KHDRBS1 RNA-Seq in K562

General Information


RBP	KHDRBS1
Cell_Line	K562
Method	shRNA
Exp_Name	KHDRBS1-BGKLV24-K562
ENCODE_series_ID	ENCSR278BRT
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR023HWI
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	KHDRBS1_BGKLV24_39_17620
Rep2	KHDRBS1_BGKLV24_40_17621
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	59.9
Rep2_qPCR	80.8
Rep1_WB	53.1
Rep2_WB	55.1
Antibody Cat#	A302-110A
Antibody Lot#
Antibody DCC ID	ENCAB974QUZ
Status	Released
Project	ENCODE3
ID	566

Experiment Information (Status: Released)

	BGKLV24-39	BGKLV24-40
idx	376	377
TRCN#_or_BGC#	TRCN0000000046	TRCN0000000046
shRNA_or_gRNA_sequence	GACGGCAGAAATTGAGAAGAT	GACGGCAGAAATTGAGAAGAT
PAM
Name	KHDRBS1	KHDRBS1
Sample_ID	BGKLV24-39	BGKLV24-40
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	KHDRBS1	KHDRBS1
qPCR_result	59.9	80.8
Ave_qPCR	70.4
RT-qPCR_primer-F	ctgtattgggaaagggctca
RT-qPCR_primer-R	agtgggcatatttggggtct
protein_conc	3783	4302
WB_result	53.1	55.1
Ave_WB	54.1
WB_DONE_date	4/1/2015
MW
IP	1	1
antibody_Cat#	A302-110A
Antibody DCC ID	ENCAB974QUZ	ENCAB974QUZ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	99.2281638	0
Rep2_TPM	92.1061008	0
Action
Library_start_date	5/22/2015	5/22/2015
repeat_library
Note
ID	433	434

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
KHDRBS1	Product_ID: A302-110A Lot_ID: 1 Source: Bethyl Labs Target Name: KHDRBS1-human

Experiment Status

	BGKLV24-39	BGKLV24-40
Sample_ID	BGKLV24-39	BGKLV24-40
Sample Name	KHDRBS1_BGKLV24_39_17620	KHDRBS1_BGKLV24_40_17621
Sample Name	KHDRBS1_BGKLV24_39_17620	KHDRBS1_BGKLV24_40_17621
RBP	KHDRBS1	KHDRBS1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	870	871

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-39	BGKLV24-40
Sample #
Sample Name	KHDRBS1-BGKLV24-39	KHDRBS1-BGKLV24-40
Sample_Name_Alias	KHDRBS1_BGKLV24_39_17620	KHDRBS1_BGKLV24_40_17621
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/A4.png	DNA_Library_LV21-24/set1/B4.png
RIN	9.6	9.3
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/E4.png	RNA_Library_LV20-22-24/set1/F4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-39	BGKLV24-40
RBP	KHDRBS1	KHDRBS1
Batch_ID	BGKLV24	BGKLV24
WB_result	53.100	55.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2558	2559

Sequencing Information

	BGKLV24-39	BGKLV24-40
Sample_ID	BGKLV24-39	BGKLV24-40
Sample Name	KHDRBS1_BGKLV24_39_17620	KHDRBS1_BGKLV24_40_17621
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	34,340,000	31,410,000
total_aligned_reads	32,381,890	29,694,804
unique_aligned_reads	29,778,562	27,260,324
percent_uniqueAligned	0.86717	0.86789
correlation_replicates	0.999025	0.999025
spikein_reads	188,536	167,564
percent_spikeins	0.00549	0.00533
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1092	1093

Data Submission Information

	BGKLV24-39	BGKLV24-39
ENCODE_alias	brenton-graveley:KHDRBS1_BGKLV24	brenton-graveley:KHDRBS1-BGKLV24-K562
ENCODE_accession	ENCSR023HWI	ENCSR278BRT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-39	BGKLV24-39
Sample Name	KHDRBS1_BGKLV24_39_17620	KHDRBS1_BGKLV24_39_17620
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2986	6788

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
KHDRBS1_BGKLV24_39_17620_GTCCGC_L008_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1092	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17204
KHDRBS1_BGKLV24_39_17620_GTCCGC_L008_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1092	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17240
KHDRBS1_BGKLV24_39_17620_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1092					GRCh38	V40	KHDRBS1_BGKLV24_39_17620_GTCCGC_L008_R1_001.fastq.gz,KHDRBS1_BGKLV24_39_17620_GTCCGC_L008_R2_001.fastq.gz		ENCORE2	17276
KHDRBS1_BGKLV24_39_17620_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1092					GRCh38	V40	KHDRBS1_BGKLV24_39_17620/Aligned.sortedByCoord.out.bam		ENCORE2	17312
KHDRBS1_BGKLV24_39_17620_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1092					GRCh38	V40	KHDRBS1_BGKLV24_39_17620/Aligned.sortedByCoord.out.bam		ENCORE2	17348
KHDRBS1_BGKLV24_39_17620_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1092					GRCh38	V40	KHDRBS1_BGKLV24_39_17620/Aligned.sortedByCoord.out.bam		ENCORE2	17384
KHDRBS1_BGKLV24_39_17620_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1092					GRCh38	V40	KHDRBS1_BGKLV24_39_17620/Aligned.sortedByCoord.out.bam		ENCORE2	17420
KHDRBS1_BGKLV24_39_17620_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1092					GRCh38	V40	KHDRBS1_BGKLV24_39_17620_GTCCGC_L008_R1_001.fastq.gz,KHDRBS1_BGKLV24_39_17620_GTCCGC_L008_R2_001.fastq.gz		ENCORE2	17456
KHDRBS1_BGKLV24_40_17621_GTGAAA_L008_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1093	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17205
KHDRBS1_BGKLV24_40_17621_GTGAAA_L008_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1093	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17241
KHDRBS1_BGKLV24_40_17621_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1093					GRCh38	V40	KHDRBS1_BGKLV24_40_17621_GTGAAA_L008_R1_001.fastq.gz,KHDRBS1_BGKLV24_40_17621_GTGAAA_L008_R2_001.fastq.gz		ENCORE2	17277
KHDRBS1_BGKLV24_40_17621_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1093					GRCh38	V40	KHDRBS1_BGKLV24_40_17621/Aligned.sortedByCoord.out.bam		ENCORE2	17313
KHDRBS1_BGKLV24_40_17621_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1093					GRCh38	V40	KHDRBS1_BGKLV24_40_17621/Aligned.sortedByCoord.out.bam		ENCORE2	17349
KHDRBS1_BGKLV24_40_17621_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1093					GRCh38	V40	KHDRBS1_BGKLV24_40_17621/Aligned.sortedByCoord.out.bam		ENCORE2	17385
KHDRBS1_BGKLV24_40_17621_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1093					GRCh38	V40	KHDRBS1_BGKLV24_40_17621/Aligned.sortedByCoord.out.bam		ENCORE2	17421
KHDRBS1_BGKLV24_40_17621_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1093					GRCh38	V40	KHDRBS1_BGKLV24_40_17621_GTGAAA_L008_R1_001.fastq.gz,KHDRBS1_BGKLV24_40_17621_GTGAAA_L008_R2_001.fastq.gz		ENCORE2	17457