title: LSD1 KO_H3K4me2

data_processing:
For ChIP-seq analysis, raw reads were aligned to hg19 or mm9 using bwa (version 0.7.2-r351) (PMID: 22569178). The resulted sam files were converted to bam with samtools (version 0.1.18 (r982:295) (PMID: 21245279). MACS2 (version 2.0.10.20131216) (PMID: 18798982) was used to call peak on the bam files. BedGraph files containing signal per million reads produced from MACS2 were converted to bigwig files with ucsctool kit (315). ChIP-seq signals were first extracted with bwtool (version 1.0) (PMID: 24489365) from bigwig files and then visualized in R.
Repeat annotation was downloaded from UCSC for hg19 and mm9, only ERVs were used for downstream analysis. To select ERVs, ERV families originated in Homo Sapien or Mus Musculus were downloaded from Repbase (http://www.girinst.org/repbase/). A peak catalogue consisting all possible peak intervals in ChIP-seq (histones and LSD1) was produced and ERVs were filtered with this catalogue. ChIP-seq signals were extracted with bwtool (version 1.0) (PMID: 24489365) from bigwig files and then visualized in R.
For RNA-seq analysis, raw reads were aligned to hg19 or mm9 using STAR (v2.4.2a) with the parameter “quantMode” set as “GeneCounts” to produce count table for each gene. Differential gene analysis was performed on gene raw counts in R with edgeR package (v3.18.1) (PMID: 22287627) from bioconductor. Read count table was filtered so that genes with at least one count across conditions were kept. The negative binomial generalized log-linear model was used in differential analysis. A FDR cut-off of 0.05 was used to determine significantly differentially expressed genes.
The function analyzeRepeats.pl from Homer (PMID: 20513432) software was used to get raw counts for repeats from RNA-seq data. Differential expression for repeats was performed with edgeR the same way as for genes.
Genome_build: hg19 and mm9

source_name: ex vivo B16 ChIP

extract_protocol:
For MCF-7 cells, cell nuclei were obtained by lysing whole cells in hypotonic buffer (10 mM HEPES pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% v/v glycerol, 1 mM DTT, and 0.1% v/v Triton X-100) supplemented with protease inhibitor. For GFP-labeled B16 cells isolated from tumor-bearing immunocompetent mice, intact cells were used for the following steps. After washing with PBS, nuclei/cells were fixed in 1% formaldehyde for 10 min at room temperature, followed by quenching in 125 mM glycine. Nuclei/cells were then washed twice with ice-cold PBS, lysed in ChIP sonication buffer (50 mM HEPES pH7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% SDS) supplemented with protease inhibitor, and were subjected to sonication to obtain DNA fragments of 300-800 bp. Subsequent procedures were carried out by following the Epigenesys protocol (https://www.epigenesys.eu/en/). The following antibodies were used to ChIP: anti-LSD1 (Abcam, cat# ab17721), anti-H3K4me1 (Abcam, cat#ab8895), anti-H3K4me2 (EMDMillipore, cat#07-030), and mouse IgG (Santa Cruz Biotechnology, cat# sc-2025). || For RNA extraction, cells weredirectly lyzed in TRIzol and total RNA was extracted according to manufacture's instructions.
ChIP-seq libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (New England Biolabs, cat#E7370L) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs, cat# E7335L) according to the manufacture’s instructions. Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for sequencing at HiSeq 2500 (Illumina) to generate 50 bp reads from single-end. || Purified total RNA from MCF-7 cells or GFP-labeled B16 cells isolated from tumor-bearing immunocompetent mice was quantified by Qubit (Invitrogen) and analyzed by Agilent Bioanalyzer to assess RNA integrity. 1 μg RNA (RIN>9) was used to generate rRNA-depleted RNA with NEBNext® rRNA Depletion Kit (New England Biolabs, cat# E6310S) or poly(A)+ RNA with Magnetic mRNA Isolation Kit (New England Biolabs, cat# S1550S) according to the manufacturer’s instructions. The rRNA-depleted or poly(A)+ RNA was subjected to Agilent Bioanalyzer to ensure the complete removal of rRNA, and then used to generate directional RNA library with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, cat# E7760L) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs, cat# E7335L) according to the manufacturer’s instructions. Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for sequencing at HiSeq 2500 or Nextseq 500 (Illumina) to generate 50 bp reads (MCF-7) or 75 bp (B16) from paired-ends.

value: B16 tumor transplanted in C56BL/6 mice

tag: molecule

value: genomic DNA

tag: antibody

value: H3K4me2 (EMDMIpplipore, cat#07-030)


title: Plasma Gel 5' Multiplex Adapter AD  MD  2

status: Public on Jun 21 2018

type: SRA

city: Huntsville

first: Richard

middle: M

last: Myers

state: AL

address: 601 Genome Way

country: USA

institute: HudsonAlpha Institute for Biotechnology

description:
Plasma Gel Extracted Multiplex 5' Adapter Adapter Dimer MAD-DASH
PlasmaGel_Samples_GSLv2-7_05_SL321729

library_source: transcriptomic

data_processing:
Fastqs from multiple lanes of the same flowcell were merged with cat.
Reads were adaptor trimmed for both 5' adaptors (4 separate) and 3' adaptors. Raw files provided are not trimmed, in accordance with GEO guidelines).
Trimmed reads less than 15 bp were considered "short fails", and within short fails reads of 0 bp length were considered "adapter dimer" (corresponding to no sequence after adapter trimming) while reads with greater than 0 bp were considered "Non AD (adapter dimer) short fails".
Trimmed reads were aligned to pre-miRNA sequences mirBase v19 using bowtie2-2.1.0 with two mismatches allowd and keeping only unique best alignments.  Reads aligning to mutliple locii were assigned to each locii proportionally to the total number of reads. Total non-miRNA aligned reads were counted and considered "non-miRNA usable reads"
Reads as processed above were read into R and library replicates for each condition were summed.  Reads were normalized by downsampling within each group of replicates to a common count value, this table is provided as processed data and named MAD-DASH_count.table.txt
Treatment group comparisons were made by taking respective intra-group downsampled replicates, summing them, downsampling to a common inter-group count, and then performing regression analysis with the R package DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text

molecule: total RNA

organism: Homo sapiens

source_name: human blood plasma

extract_protocol:
RNA was isolated from 1 mL of plasma using the Plasma/Serum Circulating and Exosomal RNA Purification Kit (Slurry Format) from Norgen Biotek using manufacturer's protocols.
Libraries were constructed exactly as detailed in "Blocking of targeted microRNAs from next-generation sequencing libraries", Roberts et al, PMID:26209131, with modification to incorporate MAD-DASH treatment. Modification to Roberts et al. 2015 protocol involves a short 4-cycle PCR amplifcation followed by Ampure bead cleanup, MAD-DASH CRISPR RNP in vitro digestion of specific sequences such as adapter dimer for 2 hrs followed by treatment with RNAse A and Proteinase K to inactivate the reaction, then a second 11-cycle PCR to complete library construction before futher cleanup with Ampure Beads or denaturing gel extraction.

treatment_protocol: Brain total RNA was purchased from Invitrogen. For human plasma RNA samples, blood was drawn from patients prior to undergoing colonoscopy. Plasma was isolated within 30 min using standard centrifugation protocol.

tag: library replicate

tag: tissue

value: blood plasma


title: Plasma Gel 5' Multiplex Adapter No MD Control 3

description:
Plasma Gel Extracted Multiplex 5' Adapter No MAD-DASH Control
PlasmaGel_Samples_GSLv2-7_03_SL321708


title: LSD1 KO_H3K4me1

city: Hangzhou

first: Wanqiang

last: Sheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Immunology

country: China

institute: Zhejiang University School of Medicine

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: MCF-7 cells were cultured in normal DMEM supplemented with 10% FBS and 1% penicillin/streptomycin in 5% CO2 incubator at 37 °C. GFP-labeled B16 cells were transplanted into WT C56BL/6 mice subcutaneously and tumor grew for 14 days.

treatment_protocol: MCF-7 cells were infected with lentiviral shRNA targeting scramble or LSD1, and selected for 6-8 days before sample collections. B16 tumors grew in mice for 14 days before being excised and digested with collagenase for single cell suspension. GFP+ B16 cells were sorted.

value: H3K4me1 (Abcam, cat#ab8895)


title: Plasma Gel 5' Multiplex Adapter No MD Control 2

description:
Plasma Gel Extracted Multiplex 5' Adapter No MAD-DASH Control
PlasmaGel_Samples_GSLv2-7_02_SL321697


title: LSD1 KO_Input


title: Scramble_H3K4me2


title: Scramble_H3K4me1


title: Rop7-II biological replicate 1 [AR7II_R1]

city: London

first: Eva

last: Frickel

address: 1 Midland Road

department: Host-Toxoplasma Interaction Laboratory

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.2.11) (Li and Dewey, 2011) was used for the alignment and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 27th May 2015.
Differential expression analysis between the triplicate groups was performed with DESeq2 (version 1.8.1) (Love et al., 2014) after removal of genes with a maximum transcript per million (TPM) value of 1 across all samples in the experiment.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

molecule: polyA RNA

source_name: CD8 T-cells_Rop7-II

growth_protocol: Cell were grown in RPMI medium 1640 supplemented with 10% fetal bovine serum, L-glutamine, penicillin/streptomycin, β-mercaptoethanol and recombinant mouse IL-2 (10 ng/ml).

extract_protocol:
RNA was isolated using Trizol and the RNeasy Micro-Kit (Qiagen).
A total of 200 ng of RNA was used to prepare the RNA library using TruSeq mRNA Library Prep Kit v2 (Illumina) according to the manufacturer’s recommendations.

treatment_protocol: Cells were incubated overnight at 37°C and 5% CO2 with ROP7 peptide (10 μM). CD3+ CD8+ H-2Ld-Rop7+ cells were sorted, maintained at 4°C and purity determined to be 90-95%.

tag: cell type

value: CD8 T-cells

tag: clone id

tag: incubated with

value: ROP7 peptide (10 μM)

tag: sorted cell type

value: CD3+ CD8+ H-2Ld-Rop7+


title: Gel 5' mod Adapter AD  MD  1

description:
Gel Extracted Modified 5' Adapter Adapter Dimer MAD-DASH
Gel_Samples_GSLv2-7_23_SL321605

source_name: Total Brain RNA (Ambion)

value: Brain


title: Scramble_Input


title: Plasma Gel 5' mod Adapter No MD Control 2

description:
Plasma Gel Extracted Modified 5' Adapter No MAD-DASH Control
PlasmaGel_Samples_GSLv2-7_17_SL321694


title: Gel 5' Multiplex Adapter mir16 MD  2

description:
Gel Extracted Multiplex 5' Adapter mir-16-5p MAD-DASH
Gel_Samples_GSLv2-7_18_SL321599


title: Gel 5' mod Adapter No MD Control 2

description:
Gel Extracted Modified 5' Adapter No MAD-DASH Control
Gel_Samples_GSLv2-7_22_SL321604


title: Gel 5' mod Adapter AD MD  2

description:
Gel Extracted Modified 5' Adapter Adapter Dimer MAD-DASH
Gel_Samples_GSLv2-7_24_SL321606


title: Gel 5' mod Adapter No MD Control 1

description:
Gel Extracted Modified 5' Adapter No MAD-DASH Control
Gel_Samples_GSLv2-7_21_SL321603


title: Gel 5' Multiplex Adapter AD  MD  1

description:
Gel Extracted Multiplex 5' Adapter Adapter Dimer MAD-DASH
Gel_Samples_GSLv2-7_15_SL321596


title: KO PAX6-TBR2- cells, replicate 2

city: Boston

first: Corey

last: Harwell

state: MA

address: 200 Longwood Avenue

department: Neurobiology

institute: Harvard Medical School

description:
LIB019993_TRA00051658_S6_L001
LIB019993_TRA00051658_S6_L002

data_processing:
Raw reads were examined for quality issues using FastQC
Sequenced reads were trimmed for adaptor sequence (if required) using Cutadapt
Trimmed reads were aligned to the UCSC genome mm10 using STAR
Counts of reads aligning to known genes were generated by featureCounts.
Raw counts were normalized and differentially expressed genes were identified  using the R Bioconductor package DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files for raw counts and normalized counts

source_name: Embryonic cerebral cortex

extract_protocol:
Sorted cells were resuspended in the lysis solution of RecoverAll total nucleic acid isolation kit (Ambion) and incubated for 3 hrs at 50oC. RNA was then purified according to manufacturer’s instructions. The concentration and quality of purified RNA was determined using BioAnalyzer (Agilent)
RNA was reverse-transcribed into cDNA and amplified by RNA-based single primer isothermal amplification (SPIA) using the Ovation RNA-seq system V2 (NuGEN). Synthesized cDNA was sonicated using a Covaris S2 ultrasonicator to reduce fragment size range to 100-600 bp. For library preparation, 100 ng of sheared cDNA was end repaired, ligated with barcoded adaptors, amplified for 9 PCR cycles and purified using the Ovation Ultralow System V2 (NuGEN).

value: Embryonic cerebral cortex

value: Cortical neurons

tag: genotype

value: Emx1Ires-Cre; Prdm16flox/flox

tag: developmental stage


title: KO PAX6-TBR2- cells, replicate 4

description:
LIB019993_TRA00051660_S8_L001
LIB019993_TRA00051660_S8_L002


title: KO TBR2+ cells, replicate 4

description:
LIB019992_TRA00051652_S8_L001
LIB019992_TRA00051652_S8_L002

value: Intermediate progenitor cell


title: KO PAX6-TBR2- cells, replicate 3

description:
LIB019993_TRA00051659_S7_L001
LIB019993_TRA00051659_S7_L002


title: KO TBR2+ cells, replicate 3

description:
LIB019992_TRA00051651_S7_L001
LIB019992_TRA00051651_S7_L002


title: Scramble_LSD1

value: LSD1 (Abcam, cat#17721)


title: KO TBR2+ cells, replicate 1

description:
LIB019992_TRA00051649_S5_L001
LIB019992_TRA00051649_S5_L002


title: KO PAX6+ cells, replicate 4

description:
LIB018752_GEN00046956_S8_L001
LIB018752_GEN00046956_S8_L002

value: radial glia


title: Gel 5' Multiplex Adapter AD/mir16  MD  2

description:
Gel Extracted Multiplex 5' Adapter Adapter Dimer  and mir-16-5p MAD-DASH
Gel_Samples_GSLv2-7_20_SL321602


title: Gel 5' Multiplex Adapter No MD Control 2

description:
Gel Extracted Multiplex 5' Adapter No MAD-DASH Control
Gel_Samples_GSLv2-7_14_SL321595


title: KO PAX6-TBR2- cells, replicate 1

description:
LIB019993_TRA00051657_S5_L001
LIB019993_TRA00051657_S5_L002


title: Gel 5' Multiplex Adapter AD /mir16 MD  1

description:
Gel Extracted Multiplex 5' Adapter Adapter Dimer  and mir-16-5p MAD-DASH
Gel_Samples_GSLv2-7_19_SL321600


title: KO TBR2+ cells, replicate 2

description:
LIB019992_TRA00051650_S6_L001
LIB019992_TRA00051650_S6_L002


title: KO PAX6+ cells, replicate 2

description:
LIB018752_GEN00046952_S4_L001
LIB018752_GEN00046952_S4_L002


title: Bead 5' mod Adapter No MD Control 1

description:
Bead Cleanup Modified 5' Adapter No MAD-DASH Control
Bead_Samples_GSLv2-7_09_SL321685


title: Gel 5' Multiplex Adapter mir16  MD  1

description:
Gel Extracted Multiplex 5' Adapter mir-16-5p MAD-DASH
Gel_Samples_GSLv2-7_17_SL321598


title: Bead 5' mod Adapter AD MD  2

description:
Bead Cleanup Modified 5' Adapter Adapter Dimer MAD-DASH
Bead_Samples_GSLv2-7_12_SL321641


title: WT PAX6-TBR2- cells, replicate 2

description:
LIB019993_TRA00051654_S2_L001
LIB019993_TRA00051654_S2_L002

value: Prdm16 flox/flox


title: Bead 5' Multiplex Adapter AD/mir16  MD  2

description:
Bead Cleanup Multiplex 5' Adapter Adapter Dimer  and mir-16-5p MAD-DASH
Bead_Samples_GSLv2-7_08_SL321684


title: KO PAX6+ cells, replicate 1

description:
LIB018752_GEN00046950_S2_L001
LIB018752_GEN00046950_S2_L002


title: WT PAX6-TBR2- cells, replicate 1

description:
LIB019993_TRA00051653_S1_L001
LIB019993_TRA00051653_S1_L002


title: Gel 5' Multiplex Adapter No MD Control 1

description:
Gel Extracted Multiplex 5' Adapter No MAD-DASH Control
Gel_Samples_GSLv2-7_13_SL321594


title: KO PAX6+ cells, replicate 3

description:
LIB018752_GEN00046954_S6_L001
LIB018752_GEN00046954_S6_L002


title: Bead 5' Multiplex Adapter mir16  MD  1

description:
Bead Cleanup Multiplex 5' Adapter mir-16-5p MAD-DASH
Bead_Samples_GSLv2-7_05_SL321681


title: Gel 5' Multiplex Adapter AD MD  2

description:
Gel Extracted Multiplex 5' Adapter Adapter Dimer MAD-DASH
Gel_Samples_GSLv2-7_16_SL321597


title: WT PAX6-TBR2- cells, replicate 3

description:
LIB019993_TRA00051655_S3_L001
LIB019993_TRA00051655_S3_L002


title: Bead 5' mod Adapter AD  MD  1

description:
Bead Cleanup Modified 5' Adapter Adapter Dimer MAD-DASH
Bead_Samples_GSLv2-7_11_SL321640


title: Bead 5' mod Adapter No MD Control 2

description:
Bead Cleanup Modified 5' Adapter No MAD-DASH Control
Bead_Samples_GSLv2-7_10_SL321639


title: Bead 5' Multiplex Adapter mir16 MD  2

description:
Bead Cleanup Multiplex 5' Adapter mir-16-5p MAD-DASH
Bead_Samples_GSLv2-7_06_SL321682


title: Bead 5' Multiplex Adapter AD /mir16 MD  1

description:
Bead Cleanup Multiplex 5' Adapter Adapter Dimer  and mir-16-5p MAD-DASH
Bead_Samples_GSLv2-7_07_SL321683


title: Bead 5' Multiplex Adapter AD MD  2

description:
Bead Cleanup Multiplex 5' Adapter Adapter Dimer MAD-DASH
Bead_Samples_GSLv2-7_04_SL321671


title: Bead 5' Multiplex Adapter No MD Control 2

description:
Bead Cleanup Multiplex 5' Adapter No MAD-DASH Control
Bead_Samples_GSLv2-7_02_SL321649


title: WT TBR2+ cells, replicate 3

description:
LIB019992_TRA00051647_S3_L001
LIB019992_TRA00051647_S3_L002


title: WT TBR2+ cells, replicate 1

description:
LIB019992_TRA00051645_S1_L001
LIB019992_TRA00051645_S1_L002


title: WT TBR2+ cells, replicate 4

description:
LIB019992_TRA00051648_S4_L001
LIB019992_TRA00051648_S4_L002


title: WT PAX6+ cells, replicate 4

description:
LIB018752_GEN00046955_S7_L001
LIB018752_GEN00046955_S7_L002


title: DNase-seq from kidney tubule cell (ENCLB626YLU)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR175IWT/
***************
biological replicate number: 2
technical replicate number: 2
description: Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures
experiment encode accession: ENCSR175IWT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB626YLU

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens male adult (62 years) kidney tubule primary cell

extract_protocol: not provided

value: kidney tubule cell

value: primary cell

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 62 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS947UTL at ENCODE; https://www.encodeproject.org/ENCBS947UTL/

value: Derived from ENCODE donor ENCDO335XPZ; https://www.encodeproject.org/ENCDO335XPZ/


title: EP2

city: WUHAN

first: Gan

last: Zhao

state: HUBEI

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using illumina Casava 1.8
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie v0.12.9
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 2.0.0.8 and srna-tools-cli v4.3 were used to obtain the potential miRNA and draw the secondary structures.
The available software miREvo and  mirdeep2 2.0.0.8  were integrated to predict novel miRNA through exploring the secondary structure
Genome_build: The cattle reference genome (UMD3.1.66) and gene model annotation files were downloaded directly from the cow genome website (ftp://ftp.ensembl.org/pub/release-69/fasta/bos_taurus/dna/).
Supplementary_files_format_and_content: tab-delimited text files include TPM (transcript per million)  values for each Sample.

organism: Bos taurus

source_name: exosomes

extract_protocol:
Blood samples sampled by coccygeal venipuncture and then collected in evacuated blood tubes containing K2EDTA as anticoagulant. Samples were placed immediately into iced water and centrifuged within 30 min at 1,500 × g for 12 min at 4°C. The plasma exosomes were isolated and characterized as described previously 70. In brief, plasma (2 mL) was diluted with an equal volume of 1x PBS (pH 7.4) and centrifuged at 2,000 × g for 30 min at 4°C. The supernatant was then centrifuged at 12,000 × g for 45 min at 4°C. The resultant supernatant fluid (4 mL) filtered through a 0.22-μm filter (Millipore, USA) and transferred to an ultracentrifuge tube and centrifuged at 100,000 × g for 75 min at 4°C (Beckman Optima XE- 90, SW32 Ti rotor). The pellet was suspended in PBS and filtered through a 0.22-μm filter (Millipore, USA) and centrifuged at 100,000 × g for 2 h at 4°C. Finally, the pellet containing the enriched exosome population was resuspended in 50 μL PBS (Hyclone, USA) and stored at -80 °C. Exosomal RNA  were isolated by exoRNeasy Serum/Plasma Midi Kit(#77044, Qiagen, Germany) according to the manufacturer’s instructions. its integrity, purity and concentration were determined using an RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), NanoPhotometer® spectrophotometer (IMPLEN, USA), and Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Chinese Holstein

tag: group

value: EARLY  PREGNANCY

value: plasma

tag: Stage


title: WT PAX6+ cells, replicate 3

description:
LIB018752_GEN00046953_S5_L001
LIB018752_GEN00046953_S5_L002

value: Embryonic cerebral cortex


title: treat_1: sh-LSD1_rep1

description:
2018-03-14_rnaseq_hs_counts.csv
2018-03-22_repeat_count_hs.csv

data_processing:
For RNA-seq analysis, raw reads were aligned to hg19 or mm9 using STAR (v2.4.2a) with the parameter “quantMode” set as “GeneCounts” to produce count table for each gene. Differential gene analysis was performed on gene raw counts in R with edgeR package (v3.18.1) (PMID: 22287627) from bioconductor. Read count table was filtered so that genes with at least one count across conditions were kept. The negative binomial generalized log-linear model was used in differential analysis. A FDR cut-off of 0.05 was used to determine significantly differentially expressed genes.
The function analyzeRepeats.pl from Homer (PMID: 20513432) software was used to get raw counts for repeats from RNA-seq data. Differential expression for repeats was performed with edgeR the same way as for genes.
For RNA-seq analysis, raw reads were aligned to hg19 or mm9 using STAR (v2.4.2a) with the parameter “quantMode” set as “GeneCounts” to produce count table for each gene. Differential gene analysis was performed on gene raw counts in R with edgeR package (v3.18.1) (PMID: 22287627) from bioconductor. Read count table was filtered so that genes with at least one count across conditions were kept. The negative binomial generalized log-linear model was used in differential analysis. A FDR cut-off of 0.05 was used to determine significantly differentially expressed genes.
The function analyzeRepeats.pl from Homer (PMID: 20513432) software was used to get raw counts for repeats from RNA-seq data. Differential expression for repeats was performed with edgeR the same way as for genes.
Genome_build: hg19 and mm9

source_name: MCF-7 RNA-seq

value: MCF-7 breast cancer cell line

tag: molecule

value: Ribosome depleted RNA


title: cKO H3K4me ChIP-seq replicate 2

data_processing:
Sequence quality was evaluated using FASTQC and if required reads were trimmed with Cutadapt
Reads were combined for each sample across multiple lanes and  mapped to the genome UCSC build mm10 using Bowtie2 v2.2.8.
Alignments were filtered to retain only reads with a unique mapping to the genome.
ChIP-seq peaks were called with MACS2 v2.1.1 using broad peak calling and a broad peak cutoff of q < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files and peak calls from MACS2 (narrowPeak format)

extract_protocol:
PRDM16 ChIP-seq was carried out using dual chromatin crosslinking with PFA and EGS, followed by sonication and antibody precipitation. H3K27ac and H3K4me ChIP-seq were carried out using native chromatin digestion with microccocal nuclease, followed by antibody precipitation of DNA-histone complexes.
For library preparation, genomic DNA was purified, end repaired, ligated with barcoded adaptors, amplified for 11 PCR cycles and purified using the Ovation Ultralow System V2 (NuGEN). Library fragments in the range of 100-800 bp were size-selected using agarose gel electrophoresis followed by DNA gel extraction and purification.

tag: developmental time

tag: tissue

value: Whole cortex lysate

value: Emx1Ires-Cre; Prdm16flox/flox

tag: chip-seq antibody

value: anti-H3K4me (abcam, Cat#ab8895)


title: ctl_2: sh-C_rep2


title: cKO H3K4me input replicate 1


title: Bead 5' Multiplex Adapter No MD Control 1

description:
Bead Cleanup Multiplex 5' Adapter No MAD-DASH Control
Bead_Samples_GSLv2-7_01_SL321638

tag: library replicate

value: Brain


title: WT PAX6+ cells, replicate 1

description:
LIB018752_GEN00046949_S1_L001
LIB018752_GEN00046949_S1_L002

tag: cell type

value: radial glia

value: Prdm16 flox/flox


title: treat_2: sh-LSD1_rep2


title: WT PAX6+ cells, replicate 2

description:
LIB018752_GEN00046951_S3_L001
LIB018752_GEN00046951_S3_L002

tag: genotype


title: ctl_1: sh-C_rep1


title: WT TBR2+ cells, replicate 2

description:
LIB019992_TRA00051646_S2_L001
LIB019992_TRA00051646_S2_L002

value: Intermediate progenitor cell

tag: developmental stage


title: Bead 5' Multiplex Adapter AD  MD  1

description:
Bead Cleanup Multiplex 5' Adapter Adapter Dimer MAD-DASH
Bead_Samples_GSLv2-7_03_SL321660


title: sh-LSD1_H3K4me2

source_name: MCF-7 ChIP

value: genomic DNA

tag: antibody

value: H3K4me2 (EMDMIpplipore, cat#07-030)


title: WT PAX6-TBR2- cells, replicate 4

description:
LIB019993_TRA00051656_S4_L001
LIB019993_TRA00051656_S4_L002

value: Cortical neurons


title: WT H3K4me input replicate 2


title: WT H3K4me ChIP-seq replicate 2


title: sh-LSD1_H3K4me1

value: H3K4me1 (Abcam, cat#ab8895)


title: sh-LSD1_LSD1

value: LSD1 (Abcam, cat#17721)


title: WT H3K4me input replicate 1


title: sh-LSD1_Input


title: WT H3K4me ChIP-seq replicate1


title: sh-Ctrl_H3K4me1


title: cKO H3K27ac input replicate 2

data_processing:
Sequence quality was evaluated using FASTQC and if required reads were trimmed with Cutadapt
Reads were combined for each sample across multiple lanes and  mapped to the genome UCSC build mm10 using Bowtie2 v2.2.8.
Alignments were filtered to retain only reads with a unique mapping to the genome.For replicates 1 and 2 data BAM files were merged across flow cells (3 different flow cells). Replicate three was only run on one flowcell
ChIP-seq peaks were called with MACS2 v2.1.1 using broad peak calling and a broad peak cutoff of q < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files and peak calls from MACS2 (narrowPeak format)


title: cKO H3K27ac input replicate 1


title: cKO H3K27ac ChIP-seq replicate1

value: anti-H3K27ac (abcam, Cat#ab4729)


title: cKO H3K27ac ChIP-seq replicate 3


title: cKO H3K27ac input replicate 3


title: sh-Ctrl_Input


title: cKO H3K27ac ChIP-seq replicate 2


title: NCI-N87_miR-seq

city: Duarte

first: Ren-Jang

last: Lin

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: City of Hope

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed using Btrim64 with parameters -l 16 -3 -P -f 3
Reads were aligned to hg38 using Bowtie version 0.12.7 with paramters -v 1
Genome_build: hg38
Supplementary_files_format_and_content: CSV file of raw miRNA read counts

source_name: NCI-N87 cells

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (QIAGEN)
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: stomach

tag: cell line


title: HeLa_1D22md_miR-seq

source_name: HeLa cells

treatment_protocol: Selected for 15 days using blasticidin

value: cervix


title: cKO H3K4me input replicate 2


title: WT H3K27ac input replicate 3


title: HeLa_1D22G1_miR-seq

treatment_protocol: Selected for 15 days using blasticidin and treated with doxycycline for 14 days


title: HeLa_2D7_miR-seq

treatment_protocol: Selected for 7 days using blasticidin


title: WT H3K27ac ChIP-seq replicate 3


title: cKO H3K4me ChIP-seq replicate1


title: HeLa_1D7_miR-seq


title: sh-Ctrl_H3K4me2

value: MCF-7 breast cancer cell line


title: WT H3K27ac input replicate 2


title: WT H3K27ac input replicate 1


title: cKO PRDM16 input replicate 2

data_processing:
Sequence quality was evaluated using FASTQC and if required reads were trimmed with Cutadapt
Reads were mapped to the genome UCSC build mm10 using Bowtie2 v2.2.8.
Alignments were filtered to retain only reads with a unique mapping to the genome.For  WT samples BAM files were merged across lanes for each sample.
ChIP-seq peaks were called with MACS2 v2.1.1 using default parameters and a narrow peak cutoff of q < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files a nd peak calls from MACS2 (narrowPeak format)


title: WT H3K27ac ChIP-seq replicate 2


title: sh-Ctrl_LSD1


title: WT H3K27ac ChIP-seq replicate1


title: H1299_TC_DBDB_6d

city: Rehovot

first: Eran

last: Kotler

address: 234 Herzl st.

country: Israel

institute: Weizmann Institute of Science

description:
processed data file: H1299_TC_DBDB.csv
Tissue culture dynamics in H1299 cells - sublib B

data_processing:
Paired-end reads were merged using Usearch (http://www.drive5.com/usearch/) setting a minimal overlap of 80 and merge length of 180-220. In runs containing multiple barcoded samples, these were un-pooled by sample barcodes (barcoded primers used for each sample are specified in Table S1). Variant sequences were extracted by matching the read-ends (primer sequences) to the wild-type p53 sequence and variants were mapped to the designed synthetic library. A minimal coverage of >200 reads for each sequence variant at the first experimental time point was required. In vitro relative fitness scores (RFS) were calculated by taking the median of the log (base 2) enrichment/depletion of each variant along the 3 latter time points. In vivo and 3D enrichment scores were defined as the median log (base 2) enrichment/depletion of each variant at the experiment end points (formed tumors/spheroids) compared to its abundance in the injected/seeded population. See STAR methods in the associated publication for details.
Genome_build: Not applicable
Lowly-processed data files:
The following files contain sequences of variants with their corresponding relative fraction of reads at different time-points or experimental conditions. Sequences were not mapped to the reference library, normalized to other sub-libraries, or filtered (other than the requirement for a minimal number of reads at first time point).
H1299_TC_DBDA.csv - Sub-library A tissue-culture time course experiment in H1299 cells.
H1299_TC_DBDB.csv - Sub-library B tissue-culture time course experiment in H1299 cells.
H1299_TC_DBDC.csv - Sub-library C tissue-culture time course experiment in H1299 cells.
H1299_TC_DBDD.csv - Sub-library D tissue-culture time course experiment in H1299 cells.
H1299_TC_DBDA_rep2.csv - Biological replication of time course experiment with sub-library A in H1299.
H1299_TC_DBDB_rep2.csv - Biological replication of time course experiment with sub-library B in H1299.
HCT116_TC_DBDD.csv - Sub-library D tissue-culture time course experiment in HCT116 cells.
HCT116_invivo_DBDD.csv - Sub-library D in vivo enrichment assay (fraction of reads of sequence variants in the injected pool (T0) and in formed subcutaneous tumors).
HCT116_3dCulture_DBDD.csv - Small-scale library measurements comparing relative growth in 2D and 3D culture settings (fraction of reads of sequence variants in the seeded pool (T0) and in 2D and 3D cultures at end-point).
Processed data files:
The following files contain further-processed data (following mapping of variants to library design, normalization, and calculation of RFS and enrichment scores). See manuscript for further details (STAR methods and additional supplementary information tables).
H1299_RFS_sequence variants.xlsx - In vitro RFS of all sequence variants. Column description: Var_seq - sequence of the variant sub-fragment; Identifier - unique identifier of each library sequence variant; SubLib - sub-library (DBD-A, B, C or D, see Methods); Backbone - background on which the mutation is presented (wt or SNP); Mut_type - mutation type; Position - nucleotide position within the CDS; Seq_change - sequence alteration in the given position; Codon_num - number of first affected codon/residue; AA_change - amino acid change, starting in Codon_num; Sec_mut_position - secondary mutation position, in variants containing multiple alterations; Sec_seq_change - sequence change in Sec_mut_position; Sec_codon_num - number of affected codon/residue by the secondary mutation; Sec_AA_change - amino acid change due to secondary mutation; MutID - Mutation ID from the IARC p53 database (Bouaoun et al., 2016); IARC_Desc - description of mutation in the IARC database; Silent - True for synonymous mutations, otherwise False; RFS_H1299 - Variant relative fitness score measured in H1299 cells. Note: IARC MutID and description are presented for mutations which are present in the database but were not covered by scanning mutagenesis of the DBD (i.e. not created by a single nucleotide substitution, insertion, deletion, amino acid deletion or substitution, dinucleotide substitutions, etc.).
HCT116_RFS_sequence variants.xlsx - in vitro RFS of sequence variants in sub-library “D”, as measured in HCT116 cells. See column descriptions for Table S2.
HCT116_invivo_enrichment_sequence_variants.xlsx - In vivo enrichment scores of single-mutation sequence variants in sub-library “D”. See column descriptions for Table S2.
HCT116_3D_enrichment.xlsx - 3D and 2D enrichment scores of sequence variants in the mini-library “D”. Corresponding in vivo enrichment scores are also shown. See column descriptions for Table S2.

source_name: Non-small cell lung cancer

growth_protocol: Pooled competition

extract_protocol:
From tissue-culture experiments: To maintain the complexity of the input libraries, PCR reactions were carried out on a genomic DNA (gDNA) amount calculated to contain an average of at least 200 copies of each variant included in the assayed library. Thus, at each time point along the time course experiments, gDNA was purified from a minimum of 1x10^7, 1.3x10^7, 2.5x10^7, and 2.5x10^7 H1299 cells infected with libraries A, B, C and D, respectively. gDNA was purified using DNeasy blood and tissue kit (Qiagen). For each measurement, a two-step nested PCR was performed: First, the entire DBD region was amplified (performed identically for all 4 sub-libraries). Then, in each experiment the relevant sub-library DBD fragment was amplified using primers specific to the modified region in that sub-library. In the first step (performed in multiple tubes to include the required amount of gDNA), each reaction contained a total volume of 100ul with 10ug gDNA, 50ul of Kapa Hifi ready mix X2 (KAPA Biosystems) and 5ul of each (10mM) primer. The parameters for PCR were 950C for 5min, 18 cycles of 94°C for 30s, 65°C for 30s, and 72°C for 30s, followed by one cycle of 72°C for 5 min. The primers used for this reaction were CTGAAGACCCAGGTCCAGATGAAG (Fw) and GGAGAGGAGCTGGTGTTGTTGG (Rv). In the second PCR step each reaction contained a total volume of 50ul with 2.5ul of the first PCR product (uncleaned), 25ul of Kapa Hifi ready mix X2 (KAPA Biosystems) and 2.5ul of each (10mM) primer. The parameters for PCR were as in the first step, performing 24 cycles. Primers used for this reaction included 5 random nucleotides at their 5’-end to increase sequence complexity and facilitate cluster calling during sequencing, and were specific for each of the 4 sub-libraries: sub-library A: Fw- NNNNNTGTCATCTTCTGTCCCTTCCCAGAAA, Rv- NNNNNATGGCGCGGACGCGGGT; sub-library B: Fw-NNNNNCTGTGCAGCTGTGGGTTGATTC, Rv-NNNNNCCAAATACTCCACACGCAAATTTC; sub-library C: Fw-NNNNNCCCTCCTCAGCATCTTATCCGAGT, Rv-NNNNNAGGATGGGCCTCCGGTT; sub-library D: Fw-NNNNNTGTGTAACAGTTCCTGCATGGG, Rv-NNNNNGCAGCTCGTGGTGAGGCT. Alternatively, for sequencing runs which included samples from various experiments or time points, this reaction was performed using alternatively barcoded Fw primers, used to barcode the different experimental samples. These primers included 3 random nucleotides at their 5' to increase sequence complexity followed by a unique 4-nucleotide barcode (see Table S1 for sequences). Amplicons were separated from nonspecific fragments by electrophoresis on a 1% agarose gel stained with EtBr, extracted from the gel and purified using a gel purification kit (Nucleospin). Products were further cleaned using a MinElute PCR Purification kit (Qiagen) and eluted in 12ul DDW. Concentration was measured using a monochromator (Tecan i-control), and sample size and purity were assessed by Tape-station using a high-sensitivity D1K screen tape (Agilent Technologies).   From mouse tumors: Primary tumors were dissected manually and flash-frozen in liquid nitrogen. Although each mouse was injected in a single location, in cases where more than a single clearly separated tumor was visible during dissection, each tumor was collected separately (labeled ‘T2a’, ‘T2b’, etc.). For DNA extraction, samples were thawed and divided to 2ml tubes each containing 25mg tissue. Genomic DNA was extracted using DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol. For lysis, each sample was suspended in 180ul ATL buffer and homogenized for 10 minutes in a Qiagen TissueLyser LT with a single 5mm stainless steel bead (Qiagen). Following removal of the bead, 20ul proteinase K were added and samples were incubated for 1 hour at 56°C. Then, after samples cooled down to room temperature, they were supplemented with 4ul RNAse and incubated for 2 minutes at RT. To avoid bias due to tumor heterogeneity, DNA from the entire tumor was purified. Thus, all lysates originating from the same tumor were pooled together and purified using the kit’s columns and the manufacturer’s protocol. Amplicons of the DBD-D region and Illumina library preparations were then prepared as described above.
50ng DNA were used for library preparation for next-generation sequencing, specific Illumina adaptors were added, and DNA was enriched by 14 amplification cycles by a protocol adopted from Blecher-Gonen et al. (Blecher-Gonen et al., 2013). Samples were reanalyzed by Tape-station prior to sequencing.

treatment_protocol: At defined timepoints, genomic DNA was extracted and subjected to PCR amplification of the relevant part of the DNA binding domain of p53

tag: growth media

value: RPMI

tag: time points / samples

value: 6 days post infection

tag: sublibrary

value: B


title: WT PRDM16 input replicate 2

value: Whole cortex lysate


title: WT PRDM16 ChIP-seq replicate 2

value: Donated by Patrick Seale (Upenn, U.S.A.)


title: cKO PRDM16 ChIP-seq replicate1

value: Emx1Ires-Cre; Prdm16flox/flox


title: WTZT20LIVER rep2

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

description: replicate 2

data_processing:
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
combine same strand txt into one file
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include original mapped reads, chromatin, gene symbol, start, end, strand, tissue and RPKM values for each Sample
Supplementary_files_format_and_content: processed data file contents: chromatin, start, end, original strand, gene symbol, given gene number, mapped reads, named strand (TS, NTS), time (for sacrificed), tissue, RPKM
Supplementary_files_format_and_content: kidneyNTSreplicate1.txt: non-transcribed strand replicate 1
Supplementary_files_format_and_content: kidneyNTSreplicate2.txt: non-transcribed strand replicate 2
Supplementary_files_format_and_content: kidneyTSreplicate1.txt: transcribed strand replicate 1
Supplementary_files_format_and_content: kidneyTSreplicate2.txt: transcribed strand replicate 2
Supplementary_files_format_and_content: DOWNSAMPLEDkidneyIntergenicDNAreplicate1.txt: intergenic DNA replicate 1
Supplementary_files_format_and_content: DOWNSAMPLEDkidneyIntergenicDNAreplicate2.txt: intergenic DNA replicate 2
Supplementary_files_format_and_content: DOWNSAMPLEDkidneyNTSreplicate1.txt: non-transcribed strand replicate 1
Supplementary_files_format_and_content: DOWNSAMPLEDkidneyNTSreplicate2.txt: non-transcribed strand replicate 2
Supplementary_files_format_and_content: DOWNSAMPLEDkidneyOvrlapGenereplicate1.txt: overlap genes replicate 1
Supplementary_files_format_and_content: DOWNSAMPLEDkidneyOvrlapGenereplicate2.txt: overlap genes replicate 2
Supplementary_files_format_and_content: DOWNSAMPLEDkidneyTSreplicate1.txt: transcribed strand replicate 1
Supplementary_files_format_and_content: DOWNSAMPLEDkidneyTSreplicate2.txt: transcribed strand replicate 2
Supplementary_files_format_and_content: liverNTSreplicate1.txt: non-transcribed strand replicate 1
Supplementary_files_format_and_content: liverNTSreplicate2.txt: non-transcribed strand replicate 2
Supplementary_files_format_and_content: liverTSreplicate1.txt: transcribed strand replicate 1
Supplementary_files_format_and_content: liverTSreplicate2.txt: transcribed strand replicate 2

source_name: Liver

growth_protocol: Wild-type animals (6 month old C57BL/6J females) were purchased from Jackson Laboratory (Bar Harbor, ME), and maintained on a light: dark 12:12 schedule for at least 2 weeks before sacrifice.

extract_protocol:
Tissue were lysed gently and small molecular weight DNA, consisting mostly of excised 26-27 mers was separated from chromosomal high molecular weight DNA by centrifugation
Briefly, the excised oligomers are immunopricipitated with anti-TFIIH (anti-XPB and anti-p62) antibodies because the excision product is released in a relatively stable complex with TFIIH, which also protects the excision product from degradation by non-specific nucleases. This is followed by extraction of the excised oligomers and ligation to adaptors and a second immunoprecipitation with either anti-CPD or anti-BPDE antibodies. Human DNA polymerases η and κ were used for primer extension in the presence of purified excised oligonucleotides containing either CPD or BPDE-dG damages, as polymerases η and κ can bypass CPD and BPDE-dG damage respectively in an error-free manner. This is followed by PCR amplification with index primers and NGS sequencing on HiSeq 2500 platform.

treatment_protocol: Cisplatin (each mL contains: 1 mg cisplatin and 9 mg sodium chloride in water for injection, Fresenius Kabi Pharmaceutical company) was administered by intraperitoneal injection at 10 mg cisplatin/kg.

value: Liver

tag: age

value: post natal day 6 months

tag: zeitgeber time

value: wild type


title: WTZT16LIVER rep2

description: replicate 2

tag: strain


title: WTZT8LIVER rep2

description: replicate 2


title: WTZT12LIVER rep2

description: replicate 2


title: WT PRDM16 ChIP-seq replicate1

value: Prdm16 flox/flox


title: WTZT16LIVER rep1

description: replicate 1


title: WTZT12LIVER rep1

description: replicate 1


title: WTZT0LIVER rep1

description: replicate 1


title: WTZT4LIVER rep2

description: replicate 2


title: cKO PRDM16 ChIP-seq replicate 2


title: WTZT0LIVER rep2

description: replicate 2


title: WTZT4LIVER rep1

description: replicate 1


title: WTZT16KIDNEY rep2

description: replicate 2

source_name: Kidney

value: Kidney


title: WTZT12KIDNEY rep2

description: replicate 2


title: cKO PRDM16 input replicate 1


title: WTZT20KIDNEY rep2

description: replicate 2


title: WTZT20KIDNEY rep1

description: replicate 1


title: WTZT12KIDNEY rep1

description: replicate 1


title: WTZT8KIDNEY rep2

description: replicate 2


title: WT PRDM16 input replicate 1


title: WTZT20LIVER rep1

description: replicate 1


title: WTZT8KIDNEY rep1

description: replicate 1


title: Plasma Gel 5' Multiplex Adapter No MD Control 1

description:
Plasma Gel Extracted Multiplex 5' Adapter No MAD-DASH Control
PlasmaGel_Samples_GSLv2-7_01_SL321686

value: blood plasma


title: WTZT4KIDNEY rep1

description: replicate 1


title: WTZT4KIDNEY rep2

description: replicate 2


title: WTZT8LIVER rep1

description: replicate 1


title: LSD1 KO_LSD1

value: B16 tumor transplanted in C56BL/6 mice

value: genomic DNA

value: LSD1 (Abcam, cat#17721)


title: WTZT0KIDNEY rep1

description: replicate 1


title: SAMPLE_106: CD3_Transcripts-R.18Siro.F

type: RNA

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

department: Medicine

institute: University of Pittsburgh

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip Rhesus Macaque Genome Array.  GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics script FS450_0001.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 scanner with 7G upgrade.

data_processing: Data from .CEL files were uploaded to the Bioconductor for further analysis and normalized using RMA (‘affy’ package).  Resulting fluorescent intensities were normalized to account for batch effects using the ‘sva’ package.

label: biotin

organism: Macaca mulatta

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3’IVT Plus protocol from 70-85 ng total RNA.

extract_protocol: CD3 T cells were lysed in RLT Buffer and total RNA was isolated using the RNAEasy kit per manufacturers instructions.

treatment_protocol: Cohorts of NHP received either an allogeneic or autologous HCT.  Allogeneic HCT recipients received various immunoprophylactic treatments for prevention of GVHD.  CD3 T cells were sorted by FACS from peripheral blood at various timepoints in the post transplant period and from healthy controls.

value: CD3 T cells

tag: individual

tag: group

tag: batch


title: WTZT0KIDNEY rep2

description: replicate 2

tag: tissue


title: SAMPLE_108: CD3_Transcripts-R.16Siro.F


title: SAMPLE_105: CD3_Transcripts-R.13Siro.F


title: SAMPLE_107: CD3_Transcripts-R.17Siro.F


title: SAMPLE_104: CD3_Transcripts-R.229NoRx.F


title: SAMPLE_102: CD3_Transcripts-R.233NoRx.F


title: SAMPLE_103: CD3_Transcripts-R.232NoRx.F


title: WTZT16KIDNEY rep1

description: replicate 1


title: SAMPLE_100: CD3_Transcripts-R.231NoRx.F


title: SAMPLE_101: CD3_Transcripts-R.230NoRx.F


title: SAMPLE_98: CD3_Transcripts-R.235NoRx.F


title: SAMPLE_97: CD3_Transcripts-R.52NoRx.F


title: SAMPLE_99: CD3_Transcripts-R.234NoRx.F


title: SAMPLE_94: CD3_Transcripts-R.53NoRx.F


title: SAMPLE_93: CD3_Transcripts-R.216Healthy.Control


title: Plasma Gel 5' Multiplex Adapter AD /mir16 MD  1

description:
Plasma Gel Extracted Multiplex 5' Adapter Adapter Dimer  and mir-16-5p MAD-DASH
PlasmaGel_Samples_GSLv2-7_13_SL321690


title: SAMPLE_91: CD3_Transcripts-R.225Healthy.Control


title: SAMPLE_92: CD3_Transcripts-R.226Healthy.Control


title: SAMPLE_90: CD3_Transcripts-R.223Healthy.Control


title: SAMPLE_96: CD3_Transcripts-R.51NoRx.F


title: Rop7-II biological replicate 2 [AR7II_R2]

value: CD8 T-cells

tag: clone id

tag: incubated with

value: ROP7 peptide (10 μM)

tag: sorted cell type

value: CD3+ CD8+ H-2Ld-Rop7+


title: SAMPLE_95: CD3_Transcripts-R.50NoRx.F


title: SAMPLE_89: CD3_Transcripts-R.254Healthy.Control


title: SAMPLE_88: CD3_Transcripts-R.237Healthy.Control


title: SAMPLE_87: CD3_Transcripts-R.227Healthy.Control


title: SAMPLE_86: CD3_Transcripts-R.224Healthy.Control


title: HCT116_3dCulture_DBDD_d9_3D_A

description:
processed data file: HCT116_3dCulture_DBDD.csv
enrichment in 2D vs 3D culture

source_name: Colorecteal cancer

value: McCoy

value: 9 days, 3D culture, replicate A

value: D ( small scale library)


title: Purified cells from mobilized peripheral blood, sorted CD45 positive CD34 positive CD38 negative, biological replicate 2

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

scan_protocol: GeneChips were scanned using  Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm and baseline transformation to the median of all samples using GeneSpring 12.5 software.

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions. Total RNA was amplified following the standard protocol at London Regional Genomics Centre.

tag: cell type

value: Purified cells from mobilized peripheral blood cells  (MPB)

tag: cell subtype


title: HCT116_3dCulture_DBDD_d9_3D_B

value: 9 days, 3D culture, replicate B


title: H9 embryonic stem cells, CD45 positive CD34 positive CD38 negative sorted population, biological replicate 2

label_protocol: In accordance with manufacturer's protocols

growth_protocol: Differentiation protocol described in Chadwick et al. Blood 2013., sorted on EB day 15

value: H9 embryonic stem cells


title: HCT116_3dCulture_DBDD_d7_3D_B

value: 7 days, 3D culture, replicate B


title: SAMPLE_84: CD3_Transcripts-R.241Healthy.Control


title: Purified cells from mobilized peripheral blood, sorted CD45 positive CD34 positive CD38 negative, biological replicate 1


title: H9 embryonic stem cells, CD45 positive CD34 positive CD38 negative sorted population, biological replicate 1


title: HCT116_3dCulture_DBDD_d9_2D_B

value: 9 days, 2D culture, replicate B


title: SAMPLE_83: CD3_Transcripts-R.228Healthy.Control


title: HCT116_3dCulture_DBDD_d9_2D_A

value: 9 days, 2D culture, replicate A


title: HCT116_3dCulture_DBDD_d7_3D_A

value: 7 days, 3D culture, replicate A


title: HCT116_3dCulture_DBDD_d7_2D_B

value: 7 days, 2D culture, replicate B


title: SAMPLE_82: CD3_Transcripts-R.242Healthy.Control


title: Purified cells from mobilized peripheral blood, sorted CD45 positive CD34 positive CD38 negative, biological replicate 3


title: SAMPLE_78: CD3_Transcripts-R.209Healthy.Control


title: SAMPLE_79: CD3_Transcripts-R.213Healthy.Control


title: HCT116_3dCulture_DBDD_d7_2D_A

value: 7 days, 2D culture, replicate A


title: SAMPLE_81: CD3_Transcripts-R.215Healthy.Control


title: SAMPLE_77: CD3_Transcripts-R.208Healthy.Control


title: SAMPLE_75: CD3_Transcripts-R.205Healthy.Control


title: SAMPLE_80: CD3_Transcripts-R.214Healthy.Control


title: SAMPLE_73: CD3_Transcripts-R.204Healthy.Control


title: SAMPLE_74: CD3_Transcripts-R.203Healthy.Control


title: SAMPLE_72: CD3_Transcripts-R.22Healthy.Control


title: SAMPLE_71: CD3_Transcripts-R.41Healthy.Control


title: SAMPLE_70: CD3_Transcripts-R.55Healthy.Control


title: SAMPLE_67: CD3_Transcripts-R.200Healthy.Control


title: SAMPLE_69: CD3_Transcripts-R.202Healthy.Control


title: SAMPLE_85: CD3_Transcripts-R.253Healthy.Control


title: SAMPLE_65: CD3_Transcripts-R.45Healthy.Control


title: HCT116_3dCulture_DBDD_T0

value: Time 0 (seeded pool)


title: SAMPLE_63: CD3_Transcripts-R.40Healthy.Control

value: CD3 T cells


title: rpb1-1/caf1_45

city: Cleveland

first: Jeff

last: Coller

state: OH

address: 10900 Euclid Ave

department: Center for RNA Science and Therapeutics

institute: Case Western Reserve University

description: Sample name: 6540

data_processing:
Basecalling was performed using Illumina CASAVA software
Reads were aligned to the reference genome using bowtie version 0.12.7 using parameters ‘-m 1 -v 2 -p 8’
Transcripts FPKMs from aligned reads were obtained using Cufflinks 1.3.0 using GTF provided by SGD (default parameters)
Unaligned reads from bowtie were aligned to control RNA sequences to obtain relative concentration
Genome_build: SacCer2
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Processed data files listing all FPKMs used in final analysis

organism: Saccharomyces cerevisiae

source_name: mid-log phase culture

growth_protocol: rpb1-1 mutant cells (yJC244) were grown to mid-log phase at 24C as described above. Cells were shifted to 37C, then cell aliquots were removed and total RNA was isolated. 10 time points were collected over 60 minutes, including an initial aliquot at time 0 collected before the temperature shift.

extract_protocol:
Cells were lysed by bead bashing in phenol and RNA was purified by acidic phenol-chlorofom extraction.
Input RNA was spiked with control RNA and libraries were prepared using either Illumina TruSeq Stranded mRNA library prep kits or Illumina TruSeq Stranded Total RNA library prep kit as indicated above

treatment_protocol: Cells were transferred to non-permissive temperature (37C) to shut off transcription

tag: genotype/variation

value: rpb1-1/caf1 mutant

tag: time point (minutes)


title: SAMPLE_57: CD3_Transcripts-R.48Healthy.Control


title: SAMPLE_66: CD3_Transcripts-R.44Healthy.Control


title: rpb1-1/caf1_20

description: Sample name: 6538


title: SAMPLE_64: CD3_Transcripts-R.35Healthy.Control


title: SAMPLE_62: CD3_Transcripts-R.43Healthy.Control


title: Untagged control #1

city: Austin

first: Arlen

middle: W

last: Johnson

state: Texas

address: 2506 Speedway

department: Molecular Biosciences

institute: The University of Texas

data_processing:
fastx_trimmer (v0.0.14) to remove bases after the 84th base (very low quality reads after as determined by fastqc)
fastx_clipper (v0.0.14) to remove adaptor sequences "CTGTAGGCACCATCAAT", discard sequences less than 5 bases, kept sequences containing "N" base
alignment: Bowtie2 (v2.2.6) default settings for single-end reads
pyReadCounters.py (0.5.3) and pyPileup.py (0.1.2) (Webb et al, Genome Biol, 2014); data available as supplementary file in (Black JJ et al, RNA, 2018, provisionally accepted).
Genome_build: Ensembl R64-1-1 May 27, 2014
Supplementary_files_format_and_content: bedgraph of alignment files

source_name: BY4741 cells

growth_protocol: Grown in liquid YPD media at 30°C to exponential phase

extract_protocol:
RNA was prepared using tandem-affinity purification via the HTP tag following the protocol adapted from (Granneman S et al, PNAS, 2009) as described in (Black JJ et al, RNA, 2018, provisionally accepted).
Library was constructed using a modified protocol adapted from (Granneman S et al, PNAS, 2009) and (Ingolia S et al, Nature protocols, 2012) as outlined in (Black JJ et al, RNA, 2018, provisionally accepted).

treatment_protocol: UV-treated using Stratalinker UV Crosslinker 1800


title: Utp14-HTP #1

source_name: Utp14-HTP cells


title: SAMPLE_60: CD3_Transcripts-R.54Healthy.Control


title: Untagged control #2

description: Raw files were merged prior to data processing


title: SAMPLE_55: CD3_Transcripts-R.30Healthy.Control


title: Utp14-HTP #2


title: SAMPLE_59: CD3_Transcripts-R.49Healthy.Control


title: SAMPLE_61: CD3_Transcripts-R.47Healthy.Control


title: SAMPLE_58: CD3_Transcripts-R.34Healthy.Control


title: rpb1-1/caf1_10

description: Sample name: 6536


title: SAMPLE_68: CD3_Transcripts-R.201Healthy.Control


title: SAMPLE_56: CD3_Transcripts-R.31Healthy.Control


title: rpb1-1/caf1_60

description: Sample name: 6541


title: rpb1-1/caf1_15

description: Sample name: 6537


title: SAMPLE_53: CD3_Transcripts-R.39Healthy.Control


title: maize_PROseq

city: Ithaca

first: Roberto

last: Lozano

state: NY

address: 358 Plant Science Building, Cornell University

department: Plant Breeding and Genetics

institute: Cornell University

description: Nascent RNA

data_processing:
Library strategy: PRO-seq
The fastq files were scanned for any residual adapter sequence (5’ TGGAATTCTCGGGTGCCAAGG -3’) using fastx_clipper from the FASTX_toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), and the 3’ molecular barcode was  removed. Reads were trimmed to a maximum length of 36bp, and the reverse complement was calculated because the Hiseq starts sequencing from the 5’ end. All downstream alignments were performed using Bowtie2. The PRO-seq method described before is not exclusive to transcripts produced by the nuclear DNA Polymerase II, therefore the reads were aligned to the chloroplast genome to eliminate transcripts produced in this organelle. The remaining reads were mapped to the Manihot esculenta reference genome v6.1 and the maize genome AGPv4 . Low-quality alignments were filtered and only reads mapping once to the genome were considered for further analysis. Bedtools was used to get bedgraph files reporting only the number of  3’ end reads at each position. Finally, bigwig files were obtained from the bedgraph files using kentUtils
Genome_build: Cassava Genome v6.1, Maize Genome AGPv4
Supplementary_files_format_and_content: Processed files are in bigwig format. There are two bigwig files for each sample, one for each strand. Each bigwig file contains normalized counts of read 3'-ends.

organism: Zea mays

source_name: seedlings

growth_protocol: Maize inbred line B73 seeds were grown in growth chambers at the Cornell Biotechnology Building.  Shoots were collected 9 days after germination.

extract_protocol:
Stem and leaves of approximately 25gr were ground with liquid nitrogen to a fine powder using a mortar and a pestle. The resulting powder was transfer to a coffee grinder containing cold 1X NIB buffer. Then, we used the CelLytica PN Plant nuclei isolation/extraction kit (Sigma-Aldrich) following the instructions for the “Highly-pure preparation of Nuclei.” The resulting solutions were frozen in liquid N2 and stored at -80° C. Most of the nuclei extraction protocol took place in a cold room (4° C) with all reagents on ice. A fraction of the nuclei preparations were stained with DAPI and visualized under a fluorescence microscope to test for concentration and nuclei integrity.
The PRO-seq protocol was performed as described by Mahat et al. Nature Protocols (2016). Briefly, nuclei isolation washes away endogenous nucleotides, halting elongating RNA polymerases bound to chromatin. Precision run-on reactions were performed in the presence of equimolar amounts of unaltered ATP and GTP, as well as biotin-11-CTP and biotin-11-UTP (Perkin-Elmer). Notably, this two-biotin run-on will produce polymerase profiles with slightly reduced (~ 2-4 bp) resolution compared to a more typical four-biotin run on, given that RNA polymerases will primarily stall when incorporating the modified CTP and UTP (Kwak et al. 2013). RNA was extracted and base-hydrolyzed with NaOH. Hydrolyzed, biotin-labelled nascent RNAs were passed through a RNase-free P-30 spin column (Bio-Rad) and then enriched using M-280 streptavidin Dynabeads (Invitrogen). T4 RNA ligase 1 (NEB) was used to attach a 3’ RNA adaptor containing a six-nucleotide unique molecular index (UMI) for the removal of duplicate sequences produced by PCR (5’-/5Phos/NNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/Inverted dT/-3’).  After a second biotin-enrichment, RNAs were submitted to RNA 5' Pyrophosphohydrolase (RppH, NEB) treatment for 5’ de-capping, and then 5’ phosphorylation with T4 polynucleotide kinase (T4 PNK, NEB), before ligation of the 5’ RNA adaptor (5'-CCUUGGCACCCGAGAAUUCCA-3’). Reverse transcription was performed with SSIII RT (Invitrogen) after a third biotin-enrichment. The cDNAs produced were PCR amplified for 13 cycles with Phusion polymerase (NEB) and size selected (120bp - 400bp) before sequencing. This protocol generated strand-specific libraries with every read starting from the 3’ end of the RNA. The RNA adapters used are TruSeq-compatible and libraries were reverse transcribed and amplified using primers from the Illumina TruSeq small RNA sequencing kit.  Amplified libraries were assessed for quality on a bioanalyzer prior to sequencing on a HiSeq2500 with 100bp single reads.

tag: accession

value: 9 days after germination

value: shoots


title: SAMPLE_52: CD3_Transcripts-R.56Healthy.Control


title: rpb1-1/caf1_30

description: Sample name: 6539


title: SAMPLE_51: CD3_Transcripts-R.60Healthy.Control


title: rpb1-1/caf1_8

description: Sample name: 6535


title: SAMPLE_48: CD3_Transcripts-R.16Healthy.Control


title: SAMPLE_49: CD3_Transcripts-R.18Healthy.Control


title: SAMPLE_50: CD3_Transcripts-R.59Healthy.Control


title: SAMPLE_44: CD3_Transcripts-R.32Healthy.Control


title: SAMPLE_41: CD3_Transcripts-R.53Healthy.Control


title: SAMPLE_45: CD3_Transcripts-R.62Healthy.Control


title: SAMPLE_40: CD3_Transcripts-R.37Healthy.Control


title: SAMPLE_54: CD3_Transcripts-R.28Healthy.Control


title: SAMPLE_46: CD3_Transcripts-R.33Healthy.Control


title: SAMPLE_42: CD3_Transcripts-R.13Healthy.Control


title: SAMPLE_38: CD3_Transcripts-R.206Healthy.Control


title: SAMPLE_39: CD3_Transcripts-R.58Healthy.Control


title: SAMPLE_43: CD3_Transcripts-R.61Healthy.Control


title: MT_NICD-ER_24h_EtOH_rep2

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description:
RNA-seq in mouse mature T-cells infected with plamids encoding for the Notch Intracellular Domain fused to the estrogen receptor binding domain (NICD-ER) and treated for 24 hours with EtOH. Replicate 1
RiboMinus - depleted total RNA

data_processing:
Quality control of FATSQ files was done using fastqc.
Removal of low-quality reads and trimming was done using trimmomatic
Read mapping was done using STAR
The aligned readswere analyzed with featureCounts  in order to obtain expression measures and differential gene expression measures.
DESeq2 was used for calling of differentially expressed genes
Genome_build: mm9
Supplementary_files_format_and_content: featureCounts output containing information about read counts per gene

source_name: mouse mature T-cells

growth_protocol: mouse mature T-cells were grown at 37°C with 5% CO2 in IMDM medium (Gibco 21980-065) supplemented with 2 % FCS, peptone, insulin, nonessential aminoacids and penicillin/streptomycin

extract_protocol:
RNeasy Mini Kit (Qiagen #74104) using the QIAshredder (Qiagen #79654) and  RNase-free DNase (Qiagen #79254)
Library-prep kit: Illumina TruSeq® Stranded Total RNA LT - Ribo-Zero Gold (RS-122-2301/2)

tag: cell line

value: hybridoma called E2-10HA

tag: integrated plasmid

value: pMIGRI Flag-NICD-ER IRES GFP

tag: selection

value: sorting

tag: treatment

value: 24 hours treatment with EtOH


title: MT_NICD-ER_24h_4-OHT_rep1

description:
RNA-seq in mouse mature T-cells infected with plamids encoding for the Notch Intracellular Domain fused to the estrogen receptor binding domain (NICD-ER) and treated for 24 hours with (Z)-4-hydroxytamoxifen (4-OHT). Replicate 1
RiboMinus - depleted total RNA

value: 24 hours treatment with (Z)-4-hydroxytamoxifen (4-OHT)


title: MT_NICD-ER_24h_EtOH_rep1


title: rpb1-1/caf1_6

description: Sample name: 6534

tag: strain


title: rpb1-1/caf1_3

description: Sample name: 6533


title: MT_NICD-ER_24h_4-OHT_rep2


title: rpb1-1/caf1_0

description: Sample name: 6532


title: MT_BioNICD_DEP_rep1

description:
RNA-seq in mouse mature T-cells infected with plamids encoding for the bacterial biotin ligase BirA and for a DEP mutant bio-tagged Notch Intracellular Domain (NICD). Replicate 1
RiboMinus - depleted total RNA

value: pLXSP-BirA / pMY-BioNICD-DEP-IRES-GFP

value: histidinol / sorting

value: no treatment


title: SAMPLE_37: CD3_Transcripts-R.27FR104.Siro.D30

tag: individual


title: SAMPLE_36: CD3_Transcripts-R.29FR104.Siro.D30

tag: group


title: MT_BioNICD_wt_rep1

description:
RNA-seq in mouse mature T-cells infected with plamids encoding for the bacterial biotin ligase BirA and for a wildtype bio-tagged Notch Intracellular Domain (NICD). Replicate 1
RiboMinus - depleted total RNA

value: pLXSP-BirA / pMY-BioNICD-IRES-GFP


title: MT_BioNICD_wt_rep2

description:
RNA-seq in mouse mature T-cells infected with plamids encoding for the bacterial biotin ligase BirA and for a wildtype bio-tagged Notch Intracellular Domain (NICD). Replicate 2
RiboMinus - depleted total RNA


title: SAMPLE_35: CD3_Transcripts-R.28FR104.Siro.D30

tag: batch


title: SAMPLE_47: CD3_Transcripts-R.36Healthy.Control

tag: tissue


title: MT_sgH2afv/H2afz_#12_rep2

description:
RNA-seq in mouse mature T-cells infected with lentiCRISPRv2 encoding for sgRNAs targeting H2afv and H2afz genes. Replicate 2
RiboMinus - depleted total RNA

value: puromycin


title: MT_BioNICD_DEP_rep2

description:
RNA-seq in mouse mature T-cells infected with plamids encoding for the bacterial biotin ligase BirA and for a DEP mutant bio-tagged Notch Intracellular Domain (NICD). Replicate 2
RiboMinus - depleted total RNA


title: SAMPLE_34: CD3_Transcripts-R.26FR104.Siro.D30


title: SAMPLE_30: CD3_Transcripts-R.249FR104.Siro.D14


title: SAMPLE_32: CD3_Transcripts-R.213FR104.Siro.D30


title: SAMPLE_31: CD3_Transcripts-R.213FR104.Siro.D14


title: MT_CRISPR_Control_rep2

description:
RNA-seq in mouse mature T-cells infected with lentiCRISPRv2 empty vector. Replicate 2
RiboMinus - depleted total RNA


title: MT_sgH2afv/H2afz_#12_rep1

description:
RNA-seq in mouse mature T-cells infected with lentiCRISPRv2 encoding for sgRNAs targeting H2afv and H2afz genes. Replicate 1
RiboMinus - depleted total RNA


title: MT_CRISPR_Control_rep1

description:
RNA-seq in mouse mature T-cells infected with lentiCRISPRv2 empty vector. Replicate 1
RiboMinus - depleted total RNA


title: SAMPLE_28: CD3_Transcripts-R.29FR104.Siro.D14


title: SAMPLE_25: CD3_Transcripts-R.24FR104.F


title: SAMPLE_26: CD3_Transcripts-R.26FR104.Siro.D14


title: SAMPLE_33: CD3_Transcripts-R.249FR104.Siro.D30


title: SAMPLE_27: CD3_Transcripts-R.28FR104.Siro.D14


title: SAMPLE_24: CD3_Transcripts-R.23FR104.F


title: orco3

city: Seattle

first: Jay

last: Parrish

state: Washington

department: Department of Biology

institute: University of Washington

description: Each sample isolated independently

data_processing:
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2
Reads were filtered for the presence of adapters using Cutadapt version 1.9.1
Reads were aligned to the transcriptome using Kallisto version 0.43.0 with default parameters.
Transcript-level counts were condensed to gene-level counts using tximport
Genome_build: FlyBase genome release 6.10
Supplementary_files_format_and_content: Tab delimited text files showing estimated counts for all isoforms for each sample
Supplementary_files_format_and_content: Tab delimited text files showing estimated counts for all genes for each sample

organism: Drosophila melanogaster

source_name: orco mutant_larval dorsal organ

extract_protocol:
Thoracic segments containing chemosensory organs were dissected from third instar larvae, enzymatically treated with type I collagenase, and GFP-positive dorsal organs were manually separated from neighboring tissue and snap frozen in RNAqueous lysis buffer (Fisher). RNA was isolated using the RNAqueous Micro Kit, diluted to 0.2ng/ul, and converted to pre-amplified cDNA libraries using Smart-seq2 template-switching reverse transcription.
RNA libraries were prepared for sequencing following Illumina protocols.  cDNA libraries were diluted to 0.25ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq4000

tag: developmental stage

value: third instar

tag: genotype

value: orco, Orco-Gal4 > UAS-mCD-8GFP

value: dorsal organ

tag: quantity

value: 20 organs


title: orco4

description: Each sample isolated independently


title: orco2

description: Each sample isolated independently


title: wildtype4

description: Each sample isolated independently

source_name: WT_larval dorsal organ

value: Orco-Gal4 > UAS-mCD-8GFP


title: orco1

description: Each sample isolated independently


title: orco5

description: Each sample isolated independently


title: wildtype3

description: Each sample isolated independently


title: SAMPLE_22: CD3_Transcripts-R.24FR104.D14

value: CD3 T cells


title: wildtype1

description: Each sample isolated independently


title: SAMPLE_21: CD3_Transcripts-R.23FR104.D14


title: SAMPLE_23: CD3_Transcripts-R.22FR104.F


title: wildtype2

description: Each sample isolated independently


title: SAMPLE_20: CD3_Transcripts-R.22FR104.D14


title: SAMPLE_29: CD3_Transcripts-R.27FR104.Siro.D14


title: SAMPLE_19: CD3_Transcripts-R.70Bela.Siro.D30


title: SAMPLE_18: CD3_Transcripts-R.66Bela.Siro.D30


title: SAMPLE_17: CD3_Transcripts-R.68Bela.Siro.D30


title: SAMPLE_16: CD3_Transcripts-R.49Bela.Siro.D30


title: SAMPLE_15: CD3_Transcripts-R.42Bela.Siro.D30


title: SAMPLE_14: CD3_Transcripts-R.38Bela.Siro.D30


title: SAMPLE_12: CD3_Transcripts-R.42Bela.Siro.D14


title: SAMPLE_10: CD3_Transcripts-R.46Bela.F


title: SAMPLE_11: CD3_Transcripts-R.38Bela.Siro.D14


title: SAMPLE_8: CD3_Transcripts-R.47Bela.F


title: SAMPLE_6: CD3_Transcripts-R.201Auto.D36


title: SAMPLE_7: CD3_Transcripts-R.202Auto.D36


title: SAMPLE_13: CD3_Transcripts-R.49Bela.Siro.D14


title: SAMPLE_9: CD3_Transcripts-R.57Bela.F


title: SAMPLE_3: CD3_Transcripts-R.202Auto.D14


title: SAMPLE_4: CD3_Transcripts-R.62Auto.D36


title: SAMPLE_2: CD3_Transcripts-R.201Auto.D14


title: Obese-LA rat 2

city: Guelph

first: David

last: Mutch

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

description: Gene expression data from tibialis anterior following 12 weeks of diet

hyb_protocol: Following fragmentation, 5.5 ug of ss-cDNA was hybridized for 20 hr on Rat Transcriptome arrays incubated at 48°C. Strips were washed and stained using the Gene Atlas Fluidics Station.

scan_protocol: Rat Transcriptome arrays were scanned using the Gene Atlas Imaging Station

data_processing:
Data were analyzed with the Bioconductor package 'oligo' (v1.32.0). Data were preprocessed (background correction and normalization) with the Robust Multichip Average algorithm ('rma' function in 'oligo') with default settings.
Signal intensity after RMA preprocessing

organism: Rattus norvegicus

source_name: rat tibialis anterior after 12 weeks of diet feeding

label_protocol: Biotinylated cRNA was prepared according to the standard GeneAtlas WT Plus Affymetrix protocol from 100 ng total RNA.

growth_protocol: Lean and obese Zucker rats (5 weeks) were received from Charles River. Rats were housed in environmentally controlled rooms with ad libitum access to water. Obese animals fed the ALA and LA supplemented diets were pair-fed to match for caloric intake of obese controls.

extract_protocol: Rats were anesthetized with an injection of pentobarbital sodium (60 mg/kg), and the red tibialis anterior muscle was excised and immediately placed in liquid nitrogen.

treatment_protocol: Lean and obese control rats were given unrestricted access to the control diet (AIN-93G). The LA diet (AIN-93G + 10% safflower oil) and the ALA diet (AIN-93G + 10% flaxseed oil) were pair-fed in comparison to obese controls.

tag: Sex

value: male

value: Zucker obese

tag: diet

value: LA

value: tibialis anterior muscle

tag: age

value: 18 weeks


title: Obese-LA rat 6


title: Obese-LA rat 5


title: Obese-LA rat 7


title: Obese-LA rat 4


title: Obese-LA rat 1


title: SAMPLE_5: CD3_Transcripts-R.200Auto.D36


title: SAMPLE_1: CD3_Transcripts-R.200Auto.D14


title: Obese-LA rat 3


title: Obese-ALA rat 5

value: ALA


title: Obese-ALA rat 7


title: Obese-LA rat 8


title: Obese-ALA rat 6


title: Obese-ALA rat 8


title: SAMPLE_76: CD3_Transcripts-R.207Healthy.Control


title: Obese-ALA rat 3


title: Obese-ALA rat 4


title: Obese control rat 5

value: control


title: Obese control rat 8


title: Obese-ALA rat 2


title: Obese-ALA rat 1


title: Obese control rat 7


title: Obese control rat 4


title: Obese control rat 6


title: epcr1/2 rep3

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using STAR-2.5.2b with parameters  --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 20  --alignSoftClipAtReferenceEnds No --readFilesCommand zcat-m 10 --best --strata
Fragments  Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cuflink2.0.0 cuffdiff with parameters -p 16 -N
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 16 h light/8 h dark photoperiod at 22ºC

extract_protocol:
Total RNA was extracted from 1 g samples of 10-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen)
libraries were prepared for mRNA-seq

value: seedlings


title: arid2/3/4 rep3


title: Obese control rat 3


title: Metformin_rep3

first: Yuan

last: Zhou

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

institute: Peking University

hyb_protocol: The microarray hybridization was performed following the standard Agilent pipeline.

scan_protocol: Array slides were scanned using Agilent G2565CA Microarray Scanner.

data_processing: Agilent Feature Extraction software (version 10.7) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX software package (Agilent Technologies).

source_name: Metformin treated (high fat diet), replicate 3

label_protocol: High quality RNA samples were Cy3 labeled by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio).

growth_protocol: Male 3-week-old C57BL/6J mice (18-21 g) were provided by the Spfanimals Company (Beijing, China). The mice were kept in a temperature- and humidity-controlled (20-24°C, 45-55% humidity) environment with free access to food and water. The protocol was approved by the Beijing Hopital Animal Ethics Committee.

extract_protocol: Total 15 mg of liver tissue was collected and flash frozen by liquid nitrogen. Then the total RNA was extracted by using the Trizol (Invitrogen, USA) following the manufacturer's recommendations.

treatment_protocol: The mice were separated into three groups and treated with different diet and drug. Control group: 17 weeks of normal chow; High fat diet group: 17 weeks of high fat diet chow, and intragastrically treated with saline saline vehicle for the last 5 weeks; Metformin treated group: 17 weeks of high fat diet chow, and intragastrically treated with 3 mg/kg/day metformin for the last 5 weeks.

value: liver

tag: gender

value: 20 weeks

value: metformin


title: Obese control rat 1


title: Metformin_rep1

source_name: Metformin treated (high fat diet), replicate 1


title: WT rep3

value: wild type


title: Lean control rat 8

value: Zucker lean


title: Control_rep2

source_name: Control (chow diet), replicate 2


title: High fat diet_rep2

source_name: High fat diet, replicate 2

value: high fat diet


title: Metformin_rep2

source_name: Metformin treated (high fat diet), replicate 2


title: High fat diet_rep3

source_name: High fat diet, replicate 3


title: epcr1/2 rep2


title: Control_rep1

source_name: Control (chow diet), replicate 1


title: arid2/3/4 rep2


title: Obese control rat 2


title: FA_CLIP_input_2

first: Lianhuan

last: Wei

address: Chengfu road 202

department: College of chemistry and Molecular Engineering

institute: Peking university

description: mRNA

data_processing:
Adapter removing (used Cutadapt).
Reads were mapped to TAIR10 by bowtie.
PARAlyzer was used to identify mutation based peaks. At least two mutations sites are needed in each peak.
To call peaks based on enrichment, a previously reported method (Lijia Ma et al. 2017) was used (FA-CLIP/input).
Genome_build: TAIR10
Supplementary_files_format_and_content: *_processed.txt: Tab-delimited text files.
Supplementary_files_format_and_content: FA_CLIP_input_1_processed.txt: RPKM abundance measurements.
Supplementary_files_format_and_content: FA_CLIP_input_2_processed.txt: RPKM abundance measurements.
Supplementary_files_format_and_content: FA_CLIP_mock_1_processed.txt: Mutation-based peaks contain at least two mutations calculated in PARAlyzer.
Supplementary_files_format_and_content: FA_CLIP_mock_2_processed.txt: Mutation-based peaks contain at least two mutations calculated in PARAlyzer.
Supplementary_files_format_and_content: FA_CLIP_1_processed.txt: Mutation-based peaks contain at least two mutations calculated in PARAlyzer.
Supplementary_files_format_and_content: FA_CLIP_2_processed.txt: Mutation-based peaks contain at least two mutations calculated in PARAlyzer.

source_name: 14-day-old seedlings

growth_protocol: All the Arabidopsis thaliana plants were grown on 1/2 Murashige and Skoog (MS) medium or soil under long day conditions (16 hr light/8 hr dark) at 22°C. The T-DNA insertion mutant line ect2 (SALK_002225) was obtained from the Arabidopsis Biological Resource Center.

extract_protocol:
Grind in Liquid N2.
NEBNext Ultra RNA Library Prep Kit for Illumina kit (NEB) for FA-CLIP input sample, NEB Next Multiplex Small RNA Library Prep Set for Illumina (NEB) for FA-CLIP and mock samples.

treatment_protocol: Formaldehyde fixation and crosslinking.

tag: ecotype/background

tag: genotype/variation

value: transgenic ECT2:ETC2-Flag/ect2

value: 14 days

tag: ip antibody


title: Control_rep3

source_name: Control (chow diet), replicate 3


title: Lean control rat 7


title: WT rep2


title: Lean control rat 5


title: FA_CLIP_input_1

description: mRNA


title: Lean control rat 6


title: R_Stellate_Ganglion_16_SHR_4

city: Oxford

last: Paterson

address: Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

data_processing:
Quality control check using FastQC (Version 0.11.7)
Quasimapping using Salmon (Version 0.8.2)
Genome_build: rn6
Supplementary_files_format_and_content: SF files containing transcript count data from Salmon Quasi-mapping

source_name: right stellate ganglion

extract_protocol:
Total RNA was extracted from isolated and cleaned stellate ganglia. Stellate ganglia were minced using dissection scissors in Qiagen RLT buffer. The protocol was then performed as described in the Qiagen Micro Kit guide.
Library was constructed by the Wellcome Trust Centre for Human Genetics (University of Oxford, UK). Total RNA was used with a Illumina TruSeq Stranded mRNA Library Prep Kit.

value: SHR

value: right stellate ganglion

value: 16 weeks old


title: High fat diet_rep1

source_name: High fat diet, replicate 1

value: male


title: Lean control rat 4

value: tibialis anterior muscle


title: Lean control rat 3

value: 18 weeks


title: HEK293T_rs199643834_EDIT_HOM [13_9]

city: New York

first: Stephane

middle: Emile

last: Castel

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
Trimmomatic v0.36 was used to clip Illumina adaptors and quality trim.
Reads were aligned to hg19 using STAR in 2 pass mode.
featureCounts  v1.5.3 was used in read counting and strand specific mode (-s 2) with primary alignments only to generate gene level read counts with Gencode v19 annotations used in GTEx v6p.
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix where lines are genes, columns are samples, and the values are the featureCounts read counts.

growth_protocol: Human 293T cell line (ATCC, cat. # CRL-3216) was adapted to and subsequently routinely grown in Opti-MEM/5% CCS (newborn calf serum), 1% GlutaMAX, 1% Penicillin/Streptomycin and sodium pyruvate. Expanded lines were grown to 70-80% confluency before harvesting.

extract_protocol:
RNA was isolated using the Qiagen RNAeasyMini kit.
RNA sequencing libraries were prepared using the TruSeq Stranded mRNA Library Sample Preparation Kit in accordance with manufacturer’s instructions.

treatment_protocol: For transfection with Cas9- and sgRNA-expressing plasmids as well as ssODN template, cells were harvested for seeding at a log growth phase (approximately 70% confluency). In a 6-well format, 300,000 293T cells were seeded a day prior to transfection. The next day 2 μg of each lentiCRISPR v2 plasmid and 0.5 μg of ssODN HDR template were delivered into the cells using Lipofectamine 3000 reagent (ThermoFisher Scientific, cat. # L3000008). At 24-hours post-transfection selective pressure in the form of 5 μg/ml puromycin was applied for 8 hours to enrich for transfected cells. This population was selected for single-cell sorting in 96-well format on SONY SH800 to obtain monoclonal edited cell lines which were genotyped.

tag: cell line

tag: rs199643834 genotype

value: ALT/ALT/ALT


title: Lean control rat 2

value: control


title: HEK293T_rs199643834_EDIT_HOM [3_F5]


title: T CD8 DN from cHL 2 [exon-level]

city: Rennes

first: Patricia

last: Amé-Thomas

address: 2 Avenue du Pr Léon Bernard

department: Faculté de Médecine

country: France

institute: INSERM UMR1236

description:
Gene expression of CXCR5- ICOS- CD8+ T cells from cHD lymph node
CD8 DN2.CEL

hyb_protocol: Following fragmentation and end-labeling, 4.7 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Human Transcriptome Array 2.0 (Affymetrix)

scan_protocol: GeneChips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 using Robust Multi-array Average (RMA) algorithms with default settings at the gene and exon levels

source_name: Ex-vivo Tfh

label_protocol: Biotinylated double strand cDNA targets were prepared with the NuGEN Ovation PicoSL WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kitaccording to manufacturer recommendations

extract_protocol: RNA was extracted using AllPrep ARN/ADN kit (Qiagen, Valencia, CA)

tag: pathology

value: Classical Hodgkin Lymphoma

tag: treatment

value: Untreated

tag: cell type

value: CXCR5- ICOS- CD8+ T cells


title: Metformin_rep3

extract_protocol: Total 15 mg of liver tissue was collected and flash frozen by liquid nitrogen. Then the total RNA was extracted by using the Trizol (Invitrogen, USA) following the manufacturer's recommendations. 5μg total RNA was digested with 2μL RNase R 10X Reaction Buffer and 0.5 μL RNase R (10U) for 30 minutes to eliminate linear RNAs.

treatment_protocol: The mice were separated into three groups and treated with different diet and drug. Control group: 17 weeks of normal chow; High fat diet group: 17 weeks of high fat diet chow, and intragastrically treated with saline vehicle for the last 5 weeks; Metformin treated group: 17 weeks of high fat diet chow, and intragastrically treated with 3 mg/kg/day metformin for the last 5 weeks.

value: liver

value: 20 weeks

tag: strain

value: metformin


title: HEK293T_rs199643834_EDIT_HET [13_21]

value: ALT/REF/REF


title: Lean control rat 1

value: Zucker lean

tag: tissue


title: R_Stellate_Ganglion_16_SHR_3


title: Metformin_rep3

data_processing: Agilent Feature Extraction software (version 10.7) was used to analyze the acquired array images. 90 percentile shift normalization and subsequent data processing were performed using the GeneSpring GX software package (Agilent Technologies).

label_protocol: High quality miRNAs were Cy3 labeled using miRNA Complete Labeling and Hyb Kit (Agilent, USA) according to the manufacturer's guidelines.

extract_protocol: Total 15 mg of liver tissue was collected and flash frozen by liquid nitrogen. Then the total RNA was extracted by using the Trizol (Invitrogen, USA) and the miRNAs were isolated by using the mirVana miRNA Isolation Kit（AM1561）, following the manufacturer's recommendations.


title: Metformin_rep1


title: Metformin_rep2


title: R_Stellate_Ganglion_16_SHR_1


title: HEK293T_rs199643834_EDIT_HET [10_61]


title: High fat diet_rep3

value: high fat


title: R_Stellate_Ganglion_16_SHR_2

value: SHR


title: High fat diet_rep2


title: High fat diet_rep3


title: R_Stellate_Ganglion_16_Wistar_4

value: Wistar

value: right stellate ganglion


title: High fat diet_rep1

value: male


title: Metformin_rep1


title: R_Stellate_Ganglion_16_Wistar_3

value: 16 weeks old


title: Control_rep3


title: High fat diet_rep2


title: T CD8 DP from cHL 3 [exon-level]

description:
Gene expression of CXCR5+ ICOS+ CD8+ T cells from cHD lymph node
CD8 DP3.CEL

value: CXCR5+ ICOS+ CD8+ T cells


title: T CD8 DN from cHL 1 [exon-level]

description:
Gene expression of CXCR5- ICOS- CD8+ T cells from cHD lymph node
CD8 DN1.CEL


title: R_Stellate_Ganglion_16_Wistar_1


title: High fat diet_rep1


title: Control_rep2


title: R_Stellate_Ganglion_16_Wistar_2


title: HEK293T_rs199643834_EDIT_HET [15_36]


title: HEK293T_rs199643834_EDIT_HET [2_70]


title: HEK293T_rs199643834_EDIT_HET [14_26]


title: T CD8 DP from cHL 2 [exon-level]

description:
Gene expression of CXCR5+ ICOS+ CD8+ T cells from cHD lymph node
CD8 DP2.CEL


title: HEK293T_rs199643834_EDIT_HET [11_38]


title: Control_rep2


title: HEK293T_rs199643834_EDIT_HET [1_53]


title: 28-5: MT2

city: beijing

first: hao

last: qingqing

address: Chinese PLA Medical School, Beijng

institute: Chinese PLA Medical School, China

data_processing:
mapping fastq to sus_scrofa ensemble release 85 with STAR
caculate read counts via htseq
Genome_build: sus_scrofa ensemble release 85
Supplementary_files_format_and_content: raw counts from htseq2

organism: Sus scrofa

source_name: otic tissue

extract_protocol:
Otic vesicles were obtained from both wild-type and mutant embryos at E28,total RNA was extracted using Trizol reagent(Invitrogen,CA, USA)following the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: inner ear

tag: developmental stage

value: 28-day old embryo

value: SOX10 p.R109W mutation


title: HEK293T_rs199643834_EDIT_WT [13_35]

value: REF/REF/REF


title: 28-2: MT1

tag: genotype


title: HEK293T_rs199643834_EDIT_WT [7_60]


title: B31 OMV (UC)

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing: All the RNA sequencing data were processed to remove adapters by using a modified version of our in-house analysis tool, sRNAnalyzer (Wu et al. 2017). Borrelia sequences were extracted from various public databases and the processed reads were first mapped to B. burgdorferi B31 non-coding RNAs including ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs). Unmapped reads were then mapped to B. burgdorferi B31 transcriptome followed by B. burgdorferi B31 genome (DNA) using Bowtie II (Langmead and Salzberg 2012).

organism: Borreliella burgdorferi

source_name: B31 OMV

growth_protocol: Borrelia burgdorferi, B31 (ATCC 3521) bacteria from ATCC were resuspended and maintained in laboratory produced media that resembles MKP/BSK-II media with 10% heat-inactivated rabbit serum (R7136-60, Sigma-Aldrich, USA) based on recipes provided Dr. K. Strle (Barbour 1984; Ruzić-Sabljić and Strle 2004). The bacteria were suspended in 10 mL of media, then 1 mL of the diluted bacteria was added to 13 mL of fresh media in 15 ml tubes. Cells were incubated at 34°C, 5.0% CO2 with the lids of the tubes tightly sealed to minimize the oxygen level.  When seeded at a density of 1 to 5 x 106 bacteria/mL, the bacteria typically quadrupled within 24 hours. When bacteria reached mid-log phase growth (about 3 to 5 x 107 bacteria/mL of density), the culture was first spun at 800 rpm for 3 minutes to pellet any aggregates that might have formed, then the supernatant was further spun at 3,500 x g at 4°C for 1 hour.  After centrifugation, the pellet was re-suspended in 20 mLs of media that was supplemented with 10% exosome depleted FBS (Thermo Fisher Scientific, Waltham MA) instead of the heat-inactivated rabbit serum and incubated for 3 hours at 34°C along with 20 mL of blank media as control for OMV analyses.  After 3 hours, the culture was spun at 3,500 x g to pellet the bacteria, the supernatant was then used for OMV purification.  The bacteria pellet was washed twice in cold PBS then re-suspended in 1 mL of PBS and transferred to a 1.5 mL Eppendorf tube.

extract_protocol:
RNA was isolated from B. burgdorferi bacteria or OMVs isolated from B. burgdorferi supernatants using the miRNeasy kit (QAIGEN, Germantown MD), with additional ribosomal depletion step using the MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher Scientific). The RNA was eluted with 30 µL of nuclease-free H20 and quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA) with a RNA (Pico) chip.
RNA library construction was performed using the NEBNext Ultra Library Prep Kit for Illumina. Individual library concentrations were measured using the NEBNext Library Quant Kit for Illumina and adjusted to an equal molar final pooled concentration of 2 nM and run on NextSeq sequencer (Illumina, San Diego CA).

treatment_protocol: OMVs were isolated from 20 mL of B. burgdorferi supernatants by using two different methods: ultracentrifugation (UC) or size-exclusion chromatography (SEC). The culture media was filtered through a 0.22 µm filter to remove bacteria and large debris, and then concentrated from 20 mL to 500 µL using Amicon Ultra-15 centrifugation filters (EMD Millipore, Billerica MA).   For ultracentrifugation (UC): The concentrated supernatants were centrifuged at 100,000 x g, 4°C for 1 hr. The supernatant was removed and pellet was washed in ice-cold PBS buffer. The pellet was centrifuged again at 100,000 x g, 4°C for 1 hr. This step was repeated one more time. After the final wash, the pellet was re-suspended in 500 µL of ice-cold PBS buffer.   Size Exclusion Chromatography (SEC): OMVs were isolated from 500 μL of concentrated supernatants using qEV size-exclusion column (Izon Science, Cambridge, MA) with de-gassed 1X PBS. Eluate fractions were collected individually and the fractions containing OMVs were pooled and concentrated to ∼100 μL using Amicon Ultra-4 centrifugation filters spun in a swing-bucket rotor at 4,000 x g at 4°C for 20 minutes. To confirm the purification of OMVs from spirochetes, SEC and Ultracentrifugation purified OMVs were examined with Transmission Electron Microscopy (TEM) at the Fred Hutchinson Cancer Center, Seattle as previously described (Théry et al. 2006)

tag: source

value: outer membrane vesicles

tag: omv isolation

value: ultracentrifugation


title: Control_rep3

value: liver

value: 20 weeks

tag: diet

value: control


title: Control_rep1

tag: age


title: 28-7: WT3

value: wild type


title: HEK293T_rs199643834_EDIT_WT [4_75]


title: B31 OMV (SEC)

value: size-exclusion chromatography


title: B31 bacterial cell

source_name: ribosomal-depleted B31 cell

value: Cell


title: 28-6: WT2


title: 28-11: WT1


title: HEK293T_rs199643834_EDIT_WT [4_38]


title: T CD8 DP from cHL 1 [exon-level]

description:
Gene expression of CXCR5+ ICOS+ CD8+ T cells from cHD lymph node
CD8 DP1.CEL

value: Classical Hodgkin Lymphoma

value: Untreated


title: cassava_PROseq

description: Nascent RNA

organism: Manihot esculenta

source_name: seedlings

growth_protocol: Cassava accession “Nase 3” (synonymous with “IITA-TMS-IBA30572” and “Migyera”) cuttings were grown in tubes containing enriched medium. Tubes were placed in growth chambers with 12 hours of light at 30°C for 6 weeks before tissue collection

tag: accession

value: Nase 3

value: 6 week after germination

value: shoots


title: T CD8 DN from cHL 3 [exon-level]

description:
Gene expression of CXCR5- ICOS- CD8+ T cells from cHD lymph node
CD8 DN3.CEL

value: CXCR5- ICOS- CD8+ T cells


title: WGS Glioblastoma patient pat_180 Surg.1 frozen [pat_180_N560_12_fv_WGS]

status: Public on Jun 20 2018

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
library strategy: WGS
Low-coverage whole genome sequencing reads were aligned to human reference genome (GRCh38) using BWA’s (v0.7.12) aln and samse commands
Samtools (v1.4) was used for sorting and indexing the aligned short reads.
Copy number aberrations were detected with CNVkit (v0.9.1). This analysis relied on generating expected read counts in each genomic window (~50,000bp) from a set of normal samples and calcu-lating the log2 ratios of the read counts from the tumor samples relative to the normal samples. We used 20 whole genome samples from the Genome Austria project (http://www.personalgenomes.org/at) to generate expected normal/germline read counts for each genomic window. In order to make the high-coverage Genome Austria data comparable with the low-coverage tumor data, we down-sampled them to 36 million reads with 50 basepair read length.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing segmented log2-ratios.

source_name: brain (tumor)

extract_protocol:
DNA samples were isolated from fresh-frozen tumor samples using the AllPrep DNA/RNA Mini Kit (Qiagen) following manufacturer’s instructions.
Concentration and fragmentation of DNA extracted from fresh-frozen tumor tissue were assessed with the Qubit 2.0 fluorometric quantitation system (Life Technologies) and agarose gel electrophoresis, respectively. One sample with an insufficiently low DNA concentration was excluded. Libraries were prepared from 1 µg input material using the TruSeq DNA PCR-Free HT Library Prep Kit (Illumina) with IDT for Illumina TruSeq UD Indexes (Integrated DNA Technologies). Briefly, genomic DNA was sheared using a Covaris S220 focused-ultrasonicator instrument, DNA fragments were cleaned, end-repaired, and 3’ A-tailed, followed by ligation of the sequencing adapters. After quality control, individual libraries were diluted, equimolarly pooled, and sequenced on Illumina HiSeq 3000/4000 machines using the 50 basepair single-read setup.

tag: idh status

value: wildtype

tag: center

value: MedUni Vienna

tag: sample group

value: Glioblastoma patient

tag: surgery number

tag: multisector

value: No

tag: sample type

value: frozen


title: WGS Glioblastoma patient pat_186 Surg.1 frozen [pat_186_N177_13_fv_WGS]


title: WGS Glioblastoma patient pat_330 Surg.1 frozen [pat_330_N1298_16_fv_WGS]


title: WGS Glioblastoma patient pat_331 Surg.1 frozen [pat_331_N1835_16_fv_WGS]


title: WGS Glioblastoma patient pat_334 Surg.1 frozen [pat_334_N570_16_fv_WGS]


title: WGS Glioblastoma patient pat_337 Surg.1 frozen [pat_337_N940_16_fv_WGS]


title: WGS Glioblastoma patient pat_173 Surg.1 frozen [pat_173_N337_13_fv_WGS]


title: WGS Glioblastoma patient pat_171 Surg.1 frozen [pat_171_N834_13_fv_WGS]


title: WGS Glioblastoma patient pat_336 Surg.1 frozen [pat_336_N724_16_fv_WGS]


title: WGS Glioblastoma patient pat_157 Surg.1 frozen [pat_157_N2085_14B_fv_WGS]


title: WGS Glioblastoma patient pat_155 Surg.1 frozen [pat_155_N1883_14_fv_WGS]


title: WGS Glioblastoma patient pat_169 Surg.1 frozen [pat_169_N579_12_fv_WGS]


title: WGS Glioblastoma patient pat_164 Surg.1 frozen [pat_164_N581_14A_fv_WGS]


title: WGS Glioblastoma patient pat_163 Surg.1 frozen [pat_163_N541_15_fv_WGS]


title: WGS Glioblastoma patient pat_165 Surg.1 frozen [pat_165_N592_15_fv_WGS]


title: WGS Glioblastoma patient pat_153 Surg.1 frozen [pat_153_N1672_14_fv_WGS]


title: WGS Glioblastoma patient pat_147 Surg.1 frozen [pat_147_N1436_15_fv_WGS]


title: WGS Glioblastoma patient pat_150 Surg.1 frozen [pat_150_N1541_14_fv_WGS]


title: WGS Glioblastoma patient pat_151 Surg.1 frozen [pat_151_N1543_14E_fv_WGS]


title: WGS Glioblastoma patient pat_146 Surg.1 frozen [pat_146_N1383_14A_fv_WGS]


title: WGS Glioblastoma patient pat_332 Surg.1 frozen [pat_332_N255_16_fv_WGS]


title: WGS Glioblastoma patient pat_333 Surg.1 frozen [pat_333_N2712_15_fv_WGS]


title: WGS Glioblastoma patient pat_187 Surg.1 frozen [pat_187_N2611_14_fv_WGS]


title: WGS Glioblastoma patient pat_183 Surg.1 frozen [pat_183_N922_12_fv_WGS]


title: WGS Glioblastoma patient pat_139 Surg.1 frozen [pat_139_N654_12_fv_WGS]


title: WGS Glioblastoma patient pat_140 Surg.1 frozen [pat_140_N2207_13_fv_WGS]


title: WGS Glioblastoma patient pat_143 Surg.1 frozen [pat_143_N1160_15_fv_WGS]


title: WGS Glioblastoma patient pat_121 Surg.1 frozen [pat_121_N2613_14_fv_WGS]


title: WGS Glioblastoma patient pat_134 Surg.1 frozen [pat_134_N466_12A_fv_WGS]


title: WGS Glioblastoma patient pat_136 Surg.1 frozen [pat_136_N1290_12_fv_WGS]


title: WGS Glioblastoma patient pat_110 Surg.1 frozen [pat_110_N1020_10_fv_WGS]


title: WGS Low-grade glioma patient pat_108 Surg.6 frozen [pat_108_N1196_13_fv_WGS]

value: mutant

value: Low-grade glioma patient


title: WGS Low-grade glioma patient pat_108 Surg.5 frozen [pat_108_N54_13_fv_WGS]


title: WGS Glioblastoma patient pat_103 Surg.2 frozen [pat_103_N1934_14_fv_WGS]


title: WGS Glioblastoma patient pat_043 Surg.1 frozen [pat_043_N486_13_fv_WGS]


title: WGS Glioblastoma patient pat_028 Surg.2 frozen [pat_028_N1164_14_fv_WGS]


title: WGS Glioblastoma patient pat_110 Surg.2 frozen [pat_110_N1917_12_fv_WGS]