CEBPZ RNA-Seq in HepG2

General Information


RBP	CEBPZ
Cell_Line	HepG2
Method	shRNA
Exp_Name	CEBPZ-BGHLV30-HepG2
ENCODE_series_ID	ENCSR301KZX
Batch_ID	BGHLV30
Pool ID	Pool-151215B
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR929PXS
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	CEBPZ_BGHLV30-19
Rep2	CEBPZ_BGHLV30-20
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	46.5
Rep2_qPCR	48.6
Rep1_WB	76.1
Rep2_WB	72.9
Antibody Cat#	A303-153A
Antibody Lot#	A303-153A
Antibody DCC ID	ENCAB660TOB
Status	Released
Project	ENCODE3
ID	683

Experiment Information (Status: Released)

	BGHLV30-19	BGHLV30-20
idx	703	704
TRCN#_or_BGC#	TRCN0000017946	TRCN0000017946
shRNA_or_gRNA_sequence	GCAGCCATGATTCTTCTTATT	GCAGCCATGATTCTTCTTATT
PAM
Name	CEBPZ	CEBPZ
Sample_ID	BGHLV30-19	BGHLV30-20
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	CEBPZ	CEBPZ
qPCR_result	46.5	48.6
Ave_qPCR	47.6
RT-qPCR_primer-F	ggaggcaccaagcaagatta
RT-qPCR_primer-R	gctgaaggtcatcgattgct
protein_conc	5160	4773
WB_result	76.1	72.9
Ave_WB	74.5
WB_DONE_date	9/18/2015
MW	121kDa
IP	1	1
antibody_Cat#	A303-153A	A303-153A
Antibody DCC ID	ENCAB660TOB	ENCAB660TOB
submitted_to_DCC_date	12/7/2015
Rep1_TPM	51.6	0
Rep2_TPM	41.7	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2790	2791

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV30-19	BGHLV30-20
Sample_ID	BGHLV30-19	BGHLV30-20
Sample Name	CEBPZ_BGHLV30-19	CEBPZ_BGHLV30-20
Sample Name	CEBPZ_BGHLV30-19	CEBPZ_BGHLV30-20
RBP	CEBPZ	CEBPZ
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1048	1049

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-19	BGHLV30-20
Sample #
Sample Name	CEBPZ-BGHLV30-19	CEBPZ-BGHLV30-20
Sample_Name_Alias	CEBPZ_BGHLV30-19	CEBPZ_BGHLV30-20
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/A10.png	DNA_Library_LV28-29-30/set1/B10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/A10.png	RNA_Library_LV29-30-31-32/set1/B5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-19	BGHLV30-20
RBP	CEBPZ	CEBPZ
Batch_ID	BGHLV30	BGHLV30
WB_result	76.100	72.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2740	2741

Sequencing Information

	BGHLV30-19	BGHLV30-20
Sample_ID	BGHLV30-19	BGHLV30-20
Sample Name	CEBPZ_BGHLV30-19	CEBPZ_BGHLV30-20
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set30	set30
total_reads	56,149,288	66,551,210
total_aligned_reads	48,945,324	58,538,314
unique_aligned_reads	46,133,072	55,262,186
percent_uniqueAligned	0.82161	0.83037
correlation_replicates	0.998316	0.998316
spikein_reads	147,786	174,692
percent_spikeins	0.00263	0.00262
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1399	1400

Data Submission Information

	BGHLV30-19	BGHLV30-19
ENCODE_alias	brenton-graveley:CEBPZ_BGHLV30	brenton-graveley:CEBPZ-BGHLV30-HepG2
ENCODE_accession	ENCSR929PXS	ENCSR301KZX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-19	BGHLV30-19
Sample Name	CEBPZ_BGHLV30-19	CEBPZ_BGHLV30-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3073	6615

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
CEBPZ_BGHLV30-19_ATCACG_L003_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1399	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20704
CEBPZ_BGHLV30-19_ATCACG_L003_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1399	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20738
CEBPZ_BGHLV30-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1399					GRCh38	V40	CEBPZ_BGHLV30-19_ATCACG_L003_001.R1.fastq.gz,CEBPZ_BGHLV30-19_ATCACG_L003_001.R2.fastq.gz		ENCORE2	20772
CEBPZ_BGHLV30-19_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1399					GRCh38	V40	CEBPZ_BGHLV30-19/Aligned.sortedByCoord.out.bam		ENCORE2	20806
CEBPZ_BGHLV30-19_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1399					GRCh38	V40	CEBPZ_BGHLV30-19/Aligned.sortedByCoord.out.bam		ENCORE2	20840
CEBPZ_BGHLV30-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1399					GRCh38	V40	CEBPZ_BGHLV30-19/Aligned.sortedByCoord.out.bam		ENCORE2	20874
CEBPZ_BGHLV30-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1399					GRCh38	V40	CEBPZ_BGHLV30-19/Aligned.sortedByCoord.out.bam		ENCORE2	20908
CEBPZ_BGHLV30-19_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1399					GRCh38	V40	CEBPZ_BGHLV30-19_ATCACG_L003_001.R1.fastq.gz,CEBPZ_BGHLV30-19_ATCACG_L003_001.R2.fastq.gz		ENCORE2	20942
CEBPZ_BGHLV30-20_CGATGT_L003_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1400	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20705
CEBPZ_BGHLV30-20_CGATGT_L003_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1400	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20739
CEBPZ_BGHLV30-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1400					GRCh38	V40	CEBPZ_BGHLV30-20_CGATGT_L003_001.R1.fastq.gz,CEBPZ_BGHLV30-20_CGATGT_L003_001.R2.fastq.gz		ENCORE2	20773
CEBPZ_BGHLV30-20_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1400					GRCh38	V40	CEBPZ_BGHLV30-20/Aligned.sortedByCoord.out.bam		ENCORE2	20807
CEBPZ_BGHLV30-20_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1400					GRCh38	V40	CEBPZ_BGHLV30-20/Aligned.sortedByCoord.out.bam		ENCORE2	20841
CEBPZ_BGHLV30-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1400					GRCh38	V40	CEBPZ_BGHLV30-20/Aligned.sortedByCoord.out.bam		ENCORE2	20875
CEBPZ_BGHLV30-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1400					GRCh38	V40	CEBPZ_BGHLV30-20/Aligned.sortedByCoord.out.bam		ENCORE2	20909
CEBPZ_BGHLV30-20_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1400					GRCh38	V40	CEBPZ_BGHLV30-20_CGATGT_L003_001.R1.fastq.gz,CEBPZ_BGHLV30-20_CGATGT_L003_001.R2.fastq.gz		ENCORE2	20943