ZNF622 RNA-Seq in HepG2

General Information


RBP	ZNF622
Cell_Line	HepG2
Method	shRNA
Exp_Name	ZNF622-BGHLV33-HepG2
ENCODE_series_ID	ENCSR552VEM
Batch_ID	BGHLV33
Pool ID	Pool-160912
Local_Set_Name	set33
ENCODE_KD_Exp_ID	ENCSR518JXY
ENCODE_CN_Exp_ID	ENCSR691IVR
Rep1	ZNF622_BGHLV33-47
Rep2	ZNF622_BGHLV33-48
CN1	NT_BGHLV33-1
CN2	NT_BGHLV33-2
Rep1_qPCR	77.7
Rep2_qPCR	76.9
Rep1_WB	68.7
Rep2_WB	68.1
Antibody Cat#	A304-075A
Antibody Lot#	A304-075A
Antibody DCC ID	ENCAB041OEQ
Status	Released
Project	ENCODE3
ID	720

Experiment Information (Status: Released)

	BGHLV33-47	BGHLV33-48
idx	855	856
TRCN#_or_BGC#	TRCN0000160244	TRCN0000160244
shRNA_or_gRNA_sequence	CAGTATGTCCAAAGGATGAAA	CAGTATGTCCAAAGGATGAAA
PAM
Name	ZNF622	ZNF622
Sample_ID	BGHLV33-47	BGHLV33-48
transduction_Date	11/17/2015	11/17/2015
days
RBP_name	ZNF622	ZNF622
qPCR_result	77.7	76.9
Ave_qPCR	77.3
RT-qPCR_primer-F	gctcacatgaccaaagacca
RT-qPCR_primer-R	aagcaaatcttgccaacacc
protein_conc	5229	4539
WB_result	68.7	68.1
Ave_WB	68.4
WB_DONE_date	3/3/2016
MW	54kDa	WES
IP	1	1
antibody_Cat#	A304-075A	A304-075A
Antibody DCC ID	ENCAB041OEQ	ENCAB041OEQ
submitted_to_DCC_date	3/8/2016
Rep1_TPM	39	0
Rep2_TPM	41.7	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	2944	2945

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ZNF622	Product_ID: A304-075A Lot_ID: 1 Source: Bethyl Labs Target Name: ZNF622-human

Experiment Status

	BGHLV33-47	BGHLV33-48
Sample_ID	BGHLV33-47	BGHLV33-48
Sample Name	ZNF622_BGHLV33-47	ZNF622_BGHLV33-48
Sample Name	ZNF622_BGHLV33-47	ZNF622_BGHLV33-48
RBP	ZNF622	ZNF622
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1227	1228

Library-Prep
Sequencing

Library-Prep Information

	BGHLV33-47	BGHLV33-48
Sample #
Sample Name	ZNF622-BGHLV33-47	ZNF622-BGHLV33-48
Sample_Name_Alias	ZNF622_BGHLV33-47	ZNF622_BGHLV33-48
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set2/A1.png	DNA_Library_LV33-34-25B-32/set1/D2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/A4.png	RNA_Library_LV32-33-34/set1/B4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV33-47	BGHLV33-48
RBP	ZNF622	ZNF622
Batch_ID	BGHLV33	BGHLV33
WB_result	68.700	68.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2912	2913

Sequencing Information

	BGHLV33-47	BGHLV33-48
Sample_ID	BGHLV33-47	BGHLV33-48
Sample Name	ZNF622_BGHLV33-47	ZNF622_BGHLV33-48
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set33	set33
total_reads	98,583,292	98,233,088
total_aligned_reads	81,793,232	81,232,802
unique_aligned_reads	77,227,692	76,588,246
percent_uniqueAligned	0.78338	0.77966
correlation_replicates	0.999417	0.999417
spikein_reads	213,416	206,452
percent_spikeins	0.00216	0.00210
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1561	1562

Data Submission Information

	BGHLV33-47	BGHLV33-47
ENCODE_alias	brenton-graveley:ZNF622_BGHLV33	brenton-graveley:ZNF622-BGHLV33-HepG2
ENCODE_accession	ENCSR518JXY	ENCSR552VEM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV33-47	BGHLV33-47
Sample Name	ZNF622_BGHLV33-47	ZNF622_BGHLV33-47
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3153	7054

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
ZNF622_BGHLV33-47_GTGGCC_L002_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1561	HiSeq2500	100	paired-ended	1				NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE3	21436
ZNF622_BGHLV33-47_GTGGCC_L002_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1561	HiSeq2500	100	paired-ended	2				NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE3	21448
ZNF622_BGHLV33-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1561					GRCh38	V40	ZNF622_BGHLV33-47_GTGGCC_L002_001.R1.fastq.gz,ZNF622_BGHLV33-47_GTGGCC_L002_001.R2.fastq.gz		ENCORE2	21460
ZNF622_BGHLV33-47_Signal.Unique.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1561					GRCh38	V40	ZNF622_BGHLV33-47/Aligned.sortedByCoord.out.bam		ENCORE2	21472
ZNF622_BGHLV33-47_Signal.Unique.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1561					GRCh38	V40	ZNF622_BGHLV33-47/Aligned.sortedByCoord.out.bam		ENCORE2	21484
ZNF622_BGHLV33-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1561					GRCh38	V40	ZNF622_BGHLV33-47/Aligned.sortedByCoord.out.bam		ENCORE2	21496
ZNF622_BGHLV33-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1561					GRCh38	V40	ZNF622_BGHLV33-47/Aligned.sortedByCoord.out.bam		ENCORE2	21508
ZNF622_BGHLV33-47_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1561					GRCh38	V40	ZNF622_BGHLV33-47_GTGGCC_L002_001.R1.fastq.gz,ZNF622_BGHLV33-47_GTGGCC_L002_001.R2.fastq.gz		ENCORE2	21520
ZNF622_BGHLV33-48_GTTTCG_L002_001.R1.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1562	HiSeq2500	100	paired-ended	1				NT_BGHLV33-1_GATCAG_L001_001.R1.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R1.fastq.gz	ENCODE3	21437
ZNF622_BGHLV33-48_GTTTCG_L002_001.R2.fastq.gz	ENCODE_DATA/set33/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1562	HiSeq2500	100	paired-ended	2				NT_BGHLV33-1_GATCAG_L001_001.R2.fastq.gz,NT_BGHLV33-2_TAGCTT_L001_001.R2.fastq.gz	ENCODE3	21449
ZNF622_BGHLV33-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1562					GRCh38	V40	ZNF622_BGHLV33-48_GTTTCG_L002_001.R1.fastq.gz,ZNF622_BGHLV33-48_GTTTCG_L002_001.R2.fastq.gz		ENCORE2	21461
ZNF622_BGHLV33-48_Signal.Unique.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1562					GRCh38	V40	ZNF622_BGHLV33-48/Aligned.sortedByCoord.out.bam		ENCORE2	21473
ZNF622_BGHLV33-48_Signal.Unique.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1562					GRCh38	V40	ZNF622_BGHLV33-48/Aligned.sortedByCoord.out.bam		ENCORE2	21485
ZNF622_BGHLV33-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1562					GRCh38	V40	ZNF622_BGHLV33-48/Aligned.sortedByCoord.out.bam		ENCORE2	21497
ZNF622_BGHLV33-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set33/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1562					GRCh38	V40	ZNF622_BGHLV33-48/Aligned.sortedByCoord.out.bam		ENCORE2	21509
ZNF622_BGHLV33-48_quant.sf	ENCODE_DATA/set33/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1562					GRCh38	V40	ZNF622_BGHLV33-48_GTTTCG_L002_001.R1.fastq.gz,ZNF622_BGHLV33-48_GTTTCG_L002_001.R2.fastq.gz		ENCORE2	21521