SND1 RNA-Seq in K562

General Information


RBP	SND1
Cell_Line	K562
Method	shRNA
Exp_Name	SND1-BGKLV13-K562
ENCODE_series_ID	ENCSR849MTM
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR232XRZ
ENCODE_CN_Exp_ID	ENCSR084SCN
Rep1	SND1_BGKLV13_59
Rep2	SND1_BGKLV13_60
CN1	non-target_BGKLV13_73
CN2	non-target_BGKLV13_74
Rep1_qPCR	87.2
Rep2_qPCR	85.3
Rep1_WB	77.0
Rep2_WB	76.9
Antibody Cat#	A302-883A
Antibody Lot#	A302-883A
Antibody DCC ID	ENCAB162GME
Status	Released
Project	ENCODE3
ID	378

Experiment Information (Status: Released)

	BGKLV13-59	BGKLV13-60
idx	194	195
TRCN#_or_BGC#	TRCN0000049653	TRCN0000049653
shRNA_or_gRNA_sequence	CCCACAGCTAATTTGGACCAA	CCCACAGCTAATTTGGACCAA
PAM
Name	SND1	SND1
Sample_ID	BGKLV13-59	BGKLV13-60
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	SND1	SND1
qPCR_result	87.2	85.3
Ave_qPCR	86.2
RT-qPCR_primer-F	GTGAAGGAAGGGCTGGTCAT
RT-qPCR_primer-R	CGCTCTTGGCTGACTCTTG
protein_conc	2118	2106
WB_result	77.0	76.9
Ave_WB	77.0
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A302-883A	A302-883A
Antibody DCC ID	ENCAB162GME	ENCAB162GME
submitted_to_DCC_date	5/4/2015
Rep1_TPM	84.5796204	0
Rep2_TPM	165.594464	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	213	214

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SND1	Product_ID: A302-883A Lot_ID: 1 Source: Bethyl Labs Target Name: SND1-human

Experiment Status

	BGKLV13-59	BGKLV13-60
Sample_ID	BGKLV13-59	BGKLV13-60
Sample Name	SND1_BGKLV13_59	SND1_BGKLV13_60
Sample Name	SND1_BGKLV13_59	SND1_BGKLV13_60
RBP	SND1	SND1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	476	477

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-59	BGKLV13-60
Sample #
Sample Name	SND1-BGKLV13-59	SND1-BGKLV13-60
Sample_Name_Alias	SND1_BGKLV13_59	SND1_BGKLV13_60
Index Well Position	S18	S19
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/B6.png	DNA_Library_LV13-14/set1/C6.png
RIN	9.3	9.4
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E2.png	RNA_Library_LV13-14-16/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-59	BGKLV13-60
RBP	SND1	SND1
Batch_ID	BGKLV13	BGKLV13
WB_result	77.000	76.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2160	2161

Sequencing Information

	BGKLV13-59	BGKLV13-60
Sample_ID	BGKLV13-59	BGKLV13-60
Sample Name	SND1_BGKLV13_59	SND1_BGKLV13_60
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	37,640,000	36,440,000
total_aligned_reads	35,818,916	34,297,580
unique_aligned_reads	33,117,386	31,587,972
percent_uniqueAligned	0.87985	0.86685
correlation_replicates	0.993712	0.993712
spikein_reads	134,552	103,572
percent_spikeins	0.00357	0.00284
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	802	803

Data Submission Information

	BGKLV13-59	BGKLV13-59
ENCODE_alias	brenton-graveley:SND1_BGKLV13	brenton-graveley:SND1-BGKLV13-K562
ENCODE_accession	ENCSR232XRZ	ENCSR849MTM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-59	BGKLV13-59
Sample Name	SND1_BGKLV13_59	SND1_BGKLV13_59
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2787	6957

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
SND1_BGKLV13_59_GTCCGC_L006_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	802	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	13404
SND1_BGKLV13_59_GTCCGC_L006_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	802	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	13456
SND1_BGKLV13_59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	802					GRCh38	V40	SND1_BGKLV13_59_GTCCGC_L006_R1_001.fastq.gz,SND1_BGKLV13_59_GTCCGC_L006_R2_001.fastq.gz		ENCORE2	13508
SND1_BGKLV13_59_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	802					GRCh38	V40	SND1_BGKLV13_59/Aligned.sortedByCoord.out.bam		ENCORE2	13560
SND1_BGKLV13_59_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	802					GRCh38	V40	SND1_BGKLV13_59/Aligned.sortedByCoord.out.bam		ENCORE2	13612
SND1_BGKLV13_59_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	802					GRCh38	V40	SND1_BGKLV13_59/Aligned.sortedByCoord.out.bam		ENCORE2	13664
SND1_BGKLV13_59_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	802					GRCh38	V40	SND1_BGKLV13_59/Aligned.sortedByCoord.out.bam		ENCORE2	13716
SND1_BGKLV13_59_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	802					GRCh38	V40	SND1_BGKLV13_59_GTCCGC_L006_R1_001.fastq.gz,SND1_BGKLV13_59_GTCCGC_L006_R2_001.fastq.gz		ENCORE2	13768
SND1_BGKLV13_60_GTGAAA_L006_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	803	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	13405
SND1_BGKLV13_60_GTGAAA_L006_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	803	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	13457
SND1_BGKLV13_60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	803					GRCh38	V40	SND1_BGKLV13_60_GTGAAA_L006_R1_001.fastq.gz,SND1_BGKLV13_60_GTGAAA_L006_R2_001.fastq.gz		ENCORE2	13509
SND1_BGKLV13_60_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	803					GRCh38	V40	SND1_BGKLV13_60/Aligned.sortedByCoord.out.bam		ENCORE2	13561
SND1_BGKLV13_60_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	803					GRCh38	V40	SND1_BGKLV13_60/Aligned.sortedByCoord.out.bam		ENCORE2	13613
SND1_BGKLV13_60_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	803					GRCh38	V40	SND1_BGKLV13_60/Aligned.sortedByCoord.out.bam		ENCORE2	13665
SND1_BGKLV13_60_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	803					GRCh38	V40	SND1_BGKLV13_60/Aligned.sortedByCoord.out.bam		ENCORE2	13717
SND1_BGKLV13_60_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	803					GRCh38	V40	SND1_BGKLV13_60_GTGAAA_L006_R1_001.fastq.gz,SND1_BGKLV13_60_GTGAAA_L006_R2_001.fastq.gz		ENCORE2	13769