title: mDA shScramble RNA-Seq Rep2

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

data_processing:
RNA-Seq analysis: All RNA-Seq data were mapped to the mm9 genome. Prior to mapping, raw RNA-Seq datasets were first trimmed using Trimmomatic (Bolger et al. 2014) (v.0.36). Illumina sequence adaptors were removed, the leading and tailing low-quality base-pairs (less than 3) were trimmed, and a 4-bp sliding window was used to scan the reads and trim when the window mean quality dropped below 15. Next, reads with a length of at least 50-bp were mapped to the genome using STAR (Dobin et al. 2013) (v.2.5.2b) with the following parameters: --outSAMtype BAM SortedByCoordinate –outSAMunmapped Within –outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999. The resulting bam files were then passed to RSEM 21 to estimate genes and isoform abundance given the Ensemble NCBIM37.67 transcriptome assembly. The differential gene expression analysis was performed using the R/Bioconductor package DESeq2. Output_format: All files are in the RSEM output format:  gene_id transcript_id(s)        length  effective_length        expected_count  TPM     FPKM
liDNase-Seq analysis: raw 100-bp single-end reads were first trimmed with Trimmomatic (Bolger et al. 2014) (v.0.36) with parameters similar to those used in RNA-Seq, except that trimmed reads were allowed to have a length of at least 25-bp. We next used Bowtie2 to map the trimmed reads to the mm9 genome without allowing any mismatches. Unmapped reads and reads with mapping quality less than 10 were filtered out using samtools 21 (v.1.3.1). DNaseq-Seq peaks were then called using macs2 with the parameters --broad --nomodel --nolambda. Peaks with a q-value < 0.05 were considered for further analysis. Output format: The called peaks are in the broadpeak format
Genome_build: mm9

source_name: mibrain

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
Nuclear Isolation: Frozen midbrain samples were homogenized in 1 ml ice-cold homogenization buffer [320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH7.6, 0.1 mM EDTA, 0.1% NP40, 0.1 mM PMSF, 1 mM β-mercaptoethanol, 1% BSA, 1:250 RNasin Plus RNase Inhibitor (Clontech)] using a 1 ml Dounce homogenizer (Wheaton); 30 times with pestle A, followed by 30 times with pestle B. After 10 min on ice, the homogenate was filtered with 40 m cell strainer (Fisher) and added 1 ml dilution buffer  [50% OptiPrep density gradient medium (Sigma), 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.6, 0.1 mM PMSF, 1 mM β-mercaptoethanol] and mixed thoroughly with pipette. Loaded 0.5 ml lysate on the top of 0.5 ml 29% iso-osmolar OptiPrep solution (in PBS) in a 1.5 ml centrifuge tube and centrifuged at 6,000 × g for 10 min at 4 °C. After removing the supernatant, the nuclei were resuspended in wash buffer [2.5 mM MgCl2, 1% BSA in PBS, 1:500 RNasin Plus RNase Inhibitor (Clontech)] for immunostaining or FANS.  Nuclear immunolabeling: Isolated nuclei suspended in wash buffer (1% BSA, 2.5mM MgCl2 in PBS) were centrifuged (5 min @1000g) and supernatant was discarded. Nuclear pellet was then resuspended with rabbit anti-HA (1:200, 3724, Cell Signaling, MA) or chicken anti-GFP (1:2000, AbCam) in 200 l wash buffer for 1 hr and centrifuged (5 min @1000g). Supernatant was discarded and pellet was resuspended in 400 l wash buffer for 5 mins and centrifuged again (5 mins @1000g). Nuclear pellet was then resuspended in donkey anti-rabbit 568 (1:500; Invitrogen, Carlsbad, CA) or rhodamine-conjugated donkey anti-chicken secondary (Vector Labs) in 200 l wash buffer for 1h and then centrifuged (5 mins @1000g). Supernatant was discarded and pellet was resuspended in 400 l wash buffer for 5 mins and centrifuged again (5 mins @1000g). Nuclei were resuspended with 1% DAPI in 300 l wash buffer. All steps for nuclear staining were performed at 4°C.
RNA-Seq: FANS-sorted nuclei were directly sorted to RLT plus buffer (Qiagen). Total RNA and DNA were prepared from the same samples. Total RNA samples from 400 nuclei were reverse transcribed and amplified using SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech). cDNAs were then fragmented using the Covaris M220 sonicator (Covaris). The fragmented cDNAs were end-repaired, adaptor ligated and amplified using NEBNext Ultra DNA Library Prep Kit for Illumina according to the manufacturer’s instruction (New England Biolabs). Single end 100 bp sequencing was performed on a HiSeq2500 sequencer (Illumina).  Low-input DNase-Seq: Low-input DNase-Seq (liDNase-Seq) libraries were prepared as previously described8. Nuclei were collected in 1.5 ml tubes in PBS with BSA during sorting. 500 nuclei were pelleted and resuspended in 36 μl lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Triton X-100) and incubated on ice for 5 min. DNase I (10 U/μl, Roche) was added to the final concentration of 40 U/ml and incubated at 37 °C for 5 min. The reaction was stopped by adding 80 μl Stop Buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.15% SDS, 10 mM EDTA) containing 2 μl Proteinase K (20 mg/ml, Life technologies). Then 20 ng of a circular carrier DNA [a pure plasmid DNA without any mammalian genes was purified with 0.5x Beckman SPRIselect beads (Beckman Coulter) to remove small DNA fragments] was added. The mixture was incubated at 50 °C for 1 hr, then DNA was purified by extraction with phenol-chloroform and precipitated by ethanol in the presence of linear acrylamide (Life technologies) overnight at -20 °C. Precipitated DNA was resuspended in 50 μl TE (2.5 mM Tris, pH 7.6, 0.05 mM EDTA), and the entire volume was used for sequencing library construction.   Sequencing library was prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufactures' instruction with the exception that the adaptor ligation was performed with 0.03 μM adaptor in the ligation reaction for 30 minutes at 20 °C, and that PCR amplification was performed using Kapa Hifi hotstart readymix (Kapa Biosystems) for 8-cycles. The PCR products were purified with x1.3 volume of SPRIselect beads (Beckman Coulter) and then size selected with x0.65 volume followed by x0.7 volume of SPRIselect beads. The samples were amplified again with Kapa Hifi hotstart readymix. The PCR product was purified with x1.3 volume of SPRIselect beads and then size selected with x0.65 volume followed by x0.7 volume of SPRIselect beads. The DNA was eluted in TE. The libraries were sequenced on a Hiseq2500 with single-end 100 bp reads (Illumina).

tag: line

value: DAT-IRES-Cre heterozygous

value: midbrain

tag: cell type

value: midbrain Dopamine neurons

tag: Sex

value: male

tag: age

value: 8-12 weeks


title: HAI52_Day 1

status: Public on May 14 2019

type: RNA

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

description: Gene expression profiling of peripheral blood from influenza infected participant

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: Influenza infection Day 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from blood collected in paxgene tubes according to manufacturer's instructions.  RNA quality assessed using Agilent Bioanalyzer.

treatment_protocol: Health volunteers were intranasally challenged with 2009 H1N1 influenza virus. Whole blood was collected pre-exposure and days 1, 2, 4, and 6 days following exposure for microarray analysis.

tag: tissue

value: Blood

tag: virus strain

value: Influenza virus infection

tag: time p.i.

value: Day 1


title: HAI31_Day 1


title: 827x4h3

type: SRA

city: Buffalo

first: Erik

last: Knudsen

state: NY

address: 665 Elm St.

department: Molecular & Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

library_source: transcriptomic

data_processing:
RNA-sequencing was performed on total RNA using Illumina HiSeq.
RNA reads were aligned using Tophat2.
Counts were generated from aligned BAM files using HTSeq.
Counts from human aligned genes were log-normalized using the edgeR R package.
Genome_build: Hg19 with mm10 concatenated
Supplementary_files_format_and_content: tab-delimited text file (gene sample expression matrix) includes gene TMM normalized values for each sample

source_name: Patient derived xenograft - pancreatic cancer

growth_protocol: Mice were implanted subcutaneously with the established PDX models. When tumors reached a volume of 200 mm3 they were randomized to treatment cohorts.

extract_protocol:
RNA was isolated from snap frozen tumor tissue using RNeasy Plus Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated by gastric gavage with vehicle control, single agent Palbociclib (PD-0332991, 100 mg/kg) diluted in 50 mM lactate buffer at pH 4.0, or the combination with TAK-228 (MLN0128, 0.5 mg/kg) diluted in 30% PEG400, 0.5% Tween 80, and 5% propylene glycol.  Mice were treated daily for 5 days then tissue was collected for sequencing.

value: Patient derived xenograft

tag: treatment

value: palbociclib + TAK228

tag: disease state

value: pancreatic cancer

tag: tumor source


title: HAI19_Day 1


title: HAI44_Day 1


title: PD39_Day 1


title: HAI26_Day 1


title: HAI2_Day 1


title: HAI68_Day 1


title: HAI35_Day 1


title: HAI70_Day 1


title: mDA shScramble RNA-Seq Rep1

organism: Mus musculus

tag: genotype


title: HAI67_Day 1


title: HAI59_Day 1


title: HAI37_Day 1


title: HAI69_Day 1


title: HAI4_Day 1


title: HAI46_Day 1


title: 827x4h1

value: vehicle control


title: 827x4j3


title: mDA shGmeb1 RNA-Seq Rep2


title: HAI74_Day 1


title: HAI72_Day 1


title: mDA shGmeb1 RNA-Seq Rep1


title: 827x4d2

value: palbociclib


title: 827x4c2


title: mDA neurons liDNase-Seq Rep2

library_source: genomic

molecule: genomic DNA


title: mDA neurons liDNase-Seq Rep1

data_processing:
liDNase-Seq analysis: raw 100-bp single-end reads were first trimmed with Trimmomatic (Bolger et al. 2014) (v.0.36) with parameters similar to those used in RNA-Seq, except that trimmed reads were allowed to have a length of at least 25-bp. We next used Bowtie2 to map the trimmed reads to the mm9 genome without allowing any mismatches. Unmapped reads and reads with mapping quality less than 10 were filtered out using samtools 21 (v.1.3.1).
DNaseq-Seq peaks were then called using macs2 with the parameters --broad --nomodel --nolambda. Peaks with a q-value < 0.05 were considered for further analysis. Output format: The called peaks are in the broadpeak format
Genome_build: mm9


title: 827x4a5


title: mDA neurons RNA-Seq Rep2


title: 810x2j3


title: mDA neurons RNA-Seq Rep1


title: mDA neurons liDNase-merged


title: HA negative RNA-Seq experiment

value: midbrain non-dopaminergic cells


title: 810x2j1


title: 810x2g4


title: HA_positive_RNA-Seq experiment

data_processing:
RNA-Seq analysis: All RNA-Seq data were mapped to the mm9 genome. Prior to mapping, raw RNA-Seq datasets were first trimmed using Trimmomatic (Bolger et al. 2014) (v.0.36). Illumina sequence adaptors were removed, the leading and tailing low-quality base-pairs (less than 3) were trimmed, and a 4-bp sliding window was used to scan the reads and trim when the window mean quality dropped below 15. Next, reads with a length of at least 50-bp were mapped to the genome using STAR (Dobin et al. 2013) (v.2.5.2b) with the following parameters: --outSAMtype BAM SortedByCoordinate –outSAMunmapped Within –outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999. The resulting bam files were then passed to RSEM 21 to estimate genes and isoform abundance given the Ensemble NCBIM37.67 transcriptome assembly. The differential gene expression analysis was performed using the R/Bioconductor package DESeq2. Output_format: All files are in the RSEM
output format:
 gene_id transcript_id(s)        length  effective_length        expected_count  TPM     FPKM
Genome_build: mm9

molecule: nuclear RNA


title: 827x4b5


title: HAI36_Day 1


title: 810x2e5


title: HAI45_Day 1


title: HAI49_Day 1


title: HAI65_Day 1


title: PD38_Day 1


title: A549 poly-IC 1h

city: Princeton

first: Alexei

last: Korennykh

state: New Jersey

address: 216 Shultz Laboratory

department: Molecular Biology

institute: Princeton University

description: The strategy is to ligate the cyclic-phosphate bearing fragment to an adapter bearing a 5'-OH using RtcB enzyme. We then enrich these chimeric RNAs by PCR during library construction.

data_processing:
Library strategy: RtcB RNA-seq
After barcode splitting, sequencing reads with quality scores ≥30 were trimmed of adaptor sequences and converted into reverse complements. The obtained reads were mapped to the human transcriptome using the FASTA algorithm with ≤1 mismatch, which accounts for possible polymorphisms. Sequences of tRNAs were modified to include CCA 3′-ends and G at the −1 position in tRNA-His. All steps past barcode splitting were conducted using software written in-house. Source code and Microsoft Windows binaries are available upon request.
18S & 28S rRNA make up the bulk of the reads. All unique reads mapping to a given site were summed. Total read counts for sites in 18S and 28S rRNA are reported in the accompanying Excel sheet.
Genome_build: HG19
Supplementary_files_format_and_content: Excel sheet of read counts observed at each rRNA fragment.

source_name: Poly I:C transfection

growth_protocol: A549 cells were grown in RPMI with 10% FBS at 37 °C, 5% CO2

extract_protocol:
Total RNA was purified using the RNeasy Kit (Qiagen)
RtcB RNA-seq was conducted as described previously (Donovan et al., 2017), but without short RNAs purification step. Briefly, 1 µg RNeasy-purified RNA was ligated to 10 µM adaptor (Table 1, oligo 1). Ligation reactions were performed using 10 µM RtcB, 20 mM HEPES pH 7.5, 110 mM NaCl, 2 mM MnCl2, 100 µM GTP, 40U RiboLock RNase inhibitor (Fermentas), 4 mM DTT, and 0.05% Triton X-100 for 1 hour at 37 °C. Reactions were quenched using 3 mM EDTA. Owing to its short length, free adapter was removed by purifying the ligated RNA with the RNeasy kit. On-column DNase treatment was omitted so that ligated adapter remained intact. Oligonucleotides were reverse-transcribed using MultiScribe reverse transcriptase (RT) and 2 pmol of RT primer complimentary to the ligation adaptor (Table 1, oligo 2). RNA, RT primer, and dNTPs were incubated for 3 min at 65°C and snap-cooled on ice. MgCl2 (3 mM f/c) was added to ensure efficient Mg2+-dependent RT reaction. A 2x mastermix containing RT buffer, RT (Applied Biosystems), and 40U Ribolock was added to snap-cooled samples to a final volume of 20 µL. Reactions were incubated at 25°C for 10 min, 37°C for 1.5 h, and 95°C for 5 min. cDNA reaction was brought up to 200 µl with water and extracted using 1 volume of 25:24:1 Phenol:Chloroform:Isoamyl Alcohol saturated with 10 mM TRIS (pH 8.0) and 1 mM EDTA (Sigma Aldrich). The aqueous phase was precipitated using 20 µg glycogen as a carrier, 2/3 5M ammonium acetate (vol/vol) and 3 volumes of 100% ethanol. Mixture was incubated at –80 °C for 30 minutes, followed by a 17,000 x g spin at 4 °C, for 30 minutes. Pellets of cDNA were washed with 75% ethanol (vol/vol) and resuspended in 25 µl DI water. Reactions contained 30% of the cDNA from the previous step, 1 µM adaptor (Table 1, oligo 3), 1 U/µl CircLigase (Epicentre), and buffer contents as per manufacturers guidelines. CircLigase reactions were incubated for 1 h at 65°C and quenched by adding EDTA to a final concentration of 8 mM. 1/3 of the quenched CircLigase reaction was PCR amplified using Phusion DNA polymerase (NEB) and primers 4-5 in Table 1. Libraries were analyzed by a BioAnalyzer high sensitivity DNA 1000 chip (Agilent). Equimolar amounts were pooled and gel purified from native page. RtcB RNA-seq was performed on an Illumina HiSeq 2500 and processed as described previously (Donovan et al., 2017).

treatment_protocol: For poly I:C transfection, 1 μg/mL poly I:C was transfected using Lipofectamine 2000 Reagent (Thermo Fisher Scientific, manufacturer's guidelines) for one hour.

tag: cell line

value: Lung carcinoma epithelium

tag: cell phenotype

value: Adherent

tag: rna fraction

value: cyclic phosphate-bearing RNAs


title: HAI57_Day 1


title: 810oix2d1


title: HAI60_Day 1


title: HAI48_Day 1


title: HAI6_Day 1


title: HAI47_Day 1


title: 810oix2b5


title: ID856_rel

city: Ulm

first: Sibylle

last: Cocciardi

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine III

country: Germany

institute: University Hospital Ulm

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-Seq reads were aligned to the human reference genome hg 19.
Reads were quantified using STAR v.2.4.2a in the 2-pass mapping mode.
The DESeq2 package from R was used to obtain normalized expression values.
Genome_build: hg 19
Supplementary_files_format_and_content: Output from DESeq2 (tab-delimited text file) which contains the normalized read counts for each Sample.

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

extract_protocol:
RNA was extracted from cryopreserved mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis and relapse using the AllPrep DNA/RNA Mini Kit (Qiagen). RNA quality was assessed using a BioAnalyzer 2100 (Agilent).
Libraries were prepared from 1µg of total RNA using the TruSeq Stranded Total RNA Kit with Ribo-Zero Human/Mouse/Rat (Illumina) according to the manufacturer’s instructions.

tag: disease status

value: relapsed AML

tag: npm1 status

value: mutated

tag: sample type

value: peripheral blood

tag: diagnosis

value: acute leukemia


title: PD37_Day 1


title: 810oix2c4


title: HAI55_Day 1


title: PD47_Day 1


title: HAI64_Day 1


title: A549 lipofectamine only

source_name: Lipofectamine mock transfection

tag: cell type


title: PD46_Day 1


title: 810oix2b2


title: PD45_Day 1


title: PD41_Day 1


title: PD44_Day 1


title: PD42_Day 1


title: 519x6c1


title: HAI24_Day 1


title: 519x6b3


title: ID856_dx

value: Leukemic cells obtained from bone marrow or blood at diagnosis

value: primary AML

value: bone marrow


title: ID659_rel


title: ID659_dx


title: ID752_dx


title: ID752_rel


title: ID584_rel


title: PD34_Day 1

value: Blood

value: Influenza virus infection

value: Day 1


title: 519x6b1

value: Patient derived xenograft

value: palbociclib + TAK228

value: pancreatic cancer


title: HAI27_Day 1


title: PD43_Day 1


title: HAI28_Day 1


title: 810oix2b1


title: HAI15_Day 1


title: ID584_dx


title: HAI21_Day 1


title: 519x6a5


title: HAI16_Day 1


title: HAI11_Day 0

description: Gene expression profiling of peripheral blood prior to virus exposure

source_name: Pre-exposure

value: Pre-exposure

value: Day 0


title: HAI9_Day 0


title: HAI10_Day 0


title: 519x5i5

value: vehicle control


title: HAI41_Day 0


title: ID1019_rel


title: HAI17_Day 1


title: 519x5h5


title: ID1019_dx


title: 519x5b3


title: ID12_dx


title: HAI42_Day 0


title: ID6034_rel

value: wild type


title: ID6034_dx


title: ID12_rel

value: relapsed AML


title: HAI51_Day 0


title: HAI50_Day 0


title: 519oix2e5

value: palbociclib


title: 519oix2b1


title: HAI39_Day 0


title: HAI5_Day 0


title: HAI62_Day 0


title: HAI63_Day 0


title: HAI61_Day 0


title: ID6111_Rem

type: genomic

description: Adult AML

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: CEL-files were generated using Affymetrix Command console software. Genotyping console version 2.0 (Affymetrix) was used for normalization and analysis of CEL files.

label: Biotin

source_name: Leukemic cells obtained from bone marrow or blood at remission

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from cryopreserved mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis, remission or relapse using the Qiagen AllPrep DNA/RNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: complete remission

tag: gender

value: female

value: wildtype

value: peripheral blood


title: 3226x5o3


title: HAI3_Day 0


title: HAI20_Day 1


title: HAI7_Day 0


title: ID6013_dx

value: Leukemic cells obtained from bone marrow or blood at diagnosis

value: primary AML

value: mutated

value: acute leukemia


title: HAI1_Day 0

value: Blood


title: ID6111_Rel

description: Adult AML

source_name: Leukemic cells obtained from bone marrow or blood at relapse

value: bone marrow


title: 3226x5o2

value: Patient derived xenograft

value: pancreatic cancer


title: ID6111_Dx

description: Adult AML


title: ID355_rel


title: HAI23_Day 0

value: Pre-exposure

value: Day 0


title: HAI53_Day 0


title: 3226x5o5


title: HAI14_Day 0


title: HAI33_Day 0


title: 3226x5k1

value: vehicle control


title: ID6107_Rem

description: Adult AML

value: male


title: HAI34_Day 0


title: ID355_dx


title: HAI22_Day 0


title: ID6013_rel

value: relapsed AML

value: wild type


title: ID103_rel


title: 3226x5e4

value: palbociclib + TAK228


title: ID6101_Rem

description: Adult AML

value: complete remission

value: female

value: wildtype


title: ID103_dx

value: Leukemic cells obtained from bone marrow or blood at diagnosis

value: primary AML

value: peripheral blood


title: ID6107_Rel

description: Adult AML

value: mutated

value: acute leukemia


title: 3226x5g1

value: Patient derived xenograft


title: ID6107_Dx

description: Adult AML

value: bone marrow


title: 3226x5d3

value: pancreatic cancer


title: JL-24hr-3

city: Philadelphia

first: Yool

last: Lee

state: PA

address: SCTR 10-165, 3400 Civic Center Blvd, Bldg 421

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Raw RNA-Seq reads were mapped to the GRCh38 build of the human reference genome using STAR v2.5.3a with the following command line arguments: --outSAMtype BAM Unsorted --outSAMunmapped Within KeepPairs --outFilterMismatchNmax 33 --seedSearchStartLmax 33 --alignSJoverhangMin 8. STAR was provided with gene models from the Ensembl v90 genome annotation (ote, the three fastq files per library (one for each sequencing lane) were aligned separately. Following alignment, the three BAM files for each library were assigned readgroups and merged together using the AddOrReplaceReadGroups and MergeSamFiles commands from Picard Tools v2.7.1 (htspectively. For both commands, BAM files were maintained in unsorted order (i.e. sorted by read ID).. Fa
Data were normalized using Pipeline Of RNA-Seq Transformations (PORT – v0.8.4-beta).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files contain PORT-normalized and quantified read counts for each gene in each sample

molecule: polyA RNA

source_name: U2OS osteosarcoma

growth_protocol: U2OS cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS and 1% penicillin-streptomycin (Invitrogen, Grand Island, NY, United States) at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted from each sample using the RNeasy Plus Mini kit (74134, Qiagen) according to the manufacturer’s protocol.
RNA quality was assessed by Bioanalyzer and samples with high RNA integrity number (>8) were used for library construction. For each sample, Illumina sequencing libraries were prepared from 100 ng of total RNA using the TruSeq Stranded mRNA Sample Prep Kit (Illumina), according to manufacturer’s protocol (TruSeq RNA Sample Preparation V2 Guide). Each library was prepared using a unique adapter barcode index to allow for multiplexing. All libraries were pooled together and sequenced across three lanes of an Illumina HiSeq 2000 Sequencer, running in single-end mode (1x100bp).

treatment_protocol: U2OS cells stably expressing Per2 promoter-driven destabilized luciferase (pPer2-dLuc) were treated with media containing100nM dexamethasone (dex) every 24hr for control (CTL) or repeated 8-h advances of the daily cycle every 2 days to simulate jet-lag (JL) for 10 days. After the final dex stimulation in the experimental schedule, control and jet-lag cells were collected at every 6 hr point (24hr, 30hr, 36hr, 42hr, 48hr) for 24hr.

tag: schedule

value: Jet Lag

tag: timepoint

tag: replicate

tag: library barcode

value: GAATTCGT-CCTATCCT


title: ID6101_Rel

description: Adult AML


title: JL-24hr-2

value: ATTCAGAA-CCTATCCT


title: 3226x5d1

tag: tissue

tag: treatment

value: vehicle control


title: HAI71_Day 0

value: Blood

tag: virus strain

value: Pre-exposure

tag: time p.i.

value: Day 0


title: ID6101_Dx

description: Adult AML

value: female


title: HAI18_Day 0


title: 226x5k5

tag: disease state

tag: tumor source


title: HAI32_Day 0


title: 226x5k2


title: HAI30_Day 0


title: HAI29_Day 0


title: ID6091_Rem

description: Adult AML

value: complete remission

value: wildtype


title: 3226x5i3


title: JL-18hr-2

value: TCCGGAGA-CCTATCCT


title: ID6091_Rel

description: Adult AML

value: relapsed AML

value: peripheral blood


title: ID6091_Dx

description: Adult AML

value: primary AML

value: mutated

value: acute leukemia


title: HAI12_Day 0


title: JL-18hr-1

value: ATTACTCG-CCTATCCT


title: 226x5i1

value: Patient derived xenograft

value: palbociclib

value: pancreatic cancer


title: ID6037_Rem

description: Adult AML

value: bone marrow


title: JL-12hr-3

value: Jet Lag

value: AGCGATAG-ATAGAGGC


title: PD40_Day 0

value: Blood

value: Pre-exposure

value: Day 0


title: JL-12hr-2

value: TCTCGCGC-ATAGAGGC


title: 226x5h4

value: vehicle control


title: ID6037_Rel

description: Adult AML

value: relapsed AML

value: female


title: HAI73_Day 0


title: JL-24hr-1

value: GAGATTCC-CCTATCCT


title: HAI56_Day 0


title: HAI58_Day 0


title: 226x5h2


title: JL-6hr-3

value: CGGCTATG-ATAGAGGC


title: JL-12hr-1

value: TCCGCGAA-ATAGAGGC


title: JL-18hr-3

value: CGCTCATT-CCTATCCT


title: 226x5g5

value: Patient derived xenograft

value: palbociclib + TAK228


title: 226x5i5

value: palbociclib

value: pancreatic cancer


title: ID6035_Rem

description: Adult AML

value: complete remission

value: wildtype

value: peripheral blood

value: acute leukemia


title: ID6037_Dx

description: Adult AML

value: primary AML

value: mutated

value: bone marrow


title: JL-6hr-2

value: Jet Lag

value: TAATGCGC-ATAGAGGC


title: 226x5a3


title: 226x5g1


title: ID6035_Rel

description: Adult AML

value: relapsed AML

value: female


title: JL-6hr-1

value: CTGAAGCT-ATAGAGGC


title: 1222x5k2

value: vehicle control


title: HAI54_Day 0

value: Blood

value: Pre-exposure

value: Day 0


title: HAI43_Day 0


title: ID6035_Dx

description: Adult AML


title: ID6014_Rem

description: Adult AML


title: 1222x5j4

value: Patient derived xenograft

value: palbociclib

value: pancreatic cancer


title: HAI74_Day 0


title: PD39_Day 0


title: ID6014_Rel

description: Adult AML


title: JL-0hr-2

value: ATTCAGAA-ATAGAGGC


title: PD48_Day 0


title: 1222x5j2

value: palbociclib + TAK228


title: JL-0hr-1

value: GAGATTCC-ATAGAGGC


title: ID6001_Rem

description: Adult AML

value: complete remission

value: unknown

value: wildtype

value: peripheral blood

value: acute leukemia


title: HAI31_Day 0


title: 1222x5i1


title: ID6001_Rel

description: Adult AML

value: relapsed AML

value: female

value: mutated

value: bone marrow


title: CTL-24hr-2

value: Control

value: TCCGGAGA-ATAGAGGC


title: 1222x5i4

value: Patient derived xenograft

value: vehicle control


title: JL-0hr-3

value: Jet Lag

value: GAATTCGT-ATAGAGGC


title: 1222x5h5

value: palbociclib + TAK228

value: pancreatic cancer


title: CTL-24hr-3

value: CGCTCATT-ATAGAGGC


title: CTL-24hr-1

value: ATTACTCG-ATAGAGGC


title: ID6001_Dx

description: Adult AML

value: primary AML


title: CTL-18hr-3

value: AGCGATAG-TATAGCCT


title: CTL-18hr-2

value: TCTCGCGC-TATAGCCT


title: 1222x5h2

value: palbociclib


title: HAI52_Day 0

value: Blood

value: Pre-exposure

value: Day 0


title: 1222x5h4


title: ID6014_Dx

description: Adult AML

value: female

value: mutated

value: bone marrow

value: acute leukemia


title: ID1214_Rel

description: Adult AML

value: relapsed AML

value: wildtype

value: peripheral blood


title: 1222x5g1

value: Patient derived xenograft

value: palbociclib + TAK228

value: pancreatic cancer


title: HAI46_Day 0


title: HAI26_Day 0


title: HAI8_Day 0


title: ID1214_Dx

description: Adult AML

value: primary AML


title: CTL-18hr-1

value: Control

value: TCCGCGAA-TATAGCCT


title: HAI2_Day 0


title: 1013x3n2

value: palbociclib


title: HAI19_Day 0

value: Blood


title: 1013x3j3


title: HAI68_Day 0

value: Pre-exposure


title: HAI69_Day 0

value: Day 0


title: CTL-12hr-2

value: TAATGCGC-TATAGCCT


title: ID1178_Rem

description: Adult AML

value: complete remission

value: male


title: ID1178_Rel

description: Adult AML

value: mutated

value: bone marrow

value: acute leukemia


title: 1013x3j2

value: vehicle control


title: ID1214_Rem

description: Adult AML

value: female

value: wildtype

value: peripheral blood


title: ID1178_Dx

description: Adult AML

value: primary AML


title: CTL-12hr-1

value: Control

value: CTGAAGCT-TATAGCCT


title: HAI70_Day 0


title: 1013x3i3

value: Patient derived xenograft

value: pancreatic cancer


title: HAI35_Day 0

value: Blood

value: Pre-exposure


title: CTL-6hr-3

value: GAATTCGT-TATAGCCT


title: 1013x3h5

value: palbociclib + TAK228


title: ID140_Rem

description: Adult AML

value: complete remission


title: CTL-6hr-2

value: ATTCAGAA-TATAGCCT


title: ID140_Rel

description: Adult AML

value: relapsed AML

value: mutated

value: bone marrow


title: 1013x3g4


title: CTL-6hr-1

value: GAGATTCC-TATAGCCT


title: CTL-12hr-3

value: CGGCTATG-TATAGCCT


title: 1013x3g2

value: palbociclib


title: ID140_Dx

description: Adult AML

value: primary AML

value: female

value: acute leukemia


title: ID133_Rem

description: Adult AML

value: male

value: wildtype

value: peripheral blood


title: HAI37_Day 0

value: Blood

value: Pre-exposure

value: Day 0


title: 1013x3e4

value: Patient derived xenograft

value: palbociclib + TAK228

value: pancreatic cancer


title: ID133_Rel

description: Adult AML

value: relapsed AML

value: mutated


title: CTL-0hr-2

value: Control

value: TCCGGAGA-TATAGCCT


title: 1013x3e2

value: vehicle control


title: ID133_Dx

description: Adult AML

value: primary AML

value: bone marrow


title: HAI67_Day 0


title: CTL-0hr-1

value: ATTACTCG-TATAGCCT


title: HAI59_Day 0


title: Sample 29_Neural induction +dox D6 rep1 ATACseq

city: Durham

first: Lee

middle: F

last: Langer

state: NC

address: 111 TW Alexander Dr

department: ESCBL

institute: NIEHS

description:
NS50590_171031_NS500489_AHMWF7BGX3.47KD_plusdox_Day6_rep1
processed data file: BAF47KD_neural_ind_ATACseq_all_peaks_11_16_17_sort.bed

data_processing:
Samples 1–12:
Quality trimmed with sickle (default parameters)
Adaptor removal with cutadapt (1.8.1 with Python 2.7.9)
Algined with STAR_2.5.1b with the following parameters: --runThreadN 5 --outReadsUnmapped Fastx   --outMultimapperOrder Random  --outSAMtype BAM   SortedByCoordinate   Unsorted --outWigType bedGraph      --outWigStrand Stranded      --outWigNorm None      --outFilterType Normal   --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1
bam file converted to positive and negative bw files
Samples 13–18:
Quality trimmed with sickle (default parameters)
Adaptor removal with cutadapt (1.12 with Python 2.7.13)
Aligned with bowtie2 VN:2.3.0 with the following parameters:  --wrapper basic-0 -x hg19 -X 2000 -N 1 -p 8 --no-mixed --dovetail --no-discordant --passthrough -1
Removal of mitochondrial reads and non-uniquely aligned reads by filtering out .bam file entries with XS tag
Deduplication with PICARD VN:1.110(1752):  MarkDuplicates.jar MAX_RECORDS_IN_RAM=5000000 VERBOSITY=DEBUG REMOVE_DUPLICATES=true ASSUME_SORTED=true
Collection of nucleosome-free reads by collecting all fragments less than or equal to 135 bp in length
Peak-calling with macs2; macs2 callpeak --nomodel -t {} -n {.} --nolambda --keep-dup all --slocal 10000 -q 0.005
Removal of regions that are prone to false positives by reverse filtering with seq.cov1.ONHG19_sort.bed; http://eqtl.uchicago.edu/Masking/
Samples 19-22:
Quality trimmed with sickle (default parameters, except for "-q 26")
Adaptor removal with cutadapt (cutadapt 1.8.1 with Python 2.7.9)
Algined with STAR_2.5.1b with the following parameters: --outReadsUnmapped Fastx   --outMultimapperOrder Random   --outSAMtype BAM   SortedByCoordinate   Unsorted      --outWigType bedGraph      --outWigStrand Stranded      --outWigNorm None      --outFilterType Normal   --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1
bam file converted to positive and negative bw files
Samples 23–30:
Quality trimmed with sickle (default parameters)
Adaptor removal with cutadapt 1.14 with Python 2.7.9
Aligned with bowtie2 VN:2.3.2 with the following parameters: --wrapper basic-0 -x hg19 -X 2000 -N 1 -p 20 --no-mixed --dovetail --no-discordant --passthrough -1
Removal of mitochondrial reads and non-uniquely aligned reads by filtering out .bam file entries with XS tag
Deduplication with Picard VN:1.122: MarkDuplicates.jar MAX_RECORDS_IN_RAM=5000000 VERBOSITY=DEBUG REMOVE_DUPLICATES=true ASSUME_SORTED=true
Collection of nucleosome-free reads by collecting all fragments less than or equal to 135 bp in length
Peak calling with macs2: macs2 callpeak --nomodel -t {} -n {.} --nolambda --keep-dup all --slocal 10000 -q 0.005
Removal of regions that are prone to false positives by reverse filtering with seq.cov1.ONHG19_sort.bed; http://eqtl.uchicago.edu/Masking/
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (sample 1-12, 19-22), bed file with called peaks (sample 13-18, 23-30)

source_name: Neural induction +dox D6

growth_protocol: Neural induction was performed as per the STEMCELL Technology instructions for neural induction using STEMDiffTM Neural Induction Media (#05835)

extract_protocol:
Cells were collected in Accutase (10 min, 27˚), rinsed 1x in PBS, and resuspended to 1e6 cells/ml in cold PBS
Cells were subjected to the ATACseq protocol as described by Buenrostro, et al. 2015, with the following parameters (Buenrostro et al., 2015). Buffer: CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100). Transposase volume/25 µl cell suspension: 5 µl.

treatment_protocol: 1 µg/ml doxycycline in sterile PBS/day

tag: cell line

value: H1 hESCs

value: human embryonic stem cells

value: Neural induction +dox D

tag: molecule subtype

value: T5-tagmented DNA


title: Sample 30_Neural induction +dox D6 rep2 ATACseq

description:
NS50590_171031_NS500489_AHMWF7BGX3.47KD_plusdox_Day6_rep2
processed data file: BAF47KD_neural_ind_ATACseq_all_peaks_11_16_17_sort.bed

extract_protocol: Cells were collected in Accutase (10 min, 27˚), rinsed 1x in PBS, and resuspended to 1e6 cells/ml in cold PBS


title: HAI4_Day 0

value: Blood

value: Pre-exposure


title: HAI40_Day 0

value: Day 0


title: CTL-0hr-3

value: CGCTCATT-TATAGCCT


title: NB1691_TMZ_72hr_n=1

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

data_processing:
Reads were quantified against transcripts using Salmon (version 0.8.2)
Gene level counts were obtained from transcript level counts using the R package tximport (version 1.4.0)
Genome_build: Gencode release 24 (GRCh38.p5)
Supplementary_files_format_and_content: Processed data file count_table.tsv is a tab-delimited text file containing a matrix of gene level counts. Rows are features (ensembl gene Ids) and columns are  samples

source_name: Neuroblastoma

growth_protocol: Cells were cultured in T75 flasks with RPMI1640 supplemented with 10% FCS.

extract_protocol:
RNeasy
Illumina TruSeq Stranded mRNA Library Prep Kit according to manufacturer's instructions. Library prep and RNASeq performed by Eurofins Genomics.

treatment_protocol: Cells were treated with DMSO, RG7388, temozolomide or RG7388 and temozolomide in combination for 24 hours or 72 hours.

tag: mycn status

value: MYCN amplified

tag: tp53 status

value: WT

value: Temozolomide 72h


title: HAI72_Day 0


title: NB1691_TMZ_72hr_n=2


title: NB1691_TMZ_72hr_n=3


title: NB1691_TMZ_24hr_n=3

value: Temozolomide 24h


title: Sample 28_Neural induction -dox D6 rep2 ATACseq

description:
NS50590_171031_NS500489_AHMWF7BGX3.47KD_plusdox_Day3_rep2
processed data file: BAF47KD_neural_ind_ATACseq_all_peaks_11_16_17_sort.bed

source_name: Neural induction -dox D6

treatment_protocol: No treatment

value: Neural induction -dox D


title: ID132_Dx

description: Adult AML

tag: disease status

value: male

tag: npm1 status

value: mutated

tag: sample type

tag: diagnosis

value: acute leukemia


title: Sample 27_Neural induction -dox D6 rep1 ATACseq

description:
NS50590_171031_NS500489_AHMWF7BGX3.47KD_plusdox_Day3_rep1
processed data file: BAF47KD_neural_ind_ATACseq_all_peaks_11_16_17_sort.bed

tag: cell type


title: ID130_Rem

description: Adult AML

value: complete remission

tag: gender

value: wildtype

value: bone marrow


title: NB1691_TMZ_24hr_n=2


title: ID130_Rel

description: Adult AML

value: relapsed AML

value: peripheral blood


title: NB1691_TMZ_24hr_n=1


title: HAI36_Day 0

value: Blood


title: HAI45_Day 0

value: Pre-exposure


title: ID130_Dx

description: Adult AML

value: primary AML


title: ID132_Rem

description: Adult AML


title: HAI48_Day 0

value: Day 0


title: HAI49_Day 0


title: HAI65_Day 0


title: NB1691_R+T_72hr_n=3

value: MYCN amplified

value: RG7388 + Temozolomide 72h


title: Sample 24_Neural induction -dox D3 rep2 ATACseq

description:
NS50590_171031_NS500489_AHMWF7BGX3.47KD_nodox_Day3_rep2
processed data file: BAF47KD_neural_ind_ATACseq_all_peaks_11_16_17_sort.bed

source_name: Neural induction -dox D3

value: H1 hESCs

value: human embryonic stem cells

value: T5-tagmented DNA


title: HAI47_Day 0


title: ID120_Rem

description: Adult AML

value: male


title: NB1691_R+T_72hr_n=2

value: WT


title: ID120_Rel

description: Adult AML

value: mutated

value: acute leukemia


title: ID120_Dx

description: Adult AML


title: Sample 17_BAF47-targeting shRNA D3 rep1 ATACseq

description:
NS50453_170420_NS500489_AHWGJTBGXY.Langer-D3_rep1
processed data file: All_considered_hESC_steady_state_ATACpeaks.bed

source_name: BAF47-targeting shRNA D3

growth_protocol: H1 hESCs were cultured in TeSR™-E8™ growth medium (STEMCELL Technologies, #05990) at 37˚ C in a 5% CO2 atmosphere. Cells were grown feeder-free on a substrate of hESC-qualified MatrigelTM Matrix (Corning™ #354277).

extract_protocol:
Cells were collected in Gentle Cell Disociation Reagent (StemCell Technologies) and resuspended in cold PBS to 1e6 cells /ml
Cells were subjected to the ATACseq protocol as described by Buenrostro, et al. 2015, with the following parameters (Buenrostro et al., 2015). Buffer: CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100). Transposase volume/25 µl cell suspension: 5 µl.

value: H1 hESCs (WA01)

tag: genotype/variation

value: BAF47-targeting shRNA

value: 1 µg/ml doxycycline in sterile PBS/day


title: NB1691_R+T_24hr_n=3

value: RG7388 + Temozolomide 24h


title: NB1691_R+T_72hr_n=1


title: Sample 18_BAF47-targeting shRNA D3 rep2 ATACseq

description:
NS50453_170420_NS500489_AHWGJTBGXY.Langer-D3_rep2
processed data file: All_considered_hESC_steady_state_ATACpeaks.bed


title: Sample 23_Neural induction -dox D3 rep1 ATACseq

description:
NS50590_171031_NS500489_AHMWF7BGX3.47KD_nodox_Day3_rep1
processed data file: BAF47KD_neural_ind_ATACseq_all_peaks_11_16_17_sort.bed

value: Neural induction -dox D


title: Sample 25_Neural induction +dox D3 rep1 ATACseq

description:
NS50590_171031_NS500489_AHMWF7BGX3.47KD_nodox_Day6_rep1
processed data file: BAF47KD_neural_ind_ATACseq_all_peaks_11_16_17_sort.bed

source_name: Neural induction +dox D3

value: Neural induction +dox D


title: Sample 26_Neural induction +dox D3 rep2 ATACseq

description:
NS50590_171031_NS500489_AHMWF7BGX3.47KD_nodox_Day6_rep2
processed data file: BAF47KD_neural_ind_ATACseq_all_peaks_11_16_17_sort.bed


title: NB1691_R+T_24hr_n=2


title: ID110_Rel

description: Adult AML

value: relapsed AML

value: bone marrow


title: NB1691_R+T_24hr_n=1

value: MYCN amplified


title: ID110_Rem

description: Adult AML

value: complete remission

value: wildtype

value: peripheral blood


title: Sample 15_BAF47-targeting shRNA D2 rep1 ATACseq

description:
NS50453_170420_NS500489_AHWGJTBGXY.Langer-D2_rep1
processed data file: All_considered_hESC_steady_state_ATACpeaks.bed

source_name: BAF47-targeting shRNA D2

value: human embryonic stem cells

value: T5-tagmented DNA


title: Sample 16_BAF47-targeting shRNA D2 rep2 ATACseq

description:
NS50453_170420_NS500489_AHWGJTBGXY.Langer-D2_rep2
processed data file: All_considered_hESC_steady_state_ATACpeaks.bed


title: ID110_Dx

description: Adult AML

value: primary AML

value: male


title: HAI60_Day 0

tag: tissue

value: Blood

value: Pre-exposure

value: Day 0


title: NB1691_RG_72hr_n=3

value: WT

tag: treatment


title: HAI55_Day 0

tag: virus strain


title: HAI64_Day 0

tag: time p.i.


title: HAI6_Day 0


title: PD41_Day 0


title: HAI57_Day 0


title: Sample 14_BAF47-targeting shRNA D0 rep2 ATACseq

description:
NS50453_170420_NS500489_AHWGJTBGXY.Langer-D0_rep2
processed data file: All_considered_hESC_steady_state_ATACpeaks.bed

source_name: BAF47-targeting shRNA D0

value: H1 hESCs (WA01)

value: BAF47-targeting shRNA


title: ID96_Rem

description: Adult AML

value: acute leukemia


title: HAI44_Day 0


title: ID132_Rel

description: Adult AML

value: relapsed AML

value: mutated


title: NB1691_RG_72hr_n=2

value: MYCN amplified


title: Sample 13_BAF47-targeting shRNA D0 rep1 ATACseq

description:
NS50453_170420_NS500489_AHWGJTBGXY.Langer-D0_rep1
processed data file: All_considered_hESC_steady_state_ATACpeaks.bed


title: Th1-rep3

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

description:
Sample 9
LM.9_S15

data_processing:
RNA-seq data were generated from three donors. Four different types of samples were taken from each donor, making 12 samples in total. Sequence reads were aligned to the GRCh38/hg38 build of the Human genome using the Subread aligner. Only uniquely mapped reads were retained. Genewise counts were obtained using featureCounts. Reads overlapping with exons in the NCBI RefSeq gene annotation for hg38 (build 38.2) were included. Read counts from sample 4 (labelled as LM-4_S10) and its technical replicate (labelled as LM-4rep_S19) were pooled together.
Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least three libraries. Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package.
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.1 or less.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read counts for genes in each sample (sample 4 and its tech replicate were merged).

extract_protocol:
RNA purification was performed following the manufacturer's protocol using the RNAeasy Plus Micro Kit (Qiagen).
Libraries were generated following the manufacturer's protocol using the Clontech Laboratories SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

treatment_protocol: Human spleen cells were stimulated with PMA and ionomycin (100ng/ml) for 3h prior to IL-17 cytokine capture and fluorescent labelling

value: Spleen


title: NB1691_RG_72hr_n=1


title: Tc17-rep2

description:
Sample 8
LM.8_S14


title: ID70_Rem

description: Adult AML

value: complete remission

value: female

value: wildtype


title: NB1691_RG_24hr_n=2


title: ID70_Rel

description: Adult AML

value: bone marrow


title: ID96_Dx

description: Adult AML

value: primary AML


title: Tc1-rep2

description:
Sample 7
LM.7_S13


title: PD47_Day 0


title: PD46_Day 0


title: PD34_Day 0


title: PD45_Day 0


title: Th17-rep2

description:
Sample 6
LM.6_S12


title: ID67_Rem

description: Adult AML

value: male

value: peripheral blood


title: NB1691_DMSO_72hr_n=2

value: DMSO 72h


title: ID70_Dx

description: Adult AML


title: NB1691_DMSO_72hr_n=3


title: ID96_Rel

description: Adult AML


title: Th1-rep2

description:
Sample 5
LM.5_S11


title: NB1691_RG_24hr_n=3


title: ID67_Rel

description: Adult AML


title: Tc17-rep1

description:
Sample 4
LM.4_S10
LM-4rep_S19 (technical replicate)


title: NB1691_DMSO_72hr_n=1


title: NB1691_RG_24hr_n=1


title: ID43_Rem

description: Adult AML


title: ID67_Dx

description: Adult AML


title: ID43_Rel

description: Adult AML


title: NB1691_DMSO_24hr_n=1

value: DMSO 24h


title: Th1-rep1

description:
Sample 1
LM.1_S7


title: PD38_Day 0

value: Blood

value: Pre-exposure

value: Day 0


title: PD44_Day 0


title: ID43_Dx

description: Adult AML

value: acute leukemia


title: Tc17-rep3

description:
Sample 12
LM.12_S18


title: PD37_Day 0


title: HAI20_Day 0


title: PD43_Day 0


title: PD42_Day 0


title: HAI17_Day 0


title: ID30_Rem

description: Adult AML


title: Tc1-rep1

description:
Sample 3
LM.3_S9


title: Th17-rep3

description:
Sample 10
LM.10_S16


title: Th17-rep1

description:
Sample 2
LM.2_S8


title: HAI28_Day 0


title: NB1691_DMSO_24hr_n=3

value: WT


title: ID30_Dx

description: Adult AML

value: mutated


title: NB1691_DMSO_24hr_n=2

value: MYCN amplified


title: HAI27_Day 0


title: ID24_Rem

description: Adult AML


title: Tc1-rep3

description:
Sample 11
LM.11_S17

value: Spleen


title: ID30_Rel

description: Adult AML

value: relapsed AML


title: ID24_Rel

description: Adult AML


title: HAI24_Day 0


title: sample F control mouse

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

description:
GeneCount_combined.tsv
F_conmtrol

data_processing:
TopHat v2
BowTie v1
FeatureCounts v1
Genome_build: mm10 & GRCm38.79
Supplementary_files_format_and_content: tsv with raw gene counts and RPKM normalized expression values

source_name: lung epithelial cells

extract_protocol:
Qiagen RNeasy kit
polyA RNA

treatment_protocol: IL-33 transgenic mice

tag: genotype

value: control

value: lung epithelial cells


title: sample E IL-33 transgenic mouse

description:
GeneCount_combined.tsv
E_IL33Tg

value: IL-33 over-expression


title: Veh_rep4

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65Â°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 Âµm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Cultured primary cells, human pulmonary fibrobalsts

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: Medium: medium 106 (Invitrogen) supplemented by 10% BCS

extract_protocol: QIAgen Rneasy mini kit

treatment_protocol: Day 1. Seeding 300000 per well (in 6-well plates) using complete media, Day 2: starvation for 24 hours, Day 3: treatment with 5nM metformin dissolved in the media 106. For the vehicle group, we just change the media

value: vehicle


title: ES_OEZ_r1

city: Beijing

first: Jie

last: Zhao

address: 2 Yuanmingyuan West Road, Haidian District

country: China

institute: China Agricultural University

data_processing:
Raw reads were mapped to the reference genome by TopHat using default parameters.
Cuffdiff was used to calculate the FPKM (fragments per kilobase of exon per million mapped reads) of each gene and to identify the differentially-expressed genes (fold change ≥ 1.5, q-value < 0.05) between ZH17 and OEZ after cold treatment.
The functional category analysis of the differentially-expressed genes was performed by the AgriGO databases.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0, MSU7
Supplementary_files_format_and_content: FPKMs

organism: Oryza sativa Japonica Group

source_name: Early seedlings

extract_protocol:
Total RNA was isolated using TRIzol according to the instructions.
Paired-end libraries were constructed using a TruSeq RNA Sample Preparation Kit v2.

value: Early seedlings

tag: development stage

value: 5 mm early seedlings

value: OsLTPL159IL112 overexpression line

value: cold treatment


title: sample D control mouse

description:
GeneCount_combined.tsv
D_conmtrol


title: ES_OEZ_r2


title: ID21_Rem

description: Adult AML

value: complete remission

value: male

value: wildtype

value: peripheral blood


title: Met_rep4

value: metformin


title: HAI21_Day 0

value: Blood

value: Pre-exposure

value: Day 0


title: ES_OEZ_r3


title: Veh_rep3


title: ES_ZH17_r3

value: wild type


title: Met_rep3


title: HAI16_Day 0


title: FaDuCR: cetuximab resistant cell lines

city: Osaka

first: Kazuko

last: Sakai

address: 377-2, Osaka-sayama

department: Dept. of Genome Biology

country: Japan

institute: Kindai University Faculty of Medicine

description: Gene expression data from cetuximab resistant cancer cell line

hyb_protocol: Samples were hybridized using Affymetrix hybridization, Wash and Stain kit.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix) according to manufacturer guidelines.

data_processing: Raw data (CEL files) were analyzed using Affymetrix Expression Console™ Software (version 1.4).

label: biotin

source_name: cetuximab resistant cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling and Control Kit and Ambion WT Expression kit (Affymetrix).

growth_protocol: Tumor cells cultured in medium and incubated at 37˚C with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Untreated parental cancer cell line and cetuximab resistant cancer cell line

value: head and neck squamous cell

tag: cell line

value: FaDu


title: ID21_Dx

description: Adult AML

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

value: primary AML

value: mutated

value: bone marrow

value: acute leukemia


title: ES_ZH17_r2

value: Early seedlings

value: 5 mm early seedlings


title: ID24_Dx

description: Adult AML


title: HAI15_Day 0

description: Gene expression profiling of peripheral blood prior to virus exposure

source_name: Pre-exposure


title: Veh_rep2

value: vehicle


title: Veh_rep1


title: Met_rep2


title: ARID1A siRNA #2

city: Fukushima

first: Mai

last: Ashizawa

institute: Fukushima medical universsity

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

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

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

source_name: N87 cells transfected with ARID1A siRNA #2

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

growth_protocol: The monolayer cells were maintained in a 37˚C incubator with 5% CO2 observed regularly under a light microscope (magnification, x40) and subcultured when they reached 80‑90% confluency.

extract_protocol: Total RNA was isolated from N87 cells using TRIzol (Thermo Fisher Scientific, Inc.).

treatment_protocol: During the exponential growth phase, cells were transiently transfected with a final concentration of 5nM siRNA using Lipofectamine RNAiMAX (Thermo Fisher Scientific, Inc.) according to the manufacture’s protocol. Following 48 hours of incubation, cells were harvested.

value: male

tag: tumor

value: gastric carcinoma


title: FaDu: Parental cell lines

description: Gene expression data from parental FaDu cell lines

source_name: Parental FaDu cells


title: ARID1A siRNA #1

source_name: N87 cells transfected with ARID1A siRNA #1


title: ID21_Rel

description: Adult AML

source_name: Leukemic cells obtained from bone marrow or blood at relapse

value: relapsed AML


title: ES_ZH17_r1

value: cold treatment


title: ID13_Rem

description: Adult AML

source_name: Leukemic cells obtained from bone marrow or blood at remission

value: complete remission

value: wildtype

value: peripheral blood


title: sample B IL-33 transgenic mouse

description:
GeneCount_combined.tsv
B_IL33Tg

value: IL-33 over-expression

value: lung epithelial cells


title: ID13_Dx

description: Adult AML


title: ID13_Rel

description: Adult AML


title: HFD-EAT_Stromal vascular cells 3

city: Seoul

first: Jae Bum

last: Kim

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Illumina 1.9 was used for base calling.
Read pairs were aligned using RSEM v.1.2.25 and Bowtie 2.2.6 to the Mus musculus genome (GRCm38/mm10).
Expected number of fragments from each transcript and gene were estimated with RSEM.
Limma (Voom) v.3.14.4 was used to perform statistical tests for pairwise differential expression between samples, calculate log2 fold change (log2FC) values and select DEGs with adjusted p-value cutoff <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include expected counts, TPM, RPKM values for each sample.

source_name: Stromal vascular cells

growth_protocol: 8 week old C57BL/6J male mice were fed HFD for 10 weeks.

extract_protocol:
EAT and IAT were isolated from HFD-fed mice. Each adipose tissues were incubated with collagenase I buffer to separate adipocyte and SVCs.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Stromal vascular cells

value: SVC


title: HFD-IAT_Stromal vascular cells 2


title: Experiment 2 DR-derived hepatocytes – GREEN 3

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

description:
Experiment 2 Sample 9
processed data file:
Experiment2.txt
RNA-16w4Green_S54

data_processing:
Samples were quantified with kallisto v0.43.1 to obtain transcript counts
using a default kmer length of 31 and an index constructed from the Ensembl Mus musculus GRCm38 cDNA transcriptome dataset.
For each library, transcript counts were consolidated into counts-per-gene using the R/BIOCONDUCTOR package tximport v1.4.03
Genome_build: Mus musculus GRCm38 cDNA
Supplementary_files_format_and_content: The values in the matrix were produced by Kallistov0.43.1 using a default kmer length of 31 and an index constructed from the Ensembl Mus musculus GRCm38 cDNA transcriptome dataset. For each library, transcript counts were consolidated into counts-per-gene using the R/BIOCONDUCTOR package tximport v1.4.0.3.

source_name: DR-derived injured hepatocytes

extract_protocol:
RNA extraction protocol not provided.
Libraries of experiment 1  were prepared starting from 150 ng of total RNA and using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA) following the standard protocol (Part#15031047 Rev.E). Libraries of experiment 2 were constructed by  starting from 150 ng of total RNA and using the KAPA RNA HyperPrep Kit with RiboErase (HMR) kit(KAPA Biosystems) according to manufacturer’s recommendations (KR1351 – v1.16)

value: liver

value: primary liver cells - hepatocytes

tag: liver status

value: Chronic injury


title: WT4

city: San Francisco

first: Sarah

last: Knox

state: California

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

data_processing:
cDNA libraries were prepared using the TruSeq RNA Library Preparation Kit v2, Set A (Illumina Inc, San Diego, CA, USA) using 1 µg RNA and were then 50 bp single-end sequenced on an Illumina HiSeq 4000. Quality control metrics were performed on raw sequencing reads using the FASTQC v0.11.6 application
Reads were mapped to the Mus musculus genome (mm10 build) using Spliced Transcripts Alignment to a Reference (STAR).  At least 90% of the reads were successfully mapped. Reads aligning to the University of California, Santa Cruz (UCSC) mm10 build were quantified against Ensembl Transcripts release 93 using Partek® E/M (Partek’s optimization of the expectation maximization algorithm, Partek Inc, St.Louis, MO, USA), which disregarded any reads that aligned to more than one location or more than one gene at a single location
Data was normalized by two procedures: 1. total count normalization, 2. addition of a small offset (0.0001).
After normalizing, differential gene expression was determined using the Differential gene expression (GSA) algorithm (Partek). This algorithm generates p values using limma-trend method. Genes were considered differentially expressed if the log2  Fold Change between samples was at least 1, with the adjusted p-value held to 0.01. We considered only genes with values of at least ten fragmetns per kilobase of transcript per million mapped reads (FPKM) in at least one biological replicate.
Gene Ontology analysis: A gene list of all significantly modulated genes (p < 0.01) was used as input for gene ontology (GO) analysis using Partek software. The resulting output was ranked by adjusted p-value (Fisher’s exact test on the underlying contingency table). We consider an attribute to be significant if its Expression Analysis Systematic Explorer (EASE) score (Fisher exact test p value) is less than 0.05 relative to an appropriate background gene set. Gene sets were selected to highlight unique features of the enrichment analysis.
Genome_build: mm10 build
Supplementary_files_format_and_content: txt , excel file and PDF files were generated. Txt files contain gene counts and gene lists; excel file contains differentially expressed genes and the PDF contains a GO list

source_name: lacrimal gland wild type

extract_protocol:
Lacrimal glands were removed, flash sonnicated in RNA lysis buffer, and RNA was harvested using RNAqueous™ Total RNA Isolation Kit (Invitrogen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Balbc

tag: age

value: 5 weeks

value: wild type

value: lacrimal gland


title: KO1

source_name: lacrimal gland mutant

value: Aire-/-


title: HFD-IAT_Stromal vascular cells 3


title: KO2


title: HFD-EAT_Stromal vascular cells 2


title: KO-Eff_Rep2

data_processing:
The 10 paired-end libraries were mapped to the GRCm38/mm10 reference genome by using Subread-1.5.1. Only uniquely mapped read-pairs were allowed in mapping. Peaks were then called from the 10 libraries by using Macs2 (v2.1.0.20150603) at an FDR cutoff of 0.01.
The peaks from the 10 libraries were merged by taking the unions of the peaks. The merged peaks were then assigned to the extended gene bodies in the NCBI RefSeq gene annotation for mm10 (build 38.1); the gene bodies were extended 20kb to their 5’ ends and 5kb to their 3’ ends. The mapped read-pairs in each library were assigned to the merged peak regions by using featureCounts.
Counts of read-pairs on the merged peaks were converted to log2 CPM values, quantile normalized and precision weighted with the “voom” function of the limma package.
A linear model was fitted to each merged peak, and empirical Bayes moderated t-statistics were used to assess differences of accessibility of the chromatin. The False Discovery Rates (FDR) was calculated for each merged peak on comparisons; a peak was called as differential between the two conditions if its FDR is less than 0.05.
The merged peaks were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1). Multiple peaks can be assigned to the same gene, and the peak that has the most significant FDR value was selected to represent the gene for drawing the scatter plots.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text files include normalized log2-CPM values in each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read-pair counts for merged peaks in each library.

source_name: KO-Eff

extract_protocol:
Cell lysates were treated with Tn5 transposease and DNA was purified following the protocol outlined in Buenrostro et al. 2015 Curr. Protoc. Mol. Biol. 109:21.29.1-9 and Buenrostro et al 2013 Nat. Med. 10(12):1213-8.
Libraries were generated following the following the protocol outlined in Buenrostro et al. 2015 Curr. Protoc. Mol. Biol. 109:21.29.1-9 and Buenrostro et al 2013 Nat. Med. 10(12):1213-8.

treatment_protocol: CD8+ T cells (30,000 cells per replicate) were FACS sorted from mouse spleen and lymph node, washed with PBS and lysed immediately prior to the transposition reaction.

tag: strain background

value: Spleen and Lymph node

value: CD8+ T cells

tag: cell subtype


title: WT-Mem_Rep2

source_name: WT-Mem


title: Experiment 2 DR-derived hepatocytes – GREEN 2

description:
Experiment 2 Sample 8
processed data file:
Experiment2.txt
RNA-16w3Green_S53


title: WT-Eff_Rep2

source_name: WT-Eff


title: HFD-IAT_Stromal vascular cells 1


title: HFD-EAT_Stromal vascular cells 1


title: WT3


title: KO3


title: negative control

source_name: N87 cells transfected with negative control

value: male

value: gastric carcinoma


title: WT2


title: Experiment 2 Native tdTomato hepatocytes – RED 4

description:
Experiment 2 Sample 6
processed data file:
Experiment2.txt
RNA-16w4Red_S51

source_name: Native injured tdTomato hepatocytes


title: WT-Mem_Rep1


title: Experiment 2 DR-derived hepatocytes – GREEN 1

description:
Experiment 2 Sample 7
processed data file:
Experiment2.txt
RNA-16w2Green_S52


title: HFD-IAT_Adipocyte 2

source_name: Adipocytes

value: Primary mouse adipocytes

value: inguinal


title: WT1


title: Experiment 2 Native tdTomato hepatocytes – RED 3

description:
Experiment 2 Sample 5
processed data file:
Experiment2.txt
RNA-16w3Red_S50


title: KO-Tc17_Rep2

data_processing:
The 10 paired-end libraries were mapped to the GRCm38/mm10 reference genome by using Subread-1.5.1. Only uniquely mapped read-pairs were allowed in mapping. Peaks were then called from the 10 libraries by using Macs2 (v2.1.0.20150603) at an FDR cutoff of 0.01.
The peaks from the 10 libraries were merged by taking the unions of the peaks. The merged peaks were then assigned to the extended gene bodies in the NCBI RefSeq gene annotation for mm10 (build 38.1); the gene bodies were extended 20kb to their 5’ ends and 5kb to their 3’ ends. The mapped read-pairs in each library were assigned to the merged peak regions by using featureCounts.
Counts of read-pairs on the merged peaks were converted to log2 CPM values, quantile normalized and precision weighted with the “voom” function of the limma package.
A linear model was fitted to each merged peak, and empirical Bayes moderated t-statistics were used to assess differences of accessibility of the chromatin. The False Discovery Rates (FDR) was calculated for each perged peak on comparisons; a peak was called as differential between the two conditions if its FDR is less than 0.05.
The merged peaks were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1). Multiple peaks can be assigned to the same gene, and the peak that has the most significant FDR value was selected to represent the gene for drawing the scatter plots.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text files include normalized log2-CPM values in each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read-pair counts for merged peaks in each library.


title: HFD-IAT_Adipocyte 1


title: embryo7-2,1,P

first: Michelle

middle: M

last: Chan

state: CA

institute: UCSF

description: CRISPR-based lineage traced embryo

data_processing:
10x cellranger v2.0.1
Normalization in Seurat ("LogNormalize")
Genome_build: mm10
Supplementary_files_format_and_content: normalized UMI counts (mtx), gene names (tsv), and cellIDs (tsv); allele table containing filtered lineage tracer calls.
Supplementary_files_format_and_content: *nwt.txt: Newick files represent the best reconstructed tree. embryo2_BestTreeGreedy.nwt.txt represents the final tree for the embryo2a and embryo2b samples merged.

source_name: E8.5 embryo

growth_protocol: Mouse embryos were cultured in vitro in KSOM at 37 ºC in 5% CO2 from the zygote to the blastocyst stage and subsequently transferred into the uterine horns of pseudopregnant females until isolation 6 or 7 days later.

extract_protocol:
Embryos were dissociated to single cell suspensions by adding 100 uL of TrypLE (Invitrogen, #12605010) and pipetting the embryo or embryo pieces every 5 minutes for ~30 minutes until complete dissociation was visually confirmed.  Trypsin was deactivated by adding 100 uL  PBS+BSA is added to the droplet and moving cells into a 1.5 mL eppendorf tube, followed by several rounds of additional collection with 100 to 200 uL of PBS+BSA to a final volume of 1 mL. Single cells were lysed in droplets using the 10x Chromium instrument.
10X Genomics Chromium Prep v2

treatment_protocol: To enable in vivo lineage tracing, B6D2F1 strain female mice (age 6 to 8 weeks, Jackson Labs) were superovulated by sequential intraperitoneal injection of Pregnant Mare Serum Gonadotropin (5IU per mouse, Prospec Protein Specialists) and Human Chorionic Gonadotropin (5IU, Millipore) 46 hours apart.  Twelve hours after delivery of the second hormone, MII stage oocytes were isolated and injected with in vitro transcribed piggyBAC transposase mRNA (100 ng/ul) prepared in an injection buffer (5 mM Tris buffer, 0.1 mM EDTA, pH = 7.4).  Decapitated sperm isolated from an 8 week old Gt(ROSA)26Sortm1.1(CAG=cas9*,EGFP)Fezh/J strain mouse (Jackson labs, PMID 25263330) was resuspended with the purified piggyBAC library in the same injection buffer at concentrations ranging from 0.5 to 1.4 ug/uL.  Transposase-injected oocytes were then fertilized by piezo-actuated intracytoplasmic sperm injection (ICSI) as previously described (PMID 17406589).  Injected embryos were cultured in 25 uL EmbryoMax® KSOM drops (Millipore) covered in mineral oil (Irvine Scientific) in batches of 25-50 embryos.  After 84 or 96 hours, successfully cavitated blastocysts were screened for uniform fluorescence of the target sequence cassette and transferred into one uterine horn of 6-10 week old pseudopregnant CD-1 strain female mice (Charles River).  Uterine transfer results in an ~24 hour lag, so the day of transfer was scored as E2.5 and embryos were dissected from euthanized animals 6 or 7 days later at ~E8.5 or E9.5, depending on the experiment.

tag: developmental stage

value: whole embryo


title: Experiment 2 Native tdTomato hepatocytes – RED 2

description:
Experiment 2 Sample 4
processed data file:
Experiment2.txt
RNA-16w2Red_S49

tag: cell type


title: HFD-EAT_Adipocyte 2

value: epididymal


title: HFD-EAT_Adipocyte 3


title: WT-Eff_Rep1


title: KO-Tc17_Rep1


title: Experiment 2 native Healthy hepatocytes - CTL 5

description:
Experiment 2 Sample 3
processed data file:
Experiment2.txt
RNA-CTL5_S48

source_name: native Healthy hepatocytes

value: Control


title: HFD-EAT_Adipocyte 1


title: KO-Mem_Rep1

source_name: KO-Mem


title: KO-Mem_Rep2


title: Tumor Endothelial Cells (TEC)

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description: 10X genomics single cell data

data_processing:
FASTQ files created from basecall files using 10X genomics Cellranger v2.0.2
Reads mapped using STAR 2.5.1b and read counts created with Cellranger 2.0.2
Filtered gene-barcode matrices were imported into R using the Seurat package, keeping all genes expressed in at least five cells and all cells with at least 200 detectable expressed genes. We employed a global-scaling normalization that normalizes gene expression measurements for each cell by the total expression and log-transforms the result, followed by identification of highly variable genes to use for downstream analyses. We used the unsupervised graph-based clustering followed by principal component analysis (PCA) and t-stochastic neighbor embedding (tSNE) to identify 10 populations overall. Furthermore, we used the canonical correlation analysis (CCA) based approach to “align” the datasets such that gene expression and differential expression could be analyzed without confounding batch effects.
Genome_build: mm10
Supplementary_files_format_and_content: csv file of raw read counts by gene for each sample (tumor or control and cell barcode per column)

source_name: Endothelial Cells

growth_protocol: Female 8 week old C57BL6/J mice (Cdh5Cre-ERT2:ZSGreenl/s/l, administered tamoxifen to induce ZSGreen expression) were injected in the mammary fat pad with 1X10^6 syngeneic EO771 mammary tumor cells. Tumors were allowed to grow for ~ three weeks at which point mice were euthanized and tumors or normal counterpart mammary glands were collected.

extract_protocol:
Normal tissues or tumors were harvested and dispersed into single cell suspensions in a collagenase/dispase/DNAse cocktail according to our published methods (Xiao et al. Cancer Research 2014). After filtering and washing the suspensions, samples were subjected to FACS (fluorescence activated cell sorting) to collect live ZSGreen+ cells from each fraction (a live/dead stain was added to exclude dead cells). The collected fractions were prepared for analysis using the 10X genomics platform.
Libraries were prepared for sequencing on the 10X chromium according to the manufacturer's instructions for the single cell 3' reagent kit.

treatment_protocol: There were no treatments used in this study.

value: Tumor Endothelial Cells


title: Experiment 2 native Healthy hepatocytes - CTL 2

description:
Experiment 2 Sample 2
processed data file:
Experiment2.txt
RNA-CTL2_S47

value: liver

value: primary liver cells - hepatocytes


title: embryo4-2,1,2

description: CRISPR-based lineage traced embryo


title: embryo6-2,1,2

description: CRISPR-based lineage traced embryo


title: embryo3-1,1,1

description: CRISPR-based lineage traced embryo


title: Experiment 2 native Healthy hepatocytes - CTL 1

description:
Experiment 2 Sample 1
processed data file:
Experiment2.txt
RNA-CTL1_S46


title: LRH-1_+OvS

city: Sherbrooke

first: Nicolas

last: Gévry

state: Québec

address: 2500 boulevard de l'université

country: Canada

institute: Université de Sherbrooke

description: 2 replicats

data_processing:
For ChIP-seq, reads were aligned to the mouse reference genome mm9 using BWA. Peak calling was performed using MACS (2.1.0) with q-value of 0.01. Bedtools intersect (2.25.0) was used to identify overlaps between conditions.
Genome_build: mm9

source_name: ovarian granulosa cells

extract_protocol:
Ovarian tissues collected following 0 and 4h post hCG (n=5 per condition) were washed in PBS, sliced in small pieces, and fixed 15 min in 1X PBS/1.1% formaldehyde with agitation. After glycine add and PBS wash, fixed tissues were incubated in lysis buffer and mechanically disrupted with an ice-cold Dounce. Chromatin was then sonicated in a Bioruptor apparatus (Diagenode) on “high”-intensity position for 30 s ON and 30 s OFF for 15 cycles at 4 °C, cleared by a 10 minutes centrifugation at 10 000 x g and checked on agarose gel. ChIP experiments were performed using 10µg of LRH-1 antibody with the use of magnetic protein A dynabeads (Life Technologies) for the immunoprecipitation. After wash, elution and decross-link, samples were purified using QIAquick® PCR purification kit (QIAGEN) and quantified with PicoGreen™ assay (Invitrogen).
Librairies were performed as previously described (Bianco et al., Methods Mol Biol, 2015)

treatment_protocol: Super stimulation was achieved in 22- to 25-day-old mice by intraperitoneal injection of 5 IU equine chorionic gonadotropin (eCG) to stimulate follicular development, followed by the injection of 5 IU of human chorionic gonadodotropin (hCG) 44 hours post eCG, to induce ovulation.

tag: antibody

value: ovarian granulosa cells


title: Normal Endothelial Cells (NEC)

description: 10X genomics single cell data

value: Normal Endothelial Cells


title: LRH-1_-OvS

description: 2 replicats


title: embryo2b-1,1,1

description: CRISPR-based lineage traced embryo


title: Experiment 1 DR-derived hepatocytes – GREEN 5

description:
Experiment 1 Sample 10
processed data file:
Experiment1.txt
RNA-16w5Green_S10

value: Chronic injury


title: mix 2302: HepG2 sgRNA CATE-seq

city: Nanjing

first: Xu

last: Xinhui

address: Sipailou 2#

institute: SEU

description: The 2302 sgRNA CATE-seq  samples of HeLa and HepG2 were mixed for sequencing, then split each sample by barcode sequence.

data_processing:
Library strategy: CATE-seq
The raw reads data were separated according to the barcode using a homemade Python scripts.
All reads were cut 25 bp at 5' by a homemade Python scripts.
The trimmed reads were aligned to the human genome (hg19) using Bowtie program (version 1.1.2)
The sorted bam files were convert to bedgraph files using genomeCoverageBed.
The bedgraph files were convert to bigwig using the program wigToBigWig.
Genome_build: hg19

growth_protocol: HepG2, HeLa cells were cultivated with the DMEM medium (HyClone) supplemented with 10% fetal bovine serum (HyClone), 100 U/mL penicillin, and 100 μg/mL streptomycin (Biosharp).  Cells were incubated at 37°C in a 5% CO2 incubator.

extract_protocol:
Cells were inoculated into a 25 cm2 culture flask and cultured in complete medium for 24 h (degree of fusion greater than 80%). Cells were then washed twice with pre-chilled PBS and collected by trypsinization. The genomic DNA (gDNA) was extracted from cells by using the TIANamp Genomic DNA Kit (Tiangen).
The extracted gDNAs of HepG2 and HeLa cells were tagmented by the Tn5 transposomes T-B-1 and T-B-6, respectively. The tagmentation reaction (30 μL) contained 150 ng gDNA, 5 μL transposome, 6 μL 5× LM buffer, and certain volume of ddH2O that supplemented the total reaction to 30 μL. The reaction was incubated at 55°C for 15 min. The reaction contained no transposome was used as control. The tagmentation products were run with agarose gel and the fragments of 200–1000 bp were recovered, which were used as the input DNA for enriching target sequences.The dCas9 protein was diluted to 0.3 μM with stock solution and stored at -20° C. The csgRNAs were mixed into four groups according to their numbering. In each mixing, about 7.5 ng of each csgRNA was used. Five μL of magnetic beads with streptavidin was added to 50 μL of PBS containing 0.5% BSA and placed on a magnetic stand for 15 s. The supernatant was aspirated. After washing three times with 50 μL of PBS-BSA solution, the beads were added with 50 μL of 1×dCas9 buffer and 2 μL of capture oligonucleotide (10 μM). The sequence of capture oligonucleotide was 5′-Biotin-TTTTTTTGCA TCTGGTATTC GTAAGGTTCC G-3′. The beads were mixing by rotation for 1 hour. The beads were washed three times with 50 μL of 1×dCas9 buffer.

tag: fragment method

value: Tagmentation


title: Experiment 1 DR-derived hepatocytes – GREEN 4

description:
Experiment 1 Sample 9
processed data file:
Experiment1.txt
RNA-16w4Green_S9

tag: tissue


title: embryo2a-1,1,1

description: CRISPR-based lineage traced embryo


title: KO-Eff_Rep1

tag: genotype/variation


title: Experiment 1 Native tdTomato hepatocytes – RED 5

description:
Experiment 1 Sample 8
processed data file:
Experiment1.txt
RNA-16w5Red_S8


title: mix 2302: HeLa sgRNA CATE-seq

source_name: HeLa

value: HeLa


title: FAIRE_+OvS

description: 2 replicats

data_processing:
For FAIRE-seq, reads were aligned to the mouse reference genome mm9 using Burrows-Wheeler Aligner (BWA). Peak calling was performed using Model-based Analysis for ChIP-Seq (MACS) with p-value of 0.0001.
Genome_build: mm9

extract_protocol:
After euthanasia, ovaries were collected and granulosa cells were isolated by ovarian puncture at 0 hours (-OvS) and 4 hours post hCG (+OvS). FAIRE-seq was performed as previously described (Bianco et al., Methods Mol Biol, 2015)
Librairies were performed as previously described (Bianco et al., Methods Mol Biol, 2015)


title: embryo1-P,1,P

description: CRISPR-based lineage traced embryo


title: embryo5-2,1,2

description: CRISPR-based lineage traced embryo


title: HFD-IAT_Adipocyte 3


title: FAIRE_-OvS

description: 2 replicats


title: Experiment 1 Native tdTomato hepatocytes – RED 4

description:
Experiment 1 Sample 7
processed data file:
Experiment1.txt
RNA-16w4Red_S7


title: Neural crest derived cells from 5 dpf , euthyroid zebrafish tails

first: David

last: Parichy

address: 409 McCormick Road, Department of Biology, PLSB 339

department: Biology

institute: University of Virginia

description:
Data collected from mCherry positive cells that were FAC sorted from single cell suspensions of cells from whole tails of 5dpf zebrafish. Single cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 2 of their single-cell solution kit.
all_NC_matrix.mtx
all_NC_genes.tsv
all_NC_barcodes.tsv
NC-deriv_5dpf_metadata.tsv

data_processing:
Expression matrix files and BAM files were generated using cellranger (10X genomics) version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries.
Genome_build: GRCz11
Supplementary_files_format_and_content: Expression matrix files and BAM files were generated using cellranger (10X genomics) version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.

organism: Danio rerio

source_name: sox10:Cre+ cells from 5 dpf zebrafish tail tissue

growth_protocol: Zebrafish were maintained at ~28.5 °C under 14:10 light:dark cycles. All thyroid-ablated (Mtz-treated) and control (DMSO-treated) Tg(tg:nVenus-v2a-nfnB) fish were kept under TH-free conditions and were fed only Artemia, rotifers enriched with TH-free Algamac (Aquafauna), and bloodworms.

extract_protocol:
10X genomics single cell gene expression V2 protocol following manufacturer recommendations.
10X genomics single cell gene expression V2 protocol following manufacturer recommendations.

treatment_protocol: Transgenic zebrafish, Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), were treated either metronidazole (10mM) or a vehicle control (DMSO) at 4dpf. Trunks or skins were collected at a stage range of 7.2-10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.

value: 2154 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from tails of 5 dpf zebrafish.

tag: treatment

value: Untreated


title: Neural crest derived cells from hypothyroid, post-embryonic zebrafish trunks, biological replicate 6

description:
Data collected from mCherry positive cells that were FAC sorted from single cell suspensions of cells from whole trunks of zebrafish, staged 7.2-10.4 SSL. Single cell RNA-seq sample and final sequencing library preparation was performed as outlined in documentation from 10X genomics for version 2 of their single-cell solution kit.
all_NC_matrix.mtx
all_NC_genes.tsv
all_NC_barcodes.tsv
NC-deriv_eu_hypothyroid_metadata.tsv

source_name: sox10:Cre+ cells from post-embryonic zebrafish trunk tissue

value: 1888 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2-10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.

value: Hypothyroid


title: Experiment 1 Native tdTomato hepatocytes – RED 3

description:
Experiment 1 Sample 6
processed data file:
Experiment1.txt
RNA-16w3Red_S6


title: Neural crest derived cells from hypothyroid, post-embryonic zebrafish trunks, biological replicate 7

value: 2650 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2-10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.


title: TBL20_3

city: Glasgow

first: Victoria

last: Gillan

address: bearsden road

institute: University of Glasgow

data_processing:
Single end sequencing reads were cleaned with quality filter, adapter cutter, and length filter, using ACGT101_miR_v4.2g from LC Sciences.
The cleaned reads were mapped to miRBase (miRBase v21) using Bowtie v1.1.1.
The un-mapped reads were mapped to multiple databases including mRNA (NCBI Bos taurus/RNA build 09/14/2010), Rfam11, and genomic DNA (NCBI Btau 4.2), using Bowtie v1.1.1.
Novel miRNA candidates were identified from genome mapped reads based on the propensity of hairpin formation in corresponding genome positions, using ACGT101_miR_v4.2g from LC Sciences.
Data were normalized by dividing sequence counts of individual samples by corresponding normalization factors which are the median values of the ratios between specific sample counts and geometric mean counts of all samples.
Genome_build: ftp://ftp.ncbi.nih.gov/genomes/Bos taurus, Btau 4.2
Supplementary_files_format_and_content: read summary and normalized data
Supplementary_files_format_and_content: Test resutls
Supplementary_files_format_and_content: final report

organism: Bos taurus

source_name: B cell lymphoma cell line

growth_protocol: Cells were routinely maintained in culture at 37°C in RPMI with 20% foetal calf serum (FCS)

extract_protocol:
100ml of cell culture was centrifuged at 300 x g for 10 minutes, 2000 x g for 10 minutes and 10,000 x g for 30 minutes, with cells and cell debris discarded at each stage. EV were then pelleted by ultracentrifugation using a Surespin 630 rotor (Sorvall) at 100,000 x g for 70 minutes, washed in sterile PBS and finally centrifuged at 100,000 x g for 70 minutes before resuspending in 100 ml of PBS.
RNA libraries were prepared for sequencing using standard Illumina protocols by LC Sciences (Texas)

value: extracellular vesicles


title: TBL20_2


title: Neural crest derived cells from hypothyroid, post-embryonic zebrafish trunks, biological replicate 4

value: 941 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2-10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.


title: Neural crest derived cells from hypothyroid, post-embryonic zebrafish trunks, biological replicate 5

value: 774 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2-10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.


title: Experiment 1 native Healthy hepatocytes - CTL 5

description:
Experiment 1 Sample 3
processed data file:
Experiment1.txt
RNA-CTL5_S3

value: Control


title: BL20_3


title: BL20_2


title: CAST liver 1

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

data_processing:
Trim Galore! 0.3.7
Bismark 0.16.1 (Bowtie2 2.1.0) [options: --bowtie2 --bam]
Bismark Methylation Extractor 0.16.1 [options: -p --ignore 5 --ignore_r2 5 --ignore_3prime 1 --ignore_3prime_r2 1]
Modmap (Modtools 1.0.2)
Genome_build: mm9 (BL6/CAST)
Supplementary_files_format_and_content: Processed read-level measurements of CpG methylation. Each file contains data on reads aligned to either the BL6 or CAST reference, and in either BL6 or CAST genomic coordinates. Each line has information on chromosome and position (forward strand) and number of methylated and total reads. Also indicated is whether each position is a retained CpG (1) or whether the CpG has been lost through mutation (0) in the BL6 or CAST genome.

source_name: Liver

extract_protocol:
Qiagen Dneasy Kit
TruSeq DNA LT Sample Preparation Kit

value: CAST/EiJ


title: Neural crest derived cells from hypothyroid, post-embryonic zebrafish skins, biological replicate 2

source_name: sox10:Cre+ cells from post-embryonic zebrafish skin tissue

value: 3033 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2-10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.


title: BL6 liver 4


title: CAST liver 3


title: BL6 liver 3


title: CAST liver 2


title: Experiment 1 native Healthy hepatocytes - CTL 3

description:
Experiment 1 Sample 1
processed data file:
Experiment1.txt
RNA-CTL3_S1

value: liver

value: primary liver cells - hepatocytes


title: Neural crest derived cells from hypothyroid, juvenile zebrafish trunks, biological replicate 1

value: 2135 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.


title: BL6 liver 2


title: CAST liver 4


title: Experiment 1 Native tdTomato hepatocytes – RED 2

description:
Experiment 1 Sample 5
processed data file:
Experiment1.txt
RNA-16w2Red_S5

value: Chronic injury


title: Neural crest derived cells from euthyroid, post-embryonic zebrafish trunks, biological replicate 6

value: 2384 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2-10.4 SSL stage zebrafish

value: Euthyroid


title: Experiment 1 Native tdTomato hepatocytes – RED 1

description:
Experiment 1 Sample 4
processed data file:
Experiment1.txt
RNA-16w1Red_S4


title: Experiment 1 native Healthy hepatocytes - CTL 4

description:
Experiment 1 Sample 2
processed data file:
Experiment1.txt
RNA-CTL4_S2


title: TBL20_0


title: TBL20_1


title: BL6 liver 1


title: Neural crest derived cells from hypothyroid, post-embryonic zebrafish trunks, biological replicate 3

value: 1073 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2-10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.


title: Neural crest derived cells from euthyroid, post-embryonic zebrafish trunks, biological replicate 5

value: 807 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2-10.4 SSL stage zebrafish


title: Neural crest derived cells from euthyroid, post-embryonic zebrafish trunks, biological replicate 4

value: 808 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2-10.4 SSL stage zebrafish


title: BL20_0


title: BL20_1


title: Neural crest derived cells from euthyroid, post-embryonic zebrafish trunks, biological replicate 3

value: 944 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2-10.4 SSL stage zebrafish


title: WT_mem_rep1

state: Victoria

address: Wellington Rd

data_processing:
Around 20 million reads were generated for each replicate and aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least two libraries.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the voom function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less and also had at least 8 RPKMs (reads per kilo exonic bases per million mapped reads) in one or both of the two cell types being compared.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-RPKM values for each gene in each library.

extract_protocol:
Total RNA was prepared from purified CD8 T cell populations using an RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Wild type

value: spleen

value: CD8 T cell

tag: cell subset

value: Memory


title: WT_naive_rep1

value: Naïve


title: WT_mem_rep2


title: WT_naive_rep2


title: WT_eff_rep2

value: Effector


title: Neural crest derived cells from euthyroid, post-embryonic zebrafish skins, biological replicate 2

value: 3008 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from skins. Zebrafish  range in stage from 7.2-10.4 SSL.


title: Neural crest derived cells from euthyroid, post-embryonic zebrafish trunks, biological replicate 1

value: 2168 cells from Tg(sox10:Cre; ubi:switch; tg:nVenus-2a-nfnB), FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage (juvenile).


title: KO_naive_rep2

value: Tcf7 Knockout


title: WT_eff_rep1