RPS21 RNA-Seq in HepG2

General Information


RBP	RPS21
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPS21-BGHcLV34-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV34
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RPS21-BGHcLV34-41B
Rep2	RPS21-BGHcLV34-42B
CN1	NT-BGHcLV34-1B
CN2	NT-BGHcLV34-2B
Rep1_qPCR	46.9
Rep2_qPCR	36.0
Rep1_WB	54.0
Rep2_WB	58.2
Antibody Cat#	A305-070A
Antibody Lot#	LOT #1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCORE2
ID	950

Experiment Information (Status: Submitting)

	BGHcLV34-41	BGHcLV34-42
idx	1111	1112
TRCN#_or_BGC#	BGC#0000820	BGC#0000820
shRNA_or_gRNA_sequence	CTCGAAATGCAGAACGACGC	CTCGAAATGCAGAACGACGC
PAM	CGG	CGG
Name	RPS21_82	RPS21_82
Sample_ID	BGHcLV34-41	BGHcLV34-42
transduction_Date	3/24/22	3/24/22
days	D6	D6
RBP_name	RPS21	RPS21
qPCR_result	46.9	36.0
Ave_qPCR	41.4
RT-qPCR_primer-F	gcgagttcgtggacctgta
RT-qPCR_primer-R	cgttcatctggatggatgc
protein_conc	2526	3077
WB_result	54.0	58.2
Ave_WB	56.1
WB_DONE_date	4/6/22
MW	9.1kd
IP
antibody_Cat#	A305-070A	LOT #1
Antibody DCC ID	NO ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library	06/22/22	06/22/22
Note
ID	7290	7291

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS21	Product_ID: A305-070A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS21-human

Experiment Status

	BGHcLV34-41	BGHcLV34-42
Sample_ID	BGHcLV34-41	BGHcLV34-42
Sample Name
Sample Name	RPS21-BGHcLV34-41B	RPS21-BGHcLV34-42B
RBP	RPS21	RPS21
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10937	10938

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-41	BGHcLV34-41	BGHcLV34-42	BGHcLV34-42
Sample #	15	51	16	52
Sample Name	RPS21-BGHcLV34-41	RPS21-BGHcLV34-41B	RPS21-BGHcLV34-42	RPS21-BGHcLV34-42B
Sample_Name_Alias
Index Well Position	G02	C07	H02	D07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-21	2022-06-17	2022-06-21
Lib_ID	Lib-220617	Lib-220621	Lib-220617	Lib-220621
Tecan_Location
Tecan
Tecan_date
Size_bp	283	268	308	269
Peak_Molarity	23.50	39.60	7.00	27.10
libSampleQC_DNA_Well		DNA_Library_set54-56/set4/G10.png		DNA_Library_set54-56/set4/H10.png
RIN		9.8		9.7
libSample_RNA_Well		RNA_Library_set54-56/set2/G2.png		RNA_Library_set54-56/set2/H2.png
SampleQC_method		TapeStation_2022		TapeStation_2022
SampleQC_date	2022-06-20	2022-07-20	2022-06-20	2022-07-20
Sample_ID	BGHcLV34-41	BGHcLV34-41	BGHcLV34-42	BGHcLV34-42
RBP	RPS21	RPS21	RPS21	RPS21
Batch_ID	BGHcLV34	BGHcLV34	BGHcLV34	BGHcLV34
WB_result	54.000	54.000	58.200	58.200
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	NotToSequence	SendToSequence	NotToSequence	SendToSequence
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
ID	3332	3368	3333	3369

Sequencing Information

	BGHcLV34-41	BGHcLV34-42
Sample_ID	BGHcLV34-41	BGHcLV34-42
Sample Name	RPS21-BGHcLV34-41B	RPS21-BGHcLV34-42B
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	65,186,364	95,633,216
total_aligned_reads	52,602,930	63,586,946
unique_aligned_reads	49,685,170	59,972,848
percent_uniqueAligned	0.76220	0.62711
correlation_replicates	0.995963	0.995963
spikein_reads	13,658	7,820
percent_spikeins	0.00021	0.00008
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2215	2216

Data Submission Information DCC submission information was not avaliable

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
RPS21-BGHcLV34-41B_S21_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2215	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1B_S23_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2B_S24_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8518
RPS21-BGHcLV34-41B_S21_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2215	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1B_S23_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2B_S24_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8568
RPS21-BGHcLV34-41B_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2215					GRCh38	V40	RPS21-BGHcLV34-41B/Aligned.sortedByCoord.out.bam		ENCORE2	17764
RPS21-BGHcLV34-41B_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2215					GRCh38	V40	RPS21-BGHcLV34-41B/Aligned.sortedByCoord.out.bam		ENCORE2	17814
RPS21-BGHcLV34-41B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2215					GRCh38	V40	RPS21-BGHcLV34-41B/Aligned.sortedByCoord.out.bam		ENCORE2	17864
RPS21-BGHcLV34-41B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2215					GRCh38	V40	RPS21-BGHcLV34-41B/Aligned.sortedByCoord.out.bam		ENCORE2	17914
RPS21-BGHcLV34-41B_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2215					GRCh38	V40	RPS21-BGHcLV34-41B_S21_R1_001.filtered.trimmed.paired.fastq.gz,RPS21-BGHcLV34-41B_S21_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17964
RPS21-BGHcLV34-41B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2215					GRCh38	V40	RPS21-BGHcLV34-41B_S21_R1_001.filtered.trimmed.paired.fastq.gz,RPS21-BGHcLV34-41B_S21_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29305
RPS21-BGHcLV34-42B_S22_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2216	NovaSeq6000	100	paired-ended	1				NT-BGHcLV34-1B_S23_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2B_S24_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8519
RPS21-BGHcLV34-42B_S22_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2216	NovaSeq6000	100	paired-ended	2				NT-BGHcLV34-1B_S23_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2B_S24_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8569
RPS21-BGHcLV34-42B_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2216					GRCh38	V40	RPS21-BGHcLV34-42B/Aligned.sortedByCoord.out.bam		ENCORE2	17765
RPS21-BGHcLV34-42B_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2216					GRCh38	V40	RPS21-BGHcLV34-42B/Aligned.sortedByCoord.out.bam		ENCORE2	17815
RPS21-BGHcLV34-42B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2216					GRCh38	V40	RPS21-BGHcLV34-42B/Aligned.sortedByCoord.out.bam		ENCORE2	17865
RPS21-BGHcLV34-42B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2216					GRCh38	V40	RPS21-BGHcLV34-42B/Aligned.sortedByCoord.out.bam		ENCORE2	17915
RPS21-BGHcLV34-42B_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2216					GRCh38	V40	RPS21-BGHcLV34-42B_S22_R1_001.filtered.trimmed.paired.fastq.gz,RPS21-BGHcLV34-42B_S22_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17965
RPS21-BGHcLV34-42B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2216					GRCh38	V40	RPS21-BGHcLV34-42B_S22_R1_001.filtered.trimmed.paired.fastq.gz,RPS21-BGHcLV34-42B_S22_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29306