title: EDI27, differentiated by PROT#1, tumor_r3


title: RIV A8 354 bp C template 2 µM dGTP and 200 µM d(A/T/C)TP

status: Public on Sep 09 2024

type: SRA

city: Konstanz

first: Melanie

last: Henkel

state: Baden-Württemberg

address: Universitätsstraße 10

department: Department of Chemistry

country: Germany

institute: University of Konstanz

description:
354 bp C template
(2*75 bp)

library_source: genomic

data_processing:
Sequencing data were processed by using the open source software KNIME 4.6.2
Raw sequence and quality values were extracted from the FASTQ file format and Phred quality scores (Q scores) were transformed into base calling error probabilities (P)
The data was preprocessed by defining the unique molecular identifier (UMI) sequence context and translating Read 1 sequence and P into the reverse complement orientation
Read 1 and Read 2 were aligned to give the expected size of the template (109 bp) and merged into one sequence for which base calls with the lower error probability were transferred for the Read 1 and Read 2 overlay segment
High quality data was filtered by removal of reads containing a base within the UMI contexts with a P value above the threshold or removal of merged reads with a mean error probability over all bases in the sequence context above the threshold value
For each filtered read, a deletion and insertion correction was performed to adjust frameshifts by employing the Levenshtein distance between the read and reference template
N base calls were replaced by reference bases to prevent false positive error detection
Reads were aligned to the reference template sequence and reads with a misalignment higher as 13% were removed from the data set
Reads were sorted into UMI family groups with identical UMIs and analysis was proceeded with UMI families containing a minimum of three reads
Error calculation of UMI families was performed by averaging over the error for each sequence position of each read in one UMI family
By employing an error cut-off of 0.9, true KlenTaq DNA polymerase derived errors were then set to 1 and errors below the cut-off were set to 0 for each UMI family
The mean error was calculated over all UMI families at each sequence position, yielding the KTq based error rate
5mC detection was facilitated by comparing the error rates of the unmodified C template data set with the error rates of the 5mC template sequencing data using the Microsoft Excel software. 5hmC detection was facilitated by comparing the error rates of the unmodified C template data set with the error rates of the 5hmC template sequencing data using the Microsoft Excel software
Assembly: CTTACCCTATCTCTTCCCTAGTTTTCGACATCCGGAGCCTAGTTCTTCTGATCCACCATATAGATATTAATGGGAGGCAGAAATGCGTGTTAGGTAAAAGTTCGTCGTC
Supplementary files format and content: excel-files include position, reference DNA sequence, error rates and base calls
Library strategy: DNA Amplicon-Seq

molecule: genomic DNA

organism: synthetic construct

source_name: DNA template generated by PCR using dCTP

extract_protocol:
artificial template generated by PCR
For samples with DNA template generated by PCR using modified dCTPs:
Reaction mixtures for linear PCR contained 2 µM dGTP and 200 µM d(A/T/C)TP (each), 100 nM 127 bp reverse primer, 50 pM 354 bp C, 5mC or 5hmC template and 250 nM RIV A8 KTq variant in 1x KTq reaction buffer (50 mM Tris HCl (pH 9.2), 16 mM (NH4)2SO4, 2.5 mM MgCl2, 0.1% (v/v) Tween 20). PCR was performed in 25 µL with an initial denaturation at 95°C for 3 min followed by amplification over 20 cycles with denaturation at 95°C for 10 s, annealing at 56°C for 30 s and elongation at 72°C for 8 min. Final elongation was performed for 10 min at 72°C. Single-stranded (ssDNA) PCR product from 109 to 127 nt was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel) in combination with the NTC binding buffer according to the manufacturer’s instructions with elution in 22 µL Milli-Q water. To verify that no original template DNA was extracted, 1 µL of purified PCR product was subsequently applied in a PCR for purity verification. Reaction mixtures contained 200 µM dNTPs (each), 500 nM 354 bp forward and reverse primer, 10% (v/v) PCR product as template and 0.02 U/µL Q5® Hot Start High-Fidelity DNA Polymerase in 1x Q5® Reaction Buffer (New England Biolabs). PCR was performed in 10 µL reaction mixtures with an initial denaturation at 98°C for 1 min followed by amplification over 25 cycles with denaturation at 98°C for 10 s, annealing at 60°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. The absence of the 354 bp PCR product was verified by agarose gel electrophoresis. 17.5 µL of purified linear PCR product ssDNA was treated with the PreCR® Repair Mix (New England Biolabs) in 20 µL according to the manufacturer’s instructions (100 µM dNTPs (each), 1x NAD+, 1 µL PreCR® Repair Mix in 1x ThermoPol® Reaction Buffer for 20 min at 37°C). Without further purification, the reaction mixture was applied in a 2-cycle UMI PCR. Reaction mixtures for UMI introduction contained 200 µM dNTPs (each), 200 nM forward and reverse UMI primer, 0.02 U/µL Q5® Hot Start High-Fidelity DNA Polymerase and 0.2x Q5® Reaction Buffer (New England Biolabs) in 25 µL end volume. PCR was performed with an initial denaturation at 98°C for 1 min followed by primer elongation over 2 cycles with denaturation at 98°C for 10 s, annealing at 48°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. 183 bp UMI PCR product was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel) according to the manufacturer’s instructions. To improve purification, NTI binding buffer was 1:1.5 diluted with Milli-Q water for solubilising agarose gel slices and the dissolved mixture was diluted in total to 1:2.5 prior to DNA binding on the purification column. Purified UMI PCR product was eluted in 15 µL Milli-Q water. DNA concentration was determined by qPCR using previously prepared 183 bp reference DNA in decadic dilution series for the quantification based on standard amplification curves. Reaction mixtures contained 0.96x NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs), 400 nM 183 bp forward and reverse primer, 1x SYBR Green I (Sigma-Aldrich) and 1.85 µL reference template or UMI PCR product elution in 5 µL end volume. qPCR was performed in a Light Cycler® 96 instrument (Roche Diagnostics) with an initial denaturation at 98°C for 1 min followed by amplification over 30 cycles with denaturation at 98°C for 10 s, annealing at 60°C for 30 s and elongation at 72°C for 30 s. High resolution melting curves were measured immediately after PCR amplification. For absolute quantification, Cq values of reactions with reference template were plotted against the logarithm of their DNA concentrations and the linear regression function was used to calculate the concentration of the UMI PCR product. Calculated concentrations were multiplied by two, because applied reference template DNA was double stranded and only one strand of UMI PCR product carried both primer binding sites. Reactions for reference and UMI DNA were performed twice and a no template control reaction was performed to determine side product signals. The minimum reaction efficiency for the standard curve was 0.9 to 1.1 and the cut-off for the correlation coefficient of linear regression was 0.98. 67.63 fM of purified UMI PCR product was treated with the PreCR® Repair Mix (New England Biolabs) in 11.25 µL according to the manufacturer’s instructions. Without further purification, the reaction mixture was applied in the Amplicon PCR. Reaction mixtures for Amplicon library preparation contained 1x NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs), 400 nM forward and reverse Amplicon primer (containing Illumina TruSeq adapter and indexes sequences) and 26.57 fM UMI PCR product (for final analysis of approximately 100 000 UMI families) in 25 µL end volume. PCR was performed with an initial denaturation at 98°C for 1 min followed by amplification over 35 cycles with denaturation at 98°C for 10 s, annealing at 70°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. 263 bp Amplicon PCR product was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel) according to the manufacturer’s instructions. To improve purification, NTI binding buffer was 1:1.5 diluted with Milli-Q water for solubilising agarose gel slices and the solved mixture was diluted in total to 1:6.5 prior to DNA binding on the purification column. The PCR product was eluted in 20 µL Milli-Q water and treated with the PreCR® Repair Mix (New England Biolabs) in 20 µL according to the manufacturer’s instructions. Repaired product DNA was purified using the QIAEX II system (Qiagen) according to the manufactures instructions and was eluted in 18 µL Milli-Q water. DNA library concentrations were determined using the Quantus™ Fluorometer (Promega). After quality control by electrophoresis with the Bioanalyzer 2100 system (Agilent), DNA libraries were pooled equimolarly and sequencing was performed in paired-end mode on a NextSeq 2000 system with 2 x 75 bp read length. Each prepared NGS library was prepared and sequenced once.

tag: tissue

value: synthetic construct


title: RIV A8 354 bp 5mC template 2 µM dGTP and 200 µM d(A/T/C)TP

description:
354 bp 5mC template
(2*75 bp)

source_name: DNA template generated by PCR using modified d5mCTP


title: RIV A8 803 bp 5mC template 10 µM dGTP and 200 µM d(A/T/C)TP

description: 803 bp 5mC template

library_source: other

data_processing:
Sequencing data were processed by using the open source software KNIME 4.6.2
Raw sequence and quality values were extracted from the FASTQ file format and Phred quality scores (Q scores) were transformed into base calling error probabilities (P)
The data was preprocessed by defining the unique molecular identifier (UMI) sequence context and translating Read 1 sequence and P into the reverse complement orientation
Read 1 and Read 2 were aligned to give the expected size of the template (bisulfite converted samples 95 bp, 5mC detection samples 109 bp) and merged into one sequence for which base calls with the lower error probability were transferred for the Read 1 and Read 2 overlay segment
High quality data was filtered by removal of reads containing a base within the UMI contexts with a P value above the threshold or removal of merged reads with a mean error probability over all bases in the sequence context above the threshold value
For each filtered read, a deletion and insertion correction was performed to adjust frameshifts by employing the Levenshtein distance between the read and reference template (OR10A2 olfactory receptor family 10 subfamily A member 2 [ Homo sapiens (human) ])
N base calls were replaced by reference bases to prevent false positive error detection
Reads were aligned to the reference template sequence and reads with a misalignment higher as 6% or 12% were removed from the data set
Reads were sorted into UMI family groups with identical UMIs and analysis was proceeded with UMI families containing a minimum of three reads
Error calculation of UMI families was performed by averaging over the error for each sequence position of each read in one UMI family
By employing an error cut-off of 0.9, true KlenTaq DNA polymerase derived errors were then set to 1 and errors below the cut-off were set to 0 for each UMI family
The mean error was calculated over all UMI families at each sequence position, yielding the KTq based error rate
5mC detection was facilitated by comparing the error rates of the unmodified C template data set with the error rates of the 5mC template sequencing data using the Microsoft Excel software
Error rates, calculated from sequencing data of human genomic DNA based NGS libraries; were processed further for 5mC detection using the Microsoft Excel software. Errors were standardised using an adapted z-score which only includes error rates at C positions but values from CpG sites were excluded
Assembly: OR10A2 olfactory receptor family 10 subfamily A member 2 [ >NC_000011.10 Homo sapiens chromosome 11, GRCh38.p14 Primary Assembly ]
Supplementary files format and content: excel-files include position, reference DNA sequence and error rates
Library strategy: DNA Amplicon-Seq

molecule: other

source_name: DNA template generated by PCR

extract_protocol: Reaction mixtures for linear PCR contained 2 µM dGTP and 200 µM d(A/T/C)TP (each), 100 nM 109 bp forward primer, 50 pM 803 bp C or 5mC template and 250 nM KTq variant in 1x KTq reaction buffer (50 mM Tris HCl (pH 9.2), 16 mM (NH4)2SO4, 2.5 mM MgCl2, 0.1% (v/v) Tween 20). PCR was performed in 25 µL with an initial denaturation at 95°C for 3 min followed by amplification over 20 cycles with denaturation at 95°C for 10 s, annealing at 62°C for 30 s and elongation at 72°C for 4 min. Final elongation was performed for 10 min at 72°C. Single-stranded (ssDNA) PCR product from 109 to 364 nt was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel) in combination with the NTC binding buffer according to the manufacturer’s instructions with elution in 22 µL Milli-Q water. To verify that no original template DNA was extracted, 1 µL of purified PCR product was subsequently applied in a PCR for purity verification. Reaction mixtures contained 200 µM dNTPs (each), 500 nM 803 bp forward and reverse primer, 10% (v/v) PCR product as template and 0.02 U/µL Q5® Hot Start High-Fidelity DNA Polymerase in 1x Q5® Reaction Buffer (New England Biolabs). PCR was performed in 10 µL reaction mixtures with an initial denaturation at 98°C for 1 min followed by amplification over 25 cycles with denaturation at 98°C for 10 s, annealing at 62°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. The absence of the 803 bp PCR product was verified by agarose gel electrophoresis. 17.5 µL of purified linear PCR product ssDNA was treated with the PreCR® Repair Mix (New England Biolabs) in 20 µL according to the manufacturer’s instructions. Without further purification, the reaction mixture was applied in a 2-cycle UMI PCR. Reaction mixtures for UMI introduction contained 200 µM dNTPs (each), 200 nM forward and reverse UMI primer, 0.02 U/µL Q5® Hot Start High-Fidelity DNA Polymerase and 0.2x Q5® Reaction Buffer (New England Biolabs) in 25 µL end volume. PCR was performed with an initial denaturation at 98°C for 1 min followed by primer elongation over 2 cycles with denaturation at 98°C for 10 s, annealing at 48°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. 183 bp UMI PCR product was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel) according to the manufacturer’s instructions. To improve purification, NTI binding buffer was 1:1.5 diluted with Milli-Q water for solubilising agarose gel slices and the dissolved mixture was diluted in total to 1:2.5 prior to DNA binding on the purification column. Purified UMI PCR product was eluted in 15 µL Milli-Q water. DNA concentration was determined by qPCR using previously prepared 183 bp reference DNA in decadic dilution series for the quantification based on standard amplification curves. Reaction mixtures contained 0.96x NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs), 400 nM 183 bp forward and reverse primer, 1x SYBR Green I (Sigma-Aldrich) and 1.85 µL reference template or UMI PCR product elution in 5 µL end volume. qPCR was performed in a Light Cycler® 96 instrument (Roche Diagnostics) with an initial denaturation at 98°C for 1 min followed by amplification over 30 cycles with denaturation at 98°C for 10 s, annealing at 60°C for 30 s and elongation at 72°C for 30 s. High resolution melting curves were measured immediately after PCR amplification. For absolute quantification, Cq values of reactions with reference template were plotted against the logarithm of their DNA concentrations and the linear regression function was used to calculate the concentration of the UMI PCR product. Calculated concentrations were multiplied by two, because applied reference template DNA was double stranded and only one strand of UMI PCR product carried both primer binding sites. Reactions for reference and UMI DNA were performed twice and a no template control reaction was performed to determine side product signals. The minimum reaction efficiency for the standard curve was 0.9 to 1.1 and the cut-off for the correlation coefficient of linear regression was 0.98. 67.63 fM of purified UMI PCR product was treated with the PreCR® Repair Mix (New England Biolabs) in 11.25 µL according to the manufacturer’s instructions. Without further purification, the reaction mixture was applied in the Amplicon PCR. Reaction mixtures for Amplicon library preparation contained 1x NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs), 400 nM forward and reverse Amplicon primer (containing Illumina TruSeq adapter and indexes sequences) and 26.57 fM UMI PCR product (for final analysis of approximately 100 000 UMI families) in 25 µL end volume. PCR was performed with an initial denaturation at 98°C for 1 min followed by amplification over 35 cycles with denaturation at 98°C for 10 s, annealing at 70°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. 263 bp Amplicon PCR product was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel) according to the manufacturer’s instructions. To improve purification, NTI binding buffer was 1:1.5 diluted with Milli-Q water for solubilising agarose gel slices and the solved mixture was diluted in total to 1:6.5 prior to DNA binding on the purification column. The PCR product was eluted in 20 µL Milli-Q water and treated with the PreCR® Repair Mix (New England Biolabs) in 20 µL according to the manufacturer’s instructions. Repaired product DNA was purified using the QIAEX II system (Qiagen) according to the manufactures instructions and was eluted in 18 µL Milli-Q water. DNA library concentrations were determined using the Quantus™ Fluorometer (Promega). After quality control by electrophoresis with the Bioanalyzer 2100 system (Agilent), DNA libraries were pooled equimolarly and sequencing was performed in paired-end mode on an Illumina MiSeq™ or NextSeq 2000 system with 2 x 75 bp read length. Each prepared NGS library was prepared and sequenced once.

value: DNA template generated by PCR


title: EDI27, differentiated by PROT#1, tumor_r2

city: Los Angeles

first: Miller

last: Huang

state: CA

address: 4640 West Sunset Blvd Off Campus

department: Pediatrics

country: USA

institute: Keck School of Medicine of Usc

library_source: transcriptomic

data_processing:
RNA-sequencing reads were mapped to the human hg38 primary assembly reference genome using the HISAT2 aligner v2.2.0
Gene expression was quantified as reads per Gene using featureCounts v2.0.2
Assembly: Ensembl Homo_sapiens.GRCh38_genome release 109
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: Neuroblastoma

growth_protocol: EDI27 iPSC were maintained on GelTrex coated 6-well plates in StemFlex media(Thermo Fisher) in a humidified 37°C incubator with 5% CO2. Cells were passaged every 4-5days using Accutase (and plated at 20-30,000 cells/cm2) StemFlex media with 2uM of ROCK inhibitor Thiazovivin.

extract_protocol:
Total RNA was extracted from flash frozen tissue using the Tissuelyzer (Qiagen) and AllPrep DNA/RNA Mini Kit (Qiagen).
Extracted RNA were sent to Novogene (https://en.novogene.com/) for library preparation (polyA enrichment)

treatment_protocol: 4 different differentiation protocol, from iPSC to tNCC, were used.

value: Neuroblastoma

tag: cell line

tag: cell type

value: sympathoadrenal cell


title: EDI27, differentiated by PROT#1, tumor_r1


title: NALM6_THAL-SNS-032_1

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

institute: St Jude Children's Research Hospital

description:
SNS_F._normD1.00.bw
SNS_R._normD1.00.bw

data_processing:
Annotated transcription start sites were obtained from human (GRCh38.99) GTF from Ensembl. After removing transcripts with (immunoglobulin, Mt, Mt tRNA, rRNA) biotypes, PRO-seq signal in each sample was calculated in the window from the annotated TSS to +150 nt downstream, using a custom script, make_heatmap.pl. This script counts each read one time, at the exact 3’ end location of the nascent RNA. Given good agreement between replicates and similar return of spike-in reads, bedGraphs were merged within conditions, and depth-normalized, to generate bigWig files binned at 10bp.
GRCh38
bigWig
Library strategy: PRO-Seq

molecule: total RNA

source_name: lymphocyte

extract_protocol:
Cell permeabilization were performed according to the protocol generated by the Nascent Transcriptomics Core at Harvard Medical School, Boston, MA. (https://ntc.hms.harvard.edu/resources)
In PRO-seq, a run-on reaction is carried out with biotin-NTPs (either all 4, or one with additional unlabeled NTPs to reduce cost) and sarkosyl, is carried out in isolated nuclei or permeabilized cells. Incorporation of the single biotin-NTP halts further elongation of nascent RNA strands by RNAPII. The RNA strands are extracted, fragmented, and purified through streptavidin pull-down. Next, 3' adapters are ligated directly to the purified sample before another streptavidin purification step. The 5' ends are repaired using TAP and PNK before ligating 5' adapters. The adapter-flanked RNA fragments are enriched through another streptavidin pull-down process before RT and PCR amplification. The resultant cDNA strands are sequenced from the 3' end.

value: lymphocyte

value: B cell

tag: genotype

value: WT

tag: treatment


title: SIRPa WT 8

city: Minneapolis

first: Christine

middle: H

last: O'Connor

address: 117 Pleasant St. SE

department: Minnesota Supercomputer Institute

institute: University of Minnesota

data_processing:
trimmomatic version 0.33 was used to clean reads for adapter contamination and low-quality sequence.
HISAT2 version 2.1.0 was used to align samples to the genome reference consortium mouse build 38 reference genome.
featureCounts v1.6.2 was used to count mapped reads to genes.
Differential Gene Expression was done using raw read counts in edgeR (via CLCGWB).
Expression heatmaps from raw counts were done using the Morpheus software (https://software.broadinstitute.org/morpheus).
Genome_build: GRCm38
Supplementary_files_format_and_content: Hogquist_thymocytes_bulkRNAseq_rawcounts.txt: Tab-delimited text file with gene expression count data.

organism: Mus musculus

source_name: murine thymocytes

extract_protocol:
Qiagen RNeasy micro kit was used to extract RNA from each sample.
Library creation was performed using the SMARTer Stranded Total RNA Pico Mammalian v2 kit (Takara Bio), according to manufacturer’s instruction. Sequencing was performed on a NovaSeq6000 using paired-end 150-base chemistry.

value: SIRPa+ CD301b+ DCs


title: NALM6_THAL-SNS-032_2

description:
SNS_F._normD1.00.bw
SNS_R._normD1.00.bw


title: RIV D15 803 bp C template 2 µM dGTP and 200 µM d(A/T/C)TP

description: 803 bp C template


title: XCR1 IFNLR 4

value: XCR1+ DCs

value: IFNLR-KO


title: NALM6_EHT 1610_1

description:
EHT_F._normD1.00.bw
EHT_R._normD1.00.bw


title: XCR1 IFNLR 3


title: RIII H20 803 bp 5mC template 2 µM dGTP and 200 µM d(A/T/C)TP

description: 803 bp 5mC template


title: RIV A8 354 bp 5hmC template 2 µM dGTP and 200 µM d(A/T/C)TP

description:
354 bp 5hmC template
(2*75 bp)

source_name: DNA template generated by PCR using modified d5hmCTP


title: SIRPa WT 7


title: EDI27, differentiated by PROT#3, tumor_r2


title: RIV A8 803 bp C template 10 µM dGTP and 200 µM d(A/T/C)TP

description: 803 bp C template


title: NALM6_EHT 1610_2

description:
EHT_F._normD1.00.bw
EHT_R._normD1.00.bw


title: XCR1 IFNLR 2


title: SIRPa WT 6


title: XCR1 IFNLR 1


title: P46

city: Houston

first: Nicholas

last: Navin

state: Texas

address: 6565 MD Anderson Blvd

department: Systems Biology

institute: MD anderson Cancer Center

data_processing:
The scATAC data were processed with scATAC-pro 1.50
The trimmed reads were alignment to the reference genomes of human (hg19 reference) with BOWTIE2
Peak Calling performed with MACS2
Assembly: hg19
Supplementary files format and content: Fragment

source_name: breast

extract_protocol:
The genomic DNA was extract from isolated single nuclei
The in house nanowell based DNA-ATAC sequencing (wellDA-seq) protocol
Single cell DNA-ATAC coassay

value: breast

value: epithelial cells


title: SIRPa IFNLR 4


title: SIRPa WT 5


title: P42


title: RIV A8 803 bp C template 2 µM dGTP and 200 µM d(A/T/C)TP

description: 803 bp C template


title: RIV D15 803 bp 5mC template 2 µM dGTP and 200 µM d(A/T/C)TP

description: 803 bp 5mC template


title: NALM6_DMSO_2

description:
dmso_F._normD1.05.bw
dmso_R._normD1.05.bw

value: DMSO


title: XCR1 WT 6


title: XCR1 WT 5


title: BCL9_CON_3

description:
RSEM_gene_TPM.tsv
2490246_BCL9_CON_3

data_processing:
trim_galore v0.6.3 remove adapter sequences
alignment with STAR2.7.3a --twopassMode Basic
read counts quantified by RSEMv1.3.1
GRCh38
TPM counts are provided in csv files for each library

extract_protocol:
Takara NucleoSpin® RNA Plus XS (740990.50) according to manufacturer instructions
TruSeq Stranded mRNA Library Prep Kit, Illumina, PN 20020595


title: XCR1 WT 7


title: P37


title: KTq wild-type 803 bp 5mC template 2 µM dGTP and 200 µM d(A/T/C)TP

description: 803 bp 5mC template


title: RIII H20 803 bp C template 2 µM dGTP and 200 µM d(A/T/C)TP

description: 803 bp C template


title: BCL9_E7820_3

description:
RSEM_gene_TPM.tsv
2490249_BCL9_E7820_3


title: NALM6_DMSO_1


title: BCL9_CON_2

description:
RSEM_gene_TPM.tsv
2490245_BCL9_CON_2


title: P47


title: P22


title: BCL9_E7820_2

description:
RSEM_gene_TPM.tsv
2490248_BCL9_E7820_2


title: RIV A8 803 bp 5mC template 2 µM dGTP and 200 µM d(A/T/C)TP

description: 803 bp 5mC template


title: BCL9_E7820_1

description:
RSEM_gene_TPM.tsv
2490247_BCL9_E7820_1


title: P44


title: P21


title: P40


title: SIRPa IFNLR 3


title: P32


title: SIRPa IFNLR 2


title: KTq wild-type 803 bp C template 2 µM dGTP and 200 µM d(A/T/C)TP

description: 803 bp C template


title: P24


title: SIRPa IFNLR 1


title: P14


title: BCL9_CON_1

description:
RSEM_gene_TPM.tsv
2490244_BCL9_CON_1


title: HN_E7820_1

description:
RSEM_gene_TPM.tsv
2490241_HN_E7820_1


title: XCR1 WT 4


title: P08


title: P20


title: P06


title: HN_E7820_3

description:
RSEM_gene_TPM.tsv
2490243_HN_E7820_3


title: P03


title: HN_CON_2

description:
RSEM_gene_TPM.tsv
2490239_HN_CON_2


title: NALM6_SF3B1_DMSO_2

data_processing:
UMIs were removed from sequencing reads and appended to read names for PCR deduplication further downstream using umi_tools v1.1.1.
Sequencing adapters were trimmed from reads using cutadapt v3.2.
Reads were mapped to Eclipsebio's proprietary repetitive element database using STAR v2.7.7a, and reads that aligned to the repetitive element database were removed.
The remaining reads were mapped to the human genome (hg38) using STAR v2.7.7a requiring end to end alignment and unique mapping.
PCR duplicates were removed using umi_tools v1.1.1
bigWig files were generated using a proprietary Eclipsebio script
Clusters of reads in IP samples were identified using CLIPper v2.1.0, and each cluster was normalized against the corresponding input sample using a proprietary Eclipsebio script
Significantly enriched peaks were annotated using transcript information from GENCODE Release 41
Motif enrichment analysis of peaks was run using HOMER v4.11. GO term and KEGG pathway enrichment analysis of genes containing peaks were run using clusterProfiler v3.8.1
GRCh38
bigWig

extract_protocol:
Approximately 20 million cells were UV crosslinked at 400 mJoules/cm2 with 254 nm radiation and stored at -80C until use. Cell pellets (20 million cells per pellet) were lysed using 1mL of eCLIP lysis mix with a modified composition of 6mL of Proteinase Inhibitor Cocktail and 20mL of Murine RNase Inhibitor.
Ligations were performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to >90%. Samples were then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (∼220 nt of RNA) above the protein size was isolated and proteinase K (NEB) treated to isolate RNA. RNA was reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5′ end) was then ligated to the cDNA fragment 3′ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample was first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder was PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

tag: antibody


title: P39


title: SIRPa WT 2


title: NALM6_SF3B1_DMSO_1


title: NALM6_input_EHT 1610_2


title: XCR1 WT 3


title: P10


title: XCR1 WT 1


title: HN_E7820_2

description:
RSEM_gene_TPM.tsv
2490242_HN_E7820_2


title: NALM6_input_EHT 1610_1


title: SIRPa WT 1


title: XCR1 WT 2


title: DMSO_input

data_processing:
Raw ChIP-seq reads were mapped to GRCh38 using bwa-mem (Version 0.7.16a) sorting, indexing and duplicates were marked using samtools(Version 1.7). MACS2(Version 2.1.1) were used for peak calling on unique mapped reads and ENCODE blacklist regions were used to filter the peaks. bamCoverage command from deeptools (Version 3.5.4) were used to generate RPGC normalized bigwig tracks.
GRCh38
bigWig

extract_protocol:
Cell were fixed with 1%formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris)
DNA was quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher). Libraries were prepared with HyperPrep Library Preparation Kit (Roche PN 07962363001). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina).


title: P07


title: SIRPa WT 4


title: XCR1 STAT1KO 4


title: NALM6_input_DMSO_2


title: NALM6_SF3B1_EHT 1610_2


title: NALM6_SF3B1_EHT 1610_1


title: HN_CON_3

description:
RSEM_gene_TPM.tsv
2490240_HN_CON_3


title: HN_CON_1

description:
RSEM_gene_TPM.tsv
2490238_HN_CON_1


title: p-Ser5_Pol II_EHT 1610_2

value: p-Ser5 Pol II (Millipore, # 04-1572)


title: SIRPa WT 3


title: XCR1 STAT1KO 3


title: EHT 1610_input


title: P17


title: Bisulfite converted 5'-3' strand gDNA mCpG

description: gDNA mCpG

source_name: HeLa human genomic DNA

extract_protocol: Reaction mixtures for linear PCR contained 10 µM dGTP and 200 µM d(A/T/C)TP (each), 100 nM 109 bp forward primer, template DNA (3 fM 803 bp C or 5mC template generated by PCR, 62.5 ng HeLa gDNA native or CpG methylated (New England Biolabs)) and 300 nM RIV A8 KTq variant in 1x KTq reaction buffer (50 mM Tris HCl (pH 9.2), 16 mM (NH4)2SO4, 2.5 mM MgCl2, 0.1% (v/v) Tween 20) in 25 µL end volume. PCR was performed with an initial denaturation at 95°C for 3 min followed by amplification over 20 cycles with denaturation at 95°C for 10 s, annealing at 60°C for 30 s and elongation at 72°C for 10 min. Reaction mixtures were purified by using the NucleoSpin® Gel and PCR Clean-up XS kit (Macherey-Nagel) in combination with the NTC binding buffer according to the manufacturer’s instructions for ssDNA PCR product purification. DNA was eluted with 18 µL Elution Buffer NE (5 mM Tris HCl (pH 8.5)). To use the linear PCR product as template for NGS library preparation, the ssDNA was exponentially amplified by a high-fidelity DNA polymerase to increase the 109 bp product concentration. Reaction mixtures contained 200 µM dNTPs (each), 100 nM 109 bp forward and reverse primer, 67% (v/v) of the PCR elution and 0.02 U/µL Q5® Hot Start High-Fidelity DNA Polymerase in 1x Q5® Reaction Buffer (New England Biolabs). PCR was performed in 25 µL reaction mixtures with an initial denaturation at 98°C for 30 s followed by amplification over 10 cycles with denaturation at 98°C for 5 s, annealing at 62°C for 10 s and elongation at 72°C for 5 s. Reaction mixtures were purified by using the NucleoSpin® Gel and PCR Clean-up XS kit (Macherey-Nagel) and a 1:2 dilution of the NTI buffer according to the manufacturer’s instructions to optimise PCR product purification and yield. DNA was eluted with 18 µL Elution Buffer NE. Note, all reactions were performed in the Thermo Scientific™ Low Profile Tubes (Thermo Scientific) and DNA was eluted in Eppendorf DNA LoBind® Tubes (Eppendorf). 16.25 µL of purified linear PCR product dsDNA was applied as template for a 2-cycle UMI PCR. Reaction mixtures for UMI introduction contained 200 µM dNTPs (each), 200 nM forward and reverse UMI primer, 0.02 U/µL Q5® Hot Start High-Fidelity DNA Polymerase and 1x Q5® Reaction Buffer (New England Biolabs) in 25 µL end volume. PCR was performed with an initial denaturation at 98°C for 30 s followed by primer elongation over 2 cycles with denaturation at 98°C for 10 s, annealing at 48°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. 183 bp UMI PCR product was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up XS kit (Macherey-Nagel) according to the manufacturer’s instructions. Purified UMI PCR product was eluted with 18 µL Elution Buffer NE. DNA concentration was determined by qPCR according to the method described for NGS library preparation using template DNA generated by PCR. DNA repair using the PreCR® Repair Mix (New England Biolabs) and Amplicon PCR were performed according to the method described for NGS library preparation using template DNA generated by PCR. Amplicon PCR was performed with an initial denaturation at 98°C for 30 s followed by amplification over 30 cycles with denaturation at 98°C for 10 s, annealing at 70°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. 263 bp Amplicon PCR product was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up XS kit (Macherey-Nagel) according to the manufacturer’s instructions. To improve purification, non-diluted NTI binding buffer was used first for solubilising agarose gel slices and subsequently the solved mixture was diluted in total to 1:6.5 with Milli-Q water prior to DNA binding on the purification column. PCR product was eluted with Elution Buffer NE. Treatment of extracted DNA with PreCR® Repair Mix (New England Biolabs) and QIAEX II system (Qiagen) purification were performed according to the method described for NGS library preparation using template DNA generated by PCR. Repaired product DNA was eluted with 22 µL Milli-Q water. DNA library concentration determination, quality control and sequencing was performed as described for NGS library preparation using template DNA generated by PCR. Note, all reactions were performed in the Thermo Scientific™ Low Profile Tubes (Thermo Scientific) and DNA was eluted in Eppendorf DNA LoBind® Tubes (Eppendorf).

value: HeLa human genomic DNA

value: HeLa

value: adenocarcinoma


title: Bisulfite converted 5'-3' strand gDNA native

description: gDNA native


title: NALM6_input_DMSO_1


title: p-Ser5_Pol II_EHT 1610_1


title: RIV A8 gDNA native 10 µM dGTP and 200 µM d(A/T/C)TP

description: gDNA native


title: IRd21-Choline-GA, scRNAseq

city: Shanghai

first: Yuan

last: Ren

state: Shanghai

address: 12 Wulumuqi Middle Road, Jing'an District, Shanghai, China.

country: China

institute: Fudan University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The cleaned FASTQ data were transformed into a single-cell expression matrix using Cellranger software (Version 6.0).
Data quality control for single-cell sequencing.
Integration of multiple samples, visualization of cell clusters, and annotation of cell types.
Scoring of single-cell gene sets and pathway analysis.
Pseudotime analysis .
Assembly: mm10
Supplementary files format and content: Matrix files and barcodes files
Supplementary files format and content: Features files

source_name: kidney

extract_protocol:
The kidneys were enzymatically digested in PBS supplemented with 5% fetal bovine serum (FBS), 0.25% trypsin and 10μg/mL lDNase I. For around 40 minutes, the renal tissues were subjected to cell dissociation at 37 °C and 50 r.p.m shaking. To maximize the yield and viability of cells, they were collected at 20-minute intervals during the dissociation process, ensuring optimal recovery and preservation. After filtration through a 40 μm nylon cell strainer, the cell suspensions were treated with 1x red blood cell lysis solution  to remove red blood cells. Then, 1x DPBS supplemented with 2% FBS was used to wash the dissociated cells. The vitality of cells was determined by staining them with 0.4% Trypan blue  and counting them with the Automated Cell Counter.
In a Gel Beads-in-emulsion (GEM) system, beads with cell barcodes and unique molecular identifiers (UMIs) were loaded almost to saturation, ensuring a one-to-one pairing of each cell with a bead. After being exposed to a cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. For reverse transcription, all of the beads were placed in a single tube. At the 5' end of cDNA synthesis, which corresponds to the 3' end of the messenger RNA transcript, each cDNA molecule was labelled with UMIs and cell labels to specify its cellular origin. The 10x beads were then subjected to universal amplification, adaptor ligation, and second-strand cDNA synthesis. Through randomly interrupted whole-transcriptome amplification, sequencing libraries were created in order to enrich the 3' end of transcripts connected with the cell barcode and UMI.

value: kidney

value: kidney cells

value: IR+choline diet feeding+gastric gavage of glycyrrhizic acid


title: IRd21-Choline, scRNAseq

description: 10x Genomics

value: ischemia reperfusion+choline diet feeding


title: XCR1 STAT1KO 1


title: p-Ser2_Pol II_EHT 1610_1

value: lymphocyte

value: p-Ser2 Pol II (Millipore, # 04-1571)


title: mTEChi IFNARKO 4

value: MHC-II-hi mTECs


title: SIRPa STAT1KO 2

value: SIRPa+ CD301b+ DCs


title: Sham, scRNAseq

description: 10x Genomics

value: sham surgery


title: mTEChi IFNARKO 2


title: SIRPa STAT1KO 1


title: SIRPa STAT1KO 4


title: p-Ser2_Pol II_EHT 1610_2

value: B cell

value: WT


title: Pol II_EHT 1610_1

value: Pol II (CST, #14958S)


title: IRd21, scRNAseq

description: 10x Genomics

value: ischemia reperfusion


title: mTEChi IFNBKO 4

value: IFNB-KO


title: mTEChi IFNBKO 3


title: RIV A8 gDNA mCpG 10 µM dGTP and 200 µM d(A/T/C)TP

description: gDNA mCpG

value: HeLa human genomic DNA


title: mTEChi WT 5


title: SIRPa STAT1KO 3


title: mTEChi IFNARKO 1


title: mTEChi WT 7


title: Pol II_EHT 1610_2


title: mTEChi IFNARKO 3


title: mTEChi WT 6


title: p-Ser5_Pol II_DMSO_2

value: p-Ser5 Pol II (Millipore, # 04-1572)

value: DMSO


title: p-Ser2_Pol II_DMSO_2


title: XCR1 DRKO 1

value: XCR1+ DCs

value: IFNAR1-KO IFNLR-KO


title: BEAF-320 D. mel. pupal heads, Hi-C rep3

city: Lausanne

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description: Hi-C library

data_processing:
FASTQ files were mapped to the dm6 reference genome using distiller v0.3.3 (https://github.com/open2c/distiller-nf).
For each biological replicate, unique pairs of reads with MAPQ ≥ 30 on both sides were aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction using cooler v0.8.11 (https://github.com/open2c/cooler).
For each sample, unique pairs of reads with MAPQ ≥ 30 on both sides from all replicates were aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction using cooler v0.8.11 (https://github.com/open2c/cooler).
Assembly: dm6
Supplementary files format and content: Multi-resolution cooler file format (mcool): unique pairs of reads with MAPQ ≥ 30 on both sides, aggregated into multiresolution contact matrices (1kb, 2kb, 4kb, 8kb, 16kb, 32kb, 64kb, 128kb, 256kb, 512kb) and normalized with iterative correction (cooler v0.8.11, https://github.com/open2c/cooler).

organism: Drosophila melanogaster

source_name: pupal head

growth_protocol: standard Drosophila culture at 25°C

extract_protocol:
30 pupal heads were homogenized in RPMI supplemented with 10% fetal bovine serum with a micropestle. Cells were crosslinked then subjected to Hi-C, cutting with Csp6I and MseI restrictrion enzymes.
NEBNext Ultra II DNA Library Prep kit for Illumina

treatment_protocol: animals were not subjected to any particular treatment.

value: pupal head


title: Pol II_DMSO_2


title: SIRPa DRKO 4


title: XCR1 DRKO 2


title: p-Ser5_Pol II_DMSO_1


title: XCR1 DRKO 3


title: Wildtype D. mel. pupal heads, Hi-C rep3

description: Hi-C library


title: SIRPa DRKO 3


title: XCR1 DRKO 4


title: BEAF-320 D. mel. pupal heads, Hi-C rep2

description: Hi-C library


title: mTEChi IFNBKO 1


title: p-Ser2_Pol II_DMSO_1


title: BEAF-320 D. mel. pupal heads, Hi-C rep1

description: Hi-C library


title: Reporter RNA-seq from synthetic insulator screen, rep2

description:
Synthetic_RNA_seq_Rep2
PCR amplicon library from total RNA
Synthetic_insulator_screen_Rep2_raw_counts.tsv

data_processing:
Cloned genomic test fragments linked to a double barcode (BC) in the DNA-seq reads were mapped to the Drosophila dm6 reference genome using Bowtie 2.
RNA-seq reads, which consisted of PCR amplicons of the uniquely barcoded SV40 3’UTR common to both eGFP and mCherry reporter genes, were attributed to either eGFP or mCherry based on the presence of a reporter gene identifier sequence (TAGG for eGFP and CGAA for mCherry) bracketing each barcode in the 3’UTR.
For the eve locus and synthetic insulator screens, RNA-seq reads additionally contained a unique molecular identifier (UMI) introduced during reverse transcription.
Assembly: dm6
Supplementary files format and content: Processed data files for BXC and eve loci screens are provided in two formats: .tsv and .bedgraph. The raw counts .tsv tables contain not normalised, not binned results of DNA and RNA sequencing merged by a barcode. The raw counts tables contain the following columns: Chromosome, Start, Stop, Barcode, mCherry, eGFP, Ratio, Strand. The mCherry and eGFP RNA-seq counts were filtered to have at least 3 reads for each gene. The .bedgraph files contain normalised, pooled, binned data for visualisation, and contain the columns Chromosome, Start, Stop, Insulator_Strength.
Supplementary files format and content: Processed data files for the synthetic insulator screen are provided as a .tsv table. The tables contain not normalised results of DNA and RNA sequencing merged by barcode. The raw counts tables contain the following columns: Name, Fragment_ID_position_in_reporter, mCherry, eGFP, Ratio. The mCherry and eGFP RNA-seq counts were filtered to have at least 3 reads for each gene.

growth_protocol: Drosophila S2R+ cells (Drosophila Genomics Resource Center stock number 150) were cultured in Schneider medium supplemented with 10% heat-inactivated FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was isolated from S2R+ cells 72h after transfection. Cells were lysed in TRIzol LS reagent (ThermoFisher 10296028) following the manufacturer's protocol. RNA was precipitated with isopropanol, resuspended in nuclease-free water, treated with DNase (ThermoFisher AM2238), purified using RNAClean XP beads (Beckman Coulter A63987), and eluted in nuclease-free water.
PCR-amplicon libraries of eGFP and mCherry mRNA 3'UTR fragments comprising a unique shared barcode were generated from total RNA using a reverse transcriptase primer complementary to the SV40 3’UTR sequence of both eGFP and mCherry reporter genes (for the BX-C locus screen) or a reverse transcriptase primer with an "8N" unique molecular identifier (UMI) (for the eve locus and synthetic insulator screens) using SuperScript IV Reverse Transcriptase (ThermoFisher 18090010) according to the manufacturer’s protocol. Sequencing-ready libraries were then generated by two successive PCR reactions using KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2602). DNA-seq libraries for all insulator-seq screens were also prepared by two successive PCRs starting from the original insulator reporter plasmid library as template.

treatment_protocol: 2 µg of insulator reporter plasmid library was transfected into 50 million S2R+ cells, seeded into a 10 cm dish at a density of 5 million cells per ml, with Effectene (QIAGEN 301425) following the manufacturer’s instructions, in biological duplicates.

value: Dissociated embryos, near hatching (Oregon R)

value: synthetic constructs

value: transient transfection


title: MUTZ-5_GNF2133_rep2 [2250125_MG]

data_processing:
trim_galore v0.6.3 remove adapter sequences
alignment with STAR2.7.3a --twopassMode Basic
read counts quantified by RSEMv1.3.1
Assembly: GRCh38
Supplementary files format and content: TPM counts are provided in csv files for each library

value: lymphocyte


title: SIRPa DRKO 2

value: SIRPa+ CD301b+ DCs


title: DNA-seq from synthetic insulator screen

description:
Synthetic_DNA_seq
DNA-seq library
Synthetic_insulator_screen_Rep1_raw_counts.tsv
Synthetic_insulator_screen_Rep2_raw_counts.tsv

tag: sample type

value: Synthetic oligo pool DNA


title: MUTZ-5_GNF2133_rep1 [2250124_MG]

value: B cell


title: Reporter RNA-seq from eve screen, rep2

description:
eve_RNA_seq_Rep2
PCR amplicon library from total RNA
eve_locus_screen_Rep2_raw_counts.tsv

value: OregonR


title: Pol II_DMSO_1

value: WT

value: Pol II (CST, #14958S)


title: Wildtype D. mel. pupal heads, Hi-C rep2

description: Hi-C library


title: MUTZ-5_EHT1610_rep3 [2250123_ME]


title: Wildtype D. mel. pupal heads, Hi-C rep1

description: Hi-C library


title: mTEChi IFNBKO 2

value: MHC-II-hi mTECs

value: IFNB-KO


title: MUTZ-5_GNF2133_rep3 [2250126_MG]


title: SIRPa DRKO 1


title: DNA-seq from BX-C screen, rep2

description:
BXC_DNA_seq_R2
DNA-seq library
BXC_locus_screen_Rep2_raw_counts.tsv

value: Genomic BAC DNA

value: y; cn bw sp (sequenced reference genome)


title: DNA-seq from eve screen

description:
eve_DNA_seq
DNA-seq library
eve_locus_screen_Rep1_raw_counts.tsv
eve_locus_screen_Rep2_raw_counts.tsv


title: XCR1 IFNBKO 2

value: XCR1+ DCs


title: MUTZ-5_EHT1610_rep2 [2250122_ME]


title: DNA-seq from BX-C screen, rep1

description:
BXC_DNA_seq_R1
DNA-seq library
BXC_locus_screen_Rep1_raw_counts.tsv


title: MUTZ-5_EHT1610_rep1 [2250121_ME]


title: XCR1 IFNBKO 1


title: patient# 136-46 sole fibroblast injection site

city: Baltimore

first: Sam

last: Lee

state: MD

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

data_processing:
Illumina's CASAVA 1.8.4 was used to convert BCL files to FASTQ files. Default   parameters were used
RSEM and STAR method were used to align and generate gene and transcript expression using hg38 in Linux
Assembly: hg38
Supplementary files format and content: DEG from bulk RNAseq in single injection (1x).xlsx.  The R package DESeq2 was used to analyze samples from patients 136-26, 27, and 28. The DESeq2 analyses were performed by comparing either the B samples to the A samples or the C samples to the A samples
Supplementary files format and content: DEG from bulk RNAseq in fractionated injections (3x).xlsx.  The R package DESeq2 was used to analyze samples from patients 136-43, 45, and 46. The DESeq2 analyses were performed by comparing either the B samples to the A samples or the C samples to the A samples

source_name: skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA library were prepared using Illumina’s TruSeq Stranded Total RNA Sample Prep (136-26,27,28) or Ovation RNA-Seq System V2 (136-43,45,46)

value: skin

value: sole fibroblast fractionated injections


title: patient# 136-46 vehicle injection site

value: media fractionated injections


title: Reporter RNA-seq from synthetic insulator screen, rep1

description:
Synthetic_RNA_seq_Rep1
PCR amplicon library from total RNA
Synthetic_insulator_screen_Rep1_raw_counts.tsv

value: Dissociated embryos, near hatching (Oregon R)

value: synthetic constructs


title: MUTZ-5_DMSO_rep3 [2250120_MD]

value: lymphocyte

value: DMSO


title: patient# 136-46 scalp fibroblast injection site

value: scalp fibroblast fractionated injections


title: SIRPa IFNBKO 4

value: SIRPa+ CD301b+ DCs


title: patient# 136-45 scalp fibroblast injection site


title: MUTZ-5_DMSO_rep2 [2250119_MD]

value: B cell


title: SIRPa IFNBKO 3


title: SIRPa IFNBKO 2


title: patient# 136-45 vehicle injection site


title: patient# 136-43 sole fibroblast injection site


title: Reporter RNA-seq from eve screen, rep1

description:
eve_RNA_seq_Rep1
PCR amplicon library from total RNA
eve_locus_screen_Rep1_raw_counts.tsv

value: OregonR

value: transient transfection


title: XCR1 IFNBKO 4


title: WTiPS_3_S3

city: Syracuse

first: Michael

middle: Scott

last: Cosgrove

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

data_processing:
Low-quality bases/reads and adaptors were removed from reads by trimmomatic v0.38.
Trimmed reads were mapped to the Gencode GRCh38 release 29 Human reference genome using STAR aligner v2.7.0d.
Reads mapped to genes were summarized by the featureCounts program in subread v1.6.3.
Genes were filtered by CPM ≥1 in at least 2 samples
Data were normalized to effective library size using  edgeR v3.22.5.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing raw or normalized count data is supplied as a matrix for the RNA-Seq study.

extract_protocol:
RNA was isolated using Trizol reagent
Sequencing libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit RiboZero Gold (Illumina), using 1 ug total RNA as input. Libraries were pooled and sequenced on the NextSeq 500 instrument (Illumina), with paired end 2 x 75 bp reads using a High Output 150 cycle reagent kit.

value: Human IPSC

value: wild type


title: SIRPa IFNBKO 1

value: IFNB-KO


title: CL39_mutant_2_S5

value: mutant


title: MUTZ-5_DMSO_rep1 [2250118_MD]

value: WT


title: WTiPS_1_S1


title: patient# 136-43 scalp fibroblast injection site

value: skin


title: CL39_mutant_3_S6


title: WTMe3

data_processing:
Processing and alignment of ChIP-seq data used Partek Flow analysis software. Reads were aligned using the BWA algorithm
Peaks were called using the MACS2 algorithm with q-value=0.05 for peak detection and annotation.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing raw peak count data is supplied as a matrix for the Chip-Seq study, with chromosome position information.

extract_protocol:
ChIP-Seq experiments were performed in duplicate for WT and MT cells (clones MT1 and MTs) using the High Sensitivity ChIP Kit (Abcam). 5x10e5 cells were used as input material for each immunoprecipitation.  Following crosslinking and cell lysis, DNA shearing was performed using Diagenode Bioruptor Sonicator at high power output, with 5 pulses of 30 seconds, followed by 30 seconds rest between each pulse. 1ug antibody was used for each reaction. Immunoprecipitated DNA was column purified and resuspended in 20ul DNA elution buffer.
ChIP-Seq was performed on technical triplicates of WT and MT cells. All purified ChIP DNA was used as input for NEBNext Ultra II Library Prep Kits for Illumina.  Libraries were pooled and sequenced on a NextSeq 500 instrument (Illumina), with paired end 2 x 75 bp reads using High Output 150 cycle reagent kits.

tag: chip antibody


title: patient# 136-45 sole fibroblast injection site

value: sole fibroblast fractionated injections


title: NALM6_GNF2133_rep1 [2250115_NG]


title: WTiPS_2_S2


title: WTIgG

value: IgG


title: NALM6_EHT1610_rep3 [2250114_NE]


title: CL39_mutant_1_S4


title: XCR1 IFNARKO 1

value: XCR1+ DCs


title: XCR1 IFNARKO 4


title: SIRPa IFNARKO 4


title: NALM6_EHT1610_rep2 [2250113_NE]


title: CL14Me3


title: CL14IgG


title: CL39Me3


title: SIRPa IFNARKO 3


title: CL39IgG


title: NALM6_EHT1610_rep1 [2250112_NE]


title: SIRPa IFNARKO 2


title: NALM6_GNF2133_rep3 [2250117_NG]


title: NALM6_GNF2133_rep2 [2250116_NG]


title: XCR1 IFNARKO 2


title: NALM6_DMSO_rep3 [2250111_ND]


title: SIRPa IFNARKO 1


title: KO

city: Hangzhou

first: Di

last: Wang

state: Zhejiang

address: Yuhgang Tang Rd No.866

department: School of Medicine

institute: Zhejiang University

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (v2.20). Sample demultiplexing, barcode processing and single-cell 3' gene counting were performed with Cell Ranger (version 3.1.0), and scRNA-seq data were aligned to Ensembl genome GRCm38 reference genome. The pipelines were run with the assistance of LC-Bio Technology co.ltd., (Hangzhou, China).
Downstream analysis was performed using Seurat package (v4.0.1). Low-quality cells with less than 200 genes or more then 5000 genes detected and cells with mitochondrial encoded transcripts represented greater than 15% were removed from analysis. The raw gene expression matrix after quality control (QC) was cell-normalized over total expression, multiplied by 10,000 and log transformed. 2000 variable genes were selected for the integration of two data sets (Kcnj2f/f and Kcnj2CKO), and anchors were identified using FindIntegrationAnchors function followed by IntegrateData function with normalization.method = SCT, dims = 30. Uniform Manifold Approximation and Projection (UMAP) of the integrated dataset was generated using the first 40 principal components determined by elbow method. Unsupervised clustering was based on a shared nearest neighbor (SNN) using Louvain algorithm with resolution = 0.8 by FindClusters function. Cluster markers were identified using the FindAllMarkers function with min.pct = 0.25, logfc.threshold = 0.25.
Genome_build: Ensembl genome GRCm38 reference genome
Supplementary_files_format_and_content: Cell Ranger output

source_name: B16F10 infiltrating CD45+ immune cells

extract_protocol:
We sorted CD45+ immune cells from Kcnj2f/f and Kcnj2CKO mice and performed 10X single cell sequencing to illustrate the impact of Kcnj2 on TME.
CD45+ tumor-infiltrating immune cells were enriched by FACS from dissociated day 10 B16F10 tumors for single-cell analysis. Tumors from three different mice were pooled per sample. The overall cell viability was confirmed by trypan blue exclusion with Countess II Automated Cell Counter and concentration was adjusted to 700-1200 cells/uL. Single-cell suspensions were loaded to 10x Chromium to capture ~6000-8000 single cell according to the manufacturer's instructions of 10X Genomics Chromium Single-Cell 3' kit (V3). The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (Hangzhou,China) with average depth of ~48000 reads per cell.

treatment_protocol: B16F10 tumor cells were s.c. injected into Kcnj2f/f and Kcnj2CKO mice, and tumors were collected at day10.

tag: strain

value: KO

value: B16F10 infiltrating CD45+ immune cells


title: NALM6_DMSO_rep2 [2250110_ND]

value: lymphocyte

value: DMSO


title: WT


title: patient# 136- 43 vehicle injection site

value: media fractionated injections


title: NALM6_DMSO_rep1 [2250109_ND]

value: B cell


title: control19

city: Beijing

first: Cheng

last: Shi

state: Beijing

address: NO.11, Xizhimen Southern Street

institute: Peking University People's Hospital

description: Endometrial tissue during the implantation window period of the endometrium (5 days after ovulation)

data_processing:
Use the fastp tool for quality control of sequencing data. Remove sequences with the following low-quality criteria: Sequences with unknown bases numbering 5 or more. Sequences with a length less than 75bp. Sequences with an average base quality value less than 15. The resulting data after this step is termed Clean Data.
Use the sortmerna tool to align the Clean Data against a ribosomal database. Exclude sequences that align to the ribosomal database. The data obtained after this step is termed de-rRNA Clean Data.
Use the STAR tool to align the de-rRNA Clean Data to the reference genome.
Use the RSeQC tool to assess the quality of the alignment results from STAR.
Use the featureCounts tool to quantify gene expression from the alignment results.
Use the edgeR tool for differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited rawcount files for each samples
Supplementary files format and content: tab-delimited FPKM files for each samples

source_name: endometrium tissue

growth_protocol: All endometrial biopsy samples were obtained with disposable uterine-cavity tissue-suction tubes (Runting), and all the collected samples were stored in All protect Tissue Reagent (QIAGEN). The samples were transported to our laboratory on ice packs and stored at -80°C before processing.

extract_protocol:
RNA was extracted from endometrial tissue using RNAprep Pure Tissue Kit (DP341; Tiangen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using a KAPA Stranded RNA-Seq Library Preparation Kit (KR0934, KAPA Biosystems), following the manufacturer’s instructions.

treatment_protocol: The estradiol administration of all patients was started from the second day of menstruation with 4 mg estradiol valerate (Progynova; Bayer, Leverkusen, Germany) per day. When endometrial thickness was at least 7 mm and endogenous progesterone level was less than 1.5 ng/ml, 90 mg progesterone sustained-release vaginal gel (Crinone; Merck-Serono, Darmstadt, Germany) was applied transvaginally per day. The initial day of progesterone administration was recognized as “P+0” and endometrial biopsies were respectively taken on days P+3, P+5, and P+7 for each patient by a dedicated physician.

value: endometrium tissue

tag: condition

value: control

tag: timing of_endometrial_biopsy


title: MN173_60_A

type: RNA

city: Chicago

first: Aaron

last: Turkewitz

state: IL

address: 920 E 58th St

department: MGCB

institute: University of Chicago

description: Mutant 60 minutes replicate 1

hyb_protocol: Hybridization and staining of arrays was carried out by Roche NimbleGen Systems, as described in Ulijasz et al 2004, J. Bacteriol 186: 8123

scan_protocol: Arrays were scanned by Roche NimbleGen using a GenePix 4000B (Molecular Devices, Sunnyvale, CA) and the data were extracted using NimbleScan software.

data_processing: Array normalization was performed using the quantile normalization method (Bolstad et al. 2003, Bioinformatics 19: 185). Normalized expression values for the individual probes were used to obtain the expression values for a given open reading frame by using the multiarray average (RMA) procedure ( Irizarry et al. 2003, Biostatistics 4: 249).  Data were analyzed based on the RMA-processed expression values.

organism: Tetrahymena thermophila

source_name: Tetrahymena thermophila MN173

label_protocol: cDNA synthesis and Cy 3 labeling was done by Roche NimbleGen Systems, as described in Nuwaysir et al. 2002, Genome Res 12: 1749

growth_protocol: Cells were grown in 1% proteose peptone, 0.2% dextrose, 0.1% yeast extract, 0.003% ferric EDTA.

extract_protocol: Pelleted cells were lysed with 5M guanidinium thiocyanate, 10mM EDTA, 50mM Tris-HCl pH7.5, 8mM 2-mercaptoethanol. RNA was precipitated with 7vol cold 4M LiCl, and the pellet was washed once with 3M LiCl and suspended in 0.5% N-lauroyl-sarkosine,1mM EDTA, 10m Tris pH7.5.  RNA was then phenol/chloroform extracted and ethanol precipitated.

treatment_protocol: Cells were grown to 150,000-200,000 cells/ml and pelleted in 50ml conical tubes for 45 sec at 800xg.  They were washed once and suspended in DMC (0.1 mM Na2HPO4, 0.1mM NaH2PO4, 0.65mM CaCls, 0.1mM MgCl2, pH7.1) for 16 h at room temperature with shaking.  50 ml aliquots were stimulated by pelleting as above, and resuspension in 5 mls.  2% Alcian Blue was added to 0.05% and the tube contents were mixed by inversion, and then diluted immediately by addition of 45mls of 0.25% proteose peptone, 0.5mM CaCl2.  Cells were then washed once in DMC and resuspended for recovery in DMC at room temperature with shaking.

tag: phenotype

value: exocytosis defective

tag: time

value: 60 minutes post stimulation


title: control20


title: control18


title: MN173_0_B

description: Mutant 0 minutes replicate 2

value: 0 minutes


title: control16


title: MN173_60_D

description: Mutant 60 minutes replicate 3

value: mutant


title: ANM_126

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

data_processing:
Basecalls performed using Perl package developed by NOVOGENE
Contaminant reads from the fq file were removed and get the final clean reads. And then summarize the length distribution of these clean reads. Normally, length of small RNA is between 18nt and 30nt. The length distribution analysis is helpful to see the compositions of small RNA sample. For example, miRNA is normally 21nt or 22nt, siRNA is 24nt, and piRNA is 30nt.
The data is processed by the following steps: 1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table); 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt; 7) Summarize the length distribution of the clean reads.
Genome_build: hg19
Supplementary_files_format_and_content: 100_samples_miRNA_RPM.txt

source_name: adjacent normal mucosa tissue

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tumor and adjacent mormal mucosa tissues excised from LSCC patients after surgery were stored with RNAlater  (Cat#AM7020，Life  technologies, Carlsbad, CA, US)  following the manufacturer’s instructions.

tag: tumor stage

value: Not Applicable

tag: tobacco smoking

tag: alcohol consumption

tag: sequencing type

value: Small RNA sequencing


title: ANM_127


title: ANM_125


title: MN173_0_C

description: Mutant 0 minutes replicate 3


title: control17

tag: tissue


title: WT_60_B

description: Wildtype 60 minutes replicate 1

source_name: Tetrahymena thermophila CU428

value: wildtype


title: WT_60_D

description: Wildtype 60 minutes replicate 3


title: WT_0_C

description: Wildtype 0 minutes replicate 3


title: WT_60_C

description: Wildtype 60 minutes replicate 2


title: ANM_124


title: pH 6.8 treated cells versus pH 7.4, replicate #3

city: Koriyama

first: Yasumasa

last: Kato

state: Fukushima

address: 31-1 Misumido, Tomitamachi

department: Department of Oral Function and Molecular Biology

country: Japan

institute: Ohu University School of Dentistry

description:
pH 6.8 treated cells versus pH 7.4 (log2), replicate #3 of quadruplicate)
Biological replicate 1 of 4. Control cells at 7.4 (7g) versus acid treatment at pH 6.8 (6c)  for 24 h.

hyb_protocol: Hybridization and wash were performed by Gene Expression Hybridization Kit (5188-5242 : Agilent) and Gene Expression Wash Pack (5188-5327 : Agilent), respectively, according to manufacture's protocols.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2505B.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent).
The data are normalized for signal intensity and are presented as the ratio of pH 5.9 to pH 7.4 or pH 6.8 to pH 7.4 (Log2).

source_name: Mouse B16-BL6 melanoma, cultured at pH 7.4 for 24 h

label_protocol: cRNA was labeled with  Cy3-CTP and Cy5-CTP using Quick Amp Labeling Kit (5190-0444 : Agilent).

growth_protocol: Cells were cultured with DMEM/F12 supplemented with 15 mM HEPES, 4 mM phosphoric acid, and 10% fetal bovine serum.

extract_protocol: Total RNA extracted using Isogen (Nippon gene) following manufacturer's instructions.

treatment_protocol: Serum starved (overnight) cells were further incubated with serum-free growth medium at pH 7.4, 6.8, and 5.9 for 24 hours.

tag: cell line

value: 24 hour

source_name: Mouse B16-BL6 melanoma, cultured at pH 6.8 for 24 h


title: WT_0_B

description: Wildtype 0 minutes replicate 2


title: WT_0_A

description: Wildtype 0 minutes replicate 1


title: pH 6.8 treated cells versus pH 7.4, replicate #4

description:
pH 6.8 treated cells versus pH 7.4 (log2), replicate #4 of quadruplicate)
Biological replicate 1 of 4. Control cells at 7.4 (7h) versus acid treatment at pH 6.8 (6d)  for 24 h.


title: control15


title: MN173_60_B

description: Mutant 60 minutes replicate 2


title: MN173_0_A

description: Mutant 0 minutes replicate 1


title: ANM_123


title: ANM_121


title: control14


title: ANM_120


title: ANM_122


title: ANM_118


title: VSMC, IFNy 24h, replicate 3

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

data_processing:
Low-quality sequences with a  Phred score of < 20 were removed by Trim_Galore(0.6.10).
Afterward, the filtered reads were aligned to the mouse genome with a  fast and efficient spliced aligner tool STAR (2.7.10).
FeatureCounts (1.6.2) was employed for the summarization of mapped reads into genomic attributes.
Genes with counts lower than 10 at any time points were filtered out.
To determine differentially expressed genes (DEG), DESeq2 (1.40.2) package in R (4.3.3) was used.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Vascular Smooth Muscle Cells

growth_protocol: The aortas were extracted from 8 to 10 week old C57BL/6 mice, primary mouse VSMC were isolated from the aorta by enzymatic digestion and maintained in DMEM supplemented with 10% FBS, 1% L-glutamine, and 1% antibiotic/antimycotic solution in humidified atmosphere with 5% CO2 at 37C. 48 hours before cell harvesting, the medium was replaced with a starving medium containing 2% FBS.

extract_protocol:
RNA was isolated by TRI-REAGENT (MRC) followed by with Total RNA Zol-Out D (A&A Biotechnology) following the manufacturer's protocols
1ug of total RNA was used for library generation. RNA libraries for RNA-seq were prepared with NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (New England Biolabs), NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), following the manufacturer's protocols.

treatment_protocol: Cells were unstimulated or treated at different time points (0,5h, 2h, 4h, 8h and 24h)  with 10ng/mL mouse IFNy (Thermo Fisher Scientific).

tag: cell type

value: Vascular Smooth Muscle Cells

value: WT

value: IFN-gamma 24h


title: pH 5.9 treated cells versus pH 7.4, replicate #3

description:
pH 5.9 treated cells versus pH 7.4 (log2), replicate #3 of quadruplicate)
Biological replicate 3 of 4. Control cells at 7.4 (7c) versus acid treatment at pH 5.9 (5c) for 24 h.

source_name: Mouse B16-BL6 melanoma, cultured at pH 5.9 for 24 h


title: ANM_119


title: ANM_114


title: ANM_115


title: ANM_113


title: control13


title: ANM_112


title: control10


title: pH 5.9 treated cells versus pH 7.4, replicate #2

description:
pH 5.9 treated cells versus pH 7.4 (log2), replicate #2 of quadruplicate)
Biological replicate 2 of 4. Control cells at 7.4 (7b) versus acid treatment at pH 5.9 (5b) for 24 h.


title: ANM_117


title: control11


title: control09


title: control12


title: ANM_111


title: VSMC, IFNy 4h, replicate 3

tag: genotype

value: IFN-gamma 4h


title: pH 6.8 treated cells versus pH 7.4, replicate #2

description:
pH 6.8 treated cells versus pH 7.4 (log2), replicate #2 of quadruplicate)
Biological replicate 1 of 4. Control cells at 7.4 (7f) versus acid treatment at pH 6.8 (6b)  for 24 h.

tag: treatment


title: ANM_107


title: pH 5.9 treated cells versus pH 7.4, replicate #1

description:
pH 5.9 treated cells versus pH 7.4 (log2), replicate #1 of quadruplicate)
Biological replicate 1 of 4. Control cells at 7.4 (7a) versus acid treatment at pH 5.9 (5a) for 24 h.


title: VSMC, IFNy 2h, replicate 3

value: IFN-gamma 2h


title: pH 5.9 treated cells versus pH 7.4, replicate #4

description:
pH 5.9 treated cells versus pH 7.4 (log2), replicate #4 of quadruplicate)
Biological replicate 4 of 4. Control cells at 7.4 (7d) versus acid treatment at pH 5.9 (5d) for 24 h.


title: ANM_105


title: ANM_110


title: VSMC, IFNy 0,5h, replicate 3

value: IFN-gamma 0,5h


title: ANM_109


title: ANM_104


title: ANM_102


title: control08


title: VSMC, IFNy 8h, replicate 2

value: IFN-gamma 8h


title: ANM_116


title: control07

value: endometrium tissue


title: ANM_106


title: ANM_108


title: VSMC, IFNy 8h, replicate 3


title: VSMC, UN, replicate 3

value: Untreated


title: Sole fibroblast from patient# 136-44_preesure

data_processing:
none provided
Assembly: hg38
Supplementary files format and content: DEG from bulkRNAseq in FB+pressure vs FB control.xlsx.  The R package DESeq2 was used to analyze samples. The DESeq2 analyses were performed by comparing either the NP (non-volar pressure) samples to the NC (non-volar control) samples or the VP (volar pressure) samples to the VC (volar control) samples
Supplementary files format and content: DEG from bulk RNAseq in Sole fibroblast vs Scalp fibroblast in the absence or presence of pressure.xlsx.  The R package DESeq2 was used to analyze samples. The DESeq2 analyses were performed by comparing either the VP (volar pressure) samples to the VP (volar pressure) samples or the NP (non-volar pressure) samples to the NC (non-volar control) samples

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA library were prepared using Ovation RNA-Seq System V2

value: skin

value: sole fibroblast

value: pressure


title: VSMC, IFNy 4h, replicate 2


title: VSMC, IFNy 24h, replicate 2


title: ANM_100


title: ANM_103


title: ANM_101


title: Sole fibroblast from patient# 136-44_no preesure

value: control


title: control05


title: control04


title: pH 6.8 treated cells versus pH 7.4, replicate #1

description:
pH 6.8 treated cells versus pH 7.4 (log2), replicate #1 of quadruplicate)
Biological replicate 1 of 4. Control cells at 7.4 (7e) versus acid treatment at pH 6.8 (6a)  for 24 h.


title: VSMC, IFNy 2h, replicate 2


title: control03


title: ANM_99

value: Not Applicable


title: control02


title: VSMC, IFNy 0,5h, replicate 2


title: control06


title: control01


title: Scalp fibroblast from patient# 136-44_no preesure

value: scalp fibroblast


title: Scalp fibroblast from patient# 136-44_preesure


title: VSMC, UN, replicate 2


title: Sole fibroblast from patient# 136-43_preesure


title: RIF20

value: RIF


title: VSMC, IFNy 24h, replicate 1


title: ANM_98

value: Small RNA sequencing


title: ANM_97


title: ANM_96


title: Sole fibroblast from patient# 136-43_no preesure


title: RIF19


title: VSMC, IFNy 8h, replicate 1

value: Vascular Smooth Muscle Cells


title: ANM_95


title: Scalp fibroblast from patient# 136-43_preesure


title: ANM_94


title: RIF18


title: Scalp fibroblast from patient# 136-43_no preesure


title: ANM_93


title: VSMC, IFNy 2h, replicate 1

value: WT


title: Sole fibroblast from patient# 136-42_preesure


title: RIF16


title: Sole fibroblast from patient# 136-42_no preesure


title: RIF15


title: ANM_92


title: VSMC, IFNy 0,5h, replicate 1


title: VSMC, IFNy 4h, replicate 1


title: RIF17


title: RIF14


title: VSMC, UN, replicate 1


title: Scalp fibroblast from patient# 136-42_preesure


title: BMDM, IFNy 24h, replicate 3

source_name: Bone Marrow Derived Macrophages

growth_protocol: Femurs and tibias were extracted from 8 to 10 week old C57BL/6 mice, bone marrow was flushed, and macrophages were differentiated in DMEM supplemented with 15% FBS, 1% L-glutamine, and 1% antibiotic/antimycotic solution, containing  20 ng/ml m-csf in humidified atmosphere with 5% CO2 at 37C. 48 hours before cell harvesting, the medium was replaced with a starving medium containing 2% FBS.

value: Bone Marrow Derived Macrophages

value: IFN-gamma 24h


title: ANM_91


title: Scalp fibroblast from patient# 136-42_no preesure


title: BMDM, IFNy 8h, replicate 3


title: ANM_90


title: ANM_89


title: RIF12


title: BMDM, IFNy 4h, replicate 3

value: IFN-gamma 4h


title: ANM_88


title: BMDM, IFNy 2h, replicate 3

value: IFN-gamma 2h


title: Sole fibroblast from patient# 136-22_preesure


title: Sole fibroblast from patient# 136-22_no preesure


title: RIF11


title: RIF13


title: RIF10


title: Scalp fibroblast from patient# 136-22_no preesure


title: BMDM, IFNy 0,5h, replicate 3

value: IFN-gamma 0,5h


title: RIF09

value: endometrium tissue


title: ANM_86


title: BMDM, UN, replicate 3

value: Untreated


title: ANM_85


title: ANM_87


title: BMDM, IFNy 24h, replicate 2


title: patient# 136-28 sole fibroblast injection site

value: skin

value: sole fibroblast single injection


title: RIF08


title: ANM_84


title: BMDM, IFNy 8h, replicate 2

value: IFN-gamma 8h


title: Scalp fibroblast from patient# 136-22_preesure

value: pressure


title: BMDM, IFNy 4h, replicate 2


title: ANM_81

value: Not Applicable


title: BMDM, IFNy 2h, replicate 2


title: ANM_80


title: RIF07


title: patient# 136-28 scalp fibroblast injection site

value: scalp fibroblast single injection


title: ANM_82


title: RIF06

value: RIF


title: patient# 136-28 vehicle injection site

value: media single injection


title: RIF04


title: patient# 136-27 vehicle injection site


title: BMDM, IFNy 0,5h, replicate 2


title: ANM_83

value: Small RNA sequencing


title: RIF02


title: BMDM, IFNy 8h, replicate 1

value: WT


title: patient# 136-26 scalp fibroblast injection site


title: RIF03


title: RIF01


title: patient# 136-26 vehicle injection site


title: RIF05


title: patient# 136-27 scalp fibroblast injection site


title: ANM_78


title: LSCC_126

source_name: LSCC tissue

value: Yes

value: No


title: BMDM, IFNy 24h, replicate 1

value: Bone Marrow Derived Macrophages

value: IFN-gamma 24h


title: BMDM, IFNy 4h, replicate 1

value: IFN-gamma 4h


title: patient# 136-27 sole fibroblast injection site


title: hiPSC-derived neuron cells, RTS 4, Day 60, replicate 2

city: Bordeaux

first: Slim

last: Karkar

address: Rue Leao Saignat

department: CBiB

country: France

institute: U. Bordeaux

data_processing:
Reads were aligned on the Human genome reference (GRCh38) using STAR (v 2.7.3).
The quantification of aligned reads over the genes was also performed by STAR (GenesCounts mode).
Using the resulting count matrix over all samples, the Differentially Expressed Genes (DEGs) were identified with the DESeq2 R package (v 1.26.0)
DEGs with a |log2Foldchange| cutoff ≥1 and a corrected p-value under 0.01 were selected for further analyses.
We used the Ensembl human gene IDs identified in the DESeq2 step as input for further analyses.
Assembly: GRCh38
Supplementary files format and content: tab-delimited CSV file includes raw counts for each Sample

source_name: hiPSC-derived neuron

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen) following manufacturer’s instructions. Quality, quantification and sizing of total RNA was evaluated using the RNA 6000 Pico assay (Agilent Technologies Ref. 5067-1513) on an Agilent 2100 Bioanalyzer system. The RNA integrity number (RIN) was calculated for each sample and only samples with RIN >9 were kept for further use.
Samples were sent to Genewiz (Azenta Life Sciences, Steißlingen, Germany) for high throughput bulk RNA sequencing according to their guidelines for sequencing on an Illumina Novaseq (2x150).

value: hiPSC-derived neuron

value: CREBBP c.3832C> T / p.Glu1278Lys variant


title: patient# 136-26 sole fibroblast injection site

value: skin


title: LSCC_125


title: BMDM, UN, replicate 2

value: Untreated


title: hiPSC-derived neuron cells, RTS 4, Day 60, replicate 1


title: hiPSC-derived neuron cells, RTS 3, Day 60, replicate 2


title: ANM_79


title: BMDM, IFNy 0,5h, replicate 1

value: IFN-gamma 0,5h


title: LSCC_124


title: SOD1G93A/PHD1+/+, replicate 1, snRNAseq

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description: 10x Genomics 3'

data_processing:
Fastq files from 10x experiments were mapped to the mouse genome (mm10-2020-A, provided by 10x genomics) using cellranger count (v5.0.2), the includeIntrons option was enabled.
Filtered count matrices were loaded into Scanpy (v1.8.1) and cells with more than 15% reads associated to mitochondrial genes or less than 250 genes expressed were filtered out, next Scrublet (v0.2.2) was used to remove doublets with thresholds being determined automatically.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lumbar spinal cord

extract_protocol:
To extract nuclei from frozen mouse lumbar spinal cords, we used a slightly modified version of the protocol described previously by Swiech et al, 2015, Nat Biotech. In brief, lumbar spinal cords from three 110 days-old littermate pairs (six samples in total) were dissected and frozen immediately in precooled RNAse-free eppendorfs. Tissue was stored at -80°C until nuclei were extracted. At the day of nuclei extraction, frozen tissues were left in homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg Acetate, 10 mM Tris pH8, 0.1 mM EDTA, 0.1% Igepal/NP-40, 0.1 mM PMSF, 1 mM β-mercaptoethanol in H2O) for 5 minutes on ice to prevent nuclei from breaking. Next, tissue was homogenized by 100 gentle manual strokes using a dounce homogenizer (Sigma-Aldrich). Subsequently, a 1:1 volume of gradient medium (5 mM CaCl2, 3 mM Mg Acetate, 10 mM Tris pH8, 0.1 mM PMSF, 1 mM β-mercaptoethanol, 50% Optiprep, in water) was layered on top of the homogenized sample before ultracentrifugation (7,700 rpm for 30 min at 4°C using a SW41Ti rotor). Subsequently, the nuclei-containing pellet was resuspended in 150 μL resuspension buffer (BSA 1%, nuclease free water 340 mM, RNasin Plus 0.2 U/ μL in 1X PBS). Number and quality of purified nuclei was controlled using a LUNA-FL Dual fluorescence cell counter (Logsbio)
After single nuclei preparation, samples were immediately processed for the single nuclei whole transcriptome analysis (WTA). The single-nucleus RNA sequencing analysis was performed using 10X genomics 3’ WTA suite, according to the manufacturer recommendation. In brief, single nuclei were encapsulated in droplets for lysis and subsequent reverse transcription of polyadenylated mRNA species. After the first cDNA amplification, the library was subjected to Truseq based library preparation to incorporate the Illumina sequencing adaptors and indices. The final library obtained at the end of the single cell RNA-sequencing workflow was sequenced on either of the Illumina Hiseq 4000 or Illumina NovaSeq6000 platforms as per the sequencing specification mentioned in the 10X scRNAseq workflow. Each lane was pooled with multiple 10X libraries which were indexed separately.

value: lumbar spinal cord

tag: age

value: 110 days


title: BMDM, IFNy 2h, replicate 1

value: IFN-gamma 2h


title: hiPSC-derived neuron cells, RTS 3, Day 60, replicate 1


title: hiPSC-derived neuron cells, RTS 2, Day 60, replicate 2


title: LSCC_123


title: LSCC_127


title: Day-14-Total-RNA-MTR4-null-Cytoplasm-rep3

first: Heng-yu

last: Fan

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
RNA-Seq was performed with biological replicates for all samples.
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1.
Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Expression level  was further normalized with the ERCC spike-in.
Assembly: mm9
Supplementary files format and content: txt file includes processed FPKM with ERCC correlation for each sample

source_name: Oocyte

extract_protocol:
Oocytes were collected from indicated genotypes from mice of different stages. Then nucleus-cytoplasm separation were performed with micromanipulation. Nuclei and cytoplasm were collected separately.
After sample collection,total RNA were extracted using TRIzol. Purified total RNA were firstly removed rRNAs using the Abclonal rRNA Depletion module, total RNA was used as input for library construction using the Abclonal Fast RNA-seq Lib Prep Kit V2. DNA fragments were selected,and the final sequencing libraries were constructed from 300–400 bp of the amplified cDNAs. Sequencing data were extracted on the Illumina HiSeq X Ten platform in the 150 bp paired-end mode.

value: Oocyte

tag: cell compartment

value: Cytoplasm


title: LSCC_122

value: Small RNA sequencing


title: hiPSC-derived neuron cells, RTS 2, Day 60, replicate 1


title: BMDM, UN, replicate 1

value: WT


title: Reporter RNA-seq from BX-C screen, rep1

description:
BXC_RNA_seq_R1
PCR amplicon library from total RNA
BXC_locus_screen_Rep1_raw_counts.tsv

value: Dissociated embryos, near hatching (Oregon R)

value: OregonR

value: transient transfection


title: LSCC_121

value: Yes


title: Day-14-Total-RNA-MTR4-null-Cytoplasm-rep2


title: SOD1G93A/PHD1-/-, replicate 1, snRNA-seq

description: 10x Genomics 3'


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [43_AppNLGF_2P-Im_6M_rep13]

city: Sendai

first: Akira

last: Uruno

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

institute: Tohoku University Graduate School of Medicine

data_processing:
Salmon quant
Assembly: GRCm38/mm10
Supplementary files format and content: CSV

source_name: Brain

extract_protocol:
Sepasol (Nakrai Tesque)
MGISP-960 sample preparation system (MGI Tech) and MGIEasy RNA Directional Library Prep Set (MGI Tech)

value: Brain

value: AppNLGF


title: LSCC_120

value: No


title: Day-14-Total-RNA-MTR4-null-Cytoplasm-rep1


title: hiPSC-derived neuron cells, RTS 1, Day 60, replicate 2

value: hiPSC-derived neuron

value: CREBBP c.3832C> T / p.Glu1278Lys variant


title: Day-14-Total-RNA-MTR4-null-Nucleus-rep3

value: Nucleus


title: hiPSC-derived neuron cells, RTS 1, Day 60, replicate 1


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [42_AppNLGF_2P-Im_6M_rep12]


title: hiPSC-derived neuron cells, Control 2, Day 60, replicate 2


title: Adult Auditory Cortex

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

description: Parse scRNA well A1-B3

data_processing:
Demultiplexing with bcl2fastq (v2.20)
Barcode deconvolution and alignment with Parse split-pipe (v1.04)
The raw files are from the Parse pipeline.
To associate cells with their raw data, we follow their documentation to import the exact files uploaded: https://satijalab.org/seurat/reference/readparsebio
Assembly: rnor7
Supplementary files format and content: all_genes.csv, cell_metadata.csv, DGE.mtx

organism: Rattus norvegicus

source_name: Auditory Cortex

growth_protocol: Rats were deeply sedated with isoflurane and then euthanized by decapitation. Brains were rapidly removed and flash-frozen in pre-chilled 2-methyl-butane for 60 sec. Frozen brains were sectioned and  auditory cortex dissected from the sections then stored at −80 °C until processed for nuclei isolation

extract_protocol:
Chromium Nuclei Isolation Kit (10X Genomics)
Parse scRNA v2

treatment_protocol: No treatment

value: Auditory Cortex

value: No treatment


title: LSCC_118


title: LSCC_119


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [41_AppNLGF_2P-Im_6M_rep11]


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [40_AppNLGF_2P-Im_6M_rep10]


title: hiPSC-derived neuron cells, Control 2, Day 60, replicate 1


title: Reporter RNA-seq from BX-C screen, rep2

description:
BXC_RNA_seq_R2
PCR amplicon library from total RNA
BXC_locus_screen_Rep2_raw_counts.tsv

data_processing:
Cloned genomic test fragments linked to a double barcode (BC) in the DNA-seq reads were mapped to the Drosophila dm6 reference genome using Bowtie 2.
RNA-seq reads, which consisted of PCR amplicons of the uniquely barcoded SV40 3’UTR common to both eGFP and mCherry reporter genes, were attributed to either eGFP or mCherry based on the presence of a reporter gene identifier sequence (TAGG for eGFP and CGAA for mCherry) bracketing each barcode in the 3’UTR.
For the eve locus and synthetic insulator screens, RNA-seq reads additionally contained a unique molecular identifier (UMI) introduced during reverse transcription.
Assembly: dm6
Supplementary files format and content: Processed data files for BXC and eve loci screens are provided in two formats: .tsv and .bedgraph. The raw counts .tsv tables contain not normalised, not binned results of DNA and RNA sequencing merged by a barcode. The raw counts tables contain the following columns: Chromosome, Start, Stop, Barcode, mCherry, eGFP, Ratio, Strand. The mCherry and eGFP RNA-seq counts were filtered to have at least 3 reads for each gene. The .bedgraph files contain normalised, pooled, binned data for visualisation, and contain the columns Chromosome, Start, Stop, Insulator_Strength.
Supplementary files format and content: Processed data files for the synthetic insulator screen are provided as a .tsv table. The tables contain not normalised results of DNA and RNA sequencing merged by barcode. The raw counts tables contain the following columns: Name, Fragment_ID_position_in_reporter, mCherry, eGFP, Ratio. The mCherry and eGFP RNA-seq counts were filtered to have at least 3 reads for each gene.


title: hiPSC-derived neuron cells, Control 1, Day 60, replicate 2


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [39_AppNLGF_2P-Im_6M_rep9]


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [38_AppNLGF_2P-Im_6M_rep8]


title: LSCC_117


title: LSCC_116


title: Day-14-Total-RNA-WT-Cytoplasm-rep3


title: LSCC_115


title: hiPSC-derived neuron cells, Control 1, Day 60, replicate 1


title: hiPSC-derived neuron cells, RTS 4, Day 20, replicate 2


title: Day-14-Total-RNA-WT-Cytoplasm-rep2


title: Day-14-Total-RNA-WT-Cytoplasm-rep1


title: hiPSC-derived neuron cells, RTS 4, Day 20, replicate 1


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [37_AppNLGF_2P-Im_6M_rep7]


title: Day-14-Total-RNA-MTR4-null-Nucleus-rep2


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [36_AppNLGF_2P-Im_6M_rep6]


title: Day-14-Total-RNA-WT-Nucleus-rep3


title: hiPSC-derived neuron cells, RTS 3, Day 20, replicate 2


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [35_AppNLGF_2P-Im_6M_rep5]


title: LSCC_114


title: LSCC_113


title: Day-14-Total-RNA-MTR4-null-Nucleus-rep1


title: Day-14-Total-RNA-WT-Nucleus-rep2


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [34_AppNLGF_2P-Im_6M_rep4]


title: hiPSC-derived neuron cells, RTS 3, Day 20, replicate 1


title: LSCC_112


title: LSCC_111


title: hiPSC-derived neuron cells, RTS 2, Day 20, replicate 2


title: Day-14-Total-RNA-WT-Nucleus-rep1


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [33_AppNLGF_2P-Im_6M_rep3]


title: Day-21-MTR4-null-Cytoplasm-rep2

source_name: Cytoplasm


title: hiPSC-derived neuron cells, RTS 2 , Day 20, replicate 1


title: hiPSC-derived neuron cells, RTS 1, Day 20, replicate 2


title: LSCC_110


title: Day-21-MTR4-null-Cytoplasm-rep1


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [31_AppNLGF_2P-Im_6M_rep1]


title: Day-21-MTR4-null-Nucleus-rep2

source_name: Nucleus


title: LSCC_108


title: Day-21-MTR4-null-Nucleus-rep1


title: LSCC_109


title: LSCC_107


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [30_AppNLGF_vehicle_6M_rep11]

value: Vehicle


title: AppNLGF mice, 6-month-old, CDDO-2P-Im-reated, Alzheimer's disease [32_AppNLGF_2P-Im_6M_rep2]


title: hiPSC-derived neuron cells, Control 2, Day 20, replicate 2


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [29_AppNLGF_vehicle_6M_rep10]


title: Day-21-WT-Cytoplasm-rep2

value: Oocyte


title: hiPSC-derived neuron cells, Control 2, Day 20, replicate 1


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [28_AppNLGF_vehicle_6M_rep9]


title: hiPSC-derived neuron cells, RTS 1, Day 20, replicate 1


title: Day-21-WT-Cytoplasm-rep1


title: LSCC_105


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [27_AppNLGF_vehicle_6M_rep8]


title: hiPSC-derived neuron cells, Control 1, Day 20, replicate 2


title: Day-21-WT-Nucleus-rep3


title: LSCC_103


title: LSCC_104


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [26_AppNLGF_vehicle_6M_rep7]


title: hiPSC-derived neuron cells, RTS 4, Day 10, replicate 2


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [25_AppNLGF_vehicle_6M_rep6]


title: Day-21-WT-Nucleus-rep1


title: hiPSC-derived neuron cells, RTS 4, Day 10, replicate 1


title: LSCC_102


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [24_AppNLGF_vehicle_6M_rep5]


title: Day-21-MTR4-null-Cytoplasm-rep2

extract_protocol:
Oocytes were collected from indicated genotypes from mice of different stages. Then nucleus-cytoplasm separation were performed with micromanipulation. Nuclei and cytoplasm were collected separately.
After sample collection,RNA-seq libraries were constructed using Smart-seq2 protocal as described previously (Picelli et al, 2014).


title: hiPSC-derived neuron cells, RTS 3, Day 10, replicate 2


title: LSCC_101


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [23_AppNLGF_vehicle_6M_rep4]


title: Day-21-MTR4-null-Cytoplasm-rep1


title: LSCC_106


title: LSCC_100


title: hiPSC-derived neuron cells, RTS 2, Day 10, replicate 2


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [22_AppNLGF_vehicle_6M_rep3]


title: hiPSC-derived neuron cells, RTS 3, Day 10, replicate 1


title: Day-21-MTR4-null-Nucleus-rep2


title: hiPSC-derived neuron cells, Control 1, Day 20, replicate 1


title: LSCC_99


title: Day-21-WT-Nucleus-rep2


title: Day-21-MTR4-null-Nucleus-rep1


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [20_AppNLGF_vehicle_6M_rep1]


title: hiPSC-derived neuron cells, RTS 2, Day 10, replicate 1


title: Day-21-WT-Cytoplasm-rep2


title: LSCC_97


title: Day-21-WT-Cytoplasm-rep1


title: hiPSC-derived neuron cells, RTS 1, Day 10, replicate 2


title: hiPSC-derived neuron cells, RTS 1, Day 10, replicate 1


title: AppNLGF mice, 6-month-old, Vehicle-treated, Alzheimer's disease [21_AppNLGF_vehicle_6M_rep2]


title: Day-21-WT-Nucleus-rep3


title: Wild-type mice, 6-month-old, Vehicle-treated, Control [17_WT_vehicle_6M_rep2]

value: Wild-type


title: LSCC_96

value: Small RNA sequencing


title: Wild-type mice, 6-month-old, Vehicle-treated, Control [18_WT_vehicle_6M_rep3]


title: hiPSC-derived neuron cells, Control 2, Day 10, replicate 1

value: WT


title: Wild-type mice, 6-month-old, Vehicle-treated, Control [19_WT_vehicle_6M_rep4]


title: Day-21-WT-Nucleus-rep2


title: LSCC_94


title: Day-21-WT-Nucleus-rep1


title: LSCC_93


title: LSCC_98


title: hiPSC-derived neuron cells, Control 1, Day 10, replicate 1


title: APP/TAU mice, 11-month-old, CDDO-2P-Im-treated, Alzheimer's disease [14_APP_TAU_2P-Im_11M_rep4]

value: APP/TAU


title: LSCC_91


title: Day-14-WT-Cytoplasm-rep1


title: patient# 136-47 sole fibroblast

data_processing:
Cell demultiplexing, alignment and filtering were performed within 10X Genomics CellRanger package version 3.0.1, mapping to hg38
CellRanger v3.0.1
Seurat
Assembly: hg38
Supplementary files format and content: 13664A.barcodes.tsv.gz, 13664A.features.tsv.gz, and 13664A.matrix.mtx files from 13664A sample. Rest of files keeps same format. Patient# following with barcode, feature or matrix file.

source_name: skin

extract_protocol:
single cell suspension was achieved using human whole skin dissociation kit (Miltenyi, cat# 130-101-540). To achieve live single cell suspension, Propidium Iodide (BioLegend, 421301) negative and Vybrant DyeCycle Violet (Invitrogen, V35003) positive single cells were sorted.
Library construction was 10x Chromium Single Cell v3. Sequencing was performed on the NovaSeq 6000, v1.5 reagents.  Basecalling and sample demultiplexing is performed within Illumina’s BaseSpace software.

value: skin

value: fibroblast

value: native fibroblast


title: hiPSC-derived neuron cells, Control 1, Day 10, replicate 2


title: LSCC_90

value: Yes


title: Day-14-WT-Cytoplasm-rep2


title: patient# 136-47 scalp fibroblast


title: APP/TAU mice, 11-month-old, CDDO-2P-Im-treated, Alzheimer's disease [13_APP_TAU_2P-Im_11M_rep3]

value: Brain


title: LSCC_92


title: Day-14-WT-Nucleus-rep1


title: APP/TAU mice, 11-month-old, CDDO-2P-Im-treated, Alzheimer's disease [12_APP_TAU_2P-Im_11M_rep2]


title: APP/TAU mice, 11-month-old, CDDO-2P-Im-treated, Alzheimer's disease [15_APP_TAU_2P-Im_11M_rep5]


title: Day-14-WT-Nucleus-rep2


title: LSCC_89

value: No


title: APP/TAU mice, 11-month-old, CDDO-2P-Im-treated, Alzheimer's disease [11_APP_TAU_2P-Im_11M_rep1]


title: hiPSC-derived neuron cells, Control 2, Day 10, replicate 2

value: hiPSC-derived neuron


title: LSCC_95


title: MTR4-Day-21-rep3

source_name: ovary

extract_protocol:
Oocytes were collected from indicated genotypes (10 oocytes per sample) from mice of different stages. Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis.
RNA-seq libraries were constructed using Smart-seq2 protocal as described previously (Picelli et al, 2014).

value: ovary

tag: Sex

value: female


title: patient# 136-62 sole fibroblast injection site at 17-month post-injection time point

value: whole skin cells

value: sole fibroblast injection


title: APP/TAU mice, 11-month-old, Vehicle-treated, Alzheimer's disease [10_APP_TAU_vehicle_11M_rep5]

value: Vehicle


title: MTR4-Day-21-rep2

value: Oocyte


title: APP/TAU mice, 11-month-old, Vehicle-treated, Alzheimer's disease [09_APP_TAU_vehicle_11M_rep4]


title: LSCC_87


title: patient# 136-62 vehicle injection site at 17-month post-injection time point

value: media single injection


title: MTR4-Day-21-rep1


title: patient# 136-62 scalp fibroblast injection site at 17-month post-injection time point

value: scalp fibroblast injection


title: MTR4-Day-14-rep3

description: MTR4-Growing GV_rep3


title: Wild-type mice, 6-month-old, Vehicle-treated, Control [16_WT_vehicle_6M_rep1]

value: Wild-type


title: LSCC_86

value: Small RNA sequencing


title: LSCC_85


title: LSCC_88


title: patient# 136-47 scalp fibroblast injection site at 5-month post-injection time point

value: skin


title: APP/TAU mice, 11-month-old, Vehicle-treated, Alzheimer's disease [08_APP_TAU_vehicle_11M_rep3]

value: APP/TAU


title: APP/TAU mice, 11-month-old, Vehicle-treated, Alzheimer's disease [07_APP_TAU_vehicle_11M_rep2]


title: MTR4-Day-14-rep2

description: MTR4-Growing GV_rep2


title: APP/TAU mice, 11-month-old, Vehicle-treated, Alzheimer's disease [06_APP_TAU_vehicle_11M_rep1]


title: LSCC_84


title: patient# 136-47 vehicle injection site at 5-month post-injection time point


title: LSCC_83


title: patient# 136-68 sole fibroblast injection site at 2-month post-injection time point


title: Wild-type mice, 11-month-old, Vehicle-treated, Control [05_WT_vehicle_11M_rep5]


title: LSCC_82


title: Wild-type mice, 11-month-old, Vehicle-treated, Control [04_WT_vehicle_11M_rep4]


title: WT-Day-21-rep3

value: WT


title: patient# 136-68 scalp fibroblast injection site at 2-month post-injection time point


title: WT-Day-21-rep2


title: patient# 136-47 sole fibroblast injection site at 5-month post-injection time point


title: LSCC_81

value: Yes


title: patient# 136-68 vehicle injection site at 2-month post-injection time point


title: patient# 136-64 sole fibroblast injection site at 2-week post-injection time point


title: Wild-type mice, 11-month-old, Vehicle-treated, Control [02_WT_vehicle_11M_rep2]

value: Brain


title: WT-Day-14_rep2

description: WT-Growing GV_rep2


title: LSCC_79

value: No


title: WT-Day-14_rep3

description: WT-Growing GV_rep3


title: Wild-type mice, 11-month-old, Vehicle-treated, Control [01_WT_vehicle_11M_rep1]


title: patient# 136-64 scalp fibroblast injection site at 2-week post-injection time point


title: LSCC_78


title: WT-Day-14_rep1

description: WT-Growing GV_rep1


title: patient# 136-64 vehicle injection site at 2-week post-injection time point