NKRF RNA-Seq in HepG2

General Information


RBP	NKRF
Cell_Line	HepG2
Method	shRNA
Exp_Name	NKRF-BGHLV27-HepG2
ENCODE_series_ID	ENCSR224WRQ
Batch_ID	BGHLV27
Pool ID	Pool-151201
Local_Set_Name	set27
ENCODE_KD_Exp_ID	ENCSR517JDK
ENCODE_CN_Exp_ID	ENCSR246RRQ
Rep1	NKRF_BGHLV27-37
Rep2	NKRF_BGHLV27-38
CN1	non-target_BGHLV27-1
CN2	non-target_BGHLV27-2
Rep1_qPCR	66.5
Rep2_qPCR	61.6
Rep1_WB	54.6
Rep2_WB	48.9
Antibody Cat#	A304-016A
Antibody Lot#	A304-016A
Antibody DCC ID	ENCAB893CIV
Status	Released
Project	ENCODE3
ID	642

Experiment Information (Status: Released)

	BGHLV27-37	BGHLV27-38
idx	657	658
TRCN#_or_BGC#	TRCN0000016432	TRCN0000016432
shRNA_or_gRNA_sequence	CCAAGAGACATCTACCAAGAT	CCAAGAGACATCTACCAAGAT
PAM
Name	NKRF	NKRF
Sample_ID	BGHLV27-37	BGHLV27-38
transduction_Date	6/9/2015	6/9/2015
days
RBP_name	NKRF	NKRF
qPCR_result	66.5	61.6
Ave_qPCR	64.1
RT-qPCR_primer-F	ccaaaccttccaaaggtcaa
RT-qPCR_primer-R	gaggtctcgcatggaatttg
protein_conc	3988	4290
WB_result	54.6	48.9
Ave_WB	51.8
WB_DONE_date	9/9/2015
MW	78kDa
IP	1	1
antibody_Cat#	A304-016A	A304-016A
Antibody DCC ID	ENCAB893CIV	ENCAB893CIV
submitted_to_DCC_date	12/7/2015
Rep1_TPM	5.1	0
Rep2_TPM	6.3	0
Action
Library_start_date	9/28/2015	9/28/2015
repeat_library
Note	x	x
ID	2744	2745

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NKRF	Product_ID: A304-016A Lot_ID: 1 Source: Bethyl Labs Target Name: NKRF-human

Experiment Status

	BGHLV27-37	BGHLV27-38
Sample_ID	BGHLV27-37	BGHLV27-38
Sample Name	NKRF_BGHLV27-37	NKRF_BGHLV27-38
Sample Name	NKRF_BGHLV27-37	NKRF_BGHLV27-38
RBP	NKRF	NKRF
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	968	969

Library-Prep
Sequencing

Library-Prep Information

	BGHLV27-37	BGHLV27-38
Sample #
Sample Name	NKRF-BGHLV27-37	NKRF-BGHLV27-38
Sample_Name_Alias	NKRF_BGHLV27-37	NKRF_BGHLV27-38
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-28	2015-09-28
Lib_ID	Lib-150928	Lib-150928
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV27/set1/A2.png	DNA_Library_LV27/set1/B2.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/G6.png	RNA_Library_LV26-27-28-29/set1/B5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV27-37	BGHLV27-38
RBP	NKRF	NKRF
Batch_ID	BGHLV27	BGHLV27
WB_result	54.600	48.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2660	2661

Sequencing Information

	BGHLV27-37	BGHLV27-38
Sample_ID	BGHLV27-37	BGHLV27-38
Sample Name	NKRF_BGHLV27-37	NKRF_BGHLV27-38
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set27	set27
total_reads	71,220,402	79,297,136
total_aligned_reads	65,010,640	73,299,568
unique_aligned_reads	61,199,998	68,980,856
percent_uniqueAligned	0.85930	0.86990
correlation_replicates	0.994691	0.994691
spikein_reads	284,032	302,518
percent_spikeins	0.00399	0.00381
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1302	1303

Data Submission Information

	BGHLV27-37	BGHLV27-37
ENCODE_alias	brenton-graveley:NKRF_BGHLV27	brenton-graveley:NKRF-BGHLV27-HepG2
ENCODE_accession	ENCSR517JDK	ENCSR224WRQ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV27-37	BGHLV27-37
Sample Name	NKRF_BGHLV27-37	NKRF_BGHLV27-37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3031	6824

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
NKRF_BGHLV27-37_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1302	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20010
NKRF_BGHLV27-37_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1302	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20032
NKRF_BGHLV27-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1302					GRCh38	V40	NKRF_BGHLV27-37_1.fastq.gz,NKRF_BGHLV27-37_2.fastq.gz		ENCORE2	20054
NKRF_BGHLV27-37_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1302					GRCh38	V40	NKRF_BGHLV27-37/Aligned.sortedByCoord.out.bam		ENCORE2	20076
NKRF_BGHLV27-37_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1302					GRCh38	V40	NKRF_BGHLV27-37/Aligned.sortedByCoord.out.bam		ENCORE2	20098
NKRF_BGHLV27-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1302					GRCh38	V40	NKRF_BGHLV27-37/Aligned.sortedByCoord.out.bam		ENCORE2	20120
NKRF_BGHLV27-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1302					GRCh38	V40	NKRF_BGHLV27-37/Aligned.sortedByCoord.out.bam		ENCORE2	20142
NKRF_BGHLV27-37_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1302					GRCh38	V40	NKRF_BGHLV27-37_1.fastq.gz,NKRF_BGHLV27-37_2.fastq.gz		ENCORE2	20682
NKRF_BGHLV27-38_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1303	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20011
NKRF_BGHLV27-38_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1303	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20033
NKRF_BGHLV27-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1303					GRCh38	V40	NKRF_BGHLV27-38_1.fastq.gz,NKRF_BGHLV27-38_2.fastq.gz		ENCORE2	20055
NKRF_BGHLV27-38_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1303					GRCh38	V40	NKRF_BGHLV27-38/Aligned.sortedByCoord.out.bam		ENCORE2	20077
NKRF_BGHLV27-38_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1303					GRCh38	V40	NKRF_BGHLV27-38/Aligned.sortedByCoord.out.bam		ENCORE2	20099
NKRF_BGHLV27-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1303					GRCh38	V40	NKRF_BGHLV27-38/Aligned.sortedByCoord.out.bam		ENCORE2	20121
NKRF_BGHLV27-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1303					GRCh38	V40	NKRF_BGHLV27-38/Aligned.sortedByCoord.out.bam		ENCORE2	20143
NKRF_BGHLV27-38_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1303					GRCh38	V40	NKRF_BGHLV27-38_1.fastq.gz,NKRF_BGHLV27-38_2.fastq.gz		ENCORE2	20683