title: NUM4039 arcA mutant

city: Kagoshima

first: Yuichi

last: Oogai

address: sakuragaoka 8-35-1

institute: Kagoshima univ.

description: Library name: AT025

data_processing:
The quality of the raw paired-end sequence reads was assessed with FastQC (Version 0.11.7; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The trimmed reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0). The HISAT2-resultant .sam files were converted into .bam files with Samtools (Version 1.9). The raw read counts were normalized with transcripts per million (TPM).
Assembly: GCF_001547775.1
Supplementary files format and content: RawCount_Matrix_ann.txt
Supplementary files format and content: FPKM_Matrix_ann.txt

organism: Aggregatibacter actinomycetemcomitans

growth_protocol: The A actinomycetemcomitans NUM4039 wild type and arcA-inactivated mutant strains were grown in 10 ml of AAGM broth until the optical density at 660 nm (OD660) reached 0.6 (mid-exponential phase).

extract_protocol:
Total RNA was extracted using Isogen II. rRNA was removed using Ribo-Zero Plus rRNA Depletion Kit.
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit.

value: arcA KO

value: aerobic culturing

tag: phase

value: exponential phase


title: H410_EPI_primary_adip

status: Public on Mar 13 2025

type: SRA

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

country: Spain

institute: CIMA

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
Samples were aligned to the Human genome (GRCh38) with STAR (v2.6.1). Gene expression was quantified with quant3p (github.com/ctlab/quant3p).
Downstream analyses were performed in R (v3.6.2). Data transformation, normalization, and differential gene expression analysis were performed with DESeq2. Genes were considered adjusted p value (p-adj)<0.05 and absolute log transformed fold-change (|log2FC|)>1, unless otherwise indicated. vst expression values were used for data visualization and unsupervised analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes filtered counts for all the cell types, treated and control.

molecule: polyA RNA

organism: Homo sapiens

source_name: epiphyseal bone (femoral head)

growth_protocol: Adipocytes and MSCs were harvested from the bone marrow portion of the femoral head and metaphysis and from the SCAT of OA patients. Tissues were minced into small pieces and treated with collagenase. Collection of the floating layer after each centrifugation provided a pure fraction of floating adipocytes and were used directly for total RNA isolation. The pellets containing MSCs after the first wash were placed in 5 cm2 cell culture flasks with DMEM medium supplemented with 10% FBS, 1% Pen-Strep, 1% L-Glutamine and basicFGF 5mg/mL in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions. The transcriptome of very low input (<10ng), degraded or high integrity samples was examined using Takara’s SMARTer Stranded Total RNA-Seq Kit v2 as indicated by the manufacturer.
RNA was fragmented according to the integrity of the sample, then reverse-transcribed (including a template-switching step) and PCR-amplified with primers bearing Illumina adapters and indexes. Next, cDNA originating from rRNA (18S, 28S as well as mitochondrial m12S and m16S) was depleted and the remaining molecules amplified through PCR. Libraries were quantified with Qubit dsDNA HS Assay Kit and their profile was examined using Agilent’s HS D1000 ScreenTape Assay.

treatment_protocol: For differentiation assays, MSCs (5x105/cm2) were cultured in DMEM High Glucose, 10% FBS, 1% Pen-Strep, 1% L-Glutamine supplemented with IBMX (3-isobutyl-1-méthylxanthine) 0.5mM, Dexamethasone 1μM and Indomethacin 50 μM.

tag: tissue

value: epiphyseal bone (femoral head)

tag: cell line

value: primary cell line

tag: cell type

value: adipocytes

tag: genotype

value: Osteoarthritis donor

tag: treatment

value: primary cell


title: Output pool, BM110 WT, Biological Replicate 4

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description:
Library name: WT_Rep4
PCR
SuppTableS4_revision.xlsx

library_source: other

data_processing:
2FAST2Q v 2.6 was used to extract and quantify the protospacer abundance in each sample (parameters: Phred score 30, no mismatches allowed).
Count data were analyzed using R version 4.0.5 and the Bioconductor package DESeq2 version 1.30.1 with default parameters (alpha 0.05, log2FCtest 1). Pairwise comparison was performed for WT, Delta CovR, CovRD53A and CovST282A samples (2 biological replicates), and raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and protospacer with an adjusted p-value lower than 0.05 were considered differentially distributed. (2 biological replicates). Sequencing data from the vectors (input pool) have been used for normalisation.
Supplementary files format and content: 2fast2q output and DESeq 2 output matrix
Library strategy: Amplicon-seq

molecule: other

organism: Streptococcus agalactiae

source_name: bacterial cell

growth_protocol: Input pools in E. coli were grown in LB supplemented with 25 µg/ml kanamycin. Ouput pools in GBS were selected on THY supplemented with 500 µg/ml kanamycin.

extract_protocol:
Plasmid purification were done with QIEprep Spin Miniprep (Qiagen) following instructions for large vector (>10kb).
PCR amplification (25 cycles) were done with Phusion+ high fidelity polymerase (NEB). PCR products were gel purified (QIAquick PCR, Qiagen). Illumina adaptaters were added (PCR-free) following provider workflow (Novogen).

value: bacterial cell

value: WT


title: NUM4039 wild type

country: Japan

description: Library name: WT

molecule: total RNA

tag: strain

value: wild type


title: H410_SCAT_primary_adip

description: Library name: Sample 6

source_name: subcutaneous adipose tissue (gluteus-femoral zone)


title: Input pool, technical replicate 4

description:
Library name: Input_rep4
PCR
SuppTableS4_revision.xlsx

organism: Escherichia coli


title: H410_EPI_diff_adip

description: Library name: Sample 1

value: adipogenic differentiation


title: H524 ASCL1 dox- #1

type: RNA

city: Hamamatsu

first: HIROFUMI

last: WATANABE

state: Select State

institute: Hamamatsu University of Medicine

description: Gene expression data from SCLC cells

hyb_protocol: Incubate the array at 45℃ for 16 hours (60 rpm) using the GeneChip™ Hybridization Oven 645 (Thermo Fisher Scientific) according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned using the GeneChip™ Scanner 3000 7G  (Thermo Fisher Scientific).

data_processing: Expression Console™ Software  (Thermo Fisher Scientific) was used.Raw data of expression values were normalized by Signal Space Transformation-Robust Multiarray Analysis (SST-RMA) method.

label: biotin

source_name: H524 ASCL1 dox-

label_protocol: Total RNA (250 ng) was isolated. Fragmented and labeled cDNA samples were prepared using the GeneChip™ WT PLUS Reagent Kit (#902281, Thermo Fisher Scientific) according to the  the manufacturer’s instructions.

growth_protocol: Cells were maintained in a 5% CO2 and 95% air incubator at 37°C.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (#74136, QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: RNA was extracted from Lu139-NEUROD1 cells, Lu139-EGFP cells, H524-ASCL1 cells, and H524-EGFP cells with or without doxycycline treatment for 72 hours (triplicate for each cell line).

value: small cell lung cancer


title: CAD, differentiated sample 15

status: Public on Mar 12 2025

city: University of Richmond

first: Omar

middle: A.

last: Quintero-Carmona

state: VA

address: 138 UR Drive

department: Biology

country: USA

institute: University of Richmond

description: Library name: CADdif15

data_processing:
Quality of FASTQ files from RNA sequencing were assessed using FastQC v.0.11.5 (Andrews, 2010). Adaptor sequences and low-quality reads were trimmed using Trimmomatic v.0.36 (Bolger, Lohse, & Usadel, 2014). Next, alignment was performed using the STAR v.2.5.1a aligner (Dobin et al., 2013) to map reads to the mouse reference transcriptome, GRCm38.p6, to create a count matrix.
Assembly: GRCm38.p6
Supplementary files format and content: Diff_v_Undiff.xlsx
Supplementary files format and content: DESEQ2 output

organism: Mus musculus

source_name: CAD

growth_protocol: Cells were maintained in growth media (DMEM/F12 media supplemented with 10% fetal bovine serum, penicillin, and streptomycin) in a humidified atmosphere containing 5% CO2 at 37°C

extract_protocol:
RNA was isolated from T25-sized cultures of CAD cells using the RNeasy Plus kit (Qiagen) according the supplied protocol for purification of RNA from animal cells, with the addition of the Qiashredder step prior to loading the lysate on the column as well as the addition of an on-column DNAse digestion prior to washing and eluting the RNA from the column.
Stranded mRNA-seq libraries were built from RNA using Kapa Stranded RNA HyperPrep Kits (Roche). Libraries were pooled in equimolar concentration and were sequenced on the Illumina HiSeq 4000 producing 50 bp single-end reads.

treatment_protocol: To induce differentiation, cells were transitioned to differentiating media (DMEM/F12 media supplemented with penicillin, streptomycin, and ITS supplement (Gemini) containing insulin, transferrin, and selenium).

value: CAD

value: CNS catecholaminergic cell line

value: differentiated, 5 days


title: H524 ASCL1 dox- #2

description: Gene expression data from SCLC cells


title: CAD, differentiated sample 5

description: Library name: CADdif5


title: CAD, differentiated sample 25

description: Library name: CADdif25


title: H410_META_primary_adip

description: Library name: Sample 4

source_name: metaphyseal bone (femoral neck)

value: metaphyseal bone (femoral neck)


title: Output pool, BM110 WT, Biological Replicate 3

description:
Library name: WT_Rep3
PCR
SuppTableS4_revision.xlsx


title: CAD,unidfferentiated sample 1

description: Library name: CADundif1

value: undifferentiated


title: CAD, undifferentiated sample 11

description: Library name: CADundif11


title: CAD, undifferentiated sample 21

description: Library name: CADundif21


title: Osteoblasts, Wild type

city: Seoul

first: Jinman

last: Kim

address: 88, Olympic-ro 43-gil, Songpa-gu

country: South Korea

institute: Asan medical center

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic 0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using TopHat 2.0.13, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.2.1 software in default options.
The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone

growth_protocol: Osteoblasts were cultured in MEMa medium containing 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using TRIzol reagent.
A library was prepared with 1ug of total RNA for each sample by Illumina TruSeq mRNA Sample Prep kit (Illumina, Inc., San Diego, CA, USA).

treatment_protocol: Osteoblast differentiation was induced by treatment of 50 μg/mL ascorbic acid and 10 mM β-glycerophosphate in culture medium for 6 days.

value: Bone

value: Primary cells

value: osteoblasts

value: osteoblast differentiation


title: mTEClo, neonate, EEDcKO, rep3

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

institute: RIKEN IMS

data_processing:
Sequence reads were trimmed to 50bp by fastx_trimmer if needed (FASTX Toolkit v0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/)
Low-quality parts and adapter sequences were trimmed by fastp (v0.20.0)
Trimmed short reads were mapped to the mm10 genome using STAR (v2.7.3a) with a GTF file from EMBL-EBI (GRCm38.99)
Unmapped reads and reads mapped with low-quality scores (MAPQ < 5) were removed by SAMtools (v1.9)
Duplicated reads were filtered out using Picard Tools (v2.21.1)
Mapped reads on each gene were counted using htseq-count (v0.11.2) with --stranded=no option and a GTF file from EMBL-EBI (GRCm38.99)
Raw counts were normalized using edgeR package in R programming language
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts for all samples
Supplementary files format and content: comma-separated values file includes edgeR normalized abundances for all samples

source_name: thymus

extract_protocol:
Mouse thymus was enzymatically  digested and then DAPI-CD45-EpCAM+Ly51-MHCII-high or MHCII-low cells were sorted by FACSAria directly into tubes containing TCL buffer (QIAGEN)
RNA-seq libraries were prepared by applying a RamDA-seq method for single-cell RNA-seq (Hayashi et al., Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, 2018) with some modifications. Specifically, RNA was isolated using RNAClean XP beads (x2.2 vol., Beckman Coulter) directly from the lysis buffer, and was eluted into 10 uL of water containing RNase inhibitor (4u/uL RNasinPlus RNase Inhibitor, Promega). The RNA was denatured by incubating at 65C for 5min, then placed on ice and treated with DNaseI (0.1U/uL DNase I, Amplification Grade, Invitrogen) in 0.25xRT Buffer (PrimeScript RT reagent Kit, Takara) at 30C for 15min. Then cDNA was synthesized in 30uL of 1xRT Buffer containing RT Enzyme Mix (1.5uL of PrimeScript RT Enzyme Mix I, Takara), oligo(dT)-RT primer (0.2uM Oligo(dT)18 Primer, Thermo Scientific), T4 gene 32 protein (0.033mg/mL, NEB) and 1st-NSR primer for mouse (3.3uM, SIGMA custom DNA oligos) by incubating 10min at 25C, 10min at 30C, 30min at 37C, 5min at 50C and 5min at 94C. Next, the second strand was synthesized by adding 5uL of 10x NEB buffer2 (NEB), 1.25uL of dNTP mix (10mM each nt, NEB), 1.5uL of Klenow Fragment (3'→5' exo-, NEB), 5uL of 2nd-NSR primer for mouse (100uM, SIGMA custom DNA oligos), and 7.25uL of DW and incubating 60min at 16C followed by 10min at 70C. The double-stranded cDNA (ds-cDNA) was purified using the AMPure XP beads (x2 vol., Beckman Coulter) and quantified using Qubit (Qubit dsDNA HS Assay Kit, Invitrogen). Then ds-cDNA less than 1ng was applied for Tn5 tagmentation in a 25uL reaction with a homemade Tn5 enzyme prepared as previously described (Picelli et al., Tn5 transposase and tagmentation procedures for massively scaled sequencing projects, 2014 and Hennig et al., Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol, 2018). DNA was purified using AMPure XP beads (x1.7 vol.) and amplified by 10~15 cycles of PCR using indexed primers and KAPA HiFi DNA Polymerase (Roche). The libraries were purified using AMPure XP beads (x1.2 vol), quantified by MultiNA (SHIMADZU) and pooled for next-generation sequencing.

value: thymus

value: MHCII-low epitherial cells

value: EEDcKO

tag: age

tag: Sex

value: female


title: mTEClo, neonate, AireEEDdKO, rep2

value: AireEEDdKO

value: male


title: mTEClo, neonate, EEDcKO, rep4

value: pooled male and female


title: Osteoblasts, Zfp462 knockout

value: Zfp462 KO


title: mTEClo, neonate, AireEEDdKO, rep3


title: Output pool, covRD53A, Biological Replicate 1

description:
Library name: D53A_rep1
PCR
SuppTableS4_revision.xlsx

value: bacterial cell


title: mTEClo, neonate, AireEEDdKO, rep1


title: mTEChi, WT, rep5 [Aire_17]

value: MHCII-high epitherial cells

value: WT


title: mTEChi, WT, rep4 [Aire_16]


title: mTEChi, WT, rep2 [Aire_14]


title: mTEChi, WT, rep1 [Aire_13]


title: mTEClo, WT, rep7 [Aire_7]


title: mTEClo, WT, rep8 [Aire_8]


title: mTEClo, WT, rep5 [Aire_5]


title: mTEClo, WT, rep3 [Aire_3]


title: mTEClo, WT, rep4 [Aire_4]


title: mTEClo, WT, rep2 [Aire_2]


title: mTEClo, WT, rep1 [Aire_1]


title: mTEChi, neonate, AireEEDdKO, rep3 [EED_19]


title: mTEChi, neonate, AireEEDdKO, rep2 [EED_17]


title: mTEChi, neonate, AireKO, rep3 [EED_18]

value: AireKO


title: mTEChi, neonate, AireKO, rep2 [EED_15]


title: mTEChi, neonate, AireKO, rep1 [EED_14]


title: mTEChi, neonate, Ctrl, rep2 [EED_7]

value: Ctrl


title: mTEChi, neonate, EEDcKO, rep1 [EED_11]


title: mTEChi, neonate, Ctrl, rep1 [EED_6]


title: OMP positive Olfactory Sensory Neurons from 72hpf Zebrafish

city: Philadelphia

first: Jonathan

middle: A

last: Raper

state: Pennsylvania

address: 105 Johnson Pavilion

department: Department of Neuroscience

institute: University of Pennsylvania

description:
Library name: 72hpfZebrafishOSNs
72 hpf Sample #97363 with two separate sequencing runs

library_source: transcriptomic single cell

data_processing:
Cell Ranger V3.0.1
Assembly: GRCz11
Supplementary files format and content: Demultiplexed 10x Genomics Files.

organism: Danio rerio

source_name: Olfactory Sensory Tissue

extract_protocol: 10X Genomics V3.3

value: Olfactory Sensory Tissue

value: Olactory Sensory Neurons

value: Neurons

tag: sample age

value: 72 hpf


title: OMP positive Olfactory Sensory Neurons from 48pf Zebrafish

description:
Library name: 48hpfZebrafishOSNs
48 hpf Sample #97364 with two separate sequencing runs

value: 48 hpf


title: Sh_PIE_Gluc

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

data_processing:
FAST5 files for each construct were base-called with Guppy version 6.0.6. Base-called sequences were aligned with Minimap2 (v2.24) (4) in unspliced mode (-x map-ont). The resulting aligned reads were filtered with samtools (v1.6) (5) to keep only primary alignments (-F 0x904) . Further filtered by samtools to keep only the full length reads alignment at least including the 5’ starting 21th bases and 3’ ending 20th bases. The filtered BAM files were calculated for mismatch, deletion and insertion rates by custom scripts. Selected Gluc sequence was used as benchmark. All primer sequences are listed in the supplementary section.
processed data files format and content: full length reads alignment files,tsv.gz
Assembly: synthetic

organism: synthetic construct

source_name: synthetic, IVT

growth_protocol: Full-length accuracy:NA

extract_protocol:
Full-length accuracy:NA
same cDNA template was used for full circular PCR amplification with respective T4, An, Sd, Cb, Sh and Po full circle F and R primers. Then these full circle fragments were sequenced using Nanopore ligation sequencing kit.

treatment_protocol: Full-length accuracy:NA

value: synthetic, IVT


title: Rnl2_PIE_Gluc


title: mTEChi, WT, rep3 [Aire_15]

value: thymus


title: OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish

description:
Library name: 36hpfZebrafishOSNs
36 hpf Sample #97366 with two separate sequencing runs

value: 36 hpf


title: Cb_PIE_Gluc


title: Sd_PIE_Gluc


title: T4_PIE_Gluc


title: SKMEL28 shp16+shATR, rep3

city: Pittsburgh

first: Katherine

last: Aird

state: PA

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

description:
Library name: Sample 9
shp16_shATR_3_fpkm

data_processing:
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCh38) using STAR (v.2.6.1)
Differential expression analysis was done using DESeq2 (v2_1.6.3)
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file includes FPKMs for all samples

growth_protocol: SKMEL28 cells were cultured in DMEM + 5% FBS

extract_protocol:
RNA was harvested by Trizol followed by a Qiagen clean up column with a DNAse step.
The cDNA libraries were prepared using NEBNext Ultra 2 RNA Library Prep Kit for Illumina (New England Biolabs; Cat.# E7775)

treatment_protocol: Cells were transduced with lentivirus expressing shRNA targeting GFP (shCont), p16 (shp16), or ATR (shATR) and selected for 3 days with 1ug/ml puromycin.

value: melanoma

value: p16+ATR knockdown


title: mTEClo, WT, rep6 [Aire_6]

value: MHCII-low epitherial cells

value: male


title: SKMEL28 shp16+shATR, rep2

description:
Library name: Sample 8
shp16_shATR_2_fpkm


title: SKMEL28 shp16, rep2

description:
Library name: Sample 5
shp16_2_fpkm

value: p16 knockdown


title: SKMEL28 shp16, rep3

description:
Library name: Sample 6
shp16_3_fpkm


title: SKMEL28 shp16+shATR, rep1

description:
Library name: Sample 7
shp16_shATR_1_fpkm


title: SKMEL28 shp16, rep1

description:
Library name: Sample 4
shp16_1_fpkm


title: Po_PIE_Gluc


title: SKMEL28 shCont, rep3

description:
Library name: Sample 3
shCont_3_fpkm

value: shGFP control


title: An_PIE_Gluc


title: mTEChi, neonate, AireEEDdKO, rep1 [EED_16]

value: MHCII-high epitherial cells

value: AireEEDdKO

value: pooled male and female


title: SKMEL28 shCont, rep1

description:
Library name: Sample 1
shCont_1_fpkm


title: IgG

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

country: China

institute: Hubei university

description: Library name: sample3

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 5 -e 100 -y -a -m 10 --best --strata
Assembly: hg19
Supplementary files format and content: .bed and .bw files
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
DNA was harvested using Vazyme Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro. 5 ug of total DNA was used for the construction of sequencing libraries.
Total DNA was isolated from HepG2 cells as the instructions provided and the quality of DNA was examined using Agilent Bioanalyzer and Fragment Analyzer according to the manufacturer’s instructions.

value: WT


title: WT_control

description: Library name: sample1


title: WT_treat_rep3

description: Library name: sample21

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 5 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg19
Supplementary files format and content: allGeneCounts.txt

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was isolated from HepG2 cells by standard phenol-chloroform extraction procedures and the quality of RNA was examined using Agilent Bioanalyzer according to the manufacturer’s instructions.


title: WT_treat_rep2

description: Library name: sample20


title: WT_treated

description: Library name: sample2


title: WT_control_rep2

description: Library name: sample14


title: WT_control_rep3

description: Library name: sample15


title: WT_treat_rep1

description: Library name: sample19


title: WT_control_rep1

description: Library name: sample13


title: Mut_treat_rep2

description: Library name: sample8


title: Mut_treat_rep3

description: Library name: sample9


title: Mut_treat_rep1

description: Library name: sample7


title: Mut_control_rep3

description: Library name: sample3


title: Mut_control_rep2

description: Library name: sample2


title: Mut_control_rep1

description: Library name: sample1


title: WT_FT671_DIF_H3K27me3_Rep2

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: patrick G Johnston Centre for Cancer research

country: United Kingdom

institute: Queen's University Belfast

data_processing:
FASTQ files were mapped against human genome (hg19) and Drosophila genome (Dm6) using Bowtie2 (bowtie-bio.sourceforge.net) and default parameters. SAM files were further filtered for uniquely mapped reads and high-quality mapping (-q 10) using SAMtools, and PCR duplicates were removed using MarkDuplicates in PICARD tools. For ChIP-Rx, the total reads in Drosophila BAM files were used to calculate the spike-in normalization factors and were used for downscaling the corresponding human BAM files as described. BAM files were then converted to BED files using BEDTools, and converted to BedGraph using the genomecov function of the BEDtools portfolio. BedGraphs were converted to BigWig files using bedGraphToBigWig from the UCSC tool suite for further visualisation using the Genome Browser hosted by the University of California, Santa Cruz (UCSC).
Assembly: hg19
Supplementary files format and content: BigWig files

source_name: Bone marrow

growth_protocol: SHSY5Y and all cell lines derived from SHSY5Y were cultured in Dulbecco’s modified Eagle’s Medium: Nutrient Mixture F-12 (DMEM/F-12) supplemented with 15% fetal calf serum (FCS), and a combination of Penicillin (100 units/ml) and 100 g/ml Streptomycin (1% Pen/Strep). Cell cultures were grown in T75 flasks and split at 65-80% confluency. After aspiration of the media of the cells, the cells were washed with PBS (Dulbeccos PBS), and then detached by adding PBS containing 0.05% Trypsin and 0.53 mM EDTA. Cells were resuspended and split.  Neuritogenesis in SHSY5Y cells was induced by culturing cells in differentiation medium; Neurobasal plus medium supplemented with 1xB27 vitamin supplement, 2mM Ultraglutamine (Glutamax) and 10µM Retinoic Acid, in the dark for 10 days. The medium was refreshed every 3-4 days.  For phase contrast imaging and immunofluorescence of neuritogenesis in SHSY5Y cells the cells were counted using trypan blue and the Countess after splitting the cell cultures. For phase contrast imaging 1.4x105 cells were split into 35mm dishes for immunofluorescence the 2.3x104 cells were split on 18mm sterilized coverslip in a 12 wells plate one day before the addition of differentiation medium. The cells were evenly dispersed into the medium by resuspending the cells gently. After 10days of differentiation medium, or 13 days for the maintenance experiment immunofluorescence was performed. Immunofluorescence of cells grown in regular culture medium was performed when the cells had reached 50%-70% confluency.   All cells were maintained in an humidified incubator with 5% CO2 at 37oC and routinely checked for mycoplasma using the MycoAlert kit.

extract_protocol:
Biological duplicates of SH-SY5Y cells were grown in two 15 cm dishes per condition, which were processed independently. SH-SY5Y cells were incubated in differentiation medium with or without USP7 inhibitor FT671 (10 M) for 3 days, after which cells were harvested by trypsinization, followed by cell counting. For crosslinking, 20 million cells were resuspended in 10 ml PBS. Cells were fixed on a roller mixer by addition of 1% formaldehyde for 10 minutes. Crosslinking  was quenched by the addition of 125 mM glycine for 5 minutes.  Next, cells were washed twice with PBS and lysed in 1.8 ml lysis buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS supplemented with aprotinin (1g/ml), AEBSF (0.2 mM), leupeptin (1 g/ml) and pepstatin A (1g/ml)). These protease inhibitors were present in all subsequent steps until elution. Cross-linked chromatin was fragmented to approximately 200 base pair (bp) DNA length in a Bioruptor® Standard sonication system. The normalization reference chromatin was prepared from Drosophila S2 cells. Approximately 80 million cells (one 15 cm dish) were harvested and subsequently fixed in 12.5 ml PBS with 1% formaldehyde for 10 minutes as above. After two wash steps with PBS, cells were lysed in 1.2 ml 50 mM Tris pH 8.0, 10 mM EDTA pH 8.0, 0.75% SDS supplemented with protease inhibitors. The Drosophila chromatin was sheared to approximately 200 bp DNA length in a Bioruptor® Pico sonication system. SH-SY5Y chromatin (185 µl) was mixed with S2 chromatin (15 µl), diluted 10 fold in dilution buffer (20 mM Tris, pH 8.0, 2 mM EDTA pH 8.0, 150 mM NaCl and 1% Triton X-100) and cleared by centrifugation at 16000 g for 25 minutes. For BCOR chIP, double amounts of chromatin (370 µl of SH-SY5Y chromatin and 30 µl of S2 chromatin) were used, divided over two tubes. The supernatant was transferred to a new 2 ml tube and incubated overnight at 4 °C with either 5 µl anti-H2AK119ub1 (D27C4, Cell Signaling Technology #8240), 15 µl anti-H3K27me3  (C36B11, Cell Signaling Technology, #9733) or 10 µl anti-BCOR (E6V3R, Cell Signaling Technology, #63972). Next morning, 50 µl of magnetic Dynabeads™ Protein A slurry, which was blocked overnight with 1% BSA in dilution buffer, was added, and incubation was continued for an additional 3.5 hour. Next, beads were washed five times with 20 mM Tris, pH 8.0, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 150 mM NaCl, followed by a final wash step with 20 mM Tris, pH 8.0, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100 and 500 mM NaCl. DNA was eluted with elution buffer (0.1 M NaHCO3, 1% SDS, 0.5 mg/ml proteinase K) for 2 hours at 37 °C, followed by overnight incubation at 65 °C. The eluted DNA was subsequently purified by phenol/chloroform extraction (2 times), followed by ethanol precipitation.
ChIP-Rx-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs, #E7645L) according to the instructions of the manufacturer. AMPure® XP Beads (Beckman Coultier) were used for cleanup. Sequencing was performed by BGI Tech Solutions (Hong Kong) Co., Ltd. on an DNBSEQ-G400 sequencing platform.

value: Bone marrow

value: neuroblastoma


title: WT_DIF_H3K27me3_Rep2


title: WT_FT671_DIF_H2AK119Ub_Rep2


title: WT_DIF_H3K27me3_Rep1


title: SKMEL28 shCont, rep2

description:
Library name: Sample 2
shCont_2_fpkm


title: WT_FT671_DIF_H2AK119Ub_Rep1


title: WT_FT671_DIF_BCOR_Rep1


title: WT_DIF_BCOR_Rep2


title: WT_DIF_BCOR_Rep1


title: SHY_USP7_hetero_UNDIF_Rep1

data_processing:
FASTQ files were aligned against the human reference genome (hg19) STAR and default setting and reads were assigned to RNAs using HTseq-count with the following settings: -m union -s reverse -t exon. DESeq2 (bioconductor.org) was used for differential gene expression analysis. Genes were considered differentially expressed if they fulfilled the following conditions: normalised read counts ≥ 25, fold change ≥ 2, and FDR < 0.05 at one or more conditions. Gene
Assembly: hg19
Supplementary files format and content: Analysed_normalized_counts_table

extract_protocol:
RNA was isolated using the TriPure isolation reagent following the manufacturers protocol for RNA-isolation. The medium was removed from the cells and the TriPure isolation reagent was added directly onto the cells (10cm dish; 5ml TRIPURE reagent,12 wells; 0.5ml TRIPURE reagent). After 5 minutes of incubation the cell lysate(1ml) was transferred into a 1.5-ml Eppedorf tube, after addition of 0.2ml chloroform the tubes were vigorously shaken and incubated at room temperature for 15minutes. Samples were centrifuged for 15 min at 12,000g at 4°C, thereafter the aqueous phase was transferred to a new 1.5-ml Eppedorf tube to which 0.5ml isopropanol was added, mixed and incubated at room temperature for 10minutes, followed by centrifugation 10 min at 12,000g at 4°C. The pellet containing the precipitated RNA was washed twice with 1ml 75% ethanol, dried for 3minutes using the SpeedVac and resuspended in 100μl of nuclease-free water. RNA concentrations and purities were determined using the Nanodrop spectrophotometer.
PolyA-total mRNA sequencing by BGI

value: Undifferentiated


title: SHY_USP7_hetero_NEURO_Rep1


title: SHY_USP7_hetero_UNDIF_Rep2


title: SHY_WT_NEUR_Rep1


title: SHY_USP7_hetero_NEURO_Rep2


title: SHY_WT_UNDIF_Rep2


title: SHY_WT_NEUR_Rep2


title: SHY_WT_UNDIF_Rep1


title: WT_FT671_NEUR_Rep3


title: WT_FT671_NEUR_Rep1


title: p53_BCOR_DKO_NEUR_Rep3


title: WT_FT671_DIF_H3K27me3_Rep1


title: WT_DMSO_NEUR_Rep1


title: p53_BCOR_DKO_NEUR_Rep2


title: p53_BCOR_DKO_UNDIF_Rep3


title: p53_BCOR_DKO_NEUR_Rep1


title: WT_DIF_H2AK119Ub_Rep2


title: p53_BCOR_DKO_UNDIF_Rep2


title: WT_DIF_H2AK119Ub_Rep1


title: WT_FT671_DIF_BCOR_Rep2


title: p53_USP7_DKO_NEUR_Rep2


title: p53_USP7_DKO_NEUR_Rep1


title: p53_USP7_DKO_UNDIF_Rep3


title: p53_USP7_DKO_NEUR_Rep3


title: p53_USP7_DKO_UNDIF_Rep2


title: p53_USP7_DKO_UNDIF_Rep1


title: p53KO_NEUR_Rep2


title: p53KO_UNDIF_Rep2


title: WT_FT671_NEUR_Rep2


title: p53KO_UNDIF_Rep3


title: WT_NEUR_Rep3


title: p53KO_UNDIF_Rep1


title: WT_DMSO_NEUR_Rep2


title: WT_NEUR_Rep2


title: WT_DMSO_NEUR_Rep3


title: WT_UNDIF_Rep2


title: WT_UNDIF_Rep3


title: WT_UNDIF_Rep1


title: H9WT_FT671_NEUR_Rep2

data_processing:
FASTQ reads were mapped against hg19 reference genome using STAR and default setting. Mapped reads were assigned to RNAs using HTseq-count with the following settings: -m union -s reverse -t exon. Samples were further analyzed  by DESeq2 (bioconductor.org) for differential gene expression analysis and with the following cut-off: log2 reads > 5 in at least one sample, FDR<0.05, log2 FC > 1.5). Graphs were generated in R version 4.3.1 on Ubuntu 16.04.5 LTS. GO-term enrichment analysis was performed using gprofiler (https://biit.cs.ut.ee/gprofiler/gost).
Assembly: hg19
Supplementary files format and content: Analysed_normalized_counts_table

source_name: Embryonic

growth_protocol: H9 hES cells were cultured in mTeSR medium supplemented with 1x mTeSR supplement and a combination of Penicillin (100 units/ml) and 100 µg/ml Streptomycin (1% Pen/Strep) using Matrigel (diluted 1:100 in DMEM:F12) coated 6wells plates. The cells were washed with PBS (Dulbeccos PBS), after aspiration of the medium, and then detached by adding TrypLE. After detaching the cells were resuspended in DMEM supplemented with 10% FCS, collected in a sterile 15ml falcon tube and centrifuged 5minutes at 1000rpm. The supernatant was aspirated and the required amount of cells were resuspended in 2ml MTSER containing ROCK-inhibitor (0.01 µM final concentration). After attachment of the cells to the Matrigel (diluted 1:100 in DMEM:F12)  coated 6-wells plate, the medium was replaced by MTSER without ROCK inhibitor.  Differentiation of H9 hES cells into neuronal progenitor cells was acquired by seeding cells on a matrigel (diluted 1:100 in DMEM:F12)  coated 12-wells plate with a density of 18.000 cells/cm2 in mTESR1 medium with ROCK inhibitor (0.01 µM final concentration). After attachment of the cells the medium was replaced by MTSER without ROCK inhibitor. When the cells have reached approximately 90% confluence the cells were washed with PBS and the medium was replaced by Differentiation medium (1x Knockout DMEM, 15% Knockout Serum Replacement, 1x L-glutamine, 1x Non-Essential Amino  Acids (NEAA), ß-mercaptoethanol (50 µM), 1% Pen/Strep) supplemented with dual SMAD inhibitors 2µM A83-10 and 2µM Dorsomorphine. The next five days the medium was refreshed daily, at the sixth day the medium was changed to differentiation medium mixed with Neuronal Stem Cell/progenitor (NSC) medium (1x KnockOut DMEM-F12, 1x L-glutamine, 20ng/ml EGF, 5ng/ml bFGF, 2% StemPro Neural Supplement, 1% Pen/Strep)in a ratio of 1:1 supplemented with 2µM A83-10 and 2µM Dorsomorphine. The medium was refreshed every other day for 4 days. Thereafter the cells could be expanded by splitting. Therefore the cells were washed with PBS, 200-250µl Accutase was used to detach the cells, subsequently the cells were collected with PBS in a sterile 15ml Falcon tube and centrifuged for 4minutes at 1200rpm. The supernatant was aspirated and the cell pellet was resuspended in NSC medium containing  ROCK inhibitor (0.01 µM final concentration) in a matrigel (diluted 1:100 in DMEM:F12) coated wells plate. After attachment of the cells the medium was replaced by NSC medium without  ROCK inhibitor.

value: Embryonic


title: p53_BCOR_DKO_UNDIF_Rep1


title: H9WT_DMSO_NEUR_Rep3


title: H9WT_FT671_NEUR_Rep1


title: H9WT_NEUR_Rep3


title: H9WT_DMSO_NEUR_Rep2


title: H9WT_DMSO_NEUR_Rep1


title: H9WT_NEUR_Rep2


title: H9WT_NEUR_Rep1


title: H9WT_UNDIF_Rep2


title: H9WT_UNDIF_Rep1


title: H9WT_UNDIF_Rep3


title: p53KO_NEUR_Rep1


title: Wh_W_Lo_2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: AA=African American, Wh=White M=male, W=women, Hi=high discrimination, Lo=low discrimination,

data_processing:
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.15 (Martin, 2011). FastQC (v0.11.9) was then performed on the FASTQ files to evaluate quality control metrics (Babraham Bioinformatics). The FASTQ files were aligned to human genome GRCh38 (hg38) Ensembl v100 using Spliced Transcripts Alignment to a Reference (STAR) software version 2.7.3a  (Dobin et al., 2013). featureCounts from the subread module version 2.0.3 were used to create gene counts, with the strand-specific option was set to reverse strand (Liao et al., 2014). Viable data for 59 of the 60 samples were generated and differential expression analysis of the gene counts was done using DESeq2 version 1.30.1 (Love et al., 2014). Only genes with greater than or equal to 10 counts in every sample were included for differential expression analysis. Significant, differentially expressed genes were defined as having a fold change absolute value of ≥ 2, and p-value and false discovery rate (FDR) adjusted p-value < 0.05
Assembly: GRCh38 (hg38) Ensembl v100

source_name: PBMCs

growth_protocol: Fasting blood samples are obtained from participants in the morning and collected in 8-ml Vacutainer® heparinized vials (BD, Franklin Lakes, NJ).  Peripheral blood mononuclear cells were isolated within 3 hours of phlebotomy as detailed previously. After isolation, PBMCs are aliquoted and stored at -80oC.

extract_protocol:
Total RNA was isolated using TRIzol® (Life Technologies) according to the manufacturer’s instructions with the addition of a DNase treatment and overnight precipitation. Samples were resuspended in 12 µl RNase-free water and frozen at -80°C until further use.
Total RNA samples were next depleted of both cytoplasmic and mitochondrial rRNA using Ribo Zero Gold (TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold; Illumina) and then fragmented using divalent cations under elevated temperatures.  Next generation RNA-seq was conducted using HiSeq® SBS Kit v4 (FC-401-4002), HiSeq® SR Cluster Kit v4 – cBotTM (GD-401-4001) and TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold Set B (RS-122-2302). The products were then purified using RNAClean XP Beads.  First strand cDNA was generated using SuperScript II Reverse Transcript (Thermo Fisher Scientific).  Second strand synthesis was achieved using DNA Polymerase I and RNaseH and the products were purified using AMPure XP Beads.
The double stranded cDNAs were prepared for ligation of the multiple indexing adapters by adenylating the 3’ blunt ends of the fragments. One adenine (A) nucleotide was added to the blunt fragments to prevent them from ligating to each other during the adapter ligation reaction. One corresponding thymine (T) nucleotide present on the 3ʹ end of each of the indexing adapters provides a complementary overhang for ligating to the fragment. This strategy ensures a low rate of chimera (concatenated template) formation.  The fragments were then purified using a 2 stage AmpPure XP bead cleanup.  Only fragments with an adapter on both ends can both bind to the surface-bound primers on a flowcell and form clusters.
To enrich the DNA for these fragments, and to amplify the amount of DNA in the library, 15 cycles of PCR were used followed by an additional AmPureXP bead cleanup.  All 60 libraries were pooled and then clustered using an eight-lane high density flowcell (HiSeq® SR Cluster Kit v4 – cBotTM), on an Illumina cBot-2.  These clustered flow cells were then sequenced on an Illumina HiSeq 2500 DNA sequencer for 141 cycles with an additional 8 sequencing cycles to identify the sample indexes (HiSeq® SBS Kit v4). The libraries were sequenced on Illumina HiSeq 2500 and the images were processed with the corresponding Illumina RTA software version v1.18.66.3 and base-calling was performed using bcl2fastq v2.18.0.12.  Libraries were generated with single-end sequencing.

value: PBMCs

tag: race

value: Wh

value: female

tag: discrimination

value: Lo


title: p53KO_NEUR_Rep3


title: Wh_M_Lo_7


title: AA_W_Hi_7

value: AA

value: Hi


title: AA_W_Lo_6


title: Wh_M_Hi_2

value: male


title: AA_W_Hi_8


title: AA_M_Lo_7


title: AA_M_Hi_6


title: AA_M_Hi_8


title: WT_NEUR_Rep1


title: AA_M_Hi_7


title: Wh_W_Lo_7


title: Wh_W_Hi_8


title: H9WT_FT671_NEUR_Rep3


title: Wh_M_Lo_1


title: AA_W_Lo_7


title: AA_M_Lo_2


title: AA_W_Lo_1


title: AA_M_Lo_1


title: AA_W_Lo_2


title: Wh_W_Hi_2


title: Wh_M_Hi_3


title: AA_W_Hi_4


title: AA_M_Hi_3


title: Wh_W_Lo_1


title: AA_M_Lo_5


title: Wh_W_Hi_1


title: AA_M_Lo_3


title: AA_W_Lo_5


title: Wh_W_Hi_5


title: Wh_M_Lo_3


title: AA_M_Lo_4


title: AA_M_Hi_2


title: AA_W_Hi_3


title: Wh_M_Lo_6


title: Wh_W_Lo_4


title: AA_W_Hi_5


title: Wh_W_Hi_4


title: AA_M_Hi_4


title: Wh_W_Hi_3


title: AA_W_Hi_6


title: AA_M_Hi_5


title: AA_W_Lo_4


title: AA_W_Hi_1


title: Wh_M_Hi_5


title: Wh_M_Hi_7


title: Wh_W_Hi_7


title: Wh_M_Hi_6


title: Wh_M_Lo_5


title: Wh_M_Lo_4


title: Wh_W_Hi_6


title: Wh_W_Lo_6


title: Wh_M_Hi_8


title: Wh_W_Lo_5


title: Wh_M_Hi_1


title: Wh_M_Lo_2


title: AA_W_Lo_3


title: Wh_M_Hi_4


title: Po_Gluc

data_processing:
Illumina Raw paired-end reads were trimmed and then mapped using BWA (2).   The Python Pysam package (3) was used to calculate the mismatch, deletion and insertion rates from aligned BAM files. The events of mismatch, deletion and insertion on each read were calculated using custom scripts. The 10 nucleotides on each side of junction site were selected to evaluate the junction accuracy.
processed data files format and content: error rates for 7 ciruclar constructs, tsv
Assembly: synthetic

growth_protocol: Junction accuracy: NA

extract_protocol:
Junction accuracy: Each junction PCR fragment was processed using NEBNext Ultra II DNA Library Prep Kit to construct libraries compatible for Illumina sequencing.
Synthesis of first-stand cDNA from circular Gluc RNA was performed using SuperScript III reverse transcriptase (Thermo Fisher) with primer junction R according to manufacturer’s instructions. Subsequently, this cDNA was used as template for PCR amplification of 6 junction fragments with respective T4, An, Sd, Cb, Sh, and Po junction F and R primers.

treatment_protocol: Junction accuracy: NA

value: synthetic, IVT


title: AA_W_Hi_2


title: Rnl2_Gluc


title: AA_M_Hi_1


title: Cb_Gluc


title: An_Gluc


title: Sh_Gluc


title: Sd_Gluc


title: T4_Gluc


title: E1E2_Po_linear

data_processing:
For data analysis, sequencing results were filtered first based on two criteria: 1) The 8-nucleotide flanking sequences beside E1 and E2 are found (Fig 3D). 2) The sequence between the 8-nucleotide flanks are exactly 60 bases in length. These 60 nucleotide sequences were then extracted, deduplicated and used for downstream sequence context analysis to identify enriched motif sequences.
processed data files format and content: PIEs linear and circular, tsv
Assembly: synthetic

growth_protocol: E1E2 circularization: IVT

extract_protocol:
These samples were resolved by agarose gel and the lower band in each sample containing circular RNA was gel extracted.
Gel extracted T4 and An PIE N60 RNA was used for first-strand DNA synthesis using SuperScript III reverse transcriptase (Thermo Fisher) with primer N60 junction R1 according to manufacturer's instructions and this cDNA was subsequently was used as template for PCR amplification with primers N60 junction F and R1. For gel extracted Sh and Po PIE N60 RNA, primer N60 junction R2 was used to synthesize first-strand cDNA with SuperScript III reverse transcriptase (Thermo Fisher) and this cDNA was subsequently used as template for PCR amplification with primers N60 junction F and R2.

treatment_protocol: T4 PIE N60 Gluc, An PIE N60 Gluc, Sh PIE N60 Gluc, and Po PIE N60 Gluc IVT RNA were folded in condition B for 15 minutes or 1 hour (55°C – 25mM NaCl, 15mM MgCl2, 25mM HEPES pH7.5, and 2mM GTP).


title: E1E2_Sh_circular


title: E1E2_Po_circular


title: Wh_W_Lo_3


title: E1E2_Sh_linear


title: E1E2_An_circular


title: E1E2_An_linear


title: Group1_Introns_Replicate3_denat

data_processing:
After obtaining sequencing data for two biological replicates for each of the eight GIIs and eight PIEs under denaturing conditions and NAI or DMSO treatment respectively the reads were aligned with the appropriate reference sequences(17,18). Shape reactivity was calculated using shapemapper 2.1.5(29) with default parameters except for a minimum read depth of 500 instead of 5000 in order to obtain the broadest possible coverage of low-read regions. To identify regions of structural divergence, we plotted the reactivities of the GII vs the reactivities of the PIE for each of the eight specimens (Fig 2A, 2D and S4A). In addition, we calculated Pearson correlation coefficients for the matching GII and PIE segments, which range from 0.65-0.82 indicating a high level of structural consistency and suggests that the split of the GIIs into PIEs did not materially disturb the structures (Fig S4B).
processed data files format and content: SHAPE-MaP data for GII and PIEs, tsv+csv
Assembly: synthetic

growth_protocol: About 0.5-1mg linearized plasmids were used as template for RNA synthesis using HiScribe T7 High Yield RNA synthesis kit (NEB) according to the manufacturer's instructions. Reactions were incubated at 37°C for 2h and IVT templates were subsequently degraded with 2mL DNase I (Thermo Fisher) per IVT reaction for 30 minutes at 37°C. The remaining RNA was then column purified. Subsequently, purified RNA was incubated for 15 minutes in following conditions with the addition of a final concentration of 2mM GTP for circularization: A. 37°C – 25mM NaCl, 15mM MgCl2, and 25mM HEPES pH 7.5; B. 55°C – 25mM NaCl, 15mM MgCl2, 25mM HEPES pH7.5; C. 37°C – 1M NaCl, 15mM MgCl2, and 25mM HEPES pH 7.5; D. 37°C – 25mM NaCl, 200mM MgCl2, and 25mM HEPES; E. 37°C – 1M NH4OAc, 100mM Mg(OAc)2, and 25mM HEPES pH 7.5; F. 55°C – 0.5M KCl, 15mM MgCl2, 40mM Tris-HCl pH 7.0, 5mM DTT, and 2mM Spermidine; G. 55°C – 15mM MgCl2, 50mM Tris-HCl pH 7.0 and 1mM DTT. All samples were column purified after folding and circularization. To enrich circular RNA, circularized RNA samples were poly A tailed using poly A polymerase (NEB) following manufacturer’s protocol. Subsequently, these samples were column purified and treated with home-made recombinant RNase R at 37°C for 30 minutes, followed by a final column clean up. For circular RNA samples that were injected into mice, they were further purified by cellulose to remove double-stranded RNA contaminants(24) .

extract_protocol:
Linear mRNA was synthesized using the HiScribe T7 High Yield RNA Synthesis Kit (NEB) with the following modifications: CleanCap AG (3’ OMe) (Trilink-7413) was added to a final concentration of 4mM and m1ΨTP (Trilink-1081) was fully substituted for UTP. For linear RNA samples that were injected into mice, they were further purified using POROSTM Oligo (dT)25 affinity resin (Thermo Fisher) according to the manufacturer's instructions.
We fragmented all the RNA in MAP fragmentation buffer (18mM MgCl2, 450mM KCl, 300mM Tris HCl pH 8.3) at 95°C for 1 minutes 45 seconds and followed by RNA purification using RNA Clean & Concentrator-5 (R1014, Zymo) according to manufacturer’s instructions. We then performed library preparation following SHAPE-MaP protocol to generate cDNA libraries compatible for Illumina sequencing

treatment_protocol: Eight group 1 intron (GII) and eight permuted intron-exon (PIE) Gluc IVT RNA were resolved by agarose gel and the largest fragment in each GII and PIE Gluc sample was extracted. These extracted RNA were separated into three reactions: (1) we added 1:30 the volume of 2M NAI (03-310, Merck, 1µL of NAI in 30µL of RNA in structure buffer (50mM Tris HCl pH 7.4, 10mM MgCl2, 150mM NaCl) to the RNA and incubated the reaction for 10 minutes at 37°C for structure probing; (2) we added 1:30 the volume of dimethyl sulfoxide (DMSO) (D2650, Sigma-Aldrich, 1µL of DMSO in 30µL of RNA in structure buffer) to the RNA and incubated the reaction for 10 minutes at 37°C as negative control; and (3) we set aside a third portion of the RNA as for the denaturing control in the downstream library preparation process.

value: SHAPE-MaP NAI


title: Group1_Introns_Replicate3_NAI


title: E1E2_T4_circular


title: Group1_Introns_Replicate2_denat


title: Group1_Introns_Replicate2_NAI


title: Group1_Introns_Replicate3_DMSO


title: Group1_Introns_Replicate1_NAI


title: Group1_Introns_Replicate2_DMSO


title: Group1_Introns_Replicate1_denat


title: Split_Group1_Introns_Replicate3_denat


title: Split_Group1_Introns_Replicate3_NAI


title: Split_Group1_Introns_Replicate3_DMSO


title: Split_Group1_Introns_Replicate2_denat


title: Split_Group1_Introns_Replicate1_denat


title: Split_Group1_Introns_Replicate2_NAI


title: Split_Group1_Introns_Replicate2_DMSO


title: Split_Group1_Introns_Replicate1_NAI


title: C. elegans, dbl-1, 24 hour S. marcescens Replicate 1

city: Flushing

first: Cathy

last: Savage-Dunn

state: NY

address: 65-30 Kissena Ave

institute: Queens College and the Graduate Center, CUNY

description:
Library name: DBL-SM-1
Column name in normcounts_alldata.tsv: DBL.SM.1_001.fastq

data_processing:
Files were processed using Galaxy. Reads were mapped to the C. elegans genome (WS273). Gene counts were generated with STAR. EdgeR was used to determine differentially expressed genes (FDR < 0.05). Analysis was done using pandas, and Venn diagrams were generated with matplotlib.
Assembly: Reads were mapped to the C. elegans genome WS273.
Supplementary files format and content: Raw counts for each sample
Supplementary files format and content: TSV file includes normalized counts for each sample from EdgeR

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C. elegans were grown at 20C.

extract_protocol:
RNA was extracted using a Trizol and chloroform precipitation, followed by Qiagen RNeasy mini kit.
RNA libraries were prepared by Azenta.

treatment_protocol: At L4, they were transferred to either control E. coli or pathogenic S. marcescens for 24 hours. Animals were collected at Day 1 adult.

value: whole organism

value: 24 hour Serratia marcescens exposure


title: C. elegans, dbl-1, 24 hour S. marcescens Replicate  3

description:
Library name: DBL-SM-3
Column name in normcounts_alldata.tsv: DBL.SM.3_001.fastq


title: C. elegans, dbl-1, 24 hour E. coli Replicate 2

description:
Library name: DBL-EC-2
Column name in normcounts_alldata.tsv: DBL.EC.2_001.fastq

value: Control


title: C. elegans, WT, 24 hour S. marcescens Replicate 2

description:
Library name: N2-SM-2
Column name in normcounts_alldata.tsv: N2.SM.2_001.fastq

value: WT


title: C. elegans, dbl-1, 24 hour E. coli Replicate 3

description:
Library name: DBL-EC-3
Column name in normcounts_alldata.tsv: DBL.EC.3_001.fastq


title: C. elegans, dbl-1, 24 hour E. coli Replicate 1

description:
Library name: DBL-EC-1
Column name in normcounts_alldata.tsv: DBL.EC.1_001.fastq


title: C. elegans, WT, 24 hour S. marcescens Replicate 3

description:
Library name: N2-SM-3
Column name in normcounts_alldata.tsv: N2.SM.3_001.fastq


title: C. elegans, WT, 24 hour S. marcescens Replicate 1

description:
Library name: N2-SM-1
Column name in normcounts_alldata.tsv: N2.SM.1_001.fastq


title: C. elegans, WT, 24 hour E. coli Replicate 3

description:
Library name: N2-EC-3
Column name in normcounts_alldata.tsv: N2.EC.3_001.fastq


title: C. elegans, WT, 24 hour E. coli Replicate 2

description:
Library name: N2-EC-2
Column name in normcounts_alldata.tsv: N2.EC.2_001.fastq


title: leaves of Potato 25℃,12h rep3

city: Xining

first: xiang

last: Li

state: Qinghai

address: No. 251 Ningda Road, Chengbei District

institute: Qinghai University

description:
Library name: GSM_KY140
Due to a long time, MetWare company(Wuhan, China) did not save my raw data. I do not have the raw sequencing data (e.g., FASTQ files) and only possess the processed expression matrix (e.g., normalized counts or FPKM/TPM values).

data_processing:
Sample collection and preparation:1.RNA quantification and qualification. 2.Library preparation for Transcriptome sequencing. 3.Clustering and sequencing.
Data Analysis:1.Data quality control. 2. Reads mapping to the reference genome. 3. New transcript prediction. 4. Quantification of gene expression levels. 5. Difference analysis. 6. Differential gene enrichment analysis. 7. Differential AS analysis. 8. SNP analysis. 9. Differential gene protein interaction analysis. 10. GSEA. 11. WGCNA
Assembly: http://spuddb.uga.edu/phased_tetraploid_potato_download.shtml
Supplementary files format and content: count.annot.xlsx

organism: Solanum tuberosum

source_name: Leaf

growth_protocol: Potato tissue culture seedlings (virus-free) were cultured on MS medium for 18 days. The light was about 2500 lx, and the light duration was 16 h per day.

extract_protocol:
RNAprep Pure Plant Plus Kit (Polysaccharides&Polyphenolics-rich)(Tiangen Biotech Co., Ltd., Beijing, China)
1) By utilizing the structural characteristic that most eukaryotic mRNAs carry a polyA tail, mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads; 2) The purified mRNAs were cleaved into small fragments with fragmentation buffer at a suitable temperature; 3) First-strand cDNAs were produced by reverse transcription using a random hexamer primer; 4) Second-strand cDNAs are synthesized (strand-specific library: dUTPs were used instead of dTTPs in the second-strand synthesis to incorporate dUTPs in the second-strand cDNAs, while the high-fidelity DNA polymerase used in this method could not amplify uracil-containing DNA templates, thus realizing the strand-specificity), while simultaneously performing end repair and dA-Tailing; 5) Sequencing adapter ligation was performed, followed by DNA magnetic bead purification and fragment selection after ligation was completed to yield a library with 250-350 bp insert fragments; 6) The ligated products were amplified by PCR and purified again using DNA magnetic beads, where the products were solubilized with nuclear-free water; 7) After the initial library was constructed, a Qubit fluorescence quantifier was used for concentration detection, followed by a Qsep400 high-throughput biofragment analyzer for fragment size detection，Finally, the effective concentration of the library was accurately quantified using Q-PCR;

value: Leaf

value: organization

tag: batch


title: leaves of Potato 25℃, 12h rep2

description:
Library name: GSM_KY130
Due to a long time, MetWare company(Wuhan, China) did not save my raw data. I do not have the raw sequencing data (e.g., FASTQ files) and only possess the processed expression matrix (e.g., normalized counts or FPKM/TPM values).


title: leaves of Potato -4℃,12h rep3

description:
Library name: GSM_CS-KY140
Due to a long time, MetWare company(Wuhan, China) did not save my raw data. I do not have the raw sequencing data (e.g., FASTQ files) and only possess the processed expression matrix (e.g., normalized counts or FPKM/TPM values).


title: Group1_Introns_Replicate1_DMSO


title: leaves of Potato -4℃, 12h rep1

description:
Library name: GSM_CS-Atlantic
Due to a long time, MetWare company(Wuhan, China) did not save my raw data. I do not have the raw sequencing data (e.g., FASTQ files) and only possess the processed expression matrix (e.g., normalized counts or FPKM/TPM values).


title: C. elegans, WT, 24 hour E. coli Replicate 1

description:
Library name: N2-EC-1
Column name in normcounts_alldata.tsv: N2.EC.1_001.fastq


title: E14.5 Pet1 neuron input

city: Cleveland

first: Evan

last: Deneris

state: Ohio

address: 2210 Circle Dr., Robbins E640

department: Neurosciences

institute: Case Western Reserve University

description: Library name: 5HT_E14.5_Input_1

data_processing:
Illumina Casava 2.20 software used for basecalling.
ChIPmentation reads were filtered and mapped using the ENCODE uniform ChIP-seq processing pipeline
Assembly: mm10
Supplementary files format and content: bed file is the filtered peaks. BigWig file is the filtered and uniquely mapped read coverage compared to input.

source_name: brain

growth_protocol: Brain tissue was taken from transgenic mice maintained under standard housing conditions.

extract_protocol:
For ChIPmentation 5-HT  neurons from E14.5 Pet1-EYFP embryos were sorted using a BD FACSAria SORP into PBS with 1% FBS.
Antibody-immunopurified DNA fragments were amplified into sequencing libraries using the ChIPmentation protocol that uses a Tn5 transposase mediated adapter ligation and amplification (Schmidl, et al. 2015).

value: brain

value: 5-HT neuron

value: Pet1::Cre; Rosa-TdTomato


title: E14.5 Pet1 neuron CTCF

description: Library name: 5HT_E14.5_CTCF_1

tag: antibody

value: anti-CTCF


title: Split_Group1_Introns_Replicate1_DMSO


title: E17.5 Pet1 neuron ATAC-seq R200Q/+ rep2

description: Library name: 5HT_E14.5_R200Q_ATACseq_2

data_processing:
Illumina Casava 2.20 software used for basecalling.
ATAC-seq reads were filtered and mapped using the ENCODE uniform ATAC-seq processing pipeline
Assembly: mm10
Supplementary files format and content: narrowPeak files are the filtered peaks for each dataset. BigWig files are the filtered, uniquely mapped, pooled reads, and downsampled to 100M reads.

extract_protocol:
Dissected tissue between the mid-hindbrain boundary to the spinal cord boundary of E17.5 hindbrains from Pet1-Cre ;SUN1-GFP, Pet1-Cre;Lmx1bN246K/+ ;SUN1-GFP, Pet1-Cre;Lmx1bDelta/+ ;SUN1-GFP, and Pet1-Cre; Lmx1bR200Q/+ ;SUN1-GFP embryos. For ATAC-seq SUN1-GFP+ Pet1 neurons were isolated using the INTACT method.
Adapter-ligated DNA fragments were purified using the NEB Monarch DNA & PCR cleanup kit , and subsequently PCR-amplified with the NEB NEBNext High-Fidelity 2x PCR Master Mix using the following conditions: (1) 5 minutes at 72°C, (2) 1 minute at 98°C, (3) 15 seconds at 98°C, (4) 30 seconds at 63°C, (5) one minute at 72°C, (6) Go to step 3 seven times, (7) hold at 10°C. All ATAC-seq libraries were sequenced on a Nextseq 550.

value: Lmx1b R200Q/fl; Pet1::Cre; Rosa-TdTomato


title: E17.5 Pet1 neuron ATAC-seq R200Q/+ rep1

description: Library name: 5HT_E14.5_R200Q_ATACseq_1


title: E17.5 Pet1 neuron ATAC-seq Delta/+ rep2

description: Library name: 5HT_E14.5_Delta_ATACseq_2

value: Lmx1b Delta/fl; Pet1::Cre; Rosa-TdTomato


title: E17.5 Pet1 neuron ATAC-seq Delta/+ rep1

description: Library name: 5HT_E14.5_Delta_ATACseq_1


title: C. elegans, dbl-1, 24 hour S. marcescens Replicate 2

description:
Library name: DBL-SM-2
Column name in normcounts_alldata.tsv: DBL.SM.2_001.fastq


title: E17.5 Pet1 neuron ATAC-seq N246K/+ rep1

description: Library name: 5HT_E14.5_N246K_ATACseq_1

value: Lmx1b N246K/fl; Pet1::Cre; Rosa-TdTomato


title: E17.5 Pet1 neuron ATAC-seq control rep1

description: Library name: 5HT_E14.5_Control_ATACseq_1


title: E17.5 Pet1 neuron ATAC-seq control rep2

description: Library name: 5HT_E14.5_Control_ATACseq_2


title: E17.5 Pet1 neuron ATAC-seq control rep3

description: Library name: 5HT_E14.5_Control_ATACseq_3


title: E17.5 Pet1 neuron Delta/+ rep3

description: Library name: 5HT_E17.5_Delta_RNAseq_3

data_processing:
Illumina Casava 2.20 software used for basecalling.
RNA-seq reads were filtered for low-quality sequence, then mapped to mm10 whole genome using hisat2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks and control samples were compared to Lmx1bN246K/+, Lmx1bR200Q/+, and Lmx1bDelta/+ samples using cuffdiff.
Assembly: mm10
Supplementary files format and content: output of cuffdiff differential gene expression analysis with RPKM values and log2 fold-change for comparison of control to the Lmx1b mutant datasets

extract_protocol:
Dissected tissue between the mid-hindbrain boundary to the spinal cord boundary of E17.5 hindbrains from Pet1-Cre ;Rosa-TdTomato, Pet1-Cre;Lmx1bN246K/+ ;Rosa-TdTomato, Pet1-Cre; Lmx1bDelta/+ ;Rosa-TdTomato, and Pet1-Cre; Lmx1bR200Q/+ ;Rosa-TdTomato embryos. For RNA-seq, E17.5 tdTomato+ 5-HT  neurons from embryos were sorted using a BD FACSAria SORP into Trizol LS.
Purified total RNA was amplified with the TRIO RNA-seq kit (Nugen)

value: Pet1 neuron

value: Lmx1b Delta/+; Pet1::Cre; Rosa-TdTomato


title: E17.5 Pet1 neuron Delta/+ rep1

description: Library name: 5HT_E17.5_Delta_RNAseq_1


title: E17.5 Pet1 neuron control rep3

description: Library name: 5HT_E17.5_Control_RNAseq_3


title: E17.5 Pet1 neuron N246K/+ rep1

description: Library name: 5HT_E17.5_N246K_RNAseq_1

value: Lmx1b N246K/+; Pet1::Cre; Rosa-TdTomato


title: E17.5 Pet1 neuron R200Q/+ rep2

description: Library name: 5HT_E17.5_R200Q_RNAseq_2

value: Lmx1b R200Q/+; Pet1::Cre; Rosa-TdTomato


title: E17.5 Pet1 neuron N246K/+ rep2

description: Library name: 5HT_E17.5_N246K_RNAseq_2


title: E17.5 Pet1 neuron R200Q/+ rep3

description: Library name: 5HT_E17.5_R200Q_RNAseq_3


title: E17.5 Pet1 neuron control rep2

description: Library name: 5HT_E17.5_Control_RNAseq_2


title: E17.5 Pet1 neuron control rep1

description: Library name: 5HT_E17.5_Control_RNAseq_1


title: E17.5 Pet1 neuron R200Q/+ rep1

description: Library name: 5HT_E17.5_R200Q_RNAseq_1


title: E17.5 Pet1 neuron N246K/+ rep3

description: Library name: 5HT_E17.5_N246K_RNAseq_3


title: leaves of Potato -4℃,12h rep2

description:
Library name: GSM_CS-KY130
Due to a long time, MetWare company(Wuhan, China) did not save my raw data. I do not have the raw sequencing data (e.g., FASTQ files) and only possess the processed expression matrix (e.g., normalized counts or FPKM/TPM values).


title: E17.5 Pet1 neuron Delta/+ rep2

description: Library name: 5HT_E17.5_Delta_RNAseq_2


title: leaves of Potato 25℃, 12h rep1

description:
Library name: GSM_Atlantic
Due to a long time, MetWare company(Wuhan, China) did not save my raw data. I do not have the raw sequencing data (e.g., FASTQ files) and only possess the processed expression matrix (e.g., normalized counts or FPKM/TPM values).


title: 207883300005_R04C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: none provided

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Following data collection, the SeSaMe normalization method was used to define beta values for each probe (W. Zhou et al 2018. PMID: 30085201). If a CpG does not map to a given species, it takes a value of 0.5. The mammalian array design is similar to the Illumina Infinium 450K array but it contains fewer up to 37492 CpGs.  Additional material on the mappability of CpGs can be found on the Github page https://github.com/shorvath/MammalianMethylationConsortium/  A vignette on using the mammal methylation array with SeSAMe is available from https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/mammal.html.

label: Cy3 and Cy5

organism: Rattus norvegicus

label_protocol: none provided

extract_protocol: none provided

tag: confidenceinageestimate

tag: specieslatinname

value: Rattus norvegicus

value: Hippocampus

tag: female

tag: condition

value: Young

tag: ageindays


title: MKs,  Becn1f/f;Pf4-iCre,3

city: Su Zhou ; Jiang Su

first: Fang

middle: Yi

last: Xuan

address: No.199, Ren Ai Road

institute: Soochow university

description: Library name: KO3

data_processing:
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results. We used HISAT to align the clean reads to the reference genome. We used Bowtie2 to align the clean reads to the reference genes.
Species: Mus_musculus Source: NCBI Reference Genome Version: GCF_000001635.27_GRCm39
Assembly: mm39
Supplementary files format and content: csv file includes raw counts, FPKM values and TPM values for each sample

source_name: bone marrow

extract_protocol:
Mouse bone marrow was taken in a sterile environment,megakaryocytes were separated from bone marrow cells by fluorescence-activated cell sorting (FACS), which were added to 500uL Trizo(vazyme)and frozen at -80"
RNA-seq

tag: tissue

value: bone marrow

value: megakaryocytes


title: MKs, Becn1f/f;Pf4-iCre,1

description: Library name: KO1

tag: cell type


title: 207883300010_R01C01


title: MKs,  Becn1f/f;Pf4-iCre,2

description: Library name: KO2


title: MKs, Becn1f/f, 2

description: Library name: WT2


title: 207883300005_R03C02


title: ∆lsrB∆oxyR, LB H2O2, biol rep3

city: Bochum

first: Franz

last: Narberhaus

state: NRW

address: Universitätstraße 150, NDEF 06/744

department: Fakultät für Biologie und Biotechnologie

country: Germany

institute: Ruhr Universität Bochum

description: Library name: Sample 24

data_processing:
Adapter sequences were removed via cutadapt 1.18 with Python 3.7.9 (options: -j 4 -q 10)
Cleaned reads were mapped with bwa (0.7.17-r1188) mem on default settings.
Duplicate reads were removed with Samtools 1.10.
Differential gene expression was analyzed  with DESeq2. A maximal adjusted p value of 0.01 was used as threshold.
Assembly: NCBI ID: 13606; 671 small RNA genes were added from Wilms et al. (2012, DOI: 10.4161/rna.17212), Lee et al. (2013, DOI: 10.1371/journal.pone.0070720) and from Möller et al. (2014, DOI: 10.1371/journal.pone.0110427)
Supplementary files format and content: Files include the binary logarithm of the fold change of each gene in the mutant and the corresponding p values.

organism: Agrobacterium fabrum str. C58

source_name: bacteria

growth_protocol: Cells were grown at 30 °C in lB medium until an optical density (OD600) of 0.8. Samples withdrawn before or after 15 min, 5 mM H2O2 stress

extract_protocol:
RNA was extracted using the hot-phenol method in accordance to Wilms et al. (2012, DOI: 10.4161/rna.17212). Residual DNA was removed with RNase-free DNase.
RNA libraries were prepared by Novogene using 1 µg of RNA and the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Index codes were added to attribute sequences to each sample. The RNA was fragmented with divalent cations in NEBNext First Strand Synthesis Reaction Buffer (5x) at elevated temperature. Then, first strand synthesis was carried out with random hexamer primers and M-MuLV reverse transcriptase. Second strand synthesis was performed with DNA polymerase I and RNase H. Blunt ends were created from overhangs via exonuclease/polymerase activities. DNA 3' ends were adenylated and NEBNext Adaptors with hairpin loop were ligated. Fragments were purified with the AMPure XP system. The cDNA was then incubated at 37 °C for 15 minutes with 3 µl USER Enzyme and then at 95 °C for 5 minutes. The subsequent PCR was performed with Phusion High-Fidelity DNA polymerase, Universail PCR primers, and Index (X) Primer. The PCR products were purified via AMPure XP system and the quality was assured via Agilent Bioanalyzer 2100.

value: bacteria

tag: genotype

value: Grown until OD 0.8, 15 min 5 mM H2O2 stress


title: MKs, Becn1f/f, 3

description: Library name: WT3


title: 207883300005_R06C01


title: 207883300005_R02C02


title: ∆lsrB∆oxyR, LB H2O2, biol rep2

description: Library name: Sample 23

tag: treatment


title: ∆lsrB∆oxyR, LB H2O2, biol rep1

description: Library name: Sample 22


title: 207883300010_R04C02


title: 207883300010_R02C02


title: MKs, Becn1f/f, 1

description: Library name: WT1


title: 207883300005_R01C02


title: 207883300010_R01C02


title: 207883300005_R06C02


title: 207883300010_R02C01


title: 207883300005_R05C01


title: 207883300010_R03C02


title: 207883300010_R06C02


title: 207883300010_R06C01


title: 207883300010_R05C01


title: 207883300010_R04C01


title: 207883300010_R05C02


title: 207883300005_R05C02


title: ∆oxyR, LB H2O2, biol rep2

description: Library name: Sample 20

value: {delta}oxyR (atu4641)


title: ∆oxyR, LB H2O2, biol rep1

description: Library name: Sample 19


title: ∆lsrB, LB H2O2, biol rep3

description: Library name: Sample 18

value: {delta}lsrB (atu2186)


title: ∆oxyR, LB H2O2, biol rep3

description: Library name: Sample 21


title: ∆lsrB, LB H2O2, biol rep2

description: Library name: Sample 17


title: ∆lsrB, LB H2O2, biol rep1

description: Library name: Sample 16


title: WT, LB H2O2, biol rep2

description: Library name: Sample 14

value: WT


title: WT, LB H2O2, biol rep1

description: Library name: Sample 13


title: ∆lsrB∆oxyR, LB, biol rep3

description: Library name: Sample 12

value: Grown until OD 0.8


title: 207883300010_R03C01


title: ∆lsrB∆oxyR, LB, biol rep2

description: Library name: Sample 11


title: ∆oxyR, LB, biol rep3

description: Library name: Sample 9


title: ∆lsrB, LB, biol rep3

description: Library name: Sample 6


title: ∆lsrB, LB, biol rep1

description: Library name: Sample 4


title: ∆oxyR, LB, biol rep1

description: Library name: Sample 7


title: ∆oxyR, LB, biol rep2

description: Library name: Sample 8


title: ∆lsrB∆oxyR, LB, biol rep1

description: Library name: Sample 10


title: WT, LB, biol rep1

description: Library name: Sample 1


title: WT, LB, biol rep2

description: Library name: Sample 2


title: WT, LB, biol rep3

description: Library name: Sample 3


title: ∆lsrB, LB, biol rep2

description: Library name: Sample 5


title: E13.5 Isl1-Cre;R26R-eYFP

city: Tsu

first: Sota

last: Torii

state: Mie

address: 2-174 Edobashi

department: Graduate School of Medicine

institute: Mie University

description: 10× Genomics

data_processing:
Demultiplexing, mapping to reference sequences, and generating the gene-barcode matrix were performed using Cell Ranger software v7.1.0 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pharyngeal arch

extract_protocol:
E13.5 embryos were collected via cesarean section from Isl1-Cre;R26R-eYFP (control) or Isl1-Cre;R26R-eYFP;Pik3caH1047R mice. The embryos were washed with 0.1 M PBS. Under a stereomicroscope, three eYFP-positive embryos were selected per group. The upper body regions, including tissues above the liver, were dissected and finely minced using scissors in 10 ml of DMEM (Fujifilm) containing 10% FBS (Gibco, 10270106), 1% antibiotic-antimycotic (AB/AM) solution (Gibco, 15240062), 0.5 mg/ml DNase I (Roche, Basel, Switzerland), and 1 mg/ml type II collagenase (Worthington). The tissue suspension was incubated at 37°C in a water bath for 30 minutes, then filtered through a 70 µm cell strainer (Falcon, 352350), followed by two passages through a 40 µm cell strainer (Corning, 431750). After centrifugation at 1000 rpm, the supernatant was discarded, and the cell pellet was resuspended in 1 ml of 2 mM EDTA/PBS/0.1% BSA for FACS sorting, flow cytometric analysis was performed using FACSCanto II and BD LSRFortessa cytometers (BD Biosciences). Data were analyzed with BD FACSDiva software. After staining, cells were washed with FACS buffer (PBS, 0.5% FBS, 2 mM EDTA), and single viable cells were gated from FSC-A/SSC-A plots, with dead cells being excluded using 7-AAD.
For the construction of single-cell RNA-Seq library, Next GEM Single Cell 5′ Library and Gel Bead Kit v2 (10x Genomics) was used according to the manufacturer’s instructions.　Libraries were sequenced on a DNBSEQ-G400 (MGI) at a read length of 28x100 in paired-end mode.

value: pharyngeal arch


title: E13.5 Isl1-Cre;R26R-eYFP;Pik3caH1047R

description: 10× Genomics


title: Control WT group sample 3

city: New York

first: Shoshana

last: Yakar

address: 345E 24th Street

institute: New York University

data_processing:
The quality of raw data was checked by FastQC (v. 0.11.9)
Read counts were quantified using Salmon (v. 1.7.0)
Differential expression analysis was performed by DESeq2 R/Bioconductor package
Assembly: GRCm38.p6
Supplementary files format and content: Salmon Output File Formats
Supplementary files format and content: quant.sf for each sample

source_name: Bone Marrow

extract_protocol:
RNA was extracted from Bone Marrow using Qiagen RNeasy plus mini kit (Qiagen, cat# 74204)
Strand-Specific mRNA Library Preparation (DNBSEQ)

treatment_protocol: AIM2 null and wildtype (WT) female mice were used for tissue dissection at 5 to 6  months of age.

value: Bone Marrow

value: tissue


title: Control WT group sample 2


title: WT, LB H2O2, biol rep3

description: Library name: Sample 15


title: Control WT group sample 4


title: Control WT group sample 1


title: Aim2 KO group sample 1

value: Aim2 knock out


title: E47-/- N1End/d  -scATACseq

city: Chiba

first: Kenta

last: Horie

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: IAAR

institute: Chiba university

description: 10x Genomics

library_source: genomic single cell

data_processing:
Read alignment was performed using CellRanger ARC analysis pilepine (v2.0.0, 10x Genomics) with mm10 whole genome reference (refdata-cellranger-arc-mm10-2020-A-2.0.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Matrix files

source_name: Fetal thymus

extract_protocol:
Nuclei isolation was performed according to the 10x Genomics Nuclei Isolation Protocol (CG000365). ~Approximately 16,000 live thymus cells were resuspended in ice-cold lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA on ice for 3 minutes. Nuclei were washed and then resuspended in nuclei buffer to target 10,000 recovered nuclei.
Sequence libraries were constructed from isolated nuclei using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits.

value: Fetal thymus

tag: cell line

value: Thymic cells

value: sorted live cells


title: Control-scRNAseq

description: 10x Genomics

molecule: nuclear RNA


title: Control-scATACseq

description: 10x Genomics


title: E47-/- N1End/d -scRNAseq

description: 10x Genomics


title: mTEChi, neonate, Aire/EED-dKO, cell265

data_processing:
Trimming reads to 50bp by fastx_trimmer if needed (FASTX Toolkit v0.0.14, http://hannonlab.cshl.edu/fastx_toolkit/)
Trimming low-quality parts and adapter sequences by fastp (v0.20.0, Chen et al., fastp: an ultra-fast all-in-one FASTQ preprocessor, 2018)
Mapping to the mm10 genome using STAR (v2.7.3a, Dobin et al., STAR: ultrafast universal RNA-seq aligner, 2013) with a GTF file downloaded from http://www.ensembl.org (GRCm38.99)
Removing unmapped reads and reads mapped with low-quality scores (MAPQ < 5) by SAMtools (v1.9, Li et al., The Sequence Alignment/Map format and SAMtools, 2009)
Removing duplicated reads using Picard Tools (v2.21.1, http://broadinstitute.github.io/picard/)
Counting mapped reads on each gene using htseq-count (v0.11.2, Anders et al., HTSeq--a Python framework to work with high-throughput sequencing data, 2015) using a --stranded=no option and a GTF file from EMBL-EBI (GRCm38.99)
Normalization of the count data for each cell, dividing by the total counts for that cell and multipling by the scale.factor 10000. This is then natural-log transformed using log1p
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw read counts for each gene by each sample
Supplementary files format and content: comma-separated values file includes normalized values for each gene by each sample

extract_protocol:
Mouse thymus was enzymatically digested and CD45+ cells were depleted using mouse CD45 MicroBeads and a LS Column (Miltenyi Biotec). After staining with an antibody cocktail, mTEChi (DAPI-CD45-EpCAM+Ly51-MHCII-high), mTEClo (DAPI-CD45-EpCAM+Ly51-MHCII-low), and cTEC (DAPI-CD45-EpCAM+Ly51+) were sorted by FACSAria into a 96well plate containing 1uL of lysis buffer (0.3% NP40; Thermo Scientific, 1U/uL RNasinPlus; Promega in 1x Lysis Buffer, Takara)
scRNA-seq libraries were prepared by a RamDA-seq method (Hayashi et al., Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs, 2018). Specifically, RNA was denatured by incubating at 70C for 90sec, then placed on ice and treated with DNaseI (0.1U/uL DNase I, Amplification Grade, Invitrogen) in 0.25xRT Buffer (PrimeScript RT reagent Kit, Takara) at 30C for 5min. Then cDNA was synthesized in 3uL of 1xRT Buffer containing RT Enzyme Mix (0.15uL of PrimeScript RT Enzyme Mix I, Takara), oligo(dT)-RT primer (0.2uM Oligo(dT)18 Primer, Thermo Scientific), T4 gene 32 protein (0.033mg/mL, NEB) and 1st-NSR primer for mouse (2.7uM, SIGMA custom DNA oligos) by incubating 10min at 25C, 10min at 30C, 30min at 37C, 5min at 50C and 5min at 94C. Next, the second strand was synthesized by adding 0.5uL of 10x NEB buffer2 (NEB), 0.125uL of dNTP mix (10mM each nt, NEB), 0.15uL of Klenow Fragment (3'→5' exo-, NEB), 0.4uL of 2nd-NSR primer for mouse (100uM, SIGMA custom DNA oligos), and 0.825uL of DW and incubating 60min at 16C followed by 10min at 70C. The double-stranded cDNA (ds-cDNA) was purified using the AMPure XP beads (Beckman Coulter) and applied for Tn5 tagmentation in a 5uL reaction with a homemade Tn5 enzyme prepared as previously described (Picelli et al., Tn5 transposase and tagmentation procedures for massively scaled sequencing projects, 2014 and Hennig et al., Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol, 2018). After dissociating Tn5 protein by adding SDS (0.04% in final), tagmented DNA was amplified by 17 cycles of PCR using indexed primers and KAPA HiFi DNA Polymerase (Roche). The libraries were purified using AMPure XP beads (x1.0 vol), quantified by MultiNA (SHIMADZU) and pooled for next-generation sequencing.

value: thymus

value: epitherial cells

value: mTEChi

tag: strain

value: Aire/EED-dKO

tag: age

value: unknown

tag: exp. batch


title: mTEChi, neonate, Aire/EED-dKO, cell268

tag: Sex


title: mTEChi, neonate, Aire/EED-dKO, cell269


title: mTEChi, neonate, Aire/EED-dKO, cell266


title: mTEChi, neonate, Aire/EED-dKO, cell264


title: mTEChi, neonate, Aire/EED-dKO, cell256


title: mTEChi, neonate, Aire/EED-dKO, cell259


title: mTEChi, neonate, Aire/EED-dKO, cell263


title: mTEChi, neonate, Aire/EED-dKO, cell257


title: mTEChi, neonate, Aire/EED-dKO, cell262


title: mTEChi, neonate, Aire/EED-dKO, cell260


title: mTEChi, neonate, Aire/EED-dKO, cell254


title: mTEChi, neonate, Aire/EED-dKO, cell261


title: mTEChi, neonate, Aire/EED-dKO, cell255


title: mTEChi, neonate, Aire/EED-dKO, cell258


title: mTEChi, neonate, Aire/EED-dKO, cell253


title: mTEChi, neonate, Aire/EED-dKO, cell251


title: Aim2 KO group sample 2


title: mTEChi, neonate, Aire/EED-dKO, cell252


title: Aim2 KO group sample 3


title: mTEChi, neonate, Aire/EED-dKO, cell248


title: mTEChi, neonate, Aire/EED-dKO, cell249


title: mTEChi, neonate, Aire/EED-dKO, cell247


title: mTEChi, neonate, Aire/EED-dKO, cell250


title: mTEChi, neonate, Aire/EED-dKO, cell245


title: mTEChi, neonate, Aire/EED-dKO, cell267


title: mTEChi, neonate, Aire/EED-dKO, cell246


title: mTEChi, neonate, Aire/EED-dKO, cell242


title: mTEChi, neonate, Aire/EED-dKO, cell244


title: mTEChi, neonate, Aire/EED-dKO, cell241


title: mTEChi, neonate, Aire/EED-dKO, cell239


title: mTEChi, neonate, Aire/EED-dKO, cell238


title: mTEChi, neonate, Aire/EED-dKO, cell237


title: mTEChi, neonate, Aire/EED-dKO, cell243


title: mTEChi, neonate, Aire/EED-dKO, cell240


title: mTEChi, neonate, Aire/EED-dKO, cell231


title: mTEChi, neonate, Aire/EED-dKO, cell236


title: mTEChi, neonate, Aire/EED-dKO, cell230


title: mTEChi, neonate, Aire/EED-dKO, cell232


title: mTEChi, neonate, Aire/EED-dKO, cell233


title: mTEChi, neonate, Aire/EED-dKO, cell235


title: mTEChi, neonate, Aire/EED-dKO, cell234


title: mTEChi, neonate, Aire/EED-dKO, cell229


title: mTEChi, neonate, Aire/EED-dKO, cell228


title: mTEChi, neonate, Aire/EED-dKO, cell227


title: mTEChi, neonate, Aire/EED-dKO, cell223


title: mTEChi, neonate, Aire/EED-dKO, cell220


title: mTEChi, neonate, Aire/EED-dKO, cell221


title: mTEChi, neonate, Aire/EED-dKO, cell222


title: mTEChi, neonate, Aire/EED-dKO, cell224


title: mTEChi, neonate, Aire/EED-dKO, cell218


title: mTEChi, neonate, Aire/EED-dKO, cell216


title: mTEChi, neonate, Aire/EED-dKO, cell217


title: mTEChi, neonate, Aire/EED-dKO, cell213


title: mTEChi, neonate, Aire/EED-dKO, cell212


title: mTEChi, neonate, Aire/EED-dKO, cell209


title: mTEChi, neonate, Aire/EED-dKO, cell207


title: mTEChi, neonate, Aire/EED-dKO, cell205


title: mTEChi, neonate, Aire/EED-dKO, cell200


title: mTEChi, neonate, Aire/EED-dKO, cell201


title: mTEChi, neonate, Aire/EED-dKO, cell202


title: mTEChi, neonate, Aire/EED-dKO, cell226


title: mTEChi, neonate, Aire/EED-dKO, cell199


title: mTEChi, neonate, Aire/EED-dKO, cell203


title: mTEChi, neonate, Aire/EED-dKO, cell206


title: mTEChi, neonate, Aire/EED-dKO, cell214


title: mTEChi, neonate, Aire/EED-dKO, cell196


title: mTEChi, neonate, Aire/EED-dKO, cell219


title: mTEChi, neonate, Aire/EED-dKO, cell225


title: mTEChi, neonate, Aire/EED-dKO, cell198


title: mTEChi, neonate, Aire/EED-dKO, cell197


title: mTEChi, neonate, Aire/EED-dKO, cell192


title: mTEChi, neonate, Aire/EED-dKO, cell208


title: mTEChi, neonate, Aire/EED-dKO, cell195


title: mTEChi, neonate, Aire/EED-dKO, cell215


title: mTEChi, neonate, Aire/EED-dKO, cell193


title: mTEChi, neonate, Aire/EED-dKO, cell194


title: mTEChi, neonate, Aire/EED-dKO, cell191


title: mTEChi, neonate, Aire/EED-dKO, cell190


title: mTEChi, neonate, Aire/EED-dKO, cell211


title: mTEChi, neonate, Aire/EED-dKO, cell210


title: mTEChi, neonate, Aire/EED-dKO, cell188


title: mTEChi, neonate, Aire/EED-dKO, cell204


title: mTEChi, neonate, Aire/EED-dKO, cell187


title: mTEChi, neonate, Aire/EED-dKO, cell186


title: mTEChi, neonate, Aire/EED-dKO, cell185


title: mTEChi, neonate, Aire/EED-dKO, cell184


title: mTEChi, neonate, Aire/EED-dKO, cell183


title: mTEChi, neonate, Aire/EED-dKO, cell180


title: mTEChi, neonate, Aire/EED-dKO, cell178


title: mTEChi, neonate, Aire/EED-dKO, cell175


title: mTEChi, neonate, Aire/EED-dKO, cell176


title: mTEChi, neonate, Aire/EED-dKO, cell174


title: mTEChi, neonate, Aire/EED-dKO, cell173


title: mTEChi, neonate, Aire/EED-dKO, cell177


title: mTEChi, neonate, Aire/EED-dKO, cell172


title: mTEChi, neonate, Aire/EED-dKO, cell165


title: mTEChi, neonate, Aire/EED-dKO, cell168


title: mTEChi, neonate, Aire/EED-dKO, cell167


title: mTEChi, neonate, Aire/EED-dKO, cell189


title: mTEChi, neonate, Aire/EED-dKO, cell166


title: mTEChi, neonate, Aire/EED-dKO, cell170


title: mTEChi, neonate, Aire/EED-dKO, cell169


title: mTEChi, neonate, Aire/EED-dKO, cell161


title: mTEChi, neonate, Aire/EED-dKO, cell162


title: mTEChi, neonate, Aire/EED-dKO, cell163


title: mTEChi, neonate, Aire/EED-dKO, cell160


title: mTEChi, neonate, Aire/EED-dKO, cell159


title: mTEChi, neonate, Aire/EED-dKO, cell158


title: mTEChi, neonate, Aire/EED-dKO, cell156


title: mTEChi, neonate, Aire/EED-dKO, cell181


title: mTEChi, neonate, Aire/EED-dKO, cell182


title: mTEChi, neonate, Aire/EED-dKO, cell179


title: mTEChi, neonate, Aire/EED-dKO, cell155


title: mTEChi, neonate, Aire/EED-dKO, cell154


title: mTEChi, neonate, Aire/EED-dKO, cell171


title: mTEChi, neonate, Aire/EED-dKO, cell153


title: mTEChi, neonate, Aire/EED-dKO, cell164


title: mTEChi, neonate, Aire/EED-dKO, cell151


title: mTEChi, neonate, Aire/EED-dKO, cell146


title: mTEChi, neonate, Aire/EED-dKO, cell150


title: mTEChi, neonate, Aire/EED-dKO, cell141


title: mTEChi, neonate, Aire/EED-dKO, cell144


title: mTEChi, neonate, Aire/EED-dKO, cell149


title: mTEChi, neonate, Aire/EED-dKO, cell145


title: mTEChi, neonate, Aire/EED-dKO, cell148


title: mTEChi, neonate, Aire/EED-dKO, cell142


title: mTEChi, neonate, Aire/EED-dKO, cell140


title: mTEChi, neonate, Aire/EED-dKO, cell137


title: mTEChi, neonate, Aire/EED-dKO, cell135


title: mTEChi, neonate, Aire/EED-dKO, cell139


title: mTEChi, neonate, Aire/EED-dKO, cell136


title: mTEChi, neonate, Aire/EED-dKO, cell138


title: mTEChi, neonate, Aire/EED-dKO, cell157


title: mTEChi, neonate, Aire/EED-dKO, cell133


title: mTEChi, neonate, Aire/EED-dKO, cell152


title: mTEChi, neonate, Aire/EED-dKO, cell132


title: mTEChi, neonate, Aire/EED-dKO, cell131


title: mTEChi, neonate, Aire/EED-dKO, cell130


title: mTEChi, neonate, Aire/EED-dKO, cell129


title: mTEChi, neonate, Aire/EED-dKO, cell128


title: mTEChi, neonate, Aire/EED-dKO, cell127


title: mTEChi, neonate, Aire/EED-dKO, cell147


title: mTEChi, neonate, Aire/EED-dKO, cell125


title: mTEChi, neonate, Aire/EED-dKO, cell126


title: mTEChi, neonate, Aire/EED-dKO, cell124


title: mTEChi, neonate, Aire/EED-dKO, cell123


title: mTEChi, neonate, Aire/EED-dKO, cell143


title: mTEChi, neonate, Aire/EED-dKO, cell122


title: mTEChi, neonate, Aire/EED-dKO, cell116


title: mTEChi, neonate, Aire/EED-dKO, cell114


title: mTEChi, neonate, Aire/EED-dKO, cell120


title: mTEChi, neonate, Aire/EED-dKO, cell134


title: mTEChi, neonate, Aire/EED-dKO, cell115


title: mTEChi, neonate, Aire/EED-dKO, cell113


title: mTEChi, neonate, Aire/EED-dKO, cell111


title: mTEChi, neonate, Aire/EED-dKO, cell107


title: mTEChi, neonate, Aire/EED-dKO, cell109


title: mTEChi, neonate, Aire/EED-dKO, cell110


title: mTEChi, neonate, Aire/EED-dKO, cell119


title: mTEChi, neonate, Aire/EED-dKO, cell121


title: mTEChi, neonate, Aire/EED-dKO, cell112


title: mTEChi, neonate, Aire/EED-dKO, cell108


title: mTEChi, neonate, Aire/EED-dKO, cell105


title: mTEChi, neonate, Aire/EED-dKO, cell104


title: mTEChi, neonate, Aire/EED-dKO, cell103


title: mTEChi, neonate, Aire/EED-dKO, cell102


title: mTEChi, neonate, Aire/EED-dKO, cell100


title: mTEChi, neonate, Aire/EED-dKO, cell99


title: mTEChi, neonate, Aire/EED-dKO, cell98


title: mTEChi, neonate, Aire/EED-dKO, cell97


title: mTEChi, neonate, Aire/EED-dKO, cell106


title: mTEChi, neonate, Aire/EED-dKO, cell96


title: mTEChi, neonate, Aire/EED-dKO, cell95


title: mTEChi, neonate, Aire/EED-dKO, cell94


title: mTEChi, neonate, Aire/EED-dKO, cell117


title: mTEChi, neonate, Aire/EED-dKO, cell118


title: mTEChi, neonate, Aire/EED-dKO, cell93


title: mTEChi, neonate, Aire/EED-dKO, cell92


title: mTEChi, neonate, Aire/EED-dKO, cell91


title: mTEChi, neonate, Aire/EED-dKO, cell90


title: mTEChi, neonate, Aire/EED-dKO, cell87


title: mTEChi, neonate, Aire/EED-dKO, cell88


title: mTEChi, neonate, Aire/EED-dKO, cell86


title: mTEChi, neonate, Aire/EED-dKO, cell89


title: mTEChi, neonate, Aire/EED-dKO, cell84


title: mTEChi, neonate, Aire/EED-dKO, cell82


title: mTEChi, neonate, Aire/EED-dKO, cell85


title: mTEChi, neonate, Aire/EED-dKO, cell83


title: mTEChi, neonate, Aire/EED-dKO, cell79


title: mTEChi, neonate, Aire/EED-dKO, cell80


title: mTEChi, neonate, Aire/EED-dKO, cell101


title: mTEChi, neonate, Aire/EED-dKO, cell76


title: mTEChi, neonate, Aire/EED-dKO, cell78


title: mTEChi, neonate, Aire/EED-dKO, cell77


title: mTEChi, neonate, Aire/EED-dKO, cell75


title: mTEChi, neonate, Aire/EED-dKO, cell69


title: mTEChi, neonate, Aire/EED-dKO, cell71


title: mTEChi, neonate, Aire/EED-dKO, cell74


title: mTEChi, neonate, Aire/EED-dKO, cell68


title: mTEChi, neonate, Aire/EED-dKO, cell72


title: mTEChi, neonate, EED-cKO, cell303

value: EED-cKO


title: mTEChi, neonate, Aire/EED-dKO, cell73


title: mTEChi, neonate, EED-cKO, cell302


title: mTEChi, neonate, EED-cKO, cell301


title: mTEChi, neonate, EED-cKO, cell300


title: mTEChi, neonate, EED-cKO, cell299


title: mTEChi, neonate, EED-cKO, cell298


title: mTEChi, neonate, EED-cKO, cell297


title: mTEChi, neonate, EED-cKO, cell296


title: mTEChi, neonate, Aire/EED-dKO, cell81


title: mTEChi, neonate, EED-cKO, cell295


title: mTEChi, neonate, EED-cKO, cell293


title: mTEChi, neonate, EED-cKO, cell292


title: mTEChi, neonate, EED-cKO, cell289


title: mTEChi, neonate, EED-cKO, cell294


title: mTEChi, neonate, EED-cKO, cell288


title: mTEChi, neonate, EED-cKO, cell291


title: mTEChi, neonate, EED-cKO, cell290


title: mTEChi, neonate, EED-cKO, cell285


title: mTEChi, neonate, Aire/EED-dKO, cell70


title: mTEChi, neonate, EED-cKO, cell283


title: mTEChi, neonate, EED-cKO, cell286


title: mTEChi, neonate, EED-cKO, cell282


title: mTEChi, neonate, EED-cKO, cell281


title: mTEChi, neonate, EED-cKO, cell275


title: mTEChi, neonate, EED-cKO, cell276


title: mTEChi, neonate, EED-cKO, cell271


title: mTEChi, neonate, EED-cKO, cell274


title: mTEChi, neonate, EED-cKO, cell273


title: mTEChi, neonate, EED-cKO, cell278


title: mTEChi, neonate, EED-cKO, cell277


title: mTEChi, neonate, EED-cKO, cell280


title: mTEChi, neonate, EED-cKO, cell287


title: mTEChi, neonate, EED-cKO, cell269


title: mTEChi, neonate, EED-cKO, cell267


title: mTEChi, neonate, EED-cKO, cell265


title: mTEChi, neonate, EED-cKO, cell270


title: mTEChi, neonate, EED-cKO, cell266


title: mTEChi, neonate, EED-cKO, cell268


title: mTEChi, neonate, EED-cKO, cell264


title: mTEChi, neonate, EED-cKO, cell263


title: mTEChi, neonate, EED-cKO, cell259


title: mTEChi, neonate, EED-cKO, cell262


title: mTEChi, neonate, EED-cKO, cell261


title: mTEChi, neonate, EED-cKO, cell258


title: mTEChi, neonate, EED-cKO, cell260


title: mTEChi, neonate, EED-cKO, cell256


title: mTEChi, neonate, EED-cKO, cell284


title: mTEChi, neonate, EED-cKO, cell255


title: mTEChi, neonate, EED-cKO, cell254


title: mTEChi, neonate, EED-cKO, cell257


title: mTEChi, neonate, EED-cKO, cell279


title: mTEChi, neonate, EED-cKO, cell272


title: mTEChi, neonate, EED-cKO, cell253


title: mTEChi, neonate, EED-cKO, cell252


title: mTEChi, neonate, EED-cKO, cell251


title: mTEChi, neonate, EED-cKO, cell250


title: mTEChi, neonate, EED-cKO, cell248


title: mTEChi, neonate, EED-cKO, cell249


title: mTEChi, neonate, EED-cKO, cell246


title: mTEChi, neonate, EED-cKO, cell243


title: mTEChi, neonate, EED-cKO, cell241


title: mTEChi, neonate, EED-cKO, cell244


title: mTEChi, neonate, EED-cKO, cell242


title: mTEChi, neonate, EED-cKO, cell245


title: mTEChi, neonate, EED-cKO, cell238


title: mTEChi, neonate, EED-cKO, cell240


title: mTEChi, neonate, EED-cKO, cell237


title: mTEChi, neonate, EED-cKO, cell239


title: mTEChi, neonate, EED-cKO, cell230


title: mTEChi, neonate, EED-cKO, cell233


title: mTEChi, neonate, EED-cKO, cell232


title: mTEChi, neonate, EED-cKO, cell228


title: mTEChi, neonate, EED-cKO, cell231


title: mTEChi, neonate, EED-cKO, cell229


title: mTEChi, neonate, EED-cKO, cell236


title: mTEChi, neonate, EED-cKO, cell226


title: mTEChi, neonate, EED-cKO, cell227


title: mTEChi, neonate, EED-cKO, cell225


title: mTEChi, neonate, EED-cKO, cell224


title: mTEChi, neonate, EED-cKO, cell223


title: mTEChi, neonate, EED-cKO, cell247


title: mTEChi, neonate, EED-cKO, cell221


title: mTEChi, neonate, EED-cKO, cell218


title: mTEChi, neonate, EED-cKO, cell220


title: mTEChi, neonate, EED-cKO, cell222


title: mTEChi, neonate, EED-cKO, cell219


title: mTEChi, neonate, EED-cKO, cell215


title: mTEChi, neonate, EED-cKO, cell235


title: mTEChi, neonate, EED-cKO, cell214


title: mTEChi, neonate, EED-cKO, cell216


title: mTEChi, neonate, EED-cKO, cell211


title: mTEChi, neonate, EED-cKO, cell210


title: mTEChi, neonate, EED-cKO, cell217


title: mTEChi, neonate, EED-cKO, cell213


title: mTEChi, neonate, EED-cKO, cell208


title: mTEChi, neonate, EED-cKO, cell212


title: mTEChi, neonate, EED-cKO, cell209


title: mTEChi, neonate, EED-cKO, cell207


title: mTEChi, neonate, EED-cKO, cell205


title: mTEChi, neonate, EED-cKO, cell206


title: mTEChi, neonate, EED-cKO, cell201


title: mTEChi, neonate, EED-cKO, cell204


title: mTEChi, neonate, EED-cKO, cell199


title: mTEChi, neonate, EED-cKO, cell198


title: mTEChi, neonate, EED-cKO, cell200


title: mTEChi, neonate, EED-cKO, cell234


title: mTEChi, neonate, EED-cKO, cell197


title: mTEChi, neonate, EED-cKO, cell202


title: mTEChi, neonate, EED-cKO, cell195


title: mTEChi, neonate, EED-cKO, cell196


title: mTEChi, neonate, EED-cKO, cell192


title: mTEChi, neonate, EED-cKO, cell191


title: mTEChi, neonate, EED-cKO, cell194


title: mTEChi, neonate, EED-cKO, cell190


title: mTEChi, neonate, EED-cKO, cell193


title: mTEChi, neonate, EED-cKO, cell189


title: mTEChi, neonate, EED-cKO, cell187


title: mTEChi, neonate, EED-cKO, cell188


title: mTEChi, neonate, EED-cKO, cell185


title: mTEChi, neonate, EED-cKO, cell183


title: mTEChi, neonate, EED-cKO, cell182


title: mTEChi, neonate, EED-cKO, cell203


title: mTEChi, neonate, EED-cKO, cell181


title: mTEChi, neonate, EED-cKO, cell180


title: mTEChi, neonate, EED-cKO, cell176


title: mTEChi, neonate, EED-cKO, cell178


title: mTEChi, neonate, EED-cKO, cell177


title: mTEChi, neonate, EED-cKO, cell179


title: mTEChi, neonate, EED-cKO, cell173


title: mTEChi, neonate, EED-cKO, cell172


title: mTEChi, neonate, EED-cKO, cell169


title: mTEChi, neonate, EED-cKO, cell168


title: mTEChi, neonate, EED-cKO, cell170


title: mTEChi, neonate, EED-cKO, cell171


title: mTEChi, neonate, EED-cKO, cell167


title: mTEChi, neonate, EED-cKO, cell166


title: mTEChi, neonate, EED-cKO, cell186


title: mTEChi, neonate, Aire/EED-dKO, cell66


title: mTEChi, neonate, EED-cKO, cell184


title: mTEChi, neonate, Aire/EED-dKO, cell67


title: mTEChi, neonate, EED-cKO, cell165


title: mTEChi, neonate, Aire/EED-dKO, cell65


title: mTEChi, neonate, EED-cKO, cell164


title: mTEChi, neonate, Aire/EED-dKO, cell63


title: mTEChi, neonate, Aire/EED-dKO, cell61


title: mTEChi, neonate, Aire/EED-dKO, cell64


title: mTEChi, neonate, Aire/EED-dKO, cell62


title: mTEChi, neonate, Aire/EED-dKO, cell58


title: mTEChi, neonate, EED-cKO, cell175


title: mTEChi, neonate, Aire/EED-dKO, cell60


title: mTEChi, neonate, Aire/EED-dKO, cell59


title: mTEChi, neonate, Aire/EED-dKO, cell55


title: mTEChi, neonate, Aire/EED-dKO, cell56


title: mTEChi, neonate, Aire/EED-dKO, cell57


title: mTEChi, neonate, Aire/EED-dKO, cell53


title: mTEChi, neonate, EED-cKO, cell174


title: mTEChi, neonate, Aire/EED-dKO, cell54


title: mTEChi, neonate, Aire/EED-dKO, cell52


title: mTEChi, neonate, Aire/EED-dKO, cell51


title: mTEChi, neonate, Aire/EED-dKO, cell50


title: mTEChi, neonate, Aire/EED-dKO, cell49


title: mTEChi, neonate, Aire/EED-dKO, cell48


title: mTEChi, neonate, Aire/EED-dKO, cell47


title: mTEChi, neonate, Aire/EED-dKO, cell45


title: mTEChi, neonate, Aire/EED-dKO, cell46


title: mTEChi, neonate, Aire/EED-dKO, cell44


title: mTEChi, neonate, Aire/EED-dKO, cell43


title: mTEChi, neonate, Aire/EED-dKO, cell42


title: mTEChi, neonate, Aire/EED-dKO, cell41


title: mTEChi, neonate, Aire/EED-dKO, cell40


title: mTEChi, neonate, Aire/EED-dKO, cell38


title: mTEChi, neonate, Aire/EED-dKO, cell37


title: mTEChi, neonate, Aire/EED-dKO, cell36


title: mTEChi, neonate, Aire/EED-dKO, cell34


title: mTEChi, neonate, Aire/EED-dKO, cell33


title: mTEChi, neonate, Aire/EED-dKO, cell31


title: mTEChi, neonate, Aire/EED-dKO, cell32


title: mTEChi, neonate, Aire/EED-dKO, cell28


title: mTEChi, neonate, Aire/EED-dKO, cell26


title: mTEChi, neonate, Aire/EED-dKO, cell21


title: mTEChi, neonate, Aire/EED-dKO, cell29


title: mTEChi, neonate, Aire/EED-dKO, cell19


title: mTEChi, neonate, Aire/EED-dKO, cell27


title: mTEChi, neonate, Aire/EED-dKO, cell23


title: mTEChi, neonate, Aire/EED-dKO, cell24


title: mTEChi, neonate, Aire/EED-dKO, cell25


title: mTEChi, neonate, Aire/EED-dKO, cell18


title: mTEChi, neonate, Aire/EED-dKO, cell17


title: mTEChi, neonate, Aire/EED-dKO, cell16


title: mTEChi, neonate, Aire/EED-dKO, cell20


title: mTEChi, neonate, Aire/EED-dKO, cell15


title: mTEChi, neonate, Aire/EED-dKO, cell13


title: mTEChi, neonate, Aire/EED-dKO, cell35


title: mTEChi, neonate, Aire/EED-dKO, cell14


title: mTEChi, neonate, Aire/EED-dKO, cell12


title: mTEChi, neonate, Aire/EED-dKO, cell39


title: mTEChi, neonate, Aire/EED-dKO, cell11


title: mTEChi, neonate, Aire/EED-dKO, cell9


title: mTEChi, neonate, Aire/EED-dKO, cell7


title: mTEChi, neonate, Aire/EED-dKO, cell8


title: mTEChi, neonate, Aire/EED-dKO, cell6


title: mTEChi, neonate, Aire/EED-dKO, cell5


title: mTEChi, neonate, Aire/EED-dKO, cell30


title: mTEChi, neonate, Aire/EED-dKO, cell4


title: mTEChi, neonate, Aire/EED-dKO, cell2


title: mTEChi, neonate, Aire/EED-dKO, cell3


title: mTEChi, neonate, Aire/EED-dKO, cell22


title: mTEChi, neonate, EED-cKO, cell161


title: mTEChi, neonate, EED-cKO, cell162


title: mTEChi, neonate, EED-cKO, cell160


title: mTEChi, neonate, EED-cKO, cell158


title: mTEChi, neonate, EED-cKO, cell156


title: mTEChi, neonate, EED-cKO, cell154


title: mTEChi, neonate, EED-cKO, cell155


title: mTEChi, neonate, EED-cKO, cell152


title: mTEChi, neonate, EED-cKO, cell153


title: mTEChi, neonate, Aire/EED-dKO, cell10


title: mTEChi, neonate, EED-cKO, cell151


title: mTEChi, neonate, EED-cKO, cell150


title: mTEChi, neonate, EED-cKO, cell147


title: mTEChi, neonate, EED-cKO, cell146


title: mTEChi, neonate, EED-cKO, cell148


title: mTEChi, neonate, EED-cKO, cell145


title: mTEChi, neonate, Aire/EED-dKO, cell1


title: mTEChi, neonate, EED-cKO, cell144


title: mTEChi, neonate, EED-cKO, cell143