SMN1 RNA-Seq in K562

General Information


RBP	SMN1
Cell_Line	K562
Method	shRNA
Exp_Name	SMN1-BGKLV24-K562
ENCODE_series_ID	ENCSR598HHA
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR129ROE
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	SMN1_BGKLV24_59B
Rep2	SMN1_BGKLV24_60B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	45.0
Rep2_qPCR	67.0
Rep1_WB	52.5
Rep2_WB	57.2
Antibody Cat#	RN077PW
Antibody Lot#	RN077PW
Antibody DCC ID	ENCAB135MQH
Status	Released
Project	ENCODE3
ID	611

Experiment Information (Status: Released)

	BGKLV24-59	BGKLV24-60
idx	396	397
TRCN#_or_BGC#	TRCN0000118704	TRCN0000118704
shRNA_or_gRNA_sequence	CAGAGCGATGATTCTGACATT	CAGAGCGATGATTCTGACATT
PAM
Name	SMN1	SMN1
Sample_ID	BGKLV24-59	BGKLV24-60
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	SMN1	SMN1
qPCR_result	45.0	67.0
Ave_qPCR	56.0
RT-qPCR_primer-F	aggaggattccgtgctgttc
RT-qPCR_primer-R	tcagtgctgtatcatcccaaa
protein_conc	3614	3364
WB_result	52.5	57.2
Ave_WB	54.9
WB_DONE_date	4/17/2015
MW	32kDa
IP	1IP	1IP
antibody_Cat#	RN077PW	RN077PW
Antibody DCC ID	ENCAB135MQH	ENCAB135MQH
submitted_to_DCC_date	5/4/2015
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	9/2/2015	9/2/2015
repeat_library
Note	x	x
ID	455	456

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMN1	Product_ID: RN077PW Lot_ID: 1 Source: MBLI Target Name: SMN1-human

Experiment Status

	BGKLV24-59	BGKLV24-60
Sample_ID	BGKLV24-59	BGKLV24-60
Sample Name	SMN1_BGKLV24_59B	SMN1_BGKLV24_60B
Sample Name	SMN1_BGKLV24_59B	SMN1_BGKLV24_60B
RBP	SMN1	SMN1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	904	905

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-59	BGKLV24-60
Sample #
Sample Name	SMN1-BGKLV24-59B	SMN1-BGKLV24-60B
Sample_Name_Alias	SMN1_BGKLV24_59B	SMN1_BGKLV24_60B
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-02	2015-09-02
Lib_ID	Lib-150902	Lib-150902
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/E7.png	DNA_Library_LV24-25-26/set1/F7.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G6.png	RNA_Library_LV20-22-24/set1/H6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-59	BGKLV24-60
RBP	SMN1	SMN1
Batch_ID	BGKLV24	BGKLV24
WB_result	52.500	57.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2592	2593

Sequencing Information

	BGKLV24-59	BGKLV24-60
Sample_ID	BGKLV24-59	BGKLV24-60
Sample Name	SMN1_BGKLV24_59B	SMN1_BGKLV24_60B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	86,936,106	82,395,400
total_aligned_reads	84,982,514	78,691,420
unique_aligned_reads	77,374,760	71,542,314
percent_uniqueAligned	0.89002	0.86828
correlation_replicates	0.998229	0.998229
spikein_reads	294,348	222,992
percent_spikeins	0.00339	0.00271
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1234	1235

Data Submission Information

	BGKLV24-59	BGKLV24-59
ENCODE_alias	brenton-graveley:SMN1_BGKLV24_B	brenton-graveley:SMN1-BGKLV24-K562
ENCODE_accession	ENCSR129ROE	ENCSR598HHA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-59	BGKLV24-59
Sample Name	SMN1_BGKLV24_59B	SMN1_BGKLV24_59B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3001	6953

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
SMN1_BGKLV24_59B_CGTACG_L003_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1234	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17490
SMN1_BGKLV24_59B_CGTACG_L003_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1234	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17514
SMN1_BGKLV24_59B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1234					GRCh38	V40	SMN1_BGKLV24_59B_CGTACG_L003_001.R1.fastq.gz,SMN1_BGKLV24_59B_CGTACG_L003_001.R2.fastq.gz		ENCORE2	17538
SMN1_BGKLV24_59B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1234					GRCh38	V40	SMN1_BGKLV24_59B/Aligned.sortedByCoord.out.bam		ENCORE2	17562
SMN1_BGKLV24_59B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1234					GRCh38	V40	SMN1_BGKLV24_59B/Aligned.sortedByCoord.out.bam		ENCORE2	17586
SMN1_BGKLV24_59B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1234					GRCh38	V40	SMN1_BGKLV24_59B/Aligned.sortedByCoord.out.bam		ENCORE2	17610
SMN1_BGKLV24_59B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1234					GRCh38	V40	SMN1_BGKLV24_59B/Aligned.sortedByCoord.out.bam		ENCORE2	17634
SMN1_BGKLV24_59B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1234					GRCh38	V40	SMN1_BGKLV24_59B_CGTACG_L003_001.R1.fastq.gz,SMN1_BGKLV24_59B_CGTACG_L003_001.R2.fastq.gz		ENCORE2	17658
SMN1_BGKLV24_60B_GAGTGG_L004_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1235	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17491
SMN1_BGKLV24_60B_GAGTGG_L004_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1235	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17515
SMN1_BGKLV24_60B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1235					GRCh38	V40	SMN1_BGKLV24_60B_GAGTGG_L004_001.R1.fastq.gz,SMN1_BGKLV24_60B_GAGTGG_L004_001.R2.fastq.gz		ENCORE2	17539
SMN1_BGKLV24_60B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1235					GRCh38	V40	SMN1_BGKLV24_60B/Aligned.sortedByCoord.out.bam		ENCORE2	17563
SMN1_BGKLV24_60B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1235					GRCh38	V40	SMN1_BGKLV24_60B/Aligned.sortedByCoord.out.bam		ENCORE2	17587
SMN1_BGKLV24_60B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1235					GRCh38	V40	SMN1_BGKLV24_60B/Aligned.sortedByCoord.out.bam		ENCORE2	17611
SMN1_BGKLV24_60B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1235					GRCh38	V40	SMN1_BGKLV24_60B/Aligned.sortedByCoord.out.bam		ENCORE2	17635
SMN1_BGKLV24_60B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1235					GRCh38	V40	SMN1_BGKLV24_60B_GAGTGG_L004_001.R1.fastq.gz,SMN1_BGKLV24_60B_GAGTGG_L004_001.R2.fastq.gz		ENCORE2	17659