CEBPZ RNA-Seq in K562

General Information


RBP	CEBPZ
Cell_Line	K562
Method	CRISPR
Exp_Name	CEBPZ-BGKcLV02-K562
ENCODE_series_ID	ENCSR156XPB
Batch_ID	BGKcLV02
Pool ID	Pool-160201
Local_Set_Name	BGKcLV02
ENCODE_KD_Exp_ID	ENCSR637EFF
ENCODE_CN_Exp_ID	ENCSR163JUC
Rep1	CEBPZ_BGKcLV02-15
Rep2	CEBPZ_BGKcLV02-16
CN1	NT_BGKcLV02-1
CN2	NT_BGKcLV02-2
Rep1_qPCR	3.9
Rep2_qPCR	23.8
Rep1_WB	75.5
Rep2_WB	76.7
Antibody Cat#	A303-153A
Antibody Lot#	A303-153A
Antibody DCC ID	ENCAB660TOB
Status	Released
Project	ENCODE3
ID	581

Experiment Information (Status: Released)

	BGKcLV02-15	BGKcLV02-15	BGKcLV02-15	BGKcLV02-16	BGKcLV02-16	BGKcLV02-16
idx	17	17	17	18	18	18
TRCN#_or_BGC#	BGC#0000014	BGC#0000014	BGC#0000014	BGC#0000014	BGC#0000014	BGC#0000014
shRNA_or_gRNA_sequence	AATACTAGTGAAGCCGAGAA	AATACTAGTGAAGCCGAGAA	AATACTAGTGAAGCCGAGAA	AATACTAGTGAAGCCGAGAA	AATACTAGTGAAGCCGAGAA	AATACTAGTGAAGCCGAGAA
PAM
Name	CEBPZ-C1-A	CEBPZ-C1-A	CEBPZ-C1-A	CEBPZ-C1-A	CEBPZ-C1-A	CEBPZ-C1-A
Sample_ID	BGKcLV02-15	BGKcLV02-15	BGKcLV02-15	BGKcLV02-16	BGKcLV02-16	BGKcLV02-16
transduction_Date	12/15/2015	12/15/2015	12/15/2015	12/15/2015	12/15/2015	12/15/2015
days	day 6	day 6	day 6	day 6	day 6	day 6
RBP_name	CEBPZ	CEBPZ	CEBPZ	CEBPZ	CEBPZ	CEBPZ
qPCR_result	3.9	3.9	3.9	23.8	23.8	23.8
Ave_qPCR	3.9	3.9	3.9
RT-qPCR_primer-F	ggaggcaccaagcaagatta	ggaggcaccaagcaagatta	ggaggcaccaagcaagatta
RT-qPCR_primer-R	gctgaaggtcatcgattgct	gctgaaggtcatcgattgct	gctgaaggtcatcgattgct
protein_conc	2763	2763	2763	3525	3525	3525
WB_result	75.5	76.0	68.3	77	68.7	75.2
Ave_WB	76.3	72.4	71.7
WB_DONE_date	12/28/2015	5/18/2022	7/6/2022
MW	121kDa	121kDa	121kDa
IP	1
antibody_Cat#	A303-153A	A303-154A	A303-155A		LOT # 1	LOT # 1
Antibody DCC ID	ENCAB660TOB	ENCAB579MFH	ENCAB432DWB
submitted_to_DCC_date	9/28/16	8/16/22	8/16/22
Rep1_TPM	62.5	0	0	0	0	0
Rep2_TPM	33.7	0	0	0	0	0
Action	Ready
Library_start_date	1/8/2016
repeat_library
Note
ID	4111	4113	4115	4112	4114	4116

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CEBPZ	Product_ID: A303-153A Lot_ID: 1 Source: Bethyl Labs Target Name: CEBPZ-human
CEBPZ	Product_ID: A303-154A Lot_ID: 1 Source: Bethyl Labs Target Name: CEBPZ-human
CEBPZ	Product_ID: A303-155A Lot_ID: 1 Source: Bethyl Labs Target Name: CEBPZ-human

Experiment Status

	BGKcLV02-15	BGKcLV02-16
Sample_ID	BGKcLV02-15	BGKcLV02-16
Sample Name	CEBPZ_BGKcLV02-15	CEBPZ_BGKcLV02-16
Sample Name	CEBPZ_BGKcLV02-15	CEBPZ_BGKcLV02-16
RBP	CEBPZ	CEBPZ
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1083	1084

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV02-15	BGKcLV02-16
Sample #
Sample Name	CEBPZ-BGKcLV02-15	CEBPZ-BGKcLV02-16
Sample_Name_Alias	CEBPZ_BGKcLV02-15	CEBPZ_BGKcLV02-16
Index Well Position	S01	S02
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/A5.png	DNA_Library_cLV02/set1/B5.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_cLV02/set1/C6.png	RNA_Library_cLV02/set1/D6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV02-15	BGKcLV02-16
RBP	CEBPZ	CEBPZ
Batch_ID	BGKcLV02	BGKcLV02
WB_result	75.500	76.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2768	2769

Sequencing Information

	BGKcLV02-15	BGKcLV02-16
Sample_ID	BGKcLV02-15	BGKcLV02-16
Sample Name	CEBPZ_BGKcLV02-15	CEBPZ_BGKcLV02-16
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGKcLV02	BGKcLV02
total_reads	52,784,974	57,472,430
total_aligned_reads	48,569,810	52,816,448
unique_aligned_reads	44,399,460	48,278,082
percent_uniqueAligned	0.84114	0.84002
correlation_replicates	0.996711	0.996711
spikein_reads	118,210	123,156
percent_spikeins	0.00224	0.00214
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1417	1418

Data Submission Information

	BGKcLV02-15	BGKcLV02-15
ENCODE_alias	brenton-graveley:CEBPZ_BGKcLV02	brenton-graveley:CEBPZ-BGKcLV02-K562
ENCODE_accession	ENCSR637EFF	ENCSR156XPB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV02-15	BGKcLV02-15
Sample Name	CEBPZ_BGKcLV02-15	CEBPZ_BGKcLV02-15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3103	6616

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_BGKcLV02-15_ATCACG_L008_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1417	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22750
CEBPZ_BGKcLV02-15_ATCACG_L008_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1417	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22770
CEBPZ_BGKcLV02-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1417					GRCh38	V40	CEBPZ_BGKcLV02-15_ATCACG_L008_001.R1.fastq.gz,CEBPZ_BGKcLV02-15_ATCACG_L008_001.R2.fastq.gz		ENCORE2	22790
CEBPZ_BGKcLV02-15_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1417					GRCh38	V40	CEBPZ_BGKcLV02-15/Aligned.sortedByCoord.out.bam		ENCORE2	22810
CEBPZ_BGKcLV02-15_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1417					GRCh38	V40	CEBPZ_BGKcLV02-15/Aligned.sortedByCoord.out.bam		ENCORE2	22830
CEBPZ_BGKcLV02-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1417					GRCh38	V40	CEBPZ_BGKcLV02-15/Aligned.sortedByCoord.out.bam		ENCORE2	22850
CEBPZ_BGKcLV02-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1417					GRCh38	V40	CEBPZ_BGKcLV02-15/Aligned.sortedByCoord.out.bam		ENCORE2	22870
CEBPZ_BGKcLV02-15_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1417					GRCh38	V40	CEBPZ_BGKcLV02-15_ATCACG_L008_001.R1.fastq.gz,CEBPZ_BGKcLV02-15_ATCACG_L008_001.R2.fastq.gz		ENCORE2	22890
CEBPZ_BGKcLV02-16_CGATGT_L008_001.R1.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1418	HiSeq2500	100	paired-ended	1				NT_BGKcLV02-1_GGCTAC_L006_001.R1.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R1.fastq.gz	ENCODE3	22751
CEBPZ_BGKcLV02-16_CGATGT_L008_001.R2.fastq.gz	ENCODE_DATA/BGKcLV02/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1418	HiSeq2500	100	paired-ended	2				NT_BGKcLV02-1_GGCTAC_L006_001.R2.fastq.gz,NT_BGKcLV02-2_CTTGTA_L006_001.R2.fastq.gz	ENCODE3	22771
CEBPZ_BGKcLV02-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1418					GRCh38	V40	CEBPZ_BGKcLV02-16_CGATGT_L008_001.R1.fastq.gz,CEBPZ_BGKcLV02-16_CGATGT_L008_001.R2.fastq.gz		ENCORE2	22791
CEBPZ_BGKcLV02-16_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1418					GRCh38	V40	CEBPZ_BGKcLV02-16/Aligned.sortedByCoord.out.bam		ENCORE2	22811
CEBPZ_BGKcLV02-16_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1418					GRCh38	V40	CEBPZ_BGKcLV02-16/Aligned.sortedByCoord.out.bam		ENCORE2	22831
CEBPZ_BGKcLV02-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1418					GRCh38	V40	CEBPZ_BGKcLV02-16/Aligned.sortedByCoord.out.bam		ENCORE2	22851
CEBPZ_BGKcLV02-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV02/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1418					GRCh38	V40	CEBPZ_BGKcLV02-16/Aligned.sortedByCoord.out.bam		ENCORE2	22871
CEBPZ_BGKcLV02-16_quant.sf	ENCODE_DATA/BGKcLV02/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1418					GRCh38	V40	CEBPZ_BGKcLV02-16_CGATGT_L008_001.R1.fastq.gz,CEBPZ_BGKcLV02-16_CGATGT_L008_001.R2.fastq.gz		ENCORE2	22891