title: Irf8-/- GMP Bulk RNA Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+ Irf8-/-

extract_protocol:
Cells were harvested from bone marrow. Mice were euthanized with carbon dioxide and cervical dislocation. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzle and subjected to flow cytrometric sorting. For G3GV mice, the sorted GMP were cultured overnight with doxycycline to induce the G3GV transgene, then sorted for Venus expression.
Bulk RNA Seq libraries were generated with Illumina TruSeq Stranded mRNA HT kits
Cells were sorted, RNA extracted, and bulk RNA Seq library construction was performed.

value: Granulocyte Macrophage Progenitor (GMP)

value: TRUseq RNA sample kit  (Illumina)


title: Gfi1-/- GMP Bulk RNA Seq

status: Public on Aug 26 2016

type: SRA

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

country: USA

institute: Cincinnati Childrens Hospital Medical Center

description: Lin- CD117+ Sca1- CD16/32+ CD34+ Gfi1-/-

library_source: transcriptomic

data_processing:
RNA reads were aligned to the reference mm9 mouse genome using Bowtie2.
Single-cell and matched bulk sorted RNA-Seq were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using a FDR adjusted empirical Bayes moderated t-test p<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values

molecule: total RNA

organism: Mus musculus

source_name: Bone Marrow

tag: cell type

tag: strain

tag: cdna synthesis

tag: library prep


title: CMP cell 1 (poor quality)

description: Lin- CD117+ Sca1- CD16/32 dim CD34+

extract_protocol:
Cells were harvested from bone marrow. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of Lin- CD117+ Sca1- CD16/32-intermediate CD34-intermediate cells (CMP).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

value: CMP Progenitors

value: Fluidigm C1 protocol

value: Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA)


title: Lineage-negative Sca1-positive c-Kit-positive (LSK) Bulk RNA Seq

description: Lin- CD117+ Sca1+ (LSK)


title: Csf1r-negative GMP ROSA-rtTA-M2-heterozygous G3-Gfi1-IRES-Venus-bright Bulk RNA Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+ CD115- ROSArtTA-M2-heterozygous Gfi1-IRES-Venus-bright


title: Csf1r-positive GMP (Csf1r+ control) Bulk RNA Seq CAG-14914

description: Lin- CD117+ Sca1- CD16/32+ CD34+ CD115+ Gfi1-IRES-Venus-negative (Csf1r+ control)


title: Csf1r-positive GMP (Csf1r+ control) Bulk RNA Seq 17Rosa-


title: Csf1r-positive GMP ROSA-rtTA-M2-heterozygous G3-Gfi1-IRES-Venus-bright Bulk RNA Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+ CD115+ ROSArtTA-M2-heterozygous Gfi1-IRES-Venus-bright


title: Csf1r-positive GMP ROSA-rtTA-M2-heterozygous G3-Gfi1-IRES-Venus-dim Bulk RNA Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+ CD115+ ROSArtTA-M2-heterozygous Gfi1-IRES-Venus-dim


title: CMP cell 2

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: Csf1r-negative GMP ROSA-rtTA-M2-homozygous G3-Gfi1-IRES-Venus-bright Bulk RNA Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+ CD115- ROSArtTA-M2-homozygous Gfi1-IRES-Venus-bright


title: Granulocyte Macrophage Progenitor (GMP) Bulk RNA Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+


title: Csf1r-positive GMP ROSA-rtTA-M2-homozygous G3-Gfi1-IRES-Venus-bright Bulk RNA Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+ CD115+ ROSArtTA-M2-homozygous Gfi1-IRES-Venus-bright


title: Common Myeloid Progenitor (CMP) Bulk RNA Seq

description: Lin- CD117+ Sca1- CD16/32-intermediate CD34-intermediate (CMP)

value: Common Myeloid Progenitor (CMP)


title: Csf1r-negative GMP ROSA-rtTA-M2-heterozygous G3-Gfi1-IRES-Venus-dim Bulk RNA Seq

description: Lin- CD117+ Sca1- CD16/32+ CD34+ CD115- ROSArtTA-M2-heterozygous Gfi1-IRES-Venus-dim


title: s7.32

city: Los Angeles

first: Ganlu

last: Hu

state: CA

address: 695 Charles E Young Dr. South

department: human genetics

institute: University of California, Los Angeles

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell by using unique barcode combinations from the Nextera XT preparation and to generate fastq files.
Raw reads past quality check were mapped by bowtie2, gene expression level was quantified as transcripts per million reads (TPM) using RSEM to known exons using Refseq gene annotation downloaded from UCSC genome browser. Ribosomal RNA annotations were removed from reference file before gene expression quantification.
In order to reduce technical noise, We filtered away genes with greater than 20% samples with TPM<10. Then we did log2 transform on the remaining data.
Genome_build: mm9
Supplementary_files_format_and_content: text files with TPM values.

molecule: polyA RNA

source_name: single DRG from SNT side

extract_protocol:
The experiment was performed on two month old adult C57BL/6 mice. All surgical procedures were performed under general anesthesia with intraperitoneal injections using a mixture of ketamine（100mg/kg) and xylazine（10mg/kg). For the sciatic nerve transection (axotomy), the right side sciatic nerve was exposed at the mid thigh level and sectioned distally. The wound was sutured in two layers, and the animals were allowed to recover. After 3 and 7 days of the surgery, animals were euthanased by CO2  and decapitated, L3-L5 DRG from both ipsilateral and contralateral side were dissected and dissociated into single cell. Single DRG soma was manually picked in the lowest possible volume (preferably ≤0.5μl, possibly 0.3μl) using a micro capillary pipette into a 0.2-ml thin-walled PCR tube contains 4μl smart-seq2 lysis buffer. Cell sizes were measured and recorded during the picking. Except for the enzyme dissociation, all the dissection procedure were performed on ice in order to reduce RNA degradation.
Whole transcriptome amplification in tubes were performed following Smart-seq2 protocol(Picelli, Faridani et al. 2014) with minor edition. Briefly, the nuclei were lysised  and ploy-A RNA was reverse transcribed by superscript III reverse transcription enzyme using a template switch fashion. cDNA were then amplified by KAPA polymerase for 18 PCR cycles. After purification, 0.2ng cDNA were used for Nextera tagmentation and library construction. These libraries were sequenced 75bp pair ended on illumina Next-seq500 pipeline.

tag: tissue

value: dorsal root ganglion

tag: gender

value: male


title: s7.33


title: CMP cell 3

description: Lin- CD117+ Sca1- CD16/32 dim CD34+


title: s7.31


title: s7.30


title: s7.29


title: s7.28


title: s7.26


title: s7.25


title: s7.27


title: s7.24


title: s7.22


title: s7.23


title: s7.20


title: s7.21


title: s7.19


title: Csf1r-negative GMP (Csf1r- control) Bulk RNA Seq 18Rosa-

description: Lin- CD117+ Sca1- CD16/32+ CD34+ CD115- Gfi1-IRES-Venus-negative (Csf1r- control)


title: Csf1r-negative GMP (Csf1r- control) Bulk RNA Seq CAG-14915


title: s7.16

value: female


title: s7.18


title: s7.8


title: s7.13


title: s7.17


title: s7.9


title: s7.7


title: s7.15


title: s7.11


title: s7.10


title: s7.12


title: s7.14


title: s7.4


title: s7.5


title: s7.6


title: n7.14

source_name: single DRG from control side


title: s7.3


title: s7.2


title: s7.1


title: n7.13


title: n7.9


title: n7.7


title: n7.5


title: n7.12


title: n7.6


title: n7.4


title: n7.3


title: n7.1


title: n7.2


title: n7.11


title: s3.26

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell by using unique barcode combinations from the Nextera XT preparation and to generate fastq files.
Raw reads past quality check were mapped by bowtie2, gene expression level was quantified as transcripts per million reads (TPM) using RSEM to known exons using Refseq gene annotation downloaded from UCSC genome browser. Ribosomal RNA annotations were removed from reference file before gene expression quantification.
Genome_build: mm9
Supplementary_files_format_and_content: In order to reduce technical noise, We filtered away genes with greater than 20% samples with TPM<10. Then we did log2 transform on the remaining data.

source_name: L5 DRG injury single cell

extract_protocol:
The experiment was performed on two month old adult CAST/Eij ♂ cross C57BL/6♀F1 mice. All surgical procedures were performed under general anesthesia with intraperitoneal injections using a mixture of ketamine（100mg/kg) and xylazine（10mg/kg). For the sciatic nerve transection (axotomy), the right side sciatic nerve was exposed at the mid thigh level and sectioned distally. The wound was sutured in two layers, and the animals were allowed to recover. After 3 days of the surgery, animals were euthanased by CO2  and decapitated, L5 DRG from both ipsilateral and contralateral side were dissected and dissociated into single cell. Single DRG soma was manually picked in the lowest possible volume (preferably ≤0.5μl, possibly 0.3μl) using a micro capillary pipette into a 0.2-ml thin-walled PCR tube contains 4μl smart-seq2 lysis buffer. Cell sizes were measured and recorded during the picking. Except for the enzyme dissociation, all the dissection procedure were performed on ice in order to reduce RNA degradation.
Whole transcriptome amplification in tubes were performed following Smart-seq2 protocol (Picelli, Faridani et al. 2014) with minor edition. Briefly, the nuclei were lysised  and ploy-A RNA was reverse transcribed by superscript III reverse transcription enzyme using a template switch fashion. cDNA were then amplified by KAPA polymerase for 18 PCR cycles. After purification, 0.2ng cDNA were used for Nextera tagmentation and library construction. ERCC RNA spike-in Mix (Ambion, Life Technologies) was added to the lysis reaction and processed in parallel with ploy-A RNA.
All libraries were sequenced 50bp single end on illumina Hi-seq2000 pipeline.

value: CAST/Eij male X C57BL/6 female


title: s3.27


title: s3.21


title: s3.22


title: s3.19


title: s3.24


title: s3.20


title: n7.10


title: s3.17


title: s3.15


title: s3.18


title: s3.23


title: s3.25


title: s3.16


title: s3.12


title: s3.11


title: s3.13


title: n7.8


title: s3.14


title: s3.10


title: s3.9


title: s3.8


title: s3.6


title: s3.7


title: s3.3


title: s3.5


title: s3.2


title: s3.4


title: n3.21

source_name: L5 DRG intact single cell


title: s3.1


title: n3.20


title: n3.22


title: n3.15


title: n3.10


title: n3.19


title: n3.13


title: n3.11


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Ioc3D mutant 7

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description:
MNase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_EdU_IOC3D_tss_aligned.txt

library_source: genomic

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling.
Time points were separated by barcode and the 5bp barcode was removed from the read sequence.
Reads were mapped to the yeast S288C genome using BLAT.
Paired end read count distribution in 1bp windows was determined separately for Watson (marked as F in the processed data files) and Crick (marked as R in the processed data files) strands.
The average read count value was calculated and the data were normalized to one.
Genome_build: S288C (S. cerevisiae)
Supplementary_files_format_and_content: Tab-delimited text files of nucleosome occupancy for every gene at indicated time points (lines), showing every 20th bp from -500bp to the end of the gene coding sequence surrounding the transcription start site (marked as tss). Occupancy data start after the GWEIGHT header.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol:
For the synchronization experiment cells were grown over night at 30°C in Synthetic Complete- URA + Dextrose media to OD 0.3. After 3.75hrs of incubation at 30°C with alpha factor (0.25μg/ml), cells were pelleted and transferred into preheated and premixed SCD-URA+ 10μM EdU(Carbosynth), with freshly added 20μg/ml pronase (Sigma). 200ml aliquots were taken at 25, 32, 40, 47 and 55 min after release. Time points were fixed with 1% formaldehyde.
In the EdU-Thymidine pulse chase experiments, cells were grown in SCD-URA over night at 30°C to an OD of 1.0. The next day the culture was diluted to OD=0.25 and cells were allowed to double once. Cell pellets were then transferred to preheated and premixed SCD-URA+ 10μM EdU media. Thymidine (to a final concentration of 5mM) was added after 5,10 or 20min incubation with EdU at 30°C and incubated for another 5 or 10 min. Cells were then pelleted and transferred into fresh media with 5mM Thymidine (and 15μg/ml nocodazole 5(Sigma) or 3μg/ml thiolutin (Abcam) when indicated) and 200ml aliquots were taken at indicated time points (after the Thymidine incubation) and fixed as above.

extract_protocol:
Cells were washed in water, cell walls were broken with bead beating and spheroplasts were treated with micrococcal nuclease. EdU from isolated nascent DNA fragments was biotinylated using Click chemistry and nascent DNA was purified with streptavidin coated beads. An input DNA aliquot was set aside prior to biotinylation.
Nascent and input DNA samples, were treated with calf intestinal phosphatase (NEB), blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors with custom 5bp inline barcodes (first 5bp in raw data read), and PCR amplified and size selected by gel purification. For nascent libraries, the nascent strand was separated from its complement with primer extension in the presence of dUTP and the dUTP strand was then digested with the USER enzyme cocktail prior to PCR amplification. All the steps for nascent libraries were done on streptavidin coated magnetic beads.

treatment_protocol: Cells were fixed in 1% formaldehyde.

value: yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and a ioc3 deletion

tag: cell cycle

value: asynchronous

tag: edu incubation

tag: thymidine incubation (min)

tag: time point

value: 25 min after Thymidine chase, nascent chromatin


title: n3.7


title: n3.16


title: n3.14


title: n3.17


title: n3.8


title: n3.18


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Ioc3D mutant 6

value: 15 min after Thymidine chase, nascent chromatin


title: n3.9


title: n3.12


title: HOS_Revived_Human

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
The Illumina HiSeq 2500 generates raw images utilizing HCS(HiSeq Control Software) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using NGS Toolkit.
Sequencing reads obtained were mapped to the human genome using TopHat (v2.0.11)
To assemble the mapped reads from RNA-seq against ENSEMBL gene structure annotation, Cufflinks (v2.2.1) was used and expression level for each transcript was estimated. A Cufflinks based probabilistic model of paired-end sequencing was used to evaluate abundances of isoforms, and detect ambiguous isoforms.
Differentially expressed transcripts were identified using CuffDiff protocol.  Fold change of 1.5 and above with a pvalue of <=0.05 was used as a cutoff to identify differentially expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: Tumor cell line

growth_protocol: All samples were cultured in MEM media with 10% FBS and 1%Penstrep. OS-R_Human cells were grown and maintained with IC50 dose of Cisplatin specifically.

extract_protocol:
TRIzol method for RNA isolation
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OS-R_Cisshock_Human cells were treated with 1mg/ml of Cisplatin and OS-R_withoutCisplatin_Human cells were grown without Cisplatin for a brief period of 14 days

value: Bone

tag: cell line

value: Osteosarcoma cell line

tag: atcc#

tag: treatment

value: Revived (without Cisplatin)


title: n3.6


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Ioc3D mutant 5

value: 8 min after Thymidine chase, nascent chromatin


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Ioc3D mutant 4

value: 6 min after Thymidine chase, nascent chromatin


title: n3.3


title: n3.5


title: OS-R_without Cisplatin_Human

value: Osteosarcoma cell line, resistant

value: without Cisplatin


title: MNase-seq of total chromatin in Ioc3D mutant

description:
MNase digest of total chromatin from asynchronous cells.
Strand-specific MNase-seq.
Processed data file: IOC3D_total_tss_aligned.txt

value: total chromatin MNase digest in asynchronous cells


title: n3.2


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Ioc3D mutant 3

value: 4 min after Thymidine chase, nascent chromatin


title: OS-R_Cisshock_Human

value: Cisshock


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Ioc3D mutant 2

value: 2 min after Thymidine chase, nascent chromatin


title: n3.1

value: dorsal root ganglion


title: DRG_bulk_SNI_3

source_name: L5 DRG intact bulk cell

value: CAST/Eij male X C57BL/6 female


title: 9Cr dCas9 silenced cells rep3

city: Milano

first: Davide

last: Cittaro

address: via Olgettina 58

department: Center for Traslational Genomics and Bioinformatics

country: Italy

institute: Ospedale San Raffaele

data_processing:
Reads were aligned to reference genome using STAR v2.3.0
Features were counted using Rsubread; gencode v19 was used as gene model; reads were summarized at gene level
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak. Features identified for MeDIP-seq samples
Supplementary_files_format_and_content: abundance measurements: raw read counts over merged features (meDIP-seq) or genes (RNA-seq)

source_name: K562 with B2M:tdTomato transgene

growth_protocol: K562 cells were grown in IMDM (Sigma) 10% Fetal Bovine Serum (EuroClone)  and 1% Pennicillin/Streptomycin (100 U/ml final concentration; EuroClone). Cells were routinely splitted every 3 days at a concentration of 10^5 cells/ml without allowing them to reach concentration higher than 8^105 cells/ml

extract_protocol:
RNA was extracted with Qiagen Kit (Cat. 74134, respectively) according to manifacturer's instructions.
Amplification of cDNA from total RNA was performed using the Ovation Human FFPE RNA-seq Library System (Nugen), cDNA was fragmented with E220 COVARIS ultrasonicator (Covaris).

treatment_protocol: K562 cells were treated with a cocktail of three plasmid each encoding for a different ATR. We used 1 ug of palsmid encoding for D3A-based ATR and then normalized the amount of the others plasmids to obtain a 1:1 molar ratio. For dCas9 based ATR treatment we used 250 ng of plasmid encoding for sgRNA.


title: 9Br dCas9 silenced cells rep2


title: DRG_bulk_Nor_3


title: DRG_bulk_SNI_2


title: HOS_Human

value: control


title: Input of replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 5

description:
Input of MNase digest time course before nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_EdU_input2_HIR1D_replicates12_tss_aligned.txt

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and the hir1 deletion

value: asynchronous

value: 8 min after Thymidine chase, total chromatin


title: 6Br Untreated cells rep2


title: 9Ar dCas9 silenced cells rep1


title: DRG_bulk_SNI_1


title: Input of replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 4

value: 6 min after Thymidine chase, total chromatin


title: Input of replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 6

value: 15 min after Thymidine chase, total chromatin


title: Input of replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 3

value: 4 min after Thymidine chase, total chromatin


title: Input of replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 7

value: 25 min after Thymidine chase, total chromatin


title: DRG_bulk_Nor_1


title: 6Cr Untreated cells rep3


title: 6Ar Untreated cells rep1


title: DRG_bulk_Nor_2


title: n3.4


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Ioc3D mutant 1

value: yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and a ioc3 deletion

value: 0 min after Thymidine chase, nascent chromatin


title: Input of replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 2

value: 2 min after Thymidine chase, total chromatin


title: HOS_Cisshock_Human

value: Bone

value: Osteosarcoma cell line


title: 4Cr TALE silenced cells rep3


title: 4Br TALE silenced cells rep2


title: mTr_rep5 (Sample 90)

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: YFP+ GFP+ Treg cells were isolated from animals treated with tamoxifen and diphtheria toxin

data_processing:
Sequences mapped using STAR 2.5.0
Expression level was quantified with refGene annotation
DESeq2 analysis was run with q-value cutoff of 0.05
Genome_build: mm9

source_name: Inflammation-experienced Treg cells

extract_protocol: Sorted cells were lysed with TRIzol and stored at -80 degree. RNA was extracted according to the manufacturer’s manual (Life Technologies). cDNA libraries were generated using SMARTer amplification (Clontech) and individually indexed. Libraries were sequenced on HiSeq 2000 platform (Illumina).

value: Spleen and peripheral lymph nodes

value: Inflammation-experienced Treg cells

tag: source

value: mixed bone marrow chimeras generated with 90% Foxp3-GFP-DTR /10% Foxp3-GFP-CRE-ERT2XR26Y bone marrow

tag: activating stimulus

value: Transient Treg cell depletion

tag: days post-stimulus

value: 60 days


title: Input of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 4

description:
Input of MNase digest time course before nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_input_HIR1D_tss_aligned.txt

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and the hir1 deletion


title: Input of replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 1

value: asynchronous

value: 0 min after Thymidine chase, total chromatin


title: aTr_rep5 (Sample 89)

source_name: Activated Treg cells

value: Activated Treg cells

value: 11 days


title: 4Ar TALE silenced cells rep1


title: Input of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 3

value: 15 min after Thymidine chase, total chromatin


title: Input of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 2

value: 8 min after Thymidine chase, total chromatin


title: 9Cm dCas9 silenced cells rep3

data_processing:
Reads were aligned to reference genome using bwa mem v0.7.5
Duplicates were processed with Picard MarkDuplicates
Peaks were identified using MACS2 (callpeak -g hs --keep-dup=1 --llocal 500000 --slocal 0 --broad)
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak. Features identified for MeDIP-seq samples
Supplementary_files_format_and_content: abundance measurements: raw read counts over merged features (meDIP-seq) or genes (RNA-seq)

extract_protocol:
DNA was extracted with Qiagen Kit (Cat.13343) according to manifacturer's instructions.
500 ng of genomic DNA was sonicated with E220 COVARIS ultrasonicator (Covaris) and sequencing libraries were prepared using NextFlex Methylseq kit 1 (Bioo Scientific). After adapter ligation step, samples were pooled and immunoprecipitated using a monoclonal antibody directed against 5-methylcytosine (MagMeDIP kit, Diagenode). Enriched and control libraries (not immumoprecipitated) were purified using the IPure kit (Diagenoide). Enrichment efficiency was evaluated by qPCR using provided internal controls (spiked-in DNA from A. thaliana). Libraries were amplified following NextFlex Methylseq kit 1 protocol


title: aTr_rep4 (Sample 88)


title: Input of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course in Hir1D mutant 1


title: rTr_rep5 (Sample 87)

description: Bulk GFP+ Treg cells were isolated from animals treated with tamoxifen only

source_name: Resting Treg cells

value: Resting Treg cells


title: 6Cm Untreated cells rep3

data_processing:
Reads were aligned to reference genome using bwa mem v0.7.5
Duplicates were processed with Picard MarkDuplicates
Peaks were identified using MACS2 (callpeak -g hs --keep-dup=1 --llocal 500000 --slocal 0 --broad)
Peaks from multiple samples were merged using bedtools multiinter -cluster; counts over merged peaks were obtained using bedtools multibamcov
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak. Features identified for MeDIP-seq samples
Supplementary_files_format_and_content: abundance measurements: raw read counts over merged features (meDIP-seq) or genes (RNA-seq)


title: 9Am dCas9 silenced cells rep1


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 7

description:
MNase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_EdU_input2_HIR1D_replicates12_tss_aligned.txt

value: yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and a hir1 deletion

value: 25 min after Thymidine chase, nascent chromatin


title: 9Bm dCas9 silenced cells rep2


title: KDEMmmB1_w11_2

first: Kenneth

last: Dorshkind

state: California

address: 10833 Le Conte Avenue

department: Pathology and Laboratory Medicine

institute: David Geffen School of Medicine at UCLA

data_processing:
Reads were aligned to the Mus musculus genome (mm10 build) using STAR v2.3.0 (Dobin et al. doi:10.1093/bioinformatics/bts635) in supervised mode using the Ensemble GRCm38.71 gene annotation as template. Relevant alignment parameters are: --outFilterMultimapScoreRange 0.75  --outFilterMultimapNmax 100 --outFilterMismatchNmax 25 --outFilterScoreMinOverLread 0.75 --outFilterMatchNminOverLread 0.75 --outFilterMismatchNoverLmax 0.25 --sjdbOverhang 99
HTSeq-count v0.5.4p3 (Simon Anders, http://www-huber.embl.de/users/anders/HTSeq/) was used to compute the matrix of raw counts (relevant paramters: --mode=intersection-strict). This matrix was used as input for DESeq v1.12.1 to assess pair-wise differential expression with "per-condition" expression estimates. Finally, moderate fold-changes (mfc) between two experimental conditions were computed from variance stabilized data (as provided by DESeq with "pooled" dispersion estimates). Genes were tagged as differentially expressed if abs(mfc)>1 and p-value<0.05.
Genome_build: GRCm38.71/mm10
Supplementary_files_format_and_content: Tab delimited, per-sample, gene expression estimates in units of FPKMs

source_name: Adult Bone Marrow B-1

growth_protocol: Lin- CD93+ CD19+ CD45R- B-1 and Lin- CD93+ CD19- CD45R+ CD43+ B-2 progenitors were collected from fetal and neonatal liver and adult bone marrow and purified by FACS

extract_protocol:
Total RNA was isolated using Qiagen miRNAeasy micro kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were lysed directly after sort

tag: Sex

value: female

tag: age

value: 11 week old adult


title: KDEMmmB2_w11_2

source_name: Adult Bone Marrow B-2

tag: strain


title: mTr_rep6 (Sample 91)

value: Spleen and peripheral lymph nodes

tag: cell type


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 5

value: 8 min after Thymidine chase, nascent chromatin


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 6

value: 15 min after Thymidine chase, nascent chromatin


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 4

value: 6 min after Thymidine chase, nascent chromatin


title: 6Bm Untreated cells rep2


title: KDEMmmB1_w11_1


title: 4Cm TALE silenced cells rep3


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 3

value: 4 min after Thymidine chase, nascent chromatin


title: 4Am TALE silenced cells rep1


title: KDEMmmB2_w9_1

value: 9 week old adult


title: 4Bm TALE silenced cells rep2


title: KDEMmmB2_w9_2


title: KDEMmmB1_w9_2


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 2

value: asynchronous

value: 2 min after Thymidine chase, nascent chromatin


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 6


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 5


title: KDEMmmB1_w9_1


title: KDEMmmB2_w11_1


title: rTr_rep4 (Sample 86)

value: mixed bone marrow chimeras generated with 90% Foxp3-GFP-DTR /10% Foxp3-GFP-CRE-ERT2XR26Y bone marrow


title: KDEMmmB2_d2_1

source_name: Neonatal Liver B-2 Progenitors

value: male and female

value: Day 1 Neonates


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 4


title: 6Am Untreated cells rep1


title: KDEMmmB1_d2_2

source_name: Neonatal Liver B-1 Progenitors


title: KDEMmmB2_d2_2


title: KDEMmmB2_e15_1

source_name: E15.5 Fetal Liver B-2 Progenitors


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 1

value: 0 min after Thymidine chase, nascent chromatin


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 2


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in CHD1D mutant 6

description:
MNase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_EdU_CHD1D_replicate_tss_aligned.txt

value: yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and a chd1 deletion


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in CHD1D mutant 7


title: KDEMmmB2_e15_2


title: KDEMmmB1_e15_2

source_name: E15.5 Fetal Liver B-1 Progenitors


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 1

value: yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase and a hir1 deletion


title: MNase-seq of total chromatin in CHD1D mutant

description:
MNase digest of total chromatin from asynchronous cells.
Strand-specific MNase-seq.
Processed data file: CHD1D_total_tss_aligned.txt

value: total chromatin MNase digest in asynchronous cells


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in CHD1D mutant 5


title: s3.48

value: CAST/Eij male X C57BL/6 female

value: dorsal root ganglion


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in CHD1D mutant 4


title: s3.47


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in CHD1D mutant 3


title: s3.46


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in CHD1D mutant 2


title: s3.45


title: KDEMmmB1_d2_1


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in ChD1D mutant 6

description:
MNase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_EdU_CHD1D_tss_aligned.txt


title: s3.43


title: s3.44


title: s3.42


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in ChD1D mutant 5


title: s3.41


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in ChD1D mutant 4


title: s3.39


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in ChD1D mutant 3


title: s3.40


title: s3.38


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in Hir1D mutant 3


title: KDEMmmB1_e15_1


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in ChD1D mutant 2


title: s3.37


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in ChD1D mutant 1


title: PTSD5

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Road

department: Pathology Microbiology and Immunology

institute: University of South Carolina School of Medicine

description: PBMCs from war veterans with PTSD as per Diagnostic and Statistical Manual for mental Disorders were isolated within one hour and total RNA extracted for RNA-Seq library preparation.

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with the default parameters. We trimmed 3 nucleotides from the 5" end.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

source_name: PBMCs

extract_protocol:
PBMCs were isolated from whole blood and total RNA was  extracted. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: PTSD +ve

value: Peripheral blood

value: Mean 38.4 years

tag: genotype


title: Replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 7

description:
MNase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_EdU_replicate_tss_aligned.txt

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase

value: 25 min after Thymidine chase, nascent chromatin


title: s3.36

tag: tissue


title: Replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 6

tag: cell cycle

value: 15 min after Thymidine chase, nascent chromatin


title: EdU pulse (5min) Thymidine chase (5min) input DNA time course in ChD1D mutant 7

value: asynchronous

tag: edu incubation


title: PTSD4


title: s3.34


title: Replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 4

tag: thymidine incubation (min)

value: 6 min after Thymidine chase, nascent chromatin


title: Replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 5

tag: time point

value: 8 min after Thymidine chase, nascent chromatin


title: PTSD3


title: s3.33


title: Replicate of EdU pulse (5min) Thymidine chase (5min) input DNA time course in CHD1D mutant 1


title: Replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 2

value: 2 min after Thymidine chase, nascent chromatin


title: 22_CP_240

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

country: Netherlands

institute: University of Groningen

description: the sample contains total RNA from the human cell line and the bacteria S. pneumoniae

data_processing:
Adapter sequences were removed, and raw reads were trimmed with sliding window every 5 nucleotides, the average value must be more than 20, final trimmed length must be more than 66.7% original length (more than 50 nucleotides out of original 75 nucleotides).
Reads were aligned to a chimeric genome, containing a concatenated S. pneumoniae D39 genome to Homo sapiens genome.
Aligned reads were counted at the gene level.
Genome_build: Streptococcus pneumoniae D39 build NC_008533 and Homo sapiens GRCh.38
Supplementary_files_format_and_content: Normalized raw counts by DESeq2 in MS Excel 2010

organism:
Homo sapiens
Streptococcus pneumoniae D39

source_name: A549_capsular mutant, more adherent_240m

growth_protocol: Human epithelial cell line A549 cells were grown in DMEM/F12 medium supplemented with 10%FBS in 37C, humidified 5% CO2. S. pneumoniae D39 were grown in C+Y, 37C. Both species were co-incubated in an infection model, in RPMI 1640 without phenol red supplemented by 1%FBS, 37C 5% CO2.

extract_protocol:
To harvest the total RNA from host and pathogen at once, we treated cellular mixture with concentrated solution of ammonium sulfate to prevent any protein-dependent RNA degradation. Each ml of the ammonium sulfate solution (pH 5.2) contains 0.7 g (NH₄)₂SO₄, 20 mM EDTA and 25 mM Na-citrate. Ammonium sulfate solution is added directly to the medium with the ratio 3:1. The suspension was vigorously pipetted to ensure the complete mixing of  ammonium sulfate and infection medium. Adherent host cells were scrapped and incubated further (room temperature, 5 min). The suspension is collected and centrifuged at full speed (20 min, 4°C). Supernatant was removed and cell pellet was snap-frozen with liquid nitrogen.  The cell mixture contains host cells, adherent bacteria and non-adherent bacteria.  With the aim of disrupting pneumococcal cells, a bead beating procedure was exercised. In a 1.5 ml screw cap tube, a PCR tube full of sterile, RNase free glass beads were added together with 50 μl  10% SDS and 500 μl phenol-chloroform. In the meantime, frozen cell pellet was resuspended in TE solution (10 mM Tris-HCl, 1 mM Na₂EDTA, pH 8.0, DEPC, diethylpyrocarbonate-treated solution). The cell suspension was added into the screw-capped tube and beat for 3 times 45s. Tubes were immediately placed in ice box and centrifuged at full speed, 4°C to separate organic and water phases. Water phase was pipetted out and back extraction were performed to the organic phase to optimize RNA yield.  The subsequent part of the RNA isolation were performed based on High Pure RNA Isolation Kit (Roche) with column. Water phase from phenol-chloroform extraction were mixed well with binding buffer and pipetted into the upper chamber of column and centrifuged. DNase mix were then added onto the filter and incubated at room temperature for 30 min to digest total genomic DNA. Total RNA were eluted according to the manufacturer protocol.   Total RNA samples were treated with a 1:1 mixture of Human/Mouse/Rat and Gram positive bacteria capture probes (Ribo-Zero rRNA Removal Kits, Illumina, US) to simultaneously deplete host and pathogen rRNA. cDNA library preparation was prepared with TruSeq® Stranded Total RNA Sample Preparation Kit (Illumina, US) according to the manufacturer protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Various co-incubation time between human epithelial cell line A549 and S. pneumoniae D39, including 0, 30, 60, 120 and 240 minutes after co-incubation/infection.

tag: cell line

value: human epithelial cell line

tag: timepoints (mpi)

tag: pneumococcal strain

value: capsular mutant, more adherent

tag: molecule subtype

value: total epithelial and pneumococcal RNA


title: Replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 3

value: 4 min after Thymidine chase, nascent chromatin


title: s3.31


title: PTSD1


title: Control5

description: PBMCs from control individuals were isolated within one hour and total RNA extracted for RNA-Seq library preparation.

value: PTSD -ve

value: Mean 42.6 years


title: Input EdU pulse (5min) Thymidine chase (5min) nascent DNA time course during Thiolutin treatment 5

description:
Input MNase digest time course during Thiolutin treatment followed before nascent DNA purification by EdU-biotin pulldown from asynchronous cells after an 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_EdU_+-Thiolutin_input_tss_aligned.txt

value: 25 min after Thymidine chase, total chromatin, with thiolutin


title: 20_WT_120

source_name: A549_capsular mutant, more adherent_120m


title: Control4


title: 21_WT_240

source_name: A549_wt, encapsulated_240m

value: wt, encapsulated


title: Control3

value: Peripheral blood


title: s3.29

source_name: L5 DRG injury single cell

value: CAST/Eij male X C57BL/6 female

value: dorsal root ganglion


title: s3.35


title: Input EdU pulse (5min) Thymidine chase (5min) nascent DNA time course during Thiolutin treatment 4

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase

value: 16 min after Thymidine chase, total chromatin, with thiolutin


title: Control2


title: 19_CP_120


title: Replicate of EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 1

value: asynchronous

value: 0 min after Thymidine chase, nascent chromatin


title: s3.28


title: Input EdU pulse (5min) Thymidine chase (5min) nascent DNA time course during Thiolutin treatment 3

value: 8 min after Thymidine chase, total chromatin, with thiolutin


title: 17_WT_120

source_name: A549_wt, encapsulated_120m


title: s3.32


title: Input EdU pulse (5min) Thymidine chase (5min) nascent DNA time course during Thiolutin treatment 2

value: 6 min after Thymidine chase, total chromatin, with thiolutin


title: 18_CP_120

value: human epithelial cell line


title: Control1


title: PTSD2

value: PTSD +ve

value: Mean 38.4 years


title: glp-1 under EV on adult day 4

city: Shanghai

first: Jing-Dong

middle: Jackie

last: Han

address: Yueyang Road 320

department: CAS-MPG Partner Institute for Computational Biology

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to ce10 genome by tophat (version 1) with parameters -p 10 -g 1.
Differentially expressed genes were identified between EV and lin-28 RNAi for each strain by Cuffdiff (version 1) based on mapped reads from above, with parameters -p 16 -u and ce10.gtf provided. EV sample are the first sample and lin-28 RNAi sample are the second for comparison.
Genome_build: ce10
Supplementary_files_format_and_content: diff file processed by cuffdiff (version 1)

organism: Caenorhabditis elegans

source_name: glp-1 worms

growth_protocol: N2 were raised at 20℃, while temperature sensitive glp-1 mutants were hatched at 20℃ and then shifted to 25℃ 12h after hatching.

extract_protocol:
Total RNA of worms fed with empty vector and lin-28 RNAi bacteria from L1 were isolated with TRIzol (Invitrogen) at adult day 4 stage and precipitated with isopropanol.
RNA sequencing libraries were constructed following the Illumina RNA-seq protocol with at least 10g total RNA

treatment_protocol: RNAi was performed on nematode growth media plates with 1 mM IPTG from L1. All RNAi bacteria were from the Ahringer library and were sequenced before use. For all RNAi assays, the same HT115 bacteria carrying the empty L4440 construct were used as control.

tag: RNAi

value: EV


title: 15_CP_60

source_name: A549_capsular mutant, more adherent_60m

value: capsular mutant, more adherent

value: total epithelial and pneumococcal RNA


title: Input EdU pulse (5min) Thymidine chase (5min) nascent DNA time course during Thiolutin treatment 1

value: before EdU addition, total chromatin, with thiolutin


title: s3.30


title: N2 under lin-28 on adult day 4

source_name: N2 worms


title: 14_CP_60


title: Input from EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 5

description:
Input of MNase digest time course before nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_EdU_+-Thiolutin_input_tss_aligned.txt

value: 16 min after Thymidine chase, total chromatin, without thiolutin


title: Input from EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 3

value: 8 min after Thymidine chase, total chromatin, without thiolutin


title: Input from EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 4

value: 12 min after Thymidine chase, total chromatin, without thiolutin


title: N2 under EV on adult day 4


title: 12_WT_60

source_name: A549_wt, encapsulated_60m

value: wt, encapsulated


title: 08_WT_30

source_name: A549_wt, encapsulated_30m


title: 09_WT_30


title: 13_WT_60


title: glp-1 under lin-28 on adult day 4


title: 11_CP_30

source_name: A549_capsular mutant, more adherent_30m


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course replicate 6

description:
MNase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 20min EdU pulse and a 10min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_20_10_EdU_replicate_tss_aligned.txt

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase

value: 25 min after Thymidine chase, nascent chromatin


title: Input from EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 1

value: asynchronous

value: before Edu addition, total chromatin, without thiolutin


title: 10_CP_30


title: Input from EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 2

value: 4 min after Thymidine chase, total chromatin, without thiolutin


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course replicate 5

value: 8 min after Thymidine chase, nascent chromatin


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course replicate 4

value: 6 min after Thymidine chase, nascent chromatin


title: 06_CP_0

source_name: A549_capsular mutant, more adherent_0m

value: human epithelial cell line


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course replicate 3

value: 4 min after Thymidine chase, nascent chromatin


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course replicate 1

value: 0 min after Thymidine chase, nascent chromatin


title: UMSCC1_ZNF750_wildtype

status: Public on Aug 25 2016

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

data_processing:
Clean paired end fastq files were aligned to human reference (hg19) using STAR aligner.
expression was estimated in terms of FPKM using cufflinks against ensemble version 75 gene model (GTF)
Genome_build: hg19
Supplementary_files_format_and_content: Output from cufflinks (genes.fpkm.tracking file)

source_name: cell line

extract_protocol: Libraries were generated using the TruSeq RNA Sample Preparation kit (Illumina)

tag: condition

value: ZNF750 wildtype overexpression


title: 05_WT_0

source_name: A549_wt, encapsulated_0m

value: total epithelial and pneumococcal RNA


title: NHC1

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Normal Human Cholangiocyte

growth_protocol: iPSC were induced to definitive endoderm (DE) for 4 days using Advanced RPMI medium changed and supplemented daily with addition of 50 ng/ml Activin A and 50 ng/ml Wnt3A in the presence of Matrigel. DE cells were treated daily with 10 ng/ml fibroblast growth factor 2 (FGF2), 20 ng/ml bone morphogenic protein 4 (BMP4) and 50 ng/ml Sonic hedgehog (SHH) for 4 days, for hepatic specification (HS). HS cells were induced to hepatic progenitor (HP) cells for 4 days with daily exposure to 50 ng/ml SHH and 100 ng/ml recombinant Jagged-1. To generate iDC, HP cells were treated for 4 days with H69 media changed and supplemented daily with 10 ng/ml transforming growth factor- β (TGF-β) and replacement of Matrigel with collagen. All growth factors were purchased from R&D Systems

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Normal Human Cholangiocyte


title: NHC2


title: NHC3


title: IDC3

source_name: iPSC-Derived Cholangiocytes

value: iPSC-Derived Cholangiocytes


title: HP3

source_name: Hepatic Progenitor

value: Hepatic Progenitor


title: 07_CP_0

value: capsular mutant, more adherent


title: HP2


title: HP1


title: DE3

source_name: Definitive Endoderm

value: Definitive Endoderm


title: HS1

source_name: Hepatic Specification

value: Hepatic Specification


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course replicate 2

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase

value: 2 min after Thymidine chase, nascent chromatin


title: 04_WT_0

value: wt, encapsulated


title: HS2


title: STSV2

source_name: iPSC

value: iPSC


title: DE2


title: ChIP_EtOH_Rep2

city: Durham

first: Christopher

last: Vockley

state: NC

address: 101 science drive rm 2193

institute: Duke University

data_processing:
Base-calling was performed on instrument using CASAVA software
Data was mapped to the hg19 version of the human genome using Bowtie
Reads were converted from .sam to .bam files using samtools view with the  "-bS" option
Bam files were sorted using Samtools sort
Bam files were indexed using Samtools Index
Reads were counted using samtools idxstats
Peaks in the DEX treated samples were called using MACS peak caller, with the EtOH treated cells as a background model
Genome_build: hg19
Supplementary_files_format_and_content: .bed files report peaks

source_name: A549 cells  treated with .02% EtOH v/v

growth_protocol: A549 cells were grown to 90% confluence according to standard protocols in F12K medium

extract_protocol:
For each replicate, 2 ×10^7 nuclei were re-suspended in 1 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS at pH 7.4). Samples were sonicated using a Diagenode Bioruptor XL sonicator at 4°C to fragment chromatin to 200-500 bp segments. Insoluble  components were removed by centrifugation for 15 min at 15000 rpm. We conjugated 5  µg of anti-GR to 200 µl of sheep anti-rabbit IgG magnetic beads  (Life Technologies). Sheared chromatin in RIPA was then added to the  antibody-conjugated beads and incubated on a rotator overnight at 4°C. After incubation,  beads were washed five times with a LiCl wash buffer (100 mM Tris at pH 7.5, 500 mM  LiCl, 1% NP-40, 1% sodium deoxycholate), and remaining ions were removed with a  single wash with 1 mL of TE (10 mM Tris-HCl at pH 7.5, 0.1 mM Na2EDTA) at 4°C.  Chromatin and antibodies were eluted from beads by incubating for 1 h at 65°C in IP  elution buffer (1% SDS, 0.1 M NaHCO3), followed by incubating overnight at 65°C to  reverse formaldehyde cross-links. DNA was purified using MinElute DNA purification  columns (Qiagen).
Illumina TruSeq adapted libraries were constructed using an Apollo 324 NGS Library  Prep System with a PrepX Complete ILMN DNA Library Kit (WaferGen Biosystems  Inc). ChIP products were amplified with 15 cycles of PCR, and fragments 150-700 bp in  length were selected using an AxyPrep MAG PCR Clean-Up Kit (Axygen MAG-PCRCL-50).  Libraries were sequenced using single end 50 bp reads on an Illumina HiSeq.

treatment_protocol: Cells were treated with 100 nM Dexamethasone or .02% EtOH as vehicle control.

tag: agent

value: etoh

tag: chip antibody

value: anti-GR (Santa Cruz Biotechnology, sc-1003)


title: Pol2SerP2_JQ1_6h_ChIP

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

institute: fondazione Istituto italiano di tecnologia

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Transcription factors peak calling with MACS version 1.4.1; macs -t samplebam -c inputbam --format="BAM" --off-auto  --mfold=7,30 --diag --fe-min=2 --fe-max=30 --fe-step=2
Histone marks peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --format="BAM" --auto-bimodal  --mfold=7,30 --broad -g hs
For Brd4 DMSO and JQ1, input gluteraldehide DMSO and JQ1 were used, respectively. For other transcription factors and histone marks, input formaldehide was used.
the largest file between input and sample is randomly downsampled to the size of the smallest
Transcription factor peaks were filtered using threshold p-value of 1e-8 and False Discovery Rate of 5% with filterpeaks.R script. Histone marks broad peaks were filtered using p-value of 1e-8 with filterpeaks.R script
Genome_build: hg19
Note: Pol2SerP2_DMSO_ChIP
Pol2SerP5_DMSO_ChIP
Pol2SerP2_JQ1_ChIP
Pol2SerP5_JQ1_ChIP
Raji_ChIPSeq_Pol2_JQ1_6h
The analyses of those files did not result in the production of a   "processed file", but in the generation of a graphical output (i.e. an   enrichment plot over genes) using only raw data (BAM files).
Supplementary_files_format_and_content: *_peaks.xls files: bed files from MACS1.4.1;  *_broad_peaks.bed files: bed files from MACS2.0.9

source_name: Raji cells

growth_protocol: RAJI cells (300000 cells/mL) were cultured in RPMI supplemented with 10% Fetal Bovine Serum, 2mM L-Glutammine and 1% penicillin/streptomycin

extract_protocol:
DNA fragments were obtained after sonication of isolated nuclei. Histone-DNA or transcription factors-DNA complexes were isolated with appropiate antibody.
For ChIPseq, 2–10 ng ChIP DNA was prepared for HiSeq2000 sequencing with TruSeq ChIP Sample Prep Kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: RAJI cells were treated with 100 nM of JQ1 or vehicle (DMSO) for 24h. JQ1 was added to the culture 6h after the initial plating

value: B cells

tag: cancer type

value: Burkitt's lymphoma

value: PolII (Santa Cruz Biotech., sc-899)


title: ChIP_DEX_rep2

source_name: A549 cells  treated with 100 nM Dexamethasone

value: dex


title: DE1

tag: cell type


title: STSV3


title: RNA_EtOH_rep2

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to gencode v19 transcripts using bowtie with the "--best" version.
Reads were converted from .sam to .bam files using samtools view with the  "-bS" option
Bam files were sorted using Samtools sort
Bam files were indexed using Samtools Index
Reads were counted using samtools idxstats
Differential expression between EtOH and DEX conditions was computed using R using the DEseq2 package with default settings
Genome_build: gencodev19 genes
Supplementary_files_format_and_content: .counts files reports the number of reads aligned to each Ensembl ID (gencode v19 genes and Ensembl IDs are congruent). Columns: 1.sequence name, 2. length, 3. number of mapped reads, 4. number unmapped reads.

extract_protocol:
Between 0.5-1 million cells were washed with PBS and then lysed using Qiagen RLT buffer. Total RNA was extracted using Qiagen RNeasy mini-columns with 1% β-mercaptoethanol in RLT buffer and a 15 min on column DNase digestion. mRNA was prepared using the Wafergen automated sample prep system with the Prep-x mRNA kit with 1 microgram of total RNA.
Libraries were prepared using the Apollo 324 liquid handling platform, as per manufacturer’s instruction using the prep-mRNAseq kit.

value: A549 cells


title: IDC2


title: ChIP_EtOH_Rep1


title: RNA_DEX_rep2


title: GR_ChIP_exo_rep3

description: ChIP-exo-enriched genomic DNA

data_processing:
Read pairs were aligned to the hg19 reference genome using Bowtie2.
Fragments mapping to adapter sequence or ENCODE blacklisted regions were removed.
PCR duplicates were removed using SAMtools.
The position of the 5'-most base pair of read 1 in each read pair was extracted.
These positions were sorted by the strand they mapped to (positive or negative).
These bed files were then converted to bedgraphs using BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files; containing the 5'-most position of read 1 for each read pair, by strand.

growth_protocol: A549 cells were grown in 15 cm plates with F-12K media (Thermo) supplemented with 10% fetal bovine serum (Thermo) and 1% penicillin-streptomycin (Thermo).

extract_protocol:
For each replicate, 2 ×10^7 cells were fixed with 1% formaldehyde for 10 minutes. Fixation was quenced with 0.125 M glycine. Cells were washed with 1X PBS and collected and spun down in 5 mL of Farham Lysis Buffer (5 mM PIPES pH 8.0 / 85 mM KCl / 0.5% NP-40). Nuclei were re-suspended in 1 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS at pH 7.4). Samples were sonicated using a Diagenode Bioruptor XL sonicator at 4°C to fragment chromatin to 200-500 bp segments. Insoluble  components were removed by centrifugation for 15 min at 15000 rpm. We conjugated 5  µg of anti-GR (Santa Cruz Biotechnology, sc-1003) to 200 µl of sheep anti-rabbit IgG magnetic beads  (Life Technologies 11203D/11201D). Sheared chromatin in RIPA was then added to the  antibody-conjugated beads and incubated on a rotator overnight at 4°C. After incubation,  beads were washed five times with a LiCl wash buffer (100 mM Tris at pH 7.5, 500 mM  LiCl, 1% NP-40, 1% sodium deoxycholate), and remaining ions were removed with a  single wash with 1 mL of TE (10 mM Tris-HCl at pH 7.5, 0.1 mM Na2EDTA) at 4°C.
Chromatin-bound IgG beads were then washed with 10 mM Tris-HCl (pH 7.5) and resuspended in 30 µL of end repair mix: 1X T4 Ligase Buffer, 0.4 mM dNTPs, 1.8 U T4 DNA Polymerase, 6 U T4 PNK, and 3 U DNA Polymerase I, Large (Klenow) Fragment. Beads were incubated at room temperature for 30 minutes, and then washed with 10 mM Tris-HCl (pH 8). Beads were then resuspended in 30 µL of A-tailing mix: 1X NEB Buffer 2, 0.2 mM dATP, and 3 U Klenow Fragment (3'->5' exo-). Beads were incubated at 37℃ for 30 minutes. Next, beads were washed with 10 mM Tris-HCl (pH 7.5) and resuspended in 30 µL adapter ligation mix: 1X Quick Ligase Buffer, 4 µL Quick Ligase, and 1 pmol of Illumina Adapter A. Beads were incubated at room temperature for 30 minutes. Next, the beads were washed with 10 mM Tris-HCl (pH 9.5), and resuspended in 20 µL of λ-exonuclease mix: 1X λ-exonuclease Buffer and 5 U λ-exonuclease. The beads were incubated at 37℃ for 30 minutes. Next, the beads were washed with 10 mM Tris-HCl (pH 8), and resuspended in 20 µL RecJf mix: 1X NEB Buffer 2 and 15 U RecJf. The beads were incubated at 37℃ for 30 minutes, and then washed with TE Buffer. The beads were resuspended in 150 µL IP Elution Buffer (1% SDS, 0.1 M NaHCO3), and incubated for 1 hr at 65℃, with vortexing every 15 minutes. The beads were centrifuged at 20,000xg for 3 minutes, and the supernatant was transferred to a new tube and incubated at 65℃ overnight. DNA was purified using a MinElute PCR Purification kit (Qiagen), using 11 µL of EB Buffer for the elution. Purified DNA was mixed with 8 µL of phi29 DNA polymerase mix: 1X phi29 Buffer, 10 pmol primer P2, 375 nM dNTPs, and 4 ug BSA. The mix was heated to 95℃ for 2 minutes, 63℃ for 5 minutes, 30℃ for 2 minutes, and held at 30℃. 10 U of phi29 DNA polymerase was added to the mix, which was then heated at 30℃ for 20 minutes, 65℃ for 10 minutes, and held at 4℃. DNA fragments were purified using AxyPrep Mag PCR Clean-Up beads at a 2:1 bead volume:sample volume ratio. DNA was eluted off beads using 30 µL A-tailing mix, and incubated at 37℃ for 30 minutes. The DNA was then purified using AxyPrep Mag PCR Clean-Up beads as described above. DNA was eluted from beads using 30 µL of adapter ligation mix (with Illumina Adapter B instead of A), and incubated at room temperature for 30 minutes. The DNA was then purified using AxyPrep Mag PCR Clean-Up beads as described above, and eluted in 50 µL of PCR amplification mix: 1X Q5 Reaction Buffer, 200 nM dNTPs, 10 pmol Primer A, 10 pmol Primer B, and 1 U Q5 polymerase. PCR was carried out according to the manufacturer's specifications, using an annealing temperature of 65℃ , and an extension time of 30 seconds, for 20 cycles. The PCR products were purified with AxyPrep Mag PCR Clean-Up beads with a 1:1 ratio, and eluted in 30 µL of EB Buffer. DNA concentration was measured on a Qubit Fluorometer (Life Technologies), and fragment size distribution was assessed on a TapeStation 2200 (Agilent Technologies). Libraries were sequenced on an Illumina HiSeq 2000 with 50 base-pair paired end reads.    Adapter A: (5'-CACTCTTTCCCTACACGACGCTCTTCCGATCT-3') + (5'-P-GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT-3')  Adapter B: (5'-ACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3')  +  (5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG-3')  Primer P2: 5'-CAAGCAGAAGACGGCATACGAGAT-3’   Primer A: 5'-AATGATACGGCGACCACCGAGATCTACACTCT-3'  Primer B: 5’-CAAGCAGAAGACGGCATACGAGATCGTGAT-3'

treatment_protocol: Cells where treated with 100 nM dexamethasone (diluted in 0.02% ethanol) for 1 hour.

tag: cell treatment

value: 100 nM dexamethasone 1 hr

value: GR Antibody E-20 (Santa Cruz Biotechnology, sc-1003)


title: A549_EtOH_B3

first: Gregory

last: Crawford

address: 101 Science Drive

department: Center for Genomic and Computational Biology

data_processing:
Single-end basecalls were done by using Illumina CASAVA 1.3 software.
First 20 bp of Dnase-seq raw reads were mapped to hg19 with Bowtie, with 2 mismatches allowed, to generate bam files, then bam files were converted to bed file by bedtools. After removing PCR artifacts bigWig files were created by using MACS2 2.1.0 (PMID: 18798982).
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

source_name: Cultured A549 cells_EtOH_1hr

growth_protocol: A549 cells were grown to 90% confluence

extract_protocol:
Cells were Lysed and nuclei were digested according to the publication PMID: 20150147.
Libraries were prepared according to the publication PMID: 20150147.

treatment_protocol: Cells were treated with 100 nM dexamethasone or .02% EtOH as vehicle control

tag: treated with

value: .02% EtOH for 1hr


title: IDC1

value: iPSC-Derived Cholangiocytes


title: HS3


title: GR_ChIP_exo_rep2

description: ChIP-exo-enriched genomic DNA


title: GR_ChIP_exo_rep1

description: ChIP-exo-enriched genomic DNA


title: ChIP_DEX_rep1


title: RNA_EtOH_rep1


title: A549_Dex_B3

source_name: Cultured A549 cells_dexamethasone_1hr

value: 100 nM dexamethasone for 1hr


title: A549_EtOH_B1


title: RNA_DEX_rep1


title: STSV1


title: A549_EtOH_B2


title: CTRL3

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

institute: IRCCS-Policlinico San Donato

data_processing:
Basecalling performed with Illumina Casava version 1.7
Quality Control performed using FastQC suite with default parameters
Alignment of reads to hg19 with SOAPSplice
Quantification of reads using HTSeq-Count
Differential Gene Expression estimated by DESeq2
Genome_build: Ensembl, GRCh37/ hg19, Feb 2009, Version 72
Supplementary_files_format_and_content: tab-delimited text file showing raw counts for each sample
Supplementary_files_format_and_content: tab-delimited text file showing DESeq2 output for mRNA, including the mean of normalized counts for all samples (baseMean), log2 fold change (hypoxia versus normoxia) and BH adjusted p-values (padj).
Supplementary_files_format_and_content: .xls file showing DESeq2 output for all detected lncRNAs and including details comprised in Ensembl data base (Ensembl ID, chromosomic location, transcription type)

source_name: HUVEC

growth_protocol: HUVEC were grown in EGM-2 (Lonza) containing 2% FBS.

extract_protocol:
Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions.
The TruSeq™ RNA Sample preparation kit (Illumina) was used to generate poly-A selected, indexed cDNA libraries, according to the manufacturer’s instructions.

treatment_protocol: HUVEC were exposed to 1% oxygen for 24 or 48 hours.

tag: experiment

value: experiment 1

tag: sequencing run

value: 1st Run

value: HUVEC


title: CTRL2


title: A549_Dex_B2


title: HYPOXIA3


title: H1

value: experiment 2

value: 2nd Run


title: H2


title: N1


title: HYPOXIA2


title: input_DNA_JQ1

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Transcription factors peak calling with MACS version 1.4.1; macs -t samplebam -c inputbam --format="BAM" --off-auto  --mfold=7,30 --diag --fe-min=2 --fe-max=30 --fe-step=2
Histone marks peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --format="BAM" --auto-bimodal  --mfold=7,30 --broad -g hs
For Brd4 DMSO and JQ1, input gluteraldehide DMSO and JQ1 were used, respectively. For other transcription factors and histone marks, input formaldehide was used.
the largest file between input and sample is randomly downsampled to the size of the smallest
Transcription factor peaks were filtered using threshold p-value of 1e-8 and False Discovery Rate of 5% with filterpeaks.R script. Histone marks broad peaks were filtered using p-value of 1e-8 with filterpeaks.R script
genome build: hg19
Note: Pol2SerP2_DMSO_ChIP
Pol2SerP5_DMSO_ChIP
Pol2SerP2_JQ1_ChIP
Pol2SerP5_JQ1_ChIP
Raji_ChIPSeq_Pol2_JQ1_6h
The analyses of those files did not result in the production of a   "processed file", but in the generation of a graphical output (i.e. an   enrichment plot over genes) using only raw data (BAM files).
processed data files format and content: *_peaks.xls files: bed files from MACS1.4.1;  *_broad_peaks.bed files: bed files from MACS2.0.9

treatment_protocol: RAJI cells were treated with 100 nM of JQ1 or vehicle (DMSO) for 24h. JQ1 or DMSO were added to the culture 24h after the initial plating


title: input_DNA


title: A549_Dex_B1


title: H3K4me3_JQ1_ChIP

value: H3K4me3 (Active Motif, 39915)


title: E2f1_JQ1_ChIP

value: E2F-1 (Santa Cruz Biotech., sc-193)


title: H3K4me1_JQ1_ChIP

value: B cells

value: H3K4me1 (Abcam, ab8895)


title: Pol2_JQ1_ChIP

value: Burkitt's lymphoma

value: PolII (Santa Cruz Biotech., sc-899)


title: Pol2SerP2_JQ1_ChIP

value: RNA PolIIS2p (ChromoTek, 3E10)


title: H3K27Ac_JQ1_ChIP

value: H3K27Ac (Abcam, ab4729)


title: Pol2SerP5_DMSO_ChIP

value: RNA PolIIS5p (Abcam, ab5131)


title: Brd4_JQ1_ChIP


title: input_DNA_DMSO


title: Myc_JQ1_ChIP

value: c-Myc (Santa Cruz Biotech., sc-764)


title: H3K4me1_DMSO_ChIP


title: H3K27Ac_DMSO_ChIP


title: N2


title: H3K4me3_DMSO_ChIP


title: Pol2SerP2_DMSO_ChIP


title: Pol2_DMSO_ChIP


title: Myc_DMSO_ChIP


title: P17 Vsx2-GFP mouse retina 5 (Batch 2)

city: Cambridge

first: Karthik

last: Shekhar

state: MA

address: 415 Main St.

institute: Broad Institute

data_processing:
Base calls performed with bcl2fastq2.15
Read 2 was aligned with Star v2.4.0
Each aligned read was tagged with its mate-pair UMI and cell barcode
Each aligned exonic read was tagged with a gene name
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample
Samples Bipolar1-6 -- prepared from P17 Vsx2-GFP mouse retinas on two separate days (Bipolar1-4 and Bipolar5-6)--were merged together into a single matrix.
Genome_build: mm10
Supplementary_files_format_and_content: compressed, flat text file with tab delimiters

source_name: Mus musculus retina, P17

extract_protocol:
Single cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.

tag: tissue

value: retina

tag: developmental stage

tag: genotype


title: P17 Vsx2-GFP mouse retina 4 (Batch 1)


title: Brd4_DMSO_ChIP


title: P17 Vsx2-GFP mouse retina 3 (Batch 1)


title: Pol2SerP5_JQ1_ChIP


title: P17 Vsx2-GFP mouse retina 6 (Batch 2)


title: ChIP_Seq MED12_2

first: Beatriz

last: Aranda-Orgilles

address: 522 First Avenue

institute: NYU School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7
Duplicates were removed with Picard tools and bedgraphs were normalized to reads per million.
MACS version 1.4.2 was used for ChIP-sequencing peak discovery.
Bedtools,  GenomicTools version 2.7.2, Seqminer and deepTools weee used for performing genomic interval mathematical operations, genomic interval annotation, ChIP-seq heatmap generation and ChIP-seq profile construction.
Genome_build: hg19
Supplementary_files_format_and_content: TDF

source_name: human CD34+

growth_protocol: CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were obtained from Dr. Shelly Heimfeld at Fred Hutchinson Cancer Research Center. The cells were maintained and differentiated as previously described (Sankaran et al., 2008). Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with 1X CC100 cytokine mix (Stem Cell Technologies Inc.) and 2% P/S for a total of 6 days.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using Med12 antibody (Bethyl A-300-774A, lot1). Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
All samples were prepared with the Illumina/Solexa Genomic DNA kit (Illumina- IP-102-1001) according to manufacture's instructions.

treatment_protocol: CD34+ cells expanded in StemSpan medium supplemented with 1x CC100 cytokine mix for 6 days

value: hematopoietis stem and progenitor cells

tag: culture

value: 6 days expanded

tag: antibody


title: ChIP_Seq MED12_1


title: Input DNA


title: E2f1_DMSO_ChIP


title: P17 Vsx2-GFP mouse retina 1 (Batch 1)


title: P17 Vsx2-GFP mouse retina 2 (Batch 1)


title: Vsx2_2b_H12_S288_R1_001

description: single cell

data_processing:
Base calls performed using bcl2fastq2.15
Reads were aligned to a reference genome (mm10 Ensembl) using Tophat v2.0.10
Expression levels were quantified using RSEM v1.2.28 (inferred counts and tpm values)
Genome_build: mm10
Supplementary_files_format_and_content: text files with tab delimiters containing inferred counts and tpm values.

extract_protocol:
Dissociated retina were FACS sorted into 96-well plates (single cells) and tubes (bulk libraries) containing lysis buffer
Smart-seq2 (Picelli et al., Nature Methods, 2014)


title: Vsx2_2b_H3_S279_R1_001

description: single cell


title: Vsx2_bulk2a_S291_R1_001

description: bulk cells (10,000)


title: Vsx2_2b_H5_S281_R1_001

description: single cell


title: Vsx2_bulk2b_S292_R1_001

description: bulk cells (10,000)


title: Vsx2_2b_H6_S282_R1_001

description: single cell


title: Vsx2_2b_H8_S284_R1_001

description: single cell


title: Vsx2_2b_H7_S283_R1_001

description: single cell


title: Vsx2_2b_H2_S278_R1_001

description: single cell


title: Vsx2_2b_H9_S285_R1_001

description: single cell


title: Vsx2_2b_H4_S280_R1_001

description: single cell


title: Vsx2_2b_H11_S287_R1_001

description: single cell


title: Vsx2_2b_H10_S286_R1_001

description: single cell


title: Vsx2_2b_G9_S273_R1_001

description: single cell


title: Vsx2_2b_G6_S270_R1_001

description: single cell


title: Vsx2_2b_G8_S272_R1_001

description: single cell


title: Vsx2_2b_H1_S277_R1_001

description: single cell


title: Vsx2_2b_G7_S271_R1_001

description: single cell


title: Vsx2_2b_G4_S268_R1_001

description: single cell


title: Vsx2_bulk1a_S289_R1_001

description: bulk cells (10,000)


title: Vsx2_2b_G2_S266_R1_001

description: single cell


title: Vsx2_2b_G3_S267_R1_001

description: single cell


title: Vsx2_2b_G11_S275_R1_001

description: single cell


title: Vsx2_2b_G10_S274_R1_001

description: single cell


title: Vsx2_2b_G12_S276_R1_001

description: single cell


title: Vsx2_2b_G1_S265_R1_001

description: single cell


title: Vsx2_2b_F8_S260_R1_001

description: single cell


title: Vsx2_2b_F9_S261_R1_001

description: single cell


title: Vsx2_2b_F7_S259_R1_001

description: single cell


title: Vsx2_2b_F6_S258_R1_001

description: single cell


title: Vsx2_2b_F10_S262_R1_001

description: single cell


title: Vsx2_2b_F4_S256_R1_001

description: single cell


title: Vsx2_2b_F2_S254_R1_001

description: single cell


title: Vsx2_2b_G5_S269_R1_001

description: single cell


title: Vsx2_2b_F12_S264_R1_001

description: single cell


title: Vsx2_2b_E8_S248_R1_001

description: single cell


title: Vsx2_2b_F3_S255_R1_001

description: single cell


title: Vsx2_2b_F5_S257_R1_001

description: single cell


title: Vsx2_2b_F1_S253_R1_001

description: single cell


title: Vsx2_2b_E4_S244_R1_001

description: single cell


title: Vsx2_2b_E7_S247_R1_001

description: single cell


title: Vsx2_2b_E3_S243_R1_001

description: single cell


title: Vsx2_2b_F11_S263_R1_001

description: single cell


title: Vsx2_2b_E11_S251_R1_001

description: single cell


title: Vsx2_2b_E12_S252_R1_001

description: single cell


title: Vsx2_2b_D9_S237_R1_001

description: single cell


title: Vsx2_2b_E2_S242_R1_001

description: single cell


title: Vsx2_2b_E1_S241_R1_001

description: single cell


title: Vsx2_2b_E10_S250_R1_001

description: single cell


title: Vsx2_2b_E6_S246_R1_001

description: single cell


title: Vsx2_2b_E5_S245_R1_001

description: single cell


title: Vsx2_2b_D7_S235_R1_001

description: single cell


title: Vsx2_2b_D5_S233_R1_001

description: single cell


title: Vsx2_2b_D6_S234_R1_001

description: single cell


title: Vsx2_2b_D4_S232_R1_001

description: single cell


title: Vsx2_2b_E9_S249_R1_001

description: single cell


title: Vsx2_2b_D8_S236_R1_001

description: single cell


title: Vsx2_2b_D3_S231_R1_001

description: single cell


title: Vsx2_2b_D10_S238_R1_001

description: single cell


title: Vsx2_2b_D1_S229_R1_001

description: single cell


title: Vsx2_2b_D12_S240_R1_001

description: single cell


title: Vsx2_2b_D11_S239_R1_001

description: single cell


title: Vsx2_2b_C9_S225_R1_001

description: single cell


title: Vsx2_2b_C6_S222_R1_001

description: single cell


title: Vsx2_2b_C4_S220_R1_001

description: single cell


title: Vsx2_2b_C8_S224_R1_001

description: single cell


title: Vsx2_2b_C2_S218_R1_001

description: single cell


title: Vsx2_2b_C11_S227_R1_001

description: single cell


title: Vsx2_2b_C3_S219_R1_001

description: single cell


title: Vsx2_2b_C12_S228_R1_001

description: single cell


title: Vsx2_2b_C1_S217_R1_001

description: single cell


title: Vsx2_2b_C5_S221_R1_001

description: single cell


title: Vsx2_2b_B8_S212_R1_001

description: single cell


title: Vsx2_2b_B5_S209_R1_001

description: single cell


title: Vsx2_2b_B7_S211_R1_001

description: single cell


title: Vsx2_2b_B9_S213_R1_001

description: single cell


title: Vsx2_2b_B3_S207_R1_001

description: single cell


title: Vsx2_2b_B6_S210_R1_001

description: single cell


title: Vsx2_2b_B2_S206_R1_001

description: single cell


title: Vsx2_2b_B4_S208_R1_001

description: single cell


title: Vsx2_2b_B12_S216_R1_001

description: single cell


title: Vsx2_2b_B10_S214_R1_001

description: single cell


title: Vsx2_2b_B11_S215_R1_001

description: single cell


title: Vsx2_2b_B1_S205_R1_001

description: single cell


title: Vsx2_2b_A9_S201_R1_001

description: single cell


title: Vsx2_2b_A5_S197_R1_001

description: single cell


title: Vsx2_2b_A8_S200_R1_001

description: single cell


title: Vsx2_2b_A4_S196_R1_001

description: single cell


title: Vsx2_2b_C10_S226_R1_001

description: single cell


title: Vsx2_2b_A6_S198_R1_001

description: single cell


title: Vsx2_2b_A3_S195_R1_001

description: single cell


title: Vsx2_2b_A2_S194_R1_001

description: single cell


title: Vsx2_2a_H9_S189_R1_001

description: single cell


title: Vsx2_2b_A1_S193_R1_001

description: single cell


title: Vsx2_2b_A12_S204_R1_001

description: single cell


title: Vsx2_2b_A10_S202_R1_001

description: single cell


title: Vsx2_2b_A11_S203_R1_001

description: single cell


title: Vsx2_2a_H6_S186_R1_001

description: single cell


title: Vsx2_2a_H5_S185_R1_001

description: single cell


title: Vsx2_2a_H8_S188_R1_001

description: single cell


title: Vsx2_2a_H4_S184_R1_001

description: single cell


title: Vsx2_2a_H3_S183_R1_001

description: single cell


title: Vsx2_2a_H12_S192_R1_001

description: single cell


title: Vsx2_2a_H10_S190_R1_001

description: single cell


title: Vsx2_2a_H1_S181_R1_001

description: single cell


title: Vsx2_2a_H2_S182_R1_001

description: single cell


title: Vsx2_2a_G6_S174_R1_001

description: single cell


title: Vsx2_2a_G7_S175_R1_001

description: single cell


title: Vsx2_2b_A7_S199_R1_001

description: single cell


title: Vsx2_2a_G9_S177_R1_001

description: single cell


title: Vsx2_2a_G3_S171_R1_001

description: single cell


title: Vsx2_2a_G5_S173_R1_001

description: single cell


title: Vsx2_2a_G2_S170_R1_001

description: single cell


title: Vsx2_2a_G4_S172_R1_001

description: single cell


title: Vsx2_2a_G10_S178_R1_001

description: single cell


title: Vsx2_2a_H7_S187_R1_001

description: single cell


title: Vsx2_2b_C7_S223_R1_001

description: single cell


title: Vsx2_2a_G11_S179_R1_001

description: single cell


title: Vsx2_2a_G12_S180_R1_001

description: single cell


title: Vsx2_2a_F7_S163_R1_001

description: single cell


title: Vsx2_2a_F8_S164_R1_001

description: single cell


title: Vsx2_2a_G1_S169_R1_001

description: single cell


title: Vsx2_2a_F6_S162_R1_001

description: single cell


title: Vsx2_2a_F5_S161_R1_001

description: single cell


title: Vsx2_2a_F2_S158_R1_001

description: single cell


title: Vsx2_2a_G8_S176_R1_001

description: single cell


title: Vsx2_2a_F10_S166_R1_001

description: single cell


title: Vsx2_2a_F12_S168_R1_001

description: single cell


title: Vsx2_2a_F4_S160_R1_001

description: single cell


title: Vsx2_2a_E8_S152_R1_001

description: single cell


title: Vsx2_2a_F11_S167_R1_001

description: single cell


title: Vsx2_2a_E6_S150_R1_001

description: single cell


title: Vsx2_2a_E7_S151_R1_001

description: single cell


title: Vsx2_2a_E3_S147_R1_001

description: single cell


title: Vsx2_2a_E5_S149_R1_001

description: single cell


title: Vsx2_2a_E12_S156_R1_001

description: single cell


title: Vsx2_2a_F3_S159_R1_001

description: single cell


title: Vsx2_2a_D9_S141_R1_001

description: single cell


title: Vsx2_2a_E4_S148_R1_001

description: single cell


title: Vsx2_2a_D7_S139_R1_001

description: single cell


title: Vsx2_2a_F9_S165_R1_001

description: single cell


title: Vsx2_2a_F1_S157_R1_001

description: single cell


title: Vsx2_2a_D2_S134_R1_001

description: single cell


title: Vsx2_2a_D11_S143_R1_001

description: single cell


title: Vsx2_2a_E9_S153_R1_001

description: single cell


title: Vsx2_2a_D4_S136_R1_001

description: single cell


title: Vsx2_2a_E11_S155_R1_001

description: single cell


title: Vsx2_2a_E1_S145_R1_001

description: single cell


title: Vsx2_2a_E10_S154_R1_001

description: single cell


title: Vsx2_2a_C8_S128_R1_001

description: single cell


title: Vsx2_2a_C7_S127_R1_001

description: single cell


title: Vsx2_2a_E2_S146_R1_001

description: single cell


title: Vsx2_2a_C9_S129_R1_001

description: single cell


title: Vsx2_2a_D5_S137_R1_001

description: single cell


title: Vsx2_2a_D3_S135_R1_001

description: single cell


title: Vsx2_2a_D1_S133_R1_001

description: single cell


title: Vsx2_2a_D12_S144_R1_001

description: single cell


title: Vsx2_2a_C6_S126_R1_001

description: single cell


title: Vsx2_2a_C5_S125_R1_001

description: single cell


title: Vsx2_2a_C4_S124_R1_001

description: single cell


title: Vsx2_2a_D8_S140_R1_001

description: single cell


title: Vsx2_2a_B9_S117_R1_001

description: single cell


title: Vsx2_2a_D10_S142_R1_001

description: single cell


title: Vsx2_2a_C2_S122_R1_001

description: single cell


title: Vsx2_2a_C3_S123_R1_001

description: single cell


title: Vsx2_2a_C1_S121_R1_001

description: single cell


title: Vsx2_2a_D6_S138_R1_001

description: single cell


title: Vsx2_2a_C10_S130_R1_001

description: single cell


title: Vsx2_2a_B8_S116_R1_001

description: single cell


title: Vsx2_2a_C12_S132_R1_001

description: single cell


title: Vsx2_2a_C11_S131_R1_001

description: single cell


title: Vsx2_2a_B11_S119_R1_001

description: single cell


title: Vsx2_2a_B6_S114_R1_001

description: single cell


title: Vsx2_2a_B1_S109_R1_001

description: single cell


title: Vsx2_2a_B10_S118_R1_001

description: single cell


title: Vsx2_2a_B5_S113_R1_001

description: single cell


title: Vsx2_2a_B2_S110_R1_001

description: single cell


title: Vsx2_2a_B3_S111_R1_001

description: single cell


title: Vsx2_2a_B4_S112_R1_001

description: single cell


title: Vsx2_2a_A9_S105_R1_001

description: single cell


title: Vsx2_2a_A5_S101_R1_001

description: single cell


title: Vsx2_2a_A7_S103_R1_001

description: single cell


title: Vsx2_2b_D2_S230_R1_001

description: single cell


title: Vsx2_2a_H11_S191_R1_001

description: single cell


title: Vsx2_2a_A6_S102_R1_001

description: single cell


title: Vsx2_2a_B12_S120_R1_001

description: single cell


title: Vsx2_2a_A3_S99_R1_001

description: single cell


title: Vsx2_2a_A2_S98_R1_001

description: single cell


title: Vsx2_2a_B7_S115_R1_001

description: single cell


title: Vsx2_2a_A1_S97_R1_001

description: single cell


title: Vsx2_2a_A11_S107_R1_001

description: single cell


title: Vsx2_2a_A12_S108_R1_001

description: single cell


title: Vsx2_1a_H8_S92_R1_001

description: single cell


title: Vsx2_1a_H6_S90_R1_001

description: single cell


title: Vsx2_1a_H9_S93_R1_001

description: single cell


title: Vsx2_2a_A10_S106_R1_001

description: single cell


title: Vsx2_1a_H4_S88_R1_001

description: single cell


title: Vsx2_2a_A8_S104_R1_001

description: single cell


title: Vsx2_1a_H11_S95_R1_001

description: single cell


title: Vsx2_1a_H10_S94_R1_001

description: single cell


title: Vsx2_1a_H3_S87_R1_001

description: single cell


title: Vsx2_1a_H1_S85_R1_001

description: single cell


title: Vsx2_1a_H2_S86_R1_001

description: single cell


title: Vsx2_1a_G9_S81_R1_001

description: single cell


title: Vsx2_2a_A4_S100_R1_001

description: single cell


title: Vsx2_1a_G8_S80_R1_001

description: single cell


title: Vsx2_1a_G7_S79_R1_001

description: single cell


title: Vsx2_1a_G4_S76_R1_001

description: single cell


title: Vsx2_1a_G2_S74_R1_001

description: single cell


title: Vsx2_1a_G3_S75_R1_001

description: single cell


title: Vsx2_1a_G12_S84_R1_001

description: single cell


title: Vsx2_1a_G5_S77_R1_001

description: single cell


title: Vsx2_1a_G11_S83_R1_001

description: single cell


title: Vsx2_1a_G6_S78_R1_001

description: single cell


title: Vsx2_1a_G10_S82_R1_001

description: single cell


title: Vsx2_1a_H7_S91_R1_001

description: single cell


title: Vsx2_1a_H5_S89_R1_001

description: single cell


title: Vsx2_1a_F8_S68_R1_001

description: single cell


title: Vsx2_1a_F9_S69_R1_001

description: single cell


title: Vsx2_1a_F7_S67_R1_001

description: single cell


title: Vsx2_1a_F6_S66_R1_001

description: single cell


title: Vsx2_1a_H12_S96_R1_001

description: single cell


title: Vsx2_1a_G1_S73_R1_001

description: single cell


title: Vsx2_1a_F5_S65_R1_001

description: single cell


title: Vsx2_1a_F2_S62_R1_001

description: single cell


title: Vsx2_1a_F3_S63_R1_001

description: single cell


title: Vsx2_1a_F4_S64_R1_001

description: single cell


title: Vsx2_1a_F12_S72_R1_001

description: single cell


title: Vsx2_1a_F1_S61_R1_001

description: single cell


title: Vsx2_1a_E7_S55_R1_001

description: single cell


title: Vsx2_1a_E8_S56_R1_001

description: single cell


title: Vsx2_1a_E9_S57_R1_001

description: single cell


title: Vsx2_1a_E5_S53_R1_001

description: single cell


title: Vsx2_1a_E4_S52_R1_001

description: single cell


title: Vsx2_1a_E2_S50_R1_001

description: single cell


title: Vsx2_1a_E6_S54_R1_001

description: single cell


title: Vsx2_1a_E11_S59_R1_001

description: single cell


title: Vsx2_1a_E1_S49_R1_001

description: single cell


title: Vsx2_1a_E12_S60_R1_001

description: single cell


title: Vsx2_1a_E10_S58_R1_001

description: single cell


title: Vsx2_1a_D7_S43_R1_001

description: single cell


title: Vsx2_1a_E3_S51_R1_001

description: single cell


title: Vsx2_1a_D6_S42_R1_001

description: single cell


title: Vsx2_1a_D5_S41_R1_001

description: single cell


title: Vsx2_1a_D12_S48_R1_001

description: single cell


title: Vsx2_1a_D2_S38_R1_001

description: single cell


title: Vsx2_1a_D11_S47_R1_001

description: single cell


title: Vsx2_1a_D3_S39_R1_001

description: single cell


title: Vsx2_1a_D10_S46_R1_001

description: single cell


title: Vsx2_1a_C9_S33_R1_001

description: single cell


title: Vsx2_1a_D1_S37_R1_001

description: single cell


title: Vsx2_1a_C8_S32_R1_001

description: single cell


title: Vsx2_1a_F10_S70_R1_001

description: single cell


title: Vsx2_1a_C6_S30_R1_001

description: single cell


title: Vsx2_1a_C7_S31_R1_001

description: single cell


title: Vsx2_1a_C5_S29_R1_001

description: single cell


title: Vsx2_1a_C3_S27_R1_001

description: single cell


title: Vsx2_1a_C4_S28_R1_001

description: single cell


title: Vsx2_1a_D9_S45_R1_001

description: single cell


title: Vsx2_1a_C11_S35_R1_001

description: single cell


title: Vsx2_1a_C10_S34_R1_001

description: single cell


title: Vsx2_1a_C1_S25_R1_001

description: single cell


title: Vsx2_1a_D4_S40_R1_001

description: single cell


title: Vsx2_1a_B9_S21_R1_001

description: single cell


title: Vsx2_1a_B4_S16_R1_001

description: single cell


title: Vsx2_1a_B3_S15_R1_001

description: single cell


title: Vsx2_1a_B5_S17_R1_001

description: single cell


title: Vsx2_1a_B7_S19_R1_001

description: single cell


title: Vsx2_1a_B8_S20_R1_001

description: single cell


title: Vsx2_1a_F11_S71_R1_001

description: single cell


title: Vsx2_1a_A9_S9_R1_001

description: single cell


title: Vsx2_1a_A8_S8_R1_001

description: single cell


title: Vsx2_1a_B6_S18_R1_001

description: single cell


title: Vsx2_1a_A7_S7_R1_001

description: single cell


title: Vsx2_1a_B12_S24_R1_001

description: single cell


title: Vsx2_1a_B2_S14_R1_001

description: single cell


title: Vsx2_1a_A5_S5_R1_001

description: single cell


title: Vsx2_1a_B11_S23_R1_001

description: single cell


title: Vsx2_1a_A2_S2_R1_001

description: single cell


title: Vsx2_1a_A6_S6_R1_001

description: single cell


title: Vsx2_1a_A12_S12_R1_001

description: single cell


title: Vsx2_1a_A1_S1_R1_001

description: single cell


title: Vsx2_1a_A4_S4_R1_001

description: single cell


title: Vsx2_1a_A3_S3_R1_001

description: single cell


title: Vsx2_1a_C12_S36_R1_001

description: single cell


title: Vsx2_1a_C2_S26_R1_001

description: single cell


title: Vsx2_1a_A11_S11_R1_001

description: single cell


title: Vsx2_1a_A10_S10_R1_001

description: single cell


title: thoracic A mut

first: Jeremy

middle: S.

last: Dasen

address: 550 First Ave

department: NYU Neuroscience Institute

institute: New York University Medical Center

data_processing:
Alignment program, Bowtie (version 1.0.0) was used with reads mapped to the Ensemble NCBIM37/mm9 (iGenome version) with two mismatches allowed.
PCR duplicates were removed with picardtools (picard-tools/1.88)
Transcripts were counted with htseq-count (version 0.6.1p1)
Counts files were analyzed with DESeq2_1.12.3
Anlayses were done on the NYULMC high performance computing cluster.
Genome_build: NCBIM37/mm9 (iGenome version)
Supplementary_files_format_and_content: comma-delimited text files, tables of CPM values for each sample

source_name: E12.5 spinal MN

extract_protocol:
E12.5 spinal cords were removed, cut into brachial and thoracic pieces by counting DRGs, then meninges and DRGs were removed and cells were dissociated with papain. Dissociated Control Hb9::GFP and PbxMNΔ; Hb9::GFP MNs were fluorescence-activated cell sorted directly into Arcturus Picopure Extraction buffer, and RNA was harvested using the Arcturus Picopure RNA isolation kit. cDNA was amplified using Nugene's Ovation RNA-Seq System V2 kit (Part No. 7102). 100ng cDNA was used as input to prepare the libraries, using the Ovation Ultralow Library system (Nugen, Parts No. 0303-05 and 0330-31) and amplified for 10 cycles of PCR and used for construction of the libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: highly mixed C57BL/6

value: embryonic spinal cord

tag: age

value: PbxMNdelta


title: Vsx2_1a_B1_S13_R1_001

description: single cell


title: thoracic C mut


title: brachial A mut


title: brachial B cnt

description:
brachial_Mutant_vs_Control_CPM_all
BR_Control_vs_TH_Control_CPM_all

value: control littermate


title: Kcng4_2la_H9

description: single end RNA-seq data

data_processing:
Reads were aligned to a reference genome (mm10 Ensembl) using Tophat v2.0.10
Expression levels were quantified using RSEM v1.2.28 (inferred counts and tpm values)
Genome_build: mm10
Supplementary_files_format_and_content: text file with tab delimiters

extract_protocol:
Dissociated retina were FACS sorted into 96-well plates (single cells) containing lysis buffer
Smart-seq2 (Picelli et al., Nature Methods, 2014)

tag: retina id


title: brachial B mut


title: thoracic C cnt

description:
Thoracic_Mutant_vs_Control_CPM_all
BR_Control_vs_TH_Control_CPM_all


title: thoracic A cnt


title: brachial C cnt


title: Kcng4_2la_H8

description: single end RNA-seq data


title: brachial A cnt


title: Kcng4_2la_H4

description: single end RNA-seq data


title: Kcng4_2la_H3

description: single end RNA-seq data


title: Kcng4_2la_H6

description: single end RNA-seq data


title: thoracic B cnt


title: Kcng4_2la_H12

description: single end RNA-seq data


title: Kcng4_2la_H2

description: single end RNA-seq data


title: brachial C mut


title: Kcng4_2la_H5

description: single end RNA-seq data


title: Vsx2_1a_B10_S22_R1_001

description: single cell


title: Kcng4_2la_G9

description: single end RNA-seq data


title: Kcng4_2la_G7

description: single end RNA-seq data


title: Kcng4_2la_G8

description: single end RNA-seq data


title: Vsx2_1a_D8_S44_R1_001

description: single cell


title: thoracic B mut


title: Kcng4_2la_G6

description: single end RNA-seq data


title: Kcng4_2la_H1

description: single end RNA-seq data


title: Kcng4_2la_H10

description: single end RNA-seq data


title: Kcng4_2la_G5

description: single end RNA-seq data


title: Kcng4_2la_H7

description: single end RNA-seq data


title: Kcng4_2la_G3

description: single end RNA-seq data


title: Kcng4_2la_F9

description: single end RNA-seq data


title: Kcng4_2la_G11

description: single end RNA-seq data


title: Kcng4_2la_F8

description: single end RNA-seq data


title: Kcng4_2la_G10

description: single end RNA-seq data


title: Kcng4_2la_F7

description: single end RNA-seq data


title: Kcng4_2la_F6

description: single end RNA-seq data


title: Kcng4_2la_H11

description: single end RNA-seq data


title: Kcng4_2la_G1

description: single end RNA-seq data


title: Kcng4_2la_F2

description: single end RNA-seq data


title: Kcng4_2la_F12

description: single end RNA-seq data


title: Kcng4_2la_F1

description: single end RNA-seq data


title: Kcng4_2la_F5

description: single end RNA-seq data


title: Kcng4_2la_F11

description: single end RNA-seq data


title: Kcng4_2la_F4

description: single end RNA-seq data


title: Kcng4_2la_F10

description: single end RNA-seq data


title: Kcng4_2la_F3

description: single end RNA-seq data


title: Kcng4_2la_E8

description: single end RNA-seq data


title: Kcng4_2la_G4

description: single end RNA-seq data


title: Kcng4_2la_E6

description: single end RNA-seq data


title: Kcng4_2la_E7

description: single end RNA-seq data


title: Kcng4_2la_E3

description: single end RNA-seq data


title: Kcng4_2la_G2

description: single end RNA-seq data


title: Kcng4_2la_E2

description: single end RNA-seq data


title: Kcng4_2la_E9

description: single end RNA-seq data


title: Kcng4_2la_E12

description: single end RNA-seq data


title: Kcng4_2la_E11

description: single end RNA-seq data


title: Kcng4_2la_E5

description: single end RNA-seq data


title: Kcng4_2la_E1

description: single end RNA-seq data


title: Kcng4_2la_E10

description: single end RNA-seq data


title: Kcng4_2la_D8

description: single end RNA-seq data


title: Kcng4_2la_G12

description: single end RNA-seq data


title: Kcng4_2la_D9

description: single end RNA-seq data


title: Kcng4_2la_D3

description: single end RNA-seq data


title: Kcng4_2la_D4

description: single end RNA-seq data


title: Kcng4_2la_D6

description: single end RNA-seq data


title: Kcng4_2la_D1

description: single end RNA-seq data


title: Kcng4_2la_D5

description: single end RNA-seq data


title: Kcng4_2la_D12

description: single end RNA-seq data


title: Kcng4_2la_C9

description: single end RNA-seq data


title: Kcng4_2la_D2

description: single end RNA-seq data


title: Kcng4_2la_D11

description: single end RNA-seq data


title: Kcng4_2la_D10

description: single end RNA-seq data


title: Kcng4_2la_C7

description: single end RNA-seq data


title: Kcng4_2la_C8

description: single end RNA-seq data


title: Kcng4_2la_E4

description: single end RNA-seq data


title: Kcng4_2la_C1

description: single end RNA-seq data


title: Kcng4_2la_C4

description: single end RNA-seq data


title: Kcng4_2la_C6

description: single end RNA-seq data


title: Kcng4_2la_C5

description: single end RNA-seq data


title: Kcng4_2la_C12

description: single end RNA-seq data


title: Kcng4_2la_C10

description: single end RNA-seq data


title: Kcng4_2la_C3

description: single end RNA-seq data


title: Kcng4_2la_B9

description: single end RNA-seq data


title: Kcng4_2la_C2

description: single end RNA-seq data


title: Kcng4_2la_B8

description: single end RNA-seq data


title: Kcng4_2la_B5

description: single end RNA-seq data


title: Kcng4_2la_C11

description: single end RNA-seq data


title: Kcng4_2la_B4

description: single end RNA-seq data


title: Kcng4_2la_B6

description: single end RNA-seq data


title: Kcng4_2la_B3

description: single end RNA-seq data


title: Kcng4_2la_D7

description: single end RNA-seq data


title: Kcng4_2la_B7

description: single end RNA-seq data


title: Kcng4_2la_B1

description: single end RNA-seq data


title: Kcng4_2la_B2

description: single end RNA-seq data


title: Kcng4_2la_B11

description: single end RNA-seq data


title: Kcng4_2la_A9

description: single end RNA-seq data


title: Kcng4_2la_B10

description: single end RNA-seq data


title: Kcng4_2la_A7

description: single end RNA-seq data


title: Kcng4_2la_A4

description: single end RNA-seq data


title: Kcng4_2la_A6

description: single end RNA-seq data


title: Kcng4_2la_A3

description: single end RNA-seq data


title: Kcng4_2la_A2

description: single end RNA-seq data


title: Kcng4_2la_A12

description: single end RNA-seq data