SAFB2 RNA-Seq in K562

General Information


RBP	SAFB2
Cell_Line	K562
Method	shRNA
Exp_Name	SAFB2-BGKLV24-K562
ENCODE_series_ID	ENCSR486SNX
Batch_ID	BGKLV24
Pool ID	Pool-160425
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR770LYW
ENCODE_CN_Exp_ID	ENCSR154OBA
Rep1	SAFB2_BGKLV24-51C
Rep2	SAFB2_BGKLV24-52C
CN1	NT_BGKLV24-1C
CN2	NT_BGKLV24-2C
Rep1_qPCR	19.0
Rep2_qPCR	36.1
Rep1_WB	60.1
Rep2_WB	68.9
Antibody Cat#	A301-112A
Antibody Lot#	A301-112A
Antibody DCC ID	ENCAB303CHK
Status	Released
Project	ENCODE3
ID	601

Experiment Information (Status: Released)

	BGKLV24-51	BGKLV24-52
idx	388	389
TRCN#_or_BGC#	TRCN0000075057	TRCN0000075057
shRNA_or_gRNA_sequence	GACATGAGTGTGCTAGACGAA	GACATGAGTGTGCTAGACGAA
PAM
Name	SAFB2_57	SAFB2_57
Sample_ID	BGKLV24-51	BGKLV24-52
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	SAFB2	SAFB2
qPCR_result	19.0	36.1
Ave_qPCR	27.5
RT-qPCR_primer-F	ggccttctcgattccttttg
RT-qPCR_primer-R	taaatccttccccatccaca
protein_conc	2803	3626
WB_result	60.1	68.9
Ave_WB	64.5
WB_DONE_date	1/19/2016
MW	107kDa	WES
IP	1	1
antibody_Cat#	A301-112A	A301-112A
Antibody DCC ID	ENCAB303CHK	ENCAB303CHK
submitted_to_DCC_date	3/8/2016
Rep1_TPM	84.3592825	0
Rep2_TPM	52.9474556	0
Action
Library_start_date	3/10/2016	3/10/2016
repeat_library
Note
ID	445	446

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SAFB2	Product_ID: A301-112A Lot_ID: 1 Source: Bethyl Labs Target Name: SAFB2-human

Experiment Status

	BGKLV24-51	BGKLV24-52
Sample_ID	BGKLV24-51	BGKLV24-52
Sample Name	SAFB2_BGKLV24-51C	SAFB2_BGKLV24-52C
Sample Name	SAFB2_BGKLV24-51C	SAFB2_BGKLV24-52C
RBP	SAFB2	SAFB2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1205	1206

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-51	BGKLV24-52
Sample #
Sample Name	SAFB2-BGKLV24-51C	SAFB2-BGKLV24-52C
Sample_Name_Alias	SAFB2_BGKLV24-51C	SAFB2_BGKLV24-52C
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-10	2016-03-10
Lib_ID	Lib-160310	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/C11.png	DNA_Library_LV33-34-25B-32/set1/D11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/A12.png	RNA_Library_LV35_LV36/set1/B12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-51	BGKLV24-52
RBP	SAFB2	SAFB2
Batch_ID	BGKLV24	BGKLV24
WB_result	60.100	68.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2882	2883

Sequencing Information

	BGKLV24-51	BGKLV24-52
Sample_ID	BGKLV24-51	BGKLV24-52
Sample Name	SAFB2_BGKLV24-51C	SAFB2_BGKLV24-52C
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set24	set24
total_reads	76,035,334	96,306,100
total_aligned_reads	53,322,738	66,596,206
unique_aligned_reads	48,439,458	60,466,848
percent_uniqueAligned	0.63707	0.62786
correlation_replicates	0.995436	0.995436
spikein_reads	117,650	177,330
percent_spikeins	0.00155	0.00184
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1531	1532

Data Submission Information

	BGKLV24-51	BGKLV24-51
ENCODE_alias	brenton-graveley:SAFB2_BGKLV24	brenton-graveley:SAFB2-BGKLV24-K562
ENCODE_accession	ENCSR770LYW	ENCSR486SNX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-51	BGKLV24-51
Sample Name	SAFB2_BGKLV24-51C	SAFB2_BGKLV24-51C
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3142	6929

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
SAFB2_BGKLV24-51C_ACAGTG_L006_001.R1.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1531	HiSeq2000	100	paired-ended	1				NT_BGKLV24-1C_TTAGGC_L006_001.R1.fastq.gz,NT_BGKLV24-2C_TGACCA_L006_001.R1.fastq.gz	ENCODE3	17214
SAFB2_BGKLV24-51C_ACAGTG_L006_001.R2.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1531	HiSeq2000	100	paired-ended	2				NT_BGKLV24-1C_TTAGGC_L006_001.R2.fastq.gz,NT_BGKLV24-2C_TGACCA_L006_001.R2.fastq.gz	ENCODE3	17250
SAFB2_BGKLV24-51C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1531					GRCh38	V40	SAFB2_BGKLV24-51C_ACAGTG_L006_001.R1.fastq.gz,SAFB2_BGKLV24-51C_ACAGTG_L006_001.R2.fastq.gz		ENCORE2	17286
SAFB2_BGKLV24-51C_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1531					GRCh38	V40	SAFB2_BGKLV24-51C/Aligned.sortedByCoord.out.bam		ENCORE2	17322
SAFB2_BGKLV24-51C_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1531					GRCh38	V40	SAFB2_BGKLV24-51C/Aligned.sortedByCoord.out.bam		ENCORE2	17358
SAFB2_BGKLV24-51C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1531					GRCh38	V40	SAFB2_BGKLV24-51C/Aligned.sortedByCoord.out.bam		ENCORE2	17394
SAFB2_BGKLV24-51C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1531					GRCh38	V40	SAFB2_BGKLV24-51C/Aligned.sortedByCoord.out.bam		ENCORE2	17430
SAFB2_BGKLV24-51C_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1531					GRCh38	V40	SAFB2_BGKLV24-51C_ACAGTG_L006_001.R1.fastq.gz,SAFB2_BGKLV24-51C_ACAGTG_L006_001.R2.fastq.gz		ENCORE2	17466
SAFB2_BGKLV24-52C_GCCAAT_L006_001.R1.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1532	HiSeq2000	100	paired-ended	1				NT_BGKLV24-1C_TTAGGC_L006_001.R1.fastq.gz,NT_BGKLV24-2C_TGACCA_L006_001.R1.fastq.gz	ENCODE3	17215
SAFB2_BGKLV24-52C_GCCAAT_L006_001.R2.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1532	HiSeq2000	100	paired-ended	2				NT_BGKLV24-1C_TTAGGC_L006_001.R2.fastq.gz,NT_BGKLV24-2C_TGACCA_L006_001.R2.fastq.gz	ENCODE3	17251
SAFB2_BGKLV24-52C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1532					GRCh38	V40	SAFB2_BGKLV24-52C_GCCAAT_L006_001.R1.fastq.gz,SAFB2_BGKLV24-52C_GCCAAT_L006_001.R2.fastq.gz		ENCORE2	17287
SAFB2_BGKLV24-52C_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1532					GRCh38	V40	SAFB2_BGKLV24-52C/Aligned.sortedByCoord.out.bam		ENCORE2	17323
SAFB2_BGKLV24-52C_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1532					GRCh38	V40	SAFB2_BGKLV24-52C/Aligned.sortedByCoord.out.bam		ENCORE2	17359
SAFB2_BGKLV24-52C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1532					GRCh38	V40	SAFB2_BGKLV24-52C/Aligned.sortedByCoord.out.bam		ENCORE2	17395
SAFB2_BGKLV24-52C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1532					GRCh38	V40	SAFB2_BGKLV24-52C/Aligned.sortedByCoord.out.bam		ENCORE2	17431
SAFB2_BGKLV24-52C_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1532					GRCh38	V40	SAFB2_BGKLV24-52C_GCCAAT_L006_001.R1.fastq.gz,SAFB2_BGKLV24-52C_GCCAAT_L006_001.R2.fastq.gz		ENCORE2	17467