title: VACO432 cells, 24h BOLD-100 treatment n1


title: ME (APS); Ctrl ; Lib4

status: Public on Jan 10 2024

type: SRA

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to hg38 and dm6 combined genome using STAR aligner. Only uniquely and concordantly aligned read pairs were used for downstream analysis. Read count mapped to each gene was measured using featureCounts with options ‘-O --fracOverlap 0.8’. For spike-in controlled analysis, reads mapped to drosophila genes were also counted using the same method.
Assembly: hg38 & dm6
Supplementary files format and content: Excel file containing read counts per genes. Columns names matche with sample titles. Drosophila genes are prefixed by "dm-"

molecule: polyA RNA

organism: Homo sapiens

source_name: Human induced pluripotent stem cells (72.3, male, RRID: CVCL_A1BW)

extract_protocol:
1 million cultured cells were dissociated to single cells with Accutase and were mixed with 100,000 of Drosophila Schneider 2 (S2) cells for a spike-in control. Cells were pelleted and lysed with Aurum Total RNA Lysis Solution (BioRad # 7326802). Total RNA was extracted by Aurum™ Total RNA Mini Kit (BioRad #7326820) and sent to Novogene for library preparation and paired-end-150bp sequencing on an Illumina NovaSeq 6000.
Novogene performed the library construction

tag: cell line

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)

tag: cell type

value: Mesendoderm

tag: treatment

value: Ctrl


title: LTBI_21810_2mo-Plasma IgA

type: protein

city: Bronx

first: Jacqueline

middle: M.

last: Achkar

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: IgA

hyb_protocol: Slides with 16 arrays on each were blocked SuperBlock (Thermo Fisher Scientific), then incubated with BALF (1:35) or plasma (1:100) diluted in phosphate buffered saline with 5% skim milk and 0.2% tween 20 (PBST) for 16 hrs at 4°C. After washing with 5% skim milk and 0.2% tween 20 (PBST) (3 x 5 min), slides were incubated with Cy3 Goat Anti-Human Serum IgA (Jackson ImmunoResearch Labs Cat# 109-165-011, RRID:AB_2337721) and Alexa 647 Goat Anti-Human IgG (Jackson ImmunoResearch Labs Cat# 109-605-008, RRID:AB_2337882; diluted at 1:200 in 5% skim milk and 0.2% tween 20 (PBST)) for 2 hrs at 4°C

scan_protocol: Slides were scanned at 635 nm and 535 nm with a Tecan PowerScanner, and images were quantified with the ArrayPro Analyzer Software (Media Cybernetics, Inc.).

data_processing: Spots were considered reactive if the ratio of the median fluorescent intensity (MFI) of the gene was greater than 1.4 x the median of negative control genes

label: Cy3 Goat Anti-Human Serum IgA

molecule: protein

organism: Macaca fascicularis

label_protocol: Cy3 Goat Anti-Human Serum IgA (Jackson ImmunoResearch Labs Cat# 109-165-011, RRID:AB 2337721)

extract_protocol: Plasma was obtained from peripheral blood samples and the BAL procedure was performed as previously described via direct visualization of the airway and lavage of ~ 40 ml normal saline (0.9%). Animal protocols and procedures were approved by the University of Pittsburgh’s Institutional Animal Care and Use Committee before the collection of samples.

tag: infection states

value: Asymptomatic controlled Mtb infection


title: LTBI_21810_Pre-BALF IgA

description: IgA

source_name: Pre-BALF


title: VACO432 cells, 3h BOLD-100 treatment n3

city: Belfast

first: Daryl

last: Griffin

address: 97 Lisburn Road

country: United Kingdom

institute: Queens University, Belfast

data_processing:
Paired 91 end sequencing was conducted with a sequencing depth of 50 million reads, resulting in 75-base pair reads.
Assembly: reads were trimmed based on Phred score from the 3-prime end and then aligned to the human genome (hg38) using TopHat21  (version 2.1.0) with default settings.
Supplementary files format and content: Merged_raw_counts.txt

molecule: total RNA

source_name: Colon adenocarcinoma

growth_protocol: Standard culture conditions

extract_protocol:
total RNA was extracted using RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol
library preparation was performed with 100ng RNA (Illumina NextSeq 500 kit, Illumina, UK)  according to the manufacturer's instructions. using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, USA).

treatment_protocol: Control - No treatment, 3H - Treatment with 24µM BOLD-100 for 3 hours, 24H - Treatment with 24µM BOLD-100 for 24 hours.

tag: tissue

value: Colon adenocarcinoma

tag: genotype

value: 24µM BOLD-100 3hours


title: LTBI_21710_Pre-Plasma IgA

description: IgA

source_name: Pre-Plasma


title: KO_pos_40

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

description:
sample ID:
Run20.120

data_processing:
Library strategy: 16S rRNA-seq
Demultiplexing for the uploaded fastq files was performed in fastq-multx
Analyses of 16S sequencing data was performed using QIIME (version 1.9.1) on the original NOT demultiplexed fastq files.
Libraries were split using split_libraries_fastq.py script (result is in processed data file seqs.fna)
Samples were rarefied to 20000 reads using multiple_rarefactions.py  script
Assembly: Silva 123 SSURef Nr99
Supplementary files format and content: counts

organism: mouse gut metagenome

source_name: fecal material [ENVO_00002003]

growth_protocol: Frozen bacterial samples were resuspended in 400 µL staining buffer before adding 250 µL 0.1 mm zirconia/silica beads (Biospec), 300 µL Lysis buffer (200 mM NaCl, 200 mM Tris, 20 mM EDTA, pH 8), 200 µL 20% SDS and 500 µL phenol:chloroform:isoamyl alcohol (25:24:1,pH 7.9; Sigma). After incubation on ice for 4 minutes, bacterial cells were homogenized by 2 rounds of bead beating with 2 minutes of incubation on ice in between before centrifugation at 6000 g at 4oC. Aqueous phase was transferred to a Phase Lock Gel tube (Light; 5 PRIME) before an equal volume of phenol:chloroform:isoamyl alcohol was added.

extract_protocol:
Samples were mixed before centrifugation at 16,100 g for 3 minutes at room temperature. DNA precipitation was performed using 1/10 volume of 3 M NaOAc (pH5.5) and 1 volume Isopropanol to the aqueous phase before overnight incubation at 20o C. DNA precipitate was pelleted at 16,100g for 20 minutes at 4oC before washing in 500 µL of absolute EtOH, centrifugation was performed 16,100 g for 3 minutes at 4oC before DNA pellet was for 15 minutes with no heat (miVac GeneVac on Auto Run setting). Lastly, DNA pellet was resuspended in 100 µL of TE buffer (pH 7) and incubated at 50oC for 30 min. 35 U/ml RNase A was added to the DNA pellet before purification and elution in 40 µL Elution Buffer (QIAquick PCRpurification; QIAGEN).
16S rRNA sequencing of the V4 region and bacterial genome sequencing were performed on an Illumina miSeq using barcoded primers.

value: feces

tag: geographic location

value: USA:Farmington, Connecticut

tag: host

value: Mus musculus

tag: host genotype

value: DOCK8 homozygous

tag: iga status

value: positive

tag: molecule subtype


title: LTBI_21810_2mo-BALF IgA

description: IgA


title: ME (APS); Ctrl ; Lib6


title: WT_pre_21

description:
sample ID:
Run20.61

value: Wild type

value: pre-sorted


title: LTBI_21710_Pre-BALF IgA

description: IgA


title: VACO432 cells, 3h BOLD-100 treatment n2


title: KO_pre_40

description:
sample ID:
Run20.118


title: LBP; FOXAKD ; Lib27

value: Liver bud progenitor

value: FOXAKD


title: LBP; FOXAKD ; Lib25


title: LTBI_21610_Pre-Plasma IgA

description: IgA


title: LTBI_21710_2mo-Plasma IgA

description: IgA


title: LTBI_21610_Pre-BALF IgA

description: IgA


title: LTBI_21710_2mo-BALF IgA

description: IgA


title: KO_pos_39

description:
sample ID:
Run20.117


title: VACO432 cells, Control n3

value: Control


title: KO_neg_40

description:
sample ID:
Run20.119

value: negative


title: LBP; FOXAKD ; Lib23

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)


title: ME (APS); Ctrl ; Lib8

value: Mesendoderm


title: KO_neg_39

description:
sample ID:
Run20.116


title: VACO432 cells, Control n2


title: LTBI_21610_2mo-BALF IgA

description: IgA


title: KO_pre_39

description:
sample ID:
Run20.115


title: KO_pos_38

description:
sample ID:
Run20.114


title: LTBI_21510_Pre-Plasma IgA

description: IgA


title: KO_neg_38

description:
sample ID:
Run20.113


title: LBP; Ctrl ; Lib26

value: Ctrl


title: VACO432 cells, 3h BOLD-100 treatment n1


title: LBP; Ctrl ; Lib22


title: LBP; Ctrl ; Lib24


title: FG_FOXACRISPRi_Low_MNase_CloneH5

library_source: genomic

data_processing:
MNase-seq sequencing reads were aligned to the USCS mouse genome, hg38, using STAR aligner like RNA-seq with options "--alignSJDBoverhangMin 999 --alignIntronMax 1 --alignMatesGapMax 2000 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05 --outReadsUnmapped None --alignEndsProtrude 2 ConcordantPair". Only uniquely and concordantly aligned read pairs were used for analysis. Aligned read 1 and 2 were connected with each other to form a fragment. Putative nucleosomal fragments with size > 150bp were selected to create stack-height profile bigwig file in read-per-million scale, where fragment were resized into 100bp centering around the fragment center.
Replicates were pooled to create a representative bigwig file per group.
Assembly: hg38
Supplementary files format and content: RPM-normalized BigWig. One representative bigwig file were created per group by pooling biological replicates.

molecule: genomic DNA

extract_protocol:
Dissociated foregut cells were washed with Wash Buffer (20 mM HEPES-NaOH [pH. 7.5], 150 mM NaCl, 0.5 M Spermidine and 1x Complete Protease Inhibitor EDTA free), centrifuged at 600 xg for 3 min, and the supernatant was removed (twice). The cell pellet was resuspended with Digitonin Buffer (0.02% Digitonin in wash buffer). Cell suspension was divided into 1.0x106 cells per reaction, added 13 U/mL (low) or 160 U/mL MNase (LS004798, Worthington), and incubated for exactly 5 min at 37°C while shaking at 300 rpm in ThermoMixer F1.5 (Eppendorf). MNase reaction was quenched by adding equal volumes of 2x Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin, 0.05 mg/ml RNaseA, and 0.05 mg/ml Glycogen). For RNase reaction, samples were incubated at 37°C for 30 min. Then, samples were treated with 0.5% SDS and 0.2 mg/mL Proteinase K for 2 hours at 37°C. Finally, DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA concentration was measured by nanodrop (ThermoFisher Scientific). Mono- and sub-nucleosomal DNA fragments were selected and purified by MagBind Magnetic Beads (M1378-01, Omega). The purified DNA concentration was measured by Quantus fluorometer (Promega).
MNase-seq libraries were prepared by using NEBNext Ultra II DNA Library Prep Kit for Illumina with dual index primer system. 10 ng of mono-nucleosomal DNA fragments were used as starting material.  Libraries were amplified by using 5 cycles on thrmocycler. Amplified libraries were size selected at 200-600 bp by using MagBind beads from Omega. Libraries were validated by using Agilent High Sensitivity DNA Kit.

value: Foregut

value: FOXA KD


title: LTBI_21510_Pre-BALF IgA

description: IgA

value: Asymptomatic controlled Mtb infection


title: VACO432 cells, Control n1

value: Colon adenocarcinoma


title: LTBI_21610_2mo-Plasma IgA

description: IgA


title: FG_FOXACRISPRi_Low_MNase_CloneA6


title: LTBI_21510_2mo-BALF IgA

description: IgA


title: LTBI_21510_2mo-Plasma IgA

description: IgA


title: hPSC; Ctrl ; Lib3

value: Pluripotent stem cells


title: KO_pre_38

description:
sample ID:
Run20.112

value: feces

value: USA:Farmington, Connecticut

value: Mus musculus


title: FG_FOXACRISPRi_High_MNase_CloneH5


title: hPSC; Ctrl ; Lib2


title: KO_pos_37

description:
sample ID:
Run20.111

value: DOCK8 homozygous

value: positive


title: hPSC; Ctrl ; Lib1


title: FG_FOXACRISPRi_High_MNase_CloneA6


title: KO_neg_37

description:
sample ID:
Run20.110


title: FG; FOXAKD ; Lib21


title: KO_pre_37

description:
sample ID:
Run20.109

value: pre-sorted


title: FG_Ctrl_Low_MNase_CloneH5


title: FG_Ctrl_Low_MNase_CloneA6


title: FG; FOXAKD ; Lib19

value: FOXAKD


title: KO_pos_36

description:
sample ID:
Run20.108


title: FG_Ctrl_High_MNase_CloneH5

value: Control


title: FG; FOXAKD ; Lib17


title: FG_Ctrl_High_MNase_CloneA6


title: KO_neg_36

description:
sample ID:
Run20.107

value: negative


title: LTBI_21408_2mo-BALF IgA

description: IgA


title: LTBI_21408_2mo-Plasma IgA

description: IgA


title: LTBI_21408_Pre-BALF IgA

description: IgA


title: LTBI_20808_Pre-BALF IgA

description: IgA


title: LTBI_20808_Pre-Plasma IgA

description: IgA


title: 90-T3

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description:
cpm.csv
logCPM.csv

data_processing:
Quality and concentration were validated with TapeStation D1000 (Agilent Technologies).
Samples were pooled in equimolar proportions, amplified by qPCR with specific primers and sequenced in a NextSeq High output 2x75 cycles run (Illumina).
Reads were mapped with STAR software (version 2.7.9a) against the human reference genome GRCh38 using the GRCh38-89 Ensembl annotation.
Counts were normalized with log2 counts per million (CPM) with the edgeR package (version 3.14.0) with a prior.count=0.5. Lowly expressed genes were filtered out (mean log2(CPM)< -2).
Assembly: GRCh38
Supplementary files format and content: cpm.csv: the first column corresponds to the gene symbol,  the second to the GeneID, and the last one to the gene biotype. All the other columns correspond to the counts per gene and sample.
Supplementary files format and content: logCPM.csv: the first column corresponds to the gene symbol,  the second to the GeneID, and the last one to the gene biotype. All the other columns correspond to the  log2 counts per million (CPM) per gene and sample.

source_name: Treatment-naive breast tumor

extract_protocol:
Multicellular suspensions were recovered and stained with directly labelled antibody cocktail including a-CD45-AF700 (clone 2D1), a-CD3-PerCP (clone SK7), a-CD56-APC (clone CMSSB), a-CD16-efluor780 (clone CB16), a-CD103-FITC (Clone B-Ly7) and DAPI as a viability die. Total RNA was isolated (RNeasy« Micro Kit, 74004, Qiagen) from purified NK cells and RNA-sequencing (RNA-seq) of bulk NK cell subsets was performed by the Genomics UPF facility at Universitat Pompeu Fabra, Barcelona.
500 ng of each sample were used to prepare NGS libraries with the NebNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) with PolyA capture.

value: Treatment-naive breast tumor

tag: patient

value: NK

tag: cell subtype

tag: Sex

value: Male

tag: her2 status

value: Negative

tag: er status

value: Positive

tag: grade

tag: tnm


title: KO_pos_35

description:
sample ID:
Run20.105


title: FG; Ctrl ; Lib18

tag: cell line

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)

tag: cell type

value: Foregut

value: Ctrl


title: 90-T2

description:
cpm.csv
logCPM.csv


title: LTBI_20808_6mo-BALF IgA

description: IgA

tag: infection states

value: Asymptomatic controlled Mtb infection


title: LTBI_20808_6mo-Plasma IgA

description: IgA


title: LTBI_20808_3mo-Plasma IgA

description: IgA


title: FG; Ctrl ; Lib16

tag: treatment


title: 90-T1

description:
cpm.csv
logCPM.csv

tag: tissue


title: KO_neg_35

description:
sample ID:
Run20.104

value: feces

tag: geographic location

value: USA:Farmington, Connecticut


title: DE; FOXAKD ; Lib15

value: Definitive endoderm


title: KO_pre_35

description:
sample ID:
Run20.103

tag: host

value: Mus musculus

value: DOCK8 homozygous


title: LTBI_19808_Pre-Plasma IgA

description: IgA


title: KO_pos_34

description:
sample ID:
Run20.102

tag: host genotype

value: positive


title: FG; Ctrl ; Lib20


title: 90-P2

description:
cpm.csv
logCPM.csv

source_name: Peripheral blood

value: Peripheral blood


title: KO_pre_36

description:
sample ID:
Run20.106

tag: iga status

value: pre-sorted


title: DE; FOXAKD ; Lib13

value: FOXAKD


title: 90-P1

description:
cpm.csv
logCPM.csv

value: NK


title: KO_neg_34

description:
sample ID:
Run20.101

value: negative

tag: molecule subtype


title: KO_pre_34

description:
sample ID:
Run20.100


title: 86-T3

description:
cpm.csv
logCPM.csv

value: Treatment-naive breast tumor

tag: patient

value: Female

value: Negative


title: DE; Ctrl ; Lib14

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)


title: DE; FOXAKD ; Lib11


title: DE; Ctrl ; Lib12

value: Ctrl


title: LTBI_19808_Pre-BALF IgA

description: IgA

value: Asymptomatic controlled Mtb infection


title: 86-T1

description:
cpm.csv
logCPM.csv

tag: cell subtype

value: Positive


title: LTBI_19808_5mo-Plasma IgA

description: IgA


title: MF317_A1_GEX_zebrafish_multiseq

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

library_source: transcriptomic single cell

data_processing:
We used the CellRanger v3.1.0 software (10x Genomics) for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2.
Assembly: GRCz11-3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes (Citrine and CFPNTR, sequences from snapgene.com).
Supplementary files format and content: compressed matrix files of CellRanger outputs
Supplementary files format and content: rds file containting Seurat object
Supplementary files format and content: hd5a file containting Seurat object

organism: Danio rerio

source_name: Kidney marrow

extract_protocol:
Each kidney marrow was split into four portions, labelled with lipid anchor plus individual barcode solution (2 μM) for 5’ on ice and then incubated with lipid co-anchor (2 μM) for 5’ on ice. Each cell portion was individually FACS-sorted to obtain one population (mmp9 NO, INT, HI or WKM). All cells were gated on live gate, for WKM debris was excluded in a FSC/SSC gate, and mmp9 NO, INT, HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine-CAAX expression.
Single cell suspensions were immediately subjected to scRNA-seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 (10x Genomics, Pleasanton, CA), according to the manufacturer’s protocols (10x Genomics) and sequenced by protocol.

value: Kidney marrow

value: Neutrophils


title: MF317_A2_GEX_zebrafish_multiseq

value: Whole kidney marrow (PBMCs)


title: LTBI_19808_5mo-BALF IgA

description: IgA


title: 86-P2

description:
cpm.csv
logCPM.csv

tag: Sex


title: ChIP-seq ; DE; FOXAKD ; SUZ12 ; Lib503

data_processing:
CUT&Run:  CUT&RUN Sequencing reads were aligned to the same genome reference as RNA-seq data for consistency using STAR aligner like RNA-seq with options ‘--alignSJDBoverhangMin 999 --alignIntronMax 1 --alignMatesGapMax 2000 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05’. Only uniquely and concordantly aligned read pairs were used for analysis. Read 1 and 2 were connected with each other to form a fragment. Downstream analysis was performed largely as previously described (Skene et al. eLife 2017). For transcription factor (TF) CUT&RUN, fragments with size < 120 bp were selected as originated from putative nucleosome-free regions. For histone modification (histone) CUT&RUN, fragments with size > 150bp were selected as originating from putative nucleosomal regions. Selected fragments were resized to 100bp to normalize bias from the sample-to-sample variabilities of fragment lengths
ChIP-seq: ChIP-seq sequencing reads were aligned to the same genome reference using STAR aligner with options ‘--alignSJDBoverhangMin 999 --alignIntronMax 1 --alignMatesGapMax 2000 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05’. Redundant fragments were deduplicated using Picard (https://broadinstitute.github.io/picard). BigWig files were generated similarly but without fragment length restriction.
Assembly: hg38 and dm6
Supplementary files format and content: RPM-normalized BigWig files. One representative bigwig files were created for each conditions by taking average of biological replicates. For CUT&Run, two bigwig files, nfr and nuc, were created: nfr using short fragments (<120bp) and nuc using longer fragments (>150bp)

extract_protocol:
Chromatin Immunoprecipitation (ChIP):  Cells were crosslinked with 1% formaldehyde in 1x PBS for 10 min at room temperature. The crosslinking reaction was stopped by adding 0.125 M glycine for 5 min at room temperature. Crosslinked cells were centrifuged at 600 xg for 5 min at 4℃, and supernatant was removed. The cell pellet was washed with ice-cold 1x PBS and centrifuge at 600 xg for 5 min at 4℃. Repeat the wash step (total twice). The cell pellet was frozen by dry ice and stored at -80℃.   Crosslinked human cells were resuspended with Lysis Buffer1 (10 mM Tris-HCl [pH. 8.0], 10 mM NaCl, 0.5% NP-40, and 1x Complete Protease Inhibitor EDTA free) and incubated for 10 min on ice. 25% crosslinked Drosophila S2 cells were reconstituted with Lysis Buffer1as a spike-in control and was mixed with the human cells. Cells were centrifuged at 665 xg for 5 min at 4℃, and supernatant was removed. Cell pellet was resuspended with Lysis Buffer2 (50 mM Tris-HCl [pH. 8.0], 10 mM EDTA, 0.32% SDS, 1x Complete Protease Inhibitor EDTA free) and incubated for 10 min on ice. Cell lysate was diluted with IP Dilution Buffer (20 mM Tris-HCl [pH. 8.0], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 1x Complete Protease Inhibitor EDTA free) and transferred into a milliTUBE ATA Fiber (Covaris). Cell lysate was sonicated by Covaris S220 (Covaris) for 3.5 min. The insoluble debris was removed by centrifuge at 12000 xg for 5 min at 4℃. Sonicated chromatin (supernatant) was transferred to a new tube and stored at -80℃.  50 to 86  uL Dynabeads Protein-G beads (10004D, Thermo Fisher Scientific) were washed twice with PBS-T (0.02% Tween-20 in 1x PBS). Desired amounts of antibodies (listed below) were conjugated to washed beads for 2 to 6 hours at 4℃ with rotation. Meanwhile, Frozen chromatin was thawed on ice. Desired amount of chromatin (listed below; determined by DNA amount) was diluted with IP dilution buffer in 4:1 ratio. Antibody conjugated Dynabeads were washed twice with IP Dilution Buffer (without Complete protease inhibitor EDTA free). Washed Dynabeads were resuspend with diluted chromatin and incubated for overnight at 4℃ with rotation. Next day, ChIPed beads were washed four times with following washing buffers: FA Lysis Buffer (50 mM HEPES-KOH [pH. 7.5], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate, 1x Complete protease inhibitor EDTA free); NaCl Buffer (50 mM HEPES-KOH [pH. 7.5], 500 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate); LiCl Buffer (100 mM Tris-HCl [pH. 8.0], 500 mM LiCl, 1% NP-40, 1% Sodium deoxycholate); and 10 mM Tris-HCl [pH. 8.0]. Chromatin was eluted with TES (50 mM Tris-HCl [pH. 8.0], 10 mM EDTA, 1% SDS) for 15 min at 65℃ while shaking at 1000 rpm in ThermoMixer F1.5 (Eppendorf). The ChIP and Input chromatin were reverse crosslinked by adding NaCl (Final concentration of 200 mM) for 2 to 8 hours at 65℃. The reverse crosslinked chromatin samples were treated with 50 ng/ul RNaseA (EN0531, ThermoFisher Scientific) for 0.5 to 1 hour at 37℃. Samples were treated with 0.2 mg/ml protease K (03115828001, Roche) for 2 to 4 hours at 37℃. Finally, DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA concentration was measured by Quantus fluorometer (Promega).  CUT&RUN:  20 uL of ConcanabalinA coated beads (BP531, Bangs Laboratories) were washed twice with Binding Buffer (20 mM HEPES-KOH [pH. 7.9], 10 mM KCl, 1 mM CaCl2 and 1mM MnCl2). Dissociated live cells were resuspended with Wash Buffer (20 mM HEPES-NaOH [pH. 7.5], 150 mM NaCl, 0.5 mM Spermidine and 1x Complete Protease Inhibitor EDTA free) and mixed with washed beads. The mixture was rotated for 10-15 min at room temperature. We then resuspend cell-bound beads with 100 ul (for histone mark CUT&RUN) and 50 ul (for TF CUT&RUN) Antibody Buffer (2 mM EDTA in Digitonin Buffer [0.02% Digitonin in Wash Buffer]). Desired amounts of antibodies (listed below) were added to cell-beads suspension and incubate overnight at 4℃ with rotation. Next day, beads were washed twice with Digitonin Buffer. Washed beads were treated with 700 ng/ml pA-MNase in Digitonin Buffer for 1 hour at room temperature with rotation. Beads were washed twice with Digitonin Buffer. Washed beads were resuspended with 100 ul of Digitonin Buffer and place on the cool block (BP361036, Fisher Scientific) for >10 min to cool down to 0℃. We then performed pA-MNase digestion by adding 2 ul of ice-cold 0.1 M CaCl2 and incubating for 30 min on the cool block. To stop pA-MNase reaction, 100 ul of 2x Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin, 0.05 mg/ml RNaseA and 0.05 mg/ml Glycogen) was added. To release CUT&RUN fragment, samples were incubated at 37℃ for 30 min with shaking at 300 rpm in ThermoMixer F1.5 (Eppendorf). The beads were removed by centrifuge at 16000 xg for 5 min at 4℃ and placing on a magnetic stand. Supernatant was transferred and treated with 0.1% SDS and 0.25 mg/ml ProteinaseK for 1 hour at 37℃. Finally, DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA concentration was measured by Quantus fluorometer (Promega).
We prepared multiplexed libraries of ChIP, Input for ChIP, and CUT&RUN samples from two replicate (two independent CRISPRi clones) using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB). The manufacture’s protocol was employed with the following changes. After the adaptor ligation, we performed cleanup by AMPure XP Beads (A63880, Beckman Coulter) or MagBind Magnetic Beads (M1378-01, Omega) without size selection. After the RCR enrichment of adaptor-ligated library, we performed two rounds of size selection by the magnetic beads.

value: Definitive endoderm


title: LTBI_20808_3mo-BALF IgA

description: IgA


title: LTBI_19808_2mo-Plasma IgA

description: IgA


title: ploop Homozygous

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

country: Germany

institute: University Medicine Greifswald

data_processing:
Paired-end reads were mapped by NextGenMap and Bowtie2 separately with default settings.
The output was sorted by Samtools.
For SNV and InDel calling we used LoFreq and VarScan2 for the rRNA precursor regions.
Assembly: As reference the specific rDNA precursor repeat of Arabidopsis thaliana was used from Sims et al. (Sequencing of Arabidopsis NOR2 reveals ist distinct organization and tissue-specific rRNA ribosomal variants)

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Seeds were grown on full strength Murashige-Skoog media containing 1% (w/v) sucrose and 0.8% (w/v) phytoagar at long-day growth conditions of 16h/8h Llight-dark cycles.

extract_protocol:
Total RNA was purified from 16 days old seedlings using E.Z.N.A Plant RNA kit.
RNA-seq library was prepared using the total RNA without performing rRNA depletion step using the manufacturer's protocol for NovaSeq 6000.

value: whole seedlings

tag: age

value: 16 DAS

tag: genotype

value: ploop KD -/-


title: 86-P1

description:
cpm.csv
logCPM.csv

value: Peripheral blood

tag: her2 status

tag: er status

tag: grade


title: 81-T3

description:
cpm.csv
logCPM.csv

tag: cell type

value: NK

tag: tnm


title: 86-T2

description:
cpm.csv
logCPM.csv


title: 81-T2

description:
cpm.csv
logCPM.csv


title: DE; Ctrl ; Lib10

tag: cell line

tag: treatment


title: heart, MI, S-DTNS treatment, 1 month

city: Chongqing

first: Xue

last: Fangchao

address: XINQIAO

country: China

institute: AMU

data_processing:
HTSeq (http://www-huber.embl.de/users/an ders/HTSeq/doc/overview.html)
Assembly: mm9
Supplementary files format and content: fpkm

organism: Rattus norvegicus

source_name: heart

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 3 μg total RNA wased for the construction of seauencina libraries
NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: After myocardial infarction, the rats (Male, 7-8 weeks) were immediately treated with SNAP/DTMS/S-DTMS in the infarcted myocardial area . One month later, the rats were killed in accordance with the ethical requirements for experimental animals, and the myocardial tissue was removed for RNA sequencing.

tag: tissue

value: heart

value: MI, S-DTNS treatment


title: BG wildtype

value: Wildtype


title: heart, MI, SNAP treatment, 1 month

value: MI, SNAP treatment


title: 81-P2

description:
cpm.csv
logCPM.csv

value: Female

value: Negative


title: 81-T1

description:
cpm.csv
logCPM.csv

value: Treatment-naive breast tumor


title: heart, MI, without treatment,1 month

value: MI, without treatment,1 month


title: LTBI_17806_6mo-Plasma IgA

description: IgA

tag: infection states

value: Asymptomatic controlled Mtb infection


title: LTBI_17906_2mo-Plasma IgA

description: IgA


title: LTBI_17906_2mo-BALF IgA

description: IgA


title: 81-P1

description:
cpm.csv
logCPM.csv

value: Positive


title: heart, normal, 1 month

value: normal


title: LTBI_17806_6mo-BALF IgA

description: IgA


title: LTBI_19808_2mo-BALF IgA

description: IgA


title: LTBI_17906_6mo-BALF IgA

description: IgA


title: SW480_acet_input

city: Palo Alto

first: Michael

last: Nshanian

state: CA

institute: Stanford University

data_processing:
Basecalls were performed using bcl2fastq (v2.17.1) for HiSeq and Novaseq output.
ChIP-seq reads were trimmed from 3' end using cutadapt (v 1.8.1) until the final base had a quality score > 30.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2 (v 2.3.1). Only uniquely mapped reads were retained with at most two mismatches.
To create ChIP-seq coverage plots, the locations of the mapped reads were extended 150 bp to denote extended fragments, renormalized to reads per million and reformatted to .bigWig file format.
Peaks were called using MACS2 (2.1.0) with the significance cut-off q-value (FDR) <= 0.01.
Assembly: hg38
Supplementary files format and content: bam, narrowPeak

growth_protocol: EMEM media containing 10 % fetal bovine serum (FBS)/1 % Pen/Strep (PS). All cell lines were maintained at 37C in a humidified atmosphere containing 5 % CO2.

extract_protocol:
Cells were trypsinized and cross-linked with 1% formaldehyde (EMD Millipore) for 10 min at RT and quenched with 2 M glycine (Thermo Fisher Scientific) for 5 min at room temperature. Chromatin corresponding to 10 million cells for histone modifications was sheared with SFX250 Sonifier (Branson). The lysates were transferred to Diagenode tubes, sonicated 16 rounds of 30 seconds on 30 seconds off, vortexing every 4th round. Protein G beads (80uL) and lysates were washed with RIPA buffer and immunoprecipitated with antibodies targeting given Kacyl marks. 5 μg for each condition, at 4 °C overnight on a nutator. For the input sample, 200 μl of sheared nuclear lysate was removed and stored overnight at 4 °C.
ChIP-DNA and input was reverse crosslinked by incubating overnight at 65 °C in 1% SDS, 1x TE buffer. On the third day, ChIP-DNA was treated with RNase A (Qiagen) and Proteinase K (ThermoFisher Scientific) and then purified using Qiagen QIAquick purification columns. The ChIP-DNA samples were end repaired using End-It DNA End Repair Kit (Lucigen) and A-tailed using Klenow Fragment and dATP (New England Biolabs). Illumina TruSeq adapters (Illumina) were ligated and libraries size-selected (200 - 400 bp) by gel extraction before PCR amplification. The purified libraries were subjected to paired-end sequencing on the Illumina HiSeq 4000/Novaseq 6000 SP to obtain an average of approximately 30 - 35 million uniquely mapped reads for each sample

treatment_protocol: Cells were treated with 10 mM Na Propionate (NaPr) or 1 mM Na Butyrate (NaBu) for 12-16 hrs followed by counting.

value: Large intestine; colon, epithelial

value: untreated


title: LTBI_17906_6mo-Plasma IgA

description: IgA


title: Sample 18_Suit.2-028 resistant to paclitaxel cells - biol rep 3

city: Amsterdam

first: Elisa

last: Giovannetti

address: de boelelaan

country: Netherlands

institute: Amsterdam UMC

data_processing:
FASTQ files were checked for quality reads and adapters were removed with Trimmomatic. Successfully quality passed reads were mapped to the human reference genome (Hg19) with STAR mapping tool and gene counts were extracted with HTSeq.
Normalization and differential analysis were performed with Bbtest (Pham T.V. et al.)
Assembly: Hg19
Supplementary files format and content: raw data in xlsx

source_name: pancreatic ductal adenocarcinoma

growth_protocol: Suit.2-028 were grown in RPMI, while Patu-T were grown with DMEM supplemented with 10% (v/v) heat-inactivated NBCS and 1% (v/v) penicilin-streptomycin. Gemcitabine and paclitaxel resitant cells were cultured without any drug treatment and periodically tested for drug resistance, to ensure their stable resistance.

extract_protocol:
Remove medium, wash the cells twice with PBS and detach by adding trypsin-EDTA and incubate at 37 °C for 5 min. Add culture medium and harvest 1-3 x 106 cells. Spin down samples at 1200 RPM for 5 min, remove supernatant and extract total mRNA using mirVana™ miRNA Isolation Kit and following the manufacturer`s protocol. Determine the concentration of total RNA by using Qubit RNA BR Assay Kit and its integrity using Agilent 2200 TapeStation system and RNA ScreenTape kit. The samples were stored at - 80 °C.
Use 500 ng of total mRNA per each sample. Follow mRNA library preparation protocol according to manufacturer's instructions. Determine quality and concentration of each library by using Agilent 2200 TapeStation system. Pool the libraries in a single sample up to a final concentration of 10 nmol/L and measure it with Agilent 2200 TapeStation system.
Libraries were paired-end sequenced (2x75bp) on a NextSeq500 (Illumina) according to the corresponding protocol.

value: pancreatic ductal adenocarcinoma

value: Suit.2-028 PR

value: immortalized cell line

value: Resistant to Ptx


title: heart, MI, DTMS treatment, 1 month

value: heart

value: MI, DTMS treatment


title: LTBI_17806_2mo-Plasma IgA

description: IgA


title: SW480_prop_input

value: 10 mM NaPr


title: Sample 16_Suit.2-028 resistant to paclitaxel cells - biol rep 1


title: Sample 17_Suit.2-028 resistant to paclitaxel cells - biol rep 2


title: LTBI_17806_2mo-BALF IgA

description: IgA


title: LTBI_17706_6mo-Plasma IgA

description: IgA


title: SW480_H4K12ac_cnt2_ChIP_2


title: Sample 15_Suit.2-028 resistant to gemcitabine cells - biol rep 3

value: Suit.2-028 GR

value: Resistant to Gem


title: LTBI_17706_6mo-BALF IgA

description: IgA


title: SW480_H4K12ac_cnt1_ChIP_1


title: Sample 14_Suit.2-028 resistant to gemcitabine cells - biol rep 2


title: ChIP-seq ; DE; FOXAKD ; PRDM1 ; Lib507

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)

value: Definitive endoderm

value: FOXAKD


title: ChIP-seq ; DE; FOXAKD ; PRDM1 ; Lib506


title: ChIP-seq ; DE; Ctrl ; RYBP ; Lib497

value: Ctrl


title: ChIP-seq ; DE; FOXAKD ; SUZ12 ; Lib502


title: ChIP-seq ; DE; Ctrl ; SUZ12 ; Lib500


title: ChIP-seq ; DE; FOXAKD ; RYBP ; Lib499


title: ChIP-seq ; DE; Ctrl ; SUZ12 ; Lib501


title: LTBI_17706_2mo-Plasma IgA

description: IgA

value: Asymptomatic controlled Mtb infection


title: ChIP-seq ; DE; FOXAKD ; RING1B ; Lib494


title: ChIP-seq ; DE; FOXAKD ; RYBP ; Lib498


title: Sample 13_Suit.2-028 resistant to gemcitabine cells - biol rep 1


title: SW480_H3K18ac_cnt1_ChIP_1


title: ChIP-seq ; DE; Ctrl ; RING1B ; Lib493


title: LTBI_17706_2mo-BALF IgA

description: IgA


title: ChIP-seq ; DE; Ctrl ; RING1B ; Lib492


title: Sample 12_Suit.2-028 WT cells - biol rep 3

value: WT


title: SW480_H4K12ac_prop_ChIP_2

value: Large intestine; colon, epithelial


title: Sample 11_Suit.2-028 WT cells - biol rep 2


title: ChIP-seq ; DE; FOXAKD ; RING1B ; Lib495


title: SW480_H3K18ac_cnt2_ChIP_2

value: untreated


title: LTBI_17606_6mo-BALF IgA

description: IgA


title: SW480_H4K12ac_prop_ChIP_1


title: ChIP-seq ; DE; Ctrl ; PRDM1 ; Lib505


title: LTBI_17606_2mo-Plasma IgA

description: IgA


title: Sample 10_Suit.2-028 WT cells - biol rep 1

value: pancreatic ductal adenocarcinoma


title: ChIP-seq ; DE; Ctrl ; RYBP ; Lib496


title: ChIP-seq ; DE; Ctrl ; PRDM1 ; Lib504


title: SW480_H3K18ac_prop_ChIP_2


title: Sample 9_Patu-T resistant to paclitaxel cells - biol rep 3

value: Patu-T PR


title: SW480_H3K18ac_prop_ChIP_1


title: CUT&Run ; hPSC; OCT4KD 2D ; H3K27me3 ; Lib490

description:
hPSC_OCT4CRISPRi-d2_CnR_H3K27me3.nfr.bw
hPSC_OCT4CRISPRi-d2_CnR_H3K27me3.nuc.bw

data_processing:
CUT&Run:  CUT&RUN Sequencing reads were aligned to the same genome reference as RNA-seq data for consistency using STAR aligner like RNA-seq with options ‘--alignSJDBoverhangMin 999 --alignIntronMax 1 --alignMatesGapMax 2000 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05’. Only uniquely and concordantly aligned read pairs were used for analysis. Read 1 and 2 were connected with each other to form a fragment. Downstream analysis was performed largely as previously described (Skene et al. eLife 2017). For transcription factor (TF) CUT&RUN, fragments with size < 120 bp were selected as originated from putative nucleosome-free regions. For histone modification (histone) CUT&RUN, fragments with size > 150bp were selected as originating from putative nucleosomal regions. Selected fragments were resized to 100bp to normalize bias from the sample-to-sample variabilities of fragment lengths
ChIP-seq: ChIP-seq sequencing reads were aligned to the same genome reference using STAR aligner with options ‘--alignSJDBoverhangMin 999 --alignIntronMax 1 --alignMatesGapMax 2000 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05’. Redundant fragments were deduplicated using Picard (https://broadinstitute.github.io/picard). BigWig files were generated similarly but without fragment length restriction.
Assembly: hg38 and dm6
Supplementary files format and content: RPM-normalized BigWig files. One representative bigwig files were created for each conditions by taking average of biological replicates. For CUT&Run, two bigwig files, nfr and nuc, were created: nfr using short fragments (<120bp) and nuc using longer fragments (>150bp)
Library strategy: CUT&RUN

value: Pluripotent stem cells

value: OCT4KD 2Day


title: LTBI_17606_2mo-BALF IgA

description: IgA


title: Sample 8_Patu-T resistant to paclitaxel cells - biol rep 2

value: immortalized cell line

value: Resistant to Ptx


title: CUT&Run ; hPSC; Ctrl ; H3K27me3 ; Lib489

description:
hPSC_Ctrl_CnR_H3K27me3.nfr.bw
hPSC_Ctrl_CnR_H3K27me3.nuc.bw


title: LTBI_17006_6mo-Plasma IgA

description: IgA


title: LTBI_17606_6mo-Plasma IgA

description: IgA


title: SW480_H3K18pr_prop_ChIP_2

value: 10 mM NaPr


title: CUT&Run ; hPSC; Ctrl ; H3K27me3 ; Lib488


title: SW480_H3K18pr_prop_ChIP_1


title: ChIP-seq ; hPSC; OCT4KD 3D ; H2Aub ; Lib445

description: hPSC_OCT4CRISPRi-d3_ChIP_H2Aub.subInput.bw

value: OCT4KD 3Day


title: hNEU-NT, Day 2, Biol Rep 3

city: Cambridge

first: Ming-Hsuan

last: Wen

address: Tennis Court Road

institute: Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge

data_processing:
Fasta files from M. musculus (mm10) and X. laevis (xla9.1) were concatenated one after the other in order to create a hybrid large mouse-Xenopus genome.
To distinguish the X. laevis chromosomes in the fasta file, they were renamed as ‘xla_chr’ instead of just ‘chr’.
Similarly, the gtf files containing the annotation of all transcripts from Mouse (mm10) and of all primary transcript from X. laevis (xla9.1) have been concatenated.
FastQ files were processed with cutadatp (version 1.9.1, options -q 10 -O 3) for adapter trimming.
Filtered reads were then aligned to the hybrid mouse-Xenopus genome with tophat (version v2.1.1).
Transcripts were assigned to gene and counted using htseq-count (HTSeq-0.5.4p3).
The M. musculus (mm10) was replaced with H. sapiens (hg38) in experiments with human cells transplanted into Xenopus oocytes.
Assembly: mm10
Assembly: hg38
Supplementary files format and content: exl files include TPM for each sample

source_name: neuroblastoma cells

extract_protocol:
RNA was extracted by Qiagen Rneasy Mini Kit and BrUTP incorporated RNA was isolated via immunoprecipitation.
RNA-seq libraries were prepared by Ovation Single Cell RNA-seq System (NuGEN) and 10 ng of BrUTP incorporated RNA was used for each library.

value: neuroblastoma cells


title: Sample 4_Patu-T resistant to gemcitabine cells - biol rep 1

value: Patu-T GR

value: Resistant to Gem


title: ChIP-seq ; hPSC; OCT4KD 3D ; H2Aub ; Lib444

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)


title: Sample 5_Patu-T resistant to gemcitabine cells - biol rep2


title: Sample 3_Patu-T WT cells - biol rep 3

value: Patu-T


title: ChIP-seq ; hPSC; OCT4KD 2D ; SUZ12 ; Lib439

description: hPSC_OCT4CRISPRi-d2_ChIP_SUZ12.subInput.bw


title: hNEU-NT, Day 2, Biol Rep 2


title: SW480_H4K12pr_prop_ChIP_2


title: CUT&Run ; hPSC; OCT4KD 2D ; H3K27me3 ; Lib491


title: Sample 7_Patu-T resistant to paclitaxel cells - biol rep 1


title: SW480_H4K12pr_prop_ChIP_1


title: LTBI_17006_6mo-BALF IgA

description: IgA

value: Asymptomatic controlled Mtb infection


title: Sample 6_Patu-T resistant to gemcitabine cells - biol rep 3


title: hNEU-NT, Day 2, Biol Rep 1


title: LTBI_11108_Pre-BALF IgA

description: IgA


title: LTBI_11108_Pre-Plasma IgA

description: IgA


title: LTBI_11108_6mo-BALF IgA

description: IgA


title: LTBI_17006_2mo-BALF IgA

description: IgA


title: LTBI_17006_2mo-Plasma IgA

description: IgA


title: Tumor biopsy, Pt98

city: Bethesda

first: Jayakumar

middle: R

last: Nair

state: MD

address: 10 center drive

department: Women malignancies Branch

institute: National Cancer Institute

data_processing:
Samples were pooled and sequenced on HiSeq4000 using Illumina TruSeq Stranded Total RNA Library Prep and paired-end sequencing
CPM files generated by sequencing each sample (n-14) was combined into a single file and processed to remove low counts, quartile normalized and log2 transformed.  The processed file is attached as a soft text file.
Assembly: HG38
Supplementary files format and content: CPM

source_name: Ovarian

growth_protocol: Tumor needle biopsies were frozen in OCT compound at -80 Celsius.  Sections were used for total RNA isolation

extract_protocol:
Qiagen micro RNA isolation kit
RNA sequencing (RNAseq) data were obtained from total RNA from fresh frozen tumor biopsy samples from 14 BRCAm PARPi-resistant HGSOC patients enrolled in the clinical trial at the National Cancer Institute (ClinicalTrials.gov, NCT02203513). RNAseq was performed using a HiSeq4000 sequencing system (Illumina) at the CCR Sequencing Facility/NCI on pre-treatment biopsy samples from 14 patients.  Paired-end sequencing was done.  Quartile normalization and log-transformation prior to analysis were performed on datasets.

value: Ovarian

tag: disease

value: Ovarian cancer

value: Homo sapiens

value: Prexasertib

tag: clinical benefit

value: NO


title: Sample 2_Patu-T WT cells - biol rep 2

value: pancreatic ductal adenocarcinoma

value: WT


title: Sample 1_Patu-T WT cells - biol rep 1

value: immortalized cell line


title: 80% sample ATAC [Fltseq_80_ATAC]

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Base calling and quality scoring were performed using Illumina Real-Time Analysis on board software (version 2.11.3).
Raw base call files were demultiplexed into FASTQ files using the mkfastq pipeline in Cellranger ARC 2.0.0
Reads were aligned to the human reference genome, filtering, barcode counting, peak calling were performed, and gene counts were generated using the count pipeline in CellRanger ARC 2.0.0.
Assembly: GRCh38
Supplementary files format and content: Detected cell-associated barcodes, features, and matrix outputs from CellRanger.

source_name: Lung adenocarcinoma

growth_protocol: The human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin.  The cells were grown independently at 37C  with 5% carbon dioxide until near 100% confluency.

extract_protocol:
Cells from each cell line were mixed in equal proportions. Cell capture was performed.
A single GEM tube of the 5 cell lines were split into 2 fractions, 80% and 20%. These 2 fractions were processed separately using the FLT-Seq protocol (https://www.protocols.io/view/massively-parallel-long-read-sequencing-of-single-81wgbpp1nvpk/v1). The GEX library was sequenced in 2 different runs on Illumina NextSeq 500. The ATAC library was sequenced on Illumina NextSeq 500 at AGRF.

treatment_protocol: Cells were dissociated into single cell suspensions in FACS buffer, centrifuged and frozen at -80 °C.

value: human lung adenocarcinoma cell lines


title: ChIP-seq ; hPSC; OCT4KD 2D ; RYBP ; Lib434

description: hPSC_OCT4CRISPRi-d2_ChIP_RYBP.subInput.bw

value: Pluripotent stem cells

value: OCT4KD 2Day


title: ChIP-seq ; hPSC; OCT4KD 2D ; RYBP ; Lib435


title: 80% sample RNA [Fltseq_80_GEX]


title: Tumor biopsy, Pt92

value: YES


title: LTBI_11008_Pre-BALF IgA

description: IgA


title: Neocuproine_rep2

city: Zurich

first: Zsolt

last: Balázs

address: Schmelzbergstrasse 26

country: Switzerland

institute: University of Zurich

description:
10x Genomics
counts.csv.gz
metadata.csv.gz

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 3.1.0  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Raw count matrix has been generated using Seurat v4.1.1 after merging all samples. The cell-type calls in the metadata are output by SingleR v1.8.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human NRAS-mutated melanoma PDX in mice

extract_protocol:
Slow-frozen PDX tissue samples were quickly thawed in the water bath set to 37°C degree, re-suspended in 10 mL of ice cold RPMI with 1% BSA  and spun down at 300g for 5 min. Further tissue samples were cut into small pieces and enzymatically digested for 30 min at 37 °C on a shaker with 5000U Collagenase IV, 15 KU DNAse I, 2 mL Accutase dissolved in RPMI with 2mM CaCl2 and 0.5% BSA 5 mL RPMI mixture. After incubation, digested tissue was filtered through 100 μm nylon and then through 35-μm cell strainers. For samples with viability below 80%, apoptotic and dead cells were removed using immunomagnetic cell separation with the Annexin Dead Cell Removal Kit and EasySepTM Magnet. If the cell pellet appeared red, red blood cell lysis was performed following the manufacturer's instructions. Cell number and viability was assessed on Luna-FLTMDual Fluorescence Cell counter using Photon slides by acridine orange propidium iodide stain and optimal cell concentrations were set to 700-1100 cells/μL according to 10x Genomics protocols.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). 6000 cells per sample were targeted and libraries were diluted to 10 nM and pooled at balanced ratios according to the target cell number. Paired-end sequencing was performed on the Illumina NovaSeq S2 flow cell. According to 10x Genomics recommendation 50,000 read pairs per cell for GEX coverage was targeted.

tag: protocol

value: xenograft

value: Neocuproine

value: human NRAS-mutated melanoma PDX in mice


title: Neocuproine_rep1


title: Tumor biopsy, Pt91


title: ChIP-seq ; hPSC; OCT4KD 2D ; SUZ12 ; Lib438

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)


title: ChIP-seq ; hPSC; OCT4KD 2D ; RING1B ; Lib430

description: hPSC_OCT4CRISPRi-d2_ChIP_RING1B.subInput.bw


title: LTBI_11108_2mo-BALF IgA

description: IgA

value: Asymptomatic controlled Mtb infection


title: Tumor biopsy, Pt87

value: Ovarian


title: original_cell_line

source_name: original cell line

value: control

value: original cell line


title: ChIP-seq ; hPSC; OCT4KD 2D ; PRDM14 ; Lib449

description: hPSC_OCT4CRISPRi-d2_ChIP_PRDM14.subInput.bw


title: MEKi_rep2

value: MEK-inhibitor


title: Tumor biopsy, Pt61

value: Ovarian cancer

value: Homo sapiens

value: Prexasertib

value: NO


title: MEKi_rep1


title: Tumor biopsy, Pt94


title: control_rep2


title: ChIP-seq ; hPSC; OCT4KD 2D ; RING1B ; Lib431


title: Tumor biopsy, Pt52


title: Tumor biopsy, Pt66


title: control_rep1


title: comb_rep2

value: combination


title: Tumor biopsy, Pt69


title: Tumor biopsy, Pt30


title: comb_rep1


title: ChIP-seq ; hPSC; Ctrl ; SUZ12 ; Lib437

value: Pluripotent stem cells

value: Ctrl


title: ChIP-seq ; hPSC; Ctrl ; SUZ12 ; Lib436


title: ChIP-seq ; hPSC; OCT4KD 2D ; PRDM14 ; Lib448

value: OCT4KD 2Day


title: LTBI_11008_6mo-BALF IgA

description: IgA


title: Tumor biopsy, Pt19


title: LTBI_11008_2mo-BALF IgA

description: IgA


title: ChIP-seq ; hPSC; OCT4KD 2D ; H2Aub ; Lib443

description: hPSC_OCT4CRISPRi-d2_ChIP_H2Aub.subInput.bw


title: ChIP-seq ; hPSC; OCT4KD 2D ; H2Aub ; Lib442


title: ChIP-seq ; hPSC; Ctrl ; RYBP ; Lib433


title: ChIP-seq ; hPSC; Ctrl ; RYBP ; Lib432


title: Tumor biopsy, Pt9


title: LTBI_10708_Pre-Plasma IgA

description: IgA


title: LTBI_10408_2mo-Plasma IgA

description: IgA


title: LTBI_10408_6mo-BALF IgA

description: IgA


title: CUT&Run ; DE; FOXAKD ; H3K27me3 ; Lib292

description:
DE_FOXA-CRISPRi_CnR_H3K27me3.nfr.bw
DE_FOXA-CRISPRi_CnR_H3K27me3.nuc.bw

value: Definitive endoderm

value: FOXAKD


title: CUT&Run ; DE; FOXAKD ; H3K27me3 ; Lib294


title: LTBI_10708_Pre-BALF IgA

description: IgA


title: ChIP-seq ; hPSC; Ctrl ; RING1B ; Lib429


title: LTBI_10708_2mo-Plasma IgA

description: IgA


title: LTBI_10708_2mo-BALF IgA

description: IgA


title: LTBI_10408_Pre-Plasma IgA

description: IgA


title: LTBI_10408_Pre-BALF IgA

description: IgA


title: LTBI_10408_6mo-Plasma IgA

description: IgA


title: LTBI_10408_2mo-BALF IgA

description: IgA


title: Tumor biopsy, Pt49


title: Tumor biopsy, Pt2


title: CUT&Run ; DE; Ctrl ; H3K27me3 ; Lib293

description:
DE_Ctrl_CnR_H3K27me3.nfr.bw
DE_Ctrl_CnR_H3K27me3.nuc.bw


title: CUT&Run ; DE; Ctrl ; H3K27me3 ; Lib291


title: ChIP-seq ; hPSC; Ctrl ; RING1B ; Lib428


title: ChIP-seq ; hPSC; Ctrl ; PRDM14 ; Lib447


title: ChIP-seq ; hPSC; Ctrl ; H2Aub ; Lib440


title: ChIP-seq ; hPSC; Ctrl ; Input ; Lib450


title: ChIP-seq ; hPSC; Ctrl ; PRDM14 ; Lib446_v2


title: ChIP-seq ; hPSC; Ctrl ; Input ; Lib451


title: CUT&Run ; hPSC; OCT4KD 3D ; H3K4me1 ; Lib370-3

description:
hPSC_d3OCT4CRISPRi_CnR_H3K4me1.nfr.bw
hPSC_d3OCT4CRISPRi_CnR_H3K4me1.nuc.bw

value: OCT4KD 3Day


title: CUT&Run ; hPSC; Ctrl ; H3K4me1 ; Lib369-2

description:
hPSC_ctrl_CnR_H3K4me1.nfr.bw
hPSC_ctrl_CnR_H3K4me1.nuc.bw

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)


title: CUT&Run ; hPSC; Ctrl ; H3K4me1 ; Lib371-2


title: CUT&Run ; hPSC; OCT4KD 3D ; H3K4me1 ; Lib372-3


title: PAIVS_PULVAL

first: Yu

last: Liu

address: 1215 Welch Road

department: CVI

description:
HealthyandPAIVS_PulValve_matrix.mtx
HealthyandPAIVS_PulValve_barcodes.tsv
HealthyandPAIVS_PulValve_features.tsv

data_processing:
The read counts of each cell was calculated by using Cellranger
The analysis of single cell RNAseq data was performed by Seurat
Assembly: hg38
Supplementary files format and content: MetaData_HealthyandPAIVS_PulValve.txt
Supplementary files format and content: MetaData_HealthyFetalValve.txt
Supplementary files format and content: healthy_matrix.mtx
Supplementary files format and content: healthy_barcodes.tsv
Supplementary files format and content: healthy_features.tsv
Supplementary files format and content: HealthyandPAIVS_PulValve_matrix.mtx
Supplementary files format and content: HealthyandPAIVS_PulValve_barcodes.tsv
Supplementary files format and content: HealthyandPAIVS_PulValve_features.tsv

source_name: Humna Fetal Pulmonary Valve

extract_protocol:
One normal human fetal heart (week 15, male) and one heart sample with underdeveloped right heart with abnormal right outflow tract and pulmonary valve (week 15, male) were manually micro-dissected. Aortic, pulmonary, mitral valve and tricuspid valves were collected, minced, and digested using the same digestion buffer as VEC isolation. Following digestion for 10 min at 37oC, EGM-2 medium was added to stop the reaction and cells were transferred through a 40 μm cell strainer. Cells with viability>90% were sent to Stanford Functional Genomics Facility (SFGF) for 10X chromium single-cell RNA-seq paired end library preparation using V2 version (10X Genomics). All samples were uniquely indexed, mixed, and evenly distributed into the Illumina HiSeq 4000 for sequencing.
10X chromium single-cell RNA-seq paired-end library preparation using V2 version (10X Genomics)

value: Day 115

value: heart valve


title: ChIP-seq ; hPSC; Ctrl ; H2Aub ; Lib441

source_name: Human induced pluripotent stem cells (72.3, male, RRID: CVCL_A1BW)


title: Control_TRIVAL

description:
healthy_matrix.mtx
healthy_barcodes.tsv
healthy_features.tsv

source_name: Human Fetal Tricuspid Valve

value: Day 105


title: ChIP-seq ; FG; FOXAKD ; SUZ12 ; Lib467

value: Foregut


title: Control_MITVAL

source_name: Human Fetal Mitral Valve


title: CUT&Run ; FG; FOXAKD ; H3K4me1 ; Lib388-2

description:
PFG_FOXACRISPRi_CnR_H3K4me1.nfr.bw
PFG_FOXACRISPRi_CnR_H3K4me1.nuc.bw


title: CUT&Run ; FG; FOXAKD ; H3K4me1 ; Lib386-2


title: ChIP-seq ; FG; FOXAKD ; SUZ12 ; Lib466


title: LTBI_10211_Pre-Plasma IgA

description: IgA

data_processing: Spots were considered reactive if the ratio of the median fluorescent intensity (MFI) of the gene was greater than 1.4 x the median of negative control genes

source_name: Pre-Plasma

value: Asymptomatic controlled Mtb infection


title: LTBI_10111_Pre-BALF IgA

description: IgA

source_name: Pre-BALF


title: LTBI_10211_3mo-Plasma IgA

description: IgA


title: LTBI_10211_Pre-BALF IgA

description: IgA


title: LTBI_10211_6mo-BALF IgA

description: IgA


title: LTBI_10211_3mo-BALF IgA

description: IgA


title: LTBI_10211_6mo-Plasma IgA

description: IgA


title: LTBI_10111_Pre-Plasma IgA

description: IgA


title: Control2_PULVAL

description: 10X Genomics

data_processing:
The read counts of each cell was calculated by using Cellranger
The analysis of single cell RNAseq data was performed by Seurat
Assembly: hg38

source_name: heart valve

value: tissue


title: Control2_TRIVAL

description: 10X Genomics


title: ChIP-seq ; FG; FOXAKD ; RYBP ; Lib463


title: Control2_AORVAL

description: 10X Genomics


title: Control_PULVAL

source_name: Human Fetal Pulmonary Valve


title: Control_AORVAL

source_name: Human Fetal Aortic Valve


title: CUT&Run ; FG; Ctrl ; H3K4me1 ; Lib387-2

description:
PFG_ctrl_CnR_H3K4me1.nfr.bw
PFG_ctrl_CnR_H3K4me1.nuc.bw


title: ChIP-seq ; FG; FOXAKD ; RING1B ; Lib459


title: CUT&Run ; FG; Ctrl ; FOXA1 ; Lib394

description:
PFG_ctrl_CnR_FOXA1.nfr.bw
PFG_ctrl_CnR_FOXA1.nuc.bw


title: CUT&Run ; FG; Ctrl ; H3K4me1 ; Lib385-2


title: LTBI_10111_3mo-Plasma IgA

description: IgA


title: Contro2l_MITVAL

description: 10X Genomics


title: DU145-miRNA-pLKO.1

city: Shanghai

first: Jianxiu

last: Yu

address: Room 202, Building 7, 280 South Chongqing Road

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University school of medicine

data_processing:
For DU145 mRNA data, paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).  The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
For MDA-MB-231 mRNA data, paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC HG19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
For DU145 miRNA data, raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.2). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
For MDA-MB-231 miRNA data, raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Assembly: hg19 for RNA-Seq, miRBase for miRNA-Seq

extract_protocol:
RNA was extracted from total cell lysates.
RNA and miRNA libraries were prepared for sequencing using standard Illumina protocols


title: ChIP-seq ; FG; FOXAKD ; RING1B ; Lib458


title: DU145-mRNA-shUSP7


title: DU145-mRNA-shUSP7shDICER


title: ChIP-seq ; FG; FOXAKD ; PRDM1 ; Lib479


title: DU145-miRNA-shUSP7shDICER


title: ChIP-seq ; FG; FOXAKD ; PRDM1 ; Lib478


title: DU145-mRNA-pLKO.1


title: S0328

city: Changchun

first: Liang

last: Han

address: Xiantai Street 126

institute: China-Japan Union Hospital of Jilin University

data_processing:
STAR 2.5.2b and CIRCexplorer2 2.2.6
CircRNA expression quantification (Backspace junction reads count) is obtained by software STAR through comparing the results to known transcriptome and detecting junction sites
calculate Backspace junction reads through CIRCExplorer2
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include count value for each Sample

source_name: GBM tumor tissues

extract_protocol:
Total RNA was isolated from the specimens using RNAiso Plus reagent (TaKaRa, Japan). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed by using pretreated RNAs with KAPA Stranded RNA-Seq Library Prep Kit (Illumina, USA) following manufacturer's protocols.

value: GBM tumor tissues


title: ChIP-seq ; FG; FOXAKD ; Input ; Lib483_v2

first: Hee-Woong

last: Lim


title: ChIP-seq ; FG; FOXAKD ; Input ; Lib482


title: ChIP-seq ; FG; FOXAKD ; RYBP ; Lib462


title: DU145-miRNA-shUSP7


title: N0284t


title: ChIP-seq ; FG; FOXAKD ; H2Aub ; Lib471


title: ChIP-seq ; FG; FOXAKD ; H2Aub ; Lib470


title: LTBI_10011_3mo-BALF IgA

first: Jacqueline

last: Achkar

description: IgA

extract_protocol: Plasma was obtained from peripheral blood samples and the BAL procedure was performed as previously described via direct visualization of the airway and lavage of ~ 40 ml normal saline (0.9%). Animal protocols and procedures were approved by the University of Pittsburgh’s Institutional Animal Care and Use Committee before the collection of samples.


title: LTBI_10011_Pre-Plasma IgA

description: IgA


title: LTBI_10111_3mo-BALF IgA

description: IgA


title: LTBI_10111_6mo-BALF IgA

description: IgA


title: LTBI_10111_6mo-Plasma IgA

description: IgA


title: LTBI_10011_Pre-BALF IgA

description: IgA


title: LTBI_10011_3mo-Plasma IgA

description: IgA


title: LTBI_10011_6mo-Plasma IgA

description: IgA


title: N0288


title: ChIP-seq ; FG; Ctrl ; SUZ12 ; Lib465


title: N0293


title: ChIP-seq ; FG; Ctrl ; SUZ12 ; Lib464


title: Han3

source_name: normal brain tissues

value: normal brain tissues


title: CUT&Run ; FG; FOXAKD ; H3K27me3 ; Lib204

description:
PFG_FOXA_CRISPRi_CnR_H3K27me3.nfr.bw
PFG_FOXA_CRISPRi_CnR_H3K27me3.nuc.bw


title: CUT&Run ; DE; Ctrl ; FOXA2 ; Lib284

description:
DE_Ctrl_CnR_FOXA2.nfr.bw
DE_Ctrl_CnR_FOXA2.nuc.bw


title: CUT&Run ; FG; FOXAKD ; IgG ; Lib208

description:
PFG_FOXA_CRISPRi_CnR_IgG.nfr.bw
PFG_FOXA_CRISPRi_CnR_IgG.nuc.bw


title: CUT&Run ; DE; Ctrl ; H3K4me1 ; Lib377

description:
DE_ctrl_CnR_H3K4me1.nfr.bw
DE_ctrl_CnR_H3K4me1.nuc.bw


title: CUT&Run ; FG; Ctrl ; FOXA1 ; Lib393


title: CUT&Run ; DE; Ctrl ; FOXA2 ; Lib283


title: CUT&Run ; FG; FOXAKD ; IgG ; Lib206


title: ko_con3

city: Jinan

first: Yue

last: Lu

state: Shandong

address: 44# Wenhua Xi Road

institute: Shandong university

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome GRCm39.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCm39.108
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Mus musculus

source_name: VSMC

growth_protocol: Primary mouse VSMCs were maintained in DMEM supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No additional treatment

value: VSMC

value: KO


title: ChIP-seq ; FG; Ctrl ; RYBP ; Lib461

city: Cincinnati

address: 3333 Burnet Ave. MLC 7024

institute: Cincinnati Children's Hospital Medical Center


title: CUT&Run ; DE; FOXAKD ; H3K4me1 ; Lib378

description:
DE_FOXACRISPRi_CnR_H3K4me1.nfr.bw
DE_FOXACRISPRi_CnR_H3K4me1.nuc.bw


title: Han2


title: CUT&Run ; DE; Ctrl ; H3K4me1 ; Lib379


title: CUT&Run ; DE; FOXAKD ; H3K4me1 ; Lib380


title: ko_con2


title: ko_con1


title: ChIP-seq ; FG; Ctrl ; RYBP ; Lib460


title: Han1


title: ChIP-seq ; FG; Ctrl ; RING1B ; Lib457


title: wt_con3

value: WT


title: N0284n


title: ChIP-seq ; FG; Ctrl ; RING1B ; Lib456

value: Ctrl


title: CUT&Run ; FG; Ctrl ; IgG ; Lib205

description:
PFG_Ctrl_CnR_IgG.nfr.bw
PFG_Ctrl_CnR_IgG.nuc.bw


title: CUT&Run ; FG; Ctrl ; IgG ; Lib207


title: CUT&Run ; FG; FOXAKD ; H3K27me3 ; Lib202


title: wt_con2


title: ChIP-seq ; FG; Ctrl ; PRDM1 ; Lib477


title: ChIP-seq ; FG; Ctrl ; PRDM1 ; Lib476


title: LTBI_10011_6mo-BALF IgA

city: Bronx

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: IgA


title: wt_con1


title: CUT&Run ; FG; Ctrl ; FOXA2 ; Lib214

description:
PFG_Ctrl_CnR_FOXA2.nfr.bw
PFG_Ctrl_CnR_FOXA2.nuc.bw


title: ChIP-seq ; FG; Ctrl ; Input ; Lib481


title: control

city: Seoul

first: Hongyoon

last: Choi

state: Seoul Teugbyeolsi

address: Daehakro 101, Jongrogu

country: South Korea

institute: Seoul National University Hospital

data_processing:
The Cell Ranger v.3.1.0 was used to perform alignment, filtering, barcode and UMI counting with default parameters.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
FACS-sorted cells were loaded onto a 10x Chromium microfluidics system according to the manufacturer’s guidelines. As the guidelines, scRNA-seq 5′ gene expression (GEX) libraries were generated using the 10X Genomics Chromium Single Cell 5′ Kit version3.1 and the 10x Chromium Controller (10x Genomics) according to the 10x Single Cell 5′ version3.1 protocol guidelines (CG000204).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type source

tag: host strain

value: BALB/c

value: vehicle liposome


title: CUT&Run ; FG; Ctrl ; H3K27me3 ; Lib203

description:
PFG_Ctrl_CnR_H3K27me3.nfr.bw
PFG_Ctrl_CnR_H3K27me3.nuc.bw


title: CUT&Run ; FG; Ctrl ; H3K27me3 ; Lib201


title: CUT&Run ; FG; Ctrl ; FOXA2 ; Lib213


title: ChIP-seq ; FG; Ctrl ; Input ; Lib480

data_processing:
CUT&Run:  CUT&RUN Sequencing reads were aligned to the same genome reference as RNA-seq data for consistency using STAR aligner like RNA-seq with options ‘--alignSJDBoverhangMin 999 --alignIntronMax 1 --alignMatesGapMax 2000 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05’. Only uniquely and concordantly aligned read pairs were used for analysis. Read 1 and 2 were connected with each other to form a fragment. Downstream analysis was performed largely as previously described (Skene et al. eLife 2017). For transcription factor (TF) CUT&RUN, fragments with size < 120 bp were selected as originated from putative nucleosome-free regions. For histone modification (histone) CUT&RUN, fragments with size > 150bp were selected as originating from putative nucleosomal regions. Selected fragments were resized to 100bp to normalize bias from the sample-to-sample variabilities of fragment lengths
ChIP-seq: ChIP-seq sequencing reads were aligned to the same genome reference using STAR aligner with options ‘--alignSJDBoverhangMin 999 --alignIntronMax 1 --alignMatesGapMax 2000 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05’. Redundant fragments were deduplicated using Picard (https://broadinstitute.github.io/picard). BigWig files were generated similarly but without fragment length restriction.
Assembly: hg38 and dm6
Supplementary files format and content: RPM-normalized BigWig files. One representative bigwig files were created for each conditions by taking average of biological replicates. For CUT&Run, two bigwig files, nfr and nuc, were created: nfr using short fragments (<120bp) and nuc using longer fragments (>150bp)


title: Breast Cancer 113 b

type: RNA

city: Brussels

first: Christos

last: Sotiriou

address: Rue Meylemeersch 90

country: Belgium

institute: Institut Jules Bordet – Université Libre de Bruxelles (ULB)

hyb_protocol: RNA extracted from FFPE specimens with Qiagen's miRNeasy FFPE Kit was processed with Affymetrix’s SensationPlus FFPE Amplification and 3'IVT Labeling Kit. The processed RNA was hybridized on the Affymetrix’s Human Genome U219 Array Plate (96 wells) using the GeneTitan instrument.

scan_protocol: The 96 well array plates were scanned using Affymetrix's automated GeneTitan system according to the manufacturer's instructions.

data_processing: The probe level intensities were background adjusted using the Robust multi-array analysis (RMA) method followed by quantile normalization as impletemented in the R/Bioconductor package affy.

label: biotin

source_name: Breast tumor

label_protocol: Biotinylated cRNA was prepared according to Affymetrix's standard protocols.

extract_protocol: RNA was extracted from FFPE specimens using Qiagen's miRNeasy FFPE Kit.

tag: filename

tag: batch

tag: dataset

value: FinHER


title: D1: Mouse_Brain_7M_AD

first: Eun Ji

last: Lee

address: 17dong-304 ho, Seoul national university hospital

department: Nuclear medicine

institute: Seoul National University

data_processing:
Library strategy: Visium spatial transcriptomics
FastQC v0.11.7 to perform quality check on the raw sequences
processed by Space Ranger v1.1.0 (10X genomics)
Aligns using STAR
implemented with spaceranger count
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: HDF5 file containing UMI counts, spatial barcodes, and feature information (*filtered_feature_bc_matrix.h5)
Supplementary_files_format_and_content: Scale factors for high and low resolution images and number of pixels in each spatial spot (*scalefactors_json.json)
Supplementary_files_format_and_content: A table for barcodes names, binary codes for differentiating the location of spots relative to the tissue (1: inside tissue, 0: outside tissue), row and column number of each spot, and row and column pixel coordinates (*tissue_positons_list.csv)
Supplementary_files_format_and_content: Tissue images (*image.png)

source_name: Brain

extract_protocol:
3-month- and 7-month-old male 5XFAD mice and wild type mice were used for spatially resolved transciptomic data. Mice were transcardially perfused using cold saline and the brains were dissected. The brain were embedded in cold OCT separately and cryosectioned to thin (10 μm) coronal sections.
10X genomics; Visium spatial gene expression

value: Brain

tag: genotype

value: transgenic

tag: age

tag: strain


title: C1: Mouse_Brain_7M_WT

value: wild type

value: Littermate


title: CUT&Run ; hPSC; OCT4KD 3D ; IgG ; Lib126

description:
hPSC_d3_OCT4CRISPRi_CnR_IgG.nfr.bw
hPSC_d3_OCT4CRISPRi_CnR_IgG.nuc.bw

extract_protocol:
Chromatin Immunoprecipitation (ChIP):  Cells were crosslinked with 1% formaldehyde in 1x PBS for 10 min at room temperature. The crosslinking reaction was stopped by adding 0.125 M glycine for 5 min at room temperature. Crosslinked cells were centrifuged at 600 xg for 5 min at 4℃, and supernatant was removed. The cell pellet was washed with ice-cold 1x PBS and centrifuge at 600 xg for 5 min at 4℃. Repeat the wash step (total twice). The cell pellet was frozen by dry ice and stored at -80℃.   Crosslinked human cells were resuspended with Lysis Buffer1 (10 mM Tris-HCl [pH. 8.0], 10 mM NaCl, 0.5% NP-40, and 1x Complete Protease Inhibitor EDTA free) and incubated for 10 min on ice. 25% crosslinked Drosophila S2 cells were reconstituted with Lysis Buffer1as a spike-in control and was mixed with the human cells. Cells were centrifuged at 665 xg for 5 min at 4℃, and supernatant was removed. Cell pellet was resuspended with Lysis Buffer2 (50 mM Tris-HCl [pH. 8.0], 10 mM EDTA, 0.32% SDS, 1x Complete Protease Inhibitor EDTA free) and incubated for 10 min on ice. Cell lysate was diluted with IP Dilution Buffer (20 mM Tris-HCl [pH. 8.0], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 1x Complete Protease Inhibitor EDTA free) and transferred into a milliTUBE ATA Fiber (Covaris). Cell lysate was sonicated by Covaris S220 (Covaris) for 3.5 min. The insoluble debris was removed by centrifuge at 12000 xg for 5 min at 4℃. Sonicated chromatin (supernatant) was transferred to a new tube and stored at -80℃.  50 to 86  uL Dynabeads Protein-G beads (10004D, Thermo Fisher Scientific) were washed twice with PBS-T (0.02% Tween-20 in 1x PBS). Desired amounts of antibodies (listed below) were conjugated to washed beads for 2 to 6 hours at 4℃ with rotation. Meanwhile, Frozen chromatin was thawed on ice. Desired amount of chromatin (listed below; determined by DNA amount) was diluted with IP dilution buffer in 4:1 ratio. Antibody conjugated Dynabeads were washed twice with IP Dilution Buffer (without Complete protease inhibitor EDTA free). Washed Dynabeads were resuspend with diluted chromatin and incubated for overnight at 4℃ with rotation. Next day, ChIPed beads were washed four times with following washing buffers: FA Lysis Buffer (50 mM HEPES-KOH [pH. 7.5], 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate, 1x Complete protease inhibitor EDTA free); NaCl Buffer (50 mM HEPES-KOH [pH. 7.5], 500 mM NaCl, 2 mM EDTA, 1% TritonX-100, 0.1% Sodium deoxycholate); LiCl Buffer (100 mM Tris-HCl [pH. 8.0], 500 mM LiCl, 1% NP-40, 1% Sodium deoxycholate); and 10 mM Tris-HCl [pH. 8.0]. Chromatin was eluted with TES (50 mM Tris-HCl [pH. 8.0], 10 mM EDTA, 1% SDS) for 15 min at 65℃ while shaking at 1000 rpm in ThermoMixer F1.5 (Eppendorf). The ChIP and Input chromatin were reverse crosslinked by adding NaCl (Final concentration of 200 mM) for 2 to 8 hours at 65℃. The reverse crosslinked chromatin samples were treated with 50 ng/ul RNaseA (EN0531, ThermoFisher Scientific) for 0.5 to 1 hour at 37℃. Samples were treated with 0.2 mg/ml protease K (03115828001, Roche) for 2 to 4 hours at 37℃. Finally, DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA concentration was measured by Quantus fluorometer (Promega).  CUT&RUN:  20 uL of ConcanabalinA coated beads (BP531, Bangs Laboratories) were washed twice with Binding Buffer (20 mM HEPES-KOH [pH. 7.9], 10 mM KCl, 1 mM CaCl2 and 1mM MnCl2). Dissociated live cells were resuspended with Wash Buffer (20 mM HEPES-NaOH [pH. 7.5], 150 mM NaCl, 0.5 mM Spermidine and 1x Complete Protease Inhibitor EDTA free) and mixed with washed beads. The mixture was rotated for 10-15 min at room temperature. We then resuspend cell-bound beads with 100 ul (for histone mark CUT&RUN) and 50 ul (for TF CUT&RUN) Antibody Buffer (2 mM EDTA in Digitonin Buffer [0.02% Digitonin in Wash Buffer]). Desired amounts of antibodies (listed below) were added to cell-beads suspension and incubate overnight at 4℃ with rotation. Next day, beads were washed twice with Digitonin Buffer. Washed beads were treated with 700 ng/ml pA-MNase in Digitonin Buffer for 1 hour at room temperature with rotation. Beads were washed twice with Digitonin Buffer. Washed beads were resuspended with 100 ul of Digitonin Buffer and place on the cool block (BP361036, Fisher Scientific) for >10 min to cool down to 0℃. We then performed pA-MNase digestion by adding 2 ul of ice-cold 0.1 M CaCl2 and incubating for 30 min on the cool block. To stop pA-MNase reaction, 100 ul of 2x Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin, 0.05 mg/ml RNaseA and 0.05 mg/ml Glycogen) was added. To release CUT&RUN fragment, samples were incubated at 37℃ for 30 min with shaking at 300 rpm in ThermoMixer F1.5 (Eppendorf). The beads were removed by centrifuge at 16000 xg for 5 min at 4℃ and placing on a magnetic stand. Supernatant was transferred and treated with 0.1% SDS and 0.25 mg/ml ProteinaseK for 1 hour at 37℃. Finally, DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA concentration was measured by Quantus fluorometer (Promega).
We prepared multiplexed libraries of ChIP, Input for ChIP, and CUT&RUN samples from two replicate (two independent CRISPRi clones) using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB). The manufacture’s protocol was employed with the following changes. After the adaptor ligation, we performed cleanup by AMPure XP Beads (A63880, Beckman Coulter) or MagBind Magnetic Beads (M1378-01, Omega) without size selection. After the RCR enrichment of adaptor-ligated library, we performed two rounds of size selection by the magnetic beads.

value: Human induced pluripotent stem cells (72.3, male, RRID:CVCL_A1BW)

tag: cell type

value: Pluripotent stem cells

value: OCT4KD 3Day


title: ChIP-seq ; FG; Ctrl ; H2Aub ; Lib468

value: Foregut


title: B1: Mouse_Brain_3M_AD


title: clodronate

value: clodronate


title: CUT&Run ; hPSC; OCT4KD 3D ; IgG ; Lib125


title: A1: Mouse_Brain_3M_WT


title: ChIP-seq ; DE; FOXAKD ; Input ; Lib486

value: Definitive endoderm

value: FOXAKD


title: ChIP-seq ; FG; Ctrl ; H2Aub ; Lib469


title: Allogeneic IL15-enhanced HSC-derived MCAR-engineered NKT (Allo15MCAR-NKT) cell 3

city: Los Angeles

first: Wenbin

last: Guo

address: 610 Charles E. Young Drive, TLSB 5000

institute: UCLA

data_processing:
The raw sequencing data underwent quality check using FastQC software (version 0.11.9), and fastp (version 0.23.2) was used to remove sequencing adapters and low-quality bases
The trimmed reads were mapped to the human reference genome (hg38) along with and annotation file gencode v32 using software STAR (version 2.7.9a)
gene count matrixes were obtained using featureCounts from Subread package (version 2.0.3)
Downstream data analysis was performed using R (version 4.2). For more details, please refer to the manuscipt
Assembly: hg38
Supplementary files format and content: raw_counts.txt: tab-delimited text file includes gene expression raw counts for each sample

growth_protocol: AlloMCAR-NKT, Allo15MCAR-NKT and PBMC-NKT cells were activated in vitro with αGC, and PBMC-αβTc cells were stimulated with CD3/CD28 T-activator beads.

extract_protocol:
RNAs were isolated from each cell sample using a miRNeasy Mini Kit (QIAGEN).
Libraries were constructed using an Illumina TruSeq Stranded Total RNA Sample Prep kit.

treatment_protocol: Cell samples were sorted using a FACSAria II flow cytometer.


title: CUT&Run ; hPSC; Ctrl ; IgG ; Lib29

description:
PFG_IgG_FOXAKD.nfr.bw
PFG_IgG_FOXAKD.nuc.bw


title: CUT&Run ; hPSC; OCT4KD 3D ; H3K27me3 ; Lib132

description:
hPSC_d3_OCT4CRISPRi_CnR_H3K27me3.nfr.bw
hPSC_d3_OCT4CRISPRi_CnR_H3K27me3.nuc.bw


title: ChIP-seq ; DE; FOXAKD ; H2Aub ; Lib475


title: CUT&Run ; hPSC; OCT4KD 3D ; H3K27me3 ; Lib131


title: CUT&Run ; hPSC; Ctrl ; IgG ; Lib28


title: ChIP-seq ; DE; FOXAKD ; H2Aub ; Lib474


title: Allogeneic IL15-enhanced HSC-derived MCAR-engineered NKT (Allo15MCAR-NKT) cell 2


title: Allogeneic IL15-enhanced HSC-derived MCAR-engineered NKT (Allo15MCAR-NKT) cell 4


title: ChIP-seq ; DE; Ctrl ; Input ; Lib485


title: CUT&Run ; FG; Ctrl ; IgG ; Lib50

description:
PFG_IgG_Ctl.nfr.bw
PFG_IgG_Ctl.nuc.bw


title: ChIP-seq ; DE; FOXAKD ; Input ; Lib487


title: Breast Cancer 26 b

description: Biotinylated cRNA was prepared according to Affymetrix's standard protocols


title: Allogeneic IL15-enhanced HSC-derived MCAR-engineered NKT (Allo15MCAR-NKT) cell 1


title: ChIP-seq ; DE; Ctrl ; Input ; Lib484


title: Allogeneic HSC-derived MCAR-engineered NKT (AlloMCAR-NKT) cell 4

source_name: MCAR-iNKT

value: MCAR-iNKT


title: CUT&Run ; FG; Ctrl ; IgG ; Lib48

description:
PFG_IgG_Ctl.nfr.bw
PFG_IgG_Ctl.nuc.bw


title: ChIP-seq ; DE; Ctrl ; H2Aub ; Lib473


title: CUT&Run ; DE; FOXAKD ; IgG ; Lib37

description:
DE_IgG_FOXAKD.nfr.bw
DE_IgG_FOXAKD.nuc.bw


title: ChIP-seq ; DE; Ctrl ; H2Aub ; Lib472


title: Allogeneic HSC-derived MCAR-engineered NKT (AlloMCAR-NKT) cell 2


title: H1299-shJOSD2-rep2

city: Hanhzhou

first: fujing

last: ge

address: No. 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38
Reads Per Kilobase The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated.
StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.


title: CUT&Run ; DE; Ctrl ; IgG ; Lib36

description:
DE_IgG_Ctl.nfr.bw
DE_IgG_Ctl.nuc.bw

data_processing:
CUT&Run:  CUT&RUN Sequencing reads were aligned to the same genome reference as RNA-seq data for consistency using STAR aligner like RNA-seq with options ‘--alignSJDBoverhangMin 999 --alignIntronMax 1 --alignMatesGapMax 2000 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05’. Only uniquely and concordantly aligned read pairs were used for analysis. Read 1 and 2 were connected with each other to form a fragment. Downstream analysis was performed largely as previously described (Skene et al. eLife 2017). For transcription factor (TF) CUT&RUN, fragments with size < 120 bp were selected as originated from putative nucleosome-free regions. For histone modification (histone) CUT&RUN, fragments with size > 150bp were selected as originating from putative nucleosomal regions. Selected fragments were resized to 100bp to normalize bias from the sample-to-sample variabilities of fragment lengths
ChIP-seq: ChIP-seq sequencing reads were aligned to the same genome reference using STAR aligner with options ‘--alignSJDBoverhangMin 999 --alignIntronMax 1 --alignMatesGapMax 2000 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.05’. Redundant fragments were deduplicated using Picard (https://broadinstitute.github.io/picard). BigWig files were generated similarly but without fragment length restriction.
Assembly: hg38 and dm6
Supplementary files format and content: RPM-normalized BigWig files. One representative bigwig files were created for each conditions by taking average of biological replicates. For CUT&Run, two bigwig files, nfr and nuc, were created: nfr using short fragments (<120bp) and nuc using longer fragments (>150bp)
Library strategy: CUT&RUN


title: CUT&Run ; DE; FOXAKD ; IgG ; Lib35


title: Allogeneic HSC-derived MCAR-engineered NKT (AlloMCAR-NKT) cell 1


title: CUT&Run ; DE; Ctrl ; IgG ; Lib34

description:
DE_IgG_Ctl.nfr.bw
DE_IgG_Ctl.nuc.bw


title: H1299-shJOSD2-rep1


title: HepG2 hepatocytes_untreated_rep2

city: Tsukuba

first: Kengo

last: Iwata

state: Ibaraki

address: 1-1-1 Tennodai

department: Alliance for Research on the Mediterranean and North Africa (ARENA)

country: Japan

institute: University of Tsukuba / Nippo., Co., Ltd.

description: Timeline for RNA extraction is the same as for the extract treatment group.

hyb_protocol: Labeled strands were hybridized to probes on Clariom S Human assay chip for 16 hours at 45 °C with constant rotation in GeneChip™ Hybridization Oven 645.

scan_protocol: The hybridized chip was washed and stained on the GeneChip™ Fluidics Station 450, and then scanned on the GeneChip™ Scanner 3000.

data_processing:
CHP files (the gene-level information) was obtained from CEL files (the probe intensity) using robust multichip analysis (RMA) summarization algorithm in Expression Console software. Subsequent data processing was carried out in Transcriptome Analysis Console (TAC) 4.0 software. Two mRNA biological samples of each group were provided for the analysis.
Signal intensities for all samples (average of the duplicates) and comparative data ('STEE30 vs Control' and 'STEE50 vs Control' fold change) generated using TAC software can be found in the additional sheets.

source_name: HepG2 hepatocytes, untreated.

label_protocol: RNAs were reverse transcribed and biotinylated with GeneChip™ WT PLUS Reagent Kit (ThermoFisher Scientific), according to the manufacturer’s instructions.

growth_protocol: Human hepatocellular carcinoma-derived HepG2 cells (ATCC) were maintained in DMEM containing 10% FBS (Gibco) and 1% anti-bacterial penicillin/streptomycin under 5% CO2 at 37°C.

extract_protocol: Total RNAs were isolated from the cells with RNeasy plus mini kit (Qiagen).

treatment_protocol: After the cells reached about 90% confluence, the cells were treated with the extract dissolved in serum-free Opti-MEM (Gibco) for 24 hours.

value: liver

value: hepatocellular carcinoma

value: untreated.


title: HepG2 hepatocytes_30 µg/mL STEE-treated_24 hours_rep2

description: Cells were exposed to serum-free Opti-MEM (Gibco) in which the extracts were dissolved.

source_name: HepG2 hepatocytes, 30 µg/mL STEE-treated, 24 hours.

value: 30 ug/mL STEE-treated, 24 hours.


title: HepG2 hepatocytes_untreated_rep1


title: HepG2 hepatocytes_15 µg/mL STEE-treated_24 hours_rep2

source_name: HepG2 hepatocytes, 15 µg/mL STEE-treated, 24 hours.

value: 15 ug/mL STEE-treated, 24 hours.


title: Allogeneic HSC-derived MCAR-engineered NKT (AlloMCAR-NKT) cell 3


title: Healthy donor PBMC-derived conventional ab T  (PBMC-abTc) cell 7

source_name: T cells

value: T cells


title: H1299-Ctrl-rep2

value: control


title: Healthy donor PBMC-derived conventional ab T  (PBMC-abTc) cell 6


title: H1299-Ctrl-rep1


title: treated Replicate 5

status: Public on Jan 09 2024

city: Madison

first: Thibaut

last: Rosay

state: Wisconsin

department: MMI

institute: UW Madison

description:
Novaseq X plus
10

data_processing:
Demultiplexing, quality control, and adapter trimming were performed with bcl-convert (v4.1.5)
Assembly: NC_013716
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Citrobacter rodentium

growth_protocol: Bacteria were grown 6h in DMEM low glucose in microaerobic conditions

extract_protocol:
Illumina Ribo-Zero Plus rRNA Depletion
Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices

treatment_protocol: treatment with or without 100uM Glucuronic acid

value: Bacteria

value: WT

value: Glucuronic acid 100uM


title: treated Replicate 4

description:
Novaseq X plus
9


title: HepG2 hepatocytes_30 µg/mL STEE-treated_24 hours_rep1


title: B13_3601

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

institute: Hospital del Mar Research Institute

hyb_protocol: Performed according to protocol GeneChip WT PLUS Reagent kit (P/N 703174 2017) and hybridized to Human Clariom S Array (Thermo Fisher Scientific).

scan_protocol: Performed according to protocol GeneChip WT PLUS Reagent kit (P/N 703174 2017).

data_processing: R programming (Version 3.4.3) Bioconductor and the Comprehensive R Archive Network (CRAN 2017) packages were used. Samples were background corrected, quantile-normalized and summarized to a gene-level using the robust multi-chip average (RMA).

label: Biotin

source_name: Breast carcinoma

extract_protocol: Total RNA was isolated according to protocol of RNeasy® Micro Kit (Qiagen).

tag: tumour-infiltrating nk cell status

value: Positive

tag: til score

tag: tumour-infiltrating nk cells

tag: g

tag: t

tag: er status

value: Negative

tag: status

value: DF

tag: cdi

value: CDI


title: treated Replicate 3

description:
Novaseq X plus
8

tag: cell line

tag: treatment


title: HepG2 hepatocytes_15 µg/mL STEE-treated_24 hours_rep1

tag: tissue


title: treated Replicate 2

description:
Novaseq X plus
7


title: treated Replicate 1

description:
Novaseq X plus
6


title: control replicate 5

description:
Novaseq X plus
5


title: control replicate 3

description:
Novaseq X plus
3


title: control replicate 2

description:
Novaseq X plus
2


title: control replicate 4

description:
Novaseq X plus
4


title: control replicate 1

description:
Novaseq X plus
1


title: RNASeq_H1Xsh_+Dox_r3

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

institute: IBMB-CSIC

data_processing:
RNA-Seq reads were mapped to the reference genome (GRCh37/hg19) using HISAT2 v2.2.1 with default parameters and specifying strand-specific information (--rna-strandness RF).
SAMtools v1.11 was used to sort BAM files and filter for properly paired-end reads (-f 2).
Aligned reads were mapped to the Ensembl GRCh37.87 gene annotation with TEtranscripts v2.1.4 (--sortByPos --mode multi --stranded reverse).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw read counts for the Ensembl GRCh37.87 gene annotation (hg19).

growth_protocol: Cells were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

extract_protocol:
Total RNA of T47D-MTVL H1Xsh Untreated or 6-days-Dox-treated cells was extracted with High Pure RNA Isolation kit (Roche)
Strand-Specific Transcriptome Library Construction Protocol (DNBSEQ). According to the manufacturer’s instructions, the first step involves the removal of ribosomal RNA (rRNA) using target-specific oligos and RNase H reagents to deplete both cytoplasmic (5S rRNA, 5.8S rRNA, 18S rRNA, and 28S rRNA) and mitochondrial ribosomal RNA (12S rRNA and 16S rRNA) from total RNA preparations. Following SPRI beads purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. This process removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. After UDG treatment, the incorporation of dUTP quenches the second strand during amplification. The products are enriched with PCR to create the final cDNA library. The libraries’ quality and quantity were assessed in two methods: check the distribution of the fragment size using the Agilent 2100 bioanalyzer and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The qualified libraries were sequenced pair end on the BGISEQ-500/ MGISEQ-2000 System (BGI-Shenzhen, China).

treatment_protocol: Initially, T47D-MTVL cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of H1X shRNA (pLVTHM). The inducible knocked-down cell line was sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Dox treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Dox (Sigma) was added at 2.5 µg/ml when indicated and treated for 6 days.

value: Breast cancer cell line

value: H1X knock-down

value: Treated with Dox (6 days)


title: RNASeq_H1Xsh_Untreated_r3

value: Untreated


title: ChIPSeq_H1.3_T47D_multiH1sh_untreated

data_processing:
Single-end reads were aligned to the human GRCh37/hg19 reference genome using Bowtie2 (v2.3.5.1) with default options.
SAMtools (v1.9) were used to filter out the low-quality alignment using the flag 3844.
Input and H1 variants genome coverage was calculated and normalized by reads per million (genomecov -bga -scale) with BEDTools (v2.28.0).
MACS2 (v2.1.2) was used to calculate input-subtracted ChIP-Seq signal coverage tracks (bdgcmp -m subtract).
Corresponding Input sample is available at GSE156036 (Input sample: GSM4720911)
Assembly: hg19
Supplementary files format and content: bigWig files include input-subtracted ChIP-Seq signal.

growth_protocol: Cells were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin and 100µg/ml streptomycin.

extract_protocol:
T47D-MTVL cells were fixed using 1% formaldehyde, chromatin was extracted and sonicated using a Diagenode Bioruptor to generate fragments between 200 and 500 bp. 30 µg of chromatin was immunoprecipitated overnight using the indicated antibody. Rabbit IgG (Milipore 12-370) was used as a nonspecific control. Input was prepared with 10% of the chromatin material used for an immunoprecipitation. Immunocomplexes were recovered using Protein A magnetic beads from Millipore. Beads with bound antibody/protein/DNA complexes were washed, decross-linked at 65ºC overnight, and immunoprecipitated DNA was recovered using the IPure Kit from Diagenode.
Library construction and sequencing were performed under BGI (Beijing Genomic Institution) ChIP-seq protocols, using combinatorial Probe-Anchor Synthesis (cPAS) and DNA nanoball sequencing.

treatment_protocol: To work with T47D-MTVL cells that carry a shRNA against multiple H1 variants (multiH1sh Sample), a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the multiple H1 variants shRNA (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Doxycycline treatment. The resulting cell line was used to perform a replicate of H1.3 ChIP under Untreated conditions (i.e. no induction of the shRNA, no Dox-induced depletion of any H1). Another replicate was performed in T47D-MTVL WT cell line.

value: Multi-H1sh (shRNA not induced)

tag: chip antibody


title: ChIPSeq_H1.3_T47D_WT


title: ChIPSeq_H1X_SKMEL147

data_processing:
All samples were treated as single-end data to homogenize the processing protocol. Single-end reads were aligned to the human GRCh37/hg19 reference genome using Bowtie2 (v2.3.5.1) with default options.
SAMtools (v1.9) were used to filter out the low-quality alignments using the flag 3844.
Input and H1 variants genome coverage was calculated and normalized by reads per million (genomecov -bga -scale) with BEDTools (v2.28.0).
MACS2 (v2.1.2) was used to calculate input-subtracted ChIP-Seq signal coverage tracks (bdgcmp -m subtract).
Assembly: hg19
Supplementary files format and content: bigWig files include input-subtracted ChIP-Seq signal.

growth_protocol: HeLa, SK-N-SH, HCT-116, and SK-MEL-147 cells were grown in DMEMGlutaMax medium, supplemented with 10% FBS, 100 U/ml penicillin, and 100µg/ml streptomycin. MCF-7 cells were grown in MEM medium containing 10% FBS, 1% penicillin/streptomycin, 1% non-essential aminoacids, 1% sodium pyruvate, and 1% Glutamine

extract_protocol:
Library construction and sequencing were performed under BGI (Beijing Genomic Institution) ChIP-seq protocols, using combinatorial Probe-Anchor Synthesis (cPAS) and DNA nanoball sequencing.
Cells were fixed using 1% formaldehyde, chromatin was extracted and sonicated using a Diagenode Bioruptor to generate fragments between 200 and 500 bp. 30 µg of chromatin was immunoprecipitated overnight using the indicated antibody. Rabbit IgG (Milipore 12-370) was used as a nonspecific control. Input was prepared with 10% of the chromatin material used for an immunoprecipitation. Immunocomplexes were recovered using Protein A magnetic beads from Millipore. Beads with bound antibody/protein/DNA complexes were washed, decross-linked at 65ºC overnight, and immunoprecipitated DNA was recovered using the IPure Kit from Diagenode.
Library construction and sequencing were performed under Illumina or BGI ChIP-Seq protocols, depending on the sample.

treatment_protocol: Some samples (indicated above) were cell-cycle synchronized in G1/S using standard double thymidine block treatment, to homogenize cell population. If not, no treatment was performed.

value: Melanoma cell line

value: anti-H1X (Abcam, ab31972)