SSB RNA-Seq in K562

General Information


RBP	SSB
Cell_Line	K562
Method	shRNA
Exp_Name	SSB-BGKLV13-K562
ENCODE_series_ID	ENCSR655TZO
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR891AXF
ENCODE_CN_Exp_ID	ENCSR084SCN
Rep1	SSB_BGKLV13_67
Rep2	SSB_BGKLV13_68
CN1	non-target_BGKLV13_73
CN2	non-target_BGKLV13_74
Rep1_qPCR	72.1
Rep2_qPCR	50.3
Rep1_WB	0.0
Rep2_WB	0.0
Antibody Cat#	RN074PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB214FIO
Status	Released
Project	ENCODE3
ID	381

Experiment Information (Status: Released)

	BGKLV13-67	BGKLV13-68
idx	202	203
TRCN#_or_BGC#	TRCN0000062194	TRCN0000062194
shRNA_or_gRNA_sequence	CCAACAAGAATCCCTAAACAA	CCAACAAGAATCCCTAAACAA
PAM
Name	SSB	SSB
Sample_ID	BGKLV13-67	BGKLV13-68
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	SSB	SSB
qPCR_result	72.1	50.3
Ave_qPCR	61.2
RT-qPCR_primer-F	TTCTCAAATCATGGTGAAATAAA
RT-qPCR_primer-R	CCAATGCTTCCTTGGCTTT
protein_conc	2290	2315
WB_result	0.0	0.0
Ave_WB	0.0
WB_DONE_date	5/27/2015
MW
IP	1	1
antibody_Cat#	RN074PW	RN074PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	218.715936	0
Rep2_TPM	126.967577	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	221	222

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV13-67	BGKLV13-68
Sample_ID	BGKLV13-67	BGKLV13-68
Sample Name	SSB_BGKLV13_67	SSB_BGKLV13_68
Sample Name	SSB_BGKLV13_67	SSB_BGKLV13_68
RBP	SSB	SSB
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	480	481

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-67	BGKLV13-68
Sample #
Sample Name	SSB-BGKLV13-67	SSB-BGKLV13-68
Sample_Name_Alias	SSB_BGKLV13_67	SSB_BGKLV13_68
Index Well Position	S25	S27
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/H6.png	DNA_Library_LV16-17/set1/H5.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C3.png	RNA_Library_LV13-14-16/set1/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-67	BGKLV13-68
RBP	SSB	SSB
Batch_ID	BGKLV13	BGKLV13
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2166	2167

Sequencing Information

	BGKLV13-67	BGKLV13-68
Sample_ID	BGKLV13-67	BGKLV13-68
Sample Name	SSB_BGKLV13_67	SSB_BGKLV13_68
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	47,160,000	47,350,000
total_aligned_reads	45,164,228	45,076,718
unique_aligned_reads	41,442,434	41,455,124
percent_uniqueAligned	0.87876	0.87550
correlation_replicates	0.998762	0.998762
spikein_reads	103,360	154,586
percent_spikeins	0.00219	0.00326
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	808	809

Data Submission Information

	BGKLV13-67	BGKLV13-67
ENCODE_alias	brenton-graveley:SSB_BGKLV13	brenton-graveley:SSB-BGKLV13-K562
ENCODE_accession	ENCSR891AXF	ENCSR655TZO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-67	BGKLV13-67
Sample Name	SSB_BGKLV13_67	SSB_BGKLV13_67
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2789	6981

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
SSB_BGKLV13_67_ACTGAT_L007_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	808	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	13408
SSB_BGKLV13_67_ACTGAT_L007_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	808	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	13460
SSB_BGKLV13_67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	808					GRCh38	V40	SSB_BGKLV13_67_ACTGAT_L007_R1_001.fastq.gz,SSB_BGKLV13_67_ACTGAT_L007_R2_001.fastq.gz		ENCORE2	13512
SSB_BGKLV13_67_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	808					GRCh38	V40	SSB_BGKLV13_67/Aligned.sortedByCoord.out.bam		ENCORE2	13564
SSB_BGKLV13_67_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	808					GRCh38	V40	SSB_BGKLV13_67/Aligned.sortedByCoord.out.bam		ENCORE2	13616
SSB_BGKLV13_67_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	808					GRCh38	V40	SSB_BGKLV13_67/Aligned.sortedByCoord.out.bam		ENCORE2	13668
SSB_BGKLV13_67_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	808					GRCh38	V40	SSB_BGKLV13_67/Aligned.sortedByCoord.out.bam		ENCORE2	13720
SSB_BGKLV13_67_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	808					GRCh38	V40	SSB_BGKLV13_67_ACTGAT_L007_R1_001.fastq.gz,SSB_BGKLV13_67_ACTGAT_L007_R2_001.fastq.gz		ENCORE2	13772
SSB_BGKLV13_68_ATTCCT_L007_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	809	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	13409
SSB_BGKLV13_68_ATTCCT_L007_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	809	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	13461
SSB_BGKLV13_68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	809					GRCh38	V40	SSB_BGKLV13_68_ATTCCT_L007_R1_001.fastq.gz,SSB_BGKLV13_68_ATTCCT_L007_R2_001.fastq.gz		ENCORE2	13513
SSB_BGKLV13_68_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	809					GRCh38	V40	SSB_BGKLV13_68/Aligned.sortedByCoord.out.bam		ENCORE2	13565
SSB_BGKLV13_68_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	809					GRCh38	V40	SSB_BGKLV13_68/Aligned.sortedByCoord.out.bam		ENCORE2	13617
SSB_BGKLV13_68_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	809					GRCh38	V40	SSB_BGKLV13_68/Aligned.sortedByCoord.out.bam		ENCORE2	13669
SSB_BGKLV13_68_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	809					GRCh38	V40	SSB_BGKLV13_68/Aligned.sortedByCoord.out.bam		ENCORE2	13721
SSB_BGKLV13_68_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	809					GRCh38	V40	SSB_BGKLV13_68_ATTCCT_L007_R1_001.fastq.gz,SSB_BGKLV13_68_ATTCCT_L007_R2_001.fastq.gz		ENCORE2	13773