title: cr2x_x_cr4x.experiment_1.RNAseq.replicate2

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description:
Capsella rubella wt2x crossed with Capsella rubella wt4x 6DAP seeds
final_RNAseq.experiment_1.RPKM.txt.gz
cr_x_cr4n.rep2

data_processing:
small-RNA: Adapters were removed from the 150-bp long on the first read of the read pair of the library using cutadapt and the resulting 18–25 bp long reads were selected. Reads belonging to chloroplast, mitochondria and to structural noncoding RNAs (tRNAs, snRNAs, rRNAs, or snoRNAs) were removed using bowtie (-v 1). Surviving reads were mapped to the Capsella rubella v1.0 genome using ShorStack (--align_only –mismatches 0 –mmap f) mismatches (command: bowtie -f -t -v0) , and sequences that did not map were discarded.
Bisulfite-seq:The 150-bp-long pair-end reads were quality trimmed by removing the first five bases from the 5’ end and the last 15 bases from the 3’ end. Reads were mapped to the Capsella rubella v1.0 reference genome in paired-end mode (–score_min L, 0, 0.6) using Bismark v0.16.3. Mapped reads were deduplicated and cytosine methylation values calculated using the Bismark Methylation Extractor.
RNA-seq: Reads were quality trimmed using Trimmomatic (--three_prime_clip_R1 15 --three_prime_clip_R2 15 --clip_R1 10 --clip_R2 10) and mapped to the C. rubella v1.0 genome in pair-end mode using HISAT2. Transcript counts and RPKM values were calculated using featureCounts.
Assembly: Capsella rubella v1.0  (also listed as 183) http://www.phytozome.org/dataUsagePolicy.php?org=Org_Crubella
Assembly: Capsella grandiflora (GEnBank JAVXYZ000000000)
Supplementary files format and content: small-RNA: Unique small RNAs (between 18-25 nts) and their accumulation number (raw reads) are represented in a two column format file: <unique_smallRNA> <number_of_raw_reads>.<length_nts>
Supplementary files format and content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format: <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>
Supplementary files format and content: RNA-seq: expression levels (RPKM) are shown for genes in the chromosome-like first eight scaffolds of the Capsella rubella genome for each condition and replicate.

organism: Capsella rubella

source_name: Cr2x x Cr4x 6DAP Seed

growth_protocol: Seeds were surface sterilized with 30% bleach and 70% ethanol, rinsed with distilled water and sown on agar plates containing ½ Murashige and Skoog (MS) medium and 1% sucrose. They were then stratified for 2 days in the darkness at 4 °C and moved into a growth chamber with long-day photoperiod (16 h and 22 °C light, 8 h and 19 °C darkness) with a light intensity of 110 µE. 7 days olds seedlings were transferred to pots filled with sterile soli and plants were grown in a growth chamber with 60% humidity and daily cycles of 16 h light at 21 °C and 8 h darkness at 18 °C with light intensity of 150 µE.

extract_protocol:
Seeds of manually pollinated crossing were taken out of siliques 6 DAP and put into 20 µl of RNA later solution (Sigma-Aldrich). Each sample consisted of 10-15 siliques. RNA was extracted with RNeasy Plant Mini Kit (Qiagen) according to manufacturer’s instruction.
500 ng of RNA was used for RNA Seq library preparation with NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra RNA LibraryPrep Kit for Illumina (E7530). For each analyzed genotype there were three biological replicates. Libraries were sequenced on HiSeqX in a 150 bp paired-end mode.

treatment_protocol: Material was generated by manually crossing of indicated genotypes

value: seed


title: ma4cell_HA

status: Public on Sep 12 2024

type: SRA

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

country: China

institute: College of Life Science,Northeast Agricultural University

library_source: genomic

data_processing:
We aligned reads of to the mm10 reference genome using Bowtie2 v2.4.4 software. Unmapped and non-uniquely mapped reads were removed by picard & samtools. Next, we pooled the biological replicates for each stage and performed downstream analysis. For quantitative analysis, we normalized the read counts by computing the number of reads using merged replicate BAM files with the bamCompare tool in deepTools software. Peaks were screened on merged replicates by the normalized RPKM in 10000bp bins. Peak annotation was performed using the R package ChIPseeker with the default parameters.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: 4cell Embryo

extract_protocol:
embryos were washed three times in 0.5% BSA-PBS solution. Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to KAPA Hyper Prep Kit for illumina platform (kk8504)

tag: tissue

value: 4cell Embryo


title: ma2cell_input

source_name: 2cell Embryo

value: 2cell Embryo


title: maMO_input

source_name: morula Embryo

value: morula Embryo


title: WT_Mice2_large_area_interaction

city: New York

first: Abdulraouf

last: Abdulraouf

state: NY

address: 1230 York Ave

country: USA

institute: Rockefeller University

library_source: other

data_processing:
cDNA data processing:
Initial Data Preparation: After the sequencing process, the data is obtained in the form of two sets of FASTQ files: R1 and R2. R1 FASTQ files contain the barcode sequences for receiver bead along with their associated Unique Molecular Identifiers (UMIs). R2 FASTQ files contain the tagmented cDNA sequences.
Barcode Mapping and Tagging: The barcode sequences from R1 are mapped to a whitelist of bead barcodes with a tolerance of 1 base pair error. The identified bead barcode is then added as an identifier (ID) for the corresponding sequences in R2.
Read2 File Generation and PolyA Trimming: New Read2 files are generated where the name of each sequence in R2 contains the corresponding Read1 barcode. Additionally, any PolyA tails present at the end of the sequences are trimmed to ensure accurate mapping and analysis.
Read Mapping to Genome: The filtered and trimmed reads are then mapped to the reference genome using a tool such as STAR(25) (Spliced Transcripts Alignment to a Reference). This step involves aligning the sequences from R2 to the genomic sequences to identify their locations and potential splice sites.
Duplicate Removal: After mapping, duplicate reads are identified and removed to eliminate redundant data and ensure accuracy in downstream analysis. This process generates new SAM (Sequence Alignment/Map) files containing the mapped reads with duplicates removed.
Gene Count Matrices Generation: From the processed SAM files, gene count matrices are generated for each associated receiver bead. This involves counting the number of reads aligned to each gene for every receiver bead, providing quantitative information about gene expression levels.
Beads Connections processing
Initial Data Preparation: Following the sequencing process, data from two beads, namely receiver bead and sending beads, are obtained. Each bead connection includes unique molecular identifiers (UMIs) which help in identifying and quantifying individual connection molecules. Additionally, there are two types of reads: R1, which contains the barcode for receiver beads, and R2, which contains the barcodes for receiver beads. The reads are mapped to a whitelist of barcodes with 1 base pair error, including the UMI sequence. Duplicated reads are then filtered, and a csv file is generated with receiver bead, UMI, and sending bead barcode, where each line represents a unique molecular connection between receiver and sending beads.
Assembly: STAR_hg19_mm10_RNAseq
Supplementary files format and content: Please check below. Annotation column has content description as well.
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Mouse Brain

extract_protocol:
10 um thick mouse brains were cryosectioned, and RNA was hybridized to a barcoded hydrogel bead based array
Barcoded beads have a PCR handle, and Template Switching Oligo was utilized to amplify bound nucleic acid molecules.

value: Mouse Brain

tag: genotype

tag: treatment

value: WT


title: A03_brain_cortex

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

library_source: transcriptomic

data_processing:
BGI’s process included filtration and removal of reads with high levels of unknown base N, adaptor sequences and low-quality reads from raw reads.
Reads were mapped to the EMBL human genome 38, patch release 13 using the splice-aware aligner STAR v2.7.10a (parameters: --twopassMode Basic , --outFilterIntronMotifs RemoveNoncanonical , --outSAMstrandField intronMotif , --outSAMtype BAM Unsorted , --alignSoftClipAtReferenceEnds No , --outFilterMatchNmin 100 , --outSAMattrIHstart 0 , --alignEndsType EndToEnd)
BAM files were sorted and indexed using SAMtools v1.9
StringTie v2.1.7 was used to extract the gene and transcript abundances of each gene (parameters: -rf , -e)
Assembly: hg38.p13
Supplementary files format and content: gene_count_matrix.csv is a csv file of the raw counts for each gene
Supplementary files format and content: transcript_count_matrix.csv is a csv file of the raw counts of each transcript for each gene

molecule: polyA RNA

organism: Homo sapiens

source_name: Brain, Cerebral Cortex

extract_protocol:
Total RNA was isolated by a modified guanidinium thiocyanate method by TaKaRa Bio, Inc. (https://www.takarabio.com/)
Library construction was performed at the Beijing Genomics Institute (BGI, Shenzhen/Hong Kong, China https://en.genomics.cn) using the DNBseq platform on a strand-specific cDNA library generating 100 bp paired-end reads. The library preparation included a mRNAs enrichment step using oligo(dT)-attached magnetic beads.
ssRNA-seq (stranded RNA-seq)

value: Brain, Cerebral Cortex

tag: reported takara_lot_number


title: cr2x_x_cr4x.experiment_1.RNAseq.replicate1

description:
Capsella rubella wt2x crossed with Capsella rubella wt4x 6DAP seeds
final_RNAseq.experiment_1.RPKM.txt.gz
cr_x_cr4n.rep1

molecule: total RNA


title: WT_Mice2_large_area_cDNA

library_source: transcriptomic single cell

data_processing:
cDNA data processing:
Initial Data Preparation: After the sequencing process, the data is obtained in the form of two sets of FASTQ files: R1 and R2. R1 FASTQ files contain the barcode sequences for receiver bead along with their associated Unique Molecular Identifiers (UMIs). R2 FASTQ files contain the tagmented cDNA sequences.
Barcode Mapping and Tagging: The barcode sequences from R1 are mapped to a whitelist of bead barcodes with a tolerance of 1 base pair error. The identified bead barcode is then added as an identifier (ID) for the corresponding sequences in R2.
Read2 File Generation and PolyA Trimming: New Read2 files are generated where the name of each sequence in R2 contains the corresponding Read1 barcode. Additionally, any PolyA tails present at the end of the sequences are trimmed to ensure accurate mapping and analysis.
Read Mapping to Genome: The filtered and trimmed reads are then mapped to the reference genome using a tool such as STAR(25) (Spliced Transcripts Alignment to a Reference). This step involves aligning the sequences from R2 to the genomic sequences to identify their locations and potential splice sites.
Duplicate Removal: After mapping, duplicate reads are identified and removed to eliminate redundant data and ensure accuracy in downstream analysis. This process generates new SAM (Sequence Alignment/Map) files containing the mapped reads with duplicates removed.
Gene Count Matrices Generation: From the processed SAM files, gene count matrices are generated for each associated receiver bead. This involves counting the number of reads aligned to each gene for every receiver bead, providing quantitative information about gene expression levels.
Beads Connections processing
Initial Data Preparation: Following the sequencing process, data from two beads, namely receiver bead and sending beads, are obtained. Each bead connection includes unique molecular identifiers (UMIs) which help in identifying and quantifying individual connection molecules. Additionally, there are two types of reads: R1, which contains the barcode for receiver beads, and R2, which contains the barcodes for receiver beads. The reads are mapped to a whitelist of barcodes with 1 base pair error, including the UMI sequence. Duplicated reads are then filtered, and a csv file is generated with receiver bead, UMI, and sending bead barcode, where each line represents a unique molecular connection between receiver and sending beads.
Assembly: STAR_hg19_mm10_RNAseq
Supplementary files format and content: Please check below. Annotation column has content description as well.


title: ma2cell_HA


title: cr.experiment_1.RNAseq.replicate3

description:
Capsella rubella wt2x 6DAP seeds
final_RNAseq.experiment_1.RPKM.txt.gz
cr_x_cr.rep3

source_name: Cr 6DAP Seed wt


title: A02_cerebellum_total

source_name: Brain, Cerebellum

value: Brain, Cerebellum


title: WT_Mice_hippo_demo_cDNA


title: Female_Young_1_Section3_2_interaction


title: Female_Aged_1_Section3_2_interaction


title: cr.experiment_1.RNAseq.replicate2

description:
Capsella rubella wt2x 6DAP seeds
final_RNAseq.experiment_1.RPKM.txt.gz
cr_x_cr.rep2


title: Female_Young_1_Section2_interaction


title: cr.experiment_1.RNAseq.replicate1

description:
Capsella rubella wt2x 6DAP seeds
final_RNAseq.experiment_1.RPKM.txt.gz
cr_x_cr.rep1


title: cr2x_x_cr4x.experiment_1.RNAseq.replicate3

description:
Capsella rubella wt2x crossed with Capsella rubella wt4x 6DAP seeds
final_RNAseq.experiment_1.RPKM.txt.gz
cr_x_cr4n.rep3


title: Female_Young_1_Section3_1_interaction


title: maZygote_input

source_name: Zygote

value: Zygote


title: Female_Young_1_Section1_interaction


title: Female_Aged_1_Section3_2_cDNA


title: cr4x_x_cr4x.experiment_1.RNAseq.replicate3

description:
Capsella rubella wt4x seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cr4n_x_cr4n.rep3

source_name: Cr4x x Cr4xn 6DAP Seed


title: Female_Young_3_Section3_2_cDNA


title: MII_input

source_name: MII

value: MII


title: pablast_input

source_name: Blastocyst

value: Blastocyst


title: Female_Young_1_Section3_2_cDNA


title: MII_HA


title: cr4x_x_cr4x.experiment_1.RNAseq.replicate1

description:
Capsella rubella wt4x seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cr4n_x_cr4n.rep1


title: WT_Mice_hippo_demo_interaction


title: cr4x_x_cr4x.experiment_1.RNAseq.replicate2

description:
Capsella rubella wt4x seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cr4n_x_cr4n.rep2


title: Female_Young_1_Section2_cDNA


title: Female_Young_1_Section3_1_cDNA


title: Female_Young_1_Section1_cDNA


title: pablast_HA


title: cr-seed.experiment_2.RNAseq.nrpd1_x_nrpd1.replicate3

description:
Capsella rubella seed 6DAP of nrpd1
final_RNAseq.experiment_2.RPKM.txt.gz
nrpd1a_x_nrpd1a.replicate3

source_name: Cr 6DAP Seed nrpd1

extract_protocol:
Seeds of manually pollinated crossing were taken out of siliques 6 DAP and put into 20 µl of RNA later solution (Sigma-Aldrich). Each sample consisted of 10-15 siliques. RNA was extracted with RNeasy Plant Mini Kit (Qiagen) according to manufacturer’s instruction.
100 ng of RNA was used for RNA Seq library preparation with NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra RNA LibraryPrep Kit for Illumina (E7530). For each analyzed genotype there were three biological replicates. Libraries were sequenced on HiSeqX in a 150 bp paired-end mode.

value: nrpd1 (Cr1GR1)


title: paMO_input


title: co4x_x_cr.seed.experiment_3.RNAseq.replicate3

description:
Capsella orientalis wt4x crossed  with Capsella rubella wt seeds 6DAP
final_RNAseq.experiment_3.RPKM.txt.gz
endo_Co4n_x_Cr_rep3

organism: Capsella orientalis x Capsella rubella

source_name: Co4x x Cr  6DAP Endosperm wt


title: co4x_x_cr.seed.experiment_3.RNAseq.replicate2

description:
Capsella orientalis wt4x crossed  with Capsella rubella wt seeds 6DAP
final_RNAseq.experiment_3.RPKM.txt.gz
endo_Co4n_x_Cr_rep2


title: maZygote_HA


title: cr-seed.experiment_2.RNAseq.nrpd1_x_nrpd1.replicate2

description:
Capsella rubella seed 6DAP of nrpd1
final_RNAseq.experiment_2.RPKM.txt.gz
nrpd1a_x_nrpd1a.replicate2


title: cr-seed.experiment_2.RNAseq.nrpd1_x_wt.replicate3

description:
Capsella rubella of wt crossed with nrpd1 seed 6DAP
final_RNAseq.experiment_2.RPKM.txt.gz
nrpd1a_x_wt.replicate3

source_name: Cr 6DAP Seed nrpd1 x wt

value: nrpd1 (Cr1GR1) x wt(Cr 48.21)


title: co_x_cr-endosperm.BSseq.replicate1

description: Capsella orientalis crossed with Capsella rubella 6DAP endosperm

source_name: Co x Cr  6DAP Endosperm wt

extract_protocol:
Seeds of manually pollinated crossing were taken out of siliques 6 DAP and the endosperm were manually dissected and absorbed by the small part of tissue paper. Samples were stored at -20 °C and then used for isolation of genomic DNA with DNeasy Plant Mini Kit (Qiagen).
Bisulfite libraries were prepared with the Accel-NGS Methyl-Seq DNA Library Kit from Illumina (Cat No. 30096, Swift), and the sequencing was performed at Novogene (Hongkong, China) on a NovaSeq 6000 platform in 150-bp paired-end mode

value: endosperm


title: cr_x_co-endosperm.BSseq.replicate1

description: Capsella rubella crossed with Capsella orientalis 6DAP endosperm

source_name: Cr x Co  6DAP Endosperm wt


title: cr-seed.experiment_2.RNAseq.nrpd1_x_nrpd1.replicate1

description:
Capsella rubella seed 6DAP of nrpd1
final_RNAseq.experiment_2.RPKM.txt.gz
nrpd1a_x_nrpd1a.replicate1


title: paMO_HA


title: co4x_x_cr-endosperm.BSseq.replicate1

description: Capsella orientalis wt4x crossed with Capsella rubella 6DAP endosperm


title: cr_x_co-endosperm.BSseq.replicate2


title: pa8cell_input

source_name: 8cell Embryo

value: 8cell Embryo


title: pa4cell_input

source_name: 4cell Embryo


title: cr-seed.experiment_2.RNAseq.wt_x_wt.replicate3

description:
Capsella rubella seed 6DAP of wt
final_RNAseq.experiment_2.RPKM.txt.gz
wt_x_wt.replicate3


title: co_x_cr.experiment_1.RNAseq.replicate3

description:
Capsella orientalis crossed with Capsella rubella seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
co_x_cr.rep3

source_name: Co x Cr 6DAP Seed wt


title: co4x_x_co4x.seed.experiment_3.RNAseq.replicate3

description:
Capsella orientalis wt4x seeds 6DAP
final_RNAseq.experiment_3.RPKM.txt.gz
endo_Co4n_x_Co4n_rep3

organism: Capsella orientalis

source_name: Co4x  6DAP Endosperm wt


title: pa8cell_HA


title: co4x_x_cr-endosperm.BSseq.replicate2


title: pa2cell_input

source_name: 2cell Embryo


title: co_x_cr-endosperm.BSseq.replicate2


title: cr-seed.experiment_2.RNAseq.nrpd1_x_wt.replicate2

description:
Capsella rubella of wt crossed with nrpd1 seed 6DAP
final_RNAseq.experiment_2.RPKM.txt.gz
nrpd1a_x_wt.replicate2


title: co_x_cr.experiment_1.RNAseq.replicate2

description:
Capsella orientalis crossed with Capsella rubella seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
co_x_cr.rep2


title: cr-seed.experiment_2.RNAseq.wt_x_wt.replicate2

description:
Capsella rubella seed 6DAP of wt
final_RNAseq.experiment_2.RPKM.txt.gz
wt_x_wt.replicate2


title: pa4cell_HA


title: co_x_cr.experiment_1.RNAseq.replicate1

description:
Capsella orientalis crossed with Capsella rubella seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
co_x_cr.rep1


title: co4x_x_cr.seed.experiment_3.RNAseq.replicate1

description:
Capsella orientalis wt4x crossed  with Capsella rubella wt seeds 6DAP
final_RNAseq.experiment_3.RPKM.txt.gz
endo_Co4n_x_Cr_rep1


title: co4x_x_co4x.seed.experiment_3.RNAseq.replicate2

description:
Capsella orientalis wt4x seeds 6DAP
final_RNAseq.experiment_3.RPKM.txt.gz
endo_Co4n_x_Co4n_rep2


title: co4x_x_co4x.seed.experiment_3.RNAseq.replicate1

description:
Capsella orientalis wt4x seeds 6DAP
final_RNAseq.experiment_3.RPKM.txt.gz
endo_Co4n_x_Co4n_rep1


title: co4x-endosperm.BSseq.replicate2

description: Capsella orientalis wt4x 6DAP endosperm


title: sperm_HA

source_name: sperm

value: sperm


title: co.experiment_1.RNAseq.replicate2

description:
Capsella orientalis seed 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
co_x_co.rep2

source_name: Co 6DAP Seed wt


title: cr-endosperm.BSseq.wt_x_wt.replicate1

description: Capsella rubella wt crossed with nrpd1 6DAP endosperm

source_name: Cr 6DAP Endosperm wt


title: co-endosperm.BSseq.replicate2

description: Capsella orientalis 6DAP endosperm

source_name: Co  6DAP Endosperm wt


title: cbp_x_cg-seed.experiment_1.RNAseq.replicate3

description:
Capsella bursa-pastoris crossed with Capsella  grandiflora seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cbp_x_cg.rep3

organism: Capsella bursa-pastoris x Capsella grandiflora

source_name: Cbp x Cg 6DAP Seed wt


title: cbp_x_cg-seed.experiment_1.RNAseq.replicate2

description:
Capsella bursa-pastoris crossed with Capsella  grandiflora seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cbp_x_cg.rep2


title: cr-seed.experiment_2.RNAseq.wt_x_wt.replicate1

description:
Capsella rubella seed 6DAP of wt
final_RNAseq.experiment_2.RPKM.txt.gz
wt_x_wt.replicate1

source_name: Cr 6DAP Seed wt


title: co-endosperm.BSseq.replicate1

description: Capsella orientalis 6DAP endosperm


title: pa2cell_HA


title: cbp_x_cg-seed.experiment_1.RNAseq.replicate1

description:
Capsella bursa-pastoris crossed with Capsella  grandiflora seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cbp_x_cg.rep1


title: K27-zygote-3.3MO [Cut&Tag]

data_processing:
library strategy: Cut&Tag
We aligned paired-end CUT&Tag reads of H3K18lac to the mm10 reference genome using Bowtie2 v2.4.4 software. Unmapped and non-uniquely mapped reads were removed by picard & samtools. Next, we pooled the biological replicates and performed downstream analysis.  CUT&Tag peaks were called on merged replicates and normalized to input using MACS2 v2.2.7.1 software. Peak annotation was performed using the R package ChIPseeker with the default parameters. For quantitative analysis, we normalized the read counts by computing the number of reads using merged replicate BAM files with the bamCoverage tool in deepTools software.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: zygote

extract_protocol:
Embryos were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG-Tn5 and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 7 µL 0.5 M EDTA, 2 µL 10% SDS, and 1.7 µL 20 mg/mL proteinase K; for single-cell CUT&Tag assays, 5 µL stop buffer was used.
CUT&Tag was performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech). Embryos were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG-Tn5 and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 7 µL 0.5 M EDTA, 2 µL 10% SDS, and 1.7 µL 20 mg/mL proteinase K; for single-cell CUT&Tag assays, 5 µL stop buffer was used. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries under the following conditions: 72°C for 3 min, 98°C for 30 s, 17 cycles of 98°C for 10 s and 60°C for 5 s, and a final extension at 72°C for 1 min with a hold at 4°C. For single-cell CUT&Tag of human embryos, CUT&Tag was performed in well of a microplate. After tagmentation, single human embryos were transferred to 200µl tubes containing 5% Proteinase K. After embryos lysis, PCR buffer and adaptors were directly added to tubes, normal PCR cycle was performed. Post-PCR clean-up was performed by adding a 1.5× volume of DNA Clean Beads (Vazyme Biotech).

tag: cell type

value: zygote


title: cr-seed.experiment_2.RNAseq.nrpd1_x_wt.replicate1

description:
Capsella rubella of wt crossed with nrpd1 seed 6DAP
final_RNAseq.experiment_2.RPKM.txt.gz
nrpd1a_x_wt.replicate1

value: seed


title: sperm_input


title: co.experiment_1.RNAseq.replicate1

description:
Capsella orientalis seed 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
co_x_co.rep1


title: cr-endosperm.BSseq.wt_x_wt.replicate2


title: cr-endosperm.BSseq.wt_x_nrpd1.replicate2

description: Capsella rubella nrpd1 crossed with wt 6DAP endosperm

source_name: Cr 6DAP Endosperm wt x nrpd1

value: wt(Cr 48.21) x nrpd1 (Cr1GR1)


title: The RNA-seq of MSL2WT-preB cells - Rep3

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

description: The RNA-seq of MSL2WT-preB cells - Replicate 3

data_processing:
The base calling was performed by using BCL2Fastq pipeline (version: 0.3.1) and bcl2fastq (version 2.20.0.422).
RNA-seq:The 151bp paired-end reads were mapped to the mouse reference genome (mm10) using the STAR aligner (2.5.3a). Total read counts for the Gencode (vM23) reference genes were calculated using featureCounts (v2.0.0). The log-transformed total count per million (CPM) was calculated for each gene and genes with values below 0 were excluded. Differential gene expression was calculated by a linear modelling approach with the use of functions available in the R package limma. For differential expression analysis, the functions lmfit, eBayes and contrast.fit available in limma were applied to the voom-transformed expression values.  A set of significant differentially expressed genes was selected with an adjusted p-value cut-off of 0.05 after the Benjamini-Hochberg correction for multiple testing was applied.
ChIP-seq:The sequencing reads of two replicates each from MSL2, YY1 and RNA polymerase II ChIP was trimmed using trim_galore and mapped to mouse reference genome (mm10) using bowtie2 (2.2.3) with the default settings. The read duplicates and reads mapping to blacklisted regions were removed using programs available in picard, samtools  and bedtools. The properly mapped reads from both the replicates of MSL2 or YY1 ChIP and their corresponding input controls were used for identifying peaks by MACS2 (v2.1.0) with a q-value cut-off 0.05.
Assembly: mouse (mm10)
Supplementary files format and content: ChIP-seq: The CPM nomalized bigWig files (bw) generated using deep tools and bedGraph files generated by makeUCSCfile tool.
Supplementary files format and content: RNA-seq: The raw read count extracted by featureCounts.

source_name: preB cells

growth_protocol: Cells from bone marrow of SLP65KO were subcloned to a single cell and cultured as a single clone. The cells were electroporated with Msl2KO gRNA under the condition 0.27kV 0.925 CAP to generate Msl2KO cell line.  SLP65KO cell lines were grown in IMDM medium with 10%FCS, 5.46 ng/µl IL7 and 2mM L‐Glutamine with penicillin and streptomycin at 37°C 5%CO2 in an incubator.

extract_protocol:
ChIP: The cells were crosslinked with EGS and formaldehyde, lysed and DNA was fragmented into pieces of average 300-500bp by sonication. Chromatin was precipitated with a specific antibody and protein A-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified via QIAquick PCR Purification Kit according to the manufacturer's manual.  RNA: RNA were extracted by Nucleospin®RNAII isolation kit (Macherey‐Nagel).
ChIP:Library preparation for ChIP analysis was performed with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (Catalog #E7370) according to the manufacturer’s protocol. No size selection was used and amplification was performed using 10 PCR cycles. RNA-seq: rRNA depleted total RNA was prepared using Ribozero magnetic beads for library preparation.

treatment_protocol: No treatment

tag: cell line

value: preB cells


title: co4x-endosperm.BSseq.replicate1

description: Capsella orientalis wt4x 6DAP endosperm


title: The RNA-seq of MSL2KO-preB cells - Rep2

description: The RNA-seq of MSL2KO-preB cells - Replicate 2


title: cr-endosperm.BSseq.nrpd1_x_wt.replicate2

source_name: Cr 6DAP Endosperm nrpd1 x wt


title: cr-endosperm.BSseq.nrpd1_x_wt.replicate1


title: cr-endosperm.BSseq.wt_x_nrpd1.replicate1


title: The RNA-seq of MSL2KO-preB cells - Rep1

description: The RNA-seq of MSL2KO-preB cells - Replicate 1


title: RNA-3.3-MO-inject

data_processing:
For RNA-seq analysis of embryos, FastQC was performed for Illumina reads. We used Fastp software to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases. Next, we downloaded the mouse reference genome (genome assembly: mm10) from the UCSC database and used bowtie2 software for read alignment. The gene-level quantification approach was used to aggregate raw counts of mapped reads using the featureCounts tool. Gene expression was quantified by calculating the normalized fragments per kilobase of transcript per million mapped reads (FPKM) value. Next, we used the R package DESeq2 for differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: count.txt

extract_protocol:
Embryos were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the Phusion Hot Start II High-Fidelity PCR Master Mix (Thermo Fisher).
Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.


title: The RNA-seq of MSL2WT-preB cells - Rep2

description: The RNA-seq of MSL2WT-preB cells - Replicate 2


title: cr-endosperm.BSseq.wt2x_x wt4x.replicate2

description: Capsella rubella wt crossed with wt 4x 6DAP endosperm

source_name: Cr2x x Cr4x 6DAP Endosperm


title: cr-endosperm.BSseq.nrpd1_x_nrpd1.replicate2

description: Capsella rubella nrpd1 6DAP endosperm

source_name: Cr 6DAP Endosperm nrpd1


title: The RNA-seq of MSL2WT-preB cells - Rep1

description: The RNA-seq of MSL2WT-preB cells - Replicate 1


title: cr-endosperm.BSseq.nrpd1_x_nrpd1.replicate1

description: Capsella rubella nrpd1 6DAP endosperm


title: The Chromatin Immunoprecipitation of MSL2 - Input- Rep2

description:
The Chromatin Immunoprecipitation of MSL2 - Input- Replicate 2
Input_H.ucsc.bedGraph.gz

tag: antibody


title: The RNA-seq of MSL2KO-preB cells - Rep3

description: The RNA-seq of MSL2KO-preB cells - Replicate 3


title: NBXH high dose 3

type: RNA

city: beijing

last: Wang

address: Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital

institute: People's Liberation Army General Hospital

description: Gene expression of MTB infected mouse treated by high dose NBXH

hyb_protocol: HybridizationKit and Instruments:Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):10X Blocking Agent25X Fragmentation Buffer2x GEx Hybridization Buffer HI-RPMHybridization Chamber, stainless (Agilent p/n G2534A)Hybridization Chamber gasket slides (Agilent p/n G2534-60003)Hybridization oven (Agilent p/n G2545A)Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029)Procedure:Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.Equilibrate water bath to 60°C.For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:2.

scan_protocol: Instrument:Agilent Microarray Scanner (Agilent p/n G2565BA)Procedure:1.

data_processing: Extract data using Agilent Feature Extraction SoftwareSoftware:Agilent Feature ExtractionProcedure:1.

source_name: Peripheral Blood, MTB infected model treated by high dose NBXH , replicate 3

label_protocol: repare labeling reactionKit:Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)Procedure:1.

growth_protocol: Sixty BALB/c 42-62-day-old female mice were purchased from Beijing Vitalriver Experimental Animal Technology Co., LTD., and put into the animal laboratory of the Eighth Medical Center of the PLA General Hospital for adaptive feeding.

extract_protocol: Three weeks after the last immunization, three mice in each group mentioned above were euthanized, and then their blood was collected in heparin sodium anticoagulant tubes. According to the manufacturer's instructions, PBMCs were isolated with the Mouse PBMC Isolation Kit (Haoyang Biological Products Technology, Tianjin, China), and total RNA was extracted from PBMCs using TRIzol Reagent (Invitrogen, USA).

treatment_protocol: 3 days after MTB infection, 50 mice were randomly divided into the following 5 groups and orally administered 5 times a week: TB model group (0.5mL distilled water/day per mouse), JHW treatment group (12mg/day per mouse), low-dose (2.4mg/day per mouse) of NBXH intermediate group, middle-dose (4.8mg/day per mouse) of NBXH intermediate group, and high-dose (9.6mg/day per mouse) of NBXH intermediate group.

value: PBMC

tag: gender

value: female


title: The Chromatin Immunoprecipitation of MSL2 - Input- Rep1

description:
The Chromatin Immunoprecipitation of MSL2 - Input- Replicate 1
Input_H.ucsc.bedGraph.gz


title: Normal 3

description: Gene expression of uninfected mouse

source_name: Peripheral Blood, Uninfected mouse, replicate 3

value: uninfected mouse


title: NBXH middle dose 3

description: Gene expression of MTB infected mouse treated by middle dose NBXH

source_name: Peripheral Blood, MTB infected model treated by middle dose NBXH , replicate 3


title: Normal 1

description: Gene expression of uninfected mouse

source_name: Peripheral Blood, Uninfected mouse, replicate 1


title: NBXH low dose 3

description: Gene expression of MTB infected mouse treated by low dose NBXH

source_name: Peripheral Blood, MTB infected model treated by low dose NBXH , replicate 3


title: The Chromatin Immunoprecipitation of MSL2 - Rep1

description:
The Chromatin Immunoprecipitation of MSL2 - Replicate 1
MSL2_H.ucsc.bedGraph.gz


title: Normal 2

description: Gene expression of uninfected mouse

source_name: Peripheral Blood, Uninfected mouse, replicate 2


title: FAD_RTP_19

city: Barcelona

first: Genís

last: Campoy Campos

state: Barcelona

address: C. Casanova 143 3rd Floor North Wing, Biochemistry Unit

country: Spain

institute: Universitat De Barcelona

data_processing:
tRAX software (http://trna.ucsc.edu/tRAX/) was used for data processing
Assembly: Mus musculusGRCm39/mm39
Supplementary files format and content: txt format. It contains the normalized read counts of mature tRNA, pre-tRNA, mitochondrial tRNA, and other small RNAs, and each column represents one animal
Library strategy: Hydro-tRNA-seq

source_name: Hippocampus

growth_protocol: The transgenic mouse line 5xFAD (MMRRC catalog #034840-JAX, RRID:MMRRC_034840-JAX) was utilized for this investigation, as well as wild type (WT) animals with a B6SJL background. All animals were housed in colony rooms with a 12:12-h light/dark cycle, maintained at 19–22 °C and 40–60% humidity, with unlimited access to food and water. All the experimental animals were male.

extract_protocol:
WT and 5xFAD mice were euthanized by cervical dislocation and both hippocampi were dissected out and stored at -80ºC until use. Total RNA was isolated using TRIzolTM Reagent (from Thermo Fisher Scientific) and following manufacturer’s instructions. Determinations of RNA quantity and quality were made with a NanoDropTM One Spectrophotometer (from Thermo Fisher Scientific) and a 4200 TapeStation System (from Agilent Technologies), respectively. All samples showed an RNA integrity number (RIN) of 8 or higher. Small RNAs (sRNAs) were isolated from total RNA with the RNA Clean & ConcentratorTM-5 kit (from Zymo Research), according to manufacturer’s instructions. This way, we could separate sRNAs (17-200 nucleotides) from long RNAs (lRNAs, >200 nucleotides). For each sample, the sRNAs were resolved on 15% urea-polyacrylamide gels and recovered within a size window of 60-100 nucleotides, corresponding to the tRNA fraction, which was used for sequencing.
In order to determine the expression levels of precursor and mature tRNA species, a sequencing protocol called Hydro-tRNA-seq, specifically designed for tRNA detection and quantification, was performed at the Centre de Regulació Genòmica (CRG). Briefly, Hydro-tRNA-seq is based on the hydrolysis of the tRNAs, which generates fragments with less structure and fewer modifications that are more amenable for sequencing. In the CRG, tRNA factions were subjected to alkaline hydrolysis, dephosphorylation and rephosphorylation with T4 Polynucleotide Kinase (PNK), to finally prepare the small RNA cDNA library. Sequencing was performed on an Illumina HiSeq 2500 platform in a 50 base pair paired-end format (40 M reads).  Analysis of the sequencing data was performed by the Bioinformatics Unit of the CRG, using the tRNA Analysis of eXpression (tRAX) software.

treatment_protocol: 6-month old WT and 5xFAD mice received bilateral hippocampal injections of  shRNA-containing adeno-associated viruses (AAVs) to genetically silence RTP801 in neurons. Summarizing, mice were injected in the CA1 and in the dentate gyrus with neuron-targeted rAAV2/8-H1-shControl-RSV-GFP (1.2 × 1013 genome copies (GCs)) or rAAV2/8-H1-shRTP801-RSV-GFP (1.07 × 1013 GCs). After 2 hours of careful monitoring, mice were returned to their cage for 4 weeks and were then euthanized for biochemical analysis.

value: Hippocampus

tag: Sex

value: male

tag: disease

value: Alzheimer's mouse model


title: Visium5xFAD_8_S8_L003

city: Irvine

first: Negin

last: Rahimzadeh

state: CA

address: 3224 Biological Sciences III

institute: UCI

description:
5XFAD_seurat_processed_annotated.rds
visium_5xFAD_11-24-21_sample_meta.csv

data_processing:
snRNA-Seq:  Gene expression quantification was performed using splitpipe (version X) from Parse Biosciences. Ambient RNA signal was quantified and corrected using Cellbender1 remove-background (v 0.2.0). Heterotypic barcode collisions were inferred using Scrublet2 (v 0.2.3). The individual snRNA-seq experiments were merged into a single anndata (v 0.8.0) object, resulting in 611,999 barcodes and 29,889 genes before quality control (QC) filtering. Various QC filters were applied, including UMIs detected, Scrublet doublet score, and percentage of mitochondrial reads. Dataset-wide cutoffs were used to remove barcodes with specific criteria. Additionally, a more stringent filter was applied to one of the snRNA-seq experiments. After QC, a total of 431,534 barcodes were retained for downstream analysis  Visium data: Sequencing reads from the human and mouse Visium experiments were processed using the 10X Genomics Spaceranger (v 1.2.1) pipeline, with GRch38 and MM10 as the respective reference transcriptomes. Spaceranger count was used to align sequencing reads to the reference, quantify gene expression, and perform a preliminary clustering analysis for each sample. Unlike the snRNA-seq dataset, we did not filter out additional spots based on sequencing QC metrics. The UMI counts matrices and fluorescent images for the human and mouse samples were combined into merged Seurat3–5 objects for the respective species.
Assembly: GRCH38, MM10
Supplementary files format and content: snRNA-Seq and Visium data were saved as R data files (.rda), with corresponding metadata as comma-separated values (.csv) files.

source_name: Brain

extract_protocol:
For snRNA-seq, single nucleus suspensions were isolated from about 50mg frozen human cortex following Parse biosciences recommendation. For spatial transcriptomics, fresh frozen mouse and human brain samples were embedded in OCT medium and cryosectioned at 10um thickness and mounted on visium slides.
snRNA-seq libraries were prepared using Parse biosciences Evercode WT kit (v1). For spatial transcriptomics, 10x genomics visium kit was used following manufacturer’s protocol.

tag: group

tag: diagnosis

value: WT

value: M

value: Brain

tag: age


title: NBXH middle dose 2

source_name: Peripheral Blood, MTB infected model treated by middle dose NBXH , replicate 2

value: MTB infected mouse treated by middle dose NBXH


title: The Chromatin Immunoprecipitation of MSL2 - Rep2

description:
The Chromatin Immunoprecipitation of MSL2 - Replicate 2
MSL2_H.ucsc.bedGraph.gz


title: NBXH high dose 1

source_name: Peripheral Blood, MTB infected model treated by high dose NBXH , replicate 1

value: MTB infected mouse treated by high dose NBXH


title: cr-endosperm.BSseq.wt2x_x_wt2x.replicate1

description: Capsella rubella wt 6DAP endosperm

source_name: Cr 6DAP Endosperm wt

value: endosperm


title: NBXH middle dose 1

source_name: Peripheral Blood, MTB infected model treated by middle dose NBXH , replicate 1


title: NBXH low dose 2

source_name: Peripheral Blood, MTB infected model treated by low dose NBXH , replicate 2

value: MTB infected mouse treated by low dose NBXH


title: Visium5xFAD_9_S9_L003


title: NBXH low dose 1

source_name: Peripheral Blood, MTB infected model treated by low dose NBXH , replicate 1


title: JHW 2

description: Gene expression of MTB infected mouse treated by JHW

source_name: Peripheral Blood, MTB infected model treated by JHW, replicate 2

value: MTB infected mouse treated by JHW


title: JHW 3

source_name: Peripheral Blood, MTB infected model treated by JHW, replicate 3


title: Model 2

description: Gene expression of MTB infected mouse

source_name: Peripheral Blood, MTB infected model, replicate 2

value: MTB infected mouse


title: cr-endosperm.BSseq.wt2x_x wt4x.replicate1

source_name: Cr2x x Cr4x 6DAP Endosperm


title: cr-endosperm.sRNA.nrpd1_x_nrpd1.replicate2

description: Capsella rubella nrpd1 6DAP endosperm

source_name: Cr 6DAP endosperm nrpd1

extract_protocol:
For each cross around 600 seeds at 6 DAP were opened and the endopserm was manually dissected. sRNAs were extracted using the mirVana miRNA isolation kit (Ambion/Life Technologies) following the enrichment procedure for small RNAs resulting in a small RNA fraction ≤200nt.
Libraries were prepared with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® using 50 -100 ng of input for each sample. Size selection was performed with 6% polyacrylamide gel; bands corresponding to about 150 bp were cut and purified from the gel for further analysis. Sequencing was performed at Novogene (Hongkong, China) on a NovaSeq 6000 platform in 150-bp paired-end mode.

value: nrpd1 (Cr1GR1)


title: cr-endosperm.sRNA.nrpd1_x_wt.replicate2

description: Capsella rubella nrpd1 crossed with Capsella rubella wt 6DAP endosperm

source_name: Cr 6DAP endosperm nrpd1 x wt

value: nrpd1 (Cr1GR1) x wt(Cr 48.21)


title: cr-endosperm.BSseq.wt2x_x_wt2x.replicate2

description: Capsella rubella wt 6DAP endosperm


title: FAD_CT_16

value: shCT


title: cr-endosperm.sRNA.nrpd1_x_wt.replicate1


title: Visium5xFAD_5_S5_L003


title: WT_RTP_17

value: Control


title: WT_RTP_10


title: Visium5xFAD_6_S6_L003


title: cr-endosperm.sRNA.nrpd1_x_nrpd1.replicate1

description: Capsella rubella nrpd1 6DAP endosperm


title: WT_CT_15


title: cr-endosperm.sRNA.WT.replicate1

description: Capsella rubella 6DAP endosperm


title: WT_RTP_21


title: FAD_RTP_14


title: cg-seed.experiment_1.RNAseq.replicate3

description:
Capsella grandiflora seed 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cg_x_cg.rep3

organism: Capsella grandiflora

source_name: Cg 6DAP Seed wt

value: seed


title: Visium5xFAD_3_S3_L003

value: F


title: Model 1

description: Gene expression of MTB infected mouse

source_name: Peripheral Blood, MTB infected model, replicate 1

value: PBMC

value: female


title: FAD_CT_18

value: Hippocampus

value: male

value: Alzheimer's mouse model


title: FAD_RTP_12


title: cr-endosperm.sRNA.WT.replicate2

description: Capsella rubella 6DAP endosperm


title: WT_CT_6

value: WT


title: WT_CT_11


title: WT_CT_5


title: cg-seed.experiment_1.RNAseq.replicate2

description:
Capsella grandiflora seed 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cg_x_cg.rep2


title: Visium5xFAD_4_S4_L003

value: Brain


title: WT_RTP_4


title: FAD_RTP_8


title: Visium5xFAD_1_S1_L003


title: FAD_RTP_7


title: Visium5xFAD_2_S2_L003


title: Visium5xFAD_7_S7_L003

value: M


title: WT_CT_3


title: FAD_RTP_2


title: cg-seed.experiment_1.RNAseq.replicate1

description:
Capsella grandiflora seed 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cg_x_cg.rep1


title: Visium5xFAD_16_S16_L003


title: cg-endosperm.sRNA.WT.replicate2

description: Capsella grandiflora 6DAP endosperm

source_name: Cg 6DAP Endosperm wt

value: endosperm


title: FAD_CT_1

source_name: Hippocampus


title: Visium5xFAD_15_S15_L003

source_name: Brain


title: SM-J39ZI_S644_E1-50

city: Chapel Hill

first: Jesse

last: Niehaus

state: NC

address: 116 Manning Drive, 7008B Mary Ellen Jones Building

department: Neuroscience Center

institute: University of North Carolina at Chapel Hill

description:
SMART-seq v2
Cell211

data_processing:
Single-cell fastq files were aligned to the mm10 mouse genome (GRCm38) using STAR version 2.7.3a (STARsolo) under suggested parameters for unstranded Smartseq data. Uniquely aligned exonic reads were used for quantification.
Assembly: mm10
Supplementary files format and content: comma-separated values file

source_name: Pontine nucleus

extract_protocol:
Two 8-week-old Snap25-IRES2-Cre;Ai14 mice (one from each sex) were perfused with artificial cerebrospinal fluid comprised of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), and thiourea (2 mM), bubbled with carbogen (95% O2 and 5% CO2). The pontine nucleus was dissected and embedded in 2% agarose, sliced into 250-µm sections with a vibratome, then subjected to enzymatic digestion with pronase (1 mg/mL) for 70 min at room temperature and trituration using fire-polished Pasteur pipettes to generate single-cell suspensions. Live single Pn neurons were isolated into 8-well strips containing SSv4 lysis buffer based on DAPI-/tdTomato+ expression using fluorescence-activated cell sorting, then stored at -80°C.
To prepare single-cell transcriptome libraries, poly-adenylated RNAs were reverse-transcribed into full-length cDNA and subjected to 18 PCR amplification cycles according to the SSv4 protocol. Single-cell libraries were indexed and prepared for Illumina sequencing using the Nextera XT DNA Library Preparation Kit. Multiplexed libraries were sequenced on HiSeq2500 sequencers to generate 100-bp paired-end reads at a depth of 2.5 million reads per cell.
SMART-seq v2 (SSv4; TakaraBio)

value: Pontine nucleus

value: Neuron


title: SM-J39ZI_S645_E1-50

description:
SMART-seq v2
Cell212


title: NBXH high dose 2

source_name: Peripheral Blood, MTB infected model treated by high dose NBXH , replicate 2

value: MTB infected mouse treated by high dose NBXH


title: SM-J39ZI_S642_E1-50

description:
SMART-seq v2
Cell210


title: Visium5xFAD_14_S14_L003


title: SM-J39ZI_S609_E1-50

description:
SMART-seq v2
Cell209


title: SM-J39ZI_S608_E1-50

description:
SMART-seq v2
Cell208


title: Visium5xFAD_13_S13_L003


title: cg-endosperm.sRNA.WT.replicate1

description: Capsella grandiflora 6DAP endosperm


title: SM-J39ZI_S605_E1-50

description:
SMART-seq v2
Cell207


title: 3-dpf Zebrafish whole embryo, Testorterone (30µM) + EGCG (100µM)  treated, clutch  4

city: Houston

first: Daniel

last: Gorelick

state: texas

address: 1 Baylor Plaza BCM229

institute: Baylor College of Medicine

data_processing:
We trimmed the raw RNA sequencing FastQ data for low-quality reads using trim_galore (version 0.6.10) (Krueger 2015).
We mapped the trimmed data using STAR (version 2.7.1a) (Dobin et al. 2013) onto the zebrafish genome assembly GRCz11, maintained by the Genome Reference Consortium (GRC).
Mapped sequence reads were aligned to genomic features using featureCounts (Liao et al. 2014).
Assembly: GRCz11
Supplementary files format and content: Excel file containing raw gene abundance counts for each sample

organism: Danio rerio

source_name: 3 dpf whole embryo

extract_protocol:
RNA was extracted using Direct-zol RNA miniprep Kit from Zymo Research (catalog #11-331) by following manufacturer 's protocol
Directional mRNA library (poly A enrichment) was prepared by Novogene America

treatment_protocol: AB zebrafish embryos were exposed beginning at 2-4 hours post fertilization until 3 days old

value: 3 dpf whole embryo

value: Testorterone (30uM) + EGCG (100uM)


title: 3-dpf Zebrafish whole embryo, Testorterone (30µM) + EGCG (100µM)  treated, clutch  2


title: SM-J39ZI_S600_E1-50

description:
SMART-seq v2
Cell205


title: Visium5xFAD_12_S12_L003


title: SM-J39ZI_S603_E1-50

description:
SMART-seq v2
Cell206


title: SM-J39ZI_S569_E1-50

description:
SMART-seq v2
Cell204


title: Visium5xFAD_11_S11_L003


title: 3-dpf Zebrafish whole embryo, Testosterone (30µM) + Calindol (5µM)  treated, clutch  4

value: Testosterone (30uM) + Calindol (5uM)


title: SM-J39ZI_S546_E1-50

description:
SMART-seq v2
Cell203


title: 3-dpf Zebrafish whole embryo, Testorterone (30µM) + EGCG (100µM)  treated, clutch  1


title: SM-J39ZI_S541_E1-50

description:
SMART-seq v2
Cell202


title: SM-J39ZI_S536_E1-50

description:
SMART-seq v2
Cell201


title: 3-dpf Zebrafish whole embryo, Testosterone (30µM) + Calindol (5µM)  treated, clutch  2


title: Undetermined_S0_L003


title: SM-J39ZI_S520_E1-50

description:
SMART-seq v2
Cell199


title: SM-J39ZI_S534_E1-50

description:
SMART-seq v2
Cell200


title: Visium5xFAD_9_S9_L002

description:
5XFAD_seurat_processed_annotated.rds
visium_5xFAD_11-15-21_sample_meta.csv


title: Visium5xFAD_10_S10_L003


title: SM-J39ZI_S517_E1-50

description:
SMART-seq v2
Cell198


title: SM-J39ZI_S516_E1-50

description:
SMART-seq v2
Cell197


title: SM-J39ZI_S511_E1-50

description:
SMART-seq v2
Cell196


title: JHW 1

source_name: Peripheral Blood, MTB infected model treated by JHW, replicate 1

value: MTB infected mouse treated by JHW


title: 3-dpf Zebrafish whole embryo, Testosterone (30µM) treated, clutch  4

value: Testosterone (30uM)


title: Visium5xFAD_8_S8_L002


title: SM-J39ZI_S509_E1-50

description:
SMART-seq v2
Cell194


title: 3-dpf Zebrafish whole embryo, Testosterone (30µM) treated, clutch  2


title: SM-J39ZI_S510_E1-50

description:
SMART-seq v2
Cell195


title: SM-J39ZI_S480_E1-50

description:
SMART-seq v2
Cell191


title: SM-J39ZI_S504_E1-50

description:
SMART-seq v2
Cell193


title: SM-J39ZI_S503_E1-50

description:
SMART-seq v2
Cell192


title: Visium5xFAD_5_S5_L002


title: 3-dpf Zebrafish whole embryo, Testosterone (30µM) + Calindol (5µM)  treated, clutch  1


title: Visium5xFAD_6_S6_L002


title: 3-dpf Zebrafish whole embryo, 0.1% DMSO control, clutch 4

value: 0.1% DMSO


title: 3-dpf Zebrafish whole embryo, Testosterone (30µM) treated, clutch  1


title: SM-J39ZI_S474_E1-50

description:
SMART-seq v2
Cell189


title: SM-J39ZI_S473_E1-50

description:
SMART-seq v2
Cell188


title: SM-J39ZI_S478_E1-50

description:
SMART-seq v2
Cell190


title: Visium5xFAD_4_S4_L002

value: F


title: 3-dpf Zebrafish whole embryo, 0.1% DMSO control, clutch 1


title: 3-dpf Zebrafish whole embryo, 0.1% DMSO control, clutch 2


title: SM-J39ZI_S466_E1-50

description:
SMART-seq v2
Cell186


title: Visium5xFAD_3_S3_L002


title: SM-J39ZI_S459_E1-50

description:
SMART-seq v2
Cell183


title: Visium5xFAD_2_S2_L002


title: cg_x_cr-endosperm.BSseq.replicate2

description: Capsella grandiflora crossed with Capsella rubella  6DAP endosperm

organism: Capsella grandiflora x Capsella rubella

source_name: Cg x Cr 6DAP Endosperm wt


title: Visium5xFAD_7_S7_L002


title: SM-J39ZI_S463_E1-50

description:
SMART-seq v2
Cell185


title: cg_x_cr-endosperm.BSseq.replicate1


title: cg_x_cr-endosperm.sRNA.WT.replicate2

description: Capsella grandiflora x Capsella rubella endosperm 6DAP

extract_protocol:
For each cross around 600 seeds at 6 DAP were opoened and the endopserm was manually dissected. sRNAs were extracted using the mirVana miRNA isolation kit (Ambion/Life Technologies) following the enrichment procedure for small RNAs resulting in a small RNA fraction ≤200nt.
Libraries were prepared with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® using 50 -100 ng of input for each sample. Size selection was performed with 6% polyacrylamide gel; bands corresponding to about 150 bp were cut and purified from the gel for further analysis. Sequencing was performed at Novogene (Hongkong, China) on a NovaSeq 6000 platform in 150-bp paired-end mode.


title: Visium5xFAD_16_S16_L002


title: SM-J39ZI_S468_E1-50

description:
SMART-seq v2
Cell187


title: cg_x_cr-endosperm.sRNA.WT.replicate1


title: Visium5xFAD_1_S1_L002


title: SM-J39ZI_S460_E1-50

description:
SMART-seq v2
Cell184


title: SM-J39ZI_S376_E1-50

description:
SMART-seq v2
Cell178


title: SM-J39ZI_S383_E1-50

description:
SMART-seq v2
Cell181


title: SM-J39ZI_S378_E1-50

description:
SMART-seq v2
Cell179


title: SM-J39ZI_S370_E1-50

description:
SMART-seq v2
Cell175


title: Visium5xFAD_14_S14_L002


title: Visium5xFAD_15_S15_L002


title: Visium5xFAD_13_S13_L002


title: SM-J39VS_S647_E1-50

description:
SMART-seq v2
Cell173


title: Patient derived organoid from sample 16 LATE PASSAGE

first: Yuan

last: Liu

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Batch A: CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.  STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.  Expression count matrix was computed using HTSeq version HTSeq-0.13.5. Parameters set were: -m intersection-strict -s no -t exon
Batch B: CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.  STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.  Expression count matrix was computed using HTSeq version HTSeq-0.13.5. Parameters set were: -m intersection-strict -s reverse -t exon
Batch C: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads. Expression count matrix was computed using HTSeq version  HTSeq-0.13.5. Parameters set were: -m intersection-strict -s no -t exon
Assembly: GRC37/hg19
Supplementary files format and content: tab-delimited file containing raw counts

source_name: Primary-Lung

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (74104, Qiagen), in accordance with the manufacturer’s protocol
Batch A: library preparation and RNA sequencing were performed by the Integrated Genomics Operation at MSK using Illumina HiSeq with 50 paired-end reads, and approximately 40 million reads were generated for each sample.
Batch B: library preparation and RNA sequencing were performed by the Integrated Genomics Operation at MSK using Illumina HiSeq with 100 paired-end reads, and approximately 20 million reads were for each sample.
Batch C: library preparation and RNA sequencing were performed by Novogene using Illumina Novaseq 6000 with 150 paired-end reads, and approximately 30 million reads were generated for each sample.

value: Primary-Lung

value: epithelial cells

value: PDO

tag: batch

value: c


title: SM-J39ZI_S379_E1-50

description:
SMART-seq v2
Cell180


title: Visium5xFAD_12_S12_L002

value: WT

value: Brain


title: Visium5xFAD_11_S11_L002

value: M


title: SM-J39VS_S643_E1-50

description:
SMART-seq v2
Cell171

value: Pontine nucleus


title: Human tumor sample 18.

value: Tumor


title: SM-J39VS_S637_E1-50

description:
SMART-seq v2
Cell169

value: Neuron


title: SM-J39ZI_S374_E1-50

description:
SMART-seq v2
Cell177


title: SM-J39VS_S635_E1-50

description:
SMART-seq v2
Cell168


title: Visium5xFAD_10_S10_L002


title: SM-J39VS_S642_E1-50

description:
SMART-seq v2
Cell170


title: Human tumor sample 16.


title: Visium8_S8_L003

description:
5XFAD_seurat_processed_annotated.rds
5XFAD_8samples.csv


title: IPFTMA5, Post-Xenium Visium HD (VUILD49LA, TILD113LA, TILD111LA, VUHD049)

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

data_processing:
SpaceRanger Count v3.0.0 (10x Genomics) with default parameters was used to align reads to the GRCh38 reference genome.
A high resolution image of H&E stained tissue was aligned using the Visium HD Manual Alignment tool on Loupe Browser v8.0.0.
Assembly: GRCh38
Supplementary files format and content: Tar archive containing Visium HD output bundle
Supplementary files format and content: High resolution image of H&E stained tissue in TIF format.
Supplementary files format and content: Cytassist image of H&E stained tissue in TIF format.
Supplementary files format and content: Alignment file in JSON format for alignment of high resolution image to spatial data.
Library strategy: Spatial Transcriptomics

source_name: lung

growth_protocol: For TMA5, a custom 3mm square punch was made to fit the specifications of the “Quick-Ray Manual Tissue Microarrayer Full Set”, and a new 3x6 layout was designed. These cores were punched and placed tissue-side down on double-sided tape in a FFPE block mold. Paraffin wax (VWR 76548-194) was then poured slowly into the back of mold with tapping to release trapped air pockets between the cores. The block was allowed to cool completely overnight. Once complete, the block was placed face down on a clean glass slide and briefly heated in a warm drawer (~45°C) to slightly melt the paraffin together and even the block face. It was then cooled to room temperature, removed from the slide, sealed in a bag, and stored at 4°C.

extract_protocol:
Slides underwent probe hybridization overnight and probe ligation for 1hr at 37℃ following manufacturer's protocols. Prior to CytAssist probe capture, the Visium HD slide was washed an d sample slides were stained in eosin briefly before placement on the instrument. The probe transfer occurred on the CytAssist instrument for 30min at 37℃. Probes were then extended on the Visium HD slide and eluted from said slide into a tube. Pre-amplification and SPRIselect were performed according to manufacturer's protocols. (10X Demonstrated Protocol CG000685)
Probe-based library was constructed using Dual Index Plate TS Set A (10X Genomics 1000251). Sample index PCR cycle number was determined by the Cq value from qPCR (Applied Biosystems QuantStudio 5). A final cleanup step with SPRIselect reagent was followed by storage at -20°C until sequencing. Next generation sequencing was carried out on Illumina's NovaSeq X platform using a 10 billion read, 300 cycle flow cell. Minimum sequencing recommendations were met using the product of tissue coverage percentage estimations and constant maximum read figure 275 million read pairs. Optimal cluster density was achieved with a lane loading concentration of 235 pM. (10X Genomics Demonstrated Protocol CG000685)

treatment_protocol: All protocol workstations and equipment were cleaned using RNase Away (RPI 147002) followed by 70% Isopropanol. All reagents, including water, were molecular grade nuclease-free. For archived slides post- Xenium and H&E staining, the 5um samples on slides were decoverslipped using a razor blade and xylene. They were then destained in 0.1 N HCl for 15 minutes at 42℃. Decrosslinking was skipped as it had already occurred as part of the Xenium protocol. (10X Genomics Demonstrated Protocol CG000684)

value: lung


title: SM-J39VS_S634_E1-50

description:
SMART-seq v2
Cell167


title: SM-J39VS_S630_E1-50

description:
SMART-seq v2
Cell164


title: Metastasis derived organoid harvested from mouse brain.  Origins from PDO6.

source_name: Metastasis-Brain

value: Metastasis-Brain

value: MDO


title: SM-J39VS_S632_E1-50

description:
SMART-seq v2
Cell165


title: Visium7_S7_L003


title: Patient derived organoid from sample 24


title: SM-J39ZI_S372_E1-50

description:
SMART-seq v2
Cell176


title: Human tumor sample 1.


title: SM-J39VS_S648_E1-50

description:
SMART-seq v2
Cell174


title: SM-J39VS_S628_E1-50

description:
SMART-seq v2
Cell163


title: Patient derived organoid from sample 18


title: SM-J39ZI_S458_E1-50

description:
SMART-seq v2
Cell182


title: SM-J39VS_S644_E1-50

description:
SMART-seq v2
Cell172


title: SM-J39VS_S627_E1-50

description:
SMART-seq v2
Cell162


title: SM-J39VS_S552_E1-50

description:
SMART-seq v2
Cell161


title: SM-J39VS_S551_E1-50

description:
SMART-seq v2
Cell160


title: Visium6_S6_L003


title: SM-J39VS_S550_E1-50

description:
SMART-seq v2
Cell159


title: Patient derived organoid from sample 12

source_name: Metastsis-Brain

value: Metastsis-Brain


title: Visium5_S5_L003


title: SM-J39VS_S548_E1-50

description:
SMART-seq v2
Cell158


title: SM-J39VS_S633_E1-50

description:
SMART-seq v2
Cell166


title: Visium4_S4_L003


title: SM-J39VS_S547_E1-50

description:
SMART-seq v2
Cell157


title: Patient derived organoid from sample 11


title: SM-J39VS_S543_E1-50

description:
SMART-seq v2
Cell156


title: Visium3_S3_L003


title: Patient derived organoid from sample 9


title: SM-J39VS_S531_E1-50

description:
SMART-seq v2
Cell152


title: SM-J39VS_S533_E1-50

description:
SMART-seq v2
Cell153


title: Visium2_S2_L003


title: SM-J39VL_S576_E1-50

description:
SMART-seq v2
Cell151


title: SM-J39VS_S540_E1-50

description:
SMART-seq v2
Cell154


title: Patient derived organoid from sample 6 W. GL


title: Visium1_S1_L003


title: Patient derived organoid from sample 16 EARLY PASSAGE


title: Patient derived organoid from sample 7


title: Patient derived organoid from sample 6


title: SM-J39VL_S572_E1-50

description:
SMART-seq v2
Cell148


title: 592_S10_L002

description:
5XFAD_seurat_processed_annotated.rds
pilot_samples.csv


title: SM-J39VL_S573_E1-50

description:
SMART-seq v2
Cell149


title: 592_S10_L001


title: SM-J39VL_S571_E1-50

description:
SMART-seq v2
Cell147


title: Patient derived organoid from sample 4


title: Patient derived organoid from sample 5


title: SM-J39VL_S570_E1-50

description:
SMART-seq v2
Cell146


title: SM-J39VL_S569_E1-50

description:
SMART-seq v2
Cell145


title: 573_S12_L002


title: SM-J39VL_S567_E1-50

description:
SMART-seq v2
Cell143


title: SM-J39VL_S575_E1-50

description:
SMART-seq v2
Cell150


title: SM-J39VL_S568_E1-50

description:
SMART-seq v2
Cell144


title: 573_S12_L001


title: SM-J39VL_S565_E1-50

description:
SMART-seq v2
Cell141


title: Patient derived organoid from sample 1


title: 342_S9_L002


title: 342_S9_L001


title: Patient derived organoid from sample 2


title: exp1, HAP1 MBD4-FLAG-Nterm, IgG

city: Paris

first: Andre

last: Bortolini Silveira

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Pipeline based on nf-core/chipseq, using FastQC 0.11.8, TrimGalore 0.6.2, BWA 0.7.17, Picard 2.19.0 and Samtools 1.9.
Assembly: hg38
Supplementary files format and content: Read depth normalized bigwig.
Library strategy: CUT&RUN

growth_protocol: IMDM [Gibco 12440053], bovine fetal serum 10% [BioSera FB-1003], Penicillin-Streptomycin 100 U/mL [Gibco 15140122]) at 37°C in 5% CO2 incubator.

extract_protocol:
CUTANA ChIC/CUT&RUN Kit (EpiCypher 14-1048), according to manufacturer’s instructions using 250,000 HAP1 nuclei per reaction.
CUTANA CUT&RUN Library Prep Kit (EpiCypher 14-1001), according to manufacturer’s instructions .Libraries were multiplexed and primer dimers were subsequently removed using SPRIselect Beads (Beckman Coulter B23317).

value: Myeloid


title: SM-J39VS_S541_E1-50

description:
SMART-seq v2
Cell155


title: SM-J39VL_S563_E1-50

description:
SMART-seq v2
Cell140


title: SM-J39VL_S566_E1-50

description:
SMART-seq v2
Cell142


title: SM-J39VL_S561_E1-50

description:
SMART-seq v2
Cell139


title: exp1, HAP1 MBD4-FLAG-Nterm, FLAG, rep2

value: FLAG (CST #14793S)


title: SM-J39VL_S480_E1-50

description:
SMART-seq v2
Cell138


title: 241_S11_L002


title: 5XFAD9_S9_L004

description:
5XFAD_seurat_processed_annotated.rds
visium_5xFAD_12-20-21_sample_meta.csv

value: F


title: SM-J39VL_S479_E1-50

description:
SMART-seq v2
Cell137


title: SM-J39VL_S478_E1-50

description:
SMART-seq v2
Cell136


title: exp1, HAP1 MBD4-FLAG-Cterm, FLAG, rep2


title: 241_S11_L001


title: SM-J39VL_S475_E1-50

description:
SMART-seq v2
Cell134


title: SM-J39VL_S473_E1-50

description:
SMART-seq v2
Cell133


title: SM-J39VL_S470_E1-50

description:
SMART-seq v2
Cell130


title: 5XFAD7_S7_L004


title: exp1, HAP1 MBD4-FLAG-Nterm, FLAG, rep1


title: 5XFAD8_S8_L004


title: 5XFAD5_S5_L004


title: SM-J39VL_S466_E1-50

description:
SMART-seq v2
Cell126


title: Model 3

description: Gene expression of MTB infected mouse

source_name: Peripheral Blood, MTB infected model, replicate 3

value: PBMC

value: female

value: MTB infected mouse


title: SM-J39VL_S384_E1-50

description:
SMART-seq v2
Cell124


title: exp1, HAP1 wt, H3K4me3

value: wt

value: H3K4me3 (EpiCypher 13-0041)


title: exp1, HAP1 wt, IgG


title: SM-J39VL_S383_E1-50

description:
SMART-seq v2
Cell123


title: SM-J39VL_S476_E1-50

description:
SMART-seq v2
Cell135


title: 5XFAD4_S4_L004

value: Brain


title: SM-J39VL_S467_E1-50

description:
SMART-seq v2
Cell127


title: 5XFAD6_S6_L004

value: WT

value: M


title: SM-J39VL_S468_E1-50

description:
SMART-seq v2
Cell128

value: Pontine nucleus


title: SM-J39VL_S465_E1-50

description:
SMART-seq v2
Cell125

value: Neuron


title: SM-J39VL_S471_E1-50

description:
SMART-seq v2
Cell131


title: SM-J39VL_S381_E1-50

description:
SMART-seq v2
Cell121


title: SM-J39VL_S469_E1-50

description:
SMART-seq v2
Cell129


title: SM-J39VL_S472_E1-50

description:
SMART-seq v2
Cell132


title: SM-J39VL_S382_E1-50

description:
SMART-seq v2
Cell122


title: SM-J39VL_S379_E1-50

description:
SMART-seq v2
Cell119


title: 5XFAD3_S3_L004


title: MECP2 mutant cerebral organoid replicate 3 [scATAC-Seq]

city: Cambridge

first: Danielle

last: Tomasello

state: Massachusetts

address: 455 Main St

institute: Whitehead Institute

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the the 10X Genomics Cell Ranger ARC software v2.0.1. We used “cellranger-arc mkfastq” to make the fastq files, and “cellranger-arc count” to align the reads, assign them to cells, remove duplicates and count.
Assembly: hg38
Supplementary files format and content: filtered_gene_bc_matrices tab separated text files  (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz),  and atac_fragments tab separated text files generated by Cell Ranger ARC software.
Library strategy: multiomics

extract_protocol:
At Day 100, organoids were flash frozen and stored in -80 °C. We followed the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (1000285) protocol. Nuclei isolation was followed according to protocol (CG000375 Rev B).  Organoids were homogenized with pestle (VWR 47747-358) with 50 strokes and incubated on ice for 5 min. After checking that cells were completely lysed, nuclei were counted with EVE automated cell counter (NanoEnTek). Nuclei were not sorted to maintain integrity. Equal number of nuclei were loaded (4500) according to protocol CG000338 Rev A.
According to 10X Genomics protocol PN-1000190
multiomics snRNA-seq plus snATAC-seq, SingleCell-10X-3P-Multiom, SingleCell-10X-ATAC-Multi

value: hESC

value: MECP2 Mutant


title: 5XFAD2_S2_L004


title: exp1, HAP1 MBD4-FLAG-Cterm, IgG


title: SM-J39VL_S377_E1-50

description:
SMART-seq v2
Cell118


title: SM-J39VL_S374_E1-50

description:
SMART-seq v2
Cell116


title: exp1, HAP1 MBD4-FLAG-Cterm, FLAG, rep1


title: 5XFAD28_S13_L002


title: SM-J39VL_S375_E1-50

description:
SMART-seq v2
Cell117


title: SM-J39VL_S380_E1-50

description:
SMART-seq v2
Cell120


title: exp1, HAP1 wt, FLAG


title: 5XFAD28_S12_L003


title: MECP2 mutant cerebral organoid replicate 4 [scATAC-Seq]


title: HEK293T cells-K700ECyto_rep3

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions.  After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets.  Raw sequences were transformed into clean reads after data processing.  These clean reads were then mapped to the reference genome sequence.  Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome.  Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two groups was performed using the DESeq R package.
Assembly: ensembl CRCh38
Supplementary files format and content: txt and counts

molecule: cytoplasmic RNA

growth_protocol: HEK293T cell line was cultured in DMEM (Gibco) supplemented with 10% FBS and streptomycin/penicillin (100 U/mL) at 37˚C in an atmosphere of 5% CO2.

extract_protocol:
Cytoplasmic and nuclear RNA was harvested using Trizol reagent. NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) was used with 1 ug of RNA per sample for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEK293T cells were transiently transfected with pIRES2-SF3B1 WT (WT) or pIRES2-SF3B1 K700E (K700E) for 48 h using Lipofectamine 2000.

value: Transient transfection with pIRES2-SF3B1 K700E


title: SM-J39VL_S280_E1-50

description:
SMART-seq v2
Cell112


title: SM-J39VL_S373_E1-50

description:
SMART-seq v2
Cell115


title: SM-J39VL_S279_E1-50

description:
SMART-seq v2
Cell111


title: MECP2 mutant cerebral organoid replicate 4 [GEX]

molecule: nuclear RNA


title: SM-J39VL_S372_E1-50

description:
SMART-seq v2
Cell114


title: SM-J39VL_S278_E1-50

description:
SMART-seq v2
Cell110


title: 5XFAD26_S11_L002


title: 5XFAD27_S12_L002


title: SM-J39VL_S369_E1-50

description:
SMART-seq v2
Cell113


title: 5XFAD27_S11_L003


title: SM-J39VL_S276_E1-50

description:
SMART-seq v2
Cell109


title: HEK293T cells-K700ECyto_rep1


title: SM-J39VL_S275_E1-50

description:
SMART-seq v2
Cell108


title: SM-J39VL_S273_E1-50

description:
SMART-seq v2
Cell107


title: 5XFAD26_S10_L003


title: SM-J39VL_S271_E1-50

description:
SMART-seq v2
Cell106


title: HEK293T cells-K700ENu_rep3


title: 5XFAD25_S9_L003


title: MECP2 mutant cerebral organoid replicate 3 [GEX]


title: HEK293T cells-K700ENu_rep2


title: 5XFAD25_S10_L002


title: HEK293T cells-K700ENu_rep1


title: SM-J39VL_S269_E1-50

description:
SMART-seq v2
Cell104


title: 5XFAD24_S9_L002


title: SM-J39VK_S767_E1-50

description:
SMART-seq v2
Cell101


title: SM-J39VL_S270_E1-50

description:
SMART-seq v2
Cell105


title: SM-J39VK_S766_E1-50

description:
SMART-seq v2
Cell100


title: SM-J39VK_S768_E1-50

description:
SMART-seq v2
Cell102


title: 5XFAD23_S8_L002


title: SM-J39VK_S765_E1-50

description:
SMART-seq v2
Cell99


title: 5XFAD24_S8_L003


title: SM-J39VK_S763_E1-50

description:
SMART-seq v2
Cell97


title: SM-J39VK_S764_E1-50

description:
SMART-seq v2
Cell98


title: HEK293T cells-K700ECyto_rep2


title: HEK293T cells-WTCyto_rep2

value: Transient transfection with pIRES2-SF3B1 WT


title: SM-J39VK_S762_E1-50

description:
SMART-seq v2
Cell96


title: 5XFAD23_S7_L003


title: SM-J39VL_S265_E1-50

description:
SMART-seq v2
Cell103


title: SM-J39VK_S761_E1-50

description:
SMART-seq v2
Cell95


title: HEK293T cells-WTNu_rep3


title: SM-J39VK_S759_E1-50

description:
SMART-seq v2
Cell93


title: SM-J39VK_S755_E1-50

description:
SMART-seq v2
Cell90


title: SM-J39VK_S754_E1-50

description:
SMART-seq v2
Cell89


title: SM-J39VK_S758_E1-50

description:
SMART-seq v2
Cell92


title: 5XFAD21_S5_L003


title: HEK293T cells-WTNu_rep2


title: 5XFAD22_S7_L002


title: HEK293T cells-WTCyto_rep1


title: HEK293T cells-WTCyto_rep3


title: 5XFAD20_S5_L002


title: MCF7 exosomes,exo-L-Re1

data_processing:
Raw data were processed through Seqtk.
The clean reads were aligned to the reference genome (GRCh38.104) using HISAT2.
The Read Counts of transcripts and ncRNAs were calculated by Stringtie（version:2.1.4）
In cells, the expression of mRNA and lncRNA was normalized to FPKM. CIRI2 was utilized for circRNA identification identification and quantification. In exosomes, the expression of mRNA and lncRNA was normalized to TPM (transcripts per kilobase million). CIRI2 was utilized for circRNA identification and quantification.
The identified circRNA was annotated using circBase. The expression of circRNA was normalized to SPRBM.
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text file includes row counts for each Sample

source_name: MCF7 exosome

extract_protocol:
Total RNA was extracted using miRNeasy Micro Kit (Cat #217084, Qiagen), and RNA quality was checked using Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US) according to standard procedures.The exosomes were isolated and total RNA was extracted using exoRNeasy Maxi Kit (#77164, Qiagen), and RNA quality was checked using Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US) according to standard procedures
Sequencing libraries were constructed by VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Cat #NR604, Vazyme) according to manufacturer's instructions. In exosomes, sequencing libraries were constructed by SMARTer Stranded Total RNA-Seq Kit for Illumina (Cat#634414, Takara) according to manufacturer's instructions.

value: MCF7 exosome


title: 5XFAD22_S6_L003


title: MCF7 exosomes,exo-L-Re2


title: SM-J39VK_S756_E1-50

description:
SMART-seq v2
Cell91


title: HEK293T cells-WTNu_rep1


title: 5XFAD21_S6_L002


title: MCF7 exosomes,exo-L-kd2


title: SM-J39VK_S753_E1-50

description:
SMART-seq v2
Cell88


title: SM-J39VD_S452_E1-50

description:
SMART-seq v2
Cell86


title: SM-J39VD_S454_E1-50

description:
SMART-seq v2
Cell87


title: SM-J39VD_S450_E1-50

description:
SMART-seq v2
Cell85


title: 5XFAD20_S4_L003


title: SM-J39VD_S449_E1-50

description:
SMART-seq v2
Cell84


title: 5XFAD19_S4_L002


title: MCF7 exosomes,exo-L-kd1


title: SM-J39VD_S352_E1-50

description:
SMART-seq v2
Cell77


title: SM-J39VD_S448_E1-50

description:
SMART-seq v2
Cell83


title: SM-J39VD_S351_E1-50

description:
SMART-seq v2
Cell76


title: SM-J39VK_S760_E1-50

description:
SMART-seq v2
Cell94


title: MCF7 exosomes,exo-L-Con2


title: MCF7 exosomes,exo-L-kd3


title: 5XFAD18_S2_L003


title: 5XFAD1_S1_L004


title: MCF7 exosomes,exo-L-Re3


title: SM-J39VD_S359_E1-50

description:
SMART-seq v2
Cell81


title: SM-J39VD_S358_E1-50

description:
SMART-seq v2
Cell80


title: SM-J39VD_S356_E1-50

description:
SMART-seq v2
Cell78


title: SM-J39VD_S357_E1-50

description:
SMART-seq v2
Cell79


title: 5XFAD19_S3_L003


title: SM-J39VD_S346_E1-50

description:
SMART-seq v2
Cell72


title: SM-J39TQ_S156_E1-50

description:
SMART-seq v2
Cell70


title: MCF7 exosomes,exo-L-Con3


title: SM-J39VD_S349_E1-50

description:
SMART-seq v2
Cell75


title: SM-J39TQ_S144_E1-50

description:
SMART-seq v2
Cell68


title: SM-J39VD_S348_E1-50

description:
SMART-seq v2
Cell74


title: MCF7 cells, cell-L-Re2


title: SM-J39VD_S446_E1-50

description:
SMART-seq v2
Cell82


title: SM-J39TQ_S159_E1-50

description:
SMART-seq v2
Cell71


title: 5XFAD16_S16_L004


title: SM-J39TQ_S149_E1-50

description:
SMART-seq v2
Cell69


title: 5XFAD17_S2_L002


title: SM-J39TQ_S137_E1-50

description:
SMART-seq v2
Cell67


title: MCF7 cells, cell-L-Re1


title: 5XFAD17_S1_L003


title: 5XFAD18_S3_L002


title: SM-J39TQ_S064_E1-50

description:
SMART-seq v2
Cell65


title: 5XFAD15_S15_L004


title: MCF7 cells, cell-L-kd3


title: SM-J39TQ_S136_E1-50

description:
SMART-seq v2
Cell66


title: MCF7 exosomes,exo-L-Con1


title: SM-J39TQ_S061_E1-50

description:
SMART-seq v2
Cell63


title: MCF7 cells, cell-L-Re3


title: SM-J39VD_S347_E1-50

description:
SMART-seq v2
Cell73


title: MCF7 cells, cell-L-kd1


title: MCF7 cells, cell-L-kd2


title: SM-J39TQ_S062_E1-50

description:
SMART-seq v2
Cell64


title: SM-J39TQ_S055_E1-50

description:
SMART-seq v2
Cell60


title: 5XFAD12_S12_L004


title: 5XFAD14_S14_L004


title: SM-J39TQ_S058_E1-50

description:
SMART-seq v2
Cell62


title: SM-J39TQ_S042_E1-50

description:
SMART-seq v2
Cell57


title: 5XFAD13_S13_L004


title: SM-J39TQ_S046_E1-50

description:
SMART-seq v2
Cell59


title: SM-J39TQ_S057_E1-50

description:
SMART-seq v2
Cell61


title: MCF7 cells, cell-L-Con2


title: MCF7 cells, cell-L-Con3


title: SM-J39RX_S054_E1-50

description:
SMART-seq v2
Cell54


title: 5XFAD10_S10_L004


title: 5XFAD11_S11_L004


title: MCF7 cells, cell-L-Con1


title: MCF7 exosomes, miRNA exo-S-Re3

data_processing:
Raw data were processed with Cutadapt.
The clean reads were aligned to the reference Database of miRBase22.1, piRNABank and RfamV14.1
The UMI Counts of miRNA ,piRNA and SmallRNA were calculated by perl.
The expression of miRNA ,piRNA and SmallRNA was normalized to CPM
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text file includes row counts for each Sample

extract_protocol:
Total RNA was extracted using miRNeasy Micro Kit (Cat #217084, Qiagen), and RNA quality was checked using Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US) according to standard procedures. The exosomes were isolated and total RNA was extracted using exoRNeasy Maxi Kit (#77164, Qiagen). RNA quality was checked using Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US) according to standard procedures.
Sequencing libraries were constructed by QIAseq miRNA Library Kit for Illumina (Cat #331505, Qiagen) according to manufacturer's instructions.


title: SM-J39TQ_S038_E1-50

description:
SMART-seq v2
Cell56


title: SM-J39RX_S056_E1-50

description:
SMART-seq v2
Cell55


title: SM-J39TQ_S043_E1-50

description:
SMART-seq v2
Cell58


title: SM-J39RX_S049_E1-50

description:
SMART-seq v2
Cell53


title: SM-J39RX_S045_E1-50

description:
SMART-seq v2
Cell51


title: 5XFAD7_S15_L003

description:
5XFAD_seurat_processed_annotated.rds
visium_5xFAD_12-13-21_sample_meta.csv


title: SM-J39RX_S043_E1-50

description:
SMART-seq v2
Cell50


title: SM-J39RX_S046_E1-50

description:
SMART-seq v2
Cell52


title: 5XFAD6_S14_L003


title: MCF7 exosomes, miRNA exo-S-Re2


title: SM-J39RX_S042_E1-50

description:
SMART-seq v2
Cell49


title: SM-J39RX_S031_E1-50

description:
SMART-seq v2
Cell47


title: 5XFAD8_S16_L003


title: SM-J39RX_S041_E1-50

description:
SMART-seq v2
Cell48


title: 5XFAD5_S13_L003


title: MCF7 exosomes, miRNA exo-S-kd3


title: MCF7 exosomes, miRNA exo-S-Re1


title: SM-J39RX_S028_E1-50

description:
SMART-seq v2
Cell45


title: SM-J39RX_S029_E1-50

description:
SMART-seq v2
Cell46


title: MCF7 exosomes, miRNA exo-S-kd2


title: SM-J39RX_S027_E1-50

description:
SMART-seq v2
Cell44


title: SM-J39RW_S740_E1-50

description:
SMART-seq v2
Cell41


title: SM-J39RW_S742_E1-50

description:
SMART-seq v2
Cell42


title: MCF7 exosomes, miRNA exo-S-Con3


title: 5XFAD3_S11_L003


title: 5XFAD4_S12_L003


title: SM-J39RW_S744_E1-50

description:
SMART-seq v2
Cell43


title: SM-J39RW_S737_E1-50

description:
SMART-seq v2
Cell39


title: SM-J39RW_S739_E1-50

description:
SMART-seq v2
Cell40


title: 5XFAD2_S10_L003


title: MCF7 exosomes, miRNA exo-S-kd1


title: MCF7 exosomes, miRNA exo-S-Con2


title: Leaves, Tre+PEG6000, 48h, repeat 2

city: Xinxiang

first: Ling

address: Eastern HuaLan Avenue, Xinxiang City , Henan Province , China

data_processing:
Use fastp (v0.20.0) to perform quality control on the raw data, with parameters set to - q 5 -n 5
Use HISAT2 (v2.1.0) to compare grape genome Vitis_vinifera.PN40024.v4 (http://ftp.ensemblgenomes.org/pub/plants/release-53/fasta/vitis_vinifera/), with parameters set to -- novelsplicesite-outfile XX.ss.. Compare the generated Sam files and use Samtools (version: 1.9) software to convert them to BAM format and sort them. Then use the rnaseq subroutine of qualimap (v2.2.1) software to calculate the comparison results and determine the comparison efficiency.
Use StringTie (stringtie-2.1.3b. Linux_x86_64) software to assemble transcripts based on the BAM file, with parameters set to - f 0.2 - a 30 - c 5 - j 5. Use StringTie to fuse all the reconstructed results of the samples to obtain the optimized transcript structure annotation file, and set the parameter -- merge.
Use StringTie to quantify gene expression based on the optimized annotation file of gene structure and the BAM file obtained from comparison, with parameters set to - e - p 4; Use Ballgown (R script) to organize the above results and obtain the readcount matrix of gene expression; Use your own script to obtain the FPKM matrix.
Assembly: Vitis_vinifera.PN40024.v4
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Vitis vinifera

source_name: leaf

growth_protocol: The self-rooted cuttings of ‘Thompson Seedless’ were grown in a greenhouse (Henan Institute of Science and Technology) at 25–30℃ and 60%–75% relative humidity.

extract_protocol:
RNA was harvested using Polysaccharide Polyphenols Plant Total RNA Extraction Kit (genepioneer, R411). 1 ug of total RNA was used for the construction ofsequencing lilbraries
RNA libraries for RNA-seg were prepared using Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (Yeasen, 12308ES) following manufacturer's protocols

treatment_protocol: Collect grape leaves from the control group, trehalose, different stresses (low temperature (4 ℃), PEG6000, NaCl), and trehalose+different stress treatments for 48 hours, and perform RNA Seq analysis. The control group and the treatment group each contain three biological replicates. 8 samples examined:  CK, 4C, NaCl，PEG6000，Tre，Tre-4C，Tre-NaCl，Tre-PEG6000.

value: leaf


title: MCF7 cells, miRNA cell-S-Re3


title: 5XFAD1_S9_L003

value: F


title: Leaves, Tre+PEG6000, 48h, repeat 3

institute: Henan Institute of Science and Technology


title: SM-J39RW_S736_E1-50

description:
SMART-seq v2
Cell38


title: SM-J39RW_S647_E1-50

description:
SMART-seq v2
Cell33


title: Leaves, Tre+PEG6000, 48h, repeat 1


title: Leaves, Tre+NaCl, 48h, repeat 3

value: Tre+NaCl, 48h


title: SM-J39RW_S735_E1-50

description:
SMART-seq v2
Cell37


title: MCF7 exosomes, miRNA exo-S-Con1


title: SM-J39RW_S734_E1-50

description:
SMART-seq v2
Cell36


title: MCF7 cells, miRNA cell-S-Re1


title: SM-J39RW_S648_E1-50

description:
SMART-seq v2
Cell34


title: MCF7 cells, miRNA cell-S-Re2


title: SM-J39RW_S729_E1-50

description:
SMART-seq v2
Cell35


title: MCF7 cells, miRNA cell-S-kd3


title: SM-J39RW_S645_E1-50

description:
SMART-seq v2
Cell32


title: Leaves, Tre+NaCl, 48h, repeat 2


title: SM-J39RW_S640_E1-50

description:
SMART-seq v2
Cell30


title: SM-J39RW_S634_E1-50

description:
SMART-seq v2
Cell27


title: SM-J39RW_S639_E1-50

description:
SMART-seq v2
Cell29


title: SM-J39RW_S638_E1-50

description:
SMART-seq v2
Cell28


title: SM-J39RW_S644_E1-50

description:
SMART-seq v2
Cell31


title: MCF7 cells, miRNA cell-S-kd2


title: Leaves, Tre+NaCl, 48h, repeat 1


title: SM-J39RW_S556_E1-50

description:
SMART-seq v2
Cell23


title: Leaves, Tre+4℃, 48h, repeat 3

value: Tre+4℃, 48h


title: Leaves, Tre+4℃, 48h, repeat 1


title: SM-J39RW_S558_E1-50

description:
SMART-seq v2
Cell24


title: Leaves, Tre+4℃, 48h, repeat 2


title: MCF7 cells, miRNA cell-S-Con3


title: MCF7 cells, miRNA cell-S-kd1


title: MCF7 cells, miRNA cell-S-Con1


title: SM-J39RW_S552_E1-50

description:
SMART-seq v2
Cell20


title: SM-J39RW_S549_E1-50

description:
SMART-seq v2
Cell18


title: MCF7 cells, miRNA cell-S-Con2


title: SM-J39RW_S547_E1-50

description:
SMART-seq v2
Cell16


title: SM-J39RW_S544_E1-50

description:
SMART-seq v2
Cell14


title: SM-J39RW_S633_E1-50

description:
SMART-seq v2
Cell26


title: #5 CMV-specific CD8+ T cells, blood, 4 hour stimulation

city: Saarbrücken

first: Fabian

last: Müller

address: Campus A 2.4

institute: Saarland University

data_processing:
Illumina RTA3 was used for basecalling.
Sequencing data was processed using the nf-core/methylseq pipeline (version 2.2.0), using default parameters, genome assembly GRCh38 and --accel=true (DOI:10.5281/zenodo.1343417, DOI:10.1038/s41587-020-0439-x). Briefly, the pipeline employs FASTQC (version 0.11.9), trimgalore (version 0.6.7) and bismark (version 0.24.0) (DOI:10.1093/bioinformatics/btr167) for read-level quality control, adapter trimming, bisulfite-aware alignment and cytosine-level DNA methylation quantification.
Assembly: GRCh38
Supplementary files format and content: *.bismark.cov.gz files contain CpG-level methylation calls in bismark covareage format

source_name: peripheral blood

extract_protocol:
PBMCs were isolated from residual blood samples from disposable kits used during routine platelet apheresis via discontinuous gradient centrifugation. CD8+ T cells were pre enriched using human anti-CD8 MicroBeads and the automated magnetic activated cell sorting (autoMACS) system (Miltenyi Biotec) according to the manufacturer’s instructions. The cells were stimulated with CMVpp65 overlapping peptide pool (Miltenyi Biotec) at a concentration of 1 µg of each peptide/ml for 4 hours. Subsequently, IFN γ secreting cells were labelled using IFN γ Secretion Assay/Detection Kit (PE) (Miltenyi Biotec; manufacturer’s protocol) and antibodies for surface protein detection. Genomic DNA was prepared from flow cytometrically sorted naive CD8+ T cells, interferon-gamma negative memory CD8+ T cells and interferon-gamma positive CD8+ T cells by using DNeasy blood and tissue kit (Qiagen, manufacturer’s protocol). Genomic DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research,  manufacturer’s protocol) and subjected to library preparation.
The bisulfite converted DNA was fragmented by sonication and served as input for library preparation using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, manufacturer’s protocol).

treatment_protocol: Pre-enriched human CD8+ Tcells were stimulated with CMVpp65 overlapping peptide pool (Miltenyi Biotec) at a concentration of 1 µg of each peptide/ml for 4 hours in TexMACS medium (Miltenyi Biotec).

tag: donor

tag: serotype

value: CMV positiv

value: peripheral blood

value: CD8 T cell

tag: marker

value: 4 hour stimulation with CMVpp65 overlapping peptide pool


title: #5 memory CD8+ T cells, blood, 4 hour stimulation

tag: tissue


title: Leaves, Tre, 48h, repeat 3

value: Tre, 48h


title: SM-J39RW_S548_E1-50

description:
SMART-seq v2
Cell17

tag: genotype


title: SM-J39RW_S542_E1-50

description:
SMART-seq v2
Cell13


title: SM-J39RW_S559_E1-50

description:
SMART-seq v2
Cell25


title: #4 CMV-specific CD8+ T cells, blood, 4 hour stimulation

tag: treatment


title: SM-J39RW_S539_E1-50

description:
SMART-seq v2
Cell11


title: SM-J39RW_S540_E1-50

description:
SMART-seq v2
Cell12


title: #4 memory CD8+ T cells, blood, 4 hour stimulation


title: Leaves, PEG6000, 48h, repeat 1


title: PN, replicate 2, scRNA-seq

description:
10x Chromium 3' v3
BPN2

data_processing:
Raw sequencing files from each library were concatenated. Final fastq files were aligned to the mm10 mouse genome (GRCm38) and converted to gene expression matrices using the Cell Ranger pipeline (Cell Ranger 5.0.1, default parameters). Intronic reads were included to increase assay sensitivity.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Pontine nucleus tissue from two 8-week-old female C57BL/6J mice was microdissected, pooled, and flash frozen with dry ice. Tissues were Dounce homogenized with 500 microliters of chilled detergen lysis buffer (0.10% Triton-X, 0.32M sucrose, 10 mM HEPES [pH 8.0], 5mM CaCl2, 3mM MgAc, 0.1 mM EDTA, 1 mM dithiothreitol [DTT]) using 5 strokes with the "loose" pestle followed by 10 strokes of the "tight" pestle (Kimble). 1 mL of sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM MgAc, 0.1 mM EDTA, 1 mM DTT) was added to the Dounce homogenizer and the combined solution was passed through a 40-μm cell strainer into a fresh tube containing 1 mL of 0.32 M sucrose buffer. An additional 1 mL of 0.32 M sucrose buffer was passed through the filter and the resulting 3.5 mL solution was centrifuged at 3,200 xg for 10 min at 4°C. The pellet was resuspended with 3 mL of 0.32 M sucrose buffer and homogenized for 30 s (Ultra-Turrax disperser, setting 1). Next, 12.5 mL of 1 M sucrose buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM MgAc, 1 mM DTT) was pipetted beneath the homogenate and the tube was centrifuged at 3,200 xg for 20 min at 4°C. After decanting the supernatant, the pellet was resuspended in 1 mL of resuspension solution (0.4 mg/mL BSA, 0.2 U/μL RNAse inhibitor [Lucigen] in 1X PBS), filtered through a 35-µm cell strainer, and diluted to a final concentration of 225 cells/µL.
Single-nuclear suspensions were loaded onto two 10x Genomics chips (Chromium v3). snRNA-seq libraries were constructed according to the protocol provided by the manufacturer (Chromium single-cell 3' v3 protocol, 10x Genomics). Multiplexed snRNA-seq libraries were spiked with a PhiX control library (5%) and sequenced twice across two NextSeq 550 high-output flow-cell runs.


title: SM-J39RW_S461_E1-50

description:
SMART-seq v2
Cell10


title: Leaves, Tre, 48h, repeat 2


title: PN, replicate 1, scRNA-seq

description:
10x Chromium 3' v3
BPN1


title: #4 naive CD8+ T cells, blood, 4 hour stimulation


title: Leaves, NaCl, 48h, repeat 3

value: NaCl, 48h


title: SM-J39RW_S460_E1-50

description:
SMART-seq v2
Cell9

value: Pontine nucleus


title: #3 CMV-specific CD8+ T cells, blood, 4 hour stimulation


title: Leaves, PEG6000, 48h, repeat 3


title: Leaves, NaCl, 48h, repeat 2


title: TADA2BKO3_E8

first: Hyein

middle: Sophia

last: Cho

address: 430 E 67th St

department: Developmental Biology

data_processing:
Alignment by STAR 2.6.1d
Duplicate removal by Picard MarkDuplicates 2.21.1
Quantification by featureCounts 1.6.4
Assembly: hg19
Supplementary files format and content: plain text table

source_name: HUES8 hESC

extract_protocol: Total RNA extraction using Quick-RNA MiniPrep kits

value: HUES8 hESC

value: TADA2B KO


title: SM-J39RW_S546_E1-50

description:
SMART-seq v2
Cell15

value: Neuron


title: #3 memory CD8+ T cells, blood, 4 hour stimulation


title: TADA2BKO2_E8


title: SM-J39RW_S457_E1-50

description:
SMART-seq v2
Cell7


title: Leaves, NaCl, 48h, repeat 1


title: Leaves, control, repeat 3

value: control


title: SM-J39RW_S454_E1-50

description:
SMART-seq v2
Cell6


title: #3 naive CD8+ T cells, blood, 4 hour stimulation


title: #2 CMV-specific CD8+ T cells, blood, 4 hour stimulation


title: Leaves, PEG6000, 48h, repeat 2


title: Leaves, control, repeat 2


title: WT3_E8

value: WT


title: SM-J39RW_S451_E1-50

description:
SMART-seq v2
Cell5


title: #2 memory CD8+ T cells, blood, 4 hour stimulation


title: WT2_E8


title: Leaves, control, repeat 1


title: WT1_E8


title: SM-J39RW_S446_E1-50

description:
SMART-seq v2
Cell3


title: Leaves, 4℃, 48h, repeat 3


title: SM-J39RW_S458_E1-50

description:
SMART-seq v2
Cell8


title: Leaves, 4℃, 48h, repeat 2


title: SM-J39RW_S445_E1-50

description:
SMART-seq v2
Cell2


title: #1 CMV-specific CD8+ T cells, blood, 4 hour stimulation


title: TADA2BKO1_E8


title: Rat, BS, rep2

first: Hanyang

department: Department of Hepatology and Gastroenterology (CCM/CVK),

institute: Charité Universitätsmedizin Berlin

data_processing:
The FASTQ files were processed and aligned to rat reference genome using MobiVision software (version2.1) with unique molecular identifier (UMI) counts summarized for each barcode. The UMI count matrix was then analyzedusing Seurat(version 4.0.0) R package.
Assembly: Rno_6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Liver

value: Primary

value: Liver cells

tag: strain

value: SD

value: wild-type

value: Bariatric surgery


title: #1 memory CD8+ T cells, blood, 4 hour stimulation

value: CMV positiv

value: peripheral blood

tag: cell type


title: Rat, BS, rep3

tag: cell line


title: Leaves, 4℃, 48h, repeat 1

value: leaf


title: Rat, BS, rep1


title: #1 naive CD8+ T cells, blood, 4 hour stimulation

value: CD8 T cell

value: 4 hour stimulation with CMVpp65 overlapping peptide pool


title: BSC3

city: Miaoli Conunty

first: Su-Fang

last: Lin

address: No 35, Keyan Road, Zhunan Town

department: NICR

country: Taiwan

institute: National Health Research Institutes, Taiwan

data_processing:
CLC Genmomic Workbench (v10)  was used for basecalling, base trimming, filtering of quality <20 and adaptor removal.
Clean reads were aligned to the human reference genome (hg38) for gene count quantitation.
After controling for batch effect, abundance measurements (TPM) for each gene (rowSums>1) in each sample were used to construct the expression matrix (Lien_MBC_2019.txt)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files comprising TPM values of 13490 genes for 8 samples

source_name: metaplastic breast cancer cell line

extract_protocol:
Total RNA was extracted from indicated cell lines using TRIzol reagent (Thermo Fischer Scientific, Waltham, MA, USA according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using MGIEasy RNA Library kit (SE50) (BGI, Shenzhen, China)

value: human metaplastic breast cancer (MBC)

tag: histological subtype

value: squamous metaplasia

tag: library preparation kit

value: MGIEasy RNA Library kit (SE50)

tag: core lab

value: Tri-I Biotech Inc., Taipei, Taiwan


title: HB7 hepatoblastoma tumoroid

city: Cincinnati

first: Peng

middle: Vijaykumar

last: Wu

state: OH

address: 3333 Burnet Ave., MLC7013

institute: Cincinnati Children's Hospital Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2
Assembly: GRCh38 3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: HB7 tumoroid

extract_protocol:
Fresh tumor specimens were obtained from patients and processed for primary tumoroid culture (Wu and Nusse, Methods Mol Biol 2022). Tumoroids grown in Matrigel were harvested at P1 or P2 for single cell RNA sequencing. Briefly, dispase was added for 30 minutes at 37C with intermittent mechanical disruption of Matrigel drops. Tumoroids released from Matrigel were spun down at 50g for 5 minutes and washed twice with liver perfusion media/5% FBS. Tryple Express was added for 10-15 minutes at 37C to digest tumoroids to single cells. Liver perfusion media/5% FBS was added at the end of the digestion and cells were collected by centrifugation at 300g x 5 minutes. Cells were resuspended in William's media/10% FBS, counted, and resuspended in the appropriate volume to target 5000 cells for 10x scRNA sequencing.
Libraries were constructed according to the manufacturer's specifications (10x Genomics 3' v2 for sample HB1 and v3 for all other samples)

value: HB7 tumoroid

value: hepatoblastoma