title: ChIPseq_HCT116_TC_EX1_HS_neg_ChIP_dCas9


title: CS_MM_4BAT_PolII_WT

status: Public on Dec 21 2024

type: SRA

city: shanghai

first: Guosheng

last: Hu

state: shanghai

address: 2005 Songhu Road, Yangpu District, Shanghai

country: China

institute: fudan university

library_source: genomic

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: mice brown adipocyte tissue

growth_protocol: BAT cells, were cultured in Medium B (Dulbecco’s modified Eagle’s medium (4.5 g/L glucose)

extract_protocol:
BAT adipocytes with forskolin treatments were used for ChIP-Seq analysis. For ChIP with anti-DDB1  antibodies, cells were fixed with 1% glutaraldehyde for 15 min at RT. For BAT tissue ChIP with  anti-Pol II and anti-Pol II-S2P antibodies, Tissue were fixed with 1% formaldehyde for 15 min at RT.Fixation was stopped by adding glycine to a final concentration of 0.14 M and incubating at RT for 10 min, followed by two washes with cold PBS.    For each ChIP, 1×107 cells or BAT tissue of 3 mice  were resuspended in Buffer A (50 mM Hepes, pH7.6, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) supplemented with protease inhibitors (Roche), incubated on ice for 10 min, and spun at 1,000 g for 10 min at 4oC. Pellet (nuclear fractions) was washed twice with Buffer B (10 mM Tris, pH7.8, 200 mM NaCl, 1 mM EDTA and 1 mM EGTA) supplemented with protease inhibitors, and resuspended in 0.3 ml Buffer C (50 mM Tris, pH7.8, 10 mM EDTA and 1% SDS) supplemented with protease inhibitors. Chromatin was fragmented to 150-300 bp on a Bioruptor for 30 cycles of 30 s on and 30 s off. Chromatin lysates were then diluted 10-fold with Buffer D (20 mM Tris, pH7.8, 150 mM NaCl, 2 mM EDTA and 1% Triton X-100) supplemented with protease inhibitors, incubated with 3 μg anti-DDB1 (Abcam, ab109027),  5 μg anti-Pol II (Bethyl, A300-653A), 5 μg anti-Pol II-S2P (Abcam, ab5095) antibodies overnight at 4oC, and then immunoprecipitated with Protein G magnetic beads (Biorad, 161-4023) with rotation at 4oC for 4 hr. Immunoprecipitations were washed once with Buffer E (20 mM Tris, pH8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS and 1% Triton X-100) for 15 min at 4oC, once with Buffer E containing 400 mM NaCl for 15 min at 4oC, and twice with Buffer F (50 mM Tris, pH8.0, 1 mM EDTA). Formaldehyde crosslinked chromatin was reversed in Buffer G (50 mM Tris, pH8.0, 10 mM EDTA, 1% SDS) at 65oC overnight, . DNA was isolated using Qiagen PCR product purification kit (#28104).
Library was generated using a KAPA Hyper Prep Kit (Roche, KK8503) following manufacturer’s instructions. Adaptors and primer sequences from Roche were used for library construction and amplification. After PCR amplification, the 250-450 bp fragments were purified using KAPA pure beads (Roche, KK8000) following manufacturer’s instructions.

treatment_protocol: 10 uM forskolin treatment for 1 hour

tag: cell line or tissue

value: mice brown adipocyte tissue

tag: chip antibody

value: anti-Pol II (Bethyl, A300-653A)

tag: treatment

value: BAT tissues harvested  from DDB1f/f mice at 4oC


title: ChIPseq_HCT116_TC_LGP_HS_neg_input

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

data_processing:
ChIP and RNA: Raw BCL output files were processed using bcl2fastq (Illumina, version 2.20)
ChIP and RNA: Quality trimming was performed using using CutAdapt1.14
ChIP: Trimmed ChIP-seq reads were aligned to the human genome (University of California at Santa Cruz [UCSC] hg38 build) using bowtie 2.4.5 with --sensitive option. Where spike-in is indicated, mm10 assembly was used for alignment. The bigwig files with reference-normalized coverage were generated using deepTools 3.5.1 bamCoverage.
ChIP: Peak calling was performed using MACS2 with the  default (narrow) option. Called peaks were annotated with HOMER program annotatePeaks.pl
ChIP: Heatmaps and metaplots from bigwig files were generated using deepTools v3.1.1
RNA: RNA-seq reads were aligned to the hg38 human genome using STAR aligner v2.5.2
RNA: Outputted bam files were sorted using samtools v1.6
RNA: exonic reads were assigned to specific genes from Ensembl release 72 and genome assembly GRCh38.p13 using the python package HTSeq-0.6.1
Assembly: hg38
Supplementary files format and content: bigwig files for ChIP-seq data

organism: Homo sapiens

growth_protocol: Human HCT116 cells were cultured in DMEM (Sigma #D6429) supplemented with 10% FBS (Sigma #F2442), 1% Pen-Strep (GIBCO #15140-122) in incubators set to 37°C and 5% CO2. Human DLD-1 cells were cultured at 37°C in DMEM supplemented with 10% FBS and 1% Pen-Strep in CO2 incubators.

extract_protocol:
For RNA: RNA from HCT116 cells was isolated using the RNeasy mini kit (Qiagen, #74106) as per manufacturer’s instructions.
For ChIP: Immunoprecipitated DNA was purified using a ChIP DNA Clean&Concentrator kit (Zymo Research, D5205). Cells were crosslinked with 1% formaldehyde (Thermo Scientific, Cat# 28908) in PBS for 10 min at r.t. To shear chromatin, sonication was performed using the E220 ultrasonicator (Covaris). The mouse embryonic fibroblast spike-in chromatin was added to the sample chromatin. Immunoprecipitation was performed using anti-Ser2P Pol II CTD (Active motif, Cat# 61083) and Dynabeads Protein G (ThermoFisher, Cat# 10004D) at 4°C. Protein degradation using proteinase K (Roche, Cat# 3115828001) and reverse crosslinking were performed at 65°C overnight. The immunoprecipitated DNA was purified using QIAquick PCR Purification Kit (Qiagen, Cat# 28106).
ChIP libraries were prepared using the KAPA HTP library preparation kit (KAPA Biosystems). RNA-seq libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, # E7760L).

treatment_protocol:
100mM biotin (Sigma-Aldrich, B4501) stock prepared in DMSO was added directly to tissue culture media at a final concentration of 100-500µM for immunostaining experiments and at 500µM for immunoblotting and proteomics experiments. Cells were incubated in biotin for 30 minutes at 37°C and 5% CO2 in the tissue culture incubator. Following this, media was removed and cells were washed with ice-cold PBS 5 times to quench the biotinylation reaction before fixation for immunostaining or harvest for endpoint assays.
Cells were either incubated at 37C (non-heat shock, HS_neg)  and 5% CO2 or 42C and 5% CO2 (heat shock/HS_pos). DLD-1 cells were treated with heat shock at 42°C for 2 h, following shRNA knockdown.

tag: cell line

tag: cell type

value: human colorectal carcinoma cells

tag: genotype

value: TurboCas no guide control

value: 37C 3 hours (no heat shock)

value: None (input)


title: CS_MM_4BAT_PolII_KODDB1

value: BAT tissues harvested  from DDB1-BKO mice at 4oC


title: ChIPseq_HCT116_TC_600_HS_pos_ChIP_dCas9

value: TurboCas FOS-600

value: 42C 3 hours (heat shock)


title: ChIPseq_HCT116_TC_600_HS_pos_input


title: E14, biol rep 1, RNAPIISer5-P, CUT&Tag

city: Pasadena

first: Yodai

last: Takei

state: CA

address: 1200 E California Blvd

institute: Caltech

data_processing:
*library strategy: CUT&Tag
Sequencing data was processed using the cutnrun pipeline v3.1 from nf-core (https://nf-co.re/cutandrun/3.1) with Nextflow v 24.04.1
Reads were aligned to the UCSC mm10 genome using bowtie2 v.2.4.2, keeping only reads with a minimum alignment q score of 20.
Aligned reads were masked using the mm10 blacklist from ENCODE.
Bigwigs were generated from masked alignments using the bamCoverage function of deeptools v3.5.1.
Assembly: mm10
Supplementary files format and content: Bigwig

growth_protocol: E14 mouse embryonic stem cells (E14Tg2a.4) (RRID:MMRRC_015890-UCD) from Mutant Mouse Regional Resource Centers were maintained on 0.1% gelatin (Sigma-Aldrich G1393) coated 6-well plates under the serum/LIF condition containing 15% ES-grade FBS (Gibco 16141061), 1,000 units/mL leukemia inhibitory factor (LIF) (Sigma-Aldrich ESG1106), 1× non-essential amino acids (Gibco 11140050), 1 mM sodium pyruvate (Gibco 11360070), 55 μM 2-mercaptoethanol (Gibco 21985023), 1× penicillin and streptomycin (Gibco 15140122) in DMEM GlutaMAX (Gibco 10566016). NMuMG mammary gland cells (ATCC CRL-1636) were maintained on 6-well plates (Thermo Scientific 150687) in 10% FBS (Corning 35-010-CV), 10 μg/mL insulin (Gibco 12585014), 1× penicillin and streptomycin (Gibco 15140122), and DMEM (Corning 10-013-CV).

extract_protocol:
Unfixed nuclei were extracted and bound to concanavalin A beads (EpiCypher), followed by an addition of primary antibody. For CUT&Tag, secondary antibody was applied, followed by an addition of pAG-Tn5 (EpiCypher). Tagmentation was then performed by an addition of magnesium. The DNA fragments were then extracted by 0.1% SDS. For CUT&RUN, pAG-MNase was applied, washed, and then activated by calcium chloride. Then DNA fragments were purified from supernatant using the column purification (EpiCypher).
The CUT&Tag libraries were prepared with i5 and i7 primers (IDT) and Q5 High-Fidelity 2× Master Mix (NEB) and amplified using 15 cycles (RNAPIISer5-P and H3K27me3) or 17 cycles (IgG) on the thermocycler. The CUT&RUN libraries were prepared with CUT&RUN Library Prep Kit (EpiCypher) and amplified using 12 cycles on the thermocycler. Post amplification libraries were purified by using magnetic beads (Omega Bio-Tek), followed by a gel electrophoresis with 1% agarose gels (Invitrogen) and a column purification (Zymo Research). Libraries were validated using the High Sensitivity DNA kit (Agilent).

value: embryonic stem cell

tag: antibody

value: RNAPIISer5-P (Cell Signaling 13523S)


title: E14, biol rep 1, H3K27me3, CUT&Tag

value: H3K27me3 (Cell Signaling 9733S)


title: CS_MM_22BAT_PolIIser2_KODDB1

value: anti-Pol II-S2P (Abcam, ab5095)

value: BAT tissues harvested  from DDB1-BKO mice at 22oC


title: CS_MM_22BAT_PolIIser2_WT

value: BAT tissues harvested  from DDB1f/f mice at 22oC


title: ChIPseq_HCT116_TC_LGP_HS_neg_ChIP_dCas9


title: ChIPseq_HCT116_TC_600_HS_neg_input


title: ChIPseq_HCT116_TC_EX1_HS_pos_ChIP_dCas9

value: TurboCas FOS-EX1


title: E14, biol rep 2, RNAPIISer5-P, CUT&Tag


title: ChIPseq_HCT116_TC_300_HS_pos_input

value: TurboCas FOS-300


title: CS_MM_22BAT_PolII_KODDB1

value: mice brown adipocyte tissue

value: anti-Pol II (Bethyl, A300-653A)


title: ChIP-seq_FUBP3_DLD1_shFUBP3_HS_Ab2

description:
Library name: ChIP-seq-APPEND_08
ChIP-seq

data_processing:
ChIP: The poor-quality bases were trimmed using Trimmomatic 0.33 (PMID: 24695404).
ChIP: Trimmed ChIP-seq reads were aligned to the human genome (University of California at Santa Cruz [UCSC] hg38 build) using bowtie 2.4.5 with --sensitive option. Where spike-in is indicated, mm10 assembly was used for alignment. The aligned read pairs with MAPQ ≥ 30 were retained for the downstream analysis. The bigwig files with reference-normalized coverage were generated using deepTools 3.5.1 bamCoverage.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: Human DLD-1 cells were cultured at 37°C in DMEM supplemented with 10% FBS and 1% Pen-Strep in CO2 incubators.

extract_protocol:
Cells were crosslinked with 1% formaldehyde (Thermo Scientific, Cat# 28908) in PBS for 10 min at r.t. To shear chromatin, sonication was performed using the E220 ultrasonicator (Covaris). The mouse embryonic fibroblast spike-in chromatin was added to the sample chromatin. Immunoprecipitation was performed using Dynabeads Protein G (ThermoFisher, Cat# 10004D) at 4°C. Protein degradation using proteinase K (Roche, Cat# 3115828001) and reverse crosslinking were performed at 65°C overnight. The immunoprecipitated DNA was purified using QIAquick PCR Purification Kit (Qiagen, Cat# 28106).
The ChIP-seq library was prepared using KAPA HTP library preparation kit (Roche, Cat# 07961901001).

treatment_protocol: Cells were treated with heat shock at 42°C for 2 h, following shRNA knockdown.

value: Colorectal adenocarcinoma

value: FUBP3 knockdown

tag: treatment 1

value: heat shock 2h

tag: treatment 2


title: ChIPseq_HCT116_TC_600_HS_neg_ChIP_dCas9

value: human colorectal carcinoma cells

value: 37C 3 hours (no heat shock)


title: NMuMG, biol rep 1, RNAPIISer5-P, CUT&Tag

source_name: NMuMG

value: NMuMG

value: mammary gland cell


title: CS_MM_BAT_DDB1_Forskolin1h

source_name: immortalized mice brown adipocyte cell

value: immortalized mice brown adipocyte cell

value: anti-DDB1 (Abcam, ab109027)

value: BAT adipocytes harvested  with forskolin treatment for 1h


title: ChIPseq_HCT116_TC_300_HS_neg_ChIP_dCas9


title: ChIPseq_HCT116_TC_300_HS_neg_input

value: None (input)


title: CS_MM_BAT_DDB1

value: BAT adipocytes harvested  without forskolin treatment


title: ChIP-seq_FUBP3_DLD1_shScr_HS_Ab2

description:
Library name: ChIP-seq-APPEND_07
ChIP-seq

value: WT

value: shScr


title: KYSE510_RNA1_sh2

city: Zhengzhou

first: Yunfeng

last: Gao

address: No.127 at Dongming road

institute: China-US (Henan) Hormel Cancer Institute

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set,then expression level of gene was calculated by RSEM (v1.2.12)
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples.
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value<= 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

molecule: total RNA

source_name: KYSE510 cells

growth_protocol: KYSE510 cells were cultured in RPMI-1640 medium with 10% FBS and penicillin-streptomycin.

extract_protocol:
Cells were collected on ice, and total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using BGISEQ-500 protocols

treatment_protocol: KYSE510 cells were transfected with lenti-virus containing shRNA for 24h, and were screened under 4μM puromycin for 48h.

value: esophageal squamous cell carcinoma (ESCC)

value: Transfected with Lenti-virus containing TCONS_02256997 shRNA#2


title: ChIP-seq_FUBP3_DLD1_shFUBP3_HS_Ab1

description:
Library name: ChIP-seq-APPEND_04
ChIP-seq


title: ChIP-seq_FUBP3_DLD1_shScr_HS_Ab1

description:
Library name: ChIP-seq-APPEND_03
ChIP-seq


title: ChIPseq_HCT116_MT_LGP_HS_pos_input

value: MiniTurbo control

value: 42C 3 hours (heat shock)


title: ChIP-seq_FUBP3_DLD1_shFUBP3_NonHS_Ab1

description:
Library name: ChIP-seq-APPEND_02
ChIP-seq

value: Colorectal adenocarcinoma

value: FUBP3 knockdown

value: control


title: ChIP-seq_FUBP3_DLD1_shFUBP3_NonHS_Ab2

description:
Library name: ChIP-seq-APPEND_06
ChIP-seq


title: KYSE510_RNA1_sh1

value: Transfected with Lenti-virus containing TCONS_02256997 shRNA#1


title: ChIPseq_HCT116_MT_LGP_HS_pos_ChIP_dCas9

value: human colorectal carcinoma cells


title: KYSE510_RNA_C

value: Transfected with Lenti-virus containing scremble shRNA


title: ChIP-seq_FUBP3_DLD1_shScr_NonHS_Ab1

description:
Library name: ChIP-seq-APPEND_01
ChIP-seq


title: C2C12_bio6_NT

city: Hong Kong

first: QIANG

last: SUN

address: Ngan Shing Street

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Adaptor sequences and poor-quality reads were removed using Trimmomatic
The filtered reads were then aligned to human (hg19) or mouse reference genome (mm9)
All aligned reads were then merged and assigned to restriction fragment, while low quality (MAPQ<30) or multiple alignment reads were discarded
Invalid fragments including unpaired fragments (singleton), juxtaposed fragments (re-legation pairs), un-ligated fragments (dangling end), self-circularized fragments (self-cycle), and PCR duplicates were removed from each biological replicate. The remaining validate pairs from all replicates of each stage were then merged, followed by read depth normalization using HOMER (http://homer.ucsd.edu/homer/ngs/) and matrix balancing using iterative correction and eigenvector decomposition (ICE) normalization to obtain comparable interaction matrix between different stages
Assembly: mm9
Supplementary files format and content: .hic: an indexed binary format designed to permit fast random access to contact matrix heatmaps.

source_name: C2C12 cell

growth_protocol: Mouse C2C12 myoblast cells (CRL-1772) were obtained from American Type Culture Collection (ATCC) and cultured in DMEM medium (Gibco, 12800-017) with 10% fetal bovine serum (Gibco, 10270-106), 100 units/ml of penicillin, and 100 μg of streptomycin at 37°C in 5% CO2. Human leukaemia K562 cells (CCL-243) were obtained from ATCC and maintained at 37°C under 5% CO2 in RPMI-1640 medium (Thermo Fisher Scientific, 22400089) with 10% fetal bovine serum, 100 units/ml of penicillin, and 100 μg of streptomycin.

extract_protocol:
RNAs were extracted 48 h after transfection.
About 300,000 C2C12 cells were cross-linked and processed to generate Hi-C libraries, following modifications of established protocols. Libraries underwent paired-end sequencing on an Illumina HiSeq X Ten instrument

treatment_protocol: For transfection, siRNA against RBFox2 or control oligos were obtained from Shanghai GenePharma Corp., China. Transfections were conducted with Amaxa Cell Line Nucleofector Kit V (Lonza, Basel, Switzerland). Briefly, K562 cells were grown for 24h and resuspended in 100 μl Nucleofector Solution V. siRNA targeting RBFox2 or control oligos were used at a concentration of 300 nM and the transfection was completed with Lonza Nucleofector™ using program T-016

value: C2C12 cell

value: no treatment


title: C2C12_bio6_ActD

value: ActD


title: C2C12_bio5_NT


title: ChIP-seq_FUBP3_DLD1_shScr_NonHS_Ab2

description:
Library name: ChIP-seq-APPEND_05
ChIP-seq


title: ChIPseq_293T_TC_LGP_HS_pos_ChIP_dCas9

value: human embryonic kidney cells

value: TurboCas no guide control


title: ChIPseq_293T_TC_LGP_HS_pos_input

value: None (input)


title: C2C12_bio5_ActD


title: ChIPseq_HCT116_TC_300_HS_pos_ChIP_dCas9

value: TurboCas FOS-300


title: ChIPseq_HCT116_MT_LGP_HS_neg_ChIP_dCas9

value: 37C 3 hours (no heat shock)


title: CS_MM_22BAT_PolII_WT

value: mice brown adipocyte tissue

value: anti-Pol II (Bethyl, A300-653A)

value: BAT tissues harvested  from DDB1f/f mice at 22oC


title: H3K27me3_8cell

city: Beijing

first: Min

last: Liu

state: Beijing

address: Yan  yuan street

institute: 北京大学

description: sample 3_H3K27me3_8cell

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to human genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Assembly: mm10
Supplementary files format and content: The processed files were aggregate bigwig file.

extract_protocol:
Following TACIT protocol.
After PCR enrichment, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Cells were collocted by centrifugation at 150-1,500g for 3 minutes

tag: tissue

value: embryo

tag: cell statement

value: fixed by methanol


title: ChIP-seq-Ser2P-DLD1-shScr-HS-Rep1

value: Colorectal adenocarcinoma

value: shScr-HS

value: pSer2 (ActiveMotif, # 61083)


title: C2C12_bio4_NT


title: K562_bio3_tech1-siRBFox2


title: ChIPseq_293T_TC_LGP_HS_neg_input


title: C2C12_bio4_ActD


title: K562_bio2_tech1-siRBFox2


title: ChIPseq_293T_TC_LGP_HS_neg_ChIP_dCas9


title: C2C12_bio3_NT


title: K562_bio4_tech1_siRBFox2


title: DKO_C14_R2_Input

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

description: Input (background) sample

data_processing:
Reads were trimmed with cutadapt v.2.8
Quality was assessed using FastQC v0.11.9 & Fastq-Screen v0.15.2
Files were mapped to GRCh38 using Bowtie2 v.2.3.5.1
Duplicates were marked using samtools markduplicates v1.10
BAMs were counted using bedtools multicov v.2.27.1 and processed in R v 4.2.2
Differential enrichment was done using edgeR v3.42.4 in R v 4.2.2
Assembly: GRCh38
Supplementary files format and content: Tab deliminated text file with counts for each OG sample minus its SES normalized input. Samples are counted over the entire genome in 1000bp bins.

growth_protocol: Cell culture in IMDM with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
Dneasy Blood and Tissue (Qiagen) according to manufacture's protocol with 0.1mM butylated hydroxytoluene and 0.1mM deferoxamine added to prevent oxidative damage during isolation.
Accel-NGS 1S Plus DNA Library Kit according to manufacturer's protocol

value: near-haploid

value: MUTYH-/ X OGG1-/


title: K562_bio4_tech1_siNC

value: siNC


title: ChIPseq_293T_TC_EX1_HS_pos_ChIP_dCas9

value: TurboCas FOS-EX1

value: 42C 3 hours (heat shock)


title: DKO_C4_R2_Input

description: Input (background) sample


title: DKO_C4_R1_Input

description: Input (background) sample


title: K562_bio2_tech1-siNC


title: C2C12_bio3_ActD

value: C2C12 cell

value: ActD


title: ChIPseq_293T_TC_EX1_HS_neg_ChIP_dCas9

value: human embryonic kidney cells


title: K562_bio1_tech1_siNC


title: K562_bio1_tech1_siRBFox2


title: DKO_C14_R2_OG

description: Pull-down sample


title: ChIPseq_293T_TC_EX1_HS_neg_input

value: 37C 3 hours (no heat shock)

value: None (input)


title: DKO_C4_R2_OG

description: Pull-down sample


title: WT_r1_L1_exit [WT_iCas9e24r1]

city: Poznan

first: Katarzyna

last: Blaszczyk

state: Wielkopolska

address: ul. Uniwersytetu Poznańskiego 6/1.87

department: Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

data_processing:
fastp for trimming, mapping with STAR, indexing bam with samtools, BigWig with deepTools, counting reads with FeatureCouts
EdgeR log2 for transforming counts, Identifying Differential Expressed Genes with DESeq2
Assembly: genome_hs_38_94/Homo_sapiens.GRCh38.94
Supplementary files format and content: Supplementary Table 1.xlsx

growth_protocol: Cells cultured in StemFlex (Thermo Fisher Scientific) medium on Geltrex (Thermo Fisher Scientific)-coated plates at 37 °C, under an atmosphere containing 5% CO2. Cells were passaged every 3-4 days using PBS-EDTA.

extract_protocol:
Total RNA was prepared with the Trizol reagent (Thermo Fisher Scientific) or phenol/chloroform method according to the manufacturer's instructions.
TrueSeq
500-1000 ng of total RNA isolated from ETV1 KO, tKO, and WT hPSCs to prepare libraries with the TruSeq RNA Library Prep Kit v2 according to the manufacturer's protocol. Libraries were prepared in duplicate. Libraries were quantified with a Qubit fluorometer (TFS), and their quality was assessed with the Agilent High Sensitivity DNA kit (Agilent Technologies, USA). Libraries were sequenced with an Illumina HiScanSQ sequencer.

treatment_protocol: Differentiation towards primitive streak was performed as follows. Ready-to-passage hPSCs were dissociated using TrypLE, resuspended in Stemflex medium plus 10 µM Y-27632 and seeded onto Geltrex-coated 12-well-plate at the density of 2 x 105 cells/cm2. The next day cells were washed and differentiation was initiated by changing medium to MCDB 131 supplemented with 10 mM Glutamax, 8.89 mM glucose, 14 mM sodium bicarbonate, 0.1% BSA, 100 ng/mL Activin A and 3 µM CHIR99021. After 24 h cells were collected for the RNA-seq experiments.

value: hPSC

value: WT

value: primitive streak stage


title: ChIPseq_293T_TC_600_HS_pos_input

value: TurboCas FOS-600


title: K562_bio3_tech1-siNC


title: C2C12_bio2_ActD


title: C2C12_bio1_NT

value: no treatment


title: WT_r2_L1_exit [WT_iCas9e24r2]


title: ChIPseq_293T_TC_600_HS_pos_ChIP_dCas9


title: ChIPseq_293T_TC_EX1_HS_pos_input


title: C2C12_bio1_ActD


title: tKO_r2_L1_exit [tKO_E1e24r2]

value: tKO


title: OGG1_C22_R2_Input

description: Input (background) sample


title: ChIPseq_293T_TC_600_HS_neg_ChIP_dCas9


title: OGG1_C1_R2_Input

description: Input (background) sample


title: Input

data_processing:
Briefly, the adapter and low-quality sequences were trimmed from 3’ to 5’ ends by Trimmomatic and the reads shorter than 36 bp were discarded
Subsequently, the preprocessed reads were aligned to the mouse genome (mm9) using Bowtie2. The aligned reads were then converted to bam format using samtools, and the duplicate reads were removed by Picard (http://broadinstitute.github.io/picard).
Peaks were then identified by MACS2 with q-value equal to 0.01 by using the IgG control sample as background.
Assembly: mm9
Supplementary files format and content: *.bw: binary signal file generated by bedGraphToBigWig

growth_protocol: C2C12  were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep in 5% CO2 37°C incubator.

extract_protocol: Sequential crosslinking was performed with the following steps: approximately 10^7 C2C12 cells were cross-linked with 0.2 mM dithiobis (succinimidyl propionate) (DSP) crosslinking solution at room temperature for 30 min, treatment with 3% final concentration of formaldehyde 15 min then quenched with 1/10 volume of 2.5 M Glycine, cells were washed and collected by centrifugation at 2,000 x g for 5 min at 4°C, flash-frozen in liquid nitrogen, and stored at -80°C. Then following our standard procedure, 6 μg of antibodies against RBFox2 (Bethyl Laboratories, A300-864A) was used for immunoprecipitation. Immunoprecipitated genomic DNA was resuspended in 25 μl of water. For DNA library construction, a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S) was used according to the manufacturer’s instructions. Bioanalyzer analysis and qPCR were used to measure the quality of DNA libraries including the DNA size and purity. Finally, DNA libraries were sequenced on the Illumina Genome Analyzer II platform.

treatment_protocol: For transcription inhibition, cells were pre-treated with actinomycin-D for indicated time before cross-linking. When the C2C12 cells’ density reached 60%-70%, added actinomycin-D (1 μg/ml) into the cell culture medium then cultured for 24 h and harvested using Trypsin. For RNA degradation, 1 × 10^7 C2C12 cells were subjected to RNase A or RNase inhibitor treatment. After cells spun down at 2,000 × g for 10 min at 4°C. The supernatant was removed, and the cell pellet was re-suspended with 1 ml of cold PBS + 0.02% Tween-20 followed by incubation on ice for 10 min. Next, either 35U of RNase A (Invitrogen, 12091-021) or 30U of RNase inhibitor (Life Technologies, 10777019) was added to the suspension and incubated at 37°C for 30 min in a thermomixer at 950 rpm. After incubation, put the cells on ice for 10 min. Then, the cells were spun down at 2,000 × g for 10 min at 4°C and washed once with 1 ml cold PBS with protease inhibitor cocktail (Cell Signaling Technology, 7012L). The subsequent cell processing was for either Hi-C or ChIP-seq experiments.


title: ChIPseq_HCT116_MT_LGP_HS_neg_input

value: human colorectal carcinoma cells

value: MiniTurbo control


title: C2C12_bio2_NT


title: tKO_r1_L1_exit [tKO_E1e24r1]


title: ChIPseq_293T_TC_300_HS_pos_input

value: TurboCas FOS-300


title: KO_r2_L1_exit [KO_H3e24r2]

value: KO


title: RBFox2_ActD


title: ChIPseq_293T_TC_300_HS_pos_ChIP_dCas9


title: OGG1_C1_R1_Input

description: Input (background) sample

value: near-haploid


title: OGG1_C22_R2_OG

description: Pull-down sample


title: ChIPseq_293T_TC_300_HS_neg_input


title: OGG1_C1_R2_OG

description: Pull-down sample


title: OGG1_C1_R1_OG

description: Pull-down sample


title: DKO_C4_R1_OG

description: Pull-down sample

value: MUTYH-/ X OGG1-/


title: KO_r1_L1_exit [KO_H3e24r1]


title: WT_r1_L1_pluri [WT_iCas9pr1]

value: pluripotency stage


title: ChIPseq_293T_TC_300_HS_neg_ChIP_dCas9


title: ChIPseq_293T_TC_600_HS_neg_input


title: ATACseq_WT_rep2

first: Chengqi

last: Yi

address: Yiheyuan Road

department: School of Life Sciences

institute: Peking University

data_processing:
After adpater was trimmed by cutadapt, reads were aligned to mm9 using Bowtie2 under the parameters -X 2000 --no-mixed --no-discordant
Duplicated reads and reads aligned to mitochondria or blacklist regions were removed, then properly alignted reads were shift.
Peak calling was performed using MACS2 with parameters callpeak --g mm --keep-dup all --q 0.01 --llocal 10000 --nomodel
Genome_build: mm9

source_name: Liver

extract_protocol:
20mg of frozen liver tissue was Dounce homogenized using a loose pestle in 2 mL ice-cold homogenization buffer. The homogenized tissue was filtered through a 40μm strainer, mixed with equal volume of 50% iodixanol density medium, underlayed with a gradient of 30% and 40% iodixanol, and centrifuged at 5,000g for 30 minutes in a swinging bucket centrifuge at 4°C with break off. Nuclei were collected in a 200μl volume and transferred to a pre-chilled tube and counted.
30,000 counted nuclei were used for ATAC-Seq library preparation. 35 μl ddH2O, 5μl 5 × TTBL, 5 μl TTE mix V50 (TD501, Vazyme) were added to the sample, which was mixed and incubated at 37 °C for 30 min and followed ATAC-seq library preparation was conducted with TruePrep Index Kit V2 for Illumina (TD202, Vazyme) and the libraries were subjected to next-generation sequencing.

tag: strain


title: ATACseq_WT_rep4


title: WT_r2_L1_pluri [WT_iCas9pr2]


title: Hmol1-3B_XBP1-OE_rep3

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

data_processing:
Expression levels for each gene were quantified from the sequencing data by Kallisto software.
The tximport package (ver. 1.18.0) was used to summarize the data.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: a txt file includes TPM counts of each sample

growth_protocol: Hmol1-3B and Hmol1-2C were maintained in a 1:1 mixture of the following DMEM and Humedia-KG2 medium: DMEM (Nacalai tesque, Kyoto, Japan) supplemented with 10% FBS and antibiotics, and Humedia-KG2 (Kurabo Industries Ltd., Osaka, Japan) supplemented with recombinant human epidermal growth factor (0.1 ng/mL), recombinant human insulin (10 μg/mL), hydrocortisone (0.67 μg/mL), gentamicin (50 μg/mL), amphotericin B (50 ng/mL) and bovine pituitary extract (0.004 mg/mL).

extract_protocol:
The total RNA of cell lines was extracted using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany).
The library construction and pair-end sequencing were conducted by Novogene, Inc. (Beijing, China).

treatment_protocol: The control and XBP1 lentiviral vectors (pLV[Exp]-Puro-EF1A>EGFP and pLV[Exp]-EGFP:T2A:Puro-EF1A>hXBP1) were purchased from Vector Builder (Chicago, IL). Transduction of the viral vectors was performed according to the protocol of the Lenti-XTM Packaging Single Shots (Takara, Shiga, Japan).

value: XBP1-OE vector


title: tKO_r1_L1_pluri [tKO_E1pr1]


title: ATACseq_WT_rep1


title: tKO_r2_L1_pluri [tKO_E1pr2]


title: Hmol1-3B_XBP1-OE_rep2


title: RBFox2_NT

value: C2C12 cell


title: MUTYH_C7_R2_Input

description: Input (background) sample

value: MUTYH-/


title: KO_r2_L1_pluri [KO_H3pr2]


title: ATACseq_HOMO_rep4


title: KO_r1_L1_pluri [KO_H3pr1]


title: Hmol1-3B_XBP1-OE_rep1


title: RNAseq_WT_rep3

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to reference genome using Tophat
Reads aligned to specific transcripts was counted by HTseq
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated and differential analysis were performed using cufflinks.
Genome_build: mm9

molecule: polyA RNA

extract_protocol:
Livers were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: MUTYH_C8_R2_OG

description: Pull-down sample


title: Hmol1-3B_Ctrl_rep2

value: Ctrl vector


title: MUTYH_C7_R2_OG

description: Pull-down sample


title: ATACseq_HOMO_rep3


title: RNAseq_WT_rep2


title: MUTYH_C7_R1_Input

description: Input (background) sample


title: Hmol1-3B_Ctrl_rep3


title: MUTYH_C8_R2_Input

description: Input (background) sample


title: MUTYH_C7_R1_OG

description: Pull-down sample


title: RNAseq_WT_rep1


title: Hmol1-2C_XBP1-OE_rep3


title: RNAseq_HOMO_rep3


title: elt-1_RNAi, smRNA-seq,bio rep3

city: hangzhou

first: li

middle: li

last: li

state: zhejiang

address: 600 Dunyu Road

institute: westlake university

data_processing:
Raw read’s adapters were trimmed via Cutadapt (version 2.5) using the adapter sequence ‘AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC’.
Reads were then mapped to the C. elegans genome (WormBase release WS279) using STAR-aligner (version 2.5.2b).
Read counts were obtained using a custom R script and normalized to library size (reads per million - RPM).
25~27nt RNA called (26G-RNAs) that are antisense to protein-coding genes.
Assembly: C. elegans WS279
Supplementary files format and content: bigWig files

organism: Caenorhabditis elegans

source_name: whole worms

extract_protocol:
Small RNAs were purified by mir-Vana miRNA isolation kit (Thermo Scientific, AM1560) from extracted Total RNAs of prepared worms. Small-RNA cloning was performed. Briefly, RNA 5’ Pyrophosphohydrolase (RppH) (NEB, M0356S) was used for trimming 5’ triphosphate of endogenous 22G-RNAs to monophosphate. The 3’ and 5’ adaptors were ligated sequentially using truncated ligase 2 (NEB, M0373S) and ligase 1 (NEB, M0437M).
cDNA was then generated by Superscript III reverse transcriptase (Invitrogen,18064022) and amplified by Q5 polymerase (NEB, M0491S) with adapter sequences added at this step. Amplified PCR products were subjected to 12.5% native PAGE and size selection. Finally, High throughput sequencing was carried out using multiple Illumina platforms.

value: whole worms

value: wild type (N2)

value: with elt-1 RNAi


title: WT_C2_R2_Input

description: Input (background) sample

value: WT


title: RNAseq_HOMO_rep2


title: elt-1_RNAi, smRNA-seq,bio rep1


title: Hmol1-2C_XBP1-OE_rep1


title: Hmol1-2C_XBP1-OE_rep2


title: WT_C11_R1_Input

description: Input (background) sample


title: ctrl_RNAi, smRNA-seq,bio rep3

value: with vector RNAi control


title: ATACseq_HOMO_rep2


title: RNAseq_HOMO_rep1


title: ATACseq_HOMO_rep1


title: Hmol1-2C_Ctrl_rep3


title: ctrl_RNAi, smRNA-seq,bio rep2


title: Hmol1-3B_Ctrl_rep1


title: WT_C2_R2_OG

description: Pull-down sample


title: A375, Replicate2, H3K27ac HiChIP

city: New York

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
We mapped HiChIP paired end reads to hg19 using HiC-Pro (Servant 2015). Default settings were using to remove duplicate reads, identify valid interactions, and generate contact maps.
We identified statistically significant contacts using FitHiChIPat a 1% FDR. We used H3K27ac ChIP-seq data as a reference set of peaks in the FitHiChIP pipeline.
Assembly: hg19
Supplementary files format and content: allValidPairs, bed
Library strategy: H3K27ac HiChIP

growth_protocol: A375 and A549 cells were cultured in Dulbecco’s Modified Eagle Medium + 10% v/v FBS + 1% Pen/Strep. HT29 cells were cultured in McCoy's 5A (Modified) Medium + 10% v/v FBS + 1% Pen/Strep. K562 cells were cultured in Iscove's Modified Dulbecco's Medium + 10% v/v FBS + 1% Pen/Strep. MDAMB231 and PC( cells were cultured in RPMI-1640 + 10% v/v FBS + 1% Pen/Strep. All cells were cultured in a humidified enviornment with 5% CO2 at 37C.

extract_protocol:
For H3K27ac HiChIP libraries, we grew NIH3T3 (mouse) cells and human cell lines A375, A549, HT29, K562, MDA-MB-231 and PC-9 in the appropriate media.  We fixed cells in 1% formaldehyde for 10min and quenched to a final concentration of 125nM glycine. We mixed 2 million fixed mouse cells with 10 million of each fixed human cancer cell line. The cells were lysed in 0.5% SDS, quenched with 10% Triton X-100, and digested with MboI (NEB R0147M). The DNA overhangs were blunted, biotinylated (ThermoFisher 19524016), and ligated. Nuclei were spun down, resuspended in nuclear lysis buffer and sonicated using a Covaris LE220 with the following conditions: Fill level 10, PIP 450, Duty factor 30, CPB 200. We incubated the sheared DNA with Dynabeads Protein A (ThermoFisher 10001D) for 2 hours at 4 °C. We then placed the tubes on a magnet and the supernatant was kept. We performed immunoprecipitation with a cross-species reactive H3K27ac antibody (Active Motif 39133). The samples were incubated with the antibody overnight at 4 °C. We then washed, eluted and treated the samples and treated with Proteinase K. We purified the samples using Zymo DNA Clean & Concentrator
Biotin capture was performed with Dynabeads M-280 Streptavidin (ThermoFisher 11205D), followed by library preparation as previously described (Gryder, Khan and Stanton, 2020). We purified the amplified libraries with Illumina Sample Purification Beads. We sequenced the libraries using paired-end reads with NovaSeq 6000 or NextSeq 500.

treatment_protocol: HT29 cells with inducible RfxCas13d were transduced with a nontargeting guide or one of two CCAT1 targeting guides. We performed H3K27ac HiChIP 72 hours after induction with 1 ug/mL  doxycycline.

value: No treatment


title: Hmol1-2C_Ctrl_rep1


title: A375, Replicate1, H3K27ac HiChIP


title: Hmol1-2C_Ctrl_rep2


title: WT_C11_R1_OG

description: Pull-down sample


title: elt-1_RNAi, smRNA-seq,bio rep2


title: ctrl_RNAi, smRNA-seq,bio rep1


title: WT_C11_R2_OG

description: Pull-down sample


title: L4 C.elegans germ cells, scRNAseq

description: BD Rhapsody™ Single-Cell Analysis System

library_source: transcriptomic single cell

data_processing:
The gene expression matrices generated from BD Rhapsody WTA Local bioinformatics pipeline.
For the quality control step, doublets from scRNA-seq data were identified and removed using Scrublet.
Cells were retained with 2000~6000 genes, 5000~50000 unique transcripts, and 0.5~10% mitochondrial transcripts.
Assembly: C. elegans WS279
Supplementary files format and content: Tab-separated values files and matrix files

source_name: germline

extract_protocol:
Germ cells were labeled with sample tags (BD Rhapsody Single-Cell Multiplexing Kit) according to the manufacturer’s protocol.
Single cells were isolated using Single-Cell Capture and complementary DNA (cDNA) Synthesis with the BD Rhapsody Express Single-Cell Analysis System, and cDNA libraries were prepared using the BD Rhapsody™ Whole Transcriptome Analysis Amplification Kit.

value: germline

value: germ cell

value: L4 worm after synchronization


title: WT_C11_R2_Input

description: Input (background) sample


title: imb_keller_2023_16_21_SoaKI_7h_SOA_Rep1

status: Public on Dec 20 2024

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

description:
Library name: Sample 21
SoaKI_7h_SOA_Rep1

data_processing:
Reads were trimmed with cutadapt (v.4.6).
Trimmed reads were mapped to the ensembl AgamP4 genome with bowtie2 (2.4.5). Duplicate and multimmapping reads were omitted from downstream analysis
Coverage signal tracks (bigWigs) of alignments were generated using Samtools (v1.10) and DeepTools (v3.5.1)
Peaks were called with MACS version 2.1.2.
DiffBind (v.3.8.4) was used to determine differential binding. Only peaks with FDR<0.05 in were considered as differentially bound.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments
Library strategy: CUT&Tag

organism: Anopheles gambiae

source_name: whole embryos

growth_protocol: A. gambiae pupae were maintained in standard insectary conditions (26–28°C, 75–80% humidity, and 12-/12-h light/dark cycle).

extract_protocol:
The experiment was performed with flash frozen tissues, which were homogenized in cold PBS and passed through a cell strainer. The cell suspension was counted and 0.4 Mio cells were used for each reaction. 100 000 cells were used for each reaction. The libraries were generated according to the following protocol: dx.doi.org/10.17504/protocols.io.bcuhiwt6). Antibodies are listed with the respective samples. We used pA-Tn5 prepared by the IMB protein production core facilty.
CUT&Tag libraries were amplified using NEBNext Ultra II Q5 Master Mix with standard protocols and 15 PCR cycles. Libraries were cleaned up using 1.3 volume Ampure XP beads and pooled together for paired-end sequencing.

tag: developmental stage

value: 7h embryo

value: whole embryos

value: SOA

tag: Sex

value: pooled male and female

value: SoaKI


title: imb_keller_2023_16_22_SoaKI_7h_SOA_Rep2

description:
Library name: Sample 22
SoaKI_7h_SOA_Rep2


title: imb_keller_2023_16_20_SoaKI_4h_SOA_Rep2

description:
Library name: Sample 20
SoaKI_4h_SOA_Rep2

value: 4h embryo


title: imb_keller_2023_16_23_SoaKI_20h_SOA_Rep1

description:
Library name: Sample 23
SoaKI_20h_SOA_Rep1

value: 20h embryo


title: imb_keller_2023_16_19_SoaKI_4h_SOA_Rep1

description:
Library name: Sample 19
SoaKI_4h_SOA_Rep1


title: imb_keller_2023_16_24_SoaKI_20h_SOA_Rep2

description:
Library name: Sample 24
SoaKI_20h_SOA_Rep2


title: ATACseq_WT_rep3


title: imb_keller_2023_16_16_WT_7h_SOA_Rep2

description:
Library name: Sample 16
WT_7h_SOA_Rep2


title: imb_keller_2023_16_17_WT_20h_SOA_Rep1

description:
Library name: Sample 17
WT_20h_SOA_Rep1


title: imb_keller_2023_16_18_WT_20h_SOA_Rep2

description:
Library name: Sample 18
WT_20h_SOA_Rep2


title: imb_keller_2023_16_13_WT_4h_SOA_Rep1

description:
Library name: Sample 13
WT_4h_SOA_Rep1


title: imb_keller_2023_16_15_WT_7h_SOA_Rep1

description:
Library name: Sample 15
WT_7h_SOA_Rep1


title: imb_keller_2023_16_14_WT_4h_SOA_Rep2

description:
Library name: Sample 14
WT_4h_SOA_Rep2


title: imb_keller_2023_16_12_SoaKI_20h_IgG_Rep2

description:
Library name: Sample 12
SoaKI_20h_IgG_Rep2

value: IgG


title: imb_keller_2023_16_11_SoaKI_20h_IgG_Rep1

description:
Library name: Sample 11
SoaKI_20h_IgG_Rep1


title: imb_keller_2023_16_10_SoaKI_7h_IgG_Rep2

description:
Library name: Sample 10
SoaKI_7h_IgG_Rep2


title: imb_keller_2023_16_06_WT_20h_IgG_Rep2

description:
Library name: Sample 6
WT_20h_IgG_Rep2


title: imb_keller_2023_16_08_SoaKI_4h_IgG_Rep2

description:
Library name: Sample 8
SoaKI_4h_IgG_Rep2


title: imb_keller_2023_16_05_WT_20h_IgG_Rep1

description:
Library name: Sample 5
WT_20h_IgG_Rep1


title: imb_keller_2023_16_07_SoaKI_4h_IgG_Rep1

description:
Library name: Sample 7
SoaKI_4h_IgG_Rep1


title: imb_keller_2023_16_03_WT_7h_IgG_Rep1

description:
Library name: Sample 3
WT_7h_IgG_Rep1


title: imb_keller_2023_16_02_WT_4h_IgG_Rep2

description:
Library name: Sample 2
WT_4h_IgG_Rep2


title: imb_keller_2023_19_32_M_SoaKI_18h_Rep4

description:
Library name: Sample 16
M_SoaKI_18h_Rep4

data_processing:
Reads were trimmed with cudadapt (1.18) to remove adapter sequences (CTGTCTCTTATACACATCT)
Reads were mapped to the AgamP4 genome using the Ensembl AgamP4 annotation (release 48)  with STAR (v. 2.7.3a) using the following parameters: outFilterMismatchNoverLmax 0.04 outFilterMismatchNmax 999. Only uniquely mapped reads were used for downstream analysis.
Coverage signal tracks (bigWigs) of primary alignments were generated using Samtools (v1.10) and DeepTools (v3.5.1).
Primary alignments were assigned to features using subread 2.0.0 with the AgamP4 annotation (release 48) as a reference.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments
Supplementary files format and content: featureCounts count matrix as tab-delimited .txt file

source_name: embryo

growth_protocol: A. gambiae mosquitoes were maintained in standard insectary conditions (26–28°C, 75–80% humidity, and 12-/12-h light/dark cycle).

extract_protocol:
RNA was extracted using Trizol (Fisher Scientific, Cat. No.15-596-026) and the Direct-zol RNA MicroPrep Kit (Zymo Research, Cat. No. R2062).
The libraries were prepared with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation ReferenceGuide (April 2021) (Document 1000000124518 v02). Libraries were prepared with a starting amount of 4 ng and amplified with 13 PCR cycles.

value: embryo

value: male

value: SOA-KI


title: imb_keller_2023_16_09_SoaKI_7h_IgG_Rep1

description:
Library name: Sample 9
SoaKI_7h_IgG_Rep1


title: imb_keller_2023_16_04_WT_7h_IgG_Rep2

description:
Library name: Sample 4
WT_7h_IgG_Rep2

value: WT


title: imb_keller_2023_19_30_M_SoaKI_18h_Rep2

description:
Library name: Sample 14
M_SoaKI_18h_Rep2


title: imb_keller_2023_16_01_WT_4h_IgG_Rep1

description:
Library name: Sample 1
WT_4h_IgG_Rep1


title: imb_keller_2023_19_31_M_SoaKI_18h_Rep3

description:
Library name: Sample 15
M_SoaKI_18h_Rep3


title: imb_keller_2023_19_29_M_SoaKI_18h_Rep1

description:
Library name: Sample 13
M_SoaKI_18h_Rep1


title: imb_keller_2023_19_28_F_SoaKI_18h_Rep4

description:
Library name: Sample 12
F_SoaKI_18h_Rep4

value: female


title: imb_keller_2023_19_27_F_SoaKI_18h_Rep3

description:
Library name: Sample 11
F_SoaKI_18h_Rep3


title: imb_keller_2023_19_26_F_SoaKI_18h_Rep2

description:
Library name: Sample 10
F_SoaKI_18h_Rep2


title: imb_keller_2023_19_25_F_SoaKI_18h_Rep1

description:
Library name: Sample 9
F_SoaKI_18h_Rep1


title: imb_keller_2023_19_23_M_WT_18h_Rep3

description:
Library name: Sample 7
M_WT_18h_Rep3

value: wild-type


title: imb_keller_2023_19_22_M_WT_18h_Rep2

description:
Library name: Sample 6
M_WT_18h_Rep2


title: imb_keller_2023_19_24_M_WT_18h_Rep4

description:
Library name: Sample 8
M_WT_18h_Rep4


title: imb_keller_2023_19_20_F_WT_18h_Rep4

description:
Library name: Sample 4
F_WT_18h_Rep4


title: imb_keller_2023_19_19_F_WT_18h_Rep3

description:
Library name: Sample 3
F_WT_18h_Rep3


title: imb_keller_2023_19_18_F_WT_18h_Rep2

description:
Library name: Sample 2
F_WT_18h_Rep2


title: imb_keller_2023_19_21_M_WT_18h_Rep1

description:
Library name: Sample 5
M_WT_18h_Rep1


title: imb_keller_2023_19_17_F_WT_18h_Rep1

description:
Library name: Sample 1
F_WT_18h_Rep1


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 180 mins (start of experiment), Rep3

first: Maricris

middle: Lanuzo

last: Zaidem

email: mzaidem@gmail.com, mz82@nyu.edu

state: New York

address: 12 Waverly Pl

department: Center for Genomics and Systems Bi8ology

institute: New York University

description: Library name: AZU_R3_SS_S6

data_processing:
Raw reads were demultiplexed from BCL into FASTQ ﬁles using bcl2fastq (Illumina) with run-appropriate settings and indexing run sheet.
Fastq files were aligned to the reference genomeOryza sativa Japonica Group (IRGSP-1.0) using STAR (Dobin et al., 2013).
Read count extraction and normalization was conducted using kallisto (Bray et al., 2016).
Assembly: GCA_001433935.1
Supplementary files format and content: tab delimited files for each processed sample that includes target_id, length, eff_length, est_counts, tpm

organism: Oryza sativa tropical japonica subgroup

source_name: leaf 3

growth_protocol: Hydroponics experiments were conducted at a controlled glasshouse bay of Lloyd T. Evans Plant Growth Facility at the International Rice Research Institute. Seedlings were grown in styrofoam floats over modified Yoshida culture solution. The non-stressed seedlings were grown at 0mM NaCl all through-out the experiment while the saline stressed seedlings were subjected to 100mM NaCl starting on the first time point of sample collection, 10 days after sowing (DAS) until 10 days after sowing (DAS). Plants were grown for a total of 15 days in a climate-controlled growth chamber with 1 kW high-intensity discharge lamps (12h days; 30°C/20°C day/night, 300-500 μmol quanta m-2 s-1 at the leaf surface).

extract_protocol:
Total RNA was extracted from RNA-later soaked leaf tissue using the Qiagen RNeasy Plant Mini Kit for RNA Extraction (#74904)
RNA libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (# E7530L) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1)

treatment_protocol: 0mM NaCl for the well-watered plants, 10mM NaCl for the salt-stressed plants

value: leaf 3

value: Azucena

value: 10mM NaCl, Yoshida culture solution

tag: time

value: 180 minutes


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 180 mins (start of experiment), Rep2

description: Library name: AZU_R2_SS_S6


title: Azucena 15DAS,  3rd leaf, collected from 10mM NaCl, 5 days (after start of experiment), Rep2

description: Library name: AZU_R2_SS_S8

value: 5 days


title: Azucena 15DAS,  3rd leaf, collected from 10mM NaCl, 5 days (after start of experiment), Rep3

description: Library name: AZU_R3_SS_S8


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 0 mins (start of experiment), Rep3

description: Library name: AZU_R3_SS_S1

value: 0 minutes


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 240 mins (start of experiment), Rep1

description: Library name: AZU_R1_SS_S7

value: 240 minutes


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 60 mins (start of experiment), Rep3

description: Library name: AZU_R3_SS_S4

value: 60 minutes


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 240 mins (start of experiment), Rep3

description: Library name: AZU_R3_SS_S7


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 240 mins (start of experiment), Rep2

description: Library name: AZU_R2_SS_S7


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 180 mins (start of experiment), Rep1

description: Library name: AZU_R1_SS_S6


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 0 mins (start of experiment), Rep1

description: Library name: AZU_R1_SS_S1


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 60 mins (start of experiment), Rep1

description: Library name: AZU_R1_SS_S4


title: Azucena 15DAS,  3rd leaf, collected from 10mM NaCl, 5 days (after start of experiment), Rep 1

description: Library name: AZU_R1_SS_S8


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 0 mins (start of experiment), Rep2

description: Library name: AZU_R2_SS_S1


title: Azucena 10DAS,  3rd leaf, collected from 10mM NaCl, 60 mins (start of experiment), Rep2

description: Library name: AZU_R2_SS_S4


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 180 mins (start of experiment), Rep3

description: Library name: AZU_R3_WW_W6

value: 0mM NaCl, Yoshida culture solution


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 60 mins (start of experiment), Rep3

description: Library name: AZU_R3_WW_W4


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 0 mins (start of experiment), Rep3

description: Library name: AZU_R3_WW_W1


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 240 mins (start of experiment), Rep2

description: Library name: AZU_R2_WW_W7


title: Azucena 15DAS,  3rd leaf, collected from 0mM NaCl, 5 days (after start of experiment), Rep 2

description: Library name: AZU_R2_WW_W8


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 60 mins (start of experiment), Rep2

description: Library name: AZU_R2_WW_W4


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 240 mins (start of experiment), Rep3

description: Library name: AZU_R3_WW_W7


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 0 mins (start of experiment), Rep2

description: Library name: AZU_R2_WW_W1


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 180 mins (start of experiment), Rep1

description: Library name: AZU_R1_WW_W6


title: Azucena 15DAS,  3rd leaf, collected from 0mM NaCl, 5 days (after start of experiment), Rep 1

description: Library name: AZU_R1_WW_W8


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 60 mins (start of experiment), Rep1

description: Library name: AZU_R1_WW_W4


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 0 mins (start of experiment), Rep1

description: Library name: AZU_R1_WW_W1


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 240 mins (start of experiment), Rep1

description: Library name: AZU_R1_WW_W7


title: Azucena 10DAS,  3rd leaf, collected from 0mM NaCl, 180 mins (start of experiment), Rep2

description: Library name: AZU_R2_WW_W6


title: Sinusoidal dura, EAE chronic, replicate 1

city: Freiburg

first: Lukas

last: Amann

address: Breisacher Straße 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

description: harmony_integrated_all_sctransform.Rdata

data_processing:
Transcriptome alignment to the GENCODE M26 genome was performed with CellRanger v.7.1.0 on a Linux workstation using the CellRanger count workflow for transcript quantification.
Filtered counts matrices were loaded with Seurat v.4.5.1. All cells with at least 200 and fewer than 4,000 detected genes but below 20% mitochondrial transcripts were included.
Doublet detection and removal were achieved using a combination of the scDblFinder v.1.18.0 and SingleCellExperiment v.1.26.1 packages.
Assembly: Gencode M26
Supplementary files format and content: Tab-separated filtered counts matrix files (h5 format).
Supplementary files format and content: Seurat objects for naïve data only and for all cells (naïve, onset, peak, chronic).

source_name: Dura mater sinus

growth_protocol: SPF breeding facility

extract_protocol:
After dissection of the cranial bone, the dura mater was first microdissected into extransinusoidal and sinusoidal compartments and then digested for 30 minutes at 37 °C in HBSS supplemented with 1:200 with murine RNAase inhibitor (New England Biolabs, M0314) and 1:2000 Actinomycin D (Sigma-Aldrich, A1410). After digestion, single cells were collected by passing the solution through a 50 µm cell strainer prior to spinning down and collected in FACS Buffer (2% BSA in PBS). CD45+ cells from the dura mater were sorted into 1.5 ml collection tubes containing 25 µl Sort Buffer (FACS Buffer supplemented with 1:200 RNAase inhibitor, New England Biolabs, M0314) using a MoFlo Astrios EQ sorter (Beckman Coulter, Brea, CA, USA).
Up to 20,000 sorted cells per reaction were loaded on a Chromium controller (10x Genomics). Complementary DNA amplification and library preparation were performed according to the user guide for the Chromium Next GEM Single Cell 3′Reagent kits v.3.1 (CG000388 RevC). The libraries were sequenced on a NextSeq 1000/2000 machine (Illumina) with a sequencing depth appropriate to reach 20,000 reads per cell.

treatment_protocol: Female C57BL/6N mice were immunized subcutaneously with 200 µg MOG35-55 peptide emulsified in Freund’s adjuvant containing 0.1 mg of Mycobacterium tuberculosis (H37RA; Difco Laboratories) at an age of 8 weeks. Mice were i.p. injected with 250 ng pertussis toxin (Sigma-Aldrich) at the time of immunization and 48 h later. Some mice were left untreated and served as controls (naïve mice ).

value: Dura mater sinus

value: CD45+ cells

value: EAE chronic


title: Sinusoidal dura, naïve, replicate 2

description:
harmony_integrated_all_sctransform.Rdata
harmony_integrated_naive_sctransform.RData

value: naïve


title: Extrasinusoidal dura, EAE onset, replicate 1

source_name: Dura mater extrasinusoidal

value: Dura mater extrasinusoidal

value: EAE onset


title: Extrasinusoidal dura, EAE chronic, replicate 1


title: Azucena 15DAS,  3rd leaf, collected from 0mM NaCl, 5 days (after start of experiment), Rep 3

description: Library name: AZU_R3_WW_W8


title: Extrasinusoidal dura, EAE peak, replicate 1

value: EAE peak


title: Sinusoidal dura, EAE peak, replicate 1


title: Extrasinusoidal dura, naïve, replicate 2


title: Sinusoidal dura, naïve, replicate 1


title: Sinusoidal dura, EAE onset, replicate 1


title: Extrasinusoidal dura, naïve, replicate 1


title: PBMC, S011327

type: RNA

city: Edinburgh

first: Max

last: Bylesjo

state: Scotland

address: BioCube 1, Edinburgh BioQuarter, 13 Little France Road

country: United Kingdom

institute: Fios Genomics Ltd

hyb_protocol: The samples were hybridized to Clariom S Human Array Plates according to standard Affymetrix GeneTitan protocol

scan_protocol: Array plates were scanned using the Affymetrix GeneTitan Scanner with AGCC and exported as CEL files

data_processing: CEL files were imported into R and the input data was normalized using RMA separately for high- and low-risk patients, resulting in normalized expression levels in log base 2

label: biotin

source_name: PBMC

label_protocol: Samples were labeled with biotin using the GeneChip WT Plus Reagent Kit according to the manufacturer's instructions.

extract_protocol: RNA was extracted from whole blood collected with PAXgene RNA tubes according to the manufacturer's recommendations

tag: pid

value: Before

tag: centre

value: CUB

tag: transplant type

value: Posterior Lamellar

tag: risk group

value: Low

tag: rejection

value: No

tag: gender

value: F

value: PBMC


title: PBMC, S010950

value: M

tag: cell type


title: PBMC, S034500

value: 12 months

value: AUH


title: PBMC, S005404


title: PBMC, S006245


title: PBMC, S005866

value: Yes


title: PBMC, S033857

value: RCSI

value: Full Thickness


title: PBMC, S045251


title: PBMC, S041346


title: PBMC, S003499


title: PBMC, S013474


title: PBMC, S034557


title: PBMC, S011971


title: PBMC, S034145


title: PBMC, S035080


title: PBMC, S041422

value: UBR


title: PBMC, S041437


title: PBMC, S032856


title: PBMC, S012026


title: PBMC, S033674


title: PBMC, S028593


title: PBMC, S033271


title: PBMC, S013429


title: PBMC, S033789


title: PBMC, S033815


title: PBMC, S003133


title: PBMC, S013024


title: PBMC, S040978


title: PBMC, S018762

value: 6 months


title: PBMC, S046092


title: PBMC, S006157


title: PBMC, S007007


title: PBMC, S011024


title: PBMC, S029747


title: PBMC, S011492


title: PBMC, S006760


title: PBMC, S006898


title: PBMC, S043903

value: NANT


title: PBMC, S042413


title: PBMC, S006184


title: PBMC, S034595


title: PBMC, S011574


title: PBMC, S006273


title: PBMC, S043479


title: PBMC, S031922


title: PBMC, S012055


title: PBMC, S034937


title: PBMC, S027672


title: PBMC, S026730


title: PBMC, S028303


title: PBMC, S029516


title: PBMC, S026493


title: PBMC, S034615


title: PBMC, S031550


title: PBMC, S027311


title: PBMC, S035735


title: PBMC, S004064


title: PBMC, S033612


title: PBMC, S003769


title: PBMC, S011515


title: PBMC, S017662


title: PBMC, S032568


title: PBMC, S004635


title: PBMC, S032541


title: PBMC, S026601


title: PBMC, S035681


title: PBMC, S038530


title: PBMC, S004340


title: PBMC, S003228


title: PBMC, S006498


title: PBMC, S031604


title: PBMC, S038121


title: PBMC, S044988


title: PBMC, S034406


title: PBMC, S007883


title: PBMC, S038461


title: PBMC, S033243


title: PBMC, S038982


title: PBMC, S007587


title: PBMC, S003472


title: PBMC, S030406


title: PBMC, S036929


title: PBMC, S029489


title: PBMC, S035799


title: PBMC, S012123


title: PBMC, S026733


title: PBMC, S039342


title: PBMC, S023130


title: PBMC, S004312


title: PBMC, S009337


title: PBMC, S035100


title: PBMC, S005619


title: PBMC, S038821


title: PBMC, S041958


title: PBMC, S034277


title: PBMC, S045420


title: PBMC, S034316


title: PBMC, S032703


title: PBMC, S005432


title: PBMC, S029033


title: PBMC, S026910


title: PBMC, S003394


title: PBMC, S010164


title: PBMC, S008631


title: PBMC, S008159


title: PBMC, S032137


title: PBMC, S032648


title: PBMC, S003003


title: PBMC, S041539


title: PBMC, S008244


title: PBMC, S008743


title: PBMC, S033134


title: PBMC, S037647


title: PBMC, S035774


title: PBMC, S009809


title: PBMC, S032110


title: PBMC, S030992


title: PBMC, S033107


title: PBMC, S007519


title: PBMC, S029837


title: PBMC, S035708


title: PBMC, S010395


title: PBMC, S012087


title: PBMC, S037171


title: PBMC, S008660


title: PBMC, S009129


title: PBMC, S035654


title: PBMC, S040877


title: PBMC, S035903


title: PBMC, S030100


title: PBMC, S011670


title: PBMC, S008300


title: PBMC, S007792


title: PBMC, S035848


title: PBMC, S031841


title: PBMC, S034218


title: PBMC, S010616


title: PBMC, S012818


title: PBMC, S029927


title: PBMC, S032056


title: PBMC, S035823


title: PBMC, S034376


title: PBMC, S004790


title: PBMC, S008047


title: PBMC, S033080


title: PBMC, S002975


title: PBMC, S009090


title: PBMC, S009532


title: PBMC, S028979


title: PBMC, S016664


title: PBMC, S004703


title: PBMC, S021267


title: PBMC, S020010


title: PBMC, S032084


title: PBMC, S037816


title: PBMC, S007451


title: PBMC, S021704


title: PBMC, S009241


title: PBMC, S038207


title: PBMC, S032595


title: PBMC, S026547


title: PBMC, S032030


title: PBMC, S001737


title: PBMC, S001049


title: PBMC, S010012


title: PBMC, S008949


title: PBMC, S009504


title: PBMC, S029809


title: PBMC, S041511


title: PBMC, S001547


title: PBMC, S022598


title: PBMC, S031334


title: PBMC, S041259


title: PBMC, S006400


title: PBMC, S003830


title: PBMC, S009592


title: PBMC, S009297


title: PBMC, S008018


title: PBMC, S026520


title: PBMC, S019605


title: PBMC, S028716


title: PBMC, S027862


title: PBMC, S020439


title: PBMC, S010478


title: PBMC, S026788


title: PBMC, S002562


title: PBMC, S005776


title: PBMC, S006060


title: PBMC, S009892


title: PBMC, S032003


title: PBMC, S028898


title: PBMC, S029895


title: PBMC, S022412


title: PBMC, S030690


title: PBMC, S001708


title: PBMC, S027833


title: PBMC, S014036


title: PBMC, S032986


title: PBMC, S027510


title: PBMC, S005703


title: PBMC, S043250


title: PBMC, S026858


title: PBMC, S029061


title: PBMC, S001975


title: PBMC, S041888


title: PBMC, S038880


title: PBMC, S039040


title: PBMC, S042943


title: PBMC, S033217


title: PBMC, S006612


title: PBMC, S022098


title: PBMC, S042188


title: PBMC, S025547


title: PBMC, S046703


title: PBMC, S029006


title: PBMC, S030926


title: PBMC, S011789


title: PBMC, S030717


title: PBMC, S011547


title: PBMC, S011998


title: PBMC, S030477


title: PBMC, S029429


title: PBMC, S004206


title: PBMC, S025606


title: PBMC, S009647


title: PBMC, S029149


title: PBMC, S008382


title: PBMC, S014291


title: PBMC, S032231


title: PBMC, S039623


title: PBMC, S009686


title: PBMC, S002934


title: PBMC, S035875


title: PBMC, S009449


title: PBMC, S003796


title: PBMC, S011412


title: PBMC, S017191


title: PBMC, S022818


title: PBMC, S030645


title: PBMC, S007711


title: PBMC, S005375


title: PBMC, S023974


title: PBMC, S029868


title: PBMC, S009908


title: PBMC, S019162


title: PBMC, S020918


title: PBMC, S008592


title: PBMC, S027720


title: PBMC, S008549


title: PBMC, S027482


title: PBMC, S026655


title: PBMC, S022481


title: PBMC, S021789


title: PBMC, S023142


title: PBMC, S026412


title: PBMC, S026088


title: PBMC, S028460


title: PBMC, S017893


title: PBMC, S026138


title: PBMC, S023605


title: PBMC, S022067


title: PBMC, S019441


title: PBMC, S024353


title: PBMC, S026574


title: PBMC, S026627


title: PBMC, S024326


title: PBMC, S029638


title: PBMC, S028926


title: PBMC, S026385


title: PBMC, S008539


title: PBMC, S022955


title: PBMC, S025181


title: PBMC, S025681


title: PBMC, S005226

value: High


title: PBMC, S007301

value: Before


title: PBMC, S026466

value: CUB


title: PBMC, S034528

value: Posterior Lamellar


title: PBMC, S013980


title: PBMC, S018843


title: PBMC, S032676


title: PBMC, S039520


title: PBMC, S040080


title: PBMC, S030457


title: PBMC, S040393


title: PBMC, S007126


title: PBMC, S004097


title: PBMC, S033302


title: PBMC, S024995

value: Low


title: PBMC, S027417


title: PBMC, S039676

value: No


title: PBMC, S034765


title: PBMC, S037702

value: F


title: PBMC, S028561

value: PBMC


title: PBMC, S028590


title: PBMC, S018573

value: M


title: PBMC, S037511

value: 12 months


title: PBMC, S029462

value: AUH


title: PBMC, S018790


title: PBMC, S033392


title: PBMC, S033449


title: PBMC, S008784


title: PBMC, S038762


title: PBMC, S024509


title: PBMC, S039079


title: PBMC, S034649


title: PBMC, S031082


title: PBMC, S034678


title: PBMC, S032915


title: PBMC, S034170


title: PBMC, S034051


title: PBMC, S039478


title: PBMC, S030012


title: PBMC, S030039

value: Yes


title: PBMC, S038397

value: RCSI


title: PBMC, S031850

value: Full Thickness


title: PBMC, S039013

value: UBR


title: PBMC, S037617

value: 6 months


title: PBMC, S036830


title: PBMC, S038735


title: PBMC, S031062


title: PBMC, S037146


title: PBMC, S033966


title: PBMC, S025647


title: PBMC, S031242


title: PBMC, S032757


title: PBMC, S034828


title: PBMC, S017099


title: PBMC, S041565

value: NANT


title: PBMC, S035408

value: High


title: PBMC, S032942


title: PBMC, S036644


title: PBMC, S036402


title: PBMC, S032730


title: PBMC, S017288


title: PBMC, S034345


title: PBMC, S029235


title: PBMC, S037119


title: PBMC, S036273


title: PBMC, S030798


title: PBMC, S031600


title: PBMC, S005986

value: Before


title: PBMC, S033584

value: CUB


title: PBMC, S005923

value: Posterior Lamellar


title: PBMC, S006962


title: PBMC, S015767


title: PBMC, S038907


title: PBMC, S004604


title: PBMC, S039316


title: PBMC, S027087


title: PBMC, S037368


title: PBMC, S007949


title: PBMC, S005468


title: PBMC, S038302


title: PBMC, S029986


title: PBMC, S032279


title: PBMC, S037092


title: PBMC, S011052


title: PBMC, S032889


title: PBMC, S015636


title: PBMC, S002421


title: PBMC, S030231


title: PBMC, S001595


title: PBMC, S007233


title: PBMC, S037427


title: PBMC, S037484


title: PBMC, S036970


title: PBMC, S004824


title: PBMC, S037397


title: PBMC, S027278


title: PBMC, S021420


title: PBMC, S010112


title: PBMC, S036771


title: PBMC, S009004


title: PBMC, S031583


title: PBMC, S005049


title: PBMC, S020203


title: PBMC, S031976


title: PBMC, S037339


title: PBMC, S026831


title: PBMC, S033558


title: PBMC, S028742


title: PBMC, S038934


title: PBMC, S019190


title: PBMC, S007194


title: PBMC, S038853


title: PBMC, S031369


title: PBMC, S030203


title: PBMC, S038032


title: PBMC, S037969


title: PBMC, S041287


title: PBMC, S010340

value: Low


title: PBMC, S019927


title: PBMC, S040457

value: No


title: PBMC, S003613


title: PBMC, S019387

value: F


title: PBMC, S015586

value: PBMC


title: PBMC, S039990


title: PBMC, S005511

value: M


title: PBMC, S004007


title: PBMC, S009931


title: PBMC, S031661


title: PBMC, S013313


title: PBMC, S003886


title: PBMC, S009477


title: PBMC, S036054


title: PBMC, S019324


title: PBMC, S011873


title: PBMC, S016155


title: PBMC, S019559


title: PBMC, S012208


title: PBMC, S037038

value: 12 months


title: PBMC, S036798

value: AUH


title: PBMC, S015030


title: PBMC, S013813


title: PBMC, S009850


title: PBMC, S016865


title: PBMC, S006004


title: PBMC, S021452


title: PBMC, S032621


title: PBMC, S003232


title: DNAm from healthy control sample162

type: genomic

city: Atlanta

first: Dawn

middle: Marie

last: Jensen

state: Georgia

address: 55 Park Place

department: TReNDS Center

institute: Georgia State University

description: DNAm from healthy control

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing:
RnBeads package in R environment (v4.1.1)
DT1 and DT2 are the deltaT1 and deltaT2 difference maps from the brain imaging and cognitive data for the analyses.

label: Cy3 and Cy5

source_name: Saliva

label_protocol: Standard Illumina Protocol

extract_protocol: DNAm was extracted from saliva according to standard instructions

tag: ursi

tag: disease state

value: Healthy

value: Saliva


title: PBMC, S015693

value: RCSI


title: PBMC, S010296

value: Full Thickness


title: DNAm from healthy control sample163

description: DNAm from healthy control


title: DNAm from healthy control sample161

description: DNAm from healthy control


title: PBMC, S002233


title: DNAm from healthy control sample160

description: DNAm from healthy control


title: PBMC, S010076


title: PBMC, S014943

value: 6 months

value: Yes


title: PBMC, S004250

value: High


title: DNAm from healthy control sample159

description: DNAm from healthy control


title: DNAm from healthy control sample158

description: DNAm from healthy control


title: PBMC, S016206

value: Before


title: DNAm from healthy control sample157

description: DNAm from healthy control


title: PBMC, S022875


title: DNAm from healthy control sample155

description: DNAm from healthy control


title: PBMC, S019760


title: DNAm from healthy control sample156

description: DNAm from healthy control


title: PBMC, S015128


title: DNAm from healthy control sample154

description: DNAm from healthy control


title: PBMC, S014349


title: PBMC, S038179

value: NANT


title: DNAm from healthy control sample151

description: DNAm from healthy control


title: DNAm from healthy control sample152

description: DNAm from healthy control


title: PBMC, S011134

value: Posterior Lamellar


title: PBMC, S038612


title: PBMC, S030373


title: DNAm from healthy control sample149

description: DNAm from healthy control


title: PBMC, S016092


title: DNAm from healthy control sample148

description: DNAm from healthy control


title: DNAm from healthy control sample146

description: DNAm from healthy control


title: PBMC, S028689

value: CUB


title: PBMC, S002733

value: No


title: PBMC, S010229


title: DNAm from healthy control sample150

description: DNAm from healthy control


title: PBMC, S014257


title: DNAm from healthy control sample147

description: DNAm from healthy control


title: PBMC, S016632

value: F


title: DNAm from healthy control sample153

description: DNAm from healthy control


title: PBMC, S026937

value: PBMC


title: PBMC, S038243

value: UBR

value: M


title: DNAm from healthy control sample144

description: DNAm from healthy control


title: DNAm from healthy control sample143

description: DNAm from healthy control


title: PBMC, S019279

value: AUH


title: DNAm from healthy control sample141

description: DNAm from healthy control

value: Healthy


title: DNAm from healthy control sample142

description: DNAm from healthy control

value: Saliva


title: DNAm from healthy control sample139

description: DNAm from healthy control


title: DNAm from healthy control sample140

description: DNAm from healthy control


title: DNAm from healthy control sample145

description: DNAm from healthy control


title: DNAm from healthy control sample138

description: DNAm from healthy control


title: PBMC, S002629

value: RCSI


title: PBMC, S037843

value: 12 months

value: Full Thickness


title: PBMC, S003803


title: PBMC, S030257


title: DNAm from healthy control sample136

description: DNAm from healthy control


title: PBMC, S036545

value: 6 months


title: DNAm from healthy control sample135

description: DNAm from healthy control


title: PBMC, S013947

value: High


title: PBMC, S006640

value: Before


title: DNAm from healthy control sample137

description: DNAm from healthy control


title: DNAm from healthy control sample133

description: DNAm from healthy control


title: DNAm from healthy control sample131

description: DNAm from healthy control


title: DNAm from healthy control sample132

description: DNAm from healthy control


title: DNAm from healthy control sample130

description: DNAm from healthy control


title: DNAm from healthy control sample129

description: DNAm from healthy control


title: PBMC, S030742


title: PBMC, S014026


title: PBMC, S013669


title: PBMC, S027800


title: PBMC, S020663


title: DNAm from healthy control sample128

description: DNAm from healthy control


title: PBMC, S027890


title: DNAm from healthy control sample127

description: DNAm from healthy control


title: PBMC, S012556


title: DNAm from healthy control sample126

description: DNAm from healthy control


title: DNAm from healthy control sample134

description: DNAm from healthy control


title: PBMC, S012627


title: PBMC, S043755


title: DNAm from healthy control sample124

description: DNAm from healthy control


title: PBMC, S020608


title: DNAm from healthy control sample125

description: DNAm from healthy control


title: PBMC, S047848

value: NANT


title: PBMC, S026964

value: Posterior Lamellar


title: PBMC, S037064

value: CUB

value: Yes


title: PBMC, S016057

value: No


title: DNAm from healthy control sample122

description: DNAm from healthy control


title: DNAm from healthy control sample119

description: DNAm from healthy control


title: DNAm from healthy control sample118

description: DNAm from healthy control


title: DNAm from healthy control sample116

description: DNAm from healthy control


title: PBMC, S036699

value: PBMC


title: PBMC, S033187

value: F


title: PBMC, S006557

value: M


title: DNAm from healthy control sample123

description: DNAm from healthy control


title: DNAm from healthy control sample115

description: DNAm from healthy control


title: DNAm from healthy control sample114

description: DNAm from healthy control


title: DNAm from healthy control sample117

description: DNAm from healthy control


title: DNAm from healthy control sample121

description: DNAm from healthy control


title: PBMC, S043534


title: DNAm from healthy control sample113

description: DNAm from healthy control


title: DNAm from healthy control sample112

description: DNAm from healthy control


title: PBMC, S025236

value: AUH


title: DNAm from healthy control sample120

description: DNAm from healthy control

value: Healthy


title: PBMC, S043560


title: PBMC, S039547


title: PBMC, S025384


title: PBMC, S038002

value: UBR


title: DNAm from healthy control sample111

description: DNAm from healthy control

value: Saliva


title: PBMC, S028596

value: 12 months

value: RCSI


title: PBMC, S027639


title: PBMC, S008272


title: PBMC, S043124

value: Full Thickness


title: DNAm from healthy control sample110

description: DNAm from healthy control


title: DNAm from healthy control sample109

description: DNAm from healthy control


title: PBMC, S027950

value: High


title: DNAm from healthy control sample108

description: DNAm from healthy control


title: DNAm from healthy control sample107

description: DNAm from healthy control


title: DNAm from healthy control sample106

description: DNAm from healthy control


title: DNAm from healthy control sample105

description: DNAm from healthy control


title: DNAm from healthy control sample104

description: DNAm from healthy control


title: DNAm from healthy control sample103

description: DNAm from healthy control


title: PBMC, S027091


title: DNAm from healthy control sample101

description: DNAm from healthy control


title: DNAm from healthy control sample102

description: DNAm from healthy control


title: PBMC, S021086

value: Before


title: PBMC, S028067

value: 6 months


title: PBMC, S033723

value: Posterior Lamellar


title: DNAm from healthy control sample100

description: DNAm from healthy control


title: DNAm from healthy control sample98

description: DNAm from healthy control


title: DNAm from healthy control sample99

description: DNAm from healthy control


title: PBMC, S028953

value: CUB


title: PBMC, S033341

value: NANT


title: DNAm from healthy control sample97

description: DNAm from healthy control


title: PBMC, S043688

value: Yes


title: DNAm from healthy control sample96

description: DNAm from healthy control


title: PBMC, S005078

value: No

value: PBMC


title: PBMC, S005546

value: M


title: DNAm from healthy control sample95

description: DNAm from healthy control


title: PBMC, S028433


title: PBMC, S027573

value: AUH

value: F


title: DNAm from healthy control sample94

description: DNAm from healthy control

value: Healthy


title: PBMC, S026979


title: PBMC, S019894


title: PBMC, S031414


title: DNAm from healthy control sample93

description: DNAm from healthy control

value: Saliva


title: PBMC, S026974


title: PBMC, S007851


title: PBMC, S022325


title: PBMC, S031133


title: PBMC, S003913


title: PBMC, S025425


title: PBMC, S017597


title: DNAm from healthy control sample88

description: DNAm from healthy control


title: DNAm from healthy control sample90

description: DNAm from healthy control


title: DNAm from healthy control sample92

description: DNAm from healthy control


title: DNAm from healthy control sample89

description: DNAm from healthy control


title: DNAm from healthy control sample87

description: DNAm from healthy control


title: DNAm from healthy control sample91

description: DNAm from healthy control


title: DNAm from healthy control sample86

description: DNAm from healthy control


title: PBMC, S021629


title: DNAm from healthy control sample85

description: DNAm from healthy control


title: PBMC, S005255


title: DNAm from healthy control sample84

description: DNAm from healthy control


title: DNAm from healthy control sample83

description: DNAm from healthy control


title: PBMC, S008953


title: DNAm from healthy control sample81

description: DNAm from healthy control


title: DNAm from healthy control sample82

description: DNAm from healthy control


title: PBMC, S040820

value: 12 months

value: UBR


title: PBMC, S032314


title: PBMC, S028847

value: RCSI


title: PBMC, S008410

value: High


title: PBMC, S039595

value: Full Thickness


title: PBMC, S030433

value: 6 months


title: PBMC, S039730

value: Posterior Lamellar


title: PBMC, S039649

value: CUB


title: DNAm from healthy control sample80

description: DNAm from healthy control


title: PBMC, S024186


title: DNAm from healthy control sample79

description: DNAm from healthy control


title: PBMC, S021113


title: DNAm from healthy control sample76

description: DNAm from healthy control


title: DNAm from healthy control sample77

description: DNAm from healthy control


title: DNAm from healthy control sample75

description: DNAm from healthy control


title: PBMC, S020639

value: Before


title: PBMC, S024286


title: DNAm from healthy control sample73

description: DNAm from healthy control


title: PBMC, S007856


title: PBMC, S023994


title: DNAm from healthy control sample72

description: DNAm from healthy control


title: PBMC, S014884


title: PBMC, S026262


title: DNAm from healthy control sample71

description: DNAm from healthy control


title: DNAm from healthy control sample69

description: DNAm from healthy control


title: DNAm from healthy control sample70

description: DNAm from healthy control


title: DNAm from healthy control sample68

description: DNAm from healthy control


title: DNAm from healthy control sample74

description: DNAm from healthy control


title: DNAm from healthy control sample66

description: DNAm from healthy control


title: DNAm from healthy control sample65

description: DNAm from healthy control


title: DNAm from healthy control sample64

description: DNAm from healthy control


title: PBMC, S027757

value: NANT


title: DNAm from healthy control sample63

description: DNAm from healthy control


title: PBMC, S018634

value: No


title: PBMC, S007732

value: PBMC


title: PBMC, S018679

value: M


title: DNAm from healthy control sample67

description: DNAm from healthy control


title: DNAm from healthy control sample62

description: DNAm from healthy control


title: PBMC, S023695


title: PBMC, S022982


title: DNAm from healthy control sample78

description: DNAm from healthy control


title: PBMC, S021546


title: DNAm from healthy control sample60

description: DNAm from healthy control


title: PBMC, S015220


title: PBMC, S022409

value: AUH


title: PBMC, S024968

value: F


title: DNAm from healthy control sample59

description: DNAm from healthy control

value: Healthy


title: PBMC, S015253


title: DNAm from healthy control sample58

description: DNAm from healthy control

value: Saliva


title: PBMC, S014654

value: Yes


title: DNAm from healthy control sample57

description: DNAm from healthy control


title: DNAm from healthy control sample61

description: DNAm from healthy control


title: DNAm from healthy control sample55

description: DNAm from healthy control


title: PBMC, S023849


title: DNAm from healthy control sample54

description: DNAm from healthy control


title: PBMC, S023887


title: DNAm from healthy control sample53

description: DNAm from healthy control


title: PBMC, S025453


title: DNAm from healthy control sample51

description: DNAm from healthy control


title: DNAm from healthy control sample52

description: DNAm from healthy control


title: DNAm from healthy control sample49

description: DNAm from healthy control


title: DNAm from healthy control sample56

description: DNAm from healthy control


title: DNAm from healthy control sample48

description: DNAm from healthy control


title: DNAm from healthy control sample47

description: DNAm from healthy control


title: DNAm from healthy control sample46

description: DNAm from healthy control


title: PBMC, S022902


title: PBMC, S022439

value: UBR


title: PBMC, S023389


title: PBMC, S018184


title: DNAm from healthy control sample45

description: DNAm from healthy control


title: PBMC, S016248


title: DNAm from healthy control sample44

description: DNAm from healthy control


title: PBMC, S023628


title: PBMC, S027536


title: PBMC, S024800

value: 12 months

value: RCSI


title: DNAm from healthy control sample43

description: DNAm from healthy control


title: PBMC, S014581

value: Full Thickness

value: High


title: DNAm from healthy control sample42

description: DNAm from healthy control


title: DNAm from healthy control sample41

description: DNAm from healthy control


title: PBMC, S024938


title: PBMC, S009537

value: Posterior Lamellar


title: DNAm from healthy control sample40

description: DNAm from healthy control


title: PBMC, S021921

value: 6 months

value: CUB


title: PBMC, S014911


title: DNAm from healthy control sample38

description: DNAm from healthy control


title: PBMC, S027455


title: PBMC, S029668


title: DNAm from healthy control sample36

description: DNAm from healthy control


title: DNAm from healthy control sample37

description: DNAm from healthy control


title: DNAm from healthy control sample35

description: DNAm from healthy control


title: PBMC, S020413


title: DNAm from healthy control sample34

description: DNAm from healthy control


title: PBMC, S031888

value: NANT


title: DNAm from healthy control sample33

description: DNAm from healthy control


title: DNAm from healthy control sample32

description: DNAm from healthy control


title: PBMC, S026321

value: No


title: DNAm from healthy control sample39

description: DNAm from healthy control


title: PBMC, S023202

value: Before

value: PBMC


title: PBMC, S028379

value: M


title: DNAm from healthy control sample31

description: DNAm from healthy control


title: DNAm from healthy control sample30

description: DNAm from healthy control


title: PBMC, S014771


title: PBMC, S025708

value: F


title: PBMC, S022378

value: AUH


title: PBMC, S025736


title: PBMC, S017515


title: PBMC, S023307


title: DNAm from healthy control sample28

description: DNAm from healthy control

value: Healthy

value: Saliva


title: DNAm from healthy control sample29

description: DNAm from healthy control


title: PBMC, S023765


title: DNAm from healthy control sample26

description: DNAm from healthy control


title: DNAm from healthy control sample50

description: DNAm from healthy control


title: DNAm from healthy control sample27

description: DNAm from healthy control


title: PBMC, S027980

value: Yes


title: PBMC, S032436


title: DNAm from healthy control sample25

description: DNAm from healthy control


title: DNAm from healthy control sample24

description: DNAm from healthy control


title: PBMC, S026294

value: 12 months


title: PBMC, S016028


title: PBMC, S012198


title: DNAm from healthy control sample23

description: DNAm from healthy control


title: DNAm from healthy control sample21

description: DNAm from healthy control


title: PBMC, S021362


title: PBMC, S019470


title: DNAm from healthy control sample22

description: DNAm from healthy control


title: Huh7.5.1 Cas9-P2A-blasticidin cells, ZEBOV minigenome replicon cells, d19, low-GFP sorted, replicate 2

city: San Francisco

first: Amy

middle: L

last: Kistler

address: 499 Illinois St, 4th floor

institute: Chan Zuckerberg Biohub

description: Library name: Sample 11

data_processing:
Demultiplexed FASTQ files were analyzed using the 'count' subcommand of MAGeCK software (v0.5.9.4; Li et al., 2014) to quantify sgRNA abundance by matching reads to the sgRNA library sequences, with the normalization method set to 'total'. The sgRNA count tables were subsequently analyzed using the ‘test’ subcommand (RRA) of MAGeCK software (v0.5.9.4; Li et al., 2014) to calculate positive enrichment scores for each gene. The two-step process was automated using Nextflow (v21.10.6). The analysis workflow standardizes metadata conventions. (Available at https://github.com/czbiohub-sf/CRISPRflow/blob/main/modules.nf)
Assembly: Brunello sgRNA library (Available at https://media.addgene.org/cms/filer_public/8b/4c/8b4c89d9-eac1-44b2-bb2f-8fea95672705/broadgpp-brunello-library-contents.txt)
Supplementary files format and content: Tab-delimited text file provides statistics for gene enrichment in GFP-low population compared to unsorted or high population, calculated from replicate 1 and replicate 2 data combined.
Supplementary files format and content: Tab-delimited text file provides statistics for sgRNA enrichment in GFP-low population compared to unsorted or high population, calculated from replicate 1 and replicate 2 data combined.
Library strategy: CRISPR Screen

source_name: cell line

growth_protocol: Huh7.5.1 cell lines stably transduced with spCas9-P2A-blasticidinR genes and a ZEBOV minigenome replicon system was maintained in DMEM media supplemented with 10% FBS and 200ug/mL zeocin antibiotic at 37C in a humidified atmosphere with 5% CO2. Cells were transitioned to antibiotic free media 24h prior to transduction with pooled lentiviral library of Brunello sgRNAs, and transitioned to media supplemented with 4ug/mL puromycin for 2-4 days post transduction, then cultured without antibiotics throughout the course of the screen.

extract_protocol:
Genomic DNA was extracted from the cell pellets of the sorted cells using the Zymo Quick-DNA Miniprep Plus kit and from cell pellets of the unsorted cells using the Qiagen Blood Maxi Kit. The genomic DNA preps were further purified from contaminants using the Zymo OneStep PCR Inhibitor Removal Kit.
Sequencing libraries were prepared from extracted genomic DNA by PCR amplification using barcoded Illumina P7 and P5 primers of the sgRNA cassettes. The entire prep of extracted gDNA was barcoded and amplified (1 µg gDNA/ 50 µl PCR reaction) for each screen condition.

treatment_protocol: pooled genome-wide sgRNA library-mediated gene depletions. Cells were harvested directly after puromycin selection, or incubated further, and subjected to FACS to harvest cells in the bottom 20% (GFP-low) or top 10% (GFP-high) range of population fluorescence on day 20 post-transduction.

value: cell line

tag: cell line

value: human hepatoma cells

tag: genotype

tag: treatment

value: Brunello lentiviral sgRNA KO library pool transduction


title: Huh7.5.1 Cas9-P2A-blasticidin cells, ZEBOV minigenome replicon cells, d0, unsorted, replicate 2

description: Library name: Sample 12

tag: tissue


title: DNAm from healthy control sample20

description: DNAm from healthy control


title: DNAm from healthy control sample18

description: DNAm from healthy control


title: Huh7.5.1 Cas9-P2A-hygromycin cells, CHIKV replicon cells, d19, unsorted endpoint, replicate 1

description: Library name: Sample 6


title: DNAm from healthy control sample16

description: DNAm from healthy control


title: PBMC, S028352

value: Posterior Lamellar

value: High


title: PBMC, S028013

value: CUB


title: DNAm from healthy control sample17

description: DNAm from healthy control


title: Huh7.5.1 Cas9-P2A-hygromycin cells, CHIKV replicon cells, d19, low-GFP sorted, replicate 2

description: Library name: Sample 7


title: DNAm from healthy control sample15

description: DNAm from healthy control


title: UntaggedU2OS_CUTnRUNseq_HA_SCAF1_Control

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

data_processing:
Fastq files were mapped to the human genome (hg38) using Bowtie v2.3.5.1 and spike-normalized based on the read counts of E.coli. mapped reads (K-12 substr. MG1655).
Assembly: hg38
Supplementary files format and content: .bedgraph, Bedgraphs were made with Bedtools genomeCoverageBed (v2.27.1), applying the calculated spike-normalization factors, and the '-bga' and '-pc' options.
Library strategy: CUT&Run

growth_protocol: U2OS SCAF1-AID and U2OS-untagged cells were grown in DMEM suplemented with 10 % FCS and 1% Penicillin/Streptomycin.

extract_protocol:
Cells were detached, and washed in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine). After washing, cells were coupled to ConA-coated magnetic beads (Polysciences Europe) and subsequently permeabilized and followed by addition of primary antibody in antibody binding buffer (wash buffer, 0.05% digitonin, 2 mM EDTA) over night at 4 °C. Cells were wased in Dig-Wash buffer (Wash buffer, 0.05% digitonin) and MNase (700ng/ml) was added to each sample for 1 hr at 4 °C. After washing with Dig-wash buffer and Low-salt Rinse buffer (20 mM HEPES pH 7.5, 0.5 mM Spermidine, 0.05% digitonin) incubation buffer (3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.05% digitoin) was added for 30 min at 4°C. STOP buffer (170 mM NaCL, 20 mM EGTA, 0.05% digitonin, 20 ug/ml RNAse A, 25 ug/ml Glycogen was added to stop the MNase digestion. DNA fragments were released at 37 °C for 30 min and proteins digested for 1 h at 50 °C after adding 0.01 % SDS and 10 mg/ml Proteinase K followed by Phenol Chloroform extraction. Precipitated DNA was resuspended in 30 ul 0.1x TE buffer
Libraries were prepared with NEBnext Ultra II DNA Library Prep Kit (New England Biolabs). Libraries were PCR amplified for 16-18 cycles. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform. Base calling was performed using Illumina’s BaseSpace platform.

treatment_protocol: Cells were treated with or without 1 µM auxin for 6 hours prior to harvest.

value: Osteosarcoma

value: Untagged

value: Control


title: SCAF1AID_CUTnRUNseq_HA_SCAF1_Control_Rep3


title: DNAm from healthy control sample13

description: DNAm from healthy control


title: PBMC, S022510

value: Before

value: NANT

value: No

value: PBMC


title: DNAm from healthy control sample14

description: DNAm from healthy control

value: Healthy


title: SCAF1AID_CUTnRUNseq_HA_SCAF1_Auxin_Rep2

value: Auxin


title: DNAm from healthy control sample12

description: DNAm from healthy control

value: Saliva


title: DNAm from healthy control sample11

description: DNAm from healthy control


title: SCAF1AID_CUTnRUNseq_HA_SCAF1_Auxin_Rep1


title: SCAF1AID_CUTnRUNseq_HA_SCAF1_Auxin_Rep3


title: SCAF1AID_ChIPseq_Input_Auxin

description:
SCAF1AID_ChIPseq_Input_pS2_RNAPII.bedgraph
SCAF1AID_ChIPseq_Input_TotalRNAPII.bedgraph

data_processing:
Fastq files were mapped to the human genome (hg38) using Bowtie v2.3.5.1 and BAM files were spike-normalized based on the read counts of corresponding mouse mapped reads (mm10).
Assembly: hg38
Supplementary files format and content: Bedgraphs were made with Bedtools genomeCoverageBed (v2.27.1) using spike-normalized bam files with '-bga' and '-pc' options.

growth_protocol: U2OS SCAF1-AID cells were grown in DMEM suplemented with 10 % FCS and 1% Penicillin/Streptomycin.

extract_protocol:
Cells were treated with 1% formaldehyde for 5 min. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using Covaris. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and eluted. Libraries were amplified for 11 cycles (pS2) or 15 cycles(Total-RNAPII). The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform. Base calling was performed using Illumina’s BaseSpace platform.

treatment_protocol: Cells were treated with or without 1 µM auxin for 6 hours prior to harvest


title: DNAm from healthy control sample9

description: DNAm from healthy control


title: Huh7.5.1 Cas9-P2A-hygromycin cells, CHIKV replicon cells, d19, unsorted endpoint, replicate 2

description: Library name: Sample 8


title: DNAm from healthy control sample10

description: DNAm from healthy control


title: DNAm from healthy control sample19

description: DNAm from healthy control


title: SCAF1AID_CUTnRUNseq_HA_SCAF1_Control_Rep1


title: Huh7.5.1 Cas9-P2A-hygromycin cells, CHIKV replicon cells, d19, low-GFP sorted, replicate 1

description: Library name: Sample 5


title: SCAF1AID_ChIPseq_Input_Control


title: DNAm from healthy control sample8

description: DNAm from healthy control


title: SCAF1AID_ChIPseq_Total_RNAPII_Auxin


title: DNAm from healthy control sample6

description: DNAm from healthy control


title: SCAF1AID_ChIPseq_Total_RNAPII_Control


title: DNAm from healthy control sample5

description: DNAm from healthy control


title: DNAm from healthy control sample3

description: DNAm from healthy control


title: DNAm from healthy control sample4

description: DNAm from healthy control


title: SCAF1AID_ChIPseq_pS2_RNAPII_Auxin


title: DNAm from healthy control sample7

description: DNAm from healthy control


title: SCAF1AID_ChIPseq_pS2_RNAPII_Control


title: SCAF1AID_4sUSeq_Control_Rep3

library_source: other

data_processing:
After adapter trimming, and removing reads mapping to rRNA, the remaining reads were aligned to a combined human+mouse genome (Ensembl v90) using STAR (version 2.5.3a) with the parameters “–outFilterMismatchNmax 20 –outFilterScoreMinOverLread 0.4 –outFilterMatchNminOverLread 0.4 –alignEndsType Extend5pOfReads12 –outSAMattributes nM MD NH'. The reads mapped to the mouse genome were counted for each library for normalization and then discarded. Human mapped read pairs, mapping inside of a gene body on the plus or minus strand were determined using the Ensembl (v90) annotation, and reads having T>C mismatches in the forward read or A>G mismatches in the reverse read were then saved. Spike normalization factors were calculated using mouse mapped reads.
Assembly: hg38
Supplementary files format and content: Bedgraphs were made with Bedtools genomeCoverageBed (v2.27.1) using the T>C coverted reads containing bam files, and applying the calculated spike factor and '-bga', '-split' options.
Library strategy: 4sU-seq

molecule: other

extract_protocol:
Cells were lysed using QIAzol and lysates were spiked with 4sU-treated mouse T-cell lysates. Total RNA was purified with the miRNeasy mini kit, precipitated to reduce volume, and then subject to fragmentation. Fragmented RNA was biotinylated. This was followed by 4sU-RNA pulldown using MyOne streptavidin beads, followed by purification with the RNeasy MinElute cleanup kit. The 4sU-RNA was subject to alkylation using iodoacetamide, and then alkylated-4sU-RNA was sequenced.
4sU-RNA was used for library preparation with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep kit. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform. Base calling was performed using Illumina’s BaseSpace platform.

treatment_protocol: Cells were treated with 1 µM auxin for 6 hours prior to harvest, and nascent-RNA was metabolically-labelled with 4-thio-uracil (4sU) 15 min prior to harvest.


title: SCAF1AID_CUTnRUNseq_HA_SCAF1_Control_Rep2


title: SCAF1AID_4sUSeq_Auxin_Rep3


title: DNAm from healthy control sample1

description: DNAm from healthy control