LSM11 RNA-Seq in K562

General Information


RBP	LSM11
Cell_Line	K562
Method	shRNA
Exp_Name	LSM11-BGKLV21-K562
ENCODE_series_ID	ENCSR435QTU
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR762FEO
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	LSM11_BGKLV21_29_17576
Rep2	LSM11_BGKLV21_30_17577
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	92.1
Rep2_qPCR	89.1
Rep1_WB	49.7
Rep2_WB	61.3
Antibody Cat#	A303-709A
Antibody Lot#	A303-709A
Antibody DCC ID	ENCAB344HWD
Status	Released
Project	ENCODE3
ID	514

Experiment Information (Status: Released)

	BGKLV21-29	BGKLV21-30
idx	300	301
TRCN#_or_BGC#	TRCN0000074440	TRCN0000074440
shRNA_or_gRNA_sequence	GCATTCGACAAGTTCTGGAAT	GCATTCGACAAGTTCTGGAAT
PAM
Name	LSM11	LSM11
Sample_ID	BGKLV21-29	BGKLV21-30
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	LSM11	LSM11
qPCR_result	92.1	89.1
Ave_qPCR	90.6
RT-qPCR_primer-F	gaatgcccttgcacgaag
RT-qPCR_primer-R	attcaccttcaccccctcac
protein_conc	2664	3207
WB_result	49.7	61.3
Ave_WB	55.5
WB_DONE_date	3/31/2015
MW
IP	1	1
antibody_Cat#	A303-709A	A303-709A
Antibody DCC ID	ENCAB344HWD	ENCAB344HWD
submitted_to_DCC_date	5/4/2015
Rep1_TPM	1.05297107	0
Rep2_TPM	1.18165639	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	335	336

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LSM11	Product_ID: A303-709A Lot_ID: 1 Source: Bethyl Labs Target Name: LSM11-human

Experiment Status

	BGKLV21-29	BGKLV21-30
Sample_ID	BGKLV21-29	BGKLV21-30
Sample Name	LSM11_BGKLV21_29_17576	LSM11_BGKLV21_30_17577
Sample Name	LSM11_BGKLV21_29_17576	LSM11_BGKLV21_30_17577
RBP	LSM11	LSM11
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	760	761

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-29	BGKLV21-30
Sample #
Sample Name	LSM11-BGKLV21-29	LSM11-BGKLV21-30
Sample_Name_Alias	LSM11_BGKLV21_29_17576	LSM11_BGKLV21_30_17577
Index Well Position	S20	S21
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/C7.png	DNA_Library_LV21-24/set1/D7.png
RIN	9.6	10.0
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/A10.png	RNA_Library_LV19-21-24/set2/E2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-29	BGKLV21-30
RBP	LSM11	LSM11
Batch_ID	BGKLV21	BGKLV21
WB_result	49.700	61.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2446	2447

Sequencing Information

	BGKLV21-29	BGKLV21-30
Sample_ID	BGKLV21-29	BGKLV21-30
Sample Name	LSM11_BGKLV21_29_17576	LSM11_BGKLV21_30_17577
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	31,870,000	50,280,000
total_aligned_reads	29,343,548	46,535,624
unique_aligned_reads	27,038,924	42,817,870
percent_uniqueAligned	0.84841	0.85159
correlation_replicates	0.998877	0.998877
spikein_reads	143,312	237,364
percent_spikeins	0.00450	0.00472
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1052	1053

Data Submission Information

	BGKLV21-29	BGKLV21-29
ENCODE_alias	brenton-graveley:LSM11_BGKLV21	brenton-graveley:LSM11-BGKLV21-K562
ENCODE_accession	ENCSR762FEO	ENCSR435QTU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-29	BGKLV21-29
Sample Name	LSM11_BGKLV21_29_17576	LSM11_BGKLV21_29_17576
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2966	6802

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
LSM11_BGKLV21_29_17576_GTGGCC_L003_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1052	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15940
LSM11_BGKLV21_29_17576_GTGGCC_L003_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1052	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15984
LSM11_BGKLV21_29_17576_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1052					GRCh38	V40	LSM11_BGKLV21_29_17576_GTGGCC_L003_R1_001.fastq.gz,LSM11_BGKLV21_29_17576_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	16028
LSM11_BGKLV21_29_17576_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	1052					GRCh38	V40	LSM11_BGKLV21_29_17576/Aligned.sortedByCoord.out.bam		ENCORE2	16072
LSM11_BGKLV21_29_17576_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	1052					GRCh38	V40	LSM11_BGKLV21_29_17576/Aligned.sortedByCoord.out.bam		ENCORE2	16116
LSM11_BGKLV21_29_17576_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	1052					GRCh38	V40	LSM11_BGKLV21_29_17576/Aligned.sortedByCoord.out.bam		ENCORE2	16160
LSM11_BGKLV21_29_17576_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	1052					GRCh38	V40	LSM11_BGKLV21_29_17576/Aligned.sortedByCoord.out.bam		ENCORE2	16204
LSM11_BGKLV21_29_17576_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1052					GRCh38	V40	LSM11_BGKLV21_29_17576_GTGGCC_L003_R1_001.fastq.gz,LSM11_BGKLV21_29_17576_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	16248
LSM11_BGKLV21_30_17577_GTTTCG_L003_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1053	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15941
LSM11_BGKLV21_30_17577_GTTTCG_L003_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1053	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15985
LSM11_BGKLV21_30_17577_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1053					GRCh38	V40	LSM11_BGKLV21_30_17577_GTTTCG_L003_R1_001.fastq.gz,LSM11_BGKLV21_30_17577_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	16029
LSM11_BGKLV21_30_17577_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	1053					GRCh38	V40	LSM11_BGKLV21_30_17577/Aligned.sortedByCoord.out.bam		ENCORE2	16073
LSM11_BGKLV21_30_17577_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	1053					GRCh38	V40	LSM11_BGKLV21_30_17577/Aligned.sortedByCoord.out.bam		ENCORE2	16117
LSM11_BGKLV21_30_17577_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	1053					GRCh38	V40	LSM11_BGKLV21_30_17577/Aligned.sortedByCoord.out.bam		ENCORE2	16161
LSM11_BGKLV21_30_17577_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	1053					GRCh38	V40	LSM11_BGKLV21_30_17577/Aligned.sortedByCoord.out.bam		ENCORE2	16205
LSM11_BGKLV21_30_17577_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1053					GRCh38	V40	LSM11_BGKLV21_30_17577_GTTTCG_L003_R1_001.fastq.gz,LSM11_BGKLV21_30_17577_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	16249