SLTM RNA-Seq in K562

General Information


RBP	SLTM
Cell_Line	K562
Method	shRNA
Exp_Name	SLTM-BGKLV13-K562
ENCODE_series_ID	ENCSR999PXW
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR234YMW
ENCODE_CN_Exp_ID	ENCSR084SCN
Rep1	SLTM_BGKLV13_57
Rep2	SLTM_BGKLV13_58
CN1	non-target_BGKLV13_73
CN2	non-target_BGKLV13_74
Rep1_qPCR	59.7
Rep2_qPCR	53.6
Rep1_WB	59.3
Rep2_WB	58.5
Antibody Cat#	A302-834A
Antibody Lot#	A302-834A
Antibody DCC ID	ENCAB526HXQ
Status	Released
Project	ENCODE3
ID	377

Experiment Information (Status: Released)

	BGKLV13-57	BGKLV13-58
idx	192	193
TRCN#_or_BGC#	TRCN0000135106	TRCN0000135106
shRNA_or_gRNA_sequence	CCCAACATTCAAGTAACGCAT	CCCAACATTCAAGTAACGCAT
PAM
Name	SLTM	SLTM
Sample_ID	BGKLV13-57	BGKLV13-58
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	SLTM	SLTM
qPCR_result	59.7	53.6
Ave_qPCR	56.7
RT-qPCR_primer-F	AGAGGAGTCATCACAGACCGA
RT-qPCR_primer-R	CTTTCCTTGGTCCGCTTGT
protein_conc	2164	1952
WB_result	59.3	58.5
Ave_WB	58.9
WB_DONE_date	5/27/2015
MW	115kDa
IP	1	1
antibody_Cat#	A302-834A	A302-834A
Antibody DCC ID	ENCAB526HXQ	ENCAB526HXQ
submitted_to_DCC_date	8/6/2015
Rep1_TPM	85.7843314	0
Rep2_TPM	77.4897075	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	211	212

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SLTM	Product_ID: A302-834A Lot_ID: 1 Source: Bethyl Labs Target Name: SLTM-human

Experiment Status

	BGKLV13-57	BGKLV13-58
Sample_ID	BGKLV13-57	BGKLV13-58
Sample Name	SLTM_BGKLV13_57	SLTM_BGKLV13_58
Sample Name	SLTM_BGKLV13_57	SLTM_BGKLV13_58
RBP	SLTM	SLTM
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	472	473

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-57	BGKLV13-58
Sample #
Sample Name	SLTM-BGKLV13-57	SLTM-BGKLV13-58
Sample_Name_Alias	SLTM_BGKLV13_57	SLTM_BGKLV13_58
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/H5.png	DNA_Library_LV13-14/set1/A6.png
RIN	9.3	9.4
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C2.png	RNA_Library_LV13-14-16/set1/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-57	BGKLV13-58
RBP	SLTM	SLTM
Batch_ID	BGKLV13	BGKLV13
WB_result	59.300	58.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2158	2159

Sequencing Information

	BGKLV13-57	BGKLV13-58
Sample_ID	BGKLV13-57	BGKLV13-58
Sample Name	SLTM_BGKLV13_57	SLTM_BGKLV13_58
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	51,000,000	43,200,000
total_aligned_reads	47,846,424	40,932,768
unique_aligned_reads	43,809,000	37,452,142
percent_uniqueAligned	0.85900	0.86695
correlation_replicates	0.991334	0.991334
spikein_reads	119,372	148,572
percent_spikeins	0.00234	0.00344
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	800	801

Data Submission Information

	BGKLV13-57	BGKLV13-57
ENCODE_alias	brenton-graveley:SLTM_BGKLV13	brenton-graveley:SLTM-BGKLV13-K562
ENCODE_accession	ENCSR234YMW	ENCSR999PXW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-57	BGKLV13-57
Sample Name	SLTM_BGKLV13_57	SLTM_BGKLV13_57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2785	6951

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
SLTM_BGKLV13_57_ATGTCA_L006_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	800	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13400
SLTM_BGKLV13_57_ATGTCA_L006_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	800	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13452
SLTM_BGKLV13_57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	800					GRCh38	V40	SLTM_BGKLV13_57_ATGTCA_L006_R1_001.fastq.gz,SLTM_BGKLV13_57_ATGTCA_L006_R2_001.fastq.gz		ENCORE2	13504
SLTM_BGKLV13_57_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	800					GRCh38	V40	SLTM_BGKLV13_57/Aligned.sortedByCoord.out.bam		ENCORE2	13556
SLTM_BGKLV13_57_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	800					GRCh38	V40	SLTM_BGKLV13_57/Aligned.sortedByCoord.out.bam		ENCORE2	13608
SLTM_BGKLV13_57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	800					GRCh38	V40	SLTM_BGKLV13_57/Aligned.sortedByCoord.out.bam		ENCORE2	13660
SLTM_BGKLV13_57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	800					GRCh38	V40	SLTM_BGKLV13_57/Aligned.sortedByCoord.out.bam		ENCORE2	13712
SLTM_BGKLV13_57_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	800					GRCh38	V40	SLTM_BGKLV13_57_ATGTCA_L006_R1_001.fastq.gz,SLTM_BGKLV13_57_ATGTCA_L006_R2_001.fastq.gz		ENCORE2	13764
SLTM_BGKLV13_58_CCGTCC_L006_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	801	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13401
SLTM_BGKLV13_58_CCGTCC_L006_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	801	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13453
SLTM_BGKLV13_58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	801					GRCh38	V40	SLTM_BGKLV13_58_CCGTCC_L006_R1_001.fastq.gz,SLTM_BGKLV13_58_CCGTCC_L006_R2_001.fastq.gz		ENCORE2	13505
SLTM_BGKLV13_58_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	801					GRCh38	V40	SLTM_BGKLV13_58/Aligned.sortedByCoord.out.bam		ENCORE2	13557
SLTM_BGKLV13_58_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	801					GRCh38	V40	SLTM_BGKLV13_58/Aligned.sortedByCoord.out.bam		ENCORE2	13609
SLTM_BGKLV13_58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	801					GRCh38	V40	SLTM_BGKLV13_58/Aligned.sortedByCoord.out.bam		ENCORE2	13661
SLTM_BGKLV13_58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	801					GRCh38	V40	SLTM_BGKLV13_58/Aligned.sortedByCoord.out.bam		ENCORE2	13713
SLTM_BGKLV13_58_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	801					GRCh38	V40	SLTM_BGKLV13_58_CCGTCC_L006_R1_001.fastq.gz,SLTM_BGKLV13_58_CCGTCC_L006_R2_001.fastq.gz		ENCORE2	13765