CSTF1 RNA-Seq in K562

General Information


RBP	CSTF1
Cell_Line	K562
Method	CRISPR
Exp_Name	CSTF1-BGKcLV21-K562
ENCODE_series_ID	ENCSR414EQZ
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR529UYQ
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	CSTF1-BGKcLV21-13
Rep2	CSTF1-BGKcLV21-14
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	66.9
Rep2_WB	69.3677307
Antibody Cat#	A301-250A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB678HIE
Status	Released
Project	ENCODE4
ID	65

Experiment Information (Status: Released)

	BGKcLV21-13	BGKcLV21-14
idx	746	747
TRCN#_or_BGC#	BGC#0000506	BGC#0000506
shRNA_or_gRNA_sequence	CTATAGGTAGCTACACGGCA	CTATAGGTAGCTACACGGCA
PAM	TGG	TGG
Name	CSTF1 _93	CSTF1 _93
Sample_ID	BGKcLV21-13	BGKcLV21-14
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	CSTF1	CSTF1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GGCTTCTGGTTCAAGGGATT
RT-qPCR_primer-R	GAAGGATGAAAAGAGATGGAACG
protein_conc	4750	5574
WB_result	66.9	69.3677307
Ave_WB	68.1
WB_DONE_date	12/11/20	JESS
MW	48.4kDa
IP	Rabbit / I
antibody_Cat#	A301-250A	Lot# 1
Antibody DCC ID	ENCAB678HIE
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	4866	4867

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CSTF1	Product_ID: A301-250A Lot_ID: 1 Source: Bethyl Labs Target Name: CSTF1-human

Experiment Status

	BGKcLV21-13	BGKcLV21-14
Sample_ID	BGKcLV21-13	BGKcLV21-14
Sample Name
Sample Name	CSTF1-BGKcLV21-13	CSTF1-BGKcLV21-14
RBP	CSTF1	CSTF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6121	6122

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-13	BGKcLV21-14
Sample #	39	40
Sample Name	CSTF1-BGKcLV21-13	CSTF1-BGKcLV21-14
Sample_Name_Alias
Index Well Position	A05	B05
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	309	308
Peak_Molarity	329.00	322.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/A5.png	DNA_Library_set45/set1/B5.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_set45/set1/A5.png	RNA_Library_set45/set1/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-25	2020-09-25
Sample_ID	BGKcLV21-13	BGKcLV21-14
RBP	CSTF1	CSTF1
Batch_ID	BGKcLV21	BGKcLV21
WB_result	67.800	61.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	813	814

Sequencing Information

	BGKcLV21-13	BGKcLV21-14
Sample_ID	BGKcLV21-13	BGKcLV21-14
Sample Name	CSTF1-BGKcLV21-13	CSTF1-BGKcLV21-14
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	104,626,594	65,963,034
total_aligned_reads	101,706,878	63,862,460
unique_aligned_reads	93,231,608	58,449,058
percent_uniqueAligned	0.89109	0.88609
correlation_replicates	0.982969	0.982969
spikein_reads	107,220	41,504
percent_spikeins	0.00102	0.00063
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	444	445

Data Submission Information

	BGKcLV21-13	BGKcLV21-13	BGKcLV21-13	BGKcLV21-13	BGKcLV21-13	BGKcLV21-13	BGKcLV21-14	BGKcLV21-14	BGKcLV21-14	BGKcLV21-14
ENCODE_alias	brenton-graveley:CSTF1-BGKcLV21	brenton-graveley:CSTF1-BGKcLV21-13	brenton-graveley:L-CSTF1-BGKcLV21-13	brenton-graveley:CSTF1-BGKcLV21-13_S33_R1_001.fastq.gz	brenton-graveley:CSTF1-BGKcLV21-13_S33_R2_001.fastq.gz	brenton-graveley:CSTF1-BGKcLV21-K562	brenton-graveley:CSTF1-BGKcLV21-14	brenton-graveley:L-CSTF1-BGKcLV21-14	brenton-graveley:CSTF1-BGKcLV21-14_S34_R1_001.fastq.gz	brenton-graveley:CSTF1-BGKcLV21-14_S34_R2_001.fastq.gz
ENCODE_accession	ENCSR529UYQ	ENCBS796QWZ	ENCLB367WDN	ENCFF302JIG	ENCFF720ZOZ	ENCSR414EQZ	ENCBS556WES	ENCLB381ZQE	ENCFF832ZXH	ENCFF083ILN
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	BGKcLV21-13	BGKcLV21-13	BGKcLV21-13	BGKcLV21-13	BGKcLV21-13	BGKcLV21-13	BGKcLV21-14	BGKcLV21-14	BGKcLV21-14	BGKcLV21-14
Sample Name	CSTF1-BGKcLV21-13	CSTF1-BGKcLV21-13	CSTF1-BGKcLV21-13	CSTF1-BGKcLV21-13	CSTF1-BGKcLV21-13	CSTF1-BGKcLV21-13	CSTF1-BGKcLV21-14	CSTF1-BGKcLV21-14	CSTF1-BGKcLV21-14	CSTF1-BGKcLV21-14
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
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		CSTF1-BGKcLV21-13.pdf	L-CSTF1-BGKcLV21-13.pdf				CSTF1-BGKcLV21-14.pdf	L-CSTF1-BGKcLV21-14.pdf
ID	2106	2167	2237	2307	2377	7160	2168	2238	2308	2378

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
CSTF1-BGKcLV21-13_S33_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	444	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1216
CSTF1-BGKcLV21-13_S33_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	444	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1266
CSTF1-BGKcLV21-13_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	444					GRCh38	V40	CSTF1-BGKcLV21-13_S33_R1_001.filtered.trimmed.paired.fastq.gz,CSTF1-BGKcLV21-13_S33_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25209
CSTF1-BGKcLV21-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	444					GRCh38	V40	CSTF1-BGKcLV21-13_S33_R1_001.filtered.trimmed.paired.fastq.gz,CSTF1-BGKcLV21-13_S33_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27163
CSTF1-BGKcLV21-13_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	444					GRCh38	V40	CSTF1-BGKcLV21-13/Aligned.sortedByCoord.out.bam		ENCORE2	27213
CSTF1-BGKcLV21-13_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	444					GRCh38	V40	CSTF1-BGKcLV21-13/Aligned.sortedByCoord.out.bam		ENCORE2	27263
CSTF1-BGKcLV21-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	444					GRCh38	V40	CSTF1-BGKcLV21-13/Aligned.sortedByCoord.out.bam		ENCORE2	27313
CSTF1-BGKcLV21-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	444					GRCh38	V40	CSTF1-BGKcLV21-13/Aligned.sortedByCoord.out.bam		ENCORE2	27363
CSTF1-BGKcLV21-14_S34_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	445	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1217
CSTF1-BGKcLV21-14_S34_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	445	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1267
CSTF1-BGKcLV21-14_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	445					GRCh38	V40	CSTF1-BGKcLV21-14_S34_R1_001.filtered.trimmed.paired.fastq.gz,CSTF1-BGKcLV21-14_S34_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25210
CSTF1-BGKcLV21-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	445					GRCh38	V40	CSTF1-BGKcLV21-14_S34_R1_001.filtered.trimmed.paired.fastq.gz,CSTF1-BGKcLV21-14_S34_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27164
CSTF1-BGKcLV21-14_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	445					GRCh38	V40	CSTF1-BGKcLV21-14/Aligned.sortedByCoord.out.bam		ENCORE2	27214
CSTF1-BGKcLV21-14_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	445					GRCh38	V40	CSTF1-BGKcLV21-14/Aligned.sortedByCoord.out.bam		ENCORE2	27264
CSTF1-BGKcLV21-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	445					GRCh38	V40	CSTF1-BGKcLV21-14/Aligned.sortedByCoord.out.bam		ENCORE2	27314
CSTF1-BGKcLV21-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	445					GRCh38	V40	CSTF1-BGKcLV21-14/Aligned.sortedByCoord.out.bam		ENCORE2	27364