title: ATRX-/- TERT-/- clone 3

city: Berkeley

first: Dirk

last: Hockemeyer

address: Li Ka Shing Center

department: MCB

institute: UC Berkeley

description: proximity ligated gDNA

data_processing:
Alignment of fastq paired end file against human hg38 index with only major chromosomes and mitochodrial chromosome using bwa mem with option -5SP, then converted to bam format with samtools view with options -Shb
Bam files are then further process with pairtools parse with the following options --min-mapq 40, -walks-policy 5unique and --max-inter-align-gap 30 to create a pairsam file
the pairsam files are sorted with pairtools sort with default option then PCR duplicates are removed using pairtools dedup then valid pair files and final bam files are created with pairtools split with default options.
Contact matrix in .mcool format are created by feading valid pairs in pairix format from pairtools into cooler cload with default bin size to 1000, then balanced with cooler balance with default options and the final multi-resolution contac matrix created with cooler zoomify with option --balance
Assembly: hg38
Supplementary files format and content: .mcool: contact matrix of proximy ligation assay at multiple resolution in cooler format

growth_protocol: E7-differentiated cultures were maintained in “E7” medium (DMEM/F12 [Gibco] supplemented with 10% FB Essence [Seradigm], 64 mg/L L-ascorbic acid [Sigma-Aldrich], 14 µg/L sodium selenium [Sigma-Aldrich], 100 µg/L FGF-Basic (AA 1-155) [Gibco], 19.4 mg/L insulin [Sigma-Aldrich], 543 mg/L NaHCO3 [Sigma-Aldrich], and 10.7 mg/L transferrin [Sigma-Aldrich]. Cells were grown on tissue culture plates treated with Matrigel matrix [Corning] and passages using Trypsin-EDTA (0.25%) [Gibco]. U2OS cells were maintained in fibroblast medium (DMEM [Gibco] supplemented with 15% FB Essence [Seradigm], 1 mM glutamine [Sigma-Aldrich], 1% non-essential amino acids [Gibco], and 100 U/mL Penicillin-Streptomycin [Gibco]) and passaged every 3-5 days enzymatically with Trypsin-EDTA (0.25%) [Gibco].

extract_protocol:
Micro-C assay was performed following Dovetail Micro-C kit protocol on 1x106 XXX  cells. Briefily, frozen cells were resuspended in 1X PBS and crosslinked with 3mM DSG and 1% formaldehyde. Washed cells were digested with 0.5 uL MNase in 100 uL of Nuclease digest buffer with MgCl2. Digestion was stop by addition of 5 µl of EDTA 0.5M. Chromatin was solubilize by addition of 3µl of 20% SDS and capture on chromatin capture beads. Chromatin bound DNA ends were repaired and A-tailed using the End Polishing enzyme mix and buffer. Dovetail bridge was then ligated to the chromatin bound DNA free ends following the Micro-C kit protocol then subjected to intra-aggregate ligation to create chromatin-chromatin long range interaction. Finally, the DNA bound to chromatin was recovered by proteinase K treatment and crosslink reversal and purify using SPRIselect beads (Beckman Coulter).
NEB NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: hESC colonies were lifted from the MEF feeder layer enzymatically with 1.5 mg/mL collagenase type IV [Gibco] and isolated by sedimentation and washing 3 times with wash medium. Colonies were suspended in E7 medium and transferred to tissue culture dishes treated with Matrigel [Corning]. After 7 days, cultures were passaged using Trypsin-EDTA (0.25%) [Gibco], triturated to single-cell suspension, and plated on Matrigel-coated tissue culture dishes. Cultures were maintained in E7 medium and were passaged every 5-7 days.

value: fibroblasts

value: ATRX-/-

value: E7 differentiation


title: U2OS

status: Public on Feb 21 2023

type: SRA

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: osteosarcoma


title: PBMC, Groupe2, J15, animal 895

city: Paris

first: Sylvain

last: Baize

address: 25-28 rue du Docteur Roux, CEDEX 15

country: France

institute: Institut Pasteur

library_source: transcriptomic

data_processing:
Bioinformatics analysis was performed using the RNA-seq pipeline from Sequana. Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11. Only sequences of at least 25 nucleotides in length were considered for further analysis. STAR version 2.5.0a, with default parameters, was used for alignment against the reference genome (Macaca Fascicularis 5 from ENSEMBL version 95). Reads were assigned to genes using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -O -s 2).
Assembly: Macaca Fascicularis 5 from ENSEMBL version 95
Supplementary files format and content: Table of read counts normalized by TPM

molecule: total RNA

organism: Macaca fascicularis

source_name: blood

extract_protocol:
Total RNA was extracted from PBMCs collected on days 0, 3, 6, 9, and 12 using the RNeasy Mini Kit with DNase treatment (Qiagen).
The libraries were prepared using the NEXTflex Rapid Directional RNA-seq (RNA sequencing) Kit (Bioo Scientific) and were quantified and qualified using a Quantus quantification kit (Promega) and a fragment analyzer advanced analytical (AATI).

tag: tissue

value: blood

value: peripheral blood mononuclear cell

value: PBMC

tag: treatment


title: ATRX-/- TERT-/- clone 2

description: proximity ligated gDNA

tag: genotype


title: ATRX-/- TERT-/- clone 4

description: proximity ligated gDNA


title: ATRX-/- TERT-/- clone 5

description: proximity ligated gDNA


title: ATRX-/- TERT-/- clone 1

description: proximity ligated gDNA


title: PBMC, Groupe2, J9, animal 852


title: PBMC, Groupe2, J9, animal 644


title: ATRX-/- TERT-/- clone 6

description: proximity ligated gDNA


title: PBMC, Groupe2, J9, animal 895


title: Knockout embryonic day 15.5 replicate 1

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Comparisons: developmental age+ genotype effect on lung gene expression

hyb_protocol: The biotinylated RNA was fragmented and hybridized to the Affymetrix array for 16 hr at 45 degree C in a hybridization oven rotating at 60 rpm. The array was washed and stained with streptavidin–phycoerythrin using an Affymetrix Fluidics Station 450.

scan_protocol: The array was scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The chip data was analyzed using Affymetrix GeneChip Operating Software (GCOS) version 1.2.

label: biotin

organism: Mus musculus

source_name: Homogenized lung tissue

label_protocol: cDNA was synthesized from RNA using a one-cycle cDNAsynthesis kit. Biotinylated RNA was then synthesized from cDNA using an IVT labeling kit after incubating at 37◦C for 16 hr.

extract_protocol: Total RNA was extracted from lung homogenates of each lung (n=3 samples per group, for E13.5, 2-3 lungs were combined for one sample.) using the Qiagen RNeasy Mini kit (Qiagen, Valencia, CA). Quality and quantity of RNAs were evaluated by an Agilent 2100 Bioanalyzer analysis (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Mice were time mated. Water and feed (AIN-76A) were provided ad libitum to time-pregnant dams and postnatal mice. The temperature (72±3 degree F) and humidity (50±15 percent) of the room were monitored and mice were exposed to a 12-hr light-dark cycle. Embryos were taken from pregnant dams by surgery and embryonic lungs were harvest at designated ages. At designated postnatal age, mouse lungs were harvested. All lungs were snap frozen in liquid nitrogen and stored at -70C until used.

tag: developmental age

value: embryo E15.5


title: Wild type postnatal day 14 replicate 1

value: juvenile PND14


title: PBMC, Groupe2, J6, animal 852


title: Wild type postnatal day 14 replicate 3


title: PBMC, Groupe2, J6, animal 895


title: Wild type postnatal day 42 replicate 2

value: adult PND42


title: Wild type postnatal day 42 replicate 1


title: Wild type postnatal day 4 replicate 2

value: neonate PND4


title: Wild type postnatal day 42 replicate 3


title: PBMC, Groupe2, J6, animal 644


title: Wild type postnatal day 4 replicate 1


title: Wild type postnatal day 3 replicate 3

value: neonate PND3


title: Wild type postnatal day 14 replicate 2


title: ATRX-/- TERT-/- clone 8

description: proximity ligated gDNA


title: Wild type postnatal day 4 replicate 3


title: PBMC, Groupe2, J3, animal 895


title: ATRX-/- TERT-/- clone 11

description: proximity ligated gDNA


title: ATRX-/- TERT-/- clone 10

description: proximity ligated gDNA


title: ATRX-/- TERT-/- clone 9

description: proximity ligated gDNA


title: ATRX-/- TERT-/- clone 7

description: proximity ligated gDNA


title: Wild type postnatal day 3 replicate 2


title: ATRX-/- TERT-/- clone 12

description: proximity ligated gDNA


title: PBMC, Groupe2, J0, animal 895


title: ATRX-/- TERT-/- clone 14

description: proximity ligated gDNA


title: ATRX-/- TERT-/- clone 13

description: proximity ligated gDNA


title: PBMC, Groupe2, J3, animal 852


title: ATRX+/+ TERT-/- clone 27

description: proximity ligated gDNA

value: ATRX+/+


title: ATRX+/+ TERT-/- clone 28

description: proximity ligated gDNA


title: CD4+ T cells, wildtype, EAE, day 9, 1

city: Urbana

first: Makoto

last: Inoue

state: Il

address: 2001 S Lincoln Ave

institute: University of Illinois at Urbana-Champaign

description: Sample 1

data_processing:
Samples were demultiplexed and adapter sequences were removed along with any reads shorter than 35 nt.
Salmon version 1.2.0 was used to quasi-map reads to the GRCm39 Annotation 109 transcriptome and quantify the counts for each transcript, then summed to gene level after adjusting for transcript lengths using the tximport package (v1.18.0) in R (v4.0.3).
Assembly: NCBI GRCm39, Annotation Release 109
Supplementary files format and content: Summed gene-level counts: Inoue_GeneCounts_forGEO.txt

source_name: CD4+ T cells

extract_protocol:
Total RNA was extracted from CD4+ T cells with QIAGEN RNeasy kit
Library construction and sequencing was done at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign using the Ovation RNASeq kit from Tecan and sequencing 100 bp single end reads on one SP lane in a NovaSeq 6000

value: CD4+ T cells

value: wildtype

tag: batch


title: ATRX+/+ TERT-/- clone 26

description: proximity ligated gDNA


title: ATRX+/+ TERT-/- clone 25

description: proximity ligated gDNA


title: PBMC, Groupe1, J12, animal 944


title: PBMC, Groupe1, J15, animal 406


title: PBMC, Groupe1, J15, animal 944


title: PBMC, Groupe1, J15, animal 841


title: PBMC, Groupe2, J3, animal 644


title: Wild type postnatal day 3 replicate 1


title: PBMC, Groupe2, J0, animal 852


title: PBMC, Groupe1, J12, animal 841


title: PBMC, Groupe2, J0, animal 644


title: ATRX+/+ TERT-/- clone 24

description: proximity ligated gDNA


title: Wild type postnatal day 2 replicate 2

value: neonate PND2


title: Wild type postnatal day 1 replicate 2

value: neonate PND1


title: Wild type postnatal day 0 replicate 3

value: neonate PND0


title: Wild type postnatal day 0 replicate 1


title: Wild type postnatal day 1 replicate 1


title: ATRX+/+ TERT-/- clone 29

description: proximity ligated gDNA

value: fibroblasts


title: Wild type postnatal day 0 replicate 2


title: PBMC, Groupe1, J9, animal 944


title: Wild type postnatal day 1 replicate 3


title: ATRX+/+ TERT-/- clone 23

description: proximity ligated gDNA

value: E7 differentiation


title: Wild type embryonic day 18.5 replicate 3

value: embryo E18.5


title: Wild type postnatal day 2 replicate 1


title: Wild type embryonic day 18.5 replicate 2


title: PBMC, Groupe1, J12, animal 406

value: blood


title: Wild type postnatal day 2 replicate 3


title: ATRX+/+ TERT-/- clone 22

description: proximity ligated gDNA


title: KO9-P-G-11

city: Singapore

first: Ying

last: Li

state: --- Select a state ---

address: 14 Medical Dr, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Reads were mapped to murine genome and quantified using Salmon.
The transcript expression was converted by tximport and normalized with “DESeq2”.
Assembly: GRCm39
Supplementary files format and content: gene expression in matrix table

source_name: B16/F10 murine melanoma tumor

growth_protocol: One hundred thousand of B16/F10 (Cas9 control or XRN1 depleted) cells was subcutaneously injected into left flank of C57BL/6. Mice were sacrificed one month after tumor inoculation.

extract_protocol:
Three largest tumors of each group (four groups and 12 samples in total) were digested for RNA extraction. Total RNAs were extracted using Rneasy Mini kit (Qiagen).
standard protocol for NovaSeq PE150 by Novogen
Three largest tumors of each group (four groups and 12 samples in total) were digested for RNA extraction. Total RNAs were extracted using Rneasy Mini kit (Qiagen).

treatment_protocol: Mice were treated with GVAX on the middle back of mice subcutaneously (injected twice at day -1 and day 1 respectively, tumor inoclulated at day 0). PD-1 antibody (100 μg per injection, Bio-X-Cell) was injected every three days with the first dose at day forth after tumor inoculation (four doses in total).

value: B16/F10 murine melanoma tumor

tag: gene manipulation

value: XRN1 depletion

value: XRN1 KO

tag: inoculation

value: XRN1 KO cells were inoculated into C57BL/6 mice

value: GVAX plus PD-1 antibody


title: KO9-P-G-12


title: ATRX+/+ TERT-/- clone 21

description: proximity ligated gDNA


title: PBMC, Groupe1, J9, animal 406

value: peripheral blood mononuclear cell

value: PBMC


title: PBMC, Groupe1, J9, animal 841


title: ATRX+/+ TERT-/- clone 19

description: proximity ligated gDNA

value: ATRX+/+


title: PBMC, Groupe1, J6, animal 944


title: PBMC, Groupe1, J6, animal 841


title: ATRX+/+ TERT-/- clone 18

description: proximity ligated gDNA


title: ATRX+/+ TERT-/- clone 20

description: proximity ligated gDNA


title: PBMC, Groupe1, J6, animal 406


title: ATRX+/+ TERT-/- clone 17

description: proximity ligated gDNA


title: KO9-5

value: MOCK


title: PBMC, Groupe1, J3, animal 944


title: ATRX+/+ TERT-/- clone 16

description: proximity ligated gDNA


title: KO9-4


title: ATRX+/+ TERT-/- clone 15

description: proximity ligated gDNA


title: PBMC, Groupe1, J3, animal 841


title: Cas9-P-G-9

value: Cas9 control

value: control

value: control cells were inoculated into C57BL/6 mice


title: PBMC, Groupe1, J3, animal 406


title: Cas9-P-G-8


title: SCLE2

city: changsha

first: zheng

last: meiling

state: Hunan

address: jiefang middle street

country: China

institute: central south university

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were aligned through 10X Genomics Cell Ranger (3.0.0) using GRCh38.
We mainly applied the Seurat package(v4.0.3) for downstream data analysis through the standard data analysis process
Assembly: GRCh38
Supplementary files format and content: cell-gene expression matrix

source_name: skin

extract_protocol:
Briefly, skin tissue samples were digested using a full-thickness skin isolation kit (Miltenyi Biotec, Germany). After 2 h of enzymatic dissociation, mechanical dissociation of skin tissue was performed using gentleMacs Dissociator (Miltenyi Biotec) in program h_skin_01.
Single-cell cDNA libraries were prepared using 10X Genomics Chromium Single cell 3' Reagent Kits (3.1) according to the manufacturer's instructions.

value: skin

tag: diagnosis

value: SCLE

tag: disease state

value: skin lesion

value: no treatment


title: KO9-P-G-10


title: PBMC, Groupe1, J0, animal 944

value: blood


title: Wild type embryonic day 15.5 replicate 2

value: embryo E15.5


title: Wild type embryonic day 15.5 replicate 3


title: Wild type embryonic day 13.5 replicate 2

value: embryo E13.5


title: Wild type embryonic day 13.5 replicate 3


title: Wild type embryonic day 13.5 replicate 1


title: Wild type embryonic day 17.5 replicate 2

value: embryo E17.5


title: Wild type embryonic day 17.5 replicate 1


title: wild type control Replicate 3

city: Guangzhou

first: Wei

last: Xiao

state: Guangdong

address: S 54 Xianlie Rd, Yuexiu District

institute: Zhongshan Ophthalmic Center

description: Gene expression in wild type lens at 3 months old

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent Gene Expression hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: wild type mouse lens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations. RNA was cleaned up using RNasey Mini Kit(Qiagen p/n 74104) and was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: BetaB2-W151C knock-in mice expressing an G to C point mutation in codon 151 of the mouse βB2-crystallin gene CRYBB2, which results in the substitution of Tryptophan 151 with Cysteine (W151C), were generated using CRISPR/Cas9 system by Shanghai Biomodel Organisms Science & Technology Development Co., Ltd. (Shanghai, China)

tag: age

value: 3 months old

value: lens

value: wild type


title: Cas9-P-G-7

value: B16/F10 murine melanoma tumor

value: GVAX plus PD-1 antibody


title: Wild type embryonic day 17.5 replicate 3


title: Wild type embryonic day 18.5 replicate 1

value: embryo E18.5


title: Cas9-3

value: Cas9 control

value: MOCK


title: Wild type embryonic day 15.5 replicate 1


title: SCLE1


title: SCLE3


title: PBMC, Groupe1, J0, animal 406

value: peripheral blood mononuclear cell

value: PBMC


title: TB8762

city: New York

first: Osama

last: Al Dalahmah

state: NY

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

description: 10X Genomics

data_processing:
snRNA samples was processed with 10X genomics software Cell Ranger
Alignment was done using the CellRanger pipeline (10X Genomics) to GRCh38.p12 (refdata-cellranger-GRCh38-1.2.0 file provided by 10x genomics). Count matrices were generated from BAM files using default parameters of the DropEst pipeline (Petukhov V et al. 2018).
Filtering and QC was done using the scater package (3). Nuclei with percent exonic reads from all reads in the range of 25-75% were included. Nuclei with percent mitochondrial reads aligning to mitochondria genes of more than 19% were excluded.
Genes were filtered by keeping features with >10 counts per row in at least in 31 cells. Further filtering of low quality cells was done to include cells with at least 400 detected genes and 10,000 reads.
Assembly: GRCh38 Ensemble 91
Supplementary files format and content: .txt files of count matrix

source_name: GBM Tissue

extract_protocol:
Briefly, frozen tissue samples measuring from 5 x 4 x 3 mm to 10 x 6 x 3 mm were homogenized using a dounce homogenizer in ice-cold 30% sucrose 0.1% Triton-X 100 based homogenization buffer. 10-15 strokes of the loose dounce pestle were followed by 10-15 strokes of the tight dounce pestle on ice. Mixing using a P1000 pipette followed before filtration through a BD Falcon 40um filters.  Filtration was repeated after a 10-minute spin at 1000g at 4c. A cleanup step followed using a density gradient step as described in [41]. The nuclear pellet was suspended in 1% BSA in PBS resuspension buffer containing RNAse inhibitors. A final filtration step using 20um Flowmi ™ filters followed before dilution to 700-1200 nuclei per ul in resuspension buffer. The nuclear suspensions were processed by the Chromium Controller (10x Genomics) using single Cell 3’ Reagent Kit v2 or v3 (Chromium Single Cell 3’ Library & Gel Bead Kit v2, catalog number: 120237; Chromium Single Cell A Chip Kit, 48 runs, catalog number: 120236; 10x Genomics).
Sequencing of the resultant libraries was done on Illumina NOVAseq 6000 platformV4 150bp paired end reads.

value: GBM Tissue

tag: Sex

value: M

value: Recurrent

tag: molecule type

value: snRNA


title: Cas9-2

value: control

value: control cells were inoculated into C57BL/6 mice


title: PBMC, Groupe1, J0, animal 841

value: blood


title: Cas9-1


title: KO9-6

value: XRN1 depletion

value: XRN1 KO

value: XRN1 KO cells were inoculated into C57BL/6 mice


title: TB5053

description: 10X Genomics

value: F


title: TB5124

description: 10X Genomics


title: Ovary, Control for Post T, biol rep 4

city: Ann Arbor

first: Hadrian

middle: M

last: Kinnear

state: MI

address: 1101 Beal Avenue

department: Biomedical Engineering

institute: University of Michigan

data_processing:
Read mapping and counts were performed by the University of Michigan Advanced Genomics Core. Reads were trimmed using Cutadapt v2.3, FastQC v0.11.8 was used to ensure data quality and Fastq screen v0.13.0  was used to screen for various types of contamination. Reads were mapped to the reference genome GRCm38 (ENSEMBL) using STAR v2.7.8a and count estimates assigned to genes with RSEM v1.3.3.
Assembly: GRCm38 (ENSEMBL)
Supplementary files format and content: tab-delimited text files of count matrices as expected counts, FPKM, or TPM for each sample (gene_expected_count.annot.txt, gene_FPKM.annot.txt, gene_TPM.annot.txt)

molecule: polyA RNA

source_name: Ovary

growth_protocol: Mice were housed in groups of five in ventilated cages and had free access to food and water and a 12-hour light/dark cycle within a non-barrier facility at the University of Michigan.

extract_protocol:
Mouse ovaries (one per mouse) were micro dissected from perigonadal fat at the time of sacrifice and stored frozen in RNAlater at -20°C. Tissue disruption and homogenization were performed using the Kimble Biomasher II and QIA shredder homogenizer. RNA was extracted following manufacturer instructions using the Qiagen RNeasy Mini Kit with Qiagen RNase-Free DNase set and subsequently stored at -80°C.
Paired-end RNA sequencing with poly-A selection was performed by the University of Michigan Advanced Genomics Core on the Illumina NovaSeq 6000 (PE150) using 7.5% of a 300 cycle S4 shared flow cell with 30–40 million reads per sample. Libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760) with NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 2, E7780). De-multiplexed Fastq files were generated with Bcl2fastq2 Conversion Software (Illumina).

treatment_protocol: Testosterone (T) therapy was administered via a weekly (Thurs PM) subcutaneous mid-back injection (100 mL). Each dose included 0.9 mg T enanthate, diluted with sesame oil from a 200 mg/mL stock (Hikma Pharmaceuticals, Portugal). Sesame oil was sterile filtered before use (USP/NF grade, Welch, Holme & Clark Co., Inc., Newark, NJ, USA).

value: Ovary

tag: strain

tag: age (weeks)

value: Control

tag: time

value: cessation


title: TB4437

description: 10X Genomics

value: Seizure epileptic brain


title: Ovary, Post T, biol rep 4

value: Testosterone


title: TB4849

description: 10X Genomics


title: βB2-crystallin W151C knock-in Replicate 4

description: Gene expression in βB2-crystallin W151C mutant lens at 3 months old

source_name: βB2-crystallin W151C knock-in mouse lens

value: 3 months old

value: lens

value: BetaB2-crystallin W151C knock-in


title: Ovary, Post T, biol rep 3


title: TB4027

description: 10X Genomics

value: GBM Tissue

value: M

value: Recurrent


title: TB4416

description: 10X Genomics

value: snRNA


title: βB2-crystallin W151C knock-in Replicate 2


title: Ovary, Control for Post T, biol rep 3


title: wild type control Replicate 1

value: wild type


title: wild type control Replicate 2


title: PANC1 RAPA-1 RNA

city: Bronx

first: Kamini

last: Singh

address: 1300 Morris Park Ave, Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

description:
RiboDiff.output.PDAC_Rapamycin.tsv.gz
RNA_cuffnorm.genes.fpkm.tsv.gz
RNA_cuffnorm.genes.count.tsv.gz
RNA_cuffnorm.isoforms.fpkm.tsv.gz
RNA_cuffnorm.isoforms.count.tsv.gz

data_processing:
Sequence Alignment: Ribosome footprint (RF) reads were filtered such that only reads with a minimum quality score of 25 were kept for at least 75% of nucleotides. The linker sequence was trimmed from the 3′ end of the reads. Reads shorter than 15 nt were filtered out. These pre-processing steps were conducted with FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index). Removal of ribosomal RNA was conducted by aligning RF reads to the ribosomal RNA sequences of GRCh37 downloaded from UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables). The reads were then mapped to GRCh37 using HISAT2 (http://daehwankimlab.github.io/hisat2/) with default parameters. Only uniquely aligned reads were used for further analysis. Similar to RF reads, total mRNA sequencing reads were similarly aligned to GRCh37 using HISAT2, and splice alignment for paired-end mRNA-seq datasets was performed with default parameters. Only uniquely aligned reads were used for further analysis. Alignment quantification of both RF and mRNA sequencing was conducted with featureCounts, using the annotations of GRCh37 protein-coding genes as input. For further analysis, we only used reads aligned to exonic regions of the protein-coding genes.
Footprint Analysis: Ribo-Diff was used to analyze translation efficiency based on ribosome foot-printing and mRNA sequencing data. Genes with significantly changed translation efficiency were defined by a q-value cut-off of 0.05.
Gene expression analysis:  The Cufflinks v2.2.1 package was used on RNA-seq replicates to identify the dominant isoforms for footprinting metagene analysis.
Assembly: GRCh37.75
Supplementary files format and content: RiboDiff.output.PDAC_Rapamycin.tsv.gz: gzipped tab-separated RiboDiff output file
Supplementary files format and content: RNA_cuffnorm.genes.fpkm.tsv.gz: gzipped tab-separated expression matrix of FPKM for 63,653 annotated genes
Supplementary files format and content: RNA_cuffnorm.genes.count.tsv.gz: gzipped tab-separated expression matrix of normalized counts for 63,653 annotated genes
Supplementary files format and content: RNA_cuffnorm.isoforms.fpkm.tsv.gz: gzipped tab-separated expression matrix of FPKM for 214,292 annotated isoforms
Supplementary files format and content: RNA_cuffnorm.isoforms.count.tsv.gz: gzipped tab-separated expression matrix of normalized counts for 214,292 annotated isoforms

growth_protocol: Pancreatic cancer cell lines were cultured in DMEM media supplemented with 10% fetal bovine serum and penicillin-streptomycin-glutamine

extract_protocol:
Total RNA and ribosome-protected fragments were isolated following published protocol (Ingolia, N.T.; Brar, G.A.; Rouskin, S.; McGeachy, A.M.; Weissman, J.S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 2012, 7, 1534–1550. https://doi.org/10.1038/nprot.2012.086)
Deep sequencing libraries were generated from these fragments and sequenced on the HiSeq 2000 platform. Genome annotation was conducted with the human genome sequence GRCh37 downloaded from the Ensembl public database (http://www.ensembl.org)

treatment_protocol: Cells were treated with DMSO (CT) or rapamycin (RAPA)

tag: cell line

value: Human pancreatic duct

value: Rapamycin treated

tag: fraction

value: Total RNA


title: TB3966

description: 10X Genomics

tag: tissue

value: F


title: PANC1 RAPA-3 RNA

tag: cell type

tag: treatment


title: PANC1 CT-3 RNA


title: PANC1 RAPA-2 RNA


title: Ovary, On T, biol rep 4

value: Ovary


title: Ovary, Control for On T, biol rep 4

value: Control


title: GC1-HDAC6-1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: Labeled cRNA sample were fragmented at 60ºC and hybridized on to Agilent Mus musculus Gene Expression Microarray 8X60K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method and gene based analysis was performed.

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: The cells were cultured in DMEM (high glucose) supplemented with 10% FBS 100 U of penicillin/100 µg of streptomycin and maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted from Trizol

treatment_protocol: The Murine HDAC6 gene under CMV promoter  with myc/DDK tag in a pCMV plasmid vector was procured. The plasmid was isolated using Midiprep kit .Cells were transfected with either Hdac6 containing vector (GC-1Hdac6) or empty vector (GC-1ev) as per manufacturer’s instructions, and incubated in the above mentioned media at 37 °C in an atmosphere of 5% CO2 for 48h, with media changed after 24h. Post transfection, cells were harvested and subjected to Microarray

value: GC1 cell line


title: βB2-crystallin W151C knock-in Replicate 1

tag: genotype


title: GC1-HDAC6-2


title: PANC1 CT-2 RNA


title: AGO1 IP sRNA rep1

city: Riverside

first: Ye

last: Xu

address: 900 University Ave

institute: University of California, Riverside

description: AGO1-bound small RNA

data_processing:
Raw reads were analyzed by a homemade pipeline pRNASeqTools v0.8 (https://github.com/grubbybio/pRNASeqTools).
Raw reads were subjected to adapter trimming using cutadapt. Reads without an adapter or shorter than 18-nt after trimming were discarded from further processing.
Trimmed reads were aligned to the Arabidopsis genome using ShortStack v3.8 with parameters (--mismatches 0 --mmap u --bowtie_m 1000 --ranmax 50).
Mapped reads were separated by size and normalization was performed by calculating the RPM (Reads per million of (total-rRNA) reads), and comparison was conducted by DESeq2 v1.30.0.
The miRNAs are annotated based on Araport11.
Assembly: TAIR10
Supplementary files format and content: bigwig (.bw) file containing CPM-normalized 18-42nt small RNA read counts along the whole genome

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: 16 hr light and 8 hr dark at 22 ˚C on MS medium

extract_protocol:
12-day-old seedlings of AGO1 truncation mutants in the ago1-36 background were ground to a fine powder in liquid nitrogen and subjected to RNA extraction using TRI Reagent, small RNAs of 18-40 nucleotides (nt) were isolated from total RNA resolved on 15% urea-PAGE gels. 12-day-old Arabidopsis seedling of  AGO1::HA-AGO1 del 1-90AA in the ago1-36 background, AGO1::HA-AGO1 del 91-189AA and  AGO1::HA-AGO1 del 1-189AA in the ago1-36 /+  backgrounds were collected and ground into powder in liquid nitrogen then subjected to immunoprecipitation using HA antibody (sigma H3663).
Small RNA library was constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (E7300).

value: seedling

tag: ecotype

tag: transgene

value: 12 days old seedlings


title: ago1-36 sRNA rep3

description: total small RNA


title: PANC1 CT-1 RNA


title: TB3864

description: 10X Genomics


title: ago1-36 sRNA rep2

description: total small RNA


title: Ovary, On T, biol rep 3

value: Testosterone


title: AGO1 IP sRNA rep2

description: AGO1-bound small RNA


title: GC1-EV1

description: GC1-empty vector

source_name: GC1-empty vector


title: ago1-36 sRNA rep1

description: total small RNA


title: TB4443

description: 10X Genomics

value: Primary


title: GC1-EV2

description: GC1-empty vector replicate

source_name: GC1-empty vector replicate


title: PANC1 RAPA-3 RF

data_processing:
Sequence Alignment: Ribosome footprint (RF) reads were filtered such that only reads with a minimum quality score of 25 were kept for at least 75% of nucleotides. The linker sequence was trimmed from the 3′ end of the reads. Reads shorter than 15 nt were filtered out. These pre-processing steps were conducted with FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index). Removal of ribosomal RNA was conducted by aligning RF reads to the ribosomal RNA sequences of GRCh37 downloaded from UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables). The reads were then mapped to GRCh37 using HISAT2 (http://daehwankimlab.github.io/hisat2/) with default parameters. Only uniquely aligned reads were used for further analysis. Similar to RF reads, total mRNA sequencing reads were similarly aligned to GRCh37 using HISAT2, and splice alignment for paired-end mRNA-seq datasets was performed with default parameters. Only uniquely aligned reads were used for further analysis. Alignment quantification of both RF and mRNA sequencing was conducted with featureCounts, using the annotations of GRCh37 protein-coding genes as input. For further analysis, we only used reads aligned to exonic regions of the protein-coding genes.
Footprint Analysis: Ribo-Diff was used to analyze translation efficiency based on ribosome foot-printing and mRNA sequencing data. Genes with significantly changed translation efficiency were defined by a q-value cut-off of 0.05.
Gene expression analysis:  The Cufflinks v2.2.1 package was used on RNA-seq replicates to identify the dominant isoforms for footprinting metagene analysis.
Assembly: GRCh37.75
Supplementary files format and content: RiboDiff.output.PDAC_Rapamycin.tsv.gz: gzipped tab-separated RiboDiff output file
Supplementary files format and content: RNA_cuffnorm.genes.fpkm.tsv.gz: gzipped tab-separated expression matrix of FPKM for 63,653 annotated genes
Supplementary files format and content: RNA_cuffnorm.genes.count.tsv.gz: gzipped tab-separated expression matrix of normalized counts for 63,653 annotated genes
Supplementary files format and content: RNA_cuffnorm.isoforms.fpkm.tsv.gz: gzipped tab-separated expression matrix of FPKM for 214,292 annotated isoforms
Supplementary files format and content: RNA_cuffnorm.isoforms.count.tsv.gz: gzipped tab-separated expression matrix of normalized counts for 214,292 annotated isoforms
Library strategy: Ribo-Seq

value: Ribosome protected RNA


title: AGO1 sRNA rep3

description: total small RNA


title: AGO1 sRNA rep2

description: total small RNA


title: Ovary, Post T, biol rep 2

value: cessation


title: Ovary, Control for On T, biol rep 3


title: TB5635

description: 10X Genomics

value: GBM Tissue


title: PANC1 RAPA-1 RF


title: AGO1 sRNA rep1

description: total small RNA


title: Ovary, Control for Post T, biol rep 2


title: PANC1 RAPA-2 RF


title: AGO1_91_IP_sRNA_rep2

description:
AGO1-bound sRNA
AGO1 delete 91-189AA IP-sRNA-seq

source_name: 12 days old seedlings

value: AGO1::3XHA-AGO1 del 91-189AA


title: TB5980

description: 10X Genomics

value: M

value: snRNA


title: PANC1 CT-3 RF

value: Human pancreatic duct


title: TB5618

description: 10X Genomics


title: PANC1 CT-2 RF


title: Ovary, On T, biol rep 2


title: AGO1_91_IP_sRNA_rep1


title: TB4100

description: 10X Genomics


title: AGO1_189_IP_sRNA_rep2

description:
AGO1-bound sRNA
AGO1 delete 1-189AA IP-sRNA-seq

value: AGO1::3XHA-AGO1 del 1-189AA


title: PANC1 CT-1 RF


title: H1975 cells, AICAR3

city: Orlando

first: Wencai

last: Zhang

state: FL

address: 6900 Lake Nona Blvd

institute: University of Central Florida

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample, differential expression

source_name: Lung tumor tissue-derived cell line H1975, AICAR1

growth_protocol: The H1975 cell line was maintained in a 5% CO2 atmosphere at 37oC. It was cultured in DMEM (high glucose) (GIBCO) with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptomycin.

extract_protocol:
RNA was harvested using mirVana miRNA Isolation Kit from Invitrogen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were treated with 1 mM AICAR for four hours

value: Lung tumor

value: Lung cancer cells

value: treated with 1 mM AICAR for four hours


title: AGO1_189_IP_sRNA_rep1


title: Ovary, Control for Post T, biol rep 1

value: Ovary

value: Control


title: Ovary, Post T, biol rep 1


title: H1975 cells, AICAR2


title: TB4567

description: 10X Genomics

value: F


title: Ovary, On T, biol rep 1


title: TB3926

description: 10X Genomics


title: TB4916

description: 10X Genomics


title: Ovary, Control for On T, biol rep 1


title: AGO1_90_IP_sRNA_rep1

description:
AGO1-bound sRNA
AGO1 delete 1-90AA IP-sRNA-seq

value: AGO1::3XHA-AGO1 del 1-90AA

value: 12 days old seedlings


title: Ovary, Control for On T, biol rep 2


title: TB4718

description: 10X Genomics

value: Primary


title: B16/F10-Cas9

data_processing:
Reads were mapped to Mus musculus genome by STAR(2.4.0i) with default parameters for paired-end
Gene expression were called by featureCounts(v1.5.0-p1)
Assembly: GRCm38.p6
Supplementary files format and content: gene expression in matrix table

source_name: murine melanoma cell line

growth_protocol: The cells were grown in DMEM medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
standard protocol for lncRNA seq by Novogen
Total RNAs were extracted using Rneasy Mini kit (Qiagen).

value: CRISPR_v2_puro empty vector was transfected into B16/F10 cells via lentivirus. Two weeks (at least) after viral transfection, total RNA was extracted for NGS seq.

tag: expression manipulation technique

value: sgRNA


title: H1975 cells, vehicle3

source_name: Lung tumor tissue-derived cell line H1975, vehicle

value: vehicle treated


title: H1975 cells, vehicle2


title: H1975 cells, vehicle1


title: B16/F10-siCtrl

value: Control siRNA (Ctrl, UCGAAGUAUUCCGCGUACG) was transfected into B16/F10 cells via RNAiMAX (cat# 13778075, Invitrogen). Total RNA was extracted for NGS seq after 48h of siRNA transfection.

value: siRNA


title: TB3652

description: 10X Genomics

value: GBM Tissue

value: M

value: snRNA


title: H1975 cells, AICAR1

value: Lung tumor


title: TB4189

description: 10X Genomics

value: Cortex with astrogliosis


title: AGO1_91_sRNA_rep1

description:
total small RNA
AGO1 delete 91-189AA

value: AGO1::3XHA-AGO1 del 91-189AA


title: Supernatant3

city: JInan

first: Mengmeng

last: Liu

address: Wenhuaxi Road

institute: Shandong University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

source_name: human oral epithelial immorted cell

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: tag

value: Human oral epithelial cell

value: Supernatant


title: MDA-MB-231L - Input2 - BRD4 (m2OE)

city: Rochester

first: Alexandre

last: Gaspar-Maia

state: MN

address: 200 First street SW

institute: Mayo Clinic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore v0.6.4 (Cutadapt v3.1)
Reads were then aligned to hg19 (mm9 for DF) whole genome using bowtie2 v2.3.3.1, alignment files were sorted and indexed using samtools v1.9, duplicate removal done using Picard v2.9.0
deepTools bamCoverage v3.5.0 was used to convert bam to bigWig
macs2 v2.2.7.1 was used to call peaks (to convert bam to bed)
Genome_build: hg19 (mm9 for DF)
Supplementary_files_format_and_content: bigWig (as produced by deepTools bamCoverage)
Supplementary_files_format_and_content: bed (as produced by macs2)

growth_protocol: Normal Human Melanocytes (NHM) were cultures in Dermal Cell Basal Medium (ATCC) with the addition of 5 µg/mL Insulin, 50 µg/mL Ascorbic Acid, 6 mM L-Glutamine, 1.0 µM Epinephrine, 1.5 mM Calcium Chloride, Peptide Growth Factor and M8 Supplement. MCF-7, DFs and MDA-MB-231L cells were grown in DMEM (Gibco) with 4.5 g/L D-glucose, 110 mg/L sodium pyruvate, 10% FBS and 1% Penicillin/Streptomycin (Hyclone). HMEC cells were grown in complete Mammary Epithelial Cell Growth Media.

extract_protocol:
Native ChIP was done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).
Libraries for ChIP-seq were done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).

treatment_protocol: MCF7 cells were treated with estradiol (E2) treatment MCF-7 cells were grown for 5 days in modified DMEM without phenol-red (Hyclone) with 4.5 g/L D-glucose, 4.0 L-glutamine, 10% charcoal-dextran–stripped FBS, 1% Penicillin/Streptomycin and 1nM of 17-β-estradiol or EtOH.

tag: ectopic expression

value: over-expressed mH2A2-GFP


title: AGO1_91_sRNA_rep2

description:
total small RNA
AGO1 delete 91-189AA


title: TB4957

description: 10X Genomics

tag: disease state

value: Focal architecture abnormalities; hippocampus with focal neuronal loss

tag: age


title: AGO1_189_sRNA_rep3

description:
total small RNA
AGO1 delete 1-189AA

value: AGO1::3XHA-AGO1 del 1-189AA

value: 12 days old seedlings


title: AGO1_189_sRNA_rep2

description:
total small RNA
AGO1 delete 1-189AA


title: B16/F10-sgXrn1

value: sgXrn1#1 was transfected into B16/F10 cells via lentivirus. Two weeks (at least) after viral transfection, total RNA was extracted for NGS seq.


title: B16/F10-siXrn1

value: siXrn1 (SASI_Mm01_00154570, Sigma Aldrich) was transfected into B16/F10 cells via RNAiMAX (cat# 13778075, Invitrogen). Total RNA was extracted for NGS seq after 48h of siRNA transfection.


title: AGO1_90_IP_sRNA_rep2

value: AGO1::3XHA-AGO1 del 1-90AA


title: D4M.3A-Cas9

value: CRISPR_v2_puro empty vector was transfected into D4M.3A cells via lentivirus. Two weeks (at least) after viral transfection, total RNA was extracted for NGS seq.

value: sgRNA


title: Supernatant1


title: Supernatant2


title: MDA-MB-231L - Input2 - p300 (m2OE)


title: MDA-MB-231L - Input2 - H3K4me1 (m2OE)


title: AGO1_91_sRNA_rep3

description:
total small RNA
AGO1 delete 91-189AA


title: D4M.3A-sgXrn1

value: sgXrn1#1 was transfected into D4M.3A cells via lentivirus. Two weeks (at least) after viral transfection, total RNA was extracted for NGS seq.


title: AGO1_189_sRNA_rep1

description:
total small RNA
AGO1 delete 1-189AA


title: MDA-MB-231L - Input2 - H3K27ac (m2OE)


title: D4M.4A-shCtrl

extract_protocol:
standard protocol for NovaSeq PE150 by Novogen
Total RNAs were extracted using Rneasy Mini kit (Qiagen).

value: Control shRNA (Ctrl) was transfected into D4M.3A cells via lentivirus. Two weeks (at least) after viral transfection, total RNA was extracted for NGS seq.

value: shRNA


title: P. gingivalis2


title: P. gingivalis3


title: MDA-MB-231L - Input2 - BRD4 (GFP)

value: over-expressed GFP-H2A


title: D4M.3A-shXrn1

value: shXrn1#1 was transfected into D4M.3A cells via lentivirus. Two weeks (at least) after viral transfection, total RNA was extracted for NGS seq.


title: P. gingivalis1


title: AGO1_90_sRNA_rep2

description:
total small RNA
AGO1 delete 1-90AA


title: MDA-MB-231L - Input2 - p300 (GFP)


title: MDA-MB-231L - Input2 - H3K4me1 (GFP)


title: B. pertussis,  8h of fermentation, replicate 3

city: Lyon

first: Paul

last: Anziani

address: 40 avenue Tony Garnier

institute: Bioaster

data_processing:
Basecalls were performed using the sequencer software (Illumina)
Sequencing QC was performed on raw data with fastqc tool
Raw data were imported in Array Studio (v11.0) software (OmicSoft Qiagen). Reads were trimmed to remove low quality bases with default parameters.
Reads were mapped to the NCBI genome of the strain of B. pertussis Tohama I (RefSeq accession number NC_002929.2)
QC was performed on aligned reads. Count table was generated with default parameters.
Counts were normlized by RLE method using R.
Assembly: RefSeq accession number NC_002929.2 ; assembly GCF_000195715.1
Supplementary files format and content: Excel matrix files including RLE normalized Log2(counts) for each sample

organism: Bordetella pertussis Tohama I

source_name: Tohama I

growth_protocol: Bordetella pertussis Tohama I were fermented in a chemically defined medium derived from Stainer and Scholte medium. Cultures were performed  in a small scale biofermenters (Ambr® 250, Sartorius) in a batch mode at constant temperature of 36°C, pH 7.3, and level of dissolved oxygen at 26%.

extract_protocol:
1 Optical density in 1ml was sampled and incubated 1h at room temperature with 33% v/v of RNAlater (Invitrogen). Then, samples were centrifuged, supernatants were discarded, and pellet were stored at -80°C. Bacteria pellets were lysed in 200 µl of TE buffer (Invitrogen™) with 15 mg.ml-1 of lysozyme (Thermo Fisher Scientific) and 1 mg.ml-1 of proteinase K (Qiagen) for 10 min at 400 rpm, at room temperature. Then RNA extraction was performed on column using RNeasy® mini kit (Qiagen) including an on-column DNase digestion. A second step of DNase digestion was performed by DNase TURBO™ (Thermo Fisher Scientific).
Libraries were prepared in triplicate for each sample by using the Universal RNA-Seq kit (Tecan Genomics). Fragmentation was performed with the Covaris® M220 Focused-ultrasonicator™ for 90 seconds at 50 W, 10% duty factor, 200 burst per cycle, to obtain 400 bp (base pair) cDNA fragments. Ribosomal RNAs were depleted using AnyDeplete technology (Tecan Genomics) with specific B. pertussis rRNA probes. Libraries were obtained after 18 cycles PCR amplification.

treatment_protocol: Fermentation were sampled at 1h, 4h, 8h, 12h, 18h45, 22h, 26h (final sampling)

value: Tohama I

value: WT

value: 8h of fermentation


title: Control2

value: Human oral epithelial cell

value: untreated


title: B. pertussis,  8h of fermentation, replicate 2


title: B. pertussis,  4h of fermentation, replicate 3

value: 4h of fermentation


title: B. pertussis,  8h of fermentation, replicate 1


title: Control1


title: MDA-MB-231L - Input1 - macro H2A.2 (m2OE)

value: over-expressed mH2A2-GFP


title: MDA-MB-231L - Input2 (GFP)


title: MDA-MB-231L - Input1 - macro H2A.2 (GFP)


title: MDA-MB-231L - Input2 - H3K27ac (GFP)


title: B. pertussis,  4h of fermentation, replicate 2


title: MDA-MB-231L - Input1 - macro H2A.1 (GFP)


title: AGO1_90_sRNA_rep3

description:
total small RNA
AGO1 delete 1-90AA

value: 12 days old seedlings


title: B. pertussis,  26h of fermentation, replicate 3

value: 26h of fermentation


title: 12667

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt version 1.12
then trimmed and filtered for quality using the FASTX-Toolkit (Hannon Lab)
Remaining reads were aligned to Plasmodium using hisat2(https://www.nature.com/articles/s41587-019-0201-4)
Reads mapping to genes were counted using htseq-count (Anders et al., 2015)
Differential expression analysis was performed using the Bioconductor package DESeq2  (Love et al., 2014)
Assembly: GCF_900002375.1_PBANKA01 and GCA_900088445.1_PbNK65E
Supplementary files format and content: tab-delimited text files include deseq2 values for each Sample

organism:
Plasmodium berghei
Mus musculus

source_name: Mus musculus infected with Plasmodium_berghei_ANKA

extract_protocol:
Mouse cheek blood samples were mixed with Trizol LS (Thermofisher) in 1:3 ratio and RNA was isolated according to manufacturer’s guidelines
TruSeq Total RNA-Seq, Globin-zero

treatment_protocol: Both Pb ANKA and Pb NK65 parasites stocks were originally grown in C57BL/6 mice. To avoid non-parasite specific immune response against infected C57BL/6 RBCs in Balb/c animals, initial Pb ANKA stock was divided into two and injected into both C57BL/6 and Balb/c donor animals. These parasites were passaged three times in respective mouse strains in order to fully adapt the parasite into the host.


title: 12670


title: 12669


title: 12668


title: Control3


title: 9701417056_R01C02

type: genomic

city: Berlin

first: David

last: Kaul

address: Augustenburger Platz 1

department: Department of Radiation Oncology

country: Germany

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: After bisulfite conversion using the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation450k BeadChip and Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
The calculations were carried out in R, version 4.2.0 "Virgorous Calesthenics"
Average beta-Values after normalization using detection p values

label: cy3, cy5

source_name: Tumor

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted form FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) , according to the manufacturer’s instructions

tag: Sex

value: Female

tag: incoming diagnosis

value: Anaplastic ependymoma (WHO grade III)

tag: tumor location

value: infratentorial

tag: progression-free survival (months)

tag: progression (0=no, 1=yes)

tag: overall survival (months)

tag: death (0=no, 1=yes)

tag: material type

value: KRYO


title: B. pertussis,  26h of fermentation, replicate 2

tag: strain

tag: time


title: 12665

source_name: Mus musculus infected with Plasmodium_berghei_NK66

tag: treatment


title: AGO1_90_sRNA_rep1

description:
total small RNA
AGO1 delete 1-90AA

tag: ecotype

tag: genotype

tag: transgene

value: AGO1::3XHA-AGO1 del 1-90AA

tag: tissue


title: MDA-MB-231L - Input1 (GFP)

tag: cell line

tag: ectopic expression


title: B. pertussis,  26h of fermentation, replicate 1


title: 12666


title: MDA-MB-231L - Input1 - H3K27me3 (GFP)


title: B. pertussis,  4h of fermentation, replicate 1


title: Normal Human Melanocytes - macro H2A.2

source_name: Normal Human Melanocytes

value: Normal Human Melanocytes


title: B. pertussis,  22h of fermentation, replicate 3

value: 22h of fermentation


title: MDA-MB-231L - ATAC (GFP)

extract_protocol:
DNA for ATAC-seq  was prepared from 20,000 cells following the OMNI-ATAC procedures from Corces et al. (Nature Methods 2017) and Buenrostro et al. (Curr Protoc Mol Biol 2016), with modifications, using the Nextera kit (Illumina).  The cells were lysed for 3 minutes on ice and transposed for 30 minutes at 37C.  DNA was cleaned-up using procedures of a DNA extraction column.
The DNA libraries were prepared with 5-9 cycles of PCR amplification with the NEB High Fidelity Master Mix (New England Biolabs).  Clean up was done using the Zymo DNA Clean and Concentrator kit (Zymo Research) and followed with AMPure XP (Beckman Coulter) bead cleanup to remove primer dimers and under-digested chromatin.

value: over-expressed GFP-H2A


title: 12663


title: Normal Human Melanocytes - macro H2A.1


title: MDA-MB-231L - ATAC (m2OE)


title: B. pertussis,  22h of fermentation, replicate 2

value: Tohama I


title: 12661


title: 12662


title: B. pertussis,  22h of fermentation, replicate 1

value: WT


title: Normal Human Melanocytes - Input


title: B. pertussis,  1h of fermentation, replicate 3

value: 1h of fermentation


title: 12660


title: MCF-7 - scATAC-seq - KO

value: macroH2A2 knockout


title: B. pertussis,  1h of fermentation, replicate 2


title: B. pertussis,  1h of fermentation, replicate 1


title: 12659


title: 12658


title: 12664


title: MCF-7 - macro H2A.2


title: B. pertussis,  18h45 of fermentation, replicate 3

value: 18h45 of fermentation


title: 12657


title: MCF-7 - Input


title: B. pertussis,  18h45 of fermentation, replicate 1


title: B. pertussis,  18h45 of fermentation, replicate 2


title: 12655


title: B. pertussis,  12h of fermentation, replicate 3

value: 12h of fermentation


title: 12654

source_name: Mus musculus infected with Plasmodium_berghei_NK65


title: Human Mammary Epithelial Cells - macro H2A.2

source_name: Human Mammary Epithelial Cells

value: Human Mammary Epithelial Cells


title: 12653


title: Human Mammary Epithelial Cells - macro H2A.1


title: B. pertussis,  12h of fermentation, replicate 1


title: Human Mammary Epithelial Cells - Input


title: iPSC-derived microglia HIV-1 (WT) rep1

status: Public on Feb 20 2023

city: Heidelberg

first: Carl

last: Herrmann

address: INF 267

department: Medical Faculty

institute: University Heidelberg

data_processing:
Filtering for reads with LTR sequence (PE on the first mate/SE) or with Linker sequence (PE, on the second mate) (allowing 2 mismatches)
Trimming with Cutadapt (v3.2) and filtering for reads longer than 15bp
Alignment to hg38/HIV genome using BLAT (parameters: -stepSize=6 -minIdentity=97 -maxIntron=0 -minScore=15)
Exclusion of BLAT results aligning less than 30 bp (SE) or 10bp (PE)
Exclusion of duplicates (distance less or equal to 10 bp) was performed on the merged set
Assembly: hg38
Supplementary files format and content: bed files of IS
Library strategy: viral integration site sequencing

source_name: Microglia

extract_protocol:
Infected C20 microglia cells were harvested 3 d.p.i and DNA was isolated and sonicated. The LM PCR protocol was adapted from (Serrao et al. 2016). Sonicated gDNA ends were repaired using End-It™ DNA End-Repair Kit (Epicentre) and A-tailing was performed using NEBNext® dA-Tailing Module (NEB). An asymmetric double stranded linker was annealed overnight at 12°C (800 U T4 ligase, 10x ligase buffer, 1.5 mM linker). After purification, first nested PCR with linker and LTR specific primers was performed. The second nested PCR with the same linker specific primer and an inner LTR specific primer containing Illumina sequencing index was performed.
Library of viral-genome junctions was constructed by PCR with in-house primers annealing to HIV-1 LTR region and linker region, containing Illumina adapters and dual indexes.

treatment_protocol: For  IS sequencing in CTCF KD conditions, the day before transfection, 2x 106 microglia cells were seeded in 10 cm dish and transfected using Lipofectamine RNAiMAX Transfection Reagent (ThermoFisher) according to the manufacturer's instructions. In brief, 22 pmol (for 10 nm siRNA end concentration) of either ON-TARGETplus Non-targeting Control siRNA (Horizon Discovery) or ON-TARGETplus Human CTCF SMARTPool (Horizon Discovery) were mixed with 500 μl Opti-MEM medium (Gibco). Then 30 μl Lipofectamine reagent were added to 500 μl Opti-MEM medium (Gibco) and mixed with the siRNA mix, incubated for 10 min at RT and added dropwise to the cells. After this treatment, C20 microglia cells were infected either with 250ng p24/ 1 mill cells with VSVG pseudotyped WT HIV-1 virus.

value: (iPSC)-derived human microglial cells (iMG)

tag: infection

value: VSV-G pseudotyped eGFP HIV-1

value: infected


title: iPSC-derived microglia HIV-1 (WT) rep2


title: Microglia HIV-1 (WT) CTCF-KD rep3

value: HIV-1 wild type

value: Infected; host cells were siRNA CTCF


title: MCF-7 - scATAC-seq - WT

value: wild type


title: Microglia HIV-1 (WT) CTCF-KD rep1


title: Microglia HIV-1 (WT) CTCF-NT rep3

value: infected; host cells were siRNA NT


title: Microglia HIV-1 (WT) infected rep3 PE

treatment_protocol: C20 microglia cells were infected either with 250ng p24/ 1 mill cells with VSVG pseudotyped WT HIV-1 virus.


title: Microglia HIV-1 (WT) infected rep2 PE


title: Microglia HIV-1 (WT) infected rep1 PE


title: 12656


title: MCF-7 - macro H2A.1


title: Microglia HIV-1 (WT) infected rep2


title: Microglia HIV-1 (WT) infected rep1


title: B. pertussis,  12h of fermentation, replicate 2


title: Microglia HIV-1 (WT) CTCF-NT rep2


title: Microglia HIV-1 (WT) CTCF-NT rep1


title: Huh-7 xenografts-2, Ad-K458R

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the sample
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads).
We use "FDR ≤0.001 and the absolute value of log2Ratio ≥1" as the threshold to judge the significance of gene expression difference.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes counts and normalized FPKM values for each Sample

source_name: Huh-7 xenografts

growth_protocol: Huh7 cells were subcutaneously injected into the flanks of NOD/SCID mice.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (foreukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). 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 fragments are enriched by PCR  amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.

treatment_protocol: when the tumors were established around 100 mm3, the mice were administered adenovirus intratumorally once every four days for eight days

value: Huh-7 xenografts

tag: cell type

value: hepatocellular carcinoma cell


title: Huh-7 xenografts-3, Ad-GK458R


title: Huh-7 xenografts-1, Ad-GFP

value: Ad-GFP


title: Huh-7 xenografts-2, Ad-GFP


title: Huh-7 xenografts-3, Ad-HNF4A


title: Huh-7 xenografts-3, Ad-GFP


title: Huh-7 xenografts-1, Ad-HNF4A


title: Huh-7 xenografts-2, Ad-HNF4A


title: Microglia HIV-1 (WT) infected rep3


title: Peri_P18, Inflamed

city: Atlanta

first: Greg

last: Gibson

state: GA

address: North Ave NW

institute: Georgia Institute of Technology

description: 10X Genomics

data_processing:
CellRanger (v.6.1.2) software was used to generate count matrices and align transcriptome to reference genome.
Seruat package (v.4.1.1) in Rstudio was used for quality control and clustering the data. MAST (v.1.24)was used for DEG analysis.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: rectum

extract_protocol:
Rectal biopsies were processed using protease protocol. Obtained single cells were encapsulated according to manufacturer's protocol using Chromium Next GEM Single Cell 3’ Reagent Kit v 3.1 Dual Index (PN-100268), targeting 10,000 cells.
Obtained cDNA were amplified for subsequent library preparation using 10x Library coonstruction kit (Part No. 1000190) and sequenced at a read depth of 50,000 reads per cell by Illumina NovaSeq S4 sequencing.

value: rectum

tag: Sex

value: M

tag: inflammation status

value: Inflamed

tag: batch

tag: disease status

value: Perianal Fistulizing CD


title: Peri_P15, Inflamed

description: 10X Genomics


title: Peri_P21, Non-inflamed

description: 10X Genomics

value: F

value: Non-inflamed


title: Peri_P19, Non-inflamed (non-IBD Control)

description: 10X Genomics

value: non-IBD Control


title: Peri_P20, Non-inflamed

description: 10X Genomics


title: Peri_P8, Non-inflamed

description: 10X Genomics


title: Peri_P17, Non-inflamed

description: 10X Genomics


title: Peri_P5, Inflamed

description: 10X Genomics


title: Peri_P7, Inflamed

description: 10X Genomics


title: Huh-7 xenografts-1, Ad-K458R

value: WT


title: RNA-Seq Donor2_EGR2_KO

city: Philadelphia

first: Inyoung

last: Jung

state: PA

address: SPE, 9-304, 3400 Civic Center Blvd, Bldg. 421

institute: University of Pennsylvania

data_processing:
Sequencing was performed on a Novaseq 6000 (Illumina) at a depth of ~20,000 reads / cell. Reads were aligned to the human reference genome (GRCh38) using Cell Ranger ARC 2.0. Subsequent quality control and downstream analyses were performed using Seurat 4.1.1 in R. Low-quality cells were eliminated based on following criteria: (1) a minimum of 1,000 genes and a maximum of 6,000 genes detected per cell, (2) less than 15% of mitochondrial gene counts, (3) a minimum 1,000 and maximum of 25,000 ATAC read counts, (4) a nucleosome signal less than two, and (5) a transcription start site enrichment score greater than two. For gene expression analysis, RNA counts were normalized using SCTransform followed by integration of four CAR T-cell datasets using SelectIntegrationFeatures, PrepSCTIntegration, FindIntegrationAnchors, and IntegrateData functions in Seurat. Data were then scaled using ScaleData, followed by principal-component analysis and graph building using the RunPCA, FindNeighbors, and FindClusters. Differential gene expression analyses between subclusters and samples were conducted using the FindMarkers command.
Supplementary files format and content: filtered_feature_bc_matrix.h5
Assembly: GRCh38

source_name: blood

extract_protocol: AAVS1 and EGR2 knockout PSMA CAR T-cells produced from two different healthy subjects were isolated from the in vitro “stress test” after multiple consecutive rounds of antigen stimulation. Dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec), and PSMA CAR-expressing T-cells were enriched by magnetic cell separation using a Biotin-goat anti-mouse IgG F(ab)2 fragment (Jackson ImmunoResearch #115-065-072) and anti-biotin beads (Miltenyi Biotech). CAR T-cells were washed with PBS supplemented with 0.04 % BSA and nuclei were isolated according to the manufacturer’s protocol (10x Genomics). Briefly, cells were incubated with lysis buffer for four minutes, washed three times and resuspended in chilled dilute nuclei buffer (10x Genomics). Absolute cell numbers were enumerated, and viability was determined using the trypan blue dye exclusion method.

value: blood

tag: cell subtype

value: CAR-T

value: T-cell

value: EGR2 KO

tag: condition

tag: biological replication

value: Normal donor 2


title: RNA-Seq Donor2_AAVS1_KO

value: AAVS1  KO


title: RNA-Seq Donor1_AAVS1_KO

value: Normal donor 1


title: ATAC-Seq Donor2_EGR2_KO

data_processing:
Sequencing was performed on a Novaseq 6000 (Illumina) at a depth of ~20,000 reads / cell. Reads were aligned to the human reference genome (GRCh38) using Cell Ranger ARC 2.0. Subsequent quality control and downstream analyses were performed using Seurat 4.1.1 and Signac 1.7.0 in R. Low-quality cells were eliminated based on following criteria: (1) a minimum of 1,000 genes and a maximum of 6,000 genes detected per cell, (2) less than 15% of mitochondrial gene counts, (3) a minimum 1,000 and maximum of 25,000 ATAC read counts, (4) a nucleosome signal less than two, and (5) a transcription start site enrichment score greater than two. For ATACseq data, peaks were called using MACS2 with the CallPeaks function followed by removal of peaks overlapping genomic blacklist regions. We then quantified counts in each peak using FeatureMatrix. Frequency-inverse document frequency (TF-IDF) normalization and dimension reduction were conducted using RunTFIDF, FindTopFeatures, and RunSVD.
Supplementary files format and content: fragments.tsv.gz
Assembly: GRCh38


title: ATAC-Seq Donor2_AAVS1_KO


title: Peri_P16, Inflamed

description: 10X Genomics


title: ATAC-Seq Donor1_EGR2_KO


title: Microglia CTCF CTCF-KD rep1

description: Sequenced on Nov 2022

data_processing:
Trimming performed with trimGalore v0.4
Read alignment with bowtie2 v2.3 (--very-sensitive -q -p 10 -X 2000) to hg38
Peaks were called using MACS2 v2.1 (-q 0.05 —nomodel) using broad cut-off=0.1 (the latter on H3K36me3).
BigWigs were produced using deeptools v3.0 function bamCompare (—normalizeUsing RPKM --ignoreDuplicates -bs 40)
Assembly: hg38
Supplementary files format and content: peak files and bigwig files with coverage

extract_protocol:
10x10^6 million microglia cells were fixed with 1% formaldehyde/PBS  followed by quenching with 0.125 M glycine. After washing with  cold PBS, pellet was resuspended in swelling buffer, cytosol was removed and nuclei sonicated. Lysates were cleared and 2-8 microgram of chromatin were incubated with corresponding amounts of antibody overnight at 4°C. The next day, chromatin was captured with Protein A/G beads, washed and eluted with TE buffer, 1% SDS, 100 mM NaCl. 0.5 mg/ml Proteinase K were added, and samples were incubated for 2 h at 55°C and overnight at 65°C. The next day, RNA was digested. Supernatant was removed from the magnetic beads and DNA was purified with AMpure beads XP clean up according to manufacturer’s instructions.
ChIP libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®  (NEB) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (NEB) according to manufacturer’s instructions.

treatment_protocol: The day before transfection, 2x 10^6 microglia cells were seeded in 10 cm dish and transfected using Lipofectamine RNAiMAX Transfection Reagent (ThermoFisher) according to the manufacturer's instructions. In brief, 22 pmol (for 10 nm siRNA end concentration) of either ON-TARGETplus Non-targeting Control siRNA (Horizon Discovery) or ON-TARGETplus Human CTCF SMARTPool (Horizon Discovery) were mixed with 500 μl Opti-MEM medium (Gibco). Then 30 μl Lipofectamine reagent were added to 500 μl Opti-MEM medium (Gibco) and mixed with the siRNA mix, incubated for 10 min at RT and added dropwise to the cells.

tag: chip antibody

value: CTCF (Cell Signaling,  #3418)

value: CTCF-KD


title: Microglia Input rep1

description: Sequenced on Nov 2022

tag: treatment

value: untreated


title: Microglia Input rep2

description: Sequenced on Nov 2022


title: Microglia CTCF CTCF-KD rep2

description: Sequenced on Nov 2022


title: Microglia CTCF NT rep2

description: Sequenced on Nov 2022


title: Peri_P11, Inflamed

description: 10X Genomics

value: rectum

value: M


title: Peri_P13, Non-inflamed

description: 10X Genomics

value: Perianal Fistulizing CD


title: Microglia CTCF NT rep3

description: Sequenced on Nov 2022


title: Microglia CTCF NT rep1

description: Sequenced on Nov 2022


title: ATAC-Seq Donor1_AAVS1_KO


title: Microglia H3K36me3 CTCF-KD rep2

description: Sequenced on Nov 2022

value: H3K36me3 (ab9050, Abcam)


title: Microglia H3K36me3 NT rep1

description: Sequenced on Nov 2022


title: Mini_screen_MV411_end_DMSO_rep2

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
20bp sgRNA sequence was extracted from each read.
Each 20bp sequence was aligned to the mini CRISPR library with Bowtie.
Count table was generated through counting the frequency of each sgRNA.
Supplementary files format and content: tab-delimited counts file
Library strategy: CRISPR screen

source_name: Human AML cell line

extract_protocol:
Cells were lysed with Tris/SDS buffer supplemented with protease inhibitor, and DNA was precipitated with 40% isopropanol
Region contatining sgRNA sequence was amplified with two sequenctial PCR and final product was gel purified--focused CRISPR mini-library was recovered

value: Blood

value: Parental

value: DMSO

tag: duration

value: 10 doublings


title: Mini_screen_MV411_start_rep1

tag: genotype


title: Microglia H3K36me3 NT rep2

description: Sequenced on Nov 2022


title: Mini_screen_MV411_end_099_rep2

value: 5uM SHP099


title: RNA-Seq Donor1_EGR2_KO

value: blood

value: CAR-T

value: T-cell


title: Microglia H3K36me3 CTCF-KD rep1

description: Sequenced on Nov 2022


title: Mini_screen_MV411_end_099_rep1


title: Peri_P6, Non-inflamed

description: 10X Genomics

value: Non-inflamed


title: Mini_screen_MV411_end_DMSO_rep1


title: Mini_screen_MOLM14_start_rep2


title: Mini_screen_MOLM14_end_DMSO_rep2


title: Mini_screen_MOLM14_end_DMSO_rep1


title: Mini_screen_MOLM14_start_rep1


title: Mini_screen_MOLM14_end_5uM_rep2


title: Mini_screen_MOLM14_end_099_3uM_rep2

value: 3uM SHP099


title: Mini_screen_MOLM14_end_099_3uM_rep1


title: Mini_screen_MV411_start_rep2


title: Mini_screen_KU812_end_DMSO_rep2

source_name: Human CML cell line


title: Mini_screen_KYO1_end_099_rep1

value: 10uM SHP099


title: Mini_screen_KYO1_end_DMSO_rep2


title: Mini_screen_KYO1_start_rep2


title: Mini_screen_KU812_end_099_rep2


title: Mini_screen_KYO1_end_099_rep2


title: Mini_screen_KU812_start_rep2


title: Mini_screen_MOLM14_end_5uM_rep1


title: Mini_screen_KU812_start_rep1


title: Mini_screen_KYO1_start_rep1


title: Mini_screen_KG1a_end_099_rep2


title: Mini_screen_KG1a_end_099_rep1


title: Mini_screen_K562_start_rep1


title: Mini_screen_KYO1_end_DMSO_rep1


title: Mini_screen_KU812_end_099_rep1


title: Mini_screen_K562_end_DMSO_rep1


title: Mini_screen_KG1a_end_DMSO_rep1


title: Mini_screen_K562_end_099_rep2


title: Mini_screen_KG1a_end_DMSO_rep2


title: Mini_screen_K562_end_DMSO_rep2


title: Mini_screen_K562_end_099_rep1


title: Mini_screen_EOL1_start_rep1


title: Mini_screen_EOL1_end_DMSO_rep2


title: Mini_screen_EOL1_start_rep2


title: Mini_screen_EOL1_end_DMSO_rep1


title: Mini_screen_EOL1_end_099_rep1


title: Mini_screen_KU812_end_DMSO_rep1


title: Mini_screen_K562_start_rep2


title: Genomic_screen_MV411_end_DMSO_rep2

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
20bp sgRNA sequence was extracted from each read.
Each 20bp sequence was aligned to the human TKOv3 CRISPR library with Bowtie.
Count table was generated through counting the frequency of each sgRNA.
Supplementary files format and content: tab-delimited counts file
Library strategy: CRISPR Screen

source_name: Huamn AML cell line

extract_protocol:
Cells were lysed with Tris/SDS buffer supplemented with protease inhibitor, and DNA was precipitated with 40% isopropanol
Region contatining sgRNA sequence was amplified with two sequenctial PCR and final product was gel purified--genomic library is recovered

value: AML

value: parental

value: 12 doublings


title: Genomic_screen_MV411_start_rep1


title: Mini_screen_BV173_start_rep2


title: Genomic_screen_MV411_end_099_rep1


title: Mini_screen_BV173_start_rep1


title: Genomic_screen_MV411_start_rep2


title: Mini_screen_BV173_end_DMSO_rep1


title: Mini_screen_BV173_end_099_rep2


title: Mini_screen_BV173_end_099_rep1


title: Mini_screen_BV173_end_DMSO_rep2


title: Genomic_screen_MV411_end_DMSO_rep1


title: primed hiPSCs cultured in 2D, E8, rep3

city: Padua

first: Alessia

last: Gesualdo

address: Via Gradenigo, 6a

department: Industrial Engineering

country: Italy

institute: University of Padua

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with RSEM 1.3.0
Differential expression analysis was performed using edgeR
Assembly: hg38
tab-delimited text files include raw counts values for all Samples

source_name: primed human induced Pluripotent Stem Cells

growth_protocol: Naïve hiPSCs were cultured in 3D in a drop of Matrigel for 4 days in RSeT medium (Stemcell Technologies). Primed hiPSCs were cultured in 3D in a drop of Matrigel for 5 days in E8 medium (Stemcell Technologies). Primed hiPSCs were cultured in 2D on 0,5% of Matrigel for 4 days in E8 medium (Stemcell Technologies). Naïve hiPSCs in priming condition were cultured in 3D in a drop of Matrigel in priming medium as described in the method section of the manuscript for up to 10 days. Medium changed was performed every day until cells were harvested for RNA extraction.

extract_protocol:
The protocol of Qiagen RNEasy Mini Kit was followed
Libraries were prepared from 600-1000 pg of total RNA using the SMART-Seq v4 Ultra Low Input Kit (Takara Bio) followed by Nextera XT DNA Library Preparation kit (Illumina), following suggested protocol

tag: days of_culture

value: 4 days


title: primed hiPSCs cultured in 2D, E8, rep1

value: primed human induced Pluripotent Stem Cells


title: STAT6_post_PBMC_GEX

city: Hongkong

first: Zhongyi

state: Hongkong

address: L7-55 Paediatrics, Lab Block, Faculty of Medicine, 21 Sassoon Road, Pokfulam, HK

institute: The University of Hong Kong

data_processing:
The raw FASTQ data was obtained and the cellranger count function was then applied to generate single cell feature counts for every single library (Cell Ranger v5.0.1). The output of filtered feature-barcode matrix containing only detected cell-associated barcodes was used for further downstream analysis. The default parameters and options were applied for cellranger count after providing the input FASTQ data and the relevant prebuilt references of the Human dataset (GRCh38) downloaded from the 10x genomic website (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest/).
The filtered expression matrix generated by CellRanger for each sample was analyzed and processed with the R package Seurat (version 3.2.0). Quality control involved first filtering for quality based on the following criteria: mapping to over 200 unique genes, the fraction of mitochondrial transcripts was less than 10%, and the fraction of unique hemoglobin transcripts was less than 1%.
Scaling and clustering was performed on PBMCs and enriched T cells separately.  Dimensionality reduction using PCA was done on the 2000 most variable genes and UMAP was based on the first 20 PCs.
Cell identities were first annotated with SingleR using fine labeling from the Novershtern hematopoietic dataset (Aran et al., 2019; Novershtern et al., 2011) and Monaco Immune dataset(Monaco et al., 2019) for PBMCs and Enriched T cells respectively. The annotation was refined manually based on the UMAP clustering patterns, grouping the SingleR labels for PBMCs into 10 main populations: Naïve B cells, Memory B cells, Naïve CD4+, Memory CD4+, Naïve CD8+, Memory CD8+, Monocytes, Dendritic cells, NK cells, and others.
For differential gene expression analyses, we utilized the Seurat implementation of negative binomial test, assuming an underlying negative binomial distribution in RNA-Seq data(Hafemeister and Satija, 2019; Robinson and Smyth, 2007).
Assembly: Homo Sapiens (GRCh38)
Supplementary files format and content: Processed counts are presented as .csv files

source_name: PBMC

extract_protocol:
scaling and clustering was performed on PBMCs and enriched T cells separately.  Dimensionality reduction using PCA was done on the 2000 most variable genes and UMAP was based on the first 20 PCs.
Single cell encapsulation and library preparation are done at Genomics Core of the Centre for PanorOmic Sciences in LKS Faculty of Medicine of The University of Hong Kong. Single cell encapsulation and cDNA libraries were prepared by Chromium™ Single Cell 5’ Reagent Kit v1 and Chromium™ Single Cell A Chip Kit, or by Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index) and Chromium Next GEM Chip K Single Cell Kit.
Cells in suspension were counted and loaded into individual wells of 10X Chromium Single Cell chip (10X Genomics, Pleasanton, United States). Single cells were then encapsulated into Gel Beads-in-emulsion (GEM) by 10X Chromium Single Cell Controller. Single Cell 5’ Reagent Kit was used to perform downstream steps: reverse transcription is performed on GEMs, followed by cDNA clean-up and amplification. The double-stranded cDNA will then go through enzymatic fragmentation, adapter ligation, index PCR and SPRIselect size selection was done as per manufacturer’s protocol. Library size and concentration are determined by Qubit, quantitative PCR and Bioanalyzer assays. The libraries were denatured and diluted to optimal concentration. Illumina NovaSeq 6000 was used for pair-end 151bp sequencing with NovaSeq 6000 S4 Reagent Kit v1.0 and v1.5 (Illumina #20012866 and #20028312, San Diego, US).

tag: tissue

value: PBMC

tag: disease

value: severe early onset allergic disease

value: two years post- dupilumab treatment


title: STAT6_post_T_GEX

source_name: Enriched T cells

value: Enriched T cells


title: primed hiPSCs cultured in 2D, E8, rep4


title: STAT6_pre_T_GEX

value: pre-treatment


title: HC_PBMC_GEX

value: healthy control


title: STAT6_pre_PBMC_GEX


title: HC_T_GEX


title: Mini_screen_EOL1_end_099_rep2

city: New York

value: Blood

value: Parental

tag: cell line

value: 10 doublings


title: 4_Naive_3D_d4_4

source_name: naive hiPSCs cultured in 3D matrigel, RSeT, rep4

value: naive human induced Pluripotent Stem Cells


title: 32_Priming_3D_D10_4

source_name: naive to primed hiPSCs in 3D matrigel, priming medium, rep4

value: naive to primed human induced Pluripotent Stem Cells

value: 10 days


title: 31_Priming_3D_D10_3

source_name: naive to primed hiPSCs in 3D matrigel, priming medium, rep3


title: 9_Primed_3D_D5_1

source_name: primed hiPSCs cultured in 3D matrigel, E8, rep1

value: 5 days


title: Genomic_screen_MV411_end_099_rep2

value: AML

value: parental

value: 5uM SHP099


title: primed hiPSCs cultured in 2D, E8, rep2

value: primed human induced Pluripotent Stem Cells

value: 4 days


title: 3_Naive_3D_d4_3

source_name: naive hiPSCs cultured in 3D matrigel, RSeT, rep3


title: 30_Priming_3D_D10_2

source_name: naive to primed hiPSCs in 3D matrigel, priming medium, rep2


title: 28_Priming_3D_D8_4

value: 8 days


title: 29_Priming_3D_D10_1

source_name: naive to primed hiPSCs in 3D matrigel, priming medium, rep1


title: 19_Priming_3D_D4_3


title: 26_Priming_3D_D8_2


title: 25_Priming_3D_D8_1


title: 21_Priming_3D_D6_1

value: 6 days


title: 24_Priming_3D_D6_4


title: 18_Priming_3D_D4_2


title: 2_Naive_3D_d4_2

source_name: naive hiPSCs cultured in 3D matrigel, RSeT, rep2


title: 20_Priming_3D_D4_4


title: 23_Priming_3D_D6_3


title: 14_Priming_3D_D2_2

value: 2 days


title: 15_Priming_3D_D2_3


title: 22_Priming_3D_D6_2


title: 17_Priming_3D_D4_1


title: 13_Priming_3D_D2_1


title: 12_Primed_3D_D5_4

source_name: primed hiPSCs cultured in 3D matrigel, E8, rep4


title: 27_Priming_3D_D8_3


title: Parental-DMSO-4

data_processing:
Base calling and demultiplexing were performed using Illumina bcl2fastq software.
The sequencing reads were adapter- and quality-trimmed with Trimmomatic.
The sequencing reads were aligned to the human genome (build hg38/GRCh38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Assembly: hg38
Supplementary files format and content: CSV files contain raw and normalized counts for all genes and samples: counts-raw.csv (raw counts), counts-normalized.csv (normalized counts), and counts-tpm.csv (TPMs: Transcript Per Million mapped reads).

source_name: Human AML cell line MOLM13

extract_protocol:
RNA was extracted from fresh cell pellets using the Qiagen RNeasy Plus Mini Kit (Qiagen: 74136), according to the manufacturer's instructions.
RNA-Seq library preps were constructed with the Illumina TruSeq® Stranded mRNA Library Prep kit (Cat #20020595) using 1000ng of total RNA as input, amplified by 10 cycles of PCR, and sequenced paired-end 50 cycles on an Illumina NovaSeq6000 SP flowcell with a 2% PhiX spike-in.

value: 0.1% DMSO for 1h

tag: driver mutation


title: 10_Primed_3D_D5_2

source_name: primed hiPSCs cultured in 3D matrigel, E8, rep2

tag: cell type


title: Parental-DMSO-3


title: Monkey exosomes - Control 6, F

city: Los Angeles

first: Brian

middle: George

last: Dias

address: 4650 Sunset Blvd

department: Division of Endocrinology

institute: Children's Hospital Los Angeles

data_processing:
alignment (STAR)
counts stranded reads aligned to MacaM genome (featureCounts)
determine gene coverage by reads (bedtools)
Assembly: MacaM, INSDC Assembly GCA_003339765.3
Supplementary files format and content: comma-separated text file, read counts, gene coverage

organism: Macaca mulatta

source_name: plasma exosomes

extract_protocol:
TRIzol extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
ssRNA-seq

treatment_protocol: Ribogone

tag: age


title: Monkey exosomes - Maltreated 6, F


title: Monkey exosomes - Maltreated 4, F


title: 11_Primed_3D_D5_3

source_name: primed hiPSCs cultured in 3D matrigel, E8, rep3


title: 16_Priming_3D_D2_4


title: 1_Naive_3D_d4_1

source_name: naive hiPSCs cultured in 3D matrigel, RSeT, rep1


title: Monkey exosomes - Maltreated 5, F


title: Monkey exosomes - Control 5, F


title: Monkey exosomes - Maltreated 3, M


title: Monkey exosomes - Control 7, F


title: Parental-DMSO-2


title: Monkey exosomes - Maltreated 2, M


title: Parental-099-1

value: SHP099 1uM for 1h


title: Parental-099-3


title: KO-MAP4K5-DMSO-4

value: MAP4K5 KO


title: KO-MAP4K5-DMSO-3


title: Monkey exosomes - Maltreated 1, M


title: Monkey exosomes - Control 3, M


title: Monkey exosomes - Control 2, M


title: Monkey exosomes - Control 4, M


title: MD

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using an in-house program (https://github.com/baj12/clean_ngs).Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 1.2.2, with default parameters, was used for alignment on the reference genome
Genes were counted using HTSeq-count version 0.6.1
Assembly: Vibrio cholerae N16961 reference genome (accession numbers AE003852 andAE003853)
Supplementary files format and content: matrix table from DESeq2 analysis

organism: Vibrio cholerae O1 biovar El Tor str. N16961

source_name: Vibrio cholerae N16961 in M63 minimal medium supplemented with 0.4% succinate, 100 μg/ml asparagine and 10 μg/ml vitamin B1

extract_protocol:
RNA was harvested using protocol published in Krin et al, 2018.
rRNA were depleted with the MICROBExpress™ Bacterial mRNA Enrichment Kit (Fisher scientific, AM1905). RNA libraries for RNA-seq were prepared using the TruSeq Stranded RNA LT prep kit, set A and B (ref 15032611, Illumina). Sequencing was performed on the Illumina Hiseq2000 platform to generate single-end 51 bp reads bearing strand specificity.

value: bacterial cells

tag: media

value: M63 minimal medium


title: KO-MAP4K5-099-4


title: KO-MAP4K5-DMSO-2


title: MC


title: Monkey exosomes - Control 1, M


title: KO-MAP4K5-099-3


title: KO-MAP4K5-099-2


title: 4S

source_name: Vibrio cholerae N16961 in Luria Broth  with NaCl  332 mM stationary growth phase

value: Luria Broth

tag: growth phase

value: stationary


title: KO-INPPL1-DMSO-4

value: INPPL1 KO


title: 4E

source_name: Vibrio cholerae N16961 in Luria Broth  with NaCl  332 mM exponential growth phase

value: exponential


title: Parental-099-2

value: Parental


title: KO-INPPL1-099-4


title: marine-A-moins

source_name: Vibrio cholerae N16961 in Marine Broth exponential growth phase

value: Marine Broth


title: KO-INPPL1-099-3


title: 3S


title: KO-INPPL1-DMSO-3


title: 3E


title: 24gtGPRC5AKOtrTNFA7FTArp3-7KOTNFA7FTA

city: La Jolla

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

data_processing:
The  fastq files  for 24 samples (made available as raw data files) were analyzed using nf-core/RNA-seq pipeline (v1.4.2 Ewels et al 2020, PMID: 32055031) written in the Nextflow domain specific language.
Reads were aligned to the reference genome using STAR v2.6.1d and gene abundance was estimated using featureCounts v1.6.4. Raw gene counts were then used to get differentially expressed genes using Bioconductor R package DESeq2 v1.20.0. Genes with BH- adjusted P-value <=0.05 found by DESeq2 were assigned as significantly differentially expressed genes.
Assembly: GRCh38(Ensembl release 98)
Supplementary files format and content: Raw gene counts in a text file format

source_name: Colon

growth_protocol: Wild-type and GPRC5A knock-out HT-29 cells were grown in 6-well plates at 500,000 cells/well to above 90% confluence.

extract_protocol:
Cells were washed with cold DPBS, and RNA were purified using RNeasy Plus Kit (Qiagen).
400 ng total RNA from each sample was used to prepare indexed sequencing libraries using the New England Biolabs Ultra II RNAseq kit for Illumina with the polyA module and 10 cycles of PCR. Libraries were size selected with Ampure beads to approximately 300 base pairs, quantitated and pooled before loading onto a NextSeq2000 sequencer (Illumnina) to generate 100 base single end reads (approximately 20M per sample).

treatment_protocol: After 24 h, cells were changed to OMEM medium containing 0.1% DMSO, 50 µM 7FTA, 10 ng/mL TNFα with or without 7FTA for 8 h.

value: Colon

value: Epithelial

value: GPRC5A knockout

value: TNFa + 7FTA


title: KO-INPPL1-099-2


title: 22gtGPRC5AKOtrTNFA7FTArp1-7KOTNFA7FTA


title: 23gtGPRC5AKOtrTNFA7FTArp2-7KOTNFA7FTA


title: marine-B-moins


title: KO-INPPL1-DMSO-2


title: 21gtGPRC5AKOtrTNFArp3-6KOTNFA

value: TNFa


title: Microglia eGFP-mKO2+ (Latent) rep1

data_processing:
Trimming performed with trimGalore v0.4.3
Read alignment with bowtie2 v2.3 (--very-sensitive --fr -X 2000 -q -p 10) to hg38
Duplicates and bad quality reads were removed after using samtools v1.9 (min MAPQ=10) to mark them
Peaks were called using MACS2 v2.1.1 (-q 0.05 -f BAMPE --nomodel)
BigWigs were produced using deeptools v2.5.4 function bamCoverage (--normalizeUsing RPKM --ignoreDuplicates --centerReads -bs 10)
Assembly: hg38
Supplementary files format and content: peak files (bed) and bigwigs with coverage

source_name: Microglia

extract_protocol:
ATAC-sequencing was performed as in Buenrostro et al. 2015
Transposed and extracted DNA was amplified by PCR with Illumina indices and adapters using NEBNext® Ultra™ II Q5® Master Mix

treatment_protocol: C20 microglia cell line was infected with 250ng p24/1 mill cells of HIVGKO reporter virus  and 3 d.p.i., cells were washed with PBS, trypsinized and filtered in 2% FBS/PBS through a 45 mm filter before sorting on BD FACSAria™ Fusion Cell Sorter into 3 populations: FITC-/PE-, FITC+/PE+ and FITC-/PE+.

tag: population

value: eGFP-mKO2+ (Latently infected)

tag: infection

value: HIVGKO reporter virus


title: Microglia eGFP-mKO2+ (Latent) rep2


title: Microglia eGFP+mKO2+ (Active) rep2

value: eGFP+mKO2+ (Actively infected)


title: Microglia eGFP+mKO2+ (Active) rep1


title: 18gtGPRC5AWTtrTNFA7FTArp3-3WTTNFA7FTA

value: Wild-type


title: Microglia eGFP-mKO2- (Uninfected) rep2

value: eGFP-mKO2- (Uninfected)


title: 17gtGPRC5AWTtrTNFA7FTArp2-3WTTNFA7FTA


title: 16gtGPRC5AWTtrTNFA7FTArp1-3WTTNFA7FTA


title: 15gtGPRC5AWTtrTNFArp3-2WTTNFA


title: Microglia eGFP-mKO2- (Uninfected) rep1


title: Microglia HIV-1 (WT) CTCF-KD rep2

value: HIV-1 wild type

value: Infected; host cells were siRNA CTCF


title: 19gtGPRC5AKOtrTNFArp1-6KOTNFA


title: 12gtGPRC5AKOtr7FTArp3-5KO7FTA


title: 11gtGPRC5AKOtr7FTArp2-5KO7FTA


title: 10gtGPRC5AKOtr7FTArp1-5KO7FTA


title: 09gtGPRC5AKOtrDMSOrp3-4KODMSO

value: DMSO


title: 08gtGPRC5AKOtrDMSOrp2-4KODMSO


title: IAD44

first: Wei

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

data_processing:
Raw reads were filtered using FastQC and Trimmomatic. Then, aligned to the GRCh38 human genome assembly using STAR.
Gene expression levels were calculated in size factor. Annotations of exlRNA in the human genome were retrieved from the Ensembl (V96).
Feature selection was performed by R package boruta to find all relevant variables for machine learning.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized values for each sample

source_name: Extracellular vesicles

extract_protocol:
EVs were purified from 0.5-1 mL serum using the exoRNeasy Midi kit (Qiagen; Cat#77144) according to the manufacturer’s instructions. For RNA extraction, EVs were lysed on column with 1 mL Trizol reagent (Invitrogen; Cat#15596026) and the RNA pellet was dissolved in 11 μL of deionized water treated with DEPC (diethylpyrocarbonate).
EV long RNA libraries were constructed using poly(A) independent extracellular RNA sequencing . Briefly, 1 ng RNA was reverse transcribed with random primer by SMART technology. cDNA was purified twice using Ampure XP beads (Beckman Coulter, Cat# A63881) and amplified with indexed primers. 200–500 base-paired PCR products were size-selected using Ampure XP beads.

value: Blood serum

tag: disease state

value: invasive adenocarcinoma


title: 07gtGPRC5AKOtrDMSOrp1-4KODMSO

state: CA


title: IAD43


title: 20gtGPRC5AKOtrTNFArp2-6KOTNFA


title: 06gtGPRC5AWTtr7FTArp3-1WT7FTA


title: IAD42


title: 04gtGPRC5AWTtr7FTArp1-1WT7FTA


title: IAD38


title: IAD39


title: IAD41


title: IAD40


title: 02gtGPRC5AWTtrDMSOrp2-0WTDMSO


title: 01gtGPRC5AWTtrDMSOrp1-0WTDMSO


title: 03idgtGPRC5AWTtrDMSOrp3-0WTDMSO


title: IAD37


title: Mini_screen_OCI_M1_start_rep2

source_name: Human AML cell line

value: Blood

value: Parental

value: 10 doublings


title: 13gtGPRC5AWTtrTNFArp1-2WTTNFA

value: Colon

value: Epithelial


title: 14gtGPRC5AWTtrTNFArp2-2WTTNFA


title: Mini_screen_OCI_M1_start_rep1


title: Mini_screen_OCI_M1_end_DMSO_rep2


title: IAD35


title: Mini_screen_OCI_M1_end_DMSO_rep1


title: IAD33


title: IAD45


title: IAD34


title: Mini_screen_OCI_M1_end_099_rep1

value: 7uM SHP099


title: IAD32


title: IAD31


title: IAD36


title: IAD29


title: Mini_screen_MOLM13_start_rep2


title: IAD30


title: 05gtGPRC5AWTtr7FTArp2-1WT7FTA


title: Mini_screen_OCI_M1_end_099_rep2


title: Mini_screen_MOLM13_end_DMSO_rep2


title: IAD28


title: Mini_screen_MOLM13_end_DMSO_rep1


title: IAD27


title: Mini_screen_MOLM13_end_099_rep2


title: Mini_screen_MOLM13_start_rep1


title: IAD25


title: IAD26


title: Mini_screen_Lu65_start_rep2

source_name: Human lung giant cell carcinoma cell line

value: Lung


title: Mini_screen_Lu65_start_rep1


title: Mini_screen_MOLM13_end_099_rep1


title: IAD24


title: Mini_screen_Lu65_end_DMSO_rep2


title: IAD23