title: Kif2b Brain met 32

value: Kif2b brain metastasis, mouse number 32


title: Jurkat single cell 109

status: Public on Jan 15 2018

type: SRA

city: Stanford

first: Ansuman

last: Satpathy

state: CA

address: 300 Pasteur Drive

department: Pathology

country: USA

institute: Stanford University

description:
singles-J2-20
Transcript-indexed single-cell ATAC-seq
Open chromatin

library_source: genomic

data_processing:
For ATAC-seq data: adapter sequence trimming, mapping to hg19 using Bowtie2, and PCR duplicate removal using Picard Tools were performed. ATAC-seq peaks were called with MACS2 and reads in each peak were counted for each sample.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.csv: Comma-separated text files; ATAC-seq counts tables; adapter trimmed, reads aligned, PCR duplicates removed, and reads in ATAC-seq peaks counted.

molecule: genomic DNA

organism: Homo sapiens

source_name: Jurkat T cells

extract_protocol:
Tn5 transposition.
Nextera

tag: cell line

value: Jurkat

tag: cell type

value: single Jurkat T cell

tag: gender

value: male


title: Control Bone 36

city: New York

first: Charles

last: Murphy

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
fpkm.geneSymbols.csv
counts.geneSymbols.csv

library_source: transcriptomic

data_processing:
The quality of the raw FASTQ files were checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). For samples originating from mouse xenographs, FASTQ reads were classified as originating from either mouse or human genomes using xenome (https://www.ncbi.nlm.nih.gov/pubmed/22689758), and human-specific reads were used for mapping. Reads were mapped to human reference GRCh38 using STAR (v2.4.1d, 2-pass mode).
Gene expression was estimated using cufflinks (v2.2.1, default parameters) and HTSeq (v0.6.1). Differential expression analyses were performed using DESeq2 (v1.14.1).
Prior to any unsupervised analyses, expression counts were transformed using variance stabilizing transformation using the DESeq2 R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited files contain FPKM and read count values for each sample.

molecule: polyA RNA

source_name: Mouse xenograft

extract_protocol:
Bulk RNA was extracted from cells using the QIAShredder (Qiagen – 79654) and the RNA extraction kit (Qiagen – 74106) and sequenced using HiSeq4000 (Illumina Inc.).
[sequencing strategy] 101bp single end RNAseq

value: breast cancer cell line MDA-MB-231

tag: originating cell line

value: Control

tag: sample type

value: Control bone metastasis, mouse number 36


title: Control Brain 36

value: Control brain metastasis, mouse number 36


title: Jurkat single cell 86

description:
singles-J1-87
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Control Lung 35

value: Control lung metastasis, mouse number 35


title: Control brain  35

value: Control brain metastasis, mouse number 35


title: Jurkat single cell 87

description:
singles-J1-88
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: WT PerC B-1a Rep2

first: Jane

last: Skok

address: 550 First Ave, Smillow 307

institute: NYU

data_processing:
Library strategy: VDJ-seq
Reads were trimmed for adaptor sequence and masked for low-complexity of low quality sequence
Reads 1 and reads 2 were overlapped and unique sequences were filtered out
These unique sequences were subject to IMGT/High V-Quest (version 1.5.5) analysis for mapping and assigning gene segment usage, Alamyar, et al. Immunome Res. 2012
IMGT/High V-Quest output was used as input for IMGT/StatClonotype (version 1.0.2) statstical analysis and visualization, Aouinti et. Al., Front. Immunol, 2016. IMGT/StatClonotype is atool that evaluates and visualizes statstical significance of pairwise comparisons of IMGT clonotype diversity per V, D orJ gene segments .
Genome_build: IMGT/GENE-DB for Mus musculus (Giudicelli, V. et al. Nucleic Acids Res. 2005)
Supplementary_files_format_and_content: tab-delimited file that contains information on AA sequence, V, D and J gene segment assignment, percent alignment, etc. This file is used as input for using the IMGT/StatClonotype tool.

organism: Mus musculus

source_name: Pertionteal B-1a cells

extract_protocol:
Cells were sorted from 6-8 week old mice. Genomic DNA was extracted from lysed cells and this gDNA was used as template for PCR prior to library prep/adaptor ligation.
Primers were used to amplify sucessfully rearranged BCR heavy chains and size selected by gel extraction for 120-280bp from an agarose gel. PCR products were end-repaired using a combination of T4 PNK and T4 polymerase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of preannelaed Illumina compatible adapters, NEXTflex DNA barcodes (Bioo Scientific) which have a single 'T' base overhang at the 3’ end. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina HISeq 4000 following the manufacturer's protocols.

tag: strain

tag: genotype

value: wild type

tag: tissue

value: Peritoneal cavity

value: peritoneal cavity B-1a cells


title: Jurkat single cell 83

description:
singles-J1-84
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 85

description:
singles-J1-86
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 84

description:
singles-J1-85
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Kif2b Bone met 32

value: Kif2b bone metastasis, mouse number 32


title: Igll1 PerC B-1a Rep1

value: Igll1 knockout


title: Jurkat single cell 95

description:
singles-J1-95
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 81

description:
singles-J1-82
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 93

description:
singles-J1-93
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Control brain met 31

value: Control brain metastasis, mouse number 31


title: Jurkat single cell 80

description:
singles-J1-81
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Kif2a brain met 56

value: Kif2a brain metastasis, mouse number 56


title: MCAK-Hypir Xeno 12

value: MCAK Hypir

value: MCAK Hypir primary tumor, mouse number 12


title: Jurkat single cell 90

description:
singles-J1-90
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: Jurkat

value: single Jurkat T cell


title: Jurkat single cell 79

description:
singles-J1-80
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: male


title: Jurkat single cell 88

description:
singles-J1-89
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Kif2a Adrenal met 56

value: breast cancer cell line MDA-MB-231

value: Kif2a adrenal metastasis, mouse number 56


title: Jurkat single cell 78

description:
singles-J1-8
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Kif2b Brain met 42MCAK -Hypir Xeno 12

value: Kif2a Brain metastasis, mouse number 42


title: Control 73 bone met

value: Control

value: Control bone metastasis, mouse number 73


title: Jurkat single cell 77

description:
singles-J1-79
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: MCAK Hypir 15 adrenal met

value: MCAK Hypir adrenal metastasis, mouse number 15


title: Jurkat single cell 75

description:
singles-J1-77
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 76

description:
singles-J1-78
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Control Bone met 72

description:
fpkm.geneSymbols.csv
counts.geneSymbols.csv

value: Control bone metastasis, mouse number 72


title: Jurkat single cell 74

description:
singles-J1-76
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 73

description:
singles-J1-75
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 72

description:
singles-J1-74
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Kif2a Bone met 56

value: Kif2a bone metastasis, mouse number 56


title: Jurkat single cell 82

description:
singles-J1-83
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Xeno 14 RNA MCAK Hypir

value: MCAK Hypir primary tumor 14


title: Bone met 2

value: MCAK Hypir bone metastasis, mouse number 4966


title: RNA Xeno 11

value: MCAK Hypir primary tumor 11


title: Jurkat single cell 71

description:
singles-J1-73
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Met 1 RNA MCAK Hypir

value: MCAK Hypir ST metastasis A 11


title: Brain met 2

value: MCAK Hypir

value: MCAK Hypir brain metastasis, mouse number 4965


title: Jurkat single cell 68

description:
singles-J1-70
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: Jurkat


title: Met 3 RNA MCAK Hypir

value: MCAK Hypir ST metastasis C 11


title: Met 2 RNA MCAK Hypir

value: MCAK Hypir ST metastasis B 11


title: Jurkat single cell 69

description:
singles-J1-71
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: single Jurkat T cell

value: male


title: Jurkat single cell 70

description:
singles-J1-72
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: RNA Xeno 5

value: breast cancer cell line MDA-MB-231

value: Control primary tumor, mouse number 5


title: RNA Xeno 2

value: Control

value: Control Primary tumor, mouse number 2


title: Jurkat single cell 66

description:
singles-J1-69
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 65

description:
singles-J1-68
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 63

description:
singles-J1-66
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Kif2a Xeno 19 replicate 2

value: Kif2a Primary tumor, mouse number 19


title: MCAK-Hypir 11 ST Met 1

value: MCAK Hypir ST metastasis, mouse number A 15


title: Jurkat single cell 64

description:
singles-J1-67
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Kif2a Xeno 16

value: Kif2a Primary tumor, mouse number 16


title: STING 20

source_name: Human cell line

value: Control STING20 shRNA


title: Jurkat single cell 60

description:
singles-J1-63
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 59

description:
singles-J1-62
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 57

description:
singles-J1-60
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: MCAK Xeno 9

value: MCAK

value: MCAK primary tumor, mouse number 9


title: Kif2a Xeno 19 replicate 1

value: Kif2a primary tumor, mouse number 19


title: Jurkat single cell 67

description:
singles-J1-7
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: STING 19

description:
fpkm.geneSymbols.csv
counts.geneSymbols.csv

value: Control STING19 shRNA


title: MCAK Xeno 8

value: MCAK primary tumor, mouse number 8


title: Jurkat single cell 53

description:
singles-J1-57
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: Jurkat


title: MKH Bone 4966

value: MCAK Hypir

value: MCAK Hypir bone metastasis, mouse number 66


title: Jurkat single cell 55

description:
singles-J1-59
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: single Jurkat T cell

value: male


title: 65 Bone MKH

value: breast cancer cell line MDA-MB-231

value: MCAK Hypir bone metastasis, mouse number 65


title: Jurkat single cell 56

description:
singles-J1-6
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 54

description:
singles-J1-58
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 52

description:
singles-J1-56
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: 66 Brain MKH

value: MCAK Hypir brain metastasis, mouse number 66


title: Tubulin

value: Control

value: Tubulin


title: Jurkat single cell 51

description:
singles-J1-55
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 62

description:
singles-J1-65
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 50

description:
singles-J1-54
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: 65 Brain MKH

value: MCAK Hypir brain metastasis, mouse number 65


title: Jurkat single cell 49

description:
singles-J1-53
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 61

description:
singles-J1-64
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: MKH_SE

description:
processed data file:
FPKM.geneSymbols.101bpSE.csv
VST.geneSymbols.101bpSE.csv
Counts.geneSymbols.101bpSE.csv
processed data column: 13

data_processing:
The quality of the raw FASTQ files were checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), then mapped to human reference GRCh38 using STAR (v2.4.1d, 2-pass mode).
Gene expression was estimated using cufflinks (v2.2.1, default parameters) and HTSeq (v0.6.1). Differential expression analyses were performed using DESeq2 (v1.14.1).
Prior to any unsupervised analyses, expression counts were transformed using variance stabilizing transformation using the DESeq2 R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited files contain FPKM, counts, or variance stabalizing transformed values for each sample.

extract_protocol: Bulk RNA was extracted from cells using the QIAShredder (Qiagen – 79654) and the RNA extraction kit (Qiagen – 74106) and sequenced using HiSeq2500 or HiSeq4000 (Illumina Inc.).

tag: chromosomal instability group

value: CIN-high

tag: genotype/variation

value: Overexpression of dominant-negative form of MCAK, leading to increased number of chromosome segregation errors during anaphase

tag: sequencing strategy

value: 101bp single end RNAseq


title: Jurkat single cell 48

description:
singles-J1-52
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: MK_SE

description:
processed data file:
FPKM.geneSymbols.101bpSE.csv
VST.geneSymbols.101bpSE.csv
Counts.geneSymbols.101bpSE.csv
processed data column: 16

value: CIN-low

value: Overexpression of MCAK which leads to suppressed chromosome segregation errors during anaphase


title: Kb_SE

description:
processed data file:
FPKM.geneSymbols.101bpSE.csv
VST.geneSymbols.101bpSE.csv
Counts.geneSymbols.101bpSE.csv
processed data column: 15

value: Overexpression of Kif2b, which leads to suppressed chromosome segregation errors during anaphase


title: Jurkat single cell 47

description:
singles-J1-51
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: Jurkat


title: Jurkat single cell 46

description:
singles-J1-50
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: 65 Lung MKH

description:
fpkm.geneSymbols.csv
counts.geneSymbols.csv

value: MCAK Hypir

value: MCAK Hypir lung metastasis, mouse number 65


title: cont_SE

description:
processed data file:
FPKM.geneSymbols.101bpSE.csv
VST.geneSymbols.101bpSE.csv
Counts.geneSymbols.101bpSE.csv
processed data column: 17

value: CIN-medium


title: Jurkat single cell 45

description:
singles-J1-5
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: single Jurkat T cell

value: male


title: Jurkat single cell 44

description:
singles-J1-49
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_M2_Input

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

description:
M2
Adapter to trim:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTG

data_processing:
Adapter and quality trimming of both ChIP-Seq and RNA-Seq reads was done using FASTX Toolkit 0.0.13. Reads below 25bp in length or reads with Phred quality scores below 20 were discarded
ChIP-seq reads were aligned to hg19 with Bowtie2 version 2.0.6, using default parameters. RNA-Seq reads were aligned to hg19 using TopHat v1.3.2
Potential PCR duplicates were removed from aligned ChIP Seq reads files
ChIP-Seq peaks were called using MACS v1.4. Cufflinks v1.3.0, run with genomic bias correction, was used to calculate transcript abundancies/FPKMs in the RNA-Seq data.
RNA-Seq FPKMs were floored to 0.3 and quantile normalized
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq WIG tracks were generated with MACS v.14. The WIG signal was divided by the number of aligned reads in millions in each sample, and the WIGs were converted to bigWIGs

source_name: lung metastasis from primary osteosarcoma tumor

growth_protocol: All cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 2mM glutamine, and 1% penicillin/streptomycin except for the Hu09 and M112 lines that were cultured in RPMI 1460 with 10% fetal bovine serum, 2mM glutamine, and 1% penicillin/streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
ChIP-Seq: 36bp single end reads (MG63 and MG63.3), 50bp single end reads (all other samples); RNA-seq: 100bp paired-end reads

treatment_protocol: To test the effects of JQ1 treatment on gene expression during metastasis, MNNG and 143B cells in ex vivo culture were treated with 250nM JQ1 or 10mM DMSO.  Media was changed and fresh JQ1 or DMSO was added every two days.

tag: chip antibody


title: Jurkat single cell 43

description:
singles-J1-48
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Ka_SE

description:
processed data file:
FPKM.geneSymbols.101bpSE.csv
VST.geneSymbols.101bpSE.csv
Counts.geneSymbols.101bpSE.csv
processed data column: 18

value: Overexpression of Kif2a, which does not affect the number of chromosome segregation errors during anaphase and serves as an additional control. Part of the CIN-medium group.


title: Jurkat single cell 42

description:
singles-J1-47
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Control 72 brain met

value: breast cancer cell line MDA-MB-231

value: Control brain metastasis, mouse number 72


title: Jurkat single cell 41

description:
singles-J1-46
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 40

description:
singles-J1-45
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: MCAK Hypir Xeno 11

value: MCAK Hypir primary tumor, mouse number 11


title: Jurkat single cell 58

description:
singles-J1-61
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_M2_H3K4me1

value: lung metastasis from primary osteosarcoma tumor

value: rabbit anti-H3K4me1 (Abcam #8895)


title: Jurkat single cell 38

description:
singles-J1-43
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_M2_H3K27ac

description:
M2
Adapter to trim:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGACTCTATCTCGTATGCCGTCTTCTGCTTG

value: rabbit anti-H3K27ac (Abcam #4729).


title: Jurkat single cell 39

description:
singles-J1-44
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_M10_Input

description:
M10
Adapter to trim:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGACTCTATCTCGTATGCCGTCTTCTGCTTG


title: Patient_P2_Input

description:
P2
Adapter to trim:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG

source_name: primary osteosarcoma tumor

value: primary osteosarcoma tumor


title: Jurkat single cell 37

description:
singles-J1-42
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_P2_H3K4me1


title: Patient_P2_H3K27ac

description:
P2
Adapter to trim:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 36

description:
singles-J1-41
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_P10_Input

description:
P10
Adapter to trim:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTG


title: Patient_M10_H3K27ac

description:
M10
Adapter to trim:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGTGGATCTCGTATGCCGTCTTCTGCTTG


title: Patient_M10_H3K4me1

description:
M10
Adapter to trim:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 34

description:
singles-J1-4
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_P10_H3K27ac


title: Jurkat single cell 33

description:
singles-J1-39
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 32

description:
singles-J1-38
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_P10_H3K4me1

description:
P10
Adapter to trim:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 31

description:
singles-J1-37
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_36087-lung_H3K4me1

description:
36087-lung
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 30

description:
singles-J1-36
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 27

description:
singles-J1-33
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 28

description:
singles-J1-34
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_36087-1_Input

description:
36087-1
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 35

description:
singles-J1-40
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 26

description:
singles-J1-32
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_36087-1_H3K27ac

description:
36087-1
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG


title: Patient_36087-lung_H3K27ac

description:
36087-lung
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 25

description:
singles-J1-31
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_33010-lung-3_Input

description:
33010-lung-3
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGAATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 24

description:
singles-J1-30
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 22

description:
singles-J1-29
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_36087-1_H3K4me1

description:
36087-1
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTG


title: Patient_33010-1_H3K27ac

description:
33010-1
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTAATCTCGTATGCCGTCTTCTGCTTG


title: Patient_33010-1_Input

description:
33010-1
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGAATCTCGTATGCCGTCTTCTGCTTG


title: Patient_33010-lung-3_H3K4me1

description:
33010-lung-3
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAATCTCGTATGCCGTCTTCTGCTTG


title: Patient_33010-lung-3_H3K27ac

description:
33010-lung-3
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 21

description:
singles-J1-28
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 19

description:
singles-J1-26
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_36087-lung_Input

description:
36087-lung
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGAATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 18

description:
singles-J1-25
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 29

description:
singles-J1-35
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_27252-lung_Input

description:
27252-lung
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGTGGATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGTGGATCTCGTATGCCGTCTTCTGCTTG


title: Patient_33010-1_H3K4me1

description:
33010-1
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCAATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCAATCTCGTATGCCGTCTTCTGCTTG


title: Patient_27252-lung_H3K4me1

description:
27252-lung
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGACTCTTATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGACTCTTATCTCGTATGCCGTCTTCTGCTTG


title: Patient_27252-1_H3K27ac

description:
27252-1
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 14

description:
singles-J1-21
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Patient_27252-1_H3K4me1

description:
27252-1
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTTATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTTATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 15

description:
singles-J1-22
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 11

description:
singles-J1-19
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: MG63.3: FOSL1/Fra-1 ChIP Seq

description:
FOSL1/Fra-1 ChIP Seq
Adapter to trim: GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTG

data_processing:
Adapter and quality trimming of both ChIP-Seq and RNA-Seq reads was done using FASTX Toolkit 0.0.13. Reads below 25bp in length or reads with Phred quality scores below 20 were discarded.
ChIP-seq reads were aligned to hg19 with Bowtie2 version 2.0.6, using default parameters. RNA-Seq reads were aligned to hg19 using TopHat v1.3.2.
Potential PCR duplicates were removed from aligned ChIP Seq reads files.
ChIP-Seq peaks were called using MACS v1.4. Cufflinks v1.3.0, run with genomic bias correction, was used to calculate transcript abundancies/FPKMs in the RNA-Seq data.
RNA-Seq FPKMs were floored to 0.3 and quantile normalized.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq WIG tracks were generated with MACS v.14. The WIG signal was divided by the number of aligned reads in millions in each sample, and the WIGs were converted to bigWIGs.

source_name: highly metastatic osteosarcoma cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
ChIP-Seq: 36bp single end reads (MG63 and MG63.3), 50bp single end reads (all other samples); RNA-seq: 100bp paired-end reads.

value: rabbit anti-FOSL1/Fra-1 (Santa Cruz #sc-605)


title: Jurkat single cell 17

description:
singles-J1-24
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 23

description:
singles-J1-3
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: HOS: FOSL1/Fra-1 ChIP Seq

description:
FOSL1/Fra-1 ChIP Seq
Adapter to trim: GATCGGAAGAGCACACGTCTGAACTCCAGTCACGACTCTATCTCGTATGCCGTCTTCTGCTTG

value: HOS


title: MG63.3: c-Fos ChIP Seq

description:
c-Fos ChIP Seq
Adapter to trim: GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG

value: rabbit anti-c-Fos (Santa Cruz #sc-52)


title: Patient_27252-lung_H3K27ac

description:
27252-lung
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCACATATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCACATATCTCGTATGCCGTCTTCTGCTTG


title: HOS: c-Fos ChIP Seq

description:
c-Fos ChIP Seq
Adapter to trim: GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCACATATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 12

description:
singles-J1-2
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: Jurkat


title: Jurkat single cell 10

description:
singles-J1-18
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: MG63: FOSL1/Fra-1 ChIP Seq

description:
FOSL1/Fra-1 ChIP Seq
Adapter to trim: GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 20

description:
singles-J1-27
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: M48

city: Louisville

first: Michael

middle: H

last: Perlin

state: KY

address: Biology, Belknap-LS 139

department: Biology

institute: University of Louisville

data_processing:
Illumina HiSeqTM 2000 for basecalling
Sequencing reads were mapped to transcripts of Ustilago maydis using bwa-0.6.2 with parameters  -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, A., B. A. Williams, et al., Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 2008.5(7): 621-8.
Genome_build: Ustilago maydis
Supplementary_files_format_and_content: Raw_counts.txt is a tab-delimited text file that includes raw counts of sequencing reads for the features of 8 samples.
Supplementary_files_format_and_content: All_rpkm.txt is a tab-delimited text file that includes normalized abundance measurements for 8 samples.

molecule: total RNA

organism: Mycosarcoma maydis

source_name: sporidial cells

growth_protocol: Each strain was grown on microarray agar medium containing either 30 mM ammonium (Hi) or 50 uM ammonium (Lo) for 48 h at 26 C

extract_protocol:
After 48h on the specific growth medium, cells were scraped off the agar and flash frozen in a cold mortar under liquid nitrogen; RNA was harvested using the Plant RNAeasy kit from Qiagen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FB1ump2Otef delta b

value: ump2 over-expressed in b deletion background

tag: treatment

value: microarray medium, 50 uM ammonium


title: M5

value: wild type a1 b1


title: M7B

value: ump2 over-expressed


title: M6

value: FB1delta b

value: b locus deleted


title: Jurkat single cell 9

description:
singles-J1-17
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: single Jurkat T cell

value: male


title: Patient_27252-1_Input

description:
27252-1
Adapter to trim R1:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTG
Adapter to trim R2:
GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTG


title: A549_Normoxia

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Mapping versus hg19 with lifescope v2.5.1 smallRNA pipeline.
Counting of smallRNAs with annotation from mirbase v18,
Genome_build: hg19
Supplementary_files_format_and_content: 144_tableCount.txt contains raw read counts for each smallRNAs identified. Annotations files are mirbase release 18 and Ensembl ncRNA release 75.

growth_protocol: A549 lung adenocarcinoma cells were grown in DMEM medium supplemented with 10% FCS

extract_protocol:
Trizol reagent
2 µg of total RNA were ligated, reverse transcribed and amplified (11 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were size-selected from 105 nt to 130 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were subjected to 4 additional PCR rounds with the primers from the 5500 W Conversion Primers Kit (Life Technologies) and converted with the enzyme kit from the 5500 W Conversion Primers Kit (Life Technologies). Libraries were then quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).

treatment_protocol: Cells were incubated for 24 hours under normoxic  (20% O2) or hypoxic (1,2% O2) conditions prior to cell lysis


title: A549_Hypoxia


title: Jurkat single cell 16

description:
singles-J1-23
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 8

description:
singles-J1-16
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: M4

value: microarray medium, 30 mM ammonium


title: Jurkat single cell 13

description:
singles-J1-20
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: MG63: c-Fos ChIP Seq

description:
c-Fos ChIP Seq
Adapter to trim: GATCGGAAGAGCACACGTCTGAACTCCAGTCACGACTCTATCTCGTATGCCGTCTTCTGCTTG


title: 143B: FOSL1/Fra-1 ChIP Seq

description:
FOSL1/Fra-1 ChIP Seq
Adapter to trim: GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG


title: M3


title: M2


title: 143B: c-Fos ChIP Seq

description:
c-Fos ChIP Seq
Adapter to trim: GATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGTGGATCTCGTATGCCGTCTTCTGCTTG


title: Jurkat single cell 7

description:
singles-J1-15
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Jurkat single cell 5

description:
singles-J1-13
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: M1


title: MNNG: FOSL1/Fra-1 ChIP Seq

description:
FOSL1/Fra-1 ChIP Seq
Adapter to trim: GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG

value: MNNG


title: Erb1_35S_1M7_2

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description:
purified 35S pre-ribosomal RNP treated with 1M7
[processed data files:]
Erb1_35S_read_counts.sgr
Erb1_35S_RT_stop_counts.sgr
Table S1.xlsx

data_processing:
Library strategy: CRAC (High-throughput RNA structure probing library)
Base-calling by Illumina
Raw data processing was performed usign the pyCRAC package for processing of aligned reads and novoalign for aligning the reads. The complete pipeline is available at: https://bitbucket.org/sgrann/chemmodseqpipeline. NOTE! The 3' adapter sequences (AGATCGGAAGAGCACACG) and 5' in-read barcodes (13 nt) have NOT been removed.
Details about the dependencies of the ChemModSeq pipeline is provided on the repositories website. All dependencies need to be in the system path. To calculate the SHAPE reactivities, the CalculateSHAPE_reactivities script was used. For this the reads for the biological replicates of the 35S_control, 35S and Erb1_35S samples were merged to increase the coverage.
An R script that runs the BUM_HMM pipeline is also provided on the bitbucket repository. All the required text files to run the pipeline (RDN37-1 gtf annotation file, novoalign index file, sequence files) are available here.
The 35S DMSO and 1M7 datasets are also available from GSE83821 (Burlacu et al Nature Communication). However, in the fastq files provided here the 5' in-read barcode (13nt) has not been removed.
Genome_build: RDN37-1 gene from SGD (yeastgenome.org)
Supplementary_files_format_and_content: sgr file with read counts and supplementary table

organism: Saccharomyces cerevisiae

growth_protocol: S.cerevisiae strains were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) or YPG/R (YP with 2% Galactose and 2% Raffinose) at 30ºC.

extract_protocol:
Immunoprecipitations with TAP-tagged Mrd1 proteins were performed with TNM150 buffer (50 mM Tris-HCl pH 7.8, 1.5 mM MgCl2, 150 mM NaCl, 0.1% NP-40 and 5 mM b-mercaptoethanol), essentially as previously described (Granneman et al., 2009). RNA was extracted using a GTC phenol solution (4 M guanidine thiocyanate, 0.05 M Tris at pH 8.0, 0.01 M EDTA, 2% sarcosyl, 1% β-mercaptoethanol, 50% [v/v] phenol) as previously described (Sambrook, 1989).
cDNA libraries were generated from purified ribosomal RNA using an RT oligonucteotide containing random hexamers (SuperScript III, Invitrogen). 5' adapters were ligated on (CircLigase II, EpiCentre) and 3' adaptors generated during PCR amplification.

tag: strain genotype

value: BY4741 with GAL::3HA-ERB1::KAN, MRD1-TAP::URA3

tag: 5' barcode sequence

value: NNNNNNGCCAATN

tag: 3' adapter sequence

value: AGATCGGAAGAGCACACG

tag: rna type

value: pre-ribosomal RNA


title: MKH

description:
processed data file:
FPKM.geneSymbols.75bpPE.csv
VST.geneSymbols.75bpPE.csv
Counts.geneSymbols.75bpPE.csv
processed data column: MKH

tag: cell line

value: CIN-high

value: Overexpression of dominant-negative form of MCAK, leading to increased number of chromosome segregation errors during anaphase

value: 75bp paired end RNAseq


title: Jurkat single cell 4

description:
singles-J1-12
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: Jurkat

tag: cell type


title: Jurkat single cell 6

description:
singles-J1-14
Transcript-indexed single-cell ATAC-seq
Open chromatin

tag: gender


title: Jurkat single cell 3

description:
singles-J1-11
Transcript-indexed single-cell ATAC-seq
Open chromatin


title: Erb1_35S_1M7_1

source_name: purified 35S pre-ribosomal RNP treated with 1M7

value: NNNNNNTTAGGCN


title: Kb

description:
processed data file:
FPKM.geneSymbols.75bpPE.csv
VST.geneSymbols.75bpPE.csv
Counts.geneSymbols.75bpPE.csv
processed data column: Kb

value: CIN-low

value: Overexpression of Kif2b, which leads to suppressed chromosome segregation errors during anaphase


title: MK

description:
processed data file:
FPKM.geneSymbols.75bpPE.csv
VST.geneSymbols.75bpPE.csv
Counts.geneSymbols.75bpPE.csv
processed data column: MK

value: Overexpression of MCAK which leads to suppressed chromosome segregation errors during anaphase


title: Ka

description:
processed data file:
FPKM.geneSymbols.75bpPE.csv
VST.geneSymbols.75bpPE.csv
Counts.geneSymbols.75bpPE.csv
processed data column: Ka

value: CIN-medium

value: Overexpression of Kif2a, which does not affect the number of chromosome segregation errors during anaphase and serves as an additional control. Part of the CIN-medium group.


title: Jurkat single cell 1

description:
singles-J1-1
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: single Jurkat T cell

value: male


title: 35S_1M7_1

description:
purified 35S pre-ribosomal RNP treated with 1M7
[processed data files:]
35S_read_counts.sgr
35S_RT_stop_counts.sgr
Table S1.xlsx
GSM2219117

value: BY4741 with mrd1-deltaRDB5-TAP::K.I.TRP1, pGAL-HA-MRD1::URA3

value: NNNNNNCGATGTN


title: 35S_1M7_2

description:
purified 35S pre-ribosomal RNP treated with 1M7
[processed data files:]
35S_read_counts.sgr
35S_RT_stop_counts.sgr
Table S1.xlsx
GSM2219118

value: NNNNNNTGACCAN


title: TREG CD4+ T cell biological replicate 3

description:
ensemble Blood T cell
Open chromatin

data_processing:
For ATAC-seq data: Adapter sequence trimming, mapping to hg19 using Bowtie2, and PCR duplicate removal using Picard Tools were performed. ATAC-seq peaks were called with MACS2 and reads in each peak were counted for each sample.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.csv: Comma-separated text files; ATAC-seq counts tables; adapter trimmed, reads aligned, PCR duplicates removed, and reads in ATAC-seq peaks counted.

source_name: Primary T cell sorted from peripheral blood

growth_protocol: Sorted from PBMCs.

value: TREG CD4+ T cell

tag: disease status

value: healthy


title: 35S_control_1

description:
purified 35S pre-ribosomal RNP treated with DMSO
[processed data files:]
35S_read_counts.sgr
35S_RT_stop_counts.sgr
Table S1.xlsx
GSM2219115

value: NNNNNNATCACGN

value: AGATCGGAAGAGCACACG

value: pre-ribosomal RNA


title: 35S_control_2

description:
purified 35S pre-ribosomal RNP treated with DMSO
[processed data files:]
35S_read_counts.sgr
35S_RT_stop_counts.sgr
Table S1.xlsx
GSM2219116


title: TREG CD4+ T cell biological replicate 2

description:
ensemble Blood T cell
Open chromatin


title: cont

description:
processed data file:
FPKM.geneSymbols.75bpPE.csv
VST.geneSymbols.75bpPE.csv
Counts.geneSymbols.75bpPE.csv
processed data column: cont

value: Control

value: 75bp paired end RNAseq


title: TREG CD4+ T cell biological replicate 1

description:
ensemble Blood T cell
Open chromatin


title: GW

city: Indianapolis

first: Bin

last: Guo

state: Indiana

address: 950 W. Walnut Street

department: Microbiology & Immunology

institute: Indiana University

description: replicate 2

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome using Tophat2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. gene_exp_(sort_order).tsv files contain the expression data for each gene in the samples of the project.  Files can have various sort orders.  "pos_sort" means file is sorted by chromosome position. Expression level is measured as FPKM (Fragments Per Kilobase of gene per Million fragments mapped). isoforms.fpkm_tracking file contains the estimated isoform-level expression values in the generic FPKM Tracking Format. genes.fpkm_tracking file contains the estimated gene-level expression values in the generic FPKM Tracking Format. FPKM tracking files use a generic format to output estimated expression values. FPKM is relative abundance in Fragments Per Kilobase of exon model per Million mapped fragments.

source_name: human cord blood

growth_protocol: CB CD34+ cells were cultured in RPMI-1640 medium (Lonza, 12-702Q) with 10% fetal bovine serum (GE Healthcare HyClone. SH30071.03), 100 ng/mL stem cell factor (SCF) (R&D Systems, #7466-SC-010/CF), thrombopoietin (TPO) (R&D Systems, #288-TP-200/CF), Fms-like tyrosine kinase 3 ligand (FL) (BioLegend, # 710802).

extract_protocol:
RNA was extracted using the RNeasy Mini Kit following manufacturer’s protocol (QIAGEN, #74106).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CB CD34+ cells were cultured in the presence of vehicle or GW9662 for 4 days.

value: cord blood

value: CD34+ cells

tag: passage

tag: treated with


title: MNNG: c-Fos ChIP Seq

description:
c-Fos ChIP Seq
Adapter to trim: GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTG

value: MNNG

value: rabbit anti-c-Fos (Santa Cruz #sc-52)


title: Vehicle

description: replicate 2

value: vehicle


title: TH17 CD4+ T cell biological replicate 2

description:
ensemble Blood T cell
Open chromatin

value: TH17 CD4+ T cell


title: Media

city: Seoul

first: Mukesh

middle: Kumar

last: Yadav

state: Seoul

department: Institute for Medical Device Clinical Trials

country: South Korea

institute: Korea University

data_processing:
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores were less than 20 and reads whose average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts. Filtered reads were mapped to the human reference genome (Ensembl release 72) using the aligner STAR v.2.3.0e.
Gene expression level was measured with Cufflinks v2.1.1 using the gene annotation database of Ensembl release 72. Non-coding gene region was removed with-mask option. To improve the accuracy of measurement, multi-read-correction and fragbias- correct options were applied and all other options were set to default values. For differential expression analysis, gene level count data were generated using HT Seq-count v0.5.4p3 tool with the option "-m intersection-nonempty” and –r option considering paired-end sequence.
Based on the calculated read count data, differentially expressed gene (DEG) were identified using the R package called TCC. TCC package applies robust normalization strategies to compare tag count data. Normalization factors were calculated using the iterative DEGES/edgeR method. Q-value was calculated based on the p-value using the p.adjust function of R package with default parameter settings. Differentially expressed genes were identified based on the q-value threshold less than 0.05.
Genome_build: human reference genome (Ensembl release 72)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, fold change with respect to control.

organism: Rattus norvegicus

source_name: Rat mucosa inoculated with media only

growth_protocol: The animals were euthanized using a 1:1 combination of nitrous-oxide and oxygen. After one week of inoculation, the rats were sacrificed using carbon-dioxide inhalation, and the bulla was aseptically acquired. Bulla were immediately dissected and middle ear was exposed and preserved in RNA latter (Qiagen, Hilden, Germany). The mucosa membrane of the bulla preserved in RNA latter solution was carefully scraped and preserved in fresh RNA latter solution till RNA extraction.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s instructions. RNA was quantified by Nano-drop, and the RNA quality was assessed by analysis of rRNA band integrality on an Agilent RNA 6000 Nano kit (Agilent Technologies, Palo Alto, CA, USA).
Ahead of cDNA library construction, the 2ug of total RNA and magnetic beads with Oligo (dT) were used to enrich poly (A) mRNA. Then, the purified mRNAs were disrupted into short fragments, and the double-stranded cDNAs were immediately synthesized. The cDNAs was subjected to end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). The suitable fragments automatically purified by BluePippin 2% agarose gel cassette (Sage Science, MA) were selected as templates for PCR amplification. The final library sizes and qualities were evaluated electrophoretically with an Agilent High Sensitivity DNA kit (Agilent Technologies, CA) and the fragment was found to be between 350–450 bp. Subsequently, the library was sequenced using an Illumina HiSeq2500 sequencer (Illumina, CA).

treatment_protocol: The bacterial cell suspensions were prepared in TSB medium. 50 µL cell suspension containing 1×107cfu of Staphylococcus aureus (MRSA) were injected into the middle ear cavity through the tympanic membrane of the right ear using a tuberculin syringe and a 27-gauge needle.

tag: strain

value: SD

value: Middle ear Mucosa

tag: inoculated with

value: media only


title: SA

source_name: Rat mucosa inoculated with SA only

tag: tissue

value: SA (MRSA)


title: Mixed

source_name: Rat mucosa inoculated with Mixed culture

value: Mixed culture (MRSA+PA)


title: Jurkat single cell 2

description:
singles-J1-10
Transcript-indexed single-cell ATAC-seq
Open chromatin

value: Jurkat

value: single Jurkat T cell

value: male


title: PA

source_name: Rat mucosa inoculated with PA only

value: Pseudomonas aeruginosa (PA)


title: TH2 CD4+ T cell biological replicate 2

description:
ensemble Blood T cell
Open chromatin

value: TH2 CD4+ T cell

value: healthy


title: TH17 CD4+ T cell biological replicate 1

description:
ensemble Blood T cell
Open chromatin


title: MG63_in_vitro: RNA Seq

description: RNA Seq

source_name: non-metastatic osteosarcoma cell line grown in vitro


title: MG63_3_in_vitro: RNA Seq

description: RNA Seq

source_name: highly metastatic osteosarcoma cell line grown in vitro


title: Infected_SG_3

city: Bethesda

first: Ilias

last: Alevizos

state: Maryland

address: 10 Center Dr., RM 1N110

institute: National Institute for Dental and Craniofacial Research (NIDCR)

data_processing:
Calibration and basecalling were performed on the Ion Torrent server with Torrent Suite version 4.4.3
Reads were mapped to the mm10 genome using the tmap aligner, version 4.4.11
Gene abundances were estimated by counting strand-specific reads using the Subread package featureCounts tool, where reads with mapq of 0 or multiple mappings were filtered out.
RPKM estimates were calculated from featureCounts results.
Genome_build: mm10
Supplementary_files_format_and_content: MCMV_Infection_RPKM.txt: Tab-separated file containing a matrix of normalized RPKM values, with genes in rows and samples in columns
Supplementary_files_format_and_content: MCMV_Infection_counts.txt: Tab-separated file contains a matrix of raw counts, with genes in rows and samples in columns

source_name: Salivary Gland

growth_protocol: All mice were purchased from the Jackson laboratory and bred in house following protocols approved by the Thomas Jefferson University Institutional Animal Care and Use Committee.

extract_protocol:
RNA was obtained with the Exiqon miRCURY RNA Isolation kit for Tissues. Prior to cDNA library preparation, RNA samples were purified using the RNA Clean & Concentrator Kit from Zymo and treated with DNase I to remove contaminating genomic DNA.
Four micrograms of total RNA per sample were used as input for the depletion of ribosomal RNA using the RiboMinus Eukaryote Kit v2 from Thermo Fisher Scientific. Library preparation was performed using the Ion Total RNA Seq Kit v2 (Thermo Fisher Scientific) according to the manufacturer’s protocol.  The barcoded cDNA libraries were diluted to a final concentration of 100 pM, and used for template preparation on the Ion Chef instrument using the Ion PI Hi-Q Chef Kit.  Sequencing was performed on the Ion Proton sequencer system using Ion Torrent PI v3 chips.

treatment_protocol: Infections were performed using 2 x 10^5 pfu and the i.p. route (100 µl per injection) for 14 days

tag: mouse strain

tag: gland type

value: submandibular salivary gland

tag: viral strain


title: TH2 CD4+ T cell biological replicate 1

description:
ensemble Blood T cell
Open chromatin


title: MG63_3_lung_culture_day_14: RNA Seq

description: RNA Seq

source_name: highly metastatic osteosarcoma cell line grown in ex vivo lung culture for 14 days


title: Infected_SG_1


title: Infected_SG_2


title: TH1-17 CD4+ T cell biological replicate 1

description:
ensemble Blood T cell
Open chromatin

value: TH1-17 CD4+ T cell


title: MG63_3_lung_culture_24hrs: RNA Seq

description: RNA Seq

source_name: highly metastatic osteosarcoma cell line grown in ex vivo lung culture for 24hrs


title: TH1-17 CD4+ T cell biological replicate 2

description:
ensemble Blood T cell
Open chromatin


title: MNNG_lung_culture_day_7_250nM_JQ1: RNA Seq

description: RNA Seq

source_name: highly metastatic osteosarcoma cell line grown in ex vivo lung culture for 7 days treated with 250nM JQ1

value: MNNG


title: Uninfected_SG_3

value: not infected


title: Uninfected_SG_2


title: TH17 CD4+ T cell biological replicate 3

description:
ensemble Blood T cell
Open chromatin


title: MNNG_lung_culture_day_7_DMSO: RNA Seq

description: RNA Seq

source_name: highly metastatic osteosarcoma cell line grown in ex vivo lung culture for 7 days treated with 10mM DMSO


title: TH1 CD4+ T cell biological replicate 3

description:
ensemble Blood T cell
Open chromatin

value: TH1 CD4+ T cell


title: MNNG_lung_culture_day_14: RNA Seq

description: RNA Seq


title: MNNG_lung_culture_24hrs: RNA Seq

description: RNA Seq


title: Uninfected_SG_1


title: MG63_lung_culture_24hrs: RNA Seq

description: RNA Seq

source_name: non-metastatic osteosarcoma cell line grown in ex vivo lung culture for 24hrs


title: TH1 CD4+ T cell biological replicate 1

description:
ensemble Blood T cell
Open chromatin


title: MNNG_in_vitro: RNA Seq

description: RNA Seq


title: Naïve CD4+ T cell biological replicate 3

description:
ensemble Blood T cell
Open chromatin

value: Naive CD4+ T cell


title: Naïve CD4+ T cell biological replicate 2

description:
ensemble Blood T cell
Open chromatin


title: Naïve CD4+ T cell biological replicate 1

description:
ensemble Blood T cell
Open chromatin


title: input

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

description: input control

data_processing:
Per cycle base call (BCL) files were converted to FASTQ format using the Illumina bcl2fastq Conversion Software v2.17.1.14
The cutadapt version 1.9 was used for read trimming and removal of Illumina adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA). Reads with less than 20 bases in length have been discarded.
ChIP-Seq reads were mapped to the human genome build hg19 with bowtie2 version 2.2.8 using the predefined ‘sensitive’ setting.
The tools from picard version 1.13 were used to convert the obtained sam files into sorted bam format (picard SortSam), for soft-clipping beyond-end-of-reference alignments and for removing unmapped reads (picard CleanSam) and for marking duplicate reads (picard MarkDuplicates).
Peak calling was perfomed using the callpeak function from MACS2 software. Minimum FDR (q-value) cutoff for peak detection was 0.01.
Genome_build: hg19
Supplementary_files_format_and_content: Peak summit files obtained by MACS2 include the genomic position of the peak summit. Scores have been calculated from normalized bigWig files for each sample using the computeMatrix function from deeptools.

source_name: cardiomyocyte progenitor cells

growth_protocol: hESCs were differentiated under defined conditions in a monolayer format according to Zhang et al. (PMID 25639979), which gives rise to near-homogeneous populations of cardiac precursor cells by day 5 of differentiation

extract_protocol:
For chromatin immunoprecipitation, differentiating day 5 cells were harvested using Accutase, resuspended in ITS/HSA-containing medium and fixed for 10 min by adding freshly thawed formaldehyde solution to a final concentration of 1% (w/v). After stopping with 125 mM glycine, pellets of 5*106 cells were stored at -80°C or processed immediately. Samples were lysed in hypotonic Tris buffer and sonicated 35 times with a 30 s on / 30 s off cycling protocol using a Diagenode Bioruptor device at high power (volume: 300 µl), to an average DNA fragment size of ~200 bp. Following 10-fold dilution with 50 mM Tris pH8 / 200 mM NaCl / 5 mM EDTA / 0.5 (v/v) NP40, sheared samples were incubated with 10 µg of antibody over night at 4°C on a rotator. The antibody used was raised against a transgenic ISL1-HA tag. Antibody/chromatin complexes were isolated using Pierce protein A/G-conjugated magnetic beads (Thermo # 26162) and washed repeatedly with high-salt (500 mM NaCl) wash buffer. ChIP samples were eluted using 65°C 1% (w/v) SDS-containing buffer, crosslink-reversed in the presence of 200 mM NaCl for 4 h at 65°C, treated with RNase A and Proteinase K, and purified on Qiagen PCR purification columns.
Illumina kit # IP-202-1012 following the manufacturer's instructions
Pooled starting material from independent experiments

treatment_protocol: 0.2 µg/ml doxycyline on days 3 and 4 in plus DOX samples

tag: cell types

value: human embryonic stem cells differentiating into cardiomyocytes

tag: passages

value: HuES6 background

tag: chip antibody


title: minus DOX

description: no DOX added, no endogenous ISL1 present

value: Cell Signaling Technology # 3724


title: plus DOX

description: DOX added to induce ISL1 expression


title: VCL3

city: CHICAGO

first: WENYANG

last: HU

state: IL

address: 909 S WOLCOTT

department: UROLOGY

institute: UNIVERSITY OF ILLINOIS AT CHICAGO

description: RNA-seq

data_processing:
Basecalls performed using Illumina Basespace
Adaptors and low-quality reads were trimmed using trimGalore 0.4.0
RNA-seq reads were aligned to the GRCh38 genome assembly with STAR 2.4.2a
Raw counts of the reads hitting the exons were quantified using Rsubread 3.2
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files were generated by Rsubread 3.2. Each column represent one sample. Each row represent one gene

source_name: Prostate

growth_protocol: Pooled primary human prostate epithelial cells from three disease-free donors were grew in 3-D matrigel culture to form prostaspheres

extract_protocol:
FACS separated CFSEHi and CFSELo cells from each replicate were subjected to cDNA synthesis using the direct cell lysis protocol of Clontech SMARTer Ultra Low Input RNA Kit for Sequencing v3. Of particular note, this direct cell lysis protocol permits RNA-seq library synthesis without mRNA purification or ribosomal RNA depletion.
The resulting cDNA was fragmented by sonication using Covaris S2 sonicator to 200-300 bp and subjected to synthesis of indexed deep sequencing libraries for Illumina NextSeq 500 sequencing using Clontech Low Input Library Prep Kit. Library quantitations and size distributions were determined using Agilent Tapestation with DNA D1000 high sensitivity tape. Paired-end sequencing (75 nt + 75 nt) yielded > 50 million raw reads (fastq format), which were aligned to the human GRCh38/hg38 reference genome sequence using the STAR aligner. The mapped reads (bam format, >48.6 million reads per sample) were subjected to quality control using the fastQC utility (Babraham Institute), and high-quality reads were normalized and annotated using DESeq R/Bioconductor package to obtain relative strength of mRNA expression.

treatment_protocol: Label-retaining prostate stem cells and non-retaining progenitor cells were separated by FACS sorting

tag: age/disease

value: Young adult/disease-free

value: Primary prostate epithelial cells

tag: cell lineage

value: Prostate progenitor cells


title: VCH3

description: RNA-seq

value: Prostate stem-like cells


title: TH1 CD4+ T cell biological replicate 2

description:
ensemble Blood T cell
Open chromatin

value: male


title: HOS_lung_culture_24hrs: RNA Seq

description: RNA Seq

tag: cell line

value: HOS


title: 143B_lung_culture_day_14: RNA Seq

description: RNA Seq


title: HOS_in_vitro: RNA Seq

description: RNA Seq


title: 143B_lung_culture_24hrs: RNA Seq

description: RNA Seq


title: MNNG: input DNA

description: input DNA

source_name: highly metastatic osteosarcoma cell line


title: VCL1

description: RNA-seq

tag: cell type


title: SaOS: H3K4me1 ChIP Seq

description: H3K4me1 ChIP Seq

source_name: non-metastatic osteosarcoma cell line

value: SaOS

value: rabbit anti-H3K4me1 (Abcam #8895)


title: VCL2

description: RNA-seq


title: VCH1

description: RNA-seq


title: 143B_in_vitro: RNA Seq

description: RNA Seq


title: 143B_lung_culture_day_5_250nM_JQ1: RNA Seq

description: RNA Seq

source_name: highly metastatic osteosarcoma cell line grown in ex vivo lung culture for 5 days treated with 250nM JQ1


title: 143B_lung_culture_day_5_DMSO: RNA Seq

description: RNA Seq

source_name: highly metastatic osteosarcoma cell line grown in ex vivo lung culture for 5 days treated with 10mM DMSO


title: MNNG: H3K27ac ChIP Seq

description: H3K27ac ChIP Seq

value: rabbit anti-H3K27ac (Abcam #4729).


title: MNNG: H3K4me1 ChIP Seq

description: H3K4me1 ChIP Seq


title: VCH2

description: RNA-seq


title: MG63: H3K27ac ChIP Seq

description: H3K27ac ChIP Seq


title: MNNG: Dnase I Hypersensitivity

description: Dnase I Hypersensitivity


title: SaOS: input DNA

description: input DNA


title: MG63: Dnase I Hypersensitivity

description: Dnase I Hypersensitivity


title: M112: H3K27ac ChIP Seq

description: H3K27ac ChIP Seq


title: M112: H3K4me1 ChIP Seq

description: H3K4me1 ChIP Seq


title: M112: input DNA

description: input DNA


title: MG63.3: H3K27ac ChIP Seq

description: H3K27ac ChIP Seq


title: MG63.3: Dnase I Hypersensitivity

description: Dnase I Hypersensitivity


title: LM7: input DNA

description: input DNA


title: M112: Dnase I Hypersensitivity

description: Dnase I Hypersensitivity


title: Spleen_boost3

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description: LCMV-specific CD4 memory T cells, isolated from spleen of LCMV-primed C57BL/6 mice, 3 days after antigenic re-challenge

data_processing:
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

source_name: Isolated from spleen of LCMV-primed C57BL/6 mice, 3 days after antigenic re-challenge

growth_protocol: 8 week old C57BL/6 male mice were immunized intraperitoneally (i.p.) with 100 μg poly(I:C) and LCMV GP61-80 coupled to murine serum albumin (MSA) and 4-Hydroxy-3-nitrophenylacetyl (NP) . Two weeks after priming, mice were immunized i.p. again with 100 μg poly(I:C) and 100 μg uncoupled LCMV GP61-80.  60 days after the last immunization, mice were boosted i.p. with 100 μg poly(I:C) and 100 μg LCMV GP61-80-MSA-NP. 3 days after the last boost, cells were isolated from BM and spleen.

extract_protocol:
Total RNA was purified with miRNeasy Micro Kit (Qiagen) from FACS sorted LCMV-specific CD4 memory T cells isolated from spleen and bone marrow. RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
For poly-A dependent cDNA synthesis and a first amplification step the Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) was used. After quality control (High sensitivity DNA Kit, Agilent) and concentration measurement (Qubit dsDNA HS Assay Kit, Invitrogen), 150 pg of the purified cDNA was used for tagmentation and library completion with the Nextera XT library preparation kit (Illumina). In the following, 2x75 nucleotides paired-end sequencing was performed on a NextSeq500 using a mid-output flow cell.

value: LCMV-specific CD4 memory T cells

tag: age

value: 8 week

tag: organ

value: spleen


title: LM7: H3K4me1 ChIP Seq

description: H3K4me1 ChIP Seq


title: Spleen_boost2


title: Spleen_boost1


title: BM_boost3

description: LCMV-specific CD4 memory T cells, isolated from BM of LCMV-primed C57BL/6 mice, 3 days after antigenic re-challenge

source_name: Isolated from BM of LCMV-primed C57BL/6 mice, 3 days after antigenic re-challenge

value: bone marrow


title: LM7: H3K27ac ChIP Seq

description: H3K27ac ChIP Seq


title: BM_boost2


title: ago18(2)_mature_panicle_Rep-1

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads.
The processed reads were aligned to the rice genome using TopHat (v2.1.1).
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: Text delimited files including FPKM for each sample.

organism: Oryza sativa

source_name: mature panicle

extract_protocol:
Total RNA from three different tissues, 4week old seedlings, young panicle and mature panicle of both wild-type and transgenic knock-down lines were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subspecies, cultivar

value: Rice, Indica, Pusa Basmati 1 (PB1)

value: mature panicle

tag: genotype


title: ago18(2)_young_panicle_Rep-2

source_name: young panicle

value: young panicle


title: Hu09: H3K27ac ChIP Seq

description: H3K27ac ChIP Seq


title: LM7: Dnase I Hypersensitivity

description: Dnase I Hypersensitivity


title: CX7_6

city: Zurich

first: Irina

last: Leonardi

address: Sternwartst. 14

department: Gastroenterology and Hepathology

country: Switzerland

institute: USZ

data_processing:
The raw reads of RNA-seq were aligned to the mm10 genome using TopHat v1.0; packages Rsamtools v1.24.0, GenomicFeatures
Genes where annotated to their Entrezid (package org.Mm.eg.db) leaving 24’451 total genes. Genes whose count per millions (CPM) was below 1 were removed from further processing, leaving 23707 total genes
The counts were analyzed for differential expression using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: Raw count table

source_name: CD103+ cells

extract_protocol:
sorting protocol: Live lineage negative (CD3, CD19, ab-TCR, SiglecF, Ly6G) CD45+MHCII+CD11b+ CD11c+ CX3CR1+ and live lineage negative CD45+MHCII+CD11b+ CD11c+ CD103+ cells were sorted from the colon of Cx3cr1GFP/+ mice
cDNAs were prepared using the SMARTer Ultra Low Input RNA Kit for Sequencing version 3 following the user manual (Clontech Laboratories).
Sequencing libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina).  Cluster generation and 75–base pair paired-end dual-indexed sequencing was performed on the Illumina NextSeq 500 system

tag: cell markers

value: DC

value: colon


title: CX7_4


title: ago18(2)_mature_panicle_Rep-2


title: Hu09: H3K4me1 ChIP Seq

description: H3K4me1 ChIP Seq


title: ago18(2)_seedling_Rep-2

source_name: Four weeks old seedlings

value: Four weeks old seedlings


title: BM_boost1

tag: strain


title: ago18(2)_young_panicle_Rep-1

tag: tissue


title: Hu09: input DNA

description: input DNA


title: HOS: input DNA

description: input DNA


title: Hu09: Dnase I Hypersensitivity

description: Dnase I Hypersensitivity


title: CX7_2

tag: mouse strain


title: ago18(2)_seedling_Rep-1


title: CX7_3

source_name: CX3CR1+ cells

value: Mononuclear Phagocytes


title: ago18(1)_mature_panicle_Rep-2


title: HOS: H3K4me1 ChIP Seq

description: H3K4me1 ChIP Seq


title: HOS: H3K27ac ChIP Seq

description: H3K27ac ChIP Seq


title: CX7_1


title: HOS: Dnase I Hypersensitivity

description: Dnase I Hypersensitivity


title: ago18(1)_young_panicle_Rep-2


title: HOXA9/IRX3 #3.2

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

data_processing:
Reads were aligned to the mouse genome (GRCm38) with Bowtie2, version 2.2.1 (Langmead et al., 2012) using default settings.
SAMtools (v 0.1.19) was used to filter out unaligned reads, non-primary alignments or alignments with a Phred quality score of <20.
There were 18.5-21.8 million input reads per sample and 8.3-10.2 million reads per sample remained after filtering.
Reads were mapped to annotated protein coding genes (ENSEMBL v76) using the Annmap database, R and Bioconductor (Gentleman et al., 2004).
RPKM (reads per kilobase per million uniquely mapped reads) was computed for each gene.
Genome_build: ENSEMBL v76
Supplementary_files_format_and_content: RPKM for each ENSEMBL gene for each sample.

source_name: KIT+Gr1+ flow sorted AML cells

extract_protocol:
RNA was extracted using QIAshredder spin columns and an RNeasy Plus Micro kit (Qiagen).
RNA was extracted and its quality confirmed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). Indexed PolyA libraries were prepared using 200ng of total RNA and 14 cycles of amplification with the Agilent SureSelect Strand Specific RNA Library Prep Kit for Illumina Sequencing (Agilent, Santa Clara, CA).
Libraries were quantified by quantitative PCR using a Kapa Library Quantification Kit for Illumina sequencing platforms (Roche). Paired-end 75bp sequencing was carried out by clustering 1.8 pM of the pooled libraries on a NextSeq 500 sequencer (Illumina, San Diego, CA).

tag: tumor type

value: AML

tag: tumor intiated by


title: HOXA9/IRX3 #3.3


title: HOXA9/IRX3 #3.5


title: 143B: input DNA

description: input DNA


title: 143B: H3K4me1 ChIP Seq

description: H3K4me1 ChIP Seq


title: ago18(1)_seedling_Rep-1


title: 143B: H3K27ac ChIP Seq

description: H3K27ac ChIP Seq


title: WT_mature_panicle_Rep-2

value: Wild type


title: WT_young_panicle_Rep-2


title: ago18(1)_seedling_Rep-2


title: WT_mature_panicle_Rep-1


title: ago18(1)_young_panicle_Rep-1


title: 42 dpi YPIII 3

city: Braunschweig

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

description: + wildtype bacteria, cecal tissue-3

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Tophat2 (V1.20) with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq)
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization. Cook distance cutoff filter disabled
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: htseqcounts*.tab files: CSV format with raw read counts per gene; des2rlog*.tab files: CSV format with DESeq2 rlog transformed read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes

source_name: infected cecal tissue

extract_protocol:
Total RNA was isolated from homogenized and tissue lysed cecal tissue using phenol extraction.
Purification of mRNA was done using human/mouse/rat ScriptSeq complete kit (Illumina). Following the purification, the RNA was used for library preparation using Script Seq v2 Library preparation kit (Illumina).

value: cecal tissue

value: Balb/c, Yersinia pseudotuberculosis

value: 6-10 weeks


title: 42 dpi YPIII deltacnfY-2

description: + cnfY mutant bactera, cecal tissue-2


title: 42 dpi YPIII deltacnfY-3

description: + cnfY mutant bactera, cecal tissue-3


title: HOXA9/MTV #1.2


title: 42 dpi YPIII deltacnfY-1

description: + cnfY mutant bacteria, cecal tissue-1


title: HOXA9/MTV #1.4


title: 143B: Dnase I Hypersensitivity

description: Dnase I Hypersensitivity


title: HOXA9/MTV #1.1


title: WT_seedling_Rep-2


title: 42 dpi YPIII 2

description: + wildtype bacteria, cecal tissue-2


title: WT_seedling_Rep-1


title: ago18(1)_mature_panicle_Rep-1


title: MG63: input DNA

description: input DNA


title: WT_young_panicle_Rep-1


title: VcoptixOMFWAsy_LM

city: ithaca

first: Linlin

last: Zhang

address: 215 TOWER RD

department: Ecology and Evolutionary Department

institute: Cornell University

description:
VcoptixOMFWAsy_SM and VcoptixOMFWAsy_LM are from the same individual
processed data file:
Vc_wtvsoptix.gene.fpkm

data_processing:
Sequencing data were subjected to quality control by removing PCR primers, adapters, and low-quality reads.
Clean reads were further aligned with reference genes with Bowtie2
Gene expression levels were calculated using FPKM (fragments per kilobase of transcript per million mapped fragments)
Genome_build: V. cardui transcriptome assembly were downloaded from butterflygenome.org and used as a reference;
http://butterflygenome.org/sites/default/files/Vanessa_cardui.unigenes.fasta.gz
In order to build a reference for J. coenia RNA-seq analysis, sequencing reads from this study and NCBI GEO Database GSE54819 were merged. Assembly was built by Trinity after in silico normalization (Jc.trinity.fasta).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Vanessa cardui

source_name: V. cardui_optix knockout large defects_forewings

growth_protocol: V. cardui caterpillars were obtained from Carolina Biological Supply. Larvae were fed on a multi-species artificial diet (Southland) and reared in a 16:8 hr light/dark cycle at 27 °C and 60% humidity. . J. coenia eggs were derived from a laboratory colony maintained at Duke university (gift of H.F. Nijhout). Larvae were fed on  a standard artificial diet with dried leaves of Plantago lanceolata, and reared in a 16:8 hr light/dark cycle at 27 °C and 60% humidity.

extract_protocol:
Both forewings and hindwings are rapidly dissected and stored in RNA later at −80 ° C (Life Technologies).RNA isolation was performed using Ambion Purelink RNA Mini Kit (Life Technology).
RNA-seq libraries were generated according to the manual of NEBNext Ultra RNA library Prep Kit for Illumina (New England Biolabs). Briefly, Poly(A) RNA was isolated with Oligo d(T)25 beads from total RNA, fragmented into 200-400 bp, added into first- and second-strand cDNA synthesis, end repaired, tailed with 3 dA, ligated with an adaptor, barcoded with a unique illumine index, selected with ~200 bp fragments using AMPure XP beads (Beckman, Fullerton, CA), and amplified with 15 cycles of PCR. Libraries were further quantified on a Qubit Fluorometer, pooled, and sequenced on Illumina Nextseq 500 lanes as 36 bp paired-end reads.

treatment_protocol: Two biological replicates were sampled from both forewing and hindwing, and in both wide type and optix knockout mutants, resulting in eight samples in each species.  Asymmetrical large and very small mosaic forewings from a V. cardui optix knockout individual were further collected as two samples to take advantage of asymmetrical mosaic information.

tag: developmental stage

value: ommochrome stage

tag: genotype/variation

value: optix knockout large defects

value: forewings


title: 42 dpi YPIII 1

description: + wildtype bacteria, cecal tissue-1


title: VcoptixOMFWAsy_SM

source_name: V. cardui_optix knockout small defects_forewings

value: optix knockout small defects


title: 42 dpi uninfected 2

description: - bacteria, cecal tissue-2

source_name: uninfected cecal tissue

value: Balb/c


title: MG63: H3K4me1 ChIP Seq

description: H3K4me1 ChIP Seq

tag: chip antibody

value: rabbit anti-H3K4me1 (Abcam #8895)


title: VcoptixHW2

description:
processed data file:
Vc_wtvsoptix.gene.fpkm

source_name: V. cardui_optix knockout large defects_hindwings

value: melanin stage

value: hindwings


title: MG63.3: input DNA

description: input DNA

source_name: highly metastatic osteosarcoma cell line


title: 5 dpi YPIII deltacnfY-2

description: + cnfY mutant bactera, cecal tissue


title: 42 dpi uninfected 1

description: - bacteria, cecal tissue-1


title: VcoptixFW2


title: VcoptixFW1


title: 5 dpi YPIII 3

description: + wildtype bacteria, cecal tissue


title: VcwtFW1

source_name: V. cardui_wide type_forewings

value: wide type


title: VcwtFW2


title: YAP1 ChIP-Seq

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
ChIP-Seq reads were aligned using Bowtie (version 1.0.0) to human genome assembly NCBI Build 37 (UCSC hg19) with the following parameters: -n 1 -m 1 --best –strata (uniquely mapped reads with one mismatch were retained).
Enriched regions were detected by Scripture package with varying window sizes (750,1500), and peaks were defined whose coverage at 0.05 significance. Collapsed repeat regions in the human genome  and "ultra-high signal suspect regions" identified by ENCODE project (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz) were masked during the peak calling procedure. Called regions were merged with BEDTools (20110278).  Intervals longer than 1500 base pair length were excluded from the final list.
Genome_build: hg19
Supplementary_files_format_and_content: wig files generated using MACS version 1.4.1, Scores represents binding strength of YAP1 at a particular locus

source_name: OVCAR5 cell line

growth_protocol: OVCAR5 cells grown as monolayer in RPMI 1460 media with 10% FBS in humidified incubator at 37C and 5% CO2

extract_protocol:
Formaldehyde fixed chromatin was isolated from cells and YAP1 bound chromatin was purified using YAP1 antibody using standard Chromatin IP method.
Libraries were prepared using NEB reagents as described earlier (Garber et al 2012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~300-500 bp (insert plus adaptor and PCR primer sequences) were size selected by SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: no treatment

value: Ovarian cancer cell

tag: antibody

value: YAP (H125)X

tag: vendor

value: Santa Cruz Biotechnologies

tag: catalog number

tag: lot number


title: JcoptixHW2

description:
processed data file:
Jc_wtvsoptix.gene.fpkm

organism: Junonia coenia

source_name: J. coenia_optix knockout_hindwings

value: optix knockout


title: 5 dpi uninfected 3

description: - bacteria, cecal tissue-3

tag: age


title: 5 dpi YPIII 1

description: + wildtype bacteria, cecal tissue


title: 5 dpi uninfected 2

description: - bacteria, cecal tissue-2


title: JcoptixHW1


title: JcwtHW2

source_name: J. coenia_wide type_hindwings


title: JcwtHW1


title: JcoptixFW2

source_name: J. coenia_optix knockout large defects_forewings


title: 5 dpi YPIII deltacnfY-3

description: + cnfY mutant bactera, cecal tissue


title: VcoptixHW1


title: JcoptixFW1


title: 42 dpi uninfected 3

description: - bacteria, cecal tissue-3


title: JcwtFW2

source_name: J. coenia_wide type_forewings


title: MG63.3: H3K4me1 ChIP Seq

description: H3K4me1 ChIP Seq

data_processing:
Adapter and quality trimming of both ChIP-Seq and RNA-Seq reads was done using FASTX Toolkit 0.0.13. Reads below 25bp in length or reads with Phred quality scores below 20 were discarded.
ChIP-seq reads were aligned to hg19 with Bowtie2 version 2.0.6, using default parameters. RNA-Seq reads were aligned to hg19 using TopHat v1.3.2.
Potential PCR duplicates were removed from aligned ChIP Seq reads files.
ChIP-Seq peaks were called using MACS v1.4. Cufflinks v1.3.0, run with genomic bias correction, was used to calculate transcript abundancies/FPKMs in the RNA-Seq data.
RNA-Seq FPKMs were floored to 0.3 and quantile normalized.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq WIG tracks were generated with MACS v.14. The WIG signal was divided by the number of aligned reads in millions in each sample, and the WIGs were converted to bigWIGs.

tag: cell line


title: JcwtFW1


title: 5 dpi YPIII deltacnfY-1

description: + cnfY mutant bacteria, cecal tissue


title: Swr1 ChIP-Exo HS12 replicate1

status: Public on Jan 14 2018

city: University Park

first: Bongsoo

last: Park

state: PA

address: 453 North Frear Building

institute: Penn State University

description:
Replicate 1
50517sacCer3_s5e10F1.gff

data_processing:
For single end reads from HiSeq, basecalls were performed using CASAVA version 1.7 and for paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.16.
ChIP-exo reads were aligned to Saccer3 genome assembly using bwa mem version 0.7.9a for paired reads.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
Genome_build: sacCer3
Supplementary_files_format_and_content: gff, gene track peak calls using (smoothing 5bp, exclusion 10bp)
Supplementary_files_format_and_content: txt, peak pair calls filtered for significance over background
Supplementary_files_format_and_content: csv, extraction of PIP-seq, ChIP-exo tag count(or ratio to NoTag) in TSS
Supplementary_files_format_and_content: tab, tag extraction from 5' end of uniquely mapped sequencing reads, tab-delimited

source_name: in vivo

growth_protocol: For ChIP-exo, cells were grown to an O.D600 of 0.8 - 1.0 at 25°C.

extract_protocol:
For ChIP-exo, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
ChIP-exo libraries were prepared for sequencing using standard SOLiD & Illumina protocols with a minor modification; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
ChIP-exo, PIP-seq

treatment_protocol: For ChIP-exo, cells were crosslinked with formaldehyde to a final concentration of 1.0%.For PIP seq 100 mMKmNO4 added.

tag: cell description

value: GRF88, MATa his4-38, S288C background


title: Swr1 ChIP-Exo HS15 replicate1

description:
Replicate 1
50518sacCer3_s5e10F1.gff


title: Swr1 ChIP-Exo HS9 replicate2

description:
Replicate 2
32331sacCer3_s5e10F1.gff


title: Swr1 ChIP-Exo HS6 replicate2

description:
Replicate 2
32330sacCer3_s5e10F1.gff


title: 5 dpi YPIII 2

description: + wildtype bacteria, cecal tissue

value: cecal tissue


title: Swr1 ChIP-Exo HS12 replicate2

description:
Replicate 2
32332sacCer3_s5e10F1.gff


title: Swr1 ChIP-Exo HS9 replicate1

description:
Replicate 1
50516sacCer3_s5e10F1.gff


title: 5 dpi uninfected 1

description: + bacteria, cecal tissue


title: Swr1 ChIP-Exo HS3 replicate1

description:
Replicate 1
HS_project_extract_tag_ratio.csv


title: Swr1 ChIP-Exo MHS replicate2

description:
Replicate 2
HS_project_extract_tag_ratio.csv


title: Swr1 ChIP-Exo MHS replicate3

description:
Replicate 3
HS_project_extract_tag_ratio.csv


title: Swr1 ChIP-Exo HS3 replicate2


title: Swr1 ChIP-Exo HS6 replicate1

description:
Replicate 1
50515sacCer3_s5e10F1.gff


title: Rsc9 ChIP-Exo HS12 replicate2

description:
Replicate 2
50505sacCer3_s5e10F1.gff


title: Rsc9 ChIP-Exo HS15 replicate2

description:
Replicate 2
50506sacCer3_s5e10F1.gff


title: Rsc9 ChIP-Exo HS9 replicate2

description:
Replicate 2
50504sacCer3_s5e10F1.gff


title: Rsc9 ChIP-Exo HS3 replicate2


title: Rsc9 ChIP-Exo MHS replicate2


title: Htz1 ChIP-Exo HS15 replicate3

description:
Replicate 3
19334sacCer3_s5e10F1.gff


title: Rsc9 ChIP-Exo HS6 replicate2

description:
Replicate 2
50503sacCer3_s5e10F1.gff


title: Swr1 ChIP-Exo HS15 replicate2

description:
Replicate 2
19326sacCer3_s5e10F1.gff


title: Swr1 ChIP-Exo MHS replicate1


title: Htz1 ChIP-Exo HS15 replicate2

description:
Replicate 2
19218sacCer3_s5e10F1.gff


title: Htz1 ChIP-Exo HS15 replicate1

description:
Replicate 1
50421sacCer3_s5e10F1.gff


title: Sth1 ChIP-Exo HS new replicate1

description:
New Replicate 1
15812sacCer3.tab

data_processing:
For single end reads from HiSeq, basecalls were performed using CASAVA version 1.7 and for paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.16.
ChIP-exo reads were aligned to Saccer3 genome assembly using bwa mem version 0.7.9a for paired reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab, tag extraction from 5' end of uniquely mapped sequencing reads, tab-delimited


title: Sth1 ChIP-Exo MHS new replicate1

description:
New Replicate 1
15805sacCer3.tab


title: Htz1 ChIP-Exo HS3 replicate2


title: Htz1 ChIP-Exo MHS replicate1


title: Htz1 ChIP-Exo HS12 replicate1

description:
Replicate 1
50420sacCer3_s5e10F1.gff


title: Htz1 ChIP-Exo MHS replicate3


title: Htz1 ChIP-Exo HS9 replicate1

description:
Replicate 1
50419sacCer3_s5e10F1.gff


title: Htz1 ChIP-Exo MHS replicate2


title: Htz1 ChIP-Exo HS6 replicate2

description:
Replicate 2
32214sacCer3_s5e10F1.gff


title: Spt16 ChIP-Exo MHS replicate2


title: Spt16 ChIP-Exo MHS replicate3


title: Htz1 ChIP-Exo HS6 replicate1

description:
Replicate 1
50418sacCer3_s5e10F1.gff


title: Sua7 ChIP-Exo HS15 replicate2

description:
Replicate 2
51834sacCer3_s5e10F1.gff


title: Rsc58 ChIP-Exo HS new replicate1

description:
New Replicate 1
15810sacCer3.tab


title: Rsc58 ChIP-Exo MHS new replicate1

description:
New Replicate 1
11855sacCer3.tab


title: Rsc6 ChIP-Exo MHS new replicate1

description:
New Replicate 1
11856sacCer3.tab


title: Sua7 ChIP-Exo HS15 replicate1

description:
Replicate 1
50432sacCer3_s5e10F1.gff


title: Rsc3 ChIP-Exo MHS new replicate 1

description:
New Replicate 1
11848sacCer3.tab


title: Sua7 ChIP-Exo HS12 replicate2

description:
Replicate 2
51833sacCer3_s5e10F1.gff


title: Rsc1 ChIP-Exo HS new replicate1

description:
New Replicate 1
15165sacCer3.tab


title: Htz1 ChIP-Exo HS12 replicate2

description:
Replicate 2
32216sacCer3_s5e10F1.gff


title: Rsc3 ChIP-Exo HS new replicate 1

description:
New Replicate 1
15815sacCer3.tab


title: Sua7 ChIP-Exo HS12 replicate1

description:
Replicate 1
50431sacCer3_s5e10F1.gff


title: Htz1 ChIP-Exo HS9 replicate2

description:
Replicate 2
32215sacCer3_s5e10F1.gff


title: Rsc1 ChIP-Exo MHS new replicate1

description:
New Replicate 1
15809sacCer3.tab


title: Rsc6 ChIP-Exo HS new replicate1

description:
New Replicate 1
15814sacCer3.tab


title: Ubp8 ChIP-Exo HS new replicate 1

description:
New Replicate 1
11963sacCer3.tab


title: Sua7 ChIP-Exo HS9 replicate1

description:
Replicate 1
51832sacCer3_s5e10F1.gff


title: Sgf11 ChIP-Exo MHS new replicate1

description:
New Replicate 1
13365sacCer3.tab


title: Ubp8 ChIP-Exo MHS new replicate 1

description:
New Replicate 1
11962sacCer3.tab


title: Sua7 ChIP-Exo HS6 replicate2

description:
Replicate 2
51831sacCer3_s5e10F1.gff


title: Sua7 ChIP-Exo HS6 replicate1

description:
Replicate 1
50430sacCer3_s5e10F1.gff


title: Sua7 ChIP-Exo HS3 replicate1


title: Sgf11 ChIP-Exo HS new replicate1

description:
New Replicate 1
13366sacCer3.tab


title: BY4741 Negative control replicate 1

description:
New Replicate 1
15941sacCer3.tab

value: NoAntibody


title: Spt7 ChIP-Exo HS new replicate 1

description:
New Replicate 1
15908sacCer3.tab


title: Spt7 ChIP-Exo MHS new replicate 1

description:
New Replicate 1
15907sacCer3.tab


title: BY4741 Negative control replicate 2

description:
New Replicate 2
15944sacCer3.tab


title: Non-specific antibody ChIP-Exo HS3 rep1

description:
Replicate 1
53802sacCer3.tab


title: Non-specific antibody ChIP-Exo HS3 rep2

description:
Replicate 2
53804sacCer3.tab


title: Sua7 ChIP-Exo HS3 replicate2


title: Non-specific antibody ChIP-Exo MHS rep2

description:
Replicate 2
53803sacCer3.tab


title: Ser7P ChIP-Exo HS6 replicate2

description:
Replicate 2
53832sacCer3.tab


title: Ser7P ChIP-Exo HS6 replicate3

description:
Replicate 3
54533sacCer3.tab


title: Ser7P ChIP-Exo HS3 replicate3

description:
Replicate 3
54532sacCer3.tab


title: Non-specific antibody ChIP-Exo MHS rep1

description:
Replicate 1
53801sacCer3.tab


title: Sua7 ChIP-Exo MHS replicate1


title: Ser7P ChIP-Exo HS3 replicate2

description:
Replicate 2
53831sacCer3.tab


title: Ser7P ChIP-Exo HS6 replicate1

description:
Replicate 1
53820sacCer3.tab


title: Ssl2 ChIP-Exo HS15 replicate3

description:
Replicate 3
matrix_for_clustering.txt


title: Ser7P ChIP-Exo HS3 replicate1

description:
Replicate 1
53815sacCer3.tab


title: Ssl2 ChIP-Exo HS15 replicate2

description:
Replicate 2
matrix_for_clustering.txt


title: Ssl2 ChIP-Exo HS15 replicate1

description:
Replicate 1
matrix_for_clustering.txt


title: Ser7P ChIP-Exo MHS replicate3

description:
Replicate 3
54531sacCer3.tab


title: Ser7P ChIP-Exo MHS replicate2

description:
Replicate 2
53830sacCer3.tab


title: Sua7 ChIP-Exo MHS replicate2


title: Ser5P ChIP-Exo HS6 replicate2

description:
Replicate 2
53829sacCer3.tab

value: Millipore, 3E8, Cat. # 04-1572


title: Ssl2 ChIP-Exo HS12 replicate2

description:
Replicate 2
matrix_for_clustering.txt


title: Ser7P ChIP-Exo MHS replicate1

description:
Replicate 1
53814sacCer3.tab


title: Ser5P ChIP-Exo HS6 replicate1

description:
Replicate 1
53813sacCer3.tab


title: Ser5P ChIP-Exo HS3 replicate2

description:
Replicate 2
53828sacCer3.tab


title: Ssl2 ChIP-Exo HS12 replicate1

description:
Replicate 1
matrix_for_clustering.txt


title: Ser2P ChIP-Exo HS6 replicate2

description:
Replicate 2
53823sacCer3.tab


title: Ssl2 ChIP-Exo HS9 replicate2

description:
Replicate 2
matrix_for_clustering.txt


title: Ser2P ChIP-Exo HS6 replicate1

description:
Replicate 1
53819sacCer3.tab


title: Ssl2 ChIP-Exo HS9 replicate1

description:
Replicate 1
matrix_for_clustering.txt


title: Ser2P ChIP-Exo HS3 replicate2

description:
Replicate 2
53822sacCer3.tab


title: Ser2P ChIP-Exo HS3 replicate1

description:
Replicate 1
53810sacCer3.tab


title: Ssl2 ChIP-Exo HS6 replicate1

description:
Replicate 1
matrix_for_clustering.txt


title: Sua7 PIP-Seq HS6 replicate2

description:
Replicate 2
Sua7_PIP-seq_extract_tag_occupancy.csv

value: GeneTex, GTX64172


title: Ser2P ChIP-Exo MHS replicate1

description:
Replicate 1
53809sacCer3.tab


title: Ssl2 ChIP-Exo HS3 replicate2

description:
Replicate 2
matrix_for_clustering.txt


title: Sua7 PIP-Seq HS3 replicate2


title: Htz1 ChIP-Exo HS3 replicate1


title: Ser2P ChIP-Exo MHS replicate2

description:
Replicate 2
53821sacCer3.tab


title: Ssl2 ChIP-Exo HS3 replicate1

description:
Replicate 1
matrix_for_clustering.txt


title: Ssl2 ChIP-Exo MHS replicate3

description:
Replicate 3
matrix_for_clustering.txt


title: Sua7 PIP-Seq MHS replicate1

description:
Replicate 1
Sua7_PIP-seq_extract_tag_occupancy.csv


title: Sua7 PIP-Seq HS3 replicate1


title: Sua7 PIP-Seq MHS replicate2


title: Rsc9 ChIP-Exo HS15 replicate1

description:
Replicate 1
53330sacCer3_s5e10F1.gff


title: Ser5P ChIP-Exo MHS replicate2

description:
Replicate 2
53827sacCer3.tab


title: Ser5P ChIP-Exo HS3 replicate1

description:
Replicate 1
53812sacCer3.tab


title: Ser5P ChIP-Exo MHS replicate1

description:
Replicate 1
53811sacCer3.tab


title: Rsc9 ChIP-Exo HS6 replicate1

description:
Replicate 1
53327sacCer3_s5e10F1.gff


title: Rsc9 ChIP-Exo HS12 replicate1

description:
Replicate 1
53329sacCer3_s5e10F1.gff


title: Rsc9 ChIP-Exo HS9 replicate1

description:
Replicate 1
53328sacCer3_s5e10F1.gff


title: Ssl2 ChIP-Exo MHS replicate2

description:
Replicate 2
matrix_for_clustering.txt


title: Rpb3 ChIP-Exo HS15 replicate2

description:
Replicate 2
RPB3_extract_tag_occupancy.csv


title: Rsc9 ChIP-Exo HS3 replicate1


title: Sua7 PIP-Seq HS6 replicate1


title: Rsc9 ChIP-Exo MHS replicate1


title: Rpb3 ChIP-Exo HS15 replicate1

description:
Replicate 1
RPB3_extract_tag_occupancy.csv


title: Ssl2 ChIP-Exo HS6 replicate2

description:
Replicate 2
matrix_for_clustering.txt


title: Rpb3 ChIP-Exo HS12 replicate2


title: Hsf1 ChIP-Exo HS12 replicate1

description:
Replicate 1
Hsf1-union-midpoint-report-strand-reversed.txt


title: Hsf1 ChIP-Exo HS6 replicate3

description:
Replicate 3
Hsf1-union-midpoint-report-strand-reversed.txt


title: Hsf1 ChIP-Exo HS6 replicate1


title: Hsf1 ChIP-Exo HS3 replicate3


title: Rpb3 ChIP-Exo HS9 replicate2


title: Rpb3 ChIP-Exo HS9 replicate1


title: Hsf1 ChIP-Exo MHS replicate2

description:
Replicate 2
Hsf1-union-midpoint-report-strand-reversed.txt


title: Hsf1 ChIP-Exo MHS replicate3


title: Hsf1 ChIP-Exo HS3 replicate1


title: Hsf1 ChIP-Exo HS3 replicate2


title: Rpb3 ChIP-Exo HS6 replicate2


title: Hsf1 ChIP-Exo MHS replicate1


title: Ssl2 ChIP-Exo MHS replicate1

description:
Replicate 1
matrix_for_clustering.txt


title: Spt16 ChIP-Exo HS6 replicate2

description:
Replicate 2
53412sacCer3_s5e10F1.gff


title: Rpb3 ChIP-Exo HS6 replicate1


title: Hsf1 ChIP-Exo HS15 replicate1


title: Rpb3 ChIP-Exo HS3 replicate2


title: Spt16 ChIP-Exo HS3 replicate1


title: Spt16 ChIP-Exo HS3 replicate2


title: Rpb3 ChIP-Exo HS12 replicate1


title: Hsf1 ChIP-Exo HS6 replicate2


title: Spt16 ChIP-Exo MHS replicate1


title: Hsf1 ChIP-Exo HS9 replicate1


title: Tbp1 ChIP-Exo HS6 replicate1

description:
Replicate 1
53321sacCer3_s5e10F1.gff


title: Tbp1 ChIP-Exo HS3 replicate2


title: Rpb3 ChIP-Exo MHS replicate3

description:
Replicate 3
RPB3_extract_tag_occupancy.csv


title: Tbp1 ChIP-Exo HS3 replicate1


title: Rpb3 ChIP-Exo HS3 replicate1


title: Rpb3 ChIP-Exo MHS replicate1


title: Tbp1 ChIP-Exo HS6 replicate2

description:
Replicate 2
53324sacCer3_s5e10F1.gff


title: Taf1 ChIP-Exo HS15 replicate1

description:
Replicate 1
50536sacCer3_s5e10F1.gff


title: Tbp1 ChIP-Exo MHS replicate2


title: Sua7 ChIP-Exo MHS replicate3


title: Tbp1 ChIP-Exo MHS replicate1


title: Taf1 ChIP-Exo HS12 replicate1

description:
Replicate 1
50535sacCer3_s5e10F1.gff


title: Rpb3 ChIP-Exo HS3 replicate3


title: Rpb3 ChIP-Exo HS6 replicate3


title: Rpb3 ChIP-Exo MHS replicate2


title: Spt16 ChIP-Exo HS6 replicate1

description:
Replicate 1
53409sacCer3_s5e10F1.gff


title: Taf1 ChIP-Exo HS9 replicate1

description:
Replicate 1
50534sacCer3_s5e10F1.gff


title: Taf1 ChIP-Exo HS6 replicate2

description:
Replicate 2
53333sacCer3_s5e10F1.gff


title: Taf1 ChIP-Exo HS12 replicate2

description:
Replicate 2
53335sacCer3_s5e10F1.gff


title: Taf1 ChIP-Exo HS15 replicate2

description:
Replicate 2
53336sacCer3_s5e10F1.gff


title: Taf1 ChIP-Exo HS6 replicate1

description:
Replicate 1
50533sacCer3_s5e10F1.gff


title: Taf1 ChIP-Exo HS9 replicate2

description:
Replicate 2
53334sacCer3_s5e10F1.gff


title: Taf1 ChIP-Exo MHS replicate1


title: Taf1 ChIP-Exo MHS replicate2


title: Spt3 ChIP-Exo HS12 replicate2

description:
Replicate 2
53419sacCer3_s5e10F1.gff


title: Taf1 ChIP-Exo HS3 replicate2


title: Spt3 ChIP-Exo HS15 replicate2

description:
Replicate 2
53420sacCer3_s5e10F1.gff


title: Spt3 ChIP-Exo HS15 replicate1

description:
Replicate 1
50530sacCer3_s5e10F1.gff


title: Spt3 ChIP-Exo HS6 replicate2

description:
Replicate 2
53339sacCer3_s5e10F1.gff


title: Spt3 ChIP-Exo HS3 replicate2


title: Spt3 ChIP-Exo HS12 replicate1

description:
Replicate 1
50529sacCer3_s5e10F1.gff


title: Spt3 ChIP-Exo HS9 replicate2

description:
Replicate 2
53340sacCer3_s5e10F1.gff


title: Spt3 ChIP-Exo HS9 replicate1

description:
Replicate 1
50528sacCer3_s5e10F1.gff


title: Spt3 ChIP-Exo HS6 replicate1

description:
Replicate 1
50527sacCer3_s5e10F1.gff


title: Spt3 ChIP-Exo MHS replicate2


title: Spt3 ChIP-Exo HS3 replicate1


title: mmu_Nrep(miR-29scr) 2

city: Paris

first: Yuvia

middle: Alheli

last: Perez Rico

address: 26 rue d'Ulm

institute: Institut Curie

data_processing:
Basecalls performed using CASAVA for all libraries.
RNA-seq FASTQ files were mapped to the zebrafish genome version danRer7 with TopHat version 2.0.6 using the global alignment option and a seed size of 22 without allowing mismatches in this region. Only the unique best hits were kept.
FASTQ files containing the small RNA sequencing data were stripped of adapter sequences using the Reaper tool and sequences between 16-24nt were selected and mapped using a command-line variant of chimiRa to known microRNA precursors from miRBase (v21). Each sequence was assigned to a mature miRNA according to which arm (5p or 3p) of the precursor was matched and to the known mature sequence. In cases where a single sequence mapped to multiple possible loci, a random locus was assigned each time. These raw counts were assembled into a table across all microRNAs from all samples (R/BioConductor) and normalized using DESeq2. Differential expression was performed using the negative binomial Wald test (DESeq2) for differences between mutant versus wild type. All derived P-values for differential expression were multiple testing corrected using the Benjamini-Hochberg method. The trimming analysis was performed by examining the fraction of nucleotides from the annotated microRNA from miRBase that was covered by each mapped read from each sample. The mean of these values was used to compute differential trimming using a paired t-test on the derived values between 17-27nt between mutant and wild type samples for miR-29b.
Genome_build: danRer7, miRBase (v21)
Supplementary_files_format_and_content: BAM files from technical duplicates of the zebrafish libraries were merged and used to generate pileup tracks with BEDTools and UCSC tools. Tab-delimited text file includes the raw read counts for microRNA precursors for all small RNA-seq libraries.

source_name: ES14 male differentiated to NPCs

extract_protocol:
Total RNA was harvested from 100zebrafish embryos and >20 million mouse NPCs for each replicate using Trizol reagent. One microgram of total RNA was used for the construction of both RNA and small RNA sequencing libraries.
RNA libraries were prepared for sequencing using standard manufacturers' protocols (Illumina TruSeq kit for RNA-Seq libraries and NEBNext Multiplex small RNA library kit for small RNA libraries).

tag: cell type

value: NPCs

tag: genotype


title: mmu-wt3

value: wild type


title: Spt3 ChIP-Exo MHS replicate1

tag: strain


title: mmu-wt2


title: zf_libra(inv)

organism: Danio rerio

source_name: 72 hpf embryos

value: AB

tag: tissue

value: whole embryos

value: 72 hours post fertilization

value: libra inversion


title: zf_wt

value: wt


title: mmu-wt1