PDCD4 RNA-Seq in HepG2

General Information


RBP	PDCD4
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PDCD4-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR381DHJ
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR580XTY
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	PDCD4-BGHcLV18-31
Rep2	PDCD4-BGHcLV18-32
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	42.6
Rep2_qPCR	54.4
Rep1_WB	92.4
Rep2_WB	90.3
Antibody Cat#	PA5-20309
Antibody Lot#	lot# TK2671263A
Antibody DCC ID	ENCAB961TZA
Status	Released
Project	ENCODE4
ID	112

Experiment Information (Status: Released)

	BGHcLV18-31	BGHcLV18-32
idx	524	525
TRCN#_or_BGC#	BGC#0000404	BGC#0000404
shRNA_or_gRNA_sequence	GCGATTCGGTCAGCGACAGT	GCGATTCGGTCAGCGACAGT
PAM	GGG	GGG
Name	PDCD4_96	PDCD4_96
Sample_ID	BGHcLV18-31	BGHcLV18-32
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	PDCD4	PDCD4
qPCR_result	42.6	54.4
Ave_qPCR	48.5
RT-qPCR_primer-F	TGGTGGGCCAGTTTATTGCT
RT-qPCR_primer-R	AAGCACGGTAGCCTTATCCAG
protein_conc	3932	4187
WB_result	92.4	90.3
Ave_WB	91.4
WB_DONE_date	9/23/19
MW	52KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-20309	lot# TK2671263A
Antibody DCC ID	ENCAB961TZA	11/24/20
submitted_to_DCC_date
Rep1_TPM	30	0
Rep2_TPM	35	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6679	6680

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

Experiment Status

	BGHcLV18-31	BGHcLV18-32
Sample_ID	BGHcLV18-31	BGHcLV18-32
Sample Name	PDCD4-BGHcLV18-31	PDCD4-BGHcLV18-32
Sample Name	PDCD4-BGHcLV18-31	PDCD4-BGHcLV18-32
RBP	PDCD4	PDCD4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5641	5642

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-31	BGHcLV18-32
Sample #	147	148
Sample Name	PDCD4-BGHcLV18-31	PDCD4-BGHcLV18-32
Sample_Name_Alias
Index Well Position	C07	D07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	4-G2	4-H2
Tecan	26.47	36.83
Tecan_date	2019-12-16	2019-12-16
Size_bp	287	275
Peak_Molarity	28.90	25.20
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/A8.png	DNA_Library_set43-44/set2/B8.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_set43-44/set4/E9.png	RNA_Library_set43-44/set4/F9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-31	BGHcLV18-32
RBP	PDCD4	PDCD4
Batch_ID	BGHcLV18	BGHcLV18
WB_result	92.400	90.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	723	724

Sequencing Information

	BGHcLV18-31	BGHcLV18-32
Sample_ID	BGHcLV18-31	BGHcLV18-32
Sample Name	PDCD4-BGHcLV18-31	PDCD4-BGHcLV18-32
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	170,405,936	145,727,964
total_aligned_reads	166,249,568	140,747,658
unique_aligned_reads	155,662,806	131,909,544
percent_uniqueAligned	0.91348	0.90518
correlation_replicates	0.997963	0.997963
spikein_reads	345,260	274,362
percent_spikeins	0.00203	0.00188
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	229	230

Data Submission Information

	BGHcLV18-31	BGHcLV18-31	BGHcLV18-31	BGHcLV18-31	BGHcLV18-31	BGHcLV18-31	BGHcLV18-32	BGHcLV18-32	BGHcLV18-32	BGHcLV18-32
ENCODE_alias	brenton-graveley:PDCD4-BGHcLV18	brenton-graveley:PDCD4-BGHcLV18-31	brenton-graveley:L-PDCD4-BGHcLV18-31	brenton-graveley:PDCD4-BGHcLV18-31_S59_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PDCD4-BGHcLV18-31_S59_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PDCD4-BGHcLV18-HepG2	brenton-graveley:PDCD4-BGHcLV18-32	brenton-graveley:L-PDCD4-BGHcLV18-32	brenton-graveley:PDCD4-BGHcLV18-32_S60_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PDCD4-BGHcLV18-32_S60_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR580XTY	ENCBS924PSY	ENCLB633RDN	ENCFF854HZB	ENCFF693SYT	ENCSR381DHJ	ENCBS432SFH	ENCLB654FZM	ENCFF455XWV	ENCFF045UGV
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	BGHcLV18-31	BGHcLV18-31	BGHcLV18-31	BGHcLV18-31	BGHcLV18-31	BGHcLV18-31	BGHcLV18-32	BGHcLV18-32	BGHcLV18-32	BGHcLV18-32
Sample Name	PDCD4-BGHcLV18-31	PDCD4-BGHcLV18-31	PDCD4-BGHcLV18-31	PDCD4-BGHcLV18-31	PDCD4-BGHcLV18-31	PDCD4-BGHcLV18-31	PDCD4-BGHcLV18-32	PDCD4-BGHcLV18-32	PDCD4-BGHcLV18-32	PDCD4-BGHcLV18-32
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
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		PDCD4-BGHcLV18-31.pdf	L-PDCD4-BGHcLV18-31.pdf				PDCD4-BGHcLV18-32.pdf	L-PDCD4-BGHcLV18-32.pdf
ID	59	198	364	614	666	7280	199	365	615	667

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-BGHcLV18-31_S59_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	229	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	201
PDCD4-BGHcLV18-31_S59_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	229	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	253
PDCD4-BGHcLV18-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	229					GRCh38	V40	PDCD4-BGHcLV18-31_S59_R1_001.filtered.trimmed.paired.fastq.gz,PDCD4-BGHcLV18-31_S59_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24921
PDCD4-BGHcLV18-31_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	229					GRCh38	V40	PDCD4-BGHcLV18-31/Aligned.sortedByCoord.out.bam		ENCORE2	24973
PDCD4-BGHcLV18-31_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	229					GRCh38	V40	PDCD4-BGHcLV18-31/Aligned.sortedByCoord.out.bam		ENCORE2	25025
PDCD4-BGHcLV18-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	229					GRCh38	V40	PDCD4-BGHcLV18-31/Aligned.sortedByCoord.out.bam		ENCORE2	25077
PDCD4-BGHcLV18-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	229					GRCh38	V40	PDCD4-BGHcLV18-31/Aligned.sortedByCoord.out.bam		ENCORE2	25129
PDCD4-BGHcLV18-31_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	229					GRCh38	V40	PDCD4-BGHcLV18-31_S59_R1_001.filtered.trimmed.paired.fastq.gz,PDCD4-BGHcLV18-31_S59_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25181
PDCD4-BGHcLV18-32_S60_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	230	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	202
PDCD4-BGHcLV18-32_S60_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	230	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	254
PDCD4-BGHcLV18-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	230					GRCh38	V40	PDCD4-BGHcLV18-32_S60_R1_001.filtered.trimmed.paired.fastq.gz,PDCD4-BGHcLV18-32_S60_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24922
PDCD4-BGHcLV18-32_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	230					GRCh38	V40	PDCD4-BGHcLV18-32/Aligned.sortedByCoord.out.bam		ENCORE2	24974
PDCD4-BGHcLV18-32_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	230					GRCh38	V40	PDCD4-BGHcLV18-32/Aligned.sortedByCoord.out.bam		ENCORE2	25026
PDCD4-BGHcLV18-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	230					GRCh38	V40	PDCD4-BGHcLV18-32/Aligned.sortedByCoord.out.bam		ENCORE2	25078
PDCD4-BGHcLV18-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	230					GRCh38	V40	PDCD4-BGHcLV18-32/Aligned.sortedByCoord.out.bam		ENCORE2	25130
PDCD4-BGHcLV18-32_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	230					GRCh38	V40	PDCD4-BGHcLV18-32_S60_R1_001.filtered.trimmed.paired.fastq.gz,PDCD4-BGHcLV18-32_S60_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25182