NIP7 RNA-Seq in HepG2

General Information


RBP	NIP7
Cell_Line	HepG2
Method	shRNA
Exp_Name	NIP7-BGHLV18-HepG2
ENCODE_series_ID	ENCSR026YCJ
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR696LLZ
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	NIP7_BGHLV18_29
Rep2	NIP7_BGHLV18_30
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	62.2
Rep2_qPCR	56.7
Rep1_WB	9.4
Rep2_WB	0.0
Antibody Cat#	A303-974A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB696XOD
Status	Archived
Project	ENCODE3
ID	452

Experiment Information (Status: Released)

	BGHLV18-29	BGHLV18-30
idx	329	330
TRCN#_or_BGC#	TRCN0000142914	TRCN0000142914
shRNA_or_gRNA_sequence	CTGGATTACCTTGCACCTTAT	CTGGATTACCTTGCACCTTAT
PAM
Name	NIP7	NIP7
Sample_ID	BGHLV18-29	BGHLV18-30
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	NIP7	NIP7
qPCR_result	62.2	56.7
Ave_qPCR	59.4
RT-qPCR_primer-F	gaggagacccgtgtcatgtt
RT-qPCR_primer-R	cggaaacagtaggtgccatc
protein_conc	4731	4484
WB_result	9.4	0.0
Ave_WB	4.7
WB_DONE_date	1/20/2015
MW	20kDa
IP	1	1
antibody_Cat#	A303-974A	A303-974A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	22.7	0
Rep2_TPM	19	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2394	2395

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV18-29	BGHLV18-30
Sample_ID	BGHLV18-29	BGHLV18-30
Sample Name	NIP7_BGHLV18_29	NIP7_BGHLV18_30
Sample Name	NIP7_BGHLV18_29	NIP7_BGHLV18_30
RBP	NIP7	NIP7
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	632	633

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-29	BGHLV18-30
Sample #
Sample Name	NIP7-BGHLV18-29	NIP7-BGHLV18-30
Sample_Name_Alias	NIP7_BGHLV18_29	NIP7_BGHLV18_30
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C3.png	DNA_Library_LV18-19/set1/D3.png
RIN	9.3	9.3
libSample_RNA_Well	RNA_Library_LV18-19/set1/A10.png	RNA_Library_LV18-19/set1/B10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-29	BGHLV18-30
RBP	NIP7	NIP7
Batch_ID	BGHLV18	BGHLV18
WB_result	9.400	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2316	2317

Sequencing Information

	BGHLV18-29	BGHLV18-30
Sample_ID	BGHLV18-29	BGHLV18-30
Sample Name	NIP7_BGHLV18_29	NIP7_BGHLV18_30
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	45,730,000	44,470,000
total_aligned_reads	41,099,664	38,461,414
unique_aligned_reads	38,830,396	36,340,634
percent_uniqueAligned	0.84912	0.81719
correlation_replicates	0.997593	0.997593
spikein_reads	155,976	123,590
percent_spikeins	0.00341	0.00278
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	958	959

Data Submission Information

	BGHLV18-29	BGHLV18-29
ENCODE_alias	brenton-graveley:NIP7_BGHLV18	brenton-graveley:NIP7-BGHLV18-HepG2
ENCODE_accession	ENCSR696LLZ	ENCSR026YCJ
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-29	BGHLV18-29
Sample Name	NIP7_BGHLV18_29	NIP7_BGHLV18_29
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2833	6823

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_BGHLV18_29_GTGGCC_L003_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	958	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14806
NIP7_BGHLV18_29_GTGGCC_L003_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	958	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14844
NIP7_BGHLV18_29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	958					GRCh38	V40	NIP7_BGHLV18_29_GTGGCC_L003_R1_001.fastq.gz,NIP7_BGHLV18_29_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	14882
NIP7_BGHLV18_29_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	958					GRCh38	V40	NIP7_BGHLV18_29/Aligned.sortedByCoord.out.bam		ENCORE2	14920
NIP7_BGHLV18_29_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	958					GRCh38	V40	NIP7_BGHLV18_29/Aligned.sortedByCoord.out.bam		ENCORE2	14958
NIP7_BGHLV18_29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	958					GRCh38	V40	NIP7_BGHLV18_29/Aligned.sortedByCoord.out.bam		ENCORE2	14996
NIP7_BGHLV18_29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	958					GRCh38	V40	NIP7_BGHLV18_29/Aligned.sortedByCoord.out.bam		ENCORE2	15034
NIP7_BGHLV18_29_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	958					GRCh38	V40	NIP7_BGHLV18_29_GTGGCC_L003_R1_001.fastq.gz,NIP7_BGHLV18_29_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	15072
NIP7_BGHLV18_30_GTTTCG_L003_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	959	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14807
NIP7_BGHLV18_30_GTTTCG_L003_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	959	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14845
NIP7_BGHLV18_30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	959					GRCh38	V40	NIP7_BGHLV18_30_GTTTCG_L003_R1_001.fastq.gz,NIP7_BGHLV18_30_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	14883
NIP7_BGHLV18_30_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	959					GRCh38	V40	NIP7_BGHLV18_30/Aligned.sortedByCoord.out.bam		ENCORE2	14921
NIP7_BGHLV18_30_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	959					GRCh38	V40	NIP7_BGHLV18_30/Aligned.sortedByCoord.out.bam		ENCORE2	14959
NIP7_BGHLV18_30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	959					GRCh38	V40	NIP7_BGHLV18_30/Aligned.sortedByCoord.out.bam		ENCORE2	14997
NIP7_BGHLV18_30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	959					GRCh38	V40	NIP7_BGHLV18_30/Aligned.sortedByCoord.out.bam		ENCORE2	15035
NIP7_BGHLV18_30_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	959					GRCh38	V40	NIP7_BGHLV18_30_GTTTCG_L003_R1_001.fastq.gz,NIP7_BGHLV18_30_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	15073