title: Limfjord, haemocytes, 1 day, Bonamia, sample 14

description:
L1T1B-14
Limfjord, gene expression at 1 day after Bonamia ostreae infection sample 14

value: Limfjord


title: P2_7_9

status: Public on Jul 27 2018

type: SRA

city: Hong Kong

first: Chee Kent

last: Lim

address: Kowloon Tong

department: School of Energy and Environment

country: Hong Kong

institute: City University of Hong Kong

description:
Itaconic acid-producing wildtype strain.
AM1_TPM_250718.txt

library_source: transcriptomic

data_processing:
Quality control (QC) of raw reads was performed using illumina-utils v2.0.2 (Eren et al. (2013) PloS One 8: e66643) and FastQC v0.11.5 (Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data).
Reads were pseudo-aligned using kallisto v0.43.1 (Bray et al. (2016) Nature biotechnology 34: 525) with 100 bootstraps per sample.
Differential analysis of RNA-Seq data was conducted in sleuth v0.29.0 (Pimentel et al. (2017) Nature methods 14: 687) integrating the bootstraps from the pseudo-alignment.
Genome_build: GCF_000022685.1 (ASM2268v1)
Supplementary_files_format_and_content: AM1_TPM_250718.txt: Tab-delimited text file includes transcripts per million (TPM) values for each sample.

molecule: total RNA

organism: Methylorubrum extorquens

source_name: whole cell

growth_protocol: Cultures were grown aerobically in minimal media adapted from Mokhtari-Hosseini et al. (Bioresource Technology (2009) 100: 2436-43) supplemented with 240 mM methanol for 96 hours at 30 oC.

extract_protocol:
RNA was extracted from biomass using RNeasy kit (Qiagen) after cell lysis with lysozyme (Sigma-Aldrich) for 10 min and followed by homogenization with autoclaved 0.1 mm zirconia-silica beads (BioSpec) for 5 min. For gDNA contamination removal, DNA digestion with DNase (Qiagen) was performed thrice.
Ribosomal RNA removal in RNA samples was done using Ribo-Zero Magnetic Kit (Illumina) and rRNA-depleted RNA samples were used as template to create cDNA libraries containing 250~300 bp inserts with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs).

tag: strain/background

tag: genotype/variation

value: wildtype strain with pTE101a-CAD plasmid


title: P1_1_3

description:
Wildtype strain with control plasmid.
AM1_TPM_250718.txt

value: wildtype strain with pTE101 plasmid


title: Whole_Brain_SLC5A8_Deficient_Old_Mice_Rep4

type: RNA

city: NICE

first: Laurent

last: SUISSA

state: (State)

address: 28, Avenue de Valombrose

country: France

institute: Faculté de Médecine

hyb_protocol: Labelled cRNA probes (400 ng) were hybridized on 8 x 60K high-density SurePrint G3 gene mouse GE 8 x 60K Agilent microarrays.

scan_protocol: standard Agilent protocol

data_processing:
standard Agilent protocol
Normalization of microarray data was performed using the Limma package (http://www.bioconductor.org). Interslide normalization was performed using the quantile methods.

organism: Mus musculus

source_name: Whole Brain SLC5A8 Deficient Old Mice Replicate4

label_protocol: Cy3 dye using the Low RNA Input QuickAmp Kit (Agilent), as recommended by the supplier.

extract_protocol: RNA was isolated with a RNeasy kit (Qiagen, Courtaboeuf, France) from freshly removed mouse brain tissue according to the manufacturer’s protocol.

tag: tissue

value: Whole brain

tag: gender

value: male

tag: strain

value: 18 months

tag: age


title: 96hQ H3K4me3 Replicate 1 ChIP-Seq

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: QMUL

library_source: genomic

data_processing:
Reads were mapped to the apis mellifera genome using bowtie2 (v2.2.8)
Reads were extended to 250bp in length and counted in 100bp windows spaced every 50bp. Creating a series of overlapping windows. Each window was then extended to 5kbp and the total number of input reads were counted.
A enrichment value for each 100bp window was calculated by dividing the total number of reads by the averaged backround count and multiplying by the fraction of mapped reads in input divided by ChIP.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: Reference Name,Start Position of Window, End Position of Window, Enrichment Value

molecule: genomic DNA

organism: Apis mellifera

source_name: Larval Head

extract_protocol:
Extracts from sonicated nuclei were cleared by centrifugation (20000×g; 10 min), histone-DNA complexes were concentrated using an Amicon centrifugal filter (Millipore) and split into 50 μl aliquots. Each aliquot was diluted ten-fold with ChIP dilution buffer (0.01% SDS; 1.1% Triton X-100; 1.2 mM EDTA; 16.7 mM Tris-HCl pH 8.0; 167 mM NaCl; protease inhibitors cocktail) and histone-DNA complexes were immunoprecipitated with antibodies overnight.
Libraries were prepared with the NEBNext Ultra II Library Prep Kit for Illumina (NEB, E7645S) according to the manufacturer’s protocol. Insert sizes were selected for 250 bp with NEBNext Sample Purification Beads (NEB, E7104S).  Libraries were PCR amplified using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, E7335S). The number of PCR cycles was selected based on the amount of input DNA. Library quality was verified by running an Agilent High Sensitivity DNA chip (Agilent, 5067-4626) on a 2100 Bioanalyzer (Agilent Genomics).

value: Larval Head

tag: chip antibody

tag: caste


title: Limfjord ,haemocytes, 1 day, Bonamia, sample 20

city: LUGO

first: Belen

middle: G

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

country: Spain

institute: University of Santiago de Compostela

description:
L1T1B-20
Limfjord, gene expression at 1 day after Bonamia ostreae infection sample 20

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to turbot custom Oligo Microarrays (G2509F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Extended dynamic range implemented in the Agilent software was applied to avoid saturation in the highest intensity range. The Agilent feature extraction was used as raw data for further preprocessing. The processed signal (gProcessed-Signal) value was chosen for the statistical analysis.

organism: Ostrea edulis

source_name: Limfjord_haemocyte cells_1 day_Bonamia

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA  of each strain and time using the Low Input Quick Amp Labeling Kit, One-Color (Cy3) (Agilent Technologies, USA)  according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Haemolymph samples were taken at three different times after the challenge (1, 30 and 90 days post-challenge, dpc); as much haemolymph as possible (from 0.2 ml to 1.5 ml) was withdrawn from the adductor muscle of each oyster with a 21 gauge needle screwed to a 2 ml cold syringe. Immediately the haemolymph was poured into a cold vial and kept in crushed ice to avoid haemocyte clumping. Haemolymph samples were centrifuged (800 g, 10 min, 4ºC) and the cell fractions (pellets) were resuspended in RNA later and stored at -20ºC after one night at 4ºC until RNA extraction. RNA was individually extracted by RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's instructions with slight modifications, including two additional RPE washes and the optional DNase digestion.

treatment_protocol: The challenge was performed by individually immersing oysters in beakers containing an aerated suspension of 300,000 B. ostreae cells in filtered seawater for 24 h at the Centro de Investigacións Mariñas. The B. ostreae cells for the challenge were isolated from heavily infected oysters collected in Lough Foyle (Ireland), following the procedure described by Mialhe et al. (1988). After challenge, oysters were kept in tanks with running, filtered (1 µm) seawater plus continuous (pumped) supply of mixed cultured algae until the end of the experiment.

tag: phenotype

value: naïve (NS)

value: haemocyte cells

tag: challenged with

value: B. ostreae cells

tag: sampling time point

value: 1 day


title: 96hQ H3K4me3 Replicate 2 ChIP-Seq


title: P2_1_3


title: ribo_blue_rep2

city: Wako

first: tomoya

last: fujita

state: Saitama

address: 2-1, Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

data_processing:
Library strategy: Ribo-Seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: tair10
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

organism: Arabidopsis thaliana

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)

tag: treatment

value: blue light condition


title: 10h_IFNa_MNase-Seq

status: Public on Jul 26 2018

city: Evanston

first: Nancy

last: Au-Yeung

state: IL

address: 2200 Campus Dr

country: USA

institute: Northwestern University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using BioScope v1.3.1
ChIP-seq peaks were called with MACS software and a p-value cutoff at 1E-5.
Direct selection MNase-seq reads were aligned to the hg19 genome assembly using Bowtie-0.12.7
Direct selection MNase-seq nucleosome peaks and statistical analysis on differential nucleosome occupancy with a p-value cutoff 1E-5 was generated with the DANPOS software.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated by MACS software and represent unique peaks enriched compared to INPUT. ChIP-seq bigwig alignment files were generated using a Northwestern University Sequencing Core internal script and bedTools. Direct selection MNase-seq bigwig files were converted with Galaxy from wig files generated from the DANPOS software normalized relative to the Mock MNase-seq sample.

organism: Homo sapiens

source_name: cervix

growth_protocol: HeLa cells were cultured in DMEM media supplemented with 10% cosmic calf serum and 1% pen-strep on adherent plates in 37C incubator with 5% CO2.

extract_protocol:
For ChIP-seq: Lysates were clarified sonicated nuclei and STAT1, STAT2, and IRF9 was immunoprecipitated with the corresponding antibody.  For Direct selection MNase-seq: Mononucleosomes were isolated following MNase digestion and direct selection via bacterial artificial chromosome hybridization isolation.
Libraries were prepared using the 5500 Series SOLiD Systems Fragment Library Preparation protocol using the ABI library preparation kit or NEBNext kit. The fragmented DNA was blunt-ended, size selected for 100-250 bp using Agencourt AMPure XP reagent, and then adding a dA tail for ligation with SOLiD adaptors. The adaptor-ligated DNA was purified using Agencourt AMPure XP reagent and PCR-amplified for 13-15 cycles. The quantity and size was verified using the Bioanalyzer .

treatment_protocol: Mock or 1000 units/ml interferon alpha

tag: cell type

value: HeLa cell line

value: 10 hr interferon alpha


title: 6h_IFNa_MNase-Seq

value: 6 hr interferon alpha


title: Input DNA

value: Mock


title: 2h_IFNa_MNase-Seq

value: 2 hr interferon alpha


title: Whole_Brain_SLC5A8_Deficient_Young_Mice_Rep2

source_name: Whole Brain SLC5A8 Deficient Young Mice Replicate2

value: 4 months


title: Limfjord, haemocytes, 1 day, control

description:
L1T1C
Limfjord, gene expresion control after 1 day

source_name: Limfjord_haemocyte cells_1 day_control

value: Limfjord

value: none (non-challenged control)


title: Limfjord, haemocytes, 1 day, Bonamia, sample 3

description:
L1T1B-3
Limfjord, gene expression at 1 day after Bonamia ostreae infection sample 3


title: IFNa_STAT1_ChIP-seq

value: STAT1 (Santa Cruz, sc-345)


title: Mock_STAT1_ChIP-seq


title: Limfjord, haemocytes, 1 day, Bonamia, sample 9

description:
L1T1B-9
Limfjord, gene expression at 1 day after Bonamia ostreae infection sample 9


title: IFNa_IRF9_ChIP-seq

value: IRF9 (Santa Cruz, sc-496)


title: Whole_Brain_SLC5A8_Deficient_Old_Mice_Rep2

source_name: Whole Brain SLC5A8 Deficient Old Mice Replicate2

value: Whole brain

value: male

value: 18 months


title: Whole_Brain_SLC5A8_Deficient_Young_Mice_Rep1

source_name: Whole Brain SLC5A8 Deficient Young Mice Replicate1


title: Whole_Brain_SLC5A8_Deficient_Old_Mice_Rep1

source_name: Whole Brain SLC5A8 Deficient Old Mice Replicate1


title: Whole_Brain_SLC5A8_Deficient_Old_Mice_Rep3

source_name: Whole Brain SLC5A8 Deficient Old Mice Replicate3


title: IFNa_STAT2_ChIP-seq

value: STAT2 (Santa Cruz, sc-476)


title: Mock_STAT2_ChIP-seq


title: Mock_MNase-Seq


title: PBMC TTTCTT mcSCRB-seq

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

description: Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the Human Genome (hg38) or Mouse genome (mm10) with STAR 2.5.3
Quantification was done with ENSEMBL gene models (GRCh38.84/GRCm38.75)
Genome_build: Human: hg38, Ensembl 84; Mouse: mm10, Ensembl 75
Supplementary_files_format_and_content: cell (columns) and gene (rows) -wise UMI expression table

source_name: peripheral mononuclear blood cells

extract_protocol:
Cells were FACS sorted into lysis buffer
Libraries were constructed using various developments of the SCRB-seq protocol, see sample description for more details

tag: protocol

value: mcSCRB-seq


title: PBMC TTTCAA mcSCRB-seq


title: PBMC TTTGGC mcSCRB-seq


title: PBMC TTTTAG mcSCRB-seq


title: PBMC TTTGTA mcSCRB-seq


title: PBMC TTTTGA mcSCRB-seq


title: PBMC TTTTCT mcSCRB-seq


title: PBMC TTTATG mcSCRB-seq


title: Mock_IRF9_ChIP-seq


title: NAC_HS_-Rapa

city: Chicago

first: David

last: Pincus

institute: University of Chicago

data_processing:
Library strategy: NAC-seq
bases called by Illumina software
quantified by htseq-count
processed data files format and content: .txt files with normalized counts
Genome_build: saccer3

organism: Saccharomyces cerevisiae

extract_protocol: Illumina tru-seq

value: Hsf1-AA, Rpb3-FLAG

tag: perturbation

value: HS 39ºC

tag: molecule subtype

value: nascent RNA


title: NAC_NHS_-Rapa

value: control 30ºC


title: NAC_HS_+Rapa

value: 1 µM rapamycin, HS 39ºC


title: PBMC TTTAGT mcSCRB-seq


title: PBMC TTTAAC mcSCRB-seq


title: PBMC TTTACA mcSCRB-seq


title: PBMC TTGTCC mcSCRB-seq


title: PBMC TTGTTA mcSCRB-seq


title: PBMC TTGATT mcSCRB-seq


title: NAC_NHS_+Rapa

value: 1 µM rapamycin, 30ºC


title: PBMC TTCCTC mcSCRB-seq


title: PBMC TTCATA mcSCRB-seq


title: PBMC TTGAAA mcSCRB-seq


title: PBMC TTATTG mcSCRB-seq


title: PBMC TTATGT mcSCRB-seq


title: PBMC TTATCA mcSCRB-seq


title: PBMC TTAGAA mcSCRB-seq


title: PBMC TTATAC mcSCRB-seq


title: PBMC TTACTA mcSCRB-seq


title: PBMC TTAACT mcSCRB-seq


title: PBMC TTAATC mcSCRB-seq


title: PBMC TTAAGA mcSCRB-seq


title: PBMC TTAAAG mcSCRB-seq


title: PBMC TGCCCC mcSCRB-seq


title: PBMC TGCGCG mcSCRB-seq


title: PBMC TCTTTC mcSCRB-seq


title: PBMC TGTTTA mcSCRB-seq


title: PBMC TTACAT mcSCRB-seq


title: PBMC TTGGAT mcSCRB-seq


title: PBMC TGATAA mcSCRB-seq


title: PBMC TGTAAA mcSCRB-seq


title: PBMC TCTGCA mcSCRB-seq


title: PBMC TCGGGC mcSCRB-seq


title: PBMC TCTAAT mcSCRB-seq


title: PBMC TCTATA mcSCRB-seq


title: PBMC TGTATT mcSCRB-seq


title: PBMC TGAAAT mcSCRB-seq


title: PBMC TCGGCG mcSCRB-seq


title: PBMC TTCAAT mcSCRB-seq


title: PBMC TCGCGG mcSCRB-seq


title: PBMC TGCGGC mcSCRB-seq


title: PBMC TGATTT mcSCRB-seq


title: PBMC TCCGGG mcSCRB-seq


title: PBMC TGAATA mcSCRB-seq


title: PBMC TCCAAC mcSCRB-seq


title: PBMC TCATTA mcSCRB-seq


title: PBMC TCTTAA mcSCRB-seq


title: PBMC TCAAAA mcSCRB-seq


title: PBMC TATTTG mcSCRB-seq


title: PBMC TCATAT mcSCRB-seq


title: PBMC TATTGT mcSCRB-seq


title: PBMC TCAATT mcSCRB-seq


title: PBMC TATGTT mcSCRB-seq


title: PBMC TATCTA mcSCRB-seq


title: PBMC TATTAC mcSCRB-seq


title: PBMC TATGAA mcSCRB-seq


title: PBMC TATTCA mcSCRB-seq


title: PBMC TAGTTT mcSCRB-seq


title: PBMC TATAAG mcSCRB-seq


title: PBMC TCGAAG mcSCRB-seq


title: PBMC TATATC mcSCRB-seq


title: PBMC TATACT mcSCRB-seq


title: PBMC TAGTAA mcSCRB-seq


title: PBMC TAGTGG mcSCRB-seq


title: PBMC TATAGA mcSCRB-seq


title: PBMC TAGATA mcSCRB-seq


title: PBMC TACTAT mcSCRB-seq


title: PBMC TAATTC mcSCRB-seq


title: PBMC TACATT mcSCRB-seq


title: PBMC TAGAAT mcSCRB-seq


title: PBMC TACAAA mcSCRB-seq


title: PBMC TAATGA mcSCRB-seq


title: PBMC TAATCT mcSCRB-seq


title: PBMC TAATAG mcSCRB-seq


title: PBMC TAAGTA mcSCRB-seq


title: PBMC TATCAT mcSCRB-seq


title: PBMC TAAGAT mcSCRB-seq


title: PBMC TAACTT mcSCRB-seq


title: PBMC TAACAA mcSCRB-seq


title: PBMC TAAATG mcSCRB-seq


title: PBMC TAAAGT mcSCRB-seq


title: PBMC TAAACA mcSCRB-seq


title: PBMC GTTTAT mcSCRB-seq


title: PBMC GTTCGA mcSCRB-seq


title: PBMC GTTTTA mcSCRB-seq


title: PBMC TAAAAC mcSCRB-seq


title: PBMC GTGGCC mcSCRB-seq


title: PBMC GTGGGG mcSCRB-seq


title: PBMC GTCGGC mcSCRB-seq


title: PBMC GTCGCG mcSCRB-seq


title: PBMC GTTAAA mcSCRB-seq


title: PBMC GTCAAG mcSCRB-seq


title: PBMC GTCCCC mcSCRB-seq


title: PBMC GTTATT mcSCRB-seq


title: PBMC GTGCGC mcSCRB-seq


title: PBMC GTATAA mcSCRB-seq


title: PBMC GTGACT mcSCRB-seq


title: PBMC GTACCG mcSCRB-seq


title: PBMC GTAAAT mcSCRB-seq


title: PBMC GGTGGC mcSCRB-seq


title: PBMC GTACAC mcSCRB-seq


title: PBMC GGGGTG mcSCRB-seq


title: PBMC GGGTCG mcSCRB-seq


title: PBMC GGGGCA mcSCRB-seq


title: PBMC GGGTGC mcSCRB-seq


title: PBMC GGGGAC mcSCRB-seq


title: PBMC GGGCGA mcSCRB-seq


title: PBMC GGGATT mcSCRB-seq


title: PBMC GGCGGA mcSCRB-seq


title: PBMC GGGAGG mcSCRB-seq


title: PBMC GGGACC mcSCRB-seq


title: PBMC GGCGCT mcSCRB-seq


title: PBMC GGCGAG mcSCRB-seq


title: PBMC GGCCAC mcSCRB-seq


title: PBMC GGCAGC mcSCRB-seq


title: PBMC GGACGC mcSCRB-seq


title: PBMC GGAGGG mcSCRB-seq


title: PBMC GGAGCC mcSCRB-seq


title: PBMC GGCACG mcSCRB-seq


title: PBMC GGCAAT mcSCRB-seq


title: PBMC GGTGCG mcSCRB-seq


title: PBMC GCTCGC mcSCRB-seq


title: PBMC GGACAT mcSCRB-seq


title: PBMC GCTGGG mcSCRB-seq


title: PBMC GCTAGA mcSCRB-seq


title: PBMC GCGGAG mcSCRB-seq


title: PBMC GCGGGA mcSCRB-seq


title: PBMC GCGCAC mcSCRB-seq


title: PBMC GCGCGT mcSCRB-seq


title: PBMC GGGCCT mcSCRB-seq


title: PBMC GCGCCA mcSCRB-seq


title: PBMC GCGCTG mcSCRB-seq


title: PBMC GCGACG mcSCRB-seq


title: PBMC GGGCAG mcSCRB-seq


title: PBMC GCCTCG mcSCRB-seq


title: PBMC GCCGGT mcSCRB-seq


title: PBMC GCCGCA mcSCRB-seq


title: PBMC GCCGTG mcSCRB-seq


title: PBMC GCCGAC mcSCRB-seq


title: PBMC GCTGCC mcSCRB-seq


title: PBMC GGACCA mcSCRB-seq


title: PBMC GCCCTC mcSCRB-seq


title: PBMC GCCCGA mcSCRB-seq


title: PBMC GCCCCT mcSCRB-seq


title: PBMC GCAGGC mcSCRB-seq


title: PBMC GCCAGG mcSCRB-seq


title: PBMC GCCCAG mcSCRB-seq


title: PBMC GCACGG mcSCRB-seq


title: PBMC GATTAA mcSCRB-seq


title: PBMC GCACCC mcSCRB-seq


title: PBMC GCAGCG mcSCRB-seq


title: PBMC GCCACC mcSCRB-seq


title: PBMC GCGAGC mcSCRB-seq


title: PBMC GATATA mcSCRB-seq


title: PBMC GAGGGC mcSCRB-seq


title: PBMC GAGCGG mcSCRB-seq


title: PBMC GATCGT mcSCRB-seq


title: PBMC GATAAT mcSCRB-seq


title: PBMC GAGGCG mcSCRB-seq


title: PBMC GAGCCC mcSCRB-seq


title: PBMC GACGGG mcSCRB-seq


title: PBMC GACCCG mcSCRB-seq


title: PBMC GACGCC mcSCRB-seq


title: PBMC GAATTA mcSCRB-seq


title: PBMC GAATAT mcSCRB-seq


title: PBMC GAAATT mcSCRB-seq


title: PBMC CTTTAA mcSCRB-seq


title: PBMC GAAGAC mcSCRB-seq


title: PBMC CTTATA mcSCRB-seq


title: PBMC CTTAAT mcSCRB-seq


title: PBMC GACCGC mcSCRB-seq


title: PBMC CTGCGG mcSCRB-seq


title: PBMC CTCCGC mcSCRB-seq


title: PBMC CTGGGC mcSCRB-seq


title: PBMC CTTCTG mcSCRB-seq


title: PBMC CTCTCC mcSCRB-seq


title: PBMC CTCCCG mcSCRB-seq


title: PBMC CTATAT mcSCRB-seq


title: PBMC CTAGTG mcSCRB-seq


title: PBMC CTAATT mcSCRB-seq


title: PBMC CTAAAA mcSCRB-seq


title: PBMC CGTCGC mcSCRB-seq


title: PBMC CGTCCG mcSCRB-seq


title: PBMC CGTGCC mcSCRB-seq


title: PBMC CGGTGG mcSCRB-seq


title: PBMC CGGGTC mcSCRB-seq


title: PBMC CGGGGA mcSCRB-seq


title: PBMC CGGGCT mcSCRB-seq


title: PBMC CGGGAG mcSCRB-seq


title: PBMC CGGCTG mcSCRB-seq


title: PBMC CGGCGT mcSCRB-seq


title: PBMC CGGAGC mcSCRB-seq


title: PBMC CGGCCA mcSCRB-seq


title: PBMC CGGACG mcSCRB-seq


title: PBMC CTGGCG mcSCRB-seq


title: PBMC CGCTGC mcSCRB-seq


title: PBMC CTATTA mcSCRB-seq


title: PBMC CGCGTG mcSCRB-seq


title: PBMC CGCGCA mcSCRB-seq


title: PBMC CGCGGT mcSCRB-seq


title: PBMC CGCGAC mcSCRB-seq


title: PBMC CGCCTC mcSCRB-seq


title: PBMC CGCCAG mcSCRB-seq


title: PBMC CGGTCC mcSCRB-seq


title: PBMC CGCAGG mcSCRB-seq


title: PBMC CGATTG mcSCRB-seq


title: PBMC CGAGGC mcSCRB-seq


title: PBMC CGCACC mcSCRB-seq


title: PBMC CGCCCT mcSCRB-seq


title: PBMC CGACTT mcSCRB-seq


title: PBMC CGAGCG mcSCRB-seq


title: PBMC CGACCC mcSCRB-seq


title: PBMC CCTTCC mcSCRB-seq


title: PBMC CGACGG mcSCRB-seq


title: PBMC CCTGGC mcSCRB-seq


title: PBMC CCTCGG mcSCRB-seq


title: PBMC CCGTGC mcSCRB-seq


title: PBMC CGCTCG mcSCRB-seq


title: PBMC CCGTCG mcSCRB-seq


title: PBMC CCGGGT mcSCRB-seq


title: PBMC CCGGCA mcSCRB-seq


title: PBMC CCGGAC mcSCRB-seq


title: PBMC CCGCGA mcSCRB-seq


title: PBMC CCGCAG mcSCRB-seq


title: PBMC CCGATT mcSCRB-seq


title: PBMC CGCCGA mcSCRB-seq


title: PBMC CCCTGG mcSCRB-seq


title: PBMC CCCGGA mcSCRB-seq


title: PBMC CCCCTG mcSCRB-seq


title: PBMC CCCACG mcSCRB-seq


title: PBMC CCCGAG mcSCRB-seq


title: PBMC CCAGGG mcSCRB-seq


title: PBMC CCCCAC mcSCRB-seq


title: PBMC CCCCCA mcSCRB-seq


title: PBMC CCCAGC mcSCRB-seq


title: PBMC CCTGCG mcSCRB-seq


title: PBMC CCACAT mcSCRB-seq


title: PBMC CATTTA mcSCRB-seq


title: PBMC CCACCG mcSCRB-seq


title: PBMC CATCAG mcSCRB-seq


title: PBMC CCAACC mcSCRB-seq


title: PBMC CATATT mcSCRB-seq


title: PBMC CATGGT mcSCRB-seq


title: PBMC CAGTCA mcSCRB-seq


title: PBMC CAGGCC mcSCRB-seq


title: PBMC CAGCGC mcSCRB-seq


title: PBMC CCGAGG mcSCRB-seq


title: PBMC CATAAA mcSCRB-seq


title: PBMC CAGCCG mcSCRB-seq


title: PBMC CATTAT mcSCRB-seq


title: PBMC CACGCG mcSCRB-seq


title: PBMC CACCGG mcSCRB-seq


title: PBMC CAGGGG mcSCRB-seq


title: PBMC CAATAA mcSCRB-seq


title: PBMC CACCCC mcSCRB-seq


title: PBMC CAAATA mcSCRB-seq


title: PBMC ATTTCA mcSCRB-seq


title: PBMC CAAGCT mcSCRB-seq


title: PBMC ATTTTG mcSCRB-seq


title: PBMC ATTTAC mcSCRB-seq


title: PBMC ATTGTT mcSCRB-seq


title: PBMC CAAAAT mcSCRB-seq


title: PBMC CACCAA mcSCRB-seq


title: PBMC ATTGAA mcSCRB-seq


title: PBMC ATTCTA mcSCRB-seq


title: PBMC ATTCAT mcSCRB-seq


title: PBMC ATTAAG mcSCRB-seq


title: PBMC ATGTAA mcSCRB-seq


title: PBMC ATGAAT mcSCRB-seq


title: PBMC ATCTAT mcSCRB-seq


title: PBMC ATCATT mcSCRB-seq


title: PBMC ATCGAG mcSCRB-seq


title: PBMC ATCAAA mcSCRB-seq


title: PBMC ATATTC mcSCRB-seq


title: PBMC ATATGA mcSCRB-seq


title: PBMC ATATCT mcSCRB-seq


title: PBMC ATATAG mcSCRB-seq


title: PBMC ATAGAT mcSCRB-seq


title: PBMC ATACTT mcSCRB-seq


title: PBMC AGGGGC mcSCRB-seq


title: PBMC ATAACA mcSCRB-seq


title: PBMC ATACAA mcSCRB-seq


title: PBMC AGTATA mcSCRB-seq


title: PBMC AGTAAT mcSCRB-seq


title: PBMC ATTACT mcSCRB-seq


title: PBMC ATAAGT mcSCRB-seq


title: PBMC ATTAGA mcSCRB-seq


title: PBMC AGGCGG mcSCRB-seq


title: PBMC ATCTTA mcSCRB-seq


title: PBMC AGGCCC mcSCRB-seq


title: PBMC ATGATA mcSCRB-seq


title: PBMC AGCGCC mcSCRB-seq


title: PBMC AGGGAT mcSCRB-seq


title: PBMC AGCCGC mcSCRB-seq


title: PBMC AGCCCG mcSCRB-seq


title: PBMC AGATTA mcSCRB-seq


title: PBMC AGAATT mcSCRB-seq


title: PBMC ATAGTA mcSCRB-seq


title: PBMC ACTTAT mcSCRB-seq


title: PBMC AGACCT mcSCRB-seq


title: PBMC ACTTTA mcSCRB-seq


title: PBMC ACTATT mcSCRB-seq


title: PBMC CCACGC mcSCRB-seq


title: PBMC ACGGGG mcSCRB-seq


title: PBMC ACGGCC mcSCRB-seq


title: PBMC AGGGCG mcSCRB-seq


title: PBMC ACGCCG mcSCRB-seq


title: PBMC ACGCGC mcSCRB-seq


title: PBMC AGCGGG mcSCRB-seq


title: PBMC ACCCGG mcSCRB-seq


title: PBMC ACCCCC mcSCRB-seq


title: PBMC ACCGCG mcSCRB-seq


title: PBMC ACATAA mcSCRB-seq


title: PBMC ACCGGC mcSCRB-seq


title: PBMC ACAATA mcSCRB-seq


title: PBMC ACAAAT mcSCRB-seq


title: PBMC AATTTC mcSCRB-seq


title: PBMC AATGTA mcSCRB-seq


title: PBMC AATTGA mcSCRB-seq


title: PBMC AATTAG mcSCRB-seq


title: PBMC AATCTT mcSCRB-seq


title: PBMC AATCAA mcSCRB-seq


title: PBMC ACTAAA mcSCRB-seq


title: PBMC AATAGT mcSCRB-seq


title: PBMC AATACA mcSCRB-seq


title: PBMC AATGAT mcSCRB-seq


title: PBMC AATAAC mcSCRB-seq


title: PBMC AATATG mcSCRB-seq


title: PBMC AAGTTA mcSCRB-seq


title: PBMC ACCGTA mcSCRB-seq


title: PBMC AACTAA mcSCRB-seq


title: PBMC AAATTG mcSCRB-seq


title: PBMC AAGATT mcSCRB-seq


title: PBMC AACAAT mcSCRB-seq


title: PBMC AAACAT mcSCRB-seq


title: PBMC AAACTA mcSCRB-seq


title: PBMC AAAATC mcSCRB-seq


title: PBMC AAGTAT mcSCRB-seq


title: PBMC AATTCT mcSCRB-seq


title: PBMC AAAGTT mcSCRB-seq


title: PBMC AACATA mcSCRB-seq


title: PBMC AAATGT mcSCRB-seq


title: PBMC AAATCA mcSCRB-seq


title: PBMC AAAACT mcSCRB-seq


title: CHOP_6522_Carrier_1

city: Los Angeles

first: Daniel

last: Nachun

state: CA

address: 695 Charles E Young Dr S

institute: UCLA

hyb_protocol: Total RNA (200 ng) was amplified, biotinylated and hybridized on Illumina HT12 v4 microarrays, as per manufacturer's protocol, at the UCLA Neuroscience Genomics Core (UNGC)

scan_protocol: Slides were scanned using an Illumina BeadStation and signal extracted using the Illumina BeadStudio software

data_processing: Array preprocessing was performed using the standard pipeline from the lumi package which is designed specifically for Illumina microarrays. Raw intensities were normalized using variance-stabilized transformation and interarray normalization was performed with robust spline normalization. Outliers were removed based upon sample-wise connectivity z-scores. Batch effect correction was performed using ComBat from the sva package. Probes were filtered by detection score P < 0.01 and unannotated probes were dropped. Duplicate probes for the same gene were dropped using the maxMean method with the collapseRows function from the WGCNA package, which only keeps probes with the highest mean expression across all of the samples.

label: biotin

source_name: Whole blood

label_protocol: Biotinylation using standard Illumina protocol

extract_protocol: Peripheral blood was collected in Paxgene tubes and frozen before RNA extraction, which was performed using a semi-automated system (Qiacube). RNA quantity was assessed with Nanodrop (Nanodrop Technologies) and quality with the Agilent Bioanalyzer (Agilent Technologies).

tag: pidn

tag: sample number

tag: batch

tag: site

value: CHOP

tag: rin

tag: status

value: Carrier

tag: Sex

value: FEMALE


title: CHOP_6503_Control_1

value: Control

tag: age


title: CHOP_6501_Control_1

value: MALE


title: CHOP_6515_Carrier_1


title: CHOP_6510_Carrier_1


title: CHOP_6511_Control_1


title: CHOP_6509_Patient_1

value: Patient

tag: onset

tag: duration


title: CHOP_6517_Patient_1


title: CHOP_6523_Patient_1


title: CHOP_6521_Carrier_1


title: CHOP_6508_Carrier_1


title: CHOP_6518_Carrier_1


title: CHOP_6506_Carrier_1


title: CHOP_6498_Control_1


title: CHOP_6520_Control_1


title: CHOP_6513_Carrier_1


title: CHOP_6516_Control_1


title: CHOP_6500_Control_1


title: CHOP_6494_Carrier_1


title: CHOP_6499_Control_1


title: CHOP_6519_Carrier_1


title: CHOP_6495_Control_1


title: CHOP_4623_Patient_1

tag: functional stage


title: CHOP_6514_Control_1


title: CHOP_6507_Control_1


title: CHOP_6493_Carrier_1


title: CHOP_50_Patient_1


title: CHOP_6502_Control_1


title: CHOP_6492_Control_1


title: CHOP_6491_Control_1


title: CHOP_4891_Patient_1


title: CHOP_4832_Patient_1


title: CHOP_206_Patient_1


title: CHOP_4848_Patient_1


title: CHOP_4871_Patient_1


title: CHOP_4856_Patient_1


title: CHOP_4830_Patient_1


title: CHOP_4862_Patient_1


title: CHOP_6481_Control_1


title: CHOP_4809_Patient_1


title: CHOP_6485_Carrier_1


title: CHOP_4741_Patient_1


title: CHOP_4685_Patient_2


title: CHOP_4869_Patient_1


title: CHOP_4859_Patient_1


title: CHOP_4808_Patient_1


title: CHOP_4860_Patient_1


title: CHOP_4835_Patient_1


title: CHOP_4635_Patient_2


title: CHOP_4842_Patient_1


title: CHOP_4682_Patient_1


title: CHOP_4454_Patient_1


title: CHOP_4193_Patient_2


title: CHOP_4770_Patient_1


title: CHOP_4081_Patient_1


title: CHOP_4092_Patient_1


title: CHOP_255_Patient_1


title: CHOP_6476_Control_1


title: CHOP_4846_Patient_1


title: CHOP_4844_Patient_1


title: CHOP_4034_Patient_1


title: CHOP_4825_Patient_1


title: CHOP_4053_Patient_1


title: CHOP_6473_Carrier_1


title: CHOP_6472_Carrier_1


title: CHOP_4051_Patient_1


title: CHOP_4037_Patient_1


title: CHOP_6470_Carrier_1


title: UCLA_51_Patient_1

value: UCLA


title: CHOP_4780_Patient_1


title: CHOP_4452_Patient_1


title: UCLA_4790_Patient_1


title: CHOP_6471_Carrier_1


title: CHOP_4766_Patient_1


title: CHOP_4052_Patient_1


title: CHOP_4841_Patient_1


title: CHOP_6468_Carrier_1


title: CHOP_6478_Carrier_1


title: UCLA_4791_Patient_1


title: UCLA_4584_Patient_1


title: CHOP_6469_Control_1


title: UCLA_6709_Carrier_1


title: UCLA_4789_Patient_1


title: UCLA_59_Patient_1


title: CHOP_6467_Carrier_1


title: UCLA_4781_Patient_1


title: UCLA_4788_Patient_1


title: UCLA_4972_Patient_1


title: UCLA_6708_Carrier_1


title: UCLA_6337_Carrier_1


title: UCLA_4973_Patient_1


title: CHOP_6486_Control_1


title: CHOP_6464_Carrier_1


title: CHOP_6479_Carrier_1


title: UCLA_6707_Carrier_1


title: CHOP_144_Patient_1


title: CHOP_6465_Control_1


title: UCLA_6705_Carrier_1


title: CHOP_4451_Patient_1


title: CHOP_4100_Patient_1


title: CHOP_4769_Patient_1


title: CHOP_6463_Control_1


title: CHOP_6462_Control_1


title: UCLA_6706_Carrier_1


title: CHOP_4750_Patient_1


title: UCLA_4786_Patient_1


title: CHOP_6466_Carrier_1


title: CHOP_4833_Patient_1


title: CHOP_4448_Patient_1


title: CHOP_4771_Patient_1


title: CHOP_4820_Patient_1


title: CHOP_4831_Patient_1


title: CHOP_4776_Patient_2


title: CHOP_4815_Patient_1


title: CHOP_4817_Patient_1


title: CHOP_4814_Patient_1


title: CHOP_4813_Patient_1


title: CHOP_6458_Carrier_1


title: CHOP_6488_Control_1


title: CHOP_6460_Control_1


title: CHOP_6461_Carrier_1


title: CHOP_4811_Patient_1


title: CHOP_6455_Control_1


title: CHOP_4250_Patient_1


title: CHOP_4806_Patient_1


title: CHOP_4749_Patient_1


title: CHOP_4755_Patient_1


title: CHOP_6457_Control_1


title: CHOP_6453_Carrier_1


title: CHOP_6446_Carrier_1


title: CHOP_4803_Patient_1


title: CHOP_6452_Control_1


title: CHOP_4687_Patient_1


title: CHOP_6451_Control_1


title: CHOP_6454_Control_1


title: CHOP_6445_Carrier_1


title: PBMC TGTTAT mcSCRB-seq


title: CHOP_6443_Control_1


title: CHOP_6448_Carrier_1


title: CHOP_6450_Control_1


title: CHOP_6449_Control_1


title: CHOP_6442_Carrier_1


title: CHOP_4684_Patient_1


title: CHOP_4805_Patient_1


title: CHOP_4801_Patient_1


title: CHOP_6490_Control_1


title: CHOP_4778_Patient_1


title: CHOP_6444_Control_1


title: CHOP_6440_Carrier_1


title: CHOP_6439_Carrier_1


title: CHOP_4049_Patient_1


title: CHOP_4658_Patient_2


title: CHOP_141_Patient_2


title: CHOP_184_mom_Carrier_1


title: CHOP_6289_Carrier_1


title: CHOP_6436_Control_1


title: CHOP_4555_Patient_2


title: CHOP_4680_Patient_1


title: CHOP_4775_Patient_1


title: CHOP_4044_mo_Carrier_1


title: CHOP_6438_Control_1


title: CHOP_4561_Patient_1


title: CHOP_6437_Carrier_1


title: CHOP_LM_Carrier_1

value: LM


title: CHOP_4502_Patient_1


title: UCLA_147_Patient_1


title: CHOP_4044_fa_Carrier_1


title: UCLA_6340_Carrier_1


title: UCLA_6336_Carrier_1


title: UCLA_4783_Patient_1


title: UCLA_6333_Carrier_1


title: UCLA_63_Patient_1


title: UCLA_6334_Carrier_1


title: UCLA_4717_Patient_1


title: UCLA_6312_Carrier_1


title: UCLA_12_Patient_1


title: UCLA_6338_Carrier_1


title: UCLA_6335_Carrier_1


title: UCLA_4716_Patient_1


title: UCLA_4714_Patient_1


title: UCLA_6332_Carrier_1


title: UCLA_4715_Patient_1


title: UCLA_4712_Patient_1


title: UCLA_4718_Patient_1


title: UCLA_4713_Patient_1


title: UCLA_200_Patient_1


title: UCLA_4597_Patient_2


title: UCLA_6327_Carrier_1


title: UCLA_6330_Carrier_1


title: UCLA_199_Patient_1


title: UCLA_6325_Carrier_1


title: UCLA_4711_Patient_3


title: UCLA_6328_Carrier_1


title: UCLA_4579_Patient_1


title: UCLA_6322_Carrier_1


title: UCLA_6314_Carrier_1


title: UCLA_33_Patient_1


title: UCLA_6323_Carrier_1


title: UCLA_4596_Patient_1


title: UCLA_6324_Carrier_1


title: UCLA_48_Patient_1


title: UCLA_6317_Carrier_1


title: UCLA_6316_Carrier_1


title: UCLA_236_Patient_1


title: UCLA_29_Patient_1


title: UCLA_4532_Patient_1


title: UCLA_6310_Carrier_1


title: UCLA_24_Patient_1


title: UCLA_6300_Carrier_1


title: CHOP_4044_Patient_1


title: CHOP_4560_Patient_1


title: CHOP_240_Patient_1


title: CHOP_4064_Patient_1


title: CHOP_4724_Patient_1


title: CHOP_4772_Patient_1


title: UCLA_14_Patient_1


title: UCLA_23_Patient_1


title: CHOP_189_Patient_1


title: CHOP_4068_Patient_2


title: CHOP_4773_Patient_1


title: CHOP_4559_Patient_1


title: UCLA_6304_Carrier_1


title: CHOP_4768_Patient_1


title: CHOP_6433_Carrier_1


title: CHOP_160_Patient_1


title: CHOP_6430_Carrier_1


title: CHOP_154_Patient_1


title: CHOP_4754_Patient_1


title: CHOP_6421_Carrier_1


title: CHOP_6360_Carrier_2


title: CHOP_6391_Control_1


title: CHOP_87_Patient_1


title: CHOP_6420_Control_1


title: CHOP_6429_Carrier_1


title: CHOP_6432_Carrier_1


title: CHOP_4765_Patient_1


title: CHOP_6428_Carrier_1


title: CHOP_6431_Carrier_1


title: CHOP_6365_Carrier_1


title: CHOP_6191_Carrier_3


title: CHOP_6370_Control_1


title: CHOP_4670_Patient_1


title: CHOP_6344_Control_1


title: CHOP_6414_Control_1


title: CHOP_4759_Patient_1


title: CHOP_6393_Control_1


title: CHOP_6413_Patient_1


title: CHOP_6417_Carrier_1


title: CHOP_6371_Carrier_1


title: CHOP_4673_Patient_1


title: CHOP_6410_Carrier_1


title: CHOP_6411_Control_1


title: CHOP_6358_Control_1


title: CHOP_6361_Carrier_1


title: CHOP_6355_Patient_1


title: CHOP_6017_Control_2


title: CHOP_6363_Patient_1


title: CHOP_215_Patient_1


title: CHOP_72_Patient_1


title: CHOP_6354_Patient_1


title: CHOP_6357_Control_1


title: CHOP_6419_Carrier_1


title: CHOP_6352_Control_1


title: CHOP_6356_Control_1


title: CHOP_6009_Carrier_1


title: CHOP_4723_Patient_1


title: CHOP_6298_Carrier_1


title: CHOP_6348_Control_1


title: CHOP_6353_Carrier_1


title: CHOP_6345_Control_1


title: CHOP_6294_Carrier_1


title: CHOP_6291_Carrier_1


title: UCLA_6286_Carrier_1


title: CHOP_6295_Carrier_1


title: CHOP_6350_Carrier_1


title: CHOP_6063_Carrier_1


title: CHOP_6349_Carrier_1


title: CHOP_6351_Patient_1


title: UCLA_6284_Carrier_1


title: UCLA_6282_Carrier_1


title: CHOP_4746_Patient_1


title: UCLA_6277_Carrier_1


title: UCLA_6278_Carrier_1


title: CHOP_6293_Carrier_1


title: CHOP_6346_Carrier_1


title: CHOP_6290_Carrier_1


title: CHOP_6271_Carrier_1


title: CHOP_6268_Carrier_1


title: CHOP_6269_Carrier_1


title: CHOP_6266_Carrier_1


title: UCLA_6276_Carrier_1


title: CHOP_6292_Carrier_1


title: CHOP_6347_Control_1


title: CHOP_6264_Control_1


title: CHOP_6265_Control_1


title: CHOP_6297_Carrier_1


title: CHOP_6267_Control_1


title: CHOP_6296_Carrier_1


title: UCLA_6283_Carrier_1


title: UCLA_6280_Carrier_1


title: UCLA_6275_Carrier_1


title: UCLA_6273_Carrier_1


title: CHOP_6270_Control_1


title: UCLA_6285_Carrier_1


title: CHOP_6263_Carrier_1r


title: CHOP_6260_Carrier_1


title: CHOP_6252_Control_1


title: CHOP_6258_Control_1


title: CHOP_6272_Carrier_1


title: CHOP_6256_Carrier_1


title: CHOP_6259_Control_1


title: CHOP_6243_Patient_1


title: CHOP_6261_Patient_1


title: CHOP_6251_Carrier_1


title: CHOP_6248_Patient_1


title: CHOP_6235_Carrier_1


title: CHOP_6253_Carrier_1


title: CHOP_6240_Carrier_1


title: CHOP_6242_Control_1


title: CHOP_6262_Control_1


title: CHOP_6249_Control_1


title: CHOP_6246_Control_1


title: CHOP_6245_Patient_1


title: CHOP_6244_Carrier_1


title: CHOP_6257_Carrier_1


title: CHOP_6250_Control_1


title: CHOP_6239_Control_1


title: CHOP_6234_Control_1


title: CHOP_4756_Patient_1


title: CHOP_6241_Carrier_1


title: CHOP_6232_Control_1


title: CHOP_6238_Control_1


title: CHOP_4757_Patient_1


title: CHOP_4763_Patient_1


title: CHOP_6233_Control_1


title: CHOP_6228_Carrier_1


title: UCLA_6226_Carrier_1


title: CHOP_6231_Control_1


title: CHOP_6230_Control_1


title: UCLA_6225_Carrier_1


title: UCLA_6219_Carrier_1


title: UCLA_6222_Carrier_1


title: UCLA_6214_Carrier_1


title: UCLA_6218_Carrier_1


title: UCLA_6213_Carrier_1


title: UCLA_6215_Carrier_1


title: CHOP_6229_Control_1


title: CHOP_6212_Control_1


title: CHOP_6211_Control_1


title: UCLA_6210_Carrier_1


title: UCLA_6208_Carrier_1


title: UCLA_6207_Carrier_1


title: CHOP_6205_Carrier_1


title: CHOP_6195_Carrier_1


title: UCLA_6203_Carrier_1


title: CHOP_6196_Patient_1


title: CHOP_6202_Carrier_1


title: CHOP_6204_Carrier_1


title: CHOP_6200_Carrier_1


title: CHOP_6198_Carrier_1


title: CHOP_6199_Patient_1


title: CHOP_6194_Carrier_1


title: UCLA_6192_Carrier_1


title: CHOP_6193_Carrier_1


title: CHOP_6206_Patient_1


title: UCLA_6188_Carrier_1


title: UCLA_6184_Carrier_1


title: UCLA_6189_Carrier_1


title: UCLA_6178_Carrier_1


title: UCLA_6190_Carrier_1


title: UCLA_6180_Carrier_1


title: UCLA_6177_Carrier_1


title: UCLA_6187_Carrier_1


title: UCLA_6185_Carrier_1


title: UCLA_6183_Carrier_1


title: CHOP_6175_Carrier_1


title: UCLA_6173_Carrier_1


title: UCLA_6186_Carrier_1


title: CHOP_6176_Control_1


title: UCLA_6182_Carrier_1


title: UCLA_6167_Carrier_1


title: UCLA_6181_Carrier_1


title: UCLA_6179_Carrier_1


title: CHOP_6162_Control_1


title: CHOP_6154_Carrier_1


title: CHOP_6163_Control_1


title: CHOP_6152_Carrier_1


title: CHOP_6153_Carrier_1


title: CHOP_6160_Control_1


title: CHOP_6161_Control_1


title: UCLA_6166_Carrier_1


title: CHOP_6158_Carrier_1


title: CHOP_6157_Carrier_1


title: CHOP_6145_Carrier_1


title: CHOP_6144_Carrier_1


title: CHOP_6159_Control_1


title: CHOP_6155_Control_1


title: CHOP_6137_Control_1


title: CHOP_6141_Control_1


title: CHOP_6147_Carrier_1


title: CHOP_6151_Carrier_1


title: CHOP_6150_Carrier_1


title: CHOP_6146_Carrier_1


title: CHOP_6127_Control_1


title: CHOP_6142_Carrier_1


title: CHOP_6131_Control_1


title: CHOP_6143_Carrier_1


title: CHOP_6148_Control_1


title: CHOP_6125_Carrier_1


title: CHOP_6135_Carrier_1


title: CHOP_6149_Carrier_1


title: CHOP_6128_Carrier_1


title: CHOP_6108_Patient_1


title: CHOP_6118_Patient_1


title: CHOP_6107_Patient_1


title: CHOP_6126_Carrier_1


title: CHOP_6123_Carrier_1


title: met-2(n4256) set-25(n5021) hrde-1(+R) F5 after hrde-1 repair small RNA-Seq

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description:
small RNA
SG0717_lib58_raw

data_processing:
Remove  the 3' linker 5'-CTGTAGGCACCATCAATC-3' and the 5' 4-nt inline barcodes
Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis.
The number of reads that map to each 1 kb window throughout the genome is calculated and then normalized to the total number of reads that map to the genome. If a read maps to multiple positions in the genome (N times), it will be counted as 1/N at each position.
Genome_build: WS190(ce6)
Supplementary_files_format_and_content: File format: MS Excel file. The content includes normalized counts for each 1 kb region (row) in the genome for each library (column) used in this study.

organism: Caenorhabditis elegans

source_name: C. elegans young adults

extract_protocol:
small RNA was extracted by using mirVana™ miRNA Isolation Kit (ThermoFisher).
Small RNA-seq was performed using a 5’-monophosphate-independent small RNA cloning procedure described in Gent, J.I. et al. A Caenorhabditis elegans RNA-directed RNA polymerase in sperm development and endogenous RNA interference. Genetics 183, 1297–1314 (2009).

tag: developmental stage

value: young adult

value: hermaphrodite

tag: inline barcode at the 5' end

value: mixture of 'CTGG','ACTG','GAAG','TGCC'


title: hrde-1(+R) F20 after hrde-1 repair small RNA-Seq

description:
small RNA
SG0717_lib46_raw


title: set-32(red11); hrde-1(+R) F20 after hrde-1 repair small RNA-Seq

description:
small RNA
SG0717_lib56_raw


title: hrde-1(+R) F5 after hrde-1 repair small RNA-Seq

description:
small RNA
SG0717_lib45_raw


title: set-32(red11); hrde-1(+R) F5 after hrde-1 repair small RNA-Seq

description:
small RNA
SG0717_lib55_raw


title: met-2(n4256) set-25(n5021) hrde-1(+R) F20 after hrde-1 repair small RNA-Seq

description:
small RNA
SG0717_lib59_raw


title: set-32(ok1457); hrde-1(+R) F8 after hrde-1 repair small RNA-Seq

description:
small RNA
SG0717_lib50_raw


title: CHOP_6119_Patient_1


title: CHOP_6124_Carrier_1


title: set-32(red11); hrde-1(+R) F20 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG1217_lib9_raw

data_processing:
Remove the 5' 4-nt inline barcodes
Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis.
The number of reads that map to each 1 kb window throughout the genome is calculated and then normalized to the total number of reads that map to the genome. If a read maps to multiple positions in the genome (N times), it will be counted as 1/N at each position.
Genome_build: WS190(ce6)
Supplementary_files_format_and_content: File format: MS Excel file. The content includes normalized counts for each 1 kb region (row) in the genome for each library (column) used in this study.

extract_protocol:
Total RNA extraction was performed using the TRIzol Reagent. Ribosomal RNA (rRNA) was removed from the total RNA using RNase H and anti-rRNA oligo mixture. 1.25 µg of anti-rRNA oligos were mixed with 0.5 µg total RNA in 1x Hybridization Buffer (100 mM Tris-HCl pH 7.4, 200mM NaCl) in a final volume of 8 µl.  The sample was denatured at 95°C for 2 minutes, and then cooled at −0.1 °C /sec to 45°C.  Equal volumes of Hybridase Thermostable RNase H (5U/µl,Epicentre) and 10x RNaseH Reaction Buffer (500 mM Tris-HCl pH 7.4, 1 M NaCl, 200 mM MgCl2) were mixed and preheated to 45°C before use. 2 µl of the enzyme mix was added to each reaction mix, which was then incubated at 45°C for 1 hr. To remove DNA oligos, 5 µl TURBO DNase buffer, 3 µl TURBO DNase (Invitrogen), and 32 µl diH2O were added to the reaction mix, followed by 37˚C incubation for 30 minutes.  To purify RNA, 300 µl STOP solution (1 M ammonium acetate, 10 mM EDTA) was added to the reaction mix, followed by phenol/chloroform (1:1) extraction and ethanol precipitation.
The resulting RNA (without poly(A) selection) was used to prepare the RNA-seq library using the standard Illumina RNA-seq library construction protocol.


title: set-32(ok1457); hrde-1(tm1200) small RNA-Seq

description:
small RNA
SG0717_lib48_raw


title: met-2(n4256) set-25(n5021) hrde-1(tm1200) small RNA-Seq

description:
small RNA
SG0315_lib39_raw


title: set-32(red11); hrde-1(tm1200) small RNA-Seq

description:
small RNA
SG0717_lib53_raw


title: N2 small RNA-Seq

description:
small RNA
SG1116_lib7_raw


title: met-2(n4256) set-25(n5021)  small RNA-Seq

description:
small RNA
SG0315_lib38_raw


title: set-32(ok1457) small RNA-Seq

description:
small RNA
SG0717_lib47_raw


title: hrde-1(tm1200) small RNA-Seq

description:
small RNA
SG0315_lib37_raw


title: set-32(red11) small RNA-Seq

description:
small RNA
SG0717_lib52_raw


title: set-32(ok1457); hrde-1(+R) F20 after hrde-1 repair small RNA-Seq

description:
small RNA
SG0717_lib51_raw


title: set-32(ok1457); hrde-1(+R) F20 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG1217_lib8_raw


title: CHOP_6136_Carrier_1


title: met-2(n4256) set-25(n5021) hrde-1(tm1200) RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib8_raw


title: set-32(ok1457) RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib9_raw


title: met-2(n4256) set-25(n5021) RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib7_raw


title: hrde-1(+R) F20 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG1217_lib7_raw


title: met-2(n4256) set-25(n5021)hrde-1(+R) F20 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG1217_lib10_raw


title: met-2(n4256) set-25(n5021) hrde-1(+R) F3 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib19_raw


title: met-2(n4256) set-25(n5021) hrde-1(+R) F5 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib20_raw


title: set-32(red11); hrde-1(+R) F5 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib22_raw


title: hrde-1(tm1200) RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib2_raw


title: set-32(red11); hrde-1(tm1200) RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib6_raw


title: set-32(red11); met-2(n4256) set-25(n5021) hrde-1(tm1200) RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib4_raw


title: set-32(red11) RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib5_raw


title: set-32(red11); met-2(n4256) set-25(n5021) hrde-1(+R) F5 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib23_raw


title: set-32(red11); hrde-1(+R) F4 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib21_raw


title: set-32(ok1457); met-2(n4256) set-25(n5021) RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib3_raw


title: CHOP_6101_Control_1


title: CHOP_6106_Patient_1


title: set-32(ok1457); hrde-1(+R) F8 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib18_raw


title: CHOP_6103_Carrier_1


title: CHOP_6104_Control_1


title: CHOP_6094_Carrier_1


title: CHOP_6100_Control_1


title: CHOP_6102_Carrier_1


title: CHOP_6095_Control_1


title: CHOP_6097_Control_1


title: CHOP_6129_Carrier_1


title: set-32(ok1457); hrde-1(+R) F5 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib17_raw


title: hrde-1(+R) F4 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib14_raw


title: CHOP_6093_Carrier_1


title: hrde-1(+R) F5 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib15_raw


title: CHOP_6092_Carrier_1


title: set-32(ok1457); hrde-1(tm1200) RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib10_raw


title: CHOP_6080_Carrier_1


title: CHOP_6086_Patient_1


title: CHOP_6088_Carrier_1


title: CHOP_6081_Carrier_1


title: N2, oma-1 RNAi for two generations ChIP-Seq

data_processing:
Map reads to C. elegans genome using bowtie 0.12.7. Only perfect alighments are used for the analysis.
The number of reads that map to each 1 kb window throughout the genome is calculated and then normalized to the total number of reads that map to the genome. If a read maps to multiple positions in the genome (N times), it will be counted as 1/N at each position.
Genome_build: WS190(ce6)
Supplementary_files_format_and_content: File format: MS Excel file. The content includes normalized counts for each 1 kb region (row) in the genome for each library (column) used in this study.

extract_protocol:
Chromatin immunoprecipitation was performed using the protocol described in BMC Genomics. 2014 Dec 22;15:1157. doi: 10.1186/1471-2164-15-1157.
Standard Illumina library was constructed as described in BMC Genomics. 2014 Dec 22;15:1157. doi: 10.1186/1471-2164-15-1157.
Standard Illumina library for genomic DNA

tag: food

value: E. coli HT115 strain expressing oma-1 dsRNA

tag: antibody used for chip


title: N2 RNA-Seq

description:
Total RNA, rRNAs are removed by RNaseH-based approach
SG0117_lib1_raw


title: N2, oma-1 RNAi for one generation ChIP-Seq


title: met-2(n4256) set-25(n5021) hrde-1(tm1200) mutant ChIP-Seq

value: E. coli OP50 strain

value: Pol II


title: set-32(red11); hrde-1(tm1200) mutant ChIP-Seq


title: set-32(red11); met-2(n4256) set-25(n5021) mutant ChIP-Seq


title: set-32(red11);  met-2(n4256) set-25(n5021) hrde-1(tm1200) mutant  ChIP-Seq


title: N2 ChIP-Seq 2


title: CHOP_6082_Carrier_2


title: met-2(n4256) set-25(n5021) mutant ChIP-Seq


title: set-32(red11) mutant ChIP-Seq


title: hrde-1 (tm1200) mutant ChIP-Seq


title: N2 ChIP-Seq 1


title: CHOP_6079_Carrier_1


title: CHOP_6078_Carrier_1


title: CHOP_6070_Carrier_1


title: CHOP_6075_Carrier_1


title: CHOP_6069_Carrier_1


title: CHOP_6068_Carrier_1


title: CHOP_6067_Carrier_1


title: CHOP_6062_Carrier_1


title: CHOP_6065_Carrier_1


title: Pem2_ell1Δ2_RNAseq

city: Kansas City

first: Dana

last: Gibbon

state: MO

institute: Stowers Institute for Medical Research

data_processing:
ChIP-seq reads were aligned to ASM294v2  with bowtie2 2.2.9
Aligned ChIP-seq reads were sorted, indexed and filtered (MAPQ > 10) with samtools 1.3.1
Broad peaks were called with macs2 callpeaks 2.1.1 with settings -nomodel -broad -f BAM -gsize 12100000 -B
RNA-seq reads were alignedReads were aligned to S. pombe ASM294v2 with TopHat (v2.1.1)
Counts were generated with a custom R script for unambiguous uniquely mapped reads with MAPQ score > 10
Differentially expressed genes were found using edgeR’s (v3.18.1) exactTest
Genome_build: ASM294v2
Supplementary_files_format_and_content: bigWig files were generated
Supplementary_files_format_and_content: normalized abundance measurements were calculated with edgeR for RPKMs

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: Yeast cells

growth_protocol: All yeast cultures were grown in rich medium (YES) supplemented with adenine, histidine, leucine and uracil (225 μg/ml) at 32°C to mid log phase.

extract_protocol:
Lysates were clarified from sonicated nuclei for ChIP experiments.
Libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Pem2 ell1-delta

tag: genotype

value: PEM-2; delta-ell1::natMX6

tag: chip antibody


title: Pem2_WT1_RNAseq

value: Pem2 (WT)

value: h- ade6-M210 leu1-32 ura4-D18 mat1_m-cyhS, smt0 rpl42::cyhR(sP56Q)


title: Pem2_WT2_RNAseq


title: WT2_RNAseq


title: WT1b_RNAseq


title: ell1Δ1b_RNAseq

value: ED666 ell1-delta

value: h+ delta-ell1::kanMX6 ade6-M210 ura4-D18 leu1-32


title: WT1_RNAseq


title: Pem2_ell1Δ1_RNAseq


title: WT3_RNAseq


title: ell1Δ2b_RNAseq


title: WT2b_RNAseq


title: eaf1Δ3_RNAseq

value: ED666 eaf1-delta

value: h+ delta-eaf1::kanMX6 ade6-M210 ura4-D18 leu1-32


title: CHOP_6058_Patient_1

tag: pidn

tag: sample number

value: CHOP

value: Patient

value: FEMALE


title: eaf1Δ1_RNAseq


title: CHOP_6061_Carrier_1

tag: batch

tag: site

value: Carrier

value: MALE


title: ebp1Δ3_RNAseq

value: ED666 ebp1-delta

value: h+ delta-ebp1::kanMX6 ade6-M210 ura4-D18 leu1-32


title: CHOP_6060_Patient_1

tag: rin

tag: status


title: CHOP_6089_Carrier_1

tag: Sex

tag: age


title: CHOP_6059_Patient_1


title: ebp1Δ2_RNAseq


title: eaf1Δ2_RNAseq


title: CHOP_6056_Patient_1

tag: onset

tag: duration


title: CHOP_6055_Patient_1


title: ebp1Δ1_RNAseq


title: WT1_input DNA


title: Ell1_WT2_ChIPSeq


title: WT2b_input DNA


title: Eaf1_WT2b_ChIPSeq


title: Eaf1_WT1_ChIPSeq


title: Ebp1_WT2b_ChIPSeq


title: WT2_input DNA


title: Ell1_WT1_ChIPSeq


title: CHOP_6071_Carrier_1


title: ell1Δ1_input DNA


title: Ell1_ell1Δ2_ChIPSeq


title: eaf1Δ2b_input DNA

value: Pem2 eaf1-delta

value: PEM-2; delta-eaf1::natMX6


title: eaf1Δ1_input DNA


title: 4H8_WT2_ChIPSeq


title: Ebp1_WT1_ChIPSeq


title: CHOP_6054_Patient_1


title: CHOP_6052_Patient_1


title: Eaf1_eaf1Δ2b_ChIPSeq


title: CHOP_6048_Patient_1


title: CHOP_6050_Carrier_1


title: CHOP_6051_Carrier_1


title: CHOP_6047_Carrier_1


title: CHOP_6049_Carrier_1


title: CHOP_6098_Carrier_1


title: CHOP_6046_Carrier_1


title: ebp1Δ2_input DNA

value: Pem2 ebp1-delta

value: PEM-2; delta-ebp1::natMX7


title: 4H8_WT1_ChIPSeq

value: Pem2 (WT)


title: ebp1Δ2b_input DNA

value: PEM-2; delta-ebp1::natMX6


title: Eaf1_eaf1Δ1_ChIPSeq


title: Ebp1_ebp1Δ2b_ChIPSeq


title: ebp1Δ1_input DNA


title: Ell1_ell1Δ1_ChIPSeq

value: Pem2 ell1-delta

value: PEM-2; delta-ell1::natMX6


title: Ebp1_ebp1Δ1_ChIPSeq


title: CD8_24_7

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Ave

department: Biochemistry

institute: Weill Cornell Medicine

data_processing:
Illumina bcl2fastq v2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using tophat-2.0.11
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Excel include RPKM values for each Sample ...

source_name: Tumor CD8 Lymphocytes

extract_protocol:
Tissue for RNA-Seq analyses was diced, ground through a 140 μm mesh, filtered through a 70 μm filter, and red blood cells lysed. Single cell suspensions were stained using standard protocols to identify CD4 and CD8 lymphocytes. Cells were sorted via flow cytometry into lysis buffer. RNA was extracted using the RNeasy kit with on column DNA digestion, and submitted for sequencing.
RNA library preparation was performed using the Illumina TruSeq RNA Sample Preparation kit, and 8 samples per lane were sequenced with single-end 50 bps on HiSeq4000 (Illumina).

treatment_protocol: For treatment studies, 250 μg of either anti-PD-1 or IgG control were diluted in sterile PBS and administered intraperitoneally in a volume of 100 μL per dose on either days 7, 10, 13, and 16 post- implantation

tag: treatment

tag: days

tag: bli group

value: Group 6


title: CD8_17_5


title: CD8_24_8

value: Group 5


title: CD8_24_6


title: S_2407_07_1.clean (paired)

city: Kumamoto

first: Yutaka

last: Okuno

state: Kumamoto

address: 1-1-1 Honko, Chuo Ku

department: Department of Hematology

institute: Kumamoto university of Medicine

description: total RNA

data_processing:
Biomedical Genomics Workbench
Raw data filtering:
Remove reads containing adapters
Remove reads containing N > 10% (N represents the base cannot be determined).
Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
We next compared the differences in gene expression between tumor cells from C?1-Cre Spi1 KO mice and those from Spi1-loxP mice.
genome build: GRCm38
processed data files format and content: fold change

source_name: Cγ1-Cre Spi1 KO mice

extract_protocol:
Total RNA was isolated from cells using the ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI, USA).
mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: C57BL/6 and Sv129 mix background

tag: cell type

value: splenic B cells from a mouse with mild splenomegaly


title: N_516_1_1.clean (paired)

description: total RNA

tag: strain

value: DLBCL cells


title: N_572_4_1.clean (paired)

description: total RNA


title: N_405_1p_1.clean (paired)

description: total RNA


title: N_1752_1_4.clean (paired)

description: total RNA

source_name: PU.1-loxP mice

value: normal B cells


title: S_540_3_1.clean (paired)

description: total RNA


title: N_1752_1_1.clean (paired)

description: total RNA


title: CD8_17_1


title: CD8_24_5


title: CD8_24_3


title: CD8_24_4

value: Group 4


title: CHOP_6040_Carrier_1

value: CHOP

value: Carrier

value: FEMALE


title: CD8_17_8


title: CD8_17_6


title: CD8_17_7


title: CD8_24_2


title: CD8_24_1


title: CHOP_6039_Carrier_1


title: CD8_17_4


title: CD8_17_3


title: CD8_14P_3

value: Group 3


title: CD8_14P_2


title: CD8_14P_8


title: CD8_14P_7


title: CD8_14P_6

value: Group 2


title: CHOP_6018_Control_1

value: Control

value: MALE


title: CHOP_6037_Carrier_1


title: CD8_14P_5


title: CHOP_6045_Carrier_1


title: CHOP_6034_Carrier_1


title: CHOP_6030_Control_1


title: CHOP_6024_Carrier_1


title: CHOP_6035_Carrier_1


title: CD8_14P_1


title: CD8_14I_8

value: IgG

value: Group 1


title: CHOP_6074_Carrier_1


title: CD8_14P_4


title: CHOP_6042_Carrier_1


title: CD8_14I_7


title: CHOP_6023_Carrier_1


title: CHOP_6038_Carrier_1


title: CHOP_6019_Carrier_1


title: CHOP_6016_Carrier_1


title: CHOP_6036_Carrier_1


title: UCLA_6031_Patient_1

value: UCLA

value: Patient


title: CHOP_6012_Control_1


title: CHOP_6008_Carrier_1


title: CHOP_6027_Carrier_1


title: CHOP_6044_Carrier_1


title: CHOP_6014_Control_1


title: CHOP_6011_Control_1


title: CD4_17_1

source_name: Tumor CD4 Lymphocytes

value: Group 6


title: CD8_14I_1


title: CD8_14I_2


title: CD8_14I_3


title: CD8_14I_6


title: CD8_14I_4


title: CD4_24_7


title: CD4_24_6


title: CD8_14I_5


title: CD4_24_8

value: Group 5


title: CD4_24_5


title: CHOP_6001_Patient_1


title: CHOP_4722_Patient_1

tag: functional stage


title: CHOP_6015_Carrier_1


title: CHOP_4743_Patient_1


title: CHOP_6007_Carrier_2


title: CHOP_4744_Patient_1


title: CD4_24_3


title: CHOP_6004_Patient_1


title: CD4_17_5


title: CD4_24_4


title: CHOP_4721_Patient_1


title: CHOP_4683_Patient_1


title: CD4_24_2


title: CD4_17_6


title: CD4_17_4


title: CD4_17_7


title: CHOP_4679_Patient_1


title: CD4_17_8


title: CD4_17_3


title: CD4_17_2


title: CD4_14P_2


title: CD4_14P_8


title: CD4_14P_3


title: CtIP-KO C27 rep1

city: Shanghai

first: Jia

last: Shou

state: Shanghai

address: 800 Dongchuan Rd

department: Institute of Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

data_processing:
Illumina GA Pipeline v1.5 was used for basecalling.
Sequenced reads (49 bp, single-read) were aligned to the human genome (GRCh37) using the TopHat software (v2.0.14) with the parameters of -N 0 –g 1 –x 1. The expression levels of each transcript were calculated using the Cufflinks software (v2.2.1) with the default parameters.
The output data were then averaged among biological replicates and normalized to reads per million (RPM) by the genomeCoverageBed program.
Genome_build: GRCh37
Supplementary_files_format_and_content: bedGraph files were generated using the genomeCoverageBed tool. Scores represent raw reads per million.

source_name: HEK293T_CtIP-KO C27

extract_protocol:
total RNA was extracted from cultured cells ( wide type control and CtIP knockout cell in duplicates) using an RNeasy plus mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: human embryonic kidney cells

tag: genotype/variation

value: CtIP-/-


title: CtIP-KO C14 rep1

source_name: HEK293T_CtIP-KO C14


title: CtIP-KO C14 rep2


title: WT rep2

value: wild type


title: CD4_14P_7


title: CD4_14P_6


title: CHOP_4676_Patient_1

tag: pidn

tag: sample number


title: CHOP_4677_Patient_1

tag: batch

tag: site


title: 15ss_Posterior_rep2

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

institute: Ecole Normale Superieure

data_processing:
paired-end reads were mapped onto the zebrafish genome assembly dn9 using STAR (outFilterMultimapNmax 1; outFilterMismatchNmax 999; outFilterMismatchNoverLmax 0.06 ; alignIntronMax 1; alignEndsType EndToEnd; alignMatesGapMax 2000).
Duplicates reads were removed using Picard (http://picard.sourceforge.net) (MarkDuplicates, REMOVE_DUPLICATES = true).
Bigwig tracks were made using DeepTools BamCoverage (1.5.9.1), keeping only fragment smaller than 100bp to exclude fragment containing nucleosomes.
Genome_build: DanRer7
Supplementary_files_format_and_content: bigwig of signal from fragments < 100bp

organism: Danio rerio

growth_protocol: All embryos were dissected in cold PBS to remove the vitellus (50 embryos at 95% epiboly) and to isolate the hindbrain and the posterior part of the embryo (80 embryos at 5s and 50 embryos at 15s).

extract_protocol:
Cells were lysed before transposition using 1 μl of transposome and purified using a Qiagen MinElute Kit with 10 μl of Elution Buffer. Transposed DNA was amplified by PCR (Picelli et al., 2014) and quantified by qPCR as previously described (Thierion et al., 2017).
Sequencing was done on multiplexed samples using 42 bp Paired-end reads on the Illumina NextSeq system according to the manufacturer’s specifications at the genomics platform of IBENS.

value: multiple cross

tag: tissue

value: Posterior


title: CHOP_4671_Patient_1

value: CHOP

tag: rin

tag: status

tag: Sex


title: CD4_14P_5


title: CHOP_4678_Patient_1

tag: age

tag: onset

tag: duration


title: 15ss_Posterior_rep1


title: CD4_14P_4

tag: treatment

tag: days

tag: bli group


title: CHOP_4668_Patient_1

tag: functional stage


title: CHOP_4667_Patient_1

value: FEMALE


title: CD4_14P_1

tag: strain


title: WT rep1

tag: cell line

tag: cell type

tag: genotype/variation


title: 5ss_Posterior_rep2


title: CHOP_4669_Patient_1

tag: pidn

tag: sample number

tag: batch


title: CHOP_4675_Patient_1

tag: site

tag: rin


title: 5ss_Posterior_rep1

tag: tissue


title: CD4_14I_8


title: CD4_14I_7


title: CHOP_4666_Patient_1

tag: status

tag: Sex

tag: age


title: CD4_14I_6

tag: treatment


title: CHOP_4665_Patient_1

tag: onset

tag: duration


title: 15ss_HindBrain_rep1

value: HindBrain


title: CHOP_4656_Patient_1

tag: functional stage


title: 5ss_HindBrain_rep1

tag: strain


title: CD4_14I_5

tag: days

tag: bli group


title: CD4_14I_4


title: CD4_14I_3


title: 95%epiboly_wholeEmbryo_rep2

value: whole Embryo

value: 95% epiboly


title: CD4_14I_2


title: CHOP_4653_Patient_1

value: MALE


title: 95%epiboly_wholeEmbryo_rep1


title: CHOP_4659_Patient_1


title: CD4_14I_1

value: IgG


title: CHOP_4654_Patient_1


title: 5ss_HindBrain_rep2


title: CHOP_4652_Patient_1


title: CHOP_4664_Patient_1


title: 15ss_HindBrain_rep2


title: CHOP_4650_Patient_1


title: CHOP_4648_Patient_1


title: Case#2_R1_Lin-cKit+

first: Harold

last: Varmus

address: 1300 York Ave

department: Department of Medicine

description:
End-stage mouse which received splenic transplant from Case#2 donor mouse and developed AML. mRNA sequencing.
AML_splicing_03202018.xlsx; AML_gene_expression_03202018.xlsx

data_processing:
Analysis of mRNA sequencing samples was the same as our previous submission (GEO: GSE80136). Briefly, reads were first mapped to these transcripts using RSEM [PMCID: PMC3163565]. Remaining unaligned reads were then mapped to a database of possible junctions between all 5' and 3' splice sites of those transcripts, and then subsequently to the GRCm38 mouse genome assembly, using TopHat [PMID: 19289445]. These read counts were then subjected to Wagenmakers’s Bayesian alternative to the binomial proportion test [PMID: 20064637]. Differentially spliced events were defined as those that exhibited a difference in absolute isoform ratio of at least 10%; differentially expressed genes (coding) were defined as those that exhibited at lease two-fold difference in a group comparison as indicated.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel tables. In the table for altered splicing events, each row corresponds to an isoform of a splicing event that is differentially spliced for the indicated comparisons that do or do not express U2af1(S34F). In each case, the isoform for which information is given is as follows: the inclusion isoform for cassette exons (type “se”), the intron-proximal isoform for competing 5' or 3' splice site events (types “a5ss” or “a3ss”), inclusion of the upstream exon for mutually exclusive exon events (type “mxe”), splicing of retained introns annotated as alternative (type “ri”) or constitutive (type “ci”), or canonical splicing of an annotated constitutive junction (type “cj”). The columns specify relevant annotations for each event as follows: “coords” specifies the genomic coordinates of the event; “gene” specifies the Ensembl gene ID; “geneName” specifies the gene name; “geneDescription” is a description of the gene as given by Ensembl; “type” specifies the type of splicing event; “nmdTarget” specifies whether the isoform is a predicted substrate for degradation by NMD (NA indicates that either all or no isoforms of the event are predicted NMD substrates). The columns prefixed by “deltaPsi_” give the absolute difference in isoform ratio (Percent Spliced In or “PSI” value) for the indicated comparisons. In the table for altered gene expression, each row corresponds to a coding gene that is differentially expressed for the indicated comparisons that do or do not express U2af1(S34F). Only those with at least 2-fold difference (logFoldChange ≥ 1 or ≤ -1) and p value (pval ≤ 0.05) were shown.

source_name: Lineage-ScaI-cKit+ cells from the spleen

growth_protocol: MEFs were cultured in DMEM, supplemented with 10% fetal bovine serum and Penicillin-Streptomycin

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) or AllPrep DNA/RNA kit (Qiagen)
TruSeq RNA Sample Preparation (Non-Stranded and Poly-A selection) for mRNA sequencing

treatment_protocol: MEFs were treated with 4OHT (500 ng/ml) or vehicle for 24 hr, incubate for 48 hr without the drug, repeat the 4OHT (500 ng/ml) or vehicle treatment for 24 hr, and incubate for another 48 hr without the drug before harvest for RNA. Mice were treated with poly (IC). Lineage-cKit+ (Lin-cKit+) cells were isolated from mouse bone marrow 4 weeks later by fluorescence-activated cell sorting (FACS). In another set of experiments, end-stage mice, which were either treated with poly (IC) and ENU or were the splenic recipients of such mice, were used for isoloation of Lin-cKit+ cells by FACS.

value: Splenic transplant recipient

tag: genotype

value: MGS34F/WT; GFP/WT; Runx1F/F; Mx1-Cre/WT


title: Case#3_R3_Lin-cKit+

description:
End-stage mouse which received splenic transplant from Case#3 donor mouse and developed AML. mRNA sequencing.
AML_splicing_03202018.xlsx; AML_gene_expression_03202018.xlsx


title: CHOP_4644_Patient_1

tag: pidn

value: Patient


title: Case#1_R5_Lin-cKit+

description:
End-stage mouse which received splenic transplant from Case#1 donor mouse and developed AML. mRNA sequencing.
AML_splicing_03202018.xlsx; AML_gene_expression_03202018.xlsx


title: AML_Cbfb-Myh11_1

description:
End-stage mouse with AML. mRNA sequencing.
AML_splicing_03202018.xlsx; AML_gene_expression_03202018.xlsx

value: poly (IC) (250 µg/moue, i.p, every other day, three doses), followed by one dose of ENU (100 mg/kg, i.p.)

value: Cbfb-Myh11/WT; Mx1-Cre/WT


title: LWmouse_Lung_72hr_2

city: Tokyo

first: Shion

last: Miyoshi

address: 5-21-16, Omori-Nishi, Ota-Ku

institute: Toho University

hyb_protocol: Agilent one-color gene expression hyb/wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G4900DA Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol.

extract_protocol: Total RNAs were extracted from the lungs of mice using Sepasol-RNA I Super G according to the manufacturer’s instructions.

treatment_protocol: BM chimeric mice were sacrificed at 72 hours after DT injection and lungs were harvested.

tag: bone marrow chimeric mice

value: BM cells of LysM-DTR mice into wild-type mice

value: Lung

tag: gender

value: Male

value: after 72hr in DT-administered mouse lung


title: WWmouse_Lung_72hr_2

value: BM cells of wild-type mice into wild-type mice


title: CHOP_4651_Patient_1

tag: sample number

tag: batch

tag: site

value: CHOP


title: CHOP_4640_Patient_1

tag: rin

tag: status


title: WWmouse_Lung_72hr_1

tag: tissue

tag: age


title: Case#1_R4_Lin-cKit+

tag: treatment


title: Case#1_R3_Lin-cKit+


title: CHOP_4632_Patient_1

tag: Sex

tag: onset

tag: duration


title: LWmouse_Lung_72hr_1


title: CHOP_4634_Patient_1

tag: functional stage


title: CHOP_4641_Patient_1


title: MP.runx1_wt-u2af1_wt.D

description:
Cells were harvested from the mouse four week after poly (IC) treatment. mRNA sequencing.
MP_splicing_03202018.xlsx; MP_gene_expression_03202018.xlsx

source_name: Lineage-ScaI-cKit+ cells from the bone marrow

value: poly (IC) (250 µg/moue, i.p, every other day, three doses)


title: CHOP_4639_Patient_1


title: LLmouse_Lung_72hr_2

value: BM cells of LysM-DTR mice into LysM-DTR mice;


title: WLmouse_Lung_72hr_2

value: BM cells of wild-type mice into LysM-DTR mice


title: CHOP_4645_Patient_1


title: MP.runx1_ko-u2af1_s34f.D


title: WLmouse_Lung_72hr_1


title: CHOP_4629_Patient_1


title: MP.runx1_wt-u2af1_s34f.D

value: MGS34F/WT; GFP/WT; Mx1-Cre/WT


title: CHOP_4628_Patient_1

value: MALE


title: mTAMs

city: Taipei

first: Chih-Chan

last: Lee

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: Molecular medicine program

description: mTAMs, metastatic tumor-associated macrophages

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA through R based affy module

label: Biotin

source_name: Isolated from matched metastatic lung

label_protocol: standard Affymetrix procedures

growth_protocol: TAMs isolated from primary tumor and metastatic lung of 5 weeks 4T1 tumor-bearing mice.

extract_protocol: Total RNA were extracted by RNeasy mini kit (Cat. 74106; Qiagen, Hilden, Germany), and 100 ng to 1 ug of total RNA were subjected into reverse transcription using the SuperScriptTM III Reverse transcriptase kit (Invitrogen) as directed by the manufacturer.

value: metastatic tumor-associated macrophages


title: pTAMs

description: pTAMs, primary tumor-associated macrophages

source_name: Isolated from 4T1 breast tumor

value: primary tumor-associated macrophages


title: CHOP_4636_Patient_1


title: MP.runx1_ko-u2af1_wt.D

value: Runx1F/F; Mx1-Cre/WT


title: MP.runx1_ko-u2af1_s34f.C

value: MGS34F/WT; GFP/WT; Runx1F/F; Mx1-Cre/WT


title: CHOP_4627_Patient_1

value: Patient

value: FEMALE


title: LLmouse_Lung_72hr_1


title: MP.runx1_wt-u2af1_s34f.C


title: BMDM

description: BMDM, bone marrow-derived macrophages

source_name: bone marrow-derived macrophages

value: bone marrow-derived macrophages


title: MP.runx1_wt-u2af1_wt.C


title: MP.runx1_ko-u2af1_wt.C


title: MP.runx1_ko-u2af1_s34f.B


title: MP.runx1_wt-u2af1_wt.B


title: TREATED [R1236_4]

city: ROME

first: FEDERICA

last: LAUDISI

address: VIA MONTPELLIER, 1

department: SYSTEMS MEDICINE

country: Italy

institute: UNIVERSITY OF ROME "TOR VERGATA"

description: gene expression data from colon samples isolated from mouse exposed to 5% Maltodextrin diluited in drinking water for 45 days

scan_protocol: Signal intensities of fluorescent images produced during GeneChip hybridizations were read by an Affymetrix Model 3000 Scanner

data_processing: Results were analyzed using Partek Genomics Suite (version 6.6 [6.15.0422]) using quantile normalization.

source_name: Mouse exposed to 5% Maltodextrin diluited in drinking water

label_protocol: not provided

extract_protocol: Total RNA was extracted from colon samples using PureLink® Purification technology kit with RNase free DNase set (Thermo Fisher Scientific, Monza, Italy). Samples with quantified cDNA were sequenced in Microarray Unit of COGENTECH Scarl (Consortium for Genomic Technologies, Milan, Italy) by hybridization to GeneChip Mouse Gene 2.0 ST microarrays.

treatment_protocol: Balb/c mice were exposed to drinking water in the presence or absence of 5% Maltodextrin for 45 days

tag: strain

value: Balb/c

value: colon


title: CTRL [R1236_2]

description: gene expression data from colon samples isolated from mouse exposed to drinking water for 45 days

hyb_protocol: Samples with quantified cDNA were sequenced in Microarray Unit of COGENTECH Scarl (Consortium for Genomic Technologies, Milan, Italy) by hybridization to GeneChip Mouse Gene 2.0 ST microarrays.

source_name: Mouse exposed to drinking water


title: TREATED [R1236_3]


title: UCLA_4595_Patient_1

value: UCLA


title: MP.runx1_ko-u2af1_wt.B

tag: genotype


title: MP.runx1_wt-u2af1_s34f.B


title: CHOP_4621_Patient_1

tag: pidn


title: UCLA_4588_Patient_1


title: CTRL [R1236_1]


title: UCLA_4591_Patient_1


title: MP.runx1_ko-u2af1_wt.A


title: UCLA_4593_Patient_1


title: MP.runx1_wt-u2af1_wt.A


title: UCLA_4590_Patient_1


title: CG32732_KO_virgins_rep1

city: Heidelberg

first: Marcel

last: Tiebe

state: Germany

address: Humboldtstr., 18

institute: DKFZ Heidelberg

description: CG32732 = dSETD3

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Drosophila (V2) Gene Expression Microarrays for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Drosophila melanogaster

source_name: CG32732 KO virgins, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling kit (Agilent, version 6.9.1) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA, p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

growth_protocol: growth controlled, synchronized Drosophila melanogaster virgins, 5 days old

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Genetic ablation of CG32732 using CRISPR-CAS9

value: female

tag: developmental stage

value: 5d old virgins


title: MP.runx1_ko-u2af1_s34f.A

value: poly (IC) (250 µg/moue, i.p, every other day, three doses)


title: CG32732_KO_virgins_rep2

description: CG32732 = dSETD3

source_name: CG32732 KO virgins, replicate 2


title: UCLA_4585_Patient_1

source_name: Whole blood


title: CtIP-KO C27 rep2

tag: cell line

tag: cell type

value: human embryonic kidney cells

tag: genotype/variation

value: CtIP-/-


title: Ctrl_virgins_rep2

source_name: w1118 virgins, replicate 2


title: MP.runx1_wt-u2af1_s34f.A

value: MGS34F/WT; GFP/WT; Mx1-Cre/WT


title: UCLA_4582_Patient_1

tag: sample number

tag: batch

tag: site

value: MALE


title: Ctrl_virgins_rep1

source_name: w1118 virgins, replicate 1


title: Oct4-GFPneg spermatogonia rep 3

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

description: #8 290514.3 GFP -

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was  fragmented at 60oC for 30 minutes in a reaction volume of 25ul containing 1x  Agilent fragmentation buffer and 2x Agilent blocking agent following the  manufacturer’s instructions. On completion 25ul of 2x Agilent gene expression  hybridization buffer was added and 43ul of sample hybridised for 17 hours at  67oC in a rotating Agilent hybridization oven. After hybridization, microarrays  were washed 1 minute at room temperature with GE wash buffer 1(Agilent) and 1  minute with 37oC GE wash buffer 2(Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray  scanner using one color scan settings for 8x60k array slides; scan area  61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1  (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid:  028005_D_F_20120201) to obtain background subtracted and spatially  detrended Processed Signal intensities.

source_name: Oct4-GFPneg spermatogonia

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.1ug total RNA using the  One-Color Low input Quick Amp labelling Kit (Agilent, v6.6 September 2012)  according to the manufacturer’s instructions, followed by RNeasy column  purification (Qiagen). Dye incorporation and cRNA yield were checked with the  NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Adult transgenic mice (6-8 weeks old) containing both Oct4-GFP and Plzf-mCherry/CreER reporters were maintained under standard conditions.

extract_protocol: Sorted cells were lysed in TRIzol LS reagent (Thermo Fisher Scientific) then RNA was purified and DNase treated using a Direct-zol RNA Miniprep kit (Zymo Research).

treatment_protocol: Testis cell suspensions were prepared by a standard two step digestion protocol with collagenase and trypsin. Cells were sorted on a BD Influx Cell Sorter (BD Biosciences). The undifferentiated population was gated according to expression of the Plzf-mCherry/CreER reporter plus surface markers c-Kit and CD9. Plzf is a well-established marker of undifferentiated spermatogonia plus cells at early differentiation stages. c-Kit marks differentiating spermatogonia and CD9 is enriched on functional stem cells. Undifferentiated cells were then isolated according to whether they were positive or negative for Oct4-GFP expression.

tag: strain background

value: mixed C57BL/6 x CBA

tag: tissue

value: Testis

value: Oct4-GFPneg spermatogonia


title: Oct4-GFPpos spermatogonia rep 3

description: #7 290514.3 GFP +

source_name: Oct4-GFPpos spermatogonia

value: Oct4-GFPpos spermatogonia


title: UCLA_4578_Patient_1

tag: rin

tag: status

value: Patient

tag: age


title: DNA-PKcs KD/KD -1

city: New Yprk

first: Zhengping

last: Shao

state: New York

address: 1130 St. Nicholas Ave

department: ICG

institute: Columbia University Medical Center

data_processing:
Library strategy: HTGTS
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 genome (mm9sr) with IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6 replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3 using Bowtie2. The best-path searching algorithm (related to YAHA; ref. 50) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads are then filtered to exclude mispriming events, germ-line (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. To plot all of the S-region junctions, including those in the repeats but unequivocally mapped to an individual switch region, we combined the ones filtered by a mappability filter but unequivocally mapped to S regions with “good” reads passing both the mappability (both deduplicated) filters (please see ref. 28 for simulation and details on plotting). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait and prey-break site. Blunt junctions are considered to have no MHs or insertions.
Mutation rate was calculated by custom Excel integrated VBA script. Mutations were determined by comparing the actual bait sequence of each IgH junction with the germ-line bait sequence based on the IgH sequence from 129/Sv strain (NCBI gene accession no. AJ851868.3). Only true mismatches (no insertion or deletion within 7 nt) were counted as a mutation.
Genome_build: mm9sr (to customized mm9 genome (mm9sr) with IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6 replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3)
Supplementary_files_format_and_content: .xlsx files generated from tab-delimited text files after analysis for reads distribution and mutation rates.

source_name: B cells

growth_protocol: Purified splenic B (CD43-) cells from mice carrying preassembled IgH and IgK loci (129Sv background) were cultured in RPMI mediume with cytokines (anti-CD40 (1 ng/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)). Due to low splenic B cell number, DNA-PKcs KD/KDTp53-/- splenic cells were used for stimulation without purification.

extract_protocol:
Genomic DNA was extracted from day 4 cultured B cells.
Libraries were prepared according to protocol in (Hu J, et al. Nat Protoc 11:853–871.(2016)) Linear amplifications were performed using Sμ-specific biotin primer  5′/5BiosG/CAGACCTGGGAATGTATGGT3′) and followed by nesting PCR with (5′CACACAAAGACTCTGGACCTC3′)  AflII is used to remove germ-line sequence.
high-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v

treatment_protocol: Cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

value: anti-CD40 and Il4 activated B cells

value: DNA-Pkcs KD/KD


title: UCLA_4575_Patient_1

tag: Sex

tag: onset

tag: duration


title: UCLA_4583_Patient_1

value: FEMALE

tag: functional stage


title: Oct4-GFPpos spermatogonia rep 2

description: #5 070414.2 GFP +


title: DNA-PKcs KD/KD -2

tag: genotype

tag: strain


title: DNA-PKcs-/- -4

value: DNA-Pkcs-/-


title: UCLA_4576_Patient_1

tag: pidn

value: UCLA


title: Oct4-GFPneg spermatogonia rep 2

description: #6 070414.2 GFP -

tag: cell type


title: UCLA_4571_Patient_1


title: DNA-PKcs-/- -1


title: DNA-PKcs-/- -2


title: mechanical stretched_rep3

city: shanghai

first: Jing

last: Wang

address: 639 Zhizaoju Road

department: Depart of Plastic & Reconstructive Surgery

institute: Shanghai 9th People's Hospital, School of Medicine, Shanghai JiaoTong University

description: mechanical stretched human IFESCs

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: isolated human interfollicular epidermal stem cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: interfollicular epidermal stem cells were cultured on the collagen I coated silicon rubber membrane for 3 days to 50% confluency.

extract_protocol: Total RNA was prepared using TRIzol reagent (QIAGEN RNeasy Mini Kit, Cat No.217004, and QIAGEN Rnase-free DnaseI kit, Cat No.79254, Germany) according to the manufacturer’s instructions.RNA integrity numbers are based on electrophoretic analysis of each RNA sample, examining 28S and 18S ribosomal RNA intensity peaks as well as amounts of RNA degradation products to provide an accurate prediction of RNA integrity. RNA concentrations were determined spectrophotometrically using a Nano-Drop ND-1000 spectrophotometer. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: Cells were cultured on the flexceable silicon membrane and subjected to the mechanical stretched.Cyclic mechanical tension (CMT) at 0.5 Hz sinusoidal curve at 10% elongation was applied using an FX-5000T™ Flexercell® Tension Plus™ unit (Flexcell International Corporation). In mechanical unloading groups, cells were cultured on the same plates in the same incubator with the mechanical stretched groups but not subjected to stretch.

tag: treatment

value: mechanical stretched for 3 hours


title: CHOP_4556_Patient_1

data_processing: Array preprocessing was performed using the standard pipeline from the lumi package which is designed specifically for Illumina microarrays. Raw intensities were normalized using variance-stabilized transformation and interarray normalization was performed with robust spline normalization. Outliers were removed based upon sample-wise connectivity z-scores. Batch effect correction was performed using ComBat from the sva package. Probes were filtered by detection score P < 0.01 and unannotated probes were dropped. Duplicate probes for the same gene were dropped using the maxMean method with the collapseRows function from the WGCNA package, which only keeps probes with the highest mean expression across all of the samples.

extract_protocol: Peripheral blood was collected in Paxgene tubes and frozen before RNA extraction, which was performed using a semi-automated system (Qiacube). RNA quantity was assessed with Nanodrop (Nanodrop Technologies) and quality with the Agilent Bioanalyzer (Agilent Technologies).

tag: sample number

value: CHOP


title: Xrcc4-/- -4


title: CHOP_4554_Patient_1

tag: batch


title: DNA-PKcs-/- -3


title: H9-O4+OPC-Rep3

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: H9-hESC derived O4+ Oligodendrocyte Progenitor Cells

growth_protocol: H9-hESCs and iPSCs were grown in E8 medium

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen), and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
TruSeq Stranded mRNA Sample prep kit

treatment_protocol: Basal medium was used to make pNSC, rNSC, IPC, and GPLC consisting of DMEM/F12 supplemented with 543μg/ml Sodium bicarbonate (sigma-aldrich), 1X B-27 Supplement without vitamin A (Thermo Fisher Scientific), 1X N-2 Supplement (Thermo Fisher Scientific), 1% penicillin-streptomycin (Thermo Fisher Scientific). 1% L-glutamine (Thermo Fisher Scientific), 1% non-essential amino acids (Thermo Fisher Scientific). To differentiate into primitive NSCs (pNSCs), medium was replaced into LSC medium containing 10ng/ml LIF (Leukemia Inhibitory Factor, Millipore), 2μM SB431542 (Tocris), and 3μM Chir99021 (Tocris) for 2 weeks. To induce ventral rosette type NSCs, pNSCs were cultured in FEP medium consisting of Basal medium supplemented with 20ng/ml FGF2 (Peprotech), 20ng/ml EGF (Peprotech), 0.5μM Purmorphamine (Tocris).

value: O4+ Oligodendrocyte Progenitor Cells


title: Xrcc4-/- -2


title: Xrcc4-/- -3


title: H9-O4+OPC-Rep1


title: UCLA_4572_Patient_1

tag: site


title: UCLA_4543_Patient_1


title: Oct4-GFPpos spermatogonia rep 1

description: #3 070414.1 GFP +

tag: strain background


title: H9-O4+OPC-Rep2


title: Oct4-GFPneg spermatogonia rep 1

description: #4 070414.1 GFP -

tag: tissue


title: mechanical stretched_rep2

description: mechanical stretched human IFESCs

value: isolated human interfollicular epidermal stem cells


title: mechanical stretched_rep1

description: mechanical stretched human IFESCs


title: mechanical unstretched_rep3

description: mechanical unstretched  human IFESCs

value: mechanical unstretched


title: CHOP_4551_Patient_1

tag: rin


title: Xrcc4-/- -1


title: CHOP_4552_Patient_1

tag: status


title: mechanical unstretched_rep2

description: mechanical unstretched  human IFESCs


title: mechanical unstretched_rep1

description: mechanical unstretched  human IFESCs


title: hiPSC-GPLC-Rep2

source_name: hiPSC derived Glial restricted Progenitor-Like Cells

value: Glial restricted Progenitor-Like Cells


title: UCLA_4540_Patient_1

tag: age


title: UCLA_4541_Patient_1

tag: Sex

value: MALE


title: hiPSC-GPLC-Rep1


title: Tp53-/- -2


title: Tp53-/- -1


title: hiPSC-IPC-Rep3

source_name: hiPSC derived Intermediate Progenitor Cells

value: Intermediate Progenitor Cells


title: wild type-4

value: wild type


title: hiPSC-IPC-Rep2


title: UCLA_4536_Patient_1

tag: onset


title: UCLA_4539_Patient_1

tag: duration


title: wild type-2


title: wild type-3


title: wild type-1


title: hiPSC-IPC-Rep1


title: hiPSC-rNSC-Rep3

source_name: hiPSC derived rosette-type Neural Stem Cells

value: rosette-type Neural Stem Cells


title: hiPSC-rNSC-Rep2


title: UCLA_4542_Patient_1

tag: functional stage


title: hiPSC-rNSC-Rep1


title: H9-rNSC-Rep3

source_name: H9-hESC derived rosette-type Neural Stem Cells


title: hiPSC-GPLC-Rep3


title: UCLA_4527_Patient_1


title: UCLA_4530_Patient_1


title: H9-rNSC-Rep1


title: H9-pNSC-Rep2

source_name: H9-hESC derived primitive Neural Stem Cells

value: primitive Neural Stem Cells


title: UCLA_4594_Patient_1

value: Patient


title: UCLA_4513_Patient_1


title: UCLA_4525_Patient_1


title: H9-pNSC-Rep3


title: UCLA_4524_Patient_1


title: UCLA_4526_Patient_1


title: MCF-7 3D Methylcellulose, biological rep2

city: Farmington

first: Nicole

last: Farra

state: Connecticut

address: 263 FARMINGTON AVE

department: Molecular Biology and Biophysics

institute: University of Connecticut Health

description: Gene expression data from MCF-7 spheroids grown in 96-well plates with methylcellulose harvested at day 3

hyb_protocol: The arrays were hybridized for 16 h at 450° in a rotisserie oven.

scan_protocol: GeneChips were scanned on a Affymetrix GeneChip Scanner 3000.

data_processing: Raw CEL files were checked for quality and RMA normalized using Affymetrix Expression Console Software (version 1.4.1.46).

label: Biotin-labeled

label_protocol: Biotin-labeled cRNA was synthesized from 1 to 5 ug of total RNA by using a one cycle target labeling kit (Affymetrix).

growth_protocol: MCF-7 cells were cultured in Dulbecco’s minimal essential medium (DMEM)–F12 supplemented with 10% FBS and were maintained at 37°C in a humidified atmosphere containing 5% CO2 and 20% O2. To generate spheroids, cells were trypsinized from monolayer cultures and cells were seeded at 8,000 cells/well (8x104 cells/ml) in appropriate plates in corresponding normal growth media. To generate 2D samples, cells were trypsanized and replated at 8x104 cells/ml

extract_protocol: RNA was isolated and purified from cells using High Pure RNA Isolation Kit (Roche Diagnostics) following the manufacturer’s instructions

value: Breast Epithelial Adenocarcinoma

tag: cell line

tag: culture method

value: 3D methylcellulose


title: CHOP_4510_Patient_1

first: Daniel

last: Nachun

tag: pidn

value: FEMALE


title: UCLA_4516_Patient_1


title: CHOP_4509_Patient_2


title: H9-hESC-Rep2

source_name: human Embryonic Stem Cells (H9)

tag: cell type

value: Embryonic Stem Cells


title: MCF-7 3D PolyHema, biological rep3

description: Gene expression data from MCF-7 spheroids grown in PolyHema coated 96-well plates harvested at day 3

value: 3D polyhema


title: CHOP_4501_Patient_1


title: CHOP_4508_Patient_1


title: CHOP_4506_Patient_1


title: MCF-7 3D Methylcellulose, biological rep3

source_name: MCF-7 spheroids grown in 96-well plates with methylcellulose harvested at day 3


title: MCF-7 3D Ultra-Low Attachment, biological rep2

description: Gene expression data from MCF-7 spheroids grown in Ultra-low attachment 96-well plates harvested at day 3

value: 3D ultra-low attachment


title: MCF-7 3D Methylcellulose, biological rep1


title: MCF-7 3D PolyHema, biological rep2

source_name: MCF-7 spheroids grown in PolyHema coated 96-well plates harvested at day 3


title: MCF-7 3D PolyHema, biological rep1


title: CHOP_4505_Patient_1

value: CHOP


title: H9-hESC-Rep1


title: CHOP_4507_Patient_1


title: MCF-7 3D Ultra-Low Attachment, biological rep3

source_name: MCF-7 spheroids grown in Ultra-low attachment 96-well plates harvested at day 3


title: MCF-7 3D Ultra-Low Attachment, biological rep1


title: hiPSC-Rep2

source_name: human induced Pluripotent Stem Cells

value: induced Pluripotent Stem Cells


title: hiPSC-Rep3


title: CHOP_4499_Patient_1

source_name: Whole blood


title: Patient_4-CD45RAneg

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

description: AML cells isolated from patient

data_processing:
Reads were aligned to the human genome (version hg38) using Bowtie v2.3.1 with default parameters
Regions of enrichment corresponding to regions of open chromatin (Peaks) were identified using MACS v1.4.2 using the parameters --keep-dup=all -w -S
Genome_build: hg38
Supplementary_files_format_and_content: WIG files generated by MACS version 1.4.2

source_name: CD34 positive AML cells from peripheral blood

extract_protocol:
Cells were thawed in a water bath at 22C for 2 minutes, prior to addition of 120ul of DNaseI buffer consisting of 60nM KCL, 15 mM NaCl and 5 mM MgCL2. Digests were performed by adding 150 uL of DNaseI buffer equilibrated at 22C, containing 0.4% Nonidet P40 (or IGEPAL CA-630), 2 mM CaCl2, and either 1.5, 3 or 5 units/mL of Worthington DPFF DNase I. The permeabilized cells were digested for exactly 3 minutes at 22C, with occasional tapping to keep tubes in suspension, and lysed by addition of 300uL of 0.3 M NA Acetate, 10 mM EDTA pH 7.4, 1% SDS and 1 mg/Ml proteinase K.
DNA was purified, size-selected, and processed for DNA-Seq with a MicroPlex library preparation kit v2 (Diagenode)

treatment_protocol: Cells were snap-frozen in a freezing buffer consisting of 1.5M sucrose, 60nM KCL, 15 nM NaCl, 5nM MgCl2 and 10 nM Tris pH 7.4. Cells were then divided into three aliquots of 30 µL containing 300.000 cells each in cold 1.5 mL tubes, and snap frozen on dry ice and stored at -80C.

tag: condition

value: AML


title: BJ-Rep3

source_name: Foreskin fibroblasts

value: fibroblasts


title: CHOP_4500_Patient_1

city: Los Angeles

address: 695 Charles E Young Dr S

institute: UCLA

tag: sample number


title: MCF-7 2D, biological rep2

description: Gene expression data from MCF-7 monolayer cells harvested at day 3

value: 2D monolayer


title: hiPSC-Rep1


title: BJ-Rep2


title: MCF-7 2D, biological rep3

source_name: MCF-7 monolayer cells harvested at day 3


title: Patient_4-CD45RApos

description: AML cells isolated from patient


title: Patient_3-CD82Hi

description: AML cells isolated from patient


title: Patient_2-CD25pos

description: AML cells isolated from patient


title: BJ-Rep1


title: Patient_2-CD25neg

description: AML cells isolated from patient


title: Patient_1-IL1RAPpos

description: AML cells isolated from patient


title: Patient_3-CD82Low

description: AML cells isolated from patient


title: CHOP_4496_Patient_1r

tag: batch


title: CHOP_4498_Patient_1

tag: site


title: CHOP_4497_Patient_1