up and Qubit quantification, the 96 pools were combined in an equimolar manner to generate a 1152-plex Illumina library.  This library was concentrated with Ampure XP beads, quantified with Qubit and assessed on the TapeStation with the High Sensitivity D1000 assay (Agilent Technologies).

treatment_protocol: Mice were euthanized by cervical dislocation, then whole brains were collected. Each cerebellum was removed and the remaining brain matter was transferred to RNAlater and stored at 4C for up to 5 days.

value: Whole brain

tag: partofsubset

value: FALSE


description: Library name: ENU5994B6G39_E8_neuro2238_S85_R1_001_2367730932


title: [bEnd.3][vehicle][replicate3]

description: Library name: BEND3-minus-Norrin-3

value: untreated


description: Library name: ENU5994B6G37_E6_neuro2238_S85_R1_001_2367731133


description: Library name: ENU5994B6G34_E3_neuro2238_S85_R1_001_2367731328


description: Library name: ENU5994B6G32_E2_neuro2238_S85_R1_001_2367731463


title: [bEnd.3][vehicle][replicate4]

description: Library name: BEND3-minus-Norrin-4


title: [bEnd.3][vehicle][replicate2]

description: Library name: BEND3-minus-Norrin-2


description: Library name: ENU5994B6G313_E11_neuro2238_S85_R1_001_2367731694


description: Library name: ENU5994B6G310_E9_neuro2238_S85_R1_001_2367730844


description: Library name: ENU5994B6G35_E4_neuro2238_S85_R1_001_2367731850


description: Library name: ENU5994B6G311_E10_neuro2238_S85_R1_001_2367731082


title: [bEnd.3][Norrin][replicate1]

description: Library name: BEND3-plus-Norrin-1


description: Library name: ENU5959B6G323_F12_neuro2238_S86_R1_001_2367731467


description: Library name: ENU5959B6G39_F3_neuro2238_S86_R1_001_2367730760


title: [bEnd.3][vehicle][replicate1]

description: Library name: BEND3-minus-Norrin-1


description: Library name: ENU5994B6G31_E1_neuro2238_S85_R1_001_2367731064


description: Library name: ENU5959B6G38_F2_neuro2238_S86_R1_001_2367731571


description: Library name: ENU5959B6G37_F1_neuro2238_S86_R1_001_2367730830


description: Library name: ENU5994B6G314_E12_neuro2238_S85_R1_001_2367731227


description: Library name: ENU5959B6G320_F9_neuro2238_S86_R1_001_2367730895


description: Library name: ENU5959B6G317_F8_neuro2238_S86_R1_001_2367731347


description: Library name: ENU5959B6G321_F10_neuro2238_S86_R1_001_2367731603


description: Library name: ENU5959B6G312_F5_neuro2238_S86_R1_001_2367731855


description: Library name: ENU5994B6G36_E5_neuro2238_S85_R1_001_2367731496


description: Library name: ENU5959B6G322_F11_neuro2238_S86_R1_001_2367731655


description: Library name: ENU5959B6G316_F7_neuro2238_S86_R1_001_2367731025


description: Library name: ENU5937B6G36_F6_neuro2237_S78_R1_001_2367731394


description: Library name: ENU5937B6G37_F7_neuro2237_S78_R1_001_2367731441


description: Library name: ENU5937B6G318_F12_neuro2237_S78_R1_001_2367731329


description: Library name: ENU5937B6G33_F3_neuro2237_S78_R1_001_2367731238


description: Library name: ENU5937B6G32_F2_neuro2237_S78_R1_001_2367731430


description: Library name: ENU5937B6G31_F1_neuro2237_S78_R1_001_2367731520


description: Library name: ENU5937B6G314_F8_neuro2237_S78_R1_001_2367731035


description: Library name: ENU5959B6G313_F6_neuro2238_S86_R1_001_2367731538


description: Library name: ENU5937B6G35_F5_neuro2237_S78_R1_001_2367731007


description: Library name: ENU5937B6G315_F9_neuro2237_S78_R1_001_2367730746


description: Library name: ENU5934B6G39_E9_neuro2237_S77_R1_001_2367731257


description: Library name: ENU5934B6G38_E8_neuro2237_S77_R1_001_2367731511


description: Library name: ENU5934B6G35_E5_neuro2237_S77_R1_001_2367730944


description: Library name: ENU5934B6G36_E6_neuro2237_S77_R1_001_2367730842


description: Library name: ENU5937B6G316_F10_neuro2237_S78_R1_001_2367731605


description: Library name: ENU5959B6G311_F4_neuro2238_S86_R1_001_2367731213


description: Library name: ENU5934B6G37_E7_neuro2237_S77_R1_001_2367730741


description: Library name: ENU5934B6G32_E2_neuro2237_S77_R1_001_2367731573


description: Library name: ENU5934B6G31_E1_neuro2237_S77_R1_001_2367731318


description: Library name: ENU5937B6G313_F4_neuro2237_S78_R1_001_2367730729


description: Library name: ENU5937B6G317_F11_neuro2237_S78_R1_001_2367731865


description: Library name: ENU5934B6G311_E11_neuro2237_S77_R1_001_2367731187


description: Library name: ENU5933B6G38_G6_neuro2237_S79_R1_001_2367731456


description: Library name: ENU5934B6G310_E10_neuro2237_S77_R1_001_2367731305


description: Library name: ENU5934B6G312_E12_neuro2237_S77_R1_001_2367731704


description: Library name: ENU5934B6G33_E3_neuro2237_S77_R1_001_2367731004


description: Library name: ENU5934B6G34_E4_neuro2237_S77_R1_001_2367731790


description: Library name: ENU5933B6G37_G5_neuro2237_S79_R1_001_2367731055


description: Library name: ENU5933B6G32_G2_neuro2237_S79_R1_001_2367731831


description: Library name: ENU5933B6G315_G10_neuro2237_S79_R1_001_2367731140


description: Library name: ENU5933B6G317_G12_neuro2237_S79_R1_001_2367731294


description: Library name: ENU5933B6G31_G1_neuro2237_S79_R1_001_2367731440


description: Library name: ENU5933B6G312_G8_neuro2237_S79_R1_001_2367731219


description: Library name: ENU59085B6G37_H7_neuro2239_S96_R1_001_2367731769


description: Library name: ENU59085B6G34_H5_neuro2239_S96_R1_001_2367731241


description: Library name: ENU59085B6G32_H2_neuro2239_S96_R1_001_2367731412


description: Library name: ENU5933B6G311_G7_neuro2237_S79_R1_001_2367731577


description: Library name: ENU59085B6G33_H4_neuro2239_S96_R1_001_2367731745


description: Library name: ENU5933B6G314_G9_neuro2237_S79_R1_001_2367731539


description: Library name: ENU59085B6G35_H6_neuro2239_S96_R1_001_2367731246


description: Library name: ENU5933B6G33_G3_neuro2237_S79_R1_001_2367731107


description: Library name: ENU59085B6G319_H12_neuro2239_S96_R1_001_2367731664


description: Library name: ENU59085B6G31_H1_neuro2239_S96_R1_001_2367731587


description: Library name: ENU5933B6G36_G4_neuro2237_S79_R1_001_2367731796


description: Library name: ENU5933B6G316_G11_neuro2237_S79_R1_001_2367731134


description: Library name: ENU59085B6G312_H8_neuro2239_S96_R1_001_2367731636


description: Library name: ENU58552B6G36_C7_neuro2231_S27_R1_001_2367731534


description: Library name: ENU59085B6G318_H11_neuro2239_S96_R1_001_2367731154


description: Library name: ENU59085B6G313_H9_neuro2239_S96_R1_001_2367731193


description: Library name: ENU59085B6G36_H3_neuro2239_S96_R1_001_2367730852