ZNF106 RNA-Seq in K562

General Information


RBP	ZNF106
Cell_Line	K562
Method	CRISPR
Exp_Name	ZNF106-BGKcLV08-K562
ENCODE_series_ID	ENCSR862FZI
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR660WRQ
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	ZFP106-BGKcLV08-87
Rep2	ZFP106-BGKcLV08-88
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	65.4
Rep2_qPCR	72.0
Rep1_WB	96.7
Rep2_WB	96.7
Antibody Cat#	A301-527A
Antibody Lot#	A301-527A
Antibody DCC ID	ENCAB444XHD
Status	Released
Project	ENCODE4
ID	213

Experiment Information (Status: Released)

	BGKcLV08-87	BGKcLV08-88
idx	308	309
TRCN#_or_BGC#	BGC#0000164	BGC#0000164
shRNA_or_gRNA_sequence	CAGCCCTTTCACCTGTTCGG	CAGCCCTTTCACCTGTTCGG
PAM	AGG	AGG
Name	ZFP106-88F	ZFP106-88F
Sample_ID	BGKcLV08-87	BGKcLV08-88
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	ZNF106	ZNF106
qPCR_result	65.4	72.0
Ave_qPCR	68.7
RT-qPCR_primer-F	ctcagactgtgatctcctcca
RT-qPCR_primer-R	agcttccttctgtgggttca
protein_conc	2383	2331
WB_result	96.7	96.7
Ave_WB	96.7
WB_DONE_date	3/14/18	wes
MW	269kDa
IP	1IP	1IP
antibody_Cat#	A301-527A	A301-527A
Antibody DCC ID	ENCAB444XHD
submitted_to_DCC_date	9/6/18
Rep1_TPM	17.2	0
Rep2_TPM	12.3	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4408	4409

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

	BGKcLV08-87	BGKcLV08-88
Sample_ID	BGKcLV08-87	BGKcLV08-88
Sample Name
Sample Name	ZFP106-BGKcLV08-87	ZFP106-BGKcLV08-88
RBP	ZNF106	ZNF106
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6197	6198

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-87	BGKcLV08-88
Sample #	33	34
Sample Name	ZNF106-BGKcLV08-87	ZNF106-BGKcLV08-88
Sample_Name_Alias	ZFP106-BGKcLV08-87	ZFP106-BGKcLV08-88
Index Well Position	A05	B05
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	274	286
Peak_Molarity	85.90	68.20
libSampleQC_DNA_Well	DNA_Library_set41/set2/A5.png	DNA_Library_set41/set2/B5.png
RIN	9.0	9.6
libSample_RNA_Well	RNA_Library_set41/set1/A5.png	RNA_Library_set41/set1/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-87	BGKcLV08-88
RBP	ZNF106	ZNF106
Batch_ID	BGKcLV08	BGKcLV08
WB_result	96.700	96.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	883	884

Sequencing Information

	BGKcLV08-87	BGKcLV08-88
Sample_ID	BGKcLV08-87	BGKcLV08-88
Sample Name	ZFP106-BGKcLV08-87	ZFP106-BGKcLV08-88
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	133,775,276	93,697,762
total_aligned_reads	130,989,882	89,864,430
unique_aligned_reads	117,878,376	80,901,942
percent_uniqueAligned	0.88117	0.86344
correlation_replicates	0.996744	0.996744
spikein_reads	238,624	155,448
percent_spikeins	0.00178	0.00166
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	289	290

Data Submission Information

	BGKcLV08-87	BGKcLV08-87	BGKcLV08-87	BGKcLV08-87	BGKcLV08-87	BGKcLV08-87	BGKcLV08-88	BGKcLV08-88	BGKcLV08-88	BGKcLV08-88
ENCODE_alias	brenton-graveley:ZFP106-BGKcLV08	brenton-graveley:ZFP106-BGKcLV08-87	brenton-graveley:L-ZFP106-BGKcLV08-87	brenton-graveley:ZFP106-BGKcLV08-87_TACCGAGG+CCTGAACT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZFP106-BGKcLV08-87_TACCGAGG+CCTGAACT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF106-BGKcLV08-K562	brenton-graveley:ZFP106-BGKcLV08-88	brenton-graveley:L-ZFP106-BGKcLV08-88	brenton-graveley:ZFP106-BGKcLV08-88_CGTTAGAA+TTCAGGTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZFP106-BGKcLV08-88_CGTTAGAA+TTCAGGTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR660WRQ	ENCBS087MOX	ENCLB647YIO	ENCFF494HST	ENCFF226HVF	ENCSR862FZI	ENCBS132FUX	ENCLB207CPD	ENCFF088FOU	ENCFF101GPO
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	BGKcLV08-87	BGKcLV08-87	BGKcLV08-87	BGKcLV08-87	BGKcLV08-87	BGKcLV08-87	BGKcLV08-88	BGKcLV08-88	BGKcLV08-88	BGKcLV08-88
Sample Name	ZFP106-BGKcLV08-87	ZFP106-BGKcLV08-87	ZFP106-BGKcLV08-87	ZFP106-BGKcLV08-87	ZFP106-BGKcLV08-87	ZFP106-BGKcLV08-87	ZFP106-BGKcLV08-88	ZFP106-BGKcLV08-88	ZFP106-BGKcLV08-88	ZFP106-BGKcLV08-88
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-BGKcLV08-87.pdf	L-ZFP106-BGKcLV08-87.pdf				ZFP106-BGKcLV08-88.pdf	L-ZFP106-BGKcLV08-88.pdf
ID	1149	1218	1288	1358	1428	7369	1219	1289	1359	1429

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-BGKcLV08-87_TACCGAGG+CCTGAACT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	289				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	565
ZFP106-BGKcLV08-87_TACCGAGG+CCTGAACT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	289				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	635
ZFP106-BGKcLV08-87_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	289	GRCh38	V40	ZFP106-BGKcLV08-87_TACCGAGG+CCTGAACT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZFP106-BGKcLV08-87_TACCGAGG+CCTGAACT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26803
ZFP106-BGKcLV08-87_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	289	GRCh38	V40	ZFP106-BGKcLV08-87/Aligned.sortedByCoord.out.bam		ENCORE2	26873
ZFP106-BGKcLV08-87_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	289	GRCh38	V40	ZFP106-BGKcLV08-87/Aligned.sortedByCoord.out.bam		ENCORE2	26943
ZFP106-BGKcLV08-87_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	289	GRCh38	V40	ZFP106-BGKcLV08-87/Aligned.sortedByCoord.out.bam		ENCORE2	27013
ZFP106-BGKcLV08-87_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	289	GRCh38	V40	ZFP106-BGKcLV08-87/Aligned.sortedByCoord.out.bam		ENCORE2	27083
ZFP106-BGKcLV08-87_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	289	GRCh38	V40	ZFP106-BGKcLV08-87_TACCGAGG+CCTGAACT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZFP106-BGKcLV08-87_TACCGAGG+CCTGAACT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27153
ZFP106-BGKcLV08-88_CGTTAGAA+TTCAGGTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	290				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	566
ZFP106-BGKcLV08-88_CGTTAGAA+TTCAGGTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	290				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	636
ZFP106-BGKcLV08-88_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	290	GRCh38	V40	ZFP106-BGKcLV08-88_CGTTAGAA+TTCAGGTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZFP106-BGKcLV08-88_CGTTAGAA+TTCAGGTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26804
ZFP106-BGKcLV08-88_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	290	GRCh38	V40	ZFP106-BGKcLV08-88/Aligned.sortedByCoord.out.bam		ENCORE2	26874
ZFP106-BGKcLV08-88_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	290	GRCh38	V40	ZFP106-BGKcLV08-88/Aligned.sortedByCoord.out.bam		ENCORE2	26944
ZFP106-BGKcLV08-88_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	290	GRCh38	V40	ZFP106-BGKcLV08-88/Aligned.sortedByCoord.out.bam		ENCORE2	27014
ZFP106-BGKcLV08-88_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	290	GRCh38	V40	ZFP106-BGKcLV08-88/Aligned.sortedByCoord.out.bam		ENCORE2	27084
ZFP106-BGKcLV08-88_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	290	GRCh38	V40	ZFP106-BGKcLV08-88_CGTTAGAA+TTCAGGTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZFP106-BGKcLV08-88_CGTTAGAA+TTCAGGTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27154