GRWD1 RNA-Seq in K562

General Information


RBP	GRWD1
Cell_Line	K562
Method	shRNA
Exp_Name	GRWD1-BGKLV21-K562
ENCODE_series_ID	ENCSR424NXX
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR528ASX
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	GRWD1_BGKLV21_15_17564
Rep2	GRWD1_BGKLV21_16_17565
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	41.2
Rep2_qPCR	66.9
Rep1_WB	85.6
Rep2_WB	87.1
Antibody Cat#	A301-576A
Antibody Lot#	A301-576A
Antibody DCC ID	ENCAB573ZJV
Status	Released
Project	ENCODE3
ID	509

Experiment Information (Status: Released)

	BGKLV21-15	BGKLV21-16
idx	286	287
TRCN#_or_BGC#	TRCN0000135333	TRCN0000135333
shRNA_or_gRNA_sequence	CTCACCAAAGAACTCGGTTTA	CTCACCAAAGAACTCGGTTTA
PAM
Name	GRWD1	GRWD1
Sample_ID	BGKLV21-15	BGKLV21-16
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	GRWD1	GRWD1
qPCR_result	41.2	66.9
Ave_qPCR	54.1
RT-qPCR_primer-F	catcttctccttcgctggac
RT-qPCR_primer-R	ccagaggtggatgttcttttg
protein_conc	3278	3466
WB_result	85.6	87.1
Ave_WB	86.4
WB_DONE_date	2/17/2015
MW	49kDa
IP	1	1
antibody_Cat#	A301-576A	A301-576A
Antibody DCC ID	ENCAB573ZJV	ENCAB573ZJV
submitted_to_DCC_date	4/2/2015
Rep1_TPM	30.3915472	0
Rep2_TPM	12.8633782	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	311	312

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GRWD1	Product_ID: A301-576A Lot_ID: 1 Source: Bethyl Labs Target Name: GRWD1-human

Experiment Status

	BGKLV21-15	BGKLV21-16
Sample_ID	BGKLV21-15	BGKLV21-16
Sample Name	GRWD1_BGKLV21_15_17564	GRWD1_BGKLV21_16_17565
Sample Name	GRWD1_BGKLV21_15_17564	GRWD1_BGKLV21_16_17565
RBP	GRWD1	GRWD1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	750	751

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-15	BGKLV21-16
Sample #
Sample Name	GRWD1-BGKLV21-15	GRWD1-BGKLV21-16
Sample_Name_Alias	GRWD1_BGKLV21_15_17564	GRWD1_BGKLV21_16_17565
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/A6.png	DNA_Library_LV21-24/set1/B6.png
RIN	8.7	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/C8.png	RNA_Library_LV19-21-24/set1/D8.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-15	BGKLV21-16
RBP	GRWD1	GRWD1
Batch_ID	BGKLV21	BGKLV21
WB_result	85.600	87.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2436	2437

Sequencing Information

	BGKLV21-15	BGKLV21-16
Sample_ID	BGKLV21-15	BGKLV21-16
Sample Name	GRWD1_BGKLV21_15_17564	GRWD1_BGKLV21_16_17565
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	35,140,000	42,200,000
total_aligned_reads	32,013,486	38,879,196
unique_aligned_reads	29,369,848	35,496,454
percent_uniqueAligned	0.83580	0.84115
correlation_replicates	0.999608	0.999608
spikein_reads	183,204	223,206
percent_spikeins	0.00521	0.00529
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1042	1043

Data Submission Information

	BGKLV21-15	BGKLV21-15
ENCODE_alias	brenton-graveley:GRWD1_BGKLV21	brenton-graveley:GRWD1-BGKLV21-K562
ENCODE_accession	ENCSR528ASX	ENCSR424NXX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-15	BGKLV21-15
Sample Name	GRWD1_BGKLV21_15_17564	GRWD1_BGKLV21_15_17564
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2961	6740

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
GRWD1_BGKLV21_15_17564_GATCAG_L001_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1042	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15926
GRWD1_BGKLV21_15_17564_GATCAG_L001_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1042	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15970
GRWD1_BGKLV21_15_17564_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1042					GRCh38	V40	GRWD1_BGKLV21_15_17564_GATCAG_L001_R1_001.fastq.gz,GRWD1_BGKLV21_15_17564_GATCAG_L001_R2_001.fastq.gz		ENCORE2	16014
GRWD1_BGKLV21_15_17564_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1042					GRCh38	V40	GRWD1_BGKLV21_15_17564/Aligned.sortedByCoord.out.bam		ENCORE2	16058
GRWD1_BGKLV21_15_17564_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1042					GRCh38	V40	GRWD1_BGKLV21_15_17564/Aligned.sortedByCoord.out.bam		ENCORE2	16102
GRWD1_BGKLV21_15_17564_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1042					GRCh38	V40	GRWD1_BGKLV21_15_17564/Aligned.sortedByCoord.out.bam		ENCORE2	16146
GRWD1_BGKLV21_15_17564_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1042					GRCh38	V40	GRWD1_BGKLV21_15_17564/Aligned.sortedByCoord.out.bam		ENCORE2	16190
GRWD1_BGKLV21_15_17564_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1042					GRCh38	V40	GRWD1_BGKLV21_15_17564_GATCAG_L001_R1_001.fastq.gz,GRWD1_BGKLV21_15_17564_GATCAG_L001_R2_001.fastq.gz		ENCORE2	16234
GRWD1_BGKLV21_16_17565_TAGCTT_L001_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1043	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15927
GRWD1_BGKLV21_16_17565_TAGCTT_L001_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1043	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15971
GRWD1_BGKLV21_16_17565_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1043					GRCh38	V40	GRWD1_BGKLV21_16_17565_TAGCTT_L001_R1_001.fastq.gz,GRWD1_BGKLV21_16_17565_TAGCTT_L001_R2_001.fastq.gz		ENCORE2	16015
GRWD1_BGKLV21_16_17565_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1043					GRCh38	V40	GRWD1_BGKLV21_16_17565/Aligned.sortedByCoord.out.bam		ENCORE2	16059
GRWD1_BGKLV21_16_17565_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1043					GRCh38	V40	GRWD1_BGKLV21_16_17565/Aligned.sortedByCoord.out.bam		ENCORE2	16103
GRWD1_BGKLV21_16_17565_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1043					GRCh38	V40	GRWD1_BGKLV21_16_17565/Aligned.sortedByCoord.out.bam		ENCORE2	16147
GRWD1_BGKLV21_16_17565_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1043					GRCh38	V40	GRWD1_BGKLV21_16_17565/Aligned.sortedByCoord.out.bam		ENCORE2	16191
GRWD1_BGKLV21_16_17565_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1043					GRCh38	V40	GRWD1_BGKLV21_16_17565_TAGCTT_L001_R1_001.fastq.gz,GRWD1_BGKLV21_16_17565_TAGCTT_L001_R2_001.fastq.gz		ENCORE2	16235