RACK1 RNA-Seq in HepG2

General Information


RBP	RACK1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RACK1-BGHcLV36-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV36
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RACK1-BGHcLV36-27
Rep2	RACK1-BGHcLV36-28
CN1	NT-BGHcLV36-1
CN2	NT-BGHcLV36-2
Rep1_qPCR	86.6
Rep2_qPCR	87.5
Rep1_WB	54.2
Rep2_WB	54.4
Antibody Cat#	5432S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1042

Experiment Information (Status: Submitting)

	BGHcLV36-27	BGHcLV36-28
idx	1158	1159
TRCN#_or_BGC#	BGC#0001047	BGC#0001047
shRNA_or_gRNA_sequence	ACCTTAGTCCGTACCTCGAG	ACCTTAGTCCGTACCTCGAG
PAM	AGG	AGG
Name	RACK1_99	RACK1_99
Sample_ID	BGHcLV36-27	BGHcLV36-28
transduction_Date	8/2/22	8/2/22
days	D6	D6
RBP_name	RACK1	RACK1
qPCR_result	86.6	87.5
Ave_qPCR	87.0
RT-qPCR_primer-F	taaccgctactggctgtgtg
RT-qPCR_primer-R	gccttgctgctggtactgat
protein_conc	4802	4261
WB_result	54.2	54.4
Ave_WB	54.3
WB_DONE_date	9/1/22
MW	35kd
IP	Rabbit / I
antibody_Cat#	5432S	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7339	7340

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RACK1	Product_ID: 5432S Lot_ID: 2 Source: Cell Signaling Technology Target Name: RACK1-human

Experiment Status

	BGHcLV36-27	BGHcLV36-28
Sample_ID	BGHcLV36-27	BGHcLV36-28
Sample Name
Sample Name	RACK1-BGHcLV36-27	RACK1-BGHcLV36-28
RBP	RACK1	RACK1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10946	10947

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV36-27	BGHcLV36-28
Sample #	5	6
Sample Name	RACK1-BGHcLV36-27	RACK1-BGHcLV36-28
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	308	307
Peak_Molarity	50.30	65.50
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/E1.png	DNA_Library_set54-56/set1/F1.png
RIN	9.3	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/E1.png	RNA_Library_set54-56/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGHcLV36-27	BGHcLV36-28
RBP	RACK1	RACK1
Batch_ID	BGHcLV36	BGHcLV36
WB_result	54.200	54.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3376	3377

Sequencing Information

	BGHcLV36-27	BGHcLV36-28
Sample_ID	BGHcLV36-27	BGHcLV36-28
Sample Name	RACK1-BGHcLV36-27	RACK1-BGHcLV36-28
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	50,416,962	38,862,330
total_aligned_reads	44,472,848	35,673,262
unique_aligned_reads	42,231,229	33,771,962
percent_uniqueAligned	0.83764	0.86902
correlation_replicates	0.998631	0.998631
spikein_reads	3,978	6,004
percent_spikeins	0.00008	0.00015
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2249	2250

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
RACK1-BGHcLV36-27_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2249	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8398
RACK1-BGHcLV36-27_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2249	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8448
RACK1-BGHcLV36-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2249					GRCh38	V40	RACK1-BGHcLV36-27_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,RACK1-BGHcLV36-27_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25639
RACK1-BGHcLV36-27_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2249					GRCh38	V40	RACK1-BGHcLV36-27/Aligned.sortedByCoord.out.bam		ENCORE2	25689
RACK1-BGHcLV36-27_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2249					GRCh38	V40	RACK1-BGHcLV36-27/Aligned.sortedByCoord.out.bam		ENCORE2	25739
RACK1-BGHcLV36-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2249					GRCh38	V40	RACK1-BGHcLV36-27/Aligned.sortedByCoord.out.bam		ENCORE2	25789
RACK1-BGHcLV36-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2249					GRCh38	V40	RACK1-BGHcLV36-27/Aligned.sortedByCoord.out.bam		ENCORE2	25839
RACK1-BGHcLV36-27_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2249					GRCh38	V40	RACK1-BGHcLV36-27_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,RACK1-BGHcLV36-27_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25889
RACK1-BGHcLV36-28_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2250	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8399
RACK1-BGHcLV36-28_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2250	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8449
RACK1-BGHcLV36-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2250					GRCh38	V40	RACK1-BGHcLV36-28_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,RACK1-BGHcLV36-28_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25640
RACK1-BGHcLV36-28_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2250					GRCh38	V40	RACK1-BGHcLV36-28/Aligned.sortedByCoord.out.bam		ENCORE2	25690
RACK1-BGHcLV36-28_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2250					GRCh38	V40	RACK1-BGHcLV36-28/Aligned.sortedByCoord.out.bam		ENCORE2	25740
RACK1-BGHcLV36-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2250					GRCh38	V40	RACK1-BGHcLV36-28/Aligned.sortedByCoord.out.bam		ENCORE2	25790
RACK1-BGHcLV36-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2250					GRCh38	V40	RACK1-BGHcLV36-28/Aligned.sortedByCoord.out.bam		ENCORE2	25840
RACK1-BGHcLV36-28_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2250					GRCh38	V40	RACK1-BGHcLV36-28_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,RACK1-BGHcLV36-28_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25890