title: Whole blood, COVID positive, rep 552


title: Whole blood, COVID positive, rep 550

status: Public on Mar 26 2025

type: SRA

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

country: Australia

institute: University of Sydney

library_source: transcriptomic

data_processing:
RNASeq-DE workflow (v1.0.0), available online at  https://github.com/Sydney-Informatics-Hub/RNASeq-DE
3’ adapter and polyA tails were trimmed from raw sequence reads with BBDuk (v37.89)
Quality checked, trimmed reads were aligned as pairs to the human reference genome, GRCh38 primary assembly and gene set release 106 (obtained from Ensembl) with STAR, setting –sjdbOverhand to 149
Sequencing batch level binary alignment (BAM) files were merged and indexed with SAMtools (v1.10) to obtain sample level BAMs.
HTSeq-count (v0.12.4) with -s reverse was used to obtain feature level raw counts.
Assembly: GRCh38
Supplementary files format and content: HTSeq-count output, containing raw counts per sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Total RNA was isolated from whole blood samples stored and stabilized in PAXgene RNA tubes according to the manufacturer's guidelines (PreAnalytiX)
Libraries were prepared with 300ng of total RNA per sample using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (RZP) as per manufacturer instructions (Illumina, CA, USA).

tag: tissue

value: Whole blood

tag: type of_infection

tag: country of_samples_collected

value: Indonesia

tag: gender

value: Male

tag: age


title: Whole blood, COVID positive, rep 549

value: Australia

value: Female


title: Whole blood, COVID positive, rep 551

value: Co-infection (Bac/Viral)

value: France


title: Whole blood, COVID positive, rep 546


title: Whole blood, COVID positive, rep 544


title: Whole blood, COVID positive, rep 548


title: Whole blood, COVID positive, rep 545


title: Whole blood, COVID positive, rep 542


title: Whole blood, COVID positive, rep 543


title: Whole blood, COVID positive, rep 541

value: Coronavirus


title: Whole blood, COVID positive, rep 540


title: Whole blood, COVID positive, rep 563


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value: Czech Republic


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value: Co-infection (Bac/Viral/Fungal)


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value: Sepsis


title: Whole blood, COVID positive, rep 467


title: Whole blood, COVID positive, rep 465


title: Whole blood, COVID positive, rep 487


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title: Whole blood, COVID positive, rep 464


title: Whole blood, COVID positive, rep 461


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value: Co-infection (Viral/Viral)


title: Whole blood, COVID positive, rep 463

value: Co-infection (Bac/viral)


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title: Meso34 cells, MCTS2

city: Nantes

first: Christophe

last: Blanquart

address: 8 Quai Moncousu

country: France

institute: INSERM UMR 1307/CNRS UMR 6075

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1)
Assembly: Hg19
Supplementary files format and content: Matrix table of raw gene counts for all genes in all samples

source_name: mesothelium

growth_protocol: Cells were grown as multicellular spheroids (MCTS) in low adherence 96-well plates in DMEM medium supplemented with 10% FCS

extract_protocol:
Nucleospin RNA kit, Macherey-Nagel
Libraries were prepared according to NovaSeq 6000 Sequencing Sytem's instructions accompanying the NovaSeq 6000 SP Reagent Kit (Ref# 20028401). Libraries were sequenced on the NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: MCTS were constituted of cancer cells alone or with monocytes from healthy donors

value: mesothelium

tag: cell line

tag: cell type

value: Mesothelioma cell line

tag: genotype

value: CDKN2A/CDKN2B del, BAP1/LATS2/NF2 mut


title: Meso34 cells, MCTS3


title: Meso34 cells + mono, MCTS2


title: Meso34 cells + mono, MCTS3


title: Meso34 cells, MCTS1


title: Meso13 cells + mono, MCTS1

value: CDKN2A/CDKN2B del


title: Meso13 cells + mono, MCTS2


title: Meso34 cells + mono, MCTS1


title: Whole blood, COVID positive, rep 398

value: Whole blood


title: Meso13 cells, MCTS2


title: Meso13 cells, MCTS1


title: hMSCs in less dynamic hydrogel, H3K18la, ChIP

city: Hong Kong

first: Boguang

last: Yang

address: Sha Tin

country: Hong Kong

institute: The Chinese University of Hong Kong

library_source: genomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software(version
0.20.1). Clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. The clean reads were mapped to
the genome using bowtie2(version 2.4.2). MACS2(version 2.2.7.1) was used to call peaks. IGV software was used to visualize called peaks from ChIP-seq samples. Called peaks were then
annotated using R package ChIPseeker. And HOMER were used to find de novo and known motif. Differential peaks analysis was performed using R package MAnorm for experimental
design without replication while using R package Diffbind for experimental design with replication.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Human Mesenchymal Stem Cells

extract_protocol:
Chromatin Immunoprecipitation Protocol 1. Add final concentration of 1% Formaldehyde solution for Cross-Linking of DNA and Protein. Then stoped the cross-linking reaction by adding final concentration of 125mM glycine. 2. Extract chromatin from cross-linked cells by adding Lysis Buffer. 3. Sonicate chromatin DNA to fragments ranging from 100 to 500 bp. 4. Immunoprecipitate chromatin DNA and antibody-associated beads by incubating them overnight at 4°C.
The sequencing libraries of immunoprecipitated chromatin DNA were generated with varied index label by NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA, cat. E7645L).

value: Human Mesenchymal Stem Cells

tag: chip antibody


title: Meso13 cells + mono, MCTS3


title: Meso13 cells, MCTS3


title: hMSCs in less dynamic hydrogel, Input


title: Whole blood, COVID positive, rep 402


title: hMSCs in more dynamic hydrogel, Input


title: Whole blood, COVID positive, rep 397

value: Indonesia


title: hMSCs in more dynamic hydrogel, H3K18la, ChIP


title: P14, non-diseased [RNA-seq]

city: Bratislava

first: Natália

last: Matyašovská

address: Ilkovičova 8

country: Slovakia

institute: MultiplexDX

data_processing:
The initial step in the RNA sequencing (RNA-seq) data processing workflow was the QC of raw sequencing data using FastQC software v0.11.9
The next step involved the removal of the adapter sequences using Cutadapt v3.4 [64] and trimming of low-quality bases using UMI-tool v1.0.0.
Sequencing reads were then aligned to the reference genome (GRCh38.104) using the STAR aligner v2.7.7a
Gene expression levels were quantified using FeatureCounts v1.5.2.
For normalization and differential expression (DE) analysis, the DESeq2 v1.36.0 (R Package)
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text file includes raw read counts data for each sample

source_name: FFPE

extract_protocol:
Total RNA was isolated from FFPE tissue, using NucleoSpin totalRNA FFPE XS extraction kit.
Total RNA libraries were prepared using TAKARA SMARTer Stranded Total RNA_x0002_Seq kit v3 – Pico Input Mammalian according to the manufacturer’s guidelines, with specific modifications recommended for highly degraded FFPE specimens, including (I) total RNA input 10 ng, (II) DNase pretreatment step, (III) omission of the fragmentation step, (IV) performing 10 PCR cycles for the first and second PCR amplification steps

value: FFPE


title: P11, non-diseased [RNA-seq]


title: P12, non-diseased [RNA-seq]


title: P13, non-diseased [RNA-seq]


title: P6, tumor [RNA-seq]


title: P10, non-diseased [RNA-seq]


title: P8, non-diseased [RNA-seq]


title: P7, non-diseased [RNA-seq]


title: P3, tumor [RNA-seq]


title: P1, tumor [RNA-seq]


title: P4, tumor [RNA-seq]


title: P5, tumor [RNA-seq]


title: P2, tumor [RNA-seq]


title: sw480_FBL-TurboID-RIP seq_rep2

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: sun yat sen university

data_processing:
Trim-galore (v0.6.10) was used to trim adapters and filter for sequences, remaining reads were then aligned to the Hg19  using Bowtie2 (v2.5.0) Hisat2 aligner (v2.1.0)
m6A peaks were identified using exomePeak2 R package (v1.6.1) under parameters: “FRAGMENT_LENGTH=140,p_cutoff = 1e-05,paired_end = TRUE” ; for epz_meRIP data , called peaks under parameters:"FRAGMENT_LENGTH=140, log2FC_cutoff = 1,p_cutoff = 1e-05,paired_end = TRUE" for shRBM15B_meRIP data.
CUT&Tag peaks were  identified using MACS2 (v2.2.7.1) under parameters:"-f BAMPE -g hs --keep-dup all -B -q 0.05 -m 5 50"
Assembly: Hg19
Supplementary files format and content: tab-delimited text files include values for each Sample
Library strategy: m6A-RIP sequencing

source_name: Colon

extract_protocol:
For Cut&Tag, 5 × 104 MOLM13 cells were sorted and washed once in 0.5 mL wash buffer (20 mM Hepes (pH 7.5); 150 mM NaCl; 0.5 mM spermidine; and 1 × protease inhibitors) and were incubated with 10 μL pre-washed concanavalin A–coated magnetic beads in a 1.5 mL microtube at 25 °C for 10 min. Cells were resuspended in 80 μL ice-cold antibody incubation buffer with 1 μg RBM15B antibody per sample (22249-1-AP, proteintech) and then rotated end-over-end at 4 °C overnight. The cells were resuspended in 100 μL of dig-wash buffer [20 mM Hepes (pH 7.5); 150 mM NaCl; 0.5 mM spermidine; 1 × protease inhibitors; 0.025% digitonin) with rabbit anti-mouse IgG (1:100 dilution, Ab6709; ThermoFisher) and rotated end-over-end at 25 °C for 1 h. After washing, home-made pA-Tn5 adapter complexes in dig-300 buffer (20 mM Hepes pH 7.5; 300 mM NaCl; 0.5 mM spermidine; 1 × protease inhibitors; 0.01% digitonin) were added to the samples at a final concentration of 1:100 and then rotated end-over-end at 25 °C for 1 h. After washing, the cells were resuspended in 300 μL fragmentation buffer (dig-300 buffer with 10 mM MgCl2) and incubated at 37 °C for 1 h. After extraction with phenol–chloroform and ethanol precipitation, the libraries were amplified by PCR.  For m6A-RIP, Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). 10μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The fragmented RNA was incubated with anti-m6A monoclonal antibody (abcam,ab208577) for 3 h at 4℃ and then with protein A/G magnetic beads (Invitrogen, 8880210002D/10004D) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was purified using TRIzol™ Reagent (Invitrogen, 15596018).
For Cut&Tag sequencing, the barcoded libraries were pooled and sequenced on the Illumina HiSeq X™ Ten platform to generate 150 bp paired-end reads. For m6A-RIP sequencing, the library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: For Cut&Tag sequencing, the MOLM-13 cells treated by 1uM epz5676 or DMSO(negative control)  for 72 hours.

value: Colon

value: colorectal adenocarcinoma cell


title: sw480_FBL-TurboID-RIP seq_rep1


title: molm13_FBL-TurboID-RIP seq_rep1

source_name: Bone Marrow

value: Bone Marrow

value: acute myeloid leukemia cell


title: sw480_TurboID-RIP seq_NC_rep2


title: molm13_FBL-TurboID-RIP seq_rep2


title: FBL_clip seq_rep1

data_processing:
Trim-galore (v0.6.10) was used to trim adapters and filter for sequences, remaining reads were then aligned to the Hg19  using Bowtie2 (v2.5.0) Hisat2 aligner (v2.1.0)
m6A peaks were identified using exomePeak2 R package (v1.6.1) under parameters: “FRAGMENT_LENGTH=140,p_cutoff = 1e-05,paired_end = TRUE” ; for epz_meRIP data , called peaks under parameters:"FRAGMENT_LENGTH=140, log2FC_cutoff = 1,p_cutoff = 1e-05,paired_end = TRUE" for shRBM15B_meRIP data.
CUT&Tag peaks were  identified using MACS2 (v2.2.7.1) under parameters:"-f BAMPE -g hs --keep-dup all -B -q 0.05 -m 5 50"
Assembly: Hg19
Supplementary files format and content: tab-delimited text files include values for each Sample
Library strategy: cut&tag

source_name: Human Embryonic Kidney

value: Human Embryonic Kidney

value: Human Embryonic Kidney 293 Cell


title: molm13_TurboID-RIP seq_NC_rep1


title: sw480_TurboID-RIP seq_NC_rep1


title: FBL_clip seq_rep2

value: Human Embryonic Kidney 294 Cell


title: PANC-1 cell, shControl3

first: Leyi

last: Huang

address: 107 Yan Jiang West Road, Guangzhou, P.R. China

institute: Sun Yat-sen University

data_processing:
Raw sequencing data were first filtered by fastp (version 0.23.1), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
UMI (version 1.0), the self-developed software of Seqhealth Co., Ltd were used to eliminate duplication.
Reads after duplication removal were mapped to the reference genome using STAR(version 2.7.6a) with default parameters.
Sambamba (version 0.7.1) was used for sam/bam format conversion and index build. The featureCounts（version 1.5.1）was used for reads distribution statistic.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include ac4C sites for each group. chr: Chromosome where the ac4C resides；start: The start position of the ac4C site. end: The end position. id: Name. strand: Strand information (positive or negative). base: Allele at the ac4C site that matches the reference genome. counts, correct, wrong: Represent the number of each base (A, C, G, T) detected at the site in each sample; the number of alleles matching the reference genome; and the number of mutated bases, respectively. misrate, snv: Represent the mutation rate of the ac4C site in the group and the type of variant, respectively. diff: The degree of difference between treatment and control samples. pvalue: The threshold for statistical testing.

source_name: pancreatic cancer

extract_protocol:
The PANC-1 cells were divided in two groups: 1.PANC-1 transfected with siRNA Ctrl; 2.PANC-1 transfected with siRNA that knockdown the expression of NAT10. 30 μg total RNA was used for mRNA capture using KAPA mRNA Capture Kit(KK8441) following the manufacturer’s instruction. Take a small amount of captured RNA as “Con”, and the remaining RNA was treated with 100 mM NaBH4 at 55℃ in the dark for 30 minutes. During the incubation time, tube lids were opened every 10 min to release pressure from NaBH4-induced bubbling. Reactions were adjusted to 200 μl with H2O, precipitated with 0.3M sodium acetate [pH 5.5], 15 mg/ml linear acrylamide (carrier) and 2.5X ethanol, briefly dried on Speedvac, resuspended in 12 μl H2O, and quantified by Qubit4.0 with Qubit™ RNA HS Assay Kit (Life Technologies, Q33224).
Total RNA was extracted from shCtrl or shNAT10 PANC-1 cells using TRIzol Reagent (Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). 30 μg total RNA was used for mRNA capture using KAPA mRNA Capture Kit(KK8441) following the manufacturer’s instruction. Take a small amount of captured RNA as “Con”, and the remaining RNA was treated with 100 mM NaBH4 at 55℃ in the dark for 30 minutes. During the incubation time, tube lids were opened every 10 min to release pressure from NaBH4-induced bubbling. Reactions were adjusted to 200 μl with H2O, precipitated with 0.3M sodium acetate [pH 5.5], 15 mg/ml linear acrylamide (carrier) and 2.5X ethanol, briefly dried on Speedvac, resuspended in 12 μl H2O, and quantified by Qubit4.0 with Qubit™ RNA HS Assay Kit (Life Technologies, Q33224).
KC Digital Stranded mRNA Library Prep Kit for Illumina（DR085-02）was used for library construction.
The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: pancreatic cancer

value: pancreatic cancer cell line

value: control

tag: treatment


title: PANC-1 cell, shNAT10 3

value: NAT10 knockdown


title: PANC-1 cell, shControl1


title: PANC-1 cell, shControl2


title: Substantia nigra from case 4851

city: San Francisco

first: Alexander

middle: James

last: Ehrenberg

state: CA

address: 675 Nelson Rising Lane

department: Memory and Aging Center

country: USA

institute: University of California, San Francisco

data_processing:
The quality of sequence files was assessed using the FastQC package before and after trimming steps.
Trimmomatic (ILLUMINACLIP: TruSeq3-PE.fa:2:30:10:2:True, LEADING: 3, TRAILING: 3, SLIDINGWINDOW: 4:15, and MINLEN: 36) was used to remove adapter sequences and any sequences with low mean quality scores.
Sequences were aligned to GRCh38 using STAR alignment and count matrices were generated using featureCounts.
The count matrices were converted to counts per million (CPM) using the edgeR package.
Assembly: GRCh38
Supplementary files format and content: Comma separated values include raw counts for each sample
Supplementary files format and content: Comma separated values include counts per million for each sample

source_name: Brain

extract_protocol:
Tissue homogenization and cell lysis was performed in TRIzol. After cell lysis, impurities removal, and inhibition of RNAse activity, total RNA was extracted by using phase separation method from cell debris.
Library preparation with poly A enrichment was done with the NEBNext Ultra II RNA Library Prep Kit for Illumina

value: Brain

tag: region

value: Substantia nigra

tag: case

tag: Sex

value: Male

tag: braak stage


title: Substantia nigra from case 3434

value: Female


title: Substantia nigra from case 3493


title: Substantia nigra from case 3361


title: Substantia nigra from case 3427


title: Substantia nigra from case 512


title: Substantia nigra from case 384


title: Substantia nigra from case 467


title: molm13_TurboID-RIP seq_NC_rep2


title: Substantia nigra from case 3406


title: Substantia nigra from case 3368


title: Substantia nigra from case 2821


title: Substantia nigra from case 475


title: Substantia nigra from case 3358


title: Substantia nigra from case 322


title: FBL_clip seq_rep3

value: Human Embryonic Kidney 295 Cell


title: PANC-1 cell, shNAT10 2


title: Substantia nigra from case 3386


title: Substantia nigra from case 3691


title: Substantia nigra from case 3411


title: Substantia nigra from case 452


title: Substantia nigra from case 334


title: Substantia nigra from case 269


title: Locus coeruleus from case 4851

value: Locus coeruleus


title: Locus coeruleus from case 3493


title: PANC-1 cell, shNAT10 1


title: Locus coeruleus from case 3361


title: Locus coeruleus from case 467


title: Locus coeruleus from case 3427


title: Locus coeruleus from case 512


title: Locus coeruleus from case 384


title: Locus coeruleus from case 3368


title: Locus coeruleus from case 3406


title: Substantia nigra from case 3603


title: Locus coeruleus from case 3358


title: Substantia nigra from case 3407


title: Locus coeruleus from case 452


title: Locus coeruleus from case 3411


title: Locus coeruleus from case 3603


title: Locus coeruleus from case 3691


title: Locus coeruleus from case 334


title: Locus coeruleus from case 3386


title: Kyse30 cell spheroids under serum-free condition_Sample 4

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Assembly: hg38
Supplementary files format and content: comma separated text file

source_name: esophageal squamous cell carcinoma

growth_protocol: Spheroids were formed from 8,000 FaDu-Dendra2 and 10,000 Kyse30-Dendra2 cells in BIOFLOAT ultra-low attachment 96-well round-bottom plates (faCellitate, Mannheim, Germany; 3000 cells/well; 72h). 35mm glass bottom u-dishes (Ibidi, Matrinsried, Germany) were pre-coated with 40 µL of serum-free medium supplemented with type I collagen (Corning, Oak Park, Bedford, MA, USA; 1.7 mg/mL). Spheroids were overlayed in serum-free medium containing type I collagen (160 µL).

extract_protocol:
Spheroids FaDu-Dendra2 and Kyse30-Dendra2 cells were embedded in type I collagen and treated with serum-free medium, high-dose EGF (EGFh, 9 nM), EGF and Cetuximab (9 nM EGF + 10 µg/mL Cetuximab), and EGF and MEK inhibitor (9 nM EGF + 100 nM AZD6244) for 72 hr. 10-12 invasive areas per spheroid and 40 spheroid per treatment were photoconverted and type I collagen degraded with 0.1 mg/mL collagenase (C9722, Sigma, Missouri, USA) for 15 mins at 37°C. Recovered spheroids were centrifuged at 400g for 4 mins, collected into RNAse-free tubes (1.5 mL) and resuspended in Accutase for 10 mins (#07922, STEMCELL Technologies, Cologne, Germany) and pipetted up down gently to prevent cell aggregation. After centrifuging and washing twice with PBS, single-cell suspensions were prepared in ice-cold FACS buffer for sorting of > 1,000 cells per group into RNAse-free tubes for RNA extraction and next-generation sequencing.
3'-RNA-seq; RNA library was generated using the Lexogen QuantSeq 3’ mRNA-Seq V2 Library Prep Kit following the manufacturers protocol

value: spheroid

value: wildtype

value: serum-free

tag: cell selection

value: unselected


title: Locus coeruleus from case 3407


title: Kyse30 cell spheroids under serum-free condition_Sample 1


title: Locus coeruleus from case 3434


title: Locus coeruleus from case 269


title: Locus coeruleus from case 322


title: Kyse30 cell spheroids under serum-free condition_Sample 2


title: Kyse30 cell spheroids treated with high-dose EGF_Photoconverted invasive cells_Sample 1

value: EGF

value: EGF photoconverted invasive cells


title: Kyse30 cell spheroids treated with high-dose EGF in combination with MEK-inhibitor_Sample 3

value: EGF and MEK-inhibitor


title: Kyse30 cell spheroids treated with high-dose EGF in combination with MEK-inhibitor_Sample 4


title: Locus coeruleus from case 2821


title: Kyse30 cell spheroids treated with high-dose EGF in combination with MEK-inhibitor_Sample 2


title: Kyse30 cell spheroids treated with high-dose EGF in combination with MEK-inhibitor_Sample 1


title: Locus coeruleus from case 475


title: Kyse30 cell spheroids treated with high-dose EGF_Photoconverted non-invasive cells_Sample 3


title: Kyse30 cell spheroids treated with high-dose EGF_Photoconverted non-invasive cells_Sample 1


title: Kyse30 cell spheroids treated with high-dose EGF in combination with Cetuximab_Sample 4

value: EGF and Cetuximab


title: Kyse30 cell spheroids under serum-free condition_Sample 3


title: Kyse30 cell spheroids treated with high-dose EGF_Photoconverted non-invasive cells_Sample 2


title: Kyse30 cell spheroids treated with high-dose EGF in combination with Cetuximab_Sample 3


title: FaDu cell spheroids under serum-free condition_Sample 3

source_name: hypopharyngeal tumor

value: FaDu


title: Kyse30 cell spheroids treated with high-dose EGF in combination with Cetuximab_Sample 2


title: Kyse30 cell spheroids treated with high-dose EGF in combination with Cetuximab_Sample 1


title: Kyse30 cell spheroids treated with high-dose EGF_Photoconverted invasive cells_Sample 4


title: FaDu cell spheroids under serum-free condition_Sample 1


title: Kyse30 cell spheroids treated with high-dose EGF_Photoconverted invasive cells_Sample 3


title: FaDu cell spheroids treated with high-dose EGF_Photoconverted invasive cells_Sample 3


title: FaDu cell spheroids under serum-free condition_Sample 4


title: Kyse30 cell spheroids treated with high-dose EGF_Photoconverted invasive cells_Sample 2


title: FaDu cell spheroids under serum-free condition_Sample 2


title: FaDu cell spheroids treated with high-dose EGF_Photoconverted invasive cells_Sample 4


title: FaDu cell spheroids treated with high-dose EGF_Photoconverted invasive cells_Sample 2


title: FaDu cell spheroids treated with high-dose EGF in combination with MEK-inhibitor_Sample 2


title: FaDu cell spheroids treated with high-dose EGF in combination with MEK-inhibitor_Sample 3


title: FaDu cell spheroids treated with high-dose EGF in combination with MEK-inhibitor_Sample 1


title: FaDu cell spheroids treated with high-dose EGF_Photoconverted invasive cells_Sample 1


title: FaDu cell spheroids treated with high-dose EGF_Photoconverted non-invasive cells_Sample 3


title: FaDu cell spheroids treated with high-dose EGF_Photoconverted non-invasive cells_Sample 2


title: Kyse30 cell spheroids treated with high-dose EGF_Photoconverted non-invasive cells_Sample 4


title: FaDu cell spheroids treated with high-dose EGF_Photoconverted non-invasive cells_Sample 1


title: FaDu cell spheroids treated with high-dose EGF in combination with Cetuximab_Sample 4


title: FaDu cell spheroids treated with high-dose EGF in combination with MEK-inhibitor_Sample 4


title: FaDu cell spheroids treated with high-dose EGF in combination with Cetuximab_Sample 3


title: FaDu cell spheroids treated with high-dose EGF in combination with Cetuximab_Sample 1


title: HeLa-Flp-In-TREx_NAT10-FLAG_R628A_DRIP

city: Austin

first: Blerta

last: Xhemalçe

state: Texas

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
The adapter sequences in each raw fastq file (fastq) were trimmed using Trim Galore. The quality of each processed fastq file was then assessed with FastQC. Subsequently, the reads were aligned to the reference human genome hg38 using the bwa mem alignment method. SAMtools was employed to remove low-quality mapped reads by filtering out reads with a mapping quality score of less than 10, as well as PCR duplicates. The RLPipes was applied to generate bw and broadPeak files.
Assembly: hg38
Supplementary files format and content: bw and broadPeak files
Library strategy: DRIP-seq

source_name: HeLa-Flp-In-TREx

growth_protocol: Cells were grown in DMEM containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 μg/mL streptomycin and 2 mM L-glutamine (PSQ) and supplemented with 10  µg/mL of Blasticidin and 400 µg/mL of Hygromycin. The cells were treated with 2 µg/mL of Doxycyclin for 24h prior to sample collection.

extract_protocol:
Cells were harvested and genomic DNA was isolated. Extracted genomic DNA was digested overnight at 37°C using a restriction enzyme cocktail (BsrGI, EcoRI, HindIII, SspI and XbaI), followed by treatment with mock or RNase H. For each DRIP, 8 µg of digested DNAs were subject to immunoprecipitation with 10 µg of S9.6 antibody and eluted. The eluates were sonicated using the bioruptor (Diagenode) and used for library preparation.
Libraries were constructed using the NEBNext Ultra II kit following manufacturer’s instructions.

treatment_protocol: Cells were treated with 2 µg/mL of Doxycyclin for 24 hrs to induce NAT10 expression.

value: HeLa-Flp-In-TREx

value: Cancer Cell Line


title: HeLa-Flp-In-TREx_NAT10-FLAG_WT__RNaseH_DRIP


title: HeLa-Flp-In-TREx_NAT10-FLAG_WT_DRIP


title: HeLa-Flp-In-TREx_NAT10-FLAG_R628A__RNaseH_input


title: HeLa-Flp-In-TREx_Control_DRIP


title: HeLa-Flp-In-TREx_NAT10-FLAG_R628A_input


title: HeLa-Flp-In-TREx_Control_RNaseH_input


title: HeLa-Flp-In-TREx_Control_input


title: HeLa-Flp-In-TREx_NAT10-FLAG_WT_input


title: HeLa-Flp-In-TREx_NAT10-FLAG_WT__RNaseH_input


title: HeLa-WT_RNaseH_DRIP

source_name: HeLa

growth_protocol: Cells were grown in DMEM containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 μg/mL streptomycin and 2 mM L-glutamine (PSQ).

treatment_protocol: Control and NAT10-KO cells were used.

value: HeLa


title: HeLa-NAT10-KO_RNaseH_DRIP


title: FaDu cell spheroids treated with high-dose EGF_Photoconverted non-invasive cells_Sample 4


title: HeLa-WT_RNaseH_input


title: HeLa-WT_input


title: HeLa-NAT10-KO_RNaseH_input


title: HeLa-NAT10-KO_input


title: ARPE-19 cells, era+vk2

city: Shanghai

first: Xiaochan

last: Dai

address: Handan Road, No.220

institute: Fudan University

data_processing:
A cDNA library was sequenced run with Illumina NovaseqTM 6000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. 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
We aligned reads of all samples to the reference genome using HISAT2 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. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown 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.
Assembly: mm10
Supplementary files format and content: Ttab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library

value: Retinal pigment epithelial cells

value: WT

value: Erastin+vk


title: ARPE-19 cells, era3

value: Erastin


title: ARPE-19 cells, era+vk1


title: FaDu cell spheroids treated with high-dose EGF in combination with Cetuximab_Sample 2


title: ARPE-19 cells, era1


title: HeLa-Flp-In-TREx_NAT10-FLAG_R628A__RNaseH_DRIP


title: ARPE-19 cells, era+vk3


title: Chromatin Immunoprecipitate of UBR7 from Wildtype Cells_REP2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
All the ChIP seq samples were analyzed using NF-CORE ChIP seq data analysis pipeline
Assembly: Hg38

source_name: Breast

growth_protocol: MDA-MB-231 cells stably transfected with lentiviral vector SCR and UBR7-Sh were maintained in RPMI supplemented with 12% fetal bovine serum (FBS), antibiotics and puromycin in 5 % CO2 incubator at 37 degree celsius.

extract_protocol:
Cells were cross-linked with 1% paraformaldehyde and then neutralised with 125mM glycine. After that chromatin fragmentation was performed by sonication.
Library preparation was done by NEBNext Ultra II DNA library preparation for Illumina sequencing.

value: Breast

value: Triple negative breast cancer

tag: antibody


title: HeLa-Flp-In-TREx_Control_RNaseH_DRIP


title: Chromatin Immunoprecipitate of H3k27Me3 from UBR7 Mutant Cells_REP2


title: Chromatin Immunoprecipitate of H3k27Me3 from UBR7 Mutant Cells_REP1


title: Chromatin Immunoprecipitate of UBR7 from Wildtype Cells_REP1


title: HeLa-NAT10-KO_DRIP


title: Chromatin Immunoprecipitate of H3k27Ac from UBR7 Mutant Cells_REP2


title: Chromatin Immunoprecipitate of H3k27Me3 from Wildtype Cells_REP2


title: UBR7 silenced cells Input / Whole Cell Extract DNA_REP1


title: UBR7 silenced cells Input / Whole Cell Extract DNA_REP2


title: Chromatin Immunoprecipitate of H3k27Ac from Wildtype Cells_REP2


title: HeLa-WT_DRIP


title: Scrambled Input / Whole Cell Extract DNA_REP1


title: Liver, STATF3

city: Strasbourg

first: Julien

last: Moehlin

address: 3 Rue Koeberlé

institute: Institute for Translational Medicine and Liver Disease (ITM)

data_processing:
Base calling was performed by CASAVA (v1.8) and raw data was stored in FASTQ format.
Raw reads were filtered to remove reads with (I) adapter contamination, (II) more than 10 % uncertain nucleotides (Ns), and (III) with more than 50 % of low quality nucleotides (base quality less than 5).
Reads were mapped using HISAT2 v2.0.5 to the human genome GRCh38.
FeatureCounts v1.5.0-p3 was used to generate gene counts.
Assembly: hg38
Supplementary files format and content: Excel file format with raw count for all samples

source_name: Liver

growth_protocol: HepaRG cells were cultured at 37 °C in a humidified 5% CO2 incubator and were differentiated in the presence of 1.8% DMSO for two weeks.

extract_protocol:
Cells were lysed in TRI reagent and total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA, USA).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis

treatment_protocol: HepaRG cells were transfected with siRNAs against STAT3, PTPRD or with control siRNA for 48 h. Subsequently, cells were treated with free fatty acids (800 µM oleic acid and 400 µM palmitic acid) for 24 h.

value: Liver

value: HepaRG

value: Hepatocytes

value: STATF


title: Chromatin Immunoprecipitate of H3k27Me3 from Wildtype Cells_REP1


title: Chromatin Immunoprecipitate of H3k27Ac from Wildtype Cells_REP1


title: Liver, STATF1


title: Poly-IC_Ctrl, rep2

city: Xiamen

first: Jun

last: Tao

state: Fujian

address: No. 4221, South Xiang'an Road

institute: XMU

data_processing:
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v2.0.5 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
The total RNA from JEG-3 cells was extracted using Trizol (Invitrogen, CA, USA).
DNBSEQ Eukaryotic mRNA library

value: Poly-IC


title: Scrambled Input / Whole Cell Extract DNA_REP2


title: Poly-IC_Ctrl, rep1


title: Liver, PTPF3

value: PTPF


title: Liver, PTPF2


title: Liver, PTPF1


title: Poly-IC_HAVCR1 KO, rep1

value: HAVCR1 KO


title: MOCK_Ctrl, rep2

value: MOCK


title: SH12L4

data_processing:
Generation of paired end reads by illumina platform.
Raw sequencing reads were filtered on the basis of quality.
Alignment of quality reads with Homo sapiens GRch38 genome was done.
Alignments were assembled into transcripts.
Normalisation of the expression values with the fragment per kilobase per million (FPKM) was performed.

extract_protocol:
RNA extraction was performed by using RNeasy kit.
Library preparation was done by using NEBNext Ultra II directional RNA library preparation kit as per manufacturer's protocol.

value: UBR7 knockdown


title: MOCK_Ctrl, rep1


title: Chromatin Immunoprecipitate of H3k27Ac from UBR7 Mutant Cells_REP1


title: SH12L3


title: MOCK_HAVCR1 KO, rep2


title: Liver, STATF2


title: MOCK_HAVCR1 KO, rep1


title: SH11L3


title: MASMCs form Hint1-/- mice treated with PDGF-BB, sample3

city: Nanjing

first: Wencheng

last: Wu

address: Longmian Street

institute: Nanjing Medical University

description:
Library name: K_r2
MASMCs treated with PDGF-BB

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: mouse aortic smooth muscle cells (MASMCs)

extract_protocol:
Transfer aortic samples to corresponding grinding tube. Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min. Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube.Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer. Stand flat for 5 min for the fully lysis of tissue cells. For BMDMs, add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells). Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking；Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃). Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
Select the corresponding testing methods for quality inspection according to the requirements of samples and products. A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. The PCR reaction system and program are configured and set up to amplify the product. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: PDGF-BB


title: SCR1L4


title: MASMCs form Hint1-/- mice treated with PDGF-BB, sample4

description:
Library name: K_r3
MASMCs treated with PDGF-BB

value: mouse aortic smooth muscle cells (MASMCs)


title: SCR2L3


title: Poly-IC_HAVCR1 KO, rep2


title: MASMCs form Hint1-/- mice treated with PDGF-BB, sample2

description:
Library name: K_r1
MASMCs treated with PDGF-BB


title: SCR1L3


title: MASMCs form Hint1-/- mice treated with PDGF-BB, sample1

description:
Library name: K
MASMCs treated with PDGF-BB


title: SH11L4


title: MASMCs form wild-type mice treated with PDGF-BB, sample4

description:
Library name: C_r3
MASMCs treated with PDGF-BB

value: wild-type


title: SCR2L4


title: MASMCs form wild-type mice treated with PDGF-BB, sample2

description:
Library name: C_r1
MASMCs treated with PDGF-BB


title: D52S_PCLS_d14

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

department: Marsico Lung Institute

institute: University of North Carolina at Chapel Hill

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
cellranger v6.1.2
SoupX
scDblFinder
Seurat v4
Minimal gene count>400, Percent mitochondrial genes<20%
Assembly: GRCh38, GENCODE v39
Supplementary files format and content: R data serialization (RDS) file, containing gene x cell (barcode) data matrices, dimension reduction embeddings, and cell meta-data.

source_name: Lung parenchyma

growth_protocol: LAE, SAE, and PCLS were placed on a media-soaked Gelfoam® sponge with the lumen exposed to air and maintained in a high humidity incubator.

extract_protocol:
LAE, SAE, and PCLS tissues were cryopreserved in CryoStor freezing medium after 0 (fresh), 2, and 14 days in culture. Cryovials were thawed, rinsed in PBS, placed into a 15 mL tube containing 5 mL of Accutase solution (Sigma-Aldrich, #A6964-100ML) with EDTA (invitrogen, #15575-038) (5 mM) and pronase (Roche, #10165921001) (1 mg/mL), and incubated on a shaker for 30 min at 37°C. Following incubation, the tube was centrifuged (600 g, 2 min, 4 oC), the supernatant was discarded, and 5 mL of Hank’s Balanced Salt Solution (Ca-, Mg-) (gibco) buffer containing liberase (Roche, #05401119001) (50 mg/mL) and DNase (Roche, #10104159001) (25 ug/mL) was added to the tube. The sample was then incubated on the shaker for 10 min at 37°C. After incubation, the cell suspension was gently pipetted 20 times using a wide-orifice pipette tip. To neutralize enzymes, 500 mL of fetal bovine serum was added to the cell suspension, and the neutralized mixture was filtered through a 100 um filter, followed by centrifugation (600 g, 2 min, 4 oC). After removing supernatant, dissociated cells were resuspended in PBS (Ca-, Mg-) containing 0.01% Ultrapure BSA (Invitrogen, #AM2616), filtered through a 40-μm cell strainer (Bel-Art, H13680-0040), and centrifuged (600 g, 2 min, 4 oC). Cell count and viability was assessed using trypan blue dye exclusion with a Countess 3 automated cell counter (Thermo Fisher Scientific), and the cell concentration was adjusted to approximately 1000 cells/uL. The dissociated cells were used for 10X Genomics scRNA-seq library preparation.
Single-cell suspensions targeting approximately 6,000 cells were loaded onto a 10x Genomics Chromium Next GEM Chip G (10x Genomics) device following the manufacturer’s instructions. After GEM generation, the library preparation was performed following the instructions for the 10x Chromium Next GEM Single Cell 3’ GEM Library kit v3.1 (10x Genomics).

treatment_protocol: LAE, SAE, and PCLS were used for scRNA-seq at 0 (fresh), 2, and 14 days after culture.

value: Lung parenchyma

value: Precision cut lung slices

value: lung cells

tag: genotype/donor

tag: time (day)


title: D52S_PCLS_Fresh

description: 10x Genomics

tag: tissue


title: MASMCs form wild-type mice treated with PDGF-BB, sample1

description:
Library name: C
MASMCs treated with PDGF-BB


title: X31-Tight-/-

city: guangzhou

first: SHI

last: JIA

state: guangdong province

address: nonglin street

institute: SUN Yat-sen university

data_processing:
The sequencing data was filtered with SOAPnuke,afterwards clean reads were obtained and stored in FASTQ format
Assembly: Mus_musculus; NCBI; GCF_000001635.26_GRCm38.p6
Supplementary files format and content: include raw counts for each sample

source_name: quadricep

extract_protocol:
Take an appropriate amount of quadriceps muscle into the grinding tube, add TRIZOL, and put it into the tissue grinder to crack the histiocytic components.Then centrifuge, transfer the supernatant to a new EP tube, add chloroform, after full shock, let stand for 10min, and centrifuge again.The supernatant was transferred to a new EP tube, isopropyl alcohol was added to assist precipitation, the supernatant was abandoned, 75% anhydrous ethanol was washed and precipitated twice, and finally the total RNA was dissolved and precipitated with enzyme-free water.The total RNA was reverse-transcribed into cDNA.
The RNA-seq libraries were sequenced on a BGIseq500 platform to generate paird-end 150 bases reads

value: quadricep

tag: strain

value: BALB/c

value: female

value: TIGIT-/-

tag: disease state

value: EAE


title: MASMCs form wild-type mice treated with PDGF-BB, sample3

description:
Library name: C_r2
MASMCs treated with PDGF-BB


title: X91-Tigit-/-


title: D52S_SAE_Fresh

description: 10x Genomics

source_name: Airway

value: Airway

value: Small airway explants


title: ARPE-19 cells, era2

value: Retinal pigment epithelial cells

value: WT

value: Erastin


title: D52S_SAE_d2

description: 10x Genomics


title: D52S_SAE_d14

description: 10x Genomics


title: X87-WT


title: D52S_LAE_Fresh

description: 10x Genomics

value: Large airway explants


title: D51S_PCLS_d14

description: 10x Genomics


title: D52S_LAE_d2

description: 10x Genomics


title: X11-Tight-/-


title: X30-WT


title: D51S_PCLS_Fresh

description: 10x Genomics


title: Tigit-/-3-total CD4

source_name: Total CD4 T cell

extract_protocol:
Collect the cells into EP tube, add TRIZOL to fully lyse the cells, then centrifuge, transfer the supernatant to a new EP tube, add chloroform, fully shake, stand for 10min, and centrifuge again.Transfer the supernatant to a new EP tube, add isopropanol to assist precipitation, discard the supernatant, wash the precipitation twice with 75% absolute ethanol, and finally dissolve the precipitation with enzyme-free water to obtain total RNA. Reverse transcription of total RNA into cDNA.
The RNA-seq libraries were sequenced on a BGIseq500 platform to generate paird-end 150 bases reads

value: Total CD4 T cell

value: Tigit-/-


title: D51S_SAE_d14

description: 10x Genomics


title: X25-WT


title: D51S_SAE_d2

description: 10x Genomics


title: Tigit-/-2-total CD4


title: D51S_SAE_Fresh

description: 10x Genomics


title: Tigit-/-1-total CD4


title: D52S_LAE_d14

description: 10x Genomics


title: D51S_LAE_d14

description: 10x Genomics


title: WT3-total CD4


title: WT2-total CD4


title: D51S_LAE_d2

description: 10x Genomics


title: WT1-total CD4


title: sorted mCherry+ tenocytes from 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 4

city: Irvine

first: Pavan

last: Nayak

address: 4462 Natural Sciences 2

institute: UC Irvine

description: Library name: P48-4

data_processing:
Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1
Assembly: GRCz10
Supplementary files format and content: csv file includes DESeq2 normalized counts for all samples

molecule: polyA RNA

organism: Danio rerio

source_name: FAC sorted mCherry+ tenocytes from whole Tg(scxa:mCherry) embryos

extract_protocol:
36 hpf and 48 hpf Tg(scxa:mCherry) zebrafish embryos (labeling tendon fibroblasts/tenocytes) were dissociated with Collagenase IV (Gibco, 17104019) at a concentration of 6.24 mg/ml without trypsin addition at a temperature of 28C for roughly 40 min, homogenizing every 5 min with a P1000 pipette. Cells were filtered through a 40um filter (Pluriselect-usa, 43-10040-50). Dissociated cell suspensions were sorted on a Bio-Rad FACS Aria II cell sorter. mCherry-positive cells were gated and sorted for those expressing at high levels.
RNEasy Micro Kit (Qiagen, 74004) was used for RNA extraction of cell lysates from FAC-sorted cells, and the Smart-seq2 protocol was utilized for cDNA library construction. Libraries were sequenced using a Hi-seq 4000 sequencer (Illumina) at a read depth of ~35M reads per replicate.

value: mCherry+ tenocytes

value: WT Tg(scxa:mCherry) background

value: 48 hpf


title: D42S_PCLS_Fresh

description: 10x Genomics

value: Lung parenchyma

value: Precision cut lung slices

value: lung cells


title: D51S_LAE_Fresh

description: 10x Genomics


title: D42S_PCLS_d14

description: 10x Genomics


title: sorted mCherry+ tenocytes from 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 2

description: Library name: P48-2

value: FAC sorted mCherry+ tenocytes from whole Tg(scxa:mCherry) embryos


title: D42S_SAE_d14

description: 10x Genomics


title: D42S_SAE_Fresh

description: 10x Genomics


title: D42S_LAE_d14

description: 10x Genomics


title: D42S_LAE_d2

description: 10x Genomics


title: sorted mCherry+ tenocytes from 36 hpf Tg(scxa:mCherry) zebrafish embryos replicate 6

description: Library name: P36-6

value: 36 hpf


title: sorted mCherry+ tenocytes from 36 hpf Tg(scxa:mCherry) zebrafish embryos replicate 5

description: Library name: P36-5


title: D42S_LAE_Fresh

description: 10x Genomics


title: sorted mCherry+ tenocytes from 36 hpf Tg(scxa:mCherry) zebrafish embryos replicate 4

description: Library name: P36-4


title: ATAC-CTCF_delta_RBR_plus_rep2

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
We performed paired-end 101-cycle sequencing on the NovaSeq 6000 sequencer (Illumina). the reads were trimmed for the Nextera adapter by cutadapt (v1.9, paired-end mode, default parameter with “ -m 6 -O 20”) and aligned to the human genome hg19(GRCh37-lite) by BWA (v0.7.12-r1039, default parameter)(Li and Durbin 2009).
The duplicated reads were then marked with biobambam2 (v2.0.87), and only nonduplicated proper paired reads were kept by samtools (parameter “-q 1 -F 1804,” v1.2)(Li, Handsaker et al. 2009).
After removing the mitochondrial DNA reads, the rest of reads were classified into nucleosome free reads and nucleosome reads by fragment size. The bigwig files were generated by using the center 80-bp fragments and scaled to 20 million nucleosome-free reads. We observed reasonable nucleosome-free peaks and patterns of nucleosome peaks surrounding the nucleosome-free peaks on the Integrative Genomics Viewer (Broad Institute).
All samples exhibited double the ENCODE criteria. Therefore, we concluded the data showed enough depth. Given that all of samples exhibited more than 20 million fragments, we were confident that most of the strong peaks were not missed.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Blood

growth_protocol: All SEM cells and derivative lines were cultured in RPMI-1640 medium (Lonza) containing 10 % fetal bovine serum (Hyclone), 2 mM glutamine (Sigma) and 1% penicillin/streptomycin (Thermo Fisher Scientific) in an incubator at 37 °C, 5 % CO2 and 95 % humidity.

extract_protocol:
ATAC-seq was performed following the protocol described previously. Nuclei were isolated from 75,000 cells in duplicate for each sample. Cell pellets were resuspended in 150 µL cold ATAC-RSB buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% TWEEN20, 0.01% digitonin and protease inhibitors) and incubated on ice for 3 minutes. One ml ATAC-RSB+ buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% TWEEN20 and protease inhibitors) was added and samples were centrifuged at 500 rpm for 10 minutes at 4°C. The nuclear pellets were resuspended in a 50 µL reaction buffer [final concentration 1X Tagment DNA Buffer (Nextera, FC-121-1030), 2.5 µL Nextera Tn5 (Nextera, FC-121-1030)] and incubated at 37°C for 30 minutes with 1,000 rpm shaking. The Qiagen MinElute PCR purification kit (Qiagen, 28004) was used to purify DNA and indexing PCR was carried out for 12 cycles with NEBNext HiFi 2X PCR Master Mix (NEB, M0541S) and indexing primers. Agencourt AMPure XP beads (Beckman Coulter, A63881) were used at a 1:3 ratio to purify DNA.
The Qiagen MinElute PCR purification kit (Qiagen, 28004) was used to purify DNA and indexing PCR was carried out for 12 cycles with NEBNext HiFi 2X PCR Master Mix (NEB, M0541S) and indexing primers

treatment_protocol: One micromolar 5-Ph-IAA (MedChemExpress) was used to induce degradation of CTCF in CTCFAID2 cells. Endogenous CTCF was removed from CTCFAID2/WT and CTCFAID2/ DRBR by a 6 h 5-Ph-IAA treatment before induction of exogenous HA tagged CTCF with 1 mg/mL doxycycline for 18 h.

value: Blood

value: SEM

value: B-ALL

value: with 5-Ph-IAA and doxycycline


title: sorted mCherry+ tenocytes from 36 hpf Tg(scxa:mCherry) zebrafish embryos replicate 3

description: Library name: P36-3


title: ATAC-CTCF_delta_RBR_plus_rep1


title: sorted mCherry+ tenocytes from 36 hpf Tg(scxa:mCherry) zebrafish embryos replicate 2

description: Library name: P36-2


title: ATAC-CTCF_WT_plus_rep2

value: CTCF-miniAID-mClover3+ TRE3G-HA-CTCF-WT


title: ATAC-CTCF_WT_plus_rep1


title: sorted mCherry+ tenocytes from 36 hpf Tg(scxa:mCherry) zebrafish embryos replicate 1

description: Library name: P36-1


title: crim1 knockdown whole eyes, 72 hours post fertilization, sample 3

city: Cincinnati

first: Anne

last: Slavotinek

state: OH

address: 3333 Burnet Ave, Room E5.253

institute: Cincinnati Children's Hospital Medical Center

description: Library name: crim1_3

data_processing:
The quality of raw single-end reads of RNA-Seq dataset was tested by FastQC (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/) to evaluate the per-base sequence quality, quality scores, sequence length distribution and overrepresented adapter/primer sequences.  After quality control with FastQC, data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome (GRCz11) using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally, DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes (DEGs) with log2 (fold change) greater than ±0.5 with an adjusted p-value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped (FPKM) ≥1 in all datasets were identified by comparing crim1-/- mutants with control datasets using an in-house Python script. Principal component analysis (PCA) was performed
Assembly: GRCz11
Supplementary files format and content: Excel; Statistically significant differentially expressed genes (DEGs) with log2 (fold change) greater than ±0.5 with an adjusted p-value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped (FPKM) ≥1 in all datasets were identified by comparing crim1-/- mutants with control datasets using an in-house Python script.

source_name: Whole eye

extract_protocol:
Whole eyes were dissected fromzebrafish at 72 hours post fertilization according to prior methods (Krall et al., 2018)
We performed ‘bulk’ RNA-Seq experiments in dissected eyes from in-crossed crim1-/- larvae and controls at 72 hpf according to prior methods (Krall et al., 2018). RNA quality and quantity was reviewed with a bioanalyzer (2100 Bioanalyzer, Agilent) and libraries were prepared with an Ovation® RNA-Seq system V2 kit (NuGEN). With this method, total RNA was reverse transcribed to synthesize first-strand cDNA using a combination of random hexamers and a poly-T chimeric primer (Krall et al., 2018). The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double-stranded DNA was then amplified using single primer isothermal amplification (SPIA). SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′-end of the double- stranded DNA, after which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′-end of the primer by displacement of the existing forward strand (Krall et al., 2018). Random hexamers were then used to amplify the second-strand cDNA linearly. Finally, libraries from the SPIA-amplified cDNA were made using the Ultralow DR library kit (NuGEN). The RNA-Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction (qPCR) prior to sequencing (KAPA library quantification kit). High-throughput sequencing was done using single-end 50 lane(s) on a HiSeq 4000 instrument (Illumina).

value: Whole eye

value: All


title: sorted mCherry+ tenocytes from 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 3

description: Library name: P48-3


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 14, induced, replicate 3

city: Helsinki

first: Juha

middle: Samuli

last: Tapanainen

state: Uusimaa

address: Haartmaninkatu 8

department: Obstetrics and Gynaecology

country: Finland

institute: University of Helsinki

description:
Library name: d14_3_ind
d14_3_ind

data_processing:
Raw reads in fastq format were processed using the fastp software (version 0.23.2)
Hisat2 (v2.0.5) was used to build the index of the reference genome and to align paired-end clean reads to the reference genome.
To quantify the gene expression level featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
The expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and the read counts mapped to this gene
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: xls file including the gene counts for each sample

source_name: cells

growth_protocol: H9-DDdCas9VP192-FOXL2 clone 24 cells were cultered in Essential 8 medium on Geltrex-coated plates and a 5%CO2 incubator at 37C.

extract_protocol:
Total RNA was extracted using the Nucleospin RNA kit (Macherey-Nagel) skipping the DNAse treatment steps. Seperated DNAse treatment was performed with the RQ1 RNAse-free DNAse (Promega) to remove gDNA after which the RNA was purified using the Nucleaspin RNA Clean-up kit (Macherey-Nagel).
RNA libraries were prepared by Novogene. Messenger RNA (mRNA) was isolated from tRNA employing poly-T oligo-attached magnetic beads (ABclonal) for mRNA library preparation. The mRNA was then fragmented and thereafter cDNA was synthetised through reverse transcription. The first cDNA strand was synthetised using random hexamer primers and the second cDNA strand with dUTP/dTTP. The non-directional library was ready after end-repair A-tailing, adapter ligation, size selection, amplification and purification. The mRNA library was subsequently quantified with Qubit (Invitrogen) and RT-PCR. Bioanalyzer was used to check the size distribution detection.

treatment_protocol: H9-DDdCas9VP192-FOXL2   clone 24 cells were single cell seeded onto human collagen coated plates and subjected to gonadal differentiation for 14-days through the addition of different small molcules, inhibitors and growth factors to the intermediate mesoderm (IM) medium. FOXL2 was induced at day 4 by adding doxycycline and trimethoprim to the IM medium.

value: cells

value: human embryonic stem cells

value: FOXL2 activation

value: Gonadal differentiation


title: ATAC-C27_plus_rep2

value: with IAA


title: crim1 knockdown whole eyes, 72 hours post fertilization, sample 2

description: Library name: crim1_2


title: sorted mCherry+ tenocytes from 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 1

description: Library name: P48-1

value: mCherry+ tenocytes

value: WT Tg(scxa:mCherry) background

value: 48 hpf


title: sorted mCherry+ tenocytes from 36 hpf Tg(scxa:mCherry) zebrafish embryos replicate 7

description: Library name: P36-7

value: FAC sorted mCherry+ tenocytes from whole Tg(scxa:mCherry) embryos


title: D42S_SAE_d2

description: 10x Genomics

value: Airway

value: Small airway explants

value: lung cells


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 14, induced, replicate 1

description:
Library name: d14_1_ind
d14_1_ind


title: crim1 knockdown whole eyes, 72 hours post fertilization, sample 1

description: Library name: crim1_1


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 14, induced, replicate 2

description:
Library name: d14_2_ind
d14_2_ind


title: ATAC-C27_plus_rep1

value: Blood

value: SEM

value: B-ALL


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 14, control, replicate 3

description:
Library name: d14_3_ctrl
d14_3_ctrl


title: ATAC-C27_minus_rep2

value: no auxn


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 14, control, replicate 2

description:
Library name: d14_2_ctrl
d14_2_ctrl


title: ATAC-C27_minus_rep1

value: no auxin


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 12, induced, replicate 3

description:
Library name: d12_3_ind
d12_3_ind

value: cells


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 12, induced, replicate 2

description:
Library name: d12_2_ind
d12_2_ind

value: human embryonic stem cells


title: wildtype whole eyes, 72 hours post fertilization, sample 2

description: Library name: wildtype_2

value: Whole eye

value: All

value: Wildtype


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 12, induced, replicate 1

description:
Library name: d12_1_ind
d12_1_ind

value: FOXL2 activation

value: Gonadal differentiation


title: hESC-SAKD_rep3

first: Li

last: Li

address: Zhen Nan Road 500

department: School of Medicine

institute: Tongji University

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads.
The clean reads were then aligned to human genome (GRCh38,Ensembl104) using the Hisat2
HTseq was used to get gene counts and RPKM method was used to determine the gene expression.
Assembly: GRCh38，Ensembl104
Supplementary files format and content: xlsx file includes raw counts for each sample

extract_protocol:
Human ESC H7 was cultured on Matrigel-coated plates (Corning, Cat#354277) in mTeSRTM Plus medium (STEMCELL Technologies, Cat#100-0276) and medium was changed every other day. Cells were cultured at 37 °C with 5% CO2, and passaged every 4~5 days in PGM1 (CELLAPY, Cat#CA1008500). Cells were tested for mycoplasma contamination (CELLAPY, Cat#CA6101096) every month.
Total RNA was extracted by Trizol reagent (Takara, Cat#9108) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction. The cDNA libraries were constructed for each RNA sample using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc.) according to the manufacturer’s instructions. Purified first-strand cDNA was enriched by PCR to create the cDNA libraries. The libraries were quality controlled with Agilent 2200 and sequenced by NovaSeq 6000 on a 150 bp paired-end run.

value: SAMD4A knockdown


title: wildtype whole eyes, 72 hours post fertilization, sample 1

description: Library name: wiildtype_1


title: hESC-SAKD_rep2


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 12, control, replicate 3

description:
Library name: d12_3_ctrl
d12_3_ctrl


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 12, control, replicate 2

description:
Library name: d12_2_ctrl
d12_2_ctrl


title: Day8 Dox

city: Singapore

first: Kiyofumi

last: Hamashima

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB)

description: Library name: SS3-_Day_8_Dox__undiluted

data_processing:
Single-cell RNA-seq data was processed as preciously described (Gautam et al., 2021). Briefly, we used counts modes of cellragner (Zheng et al., 2017) to generate read count matrices from the fastq files. The reference genome index of mm10 was downloaded from 10x Genomics. Count and fragment data were imported into Seurat (Hao et al., 2021) objects, and the QC was performed to remove outlier based on the total UMI, detected gene number and % mitochondrial genes. Major cell classes were manually annotated based on the cluster-specific markers
Assembly: mm10
Supplementary files format and content: Seurat R object (rds format)

source_name: Reprogramming cells

growth_protocol: MEFs were cultured in haematopoietic media (1× Iscove’s modified Dulbecco’s medium, 10% FBS (Gibco) 10% protein-free hybridoma medium [PFM; GIBCO], 1% L-glutamine, 1% penicillin-streptomycin, 25 ug/ml ascorbic acid, 4.5 X 10−4 M MTG, 180 mg/ml transferrin (R&D systems), 50ng SCF (PeproTech), 25ng IL-3 (PeproTech), 25ng IL-6 (PeproTech), 1% granulocyte-macrophage colony-stimulating factor, 1% thrombopoietin conditioned media, 2000 U erythropoietin, 10 ng macrophage colony-stimulating factor and 100 ng Flt3 ligand (PeproTech))

extract_protocol:
On each day of sample harvesting, the cells were trypsinised, counted and frozen in 10% DMSO containing FBS and stored in liquid nitrogen until library preparation steps.
Libraries were prepared using the Chromium Next GEM Single cell 3’ Reagents Kit v3.1 (10x Genomics) according to manufacturer instructions.

treatment_protocol: To initiate reprogramming 1 ug/ml of doxycycline was added to the haematopoietic medium.

value: Reprogramming cells

value: Indicible SCL and LMO2

value: Doxycylcine


title: hESC-SAKD_rep1


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 12, control, replicate 1

description:
Library name: d12_1_ctrl
d12_1_ctrl


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 10, induced, replicate 3

description:
Library name: d10_3_ind
d10_3_ind


title: Day4 Dox

description: Library name: SS3-_Day_4_Dox__undiluted


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 10, induced, replicate 2

description:
Library name: d10_2_ind
d10_2_ind


title: Day14 Dox cKIT-hi

description: Library name: SS3-_Day_14_Dox_ckit_plus___undiluted


title: hESC-SACTR_rep3

value: control


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 10, control, replicate 3

description:
Library name: d10_3_ctrl
d10_3_ctrl


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 10, induced, replicate 1

description:
Library name: d10_1_ind
d10_1_ind


title: hESC-SACTR_rep2


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 10, control, replicate 2

description:
Library name: d10_2_ctrl
d10_2_ctrl


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 14, control, replicate 1

description:
Library name: d14_1_ctrl
d14_1_ctrl


title: hESC-SACTR_rep1


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 8, induced, replicate 3

description:
Library name: d8_3_ind
d8_3_ind


title: Day2 Dox

description: Library name: SS2-_Day_2_Dox__undiluted


title: HEK-mKL_SCM-4hr_FGF23-4_S38

city: Indianapolis

first: Kenneth

last: White

state: IN

address: 635 Barnhill Drive

institute: Indiana University School of Medicine

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to GENCODE G31 genes using featureCounts (from subread v2.0.1) with the following parameters: “-s2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: HEK-mKL cells were grown in EMEM media supplemented with 10% fetal bovine serum (FBS) and 1% penecillin-streptomycin (PS). Cells were stored in 75cm^2 culture flasks and incubated at 37°C and 5% CO2.

extract_protocol:
Bulk RNA was extracted using the Meridian Bioscience's Isolate II RNA Mini Kit. 100ng of RNA was used for sequencing.
RNA libraries for RNAseq were prepared following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352-v4.17.

treatment_protocol: HEK-mKL cells were treated with 50ng/mL of recombinant human FGF23 protein in 1X phosphate buffered saline (PBS). Control wells were treated with an equivalent volume 1X PBS. All samples were incubated for 4 hours at 37ºC and 5% CO2.

value: Embryonic kidney

tag: time

value: 4 hours


title: Day2 Control

description: Library name: SS1-_Day_2_Control__undiluted

source_name: Fibroblasts

value: Fibroblasts

value: Untreated


title: wildtype whole eyes, 72 hours post fertilization, sample 3

description: Library name: wildtype_3


title: Replicate 3  Day 4 dox

description: Library name: GL81_09_I_S9

data_processing:
The sequencing reads were mapped to the mouse mm9 genome using STAR with the following parameters: --alignIntronMax 1 --alignEndsType EndToEnd. Peak calling was performed by MACS2 (Zhang et al., 2008). ATAC-seq read counts for each sample were then calculated using featureCounts (Liao et al., 2014). DESeq2 (Love et al., 2014) was used to visualize the PCA plot and identify the differential peaks using cutoff p-value <0.05.
Assembly: mm9
Supplementary files format and content: bedGraph file

extract_protocol:
MEFs were seeded onto 0.1% gelatin coated plates and the following day were treated with 1 ng/ml doxycycline for 48 and 96 hours. 50,000 cells of each treated and control cells were centrifuged at 350 x g for 5 minutes at 4°C and washed in cold PBS. The cell pellet was resuspended in 50 μl transposase mixture containing 25 μl 2x TD Buffer, 2.5 μl transposase enzyme, 0.01 % digitonin and 22 μl water. The resuspended cell pellet was incubated at 37°C for 60 minutes at 300 rpm. Subsequently, samples were purified using the MinElute PCR purification kit (Qiagen), according to manufacturer instructions. The elution buffer was pre-warmed to 37 °C and during the final elution step, the buffer was left to incubate on the columns for an additional 5 minutes before the final elution spin step.
ATAC-Seq library preparation was performed as described previously (Buenrostro et al., 2015)


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 8, control, replicate 2

description:
Library name: d8_2_ctrl
d8_2_ctrl

tag: cell line


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 8, induced, replicate 1

description:
Library name: d8_1_ind
d8_1_ind

tag: cell type


title: HEK-mKL_SCM-4hr_FGF23-3_S37


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 8, control, replicate 3

description:
Library name: d8_3_ctrl
d8_3_ctrl

tag: genotype


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 8, induced, replicate 2

description:
Library name: d8_2_ind
d8_2_ind


title: Day14 Dox cKIT-lo

description: Library name: SS3-_Day_14_Dox_ckit_plus__low__undiluted


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 8, control, replicate 1

description:
Library name: d8_1_ctrl
d8_1_ctrl


title: HEK-mKL_SCM-4hr_FGF23-2_S36


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 6, induced, replicate 3

description:
Library name: d6_3_ind
d6_3_ind


title: Replicate 3 Day 2 dox

description: Library name: GL81_08_H2_S8


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 6, induced, replicate 2

description:
Library name: d6_2_ind
d6_2_ind


title: HEK-mKL_SCM-4hr_FGF23-1_S35


title: Replicate 3  control - Day 2 Untreated

description: Library name: GL81_07_G2_S7


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 6, induced, replicate 1

description:
Library name: d6_1_ind
d6_1_ind


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 10, control, replicate 1

description:
Library name: d10_1_ctrl
d10_1_ctrl


title: Replicate 2 Day 4 dox

description: Library name: GL81_06_F_S6


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 6, control, replicate 3

description:
Library name: d6_3_ctrl
d6_3_ctrl


title: HEK-mKL_SCM-4hr_VEH-3_S33

value: PBS


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 6, control, replicate 2

description:
Library name: d6_2_ctrl
d6_2_ctrl

value: cells


title: HEK-mKL_SCM-4hr_VEH-2_S32


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 6, control, replicate 1

description:
Library name: d6_1_ctrl
d6_1_ctrl

value: human embryonic stem cells


title: Replicate 2 Day 2 dox

description: Library name: GL81_05_E2_S5


title: HEK-mKL_SCM-4hr_VEH-1_S31


title: Replicate 2  control - Day 2 Untreated

description: Library name: GL81_04_D_S4


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 4, replicate 1

description:
Library name: d4_1
d4_1


title: Replicate 1 Day 4 dox

description: Library name: GL81_03_C2_S3


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 4, replicate 2

description:
Library name: d4_2
d4_2


title: OEVCR3

city: Hangzhou

first: Ni

last: Zhu

state: Zhejiang

address: 54 Youdian Road

department: Hematology

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

data_processing:
Qseq100 DNA Analyzer
Data filtering:fastp software
Read alignment software:bowtie2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: T lymphocyte

extract_protocol:
RNA was extracted using the Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA).1-10μg total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq was prepared using KAPA Library Quantification Kit following manufacturer`s protocols.

treatment_protocol: Jurkat cells in both control and PTPN21 overexpressed groups were treated with VCR for 48 hours,DMSO used as control.

value: T lymphocyte

value: Jurkat

value: PTPN21 overexpression

value: vincristine


title: TSC, 48 hr rotation, rep 2

city: Edmonton

first: Meghan

last: Riddell

state: AB

country: Canada

institute: University of Alberta

data_processing:
Quality control of the samples was performed using FastQC
Trimmed sequence reads were mapped with GrCm38 uusing STAR
Feature counts for genes were obtained using the FeatureCounts package in R
Supplementary files format and content: Comma separated value files with counts for all the samples

source_name: Human TSC CT 29

growth_protocol: Single explants were placed in each well of a 48 well plate in medium consisting of Iscove's Modified Dulbecco's Medium (IMDM), 5% heat-inactivated FBS, 50µg/mL gentamicin, and 1X ITS-X supplement at 37˚C 5% CO2. To establish 3D ST spheroids, TSC were cultured 2x106 cells per 10mL High Aspect Rotational Vessels (HARVs) on rotational speed 10.8 using the Synthecon Rotary Cell Culture System.

extract_protocol:
RNA was harvetsed using the  Purelink RNA mini kit. 1g of RNA was used for library construction
Libraries were constructed using the Illumina Stranded mRNA prep kit following manufacturers instructions

treatment_protocol: For ezrin inhibitor treatments in explants, 50µM of NSC668394 or vehicle control (DMSO) was added to medium 24hrs post-trypsinization for 24hrs. The spheroids were treated after 18hrs of rotation with 25µM ezrin inhibitor (EMD Millipore; cat:341216, lot:3934373) or vehicle control (DMSO). Organoids were collected after 48hrs of total culture time for downstream analysis

value: Human TSC CT 29

value: First trimester trophoblasts

value: WT

value: 48 hr


title: TSC, 18 hr rotation, rep 2

value: 18 hr


title: Replicate 1 Day 2 dox

description: Library name: GL81_02_B2_S2

value: Reprogramming cells

value: Indicible SCL and LMO2

value: Doxycylcine


title: OEVCR1


title: TSC, 48 hr rotation, rep 1


title: TSC, Ezrin inhibitor, 48 hr, rep 2

value: Ezrin inhibitor


title: OEVCR2


title: TSC, Ezrin inhibitor, 48 hr, rep 1


title: TSC, 18 hr rotation, rep 1


title: TSC, Pre-rotation, rep 2

value: Pre-rotation


title: Replicate 1  control - Day 2 Untreated

description: Library name: GL81_01_A2_S1

value: Fibroblasts

value: Untreated


title: VCR3


title: H9-DDdCas9VP192-FOXL2 clone 24 cells, day 4, replicate 3

description:
Library name: d4_3
d4_3

value: cells

value: human embryonic stem cells

value: FOXL2 activation

value: Gonadal differentiation


title: Infected + Substance P replicate C

city: Charlotte

first: Morgan

middle: Brittany

last: Johnson

address: 9201 University City BLVD

department: Biological Sciences

institute: University of North Carolina at Charlotte

description: Library name: mOCSaSP_C

data_processing:
The adapters of the sequenced reads were adapter cut using cutadapt v. 2.6 and the reads were quality checked using fastqc v0.11.9. The GRCm39 RefSeq transcriptome (GCF_000001635.27) was used as a reference to map the quality controlled reads using Bowtie2 v 2.4.1.
Assembly: GRCm39
Supplementary files format and content: Matrix counts table, tab-delimited format.

source_name: Osteoclast

extract_protocol:
At 4 hours post-infection, RNA was isolated with TRIzol and purified using a GeneJET RNA Cleanup and Concentration Micro Kit according to the manufacturer’s guidelines (ThermoFisher Scientific).
The Genomic Sequencing and Analysis Facility at the University of Texas at Austin prepared Tag-Seq libraries using an established method and they were sequenced using an NovaSeq S1 to generate 100bp single end reads for 3’ end sequencing.

value: Osteoclast


title: Placenta, Ezrin inhibitor, rep 3

description: 1st trimester placent, GA 9-12 wks

source_name: Placenta

value: Placenta


title: TSC, Pre-rotation, rep 1

value: Human TSC CT 29

value: First trimester trophoblasts


title: Infected replicate C

description: Library name: mOCSa_C


title: VCR2

value: T lymphocyte

value: Jurkat

value: WT

value: vincristine


title: Placenta, Ezrin inhibitor, rep 2

description: 1st trimester placent, GA 9-12 wks


title: VCR1


title: Placenta, CTL, rep 3

description: 1st trimester placent, GA 9-12 wks

value: Ctl


title: Uninfected + Substance P replicate C

description: Library name: mOCuSP_C


title: Placenta, CTL, rep 2

description: 1st trimester placent, GA 9-12 wks


title: Placenta, Ezrin inhibitor, rep 1

description: 1st trimester placent, GA 9-12 wks

value: Ezrin inhibitor


title: OE3

value: PTPN21 overexpression

value: DMSO


title: Placenta, CTL, rep 1

description: 1st trimester placent, GA 9-12 wks


title: Uninfected replicate C

description: Library name: mOCu_C


title: Placenta, 72 hrs, rep 3

description: 1st trimester placent, GA 9-12 wks

value: 72 hr


title: Placenta, 72 hrs, rep 2

description: 1st trimester placent, GA 9-12 wks


title: OE1


title: Placenta, 24 hrs, rep 2

description: 1st trimester placent, GA 9-12 wks

value: 24 hr


title: Uninfected + Substance P replicate B

description: Library name: mOCuSP_B


title: h- asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX biol_rep_2

city: New York

first: Ana

middle: M

last: Sanchez

state: NY

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Library name: HASX_asp1-H397A aps1∆ siw14∆ spx1∆_biol_rep_2

data_processing:
Base calls from Illumina NovaSeq X-Plus (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2-2.1.0
Resulting SAM files were converted to BAM files using Samtools
Count files for individual replicated were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source 'ensembl')
Differential expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

source_name: Haploid

growth_protocol: Log phase cultures grown at 30˚C in ePMGT medium

extract_protocol:
Hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the NEB Ultra II Directional RNA library prep plus PolyA isolation module kit according to manufacturer's protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq X-Plus instrument at the Weill Cornell Medicine Genome Core Facility (in New York).
Stranded polyA+ RNA seq

value: Haploid

tag: growth condition

value: log phase culture, ePMGT medium

tag: developmental stage

value: Vegetative growth

value: asp1-H397A aps1 knockout siw14 knockout spx1 knockout

tag: lab strain_number


title: Placenta, 24 hrs, rep 3

description: 1st trimester placent, GA 9-12 wks

value: Placenta

tag: treatment


title: OE2


title: h- asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX biol_rep_1

description: Library name: HASX_asp1-H397A aps1∆ siw14∆ spx1∆_biol_rep_1


title: h- biol_rep_3

description: Library name: WT_biol_rep_3


title: Placenta, 72 hrs, rep 1

description: 1st trimester placent, GA 9-12 wks


title: Infected + Substance P replicate A

description: Library name: mOCSaSP_A

value: Osteoclast


title: Infected replicate A

description: Library name: mOCSa_A


title: NC3


title: Placenta, 24 hrs, rep 1

description: 1st trimester placent, GA 9-12 wks


title: NC1


title: WT_OPT_T2_B3_vs_MflgE_OPT_T2_B3

type: RNA

first: Miia

last: Lindström

address: Agnes Sjöbergin katu 2

department: Faculty of Veterinary Medicine

hyb_protocol: 300 ng of Cy3-labeled and of 300 ng of Cy5-labeld cDNA samples were mixed with 2.3 μg of salmon sperm DNA (Invitrogen), denaturized for 2 min at 95°C, then mixed with 5 μl 10x blocking agent and 26 μl 2x RPMI hybridization buffer (Agilent) and hybridized for 16 h at 65°C. After hybridization the slides were washed according to the manufacturer’s instructions.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2

data_processing:
A custom R-script was used for background subtraction and LOWESS normalization.
normalized log2 ratio (Cy3/Cy5) representing test/reference

organism: Clostridium botulinum

source_name: C. botulinum harvested cells from batch culture

label_protocol: 2 μg total RNA was reverse transcribed and labeled directly with fluorescent dye for 3 h at 46˚C. The mixture contained 5 μg of random primers, 40 U RNaseOUT™ Recombinant Ribonuclease Inhibitor, 6 μl 5x first-strand buffer, 3 μl of 100 mM DTT, 400 U SuperScript™ III Reverse Transcriptase (all Invitrogen, Life Technologies Ltd, Paisley, UK), 0.6 μl dNTP mix (25 mM dATP, 25 mM dGTP, 25 mM dTTP, 10 mM dCTP [Promega Corporation, Madison, WI, USA]), and 2 nmol Cy3-dCTP or Cy5-dCTP (GE Healthcare, Buckinghamshire, UK). The labeled cDNA was purified using a DNA purification column (QIAquick PCR purification kit; Qiagen).

growth_protocol: C. botulinum strain ATCC 19397 or derivatives were cultured in TPGY broth at 37 °C anaerobically.

extract_protocol: Total RNA extracted using Qiagen's RNeasy Midi Kit (Qiagen, Hilden, Germany), with on-column DNase treatment, following manufacturer's instructions. Additional DNase treatment using the Ambion DNA-free kit (Applied Biosystems, Life Technologies Corporation, Carlsbad, CA) according to the manufacturer’s instructions.

value: wild-type

tag: timepoint

value: ATCC 3502 cbo2654_flgE::intron-erm-


title: Donor41, GMCSF+IL6+serum starvation, CD33 high, scRNA-seq

city: Pittsburgh

first: Timothy

last: Billiar

state: PA

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

description: 10x Genomics Single Cell 3ʹ Kit v3.1

data_processing:
scMultiome-seq data were processed by Cell Ranger ARC software, and scRNA-seq data were processed by Cell Ranger software.
The BCL files generated by Illumina sequencing were demultiplexed by cellranger-arc mkfastq or cellranger mkfastq. We generated feature (GEX, ATAC)-barcode count matrix using cellranger-arc count or cellranger count (mapped to GRCh38 human reference genome) for each sample separately. The outputs of the samples from the same donor were aggregated using cellranger-arc aggr or cellranger aggr.
Assembly: GRCh38
Supplementary files format and content: UMI matrix

source_name: PBMCs, in vitro culture

extract_protocol:
Cells were harvested from dishes. Accutase 37C incubation for 10 min was used to harvest adherent cells. After CD33 beads enrichment (scMultiome) or flow sorting enrich (scRNA-seq), cells were subjected to 10x Genomics library preparation.
We followed Chromium Next GEM Single Cell Nultiome ATAC + Gene Expression protocol (CG000338 Rev C) and Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index, CG000315) to prepare the corresponding libraries.
scMultiome-seq or scRNA-seq

treatment_protocol: MDSCs were generated by treating PBMCs with GM-CSF (10ng/mL) + IL-6 (10ng/mL) at 5x10^5 cell/mL in full media at 37C with 5%CO2. Cytokines were added daily for 3 days. PBMCs cultured in full media alone were used as control. Serum starvation was performed using serum-free media.

value: PBMCs, in vitro culture

value: GMCSF+IL6+serum starvation


title: Infected + Substance P replicate B

description: Library name: mOCSaSP_B


title: Donor41, GMCSF+IL6+serum starvation, CD33 low, scRNA-seq

description: 10x Genomics Single Cell 3ʹ Kit v3.1


title: h- biol_rep_2

description: Library name: WT_biol_rep_2

value: WT


title: Uninfected + Substance P replicate A

description: Library name: mOCuSP_A


title: Infected replicate B

description: Library name: mOCSa_B


title: An.dirus Bs-treated rep3

city: Chongqing

first: Shasha

last: Yu

address: 30 Gaotanyan street

institute: Army medical university

data_processing:
Paired-end sequencing of the library was performed on the Illumina Novaseq 6000 sequencers (Illumina, San Diego, CA).
Fastp (version 0.19.5) was used for evaluating the quality of sequenced data.
Clean reads were mapped to the reference genome by HISAT2 (version 2.1.0) with default parameters.
DESeq2 (version 1.24.0) was used to determine differentially expressed genes (DEGs) between two samples.
Assembly: The reference genome downloaded from VectorBase (Anopheles dirus WRAIR2 Genome).
Supplementary files format and content: Processed data with gene expression level was provided in file " gene_expression_processed_data.txt".

organism: Anopheles dirus

source_name: whole mosquito

growth_protocol: An.dirus (Hainan strain) larvae were fed on powder mix of dry degreased pork liver and yeast in a ratio of 1:4 at 28℃ with a 12h light/dark cycle, , while the adult mosquitoes were fed on 10.0% sugar solution with the same environment conditions.

extract_protocol:
Total RNA was extracted using the Trizol Reagent (Invitrogen, Carlsbad, USA) from a pool of 30 mosquitoes treated with or without Bs.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Illumina TruseqTM RNA sample prep Kit following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Sublethal dose of Bs 2362 strain was administrated to the early 4th instar larvae of An.dirus to simulate shortage use of Bs in field circumstance. When the surviving larvae developed to pupae, they were collected and further emerged to adults in cages. The adult mosquitoes were then routinely maintained under the same environmental and rearing conditions as the group without Bs treatment.

value: whole mosquito

value: strain:Hainan strain

value: hours past blood feeding:24h

value: Bs treated


title: MhrcA_OPT_STAT_B2_vs_WT_OPT_STAT_B3

value: STAT


title: h- biol_rep_1

description: Library name: WT_biol_rep_1


title: Donor41, GMCSF+IL6, scRNA-seq

description: 10x Genomics Single Cell 3ʹ Kit v3.1


title: h- asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX biol_rep_3

description: Library name: HASX_asp1-H397A aps1∆ siw14∆ spx1∆_biol_rep_3


title: An.dirus Bs-treated rep2


title: NC2

value: T lymphocyte

value: Jurkat

value: DMSO


title: Uninfected replicate A

description: Library name: mOCu_A


title: Uninfected replicate B

description: Library name: mOCu_B


title: Donor41, control, scRNA-seq

description: 10x Genomics Single Cell 3ʹ Kit v3.1

value: control


title: WT_OPT_STAT_B2_vs_MdnaK_OPT_STAT_B3


title: An.dirus Bs-treated rep1


title: An.dirus Control rep3

value: untreated


title: Donor36, GMCSF+IL6+serum starvation, CD33 low, scRNA-seq

description: 10x Genomics Single Cell 3ʹ Kit v3.1


title: MdnaK_OPT_TRANS_B3_vs_WT_OPT_STAT_B1

value: TRANS


title: hippocampus,  Mr1-/- P301S mice 4

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

description: Library name: TauMR4

data_processing:
Raw data were processed by Cellranger. The Cellranger pipelines include Cellranger mkfastq, Cellranger count, Cellranger Aggr, and Cellranger reanalyze pipelines.
Assembly: Reference genome mouse (mm10) was used for read alignment.
Supplementary files format and content: Processed data are in the formats of mtx and tsv for processed data

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Nuclei were extracted from the hippocampus of mice.
Libraries were prepared using 3’ GEM gene expression kit (10xgenomics) following the manufacturer’s instructions.

value: hippocampus

value: hippocampus cells

tag: batch


title: WT_OPT_TRANS_B3_vs_MhrcA_OPT_TRANS_B3

value: wild-type


title: hippocampus,  Mr1-/- P301S mice 3

description: Library name: TauMR3


title: Donor36, GMCSF+IL6+serum starvation, CD33 high, scRNA-seq

description: 10x Genomics Single Cell 3ʹ Kit v3.1

value: PBMCs, in vitro culture


title: An.dirus Control rep2


title: MdnaK_OPT_TRANS_B1_vs_WT_OPT_TRANS_B2


title: Donor36, GMCSF+IL6, Ap-, scRNA-seq

description: 10x Genomics Single Cell 3ʹ Kit v3.1


title: Donor36, GMCSF+IL6, Ap+, scRNA-seq

description: 10x Genomics Single Cell 3ʹ Kit v3.1


title: hippocampus,  Mr1-/- P301S mice 1

description: Library name: TauMR1


title: WT_OPT_TRANS_B1_vs_MhrcA_OPT_TRANS_B1