DEAF1 RNA-Seq in HepG2

General Information


RBP	DEAF1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DEAF1-BGHcLV03-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV03
Pool ID	Pool-160201
Local_Set_Name	BGHcLV03
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DEAF1_BGHcLV03-13
Rep2	DEAF1_BGHcLV03-14
CN1	NT_BGHcLV03-1
CN2	NT_BGHcLV03-2
Rep1_qPCR	53.8
Rep2_qPCR	42.8
Rep1_WB	no band
Rep2_WB
Antibody Cat#	A303-187A
Antibody Lot#	A303-187A
Antibody DCC ID
Status	NotSatisfied
Project	ENCODE3
ID	571

Experiment Information (Status: NotSatisfied)

	BGHcLV03-13	BGHcLV03-14
idx	13	14
TRCN#_or_BGC#	BGC#0000016	BGC#0000016
shRNA_or_gRNA_sequence	GCACATGGACATGGGCGCCG	GCACATGGACATGGGCGCCG
PAM
Name	DEAF1-C1-A	DEAF1-C1-A
Sample_ID	BGHcLV03-13	BGHcLV03-14
transduction_Date	12/16/2015	12/16/2015
days	D6	D6
RBP_name	DEAF1	DEAF1
qPCR_result	53.8	42.8
Ave_qPCR	48.3
RT-qPCR_primer-F	aggacagctgccagatcg
RT-qPCR_primer-R	caggcagggatgtcaacac
protein_conc	3229	3116
WB_result	no band
Ave_WB
WB_DONE_date	12/28/2015
MW	59kDa
IP	1
antibody_Cat#	A303-187A	A303-187A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	22	0
Rep2_TPM	9	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	6154	6155

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV03-13	BGHcLV03-14
Sample_ID	BGHcLV03-13	BGHcLV03-14
Sample Name	DEAF1_BGHcLV03-13	DEAF1_BGHcLV03-14
Sample Name	DEAF1_BGHcLV03-13	DEAF1_BGHcLV03-14
RBP	DEAF1	DEAF1
Cell_Line	HepG2	HepG2
Exp UID
Status	NotSatisfied	NotSatisfied
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	34	35

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV03-13	BGHcLV03-14
Sample #
Sample Name	DEAF1-BGHcLV03-13	DEAF1-BGHcLV03-14
Sample_Name_Alias	DEAF1_BGHcLV03-13	DEAF1_BGHcLV03-14
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/E2.png	DNA_Library_cLV02/set1/F2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_cLV02/set1/G3.png	RNA_Library_cLV02/set1/H3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV03-13	BGHcLV03-14
RBP	DEAF1	DEAF1
Batch_ID	BGHcLV03	BGHcLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2790	2791

Sequencing Information

	BGHcLV03-13	BGHcLV03-14
Sample_ID	BGHcLV03-13	BGHcLV03-14
Sample Name	DEAF1_BGHcLV03-13	DEAF1_BGHcLV03-14
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGHcLV03	BGHcLV03
total_reads	56,175,914	52,678,850
total_aligned_reads	47,769,024	46,743,078
unique_aligned_reads	44,863,334	43,991,846
percent_uniqueAligned	0.79862	0.83510
correlation_replicates	0.998372	0.998372
spikein_reads	97,078	83,256
percent_spikeins	0.00173	0.00158
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1439	1440

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
DEAF1_BGHcLV03-13_ACAGTG_L006_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1439	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22912
DEAF1_BGHcLV03-13_ACAGTG_L006_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1439	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22930
DEAF1_BGHcLV03-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1439					GRCh38	V40	DEAF1_BGHcLV03-13_ACAGTG_L006_001.R1.fastq.gz,DEAF1_BGHcLV03-13_ACAGTG_L006_001.R2.fastq.gz		ENCORE2	22948
DEAF1_BGHcLV03-13_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1439					GRCh38	V40	DEAF1_BGHcLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	22966
DEAF1_BGHcLV03-13_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1439					GRCh38	V40	DEAF1_BGHcLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	22984
DEAF1_BGHcLV03-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1439					GRCh38	V40	DEAF1_BGHcLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	23002
DEAF1_BGHcLV03-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1439					GRCh38	V40	DEAF1_BGHcLV03-13/Aligned.sortedByCoord.out.bam		ENCORE2	23020
DEAF1_BGHcLV03-13_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1439					GRCh38	V40	DEAF1_BGHcLV03-13_ACAGTG_L006_001.R1.fastq.gz,DEAF1_BGHcLV03-13_ACAGTG_L006_001.R2.fastq.gz		ENCORE2	23038
DEAF1_BGHcLV03-14_GCCAAT_L006_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1440	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22913
DEAF1_BGHcLV03-14_GCCAAT_L006_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1440	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22931
DEAF1_BGHcLV03-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1440					GRCh38	V40	DEAF1_BGHcLV03-14_GCCAAT_L006_001.R1.fastq.gz,DEAF1_BGHcLV03-14_GCCAAT_L006_001.R2.fastq.gz		ENCORE2	22949
DEAF1_BGHcLV03-14_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1440					GRCh38	V40	DEAF1_BGHcLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	22967
DEAF1_BGHcLV03-14_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1440					GRCh38	V40	DEAF1_BGHcLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	22985
DEAF1_BGHcLV03-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1440					GRCh38	V40	DEAF1_BGHcLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	23003
DEAF1_BGHcLV03-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1440					GRCh38	V40	DEAF1_BGHcLV03-14/Aligned.sortedByCoord.out.bam		ENCORE2	23021
DEAF1_BGHcLV03-14_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1440					GRCh38	V40	DEAF1_BGHcLV03-14_GCCAAT_L006_001.R1.fastq.gz,DEAF1_BGHcLV03-14_GCCAAT_L006_001.R2.fastq.gz		ENCORE2	23039