SMAD2 RNA-Seq in K562

General Information


RBP	SMAD2
Cell_Line	K562
Method	CRISPR
Exp_Name	SMAD2-BGKcLV15-K562
ENCODE_series_ID	ENCSR271VMA
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR016WTN
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	SMAD2-BGKcLV15-55
Rep2	SMAD2-BGKcLV15-56
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	62.6
Rep2_qPCR	59.4
Rep1_WB	91.0
Rep2_WB	91.8
Antibody Cat#	700048
Antibody Lot#	LOT# TH2627538
Antibody DCC ID	ENCAB373WLA
Status	Released
Project	ENCODE4
ID	136

Experiment Information (Status: Released)

	BGKcLV15-55	BGKcLV15-55	BGKcLV15-55	BGKcLV15-56	BGKcLV15-56	BGKcLV15-56
idx	593	595	597	594	596	598
TRCN#_or_BGC#	BGC#0000368	BGC#0000368	BGC#0000368	BGC#0000368	BGC#0000368	BGC#0000368
shRNA_or_gRNA_sequence	GTTAGGATCTCGGTGTGTCG	GTTAGGATCTCGGTGTGTCG	GTTAGGATCTCGGTGTGTCG	GTTAGGATCTCGGTGTGTCG	GTTAGGATCTCGGTGTGTCG	GTTAGGATCTCGGTGTGTCG
PAM	GGG	GGG	GGG	GGG	GGG	GGG
Name	SMAD2-94	SMAD2-94	SMAD2-94	SMAD2-94	SMAD2-94	SMAD2-94
Sample_ID	BGKcLV15-55	BGKcLV15-55	BGKcLV15-55	BGKcLV15-56	BGKcLV15-56	BGKcLV15-56
transduction_Date	4/2/19	4/2/19	4/2/19	4/2/19	4/2/19	4/2/19
days	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6
RBP_name	SMAD2	SMAD2	SMAD2	SMAD2	SMAD2	SMAD2
qPCR_result	62.6			59.4
Ave_qPCR	61.0
RT-qPCR_primer-F	TAACTTCCCAGCAGGAATTGAG
RT-qPCR_primer-R	TTCAACTGTTGGTCACTTGTTTCT
protein_conc	5374	5374	5374	6091	6091	6091
WB_result	91.0			91.8
Ave_WB	91.4	NO CLEAR BAND ON THE POSION	NO CLEAR BAND ON THE POSION
WB_DONE_date	4/9/19	5/6/19	5/6/19	WES	WES	WES
MW	52kd	55kd	58kd
IP	Rabbit / I	Rabbit / I	Rabbit / I		Monoclonal	Monoclonal
antibody_Cat#	700048	701582	700050	LOT# TH2627538	SMAD2 pSer465, Ser467	SMAD2 pThr8
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	22.5	22.5	22.5	0	0	0
Rep2_TPM	22.1	22.1	22.1	0	0	0
Action	Ready			Ready
Library_start_date	05/30/19			05/30/19
repeat_library
Note
ID	4705	4707	4709	4706	4708	4710

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMAD2	Product_ID: 700048 Lot_ID: TH2627538 Source: Thermo Fisher Target Name: SMAD2-human

Experiment Status

	BGKcLV15-55	BGKcLV15-56
Sample_ID	BGKcLV15-55	BGKcLV15-56
Sample Name
Sample Name	SMAD2-BGKcLV15-55	SMAD2-BGKcLV15-56
RBP	SMAD2	SMAD2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5361	5362

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-55	BGKcLV15-56
Sample #	31	32
Sample Name	SMAD2-BGKcLV15-55	SMAD2-BGKcLV15-56
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	2-G2	2-H2
Tecan	37.66	45.64
Tecan_date	2019-12-10	2019-12-10
Size_bp	265	260
Peak_Molarity	22.10	6.41
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/G4.png	DNA_Library_set43-44/set1/H4.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set43-44/set1/G4.png	RNA_Library_set43-44/set1/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-55	BGKcLV15-56
RBP	SMAD2	SMAD2
Batch_ID	BGKcLV15	BGKcLV15
WB_result	91.000	91.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	607	608

Sequencing Information

	BGKcLV15-55	BGKcLV15-56
Sample_ID	BGKcLV15-55	BGKcLV15-56
Sample Name	SMAD2-BGKcLV15-55	SMAD2-BGKcLV15-56
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	90,264,994	125,733,128
total_aligned_reads	84,869,960	125,150,568
unique_aligned_reads	77,353,366	114,393,626
percent_uniqueAligned	0.85696	0.90981
correlation_replicates	0.995656	0.995656
spikein_reads	45,672	79,016
percent_spikeins	0.00051	0.00063
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	113	114

Data Submission Information

	BGKcLV15-55	BGKcLV15-55	BGKcLV15-55	BGKcLV15-55	BGKcLV15-55	BGKcLV15-55	BGKcLV15-56	BGKcLV15-56	BGKcLV15-56	BGKcLV15-56
ENCODE_alias	brenton-graveley:SMAD2-BGKcLV15	brenton-graveley:SMAD2-BGKcLV15-55	brenton-graveley:L-SMAD2-BGKcLV15-55	brenton-graveley:SMAD2-BGKcLV15-55_S31_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD2-BGKcLV15-55_S31_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD2-BGKcLV15-K562	brenton-graveley:SMAD2-BGKcLV15-56	brenton-graveley:L-SMAD2-BGKcLV15-56	brenton-graveley:SMAD2-BGKcLV15-56_S32_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD2-BGKcLV15-56_S32_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR016WTN	ENCBS962RKJ	ENCLB115XJC	ENCFF831YTT	ENCFF623KPK	ENCSR271VMA	ENCBS837HRP	ENCLB617RIS	ENCFF965LER	ENCFF946PFZ
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV15-55	BGKcLV15-55	BGKcLV15-55	BGKcLV15-55	BGKcLV15-55	BGKcLV15-55	BGKcLV15-56	BGKcLV15-56	BGKcLV15-56	BGKcLV15-56
Sample Name	SMAD2-BGKcLV15-55	SMAD2-BGKcLV15-55	SMAD2-BGKcLV15-55	SMAD2-BGKcLV15-55	SMAD2-BGKcLV15-55	SMAD2-BGKcLV15-55	SMAD2-BGKcLV15-56	SMAD2-BGKcLV15-56	SMAD2-BGKcLV15-56	SMAD2-BGKcLV15-56
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		SMAD2-BGKcLV15-55.pdf	L-SMAD2-BGKcLV15-55.pdf				SMAD2-BGKcLV15-56.pdf	L-SMAD2-BGKcLV15-56.pdf
ID	32	146	310	508	560	7326	147	311	509	561

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
SMAD2-BGKcLV15-55_S31_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	113	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	109
SMAD2-BGKcLV15-55_S31_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	113	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	161
SMAD2-BGKcLV15-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	113					GRCh38	V40	SMAD2-BGKcLV15-55_S31_R1_001.filtered.trimmed.paired.fastq.gz,SMAD2-BGKcLV15-55_S31_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24400
SMAD2-BGKcLV15-55_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	113					GRCh38	V40	SMAD2-BGKcLV15-55/Aligned.sortedByCoord.out.bam		ENCORE2	24452
SMAD2-BGKcLV15-55_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	113					GRCh38	V40	SMAD2-BGKcLV15-55/Aligned.sortedByCoord.out.bam		ENCORE2	24504
SMAD2-BGKcLV15-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	113					GRCh38	V40	SMAD2-BGKcLV15-55/Aligned.sortedByCoord.out.bam		ENCORE2	24556
SMAD2-BGKcLV15-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	113					GRCh38	V40	SMAD2-BGKcLV15-55/Aligned.sortedByCoord.out.bam		ENCORE2	24608
SMAD2-BGKcLV15-55_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	113					GRCh38	V40	SMAD2-BGKcLV15-55_S31_R1_001.filtered.trimmed.paired.fastq.gz,SMAD2-BGKcLV15-55_S31_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24660
SMAD2-BGKcLV15-56_S32_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	114	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	110
SMAD2-BGKcLV15-56_S32_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	114	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	162
SMAD2-BGKcLV15-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	114					GRCh38	V40	SMAD2-BGKcLV15-56_S32_R1_001.filtered.trimmed.paired.fastq.gz,SMAD2-BGKcLV15-56_S32_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24401
SMAD2-BGKcLV15-56_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	114					GRCh38	V40	SMAD2-BGKcLV15-56/Aligned.sortedByCoord.out.bam		ENCORE2	24453
SMAD2-BGKcLV15-56_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	114					GRCh38	V40	SMAD2-BGKcLV15-56/Aligned.sortedByCoord.out.bam		ENCORE2	24505
SMAD2-BGKcLV15-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	114					GRCh38	V40	SMAD2-BGKcLV15-56/Aligned.sortedByCoord.out.bam		ENCORE2	24557
SMAD2-BGKcLV15-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	114					GRCh38	V40	SMAD2-BGKcLV15-56/Aligned.sortedByCoord.out.bam		ENCORE2	24609
SMAD2-BGKcLV15-56_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	114					GRCh38	V40	SMAD2-BGKcLV15-56_S32_R1_001.filtered.trimmed.paired.fastq.gz,SMAD2-BGKcLV15-56_S32_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24661