RPS25 RNA-Seq in HepG2

General Information


RBP	RPS25
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPS25-BGHcLV20-HepG2
ENCODE_series_ID	ENCSR905LMN
Batch_ID	BGHcLV20
Pool ID	Pool-200928
Local_Set_Name	set45_H
ENCODE_KD_Exp_ID	ENCSR565ZPZ
ENCODE_CN_Exp_ID	ENCSR306EWE
Rep1	RPS25-BGHcLV20-29
Rep2	RPS25-BGHcLV20-30
CN1	NT-BGHcLV20-1
CN2	NT-BGHcLV20-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	90.7
Rep2_WB	86.1
Antibody Cat#	PA5-56865
Antibody Lot#	lot# UC2731466A
Antibody DCC ID	ENCAB558RYT
Status	Released
Project	ENCODE4
ID	79

Experiment Information (Status: Released)

	BGHcLV20-29	BGHcLV20-30
idx	579	580
TRCN#_or_BGC#	BGC#0000488	BGC#0000488
shRNA_or_gRNA_sequence	TTCTTCTTGTCGTCCTTAGG	TTCTTCTTGTCGTCCTTAGG
PAM	CGG	CGG
Name	RPS25_83	RPS25_83
Sample_ID	BGHcLV20-29	BGHcLV20-30
transduction_Date	12/10/19	12/10/19
days	D6	D6
RBP_name	RPS25	RPS25
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	AAGATTCGAGGCTCCCTGG
RT-qPCR_primer-R	GAGCATCTCCACCCTTGGTA
protein_conc	3591	3853
WB_result	90.7	86.1
Ave_WB	88.4
WB_DONE_date	8/10/20
MW	13.7kDa
IP	Rabbit / I
antibody_Cat#	PA5-56865	lot# UC2731466A
Antibody DCC ID	ENCAB558RYT
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	6734	6735

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS25	Product_ID: PA5-56865 Lot_ID: UC2731466A Source: Thermo Fisher Target Name: RPS25-human

Experiment Status

	BGHcLV20-29	BGHcLV20-30
Sample_ID	BGHcLV20-29	BGHcLV20-30
Sample Name
Sample Name	RPS25-BGHcLV20-29	RPS25-BGHcLV20-30
RBP	RPS25	RPS25
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5819	5820

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV20-29	BGHcLV20-30
Sample #	69	70
Sample Name	RPS25-BGHcLV20-29	RPS25-BGHcLV20-30
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	300	294
Peak_Molarity	82.70	81.60
libSampleQC_DNA_Well	DNA_Library_set45/set1/G8.png	DNA_Library_set45/set1/H8.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set45/set1/G8.png	RNA_Library_set45/set1/H8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGHcLV20-29	BGHcLV20-30
RBP	RPS25	RPS25
Batch_ID	BGHcLV20	BGHcLV20
WB_result	90.700	86.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	843	844

Sequencing Information

	BGHcLV20-29	BGHcLV20-30
Sample_ID	BGHcLV20-29	BGHcLV20-30
Sample Name	RPS25-BGHcLV20-29	RPS25-BGHcLV20-30
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_H	set45_H
total_reads	144,763,524	135,309,292
total_aligned_reads	140,386,156	131,059,428
unique_aligned_reads	132,157,198	123,331,288
percent_uniqueAligned	0.91292	0.91148
correlation_replicates	0.993292	0.993292
spikein_reads	103,918	80,340
percent_spikeins	0.00072	0.00059
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	474	475

Data Submission Information

	BGHcLV20-29	BGHcLV20-29	BGHcLV20-29	BGHcLV20-29	BGHcLV20-29	BGHcLV20-29	BGHcLV20-30	BGHcLV20-30	BGHcLV20-30	BGHcLV20-30
ENCODE_alias	brenton-graveley:RPS25-BGHcLV20	brenton-graveley:RPS25-BGHcLV20-29	brenton-graveley:L-RPS25-BGHcLV20-29	brenton-graveley:RPS25-BGHcLV20-29_S63_R1_001.fastq.gz	brenton-graveley:RPS25-BGHcLV20-29_S63_R2_001.fastq.gz	brenton-graveley:RPS25-BGHcLV20-HepG2	brenton-graveley:RPS25-BGHcLV20-30	brenton-graveley:L-RPS25-BGHcLV20-30	brenton-graveley:RPS25-BGHcLV20-30_S64_R1_001.fastq.gz	brenton-graveley:RPS25-BGHcLV20-30_S64_R2_001.fastq.gz
ENCODE_accession	ENCSR565ZPZ	ENCBS814FUV	ENCLB230RJR	ENCFF736MRI	ENCFF842DBS	ENCSR905LMN	ENCBS679EBD	ENCLB411SJS	ENCFF472UKZ	ENCFF092WUK
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	BGHcLV20-29	BGHcLV20-29	BGHcLV20-29	BGHcLV20-29	BGHcLV20-29	BGHcLV20-29	BGHcLV20-30	BGHcLV20-30	BGHcLV20-30	BGHcLV20-30
Sample Name	RPS25-BGHcLV20-29	RPS25-BGHcLV20-29	RPS25-BGHcLV20-29	RPS25-BGHcLV20-29	RPS25-BGHcLV20-29	RPS25-BGHcLV20-29	RPS25-BGHcLV20-30	RPS25-BGHcLV20-30	RPS25-BGHcLV20-30	RPS25-BGHcLV20-30
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45H_biosample_protocol	LV45H_library_protocol				LV45H_biosample_protocol	LV45H_library_protocol
protocol_URL		RPS25-BGHcLV20-29.pdf	L-RPS25-BGHcLV20-29.pdf				RPS25-BGHcLV20-30.pdf	L-RPS25-BGHcLV20-30.pdf
ID	2086	2127	2197	2267	2337	7313	2128	2198	2268	2338

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
RPS25-BGHcLV20-29_S63_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	474	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1320
RPS25-BGHcLV20-29_S63_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	474	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1340
RPS25-BGHcLV20-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	474					GRCh38	V40	RPS25-BGHcLV20-29_S63_R1_001.filtered.trimmed.paired.fastq.gz,RPS25-BGHcLV20-29_S63_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24861
RPS25-BGHcLV20-29_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	474					GRCh38	V40	RPS25-BGHcLV20-29_S63_R1_001.filtered.trimmed.paired.fastq.gz,RPS25-BGHcLV20-29_S63_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24881
RPS25-BGHcLV20-29_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	474					GRCh38	V40	RPS25-BGHcLV20-29/Aligned.sortedByCoord.out.bam		ENCORE2	25931
RPS25-BGHcLV20-29_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	474					GRCh38	V40	RPS25-BGHcLV20-29/Aligned.sortedByCoord.out.bam		ENCORE2	25951
RPS25-BGHcLV20-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	474					GRCh38	V40	RPS25-BGHcLV20-29/Aligned.sortedByCoord.out.bam		ENCORE2	25971
RPS25-BGHcLV20-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	474					GRCh38	V40	RPS25-BGHcLV20-29/Aligned.sortedByCoord.out.bam		ENCORE2	25991
RPS25-BGHcLV20-30_S64_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	475	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1321
RPS25-BGHcLV20-30_S64_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	475	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1341
RPS25-BGHcLV20-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	475					GRCh38	V40	RPS25-BGHcLV20-30_S64_R1_001.filtered.trimmed.paired.fastq.gz,RPS25-BGHcLV20-30_S64_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24862
RPS25-BGHcLV20-30_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	475					GRCh38	V40	RPS25-BGHcLV20-30_S64_R1_001.filtered.trimmed.paired.fastq.gz,RPS25-BGHcLV20-30_S64_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24882
RPS25-BGHcLV20-30_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	475					GRCh38	V40	RPS25-BGHcLV20-30/Aligned.sortedByCoord.out.bam		ENCORE2	25932
RPS25-BGHcLV20-30_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	475					GRCh38	V40	RPS25-BGHcLV20-30/Aligned.sortedByCoord.out.bam		ENCORE2	25952
RPS25-BGHcLV20-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	475					GRCh38	V40	RPS25-BGHcLV20-30/Aligned.sortedByCoord.out.bam		ENCORE2	25972
RPS25-BGHcLV20-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	475					GRCh38	V40	RPS25-BGHcLV20-30/Aligned.sortedByCoord.out.bam		ENCORE2	25992