ZNF106 RNA-Seq in HepG2

General Information


RBP	ZNF106
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ZNF106-BGHcLV10-HepG2
ENCODE_series_ID	ENCSR621WNM
Batch_ID	BGHcLV10
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR636DVA
ENCODE_CN_Exp_ID	ENCSR775ZWO
Rep1	ZFP106-BGHcLV10-55
Rep2	ZFP106-BGHcLV10-56
CN1	NT-BGHcLV10-1
CN2	NT-BGHcLV10-2
Rep1_qPCR	48.7
Rep2_qPCR	55.8
Rep1_WB	96.7
Rep2_WB	96.6
Antibody Cat#	A301-527A
Antibody Lot#
Antibody DCC ID	ENCAB444XHD
Status	Released
Project	ENCODE4
ID	229

Experiment Information (Status: Released)

	BGHcLV10-55	BGHcLV10-56
idx	252	253
TRCN#_or_BGC#	BGC#0000164	BGC#0000164
shRNA_or_gRNA_sequence	CAGCCCTTTCACCTGTTCGG	CAGCCCTTTCACCTGTTCGG
PAM	AGG	AGG
Name	ZFP106-88	ZFP106-88
Sample_ID	BGHcLV10-55	BGHcLV10-56
transduction_Date	4/27/18	4/27/18
days	D6	D6
RBP_name	ZNF106	ZNF106
qPCR_result	48.7	55.8
Ave_qPCR	52.3
RT-qPCR_primer-F	tcttctcctgaactcccaagtc
RT-qPCR_primer-R	attcagcagctggtcaacct
protein_conc	2339	2391
WB_result	96.7	96.6
Ave_WB	96.6
WB_DONE_date	5/24/18	wes
MW	269kDa
IP
antibody_Cat#	A301-527A
Antibody DCC ID	ENCAB444XHD
submitted_to_DCC_date	9/6/18
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	8443	8444

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ZNF106	Product_ID: A301-527A Lot_ID: 1 Source: Bethyl Labs Target Name: ZNF106-human

Experiment Status

	BGHcLV10-55	BGHcLV10-56
Sample_ID	BGHcLV10-55	BGHcLV10-56
Sample Name
Sample Name	ZFP106-BGHcLV10-55	ZFP106-BGHcLV10-56
RBP	ZNF106	ZNF106
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6309	6310

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV10-55	BGHcLV10-56
Sample #	69	70
Sample Name	ZNF106-BGHcLV10-55	ZNF106-BGHcLV10-56
Sample_Name_Alias	ZFP106-BGHcLV10-55	ZFP106-BGHcLV10-56
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	281	283
Peak_Molarity	50.60	49.20
libSampleQC_DNA_Well	DNA_Library_set41/set5/A10.png	DNA_Library_set41/set5/B10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set41/set1/E9.png	RNA_Library_set41/set1/F9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV10-55	BGHcLV10-56
RBP	ZNF106	ZNF106
Batch_ID	BGHcLV10	BGHcLV10
WB_result	96.700	96.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	919	920

Sequencing Information

	BGHcLV10-55	BGHcLV10-56
Sample_ID	BGHcLV10-55	BGHcLV10-56
Sample Name	ZFP106-BGHcLV10-55	ZFP106-BGHcLV10-56
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	91,795,168	110,732,734
total_aligned_reads	88,039,746	102,850,586
unique_aligned_reads	82,149,150	96,224,128
percent_uniqueAligned	0.89492	0.86898
correlation_replicates	0.992583	0.992583
spikein_reads	183,082	304,116
percent_spikeins	0.00199	0.00275
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	325	326

Data Submission Information

	BGHcLV10-55	BGHcLV10-55	BGHcLV10-55	BGHcLV10-55	BGHcLV10-55	BGHcLV10-55	BGHcLV10-56	BGHcLV10-56	BGHcLV10-56	BGHcLV10-56
ENCODE_alias	brenton-graveley:ZFP106-BGHcLV10	brenton-graveley:ZFP106-BGHcLV10-55	brenton-graveley:L-ZFP106-BGHcLV10-55	brenton-graveley:ZFP106-BGHcLV10-55_TCGTAGTG+AGACTTGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZFP106-BGHcLV10-55_TCGTAGTG+AGACTTGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF106-BGHcLV10-HepG2	brenton-graveley:ZFP106-BGHcLV10-56	brenton-graveley:L-ZFP106-BGHcLV10-56	brenton-graveley:ZFP106-BGHcLV10-56_CTACGACA+GAGTCCAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZFP106-BGHcLV10-56_CTACGACA+GAGTCCAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR636DVA	ENCBS611UOT	ENCLB775QSN	ENCFF096AGI	ENCFF765STJ	ENCSR621WNM	ENCBS542LFH	ENCLB225FWQ	ENCFF326ACB	ENCFF662NRV
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV10-55	BGHcLV10-55	BGHcLV10-55	BGHcLV10-55	BGHcLV10-55	BGHcLV10-55	BGHcLV10-56	BGHcLV10-56	BGHcLV10-56	BGHcLV10-56
Sample Name	ZFP106-BGHcLV10-55	ZFP106-BGHcLV10-55	ZFP106-BGHcLV10-55	ZFP106-BGHcLV10-55	ZFP106-BGHcLV10-55	ZFP106-BGHcLV10-55	ZFP106-BGHcLV10-56	ZFP106-BGHcLV10-56	ZFP106-BGHcLV10-56	ZFP106-BGHcLV10-56
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		ZFP106-BGHcLV10-55.pdf	L-ZFP106-BGHcLV10-55.pdf				ZFP106-BGHcLV10-56.pdf	L-ZFP106-BGHcLV10-56.pdf
ID	1148	1216	1286	1356	1420	7368	1217	1287	1357	1427

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
ZFP106-BGHcLV10-55_TCGTAGTG+AGACTTGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	325				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	563
ZFP106-BGHcLV10-55_TCGTAGTG+AGACTTGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	325				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	633
ZFP106-BGHcLV10-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	325	GRCh38	V40	ZFP106-BGHcLV10-55_TCGTAGTG+AGACTTGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZFP106-BGHcLV10-55_TCGTAGTG+AGACTTGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26801
ZFP106-BGHcLV10-55_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	325	GRCh38	V40	ZFP106-BGHcLV10-55/Aligned.sortedByCoord.out.bam		ENCORE2	26871
ZFP106-BGHcLV10-55_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	325	GRCh38	V40	ZFP106-BGHcLV10-55/Aligned.sortedByCoord.out.bam		ENCORE2	26941
ZFP106-BGHcLV10-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	325	GRCh38	V40	ZFP106-BGHcLV10-55/Aligned.sortedByCoord.out.bam		ENCORE2	27011
ZFP106-BGHcLV10-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	325	GRCh38	V40	ZFP106-BGHcLV10-55/Aligned.sortedByCoord.out.bam		ENCORE2	27081
ZFP106-BGHcLV10-55_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	325	GRCh38	V40	ZFP106-BGHcLV10-55_TCGTAGTG+AGACTTGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZFP106-BGHcLV10-55_TCGTAGTG+AGACTTGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27151
ZFP106-BGHcLV10-56_CTACGACA+GAGTCCAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	326				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	564
ZFP106-BGHcLV10-56_CTACGACA+GAGTCCAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	326				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	634
ZFP106-BGHcLV10-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	326	GRCh38	V40	ZFP106-BGHcLV10-56_CTACGACA+GAGTCCAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZFP106-BGHcLV10-56_CTACGACA+GAGTCCAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26802
ZFP106-BGHcLV10-56_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	326	GRCh38	V40	ZFP106-BGHcLV10-56/Aligned.sortedByCoord.out.bam		ENCORE2	26872
ZFP106-BGHcLV10-56_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	326	GRCh38	V40	ZFP106-BGHcLV10-56/Aligned.sortedByCoord.out.bam		ENCORE2	26942
ZFP106-BGHcLV10-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	326	GRCh38	V40	ZFP106-BGHcLV10-56/Aligned.sortedByCoord.out.bam		ENCORE2	27012
ZFP106-BGHcLV10-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	326	GRCh38	V40	ZFP106-BGHcLV10-56/Aligned.sortedByCoord.out.bam		ENCORE2	27082
ZFP106-BGHcLV10-56_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	326	GRCh38	V40	ZFP106-BGHcLV10-56_CTACGACA+GAGTCCAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZFP106-BGHcLV10-56_CTACGACA+GAGTCCAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27152