NKRF RNA-Seq in K562

General Information


RBP	NKRF
Cell_Line	K562
Method	shRNA
Exp_Name	NKRF-BGKLV36-K562
ENCODE_series_ID	ENCSR269TJP
Batch_ID	BGKLV36
Pool ID	Pool-180109
Local_Set_Name	set40_K
ENCODE_KD_Exp_ID	ENCSR231PWH
ENCODE_CN_Exp_ID	ENCSR619PCR
Rep1	NKRF-BGKLV36-39
Rep2	NKRF-BGKLV36-40
CN1	NT-BGKLV36-1C
CN2	NT-BGKLV36-2C
Rep1_qPCR	65.1
Rep2_qPCR	63.5
Rep1_WB	52.6
Rep2_WB	54.5
Antibody Cat#	A304-016A
Antibody Lot#	A304-016A
Antibody DCC ID	ENCAB893CIV
Status	Released
Project	ENCODE4
ID	273

Experiment Information (Status: Released)

	BGKLV36-39	BGKLV36-40
idx	762	763
TRCN#_or_BGC#	TRCN0000016430	TRCN0000016430
shRNA_or_gRNA_sequence	CCTTAACAATTCTGCCTCATT	CCTTAACAATTCTGCCTCATT
PAM
Name	NKRF	NKRF
Sample_ID	BGKLV36-39	BGKLV36-40
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	NKRF	NKRF
qPCR_result	65.1	63.5
Ave_qPCR	64.3
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3473	3368
WB_result	52.6	54.5
Ave_WB	53.5
WB_DONE_date	6/3/16	WES
MW	78kDa
IP	1	1
antibody_Cat#	A304-016A	A304-016A
Antibody DCC ID	ENCAB893CIV	ENCAB893CIV
submitted_to_DCC_date	10/26/16
Rep1_TPM	14.4	0
Rep2_TPM	8.4	0
Action
Library_start_date	07/28/16	07/28/16
repeat_library
Note
ID	855	856

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

	BGKLV36-39	BGKLV36-40
Sample_ID	BGKLV36-39	BGKLV36-40
Sample Name
Sample Name	NKRF-BGKLV36-39	NKRF-BGKLV36-40
RBP	NKRF	NKRF
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6469	6470

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-39	BGKLV36-40
Sample #	53	54
Sample Name	NKRF-BGKLV36-39C	NKRF-BGKLV36-40C
Sample_Name_Alias	NKRF-BGKLV36-39	NKRF-BGKLV36-40
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	278	278
Peak_Molarity	13.40	11.30
libSampleQC_DNA_Well	DNA_Library_LV36/set1/E3.png	DNA_Library_LV36/set1/F3.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/G6.png	RNA_Library_LV35_LV36/set1/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2016-07-29	2016-07-29
Sample_ID	BGKLV36-39	BGKLV36-40
RBP	NKRF	NKRF
Batch_ID	BGKLV36	BGKLV36
WB_result	52.600	54.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	976	977

Sequencing Information

	BGKLV36-39	BGKLV36-40
Sample_ID	BGKLV36-39	BGKLV36-40
Sample Name	NKRF-BGKLV36-39	NKRF-BGKLV36-40
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_K	set40_K
total_reads	46,227,472	62,265,572
total_aligned_reads	40,252,176	55,573,950
unique_aligned_reads	36,730,050	50,407,014
percent_uniqueAligned	0.79455	0.80955
correlation_replicates	0.999408	0.999408
spikein_reads	75,430	118,620
percent_spikeins	0.00163	0.00191
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	379	380

Data Submission Information

	BGKLV36-39	BGKLV36-39	BGKLV36-39	BGKLV36-39	BGKLV36-39	BGKLV36-39	BGKLV36-40	BGKLV36-40	BGKLV36-40	BGKLV36-40
ENCODE_alias	brenton-graveley:NKRF-BGKLV36-C	brenton-graveley:NKRF-BGKLV36-39	brenton-graveley:L-NKRF-BGKLV36-39	brenton-graveley:NKRF-BGKLV36-39_ACAGTG_ACBYWVANXX_L008_001.R1.fastq.gz	brenton-graveley:NKRF-BGKLV36-39_ACAGTG_ACBYWVANXX_L008_001.R2.fastq.gz	brenton-graveley:NKRF-BGKLV36-K562	brenton-graveley:NKRF-BGKLV36-40	brenton-graveley:L-NKRF-BGKLV36-40	brenton-graveley:NKRF-BGKLV36-40_GCCAAT_ACBYWVANXX_L008_001.R1.fastq.gz	brenton-graveley:NKRF-BGKLV36-40_GCCAAT_ACBYWVANXX_L008_001.R2.fastq.gz
ENCODE_accession	ENCSR231PWH	ENCBS199CIR	ENCLB801RLY	ENCFF031LJZ	ENCFF970FSH	ENCSR269TJP	ENCBS314LSG	ENCLB678JSW	ENCFF269CAK	ENCFF754MEZ
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	BGKLV36-39	BGKLV36-39	BGKLV36-39	BGKLV36-39	BGKLV36-39	BGKLV36-39	BGKLV36-40	BGKLV36-40	BGKLV36-40	BGKLV36-40
Sample Name	NKRF-BGKLV36-39	NKRF-BGKLV36-39	NKRF-BGKLV36-39	NKRF-BGKLV36-39	NKRF-BGKLV36-39	NKRF-BGKLV36-39	NKRF-BGKLV36-40	NKRF-BGKLV36-40	NKRF-BGKLV36-40	NKRF-BGKLV36-40
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		NKRF-BGKLV36-39.pdf	L-NKRF-BGKLV36-39.pdf				NKRF-BGKLV36-40.pdf	L-NKRF-BGKLV36-40.pdf
ID	1440	1478	1534	1653	1686	7269	1479	1535	1654	1687

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-BGKLV36-39_ACAGTG_ACBYWVANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	379	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1C_L001_001.R1.fastq.gz,NT-BGKLV36-2C_L001_001.R1.fastq.gz	ENCODE4	732
NKRF-BGKLV36-39_ACAGTG_ACBYWVANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	379	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1C_L001_001.R2.fastq.gz,NT-BGKLV36-2C_L001_001.R2.fastq.gz	ENCODE4	775
NKRF-BGKLV36-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	379					GRCh38	V40	NKRF-BGKLV36-39_ACAGTG_ACBYWVANXX_L008_001.R1.fastq.gz,NKRF-BGKLV36-39_ACAGTG_ACBYWVANXX_L008_001.R2.fastq.gz		ENCORE2	23478
NKRF-BGKLV36-39_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	379					GRCh38	V40	NKRF-BGKLV36-39/Aligned.sortedByCoord.out.bam		ENCORE2	23512
NKRF-BGKLV36-39_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	379					GRCh38	V40	NKRF-BGKLV36-39/Aligned.sortedByCoord.out.bam		ENCORE2	23546
NKRF-BGKLV36-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	379					GRCh38	V40	NKRF-BGKLV36-39/Aligned.sortedByCoord.out.bam		ENCORE2	23580
NKRF-BGKLV36-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	379					GRCh38	V40	NKRF-BGKLV36-39/Aligned.sortedByCoord.out.bam		ENCORE2	23614
NKRF-BGKLV36-39_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	379					GRCh38	V40	NKRF-BGKLV36-39_ACAGTG_ACBYWVANXX_L008_001.R1.fastq.gz,NKRF-BGKLV36-39_ACAGTG_ACBYWVANXX_L008_001.R2.fastq.gz		ENCORE2	23648
NKRF-BGKLV36-40_GCCAAT_ACBYWVANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	380	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1C_L001_001.R1.fastq.gz,NT-BGKLV36-2C_L001_001.R1.fastq.gz	ENCODE4	733
NKRF-BGKLV36-40_GCCAAT_ACBYWVANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	380	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1C_L001_001.R2.fastq.gz,NT-BGKLV36-2C_L001_001.R2.fastq.gz	ENCODE4	776
NKRF-BGKLV36-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	380					GRCh38	V40	NKRF-BGKLV36-40_GCCAAT_ACBYWVANXX_L008_001.R1.fastq.gz,NKRF-BGKLV36-40_GCCAAT_ACBYWVANXX_L008_001.R2.fastq.gz		ENCORE2	23479
NKRF-BGKLV36-40_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	380					GRCh38	V40	NKRF-BGKLV36-40/Aligned.sortedByCoord.out.bam		ENCORE2	23513
NKRF-BGKLV36-40_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	380					GRCh38	V40	NKRF-BGKLV36-40/Aligned.sortedByCoord.out.bam		ENCORE2	23547
NKRF-BGKLV36-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	380					GRCh38	V40	NKRF-BGKLV36-40/Aligned.sortedByCoord.out.bam		ENCORE2	23581
NKRF-BGKLV36-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	380					GRCh38	V40	NKRF-BGKLV36-40/Aligned.sortedByCoord.out.bam		ENCORE2	23615
NKRF-BGKLV36-40_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	380					GRCh38	V40	NKRF-BGKLV36-40_GCCAAT_ACBYWVANXX_L008_001.R1.fastq.gz,NKRF-BGKLV36-40_GCCAAT_ACBYWVANXX_L008_001.R2.fastq.gz		ENCORE2	23649