SAFB RNA-Seq in K562

General Information


RBP	SAFB
Cell_Line	K562
Method	CRISPR
Exp_Name	SAFB-BGKcLV06-K562
ENCODE_series_ID	ENCSR150DNO
Batch_ID	BGKcLV06
Pool ID	Pool-170911
Local_Set_Name	set39_K
ENCODE_KD_Exp_ID	ENCSR336TYW
ENCODE_CN_Exp_ID	ENCSR341TTW
Rep1	SAFB-BGKcLV06-29
Rep2	SAFB-BGKcLV06-30
CN1	NT-BGKcLV06-1
CN2	NT-BGKcLV06-2
Rep1_qPCR	51.9
Rep2_qPCR	52.7
Rep1_WB	49.2
Rep2_WB	60.9
Antibody Cat#	#200580
Antibody Lot#	#200580
Antibody DCC ID	ENCAB180KRZ
Status	Released
Project	ENCODE3
ID	776

Experiment Information (Status: Released)

	BGKcLV06-29	BGKcLV06-30
idx	205	206
TRCN#_or_BGC#	BGC#0000064	BGC#0000064
shRNA_or_gRNA_sequence	CCCGCAGATCGATCACTCGC	CCCGCAGATCGATCACTCGC
PAM
Name	SAFB_97	SAFB_97
Sample_ID	BGKcLV06-29	BGKcLV06-30
transduction_Date	6/9/17	6/9/17
days	Day 6	Day 6
RBP_name	SAFB	SAFB
qPCR_result	51.9	52.7
Ave_qPCR	52.3
RT-qPCR_primer-F	agctgaggaaacggaatgtg
RT-qPCR_primer-R	tccctcggaggtaatttcaa
protein_conc	518	800
WB_result	49.2	60.9
Ave_WB	55.0
WB_DONE_date	7/27/17
MW	103KD	130kD
IP	FU'S	FU'S
antibody_Cat#	#200580	#200580
Antibody DCC ID	ENCAB180KRZ	ENCAB180KRZ
submitted_to_DCC_date	11/16/17
Rep1_TPM	68.6	0
Rep2_TPM	59.1	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	4303	4304

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SAFB	Product_ID: #200580 Lot_ID: 20130304 Source: Zen Bioscience Target Name: SAFB-human

Experiment Status

	BGKcLV06-29	BGKcLV06-30
Sample_ID	BGKcLV06-29	BGKcLV06-30
Sample Name	SAFB-BGKcLV06-29	SAFB-BGKcLV06-30
Sample Name	SAFB-BGKcLV06-29	SAFB-BGKcLV06-30
RBP	SAFB	SAFB
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1369	1370

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV06-29	BGKcLV06-30
Sample #
Sample Name	SAFB-BGKcLV06-29	SAFB-BGKcLV06-30
Sample_Name_Alias	SAFB-BGKcLV06-29	SAFB-BGKcLV06-30
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/C2.png	DNA_Library_set39/set2/D2.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set39/set3/C2.png	RNA_Library_set39/set1/C2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV06-29	BGKcLV06-30
RBP	SAFB	SAFB
Batch_ID	BGKcLV06	BGKcLV06
WB_result	49.200	60.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3064	3065

Sequencing Information

	BGKcLV06-29	BGKcLV06-30
Sample_ID	BGKcLV06-29	BGKcLV06-30
Sample Name	SAFB-BGKcLV06-29	SAFB-BGKcLV06-30
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_K	set39_K
total_reads	43,640,998	45,215,316
total_aligned_reads	38,522,406	36,631,030
unique_aligned_reads	34,921,456	33,146,970
percent_uniqueAligned	0.80020	0.73309
correlation_replicates	0.997899	0.997899
spikein_reads	12,468	16,300
percent_spikeins	0.00029	0.00036
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1715	1716

Data Submission Information

	BGKcLV06-29	BGKcLV06-29
ENCODE_alias	brenton-graveley:SAFB-BGKcLV06	brenton-graveley:SAFB-BGKcLV06-K562
ENCODE_accession	ENCSR336TYW	ENCSR150DNO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV06-29	BGKcLV06-29
Sample Name	SAFB-BGKcLV06-29	SAFB-BGKcLV06-29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3224	6927

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
SAFB-BGKcLV06-29_GTGGCC_ACBE67ANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1715	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22482
SAFB-BGKcLV06-29_GTGGCC_ACBE67ANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1715	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22518
SAFB-BGKcLV06-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1715					GRCh38	V40	SAFB-BGKcLV06-29_GTGGCC_ACBE67ANXX_L006_001.R1.fastq.gz,SAFB-BGKcLV06-29_GTGGCC_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22554
SAFB-BGKcLV06-29_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1715					GRCh38	V40	SAFB-BGKcLV06-29/Aligned.sortedByCoord.out.bam		ENCORE2	22590
SAFB-BGKcLV06-29_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1715					GRCh38	V40	SAFB-BGKcLV06-29/Aligned.sortedByCoord.out.bam		ENCORE2	22626
SAFB-BGKcLV06-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1715					GRCh38	V40	SAFB-BGKcLV06-29/Aligned.sortedByCoord.out.bam		ENCORE2	22662
SAFB-BGKcLV06-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1715					GRCh38	V40	SAFB-BGKcLV06-29/Aligned.sortedByCoord.out.bam		ENCORE2	22698
SAFB-BGKcLV06-29_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1715					GRCh38	V40	SAFB-BGKcLV06-29_GTGGCC_ACBE67ANXX_L006_001.R1.fastq.gz,SAFB-BGKcLV06-29_GTGGCC_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22734
SAFB-BGKcLV06-30_GTTTCG_ACBE67ANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1716	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22483
SAFB-BGKcLV06-30_GTTTCG_ACBE67ANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1716	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22519
SAFB-BGKcLV06-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1716					GRCh38	V40	SAFB-BGKcLV06-30_GTTTCG_ACBE67ANXX_L006_001.R1.fastq.gz,SAFB-BGKcLV06-30_GTTTCG_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22555
SAFB-BGKcLV06-30_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1716					GRCh38	V40	SAFB-BGKcLV06-30/Aligned.sortedByCoord.out.bam		ENCORE2	22591
SAFB-BGKcLV06-30_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1716					GRCh38	V40	SAFB-BGKcLV06-30/Aligned.sortedByCoord.out.bam		ENCORE2	22627
SAFB-BGKcLV06-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1716					GRCh38	V40	SAFB-BGKcLV06-30/Aligned.sortedByCoord.out.bam		ENCORE2	22663
SAFB-BGKcLV06-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1716					GRCh38	V40	SAFB-BGKcLV06-30/Aligned.sortedByCoord.out.bam		ENCORE2	22699
SAFB-BGKcLV06-30_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1716					GRCh38	V40	SAFB-BGKcLV06-30_GTTTCG_ACBE67ANXX_L006_001.R1.fastq.gz,SAFB-BGKcLV06-30_GTTTCG_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22735