title: Liv_2_hi272_CDKI_Mutant

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads where first assessed for quality using FastQC v0.11.5. Trimmomatic v0.36 was used for quality trimming and adapter sequence removal, with the parameters (ILLUMINACLIP: trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36)
The resulting transcripts from the raw counts were used for further downstream analysis
Supplementary files format and content: txt containing raw counts

organism: Danio rerio

source_name: embryo livers

growth_protocol: Zebrafish larvae were kept in 6-well plate at a density of 2 larvae/ per 1 mL embyro medium in a 10:14 light/dark cycle

extract_protocol:
TRIzol/Choloform Extraction
RNA-seq libraries were prepared with Ribo-Zero kit  by the staff in the NYUAD genomics facility and quality controled by Bioanalyzer.

value: ABNYU

value: mutant uhrf1-hi272

value: CDKI

value: embryo livers


title: Liv_4_hi272_CDKI_Mutant

status: Public on Jul 28 2023

type: SRA

department: Biology

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: genotype

tag: treatment

tag: tissue


title: Liv_3_hi272_CDKI_Mutant


title: Liv_5_hi272_CDKI_Mutant


title: Zswim8 KO Placenta sRNA-seq Rep 2

city: Cambridge

first: Charlie

middle: Y.

last: Shi

state: MA

address: 455 Main St.

country: USA

institute: Whitehead Institute / MIT

description:
50 bp reads
P_DESeq2_5cutoff_output.txt

library_source: other

data_processing:
Counting of annotated miRNAs was performed as previously described (Shi et al., 2020) by string-matching the first 19 nt of each read to a dictionary derived from the set of mature miRNA names and sequences downloaded from TargetScan7 Mouse (Agarwal et al., 2015). These dictionaries were primarily generated from the mature miRNA sequences whose first 19 nt were unique, to avoid ambiguities caused by 3′ alterations.
For the 48 annotated miRNAs whose first 19 nt were not unique, all miRNAs sharing a 19-nt prefix were collapsed to create a single dictionary entry with sequence of the 19-nt prefix, and given a name that combined the names of the collapsed miRNAs (e.g., mmu-miR-466j/mmu-miR-466m-5p/mmu-miR-669m-5p). This procedure added an additional 21 entries to the dictionary.
Further analyses were performed on miRNA or passenger-strand species passing the expression threshold of at least five matching reads in each of the four libraries derived from a tissue.
Differential expression and significance levels were determined using DESeq2 v1.26.0 (Love et al., 2014) without use of the lfcShrink() function.
Supplementary files format and content: Tab-separated table of counts of miRNA-matching reads
Supplementary files format and content: Tab-separated table of output from DESeq2 v1.26.0

molecule: other

organism: Mus musculus

source_name: Placenta

extract_protocol:
Total RNA was extracted with TRI Reagent (Invitrogen) according to the manufacturer’s instructions with the following modifications. Tissues from E18.5 embryos were rapidly dissected after euthanasia of pregnant dams (CO2) and flash-frozen using liquid nitrogen. Tissue was transferred to a 50 mL conical tube, 1–2 mL of TRI Reagent was added depending on the tissue volume, and the tissue was homogenized with a TissueRuptor (QIAGEN) and disposable probes. Phase separation was performed by adding 100 μL 1-Bromo-3-chloropropane (Sigma) to 1 mL of homogenate. Aqueous phase was extracted and precipitated with isopropanol, and the pellet was washed twice with 75% ethanol. All RNA was resuspended in RNAse-free water.
Library preparation was performed as previously described (Shi et al., 2020). Briefly –5 mg of total RNA extracted from tissues was used as input. From each total RNA sample, RNAs that co-migrated within the range of 18 and 32 nt radiolabeled internal standards were isolated on a 15% polyacrylamide urea gel. Purified RNA was ligated to a pre-adenylated 3' adaptor using T4 RNA Ligase 2 KQ mutant (NEB) in a reaction supplemented with 10% polyethylene glycol (PEG 8000, NEB). To reduce ligation biases, this 3' adaptor had four random-sequence positions at its 5' end. After gel purification on a 10% polyacrylamide urea gel, RNA was ligated to a 5' adaptor using T4 RNA Ligase I (NEB) in a reaction supplemented with 10% PEG. To reduce ligation biases, this adaptor had four random-sequence positions at its 3' end. After gel purification on a 8% polyacrylamide urea gel, RNA was reverse-transcribed with SuperScript III (Invitrogen), and the cDNA was amplified by 8–12 cycles of PCR using KAPA HiFi HotStart ReadyMix (KAPA Biosystems). Amplified libraries were purified on an 8% polyacrylamide 90% formamide gel. Small RNA-seq data were generated from total RNA isolated from tissues dissected from one E18.5 Zswim8+/– embryo and one Zswim8–/– embryo selected from the same litter. This procedure was repeated with another litter, for n = 2 biological replicates.

value: Placenta

tag: age


title: platelets-ALS-nonmat-6 [06_PLT]

type: other

city: Ulm

first: Karin

last: Danzer

address: Albert-Einstein-Allee 11

country: Germany

institute: DZNE

description: isolation of platelets by differential centrifugation and subsequent clean up of the sample by depletion of CD45 positive cells using magnetic beads (MACS miltenyi)

hyb_protocol: GeneChip® CustomSeq® Resquencing Array Protocol Version 2.1 ; 270ng of fragmented mtDNA were hybridized to GeneChip™ Human Mitochondrial Resequencing Arrays 2.0 (MitoChip v2.0, Zhou et al., 2006 ).

scan_protocol: GeneChip® CustomSeq® Resquencing Array Protocol Version 2.1; The Arrays were washed using Affymetrix fluidics station FS450, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: GSEQ Version 4.1.1

label: biotin

organism: Homo sapiens

source_name: Platelets isolated from fresh EDTA blood of a fALS patient with non-maternal inheritance

extract_protocol: QiaAmp Blood Kit for DNA isolation; REPLI-g mitochondrial DNA kit (Qiagen, Hilden, Germany)  for amplification of mtDNA; Purification using Agencourt® AMPure® XP magnetic beads (QIAGEN Supplementary Protocol, REPLI-g mitochondrial DNA kit)

tag: mat vs non-mat

value: non-maternal

tag: disease state

value: ALS

tag: gender

value: m

tag: mutation

tag: cell type

value: platelets


title: Liv_1_hi272_CDKI_Mutant


title: Zswim8 KO Muscle sRNA-seq Rep 2

description:
50 bp reads
M_DESeq2_5cutoff_output.txt

source_name: Muscle

value: Muscle


title: wholeblood-ALS-mat-5 [05_WB]

description: whole blood was used for DNA isolation

source_name: whole blood (EDTA, frozen) of fALS patient with maternal inheritance

label_protocol: GeneChip® CustomSeq® Resquencing Array Protocol Version 2.1

value: maternal

value: whole blood


title: ChIP-seq Input siRad21 replicate3

city: Bunkyo-ku

first: Ryuichiro

last: Nakato

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

library_source: genomic

data_processing:
Sequenced reads were mapped to the human genome using bowtie2 version 2.4.1 with default parameters.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: BigWig files were generated with the total read normaization and with the spike-in normaization for 100-bp bins by DROMPA+ verision 1.12.1.
Supplementary_files_format_and_content: Peak files (BED) with the spike-in normaization and the total read normalization were generated by DROMPA+ verision 1.12.1.

molecule: genomic DNA

source_name: RPE cells

growth_protocol: RPE cells were routinely cultured in DMEM supplemented with penicilline-streptomycin-L-glutamine solution (Wako) and 10% FBS.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described [Izumi, K. et al. Nat Genet, 2015, doi:10.1038/ng.3229]. In Brief, ~ 8 × 106 human cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by an additional 5 min with glycine in PBS added at a final concentration of 125 mM. Fixed cells were lysed in LB1 (50 mM HEPES-KOH (pH 7.4); 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; 10 mM dithiothreitol; 1 mM PMSF) on ice. The lysate was wash with LB2 (20 mM Tris-HCl (pH 8.0); 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1mM PMSF) and LB3 (20 mM Tris-HCl (pH 7.5); 150 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; 1 × cOmplete protease inhibitor cocktail (Roche)) on ice. The lysate was resuspended in LB3 and sonicated using Branson Sonifier 250D (Branson) for chromatin shearing (12 sec with amplitude setting at 17% of the maximum amplitude, 6 times). In addition, lysate containing fragmented chromatin was also prepared from ~ 2 × 106 C2C12 mouse cells with the same procedures. Human cell lysate and mouse cell lysate (as spike-in internal control) were combined (approximately 4:1 ratio) and incubated with protein A or G Dynabeads (Thermo Fisher Scientific) conjugated with antibodies for 14 h at  4℃. The beads were then washed 5 times with cold RIPA wash buffer (50 mM HEPES-KOH (pH 7.4); 500 mM LiCl, 1 mM EDTA; 0.5% sodium deoxycholate; 1% NP-40) and once with cold TE50 (50 mM Tris-HCl (pH 8.0); 10 mM EDTA). Material captured on the beads was eluted by TE50 containing 1% SDS. The eluted material and input were incubated for 6 h at 65℃ to reverse crosslinks and treated with 100 ng RNaseA (Roche) for 1 h at 37℃, followed by treatment  with 100 ng Proteinase K (Merck) overnight at 50℃. The input and ChIP DNA were then purified by PCR purification kit (Qiagen) following manufacturer's instructions and further sheared to an average size of approximately 150 bp using Covaris S2 focused-ultrasnicator (settings: Duty Cycle, 10%; Intensity, 5; Cycle per Burst, 100; Duration, 300 sec). The sheared DNA was end-repaired, ligated to sequencing adaptors, amplified and size-selected using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and Agencourt AMPure XP (Beckman Coulter) following manufacturer's instructions.
Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).

treatment_protocol: RNAi transfection was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in accordance with the manufacturer's protocol, using final RNA duplex concentration of 50 nM.

value: RPE

tag: type

value: Spike-in (mouse)

tag: control sample

tag: chip antibody

value: none (input)


title: ChIP-seq Input Control replicate5

value: Control


title: ChIP-seq Input siNIPBL replicate4

value: siNIPBL


title: wholeblood-ALS-mat-4 [04_WB]

description: whole blood was used for DNA isolation


title: Zswim8 KO Eye sRNA-seq Rep 2

description:
50 bp reads
E_DESeq2_5cutoff_output.txt

source_name: Eye

value: Eye


title: Zswim8 KO Kidney sRNA-seq Rep 2

description:
50 bp reads
K_DESeq2_5cutoff_output.txt

source_name: Kidney

value: Kidney


title: ChIP-seq H3K27me3 siRad21

value: Input siRad21 rep3


title: Liv_4_hi272_CDKI_Control

value: ABNYU

value: CDKI

value: embryo livers


title: platelets-contr-4 [04_PLT]

source_name: Platelets isolated from fresh EDTA blood of a control person

value: control


title: wholeblood-contr-24 [24_WB]

description: whole blood was used for DNA isolation

source_name: whole blood (EDTA, frozen) of control person

value: m


title: Liv_2_hi272_CDKI_Control


title: Zswim8 KO Liver sRNA-seq Rep 2

description:
50 bp reads
LI_DESeq2_5cutoff_output.txt

source_name: Liver

value: Liver


title: wholeblood-contr-6 [06_WB]

description: whole blood was used for DNA isolation

value: f


title: wholeblood-ALS-mat-3 [03_WB]

description: whole blood was used for DNA isolation

value: maternal

value: ALS


title: ChIP-seq H3K27me3 siNIPBL

value: RPE

value: Input siNIPBL rep4


title: Zswim8 KO Intestine sRNA-seq Rep 2

description:
50 bp reads
I_DESeq2_5cutoff_output.txt

source_name: Intestine

value: Intestine


title: Liv_1_hi272_CDKI_Control

value: Control


title: ChIP-seq H3K27me3 Control

value: Spike-in (mouse)

value: Input Ct rep5


title: wholeblood-ALS-mat-2 [02_WB]

description: whole blood was used for DNA isolation

value: whole blood


title: Liv_4_hi272_DMSO_Mutant

value: mutant uhrf1-hi272

value: DMSO


title: Zswim8 KO Skin sRNA-seq Rep 2

description:
50 bp reads
SK_DESeq2_5cutoff_output.txt

source_name: Skin

value: Skin


title: Liv_5_hi272_DMSO_Mutant

value: ABNYU

value: embryo livers


title: platelets-contr-3 [03_PLT]

value: control

value: m

value: platelets


title: platelets-ALS-mat-2 [02_PLT]

source_name: Platelets isolated from fresh EDTA blood of a fALS patient with maternal inheritance

value: maternal


title: Liv_5_hi272_CDKI_Control

value: CDKI


title: Zswim8 KO Stomach sRNA-seq Rep 2

description:
50 bp reads
ST_DESeq2_5cutoff_output.txt

source_name: Stomach

value: Stomach


title: ChIP-seq Input siNIPBL replicate2

value: RPE

value: siNIPBL

value: none (input)


title: ChIP-seq Input Control replicate3

value: Spike-in (mouse)

value: Control


title: Liv_3_hi272_DMSO_Mutant


title: wholeblood-ALS-nontmat-1 [01_WB]

description: whole blood was used for DNA isolation

source_name: whole blood (EDTA, frozen) of fALS patient with non-maternal inheritance

value: non-maternal

value: ALS

value: f

value: whole blood


title: Liv_2_hi272_DMSO_Mutant

value: ABNYU

value: mutant uhrf1-hi272

value: DMSO


title: Zswim8 KO Heart sRNA-seq Rep 2

description:
50 bp reads
H_DESeq2_5cutoff_output.txt

source_name: Heart

value: Heart


title: Liv_1_hi272_DMSO_Mutant

source_name: embryo livers

value: embryo livers


title: ChIP-seq H3K4me3 siNIPBL

value: Input siNIPBL rep2


title: Zswim8 KO Hindbrain sRNA-seq Rep 2

description:
50 bp reads
HB_DESeq2_5cutoff_output.txt

source_name: Hindbrain

value: Hindbrain


title: Zswim8 KO Lung sRNA-seq Rep 2

description:
50 bp reads
LU_DESeq2_5cutoff_output.txt

source_name: Lung

value: Lung


title: Input from APCMin/+ IKK KO intestinal tumor organoids [INKO]

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

description: No use of DSP crosslink

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads
Reads were aligned to the mm10 genome assembly using Bowtie2 (see materials and methods main paper)
htseq software was used to estimate the raw gene counts
peaks were called using MACS2 with the following setting: ChIP threshold FDR (0.1)
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph and bigWig files are generated from MACS2 peak calling output using bamtools

extract_protocol:
Cells were crosslinked with 0.5% formaldehyde and lysated. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. DNA purification with GFX Kit [GE Healthcare Life Sciences Ref.28-9034-71]
Samples were digested with 0.1% collagenase and single-cell suspension was stained as described. Different subpopulations were directly sorted in a total volume of 10  ml of reaction buffer and processed for obtaining cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.

treatment_protocol: Starting material was directly extracted APCMin/+ intestine tumor organoids

tag: tissue source

value: Intestine

value: tumor organoids

value: APCMin/+ IKKa KO


title: Liv_4_hi272_DMSO_Control


title: ChIP-seq Input siRad21 replicate2

value: RPE

value: Spike-in (mouse)

value: none (input)


title: Zswim8 KO Forebrain sRNA-seq Rep 2

description:
50 bp reads
FB_DESeq2_5cutoff_output.txt

source_name: Forebrain

value: Forebrain


title: ChIP-seq H3K36me3 siRad21

value: Input siRad21 rep2


title: ChIP-seq H3K36me3 siNIPBL

value: siNIPBL


title: BRD4 ChIP-seq from APCMin/+ IKK KO intestinal tumor irradiated organoids [KOIR2]

description: No use of DSP crosslink

value: BRD4, diagenode C15410337


title: BRD4 ChIP-seq from APCMin/+ IKK KO intestinal tumor irradiated organoids [KOIR1]

description: No use of DSP crosslink


title: ChIP-seq H3K36me3 Control

value: Input Ct rep3

value: Control


title: Zswim8 Het Muscle sRNA-seq Rep 2

description:
50 bp reads
M_DESeq2_5cutoff_output.txt

source_name: Muscle

value: Muscle


title: BRD4 ChIP-seq from APCMin/+ IKK WT intestinal tumor irradiated organoids [WTIR2nd]

description: No use of DSP crosslink

value: APCMin/+ IKKa WT


title: ChIP-seq H3K4me3 siRad21

source_name: RPE cells


title: ChIP-seq H3K27ac siRad21


title: Zswim8 Het Eye sRNA-seq Rep 2

description:
50 bp reads
E_DESeq2_5cutoff_output.txt

source_name: Eye

value: Eye


title: Liv_2_hi272_DMSO_Control

value: ABNYU

value: DMSO

value: embryo livers


title: platelets-ALS-nonmat-1 [01_PLT]

source_name: Platelets isolated from fresh EDTA blood of a fALS patient with non-maternal inheritance

value: non-maternal

value: ALS

value: m

value: platelets


title: ChIP-seq H3K27ac siNIPBL

value: RPE

value: Spike-in (mouse)

value: Input siNIPBL rep2


title: BRD4 ChIP-seq from APCMin/+ IKK WT intestinal tumor irradiated organoids [WTIR1]

description: No use of DSP crosslink

value: Intestine

value: tumor organoids


title: ChIP-seq H3K4me3 Control

value: Input Ct rep3


title: Zswim8 Het Kidney sRNA-seq Rep 2

description:
50 bp reads
K_DESeq2_5cutoff_output.txt

source_name: Kidney

value: Kidney


title: Col-0, Ax, Rep2

city: Durham

first: Reza

last: Sohrabi

state: NC

address: FFSC Bldg rm 4305, 124 Science Dr,

institute: Duke University

description:
8_AX_2
Processed_data_Paasch_Sohrabi_2022_RNA_Seq_GP_updated.csv

data_processing:
Raw reads were trimmed for adapter sequence and low-quality reads using Trimmomatic version 0.39.
Leading and trailing low-quality bases were trimmed, and reads less than 36 bp in length were removed (LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36).
Trimmed sequence reads were mapped to Arabidopsis thaliana TAIR 10 reference genome using STAR version 2.7.10ac.
Extraction of read counts mapped to genomics features was done using featureCounts in Rsubread package version 2.8.2.
Assembly: Arabidopsis thaliana TAIR 10
Supplementary files format and content: comma-delimited text file includes read count values from featureCounts for each Sample

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Methods for plant growth are described in Kremer, Sohrabi et al. Nature Protocol, 2021 and Chen et al, Nature, 2020.

extract_protocol:
Leaf samples collected from three biological replicates per treatment were flash frozen in liquid nitrogen and stored in -80C until processing. A biological replicate is defined as a pool of two leaves collected from individual plants in GnotoPots within the same microbox. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to manufacturer's protocol
Stranded sequencing libraries were prepared using the TruSeq Stranded mRNA library preparation kit according to manufacturer's protocol.

treatment_protocol: Methods for plant growth are described in Chen et al, Nature, 2020.

value: Leaf

tag: ecotype

tag: growth system

value: GnotoPot

value: 26-days old

value: Axenic


title: BRD4 ChIP-seq from APCMin/+ IKK KO intestinal tumor organoids [CKO]

description: No use of DSP crosslink

value: APCMin/+ IKKa KO

value: BRD4, diagenode C15410337


title: ChIP-seq H3K27ac Control

value: Control


title: Input from APCMin/+ IKK WT intestinal tumor organoids [INWT]

description: No use of DSP crosslink

value: APCMin/+ IKKa WT


title: Zswim8 Het Liver sRNA-seq Rep 2

source_name: Liver

value: Liver


title: Col-0, Ax, Rep3

description:
9_AX_3
Processed_data_Paasch_Sohrabi_2022_RNA_Seq_GP_updated.csv


title: Liv_3_hi272_DMSO_Control

value: ABNYU

value: DMSO

value: embryo livers


title: Col-0, Ax, Rep1

description:
7_AX_1
Processed_data_Paasch_Sohrabi_2022_RNA_Seq_GP_updated.csv


title: Zswim8 Het Placenta sRNA-seq Rep 2

description:
50 bp reads
P_DESeq2_5cutoff_output.txt

source_name: Placenta

value: Placenta


title: BRD4 ChIP-seq from APCMin/+ IKK WT intestinal tumor organoids [CWT]

description: No use of DSP crosslink

value: Intestine


title: Liv_1_hi272_DMSO_Control


title: Control_24_PBMC

city: La Jolla

first: Miguel

last: Reina-Campos

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

library_source: transcriptomic single cell

data_processing:
cellranger count
Assembly: GrCh38
Supplementary files format and content: cellranger count output

molecule: polyA RNA

source_name: PBMC

growth_protocol: Human Peripheral Blood Mononuclear Cell Isolation Blood was collected in BD Vacutainer CPT tube and centrifuged at 400 x g for 25 minutes. The buffy coat layer was removed, washed, and counted. Cells were resuspended in freezing buffer (10%(v/v) DMSO, 40%(v/v) complete RPMI [RPMI +10%(v/v) fetal bovine serum (FBS) +100 U/mL penicillin/100 μg/mL streptomycin], 50%(v/v) FBS), placed into a freezing container (Mr. Frosty), and stored at -80°C. Cells were recovered, washed, and filtered, and labeled with anti-human CD45. CD45+ immune cells were sorted on a FACSAria2 (BD Biosciences). Human Intestinal Cell Isolation Four intestinal biopsies were obtained with endoscopic biopsy forceps from the rectum or ileum and collected in a conical tube with Hank's buffered saline solution (HBSS). Intestinal biopsies were transferred into freezing buffer (10%(v/v) DMSO, 40%(v/v) complete RPMI, 50%(v/v) FBS) and stored at -80°C. Biopsies were recovered, incubated in HBSS on a shaker, then incubated twice in HBSS + 5 mM dithiothreitol (DTT) with shaking, then washed in HBSS. Intestinal biopsies were mechanically dissociated, then placed into 10 mL of digestion mixture (complete RPMI + 1.5 mg/mL Collagenase type VIII + 50 µg/mL DNase I) on a rocker at 37°C for 20 minutes, filtered and stained with anti-human CD45. CD45+ immune cells were sorted on a FACSAria2 (BD Biosciences).

extract_protocol: Single cell libraries were prepared according to the protocol for 10X Genomics for Single Cell V(D)J + 5' Gene Expression. Approximately 20,000 sorted CD45+ cells were loaded and partitioned into Gel Bead In-Emulsions (GEM). scRNA libraries were sequenced on a HiSeq4000 (Illumina). The B and T cell receptor libraries were amplified according to the manufacturer's protocol and sequenced on a NovaSeqS4 (Illumina).

value: PBMC


title: Zswim8 Het Skin sRNA-seq Rep 2

source_name: Skin

value: Skin


title: Zswim8 Het Stomach sRNA-seq Rep 2

source_name: Stomach

value: Stomach


title: Control_24_Rectum

source_name: Rectum

value: Rectum


title: Control_24_Ileum

source_name: Ileum

value: Ileum


title: Control_23_PBMC


title: Zswim8 Het Intestine sRNA-seq Rep 2

description:
50 bp reads
I_DESeq2_5cutoff_output.txt

source_name: Intestine


title: Zswim8 Het Heart sRNA-seq Rep 2

description:
50 bp reads
H_DESeq2_5cutoff_output.txt

source_name: Heart

value: Heart


title: Zswim8 Het Lung sRNA-seq Rep 2

source_name: Lung

value: Lung


title: Control_23_Rectum


title: Zswim8 Het Hindbrain sRNA-seq Rep 2

source_name: Hindbrain

value: Hindbrain


title: micro midbrain organoid batch3_1

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

data_processing:
Reads were mapped to the mm10 UCSC human genome using the STAR (v2.7.9a).
Mapped reads were quantified and normalized to FPKM values using the Cuffquant and Cuffnorm tools of the Cufflinks (v2.2.1) toolset.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human embryonic stem cell , hESC

growth_protocol: To generate micro midbrain organoids (µMOs), hPSCs were dissociated into single cells using TrypLETM (Gibco), and different numbers of single cell–dissociated hPSCs, 500ESCs were plated on either ultra low–attachment U-bottom 96-well plates (Corning) or 384-well plates (Corning) for the generation of EBs using embryoid body forming medium (EBM). The EBM medium consisted of DMEM/F12 (Corning) supplemented with 20% KSR (Gibco), 1% penicillin/streptomycin (PS) (Gibco), GlutaMAXTM (Gibco), 1% NEAA (Gibco), 55 μM ß-mercaptoethanol (Gibco), 1 μg/ml of heparin (Sigma), 3% fetal bovine serum (FBS) (Seradigm), 4 ng/ml of bFGF (Peprotech), and 100 μM Y-27632 (Calbiochem). At 24 hrs after plating, the medium was changed to brain organoid generation medium (BGM) containing a 1:1 mix of DMEM/F12 (Corning) and Neurobasal Medium (Gibco) supplemented with 100× N2 supplement (Gibco), 50× B27 without vitamin A (Gibco), 1% penicillin/streptomycin (PS) (Gibco), 1% GlutaMAXTM (Gibco), 1% NEAA (Gibco), 55 μM ß-mercaptoethanol (Gibco), and 1 μg/ml of heparin (Sigma). BGM was replaced every other day for up to 9 DIVs. For early neuroectodermal commitment and mesencephalon specification (from DIVs 1 to 3), 2 μM dorsomorphin (Sigma), 2 μM A83-01 (Peprotech), 1 μM IWP2 (Biogems), and 3 μM CHIR99021 were used, as in our previous study [23]. The specification into the mesencephalic floor plate (from DIVs 4 to 7) was induced by treating EBs with 100 ng/ml of FGF8 (Peprotech) and 2 μM SAG (Peprotech) on DIV 4. From DIV 7 onward, growth factor–reduced matrigel (Corning) was added directly into BGM, supplemented with 100 ng/ml of FGF8, 2 μM SAG, 200 ng/ml of laminin (BD science), and 2.5 μg/ml of insulin (Thermo), containing µMOs at a final concentration of 1%. For the maturation of µMOs, brain organoid maturation medium (BMM) was used. BMM consisted of 1:1 mix of DMEM/F12 (Corning) and Neurobasal Medium (Gibco) supplemented with 100× N2 supplement (Gibco), 50× B27 (Gibco), 1% penicillin/streptomycin (PS) (Gibco), 1% GlutaMAXTM (Gibco), 1% NEAA (Gibco), 55 μM ß-mercaptoethanol (Gibco), 1 μg/ml of heparin (Sigma), 10 ng/ml of BDNF (Peprotech), 10 ng/ml of GDNF (Peprotech), 200 μM ascorbic acid (Peprotech), and 125 μM cAMP (Peprotech). Growth factor–reduced matrigel (Corning) was added from DIV 7 to 30.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeqStranded mRNA Sample Preparation Kit following manufacturer's protocols.

tag: group

value: micro midbrain organoid

value: human embryonic stem cell , hESC

value: WT


title: micro midbrain organoid batch2_2


title: micro midbrain organoid batch2_1


title: micro midbrain organoid batch1_2


title: micro midbrain organoid batch3_2


title: hESC2

value: hESC


title: micro midbrain organoid batch1_1


title: Control_22_PBMC


title: Control_22_Rectum


title: Zswim8 KO Placenta sRNA-seq Rep 1

description:
50 bp reads
P_DESeq2_5cutoff_output.txt


title: Zswim8 KO Muscle sRNA-seq Rep 1

description:
50 bp reads
M_DESeq2_5cutoff_output.txt

source_name: Muscle

value: Muscle


title: hESC1


title: Control_22_Ileum


title: HT-29 cells without treatment, control for E. coli treated cells rep3

city: Sydney

first: Li

last: Zhang

state: NSW

address: Botany Street

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description:
Control_Ecoli_biol_rep_3
Raw_counts_for_Ecoli.txt

data_processing:
Quality was checked using FastQC (v 0.11.9) and MultiQC (v 0.8)
Trimmomatic (v 0.40) was used to trim Illumina adapter sequences and filter the raw reads
The quality filtered reads were mapped to the reference human genome GRCh38.p14 using HISAT2 (v 2.1.0)
The Subread package Featurecount (v 2.0.1) was used to generate a set of per-gene read counts for each sample using default options
The count data files were loaded into R and analyzed with DESeq2 (v 1.32.0)
Assembly: Reference human genome GRCh38.p14
Supplementary files format and content: Tab-delimited text files of raw counts

extract_protocol:
Total RNA was extracted using the Isolate II RNA minikit (Bioline)
Libraries were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina) and sequenced on Illumina’s NextSeq 500

tag: cell line

value: intestinal epithelial cells


title: HT-29 cells without treatment, control for E. coli treated cells rep2

description:
Control_Ecoli_biol_rep_2
Raw_counts_for_Ecoli.txt


title: Ly6C- TremL4+ nonclassical monocyte

type: RNA

city: St. Louis

first: Kevin

middle: William

last: O'Connor

state: MO

address: 4925 Children's Place

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: RNA was hybridized on an Affymetrix GeneChip Mouse Gene 1.0 ST per manufacturer's instructions

scan_protocol: Genechips were scanned using Affymetrix Cytoscan

data_processing: Data were analyzed using ArrayStar software version 5 for normalization

source_name: Wild-type bone marrow

label_protocol: Samples were labeled with Nugen Encore Biotin kit per manufacturer's instructions

growth_protocol: Wild-type mice were sacrificed and the indicated cells were isolated via FACS

extract_protocol: RNA was extracted using an RNAqueous-Micro Kit per manufacturer's instructions

treatment_protocol: Cells were immediately microarrayed without any treatment

value: bone marrow

tag: sorting markers

value: Lin- CD115+ Ly6C- TremL4+

tag: genotype

value: wild type

tag: strain


title: Zswim8 KO Eye sRNA-seq Rep 1

description:
50 bp reads
E_DESeq2_5cutoff_output.txt

source_name: Eye

tag: tissue

value: Eye

tag: age


title: Common monocyte progenitor


title: Ly6C+ TremL4- classical monocyte

value: Lin- CD115+ Ly6C+ TremL4-


title: Control_10_PBMC

value: PBMC

tag: treatment


title: Monocyte-dendritic cell progenitor


title: Common dendritic cell progenitor

value: Lin- CD115+ CD117int CD135+


title: Zswim8 Het Forebrain sRNA-seq Rep 2

source_name: Forebrain

value: Forebrain


title: Zswim8 KO Kidney sRNA-seq Rep 1

description:
50 bp reads
K_DESeq2_5cutoff_output.txt

source_name: Kidney

value: Kidney


title: HT-29 cells without treatment, control for E. coli treated cells rep1

description:
Control_Ecoli_biol_rep_1
Raw_counts_for_Ecoli.txt


title: Zswim8 KO Liver sRNA-seq Rep 1

source_name: Liver

value: Liver


title: Control_10_Rectum

value: Rectum


title: HT-29 cells treated with E. coli rep2

description:
Ecoli_Treated_biol_rep_2
Raw_counts_for_Ecoli.txt

value: treated with E. coli


title: Control_9_PBMC


title: HT-29 cells treated with E. coli rep3

description:
Ecoli_Treated_biol_rep_3
Raw_counts_for_Ecoli.txt


title: Liver alcohol-gavage rep5

city: Guangzhou

last: Lin

address: No.1838, Guangzhou Avenue North, Guangzhou, China

country: China

institute: Southern Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
The rRNA mapped sequences were filtered by mapping sequence reads to rRNA Database through Bowtie.The remaining reads were mapped to Ensembl release 92 GRCm38 genome using TopHat2 with parameter
The gene expression level was normalized by using FPKM (Fragments Per Kilobase of transcript per Million  mapped reads) method
Genome_build: Ensembl release 92 GRCm38
Supplementary_files_format_and_content: xls/expression matrix

extract_protocol:
First, the mouse liver was separated for quick freezing in liquid nitrogen until analysis. The trizol method was further used to extract liver RNA, which quality was detected by agarose gel electrophoresis and Agilent 2100 detection.
RNA sequencing of mouse liver tissues was carried out using Illumina Hiseq X10 platform (San Diego, CA, US).

treatment_protocol: For alcohol induction, mice were given 20% edible alcohol (15 µL/g) by gavage daily for 2 weeks, while the control group was treated with normal saline solution.

value: alcohol


title: Liver alcohol-gavage rep4


title: Control_10_Ileum

value: Ileum


title: HT-29 cells without treatment, control for A. veronii treated cells rep3

description:
Control_Averonii_biol_rep_3
Raw_counts_for_Averonii.txt


title: HT-29 cells treated with E. coli rep1

description:
Ecoli_Treated_biol_rep_1
Raw_counts_for_Ecoli.txt


title: Zswim8 KO Skin sRNA-seq Rep 1

value: Skin


title: HT-29 cells without treatment, control for A. veronii treated cells rep2

description:
Control_Averonii_biol_rep_2
Raw_counts_for_Averonii.txt


title: Zswim8 KO Intestine sRNA-seq Rep 1

description:
50 bp reads
I_DESeq2_5cutoff_output.txt

value: Intestine


title: Zswim8 KO Lung sRNA-seq Rep 1

value: Lung


title: Liver alcohol-gavage rep3


title: Zswim8 KO Stomach sRNA-seq Rep 1

value: Stomach


title: Zswim8 KO Heart sRNA-seq Rep 1

description:
50 bp reads
H_DESeq2_5cutoff_output.txt

value: Heart


title: HT-29 cells without treatment, control for A. veronii treated cells rep1

description:
Control_Averonii_biol_rep_1
Raw_counts_for_Averonii.txt

value: intestinal epithelial cells


title: Zswim8 KO Hindbrain sRNA-seq Rep 1

value: Hindbrain


title: Liver alcohol-gavage rep2


title: HT-29 cells treated with A. veronii rep3

description:
Averonii_Treated_biol_rep_3
Raw_counts_for_Averonii.txt

value: treated with A. veronii


title: Liver alcohol-gavage rep1


title: Zswim8 KO Forebrain sRNA-seq Rep 1


title: HT-29 cells treated with A. veronii rep2

description:
Averonii_Treated_biol_rep_2
Raw_counts_for_Averonii.txt


title: Liver saline-gavage rep3

value: water


title: Liver saline-gavage rep2


title: HT-29 cells treated with A. veronii rep1

description:
Averonii_Treated_biol_rep_1
Raw_counts_for_Averonii.txt


title: Zswim8 Het Placenta sRNA-seq Rep 1

description:
50 bp reads
P_DESeq2_5cutoff_output.txt

source_name: Placenta

value: Placenta


title: Liver saline-gavage rep1


title: Zswim8 Het Muscle sRNA-seq Rep 1

description:
50 bp reads
M_DESeq2_5cutoff_output.txt

value: Muscle


title: Zswim8 Het Eye sRNA-seq Rep 1

description:
50 bp reads
E_DESeq2_5cutoff_output.txt

value: Eye


title: H2O2_1

first: Eun Jung

last: Lee

address: 50-1 Yonsei-Ro, Seodaemun-Gu

institute: Yonsei University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: human melanocyte

growth_protocol: Human melanocytes were isolated from human foreskin and cultured in M254 medium with human melanocyte growth supplements, respectively. Cells were maintained at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Primary human epidermal melanocytes were treated with H2O2 (200 μM) and incubated for 24 h

value: Foreskin

value: primary cells

value: treated with H2O2


title: cont_2

value: media only


title: cont_1


title: Control_23_Ileum

value: Ileum


title: Zswim8 Het Liver sRNA-seq Rep 1

description:
50 bp reads
LI_DESeq2_5cutoff_output.txt

value: Liver


title: Zswim8 Het Kidney sRNA-seq Rep 1

description:
50 bp reads
K_DESeq2_5cutoff_output.txt

value: Kidney


title: ChIP-seq H3K27me3 Control replicate2

data_processing:
Sequenced reads were mapped to the human genome using bowtie2 version 2.4.1 with default parameters.
Assembly: UCSC hg38
Supplementary files format and content: BigWig files were generated with the total read normaization and with the spike-in normaization for 100-bp bins by DROMPA+ verision 1.12.1.
Supplementary files format and content: Peak files (BED) with the spike-in normaization and the total read normalization were generated by DROMPA+ verision 1.12.1.

source_name: RPE cells

extract_protocol:
Chromatin preparation for ChIP was performed as previously described (Izumi, K. et al. Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin. Nat Genet 47, 338-344, doi:10.1038/ng.3229 (2015)). In Brief, ~ 8 × 106 human cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by an additional 5 min with glycine in PBS added at a final concentration of 125 mM. Fixed cells were lysed in LB1 (50 mM HEPES-KOH (pH 7.4); 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; 10 mM dithiothreitol; 1 mM PMSF) on ice. The lysate was wash with LB2 (20 mM Tris-HCl (pH 8.0); 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1mM PMSF) and LB3 (20 mM Tris-HCl (pH 7.5); 150 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; 1 × cOmplete protease inhibitor cocktail (Roche)) on ice. The lysate was resuspended in LB3 and sonicated using Branson Sonifier 250D (Branson) for chromatin shearing (12 sec with amplitude setting at 17% of the maximum amplitude, 6 times). In addition, lysate containing fragmented chromatin was also prepared from ~ 2 × 106 C2C12 mouse cells with the same procedures. Human cell lysate and mouse cell lysate (as spike-in internal control) were combined (approximately 4:1 ratio) and incubated with protein A or G Dynabeads (Thermo Fisher Scientific) conjugated with antibodies for 14 h at  4℃. The beads were then washed 5 times with cold RIPA wash buffer (50 mM HEPES-KOH (pH 7.4); 500 mM LiCl, 1 mM EDTA; 0.5% sodium deoxycholate; 1% NP-40) and once with cold TE50 (50 mM Tris-HCl (pH 8.0); 10 mM EDTA). Material captured on the beads was eluted by TE50 containing 1% SDS. The eluted material and input were incubated for 6 h at 65℃ to reverse crosslinks and treated with 100 ng RNaseA (Roche) for 1 h at 50℃, followed by treatment  with 100 ng Proteinase K (Merck) overnight at 50℃. The input and ChIP DNA were then purified by PCR purification kit (Qiagen) following manufacturer's instructions.
DNA from ChIP and input fractions was prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) according to the manufacture's protocol.

value: RPE cells

value: Normal ChIP-seq

tag: control

value: Input Ct rep4

value: Control


title: Zswim8 Het Skin sRNA-seq Rep 1

description:
50 bp reads
SK_DESeq2_5cutoff_output.txt

source_name: Skin

value: Skin


title: ChIP-seq H3K36me3 Control replicate2


title: ChIP-seq Rad21 siNIPBL replicate2

value: Input siNIPBL rep3

value: siNIPBL


title: Zswim8 Het Intestine sRNA-seq Rep 1

description:
50 bp reads
I_DESeq2_5cutoff_output.txt

value: Intestine


title: Zswim8 Het Stomach sRNA-seq Rep 1

description:
50 bp reads
ST_DESeq2_5cutoff_output.txt

source_name: Stomach

value: Stomach


title: ChIP-seq H3K27me3 siNIPBL replicate2


title: ChIP-seq H3K27ac Control replicate2


title: Zswim8 Het Lung sRNA-seq Rep 1

description:
50 bp reads
LU_DESeq2_5cutoff_output.txt

value: Lung


title: Granulosa cells from PMSG 46h +hCG 4h 2

city: Kansas city

first: praveen Chakravarthi

last: Veera raghavulu

state: Kansas

address: 3915 Booth Street, Apt 10

department: Cell Biology and Physiology

institute: University of Kansas Medical Center

data_processing:
Read quality assessed by FastQC software
Cleaned using the cutadapt software
per sequence quality score measured in the Phred quality scale
Circular RNA were obtained using the CIRCexplorer analysis toolset
Assembly: TopHat and TopHat-Fusion was used to map mouse genome GRCm38
Supplementary files format and content: Expression normalization and differential expression calculations were performed using the edgeR software

source_name: GCs from hCG 4h

growth_protocol: Granulosa cells isolated from mouse ovary was used in this study

extract_protocol:
RNA was isolated by Trizol method in the ovarian granulosa cells
Illumina True Seq Total RNA Library Preparation kit was used to prepare RNA seq library
Total transcriptome including mRNA, lnRNA and  circular RNA

treatment_protocol:
21 day old mice were injected with 5IU PMSG and 46 hours after hCG was injected
Ovarian granulosa cells were collected at 46 h after PMSG and 4h after hCG in PMSG primed mice were collected

value: Granulosa cells

value: WT

value: PMSG 46h + 4h hCG


title: H202_2

value: Foreskin

value: primary cells

value: treated with H2O2


title: Granulosa cells from PMSG 46h 3

source_name: GCs from 0h

value: PMSG 46h


title: Zswim8 Het Heart sRNA-seq Rep 1

description:
50 bp reads
H_DESeq2_5cutoff_output.txt

source_name: Heart

value: Heart


title: Granulosa cells from PMSG 46h +hCG 4h 3


title: ChIP-seq H3K27ac siNIPBL replicate2

value: RPE cells

value: Normal ChIP-seq


title: Zswim8 Het Hindbrain sRNA-seq Rep 1

description:
50 bp reads
HB_DESeq2_5cutoff_output.txt

value: Hindbrain


title: ChIP-seq Rad21 Control replicate3

value: Input Ct rep4

value: Control


title: Granulosa cells from PMSG 46h 2


title: ChIP-seq H3K36me3 siNIPBL replicate2

value: Input siNIPBL rep3

value: siNIPBL


title: prp_epidermis [n66]

city: Salt Lake City

first: Robert

last: Judson-Torres

state: Utah

institute: University of Utah

data_processing:
bcl2fastq v2.20.0.422
Trimmomatic-0.36 with standard paired-end options
STAR 2.5.3a
featureCounts 2.0.1
Assembly: GRCh38.89
Supplementary files format and content: bulk RNA-seq counts matrix in comma separated values format

source_name: epidermis

extract_protocol:
Qiagen RNA and purification kit
"Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus” using 100ng of total RNA as input and 14 rounds of amplification

treatment_protocol: Biopsy specimens were placed on sterile saline soaked gauze and placed on ice and tissue processing was done immediately. For epidermal-dermal tissues separations, tissue was rinsed in PBS and submerged in ATC (2.5mL of room temperature sterile 1x PBS with 2.5mL of 3.8% (w/v) Ammonium Thiocyanate) for 45 minutes at room temperature. Forceps were used to manually separate epidermis from dermis, which were then placed in Qiazol and homogenized with RNAse-free pestles for 2-3 minutes, and frozen at -80C.

value: epidermis

tag: subject status

value: responder


title: Granulosa cells from PMSG 46h +hCG 4h 1

value: Granulosa cells


title: mc2-Cont_1

treatment_protocol: Primary human epidermal melanocytes were treated with HMGB1 (1 μg/ml) and incubated for 24 h

tag: cell type

value: media only


title: Zswim8 Het Forebrain sRNA-seq Rep 1

description:
50 bp reads
FB_DESeq2_5cutoff_output.txt

value: Forebrain


title: mc2-HmGB1_1

value: Foreskin

value: treated with HMGB1


title: prp_dermis [n67]

source_name: dermis

value: dermis


title: Zswim8 KO Placenta RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
P_DESeq2_RNA_5cutoff_noX_output.txt

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR v2.7.1a (Dobin et al., 2013) with the parameters ‘‘–runThreadN 24 –outFilterMultimapNmax 1 –outFilterMismatchNoverLmax 0.04 –outFilterIntronMotifs RemoveNoncanonicalUnannotated –outSJfilterReads Unique –outReadsUnmapped Fastx –quantMode GeneCounts –outSAMtype BAM SortedByCoordinate”.
Aligned reads were assigned to genes using annotations from RefSeq (downloaded August 3, 2022) and counted using htseq-count v0.6.1 (Anders et al., 2015). Further analyses were performed on genes passing the expression threshold of at least five counts in each of the four libraries from a tissue.
Counts arising from Xist or Tsix were used to assign sex (one Zswim8+/- embryo was female; the other three embryos were male), and removed before proceeding with analysis.
Differential expression and significance levels were determined using DESeq2 v1.26.0 (Love et al., 2014) without the lfcShrink() function.
Assembly: mm10
Supplementary files format and content: Tab-separated table of output from htseq-count v0.6.1
Supplementary files format and content: Tab-separated table of output from DESeq2 v1.26.0

extract_protocol:
Total RNA was extracted with TRI Reagent (Invitrogen) according to the manufacturer’s instructions with the following modifications. Tissues from E18.5 embryos were rapidly dissected after euthanasia of pregnant dams (CO2) and flash-frozen using liquid nitrogen. Tissue was transferred to a 50 mL conical tube, 1–2 mL of TRI Reagent was added depending on the tissue volume, and the tissue was homogenized with a TissueRuptor (QIAGEN) and disposable probes. Phase separation was performed by adding 100 μL 1-Bromo-3-chloropropane (Sigma) to 1 mL of homogenate. Aqueous phase was extracted and precipitated with isopropanol, and the pellet was washed twice with 75% ethanol. All RNA was resuspended in RNAse-free water.
RNA libraries for RNA-seq were prepared using the KAPA RNA HyperPrep with RiboErase (HMR) kit (KAPA Biosystems) using 1 μg total RNA as input, according to the manufacturer's instructions. Bulk RNA-seq data were generated from total RNA isolated from tissues dissected from one E18.5 Zswim8+/- embryo and one Zswim8-/- embryo selected from the same litter. This procedure was repeated with another litter, for n = 2 biological replicates.

value: Placenta


title: EFZ737636AR

city: New York

first: Assaf

last: Magen

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

data_processing:
To be updated
Supplementary files format and content: CSV file containing VDJ clone information
Library strategy: TCR-seq

source_name: liver tumor biopsy

extract_protocol:
Takara Bio SMARTer Human TCR profiling kit
Libraries for TCR-seq were prepared from 100 ng of total RNA using the SMARTer Human TCR a/b Profiling Kit v.2 (Takara Bio). Eighteen cycles were used for each of the two seminested PCR ampli- fication steps. Sequencing was performed on an Illumina NovaSeq by multiplexed paired-read run with 2 × 251 cycles.
Qiagen RNA & DNA all-prep with clear up

treatment_protocol: Pre-treatment tumor biopsies and post-treatment tumor resections were analyzed used bulk TCR sequencing across patients.

value: liver tumor biopsy

tag: patient id

value: untreated


title: prp_dermis [n64]


title: ChIP-seq H3K4me2 Control

value: RPE

tag: type

value: Normal ChIP-seq

tag: control sample


title: prp_epidermis [n62]


title: ChIP-seq Input Control replicate4

tag: chip antibody

value: none (input)


title: Zswim8 KO Muscle RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
M_DESeq2_RNA_5cutoff_noX_output.txt

source_name: Muscle

value: Muscle


title: ChIP-seq H3K4me2 siNIPBL

value: Input siNIPBL rep3


title: Zswim8 KO Eye RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
E_DESeq2_RNA_5cutoff_noX_output.txt

value: Eye


title: E6_IFN-r1_H3K27ac

city: Vancouver

first: Wilfred

last: Jefferies

state: BC

address: 2260 Oak st

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

data_processing:
We aligned reads to reference genome mm10 with BWA aligner (v0.7.17)
H3k27ac peaks were called with MACS2 v2.1.2 (Zhang et al 2008) with FDR cutoff 0.01 (-f BAMPE). Input samples were used as control background
Genome_build: mm10
Supplementary_files_format_and_content: peak were were in BED format ( chromosome, start, end, peakname)

growth_protocol: 1x10^6 A9 cells were plated onto a 6 well plate in two mL of DMEM media.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Twenty-four hours after seeding, cells were cultured at the optimum concentrations of Curcuphenol 0.00167 umol, or 5.832x10-6 nmol IFN gamma or 1% DMSO vehicle for 48 hours. Cells were harvested using trypsin, and were pelleted at 200g for 5 mins before being resuspended in PBS. Cell viability was determined using Trypan Blue dye (Catalog# 15250061, Gibco) and cell counting slides (Catalog#1450015, Biorad) with Biorad TC20 automated cell counter. Once the viability was above 90%, the cells were quantified and 130K live cells were transferred into a new tube

value: 5.832x10-6 nmol IFN gamma


title: prp_epidermis [n58]

value: epidermis

value: responder


title: Zswim8 KO Kidney RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
K_DESeq2_RNA_5cutoff_noX_output.txt

value: Kidney


title: E7_curc1_H3K27ac

value: Curcuphenol 0.00167 umol


title: ChIP-seq Pol2Ser2 Control

value: Input Ct rep4

value: Control


title: prp_dermis [n60]

value: dermis


title: ChIP-seq Med1 Control


title: E12_curc1_input


title: Zswim8 KO Liver RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
LI_DESeq2_RNA_5cutoff_noX_output.txt

value: Liver


title: prp_dermis [n56]


title: B7_DMSO_control_H3K27ac

value: %1 DMSO


title: Granulosa cells from PMSG 46h 1

value: Granulosa cells

value: WT

value: PMSG 46h


title: prp_epidermis [n54]


title: Zswim8 KO Intestine RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
I_DESeq2_RNA_5cutoff_noX_output.txt

source_name: Intestine

value: Intestine


title: Zswim8 KO Skin RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
SK_DESeq2_RNA_5cutoff_noX_output.txt

value: Skin


title: ChIP-seq Pol2 Control

value: RPE

value: Normal ChIP-seq


title: C4_DMSO_control_input

source_name: DMSOcontrol-input

value: none (input)


title: Zswim8 KO Stomach RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
ST_DESeq2_RNA_5cutoff_noX_output.txt

value: Stomach


title: ChIP-seq Pol2 siNIPBL

value: Input siNIPBL rep3

value: siNIPBL


title: Lung-KO_3

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

institute: RIKEN

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Assembly: mm10
Supplementary files format and content: The detected copy number of RNA moelcules per tube (i.e., 200 cells) for each gene is listed

source_name: Lung

extract_protocol:
RNAs from cell lysate obtained by heat elevation is directly used for the next RT reaction
Libraries were prepared by using molecular barcoding technique. First, for normalization, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 100 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: Two hundred cells were directly isolated from bone marrow or lung by FACS cell sorter

value: Lung

value: CD45 KO x Rag2 KO

value: Lung ILC2


title: prp_epidermis [n50]

value: epidermis

value: responder


title: prp_dermis [n52]

value: dermis


title: Lung-KO_2


title: ChIP-seq AFF4 Control

value: Input Ct rep4

value: Control


title: prp_dermis [n48]


title: Zswim8 KO Lung RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
LU_DESeq2_RNA_5cutoff_noX_output.txt


title: Zswim8 KO Heart RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
H_DESeq2_RNA_5cutoff_noX_output.txt

value: Heart


title: ChIP-seq Input siNIPBL replicate3


title: E11_IFN-r1_input

value: 5.832x10-6 nmol IFN gamma


title: ChIP-seq Input (for Smc3ac)


title: Zswim8 KO Hindbrain RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
HB_DESeq2_RNA_5cutoff_noX_output.txt

source_name: Hindbrain

value: Hindbrain


title: prp_epidermis [n40]


title: ChIP-seq Smc3ac Control

value: RPE

value: Input for Smc3ac


title: prp_epidermis [n42]


title: Zswim8 KO Forebrain RNA-seq Rep 2

description:
50 x 50 bp reads; 2 technical replicates per ilbrary (L001, L002), sequenced on different lanes of the same flow cell.
FB_DESeq2_RNA_5cutoff_noX_output.txt

source_name: Forebrain

value: Forebrain


title: ChIP-seq Pol2Ser2 siNIPBL

value: Normal ChIP-seq


title: Lung-WT_3

value: Rag2 KO


title: prp_dermis [n41]


title: Lung-WT_2


title: ChIP-seq Input JQ1(+)

value: none (input)


title: Lung-WT_1

value: Lung


title: Zswim8 Het Placenta RNA-seq Rep 2

source_name: Placenta

value: Placenta


title: ChIP-seq AFF4 siNIPBL

value: Input siNIPBL rep3

value: siNIPBL


title: ChIP-seq BRD4 JQ1(+)

value: Input JQ1(+)


title: Zswim8 Het Muscle RNA-seq Rep 2

value: Muscle


title: prp_dermis [n38]

value: dermis

value: responder


title: prp_epidermis [n36]

value: epidermis

value: nonresponder


title: Immature-KO_2

source_name: Bone marrow

value: Bone marrow

value: CD45 KO x Rag2 KO

value: Immature ILC2 (ILC2P)


title: ChIP-seq BRD4 JQ1(-)

source_name: RPE cells

value: RPE

value: Input JQ1(-)


title: Immature-KO_3


title: prp_dermis [n34]


title: Zswim8 Het Eye RNA-seq Rep 2

source_name: Eye

value: Eye


title: prp_epidermis [n32]


title: Zswim8 Het Kidney RNA-seq Rep 2

source_name: Kidney

value: Kidney


title: ChIP-seq CTCF siESCO1

value: Spike-in (mouse)

value: input siESCO1

value: CTCF


title: Zswim8 Het Liver RNA-seq Rep 2

source_name: Liver

value: Liver


title: Lung-KO_1

value: Lung

value: Lung ILC2


title: ChIP-seq CTCF Control replicate2

value: Input Ct rep2

value: Control


title: Immature-KO_1


title: Immature-WT_2

value: Rag2 KO


title: prp_dermis [n30]

value: dermis

value: nonresponder


title: ChIP-seq Input siESCO1

value: none (input)


title: Immature-WT_3

value: Bone marrow

value: Immature ILC2 (ILC2P)


title: Zswim8 Het Intestine RNA-seq Rep 2

value: Intestine


title: prp_epidermis [n28]

value: epidermis

value: responder


title: Zswim8 Het Skin RNA-seq Rep 2

source_name: Skin

value: Skin


title: Inmature-WT_1


title: prp_epidermis [n24]


title: ChIP-seq Rad21 siESCO1

value: RPE

value: Spike-in (mouse)

value: input siESCO1


title: Zswim8 Het Stomach RNA-seq Rep 2

source_name: Stomach

value: Stomach


title: Mature-KO_3

value: CD45 KO x Rag2 KO

value: Mature ILC2


title: ChIP-seq Input Control replicate2

value: Control


title: prp_dermis [n26]


title: Zswim8 Het Lung RNA-seq Rep 2

value: Lung


title: Mature-KO_2


title: Mature-KO_1


title: prp_dermis [n22]

value: dermis


title: Zswim8 Het Heart RNA-seq Rep 2

source_name: Heart

value: Heart


title: ChIP-seq Input JQ1(-)

value: Normal ChIP-seq

value: none (input)


title: Zswim8 Het Hindbrain RNA-seq Rep 2

value: Hindbrain


title: Mature-WT_3

value: Bone marrow

value: Rag2 KO


title: prp_epidermis [n20]

source_name: epidermis

value: epidermis

value: responder


title: prp_epidermis [n18]


title: Zswim8 Het Forebrain RNA-seq Rep 2

value: Forebrain


title: ChIP-seq Input siNIPBL replicate1

value: RPE

value: Spike-in (mouse)

value: siNIPBL


title: ChIP-seq Rad21 siNIPBL

value: Input siNIPBL rep1


title: ChIP-seq Rad21 Control replicate2

value: Input Ct rep2


title: Mature-WT_2

value: Mature ILC2


title: Mature-WT_1


title: prp_dermis [n19]

source_name: dermis


title: ChIP-seq Mau2 siNIPBL

value: Mau2 siNIPBL


title: ChIP-seq Input siCTCF

value: siCTCF


title: Zswim8 KO Muscle RNA-seq Rep 1

description:
50 x 50 bp reads
M_DESeq2_RNA_5cutoff_noX_output.txt

source_name: Muscle

value: Muscle


title: prp_epidermis [n16]

value: nonresponder


title: RNA_NPC2_MLL34dCD_MLL2dTAG_rep3

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
The processed file include all sample data of the number of read counts in each gene that were calculated using HTseq (Anders et al., 2015).
Supplementary files format and content: rna_all_samples_read_count2.txt

source_name: E14 mouse neural precursor cell

growth_protocol: Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2

extract_protocol: The libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: For the dTAG treatment, 2uM ofdTAG-13 (Tocris Bioscience) was added from day 1 of NPC differentiation and cells were harvested on day 4.

value: E14 mouse neural precursor cell

value: MLL3/4 dCD+MLL2 dTAG

value: dTAG-13 + RA


title: RNA_NPC2_MLL34dCD_MLL2dTAG_rep2


title: Zswim8 KO Eye RNA-seq Rep 1

last: Shi

institute: Whitehead Institute / MIT

description:
50 x 50 bp reads
E_DESeq2_RNA_5cutoff_noX_output.txt

value: Eye


title: ChIP-seq Rad21 siCTCF

data_processing:
Sequenced reads were mapped to the human genome using bowtie2 version 2.4.1 with default parameters.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: BigWig files were generated with the total read normaization and with the spike-in normaization for 100-bp bins by DROMPA+ verision 1.12.1.
Supplementary_files_format_and_content: Peak files (BED) with the spike-in normaization and the total read normalization were generated by DROMPA+ verision 1.12.1.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described [Izumi, K. et al. Nat Genet, 2015, doi:10.1038/ng.3229]. In Brief, ~ 8 × 106 human cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by an additional 5 min with glycine in PBS added at a final concentration of 125 mM. Fixed cells were lysed in LB1 (50 mM HEPES-KOH (pH 7.4); 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; 10 mM dithiothreitol; 1 mM PMSF) on ice. The lysate was wash with LB2 (20 mM Tris-HCl (pH 8.0); 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1mM PMSF) and LB3 (20 mM Tris-HCl (pH 7.5); 150 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; 1 × cOmplete protease inhibitor cocktail (Roche)) on ice. The lysate was resuspended in LB3 and sonicated using Branson Sonifier 250D (Branson) for chromatin shearing (12 sec with amplitude setting at 17% of the maximum amplitude, 6 times). In addition, lysate containing fragmented chromatin was also prepared from ~ 2 × 106 C2C12 mouse cells with the same procedures. Human cell lysate and mouse cell lysate (as spike-in internal control) were combined (approximately 4:1 ratio) and incubated with protein A or G Dynabeads (Thermo Fisher Scientific) conjugated with antibodies for 14 h at  4℃. The beads were then washed 5 times with cold RIPA wash buffer (50 mM HEPES-KOH (pH 7.4); 500 mM LiCl, 1 mM EDTA; 0.5% sodium deoxycholate; 1% NP-40) and once with cold TE50 (50 mM Tris-HCl (pH 8.0); 10 mM EDTA). Material captured on the beads was eluted by TE50 containing 1% SDS. The eluted material and input were incubated for 6 h at 65℃ to reverse crosslinks and treated with 100 ng RNaseA (Roche) for 1 h at 37℃, followed by treatment  with 100 ng Proteinase K (Merck) overnight at 50℃. The input and ChIP DNA were then purified by PCR purification kit (Qiagen) following manufacturer's instructions and further sheared to an average size of approximately 150 bp using Covaris S2 focused-ultrasnicator (settings: Duty Cycle, 10%; Intensity, 5; Cycle per Burst, 100; Duration, 300 sec). The sheared DNA was end-repaired, ligated to sequencing adaptors, amplified and size-selected using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and Agencourt AMPure XP (Beckman Coulter) following manufacturer's instructions.
Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).

value: Input siCTCF


title: Zswim8 KO Kidney RNA-seq Rep 1

description:
50 x 50 bp reads
K_DESeq2_RNA_5cutoff_noX_output.txt

value: Kidney


title: RNA_NPC2_MLL34dCD_MLL2dTAG_rep1


title: ChIP-seq CTCF siCTCF

value: CTCF


title: prp_epidermis [n14]

value: epidermis


title: prp_dermis [n15]

value: dermis


title: ChIP-seq Input siRad21 replicate1

value: RPE

value: Spike-in (mouse)

value: none (input)


title: Zswim8 KO Liver RNA-seq Rep 1

description:
50 x 50 bp reads
LI_DESeq2_RNA_5cutoff_noX_output.txt

value: Liver


title: RNA_NPC2_WT-MLL2dTAG_rep3

value: MLL2 dTAG


title: prp_dermis [n13]


title: Zswim8 KO Intestine RNA-seq Rep 1

description:
50 x 50 bp reads
I_DESeq2_RNA_5cutoff_noX_output.txt

source_name: Intestine

value: Intestine


title: prp_dermis [n17]

value: responder


title: ChIP-seq Input Control replicate1

value: Control


title: RNA_NPC2_WT-MLL2dTAG_rep1

value: E14 mouse neural precursor cell


title: prp_epidermis [n12]


title: Zswim8 KO Placenta RNA-seq Rep 1

description:
50 x 50 bp reads
P_DESeq2_RNA_5cutoff_noX_output.txt

value: Placenta


title: Zswim8 KO Skin RNA-seq Rep 1

description:
50 x 50 bp reads
SK_DESeq2_RNA_5cutoff_noX_output.txt

value: Skin


title: prp_epidermis [n10]


title: Zswim8 KO Stomach RNA-seq Rep 1

description:
50 x 50 bp reads
ST_DESeq2_RNA_5cutoff_noX_output.txt

value: Stomach


title: RNA_NPC2_MLL34dCD_rep3

value: MLL3/4 dCD

value: dTAG-13 + RA


title: ChIP-seq Rad21 Control replicate1

value: Input Ct rep1


title: prp_dermis [n11]


title: RNA_NPC2_MLL34dCD_rep2


title: Zswim8 KO Lung RNA-seq Rep 1

description:
50 x 50 bp reads
LU_DESeq2_RNA_5cutoff_noX_output.txt

source_name: Lung

value: Lung


title: prp_dermis [n9]

value: dermis


title: ChIP-seq Mau2 Control replicate1

value: RPE

value: Mau


title: ChIP-seq CTCF Control replicate1

value: Spike-in (mouse)

value: CTCF


title: RNA_NPC2_MLL34dCD_rep1


title: Zswim8 KO Heart RNA-seq Rep 1

description:
50 x 50 bp reads
H_DESeq2_RNA_5cutoff_noX_output.txt

value: Heart


title: prp_epidermis [n8]

value: epidermis

value: nonresponder


title: RNA_NPC2_WT_rep3

value: wild type


title: Zswim8 KO Hindbrain RNA-seq Rep 1

description:
50 x 50 bp reads
HB_DESeq2_RNA_5cutoff_noX_output.txt

source_name: Hindbrain

value: Hindbrain


title: prp_epidermis [n6]


title: RNA-seq siMau2 replicate1

data_processing:
BAM-formatted map files were generated using STAR version 2.7.3a with default parameters. "Allsamples.GRCh38.xlsx" is the expression matrix.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: The expression values were estimated by RSEM v1.3.1 with the option "--estimate-rspd --strandedness reverse".

extract_protocol:
Total RNA was isolated using Trizol (Thermo Fisher Scientific) and Nucleospin RNA kit (Macherey-Nagel) following the manufacturer's instructions. Removal of rRNA was performed by using Ribo-Zero Gold rRNA Removal Kit (Illumina.)
Sequencing library preparation by NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions.

value: Mau2 siRNA

tag: treatment time


title: ChIP-seq Rad21 siRad21

value: Input siRad21 rep1


title: prp_dermis [n7]


title: RNA_NPC2_WT-MLL2dTAG_rep2

value: E14 mouse neural precursor cell

value: MLL2 dTAG


title: RNA-seq siMau2 replicate2


title: RNA_NPC2_WT_rep2

value: dTAG-13 + RA


title: RNA-seq siESCO1 replicate2

value: ESCO1 siRNA


title: Zswim8 Het Placenta RNA-seq Rep 1

value: Placenta


title: RNA_NPC2_WT_rep1


title: RNA-seq siESCO1 replicate1


title: Zswim8 KO Forebrain RNA-seq Rep 1

description:
50 x 50 bp reads
FB_DESeq2_RNA_5cutoff_noX_output.txt

source_name: Forebrain

value: Forebrain


title: RNA_ESC2_MLL34dCD_MLL2dTAG_rep3

source_name: E14 mouse embryonic stem cell

value: E14 mouse embryonic stem cell

value: MLL3/4 dCD+MLL2 dTAG


title: Zswim8 Het Muscle RNA-seq Rep 1

value: Muscle


title: prp_dermis [n5]

value: dermis


title: prp_epidermis [n2]


title: RNA-seq JQ1(+) replicate2

value: RPE

value: 1mM JQ1


title: RNA_ESC2_MLL34dCD_MLL2dTAG_rep2


title: prp_epidermis [n4]

value: epidermis

value: nonresponder


title: RNA_ESC2_MLL34dCD_MLL2dTAG_rep1


title: RNA-seq JQ1(+) replicate1


title: Zswim8 Het Kidney RNA-seq Rep 1

value: Kidney


title: Zswim8 Het Liver RNA-seq Rep 1

value: Liver


title: RNA-seq Control3 replicate2

value: mock


title: RNA_ESC2_WT-MLL2dTAG_rep3


title: prp_dermis [n3]


title: prp_dermis [n1]


title: Zswim8 Het Eye RNA-seq Rep 1

value: Eye


title: RNA_ESC2_WT-MLL2dTAG_rep1

value: MLL2 dTAG


title: ctrl_epidermis [n129]

value: ctrl


title: ctrl_dermis [n130]


title: RNA-seq siPDS5B replicate2

value: PDS5B siRNA


title: RNA-seq siPDS5B replicate1


title: RNA_ESC2_MLL34dCD_rep3

value: MLL3/4 dCD


title: ctrl_epidermis [n125]


title: Zswim8 Het Stomach RNA-seq Rep 1

value: Stomach


title: Zswim8 Het Skin RNA-seq Rep 1

value: Skin


title: RNA-seq siPDS5A siPDS5B double replicate2

value: PDS5A siRNA & PDS5B siRNA


title: Zswim8 Het Lung RNA-seq Rep 1

value: Lung


title: RNA_ESC2_MLL34dCD_rep2

value: E14 mouse embryonic stem cell


title: ctrl_dermis [n126]

value: dermis


title: Zswim8 Het Intestine RNA-seq Rep 1

value: Intestine


title: RNA-seq siPDS5A siPDS5B double replicate1

value: RPE


title: ctrl_epidermis [n107]

value: epidermis


title: Zswim8 Het Heart RNA-seq Rep 1

value: Heart


title: RNA_ESC2_MLL34dCD_rep1


title: RNA-seq Control3 replicate1


title: RNA-seq siPDS5A replicate1

value: PDS5A siRNA


title: RNA_ESC2_WT_rep2

value: wild type


title: Zswim8 Het Forebrain RNA-seq Rep 1

value: Forebrain


title: RNA_ESC2_WT-MLL2dTAG_rep2

value: MLL2 dTAG


title: RNA_ESC2_WT_rep3


title: RNA-seq siRad21 siNIPBL double replicate2

value: Rad21siRNA & NIPBL siRNA#1


title: WT_MG_L1_rep2

city: Bethesda

first: Hye Kyung

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
Raw fastq files were quality trimmed using TrimGalore (version 0.6.7). Reads were aligned to the mouse genome (mm10) using Bismark71 (version 0.23.0). Mapped BAM files were sorted by query name, deduplicated using Picard (version 2.27.3) and finally sorted coordinates using Samtools (version 1.17). Integrative Genomics Viewer63 (version 2.3.98) was used for visualization.
Assembly: mm10
Supplementary files format and content: bismark.cov.bedGraph

source_name: Mammary gland

growth_protocol: Mouse mammary gland and liver tissues were harvested at day one of lactation.

extract_protocol:
200ng of purified genomic DNA was used to create bisulfite sequencing libraries via the large DNA insert approach using the NEBNext® Enzymatic Methyl-seq Kit (New England Biolabs). In short, purified genomic DNA was fragmented, adenylated, and ligated to EM-seq adaptors. Bisulfite conversion was performed according to the manufacturer’s instructions. Internal unmethylated lambda DNA and CpG methylated pUC19 DNA controls were included with each library. Libraries were sequenced with a NovaSeq 6000 instrument (Illumina) to generate a minimum of 300 million paired-end 151 base reads per library.
Libraries for sequencing were prepared using standard New England Biolabs protocols.

value: Mammary gland

tag: developmental stage

value: Lactation day 1

value: wild-type


title: ctrl_epidermis [n105]

value: ctrl


title: ctrl_dermis [n108]


title: WT_MG_L1_rep1


title: RNA-seq siPDS5A replicate2

institute: The University of Tokyo

source_name: RPE cells


title: ctrl_epidermis [n131]


title: ctrl_dermis [n132]


title: RNA-seq siRad21 siNIPBL double replicate1


title: WT_Liver_rep2

value: Liver


title: RNA_ESC2_WT_rep1


title: WT_Liver_rep1


title: ctrl_dermis [n128]


title: ctrl_epidermis [n127]


title: Zswim8 Het Hindbrain RNA-seq Rep 1

first: Charlie

address: 455 Main St.

value: Hindbrain


title: RNA-seq siWAPL replicate2

value: WAPL siRNA


title: RNA-seq Control2 replicate2

value: mock


title: ctrl_epidermis [n103]


title: RNA-seq siNIPBL si8 replicate2

value: NIPBL siRNA#2


title: RNA-seq Control2 replicate1

value: RPE


title: sorted (GFP+CD45-) MC38 tumor cells, ctrl-treated, biol rep 3

city: Brno

first: Lucia

last: Knopfova

address: Kamenice 5

department: Department of Experimental Biology

country: Czech Republic

institute: Faculty of Science, Masaryk University

data_processing:
Using cutadapt version 1.18, the reads of the sequencing run were scanned for adapter contaminations, continuous polyA sequences and continuous polyG sequences at the 3’ end.
The reads of the samples prior to and after adapter trimming were analyzed with FastQC version v0.11.7
The alignment was performed with the splice-aware aligner STAR version 2.6.1
The alignments were quantified based on the annotations of Ensembl GRCm38 and the spike-in specific annotations of Lexogen with the FeatureCounts software program version 1.6.4 of the subread analysis package
A differential gene expression analysis was conducted using DESeq2 version v1.18.1
Assembly: The reads were aligned to the spike-in complemented Ensembl release 101 of the Mus musculus high coverage assembly GRCm38 from the Genome Reference Consortium.
Supplementary files format and content: de_summary: the output of the differential gene expression module of DESeq2, raw read counts were normalized by the median-of-ratio, formatted as a matrix table, saved as a plain tab-delimited text file  method

source_name: tumor

extract_protocol:
RNA was extracted from sorted tumor cells (GFP+CD45-) using RNeasy Plus Mini Kit (Qiagen).
Libraries were prepared according to the manufacturer’s instructions using QuantSeq 3' mRNA-Seq FWD Library Prep Kit

value: tumor


title: sorted (GFP+CD45-) MC38 tumor cells, ctrl-treated, biol rep 2


title: sorted (GFP+CD45-) MC38 tumor cells, ctrl-treated, biol rep 1


title: sorted (GFP+CD45-) MC38 tumor cells, DOX-treated, biol rep 3

value: DOX


title: ctrl_dermis [n104]

value: dermis


title: sorted (GFP+CD45-) MC38 tumor cells, DOX-treated, biol rep 4


title: ctrl_dermis [n106]


title: sorted (GFP+CD45-) MC38 tumor cells, DOX-treated, biol rep 2


title: WT_Liver_rep3


title: ctrl_epidermis [n115]

value: epidermis


title: RNA-seq siWAPL replicate1

first: Ryuichiro

last: Nakato

address: 1-1-1 Yayoi


title: Liver alcohol-gavage Stat3flox/flox;Alb-Cre rep2

address: No.1838, Guangzhou Avenue North

data_processing:
Basecalls performed using CASAVA version 1.8
The rRNA mapped sequences were filtered by mapping sequence reads to rRNA Database through Bowtie.The remaining reads were mapped to Ensembl release 92 GRCm38 genome using TopHat2 with parameter
The gene expression level was normalized by using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method
Assembly: Ensembl release 92 GRCm38
Supplementary files format and content: xls/expression matrix

extract_protocol:
The mouse liver was separated for quick freezing in liquid nitrogen until analysis. The trizol method was further used to extract liver RNA, which quality was detected by agarose gel electrophoresis and Agilent 2100 detection.
RNA sequencing of mouse liver tissues was carried out using Illumina Hiseq X10 platform (San Diego, CA, US).

treatment_protocol: For alcohol induction, the Stat3flox/flox;Alb-Cre and Stat3flox/flox mice were given 20% edible alcohol (15 µL/g) by gavage daily for 2 weeks.

value: alcohol


title: Liver alcohol-gavage Stat3flox/flox;Alb-Cre rep4


title: RNA-seq siNIPBL 72h replicate2

value: NIPBL siRNA#1


title: sorted (GFP+CD45-) MC38 tumor cells, ctrl-treated, biol rep 4


title: Liver alcohol-gavage Stat3flox/flox;Alb-Cre rep1


title: RNA-seq siNIPBL 72h replicate1


title: Liver alcohol-gavage Stat3flox/flox rep4


title: Trim33KO2_Myc_rep2

city: Tübingen

first: Nikita

last: Popov

address: Otfried-Müller-Str 14

department: Clinical Tumor Biology

institute: University Hospital Tübingen

description:
Norm_counts_vr1_12.txt
Myc_Trim33KO2_Trim33WT.txt

data_processing:
Sequencing was performed on the Illumina NextSeq 500 instrument
Basecalling and demultiplexing of the sequencing reads was performed with standard Illumina NExtseq500 software.
Reads were aligned to mouse genome (mm19) with STAR (2.5.4) and differentially expressed genes were determined using EdgeR (3.26.8).
Assembly: mm9
Supplementary files format and content: Tab-delimited text files (EdgeR output) include differential expression (log2FC) and average logCPM values for Trim33-KO vs Trim33-Ctrl  or Myc vs Ctrl samples.

source_name: liver

growth_protocol: p19Nras cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Pen-Strep in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRIzol reagent (Sigma). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's protocol.

value: liver

value: HCC


title: Liver alcohol-gavage Stat3flox/flox;Alb-Cre rep3

source_name: Liver


title: RNA-seq siNIPBL 48h replicate2


title: sorted (GFP+CD45-) MC38 tumor cells, DOX-treated, biol rep 1


title: RNA-seq siNIPBL si8 replicate1


title: Trim33KO1_Myc_rep2

description:
Norm_counts_vr1_12.txt
Myc_Trim33KO1_Trim33WT.txt


title: RNA-seq siNIPBL 48h replicate1


title: Liver alcohol-gavage Stat3flox/flox rep1


title: RNA-seq siRad21 48h replicate2

value: Rad21 siRNA


title: Trim33KO2_Myc_rep1


title: Liver alcohol-gavage Stat3flox/flox rep2


title: RNA-seq siRad21 48h replicate1


title: Liver alcohol-gavage Stat3flox/flox rep3


title: Trim33KO1_Myc_rep1


title: ctrl_epidermis [n101]


title: ctrl_dermis [n114]


title: ctrl_dermis [n102]


title: ctrl_epidermis [n113]


title: Trim33WT_Myc_rep2

description:
Norm_counts_vr1_12.txt
Trim33WT_Myc_Ctrl.txt


title: ctrl_epidermis [n117]


title: T cell_Cd47DT_2

city: Kobe

first: Yasuyuki

last: Saito

state: Hyogo

address: 7-5-1, Kusunoki-cho, Chuo-ku

department: Biochemistry and Molecular Biology, Division of Molecular and Cellular Signaling

institute: Kobe University Graduate School of Medicine

data_processing:
RNA-seq reads were aligned to the mouse reference genome (GRCm38) with the STAR aligner.
Raw read counts were obtained with RSEM and were normalized for further analysis with the use of the built-in normalization algorithms of DESeq2.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Spleen

extract_protocol: RNA was harvested using RNeasy mini kit (Qiagen). RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA LT Sample Prep Kit (Illumina) following manufacture's protocols.

value: Spleen

value: T cells


title: RNA-seq Control1 replicate2

city: Bunkyo-ku


title: ctrl_dermis [n118]

value: ctrl


title: Trim33WT_Myc_rep1


title: ctrl_dermis [n116]


title: RNA-seq Control1 replicate1


title: ctrl_epidermis [n111]


title: T cell_Cd47ff_2


title: Trim33KO2_Ctrl_rep2

description:
Norm_counts_vr1_12.txt
Trim33KO2_Trim33WT.txt


title: RNA-seq siCTCF replicate2

value: CTCF siRNA#1


title: Trim33KO2_Ctrl_rep1


title: ctrl_dermis [n112]


title: T cell_Cd47ff_1


title: RNA-seq siCTCF replicate1


title: ctrl_epidermis [n99]


title: Trim33KO1_Ctrl_rep2

description:
Norm_counts_vr1_12.txt
Trim33KO1_Trim33WT.txt


title: Trim33KO1_Ctrl_rep1


title: ctrl_dermis [n100]


title: cMoP_op9-dll1_rep2

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.  Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.7.9a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms, MSigDb, and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term.  The R/Bioconductor package heatmap3 was used to display heatmaps across groups of samples for each GO or MSigDb term with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05.  Perturbed KEGG pathways where the observed log 2 fold-changes of genes within the term were significantly perturbed in a single-direction versus background or in any direction compared to other genes within a given term with p-values less than or equal to 0.05 were rendered as annotated KEGG graphs with the R/Bioconductor package Pathview.
To find the most critical genes, the Limma voomWithQualityWeights transformed log 2 counts-per-million expression data was then analyzed via weighted gene correlation network analysis with the R/Bioconductor package WGCNA.  Briefly, all genes were correlated across each other by Pearson correlations and clustered by expression similarity into unsigned modules using a power threshold empirically determined from the data.  An eigengene was then created for each de novo cluster and its expression profile was then correlated across all coefficients of the model matrix.  Because these clusters of genes were created by expression profile rather than known functional similarity, the clustered modules were given the names of random colors where grey is the only module that has any pre-existing definition of containing genes that do not cluster well with others. These de-novo clustered genes were then tested for functional enrichment of known GO terms with hypergeometric tests available in the R/Bioconductor package clusterProfiler.  Significant terms with Benjamini-Hochberg adjusted p-values less than 0.05 were then collapsed by similarity into clusterProfiler category network plots to display the most significant terms for each module of hub genes in order to interpolate the function of each significant module.  The information for all clustered genes for each module were then combined with their respective statistical significance results from Limma to determine whether or not those features were also found to be significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: Tab-delimited text

source_name: bone marrow

growth_protocol: Ly6C+ monocytes or cMoPs were obtained from wild-type mice

extract_protocol:
RNA was isolated using a NucleoSpin RNA XS kit (Macherey-Nagel) per manufacturer's protocol.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Sorted Ly6C+ monocytes or cMoPs were cocultured with either OP9 or OP9-DLL1 cells as indicated for 6 hours.

value: bone marrow

value: common monocyte progenitor

value: wild type

value: 6 hours coculture with dll1-expressing op9 stromal cells


title: cMoP_op9-dll1_rep1


title: RNA-seq siRad21 replicate1

value: RPE


title: RNA-seq siRad21 replicate2


title: cMoP_op9_rep2

value: 6 hours coculture with op9 stromal cells


title: Trim33WT_Ctrl_rep2


title: cMoP_op9_rep1


title: Trim33WT_Ctrl_rep1

description:
Norm_counts_vr1_12.txt
Trim33KO1_Trim33WT.txt
Trim33WT_Myc_Ctrl.txt


title: ctrl_epidermis [n109]


title: HepG2 cells_rep1-240 min after insulin stimulation

city: Cambridge

first: Charalampos

last: Lazaris

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

data_processing:
RNA-seq reads were processed using nf-core RNA-seq pipeline v1.4.2 (single-end with strandedness set to reverse). Low-quality reads were trimmed using Trim Galore! v0.6.4. Alignment was performed using STAR v2.6.1d. Transcript quantification was perform using featureCounts v1.6.4. StringTie was used to calculate FPKM.
ChIP-seq reads were processed using the nf-core ChIP-seq pipeline v1.2.1. Trim Galore! v0.6.4_dev was used to trim low-quality reads. Alignment was performed against the hg19 genome assembly using BWA v0.7.17-r1188. Peak calling was performed using MACS2 v2.2.7.1 and peak annotation using Homer.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files either contain gene expression values or raw count values for the RNA-seq data. For ChIP-seq data, we provide .bigwig files for genome brower visualization. ChIP-seq peaks were called with MACS2 and annotated with Homer

source_name: HepG2 cell line

growth_protocol: EMEM 10% FBS

extract_protocol:
DNA extraction
NEBNext UltraTM II kit
75-bp single-end reads

treatment_protocol: EMEM for 16hrs, EMEM BSA and 3nM insulin for 5min

value: liver hepatocellular carcinoma


title: T cell_Cd47DT_1


title: Ly6C+mono_op9-dll1_rep2

value: Ly6C+ classical monocyte


title: microglia and myeloid cells multiplexed scRNA-seq rep2, HTO

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

description:
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
Sequencing data from each lane was processed separately and then aggregated using the Cell Ranger software package (v3.0.2), to generate matrices of UMI counts for RNA and hashtags across all cells in the experiment.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: In barcodes.tsv.gz, barcode-1 and barcode-2 correspond to samples "control microglia scRNA-seq rep1" and "control microglia scRNA-seq rep2", respectively.

molecule: protein

source_name: WTC11 iPSC-derived Microglia

growth_protocol: We used PBMCs isolated from TRIMA residuals obtained from Vitalant. The donor is healthy, and scRNA-seq has been approved by the provider and UCSF Institutional Review Board. To prepare monocyte derived dendritic cells (MoDCs) and macrophages (MDMs), we first thawed PBMCs and isolated monocytes using EasySep Human Monocyte Isolation Kit (STEMCELL Catalog# 19359) as instructed in the manufacturer’s protocol. 2x10^6 cells were seeded into 6 well plate in 4 mL complete RPMI 1640 medium (RPMI 1640, 10% FBS, 1% P/S, 1% Glutamax) containing appropriate cytokines for dendritic cells (GM-CSF: 100 ng/mL; IL-4: 100 ng/mL) and macrophage (GM-CSF: 100 ng/mL) and incubated for 5 days. On the day of IFNβ stimulation, fresh monocytes were prepared using the same procedure and resuspended in fresh complete RPMI1640 medium.

extract_protocol:
Multiplexed single-cell sequencing with cell hashing was performed following previously published protocol (30567574). In brief, each type of cells were first blocked with Human TruStain FcX (BioLegend Catalog# 422302) in cell staining buffer (BioLegend Catalog# 420201) for 10 minutes on ice, followed by staining with an individual TotalSeq-A anti-human Hashtag for 45 minutes on ice. Cells were washed three times, resuspended in PBS with 0.04% bovine serum albumin, and counted with Countess II Automated Cell Counter (Thermo Fisher Scientific). 1.25 x 10^5 cells were pooled from each group to create a pool of 1x10^6 cells with an average viability of 85%. Pooled cells were then filtered through a 40 μm filter, counted, and diluted to a final concentration of 730 cells/μL.
Single cell suspension containing 6.4x105 cells were loaded into 10X Chromium Controller following manufacturer’s user guide (Document CG000185 Rev B) using 2 lanes of Chromium Single Cell 3’ Reagent Kits v3. Single cell gene expression and hashtag barcode libraries were constructed following the manufacturer’s user guide (Document CG000185 Rev B). Final libraries were sequenced on Illumina NovaSeq 6000 sequencer using NovaSeq 6000 S4 Reagent Kit v1 to get a total of 2x109 reads.

treatment_protocol: We treated iPSC derived microglia, MoDCs, MDMs, and monocytes with IFNβ (100U/mL) for 6 hours before proceeding with scRNA-seq.

value: WTC11 iPSC derived microglia, monocyte derived dendritic cells, monocyte derived macrophages, and fresh monocytes

value: without or with treatment of IFNb


title: HepG2 cells_rep2-240 min after insulin stimulation


title: Trim33KO_E2f4

data_processing:
Basecalling and demultiplexing of the sequencing reads was performed with standard Illumina Nextseq500 software.
Reads were aligned to mouse genome (mm9) with STAR (2.5.4) and tag directories were generated using Homer (version 4.10.3)
Bedgraph files were generated using Homer makeUCSCfile script
ChIP-seq tag coverage was calculated using Homer annotatePeaks script
Assembly: mm9
Supplementary files format and content: Bedgraph

extract_protocol:
Cells were fixed with 1% formaldehyde for 5 min and quenched for 5 min with glycine. Cells were washed and resuspended in ChIP lysis buffer 1 (25 mM Tris-HCl pH 8.0, 1 % TritonX100 / 200 mM NaCl / protease & phosphatase inhibitors) and incubated 30 min on ice. Pelleted nuclei were resuspended in ChIP lysis buffer 2 (25 mM Tris-HCl pH 8.0, 1% Triton X-100, 300 mM NaCl, 0.1% SDS) and fragmented using Hilescher UP200st sonifier. Cleared lysates were incubated with E2f4 antibody overnight at 4°C on a rotating wheel. Antibodies were collected using magnetic protein A beads followed by proteinase K treatment and reversal of crosslinking. The DNA was purified by phenol/chloroform extraction and precipitated with ethanol.
Sequencing libraries were prepared using NEB Ultra II DNA library Prep kit according to the manufacturer’s instructions.

value: liver


title: Ly6C+mono_op9-dll1_rep1

address: 4925 Children's Place

institute: Washington University in St. Louis


title: HepG2 cells_rep2-30 min after insulin stimulation


title: HepG2 cells_rep1-30 min after insulin stimulation


title: HepG2 cells_rep2-10 min after insulin stimulation


title: Ly6C+mono_op9_rep2


title: microglia and myeloid cells multiplexed scRNA-seq rep2, GEX


title: microglia and myeloid cells multiplexed scRNA-seq rep1, HTO


title: Ly6C+mono_op9_rep1


title: Trim33KO_input

value: HCC


title: Trim33WT_E2f4

value: sgCtrl


title: Trim33WT_input


title: HepG2 cells_rep1-10 min after insulin stimulation


title: microglia and myeloid cells multiplexed scRNA-seq rep1, GEX


title: Hi-C siWAPL

data_processing:
Sequenced paired-end 150-bp reads were mapped to the human genome hg38 using Juicer version 1.5.7 (BWA 0.7.12-r1039) with default parameters.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: The hic files were generated by juicertools version 1.9.9 with default parameters. We used "inter_30.hic" in which low-quality reads were filtered.

extract_protocol:
Hi-C experiments were performed using MboI restriction enzyme as previously described (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014)).  Briefly, RPE cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Cells were permeabilized and chromatin was digested with MboI restriction enzyme, and the ends of restriction fragments were labeled with biotinylated nucleotides and ligated.  After crosslink reversal, DNA was purified and sheared with Covaris M220 (Covaris).  Then point ligation junctions were pulled down with streptavidin beads.
Sequencing libraries were constructed using Nextera Mate Pair Sample Preparation Kit (Illumina) according to the manufacturer’s protocol with 15 PCR cycles.

treatment_protocol: RNAi transfection was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in accordance with the manufacturer's protocol, using final RNA duplex concentration of 50 nM.

tag: enzyme

value: MboI

value: WAPL siRNA

tag: time point


title: Trim33KO_HU_rel

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20). Adapters were trimmed with Skewer (version 0.2.2).
Reads were aligned to mouse genome (mm9) with STAR (version 2.5.4) and tag directories were generated using Homer (version 4.10.3)
Bedgraph files were generated using Homer makeUCSCfile script
Sequencing tag coverage was calculated using Homer annotatePeaks script
Assembly: mm9
Supplementary files format and content: Bedgraph

extract_protocol:
The assay was performed as described previously (Lensing et al, 2016) with modifications. Cells were fixed with formaldehyde and permeabilized with 0.2% Triton X-100 in PBS. DNA end repair reaction was performed by incubation with E.Coli DNA Polymerase I Klenow fragment for 30 minutes at 25C. Cells were washed and A-tailing reaction was performed in dA-tailing buffer (NEB) with Klenow exo- for 30 minutes at 37C. dA-tailed DNA fragments were ligated to a biotinylated NEB adapter at 16C overnight. Cells were lysed in 20mM Tris pH8.5, 300mM NaCl, 0.2%SDS and treated with proteinase K, followed by sonication, phenol-chloroform extraction and ethanol purification of DNA. Biotinylated DNA fragments were captured on Streptavidin beads and used for library preparation with NEB Ultra II DNA library end prep kit.
Sequencing libraries were prepared using NEB Ultra II DNA library Prep kit according to the manufacturer’s instructions.
DSB capture and sequencing

treatment_protocol: Hydroxyurea at 1mM for 24 hours with or without subsequent release for 24 hours

tag: cell line

value: HU, release in fresh medium


title: microglia CRISPRi-hypr-seq screen rep2

description:
targeted single cell RNA-seq library
probes_hyprseq.tsv

data_processing:
Filter reads with fastp
Extract cell barcodes with UMI-Tools
Map reads to custom index with Bowtie
Convert to bam files with SAMTools
Generate count tables with UMI-Tools
Assembly: hg19
Supplementary files format and content: count tables (cells by probes or cells by genes) for all cells that passed QC
Library strategy: HyPR-seq

molecule: cytoplasmic RNA

extract_protocol:
The HyPRseq experiment was performed according to the published protocol (33376219). Briefly, cells were fixed in 4% formaldehyde solution and permeabilized in 70% ice cold ethanol. 4 pairs of ssDNA probes for each target gene were designed using HyPR-seq pipeline (https://github.com/EngreitzLab/hypr-seq). All probes were pooled at 20nM and incubated overnight at 37. After hybridization cells were washed and sequentially incubated with B1H1 hairpin (HCR tech), readout oligo, T4 ligase at 37°C for one hour individually. Following ligation, cells were resuspended in PBST and filtered through a 20 μm pluriStrainer. Single cell suspension was checked under microscope and counted for droplet generation.
To generate emulsions we first combined 1× EvaGreen Supermix (Bio-Rad Cat #186- 4033), 500 nM indexing primer, 2,000 cells and 20,000 barcoded beads (Chemgenes, as described above) in a 20 μLreaction. Once the PCR mix is made, emulsions were generated using QX200 Digital Droplet Generator (Bio-Rad #1864002) as per manufacturer’s instructions. After the droplets were generated, emulsions were gently transferred into PCR tubes and placed on ice and under the UV lamp (6.5 J/cm2 at 365 nm) about 3-8 cm away from the bulb for 5 mins. After UV exposure, the following cycling conditions were used for droplet PCR amplification: denaturation: 94°C for 30 sec; cycling: 25 cycles of 94°C for 5 sec, 64°C for 30 sec, and 72°C for 30 sec; final extension: 72°C for 5 mins. All PCR cycling steps were performed with 50% ramp rate (2 °C/min).To break down emulsions, PCR product were combined and half volume of 97% 1H,1H,2H,2H-Perfluoro-1-octanol (Sigma-Aldrich #370533) was added. Then tubes were vortexed for 5 sec and spun at 1000 g for 1 min. The top aqueous layer was carefully removed and cleaned with 1.8X SPRI beads according to manufacturer’s instructions. The amplicon libraries were sequenced with customer primers in deep sequencing. For each replicate we loaded ~50k cells in the emulsion generation step and ~15k cells could be packaged into droplets according to the Poisson distribution. We sequenced ~5000 reads/cell covering 18 target genes and 28 gRNA barcode sequences.

value: WTC11 iPSC-derived Microglia


title: HepG2 cells_rep2-5 min after insulin stimulation


title: ctrl_dermis [n110]

data_processing:
bcl2fastq v2.20.0.422
Trimmomatic-0.36 with standard paired-end options
STAR 2.5.3a
featureCounts 2.0.1
Assembly: GRCh38.89
Supplementary files format and content: bulk RNA-seq counts matrix in comma separated values format

source_name: dermis

extract_protocol:
Qiagen RNA and purification kit
"Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus” using 100ng of total RNA as input and 14 rounds of amplification

value: dermis

value: ctrl


title: Trim33WT_HU_rel

tag: genotype


title: HepG2 cells_rep1-5 min after insulin stimulation