CARHSP1 RNA-Seq in HepG2

General Information


RBP	CARHSP1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CARHSP1-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR142YHR
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR974KDR
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	CARHSP1-BGHcLV27-37
Rep2	CARHSP1-BGHcLV27-38
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	36.2
Rep2_qPCR	39.3
Rep1_WB	51.1
Rep2_WB	55.0
Antibody Cat#	A303-908A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB401VFW
Status	Released
Project	ENCODE4
ID	814

Experiment Information (Status: Released)

	BGHcLV27-37	BGHcLV27-38
idx	803	804
TRCN#_or_BGC#	BGC#0000664	BGC#0000664
shRNA_or_gRNA_sequence	ACGCCGAGAAGGTCCTCGTC	ACGCCGAGAAGGTCCTCGTC
PAM	CGG	CGG
Name	CARHSP1_96	CARHSP1_96
Sample_ID	BGHcLV27-37	BGHcLV27-38
transduction_Date	5/18/21	5/18/21
days	D6	D6
RBP_name	CARHSP1	CARHSP1
qPCR_result	36.2	39.3
Ave_qPCR	37.8
RT-qPCR_primer-F	tgtggaaggggagtatgtcc
RT-qPCR_primer-R	gcctgcagcttctcattctt
protein_conc	3013	3275
WB_result	51.1	55.0
Ave_WB	53.0
WB_DONE_date	7/13/21
MW	16kda
IP	Rabbit / I
antibody_Cat#	A303-908A	LOT# 1
Antibody DCC ID	ENCAB401VFW	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/03/21	09/03/21
repeat_library
Note
ID	6972	6973

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CARHSP1	Product_ID: A303-908A Lot_ID: 1 Source: Bethyl Labs Target Name: CARHSP1-human

Experiment Status

	BGHcLV27-37	BGHcLV27-38
Sample_ID	BGHcLV27-37	BGHcLV27-38
Sample Name
Sample Name	CARHSP1-BGHcLV27-37	CARHSP1-BGHcLV27-38
RBP	CARHSP1	CARHSP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9691	9692

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-37	BGHcLV27-38
Sample #	95	96
Sample Name	CARHSP1-BGHcLV27-37	CARHSP1-BGHcLV27-38
Sample_Name_Alias
Index Well Position	C10	D10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	289	295
Peak_Molarity	137.00	136.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/C9.png	DNA_Library_set48-49/set2/D9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set48-49/set1/E9.png	RNA_Library_set48-49/set1/F9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-37	BGHcLV27-38
RBP	CARHSP1	CARHSP1
Batch_ID	BGHcLV27	BGHcLV27
WB_result	51.100	55.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1654	1655

Sequencing Information

	BGHcLV27-37	BGHcLV27-38
Sample_ID	BGHcLV27-37	BGHcLV27-38
Sample Name	CARHSP1-BGHcLV27-37	CARHSP1-BGHcLV27-38
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	84,911,776	72,619,518
total_aligned_reads	75,329,500	66,483,508
unique_aligned_reads	70,959,174	62,711,098
percent_uniqueAligned	0.83568	0.86356
correlation_replicates	0.998306	0.998306
spikein_reads	22,616	12,454
percent_spikeins	0.00027	0.00017
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1805	1806

Data Submission Information

	BGHcLV27-37	BGHcLV27-37	BGHcLV27-37	BGHcLV27-37	BGHcLV27-37	BGHcLV27-37	BGHcLV27-38	BGHcLV27-38	BGHcLV27-38	BGHcLV27-38
ENCODE_alias	brenton-graveley:CARHSP1-BGHcLV27	brenton-graveley:CARHSP1-BGHcLV27-37	brenton-graveley:L-CARHSP1-BGHcLV27-37	brenton-graveley:CARHSP1-BGHcLV27-37_S75_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARHSP1-BGHcLV27-37_S75_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARHSP1-BGHcLV27-HepG2	brenton-graveley:CARHSP1-BGHcLV27-38	brenton-graveley:L-CARHSP1-BGHcLV27-38	brenton-graveley:CARHSP1-BGHcLV27-38_S76_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARHSP1-BGHcLV27-38_S76_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR974KDR	ENCBS842VIG	ENCLB686EUX	ENCFF211RKD	ENCFF027QCV	ENCSR142YHR	ENCBS639AFY	ENCLB764GNJ	ENCFF773VUA	ENCFF146UEM
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	BGHcLV27-37	BGHcLV27-37	BGHcLV27-37	BGHcLV27-37	BGHcLV27-37	BGHcLV27-37	BGHcLV27-38	BGHcLV27-38	BGHcLV27-38	BGHcLV27-38
Sample Name	CARHSP1-BGHcLV27-37	CARHSP1-BGHcLV27-37	CARHSP1-BGHcLV27-37	CARHSP1-BGHcLV27-37	CARHSP1-BGHcLV27-37	CARHSP1-BGHcLV27-37	CARHSP1-BGHcLV27-38	CARHSP1-BGHcLV27-38	CARHSP1-BGHcLV27-38	CARHSP1-BGHcLV27-38
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48H_biosample_protocol	LV48H_library_protocol				LV48H_biosample_protocol	LV48H_library_protocol
protocol_URL		CARHSP1-BGHcLV27-37.pdf	L-CARHSP1-BGHcLV27-37.pdf				CARHSP1-BGHcLV27-38.pdf	L-CARHSP1-BGHcLV27-38.pdf
ID	3442	3518	3652	3786	3920	7113	3519	3653	3787	3921

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
CARHSP1-BGHcLV27-37_S75_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1805	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3796
CARHSP1-BGHcLV27-37_S75_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1805	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3822
CARHSP1-BGHcLV27-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1805					GRCh38	V40	CARHSP1-BGHcLV27-37_S75_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARHSP1-BGHcLV27-37_S75_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25483
CARHSP1-BGHcLV27-37_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1805					GRCh38	V40	CARHSP1-BGHcLV27-37_S75_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARHSP1-BGHcLV27-37_S75_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25509
CARHSP1-BGHcLV27-37_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1805					GRCh38	V40	CARHSP1-BGHcLV27-37/Aligned.sortedByCoord.out.bam		ENCORE2	26447
CARHSP1-BGHcLV27-37_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1805					GRCh38	V40	CARHSP1-BGHcLV27-37/Aligned.sortedByCoord.out.bam		ENCORE2	26473
CARHSP1-BGHcLV27-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1805					GRCh38	V40	CARHSP1-BGHcLV27-37/Aligned.sortedByCoord.out.bam		ENCORE2	26499
CARHSP1-BGHcLV27-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1805					GRCh38	V40	CARHSP1-BGHcLV27-37/Aligned.sortedByCoord.out.bam		ENCORE2	26525
CARHSP1-BGHcLV27-38_S76_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1806	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3797
CARHSP1-BGHcLV27-38_S76_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1806	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3823
CARHSP1-BGHcLV27-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1806					GRCh38	V40	CARHSP1-BGHcLV27-38_S76_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARHSP1-BGHcLV27-38_S76_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25484
CARHSP1-BGHcLV27-38_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1806					GRCh38	V40	CARHSP1-BGHcLV27-38_S76_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARHSP1-BGHcLV27-38_S76_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25510
CARHSP1-BGHcLV27-38_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1806					GRCh38	V40	CARHSP1-BGHcLV27-38/Aligned.sortedByCoord.out.bam		ENCORE2	26448
CARHSP1-BGHcLV27-38_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1806					GRCh38	V40	CARHSP1-BGHcLV27-38/Aligned.sortedByCoord.out.bam		ENCORE2	26474
CARHSP1-BGHcLV27-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1806					GRCh38	V40	CARHSP1-BGHcLV27-38/Aligned.sortedByCoord.out.bam		ENCORE2	26500
CARHSP1-BGHcLV27-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1806					GRCh38	V40	CARHSP1-BGHcLV27-38/Aligned.sortedByCoord.out.bam		ENCORE2	26526