RECQL RNA-Seq in K562

General Information


RBP	RECQL
Cell_Line	K562
Method	shRNA
Exp_Name	RECQL-BGKLV08-K562
ENCODE_series_ID	ENCSR058UHM
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR310VND
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	RECQL-LV08-49
Rep2	RECQL-LV08-50
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	73.4
Rep2_qPCR	81.0
Rep1_WB	56.0
Rep2_WB	59.4
Antibody Cat#	A300-450A
Antibody Lot#	A300-450A
Antibody DCC ID	ENCAB680IWE
Status	Released
Project	ENCODE3
ID	300

Experiment Information (Status: Released)

	BGKLV08-49	BGKLV08-50
idx	50	51
TRCN#_or_BGC#	TRCN0000052001	TRCN0000052001
shRNA_or_gRNA_sequence	GCACATGCTATTACTATGCAA	GCACATGCTATTACTATGCAA
PAM
Name	RECQL	RECQL
Sample_ID	BGKLV08-49	BGKLV08-50
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	RECQL	RECQL
qPCR_result	73.4	81.0
Ave_qPCR	77.2
RT-qPCR_primer-F	TGCAAGTGACAAAGTCCACG
RT-qPCR_primer-R	TTTATCACCTTGTTCAGAATGACA
protein_conc	2788	2687
WB_result	56.0	59.4
Ave_WB	57.7
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A300-450A	A300-450A
Antibody DCC ID	ENCAB680IWE	ENCAB680IWE
submitted_to_DCC_date	5/4/2015
Rep1_TPM	19.4135066	0
Rep2_TPM	21.3402249	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note
ID	53	54

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RECQL	Product_ID: A300-450A Lot_ID: 1 Source: Bethyl Labs Target Name: RECQL-human

Experiment Status

	BGKLV08-49	BGKLV08-50
Sample_ID	BGKLV08-49	BGKLV08-50
Sample Name	RECQL-LV08-49	RECQL-LV08-50
Sample Name	RECQL-LV08-49	RECQL-LV08-50
RBP	RECQL	RECQL
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	312	313

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-49	BGKLV08-50
Sample #
Sample Name	RECQL-BGKLV08-49	RECQL-BGKLV08-50
Sample_Name_Alias	RECQL-LV08-49	RECQL-LV08-50
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-08	2014-05-08
Lib_ID	Lib-140508	Lib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set4/F2.png	DNA_Library_LV08/set4/G2.png
RIN	8.8	9.3
libSample_RNA_Well	RNA_Library_LV08/set3/G2.png	RNA_Library_LV08/set3/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-49	BGKLV08-50
RBP	RECQL	RECQL
Batch_ID	BGKLV08	BGKLV08
WB_result	56.000	59.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1932	1933

Sequencing Information

	BGKLV08-49	BGKLV08-50
Sample_ID	BGKLV08-49	BGKLV08-50
Sample Name	RECQL-LV08-49	RECQL-LV08-50
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	46,900,000	37,650,000
total_aligned_reads	42,379,814	33,650,058
unique_aligned_reads	38,674,234	30,699,554
percent_uniqueAligned	0.82461	0.81539
correlation_replicates	0.993763	0.993763
spikein_reads	309,456	260,796
percent_spikeins	0.00660	0.00693
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	632	633

Data Submission Information

	BGKLV08-49	BGKLV08-49
ENCODE_alias	brenton-graveley:RECQL-LV08	brenton-graveley:RECQL-BGKLV08-K562
ENCODE_accession	ENCSR310VND	ENCSR058UHM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-49	BGKLV08-49
Sample Name	RECQL-LV08-49	RECQL-LV08-49
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2705	6910

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
RECQL-LV08-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	632					GRCh38	V40	RECQL-LV08-49_CGTACG_L007_R1_001.fastq.gz,RECQL-LV08-49_CGTACG_L007_R2_001.fastq.gz		ENCORE2	12019
RECQL-LV08-49_CGTACG_L007_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	632	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12075
RECQL-LV08-49_CGTACG_L007_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	632	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12131
RECQL-LV08-49_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	632					GRCh38	V40	RECQL-LV08-49/Aligned.sortedByCoord.out.bam		ENCORE2	12187
RECQL-LV08-49_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	632					GRCh38	V40	RECQL-LV08-49/Aligned.sortedByCoord.out.bam		ENCORE2	12243
RECQL-LV08-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	632					GRCh38	V40	RECQL-LV08-49/Aligned.sortedByCoord.out.bam		ENCORE2	12299
RECQL-LV08-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	632					GRCh38	V40	RECQL-LV08-49/Aligned.sortedByCoord.out.bam		ENCORE2	12355
RECQL-LV08-49_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	632					GRCh38	V40	RECQL-LV08-49_CGTACG_L007_R1_001.fastq.gz,RECQL-LV08-49_CGTACG_L007_R2_001.fastq.gz		ENCORE2	13354
RECQL-LV08-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	633					GRCh38	V40	RECQL-LV08-50_GAGTGG_L007_R1_001.fastq.gz,RECQL-LV08-50_GAGTGG_L007_R2_001.fastq.gz		ENCORE2	12020
RECQL-LV08-50_GAGTGG_L007_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	633	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12076
RECQL-LV08-50_GAGTGG_L007_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	633	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12132
RECQL-LV08-50_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	633					GRCh38	V40	RECQL-LV08-50/Aligned.sortedByCoord.out.bam		ENCORE2	12188
RECQL-LV08-50_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	633					GRCh38	V40	RECQL-LV08-50/Aligned.sortedByCoord.out.bam		ENCORE2	12244
RECQL-LV08-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	633					GRCh38	V40	RECQL-LV08-50/Aligned.sortedByCoord.out.bam		ENCORE2	12300
RECQL-LV08-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	633					GRCh38	V40	RECQL-LV08-50/Aligned.sortedByCoord.out.bam		ENCORE2	12356
RECQL-LV08-50_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	633					GRCh38	V40	RECQL-LV08-50_GAGTGG_L007_R1_001.fastq.gz,RECQL-LV08-50_GAGTGG_L007_R2_001.fastq.gz		ENCORE2	13355