title: Whole Blood 48hr after 8Gy dose rep 2

status: Public on May 31 2018

type: RNA

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

country: USA

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Mouse Genome microarrays 8x60K v1 Design ID 028005 or v2 Design ID 074809 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2505C Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA). Only the 30,000+ probes that are printed on both arrays (Agilent-028005, Agilent-074809) are reported.

label: Alexa 555

molecule: total RNA

organism: Mus musculus

source_name: Whole Blood 48hr after 8Gy dose

label_protocol: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using MessageAMP II (Applied Biosystems, Foster City, CA). After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP. The quantity and quality of the cRNA were assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation.

treatment_protocol: Whole body irradiation done with X-rays using the Small Animal Radiation Research Platform (SARRP Xstrahl Ltd.). Mice were placed in plastic containers and exposed to a single surface dose of 0-12 Gy with a dose rate of 1.05 Gy/min. Control mice (0 Gy) were placed in the same plastic container as the irradiated mice and sham irradiated. 3 animals/dose/time-point have been included in the study.

tag: strain/background

tag: gender

value: female

tag: age

value: six to eight weeks

tag: tissue

value: whole blood

tag: treatment

value: 8Gy gamma rays

tag: time point


title: GT1-7cont

city: Okinawa

first: Sayomi

last: Higa-Nakamine

address: 207 Uehara, Nishihara

department: Department of Biochemistry

country: Japan

institute: Graduate School of Medicine, University of the Ryukyus

description: Gene expression after 30 min in 100 nM bradykinin treaed A549 cells

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with the Bioconductor.

source_name: GT1-7 cell, DMSO 30min

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: GT1-7 cells were grown on 60-mm Petri dishes in a culture medimum consisting DMEM and 10% FCS and 100 μg/ml gentamicin.

extract_protocol: Total RNA was extracted using an Rneasy Mini Kit (Qiagen, MD) .

treatment_protocol: GT1-7 cells were treated with 50 nM GnRH for 30 min in DMEM.

tag: cell line

value: DMSO 30min

tag: cell type

value: culltured hypothalamic neurons


title: Whole Blood 48hr after 2Gy dose rep 1

source_name: Whole Blood 48hr after 2Gy dose

value: 2Gy gamma rays


title: Whole Blood 48hr after 2Gy dose rep 2


title: Whole Blood 48hr after 8Gy dose rep 1


title: Whole Blood 48hr after 0Gy dose rep 3

source_name: Whole Blood 48hr after 0Gy dose

value: 0Gy gamma rays


title: Whole Blood 48hr after 4Gy dose rep 2

source_name: Whole Blood 48hr after 4Gy dose

value: 4Gy gamma rays


title: Whole Blood 48hr after 4Gy dose rep 3


title: GT1-7GnRH50nM30min

source_name: GT1-7 cell, 50 nM GnRH 30min

value: 50 nM GnRH 30min


title: Whole Blood 48hr after 0Gy dose rep 2


title: Whole Blood 48hr after 4Gy dose rep 1


title: Whole Blood 48hr after 8Gy dose rep 3


title: Whole Blood 48hr after 2Gy dose rep 3


title: Whole Blood 24hr after 8Gy dose rep 3

source_name: Whole Blood 24hr after 8Gy dose


title: Whole Blood 48hr after 0Gy dose rep 1


title: Whole Blood 24hr after 4Gy dose rep 3

source_name: Whole Blood 24hr after 4Gy dose


title: Whole Blood 24hr after 8Gy dose rep 1


title: Whole Blood 24hr after 4Gy dose rep 2


title: Whole Blood 24hr after 8Gy dose rep 2


title: Whole Blood 24hr after 0Gy dose rep 2

source_name: Whole Blood 24hr after 0Gy dose


title: Whole Blood 24hr after 2Gy dose rep 3

source_name: Whole Blood 24hr after 2Gy dose


title: Whole Blood 24hr after 4Gy dose rep 1


title: Whole Blood 24hr after 0Gy dose rep 3


title: Rad52_WT_60_Replicate2

type: other

city: Bordeaux

first: Pei-Yun Jenny

last: Wu

address: 1 Rue Camille Saint Saens

country: France

institute: Institute of Biochemistry and Cellular Genetics

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1). No normalization was used. Ratio IP/input.

molecule: other

organism: Schizosaccharomyces pombe

label_protocol: For amplification of the ChIP material and labeling for hybridization, the protocol from (van Bakel et al., NAR 2008) was used according to (Wu and Nurse, Mol Cell 2014). Labelling was performed with either Alexa 555/Alexa 647 dyes or Cy3/Cy5 dyes (Amersham CyDye Post-Labelling Reactive Dye pack).

growth_protocol: S. pombe cells were grown to exponential phase in EMM6S at 25˚C and synchronized using a temperature shift (blocked 4h at 36.5˚C and shifted at 25˚C for release).

extract_protocol: Chromatin immunoprecipitation experiments were performed as previously described (Wu and Nurse, Cell 2009). Cells were fixed with 1% formaldehyde, lysed in a FastPrep cell disruptor (MP Biomedicals, USA) and sonicated with a Bioruptor Plus (Diagenode) to obtain chromatin fragments of ~400-500 bp. Protein G sepharose beads (GE Healthcare) were then added to the samples and incubated for 4 h at 4 °C. IPs were then washed and eluted, and crosslinking was reversed for both IP and Input samples by incubation at 65 ºC overnight. Antibody: anti-Rad52, AB63800; Abcam, UK.

treatment_protocol: Cells were treated with 6mM HU after release from restrictive temperature and collected at time 60' after release.

tag: strain


title: Whole Blood 24hr after 2Gy dose rep 2


title: Whole Blood 24hr after 0Gy dose rep 1


title: Rad52_∆rad3_60_Replicate3

data_processing: Agilent Feature Extraction Software (v 10.7.3.1).  No normalization was used

label_protocol: RNA was amplified and labeled as described in Wu, Nurse 2014. Labelling was performed with Alexa 555/Alexa 647 dyes

extract_protocol: RNA extraction as described in the Methods section

treatment_protocol: Cells were treated with 6mM HU after release from restrictive temperature (10 min after release) and collected at time 60' after release

tag: background strain

tag: genotype

source_name: IP


title: Whole Blood 24hr after 2Gy dose rep 1


title: Rad52_WT_60_Replicate3

value: WT


title: Rad52_∆rad3_60_Replicate2


title: Rad52_∆rad3_60_Replicate1


title: Normal

city: Nanjing

first: Wang

last: Lintao

address: 163 Xianlin Avenue

department: School of Life Sciences

country: China

institute: Nanjing University

description: total RNA

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Scanned on an G2505C Agilent scanner.

data_processing: Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Normal spleens

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

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

treatment_protocol: The Normal spleens and were collected and Post-surgery spleens were collected for further microarray analysis at day 7 after the surgery operation for translocating the spleen from the abdominal cavity to a subcutaneous location. The translocated spleens injected with PBS and STH three times over 7 days were harvested and analyzed. The PBS+HepG2 spleens and STH+HepG2 spleens were harvested and analyzed during the eighth hour after HepG2 transplantation. Murine splenic macrophages were maintained in RPMI-1640 containing 50% PBS or STH (v/v) for 18 hours at 37 °C, 5 % CO2 incubator before further microarray analysis.

value: spleen

value: Female


title: Rad52_WT_60_Replicate1

hyb_protocol: Equal amounts of differentially labelled Input and IP material were mixed and hybridized for 18h-21h at 42C.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1).  No normalization was used. Ratio IP/input.


title: Post-surgery

description: total RNA

source_name: Translocated spleens

growth_protocol: Murine splenic macrophages were maintained in RPMI-1640 containing 50% PBS or STH (v/v) for 18 hours at 37 °C, 5 % CO2 incubator before further microarray analysis.


title: PN1_Cy3_PN1400_Cy5_Replicate2

type: genomic

hyb_protocol: Labeled samples were quantified and added to hybridization buffer (50 mM MES pH 6.7, 500 mM NaCl, 6 mM EDTA, 0.5% Sarcosine, 30% Formamide, 1.5 ng/µl herring sperm DNA, 0.8 µg/µl yeast tRNA, 0.05µg/µl Cot1 DNA). Samples were incubated in an Agilent hybridization oven at 42ºC for 18 to 20 hours, and washes were performed for 5 min at room temperature (2X wash 1: 6xSSPE, 0.005% N-Lauroylsarcosine, 1X wash 2: 0.06x SSPE).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1)

molecule: genomic DNA

source_name: asynchronous sample

label_protocol: Genomic DNA samples were labeled using the BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen) with either Alexa 555/Alexa 647 dyes or Cy3/Cy5 dyes (Amersham CyDye Post-Labelling Reactive Dye pack).

growth_protocol: Schizosaccharomyces pombe cells were grown to exponential phase in EMM6S at 32˚C and pellets collected at an O.D of 0.3

extract_protocol: Genomic DNA extraction was performed as in Hoffman and Winston, Gene, 1987, and samples were purified using the Qiagen Genomic Tip-20.


title: PBS

description: total RNA

source_name: The translocated spleens treated with PBS


title: PN1Cy5_PN1400_Cy3_Replicate2


title: STH (macrophage)

description: total RNA

source_name: Splenic macrophages treated with STH

value: splenic macrophage


title: PBS (macrophage)

description: total RNA

source_name: Splenic macrophages treated with PBS


title: STH

description: total RNA

source_name: The translocated spleens treated with STH


title: PBS+HepG2

description: total RNA

source_name: The PBS-treated spleens implanted with HepG2


title: STH+HepG2

description: total RNA

source_name: The STH-treated spleens implanted with HepG2


title: PN1Cy5_PN1400_Cy3_Replicate1


title: Rad52_∆rif1∆rad3_NOHU_Replicate2

source_name: input

label_protocol: RNA was amplified and labeled as described in Wu, Nurse 2014. Labelling was performed with either Alexa 555/Alexa 647 dyes or Cy3/Cy5 dyes (Amersham CyDye Post-Labelling Reactive Dye pack).

growth_protocol: Schizosaccharomyces pombe cells were grown to exponential phase in EMM6S at 25˚C and synchronized using a temperature shift (blocked 4h at 36.5˚C and shifted at 25˚C for release).

treatment_protocol: Cells were not treated with HU after release from restrictive temperature


title: Rad52_∆rad3_NOHU_Replicate1


title: Rad52_∆rif1_NOHU_Replicate2


title: PN1_Cy3_PN1400_Cy5_Replicate1


title: Rad52_∆rad3_NOHU_Replicate2


title: Rad52_WT_NOHU_Replicate2


title: Rad52_∆rif1_NOHU_Replicate1


title: Rad52_∆rif1∆rad3_NOHU_Replicate1


title: RPA_∆rad3_60_Replicate1

extract_protocol: RNA extraction as described

treatment_protocol: Cells were treated with 6mM HU after release from restrictive temperature

value: delta-rad3 cdc25-22


title: RPA_∆rad3_60_Replicate3

value: delta-rad3 cdc25-23


title: Rad52_∆rif1_Replicate2

extract_protocol:
RNA extraction as described in the Methods section
RNA was amplified and labeled as described in Wu, Nurse 2014. Labelling was performed with either Alexa 555/Alexa 647 dyes or Cy3/Cy5 dyes (Amersham CyDye Post-Labelling Reactive Dye pack).

tag: fraction

value: input

value: IP


title: Rad52_WT_NOHU_Replicate1


title: RPA_WT_60_Replicate3


title: RPA_∆rad3_60_Replicate2


title: RPA_WT_60_Replicate2


title: Rad52_∆rif1∆rad3_Replicate1


title: Rad52_∆rif1_Replicate1


title: Rad52_WT_Replicate3

label: Alexa 647


title: Rad52_∆rif1∆rad3_Replicate2


title: RPA_WT_60_Replicate1


title: Rad52_∆rad3_Replicate2

source_name: ∆rad3 cdc25-22

value: deltarad3 cdc25-22

source_name: ∆rad3 cdc25.22

value: deltarad3 cdc25.22


title: Rad52_WT_Replicate2


title: Rad52_∆rad3_Replicate1


title: Rad52_∆rad3_Replicate3


title: RPA_∆rad3_Replicate3

source_name: ∆rad3 cdc25-23

value: deltarad3 cdc25-23


title: RPA_∆rad3_Replicate2


title: Rad52_WT_Replicate1


title: RPA_∆rad3_Replicate1


title: RPA_WT_Replicate1


title: rad3∆ rif1∆_Replicate2_dye-swap2

hyb_protocol: Labeled samples from before and after S phase entry were quantified and added to hybridization buffer (50 mM MES pH 6.7, 500 mM NaCl, 6 mM EDTA, 0.5% Sarcosine, 30% Formamide, 1.5 ng/µl herring sperm DNA, 0.8 µg/µl yeast tRNA, 0.05µg/µl Cot1 DNA). Samples were incubated in an Agilent hybridization oven at 42ºC for 18 to 20 hours, and washes were performed for 5 min at room temperature (2X wash 1: 6xSSPE, 0.005% N-Lauroylsarcosine, 1X wash 2: 0.06x SSPE).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1)
BASELINE CORRECTION: To obtain origin efficiencies, the lowest ratios, which represent non-replicated DNA, were adjusted to be centered on a value of 1. This resulted in a correction of 0.25 for all datasets
1) pre-Value column:  the ratios of S phase vs. unreplicated DNA, 2) Value column: pre-VAlue is baseline corrected as part of the protocol for origin identification described in the paper.

source_name: ∆rad3∆rif1  cdc25.22

value: deltarad3deltarif1 cdc25.22

tag: time

value: 0 (unreplicated)

value: 90 (S phase)


title: rad3∆ rif1∆_Replicate3_dye-swap2

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1)
1) pre-Value column: the ratios of S phase vs. unreplicated DNA, 2) Value column: pre-Value is baseline corrected as part of the protocol for origin identification described in the paper.
BASELINE CORRECTION: To obtain origin efficiencies, the lowest ratios, which represent non-replicated DNA, were adjusted to be centered on a value of 1. This resulted in a correction of 0.25 for all datasets.

source_name: cdc25-22 rif1∆ rad3∆

treatment_protocol: Cells were treated with 6mM HU 5 minutes after release from restrictive temperature. Unreplicated DNA samples were taken at this time.

value: cdc25-22 rif1∆ rad3∆; unreplicated DNA

treatment_protocol: Cells were treated with 6mM HU 5 minutes after release from restrictive temperature. S phase DNA samples were taken after a time when cells would normally have completed S phase in the absence of HU.

value: cdc25-22 rif1∆ rad3∆; S phase DNA


title: rad3∆ rif1∆_Replicate3_dye-swap1


title: RPA_WT_Replicate3


title: RPA_WT_Replicate2


title: rad3∆ rif1∆_Replicate2_dye-swap1


title: rad3∆ rif1∆_Replicate1_dye-swap2


title: rif1∆_Replicate3_dye-swap1

source_name: cdc25-22 rif1∆

value: cdc25-22 rif1∆; unreplicated DNA

value: cdc25-22 rif1∆; S phase DNA


title: rif1∆_Replicate1_dye-swap2


title: rif1∆_Replicate1_dye-swap1

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1)
1) pre-Value column:  the ratios of S phase vs. unreplicated DNA, 2) Value column: pre-Value is baseline corrected as part of the protocol for origin identification described in the paper.
BASELINE CORRECTION: To obtain origin efficiencies, the lowest ratios, which represent non-replicated DNA, were adjusted to be centered on a value of 1. This resulted in a correction of 0.25 for all datasets.


title: rif1∆_Replicate3_dye-swap2


title: rad3∆ nda3-km311_Replicate2_Dye1

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1)
BASELINE CORRECTION:To obtain origin efficiencies, the lowest ratios, which represent non-replicated DNA, were adjusted to be centered on a value of 1. This resulted in a correction of 0.25 for all datasets
1) pre-Value column:  the ratios of S phase vs. unreplicated DNA, 2) Value column: pre-Value is baseline corrected as part of the protocol for origin identification described in the paper.

growth_protocol: S. pombe cells were grown in EMM6S to exponential phase at 32˚C and synchronized using a temperature shift (blocked 6h at 18˚C and shifted at 32˚C for release).

treatment_protocol: Cells were treated with 6mM HU after the 6 h block

value: 0  (unreplicated)

value: 80 (S phase)


title: rif1∆_Replicate2_dye-swap2


title: rad3∆ rif1∆_Replicate1_dye-swap1


title: rad3∆ nda3-km311_Replicate1_Dye2


title: nda3-km311_Replicate2_Dye2


title: rif1∆_Replicate2_dye-swap1


title: rad3∆ nda3-km311_Replicate1_Dye1


title: nda3-km311_Replicate2_Dye1


title: nda3-km311_Replicate1_Dye1


title: rad3∆ nda3-km311_Replicate2_Dye2


title: rad3∆_Replicate2_dye1

data_processing:
Agilent Feature Extraction Software (v 10.7.3.1)
1) pre-Value column:  the ratios of S phase vs. unreplicated DNA, 2) Value column: pre-Value is baseline corrected as part of the protocol for origin identification described in the paper.
BASELINE CORRECTION:To obtain origin efficiencies, the lowest ratios, which represent non-replicated DNA, were adjusted to be centered on a value of 1. This resulted in a correction of 0.25 for all datasets

source_name: cdc25-22 rad3∆

growth_protocol: S. pombe cells were grown in EMM6S to exponential phase at 25˚C and synchronized using a temperature shift (blocked 4h at 36.5˚C and shifted at 25˚C for release).

value: cdc25-22 rad3∆; unreplicated DNA

value: cdc25-22 rad3∆; S phase DNA


title: rad3∆_Replicate2_dye2


title: rad3∆_Replicate1_dye2


title: nda3-km311_Replicate1_Dye2


title: rad3∆_Replicate3_dye1


title: WT_Replicate3_dye1

value: cdc25-22; unreplicated DNA

value: cdc25-22; S phase DNA


title: rad3∆_Replicate3_dye2


title: WT_Replicate3_dye2


title: rad3∆_Replicate1_dye1


title: WT_Replicate2_dye1


title: WT_Replicate2_dye2


title: WT_Replicate1_dye2


title: Endometrium_intrauterine_MP44

city: Reno

first: Nicole

last: Ortogero

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

description:
The views expressed are those of the author(s) and do not reflect the official policy of the Department of the Army, the Department of Defense or the U.S. Government.
The investigators have adhered to the policies for protection of human subjects as prescribed in 45 CFR 46.

hyb_protocol: Affymetrix GeneChip Human Gene 2.0 ST Array

scan_protocol: Affymetrix GeneChip 1300 scanner

data_processing:
Affymetrix GeneChip Command Console Software was used for initial data collection followed by RMA normalization in oligo. Data was processed to remove control probes.
HuGene-2_0-st-v1.na35.hg19.probeset.csv
HuGene-2_0-st-v1.na36.hg19.transcript.csv

label: biotin

organism: Homo sapiens

source_name: Endometrial biopsy

label_protocol: Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay

extract_protocol: Endometrial biopsy collected from women with non-viable pregnancies at Madigan Army Medical Center

value: Endometrial biopsy

tag: pregnancy location

value: Non-viable Intrauterine


title: Endometrium_ectopic_MP24

value: Ectopic


title: Endometrium_ectopic_MP10


title: Endometrium_intrauterine_MP33


title: Endometrium_ectopic_MP15


title: Endometrium_ectopic_MP20


title: Endometrium_intrauterine_MP2


title: Endometrium_intrauterine_MP23


title: MuscleTR_rep2_1024

type: SRA

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: muscle

growth_protocol: Live cells were sorted by flow cytometry from the spleen and muscle of mice (carrying a Foxp3 reporter gene) 4 days after muscle injury with cardiotoxin.

extract_protocol:
Spleen were mechanically dissociated and muscle were digested with collagenase/dispase to single cell suspensions. Tregs were sorted by flow cytometry as DAPI- TCRb+ CD4+ GFP+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

tag: library name

tag: sample type

value: B6 Foxp3-Ires-Gfp

tag: Sex

value: male

tag: age (months)

tag: condition

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: MuscleTR_rep2_1035

value: 4 days after muscle injury with cardiotoxin.


title: MuscleTR_rep2_1027


title: MuscleTR_rep2_1028


title: MuscleTR_rep2_1037


title: MuscleTR_rep2_1032


title: MuscleTR_rep2_1025


title: MuscleTR_rep2_1038


title: MuscleTR_rep2_1026


title: MuscleTR_rep2_1029


title: MuscleTR_rep2_1031


title: Endometrium_intrauterine_MP38

tag: tissue


title: Endometrium_intrauterine_MP42


title: Endometrium_intrauterine_MP11


title: Endometrium_intrauterine_MP25


title: Endometrium_ectopic_MP37


title: Endometrium_intrauterine_MP14


title: Endometrium_ectopic_MP40


title: Endometrium_ectopic_MP1


title: MuscleTR_rep2_1023


title: MuscleTR_rep2_1020


title: MuscleTR_rep2_1019


title: MuscleTR_rep2_1021


title: MuscleTR_rep2_1017


title: MuscleTR_rep2_1015


title: MuscleTR_rep2_1022


title: MuscleTR_rep2_1012


title: MuscleTR_rep2_1013


title: MuscleTR_rep2_1010


title: MuscleTR_rep2_994


title: MuscleTR_rep2_1008


title: MuscleTR_rep2_986


title: MuscleTR_rep2_989


title: MuscleTR_rep2_988


title: MuscleTR_rep2_1004


title: MuscleTR_rep2_996


title: MuscleTR_rep2_999


title: MuscleTR_rep2_992


title: MuscleTR_rep2_1002


title: MuscleTR_rep2_1007


title: MuscleTR_rep2_990


title: MuscleTR_rep2_1001


title: MuscleTR_rep2_997


title: MuscleTR_rep2_1000


title: MuscleTR_rep2_1006


title: MuscleTR_rep2_987


title: MuscleTR_rep2_1003


title: MuscleTR_rep2_985


title: MuscleTR_rep2_982


title: MuscleTR_rep2_979


title: MuscleTR_rep2_984


title: MuscleTR_rep2_976


title: MuscleTR_rep2_975


title: MuscleTR_rep2_973


title: MuscleTR_rep2_971


title: MuscleTR_rep2_969


title: MuscleTR_rep2_968


title: MuscleTR_rep2_970


title: MuscleTR_rep2_962


title: MuscleTR_rep2_963


title: MuscleTR_rep2_961


title: MuscleTR_rep2_957


title: MuscleTR_rep2_956


title: MuscleTR_rep2_948


title: MuscleTR_rep2_947


title: MuscleTR_rep2_958


title: MuscleTR_rep2_965


title: MuscleTR_rep2_953


title: MuscleTR_rep2_945


title: MuscleTR_rep2_955


title: MuscleTR_rep2_943


title: MuscleTR_rep2_950


title: MuscleTR_rep2_959


title: MuscleTR_rep2_935


title: MuscleTR_rep2_942


title: MuscleTR_rep2_939


title: MuscleTR_rep2_937


title: MuscleTR_rep2_933


title: MuscleTR_rep2_934


title: MuscleTR_rep2_938


title: MuscleTR_rep2_928


title: MuscleTR_rep2_930


title: MuscleTR_rep2_923


title: MuscleTR_rep2_954


title: MuscleTR_rep2_918


title: MuscleTR_rep2_929


title: MuscleTR_rep2_914


title: MuscleTR_rep2_921


title: MuscleTR_rep2_919


title: MuscleTR_rep2_925


title: MuscleTR_rep2_920


title: MuscleTR_rep2_907


title: MuscleTR_rep2_917


title: Endometrium_ectopic_MP41


title: MuscleTR_rep2_904


title: MuscleTR_rep2_908


title: MuscleTR_rep2_916


title: WT_Replicate1_dye1


title: MuscleTR_rep2_902


title: MuscleTR_rep2_913


title: MuscleTR_rep2_903


title: MuscleTR_rep2_900


title: MuscleTR_rep2_899


title: MuscleTR_rep2_898


title: MuscleTR_rep2_897


title: MuscleTR_rep2_926


title: MuscleTR_rep2_890


title: MuscleTR_rep2_894


title: MuscleTR_rep2_889


title: MuscleTR_rep2_895


title: MuscleTR_rep2_888


title: MuscleTR_rep2_878


title: MuscleTR_rep2_883


title: MuscleTR_rep2_882


title: MuscleTR_rep2_884


title: MuscleTR_rep2_879


title: MuscleTR_rep2_880


title: MuscleTR_rep2_874


title: MuscleTR_rep2_873


title: MuscleTR_rep2_872


title: MuscleTR_rep2_875


title: MuscleTR_rep2_871


title: MuscleTR_rep2_869


title: MuscleTR_rep2_862


title: MuscleTR_rep2_865


title: MuscleTR_rep2_866


title: MuscleTR_rep2_868


title: MuscleTR_rep2_867


title: MuscleTR_rep2_864


title: MuscleTR_rep2_896


title: MuscleTR_rep2_859


title: MuscleTR_rep2_857


title: MuscleTR_rep2_856


title: MuscleTR_rep2_850


title: MuscleTR_rep2_851


title: MuscleTR_rep2_877


title: MuscleTR_rep2_837


title: MuscleTR_rep2_838


title: MuscleTR_rep2_833


title: MuscleTR_rep2_832


title: MuscleTR_rep2_831


title: MuscleTR_rep2_845


title: MuscleTR_rep2_844


title: MuscleTR_rep2_830


title: MuscleTR_rep2_861


title: MuscleTR_rep2_860


title: MuscleTR_rep2_824


title: MuscleTR_rep2_827


title: MuscleTR_rep2_819


title: MuscleTR_rep2_826


title: MuscleTR_rep2_818


title: MuscleTR_rep2_822


title: MuscleTR_rep2_853


title: MuscleTR_rep2_817


title: MuscleTR_rep2_812


title: MuscleTR_rep2_854


title: MuscleTR_rep2_811


title: MuscleTR_rep2_846


title: MuscleTR_rep2_810


title: MuscleTR_rep2_808


title: MuscleTR_rep2_843


title: MuscleTR_rep2_842


title: MuscleTR_rep2_839


title: MuscleTR_rep2_829


title: MuscleTR_rep2_828


title: MuscleTR_rep2_821


title: MuscleTR_rep2_806


title: MuscleTR_rep2_805


title: MuscleTR_rep2_799


title: MuscleTR_rep2_800


title: MuscleTR_rep2_797


title: MuscleTR_rep2_796


title: MuscleTR_rep2_795


title: MuscleTR_rep2_790


title: MuscleTR_rep2_791


title: MuscleTR_rep2_789


title: MuscleTR_rep2_784


title: MuscleTR_rep2_785


title: MuscleTR_rep2_786


title: MuscleTR_rep2_783


title: MuscleTR_rep2_779


title: MuscleTR_rep2_778


title: MuscleTR_rep2_807


title: MuscleTR_rep2_803


title: MuscleTR_rep2_802


title: MuscleTR_rep2_765


title: MuscleTR_rep2_771


title: MuscleTR_rep2_770


title: MuscleTR_rep2_772


title: MuscleTR_rep2_766


title: MuscleTR_rep2_775


title: MuscleTR_rep2_774


title: MuscleTR_rep2_762


title: MuscleTR_rep2_794


title: MuscleTR_rep2_793


title: MuscleTR_rep2_759


title: MuscleTR_rep2_760


title: MuscleTR_rep2_787


title: MuscleTR_rep2_755


title: MuscleTR_rep2_758


title: MuscleTR_rep2_757


title: MuscleTR_rep2_753


title: MuscleTR_rep2_751


title: MuscleTR_rep2_746


title: MuscleTR_rep2_749


title: MuscleTR_rep2_750


title: MuscleTR_rep2_745


title: MuscleTR_rep2_777


title: MuscleTR_rep2_744


title: MuscleTR_rep2_741


title: MuscleTR_rep2_761


title: MuscleTR_rep2_740


title: MuscleTR_rep2_734


title: MuscleTR_rep2_728


title: MuscleTR_rep2_739


title: MuscleTR_rep2_725


title: MuscleTR_rep2_724


title: MuscleTR_rep2_737


title: MuscleTR_rep2_718


title: MuscleTR_rep2_723


title: MuscleTR_rep2_732


title: MuscleTR_rep2_726


title: MuscleTR_rep2_711


title: MuscleTR_rep2_716


title: MuscleTR_rep2_708


title: MuscleTR_rep2_706


title: MuscleTR_rep2_714


title: MuscleTR_rep2_712


title: MuscleTR_rep2_705


title: MuscleTR_rep2_710


title: MuscleTR_rep2_703


title: MuscleTR_rep2_701


title: MuscleTR_rep2_704


title: MuscleTR_rep2_700


title: MuscleTR_rep2_702


title: MuscleTR_rep2_743


title: MuscleTR_rep2_697


title: MuscleTR_rep2_695


title: MuscleTR_rep2_696


title: MuscleTR_rep2_720


title: MuscleTR_rep2_692


title: MuscleTR_rep2_691


title: MuscleTR_rep2_688


title: MuscleTR_rep2_685


title: MuscleTR_rep2_683


title: MuscleTR_rep2_709


title: MuscleTR_rep2_684


title: MuscleTR_rep2_682


title: MuscleTR_rep2_681


title: MuscleTR_rep2_687


title: MuscleTR_rep2_680


title: MuscleTR_rep2_677


title: MuscleTR_rep2_665


title: MuscleTR_rep2_669


title: MuscleTR_rep2_673


title: MuscleTR_rep2_660


title: MuscleTR_rep2_668


title: MuscleTR_rep2_676


title: MuscleTR_rep2_664


title: MuscleTR_rep2_674


title: MuscleTR_rep2_655


title: MuscleTR_rep2_666


title: MuscleTR_rep2_656


title: MuscleTR_rep2_662


title: MuscleTR_rep2_661


title: MuscleTR_rep2_646


title: MuscleTR_rep2_643


title: MuscleTR_rep2_659


title: MuscleTR_rep2_640


title: MuscleTR_rep2_658


title: MuscleTR_rep2_653


title: MuscleTR_rep2_650


title: MuscleTR_rep2_651


title: MuscleTR_rep2_649


title: MuscleTR_rep2_647


title: MuscleTR_rep2_634


title: MuscleTR_rep2_645


title: MuscleTR_rep2_644


title: MuscleTR_rep2_625


title: MuscleTR_rep2_624


title: MuscleTR_rep2_639


title: MuscleTR_rep2_638


title: MuscleTR_rep2_635


title: MuscleTR_rep2_633


title: MuscleTR_rep2_631


title: MuscleTR_rep2_630


title: MuscleTR_rep2_629


title: MuscleTR_rep2_627


title: MuscleTR_rep2_617


title: MuscleTR_rep2_611


title: MuscleTR_rep2_626


title: MuscleTR_rep2_606


title: MuscleTR_rep2_601


title: MuscleTR_rep2_622


title: MuscleTR_rep2_598


title: MuscleTR_rep2_621


title: MuscleTR_rep2_620


title: MuscleTR_rep2_628


title: MuscleTR_rep2_619


title: MuscleTR_rep2_613


title: MuscleTR_rep2_616


title: MuscleTR_rep2_607


title: MuscleTR_rep2_603


title: MuscleTR_rep2_604


title: MuscleTR_rep2_609


title: MuscleTR_rep2_605


title: MuscleTR_rep2_592


title: MuscleTR_rep2_590


title: MuscleTR_rep2_602


title: MuscleTR_rep2_582


title: MuscleTR_rep2_577


title: MuscleTR_rep2_581


title: MuscleTR_rep2_595


title: MuscleTR_rep2_593


title: MuscleTR_rep2_573


title: MuscleTR_rep2_587


title: MuscleTR_rep2_594


title: MuscleTR_rep2_572


title: MuscleTR_rep2_575


title: MuscleTR_rep2_578


title: MuscleTR_rep2_571


title: MuscleTR_rep2_570


title: MuscleTR_rep2_567


title: MuscleTR_rep2_566


title: MuscleTR_rep2_563


title: MuscleTR_rep2_562


title: MuscleTR_rep2_564


title: MuscleTR_rep2_560


title: MuscleTR_rep2_569


title: MuscleTR_rep2_576


title: MuscleTR_rep2_550


title: MuscleTR_rep2_548


title: MuscleTR_rep2_556


title: MuscleTR_rep2_554


title: MuscleTR_rep2_559


title: MuscleTR_rep2_551


title: MuscleTR_rep2_552


title: MuscleTR_rep2_546


title: MuscleTR_rep2_542


title: MuscleTR_rep2_557


title: MuscleTR_rep2_549


title: MuscleTR_rep2_547


title: MuscleTR_rep2_538


title: MuscleTR_rep2_534


title: MuscleTR_rep2_544


title: MuscleTR_rep2_530


title: MuscleTR_rep2_531


title: MuscleTR_rep2_537


title: MuscleTR_rep2_526


title: MuscleTR_rep2_521


title: MuscleTR_rep2_522


title: MuscleTR_rep2_525


title: MuscleTR_rep2_528


title: MuscleTR_rep2_519


title: MuscleTR_rep2_517


title: MuscleTR_rep2_515


title: MuscleTR_rep2_524


title: MuscleTR_rep2_520


title: MuscleTR_rep2_512


title: MuscleTR_rep2_509


title: MuscleTR_rep2_508


title: MuscleTR_rep2_505


title: MuscleTR_rep2_511


title: MuscleTR_rep2_504


title: MuscleTR_rep2_506


title: MuscleTR_rep2_502


title: MuscleTR_rep2_491


title: MuscleTR_rep2_499


title: MuscleTR_rep2_494


title: MuscleTR_rep2_493


title: MuscleTR_rep2_488


title: MuscleTR_rep2_498


title: MuscleTR_rep2_486


title: MuscleTR_rep2_500


title: MuscleTR_rep2_492


title: MuscleTR_rep2_484


title: MuscleTR_rep2_489


title: MuscleTR_rep2_483


title: MuscleTR_rep2_479


title: MuscleTR_rep2_481


title: MuscleTR_rep2_490


title: MuscleTR_rep2_473


title: MuscleTR_rep2_471


title: MuscleTR_rep2_480


title: MuscleTR_rep2_469


title: MuscleTR_rep2_474


title: MuscleTR_rep2_470


title: MuscleTR_rep2_495


title: MuscleTR_rep2_475


title: MuscleTR_rep2_468


title: MuscleTR_rep2_466


title: MuscleTR_rep2_464


title: MuscleTR_rep2_461


title: MuscleTR_rep2_463


title: MuscleTR_rep2_465


title: MuscleTR_rep2_462


title: MuscleTR_rep2_452


title: MuscleTR_rep2_456


title: MuscleTR_rep2_450


title: MuscleTR_rep2_447


title: MuscleTR_rep2_459


title: MuscleTR_rep2_457


title: MuscleTR_rep2_443


title: MuscleTR_rep2_451


title: MuscleTR_rep2_446


title: MuscleTR_rep2_440


title: MuscleTR_rep2_445


title: MuscleTR_rep2_439


title: MuscleTR_rep2_438


title: MuscleTR_rep2_435


title: MuscleTR_rep2_431


title: MuscleTR_rep2_437


title: MuscleTR_rep2_432


title: MuscleTR_rep2_434


title: MuscleTR_rep2_430


title: MuscleTR_rep2_429


title: MuscleTR_rep2_424


title: MuscleTR_rep2_426


title: MuscleTR_rep2_419


title: MuscleTR_rep2_423


title: MuscleTR_rep2_422


title: MuscleTR_rep2_417


title: MuscleTR_rep2_418


title: MuscleTR_rep2_416


title: MuscleTR_rep2_444


title: MuscleTR_rep2_414


title: MuscleTR_rep2_442


title: MuscleTR_rep2_415


title: MuscleTR_rep2_412


title: MuscleTR_rep2_404


title: MuscleTR_rep2_407


title: MuscleTR_rep2_408


title: MuscleTR_rep2_399


title: MuscleTR_rep2_402


title: MuscleTR_rep2_406


title: MuscleTR_rep2_401


title: MuscleTR_rep2_395


title: MuscleTR_rep2_397


title: MuscleTR_rep2_400


title: MuscleTR_rep2_392


title: MuscleTR_rep2_427


title: MuscleTR_rep2_393


title: MuscleTR_rep2_396


title: MuscleTR_rep2_394


title: MuscleTR_rep2_390


title: MuscleTR_rep2_388


title: MuscleTR_rep2_387


title: MuscleTR_rep2_383


title: MuscleTR_rep2_384


title: MuscleTR_rep2_385


title: MuscleTR_rep2_380


title: MuscleTR_rep2_386


title: MuscleTR_rep2_378


title: MuscleTR_rep2_372


title: MuscleTR_rep2_369


title: MuscleTR_rep2_371


title: MuscleTR_rep2_368


title: MuscleTR_rep2_370


title: MuscleTR_rep2_362


title: MuscleTR_rep2_358


title: MuscleTR_rep2_350


title: MuscleTR_rep2_351


title: MuscleTR_rep2_398


title: MuscleTR_rep2_343


title: MuscleTR_rep2_347


title: MuscleTR_rep2_339


title: MuscleTR_rep2_353


title: MuscleTR_rep2_346


title: MuscleTR_rep2_336


title: MuscleTR_rep2_332


title: MuscleTR_rep2_366


title: MuscleTR_rep2_334


title: MuscleTR_rep2_333


title: MuscleTR_rep2_365


title: MuscleTR_rep2_325


title: MuscleTR_rep2_322


title: MuscleTR_rep2_360


title: MuscleTR_rep2_359


title: MuscleTR_rep2_321


title: MuscleTR_rep2_318


title: MuscleTR_rep2_320


title: MuscleTR_rep2_356


title: MuscleTR_rep2_352


title: MuscleTR_rep2_342


title: MuscleTR_rep2_316


title: MuscleTR_rep2_315


title: MuscleTR_rep2_314


title: MuscleTR_rep2_317


title: MuscleTR_rep2_312


title: MuscleTR_rep2_313


title: MuscleTR_rep2_311


title: MuscleTR_rep2_337


title: MuscleTR_rep2_309


title: MuscleTR_rep2_310


title: MuscleTR_rep2_329


title: MuscleTR_rep2_331


title: MuscleTR_rep2_323


title: MuscleTR_rep2_306


title: MuscleTR_rep2_307


title: MuscleTR_rep2_300


title: MuscleTR_rep2_301


title: MuscleTR_rep2_326


title: MuscleTR_rep2_295


title: MuscleTR_rep2_299


title: MuscleTR_rep2_294


title: MuscleTR_rep2_291


title: MuscleTR_rep2_289


title: MuscleTR_rep2_290


title: MuscleTR_rep2_285


title: MuscleTR_rep2_288


title: MuscleTR_rep2_280


title: MuscleTR_rep2_287


title: MuscleTR_rep2_276


title: MuscleTR_rep2_279


title: MuscleTR_rep2_275


title: MuscleTR_rep2_308


title: MuscleTR_rep2_272


title: MuscleTR_rep2_269


title: MuscleTR_rep2_267


title: MuscleTR_rep2_268


title: MuscleTR_rep2_303


title: MuscleTR_rep2_293


title: MuscleTR_rep2_296


title: MuscleTR_rep2_262


title: MuscleTR_rep2_265


title: MuscleTR_rep2_260


title: MuscleTR_rep2_259


title: MuscleTR_rep2_257


title: MuscleTR_rep2_292


title: MuscleTR_rep2_258


title: MuscleTR_rep2_255


title: MuscleTR_rep2_253


title: MuscleTR_rep2_286


title: MuscleTR_rep2_251


title: MuscleTR_rep2_248


title: MuscleTR_rep2_249


title: MuscleTR_rep2_250


title: MuscleTR_rep2_284


title: MuscleTR_rep2_246


title: MuscleTR_rep2_235


title: MuscleTR_rep2_273


title: MuscleTR_rep2_239


title: MuscleTR_rep2_245


title: MuscleTR_rep2_242


title: MuscleTR_rep2_236


title: MuscleTR_rep2_230


title: MuscleTR_rep2_227


title: MuscleTR_rep2_229


title: MuscleTR_rep2_228


title: MuscleTR_rep2_226


title: MuscleTR_rep2_224


title: MuscleTR_rep2_223


title: MuscleTR_rep2_222


title: MuscleTR_rep2_218


title: MuscleTR_rep2_214


title: MuscleTR_rep2_216


title: MuscleTR_rep2_215


title: MuscleTR_rep2_213


title: MuscleTR_rep2_207


title: MuscleTR_rep2_208


title: MuscleTR_rep2_205


title: MuscleTR_rep2_204


title: MuscleTR_rep2_237


title: MuscleTR_rep2_203


title: MuscleTR_rep2_200


title: MuscleTR_rep2_202


title: MuscleTR_rep2_199


title: MuscleTR_rep2_196


title: MuscleTR_rep2_195


title: MuscleTR_rep2_234


title: MuscleTR_rep2_193


title: MuscleTR_rep2_194


title: MuscleTR_rep2_189


title: MuscleTR_rep2_197


title: MuscleTR_rep2_188


title: MuscleTR_rep2_187


title: MuscleTR_rep2_217


title: MuscleTR_rep2_185


title: MuscleTR_rep2_182


title: MuscleTR_rep2_179


title: MuscleTR_rep2_186


title: MuscleTR_rep2_180


title: MuscleTR_rep2_178


title: MuscleTR_rep2_176


title: MuscleTR_rep2_175


title: MuscleTR_rep2_181


title: MuscleTR_rep2_174


title: MuscleTR_rep2_172


title: MuscleTR_rep2_166


title: MuscleTR_rep2_165


title: MuscleTR_rep2_162


title: MuscleTR_rep2_163


title: MuscleTR_rep2_164


title: MuscleTR_rep2_160


title: MuscleTR_rep2_159


title: MuscleTR_rep2_161


title: MuscleTR_rep2_158


title: MuscleTR_rep2_157


title: MuscleTR_rep2_156


title: MuscleTR_rep2_153


title: MuscleTR_rep2_150


title: MuscleTR_rep2_149


title: MuscleTR_rep2_148


title: MuscleTR_rep2_147


title: MuscleTR_rep2_146


title: MuscleTR_rep2_144


title: MuscleTR_rep2_142


title: MuscleTR_rep2_138


title: MuscleTR_rep2_143


title: MuscleTR_rep2_132


title: MuscleTR_rep2_137


title: MuscleTR_rep2_134


title: MuscleTR_rep2_131


title: MuscleTR_rep2_135


title: MuscleTR_rep2_127


title: MuscleTR_rep2_124


title: MuscleTR_rep2_123


title: MuscleTR_rep2_122


title: MuscleTR_rep2_125


title: MuscleTR_rep2_115


title: MuscleTR_rep2_121


title: MuscleTR_rep2_114


title: MuscleTR_rep2_111


title: MuscleTR_rep2_112


title: MuscleTR_rep2_119


title: MuscleTR_rep2_116


title: MuscleTR_rep2_151


title: MuscleTR_rep2_107


title: MuscleTR_rep2_110


title: MuscleTR_rep2_113


title: MuscleTR_rep2_108


title: MuscleTR_rep2_106


title: MuscleTR_rep2_105


title: MuscleTR_rep2_104


title: MuscleTR_rep2_101


title: MuscleTR_rep2_100


title: MuscleTR_rep2_97


title: MuscleTR_rep2_91


title: MuscleTR_rep2_96


title: MuscleTR_rep2_90


title: MuscleTR_rep2_87


title: MuscleTR_rep2_89


title: MuscleTR_rep2_80


title: MuscleTR_rep2_85


title: MuscleTR_rep2_75


title: MuscleTR_rep2_78


title: MuscleTR_rep2_74


title: MuscleTR_rep2_77


title: MuscleTR_rep2_70


title: MuscleTR_rep2_66


title: MuscleTR_rep2_72


title: MuscleTR_rep2_67


title: MuscleTR_rep2_69


title: MuscleTR_rep2_68


title: MuscleTR_rep2_65


title: MuscleTR_rep2_58


title: MuscleTR_rep2_73


title: MuscleTR_rep2_61


title: MuscleTR_rep2_51


title: MuscleTR_rep2_50


title: MuscleTR_rep2_59


title: MuscleTR_rep2_62


title: MuscleTR_rep2_55


title: MuscleTR_rep2_52


title: MuscleTR_rep2_54


title: MuscleTR_rep2_49


title: MuscleTR_rep2_48


title: MuscleTR_rep2_83


title: MuscleTR_rep2_47


title: MuscleTR_rep2_46


title: MuscleTR_rep2_43


title: MuscleTR_rep2_42


title: MuscleTR_rep2_41


title: MuscleTR_rep2_40


title: MuscleTR_rep2_37


title: MuscleTR_rep2_38


title: MuscleTR_rep2_36


title: MuscleTR_rep2_30


title: MuscleTR_rep2_44


title: MuscleTR_rep2_35


title: MuscleTR_rep2_34


title: MuscleTR_rep2_28


title: MuscleTR_rep2_29


title: MuscleTR_rep2_31


title: MuscleTR_rep2_26


title: MuscleTR_rep2_27


title: MuscleTR_rep2_21


title: MuscleTR_rep2_22


title: MuscleTR_rep2_18


title: MuscleTR_rep2_12


title: MuscleTR_rep2_14


title: MuscleTR_rep2_17


title: MuscleTR_rep2_11


title: MuscleTR_rep2_20


title: MuscleTR_rep2_15


title: MuscleTR_rep2_16


title: MuscleTR_rep2_10


title: MuscleTR_rep2_8


title: MuscleTR_rep2_7


title: MuscleTR_rep2_4


title: MuscleTR_rep2_3


title: MuscleTR_830


title: MuscleTR_rep2_1


title: MuscleTR_832


title: MuscleTR_828


title: MuscleTR_824


title: MuscleTR_820


title: MuscleTR_822


title: MuscleTR_826


title: MuscleTR_825


title: MuscleTR_821


title: MuscleTR_823


title: MuscleTR_rep2_24


title: MuscleTR_819


title: MuscleTR_818


title: MuscleTR_815


title: MuscleTR_812


title: MuscleTR_810


title: MuscleTR_808


title: MuscleTR_807


title: MuscleTR_809


title: MuscleTR_813


title: MuscleTR_816


title: MuscleTR_806


title: MuscleTR_814


title: MuscleTR_803


title: MuscleTR_rep2_45


title: MuscleTR_802


title: MuscleTR_801


title: MuscleTR_799


title: MuscleTR_800


title: MuscleTR_795


title: MuscleTR_798


title: MuscleTR_794


title: MuscleTR_790


title: MuscleTR_784


title: MuscleTR_786


title: MuscleTR_787


title: MuscleTR_788


title: MuscleTR_783


title: MuscleTR_782


title: MuscleTR_785


title: MuscleTR_791


title: MuscleTR_781


title: MuscleTR_774


title: MuscleTR_777


title: MuscleTR_775


title: MuscleTR_769


title: MuscleTR_763


title: MuscleTR_779


title: MuscleTR_772


title: MuscleTR_778


title: MuscleTR_762


title: MuscleTR_776


title: MuscleTR_765


title: MuscleTR_760


title: MuscleTR_767


title: MuscleTR_759


title: MuscleTR_797


title: MuscleTR_757


title: MuscleTR_758


title: MuscleTR_793


title: MuscleTR_756


title: MuscleTR_755


title: MuscleTR_753


title: MuscleTR_749


title: MuscleTR_752


title: MuscleTR_754


title: MuscleTR_751


title: MuscleTR_768


title: MuscleTR_750


title: MuscleTR_748


title: MuscleTR_742


title: MuscleTR_736


title: MuscleTR_741


title: MuscleTR_738


title: MuscleTR_740


title: MuscleTR_739


title: MuscleTR_745


title: MuscleTR_743


title: MuscleTR_735


title: MuscleTR_744


title: MuscleTR_737


title: MuscleTR_734


title: MuscleTR_729


title: MuscleTR_728


title: MuscleTR_727


title: MuscleTR_726


title: MuscleTR_724


title: MuscleTR_746


title: MuscleTR_721


title: MuscleTR_722


title: MuscleTR_717


title: MuscleTR_716


title: MuscleTR_715


title: MuscleTR_719


title: MuscleTR_714


title: MuscleTR_733


title: MuscleTR_730


title: MuscleTR_712


title: MuscleTR_713


title: MuscleTR_710


title: MuscleTR_707


title: MuscleTR_708


title: MuscleTR_703


title: MuscleTR_732


title: MuscleTR_699


title: MuscleTR_725


title: MuscleTR_698


title: MuscleTR_694


title: MuscleTR_700


title: MuscleTR_696


title: MuscleTR_693


title: MuscleTR_723


title: MuscleTR_692


title: MuscleTR_690


title: MuscleTR_688


title: MuscleTR_689


title: MuscleTR_687


title: MuscleTR_685


title: MuscleTR_684


title: MuscleTR_682


title: MuscleTR_711


title: MuscleTR_709


title: MuscleTR_681


title: MuscleTR_705


title: MuscleTR_702


title: MuscleTR_701


title: MuscleTR_679


title: MuscleTR_677


title: MuscleTR_668


title: MuscleTR_669


title: MuscleTR_670


title: MuscleTR_665


title: MuscleTR_659


title: MuscleTR_658


title: MuscleTR_691


title: MuscleTR_656


title: MuscleTR_648


title: MuscleTR_653


title: MuscleTR_655


title: MuscleTR_680


title: MuscleTR_647


title: MuscleTR_676


title: MuscleTR_673


title: MuscleTR_640


title: MuscleTR_645


title: MuscleTR_646


title: MuscleTR_675


title: MuscleTR_643


title: MuscleTR_664


title: MuscleTR_666


title: MuscleTR_644


title: MuscleTR_642


title: MuscleTR_634


title: MuscleTR_639


title: MuscleTR_635


title: MuscleTR_641


title: MuscleTR_636


title: MuscleTR_638


title: MuscleTR_661


title: MuscleTR_631


title: MuscleTR_637


title: MuscleTR_630


title: MuscleTR_629


title: MuscleTR_652


title: MuscleTR_649


title: MuscleTR_628


title: MuscleTR_627


title: MuscleTR_626


title: MuscleTR_624


title: MuscleTR_622


title: MuscleTR_621


title: MuscleTR_620


title: MuscleTR_614


title: MuscleTR_612


title: MuscleTR_618


title: MuscleTR_616


title: MuscleTR_617


title: MuscleTR_611


title: MuscleTR_619


title: MuscleTR_610


title: MuscleTR_608


title: MuscleTR_604


title: MuscleTR_609


title: MuscleTR_606


title: MuscleTR_605


title: MuscleTR_602


title: MuscleTR_601


title: MuscleTR_600


title: MuscleTR_597


title: MuscleTR_625


title: MuscleTR_599


title: MuscleTR_598


title: MuscleTR_623


title: MuscleTR_594


title: MuscleTR_590


title: MuscleTR_593


title: MuscleTR_592


title: MuscleTR_589


title: MuscleTR_596


title: MuscleTR_587


title: MuscleTR_588


title: MuscleTR_580


title: MuscleTR_582


title: MuscleTR_603


title: MuscleTR_585


title: MuscleTR_586


title: MuscleTR_584


title: MuscleTR_579


title: MuscleTR_574


title: MuscleTR_572


title: MuscleTR_571


title: MuscleTR_575


title: MuscleTR_578


title: MuscleTR_568


title: MuscleTR_576


title: MuscleTR_573


title: MuscleTR_570


title: MuscleTR_564


title: MuscleTR_566


title: MuscleTR_567


title: MuscleTR_565


title: MuscleTR_563


title: MuscleTR_560


title: MuscleTR_557


title: MuscleTR_559


title: MuscleTR_558


title: MuscleTR_561


title: MuscleTR_556


title: MuscleTR_554


title: MuscleTR_552


title: MuscleTR_548


title: MuscleTR_549


title: MuscleTR_555


title: MuscleTR_551


title: MuscleTR_546


title: MuscleTR_543


title: MuscleTR_542


title: MuscleTR_541


title: MuscleTR_553


title: MuscleTR_538


title: MuscleTR_537


title: MuscleTR_545


title: MuscleTR_539


title: MuscleTR_550


title: MuscleTR_534


title: MuscleTR_569


title: MuscleTR_535


title: MuscleTR_531


title: MuscleTR_533


title: MuscleTR_529


title: MuscleTR_528


title: MuscleTR_532


title: MuscleTR_527


title: MuscleTR_526


title: MuscleTR_525


title: MuscleTR_522


title: MuscleTR_521


title: MuscleTR_519


title: MuscleTR_518


title: MuscleTR_514


title: MuscleTR_516


title: MuscleTR_512


title: MuscleTR_517


title: MuscleTR_511


title: MuscleTR_510


title: MuscleTR_507


title: MuscleTR_508


title: MuscleTR_504


title: MuscleTR_503


title: MuscleTR_505


title: MuscleTR_501


title: MuscleTR_498


title: MuscleTR_496


title: MuscleTR_497


title: MuscleTR_502


title: MuscleTR_493


title: MuscleTR_499


title: MuscleTR_500


title: MuscleTR_492


title: MuscleTR_490


title: MuscleTR_489


title: MuscleTR_488


title: MuscleTR_491


title: MuscleTR_487


title: MuscleTR_484


title: MuscleTR_485


title: MuscleTR_486


title: MuscleTR_483


title: MuscleTR_506


title: MuscleTR_481


title: MuscleTR_480


title: MuscleTR_479


title: MuscleTR_478


title: MuscleTR_468


title: MuscleTR_475


title: MuscleTR_470


title: MuscleTR_474


title: MuscleTR_476


title: MuscleTR_467


title: MuscleTR_465


title: MuscleTR_463


title: MuscleTR_461


title: MuscleTR_456


title: MuscleTR_459


title: MuscleTR_462


title: MuscleTR_458


title: MuscleTR_460


title: MuscleTR_447


title: MuscleTR_455


title: MuscleTR_451


title: MuscleTR_454


title: MuscleTR_450


title: MuscleTR_445


title: MuscleTR_435


title: MuscleTR_433


title: MuscleTR_438


title: MuscleTR_436


title: MuscleTR_425


title: MuscleTR_437


title: MuscleTR_430


title: MuscleTR_428


title: MuscleTR_423


title: MuscleTR_441


title: MuscleTR_439


title: MuscleTR_422


title: MuscleTR_432


title: MuscleTR_440


title: MuscleTR_424


title: MuscleTR_421


title: MuscleTR_418


title: MuscleTR_414


title: MuscleTR_416


title: MuscleTR_415


title: MuscleTR_413


title: MuscleTR_412


title: MuscleTR_411


title: MuscleTR_417


title: MuscleTR_410


title: MuscleTR_444


title: MuscleTR_408


title: MuscleTR_419


title: MuscleTR_406


title: MuscleTR_405


title: MuscleTR_403


title: MuscleTR_401


title: MuscleTR_400


title: MuscleTR_399


title: MuscleTR_395


title: MuscleTR_397


title: MuscleTR_398


title: MuscleTR_394


title: MuscleTR_392


title: MuscleTR_388


title: MuscleTR_389


title: MuscleTR_390


title: MuscleTR_396


title: MuscleTR_391


title: MuscleTR_387


title: MuscleTR_386


title: MuscleTR_384


title: MuscleTR_374


title: MuscleTR_382


title: MuscleTR_380


title: MuscleTR_376


title: MuscleTR_375


title: MuscleTR_373


title: MuscleTR_370


title: MuscleTR_368


title: MuscleTR_371


title: MuscleTR_372


title: MuscleTR_369


title: MuscleTR_367


title: MuscleTR_363


title: MuscleTR_366


title: MuscleTR_358


title: MuscleTR_357


title: MuscleTR_365


title: MuscleTR_364


title: MuscleTR_359


title: MuscleTR_348


title: MuscleTR_361


title: MuscleTR_356


title: MuscleTR_354


title: MuscleTR_352


title: MuscleTR_381


title: MuscleTR_377


title: MuscleTR_346


title: MuscleTR_342


title: MuscleTR_347


title: MuscleTR_353


title: MuscleTR_344


title: MuscleTR_339


title: MuscleTR_340


title: MuscleTR_337


title: MuscleTR_336


title: MuscleTR_338


title: MuscleTR_335


title: MuscleTR_341


title: MuscleTR_333


title: MuscleTR_334


title: MuscleTR_350


title: MuscleTR_328


title: MuscleTR_330


title: MuscleTR_331


title: MuscleTR_327


title: MuscleTR_326


title: MuscleTR_325


title: MuscleTR_322


title: MuscleTR_321


title: MuscleTR_316


title: MuscleTR_315


title: MuscleTR_314


title: MuscleTR_313


title: MuscleTR_311


title: MuscleTR_310


title: MuscleTR_308


title: MuscleTR_307


title: MuscleTR_305


title: MuscleTR_306


title: MuscleTR_304


title: MuscleTR_332


title: MuscleTR_303


title: MuscleTR_299


title: MuscleTR_301


title: MuscleTR_318


title: MuscleTR_319


title: MuscleTR_294


title: MuscleTR_317


title: MuscleTR_298


title: MuscleTR_300


title: MuscleTR_297


title: MuscleTR_324


title: MuscleTR_289


title: MuscleTR_291


title: MuscleTR_293


title: MuscleTR_287


title: MuscleTR_288


title: MuscleTR_286


title: MuscleTR_302


title: MuscleTR_283


title: MuscleTR_281


title: MuscleTR_280


title: MuscleTR_296


title: MuscleTR_295


title: MuscleTR_276


title: MuscleTR_277


title: MuscleTR_274


title: MuscleTR_275


title: MuscleTR_273


title: MuscleTR_272


title: MuscleTR_271


title: MuscleTR_270


title: MuscleTR_290


title: MuscleTR_269


title: MuscleTR_266


title: MuscleTR_268


title: MuscleTR_264


title: MuscleTR_285


title: MuscleTR_265


title: MuscleTR_260


title: MuscleTR_261


title: MuscleTR_282


title: MuscleTR_278


title: MuscleTR_279


title: MuscleTR_256


title: MuscleTR_251


title: MuscleTR_250


title: MuscleTR_246


title: MuscleTR_247


title: MuscleTR_267


title: MuscleTR_245


title: MuscleTR_244


title: MuscleTR_241


title: MuscleTR_242


title: MuscleTR_238


title: MuscleTR_243


title: MuscleTR_237


title: MuscleTR_233


title: MuscleTR_232


title: MuscleTR_259


title: MuscleTR_226


title: MuscleTR_262


title: MuscleTR_227


title: MuscleTR_263


title: MuscleTR_234


title: MuscleTR_225


title: MuscleTR_228


title: MuscleTR_231


title: MuscleTR_222


title: MuscleTR_252


title: MuscleTR_223


title: MuscleTR_254


title: MuscleTR_230


title: MuscleTR_218


title: MuscleTR_220


title: MuscleTR_253


title: MuscleTR_221


title: MuscleTR_212


title: MuscleTR_207


title: MuscleTR_239


title: MuscleTR_208


title: MuscleTR_206


title: MuscleTR_205


title: MuscleTR_214


title: MuscleTR_216


title: MuscleTR_217


title: MuscleTR_200


title: MuscleTR_210


title: MuscleTR_196


title: MuscleTR_202


title: MuscleTR_203


title: MuscleTR_204


title: MuscleTR_199


title: MuscleTR_219


title: MuscleTR_189


title: MuscleTR_191


title: MuscleTR_195


title: MuscleTR_187


title: MuscleTR_185


title: MuscleTR_184


title: MuscleTR_194


title: MuscleTR_183


title: MuscleTR_193


title: MuscleTR_190


title: MuscleTR_186


title: MuscleTR_215


title: MuscleTR_182


title: MuscleTR_198


title: MuscleTR_181


title: MuscleTR_175


title: MuscleTR_177


title: MuscleTR_176


title: MuscleTR_171


title: MuscleTR_170


title: MuscleTR_167


title: MuscleTR_179


title: MuscleTR_178


title: MuscleTR_164


title: MuscleTR_169


title: MuscleTR_168


title: MuscleTR_174


title: MuscleTR_158


title: MuscleTR_160


title: MuscleTR_166


title: MuscleTR_161


title: MuscleTR_157


title: MuscleTR_154


title: MuscleTR_163


title: MuscleTR_152


title: MuscleTR_153


title: MuscleTR_150


title: MuscleTR_149


title: MuscleTR_151


title: MuscleTR_148


title: MuscleTR_147


title: MuscleTR_145


title: MuscleTR_146


title: MuscleTR_144


title: MuscleTR_142


title: MuscleTR_140


title: MuscleTR_137


title: MuscleTR_139


title: MuscleTR_138


title: MuscleTR_134


title: MuscleTR_136


title: MuscleTR_130


title: MuscleTR_135


title: MuscleTR_129


title: MuscleTR_127


title: MuscleTR_124


title: MuscleTR_122


title: MuscleTR_125


title: MuscleTR_126


title: MuscleTR_123


title: MuscleTR_128


title: MuscleTR_120


title: MuscleTR_121


title: MuscleTR_119


title: MuscleTR_118


title: MuscleTR_114


title: MuscleTR_116


title: MuscleTR_117


title: MuscleTR_115


title: MuscleTR_113


title: MuscleTR_109


title: MuscleTR_105


title: MuscleTR_111


title: MuscleTR_107


title: MuscleTR_106


title: MuscleTR_104


title: MuscleTR_103


title: MuscleTR_131


title: MuscleTR_101


title: MuscleTR_99


title: MuscleTR_98


title: MuscleTR_100


title: MuscleTR_96


title: MuscleTR_97


title: MuscleTR_85


title: MuscleTR_91


title: MuscleTR_83


title: MuscleTR_89


title: MuscleTR_86


title: MuscleTR_88


title: MuscleTR_81


title: MuscleTR_94


title: MuscleTR_80


title: MuscleTR_82


title: MuscleTR_78


title: MuscleTR_79


title: MuscleTR_102


title: MuscleTR_77


title: MuscleTR_73


title: MuscleTR_64


title: MuscleTR_74


title: MuscleTR_76


title: MuscleTR_75


title: MuscleTR_72


title: MuscleTR_69


title: MuscleTR_67


title: MuscleTR_71


title: MuscleTR_62


title: MuscleTR_61


title: MuscleTR_63


title: MuscleTR_59


title: MuscleTR_68


title: MuscleTR_58


title: MuscleTR_66


title: MuscleTR_57


title: MuscleTR_54


title: MuscleTR_51


title: MuscleTR_56


title: MuscleTR_50


title: MuscleTR_52


title: MuscleTR_45


title: MuscleTR_46


title: MuscleTR_49


title: MuscleTR_44


title: MuscleTR_43


title: MuscleTR_42


title: MuscleTR_41


title: MuscleTR_40


title: MuscleTR_34


title: MuscleTR_35


title: MuscleTR_37


title: MuscleTR_38


title: MuscleTR_39


title: MuscleTR_31


title: MuscleTR_33


title: MuscleTR_32


title: MuscleTR_28


title: MuscleTR_29


title: MuscleTR_26


title: MuscleTR_27


title: MuscleTR_23


title: MuscleTR_21


title: MuscleTR_20


title: MuscleTR_19


title: MuscleTR_16


title: MuscleTR_15


title: MuscleTR_17


title: MuscleTR_14


title: MuscleTR_13


title: MuscleTR_12


title: MuscleTR_11


title: MuscleTR_9


title: MuscleTR_10


title: MuscleTR_6


title: MuscleTR_24


title: MuscleTR_4


title: MuscleTR_3


title: SpMusCtrl_534

source_name: spleen


title: MuscleTR_5


title: MuscleTR_2


title: SpMusCtrl_533


title: SpMusCtrl_530


title: SpMusCtrl_531


title: SpMusCtrl_525


title: SpMusCtrl_528


title: SpMusCtrl_520


title: SpMusCtrl_519


title: SpMusCtrl_526


title: MuscleTR_22


title: SpMusCtrl_518


title: SpMusCtrl_515


title: SpMusCtrl_505


title: SpMusCtrl_506


title: SpMusCtrl_503


title: MuscleTR_18


title: SpMusCtrl_517


title: SpMusCtrl_514


title: SpMusCtrl_497


title: MuscleTR_7


title: SpMusCtrl_502


title: SpMusCtrl_495


title: SpMusCtrl_494


title: SpMusCtrl_492


title: SpMusCtrl_488


title: SpMusCtrl_486


title: SpMusCtrl_489


title: SpMusCtrl_487


title: SpMusCtrl_523


title: SpMusCtrl_482


title: SpMusCtrl_475


title: SpMusCtrl_472


title: SpMusCtrl_471


title: SpMusCtrl_468


title: SpMusCtrl_463


title: SpMusCtrl_467


title: SpMusCtrl_461


title: SpMusCtrl_460


title: SpMusCtrl_510


title: SpMusCtrl_458


title: SpMusCtrl_452


title: SpMusCtrl_453


title: SpMusCtrl_455


title: SpMusCtrl_451


title: SpMusCtrl_442


title: SpMusCtrl_447


title: SpMusCtrl_446


title: SpMusCtrl_448


title: SpMusCtrl_445


title: SpMusCtrl_437


title: SpMusCtrl_441


title: SpMusCtrl_483


title: SpMusCtrl_433


title: SpMusCtrl_431


title: SpMusCtrl_428


title: SpMusCtrl_435


title: SpMusCtrl_507


title: SpMusCtrl_420


title: SpMusCtrl_422


title: SpMusCtrl_418


title: SpMusCtrl_412


title: SpMusCtrl_414


title: SpMusCtrl_411


title: SpMusCtrl_410


title: SpMusCtrl_419


title: SpMusCtrl_404


title: SpMusCtrl_408


title: SpMusCtrl_402


title: SpMusCtrl_401


title: SpMusCtrl_396


title: SpMusCtrl_391


title: SpMusCtrl_434


title: SpMusCtrl_398


title: SpMusCtrl_387


title: SpMusCtrl_386


title: SpMusCtrl_384


title: SpMusCtrl_427


title: SpMusCtrl_382


title: SpMusCtrl_379


title: SpMusCtrl_425


title: SpMusCtrl_378


title: SpMusCtrl_376


title: SpMusCtrl_370


title: SpMusCtrl_369


title: SpMusCtrl_363


title: SpMusCtrl_407


title: SpMusCtrl_357


title: SpMusCtrl_356


title: SpMusCtrl_397


title: SpMusCtrl_353


title: SpMusCtrl_352


title: SpMusCtrl_350


title: SpMusCtrl_389


title: SpMusCtrl_348


title: SpMusCtrl_347


title: SpMusCtrl_345


title: SpMusCtrl_344


title: SpMusCtrl_343


title: SpMusCtrl_341


title: SpMusCtrl_340


title: SpMusCtrl_337


title: SpMusCtrl_334


title: SpMusCtrl_330


title: SpMusCtrl_323


title: SpMusCtrl_361


title: SpMusCtrl_316


title: SpMusCtrl_322


title: SpMusCtrl_318


title: SpMusCtrl_354


title: SpMusCtrl_310


title: SpMusCtrl_304


title: SpMusCtrl_301


title: SpMusCtrl_303


title: SpMusCtrl_296


title: SpMusCtrl_299


title: SpMusCtrl_292


title: SpMusCtrl_324


title: SpMusCtrl_325


title: SpMusCtrl_290


title: SpMusCtrl_326


title: SpMusCtrl_285


title: SpMusCtrl_331


title: SpMusCtrl_293


title: SpMusCtrl_311


title: SpMusCtrl_309


title: SpMusCtrl_283


title: SpMusCtrl_274


title: SpMusCtrl_279


title: SpMusCtrl_306


title: SpMusCtrl_280


title: SpMusCtrl_284


title: SpMusCtrl_272


title: SpMusCtrl_268


title: SpMusCtrl_399


title: SpMusCtrl_297


title: SpMusCtrl_302


title: SpMusCtrl_261


title: SpMusCtrl_294


title: SpMusCtrl_257


title: SpMusCtrl_258


title: SpMusCtrl_259


title: SpMusCtrl_254


title: SpMusCtrl_252


title: SpMusCtrl_251


title: SpMusCtrl_250


title: SpMusCtrl_246


title: SpMusCtrl_245


title: SpMusCtrl_243


title: SpMusCtrl_244


title: SpMusCtrl_239


title: SpMusCtrl_240


title: SpMusCtrl_235


title: SpMusCtrl_227


title: SpMusCtrl_231


title: SpMusCtrl_226


title: SpMusCtrl_237


title: SpMusCtrl_232


title: SpMusCtrl_234


title: SpMusCtrl_224


title: SpMusCtrl_220


title: SpMusCtrl_213


title: SpMusCtrl_214


title: SpMusCtrl_212


title: SpMusCtrl_215


title: SpMusCtrl_218


title: SpMusCtrl_210


title: SpMusCtrl_206


title: SpMusCtrl_203


title: SpMusCtrl_204


title: SpMusCtrl_201


title: SpMusCtrl_197


title: SpMusCtrl_196


title: SpMusCtrl_242


title: SpMusCtrl_230


title: SpMusCtrl_183


title: SpMusCtrl_182


title: SpMusCtrl_190


title: SpMusCtrl_178


title: SpMusCtrl_225


title: SpMusCtrl_181


title: SpMusCtrl_180


title: SpMusCtrl_194


title: SpMusCtrl_177


title: SpMusCtrl_219


title: SpMusCtrl_170


title: SpMusCtrl_179


title: SpMusCtrl_169


title: SpMusCtrl_166


title: SpMusCtrl_168


title: SpMusCtrl_167


title: SpMusCtrl_154


title: SpMusCtrl_163


title: SpMusCtrl_150


title: SpMusCtrl_156


title: SpMusCtrl_155


title: SpMusCtrl_160


title: SpMusCtrl_147


title: SpMusCtrl_142


title: SpMusCtrl_139


title: SpMusCtrl_138


title: SpMusCtrl_137


title: SpMusCtrl_132


title: SpMusCtrl_131


title: SpMusCtrl_130


title: SpMusCtrl_124


title: SpMusCtrl_136


title: SpMusCtrl_122


title: SpMusCtrl_125


title: SpMusCtrl_121


title: SpMusCtrl_114


title: SpMusCtrl_113


title: SpMusCtrl_116


title: SpMusCtrl_110


title: SpMusCtrl_109


title: SpMusCtrl_108


title: SpMusCtrl_107


title: SpMusCtrl_105


title: SpMusCtrl_102


title: SpMusCtrl_101


title: SpMusCtrl_79


title: SpMusCtrl_87


title: SpMusCtrl_88


title: SpMusCtrl_86


title: SpMusCtrl_85


title: SpMusCtrl_92


title: SpMusCtrl_84


title: SpMusCtrl_78


title: SpMusCtrl_75


title: SpMusCtrl_65


title: SpMusCtrl_72


title: SpMusCtrl_120


title: SpMusCtrl_66


title: SpMusCtrl_60


title: SpMusCtrl_59


title: SpMusCtrl_58


title: SpMusCtrl_57


title: SpMusCtrl_61


title: SpMusCtrl_48


title: SpMusCtrl_54


title: SpMusCtrl_56


title: SpMusCtrl_44


title: SpMusCtrl_42


title: SpMusCtrl_43


title: SpMusCtrl_394


title: SpMusCtrl_34


title: SpMusCtrl_40


title: SpMusCtrl_23


title: SpMusCtrl_31


title: SpMusCtrl_16


title: SpMusCtrl_25


title: SpMusCtrl_14


title: SpMusCtrl_30


title: SpMusCtrl_8


title: SpMusCtrl_364


title: SpMusCtrl_29


title: SpMusCtrl_7


title: SpMusCtrl_6


title: SpMusCtrl_1


title: SpMusCtrl_429


title: SpMusCtrl_12


title: SpMusCtrl_18


title: SpMusCtrl_4


title: IP_Male_2

city: Cold Spring Harbor

first: Jessica

last: Tollkuhn

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
Reads were base trimmed to 76bp, adapter trimmed, and quality filtered at Q > 30 using an internal Fast-X toolkit (http://hannonlab.cshl.edu/fastx_toolkit/ (Galaxy Version 1.0.1)).
Filtered reads were mapped to the mm10 reference genome using STAR (Galaxy Version 0.0.1) (Dobin et al., 2013; Yue et al., 2014).
The number of reads mapped to each gene was calculated using featureCounts (Galaxy Version 2.4.5-p1)(Liao et al., 2014).
Differential expression between IP and input samples was determined using DESeq2 with an FDR of 0.1 (Galaxy Version 1.0.0)(Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2: tab-delimited file with differential expression data between IP and input samples as derived from DESeq2
Supplementary_files_format_and_content: Normalized Counts: tab-delimited file with normalized count values for each sample as derived from DESeq2

source_name: Central Amygdala-lateral division

extract_protocol:
Microdissected tissue from 8-12 mice was pooled and frozen at -80oC for each sample. Tissue homogenization, immunoprecipitation of polysomes from SOM+ neurons, and mRNA extraction was performed as previously described (Heiman et al., 2014; Sanz et al., 2009).
Libraries were prepared according to instructions provided by NuGEN Ovation RNA-Seq kits (7102 and0344)

value: Central Amygdala-lateral division

value: SOM+ neurons

value: Male

tag: pulldown

value: IP


title: IP_Female_4

tag: cell type

value: Female


title: IP_Female_2


title: IP_Male_5


title: IP_Male_6


title: IP_Female_1


title: IP_Male_3


title: A549-KO3_Virus C

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description: The HTA 2.0 microarray data were normalized using the sst-rma approach implemented in The Affymetrix® Expression Console™ Software (version 1.4.1.46) for gene expression analysis in log2 scale.Only protein-coding genes were considered for the subsequent downstream evaluation.

hyb_protocol: Samples were hybridized to Affymetrix Human Transcriptome 2.0 array (Affymetrix) for 16 hours at 45˚C with rotation at 60rpm.

scan_protocol: Array scanning was performed using the FS450_0001 fluidics protocol and scanned using an Affymetrix 3000 7G scanncer according to the manufacturer's instruction (Affymetrix).

data_processing: All CEL files from the 12 total RNA samples hybridized to Affymetrix GeneChip Human Transcriptome 2.0 Arrays were imported into Affymetrix Expression Console (EC) for normalization and ensuring that the relative log expression signal (RLE) was comparable across all samples.  CHP files generated from Expression Console (EC) were imported into TAC3.0 software to obtain the list of differentially expressed gene in the dataset. The HTA 2.0 microarray data were normalized using the sst-rma approach implemented in The Affymetrix® Expression Console™ Software (version 1.4.1.46) for gene expression analysis in log2 scale. Only protein-coding genes were considered for the subsequent downstream evaluation. Differential gene expression between conditions was evaluated by Student’s t-test and the p-values were adjusted with Benjamini and Hochberg. Significantly differentially-expressed genes were identified with adjusted p-value < 0.05 and |log2(FC)| > 0.5. All the above statistical analysis was implemented using R version 3.1.1.

source_name: A549-KO3 cells, H1N1 virus infected, replicate C

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: A549 and A549-KO3 cells were seeded in 12-well plates for overnight culture with DMEM supplemented with 10% FBS and 1% Penn-Strep.

extract_protocol: Total RNA was extracted from 0.5 million cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. The genomic DNA was removed by in-column digestion using RNase-free DNase Set (Qiagen).

treatment_protocol: A549 and A549-KO3 cells were infected with either influenza A virus  (H1N1/A/Puerto Rico/8/34) at the MOI=0.001 or mock infected for 24 hours in triplicate wells.

tag: cell line

tag: agent

value: H1N1/A/Puerto Rico/8/34


title: A549_Mock C

source_name: A549 cells, mock infected, replicate C

value: mock


title: A549-KO3_Mock A

source_name: A549-KO3 cells, mock infected, replicate A


title: prostate tumor treated patient 507_focus-c16

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

hyb_protocol: Hybridization was performed according to Affymetrix protocols.

data_processing:
To obtain the signal values, chips were analyzed using Robust Multichip Average (RMA) method that includes background correction, quantile normalization and summarization of signal using median polish algorithm
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

source_name: prostate, tumor, treated

label_protocol: cDNA was prepared and labeled using the NuGEN Encore Biotin Module

growth_protocol: Tumor tissue was acquired from men undergoing radical prostatectomy for intermediate-risk localized prostate cancer.

extract_protocol: Total RNA was co-purified with genomic DNA from laser capture microdissected tissue using the Qiagen FFPE AllPrep kit.

treatment_protocol: Untreated tumor tissue was acquired from men receiving standard of care surgery. Treated tumor was collected from men receiving 24 weeks neoadjuvant androgen deprivation therapy (LHRHa plus abiraterone acetate plus prednisone)

value: prostate

tag: treatment group

value: treated


title: prostate tumor treated patient 516_focus-c7

scan_protocol: Hybridization was performed according to Affymetrix protocols.


title: A549_Virus B

source_name: A549 cells, H1N1 virus infected, replicate B


title: A549_Virus C

source_name: A549 cells, H1N1 virus infected, replicate C


title: A549-KO3_Virus B

source_name: A549-KO3 cells, H1N1 virus infected, replicate B


title: A549_Virus A

source_name: A549 cells, H1N1 virus infected, replicate A


title: prostate tumor treated patient 007_focus-c20


title: prostate tumor treated patient 505_focus-c20


title: prostate tumor treated patient 006_focus-c21


title: A549-KO3_Virus A

source_name: A549-KO3 cells, H1N1 virus infected, replicate A


title: A549-KO3_Mock B

source_name: A549-KO3 cells, mock infected, replicate B


title: prostate tumor treated patient 513_focus-d16


title: A549-KO3_Mock C

source_name: A549-KO3 cells, mock infected, replicate C


title: A549_Mock B

source_name: A549 cells, mock infected, replicate B


title: prostate tumor treated patient 510_focus-c13


title: A549_Mock A

source_name: A549 cells, mock infected, replicate A


title: prostate tumor treated patient 003_focus-c12f1


title: prostate tumor treated patient 003_focus-c12f2


title: prostate tumor treated patient 523_focus-s


title: prostate tumor treated patient 004_focus-a14


title: prostate tumor treated patient 516_focus-c12


title: prostate tumor treated patient 004_focus-a10


title: prostate tumor treated patient 501_focus-c20


title: prostate tumor treated patient 501_focus-c16


title: prostate tumor treated patient 513_focus-d15


title: prostate tumor treated patient 523_focus-q


title: prostate tumor treated patient 506_focus-c15


title: Aska shCt ATAC rep2

first: Cigall

last: Kadoch

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
ATAC-seq reads were processed to the human reference genome (hg19) as previously described (Buenrostro et al., 2013).
Briefly, paired-end reads were trimmed to 30bp and paired using Trimmomatic 0.35 (Bolger et al., 2014), and then mapped to hg19 using Bowtie2 version 2.1.0 with parameter -X2000 (Langmead and Salzberg, 2012). Mapped reads were subsequently filtered for duplicate reads using Picard MarkDuplicates (http://broadinstitute.github.io/picard). Reads were filtered to remove reads that overlap with ENCODE blacklisted regions (Consortium, 2012).
Tracks of ATAC-seq were generated using bedtools genomeCoverageBed with parameters -pc -bg and scaled to be per million reads using map counts generated by samtools view function with parameters -c -f 67. Tracks were generated on merged biological duplicate experiments when performed.
Genome_build: hg19

source_name: Aska shCt ATAC-seq

growth_protocol: All cell lines were cultured in DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10-20% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Cells were harvested following 48-hour exposure to lentivirus and 5 days of selection with 2 µg/ml of puromycin and ATAC-seq experiments were performed as previously described (Buenrostro et al., 2015).
All library prep and sequencing were 75bp paired end on Illuminia Nextseq 500

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). The cells were harvested following 48-hour exposure to the lenti-virus and 5-day selection with 2 μg/ml of puromycin.

value: Aska

value: Synovial sarcoma (SS) cell line

tag: infected with

value: shControl


title: Aska shSSX ATAC rep1

source_name: Aska shSSX ATAC-seq

value: shSSX vector


title: Aska-Del47 shSSX ATAC rep1

source_name: Aska-Del47 shSSX ATAC-seq


title: Aska-Del47 shCt ATAC rep1

source_name: Aska-Del47 shCt ATAC-seq


title: Aska shSSX ATAC rep2


title: Aska-Del47 shCt ATAC rep2


title: Aska shCt ATAC rep1


title: INPUT_MCF10A_ChIP-seq_siSA2

city: Madrid

first: Ana

last: Losada

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology Programme

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description: Digested/Ligated genomic DNA

data_processing:
ChIP-SEQ processing. Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 (2.3.3.1) under default parameters. Unmapped reads were removed using samtools (version 1.3.1) running 'samtools view -F 4'. Reads were sorted and replicates removed using picardtools (version 1.60). Peak calling was performed using macs2 (version 2.1.1.20160309) setting following parameters: '-q 0.05' and  '-extsize (value obtained from macs2 predictd step)' and using input as the control.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigwig files were generated using deeptools (version 2.5) 'bamcoverage' tool converting processed BAM files to bigwig. The conversion was done setting 'scaleFactor' parameter calculated using normalization algorithm from: Bin Hu, Naomi Petela, Alexander Kurze, Kok-Lung Chan, Christophe Chapard, Kim Nasmyth; Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq, Nucleic Acids Research, Volume 43, Issue 20, 16 November 2015, Pages e132, https://doi.org/10.1093/nar/gkv670.

source_name: Human Mammary Epithelial Cells

growth_protocol: MCF10A cells were grown in DMEM/F12 supplemented with 20ng/ml of EGF, 0.5mg/ml hydrocortisone, 100ng/ml of cholera toxin, 10mg/ml of insulin and 5% of horse serum.

extract_protocol:
IP step of the experiment was performed adding 20% of mouse chromatin to human chromatin (600ug)- 720ug in total per replicate.  72Ug of antibody was used per replicate.
Samples went through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7645). Adapter-ligated library was completed by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Median fragment size is 360 bp from which 120 bp correspond to adaptor sequences. Library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: Cells were transfected with 50 nM onTARGETplus SMARTpool STAG2 siRNAs (Dharmacon L-021351) at seeding in high confluency  using DharmaFECT reagent 1.

value: Transformed nontumorigenic

tag: experiment

value: ChIP-SEQ

tag: treatment

value: STAG2 siRNAs

tag: chip antibody


title: CRL7250 SS18 ATAC

source_name: CRL7250 SS18 ATAC

value: fibroblast cell line


title: CRL7250 SS18-SSX ATAC

source_name: CRL7250 SS18-SSX ATAC


title: INPUT_MCF10A_ChIP-seq_siSA1

description: Digested/Ligated genomic DNA

treatment_protocol: Cells were transfected with 50 nM onTARGETplus SMARTpool STAG1 siRNAs at seeding in high confluency (Dharmacon L-010638)  using DharmaFECT reagent 1.

value: STAG1 siRNAs


title: SA2_MCF10A_ChIP-seq_siSA2_Rep_2

description: Digested/Ligated genomic DNA

value: custom made antibody for SA2 (STAG2)


title: SA1_MCF10A_ChIP-seq_siSA2_Rep_2

description: Digested/Ligated genomic DNA

value: custom made antibody for SA1 (STAG1)


title: SA2_MCF10A_ChIP-seq_siSA2_Rep_1

description: Digested/Ligated genomic DNA


title: INPUT_MCF10A_ChIP-seq_Control

description: Digested/Ligated genomic DNA


title: SA2_MCF10A_ChIP-seq_Control_Rep_2

description: Digested/Ligated genomic DNA


title: SA2_MCF10A_ChIP-seq_siSA1_Rep_2

description: Digested/Ligated genomic DNA


title: SA2_MCF10A_ChIP-seq_siSA1_Rep_1

description: Digested/Ligated genomic DNA


title: prostate tumor treated patient 518_focus-c12

source_name: prostate, tumor, treated


title: SA1_MCF10A_ChIP-seq_siSA1_Rep_2

description: Digested/Ligated genomic DNA


title: SA1_MCF10A_ChIP-seq_siSA2_Rep_1

description: Digested/Ligated genomic DNA


title: prostate tumor control patient2

source_name: prostate, tumor, untreated

value: untreated


title: SA1_MCF10A_ChIP-seq_siSA1_Rep_1

description: Digested/Ligated genomic DNA


title: prostate tumor control patient3


title: Aska-Del47 shSSX ATAC rep2


title: SA2_MCF10A_ChIP-seq_Control_Rep_1

description: Digested/Ligated genomic DNA


title: SA1_MCF10A_ChIP-seq_Control_Rep_2

description: Digested/Ligated genomic DNA


title: SA1_MCF10A_ChIP-seq_Control_Rep_1

description: Digested/Ligated genomic DNA


title: prostate tumor control patient1


title: SS Tumor NCI17

description: RNA-seq on SS Tumor from Patient NCI17

data_processing:
RNA-seq reads were mapped to the human reference genome (hg19) using STAR(Dobin et al., 2013) version 2.3.1 with default parameters.
RPKM values for biological duplicate RNA-seq samples were generated using GFold(Feng et al., 2012) version 1.1.0.
Genome_build: hg19
Supplementary_files_format_and_content: read_cnt
Supplementary_files_format_and_content: GeneSymbol        GeneName      Read Count     Gene Exon Length     RPKM

molecule: polyA RNA

source_name: SS Tumor from Patient NCI17

growth_protocol: Fresh frozen tumor tissue was disrupted using BioMasher II Micro Tissue Homogenizers (DWK Life Sciences, Millville, NJ) and homogenized with syringes and 21-guage needles.

extract_protocol:
RNA was extracted from tissue lysate using the Animal Tissues protocol from the RNeasy Mini kit or the AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Inc., Valencia, CA), with final elution volumes of 50 µL.
All library prep and sequencing were 75bp either single end or paired end on Illumina Nextseq 500

tag: tumor

value: Synovial sarcoma


title: SS Tumor NCI21

description: RNA-seq on SS Tumor from Patient NCI21

source_name: SS Tumor from Patient NCI21


title: SS Tumor NCI14

description: RNA-seq on SS Tumor from Patient NCI14

source_name: SS Tumor from Patient NCI14


title: SS Tumor NCI12

description: RNA-seq on SS Tumor from Patient NCI12

source_name: SS Tumor from Patient NCI12


title: SS Tumor NCI5

description: RNA-seq on SS Tumor from Patient NCI5

source_name: SS Tumor from Patient NCI5


title: SS Tumor NCI7

description: RNA-seq on SS Tumor from Patient NCI7

source_name: SS Tumor from Patient NCI7


title: SS Tumor NCI18

description: RNA-seq on SS Tumor from Patient NCI18

source_name: SS Tumor from Patient NCI18


title: SS Tumor NCI8

description: RNA-seq on SS Tumor from Patient NCI8

source_name: SS Tumor from Patient NCI8


title: SS Tumor NCI13

description: RNA-seq on SS Tumor from Patient NCI13

source_name: SS Tumor from Patient NCI13


title: SS Tumor NCI20

description: RNA-seq on SS Tumor from Patient NCI20

source_name: SS Tumor from Patient NCI20


title: SS Tumor NCI3

description: RNA-seq on SS Tumor from Patient NCI3

source_name: SS Tumor from Patient NCI3


title: SS Tumor NCI16

description: RNA-seq on SS Tumor from Patient NCI16

source_name: SS Tumor from Patient NCI16


title: SS Tumor NCI4

description: RNA-seq on SS Tumor from Patient NCI4

source_name: SS Tumor from Patient NCI4


title: SS Tumor NCI15

description: RNA-seq on SS Tumor from Patient NCI15

source_name: SS Tumor from Patient NCI15


title: SS Tumor NCI11

description: RNA-seq on SS Tumor from Patient NCI11

source_name: SS Tumor from Patient NCI11


title: SS Tumor NCI9

description: RNA-seq on SS Tumor from Patient NCI9

source_name: SS Tumor from Patient NCI9


title: SS Tumor NCI6

description: RNA-seq on SS Tumor from Patient NCI6

source_name: SS Tumor from Patient NCI6


title: SS Tumor NCI10

description: RNA-seq on SS Tumor from Patient NCI10

source_name: SS Tumor from Patient NCI10


title: SS Tumor NCI2

description: RNA-seq on SS Tumor from Patient NCI2

source_name: SS Tumor from Patient NCI2


title: CRL7250 SS18-SSX1 1

description: CRL7250 SS18-SSX1 1 RNA-seq

source_name: CRL7250 (fibroblast)

extract_protocol:
All RNA was produced using the RNeasy Mini Kit (Qiagen).
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). The cells were harvested following 48-hour exposure to the lenti-virus and either 1 day (3 days post-infection) or 5 days (7 days post-infection) of selection with 2 μg/ml of puromycin.

value: CRL7250 (fibroblast)


title: CRL7250 SS18-SSX2 2

description: CRL7250 SS18-SSX2 2 RNA-seq


title: CRL7250 naive 1

description: CRL7250 naive 1 RNA-seq


title: CRL7250 SS18 2

description: CRL7250 SS18 2 RNA-seq


title: CRL7250 naive 2

description: CRL7250 naive 2 RNA-seq


title: SYO1 shSSX 2

description: SYO1 shSSX 2 RNA-seq

source_name: SYO1 (SS)

value: SYO1 (SS)


title: SYO1 shSSX 1

description: SYO1 shSSX 1 RNA-seq


title: SYO1 shCt 1

description: SYO1 shCt 1 RNA-seq


title: SYO1 shCt 2

description: SYO1 shCt 2 RNA-seq


title: HSSY2 shSSX 2

description: HSSY2 shSSX 2 RNA-seq

source_name: HSSY2 (SS)

value: HSSY2 (SS)


title: HSSY2 shCt 2

description: HSSY2 shCt 2 RNA-seq


title: CRL7250 SS18 1

description: CRL7250 SS18 1 RNA-seq


title: Aska shSSX Day3 1

description: Aska shSSX Day3 1 RNA-seq

source_name: Aska (SS)

value: Aska (SS)


title: Aska shSSX Day3 2

description: Aska shSSX Day3 2 RNA-seq


title: Aska shCt Day3 2

description: Aska shCt Day3 2 RNA-seq


title: Aska shCt Day3 1

description: Aska shCt Day3 1 RNA-seq


title: Aska BAF47KO-1 shCt 2

description: Aska BAF47KO-1 shCt 2 RNA-seq


title: HSSY2 shCt 1

description: HSSY2 shCt 1 RNA-seq


title: Aska BAF47KO-2 shCt 1

description: Aska BAF47KO-2 shCt 1 RNA-seq


title: Aska BAF47KO-2 shSSX 2

description: Aska BAF47KO-2 shSSX 2 RNA-seq


title: Aska BAF47KO-1 shSSX 1

description: Aska BAF47KO-1 shSSX 1 RNA-seq


title: Aska BAF47KO-2 shCt 2

description: Aska BAF47KO-2 shCt 2 RNA-seq


title: Aska shCt 1

description: Aska shCt 1 RNA-seq


title: Aska BAF47KO-1 shSSX 2

description: Aska BAF47KO-1 shSSX 2 RNA-seq


title: Fuji naive 2

description: Fuji naive 2 RNA-seq

source_name: Fuji (SS)

value: Fuji (SS)


title: Aska BAF47KO-2 shSSX 1

description: Aska BAF47KO-2 shSSX 1 RNA-seq


title: Aska shSSX 2

description: Aska shSSX 2 RNA-seq


title: Fuji naive 1

description: Fuji naive 1 RNA-seq


title: Aska shCt 2

description: Aska shCt 2 RNA-seq


title: YaFuSS naive 2

description: YaFuSS naive 2 RNA-seq

source_name: YaFuSS (SS)

value: YaFuSS (SS)


title: SYO1 naive 1

description: SYO1 naive 1 RNA-seq


title: Aska BAF47KO-1 shCt 1

description: Aska BAF47KO-1 shCt 1 RNA-seq


title: HSSY2 naive 1

description: HSSY2 naive 1 RNA-seq


title: Yamato naive 2

description: Yamato naive 2 RNA-seq

source_name: Yamato (SS)

value: Yamato (SS)


title: YaFuSS naive 1

description: YaFuSS naive 1 RNA-seq


title: HSSY2 shSSX 1

description: HSSY2 shSSX 1 RNA-seq


title: Yamato naive 1

description: Yamato naive 1 RNA-seq


title: Aska shSSX 1

description: Aska shSSX 1 RNA-seq


title: Aska naive 1

description: Aska naive 1 RNA-seq


title: CRL7250 naive Input

description: CRL7250 naive Input ChIP-seq

data_processing:
ChIP-seq reads were mapped to the human reference genome (hg19) using Bowtie2(Langmead and Salzberg, 2012) version 2.1.0 with parameters –k 1.
Peaks were called against input reads using MACS2(Zhang et al., 2008) version 2.1.0 at q=1e-3.
Peaks were filtered to remove peaks that overlap with ENCODE blacklisted regions, as well as peaks mapped to unmappable chromosomes (only chr1-22,X,Y included). Duplicate reads were removed using samtools rmdup for all downstream analyses.
ChIP-seq track densities were generated per million mapped reads with MACS2 2.1.0 using parameters –B –SPMR.
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed per standard protocols (Millipore, Billerica, MA) with minor modifications. Briefly, 10M cells were crosslinked with 1% formaldehyde for 10 min at 37 °C. This reaction was subsequently quenched with 0.125M glycine.
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500

tag: shRNA

value: naive

tag: antibody

value: none, input


title: CRL7250 SS18 Input

description: CRL7250 SS18 Input ChIP-seq


title: CRL7250 SS18-SSX RNAPolII

description: CRL7250 SS18-SSX anti-RNAPolII ChIP-seq

value: anti-RNAPolII

tag: antibody vendor

value: Diagenode

tag: antibody catalog

tag: antibody lot#


title: CRL7250 SS18 V5

description: CRL7250 SS18 anti-V5 ChIP-seq

value: Cell Signaling


title: SYO1 naive 2

description: SYO1 naive 2 RNA-seq


title: CRL7250 SS18-SSX SUZ12

description: CRL7250 SS18-SSX anti-SUZ12 ChIP-seq


title: CRL7250 SS18-SSX V5

description: CRL7250 SS18-SSX anti-V5 ChIP-seq


title: CRL7250 naive SS18

description: CRL7250 naive anti-SS18 ChIP-seq


title: HSSY2 shCt H3K27ac

description: HSSY2 shCt anti-H3K27ac ChIP-seq

value: shCt

value: Abcam


title: HSSY2 shCt Input

description: HSSY2 shCt Input ChIP-seq


title: HSSY2 naive 2

description: HSSY2 naive 2 RNA-seq


title: SYO1 shCt Input

description: SYO1 shCt Input ChIP-seq


title: HSSY2 shCt H3K27me3

description: HSSY2 shCt anti-H3K27me3 ChIP-seq

value: Millipore


title: HSSY2 shCt H3K4me3

description: HSSY2 shCt anti-H3K4me3 ChIP-seq


title: CRL7250 naive H3K4me3

description: CRL7250 naive anti-H3K4me3 ChIP-seq


title: SYO1 shSSX Input

description: SYO1 shSSX Input ChIP-seq

value: shSSX


title: CRL7250 SS18 SUZ12

description: CRL7250 SS18 anti-SUZ12 ChIP-seq


title: CRL7250 SS18 RNAPolII

description: CRL7250 SS18 anti-RNAPolII ChIP-seq


title: HSSY2 shCt BAF155

description: HSSY2 shCt anti-BAF155 ChIP-seq


title: SYO1 shCt H3K27me3

description: SYO1 shCt anti-H3K27me3 ChIP-seq


title: SYO1 shCt H3K27ac

description: SYO1 shCt anti-H3K27ac ChIP-seq


title: SYO1 shCt BRG1

description: SYO1 shCt anti-BRG1 ChIP-seq


title: SYO1 shCt H3K4me3

description: SYO1 shCt anti-H3K4me3 ChIP-seq


title: Aska naive 2

description: Aska naive 2 RNA-seq


title: HSSY2 shCt BRG1

description: HSSY2 shCt anti-BRG1 ChIP-seq


title: SYO1 shCt BAF155

description: SYO1 shCt anti-BAF155 ChIP-seq


title: CRL7250 SS18-SSX1 Input

description: CRL7250 SS18-SSX1 Input ChIP-seq


title: SYO1 shSSX SS18

description: SYO1 shSSX anti-SS18 ChIP-seq


title: SYO1 shCt SS18

description: SYO1 shCt anti-SS18 ChIP-seq


title: Aska-BAF47KO1 shSSX Input

description: Aska-BAF47KO1 shSSX Input ChIP-seq

source_name: Aska-BAF47KO1 (SS)

value: Aska-BAF47KO1 (SS)


title: CRL7250 naive H3K27me3

description: CRL7250 naive anti-H3K27me3 ChIP-seq

value: CRL7250 (fibroblast)


title: Aska-BAF47KO1 shSSX SS18

description: Aska-BAF47KO1 shSSX anti-SS18 ChIP-seq


title: Aska-BAF47KO1 shCt H3K27ac

description: Aska-BAF47KO1 shCt anti-H3K27ac ChIP-seq


title: Aska shCt Input

description: Aska shCt Input ChIP-seq


title: Aska shSSX SUZ12

description: Aska shSSX anti-SUZ12 ChIP-seq


title: Aska shCt SUZ12

description: Aska shCt anti-SUZ12 ChIP-seq


title: Aska shSSX RNAPolII

description: Aska shSSX anti-RNAPolII ChIP-seq


title: Aska shSSX H3K27me3

description: Aska shSSX anti-H3K27me3 ChIP-seq


title: Aska shSSX H3K27ac

description: Aska shSSX anti-H3K27ac ChIP-seq


title: Aska shCt H3K27ac

description: Aska shCt anti-H3K27ac ChIP-seq


title: Aska shCt BRG1

description: Aska shCt anti-BRG1 ChIP-seq


title: Aska shSSX BRG1

description: Aska shSSX anti-BRG1 ChIP-seq


title: Aska shSSX BAF155

description: Aska shSSX anti-BAF155 ChIP-seq


title: Aska shCt BAF155

description: Aska shCt anti-BAF155 ChIP-seq


title: Aska shSSX SS18

description: Aska shSSX anti-SS18 ChIP-seq


title: Aska shCt SS18

description: Aska shCt anti-SS18 ChIP-seq


title: Aska-BAF47KO1 shCt Input

description: Aska-BAF47KO1 shCt Input ChIP-seq


title: Aska-BAF47KO1 shSSX H3K27ac

description: Aska-BAF47KO1 shSSX anti-H3K27ac ChIP-seq


title: Aska-BAF47KO1 shCt SS18

description: Aska-BAF47KO1 shCt anti-SS18 ChIP-seq


title: Aska shSSX Input

description: Aska shSSX Input ChIP-seq


title: Aska shCt H3K27me3

description: Aska shCt anti-H3K27me3 ChIP-seq


title: Aska shCt RNAPolII

description: Aska shCt anti-RNAPolII ChIP-seq


title: HBDJKDAT02_N729_S522

city: Berkeley

first: Daniel

middle: J

last: Kramer

state: Ca

address: 291 Life Sciences Addition #3200

institute: UC Berkeley

data_processing:
Illumina CASAVA bcl2fastq_v2.17 software used for basecalling.
Reads were aligned to the GRCm38.3 (mm10, patch release 3) mouse genome assembly with Tophat2 (Version 2.1.1), and low quality reads were removed with Trimmomatic (Version 0.3.2).
Gene level counts were calculated using Tophat (Version 2.1.1) alignments and featureCounts (Version 1.5.0-p3).
Genome_build: GRCm38.3 (mm10, patch release 3)
Supplementary_files_format_and_content: tab-delimited text files include gene level count values for each sample derived from Cufflinks and featureCounts
Supplementary_files_format_and_content: ExpressionSet and matrix that include all metadata and the appropriate count data
Supplementary_files_format_and_content: Files:
Supplementary_files_format_and_content: KramerDAT_eSet_phenoData.txt: metadata on samples including experimental condition and batch
Supplementary_files_format_and_content: KramerDAT_eSet_counts_table.txt: abundance measurements (featureCounts) prior to filtering, text file
Supplementary_files_format_and_content: KramerDAT_eSet_featureData.txt: information about the genes
Supplementary_files_format_and_content: KramerDAT_eSet_protocolData.txt: QC metrics, text file
Supplementary_files_format_and_content: KramerDAT_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data, prior to filtering
Supplementary_files_format_and_content: KramerDAT_imageAfterFiltering.RData: R data object containing expressionSet of filtered count data and vector for gene filtering

extract_protocol:
single cell isolation, lysis, RT, amplification: Cells were brought to a concentration of 200,000/ml. The Fluidigm C1 system was used for single cell capture, cell lysis, and reverse transcription to make cDNA, and amplification (C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq; SMARTer Ultra Low RNA Kit for the Fluidigm C1 System). Cell capture was performed at room temperature.
sequencing library synthesis: The Nextera XT DNA Sample Preparation Kit (Illumina cat# FC-131-1096) and Index Kit A-D (cat# FC-131-2001-4) were used to synthesize sequencing libraries.
sequencing library synthesis: RNA libraries were prepared for sequencing using standard Illumina protocols.
sequencing strategy: Single-cell RNA-sequencing.  scRNA-Seq was performed on an Illumina HISEQ 2500 sequencer; up to 192 samples were sequenced per lane, often in Rapid Run mode.

treatment_protocol:
dissociation protocol: Postnatal day 26 (P26) to P34 male and female DATIRESCre;Ai9 mice were briefly anesthetized with isoflurane and decapitated, and brains were removed and placed in ice-cold, oxygenated artificial CSF. The brain was cut coronally into 275-m sections on a vibratome (Leica VT1000 S) in oxygenated ice-cold choline cutting solution.
dissociation protocol: Midbrain sections were incubated for 15 min in ACSF at 34˚C. Midbrain (including the hypothalamus) was dissected in ACSF using forceps under a dissection microscope.
dissociation protocol: Midbrain sections were incubated in 10 ml oxygenated papain solution in ACSF for 25 min at 34˚C. Following papain digestion, tissue was placed into 9 ml oxygenated STOPovomucoid inhibitor solution and bubbled gently at 34˚C. 8 ml of the supernatant solution was removed, and the tissue was triturated serially in the remaining 2 ml of solution with polished 3-, 2-, and 1-mm glass pipettes to create a single-cell suspension. The 2-mL single-cell suspension was spun down in a 20% Percoll solution at 430 g for 6 min at room temperature (RT). The supernatant was aspirated, leaving 50 l of solution and the cell pellet. The pellet was resuspended in 1 ml HEPES-ACSF with 1 mM kynurenic acid and 5% FBS. This single-cell suspension was sorted on a BD Influx cell sorter in the Flow Cytometry Facility at UC Berkeley.
dissociation protocol: Cells were gated for PI-/tdTomato and sorted into a PCR tube. Based on the number of neurons sorted and cell viability count, neurons were brought to 200,000 neurons/ml.

tag: strain

value: midbrain

value: dopamine neuron

tag: age

tag: expt condition

tag: Sex

value: M

tag: number of animals

tag: facs selection

value: TdTomato+ (PI -)

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size

value: MEDIUM

tag: c1 machine id

value: FRODO

tag: ercc spike-in dilution


title: HBDJKDAT02_N729_S517

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: Sex

tag: number of animals


title: HBDJKDAT02_N729_S518

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: library plate coordinate

tag: barcode


title: HBDJKDAT02_N729_S521

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N729_S520

tag: strain

tag: tissue

tag: cell type

tag: age

tag: expt condition

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N729_S513

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id


title: Aska shCt H3K4me3

description: Aska shCt anti-H3K4me3 ChIP-seq

tag: cell line

value: Aska (SS)

tag: shRNA

tag: antibody

tag: antibody vendor

tag: antibody catalog

tag: antibody lot#


title: HBDJKDAT02_N729_S516

tag: strain

tag: tissue

tag: cell type

tag: age

tag: library plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N729_S515

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N728_S522

tag: strain

tag: tissue

tag: cell type

tag: age

tag: library plate coordinate

tag: barcode

tag: index set


title: Aska shSSX BAF200

description: Aska shSSX anti-BAF200 ChIP-seq

tag: cell line

tag: shRNA

tag: antibody

tag: antibody vendor

tag: antibody catalog

tag: antibody lot#


title: Aska shSSX H3K4me3

description: Aska shSSX anti-H3K4me3 ChIP-seq


title: Aska shCt BAF200

description: Aska shCt anti-BAF200 ChIP-seq


title: HBDJKDAT02_N728_S518

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N728_S521

tag: strain

tag: tissue

tag: cell type

tag: age

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N728_S517

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate


title: HBDJKDAT02_N728_S516

tag: strain

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N728_S515

tag: tissue

tag: cell type

tag: age

tag: library plate id

tag: library plate coordinate

tag: barcode

tag: index set


title: HBDJKDAT02_N728_S513

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N727_S522

tag: strain

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N727_S518

tag: tissue

tag: cell type

tag: age

tag: library plate id

tag: library plate coordinate

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N727_S521

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: barcode

tag: index set


title: HBDJKDAT02_N727_S517

tag: strain

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: sequencing run id

tag: lane

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N727_S516

tag: tissue

tag: cell type

tag: age

tag: library plate id

tag: library plate coordinate

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N727_S515

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N727_S513

tag: strain

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: barcode

tag: index set

tag: sequencing run id

tag: lane


title: HBDJKDAT02_N728_S520

tag: tissue

tag: cell type

tag: age

tag: library plate id

tag: library plate coordinate

tag: c1 machine id

tag: ercc spike-in dilution


title: HBDJKDAT02_N726_S521

tag: expt condition

tag: Sex

tag: number of animals

tag: facs selection

tag: c1 batch id

tag: cdna concentration (ng/ul)

tag: dob


title: HBDJKDAT02_N726_S520

tag: strain

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: barcode

tag: index set

tag: facs & c1 date

tag: c1 chip size


title: HBDJKDAT02_N726_S522

tag: tissue

tag: cell type

tag: age

tag: library plate id

tag: library plate coordinate

tag: sequencing run id

tag: lane