ZRANB2 RNA-Seq in K562

General Information


RBP	ZRANB2
Cell_Line	K562
Method	shRNA
Exp_Name	ZRANB2-BGKLV13-K562
ENCODE_series_ID	ENCSR148OZB
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR850PWM
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	ZRANB2_BGKLV13_11
Rep2	ZRANB2_BGKLV13_12
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	67.4
Rep2_qPCR	51.8
Rep1_WB	83.2
Rep2_WB	81.5
Antibody Cat#	A301-029A
Antibody Lot#	A301-029A
Antibody DCC ID	ENCAB099IOB
Status	Released
Project	ENCODE3
ID	363

Experiment Information (Status: Released)

	BGKLV13-11	BGKLV13-12
idx	144	145
TRCN#_or_BGC#	TRCN0000013427	TRCN0000013427
shRNA_or_gRNA_sequence	CTTCACATTCACGATCTTCAT	CTTCACATTCACGATCTTCAT
PAM
Name	ZRANB2	ZRANB2
Sample_ID	BGKLV13-11	BGKLV13-12
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	ZRANB2	ZRANB2
qPCR_result	67.4	51.8
Ave_qPCR	59.6
RT-qPCR_primer-F	atgtgaattgggccagaaga
RT-qPCR_primer-R	aaaccaccaccatatcctgttc
protein_conc	1986	2066
WB_result	83.2	81.5
Ave_WB	82.4
WB_DONE_date	7/15/2015
MW	37kDa
IP	1	1
antibody_Cat#	A301-029A	A301-029A
Antibody DCC ID	ENCAB099IOB	ENCAB099IOB
submitted_to_DCC_date	8/6/2015
Rep1_TPM	33.8891918	0
Rep2_TPM	28.9160923	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note		10
ID	159	160

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ZRANB2	Product_ID: A301-029A Lot_ID: 1 Source: Bethyl Labs Target Name: ZRANB2-human

Experiment Status

	BGKLV13-11	BGKLV13-12
Sample_ID	BGKLV13-11	BGKLV13-12
Sample Name	ZRANB2_BGKLV13_11	ZRANB2_BGKLV13_12
Sample Name	ZRANB2_BGKLV13_11	ZRANB2_BGKLV13_12
RBP	ZRANB2	ZRANB2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	488	489

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-11	BGKLV13-12
Sample #
Sample Name	ZRANB2-BGKLV13-11	ZRANB2-BGKLV13-12
Sample_Name_Alias	ZRANB2_BGKLV13_11	ZRANB2_BGKLV13_12
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/B2.png	DNA_Library_LV13-14/set1/C2.png
RIN	9.2	9.6
libSample_RNA_Well	RNA_Library_LV12/set1/E10.png	RNA_Library_LV12/set1/F10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-11	BGKLV13-12
RBP	ZRANB2	ZRANB2
Batch_ID	BGKLV13	BGKLV13
WB_result	83.200	81.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2128	2129

Sequencing Information

	BGKLV13-11	BGKLV13-12
Sample_ID	BGKLV13-11	BGKLV13-12
Sample Name	ZRANB2_BGKLV13_11	ZRANB2_BGKLV13_12
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	44,090,000	46,290,000
total_aligned_reads	41,349,936	42,732,516
unique_aligned_reads	38,130,412	39,350,588
percent_uniqueAligned	0.86483	0.85009
correlation_replicates	0.998866	0.998866
spikein_reads	162,070	111,756
percent_spikeins	0.00368	0.00241
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	770	771

Data Submission Information

	BGKLV13-11	BGKLV13-11
ENCODE_alias	brenton-graveley:ZRANB2_BGKLV13	brenton-graveley:ZRANB2-BGKLV13-K562
ENCODE_accession	ENCSR850PWM	ENCSR148OZB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-11	BGKLV13-11
Sample Name	ZRANB2_BGKLV13_11	ZRANB2_BGKLV13_11
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2793	7057

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
ZRANB2_BGKLV13_11_GATCAG_L002_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	770	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13416
ZRANB2_BGKLV13_11_GATCAG_L002_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	770	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13468
ZRANB2_BGKLV13_11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	770					GRCh38	V40	ZRANB2_BGKLV13_11_GATCAG_L002_R1_001.fastq.gz,ZRANB2_BGKLV13_11_GATCAG_L002_R2_001.fastq.gz		ENCORE2	13520
ZRANB2_BGKLV13_11_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	770					GRCh38	V40	ZRANB2_BGKLV13_11/Aligned.sortedByCoord.out.bam		ENCORE2	13572
ZRANB2_BGKLV13_11_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	770					GRCh38	V40	ZRANB2_BGKLV13_11/Aligned.sortedByCoord.out.bam		ENCORE2	13624
ZRANB2_BGKLV13_11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	770					GRCh38	V40	ZRANB2_BGKLV13_11/Aligned.sortedByCoord.out.bam		ENCORE2	13676
ZRANB2_BGKLV13_11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	770					GRCh38	V40	ZRANB2_BGKLV13_11/Aligned.sortedByCoord.out.bam		ENCORE2	13728
ZRANB2_BGKLV13_11_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	770					GRCh38	V40	ZRANB2_BGKLV13_11_GATCAG_L002_R1_001.fastq.gz,ZRANB2_BGKLV13_11_GATCAG_L002_R2_001.fastq.gz		ENCORE2	13780
ZRANB2_BGKLV13_12_TAGCTT_L002_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	771	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13417
ZRANB2_BGKLV13_12_TAGCTT_L002_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	771	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13469
ZRANB2_BGKLV13_12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	771					GRCh38	V40	ZRANB2_BGKLV13_12_TAGCTT_L002_R1_001.fastq.gz,ZRANB2_BGKLV13_12_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	13521
ZRANB2_BGKLV13_12_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	771					GRCh38	V40	ZRANB2_BGKLV13_12/Aligned.sortedByCoord.out.bam		ENCORE2	13573
ZRANB2_BGKLV13_12_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	771					GRCh38	V40	ZRANB2_BGKLV13_12/Aligned.sortedByCoord.out.bam		ENCORE2	13625
ZRANB2_BGKLV13_12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	771					GRCh38	V40	ZRANB2_BGKLV13_12/Aligned.sortedByCoord.out.bam		ENCORE2	13677
ZRANB2_BGKLV13_12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	771					GRCh38	V40	ZRANB2_BGKLV13_12/Aligned.sortedByCoord.out.bam		ENCORE2	13729
ZRANB2_BGKLV13_12_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	771					GRCh38	V40	ZRANB2_BGKLV13_12_TAGCTT_L002_R1_001.fastq.gz,ZRANB2_BGKLV13_12_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	13781