title: EV_267

description: Targeted miRNA Sequencing


title: EV_292

status: Public on Mar 12 2021

type: SRA

city: New York

first: Allison

last: Kupsco

state: NY

department: Environmental Health Sciences

country: USA

institute: Columbia University Mailman School of Public Health

description: Targeted miRNA Sequencing

library_source: transcriptomic

data_processing:
Illumina CASAVA was used for base calling and generation of FASQ files
HTG EdgeSeq Parser software (version 10196100G) was used for alignment to a priori defined target sequences.  Requirements include %Q30 score >= 85% and %passing filter >= 75%.
Post-sequencing quality control using negative process control probes (ANT plant gene).  Counts are transformed to log2(counts per million) following Law et al. 2004.  Samples are removed if the average expression of negative process control probes is greater than 1.77 after log2 cpm tranformation. All samples passed the post-sequencing quality control.
Raw counts were median ratio normalized using the DESeq2 package in R version 3.5.1 (Love et al., 2014)
Following median ratio normalization, a constant (1) was added to account for zero values and counts were log2 transformed then corrected with ComBat from the sva package (Leek et al., 2012) for technical processing batch.
Genome_build: Aligment was to a priori selected target sequences
Supplementary_files_format_and_content: All processed data files are comma separated values, with the samples as columns and the miRNAs as rows. Values are normalized and/or log transformed corrected counts.

molecule: total RNA

organism: Homo sapiens

source_name: Breast milk extracellular vesicles

extract_protocol:
Breast milk samples were centrifuged at 200g for 10 mins to remove fat globules, then 3,000g for 15 mins to pellet cellular debris. Extracellular vesicle (EV) RNA was isolated with the ExoEasy Maxi Kit and the miRNeasy RNA Isolation Kit (Qiagen) according to manufacturer instructions.
Libraries were constructed with the HTG EdgeSeq WT-miRNA Assay (Tucson, Arizona). Samples were processed by adding HTG Lysis Buffer to lyse and/or permeabilize the RNA available to subsequently bind to corresponding target-specific Nuclease Protection Probes (NPPs). The lysed samples was transferred to a 96-well micro-titer plate. Target capture was done by adding NPPs to the lysed samples to hybridize to the target mRNA. Then S1 nuclease was added to digest non-hybridized miRNA and excess NPPs, leaving target mRNA/NPP duplexes. S1 digestion was terminated by heat denaturation of S1 enzyme. The processed samples were used as template to set up PCR reactions with primer tags. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation for deep sequencing. The library was prepared using HTG EdgeSeq PCR processing. Following library preparation, it was quantified using HTG EdgeSeq KAPA Library Quantification for Illumina Sequencing. All samples and controls were quantified in triplicate.
Targeted miRNA-Seq

tag: processing batch

tag: sequencing run

tag: tissue

value: Breast milk extracellular vesicles


title: EV_266

description: Targeted miRNA Sequencing


title: ALS patient_enrolment [BLT00026]

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

country: Israel

institute: Weizmann Institute

description:
BLT00026
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv

data_processing:
Data were aligned to the genome using the GeneGlobe pipeline (https://geneglobe.qiagen.com/us/)
Data were filtered using the following specifications: >50 UMIs in >60% of the samples for longitudinal analysis, >100 UMIs on average for other analyses
Data were corrected for batch using the ComBat function in R and then normalized by DESeq2
Supplementary_files_format_and_content: txt files contain raw UMI counts, after alignment
Supplementary_files_format_and_content: xls files contain batch and DESeq2 corrected UMIs, after filtration of low-abundance miRNAs. Related R code are in the same folder
Supplementary_files_format_and_content: csv files contain categorial values for miRNAs and other clinical features, to be run by an R code for calculation of hazard ratios by COX proportional hazard analysis. Related R codes are in the same folder

source_name: Blood plasma

extract_protocol:
Plasma were isolated from blood and total RNA was extracted using the Qiagen miRNeasy micro kit (Cat# 217184)
libraries were prepared from 7.5 ng of total RNA using the QIAseq miRNA library kit and QIAseq miRNA NGS 48 Index IL (Qiagen, Cat# 331505 and 331565), by an experimenter who was blinded to the identity of samples. Samples were randomly allocated to library preparation and sequencing in batches. Libraries with different indices were multiplexed and sequenced on NextSeq 500/550 v2 flow cell or Novaseq SP100 (Illumina), with 75bp single read and 6bp index read.

tag: disease

value: ALS

tag: group

value: enrolment


title: ALS patient_enrolment [BLT00021]

address: בן אליעזר 32, 17

description:
BLT00021
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: ALS patient_enrolment [BLT00059]

address: בן אליעזר 32, 17

description:
BLT00059
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: EV_265

description: Targeted miRNA Sequencing


title: EV_262

description: Targeted miRNA Sequencing


title: ALS patient_enrolment [BLT00020]

address: בן אליעזר 32, 17

description:
BLT00020
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: EV_261

description: Targeted miRNA Sequencing


title: ALS patient_enrolment [BLT00043]

address: בן אליעזר 32, 17

description:
BLT00043
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: EV_260

description: Targeted miRNA Sequencing


title: ALS patient_enrolment [BLT00018]

address: בן אליעזר 32, 17

description:
BLT00018
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: ALS patient_enrolment [BLT00008]

address: בן אליעזר 32, 17

description:
BLT00008
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: EV_259

description: Targeted miRNA Sequencing


title: ALS patient_enrolment [BLT00002]

address: בן אליעזר 32, 17

description:
BLT00002
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: ALS patient_enrolment [BLT00007]

address: בן אליעזר 32, 17

description:
BLT00007
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: EV_253

description: Targeted miRNA Sequencing


title: EV_237

description: Targeted miRNA Sequencing


title: EV_250

description: Targeted miRNA Sequencing


title: ALS patient_enrolment [BLT00023]

address: בן אליעזר 32, 17

description:
BLT00023
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: EV_244

description: Targeted miRNA Sequencing


title: EV_231

description: Targeted miRNA Sequencing


title: EV_246

description: Targeted miRNA Sequencing


title: EV_232

description: Targeted miRNA Sequencing


title: EV_230

description: Targeted miRNA Sequencing


title: EV_234

description: Targeted miRNA Sequencing


title: NT_US:E1,FF,FFa,FFd,VA1B,V1a,H4c rep2;NT_N2A:P9-E1,P9-E2,P9-E3,P9-E4,P9-E7CAG8,P9-E11CAG-11 rep2;YE1:PGM3 rep2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

library_source: genomic

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh38/hg38 human or GRCm38/mm10 mouse reference genome using BWA-MEM 0.7.9a.
Genome_build: hg38 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: base subtitutions

molecule: genomic DNA

organism:
Homo sapiens
Mus musculus

source_name: U2OS, N2A and 293FT_NT_U2OS | NT_N2A | YE1

growth_protocol: 293FT, U2OS and N2A cells from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination. All mice were housed under specific pathogen-free conditions at the animal facilities of Medical Research Institute, Wuhan University. All mouse studies were approved by the Animal Care Committees of Medical Research Institute, Wuhan University.

extract_protocol:
Target genomic sequences were PCR amplified by high-fidelity DNA polymerase PrimeSTAR HS (Clonetech) with primer sets flanking examined sgRNA target sites.
For deep target genimoc DNA sequencing, Indexed DNA libraries were prepared by using the TruSeq ChIP Sample Preparation Kit (Illumina) with minor modifications. Briefly, the PCR products amplified from genomic DNA regions were fragmented by Covaris S220, and then PCR amplified by using the TruSeq ChIP Sample Preparation Kit (Illumina). After quantitated with Qubit High-Sensitivity DNA kit (Invitrogen), PCR products with different tags were pooled together for deep sequencing by using the Illumina HiSeq X10 (2×150) at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: 293FT, U2OS and N2A cells were seeded in a 24-well plate at a density of 1E+5 per well and transfected with 250 μl serum-free Opti-MEM that contained LIPOFECTAMINE LTX (Life, Invitrogen), LIPOFECTAMINE plus (Life, Invitrogen) and expression vector. After 24 hr, puromycin (ant-pr-1, InvivoGen) was added to the medium at the final concentration of 4 μg/ml. After another 48 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) for subsequent sequencing analysis.

tag: cell line

value: U2OS, N2A and 293FT

tag: treatment

value: NT_U2OS | NT_N2A | YE1

tag: 5'-end trimming of r1

tag: 3'-end trimming of r1


title: NT_US:E1,FF,FFa,FFd,VA1B,V1a,H4c rep1;NT_N2A:P9-E1,P9-E2,P9-E3,P9-E4,P9-E7CAG8,P9-E11CAG-11 rep1;YE1:PGM3 rep1


title: tBE-V5-mA3_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep2;tBE-V5-mA3_N2A:P9-E7CAG9,P9-E11CAG-12 rep2

source_name: U2OS and N2A_tBE-V5-mA3_U2OS | tBE-V5-mA3_N2A

value: U2OS and N2A

value: tBE-V5-mA3_U2OS | tBE-V5-mA3_N2A


title: tBE-V5-mA3_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep1;tBE-V5-mA3_N2A:P9-E7CAG9,P9-E11CAG-12 rep1


title: tBE-V5-mA3_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep3;tBE-V5-mA3_N2A:P9-E7CAG9,P9-E11CAG-12 rep3


title: NT_US:E1,FF,FFa,FFd,VA1B,V1a,H4c rep3;NT_N2A:P9-E1,P9-E2,P9-E3,P9-E4,P9-E7CAG8,P9-E11CAG-11 rep3;YE1:PGM3 rep3


title: BE4max-YE1_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep3;NT_N2A:P9-E7CAG9,P9-E11CAG-12 rep3

source_name: U2OS and N2A_BE4max-YE1_U2OS | NT_N2A

value: BE4max-YE1_U2OS | NT_N2A


title: EV_229

description: Targeted miRNA Sequencing


title: EV_228

description: Targeted miRNA Sequencing


title: EV_258

description: Targeted miRNA Sequencing


title: EV_222

description: Targeted miRNA Sequencing


title: BE4max-YE1_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep2;NT_N2A:P9-E7CAG9,P9-E11CAG-12 rep2


title: EV_221

description: Targeted miRNA Sequencing


title: EV_219

description: Targeted miRNA Sequencing


title: NT:MAGEA1a,MSSK1a,MSSK1-b,MAGEA1-b,MSSK1c,MSSK1-b2 rep1;tBE-V5-mA3:P9-E1 rep1

source_name: 293FT_NT | tBE-V5-mA3

value: NT | tBE-V5-mA3


title: tBE-V5-mA3:MAGEA1-b,MSSK1c,MSSK1-b2 rep2


title: BE4max-YE1_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep1;NT_N2A:P9-E7CAG9,P9-E11CAG-12 rep1


title: NT:MAGEA1a,MSSK1a,MSSK1-b,MAGEA1-b,MSSK1c,MSSK1-b2 rep3;tBE-V5-mA3:P9-E1 rep3


title: NT:MAGEA1a,MSSK1a,MSSK1-b,MAGEA1-b,MSSK1c,MSSK1-b2 rep2;tBE-V5-mA3:P9-E1 rep2


title: tBE-V5-mA3:MAGEA1-b,MSSK1c,MSSK1-b2 rep3


title: EV_216

description: Targeted miRNA Sequencing


title: tBE-V5-mA3:MAGEA1-b,MSSK1c,MSSK1-b2 rep1


title: BE4max-YE1:MAGEA1-b,MSSK1c,MSSK1-b2 rep2


title: EV_205

description: Targeted miRNA Sequencing


title: EV_215

description: Targeted miRNA Sequencing


title: BE4max-YE1:MAGEA1-b,MSSK1c,MSSK1-b2 rep3


title: EV_218

description: Targeted miRNA Sequencing


title: EV_199

description: Targeted miRNA Sequencing


title: EV_198

description: Targeted miRNA Sequencing


title: hA3A-Y130F:MAGEA1-b,MSSK1c,MSSK1-b2 rep3


title: EV_195

description: Targeted miRNA Sequencing


title: EV_188

description: Targeted miRNA Sequencing


title: BE3:MAGEA1-b,MSSK1c,MSSK1-b2 rep1


title: hA3A-Y130F:MAGEA1-b,MSSK1c,MSSK1-b2 rep1


title: hA3A-Y130F:MAGEA1-b,MSSK1c,MSSK1-b2 rep2


title: tBE-V5-mA3:MAGEA1a,MSSK1a,MSSK1-b rep3


title: tBE-V5-mA3:MAGEA1a,MSSK1a,MSSK1-b rep2


title: BE3:MAGEA1-b,MSSK1c,MSSK1-b2 rep2


title: BE4max-YE1:MAGEA1-b,MSSK1c,MSSK1-b2 rep1


title: tBE-V5-mA3:MAGEA1a,MSSK1a,MSSK1-b rep1


title: EV_187

description: Targeted miRNA Sequencing


title: EV_185

description: Targeted miRNA Sequencing


title: EV_186

description: Targeted miRNA Sequencing


title: EV_191

description: Targeted miRNA Sequencing


title: BE4max-YE1:MAGEA1a,MSSK1a,MSSK1-b rep3


title: BE3:MAGEA1-b,MSSK1c,MSSK1-b2 rep3


title: EV_183

description: Targeted miRNA Sequencing


title: Parental M49 GAS isolate PGAS812 (3)

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

description:
rRNA-depleted total RNA
Processed file M49.xls

data_processing:
CLC Genomics Workbench version 8 RNA-seq was used for basecalling and aligning the sequence reads to the MGAS2221 (the M1 datasets) or NZ131 (the M49 datasets) genomes
Parameters for alignment were set up:  Similar fraction=0.8, Length fraction=0.8, Mismatch cost=2, Insertion cost=3.
Normalization was performed to overall sequencing depth using total mapped reads data.
Statistical significance was tested using T-test with a false-discovery rate correction.
Supplementary_files_format_and_content: Excel file containing columns for the gene name, gene border (left), gene border (right), normalized expression value for the parental strain, normalized expression value for the derivative strain, fold-change, and T-test with FDR correction value

organism: Streptococcus pyogenes

source_name: Clinical isolate

growth_protocol: GAS strains were grown in THY broth to the exponential phase of growth (an O.D.600 of 0.5) before processing for RNA isolation.

extract_protocol:
Total RNA was isolated and rRNAs were depleted using the Illumina RiboZero bacterial kit.
The rRNA depleted RNA was used to generate cDNA libraries using the ScriptSeq kit v2 (Epicentre).  Briefly, RNA was fragmented, cDNA was synthesized using random hexamers containing a 5′ tagging sequence, the RNA was hydrolyzed, and the cDNA was tagged at the 3′ end.  A limited number of PCR cycles (n=14) were used to amplify the libraries via the 5′ and 3′ tags (the libraries were barcoded by using different primers), and the libraries size-selected (170 to 300 bp).  The size-selected and barcoded libraries were run on an Illumina NextSeq550 flowcell.

tag: strain

value: Parental M49 GAS isolate


title: RD2-containing derivative of PGAS812 PGAS890 (2)

source_name: Lab-created isolate

value: RD2-containing derivative of PGAS812


title: RD2-containing derivative of PGAS812 PGAS890 (3)


title: RD2-containing derivative of MGAS2221 PGAS885 (2)

description:
rRNA-depleted total RNA
Processed file M1.xls

value: RD2-containing derivative of MGAS2221


title: RD2-containing derivative of PGAS812 PGAS890 (1)


title: Parental M49 GAS isolate PGAS812 (1)


title: EV_197

description: Targeted miRNA Sequencing


title: BE4max-YE1:MAGEA1a,MSSK1a,MSSK1-b rep2


title: Parental M49 GAS isolate PGAS812 (2)


title: EV_192

description: Targeted miRNA Sequencing


title: EV_182

description: Targeted miRNA Sequencing


title: RD2-containing derivative of MGAS2221 PGAS885 (1)


title: BE4max-YE1:MAGEA1a,MSSK1a,MSSK1-b rep1


title: hA3A-Y130F:MAGEA1a,MSSK1a,MSSK1-b rep3


title: EV_175

description: Targeted miRNA Sequencing


title: EV_178

description: Targeted miRNA Sequencing


title: EV_170

description: Targeted miRNA Sequencing


title: EV_176

description: Targeted miRNA Sequencing


title: Parental M1 GAS isolate MGAS2221 (2)

value: Parental M1 GAS isolate


title: hA3A-Y130F:MAGEA1a,MSSK1a,MSSK1-b rep2


title: Parental M1 GAS isolate MGAS2221 (3)


title: hA3A-Y130F:MAGEA1a,MSSK1a,MSSK1-b rep1


title: Parental M1 GAS isolate MGAS2221 (1)


title: BE3:MAGEA1a,MSSK1a,MSSK1-b rep3


title: RD2-containing derivative of MGAS2221 PGAS885 (3)


title: EV_168

description: Targeted miRNA Sequencing


title: BE3:MAGEA1a,MSSK1a,MSSK1-b rep2


title: EV_165

description: Targeted miRNA Sequencing


title: EV_159

description: Targeted miRNA Sequencing


title: BE3:MAGEA1a,MSSK1a,MSSK1-b rep1


title: EV_152

description: Targeted miRNA Sequencing


title: no hsg:E1,hsgFF,sgFF,hsgV1A,sgV1A,DNT1 rep1;tBE-V5-mA3:P9-E2,P9-E3,P9-E4,P9-E7CAG8,P9-E11CAG-11 rep1;NT:FF-OTsgd rep2

source_name: 293FT_no hsg | tBE-V5-mA3 | NT

value: no hsg | tBE-V5-mA3 | NT


title: EV_161

description: Targeted miRNA Sequencing


title: no hsg:E1,hsgFF,sgFF,hsgV1A,sgV1A,DNT1 rep1;tBE-V5-mA3:P9-E2,P9-E3,P9-E4,P9-E7CAG8,P9-E11CAG-11 rep1;NT:FF-OTsgd rep1


title: no hsg:E1,hsgFF,sgFF,hsgV1A,sgV1A,DNT1 rep1;tBE-V5-mA3:P9-E2,P9-E3,P9-E4,P9-E7CAG8,P9-E11CAG-11 rep1;NT:FF-OTsgd rep3


title: human sample 311

type: RNA

city: Novato

first: Yingxiang

last: Huang

state: California

address: 8001 Redwood Blvd

institute: Buck Institute

hyb_protocol: For each sample, 750 ng of total RNA were hybridized to Beadchips (HumanHT-12v3 Expression Bead Chip, Illumina, San Diego, CA) that contains 48 771 probes for around 25 000 annotated genes.

scan_protocol: The hybridized Beadchips were scanned on an Illumina BeadScan confocal scanner and were analyzed by Illumina’s GenomeStudio software, version 2.0.

data_processing: After checking the quality of each individual array, the Feature Extraction Files were imported into R Bioconductor and analyzed using the Beadarray package for probe filtering, quantile normalization, replicate probe summarization and log2 transformation.

label: biotin

source_name: serum

label_protocol: The amount of total RNA, and A260/A280- and A260/A230-nm ratios were assessed using the NanoDrop 1000 (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

extract_protocol: total RNA was extracted from PAXgene blood RNA tubes (PreAnalytiX, USA) using the QIAcube automation RNA extraction procedure according to the manufacturer’s protocol (Qiagene, Valencia, CA).

tag: age


title: human sample 310


title: human sample 303


title: human sample 312


title: human sample 306


title: hA3A-Y130F_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep3


title: human sample 307


title: human sample 305


title: human sample 308


title: hA3A-Y130F_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep1


title: EV_145

description: Targeted miRNA Sequencing


title: EV_151

description: Targeted miRNA Sequencing


title: EV_150

description: Targeted miRNA Sequencing


title: human sample 304


title: hA3A-Y130F_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep2


title: human sample 300


title: human sample 298


title: human sample 301


title: human sample 295


title: human sample 297


title: human sample 309


title: EV_137

description: Targeted miRNA Sequencing


title: EV_139

description: Targeted miRNA Sequencing


title: BE3_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep3


title: tBE-V5-mA3:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep3


title: tBE-V5-mA3:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep2


title: tBE-V5-mA3:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep1


title: human sample 296


title: BE3_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep2


title: human sample 302


title: BE4max-YE1:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep3


title: human sample 299


title: BE3_US:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep1


title: EV_133

description: Targeted miRNA Sequencing


title: BE4max-YE1:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep2


title: hA3A-Y130F:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep3


title: human sample 289


title: EV_131

description: Targeted miRNA Sequencing


title: EV_134

description: Targeted miRNA Sequencing


title: human sample 288


title: EV_130

description: Targeted miRNA Sequencing


title: human sample 293


title: human sample 291


title: EV_132

description: Targeted miRNA Sequencing


title: human sample 294


title: EV_126

description: Targeted miRNA Sequencing


title: human sample 281


title: human sample 278


title: human sample 283


title: EV_142

description: Targeted miRNA Sequencing


title: human sample 292


title: human sample 279


title: human sample 290


title: human sample 277


title: human sample 285


title: human sample 287


title: EV_129

description: Targeted miRNA Sequencing


title: human sample 286


title: human sample 275


title: human sample 274


title: human sample 284


title: EV_121

description: Targeted miRNA Sequencing


title: BE4max-YE1:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep1


title: EV_128

description: Targeted miRNA Sequencing


title: human sample 282


title: human sample 280


title: EV_118

description: Targeted miRNA Sequencing


title: human sample 276


title: human sample 271


title: BE3:CRa,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep1;no hsg:hsgDNE1,sgDNE1 rep2

source_name: 293FT_BE3 | no hsg

value: BE3 | no hsg


title: tBE-V5-mA3_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep3;dSaCas9/SgRNA+hA3A-Y130F:Sg3a,SgVAa,Sg4a rep3

source_name: U2OS and 293FT_tBE-V5-mA3_U2OS | dSaCas9/Sa-sgRNA+hA3A-BE3-Y130F

value: U2OS and 293FT


title: hA3A-Y130F:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep2


title: hA3A-Y130F:CRa,DNE1,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep1


title: human sample 273


title: human sample 265


title: BE3:CRa,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep1;no hsg:hsgDNE1,sgDNE1 rep3


title: EV_99

description: Targeted miRNA Sequencing


title: human sample 272


title: human sample 258


title: human sample 270


title: human sample 259


title: EV_113

description: Targeted miRNA Sequencing


title: human sample 268


title: human sample 269


title: tBE-V5-mA3_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep1;dSaCas9/SgRNA+hA3A-Y130F:Sg3a,SgVAa,Sg4a rep1


title: human sample 267


title: BE4max-YE1_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep2;dSaCas9/SgRNA+hA3A:Sg3a,SgVAa,Sg4a rep2

source_name: U2OS and 293FT_BE4max-YE1_U2OS | dSaCas9/Sa-sgRNA+hA3A-BE3


title: human sample 257


title: human sample 266


title: EV_111

description: Targeted miRNA Sequencing


title: EV_107

description: Targeted miRNA Sequencing


title: BE3:CRa,E1a,FFa,FFd,H4c,R2-b,S1c,V1a,V2a rep1;no hsg:hsgDNE1,sgDNE1 rep1


title: EV_114

description: Targeted miRNA Sequencing


title: EV_106

description: Targeted miRNA Sequencing


title: EV_85

description: Targeted miRNA Sequencing


title: tBE-V5-mA3_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep2;dSaCas9/SgRNA+hA3A-Y130F:Sg3a,SgVAa,Sg4a rep2


title: BE4max-YE1_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep3;dSaCas9/SgRNA+hA3A:Sg3a,SgVAa,Sg4a rep3


title: BE4max-YE1_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep1;dSaCas9/SgRNA+hA3A:Sg3a,SgVAa,Sg4a rep1


title: EV_95

description: Targeted miRNA Sequencing


title: human sample 264


title: human sample 263


title: human sample 260


title: human sample 262


title: human sample 261


title: hA3A-Y130F_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep3;dSaCas9/SgRNA+BE3:Sg3a,SgVAa,Sg4a rep3

source_name: U2OS and 293FT_hA3A-BE3-Y130F_U2OS | dSaCas9/Sa-sgRNA+BE3


title: human sample 255


title: human sample 254


title: human sample 256


title: human sample 253


title: EV_73

description: Targeted miRNA Sequencing


title: EV_112

description: Targeted miRNA Sequencing


title: hA3A-Y130F_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep2;dSaCas9/SgRNA+BE3:Sg3a,SgVAa,Sg4a rep2


title: human sample 251


title: human sample 250


title: human sample 249


title: human sample 252


title: human sample 248


title: EV_68

description: Targeted miRNA Sequencing


title: BE3_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep3;dSaCas9/SgRNA+dSpCas9:Sg3a,SgVAa,Sg4a rep3

source_name: U2OS and 293FT_BE3_U2OS | dSaCas9/Sa-sgRNA+dSpCas9

value: BE3_U2OS | dSaCas9/Sa-sgRNA+dSpCas9


title: human sample 246


title: EV_72

description: Targeted miRNA Sequencing

value: Breast milk extracellular vesicles


title: 293FT and U2OS_nSaCas9/Sa-sgRNA+tBE-V5-mA3-noTEV+1000 ng split TEV | NT_U2OS rep3

value: 293FT and U2OS


title: BE3_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep1;dSaCas9/SgRNA+dSpCas9:Sg3a,SgVAa,Sg4a rep1


title: EV_65

description: Targeted miRNA Sequencing


title: EV_64

description: Targeted miRNA Sequencing


title: EV_62

description: Targeted miRNA Sequencing


title: 293FT and U2OS_nSaCas9/Sa-sgRNA+tBE-V5-mA3-noTEV+1000 ng split TEV | NT_U2OS rep2


title: human sample 247


title: 293FT and U2OS_nSaCas9/Sa-sgRNA+tBE-V5-mA3-noTEV+1000 ng split TEV | NT_U2OS rep1


title: EV_56

description: Targeted miRNA Sequencing


title: EV_81

description: Targeted miRNA Sequencing


title: SatBEV5mA3noTV750sTV:E1,FF,VA1B,Sg3a,SgVAa,Sg4a rep3;tBE-V5-mA3:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C rep3

source_name: 293FT_nSaCas9/Sa-sgRNA+tBE-V5-mA3-noTEV+750 ng split TEV | tBE-V5-mA3


title: EV_80

description: Targeted miRNA Sequencing


title: human sample 243


title: human sample 245


title: human sample 242


title: human sample 240


title: human sample 234


title: EV_54

description: Targeted miRNA Sequencing


title: SatBEV5mA3noTV750sTV:E1,FF,VA1B,Sg3a,SgVAa,Sg4a rep2;tBE-V5-mA3:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C rep2

value: nSaCas9/Sa-sgRNA+tBE-V5-mA3-noTEV+750 ng split TEV | tBE-V5-mA3


title: human sample 241


title: human sample 244


title: human sample 239


title: human sample 238


title: EV_52

description: Targeted miRNA Sequencing


title: human sample 236


title: human sample 233


title: human sample 232


title: SatBEV5mA3noTV750sTV:E1,FF,VA1B,Sg3a,SgVAa,Sg4a rep1;tBE-V5-mA3:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C rep1


title: EV_44

description: Targeted miRNA Sequencing


title: EV_40

description: Targeted miRNA Sequencing


title: EV_39

description: Targeted miRNA Sequencing


title: SatBEV5mA3noTV500sTV:E1,FF,VA1B,Sg3a,SgVAa,Sg4a rep2;BE4max-YE1:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C rep2

source_name: 293FT_nSaCas9/Sa-sgRNA+tBE-V5-mA3-noTEV+500 ng split TEV | BE4max-YE1


title: SatBEV5mA3noTV500sTV:E1,FF,VA1B,Sg3a,SgVAa,Sg4a rep3;BE4max-YE1:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C rep3

value: nSaCas9/Sa-sgRNA+tBE-V5-mA3-noTEV+500 ng split TEV | BE4max-YE1


title: SatBEV5mA3noTV500sTV:E1,FF,VA1B,Sg3a,SgVAa,Sg4a rep1;BE4max-YE1:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C rep1


title: EV_35

description: Targeted miRNA Sequencing

source_name: Breast milk extracellular vesicles


title: EV_26

description: Targeted miRNA Sequencing


title: human sample 231


title: SatBEV5mA3noTV250sTV:E1,FF,VA1B,Sg3a,SgVAa,Sg4a rep3;hA3A-Y130F:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C rep3

source_name: 293FT_nSaCas9/Sa-sgRNA+tBE-V5-mA3-noTEV+250 ng split TEV | hA3A-BE3-Y130F


title: human sample 235


title: SatBEV5mA3noTV250sTV:E1,FF,VA1B,Sg3a,SgVAa,Sg4a rep2;hA3A-Y130F:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C rep2

value: nSaCas9/Sa-sgRNA+tBE-V5-mA3-noTEV+250 ng split TEV | hA3A-BE3-Y130F


title: human sample 226


title: human sample 228


title: human sample 237


title: human sample 229


title: human sample 225


title: human sample 224


title: human sample 223


title: human sample 227


title: SatBEV5mA3noTV250sTV:E1,FF,VA1B,Sg3a,SgVAa,Sg4a rep1;hA3A-Y130F:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C rep1


title: human sample 221


title: human sample 219


title: human sample 230


title: EV_18

description: Targeted miRNA Sequencing


title: human sample 222


title: EV_24

description: Targeted miRNA Sequencing


title: human sample 220


title: SaC9+tBE-V5-mA3:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep3


title: SaC9+tBE-V5-mA3:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep1


title: EV_1

description: Targeted miRNA Sequencing


title: human sample 218


title: EV_15

description: Targeted miRNA Sequencing


title: Clone40_NC_ASO_24hrs

city: San Francisco

first: David

last: Wu

address: 35 Medical Center Way

institute: UCSF

description:
LOC636329-miR29-deleted U87 cells with LOC646329 knockdown at T24, clone 40
counts.tsv
Clone40_NC_ASO_24hrs_R1

data_processing:
Quality assessment, adapter and quality trimming using fastp (0.13.1)
Alignment to reference genome (hisat2 2.1.0)
Gene expression quantification (featureCounts 1.5.0)
Differential gene expression analysis (DESeq2 1.22, R 3.5)
Genome_build: GRCh38.84
Supplementary_files_format_and_content: Counts matrix output of featureCounts

growth_protocol: DMEM 10% FBS 1% Antibiotics

extract_protocol:
RNA extracted by Zymo Direct-zol RNA miniprep columns
Illumina TruSeq Stranded mRNA and Nanopore Direct RNA Sequencing protocol for the nanopore sample.

treatment_protocol: Transfection using Lipofectamine RNAiMAX and collected at the respective time-point

tag: clone

tag: time

tag: condition

value: Negative Control ASO


title: human sample 217


title: Clone40_646_ASO_24hrs

description:
LOC636329-miR29-deleted U87 cells with control knockdown at T24, clone 40
counts.tsv
Clone40_646_ASO_24hrs_R1

value: ASO 646


title: human sample 215


title: Clone18_NC_ASO_24hrs

description:
LOC636329-miR29-deleted U87 cells with LOC646329 knockdown at T24, clone 18
counts.tsv
Clone18_NC_ASO_24hrs_R1


title: human sample 214


title: human sample 212


title: human sample 210


title: hA3A-Y130F_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep1;dSaCas9/SgRNA+BE3:Sg3a,SgVAa,Sg4a rep1


title: BE3_US:S4A,D1B,E1A,R2A,RIB,CAA,RB,S1-F,CRA,V2C,E1,FF,VA1B rep2;dSaCas9/SgRNA+dSpCas9:Sg3a,SgVAa,Sg4a rep2


title: human sample 216


title: SaC9+tBE-V4-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep1


title: human sample 209


title: human sample 213


title: Clone18_646_ASO_24hrs

description:
LOC636329-miR29-deleted U87 cells with control knockdown at T24, clone 18
counts.tsv
Clone18_646_ASO_24hrs_R1


title: Clone15_NC_ASO_24hrs

description:
LOC636329-miR29-deleted U87 cells with LOC646329 knockdown at T24, clone 15
counts.tsv
Clone15_NC_ASO_24hrs_R1


title: SaC9+tBE-V3-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep2


title: SaC9+tBE-V3-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep3


title: human sample 206


title: human sample 211


title: human sample 205


title: human sample 207


title: human sample 208


title: Clone15_646_ASO_24hrs

description:
LOC636329-miR29-deleted U87 cells with control knockdown at T24, clone 15
counts.tsv
Clone15_646_ASO_24hrs_R1


title: SaC9+tBE-V3-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep1


title: ASO1_24_2

description:
WT U87 cells with LOC646329 knockdown at T24, replicate 2
counts.tsv
DLDH07TruSeq_Index_25_S24

value: WT


title: human sample 204


title: human sample 202


title: SaC9+tBE-V2-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep3


title: NC_24_2

description:
WT U87 cells with control knockdown at T24, replicate 2
counts.tsv
DLDH07TruSeq_Index_22_S22


title: human sample 200


title: SaC9+tBE-V2-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep2


title: human sample 199


title: SaC9+tBE-V2-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep1


title: NC_24_1

description:
WT U87 cells with control knockdown at T24, replicate 1
counts.tsv
DLDH07TruSeq_Index_21_S21


title: human sample 201


title: human sample 198


title: SaC9+tBE-V1-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep3


title: ASO1_12_2

description:
WT U87 cells with LOC646329 knockdown at T12, replicate 2
counts.tsv
DLDH07TruSeq_Index_10_S18


title: SaC9+tBE-V1-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep2


title: human sample 203


title: ASO1_12_1

description:
WT U87 cells with LOC646329 knockdown at T12, replicate 1
counts.tsv
DLDH07TruSeq_Index_9_S17


title: human sample 196


title: human sample 194


title: human sample 192


title: NC_12_1

description:
WT U87 cells with control knockdown at T12, replicate 1
counts.tsv
DLDH07TruSeq_Index_3_S15


title: human sample 193


title: SaC9+tBE-V1-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep1


title: SaC9+hA3A-Y130F:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep3;tBE-V5-rA1:PGM3 rep3


title: human sample 195


title: human sample 190


title: human sample 197


title: human sample 188


title: human sample 185


title: ASO1_24_1

description:
WT U87 cells with LOC646329 knockdown at T24, replicate 1
counts.tsv
DLDH07TruSeq_Index_23_S23


title: human sample 186


title: ASO1_8_2

description:
WT U87 cells with LOC646329 knockdown at T8, replicate 2
counts.tsv
DLDH06TruSeq_Index_27_S12


title: human sample 191


title: human sample 189


title: human sample 187


title: SaC9+hA3A-Y130F:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep1;tBE-V5-rA1:PGM3 rep1


title: NC_12_2

description:
WT U87 cells with control knockdown at T12, replicate 2
counts.tsv
DLDH07TruSeq_Index_8_S16


title: human sample 182


title: human sample 183


title: ASO1_8_1

description:
WT U87 cells with LOC646329 knockdown at T8, replicate 1
counts.tsv
DLDH06TruSeq_Index_25_S11


title: SaC9+hA3A:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep3;hA3A-Y130F:PGM3 rep3


title: SaC9+tBE-V4-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep2


title: NC_8_2

description:
WT U87 cells with control knockdown at T8, replicate 2
counts.tsv
DLDH06TruSeq_Index_23_S10


title: human sample 184


title: NC_8_1

description:
WT U87 cells with control knockdown at T8, replicate 1
counts.tsv
DLDH06TruSeq_Index_22_S9


title: SaC9+hA3A:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep1;hA3A-Y130F:PGM3 rep1


title: ASO1_4_2

description:
WT U87 cells with LOC646329 knockdown at T4, replicate 2
counts.tsv
DLDH06TruSeq_Index_11_S6


title: SaC9+BE3:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep3;BE3:PGM3 rep3

source_name: 293FT_nSaCas9/Sa-sgRNA+BE3 | BE3

value: nSaCas9/Sa-sgRNA+BE3 | BE3


title: ASO1_4_1

description:
WT U87 cells with LOC646329 knockdown at T4, replicate 1
counts.tsv
DLDH06TruSeq_Index_10_S5


title: human sample 180


title: human sample 179


title: human sample 177


title: human sample 178


title: human sample 181


title: SaC9+BE3:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep2;BE3:PGM3 rep2


title: NC_4_2

description:
WT U87 cells with control knockdown at T4, replicate 2
counts.tsv
DLDH06TruSeq_Index_9_S4


title: NC_4_1

description:
WT U87 cells with control knockdown at T4, replicate 1
counts.tsv
DLDH06TruSeq_Index_8_S3


title: SaC9+BE3:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep1;BE3:PGM3 rep1


title: human sample 173


title: human sample 175


title: human sample 174


title: NT:Sg3a,Sg4a rep3

value: NT


title: SaC9+tBE-V5-mA3:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep2


title: SaC9+hA3A-Y130F:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep2;tBE-V5-rA1:PGM3 rep2


title: WGBS PreB2-2

city: Baltimore

first: Michael

middle: A

last: Koldobskiy

state: MD

address: 855 N. Wolfe St.

department: Center for Epigenetics

institute: Johns Hopkins University

data_processing:
base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bismark v0.12.3
InformME
Genome_build: hg19
Supplementary_files_format_and_content: bigWig format.  Tracks include mean methylation level (MML), normalized methylation entropy (NME), methylation sensitivity index (MSI), and differential quantities of the above between samples (dMML, dNME, dMSI) and Jensen Shannon Distance (JSD) to measure epigenetic discordance between samples, as well as tracks of differentially methylated regions (DMR) based on JSD.

source_name: Pre-B2 cells

extract_protocol:
Epicentre DNA extraction kit
Illumina TruSeq, NEBNext
Whole Genome Bisulfite Sequencing

tag: tissue/cell type

value: primary

tag: age (years)

tag: cytogenetics


title: NT:Sg4a rep2


title: WGBS PreB2-1


title: F73_Treated larvae 10.0 ng EE2

city: Cincinnati

first: Gregory

middle: Peter

last: Toth

state: OH

address: 26 W ML King Jr. Dr.

department: CCTE

institute: USEPA/ORD

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
The 50 base long reads in the RNA-Seq fastq(.gz) file for each sample were mapped to indexed transcripts from each of the 47,578 gene models (which include isoforms) from the newly updated FHM genome (WIOS00000000; BioSample SAMN12875914
Differential expression analysis was performed using the R limma package (version 3.40.6. Between sample normalization was conducted using the trimmed mean of M-values method implemented by the calcNormFactors function from the R edgeR package (version 3.26.8). Precision weights were calculated using the voom function from the limma package. The limma lmFit function was used to fit a generalized linear model with a term for chemical treatment effects. Moderated t-statistics were calculated for chemical treatment effects using the limma eBayes function, and the limma topTable function was used to sort features (i.e. genes) based on their nominal p-values.
Count data were filtered for features which had at least 3 samples with at least 10 counts
Genome_build: EPA_FHM_2.0.b
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Pimephales promelas

source_name: Whole 96h post-hatch larva

extract_protocol:
Larvae were removed from exposure vessels, placed into Eppendorf tubes together with a steel bead and frozen in liquid nitrogen.  MagMax lysing/binding buffer (100 μl) was added to each tube.
Libraries were prepared from 250 ng RNA using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Greenland, NH) according to the supplied protocol.

treatment_protocol: 48h post-hatch fathead minnow larvae were statically exposed to 0, 0.12, 1.2, 2.5, 5 or 10 ng ethinyl estradiol /l for 48 hours

value: whole larva

tag: experiment

tag: treatment (ng ee2/l)

tag: molecule subtype

value: mRNA


title: NT:Sg3a rep2


title: NT:Sg3a,Sg4a rep1


title: human sample 176


title: human sample 171


title: human sample 170


title: human sample 168


title: human sample 167


title: human sample 165


title: F72_Treated larvae 10.0 ng EE2

tag: tissue


title: human sample 169


title: NT:D1,R2 rep3


title: human sample 172


title: human sample 164


title: mA3CDA1-nSpCas9BE:D1,R2 rep3


title: F67_Treated larvae 10.0 ng EE2


title: F68_Treated larvae 10.0 ng EE2


title: human sample 161


title: human sample 162


title: human sample 160


title: human sample 163


title: F62_Treated larvae 10.0 ng EE2


title: SaC9+YE1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep3


title: F58_Treated larvae 10.0 ng EE2


title: hA3GCDA2-nSpCas9BE:D1,R2 rep3


title: human sample 158


title: F53_Treated larvae 10.0 ng EE2


title: hA3GBE3:D1,R2 rep3


title: mA3BE3:D1,R2 rep3


title: F57_Treated larvae 10.0 ng EE2


title: human sample 166


title: human sample 157


title: human sample 156


title: human sample 159


title: human sample 151


title: human sample 154


title: hA3FBE3:D1,R2 rep3


title: hA3DCDA2-nSpCas9BE:D1,R2 rep3


title: human sample 150


title: human sample 148


title: hA3FCDA2-nSpCas9BE:D1,R2 rep3


title: human sample 155


title: human sample 153


title: F52_Treated larvae 10.0 ng EE2


title: human sample 152


title: human sample 146


title: human sample 147


title: F47_Treated larvae 10.0 ng EE2


title: hA3BCDA2-nSpCas9BE:D1,R2 rep3


title: hA3DBE3:D1,R2 rep3


title: F43_Treated larvae 10.0 ng EE2


title: hA3BBE3:D1,R2 rep3


title: NT:T1,E1,FF,S3,S4,DNT1,DNE1,FFa,FFd rep3,R2 rep2


title: human sample 149


title: mA3CDA1-nSpCas9BE:T1,E1,FF,S3,S4 rep3,R2 rep2


title: F48_Treated larvae 10.0 ng EE2


title: F38_Treated larvae 10.0 ng EE2


title: human sample 144


title: human sample 145


title: human sample 143


title: human sample 140


title: human sample 142


title: F42_Treated larvae 10.0 ng EE2


title: F37_Treated larvae 10.0 ng EE2


title: human sample 139


title: F28_Treated larvae 10.0 ng EE2


title: hA3GBE3:T1,E1,FF,S3,S4 rep3,R2 rep2


title: hA3GCDA2-nSpCas9BE:T1,E1,FF,S3,S4 rep3,R2 rep2


title: mA3BE3:T1,E1,FF,S3,S4 rep3,R2 rep2


title: human sample 135


title: human sample 141


title: human sample 137


title: F27_Treated larvae 10.0 ng EE2


title: human sample 138


title: F33_Treated larvae 10.0 ng EE2


title: F23_Treated larvae 10.0 ng EE2


title: human sample 134


title: hA3FBE3:T1,E1,FF,S3,S4 rep3,R2 rep2


title: hA3DCDA2-nSpCas9BE:T1,E1,FF,S3,S4 rep3,R2 rep2


title: human sample 131


title: F22_Treated larvae 10.0 ng EE2


title: SaC9+hA3A:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep2;hA3A-Y130F:PGM3 rep2


title: human sample 129


title: F18_Treated larvae 10.0 ng EE2


title: hA3FCDA2-nSpCas9BE:T1,E1,FF,S3,S4 rep3,R2 rep2


title: F17_Treated larvae 10.0 ng EE2


title: human sample 128


title: human sample 123


title: human sample 126


title: human sample 124


title: human sample 127


title: human sample 125


title: human sample 122


title: human sample 130


title: F13_Treated larvae 10.0 ng EE2


title: hA3BBE3:T1,E1,FF,S3,S4 rep3,R2 rep2


title: hA3DBE3:T1,E1,FF,S3,S4 rep3,R2 rep2


title: F08_Treated larvae 10.0 ng EE2


title: NT:T1,D1,E1,FF,S3,S4,DNT1,DNE1,FFa,FFd rep2


title: hA3BCDA2-nSpCas9BE:T1,E1,FF,S3,S4 rep3,R2 rep2


title: mA3CDA1-nSpCas9BE:T1,D1,E1,FF,S3,S4 rep2


title: F12_Treated larvae 10.0 ng EE2


title: F07_Treated larvae 10.0 ng EE2


title: F03_Treated larvae 10.0 ng EE2


title: hA3GCDA2-nSpCas9BE:T1,D1,E1,FF,S3,S4 rep2


title: human sample 115


title: human sample 114


title: human sample 113


title: F02_Treated larvae 10.0 ng EE2


title: mA3BE3:T1,D1,E1,FF,S3,S4 rep2


title: human sample 118


title: human sample 116


title: human sample 121


title: human sample 133


title: human sample 111


title: hA3GBE3:T1,D1,E1,FF,S3,S4 rep2


title: human sample 119


title: E63_Treated larvae 5.0 ng EE2


title: human sample 112


title: human sample 117


title: hA3FCDA2-nSpCas9BE:T1,D1,E1,FF,S3,S4 rep2


title: human sample 109


title: human sample 110


title: human sample 107


title: hA3FBE3:T1,D1,E1,FF,S3,S4 rep2


title: E62_Treated larvae 5.0 ng EE2


title: human sample 136


title: hA3DCDA2-nSpCas9BE:T1,D1,E1,FF,S3,S4 rep2


title: E58_Treated larvae 5.0 ng EE2


title: E57_Treated larvae 5.0 ng EE2


title: human sample 106


title: E53_Treated larvae 5.0 ng EE2


title: hA3BCDA2-nSpCas9BE:T1,D1,E1,FF,S3,S4 rep2


title: hA3DBE3 :T1,D1,E1,FF,S3,S4 rep2


title: hA3BBE3:T1,D1,E1,FF,S3,S4 rep2


title: E38_Treated larvae 5.0 ng EE2


title: NT:T1,D1,E1,FF,R2,S3,S4,DNT1,DNE1,FFa,FFd rep1


title: human sample 132


title: human sample 103


title: E37_Treated larvae 5.0 ng EE2


title: human sample 101


title: human sample 102


title: human sample 96


title: human sample 97


title: human sample 99


title: human sample 93


title: E33_Treated larvae 5.0 ng EE2


title: human sample 105


title: E32_Treated larvae 5.0 ng EE2


title: human sample 98


title: human sample 91


title: human sample 95


title: human sample 92


title: human sample 100


title: human sample 94


title: human sample 108


title: E28_Treated larvae 5.0 ng EE2


title: E52_Treated larvae 5.0 ng EE2


title: E27_Treated larvae 5.0 ng EE2


title: hA3GBE3:T1,D1,E1,FF,R2,S3,S4 rep1


title: mA3BE3:T1,D1,E1,FF,R2,S3,S4 rep1


title: E12_Treated larvae 5.0 ng EE2


title: human sample 88


title: human sample 90


title: mA3CDA1-nSpCas9BE:T1,D1,E1,FF,R2,S3,S4 rep1


title: hA3FBE3:T1,D1,E1,FF,R2,S3,S4 rep1


title: hA3FCDA2BE3:T1,D1,E1,FF,R2,S3,S4 rep1


title: hA3DCDA2-nSpCas9BE:T1,D1,E1,FF,R2,S3,S4 rep1


title: E08_Treated larvae 5.0 ng EE2


title: E07_Treated larvae 5.0 ng EE2


title: human sample 87


title: human sample 89


title: human sample 86


title: human sample 81


title: human sample 85


title: E03_Treated larvae 5.0 ng EE2


title: hA3BCDA2-nSpCas9BE:T1,D1,E1,FF,R2,S3,S4 rep1


title: E02_Treated larvae 5.0 ng EE2


title: human sample 82


title: human sample 83


title: hA3BBE3:T1,D1,E1,FF,R2,S3,S4 rep1


title: human sample 84


title: hA3DBE3:T1,D1,E1,FF,R2,S3,S4 rep1


title: human sample 80


title: human sample 79


title: human sample 78


title: D63_Treated larvae 2.5 ng EE2


title: human sample 77


title: D62_Treated larvae 2.5 ng EE2


title: D58_Treated larvae 2.5 ng EE2


title: human sample 75


title: human sample 73


title: RNA-seq of DNTET1 mA3CDA1-mA3dCDI-nSpCas9-BE rep2

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh38/hg38 human or GRCm38/mm10 mouse reference genome using BWA-MEM 0.7.9a.
Genome_build: hg38 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: Number of off-target mutations (Base Substitutions)

source_name: 293FT_DNTET1 mA3CDA1-mA3dCDI-nSpCas9-BE

growth_protocol: 293FT cells from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination. All mice were housed under specific pathogen-free conditions at the animal facilities of Medical Research Institute, Wuhan University. All mouse studies were approved by the Animal Care Committees of Medical Research Institute, Wuhan University.

extract_protocol:
Total RNAs were extracted from human 293FT cells and mouse livers tissues by using TransZol® Up Plus RNA Kit (ER501-01, TransGen)
For total RNA-seq, DNA libraries were prepared by using the NEBNext Ultra II FS DNA Library Prep for Illumina, and sequencing by using the Illumina HiSeq X Ten (2×150) at CAS-MPG Partner Institute for Computational Biology Omics CoreIndexed RNA libraries were prepared by using the TruSeq Stranded Total RNA with Ribo-Zero Globin. RNA-seq libraries were sequenced on an Illumina HiSeq X Ten (2×150) at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: After 40hr after transfection, Cells in the first 15% of the fluorescence intensity were sorted by FACSAriaIII.

tag: cell line/tissue

value: DNTET1 mA3CDA1-mA3dCDI-nSpCas9-BE


title: human sample 72


title: RNA-seq of DNTET1 mA3CDA1-mA3dCDI-nSpCas9-BE rep1


title: human sample 76


title: human sample 104


title: D57_Treated larvae 2.5 ng EE2


title: RNA-seq of DNTET1 mA3dCDI-nSpCas9-BE rep1

source_name: 293FT_DNTET1 mA3dCDI-nSpCas9-BE

value: DNTET1 mA3dCDI-nSpCas9-BE


title: D53_Treated larvae 2.5 ng EE2


title: human sample 120


title: human sample 74


title: human sample 70


title: RNA-seq of DNTET1 mA3CDA1-nSpCas9-BE rep2

source_name: 293FT_DNTET1 mA3CDA1-nSpCas9-BE

value: DNTET1 mA3CDA1-nSpCas9-BE


title: D52_Treated larvae 2.5 ng EE2


title: human sample 71


title: RNA-seq of DNTET1 mA3dCDI-nSpCas9-BE rep2


title: human sample 66


title: human sample 65


title: human sample 67


title: RNA-seq of DNTET1 tBE-V5-mA3 rep3

source_name: 293FT_DNTET1 tBE-V5-mA3

value: DNTET1 tBE-V5-mA3


title: human sample 69

source_name: serum


title: human sample 64


title: human sample 68


title: human sample 63


title: RNA-seq of DNTET1 tBE-V5-mA3 rep2


title: D38_Treated larvae 2.5 ng EE2


title: RNA-seq of DNTET1 tBE-V5-mA3 rep1


title: RNA-seq of DNTET1 mA3CDA1-nSpCas9-BE rep1


title: D32_Treated larvae 2.5 ng EE2


title: D37_Treated larvae 2.5 ng EE2


title: D28_Treated larvae 2.5 ng EE2


title: RNA-seq of DNTET1 tBE-V5-rA1 rep3

source_name: 293FT_DNTET1 tBE-V5-rA1

value: DNTET1 tBE-V5-rA1


title: D33_Treated larvae 2.5 ng EE2


title: human sample 60


title: human sample 56


title: human sample 55


title: human sample 58


title: RNA-seq of DNTET1 tBE-V5-rA1 rep2


title: D12_Treated larvae 2.5 ng EE2


title: hA3GCDA2-nSpCas9BE:T1,D1,E1,FF,R2,S3,S4 rep1

tag: cell line


title: human sample 57


title: human sample 54


title: human sample 59


title: human sample 53


title: human sample 51


title: RNA-seq of DNTET1 tBE-V5-rA1 rep1

tag: treatment


title: human sample 61


title: human sample 52


title: human sample 50


title: RNA-seq of DNTET1 BE4max-YE1 rep2

source_name: 293FT_DNTET1 BE4max-YE1

value: DNTET1 BE4max-YE1


title: D27_Treated larvae 2.5 ng EE2


title: D13_Treated larvae 2.5 ng EE2


title: D08_Treated larvae 2.5 ng EE2


title: RNA-seq of DNTET1 BE4max-YE1 rep1


title: RNA-seq of DNTET1 BE4max-YE1 rep3


title: D07_Treated larvae 2.5 ng EE2


title: RNA-seq of DNTET1 hA3A-BE3-Y130F rep3

source_name: 293FT_DNTET1 hA3A-BE3-Y130F

value: DNTET1 hA3A-BE3-Y130F


title: D03_Treated larvae 2.5 ng EE2


title: D02_Treated larvae 2.5 ng EE2


title: human sample 45


title: [InflammationPLUSPanel] BALB_Brain_56dpi_rep2

city: Riverside

first: Emma

middle: Harriet

last: Wilson

state: CA

address: 900 University Avenue

institute: UC Riverside

description: 50ug RNA was loaded for each sample, Naïve samples were used as reference samples for comparison in analysis

hyb_protocol: Briefly, panel codeset probes were hybridized with 150ng of total RNA per brain over 18hr at 65C according to NanoString protocol. Inclusion of a customized PLUS codeset in the Inflammation panel required additional Reporter and Capture Plus codesets to be added during the hybridization reaction (NanoString User Manual C0019-08).

scan_protocol: Hybridized RNA was then diluted in molecular grade water and loaded into nCounter SPRINT cartridge (NanoString), placed into nCounter SPRINT Profiler, and quantified.  RNA-conjugated probes were counted via NanoString Sprint Profiler technology.

data_processing: Results from each panel were merged into one data file for comparative analysis, normalized in nSolver following best practices, and analyzed using nSolver and Advanced Analysis software according to previously published protocols (Danaher et al. 2017). nSolver-generated heat maps were created using normalized (merged) data and agglomerative clustering, a bottom-up form of hierarchical clustering (NanoString User Manual C0019-08). For Advanced Analysis, normalized merged data was used (NanoString User Manual 10030-03). Differential expression (DE) analysis was performed to identify specific targets that exhibit significantly increased or decreased expression in response to naïve control values or, in the case of BALB/c C57BL/6 comparison, to C57BL/6 control values at each time point. Gene set analysis was run to determine the change in direction of regulation within each pre-defined gene set relative to naïve controls. Global significance scores, a summary T-statistic used to measure change (NanoString User Manual 10030-03) were calculated, and the directed global significance scores were expressed via heatmap. Cell type profiling module analysis was conducted to determine the relative abundance in classically activated cell types during infection using genes assigned to each cell type: T cells (CD3e, CD6, CD3g, TRAT1, and CD3d), CD8+ T cells (CD8a), macrophages (CD68 and CD84), and microglia (GPR84, LRRC25, IRF8, NCF1, TNF, TLR2, and TNF.1). NanoString cell type profiling is a validated method to measure relative abundance of up to 24 different immune cell types, with high concordance to flow cytometry (Danaher et al. 2017). Pathway analysis was also conducted to determine overall changes in pathways based on the first principal component of the targets within a pathway as annotated by NanoString (NanoString User Manual 10030-03). Direction of pathway change (up- or downregulated) was determined by cross referencing the pathway score with the corresponding volcano plot for that pathway. Summary pathway score plot colors are based on calculated scores and are represented as downregulation (blue) to upregulation (orange). Statistical significance was determined using R software.

label: codeset probes

organism: Mus musculus

label_protocol: nCounter gene expression assays (NanoString Technologies) were performed for the NanoString Neuropathology panel. Samples were labelled with panel-specific codeset probes.

growth_protocol: The ME49 strain of T. gondii was maintained in cyst form by continuous passaging in SW and CBA background mice. Female 6-8 week old WT C57BL/6 and WT BALB/c mice were infected with 10 ME49 cysts per mouse in 200μl of sterile 1x PBS solution via intraperitoneal (IP) injection. Naïve controls received 200µl of sterile 1x PBS solution via intraperitoneal (IP) injection.

extract_protocol: RNA from brain lysate of naïve, 2 week infected, 4 week infected, and 8 week infected C57BL/6 and BALB/c mice (n=3 for all groups) was collected using Trizol extraction method. Whole brain was dissected and homogenized in 1mL Trizol. Phase separation was completed by adding 200µl of chloroform and incubating at room temperature for 2-3 minutes. Samples were centrifuged at 12,000xg for 15 minutes at 4°C, and upper aqueous phase was collected followed by RNA precipitation using 500µl isopropyl alcohol. Samples incubated at room temperature for 10 minutes followed by centrifugation. RNA pellet was washed with 1mL of 75% ethanol twice. All supernatant was discarded and RNA pellet was dissolved in 100µl of nuclease free water. RNA concentration for each sample was determined using a NanoDrop 2000, and RNA samples normalized to a concentration of 10ng/μL in molecular grade water.

treatment_protocol: At each time point, mice were sacrificed and perfused intracardially with 20mL of sterile 1x PBS.

value: Brain

tag: mouse strain

value: BALB/c

tag: infection time point


title: [InflammationPLUSPanel] BALB_Brain_56dpi_rep3


title: human sample 47


title: human sample 48


title: human sample 49


title: human sample 44


title: RNA-seq of DNTET1 hA3A-BE3-Y130F rep1


title: human sample 43


title: RNA-seq of DNTET1 hA3A-BE3-Y130F rep2


title: C73_Treated larvae 1.2 ng EE2


title: [InflammationPLUSPanel] BALB_Brain_56dpi_rep1


title: [InflammationPLUSPanel] BALB_Brain_28dpi_rep3


title: RNA-seq of DNTET1 BE3 rep2

source_name: 293FT_DNTET1 BE3

value: DNTET1 BE3


title: [InflammationPLUSPanel] BALB_Brain_28dpi_rep2


title: [InflammationPLUSPanel] BALB_Brain_28dpi_rep1


title: C68_Treated larvae 1.2 ng EE2


title: human sample 62


title: C72_Treated larvae 1.2 ng EE2


title: RNA-seq of DNTET1 BE3 rep1


title: human sample 41


title: human sample 42


title: [InflammationPLUSPanel] BALB_Brain_14dpi_rep3


title: human sample 40


title: RNA-seq of DNTET1 BE3 rep3


title: C67_Treated larvae 1.2 ng EE2


title: human sample 46


title: RNA-seq of DNTET1 Cas9 rep3

source_name: 293FT_DNTET1 Cas9

value: DNTET1 Cas9


title: [InflammationPLUSPanel] BALB_Brain_14dpi_rep2


title: RNA-seq of DNTET1 Cas9 rep2


title: RNA-seq of DNTET1 ctrl rep5

source_name: 293FT_DNTET1 ctrl

value: DNTET1 ctrl


title: C62_Treated larvae 1.2 ng EE2


title: C63_Treated larvae 1.2 ng EE2


title: [InflammationPLUSPanel] BALB_Brain_14dpi_rep1


title: C58_Treated larvae 1.2 ng EE2


title: [InflammationPLUSPanel] BALB_Brain_Naive_rep3

value: Naive


title: RNA-seq of DNTET1 ctrl rep4


title: C53_Treated larvae 1.2 ng EE2


title: [InflammationPLUSPanel] BALB_Brain_Naive_rep2


title: human sample 38


title: [InflammationPLUSPanel] B6_Brain_56dpi_rep3


title: C52_Treated larvae 1.2 ng EE2


title: RNA-seq of DNTET1 ctrl rep3


title: human sample 33


title: [InflammationPLUSPanel] BALB_Brain_Naive_rep1


title: human sample 34


title: human sample 36


title: human sample 39


title: human sample 37


title: RNA-seq of DNTET1 ctrl rep2


title: C48_Treated larvae 1.2 ng EE2


title: C57_Treated larvae 1.2 ng EE2


title: RNA-seq of DNTET1 ctrl rep1


title: [InflammationPLUSPanel] B6_Brain_56dpi_rep1


title: C43_Treated larvae 1.2 ng EE2


title: RNA-seq of PGM3 tBE-V5-mA3 rep3

source_name: 293FT_PGM3 tBE-V5-mA3

value: PGM3 tBE-V5-mA3


title: human sample 32


title: [InflammationPLUSPanel] B6_Brain_56dpi_rep2


title: C47_Treated larvae 1.2 ng EE2


title: human sample 31


title: RNA-seq of PGM3 tBE-V5-mA3 rep2


title: [InflammationPLUSPanel] B6_Brain_28dpi_rep3


title: C42_Treated larvae 1.2 ng EE2


title: RNA-seq of PGM3 tBE-V5-mA3 rep1


title: [InflammationPLUSPanel] B6_Brain_28dpi_rep2


title: RNA-seq of PGM3 tBE-V5-rA1 rep2

source_name: 293FT_PGM3 tBE-V5-rA1

value: PGM3 tBE-V5-rA1


title: [InflammationPLUSPanel] B6_Brain_28dpi_rep1


title: [InflammationPLUSPanel] B6_Brain_14dpi_rep3


title: C37_Treated larvae 1.2 ng EE2

value: whole larva


title: [InflammationPLUSPanel] B6_Brain_14dpi_rep2


title: [InflammationPLUSPanel] B6_Brain_14dpi_rep1


title: C33_Treated larvae 1.2 ng EE2

value: mRNA


title: human sample 30


title: human sample 29


title: human sample 28


title: human sample 26


title: human sample 35


title: RNA-seq of PGM3 tBE-V5-rA1 rep1


title: RNA-seq of PGM3 BE4max-YE1 rep1

source_name: 293FT_PGM3 BE4max-YE1

value: PGM3 BE4max-YE1


title: human sample 27


title: human sample 25


title: C38_Treated larvae 1.2 ng EE2


title: RNA-seq of PGM3 BE4max-YE1 rep3


title: RNA-seq of PGM3 hA3A-BE3-Y130F rep3

source_name: 293FT_PGM3 hA3A-BE3-Y130F

value: PGM3 hA3A-BE3-Y130F


title: C28_Treated larvae 1.2 ng EE2


title: C32_Treated larvae 1.2 ng EE2


title: C27_Treated larvae 1.2 ng EE2


title: human sample 24


title: [InflammationPLUSPanel] B6_Brain_Naive_rep3


title: C23_Treated larvae 1.2 ng EE2


title: RNA-seq of PGM3 hA3A-BE3-Y130F rep2


title: C18_Treated larvae 1.2 ng EE2


title: C22_Treated larvae 1.2 ng EE2


title: RNA-seq of PGM3 hA3A-BE3-Y130F rep1


title: [InflammationPLUSPanel] B6_Brain_Naive_rep2


title: C17_Treated larvae 1.2 ng EE2


title: RNA-seq of PGM3 BE3 rep2

source_name: 293FT_PGM3 BE3

value: PGM3 BE3


title: RNA-seq of PGM3 BE3 rep3


title: C13_Treated larvae 1.2 ng EE2

source_name: Whole 96h post-hatch larva


title: [InflammationPLUSPanel] B6_Brain_Naive_rep1


title: T584_T2D

city: Madison

first: Barak

last: Blum

state: Wisconsin

address: 4551 WIMR II, 1111 Highland Ave.

institute: University of Wisconsin-Madison

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X584_S21

data_processing:
bcl2fastq v2.20.0.422 was used for basecalling.
Sequencing reads were aligned to mm10 using Bowtie-1.2.2 and quantified using RSEM-1.3.0 under default RSEM parameter settings. single samples and paired-end samples were processed separately.
The expected count (EC) matrice for the single batch and paired-end batch  were combined together.
The combined EC matrix was pre-filtered where genes with average expression less than 1 were removed.
The filtered EC matrix was then normalized using median-by-ratio normalization, implemented in R package EBSeq-1.29.0.
Genome_build: mm10
Supplementary_files_format_and_content: Raw and normalized gene-by-sample count matrices in TXT format

source_name: Pancreatic β cell

extract_protocol:
Mouse islets were digested from pancreatas and purified by Histopague gradient centrifugation. The isolated islets were trypsized and sorted through flow cytometer for  mCherry+ cells (β cells). The RNA extraction was performed on sorted cells via TRIzol phenol-chloroform or Qiagen silica gel spin column.
Ultra-low RNA input libraries are generated using the Takara “SMART-Seq v4 Low Input RNA Kit for Sequencing” (Takara, Mountain View, CA, USA) for cDNA synthesis and the Illumina NexteraXT DNA Library Preparation (Illumina, SanDiego, CA, USA) kit for cDNA dual indexing.  Full length cDNA fragments are generated from 1-10ng total RNA by the Takara SMART (Switching Mechanism at 5’ End of RNA Template) technology.  cDNA fragments are fragmented  and dual indexed in a single step by taking advantage of the Nextera kit’s simultaneous transposon and tagmentation step. Libraries were standardized to 2nM.

tag: strain

value: BTBR/mix

value: Pancreas

tag: cell type

value: Pancreatic beta cell

value: adult day 71

tag: Sex

value: female

tag: blood glucose (mg/dl)

tag: weight (g)

tag: genotype

value: Cherry/+; Ins2-Cre/+; Ob/Ob

tag: disease state

value: type-2 diabetic

tag: rna extraction

value: TRIzol-phenol chloroform


title: T598.9.27.18_T2D

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X598.2019_S80

tag: age

value: adult day 70

value: male

value: Cherry/+; Ins2-Cre/Ins2-Cre; Ob/Ob


title: T569_T2D

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X569_S18

value: adult day 66


title: RNA-seq of PGM3 BE3 rep1


title: C12_Treated larvae 1.2 ng EE2

value: whole larva

tag: experiment

tag: treatment (ng ee2/l)


title: Q758_T2D

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X758_S36

tag: tissue

value: adult day 78

value: Qiagen RNeasy Plus Mini Kit


title: Q548_T2D

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X548_S17

value: adult day 60


title: RNA-seq of PGM3 ctrl rep3

source_name: 293FT_PGM3 ctrl

tag: cell line/tissue

value: PGM3 ctrl


title: RNA-seq of PGM3 ctrl rep2


title: Q279_T2D

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X279_S5

value: BTBR/mix

value: adult day 77


title: human sample 20


title: human sample 18


title: C2C12_long_1k

city: Irvine

first: Elisabeth

last: Rebboah

address: 2300E Biological Sciences 3

department: Developmental and Cell Biology

institute: University of California, Irvine

description: C2C12 myoblast cells, myoblast nuclei, and myotube nuclei were collected for Split-seq and dispersed into 48 wells of a 96 well plate containing unique barcodes per well (12 wells of myoblast cells, 12 wells of myoblast nuclei, and 24 wells of myotube nuclei). Library preparation was performed following manufacturer’s instructions for the Single Cell Whole Transcriptome Kit, where the cells are mixed for the next 2 sets of barcoding reactions followed by sublibrary generation. A mix of 1,000 cells was set aside for this sublibrary which was processed into cDNA followed by sequencing with PacBio long reads.

data_processing:
PacBio long-Split-seq: : Reads were processed into circular consensus reads using the CCS software from the SMRT analysis software suite (--skip-polish --min-length=10 --min-passes=3 --min-rq=0.9 --min-snr=2.5) (https://github.com/PacificBiosciences/ccs)
PacBio long-Split-seq: Split-seq adapters were identified with Lima (v2.0.0) (--ccs --min-score 0 --min-end-score 0 --min-signal-increase 0 --min-score-lead 0) (https://github.com/pacificbiosciences/barcoding/)
PacBio long-Split-seq: Reads were then run through IsoSeq3's Refine (v3.4.0) to yield full-length non-chimeric reads, without the polyA tail requirement, as half of the Split-seq primers used are random hexamer (https://github.com/PacificBiosciences/IsoSeq)
PacBio long-Split-seq: Reads were demultiplexed using a custom version of the Split-seq pipeline modified to work with long reads. (https://github.com/fairliereese/pacbio-splitpipe)
PacBio long-Split-seq: Reads were mapped with minimap2 (v2.17-r94) (-ax splice:hq -uf --MD)
PacBio long-Split-seq: Long-read sequencing artifacts were corrected with TranscriptClean (--canonOnly --primaryOnly)
PacBio long-Split-seq: Reads were run through TALON to annotate each read to its gene and transcript of origin with GENCODE vM21 (cb_tag branch on GitHub, https://github.com/mortazavilab/TALON/tree/cb_tag) (--cb)
PacBio long-Split-seq: Genes were quantified by using TALON's abundance matrix tool and aggregating counts for each gene
PacBio long-Split-seq: Transcripts were filtered for those that were reproducible across cells using TALON's filtering options.
PacBio long-Split-seq: Filtered transcripts were used to make the transcript-level abundance matrix using TALON's abundance matrix module
PacBio long-Split-seq: Filtered transcripts were used to create the transcriptome GTF of transcripts that were present across the entire dataset.
PacBio long-Split-seq: Scanpy was used to cluster, normalize, and generate AnnData h5ad gene and transcript-level expression matrices.
Illumina Split-seq: Reads were demultiplexed into 7 sublibraries using bcl2fastq and the provided adapter sequences.
Illumina Split-seq: Parse Biosciences' analysis software was run on the C2C12_short_1k sublibrary: split-pipe --mode all --genome_dir genomes/mm10/ --fq1 expdata/C2C12_short_1k_R1.fastq.gz --fq2 expdata/C2C12_short_1k_R2.fastq.gz --output_dir analysis/C2C12_short_1k --sample MB_cells A1-A12 --sample MB_nuclei B1-B12 --sample MT_nuclei C1-D12
Illumina Split-seq: Parse Biosciences' analysis software was run on the C2C12_short_9kA sublibrary: split-pipe --mode all --genome_dir genomes/mm10/ --fq1 expdata/C2C12_short_9kA_R1.fastq.gz --fq2 expdata/C2C12_short_9kA_R2.fastq.gz --output_dir analysis/C2C12_short_9kA --sample MB_cells A1-A12 --sample MB_nuclei B1-B12 --sample MT_nuclei C1-D12
Illumina Split-seq: Parse Biosciences' analysis software was run on the C2C12_short_9kB sublibrary: split-pipe --mode all --genome_dir genomes/mm10/ --fq1 expdata/C2C12_short_9kB_R1.fastq.gz --fq2 expdata/C2C12_short_9kB_R2.fastq.gz --output_dir analysis/C2C12_short_9kB --sample MB_cells A1-A12 --sample MB_nuclei B1-B12 --sample MT_nuclei C1-D12
Illumina Split-seq: Parse Biosciences' analysis software was run on the C2C12_short_9kC sublibrary: split-pipe --mode all --genome_dir genomes/mm10/ --fq1 expdata/C2C12_short_9kC_R1.fastq.gz --fq2 expdata/C2C12_short_9kC_R2.fastq.gz --output_dir analysis/C2C12_short_9kC --sample MB_cells A1-A12 --sample MB_nuclei B1-B12 --sample MT_nuclei C1-D12
Illumina Split-seq: Parse Biosciences' analysis software was run on the C2C12_short_9kD sublibrary: split-pipe --mode all --genome_dir genomes/mm10/ --fq1 expdata/C2C12_short_9kD_R1.fastq.gz --fq2 expdata/C2C12_short_9kD_R2.fastq.gz --output_dir analysis/C2C12_short_9kD --sample MB_cells A1-A12 --sample MB_nuclei B1-B12 --sample MT_nuclei C1-D12
Illumina Split-seq: Parse Biosciences' analysis software was run on the C2C12_short_9kE sublibrary: split-pipe --mode all --genome_dir genomes/mm10/ --fq1 expdata/C2C12_short_9kE_R1.fastq.gz --fq2 expdata/C2C12_short_9kE_R2.fastq.gz --output_dir analysis/C2C12_short_9kE --sample MB_cells A1-A12 --sample MB_nuclei B1-B12 --sample MT_nuclei C1-D12
Illumina Split-seq: Parse Biosciences' analysis software was run on the C2C12_short_9kF sublibrary: split-pipe --mode all --genome_dir genomes/mm10/ --fq1 expdata/C2C12_short_9kF_R1.fastq.gz --fq2 expdata/C2C12_short_9kF_R2.fastq.gz --output_dir analysis/C2C12_short_9kF --sample MB_cells A1-A12 --sample MB_nuclei B1-B12 --sample MT_nuclei C1-D12
Genome_build: mm10
Supplementary_files_format_and_content: Long-split-seq Scanpy h5ad file with normalized gene or transcript-level expression values
Supplementary_files_format_and_content: GTF of long-Split-seq transcript model structure
Supplementary_files_format_and_content: For Illumina Split-seq, Parse Biosciences analysis software (split-pipe) outputs are sparse cell-by-gene expression matrices in counts with corresponding cell metadata and a list of expressed genes (columns of expression matrix).

molecule: polyA RNA

growth_protocol: C2C12 cells  (ATCC, CRL-1772) were cultured on 10 cm plates  in 10 mL myoblast growth media: high-glucose DMEM with L-glutamine and without sodium pyruvate, supplemented with 20% fetal bovine serum, 100 units/mL penicillin, and 100 ug/mL streptomycin. Cells were maintained at 20-50% confluency at 37C with 5% CO2 and passaged at 1:3 or 1:4 every 2 to 3 days.

extract_protocol:
Cells were rinsed with 1X PBS and incubated with 2 mL TrypLE-Express for 5 minutes at 37C, which was then neutralized with 8 mL myoblast growth media. RNA was reverse transcribed in situ and barcoded cDNA was extracted following Parse Biosciences’ Single Cell Whole Transcriptome Kit (also called Split-seq).
PacBio long-Split-seq: SMRTbell Template Prep Kit (PacBio, 100-938-900) following manufacturer's protocol with 500 ng of amplified, barcoded cDNA. Illumina Split-seq: Parse Biosciences’ Single Cell Whole Transcriptome Kit (also called Split-seq).
scRNA-seq

treatment_protocol:
Differentiation of C2C12, ENCODE (https://www.encodeproject.org/documents/b42974fd-1490-4d51-bdcf-7db97a3e8fe0/@@download/attachment/C2C12_Wold_protocol.pdf)
To differentiate myoblasts to myotubes, cells at 90-100% confluency were rinsed with 1X PBS and myoblast growth media was replaced with 10 mL differentiation media: high-glucose DMEM with L-glutamine and without sodium pyruvate, supplemented with 2% donor horse serum, 100 units/mL penicillin, 100 ug/mL streptomycin, and freshly-added 1uM insulin. Differentiation media was replaced every 24 hours for 3 days. ENCODE protocol: https://www.encodeproject.org/documents/b42974fd-1490-4d51-bdcf-7db97a3e8fe0/@@download/attachment/C2C12_Wold_protocol.pdf

tag: celltype

value: myoblast, myotube

tag: cell line

tag: library prep protocol

value: scRNA-seq protocol; long-Split-seq (this paper).


title: human sample 19


title: human sample 21


title: human sample 17


title: human sample 23


title: human sample 16


title: C07_Treated larvae 1.2 ng EE2

tag: molecule subtype

value: mRNA


title: C03_Treated larvae 1.2 ng EE2


title: human sample 14


title: T729_T2D

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X729_S17

tag: strain

value: Pancreas

value: Pancreatic beta cell

value: adult day 58

value: female

value: Cherry/+; Ins2-Cre/+; Ob/Ob


title: RNA-seq of PGM3 ctrl rep1

tag: treatment


title: Q765_T1D

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X765_S39

value: NOD-ICR

tag: cell type

value: adult day 133

tag: Sex

value: male

value: Cherry/+; Ins2-Cre/+

value: type-1 diabetic


title: C02_Treated larvae 1.2 ng EE2

value: whole larva


title: C08_Treated larvae 1.2 ng EE2


title: human sample 15


title: human sample 22


title: Q393_T1D

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X393_S8

value: adult day 150

tag: blood glucose (mg/dl)

tag: weight (g)

value: Qiagen RNeasy Plus Mini Kit


title: Q762_T1D

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X762_S38

value: adult day 98

tag: genotype

tag: disease state


title: LUBB+1 at D6, biological rep2

city: Göteborg

first: Xin

last: Chen

address: Kemigården 4

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description: Gene expression data from day 6.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45˚C on Yeast 2.0 Array. GeneChips were washed and stained in Affymetrix  Gene Chip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: The data was analyzed by Bioconductor and R version 3.2.3.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae at day 6.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA (3' IVT Plus Reaagent Kit, PN#902415).

growth_protocol: shake flask, 30 ˚C,200rpm.

extract_protocol: Total RNA was extracted using RNAeasy Mini Kit with a FastPrep homogenizer to disrupt cells.

treatment_protocol: Samples of cells were frozen rapidly in liquid nitrogen to prevent mRNA turnover.


title: T222_T1D

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X222_S3

tag: age

value: adult day 145

tag: rna extraction

value: TRIzol-phenol chloroform


title: Q897_T1ND

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X897_S48

value: adult day 103

value: type-1 non-diabetic


title: human sample 13


title: B57_Treated larvae 0.12 ng EE2

tag: experiment

tag: treatment (ng ee2/l)

value: mRNA


title: B58_Treated larvae 0.12 ng EE2

tag: tissue


title: B53_Treated larvae 0.12 ng EE2


title: Q768_T1ND

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X768_S40

value: Pancreas

value: Pancreatic beta cell

value: adult day 212


title: Q896_T1ND

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X896_S47

value: NOD-ICR

value: adult day 82

value: female


title: LUBB+1 at D6, biological rep1

description: Gene expression data from day 6.


title: LUBB+1 at EX, biological rep2

description: Gene expression data from exponential phase.

source_name: Saccharomyces cerevisiae at exponential phase.


title: human sample 12

source_name: serum


title: B62_Treated larvae 0.12 ng EE2


title: LUBB+1 at EX, biological rep1


title: human sample 11


title: B52_Treated larvae 0.12 ng EE2


title: human sample 10


title: human sample 9


title: control at D6 (LUBB), biological rep2

description: Gene expression data from day 6.


title: control at D6 (LUBB), biological rep1

description: Gene expression data from day 6.


title: Q759_T1ND

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X759_S37

value: Cherry/+; Ins2-Cre/+


title: ZFmut ZBTB7B rep-3

city: Houston

first: Won-Seok

last: Lee

state: TX

address: One Baylor Plaza

department: MHG

institute: Baylor College of Medicine

description: Overexpression via lentiviral transduction

data_processing:
Illumina HiSeq software used for basecalling
These raw reads were first groomed by trimming adapter sequences with Cutadapt. Trimmed reads were then aligned to the Mus musculus genome (GRCh38, GENCODE, version24) using TopHat v2.0.9 with default parameters (-r 200 –p 8)
Expression level for each gene was estimated using Python program HTSeq (Anders et al., Bioinformatics 2014). Specifically htseq-count function of HTSeq accumulated the number of aligned reads that falls under
Using the obtained read counts, differential gene analyses were carried out using the DESeq2 package in the R environment.
Genome_build: GRCh38, GENCODE, version24
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

source_name: Daoy cells

growth_protocol: Cells were seeded in a 12-well plate and incubated in complete DMEM (10% FBS, 1X Antibiotic-Antimycotic) for 4 days

extract_protocol:
Total RNA was extracted using AurumTM Total RNA Fatty and Fibrous Tissue kit (Bio-Rad)
Two micrograms of total RNA was used to prepare sequencing libraries by using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB), following the manufacturer’s protocol

treatment_protocol: In the next day after seeding, concentrated lentivirus were transduced with an MOI of 15, and incubated for 72 hr

tag: disease

value: Human brain cancer

value: Daoy

value: zinc-finger domain mutant (R363L) ZBTB7B


title: human sample 8


title: control at EX (LUBB), biological rep2


title: B37_Treated larvae 0.12 ng EE2

value: whole larva


title: ZFmut ZBTB7B rep-2

tag: cell line


title: B33_Treated larvae 0.12 ng EE2


title: ZFmut ZBTB7B rep-1


title: Q225_T1ND

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X225_S4

value: adult day 131

value: Qiagen RNeasy Plus Mini Kit


title: human sample 6


title: RNA-seq of PGM3 BE4max-YE1 rep2

tag: cell line/tissue

value: PGM3 BE4max-YE1


title: B28_Treated larvae 0.12 ng EE2

tag: molecule subtype


title: WT ZBTB7B rep-2

value: wild-type ZBTB7B


title: control at EX (LUBB), biological rep1

tag: strain


title: B32_Treated larvae 0.12 ng EE2


title: human sample 4


title: T542_T2H

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X542_S16

value: BTBR

value: adult day 148

value: Cherry/+; Ins2-Cre/+; Ob/+

value: wild type

value: TRIzol-phenol chloroform


title: Q918_T2H

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X918_S50

value: Pancreas

value: Pancreatic beta cell

value: adult day 179

value: male


title: human sample 3


title: B27_Treated larvae 0.12 ng EE2

value: mRNA


title: WT ZBTB7B rep-3

value: Human brain cancer

value: Daoy


title: WT ZBTB7B rep-1


title: human sample 1


title: human sample 2


title: T539_T2H

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X539_S15

value: adult day 83

value: female


title: T549.1_T2H

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X549.1_S69

value: adult day 112


title: T509_T2H

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X509_S10

value: adult day 53

value: Cherry/+; Ins2-Cre/Ins2-Cre; Ob/+


title: T507_T2H

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X507_S9

value: BTBR


title: B13_Treated larvae 0.12 ng EE2

value: whole larva


title: T300.1_T2H

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X300.1_S62

value: adult day 141

value: Cherry/+; Ins2-Cre/+; Ob/+


title: Q891_T1ND

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X891_S46

value: NOD-ICR

value: adult day 82

value: Cherry/+; Ins2-Cre/+

value: type-1 non-diabetic

value: Qiagen RNeasy Plus Mini Kit


title: T286.1_T2H

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X286.1_S61

value: Pancreas

value: Pancreatic beta cell

value: adult day 142

value: wild type

value: TRIzol-phenol chloroform


title: B07_Treated larvae 0.12 ng EE2

value: mRNA


title: A73_Control larvae


title: B02_Treated larvae 0.12 ng EE2


title: B08_Treated larvae 0.12 ng EE2


title: B12_Treated larvae 0.12 ng EE2


title: A72_Control larvae


title: Q890_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X890_S45

value: ICR

value: adult day 162

value: male


title: A68_Control larvae

value: whole larva


title: T737_T2H

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X737_S18

value: BTBR

value: adult day 56

value: female


title: CTRL_iPSC_2

first: Bruce

middle: J

last: Aronow

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.  Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence and converted into read1 and read2 fastq files from each sample.
RNA-seq reads were aligned to a combined human + mouse transcriptome reference (Ensembl Mus_musculus GRCm38 and Homo_sapiens. GRCh38 transcriptomes v94) using the stranded library option of Kallisto v0.46.0 (Bray et al., 2016) using a concatenated mouse-human index. Based on comparisons with pure mouse and human RNA samples, the Kallisto pseudo-alignment algorithm was able to accurately distinguish and assign transcripts to the proper species reference.
From each Kallisto-processed mouse-human RNAseq sample, an expression matrix was constructed to generate human-specific TPMs (transcripts per million) as follows. Human transcript counts and TPM values were extracted and adjusted based on (1) per million human reads per mouse-human sample; (2) transcript-level TPM values were summed per gene; (3) gene TPM values were converted to log2(TPM+1) values, (4) 19,701 genes were selected with log2(TPM+1) ≥ 1 in at least one of the thirty samples, and (5) the resulting gene-level values were per-sample quantile-polished to reduce sample-sample variability (Zyprych-Walczak et al., 2015).  Genes for subsequent analyses were selected from 17,004 gene IDs with log2(TPM+1) ≥ 2 in at least one of the thirty samples. Below we refer to log2(TPM+1) values as “logTPM” values.
DEG analyses used “moderated” t-tests as implemented in limma v3.42.2 (Law et al., 2014) with the limma-trend procedure (fit = eBayes(fit, trend = TRUE)) that uses an Empirical Bayes Model to effect “shrinkage of the estimated sample variances towards a pooled estimate” (Smyth 2004) which can increase power in the face of culture-culture variability. The use of this approach on logTPM data is conservative, which we consider appropriate with a small cohort. R scripts for DEG analyses are included as supplementary material.
Genome_build: Ensembl Mus_musculus GRCm38 and Homo_sapiens. GRCh38 transcriptomes v94.
Supplementary_files_format_and_content: Kallisto output file

source_name: iPSC

growth_protocol: Neurons were generated from feeder-dependent iPS cells: (Day -1) iPS cells were plated and infected on Matrigel coated 24-well plate. Per 6-well of iPS cells grown on feeders, cells were washed 1x with PBS. 0.5 ml of CTK (0.25% Trypsin no phenol red, 0.1 mg/ml collagenase IV, 0.5 ml 1 mM CaCl2, 20% KnockOut Serum Replacement in sterile water) was added to remove the feeders at 37°C until feeder cells lift off. CTK was removed and washed 2x with PBS. iPS cells were treated with 0.5 ml Accutase briefly, resuspended in 1 ml hES media and spun down at 150 g x 5 min. Cell pellets were resuspended in 50% hES media/50% mTeSR plus Y-27632, and lentiviruses. Typically 200,000 - 300,000 cells were plated per well of a 24-well plate with 1 uL of viruses (rtTA and Ngn2-puro) in 1 ml of mixed media. (Day 0) Half of the virus-containing media was removed and fresh Neural induction medium (NIM; DMEM F12 medium supplemented with 1% N2, 1% non-essential amino acids, 10 μg/l human BDNF, 10 μg/l human NT-3, and 0.2 mg/l mouse laminin) was added supplemented with Doxycycline (2 mg/l) and Y-27632 to induce Ngn2-puro expression. (Day 1-2) 24 hours later, Puromycin (1 mg/l) was added to NIM for 24-48 hours and media was changed daily. (Day 3) neurons were washed 1-2x with PBS. Freshly isolated or previously cryopreserved mouse glial cells (~75,000 cells per well of a 24-well plate) were added in Neural differentiation medium plus Dox (NDM; Neurobasal A medium supplemented with 2% B27, 1% glutamax, 2 μM AraC, 10 μg/l human BDNF, 10 μg/l human NT-3, and 0.2 mg/l mouse laminin). (Day 5) Half of the media was changed using NDM plus Dox. Media change occurred every 2-3 days until Day 10. (Day 10) Half of media was replaced with Maturation medium (MM; MEM supplemented with 0.5% glucose, 0.02% NaHCO3, 0.1 mg/ml transferrin, 5% FBS, 0.5 mM L-glutamine, 2% B27, and 2 μM AraC). Dox was withdrawn from this time point forward. (Day 13) Additional MM (0.5 mL per well of a 24-well plate) was added and neurons were incubated for 7 days without media change. (Day 20) Half of media was replaced with fresh MM. Media change occurred weekly until RNA extraction.

extract_protocol:
Total RNA was prepared from the entire plate and thus contained both mouse and human total RNA
RNA-seq libraries were prepared from total RNA using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Neurons from engineered iPS cells were treated with the same protocol except additional treatment of lentivirus expressing Ubiquitin-Flp-GFP and Ubiquitin-Cre-GFP at Day -1.

value: WT

tag: sample group

value: ctl -iPSC

tag: culture batch pair-group

value: iPSC

tag: nrxn1 transcript mutation effect


title: C2C12_short_9kA

description: C2C12 myoblast cells, myoblast nuclei, and myotube nuclei were collected for Split-seq and dispersed into 48 wells of a 96 well plate containing unique barcodes per well (12 wells of myoblast cells, 12 wells of myoblast nuclei, and 24 wells of myotube nuclei). Library preparation was performed following manufacturer’s instructions for the Single Cell Whole Transcriptome Kit, where the cells are mixed for the next 2 sets of barcoding reactions followed by sublibrary generation. A mix of 9,000 cells was set aside for this sublibrary which was processed into cDNA followed by shallow sequencing with Illumina short reads.

tag: celltype

value: myoblast, myotube

tag: library prep protocol

value: scRNA-seq protocol; Single Cell Whole Transcriptome Kit (Parse Biosciences).


title: C2C12_short_9kB


title: C2C12_short_9kE


title: C2C12_short_9kD


title: C2C12_short_9kC


title: T880_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X880_S44

value: Pancreas

tag: cell type

value: Pancreatic beta cell

value: adult day 136

tag: Sex

tag: blood glucose (mg/dl)

tag: weight (g)

tag: genotype

value: Cherry/+; Ins2-Cre/+


title: C2C12_short_9kF


title: C2C12_short_1k

description: C2C12 myoblast cells, myoblast nuclei, and myotube nuclei were collected for Split-seq and dispersed into 48 wells of a 96 well plate containing unique barcodes per well (12 wells of myoblast cells, 12 wells of myoblast nuclei, and 24 wells of myotube nuclei). Library preparation was performed following manufacturer’s instructions for the Single Cell Whole Transcriptome Kit, where the cells are mixed for the next 2 sets of barcoding reactions followed by sublibrary generation. A mix of 1,000 cells was set aside for this sublibrary which was processed into cDNA followed by deep sequencing with Illumina short reads.


title: human sample 7

tag: age


title: B38_Treated larvae 0.12 ng EE2

tag: tissue

tag: experiment

tag: treatment (ng ee2/l)

value: mRNA


title: [Neuropathology] BALB_Brain_28dpi_rep2

description: 50ug RNA was loaded for each sample, Naïve samples were used as reference samples for comparison in analysis

hyb_protocol: Panel codeset probes were hybridized with 150ng of total RNA per brain over 18hr at 65C according to NanoString protocol.

value: Brain

tag: mouse strain

value: BALB/c

tag: infection time point


title: [Neuropathology] BALB_Brain_28dpi_rep3


title: [Neuropathology] BALB_Brain_56dpi_rep1


title: [Neuropathology] BALB_Brain_56dpi_rep2


title: [Neuropathology] BALB_Brain_56dpi_rep3


title: LNCAP-INPP4B-3

city: Miami

first: Irina

last: Agoulnik

state: FL

address: 11200 SW 8th ST

department: Human and Molecular Genetics

institute: Florida International University, HWCOM

description: Biological replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: LNCaP cells transfected with INPP4B-specific siRNA

label_protocol: Not provided

growth_protocol: LNCaP cells maintain in RPMI 1640 medium with 10% FBS.

extract_protocol: Trizol extraction, isoproponal repercipitation.

treatment_protocol: Control siRNA and INPP4B siRNA transfected with RNAIMAX for 48 hours in RPMI 1640 medium with 10% FBS.

value: prostate cancer cell line LNCaP


title: LNCAP-Cont3

description: Biological replicate 2

source_name: LNCaP cells transfected with noncoding control siRNA


title: B63_Treated larvae 0.12 ng EE2

value: whole larva

tag: molecule subtype


title: LNCAP-Cont2

description: Biological replicate 1


title: LNCAP-INPP4B-4

description: Biological replicate 3


title: LNCAP-INPP4B-2

description: Biological replicate 1


title: T843_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X843_S43

tag: strain

value: ICR

value: adult day 289

tag: disease state

value: wild type

tag: rna extraction

value: TRIzol-phenol chloroform


title: LNCAP-Cont4

description: Biological replicate 3


title: A67_Control larvae


title: Q819_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X819_S42

value: adult day 111

value: female

value: Qiagen RNeasy Plus Mini Kit


title: A62_Control larvae


title: CTRL_iPSC_1

value: WT

tag: sample group

value: ctl -iPSC

tag: culture batch pair-group

value: iPSC

tag: nrxn1 transcript mutation effect


title: CTRL_iPSC_6


title: CTRL_iPSC_5


title: Q792_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X792_S41

value: Pancreas

tag: cell type

value: Pancreatic beta cell

value: adult day 212

tag: Sex

value: male


title: A63_Control larvae

value: mRNA


title: A57_Control larvae


title: Q722.5.23.18_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X722.5.23.18_S82

value: adult day 223

tag: blood glucose (mg/dl)

tag: weight (g)

value: Cherry/+; Ins2-Cre/+


title: A58_Control larvae

value: whole larva

tag: age


title: [Neuropathology] BALB_Brain_28dpi_rep1

tag: tissue

value: Brain

value: BALB/c


title: [Neuropathology] BALB_Brain_14dpi_rep3


title: Q715_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X715_S30

value: ICR

value: adul day 364

tag: genotype

value: wild type


title: CTRL_iPSC_3


title: [Neuropathology] BALB_Brain_14dpi_rep2


title: Q709_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X709_S29

value: adult day 201

value: Qiagen RNeasy Plus Mini Kit


title: [Neuropathology] BALB_Brain_Naive_rep3

value: Naive


title: [Neuropathology] BALB_Brain_14dpi_rep1


title: T707_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X707_S28

value: adult day 289

value: female

value: TRIzol-phenol chloroform


title: A52_Control larvae

tag: experiment

tag: treatment (ng ee2/l)


title: A48_Control larvae


title: [Neuropathology] BALB_Brain_Naive_rep2

tag: mouse strain

tag: infection time point


title: CTRL_iPSC_4

value: WT

value: ctl -iPSC

value: iPSC


title: Healthy control 2

first: Zhen

last: Wang

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

data_processing:
Cell Ranger (v3.0.1, 10x Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered single-cell gene expression matrix and associated cell barcodes and gene features
Supplementary_files_format_and_content: Filtered BCR contig sequences and annotations, clonotype consensus sequences and annotations, and clonotype abundance
Supplementary_files_format_and_content: Filtered TCR contig sequences and annotations, clonotype consensus sequences and annotations, and clonotype abundance

source_name: PBMCs

extract_protocol:
Venous blood was collected on the 5th days after the onset of fever before IVIG therapy and 24 hours after IVIG therapy and subsidence of fever. PBMCs were isolated by density gradient centrifugation using the Ficoll-Paque medium.
Single-cell capturing and library construction were performed using the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: The KDs received high-dose IVIG treatment combined with oral aspirin.

value: blood

value: PBMCs

tag: treatment

value: untreatment

value: health


title: Healthy control 3

tag: disease state


title: T706_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X706_S27

tag: strain

value: Pancreas

value: Pancreatic beta cell

value: Cherry/+; Ins2-Cre/+

tag: rna extraction


title: [Neuropathology] BALB_Brain_Naive_rep1

value: Brain

value: BALB/c


title: Q703_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X703_S26

value: ICR

value: adult day 150

value: male

value: wild type

value: Qiagen RNeasy Plus Mini Kit


title: A47_Control larvae

value: whole larva

tag: molecule subtype

value: mRNA


title: A53_Control larvae


title: 595_BILs

city: Los Angeles

first: Geoffrey

last: Owens

address: 300 Stein Plaza Ste 562

department: Neurosurgery

institute: UCLA

data_processing:
10x Genomics cellranger v4.0.0 mkfastq
10x Genomics cellrangerv4.0.0 count
Genome_build: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary_files_format_and_content: Sparse matrix file of all counts for all genes per barcode
Supplementary_files_format_and_content: Excel spreadsheet of all barcodes associated with TCR Vbeta and Valpha sequences

source_name: Brain-infiltrating leukocytes

growth_protocol: not applicable

extract_protocol:
Brain-infiltrating leukocytes were isolated by enzymatic dissociation of macerated resected brain tissue with type IV collagenase and fractionation on a 30%:70% Percoll® step gradient
Chromium Next GEM single cell 5' library kit, Chromium single cell human TCR amplification kit

treatment_protocol: not applicable

value: Brain-infiltrating leukocytes

value: Pediatric


title: [Neuropathology] B6_Brain_56dpi_rep3


title: Healthy control 1

value: blood

value: PBMCs


title: Patient 6 after IVIG therapy

value: after IVIG therapy

value: acute KD


title: A42_Control larvae


title: [Neuropathology] B6_Brain_56dpi_rep1


title: [Neuropathology] B6_Brain_56dpi_rep2


title: Q594_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X594_S24

value: Pancreas

value: Pancreatic beta cell

value: adult day 179

value: female


title: Q596_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X596_S25

value: ICR

value: adult day 124

value: Cherry/+; Ins2-Cre/+


title: A37_Control larvae


title: Patient 6 before IVIG therapy

value: before IVIG therapy


title: A33_Control larvae


title: human sample 5


title: Q587_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X587_S23

value: adult day 155

value: male

value: wild type

value: Qiagen RNeasy Plus Mini Kit


title: Q899_T1ND

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X899_S49

value: NOD-ICR

value: adult day 89

value: type-1 non-diabetic


title: [Neuropathology] B6_Brain_28dpi_rep3

value: Brain


title: Q585_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X585_S22


title: A38_Control larvae

value: whole larva

value: mRNA


title: Q531_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X531_S14

value: Pancreas

value: Pancreatic beta cell

value: adult day 85


title: Q598.4.27.18_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X598.2018_S79

value: ICR


title: A28_Control larvae


title: A27_Control larvae


title: Patient 5 before IVIG therapy

value: blood

value: PBMCs

value: acute KD


title: [Neuropathology] B6_Brain_28dpi_rep1

description: 50ug RNA was loaded for each sample, Naïve samples were used as reference samples for comparison in analysis


title: Patient 4 before IVIG therapy

value: before IVIG therapy


title: Q530_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X530_S13

value: female

value: Cherry/+; Ins2-Cre/+


title: A23_Control larvae


title: Patient 5 after IVIG therapy

value: after IVIG therapy


title: Q528_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X528_S12

value: adult day 84

value: wild type

value: Qiagen RNeasy Plus Mini Kit


title: A22_Control larvae


title: [Neuropathology] B6_Brain_14dpi_rep3

value: Brain


title: [Neuropathology] B6_Brain_14dpi_rep2


title: Patient 3 after IVIG therapy


title: Q292_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X292_S7

value: adult day 158

value: male


title: [Neuropathology] B6_Brain_28dpi_rep2


title: [Neuropathology] B6_Brain_14dpi_rep1


title: [Neuropathology] B6_Brain_Naive_rep3

value: Naive


title: A18_Control larvae

value: whole larva

value: mRNA


title: A32_Control larvae


title: Patient 2 after IVIG therapy


title: Patient 4 after IVIG therapy


title: Q287_WT

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X287_S6

value: ICR

value: Pancreas

value: Pancreatic beta cell

value: adult day 207


title: A17_Control larvae


title: EZH2 knockout clone_23

city: Munich

first: Sabrina

last: Weser

address: Marchioninistraße 15

department: Department of Medicine III

country: Germany

institute: University Hospital, LMU

data_processing:
Fastq reads were processed with the zUMIs pipeline. Ensembl annotation GRCh38.84
The read count table generated by zUMIs was analysed for differential expression using the R platform
Genome_build: Hg38
Supplementary_files_format_and_content: sample (columns) and gene (rows) -wise read count table

source_name: Cell line

growth_protocol: K562 cells were cultured according to the recommendations of the DSMZ

extract_protocol:
RNA was isolated from cell lysates by digestion of residual proteins and DNA using a ProteinaseK and DNAseI digest respectively.
RNA-seq libraries were prepared using prime-seq, a bulk version of the single cell RNA-seq method mcSCRB-seq.

treatment_protocol: EZH2 knockouts were generated by CRISPR/Cas9 mediated genome editing, targeting exon 3 of EZH2

value: bone marrow

tag: cell line


title: [Neuropathology] B6_Brain_Naive_rep2


title: A13_Control larvae


title: EZH2 knockout clone_18


title: T576.1_P10

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X576.1_S75

tag: cell type

value: neonates day 10

value: TRIzol-phenol chloroform


title: T580.1_P10

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X580.1_S78

tag: Sex

value: Cherry/+; Ins2-Cre/+


title: Patient 3 before IVIG therapy

value: blood

value: PBMCs

value: before IVIG therapy

value: acute KD


title: A12_Control larvae


title: Patient 1 before IVIG therapy


title: Q573.3.9.18_P10

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X573.2018_S71

tag: blood glucose (mg/dl)

value: wild type

value: Qiagen RNeasy Plus Mini Kit


title: T573.9.5.18_P10

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X573.2019_S72

tag: weight (g)


title: A08_Control larvae

tag: age


title: EZH2 knockout clone_3

tag: tissue


title: Q526_P10

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X526_S11

tag: genotype


title: SaC9+YE1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep2

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh38/hg38 human or GRCm38/mm10 mouse reference genome using BWA-MEM 0.7.9a.
Genome_build: hg38 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: base subtitutions

extract_protocol:
Target genomic sequences were PCR amplified by high-fidelity DNA polymerase PrimeSTAR HS (Clonetech) with primer sets flanking examined sgRNA target sites.
For deep target genimoc DNA sequencing, Indexed DNA libraries were prepared by using the TruSeq ChIP Sample Preparation Kit (Illumina) with minor modifications. Briefly, the PCR products amplified from genomic DNA regions were fragmented by Covaris S220, and then PCR amplified by using the TruSeq ChIP Sample Preparation Kit (Illumina). After quantitated with Qubit High-Sensitivity DNA kit (Invitrogen), PCR products with different tags were pooled together for deep sequencing by using the Illumina HiSeq X10 (2×150) at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

tag: 5'-end trimming of r1

tag: 3'-end trimming of r1


title: SaC9+YE1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep1


title: tBE-V5-mA3:PGM3 rep3


title: EZH2 knockout clone_10


title: A07_Control larvae

tag: experiment

tag: treatment (ng ee2/l)


title: A03_Control larvae


title: EZH2 knockout clone_1


title: tBE-V5-mA3:PGM3 rep2

tag: treatment


title: Patient 2 before IVIG therapy

tag: disease state


title: Wild type clone_5

value: Wild type


title: Q574_P7

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X574_S19

tag: strain

value: neonates day 7


title: Q742_P7

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X742_S35

tag: rna extraction


title: tBE-V5-mA3:PGM3 rep1


title: Wild type clone_3