title: groupNR;Thy0;Patient_11

city: Móstoles

first: Garcilaso

last: Riesco-Eizaguirre

state: Madrid

address: Calle Río Júcar, s/n

department: Endocrinology

country: Spain

institute: Hospital Universitario de Móstoles, Universidad Francisco de Vitoria

data_processing:
Trimming - Cutadapt software (1.11) was used to extract information of adapter and UMI in raw reads. All reads containing identical insert sequence and UMI sequence (insert-UMI pair) were collapsed into a single read using an in-house script. These reads were passed into the analysis pipeline. . Expression levels are measured as Tags Per Million mapped reads (TPM).
Mapping - Bowtie2 (2.2.2) was used for mapping the reads to reference genome GRCh37 and miRBase20 was used as annotation reference.For mapping to the genome, not more than one mismatch was allowed in the first 32 bases of the read.
Prediction - The putative miRs analysis was done with in-house scripts using the MiRPara software tool
Genome_build: GRCh37
Supplementary_files_format_and_content: excel file with sheets containing rawcounts and tpm

organism: Homo sapiens

source_name: serum

extract_protocol:
RNA was isolated from 200μl serum with the miRNeasy Serum/Plasma kit (QIAGEN) according to the manufacturers instructions. Total RNA was eluted in 14μl RNAse-free water.
The library preparation was done using the QIAseq miRNA kit (QIAGEN). A total of 5μl total RNA was converted into microRNA NGS libraries. Adapters were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent).

treatment_protocol: Samples used in the transversal study included serums of patients in complete remission and with recurrent/persistent disease taken at basal TSH. In the longitudinal part, basal time point was compared with samples taken after 72h of recombinant human TSH stimulation.

tag: diagnosis

value: differentiated thyroid carcinoma

tag: rhtsh stimulation

value: Complete Remission

tag: cancer recurrence

value: basal TSH


title: groupNR;Thy2;Patient_11

status: Public on Apr 25 2021

type: SRA

library_source: transcriptomic

molecule: total RNA

value: stimulated TSH


title: groupNR;Thy2;Patient_9


title: groupNR;Thy2;Patient_10


title: groupNR;Thy0;Patient_9


title: groupNR;Thy0;Patient_10


title: groupR;Thy2;Patient_7

value: Persistent/Recurrent Disease


title: groupNR;Thy0;Patient_8


title: groupR;Thy0;Patient_7


title: groupR;Thy0;Patient_5


title: groupR;Thy2;Patient_5


title: groupR;Thy0;Patient_4


title: groupR;Thy0;Patient_6


title: groupR;Thy2;Patient_6


title: groupR;Thy2;Patient_4


title: groupR;Thy2;Patient_1


title: groupR;Thy2;Patient_2


title: groupR;Thy2;Patient_3


title: groupR;Thy0;Patient_2


title: Ago2.50_oocytes.rep2

city: Beijing

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

country: China

institute: Chinese Academy of Sciences

description:
LACE-seq
Ago2.50_oocytes.bigwig

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After sequencing of LACE-seq libraries, the adapter sequences and the polyA tails at the 3' end were removed sequentially using Cutadapt v1.15 with the following two parameters: -f fastq -q 30,0 -a ATCTCGTATGCCGTCTTCTGCTT -m 18 --max-n 0.25 --trim-n, and -f fastq -a A{15} -m 18 -n 2.
After filtering, the LACE-seq reads were first aligned to human or mouse pre-rRNA by bowtie with default parameters, and the remaining unmapped reads were then aligned to the hg19 or mm9 reference genome. For LACE-seq data mapping, two mismatches and at most 10 multiple hits were allowed (bowtie parameters: -v 2 -m 10 --best --strata).
Genome_build: hg19 (GRCh37), mm9 (MGSCv37)
Supplementary_files_format_and_content: BigWig files were generated using bedtools genomecov v2.28.0 and bedGraphToBigWig v4 software.

organism: Mus musculus

source_name: Mouse Oocytes

growth_protocol: HeLa cells were cultured in DMEM containing 10% fetal bovine serum plus 100 U penicillin/streptomycin at 37°C in 5% CO2. K562 cells were cultured in RPMI-1640 containing 10% fetal bovine serum plus 100 U penicillin/streptomycin at 37°C in 5% CO2.

extract_protocol: After UV-C irradiation, RNA cross-linked to protein is purified and ligated with an adenylated DNA linker at the 3’end. Next, cDNA fragments, which stop exactly at the cross-link site in RNA, are generated through reverse transcription (RT), followed by polyadenylation, in vitro transcription (IVT), PCR amplification and high-throughput sequencing.

treatment_protocol: Female mice at six- to eight-weeks-old were injected with 10 IU of Pregnant Mare Serum Gonadotropin (PMSG) for 48 h. Meiosis II oocytes were collected 13 hour post human chorionic gonadotropin (hCG) injection from females previously primed with PMSG.

tag: strain

tag: genotype/variation

value: Wild type

tag: Sex

value: Female

tag: cell type

value: MII oocytes

tag: treatment

value: No treatment

tag: antibody

value: anti-Ago2 (Abcam, ab186733)


title: PTBP1.100K.HeLa.rep2

description:
LACE-seq
PTBP1.100K.HeLa.bigwig

source_name: Human HeLa cells

tag: cell line

value: HeLa (ATCC CCL-2)

value: anti-PTB (monoclonal BB7)


title: PTBP1.100K.HeLa.rep1

description:
LACE-seq
PTBP1.100K.HeLa.bigwig


title: groupNR;Thy2;Patient_8


title: PTBP1.100K.K562.withoutIVT.rep2

description:
LACE-seq
PTBP1.100K.K562.withoutIVT.bigwig

source_name: Human K562 cells


title: PTBP1.100K.K562.withoutIVT.rep1


title: Leaf176_vitro_3 TN_B_039

status: Public on Apr 26 2021

city: Cologne

first: Tatsuya

last: Nobori

address: Carl-von-Linne Weg 10, Max-Planck Institute for Plant Breeding Research

country: Germany

description:
Leaf176_vitro_3
Bacteroidetes
L176_combined.txt

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the  genome of corresponding commensal strain using Bowtie2 (version 2.2.8) with the parameters -p 20 -q --phred33 and transformed into a count per gene per library by using HTSeq (version 0.6.0).
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Pedobacter sp. Leaf176

source_name: Bacteria isolated from Arabidopsis thaliana

growth_protocol: Arabidopsis plants were grown in a chamber at 22°C with a 10 h light period and 60% relative humidity for 3 weeks and then in another chamber at 22°C with a 12 h light period and 60% relative humidity.

extract_protocol:
RNA was isolated from bacterial cells using FastRNA PRO™ BLUE KIT (MP Biomedicals). For plant RNA-seq, RNA was extracted with FastRNA PRO™ KIT with Lysing Matrix E (MP Biomedicals) and DNA was digested with TURBO DNase (Ambion). RNA quality was determined using a 2100 Bioanalyzer (Agilent Technologies, USA). 500 ng total RNA has initially been used for polyA enrichment with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
For bacterial RNA-seq, cDNA libraries were generated with Ovation Complete Prokaryotic RNA-Seq kit 1-8 (NuGEN). For plant RNA-seq, cDNA libraries were generated from polyA enriched RNA using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Commensal strains were grown in the liquid 50% TSB medium. For each strain, multiple cultures were prepared with different bacterial density to ensure that unsaturated cultures are used for experiments. Bacterial cells were harvested by centrifugation, washed twice with sterile water, and resuspended in sterile water to OD600 of 0.5 (∼2.5 × 108 cfu/mL). For bacterial RNA-seq, 80–100 A. thaliana leaves (four fully expanded leaves per plant) were syringe-inoculated with bacterial suspensions using a needleless syringe. For plant RNA-seq, approximately six leaves (two fully expanded leaves per plant) were treated. Mock control (water infiltration) was included in every experiment. Leaves were harvested at 6 hours after inoculation. Sampling was conducted for each plant genotype at a time, and it took approximately 5 min per genotype. Leaves were immediately frozen in liquid nitrogen, and stored at -80°C.

tag: host genotype

tag: replicate


title: PTBP1.10M.K562.withoutIVT.rep2

description:
LACE-seq
PTBP1.10M.K562.withoutIVT.bigwig


title: PTBP1.10M.K562.withoutIVT.rep1


title: PTBP1.100K.K562_KD.rep2

description:
LACE-seq
PTBP1.100K.K562_KD.bigwig

value: PTB shRNA


title: groupR;Thy0;Patient_3


title: PTBP1.100K.K562_KD.rep1

description:
LACE-seq
PTBP1.100K.K562_KD.bigwig


title: PTBP1.100K.K562_WT.rep2

description:
LACE-seq
PTBP1.100K.K562_WT.bigwig


title: PTBP1.100K.K562_WT.rep1

description:
LACE-seq
PTBP1.100K.K562_WT.bigwig


title: VDR+/+_PBS_Ventral Tegmental Area [2V]

city: Boston

first: Lajos

last: Kemeny

address: 149 13th Street

country: USA

institute: Massachusetts General Hospitala

data_processing:
Base calling and demultiplexing were processed using CASAVA version 1.8.
Reads were filtered for adapter contamination using Trimmomatic (version 0.36).
Reads were mapped to the GENCODE mouse comprehensive gene annotation set (version CGRm38) using STAR (version 2.4.2a).
Gene level read counts were generated using the quantMode GeneCounts option in STAR (version 2.4.2a).
Genome_build: CGRm38
Supplementary_files_format_and_content: Tab-delimited text files with gene counts.

source_name: VDR+/+_PBS_Ventral Tegmental Area

extract_protocol:
RNA was extracted using a Trizol based protocol. The extracted RNA samples where checked for overall quality and only samples with high quality (RIN ≥ 8.0) and high purity (OD 260/280 = 1.8–2.0) were used to generate libraries using the Bioo Scientific NEXTflex Rapid Directional RNA-seq Library Prep Kit (Bioo Scientific, Auston TX). The final library was quantitated using the Agilent 2200 TapeStation High Sensitivity DNA Analysis (Agilent Technologies, Santa Clara, CA) for size and Qubit dsDNA HS Assay (Life Technologies, Waltham, MA) for concentration. The resulting mRNA libraries were then sequenced at the John Wayne Cancer Institute Sequencing Center on an Illumina HiSeq 2500 in Rapid Mode using 101 bp paired-end reads.
RNA-seq libraries were constructed using the Bioo Scientific NEXTflex Rapid Directional RNA-seq Library Prep Kit (Bioo Scientific, Auston TX) following the manufactures protocol.

tag: strain background

value: VDR+/+

value: PBS

tag: tissue

value: brain

tag: brain location

value: Ventral Tegmental Area

tag: tissue type

value: Frozen Tissue


title: VDR-/-_PBS_Ventral Tegmental Area [7V]

source_name: VDR-/-_PBS_Ventral Tegmental Area

value: VDR-/-


title: VDR-/-_PBS_Ventral Tegmental Area [8V]


title: VDR-/-_PBS_Nucleus Accumbens [9A]

source_name: VDR-/-_PBS_Nucleus Accumbens

value: Nucleus Accumbens


title: VDR+/+_PBS_Ventral Tegmental Area [3V]


title: VDR-/-_PBS_Nucleus Accumbens [8A]


title: VDR+/+_PBS_Nucleus Accumbens [3A]

source_name: VDR+/+_PBS_Nucleus Accumbens


title: VDR-/-_PBS_Nucleus Accumbens [7A]


title: VDR-/-_PBS_Ventral Tegmental Area [9V]


title: VDR+/+_PBS_Nucleus Accumbens [2A]


title: VDR-/-_Morphine_Nucleus Accumbens [2.2A]

source_name: VDR-/-_Morphine_Nucleus Accumbens

value: Morphine


title: VDR-/-_Morphine_Ventral Tegmental Area [2.2V]

source_name: VDR-/-_Morphine_Ventral Tegmental Area


title: VDR-/-_Morphine_Ventral Tegmental Area [2.1V]


title: VDR-/-_Morphine_Nucleus Accumbens [2.0A]


title: VDR-/-_Morphine_Ventral Tegmental Area [2.0V]


title: VDR+/+_Morphine_Ventral Tegmental Area [1.2V]

source_name: VDR+/+_Morphine_Ventral Tegmental Area


title: VDR+/+_Morphine_Nucleus Accumbens [1.2A]

source_name: VDR+/+_Morphine_Nucleus Accumbens


title: VDR+/+_Morphine_Nucleus Accumbens [1.0A]


title: VDR+/+_PBS_Ventral Tegmental Area [1V]


title: VDR+/+_Morphine_Nucleus Accumbens [1.1A]


title: VDR+/+_Morphine_Ventral Tegmental Area [1.1V]


title: VDR+/+_PBS_Nucleus Accumbens [1A]


title: VDR+/+_Morphine_Ventral Tegmental Area [1.0V]


title: Ago2_IP_Oocyte

data_processing:
library strategy: LACE-seq
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After sequencing of LACE-seq libraries, the adapter sequences and the polyA tails at the 3' end were removed sequentially using Cutadapt v1.15 with the following two parameters: -f fastq -q 30,0 -a ATCTCGTATGCCGTCTTCTGCTT -m 18 --max-n 0.25 --trim-n, and -f fastq -a A{15} -m 18 -n 2.
After filtering, the LACE-seq reads were first aligned to human or mouse pre-rRNA by bowtie with default parameters, and the remaining unmapped reads were then aligned to the hg19 or mm9 reference genome. For LACE-seq data mapping, two mismatches and at most 10 multiple hits were allowed  (bowtie parameters: -v 2 -m 10 --best --strata).
Small RNA-seq data were processed as previously described  (Yang, Q. et al.)
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Bigwig files were generated using bedtools genomecov v2.17.0 and bedGraphToBigWig v4 software. txt file contains reads id and corresponding small RNA class

growth_protocol: HeLa cells were cultured in DMEM containing 10% fetal bovine serum plus 100 U penicillin/streptomycin at 37°C in 5% CO2. Female mice at six- to eight-weeks-old were injected with 10 IU of Pregnant Mare Serum Gonadotropin  (PMSG) for 48 h.Meiosis II oocytes were collected 13 hour post human chorionic gonadotropin  (hCG) injection from females previously primed with PMSG.

value: anti-Ago2 (Sigma-Aldrich, SAB4200085)

tag: molecule subtype

value: small RNA


title: PTB_50_Oocyte_rep2

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-50oocytes-4_TGACC_L001

value: anti-PTB (Abcam, 133734)


title: PTB_50_Oocyte_rep1

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-50oocytes-3_TTAGG_L001

value: MII oocytes


title: LNCaP-SL_PBS treated rep2

city: Seoul

first: Miso

last: Park

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

data_processing:
High-throughput sequencing was performed as paired-end 251 sequencing using Hiseq 2500
The reads of RNAseq were aligned to GRCh38 genome reference using STAR aligner v2.7.1a.
The read counts mapped on each gene were obtained using HTseq v0.12.4 with Ensembl version 96 annotation GTF file.
For differential expressed gene (DEG) analysis, we used DESeq2 package (v1.26.0) in R.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: LNCaP-SL

growth_protocol: LNCaP-SL cells were routinely cultured at 37℃ in 5% CO2/95% air RPMI medium supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were treated PBS (vehicle) or csEV isolated from serial centrifugation (5 steps) for 24 hours.

value: aggressive human prostate adenocarcinoma cells (a subline of LNCaP cells)

value: PBS (vehicle) treated


title: PTB_50_Oocyte_rep3

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-50oocytes-2_adding_CGATG_L001


title: IgG_Oocyte

value: anti-IgG (Cali-Bio, CB200071)


title: LNCaP-SL_PBS treated rep1


title: cKO-4_rnaseq

data_processing:
Illumina bcl2fastq-1.8.4 conversion software was used for basecalling.
After sequencing of single-cell RNA-seq libraries, adapters and low-qaulity bases were removed by Trimmomatic 0.36 (Bolger et al., 2014).
After filtering, paired-end reads were aligned to the mouse reference genome (mm9) using HISAT2 (Kim et al., 2015) with default parameters.
The uniquely mapped reads count matrix were subject to DESeq2 (Michael, et al., 2014) to identify differential expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage.

molecule: polyA RNA

growth_protocol: Ago2 cKO (Ago2 loxP/loxP,Zp3-cre) and Control(Ago2 loxP/+) female mice were bred at six- to eight-weeks-old.

extract_protocol:
Single oocyte was picked in PCR tube and used for library construction.
Single-cell RNA-seq libraries were generated using Smart-seq2 (Simone Picelli,2014) .

value: Ago2 cKO


title: LNCaP-SL_csEV treated rep1

value: csEV treated


title: Mili_50_Oocyte_rep3

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
Mili-50oocytes-3_TGCTA_L005

value: anti-Mili (CST, 2071)


title: Mili_50_Oocyte_rep1

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
Mili-50oocytes-1_GGTTA_L005


title: cKO-5_rnaseq


title: PTB_1HeLaCells_rep2

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-1HeLa-3M_ACGGC_L007

value: HeLa (ATCC CCL-2)

value: anti-PTB (monoclonal BB7)


title: VDR-/-_Morphine_Nucleus Accumbens [2.1A]

value: brain


title: Mili_50_Oocyte_rep2

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
Mili-50oocytes-2_TGAAC_L005


title: cKO-1_rnaseq


title: Ago2_50_Oocyte

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
Ago2-100oocytes-3_TAAGA_L004

value: anti-Ago2 (Abcam, ab186733)


title: cKO-2_rnaseq


title: PTB_1HeLaCells_rep1

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-1HeLa-1_AACCC_L004


title: Leaf155_col_3 TN_B_046

institute: Max-Planck Institute for Plant Breeding Research

description:
Leaf155_col_3
Proteobacteria
L155_combined.txt

organism: Rhizobium sp. Leaf155


title: Ctrl-5_rnaseq

value: Ctrl


title: Ago2_100_Oocyte_rep2

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
Ago2-100oocytes-2_TGTTC_L004


title: PTB_10HeLaCells_rep2

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-10HeLa-3a_CACAC_L004


title: LNCaP-SL_csEV treated rep2


title: cKO-3_rnaseq


title: Ctrl-3_rnaseq


title: Ago2_100_Oocyte_rep1

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
Ago2-50oocytes-1_TGCTA_L004


title: Ctrl-4_rnaseq


title: Activation screen, Library D+E, Bin 2

city: Stanford

first: Adrian

middle: L

last: Sanborn

state: CA

address: 299 Campus Drive West

institute: Stanford University

description: Plasmid library DNA

library_source: genomic

data_processing:
cutadapt 1.18 was used to discard reads without matching paired-end sublibrary sequencing primers and trim the primers in reads with matching primers
bwa-mem 0.7.17-r1188 was used to perform a first-pass alignment of reads to the DNA fragment library
Imperfectly mapped read pairs (i.e., those without paired read SAM flags of 99 and 147) were re-mapped to the library sequence with minimal edit distance
Supplementary_files_format_and_content: Excel file containing counts of reads aligned to each protein fragment

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Library D+E, Bin 2

growth_protocol: S. cerevisiae strain BY4711 (ATCC 200873) was cultured in SC medium lacking tryptophan (SC-Trp)

extract_protocol:
Sorted cells were grown overnight and then pelleted. Pellets were treated with lyticase and then plasmid DNA was extracted using a Qiagen Miniprep kit.
The region of the plasmid encoding the variable protein fragment was PCR-amplified for 11-20 cycles (based on the OD600 of the culture) using Phusion polymerase with PCR primers that added flanking sequences corresponding to the standard Illumina sequencing primers. After a column cleanup, a second PCR was performed with primers that added sample-specific barcodes and the P5 and P7 sequences for Illumina sequencing.
OTHER:sequncing of designed plasmid library

treatment_protocol: overnight cultures were diluted to OD600 of 0.4 in SC-Trp-NAT-G418 with 10 nM beta-estradiol and grown for 4 hours at 30C before sorting on a BD Influx Cell Sorter

value: strain BY4711


title: Ctrl-2_rnaseq


title: PTB_10HeLaCells_rep1

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-10HeLa-1_AGTTC_L004


title: PTB_100HeLaCells_rep2

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-100HeLa-3_CGATT_L005


title: slt2 (BY4741) without poacid acid_3

city: Madrid

first: Javier

last: Arroyo

address: Plaza Ramón y Cajal, S/N

department: Facultad de Farmacia, Departamento de Microbiologia II

institute: Universidad Complutense de Madrid

description: slt2 3-

data_processing:
RNA-Seq data were analyzed by using the CLC Genomics Workbench (Qiagen Bioinformatics) to identify the differentially expressed genes
Expression values were measured in RPKM (Reads per kilobase of exon model per million mapped reads). The threshold p-value was determined according to the false discovery rate (FDR).
The threshold p-value was determined according to the false discovery rate (FDR). In this study, genes that were considered differentially regulated met the following criteria: FDR p-value ≤0.05 and fold change ≥ 2 for up regulated or ≤ 0.5 for down regulated genes
For RNA Seq, each study group contained three library samples. In CLC Genomics Workbench, the ‘Differential Expression for RNA-Seq tool’ performs some multi-factorial statistics on a set of Expression Tracks based on a negative binomial Generalized Linear Model (GLM).
Genome_build: Saccharomyces cerevisiae genome (R64-1-1)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

source_name: yeast

growth_protocol: Saccharomyces cerevisiae strain BY4741 was grown overnight and dilluted to 0.2 OD, allowed to grow until 0.5 and then was grown for 2 hours

extract_protocol:
Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the RNeasy kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.
DNA libraries from depleted RNA were generated with the use of the "NEBNEXT Ultradirectional RNA Library Prep Kit" (New England Biolabs) and following the instructions of the manufacturer. Briefly, depleted RNA was fragmented and copied to double-stranded cDNA. Specific adapters for Illumina sequencing were attached to the cDNAs and the library was enriched by limited PCR. DNA fragments with 300-450 bp inserts were selected for massive sequencing.

treatment_protocol: Saccharomyces cerevisiae strain BY4741 was grown overnight and dilluted to 0.2 OD, allowed to grow until 0.5 and then was grown with poacid acid for 1 hour


title: slt2 (BY4741) with poacid acid_3

description: slt2 3+

value: poacid acid for 1 hour


title: slt2 (BY4741) with poacid acid_2

description: slt2 2+


title: PTB_100HeLaCells_rep1

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-100HeLa-1_CATGT_L005


title: Ctrl-1_rnaseq


title: Ddx4_1_Oocyte_rep2

value: anti-Ddx4 (Abcam, ab108392)


title: slt2 (BY4741) without poacid acid_2

description: slt2 2-


title: PTB_1000HeLaCells_rep2

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-1000HeLa-3_ATGCT_L005


title: Ddx4_10_Oocyte


title: slt2 (BY4741) with poacid acid_1

description: slt2 1+


title: Ddx4_1_Oocyte_rep1


title: slt2 (BY4741) without poacid acid_1

description: slt2 1-


title: wild type (BY4741) with poacid acid_3

description: WT 3+

value: wild type


title: wild type (BY4741) with poacid acid_1

description: WT 1+


title: PTB_1000HeLaCells_rep1

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-1000HeLa-1_AGCAT_L005


title: wild type (BY4741) with poacid acid_2

description: WT 2+


title: wild type (BY4741) without poacid acid_3

description: WT 3-


title: PTB_10000HeLaCells_rep2

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-10000HeLa_2_ATGCT_L008


title: Ddx4_50_Oocyte


title: Ddx4_1_Oocyte_rep3


title: wild type (BY4741) without poacid acid_1

description: WT 1-


title: wild type (BY4741) without poacid acid_2

description: WT 2-


title: PTB_10000HeLaCells_rep1

description:
replicates were merged for processing and the generated processed data is linked to the corresponding replicate 1 sample records
PTB-10000HeLa_1_AGTTC_L008


title: Ddx4_30_Oocyte


title: Ex52_1to5_mouse5_HRT (cDNA)

status: Public on Apr 24 2021

city: Durham

last: Oliver

state: North Carolina

address: 101 Science Drive, CIEMAS Rm. 2323

institute: Duke University

data_processing:
Trim. The reads were trimmed for sequencing adapters and low-quality bases using Trimmomatic (v0.33).
Alignment and deduplication. Alignment of the trimmed reads was done using bwa-mem (v0.7.12) to the reference genomes (gDNA aligned to mouse genome GRCm38 + human DMD; cDNA aligned to human dystrophin cDNA). Aligned reads were tagged with their UMI using fgbio (v0.8.1) AnnotateBamWithUmis, and PCR duplicates were marked using Picard (v2.14.0) MarkDuplicates based on the UMI tag.
Alignment to reference bin sequences. Reference amplicons were built to align to the targeted locus and expected edits. To remove reads that are due to false priming, reads that do not contain the 20 bases directly adjacent to the GSP expected sequence were filtered out. To remove reads that do not extend far enough past the edit site, reads that are shorter than the required minimum length for binning were filtered out. On-site deduplicated reads were aligned to reference amplicons using bwa-mem (v0.7.12). Aligned reads were analyzed and binned based on editing outcomes using a custom-built script using python3 (https://github.com/siyansusan/DMD_integration_analysis.git). Reads that contain an indel ±15bp at the expected cute site or junction were identified. The number of distinct UMIs were counted for each edit to quantify frequency of editing events.
Genome_build: GRCm38 + human DMD
Supplementary_files_format_and_content: BAM file (curated and represents the collection of usable reads) for each sample.  Manuscript methods include a link to github for access to analysis pipeline scripts;  GEO users may find it useful to use the bam files to repeat analysis methods.
Supplementary_files_format_and_content: Matrix table with bin counts for every editing outcome and every sample

source_name: Heart

extract_protocol:
Tissue was extracted from euthanized mice. Genomic DNA was isolated using the DNeasy kit (Qiagen) according to the manufacturer’s protocol. Total RNA was isolated using QIAshredder and RNeasy Plus kits (Qiagen). First-strand cDNA synthesis was performed using 500 ng total RNA per sample using the SuperScript VILO Reverse Transcription Kit (Invitrogen) and second-strand synthesis was performed using Klenow fragment DNA polymerase (NEB).
Tagmentation of 200 ng genomic DNA or second-strand products was performed using a 1:40 dilution of assembled Tn5. To enrich the targeted sequence, first round PCR using a genome specific primer was used with a reverse primer specific for the i7 adapter sequence inserted by the transposon. Second round PCR using a barcode primer specific for the custom adapter sequence was used to add 6-nucleotide experimental barcodes and the Illumina i5 adapter was used with the Tn5-Universal reverse primer.
Tn5-based tagmentation with target enrichment.

value: Heart

tag: aav-donor

tag: aav ratio

tag: injection route

value: systemic P2 intravenous

tag: tn5 gsp


title: Ex52_1to1_mouse4_HRT (cDNA)


title: Ex52_1to5_mouse4_HRT (cDNA)


title: Super_1to1_mouse3_HRT (cDNA)


title: Ex52_1to5_mouse2_HRT (cDNA)


title: Ex52_1to1_mouse5_HRT (cDNA)


title: Super_1to5_mouse3_HRT (cDNA)


title: Super_1to1_mouse1_HRT (cDNA)


title: Ex52_1to1_mouse1_HRT (cDNA)


title: Super_1to5_mouse5_HRT (cDNA)


title: Ex52_1to1_mouse2_HRT (cDNA)


title: Super_1to1_mouse2_HRT (cDNA)


title: Super_1to1_mouse5_HRT (cDNA)


title: Ex52_1to5_mouse6_HRT (cDNA)


title: Super_1to5_mouse6_HRT (cDNA)


title: Super_1to1_mouse4_HRT (cDNA)


title: Ex52_1to1_mouse6_HRT (cDNA)


title: Ex52_1to1_mouse3_HRT (cDNA)


title: Super_1to5_mouse4_HRT (cDNA)


title: Ex52_1to5_mouse3_HRT (cDNA)


title: Super_1to1_mouse6_HRT (cDNA)


title: Ex52_1to5_mouse1_HRT (cDNA)


title: Super_1to5_mouse1_HRT (cDNA)


title: KH2 mESC diff HOXA13 3

city: ROTTERDAM

first: Vincent

last: Janmaat

address: Dr. Molewaterplein 40

department: Gastroenterology and Hepatology

country: Netherlands

institute: Erasmus MC

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.
Sequenced reads were trimmed for adaptor sequence, minimal Q score was 22, minimal read length 36, 5'or 3' trim off.
Reads were mapped against reference genome mm9 with Burrows-Wheeler Transform (Tophat version 2.0.14), and quantified using HTSeq (version 0.6.1p1).
Genome_build: mm9
Supplementary_files_format_and_content: Lists with raw gene counts for every gene per sample

source_name: KH2 mouse embryonic stem cell

growth_protocol: KH2 mESCs were maintained in DMEM with 10% FCS, Non-Essential Amino Acids, sodium pyruvate, LIF, and β-mercapto-ethanol (embryonic stem cell medium; Extended data table 5). Dishes were coated with attachment factor protein solution (Thermo-Fisher Scientific). Irradiated mouse embryonic fibroblasts (3T3-Swiss albino cells (gift of J.W.P.M. van Baal), cultured in DMEM with 10% FCS, were used as feeder cells.

extract_protocol:
RNA isolation from de-differentiated KH2 mouse embryonic stem cells (mESCs) was done using a picopure RNA isolation kit (Thermo-Fisher Scientific, Waltham, USA). Samples were tested on the Agilent 2100 Bioanalyzer to determine RNA integrity and quantity.
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample  preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for  Illumina" (NEB #E7420S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After  fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing  adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation  was measured with the Fragment Analyzer (see appendices). The size of the resulting products was  consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the Illumina NextSeq 500 was performed according to manufacturer's  protocols. A concentration of 1.6 pM of DNA was used. NextSeq control software 2.0.2 was used.

treatment_protocol: Differentiation of KH2 mouse embryonic stem cells. An optimized version of the Ogaki protocol was used[70]. Cells were plated on 50% confluent pre-cultured M15 cells, a mesoderm-derived feeder cell line[71] (gift of N. Hastie, University of Edinburgh, UK). Cells grew six days in differentiation medium consisting of ESC medium without LIF, with the addition of Activin-A, basic Fibroblast Growth Factor, CHIR, and Noggin (Extended data table 5). HOXA13-expression was induced on day four using doxycycline at 1.25 µg/ml. On day six, cells were analyzed by FACS by double staining with 0.8 µg PE Rat Anti-Mouse CD184 (CXCR4) and 2.0 µg Anti-CD324 Alexa Fluor® 488 (E-Cadherin) at 4 °C for 45 min (Extended data table 5). The cells were analysed with a BD FACSCantoTM II (BD Biosciences, USA). Data were analyzed with BD FACSDiva v8.0.1 software, which was obtained from BD Biosciences, and processed using Microsoft Excel. Double-positive cells were sorted and cultured for another day with doxycycline at 1.25 µg/ml before harvesting and RNA isolation took place, using the picopure RNA isolation kit (Thermo-Fisher Scientific).

tag: cell types

value: Embryonic stem cell

tag: strain

tag: genotype


title: KH2 mESC diff HOXA13 2


title: KH2 mESC diff HOXA13 1


title: KH2 mESC diff CONTROL 3

value: CONTROL


title: Thap1 null-D6-DIV 4D

city: Ann Arbor

first: Dhananjay

last: Yellajoshyula

state: MI

address: 5378, BSRB, 109, Zina Pitcher Place

department: Neurology

institute: University of Michigan

data_processing:
Base Calling software used --  Illumina’s Bustard
Data filtering was based upon quality scores, and quality scores over read cycles was calculated using picard-tools
Read alignment software --- STAR
Abundance measurement software - eXpress
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TPM (Transcripts Per Kilobase Million) for every gene and every sample

source_name: OPC clonal line

growth_protocol: OL differentiation media

extract_protocol:
Total RNA was extracted from cell pellet using Quick-RNA Microprep from Zymoresearch.
RNA-Seq libraries were made using the TruSeq Stranded Total RNA Library prep kit with rRNA removal mix Gold (Illumina)

treatment_protocol: T3 thyroid hormone (40 μg/ml)

tag: opc clonal line

value: Primary NSC derived OPC cells

tag: genotypye

value: Thap1 null

tag: differentiation stage - days in vitro (div)


title: Thap1 null-3F-DIV 4D


title: Control-D7-DIV 4D

value: Control


title: Control-E8-DIV 4D


title: KH2 mESC diff CONTROL 2


title: KH2 mESC HOXA13 1

treatment_protocol: No treatment was applied

tag: cell type


title: KH2 mESC CONTROL 2


title: Thap1 null-7F-DIV 4D


title: Thap1 null-D6-DIV 2D


title: KH2 mESC HOXA13 3


title: KH2 mESC CONTROL 3


title: KH2 mESC CONTROL 1


title: Control-D3-DIV 4D


title: Super_1to5_mouse2_HRT (cDNA)


title: Control-D7-DIV 2D


title: Control-D3-DIV 2D


title: Control-D3-OPC

growth_protocol: OPC  growth media

treatment_protocol: PDGF-AA

value: OPC


title: Control-D7-OPC


title: Thap1 null-7F-DIV 2D


title: Control-E8-OPC


title: bKO-3

city: Kobe

first: Okechi

last: Oduori

address: 3F, 1-5-6, Minatojima Minami-machi, Chuo-ku

department: Molecular and Metabolic Medicine

country: Japan

institute: Kobe University Graduate School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
The library used was Pre-process Core’s R library by Macrogen
Filtering criteria (exclude gene with zero FPKMs across all samples and no sample filtering), Signal+1, Log base 2 transformation and Quantile Normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: βKcnj11 -/- islets

extract_protocol: Mice were sacrificed under anesthesia and islets isolated by collagenase digestion, washed and handpicked under a microscope and cultured for 2 days in RPMI media. Following washing, three times with ice-cold PBS, Total RNA from mouse pancreatic islets was isolated using the Qiagen RNA extraction kit per the manufacturer’s instructions. RNA samples were processed as fragments per kilobase of transcript per million mapped reads (FPKM), and determined by the RNA-sequencing (RNA-seq) service provider Macrogen.

treatment_protocol: Islets were cultured in RPMI media for 2 days and washed with Ice-cold PBS before extraction began.

value: Islets

tag: age

value: 11-12 weeks

value: BetaKcnj11 -/-


title: Control-E8-DIV 2D


title: KH2 mESC diff CONTROL 1


title: Thap1 null-3F-DIV 2D


title: Thap1 null-D6-OPC


title: Thap1 null-3F-OPC


title: KH2 mESC HOXA13 2


title: Thap1 null-7F-OPC


title: WT-3

source_name: Control Islets

value: Kcnj11 fl/fl


title: WT-1


title: bKO-1


title: bKO-2


title: groupR;Thy0;Patient_1

source_name: serum

tag: diagnosis

value: differentiated thyroid carcinoma

tag: rhtsh stimulation

value: Persistent/Recurrent Disease

tag: cancer recurrence

value: basal TSH


title: CD200-AML mouse 2

city: Houston

first: Shelley

last: Herbrich

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Raw sequencing reads were pseudoaligned using Kallisto v0.44.0 with 30 bootstrap samples
Abundance data was further analyzed with Sleuth v0.30.0
Genome_build: GRCh38.92
Supplementary_files_format_and_content: comma-seperated values file includes transcript-level estimates for each sample

source_name: PBMC-humanized mouse

growth_protocol: PBMC-humanized mice were given CD200+ or CD200- AML for 10 days

extract_protocol:
Human CD3+ cells were isolated from mouse spleen. Total RNA was extracted from 5x106 cells using Qiagen RNeasy Mini Kit. RNA concentration was determined by NanoDrop 2000 and RNA quality was assessed with an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: lymphocytes

tag: disease

value: AML

tag: aml cd200 status

value: negative

tag: cell line


title: CD200-AML mouse 3


title: CD200+AML mouse 3

value: positive


title: CD200-AML mouse 1


title: CD200+AML mouse 2


title: WT-2


title: CD200+AML mouse 1


title: pclwt_mtf2wt_eb_d4

city: Nijmegen

first: Chet

middle: H

last: Loh

address: Geert Grooteplein Zuid 28

institute: RIMLS

description: Bulk-library

data_processing:
Base-calling was performed by the Illumina CASAVA software.
Reads from this study and from Perino et al, Nat. Gen (2018) were trimmed to 42bp with fastx_trimmer (version 0.0.13.2), and in case of paired-end sequencing only read_1 was used for analysis
Bulk-RNA sequencing reads were quantified using Salmon and the count tables were analysed using DEseq2
mm10
Supplementary_files_format_and_content: count table of all cell lines

source_name: mouse embyroid bodies

growth_protocol: mESC were grown in serum+LIF medium as described in Marks, H. et al. (doi:10.1016/j.cell.2012.03.026)

extract_protocol:
Standard RNA isolation protocol
Bulk-RNA libraries were prepared according to the Kapa Hyper-prep Kit (Kapa Biosystems) using NEXTflex adapters (Bio Scientific) and amplified with ten cycles of PCR. Libraries were size-selected to obtain 300bp fragments using Kapa Pure Beads and sequenced on an Illumina NextSeq machine to obtain 75bp reads

treatment_protocol: Where indicated cells were treated to directed differentiation protocol towards either mesoderm or endoderm lineage

value: embryoid bodies

tag: timepoints

value: day 4

value: Mtf2 WT


title: pclwt_mtf2wt_eb_d2

description: Bulk-library

value: day 2


title: mtf2ko_eb_d7

description: Bulk-library

value: day 7

value: Mtf2 null


title: pclwt_mtf2wt_eb_d0

description: Bulk-library

value: day 0


title: mtf2ko_eb_d4

description: Bulk-library


title: mtf2ko_eb_d2

description: Bulk-library


title: jm8_jarid2wt_eb_d7

description: Bulk-library

value: Jarid2 WT


title: jm8_jarid2wt_eb_d0

description: Bulk-library


title: jm8_jarid2wt_eb_d2

description: Bulk-library


title: CX3_2: Single cell TCR of fresh cevix biopsy/whole cell lysate/subject 3

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

department: Medicine

institute: University of Washington

description: CD8 negative selection to enrich CD8 T cells before 10x single cell gel bead emulsion

data_processing:
Library strategy: TCR-seq
The sequencing of 10x libraries for 5’ GEX and TCR-vdj for the ten cervix biopsies from eight individuals and cell ranger analysis were performed at the shared resource at Fred Hutch. Cell ranger 3.0.2 with human genome GRCh38 for gene expression and GRCh38-alts-ensembl for TCR-vdj were used in the initial steps including quality control, alignment to human genomes and counting of aligned sequence reads for individual genes.
We manually examined summary HTML files for the ten gene expression libraries and the ten TCR-vdj libraries generated from ten cervix samples. All the libraries have valid barcodes (> 85%), fraction reads in cells (> 80%) and reads mapped to genome (> 50%).
The MTX files from the output of cell ranger were imported into Monocle3, Seurat (version 3.1.2) or Scanpy (version 1.4.4) for further analysis. In all the three methods, we filtered out cells with less than 200 genes detected and genes that are only detected in less than 3 cells. We further filtered out cells with percentages of mitochondria genes more than 15%. pyVDJ (https://github.com/veghp/pyVDJ) and Scirpy is used to link TCR-vdj to gene expression in Scanpy.

source_name: Fresh human cervix biopsy

extract_protocol:
Human ectocervix biopsies were processed into single cell suspension for 10x singel cell immune profiling (5' gene expression + TCR), usually within the four hours after biopsies were collected from the UW virus research clinics (VRC). The process of cervix biopsies were a combination of collagenase, DNase and mechanical agitation (details in the associated manuscript).
Cell suspensions were loaded according to 10x Genomics Manufacturer’s instructions for Chip A to generate Gel Bead-In-Emulsion (GEMS, 10x genomics) using barcoded gel beads. RNA containing GEMS underwent barcoded cDNA synthesis. Subsequent library construction followed 10x Genomics 5’ Single Cell Immune Profiling Manufacturer’s Instructions. Libraries were constructed using the Chromium Next GEM Single Cell 5’ Library & Gel Beads Kit v1.1 with additional Chromium Single Cell V(D)J Enrichment Kit, Human T Cells kit for TCR Libraries.

value: single cell suspension from fresh cervix biopsy with CD8 negative selection


title: CX3_1: Single cell 5' gene expression of fresh cevix biopsy/whole cell lysate/subject 3

data_processing:
The sequencing of 10x libraries for 5’ GEX and TCR-vdj for the ten cervix biopsies from eight individuals and cell ranger analysis were performed at the shared resource at Fred Hutch. Cell ranger 3.0.2 with human genome GRCh38 for gene expression and GRCh38-alts-ensembl for TCR-vdj were used in the initial steps including quality control, alignment to human genomes and counting of aligned sequence reads for individual genes.
We manually examined summary HTML files for the ten gene expression libraries and the ten TCR-vdj libraries generated from ten cervix samples. All the libraries have valid barcodes (> 85%), fraction reads in cells (> 80%) and reads mapped to genome (> 50%).
The MTX files from the output of cell ranger were imported into Monocle3, Seurat (version 3.1.2) or Scanpy (version 1.4.4) for further analysis. In all the three methods, we filtered out cells with less than 200 genes detected and genes that are only detected in less than 3 cells. We further filtered out cells with percentages of mitochondria genes more than 15%. pyVDJ (https://github.com/veghp/pyVDJ) and Scirpy is used to link TCR-vdj to gene expression in Scanpy.


title: jarid2ko_eb_d7

description: Bulk-library

value: Jarid2 null


title: CX1_2: Single cell TCR of fresh cevix biopsy/whole cell lysate/subject 1

description: Whole single cell suspension to 10x gel bead emulsion

value: single cell suspension from fresh cervix biopsy


title: pclwt_mtf2wt_eb_d7

description: Bulk-library


title: jarid2ko_eb_d4

description: Bulk-library


title: CX1_1: Single cell 5' gene expression of fresh cevix biopsy/whole cell lysate/subject 1


title: jm8_jarid2wt_eb_d4

description: Bulk-library


title: jarid2ko_eb_d0

description: Bulk-library


title: EPC2-hTERT CONTROL 4

data_processing:
Reads were generated of 50 base-pairs in length.
Reads were mapped against the requested reference with Tophat (version 2.0.10).
Gene expression was quantified using both Cufflinks (version 2.1.1) and HTseq-count (0.6.1).
Genome_build: Hg 19
Supplementary_files_format_and_content: raw counts

source_name: EPC2-hTERT cell line

growth_protocol: These cells were cultured with Keratinocyte SFM medium, supplemented with bovine pituitary extract at 50 µg/ml and EGF at 1 ng/ml (Thermo-Fisher Scientific).

extract_protocol:
RNA was isolated using the NucleoSpin RNA isolation kit (Macherey Nagel, Dϋren, Germany). Samples were tested on the Agilent 2100 Bioanalyzer to determine RNA integrity and quantity.
The TruSeq Stranded mRNA Library Prep Kit was used to prpcess the samples. The resulting DNA libraries were sequenced according to the Illumina TruSeq v3 protocol.

value: Primary immortalized human squamous esophageal cell line

tag: genetic modification

value: The pEN_TmiRc3 vector was cut using AgeI and XbaI restriction sites, a gift from Iain Fraser (Addgene (Cambridge, USA) #25748). pSLIK-Venus was a gift from Iain Fraser (Addgene #25734), a version without HOXA13 was used for the control cell line. LGC Genomics (Teddington, UK) sequenced both plasmids. Next, plasmids were packaged into lentiviral particles following transfection in HEK293T cells with third generation packaging plasmids. The supernatant was collected and ultracentrifuged. EPC2-hTERT cells were transduced with the virus and Fluorescence-Activated Cell Sorted (FACS) for YFP (pSLIK-Venus) positive cells on the BD FACSCantoTM II that was bought from BD Biosciences (San Jose, USA). These cells were grown and analyzed as a cell pool. HOXA13 was induced by the addition of 1,25 µg/ml doxycycline to the culture medium. Overexpression was determined by qPCR according to scientific standards (data not shown).


title: EPC2-hTERT HOXA13 3

value: The human HOXA13 gene including its single intron was amplified using Q5 polymerase from gDNA using primers (AgeI HoxA13 F; GGTGGTACCGGTGCCACCATGACAGCCTCCGTGCTCCT, and XbaI HoxA13 R; ACCACCTCTAGATTAACTAGTGGTTTTCAGTT) and cloned into pEN_TmiRc3 using AgeI and XbaI restriction sites, a gift from Iain Fraser (Addgene (Cambridge, USA) #25748). Subsequently, the HOXA13 insert was transferred into pSLIK-Venus, using a Gateway reaction. pSLIK-Venus was a gift from Iain Fraser (Addgene #25734). LGC Genomics (Teddington, UK) sequenced both plasmids. Next, plasmids were packaged into lentiviral particles following transfection in HEK293T cells with third generation packaging plasmids. The supernatant was collected and ultracentrifuged. EPC2-hTERT cells were transduced with the virus and Fluorescence-Activated Cell Sorted (FACS) for YFP (pSLIK-Venus) positive cells on the BD FACSCantoTM II that was bought from BD Biosciences (San Jose, USA). These cells were grown and analyzed as a cell pool. HOXA13 was induced by the addition of 1,25 µg/ml doxycycline to the culture medium. Overexpression was determined by qPCR according to scientific standards.


title: EPC2-hTERT CONTROL 3


title: jarid2ko_eb_d2

description: Bulk-library


title: j1_eedwt_eb_d4

description: Bulk-library

value: Eed WT


title: j1_eedwt_eb_d2

description: Bulk-library


title: Control mouse 1

value: lymphocytes

value: control


title: EPC2-hTERT CONTROL 1


title: eedko_eb_d7

description: Bulk-library

value: eedko

value: embryoid bodies

value: Eed null


title: eedko_eb_d4

description: Bulk-library

value: day 4


title: j1_eedwt_eb_d0

description: Bulk-library


title: j1_eedwt_eb_d7

description: Bulk-library

value: day 7


title: EPC2-hTERT HOXA13 2


title: EPC2-hTERT CONTROL 2


title: EPC2-hTERT HOXA13 1


title: eedko_eb_d2

description: Bulk-library

value: day 2


title: mtf2ko_eb_d0

description: Bulk-library

value: day 0

value: Mtf2 null


title: gScbl_1to1_mouse4_HRT (cDNA)

value: Heart

tag: aav-donor

tag: aav ratio

tag: injection route

value: systemic P2 intravenous

tag: tn5 gsp


title: BAR-T HOXA13 KO 3

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.
Sequenced reads were trimmed for adaptor sequence, minimal Q score was 22, minimal read length 36, 5'or 3' trim off.
Reads were mapped against reference genome CRCh37.75 with Burrows-Wheeler Transform (Tophat version 2.1.0), and quantified using HTSeq (version 0.6.1p1).
Genome_build: GRCh37.75
Supplementary_files_format_and_content: Lists with raw gene counts for every gene per sample

source_name: BAR-T cell line

growth_protocol: These cells were grown in supplemented keratinocyte basal medium (KBM2), bought from Lonza (Basel, Switzerland), according to the method of Jaiswal et al.[65].

extract_protocol:
RNA was isolated using the NucleoSpin RNA isolation kit (Macherey Nagel, Dϋren, Germany). Samples were tested on the Agilent 2100 Bioanalyzer to determine RNA integrity and quantity.
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample  preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for  Illumina" (NEB #E7420S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After  fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing  adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation  was measured with the Fragment Analyzer (see appendices). The size of the resulting products was  consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the Illumina NextSeq 500 was performed according to manufacturer's  protocols. A concentration of 1.6 pM of DNA was used. NextSeq control software 2.0.2 was used.

value: Primary immortalized human Barrett's cell line

value: Functional HOXA13 was removed from BAR-T cells using CRISPR/Cas9-mediated gene editing. A HOXA13 sgRNA targeting exon 1 was cloned into pTLCV2, by ligating two annealed oligonucleotides, i.e. Guide1sgRNA F and R (Extended data table 4). TLCV2 was a gift from Adam Karpf (Addgene #87360)[72]. Following sequence verification, the pTLCV2-HOXA13sgRNA plasmid was packaged into lentiviral particles by cotransfection into HEK293T cells with pSPAX2 and pMD2.G, gifts from Didier Trono (Addgene #12260 and #12259). The supernatant was harvested and ultracentrifuged after which BAR-T cells were transduced. Mixed populations of transduced cells were plated at very low confluence, single cell clones could subsequently be isolated using glass cloning cylinders and low melting point agarose from Sigma-Aldrich, followed by DNA isolation using the Kleargene kit, followed by sequence verification with primers TILHOXA13R3 and Pre-HOXA13-FW2 flanking the sgRNA-site (Extended data table 4). Three cell lines in which both alleles were affected by unique out-of-frame deletions were selected.


title: BAR-T HOXA13 KO 2


title: EPC2-hTERT HOXA13 4

value: Primary immortalized human squamous esophageal cell line


title: eedko_eb_d0

description: Bulk-library

tag: strain

tag: genotype


title: Exercise Control(EC)

city: Jeju

first: Mi Gyeong

last: Jang

address: 102 Jejudaehakno

institute: Jeju National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include EdgeR-normalized read count values for each Sample

source_name: muscle

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: ICR

value: skeletal muscle

value: post natal day 42


title: Control(NC)


title: Exercise SQH(ES)


title: BAR-T CONTROL 3

value: BAR-T cells were transduced with virus made using the the pTLCV2-HOXA13sgRNA plasmid. Mixed populations of transduced cells were plated at very low confluence, single cell clones could subsequently be isolated using glass cloning cylinders and low melting point agarose from Sigma-Aldrich, followed by DNA isolation using the Kleargene kit, followed by sequence verification with primers TILHOXA13R3 and Pre-HOXA13-FW2 flanking the sgRNA-site (Extended data table 4). Three cell lines in which both alleles were not affected were selected.


title: BAR-T CONTROL 2


title: DNA_sum20.1_rep2

city: Frederiksberg C

first: Bin

last: Sun

address: Thorvaldsensvej 40

department: Department of Plant and Environmental Sciences

country: Denmark

institute: Copenhagen Plant Science Centre – University of Copenhagen

data_processing:
Library strategy: DNA-seq
Read mapping: bowtie2 v2.1.0
SNP calling: “samtools mpileup  -uD” v0.1.19
Identification of EMS-induced SNP markers: SHOREmap v3.2
Genome_build: Athaliana_167_TAIR9
Supplementary_files_format_and_content: Variant Call Format, vcf, contains gene sequence variations

organism: Arabidopsis thaliana

source_name: 12 days old seedlings

growth_protocol: Seeds were stratified 48h at 4°C, and grown on soil in a plant growth chamber under long day light conditions (16h light /8h dark) at (22°C day /18°C night).

extract_protocol:
12 days old seedling were quick freeze in liquid nitrogen, then grind with mortar. DNA were harvested.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: miP1aOX sum20

value: seedlings

tag: deveiopmental satge

value: 12 days old


title: DNA_sum20.1_rep1


title: BAR-T CONTROL 1


title: DNA_sum20.1_rep3


title: DNA_miP1aOX_rep3


title: S379

city: CAMBRIDGE

first: Aviv

last: Regev

state: MASSACHUSETTS

address: 415 MAIN ST

institute: Broad Institute

description:
single-cell RNA-Seq data
H7_S379
H5TJLBGX3_S379

data_processing:
Reads were aligned to a reference genome (mm10 Ensembl) using Bowtie
Expression levels were quantified using RSEM (inferred counts and tpm values), and log2(TPM+1) values generated.
cells were selected for subsequent analysis based on genecount and mapping rates to transcriptome (see manuscript)
Quality filtering parameters: (high-quality CD8 T) cells that had (1) 1,400-6,000 detected genes (defined by at least one mapped read), (2) at least 100,000 reads mapped to the transcriptome, (3) at least 20% of the reads mapped to the transcriptome, and (4) non-zero expression of either Cd3 or Cd8b1. Genes with non-zero expression in at least one cell were kept.
Genome_build: mm10
Supplementary_files_format_and_content: log2(TPM+1) values

source_name: Mus musculus CD8 TILs

extract_protocol:
TILs were isolated by dissociating tumor tissue in the presence of collagenase D (2.5 mg/ml) for 20 min prior to centrifugation on a discontinuous Percoll gradient (GE Healthcare).
Smart-seq2 (Picelli et al., Nature Methods, 2014)

tag: strain background

tag: genotype/variation

value: wild type

tag: cell type

value: CD8 tumor infiltrating lymphocytes (TIL)


title: S381

description:
single-cell RNA-Seq data
H9_S381
H5TJLBGX3_S381


title: S380

description:
single-cell RNA-Seq data
H8_S380
H5TJLBGX3_S380


title: S378

description:
single-cell RNA-Seq data
H6_S378
H5TJLBGX3_S378


title: S93

description:
single-cell RNA-Seq data
H9_S93
H5TJLBGX3_S93


title: S92

description:
single-cell RNA-Seq data
H8_S92
H5TJLBGX3_S92


title: DNA_miP1aOX_rep1


title: BAR-T HOXA13 KO 1


title: DNA_miP1aOX_rep2


title: Bisulfite-seq_miP1aOX rep1

data_processing:
BS-Seeker2 v2.1.0
Genome_build: Athaliana_167_TAIR9
Supplementary_files_format_and_content: BigWig format, contains methylation values over genome coordinates, can be visualized in Integrated Genome Browser, https://www.bioviz.org/

tag: developmental stage


title: Bisulfite-seq_Col-0 rep1

tag: tissue


title: S377

description:
single-cell RNA-Seq data
H5_S377
H5TJLBGX3_S377


title: SF3B1kd_ortho_3

city: New York

first: Xiuli

last: An

address: 310 E 67th St

institute: New York Blood Center

data_processing:
read counts of genes were generated using kallisto for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: orthochromatic erythroblasts

growth_protocol: CD34+ cells were purified using magnetic beads from cord blood. The CD34+ cells were differentiated towards the erythroid lineage using a three phase culture system and erythroid differentiation was monitored by analyzing the surface expression of glycophorin A (GPA), band 3 and α4 integrin.

extract_protocol:
RNA was extracted from FACS-sorted CFUE, polychromatic and orthochromatic erythroblasts
Approximately 100ng of total RNA was used as input for cDNA library preparation, which was preformed using an Illumina TruSeq kit followed by sequencing using an Illumina HiSeq 4000 platform (Beijing Genomics Institute, BGI, China). The transposed DNA was purified and amplified to generate sequencing libraries following manufacturer instructions (Nextera DNA Library Prep Kit, FC-121-1030).

treatment_protocol: Lentivirus particle preparation and shRNA-mediated knockdown in CD34+ cells was performed

value: orthochromatic

tag: treatment

value: SF3B1 knockdown

tag: cell-type

value: CB-derived HSC cultured cells


title: S88

description:
single-cell RNA-Seq data
H4_S88
H5TJLBGX3_S88


title: S376

description:
single-cell RNA-Seq data
H4_S376
H5TJLBGX3_S376


title: SF3B1kd_ortho_1


title: SF3B1kd_poly_3

source_name: polychromatic erythroblasts

value: polychromatic


title: S375

description:
single-cell RNA-Seq data
H3_S375
H5TJLBGX3_S375


title: S87

description:
single-cell RNA-Seq data
H3_S87
H5TJLBGX3_S87


title: SF3B1kd_poly_2


title: S89

description:
single-cell RNA-Seq data
H5_S89
H5TJLBGX3_S89


title: SF3B1kd_poly_1


title: S91

description:
single-cell RNA-Seq data
H7_S91
H5TJLBGX3_S91


title: S374

description:
single-cell RNA-Seq data
H2_S374
H5TJLBGX3_S374


title: S85

description:
single-cell RNA-Seq data
H1_S85
H5TJLBGX3_S85


title: SF3B1kd_CFUE_3

source_name: CFU-E progenitors

value: CFUE


title: SF3B1kd_CFUE_1


title: luci_ortho_2

value: luciferase control


title: S384

description:
single-cell RNA-Seq data
H12_S384
H5TJLBGX3_S384


title: S95

description:
single-cell RNA-Seq data
H11_S95
H5TJLBGX3_S95


title: luci_poly_3


title: S94

description:
single-cell RNA-Seq data
H10_S94
H5TJLBGX3_S94


title: S383

description:
single-cell RNA-Seq data
H11_S383
H5TJLBGX3_S383


title: luci_poly_1


title: S373

description:
single-cell RNA-Seq data
H1_S373
H5TJLBGX3_S373


title: SF3B1kd_CFUE_2


title: luci_poly_2


title: luci_CFUE_2


title: S81

description:
single-cell RNA-Seq data
G9_S81
H5TJLBGX3_S81


title: S382

description:
single-cell RNA-Seq data
H10_S382
H5TJLBGX3_S382


title: S80

description:
single-cell RNA-Seq data
G8_S80
H5TJLBGX3_S80


title: luci_CFUE_1


title: luci_CFUE_3


title: S368

description:
single-cell RNA-Seq data
G8_S368
H5TJLBGX3_S368


title: NK1_D7_SRI

city: Columbus

first: Dean

last: Lee

state: Ohio

address: 700 Children’s Drive

department: Hematology & Oncology

institute: Nationwide Children’s Hospital

data_processing:
Samples were aligned to the GRCh38 assembly of the Homo sapiens reference from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.38) using version 2.6.0c of the RNA-Seq aligner STAR (http://bioinformatics.oxfordjournals.org/content/early/2012/10/25/bioinformatics.bts635).
Features were identified from the GFF files that came with the assembly from NCBI.
Feature coverage counts were calculated using HTSeq -count
Differentially expressed features were calculated using DESeq2.
Genome_build: Homo sapiens GRCh38.p12
Supplementary_files_format_and_content: Excel spreadsheet and CSV files containing read counts for each sample and differential expression data for each feature.

source_name: blood

growth_protocol: NK cells were isolated from leukopak of healthy volunteer donors. NK cells were isolated from whole blood or buffy coats using Rosette-Sep using Ficoll. NK cells were expanded using irradiated FC21 feeder cells for period of 14-21 days. All NK cells were expanded using recombinant human IL-2 (50 IU/ml) alone, stemregenin (SR1-1uM), kynurenine (Kyn-25uM). The media was changed every 2-3 days.

extract_protocol: RNA samples were isolated using RNeasy kit and the samples were DNase treated and concentrated using RNA concentrator kit.

value: NK

tag: donor

tag: cell expansion

value: IL2+stemregenin (SR1-1uM)

tag: cell expansion period


title: S79

description:
single-cell RNA-Seq data
G7_S79
H5TJLBGX3_S79


title: NK1_D7_IL2

value: human interleukin-2 (IL2-50 IU/ml)


title: luci_ortho_3


title: SF3B1kd_ortho_2


title: S86

description:
single-cell RNA-Seq data
H2_S86
H5TJLBGX3_S86


title: A15

city: Hefei

first: Shihai

last: Xing

state: Anhui

address: No.1 Qianjiang Road, Xinzhan District

institute: Anhui University of Chinese Medicine

data_processing:
Raw reads were filtered via SOAPnuke (v1.4.0) by removing reads containing adaptors, poly-N or low quality, and then clean reads were obtained.
Trinity (v2.0.6) was used to assemble the clean reads and Tgicl (v2.0.6) to perform clustering and eliminate redundant data in the assembled transcripts to obtain unique genes. The assembled transcripts were processed for further expression analysis and functional annotation.
Clean reads were mapped to the assembled unique genes by Bowtie2 (v2.2.5)and the expression level of genes were calculated by RSEM (v1.2.8) and normalized to FPKM (Fragments per kilo base of transcript per million mapped reads). Functional annotation of genes was achieved by mapping genes to different databases (NT, NR, KOG, KEGG) using the software BLAST (v2.2.23). GO annotation was performed by Blast2GO (v 2.5.0) with NR annotations. DEseq2 was used to detect DEGs (Different expressed genes), and DEGs with fold change > 2 or <-2 and adjusted P value <= 0.001 were considered to be significantly different expressed genes. GO enrichment analysis and KEGG enrichment analysis were performed using Phyper, a function of R. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value < 0.05).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Dendrobium officinale

source_name: Protocorm-like Bodies

growth_protocol: The leaves are derived from the original plant. Protocorm-like Bodies induction of D. officinale is seed as explants, and 1/2 MS + α-NAA 0.5 mg·L-1 + 6-BA 1.0 mg·L-1 + 2, 4-D 1.5-2.0 mg·L-1 + potato juice 100 g·L-1 as the formula.

extract_protocol:
Ethanol precipitation protocol and CTAB-PBIOZOL reagent was used to purify total RNA from PLBs and leaves according to the manual instructions, and each sample has three biological duplicates. 80 mg tissue samples were ground into powder in liquid nitrogen and the powdered samples were transferred into 1.5 mL of preheated 65℃ CTAB-pBIOZOL reagents. The sample solution was incubated by thermostatic mixer at 65°C for 15 min to completely dissociate the nucleoprotein complexes. The supernatant was obtained by centrifuging the solution at 12000 × g, at 4℃ for 5 min. The supernatant was mixed with 400 uL of chloroform (per 1.5 mL of added CTAB-pBIOZOL reagent), and the sample mixture was centrifuged at 12000 × g, at 4˚C for 10 min. The supernatant was transferred to a new 2 mL tube and added 700 μL of acidic phenol and 200 μL of chloroform into it followed by centrifugation at 12000 × g, at 4˚C for 10 min. The aqueous supernatant was collected and an equal volume of chloroform was added into it followed by centrifugation at 12000 × g, at 4℃ for 10 min. An equal volume of isopropyl alcohol was added into the supernatant and the mixture was placed at -20℃ for 2 h to precipitate before centrifuging it at 12000 × g, at 4℃ for 20 min, and the supernatant was removed. The RNA pellet was washed with 1mL of 75% ethanol before being air-dried in a biosafety cabinet and dissolved in 50 uL of DEPC-treated water. Subsequently, qualification and quantification of total RNA were performed using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purify mRNA. The purified mRNA was split up into small pieces with fragment buffer at an appropriate temperature. The random hexamer-primed reverse transcription was performed to synthesize the first-strand cDNA followed by the second-strand cDNA synthesis. Then, A-Tail Mix and RNA Index Adapter were added to end the repair. The cDNA fragments obtained from above mentioned steps were amplified by PCR. The products were purified by Ampure XP Beads and dissolved in EB solution. The product was verified for quality control on an Agilent 2100 bioanalyzer. The double-stranded PCR products were denatured and cycled by the splint oligo-nucleotide sequence to obtain the final library, and the single-stranded circular DNA (ssCir DNA) was formatted into the final library.
The established library was amplified with phi29 to obtain DNA nanoball (DNB), each molecular of which had over 300 copies. The DNBs were added into the patterned nanoarray and 100 base pairs of reads generated on the BGIseq500 platform.

treatment_protocol: The culture conditions of the tissue culture were 70% relative humidity, 1600 lx illumination and a light/dark of 16/8 h for 60 d

value: Protocorm-like Bodies


title: S369

description:
single-cell RNA-Seq data
G9_S369
H5TJLBGX3_S369


title: S367

description:
single-cell RNA-Seq data
G7_S367
H5TJLBGX3_S367


title: A14


title: A13


title: NK1_D21_IL2


title: Super_1to5_mouse6_local (gDNA)

data_processing:
Trim. The reads were trimmed for sequencing adapters and low-quality bases using Trimmomatic (v0.33).
Alignment and deduplication. Alignment of the trimmed reads was done using bwa-mem (v0.7.12) to the reference genomes (gDNA aligned to mouse genome GRCm38 + human DMD; cDNA aligned to human dystrophin cDNA). Aligned reads were tagged with their UMI using fgbio (v0.8.1) AnnotateBamWithUmis, and PCR duplicates were marked using Picard (v2.14.0) MarkDuplicates based on the UMI tag.
Alignment to reference bin sequences. Reference amplicons were built to align to the targeted locus and expected edits. To remove reads that are due to false priming, reads that do not contain the 20 bases directly adjacent to the GSP expected sequence were filtered out. To remove reads that do not extend far enough past the edit site, reads that are shorter than the required minimum length for binning were filtered out. On-site deduplicated reads were aligned to reference amplicons using bwa-mem (v0.7.12). Aligned reads were analyzed and binned based on editing outcomes using a custom-built script using python3 (https://github.com/siyansusan/DMD_integration_analysis.git). Reads that contain an indel ±15bp at the expected cute site or junction were identified. The number of distinct UMIs were counted for each edit to quantify frequency of editing events.
Genome_build: GRCm38 + human DMD
Supplementary_files_format_and_content: BAM file (curated and represents the collection of usable reads) for each sample.  Manuscript methods include a link to github for access to analysis pipeline scripts;  GEO users may find it useful to use the bam files to repeat analysis methods.
Supplementary_files_format_and_content: Matrix table with bin counts for every editing outcome and every sample

source_name: Tibialis anterior muscule

value: Tibialis anterior muscule

tag: aav-donor

value: local intramuscular TA


title: S366

description:
single-cell RNA-Seq data
G6_S366
H5TJLBGX3_S366


title: S78

description:
single-cell RNA-Seq data
G6_S78
H5TJLBGX3_S78


title: A12

source_name: Leaves

value: Leaves


title: NK1_D14_SRI


title: NK1_D14_IL2


title: Super_1to5_mouse3_local (gDNA)

tag: aav ratio


title: S77

description:
single-cell RNA-Seq data
G5_S77
H5TJLBGX3_S77


title: luci_ortho_1


title: Super_1to5_mouse2_local (gDNA)

tag: injection route


title: NK126_D7_SRI


title: S365

description:
single-cell RNA-Seq data
G5_S365
H5TJLBGX3_S365


title: A11


title: S96

description:
single-cell RNA-Seq data
H12_S96
H5TJLBGX3_S96


title: S76

description:
single-cell RNA-Seq data
G4_S76
H5TJLBGX3_S76


title: Super_1to5_mouse5_local (gDNA)

tag: tn5 gsp


title: Super_1to5_mouse1_local (gDNA)


title: A10


title: Ex52_1to5_mouse6_local (gDNA)


title: Ex52_1to5_mouse5_local (gDNA)


title: NK1_D21_SRI


title: NK126_D7_Kyn

value: IL2+kynurenine (Kyn-25uM)


title: S364

description:
single-cell RNA-Seq data
G4_S364
H5TJLBGX3_S364


title: Ex52_1to5_mouse4_local (gDNA)


title: S363

description:
single-cell RNA-Seq data
G3_S363
H5TJLBGX3_S363


title: S75

description:
single-cell RNA-Seq data
G3_S75
H5TJLBGX3_S75


title: Ex52_1to5_mouse2_local (gDNA)


title: NK126_D14_Kyn


title: gScbl_1to5_mouse6_local (gDNA)


title: Ex52_1to5_mouse1_local (gDNA)


title: gScbl_1to5_mouse4_local (gDNA)


title: gScbl_1to5_mouse3_local (gDNA)


title: NK126_D14_IL2


title: S362

description:
single-cell RNA-Seq data
G2_S362
H5TJLBGX3_S362


title: gScbl_1to5_mouse2_local (gDNA)


title: S74

description:
single-cell RNA-Seq data
G2_S74
H5TJLBGX3_S74


title: S73

description:
single-cell RNA-Seq data
G1_S73
H5TJLBGX3_S73


title: gScbl_1to5_mouse1_local (gDNA)


title: Super_1to1_mouse5_local (gDNA)


title: NK124_D7_SRI


title: NK126_D7_IL2


title: S361

description:
single-cell RNA-Seq data
G1_S361
H5TJLBGX3_S361


title: Ex52_1to5_mouse3_local (gDNA)


title: NK126_D0


title: Super_1to1_mouse4_local (gDNA)


title: Super_1to1_mouse6_local (gDNA)


title: NK126_D14_SRI


title: S372

description:
single-cell RNA-Seq data
G12_S372
H5TJLBGX3_S372


title: NK124_D7_Kyn


title: gScbl_1to5_mouse5_local (gDNA)


title: Super_1to1_mouse3_local (gDNA)


title: Super_1to1_mouse1_local (gDNA)


title: Super_1to1_mouse2_local (gDNA)


title: NK124_D14_SRI


title: NK124_D7_IL2


title: Ex52_1to1_mouse6_local (gDNA)


title: Ex52_1to1_mouse5_local (gDNA)


title: Ex52_1to1_mouse4_local (gDNA)


title: S83

description:
single-cell RNA-Seq data
G11_S83
H5TJLBGX3_S83


title: NK124_D14_Kyn


title: Ex52_1to1_mouse3_local (gDNA)


title: S371

description:
single-cell RNA-Seq data
G11_S371
H5TJLBGX3_S371


title: Ex52_1to1_mouse2_local (gDNA)


title: S84

description:
single-cell RNA-Seq data
G12_S84
H5TJLBGX3_S84


title: S82

description:
single-cell RNA-Seq data
G10_S82
H5TJLBGX3_S82


title: Ex52_1to1_mouse1_local (gDNA)


title: NK124_D14_IL2


title: gScbl_1to1_mouse5_local (gDNA)

value: systemic P2 intravenous


title: gScbl_1to1_mouse6_local (gDNA)


title: gScbl_1to1_mouse4_local (gDNA)


title: S370

description:
single-cell RNA-Seq data
G10_S370
H5TJLBGX3_S370

value: wild type


title: gScbl_1to1_mouse2_local (gDNA)


title: gScbl_1to1_mouse3_local (gDNA)


title: S69

description:
single-cell RNA-Seq data
F9_S69
H5TJLBGX3_S69

value: CD8 tumor infiltrating lymphocytes (TIL)


title: gScbl_1to1_mouse1_local (gDNA)


title: S357

description:
single-cell RNA-Seq data
F9_S357
H5TJLBGX3_S357


title: Super_1to5_mouse6_TA (gDNA)


title: DEP8 [R10880_R]

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to  GRCh38 genome build
Gene counts were obtained using featureCounts on GENCODE v31 annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_counts

source_name: Healthy Control_whole blood

growth_protocol: Not Applicable

extract_protocol:
Total RNA was extracted using MagMax™ for Stabilized Blood Tubes RNA Isolation Kit (Invitrogen)
Smart-Seq V2 RNA-Seq Library Preparation Protocol

treatment_protocol: Not Applicable

tag: severity

value: Healthy Control

value: whole blood


title: S68

description:
single-cell RNA-Seq data
F8_S68
H5TJLBGX3_S68


title: Super_1to5_mouse5_TA (gDNA)


title: C_S005 Day 8 [R10866_R2]

source_name: Severe_whole blood

value: Severe


title: S356

description:
single-cell RNA-Seq data
F8_S356
H5TJLBGX3_S356


title: Super_1to5_mouse3_TA (gDNA)


title: C_N007 Day 9 [R10864_R]


title: Super_1to5_mouse4_TA (gDNA)


title: C_T112 Day 11 [R10862_R]

source_name: Moderate_whole blood

value: Moderate


title: Super_1to5_mouse2_TA (gDNA)


title: S67

description:
single-cell RNA-Seq data
F7_S67
H5TJLBGX3_S67


title: NK124_D0


title: Ex52_1to5_mouse6_TA (gDNA)


title: C_T016 Day 20 [R10836_R]

source_name: Mild_whole blood

value: Mild


title: S355

description:
single-cell RNA-Seq data
F7_S355
H5TJLBGX3_S355


title: 24F3 [R10879_R]


title: Ex52_1to5_mouse4_TA (gDNA)


title: Ex52_1to5_mouse5_TA (gDNA)


title: C_T101 Day 5 [R10860_R2]


title: Ex52_1to5_mouse3_TA (gDNA)


title: S66

description:
single-cell RNA-Seq data
F6_S66
H5TJLBGX3_S66


title: S354

description:
single-cell RNA-Seq data
F6_S354
H5TJLBGX3_S354


title: C_T011 Day 11 [R10834_R]


title: c_t301_study_day_01 [R11033]

source_name: asymptomatic_whole blood

value: asymptomatic


title: Ex52_1to5_mouse1_TA (gDNA)


title: Ex52_1to5_mouse2_TA (gDNA)


title: gScbl_1to5_mouse6_TA (gDNA)


title: gScbl_1to5_mouse5_TA (gDNA)


title: c_t300_study_day_01 [R11032]


title: Super_1to5_mouse1_TA (gDNA)


title: S65

description:
single-cell RNA-Seq data
F5_S65
H5TJLBGX3_S65


title: S353

description:
single-cell RNA-Seq data
F5_S353
H5TJLBGX3_S353


title: gScbl_1to5_mouse2_TA (gDNA)


title: S90

description:
single-cell RNA-Seq data
H6_S90
H5TJLBGX3_S90


title: Super_1to5_mouse4_local (gDNA)


title: S64

description:
single-cell RNA-Seq data
F4_S64
H5TJLBGX3_S64


title: c_t299_study_day_01 [R11031]


title: c_t298_day_1 [R11030]


title: gScbl_1to5_mouse1_TA (gDNA)


title: Super_1to1_mouse5_TA (gDNA)


title: Super_1to1_mouse6_TA (gDNA)


title: S352

description:
single-cell RNA-Seq data
F4_S352
H5TJLBGX3_S352


title: Super_1to1_mouse3_TA (gDNA)


title: c_t296_day_1 [R11029_R]


title: Super_1to1_mouse2_TA (gDNA)


title: S63

description:
single-cell RNA-Seq data
F3_S63
H5TJLBGX3_S63


title: Super_1to1_mouse4_TA (gDNA)


title: c_t293_day_2 [R11028]


title: Control mouse 2

source_name: PBMC-humanized mouse

value: lymphocytes

tag: disease

value: control

tag: aml cd200 status

tag: cell line


title: S351

description:
single-cell RNA-Seq data
F3_S351
H5TJLBGX3_S351

tag: strain background

tag: genotype/variation


title: Ex52_1to1_mouse5_TA (gDNA)


title: Super_1to1_mouse1_TA (gDNA)


title: Ex52_1to1_mouse6_TA (gDNA)


title: c_t291_day_1 [R11026_R]


title: gScbl_1to5_mouse3_TA (gDNA)


title: Ex52_1to1_mouse4_TA (gDNA)


title: Ex52_1to1_mouse2_TA (gDNA)


title: S350

description:
single-cell RNA-Seq data
F2_S350
H5TJLBGX3_S350

tag: cell type


title: c_t289_day_2 [R11024]

tag: tissue


title: c_t288_day_2 [R11023]


title: c_t285_day_1 [R11021]


title: Ex52_1to1_mouse1_TA (gDNA)


title: c_t274_day_5 [R11020]


title: gScbl_1to1_mouse5_TA (gDNA)


title: gScbl_1to1_mouse2_TA (gDNA)


title: gScbl_1to1_mouse4_TA (gDNA)


title: S61

description:
single-cell RNA-Seq data
F1_S61
H5TJLBGX3_S61


title: gScbl_1to1_mouse1_TA (gDNA)


title: S349

description:
single-cell RNA-Seq data
F1_S349
H5TJLBGX3_S349


title: S360

description:
single-cell RNA-Seq data
F12_S360
H5TJLBGX3_S360


title: Ex52_1to1_mouse3_TA (gDNA)


title: gScbl_1to1_mouse3_TA (gDNA)


title: c_t284_day_1 [R11019]


title: S72

description:
single-cell RNA-Seq data
F12_S72
H5TJLBGX3_S72


title: Super_1to5_mouse6_HRT (gDNA)

source_name: Heart

value: Heart


title: Super_1to5_mouse5_HRT (gDNA)


title: c_t281_day_1 [R11018_R]


title: S71

description:
single-cell RNA-Seq data
F11_S71
H5TJLBGX3_S71


title: Super_1to5_mouse2_HRT (gDNA)


title: S62

description:
single-cell RNA-Seq data
F2_S62
H5TJLBGX3_S62


title: c_t275_day_1 [R11017_R]


title: S359

description:
single-cell RNA-Seq data
F11_S359
H5TJLBGX3_S359


title: c_t272_day_1 [R11016]


title: Super_1to5_mouse1_HRT (gDNA)


title: S70

description:
single-cell RNA-Seq data
F10_S70
H5TJLBGX3_S70


title: gScbl_1to5_mouse4_TA (gDNA)


title: Ex52_1to5_mouse5_HRT (gDNA)


title: S358

description:
single-cell RNA-Seq data
F10_S358
H5TJLBGX3_S358


title: c_t270_day_1 [R11014]


title: Super_1to5_mouse4_HRT (gDNA)


title: Ex52_1to5_mouse2_HRT (gDNA)


title: Ex52_1to5_mouse3_HRT (gDNA)


title: Ex52_1to5_mouse1_HRT (gDNA)


title: gScbl_1to5_mouse6_HRT (gDNA)


title: S57

description:
single-cell RNA-Seq data
E9_S57
H5TJLBGX3_S57


title: Super_1to5_mouse3_HRT (gDNA)


title: S345

description:
single-cell RNA-Seq data
E9_S345
H5TJLBGX3_S345


title: gScbl_1to5_mouse5_HRT (gDNA)


title: c_t264_day_1 [R11011]


title: c_t265_day_1 [R11012]


title: gScbl_1to5_mouse3_HRT (gDNA)


title: gScbl_1to5_mouse4_HRT (gDNA)


title: S56

description:
single-cell RNA-Seq data
E8_S56
H5TJLBGX3_S56


title: gScbl_1to5_mouse2_HRT (gDNA)


title: c_t263_day_1 [R11010]


title: gScbl_1to5_mouse1_HRT (gDNA)


title: Ex52_1to5_mouse6_HRT (gDNA)


title: S55

description:
single-cell RNA-Seq data
E7_S55
H5TJLBGX3_S55


title: Super_1to1_mouse6_HRT (gDNA)


title: c_t271_day_1 [R11015]


title: S344

description:
single-cell RNA-Seq data
E8_S344
H5TJLBGX3_S344


title: Super_1to1_mouse4_HRT (gDNA)


title: Ex52_1to5_mouse4_HRT (gDNA)


title: S343

description:
single-cell RNA-Seq data
E7_S343
H5TJLBGX3_S343


title: c_t269_day_1 [R11013]


title: c_t261_day_1 [R11008]


title: Super_1to1_mouse3_HRT (gDNA)


title: S54

description:
single-cell RNA-Seq data
E6_S54
H5TJLBGX3_S54


title: Ex52_1to1_mouse6_HRT (gDNA)


title: Super_1to1_mouse2_HRT (gDNA)


title: Super_1to1_mouse1_HRT (gDNA)


title: c_t260_day_1 [R11007]


title: c_t258_day_1 [R11005]


title: Ex52_1to1_mouse5_HRT (gDNA)


title: c_t259_day_1 [R11006]


title: S341

description:
single-cell RNA-Seq data
E5_S341
H5TJLBGX3_S341


title: S53

description:
single-cell RNA-Seq data
E5_S53
H5TJLBGX3_S53


title: Ex52_1to1_mouse3_HRT (gDNA)


title: Ex52_1to1_mouse4_HRT (gDNA)


title: Ex52_1to1_mouse2_HRT (gDNA)


title: S342

description:
single-cell RNA-Seq data
E6_S342
H5TJLBGX3_S342


title: gScbl_1to1_mouse5_HRT (gDNA)


title: c_t257_day_1 [R11004]


title: c_t255_day_1 [R11003]


title: Super_1to1_mouse5_HRT (gDNA)


title: Ex52_1to1_mouse1_HRT (gDNA)


title: c_t262_day_1 [R11009_R]


title: gScbl_1to1_mouse3_HRT (gDNA)


title: gScbl_1to1_mouse4_HRT (gDNA)


title: S340

description:
single-cell RNA-Seq data
E4_S340
H5TJLBGX3_S340


title: gScbl_1to1_mouse1_HRT (gDNA)


title: gScbl_1to1_mouse2_HRT (gDNA)


title: c_t250_day_1 [R11001]


title: S51

description:
single-cell RNA-Seq data
E3_S51
H5TJLBGX3_S51


title: c_t252_day_1 [R11002]


title: Super_1to5_mouse6_DIA (gDNA)

source_name: Diaphragm

value: Diaphragm


title: Super_1to5_mouse4_DIA (gDNA)


title: S339

description:
single-cell RNA-Seq data
E3_S339
H5TJLBGX3_S339


title: c_t058_pio_day_20

description:
R10887
gene_counts.txt

data_processing:
FASTQ files were mapped using STAR to GRCh38 genome build.
Gene counts were obtained using featureCounts on GENCODE v31 annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_counts.txt

source_name: Whole blood

extract_protocol:
Total RNA was extracted using MagMax™ for Stabilized Blood Tubes RNA Isolation Kit (Invitrogen).
Smart-Seq V2 RNA-Seq Library Preparation Protocol.

value: Whole blood

tag: diagnosis

tag: gene deletion status

tag: pcr status

value: negative

tag: patient id


title: Super_1to5_mouse2_DIA (gDNA)

extract_protocol:
Tissue was extracted from euthanized mice. Genomic DNA was isolated using the DNeasy kit (Qiagen) according to the manufacturer’s protocol. Total RNA was isolated using QIAshredder and RNeasy Plus kits (Qiagen). First-strand cDNA synthesis was performed using 500 ng total RNA per sample using the SuperScript VILO Reverse Transcription Kit (Invitrogen) and second-strand synthesis was performed using Klenow fragment DNA polymerase (NEB).
Tagmentation of 200 ng genomic DNA or second-strand products was performed using a 1:40 dilution of assembled Tn5. To enrich the targeted sequence, first round PCR using a genome specific primer was used with a reverse primer specific for the i7 adapter sequence inserted by the transposon. Second round PCR using a barcode primer specific for the custom adapter sequence was used to add 6-nucleotide experimental barcodes and the Illumina i5 adapter was used with the Tn5-Universal reverse primer.
Tn5-based tagmentation with target enrichment.


title: c_t058_pio_day_1

description:
R10886_2
gene_counts.txt

value: positive


title: Super_1to5_mouse5_DIA (gDNA)


title: c_t070_pio_day_1

description:
R10884_R
gene_counts.txt


title: Super_1to5_mouse3_DIA (gDNA)


title: S50

description:
single-cell RNA-Seq data
E2_S50
H5TJLBGX3_S50

source_name: Mus musculus CD8 TILs


title: c_t039_pio_day_9

description:
R10883
gene_counts.txt


title: Super_1to5_mouse1_DIA (gDNA)


title: S52

description:
single-cell RNA-Seq data
E4_S52
H5TJLBGX3_S52


title: Ex52_1to5_mouse3_DIA (gDNA)


title: gScbl_1to5_mouse6_DIA (gDNA)


title: S338

description:
single-cell RNA-Seq data
E2_S338
H5TJLBGX3_S338


title: Ex52_1to5_mouse5_DIA (gDNA)


title: c_t070_pio_day_33

description:
R10885
gene_counts.txt


title: S49

description:
single-cell RNA-Seq data
E1_S49
H5TJLBGX3_S49


title: Ex52_1to5_mouse4_DIA (gDNA)


title: Ex52_1to5_mouse6_DIA (gDNA)


title: S337

description:
single-cell RNA-Seq data
E1_S337
H5TJLBGX3_S337


title: S348

description:
single-cell RNA-Seq data
E12_S348
H5TJLBGX3_S348


title: Ex52_1to5_mouse2_DIA (gDNA)


title: ktke_hc

description:
R10881_R
gene_counts.txt

value: Healthy

value: Not Applicable


title: gScbl_1to5_mouse3_DIA (gDNA)

value: systemic P2 intravenous


title: Ex52_1to5_mouse1_DIA (gDNA)


title: 24f3_hc

description:
R10879
gene_counts.txt


title: gScbl_1to5_mouse1_DIA (gDNA)


title: S347

description:
single-cell RNA-Seq data
E11_S347
H5TJLBGX3_S347

value: wild type

value: CD8 tumor infiltrating lymphocytes (TIL)


title: Super_1to1_mouse5_DIA (gDNA)


title: S59

description:
single-cell RNA-Seq data
E11_S59
H5TJLBGX3_S59


title: gScbl_1to5_mouse4_DIA (gDNA)


title: c_t039_pio_day_6

description:
R10882
gene_counts.txt


title: gScbl_1to5_mouse2_DIA (gDNA)


title: dep8_hc

description:
R10880
gene_counts.txt


title: Super_1to1_mouse4_DIA (gDNA)


title: Super_1to1_mouse6_DIA (gDNA)


title: S60

description:
single-cell RNA-Seq data
E12_S60
H5TJLBGX3_S60


title: S58

description:
single-cell RNA-Seq data
E10_S58
H5TJLBGX3_S58


title: S346

description:
single-cell RNA-Seq data
E10_S346
H5TJLBGX3_S346


title: Super_1to1_mouse3_DIA (gDNA)


title: gylm_hi_frozen

description:
R10877_2
gene_counts.txt


title: Ex52_1to1_mouse6_DIA (gDNA)


title: 4jv7_hi_frozen

description:
R10876_2
gene_counts.txt


title: Ex52_1to1_mouse5_DIA (gDNA)


title: gScbl_1to5_mouse5_DIA (gDNA)


title: c_t105_pio_day_18

description:
R10875
gene_counts.txt


title: S333

description:
single-cell RNA-Seq data
D9_S333
H5TJLBGX3_S333


title: Super_1to1_mouse2_DIA (gDNA)


title: Super_1to1_mouse1_DIA (gDNA)


title: Ex52_1to1_mouse4_DIA (gDNA)


title: MC38 Exosome-W

city: Shanghai

first: chunxiao

last: miao

state: Shanghai

address: Shanghai, China

institute: Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Total RNA from exosomes was prepared and quantified with a NanoDrop ND-2000. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library.
Small RNA adapters were then ligated to the 5’ and 3’ ends of total RNA. After cDNA synthesis and amplification, the PCR-amplified fragments were purified from the PAGE gel, and the completed cDNA libraries were quantified by an Agilent 2100 Bioanalyzer.
Cluster generation was performed on an Illuminac Bot, and sequencing was performed on an Illumina HiSeq 2000 platform and 50bp single-end reads were generated.
The expression level of each miRNA was calculated according to the transcripts per million reads (TPM) method. Significant differently expressed (DE) miRNAs were extracted with |log2FC|>1 and FDR < 0.05 by DEseq2.

source_name: colon cancer exosomes

extract_protocol:
Exosomes were extracted from conditioned medium of cells using Capture(TM) Exosome ELISA Kit (Streptavidin HRP) (Wako, 298-80601) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C26 and MC38 cells were cultured in exosome-free mudium.


title: MC38 Exosome-S

extract_protocol:
Exosomes were extracted from conditioned medium of cells using ExoQuick-TC Exosome Isolation Reagent (SBI,EXOTC10A-1) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: S44

description:
single-cell RNA-Seq data
D8_S44
H5TJLBGX3_S44


title: c_t105_pio_day_10

description:
R10874
gene_counts.txt


title: kpyw_hi_frozen

description:
R10878
gene_counts.txt


title: C26 Exosome-S


title: C26 Exosome-W


title: c_t100_pio_day_21

description:
R10873
gene_counts.txt


title: Ex52_1to1_mouse2_DIA (gDNA)


title: S332

description:
single-cell RNA-Seq data
D8_S332
H5TJLBGX3_S332


title: S43

description:
single-cell RNA-Seq data
D7_S43
H5TJLBGX3_S43


title: Ex52_1to1_mouse3_DIA (gDNA)


title: c_t100_pio_day_14

description:
R10872_R
gene_counts.txt


title: Treated with 100 mM NaCl, Inoculated with S. meliloti 1021, biological replicate C

city: Burlington

first: Jeanne

middle: Marie

last: Harris

state: VT

address: 63 Carrigan drive

department: Plant Biology

institute: University of Vermont

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Tophat (v2.0.13) using the Medicago truncatula genome (Mt4.0) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: Mt4.0
Supplementary_files_format_and_content: text_Raw_read_Counts
Supplementary_files_format_and_content: text_FPKM values

organism: Medicago truncatula

source_name: Whole root

growth_protocol: Seedlings were grown in growth pouches in Modified Nodulation Medium (MNM) (Chakraborty et al., 2021; MPMI), in 16/8 hour light/dark cycle, with the roots shaded.

extract_protocol:
Total RNA was extracted from ground tissue using RNeasy Plant Mini kit (Qiagen), genomic DNA removed using TURBO DNA-free kit (Ambion), and the resulting RNA further cleaned-up using RNeasy MinElute Clean-up kit (Qiagen). RNA quality was assessed with an Agilent 2100 Bioanalyzer and RNA samples with RIN (RNA Integrity Number) values higher than 8 were processed further.
RNA libraries were prepared for sequencing using Illumina Truseq protocols

treatment_protocol: Germinated seedlings were pouched in MNM or MNM + 100 mM NaCl. Respective medium was replenished after 3 days and the seedlings inoculated with a suspension of S. meliloti 1021 in 10 mM MgSO4 or mock-inoculated with 10 mM MgSO4 on day 4. Roots were harvested after 24 hours of inoculation, snap-frozen in liquid nitrogen, and stored at -80 ºC.

tag: accession

tag: genotype

value: Wild-type

tag: agent


title: S45

description:
single-cell RNA-Seq data
D9_S45
H5TJLBGX3_S45


title: gScbl_1to1_mouse5_DIA (gDNA)

first: Adrian

tag: aav-donor

tag: aav ratio

tag: injection route


title: S331

description:
single-cell RNA-Seq data
D7_S331
H5TJLBGX3_S331


title: S42

description:
single-cell RNA-Seq data
D6_S42
H5TJLBGX3_S42


title: Ex52_1to1_mouse1_DIA (gDNA)

tag: tn5 gsp


title: Treated with 100 mM NaCl, Inoculated with S. meliloti 1021, biological replicate B


title: gScbl_1to1_mouse4_DIA (gDNA)


title: Treated with 100 mM NaCl, Inoculated with S. meliloti 1021, biological replicate A (resubmission)


title: S330

description:
single-cell RNA-Seq data
D6_S330
H5TJLBGX3_S330


title: c_t017_pio_day19

description:
R10869
gene_counts.txt

tag: severity


title: c_t017_pio_day12

description:
R10868
gene_counts.txt


title: S329

description:
single-cell RNA-Seq data
D5_S329
H5TJLBGX3_S329


title: gScbl_1to1_mouse3_DIA (gDNA)


title: gScbl_1to1_mouse2_DIA (gDNA)


title: c_s005_pio_day_21

description:
R10867
gene_counts.txt


title: c_s005_pio_day_8

description:
R10866_R
gene_counts.txt


title: gScbl_1to1_mouse1_DIA (gDNA)


title: c_t057_pio_day_20

description:
R10871_R
gene_counts.txt


title: Inoculated with S. meliloti 1021, no Salt, biological replicate A

value: S. meliloti 1021, no Salt


title: S40

description:
single-cell RNA-Seq data
D4_S40
H5TJLBGX3_S40


title: c_n007_pio_day_43

description:
R10865
gene_counts.txt


title: g7_1to5_mouse4_local (gDNA)

value: Tibialis anterior muscule

value: local intramuscular TA


title: S39

description:
single-cell RNA-Seq data
D3_S39
H5TJLBGX3_S39


title: g7_1to5_mouse3_local (gDNA)


title: Treated with 100 mM NaCl, mock Inoc. biological replicate B

value: 100 mM NaCl, mock Inoc


title: S327

description:
single-cell RNA-Seq data
D3_S327
H5TJLBGX3_S327


title: c_t057_pio_day_14

description:
R10870
gene_counts.txt


title: c_n007_pio_day_09

description:
R10864_R
gene_counts.txt


title: c_t136_pio_day_34

description:
R10863_R
gene_counts.txt


title: g7_1to5_mouse1_local (gDNA)


title: S41

description:
single-cell RNA-Seq data
D5_S41
H5TJLBGX3_S41


title: Inoculated with S. meliloti 1021, no Salt, biological replicate C


title: S38

description:
single-cell RNA-Seq data
D2_S38
H5TJLBGX3_S38


title: c_t112_pio_day_11

description:
R10862
gene_counts.txt


title: Treated with 100 mM NaCl, mock Inoc., biological replicate A


title: g7_1to1_mouse4_local (gDNA)


title: No rhizobium (mock inoculation), no salt, biological replicate B

value: mock


title: c_t101_pio_day_39

description:
R10861
gene_counts.txt


title: Treated with 100 mM NaCl, mock Inoc. biological replicate C


title: S37

description:
single-cell RNA-Seq data
D1_S37
H5TJLBGX3_S37


title: No rhizobium (mock inoculation), no salt, biological replicate A


title: c_t101_pio_day_05

description:
R10860
gene_counts.txt


title: S325

description:
single-cell RNA-Seq data
D1_S325
H5TJLBGX3_S325


title: S326

description:
single-cell RNA-Seq data
D2_S326
H5TJLBGX3_S326


title: CX8_2: Single cell TCR of fresh cevix biopsy/whole cell lysate/subject 8

description: One hour plating to remove fibroblast cells before 10x single cell gel bead emulsion

source_name: Fresh human cervix biopsy

value: single cell suspension from fresh cervix biopsy with one hour plating


title: c_t081_pio_day_36

description:
R10859
gene_counts.txt


title: S48

description:
single-cell RNA-Seq data
D12_S48
H5TJLBGX3_S48


title: g7_1to5_mouse2_local (gDNA)


title: g7_1to1_mouse1_local (gDNA)


title: CX8_1: Single cell 5' gene expression of fresh cevix biopsy/whole cell lysate/subject 8


title: S336

description:
single-cell RNA-Seq data
D12_S336
H5TJLBGX3_S336


title: c_t081_pio_day_02

description:
R10858
gene_counts.txt


title: CX7B_2: Single cell TCR of fresh cevix biopsy/whole cell lysate/subject 7


title: PBS_mouse4_local (gDNA)

value: PBS


title: No rhizobium (mock inoculation), no salt, biological replicate C


title: PBS_mouse3_local (gDNA)


title: S47

description:
single-cell RNA-Seq data
D11_S47
H5TJLBGX3_S47


title: CX7B_1: Single cell 5' gene expression of fresh cevix biopsy/whole cell lysate/subject 7

description: One hour plating to remove fibroblast cells before 10x single cell gel bead emulsion. 7B refers to the same subject as 7A with two cervix biopsies 8 weeks apart


title: S335

description:
single-cell RNA-Seq data
D11_S335
H5TJLBGX3_S335


title: Inoculated with S. meliloti 1021, no Salt, biological replicate B


title: g7_1to1_mouse3_local (gDNA)


title: CX7A_2: Single cell TCR of fresh cevix biopsy/whole cell lysate/subject 7


title: c_t041_pio_day_19

description:
R10855
gene_counts.txt


title: g7_1to1_mouse2_local (gDNA)


title: S46

description:
single-cell RNA-Seq data
D10_S46
H5TJLBGX3_S46


title: g12_1to5_mouse4_local (gDNA)


title: c_t041_pio_day_13

description:
R10854_R
gene_counts.txt


title: CX6B_2: Single cell TCR of fresh cevix biopsy/whole cell lysate/subject 6


title: g12_1to5_mouse2_local (gDNA)


title: c_t034_pio_day9

description:
R10852_R
gene_counts.txt


title: g12_1to5_mouse3_local (gDNA)


title: CX6B_1: Single cell 5' gene expression of fresh cevix biopsy/whole cell lysate/subject 6

description: One hour plating to remove fibroblast cells before 10x single cell gel bead emulsion. 6B refers to the same subject as 6A with two cervix biopsies 8 weeks apart


title: S334

description:
single-cell RNA-Seq data
D10_S334
H5TJLBGX3_S334


title: S321

description:
single-cell RNA-Seq data
C9_S321
H5TJLBGX3_S321


title: c_t033_pio_day_25

description:
R10851
gene_counts.txt


title: CX6A_2: Single cell TCR of fresh cevix biopsy/whole cell lysate/subject 6


title: g12_1to1_mouse3_local (gDNA)


title: c_t034_pio_day26

description:
R10853_R
gene_counts.txt


title: S320

description:
single-cell RNA-Seq data
C8_S320
H5TJLBGX3_S320


title: S33

description:
single-cell RNA-Seq data
C9_S33
H5TJLBGX3_S33


title: CX7A_1: Single cell 5' gene expression of fresh cevix biopsy/whole cell lysate/subject 7


title: CX6A_1: Single cell 5' gene expression of fresh cevix biopsy/whole cell lysate/subject 6


title: c_t033_pio_day_7

description:
R10850
gene_counts.txt


title: g12_1to1_mouse4_local (gDNA)


title: c_t059_pio_day_8

description:
R10856
gene_counts.txt


title: g12_1to1_mouse2_local (gDNA)


title: CX5_2: Single cell TCR of fresh cevix biopsy/whole cell lysate/subject 5


title: c_t031_pio_day_15

description:
R10849
gene_counts.txt


title: S319

description:
single-cell RNA-Seq data
C7_S319
H5TJLBGX3_S319


title: c_t031_pio_day_8

description:
R10848
gene_counts.txt


title: CX5_1: Single cell 5' gene expression of fresh cevix biopsy/whole cell lysate/subject 5


title: PBS_mouse2_local (gDNA)


title: g12_1to5_mouse1_local (gDNA)


title: S31

description:
single-cell RNA-Seq data
C7_S31
H5TJLBGX3_S31


title: c_t059_pio_day_29

description:
R10857
gene_counts.txt


title: c_t030_pio_day_21

description:
R10847
gene_counts.txt


title: PBS_mouse1_local (gDNA)


title: S318

description:
single-cell RNA-Seq data
C6_S318
H5TJLBGX3_S318


title: CX4_1: Single cell 5' gene expression of fresh cevix biopsy/whole cell lysate/subject 4

description: One hour plating to remove fibroblast cells and CD8 negative selection to enrich CD8 T cells  before 10x single cell gel bead emulsion

value: single cell suspension from fresh cervix biopsy with one hour plating & CD8 negative selection


title: c_t030_pio_day_4

description:
R10846
gene_counts.txt

value: Whole blood


title: S317

description:
single-cell RNA-Seq data
C5_S317
H5TJLBGX3_S317


title: c_t062_pio_day_13

description:
R10844
gene_counts.txt


title: S30

description:
single-cell RNA-Seq data
C6_S30
H5TJLBGX3_S30


title: CX2_2: Single cell TCR of fresh cevix biopsy/whole cell lysate/subject 2

description: One hour plating to remove fibroblast cells before 10x single cell gel bead emulsion


title: c_t062_pio_day_19

description:
R10845
gene_counts.txt

value: negative


title: g12_1to1_mouse1_local (gDNA)


title: S32

description:
single-cell RNA-Seq data
C8_S32
H5TJLBGX3_S32


title: c_t028_pio_day_10

description:
R10843
gene_counts.txt


title: CX2_1: Single cell 5' gene expression of fresh cevix biopsy/whole cell lysate/subject 2


title: S29

description:
single-cell RNA-Seq data
C5_S29
H5TJLBGX3_S29


title: S316

description:
single-cell RNA-Seq data
C4_S316
H5TJLBGX3_S316


title: c_t028_pio_day_3

description:
R10842
gene_counts.txt

value: positive


title: S28

description:
single-cell RNA-Seq data
C4_S28
H5TJLBGX3_S28


title: CX4_2: Single cell TCR of fresh cevix biopsy/whole cell lysate/subject 4


title: c_t023_pio_day_19

description:
R10841
gene_counts.txt


title: S328

description:
single-cell RNA-Seq data
D4_S328
H5TJLBGX3_S328


title: S315

description:
single-cell RNA-Seq data
C3_S315
H5TJLBGX3_S315


title: T4-NSCLP

city: Miami

first: Derek

last: Van Booven

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

data_processing:
Adapters trimmed with TrimGalore
Data aligned to hg19 with Bismark2
Coverage files fed into DSS for differential methylation
Genome_build: hg19

source_name: Saliva DNA

extract_protocol:
Buccal swab
400ng per sample. Unmethylated Lambda gDNA was spiked into each sample per the Swift Accel-NGS Methyl-Seq DNA Library procotol (v.2.0). Samples were sonicated using a 500bp protocol. Sonicated products were processed overnight using the Zymo EZ DNA Methylation Gold kit. Products were purified and stored at -20C. Library preparations were carried out using the Accel-NGS® Methyl-Seq DNA Library Kit.

value: Saliva DNA

tag: disease state

value: NSCLP-Affected Twin


title: T3-Unaf

value: Unaffected Twin


title: T4-Unaf


title: c_t023_pio_day_6

description:
R10840_R
gene_counts.txt


title: S27

description:
single-cell RNA-Seq data
C3_S27
H5TJLBGX3_S27

tag: strain background

value: wild type


title: T2-Unaf


title: c_t021_pio_day_15

description:
R10839_R
gene_counts.txt