KRR1 RNA-Seq in K562

General Information


RBP	KRR1
Cell_Line	K562
Method	shRNA
Exp_Name	KRR1-BGKLV36-K562
ENCODE_series_ID	ENCSR703HFF
Batch_ID	BGKLV36
Pool ID	Pool-161129
Local_Set_Name	set36
ENCODE_KD_Exp_ID	ENCSR244SIO
ENCODE_CN_Exp_ID	ENCSR424QCW
Rep1	KRR1_BGKLV36-31
Rep2	KRR1_BGKLV36-32
CN1	NT_BGKLV36-1
CN2	NT_BGKLV36-2
Rep1_qPCR	73.5
Rep2_qPCR	71.3
Rep1_WB	75.2
Rep2_WB	60.7
Antibody Cat#	A303-898A
Antibody Lot#	A303-898A
Antibody DCC ID	ENCAB458ZFO
Status	Released
Project	ENCODE3
ID	747

Experiment Information (Status: Released)

	BGKLV36-31	BGKLV36-32
idx	754	755
TRCN#_or_BGC#	TRCN0000072296	TRCN0000072296
shRNA_or_gRNA_sequence	GCAGCATGACTGTTTGTACTA	GCAGCATGACTGTTTGTACTA
PAM
Name	KRR1	KRR1
Sample_ID	BGKLV36-31	BGKLV36-32
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	KRR1	KRR1
qPCR_result	73.5	71.3
Ave_qPCR	72.4
RT-qPCR_primer-F	atcatcattagggccagaga
RT-qPCR_primer-R	tgtcacatgcaacatcatcct
protein_conc	5004	4585
WB_result	75.2	60.7
Ave_WB	68.0
WB_DONE_date	6/21/16
MW	44kDa
IP	1	1
antibody_Cat#	A303-898A	A303-898A
Antibody DCC ID	ENCAB458ZFO	ENCAB458ZFO
submitted_to_DCC_date	11/16/17
Rep1_TPM	37.5	0
Rep2_TPM	22.8	0
Action
Library_start_date	07/28/16	07/28/16
repeat_library
Note
ID	847	848

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
KRR1	Product_ID: A303-898A Lot_ID: 1 Source: Bethyl Labs Target Name: KRR1-human

Experiment Status

	BGKLV36-31	BGKLV36-32
Sample_ID	BGKLV36-31	BGKLV36-32
Sample Name	KRR1_BGKLV36-31	KRR1_BGKLV36-32
Sample Name	KRR1_BGKLV36-31	KRR1_BGKLV36-32
RBP	KRR1	KRR1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1287	1288

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-31	BGKLV36-32
Sample #
Sample Name	KRR1-BGKLV36-31	KRR1-BGKLV36-32
Sample_Name_Alias	KRR1_BGKLV36-31	KRR1_BGKLV36-32
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-28	2016-07-28
Lib_ID	Lib-160728	Lib-160728
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV36/set1/G2.png	DNA_Library_LV36/set1/H2.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/A6.png	RNA_Library_LV35_LV36/set1/B6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV36-31	BGKLV36-32
RBP	KRR1	KRR1
Batch_ID	BGKLV36	BGKLV36
WB_result	75.200	60.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2972	2973

Sequencing Information

	BGKLV36-31	BGKLV36-32
Sample_ID	BGKLV36-31	BGKLV36-32
Sample Name	KRR1_BGKLV36-31	KRR1_BGKLV36-32
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set36	set36
total_reads	50,258,082	70,466,290
total_aligned_reads	42,094,398	56,327,500
unique_aligned_reads	38,428,964	51,385,530
percent_uniqueAligned	0.76463	0.72922
correlation_replicates	0.989888	0.989888
spikein_reads	92,898	102,218
percent_spikeins	0.00185	0.00145
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1621	1622

Data Submission Information

	BGKLV36-31	BGKLV36-31
ENCODE_alias	brenton-graveley:KRR1_BGKLV36	brenton-graveley:KRR1-BGKLV36-K562
ENCODE_accession	ENCSR244SIO	ENCSR703HFF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV36-31	BGKLV36-31
Sample Name	KRR1_BGKLV36-31	KRR1_BGKLV36-31
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3183	6794

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
KRR1_BGKLV36-31_ACTGAT_L001_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1621	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21900
KRR1_BGKLV36-31_ACTGAT_L001_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1621	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21918
KRR1_BGKLV36-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1621					GRCh38	V40	KRR1_BGKLV36-31_ACTGAT_L001_001.R1.fastq.gz,KRR1_BGKLV36-31_ACTGAT_L001_001.R2.fastq.gz		ENCORE2	21936
KRR1_BGKLV36-31_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1621					GRCh38	V40	KRR1_BGKLV36-31/Aligned.sortedByCoord.out.bam		ENCORE2	21954
KRR1_BGKLV36-31_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1621					GRCh38	V40	KRR1_BGKLV36-31/Aligned.sortedByCoord.out.bam		ENCORE2	21972
KRR1_BGKLV36-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1621					GRCh38	V40	KRR1_BGKLV36-31/Aligned.sortedByCoord.out.bam		ENCORE2	21990
KRR1_BGKLV36-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1621					GRCh38	V40	KRR1_BGKLV36-31/Aligned.sortedByCoord.out.bam		ENCORE2	22008
KRR1_BGKLV36-31_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1621					GRCh38	V40	KRR1_BGKLV36-31_ACTGAT_L001_001.R1.fastq.gz,KRR1_BGKLV36-31_ACTGAT_L001_001.R2.fastq.gz		ENCORE2	22026
KRR1_BGKLV36-32_ATTCCT_L001_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1622	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21901
KRR1_BGKLV36-32_ATTCCT_L001_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1622	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21919
KRR1_BGKLV36-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1622					GRCh38	V40	KRR1_BGKLV36-32_ATTCCT_L001_001.R1.fastq.gz,KRR1_BGKLV36-32_ATTCCT_L001_001.R2.fastq.gz		ENCORE2	21937
KRR1_BGKLV36-32_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1622					GRCh38	V40	KRR1_BGKLV36-32/Aligned.sortedByCoord.out.bam		ENCORE2	21955
KRR1_BGKLV36-32_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1622					GRCh38	V40	KRR1_BGKLV36-32/Aligned.sortedByCoord.out.bam		ENCORE2	21973
KRR1_BGKLV36-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1622					GRCh38	V40	KRR1_BGKLV36-32/Aligned.sortedByCoord.out.bam		ENCORE2	21991
KRR1_BGKLV36-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1622					GRCh38	V40	KRR1_BGKLV36-32/Aligned.sortedByCoord.out.bam		ENCORE2	22009
KRR1_BGKLV36-32_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1622					GRCh38	V40	KRR1_BGKLV36-32_ATTCCT_L001_001.R1.fastq.gz,KRR1_BGKLV36-32_ATTCCT_L001_001.R2.fastq.gz		ENCORE2	22027