RPL29 RNA-Seq in HepG2

General Information


RBP	RPL29
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPL29-BGHcLV32-HepG2
ENCODE_series_ID	ENCSR023CWM
Batch_ID	BGHcLV32
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR333JNM
ENCODE_CN_Exp_ID	ENCSR232ERY
Rep1	RPL29-BGHcLV32-45
Rep2	RPL29-BGHcLV32-46
CN1	NT-BGHcLV32-1
CN2	NT-BGHcLV32-2
Rep1_qPCR	58.1
Rep2_qPCR	56.4
Rep1_WB	69.9
Rep2_WB	70.3
Antibody Cat#	A305-056A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB581HIJ
Status	Submitted
Project	ENCODE4
ID	937

Experiment Information (Status: Released)

	BGHcLV32-45	BGHcLV32-46
idx	1046	1047
TRCN#_or_BGC#	BGC#0000794	BGC#0000794
shRNA_or_gRNA_sequence	AGGGCCCAAAAAACTTACAC	AGGGCCCAAAAAACTTACAC
PAM	TGG	TGG
Name	RPL29_81	RPL29_81
Sample_ID	BGHcLV32-45	BGHcLV32-46
transduction_Date	10/28/21	10/28/21
days	D6	D6
RBP_name	RPL29	RPL29
qPCR_result	58.1	56.4
Ave_qPCR	57.3
RT-qPCR_primer-F	accccgatcacaaagatacg
RT-qPCR_primer-R	attgttggcctgcatcttct
protein_conc	3794	2862
WB_result	69.9	70.3
Ave_WB	70.1
WB_DONE_date	1/3/22
MW	18KD
IP
antibody_Cat#	A305-056A	LOT #1
Antibody DCC ID	ENCAB581HIJ	8/4/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	2/9/22	2/9/22
repeat_library
Note
ID	7225	7226

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL29	Product_ID: A305-056A Lot_ID: 1 Source: Bethyl Labs Target Name: RPL29-human

Experiment Status

	BGHcLV32-45	BGHcLV32-46
Sample_ID	BGHcLV32-45	BGHcLV32-46
Sample Name		RPL29-BGHcLV32-46
Sample Name	RPL29-BGHcLV32-45	RPL29-BGHcLV32-46
RBP	RPL29	RPL29
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note		FPKM value of MIR1184-2 is 8936330. Correlation between RPL29-BGHcLV32-45 and RPL29-BGHcLV32-46 is 0.009340503. After set MIR1184-2 (ENSG00000221190) value to 0, the Correlation between RPL29-BGHcLV32-45 and RPL29-BGHcLV32-46 is 0.9983562. Furthermore, 0.9974246 was got using salmon counts.
ID	10373	10374

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV32-45	BGHcLV32-46
Sample #	47	48
Sample Name	RPL29-BGHcLV32-45	RPL29-BGHcLV32-46
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-02-01	2022-02-01
Lib_ID	Lib-220201	Lib-220201
Tecan_Location
Tecan
Tecan_date
Size_bp	296	288
Peak_Molarity	61.10	67.70
libSampleQC_DNA_Well	DNA_Library_set52/set2/G6.png	DNA_Library_set52/set2/H6.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set52/set3/H12.png	RNA_Library_set52/set2/D9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-02-16	2022-02-16
Sample_ID	BGHcLV32-45	BGHcLV32-46
RBP	RPL29	RPL29
Batch_ID	BGHcLV32	BGHcLV32
WB_result	69.900	70.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3224	3225

Sequencing Information

	BGHcLV32-45	BGHcLV32-46
Sample_ID	BGHcLV32-45	BGHcLV32-46
Sample Name	RPL29-BGHcLV32-45	RPL29-BGHcLV32-46
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	110,645,972	73,498,502
total_aligned_reads	95,463,240	60,797,544
unique_aligned_reads	89,647,272	57,186,010
percent_uniqueAligned	0.81022	0.77806
correlation_replicates	0.998356	0.998356
spikein_reads	6,194	4,766
percent_spikeins	0.00006	0.00006
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2019	2020

Data Submission Information

	BGHcLV32-45	BGHcLV32-45	BGHcLV32-45	BGHcLV32-45	BGHcLV32-45	BGHcLV32-45	BGHcLV32-46	BGHcLV32-46	BGHcLV32-46	BGHcLV32-46
ENCODE_alias	brenton-graveley:RPL29-BGHcLV32	brenton-graveley:RPL29-BGHcLV32-45	brenton-graveley:L-RPL29-BGHcLV32-45	brenton-graveley:RPL29-BGHcLV32-45_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL29-BGHcLV32-45_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL29-BGHcLV32-HepG2	brenton-graveley:RPL29-BGHcLV32-46	brenton-graveley:L-RPL29-BGHcLV32-46	brenton-graveley:RPL29-BGHcLV32-46_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL29-BGHcLV32-46_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR333JNM	ENCBS455JAT	ENCLB921JRQ	ENCFF727YUS	ENCFF457FNV	ENCSR023CWM	ENCBS446TXU	ENCLB533IXC	ENCFF551RYQ	ENCFF593FLM
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	BGHcLV32-45	BGHcLV32-45	BGHcLV32-45	BGHcLV32-45	BGHcLV32-45	BGHcLV32-45	BGHcLV32-46	BGHcLV32-46	BGHcLV32-46	BGHcLV32-46
Sample Name	RPL29-BGHcLV32-45	RPL29-BGHcLV32-45	RPL29-BGHcLV32-45	RPL29-BGHcLV32-45	RPL29-BGHcLV32-45	RPL29-BGHcLV32-45	RPL29-BGHcLV32-46	RPL29-BGHcLV32-46	RPL29-BGHcLV32-46	RPL29-BGHcLV32-46
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		RPL29-BGHcLV32-45.pdf	L-RPL29-BGHcLV32-45.pdf				RPL29-BGHcLV32-46.pdf	L-RPL29-BGHcLV32-46.pdf
ID	7470	7549	7659	7761	7871	7957	7550	7660	7762	7872

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
RPL29-BGHcLV32-45_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2019	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6519
RPL29-BGHcLV32-45_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2019	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6573
RPL29-BGHcLV32-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2019					GRCh38	V40	RPL29-BGHcLV32-45_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL29-BGHcLV32-45_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18440
RPL29-BGHcLV32-45_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2019					GRCh38	V40	RPL29-BGHcLV32-45/Aligned.sortedByCoord.out.bam		ENCORE2	18494
RPL29-BGHcLV32-45_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2019					GRCh38	V40	RPL29-BGHcLV32-45/Aligned.sortedByCoord.out.bam		ENCORE2	18548
RPL29-BGHcLV32-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2019					GRCh38	V40	RPL29-BGHcLV32-45/Aligned.sortedByCoord.out.bam		ENCORE2	18602
RPL29-BGHcLV32-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2019					GRCh38	V40	RPL29-BGHcLV32-45/Aligned.sortedByCoord.out.bam		ENCORE2	18656
RPL29-BGHcLV32-45_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2019					GRCh38	V40	RPL29-BGHcLV32-45_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL29-BGHcLV32-45_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18710
RPL29-BGHcLV32-46_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2020	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6520
RPL29-BGHcLV32-46_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2020	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6574
RPL29-BGHcLV32-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2020					GRCh38	V40	RPL29-BGHcLV32-46_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL29-BGHcLV32-46_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18441
RPL29-BGHcLV32-46_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2020					GRCh38	V40	RPL29-BGHcLV32-46/Aligned.sortedByCoord.out.bam		ENCORE2	18495
RPL29-BGHcLV32-46_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2020					GRCh38	V40	RPL29-BGHcLV32-46/Aligned.sortedByCoord.out.bam		ENCORE2	18549
RPL29-BGHcLV32-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2020					GRCh38	V40	RPL29-BGHcLV32-46/Aligned.sortedByCoord.out.bam		ENCORE2	18603
RPL29-BGHcLV32-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2020					GRCh38	V40	RPL29-BGHcLV32-46/Aligned.sortedByCoord.out.bam		ENCORE2	18657
RPL29-BGHcLV32-46_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2020					GRCh38	V40	RPL29-BGHcLV32-46_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL29-BGHcLV32-46_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18711