RPL11 RNA-Seq in HepG2

General Information


RBP	RPL11
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPL11-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR411BDF
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR702LIH
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	RPL11-BGHcLV16-47
Rep2	RPL11-BGHcLV16-48
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	69.2
Rep2_qPCR	56.4
Rep1_WB	93.4
Rep2_WB	97.8
Antibody Cat#	37-3000
Antibody Lot#	TB259358
Antibody DCC ID	ENCAB959BBQ
Status	Released
Project	ENCODE4
ID	156

Experiment Information (Status: Released)

	BGHcLV16-47	BGHcLV16-48
idx	477	478
TRCN#_or_BGC#	BGC#0000364	BGC#0000364
shRNA_or_gRNA_sequence	GCGGATGCGAAGTTCCCGCA	GCGGATGCGAAGTTCCCGCA
PAM	tgg	tgg
Name	RPL11-94	RPL11-94
Sample_ID	BGHcLV16-47	BGHcLV16-48
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	RPL11	RPL11
qPCR_result	69.2	56.4
Ave_qPCR	62.8
RT-qPCR_primer-F	AGCCAAGGTGTTGGAGCAG
RT-qPCR_primer-R	TGTGCAGTGGACAGCAATCT
protein_conc	3843	4350
WB_result	93.4	97.8
Ave_WB	95.6
WB_DONE_date	4/24/19
MW	20KD
IP	Mouse / Ig
antibody_Cat#	37-3000
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	2390	0
Rep2_TPM	2928	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6626	6627

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL11	Product_ID: 37-3000 Lot_ID: TB259358 Source: Thermo Fisher Target Name: RPL11-human

Experiment Status

	BGHcLV16-47	BGHcLV16-48
Sample_ID	BGHcLV16-47	BGHcLV16-48
Sample Name
Sample Name	RPL11-BGHcLV16-47	RPL11-BGHcLV16-48
RBP	RPL11	RPL11
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5431	5432

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-47	BGHcLV16-48
Sample #	65	66
Sample Name	RPL11-BGHcLV16-47	RPL11-BGHcLV16-48
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	2-G1	2-H1
Tecan	36.09	32.77
Tecan_date	2019-12-10	2019-12-10
Size_bp	271	275
Peak_Molarity	32.50	33.40
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/G3.png	DNA_Library_set43-44/set2/H3.png
RIN	9.4	9.2
libSample_RNA_Well	RNA_Library_set43-44/set3/F12.png	RNA_Library_set43-44/set1/H8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-47	BGHcLV16-48
RBP	RPL11	RPL11
Batch_ID	BGHcLV16	BGHcLV16
WB_result	93.400	97.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	641	642

Sequencing Information

	BGHcLV16-47	BGHcLV16-48
Sample_ID	BGHcLV16-47	BGHcLV16-48
Sample Name	RPL11-BGHcLV16-47	RPL11-BGHcLV16-48
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	143,020,498	125,776,674
total_aligned_reads	132,078,454	116,813,878
unique_aligned_reads	123,794,654	109,525,444
percent_uniqueAligned	0.86557	0.87079
correlation_replicates	0.998606	0.998606
spikein_reads	149,554	157,604
percent_spikeins	0.00105	0.00125
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	143	144

Data Submission Information

	BGHcLV16-47	BGHcLV16-47	BGHcLV16-47	BGHcLV16-47	BGHcLV16-47	BGHcLV16-47	BGHcLV16-48	BGHcLV16-48	BGHcLV16-48	BGHcLV16-48
ENCODE_alias	brenton-graveley:RPL11-BGHcLV16	brenton-graveley:RPL11-BGHcLV16-47	brenton-graveley:L-RPL11-BGHcLV16-47	brenton-graveley:RPL11-BGHcLV16-47_S61_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL11-BGHcLV16-47_S61_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL11-BGHcLV16-HepG2	brenton-graveley:RPL11-BGHcLV16-48	brenton-graveley:L-RPL11-BGHcLV16-48	brenton-graveley:RPL11-BGHcLV16-48_S62_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL11-BGHcLV16-48_S62_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR702LIH	ENCBS252VWD	ENCLB758JWQ	ENCFF866QCQ	ENCFF239DLV	ENCSR411BDF	ENCBS988KQS	ENCLB109GOL	ENCFF111LQS	ENCFF907HDO
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	BGHcLV16-47	BGHcLV16-47	BGHcLV16-47	BGHcLV16-47	BGHcLV16-47	BGHcLV16-47	BGHcLV16-48	BGHcLV16-48	BGHcLV16-48	BGHcLV16-48
Sample Name	RPL11-BGHcLV16-47	RPL11-BGHcLV16-47	RPL11-BGHcLV16-47	RPL11-BGHcLV16-47	RPL11-BGHcLV16-47	RPL11-BGHcLV16-47	RPL11-BGHcLV16-48	RPL11-BGHcLV16-48	RPL11-BGHcLV16-48	RPL11-BGHcLV16-48
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
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		RPL11-BGHcLV16-47.pdf	L-RPL11-BGHcLV16-47.pdf				RPL11-BGHcLV16-48.pdf	L-RPL11-BGHcLV16-48.pdf
ID	12	106	270	436	468	7303	107	271	437	469

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
RPL11-BGHcLV16-47_S61_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	143	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	23
RPL11-BGHcLV16-47_S61_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	143	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	55
RPL11-BGHcLV16-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	143					GRCh38	V40	RPL11-BGHcLV16-47_S61_R1_001.filtered.trimmed.paired.fastq.gz,RPL11-BGHcLV16-47_S61_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24186
RPL11-BGHcLV16-47_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	143					GRCh38	V40	RPL11-BGHcLV16-47/Aligned.sortedByCoord.out.bam		ENCORE2	24218
RPL11-BGHcLV16-47_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	143					GRCh38	V40	RPL11-BGHcLV16-47/Aligned.sortedByCoord.out.bam		ENCORE2	24250
RPL11-BGHcLV16-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	143					GRCh38	V40	RPL11-BGHcLV16-47/Aligned.sortedByCoord.out.bam		ENCORE2	24282
RPL11-BGHcLV16-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	143					GRCh38	V40	RPL11-BGHcLV16-47/Aligned.sortedByCoord.out.bam		ENCORE2	24314
RPL11-BGHcLV16-47_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	143					GRCh38	V40	RPL11-BGHcLV16-47_S61_R1_001.filtered.trimmed.paired.fastq.gz,RPL11-BGHcLV16-47_S61_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24346
RPL11-BGHcLV16-48_S62_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	144	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	24
RPL11-BGHcLV16-48_S62_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	144	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	56
RPL11-BGHcLV16-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	144					GRCh38	V40	RPL11-BGHcLV16-48_S62_R1_001.filtered.trimmed.paired.fastq.gz,RPL11-BGHcLV16-48_S62_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24187
RPL11-BGHcLV16-48_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	144					GRCh38	V40	RPL11-BGHcLV16-48/Aligned.sortedByCoord.out.bam		ENCORE2	24219
RPL11-BGHcLV16-48_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	144					GRCh38	V40	RPL11-BGHcLV16-48/Aligned.sortedByCoord.out.bam		ENCORE2	24251
RPL11-BGHcLV16-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	144					GRCh38	V40	RPL11-BGHcLV16-48/Aligned.sortedByCoord.out.bam		ENCORE2	24283
RPL11-BGHcLV16-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	144					GRCh38	V40	RPL11-BGHcLV16-48/Aligned.sortedByCoord.out.bam		ENCORE2	24315
RPL11-BGHcLV16-48_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	144					GRCh38	V40	RPL11-BGHcLV16-48_S62_R1_001.filtered.trimmed.paired.fastq.gz,RPL11-BGHcLV16-48_S62_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24347