title: ALS1_3WM

city: Nishinomiya

first: Kazuki

last: Yoshizumi

state: Hyogo

department: neurology

country: Japan

institute: Hyogo medical university

data_processing:
Reads were mapped using HISAT2
Alternative splicing events were quantified using rMATs, and values are showed percent spliced in (PSI)
Assembly: GRCh38
Supplementary files format and content: excel file
Supplementary files format and content: Using rMATs, inclusion, exclusion, and percent spliced in values are shown in an Excel table for the exons of genes that met the criteria. The following criteria were used: a false discovery ratio of ≤ 0.05, inclusion and exclusion reads ≥ 20, P value < 0.01 using a likelihood-ratio test, and an average level of PSI ≥ 0.2.

source_name: frontal whitematter

extract_protocol: Frozen  tissues were sectioned into 60-μm thick sections using a Leica CM1520 Cryostat. RNA was isolated using RNeasy Plus Mini.

treatment_protocol: Autopsy tissue was frozen at -80C until RNA was extracted

value: frontal whitematter

tag: disease

value: ALS


title: ALS1_3GM

status: Public on Oct 25 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: frontal graymatter

tag: tissue

value: frontal graymatter


title: ALS1_2WM


title: WT_MI rep1

city: Beijing

first: Yan

last: Liu

address: 2 Anzhen Road, Chaoyang District

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University

data_processing:
Raw reads are filtered into clean reads. Filtering steps are as follows: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose  sequencing quality  is no more than 5).
Bowtie2 was used to map clean reads to reference gene and BWA was used to reference genome.
FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes
Assembly: mm9
Supplementary files format and content: Tab-delimited text files includes FPKM values for each sample

organism: Mus musculus

source_name: Heart

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were generated using Illumina's TruSeq RNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturer’s protocols. Briefly, mRNA is enriched by using the oligo (dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The products were then purified and amplified using PCR.

value: Heart

tag: Sex

value: male

tag: age

tag: genotype

value: WT

tag: treatment

value: MI


title: ALS1_2GM


title: WT_MI rep2


title: WT_Sham rep2

value: Sham


title: KO_MI rep1

value: Card9 KO


title: BM_Michigan

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

country: USA

institute: NIAMS/NIH

data_processing:
Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of  were mapped to the mouse genome mm9 using TopHat 2.0.8.  FPKM was calculated using Cufflinks 2.1.1
Intron-less bigWig files were generated using USCS genome browser’s program bedGraphToBigWig, from bedGraph files made with the BEDtools package (Quinlan and Hall, Bioinformatics:26(6):841-2, 2010).
Assembly: mm9
Supplementary files format and content: bw files
Supplementary files format and content: Excel file containing FPKM values

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: ex vivo cells

extract_protocol:
RNA-seq was performed as described previously with slight modification (Hirahara et al., Immunity 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol following manufacture’s protocol (Thermo Fisher Scientific Inc).
Total RNA was subsequently processed to mRNA-seq library using TruSeq SR mRNA sample prep kit (FC-122-1001, Illumina). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: no treatment

value: Bone marrow

tag: cell line

value: primary cells

tag: cell type

value: Lineage negative bone marrow cells

value: {delta}CARD NOD1


title: ALS1_1WM


title: ALS1_1GM


title: wildtype heart tissue, biological replicate 2

type: RNA

city: Baltimore

first: Daniela

last: Cihakova M.D. Ph.D. D(ABMLI)

address: 720 Rutland Avenue

department: Pathology-Immunopathology

institute: The Johns Hopkins University School of Medicine

description: wildtype

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using the Affymetrix GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing: Affymetrix CEL files were extracted with the Partek GS 6.6 platform and their data RMA and quantile-normalized to create log2 transcript signal values, which were summarized by Partek from exon to genes and used in subsequent ANOVA analysis.    Transcript annotation was subsequently updated.

label: biotin

source_name: wildtype heart tissue

label_protocol: The Affymetrix Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: mouse left ventricular heart tissue dissected from 10-15 weeks old mice without perfusion

extract_protocol: Tissue was frozen at -80C. RNA was isolated with Trizol.

treatment_protocol: not applicable

value: 10.9 weeks

value: heart, left ventricle

value: wildtype


title: DM1_2WM

value: myotonic dystrophy type 1


title: DM1_2GM


title: Cyto_Fraction_Arsenite_2

city: Cleveland

first: Soon Yeul

last: Yi

state: OH

address: CWRU Wood Research Building W127A, 2109 Adelbert Rd,

department: Biochemistry

institute: Case Western Reserve University

data_processing:
*library strategy: CLIP-seq
Raw fastq files were first treated with fastX collapser to remove duplicated reads. Then, using CTK stripBarcode.pl the 7nt unique molecular identifier sequence at the 5'end was removed. Next, fastX trimmer and clipper was used to remove the barcode, spacer (GGG), and L32 sequence. Processed reads were then mapped to GRCh38.p14 genome using Bowtie2 (seed length 15nt, allow no mismatch). Mapped output (.sam) files were further processed using samtools (view, sort, index) and bedtools (bamtobed). Lastly, PCR duplicates were collapsed using CTK tag2collapse.pl.
Processed final bed files from each library were all combined into a single bed file and HOMER program was used to call peaks using makeTagDirectory and findPeaks (options: -o auto -style factor -L 2 -localSize 10000 -strand separate -minDist 50 -size 20 -fragLength 25). Finally, read counts per peak were normalized by the respective mapped depth of each library to generate the final normalized peak matrix.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file containing peak coordinates, mapped-depth normalized read counts per peaks per libraries, peak annotation, and replicate counts.

molecule: cytoplasmic RNA

growth_protocol: Huh-7.5 cell lines were grown and maintained at 37 °C and 5% CO2 in DMEM supplemented with 0.1 mM nonessential amino acids and 5% FBS.

extract_protocol:
Cell pellets were lysed with PBS lysis buffer (1x PBS, 0.1% SDS, 0.5% NaDoc, 0.5% NP-40, 1 protease inhibitor tablet (Roche)) for 10 minutes on ice. Lysate was then treated with RQ1 DNase (Promega) for 5 minutes at 37'C with shaking at 1100RPM.  The lysates were then briefly treated with RNase I at 1:100 or 1:5000 dilutions at the same condition as DNase treatment. Lysates were clarified by centrifuging on tabletop 4'C centrifuge for 10 minutes. HuR IP was performed overnight at 4'C with nutation, with an additional streptavidin capture step for coCLIP samples. Immunoprecipitated samples were labeled with radioactivity (gamma-32P-ATP (Revity)) and ran on SDS-PAGE. The gels were transferred to a nitrocellulose membrane, and bands 10-30kDa above the HuR (37kDa) were excised. The excised membranes were treated with proteinase K (Roche) to release the protein-bound RNAs from the membrane.
CLIP footprints were reverse-transcribed using the BrdU incorporation and bead-capture strategy described previously (PMID: 24613350).

treatment_protocol:
Cellular stress was induced by treating cells with 0.5mM sodium arsenite for 45 minutes. At 30 minutes prior to harvest, cells were prepared for proximity labeling  by incubating samples with 0.5mM biotin phenol for 30 minutes. Subsequently, the APEX reaction was initiated with 1mM hydrogen peroxide for 1 minute. After labeling, the reaction was stopped using ice cold quencher solution (10mM sodium ascorbate, 5mM Trolox in PBS). Quencher solution was replaced by ice-cold PBS for crosslinking using 254nm UV light, on ice, for a dose of 400mJ/cm^2 and a dose of 200mJ/cm^2. Samples were scraped into tubes, centrifuged and cell pellets stored at -80C until use.
Cellular fractions were acquired using a fractionation protocol described previously (PMID:26240403).

value: Hepatocellular Carcinoma

value: Sodium Arsenite

tag: apex-reaction

value: No

tag: hur antibody

value: HuR 3A2 (Santa Cruz, cat. #sc-5261)


title: DM1_3GM

value: frontal graymatter


title: DM1_1GM


title: DM1_1WM

value: frontal whitematter


title: ddblGATA1 IL-5 transgenic heart tissue, biological replicate 3

description: ddblGATA1 IL-5 transgenic (NJ.1638)

source_name: ddblGATA1 IL-5 transgenic heart tissue

value: 9.4 weeks

value: male

value: ddblGATA1 IL-5 transgenic (NJ.1638)


title: HEK293, pcDNA3.1_V5-TWIST1(TAL1ins), input

city: Stanford

first: Seungsoo

last: Kim

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

library_source: genomic

data_processing:
Reads were trimmed of Truseq adapter sequences and low-quality bases (-Q 10) using skewer v0.2.2.
Trimmed reads were mapped to the hg38 analysis set (human), mm39 (mouse), or a combined reference genome using Bowtie2 v2.4.1 with the options --very-sensitive -X 2000.
Reads were deduplicated with samtools v1.10 markdup and uniquely mapped reads (-q 20) mapped to the main chromosomes (excluding mitochondria and unplaced contigs) were retained using samtools view.
MACS2 v2.2.7.1 was used to call peaks using the IgG sample as a negative control, with options -f BAMPE --nomodel --keep-dup all --call-summits -g hs (human) or mm (mouse) with the -B option for H3K27ac.
bigWig tracks were generated with deeptools v3.5.0 bamCoverage -bs 10 --normalizeUsing RPGC --samFlagInclude 64 --samFlagExclude 8 --extendReads with 1h dTAG samples normalized by the fraction of reads mapping to the E. coli genome.
H3K27ac ChIP reads were counted over merged ATAC peaks using deeptools v3.5.0 multiBamSummary with options -e --outRawCounts.
Assembly: hg38 or mm39
Supplementary files format and content: bigWig, narrowPeak (except for input samples, H3K27ac ChIPs, and V5 ChIPs of dTAG-treated samples) for each sample, and tab-delimited text (.txt) files with read counts of H3K27ac ChIPs over merged ATAC peaks

molecule: genomic DNA

growth_protocol: H9 cells (WiCell, WA09, RRID:CVCL_9773) were cultured in feeder-free conditions, in mTeSR1 medium (Stem Cell Technologies, 85850) on Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix (Corning, 356231) and passaged using ReLeSR (Stem Cell Technologies, 05872) every 4-6 days. Cells were switched to mTeSR Plus medium (Stem Cell Technologies, 100-0276) prior to and during genome editing and clonal expansion, but switched back to mTeSR1 before differentiation to CNCC. hESCs were differentiated to CNCC as previously described. Briefly, hESC colonies were partially detached from the plate with collagenase IV (Gibco, 17104019) in Knockout DMEM medium (Gibco, 10829018) for 30-60 min and scraped to break up large colonies, and then cultured in Neural Crest Differentiation Medium (50%-50% v/v mixture of DMEM/F12 1:1 medium with L-glutamine, without HEPES (Cytiva, SH30271.FS) and Neurobasal medium (Gibco, 21103049) with 0.5x N2 NeuroPlex (Gemini Bio, 400-163) and Gem21 NeuroPlex (Gemini Bio, 400-160) supplements and GlutaMAX (Gibco, 35050061), and 1x antibiotic/antimycotic, and 20 ng/ml EGF (Peprotech, AF-100-15), 20 ng/ml bFGF (Peprotech, 100-18B), and 5 ug/ml bovine insulin (Gemini Bio, 700-112P)) for 11 days in bacterial-grade petri dishes, changing the plate to prevent attachment for 4 days and then leaving the cells unfed for two days to allow attachment, and then fed as needed at least every other day. At day 11, cells (now called ‘early hCNCC’) were harvested by treatment with Accutase (Sigma-Aldrich, A6964-100ML), strained to remove residual neuroectodermal spheres, and plated onto plates coated with 7.5 ug/ml human fibronectin (Millipore, FC010-10MG) and cultured in Neural Crest Maintenance Medium (Neural Crest Differentiation Medium with bovine insulin replaced by 1 mg/ml BSA (Gemini Bio, 700-104P)). These hCNCC were then passaged every 2-3 days upon reaching confluency, with cells in the third or subsequent passages defined as ‘late hCNCC’ and cultured with added 50 pg/ml BMP2 (Peprotech, 120-02) and 3 uM CHIR-99021 (Selleck, S2924). dTAGV-1 (Tocris, 6914/5) was dissolved in DMSO at 5 mM and then diluted to 250 uM in 60% DMSO/40% water (v/v) before dilution to 500 nM for acute depletions (up to 1 day) or diluted directly from the 5 mM stock for long-term depletions. RS4;11 cells (ATCC, CRL-1873, RRID:CVCL_0093) were cultured in RPMI-1640 medium (Gibco, 11875093) supplemented with 10% v/v FBS and 1x antibiotic/antimycotic. HEK293 cells (ATCC, CRL-1573, RRID:CVCL_0045) and 293FT cells (Invitrogen, R70007, RRID:CVCL_6911) were cultured in DMEM high glucose medium with sodium pyruvate and L-glutamine, supplemented with 10% v/v FBS and 1x GlutaMAX, non-essential amino acids, and antibiotic/antimycotic. O9-1 cells (Millipore, SCC049, RRID:CVCL_GS42) used for spike-in controls for ChIPs of TWIST1 depletions were cultured in Complete ES Cell Medium with 15% FBS (Millipore, ES-101-B), 25 ng/ml bFGF, and mLIF (Millipore, ESG1107).

extract_protocol:
Cells (about 1 confluent 10-cm plate or ~10-20 million cells) were crosslinked with 1% methanol-free formaldehyde (Pierce, 28908) in PBS for 10 min at room temperature and then quenched by adding 2.5 M glycine to 125 mM final concentration and incubating for 10 min. Cells were washed in PBS with 0.001% v/v Triton X-100, harvested by scraping, and collected by centrifugation for 5 min at 4°C. Cells were washed with PBS and flash frozen for storage at -80°C. Cell pellets were later thawed on ice for 30 min, and then sequentially resuspended in lysis buffer 1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Igepal CA-630, 0.25% Triton X-100, 1x cOmplete EDTA-free protease inhibitor cocktail (PIC), 1 mM PMSF), lysis buffer 2 (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x cOmplete EDTA-free protease inhibitor cocktail, 1 mM PMSF), and lysis buffer 3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 1x PIC, 1 mM PMSF), with 10 min incubations in each buffer, with rotation. Lysates were sonicated for 10-15 cycles of 30s ON/30s OFF on high power using the Bioruptor Plus (Diagenode), then diluted in additional lysis buffer 3 and clarified by centrifugation for 10 min at max speed at 4°C. Triton X-100 was added to 1%, and a small aliquot was used to extract DNA to check chromatin yield and size distribution, by dilution in elution buffer (1% w/v SDS and 100 mM NaHCO3) and incubation with 200 mM NaCl and RNase A (Thermo, EN0531) at 65°C for 1 h, then proteinase K (Thermo, EO0491) at 65°C for 1 h, and clean up with the ChIP DNA Clean & Concentrator-5 kit (Zymo, D5205). DNA was quantified by Qubit dsDNA high sensitivity kit, and the remaining chromatin was then normalized for immunoprecipitations. For TWIST1 acute depletions, chromatin from O9-1 mouse CNCCs were added prior to ChIP at ~10% of the total chromatin as a spike-in control. For H3K27ac, 5 ug of antibody was used per ChIP; for TFs, 9 ug of antibody was used per ChIP, except for dissected mouse embryos where 4.5 ug was used in half of the total ChIP volume. ChIPs were incubated overnight, then incubated for 4-6h with 100 ul Dynabeads Protein A (Invitrogen, 10002D) or Protein G (Invitrogen, 10004D) prewashed with 0.1% w/v BSA in PBS, then washed 5x with RIPA wash buffer (50 mM HEPES-KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% Igepal CA-630, 0.7% w/v sodium deoxycholate), once with 50 mM Tris-HCl pH 8, 10 mM EDTA, 50 mM NaCl, and eluted in elution buffer at 65°C for 30 min. Eluate was then reverse crosslinked and treated with RNase A and proteinase K, and then DNA was extracted with the ChIP DNA Clean & Concentrator-5 kit.
Libraries were prepared using the NEBNext Ultra II DNA kit (New England Biolabs, E7645S) using up to 50 ng of input or ChIP DNA, with ~4-8 cycles of amplification, with no pre-PCR size selection but a post-PCR double-sided 0.5x/0.9x Ampure XP bead clean-up.

treatment_protocol: DMSO or dTAGV-1 (500 nM) were added by dilution into media before changing media. HEK293 cells were transfected with Lipofectamine 2000 (Invitrogen, 11668019) at a ratio of 2.8 ul lipofectamine per ug of DNA, diluted in Opti-MEM. Cells were transfected with 2.5 ug DNA per well of a 6-well plate or 15 ug DNA per 10-cm plate 1-2 days after seeding, when they reached 70-90% confluency. Media was replaced 4-6h after transfection, and then cells were harvested for Western blot or chromatin immunoprecipitation at 24 h after transfection.

value: Human embryonic kidney

value: WT

tag: time

tag: antibody

tag: reference genome_for_alignment

tag: reference genome_for_processed_files


title: HEK293, pcDNA3.1_V5-TWIST1(L138Y) and pcDNA3.1_ALX4-Flag, input

value: transfection with pcDNA3.1_V5-TWIST1(L138Y) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(L138Y), input


title: HEK293, pcDNA3.1_V5-TWIST1(WT) and pcDNA3.1_ALX4-Flag, input, r3

value: transfection with pcDNA3.1_V5-TWIST1(WT) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(HAND2ins) and pcDNA3.1_ALX4-Flag, V5

value: transfection with pcDNA3.1_V5-TWIST1(HAND2ins) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(WT), V5, r3


title: HEK293, pcDNA3.1_V5-TWIST1(HAND2ins) and pcDNA3.1_ALX4-Flag, input


title: CD4_Millenium

source_name: Spleen and Lymph nodes

value: Spleen and Lymph nodes

value: primary cells

value: CD4 T


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1ins), input


title: HEK293, pcDNA3.1_V5-TWIST1(WT) and pcDNA3.1_ALX4-Flag, V5, r3


title: HEK293, pcDNA3.1_V5-TWIST1(WT), input, r3


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROG2ins), V5


title: HEK293, pcDNA3.1_V5-TWIST1(TAL1ins), V5


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROG2ins) and pcDNA3.1_ALX4-Flag, input

value: transfection with pcDNA3.1_V5-TWIST1(NEUROG2ins) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(L138Y) and pcDNA3.1_ALX4-Flag, V5


title: HEK293, pcDNA3.1_V5-TWIST1(TAL1ins) and pcDNA3.1_ALX4-Flag, V5

value: transfection with pcDNA3.1_V5-TWIST1(TAL1ins) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(L138Y), V5


title: HEK293, pcDNA3.1_V5-TWIST1(TAL1ins) and pcDNA3.1_ALX4-Flag, input


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROG2ins) and pcDNA3.1_ALX4-Flag, V5


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1ins) and pcDNA3.1_ALX4-Flag, input

value: transfection with pcDNA3.1_V5-TWIST1(NEUROD1ins) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(L138F), input


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1ins) and pcDNA3.1_ALX4-Flag, V5


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1ins), V5


title: HEK293, pcDNA3.1_V5-TWIST1(HAND2ins), input


title: HEK293, pcDNA3.1_V5-TWIST1(L138F) and pcDNA3.1_ALX4-Flag, input

value: transfection with pcDNA3.1_V5-TWIST1(L138F) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(L138F), V5


title: DM1_3WM

value: myotonic dystrophy type 1


title: HEK293, pcDNA3.1_V5-TWIST1(L138F) and pcDNA3.1_ALX4-Flag, V5


title: HEK293, pcDNA3.1_V5-TWIST1(WT) and pcDNA3.1_ALX4-Flag, V5, r2


title: HEK293, pcDNA3.1_V5-TWIST1(TAL1loop), input


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1M) and pcDNA3.1_ALX4-Flag, V5

value: transfection with pcDNA3.1_V5-TWIST1(NEUROD1M) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1R) and pcDNA3.1_ALX4-Flag, V5

value: transfection with pcDNA3.1_V5-TWIST1(NEUROD1R) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1R), V5


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1R), input


title: HEK293, pcDNA3.1_V5-TWIST1(TAL1loop) and pcDNA3.1_ALX4-Flag, input

value: transfection with pcDNA3.1_V5-TWIST1(TAL1loop) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(WT), input, r2


title: HEK293, pcDNA3.1_V5-TWIST1(WT) and pcDNA3.1_ALX4-Flag, input, r2


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1R) and pcDNA3.1_ALX4-Flag, input


title: HEK293, pcDNA3.1_V5-TWIST1(HAND2ins), V5


title: HEK293, pcDNA3.1_V5-TWIST1(TAL1loop), V5


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROG2ins), input


title: HEK293, pcDNA3.1_V5-TWIST1(TAL1loop) and pcDNA3.1_ALX4-Flag, V5


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROG2loop), input


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROG2loop), V5


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROG2loop) and pcDNA3.1_ALX4-Flag, input

value: transfection with pcDNA3.1_V5-TWIST1(NEUROG2loop) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1M) and pcDNA3.1_ALX4-Flag, input

value: Human embryonic kidney


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1M), input

value: WT


title: HEK293, pcDNA3.1_V5-TWIST1(HAND2loop), input


title: HEK293, pcDNA3.1_V5-TWIST1(WT), V5, r2


title: HEK293, pcDNA3.1_V5-TWIST1(HAND2loop) and pcDNA3.1_ALX4-Flag, V5

value: transfection with pcDNA3.1_V5-TWIST1(HAND2loop) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(HAND2loop), V5


title: HEK293, pcDNA3.1_V5-TWIST1(HAND2loop) and pcDNA3.1_ALX4-Flag, input


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1L) and pcDNA3.1_ALX4-Flag, input

value: transfection with pcDNA3.1_V5-TWIST1(NEUROD1L) and pcDNA3.1_ALX4-Flag


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1M), V5


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1L) and pcDNA3.1_ALX4-Flag, V5


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROG2loop) and pcDNA3.1_ALX4-Flag, V5


title: E4_3_SUM149+ETX

city: HOUSTON

first: Benny

middle: Abrhaam

last: Kaipparettu

state: TX

address: 1 Baylor Plaza T832

department: Department of Molecular and Human Genetics

institute: Baylor College Of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence using TrimGalore
Reads were mapped to the UCSC human reference genome hg38 using STAR.
featureCounts was used to evaluate gene expression level as read counts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: SUM149 breast cancer cell line

growth_protocol: Cell lines were grown in DMEM containing 5% FBS in T25 flask

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CPT1 gene was knocked-down by lentiviral shRNA or 100 uM Etomoxir(ETX) was treated for 1 week

value: breast cancer cell

value: Breast

value: 100 uM Etomoxir


title: CO_3_SUM149-Control

value: Water


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1L), V5


title: HEK293, pcDNA3.1_V5-TWIST1(NEUROD1L), input


title: CO_1_SUM149-Control


title: C1_2_SUM159-shCPT1

source_name: SUM159 breast cancer cell line

value: lentivirus for shCPT1


title: E4_1_SUM149+ETX


title: Time course experiment across morphological perturbations

city: Cambridge

first: Madeline

last: Lancaster

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Avenue

department: Cell Biology Division

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

library_source: transcriptomic single cell

data_processing:
Sequence reads from single cell and single nuclei data were demultiplexed using demuxFQ into 8 and 2 sub-libraries respectively, allowing for one mismatch in the barcode sequences. Then, each sub-library was processed using the computational pipeline provided by Parse Biosciences, spipe v.1.0.3. The output of each sub-library was combined with 'spipe combine' to create unified metadata files and count matrix.
Please refer to the publication for further details about downstream analysis.
Assembly: GRCh38.108
Supplementary files format and content: Comma separated values files and sparse matrix files. Unfiltered gell and gene metadata and count matrices.

source_name: Brain organoid

growth_protocol: For organoid growth details please refer to Methods section in the corresponding publication. Day 45, 48, 55, 70 brain organoids from hES H9 cell line were snap frozen and processed for single cells. Single cells were obtained as follows: Single organoids were incubated in 1 mL Accumax solution (Merck, A7089) supplemented with DNase I (Sigma, 04716728001) 1.25U/mL. Organoids were incubated in the solution at 37°C for 20 minutes on a shaker followed by gentle agitation and pipetting. The enzymatic activity of Accumax was stopped by adding IDM+A or FBS (fetal bovine serum Merck, F2442) 1:10. The solution was filtered through 70 µm cell strainer prior cell counting. The solution was spinned at 200g for 10 minutes at 4°C and the pellet resuspended in cell prefixation buffer (Parse Biosciences). Sample fixation and split-seq were performed according to the Evercode Fixation v3 Parse Biosciences protocol.

extract_protocol:
Nucleic acid extraction was obtained following Evercode WT v3 Parse Biosciences protocol. RT transcription was performed within each cell following single cell combinatorial barcoding. Following barcoding, cells were lysed and nucleic acid molecules extracted.
Single-cell RNA-seq libraries were generated using the Evercode WT v3 kit (Parse Biosciences).
The Evercode™ split-pool combinatorial barcoding technology, originally based on the approach published in Science and known widely as SPLiT-Seq.

treatment_protocol: Control (CO) organoids were generated according to the commercial kit (STEMdiff™ Cerebral Organoid Kit, StemCell Technologies 08570) and sampled at day45, 55, 70. Dissociated (DISS) organoids were dissociated to single cell suspension at day45, reaggregated and further sampled at day48, 55, 70. Constrained (CONS) organoids were generated by removing Matrigel from Day 13 COs and embedded in 3% low gelling temperature agarose (Sigma, A9414) solution in sterile DPBS. Agarose constrained organoids were further processed in the same way as COs. 3 independent batches of organoids were collected at day 55 for sequencing.

value: Brain organoid

value: hES H9

value: Mixed

value: Control/Dissociated/Constrained


title: CO_2_SUM149-Control


title: NSChashtag_mix_HTO

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

library_source: other

data_processing:
Cellranger count v 3.1.0 for RL1915, CITE-seq count v 1.4.3 for RL1916
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: NSC differentiation cell culture

growth_protocol: Reinhardt NSC differentiation protocol

extract_protocol:
single cell suspension via Trypsin-EDTA
10X Genomics 3prime v3

value: NSC differentiation cell culture

value: 32F primed, 32F N2P, 32F TNT, 38F primed, 38F TNT

value: NSC differentiation


title: NSChashtag_mix_scRNAseq


title: C1_3_SUM159-shCPT1


title: SC_3_SUM159-scramble

value: lentivirus for scramble


title: SC_1_SUM159-scramble


title: C1_1_SUM159-shCPT1


title: SC_2_SUM159-scramble


title: SC_4_SUM159-scramble


title: Control experiment with snRNA-seq

molecule: nuclear RNA

value: Control/Dissociated/Embed


title: EndoC-βH1 cells, AZD7762 treatment, rep 2

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
checked for quality using FastQC v0.10.1
trimmed for adaptor sequences and low-quality bases using cutadapt v1.18
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each gene

source_name: EndoC-βH1 cells

growth_protocol: EndoC-βH1 cells were maintained in DMEM containing 1g/L glucose, 2% BSA fraction V (Sigma), 50 μM 2-mercaptoethanol, 10 mM nicotinamide (Calbiochem), 5.5 μg/ml transferrin (Sigma-Aldrich), 6.7 ng/ml selenite (Sigma-Aldrich), 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using the Directzol RNA Miniprep kit (Zymo Research)
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. cDNA libraries were sequenced with pair-end 51 bps using an Illumina NovaSeq6000 platform.

treatment_protocol: EndoC-βH1 cells were starved in 0.5 mM glucose for 1 hour, and then stimulated with either 0.5 mM or 20 mM glucose for 1 hour. DMSO or AZD7762 was included during the starvation and glucose stimulation steps.

value: beta cells

value: WT


title: EndoC-βH1 cells, AZD7762 treatment, rep 3


title: E4_2_SUM149+ETX


title: CjMock3

city: Kyoto

first: Akifumi

last: Matsumoto

state: Kyoto

address: 465 Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Ophthalmology

institute: Kyoto Prefectural University of Medicine

data_processing:
initial quality assessment of raw RNA-seq data was performed using FastQC (v0.12.1) to evaluate read quality.
TrimGalore (v4.3) was conducted to remove adapter sequences, and low-quality reads.
The trimmed reads were aligned to the reference genome (GRCh38) using HISAT2 (v2.2.1).
We converted the output SAM files to sorted BAM files with SAMtools (v1.12) for downstream analysis.
FeatureCounts (v2.0.3) was utilized to assign mapped reads to their corresponding genes, generating count data for each gene.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: a text file include raw count data file for each sample

source_name: Conjunctiva

extract_protocol:
ISOLATE II RNA Mini Kit
RNA libraries for RNA-seq were prepared using “NEBNext Ultra II Direc RNA” following manufacturer's protocols.

value: Conjunctiva

value: Primary

value: Conjunctival epithelial cell

value: Mock

value: untreated


title: CjMock1


title: EndoC-βH1 cells, AZD7762 treatment, rep 1


title: EndoC-βH1 cells, DMSO control, rep 3

value: DMSO


title: EndoC-βH1 cells, DMSO control, rep 1


title: CjMock2


title: CjIR3

value: IR

value: irradiation


title: CjIR2


title: Skin_biopsy_ID_case7

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

description: 1yo_spayedFemale_AmericanStaffordshireTerrier

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler

scan_protocol: Cartridges were run on a Nanostring Sprint machine

data_processing: Data were analyzed with nSolver software version 4.0 and ROSALIND online software.

label: fluorescent probe

organism: Canis lupus familiaris

source_name: archival skin biopsy

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol

extract_protocol: RNA was isolated from 30 micron curls from archival skin biopsies using Qiagen FFPE RNEasy kit with Deparaffinization solution per the manufacturer's instructions.

tag: disease status

value: ID

tag: disease details

value: fDLE


title: Skin_biopsy_ID_case8


title: CjIR1


title: Skin_biopsy_ID_case6


title: EndoC-βH1 cells, DMSO control, rep 2


title: Human sperm swim-up replicate 2

city: Vienna

first: Roman

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.1
bowtie2 version 2.2.5 mapping against hg19, mm9 and Xenopus laevis v9.2 reference assemblies
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with Homer for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: hg19, mm9 and Xenopus laevis v9.2
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with  juicer tools pre command.

source_name: human sperm isolated from ejaculate by swim-up

growth_protocol: Xenopus laevis XL177 cells were cultured at 16-20º C in medium containing 65% Leibovitz’s L-15 (Thermo Fisher Scientific, #11415064), 15% FBS (Gibco, 10270106), 20% H2O, 100 U/ml Penicillin and 100 µg/ml Streptomycin (Sigma, P0781). Pronuclei were generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract. Human, mouse and frog sperm cells were isolated by density gradient centrifugation or swim-up.

extract_protocol:
Samples were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Hi-C was performed according to the previously described in situ Hi-C protocol (Rao et al., Cell 2014).
Hi-C libraries were prepared according to the previously described in situ Hi-C protocol (Rao et al., Cell 2014).

treatment_protocol: Some of the frog sperm samples were de-membranated. Two of the XL177 samples were crosslinked in either PBS or Xenopus egg extract (ULSS). Some of the pronuclei samples were treated by adding recombinant CTCF protein.

value: human sperm


title: Skin_biopsy_ID_case4

value: Pemphigus Foliaceous w Atopic Dermatitis


title: BMSCs, Control3

city: Chongqing

first: Zheng

last: Jing

address: #426 North Songshi Road

department: department of orthodontics

institute: Stomatological Hospital of Chongqing Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: Rnor_6.0
Supplementary files format and content: TXT file contains counts for each sample

organism: Rattus norvegicus

source_name: bone marrow mesenchymal stem cells (BMSCs) from femur

growth_protocol: bone marrow mesenchymal stem cells were maintained in αMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary BMSCs were cultured in complete growth medium to 80% confluence and treated with 3%CSE or control (serum-free culture medium) for 6h

value: BMSCs primary cell

value: mesenchymal stem cells

value: 6h of serum-free medium treatment


title: BMSCs, Control1

value: bone marrow mesenchymal stem cells (BMSCs) from femur


title: MCF7-TR2 1

hyb_protocol: standard Affymetrix prototcol

scan_protocol: standard Affymetrix prototcol

data_processing: standard Affymetrix prototcol

source_name: MCF7-TR2 Tamoxifen resistant breast cancer cell line

label_protocol: standard Affymetrix prototcol

growth_protocol: Parental MCF7 and tamoxifen-resistant MCF7 (TR) cells (TR1, TR2) were cultured in DMEM with 10% FBS, 1% penicillin/streptomycin, and concentrations of 4-hydroxy tamoxifen at 0µm, 1µM, 100nM

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Affymetrix protocols

value: Breast

value: Tamoxifen resistant


title: BMSCs, Control2

value: WT


title: 3D +dTAG+PCI

description: MboI digestion

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.4
bowtie2 version 2.2.5 mapping against hg19 reference assembly
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with Homer for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: hg19
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with  juicer tools pre command, deposited in full resolution as well as downsampled to either 190 mio. or 375 mio. valid unique ditags.

source_name: HeLa Kyoto

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were got from Narumiya S (Kyoto University; Kyoto; Japan). MEFs were generated in the lab by 3T3 methods.

extract_protocol:
Cells were cross-linked in falcon tube. The DNA was fragmented, biotynilated at both ends, and ligated at newly blunted ends together. Biotinylated DNA was captured and prepared for paired-end Illumina sequencing.
Libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa Kyoto

value: human cervical cancer cells


title: Skin_biopsy_ID_case3

description: 13yo_neuteredMale_GermanShorthairPointer

value: DLE


title: WT +dTAG+PCI

description: MboI digestion


title: BMSCs, CSE3

value: 6h of CSE treatment


title: Skin_biopsy_ID_case2


title: MCF7-TR1 2

source_name: MCF7-TR1 Tamoxifen resistant breast cancer cell line


title: MCF7-TR1 1


title: MCF7-TR2 3


title: MCF7 Ctrl 3

source_name: MCF7 parental breast cancer cell line

value: parental


title: MCF7 Ctrl 2


title: MCF7 Ctrl 1


title: Skin_biopsy_ID_case1

value: Pemphigus erythematosus


title: BMSCs, CSE2


title: BMSCs, CSE1


title: Skin_biopsy_ID_case5

value: ID

value: Hepatocutaneous syndrome


title: MCF7-TR1 3


title: WT +PCI

description: MboI digestion

value: doxycycline (+)/Auxin (+)/PCI(+)


title: MCF7-TR2 2


title: HIV JR-FL 3 Day 15

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: iPSC-derived microglial culture, infected with HIV strain JR-FL

data_processing:
Fastq files were cleaned and trimmed with fastp v0.12.2
Fastq files were aligned with grch38_tran index using HISAT2 v2.2.0
Gene counts were imported into a DESeq2 object using readCounts() from the Rsubread package using a custom GTF file, combining UCSC hg38 and HIV JR-FL genes from Genbank accession U63632
Groups were compared by Wald testing in DESeq2
Normalized counts were exported using DEseq2 counts() with normalized=TRUE
Assembly: GRCh38/release-104
Supplementary files format and content: HGNC symbol x sample ID, tab-delimited text file

source_name: Microglia

growth_protocol: Human microglia differentiated from iPSC were cultured in XVIVO15 (Lonza) supplemented with N2, Glutamax, 0.5% NEAA, interleukin-34 (IL-34, 100 ng/ml), granulocyte macrophage colony stimulating factor (GM-CSF, 10 ng/ml, and M-CSF (25 ng/ml). The medium was changed every 4 days. Cells were then detached with 20 min Accutase treatment for RNA preparation.

extract_protocol:
Total RNA was extracted using TriZol
RNA was delivered to Novogene for library construction using Illumina TruSeq kits

value: 15 days

value: Microglia

value: HIV JR-FL Infected


title: HIV JR-FL 1 Day 15


title: HIV JR-FL 2 Day 15


title: 3D +dTAG

description: MboI digestion

value: doxycycline (+)/Auxin (+)/dTAG(+)


title: 3D +PCI

description: MboI digestion


title: Control No Treatment 2 Day 15

description: iPSC-derived microglial culture, mock-infected

value: Mock-infected Control


title: WT +dTAG

description: MboI digestion


title: WT_Sham rep1

source_name: Heart

value: Heart

value: male

value: Sham


title: Control No Treatment 1 Day 15


title: Skin_biopsy_EL_case5

description: 8yo_spayedFemale_AustralianShepherdCross

value: EL

value: primary tumor


title: Skin_biopsy_EL_case4


title: Skin_biopsy_EL_case3


title: EHT3, HRA

city: Munich

first: Hengliang

last: Zhang

department: University Hospital

country: Germany

institute: LMU Munich

data_processing:
GATK (v4.1.1.0) software
Original image data file from high-throughput sequencing platforms was transformed to sequenced reads (Raw data) by Casava 1.8 base recognition (Base Calling). Raw data were stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Raw data (raw reads) of fastq format were firstly processed throughin-house perl scripts.
featureCounts v1.5.0-p3 was used to count the reads numbers mappedto each gene.
GATK (v4.1.1.0) software was used to perform SNP calling.
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: tab delimited text file includes RPKM values for each sample

growth_protocol: Cardiomyocyte differentiation was triggered when the cells reached around 85% confluence by utilizing chemically defined elements for 24 hours (Cardiomyocyte differentiation medium A) and subsequently Cardiomyocyte differentiation medium B (PSC Cardiomyocyte Differentiation Kit; Gibco) for 48 hours. After 72 hours, differentiation of hiPSC-CMs was sustained for 12 days using cardiomyocyte maintenance medium (PSC Cardiomyocyte Differentiation Kit; Gibco), which was refreshed every other day. Differentiated cardiomyocytes were collected and produced for EHT.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen). 0.2 ug of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: Different concentrations of RA (Control group without RA, LRA group with 0.05 µM and HRA group with 0.1 µM) were administered during third to sixth days of the hiPSCs differentiation process

value: 0.1 uM RA

value: hiPSC

value: WT

value: 3-6 days


title: EHT3, LRA

value: 0.05 uM RA


title: Skin_biopsy_EL_case6


title: EHT2, Control

value: DMSO


title: EHT3, Control


title: 3D +dTAG+PCI rep2

description: 5% MEF (mouse embryonic fibroblast) cells added for calibration purposes

data_processing:
Basecalling software: Illumina RTA
Aligment against hg19 reference assembly: bowtie version 1.2.2 , reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq  peak calling using MACS version 1.4.2 and version 2.2.5
TDF files for IGV and Juicebox browsers were generated from wig files using igvtools toTDF
Assembly: hg19
Supplementary files format and content: wig files for ChIP-Seq signal distributions represent genomic distribution of the factors as described in the paper.
Supplementary files format and content: tdf files for visualization in IGV and Juicebox browsers

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with Flag antibody (cell signaling 14793S); Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
Libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa Kyoto

value: human cervical cancer cells


title: Eh trophozoites+biofilm B.subtilis, 271221

city: Haifa

first: Serge

last: Ankri

address: 1 Efron street

department: Microbiology

country: Israel

institute: Technion

data_processing:
NGS QC, alignment and counting  Quality control analysis was performed using Fastqc (v0.11.8) to evaluate the sequencing data. Following this, reads were subjected to trimming for adapter sequences, removal of low-quality bases from the 3' end, and a minimum length threshold of 20 using CUTADAPT (v1.10).The resulting 100 bp single reads were aligned to the reference genome of amoeba E. histolytica (strain HM-1:IMSS). The reference genome can be accessed at the following URL: https://amoebadb.org/common/downloads/Current_Release/EhistolyticaHM1IMSS/fasta/data/. Additionally, an annotation file providing information about the genome can be found at: https://amoebadb.org/common/downloads/Current_Release/EhistolyticaHM1IMSS/gff/data/.  For the alignment process, Tophat2 version 2.1.0 (utilizing Bowtie2 version 2.2.6) was employed. Subsequently, the number of reads mapped to each gene was quantified using Htseq-count (v0.11.2).
Supplementary files format and content: Descriptive analysis
Supplementary files format and content: A statistical analysis was preformed using DESeq2 R package (version 1.28.1) (Genome Biology 2014 15:550). The number of reads per gene was extracted into merged_counts.csv and normalized_counts.csv files for raw counts and normalized counts, respectively. The similarity between samples was evaluated within DESeq2 package using correlation matrix, shown in heatmap plot.

organism: Entamoeba histolytica

extract_protocol:
Trophozoites were incubated with different forms of Bacillus subtilis (planktonic or biofilm) or serum-free Diamond's TYI S-33 medium without bacteria as a control. The trophozoites were incubated for 1 hour at 37°C in a 24-well plate that was covered with serum-free Diamond's TYI S-33 agar. After the incubation period, the trophozoites were harvested by gently tapping the glass tube, followed by centrifugation at 1900 rpm for 3 minutes. RNA extraction from E. histolytica was performed using the Monarch Total RNA Miniprep Kit ( NEW ENGLAND BioLabs, Ornat, Nes Ziona, Israel). The extraction protocol was followed according to the manufacturer's instructions, which emphasized the importance of avoiding mechanical disruption during the cell lysis step to ensure the extraction of E. histolytica RNA while minimizing extraction of B. subtilis biofilm RNA using the detergent-based lysis buffer.
Simultaneously, a total of 9 RNAseq libraries were constructed following the manufacturer's protocol (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, cat no. E7760). Each library was prepared using 400 ng of total RNA as the starting material. To enrich for mRNA, a magnetic pull-down method was employed using the Magnetic Isolation Module (NEB, cat no. E7490). Subsequently, the concentration of each library was measured using Qubit (Invitrogen), while the size distribution was determined using the TapeStation 4200 with the High Sensitivity D1000 kit (cat no. 5067-5584). To ensure equal representation, all libraries were combined into a single tube with equal molarity. The RNAseq data was generated on an Illumina NextSeq2000 platform using P2 chemistry with 100 cycles (Read1-100; Index1-8; Index2-8) (Illumina, cat no. 20046811).

treatment_protocol: Entamoeba histolytica trophozoites incubated with B.subtilis biofilm in serum-free Diamond's TYI S-33 medium for one hour at 37oC.

value: Incubation with Biofilm form of B.subtilis for 1 hour


title: WT -dTAG

description: MboI digestion

value: doxycycline (+)/Auxin (+)


title: 3D +dTAG -PCI rep2

value: doxycycline (+)/Auxin (+)/dTAG(+)


title: EHT2, HRA


title: EHT1, HRA


title: Skin_biopsy_EL_case2


title: EHT2, LRA


title: Skin_biopsy_EL_case1


title: Eh trophozoites+biofilm B.subtilis, 231221


title: H16_PD1neg_D3

city: Sacramento

first: William

last: Murphy

address: 2921 Stockton Blvd.

department: Dermatology

institute: University of California, Davis

description: Annonymous Human Blood Donor

data_processing:
Raw reads were processed with HTStream v.1.1.0 to perform raw sequence data QA/QC, remove adapter contaminatimn and low-quality bases/sequences.
Trimmed reads were aligned to Mus musculus GRCm38 genome with GENCODE v.M32 annotation or to Homo sapiens GRCh38 genome with GENCODE v.32 annotation using STAR v.2.7.0f aligner.
Supplementary files format and content: mapped read count

source_name: Leukopak human donor

growth_protocol: T cells were isolated and sorted then cultured in 96 well plate at 1.5e5-2e5 cells per well with rhIL-2.

extract_protocol:
cell pellets were extracted using Total RNA Purification Plus  Micro Kit following standard protocols and quantified using  Qubit RNA HS kit and RNA integrity  was assessed using TapeStation 2200.
Barcoded 3’ Tag-Seq libraries were created by UC Davis DNA Technologies Core facility using QuantSeq FWD kit for multiplexed sequencing according to the recommendations of the manufacturer.

treatment_protocol: Cells were compared as unculured cells versus cultured with rhIL-2

value: CD8+ CD45RO+ CD25- PD1-

value: Annonymous Human Blood Donor

tag: agent

value: In vitro with rhIL2


title: H15_PD1neg_D0

description: Annonymous Human Blood Donor

value: Untreated


title: 3D +dTAG+PCI rep1


title: 3D +dTAG -PCI rep1


title: Eh trophozoites+biofilm B.subtilis, 161221


title: Control No Treatment 3 Day 15

value: 15 days

value: Microglia

value: Mock-infected Control


title: EHT1, Control

value: hiPSC


title: H14_PD1pos_D3

description: Annonymous Human Blood Donor

value: CD8+ CD45RO+ CD25- PD1+


title: Eh trophozoites+planktonic B.subtilis, 271221

treatment_protocol: Entamoeba histolytica trophozoites incubated with planktonic cell of B.subtilis in serum-free Diamond's TYI S-33 medium for one hour at 37oC.

value: Incubation with Planktonic form of B.subtilis for 1 hour


title: H13_PD1pos_D0

description: Annonymous Human Blood Donor


title: NoMG−223579

first: Catarina

last: Martins-Costa

address: Dr.-Bohr-Gasse 3

institute: IMBA - Institute of Molecular Biotechnology of the OeAW

description: Lexogen Quantseq

data_processing:
RNAseq reads were trimmed using BBDuk v38.06 (ref = polyA.fa.gz, truseq.fa.gz, k = 13, ktrim = r, useshortkmers = t, mink = 5, qtrim = r, trimq = 10, minlength = 20) and reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Assembly: hg38
Supplementary files format and content: tab-delimited text files with per gene read counts

growth_protocol: Human telencephalic brain organoids.

extract_protocol:
Lexogen Quantseq
Library preparation was performed according to the manufacter’s instructions.

treatment_protocol: Modes of exogenous ECM addition: droplet embedding ("dropMG"), liquid embedding ("liqMG", "Laminin", "Collagen IV"), and no exogenous addition ("noMG").

value: Brain organoid

value: H9 ESCs

value: Neural progenitors and neurons

value: NoMG

value: WT


title: 3D -dTAG

description: MboI digestion

value: HeLa Kyoto

value: human cervical cancer cells

value: doxycycline (+)/Auxin (+)


title: H12_PD1neg_D3

description: Annonymous Human Blood Donor

value: CD8+ CD45RO+ CD25- PD1-

value: Annonymous Human Blood Donor


title: Eh trophozoites+planktonic B.subtilis, 231221


title: NoMG−223578

description: Lexogen Quantseq


title: EHT1, LRA

value: 0.05 uM RA

value: 3-6 days


title: H11_PD1pos_D3

description: Annonymous Human Blood Donor

value: In vitro with rhIL2


title: Eh trophozoites+planktonic B.subtilis, 161221


title: H10_PD1neg_D0

description: Annonymous Human Blood Donor

value: Untreated


title: Eh control trophozoites, 231221

treatment_protocol: Entamoeba histolytica trophozoites incubated in serum-free Diamond's TYI S-33 medium for one hour at 37oC.

value: no treatment


title: H7_PD1pos_D3

description: Annonymous Human Blood Donor

value: CD8+ CD45RO+ CD25- PD1+


title: NoMG−223577

description: Lexogen Quantseq


title: H8_PD1neg_D3

description: Annonymous Human Blood Donor


title: H5_PD1pos_D0

description: Annonymous Human Blood Donor


title: H6_PD1neg_D0

description: Annonymous Human Blood Donor


title: H4_PD1neg_D3

description: Annonymous Human Blood Donor


title: H3_PD1pos_D3

description: Annonymous Human Blood Donor


title: CollagenIV−223593

description: Lexogen Quantseq

value: CollagenIV


title: Eh control trophozoites, 161221


title: H2_PD1neg_D0

description: Annonymous Human Blood Donor


title: Skin_biopsy_EL_case6

data_processing: Data were analyzed with nSolver software version 4.0

value: EL


title: Cre_p_80

city: San Francisco

first: Jun Hyung

last: Sin

address: 513 Parnassus Ave S-1076

department: Pediatrics

institute: University of California, San Francisco

data_processing:
Aire-dependent genes and Fezf2-dependent genes were identified using previously published RNA-seq data.
Sequence alignment was performed using STAR (Version 2.7.9a) and mappings were restricted to those that were uniquely assigned to the mouse genome, and unique read alignments were used to quantify expression and aggregated on a per-gene basis using the Ensembl (GRCm39) annotation
Differentially expressed genes between expreimental groups were determined used DESeq2

source_name: thymus

extract_protocol:
Freshly sorted EPCAM+ mTECs were collected into SMART-seq lysis buffer (+RNA Inhibitor, 10X lysis buffer [Takara Biosciences], 5' SMART seq PRIMER III [Takara Biosciences], H20)
Per UCSF Genomics Core

value: thymus

value: Medullary thymic epithelial cells

value: Cre(+) Ikzf1fl/fl Pou2f3-/-


title: H1_PD1pos_D0

description: Annonymous Human Blood Donor


title: Cre_p_76


title: CollagenIV−223590

description: Lexogen Quantseq

value: Brain organoid

value: H9 ESCs

value: Neural progenitors and neurons

value: WT


title: H9_PD1pos_D0

description: Annonymous Human Blood Donor


title: Eh control trophozoites, 271221


title: NoMG−223576

description: Lexogen Quantseq

value: NoMG


title: Cre_p_45


title: Cre_m_75

value: Cre(-) Ikzf1fl/fl Pou2f3-/-


title: CollagenIV−223589

description: Lexogen Quantseq


title: Cre_m_77


title: Cre_m_48


title: CollagenIV−223587

description: Lexogen Quantseq


title: Skin_biopsy_EL_case5


title: Skin_biopsy_EL_case4


title: Skin_biopsy_EL_case2


title: CollagenIV−223588

description: Lexogen Quantseq


title: Laminin−223597

description: Lexogen Quantseq

value: Laminin


title: Foxn1-Cre (+)/Ikzf1fl/fl 40

extract_protocol:
Freshly sorted L1CAM+ thymic tuft cells were collected into SMART-seq lysis buffer (+RNA Inhibitor, 10X lysis buffer [Takara Biosciences], 5' SMART seq PRIMER III [Takara Biosciences], H20)
Per UCSF Genomics Core

value: Thymic tuft cells

value: KO


title: Skin_biopsy_EL_case3


title: Foxn1-Cre (+)/Ikzf1fl/fl 42


title: NoMG−223573

description: Lexogen Quantseq


title: Skin_biopsy_EL_case1


title: Laminin−223596

description: Lexogen Quantseq


title: Foxn1-Cre (+)/Ikzf1fl/fl 22


title: Laminin−223595

description: Lexogen Quantseq


title: Foxn1-Cre (-)/Ikzf1fl/fl 39


title: Foxn1-Cre (-)/Ikzf1fl/fl 21


title: Cre_m_46


title: LiqMG−223584

description: Lexogen Quantseq

value: LiqMG


title: Laminin−223598

description: Lexogen Quantseq


title: Laminin−223594

description: Lexogen Quantseq


title: M20_PD1neg_D3

description: Female C57BL/6 Taconic Farms

source_name: murine spleen

tag: gender

value: Female

tag: strain

value: In vitro with rhIL2


title: M19_PD1pos_D3

description: Female C57BL/6 Taconic Farms


title: Foxn1-Cre (-)/Ikzf1fl/fl 41

tag: tissue


title: LiqMG−223583

description: Lexogen Quantseq


title: Lower limb artery Test 2

city: Guangzhou

first: Yu

last: Zhou

state: Guangdong

address: No 58, Zhongshan 2nd street

department: Division of Vascular Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

source_name: Lower limb artery, atherosclerotic artery,replicate 2

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: The healthy arteries and atherosclerotic arteries were isolated and stored at -80°C for microarray.

value: Lower limb artery

value: Male

tag: disease state

value: atherosclerotic artery


title: M16_PD1neg_D3

description: Female C57BL/6 Taconic Farms


title: M18_PD1neg_D0

description: Female C57BL/6 Taconic Farms

value: Untreated


title: LiqMG−223580

description: Lexogen Quantseq

source_name: Brain organoid

tag: genotype


title: Lower limb artery Test 3

source_name: Lower limb artery, atherosclerotic artery,replicate 3


title: Lower limb artery Control 3

source_name: Lower limb artery, normal artery,replicate3

value: normal artery


title: M17_PD1pos_D0

description: Female C57BL/6 Taconic Farms


title: LiqMG−223581

description: Lexogen Quantseq

value: Brain organoid

tag: treatment


title: LiqMG−223582

description: Lexogen Quantseq

tag: cell line

value: H9 ESCs


title: DropMG−223603

description: Lexogen Quantseq

tag: cell type

value: Neural progenitors and neurons

value: DropMG


title: M12_PD1neg_D3

description: Female C57BL/6 Taconic Farms


title: Lower limb artery Control 2

source_name: Lower limb artery, normal artery,replicate2


title: Liver-SA-3

city: wuhan

first: Yan

last: Lin

address: 299 Bayi Road, Wuchang District, Wuhan City, Hubei Province

department: Department of Medical Genetics

institute: Wuhan University

data_processing:
fastQC version 0.19.7
Sequence resds were trimmed for adaptor sequences /low-quality sequnce using fastQC version 0.19.7
Trimmed sequence reads were mapped to GRCm39/mm10 using the HISAT2 software
Read count extraction and normalization were performed using  stringtie version 2.2.1
Assembly: mm10
Supplementary files format and content: table-delimited text file includes raw counts for each sample
Supplementary files format and content: table-delimited text file includes FPKM vaules for each sample

source_name: Liver

extract_protocol:
The total RNA of frozen mice liver tissues was extracted using RNAiso Plus (#9109, Takara).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: Liver


title: DropMG−223602

description: Lexogen Quantseq

value: WT


title: Liver-SA-1


title: Lower limb artery Test 1

source_name: Lower limb artery, atherosclerotic artery,replicate 1


title: Lower limb artery Control 1

source_name: Lower limb artery, normal artery,replicate1


title: Liver-ctrl-3


title: M15_PD1pos_D3

description: Female C57BL/6 Taconic Farms


title: M09_PD1pos_D0

description: Female C57BL/6 Taconic Farms


title: Liver-SA-4


title: DropMG−223605

description: Lexogen Quantseq


title: Frog XL177 nuclei PBS-crosslinking

organism: Xenopus laevis

value: nuclei isolated from Xenopus laevis XL177 cells, an immortalized non-epidermal epithelial cell line

value: crosslinking in buffer (PBS)


title: M07_PD1pos_D3

description: Female C57BL/6 Taconic Farms


title: Frog XL177 nuclei ULSS-crosslinking replicate 1

value: crosslinking in Xenopus egg extract (ULSS)


title: M14_PD1neg_D0

description: Female C57BL/6 Taconic Farms


title: S16_G3BP_Arsenite_2

city: Cleveland

first: Soon Yeul

last: Yi

address: CWRU Wood Research Building W127A, 2109 Adelbert Rd,

institute: Case Western Reserve University

data_processing:
Raw fastq reads were processed using trim-galore software for quality control and adapter trimming. Default options for paired-end sequencing data were used. Trimmed reads were then mapped to GRCh38.p13 genome using the Rsubread subjunc program using default options for paired-end sequencing data. Mapped reads were then sorted and indexed with Rsamtools sortBam and indexBam. Finally, the edgeR featureCounts program was used for annotation and count matrix generation with human GRCh38.p13 gene definitions (options: isGTFAnnotationFile = T, GTF.attrType = 'gene_name', useMetaFeatures = T allowMultiOverlap = T, strandSpecific = 1, juncCounts = T, isPairedEnd = T).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited file containing normalized read counts per gene.

extract_protocol:
RNA was isolated with trizol reagent and stored at -80C until use.
RNA seq libraries were constructed using the NEBNext Ultra II Directional RNAseq kit (NEB) with ribosomal RNA depletion.

treatment_protocol: Cellular stress was induced by treating cells with 0.5mM sodium arsenite for 45 minutes. RNA was isolated with trizol reagent and stored at -80C until use.

value: Hepatocellular Carcinoma

value: Sodium Arsenite


title: M13_PD1pos_D0

description: Female C57BL/6 Taconic Farms

value: Female


title: DropMG−223604

description: Lexogen Quantseq


title: CoIR2

data_processing:
initial quality assessment of raw RNA-seq data was performed using FastQC (v0.12.1) to evaluate read quality.
TrimGalore (v4.3) was conducted to remove adapter sequences, and low-quality reads.
The trimmed reads were aligned to the reference genome (GRCh38) using HISAT2 (v2.2.1).
We converted the output SAM files to sorted BAM files with SAMtools (v1.12) for downstream analysis.
FeatureCounts (v2.0.3) was utilized to assign mapped reads to their corresponding genes, generating count data for each gene.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: raw count data for each sample

source_name: Cornea

extract_protocol:
ISOLATE II RNA Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cornea

value: Primary

value: corneal epithelial cell

value: IR

value: irradiation


title: Liver-ctrl-2


title: Liver-SA-2


title: M05_PD1pos_D0

description: Female C57BL/6 Taconic Farms

value: Untreated


title: M11_PD1pos_D3

description: Female C57BL/6 Taconic Farms

value: In vitro with rhIL2


title: Liver-ctrl-4


title: S15_G3BP_Arsenite_1


title: DropMG−223601

description: Lexogen Quantseq

value: Brain organoid

value: H9 ESCs

value: Neural progenitors and neurons


title: M04_PD1neg_D3

description: Female C57BL/6 Taconic Farms


title: M10_PD1neg_D0

description: Female C57BL/6 Taconic Farms


title: CoMock3

value: Mock

value: untreated


title: S14_G3BP_Mock_2


title: Intratibial tumor treated with empty vector and PvP; harvested at the EOS [LCS9550_Rel_pORF0_PVP_M9]

city: West Lafayette

first: Marxa

middle: Leao

last: Figueiredo

state: IN

address: 625 Harrison St

department: Basic Medical Sciences

institute: Purdue University

data_processing:
Cutadaptand perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases, followed by sequence quality verification using FASTQC.
HISAT2 was used to map reads to the human genome.
The mapped reads of each sample were assembled using StringTie. All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown was used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM. mRNAs differential expression analysis were performed by R package DESeq2.
Assembly: GRCh38 (Ensembl release-101)
Supplementary files format and content: Tab delimited text file containing raw counts for each sample

source_name: Intratibial tumor treated with empty vector and PvP; harvested at the end of the study (EOS)

growth_protocol: Mouse adenocarcinoma cell line TC2Ras was cultured in Dulbecco’s modified Eagle’s medium–nutrient mixture F-12 (DMEM-F12) (Gibco, Waltham, Massachusetts) supplemented with 10% FBS (Hyclone, Cytiva, Marlborough, MA) and 1% antibiotic-antimycotic (Anti-Anti) (Gibco). Male C57/BL6 mice (8-10 weeks of age) were obtained from Envigo. Mice were handled in accordance with an approved study protocol by the Purdue Animal Care and Use Committee (PACUC). TC2ras cells were prepared for implantation by adding trypsin (0.25% Trypsin-EDTA, Gibco, Billings, MT) to the cells and washing with sterile 1x DPBS. The pellet was resuspended in 1x DPBS at an appropriate concentration. For the intratibial model, 105 TC2Ras-Luc cells were injected in each tibia in 10ul sterile 1xDPBS. For the subcutaneous model, 3x105 TC2Ras cells were injected in each flank in 50uL sterile 1xDPBS. Implantation was performed under 2% inhaled isoflurane anesthesia delivered by high-flow vaporizer (VetFlo, Kent Scientific, Torrington, CT). In the subcutaneous model, tumors were harvested one week post implantation for RNA-sequencing analysis. In the intratibial model, three mice per group were euthanized 14 days post implantation, whereas the rest of the mice (n=4) were allowed to progress to the ethical endpoint. Post-euthanasia, tumors were collected in RNAlater (Invitrogen, Waltham, MA) and preserved for further RNA isolation and analysis. In short, RNA was isolated using RNeasy kit (Qiagen) according to manufacturer's protocol. Poly(A) RNA sequencing library was prepared following Illumina's TruSeq-stranded-mRNA protocol and conducted by LC Sciences (Houston, TX, USA). Poly(A) tail-containing mRNAs were purified using oligo-dT Briefly, magnetic beads with two rounds of purification, and fragmented using divalent cation buffer at elevated temperature. Quality control analysis and quantification of the sequencing library were performed using an Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000. For transcript assembly and estimating transcript expression levels, software is described by Figueiredo et al. (2020) (21). For differential expression analysis of mRNAs, StringTie was used by calculating fragments per kilobase million (FPKM). The differentially expressed mRNAs were selected with log2 (fold change) > 1.5 or log2 (fold change) < -1.5 and with statistical significance (p < 0.05) by edgeR.

extract_protocol:
tumors were collected in RNAlater (Invitrogen, Waltham, MA) and preserved for further RNA isolation and analysis. In short, RNA was isolated using RNeasy kit (Qiagen) according to manufacturer's protocol.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip.

value: tumor

value: Prostate adenocarcinoma

value: Control


title: CoMock2


title: Frog pronuclei 140min +CTCF replicate 2

description: 114162_XEE-nuclei_140min_plusCTCF_merged.hic

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.1
bowtie2 version 2.2.5 mapping against hg19, mm9 and Xenopus laevis v9.2 reference assemblies
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with Homer for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: hg19, mm9 and Xenopus laevis v9.2
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with  juicer tools pre command.

source_name: pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract

extract_protocol:
Samples were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Hi-C was performed according to the previously described in situ Hi-C protocol (Rao et al., Cell 2014).
Hi-C libraries were prepared according to the previously described in situ Hi-C protocol (Rao et al., Cell 2014).

value: incubation in egg extract for 140 min and addition of recombinant CTCF protein


title: hiPSC-cardiomyocytes, doxorubicin+metformin, Day 5_4

first: Feixiong

last: Cheng

state: Ohio

address: 9500 Euclid Ave

department: Genomic Medicine

institute: Cleveland Clinic

data_processing:
Raw reads (fastq files) were first subjected to the quality filtering using fastp v0.21.070 with default parameters except multi-threading, qualified phred quality score cut-off of 20 (>=Q20) and 30% bases allowed to be unqualified.
Quality clean reads were mapped to the reference human genome hg38 (GRCh38/108 build) employing buildindex and align functions from Rsubread 2.8.171 package with default settings except multiple threads.
Gene-wise read counts were obtained with featureCounts utilizing inbuilt hg38 RefSeq annotation and duplicates were ignored in read summarization
Gene annotation (i.e., gene symbols) associated to ENTREZ gene IDs were retrieved using org.Hs.eg.db human annotation package v3.15.0.
Further, edgeR v3.38.473 and limma v3.52.474 packages were used for preprocessing, filtering, normalization and evaluating differentially expressed genes (DEGs)
Assembly: human genome hg38 (GRCh38/108 build)
Supplementary files format and content: Matrix table for reads raw counts from all the samples

source_name: hiPSC-cardiomyocytes

growth_protocol: hiPSC-cardiomyocytes were maintained in STEMdiff cardiomyocyte maintenance media supplied with antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy plus kit (Qiagen).
Libraries were constructed using the lllumina Stranded mRNA RNA (poly-a) kits following the recommended protocol

treatment_protocol: Mature cardiomyocytes were treated with DMSO (0.1%), doxorubicin (0.33 uM), or doxorubicin (0.33 uM) and metformin (0.33 mM) for 5 days. Media and drug was replenished every two days.

value: hiPSC derived cardiomyocytes

value: WT

value: doxorubicin and metformin

value: Day 5


title: mTS, NGS

city: Shanghai

first: Qinying

last: Ye

address: Haike Road #230

institute: ShanghaiTech University

description: mTS

data_processing:
The sequencing data was analyzed by the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method.
Running MAGeCK needs sgRNA library. The library file mGPCR-sgRNA.csv has been provided in the article's supplementary material.
Assembly: mGPCR sgRNA library
Supplementary files format and content: Tab-separated table file
Supplementary files format and content: Results of treatment vs control

source_name: mouse trophoblast stem cells

growth_protocol: mTS cells were cultured in TS conditioned medium. For maintenance mTO, mTS were digested by Accutase ~7min, re-suspended n growth-factor-reduced Matrigel on ice, 25µL drops were plated per well into a 48-well culture plate , 5000-8000 cells/drop, and cultured with maintenance condition medium for 7 days.

extract_protocol:
mTS were digested by Accutase and organoids were removed from Matrigel by Cell Recovery Solution, then DNAs were extracted from mTSCs or organoids for PCR amplification using the same primers for library validation.
PCR products were treated with End Prep Enzyme Mix for end repairing, then index were added using PCR reaction. The final library product for sequencing were then purified by beads.
The qualified libraries were sequenced pair end 150bp on illumina Novaseq System.

treatment_protocol: Differentiate trophoblast organoids, mTO in maintenance condition were first passaged and cultured in maintenance medium without Y27632, FGF4 for 3 days, followed by culturing in the differentiation condition medium for 16 days. mTO in maintenance condition were first passaged and cultured in maintenance medium without Y27632, FGF4 for 3 days, followed by culturing in the differentiation condition medium for 10 days.

value: mouse trophoblast stem cells

tag: stain

value: trophoblast

value: wild type

tag: condition

value: control

value: Day 2


title: Liver-ctrl-1

value: Liver


title: M08_PD1neg_D3

description: Female C57BL/6 Taconic Farms

value: Female

value: In vitro with rhIL2


title: Intratibial tumor treated with empty vector and PvP; harvested at the EOS [LCS9550_Rel_pORF0_PVP_M13]


title: CoMock1

value: Cornea

value: Primary

value: corneal epithelial cell

value: Mock

value: untreated


title: S13_G3BP_Mock_1

department: Biochemistry

growth_protocol: Huh-7.5 cell lines were grown and maintained at 37 °C and 5% CO2 in DMEM supplemented with 0.1 mM nonessential amino acids and 5% FBS.

value: Hepatocellular Carcinoma


title: hiPSC-cardiomyocytes, doxorubicin+metformin, Day 5_3

value: hiPSC derived cardiomyocytes

value: WT

tag: time


title: mTO, differentiation condition, NGS

source_name: mouse trophoblast organoids

value: mouse trophoblast organoids

value: differentiation

value: Day 10


title: CoIR3

value: IR

value: irradiation


title: mTO, maintenance condition, NGS

value: trophoblast

value: wild type

value: maintenance

value: Day 7


title: hiPSC-cardiomyocytes, doxorubicin+metformin, Day 5_2

value: doxorubicin and metformin

value: Day 5


title: M06_PD1neg_D0

description: Female C57BL/6 Taconic Farms

value: Female

value: Untreated


title: S12_NLS_Arsenite_2

value: APEX-NLS

value: Sodium Arsenite


title: CoIR1

value: Cornea

value: Primary

value: corneal epithelial cell


title: M03_PD1pos_D3

description: Female C57BL/6 Taconic Farms

value: In vitro with rhIL2


title: Intratibial tumor treated with IL-27 vector and PvP; harvested at the EOS [LCS9550_Rel_pIL27_PVP_M12]

source_name: Intratibial tumor treated with IL-27 vector and PvP; harvested at the end of the study (EOS)

value: tumor

value: Prostate adenocarcinoma


title: Frog pronuclei 140min biol. rep. 1

value: pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract

value: incubation in egg extract for 140 min


title: Intratibial tumor treated with empty vector and cabozantinib; harvested at the EOS [LCS9550_Rel_pORF0_Cabo_M23]

source_name: Intratibial tumor treated with empty vector and cabozantinib; harvested at the end of the study (EOS)

value: Cabo


title: Intratibial tumor treated with IL-27 vector and PvP; harvested at the EOS [LCS9550_Rel_pIL27_PVP_M10]


title: hiPSC-cardiomyocytes, doxorubicin, Day 5_3

value: hiPSC derived cardiomyocytes

value: WT

value: doxorubicin


title: S9_NLS_Mock_1

value: Hepatocellular Carcinoma

value: Mock


title: Intratibial tumor treated with empty vector and cabozantinib; harvested at the EOS [LCS9550_Rel_pORF0_Cabo_M19]


title: S11_NLS_Arsenite_1


title: S4_NES_Arsenite_2

value: APEX-NES


title: hiPSC-cardiomyocytes, doxorubicin+metformin, Day 5_1

value: doxorubicin and metformin

value: Day 5


title: M02_PD1neg_D0

description: Female C57BL/6 Taconic Farms

source_name: murine spleen

value: Female

value: Untreated


title: Frog pronuclei 140min biol. rep. 2


title: Frog pronuclei 60min biol. rep. 1

value: incubation in egg extract for 60 min


title: S10_NLS_Mock_2

value: APEX-NLS


title: hiPSC-cardiomyocytes, doxorubicin, Day 5_4


title: Intratibial tumor treated with IL-27 vector and cabozantinib; harvested at the EOS [LCS9550_Rel_pIL27_Cabo_M16]

source_name: Intratibial tumor treated with IL-27 vector and cabozantinib; harvested at the end of the study (EOS)

value: tumor


title: M01_PD1pos_D0

description: Female C57BL/6 Taconic Farms


title: S3_NES_Arsenite_1

value: Sodium Arsenite


title: Intratibial tumor treated with IL-27 vector and cabozantinib; harvested at the EOS [LCS9550_Rel_pIL27_Cabo_M28]

value: Prostate adenocarcinoma


title: hiPSC-cardiomyocytes, DMSO, Day 5_4

value: DMSO


title: S2_NES_Mock_2


title: S1_NES_Mock_1


title: hiPSC-cardiomyocytes, doxorubicin, Day 5_1


title: hiPSC-cardiomyocytes, doxorubicin, Day 5_2


title: Intratibial tumor treated with empty vector and PvP; harvested on day 14 [LCS9550_D14_pORF0_PVP_M7]

value: Control


title: Frog pronuclei 60min biol. rep. 2

value: pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract


title: G3BP_Enrich_Arsenite_7

data_processing:
*library strategy: CLIP-seq
Raw fastq files were first treated with fastX collapser to remove duplicated reads. Then, using CTK stripBarcode.pl the 7nt unique molecular identifier sequence at the 5'end was removed. Next, fastX trimmer and clipper was used to remove the barcode, spacer (GGG), and L32 sequence. Processed reads were then mapped to GRCh38.p14 genome using Bowtie2 (seed length 15nt, allow no mismatch). Mapped output (.sam) files were further processed using samtools (view, sort, index) and bedtools (bamtobed). Lastly, PCR duplicates were collapsed using CTK tag2collapse.pl.
Processed final bed files from each library were all combined into a single bed file and HOMER program was used to call peaks using makeTagDirectory and findPeaks (options: -o auto -style factor -L 2 -localSize 10000 -strand separate -minDist 50 -size 20 -fragLength 25). Finally, read counts per peak were normalized by the respective mapped depth of each library to generate the final normalized peak matrix.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file containing peak coordinates, mapped-depth normalized read counts per peaks per libraries, peak annotation, and replicate counts.

extract_protocol:
Cell pellets were lysed with PBS lysis buffer (1x PBS, 0.1% SDS, 0.5% NaDoc, 0.5% NP-40, 1 protease inhibitor tablet (Roche)) for 10 minutes on ice. Lysate was then treated with RQ1 DNase (Promega) for 5 minutes at 37'C with shaking at 1100RPM.  The lysates were then briefly treated with RNase I at 1:100 or 1:5000 dilutions at the same condition as DNase treatment. Lysates were clarified by centrifuging on tabletop 4'C centrifuge for 10 minutes. HuR IP was performed overnight at 4'C with nutation, with an additional streptavidin capture step for coCLIP samples. Immunoprecipitated samples were labeled with radioactivity (gamma-32P-ATP (Revity)) and ran on SDS-PAGE. The gels were transferred to a nitrocellulose membrane, and bands 10-30kDa above the HuR (37kDa) were excised. The excised membranes were treated with proteinase K (Roche) to release the protein-bound RNAs from the membrane.
CLIP footprints were reverse-transcribed using the BrdU incorporation and bead-capture strategy described previously (PMID: 24613350).

treatment_protocol:
Cellular stress was induced by treating cells with 0.5mM sodium arsenite for 45 minutes. At 30 minutes prior to harvest, cells were prepared for proximity labeling  by incubating samples with 0.5mM biotin phenol for 30 minutes. Subsequently, the APEX reaction was initiated with 1mM hydrogen peroxide for 1 minute. After labeling, the reaction was stopped using ice cold quencher solution (10mM sodium ascorbate, 5mM Trolox in PBS). Quencher solution was replaced by ice-cold PBS for crosslinking using 254nm UV light, on ice, for a dose of 400mJ/cm^2 and a dose of 200mJ/cm^2. Samples were scraped into tubes, centrifuged and cell pellets stored at -80C until use.
Cellular fractions were acquired using a fractionation protocol described previously (PMID:26240403).

tag: apex-reaction

value: Yes

tag: hur antibody

value: HuR 3A2 (Santa Cruz, cat. #sc-5261)


title: Frog sperm de-membranated biol. rep. 1

source_name: Xenopus laevis sperm isolated from testes by density gradient centrifugation (DGC)

value: Xenopus laevis sperm

value: de-membranation


title: hiPSC-cardiomyocytes, DMSO, Day 5_2

value: hiPSC derived cardiomyocytes

value: WT


title: hiPSC-cardiomyocytes, DMSO, Day 5_1

value: Day 5


title: Intratibial tumor treated with empty vector and PvP; harvested on day 14 [LCS9550_D14_pORF0_PVP_M5]


title: hiPSC-cardiomyocytes, DMSO, Day 5_3


title: Frog XL177 biol. rep. 2

value: immortalized non-epidermal epithelial cell line


title: Intratibial tumor treated with empty vector and cabozantinib; harvested on day 14 [LCS9550_D14_pORF0_Cabo_M25]

value: Cabo


title: Frog sperm de-membranated biol. rep. 2

value: Xenopus laevis sperm isolated from testes by density gradient centrifugation (DGC)


title: Intratibial tumor treated with empty vector and cabozantinib; harvested on day 14 [LCS9550_D14_pORF0_Cabo_M21]


title: Intratibial tumor treated with empty vector and PvP; harvested on day 14 [LCS9550_D14_pORF0_PVP_M3]


title: G3BP_Enrich_Mock_5

value: Hepatocellular Carcinoma

value: Mock


title: Frog sperm biol. rep. 2


title: Frog pronuclei 140min +CTCF replicate 1

value: incubation in egg extract for 140 min and addition of recombinant CTCF protein


title: Caki-1 cells, MORC2 , rep1

first: Ning

address: 600 Tianhe road

institute: Sun Yat-sen University

description: OE 1

data_processing:
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA).
The resulting libraries were multiplexed and sequenced with 100 basepair (bp) paired-end (PE100) to a depth of approximately 25–40 million reads per sample on an Illumina NovaSeq 6000 by the Institute of Genomic Medicine (IGM) .
Samples were demultiplexed using bcl2fastq v2.20 Conversion Software (Illumina).
RNAseq data was processed using kallisto (version 0.45.0) and human genome GRCh38 Ensembl version 94 annotation (Homo_sapiens GRCh38.94 chr_patch_hapl_scaff.gtf).
Assembly: hg38
Supplementary files format and content: Tab-delimited txt files is a matrix of per-gene counts for all samples.

extract_protocol:
Caki-1 cells were isolated and homogenized in TRIzol reagent (Invitrogen).Total RNA was isolated according to the manufacturer’s instructions. Total RNA concentration and purity and integrity were measured via RNA Nano 60000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Transcriptome library construction were performed by Fast RNA-seq Lib Prep Module for illumina(ABclonal Technology Co.,Ltd.,China)

value: kidney renal clear carcinoma cell

value: MORC2 overexpression

value: Overexpression


title: Frog sperm biol. rep. 1


title: Intratibial tumor treated with empty vector and cabozantinib; harvested on day 14 [LCS9550_D14_pORF0_Cabo_M27]

value: tumor

value: Prostate adenocarcinoma


title: G3BP_Enrich_Arsenite_6

value: Sodium Arsenite

value: Yes

value: HuR 3A2 (Santa Cruz, cat. #sc-5261)


title: G3BP_Enrich_Mock_6


title: Caki-1 cells, MORC2,  rep2

description: OE 2


title: G3BP_Input_Mock_4


title: Frog XL177 biol. rep. 1


title: XL177, Smc3 ChIP-Seq

data_processing:
Basecalling software: Illumina RTA
ChIP-seq reads were mapped uniquely with 0 to 2 errors against the Xenopus laevis v9.2 genome as well as the Mus musculus mm9 genome assembly using  bowtie version 1.2.2.
Peaks were called using the intersection of the peaks called using MACS version 1.4.2 with an assumed mappable genome size of 2.5e9 and a p-value threshold of 1e-10, and MACS v2.2.5 with default parameters.
TDF files for IGV and Juicebox browsers were generated from wig files using igvtools toTDF
bedGraph files (*.bedGraph) have been built using MACS v2.2.5 with -B option
Assembly: Xenopus laevis v9.2, mm9
Supplementary files format and content: bedGraph files for ChIP-Seq signal distributions represent genomic distribution of the factors as described in the paper, they can be used for visualization in IGV and Juicebox browsers
Supplementary files format and content: bed files describe genomic location and can be used as coordinates and for visualization in IGV and Juicebox browsers

growth_protocol: Xenopus laevis XL177 cells were cultured at 16-20º C in medium containing 65% Leibovitz’s L-15 (Thermo Fisher Scientific, #11415064), 15% FBS (Gibco, 10270106), 20% H2O, 100 U/ml Penicillin and 100 µg/ml Streptomycin (Sigma, P0781). Pronuclei were generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract.

extract_protocol:
Samples were crosslinked with 1% formaldehyde for 10 minutes at room temperature. After quenching with glycine and cell lysis with SDS, chromatin was sonicated using a Bioruptor sonication device.
ChIP was performed as previously described (Wendt et al., Nature 2008), and the following antibodies were used: anti-Smc3 (Bethyl, A300-060A), anti-CTCF (Millipore, 07-729). The DNA samples were submitted for library preparation and Illumina deep sequencing on HiSeq 2500 SR50 to the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria.

treatment_protocol: No treatment was applied to XL177 cells. Some of the pronuclei samples were treated by adding recombinant CTCF protein.

tag: antibody

value: anti-Smc3 (Bethyl, A300-060A)


title: Pronuclei 140min, +50nM CTCF, Smc3 ChIP-Seq

source_name: pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract for 140 min, with addition of recombinant CTCF protein


title: NES_Enrich_Arsenite_4

value: APEX-NES


title: Caki-1 cells, WT ,rep1

description: Control 1

value: Wild-type

value: Control


title: NES_Enrich_Mock_4


title: Pronuclei 140min, Smc3 ChIP-Seq

source_name: pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract for 140 min


title: NES_Enrich_Mock_3


title: Intratibial tumor treated with IL-27 vector and PvP; harvested on day 14 [LCS9550_D14_pIL27_PVP_M8]


title: G3BP_Input_Arsenite_5


title: Caki-1 cells, WT, rep2

description: Control 2


title: Pooled GEX library for 9 brain organoids replicate#1

description: 10x Genomics

data_processing:
Two CellPlex 10X libraries (named "40k" and "50k" in the metadata table) with the same CMOs were sequenced. ScRNA-seq reads were processed with cellranger multi v6.0.1 using the prebuild 10X GRCh38 reference refdata-gex-GRCh38-2020-A and setting include-introns to true. Further processing such as dimensionality reduction, clustering, and visualization of the scRNA-seq data was performed in R v4.2.2 with Seurat v4.2.0. Cells identified as stressed using Gruffi (Vertesy et al., 2022) were removed, cells with 800 to 6000 detected genes, less than 6% mitochondrial and 30% ribosomal content were retained.
Assembly: hg38
Supplementary files format and content: Seurat object containing counts and metadata of the filtered object (removal of non-telencephalic clusters, Gruffi, and quality filter), in .rds format
Supplementary files format and content: Tab-separated CMO, count, and metadata files

source_name: Brain organoid

extract_protocol:
Multiplexing was performed using the 10x Genomics 3’ CellPlex Kit.
Library preparation was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

treatment_protocol: Modes of exogenous ECM addition: droplet embedding ("drop"), liquid embedding ("liq"), and no exogenous addition ("no").

value: Brain organoid

value: H9 ESCs

value: Neural progenitors and neurons

value: WT

tag: age

value: 120 days


title: Intratibial tumor treated with IL-27 vector and PvP; harvested on day 14 [LCS9550_D14_pIL27_PVP_M6]


title: HUVECs, VmiR-1 Ago 3

city: New Haven

first: Asawari

last: Korde

state: CT

address: 300 Cedar street

institute: Yale University School of Medicine

data_processing:
The reads were trimmed using trimmomatic.
The reads were aligned to the reference genome hg19 using HiSat2.
The counts were generated using htseq.
Assembly: hg19
Supplementary files format and content: csv file with genes in the rows and samples in columns.

source_name: Human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were purchased from the Yale Vascular Biology and Therapeutics tissue culture core facility, cultured in the M199 (Gibco) medium containing 20% FBS (Heat inactivated, Gibco), 1% ECGS, and 1% penicillin, and streptomycin.

extract_protocol:
The beads were directly added to TRIzol after washing three times (wash buffer: 0.1M NaP pH 8.0) and the RNA extracted with Phenol-chloroform extraction protocol.
RNA libraries were prepapred using low-input kit

treatment_protocol: Cells were transduced with lentiviruses containing vascular-specific miR-1 (V-miR-1) overexpression or empty (V-ctrl) vector for 36-48 hours. Cells were checked for fluorescence and then collected by scraping in cold PBS, spun down (300 g for 10 min at 4°C), and resuspended in 250 µl of cold lysis buffer (10 mM Hepes, pH 7.4, 150 mM KCl, 3 mM MgCl2, 0.2 mM DTT, 10% glycerol, 0.5% NP-40, and 1 mM PMSF). Part of this lysate was kept as “input fraction,” and the rest was immunoprecipitated with anti-Ago2 antibody (Clone 11A9, Cat # SAB4200085, Sigma-Aldrich) and dynabeads protein A (Cat# 10002D, Life Technologies).

value: Human umbilical vein endothelial cells

value: V-miR-1 overexpression

tag: rip antibody


title: Subcutaneous tumor treated with IL-27 vector [LCS9574_TIL27_2]


title: HUVECs, VmiR-1 Ago 2

value: anti-Ago2 antibody (Clone 11A9, Cat # SAB4200085, Sigma-Aldrich)


title: Subcutaneous tumor treated with empty vector [LCS9574_Tctrl_2]

value: tumor


title: Pronuclei 140min, +50nM CTCF, CTCF ChIP-Seq

description: CTCF_XenopusEE.merged.macs2.2023_treat_pileup.bedGraph.gz

value: pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract for 140 min, with addition of recombinant CTCF protein

value: anti-CTCF (Millipore, 07-729)


title: Intratibial tumor treated with IL-27 vector and PvP; harvested on day 14 [LCS9550_D14_pIL27_PVP_M4]

value: Prostate adenocarcinoma


title: Subcutaneous tumor treated with empty vector [LCS9574_Tctrl_1]


title: MWIK_2

data_processing:
FASTQ files were converted into single cell matrices using 10X Cell Ranger and were transformed into a Seurat object using the Seurat package in R
Initial exclusion criteria included features that were present in less than 100 cells and cells where less than 1000 features were detected

source_name: Thymus

extract_protocol:
Freshly sorted EPCAM+Ly51- mTECs were collected in 0.04% BSA in PBS, then sent to the UCSF Genomics core for processing
Per UCSF Genomics Core
Single cells were captured using the 10X Chromium microfluidics system and cells were encapsulated and barcoded cDNA libraries were prepared using the single-cell 3'mRNA kit (10X Genomics). Single cell libraries were sequenced using a NovaSeq 6000 (lllumina)

value: Thymus

value: medullary thymic epithelial cell

value: Foxn1-Cre(+) Ikarosfl/fl


title: HUVECs, Vctrl Ago 2

value: control


title: Intratibial tumor treated with IL-27 vector and cabozantinib; harvested on day 14 [LCS9550_D14_pIL27_Cabo_M24]


title: NES_Enrich_Arsenite_3

value: Hepatocellular Carcinoma

value: APEX-NES

value: Sodium Arsenite

value: Yes

value: HuR 3A2 (Santa Cruz, cat. #sc-5261)


title: Pooled CMO library for 9 brain organoids replicate#2

description: 10x Genomics

value: Brain organoid

value: H9 ESCs

value: Neural progenitors and neurons

value: WT

value: 120 days


title: Intratibial tumor treated with IL-27 vector and cabozantinib; harvested on day 14 [LCS9550_D14_pIL27_Cabo_M22]

value: tumor


title: Pooled CMO library for 9 brain organoids replicate#1

description: 10x Genomics


title: Intratibial tumor treated with IL-27 vector and cabozantinib; harvested on day 14 [LCS9550_D14_pIL27_Cabo_M20]


title: patient_5IgM_MBC_Low_affinity

city: Indianapolis

first: Prasida

last: Holla

address: 1044 W walnut St

department: Pediatric Infectious Diseases

institute: Indiana University School of Medicine

data_processing:
Raw NGS reads were trimmed to remove adapters and low-quality regions using Trimmomatic v0.33
Trimmed reads were aligned to the human hg38 reference genome and Gencode release 26 annotation using STAR v2.5.2b
Read and alignment quality were assessed using MultiQCv1.1 to aggregate QC metrics from Picard (http://broadinstitute.github.io/picard/), FastQC v0.11.5, FastQ screen v0.9.3 and RseQC v1.1.8
Gene-level expression was quantified using RSEM v1.3.0
Assembly: Human - hg38 / Gencode Release 26
Supplementary files format and content: Text files generated using RSEM v1.3.0  containing raw counts

source_name: peripheral blood monouclear cell (PBMC)

growth_protocol: Peripheral blood draw was done, and mononuclear cells were isolated by ficoll gradient purification. B cells were further sorted into subsets by staining with fluorophore conjugated antibodies and FACS

extract_protocol:
Cells were lysed with RLT buffer (Qiagen) and RNA was isolated using the Qiagen AllPrep 96 kit as per manufacturer's instructions except treatment with 27 units DNAse I to removegenomic DNA contamination. cDAN was synthesized using SMART-Seq v4 Ultra Low Input RNA kit
600 pg sheared cDNA was used as input into the low Inout Library Prep kit v2 (Clonetech/Takara Bio) and prepared following manufacturer's protocol Final NGS libraries were assessed on a BioAnalyzer 2100 using High Sensitivity Chips. The libraries were normalized to 0.5 nM, pooled equally and prepared for sequencing on the NextSeq (illumina, San Diego) following manufacturer's guidelines  for two mid-output 2X76 cycles.

treatment_protocol: Sorted B cell subsets (Naïve, IgM MBC and IgG MBC) from each patient were stimulated under different conditions. Cells were incubated on a planar lipid bilayer embedded with either low affinity or high affinity antigens (Low_affinity and High_affinity respectively). As a control, cells were incubated with no antigen (Unstimulated). Cells were also stimulated with low- or high affinity antigens in the presence of a cocktail (IL-4+IL-21+anti-CD40 antibody) that mimics T cell help in vitro (labeled T cell or TH media). Cells were treated with T cell stimulation/ TH media only, or in addition to low- or high affinity antigens on PLB (Low_affinity+TH media and High_affinity+T cell respectively).

value: peripheral blood monouclear cell (PBMC)

value: B lymphocyte


title: HUVECs, Vctrl Ago 1

value: Human umbilical vein endothelial cells

value: anti-Ago2 antibody (Clone 11A9, Cat # SAB4200085, Sigma-Aldrich)


title: Pronuclei 140min, +123nM CTCF, CTCF ChIP-Seq

first: Roman

institute: IMP - Research Institute of Molecular Pathology

value: pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract for 140 min, with addition of recombinant CTCF protein

value: anti-CTCF (Millipore, 07-729)


title: NES_Input_Arsenite_2

value: Hepatocellular Carcinoma