SDAD1 RNA-Seq in K562

General Information


RBP	SDAD1
Cell_Line	K562
Method	CRISPR
Exp_Name	SDAD1-BGKcLV06-K562
ENCODE_series_ID	ENCSR478SZK
Batch_ID	BGKcLV06
Pool ID	Pool-170911
Local_Set_Name	set39_K
ENCODE_KD_Exp_ID	ENCSR103NNB
ENCODE_CN_Exp_ID	ENCSR341TTW
Rep1	SDAD1-BGKcLV06-31
Rep2	SDAD1-BGKcLV06-32
CN1	NT-BGKcLV06-1
CN2	NT-BGKcLV06-2
Rep1_qPCR	19.1
Rep2_qPCR	39.4
Rep1_WB	84.4
Rep2_WB	94.7
Antibody Cat#	A304-692A
Antibody Lot#
Antibody DCC ID	ENCAB322LZP
Status	Released
Project	ENCODE3
ID	777

Experiment Information (Status: Released)

	BGKcLV06-31	BGKcLV06-32
idx	207	208
TRCN#_or_BGC#	BGC#0000066	BGC#0000066
shRNA_or_gRNA_sequence	TCTAATCAAGCGAGACCCGC	TCTAATCAAGCGAGACCCGC
PAM
Name	SDAD1_97	SDAD1_97
Sample_ID	BGKcLV06-31	BGKcLV06-32
transduction_Date	6/9/17	6/9/17
days	Day 6	Day 6
RBP_name	SDAD1	SDAD1
qPCR_result	19.1	39.4
Ave_qPCR	29.3
RT-qPCR_primer-F	acctgccgcagttacagaat
RT-qPCR_primer-R	tgctgggtttatttggttgc
protein_conc	1744	1981
WB_result	84.4	94.7
Ave_WB	89.6
WB_DONE_date	7/27/17
MW
IP
antibody_Cat#	A304-692A
Antibody DCC ID	ENCAB322LZP	ENCAB322LZP
submitted_to_DCC_date	9/29/17
Rep1_TPM	41.9	0
Rep2_TPM	41.8	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	4305	4306

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SDAD1	Product_ID: A304-692A Lot_ID: 1 Source: Bethyl Labs Target Name: SDAD1-human

Experiment Status

	BGKcLV06-31	BGKcLV06-32
Sample_ID	BGKcLV06-31	BGKcLV06-32
Sample Name	SDAD1-BGKcLV06-31	SDAD1-BGKcLV06-32
Sample Name	SDAD1-BGKcLV06-31	SDAD1-BGKcLV06-32
RBP	SDAD1	SDAD1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1371	1372

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV06-31	BGKcLV06-32
Sample #
Sample Name	SDAD1-BGKcLV06-31	SDAD1-BGKcLV06-32
Sample_Name_Alias	SDAD1-BGKcLV06-31	SDAD1-BGKcLV06-32
Index Well Position	S22	S23
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/E2.png	DNA_Library_set39/set2/F2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set39/set1/E2.png	RNA_Library_set39/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV06-31	BGKcLV06-32
RBP	SDAD1	SDAD1
Batch_ID	BGKcLV06	BGKcLV06
WB_result	84.400	94.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3066	3067

Sequencing Information

	BGKcLV06-31	BGKcLV06-32
Sample_ID	BGKcLV06-31	BGKcLV06-32
Sample Name	SDAD1-BGKcLV06-31	SDAD1-BGKcLV06-32
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_K	set39_K
total_reads	46,983,316	47,025,590
total_aligned_reads	42,488,318	37,673,420
unique_aligned_reads	38,585,918	34,156,538
percent_uniqueAligned	0.82127	0.72634
correlation_replicates	0.997140	0.997140
spikein_reads	20,334	18,862
percent_spikeins	0.00043	0.00040
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1717	1718

Data Submission Information

	BGKcLV06-31	BGKcLV06-31
ENCODE_alias	brenton-graveley:SDAD1-BGKcLV06	brenton-graveley:SDAD1-BGKcLV06-K562
ENCODE_accession	ENCSR103NNB	ENCSR478SZK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV06-31	BGKcLV06-31
Sample Name	SDAD1-BGKcLV06-31	SDAD1-BGKcLV06-31
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3225	6935

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
SDAD1-BGKcLV06-31_CGTACG_ACBE67ANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1717	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	22484
SDAD1-BGKcLV06-31_CGTACG_ACBE67ANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1717	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	22520
SDAD1-BGKcLV06-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1717					GRCh38	V40	SDAD1-BGKcLV06-31_CGTACG_ACBE67ANXX_L006_001.R1.fastq.gz,SDAD1-BGKcLV06-31_CGTACG_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22556
SDAD1-BGKcLV06-31_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	1717					GRCh38	V40	SDAD1-BGKcLV06-31/Aligned.sortedByCoord.out.bam		ENCORE2	22592
SDAD1-BGKcLV06-31_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	1717					GRCh38	V40	SDAD1-BGKcLV06-31/Aligned.sortedByCoord.out.bam		ENCORE2	22628
SDAD1-BGKcLV06-31_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	1717					GRCh38	V40	SDAD1-BGKcLV06-31/Aligned.sortedByCoord.out.bam		ENCORE2	22664
SDAD1-BGKcLV06-31_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	1717					GRCh38	V40	SDAD1-BGKcLV06-31/Aligned.sortedByCoord.out.bam		ENCORE2	22700
SDAD1-BGKcLV06-31_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1717					GRCh38	V40	SDAD1-BGKcLV06-31_CGTACG_ACBE67ANXX_L006_001.R1.fastq.gz,SDAD1-BGKcLV06-31_CGTACG_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22736
SDAD1-BGKcLV06-32_GAGTGG_ACBE67ANXX_L006_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1718	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	22485
SDAD1-BGKcLV06-32_GAGTGG_ACBE67ANXX_L006_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1718	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	22521
SDAD1-BGKcLV06-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1718					GRCh38	V40	SDAD1-BGKcLV06-32_GAGTGG_ACBE67ANXX_L006_001.R1.fastq.gz,SDAD1-BGKcLV06-32_GAGTGG_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22557
SDAD1-BGKcLV06-32_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	1718					GRCh38	V40	SDAD1-BGKcLV06-32/Aligned.sortedByCoord.out.bam		ENCORE2	22593
SDAD1-BGKcLV06-32_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	1718					GRCh38	V40	SDAD1-BGKcLV06-32/Aligned.sortedByCoord.out.bam		ENCORE2	22629
SDAD1-BGKcLV06-32_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	1718					GRCh38	V40	SDAD1-BGKcLV06-32/Aligned.sortedByCoord.out.bam		ENCORE2	22665
SDAD1-BGKcLV06-32_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	1718					GRCh38	V40	SDAD1-BGKcLV06-32/Aligned.sortedByCoord.out.bam		ENCORE2	22701
SDAD1-BGKcLV06-32_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1718					GRCh38	V40	SDAD1-BGKcLV06-32_GAGTGG_ACBE67ANXX_L006_001.R1.fastq.gz,SDAD1-BGKcLV06-32_GAGTGG_ACBE67ANXX_L006_001.R2.fastq.gz		ENCORE2	22737