RPS8 RNA-Seq in HepG2

General Information


RBP	RPS8
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPS8-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR254YPW
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR994NGU
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	RPS8-BGHcLV31-9
Rep2	RPS8-BGHcLV31-10
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR	66.4
Rep2_qPCR	54.5
Rep1_WB	52.5
Rep2_WB	55.8
Antibody Cat#	A305-017A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB058SUF
Status	Submitted
Project	ENCODE4
ID	918

Experiment Information (Status: Released)

	BGHcLV31-9	BGHcLV31-10
idx	925	926
TRCN#_or_BGC#	BGC#0000826	BGC#0000826
shRNA_or_gRNA_sequence	GGAAGTAACACGCACCAGCT	GGAAGTAACACGCACCAGCT
PAM	TGG	TGG
Name	RPS8_89	RPS8_89
Sample_ID	BGHcLV31-9	BGHcLV31-10
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	RPS8	RPS8
qPCR_result	66.4	54.5
Ave_qPCR	60.5
RT-qPCR_primer-F	agtctcctggaggagcagttc
RT-qPCR_primer-R	ttgccctctagcacatagcc
protein_conc	3435	2575
WB_result	52.5	55.8
Ave_WB	54.2
WB_DONE_date	10/4/21
MW	24kd
IP
antibody_Cat#	A305-017A	LOT #1
Antibody DCC ID	ENCAB058SUF
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7104	7105

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS8	Product_ID: A305-017A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS8-human

Experiment Status

	BGHcLV31-9	BGHcLV31-10
Sample_ID	BGHcLV31-9	BGHcLV31-10
Sample Name
Sample Name	RPS8-BGHcLV31-9	RPS8-BGHcLV31-10
RBP	RPS8	RPS8
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10291	10292

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-9	BGHcLV31-10
Sample #	5	6
Sample Name	RPS8-BGHcLV31-9	RPS8-BGHcLV31-10
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	280	283
Peak_Molarity	74.90	80.90
libSampleQC_DNA_Well	DNA_Library_set52/set1/E8.png	DNA_Library_set52/set1/F8.png
RIN	9.6	9.1
libSample_RNA_Well	RNA_Library_set52/set1/E1.png	RNA_Library_set52/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-9	BGHcLV31-10
RBP	RPS8	RPS8
Batch_ID	BGHcLV31	BGHcLV31
WB_result	52.500	55.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3182	3183

Sequencing Information

	BGHcLV31-9	BGHcLV31-10
Sample_ID	BGHcLV31-9	BGHcLV31-10
Sample Name	RPS8-BGHcLV31-9	RPS8-BGHcLV31-10
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	110,487,720	74,248,232
total_aligned_reads	95,941,802	65,641,134
unique_aligned_reads	90,183,818	61,833,092
percent_uniqueAligned	0.81623	0.83279
correlation_replicates	0.998705	0.998705
spikein_reads	14,378	7,868
percent_spikeins	0.00013	0.00011
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1979	1980

Data Submission Information

	BGHcLV31-9	BGHcLV31-9	BGHcLV31-9	BGHcLV31-9	BGHcLV31-9	BGHcLV31-9	BGHcLV31-10	BGHcLV31-10	BGHcLV31-10	BGHcLV31-10
ENCODE_alias	brenton-graveley:RPS8-BGHcLV31	brenton-graveley:RPS8-BGHcLV31-9	brenton-graveley:L-RPS8-BGHcLV31-9	brenton-graveley:RPS8-BGHcLV31-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS8-BGHcLV31-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS8-BGHcLV31-HepG2	brenton-graveley:RPS8-BGHcLV31-10	brenton-graveley:L-RPS8-BGHcLV31-10	brenton-graveley:RPS8-BGHcLV31-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS8-BGHcLV31-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR994NGU	ENCBS703JUW	ENCLB809NST	ENCFF593MVD	ENCFF409OPC	ENCSR254YPW	ENCBS069KUQ	ENCLB309PHS	ENCFF433BLF	ENCFF164UHS
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	BGHcLV31-9	BGHcLV31-9	BGHcLV31-9	BGHcLV31-9	BGHcLV31-9	BGHcLV31-9	BGHcLV31-10	BGHcLV31-10	BGHcLV31-10	BGHcLV31-10
Sample Name	RPS8-BGHcLV31-9	RPS8-BGHcLV31-9	RPS8-BGHcLV31-9	RPS8-BGHcLV31-9	RPS8-BGHcLV31-9	RPS8-BGHcLV31-9	RPS8-BGHcLV31-10	RPS8-BGHcLV31-10	RPS8-BGHcLV31-10	RPS8-BGHcLV31-10
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		RPS8-BGHcLV31-9.pdf	L-RPS8-BGHcLV31-9.pdf				RPS8-BGHcLV31-10.pdf	L-RPS8-BGHcLV31-10.pdf
ID	7446	7503	7611	7721	7831	7938	7504	7612	7722	7832

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
RPS8-BGHcLV31-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1979	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6526
RPS8-BGHcLV31-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1979	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6580
RPS8-BGHcLV31-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1979					GRCh38	V40	RPS8-BGHcLV31-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS8-BGHcLV31-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18447
RPS8-BGHcLV31-9_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	1979					GRCh38	V40	RPS8-BGHcLV31-9/Aligned.sortedByCoord.out.bam		ENCORE2	18501
RPS8-BGHcLV31-9_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	1979					GRCh38	V40	RPS8-BGHcLV31-9/Aligned.sortedByCoord.out.bam		ENCORE2	18555
RPS8-BGHcLV31-9_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	1979					GRCh38	V40	RPS8-BGHcLV31-9/Aligned.sortedByCoord.out.bam		ENCORE2	18609
RPS8-BGHcLV31-9_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	1979					GRCh38	V40	RPS8-BGHcLV31-9/Aligned.sortedByCoord.out.bam		ENCORE2	18663
RPS8-BGHcLV31-9_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1979					GRCh38	V40	RPS8-BGHcLV31-9_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS8-BGHcLV31-9_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18717
RPS8-BGHcLV31-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1980	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6525
RPS8-BGHcLV31-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1980	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6579
RPS8-BGHcLV31-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1980					GRCh38	V40	RPS8-BGHcLV31-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS8-BGHcLV31-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18446
RPS8-BGHcLV31-10_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	1980					GRCh38	V40	RPS8-BGHcLV31-10/Aligned.sortedByCoord.out.bam		ENCORE2	18500
RPS8-BGHcLV31-10_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	1980					GRCh38	V40	RPS8-BGHcLV31-10/Aligned.sortedByCoord.out.bam		ENCORE2	18554
RPS8-BGHcLV31-10_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	1980					GRCh38	V40	RPS8-BGHcLV31-10/Aligned.sortedByCoord.out.bam		ENCORE2	18608
RPS8-BGHcLV31-10_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	1980					GRCh38	V40	RPS8-BGHcLV31-10/Aligned.sortedByCoord.out.bam		ENCORE2	18662
RPS8-BGHcLV31-10_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1980					GRCh38	V40	RPS8-BGHcLV31-10_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS8-BGHcLV31-10_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18716