RPL35A RNA-Seq in K562

General Information


RBP	RPL35A
Cell_Line	K562
Method	CRISPR
Exp_Name	RPL35A-BGKcLV35-K562
ENCODE_series_ID
Batch_ID	BGKcLV35
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RPL35A-BGKcLV35-39
Rep2	RPL35A-BGKcLV35-40
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	15.2
Rep2_qPCR	20.1
Rep1_WB	64.9
Rep2_WB	50.1
Antibody Cat#	A305-106A
Antibody Lot#	LOT #1
Antibody DCC ID	no ID
Status	Submitted
Project	ENCORE2
ID	960

Experiment Information (Status: Submitting)

	BGKcLV35-39	BGKcLV35-40
idx	1316	1317
TRCN#_or_BGC#	BGC#0000797	BGC#0000797
shRNA_or_gRNA_sequence	GGAAAAGTAACTCGGGCCCA	GGAAAAGTAACTCGGGCCCA
PAM	TGG	TGG
Name	RPL35A_71	RPL35A_71
Sample_ID	BGKcLV35-39	BGKcLV35-40
transduction_Date	4/28/22	4/28/22
days	D6	D6
RBP_name	RPL35A	RPL35A
qPCR_result	15.2	20.1
Ave_qPCR	17.6
RT-qPCR_primer-F	ccagagtcatctggggaaaa
RT-qPCR_primer-R	tccttgaggggtacagcatc
protein_conc	4109	3252
WB_result	64.9	50.1
Ave_WB	57.5
WB_DONE_date	5/9/22
MW	13kD
IP
antibody_Cat#	A305-106A	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
Note
ID	5462	5463

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL35A	Product_ID: A305-106A Lot_ID: 1 Source: Bethyl Labs Target Name: RPL35A-human

Experiment Status

	BGKcLV35-39	BGKcLV35-40
Sample_ID	BGKcLV35-39	BGKcLV35-40
Sample Name
Sample Name	RPL35A-BGKcLV35-39	RPL35A-BGKcLV35-40
RBP	RPL35A	RPL35A
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10877	10878

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-39	BGKcLV35-40
Sample #	43	44
Sample Name	RPL35A-BGKcLV35-39	RPL35A-BGKcLV35-40
Sample_Name_Alias
Index Well Position	C06	D06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	289	284
Peak_Molarity	20.70	31.00
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/C10.png	DNA_Library_set54-56/set3/D10.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set54-56/set2/C6.png	RNA_Library_set54-56/set2/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-39	BGKcLV35-40
RBP	RPL35A	RPL35A
Batch_ID	BGKcLV35	BGKcLV35
WB_result	64.900	50.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3360	3361

Sequencing Information

	BGKcLV35-39	BGKcLV35-40
Sample_ID	BGKcLV35-39	BGKcLV35-40
Sample Name	RPL35A-BGKcLV35-39	RPL35A-BGKcLV35-40
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	50,825,712	75,115,916
total_aligned_reads	47,876,058	69,829,624
unique_aligned_reads	43,927,348	64,318,410
percent_uniqueAligned	0.86427	0.85626
correlation_replicates	0.992824	0.992824
spikein_reads	1,716	3,108
percent_spikeins	0.00003	0.00004
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2239	2240

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
RPL35A-BGKcLV35-39_S45_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2239	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8514
RPL35A-BGKcLV35-39_S45_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2239	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8564
RPL35A-BGKcLV35-39_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	2239					GRCh38	V40	RPL35A-BGKcLV35-39/Aligned.sortedByCoord.out.bam		ENCORE2	17760
RPL35A-BGKcLV35-39_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	2239					GRCh38	V40	RPL35A-BGKcLV35-39/Aligned.sortedByCoord.out.bam		ENCORE2	17810
RPL35A-BGKcLV35-39_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	2239					GRCh38	V40	RPL35A-BGKcLV35-39/Aligned.sortedByCoord.out.bam		ENCORE2	17860
RPL35A-BGKcLV35-39_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	2239					GRCh38	V40	RPL35A-BGKcLV35-39/Aligned.sortedByCoord.out.bam		ENCORE2	17910
RPL35A-BGKcLV35-39_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2239					GRCh38	V40	RPL35A-BGKcLV35-39_S45_R1_001.filtered.trimmed.paired.fastq.gz,RPL35A-BGKcLV35-39_S45_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17960
RPL35A-BGKcLV35-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2239					GRCh38	V40	RPL35A-BGKcLV35-39_S45_R1_001.filtered.trimmed.paired.fastq.gz,RPL35A-BGKcLV35-39_S45_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29301
RPL35A-BGKcLV35-40_S46_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2240	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8515
RPL35A-BGKcLV35-40_S46_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2240	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8565
RPL35A-BGKcLV35-40_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	2240					GRCh38	V40	RPL35A-BGKcLV35-40/Aligned.sortedByCoord.out.bam		ENCORE2	17761
RPL35A-BGKcLV35-40_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	2240					GRCh38	V40	RPL35A-BGKcLV35-40/Aligned.sortedByCoord.out.bam		ENCORE2	17811
RPL35A-BGKcLV35-40_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	2240					GRCh38	V40	RPL35A-BGKcLV35-40/Aligned.sortedByCoord.out.bam		ENCORE2	17861
RPL35A-BGKcLV35-40_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	2240					GRCh38	V40	RPL35A-BGKcLV35-40/Aligned.sortedByCoord.out.bam		ENCORE2	17911
RPL35A-BGKcLV35-40_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2240					GRCh38	V40	RPL35A-BGKcLV35-40_S46_R1_001.filtered.trimmed.paired.fastq.gz,RPL35A-BGKcLV35-40_S46_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17961
RPL35A-BGKcLV35-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2240					GRCh38	V40	RPL35A-BGKcLV35-40_S46_R1_001.filtered.trimmed.paired.fastq.gz,RPL35A-BGKcLV35-40_S46_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29302