title: Input

data_processing:
Sequence reads were aligned to the mouse reference genome (version mm9) with STAR (Dobin et al. 2013, Bioinformatics , 29: 15) set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
KDM5A ChIP-seq and matching Input tag counts were normalized to 10M reads using HOMER.
Tag directories for each ChIP-seq library were generated using HOMER. BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles
Genome_build: mm9
Supplementary_files_format_and_content: H3K4me3_promoter_peaks_tags.txt: Table containing promoter H3K4me3 binding sites, including normalized tag counts for H3K4me3 libraries
KDM5A_all_peaks_tags.txt: Table containing all identified KDM5A binding sites, including normalized tag counts for KDM5A libraries
KDM5C_all_peaks_tags.txt: Table containing all identified KDM5C binding sites, including normalized tag counts for KDM5C libraries
RNA_all_genes_log2_tags_kb.txt: Table containing gene expression data for all RNA-seq libraries (reported as log2(tags/kb))


title: 1772078013_A01

status: Public on Dec 01 2016

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited file of mRNA molecule counts for each gene and cell. Cells with less than 1500 molecules have been removed from this file.

molecule: polyA RNA

organism: Mus musculus

source_name: hypothalamus

growth_protocol: C57BL/6N mice were housed conventionally (12/12-h light cycle, 55% humidity).

extract_protocol:
Mice were deeply anesthetized (5% isoflurane) and transcardially perfused with 40 ml ice-cold pre-oxygenated (95% O2/5% CO2) cutting solution containing (in mM): 90 NaCl, 26 NaHCO3, 2.5 KCl, 1.2 NaH2PO4, 10 HEPES-NaOH, 5 Na-ascorbate, 5 Na-pyruvate, 0.5 CaCl2, 8 MgSO4 and 20 glucose. A central column of the mouse hypothalamus spanning the preoptic area-Arc (rostrocaudal axis), paraventricular nucleus (dorsal) and the ventrolateral hypothalamic area (lateral) was microdissected from serial 300-micrometer-thick coronal slices under microscopy guidance and dissociated using the Papain Dissociation System (Worthington). Isolated single cells were concentrated by centrifugation to a density of 600-1,000 cells/?microlitre. After mixing C1 suspension reagent (4 microlitre; "C1 reagents", Fluidigm Inc.) to the cell suspension (7 microlitre), this mixture was loaded into a C1-AutoPrep IFC microfluidic chip (Fluidigm Inc.)
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

treatment_protocol: Formalin stress was induced by injection of 4% PFA into the left paw

tag: strain

tag: age (days postnatal)

tag: Sex

value: M

tag: acute stress

value: N

tag: cell diameter

tag: total molecules

tag: level1 class

value: oligos


title: H3K4tri shKdm5ABC Day 2 exp. 2

city: Odense M

first: Ann-Sofie

middle: Bøgh

last: Brier

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark, Odense

description: processed data file: H3K4me3_promoter_peaks_tags.txt

library_source: genomic

data_processing:
Sequence reads were aligned to the mouse reference genome (version mm9) with STAR (Dobin et al. 2013, Bioinformatics , 29: 15) set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
For normalization of H3K4me3 and matching input libraries a two-stage normalization was used. First, genome-scale normalization on background reads were done by counting tags in 10kb windows throughout the genome as described in (Lun and Smyth, 2014, Nucleic Acid Res. 42:1-11) and normalized using a relative log expression (RLE) method normalization (Love et al., 2014, Genome Bio. 15: 550). Second, the signal in peaks was normalized for each condition over time, but not across conditions.
Regions enriched for H3K4me3 were called using HOMER with the ‘-histone’ setting and requiring each putative peak to have 10-fold more normalized tags in the target experiment than the input control. For the individual H3K4me3 region files, overlapping peak regions were merged into one region and high confidence promoter proximal regions were identified as being within ±3kb of transcriptional start site (TSS) and having more than 50 tags/kb in at least one of the conditions.
Tag directories for each ChIP-seq library were generated using HOMER. BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles
Genome_build: mm9
Supplementary_files_format_and_content: H3K4me3_promoter_peaks_tags.txt: Table containing promoter H3K4me3 binding sites, including normalized tag counts for H3K4me3 libraries
KDM5A_all_peaks_tags.txt: Table containing all identified KDM5A binding sites, including normalized tag counts for KDM5A libraries
KDM5C_all_peaks_tags.txt: Table containing all identified KDM5C binding sites, including normalized tag counts for KDM5C libraries
RNA_all_genes_log2_tags_kb.txt: Table containing gene expression data for all RNA-seq libraries (reported as log2(tags/kb))

molecule: genomic DNA

source_name: 3T3-L1_H3K4tri shKdm5ABC Day 2

extract_protocol:
ChIP experiments were performed in 3T3-L1 cells essentially as previously described (Siersbæk et al. 2012, MCB, 32: 3452-3463). For cross-linking of chromatin, 0.2 mM disuccinimidyl glutarate (DSG) was applied (Proteochem, Denver, CO) for 45 min followed by cross-linking using 1% formaldehyde for 10 min.
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: Two days post confluency (day 0), 3T3-L1 cells were induced to differentiate using a standard cocktail of adipogenic inducers (dexamethasone, insulin, 3-isobutyl-1-methylxanthine, and fetal bovine serum). Two days post induction (day 2), medium was changed to DMEM supplemented with fetal bovine serum and insulin. Cells were maintained in DMEM supplemented with fetal bovine serum for the remainder of the differentiation. For knock down experiments, pre-confluent 3T3-L1 cells were transduced 4 days before induction of differentiation by incubation for 24 hours at 37°C with medium containing lentiviral constructs (shKDM5A/B/C or control shLuc) and 6 μg/mL polybrene (Sigma). After 24 hours the medium was changed to normal growth medium.

tag: cell line

tag: cell type

value: Preadipocyte cell line

tag: transduced with

tag: time point

value: Two days post induction (day 2)

tag: chip antibody

value: Anti-Histone H3 (tri methyl K4) antibody (ab8580, Abcam)


title: 1772075319_H08

value: neurons

tag: level2 class (neurons only)


title: 1772075319_H01


title: 1772075319_H02


title: H3K4tri shKdm5ABC Day 2 exp. 1


title: H3K4tri shKdm5ABC 4 hour exp. 2

source_name: 3T3-L1_H3K4tri shKdm5ABC 4 hour

value: 4 hours post induction


title: H3K4tri shKdm5ABC Day 0 exp. 2

source_name: 3T3-L1_H3K4tri shKdm5ABC Day 0

value: Two days post confluency (day 0)


title: 1772075319_G10

value: ependymal


title: H3K4tri shKdm5ABC Day 0 exp. 1


title: 1772075319_G08


title: H3K4tri shKdm5ABC 4 hour exp. 1


title: H3K4tri shLuc 4 hour exp. 2

source_name: 3T3-L1_H3K4tri shLuc 4 hour

value: control shLuc


title: H3K4tri shLuc Day 2 exp. 2

source_name: 3T3-L1_H3K4tri shLuc Day 2


title: 1772075319_G09


title: Kdm5A Day 2 exp. 1

description: processed data file: KDM5A_all_peaks_tags.txt

data_processing:
Sequence reads were aligned to the mouse reference genome (version mm9) with STAR (Dobin et al. 2013, Bioinformatics , 29: 15) set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
KDM5A ChIP-seq and matching Input tag counts were normalized to 10M reads using HOMER.
Regions enriched for KDM5A in the individual libraries were called using HOMER with the ‘-style histone’ and '-F 10' settings. For the individual KDM5A region files, overlapping peak regions were merged into one region and KDM5A peaks at each time point were identified as having 10-fold more average normalized tags over two replicates relative to the input control. Promoter proximal regions were identified as being within ±1kb of transcriptional start site (TSS) and distal binding sites between 5 and 50 kb away from TSS.
Tag directories for each ChIP-seq library were generated using HOMER. BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph formatted file that can then be uploaded as a custom track to the UCSC genome browser
KDM5A_all_peaks_tags.txt: Table containing all identified KDM5A binding sites, including normalized tag counts for KDM5A replicate libraries
KDM5C_all_peaks_tags.txt: Table containing all identified KDM5C binding sites, including normalized tag counts for KDM5C replicate libraries

source_name: 3T3-L1_Kdm5A Day 2

value: KDM5A antibody (ab70892; Abcam)


title: 1772075319_G02


title: H3K4tri shLuc Day 2 exp. 1


title: 1772075319_G03


title: 1772075319_G07


title: 1772075319_F12

value: Sst low-medium


title: 1772075319_G01


title: H3K4tri shLuc 4 hour exp. 1


title: H3K4tri shLuc Day 0 exp. 1

source_name: 3T3-L1_H3K4tri shLuc Day 0


title: 1772075319_F09


title: H3K4tri shLuc Day 0 exp. 2


title: 1772075319_F07


title: 1772075319_F03


title: RNA shKdm5ABC Day 2 exp.2

description: processed data file: RNA_all_genes_log2_tags_kb.txt

data_processing:
RNA reads were aligned to the mouse reference genome (version mm9) using Bowtie2 (version 0.12.8) (Langmead and Salzberg 2012, Nat Met 9: 357-359) with standard parameters. Splice-junction reads were handled by creation of a pseudo-splice genome, similar to the strategy utilized in RSEQTools (Habegger et al. 2011, Bioinformatics 27: 281-283). Reads were filtered post-alignment for a MAPQ score greater than or equal to 30. The number of exon reads for all RefSeq genes were counted using Subread (Liao et al. 2013, Nucleic Acids Res 41: e108) and differential expression analyses were performed using DESeq2 (FDR <0.05, paired analysis) (Love et al., 2014, Genome Bio. 15: 550).
Genome_build: mm9
Supplementary_files_format_and_content: H3K4me3_promoter_peaks_tags.txt: Table containing promoter H3K4me3 binding sites, including normalized tag counts for H3K4me3 libraries
KDM5A_all_peaks_tags.txt: Table containing all identified KDM5A binding sites, including normalized tag counts for KDM5A libraries
KDM5C_all_peaks_tags.txt: Table containing all identified KDM5C binding sites, including normalized tag counts for KDM5C libraries
RNA_all_genes_log2_tags_kb.txt: Table containing gene expression data for all RNA-seq libraries (reported as log2(tags/kb))

source_name: 3T3-L1_RNA shKdm5ABC Day 2

extract_protocol: Total RNA from 3T3-L1 cells was purified using TRIzol (Invitrogen) according to the manufacturer’s instructions. RNA was treated and the integrity of the RNA was confirmed using a Bioanalyzer 2100 (Agilent Technologies).  4 ug of total RNA was polyA-selected, and subsequently subjected to fragmentation and cDNA-synthesis using the TruSeq RNA Sample Prep kit v2 (Illumina). cDNA-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, Methods in Enzymology 2014, Vol. 537, pp. 261-279).

tag: molecule subtype

value: polyA-enriched mRNA


title: RNA shKdm5ABC 4 hour exp.2

source_name: 3T3-L1_RNA shKdm5ABC 4 hour


title: 1772075319_F02

value: GABA 2


title: Input virus

data_processing:
Sequence reads were aligned to the mouse reference genome (version mm9) with STAR (Dobin et al. 2013, Bioinformatics , 29: 15) set to not map across splice junctions (--alignIntronMax 1 --outSJfilterIntronMaxVsReadN 0)
For normalization of H3K4me3 and matching input libraries a two-stage normalization was used. First, genome-scale normalization on background reads were done by counting tags in 10kb windows throughout the genome as described in (Lun and Smyth, 2014, Nucleic Acid Res. 42:1-11) and normalized using a relative log expression (RLE) method normalization (Love et al., 2014, Genome Bio. 15: 550). Second, the signal in peaks was normalized for each condition over time, but not across conditions.
Tag directories for each ChIP-seq library were generated using HOMER. BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles
Genome_build: mm9
Supplementary_files_format_and_content: H3K4me3_promoter_peaks_tags.txt: Table containing promoter H3K4me3 binding sites, including normalized tag counts for H3K4me3 libraries
KDM5A_all_peaks_tags.txt: Table containing all identified KDM5A binding sites, including normalized tag counts for KDM5A libraries
KDM5C_all_peaks_tags.txt: Table containing all identified KDM5C binding sites, including normalized tag counts for KDM5C libraries
RNA_all_genes_log2_tags_kb.txt: Table containing gene expression data for all RNA-seq libraries (reported as log2(tags/kb))

source_name: 3T3-L1_Input virus


title: RNA shKdm5ABC Day 0 exp.2

source_name: 3T3-L1_RNA shKdm5ABC Day 0


title: 1772075319_E08

value: uc


title: 1772075319_E09

value: microglia


title: 1772075319_E07

value: M


title: RNA shLuc Day 0 exp.2

source_name: 3T3-L1_RNA shLuc Day 0


title: RNA shKdm5ABC Day 2 exp 1


title: 1772075319_E02

value: N

value: endothelial


title: 1772075319_D09


title: 1772075319_D11


title: RNA shKdm5ABC 4 hour exp 1

value: Preadipocyte cell line


title: RNA shLuc Day 0 exp 1


title: 1772075319_D12


title: 1772075319_D05


title: 1772075319_D03


title: RNA shKdm5ABC Day 0 exp 1


title: 1772075319_D01


title: 1772075319_B03


title: 1772075319_C09


title: 1772075319_A07

value: Adcyap1;Tac1 (VMH)


title: 1772075319_D02


title: 1772075319_A06


title: RNA shLuc Day 2 exp.2

source_name: 3T3-L1_RNA shLuc Day 2

value: Two days post induction (day 2)


title: RNA shLuc 4 hour exp.2

source_name: 3T3-L1_RNA shLuc 4 hour


title: 1772075317_H08

value: oligos


title: 1772075317_G12


title: 1772075317_H06

value: astrocytes


title: 1772075317_G11


title: 1772075319_E01


title: 1772075317_G09


title: RNA shLuc Day 2 exp 1


title: 1772075317_G03

value: neurons

value: Pomc+/- (ARH)


title: 1772075317_G06


title: RNA shLuc 4 hour exp 1

value: control shLuc

value: 4 hours post induction


title: 1772075317_G04


title: 1772075319_C01

value: ependymal


title: 1772075317_G02


title: 1772075317_F12


title: 1772075317_F09


title: 1772075317_F08


title: 1772075317_E10


title: 1772075317_F06

value: Hmit+/-


title: 1772075319_A11

value: Crh+/-;Gal-low (PVH)


title: 1772075317_F05


title: 1772075317_G01


title: 1772075317_E07

value: GABA 2


title: 1772075317_E09

value: uc


title: 1772075317_E05

value: M


title: 1772075317_D07

value: N


title: 1772075317_D10

value: Trh-low


title: 1772075317_E02


title: 1772075317_D06

value: endothelial


title: 1772075317_D05


title: 1772075317_G08


title: 1772075317_E01


title: 1772075317_C10

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772075317_D03

value: Vglut2 A


title: 1772075317_C03

value: oligos


title: 1772075317_C01


title: 1772075317_B12


title: 1772075317_C07


title: 1772075317_B07


title: 1772075317_B01


title: 1772075317_B02


title: 1772075317_B08

value: Qrfp


title: 1772075317_B09

value: neurons

value: Adcyap1;Tac1 (VMH)


title: 1772075317_A06


title: 1772075317_A08

value: Trh-medium


title: 1772075317_A07


title: 1772075317_A10


title: 1772075317_A05


title: 1772075317_E03


title: 1772075317_A09


title: 1772075317_A03

value: astrocytes


title: 1772075317_A04


title: 1772075310_H10


title: 1772075310_H12


title: 1772075310_H08


title: 1772075310_H05


title: 1772075310_H04


title: 1772075310_H02


title: 1772075310_G11

value: GABA 1


title: 1772075310_G10


title: 1772075310_G07


title: 1772075310_G08


title: 1772075310_G09


title: 1772075310_G06


title: 1772075310_G04


title: 1772075310_G02


title: 1772075317_A11


title: 1772075310_F09


title: 1772075310_F03


title: 1772075310_F06

value: ependymal


title: 1772075310_F12


title: HH32_whole_Input_r2

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

description: 1 lane

data_processing:
The sequencing reads of each sample were aligned to the chicken genome by BWA.
After removing PCR duplicates by samtools and removing singletons, we chose uniquely mapped reads to assess the signal-to-noise ratios for each sample using the SPP package.
The input samples of the same condition were merged, and ChIP-seq peaks for each sample were identified by the MACS2 with broad peaks mode (p<0.05).
To obtain the final peak set for each condition, we counted the aligned reads in the peak regions from each of the two replicate samples, and applied quantile normalization on the aligned reads to comparing these values across samples. We only kept reproducible intersected peaks that had an average coverage of >=1 in both replicates for each condition.
Genome_build: galgal3
Supplementary_files_format_and_content: BedGraph files were fold enrichment tracks generated by MACS2 bdgcmp; Bed files were the final peak files.

organism: Gallus gallus

source_name: chicken embryos

growth_protocol: Fertilized chicken eggs (Gallus gallus, White Leghorn) were incubated at 38°C.

extract_protocol:
Embryonic samples were dissected and dispersed by 0.05% trypsin (Gibco, 25300054) for 5 min at 37 oC. After adding an equal amount of FBS to stop the enzyme reaction, the cells were filtered using a cell strainer (BD Falcon, 352360). At least 5 x106 cells were used for the subsequent process. The cell lysates were sonicated 20 times (pulsed for 30 sec with 30 sec interval) using a Bioruptor (Cosmo Bio, UCD-300) at high power setting. Alternatively, we sonicated the lysates 17 times (pulsed for 15 sec with 60 sec interval) used a Vibra-Cell (Sonics & Materials, VCX130PB) at 20 % amplification setting. The samples were divided into four aliquot and added 10 µg of antibodies
For single ChIP enriched DNA or control DNA samples, ~10 ng genomic DNA per sample was end-repaired. Then the blunt ends fragments were treated with Klenow fragments and dATP to yield a protruding 3'-dA overhang. After adapter ligation, removal of unligated adapter and size selection, library fragments of 100~300 bp were purified from an agarose gel.

tag: tissue

value: whole embryo

tag: developmental stage


title: 1772075310_F05

value: Per2;circadian (SCH)


title: HH32_whole_H3K4me1_r2

description:
1 lane
HH32_whole_H3K4me1_overlaps.finalPeaks.bed

value: H3K4me1, abcam, ab8895


title: HH32_whole_H3K27me3_r1

description:
2 lane
HH32_whole_H3K27me3_overlaps.finalPeaks.bed

value: H3K27me3, Millipore, 07-449


title: HH32_whole_H3K27me3_r2

description:
1 lane
HH32_whole_H3K27me3_overlaps.finalPeaks.bed


title: 1772075310_E11

value: M

value: N


title: 1772075310_F04


title: 1772075310_E10


title: HH32_whole_H3K27ac_r2

description:
1 lane
HH32_whole_H3K27ac_overlaps.finalPeaks.bed

value: H3K27ac, Active Motif, 39113


title: HH32_whole_H3K4me1_r1

description:
2 lane
HH32_whole_H3K4me1_overlaps.finalPeaks.bed


title: 1772075310_E04


title: 1772075310_D12

value: endothelial


title: 1772075310_E03


title: HH32_limb_Input_r1

description: 2 lane

source_name: chicken developing limbs


title: HH32_limb_Input_r2

description: 1 lane


title: HH32_limb_H3K4me1_r2

description:
1 lane
HH32_limb_H3K4me1_overlaps.finalPeaks.bed


title: HH32_whole_H3K27ac_r1

description:
2 lane
HH32_whole_H3K27ac_overlaps.finalPeaks.bed


title: 1772075310_D10

source_name: hypothalamus


title: HH32_limb_H3K4me1_r1


title: 1772075310_E07


title: HH32_limb_H3K27me3_r2

description:
1 lane
HH32_limb_H3K27me3_overlaps.finalPeaks.bed


title: HH32_limb_H3K27ac_r1

description:
1 lane
HH32_limb_H3K27ac_overlaps.finalPeaks.bed


title: 1772075310_D09


title: HH32_limb_H3K27ac_r2


title: HH32_limb_H3K27me3_r1


title: 1772075310_D08


title: HH21_whole_Input_r1

description: 2 lane


title: HH32_whole_Input_r1

description: 2 lane


title: HH21_whole_Input_r2

description: 2 lane


title: 1772075310_D06


title: HH21_whole_H3K4me1_r2

description:
2 lane
HH21_whole_H3K4me1_overlaps.finalPeaks.bed


title: HH21_whole_H3K4me1_r1


title: 1772075310_D03

value: Trh-low


title: 1772075310_D04

value: Sst low-medium


title: HH21_whole_H3K27ac_r1

description:
1 lane
HH21_whole_H3K27ac_overlaps.finalPeaks.bed


title: 1772075310_D02

value: oligos


title: HH21_limb_Input_r2

description: 2 lane


title: HH21_whole_H3K27ac_r2


title: HH21_whole_H3K27me3_r2

description:
1 lane
HH21_whole_H3K27me3_overlaps.finalPeaks.bed


title: HH21_whole_H3K27me3_r1

description:
2 lane
HH21_whole_H3K27me3_overlaps.finalPeaks.bed


title: HH21_limb_H3K4me1_r1

description:
2 lane
HH21_limb_H3K4me1_overlaps.finalPeaks.bed


title: 1772075310_C12


title: HH21_limb_Input_r1

description: 2 lane


title: 1772075310_C11

value: neurons


title: HH21_limb_H3K27me3_r2

description:
2 lane
HH21_limb_H3K27me3_overlaps.finalPeaks.bed


title: HH21_limb_H3K27me3_r1


title: 1772075310_D01


title: HH21_limb_H3K27ac_r2

description:
1 lane
HH21_limb_H3K27ac_overlaps.finalPeaks.bed


title: HH21_limb_H3K4me1_r2


title: HH21_limb_H3K27ac_r1


title: HH16_whole_Input_r2

description: 2 lane


title: HH16_whole_Input_r1

description: 2 lane


title: 1772075310_C10


title: HH16_whole_H3K27me3_r1

description:
2 lane
HH16_whole_H3K27me3_overlaps.finalPeaks.bed


title: HH16_whole_H3K27me3_r2

description:
1 lane
HH16_whole_H3K27me3_overlaps.finalPeaks.bed


title: 1772075310_C05


title: HH16_whole_H3K27ac_r1

description:
1 lane
HH16_whole_H3K27ac_overlaps.finalPeaks.bed


title: HH16_whole_H3K27ac_r2


title: 1772075310_C04

value: Vglut2;Col9a2 (PVH)


title: 1772075310_C03


title: 1772075310_C01


title: 1772075310_C02

value: Gad-low;Gnrh-/+


title: 1772075310_B12

value: Galanin


title: 1772075310_B11


title: Astrocytes treated with Interferon from cortex at 4 hours replicate number 3

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

country: USA

institute: University of Minnesota

description: mRNA isolated from Astrocytes

data_processing:
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.2)
We then mapped all the remaining reads to the human reference genome (Homo_sapiens, NCBI, build37.1) from Illumina's igenomes using STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq.  HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed.
Genome_build: Homo_sapiens NCBI build37.1
Supplementary_files_format_and_content: [.txt] raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Astrocytes

growth_protocol: Primary human astrocytes were maintained on collagen-coated tissue culture plates in a complete astrocyte medium (ScienCell Laboratories) in 2% FBS.

extract_protocol:
mRNA was isolated using the QIAGEN miRNeasy Kit.
KAPA Stranded RNA-Seq with RiboErase workflow for Total RNA-Seq libraries (KAPA Biosystems).
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).

treatment_protocol: Primary human astrocytes were treated for 4 hours with 10U/ml recombinant human IFN-β or a PBS vehicle. Cells were then lysed in buffer RLT (Qiagen).

value: CTX

tag: treatment

value: IFN

tag: replicates

tag: time


title: 1772075310_B10

tag: strain

tag: age (days postnatal)

tag: Sex


title: Astrocytes treated with Vehicle from cortex at 4 hours replicate number 3

description: mRNA isolated from Astrocytes

value: Veh


title: 1772075310_B09

tag: acute stress

tag: cell diameter

tag: total molecules


title: Astrocytes treated with Vehicle from cortex at 4 hours replicate number 2

description: mRNA isolated from Astrocytes


title: Astrocytes treated with Interferon from cortex at 4 hours replicate number 1

description: mRNA isolated from Astrocytes


title: Astrocytes treated with Interferon from cerebellum at 4 hours replicate number 3

description: mRNA isolated from Astrocytes

value: CBL


title: Astrocytes treated with Interferon from cerebellum at 4 hours replicate number 1

description: mRNA isolated from Astrocytes


title: HH16_whole_H3K4me1_r2

description:
2 lane
HH16_whole_H3K4me1_overlaps.finalPeaks.bed

value: whole embryo

value: H3K4me1, abcam, ab8895


title: HH16_whole_H3K4me1_r1


title: 1772075310_C09

value: M

tag: level1 class


title: Astrocytes treated with Interferon from cerebellum at 4 hours replicate number 2

description: mRNA isolated from Astrocytes


title: Astrocytes treated with Vehicle from cerebellum at 4 hours replicate number 2

description: mRNA isolated from Astrocytes


title: 1772075310_B04

value: N


title: 1772075310_C08

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: Astrocytes treated with Vehicle from cerebellum at 4 hours replicate number 3

description: mRNA isolated from Astrocytes


title: MCF-7_SR2211_3

city: St Lucia

first: Tae Gyu

last: Oh

address: 306 Carmody Rd

country: Australia

institute: Institute for Molecular Bioscience

data_processing:
Reads were mapped against the reference genome (GRCh38.p2) using STAR.
SAM was tranformed to BAM with samtools.
BAM data was sorted with Picard.
read counts for each gene in the Ensembl annotation were generated using htseq-count in the HTSeq python package.
Differential expression was detected using the DESeq2.
Genome_build: GENCODE GRCh38.p2
Supplementary_files_format_and_content: text files with raw count numbers by Htseq version 0.6.1.

growth_protocol: Cell lines were maintained in complete media as described.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat. no. RS-122-2101 and RS-122-2102) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Part oo. 15031047 Rev. E October 2013).

treatment_protocol: To obtain RORC knockdown, Control-siRNA or RORC-siRNA was transfected for 48h as described. For over-expression, CMV-empty or CMV-RORC was transfected for 48h. For antagonization of RORC protein, selective inhibitor (SR2211) was treated for 24h in MCF-7 and data was compared to DMSO treated cells.

tag: cell line

value: breast cancer cell line MCF-7

tag: breast cancer subtype

value: Luminal type

tag: er status

value: ER+ve


title: 1772075310_B01

tag: level2 class (neurons only)

value: Hmit+/-


title: MCF-7_SR2211_2


title: Astrocytes treated with Interferon from cortex at 4 hours replicate number 2

description: mRNA isolated from Astrocytes


title: 1772075310_A12

value: oligos


title: MCF-7_DMSO_3

value: DMSO


title: MCF-7_SR2211_1


title: MCF-7_DMSO_1


title: MDA-MB-231_RORC_3

value: breast cancer cell line MDA-MB-231

value: Basal type

value: ER-ve

value: CMV-RORC


title: 1772075310_B08

value: neurons

value: GABA 2


title: MDA-MB-231_RORC_2


title: MDA-MB-231_RORC_1


title: 1772075310_B06

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: 1772075310_A10


title: MDA-MB-231_CMV_3

value: CMV-empty


title: MDA-MB-231_RORCKD_3

value: RORC-siRNA


title: Astrocytes treated with Vehicle from cerebellum at 4 hours replicate number 1

description: mRNA isolated from Astrocytes

value: CBL

value: Veh


title: MDA-MB-231_CMV_1


title: MDA-MB-231_RORCKD_1


title: MDA-MB-231_RORCKD_2


title: 1772075310_A04

value: M

value: N

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: 1772075310_A07


title: 1772075310_A05

value: endothelial


title: 1772075310_A03


title: MDA-MB-231_CONT_2

value: control-siRNA


title: MDA-MB-231_CONT_3


title: MDA-MB-231_CONT_1


title: 1772075310_A02

value: Vglut2;Col9a2 (PVH)


title: 1772075310_A11


title: 1772075310_A01


title: T-47D_RORCKD_3

value: breast cancer cell line T-47D

value: Luminal type

value: ER+ve


title: T-47D_RORCKD_2


title: T-47D_RORCKD_1


title: MDA-MB-231_CMV_2

value: breast cancer cell line MDA-MB-231

value: Basal type

value: ER-ve


title: 1772075309_H11

value: neurons

value: GABA 2


title: MCF-7_RORCKD_1

value: breast cancer cell line MCF-7

value: RORC-siRNA


title: MCF-7_RORCKD_2


title: 1772075310_A09

value: oligos


title: MCF-7_CONT_2


title: 1772075309_H12

value: M


title: T-47D_CONT_1


title: 1772075309_H06

value: N

value: ependymal


title: L101

city: Maebashi

first: Susumu

last: Rokudai

state: Gunma

address: Showa-machi 3-39-22

department: Molecular Pharmacology and Oncology

country: Japan

institute: Gunma University Graduate School of Medicine

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome reference using a combination of Tophat2 (http://tophat.cbcb.umd.edu), and Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
FPKM were calculated using the Cufflinks Cuffnorm package (http://cufflinks.cbcb.umd.edu).
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file includes gene symbol, gene expression (FPKM).

source_name: Lung squamous cell carcinoma

extract_protocol:
Total RNA was prepared from surgical resected samples using Qiagen RNeasy Mini kit after homogenizing with Mixer Mill MM400 (Qiagen). The quality of RNA was assessed with RNA integrity number (RIN) using Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA), for the selection of available samples for NGS analysis (RIN>7.0).
mRNA were captured using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher Scientific, Waltham, MA) and used to generate sequencing libraries of barcoded fragment using the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific) following the manufacture’s instructions. Libraries were sequenced on the Ion Proton™ System by four libraries per Ion PI™ Chip v2, using Ion PI™ Template OT2 200 kit v3 and Ion PI™ Sequencing 200 kit v3 (Thermo Fisher Scientific).

tag: disease state

value: lung SCC

tag: patient age

tag: gender

value: male

tag: pathological stage

value: IIIA

tag: smoking status

value: yes

value: resected tumor


title: T-47D_CONT_2

value: breast cancer cell line T-47D

value: Luminal type

value: ER+ve

tag: treatment

value: control-siRNA


title: MCF-7_RORCKD_3


title: 1772075309_G11

tag: strain

value: neurons

value: Sst low-medium


title: 1772075309_G06

tag: age (days postnatal)


title: 1772075309_G05

tag: Sex


title: L095

value: IA

tag: tissue


title: MCF-7_CONT_3

value: breast cancer cell line MCF-7


title: 1772075309_H07

tag: acute stress

tag: cell diameter

value: Galanin


title: MCF-7_CONT_1


title: 1772075309_H04

value: M

tag: total molecules

tag: level1 class


title: L106


title: L080


title: L100


title: 1772075309_G10

value: N


title: L075

value: female


title: CM-NEI-br2

city: Wuhan

first: Liu

last: Zheng

institute: Huazhong Agricultural University

description:
replicate 2 for ovules at nucellar embryo initiation stage
processed data file = "mandarins.rpkm.xlsx"

data_processing:
The transcriptome raw reads were filtered first, by removing the low quality reads, filtering the contaminants and trimming the adaptor sequences.
The retained high quality reads were mapped to the genome of Citrus Sinensis and Clementine by tophat, and then assembled with Cufflinks
The unigenes resulted from mRNA reads assembly were compared with the non-redundant nucleotide and protein database using BLASTN and BLASTX respectively, with the E-vaule cutoffs of 1e-5.
The differentially expressed genes were identified by Cuffdiff, with P-value ≤0.05 and fold change ≥2.0, whereas the differentially expressed miRNAs were identified by edge
Genome_build: Reference genome sequences of Citrus Sinensis were were downloaded from http://citrus.hzau.edu.cn/orange/download/data.php, while Clementine genome sequences were downloaded from http://phytozome.jgi.doe.gov/pz/portal.html.
Supplementary_files_format_and_content: files include raw counts and  RPKM values

organism: Citrus x clementina

source_name: Ovules_Nour clementina (Citrus Clementina)

extract_protocol:
Total RNA was extracted by Trizol method
Libraries were constructed for sequencing using standard Illumina protocols

tag: cultivar

value: Nour

value: ovules

tag: age

value: 7 DAF(days after flowering)


title: 1772075309_F09

value: endothelial


title: T-47D_CONT_3

tag: cell line

tag: breast cancer subtype

tag: er status


title: L092

tag: disease state

value: lung SCC

tag: patient age

tag: gender

value: male

value: IIIA

value: yes

value: resected tumor


title: L050

tag: pathological stage

value: IB

tag: smoking status


title: CgYap7, input DNA

city: Paris

first: Gaëlle

last: LELANDAIS

address: 15, rue Hélène Brion

country: France

institute: IJM/University Paris Diderot

description: processed data file: CgAP7_INPUT.txt

data_processing:
Quality of FASTQ files was controlled, using FASTQC program.
Nucleotides with a QC < 20 in 5' and 3' were trimmed using a home made Python program.
Reads were mapped on the reference genome (downloaded from Genolevures – http://genolevures.org/download.html#, C. glabrata CBS138) with default parameters, except for -m 1
Reads of replicated experiments were averaged (BAM files), and used for peak calling with bPeaks program.
Merged BAM files were converted into BED files for peak calling, using the genomeCov tool available in Bedtools.
Genome_build: C. glabrata CBS138
Supplementary_files_format_and_content: Bed files used to perform peak calling with bPeaks.  All BED files are available in a tar archive on the series record.

organism: Nakaseomyces glabratus

source_name: Candida glabrata

growth_protocol: All cultures were conducted in a rotative shaker at 28°C in YPD (Glucose 2%, yeast extract 1%, Bactopeptone 1%). Stress conditions used were: 1 mM sodium selenite, 1M NaCl, 2 mM cadmium chloride, 5 mM iron sulfate or 0.5 mM bathophenanthroline disulfonate (BPS).

extract_protocol:
Cells were lysed and DNA was sheared by sonication into ~500 bp fragments. DNA-protein complexes were selected using the antibody specifically targeting the protein of interest.
Libraries were prepared according to Illumina's instructions

treatment_protocol: For ChIP, myc-tagged CgYAP strains were grown in YPD until exponential phase (OD=0.8) and then the desired stress was added for 30 minutes. Cross-linking of the cells and ChIP were performed as described previously (Lelandais et al., Methods Mol Biol, 2016). Meanwhile, the parental HTU (untagged strain) was grown and processed the same way to provide the mock-IP samples

tag: background strain

value: HTU

tag: myc-tagged protein


title: 1772075309_F05

tag: strain

tag: age (days postnatal)

tag: Sex

value: neurons

tag: level2 class (neurons only)


title: 1772075309_G08

tag: acute stress

tag: cell diameter

tag: total molecules

tag: level1 class

value: oligos


title: CgYap5 IP, YPD

description: processed data file: CgAP5_IP_YPD.txt


title: L082

tag: tissue


title: 1772075309_F04

value: microglia


title: L078


title: ARPE19-3_D32_7dA83

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

state: CA

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

data_processing:
Base-calling was carried out using Torrent Suite and default parameters
Read alignment was accomplished using a 2-stage pipeline. The ten 5-prime bases from each sequence were trimmed using FASTX Trimmer 0.0.14. Sequences with a remaining length of  50 bases or greater were then aligned to the human genome (hg38 + 45S-RNA and 5S-RNA bait sequences) using TopHat 2.0.12 (Bowtie2 2.2.3) and settings optimized for variable read-length Ion Torrent sequences: read-mismatches = 4; read-gap-length = 4; read-edit-dist = 8; max-multihits =1; b2-i = S,1,1.15; b2-mp=6,2; b2-rdg = 5,2; and b2-rfg=5,2. Any unmapped sequences were passed to TMAP 3.4.1 and aligned using 5-prime and 3-prime soft-clipping (g = 0). The resulting TopHat and TMAP alignments were merged into a single alignment file.
Gene-level RNA quantification was determined using Partek Genomics Suite 6.6 and the hg38 RefSeq Transcript annotation (10/17/14). Only reads aligned to exons were considered in the determination of the number of reads per gene. In the case where there were two sequencing runs for the same condition (RPEC_P0_D32 and ARPE19-2) the alignments results were combined prior to quantification. Any fractional read count values were rounded to the nearest integer.
Protein coding RNA gene level results were normalized using the trimmed mean of the M-values (TMM) method of Robinson and Oshlack [Genome Biology 2010, 11:R25] as implemented by “edgeR”. Using the raw integer read counts for protein coding genes (HUGO Gene Nomenclature Database, 4/13/2015) as input and selection of genes with at least one count per million reads in 3 or more samples, the normalization factor (norm.factor) and  total number of mRNAs reads for each sample (lib.size) were determined.  The final processed normalized data for each gene is expressed as reads per million aligned reads (RPM) where RPM = (raw read count * 1 x 106) /(norm.factor * lib.size) .
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text; Annotations, mRNA  gene-level raw read counts (Reads) and TMM-normalized read counts per million mRNA alignments (RPM) for all protein coding genes

source_name: Adult RPE cell line, ARPE-19, Experimental Replicate 3

growth_protocol: RPE cells were isolated from fetal donor eyes (Advanced Biosciences Resources, Alameda, CA USA) according to the methods of Hu and Bok [Mol. Vis. 2001, 7:14-19; Methods Mol. Biol. 2010, 652:55-73]. Beyond the initial isolation, all cell culture was carried out using a base medium described by Maminiskis [Invest. Ophthalmol. Vis. Sci.2006, 47:3612-3624]. For 2-3 days post-plating the medium included 15% heat inactivated fetal calf serum. Thereafter, it was reduced to 5%. To generate a working cell bank, primary fetal RPE stocks were expanded approximately 10-fold and these working stocks were designated Passage 0. For routine serial passage, cells were harvested using trypsin digestion and plated at 4,000 cells/cm2. At approximately 80% confluence (every 3-5 days depending on passage number) the cells were enzymatically harvested and re-seeded at 4,000 cells/cm2.  For the purpose of transcriptome analysis cells were plated at 80,000 cells/cm2 and harvested after 32 days. Cultures were carried out on laminin-coated porous supports (mouse laminin, Life Technologies, Grand Island, NY USA; Millicell-HA Culture Inserts, EMD Millipore Inc., Billerica, MA USA) or laminin-coated tissue culture plastic as indicated. All cultures were fed every 2-4 days by complete exchange of the medium.

extract_protocol:
Total RNA was purified using miRNeasy mini-preps (Qiagen Inc., Valencia, CA USA)
PolyA RNA was purified from 1 microgram of total RNA using the Magnetic mRNA Isolation Kit (New England Biolabs, Inc ., Ipswitch MA USA) and mRNA-Seq libraries were constructed using the  Ion Total RNA-Seq Kit v2 (Life Technologies, Inc., Grand Island NY USA).

tag: cell line

tag: cell type

value: Adult RPE cell line

tag: plating density

tag: passage number

value: Unknown

tag: culture time

value: 32 Days

tag: treatment

tag: substrate

value: TC Plastic


title: ARPE19-2b_D32_7dA83

description:
Technical sequencing replicate of GSM2075288
processed data file: ARPE19-2_D32_7dA83.txt

source_name: Adult RPE cell line, ARPE-19, Experimental Replicate 2


title: 1772075309_F03

value: M

value: N


title: CM-NEI-br1

description:
replicate 1 for ovules at nucellar embryo initiation stage
processed data file = "mandarins.rpkm.xlsx"

tag: cultivar

value: Nour

value: ovules

tag: age

value: 7 DAF(days after flowering)


title: CM-pre-NEI-br2

description:
replicate 2 for ovules before nucellar embryo initiation stage
processed data file = "mandarins.rpkm.xlsx"

value: 3 DAF(days after flowering)


title: L087

tag: disease state

value: lung SCC

tag: patient age

tag: gender

value: male

tag: pathological stage

value: IA

tag: smoking status

value: yes


title: 1772075309_F12

tag: strain

tag: age (days postnatal)

tag: Sex

tag: acute stress

tag: cell diameter

tag: total molecules

value: neurons

tag: level2 class (neurons only)


title: MOA-RPEC_D32

description: Passage 7 RPE cells were seeded at 1 X 104 cells/cm2. On day 2, cells were treated with 250 nM A-83-01 and transduced with lentiviral vectors that co-expresses MYCN with Venus, a yellow fluorescence protein, (MOI = 1) and OTX2 with Cerulean, a blue fluorescence protein, (MOI = 0.5). After 7-14 days, Venus and Cerulean double-positive cells were enriched by fluorescence activated cell sorting. The sorted cells were then plated in basal medium supplemented with 250 nM A-83-01. After 32-40 days the cells were harvested by trypsin digestion and pigmented cells were isolated by cell sorting based on an increase in the side scatter to forward scatter ratio. The resulting pigmented MYCN/OTX2/A-83-01 reprogrammed cells (MOA-RPE) were designated as being passage 8.

source_name: Reprogrammed Fetal RPE-Donor "C"

tag: donor id

tag: plating density

tag: passage number

tag: culture time

value: OTX2-MYCN Transduced Passage 7 RPE, 250 nM A-83-01 (Days 1-7)


title: CgYap5 IP, iron excess first replicate

description: processed data file: CgAP5_IP.txt

tag: background strain

value: HTU

tag: myc-tagged protein

tag: stress condition

value: iron excess


title: CgYap4-6 IP, NaCl second replicate

description: processed data file: CgAP4-6_IP.txt

value: NaCl


title: 1772075309_E12

tag: level1 class

value: endothelial


title: 1772075309_F11


title: CM-pre-NEI-br1

description:
replicate 1 for ovules before nucellar embryo initiation stage
processed data file = "mandarins.rpkm.xlsx"

tag: cultivar

tag: tissue

tag: age


title: CgYap4-6 IP NaCl, first replicate

description: processed data file: CgAP4-6_IP.txt


title: 1772075309_E08

tag: strain

tag: age (days postnatal)


title: 1772075309_F10

tag: Sex

tag: acute stress

value: ependymal


title: 1772075309_E05

value: M

tag: cell diameter

tag: total molecules

value: Npy;Agrp (ARH)


title: CgYap3b IP, second replicate

description: processed data file: CgAP3b_IP.txt


title: L060

tag: disease state

tag: patient age

tag: gender

tag: pathological stage

value: IB

tag: smoking status

value: no

value: resected tumor


title: MCF-7_DMSO_2

tag: cell line

value: breast cancer cell line MCF-7

tag: breast cancer subtype

value: Luminal type

tag: er status

value: ER+ve

tag: treatment

value: DMSO


title: 1772075309_G01

value: N

tag: level1 class


title: RPEA_P7_D32_7dA83

source_name: Fetal RPE-Donor "A"

tag: donor id

tag: plating density

tag: passage number

tag: culture time

value: 32 Days

tag: substrate

value: TC Plastic


title: CgYap7 IP standard growth, second replicate

description: processed data file: CgAP7_IP.txt

tag: background strain

value: HTU

tag: myc-tagged protein


title: 1772075309_E03

tag: strain

tag: age (days postnatal)

tag: Sex

tag: acute stress

tag: cell diameter

tag: total molecules

value: neurons

tag: level2 class (neurons only)


title: CgYap7 IP standard growth, first replicate

description: processed data file: CgAP7_IP.txt


title: 1772075309_E01

value: Per2;circadian (SCH)


title: CgYap5, input DNA

description: processed data file: CgAP5_INPUT.txt


title: 1772075309_E11


title: Mock control

description: processed data file: Cg_MOCK.txt

source_name: Candida glabrata_parental HTU line


title: ARPE19-1_D32_7dA83

source_name: Adult RPE cell line, ARPE-19, Experimental Replicate 1

tag: cell line

tag: cell type

value: Adult RPE cell line

value: Unknown


title: 1772075309_F02

value: M

tag: level1 class

value: ependymal


title: CgYap3a IP, second replicate

description: processed data file: CgAP3a_IP.txt


title: RPEB_P7_D32_A83

source_name: Fetal RPE-Donor "B"

tag: donor id

tag: treatment


title: 1772075309_D11

value: uc


title: CgYap4-6, input DNA

description: processed data file: CgAP4-6_INPUT.txt


title: 1772075309_D08

value: endothelial


title: MOA-RPEB_D32

source_name: Reprogrammed Fetal RPE-Donor "B"

tag: plating density

tag: passage number

value: OTX2-MYCN Transduced Passage 7 RPE, 250 nM A-83-01 (Days 1-7)


title: 1772075309_D05


title: MOA-RPEA_D32

source_name: Reprogrammed Fetal RPE-Donor "A"

tag: culture time

tag: substrate


title: RPEB_P7_D32_7dA83


title: RPEC_P7_D32_7dA83

source_name: Fetal RPE-Donor "C"


title: RPEB_P4_D32 [re-analysis]

description: Reanalysis of GSM1657684


title: 1772075309_F01

value: Crh+/-;GABA;Pgr15l (PVH-PVH-galo)


title: RPED_P7_D32_A83

source_name: Fetal RPE-Donor "D"


title: CgYap1, input DNA

description: processed data file: CgAP1_INPUT.txt

tag: background strain

tag: myc-tagged protein


title: 1772075309_D01

tag: strain

tag: age (days postnatal)


title: RPEC_P4_D32_A83 [re-analysis]

description: Reanalysis of GSM1657683


title: RPEB_P4_D32_A83 [re-analysis]

description: Reanalysis of GSM1657682


title: CgYap3b IP selenite, first replicate

description: processed data file: CgAP3b_IP.txt

tag: stress condition

value: selenite


title: CgYap3a, input DNA

description: processed data file: CgAP3a_INPUT.txt


title: 1772075309_C11

tag: Sex

tag: acute stress

tag: cell diameter


title: 1772075309_D12

tag: total molecules


title: RPEC_P7_D32_A83


title: 1772075309_C10

tag: level2 class (neurons only)

value: GABA 1


title: CgYap3a IP selenite, first replicate

description: processed data file: CgAP3a_IP.txt


title: CgYap1 IP selenite, first replicate

description: processed data file: CgAP1_IP.txt


title: CgYap2 IP cadmium, second replicate

description: processed data file: CgAP2_IP.txt

value: cadmium


title: RPEC_P4_D32 [re-analysis]

description: Reanalysis of GSM1657685


title: CgYap2 IP cadmium, first replicate

description: processed data file: CgAP2_IP.txt


title: 1772075309_C08

value: N

tag: level1 class

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: PK-NEI-br1

organism: Citrus reticulata

source_name: Ovules_Ponkan ‘Huagan No.2’ (Citrus reticulata)

tag: cultivar

value: Ponkan Huagan No. 2

tag: tissue

value: ovules

tag: age

value: 7 DAF(days after flowering)


title: RPEB_P0_D32 [re-analysis]

description: Reanalysis of GSM1657678

tag: donor id

tag: plating density

tag: passage number

value: 32 Days

tag: treatment

value: Microporous support


title: 1772075309_C05

source_name: hypothalamus

value: neurons

value: Trh-low


title: 1772075309_C12

value: M

value: ependymal


title: CgYap2, input DNA

description: processed data file: CgAP2_INPUT.txt

tag: background strain

value: HTU

tag: myc-tagged protein


title: PK-pre-NEI-br1

value: 3 DAF(days after flowering)


title: RPED_P4_D32 [re-analysis]

description: Reanalysis of GSM1657686

tag: culture time

tag: substrate

value: TC Plastic


title: Neocortex tissue post-natal day 49_replicateA

city: Basel

first: oriane

last: mauger

address: Klingelbergstrasse 50/70

country: Switzerland

institute: Biozentrum of University of Basel

description:
Poly-A RNA
Processed data file: MAUGER_2015-11-12_RNA-Seq_Introns.txt

data_processing:
Reads were aligned onto mouse genome assembly mm10 using STAR aligner version 2.4.0f1.
Read alignment files (bam) were processed with custom Perl scripts using the library Bio::DB::Sam. For each segment comprising a pair of consecutive exons (exon1 and exon2) and the intermediate intron, reads that map i) exon1, ii) exon2, iii) intron, iv) exon1-intron junction, v) intron-exon2 junction and vi) exon1-exon2 junction were counted. Junction reads were accepted only if they overlapped by more than 8 nucleotides on both sides of the junction.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: MAUGER_2015_04_09_all_retentions_8nt_symbols.txt, MAUGER_2015-11-12_RNA-Seq_Introns.txt: Tab-delimited text files include raw reads counts mapping exon, intron, exon-exon and exon-intron junctions.

source_name: Neocortex tissue, post-natal day 49

growth_protocol: Dissociated cultures of neocortical cells isolated from E16.5 mouse embryos were maintained in culture for 14 days.

extract_protocol:
RNA were isolated with Trizol reagent according to manufacturer's protocol.
Library preparation was performed with 1 μg total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina # RS-122-2101).

treatment_protocol: DRB (2hrs, 50uM). Bicuculline (1hr, 20uM).

tag: strain/background

value: NMRI

tag: genotype/variation

value: wild type

value: post-natal day 49

value: neocortex

tag: drb treatment

tag: bicuculline treatment


title: RPEC_P0_D32_2 [re-analysis]

description:
Reanalysis of GSM1657680
processed data file: RPEC_P0_D32.txt


title: PK-pre-NEI-br2


title: RPEA_P4_D32_A83 [re-analysis]

description: Reanalysis of GSM1657681


title: PK-NEI-br2


title: 1772075309_C03

tag: strain

tag: age (days postnatal)

tag: Sex

tag: acute stress

value: N

tag: cell diameter

tag: total molecules

tag: level2 class (neurons only)


title: 1772075309_B11

tag: level1 class


title: DRB replicateB

source_name: primary neocortical cells, DRB

tag: age

tag: cell type

value: cultured primary neocortical cells

tag: days maintained in culture

value: 2 hours, 50 uM


title: Ctl replicateB

source_name: primary neocortical cells, control


title: CgYap3b, input DNA

description: processed data file: CgAP3b_INPUT.txt

source_name: Candida glabrata

tag: background strain

tag: myc-tagged protein


title: 1772075309_B06


title: 1772075309_B12

value: endothelial


title: 1772075309_B10


title: CgYap1 IP selenite, second replicate

description: processed data file: CgAP1_IP.txt

tag: stress condition

value: selenite


title: DRB replicateA

tag: strain/background

tag: genotype/variation


title: Neocortex tissue post-natal day 10_replicateA

source_name: Neocortex tissue, post-natal day 10

value: post-natal day 10

tag: tissue

tag: drb treatment

tag: bicuculline treatment


title: k9me3_ugal_2

city: SAN FRANCISCO

first: John

last: Liu

state: California

address: 35 Medical Center Way

institute: UCSF

description: processed data file: chip_counts.txt

data_processing:
RNA-seq: Reads were aligned to the human genome (GRCh37) using the spliced read aligner HISAT2 v2.0.3 against an index containing SNP and transcript information (genome_snp_tran). Quantification of Ensembl build 75 genes was carried out with featureCounts using only uniquely mapped reads.
ChIP-seq: Reads were aligned to the human genome (GRCh37) using bowtie v2.2.8. Enrichment at promoter regions, which were defined as +/- 1kb of each TSS and generated from Ensembl GRCh37 build 75, were quantified using featureCounts v1.5.0-p2.
Genome_build: GRCh37

growth_protocol: Cells were infected with sgRNA lentiviruses for 48 hr, followed by 4 d puromycin treatment (1 μg/mL) and 1 d recovery.

extract_protocol:
Genome-wide histone modifications were determined by ChIP against H3K9me3 (Abcam ab8898) on 5 million cells as described in (14). Cells were cross-linked by adding 37% formaldehyde to a final concentration of 1% into culture medium and gently shaking for 10 min at room temperature. Reaction was quenched with glycine, and cells were then washed twice with ice-cold PBS containing protease inhibitors (1mM PMSF, 1X Roche cOmplete EDTA-free cocktail). Cells were scraped off of the plate using a cell lifter and pelleted for 5 min at 2,000 rpm at 4°C. Pellet was snap-frozen in liquid nitrogen and stored at −80°C. Pellet was then thawed and resuspended in Cell Lysis Buffer (5 mM PIPES pH 8, 85 mM KCl, freshly added 1% IGEPAL) with protease inhibitors (Pierce Halt Protease Inhibitor Cocktail). Cells were then homogenized using a type B glass dounce homogenizer, pelleted, and resuspended in Nuclei Lysis Buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS). Chromatin was sonicated in Diagenode TPX tubes using the Diagenode Bioruptor for 20 cycles and DNA was ranged from 150–700 bps as determined by gel electrophoresis. Debris was pelleted and discarded, and an aliquot was removed for Input DNA sequencing from the sonicated chromatin within the supernatant. Sonicated chromatin was then diluted 5-fold in IP Dilution Buffer (50 mM Tris–HCl pH 7.4, 150 mM NaCl, 1% IGEPAL, 0.25% deoxycholic acid, 1 mM EDTA pH 8) with protease inhibitors and pre-cleared with Life Technologies Protein G Dynabeads for 2 hr at 4°C. 5 μg of antibody was added per million cells, and samples were incubated overnight at 4°C. Antibody-bound chromatin was then collected using Life Technologies Protein G Dynabeads and washed twice with IP Dilution Buffer, twice with IP Wash Buffer 2 (100 mM Tris–HCl pH 9, 500 mM LiCl, 1% IGEPAL, 1% deoxycholic acid), and once with IP Wash Buffer 3 (100 mM Tris–HCl pH 9, 500 mM LiCl, 150 mM NaCl, 1% IGEPAL, 1% deoxycholic acid). Precipitated chromatin was then eluted for 30 min at 65°C with Elution Buffer (1% SDS, 50 mM NaHCO3). ChIP and Input DNA crosslinks were reversed by adding 5 M NaCl and heating at 65°C overnight. The following day, 10 mg/ml RNase A was added to precipitated chromatin, and chromatin was incubated for 30 min at 37°C. DNA was then recovered using Agencourt AMPure XP Beads and quantified using the Life Technologies Qubit Fluorometer.
Kapa HyperPlus

tag: sgrna infected


title: 1772075309_B05

tag: strain

tag: age (days postnatal)

tag: Sex

tag: acute stress

value: neurons

value: Vglut2;Gad1-low;Crh-low/- (VMH)


title: Ctl replicateA


title: 1772075309_D02

value: M

tag: cell diameter

tag: total molecules

tag: level1 class

tag: level2 class (neurons only)

value: Pmch


title: 1772075309_B03

value: uc


title: DRB replicate2

description:
Poly-A RNA
Processed data file: MAUGER_2015_04_09_all_retentions_8nt_symbols.txt

tag: age

tag: cell type

tag: days maintained in culture


title: Neocortex tissue post-natal day 10_replicateB

tag: strain/background


title: DRB replicate1

tag: genotype/variation


title: k9me3_u263_1

description: processed data file: chip_counts.txt


title: k9me3_ugal_1

description: processed data file: chip_counts.txt


title: Neocortex tissue post-natal day 49_replicateB

tag: tissue


title: k9me3_u263_2

description: processed data file: chip_counts.txt


title: 1772075309_A09


title: 1772075309_A12


title: DRB+Bicuculline replicate1

source_name: primary neocortical cells, DRB+Bicuculline

tag: drb treatment

value: 1 hour, 20 uM


title: 1772075309_A11

value: Sst low-medium


title: 1772075309_B02


title: k9me3_hgal_2

description: processed data file: chip_counts.txt

value: HeLa


title: k9me3_h263_2

description: processed data file: chip_counts.txt


title: 1772075309_A08


title: DRB+Bicuculline replicate2

value: NMRI

value: wild type

tag: bicuculline treatment


title: input_ugal_2

description: processed data file: chip_counts.txt

tag: sgrna infected


title: k9me3_h263_1

description: processed data file: chip_counts.txt


title: input_ugal_1

description: processed data file: chip_counts.txt


title: C14

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3, Martin 2011) and filtered for low complexity with seq_crumbs (v. 0.1.8).
Reads were aligned against Mus musculus genome (version GRCm38) using STAR (v. 2.4.0g, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Mus musculus (Ensembl v. GRCm38.82) gene annotation.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: whole kidney

growth_protocol: Mice with floxed exon 2 of Xpr1 were obtained from Cyagen. The animals were maintained ad libitum on the standard laboratory chow diet (KLIBA NAFAG diet 3800). The conditional inactivation of Xpr1 in the nephron was induced by 2-weeks treatment with doxycycline (DOX, 2 mg/ml in drinking water) of 8-weeks old Xpr1lox/lox-Pax8-rtTA/LC-1 mice (cKO mice). In parallel the same DOX treatment was provided to their littermate controls Xpr1lox/lox mice (Control mice).

extract_protocol:
RNA from whole kidneys was isolated with the standard method of Chomczynski and Sacchi (Anal Biochem, 162: 156-159, 1987).
RNA-seq libraries were prepared using 500 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Caliper Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA) using a Caliper-developed automated script.

tag: genotype

value: Control

value: kidney


title: 1772075309_A06

tag: strain

tag: age (days postnatal)

value: N


title: KO18

value: cKO


title: KO16


title: KO20


title: KO19


title: 1772075309_A03

tag: Sex

tag: acute stress


title: C13


title: 1772075309_A01

tag: cell diameter

tag: total molecules


title: k9me3_hgal_1

description: processed data file: chip_counts.txt


title: input_u263_1

description: processed data file: chip_counts.txt


title: C11


title: input_u263_2

description: processed data file: chip_counts.txt


title: C10


title: 1772075309_A07

tag: level1 class

tag: level2 class (neurons only)


title: 1772075305_H10

value: endothelial


title: input_hgal_2

description: processed data file: chip_counts.txt

tag: cell type


title: input_hgal_1

description: processed data file: chip_counts.txt


title: input_h263_2

description: processed data file: chip_counts.txt


title: 1772075305_H06

value: ependymal


title: mESC_Alloxan_24h_RNA_rep3 RNA-seq

city: Boston

first: Wenhao

last: Zhang

state: MA

address: Warren Alpert Bldg, Rm 160, 200 Longwood Ave

department: Genetics

institute: Harvard Medical School

data_processing:
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files for RNA seq including FPKM values for each gene

source_name: mESCs

growth_protocol: Mouse ES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03), leukemia inhibiting factor (LIF) (Millipore Cat. GSE1107), penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), and non-essential amino acids (Gibco Cat. 25-025-CIR). A final concentraton of 5uM Alloxan tetrahydrate (Sigma, A6316) was added. Cell was harvested after 24 hours treatment.

extract_protocol:
Cells were lysed using TRIzol reagent (Ambion, Cat. 15596026). RNA was extracted by isopropanol precipitation and diluted in DEPC-treated water.
10ug RNA was DNase I (Fermentas, Cat. EN0521) treated at 37°C for 1 hour. RNA was purified using AMPure beads. Then ribosomal RNA was removed using Ribo-Zero Magnetic Gold Kit (Epicentre). Purified RNA was fragmented with RNA Frag. Buffer (NEB, Cat. E6186A) at 95°C for 5 min. Reaction was stopped and RNA was purified. First stand cDNA was synthesized with commercial kit using both oligo dT and random primers (Invitrogen, Cat. 18080-051). Second strand cDNA was synthesized with second strand synthesis buffer (Invitrogen, Cat. 10812014), MgCl2, DTT, dUNTP, RNase H (Fermentas, Cat. EN0202), E. coli DNA ligase (NEB, Cat. M0205S) and DNA polymerase I (NEB, Cat. M0209S). DNA was purified after 2 hour incubation on thermomixer at 16°C. Then, synthesized cDNA was end-repaired, adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG (AMPErase, Cat. N808-0096) at 37°C for 1 hour and purified before PCR amplification. 200-500bp fragments were selected for subsequent sequencing.

value: mESCs

tag: chip-antibody

value: WT


title: 1772075305_H05

value: oligos


title: input_h263_1

description: processed data file: chip_counts.txt


title: mESC_Alloxan_24h_RNA_rep2 RNA-seq

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
MethylC-seq reads performed in mESCs were mapped to the mm9 reference genome using Bsmap with parameters -r 0 -w 100 -v 0.1. Adaptor sequences were removed with parameter -A. PCR duplicates were also removed. Pair-end reads with a flag equal 177 or 129 were also removed from this data. Only samples with bisulfite conversion rates greater than 99% were accepted. 200bp bins were used for most analyses and those with total CG coverage less than 5 were removed. Methylation ratio was calculated using methylated CG verses total CG for each bin.
MethylC-seq libraries based on bisulfite TELP , the reads were mapped to the mm9 reference genome by BSSeeker2 (Guo et al., 2013). PolyG was removed in our scripts in the beginning of read2 for pair-end mapping. Alignments were performed with the following additional parameters aside from default: --bt2-p 8 --XS 0.2,3 –a CCCCCC –m 4. Multi-mapped reads and PCR duplicates were removed before calculating the methylation ratio. We also removed the unconverted reads marked by BSSeeker2 (--XS 0.2, 3) and reads with mapped region length shorter than 30bp.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited bed files including number of reads in 100bp bin in the genome for each ChIP-seq sample
Supplementary_files_format_and_content: Tab-delimited text files for RNA seq including FPKM values for each gene
Supplementary_files_format_and_content: Tab-delimited text files for methylC-seq including the average mCG level in 200bp bins.

tag: chip antibody


title: 1772075305_H04

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited file of mRNA molecule counts for each gene and cell. Cells with less than 1500 molecules have been removed from this file.

value: M


title: mESC_Tet1cs_RNA_rep2 RNA-seq

growth_protocol: Mouse ES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03), leukemia inhibiting factor (LIF) (Millipore Cat. GSE1107), penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), and non-essential amino acids (Gibco Cat. 25-025-CIR).


title: u87_nc_3150

description: processed data file: rnaseq_tpm.txt

extract_protocol:
DirectZol RNA
TruSeq HT Stranded mRNA


title: 1772075305_H02

value: neurons


title: 1772075309_A05


title: u87_nc_2727

description: processed data file: rnaseq_tpm.txt


title: 1772075305_H11


title: mESC_Tet2ko_Tet1cs_mCG_rep2 Met-seq

extract_protocol:
Cells were digested using Cell Lysis Solution (Qiagen, Cat. 1045723) and proteins were removed using Protein Precipitation Solution (Qiagen, Cat. 1045701). Genome DNA was precipitated by isopropyl alcohol and cleaned by wash with 75% ethanol.
A total amount of 6ug genomic DNA was mixed with 25ng lambda DNA and sonicated to 200-500bp.DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Bisulfite treatment is performed using commercial kit (Zymo research, Cat. D5005). DNA was amplified and 200-500bp fragments were gel selected.

value: Tet1cs/cs Tet2-/-


title: 1772075305_G12


title: 1772075305_G09


title: hela_nc_1736

description: processed data file: rnaseq_tpm.txt


title: 1772075305_G07


title: hela_nc_1688

description: processed data file: rnaseq_tpm.txt


title: mESC_Tet2ko_mCG_rep2 Met-seq


title: hela_gal4_3

description: processed data file: rnaseq_tpm.txt


title: hela_gal4_1

description: processed data file: rnaseq_tpm.txt


title: mESC_anti_Tet1cs_ChIP_rep1 ChIP-seq rep2

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication to obtain fragments 200–2000 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.

value: Tet1 (home-made; same as the one used for ChIP-seq in PMID 21514197)


title: 1772075305_G05

extract_protocol:
Mice were deeply anesthetized (5% isoflurane) and transcardially perfused with 40 ml ice-cold pre-oxygenated (95% O2/5% CO2) cutting solution containing (in mM): 90 NaCl, 26 NaHCO3, 2.5 KCl, 1.2 NaH2PO4, 10 HEPES-NaOH, 5 Na-ascorbate, 5 Na-pyruvate, 0.5 CaCl2, 8 MgSO4 and 20 glucose. A central column of the mouse hypothalamus spanning the preoptic area-Arc (rostrocaudal axis), paraventricular nucleus (dorsal) and the ventrolateral hypothalamic area (lateral) was microdissected from serial 300-micrometer-thick coronal slices under microscopy guidance and dissociated using the Papain Dissociation System (Worthington). Isolated single cells were concentrated by centrifugation to a density of 600-1,000 cells/?microlitre. After mixing C1 suspension reagent (4 microlitre; "C1 reagents", Fluidigm Inc.) to the cell suspension (7 microlitre), this mixture was loaded into a C1-AutoPrep IFC microfluidic chip (Fluidigm Inc.)
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.


title: mESC_anti_Tet1_ChIP_rep1 ChIP-seq rep2


title: mESC_anti_Tet1_ChIP_rep1 ChIP-seq rep1


title: 1772075305_G03

value: Calcr-high;VMAT+/-;Lhx1 (Sch)


title: u87_XLOC_054068_1

description: processed data file: rnaseq_tpm.txt


title: mESC_GFP ChIP-seq rep2

value: Flag (Sigma, Cat. F1804)


title: 1772075305_G01


title: u87_XLOC_051509_1

description: processed data file: rnaseq_tpm.txt


title: k562_GAL4_S23

description: processed data file: rnaseq_tpm.txt

growth_protocol: Cells were infected for 48 hr, followed by 2 d puromycin treatment (3 μg/mL) and 2 d recovery


title: mESC_Tetdko_mCG_rep2 Met-seq


title: mESC_Tet1n_delta_cxxc ChIP-seq rep2

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication to obtain fragments 200–2000 bp in length. Then chromatin was reverse-crosslinked and DNA was purifiied and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.


title: mESC_anti_Tet1cs_ChIP_rep1 ChIP-seq rep1


title: u87_XLOC_054068_2

description: processed data file: rnaseq_tpm.txt


title: 1772075305_F11


title: 1772075305_G04

value: Galanin


title: u87_XLOC_040566_2

description: processed data file: rnaseq_tpm.txt


title: mESC_cxxc ChIP-seq rep2


title: 1772075305_G06


title: 1772075305_F07


title: u87_XLOC_026118_2

description: processed data file: rnaseq_tpm.txt


title: mESC_Tet1n ChIP-seq rep2


title: u87_XLOC_029037_1

description: processed data file: rnaseq_tpm.txt


title: 1772075305_F05

value: uc


title: mESC_Tet1s ChIP-seq rep2


title: mESC_Tet1e_delta_cxxc ChIP-seq rep2


title: u87_XLOC_026118_1

description: processed data file: rnaseq_tpm.txt


title: mESC_Tet1e ChIP-seq rep2


title: u87_XLOC_015111_2

description: processed data file: rnaseq_tpm.txt


title: 1772075305_F06


title: 1772075305_F04


title: u87_XLOC_015111_1

description: processed data file: rnaseq_tpm.txt


title: CCl4_CCl4_EtOH_278

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

institute: TEXAS A&M UNIVERSITY

data_processing:
Reads were filtered such that their identical sequence could appear only up to five times, then were filtered using TagDust (Lassmann et al. 2009). Reads with a quality score greater than 20 for 90% of bases were retained, and aligned to the reference mouse genome (mm9) using GSNAP (Wu and Nacu 2010) using a k-mer size of 15, indel penalty of 5, and an allowance of 1 mismatch. Reads aligning to "blacklisted" regions of the mouse genome were removed.
Transcript abundance was estimated by computing RPKM (Mortazavi et al. 2008) using RefSeq gene models aggregated by gene symbol.
Genome_build: mm9
Supplementary_files_format_and_content: *.dat files include the raw count, the number of the bases in the exonic sequence, and the RPKM for each gene (in that order).

source_name: post CCl4 i.p. 6wks + EtOH treatment 4wks

extract_protocol:
Kidneys were removed at necropsy, flash frozen, and RNA was extracted using a QIAGEN RNeasy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Male


title: 1772075305_F03


title: u87_XLOC_014806up_2

description: processed data file: rnaseq_tpm.txt


title: 1772075305_F02


title: CCl4_CCl4_EtOH_277

tag: tissue

value: kidney


title: 1772075305_F12

value: N


title: u87_XLOC_014806up_1

description: processed data file: rnaseq_tpm.txt


title: CCl4_CCl4_EtOH_276


title: u87_XLOC_014806_2

description: processed data file: rnaseq_tpm.txt


title: u87_XLOC_014806_1

description: processed data file: rnaseq_tpm.txt


title: EtOH_272

source_name: post olive oil i.p. 6wks + EtOH treatment 4wks


title: 1772075305_E12


title: 1772075305_E11

value: astrocytes


title: EtOH_271


title: u87_TRAM2-AS1_2

description: processed data file: rnaseq_tpm.txt


title: u87_XLOC_010347_2

description: processed data file: rnaseq_tpm.txt


title: 1772075305_E08


title: u87_SNHG12_2

description: processed data file: rnaseq_tpm.txt


title: EtOH_264


title: CCl4_10W_274

source_name: post CCl4 i.p. 6wks + half dose of CCl4 i.p. 4wks


title: 1772075305_E04


title: 1772075305_E10


title: u87_SNHG12_1

description: processed data file: rnaseq_tpm.txt


title: 1772075305_F01

value: endothelial


title: u87_SNHG1_2

description: processed data file: rnaseq_tpm.txt


title: u87_SNHG1_1

description: processed data file: rnaseq_tpm.txt


title: CCl4_6W_262

source_name: post CCl4 i.p. 6wks


title: 1772075305_D12


title: OO_270

source_name: post olive oil i.p. 6wks


title: 1772075305_E02

value: ependymal


title: 1772075305_D10


title: u87_RP11-96L14.7_2

description: processed data file: rnaseq_tpm.txt


title: OO_263


title: 1772075305_D07


title: CCl4_6W_261


title: OO_260


title: 1772075305_D05


title: EtOH_273


title: u87_RP11-734K2.4_1

description: processed data file: rnaseq_tpm.txt


title: CCl4_10W_275


title: u87_RP11-734K2.4_2

description: processed data file: rnaseq_tpm.txt


title: u87_RP11-96L14.7_1

description: processed data file: rnaseq_tpm.txt


title: 1772075305_C11

value: vsm


title: mESC_Tet1wt_RNA_rep2 RNA-seq

value: mESCs

value: WT


title: u87_RP11-126L15.4_2

description: processed data file: rnaseq_tpm.txt


title: 1772075305_C07

value: M


title: 1772075305_C05


title: Oct4 GiP 2i RNA-seq

city: Urbana

first: Miroslav

last: Hejna

state: Illinois

address: 1110 West Green Street

department: Department of Physics

institute: University of Illinois

data_processing:
The reads are mapped to mm10 (igenome) genome usingTopHat2 v2.0.10
Aligned reads reads are assembled into transcripts using cufflings v2.2.1
Transcripts are merged using cuffmerge
Expresson level is calculated using cuffnorm
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with expression level.

source_name: Oct4 GiP_Embryonic stem cells_2i

growth_protocol: ES cells were grown on gelatin for 2 weeks in three different conditions.

extract_protocol:
Total RNA was extracted from 10^5 cells. 250 ng total RNA was used for mRNA purification and library preparation. All samples were spiked-in with ERCC control RNAs.
Libraries were prepared using the NEBNext Ultra Directional RNA library prep kit.

treatment_protocol: Paused cells were treated with 200 nM INK128 as mTor inhibitor for 2 weeks.

value: Embryonic stem cells

tag: passages

tag: cell line

value: Oct4 GiP

tag: treatment


title: Oct4 GiP Serum RNA-seq

source_name: Oct4 GiP_Embryonic stem cells_serum

value: Serum


title: Oct4 GiP Paused RNA-seq

source_name: Oct4 GiP_Embryonic stem cells_paused

value: Paused


title: u87_RP11-973D8.4_1

description: processed data file: rnaseq_tpm.txt

tag: sgrna infected


title: u87_RP11-1094M14.11_2

description: processed data file: rnaseq_tpm.txt


title: v6.5 Paused RNA-seq

source_name: v6.5_Embryonic stem cells_paused


title: u87_RP11-1094M14.11_1

description: processed data file: rnaseq_tpm.txt


title: 1772075305_C02

source_name: hypothalamus

tag: strain


title: 1772075305_B11

tag: age (days postnatal)


title: u87_PVT1up_2

description: processed data file: rnaseq_tpm.txt


title: OO_259


title: v6.5 Serum RNA-seq

source_name: v6.5_Embryonic stem cells_serum


title: 1772075305_B08

tag: Sex

value: neurons


title: 1772075305_B10

tag: acute stress

value: oligos


title: E14 Paused RNA-seq

source_name: E14_Embryonic stem cells_paused


title: u87_PVT1_2

description: processed data file: rnaseq_tpm.txt


title: E14 2i RNA-seq

source_name: E14_Embryonic stem cells_2i


title: 1772075305_B05

tag: cell diameter


title: u87_RP11-126L15.4_1

description: processed data file: rnaseq_tpm.txt


title: E14 Serum RNA-seq

source_name: E14_Embryonic stem cells_serum


title: 1772075305_C04

tag: total molecules


title: u87_MIR29A_2

description: processed data file: rnaseq_tpm.txt


title: 1772075305_B04

tag: level1 class


title: u87_MIR29A_1

description: processed data file: rnaseq_tpm.txt


title: u87_PVT1_1

description: processed data file: rnaseq_tpm.txt


title: u87_MIR210HG_2

description: processed data file: rnaseq_tpm.txt


title: 1772075305_B02

tag: level2 class (neurons only)

value: Sst low-medium


title: 1772075305_B03


title: E13_5_PGC_Tet1cs_4 RNA-seq

source_name: E13.5 PGCs

growth_protocol: Tet1cs/+OG2+/- mice were crossed naturally and pregnant females were identified by vaginal plug before noon, which was considered as E0.5. When pregnant females come to E13.5, their gonad were taken and PGCs were sorted out by FACS.

extract_protocol:
FACS sorted PGCs of each embryo was diluted in Hypotonic Lysis Buffer (Amresco, Cat. M334) supplied with Recombinant RNase Inhibitor (Takara, Cat. 2313A).
The Smart-seq2 RNA libraries of mouse PGCs were prepared as previously described in "Smart-seq2 for sensitive full-length transcriptome profiling in single cells" by Picelli, S., Bjorklund, A.K., Faridani, O.R., Sagasser, S., Winberg, G., and Sandberg, R. in Nature methods (2013) 10, 1096-1098.

tag: cell type

value: E13.5 PGCs

tag: genotype


title: v6.5 2i RNA-seq

source_name: v6.5_Embryonic stem cells_2i


title: E13_5_PGC_Tet1cs_6 RNA-seq

tag: chip antibody


title: 1772075305_A09


title: u87_MIR210HG_1

description: processed data file: rnaseq_tpm.txt


title: E13_5_PGC_Tet1cs_3 RNA-seq


title: u87_LINC00909_2

description: processed data file: rnaseq_tpm.txt


title: 1772075305_A08

value: Crh+/-;Lhx6;GABA (BST;MPO)


title: u87_LINC00909_1

description: processed data file: rnaseq_tpm.txt


title: E13_5_PGC_Tet1cs_2 RNA-seq


title: E13_5_PGC_Tet1cs_1 RNA-seq


title: 1772075305_A07

value: N

value: Sst-medium;Cartpt


title: u87_LINC00680_2

description: processed data file: rnaseq_tpm.txt


title: u87_PVT1up_1

description: processed data file: rnaseq_tpm.txt


title: 1772075305_A04

value: uc


title: u87_LINC00263_1

description: processed data file: rnaseq_tpm.txt


title: 1772075305_A05

value: endothelial


title: E13_5_PGC_Tet1wt_4 RNA-seq


title: E13_5_PGC_Tet1wt_5 RNA-seq


title: u87_LINC00680_1

description: processed data file: rnaseq_tpm.txt


title: u87_EPB41L4A-AS1_2

description: processed data file: rnaseq_tpm.txt


title: u87_LINC00263_2

description: processed data file: rnaseq_tpm.txt


title: u87_EPB41L4A-AS1_1

description: processed data file: rnaseq_tpm.txt


title: E13_5_PGC_Tet1cs_5 RNA-seq


title: 1772075305_A11


title: 1772075304_H11


title: u87_CTC-428G20.6_2

description: processed data file: rnaseq_tpm.txt


title: E13_5_PGC_Tet1wt_1 RNA-seq


title: 1772075304_H10


title: 1772075305_A02


title: Neuron_Tet1wt_RNA RNA-seq

source_name: mESC-derived neuron

growth_protocol: ES cells were cultured in non-adhesive bacterial dishes using ES culture medium minus LIF for 4 days. Then retinoic acid (RA) (Sigma Cat. R2625) was added in to medium to the final concentration of 2ug/ml. Medium was changed every day. On the 5th day of adding RA, embryonic bodies were dissociated by 0.25% Trypsin-EDTA (Gibco Cat. 25200-056) and plated to poly-L-ornithine (Sigma Cat. P3655) and Laminin (Invitrogen Cat. 23017-015) pre-coated dish. Cells were cultured in DMEM/F-12 (Gibco Cat. 11330-032) with B27 (Life tech. Cat. 17504-044) and were incubated for two days. The medium was switched to BME (Gibco, Cat. 21010-046) with B27 for another two days. Differentiated neurons were then harvested for subsequent analyses.

value: mESC-derived neuron


title: 1772075304_H08

value: ependymal


title: u87_CTC-428G20.6_1

description: processed data file: rnaseq_tpm.txt


title: E13_5_PGC_Tet1wt_6 RNA-seq

value: WT


title: u87_AC016831.7_2

description: processed data file: rnaseq_tpm.txt


title: 1772075305_A06

value: M


title: mESC_Tet1CS_RNA RNA-seq

source_name: mESCs

value: mESCs


title: 1772075304_H02

value: astrocytes


title: mESC_Alloxan_24h_RNA RNA-seq


title: u87_AC016831.7_1

description: processed data file: rnaseq_tpm.txt


title: 1772075304_H04


title: E13_5_PGC_Tet1wt_3 RNA-seq


title: k562_XLOC_042889_2

description: processed data file: rnaseq_tpm.txt


title: 1772075304_G11


title: E13_5_PGC_Tet1cs_mCG Met-seq

extract_protocol:
PGCs were lysed in lysis buffer (10mM Tris-Hcl PH 7.5, 10mM NaCl, 0.5% NP-40, protease K) for 3h at 55°C and heat-inactivated for 1h at 72°C.
Lamda DNA was added as control to calculate bisulfite conversion rate. The DNA mixture was digested by dsDNA fragmentase (NEB) and followed by bisulfite conversion using EpiTect Fast Bisulfite Conversion Kit (Qiagen). The bisulfite single strand DNA was subject to TELP, described in "TELP, a sensitive and versatile library construction method for next-generation sequencing" by Peng X, Wu J, Brunmeir R, Kim SY, Zhang Q, Ding C, Han W, Xie W, Xu F., published in Nucleic Acids Res. 2015 Mar 31;43(6):e35. doi: 10.1093/nar/gku818. Epub 2014 Sep 15.


title: E13_5_PGC_Tet1wt_2 RNA-seq


title: mESC_Tet1wt_RNA RNA-seq


title: k562_XLOC_042889_1

description: processed data file: rnaseq_tpm.txt


title: k562_XLOC_038702_1

description: processed data file: rnaseq_tpm.txt


title: k562_XLOC_018520_2

description: processed data file: rnaseq_tpm.txt


title: 1772075304_G03


title: 1772075304_G10

value: microglia


title: 1772075304_G02


title: mESC_Tetdko_mCG Met-seq


title: k562_RP11-392P7.6_1

description: processed data file: rnaseq_tpm.txt


title: mESC_Tet2ko_Tet1cs_mCG Met-seq

value: Tet1cs/cs Tet2-/-


title: 1772075304_G01


title: 1772075304_F12


title: 1772075304_F09


title: k562_RP11-347C12.10_1

description: processed data file: rnaseq_tpm.txt


title: k562_MIR142_2

description: processed data file: rnaseq_tpm.txt


title: Neuron_H3K27me3 ChIP-seq

value: H3K27me3 (Active Motif, Cat. 39155)


title: Neuron_H3K27ac ChIP-seq

value: H3K27ac (Active Motif, Cat. 39133)


title: k562_LINC00910_2

description: processed data file: rnaseq_tpm.txt


title: k562_MIR142_1

description: processed data file: rnaseq_tpm.txt


title: 1772075304_F07

value: oligos


title: 1772075304_G12


title: Neuron_histone_input


title: k562_LINC00910_1

description: processed data file: rnaseq_tpm.txt


title: Neuron_H3K4me3 ChIP-seq

value: H3K4me3 (Active Motif, Cat. 39159)


title: 1772075304_F05


title: mESC_GFP_input


title: k562_LINC00909_x_2

description: processed data file: rnaseq_tpm.txt


title: E13_5_PGC_Tet1wt_mCG Met-seq

value: E13.5 PGCs


title: 1772075304_F04

value: N

value: neurons

value: Trh-medium


title: mESC_GFP ChIP-seq

value: Flag (Sigma, Cat. F1804)


title: mESC_Tet2ko_mCG Met-seq


title: k562_LINC00909_2

description: processed data file: rnaseq_tpm.txt


title: 1772075304_F01


title: mESC_Tet1n_delta_cxxc ChIP-seq


title: 1772075304_E12


title: k562_LINC00909_1

description: processed data file: rnaseq_tpm.txt


title: 1772075304_E07

value: uc


title: k562_LINC00680_1

description: processed data file: rnaseq_tpm.txt


title: mESC_cxxc ChIP-seq


title: mESC_Tet1n ChIP-seq


title: 1772075304_E03


title: mESC_Tet1e_delta_cxxc ChIP-seq


title: k562_LINC00263_1

description: processed data file: rnaseq_tpm.txt


title: 1772075304_D08


title: mESC_Tet1s ChIP-seq


title: 1772075304_D07


title: mESC_Tet1e ChIP-seq


title: k562_EPB41L4A-AS1_2

description: processed data file: rnaseq_tpm.txt


title: k562_EPB41L4A-AS1_1

description: processed data file: rnaseq_tpm.txt


title: 1772075304_D05

value: ependymal


title: mESC_histone_input

value: WT


title: 1772075304_D04

value: M


title: mESC_H3K27ac ChIP-seq

value: mESCs


title: 1772075304_D03

value: Npvf


title: hela_XLOC_017263_1

description: processed data file: rnaseq_tpm.txt

value: HeLa


title: 1772075304_D02


title: mESC_H3K27me3 ChIP-seq


title: 1772075304_D01


title: hela_RP5-1148A21.3_2

description: processed data file: rnaseq_tpm.txt


title: mESC_H3K4me3 ChIP-seq


title: hela_RP5-1148A21.3_1

description: processed data file: rnaseq_tpm.txt


title: hela_RP11-1094M14.11_2

description: processed data file: rnaseq_tpm.txt


title: ES_Gmnn_66

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v1.0.0 with parameters -p 40 -S
Aligned reads were filtered, extended to 150bp by using methylQA (http://methylqa.sourceforge.net/, Li, e.tl. Methods. 2014.)
BigWig files were generated by using methylQA
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files: density of non-redundant uniquely aligned reads

source_name: Mouse embriyonic stem cell

extract_protocol:
none provided by submitter
none provided by submitter

value: Mouse embriyonic stem cell

value: Gmnn


title: ES_Gmnn_3.4


title: k562_LINC00263_2

description: processed data file: rnaseq_tpm.txt


title: hela_RP11-1094M14.11_1

description: processed data file: rnaseq_tpm.txt


title: ES_TY1_input

value: input


title: 1772075304_C09

value: oligos


title: hela_PVT1up_1

description: processed data file: rnaseq_tpm.txt


title: 1772075304_C08


title: hela_MIR17HG_2

description: processed data file: rnaseq_tpm.txt


title: hela_XLOC_017263_2

description: processed data file: rnaseq_tpm.txt


title: Day3_Zic1_8.9

source_name: Mouse neural progenitor cells

value: ES-derived neural progenitor cells


title: 1772075304_C06


title: hela_LINC00909_2

description: processed data file: rnaseq_tpm.txt


title: Day3_Zic1_6.8


title: 1772075304_C05


title: hela_LINC00680_2

description: processed data file: rnaseq_tpm.txt


title: Day3_Gmnn_66


title: hela_LINC00680_1

description: processed data file: rnaseq_tpm.txt


title: 1772075304_C03


title: Day3_Gmnn_3.4


title: 1772075304_C01


title: hela_LINC00263_2

description: processed data file: rnaseq_tpm.txt


title: 1772075304_C12


title: 1772075304_C11

value: endothelial


title: hela_LINC00263_1

description: processed data file: rnaseq_tpm.txt


title: Late stage post-radiation GBM RCAS mouse model cell T3-96

city: New York

first: Sheng

last: Li

state: New York

address: 525 East 68th Street

department: Neurological Surgery

institute: Weill Cornell Medical College

data_processing:
Data analysis was performed through the rmake pipeline, which uses STAR for alignment and TPM measurements for gene expressoin abundance quantification using Gencode mouse V7 protein coding gene model.
Cells were filtered based on number of reads mapped to the mitochondria chromosome (>=20%) and mapping rate (< 50%). In addition, cells were filtered if Pdgfra is not expressed (TPM < 3).
A expression matrix were made by log2 (1+TPM)
Genome_build: mm10
Supplementary_files_format_and_content: gene read count matrix

source_name: stage T3,  Cell # 96

growth_protocol: RCAS-hPDGFb-HA-SV40 containing human PDGFb with partially deleted 59UTR, RCAS-hPDGFb-HA, and RCAS-Cre vectors were transfected into DF-1 chicken cells (ATCC). DF1 cells transfected with RCAS-PSG were cultured in 10% FBS-DMEM media under standard conditions. For tumor induction, transfected DF1 cells were trypsinized, centrifuged and injected into the brain parenchyma of Ntva mice in heterozygous Ink4a/Arf +/-, Ptenfl/fl background at post-natal days 0– 2. The mice transgenically express RCAS binding tv-a receptor after the nestin promoter.

extract_protocol:
The tumor cells were isolated from primary or recurrent tumors from RCAS-tva mice followed by FACS. Tumor masses, which were pre-determined by MRI, were minced and then incubated at 37°C with PAPAIN in PIPES buffer, resuspending after 20 min. After quenching the digestion with fetal calf serum, the suspension was again disrupted with a pipette and passed through 70um cell filters. Samples were collected immediately by centrifugation, and then they were subjected to myelin removal (Miltenyi Biotec.). Wash the remaining cells by PBS with 2% fetal calf serum, centrifuge at 300g for 5 minutes, discard supernatant and re-suspend the pellet in the volume remaining. Follow antibody and live/dead stainings (Invitrogen) procedures. Cells were counted and one million cells in each sample were subjected to flow assisted cells sorting.  The following antibodies were used for staining: FITC-CD45, PE-CD31, APC-CD140a (PDGFRa), (eBiosciece); Pacific Blue/Mouse Lineage Panel (Biolegend). The data were analyzed by Flowjo software. The analysis was done within single cell gate after the exclusion of debris and dead cells.
Tumor cells were isolated from mouse brain tumor tissue samples. Single cells were then captured and mRNA isolated using Clontech's SMARTer chemistry on the Fluidigm C1 Single Cell Auto Prep system. Illumina's Nextera XT kit was used for library preparation.
Single cell sequencing were performed on the HiSeq2500 platform with 100 bp single-end sequencing.

treatment_protocol: Once the mice had developed radiographic high-grade tumors approximately at week 6, they were subjected to head-only fractioned ionizing radiation- 2 Gy a day, every other day for five times. To determine the progression, regression, or recurrence of tumors, high-resolution MRI images were acquired on a 7.0-T animal scanner system (Bruker Biospin). During imaging, animals were under isoflurane anesthesia and monitored for respiration and heart rate; the temperature was kept at 37°C. Images were analyzed by OsiriX DICOM viewer.

tag: tumor stage

value: Late stage post-radiation

value: Brain

tag: time point (weeks)

value: 10 weeks

tag: tumor type

value: Recurrent Tumor

tag: background strain

value: RCAS-TVA

tag: tumor grade

value: High


title: 1772075304_B12

city: Stockholm

first: Sten

last: Linnarsson

institute: Karolinska Institutet

value: N


title: 1772075305_E05

value: M

value: neurons

value: Sst low-medium


title: 1772075304_B09


title: hela_LAMTOR5-AS1_1

description: processed data file: rnaseq_tpm.txt

value: HeLa

tag: sgrna infected


title: hela_LAMTOR5-AS1_2

description: processed data file: rnaseq_tpm.txt


title: 1772075304_B10

tag: strain


title: Day3_TY1_input


title: Late stage post-radiation GBM RCAS mouse model cell T3-94

source_name: stage T3,  Cell # 94

tag: tissue


title: 1772075304_B08

tag: age (days postnatal)

tag: Sex


title: Late stage post-radiation GBM RCAS mouse model cell T3-92

source_name: stage T3,  Cell # 92


title: Late stage post-radiation GBM RCAS mouse model cell T3-93

source_name: stage T3,  Cell # 93


title: hela_KB-1471A8.1_1

description: processed data file: rnaseq_tpm.txt


title: Late stage post-radiation GBM RCAS mouse model cell T3-91

source_name: stage T3,  Cell # 91


title: Late stage post-radiation GBM RCAS mouse model cell T3-90

source_name: stage T3,  Cell # 90


title: hela_KB-1471A8.1_2

description: processed data file: rnaseq_tpm.txt


title: 1772075304_B07

source_name: hypothalamus

tag: acute stress

tag: cell diameter


title: 1772075304_B05

tag: total molecules

tag: level1 class

value: astrocytes


title: 1772075304_B06

tag: level2 class (neurons only)


title: Late stage post-radiation GBM RCAS mouse model cell T3-9

source_name: stage T3,  Cell # 9


title: Late stage post-radiation GBM RCAS mouse model cell T3-89

source_name: stage T3,  Cell # 89


title: 1772075304_A12

value: ependymal


title: Late stage post-radiation GBM RCAS mouse model cell T3-95

source_name: stage T3,  Cell # 95


title: hela_CCAT1_2

description: processed data file: rnaseq_tpm.txt

tag: cell type


title: hela_CTC-428G20.6_2

description: processed data file: rnaseq_tpm.txt


title: hela_CCAT1up_2

description: processed data file: rnaseq_tpm.txt


title: Late stage post-radiation GBM RCAS mouse model cell T3-87

source_name: stage T3,  Cell # 87


title: 1772075304_A11


title: hela_CCAT1up_1

description: processed data file: rnaseq_tpm.txt


title: 1772075304_B01


title: Late stage post-radiation GBM RCAS mouse model cell T3-88

source_name: stage T3,  Cell # 88


title: hela_CCAT1_1

description: processed data file: rnaseq_tpm.txt


title: 1772075304_A10


title: PU-NEI-br2

description:
replicate 2 for ovules at nucellar embryo initiation stage
processed data file = "pummelo-grapefruit.rpkm.xlsx"

organism: Citrus maxima

source_name: Ovules_Huanong red pummelo (Citrus grandis)

extract_protocol:
Total RNA was extracted by Trizol method
Libraries were constructed for sequencing using standard Illumina protocols

tag: cultivar

value: Huanong red pummelo

value: ovules

tag: age

value: 3 DAF(days after flowering)


title: PU-NEI-br1

description:
replicate 1 for ovules at nucellar embryo initiation stage
processed data file = "pummelo-grapefruit.rpkm.xlsx"


title: 1772075304_A09

value: oligos


title: Late stage post-radiation GBM RCAS mouse model cell T3-86

source_name: stage T3,  Cell # 86

tag: tumor stage

value: Late stage post-radiation

tag: time point (weeks)


title: 1772075304_A06


title: Late stage post-radiation GBM RCAS mouse model cell T3-85

source_name: stage T3,  Cell # 85

value: Brain

tag: tumor type

tag: background strain


title: PU-pre-NEI-br1

description:
replicate 1 for ovules before nucellar embryo initiation stage
processed data file = "pummelo-grapefruit.rpkm.xlsx"

value: 0 DAF(days after flowering), i.e anthesis


title: Late stage post-radiation GBM RCAS mouse model cell T3-84

source_name: stage T3,  Cell # 84

value: 10 weeks

value: Recurrent Tumor

tag: tumor grade


title: 1772058147_H11

tag: strain

value: Unknown

value: Avp-medium


title: Late stage post-radiation GBM RCAS mouse model cell T3-82

source_name: stage T3,  Cell # 82

tag: tissue

value: RCAS-TVA

value: High


title: Late stage post-radiation GBM RCAS mouse model cell T3-81

source_name: stage T3,  Cell # 81


title: 1772075304_A02

tag: age (days postnatal)

value: M

value: N

value: microglia


title: 1772058147_H09

tag: Sex

value: ependymal


title: 1772058147_H10

tag: acute stress


title: Late stage post-radiation GBM RCAS mouse model cell T3-8

source_name: stage T3,  Cell # 8


title: 1772058147_H08

tag: cell diameter

value: neurons

value: Pomc+/- (ARH)


title: 1772058147_H04

tag: total molecules


title: Late stage post-radiation GBM RCAS mouse model cell T3-77

source_name: stage T3,  Cell # 77


title: Late stage post-radiation GBM RCAS mouse model cell T3-76

source_name: stage T3,  Cell # 76


title: Late stage post-radiation GBM RCAS mouse model cell T3-79

source_name: stage T3,  Cell # 79


title: Late stage post-radiation GBM RCAS mouse model cell T3-80

source_name: stage T3,  Cell # 80


title: Late stage post-radiation GBM RCAS mouse model cell T3-78

source_name: stage T3,  Cell # 78


title: 1772058147_H01

source_name: hypothalamus

tag: level1 class

value: endothelial


title: Late stage post-radiation GBM RCAS mouse model cell T3-75

source_name: stage T3,  Cell # 75


title: 1772058147_H07

tag: level2 class (neurons only)


title: 1772058147_H03