SMAD4 RNA-Seq in K562

General Information


RBP	SMAD4
Cell_Line	K562
Method	CRISPR
Exp_Name	SMAD4-BGKcLV17-K562
ENCODE_series_ID	ENCSR118HZW
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR965MSX
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	SMAD4-BGKcLV17-47
Rep2	SMAD4-BGKcLV17-48
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	25.6
Rep2_qPCR	35.7
Rep1_WB	68.9
Rep2_WB	79.5
Antibody Cat#	701682
Antibody Lot#	lot# 2023880
Antibody DCC ID	ENCAB628ZTV
Status	Released
Project	ENCODE4
ID	94

Experiment Information (Status: Released)

	BGKcLV17-47	BGKcLV17-48
idx	654	655
TRCN#_or_BGC#	BGC#0000426	BGC#0000426
shRNA_or_gRNA_sequence	GTCGATGCACGATTACTTGG	GTCGATGCACGATTACTTGG
PAM	TGG	TGG
Name	SMAD4_97	SMAD4_97
Sample_ID	BGKcLV17-47	BGKcLV17-48
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	SMAD4	SMAD4
qPCR_result	25.6	35.7
Ave_qPCR	30.7
RT-qPCR_primer-F	CTGGCCCAGGATCAGTAGGT
RT-qPCR_primer-R	CATCAACACCAATTCCAGCA
protein_conc	5909	5723
WB_result	68.9	79.5
Ave_WB	74.2
WB_DONE_date	7/25/19
MW	60KD
IP	Rabbit / I	Monoclonal
antibody_Cat#	701682	lot# 2023880
Antibody DCC ID	ENCAB628ZTV
submitted_to_DCC_date
Rep1_TPM	22.8	0
Rep2_TPM	26.7	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4772	4773

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMAD4	Product_ID: 701682 Lot_ID: 2023880 Source: Thermo Fisher Target Name: SMAD4-human

Experiment Status

	BGKcLV17-47	BGKcLV17-48
Sample_ID	BGKcLV17-47	BGKcLV17-48
Sample Name
Sample Name	SMAD4-BGKcLV17-47	SMAD4-BGKcLV17-48
RBP	SMAD4	SMAD4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5521	5522

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-47	BGKcLV17-48
Sample #	111	112
Sample Name	SMAD4-BGKcLV17-47	SMAD4-BGKcLV17-48
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	2-C2	2-D2
Tecan	36.35	45.82
Tecan_date	2019-12-16	2019-12-16
Size_bp	277	277
Peak_Molarity	28.60	26.40
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C10.png	DNA_Library_set43-44/set1/D10.png
RIN	9.4	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/C5.png	RNA_Library_set43-44/set4/D5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-47	BGKcLV17-48
RBP	SMAD4	SMAD4
Batch_ID	BGKcLV17	BGKcLV17
WB_result	68.900	79.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	687	688

Sequencing Information

	BGKcLV17-47	BGKcLV17-48
Sample_ID	BGKcLV17-47	BGKcLV17-48
Sample Name	SMAD4-BGKcLV17-47	SMAD4-BGKcLV17-48
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	125,703,840	135,963,442
total_aligned_reads	125,606,312	134,878,472
unique_aligned_reads	114,120,292	122,704,440
percent_uniqueAligned	0.90785	0.90248
correlation_replicates	0.998842	0.998842
spikein_reads	35,604	34,776
percent_spikeins	0.00028	0.00026
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	193	194

Data Submission Information

	BGKcLV17-47	BGKcLV17-47	BGKcLV17-47	BGKcLV17-47	BGKcLV17-47	BGKcLV17-47	BGKcLV17-48	BGKcLV17-48	BGKcLV17-48	BGKcLV17-48
ENCODE_alias	brenton-graveley:SMAD4-BGKcLV17	brenton-graveley:SMAD4-BGKcLV17-47	brenton-graveley:L-SMAD4-BGKcLV17-47	brenton-graveley:SMAD4-BGKcLV17-47_S21_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD4-BGKcLV17-47_S21_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD4-BGKcLV17-K562	brenton-graveley:SMAD4-BGKcLV17-48	brenton-graveley:L-SMAD4-BGKcLV17-48	brenton-graveley:SMAD4-BGKcLV17-48_S22_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMAD4-BGKcLV17-48_S22_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR965MSX	ENCBS099TIX	ENCLB123NRK	ENCFF167FXP	ENCFF911VQS	ENCSR118HZW	ENCBS242OIJ	ENCLB902ZQT	ENCFF247CSK	ENCFF289QXB
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	BGKcLV17-47	BGKcLV17-47	BGKcLV17-47	BGKcLV17-47	BGKcLV17-47	BGKcLV17-47	BGKcLV17-48	BGKcLV17-48	BGKcLV17-48	BGKcLV17-48
Sample Name	SMAD4-BGKcLV17-47	SMAD4-BGKcLV17-47	SMAD4-BGKcLV17-47	SMAD4-BGKcLV17-47	SMAD4-BGKcLV17-47	SMAD4-BGKcLV17-47	SMAD4-BGKcLV17-48	SMAD4-BGKcLV17-48	SMAD4-BGKcLV17-48	SMAD4-BGKcLV17-48
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		SMAD4-BGKcLV17-47.pdf	L-SMAD4-BGKcLV17-47.pdf				SMAD4-BGKcLV17-48.pdf	L-SMAD4-BGKcLV17-48.pdf
ID	80	240	406	708	738	7328	241	407	709	739

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
SMAD4-BGKcLV17-47_S21_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	193	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	295
SMAD4-BGKcLV17-47_S21_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	193	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	325
SMAD4-BGKcLV17-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	193					GRCh38	V40	SMAD4-BGKcLV17-47_S21_R1_001.filtered.trimmed.paired.fastq.gz,SMAD4-BGKcLV17-47_S21_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24691
SMAD4-BGKcLV17-47_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	193					GRCh38	V40	SMAD4-BGKcLV17-47/Aligned.sortedByCoord.out.bam		ENCORE2	24721
SMAD4-BGKcLV17-47_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	193					GRCh38	V40	SMAD4-BGKcLV17-47/Aligned.sortedByCoord.out.bam		ENCORE2	24751
SMAD4-BGKcLV17-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	193					GRCh38	V40	SMAD4-BGKcLV17-47/Aligned.sortedByCoord.out.bam		ENCORE2	24781
SMAD4-BGKcLV17-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	193					GRCh38	V40	SMAD4-BGKcLV17-47/Aligned.sortedByCoord.out.bam		ENCORE2	24811
SMAD4-BGKcLV17-47_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	193					GRCh38	V40	SMAD4-BGKcLV17-47_S21_R1_001.filtered.trimmed.paired.fastq.gz,SMAD4-BGKcLV17-47_S21_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24841
SMAD4-BGKcLV17-48_S22_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	194	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	296
SMAD4-BGKcLV17-48_S22_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	194	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	326
SMAD4-BGKcLV17-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	194					GRCh38	V40	SMAD4-BGKcLV17-48_S22_R1_001.filtered.trimmed.paired.fastq.gz,SMAD4-BGKcLV17-48_S22_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24692
SMAD4-BGKcLV17-48_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	194					GRCh38	V40	SMAD4-BGKcLV17-48/Aligned.sortedByCoord.out.bam		ENCORE2	24722
SMAD4-BGKcLV17-48_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	194					GRCh38	V40	SMAD4-BGKcLV17-48/Aligned.sortedByCoord.out.bam		ENCORE2	24752
SMAD4-BGKcLV17-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	194					GRCh38	V40	SMAD4-BGKcLV17-48/Aligned.sortedByCoord.out.bam		ENCORE2	24782
SMAD4-BGKcLV17-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	194					GRCh38	V40	SMAD4-BGKcLV17-48/Aligned.sortedByCoord.out.bam		ENCORE2	24812
SMAD4-BGKcLV17-48_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	194					GRCh38	V40	SMAD4-BGKcLV17-48_S22_R1_001.filtered.trimmed.paired.fastq.gz,SMAD4-BGKcLV17-48_S22_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24842