|
| Status |
Public on Feb 27, 2024 |
| Title |
TF ChIP-seq from whole organism (ENCLB305OSD) |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila melanogaster strain Pdp1-MiMIC-GFP mixed sex embryo (0-24 hours) insertion targeting D. melanogaster Pdp1
|
| Organism |
Drosophila melanogaster |
| Characteristics |
antibody: Pdp1
cell_type: whole organism
biomaterial_type: whole organisms
biosample encode accession: ENCBS433YZM (SAMN40087029)
collection date: not applicable
geographic location: not applicable
encode accession: ENCBS433YZM
note: D. mel line contraining an intronic eGFP exon to create a Pdp1-GFP fusion gene
Sex: pooled male and female
dev stage: embryonic
age: 0-24 hour
donor_id: ENCDO034JNF
lab: Kevin White, UChicago
source: Hugo Bellen
link: ENCBS433YZM at ENCODE; https://www.encodeproject.org/ENCBS433YZM/
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
general protocol: https://www.encodeproject.org/documents/47d3fb40-f2e5-427a-9e29-501dfdaf41fb/@@download/attachment/modENCODE_protocols_Column_SPRI.pdf
other: https://www.encodeproject.org/documents/fd60abff-13b1-447a-b65c-88d839fe7a31/@@download/attachment/1276.pdf
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
https://www.encodeproject.org/experiments/ENCSR005MLL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on transgenic flies expressing Pdp1-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR005MLL
assay title: TF ChIP-seq
assembly: dm6, dm3
possible controls: ENCSR546LJI
encode release date: 2016-07-06
lab: Kevin White, UChicago
library encode accession: ENCLB305OSD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-800
|
| Data processing |
See GSM*_README.txt supplementary file linked below
|
| |
|
| Submission date |
Feb 24, 2024 |
| Last update date |
Feb 27, 2024 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
encode-help@lists.stanford.edu
|
| Organization name |
ENCODE DCC
|
| Street address |
300 Pasteur Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE256558 |
TF ChIP-seq from whole organism (ENCSR005MLL) |
|
| Relations |
| BioSample |
SAMN40087029 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8106147_ENCFF017VGQ_signal_of_unique_reads_dm3.bigWig |
14.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106147_ENCFF146DFE_peaks_and_background_as_input_for_IDR_dm3.bed.gz |
748.0 Kb |
(ftp)(http) |
BED |
| GSM8106147_ENCFF164QBY_control_normalized_signal_dm3.bigWig |
15.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106147_ENCFF273SRD_peaks_and_background_as_input_for_IDR_dm3.bigBed |
1.3 Mb |
(ftp)(http) |
BIGBED |
| GSM8106147_ENCFF436UQH_control_normalized_signal_dm6.bigWig |
16.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106147_ENCFF537LLV_signal_of_unique_reads_dm6.bigWig |
16.7 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106147_ENCFF685EEF_read-depth_normalized_signal_dm3.bigWig |
14.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106147_ENCFF779ORI_peaks_and_background_as_input_for_IDR_dm6.bigBed |
1.3 Mb |
(ftp)(http) |
BIGBED |
| GSM8106147_ENCFF805VGS_read-depth_normalized_signal_dm6.bigWig |
16.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM8106147_ENCFF913HEB_peaks_and_background_as_input_for_IDR_dm6.bed.gz |
748.2 Kb |
(ftp)(http) |
BED |
| GSM8106147_ENCLB305OSD_README.txt.gz |
1.9 Kb |
(ftp)(http) |
TXT |
| Raw data are available in SRA |
