NIP7 RNA-Seq in HepG2

General Information


RBP	NIP7
Cell_Line	HepG2
Method	CRISPR
Exp_Name	NIP7-BGHcLV09-HepG2
ENCODE_series_ID	ENCSR678GKV
Batch_ID	BGHcLV09
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR586YGD
ENCODE_CN_Exp_ID	ENCSR300EBW
Rep1	NIP7-BGHcLV09-5
Rep2	NIP7-BGHcLV09-6
CN1	NT-BGHcLV09-1
CN2	NT-BGHcLV09-2
Rep1_qPCR	82.8
Rep2_qPCR	82.7
Rep1_WB	70.7
Rep2_WB	75.5
Antibody Cat#	A303-974A
Antibody Lot#
Antibody DCC ID	ENCAB696XOD
Status	Released
Project	ENCODE4
ID	216

Experiment Information (Status: Released)

	BGHcLV09-5	BGHcLV09-6
idx	167	168
TRCN#_or_BGC#	BGC#0000195	BGC#0000195
shRNA_or_gRNA_sequence	GTTTCCGTCTGCACAACGAC	GTTTCCGTCTGCACAACGAC
PAM	CGG	CGG
Name	NIP7-91F	NIP7-91F
Sample_ID	BGHcLV09-5	BGHcLV09-6
transduction_Date	4/20/18	4/20/18
days	D6	D6
RBP_name	NIP7	NIP7
qPCR_result	82.8	82.7
Ave_qPCR	82.8
RT-qPCR_primer-F	cacaacgaccgggtgtacta
RT-qPCR_primer-R	gtgacgtgcaaccgaaactt
protein_conc	4776	5174
WB_result	70.7	75.5
Ave_WB	73.1
WB_DONE_date	4/27/18
MW	20kDa
IP	1
antibody_Cat#	A303-974A
Antibody DCC ID	ENCAB696XOD
submitted_to_DCC_date	9/6/18
Rep1_TPM	40	0
Rep2_TPM	69	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6310	6311

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

	BGHcLV09-5	BGHcLV09-6
Sample_ID	BGHcLV09-5	BGHcLV09-6
Sample Name
Sample Name	NIP7-BGHcLV09-5	NIP7-BGHcLV09-6
RBP	NIP7	NIP7
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6259	6260

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV09-5	BGHcLV09-6
Sample #	41	42
Sample Name	NIP7-BGHcLV09-5	NIP7-BGHcLV09-6
Sample_Name_Alias
Index Well Position	E06	F06
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	270	269
Peak_Molarity	61.40	46.20
libSampleQC_DNA_Well	DNA_Library_set41/set5/E6.png	DNA_Library_set41/set4/H10.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set41/set1/A6.png	RNA_Library_set41/set1/B6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV09-5	BGHcLV09-6
RBP	NIP7	NIP7
Batch_ID	BGHcLV09	BGHcLV09
WB_result	70.700	75.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	891	892

Sequencing Information

	BGHcLV09-5	BGHcLV09-6
Sample_ID	BGHcLV09-5	BGHcLV09-6
Sample Name	NIP7-BGHcLV09-5	NIP7-BGHcLV09-6
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	213,264,444	140,027,470
total_aligned_reads	207,930,466	137,435,026
unique_aligned_reads	192,113,718	127,324,036
percent_uniqueAligned	0.90082	0.90928
correlation_replicates	0.996331	0.996331
spikein_reads	137,660	96,726
percent_spikeins	0.00065	0.00069
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	297	298

Data Submission Information

	BGHcLV09-5	BGHcLV09-5	BGHcLV09-5	BGHcLV09-5	BGHcLV09-5	BGHcLV09-5	BGHcLV09-6	BGHcLV09-6	BGHcLV09-6	BGHcLV09-6
ENCODE_alias	brenton-graveley:NIP7-BGHcLV09	brenton-graveley:NIP7-BGHcLV09-5	brenton-graveley:L-NIP7-BGHcLV09-5	brenton-graveley:NIP7-BGHcLV09-5_ATGGCATG+AAGGTACC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NIP7-BGHcLV09-5_ATGGCATG+AAGGTACC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NIP7-BGHcLV09-HepG2	brenton-graveley:NIP7-BGHcLV09-6	brenton-graveley:L-NIP7-BGHcLV09-6	brenton-graveley:NIP7-BGHcLV09-6_GCAATGCA+GGAACGTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NIP7-BGHcLV09-6_GCAATGCA+GGAACGTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR586YGD	ENCBS386GOB	ENCLB193USD	ENCFF074YHQ	ENCFF405MOJ	ENCSR678GKV	ENCBS020ARY	ENCLB963FVX	ENCFF632ZUK	ENCFF562IPO
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	BGHcLV09-5	BGHcLV09-5	BGHcLV09-5	BGHcLV09-5	BGHcLV09-5	BGHcLV09-5	BGHcLV09-6	BGHcLV09-6	BGHcLV09-6	BGHcLV09-6
Sample Name	NIP7-BGHcLV09-5	NIP7-BGHcLV09-5	NIP7-BGHcLV09-5	NIP7-BGHcLV09-5	NIP7-BGHcLV09-5	NIP7-BGHcLV09-5	NIP7-BGHcLV09-6	NIP7-BGHcLV09-6	NIP7-BGHcLV09-6	NIP7-BGHcLV09-6
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		NIP7-BGHcLV09-5.pdf	L-NIP7-BGHcLV09-5.pdf				NIP7-BGHcLV09-6.pdf	L-NIP7-BGHcLV09-6.pdf
ID	1131	1182	1252	1322	1423	7266	1183	1253	1323	1424

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
NIP7-BGHcLV09-5_ATGGCATG+AAGGTACC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	297				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	529
NIP7-BGHcLV09-5_ATGGCATG+AAGGTACC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	297				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	599
NIP7-BGHcLV09-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	297	GRCh38	V40	NIP7-BGHcLV09-5_ATGGCATG+AAGGTACC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NIP7-BGHcLV09-5_ATGGCATG+AAGGTACC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26767
NIP7-BGHcLV09-5_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	297	GRCh38	V40	NIP7-BGHcLV09-5/Aligned.sortedByCoord.out.bam		ENCORE2	26837
NIP7-BGHcLV09-5_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	297	GRCh38	V40	NIP7-BGHcLV09-5/Aligned.sortedByCoord.out.bam		ENCORE2	26907
NIP7-BGHcLV09-5_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	297	GRCh38	V40	NIP7-BGHcLV09-5/Aligned.sortedByCoord.out.bam		ENCORE2	26977
NIP7-BGHcLV09-5_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	297	GRCh38	V40	NIP7-BGHcLV09-5/Aligned.sortedByCoord.out.bam		ENCORE2	27047
NIP7-BGHcLV09-5_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	297	GRCh38	V40	NIP7-BGHcLV09-5_ATGGCATG+AAGGTACC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NIP7-BGHcLV09-5_ATGGCATG+AAGGTACC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27117
NIP7-BGHcLV09-6_GCAATGCA+GGAACGTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	298				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	530
NIP7-BGHcLV09-6_GCAATGCA+GGAACGTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	298				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	600
NIP7-BGHcLV09-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	298	GRCh38	V40	NIP7-BGHcLV09-6_GCAATGCA+GGAACGTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NIP7-BGHcLV09-6_GCAATGCA+GGAACGTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26768
NIP7-BGHcLV09-6_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	298	GRCh38	V40	NIP7-BGHcLV09-6/Aligned.sortedByCoord.out.bam		ENCORE2	26838
NIP7-BGHcLV09-6_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	298	GRCh38	V40	NIP7-BGHcLV09-6/Aligned.sortedByCoord.out.bam		ENCORE2	26908
NIP7-BGHcLV09-6_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	298	GRCh38	V40	NIP7-BGHcLV09-6/Aligned.sortedByCoord.out.bam		ENCORE2	26978
NIP7-BGHcLV09-6_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	298	GRCh38	V40	NIP7-BGHcLV09-6/Aligned.sortedByCoord.out.bam		ENCORE2	27048
NIP7-BGHcLV09-6_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	298	GRCh38	V40	NIP7-BGHcLV09-6_GCAATGCA+GGAACGTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NIP7-BGHcLV09-6_GCAATGCA+GGAACGTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27118