ZRANB2 RNA-Seq in HepG2

General Information


RBP	ZRANB2
Cell_Line	HepG2
Method	shRNA
Exp_Name	ZRANB2-BGHLV14-HepG2
ENCODE_series_ID	ENCSR663OZZ
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR081QQH
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	ZRANB2_27_BGHLV14-71
Rep2	ZRANB2_27_BGHLV14-72
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	59.8
Rep2_qPCR	80.2
Rep1_WB	83.0
Rep2_WB	75.5
Antibody Cat#	A301-029A
Antibody Lot#	A301-029A
Antibody DCC ID	ENCAB099IOB
Status	Released
Project	ENCODE3
ID	413

Experiment Information (Status: Released)

	BGHLV14-71	BGHLV14-72
idx	167	168
TRCN#_or_BGC#	TRCN0000013427	TRCN0000013427
shRNA_or_gRNA_sequence	CTTCACATTCACGATCTTCAT	CTTCACATTCACGATCTTCAT
PAM
Name	ZRANB2_27	ZRANB2_27
Sample_ID	BGHLV14-71	BGHLV14-72
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	ZRANB2	ZRANB2
qPCR_result	59.8	80.2
Ave_qPCR	70.0
RT-qPCR_primer-F	atgtgaattgggccagaaga
RT-qPCR_primer-R	aaaccaccaccatatcctgttc
protein_conc	3220	3100
WB_result	83.0	75.5
Ave_WB	79.3
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	15.5	0
Rep2_TPM	14	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2232	2233

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

	BGHLV14-71	BGHLV14-72
Sample_ID	BGHLV14-71	BGHLV14-72
Sample Name	ZRANB2_27_BGHLV14-71	ZRANB2_27_BGHLV14-72
Sample Name	ZRANB2_27_BGHLV14-71	ZRANB2_27_BGHLV14-72
RBP	ZRANB2	ZRANB2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	550	551

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-71	BGHLV14-72
Sample #
Sample Name	ZRANB2-BGHLV14-71	ZRANB2-BGHLV14-72
Sample_Name_Alias	ZRANB2_27_BGHLV14-71	ZRANB2_27_BGHLV14-72
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set3/F1.png	DNA_Library_LV13-14/set3/G1.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E11.png	RNA_Library_LV13-14-16/set1/F11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-71	BGHLV14-72
RBP	ZRANB2	ZRANB2
Batch_ID	BGHLV14	BGHLV14
WB_result	83.000	75.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2234	2235

Sequencing Information

	BGHLV14-71	BGHLV14-72
Sample_ID	BGHLV14-71	BGHLV14-72
Sample Name	ZRANB2_27_BGHLV14-71	ZRANB2_27_BGHLV14-72
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	49,860,000	51,830,000
total_aligned_reads	45,508,108	47,079,236
unique_aligned_reads	43,014,050	44,475,918
percent_uniqueAligned	0.86270	0.85811
correlation_replicates	0.999528	0.999528
spikein_reads	265,134	269,080
percent_spikeins	0.00532	0.00519
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	876	877

Data Submission Information

	BGHLV14-71	BGHLV14-71
ENCODE_alias	brenton-graveley:ZRANB2_BGHLV14	brenton-graveley:ZRANB2-BGHLV14-HepG2
ENCODE_accession	ENCSR081QQH	ENCSR663OZZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-71	BGHLV14-71
Sample Name	ZRANB2_27_BGHLV14-71	ZRANB2_27_BGHLV14-71
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2824	7056

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_27_BGHLV14-71_GTGGCC_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	876	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13842
ZRANB2_27_BGHLV14-71_GTGGCC_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	876	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13904
ZRANB2_27_BGHLV14-71_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	876					GRCh38	V40	ZRANB2_27_BGHLV14-71_GTGGCC_L008_R1_001.fastq.gz,ZRANB2_27_BGHLV14-71_GTGGCC_L008_R2_001.fastq.gz		ENCORE2	13966
ZRANB2_27_BGHLV14-71_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	876					GRCh38	V40	ZRANB2_27_BGHLV14-71/Aligned.sortedByCoord.out.bam		ENCORE2	14028
ZRANB2_27_BGHLV14-71_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	876					GRCh38	V40	ZRANB2_27_BGHLV14-71/Aligned.sortedByCoord.out.bam		ENCORE2	14090
ZRANB2_27_BGHLV14-71_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	876					GRCh38	V40	ZRANB2_27_BGHLV14-71/Aligned.sortedByCoord.out.bam		ENCORE2	14152
ZRANB2_27_BGHLV14-71_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	876					GRCh38	V40	ZRANB2_27_BGHLV14-71/Aligned.sortedByCoord.out.bam		ENCORE2	14214
ZRANB2_27_BGHLV14-71_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	876					GRCh38	V40	ZRANB2_27_BGHLV14-71_GTGGCC_L008_R1_001.fastq.gz,ZRANB2_27_BGHLV14-71_GTGGCC_L008_R2_001.fastq.gz		ENCORE2	14276
ZRANB2_27_BGHLV14-72_GTTTCG_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	877	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13843
ZRANB2_27_BGHLV14-72_GTTTCG_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	877	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13905
ZRANB2_27_BGHLV14-72_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	877					GRCh38	V40	ZRANB2_27_BGHLV14-72_GTTTCG_L008_R1_001.fastq.gz,ZRANB2_27_BGHLV14-72_GTTTCG_L008_R2_001.fastq.gz		ENCORE2	13967
ZRANB2_27_BGHLV14-72_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	877					GRCh38	V40	ZRANB2_27_BGHLV14-72/Aligned.sortedByCoord.out.bam		ENCORE2	14029
ZRANB2_27_BGHLV14-72_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	877					GRCh38	V40	ZRANB2_27_BGHLV14-72/Aligned.sortedByCoord.out.bam		ENCORE2	14091
ZRANB2_27_BGHLV14-72_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	877					GRCh38	V40	ZRANB2_27_BGHLV14-72/Aligned.sortedByCoord.out.bam		ENCORE2	14153
ZRANB2_27_BGHLV14-72_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	877					GRCh38	V40	ZRANB2_27_BGHLV14-72/Aligned.sortedByCoord.out.bam		ENCORE2	14215
ZRANB2_27_BGHLV14-72_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	877					GRCh38	V40	ZRANB2_27_BGHLV14-72_GTTTCG_L008_R1_001.fastq.gz,ZRANB2_27_BGHLV14-72_GTTTCG_L008_R2_001.fastq.gz		ENCORE2	14277