title: leaf primordia, ospid C2, rep2

status: Public on Aug 31 2022

city: nanjing

first: Jiajun

address: Weigang no.1, Xuanwu District, Nanjing City, Jiangsu Province

institute: Nanjing Agricultural University

data_processing:
The low-quality reads in the raw data were removed by the useful Perl script: (1) Trim Smart-seq2 public primer sequence from the Reads; (2) Remove the contaminated reads for adapters; (3) Remove the low quality reads; (4) Remove the reads whose N base more than 5% for total bases
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa

source_name: leaf primordia

growth_protocol: Plant materials were cultivated in a growth chamber under a 15-h light /9-h darkness photoperiod (28°C/24°C) with 70% relative humidity.

extract_protocol:
RNA was harvested using pBIOZOL Plant Total RNA Extraction Reagent (BSC55M1). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA   Library Prep Kit for Illumina® (#E7530L, NEB, USA) following manufacturer's protocols.

value: leaf primordia

value: OsPID knockout


title: leaf primordia, ospid C1, rep2

type: SRA

last: Liu

country: China

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype


title: leaf primordia, ospin1c ospin1d, rep3

value: OsPIN1c and OsPIN1d knockout


title: leaf primordia, ospid C1, rep1


title: leaf primordia, ospid C2, rep1


title: leaf primordia, ospid C2, rep3


title: leaf primordia, ospin1c ospin1d, rep2


title: leaf primordia, WT, rep1

value: WT


title: leaf primordia, WT, rep2


title: leaf primordia, ospin1c ospin1d, rep1


title: UPMM3, Cerivastatin, 3

type: RNA

city: Genova

first: Adriana

middle: Agnese

last: Amaro

state: Italy

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale policlinico San Martino

description:
Gene expression data from uveal melanoma cells treated
Cerivastatin 0.125 microM Treated Cells

hyb_protocol: Following IVT , the RNA biotinylated were hybridized for 16 hr at 45°C on Affymetrix GeneChip™ HG-U133+ PM Array Strip in GeneAtlas Hybridization Station. GeneChips were washed and stained using  GeneAtlas™ Hybridization, Wash, and Stain Kit for 3' IVT Arrays.

scan_protocol: GeneChip were finally scanned using GeneAtlas Scanner.

data_processing: Affymetrix® Transcriptome Analysis Console (TAC) Software.  Data were preprocessed following the RMA procedure using quantile normalization

label: biotin

organism: Homo sapiens

source_name: UPMM3, Cerivastatin

label_protocol: 500 ng of total of RNA was biotin labeled using the 3′ IVT Express Kit (Affymetrix) for array strips

growth_protocol: uveal melanoma cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 100 U/ml penicillin/streptomycin

extract_protocol: Total RNA was extracted using Rneasy Plus mini kit (Qiagen) following the manufacturers protocol. RNA quantity and quality were determined using a Nanodrop-1000 spectrophotometer (Nanodrop Technology) and Agilent 2100 Bioanalyzer.

treatment_protocol: Treatment with Cerivastatin, or Trametinib or Combined Treatment of these drugs

tag: cell line

tag: cell type

value: uveal melanoma cell

tag: treatment

value: Cerivastatin


title: UPMM3, Cerivastatin, 1


title: UPMM3, Trametinib, 2

description:
Gene expression data from uveal melanoma cells treated
Trametinib 10nM  Treated Cells

source_name: UPMM3, Trametinib

value: Trametinib


title: UPMM3, Cerivastatin & Trametinib, 3

description:
Gene expression data from uveal melanoma cells treated
Cerivastatin 0.125 microM & Trametinib 10nM Treated Cells

source_name: UPMM3, Cerivastatin & Trametinib

value: Cerivastatin & Trametinib


title: UPMM3, NO, 3

description:
Gene expression data from uveal melanoma cells untreated
Control cells

source_name: UPMM3, NO

value: Control cells


title: leaf primordia, ospid C1, rep3


title: UPMM3, NO, 2


title: Hdac2-ChIP-Seq

city: New Orleans

first: Hongbing

address: 1430 Tulane Ave

country: USA

institute: Tulane University

description: E16.5 nephron progenitor cells

library_source: genomic

data_processing:
Sequencing was performed on an Illumina HiSeq 2500, running HiSeq Control Software version 2.2.58.
Quality control of sequencing reads was performed using FastQC.
Reads were then aligned to the reference genome using BWA v. 0.7.5a . Samples were filtered for regions with artificially high coverage using GreyListChIP
Subsequently samples were deduplicated using SAMtools version 1.3.1
Alignment coordinates were converted to BED format using BEDTools v.2.17 and peak calling was performed using Sicer
ChIP quality control was performed using the QHIPQC Bioconductor package
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
ChIP assays were performed on 3.75 million cells with HDAC1 and HDAC2 antibodiy using the iDeal ChIP-seq kit for Transcription Factors protocol
For each sample, a library preparation was performed on 500pg of DNA using the MicroPLEX v2 protocol. The ChIP samples (6 samples in total) were processed in 1 series of experiment.
A control library was processed in parallel of the samples using the same amount of a control Diagenode ChIP’d DNA.
According to the protocol, 12 cycles of amplification were performed to amplify the libraries.
After amplification, 1 μl of each library was loaded on Fragment Analyzer to check if enough material was generated. If not, additional cycles were performed until having enough material.
The additional PCR cycles were performed progressively until reaching enough amount of library for each sample.
Actually, the libraries were amplified for 1-3 additional cycles, then 1 μl of the libraries was analyzed on the Fragment Analyzer. The process was repeated several times until reaching enough yield of libraries

value: nephron progenitor cells

tag: chip antibody

value: Diagenode antibody, C15200201, lot 001. The Diagenode antibody H3K4me3 and IgG were used in parallel respectively as a positive and negative control IP reaction


title: UPMM3, Cerivastatin, 2


title: pRAB11

status: Public on Sep 01 2022

city: Melbourne

first: Tim

last: Stinear

state: Victoria

address: 792 Elizabeth St, Melbourne

country: Australia

institute: University of Melbourne

data_processing:
MiSeq reads from each of the five experiments (pRAB11: walRFLAG / vraRFLAG / hptRFLAG / saeRFLAG or pRAB11FLAG only) were first mapped to the S. aureus USA300 NC_007793 reference chromosome using samtools.
Read coverage plots for viewing in Artemis were created using samtools and the command %  samtools depth -aa [target_file_name].bam [subtraction_file_name].bam | cut -f3,4 | perl -nae 'use List::Util qw(max); print max(0, $F[0]-$F[1]),"\n";' > [target_peaks].userplot.
The ‘create feature from graph function’ in Artemis was then used to define sequence regions represented by the subtraction coverage plots. The resulting multi-fasta format files of these regions was the input for motif prediction using tools such as SeSiMCMC
Assembly: S. aureus USA300 NC_007793
Supplementary files format and content: userplots (Artemis)

organism: Staphylococcus aureus

growth_protocol: An overnight culture (10 ml LB in 50 ml tube) of each strain NRS384Δspa containing either pRAB11: walRFLAG / vraRFLAG / hptRFLAG / saeRFLAG or pRAB11FLAG only were grown at 37°C with shaking at 200 rpm. Overnight cultures were diluted 1:100 in fresh LB (100 ml) in a 1 L baffled flask

extract_protocol:
Bacterial cells were suspended in 1ml of lysis buffer (50 mM Tris-HCl [pH 7.4], 150 mM NaCl, 0.1% Triton X-100, 100 μg / ml lysostaphin (Ambi), 500 µg / ml RNaseA, complete mini protease inhibitor EDTA free containing 100 um zirconium beads) and incubated for 20 min at 37°C. The weakened cells were then disrupted using bead beating at 6000 rpm for 1 min and the cell lysate clarified by centrifugation (20,000xg/10min/4°C). The cation concentration of the lysate was adjusted with MgCl2 and CaCl2 to 100 mM. The DNA was sheared by the addition of a range of DNase I (NEB) concentrations (2 – 0.5 U), in a 200 uL volume, followed by incubation at 37°C for 10 min. The reaction was quenched by the addition of EDTA to 50 mM on ice. The degree of DNA fragmentation was assessed by electrophoresis of samples on a 2% (v/v) agarose TAE gel.
Samples showing maximal fragmentation at between 100-300 bp were subjected to immunoprecipitation. Lysis buffer (made up to 4 ml - omitting lysostaphin and RNaseA) containing 10 µg of M2-anti FLAG antibody was added and incubated overnight at 4°C on a rotating platform in a 15 ml tube. A 100 ul of Protein G agarose (Pierce) was added to the lysate and incubated a further 2h at room temperature. The sample was centrifuged (2,500 xg/3 min/22°C) and the agarose pellet washed three time with 4 ml of IP buffer (25mM Tris.Cl [pH 7.2}, 150mM NaCl) and finally resuspended in 200 ul of elution buffer (10mM Tris.Cl [pH 8], 1mM EDTA, 1% SDS containing 100µg of proteinase K). Crosslinks were reversed incubation for 2 h at 37°C and then 9 h at 65°C with shaking at 1400 rpm. Finally, eluted DNA was cleaned up by PCR purification (QiaQuick PCR purification kit, Qiagen). DNA libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina and sequenced using an Illumina MiSeq.

treatment_protocol: Grown to an OD600nm of 0.5, induced with 100 ng/ml of anhydrotetracycline and grown for a further hour.

value: anti-FLAG antibody

tag: culture medium

value: LB broth

tag: growth temp

tag: strain

value: 100 ng/ul aTc


title: UPMM3, NO, 1


title: DS55980254 30 mg/kg rep3

city: Tokyo

first: Hiroki

last: Goto

address: 1-16-13 Kitakasai, Edogawa-ku

country: Japan

institute: Daiichi Sankyo RD Novare

data_processing:
The sequencing reads were aligned with STAR software (2.4.2a) to the transcript reference, to both transcript references, hg19 (human reference) and mm10 (mouse reference).
The human-specific reads were difines as the following.
(human-specific reads) equals (human mapped reads with 0.04 mismatch rate) minus {(mouse mapped reads with 0.02 mismatch rate) plus (human and mouse mapped reads with 0.04 and 0.02 mismatched rate)}
Assembly: hg19
Supplementary files format and content: tab-delimited text files include expected counts, TPM and FPKM values for each Sample

source_name: xenograft

extract_protocol:
RNA was extracted from homogenized tumors with Promega Maxwell RSC simply RNA Tissue kit.
cDNA library for RNA-seq was prepared using Clontech SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian according to the manufacture’s protocol. 5 ng of total RNA was used as an input for the library preparation.

treatment_protocol: Mice baring HCT116 PTDSS2-KO tumor were orally dosed with vehicle or DS55980254 at 10 and 30 mg/kg in 0.5% methylcellulose. Tumors were collected 24 hours after the administration.

value: xenograft

value: Human cell line derived from colon cancer


title: DS55980254 30 mg/kg rep5


title: UPMM3, Cerivastatin & Trametinib, 2


title: UPMM3, Trametinib, 3


title: UPMM3, Cerivastatin & Trametinib, 1


title: UPMM3, Trametinib, 1


title: leaf primordia, WT, rep3


title: Hdac1-ChIP Seq

description: E16.5 nephron progenitor cells

value: Diagenode antibody, C15410325, lot A21-001P. The Diagenode antibody H3K4me3 and IgG were used in parallel respectively as a positive and negative control IP reaction


title: DS55980254 30 mg/kg rep6


title: DS55980254 10 mg/kg rep1


title: DS55980254 30 mg/kg rep2


title: DS55980254 10 mg/kg rep5


title: vehicle rep 6

value: vehicle


title: DS55980254 10 mg/kg rep3


title: DS55980254 30 mg/kg rep1


title: DS55980254 10 mg/kg rep2


title: DS55980254 10 mg/kg rep4


title: DS55980254 30 mg/kg rep4


title: vehicle rep 5


title: vehicle rep 4


title: vehicle rep 3


title: A375 PTDSS2-KO DS07551382 rep3

data_processing:
The sequencing reads were aligned with STAR software (2.4.2a) to the transcript reference, hg19 (human reference).
Transcripts per million (TPM), count and fragments per kilobase of exon per million reads mapped (FPKM) in each gene were estimated by RSEM software (1.2.23).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include expected counts, TPM and FPKM values for each Sample

growth_protocol: HCT116, A375, HCT116 PTDSS2-KO#3, and A375 PTDSS2-KO#54 cells were seeded at 1×10^5 cells/well onto a 12-well plate.

extract_protocol:
RNA was isolated using Qiagen RNeasy Mini Kit. 250 ng of total RNA was used as an input for the library preparation.
cDNA library for RNA-seq was prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacture’s protocol.

treatment_protocol: DMSO or DS07551382 (final concentration: 0.1 μM) was added to each well and incubated for 24 h.

value: Human cell line derived from melanoma


title: A375 PTDSS2-KO DS07551382 rep2


title: vehicle rep 2


title: vehicle rep 1


title: A375 PTDSS2-KO DMSO rep2

value: DMSO


title: DS55980254 10 mg/kg rep6


title: A375 PTDSS2-KO DMSO rep3


title: A375 PTDSS2-KO DMSO rep1


title: A375 parent DS07551382 rep3

value: wild type


title: A375 parent DMSO rep3


title: A375 parent DS07551382 rep2


title: A375 PTDSS2-KO DS07551382 rep1


title: A375 parent DS07551382 rep1


title: A375 parent DMSO rep1


title: HCT116 PTDSS2-KO DS07551382 rep3


title: A375 parent DMSO rep2


title: HCT116 PTDSS2-KO DS07551382 rep2


title: HCT116 PTDSS2-KO DMSO rep3


title: HCT116 parent DS07551382 rep3


title: HCT116 PTDSS2-KO DMSO rep1


title: HCT116 PTDSS2-KO DS07551382 rep1


title: HCT116 parent DS07551382 rep2


title: HCT116 parent DS07551382 rep1


title: HCT116 parent DMSO rep3


title: HCT116 parent DMSO rep1


title: HCT116 parent DMSO rep2


title: Tumor patient 11 saliva

city: Ulm

first: Linda

last: Hofmann

state: Deutschland

address: Frauensteige 14a, Haus 18

country: Germany

institute: University of Ulm

description:
Exosomal miRNA was analyzed using the Human v3 miRNA Assay
Nanostring SPRINT

hyb_protocol: Samples were denatured at 85°C for 5 min and then hybridized at 65°C for 12 h.

scan_protocol: Fluorescent reporter tags were scanned by an automated multi-channel epifluorescence scanner, generating the raw counts, using the SPRINT profiler and software.

data_processing: Raw counts were normalized using the positive ligation and negative controls present on the chip, using nSolver Analysis software.

source_name: Saliva-derived exosomes

extract_protocol: Exosomes were isolated from plasma and saliva by differential ultracentrifugation and RNA was isolated from exosomes using miRNeasy micro Kit (Qiagen).

tag: individual

value: Tumor patient 11

tag: disease state

value: HNSCC

tag: gender

value: male

tag: tumor site

value: Oropharynx

tag: uicc stage

value: II (low)

tag: hpv

value: positive

value: Saliva-derived exosomes


title: Tumor patient 10 saliva

value: Tumor patient 10

value: Oral cavity

value: IV (high)


title: tagcounts_noncanonical_plasmid

city: Bar Harbor

first: Kousuke

last: Mouri

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

library_source: other

data_processing:
Sequences were processed through MPRAduo pipeline (https://github.com/tewhey-lab/MPRAduo).
Supplementary files format and content: Processed data files contain raw count tables for barcode tag.
Library strategy: MPRA

molecule: other

organism: synthetic construct

source_name: plasmid vector

growth_protocol: 37C with 5% CO2 supplementation

extract_protocol:
Total RNA was purified by using Maxi RNeasy (QIAGEN) from homogenized cells. Then GFP mRNA was isolated by using biotinilated primers and magnetic beads followd by cDNA synthesis.
Libraries were initially amplified from cDNA or plasmid, and then secondarily amplified and added P5 and P7 tag sequences.

treatment_protocol: Cells were electroporated by using NEON transfection system and recovered in culture medium for 24 hours.

tag: library

value: noncanonical

tag: molecule

value: plasmid


title: Tumor patient 9 saliva

value: Tumor patient 9

value: III (high)

tag: tissue


title: Tumor patient 5 saliva

value: Tumor patient 5

value: negative


title: Tumor patient 4 saliva

value: Tumor patient 4

value: Larynx


title: HCT116 PTDSS2-KO DMSO rep2

value: Human cell line derived from colon cancer

tag: genotype

value: DMSO


title: Tumor patient 7 saliva

value: Tumor patient 7

value: HNSCC

value: female

value: Oropharynx

value: I (low)


title: Tumor patient 8 saliva

value: Tumor patient 8

value: male

value: II (low)

value: positive

value: Saliva-derived exosomes


title: Tumor patient 2 saliva

value: Tumor patient 2

value: Hypopharynx

value: IV (high)


title: tagassociations_noncanonical

value: noncanonical

value: plasmid


title: Tumor patient 3 saliva

value: Tumor patient 3

value: Larynx

value: negative


title: PPN2over_ctrl_ls_y2_r1

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

data_processing:
Mapping to the Ensemble S.cerevisiae R64-1-1 genome assembly with Ensembl R-64-1-1.107 transcript annotation was performed with STAR v2.7.6a (default parameters).
Gene-level read counts were obtained with STAR (--quantMode GeneCounts).
Assembly: Ensemble S.cerevisiae R64-1-1
Supplementary files format and content: Tab-separated plain text containing STAR-estimated read counts per gene, gene names, IDs, and descriptions.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: The cells were cultivated at 29 grad. C and 145 rpm/min to the logarithmic growth stage. The cells were cultivated for 16 hours (control medium, both strains), for 40 h (20 mM KOH, CRN), and for 25 h (20 mM KOH, CRN/pMB1_PPN2 Sc). The control medium: 2% glucose, 2% peptone , 1% yeast extract. The alkali medium: control medium with 20 mM KOH.

extract_protocol:
Total RNA was isolated using Trizol LS (Thermo Fisher Scientific) and was subsequently purified on columns Direct-zol RNA Microprep (Zymo Research).
Libraries were prepared according to the manufacturer’s protocol using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) and NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) for rRNA depletion.

treatment_protocol: The biomass samples were water-washed in triple. Samples grown in the control medium and the CRN samples grown in the alkali medium were frozen at -70 grad and homogenized with French press, and suspended in Trizol LS. The samples of CRN/pMB1_PPN2 Sc grown in the alkali medium were lyzed with Trizol LS immediately.

value: control

value: CRN/pMB1_PPN2 Sc, CRN transformed with vector pMB1/PPN2 Sc

tag: growth conditions

value: MATa ade2 his3 ura3  ppn1{delta}::CgTRP1 +pMB1_PPN2 Sc


title: wt_ctrl_ls_y1_r1

value: CRN

value: 2% glucose, 2% peptone , 1% yeast extract

value: MATa ade2 his3 ura3  ppn1{delta}::CgTRP1


title: wt_KOH_ls_y3_r2

value: KOH

value: 2% glucose, 2% peptone , 1% yeast extract, 20 mM KOH


title: wt_ctrl_ls_y1_r2


title: PPN2over_KOH_ls_y4_r1


title: PPN2over_ctrl_ls_y2_2


title: PPN2over_KOH_ls_y4_r2


title: Tumor patient 6 saliva

value: Tumor patient 6

value: HNSCC

value: male

value: Oropharynx

value: Saliva-derived exosomes


title: Tumor patient 10 plasma

source_name: Plasma-derived exosomes

value: Tumor patient 10

value: Oral cavity

value: IV (high)

value: Plasma-derived exosomes


title: Tumor patient 11 plasma

value: Tumor patient 11

value: II (low)

value: positive


title: Healthy donor 3 saliva

value: Healthy donor 3

value: healthy control

value: not applicable


title: Tumor patient 1 saliva

value: Tumor patient 1

value: negative


title: Tumor patient 9 plasma

value: Tumor patient 9

value: III (high)


title: Healthy donor 2 saliva

value: Healthy donor 2

value: male


title: wt_KOH_ls_y3_r1

value: KOH

value: CRN

value: 2% glucose, 2% peptone , 1% yeast extract, 20 mM KOH

value: MATa ade2 his3 ura3  ppn1{delta}::CgTRP1


title: Healthy donor 1 saliva

value: Healthy donor 1

value: Saliva-derived exosomes


title: Healthy donor 5 saliva

value: Healthy donor 5


title: Tumor patient 8 plasma

value: Tumor patient 8

value: HNSCC

value: Oropharynx

value: II (low)

value: positive

value: Plasma-derived exosomes


title: Tumor patient 7 plasma

value: Tumor patient 7

value: female

value: I (low)


title: Healthy donor 4 saliva

value: Healthy donor 4

value: healthy control

value: not applicable


title: Tumor patient 6 plasma

value: Tumor patient 6

value: male

value: IV (high)

value: negative


title: trachea, wildtype control, 3rd instar larvae, biol rep1

city: Weifang

first: Xiao

last: Niu

state: Shandong

address: Baotong str. 7166

institute: Weifang Medicine University

data_processing:
Resulting sequencing reads were trimmed for low-quality bases and adapters using the fastq Illumina filter and cutadapt (version 1.8.1)
Trimmed sequence reads were mapped to Drosophila melanogaster genome assembly Release 6 plus ISO1 MT (dm6) using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.5 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: dm6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Drosophila melanogaster

source_name: trachea

growth_protocol: Control animals were raised at 18 degrees. The Hop.CA expressed animals were raised in 18 degrees and then transferred to 29 degrees at the L2 larval stage for 18 hours before they were sampled.

extract_protocol:
RNA was extracted by using the PureLink RNA Mini Kit (Thermo Fisher, Waltham, MA, USA). 2 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were constructed using the TruSeq stranded mRNA kit (Illumina, San Diego, USA)

treatment_protocol: 18 degrees

value: trachea

value: btl-Gal4, UAS-GFP; UAS-Hop.CA, tub-Gal80ts

value: control


title: trachea, Hop.CA ectopic expressed trachea, 3rd instar larvae, biol rep1

treatment_protocol: animals were raised at 18 degrees and then animals were transferred to 29 degrees for 18 hours before they were sampled.

value: 29 degrees

value: Hop.CA ectopic expression


title: trachea, Hop.CA ectopic expressed trachea, 3rd instar larvae, biol rep3


title: trachea, wildtype control, 3rd instar larvae, biol rep3


title: Healthy donor 4 plasma


title: Tumor patient 2 plasma

value: Tumor patient 2

value: HNSCC

value: Hypopharynx


title: trachea, wildtype control, 3rd instar larvae, biol rep4


title: trachea, Hop.CA ectopic expressed trachea, 3rd instar larvae, biol rep2


title: Tumor patient 1 plasma

value: Tumor patient 1

value: Oropharynx

value: Plasma-derived exosomes


title: Tumor patient 4 plasma

value: Tumor patient 4

value: Larynx

value: II (low)


title: Healthy donor 2 plasma

value: Healthy donor 2

value: healthy control

value: male

value: not applicable


title: Tumor patient 5 plasma

value: Tumor patient 5

value: IV (high)

value: negative


title: trachea, wildtype control, 3rd instar larvae, biol rep2

value: trachea

value: btl-Gal4, UAS-GFP; UAS-Hop.CA, tub-Gal80ts

value: control


title: Healthy donor 3 plasma

value: Healthy donor 3


title: Tumor patient 3 plasma

value: Tumor patient 3

value: HNSCC

value: I (low)


title: Healthy donor 5 plasma

value: Healthy donor 5

value: Plasma-derived exosomes


title: Healthy donor 1 plasma

value: Healthy donor 1


title: ChIP_IGG_ILC3_2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
library strategy: CUT&TAG ChIPseq
Reads were aligned to mouse reference genome mm10 using Bowtie2.
Reads were then filtered using SAMtools
Peaks were called using SEACR (version1.1) (Meers et al., 2019) with options: 0.01 non stringent.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

treatment_protocol: ILC3s were sorted from the small intestine of Rag1-/- mice and cultured for 2 weeks to expand the cells. 100,000 ILC2s were processed and library construction according to CUT&Tag ChIP-Seq approach mentioned (version 2) (Kaya-Okur et al., 2019) (step wise protocol can be found at https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6).

tag: strain background

value: small intestine

tag: cell type

value: Group 3 innate lymphoid cells (ILC3s)

value: Rabbit normal serum IgG1


title: ChIP_IGG_ILC3_1

extract_protocol: (Kaya-Okur et al., 2019) (step wise protocol can be found at https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6).

tag: chip antibody


title: WT_ILC3_ATAC-seq_Rep2

data_processing:
Reads were aligned to mouse reference genome mm10 using Bowtie2.
Reads were then filtered using SAMtools (-F1796).
Peaks were called using MACS2 (--no model --shift -100 --ext size 200 -q 0.01) (version 2.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

extract_protocol: ATAC-seq was performed according to a published protocol (Buenrostro et al., 2015) with minor modification.

treatment_protocol: Rag1-/- or Rag1-/-Batf-/- mice were used for ATAC-seq experiments. 50,000-80,000 ILC3 cells were sorted from the small intestine.

tag: genotype/variation

tag: age


title: ChIP_BATF_ILC3_1

value: anti-BATF


title: ChIP_BATF_ILC3_3


title: ChIP_BATF_ILC3_2


title: BATF_KO_ILC3_ATAC-seq_Rep2


title: WT_ILC3_ATAC-seq_Rep1


title: BATF_KO_ILC3_ATAC-seq_Rep1


title: scRNAseq_cKO_SI_ILC

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: ILC

extract_protocol: 10x Genomics

treatment_protocol: SI ILCs were FACS-sorted from WT and cKO were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles)

tag: strain

value: Cko

value: female


title: PBS

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: RNA was isolated from the brains of 6 mice

library_source: transcriptomic single cell

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: Brain

extract_protocol:
10x Genomics Chromium single-cell preparation
NGS Illumina Next Seq

value: Brain

tag: Sex

value: male

value: 10 weeks

tag: treatment

value: PBS


title: 5xFAD.CD45

description: RNA was isolated from the brains of 8 mice

source_name: Cerebral cortex

value: Cerebral cortex

value: 5-7 months


title: WT.CD13


title: CLO

value: clodronate


title: 5xFAD.CD13


title: WT.CD45


title: Ewing_3_CITEseq

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

description: CITEseq feature barcode matrix

data_processing:
Library strategy: CITE-Seq
Demultiplexing raw reads with bcl2fastq2 (Illumina, v2.20.0)
Cellranger count (10X Genomics, v3.1.0) to generate feature barcode matrices
CITEseqCount (v1.4.3) to identify TotalSeq-C associated UMI counts for sample demultiplexing
Creation of unified feature barcode expression matrix with Seurat (v3.1.2) in R (v.3.6.0)
Assembly: GRCh38
Supplementary files format and content: Feature barcode expression matrices create with bcl2fastq and CellRanger Count; Feature barcode matrices created with CITEseqCount

source_name: peripheral blood mononuclear cells and tumor infiltrating immune cells

extract_protocol:
Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Tumor specimens were manually dissected into 1 mm2 fragments and were incubated with 50 mg/mL Liberase DL for 15 minutes at 37 degrees C. If bone fragments were present in the sample, they were incubated in Liberase with the tissue fragments. Following incubation, single-cell suspensions were passed over a 40 micro filter. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. PBMC and tumor samples were then stained with an anti-CD45::PE antibody and APC-Cy7 viability dye and live CD45+ cells were sorted on a MoFlo Astrios high-speed sorter.
Sorted live CD45+ cells resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with either the 3prime V2 or 5prime V1 chemsitry kits. In some instances samples were labeled with TotalSeq-A (3prime) or TotalSeq-C (5prime) CITEseq antibodies for sample multiplex. In these instances, two samples were pooled prior to loading cells for droplet generation. Gene expression and CITEseq libraries were generated following the manufacturer's protocols.

tag: disease state

value: Ewing sarcoma

tag: primary or recurrent

value: recurrent

tag: metastatic disease

value: yes

tag: tissue site

tag: chemistry

value: 10X Genomics 3' v2


title: Ewing_4_CITEseq

description: CITEseq feature barcode matrix

value: peripheral blood mononuclear cells and tumor infiltrating immune cells

value: primary

value: no

value: bone


title: Healthy_donor_CITEseq

description: CITEseq feature barcode matrix

source_name: peripheral blood mononuclear cells

value: peripheral blood mononuclear cells

value: Healthy donor

value: 10X Genomics 5' v1


title: tagcounts_noncanonical_K562

tag: cell line

tag: library

value: noncanonical

tag: molecule

value: GFP mRNA


title: Osteosarcoma_4_PBMC

description: Gene expression feature barcode matrix

data_processing:
Demultiplexing raw reads with bcl2fastq2 (Illumina, v2.20.0)
Cellranger count (10X Genomics, v3.1.0) to generate feature barcode matrices
CITEseqCount (v1.4.3) to identify TotalSeq-C associated UMI counts for sample demultiplexing
Creation of unified feature barcode expression matrix with Seurat (v3.1.2) in R (v.3.6.0)
Assembly: GRCh38
Supplementary files format and content: Feature barcode expression matrices create with bcl2fastq and CellRanger Count; Feature barcode matrices created with CITEseqCount

value: Osteosarcoma


title: Ewing_4_PBMC_TIL

description: Gene expression feature barcode matrix


title: Ewing_1_TIL

description: Gene expression feature barcode matrix

source_name: tumor infiltrating immune cells

value: tumor infiltrating immune cells

value: lung


title: Osteosarcoma_1_TIL

description: Gene expression feature barcode matrix


title: Ewing_2_CITEseq

description: CITEseq feature barcode matrix


title: Ewing_3_PBMC_TIL

description: Gene expression feature barcode matrix


title: Osteosarcoma_2_PBMC

description: Gene expression feature barcode matrix


title: Osteosarcoma_3_TIL

description: Gene expression feature barcode matrix


title: Osteosarcoma_3_PBMC

description: Gene expression feature barcode matrix


title: Ewing_1_PBMC

description: Gene expression feature barcode matrix


title: Healthy_donor_PBMC

description: Gene expression feature barcode matrix


title: Osteosarcoma_4_TIL

description: Gene expression feature barcode matrix


title: Osteosarcoma_1_PBMC

description: Gene expression feature barcode matrix


title: Osteosarcoma_2_TIL

description: Gene expression feature barcode matrix


title: Ewing_2_PBMC_TIL

description: Gene expression feature barcode matrix


title: scRNAseq_WT_SI_ILC

value: WT

tag: gender

value: female

tag: tissue

value: small intestine

value: Group 3 innate lymphoid cells (ILC3s)


title: Third MULTI-seq Experiment, gastruloid day 4.5 & 5, sample B

status: Public on Aug 30 2022

city: Hinxton

first: Leah

middle: Ursula

last: Rosen

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
exp6_d4.5_d5_sampleB
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz

data_processing:
For cellranger outputs: Raw FastQ files were processed with Cell Ranger 6.0.0 using default mapping arguments, and the mm10-2020-A genome and annotation (provided by 10X Genomics).
For the final Seurat, sample metadata, and feature metadata, CellRanger called cells were subjected to stringent quality control metrics on a sample-by-sample basis. They were selected for minimum number of UMI, minimum number of genes detected, as well as minimum and maximum mitochondrial percentage. Furthermore, cells that passed this initial QC were processed using the hybrid method from the scds doublet calling R package (Bais and Kostka, 2020). All cells that the method called as doublets were removed, along with any cell which had more than 10 of its 30 nearest neighbours called as doublets by the hybrid method. After stringent QC, we retained 77,683 cells. 72,176 of these cells were sequenced using MULTI-seq. The remaining 5,507 cells were sequenced using 3’ RNA sequencing. Cells were assigned MULTI-seq barcodes from the R1 and R3 fastq files using the published MULTI-seq demultiplexing method for barcode alignment and classification, with the slight modification that only cells whose barcodes passed RNA QC were included in the demultiplexing. This increased the sensitivity of the method. In all but the first MULTI-seq experiment the barcode yield was low, probably due to a loss of MULTI-seq anchor/co-anchor efficiency over time. However, it was still possible to classify these cells using the k-means based negative cell reclassification method as implemented in MULTI-seq for all but exp3C_d4_d4.5. A sample-specific reclassification stability was chosen based on identifying local maxima in diagnostic plots. Subsequently, the samples were concatenated, 1274 cell-cycle associated genes were removed based on their associated GO terms, and the samples normalised using multiBatchNorm from the batchelor R package (Haghverdi et al., 2018). Highly variable genes were selected using the modelGeneVar function from batchelor, with a minimum mean of 0.001 and a maximum p-value of 0.05. Subsequently, multiBatchPCA was used to calculate the first 50 PCs. The PCA space was then batch effect corrected using MNN, first correcting samples within a time point (ordered from most cells to fewest), and then correcting across time points (ordered from day 5 to day 3). The cells were then manually annotated.
Assembly: mm10
Supplementary files format and content: The CellRanger output files (barcodes.tsv, features.tsv, matrix.mtx)
Supplementary files format and content: The seurat_final.rds is a processed Seurat file of the cells that passed QC, with metadata, raw counts, normalised counts (using batchelor's multiBatchNorm), PCA and UMAP dimensionality reductions (after MNN integration), neighbourhood graphs, and clusterings (the latter 2 generated using the Seurat default).
Supplementary files format and content: The sample_metadata_final.txt.gz is a comma separted table, with all the metadata of the cells that passed QC
Supplementary files format and content: The feature_metadata_final.txt.gz is a comma separated table, with all the genes used, which maps ensembl ID (used in the Seurat file) to gene symbol. It also lists whether the gene was classified as a cell cycle gene (removed in many analyses, and whether it was found to be an HVG (used as the subset of genes in many analyses)

source_name: gastruloids

growth_protocol: Mouse E14Tg2A (E14) Embryonic Stem Cells (ESCs) obtained from the Cambridge Stem Cell Institute (CSCI) were cultured in ESLIF medium (DMEM (Life Technologies, 10566-016), 15% fetal bovine serum (Sigma-Aldrich, Lot #BCCC3714), 1x MEM Non-Essential Amino Acids (Life Technologies, 11140050), 2 mM GlutaMAX (Life Technologies, 35050061), 10 U/ml Penicillin-Streptomycin (Life Technologies, 15140122), 0.1 mM 2-Mercaptoethanol (Life Technologies, 31350010), and 10 ng/ml  mLIF (Department of Biochemistry, University of Cambridge)) on gelatin-coated (0.1% in H2O) tissue culture treated 10 cm plates in a humidified incubator at 37 ℃, 5% CO2. Cells were passaged every other day.     Gastruloids were grown as described previously (Girgin et al. 2018 Protocol Exchange). Briefly, ESLIF-grown mouse ESCs were dissociated to a single cell suspension using Trypsin-EDTA (Thermo Fisher Scientific, 25300096). Trypsin was inactivated in 5 ml ESLIF medium and cells were spun down. The cell pellet was washed and spun down in 5 ml pre-warmed PBS (14190144) twice to remove remaining traces of ESLIF medium. After the second wash, cells were resuspended in 5 ml N2B27 medium (50/50 mix of DMEM-F12 (Thermo Fisher Scientific, 11320033) and Neurobasal (Thermo Fisher Scientific, 21103049), supplemented with 0.5x N-2 Supplement (Cell Therapy Systems, A1370701), 0.5x B-27 (Thermo Fisher Scientific, 12587010), 2 mM GlutaMAX, 10 U/ml Penicillin-Streptomycin and 0.1 mM 2-Mercaptoethanol) and counted using a haemocytometer. Cells were diluted in N2B27 medium to a density of 7500 cells/ml. This cell suspension was transferred to a reservoir and 40 μl of the suspension was added to each well of a U-bottom suspension culture 96-well plate (Greiner Bio-One, 650185) to reach a cell density of 300 cells/well. These cells were left to aggregate for 48 hours, at which point 150 μl of N2B27 medium with 3 μM of the GSK3 inhibitor CHIR99021 (Chiron, Department of Biochemistry, University of Cambridge) was added. Subsequently, 150 μl of the medium was exchanged for N2B27 medium (without CHIR99021) every 24h and gastruloids were grown up to 120h (5 days). Gastruloids were collected for sequencing at d3, d3.5, d4, d4.5 and d5. Gastruloids for half-day time points were set up in the evening to allow collection of full- and half-day time points at the same time.

extract_protocol:
Cells were barcoded by adapting the MULTI-seq protocol (McGinnis et al., 2019) for low cell numbers, and then processed using 10x Genomics Chromium single cell 3’ RNA sequencing v3.1 according to manufacturer’s instructions. For MULTI-seq, the MULTI-seq primer was added during cDNA amplification and the supernatant was collected during 0.6x SPRI clean-up to obtain the barcode fraction as described by McGinnis et al. MULTI-seq barcode libraries were prepared according to McGinnis et al.
For scRNA-seq: Gastruloids were grown as described above. At d3 or d4, gastruloids were transferred to an eppendorf tube, washed with PBS and dissociated using Accutase (StemPro, A1110501) to obtain a single cell suspension. To remove Accutase, cells were washed twice in 5 ml PBS + 0.04% BSA (Gibco, 15260037) and filtered through a 50 um strainer (Sysmex, 1050553). Cell number and viability was assessed using the Countess II Automated Cell Counter and samples were diluted to submit for 10x 3’ scRNA sequencing at a targeted cell capture rate of 10,000 cells per lane.  For MULTI-seq: Gastruloids were grown as described above. At the collection time point, up to 32 representative gastruloids were selected and individual gastruloids were transferred to wells of a U-bottom suspension culture 96-well plate with 80 μl Accutase (StemPro, A1110501) per well. Gastruloids from multiple time points were combined on a single plate to minimise batch effect. Gastruloids were incubated at 37 ℃ for three minutes and were dissociated through repeated pipetting using a multichannel pipette. Low-retention pipette tips were used for this and all subsequent steps to minimise cell loss. Incubation and pipetting were repeated until a near single-cell suspension was achieved in each well. To label the cells of individual gastruloids with MULTI-seq barcodes, the MULTI-seq protocol (McGinnis et al., 2019) was adapted for low cell numbers as follows. First, 10 μl of unique 10x Anchor:Barcode solution was added to each well. Samples were mixed by pipetting and incubated on ice for 5 minutes. Henceforward, samples were kept on ice. Next, 10 μl 10x Co-Anchor solution was added, mixed in by pipetting and incubated on ice for 5 minutes. Anchor/Co-Anchor stock concentrations were calculated based on estimated cell numbers per gastruloid (7500 cells at d3, 13000 cells at d4, 25000 cells at d5). Used barcodes can be found in Supplementary table 1 (see supplementary note 1 for how these were selected). Barcode labelling was quenched by adding 100 μl ice cold PBS with 1% BSA (Gibco, 15260037) (PBS/BSA) per well. Next, cells from individual wells were combined into a 15 ml Falcon tube with 5 ml ice cold PBS/BSA to further quench barcode labelling. Cells were spun down at 300g in a precooled centrifuge at 4 ℃. The cell pellet was washed with 5 ml ice cold PBS/BSA and spun down again. Next, the cell pellet was resuspended in 1 ml ice cold PBS/BSA and passed through a Flowmi cell strainer (Bel-Art, H13680-0040) into a clean precooled 15 ml Falcon tube. The volume was topped up to 5 ml with ice cold PBS/BSA for a final wash and the cells were spun down again. All but approximately 50 μl of PBS/BSA was aspirated and the cells were resuspended in the remaining volume. Cell number and viability was assessed using the Countess II Automated Cell Counter and samples were diluted to submit for 10x 3’ scRNA sequencing at a targeted cell capture rate of 10,000 cells per lane.
After dissociation and labelling with MULTI-seq barcodes, cells were processed using 10x Genomics Chromium single cell 3’ RNA sequencing v3.1 according to manufacturer’s instructions. For MULTI-seq, the MULTI-seq primer was added during cDNA amplification and the supernatant was collected during 0.6x SPRI clean-up to obtain the barcode fraction as described by McGinnis et al. MULTI-seq barcode libraries were prepared according to McGinnis et al. Libraries were amplified between 11 and 16 times. The number of amplification cycles required was empirically determined for each sample. scRNA and barcode libraries were sequenced on either HiSeq or NovaSeq 6000 instruments according to 10x Genomics instructions (read 1, 28 cycles; index i7, 8 cycles; and read 2, 91 cycles).

treatment_protocol: Gastruloids were grown as described previously (Girgin et al. 2018 Protocol Exchange) for 4.5 or 5 days post-aggregation

tag: cell type

value: Differentiated ESCs

tag: genotype

value: gastruloids

tag: time

value: 4.5 & 5 days post-aggregation


title: Third MULTI-seq Experiment, gastruloid day 4.5 & 5, sample C

description:
exp6_d4.5_d5_sampleC
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz

value: E14Tg2A (E14) Embryonic Stem Cells (ESCs)


title: Third MULTI-seq Experiment, gastruloid day 3.5 & 4, sample D

description:
exp5_d3.5_d4_sampleD
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz

treatment_protocol: Gastruloids were grown as described previously (Girgin et al. 2018 Protocol Exchange) for 3.5 or 4 days post-aggregation

value: 3.5 & 4 days post-aggregation


title: Third MULTI-seq Experiment, gastruloid day 4.5 & 5, sample A

description:
exp6_d4.5_d5_sampleA
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz


title: Third MULTI-seq Experiment, gastruloid day 3.5 & 4, sample A

description:
exp5_d3.5_d4_sampleA
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz


title: Third MULTI-seq Experiment, gastruloid day 3.5 & 4, sample B

description:
exp5_d3.5_d4_sampleB
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz


title: Third MULTI-seq Experiment, gastruloid day 3, sample A

description:
exp4_d3, sampleA
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz

treatment_protocol: Gastruloids were grown as described previously (Girgin et al. 2018 Protocol Exchange) for 3 days post-aggregation

value: 3 days post-aggregation


title: MDA-MB231, 24h_#3

city: Bethesda

last: Hernandez

state: MD

address: Building 37

institute: NCI/NIH

data_processing:
Basecalling was performed by RTA (version 3.4.4).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.20) allowing 1 mismatch.
Reads were filtered with a base call quality >91% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using CutAdapt (v1.18).
STAR aligner is run in twopass basic mode to align trimmed reads to hg19 genome
Gene-level expression quantificiation  was performed using RSEM (version 1.3.3)
Assembly: hg19
Supplementary files format and content: CPM filtered TMM normalized counts are available as an excel spreadsheet

source_name: breast cancer cells

growth_protocol: Breast cancer cell lines were grown in RPMI media supplemented with 10% heat-inactivated FBS, 1% streptomycin/penicillin.

extract_protocol:
Cells were trypsinized and centrifuged at 310 x g for 5 minutes, then transferred to 1.5 ml tube, washed with PBS twice, snap frozen with ethanol-dry ice bath.
One microgram of total RNA per each time point was used as the input to an mRNA capture with oligo-dT coated magnetic beads. The mRNA was fragmented, and then a random-primed cDNA synthesis was performed. The resulting double-strand cDNA was used as the input to a standard Illumina library prep (TruSeq Stranded mRNA LT library prep kit, Illumina) with end-repair, adapter ligation and PCR amplification being performed to generate the library.

treatment_protocol: MB231 cells were seeded on four 6 well plates (1.25 x 106 cells/well). Cells in each plate were treated with ONC201 (5 μM) for different times (0, 6 h, 24 h, 48 h).

tag: cells

value: Triple Negative Breast Cancer, Basal B

tag: passages


title: MDA-MB231, 24h_#2


title: GPHR F/F

city: Bunkyo-ku

first: Yu-shin

last: Sou

state: Tokyo

address: 2-1-1 Hongo

department: Department of Cell Biology and Neuroscience

institute: Juntendo University Graduate School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: brain

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

extract_protocol: RNA extraction using TRIzol

value: brain

value: GPHR F/F

tag: strain

tag: age

value: postnatal day 10


title: MDA-MB231, 24h_#1


title: Third MULTI-seq Experiment, gastruloid day 3.5 & 4, sample C

description:
exp5_d3.5_d4_sampleC
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz


title: Third MULTI-seq Experiment, gastruloid day 3, sample B

description:
exp4_d3, sampleB
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz


title: GPHR F/F;Nes

value: GPHR F/F;Nes


title: MDA-MB231, 12h_#3


title: ATACseq_WT

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description: wildtype C57BL/6 bone marrow FACS sorted at 1:1 ratio of B220+CD43+ and B220+CD43- cells

library_source: genomic single cell

data_processing:
10X Genomics Cell Ranger (scRNAseq) software was used to demultiplex samples and generate fastq files.
Each gel bead in emulsion (GEM) was identified and all gene specific or feature barcode (e.g. HTO and ADT) reads were mapped via cellranger count (ver. 3.1.0) using the mouse mm10 reference genome (refdata-cellranger-mm10-3.0.0).
Gene level quantification was completed using cellranger count software (ver. 3.1.0).
Raw counts data was imported into R for downstream processing, including normalization, principal components analysis, differential gene expression testing, single cell clustering, etc.
Assembly: mm10 (refdata-cellranger-mm10-3.0.0, provided by 10X Genomics)
Supplementary files format and content: tab-delimited text files include raw or normalized read count values for each sample

source_name: bone marrow B cells

extract_protocol:
Bilateral femurs and tibias were harvested from two wildtype C57BL/6 mice. Bones were flushed with 1X PBS with 2% fetal bovine serum (FBS), 0.1% sodium azide and 0.5 mM ethylenediaminetetraacetic acids, pH 7.4. The cells were filtered through a 70 µm mesh, centrifuged at 1200 rpm for 5 minutes and then incubated for 5 minutes with 5 mL of ACK lysis buffer for red blood cell lysis. Cells were then washed and centrifuged at 1200 rpm and subsequently resuspended. Cells were stained with two distinct oligo-labeled antibodies that recognize CD45 and MHC class I, which allow identification of cells derived from each individual mouse (referred to as hashtag antibodies).  We further stained cells with a panel of CITE-Seq antibodies (B220, CD19, CD93, CD25, IgM, and CD43) as well as fluorescently labeled B220 and CD43. Cells were sorted at a 1:1 ratio of B220+CD43+ and B220+CD43- cells to enrich for early progenitor B cell subsets.
For 10X Genomics scRNA-seq, we generated three libraries that measure: (1) mRNA transcript expression (RNA), (2) mouse-specific hashtag oligos (HTO), and (3) cell surface marker levels using antibody derived tags (ADT). Cells were harvested and stained as described above. In order to have balanced populations of various B cell development stages, we enriched for earlier progenitor B cells (B220+CD43+) by sorting at a 1:1 ratio of Dump-B220+CD43+ cells and Dump-B220+CD43- cells. A total of 20,000 cells per mouse were sorted into a single microtube containing 1X PBS with 50% FBS and were washed and resuspended in 1X PBS with 10% FBS prior to cell capture. The sample was split into three libraries (RNA, HTO, and ADT). Reverse transcription PCR and library preparation were carried out under the Chromium Single Cell 3’ v3 protocol (10X Genomics) per manufacturer’s recommendations. After library prep, quality control was performed using a bioanalyzer (Agilent 2100 Bioanalyzer; Agilent Technologies) and preliminary sequencing of the RNA library on a MiSeq (Illumina) to determine the approximate number of cells and general quality. After passing quality control, the library was sequenced on the NovaSeq 6000 with 2x150 bp paired-end reads (Illumina). For single-cell ATAC-sequencing, we harvested bone marrow from wildtype (n = 1), Ncor1 KO (n = 1) and Ncor1/2 DKO (n = 1). Cell sorting scheme was identical as the single-cell RNA-seq cell sorting scheme, except we sorted 50,000 B220+CD43+ cells and 50,000 B220+CD43- cells, for a total of 100,000 cells for each genotype. Sorted cells were centrifuged at 300 x g for 5 minutes at 4Co. Cells were then resuspended in 100 µl of chilled lysis buffer, which consists of 10mM Tris-HCl pH 7.4 (T2914, Sigma-Aldrich), 10mM NaCl (S5150, Sigma), 3mM MgCl2 (M1028, Sigma-Aldrich), 0.1% Tween 20 (BP337, Fisher Scientific), 0.1% nonidet P40 substitute (74385, Sigma-Aldrich), 0.01% digitonin (BN2006, ThermoFisher), 1% BSA (130-091-376, Miltenyi Biotec), and nuclease-free water, and incubated on ice for 5 minutes. After incubation, 1 mL of chilled wash buffer, including 10mM Tris-HCl pH 7.4 (T2914, Sigma-Aldrich), 10mM NaCl (S5150, Sigma), 3mM MgCl2 (M1028, Sigma-Aldrich), 0.1% Tween 20 (BP337, Fisher Scientific), 1% BSA (130-091-376, Miltenyi Biotec), and nuclease-free water, was added to lysed cells, and centrifuged at 500 x g for 5 minutes at 4Co. Cells were resuspended in diluted nuclei buffer and nuclei permeabilization was determined using a Countess II (ThermoFisher). Cells were then captured on the 10X Chromium and subsequent library prep was generated using the Chromium Next GEM Single Cell ATAC library kit v1.1 (PN-1000164, 10X Genomics), following the protocol from manufacture recommendations. Post-library quality control (QC) was performed for both sizing and quantification using the Agilent Bioanalyzer (Agilent 2100 Bioanalyzer; Agilent Technologies) and KAPA library quantification kit for Illumina platforms (KR0405, Roche). All libraries were then sequenced on a NovaSeq 6000 with 2x150 bp paired-end reads (Illumina)

value: WT animal 1

value: bone marrow

value: FACS sorted 1:1 ratio of B220+CD43+ and B220+CD43-


title: MDA-MB231, 12h_#2


title: MDA-MB231, 12h_#1


title: MDA-MB231, 6h_#3


title: MDA-MB231, 6h_#2


title: MDA-MB231, 6h_#1


title: ATACseq_KO

value: Ncor1-KO animal 1


title: ADT_WT_rep1&2_Ncor1KO_rep_1&2, Ncor1&2DKO_rep1&2

value: mixed samples:WT (replicate animals 1 & 2), Ncor1-KO (replicate animals 1 & 2), Ncor1_Ncor2-DKO (replicate animals 1 & 2)


title: GEX_WT_rep1&2_Ncor1KO_rep_1&2, Ncor1&2DKO_rep1&2


title: 267-spine

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Schroeder Arthritis Institute

description: miRNA

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files is performed, followed by quality assessment for each sample using the bcl2fastq conversion tool (v2.19.1.403).
UMI tags are extracted from raw files using UMI-tools software.
The first round of alignment using Bowtie1 is performed against human miRBase (v22.1), and then unaligned reads from this step are aligned to the human reference genome to obtain reads falling in miRBase chromosomal coordinates only.
Reads are collapsed according to associated UMI to remove PCR amplification bias.
UMI-based counts for each miRNA in a sample are generated from both alignments and summed to generate a final table of miRNA expression levels for each sample.
Inference is performed on the raw counts using a negative binomial regression estimated by quasi-likelihood with trended dispersion and normalized by total aligned sequences.
Genome_build: GRCh38
Supplementary_files_format_and_content: 1 combined tab-delimited text file includes raw count values for each Sample.

source_name: plasma

extract_protocol:
RNA is extracted from 200 µL of human plasma using the QIAcube following Qiagen's instructions for sample setup of the miRNeasy Serum/Plasma Advanced Kit (Cat #217204).
miRNA libraries are prepared using QIAseq miRNA Library Kit optimized for biofluid samples (QIAseq miRNA, Cat # 331505). Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).
Libraries are multiplexed and sequenced on Illumina NextSeq550 to generate 75bp SE UMI-tagged reads.

value: plasma

tag: diagnosis

value: LSS+DS

tag: Sex

value: female

tag: % nprs20delta


title: ATACseq_DKO

value: Ncor1_Ncor2-DKO animal 1


title: 399-spine

description: miRNA

value: male


title: 311-spine

description: miRNA

value: LSS


title: 297-spine

description: miRNA


title: 324-spine

description: miRNA


title: 277-spine

description: miRNA


title: MDA-MB231, 0h_#3


title: MDA-MB231, 0h_#1


title: MDA-MB231, 0h_#2


title: 418-spine

description: miRNA


title: 404-spine

description: miRNA


title: 412-spine

description: miRNA


title: 405-spine

description: miRNA


title: 321-spine

description: miRNA


title: 328-spine

description: miRNA


title: 350-spine

description: miRNA


title: 286-spine

description: miRNA


title: 334-spine

description: miRNA


title: 300-spine

description: miRNA


title: HTO_WT_rep1&2_Ncor1KO_rep_1&2, Ncor1&2DKO_rep1&2


title: 385-spine

description: miRNA


title: 409-spine

description: miRNA


title: 308-spine

description: miRNA


title: 370-spine

description: miRNA


title: 355-spine

description: miRNA


title: 353-spine

description: miRNA


title: 343-spine

description: miRNA


title: 342-spine

description: miRNA


title: 396-spine

description: miRNA


title: 357-spine

description: miRNA


title: 361-spine

description: miRNA


title: 362-spine

description: miRNA


title: 397-spine

description: miRNA


title: 86-SPINE

description: miRNA


title: 336-spine

description: miRNA


title: 137-SPINE

description: miRNA


title: 169-SPINE

description: miRNA


title: 97-SPINE

description: miRNA


title: 195-SPINE

description: miRNA


title: 264-SPINE

description: miRNA


title: 108-SPINE

description: miRNA


title: 171-SPINE

description: miRNA


title: 172-SPINE

description: miRNA


title: 269-SPINE

description: miRNA


title: 167-SPINE

description: miRNA


title: 234-SPINE

description: miRNA


title: 283-SPINE

description: miRNA


title: 217-SPINE

description: miRNA


title: 215-SPINE

description: miRNA


title: 139-SPINE

description: miRNA


title: 289-SPINE

description: miRNA


title: 282-SPINE

description: miRNA


title: 259-SPINE

description: miRNA


title: 208-SPINE

description: miRNA


title: 237-SPINE

description: miRNA


title: 222-SPINE

description: miRNA


title: 304-SPINE

description: miRNA


title: 310-SPINE

description: miRNA


title: 263-SPINE

description: miRNA


title: 266-SPINE

description: miRNA


title: 738MIR

description: processed data file: GTavallaee_TotalRNAseq_genecounts.tsv

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files is performed, followed by quality assessment for each sample using the bcl2fastq conversion tool (v2.19.1.403).
Cutadapt (v1.18) is used to maintain minimum read length of 25 bp post trimming of adapters as well as trimming of N’s.
HISAT2 software (v2.1.0 with --rna-strandness RF –dta parameters) is used to perform splice-aware alignment of reads using a Hierarchical Graph FM index method against human reference genome (vGRCh38).
StringTie software (v1.3.5 with parameters --rffor stranded library fr- firststrand) is used to assemble the aligned reads into transcripts.
StringTie (parameters -e -B -G referencetranscripts.gtf) is used to obtain the abundance of the transcripts.
‘prepDE.py’ by StringTie software is used to extract the read count information.
Genome_build: GRCh38
Supplementary_files_format_and_content: GTavallaee_TotalRNAseq_genecounts.tsv: Tab-delimited text file includes raw count values for each Sample.

source_name: Knee OA synovium

growth_protocol: FLS are dissociated from OA synovium of 3 separate patients undergoing total knee replacement surgery (Kellgren-Lawrence Grade III/IV) by sequential enzymatic digestion. Sub-confluent primary synoviocytes are passaged three times (P3) and grown in 10-cm petri dishes to confluency in DMEM/1% PenStrep/10% FBS.

extract_protocol:
Total RNA is extracted from control or mimic-treated OA FLS (n=3 per group) by standard Trizol method and quantified using the Qubit RNA BR assay (Denovix). Quality of RNA is assessed using the Agilent RNA Nano chips on a Bioanalyzer instrument. For all the samples, RNA integrity number (RIN) was >9.7.
Total RNA libraries are prepared from 200 ηg extracted RNA using the TruSeq Stranded Total RNA Library Preparation kit with RiboZero (Illumina Cat #20020596) according to manufacturer’s protocol. Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).
Libraries are prepared for sequencing (volumetrically pooled, diluted and denatured): 75 paired end read-cycles on an Illumina NextSeq 550 sequencer.

treatment_protocol: Confluent OA FLS cultures are serum-starved for 3 h in DMEM/1% PS/0.5% FBS. Cells are then incubated with 3 µg/mL Lipofectamine RNAi MAX transfection reagent with 5 nM hsa-miR-27b-3p mimic (Qiagen #339173 YM00470553) or Control Mimic (Cel-miR-39-3p; Qiagen, #YM00479902) for 48h.

value: primary FLS

tag: treatment

value: 5 nM hsa-miR-27b-3p mimic for 48 h


title: 182-SPINE

description: miRNA


title: 211-SPINE

description: miRNA


title: 738CR

value: 5 nM Cel-miR-39-3p (control) mimic for 48 h


title: 704MIR


title: 729MIR


title: 704CR


title: 236-SPINE

description: miRNA


title: 729CR


title: First MULTI-seq Experiment, gastruloid day 5, sample 2

description:
exp1_d5, sample2
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz

treatment_protocol: Gastruloids were grown as described previously (Girgin et al. 2018 Protocol Exchange) for 5 days post-aggregation

value: E14Tg2A (E14) Embryonic Stem Cells (ESCs)

value: Differentiated ESCs

value: WT

value: gastruloids

value: 5 days post-aggregation


title: Second MULTI-seq Experiment, gastruloid day 4 & 4.5, pool C, sample 1

description:
exp3C_d4_d4.5, sample1
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz

treatment_protocol: Gastruloids were grown as described previously (Girgin et al. 2018 Protocol Exchange) for 4 or 4.5 days post-aggregation

value: 4 & 4.5 days post-aggregation


title: Second MULTI-seq Experiment, gastruloid day 4 & 4.5, pool B, sample 3

description:
exp3B_d4_d4.5, sample3
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz


title: First MULTI-seq Experiment, gastruloid day 5, sample 3

description:
exp1_d5, sample3
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz


title: 309-SPINE

description: miRNA


title: Second MULTI-seq Experiment, gastruloid day 3 & 3.5, pool C, sample 1

description:
exp2C_d3_d3.5, sample1
mRNA and lipid barcode

treatment_protocol: Gastruloids were grown as described previously (Girgin et al. 2018 Protocol Exchange) for 3 or 3.5 days post-aggregation

value: 3 & 3.5 days post-aggregation


title: 10X experiment, gastruloid day 3

description:
gastr_d3
mRNA
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz

extract_protocol:
Cells were processed using 10x Genomics Chromium single cell 3’ RNA sequencing v3.1 according to manufacturer’s instructions
For scRNA-seq: Gastruloids were grown as described above. At d3 or d4, gastruloids were transferred to an eppendorf tube, washed with PBS and dissociated using Accutase (StemPro, A1110501) to obtain a single cell suspension. To remove Accutase, cells were washed twice in 5 ml PBS + 0.04% BSA (Gibco, 15260037) and filtered through a 50 um strainer (Sysmex, 1050553). Cell number and viability was assessed using the Countess II Automated Cell Counter and samples were diluted to submit for 10x 3’ scRNA sequencing at a targeted cell capture rate of 10,000 cells per lane.  For MULTI-seq: Gastruloids were grown as described above. At the collection time point, up to 32 representative gastruloids were selected and individual gastruloids were transferred to wells of a U-bottom suspension culture 96-well plate with 80 μl Accutase (StemPro, A1110501) per well. Gastruloids from multiple time points were combined on a single plate to minimise batch effect. Gastruloids were incubated at 37 ℃ for three minutes and were dissociated through repeated pipetting using a multichannel pipette. Low-retention pipette tips were used for this and all subsequent steps to minimise cell loss. Incubation and pipetting were repeated until a near single-cell suspension was achieved in each well. To label the cells of individual gastruloids with MULTI-seq barcodes, the MULTI-seq protocol (McGinnis et al., 2019) was adapted for low cell numbers as follows. First, 10 μl of unique 10x Anchor:Barcode solution was added to each well. Samples were mixed by pipetting and incubated on ice for 5 minutes. Henceforward, samples were kept on ice. Next, 10 μl 10x Co-Anchor solution was added, mixed in by pipetting and incubated on ice for 5 minutes. Anchor/Co-Anchor stock concentrations were calculated based on estimated cell numbers per gastruloid (7500 cells at d3, 13000 cells at d4, 25000 cells at d5). Used barcodes can be found in Supplementary table 1 (see supplementary note 1 for how these were selected). Barcode labelling was quenched by adding 100 μl ice cold PBS with 1% BSA (Gibco, 15260037) (PBS/BSA) per well. Next, cells from individual wells were combined into a 15 ml Falcon tube with 5 ml ice cold PBS/BSA to further quench barcode labelling. Cells were spun down at 300g in a precooled centrifuge at 4 ℃. The cell pellet was washed with 5 ml ice cold PBS/BSA and spun down again. Next, the cell pellet was resuspended in 1 ml ice cold PBS/BSA and passed through a Flowmi cell strainer (Bel-Art, H13680-0040) into a clean precooled 15 ml Falcon tube. The volume was topped up to 5 ml with ice cold PBS/BSA for a final wash and the cells were spun down again. All but approximately 50 μl of PBS/BSA was aspirated and the cells were resuspended in the remaining volume. Cell number and viability was assessed using the Countess II Automated Cell Counter and samples were diluted to submit for 10x 3’ scRNA sequencing at a targeted cell capture rate of 10,000 cells per lane.
After dissociation and labelling with MULTI-seq barcodes, cells were processed using 10x Genomics Chromium single cell 3’ RNA sequencing v3.1 according to manufacturer’s instructions. For MULTI-seq, the MULTI-seq primer was added during cDNA amplification and the supernatant was collected during 0.6x SPRI clean-up to obtain the barcode fraction as described by McGinnis et al. MULTI-seq barcode libraries were prepared according to McGinnis et al. Libraries were amplified between 11 and 16 times. The number of amplification cycles required was empirically determined for each sample. scRNA and barcode libraries were sequenced on either HiSeq or NovaSeq 6000 instruments according to 10x Genomics instructions (read 1, 28 cycles; index i7, 8 cycles; and read 2, 91 cycles).

value: 3 days post-aggregation


title: First MULTI-seq Experiment, gastruloid day 5, sample 1

description:
exp1_d5, sample1
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz


title: scRNAseq of injured liver (8xCCl4) RS045

status: Public on Aug 26 2022

city: NEW YORK

first: Robert

middle: F

last: Schwabe

state: NY

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

description: scRNA-seq (10x) on fresh isolated liver cells

data_processing:
10x genomics' cellranger software version 2.0.0 was used to process the data.
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse).
Assembly: mm10
Supplementary files format and content: h5 format raw counts

source_name: liver

extract_protocol:
Isolation protocol (RS045 and RS046): Hepatic cell populations were obtained by perfusing and digesting the liver and enriched in non-parenchymal cells.
Isolation protocol (RS024): For the RS024 sample, non parenchymal cells from a 3 month old Mdr2 KO mouse were isolated by perfusing and digesting the liver, followed by gradient centrifucation (Mederacke et al, Nat Protocol 2015). Collagen type 1+ cells were purified by  FACS sorting using the Col1a1-GFP reporter.

treatment_protocol: Treatment protocol (RS045 and RS046): Mice were treated with 8xCCl4 (i.p. 0.5 ml/kg, diluted 1:4 in corn oil,) every 3 days and hepatic cells were isolated 2 days after the last injection of CCl4.

tag: liver damage

value: CCl4 (8 times)

value: all cell types


title: Second MULTI-seq Experiment, gastruloid day 3 & 3.5, pool A, sample 2

description:
exp2A_d3_d3.5, sample2
mRNA and lipid barcode

tag: cell line


title: 10X experiment, gastruloid day 4

description:
gastr_d4
mRNA
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz

treatment_protocol: Gastruloids were grown as described previously (Girgin et al. 2018 Protocol Exchange) for 4 days post-aggregation

value: 4 days post-aggregation


title: scRNAseq of injured liver (8xCCl4) RS046


title: snRNAseq of HCC S44

description:
snRNAseq (10x Genomics 5 prime ) frozen tissue
HSC were obtained perfusing and digesting the liver, followed by gradient centrifucation (Mederacke et al, Nat Protocol 2015) and FACS sorting for LratCre-induced TdTom.

data_processing:
snRNA SEQ: 10x genomics' cellranger software version 5.0.1 was used to process the data.
data processing step: BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference human GRCh38-2020-A
data processing step: GRCh38
genome build: h5 format unfiltered raw counts
processed data files format and content:

extract_protocol:
single nuclei isolation: nuclei were isolated from OCT-embedded tissue samples (Biermann, Melms, et al Cell 2022)
library construction: nuclei were processed and libraires constructed using the Chromium Single Cell 5'v2 kit (10x Genomics)

value: HCC; background liver cirrhosis with steatohepatitis

value: all cell nuclei


title: snRNAseq of cirrhotic liver (surrounding tissue) s43

value: non-tumour tissue; background liver cirrhosis with steatohepatitis


title: Second MULTI-seq Experiment, gastruloid day 3 & 3.5, pool A, sample 3

description:
exp2A_d3_d3.5, sample3
mRNA and lipid barcode


title: Second MULTI-seq Experiment, gastruloid day 4 & 4.5, pool C, sample 2

description:
exp3C_d4_d4.5, sample2
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz


title: scRNAseq of Col1a1+ cells (Mdr2KO)

description: scRNA-seq (10x) on FACS-sorted-HSC

value: LratCre+; TdTom+; Col1a1-GFP+ ;Mdr2KO in  Friend Virus B (FVB) background

value: Mdr2KO 3 months old

value: all Col1a1+ cells


title: snRNAseq of cirrhotic liver (surrounding tissue) S41


title: snRNAseq of HCC S42


title: Second MULTI-seq Experiment, gastruloid day 3 & 3.5, pool A, sample 1

description:
exp2A_d3_d3.5, sample1
mRNA and lipid barcode

value: E14Tg2A (E14) Embryonic Stem Cells (ESCs)


title: implanted organoid +PBMC 4, scRNAseq

status: Public on Aug 25 2022

city: Rotterdam

first: Hector

last: Tejeda Mora

address: Doctor Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

description:
Sample 7 (PBMC 4)
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
Reads containing sequence information were mapped to both the GRCh38 human genome and mm10 mouse genome (barnyard) reference
Generation of BAM files and filtered gene-barcode matrices was accomplished using the Cell Ranger Software (version 6.0.0)
Using Seurat (version 4.0.5) standard pre-processing was done. Selection and filtration of cells was done (genes that were expressed in fewer than three cells, and cells with fewer than 200 distinct transcripts were removed). Data was normalized and scaled, followed by the detection of highly variable genes.
From the generated Seurat-Object, unnormalized data (raw counts) were exported as a comma separated table in CSV files.
Assembly: GRCh38 mm10 (barnyard)
Supplementary files format and content: Comma separated values files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: human induced pluripotent stem cell-derived kidney organoid

growth_protocol: A human iPSC line was pre-treated with CHIR99201 for four days and fibroblast growth factor 9 (FGF9) for three days after which cell pellets were formed, which were placed on a Transwell membrane at the air – medium interphase. The organoids were harvested on day 18. Whole kidney organoids were then subcutaneously implanted into 4 dorsal pockets (2 per pocket) in immune deficient mice. PBMCs from healthy human donors were adoptively transferred 1 month after implantation. PBMC were thawed and 10 million PBMC were administered in 200 μL of phosphate buffered saline (PBS) via intraperitoneal injection. Two months after kidney organoid implantations and four weeks after human PBMC administration, mice were sacrificed by cervical dislocation. The organoids were harvested.

extract_protocol:
Single cell suspension of organoids were generated using TrypLE Select for 15 minutes at 37°C and stored on ice in APEL
Single cell libraries were prepared using the Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics, Pleasanton, CA, USA). Next generation sequencing (28-8-0-91 cycles) was carried out on an Illumina NovaSeq6000 platform (Illumina, San Diego, USA).

tag: mouse strain

value: BALB/c IL2Ry-/- RAG2-/-DKO

tag: protocol

value: implanted organoid +PBMC


title: implanted organoid +PBMC 1, scRNAseq

description:
Sample 4 (PBMC 1)
10x Genomics

value: human induced pluripotent stem cell-derived kidney organoid


title: implanted organoid +PBMC 3, scRNAseq

description:
Sample 6 (PBMC 3)
10x Genomics


title: implanted organoid ctrl 3, scRNAseq

description:
Sample 3 (Ctrl 3)
10x Genomics

value: implanted organoid ctrl


title: Second MULTI-seq Experiment, gastruloid day 4 & 4.5, pool B, sample 2

description:
exp3B_d4_d4.5, sample2
mRNA and lipid barcode
seurat_final.rds
sample_metadata_final.txt.gz
feature_metadata_final.txt.gz

value: Differentiated ESCs

value: WT

value: gastruloids

value: 4 & 4.5 days post-aggregation


title: implanted organoid +PBMC 2, scRNAseq

description:
Sample 5 (PBMC 2)
10x Genomics


title: implanted organoid ctrl 2, scRNAseq

description:
Sample 2 (Ctrl 2)
10x Genomics


title: implanted organoid ctrl 1, scRNAseq

description:
Sample1 (Ctrl 1)
10x Genomics


title: WThfd131

city: Shimotsuke

first: Sadahiko

last: Iwamoto

state: Tochigi

address: Yakushiji 3311-1

department: Center for Molecular Medicine

institute: Jichi Medical University

data_processing:
BaseSpace Onsite (Illumina)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BaseSpace Onsite (Illumina)
Trimmed sequence reads were mapped to GrCM38/mm10 using BaseSpace Onsite (Illumina)
The output fastq row data were assembled to the mouse genome (mm10) using the TopHat Alignment application (Illumina)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: mouse liver, WT, HFD

extract_protocol:
RNA was harvested using Trizol kit (Fisher scientific).
2 ug of total RNA was used for the construction of sequencing libraries. TruSeq mRNA sample preparation kit (Illumina) was used for the preparation of sequence libraries following manufacturer's protocols.

treatment_protocol: total RNA was extracted immediately after euthanasia

value: liver

tag: gender

value: male

tag: diet

value: high fat diet

value: 20 week old


title: KO320HFD

source_name: mouse liver, Gpr180KO, HFD

tag: tissue


title: KOhfd52

tag: genotype


title: WThfd157


title: KOhfd56


title: WThfd134


title: KO321HFD


title: KO322HFD


title: KO319HFD


title: W319HFD


title: W318HFD


title: WThfd156


title: W317HFD


title: RNA-Seq of mus musculus:adult male brain (CBSST-Seq)

city: Changchun

first: Zhengyang

last: Jin

state: Jilin

address: No. 1163 Xinmin Street

institute: Jilin University

description: CBSST-Seq

data_processing:
The filtered data was mapped to the mouse genome (mm10 mouse) using SpaceRanger V1.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Tissue was permeabilized with tissue permeabilizing enzyme for 12 minutes
RNA libraries for RNA-seq were prepared using Kapa HIFI HotStart ReadyMix PCR Kit following manufacturer's protocols.

value: Brain

value: Male

value: 10 weeks

value: Cryosection


title: F613-1, MH, 96 hour

city: Jinan

first: Guangxiang

last: Cao

address: 18877 jingshi Road

institute: Shandong Academy of Medical Sciences

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to  GCA_001693675.1 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Deseq was used to analysis
Assembly: GCA_001693675.1
Supplementary files format and content: RPKM values for each Sample

organism: Streptomyces clavuligerus

source_name: bacteria

extract_protocol:
The total RNA was harvested using  kit (Qiagen), was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell type

value: bacteria

value: MH fermentation medium

tag: time

value: Hour 96


title: F613-1, ML, 48 hour

value: ML fermentation medium

value: Hour 48


title: F613-1, MH, 48 hour


title: F613-1, MH, 24 hour

value: Hour 24


title: WT CD62L- TPEX2

status: Public on Aug 17 2022

city: Clayton

first: Wei

last: Shi

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

institute: Monash University

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Rsubread_2.2.6; only uniquely mapped read-pairs were allowed. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least 2 libraries. Counts were quantile normalized, precision weighted with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 10% or less.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read counts for genes in all the libraries.

extract_protocol:
RNA extraction from sorted P14 T cells was performed following the manufacturer’s protocol using the RNAeasy Plus Mini Kit (Qiagen)
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA)

value: wild-type

value: splenocytes

tag: collection

value: 7 days after infection with LCMV docile


title: WT CD62L-TPEX1


title: F613-1, ML, 96 hour

tag: strain

value: WT


title: WT CD62L+ TPEX1


title: WT CD62L+ TPEX2


title: WT TEX3


title: KOhfd53

value: liver

value: male

tag: age


title: KOhfd51

value: high fat diet

value: 20 week old


title: KOhfd54


title: W320HFD


title: WThfd133


title: NT from DEN+CCl4; Yap∆HSC PME010

status: Public on Aug 12 2022

description:
surrounding fibrotic liver from DEN+CCl4-treated mouse
RNAseq on surrouding liver from mice with HCC

data_processing:
20M paired-end 100bp sequencing was performed using the Illumina NovaSeq 6000
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19 or 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
A pseudoalignment to a kallisto index was created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
raw counts in TPM text file format
Genome_build: mm10

extract_protocol:
isolation protocol (RS039, RS042 and RS043): HSC were obtained perfusing and digesting the liver, followed by gradient centrifucation (Mederacke et al, Nat Protocol 2015) and HSC were purified by FACS sorting for LratCre-induced TdTom.
isolation protocol (RSB samples: HSC-  bulk RNA-seq): HSC were obtained perfusing and digesting the liver, followed by gradient centrifucation (Mederacke et al, Nat Protocol 2015) and FACS sorting for VitA and LratCre-induced TdTom and then centrifuged for RNA extraction.
isolation protocol (YAP samples: tumor -  bulk RNA-seq): One single tumor was harvested and snapped frozen with liquid nitrogen before RNA extraction; each sample correspong to 1 tumor from a different mouse.
RNA extraction protocol bulk RNA-seq: Total RNA was column purified (Qiagen mini)
library construction protocol BULK RNA Seq: construct libraries using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.
library strategy BULK RNA Seq: RNA-Seq
library strategy scRNA Seq: scRNA-seq, 10x Genomics Chromium 3' Solution
library construction protocol BULK RNA Seq: construct libraries using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.

treatment_protocol:
treatment protocol (RSB53-RSB56): Mice were treated with 12xCCl4 (i.p. 0.5 ml/kg, diluted 1:4 in corn oil,) every 3 days and hepatic cells were isolated 2 days after the last injection of CCl4.
treatment protocol (RS039): Before HSC isolation, the mouse was treated with a profound fibrosis regimen induced by 19xCCl4: first week 1x 0.50 ml/kg diluted 1:8 in corn oil; second week: 3x 0.5 ml/kg, diluted 1:4 in corn oil; third week: 3x 1 ml/kg diluted 1:4 in corn oil; fourth week: 3x 1.5 ml/kg diluted 1:4 in corn oil followed by 9 injections 2x per week 1.5 ml/kg, diluted 1:4 in corn oil. HSC isolation was performed 2 days after the last injection of CCl4.
treatment protocol (RS042): The mouse was injected by  hydrodynamic tail vein injection with pT3-EF1α-TAZS89A plasmid in combination with sleeping beauty transposase SB13, 3 weeks later it was fed with a Fructose, Palmitate, Cholesterol and Trans-Fat (FPC) in combination with high-glucose (23 g/L) fructose (19 g/L) water for 2 months.
treatment protocol (RS043): Before HSC isolation the mouse was fed with a a L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline (CDAA-diet) for 3 months
treatment protocol (RSB05-RSB08 and -RSB10): Mice were fed with a Fructose, Palmitate, Cholesterol and Trans-Fat (FPC) in combination with high-glucose (23 g/L) fructose (19 g/L) water for 16 weeks.
treatment protocol (PME001-PME010 and YAP01-YAP10): Mice were treated with DEN  (i.p. 25 mg/kg) on day 15 postpartum to male mice, followed 1 month later by 14 x CCl4 injections (i.p. 0.5 ml/kg, diluted 1:4 in corn oil) on a weekly basis. Mice were euthanied 2 days after the last injection of CCl4.

value: LratCre+,  YAP floxed mice C57BL6/J

value: adjacent fibrotic liver from mice with HCC induced by DEN+CCl4


title: KO Tpex3

value: Myb-KO


title: NT from DEN+CCl4; Yap∆HSC PME008


title: F613-1, ML, 24 hour

value: bacteria


title: NT from DEN+CCl4; Yap∆HSC PME009


title: KO Tpex4


title: KO Tex3


title: NT from DEN+CCl4; Yap∆HSC PME006


title: NT from DEN+CCl4; Yapf/f PME005

value: LratCre-,  YAP floxed mice C57BL6/J


title: mouse normal liver NL005

description:
mouse normal liver
RNAseq on normal liver

value: normal liver


title: mouse normal liver NL001


title: mouse normal liver NL002


title: mouse normal liver NL007


title: mouse normal liver NL004


title: NT from DEN+CCl4; Yapf/f PME002


title: NT from DEN+CCl4; Yapf/f PME003


title: mouse normal liver NL003


title: Tumor from DEN+CCl4; Yapf/f YAP08

description:
mouse HCC induced by DEN+CCl4
RNAseq on HCC from DEN+CCl4-HCC model

value: HCC


title: Tumor from DEN+CCl4; Yapf/f YAP09


title: Tumor from DEN+CCl4; Yapf/f YAP07


title: Tumor from DEN+CCl4; Yapf/f YAP06


title: mouse normal liver NL006


title: mouse normal liver NL008


title: Tumor from DEN+CCl4; Yap∆HSC YAP05


title: Tumor from DEN+CCl4; Yap∆HSC YAP04


title: NT from DEN+CCl4; Yapf/f PME004


title: Tumor from DEN+CCl4; Yap∆HSC YAP03


title: NT from DEN+CCl4; Yap∆HSC PME007


title: NT from DEN+CCl4; Yapf/f PME001


title: Tumor from DEN+CCl4; Yapf/f YAP10


title: HSC from injured liver (TAZ+FPC-diet) RSB042

description:
scRNA-seq (10x) on FACS-sorted-HSC
RSB042

data_processing:
10x genomics' cellranger software version 5.0.1 was used to process the data.
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse).
Genome_build: mm10
Supplementary_files_format_and_content: h5 format raw counts

value: LratCre+, TdTom+ in C57BL/6J

value: TAZ-overexpression + FPC-diet

value: Hepatic Stellate Cells


title: HSC from injured liver (FPC-diet) RSB06

description:
HSC from injured liver (FPC-diet)
RNAseq on FACS-sorted  HSC from injured liver (FPC-diet)

value: FPC-diet (16 weeks)


title: HSC from injured liver (12xCCl4) RSB56

description:
HSC from injured liver (12xCCl4)
RNAseq on FACS-sorted  HSC from injured liver (CCl4)

value: CCl4 (12 times)


title: HSC from injured liver (FPC-diet) RSB07


title: RC77T cells, prostate cancer

status: Public on Aug 05 2022

city: Tuskegee

first: Honghe

last: Wang

state: AL

address: 1200 W Montgomery Rd

department: Biology

institute: Tuskegee Universitry

description: processed data file headers: gene, RC165T, RC43T and RC77T

data_processing:
Reads trimmed using Partek and default settings
Reads aligned to hg19 using STAR 2.7.3a and defalut settings
Reads quantified using Partek E/M to hg19 - RefSeq Transcripts 90 - 2019-05-03
Assembly: hg19
Supplementary files format and content: text file. Raw gene counts

growth_protocol: Cells were maintained in Keratinocyte basal medium supplemented with 10ng/ml EGF, BPE (Bovine Pituitary Extract), 2.00 ML Insulin, Hydrocortisone, and GA-1000. The cells were incubated at 37°C, 5% v/v CO2

extract_protocol:
RNA was isolated from cultured cells using TRIzol® Reagent (Sigma Life Sciences, St. Louis, MO) following the manufacturer’s protocol
RNA library preparation and quality control were performed by Novogene Corporation Inc. (Sacramento, CA). Briefly, 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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: epithelial prostate cancer

value: WT


title: HSC from injured liver (FPC-diet) RSB05


title: HSC from injured liver (CDAA-diet) RSB043

description:
scRNA-seq (10x) on FACS-sorted-HSC
RSB043

value: CDAA-diet


title: HSC from injured liver (12xCCl4) RSB53

description:
HSC from injured liver (12xCCl4)
RNAseq on FACS-sorted HSC from injured liver (CCl4)


title: HSC from injured liver (FPC-diet) RSB10


title: P. falciparum BrdU+EdU (biol rep 1)

status: Public on Aug 04 2022

city: Cambridge

first: Michael

last: Boemo

address: Tennis Court Road

department: Department of Pathology

institute: University of Cambridge

description: R9.4.1 flowcells

data_processing:
Basecalling (Guppy v5.0.11)
Genome alignment (Minimap2 v2.17-r941)
BrdU and EdU detection (DNAscent v3.0.2)
Fork, origin, and termination calling (DNAscent v3.0.2)
Assembly: P. falciparum 3D7 ASM276v2
Supplementary files format and content: bed files (fork, origin, and termination calls at 30 hpi and 36 hpi)

organism: Plasmodium falciparum

source_name: schizonts

extract_protocol:
Qiagen MagAttract
SQK-LSK109
R9.4.1 MinION DNA sequencing

value: schizonts

value: ORC1-3xHA + pTK-BSD

value: 20 uM Edu (60 min) or 200 uM Brdu (60 min)


title: P. falciparum BrdU+EdU (biol rep 2)

description: R9.4.1 flowcells

value: 21 uM Edu (60 min) or 200 uM Brdu (60 min)


title: P. falciparum 30-36 hpi (biol rep 3)

description: R9.4.1 flowcells

value: 22 uM Edu (7.5 min), 200 uM Brdu (7.5 min)


title: HSC from injured liver (19xCCl4) RSB039

description:
scRNA-seq (10x) on FACS-sorted-HSC
RSB039

value: profound fibrosis (19xCCl4)


title: HSC from injured liver (FPC-diet) RSB08


title: RC43T cells, prostate cancer


title: EBF4 sgRNA RNA-seq rep2 [s14_2]

status: Public on Jul 27 2022

last: Lenardo

address: 9000 Rockville Pike, 10/11D14

department: NIAID

institute: NIH

data_processing:
RNA-seq data was processed using the Pipeliner workflow (https://github.com/CCBR/Pipeliner). Reads were trimmed using Cutadapt v1.18 and aligned to the human hg38 reference genome and Gencode release28 using two-pass STAR v2.7.0f.  RSEM v1.3.0 was used for gene-level expression quantification, and limma v 3.38.3 was used for voom quantile normalization and differential expression analysis.
Assembly: hg38

source_name: Jurkat T cell

extract_protocol: Total RNA from un-stimulated Jurkat T cells was extracted and were used to prepare RNA-seq libraries.

treatment_protocol: The lentiviral EBF4 plasmid was generated from pLV-EF1a-IRES-Puro (Addgene) vector by replacing the puromycin fragment with a truncated EGFR protein. The lentiviral EBF4 plasmid and plasmids containing PAX2 and VSV-G (Addgene) were transfected into 293T cells using Lipofectamine 3000 reagent (Invitrogen). EBF4 knockout plasmid was generated from the lentiCRISPRv2 vector (Addgene). Knockout plasmids and plasmids containing PAX2 and VSV-G (Addgene) were transfected into 293T cells using Lipofectamine 3000 reagent (Invitrogen). The culture supernatants containing lentivirus were harvested. Cell lines were seeded in complete medium supplemented with Polybrene (Sigma) and lentiviruses.

value: Jurkat T cell

value: EBF4 sgRNA


title: P. falciparum 30-36 hpi (biol rep 2)

description: R9.4.1 flowcells

value: 21 uM Edu (7.5 min), 200 uM Brdu (7.5 min)


title: EBF4 sgRNA RNA-seq rep3 [s14_3]


title: P. falciparum 30-36 hpi (biol rep 1)

description: R9.4.1 flowcells

value: 20 uM Edu (7.5 min), 200 uM Brdu (7.5 min)


title: P. falciparum 30-36 hpi (biol rep 4)

description: R9.4.1 flowcells

value: 23 uM Edu (7.5 min), 200 uM Brdu (7.5 min)


title: P. falciparum 30-36 hpi (biol rep 6)

description: R9.4.1 flowcells

value: 25 uM Edu (7.5 min), 200 uM Brdu (7.5 min)


title: EBF4 sgRNA RNA-seq rep1 [s14_1]


title: P. falciparum 30-36 hpi (biol rep 5)

description: R9.4.1 flowcells

value: 24 uM Edu (7.5 min), 200 uM Brdu (7.5 min)


title: non-target sgRNA RNA-seq rep3 [s37_3]

value: non target sgRNA


title: HSC from injured liver (12xCCl4) RSB55

value: LratCre+, TdTom+ in C57BL/6J

value: CCl4 (12 times)

value: Hepatic Stellate Cells


title: Tumor from DEN+CCl4; Yap∆HSC YAP02

value: LratCre+,  YAP floxed mice C57BL6/J

value: HCC


title: Tumor from DEN+CCl4; Yap∆HSC YAP01


title: RC165T cells, prostate cancer

value: epithelial prostate cancer

value: WT


title: HSC from injured liver (12xCCl4) RSB54


title: non-target sgRNA RNA-seq rep2 [s37_2]


title: non-target sgRNA RNA-seq rep1 [s37_1]


title: overexpressed EBF4 RNA-seq rep3 [EBF4_3]

value: overexpressed


title: overexpressed EBF4 RNA-seq rep2 [EBF4_2]


title: EBF4-FLAG Jurkat T cell input

data_processing:
Reads were trimmed with Cutadapt v1.18. All reads aligning to the Encode hg38 v1 blacklist regions were identified by alignment with BWA v0.7.17 and removed with Picard SamToFastq (https://broadinstitute.github.io/picard/). The remaining reads were aligned to the hg38 reference genome using BWA. Reads with a mapQ score less than 6 were removed with SAMtools v1.6 and PCR duplicates were removed with Picard MarkDuplicates.
Data was converted into bigwigs for viewing and normalized by reads per genomic content (RPGC) using deepTools v3.0.1 using the following parameters: --binSize 25 --smoothLength 75 --effectiveGenomeSize 2700000000 --centerReads --normalizeUsing RPGC. RPGC-normalized input values were subtracted from RPGC-normalized ChIP values of matching cell type genome-wide using deepTools with --binSize 25.
Peaks were called using macsNarrow (macs v2.1.1) with the following parameter: -f "BAMPE".
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak

extract_protocol:
FLAG tagged EBF4 Jurkat T cells were isolated by EGFR biotinylated antibody (R&D) and were cross-linked in 1% formaldehyde for 15 minutes at room temperature, quenched in 2.5 M glycine for 5 minutes, washed, and resuspended in 1st lysis buffer (50 mM HEPES-KOH, 140 mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100, and proteinase inhibitor cocktail) and incubated 10 minutes. The cells were resuspended with 2nd lysis buffer (20 mM Tris-HCl, 200 mM NaCl, 2 mM EDTA, 0.5 mM EGTA, and proteinase inhibitor cocktail) and incubated 10 minutes. Cells were resuspended with 3rd lysis buffer (20 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritonX-100, 0.1% Na-Deoxycholate, 0.1% SDS, and proteinase inhibitor cocktail) and incubated 10 minutes. Cross-linked chromatin was sonicated for 4 minutes using a Biruptor-Pico (30 seconds on/30 seconds off). Precleared chromatin extract was incubated overnight at 4°C with anti-FLAG antibody (Cell signaling) and immunoprecipitated with protein G sepharose beads.
DNA was used to generate a standard Illumina sequencing library.

treatment_protocol: The lentiviral FLAG tag EBF4 plasmid was generated from pLV-EF1a-IRES-Puro (Addgene) vector by replacing the puromycin fragment with a truncated EGFR protein. The lentiviral EBF4 plasmid and plasmids containing PAX2 and VSV-G (Addgene) were transfected into 293T cells using Lipofectamine 3000 reagent (Invitrogen).

tag: antibody

value: input


title: EBF4-FLAG Jurkat T cell ChIP rep2

value: Jurkat T cell

value: anti-FLAG


title: EBF4-FLAG Jurkat T cell ChIP rep1


title: overexpressed EBF4 RNA-seq rep1 [EBF4_1]


title: TE11 cells, Chloroquine and 5 Fluorouracil replicate 1

status: Public on Jul 25 2022

city: Philadelphia

first: Kelly

middle: A

last: Whelan

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

data_processing:
Rsubread 2.10
DESeq 2 1.36
Assembly: GRCm38

growth_protocol: TE11 ESCC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted and purified using RNAeasy kit (Qiagen)
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc.) following manufacturer's protocols.

treatment_protocol: The cells were treated with 0.1% DMSO (vehicle), 10 µM of Chloroquine, 25 µM of 5 Fluorouracil, or the combination of 10 µM of Chloroquine and 25 µM of 5 Fluorouracilc for 48 hours

value: Esophageal squamous cell carcinoma cells

value: 10 uM of Chloroquine + 25 uM of 5 Fluorouracil


title: Overexpressed EBF4 ATAC-seq rep2

data_processing:
Samples were trimmed for adapters using Cutadapt v 1.18 before alignment. The trimmed reads were aligned to the hg38 reference using Bowtie2 v2.3.4.1 with flag -k 10.
The peaks were called using Genrich v0.6 (https://github.com/jsh58/Genrich) with the following flags -j -y -r -v -d 150 -m 5 -e chrM,chrY. Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak

extract_protocol:
We followed the Omni-ATAC protocol. Briefly, 50000 cells were washed and lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500 x g for 10 min to remove the supernatant. Nuclei were then incubated with Tn5 transposon and tagmentation buffer (20 mM Tris-HCl (pH 7.6), 10 mM MgCl2, 20% Dimethylformamide) containing 0.1% Tween-20 and 0.005% Digitonin at 37 °C for 30 min. Stop buffer was added directly into the reaction to end tagmentation.
PCR was performed to amplify the library. Libraries were then purified with SPRI (Beckman) beads and deep sequencing was performed.

treatment_protocol: The lentiviral EBF4 plasmid was generated from pLV-EF1a-IRES-Puro (Addgene) vector by replacing the puromycin fragment with a truncated EGFR protein. The lentiviral EBF4 plasmid and plasmids containing PAX2 and VSV-G (Addgene) were transfected into 293T cells using Lipofectamine 3000 reagent (Invitrogen).


title: Empty vector ATAC-seq rep2

value: empty vector


title: Empty vector ATAC-seq rep1


title: empty vector RNA-seq rep3 [EV_3]


title: Overexpressed EBF4 ATAC-seq rep1


title: TE11 cells, Chloroquine and 5 Fluorouracil replicate 2


title: TE11 cells, Chloroquine and 5 Fluorouracil replicate 3


title: Empty vector ATAC-seq rep3


title: TE11 cells, 5 Fluorouracil replicate 3

value: 25 uM of 5 Fluorouracil


title: TE11 cells, Chloroquine replicate 3

value: 10 uM of Chloroquine


title: TE11 cells, 5 Fluorouracil replicate 1


title: TE11 cells, 5 Fluorouracil replicate 2


title: TE11 cells, Chloroquine replicate 2


title: TE11 cells, Chloroquine replicate 1


title: TE11 cells, vehicle control replicate 4

value: 0.1% DMSO


title: empty vector RNA-seq rep1 [EV_1]


title: TE11 cells, vehicle control replicate 3