RPL18 RNA-Seq in HepG2

General Information


RBP	RPL18
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPL18-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR612JXK
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR468LEL
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	RPL18-BGHcLV22-45
Rep2	RPL18-BGHcLV22-46
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	90.1
Rep2_WB	92.7
Antibody Cat#	A305-340A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB569OQM
Status	Released
Project	ENCODE4
ID	47

Experiment Information (Status: Released)

	BGHcLV22-45	BGHcLV22-46
idx	638	639
TRCN#_or_BGC#	BGC#0000536	BGC#0000536
shRNA_or_gRNA_sequence	AGTGGACATCCGCCATAACA	AGTGGACATCCGCCATAACA
PAM	AGG	AGG
Name	RPL18_90	RPL18_90
Sample_ID	BGHcLV22-45	BGHcLV22-46
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	RPL18	RPL18
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ggttgtggggaccataactg
RT-qPCR_primer-R	tggtcgaaagtgaggatcttg
protein_conc	1431	1656
WB_result	90.1	92.7
Ave_WB	91.4
WB_DONE_date	9/9/20
MW	21.6kDa
IP	Rabbit / I
antibody_Cat#	A305-340A	LOT# 1
Antibody DCC ID	ENCAB569OQM
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	6793	6794

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL18	Product_ID: A305-340A Lot_ID: 1 Source: Bethyl Labs Target Name: RPL18-human

Experiment Status

	BGHcLV22-45	BGHcLV22-46
Sample_ID	BGHcLV22-45	BGHcLV22-46
Sample Name
Sample Name	RPL18-BGHcLV22-45	RPL18-BGHcLV22-46
RBP	RPL18	RPL18
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7387	7388

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-45	BGHcLV22-46
Sample #	23	24
Sample Name	RPL18-BGHcLV22-45	RPL18-BGHcLV22-46
Sample_Name_Alias
Index Well Position	G03	H03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	284	289
Peak_Molarity	166.00	162.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/G3.png	DNA_Library_set46/set1/H3.png
RIN	9.7	9.2
libSample_RNA_Well	RNA_Library_set46/set1/G11.png	RNA_Library_set46/set1/H11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-45	BGHcLV22-46
RBP	RPL18	RPL18
Batch_ID	BGHcLV22	BGHcLV22
WB_result	90.100	92.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1398	1399

Sequencing Information

	BGHcLV22-45	BGHcLV22-46
Sample_ID	BGHcLV22-45	BGHcLV22-46
Sample Name	RPL18-BGHcLV22-45	RPL18-BGHcLV22-46
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	130,030,170	124,375,862
total_aligned_reads	111,409,350	107,578,758
unique_aligned_reads	103,706,720	100,306,550
percent_uniqueAligned	0.79756	0.80648
correlation_replicates	0.999167	0.999167
spikein_reads	36,424	32,562
percent_spikeins	0.00028	0.00026
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	504	505

Data Submission Information

	BGHcLV22-45	BGHcLV22-45	BGHcLV22-45	BGHcLV22-45	BGHcLV22-45	BGHcLV22-45	BGHcLV22-46	BGHcLV22-46	BGHcLV22-46	BGHcLV22-46
ENCODE_alias	brenton-graveley:RPL18-BGHcLV22	brenton-graveley:RPL18-BGHcLV22-45	brenton-graveley:L-RPL18-BGHcLV22-45	brenton-graveley:RPL18-BGHcLV22-45_GCAGAATT+TGGCCGGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL18-BGHcLV22-45_GCAGAATT+TGGCCGGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL18-BGHcLV22-HepG2	brenton-graveley:RPL18-BGHcLV22-46	brenton-graveley:L-RPL18-BGHcLV22-46	brenton-graveley:RPL18-BGHcLV22-46_ATGAGGCC+CAATTAAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL18-BGHcLV22-46_ATGAGGCC+CAATTAAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR468LEL	ENCBS404UWM	ENCLB955ONZ	ENCFF803RDV	ENCFF344GOP	ENCSR612JXK	ENCBS706RQK	ENCLB132KFH	ENCFF337NUA	ENCFF721BAT
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	BGHcLV22-45	BGHcLV22-45	BGHcLV22-45	BGHcLV22-45	BGHcLV22-45	BGHcLV22-45	BGHcLV22-46	BGHcLV22-46	BGHcLV22-46	BGHcLV22-46
Sample Name	RPL18-BGHcLV22-45	RPL18-BGHcLV22-45	RPL18-BGHcLV22-45	RPL18-BGHcLV22-45	RPL18-BGHcLV22-45	RPL18-BGHcLV22-45	RPL18-BGHcLV22-46	RPL18-BGHcLV22-46	RPL18-BGHcLV22-46	RPL18-BGHcLV22-46
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		RPL18-BGHcLV22-45.pdf	L-RPL18-BGHcLV22-45.pdf				RPL18-BGHcLV22-46.pdf	L-RPL18-BGHcLV22-46.pdf
ID	2406	2449	2513	2577	2607	7305	2450	2514	2578	2608

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
RPL18-BGHcLV22-45_GCAGAATT+TGGCCGGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	504	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1370
RPL18-BGHcLV22-45_GCAGAATT+TGGCCGGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	504	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1434
RPL18-BGHcLV22-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	504					GRCh38	V40	RPL18-BGHcLV22-45_GCAGAATT+TGGCCGGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL18-BGHcLV22-45_GCAGAATT+TGGCCGGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25273
RPL18-BGHcLV22-45_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	504					GRCh38	V40	RPL18-BGHcLV22-45_GCAGAATT+TGGCCGGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL18-BGHcLV22-45_GCAGAATT+TGGCCGGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25371
RPL18-BGHcLV22-45_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	504					GRCh38	V40	RPL18-BGHcLV22-45/Aligned.sortedByCoord.out.bam		ENCORE2	26021
RPL18-BGHcLV22-45_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	504					GRCh38	V40	RPL18-BGHcLV22-45/Aligned.sortedByCoord.out.bam		ENCORE2	26051
RPL18-BGHcLV22-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	504					GRCh38	V40	RPL18-BGHcLV22-45/Aligned.sortedByCoord.out.bam		ENCORE2	26081
RPL18-BGHcLV22-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	504					GRCh38	V40	RPL18-BGHcLV22-45/Aligned.sortedByCoord.out.bam		ENCORE2	26111
RPL18-BGHcLV22-46_ATGAGGCC+CAATTAAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	505	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1371
RPL18-BGHcLV22-46_ATGAGGCC+CAATTAAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	505	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1435
RPL18-BGHcLV22-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	505					GRCh38	V40	RPL18-BGHcLV22-46_ATGAGGCC+CAATTAAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL18-BGHcLV22-46_ATGAGGCC+CAATTAAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25274
RPL18-BGHcLV22-46_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	505					GRCh38	V40	RPL18-BGHcLV22-46_ATGAGGCC+CAATTAAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL18-BGHcLV22-46_ATGAGGCC+CAATTAAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25372
RPL18-BGHcLV22-46_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	505					GRCh38	V40	RPL18-BGHcLV22-46/Aligned.sortedByCoord.out.bam		ENCORE2	26022
RPL18-BGHcLV22-46_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	505					GRCh38	V40	RPL18-BGHcLV22-46/Aligned.sortedByCoord.out.bam		ENCORE2	26052
RPL18-BGHcLV22-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	505					GRCh38	V40	RPL18-BGHcLV22-46/Aligned.sortedByCoord.out.bam		ENCORE2	26082
RPL18-BGHcLV22-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	505					GRCh38	V40	RPL18-BGHcLV22-46/Aligned.sortedByCoord.out.bam		ENCORE2	26112