PDCD4 RNA-Seq in K562

General Information


RBP	PDCD4
Cell_Line	K562
Method	CRISPR
Exp_Name	PDCD4-BGKcLV17-K562
ENCODE_series_ID	ENCSR110ICH
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR469UOO
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	PDCD4-BGKcLV17-35
Rep2	PDCD4-BGKcLV17-36
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	34.5
Rep2_qPCR	51.6
Rep1_WB	67.7
Rep2_WB	70.4
Antibody Cat#	PA5-20309
Antibody Lot#	lot# TK2671263A
Antibody DCC ID	ENCAB961TZA
Status	Released
Project	ENCODE4
ID	90

Experiment Information (Status: Released)

	BGKcLV17-35	BGKcLV17-35	BGKcLV17-36	BGKcLV17-36
idx	642	642	643	643
TRCN#_or_BGC#	BGC#0000404	BGC#0000404	BGC#0000404	BGC#0000404
shRNA_or_gRNA_sequence	GCGATTCGGTCAGCGACAGT	GCGATTCGGTCAGCGACAGT	GCGATTCGGTCAGCGACAGT	GCGATTCGGTCAGCGACAGT
PAM	GGG	GGG	GGG	GGG
Name	PDCD4_96	PDCD4_96	PDCD4_96	PDCD4_96
Sample_ID	BGKcLV17-35	BGKcLV17-35	BGKcLV17-36	BGKcLV17-36
transduction_Date	7/2/19	7/2/19	7/2/19	7/2/19
days	Day 6	Day 6	Day 6	Day 6
RBP_name	PDCD4	PDCD4	PDCD4	PDCD4
qPCR_result	34.5	34.5	51.6	51.6
Ave_qPCR	43.0	43.0
RT-qPCR_primer-F	TGGTGGGCCAGTTTATTGCT	TGGTGGGCCAGTTTATTGCT
RT-qPCR_primer-R	AAGCACGGTAGCCTTATCCAG	AAGCACGGTAGCCTTATCCAG
protein_conc	4570	4570	4898	4898
WB_result	67.7	96.897	70.4	96.444
Ave_WB	69.0	96.6705
WB_DONE_date	7/23/19	6/14/23
MW	52KD	52KD
IP	Rabbit / I		Polyclonal
antibody_Cat#	PA5-20309	9535S	lot# TK2671263A	LOT # 5
Antibody DCC ID	ENCAB961TZA
submitted_to_DCC_date	8/20/19
Rep1_TPM	27.9	0	0	0
Rep2_TPM	26	0	0	0
Action	Ready		Ready
Library_start_date	12/05/19		12/05/19
repeat_library
Note
ID	4758	4760	4759	4761

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PDCD4	Product_ID: PA5-20309 Lot_ID: TK2671263A Source: Thermo Fisher Target Name: PDCD4-human
PDCD4	Product_ID: 9535S Lot_ID: 5 Source: Cell Signaling Technology Target Name: PDCD4-human

Experiment Status

	BGKcLV17-35	BGKcLV17-36
Sample_ID	BGKcLV17-35	BGKcLV17-36
Sample Name
Sample Name	PDCD4-BGKcLV17-35	PDCD4-BGKcLV17-36
RBP	PDCD4	PDCD4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5513	5514

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-35	BGKcLV17-36
Sample #	103	104
Sample Name	PDCD4-BGKcLV17-35	PDCD4-BGKcLV17-36
Sample_Name_Alias
Index Well Position	C01	D01
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-C1	2-D1
Tecan	48.94	35.32
Tecan_date	2019-12-16	2019-12-16
Size_bp	275	277
Peak_Molarity	19.40	19.80
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C9.png	DNA_Library_set43-44/set1/D9.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_set43-44/set4/C4.png	RNA_Library_set43-44/set4/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-35	BGKcLV17-36
RBP	PDCD4	PDCD4
Batch_ID	BGKcLV17	BGKcLV17
WB_result	67.700	70.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	679	680

Sequencing Information

	BGKcLV17-35	BGKcLV17-36
Sample_ID	BGKcLV17-35	BGKcLV17-36
Sample Name	PDCD4-BGKcLV17-35	PDCD4-BGKcLV17-36
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	117,647,060	481,756,482
total_aligned_reads	109,645,458	430,024,416
unique_aligned_reads	99,748,210	388,462,628
percent_uniqueAligned	0.84786	0.80635
correlation_replicates	0.998759	0.998759
spikein_reads	23,510	124,196
percent_spikeins	0.00020	0.00026
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	185	186

Data Submission Information

	BGKcLV17-35	BGKcLV17-35	BGKcLV17-35	BGKcLV17-35	BGKcLV17-35	BGKcLV17-35	BGKcLV17-36	BGKcLV17-36	BGKcLV17-36	BGKcLV17-36
ENCODE_alias	brenton-graveley:PDCD4-BGKcLV17	brenton-graveley:PDCD4-BGKcLV17-35	brenton-graveley:L-PDCD4-BGKcLV17-35	brenton-graveley:PDCD4-BGKcLV17-35_S13_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PDCD4-BGKcLV17-35_S13_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PDCD4-BGKcLV17-K562	brenton-graveley:PDCD4-BGKcLV17-36	brenton-graveley:L-PDCD4-BGKcLV17-36	brenton-graveley:PDCD4-BGKcLV17-36_S14_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PDCD4-BGKcLV17-36_S14_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR469UOO	ENCBS305PYJ	ENCLB490RGU	ENCFF363FSK	ENCFF950ZRE	ENCSR110ICH	ENCBS602WPB	ENCLB673QGO	ENCFF586XRQ	ENCFF932FIK
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	BGKcLV17-35	BGKcLV17-35	BGKcLV17-35	BGKcLV17-35	BGKcLV17-35	BGKcLV17-35	BGKcLV17-36	BGKcLV17-36	BGKcLV17-36	BGKcLV17-36
Sample Name	PDCD4-BGKcLV17-35	PDCD4-BGKcLV17-35	PDCD4-BGKcLV17-35	PDCD4-BGKcLV17-35	PDCD4-BGKcLV17-35	PDCD4-BGKcLV17-35	PDCD4-BGKcLV17-36	PDCD4-BGKcLV17-36	PDCD4-BGKcLV17-36	PDCD4-BGKcLV17-36
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		PDCD4-BGKcLV17-35.pdf	L-PDCD4-BGKcLV17-35.pdf				PDCD4-BGKcLV17-36.pdf	L-PDCD4-BGKcLV17-36.pdf
ID	76	232	398	700	730	7281	233	399	701	731

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
PDCD4-BGKcLV17-35_S13_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	185	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	287
PDCD4-BGKcLV17-35_S13_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	185	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	317
PDCD4-BGKcLV17-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	185					GRCh38	V40	PDCD4-BGKcLV17-35_S13_R1_001.filtered.trimmed.paired.fastq.gz,PDCD4-BGKcLV17-35_S13_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24683
PDCD4-BGKcLV17-35_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	185					GRCh38	V40	PDCD4-BGKcLV17-35/Aligned.sortedByCoord.out.bam		ENCORE2	24713
PDCD4-BGKcLV17-35_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	185					GRCh38	V40	PDCD4-BGKcLV17-35/Aligned.sortedByCoord.out.bam		ENCORE2	24743
PDCD4-BGKcLV17-35_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	185					GRCh38	V40	PDCD4-BGKcLV17-35/Aligned.sortedByCoord.out.bam		ENCORE2	24773
PDCD4-BGKcLV17-35_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	185					GRCh38	V40	PDCD4-BGKcLV17-35/Aligned.sortedByCoord.out.bam		ENCORE2	24803
PDCD4-BGKcLV17-35_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	185					GRCh38	V40	PDCD4-BGKcLV17-35_S13_R1_001.filtered.trimmed.paired.fastq.gz,PDCD4-BGKcLV17-35_S13_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24833
PDCD4-BGKcLV17-36_S14_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	186	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	288
PDCD4-BGKcLV17-36_S14_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	186	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	318
PDCD4-BGKcLV17-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	186					GRCh38	V40	PDCD4-BGKcLV17-36_S14_R1_001.filtered.trimmed.paired.fastq.gz,PDCD4-BGKcLV17-36_S14_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24684
PDCD4-BGKcLV17-36_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	186					GRCh38	V40	PDCD4-BGKcLV17-36/Aligned.sortedByCoord.out.bam		ENCORE2	24714
PDCD4-BGKcLV17-36_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	186					GRCh38	V40	PDCD4-BGKcLV17-36/Aligned.sortedByCoord.out.bam		ENCORE2	24744
PDCD4-BGKcLV17-36_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	186					GRCh38	V40	PDCD4-BGKcLV17-36/Aligned.sortedByCoord.out.bam		ENCORE2	24774
PDCD4-BGKcLV17-36_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	186					GRCh38	V40	PDCD4-BGKcLV17-36/Aligned.sortedByCoord.out.bam		ENCORE2	24804
PDCD4-BGKcLV17-36_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	186					GRCh38	V40	PDCD4-BGKcLV17-36_S14_R1_001.filtered.trimmed.paired.fastq.gz,PDCD4-BGKcLV17-36_S14_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24834