NIP7 RNA-Seq in K562

General Information


RBP	NIP7
Cell_Line	K562
Method	CRISPR
Exp_Name	NIP7-BGKcLV11-K562
ENCODE_series_ID	ENCSR504ORI
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR499IQB
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	NIP7-BGKcLV11-67
Rep2	NIP7-BGKcLV11-68
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	31.6
Rep2_qPCR	38.5
Rep1_WB	86.9
Rep2_WB	92.9
Antibody Cat#	A303-974A
Antibody Lot#
Antibody DCC ID	ENCAB696XOD
Status	Released
Project	ENCODE4
ID	180

Experiment Information (Status: Released)

	BGKcLV11-67	BGKcLV11-68
idx	383	384
TRCN#_or_BGC#	BGC#0000195	BGC#0000195
shRNA_or_gRNA_sequence	GTTTCCGTCTGCACAACGAC	GTTTCCGTCTGCACAACGAC
PAM	CGG	CGG
Name	NIP7_91F	NIP7_91F
Sample_ID	BGKcLV11-67	BGKcLV11-68
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	NIP7	NIP7
qPCR_result	31.6	38.5
Ave_qPCR	35.1
RT-qPCR_primer-F	cacaacgaccgggtgtacta
RT-qPCR_primer-R	gtgacgtgcaaccgaaactt
protein_conc	2824	2621
WB_result	86.9	92.9
Ave_WB	89.9
WB_DONE_date	8/13/18
MW	20kDa
IP	1
antibody_Cat#	A303-974A
Antibody DCC ID	ENCAB696XOD
submitted_to_DCC_date	2/22/19
Rep1_TPM	52.3	0
Rep2_TPM	53.8	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4485	4486

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NIP7	Product_ID: A303-974A Lot_ID: 1 Source: Bethyl Labs Target Name: NIP7-human

Experiment Status

	BGKcLV11-67	BGKcLV11-68
Sample_ID	BGKcLV11-67	BGKcLV11-68
Sample Name	NIP7-BGKcLV11-67	NIP7-BGKcLV11-68
Sample Name	NIP7-BGKcLV11-67	NIP7-BGKcLV11-68
RBP	NIP7	NIP7
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2683	2684

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-67	BGKcLV11-68
Sample #	11	12
Sample Name	NIP7-BGKcLV11-67	NIP7-BGKcLV11-68
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	1-C2	1-D2
Tecan	37.08	50.34
Tecan_date	2019-03-13	2019-03-13
Size_bp	296	295
Peak_Molarity	87.70	191.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/C2.png	DNA_Library_set42/set1/D2.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set42/set1/C2.png	RNA_Library_set42/set1/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-67	BGKcLV11-68
RBP	NIP7	NIP7
Batch_ID	BGKcLV11	BGKcLV11
WB_result	86.900	92.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	11	12

Sequencing Information

	BGKcLV11-67	BGKcLV11-68
Sample_ID	BGKcLV11-67	BGKcLV11-68
Sample Name	NIP7-BGKcLV11-67	NIP7-BGKcLV11-68
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	94,310,332	50,617,498
total_aligned_reads	91,422,236	47,894,116
unique_aligned_reads	82,476,952	43,570,008
percent_uniqueAligned	0.87453	0.86077
correlation_replicates	0.996369	0.996369
spikein_reads	151,260	51,118
percent_spikeins	0.00160	0.00101
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	39	40

Data Submission Information

	BGKcLV11-67	BGKcLV11-67	BGKcLV11-67	BGKcLV11-67	BGKcLV11-67	BGKcLV11-67	BGKcLV11-68	BGKcLV11-68	BGKcLV11-68	BGKcLV11-68
ENCODE_alias	brenton-graveley:NIP7-BGKcLV11	brenton-graveley:NIP7-BGKcLV11-67	brenton-graveley:L-NIP7-BGKcLV11-67	brenton-graveley:NIP7-BGKcLV11-67_TCTCTACT+CGCGGTTC_HK3H2DSXX_S11_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NIP7-BGKcLV11-67_TCTCTACT+CGCGGTTC_HK3H2DSXX_S11_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NIP7-BGKcLV11-K562	brenton-graveley:NIP7-BGKcLV11-68	brenton-graveley:L-NIP7-BGKcLV11-68	brenton-graveley:NIP7-BGKcLV11-68_CTCTCGTC+TATAACCT_HK3H2DSXX_S12_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NIP7-BGKcLV11-68_CTCTCGTC+TATAACCT_HK3H2DSXX_S12_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR499IQB	ENCBS844FIG	ENCLB413ZWQ	ENCFF051ETK	ENCFF042XTF	ENCSR504ORI	ENCBS176ZST	ENCLB525SZD	ENCFF393PAE	ENCFF270CKE
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	BGKcLV11-67	BGKcLV11-67	BGKcLV11-67	BGKcLV11-67	BGKcLV11-67	BGKcLV11-67	BGKcLV11-68	BGKcLV11-68	BGKcLV11-68	BGKcLV11-68
Sample Name	NIP7-BGKcLV11-67	NIP7-BGKcLV11-67	NIP7-BGKcLV11-67	NIP7-BGKcLV11-67	NIP7-BGKcLV11-67	NIP7-BGKcLV11-67	NIP7-BGKcLV11-68	NIP7-BGKcLV11-68	NIP7-BGKcLV11-68	NIP7-BGKcLV11-68
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
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		NIP7-BGKcLV11-67.pdf	L-NIP7-BGKcLV11-67.pdf				NIP7-BGKcLV11-68.pdf	L-NIP7-BGKcLV11-68.pdf
ID	765	825	907	989	1071	7267	826	908	990	1072

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
NIP7-BGKcLV11-67_TCTCTACT+CGCGGTTC_HK3H2DSXX_S11_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	39	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	371
NIP7-BGKcLV11-67_TCTCTACT+CGCGGTTC_HK3H2DSXX_S11_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	39	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	453
NIP7-BGKcLV11-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	39					GRCh38	V40	NIP7-BGKcLV11-67_TCTCTACT+CGCGGTTC_HK3H2DSXX_S11_L004_R1_001.filtered.trimmed.paired.fastq.gz,NIP7-BGKcLV11-67_TCTCTACT+CGCGGTTC_HK3H2DSXX_S11_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23710
NIP7-BGKcLV11-67_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	39					GRCh38	V40	NIP7-BGKcLV11-67/Aligned.sortedByCoord.out.bam		ENCORE2	23792
NIP7-BGKcLV11-67_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	39					GRCh38	V40	NIP7-BGKcLV11-67/Aligned.sortedByCoord.out.bam		ENCORE2	23874
NIP7-BGKcLV11-67_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	39					GRCh38	V40	NIP7-BGKcLV11-67/Aligned.sortedByCoord.out.bam		ENCORE2	23956
NIP7-BGKcLV11-67_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	39					GRCh38	V40	NIP7-BGKcLV11-67/Aligned.sortedByCoord.out.bam		ENCORE2	24038
NIP7-BGKcLV11-67_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	39					GRCh38	V40	NIP7-BGKcLV11-67_TCTCTACT+CGCGGTTC_HK3H2DSXX_S11_L004_R1_001.filtered.trimmed.paired.fastq.gz,NIP7-BGKcLV11-67_TCTCTACT+CGCGGTTC_HK3H2DSXX_S11_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24120
NIP7-BGKcLV11-68_CTCTCGTC+TATAACCT_HK3H2DSXX_S12_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	40	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	372
NIP7-BGKcLV11-68_CTCTCGTC+TATAACCT_HK3H2DSXX_S12_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	40	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	454
NIP7-BGKcLV11-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	40					GRCh38	V40	NIP7-BGKcLV11-68_CTCTCGTC+TATAACCT_HK3H2DSXX_S12_L004_R1_001.filtered.trimmed.paired.fastq.gz,NIP7-BGKcLV11-68_CTCTCGTC+TATAACCT_HK3H2DSXX_S12_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23711
NIP7-BGKcLV11-68_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	40					GRCh38	V40	NIP7-BGKcLV11-68/Aligned.sortedByCoord.out.bam		ENCORE2	23793
NIP7-BGKcLV11-68_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	40					GRCh38	V40	NIP7-BGKcLV11-68/Aligned.sortedByCoord.out.bam		ENCORE2	23875
NIP7-BGKcLV11-68_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	40					GRCh38	V40	NIP7-BGKcLV11-68/Aligned.sortedByCoord.out.bam		ENCORE2	23957
NIP7-BGKcLV11-68_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	40					GRCh38	V40	NIP7-BGKcLV11-68/Aligned.sortedByCoord.out.bam		ENCORE2	24039
NIP7-BGKcLV11-68_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	40					GRCh38	V40	NIP7-BGKcLV11-68_CTCTCGTC+TATAACCT_HK3H2DSXX_S12_L004_R1_001.filtered.trimmed.paired.fastq.gz,NIP7-BGKcLV11-68_CTCTCGTC+TATAACCT_HK3H2DSXX_S12_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24121